diff --git a/.gitignore b/.gitignore
index 241253b04ba8096cc7b5fc5c631ce1e6602fe6f0..55e199a0f4b29de5943e31ca5c56364466de0164 100644
--- a/.gitignore
+++ b/.gitignore
@@ -70,4 +70,6 @@ ost_*_tests_log.xml
rules.ninja
build.ninja
modules/gui/src/dngr.qrc.depends
+/compile_commands.json
/modules/bindings/tests/formatdb.log
+/modules/mol/mm/src/settings.hh
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 720b4ff22b90294f17ab075473c78882fb7af1dd..15cd614262cd22d3bb1a40bc3f65348e4862cfba 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,23 @@
+Changes in Release 1.5
+--------------------------------------------------------------------------------
+
+ * Added binding to 3DComb (structural alignment)
+ * Added functions to predict contacts from multiple sequence alignments
+ * Added some functions to analyze MD trajectories (pairwise distance matrices,
+ pairwise distance fluctuations, RMSD matrix etc.)
+ * Support of non-orthogonal unit cells for wrapping entities
+ * Flexible implementation of HBPlus
+ * Updated dependencies (Eigen2 to Eigen3, Boost 1.47 to 1.53)
+ * Wrapper for OpenMM. This allows for direct access to molecular mechanics
+ functionality from within OST.
+ * The compoundslib now features InChI and InChIKeys (machine readable InChI
+ hash)
+ * Names of compounds are also stored in the compoundslib now
+ * Added seq.ProfileHandle class and io.LoadSequenceProfile to work with
+ sequence profiles.
+ * Added a wrapper to HHblits.
+ * Removed levenberg_marquardt.h in img/alg
+
Changes in Release 1.4
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8141de3b24adbb7d9ab0c00cdb92c9cb30fd8b46..4ab2d74cedcb255bf1ae8f0db289c6b3c66ea16f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,9 +4,10 @@
cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
project(OpenStructure CXX C)
+set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
set (OST_VERSION_MAJOR 1)
-set (OST_VERSION_MINOR 4)
-set (OST_VERSION_PATCH 1)
+set (OST_VERSION_MINOR 5)
+set (OST_VERSION_PATCH 0)
set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
include(OST)
@@ -50,6 +51,7 @@ option(COMPILE_TESTS "whether unit tests should be compiled by default" OFF)
option(ENABLE_STATIC "whether static libraries should be compiled" OFF)
option(UBUNTU_LAYOUT "whether Debian/Ubuntu's lib and libexec directory layout should be used" OFF)
option(HIDDEN_VISIBILITY "on gcc, use -fvisibility=hidden" OFF)
+option(ENABLE_MM "whether openmm support is added" OFF)
if (CXX)
set(CMAKE_CXX_COMPILER ${CXX})
@@ -139,6 +141,12 @@ if (PROFILE)
else()
set(_PROFILE OFF)
endif()
+if(ENABLE_MM)
+ set(_OPENMM ON)
+else()
+ set(_OPENMM OFF)
+endif()
+
if (UBUNTU_LAYOUT)
set(_UBUNTU_LAYOUT ON)
@@ -146,8 +154,6 @@ else()
set(_UBUNTU_LAYOUT OFF)
endif()
-add_definitions(-DEIGEN2_SUPPORT)
-
if (COMPOUND_LIB)
set(_COMP_LIB "${COMPOUND_LIB}")
if (NOT IS_ABSOLUTE "${COMPOUND_LIB}")
@@ -226,13 +232,20 @@ else()
set (PNG_LIBRARY "")
endif()
-find_package(Eigen 2.0.0 REQUIRED)
+find_package(Eigen 3.2.0 REQUIRED)
find_package(Python 2.4 REQUIRED)
if(USE_NUMPY)
find_package(Numpy REQUIRED)
endif()
+if(ENABLE_MM)
+ find_package(OpenMM REQUIRED)
+ set(_OPENMM_PLUGINS "${OPEN_MM_PLUGIN_DIR}")
+else(ENABLE_MM)
+ set(_OPENMM_PLUGINS "NONE")
+endif(ENABLE_MM)
+
if (ENABLE_IMG)
find_package(FFTW REQUIRED)
find_package(TIFF REQUIRED)
@@ -243,7 +256,7 @@ if (ENABLE_STATIC)
set(Boost_LIBRARIES)
set(Boost_USE_STATIC_LIBS ON)
find_package(Boost ${_BOOST_MIN_VERSION}
- COMPONENTS filesystem system iostreams regex REQUIRED)
+ COMPONENTS filesystem system iostreams regex thread REQUIRED)
find_package(ZLIB REQUIRED)
if (UNIX AND NOT APPLE)
@@ -285,10 +298,11 @@ endif()
# basic environment
include_directories(${Boost_INCLUDE_DIRS}
- ${FFTW_INCLUDE_PATH}
- ${EIGEN2_INCLUDE_DIR}
+ ${FFTW_INCLUDE_DIRS}
+ ${EIGEN3_INCLUDE_DIRS}
${TIFF_INCLUDE_DIR}
- ${PNG_INCLUDE_DIR}
+ ${PNG_INCLUDE_DIRS}
+ ${OPEN_MM_INCLUDE_DIRS}
)
if(USE_NUMPY)
include_directories(${PYTHON_NUMPY_INCLUDE_DIR})
@@ -343,6 +357,8 @@ message(STATUS
" Shader support (-DUSE_SHADER) : ${_SHADER}\n"
" Numpy support (-DUSE_NUMPY) : ${_NUMPY}\n"
" SpaceNav Device support (-DENABLE_SPNAV) : ${_SPNAV}\n"
+ " OpenMM support (-DENABLE_MM) : ${_OPENMM}\n"
+ " OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : ${_OPENMM_PLUGINS}\n"
" Optimize (-DOPTIMIZE) : ${_OPT}\n"
" Profiling support (-DPROFILE) : ${_PROFILE}\n"
" Double Precision (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n"
diff --git a/build_configs/buildconfig_bc2 b/build_configs/buildconfig_bc2
index a0dd0d1a8a850c0e3615c6c7222488c39ec8f218..ae7aa9384f42215d685e16c9c8eda6389243fd08 100644
--- a/build_configs/buildconfig_bc2
+++ b/build_configs/buildconfig_bc2
@@ -1,9 +1,8 @@
-set(FFTW_INCLUDE_PATH "/import/bc2/soft/app/FFTW/current/Linux/include/" CACHE PATH "")
-set(FFTW_LIBRARIES "/import/bc2/soft/app/FFTW/current/Linux/lib/libfftw3f.so" CACHE PATH "")
-set(Boost_COMPILER "-gcc41" CACHE PATH "")
-set(PYTHON_ROOT "/import/bc2/soft/app/Python/current/Linux/" CACHE PATH "")
-set(EIGEN2_INCLUDE_DIR "/import/bc2/soft/app/eigen/current/Linux/include/eigen2" CACHE PATH "")
-set(BOOST_ROOT "/import/bc2/soft/app/boost/current/Linux" CACHE PATH "")
-set(QT_QMAKE_EXECUTABLE "/import/bc2/soft/app/Qt/current/Linux/bin/qmake" CACHE PATH "")
+set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/include/" CACHE PATH "")
+set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3f.a" CACHE PATH "")
+set(PYTHON_ROOT "/scicore/soft/apps/Python/2.7.5-goolf-1.4.10" CACHE PATH "")
+set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.2.1-goolf-1.4.10/include/Eigen" CACHE PATH "")
+set(BOOST_ROOT "/import/bc2/apps/Boost/1.53.0-goolf-1.4.10-Python-2.7.5" CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt4" CACHE PATH "")
set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
diff --git a/build_configs/buildconfig_bc2_static b/build_configs/buildconfig_bc2_static
index c26933d8ce996f93da782e919544f06312d57ff3..d25730b349840c25abf398a9b7d981d13bab5c2d 100644
--- a/build_configs/buildconfig_bc2_static
+++ b/build_configs/buildconfig_bc2_static
@@ -1,11 +1,10 @@
-set(FFTW_INCLUDE_PATH "/import/bc2/soft/app/FFTW/current/Linux/include/" CACHE PATH "")
-set(FFTW_LIBRARIES "/import/bc2/soft/app/FFTW/current/Linux/lib/libfftw3f.a" CACHE PATH "")
+set(FFTW_INCLUDE_PATH "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/include/" CACHE PATH "")
+set(FFTW_LIBRARY "/scicore/soft/apps/FFTW/3.3.3-gompi-1.4.10/lib/libfftw3f.a" CACHE PATH "")
set(DL_LIBRARIES "/usr/lib64/libdl.a" CACHE PATH "")
set(PTHREAD_LIBRARIES "/usr/lib64/libpthread.a" CACHE PATH "")
-set(ZLIB_LIBRARY "/usr/lib64/libz.a" CACHE PATH "")
-set(Boost_COMPILER "-gcc41" CACHE PATH "")
-set(PYTHON_ROOT "/import/bc2/soft/app/Python/current/Linux/" CACHE PATH "")
-set(EIGEN2_INCLUDE_DIR "/import/bc2/soft/app/eigen/current/Linux/include/eigen2" CACHE PATH "")
-set(QT_QMAKE_EXECUTABLE "/import/bc2/soft/app/Qt/current/Linux/bin/qmake" CACHE PATH "")
+set(ZLIB_LIBRARY "/scicore/soft/apps/zlib/1.2.8-goolf-1.4.10/lib/libz.a" CACHE PATH "")
+set(PYTHON_ROOT "/scicore/soft/apps/Python/2.7.5-goolf-1.4.10" CACHE PATH "")
+set(EIGEN3_INCLUDE_DIR "/scicore/soft/apps/Eigen/3.2.1-goolf-1.4.10/include/Eigen" CACHE PATH "")
+set(QT_QMAKE_EXECUTABLE "/usr/bin/qmake-qt4" CACHE PATH "")
set(COMPOUND_LIB "/import/bc2/home/schwede/GROUP/OpenStructure/ChemLib/compounds.chemlib" CACHE PATH "")
set (CMAKE_BUILD_TYPE "Release" CACHE PATH "")
diff --git a/build_configs/darwin_homebrew.txt b/build_configs/darwin_homebrew.txt
index c88a16256e5040d3cf15c1c4e288ea84ed3f3b9c..0e0b2e1793be09b6ea1f9fda1265b4ed35074db2 100644
--- a/build_configs/darwin_homebrew.txt
+++ b/build_configs/darwin_homebrew.txt
@@ -1,2 +1,2 @@
set(PNG_INCLUDE_DIR "/usr/X11/include" CACHE PATH "include path for system libpng")
-set(EIGEN2_INCLUDE_DIR "/usr/local/include/eigen3" CACHE PATH "Eigen3-compatible include path")
+set(EIGEN3_INCLUDE_DIR "/usr/local/include/eigen3" CACHE PATH "Eigen3-compatible include path")
diff --git a/build_configs/win32 b/build_configs/win32
index e315b00056d6c1fe7c835c946b40f6e0edb7e0de..7fac30a6403019e63ca30abdfff4ad28bcd697e7 100644
--- a/build_configs/win32
+++ b/build_configs/win32
@@ -10,7 +10,7 @@ set(PNG_LIBRARY "${USER_DIR}/lib/libpng13.lib" CACHE PATH "includes for libpng")
set(ZLIB_INCLUDE_DIR "${USER_DIR}/include/" CACHE PATH "zlib includes")
set(TIFF_INCLUDE_DIR "${USER_DIR}/include/" CACHE PATH "tiff includes")
set(TIFF_LIBRARY "${USER_DIR}/lib/libtiff_i.lib/" CACHE PATH "tiff includes")
-set(EIGEN2_INCLUDE_DIR "${USER_DIR}/include/eigen2" CACHE PATH "gsl includes")
+set(EIGEN3_INCLUDE_DIR "${USER_DIR}/include/Eigen" CACHE PATH "gsl includes")
set(USE_DOUBLE_PRECISION "OFF" CACHE PATH "double precision")
set(FFTW_LIBRARIES "${USER_DIR}/lib/libfftw3f-3.lib" CACHE PATH "fftw libs")
#set(FFTW_LIBRARIES "${USER_DIR}/lib/libfftw3-3.lib" CACHE PATH "fftw libs")
diff --git a/cmake_support/CopyDependencies.cmake b/cmake_support/CopyDependencies.cmake
index ddbf1ae2b39cd2b85231133e306a60f0bc32e5ea..a146c16e9b24a4bc3ea8260b472d7522c7672a9f 100644
--- a/cmake_support/CopyDependencies.cmake
+++ b/cmake_support/CopyDependencies.cmake
@@ -253,6 +253,11 @@ function(resolve_item context item exepath resolved_item_var)
if(UNIX AND NOT WIN32)
find_file(ri "${item}" ${exepath} NO_DEFAULT_PATH)
find_file(ri "${item}" ${exepath} /usr/lib)
+ if(APPLE)
+ find_file(ri "${item}" PATHS ENV DYLD_LIBRARY_PATH NO_DEFAULT_PATH)
+ else(APPLE)
+ find_file(ri "${item}" PATHS ENV LD_LIBRARY_PATH NO_DEFAULT_PATH)
+ endif(APPLE)
else(UNIX AND NOT WIN32)
find_program(ri "${item}" PATHS "${exepath}" NO_DEFAULT_PATH)
find_program(ri "${item}" PATHS "${CMAKE_INSTALL_PREFIX}/bin" NO_DEFAULT_PATH)
@@ -266,7 +271,17 @@ function(resolve_item context item exepath resolved_item_var)
if(IS_ABSOLUTE "${resolved_item}" AND EXISTS "${resolved_item}")
set(${resolved_item_var} "${resolved_item}" PARENT_SCOPE)
else(IS_ABSOLUTE "${resolved_item}" AND EXISTS "${resolved_item}")
- message(FATAL_ERROR "cannot resolve item '${item}' in context:'${context}'. Partially resolved path is: '${resolved_item}'")
+ if(APPLE)
+ # see if item is available in System frameworks
+ string(REPLACE "/Library/Frameworks" "/System/Library/Frameworks" system_resolved_item ${resolved_item})
+ if(IS_ABSOLUTE "${system_resolved_item}" AND EXISTS "${system_resolved_item}")
+ set(${resolved_item_var} "${system_resolved_item}" PARENT_SCOPE)
+ else(IS_ABSOLUTE "${system_resolved_item}" AND EXISTS "${system_resolved_item}")
+ message(FATAL_ERROR "cannot resolve item '${item}' in context:'${context}'. Partially resolved path is: '${system_resolved_item}'")
+ endif(IS_ABSOLUTE "${system_resolved_item}" AND EXISTS "${system_resolved_item}")
+ else(APPLE)
+ message(FATAL_ERROR "cannot resolve item '${item}' in context:'${context}'. Partially resolved path is: '${resolved_item}'")
+ endif(APPLE)
endif(IS_ABSOLUTE "${resolved_item}" AND EXISTS "${resolved_item}")
endfunction(resolve_item)
@@ -310,17 +325,21 @@ function(change_install_names_for_item keys_var key)
# Each referenced item's key is "rkey" in the loop:
get_filename_component(exepath ${${key}_RESOLVED_EMBEDDED_ITEM} PATH)
resolve_item( ${${key}_RESOLVED_EMBEDDED_ITEM} ${pr} exepath resolved_pr)
- get_item_key("${resolved_pr}" rkey)
- list(FIND ${keys_var} ${rkey} r_found)
- if(r_found EQUAL -1)
- MESSAGE(FATAL_ERROR "Key: '${rkey}' not found in dependency list. Cannot change install name.")
- endif(r_found EQUAL -1)
- if(NOT ${${rkey}_SYSTEMFLAG})
- get_filename_component(ref_exepath ${${rkey}_RESOLVED_EMBEDDED_ITEM} PATH)
- string(REPLACE ${CMAKE_INSTALL_PREFIX} "" ref_rel_path ${ref_exepath})
- set(diff_path @loader_path${inv_rel_path}${ref_rel_path}/)
- set(changes ${changes} "-change" "${pr}" "${diff_path}${${rkey}_ITEM}")
- endif(NOT ${${rkey}_SYSTEMFLAG})
+ # If dependency already resolves to library within install directory we don't have to do anything.
+ if(NOT (${resolved_pr} MATCHES ${CMAKE_INSTALL_PREFIX}) AND EXISTS "${resolved_pr}" )
+ get_item_key("${resolved_pr}" rkey)
+ list(FIND ${keys_var} ${rkey} r_found)
+ if(r_found EQUAL -1)
+ message("Error while trying to get dependencies for ${${key}_RESOLVED_EMBEDDED_ITEM}.")
+ MESSAGE(FATAL_ERROR "Key: '${rkey}' not found in dependency list. Cannot change install name.")
+ endif(r_found EQUAL -1)
+ if(NOT ${${rkey}_SYSTEMFLAG})
+ get_filename_component(ref_exepath ${${rkey}_RESOLVED_EMBEDDED_ITEM} PATH)
+ string(REPLACE ${CMAKE_INSTALL_PREFIX} "" ref_rel_path ${ref_exepath})
+ set(diff_path @loader_path${inv_rel_path}${ref_rel_path}/)
+ set(changes ${changes} "-change" "${pr}" "${diff_path}${${rkey}_ITEM}")
+ endif(NOT ${${rkey}_SYSTEMFLAG})
+ endif(NOT (${resolved_pr} MATCHES ${CMAKE_INSTALL_PREFIX}) AND EXISTS "${resolved_pr}" )
endforeach(pr)
execute_process(COMMAND chmod u+w "${${key}_RESOLVED_EMBEDDED_ITEM}")
@@ -414,37 +433,6 @@ function(append_unique list_var value)
endfunction(append_unique)
-#=============================================================================
-# function copy_python
-#=============================================================================
-function(copy_python include_path version new_binary_path)
-
-
- get_filename_component(real_python_include_path ${include_path} REALPATH)
- get_filename_component(python_root_dir ${real_python_include_path}/../.. REALPATH)
- file(COPY ${python_root_dir}/${LIB_DIR}/python${version}/ DESTINATION ${CMAKE_INSTALL_PREFIX}/${LIB_DIR}/python${version})
- file(GLOB py_config_files "${include_path}/pyconfig*.h")
- file(COPY ${py_config_files} DESTINATION ${CMAKE_INSTALL_PREFIX}/include/python${version})
- file(GLOB_RECURSE python_so_files "${CMAKE_INSTALL_PREFIX}/${LIB_DIR}/python${version}/*.so")
- if(NOT APPLE)
- foreach(so_file ${python_so_files})
- remove_rpath("${so_file}")
- endforeach(so_file)
- endif(NOT APPLE)
- read_config(ost_config)
- if(APPLE)
- file(COPY ${python_root_dir}/Resources/Python.app/Contents/MacOS/Python DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
- set(${new_binary_path} "${CMAKE_INSTALL_PREFIX}/bin/Python" PARENT_SCOPE)
- string(REGEX REPLACE "pyexec=\"[^\n\$]*\"" "pyexec=\"\$DNG_BINDIR/Python\"\nexport PYTHONHOME=\$DNG_ROOT" ost_config "${ost_config}")
- else(APPLE)
- file(GLOB python_libs "${python_root_dir}/${LIB_DIR}/libpython${version}.so*")
- file(COPY ${python_libs} DESTINATION ${CMAKE_INSTALL_PREFIX}/${LIB_DIR})
- file(COPY ${python_root_dir}/bin/python${version} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
- set(${new_binary_path} "${CMAKE_INSTALL_PREFIX}/bin/python${version}" PARENT_SCOPE)
- string(REGEX REPLACE "pyexec=\"[^\n\$]*\"" "pyexec=\"\$DNG_BINDIR/python${version}\"\nexport PYTHONHOME=\$DNG_ROOT" ost_config "${ost_config}")
- endif(APPLE)
- write_config("${ost_config}")
-endfunction(copy_python)
#=============================================================================
# function read_config
@@ -625,7 +613,11 @@ endfunction(get_rpath)
# function copy_qt (OSX)
#=============================================================================
function(copy_qt library_dir plugin_dir plugins)
- file(COPY "${library_dir}/Resources/qt_menu.nib"
+ find_file(QT_MENU_NIB qt_menu.nib PATHS ${library_dir}/QtGui.framework/Versions/4 ${library_dir} PATH_SUFFIXES Resources)
+ if(NOT QT_MENU_NIB)
+ message(FATAL "qt_menu.nib not found")
+ endif(NOT QT_MENU_NIB)
+ file(COPY "${QT_MENU_NIB}"
DESTINATION "${CMAKE_INSTALL_PREFIX}/${LIBEXEC_PATH}/"
FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
file(COPY ${plugin_dir}
@@ -667,12 +659,13 @@ function(copy_python include_path version new_binary_path)
get_filename_component(real_python_include_path ${include_path} REALPATH)
get_filename_component(python_root_dir ${real_python_include_path}/../.. REALPATH)
+ file(COPY ${python_root_dir}/Resources/Python.app/Contents/MacOS/Python DESTINATION ${CMAKE_INSTALL_PREFIX})
file(COPY ${python_root_dir}/${LIB_DIR}/python${version}/ DESTINATION ${CMAKE_INSTALL_PREFIX}/${LIB_DIR}/python${version})
file(GLOB py_config_files "${include_path}/pyconfig*.h")
file(COPY ${py_config_files} DESTINATION ${CMAKE_INSTALL_PREFIX}/include/python${version})
file(GLOB_RECURSE python_so_files "${CMAKE_INSTALL_PREFIX}/${LIB_DIR}/python${version}/*.so")
foreach(so_file ${python_so_files})
- file(RPATH_REMOVE FILE "${so_file}")
+ remove_rpath( "${so_file}")
endforeach(so_file)
read_config(ost_config)
file(COPY ${python_root_dir}/Resources/Python.app/Contents/MacOS/Python DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
@@ -681,6 +674,19 @@ function(copy_python include_path version new_binary_path)
write_config("${ost_config}")
endfunction(copy_python)
+#=============================================================================
+# function remove_rpath (OSX)
+#=============================================================================
+function(remove_rpath file)
+ get_rpath(${file} rpath)
+ if(${rpath})
+ execute_process(COMMAND stat -f %Mp%Lp "${file}" OUTPUT_VARIABLE permissions)
+ execute_process(COMMAND chmod ugo+wx "${file}")
+ string(SUBSTRING ${permissions} 0 3 permissions)
+ file(RPATH_REMOVE FILE "${file}")
+ execute_process(COMMAND chmod ${permissions} "${file}")
+ endif(${rpath})
+endfunction(remove_rpath)
elseif(WIN32 AND NOT UNIX)
@@ -990,13 +996,14 @@ function(copy_python include_path version new_binary_path)
endforeach()
else()
file(COPY ${python_root_dir}/${LIB_DIR}/python${version}/ DESTINATION ${CMAKE_INSTALL_PREFIX}/${LIB_DIR}/python${version} PATTERN "*.pyc" EXCLUDE)
+ if("${LIB_DIR}" MATCHES "lib64")
+ # for 64 bit systems we have to copy the python dir within lib in addition as norarch site packages might get installed there
+ file(COPY ${python_root_dir}/lib/python${version}/ DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/python${version} PATTERN "*.pyc" EXCLUDE)
+ endif("${LIB_DIR}" MATCHES "lib64")
endif()
file(GLOB py_config_files "${include_path}/pyconfig*.h")
file(COPY ${py_config_files} DESTINATION ${CMAKE_INSTALL_PREFIX}/include/python${version})
file(GLOB_RECURSE python_so_files "${CMAKE_INSTALL_PREFIX}/${LIB_DIR}/python${version}/*.so")
- foreach(so_file ${python_so_files})
- file(RPATH_REMOVE FILE "${so_file}")
- endforeach(so_file)
read_config(ost_config)
if (_UBUNTU_LAYOUT)
file(GLOB python_libs "${python_root_dir}/${LIB_DIR}/python${version}/config-${UBUNTU_ARCH_STRING}-linux-gnu/libpython${version}.so.*" FOLLOW_SYMLINKS)
@@ -1004,9 +1011,15 @@ function(copy_python include_path version new_binary_path)
file(GLOB python_libs "${python_root_dir}/${LIB_DIR}/libpython${version}.so*")
endif()
file(COPY ${python_libs} DESTINATION ${CMAKE_INSTALL_PREFIX}/${LIB_DIR})
+ foreach( additional_directory $ENV{PYTHONPATH})
+ file(COPY ${additional_directory}/ DESTINATION ${CMAKE_INSTALL_PREFIX}/${LIB_DIR}/python${version}/site-packages PATTERN "*.pyc" EXCLUDE)
+ endforeach()
file(COPY ${python_root_dir}/bin/python${version} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
set(${new_binary_path} "${CMAKE_INSTALL_PREFIX}/bin/python${version}" PARENT_SCOPE)
string(REGEX REPLACE "pyexec=\"[^\n\$]*\"" "pyexec=\"\$DNG_BINDIR/python${version}\"\nexport PYTHONHOME=\$DNG_ROOT" ost_config "${ost_config}")
+ foreach(so_file ${python_so_files})
+ file(RPATH_REMOVE FILE "${so_file}")
+ endforeach(so_file)
write_config("${ost_config}")
endfunction(copy_python)
diff --git a/cmake_support/FindEigen.cmake b/cmake_support/FindEigen.cmake
index d927ace1f8c528b80e5d0eb9696a53907fb7c2c4..36e33176aea2c6592cf9c02dc9c9612900ad82de 100644
--- a/cmake_support/FindEigen.cmake
+++ b/cmake_support/FindEigen.cmake
@@ -1,32 +1,19 @@
-# - Try to find Eigen2 lib
+# - Try to find Eigen3 lib
# Once done this will define
#
-# EIGEN2_FOUND - system has eigen lib
-# EIGEN2_INCLUDE_DIR - the eigen include directory
+# EIGEN3_FOUND - system has eigen lib
+# EIGEN3_INCLUDE_DIRS - the eigen include directories
-# Copyright (c) 2006, 2007 Montel Laurent, <montel@kde.org>
-# Redistribution and use is allowed according to the terms of the BSD license.
-# For details see the accompanying COPYING-CMAKE-SCRIPTS file.
-#adapted for OpenStructure by Juergen Haas <juergen.haas@unibas.ch>
+find_path(EIGEN3_INCLUDE_DIR NAMES Eigen/Core
+PATH_SUFFIXES eigen3
+)
-if (EIGEN2_INCLUDE_DIR)
-
- # in cache already
- set(EIGEN2_FOUND TRUE)
-
-else (EIGEN2_INCLUDE_DIR)
-
- find_path(EIGEN2_INCLUDE_DIR NAMES Eigen/Core
- PATH_SUFFIXES eigen2
- HINTS
- ${INCLUDE_INSTALL_DIR}
- )
-endif(EIGEN2_INCLUDE_DIR)
+set(EIGEN3_INCLUDE_DIRS ${EIGEN3_INCLUDE_DIR})
include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args (EIGEN DEFAULT_MSG EIGEN2_INCLUDE_DIR)
+find_package_handle_standard_args (EIGEN DEFAULT_MSG EIGEN3_INCLUDE_DIR)
-mark_as_advanced (EIGEN2_INCLUDE_DIR)
+mark_as_advanced (EIGEN3_INCLUDE_DIR)
diff --git a/cmake_support/FindFFTW.cmake b/cmake_support/FindFFTW.cmake
index b1be94c3efaf55600b8ecdb519a85cb57923f520..aadff0df4d8fa78824d3005b9d3fea57520988f4 100644
--- a/cmake_support/FindFFTW.cmake
+++ b/cmake_support/FindFFTW.cmake
@@ -1,38 +1,34 @@
# Try to find FFTW
-# adapted from FINDEIGEN.cmake of OpenStructure by Juergen Haas <juergen.haas@unibas.ch>
-# license see FINDEIGEN.cmake
#
+# Once done this will define
# - Find FFTW
# Find the native FFTW includes and library
#
-# FFTW_INCLUDE_PATH - where to find gsl/gsl_*.h, etc.
-# FFTW_LIBRARIES - List of libraries when using FFTW.
-# FFTW_FOUND - True if FFTW found.
-
-if (FFTW_INCLUDE_PATH)
- set(FFTW_FOUND TRUE)
-else (FFTW_INCLUDE_PATH)
- find_path (FFTW_INCLUDE_PATH fftw3.h)
- if (_DOUBLE_PREC)
- find_library (FFTW_LIBRARIES NAMES fftw3)
- find_library (FFTW_THREADS_LIB NAMES fftw3_threads)
- elseif(NOT _DOUBLE_PREC)
- find_library (FFTW_LIBRARIES NAMES fftw3f)
- find_library (FFTW_THREADS_LIB NAMES fftw3f_threads)
- endif()
- if(FFTW_THREADS_LIB)
- SET(FFTW_USE_THREADS TRUE)
- SET(FFTW_LIBRARIES ${FFTW_LIBRARIES} ${FFTW_THREADS_LIB} )
- else(FFTW_THREADS_LIB)
- endif(FFTW_THREADS_LIB)
-endif (FFTW_INCLUDE_PATH)
+# FFTW_INCLUDE_DIRS - FFTW include dirs.
+# FFTW_LIBRARIES - List of libraries when using FFTW.
+# FFTW_FOUND - True if FFTW found.
+find_path (FFTW_INCLUDE_DIR fftw3.h)
+if (_DOUBLE_PREC)
+ find_library (FFTW_LIBRARY NAMES fftw3)
+ find_library (FFTW_THREADS_LIB NAMES fftw3_threads)
+elseif(NOT _DOUBLE_PREC)
+ find_library (FFTW_LIBRARY NAMES fftw3f)
+ find_library (FFTW_THREADS_LIBRARY NAMES fftw3f_threads)
+endif()
+if(FFTW_THREADS_LIBRARY)
+ set(FFTW_USE_THREADS TRUE)
+ set(FFTW_LIBRARIES ${FFTW_LIBRARY} ${FFTW_THREADS_LIBRARY} )
+else(FFTW_THREADS_LIBRARY)
+ set(FFTW_LIBRARIES ${FFTW_LIBRARY} )
+endif(FFTW_THREADS_LIBRARY)
+set(FFTW_INCLUDE_DIRS ${FFTW_INCLUDE_DIR})
# handle the QUIETLY and REQUIRED arguments and set FFTW_FOUND to TRUE if
# all listed variables are TRUE
include (FindPackageHandleStandardArgs)
-find_package_handle_standard_args (FFTW DEFAULT_MSG FFTW_LIBRARIES FFTW_INCLUDE_PATH)
+find_package_handle_standard_args (FFTW DEFAULT_MSG FFTW_LIBRARY FFTW_INCLUDE_DIR)
-mark_as_advanced (FFTW_LIBRARIES FFTW_INCLUDE_PATH)
+mark_as_advanced (FFTW_LIBRARY FFTW_THREADS_LIBRARY FFTW_INCLUDE_DIR)
diff --git a/cmake_support/FindOpenMM.cmake b/cmake_support/FindOpenMM.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..d4581c95e1060c7630505e46e73a52b777ed1628
--- /dev/null
+++ b/cmake_support/FindOpenMM.cmake
@@ -0,0 +1,43 @@
+# Try to find OpenMM
+#
+# Once done this will define
+# - Find OpenMM
+# Find the native OpenMM includes and library
+#
+# OPEN_MM_INCLUDE_DIR - OpenMM include dirs.
+# OPEN_MM_LIBRARIES - List of libraries when using OpenMM.
+# OPEN_MM_FOUND - True if OpenMM found.
+# OPEN_MM_PLUGIN_DIR - Default for ressource plugins
+
+if (OPEN_MM_INCLUDE_DIR)
+ set(OPEN_MM_FOUND TRUE)
+else (OPEN_MM_INCLUDE_DIR)
+ find_path (OPEN_MM_INCLUDE_DIR OpenMM.h)
+endif (OPEN_MM_INCLUDE_DIR)
+
+if (OPEN_MM_LIBRARY)
+ set(OPEN_MM_FOUND TRUE)
+else (OPEN_MM_LIBRARY)
+ find_library (OPEN_MM_LIBRARY NAMES OpenMM)
+endif(OPEN_MM_LIBRARY)
+
+set(OPEN_MM_LIBRARIES ${OPEN_MM_LIBRARY})
+set(OPEN_MM_INCLUDE_DIRS ${OPEN_MM_INCLUDE_DIR})
+
+# handle the QUIETLY and REQUIRED arguments and set OpenMM_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (OpenMM DEFAULT_MSG OPEN_MM_LIBRARY OPEN_MM_INCLUDE_DIR)
+
+if (OPEN_MM_LIBRARY)
+ set(OPEN_MM_FOUND TRUE)
+ if (NOT OPEN_MM_PLUGIN_DIR)
+ set(OPEN_MM_PLUGIN_DIR "/usr/local/openmm/lib/plugins")
+ endif (NOT OPEN_MM_PLUGIN_DIR)
+ if (NOT EXISTS "${OPEN_MM_PLUGIN_DIR}")
+ message(FATAL_ERROR "OpenMM plugin directory does not exist: '${OPEN_MM_PLUGIN_DIR}'")
+ endif (NOT EXISTS "${OPEN_MM_PLUGIN_DIR}")
+endif (OPEN_MM_LIBRARY)
+
+mark_as_advanced (OPEN_MM_LIBRARY OPEN_MM_INCLUDE_DIR OPEN_MM_FOUND
+ OPEN_MM_PLUGIN_DIR)
diff --git a/cmake_support/OST.cmake b/cmake_support/OST.cmake
index 27b9a5eb42a27b410374ab4bcd29f343be436e2c..94cadd2ff04d812c2c8aa02e63d2ec8b72f45d06 100644
--- a/cmake_support/OST.cmake
+++ b/cmake_support/OST.cmake
@@ -661,10 +661,13 @@ macro(ost_unittest)
set_target_properties(${_test_name} PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG "${CMAKE_BINARY_DIR}/tests" )
set_target_properties(${_test_name} PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE "${CMAKE_BINARY_DIR}/tests" )
+ target_link_libraries(${_test_name} ${BOOST_UNIT_TEST_LIBRARIES} "${_ARG_PREFIX}_${_ARG_MODULE}")
if (WIN32)
- target_link_libraries(${_test_name} ${BOOST_UNIT_TEST_LIBRARIES} "${_ARG_PREFIX}_${_ARG_MODULE}")
- add_custom_target("${_test_name}_run":
- COMMAND set PATH=${STAGE_DIR}/bin\;%PATH% & ${CMAKE_CURRENT_BINARY_DIR}/${_test_name}.exe || echo
+ set(TEST_COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${_test_name}.exe || echo)
+ message(${TEST_COMMAND})
+ set(ENV{PP} ${STAGE_DIR}/bin)
+ add_custom_target("${_test_name}_run"
+ COMMAND echo %PP%
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
COMMENT "running checks for module ${_ARG_MODULE}"
DEPENDS ${_test_name})
@@ -672,8 +675,6 @@ macro(ost_unittest)
set_target_properties("${_test_name}_run" PROPERTIES EXCLUDE_FROM_ALL "1")
add_dependencies(check "${_test_name}_run")
else()
- target_link_libraries(${_test_name} ${BOOST_UNIT_TEST_LIBRARIES}
- "${_ARG_PREFIX}_${_ARG_MODULE}")
add_custom_target("${_test_name}_run"
COMMAND OST_ROOT=${STAGE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/${_test_name} || echo
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
@@ -699,7 +700,13 @@ macro(ost_unittest)
endif()
foreach(py_test ${PY_TESTS})
+ set(python_path $ENV{PYTHONPATH})
+ if(python_path)
+ set(python_path "${python_path}:")
+ endif(python_path)
+ set(python_path "${python_path}${LIB_STAGE_PATH}/python${PYTHON_VERSION}/site-packages")
if(WIN32)
+ set (PY_TESTS_CMD "PYTHONPATH=${python_path} ${PYTHON_BINARY}")
# todo fix python unit test running for Windows
#set (PY_TESTS_CMD "${EXECUTABLE_OUTPUT_PATH}/ost.bat")
#add_custom_target("${py_test}_run"
@@ -710,11 +717,6 @@ macro(ost_unittest)
#add_dependencies("${py_test}_run" ost_scripts "_${_ARG_PREFIX}_${_ARG_MODULE}")
#add_dependencies(check "${py_test}_run")
else()
- set(python_path $ENV{PYTHONPATH})
- if(python_path)
- set(python_path "${python_path}:")
- endif(python_path)
- set(python_path "${python_path}${LIB_STAGE_PATH}/python${PYTHON_VERSION}/site-packages")
set (PY_TESTS_CMD "PYTHONPATH=${python_path} ${PYTHON_BINARY}")
add_custom_target("${py_test}_run"
sh -c "${PY_TESTS_CMD} ${CMAKE_CURRENT_SOURCE_DIR}/${py_test} || echo"
@@ -825,6 +827,9 @@ macro(setup_stage)
set(HEADER_STAGE_PATH ${STAGE_DIR}/include )
set(SHARED_DATA_PATH ${STAGE_DIR}/share/openstructure )
+ if (WIN32)
+ set(ENV{PATH} ${STAGE_DIR}/bin\;$ENV{PATH})
+ endif (WIN32)
if (UNIX AND NOT APPLE)
check_architecture()
endif()
@@ -896,6 +901,7 @@ endmacro()
set(_BOOST_MIN_VERSION 1.31)
macro(setup_boost)
+ set (Boost_NO_BOOST_CMAKE TRUE)
find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS python REQUIRED)
set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
set(Boost_LIBRARIES)
@@ -919,4 +925,7 @@ macro(setup_boost)
find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS regex REQUIRED)
set(BOOST_REGEX_LIBRARIES ${Boost_LIBRARIES})
set(Boost_LIBRARIES)
+ find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS thread REQUIRED)
+ set(BOOST_THREAD ${Boost_LIBRARIES})
+ set(Boost_LIBRARIES)
endmacro()
diff --git a/deployment/macos/CMakeLists.txt b/deployment/macos/CMakeLists.txt
index 0183d8ec8ec09181350a76f15b0eb29ec3292d6a..e2e9bc675fc696960353b7e4546ab1671692c1e3 100644
--- a/deployment/macos/CMakeLists.txt
+++ b/deployment/macos/CMakeLists.txt
@@ -15,6 +15,7 @@ set(CPACK_PACKAGE_INSTALL_DIRECTORY "openstructure ${OST_VERSION_STRING}" )
install(CODE "
if(NOT ${CMAKE_INSTALL_PREFIX} STREQUAL \${CMAKE_INSTALL_PREFIX})
set(LIB_DIR ${LIB_DIR}) #pass libdir variable in install code block
+ set(LIBEXEC_PATH ${LIBEXEC_PATH})#pass libexec_path variable in install code block
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
include(CopyDependencies)
diff --git a/deployment/macos/Info.plist b/deployment/macos/Info.plist
new file mode 100644
index 0000000000000000000000000000000000000000..5169acff8e7a7856db28a8da5ba607604e489c73
--- /dev/null
+++ b/deployment/macos/Info.plist
@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN"
+ "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+ <key>CFBundleDevelopmentRegion</key>
+ <string>English</string>
+ <key>CFBundleExecutable</key>
+ <string>dng</string>
+ <key>CFBundleName</key>
+ <string>DNG</string>
+ <key>CFBundleDisplayName</key>
+ <string>DNG</string>
+ <key>CFBundleHelpBookFolder</key>
+ <string>OpenStructure Manual</string>
+ <key>CFBundleHelpBookName</key>
+ <string>OpenStructure Help</string>
+ <key>CFBundleIconFile</key>
+ <string>DNG.icns</string>
+ <key>CFBundleIdentifier</key>
+ <string>org.openstructure.OpenStructure</string>
+ <key>CFBundleInfoDictionaryVersion</key>
+ <string>6.0</string>
+ <key>CFBundlePackageType</key>
+ <string>APPL</string>
+ <key>CFBundleSignature</key>
+ <string>????</string>
+ <key>CFBundleVersion</key>
+ <string></string>
+ <key>NSMainNibFile</key>
+ <string>MainMenu</string>
+ <key>NSPrincipalClass</key>
+ <string>NSApplication</string>
+</dict>
+</plist>
diff --git a/examples/code_fragments/mm/1CRN.pdb b/examples/code_fragments/mm/1CRN.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..13ca618d438ae60a55a8ce1c532cd23bf545e200
--- /dev/null
+++ b/examples/code_fragments/mm/1CRN.pdb
@@ -0,0 +1,329 @@
+ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N
+ATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C
+ATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C
+ATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O
+ATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C
+ATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O
+ATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C
+ATOM 8 N THR A 2 15.115 11.555 5.265 1.00 7.81 N
+ATOM 9 CA THR A 2 13.856 11.469 6.066 1.00 8.31 C
+ATOM 10 C THR A 2 14.164 10.785 7.379 1.00 5.80 C
+ATOM 11 O THR A 2 14.993 9.862 7.443 1.00 6.94 O
+ATOM 12 CB THR A 2 12.732 10.711 5.261 1.00 10.32 C
+ATOM 13 OG1 THR A 2 13.308 9.439 4.926 1.00 12.81 O
+ATOM 14 CG2 THR A 2 12.484 11.442 3.895 1.00 11.90 C
+ATOM 15 N CYS A 3 13.488 11.241 8.417 1.00 5.24 N
+ATOM 16 CA CYS A 3 13.660 10.707 9.787 1.00 5.39 C
+ATOM 17 C CYS A 3 12.269 10.431 10.323 1.00 4.45 C
+ATOM 18 O CYS A 3 11.393 11.308 10.185 1.00 6.54 O
+ATOM 19 CB CYS A 3 14.368 11.748 10.691 1.00 5.99 C
+ATOM 20 SG CYS A 3 15.885 12.426 10.016 1.00 7.01 S
+ATOM 21 N CYS A 4 12.019 9.272 10.928 1.00 3.90 N
+ATOM 22 CA CYS A 4 10.646 8.991 11.408 1.00 4.24 C
+ATOM 23 C CYS A 4 10.654 8.793 12.919 1.00 3.72 C
+ATOM 24 O CYS A 4 11.659 8.296 13.491 1.00 5.30 O
+ATOM 25 CB CYS A 4 10.057 7.752 10.682 1.00 4.41 C
+ATOM 26 SG CYS A 4 9.837 8.018 8.904 1.00 4.72 S
+ATOM 27 N PRO A 5 9.561 9.108 13.563 1.00 3.96 N
+ATOM 28 CA PRO A 5 9.448 9.034 15.012 1.00 4.25 C
+ATOM 29 C PRO A 5 9.288 7.670 15.606 1.00 4.96 C
+ATOM 30 O PRO A 5 9.490 7.519 16.819 1.00 7.44 O
+ATOM 31 CB PRO A 5 8.230 9.957 15.345 1.00 5.11 C
+ATOM 32 CG PRO A 5 7.338 9.786 14.114 1.00 5.24 C
+ATOM 33 CD PRO A 5 8.366 9.804 12.958 1.00 5.20 C
+ATOM 34 N SER A 6 8.875 6.686 14.796 1.00 4.83 N
+ATOM 35 CA SER A 6 8.673 5.314 15.279 1.00 4.45 C
+ATOM 36 C SER A 6 8.753 4.376 14.083 1.00 4.99 C
+ATOM 37 O SER A 6 8.726 4.858 12.923 1.00 4.61 O
+ATOM 38 CB SER A 6 7.340 5.121 15.996 1.00 5.05 C
+ATOM 39 OG SER A 6 6.274 5.220 15.031 1.00 6.39 O
+ATOM 40 N ILE A 7 8.881 3.075 14.358 1.00 4.94 N
+ATOM 41 CA ILE A 7 8.912 2.083 13.258 1.00 6.33 C
+ATOM 42 C ILE A 7 7.581 2.090 12.506 1.00 5.32 C
+ATOM 43 O ILE A 7 7.670 2.031 11.245 1.00 6.85 O
+ATOM 44 CB ILE A 7 9.207 0.677 13.924 1.00 8.43 C
+ATOM 45 CG1 ILE A 7 10.714 0.702 14.312 1.00 9.78 C
+ATOM 46 CG2 ILE A 7 8.811 -0.477 12.969 1.00 11.70 C
+ATOM 47 CD1 ILE A 7 11.185 -0.516 15.142 1.00 9.92 C
+ATOM 48 N VAL A 8 6.458 2.162 13.159 1.00 5.02 N
+ATOM 49 CA VAL A 8 5.145 2.209 12.453 1.00 6.93 C
+ATOM 50 C VAL A 8 5.115 3.379 11.461 1.00 5.39 C
+ATOM 51 O VAL A 8 4.664 3.268 10.343 1.00 6.30 O
+ATOM 52 CB VAL A 8 3.995 2.354 13.478 1.00 9.64 C
+ATOM 53 CG1 VAL A 8 2.716 2.891 12.869 1.00 13.85 C
+ATOM 54 CG2 VAL A 8 3.758 1.032 14.208 1.00 11.97 C
+ATOM 55 N ALA A 9 5.606 4.546 11.941 1.00 3.73 N
+ATOM 56 CA ALA A 9 5.598 5.767 11.082 1.00 3.56 C
+ATOM 57 C ALA A 9 6.441 5.527 9.850 1.00 4.13 C
+ATOM 58 O ALA A 9 6.052 5.933 8.744 1.00 4.36 O
+ATOM 59 CB ALA A 9 6.022 6.977 11.891 1.00 4.80 C
+ATOM 60 N ARG A 10 7.647 4.909 10.005 1.00 3.73 N
+ATOM 61 CA ARG A 10 8.496 4.609 8.837 1.00 3.38 C
+ATOM 62 C ARG A 10 7.798 3.609 7.876 1.00 3.47 C
+ATOM 63 O ARG A 10 7.878 3.778 6.651 1.00 4.67 O
+ATOM 64 CB ARG A 10 9.847 4.020 9.305 1.00 3.95 C
+ATOM 65 CG ARG A 10 10.752 3.607 8.149 1.00 4.55 C
+ATOM 66 CD ARG A 10 11.226 4.699 7.244 1.00 5.89 C
+ATOM 67 NE ARG A 10 12.143 5.571 8.035 1.00 6.20 N
+ATOM 68 CZ ARG A 10 12.758 6.609 7.443 1.00 7.52 C
+ATOM 69 NH1 ARG A 10 12.539 6.932 6.158 1.00 10.68 N
+ATOM 70 NH2 ARG A 10 13.601 7.322 8.202 1.00 9.48 N
+ATOM 71 N SER A 11 7.186 2.582 8.445 1.00 5.19 N
+ATOM 72 CA SER A 11 6.500 1.584 7.565 1.00 4.60 C
+ATOM 73 C SER A 11 5.382 2.313 6.773 1.00 4.84 C
+ATOM 74 O SER A 11 5.213 2.016 5.557 1.00 5.84 O
+ATOM 75 CB SER A 11 5.908 0.462 8.400 1.00 5.91 C
+ATOM 76 OG SER A 11 6.990 -0.272 9.012 1.00 8.38 O
+ATOM 77 N ASN A 12 4.648 3.182 7.446 1.00 3.54 N
+ATOM 78 CA ASN A 12 3.545 3.935 6.751 1.00 4.57 C
+ATOM 79 C ASN A 12 4.107 4.851 5.691 1.00 4.14 C
+ATOM 80 O ASN A 12 3.536 5.001 4.617 1.00 5.52 O
+ATOM 81 CB ASN A 12 2.663 4.677 7.748 1.00 6.42 C
+ATOM 82 CG ASN A 12 1.802 3.735 8.610 1.00 8.25 C
+ATOM 83 OD1 ASN A 12 1.567 2.613 8.165 1.00 12.72 O
+ATOM 84 ND2 ASN A 12 1.394 4.252 9.767 1.00 9.92 N
+ATOM 85 N PHE A 13 5.259 5.498 6.005 1.00 3.43 N
+ATOM 86 CA PHE A 13 5.929 6.358 5.055 1.00 3.49 C
+ATOM 87 C PHE A 13 6.304 5.578 3.799 1.00 3.40 C
+ATOM 88 O PHE A 13 6.136 6.072 2.653 1.00 4.07 O
+ATOM 89 CB PHE A 13 7.183 6.994 5.754 1.00 5.48 C
+ATOM 90 CG PHE A 13 7.884 8.006 4.883 1.00 5.57 C
+ATOM 91 CD1 PHE A 13 8.906 7.586 4.027 1.00 6.99 C
+ATOM 92 CD2 PHE A 13 7.532 9.373 4.983 1.00 6.52 C
+ATOM 93 CE1 PHE A 13 9.560 8.539 3.194 1.00 8.20 C
+ATOM 94 CE2 PHE A 13 8.176 10.281 4.145 1.00 6.34 C
+ATOM 95 CZ PHE A 13 9.141 9.845 3.292 1.00 6.84 C
+ATOM 96 N ASN A 14 6.900 4.390 3.989 1.00 3.64 N
+ATOM 97 CA ASN A 14 7.331 3.607 2.791 1.00 4.31 C
+ATOM 98 C ASN A 14 6.116 3.210 1.915 1.00 3.98 C
+ATOM 99 O ASN A 14 6.240 3.144 0.684 1.00 6.22 O
+ATOM 100 CB ASN A 14 8.145 2.404 3.240 1.00 5.81 C
+ATOM 101 CG ASN A 14 9.555 2.856 3.730 1.00 6.82 C
+ATOM 102 OD1 ASN A 14 10.013 3.895 3.323 1.00 9.43 O
+ATOM 103 ND2 ASN A 14 10.120 1.956 4.539 1.00 8.21 N
+ATOM 104 N VAL A 15 4.993 2.927 2.571 1.00 3.76 N
+ATOM 105 CA VAL A 15 3.782 2.599 1.742 1.00 3.98 C
+ATOM 106 C VAL A 15 3.296 3.871 1.004 1.00 3.80 C
+ATOM 107 O VAL A 15 2.947 3.817 -0.189 1.00 4.85 O
+ATOM 108 CB VAL A 15 2.698 1.953 2.608 1.00 4.71 C
+ATOM 109 CG1 VAL A 15 1.384 1.826 1.806 1.00 6.67 C
+ATOM 110 CG2 VAL A 15 3.174 0.533 3.005 1.00 6.26 C
+ATOM 111 N CYS A 16 3.321 4.987 1.720 1.00 3.79 N
+ATOM 112 CA CYS A 16 2.890 6.285 1.126 1.00 3.54 C
+ATOM 113 C CYS A 16 3.687 6.597 -0.111 1.00 3.48 C
+ATOM 114 O CYS A 16 3.200 7.147 -1.103 1.00 4.63 O
+ATOM 115 CB CYS A 16 3.039 7.369 2.240 1.00 4.58 C
+ATOM 116 SG CYS A 16 2.559 9.014 1.649 1.00 5.66 S
+ATOM 117 N ARG A 17 4.997 6.227 -0.100 1.00 3.99 N
+ATOM 118 CA ARG A 17 5.895 6.489 -1.213 1.00 3.83 C
+ATOM 119 C ARG A 17 5.738 5.560 -2.409 1.00 3.79 C
+ATOM 120 O ARG A 17 6.228 5.901 -3.507 1.00 5.39 O
+ATOM 121 CB ARG A 17 7.370 6.507 -0.731 1.00 4.11 C
+ATOM 122 CG ARG A 17 7.717 7.687 0.206 1.00 4.69 C
+ATOM 123 CD ARG A 17 7.949 8.947 -0.615 1.00 5.10 C
+ATOM 124 NE ARG A 17 9.212 8.856 -1.337 1.00 4.71 N
+ATOM 125 CZ ARG A 17 9.537 9.533 -2.431 1.00 5.28 C
+ATOM 126 NH1 ARG A 17 8.659 10.350 -3.032 1.00 6.67 N
+ATOM 127 NH2 ARG A 17 10.793 9.491 -2.899 1.00 6.41 N
+ATOM 128 N LEU A 18 5.051 4.411 -2.204 1.00 4.70 N
+ATOM 129 CA LEU A 18 4.933 3.431 -3.326 1.00 5.46 C
+ATOM 130 C LEU A 18 4.397 4.014 -4.620 1.00 5.13 C
+ATOM 131 O LEU A 18 4.988 3.755 -5.687 1.00 5.55 O
+ATOM 132 CB LEU A 18 4.196 2.184 -2.863 1.00 6.47 C
+ATOM 133 CG LEU A 18 4.960 1.178 -1.991 1.00 7.43 C
+ATOM 134 CD1 LEU A 18 3.907 0.097 -1.634 1.00 8.70 C
+ATOM 135 CD2 LEU A 18 6.129 0.606 -2.768 1.00 9.39 C
+ATOM 136 N PRO A 19 3.329 4.795 -4.543 1.00 4.28 N
+ATOM 137 CA PRO A 19 2.792 5.376 -5.797 1.00 5.38 C
+ATOM 138 C PRO A 19 3.573 6.540 -6.322 1.00 6.30 C
+ATOM 139 O PRO A 19 3.260 7.045 -7.422 1.00 9.62 O
+ATOM 140 CB PRO A 19 1.358 5.766 -5.472 1.00 5.87 C
+ATOM 141 CG PRO A 19 1.223 5.694 -3.993 1.00 6.47 C
+ATOM 142 CD PRO A 19 2.421 4.941 -3.408 1.00 6.45 C
+ATOM 143 N GLY A 20 4.565 7.047 -5.559 1.00 4.94 N
+ATOM 144 CA GLY A 20 5.366 8.191 -6.018 1.00 5.39 C
+ATOM 145 C GLY A 20 5.007 9.481 -5.280 1.00 5.03 C
+ATOM 146 O GLY A 20 5.535 10.510 -5.730 1.00 7.34 O
+ATOM 147 N THR A 21 4.181 9.438 -4.262 1.00 4.10 N
+ATOM 148 CA THR A 21 3.767 10.609 -3.513 1.00 3.94 C
+ATOM 149 C THR A 21 5.017 11.397 -3.042 1.00 3.96 C
+ATOM 150 O THR A 21 5.947 10.757 -2.523 1.00 5.82 O
+ATOM 151 CB THR A 21 2.992 10.188 -2.225 1.00 4.13 C
+ATOM 152 OG1 THR A 21 2.051 9.144 -2.623 1.00 5.45 O
+ATOM 153 CG2 THR A 21 2.260 11.349 -1.551 1.00 5.41 C
+ATOM 154 N PRO A 22 4.971 12.703 -3.176 1.00 5.04 N
+ATOM 155 CA PRO A 22 6.143 13.513 -2.696 1.00 4.69 C
+ATOM 156 C PRO A 22 6.400 13.233 -1.225 1.00 4.19 C
+ATOM 157 O PRO A 22 5.485 13.061 -0.382 1.00 4.47 O
+ATOM 158 CB PRO A 22 5.703 14.969 -2.920 1.00 7.12 C
+ATOM 159 CG PRO A 22 4.676 14.893 -3.996 1.00 7.03 C
+ATOM 160 CD PRO A 22 3.964 13.567 -3.811 1.00 4.90 C
+ATOM 161 N GLU A 23 7.728 13.297 -0.921 1.00 5.16 N
+ATOM 162 CA GLU A 23 8.114 13.103 0.500 1.00 5.31 C
+ATOM 163 C GLU A 23 7.427 14.073 1.410 1.00 4.11 C
+ATOM 164 O GLU A 23 7.036 13.682 2.540 1.00 5.11 O
+ATOM 165 CB GLU A 23 9.648 13.285 0.660 1.00 6.16 C
+ATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C
+ATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C
+ATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O
+ATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O
+ATOM 170 N ALA A 24 7.212 15.334 0.966 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.614 16.317 1.913 1.00 4.49 C
+ATOM 172 C ALA A 24 5.212 15.936 2.350 1.00 4.10 C
+ATOM 173 O ALA A 24 4.782 16.166 3.495 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.605 17.695 1.246 1.00 5.80 C
+ATOM 175 N ILE A 25 4.445 15.318 1.405 1.00 4.37 N
+ATOM 176 CA ILE A 25 3.074 14.894 1.756 1.00 5.44 C
+ATOM 177 C ILE A 25 3.085 13.643 2.645 1.00 4.32 C
+ATOM 178 O ILE A 25 2.315 13.523 3.578 1.00 4.72 O
+ATOM 179 CB ILE A 25 2.204 14.637 0.462 1.00 6.42 C
+ATOM 180 CG1 ILE A 25 1.815 16.048 -0.129 1.00 7.50 C
+ATOM 181 CG2 ILE A 25 0.903 13.864 0.811 1.00 7.65 C
+ATOM 182 CD1 ILE A 25 0.756 16.761 0.757 1.00 7.80 C
+ATOM 183 N CYS A 26 4.032 12.764 2.313 1.00 3.92 N
+ATOM 184 CA CYS A 26 4.180 11.549 3.187 1.00 4.37 C
+ATOM 185 C CYS A 26 4.632 11.944 4.596 1.00 3.95 C
+ATOM 186 O CYS A 26 4.227 11.252 5.547 1.00 4.74 O
+ATOM 187 CB CYS A 26 5.038 10.518 2.539 1.00 4.63 C
+ATOM 188 SG CYS A 26 4.349 9.794 1.022 1.00 5.61 S
+ATOM 189 N ALA A 27 5.408 13.012 4.694 1.00 3.89 N
+ATOM 190 CA ALA A 27 5.879 13.502 6.026 1.00 4.43 C
+ATOM 191 C ALA A 27 4.696 13.908 6.882 1.00 4.26 C
+ATOM 192 O ALA A 27 4.528 13.422 8.025 1.00 5.44 O
+ATOM 193 CB ALA A 27 6.880 14.615 5.830 1.00 5.36 C
+ATOM 194 N THR A 28 3.827 14.802 6.358 1.00 4.53 N
+ATOM 195 CA THR A 28 2.691 15.221 7.194 1.00 5.08 C
+ATOM 196 C THR A 28 1.672 14.132 7.434 1.00 4.62 C
+ATOM 197 O THR A 28 0.947 14.112 8.468 1.00 7.80 O
+ATOM 198 CB THR A 28 1.986 16.520 6.614 1.00 6.03 C
+ATOM 199 OG1 THR A 28 1.664 16.221 5.230 1.00 7.19 O
+ATOM 200 CG2 THR A 28 2.914 17.739 6.700 1.00 7.34 C
+ATOM 201 N TYR A 29 1.621 13.190 6.511 1.00 5.01 N
+ATOM 202 CA TYR A 29 0.715 12.045 6.657 1.00 6.60 C
+ATOM 203 C TYR A 29 1.125 11.125 7.815 1.00 4.92 C
+ATOM 204 O TYR A 29 0.286 10.632 8.545 1.00 7.13 O
+ATOM 205 CB TYR A 29 0.755 11.229 5.322 1.00 9.66 C
+ATOM 206 CG TYR A 29 -0.203 10.044 5.354 1.00 11.56 C
+ATOM 207 CD1 TYR A 29 -1.547 10.337 5.645 1.00 12.85 C
+ATOM 208 CD2 TYR A 29 0.193 8.750 5.100 1.00 14.44 C
+ATOM 209 CE1 TYR A 29 -2.496 9.329 5.673 1.00 16.61 C
+ATOM 210 CE2 TYR A 29 -0.801 7.705 5.156 1.00 17.11 C
+ATOM 211 CZ TYR A 29 -2.079 8.031 5.430 1.00 19.99 C
+ATOM 212 OH TYR A 29 -3.097 7.057 5.458 1.00 28.98 O
+ATOM 213 N THR A 30 2.470 10.984 7.995 1.00 5.31 N
+ATOM 214 CA THR A 30 2.986 9.994 8.950 1.00 5.70 C
+ATOM 215 C THR A 30 3.609 10.505 10.230 1.00 6.28 C
+ATOM 216 O THR A 30 3.766 9.715 11.186 1.00 8.77 O
+ATOM 217 CB THR A 30 4.076 9.103 8.225 1.00 6.55 C
+ATOM 218 OG1 THR A 30 5.125 10.027 7.824 1.00 6.57 O
+ATOM 219 CG2 THR A 30 3.493 8.324 7.035 1.00 7.29 C
+ATOM 220 N GLY A 31 3.984 11.764 10.241 1.00 4.99 N
+ATOM 221 CA GLY A 31 4.769 12.336 11.360 1.00 5.50 C
+ATOM 222 C GLY A 31 6.255 12.243 11.106 1.00 4.19 C
+ATOM 223 O GLY A 31 7.037 12.750 11.954 1.00 6.12 O
+ATOM 224 N CYS A 32 6.710 11.631 9.992 1.00 4.30 N
+ATOM 225 CA CYS A 32 8.140 11.694 9.635 1.00 4.89 C
+ATOM 226 C CYS A 32 8.500 13.141 9.206 1.00 5.50 C
+ATOM 227 O CYS A 32 7.581 13.949 8.944 1.00 5.82 O
+ATOM 228 CB CYS A 32 8.504 10.686 8.530 1.00 4.66 C
+ATOM 229 SG CYS A 32 8.048 8.987 8.881 1.00 5.33 S
+ATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N
+ATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C
+ATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C
+ATOM 233 O ILE A 33 11.971 13.583 7.552 1.00 7.19 O
+ATOM 234 CB ILE A 33 10.790 15.535 10.085 1.00 5.49 C
+ATOM 235 CG1 ILE A 33 12.059 14.803 10.671 1.00 6.85 C
+ATOM 236 CG2 ILE A 33 9.684 15.686 11.138 1.00 6.45 C
+ATOM 237 CD1 ILE A 33 12.733 15.676 11.781 1.00 8.94 C
+ATOM 238 N ILE A 34 11.490 15.773 7.038 1.00 5.52 N
+ATOM 239 CA ILE A 34 12.552 15.877 6.036 1.00 6.82 C
+ATOM 240 C ILE A 34 13.590 16.917 6.560 1.00 6.92 C
+ATOM 241 O ILE A 34 13.168 18.006 6.945 1.00 9.22 O
+ATOM 242 CB ILE A 34 11.987 16.360 4.681 1.00 8.11 C
+ATOM 243 CG1 ILE A 34 10.914 15.338 4.163 1.00 9.59 C
+ATOM 244 CG2 ILE A 34 13.131 16.517 3.629 1.00 9.73 C
+ATOM 245 CD1 ILE A 34 10.151 16.024 2.938 1.00 13.41 C
+ATOM 246 N ILE A 35 14.856 16.493 6.536 1.00 7.06 N
+ATOM 247 CA ILE A 35 15.930 17.454 6.941 1.00 7.52 C
+ATOM 248 C ILE A 35 16.913 17.550 5.819 1.00 6.63 C
+ATOM 249 O ILE A 35 17.097 16.660 4.970 1.00 7.90 O
+ATOM 250 CB ILE A 35 16.622 16.995 8.285 1.00 8.07 C
+ATOM 251 CG1 ILE A 35 17.360 15.651 8.067 1.00 9.41 C
+ATOM 252 CG2 ILE A 35 15.592 16.974 9.434 1.00 9.46 C
+ATOM 253 CD1 ILE A 35 18.298 15.206 9.219 1.00 9.85 C
+ATOM 254 N PRO A 36 17.664 18.669 5.806 1.00 8.07 N
+ATOM 255 CA PRO A 36 18.635 18.861 4.738 1.00 8.78 C
+ATOM 256 C PRO A 36 19.925 18.042 4.949 1.00 8.31 C
+ATOM 257 O PRO A 36 20.593 17.742 3.945 1.00 9.09 O
+ATOM 258 CB PRO A 36 18.945 20.364 4.783 1.00 9.67 C
+ATOM 259 CG PRO A 36 18.238 20.937 5.908 1.00 10.15 C
+ATOM 260 CD PRO A 36 17.371 19.900 6.596 1.00 9.53 C
+ATOM 261 N GLY A 37 20.172 17.730 6.217 1.00 8.48 N
+ATOM 262 CA GLY A 37 21.452 16.969 6.513 1.00 9.20 C
+ATOM 263 C GLY A 37 21.143 15.478 6.427 1.00 10.41 C
+ATOM 264 O GLY A 37 20.138 15.023 5.878 1.00 12.06 O
+ATOM 265 N ALA A 38 22.055 14.701 7.032 1.00 9.24 N
+ATOM 266 CA ALA A 38 22.019 13.242 7.020 1.00 9.24 C
+ATOM 267 C ALA A 38 21.944 12.628 8.396 1.00 9.60 C
+ATOM 268 O ALA A 38 21.869 11.387 8.435 1.00 13.65 O
+ATOM 269 CB ALA A 38 23.246 12.697 6.275 1.00 10.43 C
+ATOM 270 N THR A 39 21.894 13.435 9.436 1.00 8.70 N
+ATOM 271 CA THR A 39 21.936 12.911 10.809 1.00 9.46 C
+ATOM 272 C THR A 39 20.615 13.191 11.521 1.00 8.32 C
+ATOM 273 O THR A 39 20.357 14.317 11.948 1.00 9.89 O
+ATOM 274 CB THR A 39 23.131 13.601 11.593 1.00 10.72 C
+ATOM 275 OG1 THR A 39 24.284 13.401 10.709 1.00 11.66 O
+ATOM 276 CG2 THR A 39 23.340 12.935 12.962 1.00 11.81 C
+ATOM 277 N CYS A 40 19.827 12.110 11.642 1.00 7.64 N
+ATOM 278 CA CYS A 40 18.504 12.312 12.298 1.00 8.05 C
+ATOM 279 C CYS A 40 18.684 12.451 13.784 1.00 7.63 C
+ATOM 280 O CYS A 40 19.533 11.718 14.362 1.00 9.64 O
+ATOM 281 CB CYS A 40 17.582 11.117 11.996 1.00 7.80 C
+ATOM 282 SG CYS A 40 17.199 10.929 10.237 1.00 7.30 S
+ATOM 283 N PRO A 41 17.880 13.266 14.426 1.00 8.00 N
+ATOM 284 CA PRO A 41 17.924 13.421 15.877 1.00 8.96 C
+ATOM 285 C PRO A 41 17.392 12.206 16.594 1.00 9.06 C
+ATOM 286 O PRO A 41 16.652 11.368 16.033 1.00 8.82 O
+ATOM 287 CB PRO A 41 17.076 14.658 16.145 1.00 10.39 C
+ATOM 288 CG PRO A 41 16.098 14.689 14.997 1.00 10.99 C
+ATOM 289 CD PRO A 41 16.859 14.150 13.779 1.00 10.49 C
+ATOM 290 N GLY A 42 17.728 12.124 17.884 1.00 7.55 N
+ATOM 291 CA GLY A 42 17.334 10.956 18.691 1.00 8.00 C
+ATOM 292 C GLY A 42 15.875 10.688 18.871 1.00 7.22 C
+ATOM 293 O GLY A 42 15.434 9.550 19.166 1.00 8.41 O
+ATOM 294 N ASP A 43 15.036 11.747 18.715 1.00 5.54 N
+ATOM 295 CA ASP A 43 13.564 11.573 18.836 1.00 5.85 C
+ATOM 296 C ASP A 43 12.936 11.227 17.470 1.00 5.87 C
+ATOM 297 O ASP A 43 11.720 11.040 17.428 1.00 7.29 O
+ATOM 298 CB ASP A 43 12.933 12.737 19.580 1.00 6.72 C
+ATOM 299 CG ASP A 43 13.140 14.094 18.958 1.00 8.59 C
+ATOM 300 OD1 ASP A 43 14.109 14.303 18.212 1.00 9.59 O
+ATOM 301 OD2 ASP A 43 12.267 14.963 19.265 1.00 11.45 O
+ATOM 302 N TYR A 44 13.725 11.174 16.425 1.00 5.22 N
+ATOM 303 CA TYR A 44 13.257 10.745 15.081 1.00 5.56 C
+ATOM 304 C TYR A 44 14.275 9.687 14.612 1.00 4.61 C
+ATOM 305 O TYR A 44 14.930 9.862 13.568 1.00 6.04 O
+ATOM 306 CB TYR A 44 13.200 11.914 14.071 1.00 5.41 C
+ATOM 307 CG TYR A 44 12.000 12.819 14.399 1.00 5.34 C
+ATOM 308 CD1 TYR A 44 12.119 13.853 15.332 1.00 6.59 C
+ATOM 309 CD2 TYR A 44 10.775 12.617 13.762 1.00 5.94 C
+ATOM 310 CE1 TYR A 44 11.045 14.675 15.610 1.00 5.97 C
+ATOM 311 CE2 TYR A 44 9.676 13.433 14.048 1.00 5.17 C
+ATOM 312 CZ TYR A 44 9.802 14.456 14.996 1.00 5.96 C
+ATOM 313 OH TYR A 44 8.740 15.265 15.269 1.00 8.60 O
+ATOM 314 N ALA A 45 14.342 8.640 15.422 1.00 4.76 N
+ATOM 315 CA ALA A 45 15.445 7.667 15.246 1.00 5.89 C
+ATOM 316 C ALA A 45 15.171 6.533 14.280 1.00 6.67 C
+ATOM 317 O ALA A 45 16.093 5.705 14.039 1.00 7.56 O
+ATOM 318 CB ALA A 45 15.680 7.099 16.682 1.00 6.82 C
+ATOM 319 N ASN A 46 13.966 6.502 13.739 1.00 5.80 N
+ATOM 320 CA ASN A 46 13.512 5.395 12.878 1.00 6.15 C
+ATOM 321 C ASN A 46 13.311 5.853 11.455 1.00 6.61 C
+ATOM 322 O ASN A 46 13.733 6.929 11.026 1.00 7.18 O
+ATOM 323 CB ASN A 46 12.266 4.769 13.501 1.00 7.27 C
+ATOM 324 CG ASN A 46 12.538 4.304 14.922 1.00 7.98 C
+ATOM 325 OD1 ASN A 46 11.982 4.849 15.886 1.00 11.00 O
+ATOM 326 ND2 ASN A 46 13.407 3.298 15.015 1.00 10.32 N
+ATOM 327 OXT ASN A 46 12.703 4.973 10.746 1.00 7.86 O
+TER 328 ASN A 46
+END
diff --git a/examples/code_fragments/mm/ethanol.pdb b/examples/code_fragments/mm/ethanol.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..4d16716e8bd096575463cc1c3bb0a13d435873d2
--- /dev/null
+++ b/examples/code_fragments/mm/ethanol.pdb
@@ -0,0 +1,10 @@
+ATOM 1 C1 ETH A 1 -0.246 0.000 1.285 1.00 0.00 C
+ATOM 2 C2 ETH A 1 0.566 0.000 -0.011 1.00 0.00 C
+ATOM 3 O ETH A 1 -0.322 0.000 -1.130 1.00 0.00 O
+ATOM 4 H11 ETH A 1 0.376 0.000 2.068 1.00 0.00 H
+ATOM 5 H12 ETH A 1 -0.847 0.866 1.302 1.00 0.00 H
+ATOM 6 H13 ETH A 1 -0.847 -0.866 1.302 1.00 0.00 H
+ATOM 7 H21 ETH A 1 1.142 0.816 -0.043 1.00 0.00 H
+ATOM 8 H22 ETH A 1 1.142 -0.816 -0.043 1.00 0.00 H
+ATOM 9 OH ETH A 1 0.209 0.000 -1.977 1.00 0.00 H
+END
diff --git a/examples/code_fragments/mm/ethanol_example.py b/examples/code_fragments/mm/ethanol_example.py
new file mode 100644
index 0000000000000000000000000000000000000000..846b2b901ace02eb8af7c44806eee9bffbe268c1
--- /dev/null
+++ b/examples/code_fragments/mm/ethanol_example.py
@@ -0,0 +1,207 @@
+from ost.mol.mm import *
+from PyQt4 import QtCore
+
+"""
+MM - Demo
+
+!!!Requires OpenStructure to be compiled with MM-Support!!!
+
+This demo should show the procedure of building a custom forcefield.
+The script can directly be started from within DNG.
+"""
+
+class Anim(QtCore.QTimer):
+ def __init__(self,sim,go):
+ QtCore.QTimer.__init__(self)
+ self.ent=sim.GetEntity()
+ self.sim=sim
+ self.go = go
+ self.ed = ent.EditXCS()
+ QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
+
+
+ def OnTimer(self):
+ self.sim.Steps(1)
+ positions = sim.GetPositions()
+ for a, pos in zip(self.ent.atoms,positions):
+ self.ed.SetAtomPos(a,pos)
+ self.go.UpdatePositions()
+
+
+#Let's create an ethanol without its hydrogens
+ent = ost.mol.CreateEntity()
+ed = ent.EditXCS()
+chain = ed.InsertChain('A')
+res = ed.AppendResidue(chain,"ETH")
+c1 = ed.InsertAtom(res,"C1",geom.Vec3(-0.246,0.0,1.285),"C")
+c2 = ed.InsertAtom(res,"C2",geom.Vec3(0.566,0.0,-0.011),"C")
+o = ed.InsertAtom(res,"O",geom.Vec3(-0.322,0.0,-1.130),"O")
+ed.Connect(c1,c2)
+ed.Connect(c2,o)
+
+
+ff = Forcefield()
+
+#generate hydrogen constructor and add it to the forcefield
+h_constructor = GromacsHydrogenConstructor()
+h_constructor.AddHydrogenRule(3,4,["H11","H12","H13"],["C1","C2","O"])
+h_constructor.AddHydrogenRule(2,6,["H21","H22"],["C2","O","C1"])
+h_constructor.AddHydrogenRule(1,2,["OH"],["O","C2","C1"])
+ff.AddHydrogenConstructor("ETH",h_constructor)
+
+#generate buildingblock and add it to the forcefield
+building_block = BuildingBlock()
+building_block.AddAtom("C1","C",-0.18)
+building_block.AddAtom("C2","C",0.145)
+building_block.AddAtom("O","O",-0.683)
+building_block.AddAtom("H11","H",0.06)
+building_block.AddAtom("H12","H",0.06)
+building_block.AddAtom("H13","H",0.06)
+building_block.AddAtom("H21","H",0.06)
+building_block.AddAtom("H22","H",0.06)
+building_block.AddAtom("OH","OH",0.418)
+
+bonds = list()
+for i in range(8):
+ bonds.append(Interaction(FuncType.HarmonicBond))
+
+bonds[0].SetNames(["H11","C1"])
+bonds[1].SetNames(["H12","C1"])
+bonds[2].SetNames(["H13","C1"])
+bonds[3].SetNames(["C1","C2"])
+bonds[4].SetNames(["C2","H21"])
+bonds[5].SetNames(["C2","H22"])
+bonds[6].SetNames(["O","C2"])
+bonds[7].SetNames(["O","OH"])
+
+for b in bonds:
+ building_block.AddBond(b)
+
+ff.AddBuildingBlock("ETH",building_block)
+
+#add masses to the forcefield
+ff.AddMass("C",12.011)
+ff.AddMass("O",15.999)
+ff.AddMass("H",1.008)
+ff.AddMass("OH",1.008)
+
+#generate bonds and add them to the forcefield
+h_c_bond = Interaction(FuncType.HarmonicBond)
+c_c_bond = Interaction(FuncType.HarmonicBond)
+c_o_bond = Interaction(FuncType.HarmonicBond)
+o_h_bond = Interaction(FuncType.HarmonicBond)
+
+h_c_bond.SetTypes(["H","C"])
+c_c_bond.SetTypes(["C","C"])
+c_o_bond.SetTypes(["C","O"])
+o_h_bond.SetTypes(["O","OH"])
+
+h_c_bond.SetParam([0.1111,269449.6])
+c_c_bond.SetParam([0.153,186188.0])
+c_o_bond.SetParam([0.142,358150.4])
+o_h_bond.SetParam([0.096,456056.0])
+
+ff.AddBond(h_c_bond)
+ff.AddBond(c_c_bond)
+ff.AddBond(c_o_bond)
+ff.AddBond(o_h_bond)
+
+#generate angles and add them to the forcefield
+h_c_h_angle = Interaction(FuncType.UreyBradleyAngle)
+h_c_c_angle = Interaction(FuncType.UreyBradleyAngle)
+h_c_o_angle = Interaction(FuncType.UreyBradleyAngle)
+c_c_o_angle = Interaction(FuncType.UreyBradleyAngle)
+c_o_h_angle = Interaction(FuncType.UreyBradleyAngle)
+
+h_c_h_angle.SetTypes(["H","C","H"])
+h_c_c_angle.SetTypes(["H","C","C"])
+h_c_o_angle.SetTypes(["H","C","O"])
+c_c_o_angle.SetTypes(["C","C","O"])
+c_o_h_angle.SetTypes(["C","O","OH"])
+
+h_c_h_angle.SetParam([1.892,297.064,0.1802,4518.72])
+h_c_c_angle.SetParam([1.922,289.5328,0.2179,18853.104])
+h_c_o_angle.SetParam([1.900,384.0912,0.0,0.0])
+c_c_o_angle.SetParam([1.920,633.4576,0.0,0.0])
+c_o_h_angle.SetParam([1.850,481.16,0.0,0.0])
+
+ff.AddAngle(h_c_h_angle)
+ff.AddAngle(h_c_c_angle)
+ff.AddAngle(h_c_o_angle)
+ff.AddAngle(c_c_o_angle)
+ff.AddAngle(c_o_h_angle)
+
+#generate dihedrals and add them to the forcefield
+x_c_c_x_dihedral = Interaction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_one = Interaction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_two = Interaction(FuncType.PeriodicDihedral)
+c_c_o_h_dihedral_three = Interaction(FuncType.PeriodicDihedral)
+x_c_o_x_dihedral = Interaction(FuncType.PeriodicDihedral)
+
+x_c_c_x_dihedral.SetTypes(["X","C","C","X"])
+c_c_o_h_dihedral_one.SetTypes(["C","C","O","OH"])
+c_c_o_h_dihedral_two.SetTypes(["C","C","O","OH"])
+c_c_o_h_dihedral_three.SetTypes(["C","C","O","OH"])
+x_c_o_x_dihedral.SetTypes(["X","C","O","X"])
+
+x_c_c_x_dihedral.SetParam([3,0.0,0.66944])
+c_c_o_h_dihedral_one.SetParam([1,0.0,5.4392])
+c_c_o_h_dihedral_two.SetParam([2,0.0,1.2552])
+c_c_o_h_dihedral_three.SetParam([3,0.0,1.75728])
+x_c_o_x_dihedral.SetParam([3,0.0,0.58576])
+
+ff.AddDihedral(x_c_c_x_dihedral)
+ff.AddDihedral(c_c_o_h_dihedral_one)
+ff.AddDihedral(c_c_o_h_dihedral_two)
+ff.AddDihedral(c_c_o_h_dihedral_three)
+ff.AddDihedral(x_c_o_x_dihedral)
+
+#add lj parameters
+c_lj = Interaction(FuncType.LJ)
+o_lj = Interaction(FuncType.LJ)
+h_lj = Interaction(FuncType.LJ)
+oh_lj = Interaction(FuncType.LJ)
+
+c_lj.SetTypes(["C"])
+o_lj.SetTypes(["O"])
+h_lj.SetTypes(["H"])
+oh_lj.SetTypes(["OH"])
+
+c_lj.SetParam([0.37,0.28])
+o_lj.SetParam([0.32,0.64])
+h_lj.SetParam([0.24,0.09])
+oh_lj.SetParam([0.04,0.2])
+
+ff.AddLJ(c_lj)
+ff.AddLJ(o_lj)
+ff.AddLJ(h_lj)
+ff.AddLJ(oh_lj)
+
+#we do not explicitely set the 1,4 interactions,
+#we rather decrease it by a certain factor
+ff.SetFudgeLJ(0.5)
+ff.SetFudgeQQ(0.5)
+
+#construct settings
+settings = Settings()
+settings.init_temperature = 310
+settings.forcefield = ff
+
+#construct integrator with tiny timesteps
+settings.integrator = VerletIntegrator(0.0001)
+
+
+#create the simulation
+sim = Simulation(ent,settings)
+
+io.SavePDB(sim.GetEntity(),'ethanol.pdb')
+
+
+go = gfx.Entity("ethanol",sim.GetEntity())
+go.SetRenderMode(gfx.CUSTOM)
+scene.Add(go)
+
+anim = Anim(sim,go)
+anim.start(2)
+
+
diff --git a/examples/code_fragments/mm/ethanol_example_using_topology.py b/examples/code_fragments/mm/ethanol_example_using_topology.py
new file mode 100644
index 0000000000000000000000000000000000000000..19a32ed0a53e6547722cf29aac347b07413eaa8f
--- /dev/null
+++ b/examples/code_fragments/mm/ethanol_example_using_topology.py
@@ -0,0 +1,166 @@
+from ost.mol.mm import *
+from PyQt4 import QtCore
+from math import sqrt
+from math import sin
+
+"""
+MM - Demo
+
+!!!Requires OpenStructure to be compiled with MM-Support!!!
+
+This demo should show the procedure building a topology from scratch and
+setting up a simulation. As an additional piece of sugar, it demonstrates
+the capabilities of altering force parameters as the simulation runs.
+The script can directly be started from within DNG.
+"""
+
+class Anim(QtCore.QTimer):
+ def __init__(self,sim,go,cc_bond_index):
+ QtCore.QTimer.__init__(self)
+ self.ent=sim.GetEntity()
+ self.sim=sim
+ self.go = go
+ self.ed = ent.EditXCS()
+ self.bond_index = cc_bond_index
+ top = sim.GetTopology()
+ param = top.GetHarmonicBondParameters(cc_bond_index)
+ self.bond_length = param[2]
+ self.force_constant = param[3]
+ self.steps = 0
+ self.counter = 0
+ QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
+
+ def OnTimer(self):
+ if self.steps % 20 == 0:
+ sim.ResetHarmonicBond(self.bond_index,sin(self.counter*3.1416/100)*self.bond_length*0.75 + self.bond_length,self.force_constant)
+ self.counter += 1
+
+ self.sim.Steps(1)
+ positions = sim.GetPositions()
+ for a, pos in zip(self.ent.atoms,positions):
+ self.ed.SetAtomPos(a,pos)
+ self.go.UpdatePositions()
+ self.steps+=1
+
+
+#create topology by only defining masses
+
+prof = io.IOProfile(dialect='PDB', fault_tolerant=False,
+ quack_mode=False, processor=conop.HeuristicProcessor())
+
+ent = io.LoadPDB('ethanol.pdb', profile=prof)
+masses = [12.011,12.011,15.999,1.008,1.008,1.008,1.008,1.008,1.008]
+top = Topology(masses)
+
+#all per atom parameters have to be set at once...
+charges = [-0.18,0.145,-0.683,0.06,0.06,0.06,0.06,0.06,0.418]
+sigmas = [0.37,0.37,0.32,0.24,0.24,0.24,0.24,0.24,0.04]
+epsilons = [0.28,0.28,0.64,0.09,0.09,0.09,0.09,0.09,0.2]
+
+top.SetCharges(charges)
+top.SetSigmas(sigmas)
+top.SetEpsilons(epsilons)
+
+#we can set the fudge parameters for 1,4 interactions also in the topology
+top.SetFudgeQQ(0.5)
+top.SetFudgeLJ(0.5)
+
+#add the bonds
+top.AddHarmonicBond(0,1,0.153,186188.0) #C-C
+top.AddHarmonicBond(0,3,0.1111,269449.6) #C-H
+top.AddHarmonicBond(0,4,0.1111,269449.6) #C-H
+top.AddHarmonicBond(0,5,0.1111,269449.6) #C-H
+top.AddHarmonicBond(1,6,0.1111,269449.6) #C-H
+top.AddHarmonicBond(1,7,0.1111,269449.6) #C-H
+top.AddHarmonicBond(1,2,0.142,358150.4) #C-O
+top.AddHarmonicBond(2,8,0.096,456056.0) #O-H
+
+#add the angles
+top.AddUreyBradleyAngle(3,0,4,1.892,297.064,0.1802,4518.72) #H-C-H
+top.AddUreyBradleyAngle(3,0,5,1.892,297.064,0.1802,4518.72) #H-C-H
+top.AddUreyBradleyAngle(4,0,5,1.892,297.064,0.1802,4518.72) #H-C-H
+top.AddUreyBradleyAngle(3,0,1,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(4,0,1,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(5,0,1,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(0,1,6,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(0,1,7,1.922,289.5328,0.2179,18853.104) #H-C-C
+top.AddUreyBradleyAngle(0,1,2,1.920,633.4576,0.0,0.0) #C-C-O
+top.AddUreyBradleyAngle(6,1,2,1.900,384.0912,0.0,0.0) #H-C-O
+top.AddUreyBradleyAngle(7,1,2,1.900,384.0912,0.0,0.0) #H-C-O
+top.AddUreyBradleyAngle(6,1,7,1.892,297.064,0.1802,4518.72) #H-C-H
+top.AddUreyBradleyAngle(1,2,8,1.850,481.16,0.0,0.0) #C-O-H
+
+
+#add the dihedrals
+top.AddPeriodicDihedral(3,0,1,6,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(3,0,1,7,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(3,0,1,2,3,0.0,0.66944) #H-C-C-O
+top.AddPeriodicDihedral(4,0,1,6,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(4,0,1,7,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(4,0,1,2,3,0.0,0.66944) #H-C-C-O
+top.AddPeriodicDihedral(5,0,1,6,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(5,0,1,7,3,0.0,0.66944) #H-C-C-H
+top.AddPeriodicDihedral(5,0,1,2,3,0.0,0.66944) #H-C-C-O
+top.AddPeriodicDihedral(6,1,2,8,3,0.0,0.58576) #H-C-O-H
+top.AddPeriodicDihedral(7,1,2,8,3,0.0,0.58576) #H-C-O-H
+top.AddPeriodicDihedral(0,1,2,8,1,0.0,5.4392) #C-C-O-H
+top.AddPeriodicDihedral(0,1,2,8,2,0.0,1.2552) #C-C-O-H
+top.AddPeriodicDihedral(0,1,2,8,3,0.0,1.75728) #C-C-O-H
+
+#we have to manually set the exclusions for the nonbonded interaction...
+
+#1,2 interactions
+top.AddExclusion(3,0)
+top.AddExclusion(4,0)
+top.AddExclusion(5,0)
+top.AddExclusion(0,1)
+top.AddExclusion(1,6)
+top.AddExclusion(1,7)
+top.AddExclusion(1,2)
+top.AddExclusion(2,8)
+
+#1,3 interactions
+top.AddExclusion(3,4)
+top.AddExclusion(3,5)
+top.AddExclusion(4,5)
+top.AddExclusion(3,1)
+top.AddExclusion(4,1)
+top.AddExclusion(5,1)
+top.AddExclusion(0,6)
+top.AddExclusion(0,7)
+top.AddExclusion(0,2)
+top.AddExclusion(6,2)
+top.AddExclusion(7,2)
+top.AddExclusion(1,8)
+
+#add lj-pairs, note, that the fudge parameters still get applied during system setup
+top.AddLJPair(3,6,0.5*(sigmas[3]+sigmas[6]),sqrt(epsilons[3]*epsilons[6]))
+top.AddLJPair(3,7,0.5*(sigmas[3]+sigmas[7]),sqrt(epsilons[3]*epsilons[7]))
+top.AddLJPair(3,2,0.5*(sigmas[3]+sigmas[2]),sqrt(epsilons[3]*epsilons[2]))
+top.AddLJPair(4,6,0.5*(sigmas[4]+sigmas[6]),sqrt(epsilons[4]*epsilons[6]))
+top.AddLJPair(4,7,0.5*(sigmas[4]+sigmas[7]),sqrt(epsilons[4]*epsilons[7]))
+top.AddLJPair(4,2,0.5*(sigmas[4]+sigmas[2]),sqrt(epsilons[4]*epsilons[2]))
+top.AddLJPair(5,6,0.5*(sigmas[5]+sigmas[6]),sqrt(epsilons[5]*epsilons[6]))
+top.AddLJPair(5,7,0.5*(sigmas[5]+sigmas[7]),sqrt(epsilons[5]*epsilons[7]))
+top.AddLJPair(5,2,0.5*(sigmas[5]+sigmas[2]),sqrt(epsilons[5]*epsilons[2]))
+top.AddLJPair(6,8,0.5*(sigmas[6]+sigmas[8]),sqrt(epsilons[6]*epsilons[8]))
+top.AddLJPair(7,8,0.5*(sigmas[7]+sigmas[8]),sqrt(epsilons[7]*epsilons[8]))
+top.AddLJPair(0,8,0.5*(sigmas[0]+sigmas[8]),sqrt(epsilons[0]*epsilons[8]))
+
+settings = Settings()
+settings.init_temperature = 310
+settings.integrator = VerletIntegrator(0.0001)
+
+#let's extract the cc_bond_index to have some fun with it
+cc_bond_index = top.GetHarmonicBondIndices(0,1)[0]
+
+#create the simulation
+sim = Simulation(top,ent,settings)
+go = gfx.Entity("ethanol",sim.GetEntity())
+go.SetRenderMode(gfx.CUSTOM)
+scene.Add(go)
+
+anim = Anim(sim,go,cc_bond_index)
+anim.start(2)
+
+
diff --git a/examples/code_fragments/mm/gb_example.py b/examples/code_fragments/mm/gb_example.py
new file mode 100644
index 0000000000000000000000000000000000000000..7939adb17600f9b2025ffdf341a44e5eae9ffb88
--- /dev/null
+++ b/examples/code_fragments/mm/gb_example.py
@@ -0,0 +1,52 @@
+from ost.mol import mm
+from PyQt4 import QtCore
+
+"""
+MM - Demo
+
+!!!Requires OpenStructure to be compiled with MM-Support!!!
+
+This demo should show the setup of a simple simulation using implicit solvent.
+The script can directly be started from within DNG.
+"""
+
+class Anim(QtCore.QTimer):
+ def __init__(self,sim,ent,go):
+ QtCore.QTimer.__init__(self)
+ self.ent=ent
+ self.sim=sim
+ self.go = go
+ self.ed = ent.EditXCS(ost.mol.BUFFERED_EDIT)
+ QtCore.QObject.connect(self, QtCore.SIGNAL("timeout()"), self.OnTimer)
+
+
+ def OnTimer(self):
+ self.sim.Steps(5)
+ positions = sim.GetPositions()
+ for a, pos in zip(self.ent.atoms,positions):
+ self.ed.SetAtomPos(a,pos)
+ self.ed.UpdateICS()
+ self.go.UpdatePositions()
+
+
+prot=ost.mol.CreateEntityFromView(io.LoadPDB('1CRN.pdb').Select('peptide=true'),True)
+
+settings = mm.Settings()
+
+settings.integrator = mm.LangevinIntegrator(310,1,0.002)
+settings.add_gbsa = True
+settings.forcefield = mm.LoadCHARMMForcefield()
+settings.platform = mm.Platform.CPU
+settings.nonbonded_method = mm.NonbondedMethod.CutoffNonPeriodic
+
+sim = mm.Simulation(prot,settings)
+sim.ApplyLBFGS(tolerance = 1.0, max_iterations = 200)
+sim.UpdatePositions()
+
+ent = sim.GetEntity()
+go = gfx.Entity("crambin",ent)
+scene.Add(go)
+
+anim = Anim(sim,ent,go)
+anim.start(1)
+
diff --git a/examples/code_fragments/mm/gb_example_traj.dcd b/examples/code_fragments/mm/gb_example_traj.dcd
new file mode 100644
index 0000000000000000000000000000000000000000..4b993c6d40109031780323513b23185fecf31343
Binary files /dev/null and b/examples/code_fragments/mm/gb_example_traj.dcd differ
diff --git a/examples/code_fragments/mm/gb_example_traj.pdb b/examples/code_fragments/mm/gb_example_traj.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..a1da60b3f73ab5a617747f15dc302a2d2ad2e5fb
--- /dev/null
+++ b/examples/code_fragments/mm/gb_example_traj.pdb
@@ -0,0 +1,643 @@
+ATOM 1 N THR 1 17.047 14.099 3.625 1.00 13.79 A N
+ATOM 2 CA THR 1 16.967 12.784 4.338 1.00 10.80 A C
+ATOM 3 C THR 1 15.685 12.755 5.133 1.00 9.19 A C
+ATOM 4 O THR 1 15.268 13.825 5.594 1.00 9.85 A O
+ATOM 5 CB THR 1 18.170 12.703 5.337 1.00 13.02 A C
+ATOM 6 OG1 THR 1 19.334 12.829 4.463 1.00 15.06 A O
+ATOM 7 CG2 THR 1 18.150 11.546 6.304 1.00 14.23 A C
+ATOM 8 HA THR 1 16.993 12.024 3.689 1.00 0.00 A H
+ATOM 9 HB THR 1 18.153 13.430 6.024 1.00 0.00 A H
+ATOM 10 HG1 THR 1 20.169 12.789 5.012 1.00 0.00 A H
+ATOM 11 HG21 THR 1 18.958 11.589 6.892 1.00 0.00 A H
+ATOM 12 HG22 THR 1 17.275 11.615 6.888 1.00 0.00 A H
+ATOM 13 HG23 THR 1 18.155 10.649 5.751 1.00 0.00 A H
+ATOM 14 H1 THR 1 17.892 14.138 3.091 1.00 0.00 A H
+ATOM 15 H2 THR 1 16.213 14.183 2.986 1.00 0.00 A H
+ATOM 16 H3 THR 1 17.040 14.869 4.345 1.00 0.00 A H
+ATOM 17 N THR 2 15.115 11.555 5.265 1.00 7.81 A N
+ATOM 18 CA THR 2 13.856 11.469 6.066 1.00 8.31 A C
+ATOM 19 C THR 2 14.164 10.785 7.379 1.00 5.80 A C
+ATOM 20 O THR 2 14.993 9.862 7.443 1.00 6.94 A O
+ATOM 21 CB THR 2 12.732 10.711 5.261 1.00 10.32 A C
+ATOM 22 OG1 THR 2 13.308 9.439 4.926 1.00 12.81 A O
+ATOM 23 CG2 THR 2 12.484 11.442 3.895 1.00 11.90 A C
+ATOM 24 HN THR 2 15.516 10.742 4.843 1.00 0.00 A H
+ATOM 25 HA THR 2 13.507 12.387 6.253 1.00 0.00 A H
+ATOM 26 HB THR 2 11.884 10.657 5.788 1.00 0.00 A H
+ATOM 27 HG1 THR 2 12.645 8.898 4.409 1.00 0.00 A H
+ATOM 28 HG21 THR 2 11.771 10.961 3.384 1.00 0.00 A H
+ATOM 29 HG22 THR 2 12.179 12.430 4.097 1.00 0.00 A H
+ATOM 30 HG23 THR 2 13.384 11.439 3.347 1.00 0.00 A H
+ATOM 31 N CYS2 3 13.488 11.241 8.417 1.00 5.24 A N
+ATOM 32 CA CYS2 3 13.660 10.707 9.787 1.00 5.39 A C
+ATOM 33 C CYS2 3 12.269 10.431 10.323 1.00 4.45 A C
+ATOM 34 O CYS2 3 11.393 11.308 10.185 1.00 6.54 A O
+ATOM 35 CB CYS2 3 14.368 11.748 10.691 1.00 5.99 A C
+ATOM 36 SG CYS2 3 15.885 12.426 10.016 1.00 7.01 A S
+ATOM 37 HN CYS2 3 12.830 11.980 8.271 1.00 0.00 A H
+ATOM 38 HA CYS2 3 14.221 9.880 9.776 1.00 0.00 A H
+ATOM 39 HB1 CYS2 3 13.733 12.504 10.850 1.00 0.00 A H
+ATOM 40 HB2 CYS2 3 14.585 11.307 11.562 1.00 0.00 A H
+ATOM 41 N CYS2 4 12.019 9.272 10.928 1.00 3.90 A N
+ATOM 42 CA CYS2 4 10.646 8.991 11.408 1.00 4.24 A C
+ATOM 43 C CYS2 4 10.654 8.793 12.919 1.00 3.72 A C
+ATOM 44 O CYS2 4 11.659 8.296 13.491 1.00 5.30 A O
+ATOM 45 CB CYS2 4 10.057 7.752 10.682 1.00 4.41 A C
+ATOM 46 SG CYS2 4 9.837 8.018 8.904 1.00 4.72 A S
+ATOM 47 HN CYS2 4 12.748 8.600 11.057 1.00 0.00 A H
+ATOM 48 HA CYS2 4 10.060 9.774 11.196 1.00 0.00 A H
+ATOM 49 HB1 CYS2 4 10.677 6.979 10.815 1.00 0.00 A H
+ATOM 50 HB2 CYS2 4 9.167 7.538 11.085 1.00 0.00 A H
+ATOM 51 N PRO 5 9.561 9.108 13.563 1.00 3.96 A N
+ATOM 52 CA PRO 5 9.448 9.034 15.012 1.00 4.25 A C
+ATOM 53 C PRO 5 9.288 7.670 15.606 1.00 4.96 A C
+ATOM 54 O PRO 5 9.490 7.519 16.819 1.00 7.44 A O
+ATOM 55 CB PRO 5 8.230 9.957 15.345 1.00 5.11 A C
+ATOM 56 CG PRO 5 7.338 9.786 14.114 1.00 5.24 A C
+ATOM 57 CD PRO 5 8.366 9.804 12.958 1.00 5.20 A C
+ATOM 58 HA PRO 5 10.312 9.323 15.424 1.00 0.00 A H
+ATOM 59 HB1 PRO 5 7.762 9.653 16.175 1.00 0.00 A H
+ATOM 60 HB2 PRO 5 8.517 10.909 15.454 1.00 0.00 A H
+ATOM 61 HG1 PRO 5 6.842 8.918 14.144 1.00 0.00 A H
+ATOM 62 HG2 PRO 5 6.686 10.540 14.031 1.00 0.00 A H
+ATOM 63 HD1 PRO 5 8.023 9.304 12.163 1.00 0.00 A H
+ATOM 64 HD2 PRO 5 8.592 10.741 12.691 1.00 0.00 A H
+ATOM 65 N SER 6 8.875 6.686 14.796 1.00 4.83 A N
+ATOM 66 CA SER 6 8.673 5.314 15.279 1.00 4.45 A C
+ATOM 67 C SER 6 8.753 4.376 14.083 1.00 4.99 A C
+ATOM 68 O SER 6 8.726 4.858 12.923 1.00 4.61 A O
+ATOM 69 CB SER 6 7.340 5.121 15.996 1.00 5.05 A C
+ATOM 70 OG SER 6 6.274 5.220 15.031 1.00 6.39 A O
+ATOM 71 HN SER 6 8.699 6.892 13.833 1.00 0.00 A H
+ATOM 72 HA SER 6 9.386 5.114 15.951 1.00 0.00 A H
+ATOM 73 HB1 SER 6 7.319 4.220 16.429 1.00 0.00 A H
+ATOM 74 HB2 SER 6 7.228 5.829 16.694 1.00 0.00 A H
+ATOM 75 HG1 SER 6 5.395 5.095 15.491 1.00 0.00 A H
+ATOM 76 N ILE 7 8.881 3.075 14.358 1.00 4.94 A N
+ATOM 77 CA ILE 7 8.912 2.083 13.258 1.00 6.33 A C
+ATOM 78 C ILE 7 7.581 2.090 12.506 1.00 5.32 A C
+ATOM 79 O ILE 7 7.670 2.031 11.245 1.00 6.85 A O
+ATOM 80 CB ILE 7 9.207 0.677 13.924 1.00 8.43 A C
+ATOM 81 CG1 ILE 7 10.714 0.702 14.312 1.00 9.78 A C
+ATOM 82 CG2 ILE 7 8.811 -0.477 12.969 1.00 11.70 A C
+ATOM 83 CD ILE 7 11.185 -0.516 15.142 1.00 9.92 A C
+ATOM 84 HN ILE 7 8.956 2.770 15.307 1.00 0.00 A H
+ATOM 85 HA ILE 7 9.620 2.297 12.585 1.00 0.00 A H
+ATOM 86 HB ILE 7 8.659 0.511 14.744 1.00 0.00 A H
+ATOM 87 HG11 ILE 7 11.253 0.733 13.470 1.00 0.00 A H
+ATOM 88 HG12 ILE 7 10.885 1.529 14.847 1.00 0.00 A H
+ATOM 89 HG21 ILE 7 9.005 -1.354 13.408 1.00 0.00 A H
+ATOM 90 HG22 ILE 7 7.781 -0.398 12.761 1.00 0.00 A H
+ATOM 91 HG23 ILE 7 9.375 -0.385 12.083 1.00 0.00 A H
+ATOM 92 HD1 ILE 7 12.159 -0.422 15.348 1.00 0.00 A H
+ATOM 93 HD2 ILE 7 10.629 -0.545 16.037 1.00 0.00 A H
+ATOM 94 HD3 ILE 7 11.019 -1.389 14.576 1.00 0.00 A H
+ATOM 95 N VAL 8 6.458 2.162 13.159 1.00 5.02 A N
+ATOM 96 CA VAL 8 5.145 2.209 12.453 1.00 6.93 A C
+ATOM 97 C VAL 8 5.115 3.379 11.461 1.00 5.39 A C
+ATOM 98 O VAL 8 4.664 3.268 10.343 1.00 6.30 A O
+ATOM 99 CB VAL 8 3.995 2.354 13.478 1.00 9.64 A C
+ATOM 100 CG1 VAL 8 2.716 2.891 12.869 1.00 13.85 A C
+ATOM 101 CG2 VAL 8 3.758 1.032 14.208 1.00 11.97 A C
+ATOM 102 HN VAL 8 6.476 2.186 14.159 1.00 0.00 A H
+ATOM 103 HA VAL 8 5.023 1.355 11.947 1.00 0.00 A H
+ATOM 104 HB VAL 8 4.286 3.040 14.145 1.00 0.00 A H
+ATOM 105 HG11 VAL 8 2.014 2.962 13.577 1.00 0.00 A H
+ATOM 106 HG12 VAL 8 2.915 3.843 12.462 1.00 0.00 A H
+ATOM 107 HG13 VAL 8 2.401 2.226 12.115 1.00 0.00 A H
+ATOM 108 HG21 VAL 8 3.013 1.143 14.866 1.00 0.00 A H
+ATOM 109 HG22 VAL 8 3.503 0.299 13.495 1.00 0.00 A H
+ATOM 110 HG23 VAL 8 4.645 0.765 14.711 1.00 0.00 A H
+ATOM 111 N ALA 9 5.606 4.546 11.941 1.00 3.73 A N
+ATOM 112 CA ALA 9 5.598 5.767 11.082 1.00 3.56 A C
+ATOM 113 C ALA 9 6.441 5.527 9.850 1.00 4.13 A C
+ATOM 114 O ALA 9 6.052 5.933 8.744 1.00 4.36 A O
+ATOM 115 CB ALA 9 6.022 6.977 11.891 1.00 4.80 A C
+ATOM 116 HN ALA 9 5.974 4.590 12.870 1.00 0.00 A H
+ATOM 117 HA ALA 9 4.672 5.963 10.759 1.00 0.00 A H
+ATOM 118 HB1 ALA 9 6.013 7.788 11.307 1.00 0.00 A H
+ATOM 119 HB2 ALA 9 5.343 7.100 12.688 1.00 0.00 A H
+ATOM 120 HB3 ALA 9 6.996 6.808 12.258 1.00 0.00 A H
+ATOM 121 N ARG 10 7.647 4.909 10.005 1.00 3.73 A N
+ATOM 122 CA ARG 10 8.496 4.609 8.837 1.00 3.38 A C
+ATOM 123 C ARG 10 7.798 3.609 7.876 1.00 3.47 A C
+ATOM 124 O ARG 10 7.878 3.778 6.651 1.00 4.67 A O
+ATOM 125 CB ARG 10 9.847 4.020 9.305 1.00 3.95 A C
+ATOM 126 CG ARG 10 10.752 3.607 8.149 1.00 4.55 A C
+ATOM 127 CD ARG 10 11.226 4.699 7.244 1.00 5.89 A C
+ATOM 128 NE ARG 10 12.143 5.571 8.035 1.00 6.20 A N
+ATOM 129 CZ ARG 10 12.758 6.609 7.443 1.00 7.52 A C
+ATOM 130 NH1 ARG 10 12.539 6.932 6.158 1.00 10.68 A N
+ATOM 131 NH2 ARG 10 13.601 7.322 8.202 1.00 9.48 A N
+ATOM 132 HN ARG 10 7.959 4.656 10.921 1.00 0.00 A H
+ATOM 133 HA ARG 10 8.654 5.464 8.342 1.00 0.00 A H
+ATOM 134 HB1 ARG 10 10.323 4.710 9.851 1.00 0.00 A H
+ATOM 135 HB2 ARG 10 9.665 3.215 9.870 1.00 0.00 A H
+ATOM 136 HG1 ARG 10 11.560 3.165 8.539 1.00 0.00 A H
+ATOM 137 HG2 ARG 10 10.248 2.948 7.591 1.00 0.00 A H
+ATOM 138 HD1 ARG 10 11.715 4.308 6.464 1.00 0.00 A H
+ATOM 139 HD2 ARG 10 10.447 5.232 6.915 1.00 0.00 A H
+ATOM 140 HE ARG 10 12.300 5.383 9.005 1.00 0.00 A H
+ATOM 141 HH11 ARG 10 11.900 6.393 5.609 1.00 0.00 A H
+ATOM 142 HH12 ARG 10 13.015 7.711 5.750 1.00 0.00 A H
+ATOM 143 HH21 ARG 10 13.746 7.071 9.159 1.00 0.00 A H
+ATOM 144 HH22 ARG 10 14.085 8.105 7.811 1.00 0.00 A H
+ATOM 145 N SER 11 7.186 2.582 8.445 1.00 5.19 A N
+ATOM 146 CA SER 11 6.500 1.584 7.565 1.00 4.60 A C
+ATOM 147 C SER 11 5.382 2.313 6.773 1.00 4.84 A C
+ATOM 148 O SER 11 5.213 2.016 5.557 1.00 5.84 A O
+ATOM 149 CB SER 11 5.908 0.462 8.400 1.00 5.91 A C
+ATOM 150 OG SER 11 6.990 -0.272 9.012 1.00 8.38 A O
+ATOM 151 HN SER 11 7.182 2.475 9.439 1.00 0.00 A H
+ATOM 152 HA SER 11 7.160 1.182 6.930 1.00 0.00 A H
+ATOM 153 HB1 SER 11 5.316 0.845 9.109 1.00 0.00 A H
+ATOM 154 HB2 SER 11 5.374 -0.149 7.815 1.00 0.00 A H
+ATOM 155 HG1 SER 11 6.617 -1.016 9.567 1.00 0.00 A H
+ATOM 156 N ASN 12 4.648 3.182 7.446 1.00 3.54 A N
+ATOM 157 CA ASN 12 3.545 3.935 6.751 1.00 4.57 A C
+ATOM 158 C ASN 12 4.107 4.851 5.691 1.00 4.14 A C
+ATOM 159 O ASN 12 3.536 5.001 4.617 1.00 5.52 A O
+ATOM 160 CB ASN 12 2.663 4.677 7.748 1.00 6.42 A C
+ATOM 161 CG ASN 12 1.802 3.735 8.610 1.00 8.25 A C
+ATOM 162 OD1 ASN 12 1.567 2.613 8.165 1.00 12.72 A O
+ATOM 163 ND2 ASN 12 1.394 4.252 9.767 1.00 9.92 A N
+ATOM 164 HN ASN 12 4.825 3.339 8.417 1.00 0.00 A H
+ATOM 165 HA ASN 12 2.957 3.271 6.289 1.00 0.00 A H
+ATOM 166 HB1 ASN 12 3.250 5.215 8.353 1.00 0.00 A H
+ATOM 167 HB2 ASN 12 2.056 5.289 7.242 1.00 0.00 A H
+ATOM 168 HD21 ASN 12 1.651 5.186 10.016 1.00 0.00 A H
+ATOM 169 HD22 ASN 12 0.830 3.707 10.387 1.00 0.00 A H
+ATOM 170 N PHE 13 5.259 5.498 6.005 1.00 3.43 A N
+ATOM 171 CA PHE 13 5.929 6.358 5.055 1.00 3.49 A C
+ATOM 172 C PHE 13 6.304 5.578 3.799 1.00 3.40 A C
+ATOM 173 O PHE 13 6.136 6.072 2.653 1.00 4.07 A O
+ATOM 174 CB PHE 13 7.183 6.994 5.754 1.00 5.48 A C
+ATOM 175 CG PHE 13 7.884 8.006 4.883 1.00 5.57 A C
+ATOM 176 CD1 PHE 13 8.906 7.586 4.027 1.00 6.99 A C
+ATOM 177 CD2 PHE 13 7.532 9.373 4.983 1.00 6.52 A C
+ATOM 178 CE1 PHE 13 9.560 8.539 3.194 1.00 8.20 A C
+ATOM 179 CE2 PHE 13 8.176 10.281 4.145 1.00 6.34 A C
+ATOM 180 CZ PHE 13 9.141 9.845 3.292 1.00 6.84 A C
+ATOM 181 HN PHE 13 5.654 5.377 6.916 1.00 0.00 A H
+ATOM 182 HA PHE 13 5.319 7.094 4.762 1.00 0.00 A H
+ATOM 183 HB1 PHE 13 6.885 7.447 6.595 1.00 0.00 A H
+ATOM 184 HB2 PHE 13 7.828 6.264 5.979 1.00 0.00 A H
+ATOM 185 HD1 PHE 13 9.176 6.624 3.999 1.00 0.00 A H
+ATOM 186 HD2 PHE 13 6.840 9.679 5.637 1.00 0.00 A H
+ATOM 187 HE1 PHE 13 10.291 8.270 2.566 1.00 0.00 A H
+ATOM 188 HE2 PHE 13 7.929 11.250 4.171 1.00 0.00 A H
+ATOM 189 HZ PHE 13 9.575 10.520 2.696 1.00 0.00 A H
+ATOM 190 N ASN 14 6.900 4.390 3.989 1.00 3.64 A N
+ATOM 191 CA ASN 14 7.331 3.607 2.791 1.00 4.31 A C
+ATOM 192 C ASN 14 6.116 3.210 1.915 1.00 3.98 A C
+ATOM 193 O ASN 14 6.240 3.144 0.684 1.00 6.22 A O
+ATOM 194 CB ASN 14 8.145 2.404 3.240 1.00 5.81 A C
+ATOM 195 CG ASN 14 9.555 2.856 3.730 1.00 6.82 A C
+ATOM 196 OD1 ASN 14 10.013 3.895 3.323 1.00 9.43 A O
+ATOM 197 ND2 ASN 14 10.120 1.956 4.539 1.00 8.21 A N
+ATOM 198 HN ASN 14 7.052 4.037 4.912 1.00 0.00 A H
+ATOM 199 HA ASN 14 7.915 4.177 2.213 1.00 0.00 A H
+ATOM 200 HB1 ASN 14 7.668 1.944 3.988 1.00 0.00 A H
+ATOM 201 HB2 ASN 14 8.250 1.772 2.472 1.00 0.00 A H
+ATOM 202 HD21 ASN 14 9.635 1.110 4.762 1.00 0.00 A H
+ATOM 203 HD22 ASN 14 11.028 2.128 4.922 1.00 0.00 A H
+ATOM 204 N VAL 15 4.993 2.927 2.571 1.00 3.76 A N
+ATOM 205 CA VAL 15 3.782 2.599 1.742 1.00 3.98 A C
+ATOM 206 C VAL 15 3.296 3.871 1.004 1.00 3.80 A C
+ATOM 207 O VAL 15 2.947 3.817 -0.189 1.00 4.85 A O
+ATOM 208 CB VAL 15 2.698 1.953 2.608 1.00 4.71 A C
+ATOM 209 CG1 VAL 15 1.384 1.826 1.806 1.00 6.67 A C
+ATOM 210 CG2 VAL 15 3.174 0.533 3.005 1.00 6.26 A C
+ATOM 211 HN VAL 15 4.956 2.932 3.570 1.00 0.00 A H
+ATOM 212 HA VAL 15 4.019 1.925 1.042 1.00 0.00 A H
+ATOM 213 HB VAL 15 2.537 2.517 3.418 1.00 0.00 A H
+ATOM 214 HG11 VAL 15 0.683 1.403 2.380 1.00 0.00 A H
+ATOM 215 HG12 VAL 15 1.077 2.791 1.514 1.00 0.00 A H
+ATOM 216 HG13 VAL 15 1.567 1.225 0.959 1.00 0.00 A H
+ATOM 217 HG21 VAL 15 2.477 0.094 3.572 1.00 0.00 A H
+ATOM 218 HG22 VAL 15 3.326 -0.026 2.124 1.00 0.00 A H
+ATOM 219 HG23 VAL 15 4.075 0.622 3.545 1.00 0.00 A H
+ATOM 220 N CYS2 16 3.321 4.987 1.720 1.00 3.79 A N
+ATOM 221 CA CYS2 16 2.890 6.285 1.126 1.00 3.54 A C
+ATOM 222 C CYS2 16 3.687 6.597 -0.111 1.00 3.48 A C
+ATOM 223 O CYS2 16 3.200 7.147 -1.103 1.00 4.63 A O
+ATOM 224 CB CYS2 16 3.039 7.369 2.240 1.00 4.58 A C
+ATOM 225 SG CYS2 16 2.559 9.014 1.649 1.00 5.66 A S
+ATOM 226 HN CYS2 16 3.633 4.958 2.670 1.00 0.00 A H
+ATOM 227 HA CYS2 16 1.937 6.253 0.824 1.00 0.00 A H
+ATOM 228 HB1 CYS2 16 2.456 7.120 3.013 1.00 0.00 A H
+ATOM 229 HB2 CYS2 16 3.993 7.398 2.538 1.00 0.00 A H
+ATOM 230 N ARG 17 4.997 6.227 -0.100 1.00 3.99 A N
+ATOM 231 CA ARG 17 5.895 6.489 -1.213 1.00 3.83 A C
+ATOM 232 C ARG 17 5.738 5.560 -2.409 1.00 3.79 A C
+ATOM 233 O ARG 17 6.228 5.901 -3.507 1.00 5.39 A O
+ATOM 234 CB ARG 17 7.370 6.507 -0.731 1.00 4.11 A C
+ATOM 235 CG ARG 17 7.717 7.687 0.206 1.00 4.69 A C
+ATOM 236 CD ARG 17 7.949 8.947 -0.615 1.00 5.10 A C
+ATOM 237 NE ARG 17 9.212 8.856 -1.337 1.00 4.71 A N
+ATOM 238 CZ ARG 17 9.537 9.533 -2.431 1.00 5.28 A C
+ATOM 239 NH1 ARG 17 8.659 10.350 -3.032 1.00 6.67 A N
+ATOM 240 NH2 ARG 17 10.793 9.491 -2.899 1.00 6.41 A N
+ATOM 241 HN ARG 17 5.356 5.756 0.706 1.00 0.00 A H
+ATOM 242 HA ARG 17 5.629 7.392 -1.550 1.00 0.00 A H
+ATOM 243 HB1 ARG 17 7.550 5.654 -0.241 1.00 0.00 A H
+ATOM 244 HB2 ARG 17 7.962 6.561 -1.535 1.00 0.00 A H
+ATOM 245 HG1 ARG 17 6.960 7.840 0.842 1.00 0.00 A H
+ATOM 246 HG2 ARG 17 8.546 7.469 0.721 1.00 0.00 A H
+ATOM 247 HD1 ARG 17 7.202 9.056 -1.270 1.00 0.00 A H
+ATOM 248 HD2 ARG 17 7.975 9.738 -0.004 1.00 0.00 A H
+ATOM 249 HE ARG 17 9.897 8.225 -0.974 1.00 0.00 A H
+ATOM 250 HH11 ARG 17 7.739 10.458 -2.656 1.00 0.00 A H
+ATOM 251 HH12 ARG 17 8.925 10.851 -3.856 1.00 0.00 A H
+ATOM 252 HH21 ARG 17 11.486 8.949 -2.423 1.00 0.00 A H
+ATOM 253 HH22 ARG 17 11.037 10.002 -3.724 1.00 0.00 A H
+ATOM 254 N LEU 18 5.051 4.411 -2.204 1.00 4.70 A N
+ATOM 255 CA LEU 18 4.933 3.431 -3.326 1.00 5.46 A C
+ATOM 256 C LEU 18 4.397 4.014 -4.620 1.00 5.13 A C
+ATOM 257 O LEU 18 4.988 3.755 -5.687 1.00 5.55 A O
+ATOM 258 CB LEU 18 4.196 2.184 -2.863 1.00 6.47 A C
+ATOM 259 CG LEU 18 4.960 1.178 -1.991 1.00 7.43 A C
+ATOM 260 CD1 LEU 18 3.907 0.097 -1.634 1.00 8.70 A C
+ATOM 261 CD2 LEU 18 6.129 0.606 -2.768 1.00 9.39 A C
+ATOM 262 HN LEU 18 4.630 4.222 -1.317 1.00 0.00 A H
+ATOM 263 HA LEU 18 5.863 3.161 -3.574 1.00 0.00 A H
+ATOM 264 HB1 LEU 18 3.399 2.486 -2.340 1.00 0.00 A H
+ATOM 265 HB2 LEU 18 3.892 1.697 -3.682 1.00 0.00 A H
+ATOM 266 HG LEU 18 5.353 1.584 -1.166 1.00 0.00 A H
+ATOM 267 HD11 LEU 18 4.330 -0.604 -1.060 1.00 0.00 A H
+ATOM 268 HD12 LEU 18 3.117 0.561 -1.113 1.00 0.00 A H
+ATOM 269 HD13 LEU 18 3.555 -0.334 -2.529 1.00 0.00 A H
+ATOM 270 HD21 LEU 18 6.622 -0.048 -2.195 1.00 0.00 A H
+ATOM 271 HD22 LEU 18 5.754 0.122 -3.626 1.00 0.00 A H
+ATOM 272 HD23 LEU 18 6.768 1.399 -3.041 1.00 0.00 A H
+ATOM 273 N PRO 19 3.329 4.795 -4.543 1.00 4.28 A N
+ATOM 274 CA PRO 19 2.792 5.376 -5.797 1.00 5.38 A C
+ATOM 275 C PRO 19 3.573 6.540 -6.322 1.00 6.30 A C
+ATOM 276 O PRO 19 3.260 7.045 -7.422 1.00 9.62 A O
+ATOM 277 CB PRO 19 1.358 5.766 -5.472 1.00 5.87 A C
+ATOM 278 CG PRO 19 1.223 5.694 -3.993 1.00 6.47 A C
+ATOM 279 CD PRO 19 2.421 4.941 -3.408 1.00 6.45 A C
+ATOM 280 HA PRO 19 2.853 4.706 -6.537 1.00 0.00 A H
+ATOM 281 HB1 PRO 19 1.173 6.696 -5.791 1.00 0.00 A H
+ATOM 282 HB2 PRO 19 0.720 5.131 -5.908 1.00 0.00 A H
+ATOM 283 HG1 PRO 19 1.194 6.619 -3.615 1.00 0.00 A H
+ATOM 284 HG2 PRO 19 0.379 5.212 -3.758 1.00 0.00 A H
+ATOM 285 HD1 PRO 19 2.850 5.468 -2.674 1.00 0.00 A H
+ATOM 286 HD2 PRO 19 2.143 4.047 -3.057 1.00 0.00 A H
+ATOM 287 N GLY 20 4.565 7.047 -5.559 1.00 4.94 A N
+ATOM 288 CA GLY 20 5.366 8.191 -6.018 1.00 5.39 A C
+ATOM 289 C GLY 20 5.007 9.481 -5.280 1.00 5.03 A C
+ATOM 290 O GLY 20 5.535 10.510 -5.730 1.00 7.34 A O
+ATOM 291 HN GLY 20 4.758 6.638 -4.667 1.00 0.00 A H
+ATOM 292 HA1 GLY 20 6.333 7.990 -5.863 1.00 0.00 A H
+ATOM 293 HA2 GLY 20 5.206 8.324 -6.996 1.00 0.00 A H
+ATOM 294 N THR 21 4.181 9.438 -4.262 1.00 4.10 A N
+ATOM 295 CA THR 21 3.767 10.609 -3.513 1.00 3.94 A C
+ATOM 296 C THR 21 5.017 11.397 -3.042 1.00 3.96 A C
+ATOM 297 O THR 21 5.947 10.757 -2.523 1.00 5.82 A O
+ATOM 298 CB THR 21 2.992 10.188 -2.225 1.00 4.13 A C
+ATOM 299 OG1 THR 21 2.051 9.144 -2.623 1.00 5.45 A O
+ATOM 300 CG2 THR 21 2.260 11.349 -1.551 1.00 5.41 A C
+ATOM 301 HN THR 21 3.816 8.548 -3.987 1.00 0.00 A H
+ATOM 302 HA THR 21 3.187 11.164 -4.110 1.00 0.00 A H
+ATOM 303 HB THR 21 3.644 9.861 -1.541 1.00 0.00 A H
+ATOM 304 HG1 THR 21 1.530 8.842 -1.825 1.00 0.00 A H
+ATOM 305 HG21 THR 21 1.786 11.016 -0.736 1.00 0.00 A H
+ATOM 306 HG22 THR 21 2.971 12.079 -1.281 1.00 0.00 A H
+ATOM 307 HG23 THR 21 1.564 11.747 -2.236 1.00 0.00 A H
+ATOM 308 N PRO 22 4.971 12.703 -3.176 1.00 5.04 A N
+ATOM 309 CA PRO 22 6.143 13.513 -2.696 1.00 4.69 A C
+ATOM 310 C PRO 22 6.400 13.233 -1.225 1.00 4.19 A C
+ATOM 311 O PRO 22 5.485 13.061 -0.382 1.00 4.47 A O
+ATOM 312 CB PRO 22 5.703 14.969 -2.920 1.00 7.12 A C
+ATOM 313 CG PRO 22 4.676 14.893 -3.996 1.00 7.03 A C
+ATOM 314 CD PRO 22 3.964 13.567 -3.811 1.00 4.90 A C
+ATOM 315 HA PRO 22 6.995 13.300 -3.174 1.00 0.00 A H
+ATOM 316 HB1 PRO 22 5.310 15.351 -2.084 1.00 0.00 A H
+ATOM 317 HB2 PRO 22 6.478 15.531 -3.211 1.00 0.00 A H
+ATOM 318 HG1 PRO 22 4.027 15.649 -3.910 1.00 0.00 A H
+ATOM 319 HG2 PRO 22 5.113 14.929 -4.895 1.00 0.00 A H
+ATOM 320 HD1 PRO 22 3.164 13.673 -3.220 1.00 0.00 A H
+ATOM 321 HD2 PRO 22 3.679 13.191 -4.693 1.00 0.00 A H
+ATOM 322 N GLU 23 7.728 13.297 -0.921 1.00 5.16 A N
+ATOM 323 CA GLU 23 8.114 13.103 0.500 1.00 5.31 A C
+ATOM 324 C GLU 23 7.427 14.073 1.410 1.00 4.11 A C
+ATOM 325 O GLU 23 7.036 13.682 2.540 1.00 5.11 A O
+ATOM 326 CB GLU 23 9.648 13.285 0.660 1.00 6.16 A C
+ATOM 327 CG GLU 23 10.440 12.093 0.063 1.00 7.48 A C
+ATOM 328 CD GLU 23 11.941 12.170 0.391 1.00 9.40 A C
+ATOM 329 OE1 GLU 23 12.416 13.225 0.681 1.00 10.40 A O
+ATOM 330 OE2 GLU 23 12.539 11.070 0.292 1.00 13.32 A O
+ATOM 331 HN GLU 23 8.415 13.468 -1.627 1.00 0.00 A H
+ATOM 332 HA GLU 23 7.836 12.177 0.754 1.00 0.00 A H
+ATOM 333 HB1 GLU 23 9.924 14.124 0.191 1.00 0.00 A H
+ATOM 334 HB2 GLU 23 9.864 13.361 1.633 1.00 0.00 A H
+ATOM 335 HG1 GLU 23 10.072 11.242 0.437 1.00 0.00 A H
+ATOM 336 HG2 GLU 23 10.327 12.097 -0.931 1.00 0.00 A H
+ATOM 337 N ALA 24 7.212 15.334 0.966 1.00 4.56 A N
+ATOM 338 CA ALA 24 6.614 16.317 1.913 1.00 4.49 A C
+ATOM 339 C ALA 24 5.212 15.936 2.350 1.00 4.10 A C
+ATOM 340 O ALA 24 4.782 16.166 3.495 1.00 5.64 A O
+ATOM 341 CB ALA 24 6.605 17.695 1.246 1.00 5.80 A C
+ATOM 342 HN ALA 24 7.447 15.598 0.031 1.00 0.00 A H
+ATOM 343 HA ALA 24 7.174 16.328 2.742 1.00 0.00 A H
+ATOM 344 HB1 ALA 24 6.206 18.365 1.871 1.00 0.00 A H
+ATOM 345 HB2 ALA 24 7.599 17.962 1.019 1.00 0.00 A H
+ATOM 346 HB3 ALA 24 6.028 17.635 0.366 1.00 0.00 A H
+ATOM 347 N ILE 25 4.445 15.318 1.405 1.00 4.37 A N
+ATOM 348 CA ILE 25 3.074 14.894 1.756 1.00 5.44 A C
+ATOM 349 C ILE 25 3.085 13.643 2.645 1.00 4.32 A C
+ATOM 350 O ILE 25 2.315 13.523 3.578 1.00 4.72 A O
+ATOM 351 CB ILE 25 2.204 14.637 0.462 1.00 6.42 A C
+ATOM 352 CG1 ILE 25 1.815 16.048 -0.129 1.00 7.50 A C
+ATOM 353 CG2 ILE 25 0.903 13.864 0.811 1.00 7.65 A C
+ATOM 354 CD ILE 25 0.756 16.761 0.757 1.00 7.80 A C
+ATOM 355 HN ILE 25 4.806 15.154 0.487 1.00 0.00 A H
+ATOM 356 HA ILE 25 2.657 15.642 2.273 1.00 0.00 A H
+ATOM 357 HB ILE 25 2.726 14.090 -0.193 1.00 0.00 A H
+ATOM 358 HG11 ILE 25 2.635 16.618 -0.178 1.00 0.00 A H
+ATOM 359 HG12 ILE 25 1.440 15.924 -1.048 1.00 0.00 A H
+ATOM 360 HG21 ILE 25 0.371 13.714 -0.022 1.00 0.00 A H
+ATOM 361 HG22 ILE 25 1.170 12.939 1.240 1.00 0.00 A H
+ATOM 362 HG23 ILE 25 0.346 14.441 1.495 1.00 0.00 A H
+ATOM 363 HD1 ILE 25 0.531 17.650 0.357 1.00 0.00 A H
+ATOM 364 HD2 ILE 25 -0.106 16.156 0.798 1.00 0.00 A H
+ATOM 365 HD3 ILE 25 1.162 16.892 1.721 1.00 0.00 A H
+ATOM 366 N CYS2 26 4.032 12.764 2.313 1.00 3.92 A N
+ATOM 367 CA CYS2 26 4.180 11.549 3.187 1.00 4.37 A C
+ATOM 368 C CYS2 26 4.632 11.944 4.596 1.00 3.95 A C
+ATOM 369 O CYS2 26 4.227 11.252 5.547 1.00 4.74 A O
+ATOM 370 CB CYS2 26 5.038 10.518 2.539 1.00 4.63 A C
+ATOM 371 SG CYS2 26 4.349 9.794 1.022 1.00 5.61 A S
+ATOM 372 HN CYS2 26 4.619 12.907 1.516 1.00 0.00 A H
+ATOM 373 HA CYS2 26 3.285 11.116 3.298 1.00 0.00 A H
+ATOM 374 HB1 CYS2 26 5.914 10.942 2.311 1.00 0.00 A H
+ATOM 375 HB2 CYS2 26 5.186 9.779 3.196 1.00 0.00 A H
+ATOM 376 N ALA 27 5.408 13.012 4.694 1.00 3.89 A N
+ATOM 377 CA ALA 27 5.879 13.502 6.026 1.00 4.43 A C
+ATOM 378 C ALA 27 4.696 13.908 6.882 1.00 4.26 A C
+ATOM 379 O ALA 27 4.528 13.422 8.025 1.00 5.44 A O
+ATOM 380 CB ALA 27 6.880 14.615 5.830 1.00 5.36 A C
+ATOM 381 HN ALA 27 5.683 13.498 3.865 1.00 0.00 A H
+ATOM 382 HA ALA 27 6.347 12.769 6.519 1.00 0.00 A H
+ATOM 383 HB1 ALA 27 7.194 14.942 6.721 1.00 0.00 A H
+ATOM 384 HB2 ALA 27 7.694 14.237 5.277 1.00 0.00 A H
+ATOM 385 HB3 ALA 27 6.409 15.398 5.305 1.00 0.00 A H
+ATOM 386 N THR 28 3.827 14.802 6.358 1.00 4.53 A N
+ATOM 387 CA THR 28 2.691 15.221 7.194 1.00 5.08 A C
+ATOM 388 C THR 28 1.672 14.132 7.434 1.00 4.62 A C
+ATOM 389 O THR 28 0.947 14.112 8.468 1.00 7.80 A O
+ATOM 390 CB THR 28 1.986 16.520 6.614 1.00 6.03 A C
+ATOM 391 OG1 THR 28 1.664 16.221 5.230 1.00 7.19 A O
+ATOM 392 CG2 THR 28 2.914 17.739 6.700 1.00 7.34 A C
+ATOM 393 HN THR 28 3.952 15.165 5.435 1.00 0.00 A H
+ATOM 394 HA THR 28 3.090 15.437 8.085 1.00 0.00 A H
+ATOM 395 HB THR 28 1.167 16.747 7.141 1.00 0.00 A H
+ATOM 396 HG1 THR 28 1.215 17.011 4.814 1.00 0.00 A H
+ATOM 397 HG21 THR 28 2.446 18.541 6.329 1.00 0.00 A H
+ATOM 398 HG22 THR 28 3.159 17.901 7.712 1.00 0.00 A H
+ATOM 399 HG23 THR 28 3.783 17.537 6.138 1.00 0.00 A H
+ATOM 400 N TYR 29 1.621 13.190 6.511 1.00 5.01 A N
+ATOM 401 CA TYR 29 0.715 12.045 6.657 1.00 6.60 A C
+ATOM 402 C TYR 29 1.125 11.125 7.815 1.00 4.92 A C
+ATOM 403 O TYR 29 0.286 10.632 8.545 1.00 7.13 A O
+ATOM 404 CB TYR 29 0.755 11.229 5.322 1.00 9.66 A C
+ATOM 405 CG TYR 29 -0.203 10.044 5.354 1.00 11.56 A C
+ATOM 406 CD1 TYR 29 -1.547 10.337 5.645 1.00 12.85 A C
+ATOM 407 CD2 TYR 29 0.193 8.750 5.100 1.00 14.44 A C
+ATOM 408 CE1 TYR 29 -2.496 9.329 5.673 1.00 16.61 A C
+ATOM 409 CE2 TYR 29 -0.801 7.705 5.156 1.00 17.11 A C
+ATOM 410 CZ TYR 29 -2.079 8.031 5.430 1.00 19.99 A C
+ATOM 411 OH TYR 29 -3.097 7.057 5.458 1.00 28.98 A O
+ATOM 412 HN TYR 29 2.206 13.257 5.703 1.00 0.00 A H
+ATOM 413 HA TYR 29 -0.203 12.388 6.857 1.00 0.00 A H
+ATOM 414 HB1 TYR 29 0.499 11.832 4.566 1.00 0.00 A H
+ATOM 415 HB2 TYR 29 1.685 10.890 5.178 1.00 0.00 A H
+ATOM 416 HD1 TYR 29 -1.820 11.281 5.833 1.00 0.00 A H
+ATOM 417 HD2 TYR 29 1.146 8.539 4.882 1.00 0.00 A H
+ATOM 418 HE1 TYR 29 -3.456 9.533 5.864 1.00 0.00 A H
+ATOM 419 HE2 TYR 29 -0.545 6.752 4.994 1.00 0.00 A H
+ATOM 420 HH TYR 29 -2.703 6.157 5.273 1.00 0.00 A H
+ATOM 421 N THR 30 2.470 10.984 7.995 1.00 5.31 A N
+ATOM 422 CA THR 30 2.986 9.994 8.950 1.00 5.70 A C
+ATOM 423 C THR 30 3.609 10.505 10.230 1.00 6.28 A C
+ATOM 424 O THR 30 3.766 9.715 11.186 1.00 8.77 A O
+ATOM 425 CB THR 30 4.076 9.103 8.225 1.00 6.55 A C
+ATOM 426 OG1 THR 30 5.125 10.027 7.824 1.00 6.57 A O
+ATOM 427 CG2 THR 30 3.493 8.324 7.035 1.00 7.29 A C
+ATOM 428 HN THR 30 3.106 11.555 7.476 1.00 0.00 A H
+ATOM 429 HA THR 30 2.164 9.501 9.237 1.00 0.00 A H
+ATOM 430 HB THR 30 4.432 8.393 8.833 1.00 0.00 A H
+ATOM 431 HG1 THR 30 5.852 9.524 7.356 1.00 0.00 A H
+ATOM 432 HG21 THR 30 4.214 7.777 6.609 1.00 0.00 A H
+ATOM 433 HG22 THR 30 2.727 7.694 7.392 1.00 0.00 A H
+ATOM 434 HG23 THR 30 3.108 9.016 6.340 1.00 0.00 A H
+ATOM 435 N GLY 31 3.984 11.764 10.241 1.00 4.99 A N
+ATOM 436 CA GLY 31 4.769 12.336 11.360 1.00 5.50 A C
+ATOM 437 C GLY 31 6.255 12.243 11.106 1.00 4.19 A C
+ATOM 438 O GLY 31 7.037 12.750 11.954 1.00 6.12 A O
+ATOM 439 HN GLY 31 3.733 12.353 9.473 1.00 0.00 A H
+ATOM 440 HA1 GLY 31 4.519 13.298 11.473 1.00 0.00 A H
+ATOM 441 HA2 GLY 31 4.552 11.835 12.198 1.00 0.00 A H
+ATOM 442 N CYS2 32 6.710 11.631 9.992 1.00 4.30 A N
+ATOM 443 CA CYS2 32 8.140 11.694 9.635 1.00 4.89 A C
+ATOM 444 C CYS2 32 8.500 13.141 9.206 1.00 5.50 A C
+ATOM 445 O CYS2 32 7.581 13.949 8.944 1.00 5.82 A O
+ATOM 446 CB CYS2 32 8.504 10.686 8.530 1.00 4.66 A C
+ATOM 447 SG CYS2 32 8.048 8.987 8.881 1.00 5.33 A S
+ATOM 448 HN CYS2 32 6.073 11.131 9.405 1.00 0.00 A H
+ATOM 449 HA CYS2 32 8.676 11.442 10.441 1.00 0.00 A H
+ATOM 450 HB1 CYS2 32 8.040 10.965 7.689 1.00 0.00 A H
+ATOM 451 HB2 CYS2 32 9.494 10.720 8.392 1.00 0.00 A H
+ATOM 452 N ILE 33 9.793 13.410 9.173 1.00 6.02 A N
+ATOM 453 CA ILE 33 10.280 14.760 8.823 1.00 5.24 A C
+ATOM 454 C ILE 33 11.346 14.658 7.743 1.00 5.16 A C
+ATOM 455 O ILE 33 11.971 13.583 7.552 1.00 7.19 A O
+ATOM 456 CB ILE 33 10.790 15.535 10.085 1.00 5.49 A C
+ATOM 457 CG1 ILE 33 12.059 14.803 10.671 1.00 6.85 A C
+ATOM 458 CG2 ILE 33 9.684 15.686 11.138 1.00 6.45 A C
+ATOM 459 CD ILE 33 12.733 15.676 11.781 1.00 8.94 A C
+ATOM 460 HN ILE 33 10.452 12.689 9.388 1.00 0.00 A H
+ATOM 461 HA ILE 33 9.516 15.293 8.459 1.00 0.00 A H
+ATOM 462 HB ILE 33 11.051 16.462 9.814 1.00 0.00 A H
+ATOM 463 HG11 ILE 33 11.781 13.927 11.065 1.00 0.00 A H
+ATOM 464 HG12 ILE 33 12.716 14.643 9.934 1.00 0.00 A H
+ATOM 465 HG21 ILE 33 10.042 16.184 11.928 1.00 0.00 A H
+ATOM 466 HG22 ILE 33 8.884 16.221 10.707 1.00 0.00 A H
+ATOM 467 HG23 ILE 33 9.369 14.724 11.431 1.00 0.00 A H
+ATOM 468 HD1 ILE 33 13.534 15.198 12.141 1.00 0.00 A H
+ATOM 469 HD2 ILE 33 13.024 16.594 11.352 1.00 0.00 A H
+ATOM 470 HD3 ILE 33 12.032 15.835 12.552 1.00 0.00 A H
+ATOM 471 N ILE 34 11.490 15.773 7.038 1.00 5.52 A N
+ATOM 472 CA ILE 34 12.552 15.877 6.036 1.00 6.82 A C
+ATOM 473 C ILE 34 13.590 16.917 6.560 1.00 6.92 A C
+ATOM 474 O ILE 34 13.168 18.006 6.945 1.00 9.22 A O
+ATOM 475 CB ILE 34 11.987 16.360 4.681 1.00 8.11 A C
+ATOM 476 CG1 ILE 34 10.914 15.338 4.163 1.00 9.59 A C
+ATOM 477 CG2 ILE 34 13.131 16.517 3.629 1.00 9.73 A C
+ATOM 478 CD ILE 34 10.151 16.024 2.938 1.00 13.41 A C
+ATOM 479 HN ILE 34 10.872 16.544 7.192 1.00 0.00 A H
+ATOM 480 HA ILE 34 12.972 14.981 5.894 1.00 0.00 A H
+ATOM 481 HB ILE 34 11.558 17.254 4.812 1.00 0.00 A H
+ATOM 482 HG11 ILE 34 11.362 14.497 3.859 1.00 0.00 A H
+ATOM 483 HG12 ILE 34 10.265 15.125 4.893 1.00 0.00 A H
+ATOM 484 HG21 ILE 34 12.745 16.830 2.761 1.00 0.00 A H
+ATOM 485 HG22 ILE 34 13.823 17.225 3.992 1.00 0.00 A H
+ATOM 486 HG23 ILE 34 13.596 15.580 3.500 1.00 0.00 A H
+ATOM 487 HD1 ILE 34 9.458 15.396 2.584 1.00 0.00 A H
+ATOM 488 HD2 ILE 34 9.693 16.908 3.284 1.00 0.00 A H
+ATOM 489 HD3 ILE 34 10.857 16.243 2.186 1.00 0.00 A H
+ATOM 490 N ILE 35 14.856 16.493 6.536 1.00 7.06 A N
+ATOM 491 CA ILE 35 15.930 17.454 6.941 1.00 7.52 A C
+ATOM 492 C ILE 35 16.913 17.550 5.819 1.00 6.63 A C
+ATOM 493 O ILE 35 17.097 16.660 4.970 1.00 7.90 A O
+ATOM 494 CB ILE 35 16.622 16.995 8.285 1.00 8.07 A C
+ATOM 495 CG1 ILE 35 17.360 15.651 8.067 1.00 9.41 A C
+ATOM 496 CG2 ILE 35 15.592 16.974 9.434 1.00 9.46 A C
+ATOM 497 CD ILE 35 18.298 15.206 9.219 1.00 9.85 A C
+ATOM 498 HN ILE 35 15.080 15.560 6.255 1.00 0.00 A H
+ATOM 499 HA ILE 35 15.537 18.356 7.118 1.00 0.00 A H
+ATOM 500 HB ILE 35 17.323 17.653 8.560 1.00 0.00 A H
+ATOM 501 HG11 ILE 35 16.670 14.938 7.940 1.00 0.00 A H
+ATOM 502 HG12 ILE 35 17.911 15.734 7.237 1.00 0.00 A H
+ATOM 503 HG21 ILE 35 16.041 16.682 10.279 1.00 0.00 A H
+ATOM 504 HG22 ILE 35 15.202 17.947 9.550 1.00 0.00 A H
+ATOM 505 HG23 ILE 35 14.825 16.297 9.181 1.00 0.00 A H
+ATOM 506 HD1 ILE 35 18.724 14.333 8.983 1.00 0.00 A H
+ATOM 507 HD2 ILE 35 19.039 15.945 9.350 1.00 0.00 A H
+ATOM 508 HD3 ILE 35 17.722 15.101 10.096 1.00 0.00 A H
+ATOM 509 N PRO 36 17.664 18.669 5.806 1.00 8.07 A N
+ATOM 510 CA PRO 36 18.635 18.861 4.738 1.00 8.78 A C
+ATOM 511 C PRO 36 19.925 18.042 4.949 1.00 8.31 A C
+ATOM 512 O PRO 36 20.593 17.742 3.945 1.00 9.09 A O
+ATOM 513 CB PRO 36 18.945 20.364 4.783 1.00 9.67 A C
+ATOM 514 CG PRO 36 18.238 20.937 5.908 1.00 10.15 A C
+ATOM 515 CD PRO 36 17.371 19.900 6.596 1.00 9.53 A C
+ATOM 516 HA PRO 36 18.272 18.552 3.859 1.00 0.00 A H
+ATOM 517 HB1 PRO 36 19.929 20.504 4.895 1.00 0.00 A H
+ATOM 518 HB2 PRO 36 18.641 20.798 3.935 1.00 0.00 A H
+ATOM 519 HG1 PRO 36 18.903 21.293 6.564 1.00 0.00 A H
+ATOM 520 HG2 PRO 36 17.658 21.684 5.583 1.00 0.00 A H
+ATOM 521 HD1 PRO 36 17.633 19.787 7.554 1.00 0.00 A H
+ATOM 522 HD2 PRO 36 16.403 20.144 6.542 1.00 0.00 A H
+ATOM 523 N GLY 37 20.172 17.730 6.217 1.00 8.48 A N
+ATOM 524 CA GLY 37 21.452 16.969 6.513 1.00 9.20 A C
+ATOM 525 C GLY 37 21.143 15.478 6.427 1.00 10.41 A C
+ATOM 526 O GLY 37 20.138 15.023 5.878 1.00 12.06 A O
+ATOM 527 HN GLY 37 19.539 17.986 6.948 1.00 0.00 A H
+ATOM 528 HA1 GLY 37 22.153 17.210 5.842 1.00 0.00 A H
+ATOM 529 HA2 GLY 37 21.777 17.196 7.431 1.00 0.00 A H
+ATOM 530 N ALA 38 22.055 14.701 7.032 1.00 9.24 A N
+ATOM 531 CA ALA 38 22.019 13.242 7.020 1.00 9.24 A C
+ATOM 532 C ALA 38 21.944 12.628 8.396 1.00 9.60 A C
+ATOM 533 O ALA 38 21.869 11.387 8.435 1.00 13.65 A O
+ATOM 534 CB ALA 38 23.246 12.697 6.275 1.00 10.43 A C
+ATOM 535 HN ALA 38 22.804 15.149 7.520 1.00 0.00 A H
+ATOM 536 HA ALA 38 21.177 12.983 6.547 1.00 0.00 A H
+ATOM 537 HB1 ALA 38 23.216 11.697 6.270 1.00 0.00 A H
+ATOM 538 HB2 ALA 38 23.226 13.063 5.287 1.00 0.00 A H
+ATOM 539 HB3 ALA 38 24.113 13.029 6.774 1.00 0.00 A H
+ATOM 540 N THR 39 21.894 13.435 9.436 1.00 8.70 A N
+ATOM 541 CA THR 39 21.936 12.911 10.809 1.00 9.46 A C
+ATOM 542 C THR 39 20.615 13.191 11.521 1.00 8.32 A C
+ATOM 543 O THR 39 20.357 14.317 11.948 1.00 9.89 A O
+ATOM 544 CB THR 39 23.131 13.601 11.593 1.00 10.72 A C
+ATOM 545 OG1 THR 39 24.284 13.401 10.709 1.00 11.66 A O
+ATOM 546 CG2 THR 39 23.340 12.935 12.962 1.00 11.81 A C
+ATOM 547 HN THR 39 21.826 14.422 9.289 1.00 0.00 A H
+ATOM 548 HA THR 39 22.079 11.922 10.782 1.00 0.00 A H
+ATOM 549 HB THR 39 22.968 14.568 11.791 1.00 0.00 A H
+ATOM 550 HG1 THR 39 25.098 13.808 11.124 1.00 0.00 A H
+ATOM 551 HG21 THR 39 24.096 13.384 13.439 1.00 0.00 A H
+ATOM 552 HG22 THR 39 22.452 13.035 13.520 1.00 0.00 A H
+ATOM 553 HG23 THR 39 23.565 11.917 12.807 1.00 0.00 A H
+ATOM 554 N CYS2 40 19.827 12.110 11.642 1.00 7.64 A N
+ATOM 555 CA CYS2 40 18.504 12.312 12.298 1.00 8.05 A C
+ATOM 556 C CYS2 40 18.684 12.451 13.784 1.00 7.63 A C
+ATOM 557 O CYS2 40 19.533 11.718 14.362 1.00 9.64 A O
+ATOM 558 CB CYS2 40 17.582 11.117 11.996 1.00 7.80 A C
+ATOM 559 SG CYS2 40 17.199 10.929 10.237 1.00 7.30 A S
+ATOM 560 HN CYS2 40 20.114 11.212 11.308 1.00 0.00 A H
+ATOM 561 HA CYS2 40 18.088 13.147 11.939 1.00 0.00 A H
+ATOM 562 HB1 CYS2 40 18.032 10.282 12.313 1.00 0.00 A H
+ATOM 563 HB2 CYS2 40 16.725 11.244 12.495 1.00 0.00 A H
+ATOM 564 N PRO 41 17.880 13.266 14.426 1.00 8.00 A N
+ATOM 565 CA PRO 41 17.924 13.421 15.877 1.00 8.96 A C
+ATOM 566 C PRO 41 17.392 12.206 16.594 1.00 9.06 A C
+ATOM 567 O PRO 41 16.652 11.368 16.033 1.00 8.82 A O
+ATOM 568 CB PRO 41 17.076 14.658 16.145 1.00 10.39 A C
+ATOM 569 CG PRO 41 16.098 14.689 14.997 1.00 10.99 A C
+ATOM 570 CD PRO 41 16.859 14.150 13.779 1.00 10.49 A C
+ATOM 571 HA PRO 41 18.859 13.521 16.218 1.00 0.00 A H
+ATOM 572 HB1 PRO 41 16.596 14.577 17.018 1.00 0.00 A H
+ATOM 573 HB2 PRO 41 17.642 15.482 16.151 1.00 0.00 A H
+ATOM 574 HG1 PRO 41 15.308 14.109 15.198 1.00 0.00 A H
+ATOM 575 HG2 PRO 41 15.790 15.625 14.828 1.00 0.00 A H
+ATOM 576 HD1 PRO 41 16.257 13.629 13.174 1.00 0.00 A H
+ATOM 577 HD2 PRO 41 17.291 14.889 13.263 1.00 0.00 A H
+ATOM 578 N GLY 42 17.728 12.124 17.884 1.00 7.55 A N
+ATOM 579 CA GLY 42 17.334 10.956 18.691 1.00 8.00 A C
+ATOM 580 C GLY 42 15.875 10.688 18.871 1.00 7.22 A C
+ATOM 581 O GLY 42 15.434 9.550 19.166 1.00 8.41 A O
+ATOM 582 HN GLY 42 18.253 12.863 18.307 1.00 0.00 A H
+ATOM 583 HA1 GLY 42 17.734 10.148 18.259 1.00 0.00 A H
+ATOM 584 HA2 GLY 42 17.729 11.077 19.602 1.00 0.00 A H
+ATOM 585 N ASP 43 15.036 11.747 18.715 1.00 5.54 A N
+ATOM 586 CA ASP 43 13.564 11.573 18.836 1.00 5.85 A C
+ATOM 587 C ASP 43 12.936 11.227 17.470 1.00 5.87 A C
+ATOM 588 O ASP 43 11.720 11.040 17.428 1.00 7.29 A O
+ATOM 589 CB ASP 43 12.933 12.737 19.580 1.00 6.72 A C
+ATOM 590 CG ASP 43 13.140 14.094 18.958 1.00 8.59 A C
+ATOM 591 OD1 ASP 43 14.109 14.303 18.212 1.00 9.59 A O
+ATOM 592 OD2 ASP 43 12.267 14.963 19.265 1.00 11.45 A O
+ATOM 593 HN ASP 43 15.413 12.652 18.517 1.00 0.00 A H
+ATOM 594 HA ASP 43 13.363 10.779 19.410 1.00 0.00 A H
+ATOM 595 HB1 ASP 43 11.949 12.570 19.635 1.00 0.00 A H
+ATOM 596 HB2 ASP 43 13.319 12.759 20.502 1.00 0.00 A H
+ATOM 597 N TYR 44 13.725 11.174 16.425 1.00 5.22 A N
+ATOM 598 CA TYR 44 13.257 10.745 15.081 1.00 5.56 A C
+ATOM 599 C TYR 44 14.275 9.687 14.612 1.00 4.61 A C
+ATOM 600 O TYR 44 14.930 9.862 13.568 1.00 6.04 A O
+ATOM 601 CB TYR 44 13.200 11.914 14.071 1.00 5.41 A C
+ATOM 602 CG TYR 44 12.000 12.819 14.399 1.00 5.34 A C
+ATOM 603 CD1 TYR 44 12.119 13.853 15.332 1.00 6.59 A C
+ATOM 604 CD2 TYR 44 10.775 12.617 13.762 1.00 5.94 A C
+ATOM 605 CE1 TYR 44 11.045 14.675 15.610 1.00 5.97 A C
+ATOM 606 CE2 TYR 44 9.676 13.433 14.048 1.00 5.17 A C
+ATOM 607 CZ TYR 44 9.802 14.456 14.996 1.00 5.96 A C
+ATOM 608 OH TYR 44 8.740 15.265 15.269 1.00 8.60 A O
+ATOM 609 HN TYR 44 14.684 11.434 16.537 1.00 0.00 A H
+ATOM 610 HA TYR 44 12.324 10.389 15.134 1.00 0.00 A H
+ATOM 611 HB1 TYR 44 14.045 12.446 14.130 1.00 0.00 A H
+ATOM 612 HB2 TYR 44 13.099 11.550 13.145 1.00 0.00 A H
+ATOM 613 HD1 TYR 44 12.989 13.999 15.802 1.00 0.00 A H
+ATOM 614 HD2 TYR 44 10.682 11.880 13.093 1.00 0.00 A H
+ATOM 615 HE1 TYR 44 11.154 15.432 16.254 1.00 0.00 A H
+ATOM 616 HE2 TYR 44 8.805 13.287 13.578 1.00 0.00 A H
+ATOM 617 HH TYR 44 7.945 14.960 14.745 1.00 0.00 A H
+ATOM 618 N ALA 45 14.342 8.640 15.422 1.00 4.76 A N
+ATOM 619 CA ALA 45 15.445 7.667 15.246 1.00 5.89 A C
+ATOM 620 C ALA 45 15.171 6.533 14.280 1.00 6.67 A C
+ATOM 621 O ALA 45 16.093 5.705 14.039 1.00 7.56 A O
+ATOM 622 CB ALA 45 15.680 7.099 16.682 1.00 6.82 A C
+ATOM 623 HN ALA 45 13.659 8.509 16.140 1.00 0.00 A H
+ATOM 624 HA ALA 45 16.233 8.130 14.839 1.00 0.00 A H
+ATOM 625 HB1 ALA 45 16.418 6.425 16.657 1.00 0.00 A H
+ATOM 626 HB2 ALA 45 15.943 7.898 17.318 1.00 0.00 A H
+ATOM 627 HB3 ALA 45 14.788 6.644 17.011 1.00 0.00 A H
+ATOM 628 N ASN 46 13.966 6.502 13.739 1.00 5.80 A N
+ATOM 629 CA ASN 46 13.512 5.395 12.878 1.00 6.15 A C
+ATOM 630 C ASN 46 13.311 5.853 11.455 1.00 6.61 A C
+ATOM 631 OT1 ASN 46 13.539 7.141 11.084 1.00 7.18 A O
+ATOM 632 CB ASN 46 12.266 4.769 13.501 1.00 7.27 A C
+ATOM 633 CG ASN 46 12.538 4.304 14.922 1.00 7.98 A C
+ATOM 634 OD1 ASN 46 11.982 4.849 15.886 1.00 11.00 A O
+ATOM 635 ND2 ASN 46 13.407 3.298 15.015 1.00 10.32 A N
+ATOM 636 OT2 ASN 46 12.893 4.996 10.485 1.00 7.86 A O
+ATOM 637 HN ASN 46 13.338 7.259 13.921 1.00 0.00 A H
+ATOM 638 HA ASN 46 14.216 4.687 12.825 1.00 0.00 A H
+ATOM 639 HB1 ASN 46 11.532 5.448 13.515 1.00 0.00 A H
+ATOM 640 HB2 ASN 46 11.984 3.984 12.949 1.00 0.00 A H
+ATOM 641 HD21 ASN 46 13.819 2.915 14.188 1.00 0.00 A H
+ATOM 642 HD22 ASN 46 13.647 2.926 15.912 1.00 0.00 A H
+END
diff --git a/examples/code_fragments/mm/gb_example_view_trajectory.py b/examples/code_fragments/mm/gb_example_view_trajectory.py
new file mode 100644
index 0000000000000000000000000000000000000000..fcdf070da18c00eb866c76b960db212c7e1096ea
--- /dev/null
+++ b/examples/code_fragments/mm/gb_example_view_trajectory.py
@@ -0,0 +1,16 @@
+from ost.gui import trajectory_viewer
+
+"""
+MM - Demo
+
+!!!Requires OpenStructure to be compiled with MM-Support!!!
+
+This demo demonstrates how to actually look at the trajectory created
+in the gb_example_writing_trajectory.py script.
+"""
+
+t = io.LoadCHARMMTraj("gb_example_traj.pdb","gb_example_traj.dcd")
+go = gfx.Entity("gb",t.GetEntity())
+scene.Add(go)
+w = trajectory_viewer.TrajWidget([t],[go])
+w.show()
diff --git a/examples/code_fragments/mm/gb_example_writing_trajectory.py b/examples/code_fragments/mm/gb_example_writing_trajectory.py
new file mode 100644
index 0000000000000000000000000000000000000000..f14f6b3fb0d792f95c3343278de1a5fe8754dc52
--- /dev/null
+++ b/examples/code_fragments/mm/gb_example_writing_trajectory.py
@@ -0,0 +1,42 @@
+from ost.mol.mm import *
+
+"""
+MM - Demo
+
+!!!Requires OpenStructure to be compiled with MM-Support!!!
+
+This demo should show the procedure of setting up a simulation and write
+the results directly to disk.
+"""
+
+
+prot=io.LoadPDB('1CRN.pdb')
+
+#set up the simulation
+settings = Settings()
+settings.integrator = LangevinIntegrator(310,1,0.002)
+settings.add_gbsa = True
+settings.forcefield = LoadCHARMMForcefield()
+settings.nonbonded_cutoff = 8.0
+settings.nonbonded_method = NonbondedMethod.CutoffNonPeriodic
+settings.platform = Platform.CPU
+settings.cpu_properties["CpuThreads"] = "2"
+
+sim = Simulation(prot,settings)
+
+#minimize it
+sim.ApplySD(tolerance = 1.0, max_iterations = 200)
+
+#create a trajectory observer and register it to the simulation
+observer = TrajWriter(10,"gb_example_traj.pdb","gb_example_traj.dcd")
+sim.Register(observer)
+
+#run the simulation
+sim.Steps(10000)
+
+#Trajectory Observer needs to finalize, otherwise you might get a corrupt dcd file
+observer.Finalize()
+
+
+
+
diff --git a/modules/CMakeLists.txt b/modules/CMakeLists.txt
index 9759f2e3bde7ae2708bd4ff61c4e0950d0a3a1db..d05c27ddb43a3b031165ea88e8e235f30b463f3d 100644
--- a/modules/CMakeLists.txt
+++ b/modules/CMakeLists.txt
@@ -1,11 +1,12 @@
# recursively process all subdirectories
file(GLOB ALL_FILES *)
-foreach(fname ${ALL_FILES})
+foreach(full_name ${ALL_FILES})
+ get_filename_component(fname ${full_name} NAME)
if(NOT ${fname} MATCHES ".*\\.svn"
AND NOT ${fname} MATCHES ".*CMakeFiles"
AND NOT ${fname} MATCHES ".*main"
AND NOT ${fname} MATCHES "doc")
- if(IS_DIRECTORY ${fname})
+ if(IS_DIRECTORY ${full_name})
add_subdirectory(${fname})
endif()
endif()
diff --git a/modules/base/pymod/__init__.py.in b/modules/base/pymod/__init__.py.in
index 4b1be9f6cdfd7c504bf4cd7b0b5094b0f5b8a147..89316b83115438dfacae9a19500b388369187001 100644
--- a/modules/base/pymod/__init__.py.in
+++ b/modules/base/pymod/__init__.py.in
@@ -18,7 +18,7 @@
#------------------------------------------------------------------------------
-__all__=['Correl', 'FileLogSink', 'FloatList', 'GetCurrentLogSink', 'GetPrefixPath', 'GetSharedDataPath', 'GetVerbosityLevel', 'Histogram', 'IntList', 'LogDebug', 'LogError', 'LogInfo', 'LogScript', 'LogSink', 'LogTrace', 'LogVerbose', 'LogWarning', 'Max', 'Mean', 'Median', 'Min', 'MultiLogSink', 'PopLogSink', 'PopVerbosityLevel', 'PushLogSink', 'PushVerbosityLevel', 'Range', 'SetPrefixPath', 'StdDev', 'StreamLogSink', 'StringList', 'StringLogSink', 'Units', 'VERSION', 'VERSION_MAJOR', 'VERSION_MINOR', 'VERSION_PATCH', 'WITH_NUMPY', 'conop', 'geom', 'io', 'mol', 'seq', 'stutil' @ALL_ADDITIONAL_MODULES@]
+__all__=['CharList','Correl', 'FileLogSink', 'FloatList', 'FloatMatrix', 'FloatMatrix3', 'FloatMatrix4', 'GetCurrentLogSink', 'GetPrefixPath', 'GetSharedDataPath', 'GetVerbosityLevel', 'Histogram', 'IntList', 'LogDebug', 'LogError', 'LogInfo', 'LogScript', 'LogSink', 'LogTrace', 'LogVerbose', 'LogWarning', 'Max', 'Mean', 'Median', 'Min', 'MultiLogSink', 'PopLogSink', 'PopVerbosityLevel', 'PushLogSink', 'PushVerbosityLevel', 'Range', 'SetPrefixPath', 'StdDev', 'StreamLogSink', 'StringList', 'StringLogSink', 'Units', 'VERSION', 'VERSION_MAJOR', 'VERSION_MINOR', 'VERSION_PATCH', 'WITH_NUMPY', 'conop', 'geom', 'io', 'mol', 'seq', 'stutil' @ALL_ADDITIONAL_MODULES@]
from _ost_base import *
from stutil import *
diff --git a/modules/base/pymod/export_generic_property.cc b/modules/base/pymod/export_generic_property.cc
index f36a12d068d85c476cfec3e12f15c24b8ef76b2d..b5fab8c7a1291ed4b56715a077e28ca7dac59831 100644
--- a/modules/base/pymod/export_generic_property.cc
+++ b/modules/base/pymod/export_generic_property.cc
@@ -34,6 +34,7 @@ void export_GenericProp()
int (GenericPropContainer::* get_int2)(const String&, int) const = &GenericPropContainer::GetIntProp;
bool (GenericPropContainer::* get_bool1)(const String&) const = &GenericPropContainer::GetBoolProp;
bool (GenericPropContainer::* get_bool2)(const String&, bool) const = &GenericPropContainer::GetBoolProp;
+ geom::Vec3 (GenericPropContainer::* get_vec3)(const String&) const = &GenericPropContainer::GetVec3Prop;
class_<GenericPropContainer, boost::noncopyable>("GenericPropContainer",no_init)
.def("HasProp",&GenericPropContainer::HasProp)
@@ -49,6 +50,8 @@ void export_GenericProp()
.def("SetBoolProp",&GenericPropContainer::SetBoolProp)
.def("GetBoolProp",get_bool1)
.def("GetBoolProp",get_bool2)
+ .def("SetVec3Prop",&GenericPropContainer::SetVec3Prop)
+ .def("GetVec3Prop",get_vec3)
.def("ClearProps",&GenericPropContainer::ClearProps)
.def("GetPropAsString",&GenericPropContainer::GetPropAsString)
;
diff --git a/modules/base/pymod/wrap_base.cc b/modules/base/pymod/wrap_base.cc
index e1a74154acc8cd264166c732533c63f9adcd9556..b0cfa84655e8574cad01d64f370d8e4ab5001163 100644
--- a/modules/base/pymod/wrap_base.cc
+++ b/modules/base/pymod/wrap_base.cc
@@ -104,10 +104,31 @@ BOOST_PYTHON_MODULE(_ost_base)
class_<std::vector<String> >("StringList", init<>())
.def(vector_indexing_suite<std::vector<String>, true>())
;
+
+ class_<std::vector<char> >("CharList", init<>())
+ .def(vector_indexing_suite<std::vector<char>, true>())
+ ;
typedef std::vector<int> IntList;
class_<std::vector<int> >("IntList", init<>())
.def(vector_indexing_suite<std::vector<int> >())
.def(geom::VectorAdditions<IntList>())
;
+
+ typedef std::vector< FloatList > FloatMatrix;
+ class_<FloatMatrix>("FloatMatrix", init<>())
+ .def(vector_indexing_suite<FloatMatrix>())
+ ;
+
+ typedef std::vector< FloatMatrix > FloatMatrix3;
+ class_<FloatMatrix3>("FloatMatrix3", init<>())
+ .def(vector_indexing_suite<FloatMatrix3>())
+ ;
+
+ typedef std::vector< FloatMatrix3 > FloatMatrix4;
+ class_<FloatMatrix4>("FloatMatrix4", init<>())
+ .def(vector_indexing_suite<FloatMatrix4>())
+ ;
+
+ ;
}
diff --git a/modules/base/src/export_helper/generic_property_def.hh b/modules/base/src/export_helper/generic_property_def.hh
index ef13e3490ac3b298fc0c50f1f192cb620672c4fd..ff02641c5a1e436a590aa8f23e0529f7dda88031 100644
--- a/modules/base/src/export_helper/generic_property_def.hh
+++ b/modules/base/src/export_helper/generic_property_def.hh
@@ -141,7 +141,9 @@ void const_generic_prop_def(O& bp_class)
Real (C::*get_float1)(const String&, Real) const=&C::GetFloatProp;
Real (C::*get_float2)(const String&) const=&C::GetFloatProp;
-
+
+ geom::Vec3 (C::*get_vec3)(const String&) const=&C::GetVec3Prop;
+
String (C::*get_str1)(const String&, const String&) const=&C::GetStringProp;
String (C::*get_str2)(const String&) const=&C::GetStringProp;
bp_class
@@ -151,7 +153,8 @@ void const_generic_prop_def(O& bp_class)
.def("GetBoolProp", get_bool1)
.def("GetBoolProp", get_bool2)
.def("GetFloatProp", get_float1)
- .def("GetFloatProp", get_float2)
+ .def("GetFloatProp", get_float2)
+ .def("GetVec3Prop", get_vec3)
.def("GetIntProp", get_int1)
.def("GetIntProp", get_int2)
.def("GetStringProp", get_str1)
@@ -179,6 +182,7 @@ void generic_prop_def(O& bp_class)
.def("ClearProps", &C::ClearProps)
.def("GetPropAsString", &C::GetPropAsString)
.def("SetFloatProp", &C::SetFloatProp)
+ .def("SetVec3Prop", &C::SetVec3Prop)
.def("SetIntProp", &C::SetIntProp)
.def("SetStringProp", &C::SetStringProp)
.def("GetPropList",&C::GetPropList)
diff --git a/modules/base/src/generic_property.hh b/modules/base/src/generic_property.hh
index 0b336e1ef8daed75e6084ef2d21d7937fa5ecae8..7c0ba516ae6068b079028e940aa5708019cfbf5e 100644
--- a/modules/base/src/generic_property.hh
+++ b/modules/base/src/generic_property.hh
@@ -36,6 +36,7 @@
#include <ost/module_config.hh>
#include <ost/invalid_handle.hh>
#include <ost/message.hh>
+#include <ost/geom/vec3.hh>
namespace ost {
@@ -45,8 +46,8 @@ struct DLLEXPORT GenericPropError: public Error
Error(m)
{}
};
-
-typedef boost::variant<String, Real, int, bool> GenericPropValue;
+
+typedef boost::variant<String, Real, int, bool, geom::Vec3> GenericPropValue;
/// \brief base class for the implementation
class TEMPLATE_EXPORT GenericPropContainerImpl
@@ -256,6 +257,13 @@ public:
return this->gp_get<bool>(key);
}
+ /// \brief returns Vec3 property, raises an exception if it does not exist
+ geom::Vec3 GetVec3Prop(const String& key) const
+ {
+ CheckHandleValidity(*static_cast<const H*>(this));
+ return this->gp_get<geom::Vec3>(key);
+ }
+
/// \brief returns String property, or the given default if it does not exist
String GetStringProp(const String& key, const String& def) const
{
@@ -364,6 +372,13 @@ public:
this->GetImpl()->GenericProp(key)=value;
}
+ /// \ brief sets Vec3 property
+ void SetVec3Prop(const String& key, geom::Vec3 value)
+ {
+ CheckHandleValidity(*static_cast<const H*>(this));
+ this->GetImpl()->GenericProp(key)=value;
+ }
+
void RemoveProp(const String& key)
{
CheckHandleValidity(*static_cast<const H*>(this));
diff --git a/modules/base/src/string_ref.hh b/modules/base/src/string_ref.hh
index 802dd594069257ba17213a02d73144018e635b32..38ab290bfa7e97e5aac93b09180dc9b89e0f0af5 100644
--- a/modules/base/src/string_ref.hh
+++ b/modules/base/src/string_ref.hh
@@ -76,7 +76,7 @@ public:
/// \brief returns a substring of the string
///
/// \param pos the starting position of the substring
- /// \param length is the length of the string. if std::string::npos, the
+ /// \param n is the length of the string. if std::string::npos, the
/// substring goes from \p pos to the end of the string
/// The function does on purpose not perform any boundary check in release
/// mode. It's the duty of the caller to make sure the string has the required
diff --git a/modules/base/tests/test_table.py b/modules/base/tests/test_table.py
index 4ee2c8b67b90b828067d46c198e504b9b4590926..347183262b12b7881631d952da072652c5407996 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -42,8 +42,8 @@ except ImportError:
print "Could not find matplotlib: ignoring some table class unit tests"
try:
- import Image
- import ImageChops
+ from PIL import Image
+ from PIL import ImageChops
except ImportError:
HAS_PIL=False
print "Could not find python imagine library: ignoring some table class unit tests"
diff --git a/modules/bindings/doc/bindings.rst b/modules/bindings/doc/bindings.rst
index 9b46608366b909a7fcee559f19ad2e3f87488ea9..966ba274fb1a28471cf1aebd34ef8b6c55725901 100644
--- a/modules/bindings/doc/bindings.rst
+++ b/modules/bindings/doc/bindings.rst
@@ -15,6 +15,7 @@ So far, the binding module includes:
dssp
blast
+ hhblits
msms
tmtools
clustalw
diff --git a/modules/bindings/doc/hhblits.rst b/modules/bindings/doc/hhblits.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c822d5bd0641d1fc6a863066f4196e3fe77f467a
--- /dev/null
+++ b/modules/bindings/doc/hhblits.rst
@@ -0,0 +1,128 @@
+:mod:`~ost.bindings.hhblits` - Search related sequences in databases
+================================================================================
+
+.. module:: ost.bindings.hhblits
+ :synopsis: Search related sequences in databases
+
+Introduction
+--------------------------------------------------------------------------------
+
+HHblits is a sequence search tool like BLAST, able to find more distant
+homologs This is achieved by performing `profile-profile searches`. In BLAST, a
+\query sequence is searched against a sequence database. That is a
+`sequence-sequence search`. HHblits works on a profile database, usually that
+one is provided, queried with a sequence profile. The latter one needs to be
+calculated before the actual search. In very simple words, HHblits is using
+per-sequence scoring functions to be more sensitive, in this particular case
+Hidden Markov models. The software suite needed for HHblits can be found
+`here <http://toolkit.tuebingen.mpg.de/hhblits>`_.
+
+
+Examples
+--------------------------------------------------------------------------------
+
+A typical search: Get an instance of the bindings, build the search profile out
+of the query sequence, run the search and iterate results. Since
+:class:`~HHblits` works with a :class:`~ost.seq.SequenceHandle` or a FastA
+file, both ways are shown.
+
+First query by sequence:
+
+.. code-block:: python
+
+ from ost.bindings import hhblits
+
+ # get a SequenceHandle
+ query_seq = seq.CreateSequence('Query',
+ 'MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGS'+
+ 'ELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGF'+
+ 'PRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPS'+
+ 'GRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYH'+
+ 'QMTAPLIGYYYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
+
+ # set up the search environment
+ # $EBROOTHHMINSUITE points to the root of a HHsuite installation
+ hh = hhblits.HHblits(query_seq, os.getenv('EBROOTHHMINSUITE'))
+
+ # now create a search profile for the query sequence against the NR20 db
+ # provided on the HHblits web page, nr20_12Aug11 is just the prefix common to
+ # all db files, so `ls hhtools/nr20_12Aug11*` would list all of them
+ a3m_file = hh.BuildQueryMSA(nrdb='hhtools/nr20_12Aug11')
+
+ # search time! we just search against NR20 again, but every HHblits db is
+ # working here, e.g. one build from all the sequences in PDB
+ hit_file = hh.Search(a3m_file, 'hhtools/nr20_12Aug11')
+
+ # lets have a look at the resuls
+ with open(hit_file) as hit_fh:
+ header, hits = hhblits.ParseHHblitsOutput(hit_fh)
+ for hit in hits:
+ print hit.aln
+
+Very similar going by file:
+
+.. code-block:: python
+
+ from ost.bindings import hhblits
+
+ # set up the search environment
+ # $EBROOTHHMINSUITE points to the root of a HHsuite installation
+ hh = hhblits.HHblits('query.fas', os.getenv('EBROOTHHMINSUITE'))
+
+ # now create a search profile for the query sequence against the NR20 db
+ # provided on the HHblits web page, nr20_12Aug11 is just the prefix common to
+ # all db files, so `ls hhtools/nr20_12Aug11*` would list all of them
+ a3m_file = hh.BuildQueryMSA(nrdb='hhtools/nr20_12Aug11')
+
+ # search time! we just search against NR20 again, but every HHblits db is
+ # working here, e.g. one build from all the sequences in PDB
+ hit_file = hh.Search(a3m_file, 'hhtools/nr20_12Aug11')
+
+ # lets have a look at the resuls
+ with open(hit_file) as hit_fh:
+ header, hits = hhblits.ParseHHblitsOutput(hit_fh)
+ for hit in hits:
+ print hit.aln
+
+The alignments produced by HHblits are sometimes slightly better than by BLAST,
+so one may want to extract them:
+
+.. code-block:: python
+
+ from ost.bindings import hhblits
+
+ # set up the search environment
+ # $EBROOTHHMINSUITE points to the root of a HHsuite installation
+ hh = hhblits.HHblits('query.fas', os.getenv('EBROOTHHMINSUITE'))
+
+ # now create a search profile for the query sequence against the NR20 db
+ # provided on the HHblits web page, nr20_12Aug11 is just the prefix common to
+ # all db files, so `ls hhtools/nr20_12Aug11*` would list all of them
+ a3m_file = hh.BuildQueryMSA(nrdb='hhtools/nr20_12Aug11')
+
+ # note that ParseA3M is not a class method but a module function
+ output = hhblits.ParseA3M(open(a3m_file))
+
+ print output['msa']
+
+
+Binding API
+--------------------------------------------------------------------------------
+
+.. autoclass:: ost.bindings.hhblits.HHblits
+ :members:
+
+.. autoclass:: ost.bindings.hhblits.HHblitsHit
+
+.. autoclass:: ost.bindings.hhblits.HHblitsHeader
+
+.. autofunction:: ost.bindings.hhblits.ParseHHblitsOutput
+
+.. autofunction:: ost.bindings.hhblits.ParseA3M
+
+.. autofunction:: ost.bindings.hhblits.ParseHeaderLine
+
+.. autofunction:: ost.bindings.hhblits.ParseHHM
+
+.. autofunction:: ost.bindings.hhblits.EstimateMemConsumption
+.. LocalWords: HHblits homologs
diff --git a/modules/bindings/pymod/CMakeLists.txt b/modules/bindings/pymod/CMakeLists.txt
index 52c855f25e792401fde6f6befa48ca443009f91f..ba312b609546b16b403236eb47396d33eac71b5f 100644
--- a/modules/bindings/pymod/CMakeLists.txt
+++ b/modules/bindings/pymod/CMakeLists.txt
@@ -8,8 +8,11 @@ dssp.py
clustalw.py
utils.py
naccess.py
+hhblits.py
blast.py
cadscore.py
kclust.py
+ialign.py
+align_3dcomb.py
)
pymod(NAME bindings PY ${OST_BINDINGS})
diff --git a/modules/bindings/pymod/__init__.py b/modules/bindings/pymod/__init__.py
index e7f855fe8211181bcf4ff603b0b6cddb4486df2e..ab3668069f13b1b3e66dbae71c895dbb4a7128fc 100644
--- a/modules/bindings/pymod/__init__.py
+++ b/modules/bindings/pymod/__init__.py
@@ -1,9 +1,10 @@
from ost.bindings import dssp
from ost.bindings import msms
+from ost.bindings import hhblits
from ost.bindings import blast
from ost.bindings import tmtools
from ost.bindings import naccess
from ost.bindings import hbplus
from ost.bindings import clustalw
from ost.bindings import cadscore
-
+from ost.bindings import align_3dcomb
diff --git a/modules/bindings/pymod/align_3dcomb.py b/modules/bindings/pymod/align_3dcomb.py
new file mode 100644
index 0000000000000000000000000000000000000000..ca709fc15fcadfe8dbb0765466cf874e3b35c231
--- /dev/null
+++ b/modules/bindings/pymod/align_3dcomb.py
@@ -0,0 +1,129 @@
+"""
+3DCOMB module
+
+Author: Niklaus Johner
+
+This module is for structural alignment from OpenStructure using the external program 3DCOMB.
+
+How To Use This Module:
+ 1. Import it (e.g. as "from ost.bindings import align_3dcomb")
+ 2. Use it (e.g. as "alignment,transformation_list = align_3dcomb.AlignStructures(view_list)")
+
+Requirement:
+ - 3DCOMB installed
+"""
+
+from ost.bindings import utils
+import subprocess,os
+from ost import settings
+from ost import io
+import ost
+import ost.geom
+
+def _GetExecutable(comb_exe, comb_env):
+ """
+ Function to check if 3DCOMB executable is present
+
+ :param comb_exe: Explicit path to 3DCOMB executable
+ :param msms_env: Environment variable pointing to 3DCOMB executable
+ :returns: Path to the executable
+ :raises: :class:`~ost.FileNotFound` if executable is not found
+ """
+ return settings.Locate(['3DCOMB_linux','3DCOMB_win.exe'], explicit_file_name=comb_exe,
+ env_name=comb_env)
+
+def _SetupFiles(structure_list):
+ """
+ Setup files for MSMS calculation in temporary directory
+
+ :param structure_list: A list of EntityView that will be aligned.\
+ each EntityView should contain a single chain and each residue needs to have a CA atom.
+ :returns: calss:settings.TempDir
+ :raises: class:`RuntimeError` if on of the Views is not valid
+ """
+
+ #write out temporary pdb files
+ if not all([ev.IsValid() for ev in structure_list]):
+ raise RuntimeError, "Invalid EntityView in structure_list"
+ tpd=utils.TempDirWithFiles(structure_list)
+
+ #Write out the file containing the list of all structures
+ outfile=open(os.path.join(tpd.dirname,'list'),'w')
+ outfile.write('\n'.join(tpd.files))
+ outfile.close()
+ return tpd
+
+
+def _Run3DCOMB(command,tpd):
+ """
+ Run the 3DCOMB alignment command
+
+ This functions starts the external 3DCOMB executable and returns the stdout of
+ 3DCOMB.
+
+ :param command: Command to execute
+ :returns: stdout of 3DCOMB
+ :raises: :class:`CalledProcessError` for non-zero return value
+ """
+ outname=os.path.join(tpd.dirname,'align.out')
+ outfile=open(outname,'w')
+ returncode=subprocess.call(command, shell=True, stdout=outfile)
+ outfile.close()
+ #check for successful completion of 3DCOMB
+ if returncode!=0:
+ print "WARNING: 3DCOMB error\n"
+ raise subprocess.CalledProcessError
+ return returncode
+
+def _ParseOutput(tpd):
+ #Read Alignment
+ ali=io.LoadAlignment(os.path.join(tpd.dirname,'list.ali'),'fasta')
+ for i in range(ali.GetCount()):
+ ali.SetSequenceName(i,'struc{0}'.format(i))
+ #Read Transformations
+ f=open(os.path.join(tpd.dirname,'list.rmt'),'r')
+ Tl=[]
+ for l in f:
+ if l.startswith('>'):
+ fl=ost.FloatList()
+ for i in range(3):
+ l=f.next()
+ sl=l.split(',')
+ fl.extend([float(el) for el in sl[0].split()+[sl[1]]])
+ fl.extend([0,0,0,1])
+ T=ost.geom.Transform()
+ M=ost.geom.Mat4(*fl)
+ T.SetMatrix(M)
+ Tl.append(T)
+ #Read standard output
+ outfile=open(os.path.join(tpd.dirname,'align.out'),'r')
+ results={}
+ for line in outfile:
+ if line.startswith('Objective function value is'):results['objective_function']=float(line.split()[-1])
+ if line.startswith('CORE_LEN'):
+ l=line.split(',')
+ for el in l:
+ s=el.split('=')
+ results[s[0]]=float(s[1])
+ return ali,Tl,results
+
+
+def AlignStructures(structure_list,apply_transform=False,name_list=None,comb_exe=None,comb_env=None):
+ comb_executable=_GetExecutable(comb_exe, comb_env)
+ tpd=_SetupFiles(structure_list)
+ command=' '.join([comb_executable,os.path.join(tpd.dirname,'list')])
+ returncode=_Run3DCOMB(command,tpd)
+ try:ali,Tl,results=_ParseOutput(tpd)
+ except:
+ print 'could not parse output'
+ raise RuntimeError
+ if apply_transform:
+ for T,ev in zip(Tl,structure_list):
+ ev.handle.FixTransform()
+ ev.handle.SetTransform(T)
+ tpd.Cleanup()
+ return ali,Tl,results
+
+
+
+
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
new file mode 100644
index 0000000000000000000000000000000000000000..dd51b1207ebb7869512dd522d16647136df3177f
--- /dev/null
+++ b/modules/bindings/pymod/hhblits.py
@@ -0,0 +1,741 @@
+'''HHblits wrapper.
+'''
+
+import subprocess
+import datetime
+import os
+import shutil
+import tempfile
+
+import ost
+from ost import settings, seq
+from ost.bindings import utils
+
+class HHblitsHit:
+ """
+ A hit found by HHblits
+
+ .. attribute:: hit_id
+
+ String identifying the hit
+
+ :type: :class:`str`
+
+ .. attribute:: aln
+
+ Pairwise alignment containing the aligned part between the query and the
+ target. First sequence is the query, the second sequence the target.
+
+ :type: :class:`~ost.seq.AlignmentHandle`
+
+ .. attribute:: score
+
+ The alignment score
+
+ :type: :class:`float`
+
+ .. attribute:: ss_score
+
+ The secondary structure score
+
+ :type: :class:`float`
+
+ .. attribute:: evalue
+
+ The E-value of the alignment
+
+ :type: :class:`float`
+
+ .. attribute:: pvalue
+
+ The P-value of the alignment
+
+ :type: :class:`float`
+
+ .. attribute:: prob
+
+ The probability of the alignment (between 0 and 100)
+
+ :type: :class:`float`
+ """
+ def __init__(self, hit_id, aln, score, ss_score, evalue, pvalue, prob):
+ self.hit_id = hit_id
+ self.aln = aln
+ self.score = score
+ self.ss_score = ss_score
+ self.evalue = evalue
+ self.prob = prob
+ self.pvalue = pvalue
+
+class HHblitsHeader:
+ """Stats from the beginning of search output.
+
+ .. attribute:: query
+
+ The name of the query sequence
+
+ :type: :class:`str`
+
+ .. attribute:: match_columns
+
+ Total of aligned Match columns
+
+ :type: :class:`int`
+
+ .. attribute:: n_eff
+
+ Value of the ``-neff`` option
+
+ :type: :class:`float`
+
+ .. attribute:: searched_hmms
+
+ Number of profiles searched
+
+ :type: :class:`int`
+
+ .. attribute:: date
+
+ Execution date
+
+ :type: :class:`datetime.datetime`
+
+ .. attribute:: command
+
+ Command used to run
+
+ :type: :class:`str`
+ """
+ def __init__(self):
+ self.query = ''
+ self.match_columns = 0
+ self.n_eff = 0
+ self.searched_hmms = 0
+ self.date = None
+ self.command = ''
+
+def ParseHeaderLine(line):
+ '''Fetch header content.
+
+ First, we seek the start of the identifier, that is, the first whitespace
+ after the hit number + 1. Since the identifier may contain whitespaces
+ itself, we cannot split the whole line
+
+ :param line: Line from the output header.
+ :type line: :class:`str`
+
+ :return: Hit information
+ :rtype: :class:`HHblitsHit`
+ '''
+ for i in range(0, len(line)):
+ if line[i].isdigit():
+ break
+ for i in range(i, len(line)):
+ if line[i] == ' ':
+ break
+ assert len(line)-i >= 31 and line[i+1] != ' '
+ hit_id = line[i+1:i+31].strip()
+ fields = line[i+32:].split()
+ prob = float(fields[0])
+ evalue = float(fields[1])
+ pvalue = float(fields[2])
+ score = float(fields[3])
+ ss_score = float(fields[4])
+ offsets = (int(fields[6].split('-')[0]), int(fields[7].split('-')[0]))
+ return (HHblitsHit(hit_id, None, score, ss_score, evalue, pvalue, prob),
+ offsets)
+
+def ParseHHblitsOutput(output):
+ """
+ Parses the HHblits output and returns a tuple of :class:`HHblitsHeader` and
+ a list of :class:`HHblitsHit` instances.
+
+ :param output: output of a :meth:`HHblits.Search`, needs to be iteratable,
+ e.g. an open file handle
+ :type output: :class:`file`/ iteratable
+
+ :return: a tuple of the header of the search results and the hits
+ :rtype: (:class:`HHblitsHeader`, :class:`HHblitsHit`)
+ """
+ lines = iter(output)
+ def _ParseHeaderSection(lines):
+ value_start_column = 14
+ date_pattern = '%a %b %d %H:%M:%S %Y'
+ header = HHblitsHeader()
+ line = lines.next()
+ assert line.startswith('Query')
+ header.query = line[value_start_column:].strip()
+ line = lines.next()
+ assert line.startswith('Match_columns')
+ header.match_columns = int(line[value_start_column:].strip())
+
+ line = lines.next()
+ assert line.startswith('No_of_seqs')
+
+ line = lines.next()
+ assert line.startswith('Neff')
+ header.n_eff = float(line[value_start_column:].strip())
+
+ line = lines.next()
+ assert line.startswith('Searched_HMMs')
+ header.searched_hmms = int(line[value_start_column:].strip())
+
+ line = lines.next()
+ assert line.startswith('Date')
+ value = line[value_start_column:].strip()
+ header.date = datetime.datetime.strptime(value, date_pattern)
+
+ line = lines.next()
+ assert line.startswith('Command')
+ header.command = line[value_start_column:].strip()
+
+ line = lines.next()
+ assert len(line.strip()) == 0
+ return header
+
+ def _ParseTableOfContents(lines):
+ assert lines.next().startswith(' No Hit')
+ hits = []
+ while True:
+ line = lines.next()
+ if len(line.strip()) == 0:
+ return hits
+ hits.append(ParseHeaderLine(line))
+ return hits
+
+ def _ParseResultBody(query_id, hits, lines):
+ entry_index = None
+ query_str = ''
+ templ_str = ''
+ def _MakeAln(query_id, hit_id, query_string, templ_string,
+ q_offset, t_offset):
+ s1 = seq.CreateSequence(query_id, query_string)
+ s1.offset = q_offset-1
+ s2 = seq.CreateSequence(hit_id, templ_string)
+ s2.offset = t_offset-1
+ return seq.CreateAlignment(s1, s2)
+ try:
+ while True:
+ line = lines.next()
+ if len(line.strip()) == 0:
+ continue
+ if line.startswith('Done!'):
+ if len(query_str) > 0:
+ hits[entry_index][0].aln = _MakeAln(\
+ query_id, hits[entry_index][0].hit_id,
+ query_str, templ_str, *hits[entry_index][1])
+ return [h for h, o in hits]
+ if line.startswith('No '):
+ if len(query_str) > 0:
+ hits[entry_index][0].aln = _MakeAln(\
+ query_id, hits[entry_index][0].hit_id,
+ query_str, templ_str, *hits[entry_index][1])
+ entry_index = int(line[3:].strip())-1
+ hits[entry_index][0].hit_id = lines.next()[1:].strip()
+ query_str = ''
+ templ_str = ''
+ # skip the next line. It doesn't contain information we
+ # don't already know
+ lines.next()
+ continue
+ assert entry_index != None
+ if line[1:].startswith(' Consensus'):
+ continue
+ if line[1:].startswith(' ss_pred'):
+ continue
+ if line[1:].startswith(' ss_conf'):
+ continue
+ if line.startswith('T '):
+ end_pos = line.find(' ', 22)
+ assert end_pos != -1
+ templ_str += line[22:end_pos]
+ if line.startswith('Q '):
+ end_pos = line.find(' ', 22)
+ assert end_pos != -1
+ query_str += line[22:end_pos]
+ except StopIteration:
+ if len(query_str) > 0:
+ hits[entry_index][0].aln = _MakeAln(query_id,
+ hits[entry_index][0].hit_id,
+ query_str, templ_str,
+ *hits[entry_index][1])
+ return [h for h, o in hits]
+ header = _ParseHeaderSection(lines)
+ # parse the table of contents. This is neccessary as some of the properties
+ # (i.e. start of alignment) we need are only given there. From the TOC we
+ # create a list of hits that is then further filled with data when we parse
+ # the actual result body
+ hits = _ParseTableOfContents(lines)
+ return header, _ParseResultBody(header.query, hits, lines)
+
+def ParseA3M(a3m_file):
+ '''
+ Parse secondary structure information and the multiple sequence alignment
+ out of an A3M file.
+
+ :param a3m_file: Iteratable containing the lines of the A3M file
+ :type a3m_file: iteratable, e.g. an opened file
+
+ :return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
+ (:class:`list`) and "msa" (:class:`~ost.seq.AlignmentHandle`).
+ '''
+ profile_dict = dict()
+ state = 'NONE'
+ pred_seq_txt = ''
+ conf_seq_txt = ''
+ msa_seq = list()
+ msa_head = list()
+ for line in a3m_file:
+ if len(line.rstrip()) == 0:
+ continue
+ elif line.startswith('>ss_pred'):
+ state = 'sspred'
+ continue
+ elif line.startswith('>ss_conf'):
+ state = 'ssconf'
+ continue
+ elif line[0] == '>':
+ if state == 'ssconf' or state == 'msa':
+ msa_seq.append('')
+ msa_head.append(line[1:].rstrip())
+ else:
+ raise IOError('The A3M file is missing the "ss_conf" section')
+ state = 'msa'
+ continue
+
+ if state == 'sspred':
+ pred_seq_txt += line.rstrip()
+ elif state == 'ssconf':
+ conf_seq_txt += line.rstrip()
+ elif state == 'msa':
+ msa_seq[len(msa_seq)-1] += line.rstrip()
+
+ profile_dict['ss_pred'] = list()
+ profile_dict['ss_conf'] = list()
+ for i in range(0, len(pred_seq_txt)):
+ profile_dict['ss_pred'].append(pred_seq_txt[i])
+ profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
+
+ # post processing
+ # MSA
+ profile_dict['msa'] = None
+ if len(msa_seq) > 1:
+ t = msa_seq[0]
+ al = seq.AlignmentList()
+ for i in range(1, len(msa_seq)):
+ qs = ''
+ ts = ''
+ k = 0
+ for c in msa_seq[i]:
+ if c.islower():
+ qs += '-'
+ ts += c.upper()
+ else:
+ qs += t[k]
+ ts += c
+ k += 1
+ nl = seq.CreateAlignment(seq.CreateSequence(msa_head[0], qs),
+ seq.CreateSequence(msa_head[i], ts))
+ al.append(nl)
+ profile_dict['msa'] = seq.alg.MergePairwiseAlignments(\
+ al,
+ seq.CreateSequence(msa_head[0],
+ t))
+ return profile_dict
+
+
+def ParseHHM(profile):
+ '''Parse secondary structure information and the MSA out of an HHM profile.
+
+ :param profile: Opened file handle holding the profile.
+ :type profile: :class:`file`
+
+ :return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
+ (:class:`list`), "msa" (:class:`~ost.seq.AlignmentHandle`) and
+ "consensus" (~ost.seq.SequenceHandle).
+ '''
+ profile_dict = dict()
+ state = 'NONE'
+ pred_seq_txt = ''
+ conf_seq_txt = ''
+ consensus_txt = ''
+ msa_seq = list()
+ msa_head = list()
+ for line in profile:
+ if len(line.rstrip()) == 0:
+ continue
+ if line.rstrip() == '>ss_pred PSIPRED predicted secondary structure':
+ state = 'sspred'
+ continue
+ elif line.rstrip() == '>ss_conf PSIPRED confidence values':
+ state = 'ssconf'
+ continue
+ elif line.rstrip() == '>Consensus':
+ state = 'consensus'
+ continue
+ elif line[0] == '>':
+ if state == 'consensus' or state == 'msa':
+ msa_seq.append('')
+ msa_head.append(line[1:].rstrip())
+ else:
+ raise IOError('Profile file "%s" is missing ' % profile.name+
+ 'the "Consensus" section')
+ state = 'msa'
+ continue
+ elif line[0] == '#':
+ state = 'NONE'
+ continue
+
+ if state == 'sspred':
+ pred_seq_txt += line.rstrip()
+ elif state == 'ssconf':
+ conf_seq_txt += line.rstrip()
+ elif state == 'msa':
+ msa_seq[len(msa_seq)-1] += line.rstrip()
+ elif state == 'consensus':
+ consensus_txt += line.rstrip()
+
+ profile_dict['ss_pred'] = list()
+ profile_dict['ss_conf'] = list()
+ for i in range(0, len(pred_seq_txt)):
+ profile_dict['ss_pred'].append(pred_seq_txt[i])
+ profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
+
+ # post processing
+ # MSA
+ profile_dict['msa'] = None
+ if len(msa_seq):
+ t = msa_seq[0]
+ al = seq.AlignmentList()
+ for i in range(1, len(msa_seq)):
+ qs = ''
+ ts = ''
+ k = 0
+ for c in msa_seq[i]:
+ if c.islower():
+ qs += '-'
+ ts += c.upper()
+ else:
+ qs += t[k]
+ ts += c
+ k += 1
+ nl = seq.CreateAlignment(seq.CreateSequence(msa_head[0], qs),
+ seq.CreateSequence(msa_head[i], ts))
+ al.append(nl)
+ profile_dict['msa'] = seq.alg.MergePairwiseAlignments(\
+ al,
+ seq.CreateSequence(msa_head[0], t))
+ #print profile_dict['msa'].ToString(80)
+ # Consensus
+ profile_dict['consensus'] = seq.CreateSequence('Consensus', consensus_txt)
+
+ return profile_dict
+
+def EstimateMemConsumption():
+ """
+ Estimate the memory needed by HHblits. By default it uses not more than 3G.
+ Also for small sequences it already uses quite some memnmory (46AA, 1.48G).
+ And since the memory consumption could depend on the iterative search runs,
+ how many hits are found in each step, we just go with 4G, here.
+
+ :return: Assumed memory consumtion
+ :rtype: (:class:`float`, :class:`str`)
+ """
+ return 4.0, 'G'
+
+class HHblits:
+ """
+ Initialise a new HHblits "search" for the given query. Query may either
+ be a :class:`~ost.seq.SequenceHandle` or a string. In the former case, the
+ query is the actual query sequence, in the latter case, the query is the
+ filename to the file containing the query.
+
+ :param query: Query sequence as file or sequence.
+ :type query: :class:`~ost.seq.SequenceHandle` or :class:`str`
+ :param hhsuite_root: Path to the top-level directory of your hhsuite
+ installation.
+ :type hhsuite_root: :class:`str`
+ :param hhblits_bin: Name of the hhblits binary. Will only be used if
+ :attr:`hhsuite_root`:file:`/bin/hhblits` does not exist.
+ :type hhblits_bin: :class:`str`
+ :param working_dir: Directory for temporary files. Will be created if not
+ present but **not** automatically deleted.
+ :type working_dir: :class:`str`
+
+ """
+ OUTPUT_PREFIX = 'query_hhblits'
+ def __init__(self, query, hhsuite_root, hhblits_bin=None, working_dir=None):
+ self.query = query
+ self.hhsuite_root = hhsuite_root
+ if os.path.exists(os.path.join(self.hhsuite_root, 'bin/hhblits')):
+ self.bin_dir = os.path.join(self.hhsuite_root, 'bin')
+ self.hhblits_bin = os.path.join(self.hhsuite_root, 'bin/hhblits')
+ else:
+ self.hhblits_bin = settings.Locate('hhblits',
+ explicit_file_name=hhblits_bin)
+ self.bin_dir = os.path.dirname(self.hhblits_bin)
+ self.hhlib_dir = os.path.join(self.hhsuite_root, 'lib', 'hh')
+ if working_dir:
+ self.needs_cleanup = False
+ self.working_dir = working_dir
+ if not os.path.exists(working_dir):
+ os.mkdir(working_dir)
+ if isinstance(query, str):
+ self.filename = os.path.abspath(os.path.join(
+ self.working_dir, os.path.basename(query)))
+ if self.filename != os.path.abspath(query):
+ shutil.copy(query, self.filename)
+ else:
+ self.filename = os.path.join(self.working_dir,
+ '%s.fasta' % HHblits.OUTPUT_PREFIX)
+ ost.io.SaveSequence(query, self.filename)
+ else:
+ self.needs_cleanup = True
+ if isinstance(query, str):
+ self.working_dir = tempfile.mkdtemp()
+ self.filename = os.path.abspath(os.path.join(
+ self.working_dir, os.path.basename(query)))
+ shutil.copy(query, self.filename)
+ else:
+ tmp_dir = utils.TempDirWithFiles((query,))
+ self.working_dir = tmp_dir.dirname
+ self.filename = tmp_dir.files[0]
+
+ def Cleanup(self):
+ """Delete temporary data.
+
+ Delete temporary data if no working dir was given. Controlled by
+ :attr:`needs_cleanup`.
+ """
+ if self.needs_cleanup and os.path.exists(self.working_dir):
+ shutil.rmtree(self.working_dir)
+
+ def BuildQueryMSA(self, nrdb, iterations=1, mact=None, cpu=1):
+ """Builds the MSA for the query sequence
+
+ This function directly uses hhblits of hhtools. While in theory it
+ would be possible to do this by PSI-blasting on our own, hhblits is
+ supposed to be faster. Also it is supposed to prevent alignment
+ corruption. The alignment corruption is caused by low-scoring terminal
+ alignments that draw the sequences found by PSI-blast away from the
+ optimum. By removing these low scoring ends, part of the alignment
+ corruption can be suppressed. hhblits does **not** call PSIPRED on the
+ MSA to predict the secondary structure of the query sequence. This is
+ done by addss.pl of hhtools. The predicted secondary structure is
+ stored together with the sequences identified by hhblits.
+
+ :param nrdb: Database to be align against; has to be an hhblits database
+ :type nrdb: :class:`str`
+
+ :param iterations: Number of hhblits iterations
+ :type iterations: :class:`int`
+
+ :param mact: ``-mact`` of hhblits
+ :type mact: :class:`float`
+
+ :param cpu: ``-cpu`` of hhblits
+ :type cpu: :class:`int`
+
+ :return: the path to the MSA file
+ :rtype: :class:`str`
+ """
+ a3m_file = '%s.a3m' % os.path.splitext(self.filename)[0]
+ ost.LogInfo('Using hhblits from "%s"' % self.hhsuite_root)
+ full_nrdb = os.path.join(os.path.abspath(os.path.split(nrdb)[0]),
+ os.path.split(nrdb)[1])
+ # create MSA
+ hhblits_cmd = '%s -e 0.001 -cpu %d -i %s -oa3m %s -d %s -n %d' % \
+ (self.hhblits_bin, cpu, self.filename, a3m_file,
+ full_nrdb, iterations)
+ if mact:
+ hhblits_cmd += '-mact %f' % mact
+ job = subprocess.Popen(hhblits_cmd, shell=True, cwd=self.working_dir,
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ sout, _ = job.communicate()
+ #lines = sout.splitlines()
+ #for l in lines:
+ # print l.strip()
+ #lines = serr.splitlines()
+ #for l in lines:
+ # print l.strip()
+ if not os.path.exists(a3m_file):
+ ost.LogWarning('Building query profile failed, no output')
+ return a3m_file
+ # add secondary structure annotation
+ addss_cmd = "%s %s" % (os.path.join(self.hhsuite_root,
+ 'lib/hh/scripts/addss.pl'),
+ a3m_file)
+ env = dict(os.environ)
+ env.update({'PERL5LIB' : os.path.join(self.hhsuite_root,
+ 'lib/hh/scripts'),
+ 'HHLIB' : self.hhlib_dir,
+ 'PATH' : '%s:%s' % (os.path.join(self.hhsuite_root, 'bin'),
+ os.environ['PATH'])})
+ job = subprocess.Popen(addss_cmd, shell=True, cwd=self.working_dir,
+ env=env, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ sout, _ = job.communicate()
+ lines = sout.splitlines()
+ for line in lines:
+ if 'error' in line.lower():
+ ost.LogWarning('Predicting secondary structure for MSA '+
+ '(%s) failed, on command: %s' % (a3m_file, line))
+ return a3m_file
+ return a3m_file
+
+ def A3MToProfile(self, a3m_file, hhm_file=None):
+ """
+ Converts the A3M alignment file to a hhm profile. If hhm_file is not
+ given, the output file will be set to <:attr:`a3m_file`-basename>.hhm.
+
+ :param a3m_file: input MSA
+ :type a3m_file: :class:`str`
+
+ :param hhm_file: output file name
+ :type hhm_file: :class:`str`
+
+ :return: the path to the profile
+ :rtype: :class:`str`
+ """
+ hhmake = os.path.join(self.bin_dir, 'hhmake')
+ if not hhm_file:
+ hhm_file = '%s.hhm' % os.path.splitext(a3m_file)[0]
+ if os.path.exists(hhm_file):
+ return hhm_file
+ ost.LogVerbose('converting %s to %s' % (a3m_file, hhm_file))
+ os.putenv('HHLIB', self.hhlib_dir)
+ if subprocess.call('%s -i %s -o %s' % (hhmake, a3m_file, hhm_file),
+ shell=True):
+ raise IOError('could not convert a3m to hhm file')
+ return hhm_file
+
+
+ def A3MToCS(self, a3m_file, cs_file=None, options={}):
+ """
+ Converts the A3M alignment file to a column state sequence file. If
+ cs_file is not given, the output file will be set to
+ <:attr:`a3m_file`-basename>.seq219.
+
+ :param a3m_file: A3M file to be converted
+ :type a3m_file: :class:`str`
+
+ :param cs_file: output file name (may be omitted)
+ :type cs_file: :class:`str`
+
+ :param options: dictionary of options to *cstranslate*, must come with
+ the right amount of '-' in front.
+ :type options: :class:`dict`
+
+ :return: the path to the column state sequence file
+ :rtype: :class:`str`
+ """
+ cstranslate = os.path.join(self.hhlib_dir, 'bin', 'cstranslate')
+ if not cs_file:
+ cs_file = '%s.seq219' % os.path.splitext(a3m_file)[0]
+ if os.path.exists(cs_file):
+ return cs_file
+ opt_cmd = list()
+ for k, val in options.iteritems():
+ if type(val) == type(True):
+ if val == True:
+ opt_cmd.append('%s' % str(k))
+ else:
+ opt_cmd.append('%s %s' % (str(k), str(val)))
+ opt_cmd = ' '.join(opt_cmd)
+ cs_cmd = '%s -i %s -o %s %s' % (cstranslate, a3m_file, cs_file, opt_cmd)
+ ost.LogVerbose('converting %s to %s' % (a3m_file, cs_file))
+ job = subprocess.Popen(cs_cmd, shell=True,
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ sout, _ = job.communicate()
+ #lines = serr.splitlines()
+ #for l in lines:
+ # print l
+ lines = sout.splitlines()
+ for line in lines:
+ if line in 'Wrote abstract state sequence to %s' % cs_file:
+ return cs_file
+ ost.LogWarning('Creating column state sequence file (%s) failed' % \
+ cs_file)
+
+ def CleanupFailed(self):
+ '''In case something went wrong, call to make sure everything is clean.
+ '''
+ store_needs_cleanup = self.needs_cleanup
+ self.needs_cleanup = True
+ self.Cleanup()
+ self.needs_cleanup = store_needs_cleanup
+
+ def Search(self, a3m_file, database, options={}, prefix=''):
+ """
+ Searches for templates in the given database. Before running the
+ search, the hhm file is copied. This makes it possible to launch
+ several hhblits instances at once. Upon success, the filename of the
+ result file is returned. This file may be parsed with
+ :func:`ParseHHblitsOutput`.
+
+ :param a3m_file: input MSA file
+ :type a3m_file: :class:`str`
+
+ :param database: search database, needs to be the common prefix of the
+ database files
+ :type database: :class:`str`
+
+ :param options: dictionary of options, must come with the right amount
+ of '-' in front.
+ :type options: :class:`dict`
+
+ :param prefix: prefix to the result file
+ :type prefix: :class:`str`
+
+ :return: the path to the result file
+ :rtype: :class:`str`
+ """
+ opts = {'cpu' : 1, # no. of cpus used
+ 'n' : 1} # no. of iterations
+ opts.update(options)
+ opt_cmd = []
+ opt_str = []
+ for k, val in opts.iteritems():
+ if type(val) == type(True):
+ if val == True:
+ opt_cmd.append('-%s' % str(k))
+ opt_str.append(str(k))
+ else:
+ opt_cmd.append('-%s %s' % (str(k), str(val)))
+ opt_str.append('%s%s' % (str(k), str(val)))
+ opt_cmd = ' '.join(opt_cmd)
+ opt_str = '_'.join(opt_str)
+ base = os.path.basename(os.path.splitext(a3m_file)[0])
+ hhr_file = '%s%s_%s.hhr' % (prefix, base, opt_str)
+ hhr_file = os.path.join(self.working_dir, hhr_file)
+ search_cmd = '%s %s -e 0.001 -Z 10000 -B 10000 -i %s -o %s -d %s'%(
+ self.hhblits_bin,
+ opt_cmd, os.path.abspath(a3m_file),
+ hhr_file,
+ os.path.join(os.path.abspath(os.path.split(database)[0]),
+ os.path.split(database)[1]))
+ ost.LogInfo('searching %s' % database)
+ ost.LogVerbose(search_cmd)
+ job = subprocess.Popen(search_cmd, shell=True, cwd=self.working_dir,
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ sout, serr = job.communicate()
+ if job.returncode != 0:
+ lines = sout.splitlines()
+ for line in lines:
+ print line.strip()
+ lines = serr.splitlines()
+ for line in lines:
+ print line.strip()
+ return None
+ return hhr_file
+
+
+__all__ = ['HHblits', 'HHblitsHit', 'HHblitsHeader', 'ParseHeaderLine',
+ 'ParseHHblitsOutput', 'ParseA3M', 'ParseHHM',
+ 'EstimateMemConsumption']
+
+# LocalWords: HHblits MSA hhblits hhtools PSIPRED addss param nrdb str mact
+# LocalWords: cpu hhm func ParseHHblitsOutput ss pred conf msa hhsuite dir
+# LocalWords: attr basename rtype cstranslate tuple HHblitsHeader meth aln
+# LocalWords: HHblitsHit iteratable evalue pvalue neff hmms datetime
+# LocalWords: whitespace whitespaces
diff --git a/modules/bindings/pymod/ialign.py b/modules/bindings/pymod/ialign.py
new file mode 100644
index 0000000000000000000000000000000000000000..d5c9f570d3a6abbaef00e2f8d1070727349b28f9
--- /dev/null
+++ b/modules/bindings/pymod/ialign.py
@@ -0,0 +1,176 @@
+#------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2009 by the OpenStructure authors
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3.0 of the License, or (at your option)
+# any later version.
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+#------------------------------------------------------------------------------
+"""
+Wrappers for the iAlign utility.
+
+References:
+
+Mu Gao and Jeffrey Skolnick, 2010. iAlign: a method for the structural comparison
+of protein-protein interfaces. Bioinformatics, 26(18):2259-65.
+Mu Gao and Jeffrey Skolnick, 2010. Structural space of protein-protein interfaces
+is degenerate, close to complete, and highly connected. PNAS 107(52):22517-22.
+
+Authors: Pascal Benkert, Marco Biasini, Martino Bertoni
+"""
+
+import subprocess, os, tempfile, platform
+from ost import settings, io, geom, seq
+
+def _SetupFiles(models):
+ # create temporary directory
+ tmp_dir_name=tempfile.mkdtemp()
+ dia = 'PDB'
+ for index, model in enumerate(models):
+ for chain in model.chains:
+ if len(chain.name) > 1:
+ dia = 'CHARMM'
+ break;
+ for res in chain.residues:
+ if len(res.name) > 3:
+ dia = 'CHARMM'
+ break;
+ io.SavePDB(model, os.path.join(tmp_dir_name, 'model%02d.pdb' % (index+1)), dialect=dia)
+ return tmp_dir_name
+
+def _CleanupFiles(dir_name):
+ import shutil
+ shutil.rmtree(dir_name)
+
+class iAlignResult:
+ """
+ Holds the result of running iAlign
+
+ .. attribute:: rmsd
+
+ The RMSD of the common Calpha atoms of both structures
+
+ .. attribute:: transform
+
+ The transform that superposes the model onto the reference structure.
+
+ :type: :class:`~ost.geom.Mat4`
+
+ .. attribute:: alignment
+
+ The alignment of the structures, that is the pairing of Calphas of both
+ structures. Since the programs only read ATOM records, residues consisting
+ of HETATMs (MSE) are not included in the alignment.
+
+ :type: :class:`~ost.seq.AlignmentHandle`
+
+ .. attribute:: IS_score
+
+ The IS-score of the structural superposition
+
+ .. attribute:: aligned_residues
+
+ The total number of aligned residues
+
+ .. attribute:: aligned_contacts
+
+ The total number of aligned contacts
+
+ """
+ def __init__(self, rmsd, transform, alignment, is_score,
+ aligned_residues, aligned_contacts):
+
+ self.rmsd=rmsd
+ self.transform=transform
+ self.alignment=alignment
+ self.is_score=is_score
+ self.aligned_residues=aligned_residues
+ self.aligned_contacts=aligned_contacts
+
+def _ParseiAlign(lines):
+ info_line=lines[18].split(',')
+ is_score=float(info_line[0].split('=')[1].strip())
+ aln_residues=int(lines[19].split('=')[1].strip())
+ aln_contacts=int(lines[20].split('=')[1].strip())
+ info_line=lines[21].split(',')
+ rmsd=float(info_line[0].split('=')[1].strip())
+
+ tf1=[float(i.strip()) for i in lines[25][1:].split()]
+ tf2=[float(i.strip()) for i in lines[26][1:].split()]
+ tf3=[float(i.strip()) for i in lines[27][1:].split()]
+ rot=geom.Mat3(tf1[2], tf1[3], tf1[4], tf2[2], tf2[3],
+ tf2[4], tf3[2], tf3[3], tf3[4])
+ tf=geom.Mat4(rot)
+ tf.PasteTranslation(geom.Vec3(tf1[1], tf2[1], tf3[1]))
+ seq1 = seq.CreateSequence("1",lines[32].strip())
+ seq2 = seq.CreateSequence("2",lines[34].strip())
+ alignment = seq.CreateAlignment()
+ alignment.AddSequence(seq2)
+ alignment.AddSequence(seq1)
+ return iAlignResult(rmsd, tf, alignment, is_score, aln_residues, aln_contacts)
+
+def _RuniAlign(ialign, tmp_dir, options={}):
+ opts = {'a' : 1, # concise output
+ 'w' : tmp_dir
+ }
+ opts.update(options)
+ cmd_opts = []
+ for k, v in opts.iteritems():
+ if type(v) == type(True):
+ if v == True:
+ cmd_opts.append('-%s' % str(k))
+ else:
+ cmd_opts.append('-%s %s' % (str(k), str(v)))
+ cmd_opts = ' '.join(cmd_opts)
+ model1_filename=os.path.join(tmp_dir, 'model01.pdb')
+ model2_filename=os.path.join(tmp_dir, 'model02.pdb')
+ if platform.system() == "Windows":
+ ialign_path=settings.Locate('ialign.pl', explicit_file_name=ialign)
+ command="\"%s\" %s %s %s" % (os.path.normpath(ialign_path), model1_filename, model2_filename, cmd_opts)
+ else:
+ ialign_path=settings.Locate('ialign.pl', explicit_file_name=ialign)
+ command="\"%s\" \"%s\" \"%s\" %s" % (ialign_path, model1_filename, model2_filename, cmd_opts)
+ ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ ps.wait()
+ lines=ps.stdout.readlines()
+ if (len(lines))<22:
+ _CleanupFiles(tmp_dir)
+ #for l in lines:
+ # print l
+ raise RuntimeError("iAlign superposition failed")
+ return _ParseiAlign(lines)
+
+
+def iAlign(model1, model2, ialign=None):
+ """
+ Compare protein-protein interfaces of the structures of two pairs of
+ protein complexes and suporpose them.
+
+
+ :param model1: The model structure. If the superposition is successful, will
+ be superposed onto the reference structure
+ :type model1: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+ :param model2: The reference structure
+ :type model2: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+ :param ialign: If not None, the path to the ialign executable.
+ :returns: The result of the tmscore superposition
+ :rtype: :class:`iAlignResult`
+
+ :raises: :class:`~ost.settings.FileNotFound` if tmalign could not be located.
+ :raises: :class:`RuntimeError` if the superposition failed
+ """
+ tmp_dir_name=_SetupFiles((model1, model2))
+ result=_RuniAlign(ialign, tmp_dir_name)
+ model1.handle.EditXCS().ApplyTransform(result.transform)
+ _CleanupFiles(tmp_dir_name)
+ return result
diff --git a/modules/bindings/pymod/msms.py b/modules/bindings/pymod/msms.py
index 60009f6070d2592ed6790521359a82684771f647..534cd3d8e0be5c80fcfa4638896ffbfa23bcdbf9 100644
--- a/modules/bindings/pymod/msms.py
+++ b/modules/bindings/pymod/msms.py
@@ -332,7 +332,8 @@ def CalculateSurfaceVolume(entity, density=1.0, radius=1.5, all_surf=False,
def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
no_hydrogens=False, no_hetatoms=False, no_waters=False,
selection='',
- msms_exe=None, msms_env=None, keep_files=False):
+ msms_exe=None, msms_env=None, keep_files=False,
+ attach_asa=None, attach_esa=None):
"""
Calculates molecular surface by using the external MSMS program
@@ -353,6 +354,8 @@ def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
:param msms_exe: msms executable (full path to executable)
:param msms_env: msms environment variable
:param keep_files: Do not delete temporary files
+ :param attach_asa: Attaches per atom SASA to specified FloatProp at atom level
+ :param attach_esa: Attaches per atom SESA to specified FloatProp at atom level
:returns: list of :class:`~ost.mol.SurfaceHandle` objects
"""
import os
@@ -385,10 +388,17 @@ def CalculateSurface(entity, density=1.0, radius=1.5, all_surf=False,
msms_data_file, msms_data_file, density, radius)
if all_surf:
command+=" -all"
+ if attach_asa != None or attach_esa != None:
+ command+=" -af %s" % os.path.join(msms_data_dir, "asa_atom")
# run msms
stdout_value=_RunMSMS(command)
+ # add sesa and asa to entity if attach_asa is specified
+ if attach_asa != None or attach_esa != None:
+ _ParseAreaFile(entity, selection, os.path.join(msms_data_dir, "asa_atom.area"),
+ attach_asa, attach_esa)
+
# parse msms output
num_surf=0
for line in stdout_value.splitlines():
diff --git a/modules/bindings/pymod/naccess.py b/modules/bindings/pymod/naccess.py
index 5a064afeecd7f86d73b4c7d378cfe2f4fcfeee57..621067e7b8c68f2242cfbf047b0932d05b24ebd9 100644
--- a/modules/bindings/pymod/naccess.py
+++ b/modules/bindings/pymod/naccess.py
@@ -105,7 +105,6 @@ def _ParseAsaFile(entity, file, asa_atom):
else:
print chain_id, resNum, atom_name
-
def _ParseRsaFile(enti,file, asa_abs, asa_rel):
"""
Reads Area file (.rsa) and attach asa (absolute + relative) per residue to an entitiy
@@ -162,7 +161,6 @@ def __CleanupFiles(dir_name):
import shutil
shutil.rmtree(dir_name)
-
def _RunNACCESS(command, temp_dir):
"""
Method to run the MSMS surface calculation
@@ -184,7 +182,6 @@ def _RunNACCESS(command, temp_dir):
return stdout_value
-
def CalculateSurfaceArea(entity, radius=1.4,
include_hydrogens=False, include_hetatm = False,
include_water = False, selection="",
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index 8763188414f2c6b83ced8a2ecb12ce71ba66872b..e2b06738372f16cf589eaa3adc1f4d0e18fca84e 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -1,7 +1,7 @@
#------------------------------------------------------------------------------
# This file is part of the OpenStructure project <www.openstructure.org>
#
-# Copyright (C) 2008-2009 by the OpenStructure authors
+# Copyright (C) 2008-2015 by the OpenStructure authors
#
# This library is free software; you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
@@ -152,7 +152,8 @@ def _ParseMmAlign(lines):
alignment = seq.CreateAlignment()
alignment.AddSequence(seq2)
alignment.AddSequence(seq1)
- return MMAlignResult(rmsd, aln_length, tm_score, tf, alignment)
+
+ return MMAlignResult(rmsd, tm_score, aln_length, tf, seq2, alignment)
def _RunMmAlign(mmalign, tmp_dir):
model1_filename=os.path.join(tmp_dir, 'model01.pdb')
diff --git a/modules/bindings/pymod/utils.py b/modules/bindings/pymod/utils.py
index 27d4008d8a543df42e21aa2c704516462fa4196c..02edd598f9b664c165f385b92429b619d7bf09fd 100644
--- a/modules/bindings/pymod/utils.py
+++ b/modules/bindings/pymod/utils.py
@@ -30,7 +30,7 @@ def SaveToTempDir(objects, seq_format='fasta', structure_format='pdb'):
continue
if isinstance(obj, mol.EntityView) or isinstance(obj, mol.EntityHandle):
name=os.path.join(tmp_dir_name, tmp_dir_name, 'mol%02d.pdb' % (index+1))
- io.SaveEntity(model, name, structure_format)
+ io.SaveEntity(obj, name, structure_format)
file_names.append(name)
continue
return file_names
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index 7b04104d9d230d61ab27b4c56dce4730bd42f49e..c443de13285adf6a7818926e29d540a258c2580c 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -1,6 +1,7 @@
set(OST_BINDINGS_UNIT_TESTS
test_msms.py
test_clustalw.py
+ test_hhblits.py
test_blast.py
test_kclust.py
)
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
new file mode 100644
index 0000000000000000000000000000000000000000..c396528b8c623d620e07f7611431760afcfd1725
--- /dev/null
+++ b/modules/bindings/tests/test_hhblits.py
@@ -0,0 +1,397 @@
+''' Unit tests for the HHblits wrapper
+'''
+
+import unittest
+import os
+import sys
+import tempfile
+import shutil
+import filecmp
+import datetime
+
+import ost
+from ost import seq
+from ost.bindings import hhblits
+
+class TestHHblitsBindings(unittest.TestCase):
+ def setUp(self):
+ self.hhroot = os.getenv('EBROOTHHMINSUITE')
+
+ def tearDown(self):
+ if hasattr(self, 'hh'):
+ self.hh.Cleanup()
+ if hasattr(self, 'tmpfile'):
+ os.remove(self.tmpfile)
+
+ def testOSTSequenceNoWDir(self):
+ # OST sequence as input, no working dir should work
+ query_seq = seq.CreateSequence('1AKE.B',
+ 'MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRA'+
+ 'AVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQ'+
+ 'EDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDV'+
+ 'PDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDV'+
+ 'TGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYYYS'+
+ 'KEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ # this works only as long as utils.TempDirWithFiles() names the first
+ # fasta file seq01.fasta
+ self.assertEqual(self.hh.filename[-11:], 'seq01.fasta')
+
+ def testOSTSequenceWDir(self):
+ # OST sequence as input, with working dir should work
+ query_seq = seq.CreateSequence('1AKE.B',
+ 'MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRA'+
+ 'AVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQ'+
+ 'EDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDV'+
+ 'PDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDV'+
+ 'TGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYYYS'+
+ 'KEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
+ tmpdir = tempfile.mkdtemp()
+ self.hh = hhblits.HHblits(query_seq, self.hhroot, working_dir=tmpdir)
+ self.assertEqual(self.hh.filename, os.path.join(tmpdir,
+ 'query_hhblits.fasta'))
+ self.assertEqual(self.hh.working_dir, tmpdir)
+ self.hh.needs_cleanup = True
+
+ def testFileNoWDir(self):
+ # we have a sequence but no working dir
+ self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot)
+ self.assertEqual(self.hh.filename[-10:], 'seq2.fasta')
+
+ def testFileWDir(self):
+ # we have a sequence and a working dir
+ tmpdir = tempfile.mkdtemp()
+ self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot,
+ working_dir=tmpdir)
+ self.assertEqual(self.hh.filename, os.path.join(tmpdir, 'seq2.fasta'))
+ self.assertEqual(self.hh.working_dir, tmpdir)
+ self.hh.needs_cleanup = True
+
+ def testDoCleanup(self):
+ # test that cleanup cleans up
+ tmpdir = tempfile.mkdtemp()
+ self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot,
+ working_dir=tmpdir)
+ self.assertTrue(os.path.isdir(tmpdir))
+ self.hh.needs_cleanup = True
+ self.hh.Cleanup()
+ self.assertFalse(os.path.isdir(tmpdir))
+
+ def testDoNotCleanup(self):
+ # test that cleanup cleans up
+ tmpdir = tempfile.mkdtemp()
+ self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot,
+ working_dir=tmpdir)
+ self.assertTrue(os.path.isdir(tmpdir))
+ self.hh.needs_cleanup = False
+ self.hh.Cleanup()
+ self.assertTrue(os.path.isdir(tmpdir))
+ shutil.rmtree(tmpdir)
+ self.assertFalse(os.path.isdir(tmpdir))
+
+ def testCleanupFailed(self):
+ # test that cleanup cleans up
+ tmpdir = tempfile.mkdtemp()
+ self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot,
+ working_dir=tmpdir)
+ self.assertTrue(os.path.isdir(tmpdir))
+ self.hh.needs_cleanup = False
+ self.hh.CleanupFailed()
+ self.assertFalse(os.path.isdir(tmpdir))
+
+ def testFileNoExists(self):
+ # test on calling with a non-existing fasta file
+ with self.assertRaises(IOError) as ioe:
+ hhblits.HHblits('notthere.fasta', self.hhroot)
+ self.assertEqual(ioe.exception.errno, 2)
+ self.assertEqual(ioe.exception.strerror, 'No such file or directory')
+
+ def testProfile(self):
+ # try to create a search profile
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ a3m = self.hh.BuildQueryMSA('testfiles/hhblitsdb/hhblitsdb')
+ self.assertTrue(filecmp.cmp(a3m, "testfiles/testali.a3m"))
+
+ def testA3mToProfileFileName(self):
+ # test A3mToProfile to work with a given hhmake_file name
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ _, self.tmpfile = tempfile.mkstemp(suffix='.hmm')
+ os.remove(self.tmpfile)
+ hhfile = self.hh.A3MToProfile("testfiles/testali.a3m",
+ hhm_file=self.tmpfile)
+ tfh = open(hhfile)
+ efh = open("testfiles/test.hmm")
+ elst = efh.readlines()
+ tlst = tfh.readlines()
+ self.assertEqual(len(elst), len(tlst))
+ for i in range(0, len(elst)):
+ if not elst[i].startswith(('FILE', 'COM', 'DATE')):
+ self.assertEqual(elst[i], tlst[i])
+
+ def testA3mToProfileWithoutFileName(self):
+ # test A3mToProfile to work without a given hhmake_file name
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ hhfile = self.hh.A3MToProfile("testfiles/testali.a3m")
+ tfh = open(hhfile)
+ efh = open("testfiles/test.hmm")
+ elst = efh.readlines()
+ tlst = tfh.readlines()
+ self.assertEqual(len(elst), len(tlst))
+ for i in range(0, len(elst)):
+ if not elst[i].startswith(('FILE', 'COM', 'DATE')):
+ self.assertEqual(elst[i], tlst[i])
+ os.remove(hhfile)
+
+ def testA3mToProfileWithExistingFile(self):
+ # test A3mToProfile to work with an existing hmm file
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ hhfile = self.hh.A3MToProfile("testfiles/testali.a3m",
+ hhm_file="testfiles/test.hmm")
+ # when the hmm file already exists, its not touched, so files should be
+ # completely equal.
+ self.assertTrue(filecmp.cmp(hhfile, "testfiles/test.hmm"))
+
+ def testA3mToProfileWithoutA3m(self):
+ # test A3mToProfile to fail if we do not have an a3m file.
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ with self.assertRaises(IOError) as ioe:
+ self.hh.A3MToProfile("doesnotexist.a3m")
+ self.assertEqual(ioe.exception.errno, None)
+ self.assertEqual(ioe.exception.message,
+ "could not convert a3m to hhm file")
+
+ def testA3mToCSFileName(self):
+ # test A3mToCS to work with a given hhmake_file name
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ _, self.tmpfile = tempfile.mkstemp(suffix='.seq219')
+ os.remove(self.tmpfile)
+ csfile = self.hh.A3MToCS("testfiles/testali.a3m",
+ cs_file=self.tmpfile, options={'--alphabet' :
+ os.path.join(self.hh.hhlib_dir,
+ 'data',
+ 'cs219.lib')})
+ self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
+
+ def testA3mToCSNoFileName(self):
+ # test A3mToCS to work with a given hhmake_file name
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ csfile = self.hh.A3MToCS("testfiles/testali.a3m",
+ options={'--alphabet' :
+ os.path.join(self.hh.hhlib_dir,
+ 'data',
+ 'cs219.lib')})
+ self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
+ self.tmpfile = "testfiles/testali.seq219"
+
+ def testA3mToCSFileExists(self):
+ # test A3mToCS to work with a given hhmake_file name
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ csfile = self.hh.A3MToCS("testfiles/testali.a3m",
+ cs_file='testfiles/test.seq219',
+ options={'--alphabet' :
+ os.path.join(self.hh.hhlib_dir,
+ 'data',
+ 'cs219.lib')})
+ self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
+
+ def testSearchWorking(self):
+ # successful search
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ search_file = self.hh.Search("testfiles/testali.a3m",
+ 'testfiles/hhblitsdb/hhblitsdb')
+ tfh = open(search_file)
+ efh = open("testfiles/test.hhr")
+ elst = efh.readlines()
+ tlst = tfh.readlines()
+ self.assertEqual(len(elst), len(tlst))
+ for i in range(0, len(elst)):
+ if not elst[i].startswith(('Date', 'Command')):
+ self.assertEqual(elst[i], tlst[i])
+
+ def testSearchNotWorking(self):
+ # successful search
+ query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
+ 'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
+ 'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
+ 'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
+ 'TSKYR')
+ self.hh = hhblits.HHblits(query_seq, self.hhroot)
+ search_file = self.hh.Search("doesnotexist.a3m",
+ 'testfiles/hhblitsdb/hhblitsdb')
+ self.assertEqual(search_file, None)
+
+ def testParseHHMWorking(self):
+ # get info from an HHM file
+ with open("testfiles/test.hmm") as hhm_fh:
+ prof = hhblits.ParseHHM(hhm_fh)
+ self.assertEqual(''.join([str(x) for x in prof['ss_conf']]),
+ '999999999999998873391557999999998639441123987788888'+
+ '856788999999999998735477789999999887650299989899889'+
+ '999999997536679989999999999999999984329')
+ self.assertEqual(''.join(prof['ss_pred']), 'CCCHHHHHHHHHHHHHHHCCCHHHH'+
+ 'HHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCH'+
+ 'HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH'+
+ 'HHHHHHHHHHHHCC')
+ self.assertEqual(str(prof['consensus']), 'xltxxxxxxixxsWxxvxxxxxxxgxx'+
+ 'xxxxlfxxxPxxxxxFxxxxxxxxxxxxxxhxxxvxxxlxxxixxldxxxx'+
+ 'xlxxlxxxHxxxxgvxxxxxxxxxxxlxxxlxxxxgxxxxxxxxxAWxxxx'+
+ 'xxixxxmxxxyx')
+ self.assertEqual(prof['msa'].GetCount(), 7)
+
+ def testParseHHMNotWorking(self):
+ # get info from an HHM file
+ with self.assertRaises(IOError) as ioe:
+ hhblits.ParseHHM(open('testfiles/testali.a3m'))
+ self.assertEqual(ioe.exception.message,
+ 'Profile file "testfiles/testali.a3m" is missing '+
+ 'the "Consensus" section')
+
+ def testParseA3MWorking(self):
+ # get info from an HHM file
+ with open("testfiles/testali.a3m") as a3m_fh:
+ prof = hhblits.ParseA3M(a3m_fh)
+ self.assertEqual(''.join([str(x) for x in prof['ss_conf']]),
+ '999999999999998873391557999999998639441123987788888'+
+ '856788999999999998735477789999999887650299989899889'+
+ '999999997536679989999999999999999984329')
+ self.assertEqual(''.join(prof['ss_pred']), 'CCCHHHHHHHHHHHHHHHCCCHHHH'+
+ 'HHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCH'+
+ 'HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH'+
+ 'HHHHHHHHHHHHCC')
+ self.assertEqual(prof['msa'].GetCount(), 253)
+
+ def testParseHHblitsOutput(self):
+ header, hits = hhblits.ParseHHblitsOutput(open("testfiles/test.hhr"))
+ self.assertEqual(header.query, 'Test')
+ self.assertEqual(header.match_columns, 141)
+ self.assertEqual(header.n_eff, 9.4)
+ self.assertEqual(header.searched_hmms, 5)
+ self.assertEqual(header.date,
+ datetime.datetime.strptime('Mon Aug 31 16:45:45 2015',
+ '%a %b %d %H:%M:%S %Y'))
+ self.assertEqual(header.command, '/import/bc2/apps/HH-suite/2.0.16-go'+
+ 'olf-1.4.10/bin/hhblits -cpu 1 -n 1 -e 0.001 -Z 1000'+
+ '0 -B 10000 -i /import/bc2/home/schwede/bienert/git/'+
+ 'ost_newenv.git/modules/bindings/tests/testfiles/tes'+
+ 'tali.a3m -o /scratch/tmp9E5dor/testali_cpu1_n1.hhr '+
+ '-d /import/bc2/home/schwede/bienert/git/ost_newenv.'+
+ 'git/modules/bindings/tests/testfiles/hhblitsdb/hhbl'+
+ 'itsdb')
+ self.assertEqual(len(hits), 4)
+ # hit 1
+ self.assertEqual(hits[0].hit_id, '3e7b90809bd446a538f9eb1a1ca0e551')
+ self.assertEqual(hits[0].score, float('222.3'))
+ self.assertEqual(hits[0].ss_score, float('16.4'))
+ self.assertEqual(hits[0].evalue, float('2.7e-42'))
+ self.assertEqual(hits[0].pvalue, float('6.9E-45'))
+ self.assertEqual(hits[0].prob, float('100.0'))
+ self.assertEqual(str(hits[0].aln),
+ 'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
+ 'MFLSFPTTKTYFPHF-DL-S----HGSAQ\n3e7b90809bd446a5... '+
+ 'VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT'+
+ 'EAEMKASED\n\nTest VKGHGKKVADALTNAVAH'+
+ 'VDDMPNALSALSDLHAHK-LRVDPVNFKLLSHCLLVTLAAHL\n3e7b908'+
+ '09bd446a5... LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHA-TKH'+
+ 'KIPIKYLEFISEAIIHVLHSRH\n\nTest PAEFT'+
+ 'PAVHASLDKFLASVSTVLTSKYR\n3e7b90809bd446a5... PGDFGA'+
+ 'DAQGAMNKALELFRKDIAAKYK\n')
+ # hit 2
+ self.assertEqual(hits[1].hit_id, 'af828e69a5f2d0fd42a2a213e09eb64f')
+ self.assertEqual(hits[1].score, float('215.7'))
+ self.assertEqual(hits[1].ss_score, float('17.2'))
+ self.assertEqual(hits[1].evalue, float('1.5e-41'))
+ self.assertEqual(hits[1].pvalue, float('3.9E-44'))
+ self.assertEqual(hits[1].prob, float('100.0'))
+ self.assertEqual(str(hits[1].aln),
+ 'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
+ 'MFLSFPTTKTYFPHFDLSHGSAQVKGHGK\naf828e69a5f2d0fd... '+
+ 'VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHG'+
+ 'SAQVKGHGK\n\nTest KVADALTNAVAHVDDMPN'+
+ 'ALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA\naf828e6'+
+ '9a5f2d0fd... KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNF'+
+ 'KLLSHCLLVTLAAHLPAEFTPA\n\nTest VHASL'+
+ 'DKFLASVSTVLTSKYR\naf828e69a5f2d0fd... VHASLDKFLASVS'+
+ 'TVLTSKYR\n')
+ # hit 3
+ self.assertEqual(hits[2].hit_id, '9287755aa6aa27583da6be3b2408bfcc')
+ self.assertEqual(hits[2].score, float('215.1'))
+ self.assertEqual(hits[2].ss_score, float('16.5'))
+ self.assertEqual(hits[2].evalue, float('3.8e-41'))
+ self.assertEqual(hits[2].pvalue, float('9.7E-44'))
+ self.assertEqual(hits[2].prob, float('100.0'))
+ self.assertEqual(str(hits[2].aln),
+ 'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
+ 'MFLSFPTTKTYFPHF-DLS-----HGSAQ\n9287755aa6aa2758... '+
+ 'HLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLST'+
+ 'PDAVMGNPK\n\nTest VKGHGKKVADALTNAVAH'+
+ 'VDDMPNALSALSDLHAHK-LRVDPVNFKLLSHCLLVTLAAHL\n9287755'+
+ 'aa6aa2758... VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHC-DKL'+
+ 'HVDPENFRLLGNVLVCVLAHHF\n\nTest PAEFT'+
+ 'PAVHASLDKFLASVSTVLTSKYR\n9287755aa6aa2758... GKEFTP'+
+ 'PVQAAYQKVVAGVANALAHKYH\n')
+ # hit 4
+ self.assertEqual(hits[3].hit_id, 'e69e1ac0a4b2554df25f2c2183b0fba0')
+ self.assertEqual(hits[3].score, float('12.6'))
+ self.assertEqual(hits[3].ss_score, float('2.6'))
+ self.assertEqual(hits[3].evalue, float('64.0'))
+ self.assertEqual(hits[3].pvalue, float('0.16'))
+ self.assertEqual(hits[3].prob, float('0.6'))
+ self.assertEqual(str(hits[3].aln),
+ 'Test VDPVNFKLLSHCLLVTLAAHL\ne69e1ac0'+
+ 'a4b2554d... ATPEQAQLVHKEIRKIVKDTC\n')
+
+# ParseHHblitsOutput
+
+if __name__ == "__main__":
+ hhsuite_root_dir = os.getenv('EBROOTHHMINSUITE')
+ if not hhsuite_root_dir:
+ print "No environment variable 'EBROOTHHMINSUITE'. To enable the "+\
+ "unit test, this needs to point to your HHsuite installation."
+ sys.exit(0)
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb.cs219 b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb.cs219
new file mode 100644
index 0000000000000000000000000000000000000000..2f7449d3cdbbf599635ab0a48a5469c68ed43617
--- /dev/null
+++ b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb.cs219
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index 0000000000000000000000000000000000000000..2ae40c6df2bc9ee6dbfcafebd6bd2da1b878504a
--- /dev/null
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diff --git a/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_a3m_db b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_a3m_db
new file mode 100644
index 0000000000000000000000000000000000000000..5ad84079c3b26ffd82cf8fc077bb9285071fadec
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diff --git a/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_a3m_db.index b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_a3m_db.index
new file mode 100644
index 0000000000000000000000000000000000000000..f98c82306c62cf5a421bfe8717dd628ce83e1822
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+4939a1cdd4b26c7d9053b02c16db7e41�� � 16608963 335082
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+5b39e5a7108ee75bcacb74b9050dfe57�� � 21698909 2462
+5b7549a440ece6efc515d1ecf5eab975�� � 21701371 72297
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+61e58fd4d97efb70b78410488ce6cac8�� � 22487009 422702
+665b4706556bcfdcefa8812b17dc787c�� � 22909711 460497
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+7bf67dbec14c0ea001ff88bc73dd7396�� � 26476092 83351
+7cff8b05889041a6d059231e4f4bc281�� � 26559443 110720
+7d7b394238d3b3e35f1bbacceedade0b�� � 26670163 498540
+7ec67cbbd85f59718803563580f1731b�� � 27168703 626803
+81e79b5741c9fbdcdbbebf2c8b14e32c�� � 27795506 427552
+8237cebaaa25ac6a2b0d49c9d5837da5�� � 28223058 28947
+84792f9cbc9eb5adabb41b1a904360bb�� � 28252005 28812
+86ed36c2fe7938800e5622d9b4acb515�� � 28280817 71227
+88117153c423d8f3cd1f072dcda24597�� � 28352044 161621
+8e30ca516d2b86076f51d1316fab39ad�� � 28513665 479192
+8fd273e25da1bf193a2bf90e2bc9fef0�� � 28992857 1618
+91ee985382113129d3975a1aa1210405�� � 28994475 459074
+9287755aa6aa27583da6be3b2408bfcc�� � 29453549 332216
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+93a4e2eb4447ccb72cf9476930f1f5df�� � 30087390 329136
+98b5ff80a113b7bb28949a2a5cd20879�� � 30416526 6636
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+9b972e307eb0d9de3734ffdbf33ed781�� � 30467521 443090
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+9c7b8409c5da2a6bc10d796287eb4c1f�� � 30931699 382334
+9f519c37964061e00a9e9906f774552e�� � 31314033 40037
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+a1369bdee466c1364c07095750be3efc�� � 31407688 237984
+a1cf9299e65402da85fa1134c4159419�� � 31645672 534291
+a251ab96460cc372677a195a346bdc79�� � 32179963 40899
+a44d747376cfd87bd0f30749697bc63b�� � 32220862 574506
+a4ffb81039c95ec205e15ab0095774e5�� � 32795368 926
+a58e5f77fe5c98ba022ce3bec19b5c22�� � 32796294 338176
+a7297e082b04c39b5ed5edf7a5889375�� � 33134470 485140
+a7d85b5797fc7c87d5f26fc1eaa87af7�� � 33619610 29371
+a9670fd5e42b822d83bb9b8a9eda5dc0�� � 33648981 285899
+aa7797cb86715b5f00dd396459cdd380�� � 33934880 106782
+abf7361a887c4e53ac97adc19e64234b�� � 34041662 507005
+ae209f299335d3708222d92bc2697502�� � 34548667 105045
+af5e37f6170ad6dd671732b9beb56903�� � 34653712 466276
+af828e69a5f2d0fd42a2a213e09eb64f�� � 35119988 319296
+b056b4c4d9017a19c3095e4c72f67a47�� � 35439284 491626
+b3693168b9f04cd2db237b30b4be5176�� � 35930910 383738
+b49b9cb98eb527401c12984cc1a2e18d�� � 36314648 551520
+b5e4c6287793467d8b047e64ec6f935b�� � 36866168 220353
+b6a8572284504b5d762ee82f90b16d91�� � 37086521 318046
+b903b162c87715ee7384e2af499c16cd�� � 37404567 231267
+b94e58bdb4361ef7c1237e2f79e9939a�� � 37635834 24068
+ba17a05f924bfd8ff94a6c5d73635b4a�� � 37659902 503778
+ba48b3cd7ebd29a9e2e367a37ac501cf�� � 38163680 331119
+bbd36c9292c799cc4a4733df8189699f�� � 38494799 461652
+bc4ef49e84c894acd9a656db73d52eeb�� � 38956451 147019
+bdf48b24c3f0fdeaa0d9654593ea6f0d�� � 39103470 425624
+be74be0e66ca7b4603630a5a17fef2a4�� � 39529094 50447
+c12ad1255bc3ed843ae21de938ab5f62�� � 39579541 547816
+c2c32c13af9575e387657a5ea9736806�� � 40127357 141801
+c5753ae3727f4c7fc5433d2395780f60�� � 40269158 369904
+c582c9c4daca574c1be2935ee4ecc45f�� � 40639062 217196
+c5863f5030b5a39b990f9179f7f8cfae�� � 40856258 142817
+c5af58a62688d809a1a0747990141890�� � 40999075 138526
+c5d10a25f4692ab6cc7c072c5ac3efcd�� � 41137601 869455
+c73204c4134fbbb074a65e8410643b7c�� � 42007056 386481
+c737dfcd8b440f4a80b15ef9f3c3a806�� � 42393537 226784
+cb13cb2555c5bacde1dc168618e48f3f�� � 42620321 702103
+cbc92a8a85651bd2fb2a8622778ceaf5�� � 43322424 436029
+cbf4a79de0130a2230da880af29a77c4�� � 43758453 432356
+cd06863eb01c4bcc5ae9b1817480cf17�� � 44190809 503963
+ced02dc66c62cb64fc91194b87a4189c�� � 44694772 339412
+cf096ff6881b75de1c34ab8525847a53�� � 45034184 1053
+cfe750d45ad9ea874e03be9e47fe8331�� � 45035237 216297
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+e130d30836eaf714deba0688836fbaec�� � 48318379 484776
+e28b3a1dbc0f15f5e8575e6ca4f6ea00�� � 48803155 654271
+e2e8d293c6308e03168e6291d88b3e9e�� � 49457426 9203
+e3d87649b2f1632f153be8830af2c4ce�� � 49466629 521432
+e44a004fd43907d485810413e310dc01�� � 49988061 13494
+e69e1ac0a4b2554df25f2c2183b0fba0�� � 50001555 491008
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+eb17077e5768f21bb26c456637a41be1�� � 50758651 75338
+eb75493f078d95ea52db97600717baa3�� � 50833989 931
+ec6d5b33f2ae17f54335ee8fce56e790�� � 50834920 286921
+ee520d2fc85e5b54c5cab5b1125d8c3b�� � 51121841 531686
+f038453661ad6048b85e5011b6e6296a�� � 51653527 604262
+f10edaeff439be4afbba7757c8cac254�� � 52257789 61589
+f22915668ca1cb3ce6b2cdc5b2a8d88f�� � 52319378 70781
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+f82cb3c7c161ae904b70948cfd869920�� � 54514404 367568
+f9eb38ef6943149426b564b15c282045�� � 54881972 557554
+fb5bff21f8955d17ec9c9ef42e3fe2a1�� � 55439526 11019
+fc94ceafa368716b735a0cc814095abc�� � 55450545 399815
+fdfbd67ee8a6a80e1c49419316279395�� � 55850360 421410
+ff5c81bfb664296a11b43497a69645cc�� � 56271770 7846
diff --git a/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_a3m_db.index.sizes b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_a3m_db.index.sizes
new file mode 100644
index 0000000000000000000000000000000000000000..08839f6bb296e888d311d8ea2f35f7ff82dd3f2d
--- /dev/null
+++ b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_a3m_db.index.sizes
@@ -0,0 +1 @@
+200
diff --git a/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db
new file mode 100644
index 0000000000000000000000000000000000000000..46062f4cfbf25492473cb0c65ec46fe5f605896c
--- /dev/null
+++ b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db
@@ -0,0 +1,100211 @@
+HHsearch 1.5
+NAME 02ae072bdd8d4b3cd3ddea7d7fd6accb
+FAM
+FILE 02ae072bdd8d4b3cd3ddea7d7fd6accb
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:20:57 2013
+LENG 149 match states, 149 columns in multiple alignment
+FILT 113 out of 1150 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCHHHHHCCCEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHH
+HHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCCC
+>ss_conf PSIPRED confidence values
+9623369997667899420778616540676589999999999999699999999998939999999999988538845333579998878999999999
+9999786777999999999843554688549999999999825799999
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxkxxsxxxrxxiixlxxxGxsxxxiaxxlgisxxtixrwxkxxxxxGxxxxxxxxxxxxxklsxxxxxxIx
+xxxxxxxxxsxxxixxxlxxxxxxxxxxxxsxstIxrxLxxxxxxxxxx
+>02ae072bdd8d4b3cd3ddea7d7fd6accb
+MDLEKNYPTPRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIA
+EYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQQPPNQ
+>gi|339493737|ref|YP_004714030.1| putative transposase [Pseudomonas stutzeri ATCC 17588 = LMG 11199]gi|339493835|ref|YP_004714128.1| putative transposase [Pseudomonas stutzeri ATCC 17588 = LMG 11199]gi|339493891|ref|YP_004714184.1| putative transposase [Pseudomonas stutzeri ATCC 17588 = LMG 11199]gi|339494626|ref|YP_004714919.1| putative transposase [Pseudomonas stutzeri ATCC 17588 = LMG 11199]gi|338801109|gb|AEJ04941.1| putative transposase [Pseudomonas stutzeri ATCC 17588 = LMG 11199]gi|338801207|gb|AEJ05039.1| putative transposase [Pseudomonas stutzeri ATCC 17588 = LMG 11199]gi|338801263|gb|AEJ05095.1| putative transposase [Pseudomonas stutzeri ATCC 17588 = LMG 11199]gi|338801998|gb|AEJ05830.1| putative transposase [Pseudomonas stutzeri ATCC 17588 = LMG 11199]
+----------------------------------REKRSTALRMREQGYTYKAIGEAVGVHPRTIAHWAQVAEHKGEkaaIAGGQrgVRQGDRRSLSSSQ
+EVLIRTLMTDKmPDQlklgfalwTRDAVRELI-RQR---CGFLMPVRTVGEYLKR--------
+>gi|260581060|ref|ZP_05848882.1| conserved hypothetical protein [Haemophilus influenzae RdAW]gi|2833479|sp|Q57066.1|Y1720_HAEIN RecName: Full=Uncharacterized protein HI_1720gi|1574576|gb|AAC23366.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]gi|260092300|gb|EEW76241.1| conserved hypothetical protein [Haemophilus influenzae RdAW]
+---------------------KVGLNNQltkvqffMTK-YNFLFKQQVIEFYLQNdKNSSLTRRHFQLAETTLERWINQFNHSGING--LALLGKKRNYS
+PEFKLNVIQAV-KNGKFSAEAACLHF---G------IANSGVVSQWLQA--------
+>gi|298674136|ref|YP_003725886.1| transposase [Methanohalobium evestigatum Z-7303]gi|298287124|gb|ADI73090.1| transposase [Methanohalobium evestigatum Z-7303]
+------------------ERKELEAIVSKGKHKSQkYQNALILLNCDEGeyqkqkHTNEVVSSVLNIGMRKIDRVKKRFVEDGLdmaLNGKEYERTYEKK
+IDGDMEAHIIALScSDPSQGhsqcSLRLLADKVVELEYI---DSISYESIKRVLKKTNL-----
+>gi|308178742|ref|YP_003918148.1| transposase of ISAar25, IS3 family, IS3 group, orfA [Arthrobacter arilaitensis Re117]gi|307746205|emb|CBT77177.1| transposase of ISAar25, IS3 family, IS3 group, orfA [Arthrobacter arilaitensis Re117]
+------------------------------QKFTPEFRAEAVELVISsQKSLVEVTASLGINEGTLGNWVRAYRT-EH--PE--SEAE---ERGPVEWaQ
+YEKLRKELLEV----------------------------------------
+>gi|313894445|ref|ZP_07828010.1| integrase core domain protein [Veillonella sp. oral taxon 158 str. F0412]gi|313441269|gb|EFR59696.1| integrase core domain protein [Veillonella sp. oral taxon 158 str. F0412]
+----------------------------TNKHLNLEERFYLEKRLLAGDPINTIAKALGRSRTTIYAEKKRGtvvqirqnkavlmyiADCGQLayERTRQ
+GSFNTLkaGSIEPSLSWVENKVRVdkwSLDAAVGYALRK----GLFVRNEMVCTKTLYNYLYQ--------
+>gi|156974440|ref|YP_001445347.1| hypothetical protein VIBHAR_02155 [Vibrio harveyi ATCC BAA-1116]gi|156526034|gb|ABU71120.1| hypothetical protein VIBHAR_02155 [Vibrio harveyi ATCC BAA-1116]
+---------------------------------------------------------MLFNNHSI---FGQFGFLSELRNK-----------ATQTMQLI
+EHLTEKTYSHTHQIVAYVKET----FGLDYTVSGMNKWLHHN-------
+>gi|332019769|gb|EGI60232.1| FLJ37770-like protein [Acromyrmex echinatior]
+--------------------------------RSLEQRYAIKFCMRLGKNATETFQMlqeaFKddcISRSQSVMWHKAFKEGREeGADEP-CSGRPtTAR
+PDENVNRVCEVLRSDRRLSIQYVADTL----------NMSTCAVHEIVTENL------
+>gi|340739047|gb|EGR73284.1| InsAB [Escherichia coli O104:H4 str. LB226692]
+-----------------------------YTASQPGTHQKIIDMAHEWRWMPGNCPHYGRWPQHDFTSLKKLRP-QSVTSRIQ-----------------
+-------------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+D 2 * * 0 * * * * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1000 0 0
+
+L 3 * * * * * * * * * 0 * * * * * * * * * * 3
+ 0 * * * * * * 1000 0 0
+
+E 4 * * * 0 * * * * * * * * * * * * * * * * 4
+ 0 * * * * * * 1000 0 0
+
+K 5 * * * * * * * * 0 * * * * * * * * * * * 5
+ 0 * * * * * * 1000 0 0
+
+N 6 * * * * * * * * * * * 0 * * * * * * * * 6
+ 0 * * * * * * 1000 0 0
+
+Y 7 * * * * * * * * * * * * * * * * * * * 0 7
+ 0 * * * * * * 1000 0 0
+
+P 8 * * * * * * * * * * * * 0 * * * * * * * 8
+ 0 * * * * * * 1000 0 0
+
+T 9 * * * * * * * * * * * * * * * * 0 * * * 9
+ 0 * * * * * * 1000 0 0
+
+P 10 * * * * * * * * * * * * 0 * * * * * * * 10
+ 0 * * * * * * 1000 0 0
+
+R 11 * * * * * * * * * * * * * * 0 * * * * * 11
+ 0 * * * * * * 1000 0 0
+
+T 12 * * * * * * * * * * * * * * * * 0 * * * 12
+ 0 * * * * * * 1000 0 0
+
+S 13 * * * * * * * * * * * * * * * 0 * * * * 13
+ 0 * * * * * * 1000 0 0
+
+R 14 * * * * * * * * * * * * * * 0 * * * * * 14
+ 0 * * * * * * 1000 0 0
+
+T 15 * * * * * * * * * * * * * * * * 0 * * * 15
+ 0 * * * * * * 1000 0 0
+
+G 16 * * * * * 0 * * * * * * * * * * * * * * 16
+ 0 * * * * * * 1000 0 0
+
+H 17 * * 1071 * * * 932 * * * * * * * * * * * * * 17
+ 0 * * * * * * 1701 0 0
+
+G 18 * * * 1071 * 932 * * * * * * * * * * * * * * 18
+ 0 * * * * * * 1701 0 0
+
+G 19 * * * 1954 * 1943 * * * * * * * 2101 2008 * * * * * 19
+ 0 * * * * * * 2893 0 0
+
+V 20 * 2594 * * * * * 1637 * * * * * * 2514 * * 2574 * 2558 20
+ 269 2558 * 1000 1000 * * 3800 1087 0
+
+N 21 * * * * * 2758 * * 2715 * * 1256 2816 * * 2847 * * * * 21
+ 0 * * * * * * 4167 0 0
+
+Q 22 * 3433 * 2463 * * * * 2499 3640 * * * 1818 3647 * * 3244 * * 22
+ 0 * * * * * * 5266 0 0
+
+L 23 3358 * * * 3752 3514 * 2720 * 1240 * * 3563 * * * * 3627 * * 23
+ 0 * * * * * * 5566 0 0
+
+G 24 * * 4017 2216 * 1207 * * 3843 * * * * 3643 * 4231 * 3529 * * 24
+ 0 * * * * * * 5894 0 0
+
+G 25 1824 * * * * 1445 * 4124 * 4062 * 4325 * 3961 * 3988 * 4163 * * 25
+ 0 * * * * * * 6825 0 0
+
+V 26 * 4459 4353 * 4243 4136 * 2481 3570 3286 4171 4188 3958 * * 3363 4430 3161 * * 26
+ 70 4399 * 2585 263 * * 6923 1018 0
+
+F 27 * * * 4614 1745 4324 * * * 4074 4313 2840 * * * 4215 * 2465 4303 3719 27
+ 70 4405 * 0 * * * 6727 1018 0
+
+V 28 4463 * * * 4513 4723 4186 3009 3686 4252 3811 * 3586 4548 * 3557 4440 2433 * 4318 28
+ 121 3633 * 2115 379 * * 7850 1194 0
+
+N 29 5032 * 5341 4403 * 4241 5302 4493 3541 4284 1547 3394 3712 5104 4545 * 4267 * * * 29
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+//
+�HHsearch 1.5
+NAME 049453f6b1ef191ef1f937c85980d483
+FAM
+FILE 049453f6b1ef191ef1f937c85980d483
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:33:30 2013
+LENG 66 match states, 66 columns in multiple alignment
+FILT 20 out of 22 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEEEECCCHHHHHHHHHEEECCCCCCCHHHHHHHHHHHHCEEECCCCEECHHHHHHCCC
+>ss_conf PSIPRED confidence values
+986435888764372155256753242077888989998986466530003887007888843479
+>Consensus
+axxxSVVAxqlIPxnTaLTlxMmxxkVxxPxGipxedixxlVgxqVnxxVxxxxTlmpxmVkxyxx
+>049453f6b1ef191ef1f937c85980d483
+ANQASVVANQLIPINVALTLVMMRSEVVTPVGIPAEDIPRLVSMQVNRAVPLGTTLMPDMVKGYAA
+>gi|113886|sp|P12100.1|ANP1_PACBR RecName: Full=Ice-structuring protein AB1; Short=ISP AB1; AltName: Full=Antifreeze peptide AB1gi|226447|prf||1513197A antifreeze peptide AB1
+--TKSVVASQLIPINTALTPAMMKAKEVSPKGIPAEEMSKIVGMQVNRAVNLDETLMPDMVKTYQ-
+>gi|62751049|dbj|BAD95785.1| type III antifreeze protein nfeAFP10 [Zoarces elongatus]
+ANQASVVATQLIPINTALTLVMMKAKVATPMGIPAEDIPRIVSMQVNQAVACGTTLMPGMVKTYTP
+>gi|76262419|gb|ABA41378.1| type III antifreeze protein [Anarhichas minor]
+AHQASIVANQLIPINTALTPIMTKAQVVTPLGIPAEDIPRIIGMQVNRAVALGTTLMPDMVKGYPP
+>gi|76262407|gb|ABA41372.1| type III antifreeze protein [Zoarces americanus]
+ANQESVVATQLIPINTALTPIMMKGKVVTPMGIPFKEMSQIVGKQVNRAVPLGTTIMPEMVKGYAP
+>gi|62751041|dbj|BAD95781.1| type III antifreeze protein nfeAFP6 [Zoarces elongatus]
+AG-ESVVATQLIPINTALTPAMMEGKVTNPSGIPFAEMSQIVGKQVNTPVAKGQTLMPGMVKTYVP
+>gi|62751053|dbj|BAD95787.1| type III antifreeze protein nfeAFP12 [Zoarces elongatus]
+ANQESVVATVLIPINTALTVGMMTTRVVSPTGIPAEDIPRLISMQVNQVVPMGTTLMPDMVKGYAP
+>gi|159163462|pdb|1WVO|A Chain A, Solution Structure Of Rsgi Ruh-029, An Antifreeze Protein Like Domain In Human N-Acetylneuraminic Acid Phosphate Synthase Gene
+---GSVVAKVKIPEGTILTMDMLTVKVGEPKGYPPEDIFNLVGKKVLVTVEEDDTIMEELVDNH--
+>gi|326935208|ref|XP_003213668.1| PREDICTED: sialic acid synthase-like, partial [Meleagris gallopavo]
+---KSVVAKVTIPEGTVLTLDMLTVKVGEPKGFAPETIFDLVGQKAKTTIEEDETITEQAV-----
+>gi|47220009|emb|CAG11542.1| unnamed protein product [Tetraodon nigroviridis]
+---KSVVAKVRIPKGTVLTADMLAVKVAEPMGVKAEEIFELVGKTVMENVEEDESVVPEEAKAWA-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 130 * * * * * * * * * * * * * * 3534 * * * * 1
+ 130 * 3534 * * * * 1687 0 0
+
+N 2 * * * * * 2309 3414 * * * * 721 * * * 3358 * * * * 2
+ 513 * 1740 * * * 0 1680 0 1000
+
+Q 3 * * * * * * * * 2344 * * * * 596 * * 2822 * * * 3
+ 158 * 3271 * * 0 * 1552 0 1159
+
+A 4 2077 * * 2412 * 3928 * * 1417 * * * * 2890 * * * * * * 4
+ 0 * * * * 0 * 2289 0 1000
+
+S 5 * * * * * * * * * * * * * * * 0 * * * * 5
+ 0 * * * * * * 2289 0 0
+
+V 6 * * * * * * * 4358 * * * * * * * * * 72 * * 6
+ 0 * * * * * * 2289 0 0
+
+V 7 * * * * * * * * * * * * * * * * * 0 * * 7
+ 0 * * * * * * 2289 0 0
+
+A 8 0 * * * * * * * * * * * * * * * * * * * 8
+ 0 * * * * * * 2289 0 0
+
+N 9 * * * * * * * * 1418 * * 2235 * * * 4544 1432 * * * 9
+ 0 * * * * * * 2289 0 0
+
+Q 10 * * * * * * * * * * * * * 795 * * * 1240 * * 10
+ 0 * * * * * * 2289 0 0
+
+L 11 * * * * * * * * 2996 676 * * * * 2657 * 3470 * * * 11
+ 0 * * * * * * 2289 0 0
+
+I 12 * * * * * * * 0 * * * * * * * * * * * * 12
+ 0 * * * * * * 2289 0 0
+
+P 13 * * * * * * * * * * * * 0 * * * * * * * 13
+ 0 * * * * * * 2289 0 0
+
+I 14 4001 * * 2251 * * * 908 3299 * 3431 * * * * * * * * * 14
+ 0 * * * * * * 2289 0 0
+
+N 15 * * * * * 1418 * * * * * 676 * * * * * * * * 15
+ 0 * * * * * * 2289 0 0
+
+V 16 * * * * * * * * * * * * * * * * 69 4429 * * 16
+ 0 * * * * * * 2289 0 0
+
+A 17 676 * * * * * * 2996 * * * * * * * * * 2007 * * 17
+ 0 * * * * * * 2289 0 0
+
+L 18 * * * * * * * * * 0 * * * * * * * * * * 18
+ 0 * * * * * * 2289 0 0
+
+T 19 * * * * * * * * * * * * * * * * 0 * * * 19
+ 0 * * * * * * 2289 0 0
+
+L 20 3299 * * * * * * * * 874 3991 * 2056 * * * * 4343 * * 20
+ 0 * * * * * * 2289 0 0
+
+V 21 2538 * 1418 * * 4343 * 2639 * * * * * * * * * 2036 * * 21
+ 0 * * * * * * 2289 0 0
+
+M 22 * * * * * * * * * * 0 * * * * * * * * * 22
+ 0 * * * * * * 2289 0 0
+
+M 23 * * * * * * * 4513 * 1418 907 * * * * * 4358 * * * 23
+ 0 * * * * * * 2289 0 0
+
+R 24 3299 * * 2580 * * * * 1842 * * * * * 3510 * 1456 * * * 24
+ 0 * * * * * * 2289 0 0
+
+S 25 2023 * * * * 2050 * * * * * * * * * 4429 3443 1418 * * 25
+ 0 * * * * * * 2289 0 0
+
+E 26 * * * 2612 * * * * 603 * * * * 3538 3443 * * * * * 26
+ 0 * * * * * * 2289 0 0
+
+V 27 * * * 3622 * * * * * * * * * * * * * 122 * * 27
+ 0 * * * * * * 2289 0 0
+
+V 28 2849 * * * * 1875 * 3449 * * * * * * * * 3080 1400 * * 28
+ 0 * * * * * * 2289 0 0
+
+T 29 * * * 1418 * * * * * * * 2290 * * * 2938 2010 * * 4552 29
+ 0 * * * * * * 2289 0 0
+
+P 30 * * * * * * * * * * * * 0 * * * * * * * 30
+ 0 * * * * * * 2289 0 0
+
+V 31 3669 * * * * * * 4720 1499 4358 2229 * * * * 2952 3443 4429 * * 31
+ 0 * * * * * * 2289 0 0
+
+G 32 * * * * * 0 * * * * * * * * * * * * * * 32
+ 0 * * * * * * 2289 0 0
+
+I 33 * * * * 3470 * * 676 * * * * * * * * * 3299 * 2456 33
+ 0 * * * * * * 2289 0 0
+
+P 34 3470 * * * * * * * 3299 * * * 307 * * * * * * * 34
+ 0 * * * * * * 2289 0 0
+
+A 35 1041 * * * 2050 * * * * * * * 1875 * * * * * * * 35
+ 0 * * * * * * 2289 0 0
+
+E 36 2684 * * 399 * * * * 4757 * * * * * * * * 4354 * * 36
+ 0 * * * * * * 2289 0 0
+
+D 37 * * 1043 1237 * * * * * * * * * * * * 3470 * * * 37
+ 0 * * * * * * 2289 0 0
+
+I 38 4354 * * * * * * 483 4513 * 2384 * * * * * * * * * 38
+ 0 * * * * * * 2289 0 0
+
+P 39 * * * * 1418 * * * * * * * 1550 * * 1814 * * * * 39
+ 0 * * * * * * 2289 0 0
+
+R 40 * * 3470 3299 * 4134 * * 3075 * * 2996 * 2050 1912 * * * * * 40
+ 0 * * * * * * 2289 0 0
+
+L 41 * * * * * * * 1433 * 667 * * * * * * * * * * 41
+ 0 * * * * * * 2289 0 0
+
+V 42 * * * * * * * 3350 * * 4738 * * * * * * 210 * * 42
+ 0 * * * * * * 2289 0 0
+
+S 43 * * * * * 278 * * * * * * * * * 2510 * * * * 43
+ 0 * * * * * * 2289 0 0
+
+M 44 * * * * * * * * 929 4596 1544 * * 3470 * * * * * * 44
+ 0 * * * * * * 2289 0 0
+
+Q 45 * * * * * * * * 1875 * * * * 676 * * 3299 * * * 45
+ 0 * * * * * * 2289 0 0
+
+V 46 3470 * * * * * * * * * * * * * * * * 136 * * 46
+ 0 * * * * * * 2289 0 0
+
+N 47 * * * * * * * * 3470 2456 3299 676 * * * * * * * * 47
+ 0 * * * * * * 2289 0 0
+
+R 48 * * * 3299 * * * * * * * * * 2953 1602 * 2262 2113 * * 48
+ 0 * * * * * * 2289 0 0
+
+A 49 1289 * * * * * * 4354 * * * 3299 3080 * * * 1875 4343 * * 49
+ 0 * * * * * * 2289 0 0
+
+V 50 * * * * * * * 2711 * * * * * * * * * 239 * * 50
+ 0 * * * * * * 2289 0 0
+
+P 51 1784 * * 1418 * * * * * 4596 * 4544 2232 * * * * * * 4705 51
+ 0 * * * * * * 2289 0 0
+
+L 52 * 4749 * 1418 * * * 4596 2290 1995 3443 * * * * * * * * * 52
+ 0 * * * * * * 2289 0 0
+
+G 53 * * 1021 * * 979 * * * * * * * * * * * * * * 53
+ 0 * * * * * * 2289 0 0
+
+T 54 * * 2456 1878 * * * * * * * * * 2283 * * 1556 * * * 54
+ 0 * * * * * * 2289 0 0
+
+T 55 * * * * * * * * * * * * * * * 3299 155 * * * 55
+ 0 * * * * * * 2289 0 0
+
+L 56 * * * * * * * 1756 * 889 * * * * * * * 2608 * * 56
+ 0 * * * * * * 2289 0 0
+
+M 57 * * * * * * * * * 4134 413 * * * * * 3470 3299 * * 57
+ 0 * * * * * * 2289 0 0
+
+P 58 * * * 1875 * * * * * * * * 459 * * * * * * * 58
+ 0 * * * * * * 2289 0 0
+
+D 59 * * 1355 1640 * 3762 * 4354 * * * 3733 * 3470 * * * * * * 59
+ 0 * * * * * * 2289 0 0
+
+M 60 3470 * * 3299 * * * * * 3991 676 * * * * 3066 * * * * 60
+ 0 * * * * * * 2289 0 0
+
+V 61 3299 * * * * * * * * * * * * * * * * 155 * * 61
+ 0 * * * * * * 2289 0 0
+
+K 62 * * 3776 2787 * * * * 355 * * * * * * * * * * * 62
+ 0 * * * * * * 2208 0 0
+
+G 63 3108 * * * 4471 2082 * * * * * 2164 * * * 3725 1718 * * * 63
+ 0 * * * * * * 2208 0 0
+
+Y 64 * * * * * * 2916 * * * * * * * * * * * 2772 472 64
+ 185 4150 3972 1000 1000 * * 2187 1000 0
+
+A 65 860 4057 * 3248 * * * * * * * * 4019 4054 4181 * 4265 4197 * * 65
+ 0 * * * * 0 * 2000 0 1000
+
+A 66 1700 * * * * * * * 2691 3670 * * 1124 * * * * * * * 66
+ 0 * * 0 * * * 1707 0 0
+
+//
+�HHsearch 1.5
+NAME 07725759f4907c8886db21d514cb9b12
+FAM
+FILE 07725759f4907c8886db21d514cb9b12
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:21:39 2013
+LENG 82 match states, 82 columns in multiple alignment
+FILT 122 out of 1045 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCHHHHHHHCCCCCEEEEECCEEEECCHHHHHCCCHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHCEEEEECCCCC
+>ss_conf PSIPRED confidence values
+9885789999976789997999999997360357649784899999759542788988369999999998576578578789
+>Consensus
+xxxxxtxxevxxhxxxxxxwvxixgxVyDvtxfxxxHPgGxxxlxxxxGxDxTxxfxxxxhsxxaxxxlxxxxIGxxxxxxx
+>07725759f4907c8886db21d514cb9b12
+AVKYYTLEEIQKHNNSKSTWLILHYKVYDLTKFLEEHPGGEAVLRAQAGGDATANFEAVGHSTDARELSKTFIIGELHPDDR
+>gi|258569831|ref|XP_002543719.1| conserved hypothetical protein [Uncinocarpus reesii 1704]gi|237903989|gb|EEP78390.1| conserved hypothetical protein [Uncinocarpus reesii 1704]
+---LTGTSREAQHRQQ-----LLGGALWKGVRC-------ANIILNLAGKDATEEYDPI-HPSGTLEenLQPEACLGTVDPA--
+>gi|12002125|gb|AAG43192.1|AF108658_1 p5327 [Homo sapiens]gi|119594381|gb|EAW73975.1| fatty acid desaturase 2, isoform CRA_b [Homo sapiens]gi|158261605|dbj|BAF82980.1| unnamed protein product [Homo sapiens]
+--GPFVCVCVLLASIPTPQTPLLQASLPPFHPASAGHP---IT-------GQQDAFRAFHPDLEfVGKFLKPLLIGELAPE--
+>gi|298710828|emb|CBJ26337.1| dopamine beta-monooxygenase, putative [Ectocarpus siliculosus]
+--PIYSVAEFNDKVLNGQSWVLVDGAILDVSEFAQRHPGGRRLIINALGTDITQELlgedlsvghamsfSPHAHSERAWTILRRLVVGYIEEEE-
+>gi|328772499|gb|EGF82537.1| hypothetical protein BATDEDRAFT_34502 [Batrachochytrium dendrobatidis JAM81]
+--IKSQSEVL-qKafRLGQQtv--pWFAAHGRYYFAEDL-mSQH--irdygpgtgqgslaly----qFQQFYGNDVSNLF--------------------
+------
+>gi|302683558|ref|XP_003031460.1| glycosyltransferase family 2 protein [Schizophyllum commune H4-8]gi|300105152|gb|EFI96557.1| glycosyltransferase family 2 protein [Schizophyllum commune H4-8]
+--HVYSTGDVAEHNyddSPDSVYTYIRGEVFNLNRISEIHgRVvsvvDQKTILDnYGGGSSDDIF--------------------------
+>gi|317050963|ref|YP_004112079.1| cytochrome b5 [Desulfurispirillum indicum S5]gi|316946047|gb|ADU65523.1| cytochrome b5 [Desulfurispirillum indicum S5]
+----MEQQKLQEYDGKDGkpAYVAYDGKIYDVST-SRMWKNGVHARVHKAGEDLTEAMKNAPHGAEVLKRFT--EVDSLEG---
+>gi|328772499|gb|EGF82537.1| hypothetical protein BATDEDRAFT_34502 [Batrachochytrium dendrobatidis JAM81]
+---GWTEQAV---ngmS-sNtKRFII-iFD----------------nvyyvspidalqnatfsLtvrNLLSPTPGSDVTAA--wkATraQSGElqqe---
+-ldtaltCLnNIFYVGTVDR---
+>gi|118420981|dbj|BAF37218.1| chitin synthase [Lentinula edodes]gi|119224826|dbj|BAF41220.1| chitin synthase [Lentinula edodes]
+---VHSWDEIQSYASDediEKIWGVYNNNLYDLTDYFYTQDQ-ndnndaylfldSgieTVFKDRSGQGITDSLNTAlgKLNETYRQqnldCLnNVFYIGQ
+TDF---
+>gi|322795632|gb|EFZ18311.1| hypothetical protein SINV_02346 [Solenopsis invicta]
+--SLIRWADLENHNRDGGLWVVVNNNVYDVQDIRNDGSwsPYEVLQRYVVGRDETSAVTqcgaPYSQLSPPRGMMDSCFVGHYC----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 2091 * * * 2030 * * * * * 1915 * * * * 1971 * * * * 1
+ 0 * * * * * * 2499 0 0
+
+V 2 * * * * 4978 * * * 4545 996 * * 4541 2924 3061 3990 * 3907 * * 2
+ 71 4375 * 1000 1000 * * 5192 1000 0
+
+K 3 5548 * 5150 4270 * 4384 4649 5538 2740 * 5511 4050 2422 4787 1976 5241 4779 5832 * * 3
+ 23 * 5960 * * * * 7343 0 0
+
+Y 4 3929 6596 4948 4900 4222 5027 5257 5114 4515 2783 5745 6710 4582 4297 4196 4365 3590 2890 * 3507 4
+ 0 * * * * 0 * 7609 0 1002
+
+Y 5 * * * * 2145 * 6279 2701 * 3132 3948 * * * 6397 4578 6143 4048 3372 2298 5
+ 0 * * * * * * 7768 0 0
+
+T 6 4792 6682 5137 5257 6696 4588 * * 5917 4290 * 6741 5660 6259 3175 2318 1308 5416 * * 6
+ 0 * * * * * * 7798 0 0
+
+L 7 2991 4765 5887 4252 6841 * 6590 3406 5741 3788 3746 6762 3555 4927 3530 4859 3229 4703 3384 * 7
+ 0 * * * * * * 7798 0 0
+
+E 8 2715 5136 3373 2144 * 4049 * * 3911 * * 3652 * 4553 4433 3274 5081 4420 * 5540 8
+ 0 * * * * * * 7798 0 0
+
+E 9 7251 5447 2503 984 * 5434 * * 6983 6256 6064 6502 * 2962 5427 6826 4976 5255 * * 9
+ 0 * * * * * * 7830 0 0
+
+I 10 * * * 6173 3830 * * 2242 * 1805 4463 * 6064 * * * 6256 1582 * 6502 10
+ 28 * 5679 * * * * 7830 0 0
+
+Q 11 1922 * 5569 3337 * 5645 * 5779 3188 4393 * 5071 * 2893 3560 3397 6819 4566 6154 6471 11
+ 0 * * 0 * 770 1274 7781 1033 1122
+
+K 12 4758 * 4668 2450 * 4593 6513 6669 2993 3819 * 3232 * 3110 3073 4007 4218 6927 * 5891 12
+ 37 5294 * 1000 1000 * 0 7821 1136 1000
+
+H 13 3807 7077 6361 4509 5694 * 992 6625 5117 3295 6521 4867 6225 4753 4900 * * * * 3775 13
+ 44 5051 * 512 1742 0 * 7821 1321 1000
+
+N 14 3926 * 3289 4042 5692 6366 * 4540 3672 4239 * 1800 * 4444 4643 3460 4390 4224 * * 14
+ 111 4749 4764 1565 595 * * 7830 1364 0
+
+N 15 3391 6590 6271 4577 5170 2445 * 5107 3021 4544 6786 3478 6229 4590 4609 2846 3611 5845 * * 15
+ 64 4519 * 1585 585 0 * 7744 1433 1280
+
+S 16 4192 * 3340 2532 * 5557 5000 6550 2774 4445 * 4194 3131 4344 3132 4195 5843 6130 * * 16
+ 154 3480 6400 783 1256 * 0 7836 1786 1000
+
+K 17 4326 * 2334 3175 * 1873 5917 * 4589 * * 3186 5290 4142 7216 4330 4529 6785 * 6798 17
+ 125 3590 * 1576 590 1390 694 7805 1786 1125
+
+S 18 4868 * 2303 3925 * 3300 6069 * 3528 6561 * 3906 3595 4760 2759 2976 5479 * * * 18
+ 59 4652 * 1172 846 * 0 7782 1268 1168
+
+T 19 3012 2507 * * 3518 6006 5082 4041 5736 2744 4497 5378 4473 4920 5161 4275 4222 5390 * 4815 19
+ 54 7050 5096 0 * 1050 952 7801 1114 1168
+
+W 20 * 4978 6616 6214 6234 * 5734 4567 6678 3246 5331 * * * 6448 * 5157 3903 1012 2963 20
+ 10 7139 * 2000 415 2054 397 7651 1000 1304
+
+L 21 5065 6674 * * 3667 5547 6694 2217 * 2878 4440 * 5650 * 6942 5937 4524 1537 * 5579 21
+ 26 * 5790 * * 0 * 7647 0 1210
+
+I 22 3270 6096 * * 6437 4178 * 1932 6623 3275 5520 * * 7193 4737 3404 4301 2217 * 6277 22
+ 22 6028 * 0 * 0 * 7798 1173 1154
+
+L 23 4541 6647 * * 3445 * 5458 1605 6936 3628 5900 * * * * 6858 6575 2274 6353 2643 23
+ 0 * * * * * * 7795 0 0
+
+H 24 5024 * 2557 3233 7250 4238 3382 * 2899 4678 * 3068 * 4312 2634 5928 * * * 5861 24
+ 6 * 7990 * * * * 7795 0 0
+
+Y 25 5205 * 3449 5139 * 931 * * 5291 * * 2730 * 4733 4284 5141 5173 * * 7132 25
+ 17 6455 * 1000 1000 * 0 7793 1012 1000
+
+K 26 4825 7410 4359 4859 5631 5063 7342 4183 2250 4193 5904 3507 * 3887 3122 3621 4492 3929 * 5573 26
+ 0 * * * * * 0 7793 0 1000
+
+V 27 4986 * * 5134 * * * 2862 * 3938 * * * * 5532 5495 6762 661 4931 5706 27
+ 0 * * * * * 0 7793 0 1000
+
+Y 28 * 4970 * * 3096 * 4883 5031 6214 3676 * * 4654 * * * 5220 * 5554 720 28
+ 12 * 6959 * * * 0 7793 0 1000
+
+D 29 * 6181 478 5728 6757 * * * 4565 6992 6028 3172 5787 6435 5430 * * * * 6507 29
+ 0 * * * * 909 1097 7782 0 1097
+
+L 30 4219 4077 * * 4797 5487 * 2473 * 1913 6896 * * * * 5532 * 1501 * * 30
+ 45 5030 * 510 1747 * 0 7793 1213 1000
+
+T 31 5042 * 5458 4948 * 5866 5710 6437 4779 6277 5660 4702 6328 4808 6233 1831 1294 6801 * * 31
+ 31 5533 * 3031 188 751 1302 7756 1106 1126
+
+K 32 4517 * 2663 2584 * 3500 7169 * 3319 6018 * 3051 4518 5736 3620 3317 4455 * * 6588 32
+ 45 * 5024 * * * 0 7793 0 1000
+
+F 33 5105 6758 * 6418 1273 4995 6320 5274 6803 4159 * * * * * * * 5062 3233 1915 33
+ 119 5072 4344 1235 798 2011 411 7647 1182 1248
+
+L 34 2923 * * 6655 5823 * 5329 3069 5485 2310 3228 6496 5781 5614 4725 4135 5967 2569 5731 5786 34
+ 123 5520 4059 0 * 1866 463 7579 1214 1680
+
+E 35 3415 5075 3669 3796 5624 5552 4461 * 2545 6222 6286 3371 3125 4192 3811 4455 4636 * * 5768 35
+ 58 4658 * 650 1463 1303 750 7513 1261 2048
+
+E 36 4399 * 3286 2981 4601 4742 * 4906 3414 4741 * 4499 * 3396 3653 3592 4053 4452 6560 4011 36
+ 27 5728 * 0 * 544 1671 7586 1066 1603
+
+H 37 5521 * * * 6202 4352 461 * * * * 4722 6767 4785 * 4084 * 6350 4846 * 37
+ 54 5199 6738 0 * * 0 7774 1129 1131
+
+P 38 4757 * 5698 5566 6960 5278 * 6577 4872 6486 * 7021 493 * 6294 3846 6331 * * 5624 38
+ 46 6321 5750 1000 1000 * 0 7750 1028 1255
+
+G 39 4643 * 3881 5585 * 725 6187 6323 6851 6369 * 5128 5057 5709 6740 3798 4408 6260 * * 39
+ 118 4190 5389 2858 214 * 0 7651 1516 1435
+
+G 40 4299 * 4801 6428 6985 542 * 7129 5765 5526 * * * * 6283 3799 4692 6330 * 5377 40
+ 126 3583 * 2994 194 731 1331 7602 1949 1670
+
+E 41 3041 * 3440 3587 7237 4959 6905 5104 3333 4567 * 4349 3964 3388 3997 2814 4915 5044 * 6861 41
+ 167 3924 4521 1818 481 748 1305 7674 1620 1217
+
+A 42 3173 * 3371 3950 5685 6244 4733 3785 3111 4772 6359 4101 6711 4664 3703 3467 3947 4930 * 4369 42
+ 62 5182 6098 751 1301 729 1334 7728 1156 1448
+
+V 43 3465 * * 6057 4604 6230 5173 2357 5238 2628 4484 5278 4185 6923 6923 3520 4411 3278 5778 4994 43
+ 54 * 4770 0 * 0 * 7747 1033 1336
+
+L 44 * 5962 * * 3750 * * 1677 6234 1370 4354 6574 * 6325 * * 5458 4095 5524 5510 44
+ 44 5577 6792 1000 1000 1017 984 7666 1130 1272
+
+R 45 4321 7151 5128 4016 4228 4804 * 4933 2664 2548 3859 5465 4658 3869 3956 5432 3946 5124 6954 6260 45
+ 46 6868 5438 3000 193 * 0 7682 1000 1175
+
+A 46 3212 7091 3791 4860 6370 5188 3313 4813 3268 4065 4957 4245 3726 3817 3771 4211 5037 * 6704 4643 46
+ 44 5459 7063 0 * 2449 292 7640 1112 1357
+
+Q 47 3161 6816 5552 6192 2891 4630 3822 6061 6421 3078 6480 4398 * 5190 4552 5915 4885 3977 6308 2335 47
+ 19 * 6223 * * 771 1273 7669 0 1351
+
+A 48 1337 5202 6714 5227 5674 3993 5714 5483 4035 3933 4896 4919 4636 7087 6478 4079 * 3373 * 6720 48
+ 0 * * * * 1414 679 7674 0 1203
+
+G 49 4485 5922 5062 * 6338 480 6090 * 5583 7023 * 3865 5460 * 6138 5013 * * * * 49
+ 18 6338 * 3322 152 * 0 7698 1010 1093
+
+G 50 7340 * * 4568 6749 2936 5863 6090 1876 5085 5617 5177 5460 3179 2423 6074 3901 5766 * 6617 50
+ 36 5338 * 715 1355 0 * 7698 1169 1093
+
+D 51 7064 6244 479 3459 * 5155 * 6707 * * * 4809 6969 * 6339 4108 * 5690 * * 51
+ 0 * * * * * * 7795 0 0
+
+A 52 1649 5024 6244 5581 * 4961 * 2738 * 2959 4594 6995 4941 5121 * 4790 * 2652 * * 52
+ 0 * * * * * * 7795 0 0
+
+T 53 6791 6244 3477 6068 * 5170 * * * * * * * 5169 6575 2180 874 4968 * 6839 53
+ 0 * * * * * * 7795 0 0
+
+A 54 3505 6555 2460 2652 * 6756 5330 * 3720 4404 6575 4086 4459 4185 3569 3859 * 5695 4920 5165 54
+ 0 * * * * * * 7795 0 0
+
+N 55 2196 5797 4999 3383 5504 5889 5297 3861 5711 3392 7072 7147 6449 4049 6147 4155 5643 3744 5011 3226 55
+ 77 5228 5297 0 * * * 7795 1234 0
+
+F 56 * 6592 * 6229 815 * 6805 4883 * 2886 3902 * * 6541 * 6845 5830 6312 4587 3802 56
+ 55 4742 * 2344 316 * 0 7660 1324 1164
+
+E 57 3411 * 2880 2973 4999 * 6166 5618 4309 4775 6013 2640 4879 4709 3645 4513 5489 5978 4985 4362 57
+ 98 3933 * 2570 266 1534 611 7498 1554 1164
+
+A 58 2569 6506 5477 3583 6760 3909 6198 5823 3157 4126 6919 4749 4205 3939 4439 3206 3672 5684 * 5576 58
+ 275 2853 4835 2030 405 * 0 7846 2132 1076
+
+V 59 2937 6415 * * 3402 * 3214 4021 5886 3452 5125 4858 4905 5197 5943 4756 5589 3880 * 2187 59
+ 575 4379 1833 1000 1000 682 1409 7510 1437 1534
+
+G 60 3336 * 5058 * 5840 3201 2130 5264 3847 5612 * 4011 2729 4766 4869 4466 5289 4455 * * 60
+ 42 5118 * 521 1721 144 3400 7305 1110 3483
+
+H 61 5273 * 5787 * 6314 * 679 5423 3793 5368 6133 5760 5156 4358 5846 4903 5873 * * 5529 61
+ 29 5646 * 1000 1000 494 1787 7614 1092 1188
+
+S 62 6428 5489 3699 7245 6007 4623 4830 * 5036 4400 * 5497 3492 5265 3756 1341 3773 * 5366 6610 62
+ 16 * 6481 * * * 0 7630 0 1000
+
+T 63 4057 6246 4109 3149 * 5615 5167 4932 2687 3808 * 4753 3025 5752 3621 3332 5952 4363 5349 * 63
+ 113 3725 * 666 1435 1307 747 7613 1617 1109
+
+D 64 2769 * 3868 2842 5337 4081 4958 * 3995 6745 * 3096 5817 4712 4055 2773 5574 4905 * 5400 64
+ 64 4532 * 264 2581 798 1235 7616 1304 1116
+
+A 65 1238 6613 * 5146 * 5103 * 4300 6614 4553 4416 * 4409 5842 5943 5007 3394 2965 * 5434 65
+ 19 6247 * 1288 760 * 0 7633 1078 1000
+
+R 66 5448 * 4863 3235 3740 5660 4030 3843 3577 3065 4776 6388 5597 5969 2784 * * 3906 4240 4114 66
+ 21 6102 * 1585 585 * 0 7617 1067 1000
+
+E 67 3691 * 5173 2428 5963 4878 5321 * 2540 4785 5969 3467 6599 3486 3883 3580 4987 6563 * 5244 67
+ 158 3268 * 1587 584 0 * 7617 1944 1000
+
+L 68 * 3972 * 5193 3775 6585 * 3167 3904 2480 2675 6253 * 4517 3916 5364 3663 5746 5665 4414 68
+ 17 6390 * 1000 1000 * * 7625 1107 0
+
+S 69 6169 * 6894 * 4567 4951 * 3680 * 778 3016 * 6958 6554 6809 5840 * 5723 5003 5418 69
+ 98 3929 * 339 2255 * * 7625 1509 0
+
+K 70 4554 6794 4123 2279 6626 * 5998 7114 2473 6644 * 3358 3196 3349 3387 4335 6392 * * * 70
+ 75 * 4297 * * * * 7625 0 0
+
+T 71 4959 6967 3906 2664 * 4794 4372 7258 2546 4541 5414 4907 4306 3377 4138 3478 3955 6006 * * 71
+ 39 5222 * 0 * 1468 647 7546 1109 1321
+
+F 72 5743 4915 * * 1961 * 4340 * 5148 2290 4403 6736 6197 6290 5818 6603 * * 5066 1897 72
+ 0 * * * * 0 * 7540 0 1173
+
+I 73 3978 3627 * 5579 4740 6956 4175 3974 2964 3306 * * 6454 5908 2685 5589 4118 4655 * 2843 73
+ 11 7042 * 0 * * * 7568 1002 0
+
+I 74 6335 5843 6394 * 5433 * 6542 1131 6454 3460 5776 * * * * * 6854 1629 * 6034 74
+ 29 5644 * 3347 149 * * 7568 1067 0
+
+G 75 3758 * 4824 * * 284 * * 6173 6297 * * * 6081 6279 * * 6055 * * 75
+ 0 * * * * * * 7560 0 0
+
+E 76 5653 * 4837 3046 6836 * 4881 3972 2652 6547 5541 4014 4753 4974 3044 6780 3561 3421 * 3521 76
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+
+L 77 6219 6397 * 5102 5470 * * 2277 * 1622 5325 * * 6016 * 5803 4255 2569 * 3152 77
+ 43 5090 * 553 1652 * * 7488 1129 0
+
+H 78 2977 4364 2184 3675 * * 5148 5667 3401 5028 4585 4774 6780 3982 4565 4199 5544 3572 * * 78
+ 20 6165 * 0 * * * 7410 1000 0
+
+P 79 4245 * 3548 2947 4509 5064 5006 * 4805 6383 * 5761 1877 6115 3534 4349 4440 5103 * 3973 79
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+D 80 2918 * 1953 1951 * 3951 5481 * * 5149 * 3836 * 5212 5231 3463 5561 * * * 80
+ 0 * * * * * * 6170 0 0
+
+D 81 * * 1245 1959 * 4274 * * 4328 * * 3809 4381 * * 3320 * * * * 81
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+
+R 82 * * * * * * * * 2707 * * * * 2719 525 * * * * * 82
+ 0 * * 0 * * * 3269 0 0
+
+//
+�HHsearch 1.5
+NAME 07e9709ec97fb9c893c6efa6db9e811b
+FAM
+FILE 07e9709ec97fb9c893c6efa6db9e811b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:49:30 2013
+LENG 224 match states, 224 columns in multiple alignment
+FILT 204 out of 1141 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCEEECCCCCHHHHHHHHCCCCCHHHHHH
+HHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEE
+EECCCCCCCCCHHHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9099997189998789999999999998799089985512476544677650358999986256754356661575377775578775045231999999
+9999853599999979885430356778999999864995899956756599999999999982899779999954788606899999999986099689
+985787899999999998664479
+>Consensus
+mxxixvxsxkggvGKTtvaxxLaxxLxxxgxkVxxxdpxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxlxx
+xlxxlxxxyDxviIDxxxxlxxxxxxxxxxxxiaxxxxxxvilVxxxxxxxxxxxxxxxxxlxxxxxxxxgvVxNxxxxxxxxxxxxxxxixxxxxxxxl
+xxIpxxxxxxxxxxxxxxlxxxxx
+>07e9709ec97fb9c893c6efa6db9e811b
+SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSA
+GLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLL
+GEIPWLAENPENAATGKYINLALL
+>gi|15616795|ref|NP_240007.1| phosphate acetyltransferase [Buchnera aphidicola str. APS (Acyrthosiphon pisum)]gi|11133754|sp|P57273.1|PTA_BUCAI RecName: Full=Phosphate acetyltransferase; AltName: Full=Phosphotransacetylasegi|25321713|pir||E84950 phosphate acetyltransferase (EC 2.3.1.8) [imported] - Buchnera sp. (strain APS)gi|10038858|dbj|BAB12893.1| phosphate acetyltransferase [Buchnera aphidicola str. APS (Acyrthosiphon pisum)]
+-RIIMLIPLDKDIGLTSIGLSIIYFFYQKKIKKKSVQSILY--FSC--TQNSSNsTSHVINKYF-SKIV--HTVDYIDF--SKVLFNS-PEYSFLLNKVI
+DEHYNN-KfLRELILIEGIKNNYCIN-SEEMNYDISQNLNAEVIFIANLENsspEyIKNKEKKINFFLKQkKYKNILGVIFNQINspflenkydfiKKLI
+VLKKiknETKTIvpKKIlknNFFSIIACIPWN-RNivtTRVIDLFNFLNIQ--
+>gi|218282221|ref|ZP_03488520.1| hypothetical protein EUBIFOR_01102 [Eubacterium biforme DSM 3989]gi|218216759|gb|EEC90297.1| hypothetical protein EUBIFOR_01102 [Eubacterium biforme DSM 3989]
+-QVITCVSTVPNEGKSTIACNLARIMAAKYKNVLLidcdlRNASVHKTLHISNR--SGLTNIISEFqeglsinS-YEgvqqVQYDggqTLTV-ITAGHRV
+PNPSEVLG-----SKRMGRFLEQARKEFGYIIIDSP-----PMAVASDTIPLSNVSD-GVLYVVDAKSSDKRRVKTAINDLKRNGGHVIGVVLNKVDM--
+-------------------------------------------
+>gi|325188235|emb|CCA22775.1| phosphate acetyltransferase putative [Albugo laibachii Nc14]
+-QRLYLTSTDYVPHTAPLLLGLASVLEQKYGRIGYFRPILPTRKS---APIDHHVPLMQKLLGLE-PHEKKPLYAVtsEEAV--DYCL-RNQQDQLIDRV
+LFTLEKAQEEHDFMIIEGSAFPSHETNsvSWQLHKQIANALGARVVLCMDAGTpdfpssdsELIdaivIRALLGREQAEADRVGYFGTLINRVGTSdPSA
+FALrLEKAFEK-HKLPYLGFLPYD-RIlasRRLNEVADRLGAK--
+>gi|333602914|gb|EGL14339.1| phosphate acetyltransferase [Gardnerella vaginalis 315-A]
+--NVTIISADCAQSRNVVALGVTKALSSH-YPTTVFRPSAKHDDAF------TSE--LIASSNTKPTLEQVIAA------CPCAV--RKNKDTLRGDIVA
+HFNELIsvTNAQGCVIVASDstSVFDPD-LFRFDASVAADLASPVFLSICAEGRDSKQILQTIEaqcaSVSKEYTKVLGVFVTDCKEDL--AKEVKENYA
+QnnN-GTPLW-TLPSI------------------
+>gi|55378027|ref|YP_135877.1| cell division inhibitor MinD-like [Haloarcula marismortui ATCC 43049]gi|55230752|gb|AAV46171.1| cell division inhibitor MinD-like [Haloarcula marismortui ATCC 43049]
+----------------------------------------------------------------------------------------------------
+---------------------------------------RTVLVSAPTRQSLTDTAKTAAIARALDAPPALTVLVGGDG-------S---vdp-SDLLSC
+SGTVHVPSV------------------
+>gi|154290868|ref|XP_001546023.1| hypothetical protein BC1G_15366 [Botryotinia fuckeliana B05.10]gi|150847185|gb|EDN22378.1| hypothetical protein BC1G_15366 [Botryotinia fuckeliana B05.10]
+---IMFVGLQ-GAGKTTTCTKLARWYQSRGFKACLV----CA-D----TFRAGAFDQLKQNATKAK----I-PYYGS---------L-TQTD-PAVVAKE
+GVDKFkKEKFEIIIVDTSGRHRQE---DALFQEMVDIQtavKpDQTVMVMDASIGqqAEAQS----KAF-KETADFGAIIITKTDGHASG--GGAISAVA
+ATHTPII------------------------
+>gi|153003842|ref|YP_001378167.1| cobyrinic acid ac-diamide synthase [Anaeromyxobacter sp. Fw109-5]gi|152027415|gb|ABS25183.1| Cobyrinic acid ac-diamide synthase [Anaeromyxobacter sp. Fw109-5]
+-RRIAFVNEKGGTCKTTLCVNVAAHLAGRGLRVLVadLDTQGhagKSLGVDVRGISPTIHDLLAGDLPLeavvvRTPVPGLD--LL--PANKELAGFpVA
+vaAAADRAERLARRLDGiPAGAYDAVLIDAPPSVSL-V---TENVLVAA--Y-ELVVPVALTylaLDGCAEIVQSLEAMRAargRAPALRLVVPTLY-RK
+TQLADEILARLRARFPAELSRtVLGWS------------------
+>gi|149240139|ref|XP_001525945.1| hypothetical protein LELG_02503 [Lodderomyces elongisporus NRRL YB-4239]gi|146450068|gb|EDK44324.1| hypothetical protein LELG_02503 [Lodderomyces elongisporus NRRL YB-4239]
+---ILILSGKGGVGKSSVTTQTALTLVNKGFRVGVLDIDLTGPSL-PRMFGVESKQVHQSVHGWVPVEvynsndtklgGSlklMSlGFLIGDRGNSVV--
+-WRGP-KKTAMIKQFLKDVVwsgndgEPLDYLLIDTPPGTSD---EHIAIAEELRYAQpiDGAIIVTTPQQVATADVRKEINFCKKVNFEILGIVENMSG
+ficPYcaecTNIFsSGGGKQMAETLQLAYLGNIPID-PL---------------
+>gi|9971822|gb|AAG10431.1| minD [Tagetes erecta]
+--PYPKPPPIRSVLQYNRKPELAGDTPRV----VAIDAD-VGLRNLDllLGLenrvnytvvevLNGDCRLDQALVR-DKRWSNFELLCISKPRSKL-PLG
+FGGKA--LVWLDALKDRQEGCPDFILIDCPAGIDAGFIT-----AITPA--NEAVLVTTPDITALRDADRVTGLLECDGIRDIKMIVNRVRTDLIRGEDM
+MSvlDVQEMLGLSLLS-DTRG------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * * * * * * * * 383 * * * * 3316 3313 4964 * * 1
+ 108 3797 * 1291 758 * * 6641 1100 0
+
+K 2 * * 6428 6598 * 5639 5099 5952 1794 6896 4292 3754 3853 3782 2183 4860 4185 5048 * 6816 2
+ 40 5756 6841 2766 229 * * 9806 1190 0
+
+R 3 3796 * * * 5497 5312 7119 2152 4859 4184 6196 5561 5799 6080 4083 3079 2768 2658 6807 * 3
+ 11 * 7047 1604 576 0 * 10185 1201 1044
+
+Y 4 7437 6138 * * 3718 * * 1154 * 2172 5580 * * * * 7490 5832 3012 * 3945 4
+ 0 * * 0 * 0 * 10265 1056 1056
+
+F 5 2707 4610 * 6198 3084 5249 * 4820 * 2958 3825 * 6089 7295 * 3236 3341 3110 7236 3942 5
+ 0 * * * * * * 10273 0 0
+
+V 6 7349 6168 * * 3137 * * 1650 6795 3241 5079 * * * * 6986 6443 1401 * 7557 6
+ 0 * * * * * * 10273 0 0
+
+T 7 2185 5391 * * 4535 3792 6215 3597 7306 3662 5430 * 5465 * * 3754 2275 3309 6321 5685 7
+ 0 * * * * * * 10273 0 0
+
+G 8 4115 6382 6956 * * 2043 6323 7065 * * 6333 2778 4153 6621 * 1367 4604 7306 * * 8
+ 25 7655 6342 0 * * * 10273 1055 0
+
+T 9 3937 6325 5499 5439 5162 3472 * 4669 6466 4106 * 4701 3249 3160 5696 3501 1960 5768 7596 7225 9
+ 19 * 6227 2807 222 0 * 10246 1001 1207
+
+D 10 4865 * 3468 4339 7510 3680 7267 4771 1124 6024 7383 4287 * 6967 4088 4015 5951 6528 6355 * 10
+ 24 7410 6550 1000 1000 0 * 10272 1000 1140
+
+T 11 6413 6295 7069 5461 7518 1022 6985 5528 4666 6972 6223 6018 3119 4961 5551 3558 3644 * * 6931 11
+ 0 * * * * 1216 812 10259 0 1165
+
+E 12 5092 * 3665 4389 5664 761 5588 * 6213 * 5721 4093 * 7402 5827 3663 7450 6937 * 7360 12
+ 0 * * * * 0 * 10277 0 1046
+
+V 13 3596 4670 6471 3600 7465 6990 * 4291 6390 6375 * 6299 6263 * 6025 2777 3428 1266 * * 13
+ 0 * * * * * * 10284 0 0
+
+G 14 7616 * 7086 6297 * 206 5968 * * 5620 7531 6967 * * * 5023 5185 * * * 14
+ 0 * * * * * * 10284 0 0
+
+K 15 7086 7496 * * * * * 7337 265 4862 * 6997 * 5877 4626 7287 5283 5904 * * 15
+ 0 * * * * * * 10284 0 0
+
+T 16 5029 * 7220 7310 7337 * * * 6575 * 6206 6303 * * 5737 1630 829 * * 6808 16
+ 0 * * * * * * 10284 0 0
+
+V 17 4420 7470 * 6607 4024 6983 5884 4983 7375 4826 5793 4513 5968 7147 * 2975 1130 3687 7302 5313 17
+ 0 * * * * * * 10284 0 0
+
+A 18 4092 5731 * * 4708 * * 2461 * 2199 5694 7375 * * 5967 4401 3145 1820 * * 18
+ 10 7220 * 1000 1000 * * 10284 1055 0
+
+S 19 1310 4402 * 5896 * 6862 * 5547 6808 4785 5760 * * * 7147 2493 2205 4736 * * 19
+ 0 * * * * * * 10284 0 0
+
+C 20 2509 4626 6359 6988 4627 5645 * 4011 5090 2061 4652 6269 6835 5826 5272 4450 3211 3227 7212 * 20
+ 9 * 7289 * * * * 10284 0 0
+
+A 21 3116 7702 * 5142 7614 2570 4031 6315 5769 4345 7655 1521 * 4729 5855 3992 5104 5753 * 5793 21
+ 0 * * 0 * 0 * 10277 1056 1056
+
+L 22 6460 * * 7519 5469 * * 2640 * 670 4867 * * * * * 4871 3712 * 5206 22
+ 24 6583 7319 0 * * * 10287 1120 0
+
+L 23 840 5059 * 6319 * 3187 * 5083 7387 4120 4716 * * * * 4132 5826 3586 * * 23
+ 7 * 7718 * * * 0 10270 0 1022
+
+Q 24 3075 6464 5878 4212 5753 4214 3817 4513 4281 4314 5754 5790 8080 4256 3396 4306 4120 3435 4732 3568 24
+ 0 * * 0 * 0 * 10263 1046 1180
+
+A 25 1984 4939 6124 4342 5334 4179 4991 4120 5921 3399 4899 * * 5474 5036 3350 4419 4024 7802 3766 25
+ 0 * * * * * * 10287 0 0
+
+A 26 3474 5874 * * 3012 * * 4989 6340 709 4420 * * * 7554 6419 6836 5979 7674 5643 26
+ 39 7510 5582 0 * * * 10287 1000 0
+
+K 27 1512 7224 7434 3984 6358 5196 5736 * 3850 4066 7129 5826 6361 3903 3939 3441 3816 4644 * 6112 27
+ 35 5839 7297 1024 976 1227 804 10272 1242 1426
+
+A 28 3807 * 4037 3123 * 5190 6782 5368 2724 3594 4969 4306 * 2798 2699 4465 5611 6377 * * 28
+ 27 * 5745 * * 1865 463 10272 0 1315
+
+A 29 3331 7161 6817 4080 4996 5577 5296 5860 2876 3431 5068 4543 * 3045 2481 4140 4696 5591 * 6291 29
+ 39 5805 6801 1431 669 919 1086 10281 1247 1538
+
+G 30 5094 7690 4281 4520 6355 681 6513 * 4651 5930 * 4368 * 5784 6738 4574 6615 6184 7424 5631 30
+ 40 5585 7233 531 1699 * 0 10264 1334 1368
+
+Y 31 4973 7086 5493 4882 4419 4950 3500 4331 2200 3640 5481 5240 5221 5299 4163 5042 4842 4415 5667 3307 31
+ 85 4219 8171 904 1103 841 1179 10258 1880 1621
+
+R 32 6694 * 4139 6071 * 5609 7201 7697 1536 6484 * 3757 4919 5457 1919 3753 4338 6297 * * 32
+ 36 6431 6260 1435 666 2245 342 10262 1272 1305
+
+T 33 4387 6456 * * 7240 7098 * 3684 6851 5063 * * 5779 * 7239 5084 3212 637 7544 * 33
+ 0 * * * * 1751 508 10255 0 1463
+
+A 34 2929 5055 7288 7233 7282 3008 5365 4295 6864 1527 4833 6490 * 5472 5133 5228 6000 3186 7246 6972 34
+ 0 * * * * * 0 10270 0 1295
+
+G 35 3917 6385 * * 3984 5498 * 2913 7306 1660 5083 * 4890 * * 6061 5659 2511 * 3219 35
+ 393 2069 * 1437 665 * 0 10270 4613 1295
+
+Y 36 4501 5712 * * 2669 5073 6482 2307 * 2245 4374 * * 7090 4523 6501 5526 2715 7547 4792 36
+ 78 4426 7416 2322 322 * 0 10270 1713 1295
+
+K 37 6282 * 937 5876 * 7229 4965 * 1975 7299 * 5833 * 5441 3605 6355 6206 * * * 37
+ 441 3213 2686 1439 664 1071 932 10261 2895 1411
+
+P 38 3133 5792 * * * 4929 4755 5738 5641 3335 5172 5643 1129 6207 5237 4001 5060 6338 6605 * 38
+ 159 4474 4069 0 * 4418 69 10073 1781 3961
+
+V 39 4202 * 2967 * 4616 4324 5716 2954 5910 4229 5028 5205 * 1873 6233 6396 4660 3233 * 7125 39
+ 159 4358 4166 202 2936 * 0 10055 1588 4587
+
+A 40 3416 5492 6933 5057 * 2570 5384 4144 4683 2805 4200 4643 4768 2862 4305 5964 4900 5019 * 6024 40
+ 154 3307 * 1942 435 426 1967 9989 2779 5152
+
+S 41 3299 5875 4880 7046 5319 4864 3585 6109 5210 4201 5997 3242 5283 4098 6439 3033 2345 4306 * 6078 41
+ 51 6557 5372 1197 827 1865 463 10246 1185 2209
+
+G 42 3395 6152 2962 4917 7143 1907 6194 5773 4722 4440 5990 4763 4903 5567 4561 3687 3670 5187 * 7225 42
+ 152 4474 4186 1543 606 3739 112 10180 1678 2296
+
+S 43 3903 4340 5030 5332 3951 5001 6082 4659 4872 2793 5569 4996 3052 5662 5008 3563 3160 3891 7223 7548 43
+ 251 6391 2759 1984 420 1182 839 10120 1105 3279
+
+E 44 5625 * 2754 4811 3960 4028 7509 3915 4502 4140 6230 3929 4402 3393 4019 3869 4216 4323 6370 5046 44
+ 249 4663 3072 1036 965 4267 77 10003 1886 4476
+
+K 45 4017 * 4110 4008 5101 3160 5086 4479 3761 3547 5095 4132 3952 6149 5370 3384 4532 3589 * 4954 45
+ 237 4126 3410 0 * * 0 9830 1663 5513
+
+T 46 4272 5503 3622 4527 3236 6903 6871 4170 4992 2984 4452 5217 4628 4197 4795 3779 3454 3899 * 5033 46
+ 579 3540 2030 1280 766 2864 213 9703 1934 6243
+
+P 47 3401 6680 2145 5036 6688 3871 4904 4950 3200 4330 6700 4424 4248 4768 4234 4510 3757 * * 5634 47
+ 466 2695 3038 2882 210 3090 180 9404 2560 7291
+
+E 48 4080 6495 3501 3719 4239 3683 5699 4297 5018 3558 6775 3570 3310 4589 3604 6133 4164 4042 * * 48
+ 208 3613 4246 309 2377 1657 550 9416 1780 7347
+
+G 49 3980 6846 3949 4803 6913 1238 5788 5858 3839 4687 5988 4244 5313 5388 6725 6013 4381 4584 * 5724 49
+ 173 4697 3750 606 1543 2281 332 9780 1467 6361
+
+L 50 4249 * 5578 5853 3855 4198 5801 4074 4130 1501 5070 5022 5591 4908 4511 4484 5860 4025 5964 * 50
+ 398 3231 2894 2140 371 3098 179 9832 2601 6074
+
+R 51 3468 6674 4014 3334 5036 3947 6664 4232 4414 3086 4745 3847 6678 5305 4781 3476 4032 3963 6413 6560 51
+ 233 4503 3252 1503 628 1778 497 9729 1731 6562
+
+N 52 4463 5620 2188 4155 5343 4166 5827 4454 3890 6642 * 2436 4968 5455 4610 4197 4201 4949 * 5971 52
+ 122 3622 * 1270 773 2302 327 9742 2025 6092
+
+S 53 3101 * 4183 3281 6656 3247 5470 6074 3835 3987 7160 4711 4868 4911 4149 3119 3807 3722 * 6907 53
+ 181 3599 4830 2214 350 1569 593 9907 2149 5317
+
+D 54 4122 * 1305 3839 7137 4371 5852 5716 4764 3668 6162 5811 5210 4966 5620 4387 4036 5203 * 6173 54
+ 185 3267 5924 697 1384 1108 900 10051 2615 4539
+
+A 55 2928 5391 5931 4631 5307 4326 6206 3974 4696 3121 6374 4781 5024 6190 4984 3225 3416 2998 * 4966 55
+ 226 2957 5949 1172 847 1034 967 10117 2916 3258
+
+L 56 4328 6066 2888 3122 6603 3191 5873 5672 4587 3849 5731 4707 5526 3407 3941 3765 5202 4491 7637 5088 56
+ 78 4920 5681 0 * 2336 318 10156 1523 2506
+
+A 57 3215 * 6460 * 3059 7422 5727 4135 5550 2156 7171 7231 5444 5787 5444 5239 4058 3212 3006 4759 57
+ 110 3889 7396 2508 279 922 1082 10173 2178 2539
+
+L 58 4601 7630 5467 6356 4140 5588 3723 2674 7463 2120 3715 5683 6417 5719 7588 4288 7368 3086 5278 4607 58
+ 82 5024 5351 1286 762 1357 714 10210 1586 1899
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+
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+L 224 * * * * * 1006 * * * 994 * * * * * * * * * * 224
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+
+//
+�HHsearch 1.5
+NAME 0895791d132888554de0d758d179b7c7
+FAM
+FILE 0895791d132888554de0d758d179b7c7
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:07:19 2013
+LENG 246 match states, 246 columns in multiple alignment
+FILT 110 out of 179 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCCCCCEEEEEEECCCCCEEEEEEECCCEEEEEEEECCEEEEECCCCHHHHHCCCCCCCC
+CEEECCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
+HHCCCCCCCCCCCEEECCCCCEEEEEEHHHHHHHHHHHHEEECCCC
+>ss_conf PSIPRED confidence values
+9489837997231999999999973758867993620799888877899999838999899999878789999998999899589964552056789987
+3588769999899998738870036307899999999996699078999999999997636652999999986312377898899999974999999999
+8538998658961365489988999667887886530511524789
+>Consensus
+xvxfxxxxatxxxYxxFIxxLRxxlxxxxxxxgipvlxxxxxxxxrxxxVxLxxxxxxxvtLaixxxnlYvvGfxxxxxxyxFxdxxxxxxxxxlfpxxx
+xxxxLxfxgsYxxLxxxagxxrxxixLGxxxLxxAixxLxxxxxxxxarxLlvxIqMvsEAaRFxxIxxxvxxxxxxxxxpxxxxxsLexnWxxlSxxIx
+xaxxxxgxfxxpvxLxxxxxxxxxvxxvxxxxxxxxxxlxxxxxxx
+>0895791d132888554de0d758d179b7c7
+DVSFRLSGADPRSYGMFIKDLRNALPFREKVYNIPLLLPSVSGAGRYLLMHLFNYDGKTITVALDVTNVYIMGYLADTTSYFFNEPAAELASQYVFRDAR
+RKITLPYSGNYERLQIAAGKPREKIPIGLPALDSAISTLLHYDSTAAAGALLVLIQTTAEAARFKYIEQQIQERAYRDEVPSLATISLENSWSGLSKQIQ
+LAQGNNGIFRTPIVLVDNKGNRVQITNVTSKVVTSNIQLLLNTRNI
+>gi|14578642|gb|AAK68928.1|AF219237_1 ribosome inactivating protein 2 precursor [Dianthus chinensis]
+TFTLDLARPTAAKYSSFLDQIRNNMRDPRLKYCsteIAVIKAPSVA-DKFLRINFQGP-RGTVSLGLARVNLYVVAYFAVDnrnvnRAYYFrtEINSA--
+ELRTVFPEVTvaNQRPLEYTEDYQSIEKNAKITtgdksRKELGLGIDLLISTIDKVNKKvrVVKDEARFLLIGIQMSAEAVRFRYIQNLVTRNFPKKFNS
+DNTVIQYQTSWGKISEAIHS-DCKNGKFNKDYNF-------------------------------
+>gi|391929|dbj|BAA02948.1| tritin [Triticum aestivum]
+TATFNVQASSA-DYVTFINGIRNKLRNPGHsSHNRPVLPPiePNVPPSRWFHIVLKTSPASTgLTLATRADNLYWEGFKSSDGTW-W------ELTPGLI
+PGAT---HVGFGGTYRDLLGDTD-KLTNVALGRQQMADAVTALYGRtkadktsgPKQQQAReAVTTLLLMVHEATRFQTVSGFVAGVLHpKekkSGKIGN
+EMKAQVNGWQDLSEALL--KTDAnappgkapAKF-TPI-------EKMGVRTAEQAAATLGILLFVQV---
+>gi|295701322|ref|YP_003610323.1| ribosome-inactivating protein [Burkholderia sp. CCGE1002]gi|295441645|gb|ADG20812.1| ribosome-inactivating protein [Burkholderia sp. CCGE1002]
+--EFSVDFTSPQKYVQSLGAIRAAMGDAMSLTNIPGnkilyqLRPDASNIVEGVTIEIIGvgrnnsPSNRDVRFVINPSDLYLTGFIVGRIFYRFSDFSD
+T-ASGRVQVNAPRhlvdfTIDMTVDSSYLSLARSAGVSADRTDLSIDRysLMKGyrdlINHVSSTrtINGAEARALLSYATVLSEAVRFRSIQGNFASTa
+LgDDAFTP--YRLSLEDsnrttRWDRLSDEIR--KAHYGAI----KIATHGAAPILLANVRD----------------
+>gi|326520397|dbj|BAK07457.1| predicted protein [Hordeum vulgare subsp. vulgare]
+----------------------------------------------LIVVELQGHNDDKSSVAVQKHDVSVAGFTDGSGQWHA--FPG---LEHLFPAST
+---TLPFGSSYSELIG--GiANLPGVPLGREAMMQAIRVLSAYrpgaDVEPVKRALAAVKVVISEAQRLEPIRKAVNDGWD-gESRVAPEHLPYIEHWDT
+MSYEILRSNRTgkwDGPFTKM----------------------------------
+>gi|254385328|ref|ZP_05000657.1| hypothetical protein SSAG_05020 [Streptomyces sp. Mg1]gi|194344202|gb|EDX25168.1| hypothetical protein SSAG_05020 [Streptomyces sp. Mg1]
+PVSFSVAHASVGDYRLLASSIRSRAALA---QCLPGRAGNEEVSARYLPVRIQLR-GLfielFIELRTQNSVLRITGFRNTFENW---QAPPEGRFRHVr
+davaPPGVHHAEALSFEGEVPALEAAAEVGRTGLSLGRRPMMKAVMWLHRNtDPKCTALGMLVLGEMLCEAASSPVLAQEMSR-----------------
+--------------------------------------------------------
+>gi|157108298|ref|XP_001650164.1| hypothetical protein AaeL_AAEL005004 [Aedes aegypti]gi|108879337|gb|EAT43562.1| hypothetical protein AaeL_AAEL005004 [Aedes aegypti]
+----------DRAYLGFIQNLISALTESDEVYgNIKVTKRK----DGITKVTLKDS-STnsQVGFIYRNRDLYIVGLVVGTTFYIDKEVYDGlgkkipTT
+WkGVINAAN--TVSLSNPFSYNQILPS----GEGTVLQIGKLGDSLTHLTKIgDtSKrsqIMTQHLGPFVVAFSEAIRFPVVAREIQGAIRKatgtvSLS
+knlvrplslghPsertsNhvFTMYSLLLNWSKLSDRVP----------------------------------------------
+>gi|334695920|gb|AEG80717.1| putative ribosome binding protein [Corynebacterium ulcerans 809]
+----------AKEYRDLLARIGNAVSH-PIVNGIGAIPENTATNAR-VDIEVLTSEGNAVTFHMLRRNMYIQAFTLSGTTYITSDAFG----RGLISG--
+--AGLPFSSDYASLGAHNtGNisDPTLFTVGGASLDTLLCNLFHAveNtqnfNRSAARALYAAAILFSEATRFSPSlgrniAQAIENGHPYnLTNADSEM
+I---RNWGQLSNwgraQLQ--SPNQPPFQ------------------------------------
+>gi|47496961|dbj|BAD20031.1| hypothetical protein [Oryza sativa Japonica Group]gi|47497865|dbj|BAD20039.1| hypothetical protein [Oryza sativa Japonica Group]
+-------RGTKNTYASLVSSIVTRITTRAMatVEGKPVCGPSG-----YFEIILFPkpgtqfaakHANGRVRLLFNYQNLYLVAFKVQGKWHKFKDLTPK
+I-----APDYAsikrkkhcEAKNLPFESNYGVRGMAANLaqlkVSRQTPLQIYKM----LSLYDPehnagmvRLSDLQKMLFKTCAVFPEVFRFPLLKKR
+VVYLMgktAdEESTVGEQHTDLFQNWGDCCMALRM--GR-QAFTPMADL-------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 5094 0 0
+
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+ 0 * * * * * * 5524 0 0
+
+S 3 * * * 2984 6627 5882 * 5994 5312 * * 3672 5764 * 3762 1769 1670 5188 * * 3
+ 116 6366 3937 1000 1000 * * 5905 1000 0
+
+F 4 * 5640 * * 434 * * 5205 * 2479 * * * * * * * * 5851 5955 4
+ 23 5987 * 0 * 0 * 6014 1355 1279
+
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+ 0 * * * * * * 6069 0 0
+
+L 6 5271 5552 * * * * * 3748 * 1674 6389 * 5697 5897 * * 2425 1662 * 6078 6
+ 22 * 6078 * * * * 6076 0 0
+
+S 7 2874 * 2605 3400 * 3409 5160 6437 4424 4707 * * 5926 4235 5334 3052 3443 3664 * * 7
+ 80 5803 4805 0 * 0 * 6068 1017 1012
+
+G 8 5202 * 4345 4966 4144 2226 4625 * 3920 6407 * 3091 6248 * 3780 3022 2705 * * 5429 8
+ 85 6248 4495 614 1528 0 * 6194 1059 1092
+
+A 9 1201 6500 6083 6098 5972 4107 * 6394 4855 4429 * * 3936 * * 2845 3543 5434 * 4495 9
+ 13 * 6854 * * 992 1008 6256 0 1089
+
+D 10 6265 * 3129 5555 * 4197 * * 5075 * * 4431 * * 5090 2701 981 5552 * 6692 10
+ 36 * 5325 * * * 0 6316 0 1065
+
+P 11 2746 5599 4312 3573 * 3403 6623 5536 3389 * * 5959 3064 4131 4029 3418 6635 3517 5751 6553 11
+ 106 5290 4456 549 1660 0 * 6530 1057 1208
+
+R 12 3766 * 3378 3690 * 2835 * 5818 2936 5795 * 3751 5793 3203 4440 3081 4460 * * 4805 12
+ 14 * 6717 * * 701 1377 6689 0 1209
+
+S 13 4330 * 3376 4729 * 3987 5804 5653 3494 * * 3929 5074 5428 4842 2072 2269 5162 * * 13
+ 17 6401 * 0 * 0 * 6721 1013 1105
+
+Y 14 * * * * 4698 * * * * * * 5704 * 6124 * * * * * 108 14
+ 0 * * * * * * 6762 0 0
+
+G 15 3554 * 6306 4274 6505 4114 * 5908 3979 4687 * 3744 4981 5488 2765 2385 2922 3968 * * 15
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+K 30 * * 3911 2553 5257 6288 3966 5011 4023 2778 4833 4350 3880 6783 4158 4485 4206 3922 * 4647 30
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+
+V 31 3457 4679 8473 6894 4081 * 5425 3070 6016 4182 6890 * 4673 6543 3976 2030 * 2309 * 5784 31
+ 125 3586 * 1466 649 0 * 6795 1893 1564
+
+Y 32 4191 3518 5006 3733 7052 5486 1712 * 6695 5695 * 4077 5353 3944 * * 4806 6400 * 2386 32
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+
+N 33 * 5917 3306 4622 * 969 * * 5826 6831 * 2308 * 7215 * 4518 4604 * * 6473 33
+ 89 4066 * 1368 707 0 * 6862 1349 1000
+
+I 34 * 6268 * * 5588 * 5678 965 4882 2564 4753 5935 * * 3838 6400 5289 3824 * * 34
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+
+P 35 5195 * 8667 * 6238 5934 * 5794 4122 6884 * 5245 608 5279 4356 4928 6930 4956 * 5236 35
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+
+L 36 4584 * * * 6943 4493 * 3368 5664 2999 4017 * * * 4864 6857 5787 886 * * 36
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+
+L 37 5777 4336 * * 6328 6227 * 3459 * 779 4216 * * * 5917 5973 3092 6299 * 5928 37
+ 103 4881 4838 1161 855 0 * 6862 1306 1000
+
+L 38 2783 * 5268 5382 * 4522 6604 * 3324 5468 * 4426 2065 6599 2155 5011 5284 4505 * 7072 38
+ 4 8643 * 0 * * 0 6823 1000 1196
+
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+
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+
+V 41 3714 * 5035 4529 6601 4119 * 4056 5158 3162 * 5663 3311 5071 * 5066 2638 2128 * 6291 41
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+
+S 42 3162 * 3633 2765 * 4440 * 6332 5291 4549 6952 4223 2855 3405 5711 2995 4210 5209 * 6154 42
+ 427 3881 2410 207 2902 1993 417 6471 1368 2410
+
+G 43 3992 * 2574 3850 * 3976 * 3713 4522 6182 * 4023 3133 3741 * 3344 3395 4085 * * 43
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+
+A 44 4695 6315 3473 5017 * 4747 * 6070 4621 4582 * 3450 1466 4684 6765 2717 5068 6658 * * 44
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+
+G 45 2255 * 3651 3589 6456 4598 * * 4064 * 6286 3666 3412 2760 3455 4771 5498 5408 6876 * 45
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+
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+
+Y 47 * * * * 1563 5240 6943 4814 * 3796 * 6435 * 6271 * 5530 * * 2231 1942 47
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+
+M 50 4080 * * * 6779 6800 * 2023 * 3539 6023 * 5660 * * 5791 5208 970 * * 50
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+H 51 4691 * 2730 2620 * 6092 4157 3524 3857 * * 3089 6617 4483 3098 6268 3972 4177 * * 51
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+Q 198 1311 5096 6161 3575 5209 4725 * * 6232 4892 4648 * 6859 2906 4992 6054 5373 4060 5316 5605 198
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+N 205 5521 * 4091 5592 5332 3645 5670 * 2690 4767 * 2714 4971 4943 3818 5848 3099 3321 * 4040 205
+ 286 4639 2838 1437 665 * 0 6287 1104 1076
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+N 206 4745 2914 3278 4675 * 3080 * * 4695 * * 1924 * 2640 6177 4774 * 6127 * 4564 206
+ 150 3652 5724 1537 610 134 3490 6029 1656 1805
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+R 210 3144 * 5124 4339 * 5665 * 6499 5031 3928 * 3799 3073 3929 5247 2299 2352 * * * 210
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+P 212 3944 * 5051 * * * * 6412 4354 4431 4500 6444 987 * 3481 3956 4340 4869 * * 212
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+ 76 * 4277 * * 858 1158 5940 0 1104
+
+V 214 4129 * 3427 3243 5213 5214 * 6563 3567 5856 * 5060 * 2249 3778 4027 3227 3370 * * 214
+ 50 4888 * 1000 1000 * 0 5912 1089 1242
+
+L 215 * * 5396 * 4600 * * 2916 * 458 * 5213 5577 * * 6254 * * * 6188 215
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+
+V 216 4492 5901 * 6036 * 3321 * 2774 4408 4156 * 5952 * 1676 4010 4390 4197 4480 * 4804 216
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+
+D 217 * * 2380 * * 5121 * 5798 4759 5474 * 2064 * 5751 3335 3585 2832 5819 5478 3625 217
+ 27 5773 * 1000 1000 2529 275 5527 1000 1374
+
+N 218 3225 * 4520 2430 * 5399 4988 4689 5924 4060 * 6001 3031 4325 4805 2642 4402 4409 * 6031 218
+ 0 * * * * * 0 5547 0 1297
+
+K 219 6134 * 2835 3407 * 2734 * * 5029 * 5540 2018 5792 6385 5073 2662 3901 5839 * * 219
+ 49 * 4898 * * * 0 5547 0 1297
+
+G 220 4963 4910 3527 5808 4055 1624 6000 * 5906 6078 * 2849 5425 4148 * * * 5631 * 2647 220
+ 29 * 5665 0 * 556 1646 5453 1000 1380
+
+N 221 5043 * 3546 2644 * 4956 6082 6078 3023 * * 2960 5645 3141 4431 3295 3166 5809 * * 221
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+R 222 * * 5814 4563 4279 * * * 3314 6031 * 5845 1774 5697 3772 5776 2385 3753 4795 4309 222
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+
+V 223 4622 * * 5796 2966 5562 * 2484 5197 4462 3965 * * * 4866 * 4353 2846 2256 4465 223
+ 26 * 5803 * * 2014 410 5478 0 1419
+
+Q 224 * 7960 5989 3778 6070 4433 5862 3428 3938 3016 * 3220 * 4507 4990 5019 3502 3360 4111 3473 224
+ 0 * * * * 911 1094 5498 0 1375
+
+I 225 * * * 5790 4782 * * 2803 5488 4413 4528 * * * * * 4947 698 * 4611 225
+ 56 4710 * 0 * 1570 593 5657 1089 1137
+
+T 226 3992 * 2741 5377 4668 5008 6114 * 4535 6057 * 2851 * * 4716 3173 1925 * 4617 5108 226
+ 133 6114 3767 1585 585 845 1173 5660 1012 1065
+
+N 227 3996 * 4237 4931 * 5681 * * 5105 * 5833 1649 * 3371 4365 3130 2271 * * * 227
+ 104 3841 * 1459 652 233 2743 5640 1527 1341
+
+V 228 3693 * 6011 * 4248 * * 4930 * 5141 3742 * * * * 5723 5972 548 * * 228
+ 137 * 3461 * * * 0 5619 0 1000
+
+T 229 3030 * 3312 2608 * 4536 * * * * * 4202 5383 5832 3216 2133 3885 5222 * 4513 229
+ 25 5867 * 365 2162 2973 197 5567 1420 1411
+
+S 230 4925 * 2547 1589 * 5266 4593 5682 4243 4972 * 5367 * 3106 4695 3704 5826 5739 * * 230
+ 325 3861 2912 1105 902 2567 267 5564 1534 1350
+
+K 231 1772 * 5244 * * 5035 * 3994 5097 2063 * 5422 3228 * * 5108 * 2643 * * 231
+ 0 * * * * * 0 4775 0 1633
+
+V 232 3078 * * * * * * 2694 3349 3553 * * * 4725 3112 * 4396 1674 * 5093 232
+ 0 * * * * 0 * 4775 0 1633
+
+V 233 3206 * * * * * * 5342 4829 3722 * 5376 2395 3887 3925 4348 3713 1821 * * 233
+ 174 * 3141 * * * * 4992 0 0
+
+T 234 2496 * 4837 * 5075 5454 * 5468 2634 4253 5288 4224 * 3626 4115 4172 2780 5018 * 4341 234
+ 86 4940 5292 1503 628 0 * 4759 1349 1279
+
+S 235 4560 5157 * * * 3216 * 2330 5259 1828 4103 5144 4466 5603 * 3698 * 3541 * * 235
+ 0 * * 0 * * 0 4757 1000 1000
+
+N 236 1302 * * * * 2087 * 5245 3812 5009 * 3044 * * * 3903 * 4560 * * 236
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+
+I 237 5270 * * * 4879 * * 1283 * 1492 3317 * * * * * * 3765 * * 237
+ 0 * * * * * * 4759 0 0
+
+Q 238 3008 * * * * 3265 * 5230 4342 1676 1720 * * 3658 * * * * * * 238
+ 0 * * * * * * 4671 0 0
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+L 239 * * * * * * * 4708 4232 280 * * * * * * * 3558 * * 239
+ 0 * * * * * * 4610 0 0
+
+L 240 * * * * 1348 5392 5229 * * 1590 4545 * * * * * * * * 2461 240
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+L 241 5072 * * 4873 3961 4405 * 5512 4772 1653 5392 * * 4853 3482 * * 1869 5230 * 241
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+
+N 242 4414 1239 5228 4551 * * * * * * * 2999 5230 4604 2909 7016 5392 * * 3287 242
+ 369 4331 2508 0 * * * 4671 1013 0
+
+T 243 3582 * * * 4949 * * 5131 2513 4423 4605 3198 * 4798 3220 3675 3090 3212 * 4763 243
+ 278 2513 * 966 1035 320 2331 4380 1509 1366
+
+R 244 4125 * 3718 * * 3671 5078 5072 4693 4819 * 4641 1789 * 3243 3241 3916 * * 4392 244
+ 227 2780 * 3322 152 0 * 4234 1000 1012
+
+N 245 1631 1742 * * * * * * * * * 2120 * * 2754 * * * * * 245
+ 0 * * * * * * 2649 0 0
+
+I 246 * * * * * * * 1908 * * * * * * * 1178 3083 2527 * * 246
+ 0 * * 0 * * * 2422 0 0
+
+//
+�HHsearch 1.5
+NAME 094af3c04fcdf9bf04bb55a97a19581b
+FAM
+FILE 094af3c04fcdf9bf04bb55a97a19581b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:18:37 2013
+LENG 56 match states, 56 columns in multiple alignment
+FILT 164 out of 1036 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCHHHHHHHHHCCCCCEEEEECCCC
+>ss_conf PSIPRED confidence values
+97413458878878888887871676995832898999998455997588753679
+>Consensus
+xxxxxxxCxxxxxxxCxxxxxPVCGsdgxTYxNxCxlcxxxcxxxxxixixxxGxC
+>094af3c04fcdf9bf04bb55a97a19581b
+LAAVSVDCSEYPKDACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC
+>gi|125986399|ref|XP_001356963.1| GA16452 [Drosophila pseudoobscura pseudoobscura]gi|54645289|gb|EAL34029.1| GA16452 [Drosophila pseudoobscura pseudoobscura]
+-----IQADddlsaekdgqtlRKFCP-CPRNYDPVCASNMVTYPNRCEYdCvRREaERRGRNLGFLRSGQC
+>gi|118360802|ref|XP_001013632.1| hypothetical protein TTHERM_00829290 [Tetrahymena thermophila]gi|89295399|gb|EAR93387.1| hypothetical protein TTHERM_00829290 [Tetrahymena thermophila SB210]
+-----GKCEDYHPEAnfcspaenrvenCTNDVDISCAYFnknikcfvppcTIQIENRCQACV-----------------
+>gi|149029561|gb|EDL84759.1| Kazal type serine protease inhibitor 5-like 2 [Rattus norvegicus]
+-----VKLSWFNKTvdPCPGLKQPICGTNFVTYDNPCILCVESF-LGDRLDITTLEDF
+>gi|118371371|ref|XP_001018885.1| hypothetical protein TTHERM_00463880 [Tetrahymena thermophila]gi|89300652|gb|EAR98640.1| hypothetical protein TTHERM_00463880 [Tetrahymena thermophila SB210]
+---QTFLCEENDRSankLCTDIFEPVCGIKqpnlqggkpiRATFSSHCNACK-----DSSVVFVAQGAC
+>gi|148678060|gb|EDL10007.1| mCG127182 [Mus musculus]
+-DPAKLNCESFKQrrkdgdFICPSDTSSVCGTDGKTYRSRCELCAENAKSQNHVDVKSEGEC
+>gi|189235796|ref|XP_970472.2| PREDICTED: similar to Mahya [Tribolium castaneum]
+--------------QCAVHRRLVCGSDGHVYPNHCELHRASCMTATDITVERGVH-
+>gi|296226165|ref|XP_002758813.1| PREDICTED: follistatin-related protein 1-like [Callithrix jacchus]
+--------------SQRKESPPVSASS------------NACLTGSKIQVDYDGHC
+>gi|327279944|ref|XP_003224715.1| PREDICTED: insulin-like growth factor-binding protein 7-like [Anolis carolinensis]
+---------------------------SLSTPTSVIAANIALLqhdlGTICLTMKLKPVI
+>gi|195453090|ref|XP_002073634.1| GK13027 [Drosophila willistoni]gi|194169719|gb|EDW84620.1| GK13027 [Drosophila willistoni]
+-----GSCRHCDAP-CPNIYSPICANRngiNYTIINKCYLERVRCKDPNsSWKIIKDSEC
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+L 1 * * * * * * * * * 0 * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+A 2 1121 * 2462 2363 * * * * * * * * * * * * 2605 * * * 2
+ 0 * * * * * * 2523 0 0
+
+A 3 2713 * * * * * * 2999 * 3153 * * 1700 * * 2736 2718 * * * 3
+ 0 * * * * * * 3119 0 0
+
+V 4 1822 * * * * 4811 * 2974 * 4594 * * * 2001 3364 4800 * 2943 * * 4
+ 0 * * * * * * 4824 0 0
+
+S 5 4922 * * 2123 * 5212 * * 2631 5038 3418 2858 * 3695 5033 3396 3568 * * * 5
+ 0 * * * * * * 5306 0 0
+
+V 6 3823 * 6018 5452 5689 2421 * 2702 * 4077 * 5425 2465 * * * 4576 2148 * * 6
+ 0 * * * * * * 6136 0 0
+
+D 7 4849 * 2665 3197 * * * 4886 2319 5806 * 2713 3895 4026 3948 3961 6349 5377 * * 7
+ 104 3852 * 582 1591 * * 6182 1189 0
+
+C 8 5949 266 * * * * * * 5934 4805 * * * 5921 * * 3965 5672 * * 8
+ 13 * 6788 * * * * 6180 0 0
+
+S 9 4322 5666 4238 2123 * 5048 * * 3515 * * 4870 3597 3666 4602 2277 3791 6088 * * 9
+ 268 3465 3663 2387 306 0 * 6195 1282 1000
+
+E 10 4340 6187 4026 2118 * 6230 3837 5097 2813 * 4324 5985 4112 4683 5278 3771 4546 5142 4113 * 10
+ 29 * 5646 * * 2186 358 5820 0 1169
+
+Y 11 5316 2890 4805 6214 3000 * 6172 * 4538 6242 4060 4437 4338 * 5212 4985 * 5876 * 1456 11
+ 0 * * * * 2012 411 5781 0 1177
+
+P 12 5781 5347 3735 4267 6420 4401 * 4752 3483 5544 6329 3152 2037 4710 3132 5645 6202 5109 * 4653 12
+ 192 3003 * 1075 929 * 0 5818 1306 1120
+
+K 13 3899 4160 4609 4363 4691 3842 * 5026 2926 4660 * 4671 3892 4604 3224 3340 5120 3717 5731 * 13
+ 211 3146 5451 2536 273 * 0 5761 1419 1120
+
+D 14 4719 * 4572 2627 4578 5660 6238 6029 3849 5426 5883 4391 2833 3428 4816 4226 3735 3942 * 4372 14
+ 667 2536 2337 1612 572 0 * 5631 1852 1207
+
+A 15 2451 5015 6022 5577 5399 3453 5768 3983 4265 4152 5416 5935 3587 4879 4951 3745 4295 3143 * 5880 15
+ 147 3371 * 2993 194 0 * 6686 1448 1752
+
+C 16 6114 204 6828 * * * 6777 6313 * * * 5356 * 5680 * 5785 * 5326 * * 16
+ 68 4711 7037 887 1123 * * 6585 1150 0
+
+T 17 4367 * 4683 5247 * 4382 7686 5345 4736 5200 6298 5586 1753 5402 4810 3360 2010 * * 6776 17
+ 49 5098 7901 1650 553 0 * 6596 1128 1000
+
+L 18 4966 5381 3848 3657 4912 4498 * 4811 3062 5039 3323 3648 4960 4853 3165 4353 3960 5816 * 4530 18
+ 66 4481 * 1198 826 * 0 6619 1211 1047
+
+E 19 4939 * 3929 2356 5432 6916 4221 3025 5886 3720 5672 3364 6681 3976 4978 4101 4582 3928 * 5781 19
+ 83 4153 * 619 1519 * 0 6986 1265 1047
+
+Y 20 5281 * 4184 4558 3239 6078 5743 6233 5216 3461 7499 5581 6084 4858 4202 3983 5489 6031 5125 1527 20
+ 16 6524 * 1130 881 605 1545 6986 1078 1047
+
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+
+P 22 4337 * * 5826 * * 5789 6603 6812 4830 6162 * 464 5420 6291 4950 6755 5721 7447 5701 22
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+
+L 23 5727 * * * 5787 * * 2734 6596 3660 * * * 5506 5384 6735 6838 601 * * 23
+ 0 * * * * * * 7109 0 0
+
+C 24 * 43 * * * * * * * * * * * * * 6041 * * * 6172 24
+ 0 * * * * * * 7109 0 0
+
+G 25 2275 6163 4908 6296 * 500 * * * * * * * * * 5255 * * * * 25
+ 29 5670 * 282 2494 * * 7109 1073 0
+
+S 26 4937 7188 5660 4628 * 5892 6832 4262 4993 * 7188 4321 5488 5772 * 1403 2006 5631 5506 5365 26
+ 72 4370 * 1859 465 * * 7109 1405 0
+
+D 27 5342 * 981 6223 4434 7290 * * 5244 6223 * 2171 7269 6341 5610 4141 5354 6848 * 6415 27
+ 259 2746 6041 2975 196 * * 7109 2116 0
+
+N 28 4994 * 5961 6723 6357 1001 5858 * 4467 5007 6394 2703 5843 6125 5027 4271 6559 5697 * 5155 28
+ 7 7740 * 1585 585 * 0 7157 1000 1065
+
+K 29 6143 6905 * 4496 7438 6726 4897 2967 2379 4173 6187 4536 * 4412 2865 4752 5801 2341 * 6022 29
+ 12 6897 * 2807 222 * 0 7157 1000 1065
+
+T 30 * * 5030 5015 6174 * * 6465 * 5161 6287 3792 * 5561 * 3145 656 5379 7030 * 30
+ 21 6126 * 759 1290 * 0 7156 1031 1065
+
+Y 31 * * * 6589 3130 6115 5737 6600 * * * * * * * 5565 6193 6423 * 348 31
+ 0 * * * * * 0 7156 0 1065
+
+G 32 3216 6905 3341 3847 4494 3355 7148 5044 5152 7408 6950 4591 3406 4649 3681 2925 4503 6807 5760 4739 32
+ 29 * 5675 * * * 0 7156 0 1065
+
+N 33 * 6588 4707 * * 6103 5806 * * * * 536 * 6481 * 2555 4391 * * * 33
+ 0 * * 0 * 1028 972 7196 1060 1176
+
+K 34 3444 * 6156 1942 5281 4950 4529 5104 3858 4406 7383 6589 3187 4700 3284 4773 6185 4526 6855 5824 34
+ 0 * * * * * 0 7156 0 1065
+
+C 35 6733 142 * * 6752 6512 * * * * * * * 6785 6061 7057 5740 6193 * * 35
+ 29 * 5675 * * * 0 7156 0 1065
+
+N 36 4353 * 5616 3010 4448 5772 3084 3624 4622 3145 4116 5324 6588 4166 4841 3936 4856 4157 * 4315 36
+ 15 6588 * 468 1852 1028 972 7196 1130 1176
+
+F 37 2585 * * * 2886 5117 4758 5545 * 1153 3481 * * * * * 6115 4459 * 6407 37
+ 271 2729 5635 0 * * 0 7156 2014 1065
+
+C 38 4521 1198 4975 3969 6643 7044 4064 6607 3784 6012 7486 4783 * 4557 3109 7455 5039 6269 * * 38
+ 37 5849 6993 513 1740 1374 704 7150 1160 1241
+
+N 39 2729 5272 5205 4136 5100 7487 6986 4322 3913 3966 4889 3888 * 4061 3324 3282 3559 4107 * 6709 39
+ 79 * 4227 * * 1389 694 7155 0 1251
+
+A 40 1947 * 3762 2426 5291 4557 4413 6012 4414 5380 6247 4991 * 4679 4523 5379 4913 4973 7155 4152 40
+ 41 5798 6687 0 * 3881 101 7271 1120 1743
+
+V 41 2107 * 7215 4043 * 5440 6741 3847 3747 5813 5452 2489 * 4941 3717 3100 4466 5532 * 6225 41
+ 83 4165 * 327 2304 2692 243 7281 1407 1777
+
+V 42 4252 1069 * 4786 6874 6328 6166 4540 4886 3201 4735 6297 * 5025 4806 5239 6291 5019 5613 7152 42
+ 103 4449 5431 1427 671 4104 86 7286 1241 1654
+
+E 43 4985 5620 4979 2870 7520 5699 * 6061 2549 2840 5476 3816 5437 4599 2742 4609 4909 5074 6601 6984 43
+ 179 3968 4248 1727 519 2626 255 7117 1348 1781
+
+S 44 4147 * 4755 4650 6062 4104 6727 5597 3463 4514 6588 3261 5729 3357 4138 2729 2989 5257 * 4714 44
+ 92 4484 5867 1327 734 487 1804 6832 1178 1980
+
+N 45 5674 * 3585 3689 * 1984 5760 5289 3560 7564 * 3418 4232 3202 3567 5335 4237 * * 6054 45
+ 36 5934 6906 1285 762 680 1411 6923 1044 1367
+
+G 46 5186 6554 4766 3743 6871 3674 5147 4215 3261 7016 5899 4879 4306 4024 3095 2938 3349 4694 * 5484 46
+ 46 5003 * 0 * 374 2131 6878 1169 1213
+
+T 47 4878 5435 3815 3624 * 4772 4789 7240 2889 6735 6225 2993 4772 3614 3763 3014 3452 6394 * 6804 47
+ 68 4444 * 544 1671 0 * 6922 1220 1009
+
+L 48 5954 * * * 4370 * * 1495 * 1762 5940 6690 * * * 6226 5540 2540 5011 5497 48
+ 43 6492 5798 1000 1000 * * 6927 1011 0
+
+T 49 4753 * 3575 2953 6308 5128 4867 5194 3901 4289 7405 5275 6504 3409 3463 3562 2754 4244 * 5992 49
+ 0 * * 0 * 0 * 6947 1060 1060
+
+L 50 5467 6677 * 5920 3322 * 6638 1791 3450 3456 3768 6226 6641 5615 * * 6229 2262 * 5040 50
+ 14 6718 * 0 * * * 6927 1000 0
+
+S 51 2997 * 4098 5052 5620 7062 * 4208 2486 3448 4778 6064 * 5249 4253 5012 3919 2721 * 4177 51
+ 0 * * * * * * 6927 0 0
+
+H 52 4465 6141 4750 * 7232 5017 1636 7051 3244 5437 6726 5400 7070 4794 4064 3119 6121 5304 * 3100 52
+ 0 * * * * * * 6905 0 0
+
+F 53 5779 * 2578 3038 5176 7503 4732 4843 3307 3754 5125 3878 6190 4965 3709 3769 5391 5635 5071 4448 53
+ 0 * * * * * * 6905 0 0
+
+G 54 7172 * 7311 4419 * 388 6625 * 5547 6911 * 5920 5059 * 6752 3939 7263 * 6894 * 54
+ 0 * * * * * * 6905 0 0
+
+K 55 3447 * 4617 2558 6420 * 4705 5144 3265 5702 6061 4620 2455 * 3232 4348 4999 4108 * 6219 55
+ 8 7578 * 1585 585 * * 6905 1000 0
+
+C 56 * 84 * * 6061 * * 5407 * * * * * * * * * * * 5779 56
+ 0 * * 0 * * * 6854 0 0
+
+//
+�HHsearch 1.5
+NAME 09ce670d46e49ba58915a7017daeb51d
+FAM
+FILE 09ce670d46e49ba58915a7017daeb51d
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:38:49 2013
+LENG 242 match states, 242 columns in multiple alignment
+FILT 141 out of 795 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEECCCCCCCCCEEEECCEEECCCCEEEECCCCCCCCCCEEEEEECCCEEEECCCCCCCCEEEEEEEEEEECCCCCCCCCEEEEEECCCCCCC
+CCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEECCCCCEEEEECCCCCCCCEEEEEEEEECCCCEEEEEEECCCCCCCEEEEEEE
+CHHHHCCCCEEEEEEEECCCCCCCEEEEEEEEEEEEECCCCC
+>ss_conf PSIPRED confidence values
+9764358980899988888799165087449808802588865474489986898685648998721279999999860799888846999925888787
+5677772343366777776768999985544776556899998587853883121232146679988999999948987999999518999733899974
+379938874799999741898763026999999998720379
+>Consensus
+xxxxxxsfxfxxFxxxxxxlxlxGxAxixxxxxlxLTxxxxxxxxxxGxvxyxxpvxlxxxxxxxxxsFstxFxFxIxxxxxxxgDGlAFxlxpxxxxxx
+xxxxGxxlGlxxxxxxxxxxxxxAVEFDTxxNxxxxxxDpxxnHigixxnsxxsxxxxxxxlxxgxxxxvxIxYdxxxxxLxVxlxxxxxxxxxxlxxxi
+dLxxxlxxxxyvGFSAsTGxxxxxxxhxIxsWsFxxxlxxxx
+>09ce670d46e49ba58915a7017daeb51d
+NLSDDLSFNFDKFVPNQKNIIFQGDASVSTTGVLQVTKVSKPTTTSIGRALYAAPIQIWDSITGKVASFATSFSFVVKADKSDGVDGLAFFLAPANSQIP
+SGSSAGMFGLFSSSDSKSSNQIIAVEFDTYFGKAYNPWDPDFKHIGIDVNSIKSIKTVKWDWRNGEVADVVITYRAPTKSLTVCLSYPSDGTSNIITASV
+DLKAILPEWVSVGFSGGVGNAAEFETHDVLSWYFTSNLEANN
+>gi|255579110|ref|XP_002530403.1| carbohydrate binding protein, putative [Ricinus communis]gi|223530052|gb|EEF31973.1| carbohydrate binding protein, putative [Ricinus communis]
+---PIYTLSLETLiTSNrnfDPQTVLLGNATISGNGsSVQLT---TPNASSSGLLLYKNPFRLHSSTPSKPMSFSTEFEFSFTGN---LI-GLSLVMGPF
+NFVSnFM---G--QGAVDS---VNKKGYLGIEFGYSRDGN------DGNSTKILV--LIRVNNEPLGhvwTERGQRMKAWIDYDASSKRIEIRINELNGK
+RPYdpFAAYALDLSKMWSDnEAFVVLGSNDgG--NPSGTCNVYSWRFRL------
+>gi|326492602|dbj|BAJ90157.1| predicted protein [Hordeum vulgare subsp. vulgare]
+-----WQFVLNGF--AGANLTLGGTSMVLPNGLLMLTN-GA-TRKMKGHAFHPSPLPFGSgsNGAGPLRSFSTTFVLAIFghGRHAdLSVRGLSFLISAS
+WEVLSTALSGQPLGLSN----gNQNASIFAMEFDTLYNAQF--SDTKNKYVGVDGDSLVSLNSASIGNyddgtgrllnlsvISWKAIQVWVDYDSKATVI
+TMTMAPLGvvRPKQPMLQTTIDLSGVVQSTAYVGFSSAMS--NITSGHFILGWSFA-------
+>gi|281211734|gb|EFA85896.1| hypothetical protein PPL_01128 [Polysphondylium pallidum PN500]
+-------YNYELL--TRSKLNLIGNCKILS-DRIELTPR---QNDQVGAFWVKDKLKVTD-----------GFVVRIKFINEmGGADGMAFVLHNHSADV
+IG-KRGSGLGY------DGIENSLAVEFDSYSSVDSC-ADPNGNHISIHCNGERKNSSHhqhSlahampVdnvPINDGRIHHAAITYNANSKTMSVWYDS
+FN----ILTDVSVDLDTLLdlPnGEAWIGMTASTG--GLCQSHHILSFEFG-------
+>gi|308081648|ref|NP_001183315.1| hypothetical protein LOC100501716 [Zea mays]gi|238010732|gb|ACR36401.1| unknown [Zea mays]
+---HVDSFSYPTFDATtTQDLVAATNTSILTSASLLFGHDAdFNFNRTEGFILLSRTVDVWRAGPGggpaREASFNTSFALSGAA-------PVAYVVLR
+DSY-PPLHGTGGLRGFANYSasdaEDgatprNASSGLASVEVGPVRS-----YGPDDPAVGLNVTVT-PTGG---TAPGG--GgggggarAVWIEYDAAK
+HRLSVYVAAAGepRPAAALLDARLGLAGrRTTETAMVGFFASAI--Q-DVLVGVRDWNLTV------
+>gi|300175631|emb|CBK20942.2| unnamed protein product [Blastocystis hominis]
+------------------rNWQCTGDGIVN-EYFVRLTPD---RQSKNGV--------LWADNTFNKGEFVTTIKFRISGQGSsLFGDGFAVFFTKHRS-
+PIP---GKMYSLTDV------YYGFAVVFSTFRNTEFSRYhrDIaiylgdgysnaftqDKDHTGCYAR-Y-RFHEKRQDFSVDNYAVVKIGYSESTGLVR
+VAIDEKNTGK-FTTCFTEAthFEPGWWREATIGISATTG--QLADNHDILSVETVE------
+>gi|134109915|ref|XP_776343.1| hypothetical protein CNBC5610 [Cryptococcus neoformans var. neoformans B-3501A]gi|50259017|gb|EAL21696.1| hypothetical protein CNBC5610 [Cryptococcus neoformans var. neoformans B-3501A]
+----------------NQALVTFGDAHWDG-STIVLTTG----NSQTSAVFHPHPIDQSD-------TFSCTVTFRLTSPPGaGEADGISIIFVPKKA-L
+GLGGyGLGYSGLGGK-------GDFAVEVDTYRTQDYA-DDPPTPHISVHsppdahhRNSIGCTAPGTLpKLSNGKEHKLQILYRGEDRRVRGYLTISSE
+gSvKdeTDIEVFDIVVPSGnEQKPWFIGVTGSCG--GLWQKQEIIDWSLQL------
+>gi|257875308|ref|ZP_05654961.1| predicted protein [Enterococcus casseliflavus EC20]gi|257809474|gb|EEV38294.1| predicted protein [Enterococcus casseliflavus EC20]
+------------------------------------------TSSVSGGVWFNKAVSFT-------RSFRLEMAFCIENT-ATDSDGLAFVMQSSGLNAL
+AQQAGPTIGVWSNTGGtNplntgAIPQSFAIEFDTFYNSGslgvhgAMDRDaPNSHHIAWNFPGSnDAYTTEGWlptykvvnhkdlvavsDISDSQWHTF
+TVTFDQPNQTLHYSVPDFGvDvtvPVDDTFKTNLNLTN--NAPVYFGFTGANG--GNVQ-----------------
+>gi|224088190|ref|XP_002308362.1| predicted protein [Populus trichocarpa]gi|222854338|gb|EEE91885.1| predicted protein [Populus trichocarpa]
+----GHSFRYPTFHEdSQTDFISHNSAIVL--NAIQATPNvkGDSIAIFSGCALYRKQFKLWAGKGRVRATLNSTFVLGISPQTKPGGEGITFILTADS-
+GLPE------------------------------------------------------------------------------------------------
+---------------------------------------------
+>gi|323347643|gb|EGA81908.1| Uip5p [Saccharomyces cerevisiae Lalvin QA23]
+--------------------HVGGATQIRNIQSIKLTQDRD--QDKHGLV-------LSNGIgDNTINDFEIVFTFRISHDPtTqLTGDGMCFAITPENG
+FLTQNlqsSYakKQYMmnsqGVIADNTDlmgFPKNlPGLFIVLDTYRNQGhdhkevpFMdvfiNVAPESDWYDINSDGELSTSLrlnsRghiKLkkNALW
+NRVTKLRIIYLESISFLKIDVQYAKE-GNYWIElFQTTENLYLPKnmhtgQRYIGCSALNG--QLTETVELLD-----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
+L 2 2757 * 4549 * 4371 * 4483 * * 3333 * * * 4508 4389 1217 4473 4318 * * 2
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+
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+
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+
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+
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+
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+ 104 5157 4584 378 2118 1307 747 7460 1136 1911
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+ 92 4188 7149 1970 425 909 1098 7450 1455 1866
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+T 45 5947 * 3191 5079 4597 3791 4569 6070 * 5394 7129 2349 4645 5848 4166 2218 4831 6049 5399 4475 45
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+S 46 5241 7029 * 5097 8203 4965 * * 2954 5027 7122 6454 4846 1843 4416 1755 4403 6193 * 7541 46
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+
+I 47 2916 4855 * 5459 5183 4844 4529 4138 6147 5137 5748 5772 * * 3694 2378 3519 2454 5556 7040 47
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+G 48 6561 6361 6313 * * 196 * * * * * * * * * 3559 7192 * * * 48
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+R 49 3473 6476 * * 5518 4154 4003 6790 * 5141 * 6861 * 4662 1484 2678 4060 5280 4435 5199 49
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+I 58 5242 * * * 2350 * * 3407 * 1147 4100 * * 5478 * 4824 7289 3198 * * 58
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+V 66 2923 * 5140 4058 4735 5159 6339 4306 6181 3149 4923 3857 4666 5634 4707 5168 4371 2006 * * 66
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+
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+ 49 * 4917 * * * * 7128 0 0
+
+N 237 5114 * 5069 4361 5964 5843 * * 2998 5857 * 3358 * 5057 4107 2003 2294 5695 * 4097 237
+ 26 5833 * 0 * 910 1096 6194 1000 1084
+
+L 238 * * 5444 * 3018 4371 * 5570 * 913 3883 * * * 4277 5320 * 5804 5566 3846 238
+ 90 4050 * 1627 564 0 * 5904 1072 1000
+
+E 239 5147 * 3423 2059 * 4792 5303 4481 3957 * * 5128 2761 3405 5063 5120 3308 4721 * * 239
+ 234 2742 * 0 * * * 5356 1002 0
+
+A 240 2512 * * * * * * * * * * 2541 * * * 1556 1677 * * * 240
+ 0 * * * * * * 2708 0 0
+
+N 241 * * * * * * * * * * * 0 * * * * * * * * 241
+ 0 * * * * * * 1000 0 0
+
+N 242 * * * * * * * * * * * 0 * * * * * * * * 242
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 0a209425cf52d1e9fc937e5aed5d7d69
+FAM
+FILE 0a209425cf52d1e9fc937e5aed5d7d69
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:45:15 2013
+LENG 169 match states, 169 columns in multiple alignment
+FILT 10 out of 12 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCHHHHHHHHHHHHH
+HCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCEEEEECC
+>ss_conf PSIPRED confidence values
+9866645789517999999998711999999999999971797654276665689999999999999866034499997612767679999999999998
+756988999999999986699877520123027999999986038751248679999970976976059
+>Consensus
+mxxxxxihxnpxRxeWxxKIaxLxtxxxaxaxlxdFRxxxtsPfrxsyxldxdxxwIExkIEervavLkxxxxxdxxllxkxxxGxdaxxVxxxxxakxx
+axxdxyEaErIxixFRxxxKPPvmPvNxFlxtdrxLgtkLMelRnxdYyxxpLeeLRkxRGvxvixlqx
+>0a209425cf52d1e9fc937e5aed5d7d69
+MAKREPIHDNSIRTEWEAKIAKLTSVDQATKFIQDFRLAYTSPFRKSYDIDVDYQYIERKIEEKLSVLKTEKLPVADLITKATTGEDAAAVEATWIAKIK
+AAKSKYEAEAIHIEFRQLYKPPVLPVNVFLRTDAALGTVLMEIRNTDYYGTPLEGLRKERGVKVLHLQA
+>gi|269980465|gb|ACZ56338.1| putative soluble di-iron monooxygenase gamma subunit [Mycobacterium chubuense NBB4]
+-----madetrsgrrrargqesvgaefrlepsPYGNTALRSDWAARAESLSDLDDAVATLMNYRSDR------wg--SEDQDSLWIEARLEERVAVLR-l
+QSMTDEEFRTRTLTGEDARHVCTDVAGRVAAAGDDYgEIERINDEFRSKYKPPVMPANLFLPTERDLSEKLMKTRTVDWYGKSLGELREERGVV------
+>gi|217977449|ref|YP_002361596.1| methane monooxygenase [Methylocella silvestris BL2]gi|74381912|emb|CAJ26294.1| protein A-gamma subunit of soluble methane monooxygenase [Methylocella silvestris BL2]gi|217502825|gb|ACK50234.1| Methane monooxygenase [Methylocella silvestris BL2]
+MPNYK-IHENPVRSDWLEKIAELKSVKDATAFIQDFRKKNTSPFRTSYALDVDYLFIEAKIEERLAVLKSSTFSAADLFTKATTGETAQAVSEDWIAKID
+AEKDKFAAEKILITFRQLYKPPVLPVNLFFKVDTYLGSRLMELRNTDYYADSLDDLRKKRGVKVLRLGN
+>gi|53804672|ref|YP_113663.1| methane monooxygenase subunit A, gamma chain [Methylococcus capsulatus str. Bath]gi|19855848|sp|P11987.4|MEMG_METCA RecName: Full=Methane monooxygenase component A gamma chain; AltName: Full=Methane hydroxylasegi|13399579|pdb|1FZ4|E Chain E, Methane Monooxygenase Hydroxylase, Form Iii Soaked At Ph 8.5 (0.1 M Tris)gi|13399580|pdb|1FZ4|F Chain F, Methane Monooxygenase Hydroxylase, Form Iii Soaked At Ph 8.5 (0.1 M Tris)gi|13399585|pdb|1FZ5|E Chain E, Methane Monooxygenase Hydroxylase, Form Ii Crystallized Anaerobically From Reduced Enzymegi|13399586|pdb|1FZ5|F Chain F, Methane Monooxygenase Hydroxylase, Form Ii Crystallized Anaerobically From Reduced Enzymegi|13399591|pdb|1FZ7|E Chain E, Methane Monooxygenase Hydroxylase, Form Iii Soaked In 0.9 M Ethanolgi|13399592|pdb|1FZ7|F Chain F, Methane Monooxygenase Hydroxylase, Form Iii Soaked In 0.9 M Ethanolgi|13399724|pdb|1FYZ|E Chain E, Methane Monooxygenase Hydroxylase, Form Ii Reduced By Soakinggi|13399725|pdb|1FYZ|F Chain F, Methane Monooxygenase Hydroxylase, Form Ii Reduced By Soakinggi|13399730|pdb|1FZ0|E Chain E, Methane Monooxygenase Hydroxylase, Form Ii Mixed-Valent Grown Anaerobicallygi|13399731|pdb|1FZ0|F Chain F, Methane Monooxygenase Hydroxylase, Form Ii Mixed-Valent Grown Anaerobicallygi|13399736|pdb|1FZ1|E Chain E, Methane Monooxygenase Hydroxylase, Form Iii Oxidizedgi|13399737|pdb|1FZ1|F Chain F, Methane Monooxygenase Hydroxylase, Form Iii Oxidizedgi|13399742|pdb|1FZ2|E Chain E, Methane Monooxygenase Hydroxylase, Form Ii Mixed-Valent Generated By Crystal Soakinggi|13399743|pdb|1FZ2|F Chain F, Methane Monooxygenase Hydroxylase, Form Ii Mixed-Valent Generated By Crystal Soakinggi|13399748|pdb|1FZ3|E Chain E, Methane Monooxygenase Hydroxylase, Form Iii Soak At Ph 6.2 (0.1 M Pipes)gi|13399749|pdb|1FZ3|F Chain F, Methane Monooxygenase Hydroxylase, Form Iii Soak At Ph 6.2 (0.1 M Pipes)gi|14278259|pdb|1FZ6|E Chain E, Methane Monooxygenase Hydroxylase, Form Ii Soaked In 1 M Methanolgi|14278260|pdb|1FZ6|F Chain F, Methane Monooxygenase Hydroxylase, Form Ii Soaked In 1 M Methanolgi|14278265|pdb|1FZ8|E Chain E, Methane Monooxygenase Hydroxylase, Form Ii Cocrystallized With Dibromomethanegi|14278266|pdb|1FZ8|F Chain F, Methane Monooxygenase Hydroxylase, Form Ii Cocrystallized With Dibromomethanegi|14278271|pdb|1FZ9|E Chain E, Methane Monooxygenase Hydroxylase, Form Ii Cocrystallized With Iodoethanegi|14278272|pdb|1FZ9|F Chain F, Methane Monooxygenase Hydroxylase, Form Ii Cocrystallized With Iodoethanegi|14278277|pdb|1FZH|E Chain E, Methane Monooxygenase Hydroxylase, Form Ii Pressurized With Xenon Gasgi|14278278|pdb|1FZH|F Chain F, Methane Monooxygenase Hydroxylase, Form Ii Pressurized With Xenon Gasgi|14278283|pdb|1FZI|E Chain E, Methane Monooxygenase Hydroxylase, Form I Pressurized With Xenon Gasgi|14278284|pdb|1FZI|F Chain F, Methane Monooxygenase Hydroxylase, Form I Pressurized With Xenon Gasgi|66360573|pdb|1XU5|E Chain E, Soluble Methane Monooxygenase Hydroxylase-Phenol Soakedgi|66360574|pdb|1XU5|F Chain F, Soluble Methane Monooxygenase Hydroxylase-Phenol Soakedgi|66360581|pdb|1XVB|E Chain E, Soluble Methane Monooxygenase Hydroxylase: 6-Bromohexanol Soaked Structuregi|66360582|pdb|1XVB|F Chain F, Soluble Methane Monooxygenase Hydroxylase: 6-Bromohexanol Soaked Structuregi|66360587|pdb|1XVC|E Chain E, Soluble Methane Monooxygenase Hydroxylase: 8-Bromooctanol Soaked Structuregi|66360588|pdb|1XVC|F Chain F, Soluble Methane Monooxygenase Hydroxylase: 8-Bromooctanol Soaked Structuregi|66360593|pdb|1XVD|E Chain E, Soluble Methane Monooxygenase Hydroxylase: 4-Fluorophenol Soaked Structuregi|66360594|pdb|1XVD|F Chain F, Soluble Methane Monooxygenase Hydroxylase: 4-Fluorophenol Soaked Structuregi|66360601|pdb|1XVE|E Chain E, Soluble Methane Monooxygenase Hydroxylase: 3-Bromo-3- Butenol Soaked Structuregi|66360602|pdb|1XVE|F Chain F, Soluble Methane Monooxygenase Hydroxylase: 3-Bromo-3- Butenol Soaked Structuregi|66360607|pdb|1XVF|E Chain E, Soluble Methane Monooxygenase Hydroxylase: Chloropropanol Soaked Structuregi|66360608|pdb|1XVF|F Chain F, Soluble Methane Monooxygenase Hydroxylase: Chloropropanol Soaked Structuregi|66360613|pdb|1XVG|E Chain E, Soluble Methane Monooxygenase Hydroxylase: Bromoethanol Soaked Structuregi|66360614|pdb|1XVG|F Chain F, Soluble Methane Monooxygenase Hydroxylase: Bromoethanol Soaked Structuregi|67464472|pdb|1XU3|E Chain E, Soluble Methane Monooxygenase Hydroxylase-Soaked With Bromophenolgi|67464473|pdb|1XU3|F Chain F, Soluble Methane Monooxygenase Hydroxylase-Soaked With Bromophenolgi|7770067|gb|AAF04157.2| soluble methane monooxygenase hydroxylase component gamma subunit [Methylococcus capsulatus]gi|53758433|gb|AAU92724.1| methane monooxygenase, A subunit, gamma chain [Methylococcus capsulatus str. Bath]
+-----MaklgIHSNDTRDAWVNKIAQLNTLEKAAEMLKQFRMDHTTPFRNSYELDNDYLWIEAKLEEKVAVLKARAFNEVDFRHKTAFGEDAKSVLDGTV
+AKMNAAKDKWEAEKIHIGFRQAYKPPIMPVNYFLDGERQLGTRLMELRNLNYYDTPLEELRKQRGVRVVHLQspH
+>gi|2098698|gb|AAC45292.1| soluble methane monooxygenase protein A gamma subunit [Methylocystis sp. M]
+MAKREPIHENSTRTEWEGKIAKLNSVEQATKFIQDFRVAYSSPFRKSYDLDVDYQYIERKIEERLSVLKTEKLSVADLITKATTGEDPAAVEATWVAKMK
+SAASKYEAERIHIEFRQLYKPPVLPVNVFLRTDAALGTILMGVRNTDYYATPLEGLRKERGVKVLHLQA
+>gi|41019262|gb|AAR98537.1| butane monooxygenase gamma subunit [Brachymonas petroleovorans]
+MMAEH-WYHTPVRDEWLEKIAALRTVQEGIAMLQQFRKEHTGPDRLTYELKKEANWIESRIEMRVAQLHSEaTIANAALLEKTIDGRDPVEITEEWLKKA
+EDIDCPIEMQRLCTAYRKAWKPPMMPINYFAPVEKKLVSKLLKLRAPNYLTTPVEELRKLHNATLISVQ-
+>gi|89572585|dbj|BAE86878.1| methane monooxygenase hydroxylase component gamma subunit [Methylomicrobium japanense]
+------manykIHDNPVRDEWVKKIGALSSLAKGVQFLKDFREQYTTPLRKSFDLELDWGWIELKIEQKLALLKHKEMNDAQILNKNADGTDAQQLANQV
+LASMDRCNDKWEAEKIHIQFRQQWKPPLMPVNVFQDTDRLLGNKLMELRNANYYDMPLEELRKARGVNVVTLQ-
+>gi|333983360|ref|YP_004512570.1| methane monooxygenase [Methylomonas methanica MC09]gi|333807401|gb|AEG00071.1| Methane monooxygenase [Methylomonas methanica MC09]
+------manIHDNPTRNAWMAKIATLDTMAKAHAFLTDFRARHMSPFKTDWSLELDGLWIELKIEEKLALLKHKEFNDSQLLNNCSCGADAQQVANAAIA
+KMEACEDMYEAERIHINFRLACKPPVMPVNVFLDTDRQLGTKLMELRNTDYYALPLEALREKRGAKVIRLQ-
+>gi|306921974|dbj|BAJ17648.1| soluble methane monooxygenase hydroxylase component gamma-subunit [Methylovulum miyakonense]
+------mpnIHDNPKRAEWANKIAGLKTLAQGHAFLKDFRAQHVSVFKTDFSLELDWLWIELKIEEKVAVLKQAEFSDHQLLNVCTCGTDAQKVANDALA
+AMAACEDMYEAERIHINFRLACKPPVMPVNVFLDTDRQLGTKLMELRNTDYYALPLEELRKARGVRVVTLQ-
+>gi|21239749|gb|AAM19730.1| butane monooxygenase hydroxylase BMOH gamma subunit [Thauera butanivorans]
+MSKQV-WYNTPVRDEWIEKITAIRTAREGTDMLARFRAEHTGPDRTTYDLKKEYNWIESRIEMRVSQLHAEaTASDEDLLTKTIDGRCAKEVAAEWLKKA
+ADIDCHYEMERLCVAFRKACKPPMMPINFFAPAEKELVAKLMKLRAPTYLTTSLDELREARGVTMISVQ-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1969 0 0
+
+A 2 1509 * * * * * * * * * 2133 * 2282 * * 2218 * * * * 2
+ 0 * * * * * * 1969 0 0
+
+K 3 2133 * * * * * * * 820 * * 2282 * * * * * * * * 3
+ 0 * * * * * * 1969 0 0
+
+R 4 * * * 2133 * * * * * * * * * 2218 1509 * * * * 2282 4
+ 0 * * * * * * 1969 0 0
+
+E 5 * * * 1509 * * 2133 * 2282 * * * * * * * * 2218 * * 5
+ 1509 * 625 4755 54 * * 1969 1063 0
+
+P 6 * * * * * * * * * * 1880 * 457 * * * * * * * 6
+ 457 1880 * 1926 441 0 * 1799 1404 1388
+
+I 7 * * * * * * * 680 * * * * * * * * * * 2040 2913 7
+ 0 * * * * * * 2534 0 0
+
+H 8 * * * * * 2913 680 * * * * * * * * * * * * 2040 8
+ 0 * * * * * * 2534 0 0
+
+D 9 * * 1519 2470 * * 2944 * * * * 2023 * * * 3400 * * * * 9
+ 0 * * * * * * 2534 0 0
+
+N 10 * * * * * * * * * * * 680 * * * * 1411 * * * 10
+ 0 * * * * * * 2534 0 0
+
+S 11 2913 * 3400 * * * * * * * * * 717 * * 2606 * * * * 11
+ 0 * * * * * * 2534 0 0
+
+I 12 * * * * * * * 3614 3600 2913 * * * * * * 1915 1191 * * 12
+ 0 * * * * * * 2534 0 0
+
+R 13 * * * * * * * * * * * * * * 0 * * * * * 13
+ 0 * * * * * * 2534 0 0
+
+T 14 3600 * 1202 * * * * * * * * 3510 * * * 2116 2606 * * * 14
+ 0 * * * * * * 2534 0 0
+
+E 15 2454 * 2116 769 * * * * * * * * * * * * * * * * 15
+ 0 * * * * * * 2534 0 0
+
+W 16 * * * * * * * * * * * * * * * * * * 0 * 16
+ 0 * * * * * * 2534 0 0
+
+E 17 2216 * * 2606 * * * 3143 * 2134 3510 * * * * * * 2384 * * 17
+ 0 * * * * * * 2534 0 0
+
+A 18 1726 * * 1552 * 3598 * * 3367 * * 2497 * * * * * * * * 18
+ 0 * * * * * * 2534 0 0
+
+K 19 * * * * * * * * 206 * * * * * 2913 * * * * * 19
+ 0 * * * * * * 2534 0 0
+
+I 20 2913 * * * * * * 206 * * * * * * * * * * * * 20
+ 0 * * * * * * 2534 0 0
+
+A 21 606 * * 2913 * 3367 * * * * * * * * * * 3143 * * * 21
+ 0 * * * * * * 2534 0 0
+
+K 22 1556 * * 3353 * 3600 * * 2606 * * * * 3400 * 2913 3510 * * * 22
+ 0 * * * * * * 2534 0 0
+
+L 23 * * * * * * * 3143 * 173 * * * * * * * * * * 23
+ 0 * * * * * * 2534 0 0
+
+T 24 * * 3510 * * * * * 2471 * * 2496 * * 2040 2122 3614 * * * 24
+ 0 * * * * * * 2534 0 0
+
+S 25 * * 2913 * * * * * * * * * * * * 1478 977 * * * 25
+ 0 * * * * * * 2534 0 0
+
+V 26 3143 * * * * * * * * 1297 3510 * * * * * * 1351 * * 26
+ 0 * * * * * * 2534 0 0
+
+D 27 1904 * 2221 2496 * * * * 3353 * * * * 2944 3143 * * * * * 27
+ 0 * * * * * * 2534 0 0
+
+Q 28 * * 2116 2040 * * * * 1839 * * * * 2019 * * * * * * 28
+ 0 * * * * * * 2534 0 0
+
+A 29 792 * * * * 1243 * * * * * * * * * * * * * * 29
+ 0 * * * * * * 2534 0 0
+
+T 30 3400 * * * * * 2554 2944 * * * * * * * * 1414 2122 * * 30
+ 0 * * * * * * 2534 0 0
+
+K 31 913 * 3143 3400 * * * * 2606 * * * * 3367 * * * * * * 31
+ 0 * * * * * * 2534 0 0
+
+F 32 * * * * 918 * * * * * 1565 * * * * * 2913 * * * 32
+ 0 * * * * * * 2534 0 0
+
+I 33 * * * * * * * 1931 * 439 * * * * * * * * * * 33
+ 0 * * * * * * 2534 0 0
+
+Q 34 3143 * * * * * * * 1867 * 2913 * * 1351 * * 3510 * * * 34
+ 0 * * * * * * 2534 0 0
+
+D 35 * * 918 * * * * * * * * 2913 * 2154 3143 * * * * * 35
+ 0 * * * * * * 2534 0 0
+
+F 36 * * * * 206 * * * * * * * * * * * * * * 2913 36
+ 0 * * * * * * 2534 0 0
+
+R 37 * * * * * * * * * * * * * * 0 * * * * * 37
+ 0 * * * * * * 2534 0 0
+
+L 38 1819 * * 3367 * * * * 2134 3614 3400 * * * * 2913 * 3598 * * 38
+ 0 * * * * * * 2534 0 0
+
+A 39 2606 * 2136 2040 * * * * 3353 * * * * 2479 3510 * * * * * 39
+ 0 * * * * * * 2534 0 0
+
+Y 40 * * * * * * 977 * * * * 3353 * * 2913 * * * * 1937 40
+ 206 * 2913 * * * * 2534 0 0
+
+T 41 * * * * * * * * * * 3325 * * * * 3416 492 3392 * * 41
+ 0 * * * * * 0 2342 0 1063
+
+S 42 * * * * * 1840 * * * * * * * * * 1006 2167 * * * 42
+ 0 * * * * * 0 2342 0 1063
+
+P 43 * * * * * * * * * * * * 144 * * * * 3392 * * 43
+ 0 * * * * * 0 2342 0 1063
+
+F 44 * * 1840 * 715 * * * * 3168 * * * * * * * * * * 44
+ 0 * * * * * 0 2342 0 1063
+
+R 45 * * * * * * * * 2358 * * * * * 313 * * * * * 45
+ 0 * * * * * 0 2342 0 1063
+
+K 46 * * * * * * * * 1735 2770 * 3165 * * * * 1179 * * * 46
+ 0 * * 1000 1000 * 0 2342 1063 1063
+
+S 47 * * 2358 * * * * * * * * * * * * 928 1840 * * * 47
+ 0 * * * * * 0 2342 0 1063
+
+Y 48 * * * * 2276 * * * * * * * * * * * * * 3325 528 48
+ 0 * * * * 0 * 2342 0 1063
+
+D 49 3353 * 1417 2154 * * * * * * * * * * * 1722 * * * * 49
+ 0 * * * * * * 2534 0 0
+
+I 50 * * * 2913 * * * 3614 * 348 * * * * * * * * * * 50
+ 0 * * * * * * 2534 0 0
+
+D 51 * * 1030 1904 * * * * 2040 * * * * * * * * * * * 51
+ 0 * * * * * * 2534 0 0
+
+V 52 * * * * * * * * 2040 1904 * 3400 * 2913 * * * 1931 * * 52
+ 0 * * * * * * 2534 0 0
+
+D 53 * * 402 2040 * * * * * * * * * * * * * * * * 53
+ 0 * * * * * * 2534 0 0
+
+Y 54 2944 * * * * 3510 * * * * * * * * * 2913 * * 2479 1089 54
+ 0 * * * * * * 2534 0 0
+
+Q 55 * * * * * 3367 * * * 1013 * 2040 * 2606 * * * * * * 55
+ 0 * * * * * * 2534 0 0
+
+Y 56 * * * * 3353 * * * * * * * * * * * * * 439 2606 56
+ 0 * * * * * * 2534 0 0
+
+I 57 * * * * * * * 0 * * * * * * * * * * * * 57
+ 0 * * * * * * 2534 0 0
+
+E 58 * * * 0 * * * * * * * * * * * * * * * * 58
+ 0 * * * * * * 2534 0 0
+
+R 59 1620 * * * * * * * * 1904 * * * * 2606 2040 * * * * 59
+ 0 * * * * * * 2534 0 0
+
+K 60 * * * * * * * * 680 * * * * * 1411 * * * * * 60
+ 0 * * * * * * 2534 0 0
+
+I 61 * * * * * * * 372 * 2136 * * * * * * * * * * 61
+ 0 * * * * * * 2534 0 0
+
+E 62 * * * 0 * * * * * * * * * * * * * * * * 62
+ 0 * * * * * * 2534 0 0
+
+E 63 * * * 600 * * * * * * 2040 * * 3367 * * * * * * 63
+ 0 * * * * * * 2534 0 0
+
+K 64 * * * * * * * * 1173 * * * * * 846 * * * * * 64
+ 0 * * * * * * 2534 0 0
+
+L 65 * * * * * * * * * 1162 * * * * * * * 854 * * 65
+ 0 * * * * * * 2534 0 0
+
+S 66 469 * * * * * * * * * * * * * * 1850 * * * * 66
+ 0 * * * * * * 2534 0 0
+
+V 67 * * * * * * * * * 2437 * * * 2040 * * * 806 * * 67
+ 0 * * * * * * 2534 0 0
+
+L 68 * * * * * * * * * 0 * * * * * * * * * * 68
+ 0 * * * * * * 2534 0 0
+
+K 69 * * * * * * 2040 * 680 * * * * * 2913 * * * * * 69
+ 206 * 2913 * * * * 2534 0 0
+
+T 70 2033 * * * * * 2244 * * * * * * 3392 * 1942 2403 * * * 70
+ 0 * * 0 * 0 * 2342 1063 1063
+
+E 71 3600 * * 1295 * * * * 2437 * * * * 2913 3400 3353 * * * * 71
+ 402 2040 * 0 * * * 2534 1229 0
+
+K 72 3400 * * 1904 * * * * 2606 * * * * * * 2913 1552 * * * 72
+ 0 * * * * * * 2534 0 0
+
+L 73 3143 * * * 1463 * * 2944 * 2606 2122 * * * * * * * * * 73
+ 0 * * * * * * 2534 0 0
+
+P 74 2944 * * * * * * * * * * 1839 3614 * * 1411 2913 * * * 74
+ 0 * * * * * * 2534 0 0
+
+V 75 3353 * 963 3400 * * * * * * * 2944 * * * * * 2606 * * 75
+ 0 * * * * * * 2534 0 0
+
+A 76 1032 * * 2023 * * 3600 * * * * * * * * 3510 * 3400 * * 76
+ 0 * * * * * * 2534 0 0
+
+D 77 2944 * 1089 2913 * * * * * * * * * 1904 * * * * * * 77
+ 0 * * * * * * 2534 0 0
+
+L 78 * * * * 2136 * * 3367 * 566 * * * * * * * * * * 78
+ 0 * * * * * * 2534 0 0
+
+I 79 * * * * 3353 * * 2606 * 970 * * * * 2136 * * * * * 79
+ 0 * * * * * * 2534 0 0
+
+T 80 * * * 2944 * * 3400 * * * * 1904 * * * * 977 * * * 80
+ 0 * * * * * * 2534 0 0
+
+K 81 * * * * * * * * 521 * * 3510 * * 2913 * * 3600 * * 81
+ 0 * * * * * * 2534 0 0
+
+A 82 1931 2554 * * * * * * * * * 3367 * * * * 1087 * * * 82
+ 0 * * * * * * 2534 0 0
+
+T 83 2384 * * * * * * 2040 * 2913 * * * * * 3510 1537 * * * 83
+ 0 * * * * * * 2534 0 0
+
+T 84 * 2554 1556 * 3400 * * * * * * * * * * * 1340 * * * 84
+ 0 * * * * * * 2534 0 0
+
+G 85 * * * * * 0 * * * * * * * * * * * * * * 85
+ 0 * * * * * * 2534 0 0
+
+E 86 3510 * * 1030 * * * * * * * * * * 2040 * 2479 * * * 86
+ 0 * * * * * * 2534 0 0
+
+D 87 * 3143 342 * * * * * * * * * * * * * 3353 * * * 87
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+
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+Q 168 * * * * * 3137 * * * * * * * 174 * * * * * * 168
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+A 169 1191 * * * * * 1743 * * * * 1926 * * * * * * * * 169
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+
+//
+�HHsearch 1.5
+NAME 0a407d4b0634f8fa863191382dd9ec39
+FAM
+FILE 0a407d4b0634f8fa863191382dd9ec39
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:34:18 2013
+LENG 210 match states, 210 columns in multiple alignment
+FILT 125 out of 1191 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEECCCCEEEECCCCEEEEEEEECCCCEEEEEECCCCCCCEEEEEECCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCEEEEEEECCCEECCCEE
+EEEEEECCCEEEEECCCCEEEECCCEEEEEEEEECCCCCCCEEEEEECCEECCCCCCCCEEEEECCCCCEEEEEEEEECCCCHHHCCEEEEEEECCCCCC
+CEEEEEECCC
+>ss_conf PSIPRED confidence values
+9399953873899889989999998279848999993899984799981254576668617888628748999940461049589999974733624379
+9999602430689628860785498099999992577999789999999997677531002586289838878999993489887918999999589985
+4899994789
+>Consensus
+xxxxxxxxxxxxxxxGxxvxLxCxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxLxIxxxxxxDxgxYxCxxxxxxxxxxxxx
+lxvxxxxxxpxvxxxxxxxxxxxgxxxxLxCxxxxxxpxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxsxLxixxxxxxdxgxyxCxxxxxxxxx
+xxxxxxxxxx
+>0a407d4b0634f8fa863191382dd9ec39
+QIVSTQSPAIMSASPGEKVTMTCSASSSRSYMQWYQQKPGTSPKRWIYDTSKLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCHQRSSYTFGGGTK
+LEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSS
+PVTKSFNRGE
+>gi|148691347|gb|EDL23294.1| mCG141185 [Mus musculus]
+----------------------------------------------------------------------------------------------------
+-------------WSHEYCSG---PRRSAKYMNFPIVPircPQTHVTHHRNGKNHTQDM-ELPDTRPAGDGTFQKWAAVLVPSGE---ELRYTGHVYHER
+LPEPLTLKWGK--
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+-------------------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne--DLRSWTAADMAAQN-----------------tqrkwe
+aagvaeqw----RAYLEGECLEWLRRYLEKGK------------------et--LQ--raePs-SQ
+>gi|62464905|gb|AAX83161.1| immunoglobulin heavy chain variable region [Aotus nancymaae]
+---------------GDPVPHLRCLWLLhrQ------willeldpPAPKGRG--WSGldisivwWVHql-qrlpQES-----sh---YFsrHVQEPVLVE
+---------A------------------------------------------------------------------------------------------
+-------------------------------------
+>gi|47227730|emb|CAG08893.1| unnamed protein product [Tetraodon nigroviridis]
+---------------GGTLVIPCNtgAIKAedILITKWKYDKGDGLSGDLLVRQ-rsqnasiIANDEYKGRVSM---AANSSLLLSDAKLSDQRTFTCMA
+VVGaNIAEYPVNVVVYKKPTELKISDKAEELEIGKLTKV-GVF------NAK-CCFYLRNFRHLKHQGktrisIHTSVLIDAMTGLSTTSSTLEYSAKKE
+DTNAQFTC---R---------------
+>gi|321457503|gb|EFX68588.1| hypothetical protein DAPPUDRAFT_63008 [Daphnia pulex]
+----------VTVQLGDTAFLNCRVLDLqDKTVSWVRRH-EQELHLLTVGMQTYSTD--SRFSLHfQHPNDWRLQIKFARPRDEGIYECQVSIHPPRIYT
+VRLIVAV----PSVEMVDDHGRVIEekiyktGSTIELKCVVSKVPGPTANIMWRHGLRILNYDTSRGGISVKTDLLPYGAVSRLYIANASQRDAGNYTCN
+ISESSWTTVVVHILNGEH
+>gi|149597420|ref|XP_001520231.1| PREDICTED: similar to butyrophilin [Ornithorhynchus anatinus]
+QFSVIGPAEPVLALEGGDTEMPCHLNPKesaeFMEVRWFRSRPSNIV--HLYDNREELFREqmeeyQGRteLVRDaMDYGSVAVRLLNVRVSDEGNYHCS
+FYDGNTVDRAPlELQVVGSTAQCSIFMEHF-----SWISLILDLFP-DWIPDlfP-ILQMRelSEGGVNIKCP--KSYGIGHTCTMFSLddifgnfisap
+lfptaLSLMVALGVT---LPVLGLIIAGglyLIWKQNMDIEKLLVklT
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+Q 1 4413 * 1466 4564 * 4625 4227 * * 3219 4595 * 4647 2538 4279 4557 * * * * 1
+ 0 * * * * * * 6618 0 0
+
+I 2 3264 * 5097 * 2994 * * 3427 * 1732 * * 4177 4123 4959 * 4148 2776 * * 2
+ 0 * * * * * * 8265 0 0
+
+V 3 5432 * 4702 3230 * 3869 4855 * 3181 4745 * 6058 * 2645 5528 3412 3142 2660 5692 * 3
+ 0 * * * * * * 8999 0 0
+
+S 4 4204 * * * 2858 * * 2682 4656 2257 5906 * * 5627 * 5842 5711 1685 5757 * 4
+ 0 * * * * * * 9205 0 0
+
+T 5 * * * 3089 5974 5848 4540 2898 4297 4388 5318 4398 * 4908 5102 5815 1571 3571 * * 5
+ 0 * * * * * * 9442 0 0
+
+Q 6 4510 * * 3073 * 4050 5887 3833 3545 3168 4139 * 4262 2453 3043 5861 6291 4319 * * 6
+ 117 * 3684 * * * * 9607 0 0
+
+S 7 3337 * 4612 4112 6269 4542 * 4283 6447 5197 6217 4923 2660 4524 5022 2073 3359 4559 * * 7
+ 44 5044 * 0 * 0 * 9762 1191 1817
+
+P 8 4341 * 5022 * 5490 4515 5673 6526 4062 6285 * 5563 1231 3446 5381 2898 5204 5240 * * 8
+ 0 * * * * * * 10048 0 0
+
+A 9 4024 * 6260 3313 * 3780 5252 6687 3633 6061 5357 5514 4875 3824 2794 2211 4186 4713 * 5932 9
+ 62 5601 5531 2025 407 * * 10053 1148 0
+
+I 10 5086 * 3853 3316 5459 4161 4745 3818 5628 3729 * 3717 2660 * 6312 3456 3356 4275 * 5002 10
+ 14 * 6670 * * 0 * 10132 0 1194
+
+M 11 5024 6750 6866 4000 4352 6402 * 3160 4955 2862 5750 6530 6285 3680 5221 5321 4174 1777 5854 6671 11
+ 0 * * * * 0 * 10187 0 1000
+
+S 12 4669 * 5042 4115 4026 5284 6948 3889 4964 3864 5196 3647 5547 4373 4830 2807 2580 4096 6671 5724 12
+ 12 6974 * 3907 100 * * 10355 1013 0
+
+A 13 2928 * * 5767 5205 3874 * 3879 4592 3135 6476 5835 6683 5237 5614 5094 4309 1491 * 6528 13
+ 0 * * * * * * 10351 0 0
+
+S 14 3813 * 5735 4160 4329 5081 5184 3892 3368 3282 6619 5026 5083 3472 3281 4838 5229 3095 * 4708 14
+ 0 * * * * * * 10382 0 0
+
+P 15 4950 * 5617 1967 5648 6569 6949 5208 5300 2871 * 5620 4249 4249 3926 3459 4076 3164 * 6559 15
+ 0 * * * * * * 10456 0 0
+
+G 16 * * 4538 5257 * 461 5681 * 4442 6667 * 4112 * * 5230 4865 * * * 6591 16
+ 0 * * * * * * 10517 0 0
+
+E 17 6733 * 2977 1950 * 3500 5800 6595 3761 5414 6397 4908 * 3613 4332 2790 4547 7162 * 5652 17
+ 13 6781 * 0 * * * 10552 1000 0
+
+K 18 4713 5414 3358 4215 6595 6870 5278 * 4231 6850 * 3058 3263 5915 4511 2450 2531 5382 * 5979 18
+ 14 6721 * 0 * * * 10552 1054 0
+
+V 19 2336 6672 * * 4197 4849 * 3514 7162 3056 6517 * 6676 6625 * * 4612 1264 * * 19
+ 0 * * * * * * 10552 0 0
+
+T 20 5854 * * 3122 5846 * 4735 3284 4856 4811 * 4353 6399 4218 3821 4054 1915 3070 * 6595 20
+ 0 * * * * * * 10552 0 0
+
+M 21 6744 * * * 3173 * 7684 2364 * 879 3957 * * * * * * 3786 * * 21
+ 0 * * * * * * 10552 0 0
+
+T 22 4595 * 4811 3908 5793 5812 5733 4899 6721 4742 5792 3753 2284 4634 3740 2982 2758 5814 * 5917 22
+ 0 * * * * * * 10552 0 0
+
+C 23 4329 187 * * * * * 6701 * 5753 * * * * 7684 * * 5141 * 6614 23
+ 0 * * * * * * 10552 0 0
+
+S 24 5996 7684 3800 3231 6899 4601 5819 4585 3676 3767 7057 3562 5328 4499 3836 3302 3118 3861 * 5395 24
+ 29 5651 * 574 1607 * * 10552 1230 0
+
+A 25 2422 6517 7057 * 3146 6820 5813 3097 7420 3455 * 4490 * 6607 * 5748 5145 1811 * 4187 25
+ 0 * * * * * * 10552 0 0
+
+S 26 4430 * 3651 3981 5992 * 5222 5259 3750 4555 5843 4902 3911 3979 4987 2411 2389 6707 6136 6625 26
+ 27 6772 6781 0 * * * 10552 1000 0
+
+S 27 3863 6580 3254 5780 6902 2019 * 6685 4119 4696 5552 3893 3884 5259 * 3209 3935 4131 * 5391 27
+ 15 6602 * 1000 1000 * 0 10542 1020 1000
+
+S 28 3440 6842 3985 3846 3959 3800 6070 5010 4587 4079 6881 4326 3709 4255 7157 2718 5970 4070 * 4012 28
+ 3361 172 6080 1371 705 * 0 10542 9623 1000
+
+R 29 3727 * 3588 4072 6706 4718 3883 5637 4168 3282 5832 4221 3721 6285 4770 3038 4156 3527 5893 6645 29
+ 55 4978 7525 1582 586 727 1336 10510 1424 1708
+
+S 30 3609 * 6577 5257 4822 4220 4988 5117 4471 2891 4547 4203 2687 * 5356 4066 3618 3696 * 4129 30
+ 39 5244 * 520 1725 808 1222 10528 1606 1441
+
+Y 31 4096 * 4555 3829 5712 4036 4784 3894 4856 4412 7036 4040 5229 4092 3929 2608 3251 4686 * 4788 31
+ 0 * * * * * 0 10540 0 1084
+
+M 32 5907 * 6815 * 3401 5411 * 2331 4833 2826 5148 * * * 6878 6587 5137 1498 5291 5250 32
+ 22 * 6047 * * * 0 10540 0 1084
+
+Q 33 4420 * * 4572 4733 5765 4189 3934 3885 4772 6699 3866 * 4253 4294 3180 2467 4663 * 3078 33
+ 15 * 6567 * * 1833 475 10519 0 1445
+
+W 34 6569 6585 * * 5405 * * 6819 * 5876 * * * 5882 6769 * 6493 7037 235 4829 34
+ 81 4744 5878 892 1116 * 0 10492 1567 1529
+
+Y 35 5088 4844 6541 5256 2615 6482 6757 3740 4969 3628 4515 4224 * 5613 4807 4861 4869 5390 4917 2008 35
+ 85 5776 4686 2265 337 1967 426 10485 1447 1846
+
+Q 36 * 5688 5213 4696 5275 6686 5325 6527 1710 3712 5124 5626 5265 4750 2231 5300 * 4002 5086 5684 36
+ 226 4981 3144 2370 310 * 0 10433 1430 2288
+
+Q 37 4855 * 3038 4170 6485 3283 4236 * 3398 4652 5247 3752 6258 2382 4635 3962 4188 6448 * 6590 37
+ 173 6986 3250 1000 1000 4243 78 10306 1000 4084
+
+K 38 6383 * 2713 4872 * 3942 6771 6005 2738 4275 5271 3522 4979 3945 5300 3601 3130 4440 * 4955 38
+ 84 6005 4618 1000 1000 1160 856 10121 1044 5163
+
+P 39 4324 5352 3086 3415 6384 3556 6425 * 3958 4016 6422 3471 2603 6272 5457 3809 4031 4818 * 6777 39
+ 71 6535 4736 0 * 800 1232 10296 1000 4023
+
+G 40 3981 * 3996 4254 * 1480 5932 * 3696 5204 * 4297 5723 4323 4536 4324 4066 4084 6499 * 40
+ 68 * 4433 0 * 2834 218 10365 1000 2938
+
+T 41 4261 6454 6513 2970 * 3354 4220 3926 2835 4593 5567 4380 4931 3389 4822 3637 4335 4781 * * 41
+ 259 * 2606 * * 1954 431 10332 0 3380
+
+S 42 3455 * 4353 4268 5027 3241 * 4714 3422 4381 4429 3672 3330 5654 3181 3969 6689 3964 * * 42
+ 102 4005 7364 1826 478 3643 120 10133 1933 5071
+
+P 43 3716 4940 6323 4607 6323 6155 * 3867 6698 2480 6676 4529 2393 5868 4597 3073 3874 3947 * * 43
+ 51 * 4858 * * * 0 10114 0 4976
+
+K 44 4792 * 4851 3303 * 4016 5465 4491 2847 4837 5697 5196 4496 3782 6201 3481 3273 3685 * 3698 44
+ 98 * 3924 * * 3141 174 10036 0 5316
+
+R 45 6390 * 5203 5619 3143 4438 5209 4274 5014 2629 * 3889 * 5314 3243 3978 3853 2997 4534 6576 45
+ 113 * 3732 * * 2396 304 10005 0 5538
+
+W 46 5362 * * 4454 5390 5255 * 2573 4040 1665 4748 6099 4759 6315 * 5772 4959 2723 6547 5521 46
+ 18 6296 * 1000 1000 3833 105 9940 1026 5550
+
+I 47 4405 6691 4052 6207 6233 3393 4316 2716 * 3175 * 4592 4377 5651 6410 3479 3721 3921 5327 3837 47
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+
+K 204 2266 * 5569 5776 3810 5808 5478 4433 2643 3175 * 5735 * 5287 3054 4739 4323 3800 * * 204
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+F 206 * * * * 2922 * * 2052 6063 2455 * * * 5554 * * 4575 2208 4685 3170 206
+ 45 5033 * 1903 449 0 * 9015 1283 1110
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+N 207 5124 * 4328 4323 * 5428 4443 * 5542 * * 2559 3626 * 3022 2323 2461 5293 * * 207
+ 27 5739 * 0 * * * 8561 1110 0
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+R 208 * * 4319 * 4644 * 4468 * 2536 1362 * * 3822 4260 3491 * 4313 4606 * * 208
+ 0 * * * * 0 * 7064 0 1110
+
+G 209 3397 * 2366 3381 * 4403 * * * * * * 2698 * * 1589 3622 * * * 209
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+E 210 * * * 758 * * * * * * * 2582 * 2050 * * * * * * 210
+ 0 * * 0 * * * 3919 0 0
+
+//
+�HHsearch 1.5
+NAME 0b91ebac43769ec865264a8281966ca6
+FAM
+FILE 0b91ebac43769ec865264a8281966ca6
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:17:59 2013
+LENG 119 match states, 119 columns in multiple alignment
+FILT 132 out of 578 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCEEEECCCCCHHHHHHHHHHHHHHHH
+HHHCCCCHHHHCCCCCCCC
+>ss_conf PSIPRED confidence values
+9899999999874899886999746877689999985523768987458899997026798762361489997995788999996999999979999999
+9978577888288966899
+>Consensus
+xlxqlxxMixxxxxxxxxxxxyxxYGCxCgxgGxGxPvDxiDxcCxxhxxCyxxxxxxxxCxxxxxxYxxxxxxxxxxCxxxxxxCxxxlCeCDxxxAxc
+xxxxxynxxxxxxxxxxxc
+>0b91ebac43769ec865264a8281966ca6
+HLVQFNGMIRCTIPGSIPWWDYSDYGCYCGSGGSGTPVDELDRCCQVHDNCYTQAQQLTECSPYSKRYSYDCSEGTLTCKADNDECAAFVCDCDRVAAIC
+FAGAPYNKENINIDTTTRC
+>gi|149410126|ref|XP_001508765.1| PREDICTED: similar to otoconin [Ornithorhynchus anatinus]
+-LPRLGEMLFCL--TQRCPEEFESVGCFCGPEERGASADILDSCCFSHHCCLEQVKT-MGCELErSSQVEVVCLDHKPECTG-WNACEKLLCSCDRTAAE
+CLAAASFNNSLPLP------
+>gi|313237065|emb|CBY25148.1| unnamed protein product [Oikopleura dioica]
+-YWQLMEQILYFNP-AFDQRKFWAYGCNCLLLgdrpmsdpGYGPPVDALDTVCKHYKDCAQCAKKKhgDECINEFKKYKFSEsfyeKGNASMCKNEANSC
+ERDLCECDFAFAKAHVQAigSFVTDYHLFW-----
+>gi|313225325|emb|CBY06799.1| unnamed protein product [Oikopleura dioica]
+-LLQLAEMVKQVQRTDYLFERYCFYGCHCIPGyavhdstaGKGPAQDGIDSVCSRLKQCYWCANDEeeGQCDGTMKSYSWNVVDndkdgkiDDIVCYNQP
+GSCRWKLCQCDRQFALQLRDVeeTYNPLL---------
+>gi|313238038|emb|CBY13157.1| unnamed protein product [Oikopleura dioica]
+--TNFRNMWHEYGYTPQQLTNLYGYGCYCLNlGGSpmsglnelnGvKPMDDIDRTCFHWTRCNRCAAIDhgEKCKAEDRSYDFEIDpdTKDITCKEKKNT
+CKWAICECDKEQVLSMKQ----------------
+>gi|313220609|emb|CBY31456.1| unnamed protein product [Oikopleura dioica]gi|313226182|emb|CBY21325.1| unnamed protein product [Oikopleura dioica]
+-LRQFRRLYTFYLVGyRLRPAHLVQYGCWCFPRgqlimGYGQPIDGIDATCRNHQLCLNCVGLDtnYECNPHTQPYRVYgqiyQNGRRLMCKDPPGSCAW
+LACQCDVNMVTTSIIeslKGYKPRFWMYDPG---
+>gi|313225706|emb|CBY07180.1| unnamed protein product [Oikopleura dioica]
+-------------------YEFHNYGCYCVApsdtkKMRGRPVDEIDRKLVakfplvknthfvtpVHFLTTDAIRKQWG--FSILIYRYKItktsSGNRI
+ECTNAADTCAYASCMCDKGLAEDLGTllmngVKVNSTYREHDGE---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
+Q 4 6474 * 3962 3753 6554 * 5746 * * * * 2210 * 993 4345 5420 5062 * * * 4
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+
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+
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+G 30 6798 * 6873 * 3743 1056 5192 7085 * 3409 5924 3913 * 4300 5380 4115 5184 6240 5173 6147 30
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+N 50 5719 2763 3707 3397 5672 5878 5726 6828 3186 4645 7308 4122 * 3280 2992 4646 4162 5019 6056 6162 50
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+
+Q 54 4144 1235 4246 3493 * 5608 7173 7419 3158 6793 * 6297 * 3979 3808 4973 6556 5213 7417 * 54
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+R 67 4948 6676 4808 6069 5078 4168 4674 4607 4196 3766 6996 3774 3112 3888 3810 2898 3373 5021 7265 6605 67
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+P 105 5594 * 4041 3467 7046 5669 4946 5295 4181 5630 6855 6671 2786 6570 5527 2676 2325 3109 * * 105
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+
+Y 106 * 5528 * 5389 2277 * 6809 5035 5867 * * * * * * * * 4985 3379 827 106
+ 0 * * * * * * 6296 0 0
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+N 107 5361 * 2939 4708 * * 4791 * 4871 * * 924 4084 5370 5146 4043 6698 5167 * * 107
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+E 109 3890 * 3388 3354 5647 4182 4956 * 2100 4899 * 3113 * 5374 4275 3294 4288 6570 * 6611 109
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+N 110 * * * 6510 2694 * 3336 5738 6469 2931 6349 2993 * 5646 * * * * * 1264 110
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+I 111 4609 * 4754 4364 3726 6443 2991 5195 2912 3933 6060 4692 5965 4417 2783 4421 4582 6502 5120 4477 111
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+N 112 5779 * 4204 4211 3112 2851 3753 6177 * 3558 4943 2847 6400 5145 4862 3343 5052 4667 * 4949 112
+ 0 * * * * * * 6127 0 0
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+I 113 * 5991 * 6072 1794 5311 4808 3784 * 3016 5196 5171 5592 * * 5503 * 3995 * 1925 113
+ 0 * * * * * * 6130 0 0
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+D 114 * * 1550 * 5385 5030 5445 6196 5250 5883 5666 3401 2805 5015 5878 3503 5067 * 4000 4710 114
+ 0 * * * * * * 6112 0 0
+
+T 115 3620 * 5204 * * 3725 * * 3112 * * 3504 5032 3711 3114 2743 2744 4715 * 4237 115
+ 0 * * * * * * 5820 0 0
+
+T 116 * * 3511 3750 5521 3478 * 3872 2713 5199 5353 3469 4834 4288 4370 2437 4492 * * * 116
+ 0 * * * * * * 5522 0 0
+
+T 117 3684 * * 2603 * * * * 1630 4726 4824 * 3536 * 3606 2676 4766 * * * 117
+ 636 * 1487 * * * * 4589 0 0
+
+R 118 * * * * * * 3462 * 2355 * * 2843 * * 1785 * 3651 * * 2289 118
+ 0 * * * * 0 * 3453 0 1314
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+C 119 * 0 * * * * * * * * * * * * * * * * * * 119
+ 0 * * 0 * * * 4006 0 0
+
+//
+�HHsearch 1.5
+NAME 0c68c5d75cc2ae618e6e5f1010b542af
+FAM
+FILE 0c68c5d75cc2ae618e6e5f1010b542af
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:13:12 2013
+LENG 91 match states, 91 columns in multiple alignment
+FILT 147 out of 815 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHCCCCHHHHCCCCCCCCCCCCHHHCCCCCCCCCCHHHHHHHCCCCCCCCCHHHCC
+>ss_conf PSIPRED confidence values
+9742113323017564504888855334432468987376578751557765688850321474313465067898705677562113049
+>Consensus
+xxxxlxxxHxxxxxCxxCHxxxxxxxxxxxxxxxCxxCHxxxxxxxxxhxxhxxxxxCxxCHxxHxxxxxxxxxCxxCHxxxxxxxxxxxx
+>0c68c5d75cc2ae618e6e5f1010b542af
+ADQKLSDFHAESGGCESCHKDGTPSADGAFEFAQCQSCHGKLSEMDAVHKPHDGNLVCADCHAVHDMNVGQKPTCESCHDDGRTSASVLKK
+>gi|303257051|ref|ZP_07343065.1| fumarate reductase flavoprotein subunit [Burkholderiales bacterium 1_1_47]gi|330999581|ref|ZP_08323292.1| hypothetical protein HMPREF9439_00917 [Parasutterella excrementihominis YIT 11859]gi|302860542|gb|EFL83619.1| fumarate reductase flavoprotein subunit [Burkholderiales bacterium 1_1_47]gi|329574434|gb|EGG56004.1| hypothetical protein HMPREF9439_00917 [Parasutterella excrementihominis YIT 11859]
+-AQQVKPYHQNIKDCAACHTKENAVAGnqfVTPDNKACLTCHQSYAAVAEktknlkngepnPHASHHygEGIACTACHSEHK---TSQVYCNNCHE----
+-------
+>gi|253701708|ref|YP_003022897.1| cytochrome C family protein [Geobacter sp. M21]gi|251776558|gb|ACT19139.1| cytochrome C family protein [Geobacter sp. M21]
+-----RSEHLPFVekRCSDCHNSNQgagsaseEGLLVKPREELCFGCHKNLLNKPFHHGPAA-VGDCLACHLPHDSAnpallvLSREKLCAKCHTERRKA
+QR----
+>gi|182412667|ref|YP_001817733.1| cytochrome b subunit of formate dehydrogenase-like protein [Opitutus terrae PB90-1]gi|177839881|gb|ACB74133.1| cytochrome b subunit of formate dehydrogenase-like protein [Opitutus terrae PB90-1]
+--KVGASVHG-SLECVDCHEGIdgeaSPH-RKQRVAVDCFSCHDDTAPKH-KFHSRLqldprpeGkDTSCTECHGTHEVQrvkSRDFAMskprltegCGQ
+CHAQAR--------
+>gi|308049069|ref|YP_003912635.1| decaheme c-type cytochrome, OmcA/MtrC family [Ferrimonas balearica DSM 9799]gi|307631259|gb|ADN75561.1| decaheme c-type cytochrome, OmcA/MtrC family [Ferrimonas balearica DSM 9799]
+-------------ACTA---chvEGE--plttRHSsYFEAETCINCH--neDRMtgkrASFqhlV----htihNTaatftdkndreytgqaaeallQNNC
+----qachVASEElaewgnwtRVPTKET------csachnN----------
+>gi|291286709|ref|YP_003503525.1| cytochrome C family protein [Denitrovibrio acetiphilus DSM 12809]gi|290883869|gb|ADD67569.1| cytochrome C family protein [Denitrovibrio acetiphilus DSM 12809]
+---FRRGRSSEKlVTCATCHDVHSKDknfLRIeAETGELCLTCHNEKEMVE--KTLHGKqklDKSCLSCHKVHNSEtkrllvKPDNDGCLDCHKKGGSAE
+KM---
+>gi|291279066|ref|YP_003495901.1| multiheme c-type cytochrome [Deferribacter desulfuricans SSM1]gi|290753768|dbj|BAI80145.1| multiheme c-type cytochrome [Deferribacter desulfuricans SSM1]
+--SMLKDIHYEKGlKCNNCHDMI-SLSKGDIATKRCNECHTINTDIIEHSiNAHIEKMECYACHSSWA-------------------------
+>gi|197121374|ref|YP_002133325.1| cytochrome C nitrate reductase, small subunit [Anaeromyxobacter sp. K]gi|220916077|ref|YP_002491381.1| cytochrome c nitrate reductase, small subunit [Anaeromyxobacter dehalogenans 2CP-1]gi|196171223|gb|ACG72196.1| cytochrome c nitrate reductase, small subunit [Anaeromyxobacter sp. K]gi|219953931|gb|ACL64315.1| cytochrome c nitrate reductase, small subunit [Anaeromyxobacter dehalogenans 2CP-1]
+-------------------------------PATCSNCHVMSGHYAgWQASAHHAVATCNDCHTPAA-------------------------
+>gi|91203484|emb|CAJ71137.1| hypothetical heme protein [Candidatus Kuenenia stuttgartiensis]
+-GVFLHNRHSPIQniECCECHNNDPANtkTHGgliieendckkchhnEATNEDCLKCHSAVNDYRngsfryaGIHSPVTGapdwmykAVLCTDCHKQEEN
+NflfRDTRSICIECHNDDYG-------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 0 * * * * * * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+D 2 1661 * 2728 4574 * 2043 * * * * * 3150 2881 * * * * * * * 2
+ 0 * * * * * * 4919 0 0
+
+Q 3 2145 * 5110 4911 * 3043 * 5175 3224 * 5173 3665 4855 2724 * 4966 4059 3811 * * 3
+ 0 * * * * * * 5852 0 0
+
+K 4 * 5502 5607 4710 3368 3470 4420 * 5754 4491 4535 3243 3607 3553 * 5368 2542 3902 * 4517 4
+ 0 * * * * * * 6554 0 0
+
+L 5 5592 * * * 5572 3332 * 5939 4587 1288 2947 * 4289 * 5481 4629 5894 2930 * * 5
+ 0 * * * * * * 6708 0 0
+
+S 6 1567 * 6366 5056 * 4234 4403 * 3168 4952 6594 4797 4140 6271 3394 2924 4907 * * * 6
+ 63 4547 * 1911 446 * * 6976 1221 0
+
+D 7 4158 * 2718 4775 4420 2665 6362 * 4446 * * 3929 5671 * 5489 1936 5255 4011 6339 5403 7
+ 0 * * * * * * 7106 0 0
+
+F 8 3104 * * 5473 4361 5169 4607 3535 4925 3351 5450 4473 6454 4135 3379 4185 5008 2535 * 4816 8
+ 14 6730 * 571 1614 * * 7164 1058 0
+
+H 9 6573 * * * * * 98 * 6673 * 6375 * * * 6434 6514 * 6519 * * 9
+ 14 6714 * 1000 1000 * * 7225 1000 0
+
+A 10 1452 * 5735 4411 * 3328 6456 6385 3592 5848 5446 6777 3783 4055 4928 4278 4663 4701 * 5762 10
+ 129 * 3543 * * 0 * 7261 0 1000
+
+E 11 3495 * 3240 2785 5842 5978 * * 4229 3532 * 4676 2166 3971 5468 5738 4552 3859 * 6853 11
+ 143 5479 3794 0 * 0 * 7241 1047 1447
+
+S 12 2730 * 3903 6506 4426 5632 5616 4414 3678 3575 3028 3641 5643 6699 4342 4100 6493 4270 * 3785 12
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+
+G 13 3614 * 4042 4176 * 1871 * 3707 5015 3107 4954 5447 * 4229 5382 4353 * 3012 * * 13
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+
+G 14 3274 * 3035 3803 6779 2814 * 6977 4369 * * 3728 4724 3962 3831 3404 3027 5971 * 6110 14
+ 32 5514 * 1357 714 0 * 7464 1145 1016
+
+C 15 * 35 * * * * * * * * * 5373 * * * * * * * * 15
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+
+E 16 2832 6841 * 3257 5511 5576 5073 4211 4659 3202 7053 3727 6939 4134 * 3877 2600 3470 * * 16
+ 9 7274 * 0 * * * 7481 1000 0
+
+S 17 3053 * 2208 4031 * 4909 7112 5929 4562 6588 6891 4259 4605 4820 5117 2172 3720 5602 * 6978 17
+ 16 * 6526 * * * * 7481 0 0
+
+C 18 * 35 * * * * * * * * 5365 * * * * * * * * * 18
+ 0 * * 0 * 587 1581 7472 1028 1075
+
+H 19 * * * * * * 0 * * * * * * * * * * * * * 19
+ 10 7128 * 0 * * 0 7476 1000 1000
+
+K 20 3905 * 2477 3283 * 2318 5369 6089 4409 4951 6986 4108 5836 4302 * 3715 3195 6318 * * 20
+ 61 5026 6521 1585 585 0 * 7476 1216 1000
+
+D 21 3157 * 2614 3145 * 3511 * 6858 5641 4960 6229 4250 2128 5329 6810 3585 5108 5485 * * 21
+ 67 4756 6867 294 2438 0 * 7447 1249 1019
+
+G 22 4533 * 4023 3345 7100 3316 2015 3733 4167 5342 7095 4501 6229 4321 4636 4579 4225 5335 * 6488 22
+ 239 3394 4118 2284 331 1038 963 7456 1684 1074
+
+T 23 3903 * 3660 2857 5971 2839 5946 5240 4120 4657 * 4480 4105 3724 4528 3370 3776 6151 * 6089 23
+ 357 2326 5651 3026 189 126 3582 7452 2426 1532
+
+P 24 3991 * 4445 4085 4993 4026 6659 6723 4164 * 5609 5121 1313 4939 6073 3212 5241 6846 5507 * 24
+ 231 3030 5278 1105 902 2335 319 7467 1845 1190
+
+S 25 4704 * 3625 4447 4762 5465 3025 4175 3741 3205 5288 3124 5389 5111 5055 3598 5007 3988 * 6163 25
+ 418 2679 3390 2347 316 1285 762 7448 2364 1407
+
+A 26 2893 * 3964 4985 6710 4428 7121 6637 3159 2689 6712 4063 4004 4616 5451 3740 3634 4094 * 5629 26
+ 234 4622 3194 1528 614 1906 448 7348 1236 2020
+
+D 27 3591 * 2381 4121 5747 3830 3896 5758 2688 3167 4337 6930 5182 6725 4290 4704 5568 5557 * * 27
+ 300 2474 6992 1753 508 919 1086 7271 2055 2506
+
+G 28 3858 * 6688 4680 5279 2110 * 4465 2986 4294 5032 5045 3866 4663 4096 4770 4692 3467 * 6767 28
+ 458 2158 4387 2695 242 925 1080 7355 2545 1754
+
+A 29 2496 * 4392 3157 4280 3945 * 6881 3054 4676 5990 5436 5688 4262 4011 4103 3558 4917 * 5060 29
+ 111 3964 6647 2450 292 815 1212 7432 1465 1716
+
+F 30 2803 * 4255 3720 4600 4915 5078 6156 3955 5024 5862 5009 2816 5513 5005 4271 4274 3070 6735 4643 30
+ 31 5555 * 1087 918 245 2678 7433 1190 1350
+
+E 31 3222 * 3064 2959 * 3570 * 4416 4591 6184 4894 5181 5063 4229 4513 3295 3829 3511 * 6627 31
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+
+F 32 3233 * 3876 4763 6181 4481 6925 4264 4493 5999 5277 2356 3398 6154 4105 3683 3852 4063 * 6085 32
+ 63 4839 7012 2256 339 0 * 7493 1212 1198
+
+A 33 2218 * 3964 2302 * 6137 * * 3251 5785 * 4555 5394 3723 5546 3715 3716 3939 * * 33
+ 8 * 7440 * * 0 * 7509 0 1000
+
+Q 34 3407 * 3819 5659 4783 4245 * 4264 4248 2155 6051 5463 * 4269 5254 3338 2966 4446 * 6913 34
+ 0 * * * * 0 * 7509 0 1000
+
+C 35 * 0 * * * * * * * * * * * * * * * * * * 35
+ 0 * * * * * * 7514 0 0
+
+Q 36 3623 * * 4899 4015 3765 * 3512 6914 1726 6090 6026 * 4165 6180 5418 3681 3243 * 4472 36
+ 53 4791 * 679 1413 * * 7514 1259 0
+
+S 37 4117 * 4124 3463 * 3412 * * 3511 * * 3929 * 3097 4575 2262 3072 4269 * 6796 37
+ 0 * * * * * * 7514 0 0
+
+C 38 * 30 * * * * * * * * * * * * * 5598 * * * * 38
+ 0 * * * * * * 7514 0 0
+
+H 39 * * * * * 5598 30 * * * * * * * * * * * * * 39
+ 64 6228 5054 2347 316 * * 7514 1087 0
+
+G 40 4089 5579 3605 3657 5894 2274 5737 5270 3648 6192 * 4045 4368 3845 4793 4037 3604 5072 * 6685 40
+ 117 4428 4989 434 1946 763 1284 7497 1329 1275
+
+K 41 4472 * 2178 3025 * 3588 6002 7139 4340 6995 5170 3335 4223 4804 7636 2790 3748 * * 6994 41
+ 56 5043 7010 969 1032 327 2302 7486 1220 1392
+
+L 42 4058 * 4410 3438 5176 5129 6788 3654 4225 3098 4575 4931 5607 3547 7159 4368 3827 3856 7403 3265 42
+ 184 3235 6198 1087 918 1285 762 7504 1917 1094
+
+S 43 2515 * 3202 2579 * 5305 5126 * 3580 4682 6022 4468 4196 4053 4107 3796 5075 5068 7042 * 43
+ 53 4792 * 2817 221 608 1539 7501 1238 1206
+
+E 44 3004 * 2692 2736 6266 3965 5537 6267 3997 6220 4835 3498 4878 4077 4379 4015 5151 5809 * 6621 44
+ 334 2275 * 1149 865 * 0 7510 2699 1028
+
+M 45 4771 * 6063 4368 3382 5567 5792 3538 4261 2235 3512 6146 5106 4598 6103 4957 5491 3302 6852 3986 45
+ 55 5333 6299 646 1470 * 0 7510 1163 1028
+
+D 46 1947 * 3295 4174 4049 4945 4862 5987 4055 5005 6136 4913 4674 4708 4823 3904 5300 3746 * 5499 46
+ 907 1261 4343 2446 292 954 1047 7511 4053 1128
+
+A 47 3953 * 5604 4451 3527 4570 6853 * 3521 5164 * 2363 4241 6175 5184 2983 5269 4416 3453 4740 47
+ 227 2779 * 3118 176 856 1160 7464 2114 1547
+
+V 48 3321 6567 6356 7065 * 6185 4210 5022 3751 3467 6149 6020 2210 4718 4829 3853 3255 3450 * 5504 48
+ 186 3321 5569 3420 142 589 1577 7501 1779 1213
+
+H 49 4654 * 6299 5454 5486 4211 834 6846 5308 * * 4805 5560 5386 3973 4247 4974 5353 * * 49
+ 144 3601 6326 848 1170 * 0 7482 1647 1202
+
+K 50 4140 * 3365 4399 5535 3242 5263 6090 3801 5735 5577 3247 3867 5299 5033 2524 3721 5752 * 5547 50
+ 211 3268 4963 3087 181 921 1084 7487 1875 1301
+
+P 51 3346 * 4717 5571 4875 5274 4649 4470 3558 3957 6238 4170 2344 6045 7061 3550 4221 3047 * * 51
+ 93 4156 7313 1475 643 1840 472 7441 1434 1431
+
+H 52 3725 * 5908 5814 7107 5154 820 5508 7617 7070 6094 4602 6940 6105 4237 7181 6561 4075 * 4459 52
+ 81 5496 4935 2064 394 543 1672 7463 1143 1352
+
+D 53 2302 * 3704 4317 4524 3546 4131 4721 6088 4117 7050 5264 3528 4447 6097 5264 5412 4572 4606 4046 53
+ 407 2166 5443 2429 296 299 2419 7467 2760 1324
+
+G 54 3696 * 3994 3235 5789 1975 * * 3318 5633 * 4531 4383 3809 4126 3223 4873 * * * 54
+ 654 1658 4392 1777 498 0 * 7482 3496 1237
+
+N 55 3905 * 3348 3534 6026 2963 5831 5585 2845 5406 6897 4288 4802 3343 4472 3847 4853 4226 * 7068 55
+ 131 4230 4911 1213 814 1656 551 7508 1381 1319
+
+L 56 2806 * 4979 5109 6015 3787 * 3580 5460 2788 3104 5681 4666 5201 6686 4851 3980 2765 * * 56
+ 44 5060 * 1590 583 0 * 7447 1179 1462
+
+V 57 3504 * 3141 3209 7073 4179 * 6711 6745 5327 7037 3681 4897 4791 4107 2576 3045 4147 * 5303 57
+ 19 6265 * 591 1573 * * 7514 1051 0
+
+C 58 * 0 * * * * * * * * * * * * * * * * * * 58
+ 7 * 7686 * * * * 7514 0 0
+
+A 59 3113 * 7250 6064 7030 5460 6318 4800 * 3224 4716 3869 * 5370 5098 3674 1761 3019 6346 6926 59
+ 0 * * * * * 0 7510 0 1000
+
+D 60 2934 * 1857 3367 * 4366 * 6292 5775 7124 * 3509 6875 6036 * 2709 3256 4870 * 7376 60
+ 0 * * * * * 0 7510 0 1000
+
+C 61 * 0 * * * * * * * * * * * * * * * * * * 61
+ 0 * * * * * 0 7510 0 1000
+
+H 62 * * * * * * 0 * * * * * * * * * * * * * 62
+ 50 4868 * 1415 678 0 * 7510 1261 1000
+
+A 63 3685 * 3386 4897 5712 3874 5397 6402 2921 3776 4382 2773 * 4155 6210 3095 4473 4675 * * 63
+ 15 * 6640 * * * * 7514 0 0
+
+V 64 3624 * 5785 3228 * 3368 * 4964 5410 4936 4128 5598 1602 5482 * 4379 4776 3522 7032 * 64
+ 15 8165 7128 0 * * 0 7491 1000 1012
+
+H 65 6241 * 6667 5491 7107 * 325 * 5392 7009 * 6523 7038 5332 5515 5455 6519 * 5723 * 65
+ 16 7631 7340 1000 1000 878 1134 7482 1028 1078
+
+D 66 2814 * 3249 3075 6994 2676 6996 * 3815 5502 7166 4636 6521 3810 4352 3614 4386 4476 * 5975 66
+ 443 4754 2138 3218 164 1108 899 7497 1213 1056
+
+M 67 3379 * 5124 3702 5094 3829 * 2951 3612 6735 4860 4358 5877 4962 6442 2220 4653 3645 * * 67
+ 215 3222 4996 2503 280 3525 131 7312 1637 2995
+
+N 68 3402 * 3217 3331 6524 3991 6691 * 2910 * * 3743 5565 3962 4738 4209 2977 4965 6588 4035 68
+ 1241 916 4415 2851 215 3732 113 7298 3951 3031
+
+V 69 3270 * 5250 4372 4986 5261 * 5534 2374 4627 4437 3874 5668 4081 4586 4766 4978 2541 6262 5577 69
+ 224 2912 6521 3462 137 242 2696 7264 1729 3140
+
+G 70 3153 * 4069 3597 * 3813 7302 * 2972 5041 4636 5993 2385 4087 5034 4128 3301 6096 * * 70
+ 138 3451 * 1499 630 * 0 7493 1645 1376
+
+Q 71 2977 * 4340 6092 5976 4366 * 3638 4595 6204 5464 5028 3324 3826 4402 2229 3930 4242 * 7228 71
+ 85 4425 6564 1934 438 * 0 7478 1282 1440
+
+K 72 4474 * 4064 3530 6099 6027 5362 * 3093 * 4938 3043 3318 3776 3543 4343 3534 3496 * * 72
+ 10 * 7228 * * 0 * 7452 0 1561
+
+P 73 3316 * 3200 2958 6988 4648 5805 5440 3531 4419 5362 3131 3813 4282 4374 4551 4777 4271 * * 73
+ 33 5445 * 2765 230 0 * 7534 1109 1009
+
+T 74 3601 * 5451 4952 5481 7251 * 4108 4974 2302 3802 4407 6810 5026 6526 4375 2674 3581 6989 3732 74
+ 38 5596 7575 1824 479 * * 7535 1119 0
+
+C 75 * 0 * * * * * * * * * * * * * * * * * * 75
+ 0 * * * * * 0 7530 0 1000
+
+E 76 3140 * 6407 5115 4956 3865 * 3973 5894 2490 5978 3575 * 5239 6057 3221 3032 4258 * 3976 76
+ 12 6947 * 0 * * 0 7530 1000 1000
+
+S 77 5291 * 3270 3327 * 3812 * 6969 3724 6689 * 3342 * 3058 4285 1955 3835 6868 * * 77
+ 0 * * * * * 0 7530 0 1000
+
+C 78 * 0 * * * * * * * * * * * * * * * * * * 78
+ 0 * * * * * 0 7530 0 1000
+
+H 79 * * * * * * 0 * * * * * * * * * * * * * 79
+ 0 * * * * * 0 7530 0 1000
+
+D 80 3188 * 3416 3234 5772 4189 4100 6756 3946 5091 6061 3592 4061 4803 5624 3467 3097 5283 * 6883 80
+ 12 6952 * 1696 533 0 * 7493 1040 1000
+
+D 81 4000 * 2462 2798 3781 3518 7068 6156 3661 6859 * 3961 5822 4153 4293 3927 5040 4596 6834 7032 81
+ 73 4345 * 1018 982 * * 7451 1241 0
+
+G 82 3867 * 4440 2775 * 3142 4945 4714 2751 4139 6458 3812 4976 3282 4965 * 4132 4908 6554 * 82
+ 0 * * * * * 0 7143 0 1001
+
+R 83 5266 * 6037 6205 4398 4494 6165 * 2760 3711 * 5068 5059 3876 1707 4852 3828 4513 * 4944 83
+ 68 4445 * 0 * 0 * 6928 1149 1001
+
+T 84 3328 * 5128 * * 1717 * * 4303 * * 5044 4490 5180 * 2120 2683 5128 * * 84
+ 0 * * * * * * 6207 0 0
+
+S 85 1821 * * * * 4756 * 3381 4286 4532 * 4280 2982 * 4451 4261 3042 3440 * * 85
+ 112 3749 * 1585 585 * * 5131 1039 0
+
+A 86 2765 * 1953 2231 * * * * 3019 * * 4257 * 2747 * * * 4133 * * 86
+ 0 * * * * * * 4559 0 0
+
+S 87 3455 * * * * 2405 3785 * 3152 * * * * * 3397 1739 * 2831 * * 87
+ 0 * * * * * * 4026 0 0
+
+V 88 * * * * * * * 2751 * * 1959 * * 2948 * * * 1106 * * 88
+ 0 * * * * * * 3524 0 0
+
+L 89 * * * * * * * 1762 * 504 * * * * * * * * * * 89
+ 0 * * * * * * 2582 0 0
+
+K 90 * * * * * * * * 0 * * * * * * * * * * * 90
+ 0 * * * * * * 1000 0 0
+
+K 91 * * * * * * * * 0 * * * * * * * * * * * 91
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 0df5dbed0f36c37f3836e114a8b5c77b
+FAM
+FILE 0df5dbed0f36c37f3836e114a8b5c77b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:17:20 2013
+LENG 55 match states, 55 columns in multiple alignment
+FILT 172 out of 1016 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCEECCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9655657888765320279978654008888887446778858240228888888
+>Consensus
+xxxxxfxxxxxxxxCxxCgxxgHxxxxCxxxxxxxCxxCgxxGHxxxxCxxxxxx
+>0df5dbed0f36c37f3836e114a8b5c77b
+MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN
+>gi|73913123|gb|AAZ91500.1| gag protein [Human immunodeficiency virus 1]
+CCREALSGAQGKSl-SVSTVAKRAPSQKLSAPRkkaV----------------------
+>gi|73913077|gb|AAZ91477.1| gag protein [Human immunodeficiency virus 1]
+DAERQFLEARKELSVSTVAKKDTYPGIAGPLEK----------------------
+>gi|270006313|gb|EFA02761.1| hypothetical protein TcasGA2_TC008494 [Tribolium castaneum]
+----------EtafgAgLLRLRKRRalSPTVPEASTgkQP-EIGAAMqllswYRSHGEILQQE------
+>gi|340034816|gb|AEK28751.1| DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 transcript variant 1 [Ornithorhynchus anatinus]
+---------------FADQPAGDFSR-------grgfgrRGGYKGANEEIMADCEKNpgkPE--
+>gi|226437753|gb|ACO56244.1| putative DEAD-box RNA helicase [Caenorhabditis elegans]
+--------------NF---SRGGYNNRDEGsdnrgsgRSynndrrDnggdgqNTRWN-------NLDAPPSR--
+>gi|323352003|gb|EGA84542.1| Dbp1p [Saccharomyces cerevisiae VL3]
+-----------MAGFFGFSKE--------RngGTSANYNRGGSSNY-----KS----
+>gi|73983191|ref|XP_866869.1| PREDICTED: similar to Splicing factor 1 (Zinc finger protein 162) (Transcription factor ZFM1) (Zinc finger gene in MEN1 locus) (Mammalian branch point binding protein mBBP) (BBP) isoform 6 [Canis familiaris]
+-----------NRILRPWQSSETR--SITNTTvfphPLPSLTGGHGGHPMQHNPNGPP-
+>gi|9627015|ref|NP_041259.1| gag protein [Squirrel monkey retrovirus]gi|120891|sp|P21411.3|GAG_SMRVH RecName: Full=Gag polyprotein; Contains: RecName: Full=Core protein p19; Contains: RecName: Full=Core protein p16; Contains: RecName: Full=Putative nucleocapsid protein p35; Contains: RecName: Full=Probable core protein p10gi|807672|gb|AAA66451.1| gag protein [Squirrel monkey retrovirus-H]
+------------AFAIIVTNPAIFQETAPKKiqpptqlptqpNapqASLiknlgpttkCPRCKKGFHWASECRSR---
+>gi|15242405|ref|NP_199353.1| replication factor-A protein 1-like protein [Arabidopsis thaliana]gi|9758730|dbj|BAB09168.1| replication protein A1-like [Arabidopsis thaliana]gi|332007861|gb|AED95244.1| replication factor-A protein 1-like protein [Arabidopsis thaliana]
+---NQYSSDARSLGgftsCNVCRSNSHVSANCPTlmsepqgqymggt-NAGGGMPRQHVGSY----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * 1812 3190 * * * * 4487 * * 948 * * * * * * * * 4549 1
+ 138 3453 * 1000 1000 * * 5440 1139 0
+
+Q 2 2206 4146 * 3917 * * * * 4545 3893 * 3868 * 1487 2997 * * * * * 2
+ 0 * * * * * * 6020 0 0
+
+K 3 4688 * * 2251 * * * * 2586 * * 4360 * 2781 1628 5108 4728 * * * 3
+ 0 * * * * * * 6563 0 0
+
+G 4 3633 * * 4741 * 1801 3396 * 3298 * * 2446 * * 3309 4066 4207 * * * 4
+ 0 * * * * * * 7032 0 0
+
+N 5 4012 * * * * 3758 * 4287 * * * 2105 4109 1865 3628 3575 3590 * * * 5
+ 65 5344 5687 0 * * * 7216 1042 0
+
+F 6 * * * * 1004 * * * * 2792 * 3958 4634 * 5079 5519 * 3765 * 2972 6
+ 59 4647 * 0 * 0 * 7549 1188 1042
+
+R 7 4154 * 5832 5114 4096 4719 * 5520 2453 4161 * 5942 * 6150 2074 2387 5451 5506 5884 5656 7
+ 20 6150 * 0 * * * 7860 1006 0
+
+N 8 3510 5166 5179 3182 * 1617 * * 5938 4385 * 3694 4221 4518 3115 5092 5791 5712 * * 8
+ 63 6300 5051 1000 1000 * * 8248 1000 0
+
+Q 9 2966 * 4623 4305 * 3207 6295 * 4444 4377 * 6222 1824 2545 5150 6632 * 5179 * 4932 9
+ 108 4013 6599 1575 590 0 * 8154 1183 1007
+
+R 10 3519 6578 4068 4072 * 3710 6241 4995 2959 5008 4690 4045 4591 4544 2460 4344 5759 * 6209 4161 10
+ 32 5515 * 1095 911 0 * 8347 1158 1005
+
+K 11 4692 * 5092 2823 6235 3103 6805 6980 2992 5843 * 4254 3637 5408 2173 3751 5477 5256 * * 11
+ 55 4743 * 2411 300 * * 8607 1284 0
+
+T 12 3823 6800 4098 4703 6513 4388 * 4834 4168 5158 5150 2710 3161 4638 3660 3165 3889 4928 6196 6853 12
+ 48 5662 6287 722 1345 * * 9191 1118 0
+
+V 13 3438 * 4294 5908 * 3498 5192 3296 4467 2974 6866 4634 4722 4819 3899 4217 3655 3557 * 4553 13
+ 115 4722 4699 208 2894 * 0 8316 1329 1000
+
+K 14 4150 * 6234 5701 4923 3363 5875 3966 2868 3996 6246 4661 4776 4556 2849 3840 3744 4202 7267 5356 14
+ 169 3574 5235 2318 323 280 2503 8126 1744 1633
+
+C 15 6040 405 6011 * 5931 5460 * * * 5809 6666 5648 * * 5331 5284 * 4076 7408 6427 15
+ 0 * * * * 3115 177 8328 0 1439
+
+F 16 4463 6806 * 6875 1509 7030 4133 4716 5557 5234 * 4655 6780 5265 4338 4527 7162 5259 4791 2334 16
+ 18 * 6305 2807 222 * 0 8173 1088 1381
+
+N 17 5963 * 5592 6253 5098 4493 6175 4483 2815 5928 7373 2042 4719 4705 2583 4452 3938 4893 6858 6150 17
+ 36 7461 5726 0 * 1766 502 8549 1042 1514
+
+C 18 6492 413 6006 6564 6669 6149 * * 5771 5523 * 6468 * 6667 5833 6537 5401 4350 5290 * 18
+ 0 * * * * 1399 688 8552 0 1502
+
+G 19 4450 * 5397 7506 5265 1158 7134 * 5629 4930 * 3799 5734 3814 3850 4290 6042 5422 4071 6570 19
+ 152 4177 4481 1914 445 1395 690 8583 1388 1287
+
+K 20 4487 * 4740 2747 * 2875 5839 * 2993 6056 6252 4038 7057 3145 3115 3336 6303 5474 7264 5387 20
+ 49 5732 6132 1000 1000 214 2858 8410 1076 1725
+
+E 21 3917 * 4160 3577 4726 4776 6131 7356 3771 4055 5181 4894 2993 5374 3728 2926 3899 5081 * 4281 21
+ 70 6726 4724 682 1409 0 * 8611 1028 1186
+
+G 22 4730 * 4143 5098 * 776 6208 6960 4932 5769 6897 4897 4513 7383 4892 5010 4680 7531 5726 * 22
+ 27 6881 6656 0 * 349 2220 8320 1028 1433
+
+H 23 5031 7013 3907 6310 6613 4530 573 5016 7922 6063 * 7084 6801 6888 * * 3810 * * 6523 23
+ 52 * 4811 * * 598 1559 8280 0 1249
+
+I 24 4546 * 6164 4415 3464 5885 5257 3431 4775 2870 4181 5535 5730 5708 3709 4970 3725 3317 4548 4187 24
+ 54 5559 5986 1000 1000 2552 270 8197 1158 1405
+
+A 25 2020 7259 * 5124 6649 4089 5038 * 3855 5675 5147 5086 3990 4121 4291 2333 5143 4414 * 5183 25
+ 9 * 7259 1000 1000 1667 546 8389 1102 1476
+
+K 26 2783 7271 4561 3937 6447 5189 7408 6542 2709 5064 * 4174 4539 4351 2068 4208 5654 5443 6278 7284 26
+ 35 6740 6126 0 * 1606 574 8456 1007 1397
+
+N 27 4045 6850 2354 3152 5394 4126 7259 5395 4133 * 7487 2655 7167 3865 4464 3702 4028 6116 * 5924 27
+ 10 7152 * 353 2204 2485 284 8526 1040 1444
+
+C 28 4691 496 6494 6288 5672 4859 * 5142 * 5286 6566 6552 * 7380 5158 4948 * 5236 * 7315 28
+ 14 6729 * 0 * * 0 8218 1000 1353
+
+R 29 4839 7277 6929 4904 5943 4686 * 5970 3466 7410 6799 5858 1446 4935 3215 4238 3285 5003 * 5099 29
+ 78 4912 5671 1993 417 748 1305 8212 1305 1426
+
+A 30 2756 7130 5102 4180 5492 2995 4763 * 3517 4660 6881 4067 5337 3743 4081 3075 4621 4322 * 6241 30
+ 410 2486 3866 3218 164 1604 576 8292 2713 1440
+
+P 31 3764 * 5550 4210 5998 3341 5686 7431 3347 4259 6440 3908 2086 4415 3753 4328 4557 5348 6718 * 31
+ 708 2155 2615 2307 326 932 1071 8461 3124 2327
+
+R 32 3967 * 4597 4930 4964 3578 * * 3125 5693 6469 4156 4204 3985 2041 3241 4456 7262 5681 7141 32
+ 436 2194 4561 2657 249 1161 855 8342 2911 3066
+
+K 33 3834 * 3916 3209 6775 2935 * 6244 2934 5897 5308 4123 4009 5053 4443 2999 3801 5355 * 6315 33
+ 283 2643 5800 2918 205 160 3249 8344 2709 2502
+
+K 34 3830 * 5217 5023 7180 2959 5352 3583 3200 3796 6213 4542 4380 4438 2822 4466 5054 3772 * 7101 34
+ 83 4363 7107 1708 527 718 1350 8410 1423 1313
+
+G 35 4305 6343 6962 5453 5447 2853 5765 3501 3590 3342 7523 4238 5061 4551 3046 4537 3392 3918 * * 35
+ 22 6035 * 2328 320 884 1127 8391 1129 1271
+
+C 36 5835 291 4856 * * 4170 * * * * * * * 6480 6257 5844 * 5893 * 5933 36
+ 15 * 6622 * * 1260 780 8400 0 1084
+
+W 37 5047 5987 * 6015 2233 5049 3553 5833 4975 3942 5861 4024 4565 5311 4134 5027 5460 4975 5610 2417 37
+ 9 * 7346 * * 725 1340 8154 0 1220
+
+K 38 5143 * 6281 4139 5677 4367 6106 3830 2732 3592 5298 3005 5440 5801 2576 4692 4373 5112 7337 4830 38
+ 46 5780 6217 2322 322 1535 611 8161 1076 1104
+
+C 39 6652 362 * * * 3469 * * * * * * * * 6349 4429 * 5803 6023 5062 39
+ 11 6995 * 1000 1000 1127 883 8100 1010 1180
+
+G 40 4240 * 6530 5911 6926 1041 4554 6218 3434 6324 * 3388 7151 4809 4493 4997 5901 5119 * 7635 40
+ 23 6679 7394 2807 222 * 0 8340 1017 1064
+
+K 41 4718 * 3857 3150 7496 3454 4989 * 2312 5364 * 4433 6023 3349 3410 3244 4992 4816 * * 41
+ 0 * * * * * 0 8100 0 1180
+
+E 42 3885 * 4802 3280 5973 3543 4628 4831 3382 4364 4900 6272 3541 4890 3639 4394 3703 3551 * 5984 42
+ 0 * * * * 1127 883 8100 0 1180
+
+G 43 5859 * 4523 4057 6014 559 6218 * 7485 * * 3868 5901 * 5693 5183 5878 * * 5907 43
+ 37 5589 7752 2000 415 * 0 8340 1116 1064
+
+H 44 6034 * 7114 5732 5627 5563 365 6597 * 6998 * 5500 * * 6305 6337 4360 5950 * 6575 44
+ 15 * 6549 * * * 0 8000 0 1130
+
+Q 45 7558 * 7215 6524 3178 5708 7512 3236 3652 3385 3401 4803 5237 6550 3357 5409 3985 3625 4149 3811 45
+ 12 * 6891 * * 622 1514 7940 0 1239
+
+M 46 1818 * 5781 5204 5852 4847 7039 5081 3752 3335 3979 4936 5788 7214 4334 2977 5784 4018 7046 5404 46
+ 0 * * * * * 0 7952 0 1097
+
+K 47 3912 7035 4660 4874 7190 4688 7054 5975 2688 5566 5577 5000 5582 4209 1902 3082 4509 5026 7043 6387 47
+ 39 5234 * 459 1876 1482 639 7936 1127 1097
+
+D 48 3734 4863 2315 3173 5725 5572 4797 6715 5370 5889 5590 3351 * 3343 4326 3308 5196 4352 * 7029 48
+ 38 5511 7937 3217 164 * 0 7926 1109 1036
+
+C 49 4403 358 5938 4405 6623 6466 * * 6886 * * 4910 * * * 6510 6590 * 5879 7060 49
+ 22 6032 * 1194 829 0 * 8016 1139 1100
+
+T 50 6339 * 6522 * 6630 5187 5080 6129 2862 4956 7290 5426 1394 5183 3198 4119 3817 5389 * 5231 50
+ 46 5235 7754 1983 421 * * 7902 1118 0
+
+E 51 4566 6237 4940 3225 4835 3873 5947 6244 3585 4585 7308 2805 5981 3386 4977 2999 3102 6258 * * 51
+ 24 5936 * 1585 585 0 * 7961 1034 1075
+
+R 52 4468 6462 4265 5328 6513 4340 * 5772 2440 5909 6780 3729 3290 4258 1990 3894 5113 * * * 52
+ 0 * * * * * * 7802 0 0
+
+Q 53 3952 * 4222 4189 5450 4294 * * 3271 6025 * 4204 1985 2356 3125 5847 * * * * 53
+ 0 * * * * * * 6895 0 0
+
+A 54 1905 * * 3413 * 3895 * * 3960 * * 2786 2088 * * 3889 * 4062 * * 54
+ 0 * * * * * * 4621 0 0
+
+N 55 * * * * * * * * * * * 0 * * * * * * * * 55
+ 0 * * 0 * * * 2363 0 0
+
+//
+�HHsearch 1.5
+NAME 0e5c9e30af579568c535c51a9a27f145
+FAM
+FILE 0e5c9e30af579568c535c51a9a27f145
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:29:09 2013
+LENG 106 match states, 106 columns in multiple alignment
+FILT 107 out of 268 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCEEEEEECCCCEEEE
+EEECCC
+>ss_conf PSIPRED confidence values
+9347888885158898056899999868857775789848889999985799778453269827878886348998724211211589982199775880
+142088
+>Consensus
+xxxxxxFxxqHidxxxxxyCnxxMxxrxxxCKxxNTFIhxxxxxVxavCxxxxxcxnxxSxxxxxxtxCxlxxpxCxYxxxxxxxxixVaCexxxPVHxd
+xxxxxx
+>0e5c9e30af579568c535c51a9a27f145
+MQNWETFQKKHLTDTRDVKCDAEMKKALFDCKQKNTFIYARPGRVQALCKNIIVSKNVLSTDEFYLSDCNRIKLPCHYKLKKSSNTICITCENKLPVHFV
+AVEECP
+>gi|164422319|gb|ABY55257.1| RNase 2 [Oncorhynchus masou formosanus]
+SHRYTHFLRQHVKgDMTIQKCQGVMGYLELtesdsaNCKVKNTFIKANSNQVRAICTGGGTPMGnslFESNNRFPVVICKHkckkktlcqhTHPRCEYEG
+SSSTRKVVIACEREWPVHYGDD----
+>gi|153791763|ref|NP_001093574.1| ribonuclease like 4 [Danio rerio]gi|146351600|gb|ABQ23785.1| RNase 3 [Danio rerio]
+SQSYNDFKRKHLApaGMKEDDCTTLIVTeRKIkeknQCKKINTFILETEDKIKGVCNTPaTDGKN-HKGTGFTVINCTKieNIIDCKYNGVKRTTDIILT
+CENRLPVHYGRS----
+>gi|18376502|emb|CAC86435.1| pancreatic ribonuclease alpha [Berylmys bowersi]
+ESSAEKFKRQHMDpdsipNSSPTYCNQMMKRREMttgSCKPVNTFVHEPLDDVKAICSQGqMTCKNgksncHKSSSTLHITECRLkgssKYPNCDYTTTD
+SQKHIIIACDGNpyVPVHFDASE---
+>gi|1330317|emb|CAA39461.1| eosinophil cationic-related protein [Homo sapiens]
+-----LRGLTSI-SRNQLQCTNAMRVINNyqrRWKNRNTFLLATFANVVNVCGNPtITCPhnrtlnNcHHSGVQVPLMYCNLttpspQnISNCRYAQTPA
+NMFYIVACDNRdqrrdppqypvVPVHLHTI----
+>gi|296214379|ref|XP_002753775.1| PREDICTED: ribonuclease-like protein 12-like [Callithrix jacchus]
+-------EHLHVDypqeGVPVpaRYCNHMIIQRIIrepdhTCKKEHVFIHERPRKINGLCTSpkKVACQNlsstfcFQSETKFKMTVCQLiegtRYPACR
+YRYFPVEGFVLITCDELGPDSFQGY----
+>gi|300872929|gb|ADK39277.1| RNase-Ginf2 [Gerrhonotus infernalis]
+-DTFESFKELHVDypktgaPNDDEYCKKVMGGRGRTKLKANTYIHAPDSELLAACNRKKYKLNheYGRTSRLPTTLCT--YGDRVFLGSSLPGTNKVLCV
+NWKPVAFRG-----
+>gi|292622086|ref|XP_002664865.1| PREDICTED: hypothetical protein LOC100332602 [Danio rerio]
+----NVFLKRHIPdGVPktwDQNAWE-AFLRKIkTCgRPTQSFFRATEkQRVENVCSKDGGKtlsGNlCISKEKFSFVTVRIdTEGACGIRSMrNETKHI
+ILACEDIgdvcQPVHFEGN----
+>gi|281345895|gb|EFB21479.1| hypothetical protein PANDA_019758 [Ailuropoda melanoleuca]
+--------------TDPEYCTAEMKMKNVhnkfRCVREHFFLQVAYEELQKLCKNIfVPCKNgvkkcHRSRQLIEGVYCNLtrgvRMSDCEYESSYRQGY
+VLITCRWQndiqeiIPAYV-------
+>gi|149568755|ref|XP_001515593.1| PREDICTED: similar to ribonuclease 13 [Ornithorhynchus anatinus]
+-SKARTFRLMHIDfprsefaPGFRGYCNGLMAYVRAqreswQCPEKHFVLHAPAATVRAICAHTdSFCEdfGefcTRSHKPLPVTTCARtpglPPSVCRY
+NATVhvQSHRVWLLCSS-------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 4292 3672 3268 1542 * * * * 3637 * 4025 2894 * * * 2767 * * * * 1
+ 0 * * 4494 66 * * 4474 1139 0
+
+Q 2 3959 * 4179 4581 * 6015 3714 * 5821 * * * 3347 2013 3808 2719 3005 * * 4814 2
+ 0 * * 1000 1000 * * 5214 1035 0
+
+N 3 3734 * 2739 5856 * 5649 * * 4907 * 4371 3528 4819 5088 1807 3108 3513 * 6031 * 3
+ 29 * 5654 * * * * 5262 0 0
+
+W 4 2265 * * 6825 3448 5795 6641 4793 * * * * 7144 * * 3209 6890 4923 2788 1617 4
+ 0 * * * * * 0 5478 0 1035
+
+E 5 4138 * 6665 2406 * * 6004 4723 3747 5201 5444 3466 * 1612 4236 4284 5626 5369 * * 5
+ 24 * 5913 * * * 0 5572 0 1035
+
+T 6 6137 * 4021 * * 6710 3701 * 2321 5769 6533 5081 5869 6587 3735 3861 2740 4543 2466 4879 6
+ 0 * * 0 * 908 1099 5626 1050 1150
+
+F 7 * * * * 61 * * * * 5449 * * * * 5781 * * * * * 7
+ 0 * * * * * 0 5641 0 1035
+
+Q 8 5227 * 6934 2685 * 5787 * 5531 3411 1615 6199 6703 * 2459 3835 5441 6830 6126 5698 6822 8
+ 23 * 5960 * * * 0 5661 0 1035
+
+K 9 6366 * * 4010 * * 5879 2566 2734 4074 * 4168 * 4263 1730 * 3184 * 6505 * 9
+ 0 * * 1738 514 0 * 5664 1150 1150
+
+K 10 * * * 6833 5719 * 4273 6164 2472 3925 5633 * * 919 3593 * 5129 * * * 10
+ 42 5982 6292 0 * * * 5667 1050 0
+
+H 11 * * 6665 * * * 41 * * * * * * * * 5764 * * * * 11
+ 17 6407 * 0 * 908 1099 5664 1003 1150
+
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+//
+�HHsearch 1.5
+NAME 0f066235c0e8814be13f086538bfd823
+FAM
+FILE 0f066235c0e8814be13f086538bfd823
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:48:16 2013
+LENG 112 match states, 112 columns in multiple alignment
+FILT 47 out of 49 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEECHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
+HHHHHHHHHCCC
+>ss_conf PSIPRED confidence values
+9500000244433566788778898378899999998588875358987443476699999999999853577878886229999999999999999999
+999999886339
+>Consensus
+GAvvGxxxGyxlGxxxxrxxxxFxnpxExrYYxenxxrypdxVyYxxxxxxvtxexFVxdCvNxTxxxxxxxxsxxxxnxsexexrvxxrvixemCvxqY
+xxxxxxxxxxxx
+>0f066235c0e8814be13f086538bfd823
+GSVVGGLGGYMLGSAMSRPLIHFGSDYEDRYYRENMHRYPNQVYYRPVDQYSNQNNFVHDCVNITVKEHTVTTTTKGENFTETDIKMMERVVEQMCITQY
+QRESQAYYQRGA
+>gi|45382625|ref|NP_990796.1| major prion protein homolog [Gallus gallus]gi|212615|gb|AAA49041.1| prion-like protein [Gallus gallus]
+GAVVGGLGGYAMGRVMSGMNYHFDRPDEYRWWSENSARYPNRVYYRDYSSPVPQDVFVADCFNITVTEYSIGPA-AKKNTSEavaaanqteveMENKVVT
+KVIREMCVQQYREYRL-------
+>gi|327284127|ref|XP_003226790.1| PREDICTED: major prion protein homolog [Anolis carolinensis]
+GAAVGALGGYLLGRSMSNMQFGFPNQYDERWWYQNRDRYSDQVYHPPYNPSVSREVFVRDCVNVTVTEY-IQPT-GNQTADEVEMRVVPLVVREMCTEQY
+---RL-------
+>gi|55667998|gb|AAV54126.1| prion protein [Xenopus laevis]
+GAAAGAIGGYMLGNAVGRMSYQFNNPMESRYYNDYYNQMPNRV-YRPMyrgEEYVSEDRFVRDCYNMSVTEYIIKPAegKNNSELNQLDTTVKSQIIREM
+CITEYRRGS--------
+>gi|82780737|gb|ABB90540.1| stPrP1 [Sparus aurata]
+GAVAGMAVGYGLGRFP-RPHFNFRNPEEEHYYNNYMYRrYGTqstdekdygrdYV-YKLPPRAETYDKFMSRCMNRTDLikDQGSSSTTPnnqgggDEDd
+dtVSIEEIgypSLIEQLKARRCVGLYMEYSEKFLE---
+>gi|47223680|emb|CAF99289.1| unnamed protein product [Tetraodon nigroviridis]
+GAVAGMAVGYGLGRFP-RPHFGFRSPSEEYYYNNYMYRQYglkstdERDYGRDYvyklpPRAESYEQFMDRCMNRTNLLKDQGSSKaeDNDTVS-IEEIG
+YPALIEQMksrrCLEEYMAKSEK------
+>gi|123303107|tpe|CAJ75791.1| TPA: doppel protein Dpl [Echinops telfairi]
+-------------------DVDLGAD-GNRYYEAHYWQFPDGIHYDGCsDANVTREMLVTRCINATQAANQAEFSAppRDQQDSRLHQRVLWRLIRELCS
+AKRCD----------
+>gi|123303103|tpe|CAJ75789.1| TPA: doppel protein Dpl [Monodelphis domestica]
+-------------------VIDFGEE-GNSYYATHYSLFPDEIHYAGCaESNVTKEVFISNCVNATRVINKLEPL-EEQNISDIYSRILEQLIKELCALN
+YCE----------
+>gi|239503711|ref|ZP_04663021.1| putative surface antigen [Acinetobacter baumannii AB900]
+GAVVGGIIGGVVGAIAGNDIAQTNNqkddsnywQEEDNYWRENYKKMP---YYTE-DKNLEYDRDYRAAYRLGY-ENRVDNN-AEINFSEVESKLKTK--
+--------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
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+
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+
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+
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+
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+
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+
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+R 110 3590 * * * * 3510 3542 * * * * * * 3439 896 * * * 3136 * 110
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+G 111 3719 * * * * 769 * * 3282 3708 * * * * 2665 * * * * * 111
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+A 112 914 * 3439 3590 * * * * * * * * * * 3510 3436 3136 * * * 112
+ 0 * * 0 * * * 1328 0 0
+
+//
+�HHsearch 1.5
+NAME 0f0e0cc97063da4305095efeb6623b6b
+FAM
+FILE 0f0e0cc97063da4305095efeb6623b6b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:55:11 2013
+LENG 98 match states, 98 columns in multiple alignment
+FILT 154 out of 1042 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEEECCCCCEEECCEEEECCCCEEEEEECCCCCEEEEEECCCCCCCCCCCCCCCCEEECCCCEEEEEECCCEEEEEEECCCCCCCCEEEEEEC
+>ss_conf PSIPRED confidence values
+94999998269861582787998799999999899983379993886655544552246358679987999948998899998987646888999989
+>Consensus
+xxxxvxxxxxxxxxxfxPxxixvxxGxxvxxxnxxxxxHxvxxxxxxxxxxxxxxxxxxxxxxxpgxxxxxxfxxxGxyxxxCxxHxxxgMxgxIxVx
+>0f0e0cc97063da4305095efeb6623b6b
+ANATVKMGSDSGALVFEPSTVTIKAGEEVKWVNNKLSPHNIVFAADGVDADTAAKLSHKGLAFAAGESFTSTFTEPGTYTYYCEPHRGAGMVGKVVVE
+>gi|319783957|ref|YP_004143433.1| hypothetical protein Mesci_4273 [Mesorhizobium ciceri biovar biserrulae WSM1271]gi|317169845|gb|ADV13383.1| hypothetical protein Mesci_4273 [Mesorhizobium ciceri biovar biserrulae WSM1271]
+--PELIIGSADSTYAVNQKDFELIAGQGYRWKitSKGGFEYkfvtdlfrNVWMDQIVINdLEVHmdG--GPAWLEFDDAGTIQVQFhtVRPGEYTWSVPD
+LADKGLKGKITIK
+>gi|342797151|gb|EGU32807.1| hypothetical protein VIS19158_17171 [Vibrio scophthalmi LMG 19158]
+-VIHVIL-SDDKPIQFKKD-VNIEENDVVQFVvmNTGTKSHEFAIGSKDELSrhnkmmTQMAGMEHdtsSSIIIAPKKARQFtwHFHGDKHVEIACNikG
+HQQHSKSLMIN--
+>gi|225558376|gb|EEH06660.1| conserved hypothetical protein [Ajellomyces capsulatus G186AR]gi|325094158|gb|EGC47468.1| extracellular serine-rich protein [Ajellomyces capsulatus H88]
+-TIDVNVGD-K-GLNFNPDIIKAKPGDDIVFHFF-PKNHDVTEgkfDAPCAP--SDGGFYSGLINADGSqpdATFTVRINNTNPIWLYCStpRHCQGGMS
+AVI---
+>gi|146343114|ref|YP_001208162.1| hypothetical protein BRADO6311 [Bradyrhizobium sp. ORS278]gi|146195920|emb|CAL79947.1| Conserved hypothetical protein [Bradyrhizobium sp. ORS278]
+-TIEISV-KD---NKFQPAELKVPADTPIVFKikNLDAAPIEFESDPL----------Q-FETIVKPNMEGVVKVkaQKPGRYEFFDDLHQN-N-KGTLV
+VE
+>gi|261857226|emb|CBE70465.1| nitrous oxide reductase [uncultured bacterium]
+-------------PHYSLDKFEVNEGDEVTVFltNTDdieNALrrrHGDRPAGDSF-----------GHLQGRSagrALVVLPVvlPRPA----------
+-----------
+>gi|152992359|ref|YP_001358080.1| multicopper oxidase [Sulfurovum sp. NBC37-1]gi|151424220|dbj|BAF71723.1| multicopper oxidase [Sulfurovum sp. NBC37-1]
+-------------KAMDMKRIDevVPLGDTEIWEvnNMMGMDHNFHIHathfrvierNDSAANVLEneKGY-KDVVYLKGNETVKLlvKMTDYTdatvPY
+MYHCHflEHENNAMMGQFTVV
+>gi|82703780|ref|YP_413346.1| cytochrome c oxidase subunit II [Nitrosospira multiformis ATCC 25196]gi|82411845|gb|ABB75954.1| Cytochrome c oxidase, subunit II [Nitrosospira multiformis ATCC 25196]
+-----------HMWYWEMDRDQVEPNQPVDIRVtSADVNHGFGIYDPDLR-----LI--AQAQAMPGYTNVIhiTFPKEGTYRVLCMeycgvAHH--NMM
+TEIKVG
+>gi|87306766|ref|ZP_01088913.1| hypothetical protein DSM3645_10542 [Blastopirellula marina DSM 3645]gi|87290945|gb|EAQ82832.1| hypothetical protein DSM3645_10542 [Blastopirellula marina DSM 3645]
+------------DYLFHPYLTFIRTSQKAKFNNLDPVGHNIKISGFA-----NSP---GPGIVPKGGQWVQSFVQeeRIPYPVHSTIYP--WMEADLLI-
+>gi|242096748|ref|XP_002438864.1| hypothetical protein SORBIDRAFT_10g027460 [Sorghum bicolor]gi|241917087|gb|EER90231.1| hypothetical protein SORBIDRAFT_10g027460 [Sorghum bicolor]
+-------------WSVPAAgaesyntwagRLRFQIGDQLLFVYPK-ETDSVLLVDAAAYNAC--NT-SSYITRFDDGSTVFTLDRSGPFFFVSGndASCR
+ANEKLIVVV-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 2146 * * 2946 * * * * * * * * * 2237 1210 * * * * * 1
+ 0 * * * * * * 4090 0 0
+
+N 2 5170 * 5130 3174 * * * * 5309 * * 3076 * 5034 * 4103 1085 2956 * * 2
+ 0 * * * * * * 6664 0 0
+
+A 3 4764 * * 5407 5086 * 2916 2131 5715 5449 * 5451 5262 5647 5452 * 4504 2091 5522 3117 3
+ 60 5647 5578 3000 193 * * 7471 1041 0
+
+T 4 5909 * 3804 2443 * * 4055 5284 3753 6239 * * 4179 5671 3817 3311 2003 4737 * 5565 4
+ 0 * * * * 1041 960 7609 0 1196
+
+V 5 4638 * * * * * * 1795 * 3185 * * * 5838 * * * 878 * * 5
+ 0 * * * * * 0 7646 0 1041
+
+K 6 4317 * 5837 2952 * * 4684 4693 4889 3446 5606 4515 * 3682 3746 3988 2401 3323 * 5008 6
+ 0 * * * * * 0 7646 0 1041
+
+M 7 * * * 5912 4380 * * 2474 * 2757 2137 * 6001 * * * 5525 1545 * * 7
+ 447 4205 2237 802 1230 * 0 7646 1298 1041
+
+G 8 3658 * 5472 3155 * 1408 * * 3514 * 4051 5175 * 5638 4420 4273 3914 4358 * * 8
+ 329 3777 2933 1018 982 783 1255 7218 1350 2668
+
+S 9 2983 5079 * 4341 * 2549 * * 5506 * * 4211 3886 * 4801 1719 3133 5239 * * 9
+ 515 4596 1950 1000 1000 2097 384 7335 1233 2470
+
+D 10 5184 * 1767 3323 * 3595 * 5036 4162 * * 3648 3561 4297 * 3236 3504 * * * 10
+ 322 * 2321 1000 1000 1811 484 6876 1028 3350
+
+S 11 2841 * 2037 3728 * 3175 * * * * * 3435 4000 5068 5141 2990 3447 * * * 11
+ 249 3513 3823 2297 328 654 1456 6866 1338 3594
+
+G 12 6234 * 4499 3772 5617 1713 4364 6143 3402 * 4881 5219 6040 3497 4572 3144 4215 * * 6263 12
+ 22 * 6049 * * 2894 208 8071 0 2274
+
+A 13 3652 * 3090 3071 6476 2377 * * 3813 6544 6585 3385 5252 3625 4458 3853 6271 4901 * 5380 13
+ 13 6813 * 523 1718 269 2557 8620 1083 2236
+
+L 14 5313 4520 5177 7244 3194 5510 6860 5238 5149 2846 3030 4251 4384 * 6975 5307 5209 5017 3475 2648 14
+ 0 * * * * 0 * 9056 0 1122
+
+V 15 2665 6070 5518 5065 * 3601 4990 5266 3232 4410 5995 5131 * 4876 3429 3373 3524 4567 * 3544 15
+ 0 * * * * * * 9173 0 0
+
+F 16 5524 * * * 842 6660 * 4773 * 5868 4656 * * * * * 6670 4423 4406 2228 16
+ 0 * * * * * * 9173 0 0
+
+E 17 4906 * 2687 2793 6127 5064 5255 5178 4593 4407 * 4291 5641 6078 5013 2640 3925 3085 7237 6283 17
+ 9 7277 * 3170 170 * * 9126 1000 0
+
+P 18 5187 * 4843 5775 6524 7098 * 6144 5287 4816 4991 6557 629 4559 6155 5059 4974 5704 * * 18
+ 10 * 7231 * * * * 9240 0 0
+
+S 19 2972 * 3026 3645 5954 4379 5325 7067 3468 6520 6836 3144 3083 5124 5007 3122 4548 * 7152 7007 19
+ 125 3870 6082 2449 292 0 * 9215 1885 1004
+
+T 20 3690 * 5627 3148 6194 4986 5469 6015 3916 4743 6504 3720 4708 4112 3685 4316 2920 2874 * 5429 20
+ 9 7366 * 1000 1000 0 * 9281 1000 1127
+
+V 21 3941 * 6496 * 3783 * 6663 1759 6719 1890 5931 4873 * 5168 * * 6084 2731 * 5458 21
+ 38 5751 7135 722 1345 * * 9333 1206 0
+
+T 22 5012 7417 4775 2550 6048 5273 4949 6112 4004 7077 * 3662 5751 4005 3740 5223 2272 3197 6199 7109 22
+ 48 4922 * 471 1843 0 * 9269 1559 1219
+
+I 23 3207 * * * 3885 * * 2078 * 2454 * * 7235 * * 7236 6736 1540 5028 7052 23
+ 0 * * * * * * 9336 0 0
+
+K 24 4352 * 4307 3322 6250 5824 4380 7021 2584 7418 * 4068 2832 3171 3573 4595 5690 4327 * 4809 24
+ 0 * * * * * * 9346 0 0
+
+A 25 2427 * 6194 4198 7360 7304 * 4915 2894 4567 * 7097 3110 4868 3981 4619 4685 2282 * 5811 25
+ 0 * * * * * * 9346 0 0
+
+G 26 * * 5396 6334 * 370 6399 * 7381 * * 3510 5823 * 5579 5296 5596 * * * 26
+ 58 4882 7545 541 1676 * * 9346 1644 0
+
+E 27 5645 * 1493 2748 * 4852 7553 * 4248 * 6762 4942 6416 2743 6534 4207 3902 4363 * * 27
+ 105 4075 6491 880 1131 0 * 9351 2007 1000
+
+E 28 4587 7468 6246 4420 * * 6013 5271 3190 4421 6692 5607 3264 4581 3290 4523 1776 3966 5838 * 28
+ 0 * * * * 0 * 9345 0 1080
+
+V 29 4773 * * 5891 5115 * * 2319 6771 2643 * * * * * * 7411 1044 * 4128 29
+ 33 5485 * 3969 95 * * 9346 1268 0
+
+K 30 4554 * 5719 3241 7566 * 5384 3814 3258 4625 6214 4870 * 4094 3043 4659 2333 3112 * 7367 30
+ 30 5621 * 1000 1000 * * 9346 1216 0
+
+W 31 6194 * * * 1527 * * 3051 * 2401 6771 * * * * 6014 * 3797 2102 * 31
+ 61 4595 * 1000 1000 * * 9346 1621 0
+
+V 32 5670 * 6314 3366 6255 * 3681 3467 3323 4857 7027 4999 6392 5179 3190 4903 3317 2341 * 4806 32
+ 418 1992 * 1089 916 * * 9346 4658 0
+
+N 33 7142 * 5475 7314 3729 7072 5738 5356 * 4604 6550 767 6343 7191 5915 5592 6886 4738 4427 4324 33
+ 102 3878 * 735 1324 * * 9346 2103 0
+
+N 34 3935 * 3226 4004 5491 4785 4757 5712 4685 4347 4716 4032 5214 3911 4307 3535 2753 4036 * 5368 34
+ 174 4218 4067 260 2600 * * 9346 1870 0
+
+K 35 3792 * 1610 4367 * 2315 7479 * 3670 * 6664 4245 6306 5656 7335 3392 3969 7310 * * 35
+ 252 3579 3708 858 1157 332 2283 9283 2362 2097
+
+L 36 3778 * 2468 4566 7463 3049 5389 5776 3367 6124 4898 3851 3998 3970 5770 3411 4333 4920 * * 36
+ 169 3298 6859 2331 320 442 1922 9147 2477 2353
+
+S 37 4353 * 5935 4323 5526 3245 4670 3289 3775 3833 3265 5138 5682 5243 6078 4328 3937 2720 6288 * 37
+ 39 5847 6761 1033 967 1117 892 9321 1361 1434
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+//
+�HHsearch 1.5
+NAME 0f1c654429f6f65b407c9e9dde84eba4
+FAM
+FILE 0f1c654429f6f65b407c9e9dde84eba4
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:25:17 2013
+LENG 87 match states, 87 columns in multiple alignment
+FILT 135 out of 1476 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 11.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCEECCCCCCCCCHHHHHHHHHHHHCCCCCEECCCCCCCCCCHHHHHHHHHHHCCCC
+>ss_conf PSIPRED confidence values
+997745798889748899999999985589871179787731307899999997358987368989794489999999999874899
+>Consensus
+xxxxxxCxxCxxxxxxxxxxxxhxxxxxxxxxxxCxxcxxxxxxxxxlxxHxxxxxxxxxxxCxxCxxxxxxxxxlxxHxxxhxxxx
+>0f1c654429f6f65b407c9e9dde84eba4
+MEKPYKCPECGKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFSRSDHLSRHQRTHQNKK
+>gi|74194495|dbj|BAE37293.1| unnamed protein product [Mus musculus]
+YTQNLSMSRSYNVCATSFGFPSSFGRYQETPVgeQHCEQKVKNCPSAKSFYIHEMNDNADIDNEHKPFGRAPSSFGSCESRGRINTRKK
+>gi|328719973|ref|XP_003246915.1| PREDICTED: transcription factor Sp8-like [Acyrthosiphon pisum]
+-------------------------------mrtkskktgSYTCpnKSCNKIYKSKG-lQSEYRRqsnls---iSYKFTCPNCCRRYSHKPRLVHHLKHE
+cGYKRF
+>gi|1363187|pir||A56229 lymphoid transcription factor Ikaros/LyF-1, form IV - mouse
+GADGFRDFHAIISDRGMPSNVKVETQSDEENGRACEMNGEEC------------------------AEDLRMLDASGEKMNGSHR--
+>gi|26338808|dbj|BAC33075.1| unnamed protein product [Mus musculus]
+------------NVAKSLHVSVLFKST---KEFILTKSPRKLINEE-----------------------------------------
+>gi|335305641|ref|XP_003360261.1| PREDICTED: transcriptional activator GLI3-like [Sus scrofa]
+------SRQSLVPTPSQRMLMLGVHSPVRRRIAGTAlsACfpenliydTTVYAVATGLFPSTQQISALNRLILRLgYLFSINILSYSAVQLlTAELMEK
+>gi|255933664|ref|XP_002558211.1| Pc12g14050 [Penicillium chrysogenum Wisconsin 54-1255]gi|211582830|emb|CAP81032.1| Pc12g14050 [Penicillium chrysogenum Wisconsin 54-1255]
+----SRAGSCLEDLVCLGVNAAYttIFPRHPDQALQVPCLPKSLyktlAK-saqrDLLKRHVAGH--------------------------------
+>gi|312383158|gb|EFR28349.1| hypothetical protein AND_03879 [Anopheles darlingi]
+--------------------------------FQSETGEDSVKADiLDVLLAGRSKDEKNQ--IAPLLGVY-FLHELKTLsNLSHQLL-
+>gi|170056553|ref|XP_001864081.1| conserved hypothetical protein [Culex quinquefasciatus]gi|167876178|gb|EDS39561.1| conserved hypothetical protein [Culex quinquefasciatus]
+-----------------MNRIFQGASDEAK-----ASLLQDF-WIPKIRFM------------------------------------
+>gi|312093630|ref|XP_003147750.1| hypothetical protein LOAG_12188 [Loa loa]gi|307757084|gb|EFO16318.1| hypothetical protein LOAG_12188 [Loa loa]
+-PTETNPQLGHTLANTRNNYGQSSLGQPNYS-------GNQA----VLRRHkkYSRRASQ--F-CKLAQF-------LHFYPPQSFSA-
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+T 54 3335 * 4975 4458 6355 5273 5001 4001 3804 4299 5094 4553 4148 4064 3589 3462 3563 3242 * 5856 54
+ 74 4319 * 2178 360 2273 334 11607 2047 2830
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+
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+ 42 5461 7372 3992 94 1328 733 11539 1291 2896
+
+K 62 4738 5625 6736 3065 * 4763 * 3899 2908 4740 6745 5739 3781 3696 3410 3354 3707 4067 6108 5773 62
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+
+C 63 * 388 * 6502 * 6739 5903 6278 6916 4705 * * 6333 * * 5228 6024 4160 6090 6163 63
+ 42 5116 * 1994 417 2486 284 11402 1440 2008
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+C 66 5218 433 6163 * 5195 5947 * 5081 * 5015 * 6216 6040 * * 5536 6202 5432 6634 5835 66
+ 47 4952 * 3889 101 2104 382 11417 1429 2152
+
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+F 70 5251 4617 * 5926 1281 * * 4512 * 2641 6677 * 5001 * * 4716 3814 6593 * 2834 70
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+H 79 * * * * * * 312 5288 5683 5199 * * 5950 5773 4903 6062 6143 * * 5305 79
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+
+Q 80 5652 6354 * 4063 5129 4860 4892 3819 3800 2490 2901 6095 6597 3377 4222 5569 5622 3467 6736 4610 80
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+
+H 83 5133 5313 5402 4552 * 5887 742 6596 5989 5363 * 4585 * 4963 4930 4541 * 4810 * 5078 83
+ 20 6197 * 1000 1000 * * 10793 1007 0
+
+Q 84 6226 4701 * 5431 6095 4518 2057 5132 4670 4318 5100 4385 6829 4368 5037 2961 2557 6326 * 4919 84
+ 36 6321 6393 2585 263 * * 10645 1000 0
+
+N 85 4131 5005 3772 4413 * 1651 * * 3304 5894 5229 3813 4392 * 3202 4574 4544 5959 * * 85
+ 0 * * * * 0 * 10683 0 1000
+
+K 86 3617 6115 3318 1751 5938 5260 * * 3288 4718 5597 3602 5998 3585 4946 5930 4655 4909 * * 86
+ 0 * * * * * * 10297 0 0
+
+K 87 5424 * * * 5410 4539 5671 * 1242 4434 * 5424 5082 4378 2626 3542 4325 * 5447 * 87
+ 0 * * 0 * * * 9440 0 0
+
+//
+�HHsearch 1.5
+NAME 0f2381e4f46aa5af8618fb2c6a96974d
+FAM
+FILE 0f2381e4f46aa5af8618fb2c6a96974d
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:33:29 2013
+LENG 162 match states, 162 columns in multiple alignment
+FILT 111 out of 666 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCEEEEEEEECEEEECCCCCEEEEEEEEEEECCCCEEEEEEEECCCHHHHHHHHHHHHHHCEEEEEECCCCEEEEEEEEECCEEEEEEECCCCCCC
+CCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHCC
+>ss_conf PSIPRED confidence values
+9822325999999663887189986999999998479986985065645068999999987741579997058600067899988799999878999886
+14739999997379674999716889778899999999984599999998819985763066
+>Consensus
+xxxxxxxxxvlxvxrvxkxtxxGrxxxfxalvvvGnxxGxvGxGxgKaxxxxxAixkAxxxAxxnlxxvxxxxxTIxxxvxgkxgsxxVxlxpapxGxGi
+xaxxxixxilxlaGixdvxxkxxGsxnxxNxvkAtfxaLxxxxtxxxiaxxrgxxxxxxxxx
+>0f2381e4f46aa5af8618fb2c6a96974d
+MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGV
+IAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG
+>gi|148680994|gb|EDL12941.1| mCG51731 [Mus musculus]
+-----FplgtslNDEVLKIMPVRKQTWAGQGTRFKALVTISDYDDHTGLGVKYSTEVPMPSEEPQSWPSFPSSLCREAtgehdwqaPR---CPMQGHrsq
+wlCAG-TSQSHPCPTGTGIVSASVLKKLLMIPSIDDCYTSARGYTaTLGNFAKATFDVISKT--------------------
+>gi|340373345|ref|XP_003385202.1| PREDICTED: 28S ribosomal protein S5, mitochondrial-like [Amphimedon queenslandica]
+----DFHSVILDMYRARWKCSMGSQFAIQTSVIVGNGKGMVGFGVARSKDMRGCIRRAKNRAVKQLRCIPIcEGHTIFHNIKSKCVRTRVLMERKEKGFG
+LRCNPKLQAVMQLIGIKDIRIKQLGSNHVGHLVRATLSGLLGQETYESLANKTGE--------
+>gi|340503743|gb|EGR30274.1| hypothetical protein IMG5_136340 [Ichthyophthirius multifiliis]
+----------LSRGLTTKVTTLQRIQSYRYLIFMGNGNGLVGYGKGKGSDFEEALDNAILHCKRNLIAIPLDlYHTVPRQLYGQYNRFEITVTPAR-TFN
+PWGSPIIASMLLLTGFRHCRFQTVSKKiNPYSMIMAYFKMITQNKTPKDICEETGQKVYR----
+>gi|242085790|ref|XP_002443320.1| hypothetical protein SORBIDRAFT_08g017450 [Sorghum bicolor]gi|241944013|gb|EES17158.1| hypothetical protein SORBIDRAFT_08g017450 [Sorghum bicolor]
+------------------------------------------------------------------------------------------MPLAPRGPGS
+SPPVSPRMSSSSLELRTSSPRPMASPrHCESNFYATFDCLMKTygfLTPEFWTETKY---------
+>gi|330802661|ref|XP_003289333.1| hypothetical protein DICPUDRAFT_80106 [Dictyostelium purpureum]gi|325080586|gb|EGC34135.1| hypothetical protein DICPUDRAFT_80106 [Dictyostelium purpureum]
+--------NLVSVGRHTSVTRAGRVFNFSATVFNGDGEGTASRGYGKGDTAVSALRRATKDAERRAFTLDRFrDYTLPSGLDMKYRSTKVRFFKSKDYDQ
+MDhSGYKQTIILPTIGLHGVTFRTYGRRNWNNVLLAIQNGLPNYTNPEEAARIMGKRFIV----
+>gi|71665096|ref|XP_819522.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]gi|70884826|gb|EAN97671.1| hypothetical protein, conserved [Trypanosoma cruzi]
+------------DMRVVKFSPKDHRQWIYCVLYVGSGKGIAGWGRAVAPSTQEAKKEAIREAFSNIIAVDLEQEGPMYPVRVNADGVRVLLYPAKR---I
+VANFRVADILCAFGFQHAGCRINlkATNNpksPTHTVEGVFEAVKALRSVSEIAASRGKVPHS----
+>gi|294932638|ref|XP_002780367.1| hypothetical protein Pmar_PMAR016562 [Perkinsus marinus ATCC 50983]gi|239890300|gb|EER12162.1| hypothetical protein Pmar_PMAR016562 [Perkinsus marinus ATCC 50983]
+-NYEGLRQHLMAVSRLCSMAPNGRVYYYRCILMVGNGKGVYGFGVGYGNTITTARADAAMQALKRLQFVDLDsSRTLHAPVIAREYGQKCKILPLPAESG
+ILCNRRYLPWVYIMGLHNVELKFEGELSWLSRTRAITRTTSMIMSRRTVANGEGKK-------
+>gi|170056144|ref|XP_001863899.1| 40S ribosomal protein S2 [Culex quinquefasciatus]gi|167875968|gb|EDS39351.1| 40S ribosomal protein S2 [Culex quinquefasciatus]
+-------------------------------------------------MIMHAIRGAIILAKLSVVPVRRGywgnkigkPHTVPCKVFGKCGSVLV--R
+PAWPCLPLTSP-----LL-ADSPDFCDARSCCSTRPFDFVAA----------------------------
+>gi|11496544|ref|NP_044554.1| ribosomal protein S5 [Toxoplasma gondii RH]gi|5231247|gb|AAD41141.1|U87145_10 ribosomal protein S5 [Toxoplasma gondii]
+-----ILQKIIEIKKISKTKQKGRIRRFKVLLLIGAKNAWIGIGVSKDFYLQEAINKARFFAFKKIYFFYiiLEklfyySNTIN--------KIKCIIIY
+KPIFYGIQVSFLIQIFLDLLGYNVLIIKIFKHTtkyTLINF-------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 2633 * * * * * * * * 1465 1617 * * 2732 * * * * * * 1
+ 0 * * * * * * 2644 0 0
+
+P 2 3277 * 3293 * * * * * 3188 * * 1060 2283 * * * * * * * 2
+ 0 * * * * * * 3456 0 0
+
+E 3 3901 * 4158 1842 * * 3351 * 2437 * * * 2686 * 4232 * * * * 3226 3
+ 0 * * * * * * 3831 0 0
+
+T 4 4746 * 3082 1722 * * * 5335 3191 * 4840 4207 4643 * 3711 3252 4371 4364 * * 4
+ 113 3732 * 1000 1000 * * 4541 1119 0
+
+D 5 6601 * 1956 2936 * 2771 * * 4237 * 6109 3280 4604 3577 4997 3073 6774 * * * 5
+ 96 3963 * 778 1263 * * 5480 1206 0
+
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+
+E 7 5114 * 3322 2135 4979 6062 5206 5803 3053 4023 * 4374 * 3549 2870 4041 * 5287 * 6265 7
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+
+E 8 * 5306 3028 1669 6134 5386 6496 * 5677 * 5502 6654 * 4240 3720 3066 3743 3641 * 4884 8
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+
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+
+M 10 * 4999 * * 5434 5420 * 2389 * 2004 5038 6195 6383 * * * 5330 1318 * * 10
+ 27 5764 * 3907 100 * * 5963 1039 0
+
+I 11 * * * * * * 5490 2078 * 1439 3523 * * * * * * 1811 * * 11
+ 0 * * * * * 0 6147 0 1039
+
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+
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+
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+
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+
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+
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+
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+ 38 5254 * 0 * 0 * 6151 1095 1105
+
+Q 20 4981 4922 5663 * * * 5542 7255 5302 5515 4734 6963 * 7286 5112 5934 872 2442 6280 * 20
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+
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+
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+
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+
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+
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+
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+
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+
+K 47 7133 5307 * 7041 4902 * * 6532 640 * * * 7119 * 3645 5123 4679 4166 * 3973 47
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+
+A 48 1322 * 3440 5651 * 2154 5200 * * * * * * 5560 * 2218 * * * * 48
+ 12 6936 * 0 * * 0 6164 1000 1024
+
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+
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+
+Q 56 3826 * 3760 3076 6919 * 5646 7197 2723 * * 4320 * 2923 1882 4526 5648 5209 * 7144 56
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+
+A 58 248 * * * * 3645 * * * * * * 5145 * * 4323 * * * * 58
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+
+Y 60 4707 6887 * 3015 5525 * 5922 3497 3063 3419 4578 3145 * 5456 2485 4358 5601 4997 5256 7279 60
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+A 160 1000 * * * * * * * * * * * * * * 1000 * * * * 160
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+Q 161 * * * * * * * * * * * * * 0 * * * * * * 161
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+
+//
+�HHsearch 1.5
+NAME 10cfcdaad4a10e98aec756d8a15574d9
+FAM
+FILE 10cfcdaad4a10e98aec756d8a15574d9
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 11:56:34 2013
+LENG 154 match states, 154 columns in multiple alignment
+FILT 103 out of 156 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEEEECCCCEEEEECCEEEEECCCCCCCCCCEEEEEEECCCCCCCCCEEEEEECCCCEEEEECCCCEEEEEEEECCHHHCCCCCCCCCEEEEE
+EECCCCCEEEEECCCCCCEEECCCCCCEEEEEECCCCCCCCCCCEEEEEEECCC
+>ss_conf PSIPRED confidence values
+9887648889961058899999999951378887554479999877887557988999974997899982499959999855735624377822006999
+963799389997116995797477799078977168987677525779976079
+>Consensus
+xxxxxxxxxixDxxqkxlvLxxxxllAxxxxxxxxxxxxxxxxxxxxxxxxxxxPVxLgIxxxnlxLsCxxgxxPxLqLeexxxxxLxxxxxxxxrFlFy
+kxxxGxtxtFESaaxPgWFIsTsxxxxxPVxLtxxxxxxxxxxxxtxFxxxxxx
+>10cfcdaad4a10e98aec756d8a15574d9
+VLSGALCFRMKDSALKVLYLHNNQLLAGGLHAEKVIKGEEISVVPNRALDASLSPVILGVQGGSQCLSCGTEKGPILKLEPVNIMELYLGAKESKSFTFY
+RRDMGLTSSFESAAYPGWFLCTSPEADQPVRLTQIPEDPAWDAPITDFYFQQCD
+>gi|291386333|ref|XP_002709615.1| PREDICTED: interleukin 1 family, member 6-like [Oryctolagus cuniculus]
+-----VLRHIQDLNHQVWVVQDQTLTA-VPRKHSMVP-ATVSLIPCQYPetlETeKGIPMYLGLDKPDVCLFCtKTREQPMLQLEDKNIMTLYHHPEPVK
+PFLFYHSKSGRTSTFESVAFPGWFIAVCSEGGCPLFLTQ-DLGK---AYTTDFELTP--
+>gi|194220472|ref|XP_001496063.2| PREDICTED: interleukin-1 family member 7-like isoform 1 [Equus caballus]
+-----EKFSIYDQDHKVLVLDCGILRAV-PDRP-YILPETFFVLASHlssACEEKGSPILLAVSKGELCLCCekDKGQsKPSLQLKKKKLTDLATEKEQA
+RQpFIFYRAEVGSKNTLESVTHPGWFICTSCNSGEPVGMTDILG----KREHTEFSFRR--
+>gi|262342547|gb|ACY54774.1| interleukin-1 beta [Hippoglossus hippoglossus]gi|262342549|gb|ACY54775.1| interleukin-1 beta [Hippoglossus hippoglossus]
+------PCNISDSQKRNFLLVQNSMelhavmLQGGSDNRKVL--LNMSTYVHPSPTIEARPVALCIKDTDLYLSChHEDGVPTLHLEPVeDKTSLKTitR
+ESEMVRFLFYKRDSGVnISTLMSARFPDWYISTSEYENRPVMMCQ-ESA----QSYQTFNIQ---
+>gi|52346210|ref|NP_001005149.1| interleukin-1 beta [Sus scrofa]gi|407900|emb|CAA52660.1| interleukin 1-beta [Sus scrofa]
+---QSVDCKLQDKDEKALVLAGpHELKALHLLKGDLKREVVFCMsfVQGD-DSDDKIPVTLGIKGKNLYLSCvMKDDTPTLQLEDVDPKS-YPKRDMEKR
+FVFYKTEIKNRVEFESALYPNWYISTSQAEQKPVFLGNSKGR----QDITDFTME---
+>gi|10241835|emb|CAC09435.1| interleukin-1 beta [Scyliorhinus canicula]gi|38145475|emb|CAC80866.1| interleukin-1-beta [Scyliorhinus canicula]
+---------MTDDQDRSLILSeNLQLLAMSLQQSKDAVQLDVRYYKTTPTTEDDLPVVMAISNQNLFLSCvGTQDSPRVQLEKWDRKLQNIsSTTDLLRF
+VFFKkvSSSGLHFELESAMYRGWYVSTSRRNRQPIELDE--KKNH--KRITIF------
+>gi|225706200|gb|ACO08946.1| Interleukin-1 beta precursor [Osmerus mordax]
+--------SLFDCNQKMLVRKDSQALQLqATHLKENMDYKKVTFklVkyVNP-QARGRDAVILWIAGSSKILSCtrpHDSNTPILKLEKENCEQLKSieA
+MGEMARFLFYRRTVDvYDTIFESVKFPGWLIRSSLSEHKPVEMCE--------------------
+>gi|183223721|emb|CAP69657.1| interleukin 1 beta [Labeo rohita]
+----TLQCTICHKYKKSLVLSDelNtqdlHLKAVTLTGGNMNLKVRISMsaYYTSTPQNIGQPVCLGISNSNLYLACtKSDDSslPKLLLKEVSgPLNII
+NvgDSDEYDSLLFFRKETGTaYNTFESVKHPGWFISTAFEDTERVEMEKTPTD-----RPSNFTLED--
+>gi|58010|emb|CAA39086.1| interleukin-1 alpha [synthetic construct]gi|208534|gb|AAA72919.1| interleukin 1-alpha [synthetic construct]gi|208633|gb|AAA72560.1| interleukin 1-alpha [synthetic construct]gi|738207|prf||1924310A interleukin 1alpha
+-----YEFILNDALNQSIIRANDQYLtAAALHN--LDEAVKFDMGAYKsSKDDAKITVILRISKTQLYVTAQDEDQPVLLKEMPEIPKTITG--SETNLL
+FFWETHGTKNYFTSVAHPNLFIATKQDYW--VCLAG---GP---PSITDFQIL---
+>gi|197927464|ref|NP_001117868.2| interleukin-1 receptor antagonist [Oncorhynchus mykiss]gi|197631658|emb|CAD88595.2| interleukin-1 receptor antagonist [Oncorhynchus mykiss]
+-----------------------------------TP-EKITIYHYKsdCVdgEFRGVPVVLNFTSSNCFLKCvKDGERVSLCVGTCDQHRLKSirkDDE
+EIQAFVFYMKAEMSkQRRFESAYCQGWFIHTSNE--TKVVLGK-PQG----------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 * * * * * * * * * * * * 2555 * * 1372 * 1173 * * 1
+ 0 * * * * * * 2228 0 0
+
+L 2 * * * * * * * * * 269 * * * * * 2555 * * * * 2
+ 0 * * * * * * 2228 0 0
+
+S 3 3177 2536 * * * 3956 * * * * * * 1879 * * 1393 * * * * 3
+ 0 * * * * * * 2513 0 0
+
+G 4 * * * 5378 * 2910 5717 * 2294 4024 3652 4217 4883 3595 2408 3058 * * * * 4
+ 33 5466 * 2000 415 * * 3928 1028 0
+
+A 5 1936 4991 * * * * * * * * 2882 * 4366 * 4126 1480 3390 6402 * * 5
+ 0 * * * * * * 4093 0 0
+
+L 6 * * 4800 4831 5233 5953 4403 4609 4412 2869 5574 * 4747 2033 2842 4894 5528 3836 5987 5009 6
+ 0 * * * * * * 4963 0 0
+
+C 7 4150 4384 3507 3625 6248 * 5969 6563 3851 3492 * 3268 4830 2878 6601 4231 3952 4874 * 3447 7
+ 0 * * * * * * 5259 0 0
+
+F 8 * 1582 * * 2159 3949 4723 6906 5736 6568 * * * 6773 4334 * * 5663 * 2164 8
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+
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+
+M 10 * * * * 5538 * * 1204 * 2254 3539 * * * * * * 2008 * * 10
+ 0 * * * * * 0 5483 0 1038
+
+K 11 5748 2911 * 5946 4754 * 4042 * 2989 * 5723 3436 * 3055 3068 4370 3595 * 3205 5798 11
+ 0 * * * * 0 * 5483 0 1038
+
+D 12 * * 63 * * * 6256 * 5926 * * 6239 * * * * * * * * 12
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+//
+�HHsearch 1.5
+NAME 1189797f72eb6f0e100dc3369ccd8ffa
+FAM
+FILE 1189797f72eb6f0e100dc3369ccd8ffa
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:20:13 2013
+LENG 122 match states, 122 columns in multiple alignment
+FILT 133 out of 572 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHHCCCCCHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCEEEECCCCHHHHHHHHHHHHHHHHHHHHH
+CCCCHHHCCCCHHHCCCCCCCC
+>ss_conf PSIPRED confidence values
+9899999999982998379996468762689999826057578862067887762268604326899989976869997689999785899999999852
+2423876278865457999898
+>Consensus
+xlxqlxxMixxxxxxxxxxxyxxYGCxCxxxGxGxPvDxiDxxCxxhxxCyxcxxxCxxxxxxYxxxxxxxxixCxxxxxCxxxlCeCDxxxAxcxxxxx
+xxynxxyxxxxxxxCxxxxxxc
+>1189797f72eb6f0e100dc3369ccd8ffa
+SLFELGKMIWQETGKNPVKNYGLYGCNCGVGGRGEPLDATDRCCFVHKCCYKKLTDCDSKKDRYSYKWKNKAIVCGKNQPCMQEMCECDKAFAICLRENL
+DTYNKSFRYHLKPSCKKTSEQC
+>gi|70907000|gb|AAZ15113.1| otoconin [Gallus gallus]
+-LLNFVNKMKCVSGFCP-RDFEDYGCSCRFEMEGLPVDEADECCFQHRKCYEEAmeMECtwDPSKISTDVTCSAENLSCENGDPCEQFLCTCDKDAIECF
+GNA--HINSSLNGLDV----------
+>gi|76468986|gb|ABA43328.1| phospholipase A21 precursor [Trichoplax sp. BZ10101]gi|76468988|gb|ABA43329.1| phospholipase A21 precursor [Trichoplax sp. BZ10101]gi|76468990|gb|ABA43330.1| phospholipase A21 precursor [Trichoplax sp. BZ46]gi|76468992|gb|ABA43331.1| phospholipase A21 precursor [Trichoplax sp. BZ264]gi|76468994|gb|ABA43332.1| phospholipase A21 precursor [Trichoplax sp. BZ264]gi|76468996|gb|ABA43333.1| phospholipase A21 precursor [Trichoplax sp. BZ413]gi|76468998|gb|ABA43334.1| phospholipase A21 precursor [Trichoplax sp. BZE8]gi|76469000|gb|ABA43335.1| phospholipase A21 precursor [Trichoplax sp. BZF1]
+SALNFQSMISYTTGRSA-LAFNGYGNWCGLGPYFstpPTVDSVDACCKAHDNCYSDT-GCNllqwEVLNPYDWHKsSTGRITCDDaPGSCDRANCECDRI
+AAECFARY--KYNCDYAPLS-----------
+>gi|313234543|emb|CBY10500.1| unnamed protein product [Oikopleura dioica]
+--SEFQTLMKFYNSNFSLDTHGQYGCKCQYMvtdrplsaGPAgpVSVDELDATCQAHKDCYRCAkekfgESCIPEFNNYQYEYVGNEIECTSsAGSCNRA
+LCECDLKFAKEHVAKIDVYDEKLTLFN-----------
+>gi|313220609|emb|CBY31456.1| unnamed protein product [Oikopleura dioica]gi|313226182|emb|CBY21325.1| unnamed protein product [Oikopleura dioica]
+-LRQFRRLYTFYLvGYrlRP-AHLVQYGCWCFPrgqliMGYGQPIDGIDATCRNHQLCLNCVgldtnYECNPHTQPYRVYgqiYQNGrRLMCKDpPGSCA
+WLACQCDVNMVTtSIIESLKGYKPRFWMYDPGRC-------
+>gi|313225501|emb|CBY06975.1| unnamed protein product [Oikopleura dioica]
+-VLTLKEIILKPTGKRNAiglErfginmGAFDYGCHCSAllagktAGFGTAVDALDMICKDYLGCTrcvQKVTNCQVS-VNYNFEMGDSGVICTEmDGSC
+EKNICECDAMFYRDLLHAAysgIVYNYKYNAdsFDpSSSCHV-----
+>gi|313212373|emb|CBY36361.1| unnamed protein product [Oikopleura dioica]
+------KLVQHFTSI-DIEKLQDYGCA-GRGyfdstepAVGLPVDEIDRSFIWWKKCIKCAqSEYSAydleynhfdYREFYEFDF--DSEICGGSETVEH
+AICQCDKSFAKRLIDL--TENNDFHNYDTDSCVRFTP--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 5013 0 0
+
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+
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+ 0 * * * * * * 5961 0 0
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ 214 2861 * 2813 221 * 0 6189 1820 1002
+
+G 32 5067 * 5771 * * 492 * * * * 4692 5028 4964 6724 4458 4884 4982 7064 * 6456 32
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+
+R 33 4863 * 5052 5246 3876 4279 4235 4562 2619 6403 6527 6044 5156 3978 3102 2633 4845 4683 * 4305 33
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+G 34 6089 * * * 7015 140 7254 * * * 7151 5809 * * 6047 6807 * 7081 * 7180 34
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+D 38 * * 61 5596 * * * * * * * 5585 * * * * * * * * 38
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+
+A 39 2216 * 3169 1801 * 3605 6586 7510 6993 5824 6899 4112 4691 4817 5191 4322 6623 6119 6623 6562 39
+ 0 * * * * 1296 755 6215 0 1148
+
+T 40 5581 * * 6823 * * * 1518 6827 2080 * 6644 * * 6822 4786 2610 2853 * 5742 40
+ 0 * * * * * 0 6213 0 1065
+
+D 41 * * 32 * * * * * * * * * 6823 * * * * * * 6249 41
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+
+R 42 3305 7355 * 3749 7195 * 5640 5541 3174 5156 6811 4797 * 3930 1732 3222 4933 5809 4015 * 42
+ 0 * * * * * 0 6206 0 1151
+
+C 43 2910 1164 * 6538 6792 5878 5262 5200 4297 4273 * 6578 * 5851 * 5071 3335 3969 * 7044 43
+ 0 * * * * 1269 773 6157 0 1151
+
+C 44 * 127 * * 5569 * * 5859 * 5976 * * * * * 5066 * * * * 44
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+H 47 6851 * * * 4229 * 944 * 5976 2715 * * * 7200 6787 6347 * * 3643 2818 47
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+K 48 5437 * 1406 6892 5394 6192 4404 7743 2308 4815 * 4776 6347 5237 3846 4719 4798 6867 6339 5345 48
+ 0 * * * * 0 * 6172 0 1065
+
+C 49 4909 3260 3670 3889 5041 6072 4875 7072 3251 4683 5290 4128 5986 3267 2788 4676 4191 6197 6947 5455 49
+ 20 6154 * 1000 1000 * * 6182 1059 0
+
+C 50 6351 76 * * * * * * * 5986 * * 6360 * * 6512 * * * * 50
+ 11 7020 * 0 * * * 6182 1000 0
+
+Y 51 7241 * * * 5480 6659 3909 5210 * 3269 * 5643 * 3942 * 6817 5505 4718 6191 746 51
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+K 52 4030 7017 3164 3589 * 3705 4530 * 1831 * 5978 4023 * 3822 3791 3591 5305 * 7199 * 52
+ 0 * * * * * 0 6184 0 1010
+
+K 53 3824 1120 4461 3796 6168 6177 * * 3549 6891 * 4383 * 4138 4457 4614 6692 5489 * 7100 53
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+L 54 1839 * 6555 7066 6913 * * 3369 6401 2160 6662 6038 5176 * * 4578 4133 2251 * * 54
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+
+T 55 4592 * 3357 3111 6283 3093 5110 5598 3616 4927 5455 4640 3769 5237 4802 3212 3335 6978 7037 5063 55
+ 64 4850 6840 1309 746 1095 911 6160 1164 1307
+
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+
+C 57 7111 222 * * 6839 * 7102 6152 7186 5170 6668 * * * * 6842 * * 5434 5112 57
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+D 58 4847 7110 2850 4759 7056 3859 5453 3190 4547 4254 7405 2904 6932 3672 5400 2988 4475 5970 5576 5602 58
+ 256 3050 4576 1840 472 663 1440 6149 1834 1511
+
+S 59 3593 * * 4446 5281 3251 4954 5543 4388 5541 7262 4744 1381 * * 3601 4393 4266 * 6988 59
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+K 60 5550 * 4389 2328 5738 5173 4341 6264 3847 3685 7258 5838 * 5711 6061 3467 4763 4970 * 1952 60
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+K 61 4897 * 4288 5902 2269 6986 7154 3727 4885 3016 5215 5134 * 4238 4624 4590 2370 5254 7083 5283 61
+ 57 5295 6244 423 1977 290 2457 6095 1106 1578
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+D 62 3977 6800 3819 5759 6265 5336 5018 4804 3481 4297 7055 3889 6568 3416 4859 3721 2693 2947 * 5685 62
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+R 63 4768 6718 4827 5589 4815 4682 4545 4208 3832 3255 6757 3785 3535 4858 3925 2605 3604 5150 * 6933 63
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+Y 64 * * * * 6410 * * 5747 * * 6734 * * * * 5636 5647 * * 120 64
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+
+S 65 7064 6278 3162 3737 7111 4675 6213 * 2547 6874 * 2996 6843 3900 3754 2586 3758 5354 * 6219 65
+ 22 6038 * 1264 777 * 0 6160 1036 1053
+
+Y 66 6001 * * 7323 2829 6730 4584 3995 * 4016 5527 * * * 6332 5505 7111 3922 2260 1627 66
+ 101 4340 5786 1673 543 1155 860 6160 1324 1053
+
+K 67 5000 * 3719 3390 4723 7264 5594 4860 3083 6868 7259 4420 4561 5116 3460 2878 2717 4827 * 4935 67
+ 134 4225 4832 2079 390 1405 684 6204 1425 1198
+
+W 68 5244 2063 * 5158 3009 5197 7554 3597 4425 3319 4667 * * 5483 6964 6124 5317 3243 4710 3897 68
+ 202 3058 6559 1878 458 3370 147 6167 1671 1340
+
+K 69 5092 * 3243 3066 6135 4085 4467 4316 3713 5363 * 3387 6572 4317 4473 2931 4953 3281 6798 * 69
+ 207 3018 6600 2199 354 1221 808 6154 1712 1424
+
+N 70 4228 * 2877 3607 * 3056 6415 * 3722 * 7261 2252 4865 4557 6648 3545 3630 6585 6931 4945 70
+ 270 2857 4925 2008 412 1346 721 6184 1849 1284
+
+K 71 4326 5489 3855 5271 * 1659 5593 * 3122 * * 2981 5222 4191 3536 5113 5086 5644 * 6994 71
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+ 39 5230 * 824 1200 234 2738 6189 1130 1286
+
+I 73 4547 * * 6588 5479 5149 5963 1468 5766 3238 5593 6735 3362 * 6571 5958 4403 2583 * 5255 73
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+
+V 74 4531 * 4972 3348 4126 6929 6925 3328 4147 6735 6254 5477 6856 3897 5049 4672 2154 2870 7120 4714 74
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+
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+
+G 76 4257 * 3597 4166 * 2933 6695 6170 3696 4158 5054 5023 7432 5400 4157 2292 3340 4763 * 4809 76
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+
+K 77 4374 6575 1942 3241 * 3285 * * 4940 * * 2867 3876 5210 6024 3011 4236 7176 * 6880 77
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+
+N 78 3404 * 4288 2470 7116 3865 6037 5518 3608 4406 * 3015 3518 4971 5093 3818 4932 4806 7247 6195 78
+ 163 3226 * 2123 376 * 0 6151 1819 1158
+
+Q 79 4278 * 2251 5863 * 1871 5880 * 5553 * * 2557 6254 5486 6862 3128 4256 5117 * * 79
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+
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+
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+
+T 102 5163 * 4532 3316 5214 5872 5400 5103 3444 5645 * 6843 3222 5433 6673 2615 2474 3073 * 6803 102
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+
+K 105 3672 5679 4863 3473 6866 5212 7035 5752 2751 4221 5476 3415 2974 3983 5333 3593 4970 4138 * 6568 105
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+
+S 106 3176 * 3188 3358 * 4951 6226 * 2123 4605 * 3879 * 5344 3878 3376 4097 6527 6813 5026 106
+ 39 6872 5784 0 * 458 1878 6206 1000 1121
+
+F 107 * * * * 2232 * 2854 * 6520 3411 * 3224 * 6573 * * * * * 1230 107
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+
+R 108 4288 * 5575 4519 4061 * 2071 6881 3111 5423 5346 4701 * 4265 3144 3708 4611 5475 4786 4863 108
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+
+Y 109 4425 * 4239 4906 3679 3195 3659 4313 * 4071 5017 2723 4966 6084 4752 3370 4882 4341 * 4483 109
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+H 110 * 6161 6283 5348 1836 6421 3847 3966 6411 2972 4451 6362 6121 6479 * 5356 * 4406 6547 2195 110
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+
+L 111 * * 1380 5075 4879 5277 5810 * 5495 4570 5960 3901 3003 6389 6309 3904 5191 * 3409 5403 111
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+
+K 112 4000 * 4819 5225 * 3870 * * 2508 * * 3273 5847 3215 2993 2789 3151 * * 5657 112
+ 108 3797 * 0 * 765 1281 6054 1218 1203
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+P 113 4131 * 4807 2706 5776 4917 * 5397 2625 4723 4370 3499 4243 4868 6466 2593 4240 5324 * * 113
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+C 115 * 0 * * * * * * * * * * * * * * * * * * 115
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+
+K 116 * * 4630 3172 5830 3771 5175 * 2935 4853 * * * 2002 2966 4652 3679 3850 * * 116
+ 0 * * * * 0 * 5555 0 1000
+
+K 117 3142 * 4319 3832 * 1740 4938 * 1993 * * 5492 * * 3368 5128 * 4820 * * 117
+ 0 * * * * * * 5213 0 0
+
+T 118 3793 * 6065 2376 4078 * 3796 * 3636 * * 4785 2878 4043 4283 5051 3162 4948 4323 * 118
+ 0 * * * * * * 4753 0 0
+
+S 119 4894 * * * * * * * 2263 * * * 3423 * 2831 2305 1827 * * 4638 119
+ 0 * * * * * * 4439 0 0
+
+E 120 * * * 2428 * * * * * 3629 4307 * 806 * * 4333 * 4029 * * 120
+ 100 3903 * 3907 100 * * 4338 1010 0
+
+Q 121 3373 * * 3194 3902 * * * 2601 * * 2664 4428 2727 * 3682 * 4040 3871 * 121
+ 102 3871 * 1391 693 * * 4234 1089 0
+
+C 122 * 0 * * * * * * * * * * * * * * * * * * 122
+ 0 * * 0 * * * 4134 0 0
+
+//
+�HHsearch 1.5
+NAME 11d0ff4d993e31f0a2ea189846a08655
+FAM
+FILE 11d0ff4d993e31f0a2ea189846a08655
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:25:41 2013
+LENG 80 match states, 80 columns in multiple alignment
+FILT 25 out of 27 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCCHHHCCC
+>ss_conf PSIPRED confidence values
+99888761999987168559999999869740999971788678745862899999999999987004568870451068
+>Consensus
+xpyxxDxSixsxLtxLGcxncidxFtxqglxxixqLxxxxmeDLxxmkIxxxxrxxIWkxlxexxqxxdyxxxpxlxrxx
+>11d0ff4d993e31f0a2ea189846a08655
+GSYHADPSLVSFLTGLGCPNCIEYFTSQGLQSIYHLQNLTIEDLGALKIPEQYRMTIWRGLQDLKQGHDYSTAQQLLRSS
+>gi|47218894|emb|CAG05660.1| unnamed protein product [Tetraodon nigroviridis]
+-PYPMDSSISSFLLRLGCAGCLDYFTAQGLTNIYQIENYNMEDLSRLKIPSEFQHIIWKGIMEHRQAMDFSPPPHIVRST
+>gi|323772104|gb|ADL27911.1| tumor suppressor p53-like protein [Branchiostoma belcheri tsingtauense]
+---DADGTVADWLTKLGCASCIETFHRKRINFLSQLEEINLQDLHEMKLTERLVDKIWKGIIEYKAAKDFSDTPSLLR--
+>gi|291224284|ref|XP_002732135.1| PREDICTED: p63-like transcription factor-like [Saccoglossus kowalevskii]
+----PDNSINEWLSKFGCENYSEIFKKKGYLSIHQLDDITIEDLDDMKISPQQKDKIWKAIIDHRAADNFSSTPSMLQ--
+>gi|217273135|gb|ACK28180.1| p63/p73 [Mya arenaria]
+---MQDNSVSTWLNALGLGAYIDGFHEQTLYSLLQLDDFSLDDLAKMKIGNSHRNKIWKSLLELRNQGFT----------
+>gi|82471258|gb|ABB77690.1| p63(62) transcription factor [Euprymna scolopes]
+---PNENTIAQWLTKLGLQAYIDNFQQKGLHNMFQLDEFTLEDLQSMRIGTGHRNKIWKSLLDYRRVLST----------
+>gi|115898454|ref|XP_001196748.1| PREDICTED: similar to p63(47) transcription factor [Strongylocentrotus purpuratus]gi|115945815|ref|XP_001184464.1| PREDICTED: similar to p63(47) transcription factor [Strongylocentrotus purpuratus]
+----QDPSIDCFLKRLGLRQHSDIFTQKNVHTVDQLEEINMEDLSS--IPHQQREILWKAILELKGGLQLNHTPTMNR--
+>gi|297522160|gb|ADI44410.1| p53-like transcription factor [Biomphalaria glabrata]
+----RDNSVAGWLDRLGLSNYIDRFHQNGYDNLFQLDECKKETLEHLGIPEVDRNKIWKSLVEFHQ--------------
+>gi|70632939|gb|AAZ05996.1| delta-N p63/p73-like protein [Mytilus edulis]gi|112819488|gb|ABI23724.1| delta-N p63/p73-like protein [Mytilus edulis]
+---NGDHSISNWLTTLGLSAYIDNFHQQNLFTMEQLDDFTVEDLQKMRIGTSHRNKIWKALVEFHSeSITISDSQSLQR--
+>gi|169349567|ref|ZP_02866505.1| hypothetical protein CLOSPI_00294 [Clostridium spiroforme DSM 1552]gi|169293642|gb|EDS75775.1| hypothetical protein CLOSPI_00294 [Clostridium spiroforme DSM 1552]
+---------------EGCSNC-EYFSKNGLPLIEeefgdhmKIVKYNMDDRESVDEVRNAYDEVVNNIIDFNQ-DDYGFGPFLV---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 0 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+S 2 * * * * * * * * * * * * 93 * * 3995 * * * * 2
+ 0 * * * * * * 1905 0 0
+
+Y 3 * * * * * * * * * * * * * * * * * * * 0 3
+ 0 * * * * * * 1905 0 0
+
+H 4 * * 3221 * * * 2631 * * 3946 2856 1926 1915 * * * * * * * 4
+ 0 * * * * * * 2842 0 0
+
+A 5 1996 * * * * 4153 * * * * 3659 4080 2637 3042 3903 3954 3390 4450 * * 5
+ 0 * * * * * * 3139 0 0
+
+D 6 * * 88 4080 * * * * * * * * * * * * * * * * 6
+ 0 * * * * * * 3139 0 0
+
+P 7 * 3789 * * * 3597 4153 4119 * * * 1601 1599 * * 3806 * * * * 7
+ 0 * * * * * * 3139 0 0
+
+S 8 * * * * * * * * * * * * * * * 220 2819 * * * 8
+ 0 * * * * * * 3139 0 0
+
+L 9 * * * * * * * 1443 * 1609 * * * * * * * 1717 * * 9
+ 0 * * * * * * 3139 0 0
+
+V 10 1529 5057 3837 * * * * * * * * 3860 * * * 2420 * 1747 * * 10
+ 0 * * * * * * 3139 0 0
+
+S 11 4119 3837 3597 3860 * 3903 * * * * * 4153 * 4080 * 1037 4281 * * * 11
+ 0 * * * * * * 3139 0 0
+
+F 12 * * * * 967 * * * * * * * * * * * * * 1034 * 12
+ 0 * * * * * * 3139 0 0
+
+L 13 * * * * * * * * * 0 * * * * * * * * * * 13
+ 0 * * * * * * 3139 0 0
+
+T 14 3789 * 3903 * * * * * 3837 3659 * 3198 * * * 3860 906 * * * 14
+ 0 * * * * * * 3139 0 0
+
+G 15 4281 * * * * 2152 4119 * 2248 * * * * * 1794 3174 4153 * * * 15
+ 0 * * * * * * 3139 0 0
+
+L 16 * * * 2363 4210 * * 4650 * 490 * * * * * * * * * * 16
+ 0 * * * * * * 3641 0 0
+
+G 17 * * * * * 0 * * * * * * * * * * * * * * 17
+ 0 * * * * * * 3641 0 0
+
+C 18 * 573 * * * * * * * 1609 * * * * * * * * * * 18
+ 0 * * * * * * 3641 0 0
+
+P 19 2516 * * 4210 * 3476 * * * * * * 2211 3379 4064 1692 * * * * 19
+ 0 * * * * * * 3641 0 0
+
+N 20 2027 * * * * 4897 * * * * * 896 * 4064 * 3014 * * * * 20
+ 0 * * * * * * 3641 0 0
+
+C 21 * 769 * * 4989 * 4064 * * * * * * * * * * * * 1635 21
+ 312 * 2363 * * * * 3641 0 0
+
+I 22 * * * * * * * 495 * 2722 * * * * * 2849 * * * * 22
+ 0 * * * * 0 * 3139 0 1332
+
+E 23 * * 953 1048 * * * * * * * * * * * * * * * * 23
+ 0 * * * * * * 3641 0 0
+
+Y 24 * 5545 * * 3746 4548 * 3135 * * * 2450 * * 4224 4408 3906 * * 1332 24
+ 0 * * * * * * 3641 0 0
+
+F 25 * * * * 0 * * * * * * * * * * * * * * * 25
+ 0 * * * * * * 3641 0 0
+
+T 26 4989 * * * * * 1765 * 4210 * * * * 4627 * 4025 948 * * * 26
+ 0 * * * * * * 3641 0 0
+
+S 27 3954 * * 2947 * * * * 2009 * * * * 2336 3906 2086 4131 * * * 27
+ 0 * * * * * * 3641 0 0
+
+Q 28 * * * * * * 4408 * 1576 * * 2528 * 1171 * * * * * * 28
+ 0 * * * * * * 3641 0 0
+
+G 29 * * * * * 516 * * * * * 2388 * * 3906 * 4548 * * * 29
+ 0 * * * * * * 3641 0 0
+
+L 30 * * * * 4650 * * 2824 * 618 * * * * * * * 4064 * 3217 30
+ 0 * * * * * * 3641 0 0
+
+Q 31 * * 4224 * 3452 * 3318 * * 3413 * 3411 2363 2086 * * 3407 * * 4548 31
+ 0 * * * * * * 3641 0 0
+
+S 32 * * * * 3906 * * * * 2363 * 1790 * * * 1909 2446 * * * 32
+ 0 * * * * * * 3641 0 0
+
+I 33 * * * * * * * 923 * 2432 3005 * * * * * * 2621 * * 33
+ 0 * * * * * * 3641 0 0
+
+Y 34 * * 4064 2472 2902 * 4210 4408 4098 4548 * * * * * 3906 * * * 1485 34
+ 312 2363 * 2807 222 * * 3641 1332 0
+
+H 35 * * * * * * 2230 * 2363 * * * * 755 * * * * * * 35
+ 0 * * * * * * 3641 0 0
+
+L 36 * * * * * * * 1662 * 548 * * * * * * * * * * 36
+ 0 * * * * * * 3641 0 0
+
+Q 37 * * 1635 2011 * * * 4098 * * * * * 2086 * * * 2879 * * 37
+ 0 * * * * * * 3641 0 0
+
+N 38 * * 2410 1650 * * 5070 * 2879 * * 1880 * * * * 4168 * * * 38
+ 0 * * * * * * 3641 0 0
+
+L 39 * 4224 * * 2221 * * 2470 * 2086 * * * * * * * * * 1662 39
+ 0 * * * * * * 3641 0 0
+
+T 40 * * 4098 * * * * * 4224 * * 1613 * * * 2066 1634 * * * 40
+ 0 * * * * * * 3641 0 0
+
+I 41 * * * * * * * 2253 4224 1785 1314 * * * * * * 4497 * * 41
+ 0 * * * * * * 3641 0 0
+
+E 42 * * 1671 691 * * * * * * * * * 3906 * * * * * * 42
+ 0 * * * * * * 3641 0 0
+
+D 43 * * 153 * * 4413 * * * * * * * * * * 4224 * * * 43
+ 0 * * * * * * 3641 0 0
+
+L 44 3746 * * * * * * * * 398 4413 * * * 4025 * 4098 * * * 44
+ 0 * * * * * * 3641 0 0
+
+G 45 2578 * 4210 2528 * 2376 3906 * * * * * * 3560 * 2607 3746 5486 * * 45
+ 0 * * * * * * 3641 0 0
+
+A 46 2279 4413 4210 3906 * * 4224 * 2898 5486 * * * * 3954 1769 4098 * * * 46
+ 163 * 3228 * * * * 3641 0 0
+
+L 47 * * * * 3595 * * * * 1187 1282 * * * * * * 3903 * * 47
+ 0 * * * * * 0 3484 0 1223
+
+K 48 * * 2741 * * 4066 * * 664 * * * * * 3386 * 3965 * * * 48
+ 0 * * * * 1007 993 3484 0 1223
+
+I 49 * * * 2977 * * * 461 3675 3874 * * * * * * * * * * 49
+ 0 * * * * * 0 3580 0 1058
+
+P 50 * * * * * 2173 * * * * * * 1155 * * 4163 3874 2285 * * 50
+ 0 * * * * * 0 3580 0 1058
+
+E 51 * * 3764 1666 * * 4040 * 2833 * * 3418 4163 * 3946 4834 2638 * * * 51
+ 0 * * * * * 0 3580 0 1058
+
+Q 52 3162 * * 3889 * 4582 5016 * 3675 * * 3946 * 1520 3874 2939 * 4114 * * 52
+ 0 * * * * * 0 3580 0 1058
+
+Y 53 2285 * 4114 * 2702 * 2173 * * 3874 * * * 3100 * 4915 * * * 2800 53
+ 0 * * * * * 0 3580 0 1058
+
+R 54 * * * * * * * * 3527 * * * * 3889 805 * * 3874 * 2285 54
+ 0 * * * * * 0 3580 0 1058
+
+M 55 * * 1603 4040 * * 2972 * * 4073 3150 1839 * * * 5016 * * * * 55
+ 0 * * * * * 0 3580 0 1058
+
+T 56 3067 * * 2977 * * 3675 2715 1309 5496 5016 * * * * * 3910 * * * 56
+ 0 * * * * * 0 3580 0 1058
+
+I 57 * * 3675 * * * * 446 * 4040 * * * * * * * 2977 * * 57
+ 0 * * * * 0 * 3580 0 1058
+
+W 58 * * * * 4413 * * 4098 * 3746 * * * * * * * 4025 398 * 58
+ 0 * * * * * * 3641 0 0
+
+R 59 * * * 3746 * * * * 811 * * 3061 * 4413 2407 * * * * * 59
+ 0 * * * * * * 3641 0 0
+
+G 60 2256 * * * * 1424 * * * * * 4025 * 3746 * 1826 * * * * 60
+ 0 * * * * * * 3641 0 0
+
+L 61 * * * * * * * 1239 * 1052 * * * * * * 4413 4408 * * 61
+ 0 * * * * * * 3641 0 0
+
+Q 62 * * * * * * * 2055 4413 2185 3445 * * 1926 * * * 2861 * * 62
+ 0 * * * * * * 3641 0 0
+
+D 63 * * 1274 890 * * * * * * * 4413 * * * * * * * * 63
+ 0 * * * * * * 3641 0 0
+
+L 64 * * * * 1775 * 2789 * * 1671 5372 * * * 4413 * * * * 2490 64
+ 0 * * * * * * 3641 0 0
+
+K 65 * * 3746 * * * 3354 * 1618 * * 2747 * * 1502 * * * * * 65
+ 69 * 4413 * * * * 3641 0 0
+
+Q 66 3011 * * * * 4040 * * 5016 * * 3418 * 929 4582 4457 * * * 3675 66
+ 707 4372 1560 0 * * 0 3580 1017 1058
+
+G 67 1742 * * 3792 * 2948 * * * 4255 4422 * * 3971 * 2241 4314 3743 * * 67
+ 0 * * 2041 402 300 2414 2986 1172 1757
+
+H 68 * * 1862 * * 3331 1844 4268 3810 3206 3818 4490 * * * * * * * * 68
+ 0 * * * * * 0 3516 0 1058
+
+D 69 4490 * 1033 3908 4409 * * * * 4257 * 4062 * 2799 * 4466 4268 * * * 69
+ 0 * * * * * 0 3516 0 1058
+
+Y 70 * * * * 1916 * * 4268 * 3985 * * * * * * 2790 * * 1073 70
+ 233 * 2746 * * * 0 3516 0 1058
+
+S 71 * * * * * 1426 * * * * * 3297 * * * 1062 4403 * * * 71
+ 194 * 2991 * * 227 2778 3300 0 1336
+
+T 72 * * 2451 * 2812 3571 2796 3892 * * * * 3426 * * 2616 4665 3580 * * 72
+ 0 * * * * 0 * 3461 0 1139
+
+A 73 2302 * * * * 1832 * * * * * * 2645 * * 3416 1927 * * * 73
+ 0 * * * * * * 3410 0 0
+
+Q 74 4044 * * * * * * * * * * * 707 1613 * * * * * * 74
+ 0 * * * * * * 3410 0 0
+
+Q 75 * * * * 2220 * 2645 * * * * * * 1767 * 2031 3522 * * * 75
+ 0 * * * * * * 3410 0 0
+
+L 76 * * * * * * * 3563 * 524 2651 * * 4044 * * * * * * 76
+ 0 * * * * * * 3410 0 0
+
+L 77 * * * * * * * 2773 * 1490 * 3522 * 3416 * * * 1658 * * 77
+ 0 * * * * * * 3410 0 0
+
+R 78 * * * * * * * * * 3773 * * * 3328 274 * * * * * 78
+ 0 * * * * * * 2843 0 0
+
+S 79 * * * * * * * * * * * * * * 3391 677 1840 * * * 79
+ 0 * * * * * * 1905 0 0
+
+S 80 * * * * * * * * * * * * 3427 * * 466 2450 * * * 80
+ 0 * * 0 * * * 1905 0 0
+
+//
+�HHsearch 1.5
+NAME 13077d2b3643cabf3bccc22d84a0a439
+FAM
+FILE 13077d2b3643cabf3bccc22d84a0a439
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:03:34 2013
+LENG 199 match states, 199 columns in multiple alignment
+FILT 138 out of 1079 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHH
+HHHHHHCCHHHHHHHHHHHHHHCCCCEEEEEEECCCEEEEEECCCCCCCCCCCCEEEEEEECHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9868999989221876770999999999989999999999996664655289999999876173348999865779998999860179999999899999
+999871899999999999997477871899997299179984267899666698647987330667688764569999999999665999999998639
+>Consensus
+xxxlpxLpyxxxxLepxgiSxxxlxxHxxkhhxxyVxxlNxxxxxxxlxxxxxxxxixxxxxxxxxxxxxxxagxxxNHxxfwxxLxpxxxxxpxxxLxx
+xIxxxFGSxdxfkxxfxxxAxxxxGsGWxwLvxxxxxLxixxtxnxxxpxxxgxxPlLxiDvwEHAYyldYxnxrxxYixxxwxxxinWxxvxxrxxxx
+>13077d2b3643cabf3bccc22d84a0a439
+AFVQEPLPFDPGALEPYGMSAKTLEFHYGKHHKGYVDNLNKLTQDTELADKSLEDVIRTTYGDAAKVGIFNNAAQVWNHTFFWNSLKPGGGGVPTGDVAA
+RINSAFGSYDEFKAQFKNAAATQFGSGWAWLVLEAGTLKVTKTANAENPLVHGQVPLLTIDVWEHAYYLDYQNRRPDFIDNFLNQLVNWDFVAKNLAAA
+>gi|153939066|ref|YP_001389886.1| Fe/Mn family superoxide dismutase [Clostridium botulinum F str. Langeland]gi|152934962|gb|ABS40460.1| superoxide dismutase, Mn/Fe family [Clostridium botulinum F str. Langeland]gi|295317969|gb|ADF98346.1| superoxide dismutase, Mn/Fe family [Clostridium botulinum F str. 230613]
+---IVAKKYPF-DNVKG-ISLKQLTEHYK-LYDGYVNMINKiwsiPNNSKDFKDSNATfSKLRCIK---L--GESYALDGVKLHELYFQNMT-SGHIPIN
+GPILDKILEDFNSVENFTELFKETGKS--MRGWVVLGIdpLDKKLHIFGSDSHDNGAIWLAYPLLVMDVYEHAYFMDFGTDKRKYMDAFLQ-NVNWNLIN
+NRLGM-
+>gi|121482735|gb|ABM53865.1| chromium (VI) response protein [Ochrobactrum anthropi]
+-YTMKPLSCDPSHIR--GMSERMIISHYENNYGGAVKRLNLIDEKlAELDYENAPGFlINGLK---R--EQLIATNSMILHEVFFDGLGDES--EPEERL
+KNALARDFGSYDRWRAEFIAMGKAlGGGSGWVLLSWspRDGKLVNQWAPDHCHT-LAGGTPILALDMYEHSYHIDYGAKAADYVGVFMA-AINWPSVQQL
+YDDL
+>gi|156057073|ref|XP_001594460.1| hypothetical protein SS1G_04267 [Sclerotinia sclerotiorum 1980]gi|154702053|gb|EDO01792.1| hypothetical protein SS1G_04267 [Sclerotinia sclerotiorum 1980 UF-70]
+-QKVPPLKHDFtKGIPEF-IGPQAFDLSWTAYQKLMVDKLTDATAGIPHlEGRQPKEIAIMTARDPDQAATFNYASMAFNNNFFFDCIQPNPAsePEMSE
+RLRVAIEASFSSVDSLKKEFVITASKMFGPGFVWLMKdRFDSLSLLTTYLAGSPFpgAhyrkqtkdmntEsenltdyhrqrlagppvntvgahgalsker
+kppgGieQTPILCVNTWEHVWIPDYGmgvdnvGGKKVYVENWWN-VIDWSVVADNAA--
+>gi|229008442|ref|ZP_04165897.1| Superoxide dismutase [Bacillus mycoides Rock1-4]gi|228752835|gb|EEM02408.1| Superoxide dismutase [Bacillus mycoides Rock1-4]
+-HRLPELSYDFHELAAF-ISPKESQLNYFEIHKWYVENLNKALSKyISYQQYSVTELMMKLKYLPGDLrqDVKKYGGMHFNYSVFWKVLTPNSRG-PIGT
+LKNAIRDTYRDFGVFKKEFTNIALDLNASdAWCWLLVQKGNLKIMKTYGYDCPISKDTYPVLCLKLWRVSSLFVKQKQNLKYINDFWN-FINWEEAENRY
+L--
+>gi|149241770|ref|XP_001526352.1| hypothetical protein LELG_02910 [Lodderomyces elongisporus NRRL YB-4239]gi|146450475|gb|EDK44731.1| hypothetical protein LELG_02910 [Lodderomyces elongisporus NRRL YB-4239]
+----------NADFEGL-FTHKALNELWFKQGEQLIQNLNQHIAQSaGLLehSadhePTVEELLAITTNKPHLHNVHKAAGRLYALTSFFENLRPMQTPl
+spvkierpsqealfqtptddfinQPTdPNLVAWISSSFGSVKEFRNLLINTAKAVKGDGTVWLVAqSkfshsnrpgasqqDyhhhpnhpnhhaspsfSEL
+ALVVTYNGGVVHDveragqlsrmreifkdkermakdeeevgesksekttealkskkevnelqlgsvqeaedrvafsnRKLIPALAIDASPRTYLVDYGVy
+GKQKYLENCWE-CIDWDVVMRRL---
+>gi|294948608|ref|XP_002785805.1| superoxide dismutase, putative [Perkinsus marinus ATCC 50983]gi|239899913|gb|EER17601.1| superoxide dismutase, putative [Perkinsus marinus ATCC 50983]
+-----DVPFStYANFFPL-VQPKALSYHYRSICGRDTARFNTGLRQLsLLPNlpthvrhMgfdallyfcEYENILSEEI--PLPLcdKLVYYGNSYIYHE
+IYFNCLRATGMyddfEEPlsleSSLLVQDITNAFGGMKELFEELLEAALSLDGYGWVWLLSlPEG-LSVITSQDYDGIHGDQIYAIFNIDLWEHAYIESH
+GANVEAYIKAWWG-AVDWNKLDVQY---
+>gi|238061592|ref|ZP_04606301.1| iron/manganese superoxide dismutase [Micromonospora sp. ATCC 39149]gi|237883403|gb|EEP72231.1| iron/manganese superoxide dismutase [Micromonospora sp. ATCC 39149]
+-YSLPDMPYAYGALKPA-MPGEILTLHRSKHHTAYAKGGNDALEQlAEVRDKgDFAGLVGLEK------TFAFTLSGHVPYSIFWPSG------------
+----------------------------------------------------------------------------------------------------
+-
+>gi|342180748|emb|CCC90224.1| conserved hypothetical protein [Trypanosoma congolense IL3000]
+-------------------------------------------------------------------RAHFLASEDFCHSLVKRCTRRVACPVP-AEWKG
+IVSRQFASEAALEAELVFRAANRREAGWTWLVYdnqrpEEQRLVVVNMPGNRTPLLLGLWPLGVVDMTDKAVV---------------------------
+----
+>gi|58267144|ref|XP_570728.1| hypothetical protein CNE01360 [Cryptococcus neoformans var. neoformans JEC21]gi|57226962|gb|AAW43421.1| hypothetical protein CNE01360 [Cryptococcus neoformans var. neoformans JEC21]
+-------------------------------------------------GLDITDLLSTTAKDRSLGLAYNYGALLANNSFFLESLNAGEPIEPSKVF--
+---------TPVLEKLEGYAEGIIGGGWLWIARtGdhEAQIDIIPTFGSGTLLVSgraqrsgavfeeplasspeppvvtsdmtgpspvsaipettappsv
+asqgsnlkrGssiyPAPLAVLNLFELAWLGdKYGVwAKRQYVRDWIK-SVDWKKVEERNS--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 2676 * 5915 5741 5630 5527 * 4683 3064 * 3875 4643 2449 5409 5754 2796 3437 4711 * * 1
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+
+K 142 4304 7088 6039 5162 5221 3907 7366 6797 4121 4673 * 3194 3480 3520 5212 3223 2387 5232 4166 * 142
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+
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+ 10 7210 * 0 * 408 2021 6999 1005 1220
+
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+ 33 6790 6202 0 * * 0 6980 1013 1006
+
+N 145 3981 * 2319 4474 6665 3976 6171 * 5549 3938 * 1136 7003 5660 * 5884 6706 6915 * * 145
+ 0 * * * * 721 1346 6974 0 1114
+
+A 146 2216 * 4533 5303 * 3834 2565 * 5941 5711 * 3601 * 1853 * 4895 6429 6454 * 5273 146
+ 0 * * * * * 0 6956 0 1006
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+ 51 * 4844 * * * 0 6899 0 1006
+
+N 148 6563 3966 4290 7261 5979 5834 4356 4773 5509 4371 6723 2234 4951 5934 * 2742 2126 5088 * * 148
+ 10 7229 * 2158 366 0 * 6870 1057 1293
+
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+ 132 4030 5253 333 2278 0 * 6949 1430 1148
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+ 400 2092 7045 4436 68 768 1276 6730 2633 1161
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+H 152 4093 * 3531 3860 4601 3804 4746 5661 4317 3815 7605 4796 4312 5186 4351 3465 4199 4326 3498 4518 152
+ 279 2714 5419 4128 85 0 * 6881 2093 1144
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+ 432 2206 4576 3637 121 0 * 6870 2550 1107
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+ 62 4707 7978 615 1526 0 * 6756 1304 1292
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+ 28 5698 * 0 * * 0 6571 1087 1110
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+D 170 * * 695 5725 * 6481 * * 2909 * * 7024 * 2804 5938 5314 6519 5983 * * 170
+ 0 * * * * * 0 6571 0 1110
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+ 45 5029 * 2622 256 0 * 6566 1176 1110
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+ 226 3015 5545 971 1029 * * 6566 1855 0
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+
+A 193 3850 7115 4085 1404 * 6373 * * 6690 * 6177 2165 * 4267 * 3268 5083 5794 6695 6057 193
+ 0 * * * * * * 6548 0 0
+
+K 194 2721 6258 4048 3181 * 6675 5299 6070 2585 6878 * 3627 * 3337 2863 4093 6074 6293 6645 5279 194
+ 0 * * * * * * 6538 0 0
+
+N 195 4342 7257 * * 6465 * 6124 6161 5329 3905 * 2813 * 5234 830 6151 6121 5290 * 5178 195
+ 23 5986 * 1330 731 * * 6528 1056 0
+
+L 196 5030 * 6831 * 2273 * * 6573 * 1664 6115 6948 * * * * * * 4730 1444 196
+ 168 3186 * 1046 955 * * 6523 1691 0
+
+A 197 3422 * 3518 2979 4767 4874 6670 5433 3736 3525 5662 4147 * 3099 3840 3775 4231 5947 6759 6328 197
+ 0 * * 1000 1000 * * 6320 1000 0
+
+A 198 2120 * 4515 3620 6178 4074 6304 6282 3063 6219 6108 3959 * 3165 3560 3594 5392 4991 * * 198
+ 32 5523 * 0 * * * 5982 1000 0
+
+A 199 1130 5294 * * 4485 3214 * 2999 * 3461 5618 * * * * 5428 4029 4492 * * 199
+ 0 * * 0 * * * 5046 0 0
+
+//
+�HHsearch 1.5
+NAME 14d53a48bb3d4cf83c4f637bd86d7e3e
+FAM
+FILE 14d53a48bb3d4cf83c4f637bd86d7e3e
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:04:19 2013
+LENG 70 match states, 70 columns in multiple alignment
+FILT 18 out of 20 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCEEEEHHHHHHHCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9877888776437887536752134443203141246657899987766589999889998866777629
+>Consensus
+GxxxsxxkxnxnssGNxGxIinNfYsnqYqnSIDlsxxxxgxxxxxxxgxxSxllgxxxsAfxxxxpLLa
+>14d53a48bb3d4cf83c4f637bd86d7e3e
+GNSTSSDKNNSSSEGNEGVIINNFYSNQYQNSIDLSANATGSDPPKTYGQFSNLLSGAVNAFSNMLPLLA
+>gi|25121875|ref|NP_740424.1| capsid protein VP4 [Theilovirus]
+GNASSSDKSNSQSSGNEGVIINNFYSNQYQNSIDLSASGGNAgDAPQNNGQLSSILGGAANAFATMAPLLM
+>gi|209363551|ref|YP_002268402.1| polyprotein [Seneca valley virus]gi|108946001|gb|ABG23522.1| polyprotein [Seneca valley virus]
+GNVQTTSKNDFDSRGNNGNMTFNYYANTYQNSVDFStsSSASGAGPGNSRG---GLAG-LLTNFSGILnPLgyLK
+>gi|239830819|ref|YP_002956075.1| polyprotein [Human cosavirus B]gi|219525340|gb|ACL15190.1| polyprotein [Human cosavirus B1]
+-MGANNSKESVNSSGNNGTTVNNFYANNYYGSIDASAQGVGTSSTPENGTVSGFLGMASSAFNAL-SLLA
+>gi|25121702|ref|NP_740361.1| VP4 [Equine rhinitis B virus 1]
+-----------NESGNNGTIVNNYYMQHYQNSVDLDGMTsqnIGGQPGSSSNPFSSIL---------------
+>gi|168480158|ref|YP_001686938.1| VP4 [Bovine rhinitis B virus]
+--------GNVNESGNSGSIINNYYMQQYQNSIDVTVGDktteggsgSGdtagsathNNTTKEdkgkDDWFSSLVSGIGSAIP-------
+>gi|82468893|gb|ABB76803.1| polyprotein [Equine rhinitis A virus]
+------TTGNQNMSGNSGSIVQNFYMQQYQNSIDADLGDnviSPegqgsntssstssSQSsgl---GGWFSSLLN--------lgtk---LLA
+>gi|130454|sp|P15072.1|POLG_FMDVT RecName: Full=Genome polyprotein; Contains: RecName: Full=Leader protease; Short=Lpro; Contains: RecName: Full=Protein VP0; AltName: Full=VP4-VP2; Contains: RecName: Full=Protein VP4; AltName: Full=P1A; AltName: Full=Virion protein 4; Contains: RecName: Full=Protein VP2; AltName: Full=P1B; AltName: Full=Virion protein 2; Contains: RecName: Full=Protein VP3; AltName: Full=P1C; AltName: Full=Virion protein 3; Contains: RecName: Full=Protein VP1; AltName: Full=P1D; AltName: Full=Virion protein 1; Contains: RecName: Full=Protein 2A; Short=P2A; AltName: Full=P52; Contains: RecName: Full=Protein 2B; Short=P2Bgi|4456720|emb|CAA24960.2| unnamed protein product [Foot-and-mouth disease virus C1]
+GAGQSsPATGSQNQSGNTGSIINNYYMQQYQNSMDTQLGDnaiSGgsnegstdttsthTTNTQNNDWFSKLAS---SAFSGLFgALLA
+>gi|254547216|gb|ACT66682.1| polyprotein [Porcine teschovirus 5]
+GTGSSRMEnGNTNNSGNTGVINYNFYSNSYTDAIDLSGAMSTQESNAAENAASgpsSLLKAGINAAARIGPLLA
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 0 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 2406 0 0
+
+N 2 2971 * * * * * * * * * 1905 1116 * * * * 2794 * * * 2
+ 0 * * * * * * 2728 0 0
+
+S 3 3988 * * * * 892 * * * * * * * * * 1892 * 2956 * * 3
+ 0 * * * * * * 2728 0 0
+
+T 4 1905 * * * * * * * * * * 3731 * 1964 * 2271 2366 * * * 4
+ 0 * * * * * * 2728 0 0
+
+S 5 * * * * * * * * * * * 1905 * * * 727 2956 * * * 5
+ 197 2971 * 0 * * * 2728 1039 0
+
+S 6 * * * * * * * * * * * 1905 2971 * 2794 1589 2956 * * * 6
+ 0 * * * * * * 2728 0 0
+
+D 7 3310 * 1669 * * * * * * * 2898 * * * * 1402 3793 * * * 7
+ 0 * * * * * * 2782 0 0
+
+K 8 * * * 2898 * * * * 529 * * * * * * * 2532 * * * 8
+ 208 2898 * 0 * * * 2782 1068 0
+
+N 9 * * * 2033 * 1490 * * * * * 1763 * * * 3251 * * * * 9
+ 0 * * * * * * 2803 0 0
+
+N 10 * * 3173 * * * * * * * * 836 * * * 1604 * * * * 10
+ 0 * * * * * * 2803 0 0
+
+S 11 * * * * 3173 * * * * * * * * 2725 * 1792 2972 1636 * * 11
+ 0 * * * * * * 2803 0 0
+
+S 12 * * 3457 * * * * * * * * 950 * 2812 * 2007 * * * * 12
+ 0 * * * * * * 2859 0 0
+
+S 13 * * * 2256 * * * * * * 4138 2771 * 3761 * 961 * * * * 13
+ 0 * * * * * * 2846 0 0
+
+E 14 * * * 3248 * * * * * * * 2899 * * 3477 576 * * * * 14
+ 0 * * * * * * 2846 0 0
+
+G 15 * * * * * 0 * * * * * * * * * * * * * * 15
+ 0 * * * * * * 2846 0 0
+
+N 16 * * * * * * * * * * * 0 * * * * * * * * 16
+ 0 * * * * * * 2846 0 0
+
+E 17 * * * 1666 * * * * * * * 2328 * 3486 * 2505 2183 * * * 17
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+
+G 18 * * * * * 0 * * * * * * * * * * * * * * 18
+ 0 * * * * * * 2846 0 0
+
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+
+I 20 * * * * * * * 224 * * 3477 * * * * * 4203 * * * 20
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+
+I 21 * * * * * * * 1283 * * * 2771 * * * * 3477 1503 * * 21
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+
+N 22 * * * * 3477 * * * * * * 500 * 4138 * * * * * 2771 22
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+
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+
+Y 25 * * * * * * * * * * * * * * * * * * * 0 25
+ 0 * * * * * * 2846 0 0
+
+S 26 2100 * * * * * * * * * 1713 * * * * 1115 * * * * 26
+ 0 * * * * * * 2846 0 0
+
+N 27 * * * * * * * * * * * 525 * 1713 * * * * * * 27
+ 0 * * * * * * 2846 0 0
+
+Q 28 * * * * * * 3218 * * * * 4203 * 841 * 2394 3477 * * * 28
+ 0 * * * * * * 2846 0 0
+
+Y 29 * * * * * * * * * * * * * * * * * * * 0 29
+ 0 * * * * * * 2846 0 0
+
+Q 30 * * * * * * * * * * * * * 588 * * 2771 * * 2408 30
+ 0 * * * * * * 2846 0 0
+
+N 31 3495 * 2771 * * 3326 * * * * * 588 * * * * * * * * 31
+ 0 * * * * * * 2846 0 0
+
+S 32 2771 * * * * * * * * * * * * * * 229 * * * * 32
+ 0 * * * * * * 2846 0 0
+
+I 33 * * * * * * * 587 * * 3761 * * * * * * 1941 * * 33
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+
+D 34 * * 0 * * * * * * * * * * * * * * * * * 34
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+
+L 35 2028 * * * 3477 * * * * 932 * * * * * * 3761 3900 * * 35
+ 0 * * * * * * 2846 0 0
+
+S 36 * * 2606 * * * * * * * * * * 3761 * 525 3900 * * * 36
+ 224 2796 * 1000 1000 * * 2846 1207 0
+
+A 37 1125 * * * * 1977 * * * 2937 * * * * * 3477 * 3900 * * 37
+ 105 3834 * 0 * * * 2846 1002 0
+
+N 38 3710 * * * * 2340 * 4254 * * 2998 2332 * 2790 * 2285 * * * * 38
+ 0 * * * * * * 2846 0 0
+
+A 39 2358 * 2340 * * 1692 * * * * 3710 * * * * 2588 4182 * * * 39
+ 678 1414 * 1984 420 * * 2846 1548 0
+
+T 40 3966 * * * * 3175 * 3218 * * * * * * * 1205 4598 2043 * * 40
+ 78 * 4254 * * * * 2846 0 0
+
+G 41 * * * * * 582 * * * * * 2393 4029 * * * 3638 * * * 41
+ 488 1800 * 3104 178 0 * 2825 1417 1000
+
+S 42 2346 * * * * 2150 * * 4205 * * 3900 * 3710 * 2269 2532 * * * 42
+ 54 4765 * 0 * * * 2846 1000 0
+
+D 43 3834 * 1712 2450 * 3477 * * * * * 3900 * 3160 * 3334 3761 * * * 43
+ 0 * * * * * * 2846 0 0
+
+P 44 3012 * * 3834 * 4675 * * * * * 2966 1999 * * 2415 2314 * * * 44
+ 84 4138 * 1585 585 * * 2846 1003 0
+
+P 45 * * * * * 2247 * * * * * 2689 1880 * * 4162 1705 * * * 45
+ 0 * * * * * 0 2822 0 1003
+
+K 46 1957 * * * * * * * 2223 * * 3425 2731 2662 3920 4049 * * * * 46
+ 0 * * * * * 0 2822 0 1003
+
+T 47 2689 * * 1890 * 4130 * * * 3920 * 3046 4162 * * 2703 3041 * * * 47
+ 110 3762 * 2000 415 0 * 2822 1018 1003
+
+Y 48 * * 3900 3114 * 4138 * * * * * 1583 * 4205 2701 2998 4254 * * 4598 48
+ 0 * * * * * * 2846 0 0
+
+G 49 * * 2829 * * 710 * * * * * 2443 * * * 3966 * * * * 49
+ 136 * 3477 * * * * 2846 0 0
+
+Q 50 3624 * * * * * * 3831 * * * 4359 2351 2157 * * 2621 * 2203 * 50
+ 0 * * * * * 0 2705 0 1095
+
+F 51 3624 * * * 1141 * * * * 2488 * * * * * * 3715 2243 * * 51
+ 0 * * * * * 0 2705 0 1095
+
+S 52 * * * 3831 * * * * * * 4114 * * * * 198 * * * * 52
+ 122 3624 * 1585 585 0 * 2705 1068 1095
+
+N 53 * * * * * 1846 * * 3761 3834 * 2561 * * * 1292 * * * * 53
+ 0 * * * * * * 2846 0 0
+
+L 54 * * * * 2733 * * 1731 * 867 * * * * * * * * * * 54
+ 0 * * * * * * 2790 0 0
+
+L 55 2557 * * * * * * * * 523 * * * * * 3932 * 3863 * * 55
+ 0 * * * * * * 2790 0 0
+
+S 56 * * * * * 756 * * 2972 * * 3910 * * * 2224 * * * * 56
+ 573 * 1609 * * * * 2803 0 0
+
+G 57 2515 * * * * 1375 * * * 2598 3495 * * * * 2430 * * * * 57
+ 0 * * * * 877 1134 2412 0 1458
+
+A 58 893 * * * 3819 2739 * 3215 * 2909 * * * * * * * * * * 58
+ 0 * * * * * 0 2691 0 1152
+
+V 59 1538 * * * * 3215 * 2739 * 2909 * * * * * 2920 * 2911 * * 59
+ 0 * * * * 816 1212 2691 0 1152
+
+N 60 * * 3846 * * * * * * * * 1427 * * * 1188 3060 * * * 60
+ 0 * * * * * 0 2809 0 1003
+
+A 61 184 * * * * * * * * * * 3060 * * * * * * * * 61
+ 0 * * * * * 0 2809 0 1003
+
+F 62 2883 * * * 355 * * 3596 * * * * * * * * * * * * 62
+ 0 * * * * * 0 2809 0 1003
+
+S 63 2004 * * * * * * * 3846 * * 2410 3596 * * 1534 3945 * * * 63
+ 0 * * * * * 0 2809 0 1003
+
+N 64 2336 * * * * 1964 * * * * * 2270 * * 2794 3857 3000 * * * 64
+ 0 * * 2000 415 * 0 2728 1003 1003
+
+M 65 2848 * * * * * * 1521 * 1968 1960 * * * * * * * * * 65
+ 317 * 2342 * * * 0 2728 0 1003
+
+L 66 2087 * * * 2743 1669 * * * 1733 * * * * * * * * * * 66
+ 505 1760 * 0 * 478 1827 2660 1243 1290
+
+P 67 2347 * * * 3839 * * * * * * * 724 * * 2964 * * * * 67
+ 0 * * * * 0 * 2728 0 1003
+
+L 68 * * * * * * * * * 0 * * * * * * * * * * 68
+ 192 3007 * 1000 1000 * * 2782 1095 0
+
+L 69 3904 * * * * * * * * 100 * * * * * * * * * * 69
+ 0 * * * * * * 2782 0 0
+
+A 70 574 * * * * * * * 2949 4026 2865 * * * * * * * * * 70
+ 0 * * 0 * * * 2773 0 0
+
+//
+�HHsearch 1.5
+NAME 17059f2501ae2a72fc19097f4d2b1341
+FAM
+FILE 17059f2501ae2a72fc19097f4d2b1341
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:45:08 2013
+LENG 86 match states, 86 columns in multiple alignment
+FILT 103 out of 186 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCEEEEEEECCCCCCCCCC
+>ss_conf PSIPRED confidence values
+98777888886066889999999999998398978981899998999999999999199300164799858999978987665679
+>Consensus
+xxxxxxxxxxxxxxexxxxxlxxxlxxFxxxxxxxlxFpxslsxxeRxxVHxlAxxxGLxsxSxGxgxxRxlvVxkxxxxxxxxxx
+>17059f2501ae2a72fc19097f4d2b1341
+MGSLNGGSPEGVESQDGVDHFRAMIVEFMASKKMQLEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSKRAGSHHHHHH
+>gi|301116633|ref|XP_002906045.1| DNA polymerase alpha-associated DNA helicase A, putative [Phytophthora infestans T30-4]gi|262109345|gb|EEY67397.1| DNA polymerase alpha-associated DNA helicase A, putative [Phytophthora infestans T30-4]
+--KTASNDEKPEAAEATAIEPAVAVQE--EEEEEEIE-------DKAVATKSVFQMMVFDSDSSDDDNDEAVDVEV----------
+>gi|294877934|ref|XP_002768200.1| DNA-binding protein SMUBP-2, putative [Perkinsus marinus ATCC 50983]gi|239870397|gb|EER00918.1| DNA-binding protein SMUBP-2, putative [Perkinsus marinus ATCC 50983]
+--TTEIGEK-pVARVDLT---ieav-DAT---ldsL---aSEETYCFDNLLSAASRRLVHERAETRGFKHGSSGDGIMRYVWVR-----------
+>gi|321472095|gb|EFX83066.1| hypothetical protein DAPPUDRAFT_316187 [Daphnia pulex]
+------DDSSGSEPDDDIDDFRELLMEWVGGEEDIFTFPDTFSLAERRQIHNICDQLKLVHKSTGEGDSRRLVVTR----------
+>gi|332017832|gb|EGI58492.1| NF-kappa-B-repressing factor [Acromyrmex echinatior]
+---------------EIKTKCRKLFKDLLQTDnySRkDIVF-LDFPKEDRIVIHQVARTMGLKSRSQGK-DQRKLIVSSK---------
+>gi|170033973|ref|XP_001844850.1| ATP-dependent RNA helicase A [Culex quinquefasciatus]gi|167875095|gb|EDS38478.1| ATP-dependent RNA helicase A [Culex quinquefasciatus]
+-------------EEDVRIAIHYMIDKFVQDEKlNEFDFPVSFTREHRAYIHDYVKNKSLKSRSHGKGNQRYLTIYK----------
+>gi|110741780|dbj|BAE98834.1| hypothetical protein [Arabidopsis thaliana]
+--------GKPTSVEATRIWATKVIEDFRASGNEVYTFEHNLSNNERGVIHQMCRKMGIQSKSSGRGEQRRLSIFK----------
+>gi|302404235|ref|XP_002999955.1| conserved hypothetical protein [Verticillium albo-atrum VaMs.102]gi|261361137|gb|EEY23565.1| conserved hypothetical protein [Verticillium albo-atrum VaMs.102]
+---------------MGIEQIAQELENFLKNSQASLALPPM-DNHARKVLHELANKFNIKSKSTGSGDQRRPTLYRT---------
+>gi|330470828|ref|YP_004408571.1| single-stranded nucleic acid binding R3H domain-containing protein [Verrucosispora maris AB-18-032]gi|328813799|gb|AEB47971.1| single-stranded nucleic acid binding R3H domain-containing protein [Verrucosispora maris AB-18-032]
+-----------------RKELAAVARNAVEkvkEHGEAVRLE-PMSAFERKCVHDVVNAiDGVESESEGVEPNRRIVVRPA---------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+G 2 * * * * * 0 * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1000 0 0
+
+S 3 3654 * 3636 3563 * * * * 1668 * * 3890 * * 4016 2194 3427 * * * 3
+ 0 * * * * * * 3920 0 0
+
+L 4 3709 * 3680 * * * 2735 * * 2193 * * * * * * 1332 3654 * * 4
+ 0 * * * * * * 3920 0 0
+
+N 5 2832 * 3680 2493 * 3654 3842 * * * * 3789 * 3376 * 2855 * 2758 * * 5
+ 92 * 4016 * * * * 3920 0 0
+
+G 6 * * * * * 3714 * 3355 3591 3550 * 3530 3695 * 2697 2772 3267 3483 * * 6
+ 0 * * * * * 0 3856 0 1000
+
+G 7 * * 2401 2658 * 2694 * 3943 3853 * * 2224 3779 * 3706 * * * * * 7
+ 0 * * * * * 0 4083 0 1000
+
+S 8 * * 2081 3515 * 3779 * * 2701 * * 3640 2639 * * 2799 3943 * * * 8
+ 0 * * * * * 0 4083 0 1000
+
+P 9 * * * 1906 * 2673 * * 2803 3953 * * 2769 3851 * 3426 4072 * * * 9
+ 118 * 3670 * * * 0 4114 0 1000
+
+E 10 4113 * 2928 1239 * * * * 2146 * * * * 3932 * 3388 * * * * 10
+ 444 3918 2330 0 * 431 1953 4013 1135 1083
+
+G 11 3902 * 3555 * * 1839 3983 * * * * * 2290 * 3630 3985 3525 3839 * * 11
+ 0 * * * * * 0 4091 0 1199
+
+V 12 3048 * 4357 2169 * 4102 * * * * * 4488 2463 * * 3077 2647 4453 * * 12
+ 0 * * * * 212 2871 4539 0 1199
+
+E 13 2956 * 4880 1272 4377 4834 * * 4742 * * * * 4857 4562 4656 * 2427 * * 13
+ 0 * * * * * 0 4867 0 1000
+
+S 14 2260 * * 3551 4569 4492 * * 3246 * * * 3535 * 3829 3294 2706 3293 * * 14
+ 0 * * * * * 0 5049 0 1000
+
+Q 15 * * 2288 1396 * * 5162 * 2819 * * * * 2899 4245 * * 4089 * * 15
+ 0 * * * * * 0 5169 0 1000
+
+D 16 2793 * 2367 2635 5220 3702 * 4865 4547 3453 4391 5665 * 5552 * 3641 * 4804 5366 * 16
+ 0 * * * * * 0 5460 0 1000
+
+G 17 4359 * 3426 4118 3896 4837 * 4517 4920 3362 4930 3781 * 5193 5963 3559 1996 5450 * 5860 17
+ 32 * 5532 * * * 0 5610 0 1000
+
+V 18 3050 * 5690 4673 * * * 3993 2276 3525 * 4956 5555 4935 1921 * 3299 6293 * * 18
+ 0 * * * * * 0 5920 0 1083
+
+D 19 3383 6398 3029 3011 * 6270 * 2533 2961 3201 6205 5528 * 5175 4131 6297 4158 4878 * * 19
+ 0 * * * * * 0 5958 0 1083
+
+H 20 3377 * 3029 1815 * 4690 5075 * 3106 5180 * 4921 * 4189 4263 3402 5199 * 6554 6322 20
+ 0 * * 2000 415 1953 431 5968 1049 1083
+
+F 21 4517 4415 * * 3179 * 6513 2401 * 1535 6370 * 4161 * * * * 3246 * 3639 21
+ 0 * * * * 0 * 5958 0 1049
+
+R 22 3281 * 3768 4061 6243 6084 4197 6443 3723 4731 5557 4933 * 4822 2387 4815 4127 5555 5119 2910 22
+ 0 * * * * * * 5930 0 0
+
+A 23 2918 6207 4782 2703 * 6460 6312 5443 2854 4701 6557 4250 * 3239 4827 3522 3768 3998 * 6249 23
+ 0 * * * * * * 5942 0 0
+
+M 24 2930 * * 3230 * * 6580 2952 4630 2749 3647 * * 3179 4227 4659 5416 3144 * 6195 24
+ 21 * 6108 * * * * 5942 0 0
+
+I 25 3646 * * * 4764 5216 * 2373 * 1242 5032 * * * * * * 2251 * * 25
+ 0 * * * * * 0 5882 0 1049
+
+V 26 5868 * 4362 2542 * * 6494 * 2573 3105 4357 5032 6671 2741 3376 * 3997 4090 * 6546 26
+ 0 * * * * * 0 5882 0 1049
+
+E 27 2806 * 3104 2175 * * * * 3511 3753 4313 3052 * 4914 4231 4211 4836 6496 * * 27
+ 78 * 4252 1585 585 0 * 5886 1049 1049
+
+F 28 3535 5247 * * 675 5648 * * * 3991 * 6072 * * * * 5363 * 4461 3415 28
+ 53 * 4784 * * * 0 5713 0 1154
+
+M 29 3130 5264 * * * * 5370 2441 2839 2478 5645 * * 6106 3406 4624 6702 2706 * * 29
+ 89 4065 * 0 * 913 1092 5659 1253 1329
+
+A 30 2489 * 2928 2105 6856 4834 5672 * 3556 5050 * 3639 * 3900 5056 3583 * * 6653 6817 30
+ 368 2152 * 1900 450 1997 416 5856 1779 1130
+
+S 31 3790 * 2051 2781 * 3185 5776 * * * * 5663 4854 5172 5453 2006 4086 * * * 31
+ 79 4231 * 428 1960 459 1876 5893 1269 1086
+
+K 32 * * 2488 2014 * 3557 5528 * 5196 6496 * 6052 3410 * 5012 2502 3602 5048 * * 32
+ 35 5377 * 3001 192 * 0 5859 1047 1000
+
+K 33 4555 6669 4210 2435 * 3599 6727 * 3348 6512 4075 3212 * 3625 3649 3687 3830 4987 * * 33
+ 60 4615 * 2010 412 * 0 5862 1114 1000
+
+M 34 3262 6448 3572 2618 * 6363 6669 6796 3980 5280 5858 4340 6032 4376 2894 4360 2806 4916 5689 6871 34
+ 457 1880 * 426 1966 0 * 5862 1993 1000
+
+Q 35 4007 * 2954 1749 * * * 4345 6363 6868 * * 4799 4073 4045 3373 3641 3202 * * 35
+ 16 6489 * 0 * * * 5723 1009 0
+
+L 36 6216 * * * 4681 * 6847 2917 5513 1442 3070 * * * 6653 * 6442 2710 * 3021 36
+ 0 * * * * * * 5695 0 0
+
+E 37 2980 6198 4759 2025 * * 4268 5072 5774 * * 6669 * 5092 4409 3354 2921 2635 * * 37
+ 78 * 4245 * * * * 5695 0 0
+
+F 38 * 5962 * * 444 * * * * 2128 5641 * * * * * * * * * 38
+ 32 * 5511 * * * 0 5506 0 1154
+
+P 39 4813 * 4672 3565 * * 6634 * 5605 5272 * * 802 6406 5448 2507 * * * * 39
+ 282 * 2492 * * 1779 497 5404 0 1236
+
+P 40 2716 * 6485 * * * 5665 * 4882 5360 * 3644 1490 * 4691 2073 5596 5291 * * 40
+ 73 * 4345 * * 402 2040 5118 0 1757
+
+S 41 6580 * 3726 3855 * 4294 4948 6120 * 6119 6066 4023 2986 6416 * 1633 2351 * * * 41
+ 31 * 5570 * * 1288 760 5491 0 1292
+
+L 42 * * * * 2375 * * 4631 * 916 2410 * * * * * 6702 5499 * 5872 42
+ 0 * * * * 2812 222 5425 0 1229
+
+N 43 4659 4634 3379 * 6531 6499 * * * 6414 * 3048 6444 * * 1545 1665 * * * 43
+ 0 * * * * * 0 5430 0 1190
+
+S 44 2062 * * * * 4665 * * 2893 5020 * 2762 2657 * 6342 2138 6602 * * * 44
+ 0 * * * * 239 2710 5430 0 1190
+
+H 45 3162 * 3225 2638 2999 * 3425 7201 6698 5280 * 4216 6723 5649 3742 4880 4849 5299 * 3208 45
+ 0 * * * * * 0 5636 0 1000
+
+D 46 5139 * 2690 1103 6633 * 5064 * 3650 * * * * 2427 * 4755 6883 * * * 46
+ 0 * * * * * 0 5636 0 1000
+
+R 47 4165 * * * * * * * * * * * * * 83 * * * * * 47
+ 0 * * * * * 0 5636 0 1000
+
+L 48 1897 * * * * 5921 5267 6520 1944 3495 4546 * * 6608 2332 6606 * 4165 6400 * 48
+ 0 * * * * * 0 5636 0 1000
+
+R 49 3036 5624 7012 5796 4348 * * 3502 4835 2371 6102 * * 3933 5928 5795 4303 2572 6029 3086 49
+ 0 * * * * * 0 5636 0 1000
+
+V 50 5462 * * * 5739 * * 1394 * 3269 * * * * * * 4189 1307 6029 * 50
+ 0 * * * * * 0 5636 0 1000
+
+H 51 * * * * * * 81 * 4189 * * * * * * * * * * * 51
+ 0 * * 3322 152 0 * 5636 1000 1000
+
+Q 52 3969 * 3010 2426 * 4575 6582 4830 5976 4783 6504 3798 * 2778 3691 3494 3980 5168 * * 52
+ 0 * * * * * * 5635 0 0
+
+I 53 4256 6454 * 5470 5201 * * 2353 6578 1739 3335 * * * 4896 6673 5333 2708 5593 4654 53
+ 0 * * * * * * 5635 0 0
+
+A 54 716 2708 * * 4190 * * 5616 * * * * * * * 3996 * 3315 * * 54
+ 0 * * * * * * 5635 0 0
+
+E 55 3285 * 3986 1992 * 5618 3518 6899 3155 5809 5359 3926 6582 2825 3954 5494 6906 * * * 55
+ 0 * * * * * * 5635 0 0
+
+E 56 3629 * 4164 2681 * * 5716 6052 1937 * 3947 3859 6482 4337 3447 4189 4294 * 5615 * 56
+ 45 5015 * 0 * * * 5635 1078 0
+
+H 57 4139 5904 6694 5555 2842 * 3993 6159 6406 1813 2373 5197 * * 4236 * * * 6403 3353 57
+ 0 * * * * * * 5635 0 0
+
+G 58 6816 * 5123 * * 585 6908 * 3733 6639 * 4310 * * 6033 4109 5389 4190 * * 58
+ 0 * * * * * * 5635 0 0
+
+L 59 * 5794 * * 2909 * * 4322 * 527 5136 * * * * * * 4169 * 5591 59
+ 15 * 6604 * * * * 5635 0 0
+
+R 60 4669 * 3593 3575 5164 4342 3895 4321 2068 * 6396 5234 6958 4677 4439 3583 4369 3694 * 5630 60
+ 0 * * * * * 0 5645 0 1004
+
+H 61 * * * * * * 1170 * * * * * * 5284 * 1012 4877 * * * 61
+ 0 * * * * * 0 5645 0 1004
+
+D 62 4026 6449 3810 2818 6492 5325 4734 6269 1741 7233 * 6672 * 3845 3882 4065 4976 3982 * 5670 62
+ 0 * * * * * 0 5645 0 1004
+
+S 63 * * * * * * * * * * * * * * * 0 * * * * 63
+ 0 * * * * * 0 5645 0 1004
+
+S 64 4416 * 6724 3412 5759 * 3567 4497 5460 5264 6641 * * 3694 3678 2542 3183 3292 * 3257 64
+ 0 * * * * 0 * 5645 0 1004
+
+G 65 * * 3941 * * 151 * * * * * * * * 6604 * * 5389 * * 65
+ 0 * * * * * * 5635 0 0
+
+E 66 5244 6786 2954 1848 * 6272 6564 * 2162 5749 6633 6541 5968 5692 4944 3797 4848 3644 6465 7456 66
+ 29 6829 6523 0 * * * 5633 1000 0
+
+G 67 5134 * 3120 3597 * 704 * * 4468 * * 5096 5525 6251 5904 5491 6397 * * * 67
+ 0 * * * * 0 * 5624 0 1000
+
+K 68 3481 * 2287 2787 * 4681 4651 6184 4744 6449 * 3145 2825 6844 4542 3695 4784 * * * 68
+ 0 * * * * * * 5633 0 0
+
+R 69 4765 * 2456 2927 6486 4690 5639 6495 4651 4857 5333 2681 * 2924 4039 3175 6615 * * * 69
+ 0 * * * * * * 5633 0 0
+
+R 70 * * * 4189 * * * * * * * * * * 81 * * * * * 70
+ 0 * * * * * * 5633 0 0
+
+F 71 4051 5785 6959 * 3431 * 2905 * 4024 * * 6869 * 3600 2339 4455 5207 3953 * 2323 71
+ 0 * * * * * * 5633 0 0
+
+I 72 5670 * * * * * * 1971 * 1392 * * 4435 * * * 6062 1822 * * 72
+ 0 * * * * * * 5633 0 0
+
+T 73 5974 5752 4189 5808 * * 4453 3345 5283 5206 5646 * * 5115 6642 4415 2080 1556 6184 * 73
+ 0 * * * * * * 5633 0 0
+
+V 74 * * * * * * * 2000 * 2625 * * * * * * * 766 * * 74
+ 27 * 5745 * * * * 5633 0 0
+
+S 75 6782 * * 3825 3942 4384 5686 5656 3677 4705 * * * 6496 3592 2050 2494 5590 5394 3409 75
+ 0 * * * * 0 * 5623 0 1030
+
+K 76 * * 5922 * 6325 6669 6233 * 1106 * * 4746 4118 6474 1942 4957 5979 3859 * * 76
+ 27 5734 * 0 * * * 5608 1000 0
+
+R 77 2873 5671 4515 4405 * 4475 * 4294 1494 4503 * * 4258 * 3035 4678 4492 * * * 77
+ 0 * * * * * * 5278 0 0
+
+A 78 2423 * 2607 2697 * 2589 * * 1604 * * * * * * * * * * * 78
+ 0 * * * * * * 2558 0 0
+
+G 79 * * * * * 0 * * * * * * * * * * * * * * 79
+ 0 * * * * * * 1000 0 0
+
+S 80 * * * * * * * * * * * * * * * 0 * * * * 80
+ 0 * * * * * * 1000 0 0
+
+H 81 * * * * * * 0 * * * * * * * * * * * * * 81
+ 0 * * * * * * 1000 0 0
+
+H 82 * * * * * * 0 * * * * * * * * * * * * * 82
+ 0 * * * * * * 1000 0 0
+
+H 83 * * * * * * 0 * * * * * * * * * * * * * 83
+ 0 * * * * * * 1000 0 0
+
+H 84 * * * * * * 0 * * * * * * * * * * * * * 84
+ 0 * * * * * * 1000 0 0
+
+H 85 * * * * * * 0 * * * * * * * * * * * * * 85
+ 0 * * * * * * 1000 0 0
+
+H 86 * * * * * * 0 * * * * * * * * * * * * * 86
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 19505167af9ebfb7eba762c056361c1f
+FAM
+FILE 19505167af9ebfb7eba762c056361c1f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:31:27 2013
+LENG 240 match states, 240 columns in multiple alignment
+FILT 126 out of 1228 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEECCCCCCCEEEEEEEECCCCCCEEEEEEEECCCEEEECHHHCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCEEEEEEC
+CCCCCCCCCCEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEECHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCEEEEEECCEE
+EEEEEEEECCCCCCCCCCCCEEEEEHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9999899987889899999916997746999999719999989889688875599981100356888607999999998998777777667768999957
+8753677644155265455557998899998366578887775568999998568993014331677886769861589966567787980799989989
+9999998657778888898559999799799999998539
+>Consensus
+ixxgxxxxxxxxPxxvxixxxxxxxxxxxCxGtlIsxxxVLTaaxCxxxxxxxxvxxgxxxxxxxxxxxxxxxvxxxxxhpxxxxxxxxxxxDiAlxxLx
+xxxxxxxxvxpiclxxxxxxxxxxxxxxxxgxgxxxxxxxxxxxlxxxxxxxxxxxxCxxxxxxxxxxxxxxxCxxxxxxxxxcxgdsGxplxxxxxxxx
+xlvGixsxxxxxxcxxxxxxxxxxxvxxxxxWIxxxxxxx
+>19505167af9ebfb7eba762c056361c1f
+VVGGTEAQRNSWPSQISLQYRSGSSWAHTCGGTLIRQNWVMTAAHCVDRELTFRVVVGEHNLNQNDGTEQYVGVQKIVVHPYWNTDDVAAGYDIALLRLA
+QSVTLNSYVQLGVLPRAGTILANNSPCYITGWGLTRTNGQLAQTLQQAYLPTVDYAICSSSSYWGSTVKNSMVCAGGDGVRSGCQGDSGGPLHCLVNGQY
+AVHGVTSFVSRLGCNVTRKPTVFTRVSAYISWINNVIASN
+>gi|74002660|ref|XP_535739.2| PREDICTED: similar to sperm-specific sodium proton exchanger [Canis familiaris]
+----------------------------------------------------------------------------------------------------
+--------YALLRVPSSPRHSSSPEDAYELIIPRRVFSYsLQQPHPPTPHLENRVSY-------------------------------------------
+-----------------------------------------
+>gi|334329721|ref|XP_001365700.2| PREDICTED: sodium/hydrogen exchanger 10-like [Monodelphis domestica]
+----------------------------------------------------------------------------------------------------
+------------NVVPkhmtkqladrc------------------ETEYAv-----------------VRvpsspQPSYSFQDEEYELIMPITHTHYPSH
+LNWMNSGNLNR----------------------------------------------
+>gi|328704879|ref|XP_003242629.1| PREDICTED: hypothetical protein LOC100575281 [Acyrthosiphon pisum]
+----------EYPYLVGLTIGgivdKTNRKTAICTGTLVSPVLVLSSAYCTlllmtTINESPEVTTLFAYWKTPTNSVKYHRATSVYTHPSYD--KATRM
+FDLSLIKLKKPFKHVE--RFVRLSSKTLSSDVELSCVVVGIGAPHERGyKVPVRVKYGRTACRIPKSNPGLEYLIGYTWADFLCSETvGPTTTRLPCDRA
+DPLVC--SGSRHQYGIFSYGydgtgaspatEATECGDPAIQGRHLFINRNAGWIAEIIANH
+>gi|329669138|gb|AEB96457.1| salivary serine protease [Simulium guianense]
+-------DNEQFPWFCTVY--SNEDFKPVCYCTILGKNAILTASKCFENrdttngdHPKYHVRFGSIAAN---GMRKLVNIEKIQGTQ-----------H
+LLMLKPKTPIE---GYHAIELAENNYVEPKNGNITVATFHSYGTKLSMKTHVHMVDMRLSkDAKNC--QFAY----PNKHFCA--AESQNRCNIGLGTAA
+VSQSpknSSRWILHGIVDQ-SPKCNGESKNADLFVKIDAeRWDFIKHNLN--
+>gi|194899249|ref|XP_001979173.1| GG13986 [Drosophila erecta]gi|190650876|gb|EDV48131.1| GG13986 [Drosophila erecta]
+--------------------RGhKPEFSVVCNATIVSPYILVTTERCFSEssiksvpstePVLYTVAEGKiygNSFLAHEPHPYKLHNVSHIVYARYL--
+----DKgivgTLVLVHLVQPLEFHMKLRPVCLTEELTDNWLtagDFTGVNPGHPIIDdRRQPGRYELREV------------------------------
+--------------------------------------------------------------
+>gi|86146281|ref|ZP_01064606.1| hypothetical protein MED222_16256 [Vibrio sp. MED222]gi|218709799|ref|YP_002417420.1| hypothetical protein VS_1811 [Vibrio splendidus LGP32]gi|85835992|gb|EAQ54125.1| hypothetical protein MED222_16256 [Vibrio sp. MED222]gi|218322818|emb|CAV18995.1| hypothetical protein VS_1811 [Vibrio splendidus LGP32]
+------------------------------SATLIDPYWVITANHVSGSKSegyENAVTCSSYEKDKNGKYNVVHTSRATTDPDgewgEYE--FTDGIYD
+FALVRLDTPIT---GIKPAKLPEKGMFDHSEVyEVNSVGFGNYNGRNGGKKFVKYNDTDK--------KWLAEYKYDPVIMPQSNL-QWLIIHGDSGSGI
+TIERDGEFYIIGEIGL---QYYGELGWQDTFDDVLGRLDSLQSDMQE-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 4648 * * * * * * 851 * * * * 3923 * * * * 1557 * * 1
+ 0 * * * * * * 7379 0 0
+
+V 2 3189 * * * 4851 * * 1946 * 3817 * 3166 5095 * * 3199 4914 2769 * 3386 2
+ 0 * * * * * * 7698 0 0
+
+G 3 5505 * 3688 * 5182 1182 * * 4390 * * 1852 * * 5080 4203 5412 * * * 3
+ 38 5284 * 0 * * * 8293 1018 0
+
+G 4 4378 * * * * 523 5430 * 5363 * * 5376 5545 4394 * 3780 * 5637 * 5467 4
+ 0 * * * * * * 8748 0 0
+
+T 5 5853 * 3724 3010 * * 5603 * 3704 * * 5746 * 2722 3043 4023 2653 4098 4777 3669 5
+ 0 * * * * * * 9030 0 0
+
+E 6 3671 * 2577 2538 * * * 4449 4353 4245 * 3917 2670 5879 3420 6197 3811 6010 * * 6
+ 0 * * * * * * 9419 0 0
+
+A 7 1883 * 3934 * 5949 * * 5931 * 5867 * * 4829 * * 4307 2349 1648 * 6305 7
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+N 240 3825 * 3661 * * * 2138 * * * * 682 * * * * * * * * 240
+ 0 * * 0 * * * 5490 0 0
+
+//
+�HHsearch 1.5
+NAME 1b2f6c29a7ee470020810a8013596703
+FAM
+FILE 1b2f6c29a7ee470020810a8013596703
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:47:25 2013
+LENG 214 match states, 214 columns in multiple alignment
+FILT 126 out of 1562 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCHH
+HHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCH
+HHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9899988999999999999999844159638997157777532169999998424344456678999999987899999999998469989995873057
+9988752133445656999999999875068877699997999999999983566553220102223299999999999999975467998999599999
+99999999997369
+>Consensus
+xxIxixGxxGsGKtTxxxxLxxxlxxxxxxvxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxixxxxxxxxxvixDrxxxxx
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxdxivxLxxxxexxxxRlxxRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxidxxxxx
+xevxxxIxxxlxxx
+>1b2f6c29a7ee470020810a8013596703
+MLIAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAFPRYGQSVAADIAAEALHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCRGYDVVILDRYVASN
+AAYSAARLHENAAGKAAAWVQRIEFARLGLPKPDWQVLLAVSAELAGERSRGRAQRDPGRARDNYERDAELQQRTGAVYAELAAQGWGGRWLVVGADVDP
+GRLAATLAPPDVPS
+>gi|21668336|emb|CAC84481.1| thymidine kinase [Heliothis virescens ascovirus 3c]
+-YVSVEGNIGSGKSSVMRSVAKHFDDCI---LFCEEPVND--W--GLLEYMYRDPT-KY-AFAFEVQVLTSkYH------KWINALDEcrrtqKRIVVME
+RsplsayKVFTRMMRERGTISSQQYHIYTQMFAEFQPQ---LKTIDHIVHIDTRASTCQVRAGERNRKAE-E-----ALSLEYLLDVESYTNNYVRDH--
+SSVYTIDGDRSREHVAGELTAFLS--
+>gi|342733037|ref|YP_004771876.1| adenylate kinase [Candidatus Arthromitus sp. SFB-mouse-Japan]gi|342330492|dbj|BAK57134.1| adenylate kinase [Candidatus Arthromitus sp. SFB-mouse-Japan]
+-RILLIGPPGVGKGTQANLICSKYN---LKHISTgdilRkYISDDSEI-GKRISNYgIDC--GKFVSDDLVNSIV------------SQLKSDKildQSY
+LLDGYPRTVS--QAEF--------YINNILNK------N-EKYLVIYLSTSNEYILNRISNRLtciNCGNIynlQNdlpkiygkcdicgn-RLIIRSDDK
+VNILkerLEIYYRITsrvvDYFRNlDVLYEIDASYGINEIFSQVKKVIG--
+>gi|297182654|gb|ADI18812.1| shikimate kinase [uncultured SAR11 cluster bacterium HF4000_37C10]
+-------MMAVGKTTLGKIVAKKQELK---FIDIDAsIEK--KN-SMTIREIFKK---------KGEKFF-----RMEeENEILKSLEKNNCVIA-----
+-----LGGGAF-----MNKTVRENILK-------NAISIWLNVDIKTLNQRVKWNQK----RP--LLK-EEN-YqKKITKLYAERKNIY-KLANHQIAcD
+KLSKDNIAEKIIAL----
+>gi|26346689|dbj|BAC36993.1| unnamed protein product [Mus musculus]
+----------------------------FGTTvpfTSRKPRED-EKDGQ-AYKFVSRSEmEADIkAGKYLEHGEYEGNLYGTkIDSILEVVQTGRTCILD
+--------------------VNPQALKVLRTS---EFMPYVVFIAAPELETLRamhKAVVDAGITT----------KLLTDSDLkktvdESARIQRAYNH
+Y-FDLIIVNDN--LDKAFEKLQTAI---
+>gi|212703228|ref|ZP_03311356.1| hypothetical protein DESPIG_01270 [Desulfovibrio piger ATCC 29098]gi|212673494|gb|EEB33977.1| hypothetical protein DESPIG_01270 [Desulfovibrio piger ATCC 29098]
+-LITVAGLVGSGRGAIINLLSEWMDSKHVQNHVFWLVTDE-----EKARPWPWRF---W-------------------RQ-LP--AAGQTAVFYDGWYGE
+AMRQRCckDVGENEFTASMHRWQALESGLAESGMAIIKLWLHLNKKDHARALKE----------------------------------------------
+----------------
+>gi|78778435|ref|YP_396547.1| dephospho-CoA kinase [Prochlorococcus marinus str. MIT 9312]gi|109824304|sp|Q31DD4.1|COAE_PROM9 RecName: Full=Dephospho-CoA kinase; AltName: Full=Dephosphocoenzyme A kinasegi|78711934|gb|ABB49111.1| dephospho-CoA kinase [Prochlorococcus marinus str. MIT 9312]
+----------------------------------------------------------------------------------------------------
+-------------------------------ICTEIWLVKCPRELQKKRLITRDKISE----------KEAYETINLQLSF-EEKSK-FSDIILDNSDDQ
+NKWINTIREIL---
+>gi|189183429|ref|YP_001937214.1| hypothetical protein OTT_0522 [Orientia tsutsugamushi str. Ikeda]gi|189180200|dbj|BAG39980.1| hypothetical protein OTT_0522 [Orientia tsutsugamushi str. Ikeda]
+---------------MILALE----KLVYVV--ILKSATD-VI-AES-QAK---gDMRPWE-Q--pDfVDKIVLTQKLRQ----MNA--VCEVQFYDRSP
+FCAYALWHY-------------------------------------------------------------------------------------------
+-----------------
+#
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+T 206 3606 * 4097 2036 * * * 4574 4623 3416 5594 5660 * 2636 4257 3645 3801 6517 6523 6354 206
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+A 208 5453 5775 6559 4083 5494 * * 3199 3506 2281 3575 5903 * 3741 4502 6391 3577 3326 6544 4691 208
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+P 213 3771 * 3524 2644 * * * * 3675 3337 * 3480 2170 * * 3390 * * * 3391 213
+ 0 * * * * * * 5134 0 0
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+S 214 * * * * * * * * * * * * * * * 0 * * * * 214
+ 0 * * 0 * * * 2765 0 0
+
+//
+�HHsearch 1.5
+NAME 1d1847456cd583e08ed67aaa11df98f2
+FAM
+FILE 1d1847456cd583e08ed67aaa11df98f2
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:56:54 2013
+LENG 59 match states, 59 columns in multiple alignment
+FILT 24 out of 26 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+96320136898766662073356768887458722433121100443103352014459
+>Consensus
+kxKxxxxKxxxgsxCxewxxgxCvPxxgDCGxGxreGtCxxxtkxxkCkiPCnwKKeFG
+>1d1847456cd583e08ed67aaa11df98f2
+KKKDKVKKGGPGSECAEWAWGPCTPSSKDCGVGFREGTCGAQTQRIRCRVPCNWKKEFG
+>gi|5031406|gb|AAD38156.1|AF149801_1 pleiotrophin 2 [Danio rerio]gi|37589708|gb|AAH59575.1| Midkine-related growth factor b [Danio rerio]
+MKKKEKGKEpKVDAECSEWQYGKCVPNSGDCGNGIREATCNEQTKKTKCKVPCNWKKDFG
+>gi|152003256|gb|ABS19628.1| midkine a [Carassius gibelio]
+KNKKEKNKGgKGGSDCAEWRFGSCVANNGDCGAGTREGTCSEQTKKVKCRVPCNWKKDFG
+>gi|73968106|ref|XP_851259.1| PREDICTED: similar to Midkine precursor (MK) (Neurite outgrowth-promoting protein) (Midgestation and kidney protein) (Amphiregulin-associated protein) (ARAP) (Neurite outgrowth-promoting factor 2) [Canis familiaris]
+KKKDKVTKGGPGERVRGVDLGALHPQQQGLRRGFPRG------------yprgpdpahpvpga--LQLKKEFG
+>gi|33312179|gb|AAQ04021.1|AF419846_1 midkine precursor [Gallus gallus]
+KAKKEKMK-KEGSECQDWHWGPCIPNSKDCGLGYREGSCGDESRKLKCKIPCNWKKKFG
+>gi|57471264|gb|AAW50957.1| truncated midkine [Mus musculus]
+KKKEKVKK---GSECQEtiRVTKPCTSKTK-------------------------------
+>gi|301625710|ref|XP_002942046.1| PREDICTED: pleiotrophic factor-beta-1 [Xenopus (Silurana) tropicalis]
+--KDKQEKKVKKSDCGEWQWSVCVATSGDCGLGTREGTrsgkeCKQTIKTQKCKIPCNWKKQFG
+>gi|260800027|ref|XP_002594938.1| hypothetical protein BRAFLDRAFT_244520 [Branchiostoma floridae]gi|229280176|gb|EEN50949.1| hypothetical protein BRAFLDRAFT_244520 [Branchiostoma floridae]
+--------KGPQEGCSGWTWQPCVPAEGDCGLGQRQGTqegpnCKILSKTIKCRIPCGRRKEYG
+>gi|72081315|ref|XP_780885.1| PREDICTED: similar to Pleiotrophin (PTN) (Heparin-binding growth-associated molecule) (HB-GAM) (Heparin-binding growth factor 8) (HBGF-8) (Osteoblast-specific factor 1) (OSF-1) (Heparin-binding neutrophic factor) (HBNF) (Heparin-binding brain mitogen) (HBBM)... [Strongylocentrotus purpuratus]gi|115960217|ref|XP_001176726.1| PREDICTED: similar to Pleiotrophin (PTN) (Heparin-binding growth-associated molecule) (HB-GAM) (Heparin-binding growth factor 8) (HBGF-8) (Osteoblast-specific factor 1) (OSF-1) (Heparin-binding neutrophic factor) (HBNF) (Heparin-binding brain mitogen) (HBBM)... [Strongylocentrotus purpuratus]
+----------------EWIWSECVPNTGSCGKGQKIGNCsgepcEVATKTVDCRVKCA------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+K 1 * * * * * * * * 160 * 3255 * * * * * * * * * 1
+ 0 * * * * * * 2167 0 0
+
+K 2 3383 * * * * * * * 985 * * 1326 * * * * * * * * 2
+ 0 * * * * * * 2167 0 0
+
+K 3 * * * * * * * * 0 * * * * * * * * * * * 3
+ 0 * * * * * * 2280 0 0
+
+D 4 * * 1239 4264 * * * * 931 * * * * * * * * * * * 4
+ 0 * * * * * * 2280 0 0
+
+K 5 * * 3936 1123 * * * * 1072 * * * * * * * * * * * 5
+ 0 * * * * * * 2280 0 0
+
+V 6 * * * * * * * * 931 * * * * 3254 * * * 1431 * * 6
+ 0 * * * * * * 2280 0 0
+
+K 7 * * * 3254 * 2655 * * 2200 * 3568 2211 * * * * 2707 3936 * * 7
+ 0 * * * * * * 2280 0 0
+
+K 8 * * * * * * * * 0 * * * * * * * * * * * 8
+ 449 * 1901 * * * * 2280 0 0
+
+G 9 * * 3172 3243 * 1258 * * 1923 * * * 3298 * * * * * * * 9
+ 688 1399 * 0 * 680 1412 2361 1174 1190
+
+G 10 4232 * * 3073 * 1288 * * 1449 * * * * * * * * 4262 * * 10
+ 0 * * * * * 0 2497 0 1029
+
+P 11 * * 4747 4584 * 1593 * * 3480 * * 5050 1595 * 4385 4403 * 4522 * * 11
+ 0 * * * * 0 * 2500 0 1029
+
+G 12 3363 * 4592 * * 621 * * 3468 * * * * 3525 * * 4886 * * * 12
+ 72 * 4366 * * * * 2542 0 0
+
+S 13 3686 * * 2159 * * * 4149 4006 * * * * * * 787 * * * * 13
+ 93 4006 * 0 * 0 * 2552 1010 1000
+
+E 14 4491 * 1749 1433 * 3530 * * 3998 * * * * * 2852 * * * * * 14
+ 0 * * * * * * 2608 0 0
+
+C 15 * 215 * * * * * * * * * * * * * * * 2852 * * 15
+ 0 * * * * * * 2608 0 0
+
+A 16 1997 * * 4097 * 3594 * * * * * * * 3811 2852 1881 2979 * * * 16
+ 154 3308 * 515 1737 * * 2608 1074 0
+
+E 17 * * 2860 622 * 2236 * * * * * * * * * * * * * * 17
+ 50 4876 * 1000 1000 * * 2690 1029 0
+
+W 18 * * * * * * * * 4135 * * * * * 4876 * 4491 2933 447 * 18
+ 0 * * * * * * 2690 0 0
+
+A 19 3648 * 2933 * * * 4983 3762 * 4979 * * * 3181 1688 * 2339 4876 * * 19
+ 0 * * * * * * 2690 0 0
+
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+
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+ 0 * * * * * * 2690 0 0
+
+P 22 2933 * * 3762 * * * * 2554 * * 3280 1578 * * 3158 * 3734 * * 22
+ 0 * * * * * * 2690 0 0
+
+C 23 * 202 * * * * * * * 2933 * * * * * * * * * * 23
+ 0 * * * * * * 2690 0 0
+
+T 24 5039 * * * * * 2933 2621 * * * * * * * * 2810 906 * * 24
+ 0 * * * * * * 2690 0 0
+
+P 25 2581 * * * * * * * * * * * 324 * * 4876 * * * * 25
+ 0 * * * * * * 2690 0 0
+
+S 26 3620 * * 3674 * * * * 4876 * * 1213 * 2933 * 2274 4748 * * * 26
+ 0 * * * * * * 2690 0 0
+
+S 27 3461 * * 3067 * * * * * * * 2400 * 2933 * 1467 3214 * * * 27
+ 0 * * * * * * 2690 0 0
+
+K 28 * * * * * 761 * * 1841 * * * * 2933 * * * * * * 28
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+
+D 29 * * 342 * * 2898 * * * * * * * * * 3706 * * * * 29
+ 0 * * * * * * 2651 0 0
+
+C 30 * 208 * * * * * * * 2898 * * * * * * * * * * 30
+ 0 * * * * * * 2651 0 0
+
+G 31 * * * * * 297 * * * * * * * * 2898 4264 * * * * 31
+ 0 * * * * * * 2651 0 0
+
+V 32 4176 * 4083 4431 * * * * 3706 1943 4086 3817 * 4916 2898 * 4627 2599 * * 32
+ 0 * * * * * * 2651 0 0
+
+G 33 * * * * * 0 * * * * * * * * * * * * * * 33
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+
+F 34 * * * * 1389 * * 4710 * 4403 4903 * * 2637 * * 2856 2943 * 3829 34
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+
+R 35 * 4166 * * * * * * 3699 * * * 2919 * 444 * * * * * 35
+ 0 * * * * * 0 2690 0 1000
+
+E 36 * * * 619 * * * 3699 * * * * * 2841 2919 * * * * * 36
+ 0 * * * * * 0 2690 0 1000
+
+G 37 2476 * * * * 286 * * * * * * * * * * * * * * 37
+ 205 * 2919 * * 0 * 2690 0 1000
+
+T 38 * * * * * * * * 4709 * * 3479 * * * 2759 465 * * * 38
+ 303 2400 * 2322 322 * 0 2348 1173 1138
+
+C 39 * 0 * * * * * * * * * * * * * * * * * * 39
+ 136 3479 * 2322 322 * 0 2348 1047 1138
+
+G 40 * * 3574 3479 * 2284 * * 1528 * * 2520 * * * 3324 * * * * 40
+ 0 * * * * * 0 2348 0 1138
+
+A 41 3840 * 2094 1864 * * * 3305 * * * * * 2899 * * 3994 3021 * * 41
+ 0 * * * * * 0 2348 0 1138
+
+Q 42 3479 * * 2922 * * 3922 * * 3305 * * * 1088 4246 * 3502 * * * 42
+ 0 * * * * * 0 2348 0 1138
+
+T 43 * * * * * * * 3502 * * 4958 4451 * * * 2521 600 * * * 43
+ 0 * * * * * 0 2348 0 1138
+
+Q 44 * * 4246 * * * * * 998 * * * * 2590 2220 * 3922 * * * 44
+ 0 * * * * * 0 2348 0 1138
+
+R 45 * * * * * * 3377 * 974 * * * * * 3840 * 1622 * * * 45
+ 0 * * * * * 0 2348 0 1138
+
+I 46 * * * * * * 3922 1620 * 2067 4451 * * 3502 * * 4642 2351 * * 46
+ 0 * * * * * 0 2348 0 1138
+
+R 47 * * 2948 * * * 3048 * 719 * * * * * 2816 * * * * * 47
+ 0 * * * * * 0 2348 0 1138
+
+C 48 * 0 * * * * * * * * * * * * * * * * * * 48
+ 0 * * * * * 0 2348 0 1138
+
+R 49 * * * * * * * * 922 * * 3922 * * 1300 * * * * * 49
+ 0 * * 3807 107 * 0 2348 1138 1138
+
+V 50 * * * * * * * 882 * * * * * * * * * 1129 * * 50
+ 0 * * * * * 0 2348 0 1138
+
+P 51 * * * * * * * * 3479 * * * 136 * * * * * * * 51
+ 0 * * * * 0 * 2348 0 1138
+
+C 52 * 208 * * * * * * * 2898 * * * * * * * * * * 52
+ 0 * * * * * * 2651 0 0
+
+N 53 3706 * * * * 3571 * * * * * 504 * 2898 * * * * * * 53
+ 0 * * * * * * 2651 0 0
+
+W 54 * * * * * * * * * 2830 * * * * 3492 * * * 376 * 54
+ 0 * * * * * * 2514 0 0
+
+K 55 * * * * * * * * 134 * * * * * 3492 * * * * * 55
+ 0 * * * * * * 2514 0 0
+
+K 56 * * * * * * * * 0 * * * * * * * * * * * 56
+ 0 * * * * * * 2514 0 0
+
+E 57 4040 * 2188 935 * * * * 3105 * * * * 3635 * * * * * * 57
+ 0 * * * * * * 2514 0 0
+
+F 58 * * * * 278 * * 3537 * * * * * * * * * * * 3492 58
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+G 59 * * * * * 0 * * * * * * * * * * * * * * 59
+ 0 * * 0 * * * 2486 0 0
+
+//
+�HHsearch 1.5
+NAME 203cc7f9db11472b54bca3769bfaf8df
+FAM
+FILE 203cc7f9db11472b54bca3769bfaf8df
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:31:50 2013
+LENG 180 match states, 180 columns in multiple alignment
+FILT 116 out of 1192 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCC
+CCCCCEEEEEEECCCCCCCCCHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9843799999798888706999999999999996487884899999789326986476667789999999976505898749999999999987554057
+88996399999289988871379887988999997885434258999999965999855997399999999999998519
+>Consensus
+xxxxDixfllDxSxSmxxxxxxxxxxxxxxxxxxlxxxxxxvxiixfxxxxxxxxxlxxxxxxxxxxxxxxxlxxxxgxtxxxxalxxxxxxxxxxxxgx
+rxxxxxxivlxTDGxxxxxxxxxxxxxvxvxxvgigxxxxxxxxxxxLxxiaxxxxxxxxxxxxxxxxLxxxxxxixxxi
+>203cc7f9db11472b54bca3769bfaf8df
+MGNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGA
+RPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVCILDTFECLKDLFTELQKKI
+>gi|260837234|ref|XP_002613610.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]gi|229298996|gb|EEN69619.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]
+------LYPYGSySGGYPPSNMEKTMG-PGNYRVPLvaGGETITIGSIKKTEETSPseslsaekQAVVAAQDTRECTMSSITiySEERLRGTKKTYSGNG
+WLPRDPS-----WVVDSAGPAWVDSNGVTWEDV-------VTVDNVQSGDQ------RQVFGGFQGKARYWKLVITQTYTGWQPYVRE-----
+>gi|317505805|ref|ZP_07963650.1| von Willebrand factor type A domain-containing protein [Segniliparus rugosus ATCC BAA-974]gi|316255887|gb|EFV15112.1| von Willebrand factor type A domain-containing protein [Segniliparus rugosus ATCC BAA-974]
+---ATVILLLDISESMRatdvkPSRVEAARAAAIKFVDGM-APTVQLGVVTFAGNAQPLVRPSTD--HETAKKVIDQMIrpdKLEKQTATGEGIYTALQQ
+IEtiAGalGGKNHA-PPARIVLVSDGKETVpdDLNAprgaYaaartaKEKHVPVCTVAFGTKAGKitldnqvdevPVDLESLKKISDLSNSPgnscRFFP
+AESQGELAQIYQSLNEDI
+>gi|268529744|ref|XP_002629998.1| Hypothetical protein CBG13361 [Caenorhabditis briggsae]gi|187028722|emb|CAP32249.1| hypothetical protein CBG_13361 [Caenorhabditis briggsae AF16]
+---LDLVLVIDNSQP--TNTIYETISGIFGAQSRIGthyedPRSSRVAIITYNNDATTVAQFPTFKSLDQLKTELTVLKNDGTsgnESYLDTGLSSA-QA
+ILNKTEDRM-NYKKVVLVFASTYDLLYDRpdyIAhalKSNGVTVITVYTGNDKT---VKGQLKSVASDG---FAFQMSVN-TTTDLQNAL----
+>gi|221107141|ref|XP_002168519.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
+VQPMDIGIAMDTSAAT-VANWPYYQQFCRNLVDKFQMgNIARIGLITFDTIAKVPVNLDTYREPTALKLHCNRLVPDPyGRRRTDAALDIARERLFAT--
+-ARPGVPKMLFLLEHGRINGGDPSinwnqqliepsQRlkQMGVNVFAVGATPI----AGVDELKTITSTIDDQsHVLPLQGYWQLPGVVPQIAA--
+>gi|227541544|ref|ZP_03971593.1| von Willebrand factor, type A [Corynebacterium glucuronolyticum ATCC 51866]gi|227182700|gb|EEI63672.1| von Willebrand factor, type A [Corynebacterium glucuronolyticum ATCC 51866]
+---AHEMFi-aVDTSSSMEGQPLERTKEILAELSKGMfEssygeyafRPGDKISffg---LTPQS----sgpSYVAYDP--EDPDSYRELEDfangLntG
+PKISTCETLIRGLLGA-----D-GMGNAVPAVIFTTGTDEDDPECEnfesnvdslpeESGPHPAYIFLLDPA-----HTEWMDTLAEITG-GQVFDATT-
+--------------
+>gi|332308254|ref|YP_004436105.1| LPXTG-motif cell wall anchor domain protein [Glaciecola agarilytica 4H-3-7+YE-5]gi|332175583|gb|AEE24837.1| LPXTG-motif cell wall anchor domain protein [Glaciecola sp. 4H-3-7+YE-5]
+--AREVVFLLDTSGSMAGESIVQAKRAVDFALTQLHPED-SVNVIEFNDAPQALWNLAMPATANNIQRARNWVASLSanGGTEMAPALSMALHKtNLEQq
+nINEGSPVQLRQVVFITDGSVSNEDALMSLienqlADSRLFTIGIGSAP----NSYFMTQAAQAGRGTFTY-IGDINQVQQKMTELFNKL
+>gi|334112791|ref|ZP_08487045.1| OmpA/MotB domain protein [Methylomicrobium album BG8]gi|333597114|gb|EGL01956.1| OmpA/MotB domain protein [Methylomicrobium album BG8]
+------YVINDSSSSMSEDylgsgftsghapaKLSVEKTILSRINQTIPDLKLTSGIRSFGFgpCSGWgstlyNLPLTAY-SKSTFNAGIDTLTCASGGS
+PMNAAAEAAASDL------SGTSGRIALLILSDGyELqASPVPAVQAlkqqygDRLCVYSVWVGnkHEE---NGKLLLNSLS------------------
+----------
+>gi|297283897|ref|XP_001104925.2| PREDICTED: integrin alpha-D-like [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+----------------TLAASTNRS-----WLLACGP------TLHRVCGENSYSKGSCLLLGSHWEIIQTVPDALPEcphqemdIV
+>gi|710012|dbj|BAA06482.1| hypothetical protein [Bacillus subtilis]
+--TARVGLVLDITGSMRPLYKNgTVQNVVERILAVADQfdDNGLLDVWVYDNEFPRlkPVSEKDFPGYVDREILNNDRLHKFGRNDEPPVMKDVLRNMLR
+RN---RARILLSLFLSMTGAV--K---SQSNRLIEassdkpvfwqF-VGIGNGNF--DFLNKLDTLEGRVIDNtNFLHIEEIDRISD---------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * 1977 * 1088 2737 * * * * * * 2992 * * 1
+ 0 * * * * * * 4173 0 0
+
+G 2 3138 * * 5276 * 1207 4802 * 5082 3905 * * 5156 3052 3489 5236 5016 * * * 2
+ 0 * * * * * * 7696 0 0
+
+N 3 3815 * 4778 5298 5368 4495 4082 * 3006 5196 6173 3721 1828 5155 3893 4353 3794 * * * 3
+ 18 * 6357 * * * * 9163 0 0
+
+V 4 2520 * * * 4542 * 6362 2760 4787 2560 4022 6384 6436 4864 3553 5610 4015 3184 * 5641 4
+ 0 * * * * * 0 9324 0 1000
+
+D 5 6641 * 662 3793 * 5840 4951 6518 5291 6701 * 3087 6651 * 6695 5618 4945 * * * 5
+ 19 * 6258 * * * 0 9338 0 1000
+
+L 6 5211 * * * 5625 * * 1480 * 2056 4637 * * * * * 4346 1920 * * 6
+ 0 * * * * 858 1158 9412 0 1207
+
+V 7 3426 5757 * * 4530 5207 5799 2944 * 2845 4198 6526 * * * 4521 5149 1734 6633 3586 7
+ 0 * * * * * 0 9617 0 1000
+
+F 8 5844 * * * 1003 * * 2784 * 2291 5209 * * * * * 6648 4224 6748 4868 8
+ 0 * * * * * 0 9617 0 1000
+
+L 9 3205 6320 * * * 6536 * 3317 * 1275 6061 * 5831 * * 6631 6457 1733 * * 9
+ 19 * 6220 * * * 0 9617 0 1000
+
+F 10 4565 * * * 5078 6561 * 2592 * 1268 5887 6471 6579 * * * * 1886 * 5194 10
+ 12 * 6928 * * * 0 9594 0 1371
+
+D 11 * * 221 4879 * 5815 4745 * 6433 * * * 6513 6593 * 5621 * * * * 11
+ 0 * * 0 * 1029 971 9579 1012 1555
+
+G 12 3268 5800 4386 4462 6692 3529 6337 4068 * 4827 5310 4113 * 5622 4887 2910 2688 2896 * 5517 12
+ 25 5848 * 0 * * 0 9610 1158 1201
+
+S 13 * 6651 6645 * * * * * * * 6829 6704 * * * 229 3208 * * * 13
+ 0 * * * * * 0 9610 0 1201
+
+M 14 3336 * 3595 3526 * 1730 5260 6750 5742 6528 6812 4908 6619 3920 5075 2789 4540 5800 * 6458 14
+ 12 * 6933 * * * 0 9610 0 1201
+
+S 15 5834 * 5043 6624 * 3943 6683 * 4691 * 6529 4473 6343 6643 5888 531 6655 5844 * 6172 15
+ 56 6928 5071 0 * 1792 492 9601 1012 1352
+
+L 16 5583 * 6479 * 7095 6564 * 2501 6495 3593 1209 6563 * 5702 * 7027 5926 2587 6767 5862 16
+ 67 4793 6769 2347 316 1011 989 9602 1875 1936
+
+Q 17 3119 * 6909 4495 * 2425 * 6802 4753 5919 * 4536 4237 4155 3682 2333 3096 5037 * 7072 17
+ 278 3918 3197 1976 423 1917 444 9636 2293 1598
+
+P 18 4950 6739 3965 2630 6373 2499 6857 * 5129 5688 * 4486 3184 4243 4575 3075 4824 4629 6440 4979 18
+ 122 4615 4636 1381 699 120 3649 9525 1506 3214
+
+D 19 3451 * 2871 2661 * 4043 5543 6853 3621 5007 5868 4332 * 5262 4465 2660 3900 5161 * 5693 19
+ 99 4717 5132 2922 204 330 2292 9618 1533 1715
+
+E 20 4220 * 3147 4005 6843 3732 6769 * 3051 6600 5575 2704 5756 5144 3407 3201 4152 6457 6722 4450 20
+ 42 5140 * 2431 296 390 2077 9614 1407 1541
+
+F 21 5661 * 6820 6753 1729 6849 6550 2960 5386 2848 4831 6947 5374 5776 5724 6339 * 4828 2909 3955 21
+ 25 5835 * 2810 222 * 0 9667 1402 1000
+
+Q 22 3523 7117 2967 2677 * 4881 5415 5249 3613 6804 7046 3750 6010 4259 3363 2941 4964 5200 * 6531 22
+ 91 4032 * 1483 639 * 0 9695 2050 1000
+
+K 23 3857 6935 3436 3768 5987 5580 5340 3836 3574 3010 5248 5115 * 3373 4000 4155 4132 4459 6009 5097 23
+ 68 4926 6252 3447 139 * 0 9695 1485 1000
+
+I 24 2310 6842 * 4379 4738 5546 * 3576 5330 3043 3134 * * 5627 5325 5120 3301 2695 * 6813 24
+ 13 * 6841 * * * 0 9672 0 1371
+
+L 25 4941 * 6683 6695 * 6626 * 4212 1706 3428 4752 4531 * 3262 2653 4665 5805 4696 6628 4839 25
+ 50 6002 5772 0 * 2009 412 9618 1099 1547
+
+D 26 2993 * 2361 3831 * 4218 * * 3100 * * 3884 5261 3100 3680 3956 4337 4767 * * 26
+ 25 * 5872 * * 2441 294 9640 0 1739
+
+F 27 1940 5685 6534 6769 1783 5889 * 5580 5549 4200 5705 5837 6640 6320 5415 3866 4477 4303 4652 6761 27
+ 0 * * * * 1054 948 9563 0 1891
+
+M 28 2961 6811 * * 3841 5782 * 2226 6654 2233 4076 * 5898 * 6591 5799 4566 2383 * * 28
+ 0 * * * * * 0 9668 0 1389
+
+K 29 3204 6913 5673 3364 5017 4590 * 5261 2688 3698 6004 4419 6903 3898 3501 3343 4132 4446 * 6939 29
+ 0 * * * * * 0 9668 0 1389
+
+D 30 3214 * 3383 3090 4846 4776 * * 3133 4842 5318 3453 * 4421 3803 3015 3617 5725 * * 30
+ 0 * * 2807 222 590 1575 9668 1201 1389
+
+V 31 3144 * 6965 * 2713 * * 2269 6343 2144 3762 * * * * 5428 4400 3280 * 4917 31
+ 0 * * * * * 0 9691 0 1012
+
+M 32 3603 * * * 5229 4690 * 2377 6660 2154 4884 5684 5715 5611 5902 4958 4865 2163 * 5271 32
+ 26 6723 6845 1585 585 * 0 9691 1004 1012
+
+K 33 6150 * 3340 3711 * 4243 5543 6729 3253 4952 5201 3935 4485 3734 3268 2742 3633 5859 6787 5845 33
+ 0 * * * * 1035 965 9637 0 1195
+
+K 34 3139 5888 4154 3703 6657 4561 4758 4902 3051 3900 5385 4326 4606 3915 3526 3676 4034 6752 * 6674 34
+ 114 3715 * 1788 493 0 * 9686 2444 1012
+
+L 35 7099 5802 * * 2179 6615 * 3104 5971 1415 4023 6038 * 5744 * 7124 5010 3718 * 5219 35
+ 567 1815 4618 1330 732 * * 9705 5260 0
+
+S 36 4399 * 3218 4736 5917 2265 5742 6589 4856 5196 6711 3522 5096 4017 4069 2507 4858 5220 7024 * 36
+ 430 2116 5206 1859 465 1396 690 9578 4520 1826
+
+N 37 4622 * 3418 2848 6653 4051 6525 4561 4122 6891 6803 3947 2000 4028 4019 5045 5767 5555 * 5585 37
+ 294 2616 5560 1270 772 0 * 9572 3651 1963
+
+T 38 5272 * 2051 3366 * 4529 6503 * 4036 4783 5237 3570 3520 4097 5068 3667 4163 4236 * 6570 38
+ 10 * 7114 * * 0 * 9670 0 1236
+
+S 39 3866 6826 3242 5221 6392 2849 5166 5884 3191 4782 6800 3433 * 4216 4301 3158 3696 4837 * 5751 39
+ 68 6749 4764 1000 1000 0 * 9709 1018 1000
+
+Y 40 3160 6629 3133 * 4676 4777 * 2976 * 4345 * 5402 6709 5225 6541 3784 2997 2300 6750 5004 40
+ 51 * 4838 * * 0 * 9718 0 1662
+
+Q 41 5427 * 5245 4130 6761 * 3061 6966 4276 5219 * 3692 6769 2841 1712 4123 4754 5771 * 4886 41
+ 0 * * * * 454 1888 9679 0 1499
+
+F 42 4379 * * * 2412 * * 2222 7206 3534 4540 * 6816 * 7309 4874 5879 1724 * 4482 42
+ 0 * * * * 0 * 9698 0 1005
+
+A 43 2106 * 4702 5772 6683 1570 * * * 5752 6930 4010 6615 6897 5865 2356 5764 * * 5264 43
+ 0 * * * * * * 9705 0 0
+
+A 44 3463 * * * 3678 * * 1792 * 1891 5225 * * * * 5456 * 2163 * * 44
+ 12 6930 * 3585 126 * * 9705 1000 0
+
+V 45 4364 * 6879 * 4746 5278 6956 1895 * 3125 4891 5738 * 5919 5682 4485 3963 1932 5692 6699 45
+ 0 * * * * * * 9705 0 0
+
+Q 46 3846 5885 5902 4490 4348 3392 6748 5841 4180 3617 5603 4508 6993 3226 4448 3563 2465 5021 6816 6148 46
+ 11 * 6993 * * * * 9705 0 0
+
+F 47 * * 6390 * 987 6604 5104 6942 5951 5287 * * * * * 5746 * 5753 * 1486 47
+ 13 6830 * 2000 415 * 0 9690 1000 1012
+
+S 48 2930 6923 3829 * * 2336 5382 6390 7095 6737 * 3259 * * 4654 1677 3762 6830 * * 48
+ 0 * * 1000 1000 0 * 9690 1012 1012
+
+T 49 3659 7006 2422 4542 5722 3142 5432 6851 5309 * 5782 3935 6743 5085 3726 2373 3423 * * 6636 49
+ 73 4343 * 2572 266 * * 9705 1751 0
+
+S 50 4664 6541 3555 3069 6923 3712 4491 4463 3310 * 6993 3962 4877 4752 4104 3274 3127 5878 5683 6088 50
+ 78 4256 * 1710 526 * * 9705 1940 0
+
+Y 51 2267 * 6767 6819 5950 4185 5723 4282 6742 5975 * 5270 2892 * 6104 3428 3374 2355 * 4399 51
+ 23 5975 * 2821 220 * * 9705 1164 0
+
+K 52 4203 6879 4385 3356 5532 6541 3617 5070 3081 5302 * 4469 6767 4133 3035 3302 3750 3845 * 5270 52
+ 62 5862 5340 1000 1000 * * 9705 1200 0
+
+T 53 4290 * 5986 3257 6522 5168 5685 3915 3969 3656 5346 5641 3646 4926 5432 5294 2575 2751 5064 6874 53
+ 159 3372 6959 1902 449 * 0 9691 2589 1338
+
+E 54 4244 * 4203 3045 5022 5086 5213 4021 5157 2926 5895 4808 4536 3941 5308 5622 4704 2536 5560 5317 54
+ 59 5009 6775 2461 289 2213 351 9676 1485 1524
+
+F 55 4062 4760 6942 * 2024 5577 5629 3812 4501 2748 3989 * * 5246 * 5139 5395 2759 5767 4787 55
+ 49 5297 6960 1054 948 982 1019 9664 1307 1555
+
+D 56 3930 7060 2944 6029 5830 3388 4587 6742 5233 4884 6889 3767 2553 4668 4614 3259 4274 4667 * 5097 56
+ 18 6334 * 3700 115 * 0 9684 1068 1357
+
+F 57 6581 6796 * 6768 2295 6780 6344 4398 * 1341 5966 * 3764 5621 6974 5194 4489 3924 * 4370 57
+ 38 5929 6721 1883 456 1616 569 9684 1334 1357
+
+S 58 3375 6882 3435 5415 6357 3807 5184 6076 5184 5388 * 2664 5958 5806 3421 3205 2638 5249 6770 6345 58
+ 98 4853 4998 1191 832 1677 541 9676 1539 1365
+
+D 59 3774 * 2626 3905 6722 5070 5184 * 4261 4409 6897 3115 4857 3919 3964 3244 3830 4791 5485 6739 59
+ 24 5943 * 642 1477 2160 365 9553 1155 1879
+
+Y 60 4839 * 3422 5869 2872 4591 4047 3473 5734 3351 5939 4627 4311 4942 5955 4743 5281 3828 6610 3189 60
+ 97 6919 4146 1039 962 * 0 9588 1185 1652
+
+V 61 4268 * 3065 3697 5249 5538 5609 4223 3289 5631 5421 3539 4019 4648 3590 3877 4132 5127 6518 4364 61
+ 322 6610 2400 2807 222 1662 548 9561 1010 2635
+
+K 62 6506 5674 2671 3805 5605 6529 * * 6553 5503 * 2966 * 5339 5631 1632 2729 * * 5034 62
+ 66 6480 4892 0 * 1697 532 9336 1007 4802
+
+R 63 3342 * 4169 3971 6360 * 5298 4081 2676 3725 5730 4652 4206 3928 3021 3888 5036 4575 * 6437 63
+ 146 5333 3803 2140 371 456 1884 9389 1212 4160
+
+K 64 3535 * 3015 2370 * 6561 6569 6653 3434 * * 4358 4472 4718 4209 2951 3475 4398 6671 6551 64
+ 98 * 3924 * * 957 1045 9553 0 2869
+
+D 65 3251 5182 2895 3165 4901 4502 4159 6543 4100 5184 * 3700 5834 3808 3654 4460 3684 5449 * * 65
+ 41 6762 5716 2807 222 2702 241 9511 1000 3037
+
+P 66 4384 * 6592 * 3396 * * 2585 4221 1879 3715 6443 5635 5480 4600 * 5797 2845 * 5257 66
+ 0 * * * * 1365 709 9513 0 2998
+
+D 67 4189 * 3320 4445 6608 5264 6280 3976 3035 3634 4814 3934 6525 3066 3779 4097 4603 3987 7042 6701 67
+ 49 5332 6847 1211 816 2908 206 9631 1306 2217
+
+A 68 2821 * 3152 3012 6619 5581 6331 5883 4024 4789 5833 3566 * 3868 3731 2975 4935 6862 5552 5135 68
+ 36 5331 * 2867 213 2089 387 9631 1306 2205
+
+L 69 2437 * 4947 4790 4870 3618 5223 3469 4663 2923 6772 5417 * 5763 4750 4534 4693 2904 5805 5561 69
+ 52 4807 * 1954 431 634 1491 9639 1874 1898
+
+L 70 3949 5816 5497 * 3550 6886 * 1978 4646 2084 6682 6985 6609 6333 5934 4842 5351 2768 6774 * 70
+ 12 * 6888 * * * 0 9676 0 1216
+
+K 71 3313 * 2630 4264 6692 4168 7122 6712 3933 5487 * 2833 5704 4271 3696 2963 4449 6797 5814 5228 71
+ 57 5914 5513 1000 1000 1642 557 9623 1158 1395
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+H 72 3060 6960 4437 3583 6019 4322 4753 * 3570 6674 * 3490 5817 4543 2988 2708 4721 5902 5981 4417 72
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+I 180 * * * * * * * 791 * 2135 3059 * * * * * * 3752 * * 180
+ 0 * * 0 * * * 7096 0 0
+
+//
+�HHsearch 1.5
+NAME 2136b1cea2992a6bf1cf63cb4e484430
+FAM
+FILE 2136b1cea2992a6bf1cf63cb4e484430
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:08:22 2013
+LENG 189 match states, 189 columns in multiple alignment
+FILT 160 out of 1133 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEEEECCCCCEECCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEECCCHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEEEECCHHHHHHHH
+HHHHCCCCCCCEEEECCHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCCCCCHHCEEEEEECCCCCCCCCCCCCCEEEEEEEECCCCC
+>ss_conf PSIPRED confidence values
+9089999998899847469987873682689999999816765466876998334776515135788999699995999878998199949999999997
+64230279981999898999999970888898999993230257612788880243999850464445324589747999999734569
+>Consensus
+xxxixxxxAxsxdGxIgxxgxlpWxxxxxdxxxfxxxtxxxxxxxxxxxvimGRkTyexxxxxxxplxxrxxiVvSxxxxxxxxxxxxvxxxxxxxlxxl
+xxxxxxxxxxxIxViGGxxlxxxxlxxxlvDelxltxipxxxxgxxxfpxxxxxxxxlxxxxxxxxxxxxxxxxxxxxfxxyxxxxxxx
+>2136b1cea2992a6bf1cf63cb4e484430
+VRSLNSIVAVCQNMGIGKDGNLPWPPLRNEYKYFQRMTSTSHVEGKQNAVIMGKKTWFSIPEKNRPLKDRINIVLSRELKEAPKGAHYLSKSLDDALALL
+DSPELKSKVDMVWIVGGTAVYKAAMEKPINHRLFVTRILHEFESDTFFPEIDYKDFKLLTEYPGVPADIQEEDGIQYKFEVYQKSVLAQ
+>gi|294155964|ref|YP_003560348.1| dihydrofolate reductase [Mycoplasma crocodyli MP145]gi|291599950|gb|ADE19446.1| dihydrofolate reductase [Mycoplasma crocodyli MP145]
+---IKLIVATDKNNLIGNVDKMPWR-IKEEFEHFRNTTIS-------HSLLFGRTTFLGLPGklDKRTiYVLSEQTLdNCITIHNETE-L----KNL---
+---FAKFKTNNEV--LFIAGGKSIYEKYF--EYADELLISRVDGDYQGNVYL-NLNLSNYEVIKK----------QKFEKFVVETYKRIQ---
+>gi|343084894|ref|YP_004774189.1| bifunctional deaminase-reductase domain-containing protein [Cyclobacterium marinum DSM 745]gi|342353428|gb|AEL25958.1| bifunctional deaminase-reductase domain protein [Cyclobacterium marinum DSM 745]
+-KKIVYYVATSLDGYIAgENGDISqFLMQGKGVDKYQADLLNF------GTVIMGRKTYEfgyQYGlvPGQPAYPHMKHHIFSTTLKIDKlSEMVKIERG
+GLDRINEIQQN----TETDIYLCGGGQFAGYLLDHGKIDQLKIKLNPIVLgKGTKLFGsSTSNANWELIDN-ES------YAEGL--QILTYNRR----
+>gi|298245066|ref|ZP_06968872.1| bifunctional deaminase-reductase domain protein [Ktedonobacter racemifer DSM 44963]gi|297552547|gb|EFH86412.1| bifunctional deaminase-reductase domain protein [Ktedonobacter racemifer DSM 44963]
+-RKVIVLEFVTLDGVIQaPGgPEEDtsggfayggWvapY-DDDVAGtVMDKQMNLP------FDLLLGRKTFEIWAP-FWPqhadgwpgVMSATKYVASN
+SMTSSEwQPSVFLGGDIAEKVSKLKHQ----PGPDLHVYGSANLLQTLMKHDLVDAFWLKIFPLTLgSGKRLFTDGTiPAAFKVTES-------------
+---------------
+>gi|2506058|dbj|BAA22616.1| fusion protein, composed of HCV p21 (NS2), N-terminal region of HCV p70 (NS3) and TAX of HTLV-I [synthetic construct]
+-----IITSLTgrdknqVDGEVQVLSTATQS-FLAtcvnGVCWTVYHGAG-------SKTLAGPKgpitqmytnvDQDLVG---WPAPPGARSMTPCTCG
+SS-DLY-LVTRHADViPVRRRGD------SRGSLLsprpvsyLKGSAGGPLLC--PSGHVVGIFRAAVCTRGVAKAVDFI--PVESME------------
+-----------------
+>gi|12045067|ref|NP_072878.1| segregation and condensation protein A [Mycoplasma genitalium G37]gi|1723127|sp|P47455.1|SCPA_MYCGE RecName: Full=Segregation and condensation protein Agi|3844813|gb|AAC71432.1| segregation and condensation protein A [Mycoplasma genitalium G37]gi|166078768|gb|ABY79386.1| segregation and condensation protein A [synthetic Mycoplasma genitalium JCVI-1.0]
+---ISLIFDKSNSFN-------PQL-CVELLNHFKVVMLT-------KTIVVDYPSFQAWKA---QLKPFKLAVFSDNLQTelTpNSKL-TVFNNYQQLL
+VD---------NNDLIIFATPTLVQLFD--NEIDQLIVinptsks-----kdQFNCN--------wNDFVLIK---------------------------
+--
+>gi|302529715|ref|ZP_07282057.1| dihydrofolate reductase [Streptomyces sp. AA4]gi|302438610|gb|EFL10426.1| dihydrofolate reductase [Streptomyces sp. AA4]
+--KVVLYSSVSADGFIADENdQpgplFDWL-TSGDvpldesgvlkvaqasYDYTRAYWDQI------GVTVAGRHVFDLTDGwDGTPPSGiDHVVVVTHR
+PAPEgwNPDAPFhFVDGVKEAVAKAQEL----AGDRVVEVAAGDVGGQVFAAGLVDEVRMDVVPVVFgAGKRYFGSVR----------------------
+---------------
+>gi|326802356|ref|YP_004320175.1| hypothetical protein Sph21_5009 [Sphingobacterium sp. 21]gi|326553120|gb|ADZ81505.1| hypothetical protein Sph21_5009 [Sphingobacterium sp. 21]
+-MKIIIVANIAANGKVLVSDH-PHHQLPqETMDFYLKLVNQI------GNLVIGVRTFENFekfPDHVkALFKNVEIVVLADKPF-ISSTY-PVVNKPTE
+AIDYFSKK----GFTEIAIGGGTGTFNTFLEGNFVTDIYF------------------------------------------------------
+>gi|158335091|ref|YP_001516263.1| riboflavin biosynthesis protein RibD domain-containing protein [Acaryochloris marina MBIC11017]gi|158305332|gb|ABW26949.1| riboflavin biosynthesis protein RibD C-terminus domain protein [Acaryochloris marina MBIC11017]
+---TTVVLAMSADGKIADAQHSPPE-FGsdEDYAHLERQVAAA------DGILFGSATLKAGETAMrvvtqDLInarlergqpEQPAQIVCTRSGDLDPn
+lkffqqavPHWLVTTQAggqswqgtshFEQiftygteaqsidwgqTLASMP----ALGIHKIAVLGGGQIVAALLAEDLIDELHLTVCP-----------
+---------------------------------------
+>gi|306836172|ref|ZP_07469157.1| riboflavin biosynthesis protein RibD [Corynebacterium accolens ATCC 49726]gi|304567955|gb|EFM43535.1| riboflavin biosynthesis protein RibD [Corynebacterium accolens ATCC 49726]
+--HVTLKFAQTLDGFTAaADGTSQWITGPKAREWVHADRARR------DAIIIGTGTALADnPSlTARf-sdgsLREHqpRRVVIGKRD--LQaagekas
+hlqrl-GF-EQYDTIEGALKELYA----SGARDVLVEGGAGLAQSFIEAGAVDTLAAYIAPILLgqgrgvLANAVAHTLADaPHFTTVRT-TSL------
+--G-PDVLIEYEAR----
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
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+I 114 5142 4887 6809 7290 6384 6793 * 1741 * 2669 6374 * * * * 7062 7115 1257 * * 114
+ 101 5979 4275 2304 327 0 * 8376 1177 1271
+
+V 115 3525 4736 5951 4065 3939 4791 5935 1599 * 3035 4544 * * * * 5151 5997 3294 6062 5239 115
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+
+G 116 4850 * 5038 * * 176 * * 5999 6509 6893 * * * * 6099 * * * * 116
+ 10 * 7191 * * 0 * 8390 0 1054
+
+G 117 6441 * 6519 * 7213 274 * * * * * 7066 * * * 3157 5379 * * * 117
+ 18 * 6306 * * 0 * 8387 0 1001
+
+T 118 1742 * 7578 4457 7581 1931 6511 6357 5762 6366 7520 7569 3473 6550 5570 3235 4405 4734 * 7500 118
+ 0 * * * * 0 * 8383 0 1048
+
+A 119 3514 * 4470 2746 7227 4306 6567 5272 3469 5889 7494 4600 6170 3280 3728 3049 3239 5053 * 5527 119
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+
+V 120 5888 * * * 5295 6007 * 1937 * 1507 5348 7645 6843 * * * 3425 2410 6720 * 120
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+
+Y 121 2616 6102 * * 4224 4459 6022 3377 * 3253 * 5399 * 7002 * 7481 5019 3717 5993 1526 121
+ 7 7639 * 0 * 0 * 8356 1000 1038
+
+K 122 2884 * 3827 3715 * 4270 5294 7704 2887 * * 4172 5480 3265 2915 3744 3542 6596 * 6020 122
+ 0 * * * * * * 8437 0 0
+
+A 123 2572 * 4101 2945 * 5163 * * 6827 3319 5918 5497 5599 2247 5619 2927 4743 5545 7262 5667 123
+ 0 * * * * * * 8437 0 0
+
+A 124 2498 4980 7300 * 1890 5907 7839 7713 * 1684 4785 * * * * 4653 5372 4287 * 5217 124
+ 0 * * * * * * 8437 0 0
+
+M 125 4105 6015 5965 7558 4936 * * 2654 7839 929 3897 * * * 7672 5615 5552 4936 5450 6098 125
+ 456 * 1883 * * * * 8437 0 0
+
+E 126 3114 7480 2914 2348 6034 6918 * 6249 3520 5752 * 4481 4433 4175 2956 3324 4953 * * * 126
+ 134 5356 3958 2127 375 * 0 8013 1157 3909
+
+K 127 1626 6217 4453 3118 6975 5079 3232 * 4946 3109 * 4426 * 4331 4207 4702 6458 * * 6772 127
+ 71 * 4388 * * 194 2991 7917 0 4296
+
+P 128 5848 * 2634 4492 * 1644 7765 * 4591 * * 3383 2438 5537 4468 4778 7436 * * 5516 128
+ 14 * 6654 * * 801 1231 8368 0 1803
+
+I 129 4601 5452 7372 4800 4203 * 4597 4028 5063 1042 7527 * * 5572 4666 5293 7444 5639 6204 3461 129
+ 10 7213 * 1000 1000 726 1338 8357 1009 1416
+
+N 130 2733 4428 * * 6582 6004 * 1976 * 3243 7293 6641 7782 6947 * 7567 5111 1706 5215 5601 130
+ 21 6098 * 1585 585 839 1182 8372 1106 1122
+
+H 131 5844 6966 592 4887 * 7437 4804 * 5225 * 6735 5302 * 5987 5277 5057 3408 6895 * * 131
+ 0 * * * * * 0 8382 0 1012
+
+R 132 7106 7233 4433 1046 7230 6309 5114 5124 3899 * * * * 3764 2983 4678 5100 4522 * * 132
+ 0 * * * * * 0 8382 0 1012
+
+L 133 4870 5713 * * 3409 * * 2057 * 1658 4613 * * * * * * 2618 6203 3679 133
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+
+F 134 6444 6349 6076 5141 3635 5515 2777 3129 6284 4524 7286 7252 * 4217 3357 5952 4255 3399 4595 2785 134
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+
+V 135 5465 5596 * 6363 4667 * 7458 2175 7396 1258 3682 * * * 7757 * * 2631 * 6641 135
+ 15 6607 * 2807 222 * 0 8380 1041 1012
+
+T 136 5499 * 5304 5204 4098 5780 5182 5296 5214 5256 4756 4910 * 6584 6127 3134 1114 5341 6100 4934 136
+ 0 * * 3170 170 1226 804 8326 1012 1128
+
+R 137 * * 6037 5352 4579 * 4521 2376 4293 3424 6076 5720 * 5592 2911 5856 3184 2450 7414 4859 137
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+
+I 138 3109 5944 7191 7421 5715 6270 4184 1902 * 3690 4596 4803 * 7683 * 4592 6146 1945 * 5278 138
+ 0 * * * * * 0 8227 0 1041
+
+L 139 4916 * 3693 3877 6708 6379 4587 6495 4423 5017 * 3962 899 6288 6724 5627 * 7128 * 5677 139
+ 33 5458 * 1415 678 * 0 8258 1202 1041
+
+H 140 4747 7091 4583 5028 * 3720 4086 3887 4447 4095 7729 5916 6340 7090 3959 5053 4184 1566 6447 4763 140
+ 8 7469 * 1821 480 0 * 8228 1162 1041
+
+E 141 3517 5111 3631 3676 5781 * 5066 3148 5685 2735 5471 5443 5574 5573 5492 4435 3265 2897 * * 141
+ 113 3936 6647 2232 345 * * 8262 1621 0
+
+F 142 4175 * * 5327 2442 5336 6268 4122 6847 1717 7429 7244 4578 * * 7262 4891 3051 * 3153 142
+ 889 1159 6344 411 2011 0 * 8233 4395 1013
+
+E 143 3270 * 3185 2395 * 3361 5559 6501 4325 5869 * 4157 4044 3858 3925 3649 4389 5597 * * 143
+ 40 5194 * 0 * 0 * 8185 1247 1032
+
+S 144 2912 3278 6983 6444 * 673 6631 * 7097 * 7468 7259 * 5983 6027 5548 6102 5600 * * 144
+ 13 6761 * 0 * * * 8225 1015 0
+
+D 145 5186 * 1405 5584 * 4047 5729 3909 4036 4745 * 4823 4766 5880 3626 5664 3734 3946 * * 145
+ 102 4100 6614 1564 596 * * 8225 1500 0
+
+T 146 3898 6029 7253 7107 * 6289 6829 5975 5169 4546 * 7202 2959 * 2251 3672 2124 2812 * * 146
+ 73 4768 6281 1614 571 * 0 8191 1328 1041
+
+F 147 5850 6944 6429 7127 1827 5847 5057 7229 4727 2024 4604 7445 5158 7438 5392 * 6216 4931 4077 2986 147
+ 23 * 6011 * * 1064 939 8151 0 1148
+
+F 148 3971 * 6630 * 767 * * 3827 * 2550 5389 * * * * * 6943 5521 6256 5047 148
+ 100 4817 5004 1217 812 694 1388 8176 1356 1228
+
+P 149 4227 * 3146 4155 * 3433 * * 4942 * * 5408 1095 5842 4470 4287 5101 5822 * * 149
+ 246 3346 4092 578 1599 427 1963 8113 1883 1373
+
+E 150 4406 * 2303 3052 5702 3489 5004 6169 3711 4426 6315 3757 3692 6333 4427 3416 6179 5914 * 7243 150
+ 134 3994 5281 1950 432 249 2659 8137 1426 1640
+
+I 151 5281 * 4745 5300 3013 3797 6589 2473 4994 2138 4786 6326 5383 6021 * 6892 4429 3252 7292 6329 151
+ 88 5471 4775 0 * 2235 344 8120 1105 1254
+
+D 152 4137 * 2180 3189 6834 4170 5323 3947 4841 4965 * 3902 3072 4766 5483 3842 4688 5161 * 6578 152
+ 485 2808 2806 589 1577 767 1278 8115 2001 1570
+
+Y 153 4523 * 3922 3605 4124 4161 6818 6267 3526 3284 4948 4624 2801 6876 3834 3711 4160 5658 6890 5149 153
+ 329 2294 * 857 1158 237 2724 7757 2532 2400
+
+K 154 4177 * 3089 4078 7018 4850 4392 4925 3673 3915 * 3432 4781 4613 3767 3027 3573 4567 * 6945 154
+ 185 3304 5714 0 * 0 * 7999 1688 1164
+
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+
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+ 67 5158 5829 3184 168 * 0 8074 1208 1006
+
+K 157 4850 * 4080 2236 6751 6566 4256 4683 2771 6910 5973 5111 * 4947 2374 4363 3627 5721 6720 * 157
+ 25 * 5867 * * 1745 511 8041 0 1169
+
+L 158 * 6845 * 4093 5072 7533 5902 4112 4547 993 5172 5615 5969 5426 4934 4980 5086 3369 * * 158
+ 42 * 5108 * * 1037 964 8046 0 1257
+
+L 159 4540 * 4875 3860 * * 6955 3120 3736 2946 5183 6271 * 4083 * 3931 3170 2000 * * 159
+ 10 7214 * 985 1015 1254 784 8000 1068 1370
+
+T 160 3754 6281 3086 2335 6116 3411 5860 6116 4569 6960 * 5099 6263 4512 5946 2186 4478 7310 * 4897 160
+ 127 5604 3979 2718 238 * 0 8013 1155 1186
+
+E 161 3488 4736 4604 3141 5909 * 4798 4370 4273 5889 * 5348 6894 3401 3990 2618 3172 3559 * * 161
+ 2431 2893 557 2753 232 * 0 7788 1587 1722
+
+Y 162 4115 * 3986 * 3926 2020 3913 * * 3054 * * * * * 3920 2940 3033 * 4025 162
+ 290 2457 * 0 * 990 1010 4726 1149 4013
+
+P 163 4443 * 4457 1805 * 5060 * 5542 4156 3813 * * 3808 4307 2835 4659 3546 4151 * * 163
+ 57 * 4686 * * 2389 306 6187 0 2618
+
+G 164 5149 * 3197 2732 4682 3322 4602 5005 4548 5595 * 5625 5485 5438 4658 2350 3687 4610 5830 * 164
+ 395 5830 2173 0 * 4583 61 6284 1000 2435
+
+V 165 * * 5185 5393 5236 4317 2749 2853 4117 3527 4345 * * 5811 * * 5542 1506 * * 165
+ 223 * 2802 * * 2870 212 5704 0 2869
+
+P 166 4036 * 4184 3264 5298 4232 * 4817 5349 5409 * 5064 2022 4064 3982 4071 3301 4117 * * 166
+ 295 5458 2626 1585 585 2286 331 5510 1046 2893
+
+A 167 2322 4898 * 3988 5073 * * 5050 3036 * * 4100 5396 4179 5497 2408 4020 3154 * * 167
+ 131 * 3525 * * 3264 159 5464 0 2916
+
+D 168 4255 * 1762 2626 5111 4980 * * * * * 4758 5122 * 3505 4170 4267 4068 4154 4231 168
+ 684 4943 1534 1000 1000 4635 59 5499 1034 2938
+
+I 169 * * * 3450 * * * 2491 * * * * * * 3526 2224 3562 1961 3501 * 169
+ 131 * 3526 * * 4195 81 5012 0 3563
+
+Q 170 * * 2851 2984 4865 4459 4390 4460 2887 4555 * * * 3459 3487 4359 4736 4559 * 3726 170
+ 0 * * * * 507 1754 5138 0 3545
+
+E 171 3845 * 2837 2414 5815 6029 3999 * 4700 5060 * 4062 5937 4477 5391 3918 3381 4370 5405 4063 171
+ 25 5841 * 3459 138 324 2313 6389 1006 1796
+
+E 172 4501 * 2441 1701 * 3993 5916 * 3565 6020 * 5125 6000 6116 4327 4120 4461 5407 * 4326 172
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+
+D 173 4708 * 3133 2869 6124 3553 3761 4895 3993 * * 2040 * 5580 4864 4351 4013 6136 * 5838 173
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+
+G 174 4570 * 2499 5522 4868 1905 4149 5558 4417 6095 * 3664 4224 4642 * 4422 5171 * * 3793 174
+ 150 * 3340 * * 1020 980 6700 0 1104
+
+I 175 4058 5713 4971 6009 3862 5771 4364 2637 5851 3268 * 4906 3862 * 5773 4237 4365 3121 5069 3485 175
+ 231 6151 2901 0 * 0 * 6551 1000 1442
+
+Q 176 3534 4821 3992 3317 * 3382 5475 4229 4877 * * 3701 3661 4237 3662 3265 3090 * * * 176
+ 31 * 5537 * * 2224 347 6465 0 1270
+
+Y 177 * 5617 4899 * 1961 * 4422 3885 * 3459 * * * * * * 4222 3992 5069 1566 177
+ 52 5787 5873 2000 415 0 * 6448 1005 1285
+
+K 178 5237 * 2984 3338 6081 * 4433 3664 2942 * * 6195 * 3491 3403 3849 3389 3319 * 5973 178
+ 0 * * * * 0 * 6787 0 1000
+
+F 179 * * * * 1014 * 4955 2601 * 3935 5701 * * 4363 * * * 3896 6010 3441 179
+ 0 * * * * * * 6805 0 0
+
+E 180 4588 4897 6205 3166 * * 5723 3572 3846 3280 5867 * 5913 4321 4017 * 2973 2239 6105 5316 180
+ 0 * * * * * * 6805 0 0
+
+V 181 * 6425 4054 4441 6101 5640 6607 2933 3377 5181 * 4490 * 6037 5031 5701 1911 2708 5455 5001 181
+ 24 5913 * 3700 115 * * 6805 1028 0
+
+Y 182 * * * * 3604 6101 * * * 3482 * * * * * 4539 * * 2685 701 182
+ 0 * * * * * * 6805 0 0
+
+Q 183 4988 6205 5923 2375 5891 * 5870 5362 2906 * * 4775 * 3293 2813 5106 3451 2856 * 6105 183
+ 0 * * * * * * 6805 0 0
+
+K 184 4698 5701 * * * * * * 1743 * * 3292 3964 4474 1359 6118 * 5155 * * 184
+ 0 * * * * * * 6805 0 0
+
+S 185 4277 * * 5659 * * 4641 3218 2080 5386 6119 4084 3832 4563 2427 3109 6214 5682 * * 185
+ 289 2460 * 973 1027 * * 6525 1075 0
+
+V 186 * * * * * * * * 3117 2008 * * * * 3130 * 3003 1332 * * 186
+ 0 * * * * * * 3508 0 0
+
+L 187 * * * * * * * * * 0 * * * * * * * * * * 187
+ 0 * * * * * * 2074 0 0
+
+A 188 0 * * * * * * * * * * * * * * * * * * * 188
+ 0 * * * * * * 1000 0 0
+
+Q 189 * * * * * * * * * * * * * 0 * * * * * * 189
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 271643171bfa4abfd3da32e2d13e3392
+FAM
+FILE 271643171bfa4abfd3da32e2d13e3392
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:29:03 2013
+LENG 186 match states, 186 columns in multiple alignment
+FILT 154 out of 1736 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 11.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEEEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEEEEECCEEEEEEEEECCCCCHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHHHHHH
+HHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCC
+>ss_conf PSIPRED confidence values
+9985489999999999999999999658876665884321579999988906999999889961034788887614878999998977301789999999
+99997479996899998834663156788887642022579999999987499759999678886999999999998520322389
+>Consensus
+xxxxxxxixvxGxxxxGKstlixxlxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxixDxxGxxxxxxxxxxxxxxxxxxixvxdxxxxxxxxxxxxxxx
+xxxxxxxxxxxxivvxnKxDxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxSaxxxxgixxxxxxixxxxxxxxxxxk
+>271643171bfa4abfd3da32e2d13e3392
+GSPQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVSLICFSLVSPASFENVRAKWY
+PEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKK
+>gi|56698355|ref|YP_168728.1| elongation factor G [Ruegeria pomeroyi DSS-3]gi|56680092|gb|AAV96758.1| translation elongation factor G, putative [Ruegeria pomeroyi DSS-3]
+-------FTVLGPSQSGKSTLVEAI--SRLDSRPTTFDLSETVHLHGFSYLEEPWCAIDVDGGSDALAFAGPAMAISDAAVIVVPPDPEAAVLCAPYLRL
+VEEA----RIPAFLFINRMDNPngRIRDIVAALQAycsHHIALRQVPIR------------------------------------------
+>gi|321473698|gb|EFX84665.1| hypothetical protein DAPPUDRAFT_194445 [Daphnia pulex]
+-GSRVLQVAILGIPNAGKSTLVNQLSGWQTcsVSRKVHTTKKMSKTVLIRDETQIV--FLDTPGlvlpaeakqfnlDKSFVIDPEVALSKANLLLVLHDI
+SNKWTRGSLSSKILRLLHLY-PDKESVLVLNKIDLLKEKRLLLDytnkltegivggksiasntdqrkrsmsRQNSDMSTVNESNAElseptnsrsmseke
+vakRIEGKMGwpnFSRVFMISAIDGDGVSDIVEHLYGAAKPGRWM--
+>gi|290974801|ref|XP_002670133.1| predicted protein [Naegleria gruberi]gi|284083688|gb|EFC37389.1| predicted protein [Naegleria gruberi]
+-----VEYLIkytpIGEHSIGKSTFFNHVQFGHYENTsLWKS---EAIkKEFTISNeSSLVQVLFD--LDPRYQtkeTFIRGLIRHNMSFLLSFGINYEC
+TFEKLGDWYHLIKQEKLETMGIMI------------------------------------------------------------------------
+>gi|291530479|emb|CBK96064.1| small GTP-binding protein domain [Eubacterium siraeum 70/3]
+--MPFGAVkGGQSHENNQYWNSCPCRRWKDDLDGEPAICQRshfrtgerrkrdnedghhVFGAAA---WdyhssgshflpgHRCKVNIVDTPGHMDFLAE
+VYRSLAVLDGAILVISAKDGVQAQTRI--LFHALRKM--NIPTVIFINKIDQAgvDLQSVVQSVRDKLSADIIikqtvslspeivleentdieawdavie
+nndellekyiagepisreklAREEQQRVQDASLFPVYHGSAKNGLGIQPLMDAVTGLFQPIGE---
+>gi|320165903|gb|EFW42802.1| conserved hypothetical protein [Capsaspora owczarzaki ATCC 30864]
+---------LLTLPALTELKLeknqITDM--GAQSI-----------AVALRNKKAQLFRLclnWNKIGD----------FGARAIAegVAVSTALASLE
+YCSlAFDLWMNN--NQIGNVGAQAIGSALS------------------------------------------------------------------
+>gi|260810141|ref|XP_002599862.1| hypothetical protein BRAFLDRAFT_127644 [Branchiostoma floridae]gi|229285145|gb|EEN55874.1| hypothetical protein BRAFLDRAFT_127644 [Branchiostoma floridae]
+--KTNISIVVIGHVNSGKSNTTGHLiykcggidkrniekyereaaearfneiQQELSAcIKKVGYDPGT--VAFVPVSAQHGDNMVEPSGNMPWYKGWSi
+ernegngSGTTLlealdsilppqrpTDKPLRLPLAdvynfrpggmgtmpvgrvetgilKPGmevtfapagltaevepvdikhESVPEALPGDTVGInfK-
+-----NADVSVKELwrgcvagdSKNDPPKEAVSFD--------AEELSACIKKVGYdpgtVAFVPVSAQHGDNMVE-----------------
+>gi|148673550|gb|EDL05497.1| Ras-related GTP binding D, isoform CRA_c [Mus musculus]
+------RILLMGLRRSGKSSIQKVVFHKMSPSETLFLESTNRICREDVsNSSFVNFQIWDFPGQIDFFDPTFDYemiFRGTGALIFVIDSQDdyMEALAR
+LH-LTVTRAYKVNTDINFEVFIHKVDGLSDDHKIETQRDIHQR-ANDDLADAGLEKIH--LSFYLTSIYDHSIFEAFSKVVQKLIPQLP---
+>gi|195998195|ref|XP_002108966.1| hypothetical protein TRIADDRAFT_52490 [Trichoplax adhaerens]gi|190589742|gb|EDV29764.1| hypothetical protein TRIADDRAFT_52490 [Trichoplax adhaerens]
+-------VLVVGHDGSGKSTLISRMKNIEEKEKYHCSGLDYRYIDVDDEdsDEIYRFGVWILHGNAEHKSLLKFAINNDNlrdtAVVLVVDLSRPWEVMS
+CLTGWTKVLKEHMQSLNIdknVIEEMKSNIVNQFQGYSEVADDADKSLKEEEKVYLPLGEDGATLAYTTLKEKKNVDILLRYLLHRLY-------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * 3264 * * 781 * * * * 1671 * * * * * * * * * 1
+ 0 * * * * * * 4652 0 0
+
+S 2 4316 * * 4598 3582 * * 4365 3376 * * 2250 2906 * * 2208 3058 * * * 2
+ 0 * * 2322 322 * * 7660 1014 0
+
+P 3 5986 * 4301 3608 * 5295 5371 * 2425 3798 3182 4473 1984 5882 * * 3418 5310 * * 3
+ 29 5650 * 1000 1000 * * 9369 1008 0
+
+Q 4 * * 4040 4171 5857 * 4041 4911 2420 6042 * 3052 5217 3507 2930 3514 3879 4998 * 5869 4
+ 42 5125 * 1406 684 * * 10088 1296 0
+
+A 5 4593 * 4950 3738 * 4670 4117 4514 3399 6535 4872 3445 3041 4104 3729 3229 3579 5477 * 6474 5
+ 19 6281 * 0 * * * 10470 1000 0
+
+I 6 5865 6301 6194 * 2968 6907 * 1788 6405 2513 3744 4785 6377 * 5237 5574 6570 3321 * 3994 6
+ 23 5972 * 4807 52 * * 10793 1116 0
+
+K 7 5626 6913 5320 4933 6891 4668 4755 5095 1910 * * 2486 * 5033 2391 4467 4282 4748 * * 7
+ 17 * 6454 * * * * 10974 0 0
+
+C 8 6813 4487 * * 5573 * * 1438 * 2538 7234 * 7001 * * 7098 5452 1648 * 5612 8
+ 0 * * * * * 0 11218 0 1038
+
+V 9 2803 4334 * 7017 4359 3538 7206 3086 * 2187 3892 * * 5830 7027 6114 4840 2486 * * 9
+ 0 * * * * * 0 11182 0 1038
+
+V 10 6057 5559 * * 3001 * * 2325 * 2107 4192 6824 * * * * 5642 1663 * 6990 10
+ 0 * * * * * 0 11235 0 1038
+
+V 11 3467 4311 7095 6721 3707 5695 * 2310 7509 1979 4175 * * 7567 6968 5114 5109 2791 7076 7065 11
+ 14 6721 * 1000 1000 * 0 11235 1024 1038
+
+G 12 6054 * * 7358 * 110 * * * * * * * 7295 6387 5352 6731 * * * 12
+ 0 * * * * 0 * 11261 0 1038
+
+D 13 3790 * 2733 4402 4968 6394 4441 6151 4177 3493 5318 4173 2932 4764 4468 3016 5215 6038 * 5461 13
+ 22 6059 * 3069 183 * * 11288 1183 0
+
+G 14 4381 6699 4584 4201 6184 5062 5126 5275 3512 5479 7039 5567 2370 4563 4737 2677 3503 3448 * * 14
+ 0 * * * * * * 11288 0 0
+
+A 15 4814 6370 3978 4481 6204 1537 6352 * 4110 6132 5505 2302 6862 4547 4999 3608 7320 * * 7424 15
+ 0 * * * * * * 11288 0 0
+
+V 16 2375 3898 7168 7148 6954 7168 5240 5009 * 5073 7360 6173 * 5867 7039 1994 3690 2030 * 7424 16
+ 12 * 6905 * * * * 11288 0 0
+
+G 17 * * 5883 6189 * 194 7102 * * * * 5635 7077 * * 4501 6723 7149 * * 17
+ 0 * * * * 0 * 11279 0 1024
+
+K 18 * * 6850 6734 * * * 6016 297 6973 6752 * 5591 4774 4555 6173 6928 6239 * * 18
+ 22 6752 7360 3170 170 * * 11288 1024 0
+
+T 19 5220 * * * 6857 6379 7170 7193 4915 5545 * 6339 6022 5049 5356 1237 1432 * * 7194 19
+ 12 6952 * 0 * * 0 11322 1009 1000
+
+C 20 3375 4461 5336 6957 * 6952 7127 5513 4712 7636 7252 6515 * 5426 6224 1718 1512 6214 6810 6145 20
+ 24 5897 * 2204 353 * 0 11322 1242 1000
+
+L 21 5598 7252 * * 2192 * * 2886 7193 1159 5513 7013 * * 6971 6948 4032 4469 * 6379 21
+ 25 5880 * 1853 468 * 0 11322 1291 1000
+
+L 22 4663 5116 * * 4595 6738 7246 1765 * 2246 3880 * * 6812 6853 6217 4711 2160 6884 * 22
+ 109 5094 4532 1284 763 * 0 11281 1482 1000
+
+I 23 4645 5838 4072 3602 6511 4231 6197 7537 3430 4184 6056 1952 6664 3811 3702 3866 4480 6826 * 5956 23
+ 0 * * * * * 0 11261 0 2114
+
+S 24 2580 5896 5373 6690 5470 5100 4795 6170 3310 4689 5886 5096 * 4267 2656 3283 3219 3902 * 7121 24
+ 14 6664 * 2000 415 * 0 11261 1038 2114
+
+Y 25 6923 * * 6694 2725 * 7192 2831 * 1107 5287 * * 6801 * * 6008 3877 5312 3719 25
+ 293 2661 5286 4203 81 * 0 11265 4034 2114
+
+T 26 4497 4331 7265 6127 3513 6549 6880 3422 3488 2788 6957 5388 6600 4773 4838 3221 2630 4074 6744 * 26
+ 10 7247 * 1585 585 * 0 11244 1000 2652
+
+T 27 4216 6898 3220 3976 5813 2673 3890 6052 3617 5959 * 3044 5318 3766 4237 4277 4342 6062 * 5405 27
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+E 173 3980 6884 4823 3836 4588 4304 4189 5184 3123 3200 5202 7308 * 4067 4578 4035 4114 5155 3478 4235 173
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+I 175 3399 5507 5828 6708 5919 4559 * 2694 3917 2610 5336 4756 * 4468 4043 4129 4732 3181 * 4643 175
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+L 179 4401 6678 4902 4905 3706 * * 3293 5477 2303 4272 5134 3869 4478 4667 4602 4547 3411 6046 4430 179
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+C 180 4306 6600 3640 2635 6106 5196 4977 5097 3746 4955 * 3232 4516 4708 3554 3641 4167 6200 * 3934 180
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+P 181 3898 5697 4901 3585 6151 3294 * 4901 3921 4297 5971 3532 3388 3173 4385 3057 4742 5951 * * 181
+ 0 * * * * * * 9916 0 0
+
+P 182 4832 5859 5740 3751 * 4639 5848 5836 2866 4118 5793 3771 2562 3665 3491 4601 4024 5914 * 4746 182
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+P 183 * 5228 * 3282 * 4618 4422 * 3883 2850 * 4033 2180 3924 4499 3655 5684 4572 5450 5569 183
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+
+V 184 5095 * * * 2916 4962 5158 2889 4376 1857 3594 4172 * * * 4210 5223 3745 5309 * 184
+ 0 * * * * * * 8756 0 0
+
+K 185 3743 * 2790 * * 3851 4667 * 1222 * * 4638 * 4962 3764 3359 * * * * 185
+ 0 * * * * * * 7966 0 0
+
+K 186 * * * * * * * * 138 * * * * * 3451 * * * * * 186
+ 0 * * 0 * * * 5347 0 0
+
+//
+�HHsearch 1.5
+NAME 2798277b8842d36de2206ba3ae8863fc
+FAM
+FILE 2798277b8842d36de2206ba3ae8863fc
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:16:48 2013
+LENG 221 match states, 221 columns in multiple alignment
+FILT 109 out of 1133 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEECCCCCHHHHHHHHHHHCCCCCEEEEECCHHHHHHHCCCCCCCCCCCCEEEECCEEEECHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
+HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHCCHHHHHHHHHH
+HHCCCCCCHHHHHHHHHCCCC
+>ss_conf PSIPRED confidence values
+9966999789990599999999986999779972743778874211368778777799899877758999999998446689999999999999999999
+9999999872671344489999999999999999999998559970569999999999999999999829112101889999999998499999999863
+740799956677764201085
+>Consensus
+MxxxxLyxxxxspxxxxvxxxlxxxxixxxxxxxxxxxxxxxxxxxxxxpxxxvPxLxxxxxxixesxxIxxyLxxxxxlxpxxxxxxxxxxxxxxxxxx
+xxxxxxxxxxxxxxxxxxxxxxxxxxxlxxxlxxlexxLxxxxxxxlxGxxxtxADixxxxxlxxxxxxxxxxxxxxpxlxxwxxxxxxxpxxxxxxxxx
+xxxxxxxxxxxxxxxxxxxxx
+>2798277b8842d36de2206ba3ae8863fc
+AGKPVLHYFNARGRMECIRWLLAAAGVEFEEKFIQSPEDLEKLKKDGNLMFDQVPMVEIDGMKLVQTRAILNYIATKYDLYGKDMKERALIDMYTEGILD
+LTEMIGQLVLCPPDQREAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGNRLTRVDVHLLELLLYVEELDASLLTPFPLLKAFKSRISSLPNVKKFLQPG
+SQRKPPLDAKQIEEARKVFKF
+>gi|241668347|ref|ZP_04755925.1| glutaredoxin 2 [Francisella philomiragia subsp. philomiragia ATCC 25015]gi|254876880|ref|ZP_05249590.1| glutaredoxin [Francisella philomiragia subsp. philomiragia ATCC 25015]gi|254842901|gb|EET21315.1| glutaredoxin [Francisella philomiragia subsp. philomiragia ATCC 25015]
+---MKIYLYHHCPYCIKVRLVADLSKLDYEMIILANDDEKSHID---RIGSKQVPFLEkDDGTFIKESDEICKFIAKTQNFEIAESTIDNYAKESVAKLA
+EHYRRIVYPRiphhpgnecdFPTQSakdyfinKKSQYIgdfDallrnpPyDSIIAINKILREIAPFVKT--PF-ING-DnFSWDDINIFPVFFILTMARD
+L-LEIPNNISNYIKNIETKTNIEL--------------------------
+>gi|195171951|ref|XP_002026765.1| GL26999 [Drosophila persimilis]gi|194111704|gb|EDW33747.1| GL26999 [Drosophila persimilis]
+MAQPlKFYFDFLNQSSRALYIFLEASKIPFEAIPISMLkesmqatatttatatTLW-RlktpiqpirsdalyavevnigfyclwgLNRNvPISSYYRIIM
+AELFNYSLSSLSSLFPFHPPEPasPldWVPFRSLGRSRIDEYLAWQqtnmgvacTDYFQQKWLVPYLQKTRPAENAVNVAGKQLEHTLNDFEQLFLN-SR
+KFMLGNNISFADLSAICEIDQPKSIGFNAFQNRNKLARWYEAVRDElgPYYKDVHAEFE--------------------
+>gi|224014714|ref|XP_002297019.1| predicted protein [Thalassiosira pseudonana CCMP1335]gi|220968399|gb|EED86747.1| predicted protein [Thalassiosira pseudonana CCMP1335]
+---MKLHVLPISANSHGCLAIVKHLNLDDKVEIIDAygktrTPEFIAMN-----PAHCCPTLQFsneSDGAIWESAAVMRCLCNSFEggeeLYPTDAIKR
+GKIDMVLDWKNStLYPDLFHIaymMFGVA-VDEDMAKTQFGKLIDTHFPMlLDTFLKD--TKFCYSDTPTIADLAVAPMITLLKGRK-KFWEKVPeGVKE
+YYGRVLeAFPGMGEYVK-----------------------
+>gi|198434929|ref|XP_002128793.1| PREDICTED: similar to methionyl-tRNA synthetase [Ciona intestinalis]
+---MMEINGQPSPEKLKVLLACFETG-------------LhkIKVN-----Skp--GSALsVRLdNEIEFTSSNAAVRYTYE------TQGVKVdVETLH
+WFEWEVTILRK-LVgsyFSLSDKKILNI----NEFPNLISSLQYLENSInsg-K--LECDFSTKISAANCVIFctisPLFCN--PG----iEGEFPVLRK
+HFAIFMNRGSFRSAW-kE----------------------
+>gi|219118467|ref|XP_002180005.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]gi|217408262|gb|EEC48196.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
+-PKITLFrdHAGWCPYCEKTMLLIEEKQVPVKIDLVPMRsygdkpQEFLRKV-----PNGLLPAIEVNGQVVTESQVIMELLDQWHSkqdgyrpMLPReg
+DTAGWERYKKLARLERDLFGWWCTLLFRPEGGNPltmlmassRDSMSGAMQGFLDCMQKVDQELLSSNGPWFFDehDYPTMIDFVYGLDLRNPKW-----
+--NLKGLNAWLEAFEKREPYLAFKSDYYTNVMDIPPQYGPGYDGGFN-
+>gi|151967130|gb|ABS19445.1| multivalent antigen sj97-23 [synthetic construct]
+MATLGTGMRCLKSCVFILNIICllcslvligagAYVEVKFSQYEANLHKVWQAA------PIAI--------IVVGVVILIVSF-------LGCCGAIKE
+NVCMLYMyafflivlLIAELVAAIVAVVYkdkiDDEINT---LMTGALENPNEEITATMDKIqtsfhcCgvkgpddykgnvpasckegQ--EVYVQGCLS
+VFSAFLKRNLIIVACVAFGVCFFQLLSIViacCLGQRIHDYQNV----------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 4504 * * * * 4469 * * * * 208 * * * * * * 4464 * * 1
+ 149 * 3349 * * * * 7434 0 0
+
+G 2 2830 * * 4845 * 4861 * * * * * 4705 1375 4843 * 2148 4757 3862 * * 2
+ 327 * 2303 * * 1326 735 8167 0 1275
+
+K 3 5252 * 2976 4285 * 5379 * 5098 2774 * 2767 5199 5341 4393 3689 2414 3567 * * * 3
+ 0 * * * * 213 2863 8776 0 2287
+
+P 4 4614 * * * 4010 5253 * 2705 * 2663 2234 5945 3235 6382 * * * 4383 * 2603 4
+ 38 5283 * 0 * 0 * 9846 1161 1015
+
+V 5 5278 6371 6226 3223 * 5796 4292 3372 2084 4743 5322 * * 6641 3465 * 2355 3612 * * 5
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+
+L 6 * * * 6215 3629 * * 3556 * 504 5165 * * * * * 5093 4102 * * 6
+ 0 * * * * * * 9937 0 0
+
+H 7 6435 * * * 3657 4285 4248 3350 6036 3571 6504 * * 6261 * 6140 5209 4114 5439 1115 7
+ 73 4748 6398 811 1218 * * 9969 1687 0
+
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+
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+ 19 6240 * 0 * * * 10015 1009 0
+
+N 10 3327 5902 3603 4869 5461 3775 4328 6579 5578 4894 * 3582 2453 5402 4120 4858 3250 * 5623 4342 10
+ 127 5551 3990 2700 241 * * 10099 1149 0
+
+A 11 3381 * 4341 5434 3934 2535 4537 4188 * 3287 5627 4810 3986 4474 6285 4707 3843 4035 6490 4787 11
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+
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+
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+
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+
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+
+E 16 4045 6400 6226 3282 4758 * 4797 4525 6237 2788 4884 6302 5402 2992 2103 * 5501 5628 4945 4897 16
+ 21 6095 * 1000 1000 0 * 10268 1037 1596
+
+C 17 2965 5625 * * * 5730 6589 4766 2401 3278 4587 6631 5052 6451 1732 5009 5494 4835 6541 * 17
+ 0 * * * * * * 10322 0 0
+
+I 18 2773 5378 * * * 5642 * 2206 * 3162 5747 6660 5011 * * 5624 4833 1449 * * 18
+ 0 * * * * * * 10310 0 0
+
+R 19 5062 5469 6625 4381 5470 6828 5061 4728 3625 2765 5085 5404 * 4050 1655 * 4668 6646 4645 4574 19
+ 16 6467 * 0 * * * 10351 1030 0
+
+W 20 3435 5710 * * 4571 4970 6709 2036 6673 2608 2690 6541 * * * 4928 5534 3770 3783 5567 20
+ 0 * * * * * * 10351 0 0
+
+L 21 2000 5797 * * 4325 6609 * 3385 * 2287 5806 * * 5489 5475 5101 4370 2595 5229 4686 21
+ 14 6705 * 0 * * * 10351 1000 0
+
+L 22 2786 3709 * * 3770 * * 3757 * 945 5185 * * * * 5633 * 5006 6722 5404 22
+ 53 4791 * 2416 299 * * 10360 1494 0
+
+A 23 2271 * 4361 2252 4314 4998 3925 6522 3362 4080 * 5053 * 5088 3217 * 4994 * 5575 * 23
+ 0 * * * * * * 10360 0 0
+
+A 24 3348 6425 6522 2135 3864 * 4584 4204 4973 2438 5084 4777 * 6683 5597 6621 * 4877 5159 3294 24
+ 14 6696 * 3585 126 * * 10360 1000 0
+
+A 25 2827 4631 * * 5625 4505 5505 5972 2043 2414 6603 6729 * 5070 3906 3399 5048 6086 5619 6647 25
+ 43 5087 * 1243 792 * * 10360 1361 0
+
+G 26 5200 6622 3709 2997 * 1484 * * 3039 * * 3560 6976 3541 4664 4608 * 6385 * 6549 26
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+
+V 27 4123 6559 6524 * 5496 6408 6674 1690 5066 2069 * 7016 5923 5117 5690 * 5437 2295 * * 27
+ 42 5129 * 2105 382 * 0 10343 1300 1321
+
+E 28 4352 * 3032 2896 * 5557 6651 6969 3459 5083 6229 4243 1769 5143 5518 3821 5166 5244 * * 28
+ 45 5029 * 383 2100 868 1145 10343 1362 1321
+
+F 29 * 6038 6536 6581 2269 6488 3582 4629 6464 3569 * * * * * * 5460 2543 4510 1799 29
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+
+E 30 3818 * 3029 1617 * 6488 6626 5011 3666 * * 4324 * 3485 4148 5291 3398 4898 * * 30
+ 15 6581 * 1000 1000 * 0 10337 1060 1036
+
+E 31 4362 5649 3943 3545 3724 5492 5772 3677 4726 2675 5527 5734 6644 4753 5749 4740 3797 2896 6665 4950 31
+ 0 * * * * * 0 10337 0 1036
+
+K 32 4598 6374 4010 3581 6751 6713 3749 3746 3453 5670 * 5688 * 5784 3475 3826 3274 2407 6941 5368 32
+ 11 * 7000 * * * 0 10337 0 1036
+
+F 33 3982 * 4082 3918 5100 5590 5708 4299 4955 3669 6683 3817 3125 5588 3308 6592 3626 3770 5071 3850 33
+ 27 5776 * 0 * * 0 10343 1139 1227
+
+I 34 3525 6625 * 5046 4201 6702 6506 2597 * 3187 3900 5113 5618 6561 4648 4644 5488 2037 * 4320 34
+ 32 6465 6557 3170 170 * 0 10343 1000 1227
+
+Q 35 3658 5556 1940 5405 * 4978 6647 5674 5581 5552 6735 3175 3310 5228 4382 3123 4025 5646 6579 6698 35
+ 111 5426 4298 2574 265 * 0 10320 1240 1410
+
+S 36 4015 6476 4994 6496 3436 4553 5689 3423 5410 2804 3350 4986 2706 * 4475 4455 6524 4605 5492 5478 36
+ 587 2194 3111 2094 385 3051 186 10215 4400 2271
+
+P 37 3161 * 3980 4364 6349 3079 4646 6374 3761 3854 * 5364 3136 5335 4054 3245 4117 * 4765 5164 37
+ 591 1700 5136 2274 334 629 1501 10017 5096 3686
+
+E 38 3004 6225 2685 2426 6424 4479 6240 * 3636 6362 * 4206 3346 4370 5634 4310 3965 6626 6319 * 38
+ 145 3968 4978 1476 643 * 0 10188 1893 2327
+
+D 39 3576 6217 2617 2986 6440 3169 4780 6682 5306 3935 * 4862 4495 4450 6499 3387 5440 4697 4716 5436 39
+ 208 3903 3886 2954 199 1338 726 10168 1832 2767
+
+L 40 5403 * 4466 4824 2285 6278 6093 4867 4379 3113 5434 * 4942 * 5056 5570 5297 4837 2477 3079 40
+ 79 6370 4595 1000 1000 1703 529 10168 1036 3034
+
+E 41 4374 * 6570 3252 3593 4794 5447 4837 3426 2546 5155 6370 3558 5959 4808 3644 4085 4194 * 5335 41
+ 33 6485 6485 0 * 778 1263 10124 1000 2958
+
+K 42 2352 * 3423 3644 * 4453 5494 5913 2650 5592 6541 3954 4589 3723 3864 4011 6971 4833 * * 42
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+
+L 43 3431 6484 * 4940 4599 4900 4521 2556 4497 2119 4481 6294 5491 5463 5422 6306 5063 3199 * 5410 43
+ 105 5013 4662 764 1282 1969 426 10230 1367 2323
+
+K 44 5389 6434 4475 4076 4921 4434 6251 5102 2515 4893 * 1973 6614 5717 4009 3180 5567 5064 6420 6486 44
+ 1185 4945 922 1479 641 * 0 10157 1347 2589
+
+K 45 3800 * 3670 3487 * * 5381 * 3133 3841 * * 2488 4366 3465 3773 3114 4416 * * 45
+ 527 3851 2078 1375 703 5937 24 8842 1348 7766
+
+D 46 3577 * 2752 3145 * 3514 * 4055 4093 4890 * 4099 2501 4970 5085 4915 4164 * 5086 * 46
+ 689 2061 2835 1072 931 2799 224 8376 2295 8270
+
+G 47 3247 * 3655 2682 * 2954 * 4271 4171 5142 * 3688 3658 5258 5379 3519 4465 4177 * * 47
+ 158 4206 4343 1498 630 3230 163 8715 1185 7981
+
+N 48 * * * 5497 3444 3450 * 4465 3374 3779 4472 5711 3872 3741 4354 5289 4375 3162 5351 3135 48
+ 68 * 4442 * * 3978 95 8938 0 7692
+
+L 49 5441 * 5240 5592 3857 5542 3918 4455 5395 2714 * 1908 * * 4477 2899 3565 5534 * * 49
+ 170 3171 * 2287 331 147 3365 9030 1818 7579
+
+M 50 3259 * 5498 5620 * 4558 6536 6605 5731 5127 5681 * 781 6697 4305 4442 6533 5390 * * 50
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+F 51 3893 * 5586 5694 3271 4245 6285 5299 3798 2637 4362 3787 5071 5476 4952 4990 5060 3490 * 3195 51
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+
+D 52 2675 * 6702 4717 * 1490 6477 5689 4017 4287 5210 6580 5022 * 3561 3948 4918 6514 * 4860 52
+ 0 * * * * 310 2370 10274 0 1764
+
+Q 53 4768 * 6647 4618 * 4999 4912 6103 2271 4175 5564 3808 * 2523 3677 3630 2997 6614 * 6619 53
+ 51 5626 6103 2004 414 * 0 10378 1264 1000
+
+V 54 4301 6546 5474 * 5506 6671 * 3191 * 2014 6169 * 4544 6559 * 5699 5112 1351 * 5665 54
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+
+P 55 5417 * * * * * * 6528 5570 7036 * * 159 * 6730 6455 6756 6425 * * 55
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+
+M 56 3049 5543 * 6468 4063 5773 * 2904 6562 3946 5088 6272 * 5567 6486 5703 2579 2173 * 3712 56
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+
+V 57 5537 * * * 4251 * 6468 3008 7066 748 4052 * * * * * * 3090 * 6665 57
+ 57 5135 6589 2012 411 * 0 10364 1423 1105
+
+E 58 5196 * 4523 2519 5031 6267 6633 3384 3513 4125 * 6640 6996 4355 4023 6466 3970 2135 6482 5783 58
+ 128 3562 * 673 1424 1395 690 10340 2431 1290
+
+I 59 5013 5678 2189 3859 4705 5818 3453 3634 6618 3147 * 6708 5496 5807 6566 5588 3509 3297 6486 5129 59
+ 381 2109 * 1567 594 * 0 10364 4742 1105
+
+D 60 5741 6509 1677 4477 6538 2347 6856 6530 3883 * * 2945 5742 5314 4912 3495 5466 * * * 60
+ 88 4079 * 747 1308 * 0 10375 1964 1105
+
+G 61 5524 * 2257 3927 * 1429 * * 4931 5574 * 3665 5896 5429 5675 3332 4629 * * * 61
+ 554 1649 * 1231 801 0 * 10375 5509 1105
+
+M 62 3780 * 4341 3882 3689 5111 5132 4230 4351 3977 6832 3815 * 3871 3702 3924 3396 3591 5585 5682 62
+ 33 5483 * 0 * 0 * 10417 1218 1009
+
+K 63 3690 5828 * 5215 4114 5357 4730 3406 4375 4387 5888 * 3982 4855 4428 5150 2942 2010 * * 63
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+
+L 64 5755 * * 6307 4862 * 6614 1757 6508 1749 4646 5398 * * 5770 * 6375 2501 6705 4660 64
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+
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+ 17 6375 * 0 * * * 10440 1032 0
+
+Q 66 * * 1827 1593 * 3687 5371 * 7023 * * 5648 5411 3023 6509 4074 5846 5443 * * 66
+ 13 * 6790 * * * * 10440 0 0
+
+T 67 3580 * 6715 4833 5768 6866 6753 5149 6294 5584 6422 4974 6785 5709 * 1017 2899 4710 6523 5326 67
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+
+Q 198 2546 * 5681 3477 * 3711 5639 6039 3222 4687 * 4191 3644 3488 3990 3312 4173 5729 * * 198
+ 60 5667 5573 2474 286 465 1859 9367 1347 1657
+
+P 199 3573 * 3535 2399 * 5496 5366 4435 3686 4614 5522 5437 3231 4568 3791 3327 5867 4431 * * 199
+ 0 * * * * 1143 870 9071 0 1239
+
+G 200 2196 * 4221 2728 4415 4264 5465 5463 4097 5920 5241 * * 4266 3607 3401 5286 * * 3693 200
+ 0 * * * * 0 * 8611 0 1041
+
+S 201 3809 4891 3693 2663 * 4190 * * 5160 3579 * 5173 2821 5126 * 2900 5315 5168 4173 4236 201
+ 0 * * * * * * 8463 0 0
+
+Q 202 * * 4653 1950 4841 4896 * * 3390 4829 * * 3714 3347 3359 * 2862 * * 3427 202
+ 0 * * * * * * 7960 0 0
+
+R 203 4731 4539 4483 3494 * * * 3448 2590 * * 2937 * * 2224 3081 4626 5324 * * 203
+ 0 * * * * * * 7239 0 0
+
+K 204 4317 * * 4139 * * * 4305 3351 3449 * 4220 * 2270 2288 * * 2906 * 4218 204
+ 0 * * * * * * 6726 0 0
+
+P 205 5167 * * 4420 * 4273 4139 * 3302 2663 4233 * 1332 4187 * * 4254 * * * 205
+ 0 * * * * * * 6726 0 0
+
+P 206 2366 * 2888 * 4734 * * * * * 3164 * 2372 * 2363 * * * * 2898 206
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+
+L 207 2239 * 3835 * * * * 3751 * 3895 * 3087 2283 * * * 2835 * * 3144 207
+ 0 * * * * * * 5942 0 0
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+D 208 * * 3700 2611 * * * * * * 3643 2128 2601 3634 2979 3676 * * * * 208
+ 0 * * * * * * 5688 0 0
+
+A 209 3700 * * 3646 3634 2703 * * * * * * 3557 3633 * 3611 1804 * * 3733 209
+ 0 * * * * * * 5688 0 0
+
+K 210 2581 * 3519 3616 * * 3504 * 1954 * * * * 2464 2873 * * * * * 210
+ 0 * * * * * * 5483 0 0
+
+Q 211 3393 * * * 2386 3494 * * * 3455 * * * 3393 * * 3372 4209 * 1797 211
+ 0 * * * * * * 5233 0 0
+
+I 212 3365 * * 2617 * 3184 * 3182 2236 3318 * 3227 * * * 3316 * * * * 212
+ 0 * * * * * * 4950 0 0
+
+E 213 * * 2661 2425 * 2638 * * 2606 * * 2635 2558 * * * * * * * 213
+ 0 * * * * * * 3814 0 0
+
+E 214 * * * 1279 * 2328 2372 * * * * * * * * * * * * 2354 214
+ 0 * * * * * * 3437 0 0
+
+A 215 1271 2373 * * * * * * * * * * * * * * * 2372 * 2328 215
+ 0 * * * * * * 3437 0 0
+
+R 216 * * 1628 * * * * * * 1665 * * * * 1470 * * * * * 216
+ 0 * * * * * * 2400 0 0
+
+K 217 * * * * * 1628 * * 564 * * * * * * * * * * * 217
+ 0 * * * * * * 2400 0 0
+
+V 218 * * * * * 1081 * * * * * * * * * * * 923 * * 218
+ 0 * * * * * * 1788 0 0
+
+F 219 * * * * 0 * * * * * * * * * * * * * * * 219
+ 0 * * * * * * 1788 0 0
+
+K 220 * * * * * * * * 923 * * 1081 * * * * * * * * 220
+ 0 * * * * * * 1788 0 0
+
+F 221 * * * * 0 * * * * * * * * * * * * * * * 221
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 2a3d9802bfcbb4c8a6063b33f02f6538
+FAM
+FILE 2a3d9802bfcbb4c8a6063b33f02f6538
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:04:17 2013
+LENG 132 match states, 132 columns in multiple alignment
+FILT 111 out of 603 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCCCEEEECCCEEEEECC
+CCCEEEEEEECCCCHHHHHHCHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9875465111405768999945799848999998164684465776641879999998632676897888999987045204899789848888999959
+99893617853504998740348865223109
+>Consensus
+xxxxxxxxxxmIqxxTxlxVxDNSGakxvxcIxvxxxxgxxxrxxxaxvGDxIxvsVkkxxxxxkgxvxxAvIVrtkkxxxRxdGxxixFxxNaxVLinx
+kxxpxGtrIxGpvxxElrxkxxkixslaxxii
+>2a3d9802bfcbb4c8a6063b33f02f6538
+MEALGADVTQGLEKGSLITCADNTGARELKVISVHGYSGTKNRHPKAGLGDKITVSVTKGTPEMRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDE
+NEDPRGTELKGPIAREVAQRFGSVASAATMIV
+>gi|301353215|ref|YP_003795212.1| ribosomal protein L14 [Proteromonas lacertae]gi|301353235|ref|YP_003795232.1| ribosomal protein L14 [Proteromonas lacertae]gi|290573163|gb|ADD46350.1| ribosomal protein L14 [Proteromonas lacertae]gi|290573183|gb|ADD46370.1| ribosomal protein L14 [Proteromonas lacertae]
+----------MIQMNTILKVADNSGAKTVFCFKFPN--KLKHN--ATFFNEKAKVSIRSLRKRGslkikKGDIYTALVLRQKINLRRFNGSFIKFSNNSV
+ILFDPKKdnTPLGTRIFGIVNKELRLKkYLKIISLASCLI
+>gi|119614253|gb|EAW93847.1| hCG2041309 [Homo sapiens]
+-------------------------------------------------hGDG--HSQERQTRAQKKGTSSSGHLTTKVIW-RKDGVFLYFEGNAGVIIK
+NKDEMKGSAITGPVAKECADLWPRIAFNTGSIA
+>gi|260076070|gb|ACX30948.1| ribosomal protein L14 [Euplotes minuta]
+-----------IQRLTWLKVADSSQAQWLKTFHL--YGGFSRAV--SAVGDLVRGSVRVIQA--ipdpykgftvrrinKGRILAGIIIRQTYKAQLKSTT
+TVQAKTNGVVILKDDRSVLIKHVVGPCFSLL---------------
+>gi|32563935|ref|NP_495527.2| hypothetical protein F45E12.5 [Caenorhabditis elegans]gi|24418262|gb|AAA68795.2| Hypothetical protein F45E12.5b [Caenorhabditis elegans]
+-------PSMGIHRRTRLNVVDNSAlgkeadttGKLPYCIHVYKQGRRAKHMPHAELGDKILVAI-------RGQMRKAYVVGANThVHYRKHGVP-VTD
+QNMIVLLDEEGNPLGNRITAPIPTKLMAnrgnvQFSKVLALANKFI
+>gi|114329853|ref|YP_740757.1| ribosomal protein L14 [Tetrahymena malaccensis]gi|114150086|gb|ABI51666.1| ribosomal protein L14 [Tetrahymena malaccensis]
+----------MVQKETNLKPIDKCGVWSVRVFHLYG--GSFRK--QSYISNFVKVSVKKTRPNNwvpKKTKLKSIIVTGKNEIKKIDGSYIKFRSLNTVL
+LKKRLTPKGKILMGPVSVSLKRkKFL----------
+>gi|49147208|ref|YP_025801.1| ribosomal protein L14 [Pseudendoclonium akinetum]gi|33439223|gb|AAQ18760.1| ribosomal protein L14 [Pseudendoclonium akinetum]
+----------MLISRSKLIVKDNSGIILAQCIQVQRSKKSQK---PCKIGDFLKATVKKGSAKSqtqrlkkltgSERLRNLVVIQTKSALRRLDGGAIRF
+NANCGITVNERKLPLFKRVTSVVPFELKKKCNPVLNLARAVI
+>gi|1171600|emb|CAA64584.1| rpl14 [Plasmodium falciparum]
+----------MIYINSILDVIDNSGIFKFKYICTLN------KYKNPKYGDIVIGVVYSLYNNnlyKKSDKCKGILVQQKKFLNFKKYYSIKFNKNAVII
+INNKLNFVGTKSNNYISK-----------------
+>gi|224140519|ref|XP_002323630.1| predicted protein [Populus trichocarpa]gi|222868260|gb|EEF05391.1| predicted protein [Populus trichocarpa]
+---------------THLNVAYNSEVRELMF--------SNRR--YIYIGDVIIIVIKKVVPNSpleRFEVIRAVIMHTLKELKCDNSMIKRYNDNAT--
+-----------------------------------
+>gi|10802917|gb|AAG23665.1|AF288091_10 ribosomal protein L14 [Thraustochytrium aureum]
+----------MVYPETNVFIVDNSNVKEVRCVHVYN--QSSNN--FGSTGSFIIGVITKLKKNnlkstqKRGDLVKVLIVFTRKEKNniKGSGIFVKAPK
+NFGILFDKK-IAVGSRCKGVLPIKIKP-------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 3052 * * 3994 * * * * * * 981 * 4164 * 2844 * * 3121 * * 1
+ 0 * * * * * * 2875 0 0
+
+E 2 * * * 3128 * * * 4106 643 4134 * 4000 * * 3885 * * * * * 2
+ 0 * * * * * * 2875 0 0
+
+A 3 3115 * * 3121 * 2318 * * 2896 4106 * * 2391 * 3885 * 4164 4000 * * 3
+ 0 * * * * * * 2875 0 0
+
+L 4 3835 * * * 2846 * * 1625 2817 4459 * * * * 3461 4515 4584 3279 * * 4
+ 0 * * * * * * 3004 0 0
+
+G 5 4373 * * * * 1839 * * 3835 * * * * 4459 2060 2160 4584 4275 * * 5
+ 163 3230 * 1826 478 * * 3004 1077 0
+
+A 6 2859 4633 * 4429 2346 2888 * * * * * * 3655 * * 2478 4486 4706 * 3297 6
+ 0 * * * * * * 3278 0 0
+
+D 7 * * 3754 * * 3755 3368 * 3118 * * 3936 * * 1663 2741 3805 * * 4735 7
+ 53 4806 * 1000 1000 * * 3476 1016 0
+
+V 8 5044 * * 5140 4039 * * 1799 * 4119 4979 * 3903 * 4006 * 5064 1776 * 4243 8
+ 0 * * * * * * 3858 0 0
+
+T 9 * 4830 5172 * * * * 5706 3870 4242 * * 3644 4573 3193 1440 2575 5107 * * 9
+ 0 * * * * * * 4001 0 0
+
+Q 10 4281 4651 * * * * * * 2657 2528 4454 2911 5072 5382 1899 * * 5298 * 4295 10
+ 0 * * * * * * 4060 0 0
+
+G 11 4000 6015 * * 5761 2320 6546 * 6216 * 839 * * 6378 * 4697 4503 7141 5784 * 11
+ 0 * * * * * * 5096 0 0
+
+L 12 * 6469 * * 5657 * * 717 * 1844 * * * * * * 5140 4217 * * 12
+ 0 * * 0 * * * 5372 1022 0
+
+E 13 * * 6073 7251 5602 4878 5279 3795 5197 4632 6049 5636 3670 1130 4662 5781 5832 5782 6126 3642 13
+ 12 6894 * 0 * * * 5396 1000 0
+
+K 14 4945 6563 7681 6352 6284 * 5585 4237 2065 2984 4398 5567 3889 4858 4380 4070 4359 2635 * * 14
+ 0 * * * * * * 5420 0 0
+
+G 15 * 5342 * 3151 5935 1604 * * 3491 3815 5876 3720 * 2499 4367 5798 6772 * * 6372 15
+ 0 * * * * * * 5420 0 0
+
+S 16 3196 * * * * * * * * 6705 * * * * * 1647 912 5031 * * 16
+ 0 * * * * * * 5450 0 0
+
+L 17 7104 6894 7425 4566 4529 5703 6201 3305 3156 3718 5170 4054 6705 4727 2693 7436 * 2858 5440 3132 17
+ 25 5871 * 2000 415 * * 5450 1084 0
+
+I 18 6073 7302 * * 3971 * * 3541 * 712 4566 * * * * 5437 * 2705 * * 18
+ 0 * * * * * * 5450 0 0
+
+T 19 6060 * 4397 5186 5104 5828 5560 5933 1894 7393 * 2092 6644 4485 3540 6142 3445 4792 * 4900 19
+ 0 * * * * * * 5450 0 0
+
+C 20 * 2476 * * * * * 2283 * 6783 * * 6044 * 6064 * 7353 812 * * 20
+ 0 * * * * * * 5450 0 0
+
+A 21 1423 6189 * * * 4583 * 2844 5933 4466 6898 6674 * * * 4054 3664 2406 * 5342 21
+ 0 * * * * * * 5450 0 0
+
+D 22 * * 54 * * * * * * * * * * * * * 5437 * * 6201 22
+ 0 * * * * * * 5450 0 0
+
+N 23 * * * * * * * * 6044 * * 151 * * * 5123 4166 * * * 23
+ 0 * * * * * * 5450 0 0
+
+T 24 * 4783 * * * * * * * * * * * 5437 * 461 2224 * * * 24
+ 16 6481 * 3000 193 * * 5450 1010 0
+
+G 25 5530 * 5693 4214 * 279 * * 6552 * * 6131 * 6184 * 5341 5812 * * * 25
+ 84 4142 * 2686 244 * * 5450 1285 0
+
+A 26 812 * * * * 3285 * 3578 * 4889 * * 6032 * * 6510 6064 2753 * 5597 26
+ 37 5322 * 2257 339 * * 5450 1096 0
+
+R 27 6879 6032 * * 5035 * * 4344 1016 5005 * 5309 * 4401 2433 6588 4471 6632 4998 5934 27
+ 0 * * * * * * 5450 0 0
+
+E 28 4982 * * 3273 4884 * 5847 3042 2713 2364 5874 4194 4871 4764 5308 6045 4485 3828 4957 6039 28
+ 0 * * * * * * 5452 0 0
+
+L 29 2420 * * * 5913 3962 * 3425 * 2590 * * 3791 * * * 5847 1383 * * 29
+ 0 * * * * * * 5452 0 0
+
+K 30 6851 4343 * 3416 5279 5898 * * 2194 3845 3378 5954 * 3089 2521 5137 * 5564 * 3963 30
+ 0 * * * * * * 5452 0 0
+
+V 31 6045 885 * * 5372 * * 2302 * 5196 * * * * * 5874 4877 3042 * 5913 31
+ 20 * 6202 * * * * 5452 0 0
+
+I 32 5838 * * * 3055 * * 416 * 4653 * * * * * * * 3778 * * 32
+ 0 * * * * * 0 5434 0 1040
+
+S 33 6296 5293 7036 * * 2782 2912 * 1884 6911 6768 4901 * 2804 3759 2962 6864 * * * 33
+ 12 * 6861 * * * 0 5434 0 1040
+
+V 34 5254 * * * 4998 * * 2556 5584 3607 6157 3979 * * * 5858 4432 966 * 5916 34
+ 24 * 5893 * * * 0 5427 0 1084
+
+H 35 * 6468 5455 * 4975 5169 5378 3859 3128 1558 6146 5108 4312 5922 5290 6252 * 6902 * 2306 35
+ 196 5847 3187 945 1057 * 0 5398 1042 1163
+
+G 36 * * 5578 5265 * 1562 6885 * 2525 * * 2810 4466 4706 2981 5199 4263 * * * 36
+ 1149 * 865 * * 3376 146 5342 0 1743
+
+Y 37 * * * * 6076 * 4343 3473 2323 5676 * * 5077 4047 4288 3350 5229 4818 4899 1778 37
+ 232 3911 3611 1544 606 * 0 4552 1052 3621
+
+S 38 5237 * * * 4665 2791 3082 * 1398 * * 5180 * 3835 4475 3039 5164 * * * 38
+ 0 * * * * 374 2129 4470 0 3718
+
+G 39 4543 * 6335 * * 907 5947 * 2853 * * 4824 7204 5998 4908 3294 3966 * * * 39
+ 120 * 3646 * * 1507 625 5306 0 1673
+
+T 40 4826 * * * 3592 5413 5452 * 3094 6503 * 3725 6582 5051 2222 2339 3862 4048 5244 5408 40
+ 105 * 3837 * * 1424 673 5335 0 1793
+
+K 41 4381 * * * 4758 4701 4853 * 2173 3099 * 3056 4824 3774 2778 3903 4982 6940 6940 6124 41
+ 21 * 6124 * * 950 1052 5324 0 1768
+
+N 42 4636 7171 4501 * * 3414 5244 7223 2060 * * 2820 5920 4622 1852 5176 5386 * * 6092 42
+ 56 * 4719 * * 2479 285 5370 0 1411
+
+R 43 5217 * 6335 * 5196 5774 4916 6987 2078 * 5934 4545 * 5942 1079 4195 5436 6533 * * 43
+ 1335 6211 761 0 * * 0 5372 1010 1516
+
+H 44 4683 * * * 5876 4341 4177 3161 * 1875 4110 * * 4450 5063 5259 5377 4635 * 2114 44
+ 480 * 1822 * * * 0 4582 0 3753
+
+P 45 2946 4165 5463 * * 4137 * * 2802 * * 3241 1041 * * * * * * * 45
+ 0 * * * * 385 2094 4104 0 4070
+
+K 46 2875 7110 * * 3892 4383 4527 4549 3977 4164 * 3734 4698 * 5533 4277 2898 3795 6276 2946 46
+ 0 * * * * 484 1810 5370 0 1802
+
+A 47 765 5285 * * * 2545 * 5421 * 5256 6991 * 5873 * * 4209 5057 4153 * * 47
+ 0 * * * * * 0 5418 0 1201
+
+G 48 4077 * 6649 4806 5138 2335 7189 7254 2672 * * 4339 5919 6476 3457 2500 3231 5267 * 5598 48
+ 0 * * * * 1812 484 5418 0 1201
+
+L 49 5311 6397 * * 4601 * * 1742 * 3097 * * 5157 6488 * 5362 4454 1396 * 5891 49
+ 0 * * 0 * 0 * 5410 1037 1130
+
+G 50 5249 * * * * 171 * * * * * 4656 6145 * * 6069 5901 * * * 50
+ 0 * * * * * * 5482 0 0
+
+D 51 6612 6798 399 4957 6145 * 6141 * * 5878 * 4311 * 6587 * 4043 6660 * * 6183 51
+ 0 * * * * * * 5482 0 0
+
+K 52 5339 * * 5643 3397 6305 6121 2577 3200 2714 3906 * * 6696 4441 * 3284 2539 * 7076 52
+ 18 * 6305 * * * * 5482 0 0
+
+I 53 4750 * * * 5394 * * 993 * 5211 6041 * * * * * * 1343 * * 53
+ 0 * * * * * 0 5458 0 1037
+
+T 54 * * * * 6118 * * 2788 2470 2451 3658 * * * 3707 7055 3572 2120 * * 54
+ 0 * * * * 0 * 5458 0 1037
+
+V 55 2717 4907 * * * 3264 4464 3773 * 4569 6183 * * * * * 7167 918 * * 55
+ 0 * * * * * * 5482 0 0
+
+S 56 3104 * * * * * * 5901 6108 * * * * * * 1101 2470 2281 * * 56
+ 0 * * * * * * 5482 0 0
+
+V 57 5802 6664 * * * * * 1657 * 6928 * * * 6305 * * 5857 697 * * 57
+ 17 * 6446 * * * * 5482 0 0
+
+T 58 * * * 6303 6619 5871 * * 776 3925 * 5995 * 3099 3031 * 5057 6770 * 5939 58
+ 32 * 5495 * * * 0 5462 0 1015
+
+K 59 3857 * 3935 2767 * 4289 * * 1330 * * 7413 * 6319 3479 3284 5026 6183 * 6092 59
+ 50 5545 6301 1256 783 * 0 5422 1060 1142
+
+G 60 2552 5337 * 5997 * 2263 * 3241 4035 2768 5264 * * 4656 * 3935 4027 3741 * * 60
+ 0 * * * * * 0 5399 0 1240
+
+T 61 6445 * 5263 6706 * * 5011 3974 1978 4935 5343 4529 6680 7228 2528 3391 3331 3644 * 4667 61
+ 30 * 5605 * * * 0 5399 0 1240
+
+P 62 3042 * * * 5334 5558 * 5629 3586 5015 6969 4914 1352 4393 3522 3640 5001 * * 5702 62
+ 219 4486 3380 2994 194 1565 595 5397 1216 1370
+
+E 63 5053 * 3542 2743 7382 5239 4905 4773 2681 5667 7170 3104 * 3191 2980 4836 5002 5020 * * 63
+ 307 2563 5487 2902 207 * 0 5294 1677 1690
+
+M 64 5342 4814 * * 4728 3884 5132 4968 2581 2931 3670 4840 5101 4298 4884 2939 4427 5345 * 4419 64
+ 1100 907 * 2308 325 816 1211 5279 3397 1783
+
+R 65 5306 * * 6311 * * * 5295 906 * 5810 * * 6226 1810 4762 6329 6729 * 5168 65
+ 39 6329 6139 1000 1000 1558 599 5418 1009 1319
+
+R 66 6643 * * 5970 6090 970 5224 * 2305 * * 5973 * * 4300 2709 * * * * 66
+ 0 * * * * * 0 5439 0 1251
+
+Q 67 * * 2641 2321 * 5340 6029 6712 2469 * 7209 6681 * 2109 4326 4135 4564 6377 * * 67
+ 11 7007 * 1000 1000 * 0 5439 1000 1251
+
+V 68 * 5940 * * * * * 1825 3503 3097 5001 * 5130 * * * 5108 1295 * * 68
+ 0 * * * * 1765 503 5439 0 1251
+
+L 69 * 3477 * 7002 3588 5967 3019 4973 4769 3383 4993 5696 5989 7459 3395 4680 6375 2397 * 3220 69
+ 20 6172 * 0 * 0 * 5446 1021 1163
+
+E 70 7127 * 6898 7344 5091 6795 4414 * 1591 4777 * 3600 4089 5209 2353 4557 5951 * 5387 3680 70
+ 0 * * * * * * 5486 0 0
+
+A 71 568 5722 * * * 2163 * * * 6009 * * * * * 4912 6048 5705 * * 71
+ 0 * * * * * * 5486 0 0
+
+V 72 6637 * * * 5903 6306 * 2145 * 2247 5629 * * * * * * 1202 4712 5011 72
+ 0 * * * * * * 5486 0 0
+
+V 73 * 6130 * * 5998 * 6306 996 * 3618 * * * * * * * 1417 * * 73
+ 0 * * * * * * 5486 0 0
+
+V 74 * 6048 * * * 5722 * 1970 * 3901 6209 * * * * * * 693 * 6394 74
+ 0 * * * * * * 5486 0 0
+
+R 75 5722 6637 * 3981 4790 3834 5485 * 4607 * * * * 3943 653 * 4756 * * * 75
+ 0 * * * * * * 5486 0 0
+
+Q 76 5414 5550 * 6637 5452 * 7413 6130 * 3702 5311 * * 2075 6003 3842 1209 4865 6552 * 76
+ 21 * 6130 * * * * 5486 0 0
+
+R 77 4199 * * * 5441 * * 6051 1050 5071 * 6443 5706 5278 1968 4176 6016 6384 * * 77
+ 33 5993 7248 348 2221 0 * 5465 1100 1022
+
+K 78 4549 * * * 4464 * 5384 4700 1198 * 4682 5100 * 4472 3602 4062 5158 6296 * 3090 78
+ 79 4867 5737 0 * * 0 5488 1130 1000
+
+P 79 4758 6926 * 2315 4478 4032 5500 6280 3437 6901 6106 3923 2407 4363 5688 3551 4234 5164 6810 * 79
+ 16 6462 * 0 * * 0 5466 1010 1100
+
+I 80 7295 5638 * * 4905 7378 4727 2492 4194 2731 6175 5683 6926 4033 4832 5181 3759 3483 4188 2944 80
+ 65 7219 4745 0 * 628 1502 5466 1000 1100
+
+R 81 5230 * * * * 4779 5196 6325 2744 5219 5922 3531 3970 3183 1610 4433 5190 5244 * 5938 81
+ 76 4917 5787 3163 171 801 1231 5418 1180 1228
+
+R 82 * 6111 * * 5292 * * 5068 3144 5405 6498 6863 5981 5978 556 5761 * 6695 * 4887 82
+ 9 * 7326 * * 2016 410 5446 0 1165
+
+P 83 4154 * 4501 4733 4446 5534 5271 4655 1816 3725 * 4710 3313 4703 4022 4405 5638 5230 5678 5866 83
+ 22 * 6064 * * 1016 984 5457 0 1162
+
+D 84 6669 6728 924 * * 6650 5339 5816 5262 6771 6512 2206 7241 6549 * 3531 5350 6617 * * 84
+ 9 * 7293 * * 1790 492 5466 0 1146
+
+G 85 * * 6624 4944 * 337 * * 5772 * * 4496 6535 * 5879 4723 5557 * * 5927 85
+ 0 * * * * 991 1009 5479 0 1129
+
+T 86 5575 6497 * 5717 4451 5528 5756 3452 * 4720 3469 4615 * 4376 5903 1923 2870 3404 * 4546 86
+ 29 6571 6776 0 * 0 * 5484 1003 1039
+
+R 87 5967 * * 7411 3353 5418 4413 3876 5639 4455 5986 4958 5022 5129 2800 3357 3641 3627 4181 3165 87
+ 32 * 5494 * * 0 * 5480 0 1006
+
+V 88 5988 * * * 4952 * * 1331 6202 2677 * 6705 3856 6874 * 6842 6768 2047 * 4734 88
+ 14 * 6727 * * 0 * 5438 0 1076
+
+K 89 5355 6945 * 5387 6791 6660 * 5887 1987 6609 * 4744 * 4201 1783 2878 6484 4916 * 3598 89
+ 0 * * * * 0 * 5484 0 1000
+
+F 90 4641 6048 * * 278 * 6394 * * * * 5957 * * * 5608 5196 * 6733 4844 90
+ 0 * * * * * * 5486 0 0
+
+E 91 6048 * 1662 2153 6877 4400 6515 6776 5364 5119 * 2963 6233 4528 5225 3411 6749 * * * 91
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+
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+A 128 689 6428 * * * 4816 * 6097 * * * * * * * 2041 4234 5521 * * 128
+ 0 * * * * * * 5138 0 0
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+T 129 4123 * 6000 5460 * 3186 6504 * 2963 4815 * 4656 2511 4354 3746 2287 4000 6196 * * 129
+ 0 * * * * * * 5104 0 0
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+M 130 3883 6283 5016 2985 6058 3640 5705 3939 3206 6761 4699 4334 * 5497 3671 2916 4427 4406 * 4321 130
+ 0 * * * * * * 5068 0 0
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+I 131 6876 6767 * * 3016 * * 1380 * 3965 * 4559 * 6608 * 5527 4697 1878 * 5287 131
+ 0 * * 2000 415 * * 4984 1022 0
+
+V 132 3546 * * * 3606 6514 6789 1568 * 2861 6266 6066 * * * * * 1768 5982 * 132
+ 0 * * 0 * * * 4908 0 0
+
+//
+�HHsearch 1.5
+NAME 2aaa64efe58cc449ac3f69c82cc966f0
+FAM
+FILE 2aaa64efe58cc449ac3f69c82cc966f0
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:08:35 2013
+LENG 156 match states, 156 columns in multiple alignment
+FILT 113 out of 646 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCEEEEEEECCCEEEEEEEEECHHHHHHHH
+HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9998888757789996437899999999988563199999999999999998748858999999999658808999971198899995771799999999
+99999999756999889999999999980873777689999999999685620679
+>Consensus
+mxrxxxxxxxxxxxdxxxxxxxvxkxinxlmkxGKKxxAxxixxxalxxixxxxxxnpixilxxAixnxxPxxxvxxxrxggxxyqvPvxixxxrrxxlA
+irWiixaaxxrxxxxxxxxLaxEiixaxxxxgxaikkKxexhkxAxaNRaxxxxRw
+>2aaa64efe58cc449ac3f69c82cc966f0
+MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLA
+LRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW
+>gi|87043010|ref|YP_492624.1| ribosomal protein S7 [Dictyostelium citrinum]gi|122074018|sp|Q2LCR8.1|RT07_DICCI RecName: Full=Ribosomal protein S7, mitochondrial; Short=MRP-S7; Short=S7mtgi|84682110|gb|ABC60375.1| ribosomal protein S7 [Dictyostelium citrinum]
+----------------------EKRLINAFMRKGNYIKAERIYFTVLNRLTTLGIQNPYKFLRETLIKMTPIMGVVKKKRGVKEKIYPKYLEPRMGEKYA
+IKWLLKKLEKSKGDLLINNIVDEFLKASKDQGEVLKEKWALY--------------
+>gi|119623074|gb|EAX02669.1| hCG18724, isoform CRA_a [Homo sapiens]
+----------------------------------------------------ISLQDYIAVkekytKQEPSAGSGecqhqmwPWEDSTYIEQAETVRQQD
+VDMSPLYHVNQAIWLLYTGTSEaafQNIKTITEYLADKLISIAKNSSnyYAIE-KNNLELMAKSNC-------
+>gi|336378070|gb|EGO19229.1| hypothetical protein SERLADRAFT_479598 [Serpula lacrymans var. lacrymans S7.9]
+-----------------PEDPLLQYLTSALLHHGHRAKAARMTSLTLLHIHAFTRAPPLPILREAIMAAAPAVRCMSHKHGSKNVAKPIALGEKQRVRTA
+VQMIIKASEKKNGKTIAERLAREMIAVVQGDSRALEERETIHRFAMVNRGNTLL--
+>gi|11465896|ref|NP_066445.1| ribosomal protein S7 [Ochromonas danica]gi|10505229|gb|AAG18411.1|AF287134_36 ribosomal protein S7 [Ochromonas danica]
+---------------------IYKNLLGNIIKRGKKVKAKLILNSSIEIVSSRLNSNSDILLQRLAQKIGSLVELRKIKIRKNVHIVPFPVKSYRRKFLF
+SKELVSYIFSdKKKTNSVEKLNFNIFSYLIKKGSNYNKKDATLKEVIINRSNIHYRW
+>gi|324309737|gb|ADY18518.1| ribosomal protein S7 [Phaeodactylum tricornutum]
+---------------------IKNKLTNHLTTSGKKTKGEKILFKSVKTIQRQSRKQVNSLIKLAIFSSSPVFKLHiltqKKRKKKKSKEIPAFmQSPQA
+RVSLSIKLIILSIRKRKLNNFSIGLGKEILLNANCKGETIKIKNKLQEQVFAKKHLLkYYRW
+>gi|319412297|gb|ADV41834.1| ribosomal protein S7 [Bigelowiella natans]
+-------------HDPLYKSWFFRKIIGGLPLKS-RSRNKALFRRALARLRHEhHSLDTPFALVWSIHKIRPLFWIRTVKKGKREYKIPFKLTPRGQYRR
+ALYWVVKSFRGRTEPRLETRLFLELKDLLDGKSKVFSWRDTLYNEVGRNRHNANFRW
+>gi|301500888|ref|YP_003795300.1| ribosomal protein S7 [Chromera velia]gi|300069434|gb|ADJ66542.1| ribosomal protein S7 [Chromera velia]
+------------------------FMVNRIQRRGCNSLARKIWSKTLLKVEKQLNRSIKDILEEIFRFLIPPVGITFLKKANQVTELPVIQPYYRAVPMA
+INWILEAARKKRGVKFVNALVTEFVDLYNFTGAASSQRNKYLR-------------
+>gi|11467069|ref|NP_042545.1| ribosomal protein S7 [Acanthamoeba castellanii]gi|1173306|sp|P46756.1|RT07_ACACA RecName: Full=Ribosomal protein S7, mitochondrialgi|562050|gb|AAD11838.1| ribosomal protein S7 [Acanthamoeba castellanii]
+---------------------------QGLTSRGKKKLSISIFKTLFLLLKFKYKRKFIDCYLQFLEKVRPLIYYKVMFIGGKKYKIPTLMPISKSYSTS
+IRWLINNADKR---DIATSLFSQINISLKNEGSLIKYRKEYHSASFENKSYIRF--
+>gi|301353213|ref|YP_003795210.1| hypothetical protein PROLAC_032 [Proteromonas lacertae]gi|301353237|ref|YP_003795234.1| hypothetical protein PROLAC_057 [Proteromonas lacertae]gi|290573161|gb|ADD46348.1| hypothetical protein PROLAC_032 [Proteromonas lacertae]gi|290573185|gb|ADD46372.1| hypothetical protein PROLAC_057 [Proteromonas lacertae]
+--------------------YILILFLNYLNKTGNKVLAESIIYRLLFLLKKTsltknsilfsQQESSLCILNQAFINVMPSFKLILKNkkeytvvsfqd
+likdhsillnkqqftdsknsnnknsfdLLNIITVIPVPLNLNTRCLKGCTFLFKSAVLhKNSFDFASKLYEELLLAYYSCGRSVYLKNEIDKIACIHRSN
+IKF--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 4131 0 0
+
+A 2 3044 * * 4596 * 4973 * * * * * 4185 3334 * 4004 763 * * * * 2
+ 0 * * * * * * 4131 0 0
+
+R 3 * * * * * * * * 2883 * * * * * 383 4185 4544 * * * 3
+ 0 * * * * * * 4131 0 0
+
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+ 200 * 2947 * * * * 4131 0 0
+
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+ 163 3228 * 212 2869 0 * 3904 1247 1210
+
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+ 0 * * * * * * 4131 0 0
+
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+ 198 5069 3343 1000 1000 * * 4131 1000 0
+
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+ 0 * * * * 0 * 3936 0 1165
+
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+ 103 3854 * 0 * * * 4260 1118 0
+
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+ 59 * 4638 * * * * 4260 0 0
+
+Q 11 4764 * * 3314 4967 3399 5094 3293 2997 5408 * 3599 5034 4178 4108 4632 3555 3263 * * 11
+ 0 * * * * * 0 4214 0 1044
+
+L 12 3494 4842 * 5074 5084 5159 * 2047 * 1984 * * 5073 * 4760 4768 4351 3191 * 4938 12
+ 0 * * 3235 162 * 0 4387 1109 1044
+
+Q 13 3802 * * 4231 4248 * * 4259 2593 1789 4082 * 4098 5620 * 3916 * 3170 * * 13
+ 296 5307 2642 0 * 0 * 4500 1000 1044
+
+P 14 3237 * * 5760 5653 5542 4426 * 4769 * * 3427 1637 4461 * 4070 2273 * * 5350 14
+ 67 4468 * 2193 356 510 1748 5089 1057 1312
+
+D 15 * 4142 794 4100 * 6720 4624 4902 5676 4318 5528 * 4105 * * 4280 * * * 5396 15
+ 0 * * * * * 0 5316 0 1043
+
+L 16 4840 * 4455 4706 * 5871 * 6321 * 6591 * 5649 1196 5011 5539 1803 6063 5019 * * 16
+ 0 * * * * * 0 5372 0 1043
+
+V 17 * * 4747 4779 3705 5871 * 2170 2750 2739 5239 * 4975 3901 6163 * 4557 2940 * * 17
+ 117 5839 4048 0 * * 0 5372 1000 1043
+
+Y 18 3875 5988 * * 1601 * * * * 4713 * 5330 4555 4996 5655 5617 * * * 1288 18
+ 28 5710 * 1750 509 636 1487 5397 1109 1250
+
+G 19 * 5638 4798 3101 6089 3690 * * 3696 * * 2064 * 3476 2856 3834 * 6029 * 3246 19
+ 22 6065 * 0 * * 0 5668 1000 1043
+
+D 20 6145 4831 1303 * * 5340 4859 4473 4502 5612 5096 4065 * 6277 6301 1932 * * * * 20
+ 0 * * * * * 0 5893 0 1043
+
+V 21 4463 * 6396 3461 5886 * 5676 5528 3861 3941 6377 4850 1565 5802 4499 4472 4880 4445 5256 4013 21
+ 18 6343 * 3170 170 * 0 6103 1006 1043
+
+L 22 6697 * 6655 5793 3628 * * 2080 6635 1555 4939 * * 5839 6796 6899 4339 2578 * 6615 22
+ 0 * * * * 0 * 6419 0 1043
+
+V 23 5127 * * 4451 4994 * * 2391 4742 2244 5586 * * 6754 * 6655 6374 1444 * 4808 23
+ 19 * 6231 * * * * 6468 0 0
+
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+ 20 6172 * 1000 1000 0 * 6505 1010 1020
+
+A 25 7567 * * 6524 4741 * 4419 7268 1314 4402 4184 5018 * 4422 2330 5137 4288 * * 4936 25
+ 0 * * * * * * 6588 0 0
+
+F 26 7042 6680 * * 1477 * * 3277 * 1368 4517 * * * * * 6983 3861 * 6343 26
+ 0 * * * * * * 6627 0 0
+
+I 27 4866 * * 5703 * 6767 * 1433 5170 3209 5900 * * * * 5683 2623 2106 * * 27
+ 0 * * * * * * 6627 0 0
+
+N 28 6503 6343 5983 * * 3499 6734 * 4532 6100 * 751 * 5408 3734 3617 5358 7283 * * 28
+ 0 * * * * * * 6703 0 0
+
+K 29 4783 4421 * * 4046 4967 3420 4602 3669 2841 3435 4055 * 5343 2939 4598 5169 3967 * 5013 29
+ 0 * * * * * * 6703 0 0
+
+I 30 * 4538 * * 4032 * * 2155 * 1022 3338 * * * * * * 3643 * * 30
+ 0 * * * * * * 6703 0 0
+
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+ 0 * * * * * * 6713 0 0
+
+R 32 * * 6890 * 5831 * 4456 4143 1354 3684 5593 5434 * 6006 2341 4294 4630 4402 7070 * 32
+ 47 4977 * 3014 191 * * 6713 1148 0
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+ 103 3859 * 2525 275 * * 6713 1399 0
+
+G 34 * * * * * 47 * * * * * * * * * 5837 * * 6083 * 34
+ 56 5618 5837 1585 585 * * 6748 1073 0
+
+K 35 6395 6236 4643 5263 * * 4642 * 620 6136 * 2956 * 6645 4333 6017 * * * * 35
+ 0 * * * * 0 * 6693 0 1052
+
+K 36 * * * * 5289 6722 * * 529 6649 * 6250 * 5360 2530 * * 5977 * 4812 36
+ 0 * * * * * * 6748 0 0
+
+N 37 2946 * 6997 3671 6125 4700 4649 3992 4237 5628 * 4264 * 3441 4577 2079 3384 4768 * * 37
+ 0 * * * * * * 6748 0 0
+
+L 38 5865 * * * * * 6231 4424 1687 1891 6125 5219 * 7264 3171 5612 4498 3068 * * 38
+ 30 5618 * 3585 126 * * 6748 1073 0
+
+A 39 539 6231 * * * 5510 * 5562 * 4972 * 5837 * * * 2651 5419 5410 * * 39
+ 0 * * * * * * 6748 0 0
+
+A 40 4318 * * 1869 5054 * 4694 3504 4298 5954 6822 5545 * 3184 2844 5014 5109 5485 5618 3834 40
+ 9 * 7319 * * * * 6748 0 0
+
+R 41 4447 * * 5321 * 4342 6810 6025 1655 5176 6781 3369 * 4939 2230 3246 4457 * * 7022 41
+ 0 * * * * * 0 6753 0 1000
+
+I 42 6226 * * * 5094 * 5443 1130 * 2169 4790 4831 * * * 5352 5034 3334 * 5076 42
+ 0 * * * * * 0 6753 0 1000
+
+F 43 * 4957 * * 2613 * * 3194 6227 1938 3426 * 6032 * * * 5141 2226 5096 4601 43
+ 0 * * * * * 0 6719 0 1000
+
+Y 44 5152 6087 5404 3998 3877 * 5014 5177 3506 4066 5237 3348 * 5308 3975 3334 4569 6482 * 2116 44
+ 0 * * * * * 0 6719 0 1000
+
+D 45 4722 * 3335 3492 * 3993 5332 5565 2204 4778 6818 3331 * 4248 2991 4033 4667 6845 * 5963 45
+ 0 * * * * * 0 6719 0 1000
+
+A 46 1335 * * * * * * 3743 * 3285 5065 6016 * * * 2883 2639 3557 * * 46
+ 0 * * * * * 0 6719 0 1000
+
+C 47 * 4383 * * 1856 7127 * 3504 * 1337 3062 * * * * * * 4230 * 6410 47
+ 12 * 6870 * * 0 * 6719 0 1000
+
+K 48 4639 * 3573 2462 4335 7491 5018 4540 3218 2912 * 3627 * 4737 4163 3883 5937 5988 * 4295 48
+ 0 * * 0 * 0 * 6706 1000 1000
+
+I 49 5622 6958 7384 4200 4823 7130 3663 2538 3568 2295 5458 3872 * 6588 4580 4371 4733 4653 * 4044 49
+ 0 * * * * * * 6714 0 0
+
+I 50 4824 * * * 5980 * * 1204 * 1635 4669 * * * * * * 2705 * * 50
+ 64 5177 5998 2778 227 * * 6714 1132 0
+
+Q 51 3988 * 5077 3178 5715 6029 3441 7484 1600 5927 * 4647 * 3199 4054 3730 * * * 4873 51
+ 56 5247 6419 3231 162 0 * 6716 1236 1056
+
+E 52 4540 5980 5060 3341 5470 6144 4089 5846 1966 3959 6775 5366 5647 3677 3343 4327 3756 5291 * * 52
+ 35 7398 5788 1585 585 0 * 6698 1000 1003
+
+K 53 3994 * 4654 3336 6586 5791 * 3186 1975 4222 4936 4621 * 3960 3556 5397 4178 5129 * 5496 53
+ 339 2486 5009 3701 115 1328 733 6781 2200 1096
+
+T 54 5459 * 5056 7385 5985 4929 5789 3321 3584 3449 6971 5342 7160 4147 6557 4582 1632 4911 * 3394 54
+ 65 4690 7526 1581 587 1214 813 6748 1230 1271
+
+G 55 * * * 3287 * 2728 5871 4853 2660 5852 * 2568 3430 4784 3091 4642 5453 4591 * * 55
+ 63 4557 * 3902 100 1125 885 6775 1287 1178
+
+Q 56 4131 * 7367 3034 * 4912 * 3988 2258 2953 6952 5060 * 2800 3552 4657 5664 4208 * * 56
+ 23 5956 * 2950 200 1734 516 6764 1085 1064
+
+E 57 7536 * 1879 6080 * 6920 6014 5861 4780 * * 1331 3375 4969 5057 4598 6175 5666 * * 57
+ 0 * * * * * 0 6744 0 1023
+
+P 58 3350 * * 5941 6157 5912 * 5130 6096 * * * 717 * * 3511 5355 4077 * 4959 58
+ 9 7411 * 0 * * 0 6744 1006 1023
+
+L 59 * * 5322 5550 4386 * * 1773 5132 1675 4963 5496 5825 * 7009 6586 5435 3336 * 4073 59
+ 0 * * * * * 0 6744 0 1023
+
+K 60 4669 5563 3589 3322 5135 7539 4890 3998 3206 5067 6567 7366 3766 2616 4898 3550 4633 4027 * 6133 60
+ 21 * 6113 * * 0 * 6740 0 1023
+
+V 61 4911 6203 * * 4050 * 6936 1800 6276 2438 7637 * * 6048 6878 * 5191 1723 * 4604 61
+ 24 5897 * 2322 322 * 0 6770 1074 1050
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+F 62 6017 * * * 1844 * * 2882 5897 1147 * * 6159 * * * * 4245 6135 5576 62
+ 0 * * * * * 0 6770 0 1050
+
+K 63 * * 7021 3599 5338 * 2890 4638 2906 3783 6310 3964 6878 3532 3635 7085 4051 3038 6175 4366 63
+ 0 * * * * 0 * 6770 0 1050
+
+Q 64 5888 * 3661 2932 5533 5941 5732 5575 2598 3657 5454 4906 6936 2481 4080 4793 4206 5621 5836 5629 64
+ 0 * * * * * * 6768 0 0
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+A 65 465 6475 * * 5372 4317 * 4840 * 6007 * * 5913 * 6183 3952 6635 4866 * * 65
+ 0 * * * * * * 6768 0 0
+
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+ 0 * * * * * * 6768 0 0
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+ 0 * * * * * * 6768 0 0
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+N 68 5630 * 5245 4762 6321 5336 * * 2471 5167 6051 854 * 5480 5588 4772 6755 * * 6170 68
+ 0 * * * * * * 6768 0 0
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+L 101 6184 5390 * * 4801 * * 1240 * 1922 2764 7158 * * * 5351 6049 5698 5261 * 101
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+Q 106 4725 * 3212 2228 * 5432 * 6288 2144 5501 7626 4499 * 3556 5532 3894 3219 6384 6161 * 106
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+N 109 5746 * 4699 4230 5291 * 6470 5472 2189 4271 6035 3838 * 7487 1505 4651 6288 5414 6810 5008 109
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+Q 110 5733 * 5031 2772 6792 4658 * 6256 1614 3666 * 3498 * 3902 4168 3587 6550 5357 7035 * 110
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+
+R 111 7512 * * 6671 6661 5600 6760 6180 1417 5814 * 4597 * 4840 1218 7540 6897 6504 * 6927 111
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+P 112 4166 * 6111 7169 5974 5175 5385 6582 2368 * * 2559 3220 5888 3763 2340 4164 5039 * * 112
+ 148 3544 6400 1304 749 2122 376 6704 1595 1157
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+E 113 5847 * 3461 2743 6345 2111 4585 5116 3215 5024 * 5696 4726 * 3831 3233 4896 6945 * 6132 113
+ 196 3044 7436 1429 670 * 0 6685 1816 1188
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+R 114 6915 * 5608 4018 6230 6441 5706 4728 1757 4661 4527 3416 5737 4848 2875 3719 4220 4799 * * 114
+ 74 4322 * 574 1608 1669 545 6696 1316 1228
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+R 115 6998 6612 3726 5013 5015 4814 5236 * 3769 4519 6882 3385 3531 5087 3492 2313 2776 * * 6777 115
+ 16 6497 * 1714 524 2337 318 6766 1061 1134
+
+A 116 3818 * * * 1738 * * 2381 5434 2895 2443 * * * * 5266 5000 5528 * 5876 116
+ 0 * * * * 987 1013 6717 0 1093
+
+A 117 2357 6973 4755 4055 * 4629 4651 4044 4425 6409 6982 * 3367 5390 5986 2920 4985 3403 4123 4627 117
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+D 126 2587 * 1787 3538 * 6066 * 6231 4899 3203 6172 3322 * 3860 * 3379 6856 * * * 126
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+
+A 127 765 * * 6202 * * * 3921 * 3820 * 6469 * * * 4043 4241 3050 * 6016 127
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+A 128 2332 * * * 3960 * 4639 4095 5302 2756 * * * 5547 * 2194 6037 4046 * 2743 128
+ 10 7184 * 0 * * * 6748 1000 0
+
+E 129 4724 5979 4280 3663 6604 * 4201 6016 1999 4900 * 2200 * 3366 4143 5003 5162 * * 5524 129
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+G 130 6742 6469 5034 5350 6344 2035 5575 5292 2772 5294 * 1603 * 6206 5223 4053 5658 * * * 130
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+K 138 6568 6548 * * 6638 * * * 756 6536 * * * 6104 1669 * 6491 6160 * 6403 138
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+
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+
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+A 147 1469 * 7217 4890 * 5507 6228 4640 * 4378 6564 4713 5851 4513 4737 2234 3908 4371 * * 147
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+N 148 3770 * * * 6172 6541 4627 7081 4975 7112 * 508 * 6255 * 4129 6663 5704 * 6278 148
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+
+R 149 * 5671 * * * * 6962 * 2238 6209 * 6530 * 4559 543 7135 * * * * 149
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+
+A 150 1232 * * * * 4244 4383 4353 5529 5397 6800 6112 5034 6540 4361 2583 4289 4699 * 6753 150
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+Y 151 * * * * 1749 * 6108 5924 * 3089 * 2054 * * 5310 5397 * * * 1920 151
+ 0 * * * * * * 6310 0 0
+
+A 152 1377 * * * 5464 * 5387 2359 5980 3802 5320 * * * 6673 3116 4823 3561 * 5997 152
+ 44 5062 * 2179 360 * * 6199 1089 0
+
+H 153 6571 * * * * * 1154 5500 3388 5575 * 2894 5167 4904 3297 6382 * * * 3441 153
+ 0 * * * * * * 6126 0 0
+
+Y 154 6698 6328 * * 1970 * * 5184 5406 3194 6313 * 6392 6177 5802 4546 * 4783 * 1228 154
+ 21 6099 * 1000 1000 * * 6071 1003 0
+
+R 155 6406 * * * * 4878 6132 * 3791 * * 4686 * * 271 * * * * * 155
+ 39 5218 * 1000 1000 * * 5570 1050 0
+
+W 156 4632 * * * 2910 * * 4545 5752 6272 * * * 5202 * * * 5099 561 5802 156
+ 0 * * 0 * * * 5499 0 0
+
+//
+�HHsearch 1.5
+NAME 2b78356947507e56ed56d054e1215b8c
+FAM
+FILE 2b78356947507e56ed56d054e1215b8c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:10:25 2013
+LENG 120 match states, 120 columns in multiple alignment
+FILT 108 out of 1047 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCEEECCHHHHHHHHHCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHCCCCCCCEEEEEECCCEEEEEEEC
+CCCCHHHHHHHHHHHHCCCC
+>ss_conf PSIPRED confidence values
+9977899839938899999985699299999899986899999999999999773088689999976668999998499853389999899178999953
+88999999999998655899
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxvvxfxxxxCxxCxxxxxxlxxxxxxxxxxxxxixxxxxdxxxxxxxxxxxxixxxPxxxxxxxgxxxxxxxxx
+gxxxxxxxxxxixxxxxxxx
+>2b78356947507e56ed56d054e1215b8c
+DAPEEEDHVLVLRKSNFAEALAAHKYLLVEFYAPWCGHCKALAPEYAKAAGKLKAEGSEIRLAKVDATEESDLAQQYGVRGYPTIKFFRNGDTASPKEYT
+AGREADDIVNWLKKRTGPAA
+>gi|239636570|ref|ZP_04677572.1| thioredoxin [Staphylococcus warneri L37603]gi|239597925|gb|EEQ80420.1| thioredoxin [Staphylococcus warneri L37603]
+-----------SIEIDDVTENFGEEKHLIFGYTPTCGTCKVSE----RMLDIANEILK-LPVKKIDMNFHPKFSETHQIMSVPVLMLMNKD---------
+--------------------
+>gi|71020229|ref|XP_760345.1| hypothetical protein UM04198.1 [Ustilago maydis 521]gi|46099969|gb|EAK85202.1| hypothetical protein UM04198.1 [Ustilago maydis 521]
+----SSQGFIDVDTNE-fSQII-QVPrdyAVTALLTTttGGikC-pPCQVFQPE--feK-lAQQWNknkSVKSKNVFI--kaEFSRAQGVFARYQLQHAP
+VLYTFpAPtASNgspd--HVSFDfneRSFSAPDVADHLNKL-lN---
+>gi|313898805|ref|ZP_07832339.1| putative bacteriocin transport accessory protein [Clostridium sp. HGF2]gi|312956387|gb|EFR38021.1| putative bacteriocin transport accessory protein [Clostridium sp. HGF2]
+---DEPGRVENITVAKMQEMVDKKESFAIVFTQTTCSHCIEFKKMLDGYLL-----DHNVVLYDVVLDEAPASQRKSDLNtirktfpgmnETPSLYYVKE
+GK--LENLLEngdDGLTEEKFDSWVQRY-----
+>gi|256421245|ref|YP_003121898.1| alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Chitinophaga pinensis DSM 2588]gi|256036153|gb|ACU59697.1| alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Chitinophaga pinensis DSM 2588]
+DKPAPGFALRDLNGKKWSLKNLKGKVVVLNFWFVTCPPCIQEMPELNELTKDYQSKEVVFLAMTYNDKEevtdfledhtfdynllvdSHDTDQAYNVASW
+PVSFVIdKEGIVKFVVKGGQATIRQQLTKAIEQVL----
+>gi|317121579|ref|YP_004101582.1| hypothetical protein Tmar_0740 [Thermaerobacter marianensis DSM 12885]gi|315591559|gb|ADU50855.1| hypothetical protein Tmar_0740 [Thermaerobacter marianensis DSM 12885]
+------------TVADLERALRDPQPVMIFKHSTACPISARAYRAFRQFVARQpAAARYYLVQVIEQRPLSNEIARRLGVPhASPQVLLWHRGA-VRWHA
+SHGAITERALATALAAVRAP--
+>gi|302348009|ref|YP_003815647.1| Protein-disulfide oxidoreductase [Acidilobus saccharovorans 345-15]gi|302328421|gb|ADL18616.1| Protein-disulfide oxidoreductase [Acidilobus saccharovorans 345-15]
+------------LIKELKDTLAymVSPVTVDLFIDdASrCETCEDAYKLVKTIADASPVRDGKKMLQLRVFSKskpeDLEEFKRQNVERVPTVTLLGGV-
+----IRYTGTPAGEEIRGFIETIMR---
+>gi|70726027|ref|YP_252941.1| hypothetical protein SH1026 [Staphylococcus haemolyticus JCSC1435]gi|68446751|dbj|BAE04335.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
+------------SDDRINQLKDSSYSKVLVISEDWCGDAMMNLPILKRISES-----LQLEVRVFHRDEDTNLIDQYltnGtARSIPIFIFMNDQF--EQ
+VSVWGPRA-REAQEFVTQ------
+>gi|221059209|ref|XP_002260250.1| hypothetical protein, conserved in Plasmodium species [Plasmodium knowlesi strain H]gi|193810323|emb|CAQ41517.1| hypothetical protein, conserved in Plasmodium species [Plasmodium knowlesi strain H]
+------------NEEEYKKLFeeKNDILYIVDVYTKWCGPCLFTFEIINKIYKANFTFTESVKIVAV-CAQNIASLKNYDNNSKPFYIILKNGE--IIRQ
+IQGCNTPH-IFALIDEHL----
+>gi|123448520|ref|XP_001312989.1| hypothetical protein [Trichomonas vaginalis G3]gi|121894856|gb|EAY00060.1| hypothetical protein TVAG_196200 [Trichomonas vaginalis G3]
+DRREQVDVVIEMTDQNFQFKTSDGRPWVILVYQHYYDY-QSNKPFLEDLFQ---KTGLLFGIARMQISQSPKIVEKFGIRYSPQLVVYDSKT-NNHFLFN
+GEMKLGKVINFATRKFGADV
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+D 1 3370 * 724 * * * * * * * * * * * * 2393 * * 3219 * 1
+ 0 * * * * * * 5211 0 0
+
+A 2 2648 * 4501 3026 * 3743 3492 * 2910 4774 * 3065 3601 4560 4367 * 4392 * * * 2
+ 0 * * * * * * 7730 0 0
+
+P 3 3228 * * * 3857 3652 * 3618 4832 3087 4456 4723 2796 * 4449 * 3131 * * 3022 3
+ 0 * * * * * * 7937 0 0
+
+E 4 2934 * 2157 2602 4877 4058 * 4698 4998 5067 5000 3913 3977 4950 * 4091 * * * 4861 4
+ 0 * * * * * * 8298 0 0
+
+E 5 5272 * 5071 2174 * 3400 5207 5061 5282 5327 * 5215 3557 3101 5206 2505 4082 5069 * * 5
+ 52 4832 * 0 * * * 8662 1107 0
+
+E 6 5308 * 3064 2684 * 4123 * 5228 3553 * * 3162 3311 4167 5014 2967 5457 4167 * 5327 6
+ 0 * * * * * * 8823 0 0
+
+D 7 5608 * 2583 3284 4771 2614 4751 4918 3398 * * 4611 4284 4566 * 2540 5913 5510 * * 7
+ 23 5956 * 3907 100 * * 9585 1000 0
+
+H 8 4893 * 3162 2984 5743 3668 4908 5911 3094 * 5784 3282 6031 4883 3308 * 3713 3888 * 4353 8
+ 81 4661 6022 551 1656 * * 9740 1262 0
+
+V 9 5631 6027 * 5051 4501 5978 * 2826 5019 2456 4013 6087 5941 5462 5907 6036 * 1566 * 4842 9
+ 0 * * 0 * 0 * 9885 1057 1057
+
+L 10 4019 * 5056 4090 * 5499 4104 3027 4048 3493 * 6035 * 4561 3348 * 3173 2424 * 4499 10
+ 0 * * * * * * 9960 0 0
+
+V 11 3448 * 2894 2083 5897 * * 5231 4544 4132 4866 4565 4379 * 5948 4080 3718 3278 * 6004 11
+ 22 6072 * 0 * * * 10060 1000 0
+
+L 12 6058 * * * 4063 * * 2296 4609 1694 4554 5193 * 5080 6326 * 4774 2502 4939 6171 12
+ 17 6434 * 1000 1000 * * 10229 1040 0
+
+R 13 4399 5297 2858 5985 6222 4167 6152 * 6200 6065 * 2658 * 5323 6734 2488 1971 5345 * 6506 13
+ 15 6557 * 2807 222 * * 10438 1000 0
+
+K 14 3774 5904 2256 2980 * 3586 6504 4689 6815 5286 5510 4786 4126 3691 3862 4456 4886 5005 6271 5545 14
+ 13 * 6827 * * * * 10536 0 0
+
+S 15 3185 * 2623 2794 * 4458 6317 6168 3291 4737 * 4130 4833 3108 4445 4005 4858 6547 * 6586 15
+ 18 6324 * 1000 1000 * 0 10535 1015 1000
+
+N 16 2962 * 3212 2862 * 4262 6545 6379 3754 5270 * 2666 5346 4505 4850 3662 3344 6257 * * 16
+ 0 * * * * * 0 10535 0 1234
+
+F 17 4063 * * 5974 1637 * * 3577 6568 2481 5429 6593 * 5476 6365 6477 * 3917 4509 2839 17
+ 13 6772 * 0 * 936 1067 10536 1000 1234
+
+A 18 3392 * 2926 2482 * 6547 5509 4553 2802 4909 * 3502 6320 4116 4445 3906 4416 6176 * 6574 18
+ 66 4885 6526 0 * * 0 10670 1506 1000
+
+E 19 3487 * 3558 2330 5485 4787 6406 5318 3009 4399 5554 4804 6665 3730 3921 3759 4970 4448 * * 19
+ 17 6406 * 0 * * 0 10681 1030 1215
+
+A 20 2554 * 6485 5599 3604 6260 * 3301 4771 2426 4384 6583 * 5662 4119 4928 3712 3340 5346 6599 20
+ 0 * * * * * 0 10681 0 1215
+
+L 21 3619 6496 6424 * 5077 * * 2424 3551 2432 4993 5246 * 4957 5037 4418 3957 2595 * 6371 21
+ 168 3351 6424 1619 568 1006 994 10711 2809 1215
+
+A 22 2950 6783 3644 3550 6762 4357 4984 * 2757 4556 * 3988 * 3240 3962 3489 4551 6760 5557 5582 22
+ 113 3728 * 1734 516 * 0 10683 2579 1236
+
+A 23 4014 * 3564 3053 6052 3171 * * 2977 5566 * 3821 6656 3310 3626 2813 5127 5298 * * 23
+ 25 5845 * 1228 803 0 * 10779 1453 1236
+
+H 24 5836 5755 3648 4450 5067 1978 4477 6623 3450 6517 * 3055 3582 5631 6854 3113 5057 * * 5721 24
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+
+K 25 4911 6650 3413 3604 * 4367 5696 6692 2013 5644 6737 5427 3608 4055 2694 4742 5000 5954 * 5548 25
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+
+Y 26 4206 7022 4706 5684 6740 5788 6420 5053 4018 3774 * 4633 2309 6607 4921 3967 4021 2582 6691 3495 26
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+
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+
+L 28 4579 5669 * * 2903 6706 * 2850 * 2029 5085 * * * * * 6359 1518 * 5600 28
+ 11 * 7074 * * * 0 10909 0 1107
+
+V 29 4584 6558 6350 * 6263 * * 2007 * 1820 5648 * * * * * 5743 1626 * 5163 29
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+
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+
+F 31 6780 5801 * * 1042 6626 6321 3089 5843 3542 6396 * * * * 6876 * 2687 6394 4153 31
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+
+Y 32 6759 6445 * 5533 2827 3294 3525 6368 5770 5742 * 6482 * 6944 5771 3971 3326 4913 2886 2256 32
+ 72 4662 6719 346 2229 * 0 10959 1648 1000
+
+A 33 2481 5735 3287 5223 6687 3455 5526 * 3956 4347 6634 4036 * 4769 4643 2523 3700 5790 6598 6707 33
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+
+P 34 4083 * 3255 2973 4966 6507 5710 * 4757 5691 6905 4804 2315 5033 4553 2903 3728 4493 * 5748 34
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+C 36 5678 559 4473 6282 5669 6321 5244 * * * * 6515 * 5633 6746 3095 6644 6832 * 6794 36
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+
+G 37 3785 * 5064 3249 5595 3164 5102 6971 4020 4931 5674 * 2250 4404 4030 3099 6276 4955 * 5125 37
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+
+H 38 3711 * 3739 4249 5229 6962 3886 5043 4154 5077 4969 3902 2665 5109 5083 4708 4252 4191 5237 3464 38
+ 23 * 5955 * * * * 10964 0 0
+
+C 39 4236 559 6260 6507 6392 * * * 5606 * * * * 6523 6717 2769 5929 5678 * 6824 39
+ 0 * * 0 * 0 * 10955 1057 1331
+
+K 40 4364 6433 5682 3600 6532 5713 4345 3277 2870 3780 4760 5841 6741 3442 2979 4828 5283 3750 * 5142 40
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+
+A 41 2609 6321 4040 3149 6819 4624 5141 5199 3115 4387 4500 4587 * 3876 3179 4905 4132 5201 * * 41
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+
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+P 44 3643 6539 3802 3036 6543 5889 6276 5569 3208 5647 * 4806 1918 4728 4337 3963 4421 5186 * * 44
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+E 45 3390 * 4402 3284 5191 3924 4522 3807 3717 4492 4836 4804 * 4834 4807 4059 3542 3050 * 5813 45
+ 16 6523 * 4700 57 * * 10964 1000 0
+
+Y 46 5523 * * * 2544 * * 3163 * 1431 4531 6394 * * * * 5618 2629 4446 4597 46
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+
+A 47 4038 7008 3596 2518 4599 5027 * 5168 2672 4057 6727 4305 5645 4407 3997 3839 5271 4242 6450 7062 47
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+K 48 3923 * 3327 2798 7056 4244 5806 5101 3047 5579 * 3594 4539 3392 3337 4609 4400 5636 * 6276 48
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+
+A 49 3327 * 4903 6793 3864 6725 6501 2413 * 1954 5188 5685 * 5079 5874 4634 5786 3234 5659 4474 49
+ 27 6662 6890 2322 322 * 0 10946 1000 1429
+
+A 50 2337 6594 7047 4107 5016 4893 5662 4657 4240 3480 7006 4421 4314 5009 5104 3722 5269 3597 * 3179 50
+ 11 7104 * 1000 1000 1067 936 10938 1057 1606
+
+G 51 3804 * 3822 2664 * 4471 4968 * 2771 7176 * 4162 3776 3476 3365 3849 4259 5475 * 6707 51
+ 206 * 2911 * * * 0 10950 0 1215
+
+K 52 3368 * 3389 3021 5593 6460 * 4506 3004 4467 5643 5449 6482 3411 4705 3676 3716 3888 * 5049 52
+ 174 6405 3297 2807 222 3153 172 10698 1001 4058
+
+L 53 4017 * * * 2470 6386 5511 4413 * 2481 4636 6388 6404 5386 4434 4751 6114 3510 6145 2251 53
+ 209 * 2889 * * 3333 151 10608 0 5140
+
+K 54 5292 * 3604 3669 * 5944 4591 * 2376 4618 * 5182 3229 3729 3381 3672 4481 3625 * 6303 54
+ 382 5243 2277 1776 498 1932 438 10449 1227 6269
+
+A 55 3281 * 3290 2974 5135 3686 5033 * 2972 4172 5749 4193 5231 3857 4323 4008 * 4909 * 4887 55
+ 236 5077 3044 1277 768 3973 95 10309 1474 7025
+
+E 56 3389 * 3398 4571 5021 4276 5933 4395 3001 3556 * 4369 5885 4301 4283 3497 4340 6036 4832 4170 56
+ 194 6179 3155 0 * 2059 396 10147 1000 7571
+
+G 57 5221 * 2866 3409 5711 2252 4844 5848 5737 4499 * 2508 3849 6575 5066 4871 4323 * * 5154 57
+ 159 4008 4557 1056 946 438 1932 10219 1653 7229
+
+S 58 5311 6452 3222 4737 5037 2860 4975 4004 3753 3741 * 4479 3400 5648 5008 3227 4444 4286 * 6284 58
+ 13 6758 * 1585 585 1034 967 10753 1242 3986
+
+E 59 3708 * 3204 3888 * 4534 4303 6640 2724 5096 5528 3199 6428 4169 3304 6481 4331 4306 6592 4568 59
+ 16 6481 * 0 * 0 * 10894 1035 2557
+
+I 60 5323 5113 * * 3128 5487 * 2164 6371 2408 5655 * * * 6874 6515 4550 2086 5862 4290 60
+ 0 * * * * * * 10964 0 0
+
+R 61 3820 6673 4755 4142 6983 4405 6668 3221 2858 3261 6371 4254 6515 5244 3928 5242 3916 3106 * 4835 61
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+
+L 62 3963 6673 * * 2225 4643 6523 2828 6764 2853 4288 6626 * * * 4518 5849 2573 5677 3990 62
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+
+A 63 3121 6825 * 5864 5026 3351 5600 3031 4413 2738 5131 6803 * 5389 6751 6916 6377 2421 * 3148 63
+ 0 * * * * * 0 10916 0 1050
+
+K 64 3672 6941 4552 4506 5881 4246 5193 4370 2942 5372 5872 5494 6841 3925 3358 3252 3895 3587 6527 4336 64
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+
+V 65 3886 4765 * 5284 3811 5770 * 2642 6901 2720 3766 6522 * 5495 5500 4792 5728 2219 6472 4314 65
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+
+D 66 5425 * 1437 3979 5546 4290 6751 5785 6411 * 6892 2046 4528 5837 6541 5282 5240 4673 * 5738 66
+ 173 3395 5821 5189 40 * 0 10916 2896 1050
+
+A 67 3420 3029 6683 5715 4308 4696 * 3273 6496 3151 7036 5244 5100 4764 3918 3936 5120 2836 6525 5158 67
+ 59 5163 6366 1709 527 * 0 10907 1400 1498
+
+T 68 3874 * 2114 2970 6465 4987 5118 5075 3873 4676 * 3958 5256 7004 6340 3288 3390 5657 5693 5891 68
+ 67 4966 6207 4475 66 801 1231 10846 1686 1972
+
+E 69 5501 * 2831 2448 6662 * 5517 5257 3259 4563 6026 3927 5038 3040 4413 3926 3796 5529 * 6645 69
+ 129 3549 * 4762 54 1521 618 10854 2615 1572
+
+E 70 3307 4389 3396 2750 6939 4922 3753 5328 6420 5624 6885 3132 5141 3832 5085 3672 4686 4724 6500 5742 70
+ 39 7072 5711 1000 1000 1075 929 10906 1000 1299
+
+S 71 4282 * 3956 3736 * 5748 5128 6746 2944 4962 6402 3964 2687 3446 4092 3246 3999 5770 * 5453 71
+ 247 2755 6788 2624 255 0 * 10893 3864 1492
+
+D 72 3140 * 3144 2236 6539 3982 * * 3633 5731 6976 4777 4665 4482 4786 3018 4122 5517 6832 6458 72
+ 38 5767 6976 1590 582 * 0 10946 1216 1000
+
+L 73 3753 * 6838 5050 3194 * 6661 2451 5108 1857 5209 * 5657 * 6469 5767 3996 3605 4931 5286 73
+ 27 * 5747 * * * 0 10957 0 1214
+
+A 74 2412 3166 5657 4256 3363 3776 6728 3896 4418 4411 * 5914 4123 4992 4805 4497 * 3705 * 5274 74
+ 41 5678 6881 1282 765 0 * 10927 1259 1606
+
+Q 75 3833 * 3486 3330 * 5139 5070 * 2540 6455 4913 4485 4401 2793 2865 5358 5312 * 6801 4856 75
+ 30 6443 6837 4700 57 0 * 10948 1007 1000
+
+Q 76 4794 * 3477 3440 5775 5722 5976 6755 2827 4449 5581 5630 5628 2893 2687 3879 4374 5635 * 4461 76
+ 41 5767 6684 1265 776 * 0 10958 1191 1000
+
+Y 77 3847 5611 6475 * 2028 * 4537 6020 6356 2280 5770 6696 5826 5589 * 5210 6736 5212 5939 2113 77
+ 131 3674 6898 2162 365 0 * 10944 2478 1189
+
+G 78 5196 * 4584 3954 6755 1673 5058 * 3576 6478 6734 3111 4847 3402 4100 4316 5152 5652 * 7052 78
+ 57 5139 6639 450 1901 0 * 10948 1423 1000
+
+V 79 4323 * 5122 * 5220 5845 * 1732 5825 3054 5728 * 4388 5621 6731 4275 * 1921 5959 6660 79
+ 14 * 6660 * * 0 * 10937 0 1000
+
+R 80 3790 * 4000 4028 4750 6469 4651 4650 4273 4746 5289 3843 5041 4099 2931 4199 2781 4791 * 4809 80
+ 139 3793 5667 1395 690 0 * 10946 2324 1000
+
+G 81 3398 5730 5677 3497 4488 2247 4792 5562 4395 * 5853 4213 * 5182 4622 2899 3624 4794 * 5178 81
+ 58 5063 6709 2780 227 732 1329 10898 1656 1463
+
+Y 82 3852 * * 5136 3465 6496 * 3020 * 3668 6683 * 4912 4889 * 4696 2891 2276 4797 3235 82
+ 48 4945 * 1397 689 1148 866 10905 1472 1277
+
+P 83 6517 * * * * 6692 * 6513 * 6482 * * 198 6541 5578 6803 5663 5323 * * 83
+ 0 * * * * 0 * 10916 0 1050
+
+T 84 2750 5810 4716 6667 4235 5232 5235 4738 5498 5028 * 6421 * 3765 4658 3083 1919 3838 * 6396 84
+ 0 * * * * * * 10964 0 0
+
+I 85 4413 * * * 2497 6746 * 3722 * 1812 3871 6532 * 6932 * 5828 3311 2944 6396 4099 85
+ 21 * 6122 * * * * 10964 0 0
+
+K 86 4161 5736 * 5797 2727 * * 2935 4727 2391 4825 * 6815 4348 6309 5912 5399 2714 * 3341 86
+ 0 * * * * 0 * 10957 0 1274
+
+F 87 4793 6560 * 6668 2255 5557 5505 2887 * 2356 5588 * * * 6747 5655 6818 2067 6928 4196 87
+ 71 * 4386 * * * * 10964 0 0
+
+F 88 5673 * 6464 6507 1959 * 5678 3089 6700 2785 4756 * 5647 6697 * 5750 6509 3786 * 2055 88
+ 379 2311 5088 824 1200 * 0 10891 4592 1879
+
+R 89 4228 * 3307 4956 6189 3235 5079 * 2328 4298 6893 4455 4115 3736 2847 6686 6612 4622 * 5178 89
+ 59 5902 5429 3450 138 664 1438 10859 1215 2624
+
+N 90 3485 * 2473 3431 * 3581 4782 6722 3668 * 6783 2536 4552 4036 6605 4187 4698 6413 * 5093 90
+ 0 * * * * 343 2239 10860 0 1939
+
+G 91 4838 4684 2992 4938 6315 878 6901 * 5801 6945 * 3487 6387 4434 * * 5862 6362 * * 91
+ 258 5390 2840 2215 350 0 * 10943 1366 1028
+
+D 92 5587 * 4617 3298 6573 3202 * 4452 2183 6334 5490 3358 * 4572 3787 3452 3635 4913 * * 92
+ 1274 6464 798 1000 1000 * 0 10738 1000 3689
+
+T 93 4171 * 4217 3762 5196 4335 5010 5021 3229 5379 4125 3246 2881 * 3638 * 5731 2987 5391 * 93
+ 122 * 3628 * * 3077 182 9163 0 9140
+
+A 94 4688 * 4464 * * 3769 * 5300 2247 3056 4451 4330 4360 4489 3143 5531 3343 4534 * 5568 94
+ 0 * * * * 101 3890 9402 0 8869
+
+S 95 5530 * 5774 3185 4325 * 4446 3597 3268 3211 6601 5725 3876 3992 3879 3886 4778 3212 * 5661 95
+ 14 6719 * 0 * * 0 10915 1029 1738
+
+P 96 4166 5827 5619 4475 4994 3987 5091 3276 4650 3098 5827 * 3730 5209 5598 5613 4510 2274 6901 4118 96
+ 19 * 6229 * * 1870 461 10915 0 1738
+
+K 97 3509 * 3879 3753 3977 3820 3887 3217 4753 3778 5207 4568 6602 4707 5649 4509 5235 3176 6376 5667 97
+ 77 4573 6658 819 1207 517 1731 10881 1636 1774
+
+E 98 4927 * 4741 3216 4957 5129 6482 4604 3758 4229 6504 4901 6868 2979 2553 4106 4134 3493 6653 5819 98
+ 57 5893 5508 0 * 1716 524 10892 1149 1497
+
+Y 99 3957 5780 4968 5290 2723 4761 5112 4196 5150 3298 4993 * 6605 4788 5324 3995 5693 3333 5089 2789 99
+ 34 6247 6655 1585 585 1210 817 10857 1056 1744
+
+T 100 4639 6982 3759 3567 6693 4160 4462 3497 4280 4877 5646 4051 3625 5747 5110 3487 3524 3541 6717 5151 100
+ 98 3923 * 1258 782 719 1349 10869 2367 1549
+
+A 101 4884 * 4091 3386 5314 1002 * * 4757 6576 6613 4115 5583 6693 4796 4181 5583 6563 * 5715 101
+ 68 4738 6832 770 1274 * 0 10905 1695 1082
+
+G 102 4410 * 4048 3225 4513 3038 * 4406 6410 4807 5699 4016 3461 3565 4112 3897 5615 4283 5837 4189 102
+ 75 5071 5573 612 1532 1181 839 10895 1474 1323
+
+R 103 3481 * 4645 4617 5562 6591 4519 4235 5651 2447 4694 5694 3874 4277 4004 4683 3956 3266 4572 6832 103
+ 109 3780 * 905 1102 539 1683 10833 2775 1539
+
+E 104 4566 * 2901 3409 * 5670 * 4928 4473 5548 6498 3061 3442 5135 * 2529 2682 * * 5035 104
+ 63 5974 5234 0 * 0 * 10919 1178 1015
+
+A 105 3200 * 4090 3935 5713 3880 5049 4304 3539 3469 6732 6422 3214 5084 4983 4960 4425 3299 5568 4982 105
+ 0 * * * * 0 * 10915 0 1381
+
+D 106 3898 * 3093 1967 5603 3907 5537 * 3724 4189 * 4582 3980 4176 4598 3629 5614 5811 * * 106
+ 31 5579 * 1866 463 * * 10940 1289 0
+
+D 107 3821 6521 3303 2535 5752 5657 5064 6859 3048 6608 4521 4045 6642 3465 4528 3736 3972 5713 6361 5755 107
+ 19 6268 * 0 * * * 10940 1082 0
+
+I 108 5799 6760 * 5510 2803 * * 2677 6531 1844 3793 * * 6625 6537 5923 5557 2933 4993 3859 108
+ 0 * * * * * * 10940 0 0
+
+V 109 3712 * 3683 3015 6801 * 5602 2965 3634 3006 5194 5570 * 3997 3180 5110 4808 4498 5614 6845 109
+ 0 * * * * * * 10934 0 0
+
+N 110 3327 * 3206 2710 * 4980 * 6666 3107 4538 5723 3592 * 3670 3772 3414 4222 5686 * 5794 110
+ 15 6637 * 1585 585 * * 10920 1000 0
+
+W 111 2912 6601 5701 4375 2069 * * 5570 5449 3417 3985 * * 6837 3630 * 4631 5094 2783 4446 111
+ 0 * * * * * * 10927 0 0
+
+L 112 5039 5657 * * 4254 * * 1759 5421 1639 4538 * * 6459 * * 5500 2557 * 6489 112
+ 0 * * * * * * 10876 0 0
+
+K 113 4212 * 3083 3081 * 4831 5119 6259 3914 3893 * 3466 * 2748 3741 3399 4512 4947 * 6156 113
+ 17 * 6375 0 * * * 10652 1000 0
+
+K 114 3783 * 3470 2371 * 6463 * * 2697 5242 5571 3283 5509 3233 3859 3564 5334 * * 5538 114
+ 0 * * 0 * 0 * 10501 1000 1000
+
+R 115 2747 6229 * 4638 4150 6290 3233 3205 4163 2467 * 3745 * * 4720 6360 5492 3941 5970 4355 115
+ 24 5918 * 0 * * * 10284 1000 0
+
+T 116 3785 3870 * 6151 4293 5873 5856 3627 4909 1717 3809 * 5053 * 4193 3740 3375 6176 * * 116
+ 0 * * * * * * 9981 0 0
+
+G 117 3410 * 3115 4414 * 2216 * * 3932 4449 * 3958 4311 5163 3067 4441 3471 * * 5720 117
+ 0 * * * * * * 9419 0 0
+
+P 118 3339 * 3172 3013 * 3219 * * 3392 4030 4789 * 1935 * 4774 3873 * * * * 118
+ 0 * * * * * * 8443 0 0
+
+A 119 2097 * 4188 4365 * * * 4197 * 4248 4460 3398 1674 4438 * * * 4163 * * 119
+ 0 * * * * * * 7340 0 0
+
+A 120 1671 * * 3911 * * * * * * * * * * * 3843 3809 1064 * * 120
+ 0 * * 0 * * * 6609 0 0
+
+//
+�HHsearch 1.5
+NAME 2b86eaed0dd0462632e7bb6e0a56ceb8
+FAM
+FILE 2b86eaed0dd0462632e7bb6e0a56ceb8
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:12:52 2013
+LENG 118 match states, 118 columns in multiple alignment
+FILT 143 out of 1887 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHHCCCCCCCCCCC
+CCCHHHHHHHHCHHHHHC
+>ss_conf PSIPRED confidence values
+9853999999958999999999849997756889998999999949999999999839987764889998999999949999999999859997766889
+998999999827998849
+>Consensus
+xxxxxlxxaxxxxxxxxxxxllxxxxxxxxxxxxgxxxlxxAxxxxxxxxxxxLlxxxxxxxxxdxxgxtxlxxaxxxxxxxxxxxLxxxgxxxxxxxxx
+gxtxlxxaxxxxxxxxlx
+>2b86eaed0dd0462632e7bb6e0a56ceb8
+MCDKEFMWALKNGDLDEVKDYVAKGEDVNRTLEGGRKPLHYAADCGQLEILEFLLLKGADINAPDKHHITPLLSAVYEGHVSCVKLLLSKGADKTVKGPD
+GLTALEATDNQAIKALLQ
+>gi|123416765|ref|XP_001304968.1| hypothetical protein [Trichomonas vaginalis G3]gi|121886455|gb|EAX92038.1| conserved hypothetical protein [Trichomonas vaginalis G3]
+----CLTQAVRESSLEVVEFLLSLGASILEGDDNEFTPFITSFAYNRKDMAYSMLFYKSNV----------LTYCYGL----IVMLILFILLKFMKR---
+------------------
+>gi|281351399|gb|EFB26983.1| hypothetical protein PANDA_009999 [Ailuropoda melanoleuca]
+--------RQHRGVTLCQRY--REGIAEEEEGKLGMCAARGDTGAAcrrregtTRQVCS---KTRTWPGRTDAQDGGPGSQASEAHASWVRRRLASQGER
+STGFVHRVEAP--------------
+>gi|123453151|ref|XP_001314609.1| hypothetical protein [Trichomonas vaginalis G3]gi|121897165|gb|EAY02294.1| hypothetical protein TVAG_275680 [Trichomonas vaginalis G3]
+--NECFIHSTMFNIPSFSEYFFQELKTSILK-INMELRLSIMQLFSIVKKQPNFLFHMVQIsmkkmkk--------------------------------
+-------------------------
+>gi|281202058|gb|EFA76263.1| hypothetical protein PPL_10024 [Polysphondylium pallidum PN500]
+---KLLEISPKSHNLEMVQYIAKIY-KQRLPAHHKIDKDSCrvlntVAFVGRLDMFNWAIANEF----DEFRVKRLLRESAQGGNIEFFQYLMVHYPRK-
+LDSHHFQKFMVCAASADSLELMK
+>gi|123474918|ref|XP_001320639.1| hypothetical protein [Trichomonas vaginalis G3]gi|121903449|gb|EAY08416.1| hypothetical protein TVAG_354750 [Trichomonas vaginalis G3]
+---TPYLYACIYGKPETLRILEKHGADPYFrlvrasdhviyhapkckidtkeyfeqcqeeakKKQSGLNAVALSIMKDNIDVLVYLHREKKFSLDEKSNG
+FYPIHIAARQNASKCFEYLKNNmeNCDPNLRTGEHST---------------
+>gi|86143535|ref|ZP_01061920.1| periplasmic protease [Leeuwenhoekiella blandensis MED217]gi|85829982|gb|EAQ48443.1| periplasmic protease [Leeuwenhoekiella blandensis MED217]
+-----LDYTISTNNNTLYTLLLEQGIYADAGANKTYTALQEAVKEANTGWVVKLVDAGADAQVKDDGDNNLLHLAAATGNTTLINYLYGLEPQlIDSENR
+AGDLPERVAKDKGYKKVFK
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * 3298 * * 2806 * 4268 1992 * * 1330 * * * * * 4205 1
+ 0 * * * * * * 6668 0 0
+
+C 2 5651 4007 * 5619 * 912 * 5522 4641 * * 3868 * 5490 4447 2766 5587 * * * 2
+ 30 5591 * 3170 170 * * 8736 1000 0
+
+D 3 * * 3195 2864 5887 3989 5895 6027 3893 5159 5120 2866 4947 3939 3371 3479 5062 6048 4916 5800 3
+ 0 * * * * * * 9289 0 0
+
+K 4 5116 * * 3688 6156 5277 * * 3677 5404 * 3006 4635 * 4919 2422 1644 * * 4392 4
+ 30 5585 * 1701 530 * * 9856 1153 0
+
+E 5 2154 4882 4847 5007 * 6777 * 4960 * 2933 * 6291 2039 5432 6429 3618 5754 3636 * 4964 5
+ 17 * 6449 * * * * 9975 0 0
+
+F 6 6326 * 6633 6613 2898 * * 2580 * 919 4412 * 5741 * * * 5921 4508 6531 * 6
+ 0 * * * * * 0 10517 0 1015
+
+M 7 6793 5194 4832 5040 2934 6346 1731 3165 6814 4426 4656 5235 6831 4395 5723 4200 * 4865 6835 4385 7
+ 13 * 6831 * * * 0 10554 0 1015
+
+W 8 4131 7011 5538 4115 3548 6582 4671 2751 4273 2962 6824 4877 * 4098 5067 4526 4633 4103 5072 3483 8
+ 0 * * * * * 0 10631 0 1186
+
+A 9 787 4100 5336 * * 6087 * 5328 * 5587 6792 6618 6984 7245 4464 3252 5266 4079 * 6998 9
+ 25 6770 6931 3320 152 917 1088 10785 1168 1186
+
+L 10 1928 3738 * 6979 * 5158 * 2193 5663 3973 6867 * 5628 6062 4656 4972 4179 2784 * 6859 10
+ 16 6464 * 2322 322 * 0 10938 1048 1161
+
+K 11 4331 5769 4504 3832 5082 5988 4728 4555 2778 3569 3933 6552 * 4269 2848 3705 5037 4627 6774 4704 11
+ 22 7139 6987 4524 64 * 0 10946 1047 1161
+
+N 12 4427 4659 5223 3709 3818 4807 4907 5746 3888 4473 * 2595 6962 5423 3988 3221 3956 5807 * 3472 12
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+
+//
+�HHsearch 1.5
+NAME 2c276c7332b4ac4757cbea933e3f987e
+FAM
+FILE 2c276c7332b4ac4757cbea933e3f987e
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 11:56:55 2013
+LENG 78 match states, 78 columns in multiple alignment
+FILT 106 out of 1048 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEEEECCCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEECCEECCCCCCHHHCCCCCCCEEEEEEECCCC
+>ss_conf PSIPRED confidence values
+957999990899899999699890999999999987979689799999999789883899599999899999947999
+>Consensus
+xxmxixvkxxxxxxxxxxvxxxxtvxxlkxxixxxxxxxxxxxxlxxxgxxLxdxxxlxxxxixxxxxixxxxxxxxx
+>2c276c7332b4ac4757cbea933e3f987e
+MGMIVFVRFNSSYGFPVEVDSDTSILQLKEVVAKRQGVPADQLRVIFAGKELPNHLTVQNCDLEQQSIVHIVQRPRRR
+>gi|154417020|ref|XP_001581531.1| hypothetical protein [Trichomonas vaginalis G3]gi|121915759|gb|EAY20545.1| hypothetical protein TVAG_239180 [Trichomonas vaginalis G3]
+-GYRVKVNCMDHFIInVSGVRDDMSSTEFLQQIAQAAVLTPNDFKIVFGIRQFFENHPLSDYKMHDGSVLKLSLRNRG-
+>gi|118353549|ref|XP_001010040.1| Ubiquitin family protein [Tetrahymena thermophila]gi|89291807|gb|EAR89795.1| Ubiquitin family protein [Tetrahymena thermophila SB210]
+--ISIQIKTLTGQTLAFKCKLNQKVYQLKNQIQEQFQISPSQQKLIYAEQQLEDDQQLYCYNLQSDCVVHLAQTLKK-
+>gi|242010787|ref|XP_002426140.1| ubiquitin domain-containing protein, putative [Pediculus humanus corporis]gi|212510187|gb|EEB13402.1| ubiquitin domain-containing protein, putative [Pediculus humanus corporis]
+--CTLKLRLSTScTDVKLLINSNKTIGMAKKKLcqqlkNSDINLEPSGQRWYFGGRLLVDKMKINEIHIQPGYVIQVIYN----
+>gi|254585453|ref|XP_002498294.1| ZYRO0G06864p [Zygosaccharomyces rouxii]gi|238941188|emb|CAR29361.1| ZYRO0G06864p [Zygosaccharomyces rouxii]
+--MNLTISnETNEEVYgPLEVSDDMTLPDLVALIELECGFDRSKHDLYHSVTLLDpNDTkSLTAIGMGDNELLLI-------
+>gi|194223268|ref|XP_001490596.2| PREDICTED: ubiquitin D-like [Equus caballus]
+------VHSEQWKLMTFNANSYDRVKKINEHVRSKTKVPVQDQILLLGSKTLKPMRKLSSYGIDKETTIHLTLK----
+>gi|297719771|ref|NP_001172247.1| Os01g0234850 [Oryza sativa Japonica Group]gi|255673035|dbj|BAH90977.1| Os01g0234850 [Oryza sativa Japonica Group]
+---RTAVRTVYGRKFKFQVDQRRNARYMKQEISrnveSPNGIG-ESMTL-VNGEKLDESTLISTICETNTSDTDFLANK---
+>gi|297823061|ref|XP_002879413.1| hypothetical protein ARALYDRAFT_321011 [Arabidopsis lyrata subsp. lyrata]gi|297325252|gb|EFH55672.1| hypothetical protein ARALYDRAFT_321011 [Arabidopsis lyrata subsp. lyrata]
+--ITLKVKNQQGAEDLYKIGAHAHLKKLMSAYCMKRNLDYGSVRFVYNGREIKARQTPAQLKMEEEDEICSVM-----
+>gi|335282306|ref|XP_003123059.2| PREDICTED: midnolin-like [Sus scrofa]
+--VPQFIGGVPHGKTGVPGGVEVPAAGVGGAAAASFACVPAGfrICLAAPSARLSSG-KLQEFGVGDGSKLTLV------
+>gi|149634203|ref|XP_001511134.1| PREDICTED: hypothetical protein [Ornithorhynchus anatinus]
+--KKVEILDyKTKKQLCFldKVEPHASINDIRLMFHkFYPQWYPARQSIRldPKGKSLRNEEILQRLPVGTTATLYF-------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * 3156 * * 3182 * 363 * * * * * * * * * 1
+ 0 * * * * * * 4649 0 0
+
+G 2 4777 * 2843 4423 * 2062 * * * 5067 4507 * 3420 4626 * 2617 2942 4747 * * 2
+ 82 4182 * 2000 415 * * 7258 1138 0
+
+M 3 6147 6171 * * 4756 5859 * 2487 6203 3457 1417 6023 6376 5308 6349 5746 5268 3057 * 5033 3
+ 0 * * * * * * 9346 0 0
+
+I 4 * * 4666 3144 5841 * 4928 4518 3106 6353 5597 5093 3907 2387 3085 3877 3340 5461 * 6628 4
+ 0 * * * * * * 9573 0 0
+
+V 5 * * * * 4357 * * 1633 * 2022 6413 5527 * 5938 * 5087 * 1721 * * 5
+ 14 6689 * 0 * * * 9684 1000 0
+
+F 6 4850 5554 6584 5067 2689 * 4429 3393 2990 3493 6556 4262 * 6345 3939 4244 3052 4084 * 5653 6
+ 0 * * * * * * 9695 0 0
+
+V 7 6428 4224 * * 5393 6429 5574 2017 * 2495 6145 * * 6673 * 6171 6636 1397 * 5238 7
+ 0 * * * * * * 9731 0 0
+
+R 8 5568 6604 * 4790 * 4720 5538 6519 1573 4067 6600 3444 5414 5555 2090 4703 4749 6812 * * 8
+ 125 3596 * 2010 412 * * 9753 2369 0
+
+F 9 4278 4920 3455 5644 4331 4085 4298 4991 5490 3827 5583 4167 6361 4255 5723 2522 3002 4976 5579 6798 9
+ 119 4886 4466 0 * * 0 9666 1400 1106
+
+N 10 3947 6232 6598 4972 3977 4926 4605 3947 3809 3322 4107 5664 3226 3768 4903 3779 3951 4214 6281 6598 10
+ 48 5565 6398 1000 1000 479 1822 9726 1148 1861
+
+S 11 4902 5739 2936 4346 * 2595 5650 6453 3403 4991 6642 2802 5447 6184 3925 3920 3365 5973 * 6622 11
+ 52 4822 * 0 * 1301 751 9791 1533 1316
+
+S 12 5402 * 3368 3754 * 1495 4545 * 3817 6649 6092 3526 6676 4637 4697 3700 5115 6801 * 5502 12
+ 78 6421 4611 0 * * 0 9805 1009 1106
+
+Y 13 4310 * 4335 2742 6303 3973 4140 * 3001 6408 * 4649 4406 3542 2999 3484 4259 4938 * 6848 13
+ 176 3791 4548 503 1763 779 1262 9896 2134 2007
+
+G 14 5774 5477 3275 3914 5172 5571 4006 3116 3680 4128 6405 * 5607 4299 5576 3505 3004 3487 6778 6257 14
+ 44 5044 * 527 1708 854 1162 9852 1404 2096
+
+F 15 4041 6800 6146 4188 2661 5714 4668 2947 4132 3370 5623 5643 6408 5663 4885 5101 3731 3459 5490 4714 15
+ 69 4420 * 272 2540 0 * 9967 1600 1397
+
+P 16 5028 5626 5375 2811 4277 4431 * 4470 4887 4087 7158 5078 3688 4388 4035 3094 3486 3234 * 6478 16
+ 0 * * * * * * 10097 0 0
+
+V 17 5759 6758 * * 2429 * 6848 2583 4795 2055 5346 5802 6669 6688 6855 4696 6836 2591 * 4312 17
+ 66 4834 6725 816 1211 * * 10097 1527 0
+
+E 18 3842 * 2977 2775 * 4515 4816 6608 3537 5099 * 4121 3798 4482 4605 3425 3483 4839 6521 6834 18
+ 79 4582 6413 681 1411 0 * 10078 1643 1000
+
+V 19 4919 4739 * * 2893 4516 * 2370 6054 3329 6873 * 5718 6388 * 5525 4225 1659 * 6415 19
+ 64 5668 5381 0 * * 0 10065 1283 1029
+
+D 20 5182 * 2941 2932 * 3402 5441 * 4415 5017 * 3973 3502 4380 4170 2428 4164 * * 5744 20
+ 41 5161 * 1977 423 1671 544 9991 1352 1529
+
+S 21 4270 * 4220 3445 6539 4554 5829 * 3633 3204 * 4548 1959 4353 4947 3889 4700 4435 6768 * 21
+ 0 * * 1585 585 * 0 10022 1106 1303
+
+D 22 5051 6549 2756 3433 5661 3572 4264 6844 5260 5759 7072 2619 6859 4434 * 3493 3275 4523 * 4362 22
+ 0 * * * * 0 * 10022 0 1303
+
+T 23 2718 5086 2744 3437 * 5180 * 5604 4499 4262 4685 4344 6556 3846 5757 4356 3340 4153 4933 6763 23
+ 10 7135 * 1000 1000 * * 10097 1000 0
+
+S 24 6386 5853 5117 6058 6684 * 6250 5346 4319 4870 5807 4846 3362 5849 5634 2448 1262 * * 7078 24
+ 25 5847 * 2865 213 * * 10097 1178 0
+
+I 25 4716 * * * 5614 5115 * 1836 * 2705 5240 * 6286 5300 * 4727 5421 1501 * * 25
+ 0 * * * * * * 10097 0 0
+
+L 26 3612 * 6909 2941 6646 2404 6610 6809 3171 4121 * 4993 6921 3858 3513 3325 5113 6162 * 4203 26
+ 0 * * * * * * 10097 0 0
+
+Q 27 4122 * 2434 2374 * 6417 6215 6860 3934 4559 5153 4569 * 2548 * 3570 4796 4538 * 5757 27
+ 0 * * * * * * 10097 0 0
+
+L 28 5766 * * 6162 2940 * * 2518 * 1295 6534 * * * * 5300 * 2190 * * 28
+ 0 * * * * * * 10097 0 0
+
+K 29 6162 6843 * 6690 5601 5721 6031 4606 828 4365 5483 * * 4232 2843 5312 * 5668 * * 29
+ 0 * * * * * * 10097 0 0
+
+E 30 3080 * 3618 2603 * 5443 5884 7026 2652 5114 5248 4339 6040 3514 4794 3312 4128 5168 * * 30
+ 15 6591 * 4459 67 * * 10097 1037 0
+
+V 31 2945 * 6418 3952 4765 * 4622 5231 2682 3719 4183 * 6275 2973 2987 5599 4597 4804 * 4683 31
+ 10 * 7213 * * * 0 10073 0 1037
+
+V 32 6412 * * * 3705 6267 5791 1514 5881 1803 5606 6364 * * * 6667 * 2651 * 5320 32
+ 79 4894 5672 1024 977 1497 631 10071 1607 1169
+
+A 33 1818 5468 5818 3741 4454 6526 4509 6870 4667 5260 * 5867 * 3352 4177 3385 5410 4337 6392 3720 33
+ 54 4772 * 277 2515 * 0 10037 1518 1444
+
+K 34 3565 6350 3427 2615 5714 * * 5913 3244 4803 6209 4608 5420 2848 3951 2786 4886 6674 * * 34
+ 45 5015 * 2552 270 * 0 10037 1581 1444
+
+R 35 3326 * 4747 3326 * 6647 5252 3842 2358 3875 6661 6733 5607 3559 2896 4872 5191 4952 * 4595 35
+ 40 5183 * 0 * * 0 10037 1339 1444
+
+Q 36 5032 4911 6676 3284 3358 4581 5068 4254 3721 3872 6742 6452 5191 5965 4168 4222 2840 5056 6725 3245 36
+ 38 7173 5736 1000 1000 * 0 10037 1000 1444
+
+G 37 4568 * 4157 4869 6459 1326 4764 * 3793 5760 6226 3529 5392 3757 4648 3906 6161 6423 * * 37
+ 190 3016 * 2116 378 1396 689 10027 3201 1853
+
+V 38 5666 4750 6372 5773 4364 5298 * 2177 4386 2607 5467 5731 4573 5678 6667 4756 4311 3134 4931 4086 38
+ 102 4986 4766 1607 574 636 1488 10065 1452 1464
+
+P 39 4052 * 3451 3384 6662 6468 5006 5570 4992 4694 6792 4814 2235 4226 6161 2646 4873 4259 * 4699 39
+ 78 5092 5419 0 * 1001 999 10012 1326 1797
+
+A 40 2378 * 4572 4007 5596 6666 6632 3850 7064 4561 6525 6146 2231 5678 4776 4558 3705 3556 5517 5409 40
+ 48 5698 6192 0 * 1137 875 9973 1179 1719
+
+D 41 3611 * 2699 3326 * 3080 4854 6160 4122 5370 6356 3136 5835 3633 5519 3247 4426 5779 * * 41
+ 55 5835 5665 0 * * 0 9986 1219 1577
+
+Q 42 4061 * 2776 3409 4924 4603 5865 6748 3566 4714 * 3779 6638 3144 2790 4399 4672 6329 * 4751 42
+ 18 6334 * 1000 1000 * 0 9944 1051 1950
+
+L 43 * 6768 6485 6329 4208 * 5365 2531 6153 2780 3527 6686 * 1646 * * 6656 3508 6454 5016 43
+ 16 6485 * 2108 381 1500 629 9944 1242 1950
+
+R 44 * 5653 6011 3877 * 5676 5914 5777 2250 5643 6622 4971 * 5152 1603 3823 4301 3872 6629 6279 44
+ 24 5939 * 0 * 1816 482 9992 1106 1557
+
+V 45 * 6561 * * 3549 * 6191 2145 * 875 6896 * * 6023 * * * 3810 5387 * 45
+ 29 6736 6561 0 * 1013 987 10010 1010 1345
+
+I 46 4556 4746 * 4754 3665 * 5845 3154 6678 2486 4516 5152 * 4592 4750 3982 3895 2678 5558 5167 46
+ 97 4161 6744 1000 1000 * 0 10046 1865 1313
+
+F 47 4183 4742 6437 6824 2514 * 3348 4216 5538 3044 * 6797 4838 7063 6633 4073 4941 4236 * 2246 47
+ 63 5121 6144 2047 400 0 * 10040 1545 1520
+
+A 48 3496 6145 3301 4892 6174 2409 5814 6752 2842 5675 5884 2818 5137 3639 4596 5614 5567 * * 5398 48
+ 39 5215 * 1730 517 * 0 10047 1426 1067
+
+G 49 5803 * 4262 4925 * 876 7093 6459 5076 6191 6898 4128 * 4754 5693 3287 5567 * * 4492 49
+ 187 3219 6174 1530 613 0 * 10047 2758 1067
+
+K 50 4376 * 5773 4015 4849 4806 4497 6678 2017 4901 * 5072 5474 3704 2420 3415 5121 5135 * * 50
+ 41 5876 6502 0 * 0 * 10037 1128 1054
+
+E 51 5223 7117 4417 3739 3907 * * 3486 4334 2934 * 6416 3330 3350 3873 4435 4693 3021 6363 6627 51
+ 48 4940 * 1144 869 * 0 10063 1443 1008
+
+L 52 * * 6794 6172 4411 * 5796 4115 6408 670 4391 * 5069 6449 6363 6729 * 3272 * * 52
+ 159 3261 * 1185 836 * 0 10063 3027 1008
+
+P 53 3807 6201 3228 2831 6459 6468 4497 * 2534 4711 6584 3746 4029 5632 3828 3361 6556 4821 6679 * 53
+ 91 4265 6752 1779 497 * 0 10063 1760 1008
+
+N 54 4357 * 1132 3490 * 5022 5828 6628 5761 5099 6718 3065 3500 * * 3822 6403 * * * 54
+ 45 5022 * 2179 360 1024 977 10044 1628 1227
+
+H 55 4350 6835 2358 2733 * 3711 4788 * 4977 * * 2748 6285 4676 3879 3788 3676 5432 * 6672 55
+ 17 * 6393 * * * 0 10078 0 1015
+
+L 56 4097 6387 4330 4659 6824 6679 4437 4522 2347 3846 4849 3845 * 3274 3935 3564 4106 5794 6523 5542 56
+ 99 3914 * 674 1422 895 1113 10036 2012 1269
+
+T 57 4896 * 4371 6199 * * * 4087 3655 3085 6726 6545 4095 5346 5086 2567 1769 4579 * 6418 57
+ 47 4974 * 1388 694 * 0 10078 1460 1015
+
+V 58 7029 6845 * * 4065 * * 2425 * 933 5493 6545 5311 * 5515 5409 * 3360 6251 * 58
+ 0 * * * * * 0 10078 0 1015
+
+Q 59 2837 * 4680 3251 5358 3487 6418 * 3400 5371 * 4594 5372 3603 4329 2599 3750 5262 * 6824 59
+ 18 * 6366 * * * 0 10078 0 1015
+
+N 60 4507 * 1731 2648 5667 5547 5681 * 5525 5488 * 3812 * 3514 5808 2762 5739 6607 * 4724 60
+ 16 6530 * 3807 107 * 0 10052 1000 1292
+
+C 61 4463 3962 * * 4125 6138 6669 3762 5897 2273 6537 4719 6580 5238 6149 4594 5835 4304 * 1725 61
+ 50 5328 6791 1968 426 837 1184 10052 1549 1292
+
+D 62 4604 4776 4153 4062 * 1606 4913 6129 3669 4789 * 2753 4729 4351 5666 4818 5311 * * * 62
+ 65 6611 4879 1000 1000 1563 596 10064 1021 1357
+
+L 63 5475 5056 * 6654 5737 6540 * 1537 * 2473 4162 6792 6206 5390 5584 5707 5005 2479 5033 * 63
+ 19 6241 * 3323 152 2056 397 9987 1339 1896
+
+E 64 4430 * 3921 3296 4020 3680 4652 5167 3027 5886 * 3878 4294 3820 4045 4047 3455 4760 * * 64
+ 54 5005 7418 0 * 2485 284 10032 1365 1642
+
+Q 65 4835 * 2295 2806 * * 4645 5581 4123 4139 5700 2547 4112 5165 5276 3221 5467 * * 6455 65
+ 16 * 6533 * * 0 * 9917 0 1649
+
+Q 66 5071 5568 3003 4618 * 1608 6686 6717 4240 4915 * 2768 5593 4701 3820 5079 4827 6839 * * 66
+ 89 5546 4706 2340 317 * 0 10001 1233 1000
+
+S 67 3422 4298 2121 5633 6066 4328 5229 5315 6000 * 4854 5612 5592 5479 * 2039 4515 3937 * 5439 67
+ 21 6138 * 1585 585 1219 810 9861 1069 1827
+
+I 68 6942 * 5497 3914 5140 6482 5612 2937 3893 3815 4704 5083 6154 4271 3494 4900 2584 2817 * 6663 68
+ 0 * * * * 2141 371 9830 0 1657
+
+V 69 6447 * * * 4918 * * 1514 * 1616 5668 6601 6243 * * * * 2142 * 6738 69
+ 28 5723 * 561 1635 745 1310 9857 1349 1468
+
+H 70 4689 4613 3722 5639 4999 * 2578 3711 5437 4327 5508 4653 * 3764 4720 5568 4092 3306 * 3031 70
+ 0 * * * * * 0 9864 0 1070
+
+I 71 4934 4247 * * 4270 * 6129 3236 * 1828 3912 * * 6274 * 5371 6132 1755 5109 5825 71
+ 17 6439 * 0 * * 0 9864 1093 1070
+
+V 72 4951 6545 6067 4687 5619 * 4508 2124 5228 3126 4257 5269 * 5126 * 4676 4272 2256 4648 5556 72
+ 0 * * * * * 0 9666 0 1070
+
+Q 73 5944 4181 * 5153 5093 5901 * 2767 4768 2518 5583 * 5114 6161 3649 3500 4845 2440 5135 5877 73
+ 25 5883 * 2000 415 * 0 9148 1021 1070
+
+R 74 * 5608 4111 3801 * * 5037 * 2057 * * 4089 4710 5860 1506 3806 5600 5588 * * 74
+ 0 * * * * 0 * 8798 0 1070
+
+P 75 5111 * * 4250 * 5337 4242 5035 3159 2235 * 3638 2591 4001 5516 3335 * 5052 * 5249 75
+ 0 * * * * * * 8115 0 0
+
+R 76 3895 * * 3670 * * 4807 * 3280 * * * 3055 4639 1140 3807 5060 * * * 76
+ 0 * * * * * * 7139 0 0
+
+R 77 4260 * * 4622 * 1366 * 4376 3221 * * 3334 * * 2181 4502 * * * * 77
+ 0 * * * * * * 6461 0 0
+
+R 78 * * * * * 2682 * * 1781 * * * * 2976 2778 1836 * * * * 78
+ 0 * * 0 * * * 4071 0 0
+
+//
+�HHsearch 1.5
+NAME 2cf47989aa11bbeeda0f0b4af2c1f1ad
+FAM
+FILE 2cf47989aa11bbeeda0f0b4af2c1f1ad
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:11:37 2013
+LENG 136 match states, 136 columns in multiple alignment
+FILT 142 out of 1017 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 11.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHCCCCE
+EEECCCCHHHHHHHHHHHHHHHHCCCCHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9975799996999999999999997797899978999999998618998899956888875899999999718997099996798879999999689869
+992899999999999999975133696334141209
+>Consensus
+xxxxxvliixxxxxxxxxlxxxlxxxxxxxxxxxxxxxxxxxxxxxxxdlvlxdxxxxxxxxxxxxxxlxxxxxxxxxixlxxxxxxxxxxxxxxxgxxx
+xlxkpxxxxxlxxxlxxxxxxxxxxxxxxxxxxxxx
+>2cf47989aa11bbeeda0f0b4af2c1f1ad
+HMNKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADD
+YMTKPFSPREVNARVKAILRRSEIRAPSSEMKNDEM
+>gi|258405286|ref|YP_003198028.1| response regulator receiver protein [Desulfohalobium retbaense DSM 5692]gi|257797513|gb|ACV68450.1| response regulator receiver protein [Desulfohalobium retbaense DSM 5692]
+--DYKVRIEIGNRLVRRQFETVV--------GQk------------selsilegqslERPDLLIKEISDDPDHIFDLVQNS-------lyndeagEIFLT
+SESKDQNLVLKAMRSGAREFFGPYTVEDEISSALDRFMTRQa--------------
+>gi|119897298|ref|YP_932511.1| signaling protein [Azoarcus sp. BH72]gi|119669711|emb|CAL93624.1| hypothetical signaling protein [Azoarcus sp. BH72]
+--PKEPFRPDLSEgAETGVY---LALLELLD-EGLIITGDETVLDANSAACALLqrDYRELAGQPLANLFPSER-AFIeARARLFIQGQMRGTLTVALPA
+GGTAALRfiaaprlRPGIHALILSPLPSATaAAQP-------------
+>gi|261251799|ref|ZP_05944373.1| response regulator VbsA [Vibrio orientalis CIP 102891 = ATCC 33934]gi|260938672|gb|EEX94660.1| response regulator VbsA [Vibrio orientalis CIP 102891 = ATCC 33934]gi|342816460|gb|EGU51357.1| LuxR family transcripitonal regulator [Vibrio orientalis CIP 102891 = ATCC 33934]
+---IHFIVIEPQPLLRHSLTELVASQPfvgnvYALSDCSDVE----ailqTKPVHGIIFDPTNDLSAASELMTFLAE---Srp--HI----------yti
+aysmnmtSSYRR-lFDTmnimgivsrldsi-------------ETLQASLMAAAHGYA-------------
+>gi|293606334|ref|ZP_06688694.1| response regulator [Achromobacter piechaudii ATCC 43553]gi|292815194|gb|EFF74315.1| response regulator [Achromobacter piechaudii ATCC 43553]
+-CGIELITFGPASVSSDAVDALLKNGALREVrAACGLDALIEALCQQDADVILCEVHGVPCEALLLPGHLqrefdaGRLRRLPAVLWISDLPRSIleaca
+GSFRTAGGKLQIATIATGVAASLDLFAKAGRG--GAPAAAA-------
+>gi|119487283|ref|ZP_01621034.1| Putative diguanylate cyclase (GGDEF domain) [Lyngbya sp. PCC 8106]gi|119455838|gb|EAW36973.1| Putative diguanylate cyclase (GGDEF domain) [Lyngbya sp. PCC 8106]
+--ETQFLLqaiwaIEKSQT-LEEAISSI-LDVICQNICWDYGEGWLPNPdKGVLEYIpqfqSCSAAFERFQKQSrlitfasgegLPGRIWQsHKpewied
+cstcsepvylrtqlvvDAglkavfgVPVVESEKLLAILVFYHTQAIPYQSRIVELI--QAVATQLSSSLQQAQLK-----------
+>gi|288573489|ref|ZP_06391846.1| response regulator receiver modulated diguanylate cyclase [Dethiosulfovibrio peptidovorans DSM 11002]gi|288569230|gb|EFC90787.1| response regulator receiver modulated diguanylate cyclase [Dethiosulfovibrio peptidovorans DSM 11002]
+--NSQLQKLSGDYRSALDDVKRV-QANFQTIMETTGDGIVVVDDAGLVRYVnpaaelLFESSSSEMIGNPF--SYDVdeDGDW--EISIKTSKGE-IYV-
+--DMRVVGS-NWDGDLVRLATLR-DISETVCLR-----------
+>gi|307721789|ref|YP_003892929.1| response regulator receiver modulated diguanylate cyclase [Sulfurimonas autotrophica DSM 16294]gi|306979882|gb|ADN09917.1| response regulator receiver modulated diguanylate cyclase [Sulfurimonas autotrophica DSM 16294]
+--NSISVIASTQH--VSFASKSF-LKYFGVADADEFNEKY----AS-----IINIFENNEDSintkniksyLHegksLYDFINFldETQRiTII----QN
+SENEQKSFLINIS-QI------NETQFLMNFTDVTEIEKQR-----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+H 1 1638 * * * * 1555 1563 * * * * * * * * * * * * * 1
+ 0 * * * * * * 2441 0 0
+
+M 2 3906 4349 4743 * 4700 * * 3665 3732 * 1196 4701 * * 4764 3770 3855 * * * 2
+ 52 * 4810 * * * * 8246 0 0
+
+N 3 4417 * 5488 3854 5750 2560 5799 5064 3306 * 4408 3108 3090 4217 3512 4030 4592 * * * 3
+ 161 3736 5044 2224 347 * 0 11054 2079 1000
+
+K 4 3636 * 6443 4471 5546 5505 6105 2938 2867 3780 4060 4495 4136 4812 3993 4137 3952 4947 6190 4734 4
+ 65 4513 * 1674 542 1846 470 11631 1663 1412
+
+K 5 3881 * 4837 4091 5625 6857 4055 5843 3021 5315 6524 3433 6099 4030 2302 3403 3687 5084 * * 5
+ 54 5434 6189 1481 640 0 * 11932 1441 1246
+
+I 6 3836 6941 * 6973 4609 * 6854 1977 5667 2612 5531 7043 5575 * 5516 7194 4529 1797 * 5888 6
+ 57 5217 6431 4938 48 0 * 11936 1645 1157
+
+L 7 3211 5013 * * 5565 * 6975 2856 * 1155 6971 * 7090 6650 5813 * 4290 2898 6635 7279 7
+ 46 5924 6041 2389 306 * 0 11917 1261 1087
+
+V 8 4846 6121 * * 4139 * 6386 2019 6640 2093 4606 * * * 5655 * 5169 1987 6667 4634 8
+ 86 4369 6764 2198 355 525 1712 11907 1903 1432
+
+V 9 2998 4182 * 4836 4513 5668 * 2077 * 2641 5114 * 6448 * 6808 5691 5313 2291 6652 5977 9
+ 27 6984 6589 0 * * 0 11947 1000 1235
+
+D 10 4431 * 1992 2185 6884 4013 5409 5423 4986 * 4924 4987 * 4480 6807 3539 3410 5906 * 5759 10
+ 0 * * * * 1827 477 11917 0 1483
+
+D 11 4551 5085 2102 3553 6955 3532 4843 5752 4126 4998 6684 3967 3462 4558 4591 3312 5889 7076 * * 11
+ 0 * * 3459 138 * 0 11935 1000 1296
+
+E 12 4217 * 2214 4422 5472 4362 4245 6659 5509 4803 * 3049 4499 4297 4605 2663 5197 4951 * 5788 12
+ 35 5860 7183 2000 415 1054 948 11943 1203 1296
+
+E 13 3525 * 4788 2569 6183 4340 7586 4710 3882 3929 * 5611 2766 3900 4022 3607 5083 5105 7013 5373 13
+ 67 6473 4865 850 1168 752 1300 11967 1240 1234
+
+S 14 3594 * 3325 3073 5424 4127 5679 4984 5057 2800 6374 4098 5126 5225 4303 3874 4397 4143 5848 5204 14
+ 79 6403 4589 1000 1000 2284 332 11906 1079 1818
+
+I 15 3991 5401 4417 3749 3510 5363 7452 4264 5552 2927 6149 4698 5856 3955 4449 3674 4238 3461 5969 4286 15
+ 68 5649 5249 1948 433 0 * 11755 1396 2507
+
+V 16 2798 4468 4485 5530 4721 4559 6279 4246 4901 2968 5971 5138 5613 4797 2753 4004 4536 3843 7533 6985 16
+ 10 * 7177 0 * 434 1945 11965 1082 1507
+
+T 17 3683 6830 3107 2717 4734 4711 5685 5211 4150 4441 * 3968 5417 4214 3634 3653 3903 5135 7019 5935 17
+ 75 7038 4544 1023 978 1064 939 12004 1155 1160
+
+L 18 3455 6070 4936 3428 5010 3764 4772 4535 4138 3476 5665 5447 5491 3632 4326 3991 4802 4073 4843 4355 18
+ 24 6767 7138 1097 909 0 * 11903 1248 1959
+
+L 19 3962 6325 5766 6493 5447 * * 2515 6028 1363 4165 * * 6077 6352 7434 4833 2889 5518 6462 19
+ 35 * 5389 * * * 0 12023 0 1000
+
+Q 20 2645 5433 5008 3584 5245 5744 6087 5083 3345 3844 6406 4424 5341 3880 3216 4542 4572 3412 * 7002 20
+ 24 7126 6722 1000 1000 * 0 11966 1000 1550
+
+Y 21 3100 6995 3783 2314 * 4865 4884 5850 3546 4917 * 3994 6335 4047 4377 3154 4262 5582 7059 5582 21
+ 44 7235 5423 0 * * 0 11927 1000 1766
+
+N 22 3209 5351 5617 5457 6328 5941 6379 3694 7050 1659 5122 7525 6737 3504 4875 4576 4993 3825 7082 3943 22
+ 0 * * * * 1359 713 11879 0 2301
+
+L 23 5389 5271 * 6831 3525 6718 * 2763 * 1087 4423 * 6741 5415 6828 5827 5752 3286 * * 23
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+//
+�HHsearch 1.5
+NAME 2dc7af2028fa424ea0f21cfb017ac190
+FAM
+FILE 2dc7af2028fa424ea0f21cfb017ac190
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:25:20 2013
+LENG 145 match states, 145 columns in multiple alignment
+FILT 142 out of 652 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCCCEEEEEEEEECCEECCCEEEEEEEEEECCCCCCCCCEEEEECCCCCCCCCC
+CCCCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCC
+>ss_conf PSIPRED confidence values
+9468899997630378888999999999997889863875178889990043799999575487988836799995888999999899958987312888
+879999889434242689666859999999999980489976788
+>Consensus
+xxxxxxxxxxxxxxYxxxxxxxxdxxxxlxxyxxLxpxxxxxxxxdGxxxxLlxlxGtIpxxyxgxxyxiPvxixlpxxYPxxpPxvxvxptxxmxixxh
+pxVdxxGxvxlpxLxxWxxxxxxLxxllxxlxxxfxxxpPxxxxx
+>2dc7af2028fa424ea0f21cfb017ac190
+MAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTG
+KHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRP
+>gi|224066317|ref|XP_002302080.1| predicted protein [Populus trichocarpa]gi|222843806|gb|EEE81353.1| predicted protein [Populus trichocarpa]
+--------------------FIRKhLLSLIQDYPTFTLSTNTFFHDDGTTVNLLYATGHLHVANHT--PSIPLTIWIHENYPCMPPMVYVLSDSTSPIHQ
+DhPFVHSSGATSSPYLQTWVFPRCHLTELVHNLVRIFSHDHPFVY--
+>gi|50289071|ref|XP_446965.1| hypothetical protein [Candida glabrata CBS 138]gi|49526274|emb|CAG59898.1| unnamed protein product [Candida glabrata]
+------LFKVIQPIYKQPKLVFHDAVQTLTEFKNLRPRTRVFTDEDGSPRLLLCLYGGIPIEQ---GLDVPVLIWIPESYPIAKPLLFIDlelLDKDLQL
+ATNESVEPDGRVHTRLLRQWNPQSANLFNVIQDLADMCNAIAPIQpvtfsstvapgT--
+>gi|156087172|ref|XP_001610993.1| hypothetical protein [Babesia bovis T2Bo]gi|154798246|gb|EDO07425.1| hypothetical protein BBOV_IV010720 [Babesia bovis]
+------------RHFYDELIVCNDVTDVLKKYKSLSVALDRI---GG--EVVLNLKGTLPYTHANVEYHCPIGITIGTLYPKTPPLFKVISSGTIRIATN
+hPCVAKNGNIVMAYFDKWSA-RCTVMDAINLVLGEFNKQSPIYQ--
+>gi|154416614|ref|XP_001581329.1| hypothetical protein [Trichomonas vaginalis G3]gi|121915555|gb|EAY20343.1| hypothetical protein TVAG_193190 [Trichomonas vaginalis G3]
+--------------------ICRDIELFIQRYNTLQPR--QFSSSVGN---LIAISGYLLFNIGGTQSYVNLDITLTPKFPMKSPYIQFRIDPS-QICPS
+HGLTPQGVVNMPVVHNWVFRQSTLLQMGDDLYRFFMQNPPIM---
+>gi|145487706|ref|XP_001429858.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124396952|emb|CAK62460.1| unnamed protein product [Paramecium tetraurelia]
+-----ELYRVISqCAYRNHSQVATDAANILYNYPKLFNPLITQTSENGVIKQLLELKGELPIKYKGSTYSIITSIQFPFIYSDAPAVIRIyNPDISKfSV
+NqyfiQGASQDQSvVNIHNTELQSWYQHRSiarVMVALVRELEGHF----------
+>gi|300175628|emb|CBK20939.2| unnamed protein product [Blastocystis hominis]
+------------------------------------SKCEVYDINiNGVNTR--CLKCSVnhYCTYYNQKYLIPIDLFVPNSFPYVDPILYIRPPAGSKI
+VPIpNVVDADGRIIYILVSNIK--NITLNQFFASLDSCFATCFPI----
+>gi|340713047|ref|XP_003395063.1| PREDICTED: ubiquitin-conjugating enzyme E2-17 kDa-like isoform 2 [Bombus terrestris]
+------------------------------------PPTGVSGAPTDN--NIMIWNAVIFgphdTPFEDGTFK--LTIEFTEEYPNKPPTVRfISKMF--
+----HPNVYADGGICLDILQNrWSP-TYDVSAILTSIQSLLDE--------
+>gi|32967283|ref|NP_861515.1| ubiquitin-conjugating enzyme E2 C isoform 2 [Homo sapiens]gi|114682254|ref|XP_001156756.1| PREDICTED: ubiquitin-conjugating enzyme E2 C-like isoform 2 [Pan troglodytes]gi|119596211|gb|EAW75805.1| ubiquitin-conjugating enzyme E2C, isoform CRA_b [Homo sapiens]
+--------------------------------------KGISAFPESD--NLFKWVGTIHGaagtAVGSIRTS--STVCLLSGPRETQDSSkPLV-----
+---------------------WGL-GWDMRLLLeLTLQLFLQ---------
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
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+S 122 5262 3283 * * * 5773 4362 4275 4925 3670 4424 4925 6508 6435 * 1655 4051 5162 5185 3239 122
+ 28 5677 * 1585 585 1414 679 6987 1062 1113
+
+D 123 * * 2832 5781 * 6331 5090 * 4047 * * 1976 6257 5478 4669 2697 2108 5386 * * 123
+ 7 * 7770 * * * 0 6985 0 1049
+
+L 124 6548 6655 * * * * * 2667 * 778 4524 * * * * 6526 5366 2642 * * 124
+ 16 6500 * 0 * * 0 6983 1009 1083
+
+L 125 4204 6620 5007 4466 4319 6195 5927 5219 4200 2786 5932 5261 6854 4436 3780 3182 4017 2474 * 5029 125
+ 18 * 6349 * * * 0 6983 0 1083
+
+G 126 4082 * 3106 2784 * 3146 5445 6850 4654 4602 5873 4109 7582 2878 4510 2960 4345 7160 * 6761 126
+ 0 * * * * * 0 6951 0 1165
+
+L 127 4545 5180 * * 4300 6652 * 3224 * 1070 5329 * * * * * 7109 2197 * 4822 127
+ 0 * * 1365 709 938 1065 6951 1059 1165
+
+I 128 4811 5441 6527 * 4259 6327 * 1922 * 1644 5148 * * * * * 5309 2130 * * 128
+ 38 5262 * 0 * * 0 6984 1133 1049
+
+Q 129 3788 6491 4352 2922 7247 4750 4746 4347 3856 3508 6034 4711 * 2269 3324 4774 5450 5144 * * 129
+ 15 * 6642 * * * 0 6978 0 1049
+
+V 130 3664 * 3800 3210 5330 3734 5110 3987 5932 5362 * 4440 6488 4735 5456 2746 4046 2578 7330 7017 130
+ 0 * * 0 * 932 1071 6990 1060 1166
+
+M 131 5837 5330 * * 4511 * 6652 2581 * 1037 2815 6525 * * * 6491 * 3549 * * 131
+ 0 * * * * * 0 6978 0 1049
+
+I 132 3660 4357 5278 5135 * 5146 5784 3241 5015 3455 4933 * 7051 2725 3531 3296 5489 3839 * 3802 132
+ 0 * * * * * 0 6978 0 1049
+
+V 133 3171 6317 3132 3661 5047 4233 4793 5720 4692 4327 5818 5290 7125 3333 3729 2719 5935 4767 * 5245 133
+ 0 * * * * * 0 6974 0 1049
+
+V 134 3337 5319 6385 4892 4241 * 4969 3230 4899 1797 4129 * * 5149 * 5180 4400 2790 * 6292 134
+ 15 * 6601 4087 87 0 * 6974 1049 1049
+
+F 135 * 5834 * * 979 * * 4222 * 1513 6151 * * * 6469 6932 * 5581 6773 7017 135
+ 0 * * * * * 0 6971 0 1010
+
+G 136 3205 6555 5148 5078 * 2346 5565 4922 5265 5383 5122 4027 7374 3817 4789 1868 4919 * * 6374 136
+ 14 6666 * 3964 96 0 * 6734 1074 1010
+
+D 137 2876 5513 3544 2306 6536 * 4122 5277 4006 5101 6043 3745 * 4388 3763 3722 4161 6367 * 6203 137
+ 0 * * * * * 0 6587 0 1006
+
+E 138 6223 4573 2822 1497 5596 * 6360 4297 5597 * 5546 3475 5675 3858 4926 5014 5149 6724 * 4534 138
+ 0 * * * * * 0 5915 0 1006
+
+P 139 5909 4382 * * 4246 * 4059 5287 * 5490 5112 * 641 * * 4329 5193 * * 5181 139
+ 0 * * * * * 0 5834 0 1006
+
+P 140 * * * * * 6331 * * * * * 5653 47 * * * * * * * 140
+ 0 * * * * * 0 5834 0 1006
+
+V 141 * 6190 * * 3734 * * 2856 5645 1484 6254 * * 5765 * 6326 * 1508 * * 141
+ 0 * * * * * 0 5831 0 1006
+
+F 142 * * * * 2007 6250 * 5135 * 3900 4568 * * 5445 4147 4575 4298 4789 * 1351 142
+ 39 5245 * 3459 138 * 0 5411 1004 1006
+
+S 143 1845 * 5307 * * * 5212 * 5394 5119 5409 6005 5991 4221 * 1444 3086 * * 5438 143
+ 24 5893 * 0 * * 0 5046 1018 1006
+
+R 144 * * * * * * * * 1065 4641 * * * 4570 1523 5899 4194 5617 * * 144
+ 0 * * * * 0 * 4543 0 1006
+
+P 145 4442 * * * 4096 * * 5023 4785 * * * 758 4025 * 2907 * * * 4559 145
+ 0 * * 0 * * * 4230 0 0
+
+//
+�HHsearch 1.5
+NAME 2ebbe0783d204f9b6a288ba6e9641f90
+FAM
+FILE 2ebbe0783d204f9b6a288ba6e9641f90
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:23:44 2013
+LENG 128 match states, 128 columns in multiple alignment
+FILT 133 out of 1234 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEEEECCCCEEECCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEE
+EEECCHHHEEECCEEHHHHHHCCCCCCC
+>ss_conf PSIPRED confidence values
+9999993899999999999999999999849892796999999676036707999897699999987899999999999999999999969390639999
+9987989946988998998762797779
+>Consensus
+xixixxxxgxxxexxxxlxxxixxxxxxxxxxPxxxxxvxxxxxxxxxxxxgxxxxxxxxxIxvxxxxgrxxexkxxlxxxixxxlxxxlgixxxxvxix
+ixexxxxxwxxxGxxxxxxxxxxxxxxx
+>2ebbe0783d204f9b6a288ba6e9641f90
+MITVFGLKSKLAPRREKLAEVIYNSLHLGLDIPKGKHAIRFLCLEKEDFYYPFDRSDDYTVIEINLMAGRMEGTKKRLIKMLFSELEYKLGIRAHDVEIT
+IKEQPAHCWGFRGMTGDEARDLDYDIYV
+>gi|334881627|emb|CCB82523.1| 4-oxalocrotonate tautomerase [Lactobacillus pentosus MP-10]gi|339638689|emb|CCC17842.1| 4-oxalocrotonate tautomerase [Lactobacillus pentosus IG1]
+-MRIDMIRGRSQSEIKQILDIAYHAASTALHLRPRDRYQIVTQHDPDEMIIEDvglgfERTSAFLMFSL-T-sSPRKVEDKQQFYQLLVHDLHQQLGIAP
+ADVMINITTNSYEDWSFGDG--------------
+>gi|197123365|ref|YP_002135316.1| tautomerase [Anaeromyxobacter sp. K]gi|196173214|gb|ACG74187.1| tautomerase [Anaeromyxobacter sp. K]
+--LFDLSVSPPDDDRARFGAAVARRFGEIMDTGTDHVAVLVRAHSQGSLTLGLAsdPARGVALASADIRVGRTQDQERRLCLAFIEELERWFGIPKDQVY
+VVLTRHDGPEF-------------------
+>gi|182676840|ref|YP_001830987.1| hypothetical protein Bind_3691 [Beijerinckia indica subsp. indica ATCC 9039]gi|182636470|gb|ACB97243.1| hypothetical protein Bind_3691 [Beijerinckia indica subsp. indica ATCC 9039]
+--RLTLTSIPTLDQANHLATELTELIAHDLGKRQELTSILVETSGISHWAIGAegRLTAAHLEVCVTA-GTNSEQEKRAFIANAMTILRTVLPGLNPATY
+VVIRELPATDWGYDGRTQADRA--------
+>gi|127512436|ref|YP_001093633.1| 5-carboxymethyl-2-hydroxymuconate isomerase [Shewanella loihica PV-4]gi|126637731|gb|ABO23374.1| 5-carboxymethyl-2-hydroxymuconate isomerase [Shewanella loihica PV-4]
+-------------AIDNLVEQVHRGAIESELFEPASIKSRAYSA--EHYCVGEAKAASFIHISFKIMPGRSSEQKLHLMQCVDRLIAPL-CASVSSITME
+VLDIEREHYFK-----------------
+>gi|239820694|ref|YP_002947879.1| 4-oxalocrotonate tautomerase family enzyme [Variovorax paradoxus S110]gi|239805547|gb|ACS22613.1| 4-oxalocrotonate tautomerase family enzyme [Variovorax paradoxus S110]
+-VIVEMWEGRTVDQKRNLVKAITQAMVDHAGCKPDHLHVVIHDTPKESWGRNG-----------------------------------------------
+----------------------------
+>gi|336380645|gb|EGO21798.1| hypothetical protein SERLADRAFT_474679 [Serpula lacrymans var. lacrymans S7.9]
+--------------TKAFVSEFSKFCATTIDKPEK--AFSVNFIYNPHLTFA-GTFDPAIMLNVMSLYNTNPTSVQKWSKAFADYFEEKLGVTSDRGYMA
+FQDPGPAFIGTRGSTVEVL---------
+>gi|262202814|ref|YP_003274022.1| 4-oxalocrotonate tautomerase [Gordonia bronchialis DSM 43247]gi|262086161|gb|ACY22129.1| 4-oxalocrotonate tautomerase [Gordonia bronchialis DSM 43247]
+QIQLTVPAGaLTDQGRTTIQQDLARALLKWEGAPDNDFFKAlgwsyLHELPEGAQVTA-ADTEPRFRVDVTVPQFaLNDERKAGLSKEVTGLVLAAAGLG
+PEhalRVWVLINEQTDGTWSVGGQ--------------
+>gi|28378091|ref|NP_784983.1| hypothetical protein lp_1348 [Lactobacillus plantarum WCFS1]gi|342241468|emb|CCC78702.1| hypothetical protein lp_1348 [Lactobacillus plantarum WCFS1]
+-------------------------------VPGKSEEVLMVGIEDQYDLYLHGDdRVNLAYISVAIYGIPHHEGYVNLNLAITKLFYEVLKIHPENIFI
+DYADI--RAWGNSGYFIDGK---------
+>gi|54024265|ref|YP_118507.1| hypothetical protein nfa22960 [Nocardia farcinica IFM 10152]gi|54015773|dbj|BAD57143.1| hypothetical protein [Nocardia farcinica IFM 10152]
+--HIYHPPAtYTEADKQQFAQAVTRSYRSWG-LPDFYVVVLFHEIAAVDCYVGGRPADSTVRVVVEHLARqlEDPDMRRIMTEKLDTVMAPFTHDRGLHC
+EFHVDETPRDLWMIGGL--------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * 4011 * * 4154 * 1284 2762 3639 * 2918 * * 4217 4126 * * 1
+ 0 * * * * * * 5049 0 0
+
+I 2 5741 * * * 4490 * * 1377 * 2984 5252 * * * * * 4001 1571 * * 2
+ 0 * * * * * * 7163 0 0
+
+T 3 * * 5216 5656 * * 3095 5457 2833 3825 * 3092 * 3618 2004 * 2693 * * * 3
+ 0 * * * * * * 7827 0 0
+
+V 4 4981 4919 * * 3521 * * 1175 * 3506 * * * * * * 5501 1760 * * 4
+ 0 * * * * * * 7928 0 0
+
+F 5 5501 * 2312 3261 5437 * 3066 * 3746 * * 4920 * 4571 * 3052 2916 5438 5933 3512 5
+ 22 * 6063 * * * * 7928 0 0
+
+G 6 4616 * * 5491 * 4468 5725 2683 * 1977 3055 * * * * 4907 5977 2301 4703 4254 6
+ 67 4471 * 0 * 0 * 7923 1339 1000
+
+L 7 3560 5527 * * 4299 5433 6026 3484 4241 3024 * * 2556 4151 3312 3642 5136 3826 4925 * 7
+ 0 * * * * * * 7928 0 0
+
+K 8 2776 * 5661 2729 * 5018 5498 * 2135 * * 6063 3947 3368 3434 5136 3611 5430 * * 8
+ 29 5631 * 0 * * * 7928 1030 0
+
+S 9 4458 * 4691 4358 * 815 * 4480 4484 * * 5295 5501 4831 4679 3883 5664 * * * 9
+ 318 2436 6263 0 * * * 7928 2121 0
+
+K 10 5488 * * * 4083 5657 4697 3847 3568 2470 5513 5739 4271 5523 1926 * 3883 5738 5422 4685 10
+ 79 5270 5204 0 * 0 * 7938 1018 1057
+
+L 11 * * 3517 4862 * * * * 5995 5480 * 3620 3029 * 5532 1905 1674 5995 5743 * 11
+ 0 * * 0 * 0 * 8158 1027 1027
+
+A 12 2785 * 2539 3653 * 4430 5075 * 4671 3324 * * 2958 3466 3536 5305 4841 5466 * * 12
+ 27 5729 * 0 * * * 8654 1000 0
+
+P 13 2992 * 2854 1411 5135 * * * * 4327 * 5904 4687 3709 4802 4538 5896 4216 * * 13
+ 0 * * * * * * 8654 0 0
+
+R 14 3211 * 3109 3096 * 5941 5874 6081 4970 5347 4994 3993 5881 2129 5938 5132 3625 5313 * 3968 14
+ 0 * * * * * * 9002 0 0
+
+R 15 4149 6135 * 4301 6321 5370 * 3624 2138 3730 5340 5864 3594 6419 2215 6557 4148 4666 * * 15
+ 0 * * * * * * 9527 0 0
+
+E 16 2893 * 4039 2825 * 5562 * * 2648 6528 * 3544 6637 3170 2911 4818 4267 4483 * * 16
+ 0 * * * * * * 9628 0 0
+
+K 17 2235 * 3952 3188 6642 3617 5770 * 3027 5234 * 4136 * 3748 3054 4133 4859 6512 * * 17
+ 0 * * * * * * 9628 0 0
+
+L 18 5544 5753 * * 2543 * * 1958 * 1301 5113 * * * * * 6422 3821 6162 * 18
+ 0 * * * * * * 9628 0 0
+
+A 19 2356 5435 * * 6281 4227 5084 3952 5251 2196 3599 5184 * 4473 * 3498 6474 3037 * * 19
+ 0 * * * * * * 9652 0 0
+
+E 20 3184 * 2689 2522 * 6499 5897 * 3108 4308 6462 5956 6735 3925 3422 3726 3932 5092 * * 20
+ 26 * 5799 * * * * 9652 0 0
+
+V 21 2478 6149 4117 2265 * 4548 * 4647 3512 4446 * 6269 * 4149 3745 3932 3998 4253 * * 21
+ 0 * * 0 * 0 * 9634 1065 1065
+
+I 22 4001 * * * 3788 * * 1842 * 1921 * * * * * 6097 3540 2249 * 6485 22
+ 0 * * * * * * 9652 0 0
+
+Y 23 3973 6486 * 5450 6211 5044 2009 6076 * 6566 * 4703 * 5489 6374 2382 2130 5313 * 3913 23
+ 0 * * * * * * 9652 0 0
+
+N 24 3539 * 2951 2421 6647 5452 4155 * 3294 4330 * 4295 5799 3340 3035 5092 5259 * * 6343 24
+ 0 * * * * * * 9652 0 0
+
+S 25 1779 4051 * 5456 3593 4630 * 4137 * 3347 5363 * * 5616 5476 3188 4508 2987 * * 25
+ 0 * * * * * * 9652 0 0
+
+L 26 2870 6268 * * 6323 * 4343 2545 * 1852 3846 * * * 6525 6622 4387 2557 * 4970 26
+ 0 * * * * * * 9652 0 0
+
+H 27 2338 3991 6673 6021 5378 5609 4111 4100 * 4749 5847 * * 6725 4733 2699 4199 2167 * 5591 27
+ 0 * * * * * * 9652 0 0
+
+L 28 3423 * 3273 1850 * 6198 5782 6068 3349 5173 * 4000 * 3611 3626 4282 3708 * * * 28
+ 20 6198 * 0 * * * 9652 1003 0
+
+G 29 2828 5847 4631 4525 5556 4921 4712 2787 6977 3370 * 6012 6198 * * 4275 2333 3331 5469 6076 29
+ 15 * 6622 * * * * 9652 0 0
+
+L 30 4476 6175 * 3588 2622 3220 * 3896 * 1898 3601 6705 5039 * * 5353 4037 5784 6518 5967 30
+ 17 6408 * 0 * 0 * 9664 1000 1000
+
+D 31 4102 6532 2785 4403 * 1744 4122 4805 3684 3965 * 3247 * 4953 6525 6724 6374 5456 * 6356 31
+ 26 * 5799 * * * * 9652 0 0
+
+I 32 2672 4120 * * 3286 * * 3956 1839 4621 5266 6039 * * 5579 * 4259 2606 * 5650 32
+ 0 * * 0 * 0 * 9736 1065 1065
+
+P 33 5004 * 3581 4751 * 5163 * * 4296 * * 5250 736 5031 5805 4267 4562 * * * 33
+ 0 * * * * * * 9761 0 0
+
+K 34 3809 * 4211 1860 * 5210 6110 4915 3760 4574 4759 5409 2882 4288 4972 5035 4708 4040 * * 34
+ 0 * * * * * * 9761 0 0
+
+G 35 2758 * 2788 2467 5618 3810 * 5451 3518 6736 6092 3632 5993 4785 5447 3915 4266 * 5769 6897 35
+ 318 * 2339 * * * * 9761 0 0
+
+K 36 3800 * 1482 4715 4944 4085 4407 * 4302 4492 * 4602 5044 * 5135 3948 4674 6199 5053 4295 36
+ 25 5879 * 2322 322 * 0 9295 1000 2969
+
+H 37 5746 4613 5999 5117 5256 * 6093 2330 4617 3030 6516 * * 3706 3613 * 4363 1960 * 5777 37
+ 0 * * * * 0 * 9295 0 2969
+
+A 38 3544 * 6033 4947 2525 6533 5494 6527 2924 * 4139 4380 * 4396 3040 5805 5242 4422 6592 2816 38
+ 0 * * * * * * 9761 0 0
+
+I 39 4770 * * * 6317 6143 4582 2234 6446 5456 4645 6598 * 3058 6008 4907 3451 1567 * * 39
+ 0 * * * * * * 9761 0 0
+
+R 40 3685 5194 * * 4435 6120 6087 2695 * 3024 3317 * * 6835 2242 5464 3809 3390 5406 6818 40
+ 55 4732 * 2322 322 * * 9765 1320 0
+
+F 41 3090 * * * 2386 6454 * 2684 * 2656 4486 * * * * 5477 5846 1996 5879 6206 41
+ 84 * 4139 * * * * 9765 0 0
+
+L 42 4876 * 4681 3791 * 6987 3017 4870 * 3507 5360 3241 * 3738 3312 3847 3173 3498 * 5235 42
+ 0 * * * * * 0 9622 0 1473
+
+C 43 4525 5071 3977 1882 6215 5593 6619 4828 6315 3592 6431 * 3312 5082 3751 5565 4901 3395 5123 5469 43
+ 93 * 3998 * * 0 * 9627 0 1473
+
+L 44 5102 5843 4156 3861 3881 * 3020 2803 5111 3226 4845 5884 * 6285 4690 5774 4983 3002 * 3638 44
+ 145 * 3388 * * * 0 9644 0 1492
+
+E 45 3748 * 3078 2421 * 4135 5961 * 4612 5656 * 5576 2371 4949 7873 3226 3469 * * 4695 45
+ 0 * * * * 1333 729 9356 0 2346
+
+K 46 2688 6271 2667 3853 * 4317 6131 5728 4746 6378 6331 4516 2452 3871 4622 3790 6405 4620 * * 46
+ 45 5917 6131 2322 322 0 * 9567 1050 1794
+
+E 47 4359 * 2859 2568 * 3064 6508 * 3896 5768 5604 4633 5206 3625 5376 3460 3732 5198 * 4563 47
+ 13 * 6777 * * * 0 9732 0 1000
+
+D 48 4642 6101 2364 3431 6611 6000 2734 6038 4722 4490 * 3078 4382 4147 3864 5003 6587 6356 6721 5069 48
+ 0 * * * * 0 * 9723 0 1100
+
+F 49 4729 5781 6712 * 2682 * 5872 3492 * 2789 2561 * * 5461 6337 4772 6051 3981 3177 3353 49
+ 99 4058 7337 1930 439 * * 9770 1757 0
+
+Y 50 3080 5622 6449 5630 3986 4620 6582 3121 5866 3617 4626 5338 6212 6526 4116 4490 3313 3200 5669 3626 50
+ 0 * * * * * 0 9709 0 1172
+
+Y 51 5034 * * * 1925 * 5320 2785 5738 3556 4691 * 5334 6829 4463 * 4104 2882 * 3048 51
+ 0 * * * * 1250 787 9709 0 1172
+
+P 52 2589 6288 4204 5274 6626 1349 6410 * 5136 5053 5290 5415 3504 4671 4745 4209 * * * * 52
+ 455 * 1887 * * * 0 9697 0 1050
+
+F 53 3880 * 2553 4034 5884 1677 6522 * 4510 4100 * 4620 3232 * 4186 4606 6092 * * * 53
+ 1389 694 * 1883 456 69 4424 9003 4774 3922
+
+D 54 2553 * 3393 3742 * 1850 6733 * 3841 * * 4058 4041 3928 4747 5917 3990 * * * 54
+ 39 6128 6326 1000 1000 * 0 8996 1028 1050
+
+R 55 3822 * 4271 3537 * * 6310 6538 3559 5088 6529 5686 3592 5476 1956 3175 3087 5489 * 6684 55
+ 93 4356 6173 192 3002 704 1373 9022 1670 1315
+
+S 56 3198 * 2785 3278 5291 3480 5149 6228 4799 5350 5260 4489 6670 5199 5241 2690 2871 * * * 56
+ 98 6398 4212 0 * 1183 838 9004 1000 1182
+
+D 57 3164 * 2194 2358 * 4308 4777 6687 4876 6115 5851 4492 3564 4009 4403 4804 * 4709 * * 57
+ 75 * 4311 * * 385 2094 8994 0 1586
+
+D 58 3738 * 3320 5242 6050 3572 4936 * 4185 * * 3346 1754 4796 3807 4234 7001 6062 * 4897 58
+ 0 * * 0 * 1201 824 8937 1050 1525
+
+Y 59 3384 3085 * * 2390 4851 4813 5107 * 4031 3062 6462 6630 6530 4406 * 4105 3562 * 3424 59
+ 15 6550 * 0 * 1642 557 9044 1264 1250
+
+T 60 2556 4577 * * 5403 6343 * 2116 * 2847 4227 * 3817 * 6027 6249 3960 2598 * * 60
+ 32 6638 6383 1000 1000 0 * 9035 1000 1133
+
+V 61 6812 5474 5811 5159 2687 6806 3280 3616 5948 3387 3670 4571 * 4829 4579 6070 5159 3053 7130 3409 61
+ 0 * * * * 0 * 8670 0 1050
+
+I 62 4696 5163 * * 4700 5424 * 1094 * 3533 4948 * * * 6927 * * 1856 * * 62
+ 26 * 5824 * * * * 8740 0 0
+
+E 63 5552 6445 4162 2699 5090 6527 3545 5452 3951 * * 3085 * 3167 4716 2903 3033 6562 * 6612 63
+ 0 * * * * * 0 8745 0 1165
+
+I 64 4617 5951 * * 4508 4465 * 1689 * 2734 6605 * * * * * 6414 1429 * * 64
+ 28 * 5726 * * * 0 8745 0 1165
+
+N 65 3601 6445 4000 3932 5306 * 4326 * 2495 5005 6077 5660 * 4117 3587 3873 2543 4601 6565 5194 65
+ 0 * * * * 0 * 8717 0 1439
+
+L 66 3399 4374 5858 * 5250 4514 4841 2640 5779 2377 4329 * * * 5821 2869 3859 3738 6005 * 66
+ 216 * 2845 * * * * 8740 0 0
+
+M 67 3861 6925 * * 2953 4724 * 2298 6455 2913 3502 5411 4999 6678 3258 5194 6517 5474 5044 4057 67
+ 63 * 4556 0 * 0 * 8501 1163 2809
+
+A 68 3057 * 5452 3217 * 2289 4754 * 4125 * * 4255 2619 4763 4425 3760 5093 4911 * 6008 68
+ 40 6315 6095 0 * 0 * 8689 1174 1312
+
+G 69 5000 * 6374 6588 6886 941 5969 6157 3966 6868 6839 4973 4587 5444 3802 4543 4061 4848 * * 69
+ 71 4377 * 493 1790 0 * 8755 1530 1136
+
+R 70 5845 * 5139 * 4388 6914 6607 3777 5198 2974 * 4571 5015 7366 1125 7192 4591 4167 * 5709 70
+ 67 4459 * 0 * * * 8740 1333 0
+
+M 71 6679 * 2766 4655 * 3998 6163 * 5139 * 6423 3420 4091 6693 6563 1818 2113 * * * 71
+ 17 * 6385 * * * * 8740 0 0
+
+E 72 3346 * 2550 3073 7233 5939 4776 4626 4242 3895 6669 * 3360 3916 4138 5806 3821 3771 * * 72
+ 9 7276 * 0 * 0 * 8749 1224 1148
+
+G 73 3037 * 3304 1090 * 4538 5945 * 4293 * * 5712 5719 3911 * 4346 5109 6129 * * 73
+ 0 * * * * * * 8740 0 0
+
+T 74 3542 * 4215 3602 5682 6163 6891 6218 4018 4216 5671 5161 * 1541 4248 4979 3750 4601 * 5973 74
+ 0 * * * * * * 8740 0 0
+
+K 75 6869 4810 6779 5741 6822 * * 4561 947 4492 6642 3371 6758 5499 3213 * 5024 5441 * 6163 75
+ 62 4581 * 1192 831 * * 8740 1375 0
+
+K 76 3128 * 3809 3083 * 6104 6209 * 2515 4308 6129 5914 6215 3036 2529 4371 4955 5460 * * 76
+ 0 * * * * * * 8740 0 0
+
+R 77 2670 * 4498 2675 * 4945 5183 5318 2527 7078 5569 3868 * 4031 2616 5268 4785 * * * 77
+ 0 * * * * * * 8740 0 0
+
+L 78 5150 * * * 2734 * 6416 3103 * 1067 3710 * * * * * 6052 5032 6106 3653 78
+ 0 * * * * * * 8740 0 0
+
+I 79 2433 6524 * * 4616 5104 6642 2981 * 3874 4095 5385 * * 7953 2457 4379 3347 * 3130 79
+ 0 * * * * * * 8740 0 0
+
+K 80 2535 * 3806 2567 * 5825 5770 * 2082 4129 * * 6758 3634 3524 5239 4920 5528 * * 80
+ 7 * 7600 * * * * 8740 0 0
+
+M 81 1943 6522 3559 2653 * 4011 * * 3349 3850 4973 6448 * 4253 3641 5076 5489 5750 * 6739 81
+ 0 * * * * * 0 8745 0 1065
+
+L 82 5169 * * * 3463 * * 1722 * 1726 4240 * * * * * 5560 2308 * * 82
+ 0 * * 1000 1000 0 * 8745 1065 1065
+
+F 83 2709 4127 6527 6247 3919 * 5110 5628 6497 5234 4345 7052 * * 5185 3485 1636 3470 * 5189 83
+ 19 7953 6816 0 * * * 8740 1000 0
+
+S 84 2943 6436 2533 2157 * 4997 5217 6628 3850 6865 * 5228 5485 3818 3614 4457 4359 6748 * 6636 84
+ 16 6521 * 0 * 0 * 8725 1019 1025
+
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+D 125 2620 * 1326 * * * * * 2853 * * 2727 * * * * 2746 * * * 125
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+I 126 * * * * * * * 732 * * * * * * * * * 1329 * * 126
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+Y 127 2290 * 1370 * * * * * * * * * * * 2335 * * * * 2249 127
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+V 128 * * * * * * * * * 2023 * * * * * * * 408 * * 128
+ 0 * * 0 * * * 2467 0 0
+
+//
+�HHsearch 1.5
+NAME 2f38e0381f5a1497aa929335a94cdbc7
+FAM
+FILE 2f38e0381f5a1497aa929335a94cdbc7
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:18:21 2013
+LENG 89 match states, 89 columns in multiple alignment
+FILT 113 out of 1640 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCC
+>ss_conf PSIPRED confidence values
+98999999999983670089999999998778999938699999999993799999999999998688999949699999999867899
+>Consensus
+ixxxeFxxxxxxxxxxxxxxxxxxxxFxxxDxxxxgxixxxexxxxxxxxxxxxxxxxxxxxxxxxdxxxxgxixxxefxxxxxxxxxx
+>2f38e0381f5a1497aa929335a94cdbc7
+MNFGDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKRVAKELGENLTDEELQEMIDEADRDGDGEVSEQEFLRIMKKTSLY
+>gi|66808853|ref|XP_638149.1| EF-hand domain-containing protein [Dictyostelium discoideum AX4]gi|74996819|sp|Q54MZ4.1|MCFB_DICDI RecName: Full=Mitochondrial substrate carrier family protein Bgi|60466585|gb|EAL64637.1| EF-hand domain-containing protein [Dictyostelium discoideum AX4]
+---------------------------------------MSNNNNNNNNNNNNNNNNNN----NNNNNNNNDKNNNNNIDSSIK-----
+>gi|330796947|ref|XP_003286525.1| hypothetical protein DICPUDRAFT_77398 [Dictyostelium purpureum]gi|325083506|gb|EGC36957.1| hypothetical protein DICPUDRAFT_77398 [Dictyostelium purpureum]
+ITKDEAISYF-KNSGSKFPERNASYLFKAMDLDHDGKLTLDEIRAGLIKEYSEkledTIELDIDAFFLKHDINKDQKIHKKEMIQYFEDLGT-
+>gi|313213218|emb|CBY37065.1| unnamed protein product [Oikopleura dioica]gi|313233994|emb|CBY10162.1| unnamed protein product [Oikopleura dioica]gi|313246556|emb|CBY35452.1| unnamed protein product [Oikopleura dioica]
+-------------LEDDELQSRLRKLVVRMDHNRDGYVDKEELTSWGLVSIYNIQGKDGREDYEFLLHDGASg-LDFDHLSDDI------
+>gi|74189848|dbj|BAE24569.1| unnamed protein product [Mus musculus]
+---------------EKEPIAASTNRGKDLIGVQNLLKKHQALQAEIAGHEPRIKavt----------------------------------
+>gi|67471481|ref|XP_651692.1| EF-hand calcium-binding domain containing protein [Entamoeba histolytica HM-1:IMSS]gi|56468461|gb|EAL46305.1| EF-hand calcium-binding domain containing protein [Entamoeba histolytica HM-1:IMSS]
+ISFYEYMGMHK-------FLEICYNVFIQCDTNRSGTMEPHEIIPALRILGFFVNQRTAIVLHRLFAHGs---tICDLNCWIALCA-----
+>gi|256075808|ref|XP_002574208.1| mitochondrial solute carrier [Schistosoma mansoni]gi|238659407|emb|CAZ30441.1| mitochondrial solute carrier, putative [Schistosoma mansoni]
+IHYDEFTQIIH-V-----KYNFSYTCIYFSYK--TGTITVDQFKSIILQLkSRLLTPLIKENLLTVVlqsemdGGR----ITFAYYMAF-------
+>gi|221117548|ref|XP_002159552.1| PREDICTED: similar to apoptosis-inducing factor (AIF)-like mitchondrion-associated inducer of death [Hydra magnipapillata]
+-------------VQYTKISDYVEMLY---DTEIKNGKNLSQFEELIEKGKMKYPHLSyhfkelkklynSKVLKLESEGs-----LSLKDLHSLAKIVDS
+-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 43 5080 * 0 * * * 9486 1202 0
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+
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+
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+
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+
+I 38 * * * * 5540 * * 1605 4934 1538 4473 * * 6479 * 6140 * 2304 * * 38
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+
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+
+A 47 4104 4497 6733 * 4124 * 6643 2522 * 1900 2930 6196 * 6792 6898 6769 4834 2711 * 5670 47
+ 30 7053 6266 2807 222 * 0 10624 1000 1299
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+K 48 5489 6653 4196 3557 * 3707 5716 6018 3117 4480 5199 3584 * 3595 2838 3273 4682 3769 * 6917 48
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+
+T 55 3423 5767 2991 6577 5920 5086 5260 5302 3723 4985 7051 3398 3235 6819 5693 2964 2958 4902 * 5619 55
+ 64 4537 * 2576 265 * 0 10516 1795 1290
+
+D 56 3976 * 3422 2542 * * 4933 4489 3170 4171 5889 4064 3653 3862 4048 * 4064 4788 * 4433 56
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+
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+I 63 5626 5737 * 6443 1959 7029 5432 2911 5673 2023 3674 * * * * * 5480 3922 4263 4507 63
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+
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+D 71 5037 * 1543 3583 6812 4500 6404 * 3389 5717 * 3181 * 4552 5145 3311 4063 * * 5527 71
+ 32 5522 * 378 2117 1106 901 10337 1371 2371
+
+G 72 5416 * 3655 3631 5943 1141 5611 6721 4496 6516 * 3622 5034 4488 5796 4780 5729 5481 6684 * 72
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+E 73 4131 6456 5777 4249 5306 5033 3756 4968 2449 5140 5455 5858 * 3199 3076 4021 3574 4971 * 4561 73
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+
+V 74 * 4820 * * 4201 * * 1553 6357 1788 3839 6145 * * * * * 2446 * * 74
+ 0 * * * * 1097 909 10446 0 1229
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+S 75 6688 6500 2368 4195 * 4884 6467 * 5225 6783 * 2508 3903 6789 5019 2189 2856 6636 * * 75
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+
+E 76 5542 * * 5581 2000 5064 * 3675 3944 2685 4294 6143 * 5881 4298 6728 * 4802 4536 2666 76
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+
+Q 77 3656 * 2288 2229 * 6165 * 5323 3781 4463 * 3938 5175 3862 6773 3432 4781 5946 6911 5554 77
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+
+E 78 4676 6227 2279 1218 4237 3809 7000 * 4829 6753 * 6145 * 4167 6760 4466 * * * 6566 78
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+I 82 3734 3960 * 5478 2882 6612 5599 3668 5670 2261 3388 6716 6459 6829 6493 4363 6127 3520 4989 4417 82
+ 0 * * * * * 0 10424 0 1024
+
+M 83 4325 4281 * 6062 4296 5327 * 2897 6232 1929 2936 6432 * * * * 5712 2783 5507 3853 83
+ 0 * * * * * 0 10348 0 1024
+
+K 84 3620 6264 6408 4150 5474 6717 5539 4365 2472 4345 6416 3260 5270 3388 3514 3498 3879 6399 * 6305 84
+ 0 * * * * 0 * 10061 0 1024
+
+K 85 4458 * 3824 3706 * 3229 5430 5850 2643 6131 * 3222 * 4714 2550 3030 4402 * * * 85
+ 47 * 4969 * * * * 9835 0 0
+
+T 86 4203 5781 4267 4492 4732 * * 3895 3336 2369 * 3681 * 4853 4468 4631 4253 2989 4643 5868 86
+ 25 5868 * 501 1769 0 * 9291 1142 1207
+
+S 87 3812 * 2696 3843 * 4050 * * 5542 5264 * 4526 1985 * 5553 3086 2850 5428 * * 87
+ 0 * * * * * * 9120 0 0
+
+L 88 4896 * 4872 5062 5116 * * 3111 3868 2192 * 2802 * 4835 4882 3317 3985 3402 * * 88
+ 0 * * * * * * 8191 0 0
+
+Y 89 * 4007 * * 2515 * 4010 * 3054 2103 * * * 4051 * * * * 4013 2150 89
+ 0 * * 0 * * * 6487 0 0
+
+//
+�HHsearch 1.5
+NAME 2f4c86088a47ef73c12ffc801e19fb3c
+FAM
+FILE 2f4c86088a47ef73c12ffc801e19fb3c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:14:23 2013
+LENG 227 match states, 227 columns in multiple alignment
+FILT 149 out of 1419 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEECCCCCCEECCCCCCCEEEEECCCCCCEEEEEECCCCCCCEEEEEEEEC
+CCCCEEEEEEEEEEEECCCCCCEEEECCCCCEECCCCEEEEEEEECCCCCCCEEEEECCCCCCCCCCCEEEEECCCCEEEEEEEEEEECCCCCCEEEEEE
+EECCCCEEEEEEEECCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9399576868996899899999972888888589999918999828999995478850105555772899852778705799812531143548999942
+8862561248999974033364488618742211697599999945757998699988995457731103485499789999999960456797799999
+948898789999920569999498999
+>Consensus
+xxxxxxpxxxxvxxGxxvxLxCxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxxLxIxxvxxxDxgxYxCxvxx
+xxxxxxxxxxxlxvxxxxxxxpxxxxxxxxxxxxxgxxxxlxCxxxxxxPxxxxvxWxxxxxxxxxxxxxxxxxxgxxxxxsxLxixxxxxdxgxyxCxv
+xxxxxxxxxxxxxxxxxxxxxxxxxxx
+>2f4c86088a47ef73c12ffc801e19fb3c
+EVQLQQPGAELVKPGASVKLSCKASGYTFTNYWINWVKQRPGQGLEWIGNIYPGSSYTHYNEKFKNKATLTVDTSSSTAYMQLSSLTSDDSAVYYCANKL
+GWFPYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNV
+AHPASSTKVDKKIEPRGPTIKPCPPCK
+>gi|1853|emb|CAA32113.1| mu-immunoglobulin C(U) [Suncus murinus]
+----------------TSQLICQASGFSPRTIVMSWL--QRGEPVQPSL-VSTSAVEAEPKGSGPTTFRVI-------SRLTITENEWLSQREFTCQALH
+KG-LTFQKNVSSVCmGDDTSTGISVFLLPPTFANIfLTQSAQLTCLVTGLATyDSLDISWsrQNGEALQTHVNISESHPNSTFTAKGHASVCREEWEsGE
+KFTCTVQHSDLPSPLKQSLSR------------
+>gi|332835951|ref|XP_003312984.1| PREDICTED: b7 homolog 6-like [Pan troglodytes]
+KVEMMAGGTQITPLNDNVTIFCNIFYSQPLNitsmgITWFWKSLTFDKEVKVFEFF----GDHQEAFRPGAIVSPWRLKSG-DASLRLPGIQLEEAGEYR
+CEVVVTPLKAQGT-VQLEVV-----ASPASRLFLDQVGVKENEGKYMCESSGFYPEAINITWekqtqkfpHPIEISEDVITGPTIKNmDGTFNVTSCLKL
+NSSQEDpGTVYQCVVRHASLHTPLRSNF--------------
+>gi|334323375|ref|XP_001366403.2| PREDICTED: butyrophilin subfamily 2 member A2-like [Monodelphis domestica]
+QFTVVAPAKPLlVMVGEDAILHCHLFPKKNAEQmEVRWFRSQFSPAIYVY--KDGKNRDEEQMEEYRSRTTFMRDnIKDGSVALKIHNVTAFENGRYHCY
+FQE--GRSYDEAFIDLKVASMGSDPLIEI-----TGYEYGWIQLECTSAGWYPQP-RVEWrnLSEETIPSLEENLVPSEDGLFIVKLSVNITDHT--VVS
+VFCSIQNSLLSQELLAMMSIPE----------
+>gi|148690707|gb|EDL22654.1| mCG22132, isoform CRA_c [Mus musculus]
+---LQVQRIVKAQEGLCIFVPCSFSSPEGkwlnRSpLYGYWFKGIRKPSLSFP--VATNNKDKVLEWEARGRFQLLGDISKKNCSLLIKDVQWGDSTNYF
+FRMERGfERFSF-K-EEFRLQVeVpdLHENPSHLE------VQQGQSLRLLCtadsqppaTLSWVLEDqvlswsSPVgsrtlaleLPW----------VK
+AG------------dsghytcqaenrlgsqqhtldlsvlceyd---lpkVPGPKkDkGVTSGYKqsdycAACVGDPMSDAPThpqlpslggmfcperraw
+pvwnqFP-------------
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+-------------------------------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne--DLRSWTAADMAAQN-----------
+---tqrkweaagvaeqw----RAYlEGECLEWLRRYLEKGK-----------------et--LQ--raEPs-SQSTIP-----
+>gi|47215549|emb|CAG06279.1| unnamed protein product [Tetraodon nigroviridis]
+--------------------------------------------------------------------------------ILIRNLQPSFNADYVCTAKV
+KGVEKTSKAFSINVIQKLRFPPYVFLEMDEYVRIVGEELKIRCMTHNP-NFNYNVTWNYTTKSVSMRHHAVYLHREnRLDIQSILTISAVVLaDTGNISC
+IGTNEAGVNSSNTYLL-------------
+>gi|301623029|ref|XP_002940823.1| PREDICTED: beta-2-microglobulin isoform 1 [Xenopus (Silurana) tropicalis]gi|301623031|ref|XP_002940824.1| PREDICTED: beta-2-microglobulin isoform 2 [Xenopus (Silurana) tropicalis]
+----------------------------------------------------------------------------------------------------
+----------------SNISPPVVKVYTAEPVE-FGKKNELICYAYDYHPPRMEISLlkNGVEIPDT-kQKDPSFHHNWKYYTMMSAHVHIDS--DD--k
+vE-----clvah-------------------------
+>gi|312373456|gb|EFR21197.1| hypothetical protein AND_17411 [Anopheles darlingi]
+------KPVMDAVEGQSFSVMCNATGKPV--PEFQWIKQGTQQNAADL-----------------DRFSVN----AITGQLDISKVEQQDHDSYACIARN
+P-AGQSESVMKPNVL----IRPKIIELINITVSEDTE-AVFVCKAFGRPEPEITFRRygtleeysIGLQVSDDRIQLEQSVDVDKGESVGTLRISKVTTt
+DDGLYECIARNRGDvafkAGHITVEYSPI-----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 7596 0 0
+
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+ 0 * * * * * * 8786 0 0
+
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+ 0 * * * * * * 9045 0 0
+
+L 4 5838 * * * 4226 * * 2851 5966 1715 3921 * * * * 5640 3376 1798 * * 4
+ 23 5966 * 0 * * * 9577 1016 0
+
+Q 5 * * 5107 3610 6218 6606 6108 4263 5022 4813 * 3946 4904 2731 6021 2719 2313 3120 * * 5
+ 0 * * * * * * 9856 0 0
+
+Q 6 3102 * 5981 4155 * 4465 5253 * 3525 3683 5893 4811 5200 1855 5179 4302 4587 3332 * * 6
+ 89 4066 * 0 * * * 9939 1535 0
+
+P 7 5952 * 5266 5296 * 6498 4683 5909 4305 5431 * 4482 924 4546 5918 3323 4038 * * * 7
+ 15 6572 * 0 * * * 10107 1015 0
+
+G 8 3267 6495 5632 2591 * 3536 5524 * 4622 4827 * 4201 2315 5713 5111 3632 4008 4187 * 6148 8
+ 46 5783 6260 588 1578 * * 10243 1101 0
+
+A 9 4089 * 3572 3620 6475 4679 4186 5902 4650 3574 * 3698 4640 4024 5445 2330 3401 4837 * * 9
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+
+E 10 5089 * 5451 3733 6600 4836 6480 2855 5737 2377 5121 * 6039 4243 5499 4283 4777 1945 * * 10
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+
+L 11 5665 6565 4716 4605 4808 6808 6376 3758 4911 3914 4743 5093 4808 4772 3821 2660 2678 3032 * 6160 11
+ 64 4524 * 0 * * * 10476 1496 0
+
+V 12 2149 6616 * 6986 * 4497 5950 3753 5743 3787 5696 6689 4744 5668 5768 5208 4684 1539 * 5935 12
+ 0 * * * * * * 10520 0 0
+
+K 13 3552 * * 4522 7096 5692 * 6826 2975 3758 4447 4476 4412 3000 3893 3484 3527 3589 5029 6096 13
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+
+P 14 4709 * 5986 2121 * 5653 * 5048 3567 3064 * * 3170 4708 4100 3660 4372 3464 6893 5158 14
+ 0 * * * * * * 10685 0 0
+
+G 15 6664 * 5147 4265 7193 426 * * 5797 * * 4540 * 5450 5541 4768 * 6940 * 6906 15
+ 11 7047 * 1585 585 * * 10735 1000 0
+
+A 16 4656 * 2913 2217 * 3164 6714 * 3347 5912 6841 5074 * 3385 5987 2792 3960 5795 * * 16
+ 0 * * * * * * 10749 0 0
+
+S 17 4537 5315 3517 4294 6386 7283 6105 * 4264 * * 3052 3225 4174 4427 2470 2722 4408 * * 17
+ 25 * 5850 * * * * 10770 0 0
+
+V 18 2067 * * 6145 4998 5717 7187 3687 6518 3837 4053 * 6225 * * 6280 4895 1311 * 6930 18
+ 0 * * * * 0 * 10799 0 1169
+
+K 19 6108 * 5017 4191 5844 6630 5525 3481 4301 5080 6387 4007 5081 4822 4318 3244 1811 3541 * 6046 19
+ 0 * * * * * * 10804 0 0
+
+L 20 * * * * 3303 * * 2553 * 695 4869 * * 6723 * * * 3900 * * 20
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+
+S 21 * * 3790 4798 6049 6884 4715 4815 4826 4256 5031 3958 2685 4477 3300 2783 3189 4488 * 6551 21
+ 0 * * * * * * 10804 0 0
+
+C 22 5655 135 * * 5839 6871 6420 5917 * * * * * * * 6815 * 7327 * * 22
+ 10 7191 * 0 * * * 10804 1000 0
+
+K 23 4380 * 5131 3636 6131 4978 4276 5380 3569 3960 * 3185 4386 4474 3951 2548 3538 4896 6970 7207 23
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+
+A 24 3357 6888 * 6603 2862 6229 6955 3189 5841 2862 * 7055 4476 7091 * 4994 4626 2365 * 2896 24
+ 118 4456 4922 695 1387 * 0 10798 1670 1000
+
+S 25 5297 * 3975 3562 6499 4803 4436 4559 4468 5194 6676 3882 3893 4117 4493 2903 2438 4676 7428 6944 25
+ 191 3920 4102 1412 680 751 1300 10752 2026 1563
+
+G 26 3814 7242 4451 3931 * 1905 6758 5329 4598 4491 5171 3069 5589 3877 5289 3560 4225 6215 * 6492 26
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+
+Y 27 4289 7138 4569 4760 3156 4192 4635 7041 4147 4141 5962 4543 4115 3924 4841 2872 3614 4496 6734 4458 27
+ 68 * 4447 * * 208 2896 10667 0 2891
+
+T 28 4542 6951 3406 4145 6875 5047 6736 5949 3603 4169 * 4087 2502 4470 5424 2883 3295 4695 7430 6614 28
+ 226 5771 2984 2664 248 786 1251 10724 1226 1906
+
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+ 413 5915 2107 536 1689 2140 371 10657 1113 3577
+
+T 30 4103 * 2987 4321 5338 3414 5590 * 3379 5321 6249 4232 3590 4762 4144 3424 2920 6193 * 5421 30
+ 138 4372 4548 953 1048 3658 119 10362 1464 6153
+
+N 31 6843 * 2360 3614 * 4197 4179 4549 4332 3866 * 3504 4060 4502 4441 3976 4548 3856 6937 5481 31
+ 189 3023 * 645 1471 352 2208 10368 2638 6149
+
+Y 32 7413 * 4001 4837 3894 4815 5294 3556 5003 3161 5385 5061 3112 4620 5615 3809 3784 3218 * 4100 32
+ 111 3911 7003 796 1237 1143 870 10719 2066 2340
+
+W 33 4173 * 4529 4892 5678 5422 4857 3339 4952 5043 4508 5311 5083 4042 4330 2796 3297 3472 6027 3868 33
+ 16 6516 * 0 * * 0 10755 1079 1845
+
+I 34 5352 7078 * * 5016 5950 * 2095 5511 2061 5773 * * * 6942 7006 6159 1459 * 6234 34
+ 0 * * * * 2640 252 10755 0 1845
+
+N 35 5044 * * 3560 3480 5046 4901 4558 4566 4327 6746 4092 * 4102 3897 3052 2851 4562 6793 3425 35
+ 24 5896 * 0 * * 0 10761 1186 1691
+
+W 36 * * * * 5047 6912 * 5975 6407 5306 * * * * * * * 4551 208 * 36
+ 40 * 5205 * * * 0 10761 0 1691
+
+V 37 6896 5858 6025 5372 2376 * 5179 4820 3965 3335 7049 * * 4552 4886 4474 4190 4572 5848 1874 37
+ 48 * 4932 * * * 0 10728 0 2176
+
+K 38 * 6354 * * 4931 6766 4870 5145 1805 4604 5915 5034 * 3495 2121 5152 5308 4144 4283 5104 38
+ 63 7086 4824 1585 585 1971 425 10690 1000 2800
+
+Q 39 5258 * 2982 4559 7386 3849 5209 6891 4604 4676 5336 4219 6186 2042 4137 3965 4058 3619 7066 6810 39
+ 168 7150 3284 0 * 2847 216 10710 1000 2944
+
+R 40 4408 6293 3511 4204 5820 3705 4821 5054 3024 4732 5129 4379 4134 4626 2938 4181 3889 5800 * 4940 40
+ 355 * 2197 * * 2225 347 10590 0 4317
+
+P 41 4920 * 3430 3707 4653 4385 6573 4702 3809 4021 * 4015 1919 5007 5445 3334 5252 5481 * * 41
+ 99 4109 6917 1280 766 701 1377 10375 1598 6200
+
+G 42 4922 * 3329 3896 * 1449 6697 * 4872 6354 * 3484 5683 4644 4181 3580 4179 5145 * 7152 42
+ 27 7154 6412 1000 1000 2422 298 10723 1007 3470
+
+Q 43 3937 * 3984 3964 7100 3351 5369 * 2487 4451 6983 3261 4721 2802 5820 4155 3899 5678 * * 43
+ 104 6850 4044 1585 585 * 0 10668 1000 3222
+
+G 44 3132 * 3988 3339 5464 3164 5534 4846 5943 4796 * 4076 3023 4446 4191 3244 3931 5799 6757 * 44
+ 84 4807 5606 542 1675 1981 421 10607 1420 4178
+
+L 45 5378 * 5133 4828 5287 6660 6999 3043 5282 2601 4916 5503 2229 5262 3894 4461 4713 3300 6608 * 45
+ 0 * * 0 * 1953 431 10613 1000 3746
+
+E 46 4968 * 3863 2479 5589 4960 6939 4771 4302 4503 * 4417 5167 3042 3446 3192 4102 4236 * 5717 46
+ 131 7905 3601 2585 263 2107 381 10674 1000 3087
+
+W 47 4738 7068 4249 5105 2941 6153 5883 5016 4545 2654 4627 5616 4433 5414 4240 4212 4323 3604 3947 4470 47
+ 13 * 6811 * * * 0 10608 0 3901
+
+I 48 6921 5897 6900 4301 4548 6535 5995 2285 6673 1904 5968 6858 4710 6710 7008 3233 * 2590 * 6403 48
+ 648 5945 1532 1001 999 1816 482 10605 1172 4001
+
+G 49 2442 4809 6189 6394 3248 3062 5332 3513 * 3223 * 6493 * 4636 * 3996 3764 3785 5174 5493 49
+ 96 6253 4278 1585 585 5224 39 10051 1101 6797
+
+N 50 4168 * * 3775 3626 4798 5189 5336 4005 4792 5168 6515 4654 6118 4108 2993 3516 4672 4507 2673 50
+ 0 * * * * 833 1188 10055 0 6944
+
+I 51 5153 6585 5505 6383 3674 6782 5809 2237 4277 3372 5288 5816 * 5106 4132 5058 4167 2704 6007 3685 51
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+ 461 5936 1960 1712 525 4805 53 10575 1149 4390
+
+P 53 3278 * 4843 4477 5248 3548 5218 5557 3265 5479 6410 4363 3357 5393 6177 2987 3498 3896 * 4226 53
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+
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+
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+ 153 5002 3846 1240 795 2037 403 10091 1327 6971
+
+S 56 6410 * 3641 5339 * 2026 6589 5267 2966 5375 * 3479 4119 4591 4223 3608 4423 4505 * 4860 56
+ 136 5256 3972 2186 358 3292 155 10329 1161 6372
+
+Y 57 4523 6677 3491 4949 6474 3746 5015 4551 4363 4808 * 4897 5840 4809 3510 2695 3011 3072 * 6663 57
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+
+T 58 5514 * 4884 4824 5552 5151 4680 4127 3082 4746 6498 4458 3592 5560 3724 2708 3296 3209 6868 * 58
+ 89 5044 5093 1852 468 3252 160 10450 1271 5951
+
+H 59 4137 * 3918 2825 4157 6562 4826 5214 4182 3677 * 3364 6596 3601 3993 4076 4193 3793 * 4836 59
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+
+Y 60 4632 5080 5174 4675 3037 3921 5610 5469 5769 4113 * 3883 5607 4010 4005 4283 4224 3200 * 2945 60
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+
+N 61 3806 * 4159 3585 4952 4158 5305 5070 4189 4818 5104 3598 3685 4299 4164 3280 4083 3830 6554 5910 61
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+ 49 4897 * 1513 623 * 0 10623 1480 4406
+
+K 63 4688 * 3026 3188 * 2899 6728 5350 4152 5694 * 5044 3618 4142 5721 3000 3484 3586 * * 63
+ 45 7024 5432 2178 360 3993 94 10623 1112 4406
+
+F 64 5049 * 5306 4873 3235 4361 4745 4145 6277 3099 5926 5054 6906 5273 4123 4315 3884 3271 * 2537 64
+ 52 5169 6980 4665 58 5037 45 10630 1527 4519
+
+K 65 4661 7131 2841 3138 5476 5779 4759 7123 2885 5601 4730 4061 4020 3846 3717 3827 4134 6748 * 5802 65
+ 67 4463 * 494 1787 297 2426 10625 1574 4519
+
+N 66 3822 6518 3042 3387 * 2170 5402 6455 3911 5264 * 3426 4499 4678 4538 3311 5324 7290 * * 66
+ 29 6941 6434 0 * 2383 307 10806 1000 1656
+
+K 67 6850 * 5424 4437 * 4858 5508 5967 3762 7059 6439 5048 4463 4716 887 4747 4468 5661 * * 67
+ 25 5868 * 0 * 1859 465 10772 1155 1746
+
+A 68 3053 5938 * 6617 1912 4496 4767 3438 6807 3374 5852 7189 * * 5398 6360 4445 3330 7274 3368 68
+ 12 * 6914 * * 2312 324 10820 0 1505
+
+T 69 5392 * 4509 4349 4986 4715 4375 5074 4201 4101 * 4755 7478 3945 3579 2301 2702 5013 6008 5128 69
+ 51 5918 5799 0 * * 0 10816 1129 1533
+
+L 70 3459 5772 5978 5488 3487 5308 * 3219 4570 2337 4533 6616 * 5102 6801 4413 6145 2515 6053 4375 70
+ 33 * 5447 * * 3039 187 10820 0 1851
+
+T 71 5016 * 3473 3233 4276 5381 5713 4462 5949 4009 6500 4730 5059 3478 4193 2743 2846 4774 * 7354 71
+ 274 7142 2593 1585 585 2093 385 10793 1000 2160
+
+V 72 4460 6914 4337 4472 3836 2823 6689 5024 3299 4467 * 4783 3624 4564 3240 3686 4789 4490 5733 6598 72
+ 63 6754 4897 0 * 4797 53 10635 1011 4520
+
+D 73 5254 6617 2176 3331 5848 4797 6912 4694 3645 4914 5235 3408 4569 4006 4381 4214 4421 5927 6486 5141 73
+ 489 3189 2493 586 1582 983 1017 10627 2397 4796
+
+T 74 3981 * 4237 3636 6440 3014 4915 5239 3385 4635 6480 3891 3368 4483 4588 3791 4799 3920 * 4780 74
+ 61 * 4588 * * 3790 108 10622 0 5408
+
+S 75 3494 * 3662 4071 4363 3946 6134 6547 5309 4414 6955 3968 4369 4146 5164 2567 3642 5600 3907 5549 75
+ 203 4682 3442 379 2114 1153 862 10556 1486 5548
+
+S 76 4101 * 3843 3491 * 2755 4638 6733 3421 3944 6534 3594 4773 3499 4379 3723 4379 5117 6998 * 76
+ 47 * 4965 0 * 1306 748 10626 1000 4746
+
+S 77 4135 6415 4183 4291 6564 2405 6743 6117 3913 5397 6666 3514 6594 4472 3637 2741 3065 6707 * * 77
+ 138 6827 3602 0 * 3581 126 10721 1000 3797
+
+T 78 4248 5698 2630 6045 * 4447 5559 4429 3994 5247 5368 3230 5254 4429 4059 3066 3006 5014 6563 * 78
+ 33 * 5456 * * 1134 878 10618 0 4678
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+
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+D 210 5381 * 3194 3556 * * 5317 4893 3798 4756 * 3912 * 3985 4771 2817 2259 3820 * 5253 210
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+ 44 6680 5630 2129 374 0 * 9513 1116 1006
+
+K 212 * * 6126 3173 5931 * 3624 5219 4199 6237 5809 4075 4178 4567 4566 2566 2110 5171 * 4730 212
+ 0 * * * * 1831 476 9500 0 1332
+
+I 213 5731 * * * 2869 * * 2133 6001 1668 4275 * 5828 5723 * 5001 5911 2915 * 5845 213
+ 0 * * 1000 1000 0 * 9278 1197 1197
+
+E 214 * * 3944 2844 * 5694 5620 5617 4574 2922 * 2563 5694 3806 4186 2738 3631 5953 * * 214
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+
+P 215 * 4825 5100 * * * * 3529 2749 4837 * 4023 2705 3919 4354 3604 4854 2432 4912 * 215
+ 22 6046 * 0 * * * 7762 1197 0
+
+R 216 3431 * 4686 * * 3653 * 2170 4651 4598 * * 4202 3558 2828 3000 3634 * * * 216
+ 0 * * * * 0 * 6963 0 1197
+
+G 217 2811 * 3593 2412 * 4287 * * 3311 * * 4474 4121 4393 * 2120 4197 * * * 217
+ 85 4136 * 4858 51 * * 6553 1119 0
+
+P 218 * 1516 * 3535 * * 4147 * * * * * 2063 5769 4225 * 3824 2990 * * 218
+ 104 3841 * 4087 87 * * 5876 1101 0
+
+T 219 3958 * * * * * * 4191 3664 * * * 1533 * 4000 3350 2542 3011 * * 219
+ 0 * * * * * * 5426 0 0
+
+I 220 * * 1964 * * * * 3350 3736 * * * 1947 * * 2553 5322 3112 * * 220
+ 0 * * * * * * 4897 0 0
+
+K 221 3655 * * * * * 2705 5322 2475 * * 3639 1373 * * 3380 * * * * 221
+ 146 * 3380 * * * * 4897 0 0
+
+P 222 * * * 3540 * * * * * * * * 323 * * 3128 * * * * 222
+ 518 1730 * 2501 280 0 * 4622 1354 1123
+
+C 223 * 1259 * * * * * * * * * * * * * 2984 1709 2739 * * 223
+ 0 * * * * * * 3788 0 0
+
+P 224 2907 * * * * * 2739 * 3013 * * * 754 * * * * * * * 224
+ 223 2806 * 1585 585 * * 3788 1101 0
+
+P 225 2907 2739 1906 * * * * * * * * * 1628 * * * 2984 * * * 225
+ 0 * * * * * * 3788 0 0
+
+C 226 * 493 * * * * * * * * * * 1789 * * * * * * * 226
+ 0 * * * * * * 3788 0 0
+
+K 227 * * * * * * * * 0 * * * * * * * * * * * 227
+ 0 * * 0 * * * 1652 0 0
+
+//
+�HHsearch 1.5
+NAME 2ff05444e7145a5dd540ec42015fcba1
+FAM
+FILE 2ff05444e7145a5dd540ec42015fcba1
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:29:31 2013
+LENG 177 match states, 177 columns in multiple alignment
+FILT 110 out of 1146 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
+CCEEEEEEECCCCCCCCCHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9499999788888806999999999999996498885899999889026986477767899999999975505898759999999999987554058889
+96299999179988885758887988999997884334248999999966999853997199999999999999649
+>Consensus
+xDvxfllDxSxSmxxxxxxxxxxxixxxxxxlxxxxxxvxvixfxxxxxxxxxlxxxxxxxxxxxxxxxlxxxxgxtxxxxalxxaxxxxxxxxxxxrxx
+xxxxiilxTdGxxxxxxxxxxxxxixvxxigxgxxxxxxxxxxxLxxiaxxxxxxxxfxxxxxxxLxxxxxxixxxi
+>2ff05444e7145a5dd540ec42015fcba1
+VDLVFLFDGSMSLQPDEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPD
+ATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLCTELQKKI
+>gi|260837234|ref|XP_002613610.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]gi|229298996|gb|EEN69619.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]
+---LYPYGSySGGYPPSNMEKTMG-PGNYRVPLvaGGETITIGSIKKTEETSPseslsaekQAVVAAQDTRECTMSSITiySEERLRGTKKTYSGNGWLP
+RDPSW-----VVDSAGPAWVDSNGVTWEDV-------VTVDNVQSGDQ------RQVFGGFQGKARYWKLVITQTYTGWQPYVRE-----
+>gi|21675085|ref|NP_663150.1| hypothetical protein CT2279 [Chlorobium tepidum TLS]gi|21648325|gb|AAM73492.1| conserved hypothetical protein [Chlorobium tepidum TLS]
+IDIIFM-------ldisnsmLardtaPDRLTH-------aktellqISRRL--GDGRKALLLFAGTPVVQCPLTDDE--E-----dfeilLD-mA-apeL
+ITTqGTD------yrrafdA-aLKL-TNSGG-ELSSNETV------lvlasdGE--dhg-NDLGDIatamkTRG------vhlhviGVG--gvqpvpipm
+qggpkrdqqgkiVLTSFKPEPLASLIKTAKG-KFYYSRPDAp-vHDAVADDI----
+>gi|317505805|ref|ZP_07963650.1| von Willebrand factor type A domain-containing protein [Segniliparus rugosus ATCC BAA-974]gi|316255887|gb|EFV15112.1| von Willebrand factor type A domain-containing protein [Segniliparus rugosus ATCC BAA-974]
+--VILLLDISESMRatdvkPSRVEAARAAAIKFVDGM-APTVQLGVVTFAGNAQPLVRPSTD--HETAKKVIDQMIrpdKLEKQTATGEGIYTALQQIEt
+iAGalGGKNHA-PPARIVLVSDGKETVpdDLNAprgaYaaartaKEKHVPVCTVAFGTKAGkitldnqvdeVPVDLESLKKISDLSNSPgnscRFFPAES
+QGELAQIYQSLNEDI
+>gi|341895816|gb|EGT51751.1| hypothetical protein CAEBREN_12317 [Caenorhabditis brenneri]
+LDIVLVIDNTKIMQMDGVYQTIQLMFGASVRIGtdyqdPRSTRVAIVTYNEKATVVADFNKFKSLKQLNDELEMLNGTEKsdsfSAYMDLGLQSA-YDLI
+QDVNNANDrrRYKKLIILFTSNYAYKNKRPdvlAltiRQSGVDIATVYTGTGTT---RNTQFQlTfVGNYN---MNFHMADATpIVKELQGAT----
+>gi|227541544|ref|ZP_03971593.1| von Willebrand factor, type A [Corynebacterium glucuronolyticum ATCC 51866]gi|227182700|gb|EEI63672.1| von Willebrand factor, type A [Corynebacterium glucuronolyticum ATCC 51866]
+AHEMFi-aVDTSSSMEGQPLERTKEILAELSKGMfEssygeyafRPGDKISffg---LTPQS----sgpSYVAYDP--EDPDSYRELEDfangLntGPKI
+STCETLIRGLLGA-----D-GMGNAVPAVIFTTGTDEDDPECEnfesnvdslpEeSGPHPAYIFLLDPA-----HTEWMDTLAEITG-GQVFDATT----
+-----------
+>gi|332308254|ref|YP_004436105.1| LPXTG-motif cell wall anchor domain protein [Glaciecola agarilytica 4H-3-7+YE-5]gi|332175583|gb|AEE24837.1| LPXTG-motif cell wall anchor domain protein [Glaciecola sp. 4H-3-7+YE-5]
+-EVVFLLDTSGSMAGESIVQAKRAVDFALTQLHPED-SVNVIEFNDAPQALWNLAMPATANNIQRARNWVASLSanGGTEMAPALSMALHKtNLEQqniN
+EGSPVQLRQV-VFITDGSVSNEDALMSLienqlADSRLFTIGIGSAP----NSYFMTQAAQAGRGTFTY-IGDINQVQQKMTELFNKL
+>gi|297283897|ref|XP_001104925.2| PREDICTED: integrin alpha-D-like [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+--------------LAASTNRS-----WLLACGP------TLHRVCGENSYSKGSCLLLGSHWEIIQTVPDALPEcphqemdIV
+>gi|311103581|ref|YP_003976434.1| von Willebrand factor type A domain-containing protein 1 [Achromobacter xylosoxidans A8]gi|310758270|gb|ADP13719.1| von Willebrand factor type A domain protein 1 [Achromobacter xylosoxidans A8]
+--T---------lvlldlsasA---ndlAsdagttvLDLEKQAAMLLAQATSGEGDRIAVHGFCSDTRAAVyyyRLLEPGAPVA-TALG-RIGAAQARys
+TRLGAALRHAGGLA-----LLVPGERRAIIVVTDGEPSDVDahdprylvddareavLEL----rgrgVSVHCVALDAK-----AEPQLRAMFGF---RGY
+RIVTNPA-aLPQALVRV----
+>gi|156404021|ref|XP_001640206.1| predicted protein [Nematostella vectensis]gi|156227339|gb|EDO48143.1| predicted protein [Nematostella vectensis]
+IDIVFVLSASSMKSSTTFSLMQNCILKIGSKFGVYTFHYSVILYGSSSVKKFDFNtAFPYREALIEESNNLVKENGSSAITEALSFARTVLNDASA--RS
+NVRRGVAVIFDKATGKTVqqlqsaaRPLHDEGIIVVASGVGPE----VTKEEARAMTSRR--NDATHVNDTYQPGPLGDHIVRRI
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 2347 * * * 4932 * * 2822 * 2186 4105 * 6052 * 4239 6086 6298 2250 * 4450 1
+ 0 * * * * * * 8772 0 0
+
+D 2 * * 574 3158 * 6353 4339 * * * * 3471 * 5034 6360 6553 6483 * * * 2
+ 18 * 6353 * * * * 9165 0 0
+
+L 3 5916 6868 * 6350 6664 * 6504 1881 * 2003 4874 * * * * * 4778 1551 * 6808 3
+ 0 * * * * 0 * 9474 0 1036
+
+V 4 3221 4386 * * 5335 4825 * 3085 * 2914 4457 6511 * * * 5732 3775 1790 5681 3693 4
+ 0 * * * * * * 9593 0 0
+
+F 5 6433 6642 * * 906 * * 2911 * 2259 5869 * * * * * * 3876 * 5814 5
+ 17 6423 * 0 * * * 9593 1051 0
+
+L 6 3549 6284 * * * 6469 * 2909 * 1161 * 6505 5784 * * 6399 6543 1953 * * 6
+ 9 * 7381 0 * 0 * 9554 1051 1051
+
+F 7 5886 * * * 5055 * * 2417 * 1288 4866 6407 6604 * * * * 1875 * 5197 7
+ 0 * * * * * 0 9590 0 1020
+
+D 8 * * 264 4412 * 5273 5201 * 6542 * * 6654 5425 6641 * 6252 * * * * 8
+ 0 * * * * * 0 9590 0 1020
+
+G 9 3270 5705 5492 4740 6685 3489 5668 4053 5799 4509 6825 4313 * 4651 3997 3113 2747 2900 * 5886 9
+ 41 5811 6654 0 * * 0 9590 1182 1020
+
+S 10 6537 6671 6503 * * * 6374 * * * * 6542 * * * 253 3234 * * * 10
+ 0 * * * * 1088 917 9578 0 1204
+
+M 11 3667 * 3394 3995 * 1624 5577 6544 5085 6390 7003 4619 6641 4795 5032 2597 4483 6554 6689 6563 11
+ 29 * 5628 * * * 0 9590 0 1020
+
+S 12 4878 * 4568 * 6619 3864 6687 * 4473 * 5502 5164 * 6656 5766 612 5542 5700 * 5866 12
+ 16 * 6535 * * 1784 495 9561 0 1398
+
+L 13 4408 * 6388 * 7033 * * 2824 6282 3323 1266 6612 * 5816 * 5819 5015 2565 * 5788 13
+ 64 4808 7013 3144 173 1574 591 9567 1686 1423
+
+Q 14 3169 6831 5058 4561 * 2432 * 6773 4402 5083 * 3633 4740 4324 3725 2442 3332 6722 * * 14
+ 252 4045 3324 2017 409 * 0 9575 2093 1410
+
+P 15 3959 * 3623 2635 6550 2438 5408 6932 3904 5768 6515 3606 3267 5692 5504 3161 5687 6392 * * 15
+ 120 4895 4442 1872 460 595 1565 9439 1339 3056
+
+D 16 3404 * 2930 2486 * 5371 5504 5619 3150 5002 6490 4189 5797 4591 4571 2915 4195 5535 * 6768 16
+ 96 4376 5972 2590 262 972 1029 9408 1790 2343
+
+E 17 3720 * 2723 3521 * 3654 * 6952 3153 6375 5492 2978 5522 5625 3436 3987 4005 5596 6494 4926 17
+ 41 5153 * 1609 573 672 1425 9439 1331 1916
+
+F 18 5614 * * * 1631 6520 * 3251 * 2683 4684 * 5726 6745 5274 5121 * 4049 2788 4104 18
+ 13 6793 * 0 * 1009 991 9567 1000 1237
+
+Q 19 3270 * 2819 2661 * 4504 4855 5765 3965 5234 6844 4422 7091 3487 4266 3020 5293 4798 * 5619 19
+ 93 4006 * 2874 212 * 0 9589 2020 1027
+
+K 20 3087 * 3145 4131 6840 4648 5229 4362 3158 2776 5813 5562 * 3677 3773 4122 4521 5098 * 6677 20
+ 33 5917 7420 2749 232 0 * 9589 1396 1027
+
+I 21 2273 * * 5036 4594 * 6640 3866 6303 2821 3651 * * 4713 * 4024 3120 2364 * * 21
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+
+L 22 6438 * 6670 5820 * * * 4509 1586 3624 5206 4467 * 3580 2338 4558 5674 4357 6441 5224 22
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+
+D 23 2903 * 3324 3547 6865 3803 5267 * 2826 6897 6735 4278 5954 3222 3118 4203 4707 4911 * * 23
+ 26 * 5811 * * * 0 9591 0 1217
+
+F 24 2177 5612 5117 6750 1579 5650 * 4596 6506 4113 5490 5571 * * 6288 3782 4410 4361 5012 * 24
+ 0 * * * * 449 1903 9505 0 1574
+
+M 25 2897 6912 * * 3626 6966 * 2155 * 2376 3934 * 5820 * * * 4571 2202 * 6855 25
+ 0 * * * * * 0 9606 0 1020
+
+K 26 3634 6841 4505 2812 5675 4426 5263 4693 3765 3792 5826 4101 * 3624 3658 3697 4657 3655 * 6026 26
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+
+D 27 3480 * 2792 2839 4862 3943 6914 * 4243 4531 5597 3577 6564 4827 4184 2976 3989 5208 * * 27
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+
+V 28 3445 * * * 2877 * * 2488 6332 1978 3708 * * * * 6905 4175 2712 * 4848 28
+ 0 * * * * * * 9609 0 0
+
+M 29 3381 * * * 5498 5369 6422 2454 * 2153 3701 6483 * * 4793 4506 4733 2226 * 5707 29
+ 44 6447 5742 1585 585 * * 9609 1039 0
+
+K 30 6829 * 3529 3172 * 4670 5269 6741 3288 4322 6833 4080 4504 3283 3514 2925 3556 5106 6884 6625 30
+ 17 6443 * 1585 585 1068 935 9472 1008 1232
+
+K 31 3729 5702 4527 3834 6425 3766 4517 4805 3584 4258 6806 4367 4756 3526 3351 2849 4509 6652 * 5662 31
+ 80 4451 6914 1735 515 * 0 9605 1746 1033
+
+C 32 6522 4724 * * 1896 * * 2933 * 1438 4183 5970 * 5530 * 6897 * 4031 * 5623 32
+ 556 1884 4358 1366 708 1037 964 9612 5002 1241
+
+S 33 5152 * 2855 4350 6879 2112 5571 5895 6681 6958 6567 3704 4996 4196 4491 2338 5148 5206 6863 6677 33
+ 430 2121 5163 1841 472 765 1281 9488 4400 2094
+
+N 34 4857 * 2971 2951 6451 3992 6448 5711 3987 5606 * 3961 1963 4454 4546 4064 * 4984 * 5663 34
+ 275 2608 6711 1044 957 0 * 9540 3681 1849
+
+T 35 3980 * 2329 2945 * 4515 5704 6784 3913 5681 5068 3824 3704 5177 5473 3281 3784 4858 * 6314 35
+ 12 * 6927 * * 0 * 9610 0 1000
+
+S 36 3917 6736 3377 4044 6576 2730 4534 * 3070 4139 5717 3554 6787 4847 5624 3014 4101 6580 7181 5656 36
+ 65 6661 4870 1000 1000 0 * 9622 1016 1005
+
+Y 37 3324 * 3411 5617 4544 5083 * 2677 * 3525 6726 6769 6706 4401 6513 4134 2936 2629 6600 5378 37
+ 52 6805 5256 1000 1000 0 * 9597 1000 1619
+
+Q 38 4855 * 4813 4831 6801 * 3903 * 3276 5236 6957 4489 6871 2903 1532 4241 4629 5556 * 4877 38
+ 0 * * * * 0 * 9614 0 1337
+
+F 39 4889 * * * 2293 * * 2276 * 3138 4941 * * * 7486 6400 5715 1662 * 4128 39
+ 13 * 6819 * * * * 9518 0 0
+
+A 40 1961 5115 5475 5621 6945 1811 * * * 6419 6720 3945 * * 6002 2255 4373 * * 5720 40
+ 17 6447 * 1585 585 * 0 9617 1051 1000
+
+A 41 4379 * * * 3847 * * 2111 * 1946 4369 * * * * 5059 * 1675 * * 41
+ 24 5923 * 3585 126 1184 837 9579 1158 1236
+
+V 42 3826 * * * 4388 5626 * 1868 * 2797 4730 5569 * 6682 6480 5296 4992 1908 5566 5675 42
+ 0 * * * * * 0 9583 0 1051
+
+Q 43 3952 * 5884 4134 5277 3558 5959 4752 4464 3543 4713 4444 * 2974 5145 3077 2602 5264 6645 7023 43
+ 0 * * * * 0 * 9583 0 1051
+
+F 44 * * * * 1094 * 5098 6782 5807 5642 * * * * * 5131 * 4994 * 1338 44
+ 0 * * * * * * 9518 0 0
+
+S 45 3187 5848 4768 * * 2302 5513 * 6627 6768 * 2783 6086 * 4813 1609 4129 * * 6415 45
+ 11 7042 * 3170 170 * * 9518 1006 0
+
+T 46 4528 6854 2730 3469 6400 3627 4810 * 4858 * 5557 3289 4989 5019 4362 2796 2942 5747 6931 6858 46
+ 46 5003 * 2411 300 * * 9518 1388 0
+
+S 47 4376 6400 3749 2810 6009 3548 5847 4649 3614 6689 * 3682 5578 3746 3811 3325 3446 6750 6768 5736 47
+ 129 3546 * 2075 391 * * 9518 2427 0
+
+Y 48 2005 * 6907 * 4760 4378 6653 5349 5874 6497 * 5312 3156 * 6858 3227 3412 2342 * 4294 48
+ 47 5620 6416 563 1630 * * 9518 1196 0
+
+K 49 4378 6537 4174 3474 6525 5669 3603 5266 3137 4883 6900 4596 4732 3635 3008 3541 3868 4406 * 5999 49
+ 0 * * * * * 0 9583 0 1051
+
+T 50 3913 * 5230 3636 5643 5159 6887 4064 4286 3841 4888 5499 3384 5106 4492 5257 2951 2695 4206 * 50
+ 174 3393 5765 1748 510 * 0 9583 2600 1051
+
+E 51 5458 6063 3965 3176 5313 4517 5175 3432 5055 3208 6627 5922 5560 3940 5115 4889 4652 2276 * 4706 51
+ 57 5193 6463 2135 373 * 0 9453 1396 1397
+
+F 52 3401 7419 6635 * 2277 4980 5716 2804 5968 3001 4485 * 6893 4731 * 4337 5300 3112 5682 4392 52
+ 51 5851 5833 1306 748 827 1197 9428 1373 1604
+
+D 53 3723 7003 3077 4584 6583 3597 5119 6871 3977 5291 6845 4138 2630 4446 4797 3171 4271 4551 * 5475 53
+ 32 6412 6613 3700 115 1838 474 9481 1052 1491
+
+F 54 5729 5889 7099 5069 2472 6598 * 3956 6502 1376 5746 * 4324 4759 6534 5723 5526 3842 * 4344 54
+ 28 5709 * 1904 448 * 0 9586 1168 1460
+
+S 55 3522 * 3799 5772 * 4747 5210 6507 4178 5421 6534 2875 5688 4258 3184 3146 2696 5011 6863 4909 55
+ 121 3843 6502 1192 830 925 1079 9586 2082 1460
+
+D 56 3825 * 2823 3478 6444 3576 5681 * 4397 4616 6832 3434 4436 3811 4158 3647 3399 5699 5937 6606 56
+ 38 5979 6617 1309 746 * 0 9482 1162 1337
+
+Y 57 4319 * 3212 6965 2638 6382 4128 3723 6692 3250 * 4629 4042 4767 5010 4365 5262 5090 5836 3020 57
+ 76 * 4287 * * 1259 781 9464 0 1543
+
+V 58 4098 6623 3298 4120 5131 5191 5566 4610 2949 4970 5334 3450 4444 5323 4455 3387 3929 4739 * 4025 58
+ 310 5810 2508 555 1646 * 0 9496 1142 2260
+
+K 59 4817 5602 2479 3766 6517 * 6307 * 5452 * * 2718 5325 4810 5183 2044 2874 * * 5291 59
+ 82 5252 5111 599 1556 1431 668 9226 1190 4799
+
+R 60 4140 * 3459 5141 6307 5645 5620 3986 2572 4385 6615 4067 4831 4022 3016 3621 4165 4261 * 6317 60
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+
+K 61 3284 * 3013 2621 6636 * * 6365 3642 6197 5058 4266 4054 4914 4610 3010 3534 4665 6763 5676 61
+ 66 * 4475 * * 1448 659 9442 0 2799
+
+D 62 2923 5052 3167 2803 5358 4090 4286 * 4379 5178 * 3649 6716 3659 4054 4555 3455 6505 * * 62
+ 59 6666 5041 2807 222 2046 400 9390 1000 2923
+
+P 63 4391 * 6279 * 3117 6481 * 2748 6672 1957 4152 6399 4595 * 4329 * 4756 2635 6527 5120 63
+ 0 * * * * 575 1605 9414 0 2907
+
+D 64 3865 * 3606 4411 6550 5497 5868 4070 2823 3585 4697 4397 5414 3137 3168 3875 4510 6626 * 6437 64
+ 29 5648 * 498 1776 * 0 9486 1196 1557
+
+A 65 3033 * 3016 3159 6503 4554 5635 4974 4036 5090 5857 4351 * 4237 3477 2958 4212 5795 5926 5636 65
+ 12 6894 * 4392 70 1060 942 9486 1000 1557
+
+L 66 2174 6902 5292 5028 4952 4542 6521 3203 4182 2952 5071 6553 * 4778 5822 4067 4974 3156 5867 5679 66
+ 40 5208 * 1452 656 0 * 9606 1578 1206
+
+L 67 4416 5688 6564 * 3588 6519 * 2040 5889 1884 6776 5588 * 6323 5382 4628 5249 2800 6654 6440 67
+ 29 6713 6564 2585 263 0 * 9588 1000 1224
+
+K 68 4106 * 2639 3753 6469 4179 6876 6606 3588 * * 2718 6934 3515 3770 3132 4007 6655 5395 6988 68
+ 35 5790 7472 1000 1000 * 0 9493 1182 1013
+
+H 69 3578 * 3911 3514 5748 4444 5270 * 3911 * 5280 2939 * 3584 3137 2803 4018 5718 6868 5673 69
+ 13 6837 * 0 * 977 1024 9491 1217 1220
+
+V 70 4303 * * 5171 4078 6458 6750 2009 6839 1557 3991 * * * * 6884 4811 3288 * 4820 70
+ 77 4437 7472 1980 422 * 0 9493 1701 1013
+
+K 71 4023 * 4748 3191 5594 5135 5276 5716 3044 5248 5725 4151 3546 3799 2930 3634 3889 4705 * * 71
+ 86 5325 4927 1470 646 977 1024 9491 1535 1220
+
+H 72 4520 5558 3417 4727 3802 5690 5712 4997 3619 4975 * 4775 3173 3255 4191 4377 4775 5063 5831 3182 72
+ 334 2728 4163 2029 406 0 * 9463 3453 1737
+
+M 73 3254 * 4746 3282 6757 5706 * 3048 3738 2545 3572 5228 4457 5554 5634 3552 4463 5555 * 6660 73
+ 218 3598 4115 934 1069 240 2707 9600 2275 1914
+
+L 74 4639 * 3848 4278 * 1934 6593 6725 3659 5725 6973 3583 4393 5519 3541 2957 5257 4404 * 6588 74
+ 259 2603 * 1261 779 0 * 9530 3709 2049
+
+L 75 3920 * 5152 5710 6849 1136 5651 * 4540 5808 6708 * 5416 4352 4669 3298 3814 * 5118 5681 75
+ 90 4050 * 2293 329 * * 9518 2118 0
+
+L 76 3836 6942 4442 4196 5121 1663 5726 5944 4485 3641 5907 4198 4646 5981 6627 3911 4045 5967 5144 6882 76
+ 159 3258 * 1125 885 * * 9518 2696 0
+
+T 77 3475 6609 6558 5734 * 5211 * 5591 5250 5117 * 3960 4397 5627 4772 3157 1133 5006 * * 77
+ 0 * * * * * * 9518 0 0
+
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+
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+L 173 5764 * * 6027 4934 * * 1434 * 1436 3973 * * * * * * 2941 * * 173
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+K 175 * * 2849 2985 4151 * * * 2567 * 5240 2789 * 4107 3681 3782 3307 * 5106 * 175
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+K 176 3529 5111 4078 3326 * 5115 * * 1783 3448 * * * 4081 2756 3646 5183 * * * 176
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+
+I 177 * * * * * * * 849 * 2147 3179 * * * * * 4785 3786 * * 177
+ 0 * * 0 * * * 7159 0 0
+
+//
+�HHsearch 1.5
+NAME 3067be314a806ff137315081e104742e
+FAM
+FILE 3067be314a806ff137315081e104742e
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:26:38 2013
+LENG 171 match states, 171 columns in multiple alignment
+FILT 188 out of 1401 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEEEEECCCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
+CCEEEEEEEEEEECCCEECCCEEEEEEEEEEEEEECCCCEEEEEEEEEECCEEEEEEEEEEEEEECCCCCC
+>ss_conf PSIPRED confidence values
+9866789999998655877579960008999879999999993799820156999999937987400367899983778999999999999998633578
+86158555589981660079989999999999985479889999999999999999986099993688889
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxLPxxpxlxvDxvxxxxxxxGxxxxgxixxxxxvxxdxxxfxgHFpxxpvxPGvlxiExxaQxxxxxxxxxxxx
+xxxxlxgixxxkFxxpVxPGdxxLxxxvxvxxxxxxxxgxxxxxxxxxxxgxxvxxxxxxxvxxxxxxxxx
+>3067be314a806ff137315081e104742e
+VDKRESYTKEDLLASGRGELFGAKGPQLPAPNMLMMDRVVKMTETGGNFDKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGE
+GKGRALGVGEVKFTGQVLPTAKKVTYRIHFKRIVNRRLIMGLADGEVLVDGRLIYTASDLKVGLFQDTSAF
+>gi|149174078|ref|ZP_01852706.1| probable hydroxymyristoyl-(acyl carrier protein) dehydratase [Planctomyces maris DSM 8797]gi|148847058|gb|EDL61393.1| probable hydroxymyristoyl-(acyl carrier protein) dehydratase [Planctomyces maris DSM 8797]
+-------------------------------RFSLVDQILEMEKG--K----SITAVKNLSLSEEYLQDHFPGFAVMPGVLMVESIVQAGAWLMRYTNDf
+QYSTILLkQTKAIRFNSFVTPGKQ-LRVSLSIQKWE---DNLCTLKASSQVEGEAAVSGR-------------
+>gi|269967927|ref|ZP_06181967.1| putative beta-hydroxydecanoyl-ACP dehydrase [Vibrio alginolyticus 40B]gi|269827450|gb|EEZ81744.1| putative beta-hydroxydecanoyl-ACP dehydrase [Vibrio alginolyticus 40B]
+------------------------EQLLPhDKPMILVDRALDVQQD-------TIHCQVDIAEHNPFFD---STSQTVPAYVGIEFMAQSVAAWSGYHAl
+mkEQapPIGFLLGSRRYTSECDTFSRGQ--VLDVYAEKVMED-NGMAVFSARIELQGTVVATCQ-------------
+>gi|325300363|ref|YP_004260280.1| hypothetical protein Bacsa_3281 [Bacteroides salanitronis DSM 18170]gi|324319916|gb|ADY37807.1| hypothetical protein Bacsa_3281 [Bacteroides salanitronis DSM 18170]
+----------------------------------------------------TPSFHVELLPGCDVYRGHFPGHPVCPGVCNIGM----LKECMEEAVG-
+VKLAIETIKQCRMTAVASPEICsELDIRMHIQSL--GEA-RWAVQAKLYDAERTYMEYK-------------
+>gi|300726872|ref|ZP_07060300.1| conserved hypothetical protein [Prevotella bryantii B14]gi|299775819|gb|EFI72401.1| conserved hypothetical protein [Prevotella bryantii B14]
+-------------------------ELLLqQEPFVFIDQLTYYDER-------LTTSVFRVSPNHLYV-----EEGKLQTCALAEVIAQTCAARIGYINk
+yilKrTIqMGFIGAIRNLKVYATPLVGDL-LETQVEIKEE---IMGMLLVEAQIKRGEDLIAEGT-LKMSLT------
+>gi|94265785|ref|ZP_01289519.1| conserved hypothetical protein [delta proteobacterium MLMS-1]gi|93453677|gb|EAT04061.1| conserved hypothetical protein [delta proteobacterium MLMS-1]
+-----------------------------------------------------LVGNYSFALDFPGFIGHFPELPILPAVVQLAAVRYLAELAVAS----
+-NLQTVGCQGAKFRGMVRPRE-LLSVSLTL--VQRAEPPGCQAKFKLTRADVLVAGG--------------
+>gi|312114350|ref|YP_004011946.1| MaoC domain-containing protein dehydratase [Rhodomicrobium vannielii ATCC 17100]gi|311219479|gb|ADP70847.1| MaoC domain protein dehydratase [Rhodomicrobium vannielii ATCC 17100]
+-----------------------------------------------------------VHLDEAFAATTPFKQRIAHGMLSAAYI---SAVFGTKLPGP
+GCIYI--SQTLNFKGPVHIGDE-VVTTVRVTDLITEKR-RAIFHCECKVGGKTVVVGEA------------
+>gi|52840605|ref|YP_094404.1| 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases [Legionella pneumophila subsp. pneumophila str. Philadelphia 1]gi|52627716|gb|AAU26457.1| 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratases [Legionella pneumophila subsp. pneumophila str. Philadelphia 1]
+-------------------------------RFLFVDRIVQLSP--GEWIKG----IKHVTRDDAYLTTDDHGRLCFMPSLIGETLGQLAAWNVMQHN-H
+FTARpVAGVvSSARLYRPAYVGET-ILLESNIDSLDE---KAVQYHSIAKVGNDIIFTIDG------------
+>gi|301062223|ref|ZP_07202900.1| FabA-like domain protein [delta proteobacterium NaphS2]gi|300443655|gb|EFK07743.1| FabA-like domain protein [delta proteobacterium NaphS2]
+--------------------------LIPHrGLMRLVDEIISVDEK-------TAVTASTVTESWPMVEGGA-----ANCIVLVELIAQTAGICLGWKEP
+RkkeeelaGTGWIVGVKEAVFHHSEIPLNSRII-TA-SDRVFQV-EFYSEIAGTARVGDETLAEV---KLQMVQSDS--
+>gi|334140009|ref|YP_004533209.1| MaoC-like dehydratase [Novosphingobium sp. PP1Y]gi|333938033|emb|CCA91391.1| MaoC-like dehydratase [Novosphingobium sp. PP1Y]
+--------------------------------------------------------------DAELAKKSEFGRILVNSTFTF-SLA--IGLSVADT-TV
+GTlVANLGFDKVVTPKPTFIGDT-LTCTSEVIELREsksRPgQGIVVFRHELTNqKGEVVLSCQR------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+
+//
+�HHsearch 1.5
+NAME 3155c91c2cbf7967cb4ba20d80ff989c
+FAM
+FILE 3155c91c2cbf7967cb4ba20d80ff989c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:34:41 2013
+LENG 142 match states, 142 columns in multiple alignment
+FILT 169 out of 1174 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC
+CCCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCC
+>ss_conf PSIPRED confidence values
+9689999999999999999299940599999999868579999999399999999998988873044567777767777699999999999999998599
+854799999999826430899999996999999999987359
+>Consensus
+xxtxxxxxxlxxAxxxAxxxxxxxixxeHlLxallxxxxxxxxlxxxgxxxxxlxxxlxxxlxxxxxxxxxxxxxxxxxxsxxxxxxlxxAxxxaxxxxx
+xxixxxhLllalxxxxxxxxxxxLxxxgixxxxxxxxixxxx
+>3155c91c2cbf7967cb4ba20d80ff989c
+MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGR
+NEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGT
+>gi|58270056|ref|XP_572184.1| chaperone [Cryptococcus neoformans var. neoformans JEC21]gi|57228420|gb|AAW44877.1| chaperone, putative [Cryptococcus neoformans var. neoformans JEC21]
+-------------------------------------------------------------------------------------------------MLA
+RKHLIRTARLSI-PRPSV--ATRAVALGFVRTYAQGPP----
+>gi|257440207|ref|ZP_05615962.1| Clp protease, ATP-binding subunit ClpC [Faecalibacterium prausnitzii A2-165]gi|257197241|gb|EEU95525.1| Clp protease, ATP-binding subunit ClpC [Faecalibacterium prausnitzii A2-165]
+-PAIIFVQRMENGQMKNEGYCLHCAREMHI--------kPVDDLMKQFGMSDEDM-DAMEDRMENmM-QEM---------gdmSNMNPFSMMMGMGQPDQ
+SEEDGDLVPGSSATFPL-gVNGGA-------QNGKNEKK---------
+>gi|303273680|ref|XP_003056193.1| predicted protein [Micromonas pusilla CCMP1545]gi|226462277|gb|EEH59569.1| predicted protein [Micromonas pusilla CCMP1545]
+----------------------------------MTSDverVRVALMMSAGVTTAAVLVLSSKTVRGA----IaG-TL-KSVA-STiQPTELIEAFDKSD
+TPV----INTKMTNISSVqS--QAS-EP--LNTGIPHDIAPKNM----
+>gi|302664673|ref|XP_003023964.1| hypothetical protein TRV_01906 [Trichophyton verrucosum HKI 0517]gi|291187987|gb|EFE43346.1| hypothetical protein TRV_01906 [Trichophyton verrucosum HKI 0517]
+---KEEEKDFFPSERSGDRGGRLPWATRRELGGELHGWdRTAAFWS-------L---REGPSTRGR-PSQ-------RL-dI--iyiyikgkawyvglqq
+vkahtmscrlvmRGSRQLLQAPRAAAHInttarRGLYgllprqlskqyVPASGFVRHY-A--NGR-PH--PPGGTHRMN---------
+>gi|50294636|ref|XP_449729.1| hypothetical protein [Candida glabrata CBS 138]gi|49529043|emb|CAG62705.1| unnamed protein product [Candida glabrata]
+-------------------------------------------------------------------------------M---LS-RVCRSSLRNSVARV
+-SRYAGPRALALSMV---VSGRQVSG------S---------
+>gi|55376027|gb|AAV50022.1| heat shock protein 104 [Pleurotus ostreatus]
+-FTDKTRRTITAAVQLAKDYANAQVHPVHIASALLNDTgedeqsgglgdtssssrsqsLFHSAISKAGGDPAVVKRGIQRAVVRL-PTQD-P-PPEEVYF
+SGPALKVVREAQSLQKTMHDSYIAQDHLLLAVLKDA--TIQAIIKEAGLTEATLKTAI----
+>gi|342839815|ref|ZP_08713678.1| ATP-dependent Clp protease ATP-binding subunit clpE [Streptococcus criceti HS-6]
+-------------------------------------------------------------MLCQnCKLN----DASIHLYANVNGQ-------------
+QKQIDLCQNCYRIMKaDPENILNSNLTSqnpQNQSMDSFFD------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
+D 77 3922 * 3423 2874 7347 4384 4126 4085 4085 4017 * 3525 4723 3159 3704 4179 5980 7067 * 5537 77
+ 85 4283 7415 2085 388 1767 502 9482 1739 3564
+
+T 78 4902 * 6019 5832 4954 6165 6067 2801 * 2305 6003 * 2356 4687 4937 4233 4579 3008 * 5326 78
+ 142 4607 4253 2741 234 70 4396 9529 1734 2949
+
+Q 79 4158 * 4082 3886 4864 3742 6208 4510 4487 4147 7211 5700 3086 4288 3486 3561 4529 4298 6658 3703 79
+ 24 * 5934 0 * 1552 602 9621 1144 1981
+
+P 80 4335 * 7261 7163 2315 * * 3257 6005 1826 3770 5462 3804 5353 * 6034 6207 4264 6082 4440 80
+ 59 7265 4900 2000 415 1131 880 9646 1000 1979
+
+T 81 3801 * 4420 5552 * 4036 7306 5068 7035 6963 6465 4713 * 7026 6060 941 2694 * * * 81
+ 0 * * * * 3768 110 9631 0 2272
+
+L 82 3880 * 3626 3535 7001 3982 5233 6873 4861 5680 * 3810 2461 3284 3759 3791 4176 5757 * 5095 82
+ 40 5181 * 3122 176 2338 318 9634 1795 2176
+
+S 83 3354 * 3603 2979 7606 4089 4890 6268 4038 5219 6987 4335 5282 3694 3018 2974 3967 6282 * 7191 83
+ 0 * * * * 916 1090 9736 0 1933
+
+F 84 2725 6286 * 7100 3536 5292 * 3843 * 1628 4768 6085 6726 6036 * 4259 3702 3266 * 6084 84
+ 0 * * * * 1001 999 9922 0 1385
+
+Q 85 4120 * 4435 3102 5751 5719 6025 4964 2684 5635 5105 4273 7151 3898 3379 3601 3432 3530 * 7275 85
+ 21 * 6099 * * * 0 9960 0 1132
+
+R 86 3425 * 4594 2308 7238 6220 6126 7163 2963 4803 5879 4476 5533 3858 2633 4264 4002 5984 * 6139 86
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+
+V 87 2574 7449 * * 7532 * 6954 2621 * 2191 4282 6986 * 4965 5960 4653 5398 2163 4744 * 87
+ 18 7292 7367 0 * 2273 335 9765 1059 1765
+
+L 88 6329 * * 7014 3318 * * 2554 * 996 4169 * 7191 * 5774 * 6891 3362 6728 6389 88
+ 0 * * * * 2700 241 9768 0 1760
+
+Q 89 3841 7731 3594 2022 * 4049 * 5356 3829 4145 6238 4043 7930 3272 3369 4282 5168 5686 * 7007 89
+ 14 6702 * 455 1887 2065 394 9760 1166 1629
+
+R 90 3135 7245 3241 3466 5268 5463 5049 4697 3434 3735 5891 3513 7336 4216 2947 4543 5580 6314 7039 5635 90
+ 15 * 6612 * * * 0 9712 0 1557
+
+A 91 593 7677 * * 6829 4075 * 6076 6803 5470 6052 * * * 6329 3012 5093 4752 * * 91
+ 11 * 7010 * * 3029 189 9718 0 1736
+
+V 92 4722 6149 4810 2815 4421 5274 5802 4428 4453 3521 8191 5075 6229 4163 4268 3666 4731 3300 3760 4192 92
+ 0 * * * * * 0 9779 0 1761
+
+F 93 4024 * 3658 3734 5809 4873 5310 4167 3107 3228 5124 3972 5818 3318 3443 4065 5335 4840 * 7195 93
+ 0 * * * * * 0 9779 0 1761
+
+H 94 4903 * 5553 2622 5754 5571 5213 2842 5103 3031 5202 5056 7449 5774 4495 4142 4206 4389 6214 2967 94
+ 24 * 5947 2000 415 3523 131 9779 1000 1761
+
+V 95 1055 6213 5483 6899 * 5579 7120 5534 3966 4332 4185 6272 * 4108 4995 3361 5747 4719 * * 95
+ 68 5352 5520 816 1211 3455 138 10269 1309 2035
+
+Q 96 3445 * 4699 3346 6689 6884 4599 4879 2914 4448 6962 3883 7344 3600 2848 3488 4084 5906 * 4996 96
+ 40 5659 7038 782 1257 4148 84 9669 1311 2653
+
+S 97 3203 * 4376 3240 6729 6273 5687 5527 2960 3643 6236 4810 6308 4509 2887 3459 3960 4647 * 5080 97
+ 183 3068 * 1078 926 3927 98 9829 2911 2739
+
+S 98 3687 6008 * 4959 3791 5135 5563 5582 6996 2276 2897 4519 * 5075 3591 3855 5070 4582 5014 4173 98
+ 62 5351 5835 1778 497 341 2246 9717 1360 3560
+
+G 99 5373 * 3549 5019 7241 1460 4750 7177 3546 5056 * 3581 5557 4123 4105 3550 6285 6486 * * 99
+ 38 6954 5818 2980 196 1660 549 9875 1154 1878
+
+R 100 2998 5858 1889 4464 7098 4200 4408 * 4799 5479 * 4592 6768 4335 3325 3024 5660 5468 * 6655 100
+ 9 * 7353 * * 2927 203 10603 0 1870
+
+N 101 3908 * 3397 2571 7201 4697 5544 * 3750 4636 7682 3902 4689 4601 3759 2651 3939 4685 * * 101
+ 169 4749 3767 2018 409 1661 548 10219 1620 1878
+
+E 102 4007 * 6851 3538 3265 * 5471 4948 4401 3442 5660 5687 5526 3944 4493 4182 4719 3495 7297 2424 102
+ 69 4424 * 2049 399 232 2752 10589 1868 2847
+
+V 103 3945 7639 * * * 7038 7805 1532 * 2533 4421 6039 * * 6090 7226 5531 1763 * * 103
+ 10 7226 * 2322 322 * 0 10799 1000 1193
+
+T 104 3366 * 2763 3962 * 2922 6357 7105 5389 4634 * 4371 4414 7447 3993 2406 3239 7416 * 6400 104
+ 0 * * * * 1500 629 10799 0 1193
+
+G 105 3852 4960 7122 4423 * 4153 * 3358 6670 4351 * 5490 3009 6773 * 3145 2422 2596 6422 * 105
+ 0 * * * * * 0 10809 0 1080
+
+A 106 3876 5480 3302 1791 6248 3301 7094 4318 5112 5598 5950 6418 4745 4600 4249 3655 5310 4884 * * 106
+ 30 5585 * 553 1651 * 0 10809 1328 1080
+
+N 107 3919 6112 2957 6394 6016 6146 1165 5609 7933 4942 5484 5173 5063 5413 6874 4567 4511 5691 6550 5800 107
+ 0 * * * * 0 * 10804 0 1188
+
+V 108 5024 * 7488 * 3565 * * 2759 7991 964 6514 6941 * 7423 6446 5455 6561 2854 * 7191 108
+ 0 * * * * * * 10854 0 0
+
+L 109 4555 6941 * * 3561 7179 * 3672 5953 940 6580 6561 6658 5390 6053 7142 5242 2921 7270 * 109
+ 6 7974 * 0 * * * 10854 1000 0
+
+V 110 3916 5072 * 5670 5530 5495 6157 2764 5289 1509 4553 5401 6695 4345 4123 5325 5793 5699 5956 4592 110
+ 0 * * * * * 0 10730 0 1000
+
+A 111 917 5479 * 6259 7001 2606 5866 * 5084 6740 * 5326 6304 5574 6123 3410 5619 5683 * * 111
+ 10 * 7184 * * * 0 10730 0 1000
+
+I 112 5050 7445 * * 4026 * * 2393 6871 1276 3065 * * 6465 * 4799 4766 3930 7358 6002 112
+ 113 6691 3929 0 * * 0 10722 1059 1101
+
+F 113 3348 5859 7113 * 2966 * 7091 3949 * 1572 3435 * 6802 7051 * 5431 5009 3180 4436 5552 113
+ 126 3703 7195 1344 723 72 4363 9639 2782 2907
+
+S 114 3789 * 3212 3059 6272 5787 4653 7541 3314 4337 5788 3959 7291 3142 3318 3467 4237 6755 * 5766 114
+ 145 5064 3934 444 1917 1543 606 10700 1515 1198
+
+E 115 4675 5738 2427 2919 * 5034 5607 6374 4238 3317 * 3639 5436 4149 6344 3956 3469 4244 * 5167 115
+ 156 7267 3383 0 * * 0 10507 1000 2569
+
+Q 116 4877 * 3184 3054 * 3443 5641 5711 3145 * 6721 3988 2768 4497 4539 3285 4065 5473 * * 116
+ 138 * 3450 * * 937 1066 9452 0 3907
+
+E 117 4787 * 2487 3234 * 3944 5200 6893 5487 5459 * 3067 5644 4290 3752 2492 4110 5109 * 7897 117
+ 93 5072 4925 0 * 597 1561 10277 1308 3569
+
+S 118 4597 4041 4456 5128 7152 2795 6999 7145 4377 3735 7527 3949 5537 5576 4770 1997 3686 4591 * 6027 118
+ 262 4099 3212 862 1153 613 1530 9828 1796 2524
+
+Q 119 3910 * 4951 4442 4321 4713 5911 3893 6937 3691 5391 4569 4206 4859 3410 4113 4143 3575 4377 3289 119
+ 101 * 3888 * * 1398 688 9698 0 3683
+
+A 120 1538 6904 * * 4315 4175 * 3619 6326 3554 6923 * 5351 5071 5860 3407 3874 3054 * * 120
+ 16 * 6470 * * 713 1359 9325 0 3860
+
+A 121 2771 4325 * 5298 6118 3642 5161 5384 3522 4367 7266 3508 5219 5097 3247 3386 4255 4382 * 4492 121
+ 83 4384 7012 0 * 468 1851 9766 1912 2365
+
+Y 122 4284 7194 4434 3437 5982 5056 5218 5482 3101 4429 7433 4357 4836 4065 2628 3861 4107 4607 * 3916 122
+ 62 * 4561 * * 1295 755 10624 0 1426
+
+L 123 4736 5929 7463 6389 4281 6921 6910 2402 6276 1864 5597 6104 6777 5240 4325 4931 5132 3460 4855 3712 123
+ 0 * * * * 2832 218 10434 0 2214
+
+L 124 4936 7495 * * 3275 7345 * 3932 5966 719 4217 * 5975 7013 6151 6119 * 4554 * 6063 124
+ 26 6624 7079 2302 327 290 2459 10424 1066 2038
+
+R 125 3034 * 5094 3294 5653 4561 4837 5109 2606 3898 6308 3625 5967 4187 3547 4175 4099 5303 * * 125
+ 31 6000 7472 2882 210 608 1540 10640 1351 1209
+
+K 126 3404 * 3791 2567 6057 6582 7140 7173 2764 6031 6882 4086 5819 3311 3320 3212 4149 6344 * * 126
+ 87 6155 4495 1585 585 * 0 10425 1164 1212
+
+H 127 2738 6068 7203 4966 3827 4692 5250 4542 5019 2463 5114 4143 5877 4156 7174 3806 4741 5350 * 3225 127
+ 167 3550 5385 111 3749 886 1124 9792 2284 2172
+
+E 128 5099 * 4822 3863 * 884 5584 6828 6937 7137 * 3211 4341 4969 6479 4388 5325 7189 * * 128
+ 0 * * * * 585 1584 10343 0 1937
+
+V 129 3851 7049 7039 6069 3896 7264 * 1759 5446 2668 5308 * 6027 5005 * 5408 5206 2219 * 6166 129
+ 55 * 4739 * * * 0 10324 0 1240
+
+S 130 5640 * 2517 5017 6487 5524 5852 6526 4186 6174 5848 2854 5661 4140 4973 2703 2498 4324 * * 130
+ 65 5382 5620 2300 327 1493 633 10617 1425 1853
+
+R 131 3994 * 6811 3526 6198 5888 4404 3958 3843 3094 4818 6799 3536 4676 3361 4596 3700 4052 * 3898 131
+ 0 * * * * 1542 607 10581 0 1829
+
+L 132 3352 6626 3110 2894 5744 6741 5198 4433 2947 4596 5039 4052 4116 3811 4870 4182 4514 5935 * * 132
+ 11 * 7050 1000 1000 0 * 10628 1372 1511
+
+D 133 3388 * 2932 3470 5095 4837 6965 4742 3012 5933 6051 3635 5504 3473 4589 3582 5132 4163 * 5945 133
+ 14 6652 * 1000 1000 * 0 10623 1000 1000
+
+V 134 3596 * * * 3183 * 6283 2179 6493 1720 6706 * 6598 * 6331 5299 5142 2631 * 6470 134
+ 0 * * * * 0 * 10216 0 1000
+
+V 135 5870 * 4835 3128 4659 6343 * 3972 4476 2281 5775 4557 5955 4364 2909 3890 4486 3883 * 5124 135
+ 77 * 4275 * * * * 10223 0 0
+
+N 136 3340 * 5427 2125 * 4245 5443 * 2830 4828 * 4221 * 3188 4102 2883 4642 * * * 136
+ 0 * * * * * 0 9678 0 1528
+
+F 137 1900 * 4070 4113 5831 * 6251 4160 4405 2391 * 4258 5659 3029 5407 6757 6771 4220 * * 137
+ 191 3014 * 1453 656 0 * 9122 2107 1528
+
+I 138 5199 6427 * 5264 4720 6057 6875 1764 * 2206 3647 6990 4245 6347 5505 4991 * 3075 * 4734 138
+ 0 * * * * * * 9827 0 0
+
+S 139 3425 * * 3341 5965 * * 3785 3053 3666 * 3212 4881 4930 5255 2899 3524 3343 * * 139
+ 217 2840 * 2681 245 * * 7179 1652 0
+
+H 140 * * * 4254 4645 * 1867 4519 4240 4277 * 3167 4125 3127 4163 3784 4803 4717 * * 140
+ 0 * * * * * * 6676 0 0
+
+G 141 3207 * * 3981 * 1990 4562 2731 * * * * 4075 4192 2649 3987 4403 * * * 141
+ 1740 513 * 2759 231 * * 6174 1762 0
+
+T 142 * * * * * * * * * * * * * * 1042 * 960 * * * 142
+ 0 * * 0 * * * 1717 0 0
+
+//
+�HHsearch 1.5
+NAME 3472662a6001a05156368eef829706af
+FAM
+FILE 3472662a6001a05156368eef829706af
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:26:29 2013
+LENG 237 match states, 237 columns in multiple alignment
+FILT 133 out of 1363 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEECCCCEEEECCCCEEEEEEECCCCCEEEEEEECCCCCCEEEEEECCCCCEECCCCCCCEEEEECCCCEEEEEECCCCHHHCCEEEEEEECCCCCE
+ECCCEEEEEEEEECCEEEEEEEEECCCCEEEEECCCEEEEEEECCCCCCCEEEEEEECCEECCCCCEEEEEEEECCCCCEEEEEEEEEECCCCCCCCCEE
+EEEEECCCCCCCEEEEECCCCCCEEEECHHHCCCCCC
+>ss_conf PSIPRED confidence values
+9879935972899789989999997189977999994799984899996378722256667747997267716899991357533956999998588630
+1351488999861100001248972674367621308899999178899829999999999768713500489738994999999999145520499479
+9999807888555998647898424888135142679
+>Consensus
+xxxvxxxpxxxxvxxGxxvxLxCxxxxxxxxixWxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxLxIxxvxxxDxgxYxCxvxxxxxxx
+xxxxxxlxvxxxxxxxxxpxxxxxxxxxxxxxxgxxxxlxCxxxxxxpxxxxxxWxxxxxxxxxxxxxxxxxxxxxxgxxxxxsxLxixxxxxxxxxxxy
+xCxvxxxxxxxxxxxxxxxxxpxxxxxxxxxxxxxxx
+>3472662a6001a05156368eef829706af
+EAAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGGGGTLY
+FGAGTRLSVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHF
+RCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADC
+>gi|34364807|emb|CAE45841.1| hypothetical protein [Homo sapiens]
+----------------------------------------------------------------------------------------------------
+----------------E----------------------------LKtPLGDTTHtCPRCPEPKPCDTPPP-CPRCPEPKSCDTPPPCP-----------
+---RCPEP-KSC---------------------------
+>gi|332245853|ref|XP_003272066.1| PREDICTED: patr class I histocompatibility antigen, CH28 alpha chain-like isoform 2 [Nomascus leucogenys]
+----------------------------------------------------------------------------------------------------
+-----------------------------------htlqgmngcdmgpdgrllrgyhqhaydgrdyislne--DLRSWTAADTVAQI-------------
+---tqrfyeaeeyaeef-----RTYLEGECLELLRRYLENGK-------------------et--LQ--raEPs-SQPTIPI----------
+>gi|47227730|emb|CAG08893.1| unnamed protein product [Tetraodon nigroviridis]
+---------------GGTLVIPCNtgAIkaEDILITKWKYDKGDGLSGDLLVRQ-RSqnAsiIANDEYKGRVSMAAN----SSLLLSDAKLSDQRTFTCM
+AVV-GANIAEYPVNVVVYK------KPTELKISDKAEELEIGKLTKVGvF------N-AKCCFYLRNFRHLKHQgktriSIHTSVLIDAMTGLSTTSSTL
+EYSAKKEDTN-AQFTC---RTVEEDLV---SQP------------------
+>gi|149754992|ref|XP_001496343.1| PREDICTED: butyrophilin subfamily 1 member A1 [Equus caballus]
+---VIGPPEPILAIVGEDAELPCHLSpnvsAEDMELRWFRKKVSPAVFVHREGREQEGEQMAEYRGRATLVKTNvtAGRVAVKIHGVKASDDGEYRCFFR
+---QEDSFEEAIVQLKVA-ALGSDPHIHMEVQE------SGEIWLQCTSVGWYPEPQ-VQWRtPKGEKFPS---MSEARNPDEEGLFTVTASVVIRDTSM
+KN----VSCCIQNLLLGQEKEGEISIPAPFFPRLTP--WMVA--
+>gi|301610340|ref|XP_002934715.1| PREDICTED: vascular endothelial growth factor receptor 2-like [Xenopus (Silurana) tropicalis]
+--------------ERDNITLICTADkFTYGNVMWFKLSPstvekhhMGWPIPVCKNLVG---LVR-MHATTTNTNGDNVTSALVLHNISMREQGNYVCV
+AQD-----KKTQKKYCLIRHIRIQAQKVPFIYQdLKNQTRNVSETVVVKCQASGTPDPQII--WFKDDDSL---VEDSGIILKDHNRT------LTIQRV
+RKEDE-GIYSCRA---------------------------------
+>gi|158298944|ref|XP_319079.4| AGAP009947-PA [Anopheles gambiae str. PEST]gi|157014131|gb|EAA14041.5| AGAP009947-PA [Anopheles gambiae str. PEST]
+------------VRRGDPVHLFCEYEledNErLYSIKWYKGKRE------FYRYTPQVHpSVQVFStVSgIDVEVryfSISQHSVWNLQK--RTRSQKIP
+TKLSFGAiFFVDLISVRFLLAH--FPSHCPTVTGVQARYRP---GDILRANCTSHNSKP-AANLTWTINDVPIPAqYVKLYRPIRDTFTGLETSIAGVNf
+mVAHDHFVKGKLKLKCSAS--------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+E 1 2268 * 2764 2220 * 2177 * * 2790 * * * * * * * * 3946 * * 1
+ 0 * * 0 * * * 6107 1000 0
+
+A 2 1614 * 4692 * * * * 2550 * 2738 * * 4073 3863 * 3196 4718 * 4689 * 2
+ 0 * * * * * * 7863 0 0
+
+A 3 5661 * 4203 4904 5695 3871 5835 5711 2359 4518 * * * 2402 4054 5578 3673 2467 * * 3
+ 0 * * * * * * 9276 0 0
+
+V 4 6044 * * * 2977 * 4961 2263 * 3004 5035 * 4751 * 5807 6091 4018 1755 * 4852 4
+ 51 6138 5595 0 * * * 9764 1006 0
+
+T 5 * * 6099 4388 4829 * 6118 3962 4987 2872 4283 4950 4461 4990 5402 6193 1651 2843 * * 5
+ 37 6016 6656 0 * * 0 9639 1000 1056
+
+Q 6 4388 * * 3139 5895 * 4558 5180 3568 4442 5885 6225 4096 2088 3358 5318 4196 3055 * * 6
+ 41 * 5155 * * 710 1363 10113 0 1196
+
+S 7 3899 6008 5145 3524 6118 4543 5324 4639 4386 4722 5040 5121 2965 3500 5426 2839 2943 5297 * * 7
+ 0 * * * * 432 1951 10134 0 1376
+
+P 8 4664 * 4386 3477 6226 5501 6431 5464 5408 6203 * 6606 1042 4229 6342 3369 4850 5426 * * 8
+ 19 * 6226 * * * 0 10157 0 1000
+
+R 9 3314 * 6597 3118 * 3400 5364 * 3100 4086 * 4325 3202 6227 4104 2670 4885 4550 * 5998 9
+ 18 6351 * 0 * * 0 10155 1000 1125
+
+N 10 6025 * 3242 3553 4651 5355 5171 3563 5527 4437 * 4094 3661 4794 4114 2592 3490 4712 * 5329 10
+ 0 * * * * 957 1044 10170 0 1125
+
+K 11 6493 * * 4562 6869 5134 6557 3575 3471 2262 4408 * 6674 4137 5364 3318 4351 2288 6501 6246 11
+ 15 * 6554 * * * 0 10224 0 1000
+
+V 12 6503 5390 4156 4001 * * 4225 4059 3965 3881 4933 3860 5411 4773 6811 3346 2889 2861 * 4069 12
+ 13 6793 * 3468 137 0 * 10264 1156 1137
+
+A 13 2102 * * * 5059 4704 * 4465 4277 3990 6514 * * 5800 6364 4645 4147 1412 * 5290 13
+ 0 * * * * * * 10335 0 0
+
+V 14 3552 * 5887 4163 3902 4279 6813 4895 3179 3211 5028 4694 4415 4134 4651 3901 4170 3211 6798 6596 14
+ 26 * 5792 * * * * 10383 0 0
+
+T 15 4334 * 5495 1979 6350 5976 * 5288 5500 3249 5622 * 3144 5257 3354 3470 5176 3496 * 5077 15
+ 16 6532 * 1462 651 * 0 10427 1173 1196
+
+G 16 6957 * 5101 4337 * 492 * * 5212 * * 4211 * 3952 7155 4328 * * * * 16
+ 21 * 6084 * * * 0 10490 0 1196
+
+G 17 5068 6922 2803 2155 * 3874 * * 4722 6844 6217 4795 * 2750 4558 2716 3845 5873 * * 17
+ 0 * * * * 1194 829 10512 0 1472
+
+K 18 4007 6875 3502 4093 6823 * 4897 * 3621 6006 5873 3232 3253 4750 4717 2430 3318 4790 * 5825 18
+ 12 6976 * 1000 1000 710 1363 10513 1012 1196
+
+V 19 2034 * * 6767 4582 5108 * 4904 6952 2943 5289 * * * 6480 5679 5140 1253 * * 19
+ 12 6919 * 0 * * 0 10544 1012 1000
+
+T 20 4663 * 5214 3843 7078 * 5847 4082 5220 4486 7114 4541 4942 5845 3822 3072 1691 3315 * 6824 20
+ 0 * * * * * 0 10544 0 1000
+
+L 21 6777 * * * 3165 * 7558 3043 6986 666 4408 * * * * 6474 6423 4879 * 6546 21
+ 0 * * * * * 0 10544 0 1000
+
+S 22 6212 6588 4437 4190 6795 5341 5299 5708 6480 5122 6022 3688 2562 4596 3479 2667 2750 5194 * 5051 22
+ 0 * * 2807 222 0 * 10544 1000 1000
+
+C 23 5567 178 * * 5661 * * 5966 6988 * * * * * 6118 6686 6819 5757 * * 23
+ 19 7051 7535 0 * * * 10546 1006 0
+
+N 24 5964 7558 4566 4063 * 4232 3920 5731 3599 4134 6636 3268 3869 5491 3656 3054 3194 3861 6888 6924 24
+ 39 6718 5876 638 1484 0 * 10544 1152 1000
+
+Q 25 3136 * 7021 6669 3317 7087 4970 3513 * 3174 * 6667 4759 5226 6575 4337 5165 1864 * 3401 25
+ 93 4198 6942 1157 859 1338 726 10516 1799 1162
+
+T 26 5085 * 3178 4322 6252 4167 6457 4478 3900 6658 * 3629 3758 4990 3956 2617 2700 * 5929 5371 26
+ 1744 528 6950 1437 665 0 * 10512 8381 1312
+
+N 27 3568 * 3550 4068 4144 3853 4357 4813 4335 3284 * 3778 3365 5626 4948 3549 4565 4747 * 5587 27
+ 70 5322 5474 474 1837 * 0 10584 1304 1000
+
+N 28 4820 * 3000 4031 * 3487 * * 3209 5226 * 4435 2637 6592 4367 2837 4023 4637 7032 4668 28
+ 47 5894 6006 607 1542 969 1032 10527 1128 1454
+
+H 29 6565 * 3459 4154 6775 4601 3634 5078 5845 2773 * 3610 3289 5021 5032 3829 4288 3534 7001 4138 29
+ 150 3566 6155 1644 556 * 0 10555 2289 1461
+
+N 30 4787 * 4650 4755 4936 5030 4512 4571 5436 2934 3909 4417 2511 4676 5408 6803 3578 4258 6511 3711 30
+ 30 5607 * 626 1505 1365 709 10516 1297 2084
+
+N 31 4045 * 5416 3599 5800 4519 6029 3654 4882 4772 4791 4684 5924 3891 4372 2406 2905 4822 7000 4875 31
+ 9 7376 * 0 * 2366 311 10525 1000 1617
+
+M 32 5770 6594 * 6948 3847 4781 * 1947 5211 2376 5195 * 6634 * * * 5048 1842 * 4976 32
+ 0 * * * * * 0 10525 0 1469
+
+Y 33 4322 * * 4192 3990 6065 5416 3956 3463 5288 5774 4089 6746 3306 4779 2939 3026 4887 6542 3446 33
+ 14 6746 * 1000 1000 2194 356 10525 1004 1469
+
+W 34 * * * * 6529 * * * 6652 * * * * 5814 6541 6470 * 4856 168 6078 34
+ 75 6682 4603 0 * * 0 10523 1000 1333
+
+Y 35 * 6490 6712 6355 2306 * * 3689 3831 3190 6486 5141 * 5421 4020 4203 4426 4376 6615 2159 35
+ 14 * 6674 3000 193 2848 216 10433 1013 2078
+
+R 36 5802 6822 6761 6472 4721 5706 4394 5848 1731 3959 * 5596 6380 4457 1910 5624 5563 5431 5052 5260 36
+ 233 5640 2953 704 1372 1037 964 10425 1186 2064
+
+Q 37 5552 * 2854 3643 * 3417 5036 5517 3879 5402 4556 5284 5574 2062 5096 5532 4098 3952 5626 * 37
+ 300 6550 2496 0 * 4177 82 10327 1000 3478
+
+D 38 6206 * 2969 4544 5332 3892 6418 6273 3107 6112 5311 4283 3766 6107 2682 4118 3582 4508 * 3987 38
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+V 166 4816 * 7222 4243 6181 3901 4304 3899 5154 4051 6780 4021 5707 3883 5023 3423 2742 2498 * 6635 166
+ 13 * 6788 * * 1614 571 10071 0 2563
+
+S 167 4716 * 4504 3248 4271 5188 5947 3730 4468 5075 * 4283 5004 3556 3403 3177 3499 4406 * 4093 167
+ 43 5095 * 1575 590 2338 318 10037 1282 2175
+
+T 168 5896 * 5111 5890 7025 4913 4076 3847 4311 3990 5278 3969 3856 3769 3780 3867 2281 4464 6384 5796 168
+ 56 6523 5188 3322 152 2763 230 10047 1157 1924
+
+D 169 3789 * 3064 5218 4655 3589 4702 6766 6622 3873 5976 3872 6428 7000 4232 3399 3008 4333 * 3226 169
+ 252 6445 2747 1000 1000 3213 165 10055 1028 2205
+
+P 170 6574 * 4423 4279 4196 3263 6273 4880 5142 4741 5450 3851 2459 4016 5536 2616 4680 4045 * * 170
+ 182 * 3080 * * 1244 791 9791 0 4489
+
+Q 171 4763 6861 6417 3594 6580 6612 6619 4074 4898 3659 5474 4018 3440 3475 4133 2922 3358 3985 * 4602 171
+ 18 6309 * 0 * 2641 252 9946 1134 4409
+
+A 172 4339 * * 4446 * 4589 4215 3534 4478 3410 4558 * 3136 3891 4955 3558 3418 2740 * * 172
+ 143 6121 3648 0 * 4789 53 9794 1023 3936
+
+Y 173 4736 6325 5720 4168 3936 6385 4181 3960 6969 2684 6548 5339 * 4333 3394 3971 3617 2771 * 4531 173
+ 68 4444 * 1751 508 2596 261 9725 1594 4676
+
+K 174 5377 6384 3903 4266 * 5497 4349 3668 2838 4154 6565 4768 3199 3993 2585 4967 4752 4490 * * 174
+ 269 5536 2750 1832 476 * 0 9797 1131 4161
+
+E 175 3439 * 2921 2898 6019 4804 4737 * 6256 5153 5766 2525 5180 4286 3674 3711 4036 6435 * 6217 175
+ 174 4411 3908 1355 715 888 1121 9967 1489 5537
+
+S 176 3263 * 3049 3696 6767 3258 5090 5260 4339 4531 5493 4093 4693 5471 6399 3098 3025 4557 * * 176
+ 18 * 6354 * * 589 1577 9952 0 3939
+
+N 177 5314 * 1754 3597 * 2899 * * 4630 6551 * 3219 5098 5536 4462 2677 4300 * * * 177
+ 90 5743 4588 0 * * 0 10021 1182 2229
+
+Y 178 * * 4719 4282 5280 1166 4711 * 3802 6895 6200 3246 * * 4735 3740 5197 5058 5456 6697 178
+ 135 4209 4834 325 2311 2207 352 9987 1636 2860
+
+S 179 4507 * 5696 * * 5689 * 5268 3341 2327 * 3586 * 5079 4089 3169 1909 5627 * 5366 179
+ 309 * 2373 * * 2564 267 9963 0 2987
+
+Y 180 * 4735 * 4308 2081 5580 5866 4615 6694 3553 6279 6223 6313 * 6764 5078 5142 5136 7237 1470 180
+ 45 * 5023 * * 3384 145 9667 0 4880
+
+C 181 5480 5341 3490 4088 6278 5236 6139 5238 6381 5270 6281 3695 * 4318 5002 2022 2065 6156 * 5922 181
+ 81 5136 5261 1644 556 3363 147 9631 1192 4827
+
+L 182 3822 6389 * 6188 4278 5881 * 3351 4740 3417 4013 4846 6454 5403 4488 3413 3041 2497 6447 5273 182
+ 0 * * * * * 0 9670 0 4725
+
+S 183 6584 * 6232 4725 5120 * 4740 5357 5445 4721 6096 6231 4438 4531 4656 2521 2046 2771 4812 4990 183
+ 0 * * 2322 322 4004 93 9670 1000 4725
+
+S 184 3899 5403 5585 5853 * 3684 * 6279 6807 3911 6428 6278 5463 * * 763 4696 5048 * * 184
+ 90 * 4051 * * 2035 404 9689 0 4534
+
+R 185 5449 * 5180 4153 5600 6182 5506 3241 5598 4145 * 4453 5607 4088 3474 2878 2403 4027 * 4252 185
+ 0 * * 0 * 656 1453 9703 1000 4329
+
+L 186 4860 6529 * 6854 5264 * 6626 3822 * 523 5412 * * * * * 6439 3674 * 5072 186
+ 0 * * * * 454 1889 9912 0 2285
+
+R 187 * * 4505 4998 6926 6705 4008 4177 5984 3615 5306 3478 5314 5300 3261 2919 2389 3596 * 5940 187
+ 46 5600 6565 1308 746 * 0 10050 1145 1245
+
+V 188 5797 * * 6686 3573 6640 * 1665 * 1999 5226 5710 * 5781 * 5856 6801 2616 6971 4281 188
+ 0 * * * * * 0 10001 0 1591
+
+S 189 4403 * 4047 5390 * 5246 5292 5777 4500 6691 5879 3377 2466 4894 3696 2435 3094 5833 * 5662 189
+ 14 * 6656 * * * 0 10001 0 1591
+
+A 190 3428 * 4665 4752 6652 5637 3794 6074 3795 3645 4979 4220 2461 5420 4568 2847 4045 5083 * * 190
+ 13 * 6799 * * * 0 9994 0 1762
+
+T 191 4427 5645 4776 4339 6599 4196 5534 4846 4381 3820 6697 5577 6882 3851 4303 2489 3205 2708 * 6822 191
+ 125 * 3590 * * * 0 9974 0 1903
+
+F 192 3804 6677 2966 4004 6677 4236 5318 * 3813 5361 6554 3968 4675 3297 3318 3666 3541 3953 * * 192
+ 99 * 3912 * * 1881 457 9844 0 3271
+
+W 193 4433 * 5781 2871 3977 6871 4648 5587 5234 4255 4225 * 5582 5498 3258 4388 5049 4179 2292 4356 193
+ 57 6526 5172 1000 1000 * 0 9803 1000 3553
+
+H 194 4672 * 2426 2544 * 4394 4644 5416 5486 4580 * 4906 * 4912 3645 2531 3931 5496 * 5577 194
+ 31 6536 6599 3007 192 2972 197 9781 1267 3930
+
+N 195 5798 * 1523 4226 * 3948 4095 5373 3245 5731 5050 3997 4694 4961 5751 3904 4336 6594 * * 195
+ 151 * 3333 * * 2845 216 9785 0 3690
+
+P 196 3022 * 2842 3924 6890 2503 6403 5661 6316 4869 5406 3636 6486 5427 5211 2518 4937 * * 4811 196
+ 1542 * 607 * * 1244 791 9674 0 4517
+
+R 197 4253 * 3675 4356 * 1372 * 4159 5360 6093 * 3529 * 4070 3654 3597 5023 * * * 197
+ 0 * * * * 282 2495 8470 0 7912
+
+N 198 3233 * 4900 4706 * 1556 5952 6633 3003 5343 * 3520 * 5282 5792 4754 3858 4032 * 6947 198
+ 236 * 2729 * * 3678 117 9915 0 2793
+
+H 199 5657 * 4045 4179 6145 6449 5487 3763 4005 3473 6232 3823 6346 4842 4530 3586 2131 3628 * 5403 199
+ 0 * * * * 209 2892 9859 0 4548
+
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+
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+
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+ 16 * 6468 * * * * 10093 0 0
+
+Q 203 4329 4585 * 3018 * 6809 5469 3255 4038 4124 4678 5938 6672 3838 3019 4906 3175 3103 * 6420 203
+ 12 * 6934 * * * 0 10058 0 1010
+
+V 204 2075 6672 * 5642 4276 6453 * 3783 * 5167 * * 6486 * * 3899 * 1026 * * 204
+ 26 5793 * 5136 42 1128 883 10010 1156 1160
+
+Q 205 4920 * 4665 2936 * 4899 4705 6646 2827 6032 6241 4851 * 3736 3075 2792 2703 5696 * * 205
+ 21 6109 * 0 * 0 * 9955 1023 1010
+
+F 206 6390 * 5237 6738 4254 4729 1667 * 6434 * 6564 1639 6319 5704 5412 3835 5522 * * 4131 206
+ 64 * 4520 * * * * 9844 0 0
+
+H 207 4645 6318 5006 2652 6084 3753 4634 5124 3275 4498 * 4450 3477 4585 4370 3256 4214 4911 * 4862 207
+ 0 * * * * 377 2120 9654 0 1894
+
+G 208 2374 * 4973 4831 4544 2388 5613 6372 6086 5372 * 4072 * 4686 6446 2613 3493 4826 6269 5353 208
+ 0 * * * * * 0 9626 0 1085
+
+L 209 5267 * * 4746 5593 2009 * 5439 6279 1815 4631 6378 5192 4804 6604 2754 5433 4725 * 6324 209
+ 0 * * * * * 0 9518 0 1085
+
+S 210 5194 6016 4711 2913 6164 5292 5336 * 4821 6327 * 3347 2942 3181 5237 2550 3373 5166 * 6169 210
+ 20 6202 * 0 * 0 * 9506 1001 1085
+
+E 211 5021 * 2996 2824 * 3860 4649 5016 4540 4580 5215 4023 * 3711 5034 3698 3752 3177 * 5572 211
+ 19 * 6279 * * * * 9424 0 0
+
+E 212 4557 * 5990 3108 * 4284 5682 * 5083 5771 5679 3128 2347 3056 3606 3148 4995 5045 * * 212
+ 241 2700 * 2192 356 * 0 9392 2340 1006
+
+D 213 3655 * 2925 4513 * * 4928 * 2567 2947 * 4883 6027 4063 2981 3868 4819 4159 * 5777 213
+ 180 3659 4708 1411 680 * 0 9185 1618 1006
+
+K 214 4077 * 5666 5238 * * 5674 5020 4338 4702 * 3471 5675 4063 4846 2800 1938 2939 * 5885 214
+ 56 5814 5614 2322 322 1308 746 9006 1043 1417
+
+W 215 3687 5550 5830 * 3541 5591 * 2265 * 2725 4506 * * 5787 * * 3390 2959 3733 4152 215
+ 0 * * * * * 0 8878 0 1332
+
+P 216 * * 3371 3924 * 4371 * 5494 3894 4722 5495 4449 3268 3988 3285 2741 2949 4463 * * 216
+ 29 5644 * 3459 138 1499 630 8782 1015 1332
+
+E 217 3813 * 4552 3737 5353 5253 * 4346 3131 1948 * 5623 * * 2958 3026 5765 * 5532 5246 217
+ 64 4524 * 3081 181 * 0 8649 1294 1157
+
+G 218 4239 * 3797 3864 * 5444 * 4359 5174 * * 2640 4402 3872 4341 2440 4355 2993 * 5445 218
+ 97 3937 * 771 1272 * 0 8649 1338 1157
+
+S 219 5364 * * 4414 * * 5209 3479 * 3846 4219 * 2042 * 3690 3284 4532 2167 * * 219
+ 0 * * * * * 0 8537 0 1157
+
+P 220 * * * 4460 5392 5138 3214 5209 4956 4316 * 3599 2532 5486 4262 3186 4243 3122 * 3685 220
+ 79 4238 * 0 * * 0 8291 1195 1157
+
+K 221 5226 * 5271 2831 * 4262 3953 5392 3469 * * * 3273 2897 2665 5312 3620 * * 3751 221
+ 39 5246 * 0 * 0 * 8291 1000 1157
+
+P 222 * * * 3563 5630 * * * 5016 4375 * * 908 4297 4249 2688 5358 * * * 222
+ 38 5280 * 1000 1000 * * 8353 1001 0
+
+V 223 3410 * 5282 3630 * 3449 * 2823 4163 3187 * * 2949 * 4174 5149 5246 2901 * 5187 223
+ 0 * * * * * * 8201 0 0
+
+T 224 5175 5187 5267 3080 4102 * 5250 3552 * 3209 * 5293 3952 5140 4286 2616 4178 4373 * 3534 224
+ 0 * * * * * * 8201 0 0
+
+Q 225 5185 * * * * * * 3510 4329 2882 * 5238 4803 2588 4132 3624 * 1712 * 5187 225
+ 41 5155 * 0 * * * 8201 1001 0
+
+N 226 * * 4028 4042 * * * 2696 4984 * * 2220 4071 3935 4952 3087 2519 * * 5164 226
+ 0 * * * * * * 7949 0 0
+
+I 227 4075 * * * * * * 1595 4890 2066 * * * 4092 * * 3104 2999 4755 * 227
+ 0 * * * * * * 7949 0 0
+
+S 228 4869 * 4887 * 3878 5105 4818 4770 4765 * * 5002 4853 4871 * 1223 2606 4900 * * 228
+ 0 * * * * * * 7611 0 0
+
+A 229 1758 4732 * 3641 * 4682 * 4896 * 3588 * * 2069 * 3715 3102 * * * * 229
+ 0 * * * * * * 7316 0 0
+
+E 230 * * 3685 1125 * 4619 * * 4843 * 4543 4700 * 4558 * 2906 * 2932 * * 230
+ 0 * * * * * * 7126 0 0
+
+A 231 1798 * 3306 2618 3523 * * * * * * 2484 * * * * 2453 * * * 231
+ 0 * * * * * * 5187 0 0
+
+W 232 * 3095 * * * * 3100 3178 * * * * * * * * 2835 * 955 * 232
+ 0 * * * * * * 4342 0 0
+
+G 233 * * * * * 1456 * * * * * 2636 * * 2538 2727 * 2723 * * 233
+ 0 * * * * * * 3631 0 0
+
+R 234 * * * 2232 * * * * * * 2405 * * * 1322 * 2332 * * * 234
+ 0 * * * * * * 3307 0 0
+
+A 235 425 * * * * * * * * * * * * * * * * 1972 * * 235
+ 515 * 1735 * * * * 2901 0 0
+
+D 236 * * 942 * * * * * * 1060 * * * * * * * * * * 236
+ 0 * * * * 0 * 1725 0 1086
+
+C 237 * 0 * * * * * * * * * * * * * * * * * * 237
+ 0 * * 0 * * * 2256 0 0
+
+//
+�HHsearch 1.5
+NAME 377b625a8e52f94cba9ef9a525219056
+FAM
+FILE 377b625a8e52f94cba9ef9a525219056
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:22:57 2013
+LENG 161 match states, 161 columns in multiple alignment
+FILT 122 out of 212 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEEEECCCCEEEECCHHHHHHHHHHHH
+CCCCCCHHHHHHHHHHHHHCCCEEECCCCEEEEECCCCHHHHHCCCHHHHHHHHCCCCCCC
+>ss_conf PSIPRED confidence values
+9863444403388886868999989999786666257888887443568789987349999999854912257279978988899659999999999872
+8999888999699998860686675578878987486899995899999998845498999
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxsxxxxvxxxxxxxxxxpxxPxxxxxxxxxxgxxxLwqFLxxLLxdxxxxxxIxWtxxxxeFklvdpxxVAxlWGxxK
+nkxxMtYeKLSRaLRyYYxkxIlxKvxGkrxxYrFxxxxxxxxgxsxxxxxxxxxxxpxxx
+>377b625a8e52f94cba9ef9a525219056
+VPSYDSFDYEDYPAALPNHKPKGTFKDYVRDRADLNKDKPVIPAAALAGYTGSGPIQLWQFLLELLTDKSCQSFISWTGDGWEFKLSDPDEVARRWGKRK
+NKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQSLLGYTPEELHAMLDVKPDAD
+>gi|340380278|ref|XP_003388650.1| PREDICTED: hypothetical protein LOC100638140 [Amphimedon queenslandica]
+------------PSPPCFPppPPPFTTEDFIRPHHPpkpnKRPRKPKPPATVDPSEIKDipASAQLWEFLLKVLKKPKYAYMVSWENqqDG-LFRFHDPP
+AFAALWGRHRNRPSMTYDKVARALRYYYRRDILE-QVGGRLTYKFSPRLCKQFS-----------------
+>gi|268579031|ref|XP_002644498.1| Hypothetical protein CBG14386 [Caenorhabditis briggsae]gi|187027866|emb|CAP32937.1| hypothetical protein CBG_14386 [Caenorhabditis briggsae AF16]
+----------------------------------SYVPSPVYPSPIMNDepmtddelVKMKGPSRLIGFLVHIAMNEKARRALRWTGNGLEFVLVNKELV
+AKMWGNRKhNTKDMDYYKLSRAIREKYEKKnSSNSRgGGKlkkgtrTYSYVFtenaYPDLINQTEKSIE-------------
+>gi|291389803|ref|XP_002711338.1| PREDICTED: Spi-C transcription factor (Spi-1/PU.1 related)-like [Oryctolagus cuniculus]
+---------------------EGNVHQSLQNATENQLVQPAIFP--QKGGKGRKKLRLFEYLYDSLCNPEMASCIQWVDKnKGIFQFVskNKEKLAELWG
+KRKgNRKTMTYQKMARALRNYGRTGEITKIR-RKLTYQFSEAIlqrlspSYILG---KEIFYSQYLQPDQE
+>gi|309366055|emb|CAP22188.2| hypothetical protein CBG_00832 [Caenorhabditis briggsae AF16]
+-----------------------------------------------------SKLCLLPFLRGLLEDESNQHLICWTDKsRLQFRFVDHMKVTELWAAT
+KpgRKVRaMKYDNMCKSLRTFCKQDkTLEKVEGKLFEWRFLES-----------------------
+>gi|189234183|ref|XP_967290.2| PREDICTED: similar to DNA polymerase delta catalytic subunit [Tribolium castaneum]
+-----------------------------------------------------VPPSAPLLYVSNATSSSILLKWKIGNDGgApvSGFTLNYR-------
+----------------------------------------------------------------
+>gi|256077175|ref|XP_002574883.1| hypothetical protein [Schistosoma mansoni]gi|238660099|emb|CAZ31116.1| conserved hypothetical protein [Schistosoma mansoni]
+----------------------------------------------------------DEFILHLFNPnSQYLNCVQWIDKqARIFQIRNPQKLSQLWGY
+YRKNVNMTFESVSRSLRLYYVSGKLERIRGQRNQYRFL-------------------------
+>gi|341878556|gb|EGT34491.1| hypothetical protein CAEBREN_21643 [Caenorhabditis brenneri]
+-----------------------------------------------------RTHRLLRFIPRLINSGDYPDKIIWVNEeEREFRFLEPHFFAKLYGKA
+IGNPDMKYDNMTRSLREYCKQGFAVKTEGQ-SSWRILNNPVALEV-----------------
+>gi|123123380|emb|CAM24571.1| E74-like factor 5 [Mus musculus]gi|123123589|emb|CAM17513.1| E74-like factor 5 [Mus musculus]
+---------------------------------------------------SLQSSHLWEFVRDLLLSPeENCGILEWEDReQGIFRVVKSEAL------
+---------------------------------------------------------------
+>gi|341903063|gb|EGT58998.1| hypothetical protein CAEBREN_15325 [Caenorhabditis brenneri]
+-------------------QSVGSLETFVKKVNLKSVKSPKLP-----------KVNILDFIRDTIESGEHSEVITWVDQnKSGSQIVDPMAVVELYNKA
+TGKRYTKFDNFCRPLRRLAEEGVLFKPKTMRSTWYFVETV----------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 * * * * * * * * * * * * * * * * * 0 * * 1
+ 0 * * * * * * 1553 0 0
+
+P 2 * * * * * * * * * * * * 0 * * * * * * * 2
+ 0 * * * * * * 1553 0 0
+
+S 3 * * * 2673 3605 * * * * * * * * * * 394 * * * * 3
+ 0 * * * * * * 1553 0 0
+
+Y 4 * * * * 2213 * * * * * * * * * * * * * * 350 4
+ 246 * 2673 * * * * 1553 0 0
+
+D 5 * * 425 1970 * * * * * * * * * * * * * * * * 5
+ 0 * * * * * 0 1496 0 1031
+
+S 6 * * * * * 2572 * * * * * * * * * 266 * * * * 6
+ 0 * * * * * 0 1496 0 1031
+
+F 7 * * * * 0 * * * * * * * * * * * * * * * 7
+ 0 * * * * * 0 1496 0 1031
+
+D 8 * * 1334 968 * * * * 3439 * * * * * * * * * * * 8
+ 1334 * 729 * * * 0 1496 0 1031
+
+Y 9 * * * * * * * * * * * * * * * 1171 * * * 847 9
+ 0 * * * * 244 2685 1217 0 1352
+
+E 10 * * * 0 * * * * * * * * * * * * * * * * 10
+ 0 * * * * * 0 1496 0 1031
+
+D 11 * * 458 2474 * * * * * * * 3439 * * * * * * * * 11
+ 0 * * * * 0 * 1496 0 1031
+
+Y 12 * 2213 * * * 2844 * * * 2740 * * * * * * * * * 1013 12
+ 234 * 2740 * * * * 1553 0 0
+
+P 13 * * * * * 3103 * * * * * * 491 * * 2539 * * * * 13
+ 0 * * * * 0 * 1920 0 1036
+
+A 14 3349 * * * * * * * * 3199 * * * 2048 * 1856 1863 * * * 14
+ 0 * * * * * * 1943 0 0
+
+A 15 1515 * * * 3032 * * * * * * * 1055 * * 4435 * * * * 15
+ 0 * * * * * * 1943 0 0
+
+L 16 * * * * * * * * * 1109 * * 1877 3291 * 2627 * * * * 16
+ 0 * * * * * * 2071 0 0
+
+P 17 * 1206 * * * 3460 * * * * * * 2240 * 1921 * * * * * 17
+ 0 * * * * * * 2071 0 0
+
+N 18 * * * * 2069 * * * * 1159 * 1672 * * * * * * * * 18
+ 0 * * * * * * 2071 0 0
+
+H 19 * * * * * * 2240 * 4878 * * 3623 2069 1984 * 3644 3291 * * * 19
+ 393 2069 * 1000 1000 * * 2071 1049 0
+
+K 20 * * * * * * * * 1238 * * * 2506 2212 2440 * * * * * 20
+ 0 * * * * * * 2590 0 0
+
+P 21 * * * * * * 4074 * * 5107 * * 676 * * 1807 * * * * 21
+ 105 3830 * 2322 322 * * 2590 1031 0
+
+K 22 * * 3464 2218 * 4440 4204 * 2963 * * 4147 2523 * * * 3927 2559 * * 22
+ 0 * * * * * * 3004 0 0
+
+G 23 * * * * 2924 813 * * * * 3211 * 3464 * 3317 * * * * * 23
+ 0 * * * * * * 3004 0 0
+
+T 24 * * 4298 * * * * 3647 * * * 3397 5609 * * 965 2050 * * * 24
+ 0 * * * * * * 3109 0 0
+
+F 25 * * * * 1038 * * 3548 * 2711 * * * * * * 3150 3515 * 3740 25
+ 0 * * * * * * 3209 0 0
+
+K 26 * * * 1675 * * 2699 * 1647 3386 * 4642 * * * 3680 * * * * 26
+ 0 * * * * * * 3382 0 0
+
+D 27 * 2743 1321 4724 4079 * * * * * * * * 2791 * * 2258 * * * 27
+ 0 * * * * * * 3446 0 0
+
+Y 28 3942 * * * 1648 * 3982 * * 4136 3529 * * * * 2826 * * * 1900 28
+ 0 * * * * * * 3454 0 0
+
+V 29 * * * * * * * 2141 * 2332 4136 * * * * 3803 * 1164 * * 29
+ 0 * * * * * * 3454 0 0
+
+R 30 * * * * 4963 4824 3942 * 2850 4121 * 3982 * 1445 2054 * * * * * 30
+ 0 * * * * * * 3454 0 0
+
+D 31 * * 3201 3075 * * * * 1852 * * 1668 3569 * * 4763 4064 * * * 31
+ 43 * 5091 * * * * 3644 0 0
+
+R 32 2860 * * * * * 3540 * * * * * 4662 4901 984 * * 2338 * * 32
+ 0 * * * * * 0 3657 0 1031
+
+A 33 1917 3766 * * * * 3563 3436 * * * 2681 4168 4328 * 2971 3385 * * * 33
+ 0 * * * * * 0 3646 0 1031
+
+D 34 4328 * 2768 2320 * * * * 3487 2174 * 3496 3563 5225 4770 4168 * * * * 34
+ 520 2640 2814 932 1071 * 0 3646 1225 1031
+
+L 35 3571 * * * * 3079 * * 1952 3641 * 3358 * 5182 * 3251 3960 3083 * 4423 35
+ 0 * * 1950 432 969 1031 3759 1139 1344
+
+N 36 4695 * * 2053 4717 * * * 4359 * * 3292 * 2584 3955 2665 * 4716 * 3257 36
+ 186 * 3045 * * 2334 319 3868 0 1156
+
+K 37 * * 3795 * 4736 * 4778 * 3490 2427 * * 3235 3432 * * 2718 2294 * 5364 37
+ 48 * 4948 * * 2298 328 3799 0 1207
+
+D 38 4808 * 2611 5778 * 2069 * * 3284 5119 * * 3414 4584 4148 5314 2785 4310 * * 38
+ 0 * * * * 2460 289 3923 0 1193
+
+K 39 * 5389 5205 5237 4680 * 4775 * 2719 4566 * 3831 4952 3269 3303 1908 * 4113 5573 * 39
+ 39 * 5218 * * * 0 4082 0 1153
+
+P 40 5886 * * * * * * * 5801 4784 * 3889 473 4273 * 4418 * 4559 * * 40
+ 0 * * * * * 0 4081 0 1190
+
+V 41 3214 * 4600 * * * * 5152 2143 5434 4916 * 4189 4818 * 3158 4533 1762 * * 41
+ 27 * 5773 * * 2565 267 4120 0 1190
+
+I 42 4943 * 5498 * 3802 * 4849 1972 4056 2837 4022 * 4039 * 5395 4082 4490 3841 5399 4615 42
+ 0 * * * * * 0 4152 0 1184
+
+P 43 5139 * 5106 * 5320 5655 * * * * * 5341 421 6296 * 3700 * 4775 * * 43
+ 141 * 3427 * * 2800 224 4148 0 1184
+
+A 44 1796 * 5328 * 4825 4922 4955 * 5026 * * 4691 3245 4106 * 3108 2463 4149 * * 44
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+
+//
+�HHsearch 1.5
+NAME 37afc7acd88623f9df7bf8f423af00c0
+FAM
+FILE 37afc7acd88623f9df7bf8f423af00c0
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:51:38 2013
+LENG 74 match states, 74 columns in multiple alignment
+FILT 107 out of 1036 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEEECCCCCCCHHHHHHHHHHHCCEEEEECCCCCEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEECCC
+>ss_conf PSIPRED confidence values
+97499996899999999999999970938999708875899997999999999998289868985899996899
+>Consensus
+xxxxlxvxxlpxxxxxxxlxxxxxxxgvxxxxxxxxxxxafvxfxxxxxaxxaxxxlxxxxxxgxxlxvxxxxx
+>37afc7acd88623f9df7bf8f423af00c0
+HMRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT
+>gi|115402163|ref|XP_001217158.1| polyadenylate-binding protein 2 [Aspergillus terreus NIH2624]gi|114189004|gb|EAU30704.1| polyadenylate-binding protein 2 [Aspergillus terreus NIH2624]
+--RSIFVGNVDYGASPEEIQAHFQSCGsINRVTIlldkftGQPKGMPTSNLQSPVWWPNSGV-KRKCVPWSQS-EVVPKRT
+>gi|335282457|ref|XP_003123153.2| PREDICTED: scaffold attachment factor B1 [Sus scrofa]
+-MAKFCRTGRSIAKESRAVTIVQPALGpSFG--VapcGERsggPAAG---RGTQGEPASFLPLWPVPPAGG----------
+>gi|338723967|ref|XP_001497902.3| PREDICTED: insulin-like growth factor 2 mRNA-binding protein 3-like [Equus caballus]
+-LGSLYLESemgvssvVGARCVGAPSLRSSSHSRlSLPGrpeqgegpgrPHLKKvnvapsPGSVCGESPRR-WAggqRPSCGCRGSkVELHGKLIEVEHS
+--
+>gi|194222666|ref|XP_001498933.2| PREDICTED: insulin-like growth factor 2 mRNA-binding protein 2-like isoform 1 [Equus caballus]
+-DYELPMEAFPSWSRLSTYTKcrfqlwLYlgsdpGSPPpPSSSQdpgrpPSFPLGTKFAQLEPGRRSLEGARRRSRsveFCKVElhgKIMEVDYS--
+>gi|302763791|ref|XP_002965317.1| hypothetical protein SELMODRAFT_406603 [Selaginella moellendorffii]gi|300167550|gb|EFJ34155.1| hypothetical protein SELMODRAFT_406603 [Selaginella moellendorffii]
+NQGTLVVFNLDVAISIETINSVFKKYGdVKEIREtPIKRTHKFVEFFDVRDAARAKEALDGEDILGSTVKIEFSRP
+>gi|7498075|pir||T30930 hypothetical protein D1007.7 - Caenorhabditis elegans
+--RTLWLKKIPTNIVENDLKQAVESCGeASRVKVIGNRACAYITMENRRSANDVVSKMREVSVAKKMVKVYWA--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+H 1 4182 * 4232 * * * 3215 * * * * 887 3905 * * 3873 4122 4296 * * 1
+ 0 * * * * * * 5669 0 0
+
+M 2 3753 4779 4058 * 4903 5045 * * * 3517 1982 3883 * 4854 2735 3318 * 4950 * 4649 2
+ 0 * * * * * * 7451 0 0
+
+R 3 3515 4135 * 5739 5632 4384 * * 2620 5765 6030 6206 5899 6008 1671 4802 3143 5694 * 4497 3
+ 0 * * * * * * 9159 0 0
+
+K 4 5989 5191 6181 4508 6188 * * 6347 2708 4967 * 4654 6469 5263 3185 2924 1706 4411 * 5980 4
+ 0 * * * * * * 9964 0 0
+
+I 5 5072 5119 * * 5038 6275 6641 2072 * 1424 6556 * * * 5078 5882 6816 2241 * * 5
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+
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+
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+
+R 8 4280 * 5109 4415 4544 1968 5880 * 3717 6337 * 5515 * * 2892 2662 3287 6560 6447 5072 8
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+
+G 9 5124 * 5448 5336 * 1993 4645 6501 4508 6029 6684 1618 4780 6872 4639 3483 4891 * 6620 6920 9
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+//
+�HHsearch 1.5
+NAME 389317ac7330494edc8db3812c39f6d3
+FAM
+FILE 389317ac7330494edc8db3812c39f6d3
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:11:32 2013
+LENG 97 match states, 97 columns in multiple alignment
+FILT 109 out of 310 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEEECCCCCCEEEEEEEEEEEEEEECCCEEEEEEEEECCCCEEEEECCCCCCCC
+>ss_conf PSIPRED confidence values
+9987798899899999999999987636587549999999999763035636359864899999998078739999998279918989702789998
+>Consensus
+xGgwxxidvxxxvqxlaxfAVxexNkxxxxxxLxxxxVvxxxxxxxxxxxxgxQvVaGxnYxLxixaxxxxyxaxVxxxpwxxxxkLxsFxpxxxxx
+>389317ac7330494edc8db3812c39f6d3
+MGEWEIIDIGPFTQNLAKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEGFREIKGYEYQLYVYASDKLFRADISEDYKTRGRKLLRFNGPVPPP
+>gi|224089663|ref|XP_002308795.1| predicted protein [Populus trichocarpa]gi|222854771|gb|EEE92318.1| predicted protein [Populus trichocarpa]
+-DGWIPIkNLEnKHVVKIAEFAVKEHNRQA-GSELRLYSIHKGEL----------QVKEGTDYRLLLAVI--GagglHEAVVHE-SYDYSTVLISFVP-L
+---
+>gi|15225164|ref|NP_180758.1| cysteine proteinase inhibitor 2 [Arabidopsis thaliana]gi|125991828|sp|Q8L5T9.2|CYT2_ARATH RecName: Full=Cysteine proteinase inhibitor 2; Short=AtCYS-2; Flags: Precursorgi|4263720|gb|AAD15406.1| putative cysteine proteinase inhibitor B (cystatin B) [Arabidopsis thaliana]gi|110738361|dbj|BAF01107.1| putative cysteine proteinase inhibitor B [Arabidopsis thaliana]gi|330253521|gb|AEC08615.1| cysteine proteinase inhibitor 2 [Arabidopsis thaliana]
+-GGKSGVpNIRtnREIQQLGRYCVEQFNQQA-qneqgnigsiaktdtaiSNPLQFSRVVSAQK----------QVVAGLKYYLRIEVTQPngstrMFDSV
+VVIQPWLHSKQLLGFTP-VVSP
+>gi|47115697|sp|Q7M429.1|CYTL_TACTR RecName: Full=L-cystatin; Flags: Precursorgi|1587012|prf||2205298A L-cystatin
+-GGWIDANVGdTDVKEAARFATEAQSSRS-NSLYHHklLKIHKART----------QVVSGINYEVFIETGTttckksevpledlkrcavpenGvKhlCQ
+AIVWVQAWIPRTKVTKLE------
+>gi|242036759|ref|XP_002465774.1| hypothetical protein SORBIDRAFT_01g045610 [Sorghum bicolor]gi|241919628|gb|EER92772.1| hypothetical protein SORBIDRAFT_01g045610 [Sorghum bicolor]
+--AWVPVlDVNeLVIKQVAQFAVLVYG-LAHHRDLAYVGVVRGQTEQA--------VGGGTNFRLVVVAarpDDGgstaQYDCLVWGVPgsRSDTWKLRR
+FRK-----
+>gi|225717196|gb|ACO14444.1| Cystatin-F precursor [Esox lucius]
+-GAPHEISRNdSGVLKAALHGTYSFNNKT-NDAFLFkpSAIEKAER----------QIVKGLNYIMEVDISRTvchkngqnntdlarcvfqpdgLlkqtf
+hCHFEVWTIPWLNFMKTI---------
+>gi|241999596|ref|XP_002434441.1| secreted cystatin, putative [Ixodes scapularis]gi|215497771|gb|EEC07265.1| secreted cystatin, putative [Ixodes scapularis]
+-GGYTRKtDhQTnPKYLELAHFATSSWSAGQ-ANKAYYDTVEEVLEAQT-------QVVAGINYKLTLKVAESvceitsqytkeactpkpdavrkTCTTV
+IYEKVWENMKSVSSFS------
+>gi|109093141|ref|XP_001097898.1| PREDICTED: cystatin-D [Macaca mulatta]
+-GDIHAADLNdKSVQRVLNFTIREYNKDiS-KDEYYSrpLQVMAA--YQ--------QVVGGVNYYFNVKfgrttctKSQPNldncpfndqpelkeeefC
+SFQINEVSQENKISILNYK------
+>gi|123408571|ref|XP_001303223.1| Clan IH, family I25, phytocystatin-like peptidase inhibitor [Trichomonas vaginalis G3]gi|121884585|gb|EAX90293.1| Clan IH, family I25, phytocystatin-like peptidase inhibitor [Trichomonas vaginalis G3]
+-GAAKPANVQdEHVIQAFKDAIALGNQKN-GTTLEYIQLLSATQ----------KVVSGYIFEGVVKTNDGDYKVKIWCKPGNTEKELQLFE------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
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+ 68 5112 5841 1845 471 0 * 5680 1077 1051
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+ 46 4993 * 3868 102 244 2684 4142 1096 4194
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+ 13 6772 * 1000 1000 * * 5688 1000 0
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+ 218 2835 * 1000 1000 * * 5688 1683 0
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+ 63 4556 * 2467 288 * * 5688 1165 0
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+
+G 92 4384 * * * * 2995 5511 * * 3851 * * 718 4745 4675 5555 5066 * * * 92
+ 1951 * 432 * * 0 * 4306 0 1204
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+P 93 * * 3024 * * * * * 3153 * * * 735 * * 2610 * * * * 93
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+
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+P 95 3846 * * * * * 3895 * * * * 2075 1435 * 3822 4033 4057 3961 * * 95
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+P 96 * * * * * * * * * * * * 1175 * * 844 * * * * 96
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+
+//
+�HHsearch 1.5
+NAME 38a44a0cf7d477bebe8b2606d936e643
+FAM
+FILE 38a44a0cf7d477bebe8b2606d936e643
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:20:43 2013
+LENG 102 match states, 102 columns in multiple alignment
+FILT 113 out of 510 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCC
+CC
+>ss_conf PSIPRED confidence values
+9988788888766523689988740578986799999997799634399999999999999999999999999982997675999999999759867787
+98
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxixxaxixrlaxxxgvxxisexalexlxeaxexxxrxVixxaxxxaxhaxRktVtxxDIxxAlkxxgxxxygf
+xx
+>38a44a0cf7d477bebe8b2606d936e643
+SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF
+GG
+>gi|222823380|ref|YP_002574954.1| NADP-dependent alcohol dehydrogenase [Campylobacter lari RM2100]gi|222538602|gb|ACM63703.1| NADP-dependent alcohol dehydrogenase [Campylobacter lari RM2100]
+-----------------------------------DFSLEHGIYPEIElIKPSEIDKAYENLTsgkakfRYVIdmseqD---------------------
+--------------
+>gi|281210047|gb|EFA84215.1| hypothetical protein PPL_03292 [Polysphondylium pallidum PN500]
+-----------------------------------QFIDEGkllksPLIGKV-fKGIESVPSAHDYLEnnqesfgKVQV-----YSYFFD-------LIV
+CPLNKIVDDKVD---
+>gi|313903307|ref|ZP_07836699.1| zinc-binding alcohol dehydrogenase family protein [Thermaerobacter subterraneus DSM 13965]gi|313466395|gb|EFR61917.1| zinc-binding alcohol dehydrogenase family protein [Thermaerobacter subterraneus DSM 13965]
+-----------------------------------AVAASVPLQVAVQrYPFEQANQALAAVKesrvrgAAVLvldepagr-------------------
+-----------------
+>gi|254504613|ref|ZP_05116764.1| Alcohol dehydrogenase GroES-like domain family [Labrenzia alexandrii DFL-11]gi|222440684|gb|EEE47363.1| Alcohol dehydrogenase GroES-like domain family [Labrenzia alexandrii DFL-11]
+-----------------------------------AFAAEGKVASHYAtESLDNINDIFGRMElgkidgRIVMtl-------------------------
+-----------
+>gi|303391124|ref|XP_003073792.1| transcription initiation factor TFIID subunit TAF6 [Encephalitozoon intestinalis ATCC 50506]gi|303302940|gb|ADM12432.1| transcription initiation factor TFIID subunit TAF6 [Encephalitozoon intestinalis ATCC 50506]
+----------------------------FSKETLKSFAQSKGISNIDDDALRVLSQDLEYRIKEVCQEGSKFMVGSKRTKLSIDDINYALISRnVDPLFG
+YDP
+>gi|50423321|ref|XP_460243.1| DEHA2E21626p [Debaryomyces hansenii CBS767]gi|49655911|emb|CAG88519.1| DEHA2E21626p [Debaryomyces hansenii]
+---------------------IKEQDRFLPIANVGRVMKKALPPhaKLSKESKECIQECVSEFISFITSHASDRGRLEKRKTLNGEDILWSMYILGFENY
+----
+>gi|328769656|gb|EGF79699.1| hypothetical protein BATDEDRAFT_7075 [Batrachochytrium dendrobatidis JAM81]
+---------------------------------ISLILQAAEVDDYEPRIIPQLLEFAHRYVQDVLQDSQVFADHAGHKDLEVDDIRLAIES--RVAHSF
+--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+
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+
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+
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+ 0 * * * * * * 1840 0 0
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+E 52 3729 6842 2268 1489 * 6153 * 5243 3770 4583 * 5037 5459 5457 6482 3739 6364 5483 * * 52
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+
+E 53 3129 6990 3069 2185 * * 6345 * 3732 4898 6068 5378 5607 3005 5727 4062 3615 4787 * 4756 53
+ 29 5645 * 4597 61 * * 9092 1009 0
+
+T 54 3322 * * * 4602 4650 * 2305 * 1514 4757 * * 6254 * 6530 6831 2438 * 6334 54
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+
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+V 81 * 5411 * * * * * 1581 * 2481 6149 * * * * 5364 * 1236 * * 81
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+
+R 95 * * 4120 2089 3115 * 4826 3045 4512 4629 5717 5709 * 4659 2633 5239 5493 * * 3970 95
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+
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+ 0 * * * * * * 6621 0 0
+
+L 97 3179 * * * * * * 3401 4333 1717 5287 4453 * 4739 4856 5204 4306 2741 * 3823 97
+ 0 * * * * * * 6112 0 0
+
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+ 0 * * * * * * 4252 0 0
+
+G 102 2910 * * * * 1622 * * * * * * 2801 * * 1327 * * * * 102
+ 0 * * 0 * * * 3018 0 0
+
+//
+�HHsearch 1.5
+NAME 38dd9955ccfba0d5be1c28ca6ce0751d
+FAM
+FILE 38dd9955ccfba0d5be1c28ca6ce0751d
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:54:43 2013
+LENG 76 match states, 76 columns in multiple alignment
+FILT 134 out of 700 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCHHHEEEEEECCCCCCCCCEEEEEECCCCEEECCCCCHHHHHHHHHHHHCCCCCCC
+>ss_conf PSIPRED confidence values
+9876579998135771681795692599990899999737999987899897598708999999999863457899
+>Consensus
+xxxxxxxxxxCCxxxxxxxIpxxxIxxyxxxtsxxCxxxaVIfxtkxgxxiCxdPxxxWVkxxixxlxxxxxxxxx
+>38dd9955ccfba0d5be1c28ca6ce0751d
+QPDAINAAVTCCYNFTNRKISVQRLASYRRITSSKCPKEAVIFKTIVAKEICADPKQKWVQDSIDHLDKQTQTPKT
+>gi|293630689|gb|ADE58987.1| CC chemokine CK7 [Sparus aurata]
+IVEPESINKSCCLMATRKPVPGKIIQNVER-SHSSCPVPAIILTTTRGRQICLDGSWIWAERVLRAFETSP-----
+>gi|229365878|gb|ACQ57919.1| C-C motif chemokine 19 precursor [Anoplopoma fimbria]
+----AEVPRDCCLSVKNKEVKKILVVDYSRQISGgGCSIDATVLVTRGGRKLCVPADESWIQAVMKHVDHL------
+>gi|297673795|ref|XP_002814937.1| PREDICTED: c-X-C motif chemokine 10-like [Pongo abelii]
+-----------CISISNQPVNPRSLEKLEIIpASQFCPHVEIIATMKKkGEKRCLNPESKAIKNLLKAVSKERS----
+>gi|327281413|ref|XP_003225443.1| PREDICTED: stromal cell-derived factor 1-like [Anolis carolinensis]
+--------YRCPCRYVESSVAKSHIKHLKILTVPGCSLQ-IIARLKNSsKQICIDPKLKWIQEYLEKYLH-------
+>gi|139472813|ref|YP_001129363.1| K4.1 [Human herpesvirus 8]gi|1778606|gb|AAC56951.1| similar to beta-chemokine genes [Human herpesvirus 8]gi|2246547|gb|AAB62672.1| ORF K4.1 [Human herpesvirus 8]gi|87196834|gb|ABD28860.1| K4.1 [Human herpesvirus 8]gi|261853486|gb|ACY00408.1| K4.1 [Human herpesvirus 8]gi|312275154|gb|ADQ57891.1| K4.1 protein [Human herpesvirus 8]
+-----IMASDCCENSlSSARLPpDKLICGWYW-TStVYCRQKAVIFVTHSGRKVCGSPAKRRTRLLME-----------
+>gi|149639456|ref|XP_001507067.1| PREDICTED: similar to shroom family member 3 protein [Ornithorhynchus anatinus]
+-----LMPRTCnCLKHTSNFIHPRFIRRLEKFeAGPYCRRLELLVILKSNQIVCVDPDAQWMKELLRYMDQRSREP--
+>gi|327274220|ref|XP_003221876.1| PREDICTED: c-X-C motif chemokine 11-like [Anolis carolinensis]
+-----------CQGRRMIRVNMLDVAEVEYHrSSPSCSEDELIIFFKTNGkTGCLDITKKQGRIIKEAIMRKR-----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 5346 0 0
+
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+
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+ 71 5247 5546 0 * * 0 5434 1020 1342
+
+A 4 1962 * 5292 5076 5221 2023 * * 5103 * 3088 * 4798 4109 * 2991 * 4981 5843 * 4
+ 133 4109 5040 1435 666 1690 535 5435 1376 1404
+
+I 5 2200 * * 4234 5267 * 5070 3185 4719 5308 * 4489 3765 5399 4327 3079 4017 3233 5482 * 5
+ 35 * 5370 * * 363 2168 5476 0 1445
+
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+ 59 4642 * 0 * * 0 5856 1051 1167
+
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+
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+
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+
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+ 0 * * * * 0 * 6698 0 1084
+
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+
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+ 35 7169 5879 0 * 0 * 7191 1060 1000
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+
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+
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+
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+
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+R 30 7481 * * 3753 5683 * 4868 2371 3584 3587 4869 6169 5918 3873 3664 7367 4827 2661 4475 4312 30
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+
+I 31 * * * 4999 3522 * 4466 2504 5571 3408 4493 * * 1497 6045 4995 4045 5310 * 6156 31
+ 1606 575 * 46 5008 119 3657 6840 3879 4249
+
+T 32 3238 * 6301 5006 * * 5869 4930 5063 5089 6130 4669 2748 6131 6048 3685 1463 3861 * * 32
+ 99 4067 7243 0 * 1750 509 7212 1491 1252
+
+S 33 5813 * 3330 6384 6002 2663 5623 6795 4650 6801 7153 4744 4502 6648 4450 1345 3856 6357 * * 33
+ 32 6095 7090 346 2231 299 2416 7201 1124 1209
+
+S 34 5613 6782 5120 4211 6686 2758 5931 4837 5546 4874 * 4195 2326 3901 4792 2130 5646 5813 * * 34
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+
+K 35 5548 * 3589 4148 6708 3048 3118 6397 7114 4147 6304 3732 4356 3679 4211 2573 4929 6103 * 4891 35
+ 0 * * * * 1187 835 7194 0 1050
+
+C 36 6306 52 * * * 6305 * * * * * * * * * * * 6645 * * 36
+ 86 * 4115 * * 0 * 7196 0 1000
+
+P 37 4206 * 3487 4752 * 4860 4749 7191 3743 5116 * 3506 2371 5367 3241 2483 4401 * * * 37
+ 19 * 6253 * * 0 * 7081 0 1401
+
+K 38 * * 7253 5381 4542 * 5428 2979 2775 2943 5303 3786 * 3442 2890 7017 4436 3231 * 6041 38
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+
+E 39 4936 * 3302 4216 * * 6740 5931 2948 5128 5061 4106 2261 3893 3695 5585 3084 5207 7436 6017 39
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+
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+ 0 * * * * 0 * 7168 0 1035
+
+F 43 2801 * * * 1070 * * 3967 * 2622 * * * * * * * 2701 * * 43
+ 9 * 7337 * * * * 7247 0 0
+
+K 44 5187 6454 * 4741 4238 6934 3800 3879 3071 4101 6601 7347 * 4911 4589 5786 1607 3919 6827 4925 44
+ 20 * 6215 0 * 0 * 7244 1000 1000
+
+T 45 * * * * 4463 6038 * 6001 * 1831 3798 * 6127 * 6302 5954 1044 4545 * * 45
+ 7 * 7679 * * 0 * 7226 0 1034
+
+I 46 5975 * 6917 6630 5474 5358 4738 5047 1092 5422 6780 4311 5022 5368 3005 5280 5426 3823 * * 46
+ 78 5227 5278 727 1337 0 * 7254 1150 1000
+
+V 47 4324 6328 4976 4393 * 4743 6273 * 2149 7224 5950 2596 * 5264 2168 3540 4249 7119 * * 47
+ 111 6986 3915 0 * 0 * 7223 1119 1139
+
+A 48 5715 * 4587 5039 6787 813 5635 5373 3934 6475 * 2754 * 5363 5860 5638 * * * * 48
+ 65 5479 5525 1690 535 0 * 7145 1099 1434
+
+K 49 5343 * 6503 4427 5699 5191 7383 4183 1939 4706 5576 5336 6125 4377 1631 5337 5287 5976 * 6182 49
+ 190 4065 3978 597 1561 0 * 7236 1392 1102
+
+E 50 4670 * 6040 2520 4891 * 5274 5581 2199 5258 5192 5002 * 2668 3657 3867 3879 6037 * * 50
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+
+I 51 5090 * * * 3409 6053 * 1810 4644 2773 5972 * * * 5214 6228 4802 2006 * 4353 51
+ 9 7366 * 0 * * * 7247 1000 0
+
+C 52 6377 53 * * * * * * * * * * * * 5368 * * * * * 52
+ 0 * * * * * * 7247 0 0
+
+A 53 1878 * * * * 4661 * 4430 * 2130 6531 * * * * 3457 4300 2090 * 5257 53
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+
+K 56 4959 * 3015 2968 6970 5329 4507 6655 2592 * * 2959 * 3901 3714 3307 3581 7085 * * 56
+ 37 5307 * 959 1042 * * 7236 1179 0
+
+Q 57 2306 * 3041 3027 6337 4980 * 6605 3750 4483 5918 3870 * 3323 6740 3192 5740 5030 5564 7330 57
+ 10 7164 * 2000 415 0 * 7238 1000 1021
+
+K 58 4828 * 4371 3448 5800 4439 4928 6920 2200 5155 * 4749 2007 5882 4071 4591 3970 7319 * * 58
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+
+W 59 7143 6807 * * 5204 5677 * 6591 5441 4938 5399 7263 6729 4679 5139 6221 5707 6001 482 * 59
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+D 62 4521 * 4122 2851 * * 6689 4989 1732 5342 5724 3328 6994 3681 2797 5232 6773 6711 * * 62
+ 0 * * * * * * 7184 0 0
+
+S 63 3216 6128 * * 5968 5957 4499 2810 4626 1933 6286 5052 * 6270 5441 7116 5624 3186 5270 3126 63
+ 9 * 7279 * * * * 7184 0 0
+
+I 64 * * * * 5271 7143 * 1734 5497 2048 2408 * * 6729 * * 5204 2711 6335 6339 64
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+
+D 65 5005 * 4345 2836 5900 * 5447 * 1808 6132 5113 3716 * 3265 3311 4264 4128 6137 * 7211 65
+ 8 7414 * 2102 382 1178 842 7181 1073 1041
+
+H 66 3699 5383 5584 3863 4603 4792 4531 4495 2146 5169 4640 4257 * 4338 2990 5470 4995 6992 * 4025 66
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+L 67 5085 * * 6955 3622 * * 2751 4521 1263 3751 * 5931 4537 6255 6682 * 3921 5774 4982 67
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+D 68 7077 * 2269 3022 7239 5380 * 5625 2572 3865 5230 3629 4837 3864 4681 3556 5148 * * 6519 68
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+
+K 69 4088 * 5029 3099 * * 4656 6679 2012 4463 5155 3538 5056 4450 3734 3696 3897 4901 6906 * 69
+ 24 5937 * 2000 415 * * 7064 1034 0
+
+Q 70 4392 4927 6739 4323 * 5734 * 6793 1861 4761 6019 4841 5749 4075 2017 3114 5095 * * * 70
+ 44 5046 * 0 * * * 6983 1062 0
+
+T 71 3125 6249 4857 * 5966 5696 6186 5964 2439 4216 4213 3193 3464 4825 4277 3208 3547 * * * 71
+ 0 * * * * * * 6458 0 0
+
+Q 72 3075 * 5413 4368 5129 * 4289 * 2688 * 4556 5086 * 1906 3889 4620 3807 5198 * 5112 72
+ 59 4642 * 1000 1000 * * 5914 1000 0
+
+T 73 4785 * * 3580 * * * 4887 1346 * * * 3645 3472 3608 4494 2675 * * * 73
+ 0 * * * * * * 5394 0 0
+
+P 74 2878 * * * * 2560 * * 3592 3839 * 4031 2008 2632 3826 * * * * * 74
+ 0 * * * * * * 4196 0 0
+
+K 75 * * * * * * * * 1219 * 2522 * * 2884 * 1938 * * * * 75
+ 0 * * * * * * 2968 0 0
+
+T 76 2615 * * * * * * * * * * * 1038 * * * 1515 * * * 76
+ 0 * * 0 * * * 2838 0 0
+
+//
+�HHsearch 1.5
+NAME 3b63735b431780c58c19dd032083016e
+FAM
+FILE 3b63735b431780c58c19dd032083016e
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:32:41 2013
+LENG 185 match states, 185 columns in multiple alignment
+FILT 122 out of 1583 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEECCCCEEEEEEEECCCCCEEEECHHHCCCCCEEEEECCCCEEEEEEECCCCCCCCEEEEEECCCCCCCCCEEEEECCCCCCCCCCCCEEEEE
+EECCCCCCCEEEEEEEEEECCCCCEECCEEECCCCCCCCCCCCEEEECCEEEEEEEECCCCCCCCCCEEEEEHHHHHHHCCEEEC
+>ss_conf PSIPRED confidence values
+9487789949987888999982987899989678579868999758963888996567898888999988877468553354436876778999999999
+8069987647999887870555715405365021258998578499999999999734788877787899998998976591989
+>Consensus
+xxxGxxixxxxxxctxGxxvxxxxxxxiLTaxHcxxxxxxvxxxxxxxxxigxxxxxxxxxxDiAllxlxxxxxxxxxixxxxxxxxxxxxxxgxxvxxx
+GxxxgxxxgxixxxxxxxxxxxxxxxxxxxxxxxxxxxGDSGgPvxxxxxxvGixsxgxxxxxxxxxxxxxxixxxxxxlxxxxx
+>3b63735b431780c58c19dd032083016e
+ISGGDAIYSSTGRCSLGFNVRSGSTYYFLTAGHCTDGATTWWANSARTTVLGTTSGSSFPNNDYGIVRYTNTTIPKDGTVGGQDITSAANATVGMAVTRR
+GSTTGTHSGSVTALNATVNYGGGDVVYGMIRTNVCAEPGDSGGPLYSGTRAIGLTSGGSGNCSSGGTTFFQPVTEALVAYGVSVY
+>gi|183981692|ref|YP_001849983.1| hypothetical protein MMAR_1678 [Mycobacterium marinum M]gi|183175018|gb|ACC40128.1| conserved hypothetical membrane protein [Mycobacterium marinum M]
+--PGLEIHQGSVVCVIGFV--EPQMRIAFSAGRCNGDP-MVT--DRYGNAVGAVTLAGqatvsevavdgaAAGVDYEVITLAPEVAA-TDLLPTGLRLQs
+kpGFRVQPGARVCE-ATAARQSCGRVDTVT------E-----SRFVIAgMDADQHEIGAPVYVlddDnHaLIAGLLDGVRGST-----------------
+------
+>gi|163757015|ref|ZP_02164121.1| hypothetical protein KAOT1_09946 [Kordia algicida OT-1]gi|161323019|gb|EDP94362.1| hypothetical protein KAOT1_09946 [Kordia algicida OT-1]
+--SGQEISMtnaSQAKGTIGAIVELEnhKGDFILSNWHVMMQSSGdLGAGIdNKsDEKIAELfWGLNNEYYDIALSKIISKKQIIKER-KIDTVKKYKDI
+RIGDSVKIEGFKSGFDKNTIYSKNAYVKVGNEERIfKNQIMTGKLSVSGDSGSIVLNKKnEIIGIVCAGDNkKF-----SICNHLHSLLSS------
+>gi|313224875|emb|CBY20667.1| unnamed protein product [Oikopleura dioica]
+-------------------------------------------------------------QYSCMLHFKEDILWsgtdDSYTN-TPCM-PQEPIVah-D
+QECWIAgwGSTAV-igiPSDELRSRGVRLrNDTDcQDQFl--YKNSGACiEGeypvsgeiyheapscGNDIGGPVICpiDGkaVLAGVMGPGG--CGIyG
+RKSLYLDVFTQM--------
+>gi|281357362|ref|ZP_06243851.1| peptidase S1 and S6 chymotrypsin/Hap [Victivallis vadensis ATCC BAA-548]gi|281316393|gb|EFB00418.1| peptidase S1 and S6 chymotrypsin/Hap [Victivallis vadensis ATCC BAA-548]
+------------GSGTGFVIDGNR---IITNAHVVAYPTFITVRKP-GDQTRYPAKVVAVNHecDLAILTVEDPKFFDG--IKPLELA--DLPPMQSSVA
+AVGYPVGgdnvsITVGVLSRVEPL-EYShSGKEL-LGAQIDAAINPGNSGGPVLHEGKVVGIAFQGLgesQNI-----GYMIPC------------
+>gi|156378061|ref|XP_001630963.1| predicted protein [Nematostella vectensis]gi|156217994|gb|EDO38900.1| predicted protein [Nematostella vectensis]
+------------------------PLWLLTAAHCvirSNNSADYTVIVGAHKrvldgTehkLStFYKHEKYvggkdKKHDLALIKLAKPATFSTKVSPVc
+LPKQGDLMKE-RE-NCFAtgwGRVSSSLlhsrAKKLQQGKAPIvDHQTcirkISQWkDGIDQQsMVCAGgagnsvcHGDSGGPLVCeesgHWVLRGAASW
+vSSMTCPGKKYAIYVRVSS----------
+>gi|158299042|ref|XP_001238092.2| AGAP010015-PA [Anopheles gambiae str. PEST]gi|157014178|gb|EAU76076.2| AGAP010015-PA [Anopheles gambiae str. PEST]
+----------QFLCS-GNIITPS---HVLSLEYCFEiFVFQMSIYGGgtsplsggisiPVNKITIHPNf-EYrygrSDFDVAVISVPINTFQgMANMASI
+ALQ--TSEVLPGSRcyVIGWGVSKifgpidlnGLHYGTMNIVSQSAcsrSWAsvNENVTSNMICAKYcfgvDICYGDLGGPLVCDGKLTGIIGYTEYGCT
+KNNPAVFTRIMApsIR--------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+I 1 * * * * * * * 0 * * * * * * * * * * * * 1
+ 0 * * * * * * 2177 0 0
+
+S 2 2674 * * * * * * 2633 2487 * * * * * 3357 2599 * 3617 * 2648 2
+ 0 * * * * * * 4916 0 0
+
+G 3 2714 * * * * 658 * * * * * * 2707 * * 4039 * * * * 3
+ 0 * * * * * * 6060 0 0
+
+G 4 * * * * * 0 * * * * * * * * * * * * * * 4
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+
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+ 0 * * * * * * 6498 0 0
+
+A 6 1999 * * 2500 * * * * 1910 * * * * 4618 3586 3484 4475 4360 * * 6
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+
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+
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+
+S 9 * * 4636 4529 * 2943 4441 3014 * 3504 3485 4703 * 3470 4579 3552 4682 3333 * 4467 9
+ 915 1090 * 1165 852 * * 6498 2894 0
+
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+ 52 4834 * 0 * * * 6928 1000 0
+
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+ 104 3848 * 1908 447 * * 7943 1410 0
+
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+ 129 3991 5449 1391 692 * * 8385 1378 0
+
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+ 0 * * * * 0 * 8688 0 1085
+
+C 14 3598 1003 * 6081 * 1596 * * * * * * * * 5364 5864 * 6021 * 5972 14
+ 0 * * * * * * 8759 0 0
+
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+ 205 * 2919 * * * * 8844 0 0
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+
+F 18 2396 4103 * * 1525 * 6469 6115 * 4059 6498 5121 4856 * * 5335 4645 3523 5359 3875 18
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+L 29 5331 * * * 4601 6539 * 3420 * 765 5998 * * * * * 4496 2609 * 5825 29
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+A 31 800 5627 * * * * * 6624 * 6331 * 2751 * * * 3084 3517 5114 * * 31
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+G 32 1523 6792 * 5489 6591 2016 6601 * 3700 * 5451 3731 * * 4131 4318 * * 5651 4305 32
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+H 33 6492 * 6591 * * * 226 * * 6791 * * * 4192 6442 6574 6211 6373 * 6331 33
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+C 34 5687 807 * * 6666 * * 4577 * 5456 * * * * * * 6211 1753 6507 6249 34
+ 29 5654 * 2641 252 * * 9706 1173 0
+
+T 35 3117 * 5009 6464 3498 2924 6771 3818 6495 2810 5320 6428 6230 * 6604 6610 4966 2139 6623 4363 35
+ 17 6457 * 0 * 0 * 9671 1000 1028
+
+D 36 2975 6591 4101 3227 5620 2904 5154 6246 3538 5576 4347 3800 5882 4242 5721 3928 3994 5073 * 5196 36
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+G 37 3605 * 2579 5265 6292 2430 6877 6803 4183 5078 5838 3658 3660 3439 5646 4279 4905 4616 * 6602 37
+ 86 4376 6698 1074 930 1885 455 9655 1697 1329
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+A 38 2677 5779 3735 4165 4903 2464 5292 6703 4815 4611 5852 4362 4388 6451 6332 3537 5054 3727 6367 5218 38
+ 82 4995 5400 1770 501 1148 866 9647 1285 1338
+
+T 39 3820 * 2968 4295 6284 3169 6585 4411 3680 5319 6450 3265 5659 4038 4726 3526 3285 5526 * 5582 39
+ 165 3507 5657 1672 543 294 2438 9633 2176 1551
+
+T 40 3612 6586 4127 3781 4924 4957 5596 4555 3671 * 4966 3605 4849 3951 4486 3554 2585 5172 * 4910 40
+ 388 2085 * 2466 288 747 1307 9675 4166 1334
+
+W 41 3623 6571 6848 5388 5259 * 5729 3096 5730 3086 6325 * * 5421 4359 5663 4443 1568 4438 4523 41
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+W 42 5133 6464 4566 4495 5132 3742 4214 4247 4400 5359 * 7030 4984 3894 4025 4036 3418 3223 5188 2889 42
+ 144 4042 4874 1960 429 * 0 9682 1782 1069
+
+A 43 3579 6873 5045 4944 5036 3697 * 3110 5492 3399 6638 * 3796 5381 6096 4141 3769 2219 * 4677 43
+ 182 3578 4836 582 1591 1090 916 9613 2110 1665
+
+N 44 6523 * 4976 3538 * 2308 4534 5555 4041 5284 * 3249 4701 4071 3853 3415 4905 3576 * 4831 44
+ 190 4802 3513 1329 732 423 1976 9644 1421 2094
+
+S 45 4422 * 3055 4370 5587 3289 5578 5384 5600 2267 6412 4927 5098 4635 4046 3717 3592 4485 * 6630 45
+ 388 2420 4345 1935 437 1377 701 9594 3357 2673
+
+A 46 3737 * 4394 5476 5123 1579 3928 6080 5654 6105 * 4323 6450 6911 3713 3467 4763 5655 * 3579 46
+ 558 1870 4406 2155 367 1065 938 9553 4213 2696
+
+R 47 3488 6495 3043 3384 6801 3360 5836 5462 3140 5391 6156 4149 4375 4126 4132 4420 3513 5715 * 6312 47
+ 420 2099 5710 1867 462 552 1654 9533 3840 2606
+
+T 48 3792 * 3417 4248 4848 2527 6431 * 4274 4845 * 3646 6036 5613 4137 2825 5762 3929 6238 3956 48
+ 187 3037 * 1627 564 812 1217 9615 2612 1849
+
+T 49 4420 * 5455 4174 * 3973 4514 4499 4383 4442 6558 3217 5634 4439 4223 3578 2483 3212 * 5577 49
+ 100 3894 * 1947 433 2019 409 9665 1845 1413
+
+V 50 3569 6566 3478 4478 6216 4468 5584 * 3526 4230 * 4394 2438 4637 3369 3720 5799 3682 * 6636 50
+ 79 4238 * 1521 618 1705 529 9673 1706 1272
+
+L 51 * * 6726 6468 4200 6862 5559 1949 4398 3049 5055 * 4896 5845 4978 6714 4507 2006 * 4249 51
+ 16 * 6519 * * 543 1673 9685 0 1271
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+G 52 3368 * 6656 4386 6897 1119 6447 6217 3177 6223 * 5767 5050 6481 6718 4250 4834 4276 * 5697 52
+ 89 4679 5593 1626 565 0 * 9658 1460 1238
+
+T 53 3467 6317 4652 3147 3904 6833 6808 4299 3534 6906 6528 4306 4651 5151 4056 4169 2912 3428 5541 5500 53
+ 89 4628 5679 551 1656 803 1228 9661 1427 1245
+
+T 54 5156 6617 * 4597 3705 6874 3725 3204 4267 3189 5057 5715 6134 5540 4339 4960 3978 1945 * * 54
+ 159 3358 7164 1543 606 * 0 9633 2168 1350
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+S 55 2920 * 5436 4019 6170 4581 4731 4688 3804 5079 6880 4977 5457 4203 3923 3244 3410 2897 6399 5583 55
+ 119 4561 4770 987 1013 0 * 9637 1460 1455
+
+G 56 4033 * 4481 3959 4939 3639 2830 3073 5399 4024 * 4885 5436 6560 3363 6652 5716 3497 4733 4253 56
+ 249 3609 3713 2718 238 1031 970 9667 2143 1501
+
+S 57 3689 6467 * 3736 4963 4983 4813 4885 4959 5323 * 5629 2876 3539 4148 2362 4878 3648 * 4688 57
+ 203 4522 3512 1856 466 169 3177 9529 1497 2457
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+S 58 4730 6403 3861 4053 5642 3012 6536 4635 3451 4480 * 3421 5656 4058 3502 2862 3873 5456 * * 58
+ 85 4429 6528 3084 181 181 3081 9590 1725 2362
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+F 59 3651 5567 3325 4940 2955 5694 3967 3972 6770 4748 5703 4163 * 6689 5717 5292 3602 6928 5281 2328 59
+ 308 2381 * 1798 489 975 1026 9687 3489 1222
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+P 60 4175 6727 3748 3904 6924 3164 4816 * 5356 4452 5517 3780 2211 5768 4874 3152 4360 5471 * 5521 60
+ 190 3106 7083 2437 295 0 * 9722 2424 1023
+
+N 61 3362 * 2592 3526 5708 2915 5778 5238 4228 4236 * 3600 5574 5464 6727 3871 3817 4719 * 4862 61
+ 96 4146 6971 2047 400 0 * 9752 1863 1000
+
+N 62 3843 6263 3565 * 4876 4983 3531 6845 5627 4417 * 1763 4781 5124 4117 4606 4641 4916 6430 4019 62
+ 460 1873 * 957 1044 0 * 9886 5326 1021
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+D 63 * * 188 5690 * 5437 6480 * * * * 4138 * * * * * * * 6408 63
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+Y 64 3066 6044 6968 * 4112 6935 6853 1660 * 2503 5065 * * * * 5559 * 2793 4710 4146 64
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+G 65 595 5731 5365 4593 * 3600 * * 7081 6893 3972 * 6480 5871 * 5382 7280 4936 * * 65
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+I 66 5425 * * * 4031 * * 2529 * 1154 5140 * * 6220 6442 * 7270 2404 4505 * 66
+ 0 * * * * * * 9887 0 0
+
+V 67 4433 6515 * * 4753 6972 6835 1791 * 1469 5836 * * * * 5393 * 2659 6126 5341 67
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+R 68 5859 * 4934 2291 6685 6899 6408 6978 2169 4186 * 6977 5738 4202 2475 3976 4700 5615 * 4405 68
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+
+Y 69 5099 * * 6835 3989 5718 * 3210 7013 1475 6030 * 3705 * * 5246 3890 2555 7213 4573 69
+ 17 6414 * 0 * * * 9887 1061 0
+
+T 70 3903 5765 2961 3130 6729 4912 * 4900 3667 7145 6515 3576 4046 4651 5034 2857 3663 4148 * 6480 70
+ 39 5220 * 2677 245 * * 9887 1355 0
+
+N 71 4736 * 3031 3353 * 4505 5926 6071 4033 5095 * 3244 3282 4741 3757 3028 3351 5297 * 6536 71
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+
+T 72 3197 * 4069 3363 * 3224 7007 5973 3497 5561 6703 4054 2519 5461 5839 3276 4116 4717 * 6590 72
+ 43 6703 5667 1412 680 1767 502 9858 1204 1393
+
+T 73 2959 * 4147 5596 4300 4501 * 3783 5198 3620 6693 3817 6131 5289 4119 4432 4779 2430 4910 4692 73
+ 56 5547 5918 1057 945 870 1143 9814 1419 1817
+
+I 74 4446 * 3949 3538 3993 5840 6046 4450 3854 4111 * 3901 3791 4868 5328 3882 2700 3120 * * 74
+ 142 3681 5984 2266 336 553 1652 9837 2348 1608
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+P 75 3878 5997 5378 * 2748 4269 7148 3669 5413 3345 5317 7043 4162 4911 5793 4113 4467 2939 4226 4123 75
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+
+K 76 4451 * 3727 4449 6822 4462 6762 5768 4879 6939 6916 2208 4288 7089 5171 1999 3286 7059 * 4721 76
+ 132 4550 4480 1432 668 1196 828 9773 1683 2161
+
+D 77 3885 * 2868 4244 5990 4426 5922 5838 4505 4932 6744 3450 2408 5649 6866 2887 3933 5126 * 5478 77
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+G 78 3884 * 4047 4185 4557 4140 4354 * 4090 4820 5660 2759 5343 4372 3421 4080 3881 5735 * 3396 78
+ 127 5742 3932 720 1348 1312 744 9747 1311 2934
+
+T 79 5434 * 6736 6937 4796 6632 * 1981 5667 3486 4663 6807 4722 4895 5286 4677 3350 2081 6675 5493 79
+ 173 4865 3663 1800 489 2186 358 9721 1568 3227
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+V 80 3152 * 5169 5802 6202 4080 5567 4228 3067 3074 * 3702 4954 4756 3898 4831 5810 3489 6394 3484 80
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+G 81 3634 * 6539 4719 3770 4174 6413 4975 4430 4978 * 5408 2486 6142 4776 3057 3083 4473 5273 4092 81
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+
+G 82 4308 * 5997 5275 4393 4929 * 2158 6562 2749 6248 5400 3200 6433 5243 5661 3104 3366 * 5192 82
+ 141 3566 6889 1235 798 2750 232 9770 2291 3555
+
+Q 83 3177 4190 4369 4651 6984 2741 6854 3712 4733 3429 5219 5255 3843 6085 4821 4290 4479 3381 * 6828 83
+ 54 * 4761 * * 2000 415 9769 0 3474
+
+D 84 4159 4784 3538 3829 5632 4834 * 5154 3905 2181 5521 4489 3574 4491 6397 4269 3629 4907 * 6957 84
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+I 85 4685 * 6457 6978 4865 * * 2901 * 2466 5117 5476 2147 5327 4723 6024 5560 2354 * 5604 85
+ 315 4480 2723 1114 894 1171 847 9821 1535 2384
+
+T 86 3378 6721 4077 5167 5313 3911 * 6995 3844 3277 * 4762 3844 4151 3943 2814 3336 4532 * 5468 86
+ 211 4346 3523 1317 741 1023 977 9658 1634 3955
+
+S 87 3009 6816 3579 6901 4941 1797 * 5851 4593 3926 * 4003 5051 5158 * 2902 4560 6821 6441 6279 87
+ 118 4261 5250 1871 461 654 1456 9641 1985 3545
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+A 88 4216 * 3637 4033 5237 4161 5999 4362 4499 4165 5332 5012 3856 4882 5636 3159 3704 3523 4530 4054 88
+ 88 4293 6964 1665 547 745 1310 9767 1628 2321
+
+A 89 3010 * 4238 3405 4859 3585 6951 6603 4015 5244 5338 4064 7022 5847 4948 3066 3545 3350 6595 4364 89
+ 142 3531 7111 624 1510 599 1556 9798 2601 1610
+
+N 90 2988 * 2834 3595 5464 4618 6017 4743 5086 4067 5784 3739 4096 5486 4461 3627 3821 4123 * 5848 90
+ 42 6145 6076 2479 285 572 1611 9876 1165 1231
+
+A 91 2729 * 5323 6833 5627 * 6649 3476 6425 3204 5300 5173 1740 5753 5631 4750 6520 3082 * 5801 91
+ 64 4812 7043 557 1643 493 1789 9885 1468 1283
+
+T 92 3433 5641 5061 3727 6282 5370 4379 6562 2902 3916 6808 4475 3737 3801 4248 3576 4510 3869 6422 5316 92
+ 41 5143 * 916 1089 879 1132 9877 1513 1119
+
+V 93 4101 * 4256 3723 * 5749 4756 3953 4663 2653 * 4841 2669 6213 6418 4958 3702 2720 6871 6908 93
+ 60 5763 5489 1387 695 737 1321 9854 1181 1159
+
+G 94 4258 * 3748 5160 * 713 * * 4759 * * 3201 * 4431 6192 5725 6577 * * * 94
+ 40 5176 * 2399 303 0 * 9878 1357 1421
+
+M 95 3721 * 3142 2852 * 4452 * 4781 4224 4287 5055 6347 6101 3038 4784 3317 2693 6922 * 7066 95
+ 121 4911 4395 1000 1000 * * 9895 1375 0
+
+A 96 3494 * 4236 4248 * 6785 5255 4862 4281 3728 4601 4611 3267 4102 3002 5210 3155 3915 6067 5680 96
+ 144 3555 6696 1230 802 0 * 9863 2246 1786
+
+V 97 3739 3950 * 6954 4990 5053 * 2984 * 3097 7077 * 6576 7182 7040 * 5182 1083 * 6001 97
+ 97 4176 6661 882 1129 1041 960 9862 1817 1146
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+T 98 3508 2129 * 5671 4919 5709 5770 3719 4798 3842 7012 6643 * 4706 3683 3899 3987 4140 5227 3960 98
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+
+R 99 3779 * * 6828 3865 2662 6880 3761 2456 4706 5255 7149 6609 4453 4821 5503 3448 3007 5740 7042 99
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+G 101 4899 * 6491 7073 * 194 * 6815 * * * 6904 * 6314 6650 7133 5899 6610 * * 101
+ 193 3238 5709 1825 479 606 1544 9883 2752 1323
+
+S 102 2791 6707 4594 4293 4428 7087 5762 5345 5230 5470 6961 4319 * 4987 2341 3331 4960 4316 4615 3352 102
+ 99 4367 5814 1694 533 * 0 9859 1727 1371
+
+T 103 3951 * 5003 * 5231 4253 5693 4077 4792 5404 5129 4885 3443 4999 3500 3092 2048 4518 * 6642 103
+ 91 4425 6116 1793 491 652 1459 9808 1704 1829
+
+T 104 4555 6712 4792 4418 * 3397 5962 * 5784 5375 * 3947 5417 4621 3956 1780 2524 5161 * 5294 104
+ 216 3203 5025 2111 380 1174 845 9843 2737 1494
+
+G 105 4885 * 3706 3610 6671 1225 * * 4276 6363 * 4186 4523 5956 4436 5040 4803 4019 5839 * 105
+ 474 2250 3844 1802 487 506 1758 9839 4124 1792
+
+T 106 4723 * 6535 3985 3767 4386 4375 4194 5356 2672 * 4552 4288 4394 3515 5681 4873 3354 5837 3555 106
+ 121 3791 6944 1065 938 679 1413 9702 2337 2517
+
+H 107 5439 * 5121 4884 5288 5348 4003 4822 4754 3479 6800 4380 5682 3636 3917 2854 2256 3861 * * 107
+ 104 4031 6956 813 1215 907 1099 9829 2009 1661
+
+S 108 4113 2235 5309 3883 6226 6520 7128 5737 5855 4857 6878 4104 3143 4745 4985 2655 3751 6599 * 4549 108
+ 83 4881 5504 770 1274 750 1303 9848 1371 1385
+
+G 109 4425 7034 3944 5555 5936 946 5718 * 5226 4941 7124 6639 * 5286 6504 3385 5398 4205 * 5776 109
+ 122 3626 * 1306 747 267 2567 9813 2197 1616
+
+S 110 4492 5719 4686 3980 6117 5526 5939 3559 3420 7022 * 4489 5457 4535 3127 3534 2759 3797 7020 4123 110
+ 51 4856 * 566 1625 * 0 9890 1500 1000
+
+V 111 7152 * * * 5152 5521 * 1907 5732 1897 5395 6676 5243 6873 6734 * 5665 1950 * 4943 111
+ 44 5481 6980 0 * * 0 9890 1292 1000
+
+T 112 4089 5401 5737 5430 7005 4328 7053 4224 3207 3613 7039 4991 * 3041 3420 3412 3061 3794 7139 5643 112
+ 28 5719 * 1056 946 * 0 9881 1224 1172
+
+A 113 3452 7053 4268 3797 7159 3574 4669 5310 3719 5564 4974 4346 7059 4973 4385 2443 3442 4539 6448 5255 113
+ 36 5749 7335 0 * * 0 9881 1141 1172
+
+L 114 3128 6274 * 6835 * 7039 7052 2767 4443 2859 4243 6161 5419 5933 4527 4963 2906 2523 6624 5748 114
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+
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+G 122 5783 5774 2961 2792 5187 3604 4632 * 3913 5936 6405 3313 4758 3517 6645 3220 3964 4649 * * 122
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+M 129 5506 * 6939 3996 3452 5796 5601 3119 5287 3055 4465 5486 5068 2608 5660 4375 4642 3373 7220 4522 129
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+I 130 4777 * 4871 * 4089 4813 6535 2281 4296 2466 4856 6561 * * 6939 4463 3324 3146 7085 3884 130
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+ 37 5289 * 652 1460 0 * 9406 1189 2792
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+A 176 3239 * 5978 * 3445 * 4934 2626 * 3302 5637 6283 6439 5604 6108 4757 4643 2389 * 2807 176
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+A 179 2267 * 2778 3004 * * 4752 * 4047 3899 4901 5630 * 4157 4548 3292 5586 4618 4604 * 179
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+Y 180 5694 * * * 2706 5692 * 4636 * 970 3986 * * 5318 5617 * * 5754 3435 4719 180
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+ 0 * * 0 * * * 4701 0 0
+
+//
+�HHsearch 1.5
+NAME 3dddac6f1a46a0d944548b4f8648c5d1
+FAM
+FILE 3dddac6f1a46a0d944548b4f8648c5d1
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:39:16 2013
+LENG 107 match states, 107 columns in multiple alignment
+FILT 107 out of 267 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCHHHHCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCC
+CCCCCCC
+>ss_conf PSIPRED confidence values
+9989887655578779845785886568353345878887774533255456565566766101999975541467603657767765321347898756
+6888869
+>Consensus
+xxxxpxxxxxxxxxxxxVxFxHxxHxxxxCxxCHHxxxxxxxxxxCxxxxCHxxxxxxxxxxxxxxxAxHxkxxxxxxCxgCHxxxxxxxxxxxxgpxxC
+xxxxCHx
+>3dddac6f1a46a0d944548b4f8648c5d1
+APKAPADGLKMEATKQPVVLNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGC
+KKSKCHE
+>gi|258404546|ref|YP_003197288.1| cytochrome c class III [Desulfohalobium retbaense DSM 5692]gi|257796773|gb|ACV67710.1| cytochrome c class III [Desulfohalobium retbaense DSM 5692]
+AQMPPSNityeAPEIMPRLGPSHFSHDSHYAHDCMTCHHMWDGFSEIKSCSAEGCHDQRGT--MkmEGSTIYYAFHKKSSQAS-CLGCHMQL--KKAGEP
+TGPIGC--TTCHE
+>gi|224371554|ref|YP_002605718.1| TmcA2 [Desulfobacterium autotrophicum HRM2]gi|223694271|gb|ACN17554.1| TmcA2 [Desulfobacterium autotrophicum HRM2]
+------------RQRSAVFFPHGLHMDnLECLDCHHVY-EGGkNlqdedelyednpDIRCQ--DCHNTDAS-----IDTTKAFHH-----Q-CMGCHIKS
+--TKEQaKIKTPEMC--GDCHT
+>gi|95929129|ref|ZP_01311874.1| conserved hypothetical protein [Desulfuromonas acetoxidans DSM 684]gi|95135030|gb|EAT16684.1| conserved hypothetical protein [Desulfuromonas acetoxidans DSM 684]
+----KGKSLTFAgSSMGAVTFDGTLHNNAaeKgCRDCHNP-----DVF-----------PKM-KQgtvK----ITMAQIYAGKQ-CGICHDG---GR---
+AFAAKgHC--AKCHK
+>gi|224371107|ref|YP_002605271.1| hypothetical protein HRM2_40490 [Desulfobacterium autotrophicum HRM2]gi|223693824|gb|ACN17107.1| conserved hypothetical protein [Desulfobacterium autotrophicum HRM2]
+-------------KKGIVQFTHQKHVadyKIGCGECHHGDDGSpladmkagDDAVGCA--ECHAEPGTApkskDKKLSdSEKLEYHAEALHEN-CITCHK
+AYNKEN-NTKDAPASC--AKCHP
+>gi|220918631|ref|YP_002493935.1| hypothetical protein A2cp1_3539 [Anaeromyxobacter dehalogenans 2CP-1]gi|219956485|gb|ACL66869.1| conserved hypothetical protein [Anaeromyxobacter dehalogenans 2CP-1]
+------------AEQPAVEFTHEAHimAEVACLDCHSGIDKATRLepkrhvsVSCS--DCHDDARGQVKvperVKqvrFTFSHQDHLAKV-KD-CKTCHQ
+ALPEpGDKEIKaPPMAAC--TSCHN
+>gi|320449434|ref|YP_004201530.1| chaperone protein HtpG [Thermus scotoductus SA-01]gi|320149603|gb|ADW20981.1| chaperone protein HtpG [Thermus scotoductus SA-01]
+-------------VEQPVPFSHAFHAGglgLSCRYCHSSVERAayaglPPTEACM--TCHTFIKPDSpnlalvrrswetgeplrwnrvinlPDFVYFNHG
+AHV-AKGVG-CAECHGRVDqmaVVRQPQAFTMKFC--LDCH-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 428 * 3374 * * 2644 * * * * * * * * * * * * * * 1
+ 148 3356 * 2585 263 * * 3302 1025 0
+
+P 2 4052 * * * * * * * * * 2873 * 2070 1760 * * * 2279 * 3975 2
+ 85 * 4127 * * * * 3833 0 0
+
+K 3 3257 * 3056 1648 * * * * 2511 * 3983 4338 * * * * 3322 3882 * * 3
+ 0 * * * * * 0 4013 0 1009
+
+A 4 1050 * * * * * * 4071 * * * 4080 4139 3243 * * * 2083 * * 4
+ 0 * * * * * 0 4191 0 1009
+
+P 5 4904 * 3740 * * 4044 * 3448 3794 * * * 583 * * * * * * * 5
+ 0 * * 1585 585 0 * 4660 1009 1009
+
+A 6 2605 4673 2678 3844 * 2680 4798 5497 3860 * * 4224 4862 3230 * 3716 5871 * * * 6
+ 0 * * * * * * 4967 0 0
+
+D 7 3401 * 1681 3776 * 4449 * * 1831 4798 * 3950 * * 4918 4941 5189 * * * 7
+ 443 2112 4918 2138 372 * * 4967 1486 0
+
+G 8 4043 * 4878 5231 * 3198 * * 3304 * * 5206 1523 * 4820 4395 3551 2999 * * 8
+ 0 * * * * 0 * 5513 0 1009
+
+L 9 3176 * 5274 4063 * * * 2656 5908 2347 4242 3619 3823 * 5683 5823 5267 3557 5308 4220 9
+ 0 * * * * * * 5602 0 0
+
+K 10 5335 * 4598 1460 * 3674 * 6102 3487 5277 * * 3082 * 5547 5726 2691 4345 * * 10
+ 161 3527 5726 1198 826 * * 5623 1213 0
+
+M 11 4527 * 5845 4373 2593 * * 2851 4085 2690 2317 5537 5705 * * * 5620 4466 5955 4333 11
+ 113 5086 4436 440 1928 814 1213 5240 1116 1066
+
+E 12 3800 * 3295 2219 * 3648 4917 * 2186 * 5002 3284 3910 6027 * 5945 4413 * * * 12
+ 320 2329 * 1519 619 * 0 5179 1706 1149
+
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+ 61 * 4584 * * 446 1910 6151 0 1149
+
+T 14 4517 * * 4008 * 5123 * * 2017 3443 6583 6302 4139 4183 4241 3573 2449 5147 4890 6711 14
+ 99 4372 5797 979 1021 698 1383 6323 1231 1216
+
+K 15 5584 * 4937 5050 4378 3817 5820 4698 2442 3923 2744 4859 5707 3948 3573 5172 7045 5483 * 3613 15
+ 0 * * 2000 415 840 1181 6463 1042 1232
+
+Q 16 3296 * 5087 5146 * 1540 * * 3218 5033 4849 6509 2786 3717 * 4736 4583 * * 6303 16
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+
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+
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+
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+
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+ 0 * * * * * * 6530 0 0
+
+N 21 6045 * 1911 6017 * 5151 7014 * * * 6760 2507 2615 * * 2305 3098 * * * 21
+ 21 6127 * 1585 585 * * 6530 1014 0
+
+H 22 * * * * 5746 4753 83 * * * * * * * * * * * * * 22
+ 10 * 7144 * * * * 6530 0 0
+
+S 23 2806 * 2949 4196 5795 4147 * 6263 2219 4471 * 6895 * 3397 4948 3253 5258 5940 * 4553 23
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+
+T 24 2222 * 3845 4349 5970 6407 7392 5060 2539 3283 5421 7050 6638 4884 4466 3703 3637 4282 * * 24
+ 0 * * * * * 0 6531 0 1000
+
+H 25 * * * * * * 0 * * * * * * * * * * * * * 25
+ 148 3555 6310 1173 846 * 0 6531 1524 1000
+
+K 26 1833 * 5736 2814 5094 4442 7431 5282 4069 5841 4203 4440 * 3590 4470 4280 4394 4881 * 6261 26
+ 120 3652 * 1322 737 2048 399 6526 1577 1093
+
+S 27 2867 * 3196 2707 * 2633 * 6166 3153 * 7624 4027 6437 4207 5009 3504 4015 * * * 27
+ 478 1825 * 1703 529 0 * 6528 2712 1055
+
+V 28 3446 * * 5370 4337 6574 6304 2980 3461 3282 4678 6040 * * 6534 6841 4462 2043 * 2952 28
+ 769 1275 * 947 1055 * * 6530 3530 0
+
+K 29 3420 * 1562 2595 * 6493 * * 3747 6486 * 4299 6606 6935 5099 2873 3823 * * * 29
+ 29 5650 * 0 * 667 1434 6520 1125 1054
+
+C 30 * 0 * * * * * * * * * * * * * * * * * * 30
+ 0 * * * * * 0 6531 0 1000
+
+G 31 3526 * 4807 4411 5179 3163 * 6718 3634 3786 4913 4435 * 4123 3270 3510 3067 3624 * * 31
+ 0 * * 2000 415 0 * 6531 1000 1000
+
+D 32 3936 * 2197 3665 6476 5981 * 6460 4391 4255 6411 7394 * 3967 7766 3445 2146 3652 * 5988 32
+ 0 * * * * * * 6530 0 0
+
+C 33 * 0 * * * * * * * * * * * * * * * * * * 33
+ 10 * 7144 * * * * 6530 0 0
+
+H 34 * * * * * * 0 * * * * * * * * * * * * * 34
+ 34 * 5438 0 * 0 * 6531 1000 1000
+
+H 35 4230 * 4917 5228 * 6821 392 * 5365 * * 5658 * * * 4672 4925 * * * 35
+ 58 4661 * 1111 897 1484 638 6498 1183 1139
+
+P 36 4723 * 3089 3734 6088 2826 4249 5715 3010 5185 3750 4966 5091 5486 5675 4774 3202 4095 * 6744 36
+ 309 5144 2605 939 1064 0 * 6516 1180 1066
+
+V 37 3804 * 4357 3922 4442 3218 * 4680 3594 4423 6133 4579 5879 6758 4972 4863 3709 3645 4014 3002 37
+ 54 6941 5118 4524 64 3835 105 6388 1000 2175
+
+N 38 4467 * 1624 2580 * 5159 * 6651 3770 6075 * 5224 2896 6163 * 5299 3364 6098 * 5330 38
+ 160 3251 * 1580 588 3583 126 6040 1574 2248
+
+G 39 3924 * 3143 2412 * 1914 * 4000 4919 5056 5464 6176 3655 5528 5498 4580 5957 5349 * * 39
+ 252 3991 3356 3278 157 * 0 6061 1279 2146
+
+K 40 3564 6094 3288 2830 6019 2440 * * 2195 5689 * 6218 4575 6094 5069 4134 4328 * * 6190 40
+ 595 1965 3608 2412 300 1951 432 6196 2160 2686
+
+E 41 3933 * 3340 2933 * 2065 * * 5194 * 5439 4796 3093 4650 7542 3309 3652 6803 6014 6358 41
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+
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+
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+
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+
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+
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+
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+
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+
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+ 124 * 3601 0 * 430 1956 4381 1042 5004
+
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+
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+
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+
+K 58 2571 * 3092 3291 * 6221 5698 5736 1993 * 4047 5649 4906 4710 3602 6323 3992 * * * 58
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+
+D 59 5176 * 2059 3071 6062 4668 6030 4906 2839 * 5976 4421 3959 6254 3118 5363 3826 5592 * * 59
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+
+A 62 3585 6604 4288 2529 3754 5450 * 3863 3427 3577 * 5038 3651 5553 4172 6962 3939 4764 * 4556 62
+ 152 5969 3575 3866 102 2333 319 6310 1095 2190
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+K 63 5066 * 4026 4379 4499 6269 5054 3546 3773 3241 4322 4563 2934 * 5335 3189 4200 3367 * * 63
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+
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+
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+
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+ 0 * * * * * 0 6387 0 1574
+
+V 68 697 * 5738 4335 6127 5834 * * 5669 5554 * * * 5164 * 4960 3749 3218 * * 68
+ 56 4725 * 2322 322 2128 375 6387 1123 1574
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+
+N 73 3113 * 2503 3489 * 4573 * * 2605 * * 2960 5603 3298 5527 4129 4671 6172 * 5063 73
+ 51 4849 * 2316 323 3772 110 5968 1053 3374
+
+T 74 2417 * 5098 6344 * 4152 * * 4362 3954 5896 4118 5407 6384 * 1993 2839 3651 5542 * 74
+ 129 * 3543 * * 3226 163 6000 0 3220
+
+K 75 2921 5173 3005 2848 5408 2572 4791 5610 3531 6274 3801 * 3851 5476 * * 5705 * * 4429 75
+ 73 5477 5224 1729 518 1927 440 5880 1245 3280
+
+F 76 2775 * 6265 3869 4246 5551 2534 4662 2576 * * 4510 4131 4478 3248 6041 6019 4768 * * 76
+ 84 4146 * 668 1432 0 * 6102 1232 2827
+
+K 77 4868 * 6248 5457 * 4541 5381 * 3632 4409 6579 3371 4772 2894 4493 1693 4245 5901 6047 5739 77
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+S 78 * * * * * * 4152 * 3768 2760 * 4224 * * 2715 2293 1677 * * * 78
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+
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+E 85 2977 * 3237 2682 * 3925 * * 1900 5099 * 5361 * 3428 4248 6714 3859 * * * 85
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+
+V 86 4420 * * 2889 6761 5848 6226 4611 3503 2541 2334 4798 * 4798 5922 4629 * 3310 6456 4719 86
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+A 87 2675 * 5158 5241 2963 4698 * * 2901 5815 * 3691 4454 2907 4815 * 5068 2962 * 5600 87
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+
+G 88 3281 * 3823 2566 * 2216 * * 2680 * * 4520 * 5083 4956 4730 * 2802 * * 88
+ 191 3333 5329 1907 447 755 1295 5336 1170 4078
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+A 89 3645 * 3795 2771 * 2878 * * 1533 5834 * * * 4913 4420 * 3536 4787 * * 89
+ 206 * 2913 * * 3165 171 5990 0 2429
+
+D 90 4065 * 2834 3874 5848 6439 6135 * 1922 5152 * 4744 * 4493 2275 5580 4366 * * 4683 90
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+
+A 91 2275 * 5913 2567 * 5887 4671 * 2624 * * * 2134 3508 5783 4916 5459 * * * 91
+ 97 5307 4661 0 * 5380 35 5603 1042 3377
+
+A 92 4417 * 3336 3085 * 1368 5268 * 2945 * * 4347 4768 4554 5150 5723 5839 * * * 92
+ 421 4402 2279 1817 482 * 0 5589 1077 3408
+
+K 93 * * 4557 3196 * 5024 5140 4947 1552 2168 * * 5439 4477 4124 * 4887 * 4865 * 93
+ 196 5140 3338 0 * 1032 969 5285 1000 3883
+
+K 94 2510 * * 5900 * 3348 * 5778 1397 * * 4163 3385 4578 5759 4620 4081 * * * 94
+ 169 3532 5361 486 1805 757 1292 5755 1323 2811
+
+K 95 2843 * 3972 5863 3150 5530 * 5898 2437 5142 5295 3531 3502 * 5636 5091 2819 5366 * * 95
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+
+D 96 2759 * 4280 6560 5949 1141 * 5969 3723 * 6522 5250 3894 6433 * 4389 4517 5544 * * 96
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+
+L 97 5017 * * * 5160 5732 * 5515 * 3120 3402 6149 718 6137 * 5642 * 4857 * * 97
+ 0 * * * * 0 * 6147 0 1009
+
+T 98 3287 * 5890 5373 * * * 4215 2498 3247 * 6681 6867 6763 6544 5217 1888 2517 * 6590 98
+ 126 3584 * 0 * * * 6158 1539 0
+
+G 99 2991 * 4427 4531 5586 1965 4912 * 3364 5657 5653 4613 6054 * 4364 2825 3443 * * * 99
+ 11 7011 * 0 * * * 6158 1000 0
+
+C 100 * 0 * * * * * * * * * * * * * * * * * * 100
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+
+K 101 1714 * * * * * * * 2211 3099 * * * * * 3008 2070 * * * 101
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+
+K 102 * * * * * 2996 * * 1680 * * 1776 * 2916 * * 2854 * * * 102
+ 205 * 2916 * * 0 * 2930 0 5091
+
+S 103 3057 * 6861 5613 6038 2906 6132 * 3144 4827 6532 3051 6412 5426 4551 2693 2590 6689 * * 103
+ 0 * * * * 0 * 6127 0 1042
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+K 104 3789 * 2660 2751 * 2911 * * 2973 7057 * 6704 4331 4066 4463 3095 4400 5358 * * 104
+ 35 5371 * 0 * * * 6158 1093 0
+
+C 105 * 0 * * * * * * * * * * * * * * * * * * 105
+ 0 * * * * * * 6158 0 0
+
+H 106 * * * * * * 0 * * * * * * * * * * * * * 106
+ 0 * * * * * * 6158 0 0
+
+E 107 4384 * 5773 3519 * 6552 6193 6426 1881 * * 4650 2526 3971 5040 4707 2962 3944 * * 107
+ 0 * * 0 * * * 5957 0 0
+
+//
+�HHsearch 1.5
+NAME 3e7b90809bd446a538f9eb1a1ca0e551
+FAM
+FILE 3e7b90809bd446a538f9eb1a1ca0e551
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 11:58:24 2013
+LENG 153 match states, 153 columns in multiple alignment
+FILT 118 out of 1086 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
+HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9699999999999999985388899999999999894377668002466768988609888899999999999999815236999999999888872999
+89999999999999998765369999999999999999999999998758899
+>Consensus
+xltxxexxxixxsWxxvxxxxxxxgxxxfxxlFxxxPxxxxxFxxfxxxxxxxxlxxxxxxxxhxxxvxxxlxxxixxldxxxxxlxxlgxxHxxxxgvx
+xxxfxxxxxxlxxxlxxxlgxxxtxxxxxAWxxxxxxixxxxxxxxxxxxxxx
+>3e7b90809bd446a538f9eb1a1ca0e551
+VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIP
+IKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
+>gi|194015055|ref|ZP_03053672.1| oxidoreductase, FAD-binding domain protein [Bacillus pumilus ATCC 7061]gi|194014081|gb|EDW23646.1| oxidoreductase, FAD-binding domain protein [Bacillus pumilus ATCC 7061]
+MLSKDQMNAIKQSAPLLKAEGTKLVTVFYQNMIRQHPELLNQFN----Q-------TNLMNGSQPEALAVTLYQAALHIDRLEellPVVKQIAHKHVS-V
+MVKKEQYPIVGYHLIEAMKEVFGLTEKDDTLLAWKAAYDIIANIFITieaeMMEVnvkqpGGWAD
+>gi|297697626|ref|XP_002825953.1| PREDICTED: hemoglobin subunit alpha-like [Pongo abelii]
+-----------------------------------------------------------------------------------------GQRDGRDFQWD
+PVKIKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------
+>gi|108797450|ref|YP_637647.1| oxidoreductase FAD-binding region [Mycobacterium sp. MCS]gi|119866535|ref|YP_936487.1| oxidoreductase FAD-binding subunit [Mycobacterium sp. KMS]gi|108767869|gb|ABG06591.1| Oxidoreductase FAD-binding region [Mycobacterium sp. MCS]gi|119692624|gb|ABL89697.1| Oxidoreductase FAD-binding domain protein [Mycobacterium sp. KMS]
+-----ALAVLRDAVDP-RRGSDPLIADFYTRWFAADLSVRDLFPP--DM------------ARQRTAFAEAMTWLFGELiaQraeEPVAFLAQLGRDHR-
+KYGVVQRHYDTMGDALYAALRSGLADQWSDRVAEAAHDAVALATGVMRGA--------
+>gi|198419488|ref|XP_002119301.1| PREDICTED: hypothetical protein [Ciona intestinalis]
+PLTEIEIEGVQESWEKVSSgGPKTTGLILMEKLFNTYPASIAVFSHLGIPSKPdgaitvSDLASIGGVSNHAVSLASRIGKLVGLLNNeteLKESSTEVG
+RIHVK-YGVTSEHVDLLGSVLLSVISENQGLSNTSELIGWWSKTWNIIGNYVKTGL-------
+>gi|119474700|ref|ZP_01615053.1| hypothetical protein GP2143_12811 [marine gamma proteobacterium HTCC2143]gi|119450903|gb|EAW32136.1| hypothetical protein GP2143_12811 [marine gamma proteobacterium HTCC2143]
+--DQ-----IVSCLEQVGDRCKDPTALVYERLFSANPEMKPLFI----M-D-----GNDAVKGQM--LFQVLDGIIDFVGDRRYaetLFLSELINHDI-I
+GVPPRVFSTFFRTIMETFRDIMGADWTAEFDQAWAQLLSDLDEMIREKAEVA----
+>gi|341887822|gb|EGT43757.1| CBN-GLB-25 protein [Caenorhabditis brenneri]
+----RDFFTLKNWWKSVDRKRVEASTYMFSRYLNDFPENKAFYAKLKNVNAqtVDMNCSDPGFEAMAAQYLKVFDDVITAveekPGDVQSacdRLSAVGK
+MHRAKvSGagMESSMFQNMEEPFIQMVKYILQDRFNEKAEMLYRKFFQFCLKYLLEGF-------
+>gi|339235297|ref|XP_003379203.1| putative WAP-type 'four-disulfide core' [Trichinella spiralis]gi|316978179|gb|EFV61192.1| putative WAP-type 'four-disulfide core' [Trichinella spiralis]
+-LSVYDKRLIEESWCALR-DKDEVAKQIFLRVLTSNEKIRTIFDLH--TCPDDELEENSAFQRHVKSLSLFLSICADSlsvsPDRLVSIARSIGEKHVNF
+RWvsFDAEYWLLMKCAMVEVISSKQRPKISHLVNTAWNSLLSFVIFEIKHSFLEA----
+>gi|294979326|pdb|2WTG|A Chain A, High Resolution 3d Structure Of C.Elegans Globin-Like Protein Glb-1gi|294979327|pdb|2WTH|A Chain A, Low Resolution 3d Structure Of C.Elegans Globin-Like Protein (Glb-1): P3121 Crystal Formgi|294979328|pdb|2WTH|B Chain B, Low Resolution 3d Structure Of C.Elegans Globin-Like Protein (Glb-1): P3121 Crystal Form
+--------------------NIENGNAFYRYFFTNFPDLRVYFKGAEKY-TADDVKKSERFDKQGQRILLAChllANVYTNEEVFKGYVRETINRHR-IY
+KMDPALWMAFFTVFTGYLESVG--SLNDQQKAAWMA--------------------
+>gi|194745446|ref|XP_001955199.1| GF16359 [Drosophila ananassae]gi|190628236|gb|EDV43760.1| GF16359 [Drosophila ananassae]
+-FTLSERLALRQAWNIVRPFTRRYGQEIFFNYLNDAYLRISKFKHTKGN-------YLHVLHNHFRGFLCFIGSLIEEQDPvmFQLMLNDNNMTHSR-CK
+VGAAFILELAQAMTDYILKVFEKVSSASLESGFRKIVD-----------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 4865 4754 4858 * * 3862 3292 * * 4864 3522 4800 1479 4967 * 2877 * 4673 * * 1
+ 102 3874 * 1671 544 * * 6449 1270 0
+
+L 2 6390 * * * 2775 6389 * 5187 * 682 3753 * 6579 * * * 6479 3809 6378 * 2
+ 0 * * * * * * 8204 0 0
+
+S 3 6541 * 4492 * * * * * * * 6481 4585 * 6363 * 1359 1102 5361 * * 3
+ 0 * * * * * * 8310 0 0
+
+E 4 2557 6360 3279 2616 7155 3864 6687 5062 4276 5145 * 5648 2532 5497 6324 3964 4639 6356 * 6304 4
+ 18 * 6335 * * * * 8407 0 0
+
+G 5 2722 * 2843 2457 6074 5096 5716 5449 2938 6621 * 5674 5400 4590 3271 3661 5582 * * 6378 5
+ 0 * * * * * 0 8452 0 1024
+
+E 6 6454 * 2184 1467 * * 6212 6708 5569 * 6568 6362 * 1642 * * 5690 * * * 6
+ 0 * * * * * 0 8463 0 1024
+
+W 7 5154 6134 * 5125 6048 * 6292 2129 2183 4193 6623 * * 6425 2330 * 4822 3095 6575 6147 7
+ 0 * * * * * 0 8612 0 1024
+
+Q 8 2803 * 3879 2981 4661 6930 4651 5002 2408 4909 * 5445 6434 3338 3494 4510 5008 7035 * 5882 8
+ 0 * * * * * 0 8629 0 1024
+
+L 9 2405 * 4117 4868 6693 5529 5699 3435 * 1432 6132 4374 * 5487 6950 * 3746 4707 * * 9
+ 0 * * * * 0 * 8649 0 1024
+
+V 10 5091 * * * * * * 1496 * 1888 4857 * * * * * 5622 1780 * * 10
+ 0 * * * * * * 8761 0 0
+
+L 11 4500 * * 4806 * 6751 5076 4926 2433 3991 * 5755 * 2135 1916 * 5171 4028 * * 11
+ 16 * 6532 * * * * 8761 0 0
+
+H 12 3400 * 3547 2937 * 4959 5215 * 2998 6826 * 3621 * 3138 3676 2631 4387 * * 6176 12
+ 0 * * * * * 0 8740 0 1020
+
+V 13 3838 5621 4678 * 6505 * 6310 4845 * 5286 6826 4975 * * * 1069 2183 4834 6134 * 13
+ 0 * * * * * 0 8740 0 1020
+
+W 14 * * * * 3514 6928 * 5163 * 4954 6549 * * * * * * 4956 338 6606 14
+ 0 * * * * 0 * 8740 0 1020
+
+A 15 2719 5190 3530 2903 6325 3891 * * 3624 6943 * 3074 4001 4973 3719 3319 4568 * * * 15
+ 0 * * * * * * 8761 0 0
+
+K 16 3505 * 6551 4948 4749 4499 * 3823 2666 3586 4723 4454 5815 3907 3481 4121 4160 3252 * * 16
+ 33 5479 * 1000 1000 * * 8761 1169 0
+
+V 17 3681 * 6528 6932 5178 * * 2136 * 2225 4439 6341 6282 7064 6538 * 5736 1618 * * 17
+ 106 6454 4071 1000 1000 * * 8774 1024 0
+
+E 18 3667 5822 4781 3720 5269 4283 5729 4751 2855 4537 5200 6531 * 5636 3218 2893 5207 5090 4570 3681 18
+ 107 4386 5415 1298 753 2629 254 8694 1503 1685
+
+A 19 2939 * 3758 4364 6453 3505 5646 6147 2648 5065 5914 5287 3183 3845 3815 3847 4404 6107 * * 19
+ 88 4870 5328 450 1900 0 * 8658 1300 1849
+
+D 20 5307 6638 1826 4387 5272 3443 4482 * 3440 4414 * 2491 6452 5149 4047 5970 6233 5272 * * 20
+ 63 4940 6601 947 1055 * 0 8765 1318 1221
+
+V 21 3144 5912 4997 6577 6002 3779 5868 4239 2819 2832 4588 7453 3425 4640 4063 5348 4900 4746 5001 5578 21
+ 108 4240 5687 2026 406 1843 471 8773 1608 1355
+
+A 22 3786 * 2651 3075 * 5746 6148 4678 3851 6379 5840 4097 3909 3514 4265 6329 3316 3466 * 6470 22
+ 42 5123 * 721 1346 934 1069 8789 1247 1598
+
+G 23 3489 * 3421 2161 6242 4041 4741 6928 3601 6510 * 4625 6437 3507 4231 4510 3510 4156 * * 23
+ 0 * * * * 0 * 8781 0 1221
+
+H 24 3198 6827 7050 * 2932 * 3737 2797 * 3408 5955 3112 4999 6621 * 5103 3767 3352 5666 4744 24
+ 0 * * * * * * 8790 0 0
+
+G 25 2406 6316 6039 6930 6322 850 6612 6908 6217 * * * * 7145 * 4343 4581 3906 * 6463 25
+ 11 7048 * 3000 193 * * 8790 1000 0
+
+Q 26 4038 * 4193 4481 5913 5850 7112 3850 3690 3530 5322 4625 4704 3881 4007 3102 3342 3205 * 7049 26
+ 34 5405 * 2860 214 * * 8790 1177 0
+
+D 27 3117 6316 3485 3178 * 4715 5281 3858 3377 3646 6954 3991 * 4399 3479 4472 3929 5016 * 6163 27
+ 0 * * * * * * 8790 0 0
+
+I 28 3684 6267 * * 1946 * * 1899 * 2828 3942 * * * * 6322 5455 2832 * * 28
+ 0 * * * * * * 8790 0 0
+
+L 29 * * * * 1143 * * * * 2342 4442 * * * * * * 5646 * 1815 29
+ 0 * * * * * * 8790 0 0
+
+I 30 3597 * 4243 3842 4209 4594 4517 3121 3475 2863 5806 5889 * 5017 4459 4208 3814 4460 * 4989 30
+ 35 5388 * 3073 183 * * 8790 1206 0
+
+R 31 3621 5588 4493 5433 6573 4316 5404 6017 2365 4730 5657 3901 * 5196 1720 4684 5650 * 6516 6460 31
+ 20 6217 * 3000 193 * * 8790 1045 0
+
+L 32 * * * * 2442 * * 3583 * 1064 3846 * * * * * 6513 3971 5487 3511 32
+ 0 * * * * * * 8792 0 0
+
+F 33 6904 5418 * * 514 * 5527 4198 * 2583 * * * 6837 * * * 5957 * * 33
+ 0 * * * * * * 8792 0 0
+
+K 34 3450 * 4730 1918 5595 6667 6038 * 2826 5761 6604 4048 * 4448 4290 4170 2779 5490 * 6676 34
+ 14 * 6725 * * * * 8792 0 0
+
+S 35 2600 * 3727 3448 * 6944 4687 4089 3307 3201 4673 4463 * 4429 3774 4139 3571 7065 * * 35
+ 0 * * * * 0 * 8786 0 1000
+
+H 36 3400 5443 3550 5626 3640 * 2591 * 5641 6049 * 2766 * 5739 4587 4415 5910 4359 * 2509 36
+ 0 * * * * * * 8792 0 0
+
+P 37 6778 * 6700 4710 * 6837 * * 5602 6567 * * 272 6468 * 5807 4916 * * 6305 37
+ 0 * * * * * * 8792 0 0
+
+E 38 4097 * 2285 2246 6225 4249 5139 6955 4669 5468 5111 3919 * 4103 5224 3219 4453 6505 5860 * 38
+ 0 * * * * * * 8792 0 0
+
+T 39 3259 6225 5703 6827 3912 * * 2966 * 2901 4433 4360 * 6910 6305 3742 3041 3386 6831 3194 39
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+G 153 * * * * * 384 * * * * * * * * * * 2096 * * * 153
+ 0 * * 0 * * * 2910 0 0
+
+//
+�HHsearch 1.5
+NAME 3efa288e683aab27e0db9e3baf300765
+FAM
+FILE 3efa288e683aab27e0db9e3baf300765
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:25:08 2013
+LENG 219 match states, 219 columns in multiple alignment
+FILT 133 out of 1330 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEECCCEEEEECCCCEEEEEEEECCCCCCCCCCEEEEEEECCCCCCEEEEEECCCCCCCCCCCEEEEECCCEEEEEEEECCHHHCCEEEEEEECCCC
+CEEEEEEEEEEEECCCCEEEEECCCCEEEECCCEEEEEEEEECCCCCCCEEEEEECCEECCCCCCCCEEEEECCCCCEEEEEEEEECCCCHHHCCEEEEE
+EECCCCCCCEEEEEECCCC
+>ss_conf PSIPRED confidence values
+9299937972899789979999997078766678878999990899973799970454466778617875047657999950565549589999853888
+4241358999971132116896288517861982999999816779986899998998977775432036863898288899999824887769389999
+9968888228999845779
+>Consensus
+xxxvxxxxxxxxvxxGxxvxLxCxxxxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxLxixxxxxxDxgxYxCxvxxxxx
+xxxxxxxxlxvxxxxxxpxvxxxxxxxxxxxxxxxxlxCxxxxxxpxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxsxLxixxxxxxdxgxyxCx
+vxxxxxxxxxxxxxxxxxx
+>3efa288e683aab27e0db9e3baf300765
+DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVP
+RTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGKERQNGVLNSWTDQNSKDSTYSMSSTLTLTKDEYERHNSYTCE
+ATHKTSTSPIVKSFNRNEC
+>gi|34536129|dbj|BAC87548.1| unnamed protein product [Homo sapiens]
+--------------DNSPVVLACLITGYH--PT-SVTVTWYMGTQSQP-----------QRTFPEIQRRDSYYMtSSQLSTPLQQW-RQGEYKCVVQHTA
+SK----SKKE------I---------------------------FR-------WPESPKAQASSV-PTAQPQAEGSLAKATTAPATTRNTGRGGEEKKKE
+KEKE----------------
+>gi|118129764|ref|XP_001233426.1| PREDICTED: hypothetical protein [Gallus gallus]
+--KIMPPNKPVVGVIGKGVVLPCQLEAKT----VSERLlvQWif--TGKSPNigvTTYDGINTLnpvREEKTYQGRthfFQSEVNRGNLSLHLKNVMLSD
+KGKYICFV-SLENWYDEVVVDLDVAAQSE-eSEVFL-----DGHMGQGIGLTCKSQGWFPQP-EVIWLdSKGQTRKE---KVVTqSLQTSSGLFDVVSSM
+TLEPGS---DMEVSCRIVNDLLNTACES-------
+>gi|242010303|ref|XP_002425908.1| beat protein, putative [Pediculus humanus corporis]gi|212509884|gb|EEB13170.1| beat protein, putative [Pediculus humanus corporis]
+---------PKIIDVRESGILTCEFDLENGK---LYSVKWYK----NDLEFFRFMPNGNPIvqifKVDG-INLTdKDCNMTTVVLNRLEFTTSGLYTCEV
+STegPYFKTVQTSSNMTVLGiPEKNPTITG--IENIYNVGDYVRGNCTSDLSYPVS-NIDWYINDNKVESWQLEKYPVIIFNDKMIISTLGISF------
+---------------------------
+>gi|185135274|ref|NP_001118211.1| macrophage colony stimulating factor receptor-like [Oncorhynchus mykiss]gi|34392449|dbj|BAC82552.1| macrophage colony stimulating factor receptor [Oncorhynchus mykiss]
+--SVLIEVDGYVSIVGEELRIPCITSNPNH----FYNVTWKHSSLKA------------LNFFQTVIQDKQVHITSTVTIPAVTMSDTGNFTCTAMNE--
+--AGASRSTIYLEVVDEPYIRFIPRlspnlyqNGSLVNvkeGENLEISILIEAY-PQIKKHWWDVPMSHSQNIS--THgDTWTA-QDNNRYESSLLLHRV
+RSEERGQYTLHTRSTRLNSSITFNI-----
+>gi|327265502|ref|XP_003217547.1| PREDICTED: macrophage colony-stimulating factor 1 receptor-like [Anolis carolinensis]
+--KIGLIVKGFIIFYYIFTYFFVTAHCIVL----AFGSY-----CKC------------HIKLELSFK-----------------------ICILTK---
+-----KQSALIKTINTPISVTIGAKDNVRIQGEPFNISCNV-SY-PSFGyQIRWDYPSTANVSLE-SRESFDDS-SESYNTQHILSIPAVQLNDSGKYTC
+FASTNARVSNSSANL-----
+>gi|170037717|ref|XP_001846702.1| fasciclin [Culex quinquefasciatus]gi|167881048|gb|EDS44431.1| fasciclin [Culex quinquefasciatus]
+GLTVRDD-----TEGd-VSDSRFTVA---------AAATPSTtFTLPSSSQQVALTPGQPAANGL-QYFGEGYQKGQCGV--tiDRITTAHNGQVKCSVF
+vDGLSAE----glIDVVVAVSPSQPTIQLEPETTYFEAGKQITAHCV---ttgG-nPDP-QLAWFLE-nDPIYDG----Vdk-qqdFEQDGTTGTAL--T
+L-rRIINGNDN-gKRLICQARHLAYpEGSSQTSL-----
+#
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+F 123 7209 * 6584 4113 3425 4961 4134 4026 3585 2478 5004 4507 5437 4570 5009 3146 4208 4950 5833 5046 123
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+
+P 124 3656 * 5862 3680 6855 4252 5063 7166 3693 4240 * 4933 2430 4531 3528 2990 4276 5095 7176 4826 124
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+
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+ 77 * 4260 1000 1000 945 1057 10612 1017 2408
+
+S 126 3921 * 3526 3947 6555 6605 * 6775 3768 4971 5162 5021 2996 4322 4493 2221 3296 5169 * 5357 126
+ 77 5832 4863 1585 585 2219 349 10627 1177 2602
+
+S 127 5988 5338 5491 3672 6836 4243 5186 4049 4639 3211 * 3498 3376 4803 3857 3128 4314 3225 * * 127
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+
+E 128 4451 * 4885 3084 5280 * 5897 4436 3867 3437 4512 5676 4228 4431 4735 2688 3765 3141 6616 * 128
+ 48 7111 5278 0 * 1546 605 10499 1000 3765
+
+Q 129 4280 * 3809 3023 * 4214 * 3955 5400 3105 6810 5280 5919 4233 5895 4218 2612 3392 * 4007 129
+ 79 * 4237 1000 1000 2321 322 10527 1001 3275
+
+L 130 4507 * 5729 4519 4824 5784 5852 2843 4099 2624 3698 4695 4644 4808 4308 4509 5739 3232 5914 4819 130
+ 126 3854 6084 720 1347 1839 473 10541 2060 3788
+
+T 131 3483 * 4258 2760 * 5873 5437 7118 3356 3920 5116 4745 3816 5680 3261 3450 4825 3161 * * 131
+ 111 4165 5777 2312 324 683 1407 10580 1843 3297
+
+S 132 4083 6604 3684 3503 * 1393 5726 6969 * 4769 6927 4157 4887 4374 6727 4626 4500 4205 6863 5864 132
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+
+G 133 5108 6912 2983 2586 * 2017 6334 7095 4079 5810 * 3566 5471 3308 5983 4084 5954 5766 * 6856 133
+ 396 2058 * 250 2651 2081 389 10691 5157 1623
+
+G 134 4889 * 3709 2764 * 7027 5271 5886 3845 5825 6633 3312 3600 5497 5562 2652 2894 4097 6962 6932 134
+ 23 5973 * 2975 196 1275 769 10699 1207 1603
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+A 135 2286 6834 * 6910 4576 5358 * 3634 6762 3266 6717 5037 5221 5967 5057 5951 4682 1678 6541 5227 135
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+
+S 136 5270 * 4861 3782 7133 6541 6973 4363 5133 4377 5438 3476 5888 4612 4424 3203 1865 3230 6803 * 136
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+
+V 137 4153 * 7142 6834 2802 6954 6807 2841 * 1101 4989 * * * 8005 5937 * 3260 * 7454 137
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+C 139 6037 97 * * * * * * * 6567 * * * * 6891 * 6965 5954 * 7237 139
+ 23 5957 * 992 1008 605 1545 10650 1362 1425
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+ 59 5362 5980 1874 460 689 1397 10624 1428 1704
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+N 143 3384 * 2997 5177 6839 1799 4926 * 5996 5400 * 3604 6058 6021 4160 2862 4574 6670 5860 6987 143
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+K 147 4081 6647 3125 2673 5812 4882 6017 6657 2953 5286 6680 5332 3308 4359 4181 4228 5174 3622 * 5268 147
+ 172 4779 3718 731 1331 339 2256 10566 1850 3227
+
+D 148 3019 6585 3358 3758 5134 4252 4467 6007 5682 5745 5670 3668 2155 4979 5778 3184 7025 7192 6888 6780 148
+ 601 5241 1669 757 1292 3705 115 10625 1332 2700
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+I 149 3947 * * * 4727 5543 6118 2602 5210 2687 * 6165 3719 6050 6260 5345 3761 2170 5178 4368 149
+ 37 6456 6141 0 * 72 4356 9975 1047 6719
+
+N 150 5909 6700 4005 3387 4576 4795 4246 4813 4284 4911 6985 3382 6000 4049 4615 3330 2385 5365 * 5090 150
+ 35 6045 6879 0 * 627 1505 10692 1163 1409
+
+V 151 * 5933 6805 6705 3467 * 7034 2014 5943 2248 6664 * 6900 * * 5988 6353 1861 6978 3982 151
+ 0 * * * * * 0 10660 0 1222
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+W 153 * 7945 6795 * 4851 * 7321 7044 6120 5089 * * * * * 5401 * 7047 242 5793 153
+ 24 * 5949 * * 0 * 10666 0 1200
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+K 154 6407 7051 6963 4239 3140 * 5634 5052 3748 2423 4806 6704 6667 4206 7363 3843 3894 6203 4765 2378 154
+ 139 4153 4821 1103 904 * 0 10670 1967 1180
+
+I 155 4828 * 6686 4144 3764 * 5028 4441 2255 3922 * 4937 6665 4478 2022 6733 * 3547 6766 4837 155
+ 121 3744 7422 3393 144 2882 210 10638 2246 1928
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+D 156 6629 * 2466 3375 * 2976 4625 7850 4880 5340 5822 1651 5926 5624 4736 4842 4767 * * * 156
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+G 157 6055 6642 3232 4239 6902 1406 * * 6214 * 6870 3162 4840 5296 5437 3060 4593 6741 7092 4851 157
+ 60 4942 6962 3678 117 594 1568 10585 1466 1896
+
+K 158 4423 * 4641 2719 * 4048 5749 5894 2462 3994 7104 3415 * 4648 4379 4303 3512 3679 7167 6803 158
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+E 159 4770 * 5077 2471 * 4912 6765 4657 3588 4126 6735 4095 3234 4731 4233 4565 3147 3777 6897 5085 159
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+R 160 * * 5785 4122 4699 * 7296 2658 6995 1916 4465 4570 5260 4959 5075 4698 6119 2404 * 5008 160
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+ 167 4400 4013 0 * 1444 661 10595 1774 2142
+
+N 162 5770 * 3225 3361 6881 3756 7007 6440 3876 4479 * 3157 3129 4887 4429 2871 4137 5253 6767 5208 162
+ 279 6919 2576 1585 585 3959 96 10487 1000 3044
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+G 163 4790 * 3510 3382 * 2178 4985 6403 4503 4565 5419 3425 4804 4513 4267 3692 5032 4278 6553 6482 163
+ 86 * 4111 0 * 1533 612 10283 1054 5273
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+V 164 4304 * 5077 4262 4026 4380 5127 3415 4826 3697 4702 5069 4763 4999 5451 2926 3490 3431 5022 5624 164
+ 982 5536 1082 508 1753 4031 91 10333 1180 4728
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+L 165 3982 * 4734 3530 4775 5758 5777 4088 5852 3139 * 4144 3635 5762 3291 3471 4131 3815 * 3760 165
+ 193 5030 3399 0 * 292 2449 9257 1112 8416
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+ 41 6512 5855 2807 222 2208 352 10465 1000 3687
+
+S 167 4618 * 5221 4041 * 3706 5573 5769 3934 5464 6538 3661 5223 4155 3031 4055 2152 4726 * 4335 167
+ 49 6947 5299 2585 263 2441 294 10479 1000 3403
+
+W 168 4591 * 3944 4652 3143 4266 4429 4441 6730 3946 5581 3800 3957 6680 5023 2776 4460 3846 5786 4469 168
+ 29 5672 * 0 * * 0 10461 1206 3381
+
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+ 14 6706 * 2347 316 2126 375 10461 1179 3381
+
+D 170 3647 * 4460 3893 5821 4273 4684 3928 3844 4410 * 4754 3152 5823 4334 3049 4046 3289 * 5944 170
+ 13 6811 * 1581 587 3778 109 10497 1145 2856
+
+Q 171 4174 6704 4831 3900 4137 5320 6754 3844 4092 3813 5285 5812 5166 3742 4029 3211 4022 2960 6674 5198 171
+ 75 5237 5360 1200 824 * 0 10498 1339 2721
+
+N 172 5831 * 4147 3238 5785 5164 4490 4234 3207 3438 * 4460 3537 3727 3573 3933 4853 3927 * 5738 172
+ 24 5933 * 574 1607 3760 111 10454 1112 3166
+
+S 173 3756 * 3056 2794 4858 5841 5095 * 4179 5983 6636 2762 5602 4930 3808 3356 4632 4505 6765 4803 173
+ 171 3951 4402 1919 443 1923 442 10465 2125 3013
+
+K 174 3349 * 3709 2513 * 3113 5087 5820 3700 5129 * 4071 6795 4887 4448 3501 3120 5648 6555 * 174
+ 83 6581 4453 1000 1000 867 1147 10431 1158 3295
+
+D 175 4711 5129 1847 4290 6530 3660 4930 6683 4865 5708 * 3345 4068 5966 4472 2874 4845 5155 * * 175
+ 76 * 4275 * * * 0 10487 0 2804
+
+S 176 5289 * 5209 3240 6637 1356 * * 3627 6812 5587 2643 6513 5691 * 3578 5207 6460 5826 * 176
+ 86 5869 4616 0 * 1654 551 10411 1175 3630
+
+T 177 5256 5611 5620 4203 4728 5819 * 4848 3538 3049 5746 3673 * 6937 3139 3151 2420 4538 * 5608 177
+ 132 * 3513 * * * 0 10395 0 3413
+
+Y 178 4951 5673 5572 5184 2471 6825 4711 4880 5625 4183 5573 4190 6568 6427 5148 4600 4039 4304 * 1816 178
+ 120 * 3642 * * 3539 130 10297 0 4541
+
+S 179 4121 5407 3628 4361 5477 5082 4909 5461 4203 5380 * 3209 6537 5243 6679 2070 2691 4912 6420 6612 179
+ 82 5319 5051 3659 119 1738 514 10225 1176 5135
+
+M 180 3088 * * 6948 4688 3872 6404 3503 4805 3627 4269 6369 5537 4481 5152 3683 3178 2857 5522 4506 180
+ 16 * 6488 * * 3653 120 10308 0 4438
+
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+ 14 * 6745 * * 2258 338 10331 0 4331
+
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+ 96 4151 6919 2920 204 2828 219 10401 1754 3820
+
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+ 11 * 7065 * * 479 1824 10427 0 3583
+
+L 184 5755 6459 * * 4151 * * 3384 * 532 6213 * * 5731 * 6994 6918 4224 * 5339 184
+ 12 6948 * 2322 322 2686 244 10561 1000 1832
+
+T 185 * * 5495 4770 * 7080 4272 4310 3932 3179 4797 4484 5283 4563 2891 3096 2520 3974 6903 6804 185
+ 74 5454 5191 1784 495 526 1710 10550 1511 1832
+
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+ 0 * * * * 2578 264 10529 0 1979
+
+K 188 2931 * 4494 4848 * 4533 5281 4453 3520 4079 5139 3253 2954 5407 3456 3380 4416 6814 * * 188
+ 0 * * * * 1600 577 10546 0 1794
+
+D 189 3070 * 4419 5559 * 5090 7018 4112 7381 3154 7062 5263 5226 4488 4651 2695 3130 2529 * 6254 189
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+
+E 190 3895 7773 4058 4216 6574 4933 4323 5888 4142 4791 5635 5368 4004 2872 3372 3446 3458 4016 6829 5780 190
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+ 70 5141 5694 0 * 2696 242 10516 1309 2755
+
+E 192 3693 * 2354 2272 6881 4202 * 5833 4192 5715 7012 3509 5781 5975 4886 2862 4452 6638 * 6759 192
+ 48 5342 6921 473 1840 2070 393 10503 1286 2796
+
+R 193 6813 * 1219 3610 * * 3489 5721 4221 6727 6700 3142 5113 6665 4807 4069 5046 * * 5547 193
+ 38 5932 6652 0 * 174 3136 10523 1203 2542
+
+H 194 3478 * 3316 3991 7048 2472 5353 6775 4323 5642 4892 3110 5722 5815 4082 2416 6810 * * 6155 194
+ 12 * 6866 * * * 0 10576 0 1231
+
+N 195 3247 * 4783 5378 * 1138 5597 6665 3874 4622 5900 5240 * 5640 4999 4950 3532 5192 * * 195
+ 21 6091 * 1574 590 1770 501 10560 1128 1397
+
+S 196 6134 * 3602 3196 6882 * 5195 3876 3415 5431 5241 3290 4882 4637 3725 3820 3509 3254 5987 5979 196
+ 11 7028 * 2585 263 1025 976 10576 1000 1231
+
+Y 197 * * * * 2763 * * 4219 * 2946 6750 * * * * * * 3890 5270 820 197
+ 0 * * * * 1201 824 10577 0 1190
+
+T 198 5217 * 6155 3964 4815 6890 4823 5251 4662 6672 5208 6151 * 3220 3185 4592 1653 3874 6571 4522 198
+ 11 7046 * 0 * 0 * 10595 1000 1030
+
+C 199 * 112 * 7135 6626 7178 * 7081 * 6923 6777 * * 7006 * * * 5799 * * 199
+ 0 * * * * 0 * 10592 0 1000
+
+E 200 4247 5917 6657 2511 5243 6754 5291 4371 4068 4054 5604 * * 3198 3326 4813 3598 2734 * 5775 200
+ 0 * * * * * * 10598 0 0
+
+A 201 1889 * * 5882 4768 * * 4085 6686 4167 * 6634 6687 * * 5253 5836 1034 * * 201
+ 64 * 4529 * * * * 10589 0 0
+
+T 202 4343 * 5632 3010 4028 4421 * * 3956 6779 6722 5102 5662 3233 4683 2622 2428 5243 4681 7071 202
+ 15 6555 * 390 2077 319 2333 10409 1388 1671
+
+H 203 4650 * 4686 * 4821 4614 1640 * 6666 6434 * 1559 6759 4210 5738 5585 5723 5634 * 5535 203
+ 28 5696 * 3314 153 * 0 10340 1188 1000
+
+K 204 5678 6244 4979 1888 6435 3814 * 5492 3612 4971 * 4547 2881 5593 4154 3395 6325 4355 * 4833 204
+ 0 * * * * * 0 10216 0 1000
+
+T 205 2307 * 4286 4065 5361 2564 4798 6343 5222 5370 * 3635 6211 6150 5303 2412 4751 4807 * * 205
+ 0 * * * * 0 * 9970 0 1000
+
+S 206 4628 * 6156 4522 4587 3383 * 5141 4092 1612 4187 6138 * 4565 4678 3029 4300 6306 * 6144 206
+ 45 6069 5989 0 * * * 9805 1000 0
+
+T 207 4525 * 5048 4490 * 3556 4138 6133 3840 6113 * 5039 2525 4005 4969 2151 3529 4997 * * 207
+ 200 4215 3723 639 1483 0 * 9639 1764 1054
+
+S 208 3168 * 4926 2517 * 4317 4958 * * * 5021 4402 5901 3332 3911 2513 4313 3383 * 5885 208
+ 0 * * * * 2300 327 9502 0 1777
+
+P 209 4963 * 5765 5163 4794 5905 * 4743 4822 5773 * 3281 1359 3929 4703 2939 4908 5849 * * 209
+ 0 * * * * 0 * 9370 0 1590
+
+I 210 3274 * 5694 * * * 6659 2259 3858 2201 4965 5346 * 5899 5661 4952 4919 2344 * 5915 210
+ 28 * 5722 * * * * 9392 0 0
+
+V 211 * 4646 5021 3800 * * 5708 * 6021 4930 * 3479 5725 4644 3463 3204 1535 3362 * * 211
+ 0 * * * * 0 * 9331 0 1045
+
+K 212 2317 * 4778 5733 5547 * 4671 3913 3155 4293 5844 5734 * 4744 3639 3877 4137 2514 * * 212
+ 0 * * * * * * 9304 0 0
+
+S 213 4865 * 4097 4351 5702 5712 * 5707 6271 * 5658 3377 5038 * 5642 1684 1971 4182 * * 213
+ 0 * * * * * * 9247 0 0
+
+F 214 4925 5496 * * 2637 * * 2954 * 1976 4536 * * * 5591 5558 6062 2314 4799 3968 214
+ 0 * * * * * * 9078 0 0
+
+N 215 5175 * 4327 2841 * 5850 * * 3446 * * 2608 5212 4430 3188 2293 3027 * * * 215
+ 69 4427 * 3585 126 * * 8555 1027 0
+
+R 216 4491 * * * 3686 * 4436 * 2560 2588 3616 * 3744 4407 2333 * 4285 * 4549 * 216
+ 0 * * * * * * 7204 0 0
+
+N 217 * * 4355 3528 * 2981 * * 3501 3591 * 2580 3492 * * 1928 * 4396 * * 217
+ 0 * * * * * * 7190 0 0
+
+E 218 * * 3516 1173 * * * * 3417 * * * * * * 3463 2444 3307 * * 218
+ 0 * * * * * * 5257 0 0
+
+C 219 * 389 * * * * * * * * * * * * * 2080 * * * * 219
+ 0 * * 0 * * * 2856 0 0
+
+//
+�HHsearch 1.5
+NAME 409d1b78279b50a32005612fe5003760
+FAM
+FILE 409d1b78279b50a32005612fe5003760
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:03:42 2013
+LENG 200 match states, 200 columns in multiple alignment
+FILT 196 out of 1298 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCEEEECCCCEEECCCCEEEEEECCCCCCEEEEEECCEECCCCCCCCCCCCCCCCCEEEECCCCHHHCEEEEEEEEECCCCCCCCCCCCCEEEE
+EEECCCCCEEEECCCCCCCCCCEEEEEEEECCCCCEEEEEECCCCCCCCCCCEEECCCCCEEEEEECCCCCCEEEEEEEEECCCCCCCCCCCCCEEEEEC
+>ss_conf PSIPRED confidence values
+9887699999958998662799099999788998589999899375431014310256655479984467778856999999477887531127719999
+9820478779978987301698299999837998579999899104542231231278630089975668897999999969998405578888999969
+>Consensus
+xxxxxxxPxixxxpxxxvxxGxxVtLxCxxxxxxxxxxxxkxgxxxxxxxxxxxxxxxxxxxxlxixxvxxxdsGxYxCxaxxxxxxxxxxxxSxxxxlx
+VxxxxxxpxlxxxpxxxvxxGxxvtLxCxxxxxxxxxxwxkxgxxxxxxxxxxxxxxxxxxxxlxixxvxxxGxYxCxaxxxxxxxxxsxxSdxxxlxVx
+>409d1b78279b50a32005612fe5003760
+HEGVHRKPSLLAHPGPLVKSEETVILQCWSDVRFEHFLLHREGKYKDTLHLIGEHHDGVSKANFSIGPMMQDLAGTYRCYGSVTHSPYQLSAPSDPLDIV
+ITGLYEKPSLSAQPGPTVLAGESVTLSCSSRSSYDMYHLSREGEAHERRFSAGPKVNGTFQADFPLGPATHGGTYRCFGSFRDSPYEWSNSSDPLLVSVT
+>gi|148699261|gb|EDL31208.1| leukocyte-associated Ig-like receptor 1, isoform CRA_d [Mus musculus]
+QLCSLPDITIFPNSSLMISQGTFVTVVCSYSDKHDLYnmvRLEKDGSTFME----KSTEPYKTEDEFEIGPVNETITGHYSC---IYSKGITWSERSKTL
+ELKVI-----------------------------------------------------------------------------------------------
+---
+>gi|297701545|ref|XP_002827772.1| PREDICTED: platelet endothelial cell adhesion molecule-like [Pongo abelii]
+-----------SLPDWTVQNGKNLTLQCFADVSTtshvkpqHQMLFYKDDVLFYN------ISSMKSTESYFIPEVRIYDSGTYKCTVIVN----NKEKT
+TSEYQVLVEG-VPNPRVTLDKK-EAIQGGVVRVNCSVPEEKapIYFTIEKLELNkKMAKQ----KREKASRDqNFVIleFPVEEQdrvLSFRCQARII--
+----------------
+>gi|7650326|gb|AAF65994.1|AF226640_1 pregnancy-specific glycoprotein 70 [Papio hamadryas]
+-----AQVMIEAQPTK-VSEGKDVlLPVRNLPQEVAAYIWYKGQIMDF-HQFItaytidteriifGAAYSGRetvySNGSLLIRNVTKNDTGSYTVKIR-
+-KPAEETKGVTVHFTL--YLETPKPYISSSNLNPREGTETVILSCDPETQDVSYLWWINGQSLPISRP-WQLSE--NNRILMLYGVTKdiAGPYECEMK-
+--NP-VSSSRSDPVTLNL-
+>gi|332031157|gb|EGI70734.1| Tyrosine-protein kinase-like 7 [Acromyrmex echinatior]
+----------QRERVGlAMRGKKRLRVPCRSTAISArLFAAvlgDVDDAPF---LQAPSTT---dDDvereeigsggcgdrlSRPSLLSFDVTaLYSDFL
+CRSTRRN---lVEKRRNVDGKKSFGiseAivQLQQPKLP----STIHVDNEIELRCHVDGSGDmKYEWFKNTVSVA--K---SDRVEIKKKKLHIHRAIP
+edSGMYTCVA---------------------
+>gi|213982747|ref|NP_001135545.1| v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog [Xenopus (Silurana) tropicalis]gi|195539639|gb|AAI68021.1| Unknown (protein for MGC:185004) [Xenopus (Silurana) tropicalis]
+-----AVPKINEgQDRFTIKVGERFQLICRDAQLVKWTFqKsglvKKPRDVQ------SR-SYNKSEtdQILFIGKADLKHVGRYTCTNTE------TY-
+ENTSISLFVKDP-ARPFLDVPF-IDVIEGSDAVGMCFPSDPDiVDIAIEKCDGSPLAEDFT---FTTDIEAGITIKMVQVsfDGCYVCTGNQSG------
+-----------
+>gi|281371402|ref|NP_001163795.1| carcinoembryonic antigen-related cell adhesion molecule 20 [Rattus norvegicus]
+---SLAKPILTVRQRVVTEQRDMADFYCATNAV--NATIHWVFNNS-LLVLNERMKLSADNKNLTVLVVQREDSGSYLCEVQS----GFEVGRSDDTLLE
+VNYGPDPVSIKLDSgvatGDVveVMEGNTVNF-wVETQsypaPTYTWYLPT--DS---IQP---------PpiTGQLTIPAISreQEGMYRCLVS-----
+---------------
+>gi|157888749|emb|CAP09304.1| novel immunoglobulin domain containg protein [Danio rerio]
+----TAPPVLTETSPPEVevFVGRSLTLKCAAQGnPRPTITWSKDGAPIKPQHK-----VKMVNGSVSFHAVSREAAGQYQCYTSNSE-----GNATHVT
+RLKIIG---PPVIIIPPSdTVLNMSQDAKLKCQAEADppNMTYVWQRQGVDIYhidsLKSRIKVIVDG----TLLISRLAPedSGNYTCMPT--N--GLP
+VSPSASAVL---
+>gi|312385976|gb|EFR30357.1| hypothetical protein AND_00104 [Anopheles darlingi]
+----------------YYKDGSEVFITCSINCtDPFNVIWLHDNREIKNSADFEYLND--GDIyTLHIAEIFPEDAGTYTCEAF-NK----GGESFSSCT
+ISVLapeDQKEKATFAKFPASLsVLDGAKAVFSCETY-ePPSKLQWYKDGEPI--Ne-SSnrYRFVKKDNKYTFSVAKCSFedIGQYQVR----------
+------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+H 1 * * * * * * 1851 * * * * * * 468 * * * * * * 1
+ 0 * * * * * * 2438 0 0
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+M 136 4504 * 4305 3701 6670 4865 6638 5027 3909 4687 5257 3944 5524 4066 3999 3441 2464 3675 4671 6363 136
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+G 153 4318 6267 5384 4034 4263 4591 * 3428 5980 4289 * 5193 3776 5135 4141 2630 2954 3685 5890 5173 153
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+G 158 4596 * 5970 3482 4855 1841 5618 * 5060 4461 5108 4050 4378 3951 6221 3772 3970 4498 * 4411 158
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+T 159 4476 * 3183 3277 * 2913 * 4493 4376 5840 6832 3996 6546 3499 4151 3133 3717 4394 5346 6659 159
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+R 182 * * 4448 4297 6444 3750 5739 4980 3907 4403 * 4600 3146 5021 2082 3260 3695 * 4528 7138 182
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+W 188 4436 * 5750 5566 5751 3238 5464 4189 * 5859 * 4317 4653 4217 5675 2914 3818 4235 2306 3780 188
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+ 0 * * * * 1040 961 8054 0 1832
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+N 190 3408 * * 2006 4761 4408 4303 * 3324 4855 * 5887 3505 3329 3871 3598 5900 * * 6012 190
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+S 191 5184 * 4779 3766 * * 6256 4786 4804 3066 * 5899 2276 4925 2220 4350 3959 4919 * 4618 191
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+S 192 * * * * * 5878 * * * 5561 * * * * 4849 133 6053 * * * 192
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+D 193 4040 * 1140 3304 * * 4836 * 4357 * * 2650 5149 5650 * 4553 5938 4883 * * 193
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+L 195 3390 * * 5711 6233 * * 2781 4939 1496 * * * * * * 5858 1634 * * 195
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+
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+V 197 * * * * * * * 1576 * 956 * * * * * * 5754 2935 * * 197
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+S 198 5655 * 5085 4686 * * 4855 3586 3643 * 5464 3930 * 4162 3704 3354 2418 2579 4619 * 198
+ 0 * * * * * 0 7866 0 1016
+
+V 199 5565 * * * 5767 * * 2389 * 4395 5427 * * * * * * 517 * * 199
+ 0 * * * * 0 * 7841 0 1016
+
+T 200 3191 * * 3091 * * * 4033 * * * * * * * 2546 887 * * * 200
+ 0 * * 0 * * * 5434 0 0
+
+//
+�HHsearch 1.5
+NAME 4162710e327474bbbd96cdac5a602313
+FAM
+FILE 4162710e327474bbbd96cdac5a602313
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:20:50 2013
+LENG 159 match states, 159 columns in multiple alignment
+FILT 160 out of 1038 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEECCCCCEECCCCCCCCCHHHHHHHHHHHCCCEEEEECCHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCHHHHHHHHCCCCCEEEECCHHHH
+HHHHHHCCEEEEEEEEEEECCCCCCCCCCCHHCEEEEEEEECCCCCCCCCEEEEEEEEC
+>ss_conf PSIPRED confidence values
+9999999968984847998786587999999997439879990776762865579996999979998899979989999999986079969999889999
+99997669999999637505761279888013299998860245678965899999979
+>Consensus
+mixxxxAxsxdGxIgxxgxlxWxxxxdxxxfxxxtxxxxvlmGrxTyexxxxxxxxxxxxVvSxxxxxxxxxxxxxxxxxxlxxxxxxxxixvxGGxxlx
+xxxlxliDelxltxxpxxxxGxxxfpxxxxxxxxlxxxxxxxxxxxxxxxxxxxxyxrx
+>4162710e327474bbbd96cdac5a602313
+MISLIAALAVDRVIGMENAMPWNLPACLAWFKRNTLDKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVY
+EQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR
+>gi|2506058|dbj|BAA22616.1| fusion protein, composed of HCV p21 (NS2), N-terminal region of HCV p70 (NS3) and TAX of HTLV-I [synthetic construct]
+---IITSLTgrdknqVDGEVQVLSTATQSFLAtcvnGVCWTVYHGAGSKTLAGPKgpitqmytnvDQDLVGWPAPPGARSMTPCTCGSSDLYLVTRHADV
+iPVRRRGDSRGSLLsprpvsyLKGSAGGPLLCPSGHVVGIFRAAVCTRGVAKAVDFIP--VESMETTMRSPVFTDNSSLVA------
+>gi|330723554|gb|AEC45924.1| dihydrofolate reductase [Mycoplasma hyorhinis MCLD]
+MIISILAMGKNNLIGKGDDLPWYVKEDFDFYREQTKHHDILVGKNTFFTLPKSLQKWSKIYIVSddkNFNYEnENVKTINNFSNLIKEYQNhpSKHLFVS
+GGYTLYKSIINKCDQLIISFIKGEHSGDIFLNELKWEKFEEISSKDK-------GKFIVKKYKK-
+>gi|158316784|ref|YP_001509292.1| deaminase-reductase domain-containing protein [Frankia sp. EAN1pec]gi|158112189|gb|ABW14386.1| bifunctional deaminase-reductase domain protein [Frankia sp. EAN1pec]
+-LVYFVASTVDGFVaGPDGADptgpdGFWPvPQDyvehlAtEYPETLpgparaalgvtaagIHFDTVLEGRRSYEVglrvgLTNAFPHLRHLVFSRTLTV
+SpdPGVELVAdDPVATVRELKrqDGKDVWLVGGGELAGALYQEIDELVVKLGPLTLgTGIPLFSrtAAFDpRIWVLADHSVLK----SG--AVFLTYRR-
+>gi|258650872|ref|YP_003200028.1| riboflavin biosynthesis protein [Nakamurella multipartita DSM 44233]gi|258554097|gb|ACV77039.1| putative riboflavin biosynthesis protein [Nakamurella multipartita DSM 44233]
+-VVMYSSVSVDGFIAdENDQpgplFDWLVSgdvplddsgalkvsqTSYDYVRPYWDeIGVTVVGRHVFDLTDgwdgQPPSGIDhVVVVTHRPAPEgwdpE
+APfHFVGDVESALASAQelaGERTVEVAAG-DVGGQVLAagLIDEVRMDVVPVVFgSGKRFFGSVDAPHL--------------------------
+>gi|254389245|ref|ZP_05004474.1| conserved hypothetical protein [Streptomyces clavuligerus ATCC 27064]gi|326444933|ref|ZP_08219667.1| putative riboflavin-specific deaminase/reductase [Streptomyces clavuligerus ATCC 27064]gi|197702961|gb|EDY48773.1| conserved hypothetical protein [Streptomyces clavuligerus ATCC 27064]
+-VVLSAAMTVDGYLDDASPERLLlsNAADFDRVDQVRAQsDAILIGATTVRKDNprllvnsdERRAKrvadgksayPLKVTVTRTGDLSADLnfwhhggk
+klVIt-VDdavekvrttlgdLADVVsvgpdlrdwglvl---delgRrNVGQLMVEGGGTIHTQLMaaDLADEVHLAIAPLLVG-qpGAArflgaadYPGG
+STARMKVLEVRA-------------------
+>gi|326802356|ref|YP_004320175.1| hypothetical protein Sph21_5009 [Sphingobacterium sp. 21]gi|326553120|gb|ADZ81505.1| hypothetical protein Sph21_5009 [Sphingobacterium sp. 21]
+-IIIVANIAANGKVLvSDH--PHHqlPQETMDFYLKLVNqIGNLVIGVRTFENFekfPdhvkALFKNVEIVVLADKPFISSTYPVVNKPTEAIDYFSkkG
+FTEIAIGGGTGTFNTFLEgnFVTDIYFNISPIIT----------------------------------------
+>gi|338707733|ref|YP_004661934.1| riboflavin biosynthesis protein RibD [Zymomonas mobilis subsp. pomaceae ATCC 29192]gi|336294537|gb|AEI37644.1| riboflavin biosynthesis protein RibD [Zymomonas mobilis subsp. pomaceae ATCC 29192]
+-ITLKLATSLDGCIAlENGKSHWITGErARAhaHLERM-RSELIVVGRGTWEVDnPrldvRlLgLEHRspIRAVLGHGSLP-PDWIGLEQ-PTDVSLTAA
+-DHVLVEGGAKAAAAFIkaDIVDRILFYRAPILIgGGiaslsDIGLQNLAEThgRWCHKETRMLGN-------DQLDAYVR-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 3785 * * * * * * 5171 * 4730 332 4943 * * * * * 4823 * * 1
+ 232 2753 * 977 1023 * * 5430 1320 0
+
+I 2 * 6890 * * 4411 * * 1204 6808 2321 4715 * * * 6750 * 5859 2127 * 7003 2
+ 0 * * * * * * 7963 0 0
+
+S 3 4080 * * 4224 5795 6218 5767 2356 2984 5047 7068 4605 * 5377 3455 3400 3368 3155 * 5801 3
+ 0 * * * * * * 8030 0 0
+
+L 4 3588 * * * 4422 5199 * 3061 * 1548 3373 * * * * 4148 * 3143 * 3118 4
+ 26 6251 7804 711 1362 * * 8277 1087 0
+
+I 5 6124 7113 5197 6375 3960 6040 5135 1549 4289 6370 4299 4386 * 6553 * 4167 7045 3163 5798 3010 5
+ 11 7045 * 0 * 0 * 8273 1000 1000
+
+A 6 2657 5388 * 6081 4109 5753 * 3167 * 3328 3472 4859 * 5644 7725 4815 4207 2405 3816 5908 6
+ 7 * 7660 * * * * 8264 0 0
+
+A 7 630 5377 6431 * 4729 6338 5497 4807 * 7124 6383 4218 7233 6559 7226 4321 5756 4695 7350 * 7
+ 0 * * * * 0 * 8264 0 1011
+
+L 8 4024 5268 * 5933 6799 * 7196 2577 5833 3267 3048 7183 * 4030 6505 4898 3367 2048 * 5709 8
+ 0 * * * * * * 8279 0 0
+
+A 9 4497 6035 2913 6307 * 3599 * * * * * 5578 * * 7085 1145 2108 * * * 9
+ 97 4273 6212 3309 153 * * 8279 1630 0
+
+V 10 3518 * 6252 3849 7270 6871 * 4108 3407 1509 4975 5217 4701 5004 4286 5338 * 3219 * * 10
+ 32 5518 * 1306 748 604 1548 8275 1314 1117
+
+D 11 6251 * 872 5320 * 7020 6148 * 4793 * * 2086 * 5401 5592 4790 5177 7243 * 7090 11
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+
+R 12 * 7139 * 6899 5510 397 5516 * 6050 5014 5484 4763 * * 4720 7090 * * 5350 7376 12
+ 9 7273 * 1000 1000 * 0 8285 1000 1000
+
+V 13 4602 5227 * 4194 2304 3341 5388 6104 4048 3752 5594 4959 * 5124 6273 * 7182 3173 * 2389 13
+ 16 * 6462 * * * 0 8285 0 1000
+
+I 14 5547 5390 * * 4087 * 7313 776 * 3083 4609 7103 * * * * 6167 3232 * 5730 14
+ 298 2421 * 449 1904 * 0 8244 2998 1128
+
+G 15 1878 * 3692 4977 * 1086 7258 * * 6148 * * 6923 4953 6086 4684 5270 7142 * * 15
+ 502 1800 7177 561 1633 * 0 8244 3907 1128
+
+M 16 3328 * 4668 3388 4678 5522 4988 4965 2783 3393 5515 4332 2893 5020 4196 4954 5445 4755 * 5878 16
+ 0 * * * * * 0 8232 0 1295
+
+E 17 3419 6469 2125 4497 * 2830 7126 * 4465 4949 7325 2264 4847 4489 6028 4553 4747 * 7069 * 17
+ 58 4917 7325 1823 479 * 0 8232 1284 1295
+
+N 18 4814 * 3023 * 7121 1204 5078 6738 4875 * 6785 2519 7035 5641 6006 3679 7108 7000 * 7141 18
+ 69 5262 5581 2061 395 2517 277 8232 1285 1365
+
+A 19 4568 * 2512 3392 7052 2612 5748 * 3275 6941 5690 5346 * 4183 3324 3671 4142 5101 6074 6963 19
+ 134 3754 6117 2742 234 2776 228 8213 1824 1523
+
+M 20 5173 * 4738 6430 4349 5094 6329 3171 6752 1315 3100 6035 5189 * 6339 5066 4723 4155 * 6106 20
+ 95 4082 7670 1501 629 330 2289 8201 1579 1592
+
+P 21 4973 * 2498 4513 6790 4109 7086 7309 5026 4314 7134 6221 1245 6241 5227 3823 5363 6883 * * 21
+ 126 4643 4509 1767 502 590 1576 8284 1463 1121
+
+W 22 7359 * 6998 6924 3932 * 7073 * 6121 4998 6712 * * 4759 6223 5895 * 5104 499 4452 22
+ 301 2558 5763 639 1482 * 0 8260 2727 1475
+
+N 23 3938 6528 6227 5279 4593 * 2659 4252 4724 2485 6225 5123 5061 5101 3894 3268 5622 4493 7321 3776 23
+ 263 2661 6924 1611 572 194 2991 8243 2690 1935
+
+L 24 5803 4835 5169 4307 2757 5063 5179 2775 7073 2445 5665 5992 5238 7261 6918 3517 4889 3929 6586 4257 24
+ 188 3425 5104 1510 624 1830 476 8272 2109 1145
+
+P 25 4789 * 4098 3313 7311 3521 * 6567 2904 4941 * 5779 1738 5575 4487 3789 4263 5664 * 7157 25
+ 82 4454 6660 1813 483 1015 985 8240 1545 1534
+
+A 26 2922 * 3007 2025 6166 3251 6247 * 4084 7227 * 4669 4817 3939 6188 4030 4393 5745 * 5717 26
+ 351 2276 6724 2103 382 1339 726 8279 3180 1378
+
+C 27 4243 6486 1075 2406 5428 3632 5703 7167 7835 5164 * * 5096 * 7374 4700 5890 5666 * * 27
+ 105 3836 * 2352 314 905 1101 8271 1854 1313
+
+L 28 4816 7170 5967 6440 3034 6074 5879 * 4928 1983 2887 6218 6431 5281 4368 4829 5001 3103 6532 4005 28
+ 96 3958 * 1246 790 * 0 8279 1724 1102
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+
+//
+�HHsearch 1.5
+NAME 4186931bf3bd591aa12aac05cbb54275
+FAM
+FILE 4186931bf3bd591aa12aac05cbb54275
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:15:10 2013
+LENG 69 match states, 69 columns in multiple alignment
+FILT 106 out of 1048 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEEEEECCCCEEEEECCCCCEEEEEEHHHHHCCCCCCCCCCCEEEEEEEECCCCCEEEEEEEC
+>ss_conf PSIPRED confidence values
+997879999987999826895389971489876780045877689999999999989999587899979
+>Consensus
+xxxxxGxVkxxxxxkgyGfIxxxxxxxdiffhxsxxxxxxxxxlxxGxxVxfxxxxxxxGxxAxxVxxx
+>4186931bf3bd591aa12aac05cbb54275
+SGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL
+>gi|288961931|ref|YP_003452241.1| cold-shock DNA-binding domain protein [Azospirillum sp. B510]gi|288914211|dbj|BAI75697.1| cold-shock DNA-binding domain protein [Azospirillum sp. B510]
+---mAYGTVRWYNLDSQSGLIEPWEDGATVYFDRATLRQSGLDIVADGEDVRYLAVGSEDAPVAQRVELI
+>gi|57339988|gb|AAW49981.1| hypothetical protein FTT1051 [synthetic construct]
+--MKIKAASVCNDSKTIKktWQTP-------MLSTQHQESE---SI-EGKAPAGNEQFGTQG-------LS
+>gi|242032877|ref|XP_002463833.1| hypothetical protein SORBIDRAFT_01g007080 [Sorghum bicolor]gi|241917687|gb|EER90831.1| hypothetical protein SORBIDRAFT_01g007080 [Sorghum bicolor]
+-----------------------------MAIRITMSYSGYvaQNLAASFGLRCTTA--------------
+>gi|307152296|ref|YP_003887680.1| cold-shock protein DNA-binding protein [Cyanothece sp. PCC 7822]gi|306982524|gb|ADN14405.1| Cold-shock protein DNA-binding protein [Cyanothece sp. PCC 7822]
+----EALVVRLFPEQDYGFLKTLDG-EEIYFHRNSVLHNDFERLAVGTGVRYSAIEDDQGPRATTVQI-
+>gi|82914243|ref|XP_728783.1| hypothetical protein [Plasmodium yoelii yoelii str. 17XNL]gi|23485305|gb|EAA20348.1| hypothetical protein [Plasmodium yoelii yoelii]
+-------------VQAHGpdFPADSGG-RLRHHRDAGRPG---NLFSPAQRVRFAEEMGEEGPQASSVRV-
+>gi|323498541|ref|ZP_08103534.1| hypothetical protein VISI1226_09719 [Vibrio sinaloensis DSM 21326]gi|323316430|gb|EGA69448.1| hypothetical protein VISI1226_09719 [Vibrio sinaloensis DSM 21326]
+--MaIQGTISEWDQHKGYGYIAVDDQEAQIRFHLFDFEAFGHP-PQLRDRVQFRLAKDDQGeLRAVHVER-
+>gi|294788309|ref|ZP_06753552.1| membrane protein,putative [Simonsiella muelleri ATCC 29453]gi|294483740|gb|EFG31424.1| membrane protein,putative [Simonsiella muelleri ATCC 29453]
+----SGKIVKWNSERGFGFVKTAEVANDIFFHVNTLVGKDEISPQQNESVtvYAKYDDDKKRWSATKITS-
+>gi|50085859|ref|YP_047369.1| hypothetical protein ACIAD2809 [Acinetobacter sp. ADP1]gi|49531835|emb|CAG69547.1| hypothetical protein; putative membrane protein [Acinetobacter sp. ADP1]
+---MKGKILDYSIQTSTGIIRAENQ-QRYSFSGSAWKEQ--QAPMRGMHVDFEID--------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * * * * * * * * * * * * * 0 * * * * 1
+ 0 * * * * * * 3105 0 0
+
+G 2 3654 * 2230 * * 1415 * * 1985 * * 3646 * * * * * * * * 2
+ 101 3888 * 2000 415 * * 4582 1000 0
+
+K 3 * * * 5537 * * * 5588 4015 3509 1274 * 5030 * 1458 * * * * * 3
+ 83 4162 * 0 * * * 6947 1281 0
+
+M 4 4526 * * 4366 4208 * 4824 3400 3951 3428 3512 * 4663 4137 3562 4077 5588 3472 * 2970 4
+ 0 * * * * * * 7872 0 0
+
+T 5 4213 * * 6778 4879 * 4784 4226 3256 4127 5759 4765 * 2720 3125 4159 2616 5325 * 3545 5
+ 0 * * 1000 1000 * * 7719 1000 0
+
+G 6 3651 * 6592 * * 296 * * 5310 * * * * * 5400 6602 6369 5369 * * 6
+ 0 * * * * * * 7755 0 0
+
+I 7 4006 * * * 5363 * * 4185 2392 5488 6876 5676 * * 3180 5678 1453 3293 6474 6743 7
+ 0 * * * * * * 7755 0 0
+
+V 8 5310 4775 * * * 5400 * 1510 * 3566 * * * * * * * 1062 * * 8
+ 0 * * * * * * 7755 0 0
+
+K 9 4722 6546 5781 * 6769 5400 7091 4407 1364 4579 * 6980 * 6402 3090 3176 4026 3673 * 5159 9
+ 0 * * * * * * 7755 0 0
+
+W 10 6337 6212 4220 4113 3705 * 5091 6918 3875 6702 * 4834 * 5884 3153 2369 4668 4832 2069 * 10
+ 12 * 6914 * * * * 7755 0 0
+
+F 11 * 4789 * * 1536 5395 * 4847 * 3423 5554 * * * * * 6745 5088 2240 2354 11
+ 63 * 4553 0 * 0 * 7740 1000 1000
+
+N 12 * 6753 1887 6754 4039 6783 5381 5659 3966 4995 5723 1707 * 6943 4843 3654 * 4202 * * 12
+ 55 6783 5144 2807 222 * 0 7711 1000 1319
+
+A 13 4813 * 2833 3619 6740 6398 4123 5610 5573 6258 5986 5663 2299 4294 3525 3320 3961 4176 * 6245 13
+ 35 5365 * 2000 415 198 2963 7777 1114 1583
+
+D 14 3361 * 2942 2498 * 5054 5678 6599 3146 6051 * 4806 5989 4028 3843 3934 3648 3860 * 6515 14
+ 0 * * * * 0 * 7824 0 1000
+
+K 15 6031 * 4455 3467 * 4087 6438 6777 1595 5930 5656 3805 * 3685 2410 4829 5087 * * * 15
+ 0 * * * * * * 7824 0 0
+
+G 16 5446 * 4933 5740 * 656 5710 * 4582 * 6330 4754 * 5095 3495 5073 5356 6898 * * 16
+ 0 * * * * * * 7824 0 0
+
+F 17 6707 * * * 1594 * 4763 4720 6745 5307 * * 6232 * 6613 6436 4253 6373 4553 1294 17
+ 33 5459 * 0 * * * 7824 1114 0
+
+G 18 6373 * * 5459 * 163 * * 5356 6393 * * * * 5487 * 6232 * * * 18
+ 59 4635 * 1000 1000 * * 7824 1384 0
+
+F 19 4971 * * * 688 * * 4955 * 4217 5930 * * * 5566 6310 6107 3989 4407 3532 19
+ 0 * * * * * * 7824 0 0
+
+I 20 6393 6673 * * * 5459 * 633 * 3239 * * 5980 5356 * * 6629 2921 * 5487 20
+ 0 * * * * * * 7824 0 0
+
+T 21 3574 6472 4637 3001 * * 6383 4948 3580 4559 * 4539 6467 4084 3409 3495 2509 3517 * 6620 21
+ 15 * 6629 * * * * 7824 0 0
+
+P 22 3834 5018 3781 4387 * 3999 6641 5929 * 6789 * 4693 2207 4462 3558 3238 3740 3270 * 6566 22
+ 69 6454 4836 2322 322 * 0 7820 1059 1005
+
+D 23 4171 * 1844 2852 4697 5066 5478 5938 5124 4085 * 4103 3115 6924 4320 4729 5657 4988 6414 * 23
+ 79 4226 * 2114 379 2328 320 7661 1553 1421
+
+D 24 3969 * 2205 2925 5113 2508 4523 * 5361 5300 * 3492 4840 6307 4296 4105 4874 * * 6624 24
+ 83 4368 7069 810 1218 * 0 7676 1375 1318
+
+G 25 3996 6541 3812 5082 5094 1376 6841 6925 4953 5451 6822 5214 4317 4454 5281 4088 3455 6827 * 5435 25
+ 426 * 1968 * * * 0 7679 0 1440
+
+S 26 3472 * 3124 3119 * 1602 6195 6610 5922 6051 * 5675 3756 3669 3675 5647 6512 6170 * * 26
+ 37 5309 * 993 1008 237 2724 7363 1078 3724
+
+K 27 4662 * 3080 2418 6284 3265 6538 6494 2855 6017 5002 4401 3521 3908 4613 4663 4678 6502 * * 27
+ 0 * * * * 1423 673 7676 0 1388
+
+D 28 4591 * 1173 2928 * 5375 * * 5205 4330 * 3677 * 4904 3462 4497 5443 6264 * * 28
+ 0 * * * * * 0 7683 0 1205
+
+V 29 4676 5708 * * 4877 5321 * 1517 * 3742 5098 * * 6345 5080 * * 1780 * 3378 29
+ 0 * * * * 0 * 7683 0 1205
+
+F 30 4428 * 6675 * 845 * 5983 * 6806 3971 4252 * * 5503 4409 5733 * * 4665 3075 30
+ 0 * * * * * * 7854 0 0
+
+V 31 4789 6334 5460 * 1078 6327 5983 3901 * 3206 5141 * * * 6304 5531 * 2404 * * 31
+ 0 * * * * * * 7854 0 0
+
+H 32 6968 * 4409 6628 7158 5969 773 6886 6322 6362 6821 4869 4518 5397 4539 3181 6980 * * 5519 32
+ 0 * * * * * * 7854 0 0
+
+F 33 2616 * 5983 * 3339 5546 * 2829 3578 4265 5839 6424 6469 4279 2917 5216 4568 3711 * 4193 33
+ 0 * * * * * * 7854 0 0
+
+S 34 3099 6806 4826 4248 6783 6622 5849 5406 3991 * * 3162 * 4876 4285 1655 2748 * * * 34
+ 0 * * * * * * 7854 0 0
+
+A 35 2232 6903 2370 3964 * 3783 4550 5614 5737 5001 * 3160 * 4250 * 4045 3805 4683 * * 35
+ 0 * * * * * * 7854 0 0
+
+I 36 6970 * * 6469 2662 * * 2567 * 1669 5697 * * 5365 5983 5943 5578 2158 5721 * 36
+ 51 5751 5939 1780 496 * * 7854 1087 0
+
+Q 37 4093 5784 4488 2661 * 5662 6208 5144 3318 4521 * 6010 3996 3513 3456 3193 4849 4255 * 4013 37
+ 58 5743 5577 0 * * 0 7839 1081 1080
+
+N 38 3631 6647 3254 4358 * 2512 4405 6746 3141 5912 6222 4413 4317 3679 4171 3289 5626 6925 * 5719 38
+ 114 6283 3986 885 1126 1572 592 7860 1105 1309
+
+D 39 3479 4944 3656 3300 4811 4694 5631 5338 4025 5504 6788 3607 3931 4467 4564 3349 3577 5247 6619 4974 39
+ 396 6854 2112 0 * 1063 940 7772 1000 1828
+
+G 40 4155 * 2336 5242 * 1637 5488 * 6527 6139 6228 3442 5341 5287 6286 2894 4398 * * * 40
+ 280 3057 4158 1748 510 1522 618 7354 1778 3521
+
+Y 41 4394 5615 * 5632 2832 6255 3793 4297 * 2842 5453 5475 5264 4036 3209 5523 5609 3328 6586 3277 41
+ 428 4488 2238 1489 636 580 1596 7354 1427 3076
+
+K 42 4627 6157 3263 3740 6325 3791 5368 5453 3750 4761 * 3972 3804 4065 2531 3801 5536 5412 * 4695 42
+ 120 6671 3831 0 * 225 2793 7489 1000 3306
+
+S 43 3925 6647 3572 3775 * 5471 6341 4830 4377 4032 5232 5862 4418 5156 3341 2683 2805 4873 6893 5102 43
+ 13 * 6769 1000 1000 0 * 7747 1000 1836
+
+L 44 5679 * * * 4670 * * 2951 * 1342 5422 * 1949 6401 * * 6080 3343 * 6648 44
+ 36 * 5354 0 * 0 * 7808 1000 1000
+
+D 45 3551 4802 4432 4406 6513 4861 5544 5206 2821 5938 6670 5647 5992 3142 3613 2905 3849 4187 6347 5442 45
+ 25 6796 6946 1000 1000 0 * 7680 1000 1205
+
+E 46 3949 6448 3817 2576 6080 * * 4278 4725 4402 5761 4490 2822 4495 4821 4244 4683 2737 * 6966 46
+ 0 * * 0 * 0 * 7808 1000 1000
+
+G 47 5963 * 4078 * * 483 * * 5445 * * 2981 * * 6778 4661 * * * 6488 47
+ 0 * * * * * * 7821 0 0
+
+Q 48 3815 * 1904 2516 6904 * 6496 6160 4472 6111 3732 6961 * 2782 6398 4664 3578 5719 * 6470 48
+ 0 * * * * * * 7821 0 0
+
+K 49 3920 * 3943 3190 * 5667 5517 5022 4523 4885 5413 * 3407 3997 2104 4075 4166 4325 6504 5587 49
+ 13 6841 * 1000 1000 * * 7821 1000 0
+
+V 50 * 6820 * * 6327 6290 * 3649 * 3157 5902 * 5357 * * * * 448 * * 50
+ 13 6855 * 1000 1000 * * 7821 1000 0
+
+S 51 4968 5624 5069 1973 6509 6810 5773 5226 4976 4516 * * * 4697 3712 2609 2843 4579 6111 4367 51
+ 0 * * * * * * 7821 0 0
+
+F 52 4977 5897 * 6083 756 4905 * 6111 * 5139 * * * * * * * 3601 * 2426 52
+ 14 6664 * 1000 1000 * * 7821 1000 0
+
+T 53 4496 6202 3460 1889 * 6354 6888 5554 3784 5653 7040 3920 * 3893 3789 3562 3496 4383 * 6356 53
+ 27 * 5748 * * * * 7821 0 0
+
+I 54 4646 6398 6948 4140 4937 * * 2391 5860 2329 4716 * 4231 * 5815 6664 4106 2117 6378 5364 54
+ 30 6594 6584 1585 585 0 * 7854 1001 1099
+
+E 55 3547 4769 4066 2592 5400 2876 5567 5907 4352 6034 * 7170 5147 3689 3987 5119 4458 2834 * * 55
+ 0 * * * * 1052 950 7786 0 1105
+
+S 56 4001 4857 3705 2642 5356 5648 5073 5402 3724 5399 4826 4459 3575 3723 3462 6103 3563 5001 7042 * 56
+ 14 * 6737 * * * 0 7650 0 1001
+
+G 57 * * 2227 6778 6873 1966 * 5471 5829 6232 4459 3839 * 5265 4191 3220 3236 4328 * * 57
+ 62 5039 6451 1265 776 971 1030 7599 1282 1108
+
+A 58 3857 * 2754 3188 6650 4246 6765 5499 3582 * 5545 4690 2602 3764 3588 4118 4965 5355 * * 58
+ 116 3693 * 2125 376 959 1042 7651 1654 1110
+
+K 59 6021 * 4373 3625 5869 3884 5689 * 1930 6490 6230 4225 6185 3253 2230 4953 5286 * * 5583 59
+ 32 5490 * 1251 786 * 0 7660 1119 1000
+
+G 60 4827 5259 * 6468 * 533 * * 3747 6226 * 5645 * * 4520 3560 * * * * 60
+ 591 1766 4575 627 1504 * 0 7650 3483 1000
+
+P 61 4907 4853 5602 4700 4806 6268 * 4663 3274 2236 5828 * 1932 5624 4383 * 6241 4419 5188 4886 61
+ 19 6266 * 0 * 1882 457 7463 1003 1461
+
+A 62 3992 6471 6448 3673 * * 5808 5066 3203 5244 4576 5109 * 2176 2711 3493 5592 3466 6905 * 62
+ 30 5617 * 0 * * 0 7499 1113 1310
+
+A 63 208 6459 * * * 5238 * * * * * * * 5063 * 5953 * 4319 * * 63
+ 0 * * 1000 1000 1988 419 7499 1000 1310
+
+G 64 3115 * 6459 3367 4348 6140 6878 3918 3633 3642 * * 6711 5488 4958 3939 3239 2283 * 4756 64
+ 0 * * * * * 0 7510 0 1205
+
+N 65 4053 * 2916 3403 * 6387 4860 * 3941 * * 1916 * 3732 3562 3307 4733 5544 * 5942 65
+ 0 * * * * * 0 7510 0 1205
+
+V 66 4315 * * 5689 5882 * * 1709 * 4089 * * * * * * * 866 * * 66
+ 18 6356 * 0 * * 0 7471 1000 1205
+
+T 67 4703 4837 * 3490 6772 * 3740 5382 3359 4647 * * * 2999 2266 4190 2729 5311 * 5134 67
+ 0 * * * * 0 * 7443 0 1205
+
+S 68 4566 * * 6820 5243 * * 3567 3524 1835 * * 3173 6269 3331 4307 * 2590 6002 6003 68
+ 0 * * * * * * 7215 0 0
+
+L 69 * * * * * * * 1596 * 1521 4239 * * * * 3755 * 2845 * 4192 69
+ 0 * * 0 * * * 5467 0 0
+
+//
+�HHsearch 1.5
+NAME 448f640ce08539f9f492ab947cf5c879
+FAM
+FILE 448f640ce08539f9f492ab947cf5c879
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:10:18 2013
+LENG 196 match states, 196 columns in multiple alignment
+FILT 117 out of 167 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCEEEEEEEECCCEECCEEEECCCEEEEECCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCEEEECC
+CCCCCCCCCCCCEEEECCCCEEEECCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9854554578996599999745976715289509989993762799998777645778898789999997447738999989989999878998897179
+777302688785289699986998177999999999862478765673010479999976779987868835588599999385899999998619
+>Consensus
+xxxxxvxxxxxxxWcxIxYyExxxrVGexfxxxxxxvxIDGfxdxxxxxrfcLgxlxnxxrxxxxxxxRxxIGxGvxLxxxxgxVxxxnxsxxxIFVqSx
+xxnxxxxxxxxtVxKvxpgxxxkvFdxxxfxxxlxxxxxxxxxxxxxlxxxcxiRISFvKGWGxxYxRqxItxxPCWiEIxlxxplxxlDxvlxxm
+>448f640ce08539f9f492ab947cf5c879
+LDLQPVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNATVEMTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSP
+NCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQM
+>gi|308489650|ref|XP_003107018.1| CRE-DAF-3 protein [Caenorhabditis remanei]gi|308252906|gb|EFO96858.1| CRE-DAF-3 protein [Caenorhabditis remanei]
+-----------VRWGVVSYYEEGDCYIER-ECYRGNFHIDSgFI--ISEQRLSLGLIQNPSRSTMAFKIRKAMIDGIRFSYKtDGSVWLQNNMRLPIFVT
+SGYLDDqCPGIRVNKVHKLYGHAKVKVFGFTRVKQIIRDrlyskqmarLYLQqnGnrnpMFEVYhripliaiqrearvttdSLVKYCCVKVSFGKGFGDA
+YPeRPIVSQCPVWLELKINSAFDYMDAILNDL
+>gi|24652852|ref|NP_725091.1| CG13188, isoform A [Drosophila melanogaster]gi|23240327|gb|AAF58603.2| CG13188, isoform A [Drosophila melanogaster]
+-------QIDDEIWAKVIVFERNRRVAKAY-ARAPVLTINGSDDGFDGMRIGLCGFDNPMRDQKTDEMKRVIGQGVKIKMDdAGNILIRRYAKSNVYVKS
+TASSPnEETSIGAEILKLPNQAlesekIVKLFDMKKFQSNVNRELRRAYPDRRRLETQCLSAVAFVKS------ENDILECPIWVLIVNVVAMDMLK---
+---
+>gi|268552851|ref|XP_002634408.1| C. briggsae CBR-DAF-14 protein [Caenorhabditis briggsae]gi|187035781|emb|CAP25118.1| CBR-DAF-14 protein [Caenorhabditis briggsae AF16]
+------------TWCHVQTFQLGVkkkaQAKEVFQTSQPTFTIEGGitTVGSTSSRMQLTC----GNSSKIQGIHQTFGEGIRMTKEKGTVWLTVLTaKC
+VVFIQSPFFNHINGKPLDTVIRVQNEHdelgnllhedklpTIKLFDSELYASELNAARSDPINRMETMEAFCKTRVSLAKGFNGDYAKK-----------
+----------------
+>gi|313232554|emb|CBY19224.1| unnamed protein product [Oikopleura dioica]
+------------DWARVSFYQKKMKRGPDFIARSRSFTIDGMTGPRCTsTRMPLGIRTLGLRgCPDTDRLLETVGHGIVIENKENCVLLRNISPVSVYVK
+SCQID-------STPIRIPAAHEVDLFFYDEFSRSIAER--NTLADLWQLREHCTLFISFGLCWGSStVQVESVDGLPCWLKLDLQHCW----------
+>gi|221125810|ref|XP_002162815.1| PREDICTED: hypothetical protein [Hydra magnipapillata]
+----------VSGWCRVDCYERQHHVAT-FRMDEPVICIDGIHPVSDKHRISFAGLPTRSEDLKVLKVKSCIGKGVQLHQDErQNLWATRLGKNPIFVRG
+HTLCPELVK---LNGKLTQGVPMKVLDTSAFKEYMKKECeTSGLV-DDELRDKIMsrlkVCMSFIKD------TVVDEETPCWFEVWLI-----------
+--
+>gi|167517705|ref|XP_001743193.1| hypothetical protein [Monosiga brevicollis MX1]gi|163778292|gb|EDQ91907.1| predicted protein [Monosiga brevicollis MX1]
+----------RDVVASITYHERDSPLAQFY-LNQPIFNISCFRPVEDNtTTVSLSDIDNPCRDSRTEKIRRFIGSGLQVSIRRKCLYVTRLSRNPVFLKN
+YQSPStvSDSILLRENGELPDGAEVCLFDYQVFSKEIARMPAE-----L-ALKMATVSLAFVRT------GEFDDKIPCWIRIRMGDALR---------
+>gi|313217634|emb|CBY38686.1| unnamed protein product [Oikopleura dioica]gi|313218130|emb|CBY41437.1| unnamed protein product [Oikopleura dioica]gi|313231875|emb|CBY08987.1| unnamed protein product [Oikopleura dioica]
+----------EKPWCNVSVYECNNKIevystaktqlGVEYKVADanryaKKEAMKG-KNATQSDVFDLSSISNVNRSTDTWDLLEKLQRGLTLVYDREKR
+IVSChnNcKNLKIYVLSYLMNVECGKHEQSLIQVGPGASRVVYDGYQLAKTIEG-VNSTT--QNDLQKwalisqyanyFTVFRISFQP-WGPEYTKKRLT
+DCDLWLEIFMREYLDWINQIE---
+>gi|256052771|ref|XP_002569925.1| smad [Schistosoma mansoni]gi|227284678|emb|CAY17438.1| smad, putative [Schistosoma mansoni]
+-----------KPWANISYWESHHHVGRRWISGNNsSVIrssskqckkcynyVDSFNDTSL--------IPNLivHssmykSSSGWKQCCRLGSQGISLT
+LTTyGCVWLSNQAlatNLPIFVSSPCFHFHNAncssssssslnssaedFLvDRPVYRVPAGYSLLVFDLSSYENWLQQHSSssssassssyRQYsgnnhn
+gdnsnlsgnsnnsnnIDFDelhkthlwaknnNLCKNPIIHISLGKGWGPSYRRPDVTHCPARLEVWIN-------------
+>gi|71985803|ref|NP_492746.2| Temporarily Assigned Gene name family member (tag-68) [Caenorhabditis elegans]gi|38422270|emb|CAB70215.2| C. elegans protein F37D6.6, confirmed by transcript evidence [Caenorhabditis elegans]gi|38422275|emb|CAB70221.2| C. elegans protein F37D6.6, confirmed by transcript evidence [Caenorhabditis elegans]
+----------NRSWAKMTRYERKEQIGDTVWLHGPFAAV-GVLSKSvhDAQLECSpWDLKN----EVSfALIRQadPIG-----STNPEDVWLYNSGTRP
+LFL-SMTPNVSS--TKDTLRRLSPGYCIRVHRGEVSASAPASERTKVrRPSKDPALAQQNLVISVGKGWGPNYSRLYLTDIPCRYEVSF-----------
+---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+L 1 * * * * * 2943 * * * 1740 * * 1928 * 2730 * 2670 * * * 1
+ 0 * * * * * * 1984 0 0
+
+D 2 * * 1821 2520 * 3783 3882 * * * * 1993 4377 3938 * * * 4732 * * 2
+ 0 * * 2000 415 * * 2712 1030 0
+
+L 3 4933 * * * 3260 * * 2184 * 3327 3826 * 4817 4156 * 4179 4386 2148 * 4254 3
+ 0 * * * * * * 2954 0 0
+
+Q 4 * * 2555 5313 * 4241 3572 3308 * 4803 * * 5352 2546 2658 5212 2740 * * * 4
+ 211 3093 5707 915 1090 * * 3000 1093 0
+
+P 5 3324 3214 5328 3863 * * * * * 4389 * 4926 1449 * * 2312 * * * 4309 5
+ 26 * 5823 * * 0 * 3359 0 1000
+
+V 6 * * * * 4152 4060 * 3524 * * * * 4526 * * * * 408 * * 6
+ 0 * * 3322 152 0 * 3359 1000 1000
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+
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+
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+
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+A 164 2430 * 4506 3091 * 4626 5658 * 4875 * * 4901 1492 4751 5830 3843 * 4739 * 7006 164
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+E 165 4236 3848 2112 2574 6572 3368 5573 * 3423 6570 7015 4300 * 4585 6379 3536 4922 6087 * * 165
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+T 174 5595 1348 * * * * 6303 4320 5945 4416 * * * * * 4497 1297 6717 * * 174
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+W 177 * * * * * * * * * 6303 * * * * 4330 5409 * * 153 6078 177
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+L 182 * * * * 2533 * * 3441 * 768 4126 3714 6136 * * * * * * * 182
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+G 184 3976 * 4155 4074 * 2732 4634 5036 4983 * * 3538 4288 4569 2469 3688 6808 3040 * * 184
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+W 188 * * 4950 4997 4760 * * 5685 5459 2372 4004 * * * * * * 3821 1121 3813 188
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+K 191 3322 * 4167 3382 * * * * 2325 * * 3606 * 2424 2548 3748 4844 * * * 191
+ 0 * * * * * * 4659 0 0
+
+V 192 5101 * * * 5424 5366 * 2864 5844 3388 * * * * * * 4882 740 * 4635 192
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+
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+ 0 * * * * * * 4569 0 0
+
+T 194 4709 7061 * * * * 3436 6727 2727 5193 * 3228 * 3790 2870 2959 2347 6522 * 5494 194
+ 0 * * * * * * 4409 0 0
+
+Q 195 4293 3461 4187 4209 * 5175 5622 6714 5022 * * 5230 * 1190 6708 6323 2733 * * 5402 195
+ 0 * * * * * * 4287 0 0
+
+M 196 * * * 6263 * * * 3366 * 2521 482 * * * * * * * * * 196
+ 0 * * 0 * * * 3887 0 0
+
+//
+�HHsearch 1.5
+NAME 482b4b12963f255ad7693a467b7af4cc
+FAM
+FILE 482b4b12963f255ad7693a467b7af4cc
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:08:02 2013
+LENG 173 match states, 173 columns in multiple alignment
+FILT 128 out of 686 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEECCCCCCEEEEECCCCCCHHHHCCCEEEEEECCCCEEEEECCCCCCCEEEECCCCCCCHHHHCCCCCCEEEEEEEECCCCCEEEEEECCCCCCE
+EEEECCCCCCHHHCCCCCCEEEEEECCCCEEEEECCCCCEEEEEECCCCCCCHHHHCCCCCCEEEEEEECCCC
+>ss_conf PSIPRED confidence values
+9599996799886089988875222662585468996688689995488752389976884387347246787103689840168735999965887553
+8998567856666426783207896389889995699711699979864599789378997240489833679
+>Consensus
+xxixxyxxxxfxGxxxxxxxxxxxlxxxxxxisSixVxxgxwvxYexxnfxGxxxxlxxGxyxxxxxxxxxndxisSxrxxxxxxxxxixlyexxxfxGx
+xxxxxxdxxxlxxxxxndxisSixVxxGxwvxyexxxfxGxxxxlxxGxyxxxxxxgxxxxxisSirxixxxx
+>482b4b12963f255ad7693a467b7af4cc
+GKITFYEDRGFQGRHYECSSDHSNLQPYFSRCNSIRVDSGCWMIYEQPNFQGPQYFLRRGDYPDYQQWMGLNDSIRSCRLIPHTSSHRLRIYEREDYRGQ
+MVEITEDCSSLHERFHFSEIHSFHVLEGWWVLYEMPNYRGRQYLLRPGDYRRYHEWGAVDARVGSLRRAVDFY
+>gi|229895166|ref|ZP_04510342.1| putative exported protein precursor [Yersinia pestis Pestoides A]gi|229701928|gb|EEO89951.1| putative exported protein precursor [Yersinia pestis Pestoides A]
+-KVCFYMDDDYNGESLCAAqgNSVASIPDKwNDRISSISIPHGLVVtVYEDVDFLGASRSFEADvDLVSDKDLIYLNDNISAFKI-----KKAVCFYGES
+NFTGDSLCLSSgEQFDLYrgnyperkqsHlvNPLNDEVYSIKIPPGMQtTVYEDDDYNGKYFVLTEDYTPdDLLII-RMNNKISSMRVSQD--
+>gi|156384196|ref|XP_001633217.1| predicted protein [Nematostella vectensis]gi|156220284|gb|EDO41154.1| predicted protein [Nematostella vectensis]
+--AVVFEHAYYGGSRKAFDDyGCPDVTALFppgdiGGASS-LIInqTKKWELFTETQYKGLVKTEEPGWYATPEEMKFPNDRLKSIRPR-----------
+---------------------------------------------------------------------------------
+>gi|238798360|ref|ZP_04641843.1| hypothetical protein ymoll0001_1640 [Yersinia mollaretii ATCC 43969]gi|238717818|gb|EEQ09651.1| hypothetical protein ymoll0001_1640 [Yersinia mollaretii ATCC 43969]
+----------------------------------------mknkrillslLIyLSSTEIALAENNLTrnvidrihhdma-------------------vr
+sa----I-----TSPVCFYYENYFqgekfclsspelid-----------fTREnniqihtnkiksisipkssqitvyqgehfftlt--------------
+---------------------DNilq--EAWQKMIA---------gdevteifT-----
+>gi|238754017|ref|ZP_04615376.1| hypothetical protein yruck0001_29380 [Yersinia ruckeri ATCC 29473]gi|238707769|gb|EEQ00128.1| hypothetical protein yruck0001_29380 [Yersinia ruckeri ATCC 29473]
+----------------------------------------mkrknkilllILfISIPEIVFSQYLSVsnnideig-------------------ptyt--
+--L-----DNDEKLSTESFS-----------fNQPeeitll-----------------------------------GSqpg--EQWQEPV----------
+M-----
+>gi|294817978|ref|ZP_06776620.1| Hypothetical protein SCLAV_p1446 [Streptomyces clavuligerus ATCC 27064]gi|326446897|ref|ZP_08221631.1| hypothetical protein SclaA2_37770 [Streptomyces clavuligerus ATCC 27064]gi|294322793|gb|EFG04928.1| Hypothetical protein SCLAV_p1446 [Streptomyces clavuligerus ATCC 27064]
+------------------------------------------TAWEHSNYGGAYLQFFSdingcspttpSHKYDQLPQ-GWNDKISSMR-ipG---SLCG
+GYAFDHIKRYGPMTR-vDGNIPA-mpA--GWNDRVSSLEVLYA---------------------------------------------
+>gi|238754019|ref|ZP_04615378.1| hypothetical protein yruck0001_29400 [Yersinia ruckeri ATCC 29473]gi|238707771|gb|EEQ00130.1| hypothetical protein yruck0001_29400 [Yersinia ruckeri ATCC 29473]
+--TSIYSCGARPHDFISMIDIKEPLQSKg-------KTVAPI-CFYTEDHFQGEHFCLNPPEMIDLYNTEnqNl-NDKLSSIKIPD---GMQVTIYKNDK
+FNAPHYSFTESVNlaGLDKIGMAGQISSIKTFE----------------------------------------------
+>gi|238783059|ref|ZP_04627086.1| hypothetical protein yberc0001_4180 [Yersinia bercovieri ATCC 43970]gi|238716060|gb|EEQ08045.1| hypothetical protein yberc0001_4180 [Yersinia bercovieri ATCC 43970]
+--YQLFIGIAFATENKTkstiygid---------------ntsk----ENTQN-CLYYK------------------yNTQdnipcqnt-----------
+--------------------------SNiid--eTWVPI----------gkdsKSG--------------------------------------------
+--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 4007 * 3026 * * 1354 4182 * * * * 2508 3983 * * 2948 * * * * 1
+ 0 * * * * * * 4945 0 0
+
+K 2 * * * 4631 * 4382 * * 1128 5696 * 5080 * 4044 3570 2298 4134 * * * 2
+ 0 * * * * * * 6189 0 0
+
+I 3 2900 * * * 5489 * * 1509 * 3240 4184 * * * * * 4351 1941 * 5496 3
+ 0 * * * * * * 7162 0 0
+
+T 4 5645 3120 6438 4463 * * 6523 2771 4847 5661 * 6499 * 5485 4263 3522 1895 2820 * 6237 4
+ 0 * * * * * * 7496 0 0
+
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+
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+
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+
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+
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+
+G 10 4678 5446 3167 * 4893 2385 4903 * 5290 * * 1335 * 5365 * 4378 * 5879 * 4137 10
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+
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+
+Q 12 4653 * 5236 4231 * 2514 5039 * 3396 5552 4940 4388 5625 2473 3029 3780 4135 6421 6163 * 12
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+
+G 13 5569 * * 5464 * 160 5636 * * * * 6122 * 5884 * * 6710 * * * 13
+ 0 * * * * * * 7597 0 0
+
+R 14 3464 * 3588 3036 5362 5931 5195 6014 3179 3972 * 4232 6226 3960 2311 3805 5272 * * 5884 14
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+
+H 15 4177 4273 5931 4227 5636 * 3593 * 3775 4124 4188 4693 6431 5029 4024 1608 * * 6199 4299 15
+ 0 * * * * * * 7597 0 0
+
+Y 16 * * * 6224 2996 6484 4943 2464 3385 2760 4274 * * 4707 4103 5192 4125 3075 * 4594 16
+ 13 * 6760 * * * * 7597 0 0
+
+E 17 4267 3336 2920 1796 * 6415 5422 5055 5668 6238 * * 5447 6002 5487 3337 3367 4487 6221 5950 17
+ 52 4826 * 3168 170 * 0 7591 1360 1000
+
+C 18 4293 6583 * * 1670 * * 2598 * 2109 4849 * * * * 6021 6597 2712 * 6144 18
+ 14 6699 * 1000 1000 * 0 7467 1000 1420
+
+S 19 5586 5957 4375 3517 5166 * * 4469 3731 5376 6205 4149 5195 4739 5075 3321 2092 4729 5337 3415 19
+ 337 2263 * 767 1278 2909 206 7468 2254 1496
+
+S 20 4178 6670 2707 2307 6391 3096 5225 6369 5202 * * 3401 4683 5279 3794 3142 4639 * * * 20
+ 112 3747 * 954 1048 1929 439 7445 1412 1516
+
+D 21 4886 * 1532 3573 6413 4358 5736 4941 5409 6325 * 3213 5115 * * 2993 3688 * * 4365 21
+ 47 4951 * 1000 1000 * 0 7485 1118 1360
+
+H 22 4502 2262 6290 5394 6214 * 6613 3216 5471 4387 5970 4854 * 3231 5083 5107 4520 2067 * 6447 22
+ 0 * * * * * 0 7485 0 1360
+
+S 23 2946 * 3302 3758 * 4225 5523 * 4630 5607 6248 4584 2124 * 3400 2834 5582 * * 5748 23
+ 0 * * * * * 0 7485 0 1360
+
+N 24 * 6474 2047 5360 6689 5599 * 5035 5390 6240 4712 2282 3923 5026 5185 2559 3732 * 6406 * 24
+ 42 5133 * 3000 193 * 0 7615 1093 1360
+
+L 25 4524 * 4960 * 3775 * * 3652 * 930 * 5528 * 6240 * 4924 5257 3038 * 5000 25
+ 0 * * * * * 0 7615 0 1360
+
+Q 26 4544 6261 4480 4122 5399 4014 4980 * 3733 6375 5545 3565 3301 2764 4995 3258 2991 * 6540 6606 26
+ 121 3635 * 3079 182 * 0 7615 1466 1360
+
+P 27 3558 * 2485 4172 6710 4127 4551 * 5442 4470 5326 5138 3422 4071 4885 2718 3836 * 5313 5939 27
+ 131 3897 5655 835 1187 * 0 7641 1420 1360
+
+Y 28 4160 * 4928 4718 3845 2807 5632 5434 3988 2782 6313 3799 6350 4958 3729 4264 6511 4117 5031 4221 28
+ 1799 512 6485 793 1242 2915 205 7633 4959 1533
+
+F 29 5246 6524 5223 4988 1764 5394 5440 5324 * 4050 5330 1698 5457 5158 6579 * 6165 5420 5443 5418 29
+ 226 2784 * 557 1643 2069 393 7541 1994 1671
+
+S 30 6456 * 1412 * 5251 6197 5520 6442 6158 6500 * 1823 4238 5068 * 3174 * 4707 * * 30
+ 111 5338 4342 0 * 2481 285 7555 1074 1618
+
+R 31 * 6627 2479 3388 * 3785 6429 * 2187 * * 5035 6264 4578 2370 4272 4148 * 6402 6331 31
+ 123 3615 * 0 * 1259 781 7472 1521 1893
+
+C 32 2820 3835 * * 4138 * * 1661 5701 4788 4814 * * 6367 * * 4231 2022 * 6298 32
+ 162 3818 4814 1861 464 * 0 7560 1952 1495
+
+N 33 3348 5835 * 5127 6603 4532 4496 6202 6840 6449 * 3855 * 4866 4138 1002 4354 * * 6014 33
+ 0 * * * * 1593 581 7528 0 1772
+
+S 34 * * * * * * * * 5378 * * * 5993 5795 5261 126 * * * * 34
+ 20 * 6179 * * * 0 7791 0 1495
+
+I 35 3076 4257 * * 3562 6280 * 1610 * 3055 4008 * * * * 4557 * 2696 * 5353 35
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+
+R 36 5155 6216 5207 5448 * * 4517 4813 2052 4236 * 4610 * 3890 1855 4291 5285 5662 6381 4583 36
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+
+V 37 * * * 6989 * * 6309 2389 * 3992 5911 6305 * * * 5956 5824 594 * * 37
+ 24 5911 * 825 1199 695 1388 7900 1180 1071
+
+D 38 6697 * 5266 4219 4765 4653 5622 3907 4696 3364 3845 5690 2656 4252 3811 5642 3316 3257 * 6052 38
+ 49 4913 * 328 2298 0 * 7775 1243 1000
+
+S 39 3559 6360 4469 4245 6512 2566 4493 * 4389 5574 * 4927 3490 5738 3326 2140 5542 5416 * * 39
+ 44 5063 * 2743 233 * * 7778 1128 0
+
+G 40 4197 * 4876 5359 * 667 * * 4673 6176 * 6266 5141 3859 6072 5363 * 5556 * 4905 40
+ 66 5517 5431 3192 167 * * 7778 1440 0
+
+C 41 3981 2857 * 4611 6316 * 5772 3346 6258 3457 4125 7010 3654 5290 5105 4117 3923 3111 4490 4591 41
+ 145 * 3384 0 * 2181 359 7907 1000 1189
+
+W 42 5900 * 5108 5081 4935 6097 6144 4740 5777 4563 * * 6177 6374 6329 6019 5414 3651 777 5336 42
+ 515 1812 6023 182 3077 296 2430 7601 2840 2035
+
+M 43 5769 3809 5523 3853 * * * 2299 6856 2927 5747 * * 7006 4498 4860 4167 1791 * 5246 43
+ 104 3846 * 181 3083 * 0 8095 1556 1264
+
+I 44 2391 6372 * * 2587 4442 * 3804 * 1808 4547 * * * * 5510 6366 2730 * * 44
+ 0 * * * * * 0 8097 0 1264
+
+Y 45 * 3800 * * 2276 * 4976 6354 * * * * * * * 5769 * * 6329 628 45
+ 0 * * * * * 0 8095 0 1264
+
+E 46 5437 * 4127 1292 * 6303 6965 5925 4130 6646 5154 5845 4648 3390 5906 3820 3453 6480 * 4785 46
+ 0 * * * * * 0 8095 0 1264
+
+Q 47 6403 5606 2133 2975 * 4133 2220 * 4120 5546 6720 3981 * 3286 6303 6547 6382 * * 4287 47
+ 5 * 8207 * * * 0 8095 0 1264
+
+P 48 3353 5990 3242 4212 5838 4262 * 3727 3746 4922 6631 4544 2568 6212 6773 3253 4206 4373 * 5467 48
+ 0 * * * * * 0 8090 0 1400
+
+N 49 4718 6755 2419 5521 4021 3435 4666 * 4950 * * 1368 * 5431 5469 4632 * 6353 6302 5659 49
+ 0 * * * * * 0 8090 0 1400
+
+F 50 6302 6936 * * 1130 5253 6803 * * 5657 6257 * * 6484 4314 6849 * * * 1380 50
+ 17 8464 6849 3807 107 * 0 8090 1021 1400
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+ 20 6173 * 2000 415 2562 268 8064 1029 1699
+
+G 52 5170 * 5076 6437 * 261 5597 * * * * * 6378 6355 * 6173 5411 * * 6131 52
+ 23 5997 * 1585 585 * 0 8067 1024 1570
+
+P 53 3410 * 3463 3330 6853 4519 4668 6516 4097 4967 5997 4572 3941 3838 2562 4550 4120 5057 * 5037 53
+ 79 4382 7525 2239 343 * 0 8067 1342 1570
+
+Q 54 4484 3480 6169 5743 3881 5464 6527 7234 3871 5423 4630 5687 5612 2193 4221 2594 4789 5498 * 4131 54
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+
+Y 55 4844 5297 * 5679 4125 * 5091 3371 4430 3250 5742 * * 4691 4684 5261 3236 3344 3984 2356 55
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+F 56 4988 3938 5384 5200 4738 * 5300 3452 4669 3425 5648 * 6536 5288 3850 4259 3148 2576 5063 3697 56
+ 109 4983 4611 3185 168 * 0 8076 1297 1640
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+L 57 5766 * 6326 6224 3402 * 6690 3828 5689 784 4897 * * * 5064 * * 3668 6016 5418 57
+ 41 * 5150 * * 3853 103 7894 0 2271
+
+R 58 5074 * 4633 1844 5223 3191 5861 5413 3547 * * 4262 4176 6015 4052 3600 4799 6110 5739 4202 58
+ 105 5652 4322 2068 393 3013 191 7863 1092 2349
+
+R 59 3458 5789 4729 2495 * 3698 6506 5581 3621 * 5663 5867 2180 * 3866 3429 5215 5370 6012 * 59
+ 239 2874 5945 2064 394 2505 280 7854 1873 2506
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+//
+�HHsearch 1.5
+NAME 4939a1cdd4b26c7d9053b02c16db7e41
+FAM
+FILE 4939a1cdd4b26c7d9053b02c16db7e41
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:30:19 2013
+LENG 90 match states, 90 columns in multiple alignment
+FILT 165 out of 1035 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCEEEEEEEECCCCCCCCCCCCEEEECCCCEEEEEECHHHHHHHC
+>ss_conf PSIPRED confidence values
+988999999999839899999999999999999999769969976874899987357324389998789965976089988889999649
+>Consensus
+mxkxelxxxiaxxxxxsxxxxxxvlxxxxxxixxxLxxgxxVxlxxxGxFxxxxxxxrxxxnpxtxexixixxxxxvxFxpskxlkxxvn
+>4939a1cdd4b26c7d9053b02c16db7e41
+MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFVSGKALKDAVK
+>gi|257470064|ref|ZP_05634156.1| hypothetical protein FulcA4_12035 [Fusobacterium ulcerans ATCC 49185]gi|317064288|ref|ZP_07928773.1| predicted protein [Fusobacterium ulcerans ATCC 49185]gi|313689964|gb|EFS26799.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
+MTETEFIRFYKKKIKlRNVKEVQERIDTFWKTIFKALEIDGKVTFKDWGVFEKRKHGARRYILASLGIDNMTENKEVIKFRAGKGFENKIN
+>gi|189465367|ref|ZP_03014152.1| hypothetical protein BACINT_01716 [Bacteroides intestinalis DSM 17393]gi|189437641|gb|EDV06626.1| hypothetical protein BACINT_01716 [Bacteroides intestinalis DSM 17393]
+-ERKEFLNRVHLFTGISRSLLEGAMASFMDELRDCLADGWTVEFGELGYFTPSLNCRREVMEKKelRAASVTLRG---LNFRLGKEFYKEL-
+>gi|157325091|ref|YP_001468516.1| gp136 [Listeria phage A511]gi|66732779|gb|AAY53370.1| gp67 [Listeria phage P100]gi|66733099|gb|AAY52917.1| gp136 [Listeria phage A511]
+-NRTDIAREVAQRTGFYIKDVEQILAERDTVIIDALQGGVtKIKEHKLYQIEVETKPaKKNAWNGLDKVYFSIPEKKIIKFKPLVAVEEVI-
+>gi|261881157|ref|ZP_06007584.1| conserved hypothetical protein [Prevotella bergensis DSM 17361]gi|270332024|gb|EFA42810.1| conserved hypothetical protein [Prevotella bergensis DSM 17361]
+LSPRELEEKISHNCTLTASDIRSVLAALNHVMTTELSAGRRLHLSSIGYFSLKVRSIKlEDRKKMRGNHLYA---SGILFRPEASVMSDM-
+>gi|232236|sp|Q01239.1|HCC1_CRYCO RecName: Full=Major basic nuclear protein 1; AltName: Full=Protein p14 alpha/beta chaingi|17961|emb|CAA41349.1| p14 (alpha and beta) [Crypthecodinium cohnii]
+MTKTGLAEAWRRRPSFLRRTAGQSWRAWPRSCAAEVKKTGKLTIPGLVMVKTRKKPATKaGKREMFGKVVLVkaSCQDVVKAYPVKALKT---
+>gi|194337423|ref|YP_002019217.1| Sporulation domain-containing protein [Pelodictyon phaeoclathratiforme BU-1]gi|194309900|gb|ACF44600.1| Sporulation domain protein [Pelodictyon phaeoclathratiforme BU-1]
+MTNHDCVGELAGLLDVERQVASSFLIDFSSAMVAELLAVRKLSLKGLGSFTVTHHPAE--KKNTASAIIYTPPSDRLTFSRQLSGAD---
+>gi|12045213|ref|NP_073024.1| DNA-binding protein HU, [Mycoplasma genitalium G37]gi|255660275|ref|ZP_05405684.1| DNA-binding protein HU, putative [Mycoplasma genitalium G37]gi|1351556|sp|P47595.1|Y353_MYCGE RecName: Full=Uncharacterized protein MG353gi|3844937|gb|AAC71578.1| DNA-binding protein HU, putative [Mycoplasma genitalium G37]gi|166078767|gb|ABY79385.1| DNA-binding protein HU, putative [synthetic Mycoplasma genitalium JCVI-1.0]
+-SRSEINKIIAVATGIKEKKIKEIFKYLNTLLLNELVSRSVCILpENLGKLRITIRNARYQKDMQTGEIRHIPPKPLVRYSPSKTIKET--
+>gi|288802083|ref|ZP_06407524.1| putative non-specific DNA binding protein [Prevotella melaninogenica D18]gi|288335518|gb|EFC73952.1| putative non-specific DNA binding protein [Prevotella melaninogenica D18]
+MSLAQIVKRVEKRSTVSSADVKAVLDALQYEVMEALENGNTVRLGDLGSFRLTMKSqGAPTAAEAKKKGAQLIKQVNVQFTKSTTMRDTL-
+>gi|298373791|ref|ZP_06983780.1| conserved hypothetical protein [Bacteroidetes oral taxon 274 str. F0058]gi|298274843|gb|EFI16395.1| conserved hypothetical protein [Bacteroidetes oral taxon 274 str. F0058]
+VTKQDIISNLSQKLDMPEEQVGIFISKLNDLLLKNLPTNKEITIDGVGTFSLVWSTYHKNTKLKDGEPREF---YKLKFEPAESLKSTVN
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 6440 * * * 4927 * * 4538 6627 3043 746 * 6137 5530 6431 * 6289 3003 * * 1
+ 0 * * 2000 415 * * 7639 1000 0
+
+N 2 5220 * 3424 6928 * 4914 6737 6664 3613 6187 * 2191 * * 5967 2988 1497 6838 * * 2
+ 12 6896 * 0 * * * 8064 1012 0
+
+K 3 4407 * 6307 4707 4396 * 7040 5376 1261 3903 6093 5179 6724 5576 2711 5785 3942 5489 * 7008 3
+ 10 * 7118 * * * * 8163 0 0
+
+T 4 3647 * 3150 2736 * 6946 6563 4661 2114 5750 * 4818 5916 3849 4300 3083 4809 5391 * * 4
+ 0 * * * * 0 * 8272 0 1000
+
+Q 5 4503 * 2279 1380 7344 5249 5179 6270 4087 * 6040 7599 * 3696 4206 4974 5173 * 6340 6587 5
+ 10 7154 * 2000 415 * * 8266 1000 0
+
+L 6 6169 7047 * * 2593 * * 2184 7303 1172 3925 * * * * 7334 * 3825 * * 6
+ 0 * * * * * * 8322 0 0
+
+I 7 2067 4184 * 5207 6495 * * 1778 7288 3625 5850 6167 * * 7495 5194 4393 2495 * * 7
+ 15 7347 7881 2000 415 * * 8328 1001 0
+
+D 8 3733 * 3285 2048 * 7417 5036 6156 2483 6937 6243 4738 * 4573 2918 3970 4796 6297 * 7527 8
+ 0 * * 0 * 0 * 8328 1000 1000
+
+V 9 3729 * 4583 2775 6603 6354 4879 3974 3669 3225 5349 5543 * 4016 2493 4887 4492 5728 * 4365 9
+ 9 7338 * 2585 263 * * 8328 1021 0
+
+I 10 4315 * * * 6182 * 7338 1582 6937 1945 4990 * * * * * 5804 2210 * 3998 10
+ 19 7314 7176 0 * * * 8328 1012 0
+
+A 11 1293 * * 3665 5766 7310 6502 7270 4176 6313 6311 7677 7343 4862 5276 2160 4345 5308 7284 6101 11
+ 0 * * * * 0 * 8315 0 1016
+
+E 12 3952 * 5142 2123 * 5702 4860 5876 2800 5395 6494 4134 7736 3323 3096 3534 4724 6165 * 6400 12
+ 106 3937 7452 1657 550 * * 8328 1824 0
+
+K 13 4065 7569 6510 3119 5573 5062 4502 4168 2858 4794 5501 3471 7441 4181 2246 4353 6175 6107 * 5439 13
+ 27 5758 * 0 * * 0 8328 1254 1000
+
+A 14 4417 4279 * * * 4889 4483 6187 6186 2940 4909 4244 6250 4801 5293 2258 1992 5177 * 5901 14
+ 28 6133 7725 321 2327 * 0 8348 1191 1000
+
+E 15 4588 6977 4135 4042 7159 1594 5366 * 4102 * * 3579 5420 5583 5490 2781 3102 * * * 15
+ 80 4213 * 1162 855 1087 918 8353 1741 1059
+
+L 16 5224 5730 * 7228 3121 6767 6868 2834 4785 1733 4074 7018 6097 7268 * 5674 4542 2775 * 4611 16
+ 34 5433 * 0 * 0 * 8348 1349 1000
+
+S 17 5904 * 4377 4539 6293 4856 4598 * 4424 6480 * 4562 3403 * 5997 1674 1920 * * 6004 17
+ 10 7229 * 2000 415 * * 8346 1000 0
+
+K 18 4907 * * 2583 * 6376 5984 4432 2035 4920 * 4855 4407 3446 2754 4089 6376 4775 7379 6221 18
+ 0 * * * * * * 8346 0 0
+
+T 19 2663 * 5168 3299 6013 2576 6339 6738 2097 7507 7293 5250 5732 5333 5414 3806 4706 4254 * 7236 19
+ 7 7737 * 1000 1000 * * 8346 1000 0
+
+Q 20 4308 7585 1704 2607 7492 6038 5843 5134 4126 5801 5243 5370 * 3130 5289 5807 4256 3819 * * 20
+ 0 * * * * * * 8346 0 0
+
+A 21 1719 4817 * * * * * 2532 * 3940 * * * * * 4634 3682 1746 7288 * 21
+ 0 * * * * * * 8346 0 0
+
+K 22 4315 * 4943 2528 7172 4757 6335 4875 2465 3748 7490 5179 6954 5019 2882 3805 4403 4595 * 5061 22
+ 0 * * * * * * 8346 0 0
+
+A 23 2796 7379 4522 2735 7227 3278 4856 5464 3204 5133 5157 4364 5866 3856 3854 4006 5035 5546 * 7337 23
+ 0 * * * * * * 8346 0 0
+
+A 24 3077 5328 5691 7169 3524 * 6756 2728 6138 3166 6861 7551 * 6911 7231 5433 5158 1498 5903 7224 24
+ 0 * * * * * * 8346 0 0
+
+L 25 5431 * * * 3441 6768 * 2594 * 1447 4536 * * * * * 6653 1909 6480 6319 25
+ 12 6954 * 2807 222 * * 8346 1027 0
+
+E 26 3993 7518 1868 2608 * 4981 5855 4864 3426 7024 5381 3837 * 4360 4003 5731 3658 * * 7235 26
+ 0 * * * * * * 8346 0 0
+
+S 27 2150 7261 3693 2995 * 3460 5763 5116 7148 3990 5044 4570 * 5770 4522 3581 3598 4348 * 7013 27
+ 0 * * * * * * 8346 0 0
+
+T 28 4625 * * * 1945 * * 2906 * 1567 4311 * * * 6511 * 5711 2927 * 5880 28
+ 0 * * * * * * 8346 0 0
+
+L 29 3898 7028 5716 4125 2786 4592 * 3763 6285 2654 4182 5157 7283 4847 4632 5036 3875 3070 5583 6172 29
+ 0 * * * * * * 8346 0 0
+
+A 30 3793 * 2180 2205 7187 4160 4878 * 3550 5734 * 4076 * 5055 4828 3722 4168 7164 * 5248 30
+ 12 6954 * 1585 585 * * 8346 1027 0
+
+A 31 3181 6299 7416 2867 5016 4257 * 3829 4700 2953 5409 6627 * 7547 6687 4006 3812 2522 7132 4336 31
+ 0 * * * * * * 8346 0 0
+
+I 32 5755 * * * 5420 * * 1390 * 2048 2808 * * * 6738 7132 5647 2684 * * 32
+ 0 * * * * * * 8346 0 0
+
+T 33 2948 6759 6970 3743 7231 4084 * 3611 2637 3920 6213 5979 6213 4782 4121 3416 4358 3254 * 5622 33
+ 0 * * * * * * 8346 0 0
+
+E 34 3369 7181 2486 1974 6970 6327 5462 7718 3508 6675 6756 3967 * 4167 3752 3934 4769 * * 6326 34
+ 7 * 7604 * * * * 8346 0 0
+
+S 35 2141 4738 6242 2832 * 4441 4030 6908 5767 3868 6454 5160 * 4081 5678 3995 3847 3781 * 4137 35
+ 0 * * * * 0 * 8346 0 1000
+
+L 36 5946 * * * 4726 * * 3320 * 509 4310 * * 7465 * * 8287 3575 * * 36
+ 9 7333 * 0 * * * 8346 1002 0
+
+K 37 2795 5936 4261 3405 * 3752 6239 4735 3045 3137 5732 6148 6363 4345 5060 2989 6437 4053 * 6473 37
+ 9 7283 * 1585 585 * * 8346 1001 0
+
+E 38 3678 * 2628 2671 * 5808 6187 6365 3118 4960 5255 3415 * 4291 3622 3707 3802 * * 6431 38
+ 48 5571 6421 2064 394 * * 8346 1218 0
+
+G 39 4873 7005 4345 3798 * 733 5204 * 4880 * * 3937 * 7394 4779 5218 5229 * * 6246 39
+ 17 7591 7318 1400 687 1615 570 8313 1170 1248
+
+D 40 6483 7152 4007 2202 7243 3182 4081 * 2836 * * 3130 6359 4804 3302 5235 6950 5247 * 4017 40
+ 47 4968 * 793 1242 914 1091 8332 1416 1229
+
+A 41 5546 7172 4675 2960 7003 5395 5710 3415 3152 * * 4038 6559 5760 2574 2297 4177 5560 * 6759 41
+ 9 7282 * 1000 1000 * 0 8330 1006 1061
+
+V 42 7316 6150 * * 4028 * * 2597 * 3150 * * * * * * 6635 666 * * 42
+ 0 * * * * 0 * 8330 0 1061
+
+Q 43 5218 5552 4166 2991 6444 6399 4129 4954 2873 5823 7276 3936 * 4694 2785 3664 3109 4891 * 5686 43
+ 17 6432 * 1297 754 * * 8346 1080 0
+
+L 44 * 6670 * 6507 3340 * * 1805 * 1073 7044 * * * * * * 3169 * * 44
+ 20 6176 * 0 * 0 * 8343 1184 1000
+
+V 45 5643 * 3969 4082 6173 2365 4768 * 3362 6063 6044 4705 2613 4726 3185 4327 4436 4667 * * 45
+ 0 * * * * 0 * 8344 0 1000
+
+G 46 7337 7325 2643 3497 * 1212 * 6751 4091 6461 * 2951 6296 6379 5418 4852 6971 * * 6986 46
+ 0 * * * * * * 8346 0 0
+
+F 47 * * * * 1258 * * 3154 7014 1626 5787 * 6751 * 7160 * * 3816 5323 7058 47
+ 0 * * * * * * 8346 0 0
+
+G 48 4818 5929 * * 5053 199 * 6876 6738 7566 7316 7283 * * * * * * * 6511 48
+ 0 * * * * * * 8346 0 0
+
+T 49 4810 * 7264 * 7415 5798 5323 4213 3104 4360 6907 5692 * 5148 3919 2873 1663 4163 7098 4243 49
+ 0 * * * * * * 8346 0 0
+
+F 50 * 6751 * * 484 * * 4046 * 2680 7277 * * * * * * 5370 5747 6676 50
+ 14 * 6732 * * * * 8346 0 0
+
+K 51 7537 6306 6319 2827 6612 5431 5801 4084 3041 5970 8027 6312 * 4219 2845 2368 3214 5632 6306 4750 51
+ 8 7496 * 1000 1000 0 * 8313 1000 1036
+
+V 52 4714 7820 * * 7175 6346 7891 2782 4971 2412 4360 7368 3260 7328 5558 4954 3522 1983 * 6644 52
+ 7 * 7695 * * * * 8327 0 0
+
+N 53 3747 6060 7175 4706 7334 4477 5041 4725 2317 5554 * 5353 * 5925 3132 2781 3744 3000 7268 5844 53
+ 63 4540 * 1714 525 * 0 8327 1526 1000
+
+H 54 3496 * 4184 3109 3997 6227 4153 3668 3862 2973 6132 7318 5249 5480 5415 5140 3513 3575 7157 4887 54
+ 27 7558 6241 1585 585 0 * 8327 1000 1000
+
+R 55 5393 7249 * 4675 6988 3625 6321 6550 2163 5611 7305 5313 6151 4100 2223 4428 3143 3703 * 5635 55
+ 98 6344 4228 1034 967 * 0 8311 1094 1106
+
+A 56 3095 5637 4799 4611 7139 4705 6016 6886 2164 5154 * 4814 3063 6836 4150 2657 4117 5854 * 6408 56
+ 120 4504 4802 203 2926 436 1938 8246 1476 1920
+
+E 57 2285 7446 5865 2627 6968 3609 * 6437 3639 5336 * 7669 2759 6233 4128 3277 5127 4942 * 5954 57
+ 91 5221 4866 1275 769 991 1009 8310 1253 1686
+
+R 58 5585 5739 5511 4502 6608 4180 5079 * 2160 7447 * 6151 7044 5067 1256 4210 5255 * 6554 6843 58
+ 189 4414 3725 187 3040 2071 392 8275 1572 1758
+
+T 59 5063 * 7141 3348 4684 5492 6990 4426 2646 4170 4272 4637 3940 4345 3970 4283 3255 3464 * 5874 59
+ 24 5949 * 0 * 649 1464 8154 1142 2507
+
+G 60 2892 * 5751 4517 6832 1716 7040 4032 6979 5865 5474 5137 6947 5439 4750 4128 4468 2838 * 4856 60
+ 20 * 6208 0 * 900 1108 8210 1061 1666
+
+R 61 4320 7137 5056 4310 5457 6926 5058 3925 3487 4844 5508 7294 5483 6244 1873 4782 3254 3583 6478 4693 61
+ 222 4705 3259 700 1379 * 0 8288 1429 1445
+
+N 62 5029 * 2819 4718 6773 6544 4679 6657 4658 6433 * 927 7040 6078 5509 4313 4839 6147 * * 62
+ 41 6067 6252 2224 347 3774 110 8192 1193 2757
+
+P 63 4966 * 6653 3224 4816 5192 7320 4276 4307 4210 6050 7107 1014 * 4780 6517 4854 5718 * 7114 63
+ 74 4331 * 1000 1000 1084 921 8200 1525 2769
+
+Q 64 4279 7290 4487 3572 4195 4144 6161 6418 2250 3995 6083 5820 7085 3719 2895 4115 4735 4105 * * 64
+ 129 3545 * 881 1129 1018 982 8250 2131 1944
+
+T 65 4497 5998 3453 5983 6231 5840 7242 7126 3561 5915 * 4105 6705 7324 4384 4640 946 7349 * * 65
+ 47 5571 6482 707 1369 692 1393 8272 1196 1591
+
+G 66 3070 * 7191 4034 6745 1213 7016 6252 2862 6299 6388 4979 5657 5720 4326 4784 6178 5726 * * 66
+ 39 5611 7305 1000 1000 1463 650 8323 1193 1323
+
+K 67 4527 * 5742 1348 7222 4074 5247 7465 2548 * 7267 6558 7233 3758 4612 4935 4231 4277 * * 67
+ 24 6755 7116 606 1544 * 0 8312 1046 1261
+
+E 68 5398 7033 4286 3039 6997 7128 7014 5270 3465 4931 4273 4542 3528 5854 3503 3002 2899 4365 5773 6464 68
+ 50 6129 5673 0 * * 0 8304 1116 1358
+
+I 69 5627 5614 * 5871 3660 * 7234 1950 4914 3547 3279 6876 * 6957 5087 5469 4782 2050 6728 5639 69
+ 20 6192 * 507 1754 1254 784 8292 1106 1610
+
+K 70 4917 7303 4506 3502 4967 6740 4790 4224 2777 5207 4729 4907 6319 3935 4003 4256 2818 3878 6897 4554 70
+ 172 5602 3447 1742 513 1464 649 8310 1234 1402
+
+I 71 4568 7365 * 6910 3789 * * 1540 4533 2962 4958 6896 5957 5895 6640 4595 4826 2466 * 6096 71
+ 200 4834 3402 1585 585 3274 157 8201 1361 2410
+
+A 72 4274 * 5438 3641 6873 6293 * 5687 2816 7293 * 4239 1250 4825 4999 4238 5753 5644 6779 6020 72
+ 130 4286 4830 1000 1000 * 0 8059 1460 3368
+
+A 73 1745 6714 5570 2840 6478 3647 * * 3944 * * 4675 2363 * 5641 3821 4288 * * * 73
+ 93 5585 4596 1242 793 737 1322 8013 1275 3674
+
+A 74 4399 7037 7111 5442 5441 4219 3151 5756 1853 5944 * 5183 * 5966 2195 4095 4394 5004 * 6088 74
+ 35 * 5389 * * 502 1768 8191 0 2509
+
+N 75 3498 6968 4269 7158 * 6199 5162 6798 1881 4187 7143 3996 4244 5064 3173 5028 3770 4476 7479 4328 75
+ 0 * * * * 2234 345 8261 0 1675
+
+V 76 5426 * 5109 6587 * 4006 5100 3676 2527 5142 7177 4363 * 6427 2759 4296 3354 2401 * 6270 76
+ 8 7451 * 1000 1000 0 * 8289 1000 1518
+
+P 77 5837 6961 * * 5378 * 6871 2039 * 3514 5503 * 3245 * * * 7195 1069 * * 77
+ 0 * * * * * * 8334 0 0
+
+A 78 4961 6664 7227 7285 7536 5859 4362 5116 1662 4277 7215 3643 * 5776 2706 4671 4335 3417 * 4776 78
+ 0 * * * * * * 8334 0 0
+
+F 79 5462 * * * 359 * * * * 3915 7078 * * * * * 6846 4385 5441 4489 79
+ 0 * * * * * * 8334 0 0
+
+V 80 6210 7211 * 5984 6321 * 5740 5203 1575 5938 * 6368 * 5136 2020 4286 2749 4751 * 5095 80
+ 0 * * * * * * 8332 0 0
+
+S 81 2398 5901 * * 4570 * 7476 4183 7142 6145 6377 * 1013 6203 * 4610 5039 4015 6039 * 81
+ 0 * * * * * * 8332 0 0
+
+G 82 3645 6208 3896 4617 * 2564 * * 5093 4637 * 5099 6328 * 4817 1246 5150 5666 * 6235 82
+ 15 * 6618 * * * * 8319 0 0
+
+K 83 3709 * 5737 4228 7130 5093 * 7232 1205 6738 5868 5353 3874 5080 3900 3421 5189 5102 * 6823 83
+ 0 * * * * 0 * 8272 0 1056
+
+A 84 3338 * 4500 2525 * 4507 5989 5721 2992 5087 4951 4788 6026 4359 4620 2943 3694 4020 * 7144 84
+ 0 * * * * * * 8312 0 0
+
+L 85 6309 * * * 2806 * * 3317 7162 927 4615 * * * 5772 * * 3134 5880 5567 85
+ 8 7455 * 2000 415 * * 8312 1000 0
+
+K 86 4840 * 7093 5190 5603 6590 * 4675 1218 3937 6990 7163 6888 5680 2264 4899 4609 4921 * 7265 86
+ 0 * * * * * * 8267 0 0
+
+D 87 4161 * 2566 2406 * 4697 6868 7327 2461 5170 * 4201 7168 4216 3096 4943 4995 6055 * 6282 87
+ 38 5256 * 3062 184 * * 8266 1377 0
+
+A 88 1959 * 7209 3738 4915 5429 6143 5571 2873 3329 3807 6790 6781 4810 3605 5149 4106 4929 * 7173 88
+ 32 6178 6990 0 * * * 8167 1061 0
+
+V 89 4951 5823 * * 6715 * * 2088 6367 1939 3714 * * * 6486 6666 5100 1709 * * 89
+ 99 3920 * 0 * 0 * 7836 1202 1000
+
+K 90 3506 * 3751 3742 * 5776 * * 3180 * * 987 * 4321 * 4488 4831 * * * 90
+ 0 * * 0 * * * 6868 0 0
+
+//
+�HHsearch 1.5
+NAME 497673b84b7766fe2450fe095360affb
+FAM
+FILE 497673b84b7766fe2450fe095360affb
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:23:20 2013
+LENG 182 match states, 182 columns in multiple alignment
+FILT 149 out of 540 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHHHHHHHHHHHHHHHHHCCCCHHHCCEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCEEEEEEEEECHHHH
+HHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECHHHHHCCCCCCCCCCCCCCCCEEEEEEEECCHHHHHHHHHHCCCCCCC
+>ss_conf PSIPRED confidence values
+9974689999999989999997488981226657899999568413314689999999999987998376652555533354799888899999458699
+9999999986443302455774446898678751078764846110456895565499996009889999999984993359
+>Consensus
+xxxxxxlxxxYxxxvxxxLxxkxxxxnxxxiPkixKIvinxxxxxxxxdxxxlxxaxxxLxxItGQkpxxtxakksiaxfkiRkgxxiGxkvTLRgxxmy
+xFLxklixxvlPrirdfxgixxxsfdxxGnxsfGixxxxxFPEixxdxxxxxxGxxItivtxaxxxxeaxxLlsxxgxPfxx
+>497673b84b7766fe2450fe095360affb
+MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMW
+IFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK
+>gi|74325185|ref|YP_316605.1| ribosomal protein L5 [Thalassiosira pseudonana]gi|74100251|gb|AAZ99412.1| ribosomal protein L5 [Thalassiosira pseudonana]
+-----FFNSYLNNVVKHDLINKFFYTNLKQIPKLETIVLNFGYQ--NSNFKHLISGLLALELLSSKKSRLTRSKHLNVFLKIKKGNPVGCKIVLKKTTMH
+VFYLKLITSVFPKIKHNKTAQS-QQNVKsvKSISIIIKNPLLFLELEsqYQFFKDIPKLDITILTDSKSQNEIFFLLKSVKFFI--
+>gi|300706059|ref|XP_002995340.1| hypothetical protein NCER_101808 [Nosema ceranae BRL01]gi|239604376|gb|EEQ81669.1| hypothetical protein NCER_101808 [Nosema ceranae BRL01]
+-------------------------KiNPMREIKIKKLSIVINVGgGSSN---KLNNAAKVLKQLTDQDCLFSKARYTLRNFGIRRNEKISVHVNISGEK
+AMEVLKKAL-----KVREYE-LSKSCFNATGCFGLGINEHIDL-GMKYDPDIGIFGMNFYVDLK--------------------
+>gi|15150728|ref|NP_150394.1| ribosomal protein L5 [Pylaiella littoralis]gi|15147734|emb|CAC50835.1| ribosomal protein L5 [Pylaiella littoralis]
+------LKNHYHDVIQKDLILSENTSTVAMLPALKKIDLA--LGGSHSDENFVIASLGSLNILTGQKPYLTQQKPV---GQKSSChkEAVGGKLTLRGSS
+MFNFLHKLLFGVFPHMRQFEGLRAPL--HKDLYCFVIKDIFSFQELVplFIYFESVGSLQCQFYFTTKSESEVVVLGNSLQL----
+>gi|321268737|gb|ADW79186.1| ribosomal protein L5 [Cyanophora paradoxa]
+-----RLQYHINHIVNYELISRLNINNIYKIPKKESIIIQSSQKKLVHDQTLLYPLYGCFELMSFQRPVFSISKNAISAYQLRKKQVLGCKTTLRNKYAL
+IFLDKLIYLYFPKVKALNLYKYKLNQNNINFAFGLNSIIPFEDIEnqYSKIDMNFGINVFINfvKYQNiNNQNILLYLSSIQFPIA-
+>gi|30351950|emb|CAD62688.1| mitochondrial ribosomal protein L5 [Zea mays]gi|194703766|gb|ACF85967.1| unknown [Zea mays]gi|195635755|gb|ACG37346.1| mitochondrial 60S ribosomal protein L5 [Zea mays]
+--MMLPLHIHYEDVLRQDLLLKQNHANIMQVPGLFEVKL---APKAGSDL-KIPIGKMAMEVLSGQRFKeakidpFAKARKSSRTnpfIGADKdGStVFA
+QPTVLRGHAMYNFLVRMLTVMsmLNSRADIRENT-------VKFFMETEFCEFSPELEdhFEIFEHIRGFNVTIVTSANTKDETSLLWSGFM-----
+>gi|110225686|ref|YP_665691.1| ribosomal protein L5 [Mesostigma viride]gi|17222557|gb|AAL36730.1|AF353999_10 ribosomal protein L5 [Mesostigma viride]
+---------------------KQNSKNIERNSSLEKLIIRFPFNTMKSER-DFLLHWTALGIISGQKPKIVFSTTADAKEKIKKGDPLFCFVTLRNSKMI
+EFLNKFYHAVFPILN-MEKNSFRFFKEETKqffgYSFFWEQGLLFPELEdrFELFKSSFEFQLFVKAEKKNN--SDIFLTALNIPL--
+>gi|323398663|ref|YP_004222738.1| ribosomal protein L5 [Glaucocystis nostochinearum]gi|321401356|gb|ADW83110.1| ribosomal protein L5 [Glaucocystis nostochinearum]
+-------KEYNDNVLKYDFSLRYFCPNNYYSLRIKKINIQILLSEILINENLFFFIISILKIISYQHSLPIFSKKAIANFSLKKHMIIGAIVCLRKLSLL
+CFISKFQNLLnqnLDLSKNYT-YK-EAENNLLNITIGLKNISVFPEIEsqFSKISRKIGADIMFTF---------------------
+>gi|49147184|ref|YP_025777.1| ribosomal protein L5 [Pseudendoclonium akinetum]gi|33439199|gb|AAQ18736.1| ribosomal protein L5 [Pseudendoclonium akinetum]
+----------------------------LNSYGLEKIILHSSSGKLLQAPSSSTTIDLAFSTVGCQTPTKVYSRRSIAGFKLSKSALLGAKATLRNLAKY
+DFFYKFYFLGagetnvtaMtrqSRITlgeqklaaPY-GLQ--SIQQQPNlstTSLAVKNVFLFNELDsldYDVFSNMAGFEIVFI---------------
+-------
+>gi|200004035|ref|YP_002221370.1| hypothetical protein BlDMPOM_p17 [Blastocystis sp. DMP/02-328]gi|198385459|gb|ACH86053.1| hypothetical protein [Blastocystis sp. DMP/02-328]
+----------YFQQINHNRYLKMLYKTPYQISNIDRISMFIRFDTQLNNKFIVLCSFflfKTTLFKTGHYIVINKKT----------KQILGLNYYFTKQ
+LIINFFNIFLLNLLiqPEIQN--SINLTSFDSDANFNFTIINSncYFFERILinqfYKRALQSCNFHITIKFKKNqNIYDHILLLNFFKFYF--
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
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+ 120 4444 4875 1000 1000 * 0 6357 1215 1019
+
+E 137 4088 * 1938 1640 4820 5870 * * * 6454 * 3031 3990 4560 * 3882 * * * * 137
+ 24 5907 * 370 2145 349 2218 6368 1301 1267
+
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+ 136 3474 * 1000 1000 * 0 6358 1498 1019
+
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+ 60 4626 * 1467 648 0 * 6358 1196 1019
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+
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+
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+ 0 * * * * * * 6375 0 0
+
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+ 84 5433 4901 1000 1000 * * 6375 1105 0
+
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+ 885 1124 * 1105 902 2394 304 6387 3391 1258
+
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+ 72 5459 5286 1000 1000 * 0 6388 1086 1200
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+ 0 * * * * * 0 6324 0 1352
+
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+ 167 3191 * 1685 537 381 2106 6324 1801 1352
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+ 14 6645 * 1000 1000 * 0 6320 1018 1045
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+ 0 * * 0 * 0 * 6305 1018 1112
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+ 0 * * * * 0 * 6352 0 1075
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+ 0 * * * * * * 6372 0 0
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+D 156 * 6427 1630 4406 * 5462 3152 * 6212 * * 1791 * 3544 5799 4249 5951 * 6971 * 156
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+ 0 * * * * * * 6372 0 0
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+V 159 7122 5103 * * 2010 6666 * 1315 * 3426 6204 * * * * * * 2385 7477 * 159
+ 0 * * * * * * 6372 0 0
+
+V 160 6077 5526 5807 * * * 3153 3897 3437 5412 * 4104 * 5197 6773 6328 3283 1314 * 4708 160
+ 20 6214 * 1000 1000 * * 6372 1028 0
+
+T 161 6002 5982 * * 3005 6877 * 4487 6186 2715 5183 * * * * 6088 835 5494 * * 161
+ 12 * 6884 * * * * 6342 0 0
+
+T 162 5885 * 5232 3504 6867 4869 7141 * 3899 6166 * 2749 * * 4694 2163 1787 6609 * 5220 162
+ 0 * * * * 0 * 6278 0 1006
+
+A 163 927 6565 * * * 5991 * * 4444 6163 * 4432 * 5138 4295 3018 2933 6987 * * 163
+ 12 * 6901 * * * * 6094 0 0
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+E 164 6474 * 5976 4387 * 5923 6169 * 1654 5818 * 2479 4638 4017 3391 4089 3380 5171 * * 164
+ 126 3753 6700 1026 974 0 * 6072 1322 1013
+
+T 165 4463 5994 4132 6474 * 4518 * * 6217 5523 * 1995 * * * 2379 1584 6030 * * 165
+ 105 4078 6517 1975 424 0 * 6016 1292 1000
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+D 166 7757 * 1723 5982 6260 5961 6884 4702 4108 4776 * 3124 5071 3293 3875 3815 4702 3817 * 6484 166
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+
+E 167 3512 * 2756 2663 6195 5828 5869 7374 2851 4765 6084 3931 * 3341 4243 3746 * 5541 5856 4985 167
+ 9 7334 * 1585 585 * 0 5968 1001 1041
+
+E 168 5251 * 2993 1108 5896 7347 3194 7281 4301 5319 7640 4611 * 3725 5494 6767 7599 * * 6419 168
+ 31 5571 * 2224 347 0 * 5925 1072 1041
+
+A 169 1277 7064 * * 6177 3021 5643 4451 * 4425 5274 5771 * * 5688 3243 2782 5976 * * 169
+ 0 * * * * * * 5989 0 0
+
+R 170 4325 * 5641 6117 3787 7955 5820 3350 2640 3114 6398 5174 * 4606 1855 4936 * 4803 * 5512 170
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+A 171 2714 * 5921 3775 3412 7549 * 3920 5295 1844 5973 6890 6218 6861 3868 5546 3477 3995 * * 171
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+L 173 * 4634 * * 5263 4129 * 4574 * 577 6721 * * * * * 5307 4839 3654 6039 173
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+E 174 4932 * 7215 3818 * 5392 5821 * 2762 5825 5955 3348 * 4473 4212 1370 3682 7727 * * 174
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+L 175 3019 5137 6861 4467 4961 2034 5984 * 4252 3175 4874 7320 * 5422 5525 2250 5514 * * 5531 175
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+L 176 * * * * 1490 * * 3103 * 1511 3232 * * * 6628 * * 5116 * 5000 176
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+G 177 5797 * 5791 7056 5907 914 5711 * 3194 * 5504 4624 * 2499 4604 * * * * * 177
+ 0 * * * * 0 * 5798 0 1000
+
+F 178 7362 6887 * * 1581 * * 2882 * 2060 2477 * * * * * 5394 3786 * * 178
+ 0 * * * * * * 5680 0 0
+
+P 179 6679 * * * 5000 * * * 7135 * * * 316 4109 5895 * * 5442 * 4296 179
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+
+F 180 * * * * 634 5860 6555 3629 * 3363 6979 * * * * * 4753 3705 * 5148 180
+ 75 4301 * 0 * * * 5364 1076 0
+
+R 181 3100 * 5660 4112 5747 * 5808 3664 3053 * 4657 5773 * 3845 2574 3798 6698 4445 * 2765 181
+ 0 * * * * 0 * 4568 0 1012
+
+K 182 4193 * 2469 3133 * 4410 * * 1627 * * 3533 4656 3873 5159 * 4115 * * * 182
+ 0 * * 0 * * * 3907 0 0
+
+//
+�HHsearch 1.5
+NAME 4bc967f8d6c71174670a6efb6d0861ff
+FAM
+FILE 4bc967f8d6c71174670a6efb6d0861ff
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:00:28 2013
+LENG 222 match states, 222 columns in multiple alignment
+FILT 117 out of 1276 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEECCCCCCCCEECCCCCCCEEEEECCCCCEEEEEECCCCHHHCEEEEEEE
+ECCCCCCCCCEECCEEEEEEEECCCCCCEEEECCCCCCCCCCEEEEEEEECCCCCCCCEEEEEEECCEEEEECCCCEEECCCCCEEEEEEEEEECCCHHH
+CCEEEEEEEECCCCCEEEEEEC
+>ss_conf PSIPRED confidence values
+9389926987996899799998965888998469999958999827999994268755410266668738999614788078997568878884899978
+7378875533132216878873124575699605543323542899998158888997499999899382000353067079969888999990589643
+9489999993788977999989
+>Consensus
+xxxxxxxxxxxxxxGxxvxLxCxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxsLxIxxxxxxDxgxYxCxv
+xxxxxxxxxxxxxxxxxlxvxxxxxxxpxixxxxxxxxxxgxxxxlxCxxxxxxpxxxxxvxWxxxgxxxxxxxxxxxxxxxxxxxxxsxLxixxxxxxd
+xgxyxCxvxxxxxxxxxxxixx
+>4bc967f8d6c71174670a6efb6d0861ff
+EVKLVESGGGLVQPGGSLRLSCATSGFTFSDFYMEWVRQPPGKRLEWIAASRNKGNKYTTEYSASVKGRFIVSRDTSQSILYLQMNALRAEDTAIYYCAR
+NYYGSTWYFDVWGAGTTVTVSSESARNPTIYPLTLPPALSSDPVIIGCLIHDYFPSGTMNVTWGKSGKDITTVNFPPALASGGRYTMSNQLTLPAVECPE
+GESVKCSVQHDSNPVQELDVNC
+>gi|5305517|gb|AAD41690.1|AF091139_1 immunoglobulin alpha heavy chain constant region [Trichosurus vulpecula]
+QMNSLDTGDTGL----YYCARANDYRTDVHRVPLDVWGKGTMVTVS------------------------------------------------------
+----------------------------------------------------------------------------------------------------
+----------------------
+>gi|281349765|gb|EFB25349.1| hypothetical protein PANDA_021873 [Ailuropoda melanoleuca]
+--SVSQmKNQVTLSERAFLIVNHSFA--ANKsappfsgvFSVLVKLCSCPENH--------------KRKCDGSNKG-FEATNEE-KTTFPWEKLSVPMA
+DMAVCHCA--------------------------------------------------------------------------------------------
+-------------------------------
+>gi|18858393|ref|NP_571075.1| CD166 antigen homolog A precursor [Danio rerio]gi|2497299|sp|Q90460.1|C166A_DANRE RecName: Full=CD166 antigen homolog A; AltName: Full=Activated leukocyte cell adhesion molecule A; AltName: Full=DM-GRASP homolog; AltName: Full=Neurolin; AltName: CD_antigen=CD166; Flags: Precursorgi|452158|gb|AAA50024.1| transmembrane glycoprotein [Danio rerio]
+--------------GETIEVPCNngNNK-PDGLIFTKWKYAKDDGSPGDLLIKQAQKD--DPtvSAMDGYKTRVSIAAN-----SSLLIAQGSLTDQRVF
+TCMVV--S---STNLEEFSVEVKVH-KKPSAPVIKNKVKELENGKLTQLGECVVESANP--AADLIWMKNNQALvddgkTIIITSDVTKDpvTGLSSTSS
+RLQYTARKEDVASQFTCVAKHVTGPNQV-----
+>gi|334350079|ref|XP_001376500.2| PREDICTED: v-set and immunoglobulin domain-containing protein 1-like [Monodelphis domestica]
+-VEVTIPVKVMnVTVGTDATFLCTYtTTAATTKLTIQWsFYHIKKFDIIThspclniqsmeektisqclkmvhtrdargrcswtsqVYYS--QDG--QAS
+GIGKYKDRVTGT--STPGNASITISNMQPSDSGVYVCDVT--N---PPDFQGINQGLIVANVLVKPSKPYCSIRGTPEANHAISLSCFSAEGAP--PPKY
+QWFkLEEDTIKPVNEQYNPTTGLLV-------IGNLTTFEKGHYQCIASN-SLGNSSCEID-
+>gi|56207974|emb|CAI21226.1| novel immune-type receptor 9, allele 1 [Danio rerio]
+-------------SGDSVSLTCTVlNQKCVGNHSMYWLIIESQDYRPRIISTHGTP---VDQCEWISDADFRAL----RCVYSFSRKDFRLSNSATYSCT
+VTACG----EKLDRNVSKLDI-------------------------------------------------------------------------------
+-----------------------
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+------------------------------------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne--DLRSWTAADMAA-QN-----
+------tqrkweaagvaeqw----RAYL---EGECLEWLRRYLEKGK-------------------------
+>gi|31339976|sp|Q8AXA0.1|B2MG_RAJEG RecName: Full=Beta-2-microglobulin; Flags: Precursorgi|24528462|gb|AAN62852.1| beta-2 microglobulin [Raja eglanteria]
+----------------------------------------------------------------------------------------------------
+---------------------AVP-SPPQVVVYTYKPVVHGEKNTLLCHAKEFNP-PNVELQLFEDGNVFsQANQTDLSFESNWKFKLTKFIELIPRE--
+-DVEYSCHVMYMGKT--------
+>gi|321475782|gb|EFX86744.1| hypothetical protein DAPPUDRAFT_44172 [Daphnia pulex]
+-------------NHHRRHSTSTAGYDHPSeltm--DdgylVLWFV-DPDRKPFYSLDVRRGRsgrH--WWNEE-rFgr-RVRFL----AstL--arLQI
+VNVTR---QDGGDYRCRVD----------FNSApsrnfkYRLVVIE-PPSSVVI--ldGFLQQLSVvagpleeGNDLILTCKAYGGYP-QP-WVTWWQGG
+QL-ldN--ttDARSPES-vSNLL---VVPRVGRQHL--HDAFTCQVTS------------
+>gi|5327167|emb|CAB46330.1| immunoglobulin light chain variable region [Mus musculus]
+----------------------------------------------------------------------------------------------------
+--------------------------------PAILSVSPGERVSFSCRASQS-iGT---SIHWYqqRTNGSPRLLIKYasesi----------------
+-------SG---------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+E 1 * * 2022 2035 * * 4260 * * * * * * 1503 * 3490 5990 * * * 1
+ 0 * * * * * * 6914 0 0
+
+V 2 * * 4945 * 3577 * * 1840 * 2032 6107 * * 5103 * * * 1945 * 4143 2
+ 0 * * * * * * 8200 0 0
+
+K 3 5045 * 4473 2846 4032 5546 4227 4040 3304 5390 * 4759 * 3176 4647 5527 4974 2166 * * 3
+ 0 * * * * * * 8733 0 0
+
+L 4 * * 4509 * 4817 * 5765 3437 * 1737 3930 5900 4904 5650 * 4949 5805 1627 * * 4
+ 0 * * * * * * 9333 0 0
+
+V 5 4367 * * 3939 * * * 3805 4852 5558 4749 4896 * 3634 5247 3022 1712 2709 * * 5
+ 0 * * * * * * 9230 0 0
+
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+ 21 * 6143 * * * * 9258 0 0
+
+S 7 6296 * * 3593 6169 4111 4430 * 6646 4365 * 4338 1642 5112 * 3033 2421 5638 * * 7
+ 18 6316 * 0 * 0 * 9637 1205 1018
+
+G 8 4633 * 4913 3917 * 3470 5693 6162 3295 6056 * * 1660 3182 4518 3503 4596 5632 * * 8
+ 0 * * * * * * 9799 0 0
+
+G 9 3687 * 3391 3052 5951 4411 * 5954 3459 4568 * 3515 3069 3733 3974 3027 5275 * * * 9
+ 42 5112 * 0 * * * 9869 1230 0
+
+G 10 5471 * 4746 3407 * 5127 * 3606 6462 3064 * 6267 4450 3662 5971 3552 4076 1769 6307 * 10
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+
+L 11 5558 * 4437 3670 6013 5074 5600 3698 5120 3491 4661 4691 6128 6017 3642 3141 3506 2519 * 5081 11
+ 415 2001 * 0 * * * 10046 4131 0
+
+V 12 2778 6537 * 6374 6519 3946 * 3585 4662 3664 * * 4164 6290 5227 4070 4003 1619 * 6506 12
+ 16 * 6475 * * * * 10190 0 0
+
+Q 13 4673 * 5758 4483 6602 4486 4513 3927 2953 4847 4624 5216 5460 3785 4225 3311 3515 3109 5280 5425 13
+ 0 * * * * * 0 10181 0 1391
+
+P 14 4994 * 5107 1767 5753 6530 * 4342 5518 3142 * * 3019 5895 4976 3882 4426 2989 * 5658 14
+ 0 * * * * * 0 10308 0 1391
+
+G 15 * * 5026 3532 * 521 6805 * 5752 5689 * 3709 * 6307 * 4317 * * * * 15
+ 0 * * * * * 0 10427 0 1391
+
+G 16 5223 * 3080 2013 * 3244 5291 * 4512 6301 6624 5819 * 2870 4541 2880 4313 6219 * 6346 16
+ 0 * * * * 916 1089 10427 0 1391
+
+S 17 4465 6324 4712 3770 * 6992 6360 6679 3728 * * 2730 2769 4302 6673 2634 2475 5651 * 7220 17
+ 0 * * * * 0 * 10478 0 1086
+
+L 18 2341 * * 6665 5737 6789 * 3430 6286 3093 * * 5854 * * 5345 5799 1081 * 6712 18
+ 0 * * * * * * 10483 0 0
+
+R 19 6446 6712 5593 3018 5824 * 5913 3925 4801 5443 * 4732 4454 5178 3972 3143 1607 4063 * * 19
+ 10 7206 * 1000 1000 * * 10483 1003 0
+
+L 20 5808 * * 8158 3827 * 7206 2701 * 581 4862 * * * * 6193 * 5005 * * 20
+ 0 * * * * * * 10483 0 0
+
+S 21 6719 * 4674 3361 5149 6180 5272 6516 * 3957 * 3970 2487 4421 3140 2824 3095 5298 6362 6286 21
+ 0 * * * * * * 10483 0 0
+
+C 22 4732 137 * * 6530 * * 6264 * * * * * * 6605 5725 * * * * 22
+ 0 * * * * * * 10483 0 0
+
+A 23 4007 7206 3963 4219 * 4874 4771 5347 4434 4629 * 3120 4366 3700 4307 2611 3325 3889 * 6743 23
+ 90 4043 * 797 1236 * * 10483 1924 0
+
+T 24 2590 6665 7373 6264 3189 6054 5193 3775 6758 3528 * 5719 4775 6496 * 4363 4852 2209 * 3083 24
+ 89 5245 4892 440 1927 * * 10483 1325 0
+
+S 25 3979 * 3749 3431 5418 5636 6964 6680 4903 5184 * 3275 3300 4853 5172 2496 2726 5146 7141 5924 25
+ 189 3856 4218 1531 612 1479 641 10414 2021 1455
+
+G 26 3414 6679 3607 3978 6249 2199 5324 * 4755 3698 * 3212 4046 4104 5110 4973 3834 * 6220 6644 26
+ 390 5568 2213 0 * 2622 256 10359 1165 2337
+
+F 27 4704 * 4055 6144 3218 5375 4704 5212 3765 3222 * 4198 3478 4489 4366 2874 3745 6369 * 4340 27
+ 118 5924 4008 0 * 181 3087 9993 1000 4939
+
+T 28 3999 6330 3632 4709 4428 4651 4893 5694 3508 4223 * 3525 3220 4845 6042 3042 3054 4804 8060 * 28
+ 91 6723 4272 1000 1000 2780 227 10369 1000 2255
+
+F 29 4553 4357 3573 3615 4349 3937 5095 4684 5129 3611 * 6551 2992 4697 5622 5006 4628 3900 6180 3287 29
+ 132 4128 5061 1672 543 1056 946 10349 1761 2841
+
+S 30 3566 * 3010 3931 5815 3446 5964 * 4227 5453 * 4495 2935 4116 4266 3408 3362 5454 * 5317 30
+ 291 4534 2840 291 2454 1380 699 10348 1543 2612
+
+D 31 4624 * 3464 4584 6372 4538 3337 6473 3474 3042 * 3594 3635 4289 7138 3248 4499 4259 * 5209 31
+ 202 3784 4108 649 1464 4313 74 10118 1850 4136
+
+F 32 3930 * 4360 4144 3988 4677 6201 3182 6144 3212 6303 3929 3333 * 6186 4483 3330 5080 * 3105 32
+ 121 3641 * 0 * 137 3469 9811 2031 4590
+
+Y 33 5202 * 5015 4672 4924 5168 5003 3848 5537 3527 5396 4359 5609 3809 4860 2891 3178 3523 * 3294 33
+ 33 5487 * 0 * * 0 10454 1226 1228
+
+M 34 * 5792 * * 4045 6145 6288 2288 5623 2127 4332 * 6740 * * 6335 5735 1592 5744 * 34
+ 14 * 6743 * * * 0 10448 0 1228
+
+E 35 5551 * 7591 3865 3752 5383 5023 4710 3381 3743 6407 4747 * 3699 3815 2953 3293 6495 * 2969 35
+ 0 * * * * 1736 515 10165 0 1403
+
+W 36 * * * * 5219 * * 6288 * 5103 * * * * * 6145 * 4311 244 5465 36
+ 137 4207 4787 646 1470 * 0 10448 1817 1228
+
+V 37 * 5582 6565 4634 2155 * 6831 5282 3486 3060 6889 6515 * 5084 4580 4996 5498 4518 4612 2112 37
+ 46 * 4982 3170 170 2579 264 10396 1003 1921
+
+R 38 6941 * * 6185 5691 7165 4606 6234 2131 3712 5184 4987 * 3759 1970 4273 * 5597 3921 3914 38
+ 126 5130 4177 0 * 2053 398 10349 1256 2220
+
+Q 39 4487 * 3157 4066 5822 4902 4190 4484 3751 4571 5683 4581 * 1802 4984 4357 5286 4809 6234 6195 39
+ 65 5979 5141 0 * 1448 659 10283 1086 2751
+
+P 40 3731 * 3007 4910 5565 3292 6696 4104 2924 3984 5553 4123 4036 5579 3466 3819 4357 * 6605 * 40
+ 89 * 4058 * * * 0 10314 0 2562
+
+P 41 4040 * 3363 3920 6719 3804 5568 * 3732 3472 * 3823 2337 4384 5132 3214 4168 * * * 41
+ 143 4406 4399 2213 350 902 1106 10283 1477 3540
+
+G 42 4940 * 3018 3426 * 1946 * 6560 4316 4981 7086 3943 4422 4869 4106 3368 4454 5428 5512 * 42
+ 67 4452 * 297 2427 638 1484 10264 1496 2850
+
+K 43 4655 7313 4122 3694 6795 2735 4616 4690 2766 5133 * 4174 3600 3644 4255 4147 4665 4683 * * 43
+ 50 4877 * 756 1294 1878 458 10390 1406 1592
+
+R 44 3715 * 3824 3310 6937 2681 5935 4622 4761 5228 6708 4977 3529 4651 5035 2917 3378 5149 * 6291 44
+ 145 4002 4904 878 1133 * 0 10409 1844 1385
+
+L 45 5400 6673 4733 6544 5575 5174 * 3844 6787 2754 * 4061 1938 5089 3355 4621 4153 3562 * 6263 45
+ 30 6421 6839 0 * 2186 358 10354 1031 2052
+
+E 46 3905 * 4833 2902 * 3041 5026 4445 3189 5319 5603 5137 6488 3167 4903 5315 3663 3407 * 5141 46
+ 39 * 5229 * * 1529 614 10357 0 1962
+
+W 47 4938 * 5097 5377 2441 5743 5841 4443 6669 2383 4974 4413 * 4914 3400 4265 4070 4906 4244 4574 47
+ 33 5479 * 4235 79 * 0 10304 1169 2163
+
+I 48 4994 6435 5944 4864 4113 5684 6551 2733 6440 2129 4503 4528 5473 5487 * 4748 4872 2345 * 5183 48
+ 124 5181 4185 1000 1000 * 0 10304 1326 2163
+
+A 49 2758 4540 4224 5470 5839 3598 4879 3004 * 2846 6079 * * 6446 3988 3745 4443 3707 * 4351 49
+ 0 * * * * 1947 433 9927 0 3000
+
+A 50 3308 * 3920 5601 4230 4102 5548 3752 4619 4881 5341 4518 6453 5604 4570 3235 4162 5152 5183 2551 50
+ 80 * 4218 * * 2194 356 10290 0 2483
+
+S 51 4595 6523 4653 5224 3269 4468 4102 3524 3744 4409 5254 5647 * 4899 4227 3023 4334 3654 * 3637 51
+ 213 * 2864 * * * 0 10303 0 3066
+
+R 52 6195 * 3937 4095 4284 5071 4971 4468 3878 3543 * 3103 4666 4431 3835 2667 4703 6612 * 3790 52
+ 394 * 2063 * * * 0 10057 0 4798
+
+N 53 5006 5661 4702 4305 * 3423 5949 6508 3826 4466 * 2577 3254 4014 3906 3732 3617 4392 5752 * 53
+ 89 5202 4950 0 * 2671 246 9399 1171 6608
+
+K 54 5097 * 4347 5102 * 3206 5028 * 3862 4542 6071 3975 6094 3473 4106 2276 3011 4941 5460 6074 54
+ 203 * 2929 * * 4223 79 9462 0 6282
+
+G 55 3932 * 3193 3676 4790 2485 5958 5840 3665 4678 * 4768 * 4749 5004 3076 3422 * * 3972 55
+ 681 4252 1627 1929 440 * 0 9287 1376 6736
+
+N 56 5005 5516 3103 3644 * 1573 * * 4428 4232 * 3113 4895 3653 * 4084 * 5195 * * 56
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+M 187 3697 5096 * 5888 4889 5306 * 3183 6730 3206 4736 4788 6628 6221 3513 4155 2912 2346 5700 * 187
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+
+S 188 4100 * 4955 6962 5706 4610 7417 5008 5640 6312 4243 4623 6402 5701 3780 2087 2207 3518 6133 5564 188
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+N 189 3788 5605 6579 6733 3773 5055 4907 5670 5507 4198 5668 3979 4965 5709 5414 1188 5191 * * 5036 189
+ 49 4915 * 1684 538 2695 242 9875 1477 2096
+
+Q 190 4104 6468 6536 3666 4834 5912 4978 4076 5502 5369 * 4925 * 3780 2848 3266 2769 3699 5068 4323 190
+ 30 5590 * 1312 743 2280 332 9888 1176 1908
+
+L 191 4742 * * * 4465 * 6505 3904 * 473 6802 * 6657 * 7741 * 6482 3932 6724 6774 191
+ 18 * 6370 * * * 0 9926 0 1692
+
+T 192 * * 5387 4341 5725 * 6339 4512 4222 3292 4592 3766 6646 3722 3328 3686 2106 4303 * 4834 192
+ 0 * * * * 1714 524 9910 0 1867
+
+L 193 * * * * 3804 * * 1331 6397 1989 * * 6193 6488 * * 6331 2619 6500 4155 193
+ 0 * * * * * 0 9927 0 1557
+
+P 194 4171 6346 4930 5340 6251 5154 5254 5586 3210 4482 7487 3275 3863 3792 3428 2988 3094 4818 * 6331 194
+ 0 * * * * * 0 9906 0 1557
+
+A 195 2747 * 3862 5407 6630 5265 3915 6468 3890 3686 6182 3680 2903 5466 3825 3250 5029 5345 6502 6663 195
+ 28 5678 * 0 * 2005 413 9906 1143 1557
+
+V 196 3173 5741 5501 * 5726 4313 5682 5688 4920 2697 6086 5512 5033 3708 4455 3482 3369 2494 * * 196
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+
+E 197 3965 6677 2843 3051 6664 4872 6336 * 3018 4600 * 4734 4572 3875 3814 3414 3230 5275 * * 197
+ 79 6127 4686 0 * * 0 9853 1095 1787
+
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+ 34 * 5435 * * * 0 9777 0 2619
+
+P 199 4333 * 2070 2363 4551 6375 * * 7252 5491 5413 3418 6153 3392 4261 3533 4396 * 6429 6584 199
+ 9 * 7252 4322 74 1372 705 9745 1074 2922
+
+E 200 * * 920 3852 6197 * 3860 5245 6432 5485 * 3822 4359 * 6420 3909 6225 5554 * 5196 200
+ 0 * * * * 537 1687 9824 0 2354
+
+G 201 2762 * 4358 4529 * 1919 6689 5647 5675 6471 5379 3421 4434 5436 5203 3130 3793 5556 * 6154 201
+ 17 6449 * 0 * * 0 9900 1000 1316
+
+E 202 3193 * 7345 4458 * 1205 * * 2874 6813 5951 4991 * 5659 4118 5394 4794 4551 * 4949 202
+ 115 4329 5223 0 * * 0 9900 1585 1316
+
+S 203 6207 * 4397 3722 6653 * 5078 4223 3362 3294 * 3832 5698 4184 3871 3381 3618 2659 6262 6746 203
+ 0 * * * * 1318 740 9844 0 1928
+
+V 204 * 7328 * * 2183 * 7450 4090 * 4008 * * * * * * * 3367 6268 897 204
+ 0 * * * * 1175 844 9894 0 1494
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+K 205 5652 * 7333 4932 4972 * 5157 3264 4075 5477 6854 * * 4163 3452 3265 1874 4241 5298 3567 205
+ 0 * * 1585 585 1106 901 9922 1000 1196
+
+C 206 * 68 * * * 6905 * 6818 * 5765 * * * * * * * 6627 * * 206
+ 18 * 6334 * * * 0 9930 0 1018
+
+S 207 3570 * * 3365 * 6549 5759 2851 4026 6487 5451 5189 * 2873 3464 3672 3564 3081 * 5645 207
+ 0 * * * * * 0 9904 0 1248
+
+V 208 1464 6664 * * 6478 6155 * 4581 6231 3850 * * 5130 6503 * 5017 6136 1393 * 6301 208
+ 10 7187 * 0 * 1086 919 9864 1000 1248
+
+Q 209 4497 * 4071 3532 6161 5241 * 5825 3321 5337 * 4623 * 4339 3347 2073 2942 4035 * 6680 209
+ 10 7112 * 0 * 0 * 9726 1000 1043
+
+H 210 * * * 5971 4716 * 1581 * 6598 6136 * 1423 * 4143 4288 6390 4216 6133 * 5238 210
+ 457 * 1880 * * * 0 9595 0 1000
+
+D 211 5472 * 4044 1793 4519 3465 * * 3091 5360 * 5256 3710 5329 3923 4348 4491 5634 * 4464 211
+ 70 4407 * 0 * 123 3614 8420 1143 4006
+
+S 212 3085 5809 6209 4842 5856 2507 5733 5723 4179 4295 * 5662 4192 * 5613 2065 3526 4105 * * 212
+ 29 5665 * 1585 585 * 0 8869 1008 1118
+
+N 213 4415 * 5599 4575 5291 3631 * 4555 * 1808 * 2895 5310 3386 * 3434 4401 4672 * 5519 213
+ 33 * 5465 * * * 0 8602 0 1118
+
+P 214 3821 * * 5350 * 1610 * * 4935 3842 * 4458 2632 3558 5621 3376 4589 5330 * * 214
+ 61 4601 * 1701 530 889 1121 8486 1220 1470
+
+V 215 3572 * 4190 2422 * 3792 * * 3706 * * 3897 5842 5415 5166 2649 2458 4367 * * 215
+ 33 5450 * 0 * 0 * 8327 1000 1294
+
+Q 216 3466 * 3381 3315 * * * * 3497 3629 5391 3494 5245 2858 * 3939 3438 3194 * * 216
+ 0 * * * * * * 8519 0 0
+
+E 217 5171 * 3652 2597 * 5466 4263 4252 4184 4086 * 4194 5304 3455 3368 3181 4612 3898 * * 217
+ 33 5468 * 0 * * * 8472 1000 0
+
+L 218 3082 4338 5270 * * 4327 5227 4083 2601 2182 * 5140 * 5016 * 4092 3935 3287 * * 218
+ 0 * * * * * * 8117 0 0
+
+D 219 5176 * 3039 3046 * * 4812 5089 * * * 2513 * 5100 3509 3609 1936 5107 * * 219
+ 0 * * * * * * 7972 0 0
+
+V 220 * * * * 4125 * * 1241 * 3133 * * * * 4736 * 3320 2356 * 3780 220
+ 0 * * * * * * 7898 0 0
+
+N 221 3879 * 3230 4355 * * * * 3943 * * 3407 3426 3299 3652 2209 2980 * * * 221
+ 0 * * * * * * 6940 0 0
+
+C 222 * 2633 * * * * * 1477 * 3224 * * * * * * 3023 3026 * 2978 222
+ 0 * * 0 * * * 4192 0 0
+
+//
+�HHsearch 1.5
+NAME 4c402988a256f524c3b41ec989161202
+FAM
+FILE 4c402988a256f524c3b41ec989161202
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:35:57 2013
+LENG 58 match states, 58 columns in multiple alignment
+FILT 161 out of 1130 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEECCCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEEEEHHHEEECC
+>ss_conf PSIPRED confidence values
+9889992452899988435369999999784489969999579977987876789987
+>Consensus
+xxxxxalxxxxxxxxxxlxxxxgxxxxvxxxxxxxwxxxxxxxxxxGxxPxxxvxxxx
+>4c402988a256f524c3b41ec989161202
+AEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYG
+>gi|193586979|ref|XP_001952482.1| PREDICTED: tyrosine-protein kinase CSK-like [Acyrthosiphon pisum]
+---NTGRTHFGTTPQQLVTHSFCDRASPVSpVTNIGSYSSF----------VQHVKD--
+>gi|119593683|gb|EAW73277.1| protein kinase C and casein kinase substrate in neurons 2, isoform CRA_a [Homo sapiens]gi|119593684|gb|EAW73278.1| protein kinase C and casein kinase substrate in neurons 2, isoform CRA_a [Homo sapiens]
+---SyEKTQSYPTDWSDNESNNPfsstdangeLQSIRrQRHLGERSSIPGPV-----------------
+>gi|302414846|ref|XP_003005255.1| AbpA [Verticillium albo-atrum VaMs.102]gi|261356324|gb|EEY18752.1| AbpA [Verticillium albo-atrum VaMs.102]
+--QQELREANIPAAQPPAGAQAGGQRALIHSARANtsptlkWstrtggWAPTRrARAASSLATTSSSSRT-
+>gi|32565949|ref|NP_502695.2| Lateral Signaling Target family member (lst-4) [Caenorhabditis elegans]gi|24817571|emb|CAA19487.2| C. elegans protein Y37A1B.2b, confirmed by transcript evidence [Caenorhabditis elegans]
+---LRKAVENYPtPPGGSSEDAHRQLLerrrkQMLRrHTCSTLIKQDTSASPHKMKPpilmeeedEQHSTGK-
+>gi|161077253|ref|NP_001097376.1| endophilin B, isoform D [Drosophila melanogaster]gi|157400406|gb|ABV53852.1| endophilin B, isoform D [Drosophila melanogaster]
+---DKSLTNLLEDFHIEFDTTAvSTVIFVTECSpvNEDYMYGK-QGLLKGLVPRAFVEML-
+>gi|328776214|ref|XP_393399.3| PREDICTED: tyrosine-protein kinase CSK [Apis mellifera]
+-------------MTTHSNVTTPNITSHMNtGSTPVILTSNVTNPSNPAALS--VNP--
+>gi|226228854|ref|YP_002762960.1| hypothetical protein GAU_3448 [Gemmatimonas aurantiaca T-27]gi|226092045|dbj|BAH40490.1| hypothetical protein [Gemmatimonas aurantiaca T-27]
+---------------------HHSEVTLLSRYNSEWALIRSANNEEGYCSLKYLTAI-
+>gi|125805800|ref|XP_694393.2| PREDICTED: myosin-VIIa [Danio rerio]
+--YAVAIQD-lsRqgASSALAIFWQGSHIAELQTrrcAVYHkGWRIFSRRrVDKSKeredksnwgsflRCNSDSA----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 1724 * * * * 5313 * * 4324 * 5402 3902 * 4100 4064 3087 3618 2222 * * 1
+ 40 5186 * 1000 1000 * * 6926 1021 0
+
+E 2 * 4593 4865 2730 6419 * 5147 * 3129 * * 5170 2957 3140 2893 3025 5064 4011 * * 2
+ 0 * * * * * * 7974 0 0
+
+Y 3 * 6739 6407 5948 4398 5482 4689 5663 3593 2939 4684 7045 6414 3764 2613 5113 4904 4318 5573 2378 3
+ 24 7109 6796 3501 133 * * 8995 1148 0
+
+V 4 2270 3045 6672 6790 4172 4746 * 5026 * 3454 5236 5606 6623 6456 6682 4378 6877 2369 6374 3359 4
+ 33 6041 7138 0 * 0 * 9972 1184 1000
+
+R 5 4297 * * 4011 7549 4992 * 3996 2840 3914 7427 * 6726 4764 2009 5206 3904 2471 * 7177 5
+ 0 * * * * * 0 10009 0 1046
+
+A 6 1136 4424 6000 6019 * 4477 * 6380 4504 4884 5324 * 4812 * 5420 4486 4117 2888 * 6493 6
+ 24 7054 6825 3585 126 * 0 10078 1000 1046
+
+L 7 5722 * 7214 5021 * * 5677 2425 4496 1444 3661 6928 6449 4381 4218 4400 4598 4761 * * 7
+ 8 * 7489 * * * 0 10054 0 1249
+
+F 8 4510 4465 5047 4420 3703 5287 3998 * 4155 5159 7002 6900 * 4097 5864 5013 3753 4347 4928 1709 8
+ 39 5840 6718 1358 713 * 0 10069 1183 1363
+
+D 9 4193 6803 1721 3394 * 5437 4600 * 4822 * * 3498 3369 6004 4559 2766 4385 * * * 9
+ 30 7685 5999 1000 1000 2620 256 10029 1000 1568
+
+F 10 6936 5310 5312 6403 1840 6430 3690 * * 4957 * 4540 4919 6203 6390 3969 * * 7405 1483 10
+ 32 5504 * 3811 107 353 2202 9929 1647 1697
+
+N 11 4519 5844 3696 2900 7087 4412 4610 4926 3834 4991 6340 4566 4604 3848 3769 3697 3430 3890 * 5492 11
+ 36 5343 * 810 1219 * 0 10103 1308 1046
+
+G 12 2130 6976 5594 4805 * 2693 * 7151 4453 * * 6458 2257 6105 5518 2731 4093 5256 * 7097 12
+ 101 4313 5863 276 2524 1418 676 10143 1832 1158
+
+N 13 3493 6863 3640 3852 7326 4819 5452 5574 3730 5822 7259 4512 4502 3410 3400 3015 3080 4341 * * 13
+ 19 6239 * 614 1529 * 0 10132 1156 1414
+
+D 14 3775 7058 3262 4048 5818 3210 4150 6902 4139 7014 5191 3388 3571 5007 4607 3183 4576 4873 6259 5550 14
+ 95 4378 6002 1651 553 * 0 10218 1822 1414
+
+E 15 3022 7001 3340 3091 * 4155 4849 5665 4700 * 5919 4341 2446 4528 4384 3990 3479 6563 * * 15
+ 31 5566 * 1497 631 811 1218 10176 1303 1748
+
+E 16 4993 5956 2434 3847 * 2654 4872 5980 3881 5678 6572 3704 3958 4502 4203 3852 4461 5749 6377 7293 16
+ 76 4617 6550 1907 448 * 0 10202 1682 1251
+
+D 17 3996 7090 3281 1552 6048 3806 5161 * * 4376 7396 5670 3768 3763 4965 3775 6246 5709 * 6232 17
+ 27 7672 6204 0 * 1552 602 10148 1000 1456
+
+L 18 4992 * * 6195 5782 5508 7100 2410 7322 1081 5064 7141 5566 5804 5296 4406 7131 3914 6977 6583 18
+ 54 5588 5976 2349 315 * 0 10168 1317 1552
+
+P 19 3210 6439 4006 4251 5383 3843 7171 7308 5100 6211 5770 3813 4012 4805 5235 1820 3570 5247 6862 * 19
+ 39 6049 6441 963 1038 2348 315 10127 1217 1857
+
+F 20 4870 6187 6161 * 1954 * 4981 3549 6044 2002 4434 6876 4984 6054 6340 5462 6258 3407 5434 5007 20
+ 12 6946 * 3585 126 760 1288 10100 1011 1875
+
+K 21 4574 5709 3922 3137 * 5318 5317 7024 3034 5285 7048 4289 4187 3363 3195 3305 3758 4362 * 6661 21
+ 30 6422 6852 1000 1000 * 0 10233 1135 1288
+
+K 22 3258 * 5814 3064 5460 5582 5171 4233 2200 5520 * 5343 3667 3944 3704 4163 4661 4216 * * 22
+ 49 5469 6566 2008 412 1927 440 10222 1351 1451
+
+G 23 5044 5677 3660 5374 * 897 7441 * 4309 5561 * 3688 5461 5097 4405 4325 7409 * * * 23
+ 39 6233 6221 2967 197 683 1406 10239 1172 1538
+
+D 24 4059 7272 1515 2287 * 3887 5625 6063 6784 * 7370 5302 5431 3355 4726 4758 5625 6470 * 6926 24
+ 12 6871 * 1000 1000 * 0 10225 1024 1434
+
+I 25 4400 5438 * 4071 5020 7054 5421 2543 4078 2902 6320 5910 7256 5212 3934 3878 4597 2482 7452 5531 25
+ 24 * 5933 3178 169 2261 338 10225 1104 1434
+
+L 26 4881 * * * 4281 5701 6665 2190 * 1869 5505 * 5169 7308 4876 * 6365 2072 6501 4595 26
+ 30 5588 * 2733 235 * 0 10187 1309 1674
+
+R 27 4597 * 4534 2928 5407 5224 4601 3999 4151 3771 6354 4616 5551 4060 3885 3594 3618 3894 6686 4124 27
+ 29 6163 7385 457 1881 2613 257 10187 1158 1674
+
+I 28 5277 7136 5890 5962 6348 6413 5292 2388 * 2352 4670 5909 4931 4824 6658 6835 6868 1529 * * 28
+ 40 5604 7254 0 * * 0 10181 1299 1683
+
+R 29 4403 6868 5265 5142 5656 4653 5790 3261 4714 1899 6328 5950 5112 5576 4529 4560 4059 2819 6140 5532 29
+ 28 * 5694 * * 2132 373 10164 0 1857
+
+D 30 5163 6015 3786 2476 5628 3920 4139 5975 3469 5682 6993 3955 4966 3640 3474 3301 6063 5582 * 5386 30
+ 348 2263 7406 696 1385 1359 713 10179 4789 2019
+
+K 31 4753 4765 3238 3145 7235 3990 6254 5693 2414 4654 6770 4769 5516 3823 4098 3964 3958 4859 7056 6555 31
+ 166 4658 3859 2249 341 * 0 10238 1695 1694
+
+P 32 5401 6000 3015 3965 7124 3567 4803 4057 4913 3806 5281 4204 4667 4666 4910 3061 3299 4185 * 6325 32
+ 161 4568 3979 3833 105 699 1381 10116 1746 3003
+
+E 33 5134 4904 2392 2938 5220 4010 5092 * 4787 6561 7224 2988 4826 5545 3772 3903 3625 6326 6221 5993 33
+ 36 5346 * 2383 307 756 1294 10174 1316 2891
+
+E 34 4177 6863 2965 2928 6437 3407 5071 5465 3755 6501 5727 3871 3786 6761 4235 2724 4413 7388 7136 * 34
+ 185 3430 5172 1125 885 2194 356 10197 2759 1743
+
+Q 35 4908 * 2424 3841 * 1427 5691 6698 5718 5366 * 3893 5599 6529 5692 4584 4710 4366 6282 7162 35
+ 70 5142 5727 3250 160 1111 897 10179 1623 2124
+
+W 36 7451 * * 5692 4131 4918 7053 6286 5959 4862 5909 7471 * 5152 6032 4524 6388 4902 734 4106 36
+ 22 6723 7413 2585 263 3074 182 10213 1059 1950
+
+W 37 5293 5267 5525 * 4569 5451 * 3779 6105 3054 5282 6872 6009 6434 5131 5836 6698 4061 1488 3051 37
+ 42 5716 6694 2547 271 1437 665 10195 1255 1961
+
+N 38 4725 7617 6112 4818 4365 5358 7892 4627 2740 2735 6183 5823 4475 3711 2971 4247 4679 5969 3998 4678 38
+ 21 7047 7166 5392 35 1419 676 10182 1049 1768
+
+A 39 3139 4106 6999 7411 6225 1609 * 5894 5249 6274 7295 * 5637 5576 5078 4923 4255 2005 * 7345 39
+ 45 6720 5549 1035 966 1179 841 10228 1094 1565
+
+E 40 5251 6099 4604 3048 5394 5331 5333 7435 2876 4653 5999 6322 6869 4515 2080 3911 3759 3968 * 5583 40
+ 543 3557 2127 2165 364 1146 867 10225 2528 1769
+
+D 41 4628 6154 3456 4626 6817 4904 4230 6005 4247 3506 * 2493 7165 * 3062 3248 4103 3581 * 6534 41
+ 54 4973 7693 565 1625 208 2895 9839 1437 5097
+
+S 42 3937 4734 5284 4522 6473 4571 5436 5001 3279 2446 6478 6239 5143 4431 4289 3672 4248 3020 * 5104 42
+ 483 1814 * 389 2080 3025 189 10194 5552 1667
+
+E 43 3851 7034 3681 3864 6494 2795 5144 * 4094 5766 7025 2967 4832 5228 3770 3566 3139 4672 * 6926 43
+ 129 3648 7519 944 1058 * 0 10164 2389 1571
+
+G 44 4629 5455 4396 4650 * 1264 7147 * 3914 5835 7236 3448 5005 4195 4196 3606 6747 7337 * 7367 44
+ 9 7256 * 2322 322 2171 362 10134 1000 1685
+
+K 45 4489 6643 5202 3048 6062 5134 5066 4965 2195 4855 5910 4747 5154 3420 3136 3251 5884 5705 * 6826 45
+ 57 5347 6115 687 1401 2064 394 10155 1391 1508
+
+R 46 3955 6581 6247 2417 7072 5682 6123 4056 3894 4073 7243 5338 4786 4148 3710 3317 3669 3602 6276 5504 46
+ 68 4604 7596 3393 144 672 1425 10084 1650 1615
+
+G 47 4202 6091 6091 5161 6116 609 * 7173 4519 * * 5898 5007 7394 4532 4325 * 7306 * 6088 47
+ 91 4678 5517 2839 217 * 0 10108 1590 1295
+
+M 48 4557 7168 6714 6409 2918 7309 6555 3949 6138 2132 4822 6165 5569 * 5692 3989 5765 5166 2667 3101 48
+ 42 5134 * 4157 83 2157 366 10012 1392 1745
+
+I 49 4176 5114 5872 * 1935 6096 * 2850 5474 3359 7246 * 5262 * * 5063 5903 1930 * 5488 49
+ 36 5346 * 1836 474 1538 609 10053 1474 1553
+
+P 50 5798 * 5607 5687 5790 5549 5780 * 6118 4808 6798 6050 465 7041 5775 4587 6718 * * 6830 50
+ 38 5269 * 2266 336 1478 641 10046 1344 1319
+
+V 51 2505 6519 * 4288 5591 3591 6534 5644 3554 4009 * 5503 6505 4682 4321 2179 4414 3575 * 7290 51
+ 39 6979 5749 1000 1000 * 0 10066 1000 1156
+
+P 52 3681 * 4166 4219 * 4607 7092 6847 4132 * * 2318 5454 3463 3980 2229 3574 6904 * 6013 52
+ 0 * * * * 2189 357 9866 0 1532
+
+Y 53 6237 4719 7243 6058 2439 5663 3550 4228 6292 3937 5473 5369 5867 5689 5828 3682 7186 5270 5431 1881 53
+ 50 4870 * 2683 244 463 1865 9812 1599 1388
+
+V 54 3740 7240 * 6418 4963 5991 * 2843 * 2353 6411 * * 6729 6989 3957 4414 1451 6714 6889 54
+ 37 5320 * 2633 254 * 0 9812 1282 1006
+
+E 55 3937 4997 4591 1864 * * 5468 6668 3112 5347 7188 5373 5772 3851 3343 3766 3764 5364 6425 6127 55
+ 41 5157 * 0 * 1210 816 9671 1322 1118
+
+K 56 4976 * 4158 2713 5038 5238 7115 3731 3903 3077 5764 6202 2585 4550 4188 4340 5718 4176 * 6070 56
+ 45 5026 * 3785 109 0 * 9476 1257 1006
+
+Y 57 5390 6737 * 4409 4629 * 6709 2627 4862 1796 4650 6812 * 6748 * 5922 4399 2285 * 4095 57
+ 134 3494 * 0 * * * 8915 1227 0
+
+G 58 3465 * 2982 5455 * 1638 4170 * 5196 * * 3772 5027 * * 2608 4074 5117 * * 58
+ 0 * * 0 * * * 6974 0 0
+
+//
+�HHsearch 1.5
+NAME 4e1e30ab1e15c9c1545ff8328bcfebeb
+FAM
+FILE 4e1e30ab1e15c9c1545ff8328bcfebeb
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:42:23 2013
+LENG 75 match states, 75 columns in multiple alignment
+FILT 64 out of 66 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEEEEEEEEECCCCCCCCCCCCCCEEEEEEEEEECCCCEECCCCCEEEEECCCEEEEECHHHEEECCC
+>ss_conf PSIPRED confidence values
+999999999100899957866899823216788899998614697965996499998402168963202888369
+>Consensus
+mkxGdrVrVxxsvxVyhxPxxrxxxfDlxGmEGeVxxxvxxwkGrxISanlPxxVxFxxkFxaHlredElExixx
+>4e1e30ab1e15c9c1545ff8328bcfebeb
+MNVGDRVRVTSSVVVYHHPEHKKTAFDLQGMEGEVAAVLTEWQGRPISANLPVLVKFEQRFKAHFRPDEVTLIED
+>gi|254423582|ref|ZP_05037300.1| Ferredoxin thioredoxin reductase variable alpha chain [Synechococcus sp. PCC 7335]gi|196191071|gb|EDX86035.1| Ferredoxin thioredoxin reductase variable alpha chain [Synechococcus sp. PCC 7335]
+MKVGDRVRVKAPLTLFNHPKFRNQPHNVEGMEGVISAILTDWEGRPISANYKIVASFEvegakRPFK-aHLHEDELEV-iE-
+>gi|158334553|ref|YP_001515725.1| ferredoxin-thioredoxin reductase variable alpha chain [Acaryochloris marina MBIC11017]gi|158304794|gb|ABW26411.1| ferredoxin-thioredoxin reductase variable alpha chain [Acaryochloris marina MBIC11017]
+MQVGDQVRVKESVIIYHHPEHRNNPFDIKGTEGELIQVIKDWQGREVSANYPYLVKFSKKLRIHLGEHEIESV--
+>gi|302772070|ref|XP_002969453.1| hypothetical protein SELMODRAFT_170523 [Selaginella moellendorffii]gi|300162929|gb|EFJ29541.1| hypothetical protein SELMODRAFT_170523 [Selaginella moellendorffii]
+-GVGSRIRVKGPLKVFHVPK--NPEFDLGGQEGEVKEVLTSWKGKIISANLPYKTQFAlsidgkeVKLIAHLREDEFEVIG-
+>gi|729538|sp|P38365.2|FTRV_SPIOL RecName: Full=Ferredoxin-thioredoxin reductase, variable chain, chloroplastic; Short=FTR-A; Short=FTR-V; Short=Ferredoxin-thioredoxin reductase subunit A; Flags: Precursorgi|474766|emb|CAA55480.1| ferredoxin:thioredoxin reductase [Spinacia oleracea]gi|861138|emb|CAA54408.1| ferredoxin-thioredoxin reductase SU A [Spinacia oleracea]
+-KVGCKVKVKSPLKVYHVPKL--PEVELTpDMVGVIKQYVGFWKGKYISPNYPFKVEYRidvpdrgsVKLVVHLKEEEFEIIA-
+>gi|195655467|gb|ACG47201.1| ferredoxin-thioredoxin reductase, variable chain [Zea mays]
+-KIGRRVRVTAPLRVYHVLKA--PDLDIQGMEGVVKQYVCVWKGKRVTANFPFKVEFElavegqpkpVRFFAHLREDEFEFVDG
+>gi|255074043|ref|XP_002500696.1| predicted protein [Micromonas sp. RCC299]gi|226515959|gb|ACO61954.1| predicted protein [Micromonas sp. RCC299]
+-EAGDKVKVVSKVLVYHVpKGDRKNGTDLSGWEGVVDSRADDYNGTYISANLEVKVAFavpndpkGKTFIVHCKENELEK---
+>gi|53801456|gb|AAU93930.1| plastid ferredoxin-thioredoxin reductase variable chain subunit A [Helicosporidium sp. ex Simulium jonesi]
+-REGATVRVTSPITVWHVPKFR-KGMNVQGLQGKIMQNVSVFRGVPLSPSKPWKVAIDakdpagqaFKFVMHLGDEEMEVLN-
+>gi|307110609|gb|EFN58845.1| hypothetical protein CHLNCDRAFT_140698 [Chlorella variabilis]
+-AEGARVKVKAPVKVYHVGKYK-AGLELEGMEGTVVQPnVCDYKhhdGKkhDLSATLPVKVQFmvpapdggkDVKVLVHLVsslagvaDDEVEA---
+>gi|219111423|ref|XP_002177463.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]gi|217411998|gb|EEC51926.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
+-EKGALVRVCvEGVKAFQVPKKGQGTFDAdknfvlgekflllpVGMRGTITKIY---NQDEVSANFPVQVKFQpgtnleegydapVAFMMHMETYEIEVI
+--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * 4653 * * * 4076 4985 202 * * * * * * * * * 1
+ 0 * * * * * * 2473 0 0
+
+N 2 5248 * * 2740 * 5857 * * 964 * * 4650 5610 2541 4450 5954 * * * * 2
+ 0 * * * * * * 3275 0 0
+
+V 3 3271 * * 3212 * * * 2383 3617 5183 * * 3659 6449 * * 5826 1398 * * 3
+ 0 * * * * * * 3316 0 0
+
+G 4 * * * * * 0 * * * * * * * * * * * * * * 4
+ 0 * * * * * * 3316 0 0
+
+D 5 2369 5482 897 6281 * * * * 4225 5997 * * * 4594 5194 3866 5184 * * * 5
+ 0 * * * * * * 3316 0 0
+
+R 6 * * * * * * * * 1985 4238 * * * 3851 779 * 4558 * * * 6
+ 0 * * * * * * 3316 0 0
+
+V 7 * * * * * * * 3895 * * * * * * * * * 100 * * 7
+ 0 * * * * * * 3316 0 0
+
+R 8 * 5087 * * * * * * 2027 * * * * 5826 672 * 4674 4613 * * 8
+ 0 * * * * * * 3316 0 0
+
+V 9 * * * * * * * 3827 * * * * * * * * * 105 * * 9
+ 0 * * * * * * 3316 0 0
+
+T 10 4960 3960 * 5158 * * * 3684 1543 * * 4464 * 6270 4794 3918 2151 3857 * * 10
+ 79 4238 * 0 * * * 3316 1095 0
+
+S 11 2038 * 6722 2119 * 4020 * * 5205 * * 5924 * 4718 5680 2592 3280 3550 * * 11
+ 0 * * * * * * 3316 0 0
+
+S 12 4982 * * * * 4238 * * 4820 * * 6022 1476 * * 985 * * * * 12
+ 15 6582 * 0 * * * 3316 1000 0
+
+V 13 * * * * * * * 3480 * 2266 * * * * * * 5156 568 * * 13
+ 0 * * * * * * 3316 0 0
+
+V 14 * * * * * * * 2687 1692 4820 * * * * 3630 * 3332 1645 * * 14
+ 0 * * * * * * 3316 0 0
+
+V 15 4238 * * * * * * 4872 * 5143 6472 * * * * * * 195 * * 15
+ 0 * * * * * * 3316 0 0
+
+Y 16 * * * * 2345 * 4499 * * * * * * * * * * * 4558 481 16
+ 0 * * * * * * 3316 0 0
+
+H 17 * * * * * * 483 5295 * * * 2695 * 4238 * * 4860 5876 * * 17
+ 0 * * * * * * 3316 0 0
+
+H 18 4594 * * 5710 * * 1074 * * * * 5142 * * * * * 1197 * * 18
+ 96 4820 5103 0 * * * 3316 1049 0
+
+P 19 5945 * * * * 5312 * 5889 4808 4630 6348 * 252 * * 6210 * * * * 19
+ 0 * * * * * 0 3309 0 1034
+
+E 20 6434 * 4597 1691 * 3950 * * 1332 * * * * 3019 4262 * * * * * 20
+ 72 * 4357 * * 0 * 3309 0 1034
+
+H 21 3570 6112 4792 * 3767 * 1034 * 4222 5380 5095 3862 * * * * * 3286 * 5306 21
+ 206 * 2908 * * * 0 3302 0 1078
+
+K 22 5757 * * * * 3786 4374 * 2746 * * * 3808 * 643 * * * * * 22
+ 385 * 2094 * * 1700 531 3238 0 1421
+
+K 23 5498 * * * * 1633 * * 3129 * * 1771 * 2990 * 4803 5089 4136 * * 23
+ 0 * * 0 * 240 2707 3020 1000 1718
+
+T 24 3962 * 4893 2124 * 4201 * * 3249 * * 4215 2259 2144 * * 5374 * * * 24
+ 37 * 5309 * * 0 * 3297 0 1080
+
+A 25 1936 * 3884 2501 * 2434 * * * * * * 2131 * * 5265 4188 * * * 25
+ 0 * * * * 0 * 3326 0 1026
+
+F 26 * * * * 875 * 5143 * * 2371 3996 * * * * 5876 4820 3082 * * 26
+ 0 * * * * * * 3316 0 0
+
+D 27 * * 235 4017 * 5802 * * * * * 3821 * * * * * * * * 27
+ 0 * * * * * * 3316 0 0
+
+L 28 3836 * * * * * * 2334 * 850 3838 * * * * * * 3225 * * 28
+ 79 4238 * 3807 107 * * 3316 1095 0
+
+Q 29 * 4819 4991 3662 * 4872 * 5680 1492 6281 5233 4330 * 2603 5121 4820 4088 3875 * * 29
+ 33 5482 * 0 * * * 3316 1017 0
+
+G 30 * * 4358 * * 72 * * * * * * * * * * * * * * 30
+ 0 * * * * * * 3316 0 0
+
+M 31 5339 * * * * * 6209 5190 5199 2630 1047 * * 3029 5710 4368 4788 * 4820 * 31
+ 0 * * * * * * 3316 0 0
+
+E 32 * * 6022 415 * * * 5710 * * * 5826 * 3402 4238 6208 6108 5482 * * 32
+ 0 * * * * * * 3316 0 0
+
+G 33 * * * * * 0 * * * * * * * * * * * * * * 33
+ 0 * * * * * * 3316 0 0
+
+E 34 * * 4213 1057 6028 * 6259 * 4153 * * * * 6404 * * 2545 2338 * * 34
+ 0 * * * * * * 3316 0 0
+
+V 35 * * * * * * * 1587 * 3504 * * * * * * * 788 * * 35
+ 0 * * * * * * 3316 0 0
+
+A 36 4018 5997 4820 6127 4612 * 5132 3611 1865 4775 4218 5802 * * * 4383 3585 2267 * * 36
+ 0 * * * * * * 3316 0 0
+
+A 37 2665 * 4124 3801 * 4605 * * 3221 * * 4082 * 1710 * 2956 3808 * * * 37
+ 0 * * * * * * 3316 0 0
+
+V 38 * * 4594 * * * * 1636 * 6485 * 4558 5377 5680 3968 * * 2014 * 2132 38
+ 35 5378 * 0 * * * 3316 1021 0
+
+L 39 3562 * * * * * * 2992 * 1827 * * * * * * * 1137 * 4238 39
+ 101 * 3893 * * * * 3316 0 0
+
+T 40 4053 4766 3173 6258 * 2824 5877 * 5719 6217 * 3285 * * 4989 3198 1602 5977 * * 40
+ 0 * * * * * 0 3184 0 1132
+
+E 41 * * 1459 2525 5424 * 4106 6185 * 3816 * 6500 * 4048 * 5061 5064 2599 * * 41
+ 0 * * * * * 0 3184 0 1132
+
+W 42 * * * * 3366 * 5645 * * 4946 * * * * * * * * 416 3308 42
+ 0 * * * * 347 2226 3184 0 1132
+
+Q 43 * * 5123 3980 * * 5910 * 975 * * 2712 * 2590 3969 * * * * * 43
+ 35 5367 * 1585 585 0 * 3314 1021 1000
+
+G 44 * * * * * 79 * * * * * * * 4238 * * * * * * 44
+ 0 * * * * * * 3316 0 0
+
+R 45 * * 4238 * * * * * 1490 * * * * * 1045 * 4820 3816 * * 45
+ 35 5378 * 1000 1000 * * 3316 1021 0
+
+P 46 * * 5377 3480 * * * 4740 6028 * * * 1193 5710 2546 * 3641 4670 * 3535 46
+ 0 * * * * * * 3316 0 0
+
+I 47 * * * * * * * 835 * 2949 * * * * * * * 1689 * * 47
+ 0 * * * * * * 3316 0 0
+
+S 48 * * * * * * * * * * * * * * * 172 3157 * * * 48
+ 0 * * * * * * 3316 0 0
+
+A 49 456 * * * * * * * * * * * 1885 * * * * * * * 49
+ 0 * * * * * * 3316 0 0
+
+N 50 * * * * * * * * * * * 494 * * * 4558 2015 * * * 50
+ 0 * * * * * * 3316 0 0
+
+L 51 * * * * 2678 * * * 4558 613 6172 * * * 6157 * * * 5924 3280 51
+ 0 * * * * * * 3316 0 0
+
+P 52 * * * 3968 * * * * 5143 * * * 140 * * * * * * * 52
+ 0 * * * * * * 3316 0 0
+
+V 53 * * * * 2431 * * 2254 * 4881 * * * * * * * 1502 4558 2511 53
+ 0 * * * * * * 3316 0 0
+
+L 54 * 5680 * * * * * 3139 1239 2462 * * * 2784 6157 * * 3285 * * 54
+ 0 * * * * * * 3316 0 0
+
+V 55 5143 * * * * * * 3459 * * * * * * * * 5141 230 * * 55
+ 0 * * * * * * 3316 0 0
+
+K 56 2152 * * 2560 * 6271 * * 2472 * * * * 1664 4600 4601 * 6143 * * 56
+ 0 * * * * * * 3316 0 0
+
+F 57 * * * * 201 * * 3966 * 5184 * * * * * * * 5928 * 5482 57
+ 267 2567 * 2767 229 * * 3316 1389 0
+
+E 58 5934 * 2524 3275 6141 2031 6405 * * 4255 * 5052 4962 3842 5475 2686 5323 4363 * * 58
+ 1107 1474 2507 3123 176 0 * 3319 1856 1000
+
+Q 59 * * 5805 5400 4347 5312 * 5631 1808 * 5308 5035 3504 5845 3933 * * 1508 * * 59
+ 0 * * * * 0 * 3189 0 1398
+
+R 60 4238 * * * * * * * 697 * 5132 * 5143 * 2071 * 4820 * * * 60
+ 0 * * * * * * 3316 0 0
+
+F 61 * * * * 354 * * * * 4166 * * * * * * * 5377 * 2861 61
+ 0 * * * * * * 3316 0 0
+
+K 62 6127 * * * 2852 * * 3398 1745 4159 4238 * * 5559 2684 4088 * 3192 * * 62
+ 41 * 5143 * * * * 3316 0 0
+
+A 63 833 * * * * 5272 * 5818 6602 * 3322 * * * * 6134 5036 2058 * * 63
+ 15 6602 * 0 * 0 * 3299 1056 1031
+
+H 64 * * * * * * 0 * * * * * * * * * * * * * 64
+ 0 * * * * * * 3316 0 0
+
+F 65 * 4820 * * 1937 * * * * 736 3617 * * * * * * 5537 * * 65
+ 0 * * * * * * 3316 0 0
+
+R 66 5630 5537 * 4238 * 3630 4021 * 1818 * * * * 5081 1232 * * 5377 * * 66
+ 35 5378 * 2807 222 * * 3316 1021 0
+
+P 67 3229 * 2765 701 * * * * * * * * 4664 * * 4700 4238 * * * 67
+ 0 * * * * * * 3316 0 0
+
+D 68 * * 833 2730 5415 5444 5082 * * * * 3148 * 6086 * 4997 * * * 4238 68
+ 0 * * * * * * 3316 0 0
+
+E 69 * * * 0 * * * * * * * * * * * * * * * * 69
+ 0 * * * * * * 3316 0 0
+
+V 70 * * * * 2094 * * 2990 * 1081 4558 * * * * * * 3002 * * 70
+ 0 * * * * * * 3316 0 0
+
+T 71 5630 * 4593 328 * * * * 6108 * 5826 6022 * 4444 * * 4367 * * * 71
+ 0 * * * * * * 3316 0 0
+
+L 72 2793 * * * 3018 * * 3364 3963 3471 * * 6165 * * 4387 5295 1394 * 6237 72
+ 47 * 4972 * * * * 3323 0 0
+
+I 73 3361 * * * * * * 1222 * 1983 * * * * * * * 2178 * * 73
+ 128 3555 * 183 3067 0 * 3173 1158 1031
+
+E 74 3266 * 2125 2610 * 2522 * * * * * 3177 5227 4565 4715 3167 * * * * 74
+ 0 * * * * * * 3006 0 0
+
+D 75 * * 895 1499 * 3204 * * * * * * * * * * * * * * 75
+ 0 * * 0 * * * 1734 0 0
+
+//
+�HHsearch 1.5
+NAME 4f78b9c2edbc3ae2d8e9a0de15b7225f
+FAM
+FILE 4f78b9c2edbc3ae2d8e9a0de15b7225f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:28:29 2013
+LENG 73 match states, 73 columns in multiple alignment
+FILT 107 out of 1112 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 11.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEECCCCCHHHHHHHHHHHHCCCCEEEEEEECCCCEEEEEECCCCHHHHHHHHHHCCCCCEECCCCC
+>ss_conf PSIPRED confidence values
+9857999967976658999999998406864479875258669998478899999999998499712323269
+>Consensus
+xxxxxxxxxxxxxcxxcxxxxxxxxxxxxxvxxxxxxxxxxxxxvxxxxxxxxxxxxxlxxxgxxxxxxxxxx
+>4f78b9c2edbc3ae2d8e9a0de15b7225f
+SGTRYSWKVSGMDCAACARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESALQKAGYSLRDEQAAE
+>gi|289762151|ref|ZP_06521529.1| metal cation transporter P-type ATPase G ctpG [Mycobacterium tuberculosis GM 1503]gi|289709657|gb|EFD73673.1| metal cation transporter P-type ATPase G ctpG [Mycobacterium tuberculosis GM 1503]
+-DDDPGAMARGYQCAGIRDIATISDRCAlrQRHLVLAAAVPAYASRSASNRKAgvVQKIIDwstrtlsgvrrdvaaqpsgeTSDACcDGED-------
+>gi|84488951|ref|YP_447183.1| cation transport ATPase [Methanosphaera stadtmanae DSM 3091]gi|84372270|gb|ABC56540.1| predicted cation transport ATPase [Methanosphaera stadtmanae DSM 3091]
+------KVDKICDCaDDCCTGNTHHEHNHEHNHehnhehnhedCCDDDCCSDikicncgDCDD---------DDEEEEEVIKEGipllK------
+>gi|108763657|ref|YP_629240.1| copper-translocating P-type ATPase [Myxococcus xanthus DK 1622]gi|108467537|gb|ABF92722.1| copper-translocating P-type ATPase [Myxococcus xanthus DK 1622]
+-----SHVPHSRT---PPPSPAGEAPAIDPVCGMKVDPNApkggHLEHAGLTYAfCNPRCRERFRADPerYL--------
+>gi|304384108|ref|ZP_07366561.1| P-ATPase superfamily P-type ATPase cadmium transporter [Prevotella marshii DSM 16973]gi|304334735|gb|EFM01012.1| P-ATPase superfamily P-type ATPase cadmium transporter [Prevotella marshii DSM 16973]
+----------MDAGKYIGRENKCQMMfatELQPFFYYLCNKEEK--------------------------------
+>gi|340622612|ref|YP_004741064.1| putative cation-transporting P-type ATPase [Capnocytophaga canimorsus Cc5]gi|339902878|gb|AEK23957.1| Putative cation-transporting P-type ATPase [Capnocytophaga canimorsus Cc5]
+----NEa----QSYTYFVKgmscsgceqtvgerletisgvtvsq--inaKNKTVTLNAPSTISFHKLSQTlegthysihktleeattiSQKTssnngVFY
+---cpMqCEGDKtyskagd-CPICGMDLV------
+>gi|187928736|ref|YP_001899223.1| heavy metal translocating P-type ATPase [Ralstonia pickettii 12J]gi|241114288|ref|YP_002973763.1| heavy metal translocating P-type ATPase [Ralstonia pickettii 12D]gi|187725626|gb|ACD26791.1| heavy metal translocating P-type ATPase [Ralstonia pickettii 12J]gi|240868861|gb|ACS66519.1| heavy metal translocating P-type ATPase [Ralstonia pickettii 12D]
+---EVGHQRYWFCSRHCEKTFLADPARYlshdahdahdhDGAAHDHAPTGVAAVSastkqLAKDPicGmmVDKATALSAERGGRKY-------
+>gi|120610206|ref|YP_969884.1| heavy metal translocating P-type ATPase [Acidovorax citrulli AAC00-1]gi|120588670|gb|ABM32110.1| heavy metal translocating P-type ATPase [Acidovorax citrulli AAC00-1]
+-------------mCPGGWAHSLGaml-SD--PSESPAASSAidrealpgSPSVDGdaLLDDPQEWpsfgrPHASATgPAQ------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * * * * * * * * * * * * * 0 * * * * 1
+ 0 * * * * * * 1000 0 0
+
+G 2 3215 * 2911 2142 * 3250 * * * * * * * * 3513 2165 * 3094 * * 2
+ 0 * * * * * * 5380 0 0
+
+T 3 * * 2673 2749 * 3925 * * 2804 * 3777 * 3712 * 3760 3882 3075 3721 * * 3
+ 238 2718 * 1815 482 * * 6659 1437 0
+
+R 4 5305 * 3625 4059 * * 4091 * 3019 3935 * * 5318 2768 2105 * 2994 4151 * * 4
+ 0 * * * * * * 9215 0 0
+
+Y 5 2861 5659 4623 * * * 4139 4086 4675 3738 4804 4225 3885 4752 4430 5044 3463 2635 * 4327 5
+ 97 3945 * 2722 237 * * 11091 1833 0
+
+S 6 6256 5672 5262 2709 * 4015 4615 4365 3733 3702 4054 4459 4345 3991 3622 4714 3379 4271 * * 6
+ 31 5543 * 1202 823 0 * 12036 2109 1000
+
+W 7 3324 5405 * 4998 3007 4628 5030 3204 4329 2848 5424 6219 * 5164 5556 4227 5090 3843 5352 3476 7
+ 41 5899 6448 1000 1000 * 0 12803 1092 1072
+
+K 8 4020 * 4213 3615 6598 5383 3964 5308 3345 4809 4898 5322 3939 3369 3684 3046 4616 4865 * 4303 8
+ 0 * * * * * 0 12810 0 1304
+
+V 9 4652 * 3848 4495 3983 6094 6358 2378 4951 2882 6360 4526 5094 5037 5788 5361 3920 2538 * * 9
+ 0 * * * * * 0 12810 0 1304
+
+S 10 3671 6080 3284 3468 6206 5535 4117 6170 3127 5320 6281 4586 3826 4234 4544 3465 3985 5094 6521 4247 10
+ 224 4864 3188 0 * 756 1294 12810 1289 1304
+
+G 11 5349 * 3673 4442 * 1599 4515 4314 5036 5880 6020 3582 4026 4425 4990 5169 4133 5888 6098 5328 11
+ 97 5225 4696 1876 459 734 1326 12764 2100 2938
+
+M 12 3666 5580 4857 5307 4372 4364 6051 2676 * 3475 2594 5338 4368 4952 6190 4786 * 3168 6133 4813 12
+ 24 * 5903 * * 1842 472 12905 0 2397
+
+D 13 3858 3855 3018 4003 6553 6352 3266 5704 4307 * 4318 6546 4157 3678 4096 3463 4014 4194 * 5738 13
+ 101 3889 * 1264 777 920 1084 12903 2311 2245
+
+C 14 4764 1225 3936 6080 5844 4545 4716 5417 4450 4775 5270 5660 4837 * 5179 3845 4430 5972 6475 * 14
+ 42 5112 * 0 * * 0 13122 1296 1469
+
+A 15 2824 6001 3525 3984 * 3635 * 6523 5403 5446 4047 3762 3328 4189 3374 4278 4601 4908 6324 4988 15
+ 36 6149 6577 1585 585 * 0 13316 1018 1469
+
+A 16 3292 * 5099 5155 5125 2704 4339 * 6256 5075 4774 3694 4278 6151 4221 3035 2904 4014 * 5982 16
+ 47 5450 6818 0 * 488 1801 13298 1298 1702
+
+C 17 6735 1047 4658 4638 * 4133 5712 4147 5853 4315 4643 6656 4821 4883 6526 6513 5800 4217 6148 * 17
+ 25 6034 9260 3079 182 1012 988 13364 1325 1292
+
+A 18 2652 5938 5844 3379 5103 3265 * 4782 2868 4224 6909 4839 3567 6223 4536 5352 4786 3655 * 5218 18
+ 114 3925 6663 2769 229 * 0 13350 2247 1265
+
+R 19 3259 6032 3542 5154 * 3306 5793 6780 3239 4540 5308 3722 4380 4345 3512 3311 4222 5577 5158 * 19
+ 11 * 7090 * * 3255 160 13146 0 2431
+
+K 20 4298 4548 3982 4106 5412 3966 4660 4972 2764 3672 6786 4381 5000 4573 3240 5394 4440 3843 * 5334 20
+ 0 * * 870 1143 789 1247 13183 1774 2478
+
+V 21 3832 6696 * 6456 3733 * 4393 2306 5971 2929 4040 4390 4157 5057 6622 4580 4861 2793 * 6463 21
+ 38 6240 6321 2000 415 * 0 13367 1014 1499
+
+E 22 3753 * 4143 2560 * * 4511 5936 3457 3778 6995 3525 4421 4656 3021 4379 3422 5069 * * 22
+ 18 6355 * 1000 1000 * 0 13307 1000 1744
+
+N 23 2865 6021 3551 3706 * 4258 3755 5149 3254 5297 * 3788 5077 6793 3322 4052 3505 4598 * * 23
+ 181 4148 4020 916 1090 2003 414 13307 1940 1744
+
+A 24 3152 * 4298 4968 5066 4705 3427 4519 4581 4080 * 4278 4478 3605 4306 3019 3898 3655 * * 24
+ 59 4632 * 2124 376 401 2043 13091 1507 3320
+
+V 25 3485 6366 4303 5260 4141 5505 4108 3260 5254 1964 3660 * 4167 4902 * 5624 * 3839 5941 5414 25
+ 34 5423 * 341 2247 * 0 13506 1649 1416
+
+R 26 3999 6103 3359 2752 * 4457 4255 6575 3929 4648 4877 5746 4848 3724 2798 3410 4340 * * 6285 26
+ 144 4451 4342 1831 476 1914 445 13533 2128 1654
+
+Q 27 3653 5963 4717 3238 6036 3385 3879 5055 3596 4522 6239 3895 4439 3736 3304 4194 4130 6558 * * 27
+ 75 4646 6558 1877 458 * 0 13552 1704 2524
+
+L 28 3343 * 6715 4786 4725 4400 3856 3914 5064 2840 4233 3642 6280 4167 4351 4394 5072 3337 * 4700 28
+ 214 4016 3716 2211 351 379 2115 13556 2186 2729
+
+A 29 3070 6701 3203 3148 5802 4264 3650 * 3876 5002 * 4517 3460 4605 4591 3148 4048 * * 6567 29
+ 87 4603 5872 2240 343 1680 540 13527 1642 2982
+
+G 30 3392 6246 4191 4765 6023 1610 4873 6097 4842 5226 * 4921 3610 4800 4346 4906 3714 6136 6665 6244 30
+ 13 6856 * 0 * 2828 219 13531 1000 2753
+
+V 31 3454 6311 4847 6130 5960 4204 4354 2460 * 3013 * 5191 6613 5225 6249 4248 5833 1865 * * 31
+ 17 * 6436 * * 2039 402 13540 0 2490
+
+N 32 3627 4794 3855 3550 6129 5096 4146 5132 3402 3539 6167 5241 4330 5270 4016 3844 3198 4362 * 6127 32
+ 122 3997 5779 2416 299 236 2729 13490 2250 2261
+
+Q 33 3623 4552 3584 3653 * 3288 3366 6047 4044 6552 * 4303 3781 4035 5371 3196 4202 6106 6869 4947 33
+ 14 6922 9272 1585 585 1920 443 13691 1011 1436
+
+V 34 2896 3892 5493 5131 4733 4821 4292 5891 6280 3894 3843 4743 4738 6671 5242 3343 4346 2825 5011 5267 34
+ 0 * * * * 1456 654 13669 0 1498
+
+Q 35 3926 4960 3653 3779 6027 3713 4608 6642 3480 3963 * 5022 4125 3636 4086 2993 4396 4945 * 5617 35
+ 50 5545 6278 0 * * 0 13704 1350 1223
+
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+A 58 2561 5008 4949 3715 4851 4877 5555 4476 3782 4376 * 4355 3887 4836 4478 3983 3131 4021 * * 58
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+L 59 3882 4477 5165 4691 5267 6087 5784 2077 * 1725 6221 * 5934 5315 5376 3979 * 3645 * * 59
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+G 63 3817 7223 3945 3975 * 1179 * 5663 4581 * * 3754 3964 6253 4373 4279 4657 * * * 63
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+
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+S 65 3514 * 3319 2948 * 3599 6289 5968 3698 4133 6444 * 3925 3980 4290 3805 3278 4055 * 6539 65
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+L 66 2416 4553 3973 4732 4954 3396 5762 3071 * 3142 6183 * 4596 5825 6068 6392 5183 3271 * 4057 66
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+
+D 68 3705 * 3699 3424 * 3824 * 4596 4882 2906 4075 * 3284 4833 * 3923 3103 3405 * * 68
+ 0 * * * * * * 9099 0 0
+
+E 69 1784 * * 2900 * * * 2765 * * 2778 * 2879 * * 2767 * * * * 69
+ 0 * * * * * * 4825 0 0
+
+Q 70 * * 1000 * * * * * * * * * * 1000 * * * * * * 70
+ 0 * * * * * * 1752 0 0
+
+A 71 0 * * * * * * * * * * * * * * * * * * * 71
+ 0 * * * * * * 1000 0 0
+
+A 72 0 * * * * * * * * * * * * * * * * * * * 72
+ 0 * * * * * * 1000 0 0
+
+E 73 * * * 0 * * * * * * * * * * * * * * * * 73
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 5039b5951b98074071f6c69dc58114cc
+FAM
+FILE 5039b5951b98074071f6c69dc58114cc
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:00:59 2013
+LENG 127 match states, 127 columns in multiple alignment
+FILT 147 out of 1021 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCEEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEECCCCCEEECCCCCCCEEEEECCCCCEEEEEECCCCHHHCEEEEEEECC
+CCCCCCEECCCEEEEECCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9289914859995899899998974888888349999979999968999995578831326766762588754888789999987996569899999836
+998766799999999826998987589
+>Consensus
+xxxvxqxxxxxxxxGxxvxlxCxxxxxxxxxxxvxWxxxxxxxxxxxlxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxxLxixxxxxxDsgxYxCxxxx
+xxxxxxxfgxgtxLxVxxxxxxpxxxx
+>5039b5951b98074071f6c69dc58114cc
+EVKLQESGGDLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVASINNGGGRTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHE
+YYYAMDYWGQGTTVTVSSAWRHPQFGG
+>gi|62464905|gb|AAX83161.1| immunoglobulin heavy chain variable region [Aotus nancymaae]
+--------------GDPVPHLRCLWLLHRQ-------willeldpPAPKGRG--WSGldisivwWVHQl-QRLPQES-----sh---YFSRHVQEPVLVE
+---------AE-LCDR-----------------------------
+>gi|50428758|gb|AAT77091.1| anti-HCC scFv antibody [synthetic construct]
+EIVMTQTPLsSPVTLGQPASISFRSSQS-LVHsdgNtYLSWLQQRPGQPPRLL--IYK---VSNRFSGGPRQIQ--WQwGQGQIFTLKNQQGWKLRMSGF
+ITARKL--HNFRvgTFGPRDQAGNRRAAAH-----
+>gi|6840832|gb|AAF28780.1| immune-type receptor 2 [Sphoeroides nephelus]
+---HPKRVLVFANVGDNITLGCSSEDSSAN--TFRWFKQTLGEKPRIISSFFKHEKKLEYAKEFQNsQISTNITEGNYHL--KIANLSISDSSTYYCGCI
+--FSYAIEFEEIYMVHV-----------
+>gi|309262028|ref|XP_003085513.1| PREDICTED: ig alpha chain C region [Mus musculus]
+---------------------------------------------------------------------VFLLTLLHGIQCEVKLVESGGGLVqpggSLR
+LScatsgftfSDFY--MEWVRQPPGKRLEwiaakSA--------
+>gi|255709618|gb|ACU30711.1| CD8 alpha chain [Ctenopharyngodon idella]
+----------IYKEGEKVQVDCDLKQSG----TLTFWFRINSKGADYLFSVKS---ADIKENDlNSEHYTVNTNsGK---VQLDIKSFKKkTDSGVYVCA
+AM--NSNKLFFGGLTRIEGEPDPT------
+>gi|149632037|ref|XP_001512632.1| PREDICTED: similar to T cell receptor gamma chain [Ornithorhynchus anatinus]
+---------------------------------------------------------------------ACGHRVSTVSGVKYFGTGTKLVVTGFKHCaL
+QSGAYIKVFGSGTKLIVENTTP------
+>gi|74218336|dbj|BAE23783.1| unnamed protein product [Mus musculus]
+----------------------------------------------------------------------------MLEMIRKLLLYDDHKSNLVSSPS-
+QLS-iQHKLC----FTMRNKDK------
+>gi|149602051|ref|XP_001518834.1| PREDICTED: similar to OB binding protein-2 [Ornithorhynchus anatinus]
+-FQLVVPNSVTVEEGLCVLIPCTFTYplsfQNSHEALAFWFQE-EGGSQGDP--VATNDPNRPVKDWSRDRFNLTGNPQMDNCSLSIDYARAGDSRKYL-
+-------------------------------
+>gi|6013137|gb|AAF01256.1| coxsackie-adenovirus-receptor homolog [Canis lupus familiaris]
+-LSITTPEqMIEKAKGETAYLPCKFTL-SPEDQGpldIEWLLSPADNqkvDQVIILYSGDKIYDDYYQ-DLKGRVHFTsNDLKSGDASINVTNLRLSDIG
+TYQCKVKKA---PGVGNKKIQLTVLVKPSGI----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 100 3902 * 0 * * * 6504 1072 0
+
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+ 0 * * * * * * 8628 0 0
+
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+ 35 5366 * 1000 1000 * * 8869 1072 0
+
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+
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+
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+
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+
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+
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+
+G 26 3817 * 3180 4586 5264 2432 5114 4499 5472 4189 6825 4018 5529 3350 5296 3839 4057 5211 6115 5147 26
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+
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+
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+ 129 5987 3845 587 1581 1615 570 10175 1129 3811
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+Y 32 4202 * 4082 5756 5224 4948 4678 6012 4894 3482 4580 4434 3159 4907 4160 3832 3359 4768 6868 2955 32
+ 75 5513 5132 0 * 251 2645 10030 1226 4621
+
+T 33 5233 7144 4544 5210 5598 4283 5757 5967 5523 4319 5494 4411 3719 4699 3591 3173 3295 3220 4463 3539 33
+ 47 5687 6343 1036 965 716 1355 10213 1239 2057
+
+M 34 6668 6289 * * 4293 7179 * 2529 4856 2369 2900 * * 7411 7198 * 5920 1607 5701 7059 34
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+
+S 35 3801 6917 7151 4626 3010 6831 3581 5923 4697 3794 7528 4267 7367 4484 4958 2956 3792 5185 6775 2728 35
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+
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+
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+
+R 38 5256 6375 * * 4330 * 5287 6432 2125 4247 * 7905 7026 2705 1713 4986 5953 5125 5388 5486 38
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+
+Q 39 5580 * 4661 4588 6052 4525 4424 * 3389 4031 5430 6342 5655 1542 3723 3884 7072 4256 5552 6252 39
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+
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+E 42 5454 * 3054 3443 * 1623 6115 5999 4903 5763 7027 4429 4759 4871 4609 3143 4614 5042 * 7035 42
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+
+K 43 4006 6927 4341 3397 * 3273 5959 6899 3264 4173 * 3506 5277 3323 3303 3435 4054 5974 * 6139 43
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+
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+W 47 5576 5559 5792 5824 2676 5124 6192 4211 4473 2456 5297 5210 6101 5110 4069 4340 7060 3716 3557 3868 47
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+
+A 49 2673 7250 * 6026 3199 2708 5338 2868 * 3029 5082 6718 6780 * * 4662 5214 3226 * 4218 49
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+I 51 5068 5238 * * 3686 4504 5166 2815 4784 3201 4809 6171 * 4163 6044 3077 4151 3089 6640 3572 51
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+
+G 54 4200 * 4028 4884 6964 3208 5904 4958 3420 5597 5645 2907 4241 5115 4225 2582 4050 4809 * 5667 54
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+
+G 55 5941 * 3593 4331 5593 2224 5453 5661 3970 5649 6966 4057 5966 4265 3829 3265 3326 4609 * 4683 55
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+ 43 * 5085 * * 4305 75 10116 0 4686
+
+Y 60 4787 6087 4984 4362 4817 3383 * 4046 4495 3936 4647 4335 4871 5929 3976 4742 4137 3292 5751 2749 60
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+
+P 61 4408 6978 3909 3072 5243 3453 6127 6026 3765 3731 5410 4301 4725 4194 4404 3276 4113 4614 6970 4665 61
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+
+D 62 4096 * 3670 3246 6185 2624 6096 6339 4025 5004 6036 4512 2707 4678 7270 3270 3436 6940 * * 62
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+K 65 4919 * 3960 3352 6337 3892 5467 * 2902 5991 5511 4781 3821 3562 3358 2876 3626 6105 * 6665 65
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+
+G 66 3777 * 2885 3452 * 2242 * * 3394 7064 * 4070 4297 4382 3830 3193 4900 6088 * * 66
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+R 67 * * 4762 5104 * 4693 4668 5472 3425 6866 7016 5216 4766 4257 1115 3435 5431 5987 6062 * 67
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+ 22 * 6053 * * 2947 200 10235 0 1686
+
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+ 39 5966 6568 1287 760 806 1224 10229 1173 1836
+
+I 70 3458 4993 * 6992 3488 3962 5259 2864 6039 2465 4038 5900 6183 6012 5373 3756 6239 3167 7169 5637 70
+ 48 5342 6981 1013 987 1354 716 10285 1404 1650
+
+S 71 4715 6984 * 3709 4989 6587 4951 4208 3853 3474 5213 4669 * 4743 3655 2335 2930 4144 * 5567 71
+ 54 7186 5073 0 * 1110 898 10265 1000 1656
+
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+ 29 * 5643 * * * 0 10347 0 2017
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+ 154 4616 4049 0 * 700 1380 10318 1638 2385
+
+N 74 3785 * 5199 4219 6124 3030 4537 5422 3814 4525 6813 3460 3007 5432 3844 3597 3496 4897 7163 * 74
+ 330 3455 3145 1169 849 609 1537 10297 2341 2614
+
+A 75 4098 * 3223 3530 * 4073 5168 5015 4555 4559 * 4752 5842 3437 4293 2282 3282 4984 * 7176 75
+ 214 * 2861 * * 1550 603 10265 0 3407
+
+K 76 3396 * 4097 3329 * 3316 6737 * 2776 4506 6491 4395 5374 3344 3974 3031 5018 4955 * 5887 76
+ 49 5866 5958 538 1684 500 1772 10186 1133 4534
+
+N 77 5214 6145 4710 4354 7072 2619 4323 5593 3870 4450 6276 3351 5409 4529 3582 3917 2687 5699 * 6072 77
+ 62 6292 5085 498 1777 1674 542 10331 1105 2321
+
+T 78 5828 6332 2871 4457 4242 4967 5229 4698 4549 4028 7196 4153 4497 4464 4000 3076 2857 4332 * 6340 78
+ 0 * * 1585 585 271 2545 10251 1000 2360
+
+L 79 3473 4387 6766 7526 1822 4618 5527 6205 7054 3573 5133 5869 6001 * * 3360 5194 3362 7147 3226 79
+ 63 5089 6260 1563 596 1142 871 10365 1365 1125
+
+Y 80 6258 7391 5574 4904 4377 5211 4977 4405 4739 4734 6379 3929 4034 4749 4373 2375 2205 5097 * 4857 80
+ 63 4709 7902 590 1575 1940 436 10312 1742 1486
+
+L 81 7198 6451 * 5935 4401 * 6758 3927 * 472 6251 * 6542 * * * * 3530 6410 * 81
+ 0 * * 0 * 1073 931 10320 1000 1442
+
+Q 82 6551 * 5326 3387 6216 5950 4217 3799 3460 4398 6076 4637 4695 4272 3152 3759 2552 3777 * * 82
+ 57 * 4685 * * 939 1063 10322 0 1164
+
+M 83 * * * * 5066 * * 1106 4465 2243 3936 6618 6052 * 7024 5415 6032 3363 * 6080 83
+ 0 * * * * 2925 204 10300 0 1810
+
+S 84 4849 * 5382 3425 7005 5663 3637 4644 3074 4016 6059 4034 4584 4350 3447 3215 3264 5129 6239 7018 84
+ 0 * * * * 2469 287 10302 0 1688
+
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+ 0 * * * * * 0 10302 0 1542
+
+L 86 2505 5919 7128 * 4604 5674 * 3430 * 1831 6368 6976 6405 * * 4620 3913 2141 * * 86
+ 0 * * 3585 126 2227 347 10302 1000 1542
+
+K 87 6050 * 4144 3263 6793 5223 4845 6622 3264 5282 7034 6999 4847 2454 2968 3717 2627 * 6651 7543 87
+ 0 * * * * * 0 10317 0 1398
+
+S 88 3730 * 6546 3297 5641 5268 * 4594 4347 3003 4125 * 2377 5620 5378 3558 3731 3564 6377 * 88
+ 20 6152 * 0 * * 0 10317 1143 1398
+
+E 89 3584 7052 4207 2411 * 4023 6093 6958 3547 6648 * 3548 * 4354 4503 2030 4384 7032 * 6917 89
+ 0 * * * * * 0 10317 0 1398
+
+D 90 6980 * 389 5061 * 4865 4590 * 6361 7007 * 5849 * 4639 5115 7149 6717 * * * 90
+ 8 * 7444 * * * 0 10317 0 1398
+
+T 91 2986 * 5267 3827 * 4803 5506 * 6232 6034 4417 4461 6974 4825 6121 1458 2702 5411 * * 91
+ 11 * 7052 * * 1301 751 10313 0 1509
+
+A 92 1842 * 7283 5668 * 870 * * * 5170 * * 6694 * 5827 3738 * 5827 * * 92
+ 16 6536 * 480 1820 2275 334 10338 1144 1406
+
+M 93 6265 6967 6219 4010 4738 6629 6094 3295 4560 2826 4404 5566 7321 6072 4706 4466 2697 2498 6306 4677 93
+ 28 7304 6299 2000 415 1481 640 10339 1131 1293
+
+Y 94 * 5313 * * 4255 5989 5336 * * 5457 * * * * * 7322 6715 5552 6949 297 94
+ 19 * 6278 * * 1037 964 10309 0 1402
+
+Y 95 6257 6901 * 4757 2562 6898 5791 4585 5724 2804 6831 6963 * 4341 5279 4091 4239 4923 5110 1855 95
+ 0 * * 3700 115 356 2194 10348 1000 1376
+
+C 96 * 116 * * * 6731 * * 7008 5512 * * * * 7307 6100 5851 * * * 96
+ 19 6944 7735 0 * * 0 10331 1004 1000
+
+V 97 1577 4831 5485 4057 * 3143 5906 5399 4567 5826 5309 * * 3404 4524 3637 6875 3612 * * 97
+ 52 6893 5209 1976 423 1037 964 10059 1099 1088
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+R 98 2553 4789 * 5815 5176 6811 6659 4153 3994 3581 5472 5050 5979 5577 3650 3681 4994 2109 6985 6871 98
+ 146 3695 5724 1433 667 2243 342 9895 2253 1421
+
+H 99 4718 6567 4526 3750 3955 3132 7054 3968 3803 4355 6861 6700 * 4914 3821 2350 5132 5830 4320 4358 99
+ 450 3033 2776 1545 605 1620 568 9896 2393 1715
+
+E 100 3679 6537 3380 4299 6450 4246 4013 5439 4337 3794 6579 3813 4206 4019 3809 3482 3498 4783 6588 * 100
+ 300 4624 2764 3011 191 2345 316 9455 1435 3403
+
+Y 101 4743 5371 4578 5293 6199 2946 6009 5218 4635 4601 5387 3723 4070 6449 3456 2535 3318 6205 6167 4575 101
+ 523 2451 3042 1178 842 874 1137 9306 2819 4415
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+Y 102 5793 * 4809 4340 6277 2545 * 6458 5152 4778 5288 3158 * 4332 4205 2404 3914 5203 5221 3538 102
+ 465 5411 1988 1239 795 2043 401 9426 1502 3684
+
+Y 103 4614 * 4475 5151 4930 3145 5450 6097 3999 3701 * 3174 6273 * 4327 2661 3980 5071 6196 3002 103
+ 216 4483 3404 935 1068 3579 126 9085 1421 5184
+
+A 104 4542 * 2896 4146 5862 2892 * * 5842 4718 5932 2712 2944 5877 5716 3290 5205 5982 * 3667 104
+ 77 4949 5672 900 1108 316 2346 8846 1649 5555
+
+M 105 4053 * 4575 2992 4710 5421 5553 4317 3650 4153 5025 6671 2916 3278 3932 4887 5006 3558 * 6409 105
+ 71 5016 5879 2357 313 608 1539 9573 1433 2225
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+D 106 3748 * 4031 3733 5409 4174 5542 3135 4270 2675 5045 6699 4500 4097 4422 5821 3718 4961 6835 4546 106
+ 108 4294 5573 1332 730 2530 274 9664 1583 1587
+
+Y 107 6573 6592 * 4962 4218 6562 4820 2871 4365 3542 5104 6524 5591 4233 5022 5602 3485 2700 6440 2677 107
+ 79 5070 5412 654 1457 561 1633 9623 1355 1755
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+W 108 6323 5505 6576 * 1091 6441 4930 4930 5681 4039 5443 * * 6510 4545 4994 5699 4982 3054 4363 108
+ 93 4494 5779 1784 495 661 1443 9653 1500 1648
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+G 109 5071 6672 * 5453 6330 1008 5454 6444 5649 6481 * 6599 5648 4628 4861 2645 4622 6598 6203 4925 109
+ 23 * 5955 0 * * 0 9662 1005 1436
+
+Q 110 4642 6686 4222 3770 * 3617 6687 * 3991 6532 * 2823 2871 3264 3561 2652 4947 * * * 110
+ 48 4935 * 1038 963 1841 472 9596 1413 1813
+
+G 111 3415 * 5425 * * 728 6449 5494 6202 5729 * 6598 4566 6469 4521 4081 5499 6526 6189 * 111
+ 50 4878 * 2493 282 711 1362 9642 1268 1554
+
+T 112 3802 * 4827 * * 6238 * 4257 * 4546 6316 5136 5502 5383 * 4255 822 4393 * 4961 112
+ 15 6603 * 1000 1000 * 0 9514 1018 1129
+
+T 113 5626 6596 6335 4874 4231 5441 4210 5700 1991 3745 5550 5017 4652 3007 2678 4745 5952 * 6644 6486 113
+ 15 6603 * 0 * 0 * 9514 1018 1129
+
+V 114 4479 * * 6586 6656 5290 * 3663 6401 600 * * * 4979 * * 6476 3111 * * 114
+ 0 * * * * * * 9560 0 0
+
+T 115 6297 * 4303 4910 5610 5022 4214 3213 6586 4137 * 5542 5407 6312 3903 3238 2268 2756 * 4758 115
+ 16 6463 * 2322 322 * * 9462 1000 0
+
+V 116 * 5245 * 6483 * 5442 * 3079 6387 4859 4609 5879 4842 * 6069 5189 * 645 * * 116
+ 37 5319 * 588 1579 * * 9453 1160 0
+
+S 117 6016 5075 * 3247 * 5285 6440 3768 4007 2859 6370 * 5368 4296 3526 2506 2723 5243 * 6505 117
+ 41 5174 * 1901 450 * * 9263 1259 0
+
+S 118 3392 * 3548 4085 * 2768 6026 6157 5033 4608 * 4574 3076 4164 4305 2800 4462 4534 * 6211 118
+ 120 3952 6014 2698 241 * * 9080 1459 0
+
+A 119 2336 4953 4822 4982 5846 3907 4352 5963 2938 5116 * 4273 3494 4496 4496 3675 4367 4707 * * 119
+ 0 * * * * * 0 8866 0 1000
+
+W 120 3277 * 4332 3322 * * 5577 3633 4178 4794 * * 2059 * 4057 3489 3717 3785 5911 * 120
+ 0 * * * * 0 * 8633 0 1000
+
+R 121 3642 5568 5794 4220 * 5767 * * 2967 4759 * 5568 2474 3210 4797 3640 2478 5624 * 5728 121
+ 0 * * * * * * 8612 0 0
+
+H 122 4730 5301 3924 3831 5571 * 2932 * 5313 2856 5387 2421 4449 5382 5358 3164 4315 5724 * * 122
+ 0 * * * * * * 8190 0 0
+
+P 123 5174 5195 * * * * 5124 5088 5048 5472 * * 590 * 5088 3586 5220 5032 * * 123
+ 0 * * * * * * 7650 0 0
+
+Q 124 * * 4337 2814 * * * * 4511 3298 * 4405 * 1626 3236 3271 4710 4517 * * 124
+ 92 4015 * 0 * * * 6387 1000 0
+
+F 125 * * * * 1912 * * 4413 * 1438 4098 * * * * 4404 4215 3272 * 4181 125
+ 0 * * * * * * 6143 0 0
+
+G 126 * * * 3630 * 1240 * * * * * * * * * 1630 3587 3480 * * 126
+ 0 * * * * * * 4393 0 0
+
+G 127 * * * 3101 * 390 * * * * * * 3057 * * * * * * * 127
+ 0 * * 0 * * * 3453 0 0
+
+//
+�HHsearch 1.5
+NAME 52f7b42c2dd929be3683545ebc8d1362
+FAM
+FILE 52f7b42c2dd929be3683545ebc8d1362
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 11:59:00 2013
+LENG 140 match states, 140 columns in multiple alignment
+FILT 112 out of 736 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEEEEEECCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCEEEEECCCCHHHHHHHHHCCCCCCCCCCCEEEEEEC
+HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEEEC
+>ss_conf PSIPRED confidence values
+9837999999986175068996530012679899999999999860036984668999818981899988988899999982988677899985770454
+9999999999877516637999999999777423579719
+>Consensus
+xkxxxxxiklxvxaGxAxpxPplGpxLGxxGinixxfxkxfNxxTxxxxgxxvpVxixvxxdrsfxxxvxxPxxsxllxkaagxxxgsxxpxxxxxGxit
+lxxvxeIAkxKxxdxxxxxlxxxvkxVxGTaxSmGixVxx
+>52f7b42c2dd929be3683545ebc8d1362
+AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVT
+RKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD
+>gi|156937968|ref|YP_001435764.1| 50S ribosomal protein L11P [Ignicoccus hospitalis KIN4/I]gi|156566952|gb|ABU82357.1| LSU ribosomal protein L11P [Ignicoccus hospitalis KIN4/I]
+-----KVLTFSVEGGNAKPAPPIKPALESVGLDPNEVVQKINEVTKRYKGFTVTVKVIVdPDTKEYEIEVEPPNITELLLKLAGAKAPSGDPIHQKVGDL
+PFEKVIEAALLKAPELTAKTLKGAVKTVLGTARAIGLTVDK
+>gi|76802860|ref|YP_330955.1| 50S ribosomal protein L11P [Natronomonas pharaonis DSM 2160]gi|119390738|sp|Q3INI5.1|RL11_NATPD RecName: Full=50S ribosomal protein L11Pgi|76558725|emb|CAI50318.1| ribosomal protein L11 [Natronomonas pharaonis DSM 2160]
+-----GTIEVLVAGGQADPGPPLGPELGPTPVDVQAVVNEINDQTEAFDGTEVPVTIDYDDDGSFDIDVGVPPTAALIKDELDFETGSGEPNEEFVADMS
+AEQLKTVAEQKLPDLLAYDTRNAAKEVAGTCVSLGVTIEG
+>gi|116335068|ref|YP_802563.1| ribosomal protein L11 [Candidatus Carsonella ruddii PV]gi|13272288|gb|AAK17071.1|AF274444_1 ribosomal protein L11 [Candidatus Carsonella ruddii]gi|116235349|dbj|BAF35197.1| ribosomal protein L11 [Candidatus Carsonella ruddii PV]
+---LKFKLKLILKPNKATPSSGIGPILGQYGINLIDFCNKFNDLT-KFIcLEKINVKIAIFNDNSYQILINTMSLSDYIKEKKNILSFSKKPGYNQLTNI
+NLNDVVEISYF------------------------------
+>gi|156098390|ref|XP_001615227.1| 50S ribosomal protein L11 [Plasmodium vivax SaI-1]gi|148804101|gb|EDL45500.1| 50S ribosomal protein L11, putative [Plasmodium vivax]
+---RIGRFNLVVLSGSAKPSASIGQTLGPLGINMMTFFKEFNERTKNIsKNVPIQVTLEPLNDRTYRFYLRTPTVVWFIRRCARVPMFSPTAKHHTVGSI
+TLAEVFHIAKCKRMDppLINLTLKSICKYIIGTCNSMGIKVC-
+>gi|7524989|ref|NP_050087.1| ribosomal protein L11 [Dictyostelium discoideum]gi|74894767|sp|Q23884.1|RM11_DICDI RecName: Full=60S ribosomal protein L11, mitochondrialgi|1088423|dbj|BAA04733.1| ribosomal protein L11 [Dictyostelium discoideum]gi|4958892|dbj|BAA78069.1| ribosomal protein L11 [Dictyostelium discoideum]
+----LVRLKLIIGAGTASMTPPLGPNLGQYGINSIEFFNDFNTETKe-lFEtGLALRVILWINVMKAFYFELQMPKISNLLKEYYKVECEAAKGGNVYIe
+KERLLKDCFKIAILLCTfnkaekQweqIEKKYLRITVLEILGTCRSCKIYVK-
+>gi|340052452|emb|CCC46732.1| putative ribosomal protein L11 [Trypanosoma vivax Y486]
+--RVLHNWRFFIRAGKATTGPPVGQEFSKLGLKAMDFAKSFNDRTKPFfkDDVELIVRIQVYFDKSYLFAIEPPPTAWFILRALRKKRRETGPVgvrGHY
+CALMTLEMAYEIAKMKPLCwgrPEYPLLETRVRRVVGQARRMGVCFI-
+>gi|71013111|ref|XP_758556.1| hypothetical protein UM02409.1 [Ustilago maydis 521]gi|46098214|gb|EAK83447.1| hypothetical protein UM02409.1 [Ustilago maydis 521]
+---AVNIIYLRATGGEVGASSALAPKIGPLGLSPKKVGEDIAKATGDWKGLRVTVQLTV-QNRQAAVSV-VPSASSLVIKALKEPPRDRKKEKNIKhgGN
+IPLDEIVEIARKMRFKSFAKSLSGTVKEILGTAQSVGCTVNG
+>gi|11496550|ref|NP_044561.1| ribosomal protein L11 [Toxoplasma gondii RH]gi|5231253|gb|AAD41147.1|U87145_16 ribosomal protein L11 [Toxoplasma gondii]gi|3377956|emb|CAA72240.1| ribosomal protein L11 [Toxoplasma gondii]
+-----KIIKLILHTELTNFLSSLSSILGPIGININLFFQEYNKRIKLKNNIDLPLHIIVYNDKSYVLNFNLIYTSFFFITkLQKVFKKK--QNKQYL---
+----IKKFSFLKQIKLFPKSNISICKTIKATLNS-------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 1276 * * 4916 * * * * 4058 * 4330 * 4692 * * 2034 3317 5048 * 5032 1
+ 104 5049 4676 2487 283 * * 3727 1039 0
+
+K 2 3723 * * * * 3893 * * 537 * * 5089 5215 * 3525 * 5332 * * * 2
+ 0 * * * * * 0 3883 0 1000
+
+K 3 3815 * * 3669 5675 * * * 1171 5584 * * 3685 5917 2741 5294 4151 4635 * * 3
+ 144 3393 * 1440 663 0 * 4176 1138 1000
+
+V 4 4647 * 5368 * 4754 * * 2120 3561 2886 5559 * * * 5651 * * 1386 * 5325 4
+ 0 * * * * * * 4662 0 0
+
+A 5 4517 * * 6092 6190 6185 * 3117 2550 2352 6030 6200 * 3909 5026 5014 3911 2260 * * 5
+ 18 * 6363 * * * * 4810 0 0
+
+A 6 2465 * * 4603 6334 2704 5732 4137 2815 6352 * 5056 5308 4893 2831 4808 4281 4446 * 5683 6
+ 83 5011 5309 1756 506 0 * 5619 1124 1000
+
+Q 7 6928 6904 * 6379 4604 * 6656 2855 3014 3238 6294 4695 6781 6297 3197 * 3001 2362 * 4298 7
+ 0 * * * * 1147 866 5591 0 1092
+
+I 8 4915 * * * 4191 * * 1486 * 2214 6323 * 7046 * * * * 1824 5770 5727 8
+ 0 * * * * * 0 5594 0 1025
+
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+ 0 * * 1585 585 0 * 5594 1025 1025
+
+L 10 5532 7435 * * 4404 6597 * 2436 * 993 4984 * * * * 7265 3445 3351 * * 10
+ 0 * * * * * * 5641 0 0
+
+Q 11 5515 * * 4869 5793 * 5832 2934 3333 3499 6120 4599 5168 2814 2714 4774 3859 3623 6492 6148 11
+ 12 6861 * 0 * * * 5641 1000 0
+
+L 12 5670 4691 * * 6123 * * 1746 * 2480 5736 * * 6718 * 6475 6127 1336 * * 12
+ 0 * * * * * * 5682 0 0
+
+P 13 4409 * 7111 2649 5579 3928 5253 4872 3676 3995 * 5297 2159 4885 3820 5401 4000 4538 7737 6575 13
+ 30 * 5605 * * * * 5682 0 0
+
+A 14 877 * * * * 1513 * * * * * * 5353 * * 4053 5597 * * * 14
+ 0 * * * * * 0 5634 0 1065
+
+G 15 5733 * * 5597 * 273 * * 6575 * * 5500 * 3547 * 6065 * * * * 15
+ 0 * * * * * 0 5634 0 1065
+
+K 16 3760 * 4567 3529 * 5331 * 5510 1656 4829 4192 4321 * 3045 5039 3613 4923 5212 * * 16
+ 0 * * * * * 0 5634 0 1065
+
+A 17 396 * * * 6159 * * 4986 * 6456 6704 * 5109 6091 * 5875 5597 3439 * * 17
+ 94 * 3983 * * * 0 5634 0 1065
+
+T 18 3486 * * * * 4637 * * 2442 5589 5988 2873 5154 * 4886 2162 2237 5953 * * 18
+ 0 * * * * 551 1656 5538 0 1413
+
+P 19 2323 * * * 5561 7422 * * * 5261 4968 * 721 * * 4616 4460 5488 * * 19
+ 42 * 5108 * * 0 * 5642 0 1095
+
+A 20 2056 * * 5710 * 1718 5598 * 6075 5576 * 4304 5197 6323 * 2471 3194 * * * 20
+ 42 * 5132 * * * 0 5690 0 1110
+
+P 21 4139 * * 6040 * 6254 * * 5535 * * 6278 360 7368 * 3905 * * * 5119 21
+ 31 * 5535 * * 995 1005 5635 0 1276
+
+P 22 3846 * * 6158 * 6389 5594 * 4480 5696 * * 689 4542 * 3163 5538 5423 * * 22
+ 26 * 5802 * * 1290 759 5681 0 1225
+
+V 23 5156 * * * 4229 * * 2340 * 1255 5600 * * * * 5555 * 1943 * * 23
+ 0 * * 0 * 188 3036 5674 1025 1225
+
+G 24 2717 * * * * 470 * * 6506 5574 6125 * * 5206 * 4630 * 6337 * * 24
+ 0 * * * * * 0 5686 0 1000
+
+P 25 * * 5206 * * * * * 5536 * * * 569 2428 * 3894 6665 6154 * * 25
+ 0 * * * * * 0 5686 0 1000
+
+A 26 1583 * 6726 5231 * * * 3834 3029 5125 4812 5315 * 3494 6500 3721 3535 3537 * * 26
+ 0 * * * * * 0 5686 0 1000
+
+L 27 4852 * * * 4010 * * 3528 * 398 6154 * * * * * * 5470 5574 * 27
+ 0 * * * * * 0 5686 0 1000
+
+G 28 4492 * 5605 6529 5805 358 * * 5236 * * * 6090 6151 * 4288 5689 * * * 28
+ 0 * * * * * 0 5713 0 1000
+
+Q 29 4704 * 6968 5298 7220 4433 * * 4346 6836 6455 6245 1624 1487 6776 3425 6741 * * * 29
+ 10 7181 * 0 * * 0 5713 1000 1000
+
+H 30 3795 * * 7181 3347 * 5025 5621 3332 1832 5059 * * 7281 2895 6869 5310 4504 6537 2921 30
+ 0 * * * * * 0 5713 0 1000
+
+G 31 7118 * 5805 6090 * 215 * * 5547 * * 6081 6852 7084 5265 * * 5605 * * 31
+ 21 * 6126 * * * 0 5713 0 1000
+
+V 32 7053 * * * 5754 6083 * 1428 * 1747 * * * * * * * 1788 * * 32
+ 27 5754 * 1585 585 * 0 5678 1046 1087
+
+N 33 7049 * 3924 5754 * * * 5593 3553 * * 613 3755 5751 * 4607 * 6083 * * 33
+ 0 * * * * * 0 5678 0 1087
+
+I 34 3376 * * * * 5387 * 1479 * 3274 2773 * 3110 5593 * 4630 6048 3654 * * 34
+ 0 * * * * * 0 5678 0 1087
+
+M 35 3129 * * * * 3873 * 3893 2799 5856 1748 3125 4426 4732 4627 6234 6655 5105 * * 35
+ 0 * * * * * 0 5682 0 1087
+
+E 36 3228 * 2617 2240 5178 5223 * * 2820 4511 * 4929 * 2870 * 4523 6685 4165 * * 36
+ 0 * * * * * 0 5682 0 1087
+
+F 37 * * * * 617 * * 3264 * 5597 * * * * * * 6483 2237 * * 37
+ 0 * * * * * 0 5682 0 1087
+
+C 38 4096 1185 * * 4425 3296 * 3989 6405 6090 6738 5915 * * * 4687 4202 2789 * * 38
+ 14 * 6738 * * * 0 5682 0 1087
+
+K 39 5379 * 5403 2935 * * * 5596 949 * * 3102 6082 3561 5224 6613 5057 * * * 39
+ 21 * 6082 0 * 1824 479 5676 1000 1143
+
+R 40 3284 * 1906 1957 * * * * 2871 4854 * 6221 6525 3634 4180 4993 6605 * * * 40
+ 0 * * * * * 0 5655 0 1188
+
+F 41 6976 6461 * * 806 * * 2121 * 4283 * * * * * * * 4831 * 3439 41
+ 0 * * * * * 0 5655 0 1188
+
+N 42 4536 * 6378 * * * 6311 6375 4830 5567 * 318 * 5206 * 5714 6003 * * * 42
+ 0 * * * * * 0 5655 0 1188
+
+A 43 2333 * 2456 1898 6870 6019 * * 2702 4699 * 3841 * * 5902 5891 4993 * * * 43
+ 0 * * * * * 0 5655 0 1188
+
+E 44 2357 * * 3850 * * * 5714 2256 3060 5825 5623 * 3933 2158 4766 * 5440 * * 44
+ 0 * * * * 1264 777 5655 0 1188
+
+T 45 6090 5598 * * * * * 4458 * 6222 * * * * * 4990 277 4344 * * 45
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+I 107 6529 * * * 5585 * * 297 * 5037 * * * * * * * 3015 * * 107
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+
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+ 0 * * * * * * 5628 0 0
+
+K 111 6478 * * * * * 6396 5248 316 3839 4476 * * * * * * 4947 * * 111
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+
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+ 107 3813 * 969 1031 2295 329 5620 1340 1220
+
+N 116 5912 * 7554 4347 3884 5075 * 5541 3714 3895 4207 1893 6205 4494 3886 4582 3539 5149 6578 4285 116
+ 39 5245 * 1000 1000 0 * 5615 1088 1164
+
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+ 46 5312 7326 1000 1000 * 0 5608 1085 1000
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+
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+
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+K 125 * * * 5280 * 6157 * 6426 1017 4185 6478 4480 * 4744 2136 4267 6396 * * 6077 125
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+
+I 126 6207 7048 * 2546 * * * 3462 6728 6451 2608 * * 2923 4093 2203 3362 5849 * 6679 126
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+
+I 127 * * * * * * * 1496 * 2930 6980 * * * * * * 982 * * 127
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+
+E 128 2723 6152 * 5177 * * * 2342 4140 1487 4915 * * 6576 6225 5820 5028 3609 6834 * 128
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+
+G 129 3666 * * 6439 * 364 * * 6043 6204 * 5934 * * * 4025 * 5825 * 6910 129
+ 0 * * * * * * 5607 0 0
+
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+ 20 * 6201 * * * * 5607 0 0
+
+A 131 780 1881 * * * * * 7064 * 3626 * * * * * 6848 6909 4619 * * 131
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+
+K 132 4651 6373 * * 7341 5687 4842 7115 2335 3884 * 3822 * 3572 1394 6163 6686 5362 * 4997 132
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+
+S 133 3133 * * * * 6848 * * 6705 * * 4347 * 5184 4188 539 4379 * * * 133
+ 0 * * * * * 0 5584 0 1025
+
+M 134 7070 3946 * * * * * 2732 * 2875 938 6163 * * * * 7169 3488 6806 * 134
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+
+G 135 6806 * * * * 112 6821 * 5302 * * 5947 * 6012 * * * * * * 135
+ 0 * * * * * 0 5512 0 1025
+
+I 136 5567 2899 * * 6378 * * 935 * 3291 * * * * * * 5327 2453 * * 136
+ 11 6983 * 2104 382 0 * 5533 1067 1025
+
+E 137 4211 5818 5075 2958 * 6113 7273 5991 2142 4645 * 3994 * 4009 5203 5203 2072 5852 * 4950 137
+ 59 * 4634 * * * * 5556 0 0
+
+V 138 6699 6560 * * 5772 * * 1435 * 5572 * * * * * * 6671 835 * * 138
+ 0 * * 0 * 0 * 5505 1164 1164
+
+V 139 5070 6573 2412 2286 6827 5106 * 4754 4612 6341 6726 4204 * * 6605 6284 3717 1858 * * 139
+ 101 3891 * 907 1099 * * 5529 1214 0
+
+D 140 * * 2753 3905 * 1303 * * 2812 * * 4438 4068 6698 3525 * 6212 * * 5539 140
+ 0 * * 0 * * * 5142 0 0
+
+//
+�HHsearch 1.5
+NAME 530957bbdb4e54c1b80f11ba55b52a90
+FAM
+FILE 530957bbdb4e54c1b80f11ba55b52a90
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:30:49 2013
+LENG 241 match states, 241 columns in multiple alignment
+FILT 117 out of 2257 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEEEEECCCCCEEEEEEEEEECCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCEEEECCEECCCCCHHHHHHCEEEEECCCCCCCCCHHHHHHHC
+CCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCHHH
+HHHCCEEEEEECCEEEECCCHHHHHHCHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9799999998179984467423799849979999999999889999999488878887299999974426878885227999413433556499999740
+3445789999999982859999875543344541660318999999999999996099999995876569999999999999997289989999788899
+96388899998997985089999874707899999875249
+>Consensus
+xixxxxlxxxxxxxxxxxlxxxsxxixxGxxxxlxGxnGsGKStLlxxlxGxxxxxxGxixxxgxxxxxxxxxxxxxxixxxxqxxxxxxxtxxenlxxx
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxlxxxxxxxxxxLSxGxxxrlxlaxalxxxpxllllDEPxxxLDxxxxxxlxxxlxxxxxxxtiixxthxxxx
+xxxxdxvxxlxxgxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+>530957bbdb4e54c1b80f11ba55b52a90
+DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLA
+NPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLST
+VKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD
+>gi|258578069|ref|XP_002543216.1| hypothetical protein UREG_02732 [Uncinocarpus reesii 1704]gi|237903482|gb|EEP77883.1| hypothetical protein UREG_02732 [Uncinocarpus reesii 1704]
+RLEVTDLVVGYARDLPAVLRGLSFTVEKNQRNEC-------------NLFPLCPLKAHVQLHPPTQLSRPQ--GYRTAL-HQP-----------------
+----------------------------------------------------------------------------------------------------
+-----------------------------------------
+>gi|3644002|gb|AAC69488.1| ATP-binding protein [Pseudomonas aeruginosa]
+-LQTQALIKRYG--GLLVTDSVSIDVREGELHAIIGPNGAGKTTLINQLSGNFGRMRAMLCMRVRKSLHYLFTIGLAeGCCvrirsPPFSKSSQCSRtRC
+SAAMGaksqpvLLLAsYVGPGRS--RQSCPSCARDHPAVASd--------RCIGSRAGlwRTSSIGASHGFAAKPRVLLLDEPMAGMSPQESTSVIELLK
+SLKGSHSILLIEHDMEAvFALADRITVLVYGKVLCTGTPDEIRNNPEVKTVYL------
+>gi|170017200|ref|YP_001728119.1| ABC-type multidrug transport system, ATPase component [Leuconostoc citreum KM20]gi|169804057|gb|ACA82675.1| ABC-type multidrug transport system, ATPase component [Leuconostoc citreum KM20]
+-MEIKNYSVTFGNR--QLSTNLNVSFSKSKMNIVMGANGAGKSTLLDFVAGVGPKGAVGEKVG-----I----PSYKKIAYQLQQVHFFPtLTVAQTVEF
+YskltnKPKTKMYENAQTVRENLLDPI-----------WDTKMGQLSGGERQIVLTYGQCLLDKEVYIFDEPTSGVDETNAPVILSMINDLVINEHKIVI
+MTSHHSDQLKQFDLNLIT-----------------------------
+>gi|332716583|ref|YP_004444049.1| ABC transporter, nucleotide binding/ATPase protein [Agrobacterium sp. H13-3]gi|325063268|gb|ADY66958.1| ABC transporter, nucleotide binding/ATPase protein [Agrobacterium sp. H13-3]
+-IRLRSVTIC-RDAGgqdlerGFRLREAEVEIGRGDRLMINGEQGVNRRLLFAAMAGLWPWGQGSIEMPEQSDTL-----------FIAQHGYLPTGTLR
+EILAYPRapQRFVEADYVAALTACGLGEMAPRLDE-----HIRWDKKLDSDEQASIRIANALLLKPKFIVIDDLLEGLEKQTQDTLAEVLNG-IDGVAII
+YIGRSE---TFLSVLTPALAH----------------------------
+>gi|120436602|ref|YP_862288.1| ABC-type transporter ATP-binding protein [Gramella forsetii KT0803]gi|117578752|emb|CAL67221.1| ABC-type transporter ATP-binding protein [Gramella forsetii KT0803]
+-LNIEGLEASIE-GET-LFKNVDINLAKGDKVVVFSKDSRATSAFYEIINGKQNAVNGKFQWGVT-----------TSQSYLPADNSdffDNDLTLVDWL
+RQWatsEEEREEVYIRGFLGKMLF----------SGEEALKTCRVLSGGEKVRCMLSRMMMIRANVLMLDEPTNHLDLESITAFNNSLKNF--KGTVLFT
+THDHEFAQTlANRVIELtPGGVIDRYLSFDEYMSD--------------
+>gi|295115774|emb|CBL36621.1| ABC-type sugar transport system, ATPase component [butyrate-producing bacterium SM4/1]
+---------------EPYLQDVSFDVREGEIFGLYGLVGAGRTELLETMFGICTRAAGRVYFRNRLMNFNSAkEAIEHGFALITEErkanGLFLKGDLTF
+NTTIANLDQYKVGmaLSDQKMVKATAQEIKIMHTKCMGPD-DMISSLSGGNQQKVIFGKWLERSPQVFMMDEPTRGIDVGAKYEIYELIIKMANrERPLL
+LFPLRCRRFWESQTVSELCQTVIFLELSTRR------------------
+>gi|254674125|emb|CBA09909.1| ABC transporter, ATP-binding protein, putative [Neisseria meningitidis alpha275]
+AIKFEHVDFSYEAGKP-LLNGFNLTIRPGEKVGLIGRSGAGQIHHRQPAFALLRTAKRHG-FDRRAGHKRRHPRIFTRPNRFGHARYLAAAPFRARQHYL
+RPPRRDRCRNGFRRRTRRSR--------------------------------------------------------------------------------
+-----------------------------------------
+>gi|330961459|gb|EGH61719.1| ABC transporter family protein 61 [Pseudomonas syringae pv. maculicola str. ES4326]
+-VTLEH------CELPYgpPDSRFIdLTLHGPMRVAVIGPNGCGKSTLLKVIAGQLAP-ASGIARHIL------------RTHLIDQHAQTFDPehGIEQ
+VLRNELGTVEEGRFrQVFANA------------GLDARQMAtPFGRLSGGERLRATLAWLAGGrprTDATVAARRSEQSSRHRGAGSSRAVARTIQR--R
+AHRECSRS-------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+D 1 2636 * 2895 3506 * 4971 * * 4303 * * 4478 2811 * 3117 2436 4418 * * * 1
+ 62 4566 * 2157 366 * * 6672 1209 0
+
+I 2 * * * * 4108 * * 1384 * 1473 4140 * * * * * * 2914 * 6739 2
+ 0 * * * * * * 9053 0 0
+
+T 3 4443 6773 3916 2366 * 5220 4739 6862 3045 4715 6264 3978 * 4407 4288 3185 3351 3841 * * 3
+ 43 5099 * 1374 703 * * 9060 1276 0
+
+F 4 3585 6537 6598 * 3073 6137 * 2295 * 2203 4069 * * * * * * 2154 6837 4361 4
+ 13 * 6827 * * * * 9130 0 0
+
+R 5 5706 * 4048 1829 6106 * 4859 5523 3252 * * 3447 * 4224 2892 3371 3710 6603 * * 5
+ 51 6255 5516 1585 585 0 * 9153 1028 1042
+
+N 6 4719 * 2265 5757 * 3063 3542 * 4625 * 6570 1721 6076 4805 4547 5126 5439 6516 * 5669 6
+ 45 6605 5629 1000 1000 619 1520 9079 1000 1368
+
+I 7 4272 6582 6297 * 4123 6370 * 2679 * 1203 * * 5701 * * * * 2083 * 6668 7
+ 0 * * * * * 0 9074 0 1504
+
+R 8 3180 5679 4735 4660 6320 3870 6519 5674 4347 * * 4217 * 4895 3224 2188 2847 4338 5641 6615 8
+ 16 6480 * 0 * 1861 464 9074 1024 1504
+
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+//
+�HHsearch 1.5
+NAME 530b8b90a2b272c2660145f9c38cb283
+FAM
+FILE 530b8b90a2b272c2660145f9c38cb283
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:10:30 2013
+LENG 60 match states, 60 columns in multiple alignment
+FILT 153 out of 1152 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEEEECCCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEEEEHHHEEECC
+>ss_conf PSIPRED confidence values
+997799992251899988135579999999881599979999679978987666689985
+>Consensus
+xxxxxxxalxxxxxxxxxelxxxxgdxixvxxxxxxxwxxxxxxxgxxGxxPxxxvxxxx
+>530b8b90a2b272c2660145f9c38cb283
+CGAEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYG
+>gi|193586979|ref|XP_001952482.1| PREDICTED: tyrosine-protein kinase CSK-like [Acyrthosiphon pisum]
+-----NTGRTHFGTTPQQLVTHSFCDRASPVSpVTNIGSYSSF----------VQHVKD--
+>gi|119593683|gb|EAW73277.1| protein kinase C and casein kinase substrate in neurons 2, isoform CRA_a [Homo sapiens]gi|119593684|gb|EAW73278.1| protein kinase C and casein kinase substrate in neurons 2, isoform CRA_a [Homo sapiens]
+----SSyEKTQSYPTDWSDNESNNPfsstdangeLQSIRrQRHLGERSSIPGPV-----------------
+>gi|302414846|ref|XP_003005255.1| AbpA [Verticillium albo-atrum VaMs.102]gi|261356324|gb|EEY18752.1| AbpA [Verticillium albo-atrum VaMs.102]
+---AQQELREANIPAAQPPAGAQAGGQRALIHSARANtsptlkWstrtggWAPTRrARAASSLATTSSSSRT-
+>gi|161077253|ref|NP_001097376.1| endophilin B, isoform D [Drosophila melanogaster]gi|157400406|gb|ABV53852.1| endophilin B, isoform D [Drosophila melanogaster]
+-----DKSLTNLLEDFHIEFDTTAvSTVIFVTECSpvNEDYMYGK-QGLLKGLVPRAFVEML-
+>gi|32565949|ref|NP_502695.2| Lateral Signaling Target family member (lst-4) [Caenorhabditis elegans]gi|24817571|emb|CAA19487.2| C. elegans protein Y37A1B.2b, confirmed by transcript evidence [Caenorhabditis elegans]
+-----LRKAVENYPtPPGGSSEDAHRQLLerrrkQMLRrHTCSTLIKQDTSASPHKMKPpilmeeedEQHSTGK-
+>gi|55648067|ref|XP_512320.1| PREDICTED: cdc42-interacting protein 4 isoform 6 [Pan troglodytes]
+----HCVAIYHFEDlGPPPPPSQGPARALSLWPrVKTSVlWKKTKGTAGP-GSGGKREAR---
+>gi|328776214|ref|XP_393399.3| PREDICTED: tyrosine-protein kinase CSK [Apis mellifera]
+---------------MTTHSNVTTPNITSHMNtGSTPVILTSNVTNPSNPAALS--VNP--
+>gi|125805800|ref|XP_694393.2| PREDICTED: myosin-VIIa [Danio rerio]
+-RSMYAVAIQD-lsRqgASSALAIFWQGSHIAELQTrrcAVYHkGWRIFSRRrVDKSKeredksnwgsflRCNSDSA----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 4997 0 0
+
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+ 26 5826 * 3907 100 279 2507 10036 1542 1807
+
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+ 43 5099 * 869 1144 * 0 10180 1445 1026
+
+G 14 2165 6924 6188 4784 * 2534 * 5989 4692 * * 6341 2199 6191 5787 2811 3731 6391 * * 14
+ 131 4044 5256 214 2860 1413 679 10216 2096 1130
+
+N 15 3575 7536 3916 3252 6368 4823 4985 6731 3486 6801 5521 4184 4077 3723 3269 3258 3485 5050 * 6225 15
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+
+E 17 3141 6956 3307 3161 * 3654 4990 6090 4746 7083 6375 4352 2558 4058 4913 4108 3358 6558 7557 * 17
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+
+E 18 5300 6698 2095 4558 7267 2342 5406 5612 4422 5802 * 4229 4031 5064 3977 4069 3883 5146 7184 7481 18
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+D 19 4221 * 3147 1417 6960 4194 5416 * 6962 4353 5506 5830 3736 4518 4947 3795 4742 5971 * * 19
+ 49 5717 6152 1681 539 1555 600 10220 1247 1424
+
+L 20 5331 7470 * 6002 5553 6344 7037 2652 7252 1072 5125 7314 5477 5708 5269 4104 * 3455 7076 6381 20
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+P 21 3166 5858 4332 3935 5776 3832 7537 6960 4978 7006 6379 4020 4142 4679 5159 1861 3123 5720 6853 * 21
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+F 22 4456 * 6071 * 1925 * 4950 3207 5875 2039 4297 6608 5089 6034 6401 5446 6796 3255 5578 * 22
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+K 23 4781 7358 4306 3534 7424 5367 4969 * 3005 5472 * 4159 4327 3239 2847 3198 3358 4462 * 6807 23
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+
+K 24 2875 7195 5951 3021 5268 6302 6101 4562 2270 5433 * 5189 3696 4961 3459 4033 4389 4186 * * 24
+ 44 5290 7799 2143 370 1772 500 10279 1373 1345
+
+G 25 5238 5647 3736 5720 * 823 * * 4646 5788 6625 3691 5445 5432 4541 4067 * * * * 25
+ 28 6307 7183 2862 214 0 * 10290 1146 1311
+
+D 26 3852 7250 1488 2251 * 3973 5661 5938 6815 * 7221 5241 5455 3613 4679 4961 4928 * * 7091 26
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+
+I 27 4440 6046 * 4009 5028 7119 5529 2708 3748 3598 5554 6265 5275 5235 3690 3723 5043 2311 * 4823 27
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+
+L 28 4863 6688 * * 4133 5588 6631 1973 * 2083 7225 * 5165 6158 4819 * 6490 2116 6323 4678 28
+ 33 5458 * 2719 238 * 0 10237 1335 1404
+
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+D 32 5101 5590 3976 2443 6027 3846 4125 7111 3487 5246 * 4143 4878 3903 3417 3514 5031 4752 * 4989 32
+ 353 2247 7339 600 1555 1608 574 10232 4792 1657
+
+K 33 4776 5314 3305 3216 6702 4034 5684 4842 2832 4984 6237 5151 5095 3971 3605 3860 3586 4459 7093 6499 33
+ 178 4374 3878 2139 372 * 0 10286 1933 1548
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+P 34 4480 5551 2916 3630 * 3311 4762 4200 5281 4241 6342 5074 4736 4601 5095 2992 3069 4515 * 6454 34
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+E 35 7247 4791 2741 2842 5480 3567 4667 * 5195 6336 7135 2874 4235 5213 3854 3914 3599 7166 7058 5249 35
+ 47 4971 * 2202 353 1024 976 10180 1561 2562
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+E 36 4520 6743 2567 3308 6353 3230 5038 5428 3911 4806 6261 4048 4102 5818 4396 2999 4177 6411 7176 7233 36
+ 182 3449 5212 1113 895 2044 401 10235 2693 1761
+
+Q 37 5548 7121 2628 4081 * 1331 5278 5980 4944 5115 7584 4035 5864 6598 6986 4715 4857 4573 7180 5206 37
+ 58 5017 6894 3638 121 1115 894 10238 1605 2078
+
+W 38 7601 * * 5909 3870 5000 6033 5781 6406 4395 5525 * * 6965 5845 5163 6348 5229 706 4089 38
+ 13 6845 * 2585 263 * 0 10258 1047 1671
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+ 44 5621 6655 2555 269 1587 584 10258 1268 1671
+
+N 40 4453 * 5007 4675 4554 5604 7621 4745 2850 3294 5512 5771 4317 3774 3046 4189 4598 5083 4092 3856 40
+ 30 6221 7116 4731 55 1994 417 10243 1153 1631
+
+A 41 2941 4222 6105 * 6335 1414 * 5333 5522 * 6248 7330 5693 5444 4741 4922 4508 2440 * 7137 41
+ 46 6649 5540 0 * 1254 784 10268 1105 1570
+
+E 42 4483 5704 4483 3125 5810 5836 4916 7070 2834 5107 6185 5833 6556 4485 2299 3888 3279 4234 * 5787 42
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+
+D 43 4391 6869 3480 4984 6960 4585 3812 6024 3746 3348 * 2841 * 6003 3011 3507 3603 4219 * 6595 43
+ 91 4030 * 1079 925 245 2680 9833 1843 4890
+
+S 44 3760 4454 4518 4709 7247 4290 5536 4939 3521 2449 4939 6362 4786 4264 4539 4234 3854 3355 * 5604 44
+ 507 1773 7993 385 2095 * 0 10204 5624 1626
+
+E 45 4231 6751 3172 3732 6162 3135 5295 * 4097 6238 6938 3235 4499 5440 3725 3271 3069 4956 * 6154 45
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+G 46 5152 5998 4534 4393 6147 1099 6925 * 3688 5749 7629 4195 4754 4328 4807 3598 6029 * * * 46
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+
+K 47 3850 6514 5519 3033 6145 5405 5278 4584 2437 5284 7591 4737 4689 3429 2907 3413 5135 5554 * 6806 47
+ 33 7143 6024 0 * 1691 535 10195 1000 1447
+
+R 48 3533 * 6160 2660 6172 5617 6013 4184 3774 4136 7198 4577 5079 4071 3370 3172 3852 4005 6298 5889 48
+ 72 4367 * 2764 230 435 1942 10120 1749 1530
+
+G 49 4555 6060 6051 5144 6924 621 * 6990 4519 7447 * 6227 4473 7072 4792 4156 * * * 5308 49
+ 91 4707 5447 2812 222 * 0 10147 1573 1032
+
+M 50 4286 6572 6773 6372 3110 * 5915 3541 7134 2234 4619 6300 5549 * 5821 3642 6330 4820 2707 3246 50
+ 46 4980 * 4186 82 1766 502 10064 1439 1521
+
+I 51 4165 5515 6392 * 1757 6036 * 3113 5405 3279 6036 * 5213 * * 5118 6502 2004 * 5274 51
+ 46 4987 * 1484 638 1863 464 10096 1513 1329
+
+P 52 5608 * 5547 5669 6432 5520 5828 * 6301 5064 6787 5675 473 7012 6235 4604 5292 * * 6895 52
+ 51 4849 * 2001 415 956 1045 10087 1526 1200
+
+V 53 2697 6314 * 4659 5386 3886 6535 4485 3577 3761 7291 5491 5819 4458 4292 2351 3825 3653 * * 53
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+
+P 54 4275 * 3763 4492 6078 4370 6810 5566 4887 7045 6223 2595 5493 3574 3685 2357 3203 6160 * 6051 54
+ 0 * * * * * 0 9931 0 1255
+
+Y 55 7321 4211 7169 6049 2712 5315 3261 3985 6981 4097 6868 4544 5731 5469 6054 3727 * 4987 5808 1871 55
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+
+V 56 3603 6191 * 6093 5231 5347 * 3210 * 2400 6293 * * 5875 * 3893 4681 1372 6724 6836 56
+ 9 7254 * 0 * * 0 9872 1000 1021
+
+E 57 3512 6611 4260 2251 * * 4972 6923 2600 4892 * 5073 5866 3736 3695 3421 3931 5440 6401 6920 57
+ 21 6080 * 0 * 1388 695 9692 1092 1125
+
+K 58 4753 * 4908 2402 6884 4856 * 3475 4135 3467 4640 6040 2621 4691 3987 4672 5748 3724 * 7189 58
+ 53 4802 * 3768 110 0 * 9505 1258 1021
+
+Y 59 4614 6726 * 4065 5863 * 6562 2495 5193 1720 6600 * * 6435 6387 5764 4965 2294 * 3927 59
+ 74 4318 * 0 * * * 8876 1089 0
+
+G 60 3639 * 2889 * * 2045 5184 * 4430 * * 4321 5026 * * 1615 4026 * * * 60
+ 0 * * 0 * * * 7177 0 0
+
+//
+�HHsearch 1.5
+NAME 5364a334c335e7d706a5569fbc3f602d
+FAM
+FILE 5364a334c335e7d706a5569fbc3f602d
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:04:47 2013
+LENG 165 match states, 165 columns in multiple alignment
+FILT 114 out of 1143 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEEEEEEEECCEECEEEEEEEECCCCCHHHHHHHHHHHCCCCCEECCCEEEEEECCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEE
+EECCCCCCCCEEEEEECCCCCCCCCCEEEEEEEECHHHHHHHHHCCCCCCCCCCCEEEEEEEECC
+>ss_conf PSIPRED confidence values
+9988899999999880216999996776917999999885236782536988899877957981672578888887545752255553104688769998
+43799985556999936884348981699998837999999985688899893457999928309
+>Consensus
+xxxxxvxxdixixxtxxGxixixLxxxxaPxxxxnFxxlxxxxxgxxYxgxxfxrixxxxxiqxGxxxxxxxxxxxsxxxxxxxxexxxxxxxxxGxvsx
+xxxxxxxxxsxFfIxlxxxxxldxxxxvfGxVxxGxxvlxxIxxxxxxxgxPxxxixIxxcgxlx
+>5364a334c335e7d706a5569fbc3f602d
+MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSM
+ANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
+>gi|156848109|ref|XP_001646937.1| hypothetical protein Kpol_2000p44 [Vanderwaltozyma polyspora DSM 70294]gi|156117619|gb|EDO19079.1| hypothetical protein Kpol_2000p44 [Vanderwaltozyma polyspora DSM 70294]
+---------------TIGSFGVTLDCKDSSVEAYNFLKLCKAN---YYNYQCFYDIRKGHSIEFGDGLYR-FKDRKELrvHSTFINsllNknnvdtivpe
+latcsSSVNTKEADMGRIGfktTFKDKERLIGSKVVVAlTDwDSNDGSV--SFFGRVnRRNWDVLDNFNRaIIDEKNELVTDIRI-------
+>gi|85710701|ref|ZP_01041765.1| putative secreted peptidyl prolyl cis-trans isomerase, cyclophilin type [Erythrobacter sp. NAP1]gi|85687879|gb|EAQ27884.1| putative secreted peptidyl prolyl cis-trans isomerase, cyclophilin type [Erythrobacter sp. NAP1]
+---------------NARKVVIQLMPApFSQGWTQNIRTLAR--AEW-YDGISVNRVQDNYVVQWGDPgydnpesgetetkplpdglnvmseadyaatgl
+isvpdprgrprinytlgaammrnamiaangaielpatftealeSGETPPPIKLETGDAYGELATLALgwpvtgsfgnaeepanqfwpvHC-YGMVGVGRN
+ySPDTGsGAELYTVIGHAPrHLDRNIALVGRIVSGMEHLSSLPRGSGTLGfyteeeadkrMPILSIRVAS-----
+>gi|328865705|gb|EGG14091.1| phosphoglycerate/bisphosphoglycerate mutase [Dictyostelium fasciculatum]
+--------------TSKGGIIVELYRDKARLSCERFTNQI--EVGR-YQDTIIHRIVKNLFIQCGRYSINSSSLDNSLMNNNDSSsnsnnddsitsftst
+stttsiydnnnnnnntqptslnssstilnqlyvdssdddeleqeqqqddivyisdnkesnltnskkesssskqqelldkdqfkrlikenNDNGLSFNERG
+LVAMGSYN------QIIFTLDACGALNRKYPIIGRVHpSTMQMLCILESTPTnESNCPIDPIFLTN-----
+>gi|156839035|ref|XP_001643213.1| hypothetical protein Kpol_457p6 [Vanderwaltozyma polyspora DSM 70294]gi|156113813|gb|EDO15355.1| hypothetical protein Kpol_457p6 [Vanderwaltozyma polyspora DSM 70294]
+--------------TSKGNLNVELWAKECPIASKLFIETCL--SKF-WVGSSLGEFgedGSKLYIDFDGDTKF---------KDSIAMEsNSRLLFNREG
+LLGW-----DIDAGLWFVTTSEKC-DGKRKILIGKIV--------------------------------
+>gi|309366416|emb|CAR98339.1| hypothetical protein CBG_27914 [Caenorhabditis briggsae AF16]
+----RIIFDVVSGNLMMGRIIIMLSN-FEPELRKHFYKMADGNRTnRSFSGTIFHRKTNKFIEGGVLTSSNDTSTVESLYTTKPVNNPKFYSKY--VMIA
+NRNIHDDYRGTRFLITTSPLLHCDQDHIPLGTIVCGREIFDQIAELPcDQDGKFLSTLSIHHS----
+>gi|321456758|gb|EFX67858.1| hypothetical protein DAPPUDRAFT_330682 [Daphnia pulex]
+----KCYFRMNINGVMSERIIVQLEKAKAPIMCAKFIEMCTKKDG--YKGSKIYKTIKGesVFCSSGWFHTYDLDQRCDVFTADKSDVAEQRGSM-RFQI
+KKSENGIAQVSTEFNVILANRPRHHRSTSVFAQIIEGLTVFDQISGMDMKQNR----VIFAECGV--
+>gi|159482122|ref|XP_001699122.1| hypothetical protein CHLREDRAFT_193502 [Chlamydomonas reinhardtii]gi|158273185|gb|EDO98977.1| predicted protein [Chlamydomonas reinhardtii]
+---------------EMGDVVVKLLPDLAPASVRELRRMAALLAleGTGCDGCKLYRSEVNFLVQGVIRHPG------AYVATPRRPNPPQKKMMERGLA
+CWAGGM---GGPDWFVNLIDQSGFGDDHLCWGKI-DDMSLLDAIVKLPTK-----------------
+>gi|308813275|ref|XP_003083944.1| peptidyl-prolyl cis-trans isomerase TLP38, chloroplast / thylakoid lumen PPIase of 38 kDa / cyclophilin / rotamase (ISS) [Ostreococcus tauri]gi|116055826|emb|CAL57911.1| peptidyl-prolyl cis-trans isomerase TLP38, chloroplast / thylakoid lumen PPIase of 38 kDa / cyclophilin / rotamase (ISS) [Ostreococcus tauri]
+--------------LNEATLEITVDGYNAPLTAGNFVDNVR--RGV-YRNAPMRRSET--AILGGASN--pDAPSVPleikasdafdPSYRFPLDvqnGE
+aIPSIPLSINGSVAMARS-sdGQSDKDQFFVYLFDkrsaglggLSFEEGEFSVFGYVTKGEEYLGSI-----------------------
+>gi|342181197|emb|CCC90675.1| putative RNA-binding protein [Trypanosoma congolense IL3000]
+-PRPIVTAAVLIE-TSVGTFVVDLYGADCPAATGELVNLCRCK---YFNGCIATEVIPDSvlifshpveALQQQTFASLLDMgGMRHLPLRDGTLdatst
+rqavyaewkrmrrhvarpqdgakgavgaenvefvirpplEAPGTIRY-SGLLLLevpqvesgATTVCHPLKMRLLITLSnrHLDYLEGQFIVVGEVREGC
+DVVEKMRAAPhrrltTSSGittRPSRLVRIKHTTVLP
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 344 2239 * 0 * * * 2117 1037 0
+
+V 2 * * * * * 3061 * 2712 3104 * * * 2371 * * 2840 * 1846 * * 2
+ 0 * * * * * * 3309 0 0
+
+N 3 * * * * 4533 * * * 3628 * * 1243 * * 2108 4399 2936 * * 4530 3
+ 198 2963 * 0 * * * 5539 1342 0
+
+P 4 4745 * 4923 * * * * * 2980 4963 * * 928 3886 3333 3668 * * * * 4
+ 0 * * * * * * 6329 0 0
+
+T 5 * 5213 * 5386 * * 4415 2952 2786 5277 * 4128 * 5241 2765 4350 3611 2971 * 3144 5
+ 0 * * * * * * 7053 0 0
+
+V 6 3528 3743 * * 5320 * * 2644 * 5411 * * 5627 * 4958 * 5257 1025 * 4054 6
+ 0 * * * * * * 7121 0 0
+
+F 7 * * * 5571 1787 * * 5243 * 5438 * 4730 * * 5333 3653 4105 5060 5006 1402 7
+ 0 * * * * * * 7151 0 0
+
+F 8 5021 * * * 1512 * * 3770 * 1710 2538 * * 5538 * * 5427 5464 * * 8
+ 0 * * * * * * 7159 0 0
+
+D 9 5021 * 957 3194 4572 * 4317 * 4787 * * * 5618 4766 4986 * 3931 4011 * * 9
+ 134 * 3492 * * * * 7159 0 0
+
+I 10 * 5409 * * 3094 * * 1576 5528 3593 3517 * 5403 * * 4996 * 1851 * * 10
+ 76 5166 5419 0 * * 0 7074 1034 1328
+
+A 11 2065 * * 2512 * 4080 * 4214 3276 5035 * 4930 * * * 2803 3851 3420 * * 11
+ 0 * * * * * 0 7084 0 1445
+
+V 12 5347 * * 5365 * * 5132 1439 3998 4637 5789 * * * 4620 3550 5798 1791 * * 12
+ 40 5188 * 1000 1000 * 0 7207 1028 1445
+
+D 13 4344 * 2461 2987 4794 3061 * 4721 5855 3758 * 2225 5635 * 5479 4151 5723 * * 5245 13
+ 152 3739 5300 750 1303 * 0 7237 1333 1445
+
+G 14 6053 * 3200 3171 * 1926 6010 * 4208 6037 * 2897 6221 5792 4424 4450 3217 4276 * * 14
+ 44 5062 * 957 1045 248 2661 7365 1111 1631
+
+E 15 4673 6260 6287 3831 * 6295 * 4398 3668 4853 * 5579 * 4419 4213 6097 985 4777 * 6218 15
+ 37 5312 * 2010 412 0 * 7893 1166 1005
+
+P 16 5243 * 3940 4392 4600 6766 6673 5580 5104 4641 5280 2984 3055 5048 5079 2210 2884 6744 * 5854 16
+ 0 * * * * * * 8197 0 0
+
+L 17 3071 5943 6549 4058 4148 6004 6910 4287 2767 2513 4514 * 6736 4315 5657 5072 4664 3341 * 4344 17
+ 0 * * * * * * 8240 0 0
+
+G 18 5765 * * 5698 * 166 6299 * 6761 * * * * 6558 5571 * 7005 6694 * * 18
+ 27 6334 7340 0 * * * 8249 1060 0
+
+R 19 6314 6360 2525 4852 6713 6526 * 7170 3645 5871 * 3863 4917 6954 1759 3543 3195 4567 * * 19
+ 0 * * * * 0 * 8273 0 1000
+
+V 20 * * * * 2875 * * 1530 * 2088 3856 * * * * * * 2230 * * 20
+ 0 * * * * * * 8262 0 0
+
+S 21 6937 * 4117 3945 6778 5492 * 2852 4764 4080 * 4577 6915 5372 4673 3896 2931 1866 * 5856 21
+ 0 * * * * * * 8262 0 0
+
+F 22 4437 7016 * * 3058 * * 1086 * 3285 4796 * * * * * * 2207 * * 22
+ 0 * * * * * * 8262 0 0
+
+E 23 5717 * 2962 1499 * 3400 * 4754 4882 5112 5727 * * 3030 3920 6894 4440 4557 * * 23
+ 16 * 6480 * * * * 8262 0 0
+
+L 24 6453 * * * 5721 * * 4364 * 364 6335 * * * * 6613 * 3040 * * 24
+ 14 * 6709 * * * 0 8233 0 1016
+
+F 25 5073 * 2802 5082 2071 6585 5234 * 5673 4264 6432 4645 * * 4506 5436 * * 4081 1873 25
+ 0 * * * * 896 1112 8216 0 1129
+
+A 26 3480 4683 4285 4911 * 2502 5933 * 4547 5742 * 3538 2637 * 3505 4520 3798 4200 * 5176 26
+ 62 5973 5262 617 1523 * 0 8268 1080 1000
+
+D 27 4513 6828 1490 2538 * * 6061 * 3046 6811 * 4042 * 6016 4998 4419 4201 5423 * 4563 27
+ 71 5616 5173 498 1777 370 2143 8257 1116 1309
+
+K 28 3328 6326 3837 2776 4365 4331 5053 4460 3384 3349 5600 6048 * 5084 5215 4686 5204 3521 4302 6892 28
+ 0 * * * * 0 * 8280 0 1331
+
+V 29 1292 3408 * 5053 4919 6779 5777 5986 5445 5157 6818 7157 * 6882 6515 2658 4297 3388 * * 29
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+
+P 30 5545 6880 6480 5862 6722 * 6811 * 5635 * * 6978 300 5487 5703 6369 5089 * * * 30
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+
+K 31 3397 4511 4936 4058 * 5769 6463 4240 2690 2645 4566 3481 6525 4115 4104 5805 5794 3916 * 6592 31
+ 0 * * * * * 0 8276 0 1000
+
+T 32 2673 * * 5002 6366 3341 4438 4998 * 3703 4173 5918 6706 5771 * 2892 2180 4305 6449 5075 32
+ 0 * * * * 0 * 8276 0 1000
+
+A 33 2193 2807 * * * 4820 6707 6779 6622 6397 * * * * 4547 3143 3461 1665 * * 33
+ 0 * * * * * * 8285 0 0
+
+E 34 3147 * 2982 2703 5884 3973 7034 6880 3601 4208 5820 4633 * 3537 3075 4277 5085 * * 5065 34
+ 0 * * * * * * 8285 0 0
+
+N 35 5308 7414 * 4189 5655 6641 3889 5690 5047 4409 * 1258 * 4763 3113 4841 5279 5265 6935 4195 35
+ 0 * * * * * * 8285 0 0
+
+F 36 * * * * 284 * * 4020 * 4110 6668 * * * * * * 4648 * 6700 36
+ 0 * * * * * * 8285 0 0
+
+R 37 4035 5625 6622 4582 6515 5964 5175 3096 4013 1679 4987 * * 5383 4490 7250 5866 2769 6886 4570 37
+ 0 * * * * * * 8285 0 0
+
+A 38 3953 * 3758 3070 5704 4638 4826 * 2604 6817 * 3532 * 3318 3032 3677 4105 6962 * 5562 38
+ 41 5572 7185 627 1504 * * 8285 1159 0
+
+L 39 4432 * * 5812 5283 * 5238 4590 * 879 3447 4235 * 6596 3990 6650 5393 * 6335 4871 39
+ 14 6695 * 710 1363 * 0 8287 1127 1000
+
+S 40 2072 1497 * 6390 6824 * * 3347 * 4910 * 6484 * * * 7522 4770 2362 * 7027 40
+ 227 5969 2947 1558 599 * 0 8287 1098 1000
+
+T 41 4257 6517 4423 4684 * 6667 5418 5901 2851 3066 6361 4290 5616 4085 2402 4153 2983 5115 * * 41
+ 753 5656 1371 2000 415 * 0 8153 1114 2449
+
+G 42 2988 5457 5047 5826 * 1225 5114 4892 4753 4520 * 4921 5782 4886 4670 3210 * * * * 42
+ 181 4288 3911 2248 341 1810 485 7693 1317 5269
+
+E 43 * * 2599 2484 * 3598 * 4536 2407 5856 * 2839 6225 5143 4424 4093 5300 * * 6294 43
+ 401 3748 2569 2219 349 289 2460 7909 1636 4587
+
+K 44 3308 * 3666 3545 6677 5500 5328 6710 2163 4372 * 3837 5721 4639 2858 3329 6705 5597 * * 44
+ 111 4921 4609 2271 335 2677 245 7956 1221 2857
+
+G 45 5043 6373 3787 4695 * 816 5875 6670 4105 6115 * 4531 6211 * 4845 4541 4878 * * 6530 45
+ 265 3395 3783 2785 226 4123 85 7968 2058 2895
+
+F 46 4392 * 6413 6500 2260 5418 5493 3495 5395 2943 * 5174 5498 5596 4220 4795 4117 4616 5421 2729 46
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+//
+�HHsearch 1.5
+NAME 53ff759256b5d7f5f74b908ef8b7590f
+FAM
+FILE 53ff759256b5d7f5f74b908ef8b7590f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:43:32 2013
+LENG 239 match states, 239 columns in multiple alignment
+FILT 133 out of 556 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEECCCCCCCEECCCCEEECCCCCCEECCCCCEEEEEEEEEECCCCCEEEEEEEECCCCEEEEEECCCCCCCEEEEECCCCCCCCCCEEHHHCCC
+CCCEEEEEEECCCCCCEEEEECCCCEEEEEECCCEEEEECCCCCEEEECCCCEEEEEEEECCCCCCEEECCCHHHHHHHHHCCCCCCCCCEEECCCCCCC
+CCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCC
+>ss_conf PSIPRED confidence values
+9874340258999835077720777621340316688008999999879888378999824897799980147702639997987776665461312379
+9988987874089970688707981899995499999987898748885426599878726760100502011243445411799970251841655588
+689899889971257576999864131210135778789
+>Consensus
+gkxxxxqrrgxgxxxxrxxxxxxxxxxxyrxidxxxxxxgxVxxIxyDPxRsaxIAlvxxxxgxxxYIlAxxglxxGdxIxxgxxxxixxGnxlpLxxIP
+xGtxIxNIExxpgxGgklxRaAGtxAxIixkxxxxxxvkLPSGexkxixxxcxAtIGxVsnxxxxxxxxxKAGxxrxxxxxxxxxxPxVRGvAMNpvdHP
+hGGgxxxxxgxpxxxxrxxxpgxkvgxixxrrtgxxxxx
+>53ff759256b5d7f5f74b908ef8b7590f
+GRRIQGQRRGRGTSTFRAPSHRYKADLEHRKVEDGDVIAGTVVDIEHDPARSAPVAAVEFEDGDRRLILAPEGVGVGDELQVGVDAEIAPGNTLPLAEIP
+EGVPVCNVESSPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVGGGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHP
+FGGGGRQHPGKPKSISRNAPPGRKVGDIASKRTGRGGNE
+>gi|11496537|ref|NP_044547.1| ribosomal protein L2 [Toxoplasma gondii RH]gi|74824921|sp|Q9MTE5.1|RK2_TOXGO RecName: Full=50S ribosomal protein L2, apicoplastgi|5231240|gb|AAD41134.1|U87145_3 ribosomal protein L2 [Toxoplasma gondii]
+---------------------------LYKILDSNfanYGmsFSSAFYvNIIYDSFRRIFLAVYFIi--NsiiKNiyRYFLLTKNLKIGSQIN-fG-FkA
+PLKIGNALPLYKILLGSFIYNIEIRYKGKGSLVKNANHNAIILMIgD-IYVTVKLPSGEIKLLLKNLFCILGqLEIRRKVNKNIKKHAGFNRKL-----S
+IRPKIRGAAMNAVDHPHGGGEG---------------------------------
+>gi|295791976|gb|ADG28988.1| ribosomal protein L2 [Vandenboschia radicans]
+-------------------------------------NRGIITSRHRGGGHKRLYRKIDFERNKMEI--------------CGII-----GSIEYDTKVP
+LGTIIHNIEIIPGRGGRLARAAGTTAKVIAKEGQLATLRLPSGEVRSISQNCIATVGRVGNVDINNKDLGKAGSKRW-----------------------
+---------------------------------------
+>gi|149195350|ref|ZP_01872436.1| 50S ribosomal protein L2 [Caminibacter mediatlanticus TB-2]gi|149134482|gb|EDM22972.1| 50S ribosomal protein L2 [Caminibacter mediatlanticus TB-2]
+----------------------------YRIIDFKrnkFGVPGKVVTIEYDPYRNCRICLISY-------------------------------------
+----------------------------------------------------------------------------------------------------
+------------------------------------------
+>gi|115756514|ref|XP_001202571.1| PREDICTED: similar to MGC84466 protein [Strongylocentrotus purpuratus]gi|115938363|ref|XP_789607.2| PREDICTED: similar to MGC84466 protein [Strongylocentrotus purpuratus]
+-----SGRRGGGaKRNYRMVDFKRVGPVEGPPME------EKVLAVRYDPNRTANIAIVA-GGNKKRYIIASANMEPGDIIRtsghIGRMtVVANEGDAY
+PLGALPIGSLVHCVEIYPGEGAIRVRSGGTSAQILRKVGGQVILQLPSKLQISVNERCVATVGRASGDQHNRMVIGKAGRSRWFgRRPSSGLWQRKGG--
+----------------------------------------------
+>gi|11466313|ref|NP_051141.1| ribosomal protein L2 [Cafeteria roenbergensis]gi|6180095|gb|AAF05792.1|AF193903_15 ribosomal protein L2 [Cafeteria roenbergensis]
+-------------------------------------------GVSYNPIKSGMLFQfINKESGEIFYQPATskfsllEGLNLNETSS---QD----SFR
+EPLSNFNIGEFCSHI----GSSSKinYIKASGSVGKVLQRytwIKNYMLIVLPSGEQKLFLKTQSAVKGANLGNTKLFEKLKMAGRSRWLS-----KRPS
+VRGVAMNPIDHPHGGGEGKTSgGRPS-VSK----------------------
+>gi|23464625|ref|NP_696993.1| ribosomal protein L29 [Monosiga brevicollis ATCC 50154]gi|23344087|gb|AAN28363.1| ribosomal protein L29 [Monosiga brevicollis]
+---------------------------RLRLIDRSrelgIYTKSEIIDIQYNPNISSNIALLSTLNtpSIKFYILASNTMKIGDIIEGYKyndieklnNV
+nlnnnEINNnkIESNYLYNLPIGTNIYNITSLsnknilnekslnniklntkqtylseknlknklknsyltnhlNKNNGVYSRAAGTFSILLKNiEennEL
+RSIVRLPSKKIINIPSNNIASIGKVSNELHKYEIKGKAGTNRLL-----NNRPKVRGKAQNPVDHPMGGKTSGsgGLGKPKKTAW---------------
+-------
+>gi|8928598|ref|NP_059403.1| ribosomal protein L2 [Paramecium aurelia]gi|133115|sp|P15765.1|RM02_PARTE RecName: Full=60S ribosomal protein L2, mitochondrialgi|578755|emb|CAA34047.1| unnamed protein product [Paramecium aurelia]gi|1019633|gb|AAA79258.1| ribosomal protein L2 [Paramecium aurelia]
+--------------------------------------------------KKPYVALVRDSYNSLSYYIAPAGFFVGRTLKTLPtkhdyykkggwKFYIr
+GLGTYVMLRVLRVNDVIFNLLSPSRVLYRLALAAGTYFKILYQSfcKTFYVMTIPSGLIIRVPSEGLAVMGRNSNTQNNKRVLGLAGVNFFN-----GTN
+PRVRGVAMNPVDHPNGGRTK---------------------------------
+>gi|66773824|sp|Q5DUX7.1|RL2H_NYCOV RecName: Full=60S ribosomal protein L2, hydrogenosomalgi|60416551|emb|CAI38861.1| ribosomal protein L2 [Nyctotherus ovalis]
+----------------------------------------------------------------------------------------------------
+--TLVSYVPNILNGRPLFARARGSACLVRYRNklqhLGLIWVKLPSGKYRRVSNGNSVLLGKIAPKLRSELGNTRAG--YWV---NRGIKPQVRGIVKNP
+VDHPNGGRA----------------------------------
+>gi|74002880|ref|XP_545130.2| PREDICTED: similar to Cystatin A (Stefin A) (Cystatin AS) [Canis familiaris]
+--------------------------------------------------------------GRLRTYFSELQLPQGWFLSCGKKAQLSISHVLPTGTIP
+EImrhHRVCCLEEKAATEASWPE----PPQMMSLsppttrdqgDPGEAALGLQEGHHLS-QQSC----GRCSGQKWLHLQAHPEGhCAYHKYVDKRDCWP
+RMQGVAMSPVGHPFS-------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 5046 * * * * 141 * * * * * * * * * 3998 * * * * 1
+ 0 * * * * * * 3470 0 0
+
+R 2 * * * * * * 3466 * 511 * * * * * 2545 * 4789 * * * 2
+ 48 4947 * 0 * * * 3470 1000 0
+
+R 3 * * * * * * 3938 2241 2877 * * 5111 4876 * 1269 4710 * 3819 * * 3
+ 0 * * * * * * 3542 0 0
+
+I 4 * * * * * * * 966 * 2101 * * 4833 * * * 2791 3727 * * 4
+ 143 * 3403 * * * * 3542 0 0
+
+Q 5 * * * * * * * 2227 4745 2198 * * 4369 5421 1533 3696 * 4766 * * 5
+ 0 * * * * * 0 3436 0 1136
+
+G 6 2232 * * * * 5556 * * * * * 3012 3774 3290 4524 2542 4249 2331 * * 6
+ 0 * * * * * 0 3682 0 1136
+
+Q 7 * * * * * 4487 * * * * * * * 245 3880 4524 * * * * 7
+ 0 * * * * * 0 3682 0 1136
+
+R 8 * * * * * * * * * * * 3681 * * 213 4076 * * * * 8
+ 0 * * * * * 0 3682 0 1136
+
+R 9 4281 * * * * * 5290 5079 2244 * * * * * 666 * * 4258 * * 9
+ 71 * 4386 * * * 0 3682 0 1136
+
+G 10 * * * * * 66 * * * * * * * * 4476 * * * * * 10
+ 71 * 4387 1000 1000 1594 581 3598 1046 1223
+
+R 11 4352 * * * * 2780 3952 * 1885 * * 4969 * * 1190 * * * * * 11
+ 0 * * * * 1714 525 3669 0 1213
+
+G 12 4190 * * * * 347 * 4518 4524 * * * * * * 3795 * * * * 12
+ 495 4487 2023 0 * * 0 3682 1010 1136
+
+T 13 * * * * * 1771 * * 4043 * * 4570 * * * 1253 2437 * * * 13
+ 0 * * * * 0 * 3293 0 1534
+
+S 14 * * * * 4968 3811 * 4441 5055 4153 * 4842 2003 6289 2596 2117 5731 * * 4253 14
+ 0 * * * * * * 3972 0 0
+
+T 15 * * * * 4711 * * 4686 2114 * * 3725 * 2937 3682 * 2625 2209 5083 * 15
+ 0 * * * * * * 4365 0 0
+
+F 16 * * * * 1032 * * * * 5295 * 4727 * 4711 * * 5110 * 5468 1482 16
+ 0 * * * * * * 4365 0 0
+
+R 17 * * 4615 * * 5159 3858 5414 3412 * * * * 4437 646 * 4064 * * * 17
+ 60 4615 * 1000 1000 * * 4365 1016 0
+
+A 18 1729 * * 5110 * * * * 4914 5295 5018 4635 * 3944 * 2316 5671 3883 2423 * 18
+ 0 * * * * * * 4365 0 0
+
+P 19 * * * * * 4711 3781 2860 5674 4092 * 3860 1716 5222 5468 3574 5061 2872 * * 19
+ 0 * * * * * * 4365 0 0
+
+S 20 * * 2597 * * 3988 * 5159 2845 * * 6439 4914 5547 4860 1352 3156 * * * 20
+ 167 * 3195 * * * * 4365 0 0
+
+H 21 * * * * 3172 4376 1163 * * * * 3969 * * 4430 4555 4878 4995 2794 4965 21
+ 0 * * 0 * 0 * 4203 1223 1223
+
+R 22 * * * * * 4109 3702 5671 2140 3625 3858 * * 4502 1538 * 4914 4404 * * 22
+ 0 * * * * * * 4365 0 0
+
+Y 23 4266 * * 5110 3544 * 3792 5222 3279 * * 4686 * * 1139 5457 * * * 3110 23
+ 0 * * * * * * 4365 0 0
+
+K 24 4650 * 3138 * * * * 2317 2387 4474 * * 4727 4185 3509 4807 * 2558 * 5414 24
+ 79 5061 5414 0 * * * 4365 1009 0
+
+A 25 1661 * * * * 1016 * * * * * 5200 * 5079 5238 4081 4415 * * * 25
+ 0 * * * * 0 * 4363 0 1010
+
+D 26 3186 * 4815 3774 * * * * 2859 4880 4177 * 1186 * 5848 4482 4246 * * * 26
+ 76 * 4285 * * * * 4393 0 0
+
+L 27 2319 * * * * 4893 * 3936 4064 3319 * 4706 3929 * 4923 4044 3376 2019 * * 27
+ 161 * 3240 * * * 0 4387 0 1064
+
+E 28 5792 6455 4514 4482 5414 6243 5482 4345 2539 2415 4985 3824 * 4627 2154 4418 * * * * 28
+ 35 5395 * 598 1559 1816 482 5506 1034 1327
+
+H 29 * 6478 * 6413 3465 4029 4858 4968 * 3543 * 6968 * 5016 * 6334 6868 4384 * 823 29
+ 0 * * * * * 0 5611 0 1223
+
+R 30 5498 * * * 6643 6242 * 3593 3734 5858 * * 2427 6368 960 6907 5108 5808 * 6374 30
+ 43 * 5077 1585 585 0 * 5627 1223 1223
+
+K 31 4967 * * * 6648 5596 5011 3563 3060 2957 5228 3348 3144 4373 4507 4038 3553 4513 6508 4576 31
+ 270 3373 3753 1194 829 * 0 5125 1458 1096
+
+V 32 * * 6487 * 4026 * * 1122 6384 2705 4902 * * * * 5585 5636 2521 * 4208 32
+ 104 4495 5305 1585 585 * 0 5013 1223 1473
+
+E 33 6463 * 693 3748 * 6360 * * 4719 * * 2812 * * * 3958 4686 * * * 33
+ 80 * 4219 * * 1302 750 4942 0 1797
+
+D 34 6330 * 4941 5015 1301 5448 4720 4525 5582 3777 5383 4387 5660 5102 5299 4195 * * 6805 3178 34
+ 105 4643 5051 830 1193 2948 200 4968 1071 1661
+
+G 35 3489 * 4275 3249 5170 4228 5664 * 1962 4194 * 3091 5133 6766 4337 3777 6601 7914 5724 5011 35
+ 1628 564 * 1535 611 984 1016 4980 2849 1671
+
+D 36 5484 * 3579 3081 4856 3528 5913 3752 3126 6515 5634 4305 4355 4488 3939 4175 3928 6410 * 3716 36
+ 244 3397 4037 724 1342 1919 443 5005 1416 1473
+
+V 37 5210 * 3202 4200 6295 2931 5028 * 4243 3726 * 2821 3985 5419 6714 4423 3756 3699 * 3800 37
+ 123 3811 6587 997 1003 1783 495 5535 1285 1863
+
+I 38 4724 * * 5151 4802 5595 4913 2091 4201 3649 5188 4728 7704 5077 * 3744 4056 2676 * 3563 38
+ 42 5785 6539 1049 952 1359 713 5537 1336 1691
+
+A 39 4957 * 6209 3050 4566 5602 * 3831 2627 5088 * 4414 2811 5314 3441 3428 4348 4534 6638 7074 39
+ 95 4182 6845 532 1696 189 3029 5593 1205 1440
+
+G 40 2870 5899 4775 3137 5435 1207 5755 * 4679 5703 6715 5590 * 6915 * 3400 * * * 5068 40
+ 11 7022 * 1000 1000 * 0 5690 1000 1043
+
+T 41 4852 6611 5974 4013 5900 * * 2946 2179 3701 6258 7210 * 5776 3899 5336 3209 2585 * 5141 41
+ 0 * * * * 1756 506 5690 0 1043
+
+V 42 * * * * 4142 * * 1664 * 6014 * * * * * * * 708 * * 42
+ 0 * * * * * 0 5689 0 1017
+
+V 43 5004 5082 6776 3076 7500 * 7026 2648 3253 2229 6817 7140 * 6662 7167 4628 4691 2632 * 4401 43
+ 125 3596 * 760 1288 * 0 5689 1217 1017
+
+D 44 3976 * 2720 2883 * 4619 5060 * 3759 6768 * 3977 * 4309 2351 2890 4310 * * * 44
+ 0 * * * * * 0 5707 0 1017
+
+I 45 * * * * 4820 * * 1000 5222 2287 * * * * 6464 6183 5749 2401 * * 45
+ 0 * * * * * 0 5700 0 1017
+
+E 46 * * 6675 1377 4647 5896 5449 3120 4448 3448 5031 5744 * 4149 4698 4616 * 3504 * * 46
+ 0 * * * * * 0 5700 0 1017
+
+H 47 * * 6569 5638 * * 1935 6435 4320 6678 * 5303 * 6808 4448 5566 * * * 902 47
+ 0 * * * * * 0 5700 0 1017
+
+D 48 5888 5854 473 4441 * 6464 6623 * 6041 5744 * 4185 * 6771 * 4924 4662 7073 * * 48
+ 0 * * * * * 0 5700 0 1017
+
+P 49 7236 * 6902 5566 * 4450 * * * * * 5744 481 6414 4517 3970 5101 * 5764 5946 49
+ 0 * * * * * 0 5700 0 1017
+
+A 50 4014 4248 * * 4509 2120 * 4312 5251 * * 1290 * * * 5041 5765 6435 5764 4403 50
+ 0 * * * * * 0 5700 0 1017
+
+R 51 * * * * * * 4426 6332 3795 5151 * 4693 * 6392 353 * * 7086 * * 51
+ 0 * * * * * 0 5759 0 1017
+
+S 52 * * 6711 6829 * 3628 4120 6056 4611 * 6448 3055 6984 * 5844 1428 2106 7245 6275 7183 52
+ 0 * * * * * 0 5759 0 1017
+
+A 53 806 3805 * * * 3746 * 5844 * * 5608 * 4787 * 5465 3252 4156 5367 * * 53
+ 0 * * * * * 0 5759 0 1017
+
+P 54 * * * 6925 2664 * 3335 6611 4472 4407 5776 3247 2004 * 3408 6914 * * 6956 2747 54
+ 0 * * * * * 0 5759 0 1017
+
+V 55 5744 * * * * * * 930 * 1933 * * * * 5608 * 5526 2824 * 6482 55
+ 0 * * * * * 0 5759 0 1017
+
+A 56 625 4597 * * 5776 3851 * 5315 6056 5919 4716 4970 * * 6482 4006 * 5478 * * 56
+ 34 5441 * 0 * * 0 5759 1029 1017
+
+A 57 7642 5018 * 5370 * * 6165 3240 3243 1004 * * 6129 5247 4004 5622 5024 4011 * * 57
+ 27 5776 * 0 * * 0 5759 1017 1017
+
+V 58 5298 5625 * * 5447 * * 1958 5608 2885 7307 6338 * * * * 7129 1121 * 4942 58
+ 96 4983 4945 1409 681 * 0 5759 1101 1017
+
+E 59 2962 5151 4406 4486 4651 5723 3832 4664 2453 3907 6963 5053 * 6120 3166 5004 * 3902 6525 4028 59
+ 219 4699 3287 598 1560 1089 916 5709 1087 1125
+
+F 60 6640 * 4569 7171 2302 4112 4634 4128 4803 3692 6755 3981 * * * 4148 6164 6129 5882 1759 60
+ 207 3416 4654 3040 187 844 1175 5658 1296 1592
+
+E 61 * 6376 3825 2142 * 3297 6799 4541 3660 4049 * 4003 4598 5494 4044 3098 4388 5243 * 5636 61
+ 48 6882 5371 0 * 1948 433 5517 1046 1532
+
+D 62 * * 1910 5313 * 3537 4968 5028 5672 * * 2019 4123 4741 6350 3467 5146 4809 * 4956 62
+ 142 4394 4442 357 2189 1200 824 5537 1131 1469
+
+G 63 6394 * 6156 5179 6578 898 7154 * 4114 5443 * 2948 5292 6364 5398 4783 3691 7150 * * 63
+ 343 2298 6944 2294 329 1138 874 5796 2074 1439
+
+D 64 4729 * 4442 2580 5269 4627 4749 3763 2582 3858 * 4880 * 3802 4510 3290 5387 4347 * 6503 64
+ 0 * * * * * 0 5812 0 1335
+
+R 65 6768 * 7203 3958 4328 5119 5884 4629 2257 2647 4390 4252 4938 5343 4196 4822 4348 4863 * 3572 65
+ 201 2943 * 1084 921 2296 328 5812 1409 1335
+
+R 66 4686 6620 * 4422 3074 4999 6226 7249 3240 6001 6189 4920 * 6951 1885 2220 4244 6333 * 7064 66
+ 0 * * * * 169 3176 5810 0 1283
+
+L 67 * * * 6863 4099 * 6023 5388 * 3445 6794 5187 * * * 6103 4666 * 3793 645 67
+ 16 * 6525 * * 0 * 5836 0 1000
+
+I 68 7211 * 6416 * 4334 * 6774 829 * 3904 4442 * * 5312 6900 * 6507 2843 * 3984 68
+ 0 * * * * * 0 5831 0 1003
+
+L 69 6292 6054 * * 5407 * * 1535 5835 1212 7191 * 3136 * * * * 4893 * * 69
+ 0 * * * * * 0 5857 0 1003
+
+A 70 628 4608 * 7577 * * 5021 5428 4365 3773 * * 5679 5258 6968 4203 6496 * * 6379 70
+ 0 * * * * * 0 5857 0 1003
+
+P 71 4536 5262 7052 5407 4894 * 7588 * * 7191 7564 6224 1309 5056 * 3931 1915 3815 * * 71
+ 26 5813 * 2585 263 * 0 5857 1017 1003
+
+E 72 3531 * 3827 1592 * * 4129 7489 3015 4258 * 3523 * 4219 6236 4172 5102 5817 * 5933 72
+ 0 * * * * * 0 5857 0 1003
+
+G 73 * * 5237 5061 * 1000 * * 3187 6702 * 2240 * 5407 6018 7633 3873 * * * 73
+ 0 * * * * * 0 5857 0 1003
+
+V 74 3799 6460 * * 4708 * 6496 3344 4765 1667 2128 * * * * 5039 3906 3721 * 6005 74
+ 0 * * * * * 0 5857 0 1003
+
+G 75 4537 * 6968 5381 3601 5400 4814 * 1591 5335 5398 4566 5407 4310 3749 3605 5294 7272 * 3347 75
+ 0 * * * * * 0 5857 0 1003
+
+V 76 3386 * * 4340 * 6930 * 2167 4259 4130 * * 3255 4477 * 7207 3760 1875 * 6401 76
+ 0 * * * * * 0 5857 0 1003
+
+G 77 * * 7224 * * 129 * * * * * 3670 * * * * * * * * 77
+ 0 * * * * * 0 5857 0 1003
+
+D 78 * * 1071 4825 * * * 6178 4843 * 5990 3369 * 2490 5625 3671 5842 * 5407 6663 78
+ 51 * 4837 * * * 0 5857 0 1003
+
+E 79 7252 7036 * 3575 3783 * * 2223 3506 3931 6524 5066 6957 4914 5678 4555 3152 2614 6844 4925 79
+ 0 * * 0 * 229 2770 5832 1223 1268
+
+L 80 8454 * * * 5433 * * 925 * 2841 7260 * * * * 5813 5835 2064 * 5230 80
+ 0 * * * * * 0 5857 0 1003
+
+Q 81 4698 * * 2972 4350 6881 7194 3546 2861 4839 4983 4553 * 3688 3913 3760 4069 4319 * 3188 81
+ 143 7121 3517 2000 415 0 * 5857 1010 1003
+
+V 82 3195 3455 6149 * 4735 6285 * 2969 * * * 3425 6491 * 6271 1811 2838 6015 6162 4797 82
+ 205 3063 6287 1702 530 807 1223 5619 1582 1249
+
+G 83 * 6642 4292 * 5421 893 5329 5150 6932 5008 6961 5501 6608 6800 6822 2829 4311 * * 4810 83
+ 270 3204 4009 3344 150 2274 334 5767 1391 1117
+
+V 84 4212 6302 3632 2995 5506 5233 * 3608 2654 5549 5685 4158 2933 * 4382 3581 5875 4277 * 6669 84
+ 459 1953 6152 2393 305 135 3486 5605 1862 1278
+
+D 85 6003 * 3057 2866 5332 3797 4472 6537 2679 6411 7172 2011 5945 4103 * 5195 5255 5404 * * 85
+ 391 2174 5990 1621 567 * 0 5804 1818 1046
+
+A 86 1532 6406 4446 4833 4450 5369 5861 3439 6176 4970 * 4650 4481 5344 5957 4236 4807 3032 * * 86
+ 65 5220 5838 3288 156 1702 530 5836 1081 1110
+
+E 87 4281 * 3766 2681 * 5895 * 5365 4319 4332 6043 3503 2808 4465 4341 3365 3554 5260 * 5096 87
+ 12 6900 * 0 * * 0 5781 1000 1123
+
+I 88 3997 * * * 3802 * * 1706 5663 2313 5964 5097 3451 7020 5703 5208 4456 3438 * 6692 88
+ 88 4339 6660 0 * * 0 5781 1122 1123
+
+A 89 3574 * 6018 3911 * 5795 4603 5582 1650 7251 6701 3734 * 4170 3977 3673 3599 4693 7271 5717 89
+ 48 * 4946 2322 322 1781 496 5776 1017 1164
+
+P 90 5534 * 5229 3111 4966 * * 2692 5999 3745 * 3240 2509 * 5099 5634 3822 2737 * 7061 90
+ 62 4577 * 633 1493 0 * 5759 1198 1231
+
+G 91 * * * * * 146 * 6453 * * 6760 5767 * * 6521 4432 * * * * 91
+ 0 * * * * * * 5861 0 0
+
+N 92 * 5612 2424 6453 4803 6637 3778 6563 * * * 1044 6760 5601 7147 3487 4908 * * 6954 92
+ 0 * * * * * * 5861 0 0
+
+T 93 2442 4029 * 6816 5198 * 6937 2784 * 5752 6445 * * * 4485 2366 3725 2524 6781 4715 93
+ 0 * * * * * * 5893 0 0
+
+L 94 7001 * 6429 5238 6047 * 5687 4034 6013 1216 4056 4721 6422 5607 * 4969 3740 4027 5825 3374 94
+ 0 * * * * * * 5895 0 0
+
+P 95 5963 6157 * 6383 5260 6578 7075 5534 4333 4610 5251 5629 792 4743 5944 5008 5422 6149 * 4160 95
+ 13 * 6801 * * * * 5895 0 0
+
+L 96 * * 6574 * 4938 * * 3004 * 498 5911 * * * * 5666 5443 3941 * * 96
+ 0 * * * * * 0 5889 0 1000
+
+A 97 3675 7398 5506 4557 5071 2267 5747 * 2608 5781 7245 4649 * 4604 3316 3284 4278 * 4987 4669 97
+ 0 * * * * * 0 5889 0 1000
+
+E 98 3323 * 3818 4084 5264 5578 4851 * 2869 4440 5674 1915 * 4503 7324 4046 5443 5900 * 3832 98
+ 0 * * * * * 0 5889 0 1000
+
+I 99 5866 6200 * * 4030 * * 922 * 2194 4289 * * * * * 6695 3310 * * 99
+ 0 * * * * 0 * 5890 0 1000
+
+P 100 5931 * 5951 6958 * * * * 5200 5142 * 4730 392 6941 4712 4809 6492 6475 * * 100
+ 13 * 6759 * * * * 5923 0 0
+
+E 101 4763 6643 4704 2229 * * * 2477 4921 2892 * 6567 4785 * * 4981 4219 2246 * 6477 101
+ 0 * * * * * 0 5920 0 1000
+
+G 102 7298 * * * * 227 5302 5421 * * * 4005 * 6876 6181 7392 * * * * 102
+ 34 5421 * 1585 585 * 0 5920 1075 1000
+
+V 103 5911 6919 4591 5945 5755 7133 5422 4887 6484 5961 5886 6433 * * 6395 2575 916 3853 * * 103
+ 0 * * * * * 0 5946 0 1000
+
+P 104 5199 7169 6935 4153 3833 * * 2942 3686 2822 5990 4861 4131 4731 4445 5774 4986 2672 5600 3966 104
+ 0 * * * * * 0 5928 0 1000
+
+V 105 6499 5966 * 7107 6070 * * 1041 * 4645 5442 * * * 6782 * * 1348 * * 105
+ 0 * * * * * 0 6017 0 1000
+
+C 106 7403 2362 * * 4760 7107 1514 6147 * * * 3235 * * 6476 3540 6753 * 6782 2562 106
+ 0 * * * * * 0 6017 0 1000
+
+N 107 5334 3080 * * * 5339 5524 * * 6782 6029 658 * 6121 * 3055 7111 * * 6565 107
+ 0 * * * * * 0 6017 0 1000
+
+V 108 * * * * 6121 * * 901 * 3023 6055 * * * * * 6499 1732 * * 108
+ 38 * 5271 * * * 0 6017 0 1000
+
+E 109 5126 * 5909 442 * 4658 * 5986 * 5851 * * 6508 4965 6106 4249 6400 6447 * 6312 109
+ 27 * 5739 * * 1876 459 5954 0 1096
+
+S 110 5048 6290 6005 3208 4870 7952 5779 3415 3616 1949 4244 4455 5667 6371 5944 3460 4110 5634 5702 6948 110
+ 0 * * * * * 0 5998 0 1138
+
+S 111 5869 * 5305 5563 5281 * 4435 3395 2177 5590 5465 3506 5842 4261 2768 4541 4411 4845 * 3723 111
+ 30 6516 6652 5358 36 * 0 5998 1006 1138
+
+P 112 4387 * 5920 5093 4501 * * 5282 4441 4507 * 5136 898 6461 5159 4332 6277 5590 * 4085 112
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+//
+�HHsearch 1.5
+NAME 55e5f4d58d11858b673e58b73804fab3
+FAM
+FILE 55e5f4d58d11858b673e58b73804fab3
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:19:11 2013
+LENG 155 match states, 155 columns in multiple alignment
+FILT 124 out of 1153 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEECCCCCCCCEECCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHCCCCCHHHHHHHHHHCCCCC
+CCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCCCCHHCCCCCC
+>ss_conf PSIPRED confidence values
+9621207998741312798766628899999836888677886789999999998749863888888889986420444045589999999998488888
+8765568999999999999997267888763536988705568998011145569
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGxxlyxxxCxxCHgxxgxgxxgPxLxxxxxxxxxxxxxxxlxxxixxgxxxx
+MpxxxxxlsdeeixxlxxYlxslxxxxxxxxxxxxxxxxxxxxpxxxxxxxxxxx
+>55e5f4d58d11858b673e58b73804fab3
+APQFFNIIDGSPLNFDDAMEEGRDTEAVKHFLETGENVYNEDPEILPEAEELYAGMCSGCHGHYAEGKIGPGLNDAYWTYPGNETDVGLFSTLYGGATGQ
+MGPMWGSLTLDEMLRTMAWVRHLYTGDPKDASWLTDEQKAGFTPFQPKSSGEDQS
+>gi|148555142|ref|YP_001262724.1| pyrrolo-quinoline quinone [Sphingomonas wittichii RW1]gi|148500332|gb|ABQ68586.1| Pyrrolo-quinoline quinone [Sphingomonas wittichii RW1]
+-------NSERLIVFRIGGpA-PRLPP-LREARPftVAPAQYRGTQAQEQHGAALYGENCGRCHGGPTGAGGYPNLW---KM--TPETHAAFESIVLDGA
+faYAGMASFADVLSKQDARDIHAFLAKP--------------------------------
+>gi|159043030|ref|YP_001531824.1| cytochrome c class I [Dinoroseobacter shibae DFL 12]gi|157910790|gb|ABV92223.1| cytochrome c class I [Dinoroseobacter shibae DFL 12]
+-------------------------------------------GditvDAAAGEKVFR-TGKAYHQVSVdaESRASPRLNGavdravgsiEGFSYSDAFv
+vlnaegtirSTEKFAAFLAKPKnfeKGTMIAFAGLRKKEDRKNMIAYLATCWV------------------------------
+>gi|209486095|gb|ACI48510.1| nitrite reductase [uncultured bacterium]
+---------------------------------------------------------------LRKGATGKPLTPDITLGKG---TDYLKVFISYGSPGG
+MPNWPtsGEMSEKLVDVMARYVQQDPPQP---PEWGMEQMKQTWK------------
+>gi|255034827|ref|YP_003085448.1| heme-binding protein [Dyadobacter fermentans DSM 18053]gi|254947583|gb|ACT92283.1| heme-binding protein [Dyadobacter fermentans DSM 18053]
+-----------------------KGP-GRAWKVEQAVELVEDSLAnrdFERGKQIFSAvLCSRCHAIQGEGAdVGPELTQ----LGTRFSVKDMLEAIII
+PdkavsdqyasisfqmkdgqsivgRevnqdanfyyvsqnpfdpktirkvakkdvassrlspVSIMLPGlINGLNPNELRDLVAYLM--AGGNKN------
+--------------------
+>gi|162448635|ref|YP_001611002.1| cytochrome b6 [Sorangium cellulosum 'So ce 56']gi|161159217|emb|CAN90522.1| cytochrome b6 [Sorangium cellulosum 'So ce 56']
+-----------------------RTARAVALFKQGVPPegalamLRNDP--ETRGEDLYKKECASCHRLNDLGPpkdkQtAPDLTgfgTKAWALEVLRDP
+--DADHLFGKtafkemmpSAVKPPADPeAAkv-FTPMSEADQETIAA---------------------------------
+>gi|320332835|ref|YP_004169546.1| class I cytochrome c [Deinococcus maricopensis DSM 21211]gi|319754124|gb|ADV65881.1| cytochrome c class I [Deinococcus maricopensis DSM 21211]
+-VVFRNGVRPSDVMAPIarRLSDQDVADLAAYYARQPLGPaWPTNAADRERGRALFtrgdpnrnLMACAVCHGADGRGTEGgvASIARLPAAYAQ--KAM
+GVFRDLP--GFGGIPHAEamrialHPLTDTELQQLAAYVSSM--------------------------------
+>gi|94495110|ref|ZP_01301691.1| Cytochrome c, class I [Sphingomonas sp. SKA58]gi|94425376|gb|EAT10396.1| Cytochrome c, class I [Sphingomonas sp. SKA58]
+----------------SSLSDAEMQRLANHFSALP--GL--KPTILLSDLPMLkdQAGipvpaCVNCHAP---GKAGPILAGQRSSYVA--ARLKGWQQE
+KAVVDArqspeTMAMIARRIPLSDVDSLAAAIGQS--------------------------------
+>gi|313681723|ref|YP_004059461.1| sulfite dehydrogenase (cytochrome) subunit sorb [Sulfuricurvum kujiense DSM 16994]gi|313154583|gb|ADR33261.1| sulfite dehydrogenase (cytochrome) subunit SorB [Sulfuricurvum kujiense DSM 16994]
+-------------------------------------PYVDYPIEAGDHDEVAQQYCLICHSFGYVLNQGKK-SRPYWT-----GT----------VQKM
+VNEFKAPIPKEDQQTIINYLVKHYGYE----------------------------
+>gi|291280072|ref|YP_003496907.1| cytochrome c family protein [Deferribacter desulfuricans SSM1]gi|290754774|dbj|BAI81151.1| cytochrome c family protein [Deferribacter desulfuricans SSM1]
+------------------------------LIMIFSAVSYSK-kYPADYGRNTWKKNCRlAC-HDGSKTGvpkLAPNSkTQQQW--------ENVFA-qn
+rkyIYEMHKGVD---fSH--lSEKDWNMIKLFVIQHAYDSDQPES-----------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+S 155 * * * * * * * * * * * * * * * 0 * * * * 155
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+
+//
+�HHsearch 1.5
+NAME 564c9b9e5d4cd66b1fd7f125a716af4e
+FAM
+FILE 564c9b9e5d4cd66b1fd7f125a716af4e
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:34:38 2013
+LENG 113 match states, 113 columns in multiple alignment
+FILT 158 out of 1138 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEECCEEEEECCCCEEEEEEECCCCCCCCCCCEEEEEEECCCCCCEEEEEECCCCCCCCCCCEEEEECCCEEEEEECCCCHHCCEEEEEEECCCCC
+CEECCCEEEEECC
+>ss_conf PSIPRED confidence values
+9789980986999689989999998588656667855999998999996899996465487758848998415489999987783009799999925998
+8899999999719
+>Consensus
+xxxvxqxpxxvxxxxGxxvxLxCxxxxxxxxxxxxxxvxWyrxxxxxxxxxlxxxxxxxxxxxxxrxxxxxxxxxxxLxixxxxxxDsgxYxCxxxxxxx
+xxxgxgtxlxvxx
+>564c9b9e5d4cd66b1fd7f125a716af4e
+DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVP
+PTFGGGTKLEIKR
+>gi|3002929|gb|AAC08955.1| T cell receptor beta chain [Homo sapiens]
+-AQVTQNPRYLITVTDKGdvpegYKVSRKE--KR----NFPLIL---ESPSPNQTSLYFCARsfeQGYEQYFGPGTRLTvTEKRNfPLILESPSPNQTSL
+YFCASSlLgTg-dlwpAQHFGDGTRLSI--
+>gi|291010643|gb|ADD71699.1| immunoglobulin gamma heavy chain [Pteropus alecto]
+QVTLKES-GPGLMRPTQTLTLTCSFSGFSLST-ADMGVSWVRQPPGKALEWLATIWwdddKNYSPSLKSRLTMTKdtSKNQVLLTLTNTDPRDTATYYCA
+RTGlkvGysYVDVWGQGSPVTVS-
+>gi|281349765|gb|EFB25349.1| hypothetical protein PANDA_021873 [Ailuropoda melanoleuca]
+--SVSQMKNQVTLSERAFLIVNHSFAANKSAPpfsGVFSVLVKLCSCPENH----KRKCDGSNKG----FEATnEEKTTFPWEKLSVPMADMAVCHCA--
+-----------------
+>gi|62464905|gb|AAX83161.1| immunoglobulin heavy chain variable region [Aotus nancymaae]
+---------------GDPVPHLRCLWLLHR----Q------willeldpPAPKGRG--WSGldisivwWVHql-qrlpQES-----sh---YFSrhVQEP
+VLVE---------A------------------------
+>gi|321468336|gb|EFX79321.1| hypothetical protein DAPPUDRAFT_212574 [Daphnia pulex]
+--TISYISQEKVIDIGGSIELECSVQYVR-----DFPVLWIKIDNVDPSRTIPLSTGSNLIVKDSRFSLRYDQasSTYTLQIKDIQENDAGKYQCQ----
+---------------
+>gi|328702162|ref|XP_003241824.1| PREDICTED: roundabout homolog 2-like [Acyrthosiphon pisum]
+--RITEHPTDITVPKNEPITLGCKAEGRP-----EPTIEWYKDG-----ELLKippnGAAAGGGGDNgarsSQKVILSDGSLFFLRVAHNKKEQDSGVYW
+CVAKNVAGTEVSRNATLQVAE
+>gi|74218336|dbj|BAE23783.1| unnamed protein product [Mus musculus]
+-------------------------------------------------------------------------MLEMIRKLLLYDDHKSNLVSSPSqLS-
+iQHKLC----FTMRN
+>gi|73972829|ref|XP_851243.1| PREDICTED: similar to triggering receptor expressed on myeloid cells-like 4 [Canis familiaris]
+----EQKPELLRKLEGETISVKCLYQSWQDS---KSVKAWCRQVSARTCTVLASYPRIQGMQWKPGNSIQDwvRLGYFIVTMTKLKVEDSGFYSCGIYKS
+SE-ILT---------
+>gi|149546673|ref|XP_001515336.1| PREDICTED: similar to small intestinal receptor adhesion molecule, partial [Ornithorhynchus anatinus]
+QFSVIGPAEPILALEGKDVELPCHLKPKMNA--ESMEVRWFRSQPSDIVHLYENRKdrfQQQMEEYHKRTKLVTdamDYGSVAVRVYNVTVSDEGQFRCS
+-------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
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+
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+ 0 * * * * * * 9493 0 0
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ 67 5910 5104 354 2199 1511 624 9973 1310 2246
+
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+
+A 45 3702 6833 3942 3173 4555 3973 6186 5975 4610 3639 6964 4210 2013 5218 5551 4241 4702 6030 5889 * 45
+ 79 6181 4653 2241 343 2365 311 9819 1122 3645
+
+G 46 4225 * 3654 3962 5710 1665 6782 5631 4645 7453 * 4139 5960 5406 4245 2857 3775 5661 6211 * 46
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+
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+
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+ 106 4635 5024 532 1697 * 0 9841 1706 3228
+
+P 49 4535 5152 5140 4797 4931 4906 6601 4670 6533 2547 6920 5527 1579 4403 5776 5594 4440 4648 * 5057 49
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+
+R 66 6108 * 6002 4615 6659 4572 4401 * 3254 5940 * 5158 4536 4503 1077 4262 5622 4406 * * 66
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+S 68 4655 * 4262 3721 6522 5730 5162 4582 3405 3959 6919 4181 7212 4702 4013 2541 2534 4479 * 6116 68
+ 30 5617 * 2172 362 2207 352 10027 1335 1765
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+G 69 3012 6879 5707 5622 4035 3418 5140 2957 6982 3053 4272 5587 5117 6283 5171 4030 3805 3457 7548 5891 69
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+G 71 5077 7302 4055 4442 5312 2874 4724 4955 3155 4604 5175 4880 6245 4461 2605 3835 3648 4708 * * 71
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+
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+ 60 4871 7255 287 2472 1257 782 10151 1528 1537
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+T 77 6085 * 4760 5213 5318 4975 4679 5503 3965 4654 5808 4494 3955 4728 4995 1961 2518 4267 7294 6145 77
+ 31 5573 * 2173 362 1234 799 10134 1344 1423
+
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+ 0 * * * * * 0 10133 0 1187
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+K 79 5305 7665 5620 3470 5521 5623 3986 3505 4338 4403 7552 5090 5098 4444 3254 4580 1996 4355 7088 7394 79
+ 21 * 6127 * * 958 1043 10133 0 1187
+
+I 80 7131 * 6865 7433 4617 * * 981 5135 2331 4593 * * * 7218 4764 5691 3556 7056 7151 80
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+
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+
+E 84 4911 * 5420 3420 * 6149 6100 7602 3104 5777 7619 5036 5415 2489 3018 2829 2634 6268 * 7364 84
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+
+A 85 4179 * 5729 3220 4628 7232 6345 4628 3553 2947 4186 * 2704 4908 4364 4484 4131 3502 * 5406 85
+ 16 6540 * 0 * * 0 10107 1083 1485
+
+E 86 3643 7220 3706 2160 * 4694 * 6234 4151 * 6013 3585 * 4875 4164 2096 3940 5888 * * 86
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+
+D 87 6861 * 381 5789 * 5809 4007 * 6357 7150 * 4840 * 5575 5596 7250 5882 * * 7391 87
+ 0 * * * * 1675 542 10106 0 1363
+
+L 88 3056 7285 5290 3224 7712 4215 5520 6296 7424 6453 4970 4508 6397 7721 5743 1552 2824 5095 * 7047 88
+ 10 * 7223 * * 785 1253 10120 0 1208
+
+G 89 1968 * 5811 5827 * 750 6325 * * 6908 * 5681 6808 * 7071 4614 * 5892 * * 89
+ 0 * * * * * 0 10118 0 1175
+
+I 90 5620 6926 5549 4962 4054 6453 5851 3271 5026 3216 4446 3652 * 4960 4939 4738 2192 3173 6861 5561 90
+ 0 * * * * 1106 901 10079 0 1175
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+Y 91 * 5489 * * 4055 7124 4974 * * 5642 * * * * * * 5867 5905 6912 293 91
+ 10 * 7221 * * * 0 10094 0 1030
+
+F 92 5508 7000 * 4816 2701 6926 4945 3464 7351 4130 6784 6827 * 4665 4543 4370 3245 4761 4792 1947 92
+ 0 * * * * 958 1043 10080 0 1187
+
+C 93 7173 108 * * * * 6310 7147 7122 6086 * * * * * 5979 * 6997 * * 93
+ 11 6995 * 1282 764 0 * 10053 1140 1020
+
+S 94 1827 6288 6118 3594 * 3212 6705 5634 4671 5241 4464 * * 3350 4524 3929 4994 3312 * 5618 94
+ 35 6030 6849 1147 866 * * 9730 1114 0
+
+Q 95 2649 5282 * 5929 4313 6721 6680 3710 3895 3406 5718 6109 6781 4506 4638 3781 4714 2039 * 6643 95
+ 232 3274 4466 1497 631 * 0 9573 2323 1000
+
+T 96 3736 5704 4517 4313 4895 3532 5982 4598 3947 5654 5775 4206 * 5152 3657 2332 3940 4677 4759 5046 96
+ 447 2025 5574 1242 793 2979 196 9582 3705 1728
+
+T 97 3427 5657 3057 4236 4260 3673 * 5134 6503 4634 6305 3169 3749 5635 5308 3449 3303 5145 * 4682 97
+ 172 3749 4714 2233 345 2950 200 9314 1792 1893
+
+H 98 4891 4867 3644 5516 6604 2853 4911 * 4797 4595 5400 3060 3639 6526 4253 2841 3536 5424 * 4847 98
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+
+V 99 4672 * 3760 5279 * 2550 5804 6574 4294 4769 6790 2932 4032 4960 4893 3514 4634 4518 5306 3175 99
+ 149 3657 5754 1296 755 1602 577 9230 2341 2244
+
+P 100 3045 * 4265 3392 5376 3999 * 4543 3716 4874 7004 4668 3959 2993 4909 3710 4391 4280 * 4448 100
+ 242 3275 4282 1420 675 290 2455 9281 2192 2197
+
+P 101 3886 * 4313 5189 5010 6021 5006 4300 3456 2068 5210 5649 5038 4032 5947 4620 3904 4044 * 3757 101
+ 69 4427 * 2001 415 578 1600 9289 1643 1638
+
+T 102 6237 6606 4950 4620 5640 4505 5836 3557 4318 3053 4674 * * 4367 4924 3859 4135 2237 * 3215 102
+ 12 6929 * 1399 688 1238 796 9337 1220 1471
+
+F 103 5656 5343 5842 5975 1306 * * 4405 * 4037 5614 * 6222 4873 4507 4339 4104 4620 3383 4223 103
+ 34 6213 6668 1000 1000 * 0 9375 1009 1217
+
+G 104 4535 5525 6459 5614 * 855 6462 6637 4652 5330 * 5695 4386 * 6424 3064 4694 6738 6942 6656 104
+ 33 6403 6550 0 * * 0 9362 1349 1352
+
+G 105 5371 4897 3968 3064 * 3142 5123 * 4279 6550 5539 3254 3482 3336 3897 3400 3913 6427 * * 105
+ 0 * * * * 921 1083 9161 0 1765
+
+G 106 3681 6707 * * 6482 636 5475 6765 * 6654 6485 4940 5581 6228 5415 4697 5518 5121 5295 * 106
+ 0 * * * * 1667 546 9242 0 1298
+
+T 107 4097 * 6290 6761 * 4915 * 4467 5354 4804 6572 6781 6482 5510 * 3708 903 4010 * 4188 107
+ 43 5081 * 448 1905 * 0 9247 1240 1162
+
+K 108 * 6621 6311 5658 4304 * 5644 4988 2278 4410 4363 5014 4969 3169 2280 6534 3453 * * 3809 108
+ 17 6452 * 0 * 0 * 9123 1000 1162
+
+L 109 * * * * 6455 4813 6525 3443 6318 872 * * 6354 6473 6550 6692 6722 2070 * * 109
+ 16 6463 * 2000 415 * * 9102 1000 0
+
+E 110 6293 6351 4810 4049 * 5107 6399 3460 6500 3828 * 4710 5404 3812 3804 3651 2083 3506 * 4120 110
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+I 111 4511 6097 * * 5193 * * 3156 * 4356 5355 * 5271 * 6522 4081 6284 690 * * 111
+ 0 * * * * * * 8823 0 0
+
+K 112 4766 * 4123 2599 * * 5608 4857 2703 2760 4925 * * 4612 3275 3092 3768 5897 * * 112
+ 0 * * * * * * 8240 0 0
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+R 113 * * 3597 3402 * 1653 * * 5011 * * 4316 2983 * 2509 5207 4069 4841 * * 113
+ 0 * * 0 * * * 7078 0 0
+
+//
+�HHsearch 1.5
+NAME 56a96aae83069ea95d56b56dc6e8cd1a
+FAM
+FILE 56a96aae83069ea95d56b56dc6e8cd1a
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:44:52 2013
+LENG 172 match states, 172 columns in multiple alignment
+FILT 146 out of 1066 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCEEEEEEECCCCCCEECCHHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCC
+CHHHHHHHHHCCCCCCHHHHHHCCCCEECCEEEEECCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9988889888589999951888827525799999999987995889987289999999999999854898989981998899985579999998578787
+659999885043688225565440536999899988999899999999999999986606664766323799
+>Consensus
+xxxxxxxxxxxrvxIixtGdExGxxxDxnxxxlxxxLxxxGxxvxxxxxvxDdxxxIxxxlxxxxxxxxxDlVittGGtgxgxxDxtxxalxxxxxxxlx
+gxxxxxxxixxxxpgxxxxlsrxxxgxxxxxxixxLPGxPxaxxxxxxxxlxpxlxxxxxxxxxxxxxxxxx
+>56a96aae83069ea95d56b56dc6e8cd1a
+MSQVSTEFIPTRIAILTVSNRRGEEDDTSGHYLRDSAQEAGHHVVDKAIVKENRYAIRAQVSAWIASDDVQVVLITGGTGLTEGDQAPEALLPLFDREVE
+GFGEVFRMLSFEEIGTSTLQSRAVAGVANKTLILAMPGSTKACRTAWENIIAPQLDARTRPCNFHPHLKKGS
+>gi|213966091|ref|ZP_03394279.1| molybdenum cofactor biosynthesis protein [Corynebacterium amycolatum SK46]gi|213951289|gb|EEB62683.1| molybdenum cofactor biosynthesis protein [Corynebacterium amycolatum SK46]
+--------QVRNAFVVLVGDHFE-NPDGAASLMVELLEEDGYSVDAVVSTGAVKREIRKALDTAV-VGGADLVVTVGGVGVGPRAKTPDATRKVLDVRLQ
+GIEQAIRNSGMGAGALDAGLSRGLAGVSGQTVIINLAESRAAVRDGMATI----------------------
+>gi|145608252|ref|XP_360715.2| hypothetical protein MGG_03258 [Magnaporthe oryzae 70-15]gi|145015744|gb|EDK00234.1| hypothetical protein MGG_03258 [Magnaporthe oryzae 70-15]
+-------QPMPIVRVFSTGKELlreqnevanganqphgrdklhtadpreSSIRDVNGVFLTAAFREVGAESQFLGQLADETKDIADAVSHILSSNPTpNV
+IVTSGGVSVGKFDHVRGALEQHV----HGTRILFHGLAIR-PGHPVLFAMLPNMAGRETAFFGFPGNPGAAAACFRFLAVPYVRHL--------------
+>gi|220905312|ref|YP_002480624.1| MoeA domain-containing protein domain I and II [Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774]gi|219869611|gb|ACL49946.1| MoeA domain protein domain I and II [Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774]
+-------WDRLQLHLAAVADPAptpkkngpavtaaaDGII----PALAALAQDIDCHVQTAPCLPADAGVVRDFLQSALK--AGAHALLLCATGDDALTA
+VRDLMERE------G-RIVAPDIGLL-PGAPAMT-----AVYEGRPVFCLPCSPAGSLTAFDALVAPALLL---------------
+>gi|315161293|gb|EFU05310.1| molybdenum cofactor synthesis domain protein [Enterococcus faecalis TX0645]
+-------GKSMKAEIIAVGTEllLGQVVNTNATFLSEELAALGIDVYYQTVVGDNGGRLETLLTEAEQR--SDLIVLCGGLGPTEDDLTKQVVAQHLHKS
+LVEDQEGLNRLhqffqqsKR-PMTeNNLRQVLAIEGGqvlqnptglavgsfvtEGTTSYLLLPGPPNELIPMFQQAARPLLIDA--------------
+>gi|331003726|ref|ZP_08327220.1| hypothetical protein HMPREF0491_02082 [Lachnospiraceae oral taxon 107 str. F0167]gi|330412109|gb|EGG91504.1| hypothetical protein HMPREF0491_02082 [Lachnospiraceae oral taxon 107 str. F0167]
+------PYRQKKVGIVTTGNEvyYGRIKDTFTPVVINKMKQYGAEIIAHEISSDDVEMEIECIKKVMAA-GADIVLCTGGMSVDPDDKTPYAIGQN----
+--ASRVITYGAPVL-PGAMFML-----AY-ggENenITFMGLPGCVMYEKKTIFDIVLPRI-----------------
+>gi|150377598|ref|YP_001314193.1| molybdopterin binding domain-containing protein [Sinorhizobium medicae WSM419]gi|150032145|gb|ABR64260.1| molybdopterin binding domain [Sinorhizobium medicae WSM419]
+-------VRSPRIRVIDVASV--NHETFSTRLVAECVMTSNGTIAAIETANRDAASIAAALAGE----ACDLLLLIGGTGAGRLDATAEALTLS------
+G-ASIAHGIAVRP-GDTTAI-----GRLGSTPLVALAGAPDHVFAGFLAFVQPVLDRL--------------
+>gi|329120716|ref|ZP_08249378.1| CinA family protein [Neisseria bacilliformis ATCC BAA-1200]gi|327460513|gb|EGF06849.1| CinA family protein [Neisseria bacilliformis ATCC BAA-1200]
+----------TRdFNLIIIGDEilHGSRQDKHFPYFKNLLETHGLRLNSVQYLPDERPQLAKQLERSFSDG--LPAFVTGGIGATPDDHTRQAAAEAAKC
+PLQRHPEAAALIEAVtrKRGestdspehrQRLHMADFPQGAqiipnpYNGIagftllHHHFLPGFPVMAHPMAEWVLHTHYAESF-------------
+>gi|332025568|gb|EGI65731.1| Gephyrin [Acromyrmex echinatior]
+---------QLSIGVLSIGNNLeepgkplksGYVYDISRIIIISLLKNNDFSSLDFGIVNNTSSSIKENIKKALD--KVDILVTLGSAN--DKDLLKQIL
+LEYFEAEI-----YFGNINIK-PGKSTTL--ATCKINDkIKYLLCLSGNPVTAFIIAQALLLPFLKNM--------------
+>gi|262197738|ref|YP_003268947.1| 4-diphosphocytidyl-2C-methyl-D-erythritolsynthas e [Haliangium ochraceum DSM 14365]gi|262081085|gb|ACY17054.1| 4-diphosphocytidyl-2C-methyl-D-erythritolsynthas e [Haliangium ochraceum DSM 14365]
+------GFRPRRVGMVLTELPgvKESQLGRAAANMRARLQRFDCELSDELRCAHTPEAVAAAIVRLRQG-GAGMVLVLGASAIVDrRDVVPSAIEDI---
+---G--GVVEHFGMPvDPGNLLLI-----ARLDEIPVLGVPGCARTLKPsGFDWVLARLCAD---------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+S 2 * * * * * * * * * * * * * * * 0 * * * * 2
+ 0 * * * * * * 1000 0 0
+
+Q 3 * * * * * * * * * * * * * 0 * * * * * * 3
+ 0 * * * * * * 1000 0 0
+
+V 4 * * * * * * * * * * * * * * * * * 0 * * 4
+ 0 * * * * * * 1000 0 0
+
+S 5 * * * * * * * * * * * * * * * 0 * * * * 5
+ 0 * * * * * * 1749 0 0
+
+T 6 * * * * * * * * 1020 * * * * * * * 980 * * * 6
+ 0 * * * * * * 1749 0 0
+
+E 7 * * * 2148 * 2937 * * 2181 * * * 1240 * * * * * * * 7
+ 0 * * * * * * 3120 0 0
+
+F 8 5847 * 5781 * 2633 4027 4322 5700 3660 4190 6536 * 5258 6450 4081 5800 5091 3032 4815 2144 8
+ 46 * 5003 * * * * 7444 0 0
+
+I 9 4140 6682 4256 4240 * 4389 5529 5193 2138 6313 6661 6055 3614 3790 2060 5337 5133 5659 * * 9
+ 15 6548 * 2516 277 0 * 7447 1071 1128
+
+P 10 6920 * 7053 5618 * 6166 5661 * 2762 5974 5707 6836 2123 4581 1852 3532 3659 5326 * * 10
+ 45 6779 5550 1314 742 0 * 7557 1075 1001
+
+T 11 6316 6553 * 6789 5430 6037 * 3279 5802 2638 2941 * 1642 * 4972 * 5955 3130 6466 5411 11
+ 29 5996 7832 1034 966 0 * 8044 1130 1056
+
+R 12 5430 * 7579 6173 6701 6080 7232 7226 2343 5123 * 3273 * 5745 1560 4115 2969 4914 * 6123 12
+ 25 5877 * 1125 885 0 * 8143 1137 1051
+
+I 13 2028 6185 * * 4040 6083 * 2486 * 4416 * * * * * 5033 5712 1422 * 5835 13
+ 11 7014 * 2322 322 * * 8156 1009 0
+
+A 14 1942 3904 * 3950 5639 2134 6419 4836 5286 4802 * 6694 * * 4612 3518 4904 4418 6818 5310 14
+ 0 * * * * * * 8156 0 0
+
+I 15 6761 7089 * * 4348 * * 1258 * 2242 4625 * * * * 6547 * 1980 * * 15
+ 15 * 6596 * * * * 8156 0 0
+
+L 16 5288 * * * 3545 * * 1392 * 1701 5572 * * * * * 6965 2547 * * 16
+ 6 * 7960 * * 0 * 8130 0 1039
+
+T 17 2679 7500 6063 * 7086 5365 * 3446 * 3746 7411 6254 3872 * 6730 2199 2612 2762 * * 17
+ 52 * 4828 0 * 0 * 8156 1000 1000
+
+V 18 5606 * * * 6786 7024 * 2365 * 4667 7142 * * * * 5020 1254 1934 * 6571 18
+ 0 * * * * * 0 8144 0 1269
+
+S 19 4486 * * 7121 * 486 * * * * 7015 5652 * * * 2522 5327 * * 7024 19
+ 0 * * * * * 0 8144 0 1269
+
+N 20 5043 * 1008 7605 6756 4636 7080 * 5517 5527 * 2752 7285 7486 * 3142 3422 * * * 20
+ 44 5065 * 834 1187 0 * 8150 1227 1269
+
+R 21 * * 5618 668 * 6734 6059 * 5253 6862 * 5195 4160 7515 5007 3380 3894 6964 * * 21
+ 845 1223 6073 1426 671 * * 8162 4378 0
+
+R 22 3758 6719 6994 4364 6985 4053 4860 3172 4168 2538 5474 4270 7194 5668 3500 3496 6089 3220 * 5720 22
+ 695 1423 6738 3027 189 * 0 8137 3971 1071
+
+G 23 3864 * 3713 4965 7441 652 7389 * 7125 7341 5742 5633 7034 * 6086 4683 4781 5808 7088 * 23
+ 121 4179 5291 2613 257 354 2200 8119 1461 1232
+
+E 24 6142 7563 4587 2184 * 4604 5388 4970 2813 4251 5949 6914 5624 2941 3388 4737 3654 6804 * 5025 24
+ 139 3448 * 2486 284 279 2507 8130 2039 1300
+
+E 25 4542 6080 4937 5198 * 5913 6943 2292 3908 5080 6913 4980 6073 5466 3348 4364 3122 2401 * 5116 25
+ 73 4336 * 1885 455 973 1027 8162 1456 1060
+
+D 26 4288 6280 4469 3642 5345 7016 7130 3455 4459 3017 * * 4214 4747 2745 5505 4410 3262 * 3360 26
+ 47 5943 5994 619 1519 * 0 8166 1073 1000
+
+D 27 4781 * 809 3648 * 5002 * * * 6715 * 2490 6846 6482 5768 4959 5383 * * * 27
+ 14 * 6727 0 * 2044 401 8138 1000 1165
+
+T 28 3633 5852 7191 4459 5961 4525 5694 5741 3701 4190 6930 * 5441 7119 4257 2122 2075 4464 * 5833 28
+ 27 7191 6426 3322 152 * 0 8140 1000 1190
+
+S 29 3540 6215 6068 * 4881 6782 4158 4051 * 5567 * 1027 * * 6715 2972 3849 6939 * * 29
+ 13 6825 * 0 * 2817 221 8128 1063 1333
+
+G 30 2645 * 7428 6464 5042 2101 6198 5272 6894 4106 6236 * 7056 6107 4484 2081 3153 5699 * 7445 30
+ 22 * 6024 * * 409 2018 8128 0 1276
+
+H 31 2974 * 5535 5152 5218 5103 4226 4864 5628 3971 7130 7273 2060 4293 3728 4117 4744 4668 6250 3878 31
+ 0 * * 0 * 590 1576 8145 1097 1184
+
+Y 32 3490 7166 7096 5986 3062 5313 * 3465 4497 2531 3642 6042 * 6262 7407 4861 4189 3558 4350 3462 32
+ 15 * 6590 2000 415 0 * 8171 1012 1012
+
+L 33 4394 6803 * * 4405 * 6885 1890 * 1104 5334 * * 7242 * * 6087 3230 * * 33
+ 12 6921 * 1000 1000 * 0 8155 1005 1039
+
+R 34 1973 4859 6872 4224 7480 4618 * 4258 3338 5839 4969 6580 5135 4224 3688 3963 3929 3450 * 6559 34
+ 12 6900 * 2000 415 * 0 8170 1002 1039
+
+D 35 2239 * 3939 2509 * 4244 6931 * 4035 6277 * 4130 5750 4628 3471 2705 5347 6263 7094 6996 35
+ 0 * * * * * 0 8170 0 1039
+
+S 36 3849 6069 * 3748 4129 7211 6034 3888 5440 1720 5784 7440 * 5022 3602 4699 4394 4246 4942 4068 36
+ 11 7001 * 2000 415 * 0 8170 1000 1039
+
+A 37 3773 5002 7125 * 3936 7398 * 3470 * 816 5336 * * * * 7098 * 3243 7290 6056 37
+ 14 * 6684 2322 322 0 * 8170 1039 1039
+
+Q 38 4103 6892 4391 2377 4850 5940 5079 6025 3495 4648 6278 4772 5963 3550 2758 3620 3855 * 7036 6382 38
+ 42 * 5137 * * * 0 8174 0 1017
+
+E 39 3348 * 4078 2321 7147 4177 6885 * 3170 4976 5454 4180 6918 4224 2828 3134 4861 * * * 39
+ 74 4477 7623 192 3008 * 0 8107 1387 1297
+
+A 40 2892 5331 5580 5504 4122 * 3775 4224 5503 3262 5377 4924 5514 4531 3146 4869 7294 5378 3643 3220 40
+ 65 4936 6437 1556 600 1548 604 8109 1398 1350
+
+G 41 5542 * 4172 4954 6696 479 6996 * 5704 5563 6152 5999 6293 6970 5417 5504 7069 * * 6340 41
+ 69 4942 6122 581 1593 488 1800 8130 1288 1319
+
+H 42 2882 3995 6045 7651 3449 3211 4394 3120 5086 3478 5410 * * * 7302 5570 7451 3083 4756 3497 42
+ 53 5000 7651 2540 272 642 1477 8155 1208 1241
+
+H 43 5973 * 3416 1855 6837 6809 3967 5541 3297 4631 * 4489 5309 4702 3878 3652 3939 4385 * * 43
+ 34 5405 * 342 2246 1748 510 8172 1170 1087
+
+V 44 4119 5671 7156 * 5207 7214 5118 2967 * 2590 * 7589 3874 * 7165 4760 4092 1416 * 6881 44
+ 39 6737 5862 3408 143 0 * 8170 1121 1039
+
+V 45 3958 6978 4594 3868 5401 4739 6318 2736 3916 4260 7221 4354 7006 4969 4008 4495 3291 2753 6368 6472 45
+ 21 * 6128 * * 0 * 8192 0 1102
+
+D 46 3053 * 3077 4447 4244 3304 5606 5798 4258 5291 6434 6026 6754 4697 2969 3606 4683 4908 6335 3725 46
+ 0 * * * * 0 * 8190 0 1061
+
+K 47 3722 6242 7003 3909 4389 4664 4597 3093 5507 3715 5363 6266 5570 5613 3915 4378 3162 3157 7386 3838 47
+ 45 6097 5979 0 * * * 8196 1086 0
+
+A 48 3809 6132 7482 3182 4670 2503 5792 4345 3899 3424 7380 6855 4013 5389 3812 4588 3532 4349 * 7199 48
+ 8 * 7473 * * 0 * 8172 0 1153
+
+I 49 4809 5865 6892 * 7039 * 4259 1942 5263 4206 6368 6876 4194 7267 3898 4453 3034 2457 * 4654 49
+ 0 * * * * 0 * 8197 0 1000
+
+V 50 3702 3929 * 6101 7474 6458 7451 2728 7200 2501 6273 * 7117 * * 4314 5717 1374 7386 7748 50
+ 0 * * * * * * 8196 0 0
+
+K 51 3434 * 5058 4505 * 3267 * * 2757 * * 5540 1653 5238 3061 4407 5149 * 7360 6118 51
+ 0 * * * * * * 8196 0 0
+
+E 52 5221 * 445 3751 * 7093 5578 * * 6273 * 4820 5843 5967 5225 5938 * 7429 * 7526 52
+ 22 * 6068 * * * * 8196 0 0
+
+N 53 7087 * 1147 2932 6953 4363 5342 7414 5677 * * 3261 * 6805 5783 3812 3670 5492 * * 53
+ 30 7228 6152 0 * 978 1023 8180 1077 1096
+
+R 54 3079 * 7351 3298 4669 5461 5538 3818 5168 3869 4098 * 2388 5900 3181 4682 5098 4494 * 4870 54
+ 6 * 7980 * * 0 * 8182 0 1160
+
+Y 55 3653 * 2472 2105 * 4156 5636 6904 5150 5938 7465 3840 5390 4599 5487 3927 5331 3630 5662 5337 55
+ 0 * * 0 * 0 * 8196 1000 1000
+
+A 56 2118 * 3843 2719 * 5648 * 6889 5680 3120 6206 7155 5611 3344 4098 3605 4833 3970 * 7335 56
+ 10 7132 * 0 * * * 8196 1000 0
+
+I 57 * * * 6813 4180 * 7519 1003 * 2004 4958 * 7033 7507 * * 7477 3008 * 7132 57
+ 6 * 8008 * * * * 8196 0 0
+
+R 58 2541 6298 6616 3684 6878 5884 6547 4986 2564 3598 6286 7106 * 3905 3089 4176 4075 3692 * 6419 58
+ 0 * * 0 * 0 * 8196 1000 1000
+
+A 59 3083 * 3491 2471 7358 4132 5689 7032 3504 5544 6877 3706 * 3681 3639 3281 4452 * 7100 6185 59
+ 24 6273 8008 0 * * * 8196 1043 0
+
+Q 60 1978 4414 * 3262 5785 5341 6339 4116 4418 4075 5244 7047 * 4018 4301 5335 3069 4221 6204 5750 60
+ 22 6687 7448 0 * * 0 8196 1017 1000
+
+V 61 4653 6941 * * 3794 * * 2189 * 1411 4403 * * 6267 * * * 2256 * 6059 61
+ 30 6305 6941 791 1245 0 * 8198 1124 1044
+
+S 62 3547 6168 4006 2894 6586 6305 5680 7408 3139 3637 5465 3898 7094 3640 3203 3635 4181 5306 * 6089 62
+ 24 6447 7673 1000 1000 * 0 8180 1040 1005
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+C 162 2829 1059 3612 * * * * 3942 * * * * 3644 * * * 3885 3560 * * 162
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+N 163 * * 3462 * * * 3348 * 2246 * * 1706 * 3224 3417 3424 * * * * 163
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+F 164 * * * * 571 * * * * 1614 * * * * * * * * * * 164
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+H 165 * * * * * * 1541 * * * * * * * * 1601 * 1614 * * 165
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+P 166 * * * 1614 * * * * * 1601 * * 1541 * * * * * * * 166
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+H 167 * * * * * * 1541 1601 * 1614 * * * * * * * * * * 167
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+L 168 1614 * * * * * * * 1601 1541 * * * * * * * * * * 168
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+K 169 * * * * * * * * 571 * * * * * 1614 * * * * * 169
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+K 170 * * 1024 * * * * * 2024 * * * * * 1930 * * * * * 170
+ 0 * * * * * * 2547 0 0
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+G 171 * * * * * 0 * * * * * * * * * * * * * * 171
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+S 172 * * * * * * * * * * * * * * * 0 * * * * 172
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 5b39e5a7108ee75bcacb74b9050dfe57
+FAM
+FILE 5b39e5a7108ee75bcacb74b9050dfe57
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:02:50 2013
+LENG 152 match states, 152 columns in multiple alignment
+FILT 7 out of 9 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 1.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHCCCEEEEEECHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHH
+HHHHHHHHHCCCCCCHHHHHHHHHHEEECCCCCCHHHHHHHHHHHHHHCCCC
+>ss_conf PSIPRED confidence values
+9721477899999999999998766523530012333256169960606889999999742532046889997099999999885042103666777511
+0767877533336504888766752131478330022887699998863489
+>Consensus
+mxxxxxxxvxfxtaxasikliqasxvldlteddfdfltxdxvwiatdrxrarrxveacvygtldfvgyprfpapvefiaaviayyvhpvniqtaclimeg
+aefteniingvexpvkAAElfafTLrvrAGxkexvxxAEeNxRqkLRAxGvm
+>5b39e5a7108ee75bcacb74b9050dfe57
+MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEG
+AEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM
+>gi|89888099|ref|YP_512793.1| gpD [Enterobacteria phage ID18 sensu lato]gi|71843204|gb|AAZ49372.1| gpD [Enterobacteria phage ID18]gi|71843217|gb|AAZ49384.1| gpD [Enterobacteria phage WA14]
+MK-ANENAVAFQTAIASIKLIQASSVLDLTEDDFEFLTRDRVWIATDRSRARRAIEACVYGTLDFVGYPRFPAPIEFIAAVIAYYVHPVNIQTACLIMEG
+AEFTENIINGVDAPVKAAELFAFTLRVRAGNTELITYAENNAREKLRAQGVM
+>gi|262064213|gb|ACY07191.1| D [Enterobacteria phage G4]gi|262064224|gb|ACY07201.1| D [Enterobacteria phage G4]
+MSKSNESAVAFQTAIASIKLIQASSVLDLTEDDFDFLTRDRVWIATDRSRARRAIEACVYGTLDFVGYPRFPAPVEFISAVIAYYVHPVNIQTACLIMEG
+AEFTENIVNGVERPVKASELFAFTLLVRAGNKDLIGHAETNIREQLRAQGAM
+>gi|89888658|ref|YP_512413.1| gpD [Enterobacteria phage WA13 sensu lato]gi|71842768|gb|AAZ48973.1| gpD [Enterobacteria phage ID32]gi|71842779|gb|AAZ48983.1| gpD [Enterobacteria phage NC35]gi|71842791|gb|AAZ48994.1| gpD [Enterobacteria phage WA13]gi|71842801|gb|AAZ49003.1| gpD [Enterobacteria phage WA45]
+MSNLVATDVNFATSVAALKMLQASAVLDITEEDFDFLTGDKIWIATDRNRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEG
+AEFTENIVNGVERPVKAAELFAYTLRVKAGFKETVLSAEENARQKLRASGV-
+>gi|89888612|ref|YP_512373.1| gpD [Enterobacteria phage ID2 Moscow/ID/2001]gi|71842745|gb|AAZ48952.1| gpD [Enterobacteria phage ID2 Moscow/ID/2001]
+MN-SNESAVAFATALASIKLIQASSVLDLTEDDFDFLTRDRVWIATDRSRARRAIEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEG
+AEFTENIINGIDQPVKAAELFAFTLRVRAGNTDHVTHAETNVREQLRAQGVM
+>gi|242346747|ref|YP_002985209.1| gpD [Enterobacteria phage St-1]gi|240129558|gb|ACS44791.1| gpD [Enterobacteria phage St-1]
+MN--IVSDVNYATSVAALRMLQASAVLDITEEDFDFLTGDKIWIATDRNRARRCVEACVYGALDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLVMEG
+AEFSENIINGVERPVNAAELFAYTLRIKAGFKETVIDAEENARQKLRANGL-
+>gi|15432|emb|CAA25348.1| unnamed protein product [Enterobacteria phage alpha3]
+----------------------------------------------------------------------------------------------------
+---------------NAAEPLRYTLRIKAGFKETVMDAEENARQKLRANGL-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1326 0 0
+
+S 2 * * * * * * * * 2627 * * 1558 * * * 1004 * * * * 2
+ 1004 * 996 * * * * 1326 0 0
+
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+//
+�HHsearch 1.5
+NAME 5b7549a440ece6efc515d1ecf5eab975
+FAM
+FILE 5b7549a440ece6efc515d1ecf5eab975
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:12:57 2013
+LENG 95 match states, 95 columns in multiple alignment
+FILT 103 out of 270 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHCCCCCEEEEEECCCEECCCCCCCCCCCCEEEEEECCCEEEEEEEECCCCEEEEECHHHCCCCC
+>ss_conf PSIPRED confidence values
+98877756304766778653688788998862158988999866860179987543898868985879689999986990159997868810479
+>Consensus
+xxSxGxRxxTRxxxxkxxRxxGxxxxsxxlxxfxxGDxVxIxidpsvxkGmPhxxyhGkTGxVxxxxgxAxxVxvxxgxxxKxixvrxeHlkxxx
+>5b7549a440ece6efc515d1ecf5eab975
+PSSNGPLEGTRGKLKNKPRDRGTSPPQRAVEEFDDGEKVHLKIDPSVPNGRFHPRFDGQTGTVEGKQGDAYKVDIVDGGKEKTIIVTAAHLRRQE
+>gi|159042508|ref|YP_001541760.1| 50S ribosomal protein L21e [Caldivirga maquilingensis IC-167]gi|157921343|gb|ABW02770.1| Ribosomal protein L21e [Caldivirga maquilingensis IC-167]
+ARTHGYRFKSRKLLSKTPREKGRPGLFKWLLAryYRVGDKLAIDIDPVYVSTAPHKRYQGRVGTLIGWRGRALVLEVNFMGERRIIITTPEHVKPLN
+>gi|296241777|ref|YP_003649264.1| 50S ribosomal protein L21E [Thermosphaera aggregans DSM 11486]gi|296094361|gb|ADG90312.1| LSU ribosomal protein L21E [Thermosphaera aggregans DSM 11486]
+RAPRGLRHRTRKLLRKNVRERGsIPPLSLLLVEYKEGDVVHIKINPSVHEGMPHRRYHGRTGVIVGRRGLSYIVKVMAGDKEKILFVRPEHLRLAS
+>gi|167042538|gb|ABZ07262.1| putative ribosomal protein L21e [uncultured marine microorganism HF4000_ANIW133F6]gi|167043078|gb|ABZ07789.1| putative ribosomal protein L21e [uncultured marine microorganism HF4000_ANIW141C7]
+RRSHGTRQGTRSILRRSKTQRGRINIARVMHQYEIGDRVAVVLDGAQQKGMPHRRFQGATGIIQAQQGRAWVIDLHDKNMAKTVVARAEHLRPLE
+>gi|48477461|ref|YP_023167.1| 50S ribosomal protein L21e [Picrophilus torridus DSM 9790]gi|73914084|sp|Q6L228.1|RL21_PICTO RecName: Full=50S ribosomal protein L21egi|48430109|gb|AAT42974.1| large subunit ribosomal protein L21E [Picrophilus torridus DSM 9790]
+KMSKGPRSGSRRVMTKSVKNKGMPKVNEMMKTFEVGDRAAIVINSAVPDGMPHHDFQGITGVITGMQGSCYILSFKVGNVEKKVIAAPVHLRKV-
+>gi|339757944|gb|EGQ43201.1| ribosomal protein L21E [Candidatus Nanosalina sp. J07AB43]
+QKSQGSQQGARKKLKRDSREKT--TVNDRLQSFEQGDKALIHVDSSVQEGRPHMRFHGKTADVTGQRGDAYIVEFDEGDETKTLQIDPAHLNE--
+>gi|148688544|gb|EDL20491.1| mCG5613 [Mus musculus]
+TNTKGKRRGTRYMFSRPFRKHGIVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQHAVGIIVNkqVKGkiLAKRINVRIEHIKHS-
+>gi|290559669|gb|EFD92995.1| Ribosomal protein L21e [Candidatus Parvarchaeum acidophilus ARMAN-5]
+--GNGIHKRSRKRLKLDINERGKIDIKKALQSFDVGDKVVIDPDSRIQRNLPQRSFFGAVGVVLNKKGKAYTIEVKQQGKyPKKIDVLPVHMKRL-
+>gi|162606458|ref|XP_001713259.1| 60S ribosomal protein L21 [Guillardia theta]gi|12580725|emb|CAC27043.1| 60S ribosomal protein L21 [Guillardia theta]
+SRSKGKKSNTRYILTKSKKLTGIK-SNIIINNVSIGDLVDIVIDPSFQSTMPFKFYHGKTGEVFSLNSNSLGIKIQkiVGNRkvCKKINIGLEHLRI--
+>gi|255514076|gb|EET90339.1| Ribosomal protein L21e [Candidatus Micrarchaeum acidiphilum ARMAN-2]
+------------------------SIRDYIKDFQIGERVAIVPKGNF-GNIPHPRYKGKIGEVVERRGKAYVVQIKVMNATRKLVVPAVHLEK--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 3951 0 0
+
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+ 0 * * * * * * 4274 0 0
+
+S 3 4815 * * * * 4301 4688 * * * * * 3814 * * 558 3006 * * * 3
+ 0 * * * * * * 4327 0 0
+
+N 4 6161 * * 4794 3331 5839 2123 * 1765 * * 3022 * 4568 4410 5639 5854 * 6729 4314 4
+ 0 * * * * * * 4327 0 0
+
+G 5 * * * 5009 * 63 * * * * * * * * * 6427 * * * * 5
+ 0 * * * * * * 4327 0 0
+
+P 6 * * * 4984 2610 * * 4901 3243 3011 6411 5775 3199 6755 4618 5625 4376 5538 6603 1986 6
+ 0 * * * * * * 4327 0 0
+
+L 7 * * * * * 5189 5426 * 3919 4600 * 6762 * 4666 334 * * * * * 7
+ 0 * * * * * * 4382 0 0
+
+E 8 2968 4906 * 6180 5247 4857 3116 * 3331 * * 5605 * 5026 2163 2149 5419 * * 5257 8
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+
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+ 0 * * * * * * 4382 0 0
+
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+ 40 5189 * 1000 1000 * * 4382 1072 0
+
+R 11 * * * * * 5244 * * * * * * * * 39 * * * * * 11
+ 0 * * * * * 0 4327 0 1072
+
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+ 0 * * * * 0 * 4327 0 1072
+
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+
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+
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+
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+ 82 * 4173 1585 585 * 0 4397 1000 1000
+
+K 17 3814 * 2506 6743 * 4035 4371 * 2467 * * 4899 2568 6863 4851 2762 4330 6547 * * 17
+ 0 * * * * * 0 4317 0 1226
+
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+ 73 * 4345 1000 1000 803 1228 4317 1000 1226
+
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+
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+
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+
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+ 201 3597 4409 0 * * * 4403 1286 0
+
+T 23 4518 5217 * 6312 6571 5852 6162 3060 4330 3343 2868 4577 4566 6041 3742 6537 4092 2263 * 5778 23
+ 45 * 5018 * * * 0 4329 0 1150
+
+S 24 4630 6292 * 5945 * 6191 * 3171 5974 4030 * 4050 1604 5660 * 2804 6944 2708 * 6027 24
+ 23 * 5974 * * 633 1494 4305 0 1279
+
+P 25 5615 5222 5539 6970 * 3435 4190 6324 4029 5106 7401 3762 1720 6887 3796 2938 4176 6243 * 6560 25
+ 0 * * * * 1527 615 4357 0 1135
+
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+ 0 * * 0 * 0 * 4387 1074 1074
+
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+
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+
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+
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+
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+ 0 * * * * * * 4425 0 0
+
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+ 40 5825 6687 1000 1000 * * 4425 1029 0
+
+F 33 * * * * 1061 * 5140 6360 * * * * * * * 5224 * 5185 * 1232 33
+ 0 * * * * * 0 4418 0 1000
+
+D 34 7018 * 3313 2480 * * 4639 * 1341 * * 3620 * 4337 3316 4791 6620 * * * 34
+ 0 * * 1000 1000 0 * 4418 1000 1000
+
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+
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+ 11 7061 * 0 * * * 4437 1000 0
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+G 50 * * * 6061 * 252 * * * * * 4523 * * 5300 * 3712 * * * 50
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+
+H 53 6653 * 6463 * 3187 * 644 * * * * 5615 4187 4799 * * * * * 3084 53
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+
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+ 0 * * * * * 0 4420 0 1037
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+G 61 4463 6595 * * * 166 * * * * * * * * 5219 * * * 5251 * 61
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+
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+
+V 63 * 6653 * * * * * 1843 * 5813 * * * * * 5251 * 584 * * 63
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+
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+ 0 * * * * 0 * 4420 0 1037
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+G 65 5692 * 4881 4636 * 1297 6369 7048 5573 * * 1464 * * * 3650 5883 * * * 65
+ 0 * * * * * * 4403 0 0
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+K 66 6368 * * * 6523 * * 3232 2196 5392 4970 * 6315 3819 4114 * 4389 1364 5701 * 66
+ 17 6455 * 1000 1000 * * 4403 1004 0
+
+Q 67 6193 * * * 5866 4174 * * 4397 * * 3225 * 3121 1572 4982 1855 * * * 67
+ 0 * * * * * * 4394 0 0
+
+G 68 * * * * * 970 * * 2780 * * 5413 2819 3522 3841 6025 7285 * * * 68
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+
+A 70 487 3808 * 6036 * 4314 * * * * * * * * * 2915 5859 * * * 70
+ 0 * * * * * * 4355 0 0
+
+Y 71 * * * * 4497 * * 3954 * 3002 4062 * * * * * * 1787 4727 1399 71
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+
+V 76 7019 * 5488 6265 6724 6027 4103 * 2347 * 5250 1824 6016 4773 3326 5757 3776 5182 6575 3514 76
+ 731 1331 * 1000 1000 * 0 4334 2341 1022
+
+D 77 * * 2127 5488 4313 * 6928 3838 3687 3870 6858 6431 * 5566 * * * 1263 5941 * 77
+ 0 * * * * 0 * 4334 0 1022
+
+G 78 * 6953 6273 * * 909 * 6667 3374 * 4570 3658 * 3601 2989 6588 * * * * 78
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+
+G 79 * * 2982 5272 * 1580 3825 * 6588 * * 1845 6163 * 6985 4143 5671 4167 * * 79
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+
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+
+E 81 2814 6006 5742 2210 6828 5892 * 5023 3375 4565 6511 5398 3981 5040 3328 7007 3259 4422 * 5294 81
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+
+K 82 * * * * * * * * 113 * * * * 6036 4050 * * * * * 82
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+
+T 83 * * 6588 4690 * * 5279 3666 2345 4877 * * * 5827 1545 * 2354 4869 * 5299 83
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+
+I 84 * * * * 4746 * * 1165 * 1772 * * * * * * * 2159 * * 84
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+
+V 86 3013 * * * * * * 2551 * 4676 * * * * * 4673 3389 911 * * 86
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+
+T 87 5423 * 5562 * * 4868 4616 * 4983 3256 * 6001 5594 * 747 4855 3975 * * 6168 87
+ 0 * * * * * * 4355 0 0
+
+A 88 3322 * * * 4386 * * 2008 6363 5245 * * 1305 6776 * * 4635 3171 * * 88
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+
+A 89 3564 * 3651 634 * * * * * * * 5859 * 4256 * * * 3038 * * 89
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+H 90 * * * * * * 45 * * * * * * 5017 * * * * * * 90
+ 0 * * * * * * 4355 0 0
+
+L 91 * * * * * * * 2183 * 1139 5086 * * * * * * 1755 * * 91
+ 0 * * * * * * 4355 0 0
+
+R 92 7315 * * 5383 6474 * 6533 6750 1352 6881 * 5253 * 4971 1408 5307 5344 4228 * * 92
+ 24 5892 * 2000 415 * * 4355 1037 0
+
+R 93 4371 * * 4635 * 5882 3307 6006 2169 4848 6158 * 1446 4779 3564 * 5742 * * * 93
+ 21 * 6101 * * * * 4355 0 0
+
+Q 94 6284 5924 5704 * 3860 * 6441 4586 * 2583 * 6850 * 2296 * 1409 * 4237 * 5593 94
+ 0 * * * * 0 * 4177 0 1011
+
+E 95 4623 * * 2949 * 4265 * * 1243 * * 3367 5691 4605 4773 4514 4290 3909 * * 95
+ 0 * * 0 * * * 3401 0 0
+
+//
+�HHsearch 1.5
+NAME 5b8f9d914431e9d2b55e563b03e7b909
+FAM
+FILE 5b8f9d914431e9d2b55e563b03e7b909
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:30:08 2013
+LENG 206 match states, 206 columns in multiple alignment
+FILT 56 out of 58 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHHHCCCC
+CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCEECEECCCCCCCCCCCCEEECCCCEEEEEEEEECCCCCCCCCEEEEECCCEEE
+EEECCC
+>ss_conf PSIPRED confidence values
+9854335689867887635667987356978100899999998653438683242066445556654546755402113120347542036999828474
+6478875015089999999999887426837998853586538761200304588775789994164177568999888658998885127984666897
+776279
+>Consensus
+xqxxxxlrpxpsdxlpxxxlxexpdpxxxPkxxdLxxxxLrxxLGxxfDxxxmSixxPxxxxxxxxxxxxxxxxlxxxdxxxrxxxxxxlpxexxxlxfx
+xxxxxGxxxxxsxxxxrxlrxWLxxxtxCpvxyxWxDLGxxFWPRwIKxGxCxxxxSCSxPxGMxCkpsxsxxlxlLRWxCxxxxxxxCxWxxvxyPiit
+eCxCsC
+>5b8f9d914431e9d2b55e563b03e7b909
+MQHYLHIRPAPSDNLPLVDLIEHPDPIFDPKEKDLNETLLRSLLGGHYDPGFMATSPPEDRPGGGGGAAGGAEDLAELDQLLRQRPSGAMPSEIKGLEFS
+EGLAQGKKQRLSKKLRRKLQMWLWSQTFCPVLYAWNDLGSRFWPRYVKVGSCFSKRSCSVPEGMVCKPSKSVHLTVLRWRCQRRGGQRCGWIPIQYPIIS
+ECKCSC
+>gi|99030980|gb|ABF61775.1| noggin1 [Nematostella vectensis]
+--------------DPPVRLSLPPELNFGILPTNINREELLAILGQDYDREYVAETFSEVLLR------KTNKSIYDNENFYRKTLVKSMPEGLRKLDFQ
+--M-PGEGRNLGPKASRKLQLWLWELSSCPVYQKWKDQGQLIWPRYRNIGRCSRKSTCSYPGGMKCKRSKTKRVALLRWFCRG---KLCQWLKFFVSVIT
+ECSCQC
+>gi|225691084|gb|ACO06226.1| noggin 2 [Schmidtea mediterranea]
+--------------------------NFKTEEIARAAfkltngQLLKLLNRKNFNSNFMSITEPESSNDIKQ--FYISKSLNLIE-KQNQ-------KSF
+lrKAL----QLFHLKKFRKTinRDFRRKLRTFLDLFSWCPVTYQWKDMGPKFWPRWIKQGSCaNLSKSCSYPEGLVCQEYEHKNIAVLRFLCmSDWAIDK
+CKWYKIYIPFLLTCRCGC
+>gi|225713144|gb|ACO12418.1| Noggin precursor [Lepeophtheirus salmonis]gi|290462987|gb|ADD24541.1| Noggin [Lepeophtheirus salmonis]
+------------DTGPLQRAITYTNPLVplefwekakrKPRRKHLKIDLLLRKMGQDFDSSWMSASKPQKDL-------KSVVEISddQVAELVEQVSDL
+NLKEDLSNIlsisPFNnesekdddtKTRdDDGEpRIKeeivSSKDitqMANLLQQWLIKKSSCPVTYKWKDLGEYFWPRWIRMGSCTQEKsgfvdkkpNC
+SWPKGLHCVPGEALTLQILRWHCKRRRphigsskrdrPMKCKWYKVPYPVTSSCKCDC
+>gi|225691090|gb|ACO06229.1| noggin-like protein 4 [Schmidtea mediterranea]
+--------------LKVKVLSEKIDPILfndlMPESHSLHEGRLMKILGDRFDSFWTSVNTPHN--------LGYETEVS-YDPKLE--------IFLDS
+LNITEI----RGQPISFEMKRLIQNWLVNKATCKISYYWEDLGNLFWPRFIKKTICVntNSESCSWPPGMKCGLSGPMKIHHLRWTC-------------
+------------
+>gi|118344598|ref|NP_001072068.1| noggin4 [Takifugu rubripes]gi|59800376|gb|AAX07475.1| noggin4 [Takifugu rubripes]
+---FLQLRAsLPSYSQPIRtytllANIED--YHYMPKPTERRASRLLRLLGSSLDLFWMSIEKPSEVS--GSHPddlvpLHGDKRLEKAAALNQQK----
+LEKEAEALELGF-LP--------PQVASSVRAWLVHSAICRLRHRWVDLGPAFWPRWLRQTDCEswdGGRSCSFPGGMECVRAKTTHIKILAWHCsESRG
+EdgsrgnksdvrtgaemgevmKRCVWRQVPYPVVTACTCSC
+>gi|225691092|gb|ACO06230.1| noggin-like protein 5 [Schmidtea mediterranea]
+-------------------------------------KKLKKILDSDhlFD-NWLALTKPAEIYIP----LNGT---NKID--SRLRNLIK----MKNFV
+FKN--KRGEKMNLTSDILDSIKLWLEEESSCQMEYIWHELEPSFWPRWIKKGLCVSLTSCSWPPGMSCKAKKTKNLDLLQFRC-----------------
+--------
+>gi|27374944|emb|CAD59735.1| noggin-l [Suberites domuncula]
+-----------------------------SRAQSLDVQlTLLNILGADLNQGLQSITEMTGS---SPTVCTNETALEQSDEGLR--P-SDVPEFFQDRYF
+EEGFNNTAVYSIHsgdtRmAIRRTL-----NTLNCRVTYNWADAGVNFFPRYFSAGSCFE-RRCSIPDraDFLCRPDVfnqeqMGTLTALRWDCCwevve
+tivrgRRgrtfrrLSRRynCGWRRIRFPIVCDCDCNC
+>gi|340374294|ref|XP_003385673.1| PREDICTED: noggin-2-like [Amphimedon queenslandica]
+----------------------------------LDIALLYGHLGPDFDSTYTQLEDPTAMNPP------INPPIP--P---E---LVTLPRTMVNRTFF
+---P-DMVYNASEQF--TIRRWVGDQLGCKLEAGWVDLRQNFFPRWYAGRKCLpIRGNCSIPSgGQQCWPDLtdLDYVTMLAWDACyvpvGTTEaYTFGW
+RKVSVPIIRRCSCTC
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+Q 2 * * * * * * * 3682 * 3921 * 4057 * 329 * * * * * * 2
+ 0 * * * * * * 2980 0 0
+
+H 3 * * 3921 * * * 1320 * * 4287 * * 1503 2948 * * * * * * 3
+ 0 * * * * * * 2980 0 0
+
+Y 4 * * * * 2652 * 3499 * * * * * * 3166 4151 3917 3873 * * 1151 4
+ 0 * * * * * * 3119 0 0
+
+L 5 * * * * 4995 * * * 4054 489 * * * * * * 4151 * * 2838 5
+ 0 * * * * * * 3119 0 0
+
+H 6 * * 3873 * 3917 * 2177 * * 2136 * * 4044 3652 1854 * * * * * 6
+ 0 * * * * * * 3119 0 0
+
+I 7 * * * * * * * 3102 * 373 * * * * * * * 3166 * * 7
+ 0 * * * * * * 3119 0 0
+
+R 8 * * * * * * 3917 * 3976 * * * * * 201 * * * * * 8
+ 0 * * * * * * 3119 0 0
+
+P 9 3652 * 3917 * * * * * * * * * 227 * * * * * * * 9
+ 120 3652 * 0 * * * 3119 1025 0
+
+A 10 3102 * * * * * * 2546 * 2611 * * * 3015 4489 1991 * 2956 * * 10
+ 0 * * * * * * 3119 0 0
+
+P 11 * * * * * * * * * * * * 0 * * * * * * * 11
+ 0 * * * * * * 3256 0 0
+
+S 12 * * * * * * 4180 * * * * * * * * 82 * * * * 12
+ 0 * * * * * * 3256 0 0
+
+D 13 * * 563 3764 * * 4361 * * * * 4255 * * * 4183 5189 * * 3925 13
+ 84 4146 * 3000 193 * * 3381 1025 0
+
+N 14 * * 1967 * * 5379 3941 * 4261 * * 2128 * * 3883 2531 2907 * * * 14
+ 0 * * * * * * 3381 0 0
+
+L 15 * * 4024 * * 4177 * 4695 * 644 * * 4494 4185 * * * 3244 * * 15
+ 73 * 4335 * * * * 3745 0 0
+
+P 16 4344 * * * * 4413 * * 4526 * 4072 * 396 * 4615 * * * * * 16
+ 73 4344 * 2322 322 * 0 3665 1033 1035
+
+L 17 * * * * * * * 2573 * 1781 * * 2989 * * * * 1269 * * 17
+ 0 * * * * * 0 3665 0 1035
+
+V 18 * * * * * * * 3463 2884 2564 * * 2956 2808 4060 * * 1872 * * 18
+ 89 4060 * 2322 322 * 0 3665 1025 1035
+
+D 19 4060 * 896 3189 * * * * * * * * 3585 * 2995 * * 3570 * * 19
+ 0 * * * * * 0 3665 0 1035
+
+L 20 4147 * * * * * * 2959 * 397 * 4165 * * * * * * * * 20
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+//
+�HHsearch 1.5
+NAME 5ce3a21f2652f5e4378c3552cceb2340
+FAM
+FILE 5ce3a21f2652f5e4378c3552cceb2340
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:28:08 2013
+LENG 139 match states, 139 columns in multiple alignment
+FILT 103 out of 548 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEHHHCCCCCEEECCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCC
+CCCEECEEECCEEEEEEECCCCEEEEEECCEEEEECCCC
+>ss_conf PSIPRED confidence values
+9887666777678877223110003566665556787445447988888788640676795486776402798541347886048999998864867686
+875614243167899993899699999389288640159
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxCxrxxlxVdFxdlGWxxwIixPxxyxaxyCxGxCxxpxxxxxxxtnhaixxxlxxxxxxxxxx
+xpCCvPxxxxxlxilyxdxxxxixxxxlxxMvvxxCgCx
+>5ce3a21f2652f5e4378c3552cceb2340
+STGSKQRSQNRSKTPKNQEALRMANVAENSSSDQRQACKKHELYVSFRDLGWQDWIIAPEGYAAYYCEGECAFPLNSYMNATNHAIVQTLVHFINPETVP
+KPCCAPTQLNAISVLYFDDSSNVILKKYRNMVVRACGCH
+>gi|335280265|ref|XP_003353533.1| PREDICTED: bone morphogenetic protein 4-like [Sus scrofa]
+----------------------------------IEGLYIDGCYVEPKEEtgpigdGCNHfWIReeragAEEGRELLTIvslLGSDPLEPKPSGRAQKKS
+TL----------------------------------------------------
+>gi|73961483|ref|XP_854725.1| PREDICTED: similar to left-right determination, factor B preproprotein [Canis familiaris]
+----------------PRLELHTLDLGTYGAQgdcdpevpvTQAARCCRQEVYIDLRGMKWaENWVLEPPGFLAYECVGTCQQPPRPL-P-F-------E
+WPLLGPR-----QCVPSETTSLPMIITVKEGGrprPPVVSLPNMRVQKCSCS
+>gi|40556096|ref|NP_955181.1| CNPV157 TGF-beta-like protein [Canarypox virus]gi|40233921|gb|AAR83504.1| CNPV157 TGF-beta-like protein [Canarypox virus]
+----------------------------------DAICNIRSINIKFADYGM-KWILSPLSTVLTYCYGICSISS---YQKTSL-MYGTIITNHMPDNTI
+PQCCYPITRSNFTIRYKVGR-NIKTDVINNFMPLECACG
+>gi|162424750|gb|ABX90061.1| Tgf-beta [Amphimedon queenslandica]
+--------------------------------GDSEECSKSSLSIDKGQLAQilDIEIDFPETFDLNVCGGHCPGS---KYINQFHSKITYLLLATseve
+hlANKHHYSKTCVPTKYHSLNYIKFDQNGSV-IKTLDQFSVAECSC-
+>gi|291395261|ref|XP_002714159.1| PREDICTED: glial cell derived neurotrophic factor [Oryctolagus cuniculus]
+--------------------------------GKNRGCVLTAIHLNVTDLGLG--YETKEELIFRYCSGSCDAAE------TMyDKILKNLSKSrrLVSD
+KAGQACCRPIAFDDD-LSFLDD--NLVYHILRKHSAKRCGC-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+
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+
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+
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+
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+
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+
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+
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+
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+H 84 4704 * 5135 6723 5555 * 770 5543 4648 5270 5247 5154 6988 * 5361 4463 5053 * * 3903 84
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+
+L 90 4444 * * 6460 5038 * * 3479 4980 1111 3903 6391 7080 6210 3490 5253 5467 3663 * 6456 90
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+ 64 * 4521 * * 1539 609 7192 0 1405
+
+H 92 3565 * * 6361 5554 6257 2094 6412 3633 4062 * 2754 4909 4047 3412 3967 3969 * * 5735 92
+ 223 6740 2900 639 1483 1016 985 7198 1040 1521
+
+F 93 3365 * 4869 3517 3741 3857 4805 4894 4072 3341 6601 3972 5364 3385 5461 4045 4940 4046 * 4660 93
+ 123 3921 5998 414 2002 1540 608 7140 1566 2026
+
+I 94 4582 * * 4406 4647 5567 4566 2884 4064 2430 3384 6925 6166 4284 3791 6363 5594 3572 * 3868 94
+ 175 3721 4692 1605 575 1123 887 7204 1436 1762
+
+N 95 4018 5270 3572 4552 * 2981 6125 5384 4409 4726 6014 3178 5926 3548 3421 3504 4090 4513 * 5383 95
+ 234 3008 5296 1307 747 753 1299 7188 1678 1604
+
+P 96 3608 * 4549 3683 * 4896 6082 * 3913 3916 6574 4665 1611 5036 3672 3558 5734 5231 * * 96
+ 183 4077 4064 2064 394 930 1073 7291 1267 1352
+
+E 97 4196 * 2645 4410 6194 3085 4725 * 3604 4463 * 3018 5125 4895 3226 3986 5356 6659 5455 5117 97
+ 263 3999 3262 1569 593 355 2197 7194 1301 1563
+
+T 98 2698 * 3997 4515 * 3692 5195 6145 3498 3718 * 3250 6307 5038 4201 3323 3728 4294 5897 6573 98
+ 86 4870 5385 1357 714 1963 428 7003 1173 1833
+
+V 99 4085 * 5304 4033 6613 5069 4258 3106 6095 4812 6435 4799 * 4690 3368 3786 4119 1882 * 6442 99
+ 136 3653 6591 1370 706 1407 683 7180 1443 1742
+
+P 100 3970 * 4768 4478 5982 3962 5006 5015 5083 3948 5107 * 1622 5081 3464 4207 4930 4734 * 5655 100
+ 14 6742 * 1000 1000 1029 971 7267 1000 1549
+
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+ 32 6904 6195 0 * 2053 398 7288 1000 1245
+
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+ 16 6532 * 2585 263 575 1606 7277 1000 1287
+
+C 103 4573 379 * * * * * * 4962 * * * * 5706 6348 3749 4292 * * * 103
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+ 19 6286 * 0 * * * 7344 1181 0
+
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+ 13 6774 * 1000 1000 * * 7135 1000 0
+
+Q 108 3190 * 5190 3034 6086 * 5890 * 2330 6459 * 5056 6995 3656 2520 3048 4171 6829 * 5488 108
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+L 109 * 5823 * * 3338 * * * * 1842 2939 * * 5804 4276 5584 4251 * 6026 1663 109
+ 0 * * * * * * 7135 0 0
+
+N 110 3832 * 3100 2877 * 3760 5292 4630 3388 5823 6845 5502 * 5530 3634 2188 4394 * * 5369 110
+ 0 * * * * * * 7135 0 0
+
+A 111 2917 * 3451 5166 * 4745 5421 * 7260 * 5113 5003 1929 5066 6814 1913 4516 * * 6580 111
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+I 112 * 6315 5353 7011 4768 6550 6927 2405 6444 1346 3053 * * 3991 * 6358 * 3306 * 6768 112
+ 99 6468 4177 1585 585 * * 7135 1003 0
+
+S 113 6191 * 4211 4802 * 5664 5538 4990 4046 4201 * 3859 4044 5123 4704 1854 2443 4859 * 5850 113
+ 0 * * * * 0 * 7020 0 1253
+
+V 114 4632 5674 * * 3868 * * 1969 * 2583 2296 * * * * 6083 * 2342 * 4891 114
+ 18 * 6302 * * * * 7126 0 0
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+
+F 117 6479 * * 5575 2922 * 4719 4042 5372 2117 4051 5414 5488 5299 4353 5243 5743 3591 5236 2761 117
+ 65 6405 4968 1000 1000 * * 7002 1000 0
+
+D 118 * * 1400 3867 * 5028 6194 5525 4647 4794 5020 2588 5641 4845 4755 4337 4736 4859 * * 118
+ 54 5615 5950 748 1306 0 * 6977 1086 1130
+
+D 119 3994 * 2930 2528 * 3014 4117 * 4009 * * 3219 5141 3693 4535 3147 5641 * * * 119
+ 47 * 4952 * * 0 * 6973 0 1016
+
+S 120 * * 2501 2965 5765 3821 5082 6388 3381 5805 * 2452 5759 4623 3591 3566 4589 * * * 120
+ 286 * 2475 0 * 814 1213 6965 1000 1122
+
+S 121 * * 4831 6050 * 1276 4699 6595 4076 6146 * 3065 * 5237 4183 3865 3608 6046 5998 4962 121
+ 115 5517 4188 1000 1000 371 2142 6711 1030 2029
+
+N 122 5579 * 3975 4006 5431 3326 6465 5783 3474 * * 2623 5254 3565 3895 3217 3172 4607 * 6503 122
+ 29 5632 * 1084 921 136 3475 6816 1118 1553
+
+V 123 4964 * * 6659 4735 * 6159 1738 6392 2475 5094 6416 4466 5433 6603 5625 5021 2366 * 4319 123
+ 28 * 5715 * * * 0 6893 0 1000
+
+I 124 5033 * 5555 3417 5368 5620 6130 3503 3262 4367 5456 6471 6567 3668 3707 4516 3690 2229 * 5613 124
+ 80 5537 4940 1585 585 0 * 6832 1087 1081
+
+L 125 6226 * * * 3622 5021 * 3026 4060 2572 4213 5701 * 6103 6279 5123 3002 2579 5330 3691 125
+ 44 5058 * 637 1485 580 1595 6860 1137 1109
+
+K 126 3973 * 4407 4223 * 4689 3783 5166 2300 6815 6211 6694 * 3478 2708 3352 3812 4343 * * 126
+ 44 5056 * 435 1942 * 0 6865 1132 1000
+
+K 127 6718 * 4342 3155 5257 * 4101 3931 3398 6348 6324 3663 4995 4812 3527 3688 2596 3746 * 6762 127
+ 13 * 6815 * * * 0 6865 0 1000
+
+Y 128 6294 * * * 3670 * 6646 2887 6451 1446 5789 * 5328 6950 * * * 3167 4888 2404 128
+ 28 * 5720 * * 0 * 6867 0 1038
+
+R 129 6672 * 3066 2894 * 6713 4061 * 4398 * * 3782 1727 4425 3526 3657 * 4960 * * 129
+ 0 * * * * * 0 6814 0 1029
+
+N 130 6672 * 1850 3552 * 3418 * * 3678 * * 1430 * 4020 * 6350 6532 * * * 130
+ 0 * * * * 0 * 6814 0 1029
+
+M 131 6656 * * * 3541 * 6056 3648 * 3106 749 * * 5733 * 4698 * 4607 * * 131
+ 0 * * * * * * 6867 0 0
+
+V 132 6793 * * 4743 * * * 2137 4312 4061 4604 * * 6487 3017 3014 4976 1813 * * 132
+ 28 * 5703 * * * * 6867 0 0
+
+V 133 1545 * * * * * * 3158 * * * * 4552 * * * 5122 1077 * * 133
+ 0 * * * * * 0 6867 0 1038
+
+R 134 3591 * 3833 2391 * 5650 * * 2374 2957 5906 5507 * 5561 3576 4336 3904 4197 * * 134
+ 0 * * * * * 0 6867 0 1038
+
+A 135 3498 * 4156 1550 * 4246 4584 * 2828 5578 * * * 6711 4762 2740 4021 * * * 135
+ 0 * * * * * 0 6869 0 1038
+
+C 136 * 0 * * * * * * * * * * * * * * * * * * 136
+ 0 * * * * * 0 6860 0 1038
+
+G 137 2943 * 5062 * * 932 5038 * 4762 * * * * * 6651 2416 4916 5783 * * 137
+ 0 * * * * * 0 6860 0 1038
+
+C 138 * 31 * * * 5541 * * * * * * * * * * * * * * 138
+ 38 5281 * 2663 248 0 * 6836 1108 1038
+
+H 139 4916 * * * * 3325 3308 5224 5415 5369 * 5523 5569 5545 1729 1715 5562 * * * 139
+ 0 * * 0 * * * 5894 0 0
+
+//
+�HHsearch 1.5
+NAME 5d895b2caff816955040ab755eaf5b19
+FAM
+FILE 5d895b2caff816955040ab755eaf5b19
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:01:04 2013
+LENG 167 match states, 167 columns in multiple alignment
+FILT 119 out of 452 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCHHH
+CCCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEECCCHHHHHHHHHHHHCCCCCCEEEEEECCCCC
+>ss_conf PSIPRED confidence values
+9600111688999875101489998736888666634677798589999886664188899999999999999863776657999978884103060221
+4563200243457778950899997389889999634899999999997532899479999257789
+>Consensus
+rPxxxyrxxxxxxYtrxxyxxgxpxxKixxfxxGxxxxxxxfxxxxxLxaxexxxixxxxiEAaRixxnrxlxkxxGxxxxkxxIrvfPxxxxtxkpxxx
+xagadrxexrMgxgkGkpxxwxArVxxGqvifeixxxxxxxakeALxxAxxKlPxxxkivxxxxxxx
+>5d895b2caff816955040ab755eaf5b19
+KPGAMYRNSSKPAYTRREYISGIPGKKIAQFDMGNNGAGPTYPAQVELVVEKPVQIRHNALEAARVAANRYVQNSGAAANYKFRIRKFPFHVIRENKAAA
+AAAAAAAADGMRAPFGKPVGTAARVHGANHIFIAWVNPDPNVEEAWRRAKMKVTPTINIDSSPAGNA
+>gi|339758767|gb|EGQ44020.1| ribosomal protein L16/L10E [Candidatus Nanosalina sp. J07AB43]
+RPASIYREQPSQPYTRkaqnkrDNYVAGAPAPRVTQYEMGARNK--EFEQDVVLISEEDCSIRSEALESGRVAANSFLSKEFNmEEDYKLKIRPYPHHIL
+RYHPLAGIAQADRYYEGMRKPFGRPIGRAAIVDEGDVVFKVSIDSEnvQEARKALERTNHKMPVTCRVKLA-----
+>gi|242824789|ref|XP_002488329.1| 50S ribosomal protein L10e, putative [Talaromyces stipitatus ATCC 10500]gi|218713250|gb|EED12675.1| 50S ribosomal protein L10e, putative [Talaromyces stipitatus ATCC 10500]
+RPARCYHYCKNKPFPKSRFNRGVPDHKIRFFDTGRKKATVDdFPCCIHLVSSEYEQLSSEALEAALICANKYLVKTAGKESFHLRIRVHPYHTTRINKML
+SVAGADRLQTGMRGTWGKPVGKVARVNVDQILVSVRTTDRhrLVAIEALRRSMYKFPGRQKVIVSK----
+>gi|73997710|ref|XP_854316.1| PREDICTED: similar to ribosomal protein L10 [Canis familiaris]
+-----------------------------------------FGVCVHK---QTKIFKKEHLEKKSINTNSNVDHMEtNEDE--------IFDLSREKPLL
+AMYLVYFlTQLSIQGAFGKPQGTVARGHIGQVIMSICTKLQnkEHVIEALHRAKFKFPDCQKIHSSKK---
+>gi|25987151|gb|AAN75748.1|AF319171_3 ribosomal protein L16 [Magnolia x soulangeana]
+----------------------MLYPKRTKYSKYR-kgrcSRGrepdgtqLGFG-RYGTKSCRAGRLSYRAIEAARRAtigqfhraMSGQFRR-NG----
+KIWVRVLADLPITGKPT---------EVRMGRGKGNPTGWIARVSTGQIPFEMDGVSLSNARQAATLAAHKPCSSTKFVQWS----
+>gi|328766533|gb|EGF76587.1| hypothetical protein BATDEDRAFT_7062 [Batrachochytrium dendrobatidis JAM81]
+---------------------------------------------YGLQLFEPGRLKDKQLDTVRTMVNRILKseK-----GSKLILRIFPHRPVTAKGA
+---------ETRMGKGKGAVEYYATWVSEGVVIMEITGARKDVALKALNVAAQALPLRTRVV-------
+>gi|10802927|gb|AAG23675.1|AF288091_20 ribosomal protein L16 [Thraustochytrium aureum]
+---------KNTSFTKS--Q-rkkrflvDLDSSKICSVNKL------TF-GSMGLMLLEDSFIQAKHFKIAYDFLKKNISK-RG----LFWILKFPDQSF
+TKKPLG---------SRIGKGKGNVAFWAIFVNKGNVFIEIESDSYQKSILLLKKLEKRFPFSGKII-------
+>gi|11466316|ref|NP_051144.1| ribosomal protein L16 [Cafeteria roenbergensis]gi|6180098|gb|AAF05795.1|AF193903_18 ribosomal protein L16 [Cafeteria roenbergensis]
+---------PRKKYKKNF-SKHLSFRKTTQNNGL------VY-GNIGLQVAEYGKISHLRLNALKKILTFSLQR-KG----KIWLRVYPMIPKTKKPLE-
+--------VRMGKGKGNLHYWETTIFPGEILFELTTVDSKIAVNGLKQVMKRLGLKSRII-------
+>gi|21450002|ref|NP_659264.1| ribosomal protein L16 [Laminaria digitata]gi|21425327|emb|CAC87960.1| ribosomal protein L16 [Laminaria digitata]
+---------KKTKYRKYFKPRGLPNTSTKTQKLA------EL-TCFALIAMESSYLNGRQIEAARQNIRRKVKR-EG----KLEILVFPDIAISRKASA-
+--------ARMGKGKGKVDHWIASVSAGQTMFLLYGIHAEQGIPALSSGANKLPLKVKIY-------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+K 1 * * * * * * 3808 * 1751 * * * * * 663 * * * * * 1
+ 0 * * * * * * 3463 0 0
+
+P 2 * * * * * * * * * * * * 0 * * * * * * * 2
+ 0 * * 1297 754 * * 3463 1261 0
+
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+ 0 * * * * * * 3707 0 0
+
+A 4 3697 * * * * * 4768 * 2681 * * * * 5074 1041 3007 * 5169 4006 * 4
+ 54 * 4768 * * * * 3707 0 0
+
+M 5 * 1035 * * * * * 3352 5274 * 2319 3282 * * * 4533 4583 * * * 5
+ 0 * * * * * 0 3655 0 1029
+
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+ 0 * * * * * 0 3655 0 1029
+
+R 7 * * * * * * 4658 * 4533 * * * * 3968 509 5185 3023 * * * 7
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+
+N 8 * * 3769 2843 4347 5699 3347 * 3523 * * 3308 * * 2832 4583 * 4800 * 2220 8
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+
+S 9 * 2698 * * 2804 3914 * 2061 * 3381 * * 4724 4545 * 4532 5102 2760 * * 9
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+
+S 10 5618 * 3492 3324 * 5290 * * 1472 * 5530 4621 3659 * 4511 2793 3733 * * * 10
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+
+K 11 * * * * * 1963 * 5021 2008 * * 2088 * 4170 3322 4275 * 5530 * * 11
+ 0 * * * * * 0 4361 0 1029
+
+P 12 * * * * * * 5636 * 2004 * 4296 * 1603 3321 4468 4966 2528 * * * 12
+ 122 3993 5769 1728 518 * 0 4361 1172 1029
+
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+ 0 * * * * 1347 721 4369 0 1074
+
+Y 14 * * * * 2966 * * * * * * * * * * * 4916 * * 253 14
+ 0 * * * * * 0 4406 0 1029
+
+T 15 5061 5308 * * * * * * 2807 * * * 2512 * 4436 4999 970 4700 * * 15
+ 46 4999 * 1813 483 * 0 4406 1102 1029
+
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+
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+ 174 * 3139 * * * * 4474 0 0
+
+E 18 * * 3731 1332 3135 * 4299 * 3093 * * 3465 * * 3014 5004 * * * * 18
+ 84 * 4144 * * * 0 4233 0 1156
+
+Y 19 * * * * 2124 * * * 3948 * * * * * * * * * * 503 19
+ 0 * * 0 * 0 * 4074 1064 1236
+
+I 20 * 2593 * * * * * 1282 * * 3462 4096 4485 3139 * 4593 * 3750 * * 20
+ 72 * 4355 * * * * 4474 0 0
+
+S 21 4491 * 5948 * * 3121 3308 * 2432 * * * 4158 * 1216 4964 5671 * * * 21
+ 45 5036 * 3842 104 0 * 4511 1104 1045
+
+G 22 4577 * 3510 4981 * 580 4693 5284 4366 * 5222 * 5058 * * * * * * * 22
+ 0 * * * * * 0 4574 0 1018
+
+I 23 2436 5133 * * 5248 * * 3189 4203 3452 2482 5662 5398 * * * 4935 2001 * * 23
+ 27 * 5750 * * * 0 4909 0 1018
+
+P 24 * * 4750 * * 4441 * * 5544 2279 * * 642 5665 * 5107 * * * * 24
+ 0 * * * * * 0 4897 0 1063
+
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+ 0 * * * * * 0 4897 0 1063
+
+K 26 3108 * * * * * 5510 4271 4319 6100 5520 * 1265 * 5155 2741 3379 4890 * * 26
+ 0 * * * * * 0 4920 0 1063
+
+K 27 * * * * 5529 * * 5520 517 5264 5561 * * 4780 3000 4354 * * * * 27
+ 28 5721 * 0 * * 0 4920 1000 1063
+
+I 28 * * * * * * * 807 5700 4734 * 5476 * * 2943 * 3584 2880 * * 28
+ 0 * * * * * 0 4907 0 1103
+
+A 29 3412 3136 * * 5476 * * 4748 3539 5449 * * 5695 * 2850 6024 1443 3598 * * 29
+ 0 * * * * * 0 4907 0 1103
+
+Q 30 * * * * 4499 * 3891 2828 1869 3989 5097 * * 2773 3814 4146 3558 5449 * * 30
+ 118 4313 5139 766 1280 * 0 4907 1045 1103
+
+F 31 * * * * 954 * * 5133 * * 4467 4388 * 5155 * 5547 * 4754 5795 1955 31
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+
+D 32 * * 1734 3152 * * 3953 4832 3802 * 5952 2886 5738 4725 3694 4678 4484 4426 * * 32
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+
+M 33 4645 * * * * 4346 * 4310 1929 3969 1485 * * 5151 * 3912 4606 4612 * * 33
+ 0 * * 1000 1000 661 1443 4854 1029 1238
+
+G 34 5407 * * * * 482 * * 5331 3626 5891 * 5615 * 4932 * * * * 3565 34
+ 193 * 3001 * * 807 1223 4951 0 1063
+
+N 35 4358 * 3666 * * * 4034 * 5542 * * 1822 * 2876 2319 4910 3481 4389 * * 35
+ 322 2935 3849 1841 472 * 0 4719 1261 1357
+
+N 36 4159 * 5494 * 5703 * * 4799 1944 2955 4256 3836 3212 5009 3957 * 4820 4473 * 3800 36
+ 386 2089 * 1785 494 1132 879 4524 1591 1582
+
+G 37 3898 * 5856 5018 * 4483 4776 * 1699 5027 5896 3756 * 5119 3315 3328 3348 5848 5974 6189 37
+ 209 * 2887 * * 3652 120 4699 0 1333
+
+A 38 1646 * 5838 * * 3442 * * 3514 * 6093 4113 4185 4570 2165 4414 5200 5890 * * 38
+ 747 * 1306 * * * 0 4623 0 1671
+
+G 39 5272 * 4878 * * 1082 4496 * 2488 3455 * 4017 * * * 4306 4583 * * * 39
+ 781 1258 * 1784 495 3684 117 4123 1525 2527
+
+P 40 3605 4719 * * * * * 3190 4304 2348 4016 * 4111 4429 * * 4578 1666 * * 40
+ 155 3292 * 0 * 173 3145 4323 1117 2415
+
+T 41 3606 4535 2414 2347 * 4333 4440 * 4227 * 6160 3174 * 6042 5679 5404 3434 3925 * * 41
+ 441 2037 5671 723 1343 2108 381 4912 1767 1190
+
+Y 42 5884 * * * 654 * * * * 4264 * * * * * * * * 6192 1828 42
+ 134 * 3493 0 * 414 2003 4968 1029 1195
+
+P 43 * * 2935 2924 6031 1592 * * * * * * 1655 5682 * 6118 4680 * * * 43
+ 492 * 1792 * * 0 * 4875 0 1304
+
+A 44 5005 4173 * * 5854 2699 5341 3396 * 4211 4705 * 4690 4337 * 4208 3971 2342 * 2979 44
+ 0 * * * * 0 * 4729 0 1557
+
+Q 45 6548 2241 3582 2531 * * * 5426 3433 * * 4154 * 3336 3616 3338 4626 5095 * * 45
+ 0 * * * * * * 5091 0 0
+
+V 46 5023 6057 * * 2941 3667 5484 3284 * 3659 3664 * * * * * * 1861 * 2419 46
+ 0 * * * * * * 5050 0 0
+
+E 47 3420 * 7214 4286 5670 1326 3147 * * 5954 6867 5798 * 3885 3961 3420 5571 6035 * 6268 47
+ 0 * * * * * * 5125 0 0
+
+L 48 * * * * 7250 * * 2498 4887 520 3786 * * * * * 6302 * * * 48
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+
+V 49 5404 * * * 6711 * 5583 3054 2322 4443 4839 6262 * 2292 4304 * * 1853 * * 49
+ 0 * * * * * 0 5003 0 1077
+
+V 50 1406 6451 * * * * * 4525 * 3408 6907 5771 5901 * * 1907 4592 3034 * * 50
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+
+E 51 5005 5155 4065 2955 6719 * 4835 4322 3283 1839 4528 5478 * 6262 7199 4610 3760 3921 * 6815 51
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+
+K 52 4190 6102 4277 943 * 3766 * * 4042 * * 6772 * 3198 6302 4679 4193 * * * 52
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+
+P 53 3793 5851 3921 5389 6496 4105 5686 6955 4939 6785 5762 4188 2548 6573 2970 2856 4184 * * 3228 53
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+
+V 54 3361 3785 * 3837 5290 1496 5331 4409 3890 5151 5701 * * * 6102 4125 6570 3172 * * 54
+ 40 5193 * 1000 1000 * * 5125 1064 0
+
+Q 55 5758 6537 * 5401 4639 * 5944 4239 4444 7076 * 4760 6049 1377 2856 5972 6419 * 3056 4027 55
+ 0 * * * * 0 * 5089 0 1064
+
+I 56 * 6268 * * 4058 * * 1016 * 1965 5607 * 5194 * 6102 * * 3133 * * 56
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+
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+
+A 60 1333 5338 * * * * 3902 * * * 6869 * * 1310 6034 5743 4448 5651 * * 60
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+
+L 61 * * * * 5734 * * 1105 * 1092 * * 5194 * 6102 * * 7518 * * 61
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+
+E 62 * * 6740 127 * 6714 * * 5734 * * 6114 * * 6102 * 5811 * * * 62
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+A 63 768 * * * * * * 5734 4887 * * * 4639 * * 2161 3376 * * * 63
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+A 64 758 4343 * * * 4139 * 5169 4887 5524 7134 * * * * 4992 3360 3585 * * 64
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+S 162 3974 * 3964 3987 * 7214 7389 5335 3020 4967 7332 6564 4995 * 2261 2006 4627 5788 4771 6002 162
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+A 164 1829 * * * * * * * 477 * * * * * * * * * * * 164
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+A 167 0 * * * * * * * * * * * * * * * * * * * 167
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+
+//
+�HHsearch 1.5
+NAME 60dd783edaf524b39db3af7ecfd53a48
+FAM
+FILE 60dd783edaf524b39db3af7ecfd53a48
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:17:44 2013
+LENG 114 match states, 114 columns in multiple alignment
+FILT 132 out of 875 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEEECCCCEEECCCCCCEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEE
+CCHHHEEECCEECC
+>ss_conf PSIPRED confidence values
+9899996378625589999999999999879594479999986986797898986699999998289999999999999999999969393649999998
+89999578779886
+>Consensus
+PxixixTNxxxxxxxxxxxxxlsxxiaxxlxkpexxixvxvxxxxxmxxggxxxpxxxvxixxxxgxxxxxxxxxxxxixxxlxxxlgvxxxrixIxfxx
+xxxxxwgxxGxtxx
+>60dd783edaf524b39db3af7ecfd53a48
+PMFIVNTNVPRASVPEGFLSELTQQLAQATGKPAQYIAVHVVPDQLMTFSGTNDPCALCSLHSIGKIGGAQNRNYSKLLCGLLSDRLHISPDRVYINYYD
+MNAANVGWNGSTFA
+>gi|225698066|pdb|3FWT|A Chain A, Crystal Structure Of Leishmania Major Mif2
+PFLQTIVSVSLDDQKrANLSAAYGMICr-EELGKPEDFVMTAFSDKTPISFQGSTAPAAYVRVESWGEYAPSKPKMMTPRIAAAITKECGIPAERIYVFY
+YSTKHCGW--NGT---
+>gi|319935323|ref|ZP_08009761.1| hypothetical protein HMPREF9488_00592 [Coprobacillus sp. 29_1]gi|319809731|gb|EFW06132.1| hypothetical protein HMPREF9488_00592 [Coprobacillus sp. 29_1]
+PFMRFTTTKTLTLKQeKALKESAGKFISILPNKKEEQLMIHIEDNQVMYFKGKEMDCMKIECQLFHHIEISYKQEFVKAMMNEIEMITKIPVSHQYMTID
+EYD--NWGKNGELA-
+>gi|336255477|ref|YP_004598584.1| 4-oxalocrotonate tautomerase [Halopiger xanaduensis SH-6]gi|335339466|gb|AEH38705.1| 4-oxalocrotonate tautomerase [Halopiger xanaduensis SH-6]
+PLLQFDTTLSlSADEKEALADRVTAIYTEEMATTAGHVAVTIREhePAALHLGRaVEGPLCFLDAEIRQGRPFERKRAFALETMAYVGERFDVPDENMKV
+VFTEHPGESM--------
+>gi|312219511|emb|CBX99454.1| similar to MIF domain containing protein [Leptosphaeria maculans]
+---ELRTNVIIK-DEYTLVTDLSHHLSTRYQRPETSIMITVNHSACLLLGGSFEPTYILAINALPvQLQPTTNKRNAAMIQTFMAESIGVSPERGIIKFL
+PIPEDSLAMNGMTI-
+>gi|296136495|ref|YP_003643737.1| 4-oxalocrotonate tautomerase [Thiomonas intermedia K12]gi|295796617|gb|ADG31407.1| 4-oxalocrotonate tautomerase [Thiomonas intermedia K12]
+PFITLHLSGSPDPElSRDLSKRIGALACKLLRKDLRRTSVLVRYVphADWFIADQSlqelgRNAFRLEVTVTDETNTRdEKAIFQREAFQALSTWIGNVH
+PHSNIHVIDCRATAYGYGGVT--
+>gi|302876815|ref|YP_003845448.1| 4-oxalocrotonate tautomerase family enzyme [Clostridium cellulovorans 743B]gi|307687498|ref|ZP_07629944.1| 4-oxalocrotonate tautomerase family enzyme [Clostridium cellulovorans 743B]gi|302579672|gb|ADL53684.1| 4-oxalocrotonate tautomerase family enzyme [Clostridium cellulovorans 743B]
+PYINVKLVKeQTSLEqQKKIIEGLTDLVVTVMGREKSLTVITLDELsaNQWSIGGETleqsadkKAVSFVNIKVSKGTTDAeEISKMMKATKELLAEVLG
+NNEEANYFILDELNPDAWGFDGisMT--
+>gi|315303670|ref|ZP_07874195.1| 4-oxalocrotonate tautomerase [Listeria ivanovii FSL F6-596]gi|313627960|gb|EFR96568.1| 4-oxalocrotonate tautomerase [Listeria ivanovii FSL F6-596]
+---------------ENINRAIHNALIECFQIPENDSFQLWvsTDATANfvdaHYllPTgkRNNEFLYLEIFCGPGRSIEQKRSLYQTIVAQMEQATSLS
+KQNIFILLNEVSLENWSFGDG---
+>gi|293606869|ref|ZP_06689217.1| 4-oxalocrotonate tautomerase [Achromobacter piechaudii ATCC 43553]gi|292814721|gb|EFF73854.1| 4-oxalocrotonate tautomerase [Achromobacter piechaudii ATCC 43553]
+PILNVQILQGHSAAQkAALLRAASDAVVQSIAAPLPSVRIVLqeVPAENVIVAGEIGkRMVRVDVALIEGRDEAKKAALIAALNQAVCSSIDISGEDVRV
+LIRDVPKVDMGVANG---
+>gi|338811969|ref|ZP_08624168.1| 4-oxalocrotonate tautomerase [Acetonema longum DSM 6540]gi|337275938|gb|EGO64376.1| 4-oxalocrotonate tautomerase [Acetonema longum DSM 6540]
+--------------------------------------------------------------------QAQKDEISQTFTREISRILKGDHGPVTVEFNE
+IPRPEADSKQTP--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+P 1 * * * * * * * * * * * * 30 * * 5619 * * * * 1
+ 30 * 5619 * * * * 7763 0 0
+
+M 2 6639 3370 * 6240 2153 * 5038 3355 6260 2941 5548 6442 * * 6346 * 4293 3306 * 2423 2
+ 0 * * * * 0 * 7845 0 1084
+
+F 3 3638 3881 * * 4723 * * 1606 * 1706 5743 * * * * * * 2820 * 5735 3
+ 0 * * * * * * 7907 0 0
+
+I 4 6121 * 5348 2649 6117 * 6522 4394 3964 6220 4640 4061 * 2677 2836 3707 2891 5038 * 6258 4
+ 0 * * * * * * 8093 0 0
+
+V 5 5126 6326 * * 3560 * * 1906 * 1767 5209 * * * * * 4572 2032 * * 5
+ 0 * * * * * * 8126 0 0
+
+N 6 4804 * 3209 3428 4053 * 4043 4968 2619 6671 * 5293 * 3420 4680 4107 2525 5517 * 5258 6
+ 0 * * * * * * 8126 0 0
+
+T 7 5827 6446 * * * * * 5090 * 3370 * * * * * 4096 539 3348 * * 7
+ 0 * * * * * * 8126 0 0
+
+N 8 4450 * * * * 6382 * * 5554 * * 455 6446 * * 3458 3743 6111 * * 8
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+
+V 9 4736 5973 5395 4684 5236 5963 6279 4233 4103 2155 6159 * * 4455 5847 4802 5324 1495 * * 9
+ 87 4362 6682 256 2623 * * 8126 1398 0
+
+P 10 3740 * 4106 5890 6558 5817 5387 4811 2831 6624 * 3560 2430 3941 4733 2343 5014 6571 * * 10
+ 340 2348 6232 103 3855 0 * 8133 2937 1000
+
+R 11 2528 * 4589 4154 6290 * 6464 3544 3643 3157 4834 5410 4054 6686 5651 2994 3477 5059 * 4913 11
+ 35 * 5372 * * * 0 8073 0 1029
+
+A 12 3610 6110 2309 4678 * 4580 * 6709 4888 5264 * 3349 6362 5786 6633 2085 2790 5543 * 6446 12
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+
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+
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+
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+ 72 4743 6489 1000 1000 0 * 8857 1382 1000
+
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+
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+
+Q 45 3147 4852 4348 3229 * 4512 5219 5056 3651 3626 5787 5035 5171 2868 4670 4987 4320 3484 * 6400 45
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+
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+
+M 47 5542 6358 * * 3796 6458 * 2741 * 2238 1503 6376 * * * * 6866 4453 3635 5518 47
+ 134 4119 5009 1441 663 * * 8854 1618 0
+
+T 48 4128 4040 5544 * 3236 4866 4414 4893 * 3157 5181 * * * 4362 3604 2938 3776 4699 2976 48
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+
+F 49 5367 * * * 1638 * 5033 3041 6529 3509 4232 6450 5299 * 2814 5694 6467 4485 4919 3984 49
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+G 51 3570 * 4651 5436 4928 722 * * 6710 4218 * 4813 5549 * 4202 6341 5219 * * * 51
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+
+T 52 7012 * 4246 3284 * 6835 6554 * 3947 5109 * 4138 6211 4686 2916 1859 2532 4903 * * 52
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+
+N 53 4606 6437 2934 3178 4003 4769 5129 6447 5026 5586 6971 3987 2869 5663 5638 3277 2701 6533 * * 53
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+V 106 6319 5522 * * 3403 * * 3096 6591 4757 4262 * * * 5951 * 5579 3265 1101 4398 106
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+G 107 2123 * 6307 * 5715 733 6315 * * 6344 5710 * * 6147 6074 4177 * * * 6787 107
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+W 108 6778 * * 5802 2315 6984 5720 2712 3334 5150 4891 5094 * * 6600 5071 3667 3584 3487 3174 108
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+N 109 4149 * 3386 5740 * 1949 6602 6105 3563 5145 * 1908 6684 4664 4146 4437 * * 6121 * 109
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+
+G 110 * 6062 4479 5522 * 288 5075 * * * * * 6363 6277 5410 6957 * * * 6267 110
+ 38 6378 6151 1000 1000 0 * 8364 1027 1023
+
+S 111 4944 * 6833 4247 6610 2958 5225 5908 2737 6989 4351 * 6249 6021 3686 2818 2498 3693 * 6119 111
+ 19 6249 * 0 * 0 * 8334 1020 1059
+
+T 112 6485 * * * 5287 * 5761 5480 5989 2426 * 4949 5335 * 6860 4544 839 4653 * 6259 112
+ 0 * * * * * * 7954 0 0
+
+F 113 3755 * * * 1472 * 4486 2920 5052 2447 4565 4860 * * * 5514 * 4493 6210 5742 113
+ 205 2918 * 2071 392 * * 7452 1402 0
+
+A 114 1573 * 4292 3511 * 1938 3926 * 3342 * * * 4998 * * 3868 * * * * 114
+ 0 * * 0 * * * 5846 0 0
+
+//
+�HHsearch 1.5
+NAME 61affadfde1fab540b7313adbf4ebfda
+FAM
+FILE 61affadfde1fab540b7313adbf4ebfda
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:03:26 2013
+LENG 231 match states, 231 columns in multiple alignment
+FILT 155 out of 321 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEEECCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCEEECCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCHHHHHHHHH
+HCCEEEEEEEEEEEEECCCCCEEEEEEEECCCCCCCCCHHHHCCCCEEEEECCCCCCEEEEECCCCCCEEEECCCCCCCEEECCEEEEEEEECCCCCCCC
+CCCCEEEEEEECCCCCCEEEEECCCHHCCCC
+>ss_conf PSIPRED confidence values
+9958802478765374699977661688779986788743003757146682520786688664898663789868999983377676640289999976
+3026412999999980573446899999699999988978960671899997899738999603177025761379885064457999998287588999
+9995799999823899189834492311579
+>Consensus
+xxxpxxxxpgsxxfxttxxxxsxxxxxxxxxxxxxxxpgxvxnxlxiaxvxsxxxxxxxxxxxxfxxxxxxxxxxxLxxxxvxPxxxxxxxTxlxxlsxx
+fxxWrGslxxxfxfxgsxxxxGklliayxPpgxxxpxtxxxamxxxhvixDlgxxsxxxfxVPxisxtxxxxxxxxxxxxxxxxGxlxvxvxtxLvxpxx
+xxxtvxixvxxsagxDFxxxxpxxpxxxxxx
+>61affadfde1fab540b7313adbf4ebfda
+SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQIPTFIGNKMPNAVPYIEASNTAVKTQPLAVYQVTLSCSCLANTFLAALSRN
+FAQYRGSLVYTFVFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIWDLGLNSSYSFTVPFISPTHFRMVGTDQANITNVDGWVTVWQLTPLTYPPG
+CPTSAKILTMVSAGKDFSLKMPISPAPWSPQ
+>gi|3002544|gb|AAC12265.1| polyprotein [Clethrionomys glareolus picornavirus]
+---DIAEGPGAlniANVLSTTGGQTVALVGEraFYDPRTAGAAVRCKDLMEIARMPSVYKgERTePGGtNGYF-QWSHTHsPINWVFDGGIHLEDMPN--
+--LNLFSSCYNYWRGSTVLKLTVYASTFNKGRLRMAFFPNHDARY-TEEEAQNAIFMVCDIGLNNTFEMTIPYTWGNWMRPTRGS------VIGWLRIDV
+LNRLTYNSSSPNAVNCILQVKMGNDAKFMVPTTSN-----
+>gi|237769644|dbj|BAH59290.1| capsid protein VP1 [Human echovirus 24]
+----------------------------------------------------------------------------------------------------
+-------------------------------------------------------------------CFVRALDKPDALqVCCRRRLHGCWIcnllvSNK
+VVAPADAQSACYILGFVSACNDFSVRLLKDTPFISQQ
+>gi|38224698|gb|AAR14150.1| polyprotein [Maize chlorotic dwarf virus]
+--------------------------------------------------------------------------TNLMELNIHPTscaiqNGLITQTPLS
+VLAHAFARWRGSLKISIIFGASLFTRGRILAAAVPVAKRKgTMSLDE-ISGYHNvCCLLnGQQTTFELEIPYYSVGQDSFVYRDALFDISAhdgnfmITR
+LHLVILDKLVMSANASSSINFSVTLGPGSDLELKYLAG-------
+>gi|72170202|gb|AAZ66774.1| capsid protein [Norwalk virus]
+------------------------------------------------IIDPWIMNNfVQAPGGEFTVSPRNSPGEVLLNLELGPEINPY----LAHLAR
+MYNGYAGGFEVQVVLAGNAFTAGKVIFAAIPPNFPiDNLSAAQITMCPHVIVDVRQLEPINLPMPDVRNNFFHYNQGSD-----SRLRLIAMLYTPLRAN
+NSgdDVFTVSCRVLTRPSPDFSFNFLVPP------
+>gi|336391070|dbj|BAK40204.1| putative structural protein [Chaetoceros sp. RNA virus 2]
+-----------------------------IDTRVMGLGGEDElAISAIAQRPSFWQ--------QFDWAESATTDTLLASMVVTPALvrtltaspvTEVH
+PTALCFASNPFGAWQGSIKFRFNIVCSEYHRGRLRIVYNPRSNnSGPVAYN---QVYSTTIDISEDRDFEYEVKWADIRAWNVLlGADaaplfptfstva
+nvTAGEAFDNGSLSVYVVNELATPSNTNAAVKVQVWVSGGEDIAFAVPTVN------
+>gi|9632406|ref|NP_049374.1| polyprotein [Sacbrood virus]gi|4416207|gb|AAD20260.1| polyprotein [sacbrood virus]
+------------------------------------YPDEPRTTLDIARIWGLRS--------TF-NWGSGDdHGKELFNTVLDPGLrfydqdYEGQITP
+MEYVTGLYNFWSGPIELRFDFVSNAFHTGTVIISAEYNRS--STNTDECQsHSTYTkTFHLGEQKSVHFTVPYIYDTVVRRNTASAYLpvtdydkvdnvs
+RAQAMGiraeskmRVKVRVVNVLRPVASTTSTIEVLVYMRGGKNYALHGLKQST-----
+>gi|185871627|gb|ACC78151.1| structural protein VP0 [Duck hepatitis A virus]gi|189007748|gb|ACD68184.1| VP0 [Duck hepatitis A virus]
+----------------------------------------------------------------------------------------------YGQTRY
+FRFIRCGFHFRLLVNAPSGSAGALMLVWMPypycrvlSGANqihTNVERRSLMNLPYAILDLRTNTEIDLVVPYVNYRNYVEItTSDT-----TGGAICV
+IVLGKYRHGNGTSNTVDFTLFGEL-LETDLQCPRPFD-----
+>gi|297615108|gb|ADI48872.1| coat protein [Taura syndrome virus]
+-------------------GVPLSLFPNNAIDPTIAVPEGLDEMSieYLAQRPYMLN--------RY-TIRGGDtpdaHGTIIADIPVSPVNFSLYgkvi
+akyRTLfaapVSLAVAMANWWRGNINLNLRFAKTQYHQCRLLVQYLPYGSGvQPI---ESILSQ--IIDISQvdDKGIDIAFPSVYPNKWMRVYDPAKVG
+YTadcAPGRIVISVLNPLISASTVSSNIVMYPWV--------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * * * 1332 * * * * * * * * * 1078 2952 * * * 1
+ 0 * * * * * * 2969 0 0
+
+P 2 5380 * * * * 944 3191 3712 * * * * 1887 * * * * * * * 2
+ 0 * * * * * * 4473 0 0
+
+I 3 * * * * 3120 * * 2147 * 1443 * * * * * * * 2218 3711 * 3
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+
+H 169 4413 7016 2820 3683 4123 * 3205 * 5372 4276 4462 3846 2563 4757 7017 5340 7187 5677 4443 4099 169
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+ 94 4194 6836 2534 273 2132 374 6752 1301 1426
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+T 175 3447 5734 2865 5938 * 3107 8260 5441 4698 5022 5926 5273 3660 5287 3404 3060 3501 3998 * 6393 175
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+
+D 176 3601 * 1457 3889 * 4063 5451 6590 * 5472 * 4098 4110 5472 5278 2984 3962 7693 * 6606 176
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+
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+
+A 178 3061 * 4358 6727 6141 4185 * * 3800 4249 * 3724 1836 6499 6101 3744 4109 6955 6301 3415 178
+ 235 2903 5911 1903 449 4029 91 6111 1443 3672
+
+N 179 4801 * 4000 4384 4202 4299 * * 4195 3264 * 3876 5823 5527 5993 2186 2861 4929 4232 5428 179
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+ 44 5044 * 1721 521 1417 677 6149 1150 3481
+
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+ 122 4120 5423 2532 274 5688 28 6258 1227 2628
+
+N 182 4040 7195 4940 6240 4361 6065 5704 6371 6196 5169 5887 2658 * 5236 * 2219 2819 4643 6351 2839 182
+ 133 3503 * 1048 953 317 2341 6171 1473 2639
+
+V 183 1801 6429 3676 4827 5260 5694 7062 8114 5829 6716 * 4943 3576 4730 6244 2774 4724 3503 * 3946 183
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+
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+
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+ 164 3220 * 899 1109 * 0 6829 1640 1108
+
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+
+P 202 3118 * 4505 6238 * 4433 7053 5982 7335 6668 * 4896 1627 6023 * 2214 3354 4166 * * 202
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+
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+M 210 7288 4996 5308 2592 2174 * 6826 * 6628 2420 4181 * * 5714 * 4085 4541 6433 4252 3270 210
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+
+K 220 2767 4437 * 7122 4310 6325 5042 6187 4392 5350 5068 6004 * 4894 1323 4594 4204 5230 * 5678 220
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+
+M 221 4023 3856 * 6481 3642 3860 7186 4064 * 1926 2729 7619 * 5233 * 5247 * 2982 * 4504 221
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+
+P 222 5289 6111 * * 7212 * * 5086 * 1770 4028 * 1009 5717 4223 * * * * * 222
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+
+I 223 4268 5550 6510 * * * 6260 2630 2512 5128 7170 5204 * 4921 2092 4286 3648 3257 * * 223
+ 19 * 6238 * * * * 6763 0 0
+
+S 224 3924 5732 1803 4353 * 4097 5586 * * 7156 6891 3457 2630 3732 * 3663 4482 4901 * * 224
+ 24 5945 * 0 * * 0 6449 1031 1033
+
+P 225 * 6803 * 5280 5770 5061 * 6041 * 6796 * 4616 1016 * 4574 3282 2232 * * * 225
+ 17 6416 * 1000 1000 0 * 6282 1007 1115
+
+A 226 3420 * 3468 4549 * 2956 6573 6186 4663 5924 * 3484 2555 4830 4072 4162 3296 4722 * 6080 226
+ 72 * 4358 * * * * 6038 0 0
+
+P 227 5196 * 3752 5435 2567 * 5100 5886 4604 2329 3905 * 3978 3511 5525 7102 4571 * 4157 3732 227
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+
+W 228 4358 * * * 3427 * 4477 2018 5559 4914 3476 * * 2470 4094 * 4688 5914 4249 3733 228
+ 73 4340 * 0 * * * 4738 1106 0
+
+S 229 3555 * 6793 3510 * 4227 6500 4544 3750 4856 6494 4536 * 3463 6816 2244 2725 3544 * * 229
+ 0 * * * * * * 4418 0 0
+
+P 230 * * * 5387 4663 * * * * 5169 * 4897 3214 382 * * * * * * 230
+ 0 * * * * * * 3578 0 0
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+Q 231 4007 * * 4037 * 2428 2737 * 2786 * * * * 1591 * 3965 * * * * 231
+ 0 * * 0 * * * 2919 0 0
+
+//
+�HHsearch 1.5
+NAME 61e58fd4d97efb70b78410488ce6cac8
+FAM
+FILE 61e58fd4d97efb70b78410488ce6cac8
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:20:36 2013
+LENG 179 match states, 179 columns in multiple alignment
+FILT 109 out of 1185 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCC
+CCCCEEEEEECCCCCCCCCCHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9747999997988888069999999999999963878848999997893369864776677899999998754158987599999999999865540578
+8996299998579989970569888988999997886434248999999966999854998099999999999999619
+>Consensus
+xxxdivfllDxSxSmxxxxxxxxxxxxxxxxxxlxxxxxxvxivxfxxxxxxxxxxxxxxxxxxxxxxixxlxxxxgxtxxxxalxxaxxxxxxxxxxxr
+xxxxxxvilxTDGxxxxxxxxxxxxxixvxxigigxxxxxxxxxxxlxxiaxxxxxxxxxxxxxxxxLxxxxxxixxxi
+>61e58fd4d97efb70b78410488ce6cac8
+GNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGAR
+PDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLCTELQKKI
+>gi|260837234|ref|XP_002613610.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]gi|229298996|gb|EEN69619.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]
+-----LYPYGSySGGYPPSNMEKTMG-PGNYRVPLvaGGETITIGSIKKTEETSPseslsaekQAVVAAQDTRECTMSSITiySEERLRGTKKTYSGNGW
+LPRDPS-----WVVDSAGPAWVDSNGVTWEDV-------VTVDNVQSGDQ------RQVFGGFQGKARYWKLVITQTYTGWQPYVRE-----
+>gi|317505805|ref|ZP_07963650.1| von Willebrand factor type A domain-containing protein [Segniliparus rugosus ATCC BAA-974]gi|316255887|gb|EFV15112.1| von Willebrand factor type A domain-containing protein [Segniliparus rugosus ATCC BAA-974]
+--ATVILLLDISESMRatdvkPSRVEAARAAAIKFVDGM-APTVQLGVVTFAGNAQPLVRPSTD--HETAKKVIDQMIrpdKLEKQTATGEGIYTALQQI
+EtiAGalGGKNHA-PPARIVLVSDGKETVpdDLNAprgaYaaartaKEKHVPVCTVAFGTKAGkitldnqvdeVPVDLESLKKISDLSNSPgnscRFFPA
+ESQGELAQIYQSLNEDI
+>gi|224080450|ref|XP_002190370.1| PREDICTED: von Willebrand factor A domain containing 5B1 [Taeniopygia guttata]
+---EFIFLVDRSRSMSGVNISHAKDALLVILKSLMPA-CLFNVIGFGSTFKTLFPVSQAYCEESLLMACQSIRRIRadmGSINLLSPLKWVTRQPL----
+--HRGHPRLLFLLTGGAISNTGKVLEllrttPCSTRCYSFGIGPN----ACRRLVRGLAAVSRGVSEFLAEGERLQPKMIRSLKKAM
+>gi|327441394|dbj|BAK17759.1| uncharacterized protein containing a von Willebrand factor type A domain [Solibacillus silvestris StLB046]
+QGRDIVFVIQDTPDIQSHDPDQSR--VTEVLSLMDDasSKDRFGFVGFNKEVTKELALTNNI--VQAKSKLNEFGKnisPYMANDLSKGLEKAVDELTKK
+ST----SNDKVIVIMTVGNSiYNEVSKklaakAYEEDITIHTISFGDPL-YA-DAPFLTEIAKLTGGNYT-HSPNAAFLKDVLSKLS---
+>gi|156404021|ref|XP_001640206.1| predicted protein [Nematostella vectensis]gi|156227339|gb|EDO48143.1| predicted protein [Nematostella vectensis]
+-QIDIVFVLSASSMKSSTTFSLMQNCILKIGSKFGVYTFHYSVILYGSSSVKKFDFNtAFPYREALIEESNNLVKENGSSAITEALSFARTVLNDASA--
+RSNVRRGVAVIFDKATGKTVqqlqsaaRPLHDEGIIVVASGVGPE----VTKEEARAMTSRR--NDATHVNDTYQPGPLGDHIVRRI
+>gi|288918847|ref|ZP_06413192.1| conserved hypothetical protein [Frankia sp. EUN1f]gi|288349809|gb|EFC84041.1| conserved hypothetical protein [Frankia sp. EUN1f]
+----LLLVIDHSTSMA-ETWAggtmskadqlalAVNRLLGNAVLLCSrgddrvYDYFEVGILGYGRGVAPVLYgssvsrpllpiseVALNP--NRVDHVL
+RKVPDgagglvevqtpipawvdpvADGWTPMVEALRVAAWVVDGWCRTHTASFPPIVVNVTDGQSTDGDPRAAAAQVRAAGTADGNAL-------LFNAH
+LSATMRRAVTFPRDRADLPGEFAQVLFDM
+>gi|237801322|ref|ZP_04589783.1| magnesium chelatase subunit ChlD [Pseudomonas syringae pv. oryzae str. 1_6]gi|331024181|gb|EGI04238.1| magnesium chelatase subunit ChlD [Pseudomonas syringae pv. oryzae str. 1_6]
+------VIVDASASTrRHQALSQAKGLLSQVFDDAYRRRARLALLTASGAvPRWQHQGLKAS-----AALVPWLDGLGagGGTPLTAALEQA-RAWLEQR
+QKRYPAEQHRVLVMTDGRIKQLPVLSAFTCASLLI------------------------------------------------
+>gi|268576625|ref|XP_002643292.1| Hypothetical protein CBG08168 [Caenorhabditis briggsae]gi|187032944|emb|CAP28053.1| hypothetical protein CBG_08168 [Caenorhabditis briggsae AF16]
+-KMDIIIAFDSSDTISQEMYYSTIGAVKKIGNSItiGQDKSRIIVGTYDATSHFNGNLNTIDSFDRYQEKIADLFSLGYTGINGNNVQSVLDFIIVENST
+apLRQaPVRKLLILLSSqGWDQGNFvegkeqgfqdPTNSAQslqkiGLETFAIGLGNT----ANMSQLSAIAKCST-----KVMSESALYNVVFQIISNI
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 885 4104 * * 4202 * * * 2017 4391 * 4285 * * * 1
+ 0 * * * * * * 6626 0 0
+
+N 2 5941 * 4547 5108 5047 5922 4457 * 2865 5816 * 3989 1543 3616 4162 4096 4468 5839 * * 2
+ 22 * 6074 * * * * 8798 0 0
+
+V 3 2394 * * * 4424 * 6272 3643 5077 2408 3870 6415 4837 6512 4006 4371 4264 2943 * 4896 3
+ 0 * * * * * 0 9217 0 1006
+
+D 4 6388 * 748 3560 * 5218 4365 6559 6032 5686 6541 3128 6526 * 6636 * 4607 * * * 4
+ 20 * 6200 * * * 0 9221 0 1006
+
+L 5 5517 * * 6303 6600 * 6666 1446 * 2169 6879 * * * * * 4749 1729 * 6849 5
+ 0 * * * * 838 1183 9330 0 1254
+
+V 6 3320 5113 * * 4807 5617 * 2720 * 3230 4156 6566 * * * 5175 4458 1634 6519 3581 6
+ 0 * * * * * 0 9461 0 1006
+
+F 7 5706 * * * 1054 * * 2663 * 2173 7074 * * * * * 6570 3779 * 5120 7
+ 18 6361 * 0 * * 0 9526 1049 1006
+
+L 8 3371 4638 * * * 6503 * 2606 * 1569 6610 6665 5723 * * 6613 6319 1843 * 6592 8
+ 0 * * 0 * 866 1148 9483 1049 1243
+
+F 9 6014 6700 * * 5088 * * 2238 * 1441 4677 * 6413 * * * * 1804 * 5156 9
+ 12 * 6956 * * * 0 9526 0 1006
+
+D 10 * * 241 4256 * 5731 5190 * 6333 * * * 6510 6661 * 5488 * * * * 10
+ 0 * * 0 * 0 * 9512 1011 1207
+
+G 11 2993 6766 4094 5174 6657 3690 6416 4113 * 5201 6891 4160 * 5088 4550 2701 2621 2980 * 6025 11
+ 26 5781 * 0 * * * 9537 1190 0
+
+S 12 6857 6517 6528 * * * * * * * * 6658 * * * 224 3272 * * * 12
+ 0 * * * * * * 9537 0 0
+
+M 13 3251 * 3684 3905 * 1782 5718 6589 5251 * 6869 4463 6696 3908 4685 2784 4071 6658 * 5613 13
+ 0 * * * * * * 9537 0 0
+
+S 14 6546 * 4614 * 6654 3689 6760 * 5613 * 5649 4676 * 6517 6570 503 5629 6677 * 6025 14
+ 27 6962 6589 0 * * * 9537 1011 0
+
+L 15 4385 * * * 6968 * * 2706 6379 3743 1152 6410 * 5733 * * 5168 2580 6663 5748 15
+ 66 4884 6532 3128 175 1035 966 9509 1505 1221
+
+Q 16 3172 6914 6776 4082 6620 2670 6781 6789 3761 5197 * 4165 4372 3453 3940 2879 3172 6731 * 6730 16
+ 318 3830 2974 2258 338 983 1018 9513 2229 1236
+
+P 17 3705 * 4115 2848 5357 2394 5562 * 4345 5113 * 4000 3332 5417 4672 3025 5748 4832 * 6396 17
+ 160 4824 3840 2094 385 265 2577 9311 1381 3209
+
+D 18 3277 * 3214 2713 6601 4891 4993 * 3533 6114 6693 3434 5709 4579 4926 2683 4305 4700 * 5672 18
+ 75 5678 5017 2030 405 582 1590 9441 1163 2371
+
+E 19 3905 * 3134 3498 6902 3401 6679 6873 3603 6491 5511 2904 4975 5522 3424 3298 4639 5568 6673 4599 19
+ 57 4695 * 1317 740 626 1506 9467 1535 1901
+
+F 20 5634 * * 4674 1844 6753 * 3240 6693 2738 4168 * 4241 6747 6546 6188 * 4456 2900 3927 20
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+ 42 6653 5742 0 * * 0 9394 1000 1000
+
+K 153 3565 5476 3345 3867 * 3127 4694 6252 3492 3941 6509 4623 4937 3976 4360 3111 4544 5562 * 5081 153
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+ 144 * 3401 0 * 1220 809 8974 1018 5319
+
+S 156 5272 * 4869 2861 * 1489 6141 6023 4000 6212 * 4122 5204 5040 3728 3343 6093 6269 * 5397 156
+ 245 * 2680 * * 414 2004 9070 0 4503
+
+E 157 4339 * 4327 2689 * 3133 4856 4938 3287 4596 * 2971 6304 3279 4577 4727 4413 6115 5454 6199 157
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+ 32 6435 6579 1000 1000 546 1667 9322 1000 1927
+
+I 161 4917 * 6196 4225 4851 5708 3942 3093 3697 5515 5455 4620 4507 4075 3709 3540 3259 3748 * 4141 161
+ 0 * * * * 0 * 9370 0 1353
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+L 162 2437 * 5824 6544 6312 6441 6409 3336 6513 2323 5568 5003 4777 * * 4583 4634 1982 * 5846 162
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+D 163 4824 6440 2557 3184 * 4009 6413 * 4273 4887 6293 3078 3511 4585 4118 4040 2891 * * * 163
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+
+T 164 6758 * 1863 3658 * 3523 * * 4398 6576 6643 2665 6322 5743 4986 2529 3505 * * * 164
+ 17 * 6446 0 * 0 * 9245 1058 1058
+
+F 165 3551 * 6233 4467 2459 4652 * 4393 5564 4587 4812 4436 3114 5667 5201 4309 4862 3921 6406 3090 165
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+
+E 166 3210 6465 2790 2458 * 4442 6390 * 4231 6298 * 3827 5217 4002 6143 3192 3682 5710 6296 4754 166
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+ 20 6205 * 0 * * * 9209 1006 0
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+D 170 5304 * 2962 3406 * 3330 6235 * 3924 6205 6404 3289 4241 2958 4213 3141 4011 5507 * 6267 170
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+
+L 171 2661 6283 * 5156 4713 * * 2250 4598 2370 5272 5160 * 5153 4718 * * 2756 * 4327 171
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+C 172 5342 6218 * * 2285 5978 * 2745 6203 2734 4696 6356 * 4726 5188 5171 4681 2185 * 5312 172
+ 0 * * * * * * 9084 0 0
+
+T 173 4186 * 2587 3719 5203 5083 * * 3243 4569 6319 2771 4190 3879 4002 4116 3904 6122 * 6044 173
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+E 174 5130 5178 4195 2510 * 4585 4557 5204 3199 4551 6402 5139 5127 2769 3643 3234 4350 * * * 174
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+
+L 175 5952 * * 5108 4139 * * 1269 * 1599 3823 * * * * * * 3602 * * 175
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+
+Q 176 2869 * * * 4085 4735 * 3338 4097 2971 4854 5760 * 2501 3924 3724 * 3727 * 4835 176
+ 0 * * * * * * 8381 0 0
+
+K 177 5457 * 2286 2968 4298 5543 * * 2926 * 5504 3947 * 3751 3794 2880 4398 * 5381 * 177
+ 0 * * * * * * 8134 0 0
+
+K 178 4190 5176 3225 2840 * 4304 * * 2084 4173 * 5155 * 4335 3241 3349 5324 5473 * * 178
+ 0 * * * * * * 7957 0 0
+
+I 179 * * * * * * * 853 * 2035 3787 * * * * * * 2945 * * 179
+ 0 * * 0 * * * 7385 0 0
+
+//
+�HHsearch 1.5
+NAME 665b4706556bcfdcefa8812b17dc787c
+FAM
+FILE 665b4706556bcfdcefa8812b17dc787c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:15:57 2013
+LENG 233 match states, 233 columns in multiple alignment
+FILT 122 out of 1206 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEECCCCCCCEEEEEEEECCCEEEEEEEECCCEEEECHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEEEECCCCCC
+CCCEEEEECCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEEEEEECHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEEEECCEEEEE
+EEEECCCCCCCCCCCEEEEEHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9999999987898699999818985999999719999989899377885699994121356788717999999997987877766565899992575436
+7744446747765432344679879999856657888777556899999867899765415777867599632789974445788882799309939999
+999737787888986189997997999999859
+>Consensus
+ixxgxxxxxxxxPxxvxixxxxxxxxCxGtlIxxxxVLTaaxCxxxxxxxxvxxgxxxxxxxxxxxxxxxvxxxxxxpxyxxxxxxxDiallkLxxxixx
+xxxvxpxxlxxxxxxxxxxxxxxxxxxxgxgxxxxxxxxxxxxxxxxxxxxxxxxCxxxxxxxxxxxxxCxxxxxxxxxxcxgdsGxplxxxxxxxxxlx
+GixsxxxxcxxxxxxxvxxxvxxxxxWIxxxxx
+>665b4706556bcfdcefa8812b17dc787c
+IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
+RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
+GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
+>gi|339237293|ref|XP_003380201.1| putative ovochymase-2 [Trichinella spiralis]gi|316977003|gb|EFV60183.1| putative ovochymase-2 [Trichinella spiralis]
+-----KASPYSMPWSVII-QTKDK-VCGGVLIrlektanSSNTVLASSYCFSQKfgkmysyVNTKVHLGVHTFPSDS-DKVTVGIKQVTSTP-YEQGMIK
+KDIALITLLSEVEFNEKIRPICLPSINY---KPPTATKYPLVGWVLSKLTRfRKIPYLLQVPIILFEPSECAMMLEIFSDDDHICGYFYDPHMfnNSVPL
+DLGSALISTYRRNLFIIGLFSAMIRfENMTGHILLFSRISTSVEWI-----
+>gi|319891581|ref|YP_004148456.1| hypothetical protein SPSINT_0291 [Staphylococcus pseudintermedius HKU10-03]gi|317161277|gb|ADV04820.1| hypothetical protein SPSINT_0291 [Staphylococcus pseudintermedius HKU10-03]
+------------------YESGTHKQCTAILISSSVALTAKHCGGDHpttYNGTIYPGESGLSTPFG---YMNISTYIPNPDY-------DIAILKgteQ
+DKTNAYKYYIKPFKT----------------PVTAFSDETLSSFIGQDVYSYGYPSKYGGYKQYRSDGKMNFYEKNNKLFLTSLPTFEGQSGSGIF-KKD
+GQ--FVGLLITRTQDYEGNFLPFTQEVA---EWVNTNSN
+>gi|157130425|ref|XP_001655710.1| hypothetical protein AaeL_AAEL002577 [Aedes aegypti]gi|108881970|gb|EAT46195.1| conserved hypothetical protein [Aedes aegypti]
+-------------------------------------------------------------------VFQTAKKVVHPDFNPASNVANIALLFLKERSEI
+NHLACTFDINET-------FNDQTCLIVGWNNDNFENIRSTSVTPNKQPISILQSSDSYLHTLSTAR-------NQSKQSCNRWRGATIICldQKDQNWK
+IIGIAAKNNErCDANGIPETLVAIPQLSPWIREQL-
+>gi|313236555|emb|CBY19847.1| unnamed protein product [Oikopleura dioica]
+---------------------NNFRLCTATLLTPTTLITTAGCTGSDanNRLFAKIGQANFDPraPSDHVQTIMIRRCVAHPKYVRGEPNNDLQICFLAE
+SIKQAKGIMIPCLTDTQ----IKLNDGDIVVTESRTNFNKGKTEGYPMRTHIPISGKYSQGKTDKER---------GYAFGDPLCMKEVGSPVFREDVNQ
+RTLVGLVQGALTpenqC--PTRLFNIVDLRDHVDWITATTK
+>gi|325194105|emb|CCA28172.1| AlNc14C1403G12929 [Albugo laibachii Nc14]
+-------------------------VCAACLIDTMNVATSSSCIrYQVQSPGDRWQFKFQKVGGGFKKSRFVTQITHAPNFQMYQMTGDFAILKLDTPIV
+---EIHPVLISNKAPR-----VGSKLHIFG---VAPANPETEKMIMGTLTVQSTDTCQLAFEGkppnlytpkYDGKQLFCAK--SQCSAVCEGELGMPFa
+redIVNNTVRLILYGIQASASVECDPRKTSSYGVPFSHENFFESYSK
+>gi|195112812|ref|XP_002000966.1| GI10530 [Drosophila mojavensis]gi|193917560|gb|EDW16427.1| GI10530 [Drosophila mojavensis]
+-------------HLVYL-RFNYNIICSGIVVNNRTVLTVTSCLDRKEPPKIIVHFTD-------GTAQTASSSSPSSDYTMSSGSNLLSFLHLEKPLDQ
+EfDTPPPFCT-------QAVRPQDNVMQLNWDKNY------SRPIPRFVPQMPLDQCQTLNRDarMLAPAVHCVE-NTQYTDECIRSYGLPYVWKGA---
+-FCGMNINGHNCSVPSNADVYVRLLREKRLISKMLR
+>gi|301166151|emb|CBW25726.1| conserved hypothetical protein [Bacteriovorax marinus SJ]
+--------------------------CTATLVGKSCIITSSVCAKLDrvVEFNIPSSEDGVPALAKAEDTYEVDPSSFSYDNSG--IGKFWAVAKLKRNA
+LTGKLPGEVQGYFPVISK-KPRKNDKIYILQYANTNPDRYdvisgevganpngys-lNYSQSSANGVLV-------KAGIFLIPEII-----YHNVDVSH
+GGAGAPLINSSTHE--VVGVHTHG-GCQSGqgrGR-------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+I 1 4685 * * * * * * 816 * 3743 * * * * * 4687 3708 2300 * * 1
+ 0 * * * * * * 7293 0 0
+
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+
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+ 40 5194 * 0 * * * 8064 1000 0
+
+G 4 4363 * 5335 * * 522 5216 * 4264 * * 4378 5319 * 5291 4244 * * * * 4
+ 66 4473 * 1806 486 * * 8373 1192 0
+
+Q 5 5340 * 5375 2602 5385 5610 * * 3876 5471 * 5566 4668 3451 2558 4480 2943 3198 * 4445 5
+ 20 * 6189 * * * * 8547 0 0
+
+E 6 4736 * 2986 3008 * * * 5766 3728 4062 * 4831 2217 4155 3316 4215 4127 4626 * * 6
+ 0 * * 0 * 0 * 8910 1000 1000
+
+C 7 1833 4754 3847 4862 * * * 5828 5823 5734 * * 3824 * * 3988 2789 2224 5920 6028 7
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+
+K 8 4988 * 3092 4032 5620 3965 * 4522 3619 4390 * 2999 2687 6085 4427 2793 5011 * * 5938 8
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+
+D 9 3498 * 3692 3901 6340 4102 6098 4156 4933 5994 5870 3438 3257 4362 3639 3157 4813 4542 4505 * 9
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+
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+
+E 11 4442 * 4001 1973 * 4022 6704 6160 3612 * 5957 4156 4641 2889 3274 3535 5806 * * 6049 11
+ 0 * * * * 0 * 9470 0 1001
+
+C 12 3903 6429 6273 * 2236 * 3506 5017 6303 4659 5279 * * 5032 6153 3797 5129 5152 3088 2261 12
+ 27 6712 6842 2000 415 * * 9564 1000 0
+
+P 13 3946 * 6325 * * 6406 6147 6022 * * * 5416 416 4302 * 4464 * * * 6310 13
+ 17 6448 * 2322 322 * 0 9699 1019 1150
+
+W 14 6186 * 6438 * 3387 6412 3706 * * * * 4745 5054 * * 4590 * * 1158 2098 14
+ 0 * * 2322 322 862 1153 9873 1000 1150
+
+Q 15 4121 * * * 4653 6416 4177 3854 * 2448 3343 4846 6280 3987 5523 3464 4565 2413 * 4975 15
+ 0 * * * * * 0 10038 0 1000
+
+A 16 1958 4674 * * * 3402 * 6546 * 3845 5495 6613 * * * 6617 4995 1137 * * 16
+ 58 4939 7181 2361 312 0 * 10038 1423 1000
+
+L 17 3495 * * 4214 4961 3752 6328 4469 5330 3464 4926 * 5858 4469 2830 2603 3779 3640 * 5353 17
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+
+L 18 6468 * * * 3473 4318 * 1612 6357 2098 4926 * * 6618 5858 5519 5425 2857 * 4954 18
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+
+I 19 5825 * 5337 5830 2677 4304 4294 4267 3617 3545 5022 * * 5786 3617 4194 * 3571 5908 2498 19
+ 287 2469 * 1559 598 202 2939 9329 2758 5572
+
+N 20 5491 * 3276 4099 4544 4491 5291 3891 4080 4138 6344 3912 * 4352 4171 3985 3750 3905 5373 3206 20
+ 32 6716 6349 1000 1000 2029 406 9991 1007 1602
+
+E 21 5299 * 5006 3653 5279 3418 * 4903 3433 5246 * 2996 3738 5550 3648 3358 3696 3626 * 4829 21
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+
+E 22 4954 6507 3028 3533 4442 3094 6695 * 3864 4938 6283 3043 3569 4944 3438 3494 4983 * * 6623 22
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+
+N 23 5505 * 3364 3859 5093 2021 5586 6390 4570 6651 * 3377 6386 4340 4296 2963 4093 * 5453 4911 23
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+
+E 24 4495 5135 6169 5602 4578 3225 4881 * 2840 5633 * 3293 4930 3921 3507 3217 3496 5599 * 4491 24
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+
+G 25 4629 * 6514 5644 2658 4215 3129 4852 4909 4932 6744 5058 4129 3915 3414 3794 6465 3798 6163 3727 25
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+
+F 26 3923 * * * 3122 6826 4187 3444 5293 2776 * 4982 4637 4378 4261 4563 3798 2708 4956 5594 26
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+
+C 27 5938 252 * * 5783 4640 6550 * * 6249 * * * * * 4246 6805 * * * 27
+ 9 * 7406 * * * * 10349 0 0
+
+G 28 3791 * * 6774 6718 2700 6729 5162 * 4754 5880 4232 5581 5161 5778 2060 2223 4499 * 4465 28
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+
+G 29 2073 5476 * * * 594 * * * 6756 * * * 6269 * 5747 * 4779 * * 29
+ 0 * * * * * 0 10383 0 1000
+
+T 30 2948 5034 * * 4785 6232 6713 4839 * 4686 * 5230 * * * 3086 1427 2464 * 6730 30
+ 0 * * * * * 0 10383 0 1000
+
+I 31 5346 * * * 4305 * * 2303 5714 1174 4154 * * * * * * 2956 5643 4192 31
+ 0 * * 2000 415 0 * 10387 1000 1000
+
+L 32 * * * * * * * 1156 * 2080 7102 * * * * * 4824 1988 * 5641 32
+ 53 4791 * 2894 209 * * 10391 1571 0
+
+S 33 3903 6844 3563 6704 5446 2778 4323 * 5211 * * 2796 * 6907 5429 1843 3049 * * 6711 33
+ 0 * * * * * * 10391 0 0
+
+E 34 5275 * 3523 3641 * 4322 * * 4137 6985 * 3019 1904 5774 3700 3144 3989 5492 * 6937 34
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+
+F 35 * * 2738 4456 7157 5110 * 5348 3821 5913 6779 2643 6772 4086 1962 3824 4439 6884 * 4736 35
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+
+Y 36 5464 6659 6929 * 3413 * 2348 4791 * 3834 5853 6776 * 5962 5988 4936 3454 3405 2401 3369 36
+ 33 5451 * 2755 231 0 * 10435 1270 1000
+
+I 37 3697 * * * 5072 * 6774 1978 * 3697 5862 * * * * * 6844 999 6738 5848 37
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+
+L 38 4928 * * * 6539 * * 2685 * 797 5089 * * * 6767 * 6734 2493 * * 38
+ 0 * * * * * 0 10448 0 1000
+
+T 39 5082 * 6767 * * * * 5233 6309 * * 6596 6327 * * 3375 348 5862 * * 39
+ 15 * 6587 * * * 0 10448 0 1000
+
+A 40 957 * * * * * * * 5096 * * 7136 5743 * * 2035 3163 4585 5524 6527 40
+ 0 * * * * 956 1045 10434 0 1196
+
+A 41 905 6857 * 6655 * 3584 6734 5530 3748 5790 * 4839 * * 4500 3311 4536 6843 * 6818 41
+ 0 * * 2000 415 0 * 10448 1000 1000
+
+H 42 5918 * 4375 5380 5972 5254 1289 5870 4232 6675 * 4402 6350 4331 5198 3002 3870 * * 4323 42
+ 18 7136 7481 1000 1000 * * 10452 1000 0
+
+C 43 6160 321 6626 * * 6896 * 4713 * * * 4928 6850 * * 5078 * 4114 * * 43
+ 70 * 4395 * * * 0 10448 0 1000
+
+L 44 4683 5877 * * 2728 6882 * 2783 6602 2229 5067 6017 * * * 4719 3934 2001 * 5847 44
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+
+Q 46 5206 5887 2774 4267 6749 3119 5700 6237 3493 4748 5659 4609 3993 3932 4571 2831 4833 5923 6510 4620 46
+ 126 4414 4760 2320 322 2175 361 10391 1947 2477
+
+A 47 4429 * 3551 4777 6536 3269 5884 5846 3444 3863 4900 3758 3685 3906 3945 3910 3801 5146 * 4679 47
+ 956 1139 5038 2564 267 800 1233 10363 7045 2874
+
+K 48 4693 * 3494 3510 * 3492 6704 * 3653 7045 6612 3700 3649 4133 3735 3105 2942 5867 7113 5081 48
+ 53 5598 6016 1000 1000 2931 203 10349 1208 2321
+
+R 49 4118 * 3503 2959 7062 3543 5628 5923 3933 4281 6768 3841 3251 4005 4102 4172 4167 5813 6439 4891 49
+ 51 6939 5246 1000 1000 1472 645 10367 1006 2483
+
+F 50 4835 * 5408 5734 3146 4834 5126 3673 6713 2376 5349 4286 4430 5066 6990 4314 4020 3303 * 3439 50
+ 25 5884 * 1659 549 2148 369 10363 1345 2514
+
+K 51 4995 * 4238 3938 4374 4764 3879 3780 3336 4534 6944 5058 4508 4603 3546 3768 3419 4217 5844 4815 51
+ 22 6760 7418 2461 289 1875 459 10383 1175 2155
+
+V 52 3415 * 6707 4821 4290 4574 * 2833 4874 4243 5149 5603 * * * 6704 4803 1249 6897 5828 52
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+
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+
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+ 0 * * 2093 385 1924 441 10382 1221 2301
+
+G 55 5160 * 4056 4081 4525 1185 5729 7331 4864 4629 5857 5892 5810 5188 4339 4117 6497 5687 * 4242 55
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+
+D 56 4106 * 3600 4154 3959 4431 5882 4107 5196 5518 5353 3941 4184 5019 4511 2834 3525 4005 6221 4428 56
+ 46 * 4990 * * 3398 144 10347 0 2616
+
+R 57 3283 * 3359 5807 5661 3945 3792 4260 5054 4443 6642 4053 3897 5163 4816 3435 3787 3963 6694 4124 57
+ 12 6918 * 0 * 2696 242 10330 1043 3087
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+N 58 4008 5755 2736 3871 5066 4038 6393 5782 4046 4172 6582 3183 5932 5376 3827 3142 4186 5067 * 4855 58
+ 69 * 4414 * * 3827 105 10352 0 2770
+
+T 59 4802 5452 6791 6482 3871 3939 * 3509 4654 3006 5805 6681 4466 4603 3813 2971 3649 5307 4467 3783 59
+ 29 6655 6614 0 * 4027 91 10257 1176 3532
+
+E 60 5713 * 3427 3958 6905 3509 4072 5005 5646 4763 6636 3160 3911 5249 4486 3623 3024 4282 5406 4587 60
+ 34 6006 6961 3700 115 * 0 10251 1076 3530
+
+Q 61 4178 5575 3194 3956 5775 4195 6522 4790 5635 4285 5636 4555 4321 5239 3081 3733 3215 3680 5768 5490 61
+ 26 5804 * 647 1469 4057 89 10260 1162 3668
+
+E 62 4775 6017 3719 5353 4413 4217 6597 5198 4848 4411 4831 3186 3418 5554 3753 2887 3840 3685 6526 * 62
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+
+E 63 3411 * 3084 3784 4170 3923 5336 5447 4247 5244 * 3885 4240 4916 3781 3386 3602 5231 * 4791 63
+ 332 4932 2534 2573 266 * 0 10418 1518 2966
+
+G 64 4081 * 3501 3943 * 2525 * 5725 3927 4304 6494 3886 4361 5491 4345 3323 2981 6823 * 4501 64
+ 144 4874 4043 4478 66 1935 437 10174 1352 5434
+
+G 65 5347 4075 2861 4547 4848 3568 4770 6264 4430 6678 6433 3147 3248 * 5492 3006 3819 * * 3978 65
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+
+E 66 3211 * 4238 3219 6350 3239 6812 4225 4430 5512 6498 5523 5524 4616 3896 3098 3438 4048 5580 5064 66
+ 70 5200 5630 2721 237 1032 968 10257 1381 4684
+
+A 67 3284 * 4332 3718 6736 4272 5213 4153 3768 5232 * 4398 4840 2276 3628 7021 3553 4402 * 5830 67
+ 54 5178 6755 1949 433 846 1172 10292 1380 3333
+
+V 68 5172 * 4546 5327 5473 4434 5123 2894 4867 4528 4767 6088 6841 4642 3110 3769 3044 3192 6885 3911 68
+ 26 6858 6807 1585 585 1355 715 10496 1007 2185
+
+H 69 3502 7051 5134 6934 3146 5255 3554 3069 5061 3537 5815 6773 * 4801 2844 5214 5933 4044 6744 3434 69
+ 21 6097 * 1927 440 2500 281 10511 1320 1845
+
+E 70 4093 * 3861 5378 6767 3608 6778 4605 3035 4864 6677 4184 3661 3817 3830 3926 3075 4859 * 4420 70
+ 21 6120 * 1305 748 * 0 10514 1177 1669
+
+V 71 3219 * 5809 5537 5955 7106 * 1742 * 5329 * 6751 5906 * 5833 4530 6005 1423 5937 6105 71
+ 0 * * * * 2202 354 10514 0 1669
+
+E 72 3886 6836 2924 3034 * 5720 4330 4780 3554 4650 * 6988 5075 4229 3632 2791 3663 4771 * 6954 72
+ 12 6914 * 1000 1000 * 0 10520 1006 1487
+
+V 73 4212 * 5128 3339 5995 5773 4277 5504 2998 5477 5902 4182 5557 3505 3007 3176 3340 5982 5975 5900 73
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+
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+ 85 4658 5838 1006 994 307 2381 10350 1564 1745
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+ 98 5745 4418 2077 390 1665 546 10192 1368 1401
+
+E 207 3973 * 4329 3511 4668 4569 4354 4957 4023 4488 6398 3844 3397 5706 4494 3193 3466 5404 * 3902 207
+ 269 3079 4275 1617 569 1636 560 10182 2836 2087
+
+G 208 3592 5537 3327 3506 4570 3054 5527 6336 3590 5230 6456 2953 5533 5379 4229 4291 4467 5046 * 4811 208
+ 366 2246 6241 1035 966 1676 541 10059 3965 2603
+
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+A 210 3931 3011 3994 3763 4711 2642 6641 * * 5007 6502 4166 4778 4899 4859 3150 3442 5720 * 4658 210
+ 71 * 4371 * * 3626 122 9973 0 3372
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+ 46 5370 7149 2183 359 875 1136 9926 1372 3663
+
+G 213 5061 6703 3372 3728 4438 1979 5414 5749 4791 6460 * 3808 6195 5064 3581 3347 3455 6501 * * 213
+ 136 * 3471 1585 585 701 1378 10064 1033 2384
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+K 214 3929 * 3390 4829 4555 3721 6423 3979 3885 3335 6474 4000 4959 6515 3722 4048 3982 6126 5409 3486 214
+ 10 * 7208 * * 1121 888 10086 0 3003
+
+Y 215 3929 * 5535 5136 3952 5102 6608 3698 6585 3754 5590 5691 1316 5379 * 6563 4387 6783 * 3548 215
+ 16 * 6518 * * 1688 536 10059 0 2225
+
+G 216 2866 6223 2735 3244 5037 2898 5612 4942 * 4055 7049 4479 4518 * 4986 3181 5545 5303 * 4997 216
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+
+I 217 4336 * * 6573 5029 4304 6923 2992 6311 2489 5682 6438 6364 * 5476 4886 4681 1535 7084 4536 217
+ 0 * * * * 1342 724 10112 0 1778
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+Y 218 4242 6738 6611 6587 1551 4332 5093 4995 * 4805 6312 5504 * * 6389 4731 6499 3826 * 1922 218
+ 0 * * * * 542 1675 10140 0 1405
+
+T 219 3014 * 6347 * 6551 4909 6558 3733 6797 3843 5139 4358 * 4606 * 3532 1579 3107 * * 219
+ 15 6641 * 0 * * 0 10185 1028 1000
+
+K 220 4052 * 2557 4388 5551 4992 6481 * 3632 6687 6763 2922 4608 5228 2003 4157 6420 6442 6750 5584 220
+ 0 * * * * * 0 10185 0 1000
+
+V 221 6534 * * * * * * 1950 * 2264 5611 * 6442 * * 6477 4138 1283 * 6481 221
+ 38 5251 * 481 1819 * 0 10185 1321 1000
+
+T 222 2632 6685 4204 5694 4022 4043 4641 6470 5644 5420 4939 5627 4740 6841 3348 2650 3823 4311 5534 4666 222
+ 16 * 6502 3000 193 0 * 10170 1000 1000
+
+A 223 3385 6742 4116 5181 4273 4919 4570 6607 4268 4961 6539 5047 3060 4352 3698 2848 4337 6719 * 3268 223
+ 14 6650 * 1000 1000 * 0 10145 1000 1017
+
+F 224 * * 5010 5430 2641 * 2528 5131 6961 4660 6320 5502 * 5610 4602 4216 6541 4605 * 1582 224
+ 14 6723 * 1585 585 * 0 10129 1006 1017
+
+L 225 3339 6806 6530 4606 4956 5958 6464 3701 3909 2604 4996 6650 * 6591 3166 3899 3493 3084 5976 5654 225
+ 0 * * * * 0 * 10129 0 1017
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+K 226 4783 * 1949 3518 * 5753 4731 * 3288 * * 3797 2532 4549 4057 3825 5006 6713 * * 226
+ 0 * * * * * * 10162 0 0
+
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+ 0 * * * * * * 10094 0 0
+
+I 228 * * * * 4540 * * 493 * 2836 5075 * * * 6263 * * 3972 * * 228
+ 19 * 6260 * * * * 10038 0 0
+
+D 229 4955 6124 4681 2274 * 5552 6559 5266 2733 3385 5516 5476 * 3134 3399 4796 4770 3682 * * 229
+ 0 * * * * 0 * 9938 0 1020
+
+R 230 4345 * 2817 3143 * 4589 4832 * 4056 6184 * 3191 * 2989 4434 2311 4780 * * 5291 230
+ 0 * * * * * * 9758 0 0
+
+S 231 3902 * 5891 4677 4684 * 6120 3965 6277 5576 6127 2772 * 3833 6185 4744 2188 2262 * 5952 231
+ 0 * * * * * * 9731 0 0
+
+M 232 6082 * * * 5975 * * 1846 * 2304 2488 * * 5988 * 4327 3079 2984 * * 232
+ 0 * * * * * * 9536 0 0
+
+K 233 3228 * 3557 2988 * * 5733 5813 2181 * * 2245 * 3000 4477 * 5719 5309 * * 233
+ 0 * * 0 * * * 8916 0 0
+
+//
+�HHsearch 1.5
+NAME 674c81cff4c6c504dd50e35c2bf78401
+FAM
+FILE 674c81cff4c6c504dd50e35c2bf78401
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:42:54 2013
+LENG 150 match states, 150 columns in multiple alignment
+FILT 72 out of 74 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEECCCCCCCCCCCCCCEEEEECHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEE
+CCCCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCCCCEEECCC
+>ss_conf PSIPRED confidence values
+9757705888886657655410568799999987548987786788898131277555443235677864463457873123445677788767884220
+47873578877668899971899968998899998505688897040689
+>Consensus
+xxxxtCxxxxxxxxxxxxxxkxxxxxqxxAxxxaxxAxxtxGkxxsxYPHxFxNxxxxxxxxxxxxexixFxxxxCxxpxxxxxxxxgxxxxxlxEfPix
+xxgxxYxxxskxxxxxPGpxRVIyxxxxxxfCGiitHtgxnxgxFxlCsx
+>674c81cff4c6c504dd50e35c2bf78401
+AVTWTCLNDQKNPKTNKYETKRLLYNQNKAESNSHHAPLSDGKTGSSYPHWFTNGYDGDGKLPKGRTPIKFGKSDCDRPPKHSKDGNGKTDHYLLEFPTF
+PDGHDYKFDSKKPKENPGPARVIYTYPNKVFCGIIAHTKENQGELKLCSH
+>gi|262367755|pdb|2KAA|A Chain A, Solution Structure Of Hirsutellin A From Hirsutella Thompsonii
+-PIVTCRPKLDGR------EKPFKVDVATAQAQARKAGLTTGK--SGDPHRYFAG-----------DHIRWGVNNCDK-----------ADAILWEYPIY
+WVGKnaEWAKDVKTSQQKggPTPIRVVYANSRgaVQYCGVMTHSKvdkNNQgkEFFEKCD-
+>gi|115388805|ref|XP_001211908.1| predicted protein [Aspergillus terreus NIH2624]gi|114195992|gb|EAU37692.1| predicted protein [Aspergillus terreus NIH2624]
+-QVYTCKRGANND-----GELIGKVPQDKAIGHFREAKTKAGK--SGYPKRFYNN-----------ENLKFKKG-CRD-----------KKVELWELPVL
+NGGQRYAYDKPKQEAPPGPMRVYYTKD-LKFCGIGTKSNrDNSGPVHLCK-
+>gi|238501164|ref|XP_002381816.1| conserved hypothetical protein [Aspergillus flavus NRRL3357]gi|220692053|gb|EED48400.1| conserved hypothetical protein [Aspergillus flavus NRRL3357]
+---------------------------------------------RRYPHQFFNK-----------DEITWGNERCNKPE-------GGEQPVLLEFPIL
+LDKSqkkaiqeLYNYKQLKPRPEPGPCRIVTRKKGDDLCGVMCHIEygkKDAkPGFKRC--
+>gi|3915848|sp|P00654.4|RNU2_USTSP RecName: Full=Ribonuclease U2; Short=RNase U2gi|257472077|pdb|1RTU|A Chain A, Ustilago Sphaerogena Ribonuclease U2gi|300193153|pdb|3AGN|A Chain A, Crystal Structure Of Ustilago Sphaerogena Ribonuclease U2 Complexed With Adenosine 3'-Monophosphategi|300193154|pdb|3AGO|A Chain A, Crystal Structure Of Ustilago Sphaerogena Ribonuclease U2 Complexed With Adenosine 3'-Monophosphategi|300193158|pdb|3AHW|A Chain A, Crystal Structure Of Ustilago Sphaerogena Ribonuclease U2 Complexed With Adenosine 2'-Monophosphate
+-------------------------DINTAIQGALDDVA-NGDRPDNYPHQYYDE-----------ASEDITLC-CgSG--------------PWSEFPL
+VYNGPYYSSRD--NY-vSPGPDRVIYQTNTGEFCATVTHTGAASyDGFTQC--
+>gi|115402733|ref|XP_001217443.1| predicted protein [Aspergillus terreus NIH2624]gi|114189289|gb|EAU30989.1| predicted protein [Aspergillus terreus NIH2624]
+--------------NRQYAAHKYTVNQIQAAFRAGINLQSKGKqTgDNHYPHNFRNG-----------DRLALGA--CGN------------TRTKSEFP
+IQIDGKTYSGG----KVDAVPDRVIYEYKEskktleVWFCGIVRHGTGN--NFLNC--
+>gi|336364646|gb|EGN93001.1| hypothetical protein SERLA73DRAFT_146126 [Serpula lacrymans var. lacrymans S7.3]
+------------------------------------NPTPTATNGVIYPHRFSNN-----------ERITFHN--CPA------------AQTLVEYPLR
+L-----------PTEvGAARHRVVYDYNKpHQFCGCMTHDGAIGNQFVAC--
+>gi|83766539|dbj|BAE56679.1| unnamed protein product [Aspergillus oryzae RIB40]
+-------------------------------------NTQVGR--NRYPHQFNNR-----------EALQIPEE-FR-------------NRRLQEFPIL
+RG-QIY------SGQAPGAMRVILAQVGnnWLLAGVMRHPTGRGNAFELCQ-
+>gi|154296967|ref|XP_001548912.1| predicted protein [Botryotinia fuckeliana B05.10]gi|150843099|gb|EDN18292.1| predicted protein [Botryotinia fuckeliana B05.10]
+-----------------------TYDQSAIDAACKQALLlasekkTVGK--DKYPHAYNDY-----------EKFTFIPA--A------------KKPYL
+-EFPILSNGATYTGSD---PASPGADRIVIGSiatdyKSAIFCAVITHDGSTKNGFTEC--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 423 * * * * * * * * * * * * * 1976 * * * * * 1
+ 0 * * * * * * 1206 0 0
+
+V 2 2130 * * * * * * * * * * * 2496 1442 * * * 2143 * * 2
+ 0 * * * * * * 2162 0 0
+
+T 3 * * * * * * * 3985 * * 2766 * * * * 3797 890 3185 * 3875 3
+ 0 * * * * * * 2567 0 0
+
+W 4 * * * * * * * 3898 * * * * * * * 4181 * 1719 1094 3243 4
+ 0 * * * * * * 2596 0 0
+
+T 5 * * * * * * * 4417 2874 * * * * * * * 292 * * * 5
+ 0 * * * * * * 2661 0 0
+
+C 6 * 0 * * * * * * * * * * * * * * * * * * 6
+ 0 * * * * * * 2661 0 0
+
+L 7 * * * 3217 * * * 3611 1278 2694 3700 * * * 4293 4343 3911 * * * 7
+ 0 * * * * * * 2661 0 0
+
+N 8 * * * * * * * * * * * 1153 1338 * 3357 * 4135 * * * 8
+ 0 * * * * * * 2661 0 0
+
+D 9 * * 2809 2752 * 3357 4417 * 2486 * * * * 2196 4042 * 3226 * * * 9
+ 0 * * * * * * 2661 0 0
+
+Q 10 3357 * * 4323 * * * * 4343 2568 * 2266 * 1229 * * * * * * 10
+ 0 * * * * * * 2661 0 0
+
+K 11 * * 2657 3676 * * * * 2706 3611 * 1579 2874 * * 4135 * * * * 11
+ 0 * * * * * * 2661 0 0
+
+N 12 * * * 3807 * 3212 * * * * * 869 * 3911 * 2644 4417 * * * 12
+ 0 * * * * * * 2661 0 0
+
+P 13 * * 3357 3217 * * * * 4135 2874 * * 2111 * 4293 2076 3611 * * * 13
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+
+K 14 * * * * * * * * 0 * * * * * * * * * * * 14
+ 0 * * * * * 0 1206 0 1548
+
+T 15 * * * * * * * * * * * 1891 * * * * 453 * * * 15
+ 0 * * * * * 0 1512 0 1548
+
+N 16 * * * * * 2407 * * * * * 884 * * 1891 * * * * * 16
+ 0 * * * * * 0 1512 0 1548
+
+K 17 * * * * * * * * 453 * * * * 1891 * * * * * * 17
+ 0 * * * * * 0 1512 0 1548
+
+Y 18 * * * * * * * * * * * * 2407 * * * * * 2451 670 18
+ 0 * * * * 530 1701 1512 0 1548
+
+E 19 2653 * 3706 1446 * 2553 * * * * * * 3209 * * * 3075 * * * 19
+ 409 3075 2967 1000 1000 1943 435 2531 1066 1150
+
+T 20 3140 * 3326 2528 * * * 2989 * * * 3406 * * * * 1697 3557 * * 20
+ 0 * * * * 0 * 2448 0 1198
+
+K 21 * * 2969 * * * 3483 * 656 3488 * * * * * * * 4078 * * 21
+ 0 * * * * * * 2820 0 0
+
+R 22 * * * * * * * 3488 2018 * * 2969 3473 * 1810 2633 * * * * 22
+ 0 * * * * * * 2820 0 0
+
+L 23 * * * * 1479 3488 * * * 1277 * * * * * * * * * 2843 23
+ 0 * * * * * * 2820 0 0
+
+L 24 * * * 4409 * * * * 2244 2431 * 3934 * 3052 3232 * 1922 * * * 24
+ 55 * 4745 * * * * 3029 0 0
+
+Y 25 * * * * * * * 3904 * * * * * * * * * 1140 * 1061 25
+ 0 * * * * * 0 3009 0 1010
+
+N 26 * * 1693 * * * * * 4321 * * 1940 4479 4942 * 1724 * * * * 26
+ 0 * * * * * 0 3443 0 1010
+
+Q 27 * * * 4630 * * * 3328 * * * * * 1150 4541 * * 1448 * * 27
+ 0 * * * * * 0 3445 0 1010
+
+N 28 2660 * 1900 * * 4133 * 4525 3783 * * 1953 5227 * 5221 3951 5356 * * * 28
+ 0 * * 3459 138 * 0 3445 1000 1010
+
+K 29 4064 * 3014 * * * * * 2396 * * 1805 * 4532 3794 4812 2911 4149 * * 29
+ 0 * * * * * 0 3446 0 1010
+
+A 30 143 * * * * * * 3874 * * * * * * * * * 5257 * * 30
+ 0 * * * * * 0 3455 0 1010
+
+E 31 3315 * 4217 1979 * 5110 * 2608 2810 3136 * * * 3313 4570 * * * * * 31
+ 0 * * * * * 0 3455 0 1010
+
+S 32 2237 * 3701 3774 4595 4575 * * 4570 * * 4200 * 4393 3978 1987 * * 3926 5110 32
+ 0 * * * * * 0 3455 0 1010
+
+N 33 4709 * 6544 5419 * 4756 4718 * * 2983 * 1945 * 1676 4222 3577 5952 * * * 33
+ 0 * * * * 0 * 3441 0 1010
+
+S 34 1270 4723 * * 4735 * 4864 3354 * 2795 * * * * * 2768 * 4973 * 4187 34
+ 16 * 6469 * * * * 3451 0 0
+
+H 35 3349 * * 5893 * 3149 2256 5489 2943 4192 * * * 5269 2377 * * 4396 * 3474 35
+ 53 * 4791 * * * 0 3452 0 1000
+
+H 36 5713 * 4790 3787 * 5981 1983 4869 2614 6430 * 4075 * 2382 5613 3853 5485 4999 * * 36
+ 49 * 4899 * * * 0 3398 0 1048
+
+A 37 539 * 4012 * * 5906 * 4503 * * * 3642 5370 6449 * 3977 6705 * * * 37
+ 0 * * * * * 0 3417 0 1098
+
+P 38 6469 * 4414 * * 1721 5525 * 5000 4155 5265 4103 1310 * * 6650 * 4977 * * 38
+ 0 * * * * * 0 3416 0 1098
+
+L 39 4574 * 4086 4424 3218 7261 * 3895 6183 1437 * * 5718 4165 * 4570 2737 * 5547 * 39
+ 88 5176 4977 2154 367 1217 812 3416 1056 1098
+
+S 40 6134 * 3947 4179 * * 5065 * 3986 * * * 4526 4229 6321 2027 1344 5360 * * 40
+ 0 * * * * 296 2430 3380 0 1097
+
+D 41 2398 * 2048 * * 4494 5874 5452 3071 6575 * 5179 5026 * 6717 * 2437 3290 * * 41
+ 86 * 4118 * * * 0 3447 0 1000
+
+G 42 5315 5291 5544 * * 384 5462 * * * * * * 6131 * 5062 3403 * * * 42
+ 148 4676 4104 1000 1000 * 0 3441 1064 1117
+
+K 43 6349 * 4533 3383 * 4384 * * 1123 * * * * * 3025 2769 4195 * * 5854 43
+ 1442 5163 727 0 * 2515 277 3399 1041 1231
+
+T 44 * * * * * 2921 * * * * * 2003 * * 3187 3643 1222 * * * 44
+ 366 3442 2921 0 * 3535 130 2544 1041 2220
+
+G 45 4552 * 3798 2781 * 843 * * * * * * 3554 * * 3361 * * * * 45
+ 63 4552 * 0 * 82 4170 2678 1000 2160
+
+S 46 * * 3982 * * 4474 7055 * * * * 3476 * * 3623 715 4308 4219 * * 46
+ 0 * * * * 603 1549 3653 0 1038
+
+S 47 6079 * 4005 4901 * 1640 5721 5692 4402 5190 * 3340 * * 4183 2104 3854 * * * 47
+ 0 * * * * * 0 3667 0 1000
+
+Y 48 * * 3461 * * * * * * * * * * * * * * * * 137 48
+ 0 * * * * * 0 3667 0 1000
+
+P 49 * * * * * * * * * * * * 0 * * * * * * * 49
+ 0 * * * * * 0 3667 0 1000
+
+H 50 * * * * * * 209 * 5242 * * * * 5238 * * * * * 3604 50
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+
+W 51 5805 * 4204 3991 3604 5040 * 5190 5691 5994 * 5039 4994 2538 2658 * 3945 4165 2637 5950 51
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+
+F 52 * * * * 655 * * * * * * * * * * * * * * 1454 52
+ 0 * * * * * 0 3667 0 1000
+
+T 53 * * * * 4352 3351 3457 * 4783 6377 4275 1763 * 5190 3609 5692 2637 * * 3683 53
+ 0 * * * * * 0 3667 0 1000
+
+N 54 5840 * 3063 * * * * * * * * 239 * * * 6002 * * * * 54
+ 22 6079 * 0 * * 0 3667 1003 1000
+
+G 55 * * 4343 5294 5369 1423 6580 * 3652 4572 * 3836 * * 3454 * * * * 2090 55
+ 2012 * 411 * * 743 1313 3648 0 1028
+
+Y 56 * * * * * * * * * * * * 2340 * * * * * * 317 56
+ 317 * 2340 * * * 0 1769 0 2639
+
+D 57 * * 0 * * * * * * * * * * * * * * * * * 57
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+
+G 58 * * * * * 517 * * * * * 1731 * * * * * * * * 58
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+
+D 59 * * 1883 * * 2288 * * * 2027 * 1843 * * * * * * * * 59
+ 330 * 2289 * * * 0 1789 0 2619
+
+G 60 * * * * * 0 * * * * * * * * * * * * * * 60
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+
+K 61 * * * * * * * * 517 * * * * * 1731 * * * * * 61
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+
+L 62 * * * * * * * 2525 * 929 * * * * * * * 1731 * * 62
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+
+P 63 * * * * * * * 2511 * 1498 * * 1088 * * * * * * * 63
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+
+K 64 * * * * * * * * 0 * * * * * * * * * * * 64
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+
+G 65 * * * * * 517 * * * * * 1731 * * * * * * * * 65
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+
+R 66 * * * * * * * * * * * 2021 2147 * 922 * * * * * 66
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+T 67 5327 * 2517 1154 * 4214 * * 4726 * * * 3604 4204 * * 3024 * * * 67
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+
+I 69 * * * 5327 1784 * * 1482 * 1614 * * * * * * * * * * 69
+ 46 4994 * 2000 415 * 0 3667 1064 1000
+
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+F 71 * * * * 537 * * 4260 * 4702 4589 * * * * * * * 2728 5171 71
+ 48 5446 6649 2916 205 * 0 3642 1052 1088
+
+G 72 3846 * 7484 * * 1486 4583 6066 4597 4084 * 7514 1755 7476 * 4022 5249 * 7088 6874 72
+ 150 4450 4240 1229 802 278 2511 3638 1163 1113
+
+K 73 2991 5934 6063 5652 * * * 6089 2286 3295 * 2750 4956 5022 6053 3680 5666 2601 6354 * 73
+ 425 * 1970 * * 1069 934 3637 0 1148
+
+S 74 2224 4733 * 3933 * 2264 4466 * 5079 * * 3888 4891 * 5538 2102 * * * 4501 74
+ 1042 * 959 * * * 0 3597 0 1607
+
+D 75 * * 2064 3659 * 3789 2829 * 2955 * * 1929 * * 3699 * * * * * 75
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+
+C 76 * 49 * * 4911 * * * * * * * * * * * * * * * 76
+ 118 3673 * 0 * 328 2297 3579 1120 1533
+
+D 77 4938 * 1501 6882 * 4330 * * 4419 * * 2436 4387 * 3462 2694 5001 * * * 77
+ 620 * 1516 * * * 0 3654 0 1085
+
+R 78 4869 * 3400 * * 2995 * * 2198 * * 2437 5169 * 2095 3622 * * * * 78
+ 1292 * 757 * * * 0 3365 0 1804
+
+P 79 * * * * * * * * * * * * 271 * * * 2546 * * * 79
+ 0 * * * * * 0 2060 0 2558
+
+P 80 * * * 2491 * * * * * * * * 698 * * * 2280 * * * 80
+ 283 * 2491 * * * 0 2060 0 2558
+
+K 81 * * * * * * * * 369 * * * * 2147 * * * * * * 81
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+
+H 82 * * * * * * 408 * * * * * * * 2021 * * * * * 82
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+
+S 83 * * * * * * * * 2147 * * * * * * 369 * * * * 83
+ 0 * * * * * 0 1809 0 2608
+
+K 84 * * * * * * * * 637 * * * 2147 2931 * * * * * * 84
+ 369 * 2147 * * * 0 1809 0 2608
+
+D 85 * * 1516 * * 1731 * * * * * 1518 * * * * * * * * 85
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+
+G 86 * * * * * 0 * * * * * * * * * * * * * * 86
+ 0 * * * * * 0 1557 0 2669
+
+N 87 * * 1498 * * 1731 * * * * 2511 2561 * * * * * * * * 87
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+
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+
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+
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+
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+
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+
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+
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+
+D 109 5458 * 1463 4108 * 1611 * * 4771 * * 4072 * 4822 5004 3908 * * * * 109
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+
+S 110 5340 * 4102 3152 * 5569 5224 * 4066 * 5889 3361 * 3759 * 1224 4539 4725 * * 110
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+
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+ 27 5758 * 1000 1000 0 * 3674 1015 1136
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+G 118 5697 * 5191 * * 381 * * * 5083 * * * * * * 2866 5726 * * 118
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+P 119 1859 * * * * * * * * 3606 * * 813 * 4454 * 5191 * * * 119
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+A 120 1944 4996 1340 * 4085 * 5697 3104 * 5587 4486 5191 * * * * * 5245 * * 120
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+T 125 2363 * 3170 4365 5583 4406 * * 4899 6447 * 3159 * 4653 4984 3926 1816 * * * 125
+ 187 * 3041 * * 0 * 3670 0 1000
+
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+H 137 * * * * * * 78 * 4249 * * * * * * * * * * * 137
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+K 139 * * * 3548 * 1088 * * 3189 * * 4205 * * 2601 5727 4083 4744 * * 139
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+E 140 1587 * 3486 3531 * 2035 * * 4397 * * 3431 3811 * * 4801 * * * * 140
+ 0 * * * * 0 * 3596 0 1006
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+N 141 5275 * 4630 * 4677 5876 * 5652 6542 * * 1227 6530 6249 5085 1767 5724 * * 4216 141
+ 29 * 5642 * * * * 3611 0 0
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+Q 142 3383 * 5741 6778 * 1940 5426 * 5150 * * 4199 5111 1602 6560 3136 5197 * * * 142
+ 388 2085 * 738 1320 * 0 3564 1524 1041
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+G 143 5531 * 3269 5784 * 1023 * * 4717 * * 1901 4863 * * 5366 * * * * 143
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+E 144 4978 * 2260 4271 3837 2260 * * * 4893 * 2091 5177 5641 * 3147 * * * * 144
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+L 145 * * * * 527 * * * * 1989 * * 5245 * * * * 5177 * * 145
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+L 147 2818 * * 4202 * 4762 * * 2945 1149 * 4343 * 3672 4901 5327 * * * * 147
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+C 148 * 0 * * * * * * * * * * * * * * * * * * 148
+ 0 * * * * * * 3622 0 0
+
+S 149 * * 4161 5375 * 7052 * * 3301 * * 3788 5297 2791 4221 1243 3434 * * * 149
+ 0 * * * * * * 3321 0 0
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+H 150 * * * * * * 0 * * * * * * * * * * * * * 150
+ 0 * * 0 * * * 1152 0 0
+
+//
+�HHsearch 1.5
+NAME 679a9284ef0ef040ad53936c4c1e9d7d
+FAM
+FILE 679a9284ef0ef040ad53936c4c1e9d7d
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:09:07 2013
+LENG 204 match states, 204 columns in multiple alignment
+FILT 92 out of 106 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEECHHHHHHHHHHCCCCEEEEEEEEEEECCCCCEEEEEEECCEEEEEEEECCHHHHHHCCCCCCEEEEEEEECCCCCCCEEEECCEEECCCC
+CCCCCCCCEEEEEEEECCCEEEECCCEEEEECCEEEHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCEEEEECHHHHHHHCCCCEEECCCEEEEE
+EEEC
+>ss_conf PSIPRED confidence values
+9877605673663899999766897789956999970899489999778669999998638877625888967899988034777629998989938987
+5667642105899990795279766168970659962455489999999973756699765489999889987999806844453589836114416899
+9979
+>Consensus
+xxxxxxxxxxxxxxxdLkxYYsxxxxexxNxxgxxxxxxgxxxxxxxxxxxxxxixlxgxdxxxfkxxxxkxVDVFgvxxxxxxxxxxxxyGGVTxxnxx
+xxxdxxxxixlxvxxxxgxxtxxxxxxxxixKexvTlkELDfKiRkxLixxxxLYxxxxxxGxIxixmkdgxxytxDLxkkLqxxrmxxxIdsxxixxIe
+Vxlx
+>679a9284ef0ef040ad53936c4c1e9d7d
+SEHKAKYENVTKDIFDLRDYYSGASKELKNVTGYRYSKGGKHYLIFDKHQKFTRIQIFGKDIERLKTRKNPGLDIFVVKEAENRNGTVFSYGGVTKKNQG
+AYYDYLNAPKFVIKKEVDAGVYTHVKRHYIYKEEVSLKELDFKLRQYLIQNFDLYKKFPKDSKIKVIMKDGGYYTFELNKKLQPHRMSDVIDGRNIEKME
+ANIR
+>gi|334277106|gb|EGL95345.1| toxin, beta-grasp domain protein [Staphylococcus aureus subsp. aureus 21310]
+-----------TNINELIKYYTQKPLTFSNRWLYQ-YDDGNIYVEFKRYSWSAHIRLWGAESWgNINQLRDRYVDVFGLKDKDTRRLWWvytdTFTGGVT
+PAASSS--D--KPYNIYVQYKDKLQTFIGAHkIYQGNKPVLTLKEIDFRVRESLIKNKILYNENRNKGNIHIT-GGGNNFTIDlskrlhsdlanvyvknp
+qkitvevlid---------------------------
+>gi|34536505|dbj|BAC87686.1| exotoxin G variant 5 [Streptococcus dysgalactiae subsp. equisimilis]gi|34536507|dbj|BAC87687.1| exotoxin G variant 6 [Streptococcus dysgalactiae subsp. equisimilis]
+--YGSKLVYADEILNDlkasLRFAYDVTPLEYENVEItFVTT--NNIHINTGQ-KKSGCVLYVDSIVslgitDNFIKG--DKVDVFGLPYNFSSPNVDNI
+YGGVVKHSDDKLQ---SLQFVGILNQDGEETSLPSYTILIKHKQFTLQEFDFKIRKFLMETYSIYDSEsrYISGSFFLATKDSKHYEVDLF---------
+----------------
+>gi|145386879|gb|ABP65290.1| mitogenic exotoxin Z-43 [Streptococcus pyogenes]
+----------------levdnnslLRNIYSTIVYEYSDTVIdFKTS--HNLVTKKLD-VRDARDFFINSEMdeyaaNDFKAG--DKIAMFSVPFDWN--y
+lskgkVTAYTYGGITPYQK-tSIP---KNIPVN-LWINGKQISVPYNEISTNKTTVTAQEIDLKVRKFLIAQHQLYSSGssYKSGKLVFHTNNns-DKYS
+LDLF-------------------------
+>gi|4206380|gb|AAD11625.1| exotoxin C [Streptococcus pyogenes]gi|4206384|gb|AAD11627.1| exotoxin C [Streptococcus pyogenes]
+--------------SDLLYAYTITPYDYKDCRVNFS---TTHTLNIdtqKYRGKDYYISSemSYEASQKFKRD--DHVDVFGLFYILNSHTGEYIYGGIT
+PAQNNKV-NHKLLGNLFISGESQQNLNN---KIILEKDIVTFQEIDFKIRKYLMDNYKIYDATSpyVSGRIEI---------------------------
+-----------
+>gi|166409297|dbj|BAG06666.1| enterotoxin T [Staphylococcus aureus]
+--------------EGLKDFYSKKIDVYTNKKIN---EKDKYSVDIEVDNYVYRINTLDDKILnQFKVG--DYVDAWGHIINNKPIgkVIKFYDGDISKH
+SPL---DKPTniSYRINLFK-EQKQTEVTPEkELEIGNRYLTMKQIDYRIKSYLVKKQQLYT-EFYNGKIEISMLDGKKHFIDLSTYY------------
+----------
+>gi|341844123|gb|EGS85342.1| enterotoxin type C-2 [Staphylococcus aureus subsp. aureus 21269]
+--------------------------------------------------------------------DGKEVDIFGVNYFDqcyfsneniqcdSNQggg
+sKKTCMYGGITLNENNTN-NRIQPIVVKVYE-NDSVTLSF--DINIDKETVTIQELDYKVRNKLISKINLYHLggtSYETGYIKFIENGNRYYWYDMMpd
+pgftqsKYLMIYRGNETVESAK-TEIEVHL-
+>gi|297589926|ref|ZP_06948566.1| toxic shock syndrome toxin-1 [Staphylococcus aureus subsp. aureus MN8]gi|297577054|gb|EFH95768.1| toxic shock syndrome toxin-1 [Staphylococcus aureus subsp. aureus MN8]
+---------TNDNIKDLLDWYSSGSDTFTNSEVLDNslgsmrikNTDGSISLIIFP-SPYYSPA--------FTKGE--KVDLNTKRTKksqHTSEGTyi
+HFQISGVTNTEKLPTP---IELPLKVKVHGK--DSPLKYWPKFDKKQLAISTLDFEIRHQLTQIHGLYRSSDKTgGYWKITMNDGSTYQSDLSKKFEYNT
+EKPPINIDEIKTIEAEIN
+>gi|304388588|gb|ADM29185.1| Enterotoxin [Staphylococcus aureus]
+---------------------------------------------------------------------SKNVDVYAIRYSIncyggEIDKTACTYGGVT
+PHEGNKL-KERKKIPINLWINGVQKEVSLD-KVQTDKKNVTVQELDAQARRYLQKDLKLYNNDtlggkIQRGKIEFDSSDGSKVSYDL------------
+--------------
+>gi|225871304|ref|YP_002747251.1| exotoxin H precursor [Streptococcus equi subsp. equi 4047]gi|8117875|gb|AAF72809.1|AF186180_3 SeeH [Streptococcus equi]gi|225700708|emb|CAW95321.1| exotoxin H precursor [Streptococcus equi subsp. equi 4047]
+--------------------------------------------------------------------KDKEVDIYALSAQEACecPGkRYEAFGGITLT
+NSEK-KE--IKVPINVWDKSKQH----PPMFiTVNKPKVTAQEVDIKVRKLLIKKYDIYNNreqKYSKGTVTLDLNSGKDIVFDLyyfgngdfNSMLKIY
+SNNERIDSTQF--------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * * * * * * * * * * * * * 0 * * * * 1
+ 0 * * * * * * 1000 0 0
+
+E 2 * * * 0 * * * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1000 0 0
+
+H 3 * * * * * * 696 * * * * * * * * * * * * 1385 3
+ 0 * * * * * * 2187 0 0
+
+K 4 * * * * * 409 * * 2019 * * * * * * * * * * * 4
+ 0 * * * * * * 2580 0 0
+
+A 5 2275 * * * * * * * * * * * * * * 742 * * * 2355 5
+ 0 * * * * * * 2659 0 0
+
+K 6 * * * 2131 * 4224 4513 4967 1687 * * 4767 * 4603 3641 4567 3355 4889 * * 6
+ 348 2221 * 1000 1000 * * 3900 1357 0
+
+Y 7 4237 * * * * * 4778 * * 1330 * * 3085 * * 2601 * 2660 * 3798 7
+ 114 3714 * 0 * * 0 3869 1049 1357
+
+E 8 3651 * * 2373 * * * 3782 2093 * * * * 4237 * 3209 2620 3376 * * 8
+ 0 * * * * 0 * 3869 0 1357
+
+N 9 5523 * 4280 4008 * * * 5622 4949 * * 3419 * 2207 3813 3162 * 2115 * 3506 9
+ 0 * * * * * * 4291 0 0
+
+V 10 3866 * 4662 * * 4193 * 2748 * * 4427 * * 3202 3586 4617 2562 2060 * * 10
+ 0 * * * * * * 4186 0 0
+
+T 11 * * 3866 * * * 4779 * 4617 * * 2175 * 2722 * 1335 3560 * * * 11
+ 0 * * * * * * 4186 0 0
+
+K 12 * * 4233 2144 * * 3330 * 2313 * * 4011 3911 3537 4572 5166 3110 * * 5676 12
+ 358 2898 3542 758 1292 * * 4882 1357 0
+
+D 13 3698 * 1798 4441 * * * 4755 2901 * * 1479 * 4794 * * * * * 5399 13
+ 79 4739 5958 2313 324 * 0 4865 1084 1202
+
+I 14 3847 * * * 4633 * * 1572 4276 3810 * * * * * 3886 2263 3953 * 3467 14
+ 0 * * * * 824 1201 4812 0 1399
+
+F 15 4468 * 3835 3302 4784 * * * 1743 * * 2796 * 2618 5852 3009 * * * * 15
+ 0 * * * * * 0 5114 0 1143
+
+D 16 4557 * 1318 2237 * 4053 * * 3773 * 5617 3633 * 5155 * 3607 * * * * 16
+ 179 3103 * 2254 339 0 * 5114 1419 1143
+
+L 17 * * * * * * * * * 0 * * * * * * * * * * 17
+ 0 * * * * * * 5241 0 0
+
+R 18 * * * * * * 3310 3905 1273 3204 * 5139 * * 2476 4798 4855 * * 4991 18
+ 0 * * * * * * 5241 0 0
+
+D 19 3717 * 2440 3788 4238 5146 4387 * 2714 5136 * 4819 * 4730 3402 4558 4989 * * 3112 19
+ 0 * * * * * * 5241 0 0
+
+Y 20 2962 * * * 4589 * 4778 4819 * * * * * * * * * * 4504 486 20
+ 66 * 4493 * * * * 5241 0 0
+
+Y 21 * * * * * * * * * * * * * * * * * * * 0 21
+ 0 * * * * * 0 5195 0 1143
+
+S 22 4748 * 5091 5078 * * * * 5265 * * 3124 * * * 1125 1715 * * * 22
+ 0 * * * * * 0 5195 0 1143
+
+G 23 * * * 5649 * 1966 * 3280 2245 * * * * 2151 5297 3415 4772 5091 * * 23
+ 0 * * * * * 0 5195 0 1143
+
+A 24 4798 * * 3558 * 4442 * 4772 2847 * * 5692 1682 5029 4072 6007 2178 * * * 24
+ 0 * * 2000 415 0 * 5195 1143 1143
+
+S 25 * * * * 3676 4136 3941 3923 * * * * 2509 * * 1241 4507 4819 * 4162 25
+ 0 * * * * * * 5241 0 0
+
+K 26 * 5368 3546 3945 1717 * * 4712 4303 2420 4991 * * * * * 4923 4121 * 3016 26
+ 0 * * * * * * 5241 0 0
+
+E 27 5933 * 2671 952 * * * 5134 * * * 4461 * * * 4489 3141 3681 * * 27
+ 0 * * * * * * 5241 0 0
+
+L 28 * * * * 1777 * 4663 * * 2365 4821 * 5713 * 4753 * * * * 1384 28
+ 0 * * * * * * 5241 0 0
+
+K 29 * * * 3634 * * * 5646 1482 * * 5279 * 4461 5042 2245 2127 * * * 29
+ 0 * * * * * * 5241 0 0
+
+N 30 * * 3602 * * 5827 * * 3906 * * 308 * * * 5279 * * * * 30
+ 0 * * * * * * 5241 0 0
+
+V 31 * 3731 * 5035 * * * 3013 2543 3611 * * * 4669 5728 4025 4298 1529 * * 31
+ 0 * * * * * * 5241 0 0
+
+T 32 * * 4630 2905 5181 6199 * 4338 3581 6063 * 4078 * * 4025 2419 2252 4819 3574 * 32
+ 0 * * * * * * 5241 0 0
+
+G 33 4356 * * * * 953 * 2659 * 2946 * * * * * * * 2771 * * 33
+ 219 2830 * 0 * * * 5241 1419 0
+
+Y 34 * * * * 2584 * * 5035 3947 2907 * 3951 * 5747 * * 3945 * 3925 1356 34
+ 160 6221 3451 1585 585 * * 5241 1000 0
+
+R 35 * * 4285 * 5283 5149 5826 3320 2247 4979 5089 * * 2812 3381 3902 5731 2872 * 4485 35
+ 170 * 3173 * * * 0 5010 0 1274
+
+Y 36 * * * 1930 4982 * 4385 5739 5558 4313 * 4159 * 4639 4332 3532 2548 4377 * 3102 36
+ 734 2691 2035 2080 389 1052 950 4786 1315 1574
+
+S 37 * * 4281 * 5431 3701 * 5813 2938 * * 3016 4154 4146 * 2497 2048 * * 4477 37
+ 534 3504 2177 1817 482 1615 570 4846 1176 1925
+
+K 38 * * 2263 2654 * 3665 5025 * 3141 * * 3590 5537 * * 5288 3538 * 3946 2958 38
+ 0 * * * * 3063 184 4634 0 2110
+
+G 39 * * 2609 5412 * 4525 4552 3830 2572 5118 * 2353 5760 * * * 3196 3612 * 4207 39
+ 77 * 4272 * * 0 * 4716 0 1978
+
+G 40 * * 4035 4648 * 1038 3500 * 3196 * * 3454 * * 5988 * 3215 * * * 40
+ 0 * * * * * 0 5245 0 1029
+
+K 41 * * 2853 4765 3936 4414 * 6032 2529 5773 * 2461 * 6141 * 2559 3156 5150 * * 41
+ 97 * 3936 * * * 0 5245 0 1029
+
+H 42 * * 5280 5665 5048 * 3826 1969 2251 3986 * 2465 * * 3586 5808 * * * 4542 42
+ 207 * 2904 * * * 0 5189 0 1263
+
+Y 43 * * * * 2776 4279 2611 * * 4808 * 3459 * * * 3395 5129 2783 * 2040 43
+ 34 5409 * 0 * 0 * 5154 1000 1636
+
+L 44 3598 * * * 5944 * * 2605 * 2241 2487 * * * * 5279 4819 1807 * * 44
+ 66 4493 * 2322 322 * * 5241 1143 0
+
+I 45 * * 2664 3437 * * * 3396 3921 5647 * 1946 * * 3486 * 2902 4488 * 4579 45
+ 0 * * * * * 0 5195 0 1143
+
+F 46 * * * * 1771 * * 2097 4772 3372 5818 * * * * * 3108 2276 * * 46
+ 35 5386 * 1585 585 * 0 5195 1021 1143
+
+D 47 6254 * 4837 4564 4126 5091 * 2231 2443 3491 * 3885 5779 3839 * 5078 3680 4972 4579 * 47
+ 0 * * * * * 0 5195 0 1143
+
+K 48 * * 3211 5818 4778 * * * 3300 * * 6226 2508 2235 4770 3830 5116 2956 * 3836 48
+ 359 * 2182 * * * 0 5195 0 1143
+
+H 49 * * 2058 5639 5436 2889 3467 5540 5612 5445 * 2428 * 5294 2755 * * * 5651 4412 49
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+A 201 3698 * * * 5319 * * 2848 * 6268 * * * * * * * 423 * * 201
+ 0 * * * * * * 4717 0 0
+
+N 202 * * 5015 2249 4628 * 3245 * 3942 * * 1975 * * * 5898 4290 * * 2149 202
+ 0 * * * * * * 4717 0 0
+
+I 203 * * * * * * * 2313 * 554 4667 * * * * * * 3671 * * 203
+ 26 5828 * 0 * * * 4296 1000 0
+
+R 204 * * * 3791 * * * * 1210 * * 1825 * * 3381 * 4138 4973 * 5118 204
+ 0 * * 0 * * * 3759 0 0
+
+//
+�HHsearch 1.5
+NAME 68a5857c951cd0795a2bfc79e65a0c63
+FAM
+FILE 68a5857c951cd0795a2bfc79e65a0c63
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:21:28 2013
+LENG 88 match states, 88 columns in multiple alignment
+FILT 121 out of 1407 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHHHHHHHHHHHHHHCCCCCCCEECHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9579999999999999825389989777999999999986765178898999999999866799991949999999999999998619
+>Consensus
+xxxxxxxxxlxxxFxxxdxxxxxxgxixxxelxxxlxxxxxxxxxxxxxxxxxxxxxxxxdxxxdgxixxxeFxxxxxxxxxxxxxxx
+>68a5857c951cd0795a2bfc79e65a0c63
+SELEKAVVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMITTACHEFF
+>gi|60097902|ref|NP_002007.1| filaggrin [Homo sapiens]gi|84028206|sp|P20930.3|FILA_HUMAN RecName: Full=Filaggringi|56205087|emb|CAI19595.1| filaggrin [Homo sapiens]gi|260158880|gb|ACX32320.1| filaggrin [synthetic construct]
+------------------SEESDTQSVSAHGQAGPHQQSHQESTRGQsgERSGRSGSFL--------------------------YQV--
+>gi|196016045|ref|XP_002117877.1| hypothetical protein TRIADDRAFT_51129 [Trichoplax adhaerens]gi|190579546|gb|EDV19639.1| hypothetical protein TRIADDRAFT_51129 [Trichoplax adhaerens]
+------EDILMKALEVLD-QEHK-EHLTIDEITKFMTE-----YGEAFTQDELEEMKSAAVDQEKGVIYYKDYVSLLVV---------
+>gi|1396048|dbj|BAA12908.1| troponin C [Chlamys nipponensis akazara]
+---EKQISDAKQAFCNFD-KKKE-GTVSCKDLGAIFKS-----LGLVMKDDKIKDWSDEVDEEATGRLSCEQWLKLFEWKLKE-----
+>gi|242033981|ref|XP_002464385.1| hypothetical protein SORBIDRAFT_01g017320 [Sorghum bicolor]gi|241918239|gb|EER91383.1| hypothetical protein SORBIDRAFT_01g017320 [Sorghum bicolor]
+---EDELIYIRAQYNLLE-PDSGDGRICIDNFSTALLQN----CTDAMKESRTLEILNALEPLAYRRMDFEEFCAATISPYQ------
+>gi|66808853|ref|XP_638149.1| EF-hand domain-containing protein [Dictyostelium discoideum AX4]gi|74996819|sp|Q54MZ4.1|MCFB_DICDI RecName: Full=Mitochondrial substrate carrier family protein Bgi|60466585|gb|EAL64637.1| EF-hand domain-containing protein [Dictyostelium discoideum AX4]
+----------------------------MSNNNNNNNN-----NNNNNNNNNN----NNNNNNNNDKNNNNNIDSSIK----------
+>gi|220908286|ref|YP_002483597.1| Calcium-binding EF-hand-containing protein [Cyanothece sp. PCC 7425]gi|219864897|gb|ACL45236.1| Calcium-binding EF-hand-containing protein [Cyanothece sp. PCC 7425]
+-KLYATQMAWWENLRAATDKDNN-GQVTLEEWSAFWEAWLTSV---ANEAATgqtpsleaikgsAAVTFDMIDSNQDGQVTSDEYASWFQTLN-------
+>gi|334328558|ref|XP_001367800.2| PREDICTED: calpain-12 [Monodelphis domestica]
+---SAPLDFdLEQLFHELA---GEEEAISTAQLQALLSLALEPgdwgsswTHPPGeIGFRTCEQLIHCFGqRG--HCLTLPEFQQLWYRL--------
+>gi|241711501|ref|XP_002413417.1| Ca2+ sensor, putative [Ixodes scapularis]gi|215507231|gb|EEC16725.1| Ca2+ sensor, putative [Ixodes scapularis]
+---------MLRRYKGFV-KDCPSGHLTEQGFLRIYKL----FFPQGDPSKFTSLIFRVFDENKVRLFSYQWFLrwrPVVLLLCVS-----
+>gi|195012466|ref|XP_001983657.1| GH15448 [Drosophila grimshawi]gi|193897139|gb|EDV96005.1| GH15448 [Drosophila grimshawi]
+---EESKRRLGLIVDRID-ADKN-VFITLAELKAWIQY-----TQRRYIDEDVSRIWRQHNPDNNKTISWDVYRKSIYG---------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * 3052 * * * * * * * * * * * 1047 1338 * * * 1
+ 0 * * * * * * 4488 0 0
+
+E 2 4650 * 2293 2928 * * * 4553 3118 * * 4496 4559 4451 2337 3317 * 4793 * * 2
+ 0 * * * * * * 7065 0 0
+
+L 3 3387 * 4818 * 4777 * * 2853 * 1085 * * * * * * 4500 2486 * * 3
+ 0 * * * * * * 7381 0 0
+
+E 4 5747 5712 4509 1683 * 4754 4176 * 4962 6177 4259 3714 3698 4204 5756 3381 5780 5545 5873 4727 4
+ 0 * * * * * * 9101 0 0
+
+K 5 3173 * 3199 1817 5676 * * * 3249 4079 * 4148 * 4004 4531 3541 5936 5382 * 5363 5
+ 0 * * * * * * 9266 0 0
+
+A 6 3054 6400 3603 2741 * 6473 5356 5978 5281 4607 * 4611 6378 2755 4691 2994 3517 4894 * 4996 6
+ 34 6318 6537 2807 222 * * 9594 1000 0
+
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+ 16 6529 * 1000 1000 * 0 9739 1092 1000
+
+V 8 2958 6365 2636 2681 6796 * 4971 4762 3576 5581 5118 4216 * 3954 3617 4907 4444 5364 * 5179 8
+ 15 6623 * 1585 585 0 * 9919 1095 1000
+
+A 9 3616 * 3191 2630 * 3682 * 5426 2995 5227 6511 5015 5207 3873 3285 5747 3452 4930 * 6443 9
+ 51 6060 5681 3450 138 * * 10045 1298 0
+
+L 10 4207 6129 * * 3621 * * 2484 * 1484 4739 * * * 6319 * 4860 3099 4609 3798 10
+ 15 * 6559 * * 710 1363 10028 0 1273
+
+I 11 4213 7039 5916 3488 5104 4309 5527 3013 2681 4852 6159 5722 * 4612 3248 4363 5302 3874 3382 * 11
+ 0 * * * * * 0 10053 0 1223
+
+D 12 3839 * 3392 2952 5011 * 5348 4979 2283 4074 * 3786 * 4481 3095 4756 4618 4984 6652 * 12
+ 22 * 6020 1286 762 0 * 10126 1223 1223
+
+V 13 2232 6047 5614 5036 4986 7004 7353 3028 4663 2656 4852 4945 * 4012 5807 3879 5980 3272 6569 6629 13
+ 17 6450 * 0 * 1051 951 10148 1020 1163
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+F 14 6370 6822 * * 658 * * * * 2930 6245 * 6574 * * * * 4961 3749 3578 14
+ 32 6338 6687 5334 36 * 0 10164 1178 1001
+
+H 15 4545 6988 2962 3577 5184 5084 3779 4977 2388 3861 6796 3252 * 3991 4365 4788 * 4822 6826 6653 15
+ 10 * 7179 * * * 0 10184 0 1416
+
+Q 16 3456 4976 6283 4081 5054 6486 5374 4631 3464 2714 4008 4401 * 3604 3599 3634 4344 5248 * 5262 16
+ 11 7057 * 1792 492 2655 249 10199 1127 1523
+
+Y 17 3999 5707 6680 6576 1980 6680 5442 3489 6582 2346 5673 5188 5666 * * 5544 6322 5194 5258 2630 17
+ 38 7074 5750 1585 585 1774 499 10174 1000 1416
+
+S 18 3203 5947 1042 4556 5162 6673 5755 * 5600 6292 * 5156 6333 * 5314 3601 4685 4305 6660 6615 18
+ 2267 * 336 * * 2351 315 10150 0 1779
+
+G 19 3757 * 1412 4366 * 2517 * * * 3373 * * 4350 * * 2911 * 4367 * * 19
+ 127 4361 4813 2807 222 199 2955 6806 1023 8699
+
+R 20 4240 6449 4089 3951 6568 5042 5281 5197 2141 4691 6697 5166 3833 4348 3078 5385 3432 4035 * * 20
+ 60 7046 4904 271 2546 744 1311 9987 1650 2894
+
+E 21 5318 6824 1686 3117 * 4831 5537 * 3341 6279 * 2614 4726 4520 5251 4616 4056 * * * 21
+ 33 7326 5919 3000 193 743 1313 10154 1000 2275
+
+G 22 4036 6278 3634 3690 6713 1973 5795 * 2717 6697 7099 3590 5699 4953 3881 3986 5520 6317 * 5892 22
+ 165 7060 3314 2000 415 1092 913 10248 1000 1708
+
+D 23 * 4937 2018 3401 6311 5209 6822 6044 3583 7042 * 3214 4673 3813 5359 2730 3886 6600 * * 23
+ 2532 6690 291 0 * 1203 822 10163 1000 3039
+
+K 24 4366 5133 2424 * * * 4341 4471 2187 * * * * 4678 3442 2952 3033 * * 4639 24
+ 80 4207 * 1000 1000 73 4344 7121 1012 8690
+
+H 25 4637 * 4224 3468 * 945 5250 * 4940 * 5012 4311 6593 4486 4703 5041 * 4941 * * 25
+ 49 6947 5308 0 * 905 1101 10181 1256 1602
+
+K 26 4442 5511 5989 3582 4763 5505 6788 4897 2691 4543 * * * 3886 2942 3213 3376 4704 * 3420 26
+ 0 * * * * 0 * 10244 0 1650
+
+L 27 6287 6986 * * 5703 * * 1571 5835 1480 3931 * * 6527 * 6372 * 2652 * * 27
+ 8 7448 * 2322 322 * * 10297 1000 0
+
+K 28 5752 5361 2665 3696 7170 4449 * * 4441 7132 6038 3284 5027 5569 4629 2271 2489 6201 * 7057 28
+ 20 6209 * 1571 592 * * 10297 1092 0
+
+K 29 3111 7006 5882 4539 4907 5790 * 4635 2955 2593 4848 7052 4567 4376 3225 5611 4677 3355 7192 5240 29
+ 0 * * * * 0 * 10346 0 1000
+
+S 30 2981 * 2765 2437 5004 5427 5775 6549 3805 * 5575 3864 5448 4193 4123 3035 5476 6617 7070 * 30
+ 41 5706 6785 0 * * * 10357 1187 0
+
+E 31 4402 7067 2961 1035 * 5975 5573 6887 5174 6697 7253 4603 7170 3679 6730 4328 4855 6806 6546 * 31
+ 0 * * * * 1969 426 10301 0 1387
+
+L 32 5922 6793 * * 2017 * * 3221 * 1464 4721 6480 * 6631 6547 6784 6292 2908 6544 5503 32
+ 0 * * * * * 0 10310 0 1246
+
+K 33 4143 7095 6378 4170 6632 4379 5768 4162 2602 3487 5436 5603 5653 3262 2947 4254 4444 4070 * 5217 33
+ 31 6568 6540 1000 1000 * 0 10310 1013 1246
+
+E 34 3456 * 3508 3189 6879 5064 4997 5475 3389 4716 5857 3274 5598 3292 4040 3641 3828 5470 * 6898 34
+ 29 6449 6906 2807 222 * 0 10213 1012 1460
+
+L 35 2710 5289 6440 6713 3797 4475 6593 2689 5751 2323 4161 6471 5960 * 6105 4409 6203 3367 4979 6296 35
+ 40 6037 6375 557 1643 * 0 10194 1104 1613
+
+I 36 5315 5335 * 5664 3240 5046 6563 2936 6580 1565 3482 5572 6668 * * * 5983 2969 5553 5683 36
+ 82 4679 5922 346 2229 2178 360 10152 1605 1796
+
+N 37 4627 6270 4625 3232 * 5915 6858 5344 3091 4280 7068 3421 6338 3536 2410 3750 4045 4629 * 5785 37
+ 43 * 5105 * * * 0 10181 0 1878
+
+N 38 2991 5634 4227 3213 * 5887 7524 6158 3104 3886 5829 4035 6839 3514 3970 3386 3577 4871 * 5621 38
+ 1357 5853 755 2440 294 1200 824 10135 1137 2388
+
+E 39 3077 5198 * 3952 * 5403 5440 4458 5287 3235 5683 3157 * 3533 3953 3469 3629 4601 5428 4396 39
+ 176 5447 3446 1585 585 4733 55 8520 1028 7836
+
+L 40 4459 5535 4766 4242 2309 5484 5529 5367 5605 1775 4421 5612 * * 5419 3675 5938 5697 * 4156 40
+ 175 4528 3822 1245 790 5363 35 8479 1260 7894
+
+S 41 3568 * 4559 3889 * 2857 4864 * 4021 * 5380 3361 2308 4599 3852 3831 3886 * * * 41
+ 246 5653 2868 2000 415 * 0 8461 1000 7913
+
+H 42 5272 * 3686 2770 4260 4075 3313 5015 4210 4170 * 2352 * 4682 * 4147 4193 4288 * * 42
+ 314 3279 3435 686 1402 4197 81 8067 1426 8173
+
+F 43 5059 * 5055 5220 2405 3076 * 5214 * 3135 4255 4344 4112 5375 4246 4245 * 3581 5070 3998 43
+ 514 3584 2209 1749 510 337 2262 8086 1328 8181
+
+L 44 5425 6437 * 4908 3595 4903 4533 3348 4521 1805 3875 5408 6998 5939 6129 4504 3676 3899 6927 5895 44
+ 78 5138 5380 0 * 3065 184 9846 1231 4446
+
+E 45 5098 * 4142 3479 6086 1606 5066 6198 3178 4882 * 3876 4842 4594 4766 4626 5519 5422 * 5239 45
+ 59 5012 6781 381 2106 1883 456 9796 1291 4352
+
+E 46 4319 5190 2819 3143 3918 4296 4991 5564 3992 3736 6536 3875 * 4705 3720 5501 4818 4543 6551 4165 46
+ 144 4657 4177 404 2032 3963 96 9882 1441 3658
+
+I 47 3658 5487 4512 4936 5701 4109 5535 4910 3304 4926 4889 2978 3663 3768 3598 3866 5449 4419 6247 6817 47
+ 87 5026 5176 1277 767 1292 758 9779 1630 4251
+
+K 48 5650 * 4131 4167 5053 4458 5991 3242 4529 2621 4304 4443 2833 5544 5643 4436 4496 4757 6395 4423 48
+ 27 6785 6743 2000 415 2084 388 9946 1000 3396
+
+E 49 3774 * 3219 4677 * * * 5041 3742 4871 5261 3687 3572 5520 4125 2534 2644 6763 6431 5586 49
+ 82 5127 5217 1305 748 2667 247 10004 1301 2989
+
+Q 50 4077 * 3253 2566 * 4308 5953 5182 2923 4201 7075 4191 4096 4242 4362 4413 3652 4719 * * 50
+ 35 5367 * 1198 826 1371 705 10008 1247 3129
+
+E 51 3768 * 3285 2513 6922 4388 5293 6063 3125 4731 * 4749 4472 3988 4291 3574 4696 4359 * 4947 51
+ 0 * * * * * 0 10099 0 2313
+
+V 52 4094 6808 3004 2216 4389 4854 5890 5005 3807 4005 5124 5256 5644 4998 4518 5506 3995 4715 5360 4979 52
+ 76 4291 * 2973 197 933 1071 10099 2629 2313
+
+V 53 2748 4670 6808 6593 4878 5704 * 2506 6492 2492 5493 6453 6352 6539 5650 5858 3954 2701 5191 4830 53
+ 30 6821 6453 0 * 1950 432 10212 1000 1564
+
+D 54 4630 5439 3025 2811 * 4485 6984 4665 3868 4189 * 4984 6726 3076 2552 3630 4766 * * 6907 54
+ 60 4618 * 1839 473 * 0 10184 1622 1616
+
+K 55 3250 5863 4203 2283 6816 4448 5801 4892 3476 4539 5374 4557 7032 3196 3285 4659 5913 5104 7054 * 55
+ 0 * * * * * 0 10184 0 1616
+
+V 56 4175 * 6420 5775 3959 * 6854 2125 6549 1839 3422 * * * * * 3773 3257 4546 6896 56
+ 30 7356 6129 3077 182 2573 265 10184 1100 1616
+
+M 57 6545 6490 * * 1928 6823 6424 2470 6093 2051 3972 7020 * * * 5625 5701 4218 4024 4946 57
+ 70 * 4409 * * 1859 465 10172 0 1709
+
+E 58 3449 6909 3251 3122 6527 5003 5409 * 2364 5877 * 3417 5922 3503 3417 3723 4807 * * * 58
+ 71 6058 4925 2552 270 1040 961 10135 1101 2421
+
+T 59 4166 6445 3675 2448 6366 4474 5081 4703 3862 4414 4830 3982 6720 4066 4612 4104 5860 3436 * 4204 59
+ 34 * 5419 1000 1000 1853 468 10213 1001 2304
+
+L 60 3140 4545 * 4851 3060 5479 6135 3636 5544 2300 3941 4246 5814 5953 * 6870 5131 3506 6821 4013 60
+ 50 5316 6796 1132 879 1551 602 10209 1787 2286
+
+D 61 6888 6780 1082 3709 * 4544 * 5005 6931 4796 6806 3212 5142 5302 5204 4357 5178 5818 * 5399 61
+ 52 5729 5896 1893 453 * 0 10195 1294 1973
+
+S 62 4932 6750 5671 3676 6196 5505 4859 3751 3420 4235 * 5026 3378 3750 4368 2912 3086 3860 * * 62
+ 32 * 5517 * * 1043 958 10174 0 2239
+
+D 63 5524 * 1913 3460 * 3947 7257 6775 4380 4873 6654 1914 4659 4498 6536 4026 6877 6684 * 6693 63
+ 34 5419 * 414 2004 1597 579 10183 1230 1931
+
+G 64 4284 6567 4373 3448 * 2371 5205 * 2822 4394 7100 2786 4797 4676 4553 3930 4891 6607 * 6764 64
+ 19 7180 7305 2141 371 2141 371 10236 1122 1580
+
+D 65 5225 * 1457 3541 * 3500 5650 6812 4447 5644 * 2800 6717 6888 4294 4769 3802 * * 5707 65
+ 59 5282 6105 1916 444 2619 256 10249 1514 1525
+
+G 66 4907 * 3398 4655 * 915 * * 3375 * * 4560 7161 4249 5568 4134 * * * 5308 66
+ 51 6358 5467 0 * 2840 217 10225 1039 1829
+
+E 67 5286 * * 3947 4935 3694 4681 4614 2253 5079 4921 5314 7078 4338 3113 4037 3658 4944 * 3692 67
+ 34 5893 7212 585 1585 501 1769 10181 1116 2249
+
+C 68 6542 6914 * * 5219 * * 1489 6289 1960 3856 6451 * * * 6769 * 2109 7240 * 68
+ 0 * * 2585 263 2090 386 10251 1000 1398
+
+D 69 5530 5957 2209 4068 6175 4397 5595 * 4706 * * 2945 4541 5409 7109 2404 2661 * * 6011 69
+ 0 * * * * * 0 10260 0 1266
+
+F 70 4989 6998 * 5008 1546 7345 * 4409 4645 2474 7240 6470 * * 4001 5503 5397 4944 5100 2985 70
+ 28 6295 7332 1000 1000 * 0 10260 1044 1266
+
+Q 71 3666 * 2537 1734 5577 5157 5590 6899 3727 5924 6863 4585 6013 4385 5106 4000 4723 5272 * 6727 71
+ 9 * 7343 0 * 2270 335 10257 1000 1378
+
+E 72 5055 * 2565 1116 6861 4981 6425 5856 5597 * * 5122 5952 2875 * 6194 4395 7120 * * 72
+ 0 * * * * * 0 10251 0 1398
+
+F 73 5573 * * * 655 * 6691 4695 * 3590 6708 * 6769 * * * * 5324 4974 2867 73
+ 28 6656 6757 2585 263 * 0 10251 1000 1398
+
+M 74 4334 4732 6411 4622 5827 5869 * 3217 4352 2348 4180 6843 * 4287 4247 3962 4478 2750 4602 7344 74
+ 0 * * * * * 0 10188 0 1795
+
+A 75 3722 * 3049 4090 6403 7086 5051 4220 2889 4923 * 4733 5247 3310 3090 3660 4238 4705 * 5571 75
+ 25 6533 7229 0 * * 0 10188 1043 1795
+
+F 76 3783 5642 6319 6424 2899 5738 6606 3235 4629 2007 3100 5888 * * 5877 4147 6771 4180 6463 4576 76
+ 21 6142 * 2624 255 3270 158 10135 1190 1900
+
+V 77 4150 4337 * 5819 3750 6410 5892 2318 6822 1912 3279 * * 6474 6591 * 6455 3246 6449 4455 77
+ 48 5433 6659 1443 662 * 0 10128 1213 1795
+
+A 78 3708 5296 5458 3891 6901 3408 5296 3696 3845 3597 5170 5246 * 4884 3887 2918 4046 5184 6517 3976 78
+ 13 6767 * 1570 593 461 1871 9986 1238 1938
+
+M 79 4647 6000 3669 4684 5533 3538 4464 5516 2601 6830 5549 4823 5086 4339 3450 2913 6111 3931 6627 5138 79
+ 0 * * * * * 0 9910 0 1142
+
+I 80 5165 * 4647 4966 4115 * 6039 2983 4087 2188 4656 5291 4723 4001 4600 4245 4684 3661 4476 * 80
+ 0 * * 1000 1000 * 0 9566 1010 1142
+
+T 81 3363 * 5585 5935 * 3540 5776 5096 5063 3419 3866 4626 4238 3911 4877 3799 2907 3291 * 4687 81
+ 41 5152 * 0 * * 0 9036 1048 1142
+
+T 82 3000 5325 * 5438 * 5195 4083 3872 2715 2959 * 2862 5506 5004 3450 * 4243 4147 * * 82
+ 0 * * * * * 0 8441 0 1142
+
+A 83 3516 * 2829 1832 4713 3661 * * * 3090 * 4630 * 4457 3251 4976 4899 * * * 83
+ 0 * * * * 0 * 7091 0 1142
+
+C 84 2517 2607 * * 4481 * * * * 4152 * * * 4119 * * 4132 3118 * 1598 84
+ 0 * * * * * * 6141 0 0
+
+H 85 * * 3758 * 2777 4275 2300 3827 3679 4014 * * * 4179 2405 * * * 3817 * 85
+ 0 * * * * * * 5628 0 0
+
+E 86 * * * 2892 * * * 3039 1182 * * 3618 * * 3118 * * 3236 * * 86
+ 0 * * * * * * 4399 0 0
+
+F 87 * * * * 1244 * 2876 * * 2502 * * * 3102 * * 2752 * * * 87
+ 0 * * * * * * 3156 0 0
+
+F 88 * * * * 0 * * * * * * * * * * * * * * * 88
+ 0 * * 0 * * * 2396 0 0
+
+//
+�HHsearch 1.5
+NAME 6a5d2aa2a4dfa511f1b7a6417307a0bf
+FAM
+FILE 6a5d2aa2a4dfa511f1b7a6417307a0bf
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:59:12 2013
+LENG 225 match states, 225 columns in multiple alignment
+FILT 124 out of 1363 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEECCCCCEEECCCCCCCEEEEEECCCCCEEEEEECCCHHCCCCEEEEEEC
+CCCCCCCEEECCCCEEEEEEECCCCCCEEEECCCCCEEECCCEEEEEEEEECCCCCCEEEEECCCCCCCCCCCEEEEECCCCEEEEEEEEEEECCCCCCE
+EEEEEEECCCCEEEEEEEECCCCCC
+>ss_conf PSIPRED confidence values
+9379688878995799899998963888889789999958999858999995378840444666872688750588948699944542009847999973
+8987521120378557778602356404785288621205855999999827779976999899842577321024754997899999999503457976
+9999993889888999980579839
+>Consensus
+xxxxxxpxxxxxxxGxxvxLxCxxxxxxxxxxxixWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxsLxIxxvxxxDxgxYxCxvxx
+xxxxxxxxxxxxxxxxlxvxxxxxxxPxvxxxxxxxxxxxgxxxxlxCxxxxxxPxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxsxLxixxxxxdxgx
+ytCxvxxxxxxxxxxxxxxxxxpxx
+>6a5d2aa2a4dfa511f1b7a6417307a0bf
+EVNLQQSGTVLARPGASVRMSCKASGYSFTSYWLHWIKQRPGQGLEWIGGIYPGNRDTRYTQRFKDKAKLTAVTSANTAYMELSSLTNEDSAVYYCSIIY
+FDYADFIMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQS
+ITCNVAHPASSTKVDKKIEPRGPTI
+>gi|2707433|gb|AAB92274.1| T-cell receptor gamma chain Vg2-Jg1 [Gallus gallus]
+---------ITMSRVNT-DLKCHFKdfSGNFDNTVIHWYQQKENKAPVRMIYFTSG--RTKVNESFQRhRYRIQTIPTQRLCTLTIRNVIPDDAATYYCA
+YW-DP-RRILLQSFRLWYKAHCIRQRKFSTREL-------------------------------------------------------------------
+----------------------------
+>gi|145408204|gb|ABP65664.1| MHC class I antigen [Sus scrofa]
+----------------------------------------------------------------------------------------------------
+------------------------------------------htyqwmygcylgpdglflrgysqfgydgadyvalne--DLRSWTAADMAAQI------
+--------skrkweaadeaerm----RSYlQGRCVEWLQKYLEMGK-----------------dt--LQ--hadP-PQPPV
+>gi|194039786|ref|XP_001927231.1| PREDICTED: butyrophilin subfamily 1 member A1-like [Sus scrofa]
+HFDVIGPPEPIlAVVGEDAELPCRLSPNVSAeRMELRWFRK--KVSPAVFVRREGREQAGEQMPEYRGRVTLVEDDiAAGHVAVRIQGVKASDDGEYRCF
+FRQD-------ENYEEAIVHLKVAALGSDPQIHMEV-----QESGEIQLECTSMGWYPEP-WVQWrtPKGEEFPSMSESKSPNEEGLFTVAASVIIRDPS
+--VKNVSCYVRNLLLGQEKEVEISIPAPF-
+>gi|297295448|ref|XP_001107711.2| PREDICTED: macrophage colony-stimulating factor 1 receptor-like isoform 1 [Macaca mulatta]
+--------------------------------------------------------------------------------FTIHRAKFIQGQDYQCSALM
+GS-----RKVMSISIRLKVQKVIPGPPALTLVPEELVRIRGEAAQIVCSASNI-DVDFDVFLQHNTTKLAIPQRSDFH-DNRYQKVLTLSLGQVDFqHAG
+NYSCVASNVQGKHSTSMFFR------
+>gi|242008252|ref|XP_002424921.1| down syndrome cell adhesion molecule, putative [Pediculus humanus corporis]gi|212508527|gb|EEB12183.1| down syndrome cell adhesion molecule, putative [Pediculus humanus corporis]
+---KIEPVDTNVTSGQELILNCQGNGYPTPTTTWKK---STGEFL-----------GEYKDFLYDSNISIYPNGS-----LKFSKIFKENQGHYLCELKN
+E---------VGSGLSKLIYLKVNVPVYFPQKFKQIQVIQGKEAHMQCPAIGETP--IEIEWriKGQKIQENKhSRYIINKQILTDGLVSEISIPKTYRh
+DTGIFTCYATN------------------
+#
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+I 225 3746 * * * * * * 1254 * 3576 * * 3528 * * * * 1575 * * 225
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+
+//
+�HHsearch 1.5
+NAME 6dc27b301d7556991a74587deb3a9692
+FAM
+FILE 6dc27b301d7556991a74587deb3a9692
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:24:35 2013
+LENG 232 match states, 232 columns in multiple alignment
+FILT 135 out of 1524 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEECCCCEEECCCCCCCEEEEEECCCCEEEEEECCCCCCCCCEEEEEEEEC
+CCCCCCCCCCCCCEEEEEECCCCCCCEEEEECCCCCCCCCCCEEEEEEECCCCCCCCEEEEEEECCEECCCCCCCCCEEECCCCEEEEEEEEEECCCCCC
+CCCCEEEEEEECCCCCEEEEEEECCCCCCCCC
+>ss_conf PSIPRED confidence values
+9089887848996799899998961788888679999968999847999980478604456668857999614675378998035304572799999851
+5887542201531132110012342014770775310027742899997378889983999998991725784002117538958998899996110002
+89988999999089868999994898988979
+>Consensus
+xxxvxxpxxxxxxxGxxvxLxCxxxxxxxxxxxixWxkxxxxxxxxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxxsLxIxxvxxxDxgxYxCxvxxx
+xxxxxxxxxxxxxxxlxVxxxxxxxpxxxxxxxxxxxxxxxxxxxlxCxxxgxxpxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxsxlxixxxxxxx
+xxxxxxtCxvxxxxxxxxxxixxxxxxxxxPx
+>6dc27b301d7556991a74587deb3a9692
+EVQLQQWGAGLLKPSETLSLTCAVYGGSFSDYYWSWIRQPPGKGLEWIGEINHSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARPPH
+DTSGHYWNYWGQGTLVTVSSGSASAPTLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVMA
+GTDEHVVCKVQHPNGNKEKNVPLPVIAELPPK
+>gi|62464905|gb|AAX83161.1| immunoglobulin heavy chain variable region [Aotus nancymaae]
+--------------GDPVPHLRCLWLLHRQ-------willeldpPAPKGRG--WSGldisivwWVHql-QRLPQES-----sh---YFSRHVQEPVLVE
+---------AE-LCDRR-----------------------------------------------------------------------------------
+---------------------------------------------------
+>gi|241177585|gb|ACS66861.1| MHC class II antigen beta chain [Amblyrhynchus cristatus]
+----------------------------------------------------------------------------------------------------
+---------YGVYEPFARKRLVQPKMSITPAEHDSSSQKT----LLICDVAGFWPSGINITWLRNGKEEEGtKVMTTDLIRNGDwTFQIQVMLETKAEWG
+-----DVYACQVEHPSFPTPARVQWEPQSD----
+>gi|296485480|gb|DAA27595.1| butyrophilin-like 9 [Bos taurus]
+EIRVVGhEEPILAHVGDEVEFSCHLSPYRDAqHMEILWFWSQASNV-VHLYREQQEFYGWQMKQFQNRTQLIRDdIIDGSVTLRLHLVVPADQGLYGCRF
+LS---S----DFTGEATWELEVAGLGSDPHISIEGF------KEGGIQLRCHSNGWYPKP-QAQWRDRHGRCLPPETENITEDVQGLFSLETSVVVQEGA
+H----SNVS-CSIQNhlLGQKKEFVVHIADV------
+>gi|56207974|emb|CAI21226.1| novel immune-type receptor 9, allele 1 [Danio rerio]
+-------------SGDSVSLTCTVlNQKCVGNHSMYWLIIESQDYRPRIISTHGTPVDQCEWISDADFRAL----RCVYSFSRKDFRLSNSATYSCTVTA
+--CG---EKLDRNVSKLDIDADST-Ee-MMILVLLS----------------------------------------------------------------
+----------------------------------
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+------------------------------------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne--DLRSWTAADMAAQN------
+----------tqrkweaagvaeqw----RAYLeGECLEWLRRYLEKGK--------------------et--LQ--raePs-SQSTIPI
+>gi|309362790|emb|CAP27555.2| CBR-SYG-2 protein [Caenorhabditis briggsae AF16]
+QLFLESPSNLSTIAGESITFRCAAEKSPEPIVYSQW-KSNTGS---LLGY----HQEGVLPGHQGRFSYVKQN-AEELHLKITHVNLDDDGEYECQMLHP
+EEG-----PIRAKAFLNIL---VPPQLVYFSnyqPNSVIAVKENTPLNITCVVPNVKPDPQ-VSWYMDGKVMSRDVKQASMPHLNKTFTVYTSLVIQPGR
+S--DHGKIVTCEVVQKETETRITTNTTLDVLFPPS
+>gi|221330930|ref|NP_001137898.1| CG42256, isoform F [Drosophila melanogaster]gi|220902492|gb|ACL83253.1| CG42256, isoform F [Drosophila melanogaster]
+--------------------vaknpaaeikytallqvKGSVLAYPS--QKLN-TEHK-KRKPHKYRshllskl-----K-------------------LS
+QCSLTLAA----slkp----FI------------------------------------------------------------------------------
+------------------------------------------------------------
+>gi|326678203|ref|XP_001337469.4| PREDICTED: hypothetical protein LOC797033 [Danio rerio]
+-----------VKEGDSVTLNSGLTE-VKDTDLILWwF--RDEDTLIAEINVTTDSTFVFDDVLDGRFRDRLKLDNKTGSLTITDAGTEHDGDYKLLIIG
+---AKWAVDWF----SVSVC-AHLRFPVISRNssqCSSSSSSSV-QYCSVLCSVVNVN--HATLSWYKENSLLSSISVSDFSI------SLSLPLEV---
+EY--QDNNTYSCVIDNpfSNltQLLNISQLCRTCSD----
+>gi|269115798|gb|ACZ26466.1| Down syndrome cell adhesion molecule [Litopenaeus vannamei]
+---IVEPADKAFALGSDARLECKADGFPRPTLGWKK---AAGHTP----------GDYRDLDVNNpNIKVTDDG-----TLHISSIQKSHEGYYLCEANN
+---G------IGAGLSTVIY-VRVQAPPQFKIQYRNQTARHGDDAVLECEAGGETP--IGILWSKDKHSVDQAAePRYTIREEMRGGSVHSSLSIKTTDR
+--TDSAVYTCIATNAFGSADTNINLIIQERPEQ-
+#
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+ 0 * * 0 * * * 5862 0 0
+
+//
+�HHsearch 1.5
+NAME 6e235e11f9c330891bd4a7eac552e81b
+FAM
+FILE 6e235e11f9c330891bd4a7eac552e81b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:02:52 2013
+LENG 187 match states, 187 columns in multiple alignment
+FILT 10 out of 12 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEECCCCCCCCCCCEEEEEEEECCCCCCCCEECCCCCCCCEEEEEEEEEEEEEECCCCCEEEEEEECCCCCCCCEEEEEEEEEECCCCCCCEEEEE
+EEEECCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEHHHEEEEEEEEECCC
+>ss_conf PSIPRED confidence values
+9417433045643457512341165317767586663796464248999987776776389717999991799989864899998863267988378999
+987457888856744245898787307874788986688324463258867999999867754242799998054333478740179
+>Consensus
+MfQxfvsKHxxxxxxapfssxxxxxxxtPaxxxpVvxtxxixxxrstxxxxxsxtaxtxxxGxfxxxxxxDxsxpxxnqVxSvxasLSfxvxsxxixxxV
+RFExaxxxxxtxxpxxxdxyPiexxxxsgxaxSxrDcvTidxhprtxGNnVyvGvxxxSxxwtagxvxGxiSxxQVxxExtvLQPLK
+>6e235e11f9c330891bd4a7eac552e81b
+MYQNFVTKHDTAIQTSRFSVTGNVIPAAPTGNIPVINGGSITAERAVVNLYANMNVSTSSDGSFIVAMKVDTSPTDPNCVISAGVNLSFAGTSYPIVGIV
+RFESASEQPTSIAGSEVEHYPIEMSVGSGGVCSARDCATVDIHPRTSGNNVFVGVICSSAKWTSGRVIGTIATTQVIHEYQVLQPLK
+>gi|2493330|sp|Q38042.1|G_BPPHK RecName: Full=Major spike protein G; AltName: Full=G protein; AltName: Full=GPGgi|1478127|emb|CAA42892.1| G [Enterobacteria phage phiK]
+MYQIFVTKHDTAIQTSRFSVTGSITPVAPTGNIPVINTGNI--taEHAVVSLYANLTAGTSSDGSFIVAMKVDTSPADPNCVISAGVNLSFAGTSYPIVG
+IVRFESASDQPTSIags---QIEHYPIEMSv-GSGGVCSARDCVTVDIHPRAFGNNVFVGVICSSAKWTSGRVLGTIATTQVIREYQVLQPLK
+>gi|71842816|gb|AAZ49017.1| gpG [Enterobacteria phage NC28]
+MFQVYVSKH-----VAPFTSKNRAFSIAPAANPQVVNSGEI--vaGRSTFRIASSIASAVNGSG-FAFVQMMDPNSPDSQQVFSVAASLSFSVDSNYIPC
+VVRFEDNAAQPTDFdia---TADFIPVEVSa-ISPRALSVRDCVTVDVKPRTQGNNVFVGVVFFSASANAGNVTGVVSMAQVDHEVTALQPLK
+>gi|71842783|gb|AAZ48987.1| gpG [Enterobacteria phage NC35]
+MFQVYVSKH-----VSPFTSMNRAFGITPSSNPTVVNSGEI--qaGRSTFRIASSIGAASNGQG-FAFVQMMDPYSPDNQQVFSVAASLSFSVDSNYVPC
+VIRFETASTQPTNIdvs---TADFIPLESSa-LSARALSVRDCVTVDVKPRIEGNNVFVGVVFCSAGASAGNVTGAVSMAQVDHEVTALQPLK
+>gi|71842861|gb|AAZ49058.1| gpG [Enterobacteria phage NC29]
+MFQVYVAKH-----VAPFTSMNRTFSISPAAAPQVVNSGEI--vaGRSTFRIASSIGSASNGNG-FAFVQMMDPNSPDSQQVFSVAASLSFSVDSNYVPC
+VVRFESSFSQPGQFaia---EADFIPVESSa-LSARALSVRDCVTVDVKPRAEGNNVFVGLFLSSAAANAGNVTGVISMAQVDHEVTALQPLK
+>gi|89888617|ref|YP_512377.1| gpG [Enterobacteria phage ID2 Moscow/ID/2001]gi|71842750|gb|AAZ48957.1| gpG [Enterobacteria phage ID2 Moscow/ID/2001]
+MFQKFIKKH-----NAPLTSQpAISKAVTPSMTaAPLVTTPL-GVSSTQLFLELTTTAAA--GG-FAYAIRVDNSNPTDNQVFSVCAHItS-DVDPKYIA
+CLVRFEVTAGTTPTAMPPVYDAYPIA-GYYDAGSYTVEDCATIPTHAVSSGNDVYVGLMLFSRMWPVAKLSGIASLNQVNKEVTVLQPLK
+>gi|71843197|gb|AAZ49366.1| gpG [Enterobacteria phage NC6]
+MFQKFISKH-----NAPISSTQVTVTETPAATAPILGVP--GLSRSTIQINVTTTAVTTHSG-LCHVVRIDETNPTNHHALSVAGSLS-HVSADMIAFAI
+RFEVADGFVPTAVPTLYDVYPIE-IVNTGKAISFKDVVTIDSHPRTVGNDVYAGIMLWSNAWSATTTSGVLSVNQVNREATVLQPLK
+>gi|71843149|gb|AAZ49322.1| gpG [Enterobacteria phage ID41]
+MFQKFISKH-----NAPINSTQLAATKTPAVTAPVLSVP--DLSRSTIQINATTTAVTTHSG-LCHVVRIDETNPTNHHALSIAGSLS-NVPADMIAFAI
+RFEVADGVVPTAVPALYDVYPIE-TFNNGKAISFKDAVTIDSHSRTVGNDVYAGIMLWSNAWTASTISGVLSVNQVNREATVLQPLK
+>gi|71843221|gb|AAZ49388.1| gpG [Enterobacteria phage WA14]
+MFQTYLSKH-----NSPLTSQSITATKTPAAAAPIISTP--ELSRSTIFAGLTLTAATTHSG-VAHVVRIDETNPTDNQVLSVAASLS-GVPSDAIAIAI
+RFEVADGTVPTALPALYSAYPVE-FFTSGAALSCKDAVSIPTHPVTAGNDVYAGILIWSKSWAAGVVSGLLSVNQVNRETTVLQPLK
+>gi|304269275|gb|ADM16612.1| protein G [Enterobacteria phage phiX174]
+MFQTFISRHN----SNFFSDKLVLTSVTPASSAPVLQTP--KATSSTLYFD-SLTVNAGNGG-FPHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLV
+RFESSS--VPTTLPTAYDVYPLN-GRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSN-FTATKCRGLVSLNQVIKEIICLQPLK
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ 0 * * * * * 0 1085 0 1994
+
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+
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+
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+
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+ 0 * * * * * * 2517 0 0
+
+S 158 * 3595 * * 2338 * * * * * * * * * * 1640 * * 1327 * 158
+ 0 * * * * * * 2517 0 0
+
+S 159 * * * * * * * * * * * * * * * 0 * * * * 159
+ 0 * * * * * * 2517 0 0
+
+A 160 1044 * * * * * * * 3391 * * 1721 * * 3103 * * * * * 160
+ 197 * 2970 * * * * 2517 0 0
+
+K 161 1771 * * * * 3413 * * 1884 * 2819 * * * * 2319 * * * * 161
+ 0 * * * * 0 * 2367 0 1046
+
+W 162 2021 * * * 2970 * * * * * * * * * * * * * 676 * 162
+ 0 * * * * * * 2517 0 0
+
+T 163 3391 * * * * * * * * * * 2612 3103 * * 2560 1136 * * * 163
+ 0 * * * * * * 2517 0 0
+
+S 164 633 * * * * * * * * * * * * * * 2067 * 3103 * * 164
+ 0 * * * * * * 2517 0 0
+
+G 165 3103 * * * * 785 * * * * * * * * * 3493 2221 * * * 165
+ 0 * * * * * * 2517 0 0
+
+R 166 * * * * * * * * 2035 * * 2021 * * 2067 * 2509 3391 * * 166
+ 0 * * * * * * 2517 0 0
+
+V 167 * 2970 * * * * * 3493 * 3103 * * * * * * 3525 785 * * 167
+ 0 * * * * * * 2517 0 0
+
+I 168 * * * * * * * 3002 * 3135 * * * * 2970 1368 2021 * * * 168
+ 0 * * * * * * 2517 0 0
+
+G 169 * * * * * 0 * * * * * * * * * * * * * * 169
+ 0 * * * * * * 2517 0 0
+
+T 170 3595 * * * * * * 3103 * 2165 * * * * * * 2067 1559 * * 170
+ 0 * * * * * * 2517 0 0
+
+I 171 3103 * * * * * * 1640 * 1883 * * * * * * * 1777 * * 171
+ 0 * * * * * * 2517 0 0
+
+A 172 2067 * * * * * * * * * * * * * * 393 * * * * 172
+ 0 * * * * * * 2517 0 0
+
+T 173 * * * * * * * * * 2035 2021 * * * * * 2067 1883 * * 173
+ 0 * * * * * * 2517 0 0
+
+T 174 2021 * * * * * * * * * * 957 * * * * 2067 * * * 174
+ 0 * * * * * * 2517 0 0
+
+Q 175 * * * * * * * * * * * * * 0 * * * * * * 175
+ 0 * * * * * * 2517 0 0
+
+V 176 * * * * * * * * * * * * * * * * * 0 * * 176
+ 0 * * * * * * 2517 0 0
+
+I 177 * * 2021 * * * * 1449 * * * 1368 * * * * * * * * 177
+ 0 * * * * * * 2517 0 0
+
+H 178 * * * * * * 1430 * 2035 * * * * * 1378 * * * * * 178
+ 0 * * * * * * 2517 0 0
+
+E 179 * * * 0 * * * * * * * * * * * * * * * * 179
+ 0 * * * * * * 2517 0 0
+
+Y 180 2509 * * * * * * 2970 * * * * * * * * 3391 1463 * 2067 180
+ 0 * * * * * * 2517 0 0
+
+Q 181 * * * * * * * 2970 * * * * * 2067 * * 658 * * * 181
+ 0 * * * * * * 2517 0 0
+
+V 182 2021 2970 * * * * * * * * * * * * * * * 676 * * 182
+ 0 * * * * * * 2517 0 0
+
+L 183 * * * * * * * * * 0 * * * * * * * * * * 183
+ 0 * * * * * * 2517 0 0
+
+Q 184 * * * * * * * * * * * * * 0 * * * * * * 184
+ 0 * * * * * * 2517 0 0
+
+P 185 * * * * * * * * * * * * 0 * * * * * * * 185
+ 0 * * * * * * 2517 0 0
+
+L 186 * * * * * * * * * 0 * * * * * * * * * * 186
+ 0 * * * * * * 2517 0 0
+
+K 187 * * * * * * * * 0 * * * * * * * * * * * 187
+ 0 * * 0 * * * 2517 0 0
+
+//
+�HHsearch 1.5
+NAME 6f8bf45e3bf355ef54d788898343cb1c
+FAM
+FILE 6f8bf45e3bf355ef54d788898343cb1c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:41:56 2013
+LENG 65 match states, 65 columns in multiple alignment
+FILT 16 out of 18 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 1.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEEC
+>ss_conf PSIPRED confidence values
+97533343444179999966303257888878889999999870578640887246656788109
+>Consensus
+xxxxxxxxxxxxtykLiinxxtxxxtteAvdAatAekxfKxYaNxngVdGeWtYddatkTFTvTE
+>6f8bf45e3bf355ef54d788898343cb1c
+MHHHHHHAMDTYKLVIVLNGTTFTYTTEAVDAATAEKVFKQYANDNGVDGEWTYADATKTFTVTE
+>gi|24159073|pdb|1MI0|A Chain A, Crystal Structure Of The Redesigned Protein G Variant Nug2gi|24159074|pdb|1MI0|B Chain B, Crystal Structure Of The Redesigned Protein G Variant Nug2
+------------TYKLVIVLNGTTftYTTEAVDAATAEKVFKQYANDNGVDGEWTYADATKTFTVTE
+>gi|198443040|pdb|2JWS|A Chain A, Solution Nmr Structures Of Two Designed Proteins With 88% Sequence Identity But Different Fold And Function
+------------TYKLILNLKQAKeeAIKELVDAGIAEKYIKLIANAKTVEGVWTLKDEILTFTVTE
+>gi|119389519|pdb|2FS1|A Chain A, Solution Structure Of Psd-1
+-------------------meavdans------LAQAKEAAikelkqygIGDYYIKLINNAKTVEGVESLKNEIL------
+>gi|64174789|gb|AAY41168.1| protein G/SspDnaE fusion protein [Expression vector pJJDuet30]
+----------HMQYKLILNGKTLKgeTTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTYTVTE
+>gi|195977828|ref|YP_002123072.1| IgG binding protein Zag [Streptococcus equi subsp. zooepidemicus MGCS10565]gi|195974533|gb|ACG62059.1| IgG binding protein Zag [Streptococcus equi subsp. zooepidemicus MGCS10565]
+-----------SevidaaeltpaltSYKLVIKGATFSgeTATKAVDAAVAEQTFRDYANKNGVDGVWAYDAATKTFTVTE
+>gi|195977828|ref|YP_002123072.1| IgG binding protein Zag [Streptococcus equi subsp. zooepidemicus MGCS10565]gi|195974533|gb|ACG62059.1| IgG binding protein Zag [Streptococcus equi subsp. zooepidemicus MGCS10565]
+-----------TTYRLVIKGVTFSgeTATKAVDAATAEQTFRQYANDNGITGEWAYDTATKTFTVTE
+>gi|15824801|gb|AAL09476.1|AF354651_1 Mig precursor [Streptococcus dysgalactiae]
+------------TYKLIVKGNTFSgeTTTKAVDAETAEKAFKQYATANNVDGEWSYDDATKTFTVTE
+>gi|313885225|ref|ZP_07818977.1| B domain protein [Eremococcus coleocola ACS-139-V-Col8]gi|312619916|gb|EFR31353.1| B domain protein [Eremococcus coleocola ACS-139-V-Col8]
+---------------LVVNSEDAQITSEytASSVELAGQYFRDYVNNNGLgDLEWSYDPATYTFTATD
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+H 2 * * * * * * 0 * * * * * * * * * * * * * 2
+ 0 * * * * * * 1000 0 0
+
+H 3 * * * * * * 0 * * * * * * * * * * * * * 3
+ 0 * * * * * * 1000 0 0
+
+H 4 * * * * * * 0 * * * * * * * * * * * * * 4
+ 0 * * * * * * 1000 0 0
+
+H 5 * * * * * * 0 * * * * * * * * * * * * * 5
+ 0 * * * * * * 1000 0 0
+
+H 6 * * * * * * 0 * * * * * * * * * * * * * 6
+ 0 * * * * * * 1000 0 0
+
+H 7 * * * * * * 0 * * * * * * * * * * * * * 7
+ 0 * * * * * * 1000 0 0
+
+A 8 0 * * * * * * * * * * * * * * * * * * * 8
+ 0 * * * * * * 1000 0 0
+
+M 9 * * * * * * * * * * 0 * * * * * * * * * 9
+ 0 * * * * * * 1000 0 0
+
+D 10 * * 0 * * * * * * * * * * * * * * * * * 10
+ 0 * * * * * * 1000 0 0
+
+T 11 * * * * * * 1000 * * * * * * * * * 1000 * * * 11
+ 0 * * * * * * 1178 0 0
+
+Y 12 * * * * * * * * * * 2379 * * * * 2250 1383 * * 2224 12
+ 341 2250 * 3700 115 * * 1454 1000 0
+
+K 13 * * * * * * * * 3729 * * * * 4272 * 3632 336 * * * 13
+ 0 * * * * * * 1806 0 0
+
+L 14 * * * * 2948 * * * * 3729 * * * * * * * * * 331 14
+ 0 * * * * * * 1806 0 0
+
+V 15 * * * * * * * * 241 * * * * * 3673 * * 3729 * * 15
+ 0 * * * * * * 1806 0 0
+
+I 16 * * * * * * * 3899 * 100 * * * * * * * * * * 16
+ 0 * * * * * * 2026 0 0
+
+V 17 * * * * 3920 * * 1022 * * * * * * * * * 1179 * * 17
+ 0 * * * * * * 2026 0 0
+
+L 18 * * * * * * * 1334 * 1341 * * * * * * * 2261 * * 18
+ 0 * * * * * * 2026 0 0
+
+N 19 * * * * * * * * 2378 * * 536 * * * * * 3086 * * 19
+ 0 * * 3000 193 * * 2026 1050 0
+
+G 20 * * * * * 834 * 3920 * 2164 * * * * * 2737 * * * * 20
+ 0 * * * * * * 2026 0 0
+
+T 21 3902 * * 2737 * 3920 * * 1081 * * 3181 * * * * 3899 3901 * * 21
+ 0 * * * * * * 2026 0 0
+
+T 22 * * 2210 * * 4274 * * * * * * * 2544 * * 834 * * * 22
+ 0 * * * * * * 2026 0 0
+
+F 23 1637 * * * 1947 * * * * 1730 * * * * 3920 * 4274 * * * 23
+ 0 * * * * * * 2026 0 0
+
+T 24 * * * * * * * * 1081 * * * * 2737 * 2378 3075 3920 * * 24
+ 2204 353 * 1000 1000 * * 2026 1500 0
+
+Y 25 2544 * * * * * * 2319 * * * * * * * * 1174 3920 * 3075 25
+ 0 * * * * * * 2026 0 0
+
+T 26 3106 * * * * * * 2895 * 3135 * * * * * * 654 * * * 26
+ 0 * * * * * * 2218 0 0
+
+T 27 3135 * * * * * * 4475 2895 * * * * * * 2816 824 * * * 27
+ 0 * * * * * * 2218 0 0
+
+E 28 * * * 558 * * * * 2273 * * * * 3135 * * * * * * 28
+ 221 2816 * 1000 1000 * * 2218 1050 0
+
+A 29 208 * * * * * * * * 2895 * * * * * * * * * * 29
+ 0 * * * * * * 2218 0 0
+
+V 30 * * * * * * * * 3135 * * * * * * 2816 * 426 * * 30
+ 0 * * * * * * 2218 0 0
+
+D 31 * * 426 3135 * * * * * * * * * * * 2816 * * * * 31
+ 0 * * * * * * 2218 0 0
+
+A 32 221 * * * * * * * * * * * * * * * * 2816 * * 32
+ 0 * * * * * * 2218 0 0
+
+A 33 645 * * 1832 * 3651 * * * * * * * * * * * * * * 33
+ 174 3135 * 3000 193 * * 2218 1050 0
+
+T 34 * * * 4475 * * * 2370 * 2816 * * * * * * 834 4092 * * 34
+ 0 * * * * * * 2218 0 0
+
+A 35 174 * * * * 3135 * * * * * * * * * * * * * * 35
+ 0 * * * * * * 2218 0 0
+
+E 36 * * 3135 426 * 2816 * * * * * * * * * * * * * * 36
+ 0 * * * * * * 2218 0 0
+
+K 37 * * * * * * * * 786 * * * * 1954 4377 * * * * 3135 37
+ 0 * * * * * * 2218 0 0
+
+V 38 3461 * * * * * * 4475 * * * * * * * * 3106 1483 * 1357 38
+ 0 * * * * * * 2218 0 0
+
+F 39 * * * * 402 * * 2370 * 4331 * * * * * * * * * * 39
+ 0 * * * * * * 2218 0 0
+
+K 40 * * * * * * * * 431 * * * * * 1954 * * * * * 40
+ 0 * * * * * * 2218 0 0
+
+Q 41 * * 2318 4377 * * 4101 * * 2010 * * * 1169 * * * * * * 41
+ 0 * * * * * * 2218 0 0
+
+Y 42 * * * * * * * 2370 * * * * * * * * * * * 310 42
+ 0 * * * * * * 2218 0 0
+
+A 43 526 * * * * * * 4331 * * * 3135 * * * * * 2816 * * 43
+ 0 * * * * * * 2218 0 0
+
+N 44 * * * * * * * * 4377 * * 157 * * * * 4178 * * * 44
+ 0 * * * * * * 2218 0 0
+
+D 45 1720 * 1360 4101 * * * * 3228 * * 2816 * * * * * * * * 45
+ 0 * * * * * * 2218 0 0
+
+N 46 * * * * * * 4101 * 2010 * * 528 * * * * * * * * 46
+ 0 * * * * * * 2218 0 0
+
+G 47 * * * * * 522 * * * * * 4178 * * * * 2010 * * * 47
+ 0 * * * * * * 2218 0 0
+
+V 48 * * * * * * * 2716 * 2816 * * * * * * * 502 * * 48
+ 221 2816 * 0 * * * 2218 1050 0
+
+D 49 * * 653 2010 * * 4101 * * * * * * * * * 4121 * * * 49
+ 0 * * * * * * 2218 0 0
+
+G 50 * * * * * 221 * * * 2816 * * * * * * * * * * 50
+ 0 * * * * * * 2218 0 0
+
+E 51 * * * 739 * * 4101 * * * * * * * * * * 1546 * * 51
+ 0 * * * * * * 2218 0 0
+
+W 52 * * * 3135 * * * * * * * * * * * * * * 174 * 52
+ 0 * * * * * * 2218 0 0
+
+T 53 3106 * * * * * * * * * * * * * * 1685 804 * * * 53
+ 0 * * * * * * 2218 0 0
+
+Y 54 * * * * * * * * * 2370 * * * * * * * * * 310 54
+ 0 * * * * * * 2218 0 0
+
+A 55 3333 * 616 * * * * * 2010 * * * * * * * * * * * 55
+ 0 * * * * * * 2218 0 0
+
+D 56 4092 * 811 * * * * * * * * 3135 2320 * * * 4121 * * * 56
+ 0 * * * * * * 2218 0 0
+
+A 57 528 * * 1706 * * * * * * * * * * * * * * * * 57
+ 0 * * * * * * 2218 0 0
+
+T 58 3941 * * * * * * 2370 * * * * * * * * 432 * * * 58
+ 0 * * * * * * 2218 0 0
+
+K 59 * * * * * * * * 589 2370 * * * * * * * * * 2816 59
+ 0 * * * * * * 2218 0 0
+
+T 60 * * * * * * * * * * * * * * * * 0 * * * 60
+ 0 * * * * * * 2026 0 0
+
+F 61 * * * * 152 * * * * * * * * * * * * * 4171 4498 61
+ 0 * * * * * * 2026 0 0
+
+T 62 * * * * * * * * * * * * * * * * 0 * * * 62
+ 0 * * * * * * 2026 0 0
+
+V 63 2737 * * * * * * * * * * * * * * * * 234 * * 63
+ 0 * * * * * * 2026 0 0
+
+T 64 * * * * * * * * * * * * * * * * 0 * * * 64
+ 0 * * * * * * 2026 0 0
+
+E 65 * * 2737 234 * * * * * * * * * * * * * * * * 65
+ 0 * * 0 * * * 2026 0 0
+
+//
+�HHsearch 1.5
+NAME 70185c53b564a6651b730e4dcf340af6
+FAM
+FILE 70185c53b564a6651b730e4dcf340af6
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:19:29 2013
+LENG 54 match states, 54 columns in multiple alignment
+FILT 104 out of 210 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCHHHHHHHHHHCCC
+>ss_conf PSIPRED confidence values
+908789898733999999998878999999999999949976999999972349
+>Consensus
+xxxxxxxxxxxxxxxxxxLxxMFPxldxxvIxxvLxxxxgxxdxaIdxLLxmsx
+>70185c53b564a6651b730e4dcf340af6
+SSLIKKIEENERKDTLNTLQNMFPDMDPSLIEDVCIAKKSRIEPCVDALLSLSE
+>gi|281343012|gb|EFB18596.1| hypothetical protein PANDA_003683 [Ailuropoda melanoleuca]
+-RPARQVRRLEFNQAMDDFKTMFPNMDYDIIECVLRANSGAVDATIDQLLQMN-
+>gi|51535464|dbj|BAD37361.1| hypothetical protein [Oryza sativa Japonica Group]gi|222635963|gb|EEE66095.1| hypothetical protein OsJ_22122 [Oryza sativa Japonica Group]
+----------------iEVLQLIF------phedpq-lLKSFFEASGNVLDA-aIRGFKHR--
+>gi|334184040|ref|NP_001185446.1| uncharacterized protein [Arabidopsis thaliana]gi|332198229|gb|AEE36350.1| uncharacterized protein [Arabidopsis thaliana]
+------------SSSLDQLHSAFPHIELTVaskihvsvaqvLVKALEDNGSDFNAAMKSLYSF--
+>gi|330922638|ref|XP_003299915.1| hypothetical protein PTT_11019 [Pyrenophora teres f. teres 0-1]gi|311326207|gb|EFQ91994.1| hypothetical protein PTT_11019 [Pyrenophora teres f. teres 0-1]
+------------PTKELLLAETFPGLRVSQVTYTLKKCGYDYDKATDELLNQV-
+>gi|302407576|ref|XP_003001623.1| conserved hypothetical protein [Verticillium albo-atrum VaMs.102]gi|261359344|gb|EEY21772.1| conserved hypothetical protein [Verticillium albo-atrum VaMs.102]
+------------DFQIRQLQDMFADLKTHDIQLAFKKSHG--------dfftamdsLLNTQ-
+>gi|255932461|ref|XP_002557787.1| Pc12g09600 [Penicillium chrysogenum Wisconsin 54-1255]gi|211582406|emb|CAP80587.1| Pc12g09600 [Penicillium chrysogenum Wisconsin 54-1255]
+------------ADKAQNLISMFPSITRLEAERILEDCHDNLSRSMDVLLNLA-
+>gi|255713396|ref|XP_002552980.1| KLTH0D05962p [Lachancea thermotolerans]gi|238934360|emb|CAR22542.1| KLTH0D05962p [Lachancea thermotolerans]
+----------SLSNntdgrsegegmgsrHAKALSEEnFPDENHTKARKGAVNLKKRMWRPIHSFTK---
+>gi|194667823|ref|XP_587938.4| PREDICTED: phosphonoformate immuno-associated protein 5-like [Bos taurus]gi|297475788|ref|XP_002688251.1| PREDICTED: phosphonoformate immuno-associated protein 5-like [Bos taurus]gi|296486625|gb|DAA28738.1| phosphonoformate immuno-associated protein 5-like [Bos taurus]
+--LPSVYETkVDQEELFTSVSEMFSDLDPDVVYLMLSECDFKVENAMDCLLELSA
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 2856 * 2728 * * * * * * * * * * * * 1791 1245 * * * 1
+ 0 * * * * * * 2056 0 0
+
+S 2 * * * 2047 * * * * * * * * * * 1202 2175 * 3295 * * 2
+ 0 * * * * * * 2424 0 0
+
+L 3 * * * 2289 * * * * * 743 3917 * 2926 * * * * * * * 3
+ 0 * * * * * * 3140 0 0
+
+I 4 686 * * * * 3477 * 2602 * * * * 3011 * * * * * * * 4
+ 0 * * * * * * 3494 0 0
+
+K 5 * * * 2784 * * * * 3308 * * * * 1883 1826 2317 * * * * 5
+ 0 * * * * * * 3494 0 0
+
+K 6 2845 * * 4280 * * * 4210 2171 * * * * 2794 1747 * * 3455 * * 6
+ 0 * * * * * * 3676 0 0
+
+I 7 * * * * * * * 2280 * 1603 3483 * * * * 3718 3965 2792 * 3455 7
+ 0 * * * * * * 3676 0 0
+
+E 8 * * * 1172 * 4298 2834 * 4282 * * 4373 * 2226 4274 * * * * * 8
+ 74 4324 * 1585 585 * * 4032 1002 0
+
+E 9 3058 * 4899 2511 * * 3762 * * * * 4490 4105 3423 1880 4102 3807 * * * 9
+ 107 3807 * 2660 249 * * 4032 1188 0
+
+N 10 3513 * * 2912 * * * * 2962 4298 * 3633 * 2096 2956 4695 4388 3822 * * 10
+ 59 4630 * 3459 138 * * 4056 1027 0
+
+E 11 4280 5131 4711 1327 * * * * * * * 4850 3732 2458 5205 2607 * * * * 11
+ 0 * * 4790 53 * * 5298 1097 0
+
+R 12 4040 * * 5280 3532 * 2588 4990 5835 3185 4348 4537 5006 3192 3956 3702 3448 5710 * 5873 12
+ 0 * * * * * * 5539 0 0
+
+K 13 3665 * 3179 1863 * * 6754 6213 4294 * 6930 4223 3774 3480 3585 3235 4665 6862 * * 13
+ 0 * * * * * * 6074 0 0
+
+D 14 2804 * 2778 1955 5868 5878 6289 * 5629 5604 * 3504 6015 4337 5694 3041 4189 5908 * * 14
+ 158 3266 * 2898 208 * * 6029 1423 0
+
+T 15 2928 * 3645 3738 6778 6625 3974 5310 2986 3461 6903 5585 5160 4018 6811 3514 3187 3979 * * 15
+ 0 * * * * * * 6070 0 0
+
+L 16 4133 * * 4046 4831 * 4793 2750 * 1650 4654 * * 6292 5197 * 5698 2306 * 4549 16
+ 19 * 6220 1638 559 * * 6030 1100 0
+
+N 17 3418 * 2909 2614 5594 6045 6828 6897 2684 4468 * 4333 * 3374 3988 3686 4589 5167 * * 17
+ 12 6857 * 2585 263 0 * 6069 1027 1001
+
+T 18 3469 * 4781 3139 5020 6864 5973 5705 * 5091 * 3880 * 2216 4468 3792 2357 4618 * 5671 18
+ 28 5705 * 1585 585 * * 6088 1028 0
+
+L 19 * * * * 5124 * * 3754 * 287 4579 * * * * * * 4797 * * 19
+ 0 * * * * * * 6088 0 0
+
+Q 20 3825 6059 * 6731 * * 3706 4443 2215 4215 4846 * * 2624 3183 3354 4230 4786 * 5727 20
+ 0 * * * * * * 6088 0 0
+
+N 21 2760 * 4049 1627 * 3577 * * * 5345 * 6072 6173 3995 6483 2375 4276 6281 * * 21
+ 0 * * * * * * 6088 0 0
+
+M 22 4587 * * 4697 * * * 3026 * 3848 682 * * 6636 6173 * 4290 5096 * * 22
+ 57 4697 * 0 * * * 6088 1118 0
+
+F 23 * 5870 * * 53 * * * * * * * * * * * * * * 5705 23
+ 28 * 5715 * * * * 6088 0 0
+
+P 24 5634 * * 5024 * 6586 * * * * * * 170 * * 4321 * * * * 24
+ 0 * * * * * 0 6031 0 1058
+
+D 25 4674 * 1767 5429 * 4010 4923 5533 6200 5236 * 2374 * 4226 * 2911 3215 * * * 25
+ 27 5772 * 0 * * 0 6031 1029 1058
+
+M 26 6935 * * 4625 4130 * 6435 2634 * 1599 2362 * * * 6026 * 6744 2723 5586 * 26
+ 0 * * * * * 0 6031 0 1058
+
+D 27 6295 * 733 3548 * 5672 5913 * 3623 * * 4625 6621 6435 5758 3895 4850 * * * 27
+ 0 * * * * * 0 6031 0 1058
+
+P 28 4393 * 5268 3527 6653 5234 4293 6026 3336 4239 6489 5648 2797 4574 2654 3995 4442 3465 * 6670 28
+ 0 * * * * * 0 6031 0 1058
+
+S 29 4165 * 3064 1632 4577 6011 5267 * 5507 5933 * 4753 5173 3322 * 3279 3898 6109 * 5010 29
+ 0 * * 2585 263 * 0 6031 1058 1058
+
+L 30 5745 * 3745 5933 * * 6820 2654 4310 2658 5669 * * 5758 * 5076 3333 1579 * 6392 30
+ 18 6317 * 2112 379 0 * 6031 1116 1058
+
+I 31 4188 * * * * * * 1058 * 2385 * * * * * * * 1872 * * 31
+ 0 * * * * * * 6088 0 0
+
+E 32 5827 6452 5408 1693 * 7059 6021 5828 2236 5985 * 6268 * 3458 2640 5705 4799 4726 * 6350 32
+ 0 * * * * * * 6088 0 0
+
+D 33 3546 5230 2687 5242 5793 5178 4358 * 3025 4438 4895 6173 * 5410 3945 2634 3620 5856 5931 5029 33
+ 0 * * * * * * 6088 0 0
+
+V 34 2883 6512 * * 5715 4697 * 3540 * 4876 5573 * * * * 5435 3250 925 * * 34
+ 0 * * * * * * 6088 0 0
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+C 35 4142 4707 * * 4142 * 6240 3746 * 673 * * * * * 6993 * 4266 5919 4131 35
+ 42 5648 6837 1824 479 * * 6088 1049 0
+
+I 36 4577 * 3555 1969 5337 5477 5078 3478 3233 5250 * 6899 * 4169 3233 4423 6486 3761 * 5910 36
+ 0 * * * * 0 * 6078 0 1000
+
+A 37 1818 * 3841 2783 * 6162 * 5030 3107 6737 6502 3664 * 4356 5406 3012 4477 * * * 37
+ 0 * * * * * * 6088 0 0
+
+K 38 5787 2043 6837 * * * 4415 * 2857 4697 * 2453 * 3979 4634 2878 4827 4864 * 6059 38
+ 28 7956 6042 1585 585 * * 6088 1000 0
+
+K 39 6837 * 3044 4805 6698 2336 4852 * 2771 6640 * 2104 * 3593 3280 5869 * * * * 39
+ 20 6164 * 1950 432 * 0 6010 1103 1035
+
+S 40 5251 5655 4486 6284 4828 911 7163 * 4399 * * 2727 * 6325 * 5250 * * 7126 3676 40
+ 44 * 5054 * * 0 * 6009 0 1035
+
+R 41 4726 * 1733 6050 * * 3712 * 3528 * * 1760 * * 2993 5934 6815 5486 * 6073 41
+ 0 * * * * * 0 5994 0 1108
+
+I 42 6790 * * * 4171 * * 2740 3568 2267 2843 * * 4688 5506 * 4617 2243 5627 5550 42
+ 0 * * * * * 0 5950 0 1108
+
+E 43 5642 * 1104 2139 * 3221 5627 * * * * 4391 6059 5490 * 4843 * * 4625 * 43
+ 0 * * * * * 0 5950 0 1108
+
+P 44 2322 * 4081 5013 * * 6227 6915 3415 4002 * 3790 4246 4356 2725 3182 4887 4264 * 6497 44
+ 33 * 5482 * * * 0 5950 0 1108
+
+C 45 907 3240 * * * * * 6502 * * * * 4583 * * 3376 2445 5146 * * 45
+ 0 * * 0 * 1279 766 5937 1058 1224
+
+V 46 4982 * * * 5048 * * 947 * 4738 2948 * * * * * 5550 2113 * * 46
+ 0 * * * * * 0 5950 0 1108
+
+D 47 5864 * 1337 2775 * 6528 4270 * 3121 * 6111 2936 * 6453 4443 5817 5276 5853 * * 47
+ 0 * * * * * 0 5950 0 1108
+
+A 48 2092 4571 4269 3756 5317 5482 * 5552 5681 * 5847 6730 * 4236 5448 2038 4358 3501 * 5270 48
+ 0 * * 3000 193 0 * 5950 1108 1108
+
+L 49 * 3427 * * 3812 * * 5400 * 300 * * * * * * * * * * 49
+ 0 * * * * * * 5991 0 0
+
+L 50 * * * * * * 5657 * 5538 287 6188 4073 * * * 6251 4643 * * 6298 50
+ 0 * * * * * * 5991 0 0
+
+S 51 4408 6469 5037 1950 6414 4725 5535 * 3930 6666 6599 2380 * 2787 * 3384 4261 6571 * * 51
+ 0 * * * * * * 5995 0 0
+
+L 52 * * * * 4454 * 4832 3983 * 1346 1436 * * 4431 5389 * 6335 6581 * * 52
+ 0 * * * * * * 5697 0 0
+
+S 53 3529 5075 6289 * * 6814 * * 4710 * 6068 3250 * 3690 * 1332 3040 3218 * * 53
+ 0 * * * * * * 5429 0 0
+
+E 54 2981 * 1516 2008 * * * * * * * 4468 * * * 2892 3394 * * * 54
+ 0 * * 0 * * * 4412 0 0
+
+//
+�HHsearch 1.5
+NAME 717d981e28459396ae1133448788c53e
+FAM
+FILE 717d981e28459396ae1133448788c53e
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:34:14 2013
+LENG 238 match states, 238 columns in multiple alignment
+FILT 84 out of 86 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHCHHHHCCCEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEECCCEEEEECCCCCCCEEEEEEEEECCCCCCCEEEEEEECCCHHHHC
+CHHHHHHCCHHHHCCCCCHHHHHHHHHHCCCCCEEEEECCCCEEEHHHEEEEEEECCHHHHHHCCCCCCCCCEEEEEEEECCCCCCCCEEEHHHHHHHHH
+HCCHHHHHHHHHHCEEECCCCCCCCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9422217366378679994577787769976454458867389998469979977879999278889960899999972778873689999814888917
+6122210382440445533566444442168643788565131674230201388459997430467658937999978828888404077999999998
+47989999999840532434544557733241244569
+>Consensus
+xxxMAxxxkdlxGWxixxxdxxxxxixxxxrRxRrxxxxxxixLxRxxdxxxxxxGDsVlxkxxxxxxxxVxlIxeIxxxtxxnxvEixvxWyxrxxEix
+xxxxxxxxxPxxxxxxxrxdxxxxxxxxxxxxnELfLTxxxdeixLxxIigkaxVlSxxefxxlxxxxxxxxxFxcRxxcxxxxxxftxfdxxdxxxxix
+xxxpkxxxexlkxltxxxxxxxxkxxxxxxxxxxxxxx
+>717d981e28459396ae1133448788c53e
+AMTMAKTLKDLQGWEIITTDEQGNIIDGGQKRLRRRGAKTEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVN
+PLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIK
+KVEPREAQEYLKDLTLPSKKKEIKRGPQKKDKATQTAQ
+>gi|294656587|ref|XP_458878.2| DEHA2D09504p [Debaryomyces hansenii CBS767]gi|218511733|sp|Q6BSE2.2|ORC1_DEBHA RecName: Full=Origin recognition complex subunit 1gi|199431584|emb|CAG87030.2| DEHA2D09504p [Debaryomyces hansenii]
+---MAKSQRDLKGWQYFLDDAELNNtdsVNGePTTPSRrsRRgksTSSQKISLKREEDELEIKEGDFLLVQQDN-NSPEVAIVKEIKFGN-DNFLDIIVS
+WFIRMRDIEEA-----DLPKVEEY-KERSQ--------LNENELFITSYLDEVKLGEIIDKVNILSEEEFNnDIVIDDSNKaSTFICRRGCDSAGELFTd
+VFDFRDLCVLFE-KNHHEFIEFIRRKTVPV--------------------
+>gi|242768097|ref|XP_002341502.1| origin recognition complex subunit Orc1, putative [Talaromyces stipitatus ATCC 10500]gi|218724698|gb|EED24115.1| origin recognition complex subunit Orc1, putative [Talaromyces stipitatus ATCC 10500]
+-----------------------------------------------MGKFECRLGHVVLLKSPEAGKDWVGLITEFLEEE-DDDDEeemIKSAnimWFA
+SAEEFLSTK----------TKNRkRVD---------ALPNEQYLTTDFNVNPLTSINGRGKVMSKDAFFAKYpngtPPrnkAelaEYKKCIVCRRGVNQl
+QGK-YTeEFVWEDVY------------------------------------------
+>gi|50550345|ref|XP_502645.1| YALI0D10104p [Yarrowia lipolytica]gi|49648513|emb|CAG80833.1| YALI0D10104p [Yarrowia lipolytica]
+--------------------------------------KAAVRAIRDQDNVEISAGDVVLLKDDPdVEGKEFALIQGLKHGD--QGLEAKCVLMKLFNDA
+EA------LTPKHVIPNTNKNRY-------SKGQELVMMNSIVDVLVEELHLPVNCYSFAEFEALSREDKKGdNVYFCRYVFDNDANKTSvEFDWQDITK
+DMC--------------------------------------
+>gi|255631163|gb|ACU15947.1| unknown [Glycine max]
+--------------------------------------------VKHISKT-IRAGDCVLMRPSDLSKPSyVARIERIEADARGSNVKIHVRWYYRPEES
+IG---------------GRRQF--------HGSKEVFLSDHFDVQSADTIEAKCTVHSFKSYTKL--DAVGNDDFFCRFEYNSSTGAFN-----------
+---------------------------------------
+>gi|145507041|ref|XP_001439481.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124406665|emb|CAK72084.1| unnamed protein product [Paramecium tetraurelia]
+------------------------------------------------CGEIIKLNDKVIIKNE--DSNVedyIGSIQKIcSIVE-PRTLKLiclcEVQW
+FMRKNEIIC------HKPRAR------SW--------IGNQEIFSTNTNDYVLAQTIVQRCTVVDCEEYFNM--ENCDSTTYYNRLEWDVECKKFTNMN-
+----------------------------------------------
+>gi|145539714|ref|XP_001455547.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124423355|emb|CAK88150.1| unnamed protein product [Paramecium tetraurelia]
+------------------------------------------------QNQEYHVGQNLCIR-gD--NGS-eyVAKLIKVvKLID-NED-N-clpfiKVQ
+WYYRKTELTG------LPKDYL------EC--------ISENEVFKTNELDYIEIESIIGLAIILSYEEYDKI--EELNENVYFMRATY-FDQ-kLFPSF
+E-----------------------------------------------
+>gi|19112852|ref|NP_596060.1| origin recognition complex subunit Orc1 [Schizosaccharomyces pombe 972h-]gi|1709487|sp|P54789.1|ORC1_SCHPO RecName: Full=Origin recognition complex subunit 1gi|1127741|gb|AAC49129.1| Orp1 [Schizosaccharomyces pombe]gi|1161930|gb|AAC49141.1| orc1+ protein [Schizosaccharomyces pombe]gi|4007803|emb|CAA22443.1| origin recognition complex subunit Orc1 [Schizosaccharomyces pombe]
+-----------------------------------------------KNDVIYRVGDDITVHDGD-SSFYLGVICKlyekaIDKHSGKKYVEA--IWYSR
+AYakrmEIKPE----YLLPD------------------RHINEVYVSCGRDENLTSCIIEHCNVYSEAEFFskfpaGIPTKrkDLFPCNFFIRRGVHLKV
+NKYTePLDWSYYAHNLE--------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 963 * * * * 1038 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1433 0 0
+
+M 2 * * * * * * * * * * 963 * * * * 1038 * * * * 2
+ 0 * * * * * * 1433 0 0
+
+T 3 * * * * * * 1038 * * * * * * * * * 963 * * * 3
+ 0 * * * * * * 1433 0 0
+
+M 4 * * * * * * * * * * 0 * * * * * * * * * 4
+ 0 * * * * * * 4504 0 0
+
+A 5 326 * * * * * * * * * * 3212 * * * 3406 * * * * 5
+ 0 * * * * * * 4504 0 0
+
+K 6 3411 3660 * 3588 * * 3379 * 2134 * * * * 3465 3321 2126 * * * * 6
+ 0 * * * * * * 4504 0 0
+
+T 7 * * * * * * * 4471 3440 3184 * 3295 * * 4313 2243 1361 * * * 7
+ 67 * 4471 * * * * 4504 0 0
+
+L 8 3454 * * * * * * 3352 * 1696 * * 3061 1591 * 4309 * * * * 8
+ 75 * 4309 * * 0 * 4429 0 1063
+
+K 9 3322 * * * * * * * 685 * * * * * 3521 2825 4330 * * * 9
+ 177 * 3117 * * * 0 4410 0 1068
+
+D 10 * * 872 2120 * * * * 4210 * * 4044 * 3200 * * * * * * 10
+ 90 4044 * 0 * 1717 523 4234 1071 1354
+
+L 11 * * * * 1982 * * 3417 * 614 * * * * * * * * * * 11
+ 0 * * * * * 0 4350 0 1230
+
+Q 12 4256 * 4722 1482 * * * * 1745 * * 3135 * 2841 * * * * * * 12
+ 83 4160 * 0 * 0 * 4350 1067 1230
+
+G 13 4444 * 4313 * * 230 * * * * * * * 4282 * * * * * * 13
+ 0 * * * * * * 4504 0 0
+
+W 14 * * * * * * * * * * * * * * * * * * 68 4444 14
+ 0 * * * * * * 4504 0 0
+
+E 15 * * 4433 1906 * 4471 * * 3337 * * 3202 * 1539 4380 4568 * * * * 15
+ 0 * * * * * * 4504 0 0
+
+I 16 * * * * 2330 * * 1089 * 4557 * * * * * * * 3118 * 2529 16
+ 134 * 3499 * * * * 4504 0 0
+
+I 17 * * * 4196 4469 * 4388 1297 * 4058 * * * 4169 4291 * 3814 2652 * 4364 17
+ 0 * * * * * 0 4346 0 1178
+
+T 18 * * * * 3376 * * 1684 3220 2267 * * * * * * 2567 3203 * * 18
+ 195 2980 * 758 1291 0 * 4346 1359 1178
+
+T 19 * * 2615 2905 * * 4568 * 2799 4160 * 4978 * 4433 * * 1383 * * * 19
+ 0 * * * * * * 4504 0 0
+
+D 20 * * 724 2828 4568 * * * * * * 3715 * * * 3439 * 4530 * * 20
+ 0 * * * * * * 4504 0 0
+
+E 21 3079 * 3694 1737 * 4396 * * * 4282 * * 3346 4403 * 3401 4557 3026 * * 21
+ 0 * * * * * * 4504 0 0
+
+Q 22 * * 3018 1969 4396 4557 4879 * 2803 * * 4503 * 3005 * 2433 * * * * 22
+ 0 * * * * * * 4504 0 0
+
+G 23 * * 3234 * * 1080 * * 4380 4694 * 4361 * 3481 * 2737 * 4444 * * 23
+ 0 * * * * * * 4504 0 0
+
+N 24 * * 2475 3350 * 4380 * * * * * 1254 4313 * 3582 3478 5009 * * * 24
+ 207 * 2905 * * * * 4504 0 0
+
+I 25 * * 3438 * * 3192 * 2051 * 3051 * 3538 * * * 3149 * 2074 * * 25
+ 738 1320 * 1638 559 664 1438 4267 1869 1282
+
+I 26 * * * * * * * 1218 * 2321 4222 * * 4249 * * 3145 2731 * * 26
+ 0 * * * * * 0 4229 0 1305
+
+D 27 4100 * 1461 * * * 4738 * 4278 * * 3454 3213 3679 4108 4335 4335 4182 * * 27
+ 0 * * * * * 0 4229 0 1305
+
+G 28 * * 1859 2631 * 1837 * * * * * 4229 * * * * 2594 * * 3965 28
+ 1005 995 * 185 3057 593 1570 4229 2005 1305
+
+G 29 * * * 4098 * 4546 * * 4465 * * 3765 3506 * 1962 2438 1996 * * * 29
+ 0 * * * * * 0 4404 0 1064
+
+Q 30 4335 * 4351 * * 3453 * * 3549 * * 4782 2175 2325 2484 * 3497 * * * 30
+ 0 * * * * 0 * 4404 0 1064
+
+K 31 4433 * * * * * * * 2791 * * * * * 557 4444 4694 4471 * * 31
+ 0 * * * * * * 4504 0 0
+
+R 32 * * 4433 * * * * * 4403 * * * 4694 * 364 * 3457 * * * 32
+ 124 3601 * 0 * * * 4504 1194 0
+
+L 33 4303 * * * * * * * 4387 4529 * * 3246 * 1801 1411 3473 * * * 33
+ 0 * * * * 0 * 4512 0 1078
+
+R 34 * * * * * * * * 4433 * * * * * 123 4831 * * * * 34
+ 914 1379 3562 895 1113 * * 4504 1923 0
+
+R 35 3180 * * * * * * 4328 2994 * * * * * 755 * 4829 3526 * * 35
+ 55 * 4731 * * * 0 4374 0 1152
+
+R 36 4187 * * * * 3194 * * * * * 3262 * 3814 1005 3258 * 4119 * * 36
+ 695 1607 4208 1363 710 533 1695 4380 1881 1287
+
+G 37 2674 * 4169 * * 1180 * * * * * 3294 * * 3348 * 2774 * * * 37
+ 419 2211 4796 1001 999 * 0 4346 1512 1178
+
+A 38 1728 * * 2613 * 3037 * * * 4319 * 3247 4206 * * 2750 * 4195 * * 38
+ 91 4027 * 2322 322 * 0 4354 1095 1260
+
+K 39 4262 * * 4335 * 4639 4181 * 1718 * * 4401 * * * 1646 3563 4391 * * 39
+ 0 * * 1000 1000 1947 433 4475 1024 1260
+
+T 40 4278 * 3292 1326 * * * * * 4485 4363 * 3097 4547 * 4274 2807 * * * 40
+ 0 * * * * * 0 4467 0 1178
+
+E 41 3320 * 4356 4602 * * 4347 3646 4547 4394 * 3201 * 2712 4463 3340 4863 3287 * 4373 41
+ 0 * * * * * 0 4467 0 1178
+
+H 42 * * * * 4846 * 4602 1276 * 2796 * * * * * * 4730 1602 * * 42
+ 0 * * * * * 0 4467 0 1178
+
+Y 43 * * * * 2156 * 4373 * 3300 * * 4235 * 4863 2449 2870 4447 4347 * 3017 43
+ 178 3106 * 2099 383 0 * 4467 1461 1178
+
+L 44 4378 * * * * * * 3464 * 215 * * * * * * * * * * 44
+ 0 * * * * * * 4621 0 0
+
+K 45 * * * 4538 4895 * 4774 1813 2672 * * * * 2828 3039 5140 4295 3765 * 5056 45
+ 0 * * * * * * 4917 0 0
+
+R 46 * * * * * * * * 2899 * * 5056 * 4570 333 * * * * * 46
+ 64 * 4524 * * * * 4917 0 0
+
+S 47 * * 3623 2121 * 2081 5570 4109 3505 3761 * 5068 * 4102 * 4475 3667 * * * 47
+ 45 * 5037 * * 0 * 4842 0 1067
+
+S 48 4213 * 4022 5854 * 5669 * 4855 3121 5058 2678 6674 6703 3882 * 2267 2718 5533 * 4534 48
+ 0 * * * * * 0 5408 0 1003
+
+D 49 * 5735 935 4282 * 2391 7408 * * * * 3108 * 4181 5873 6421 6612 * * * 49
+ 0 * * 1000 1000 * 0 5754 1003 1003
+
+G 50 4438 * 4146 3516 * 1351 7314 * 2860 5153 * 3346 7284 5150 * 3248 7026 * * * 50
+ 0 * * * * * 0 5754 0 1003
+
+I 51 * * * 4524 2403 * * 2899 6167 1976 4400 * * 3943 6038 * 4465 2377 * * 51
+ 172 * 3155 * * * 0 5754 0 1003
+
+K 52 * * 5191 1425 * * 5325 3770 3810 4950 * * * 4497 3214 3870 4055 3088 * * 52
+ 0 * * * * 182 3077 5618 0 1459
+
+L 53 * 2319 * * 2145 * * 2257 * 2259 * * * * * * * 3361 * 4108 53
+ 0 * * 0 * 0 * 5754 1003 1003
+
+G 54 7118 6416 * 4695 * 2912 5264 * 1817 6690 * 6050 * * 2009 3127 4196 * * 4119 54
+ 0 * * * * * * 5768 0 0
+
+R 55 3541 4186 * 6161 * * 7058 3184 4733 2929 * * 3719 * 2570 * 4911 1831 * * 55
+ 0 * * * * * * 5768 0 0
+
+G 56 4711 * * * * 84 * * * * * 5758 * * * * * * * * 56
+ 0 * * * * * * 5768 0 0
+
+D 57 * * 532 3755 * * 6012 * * * * 5516 * 2883 * 6061 5899 5071 * * 57
+ 0 * * * * * * 5768 0 0
+
+S 58 3209 2897 5841 * 6161 * * 6039 5758 * * 3260 * * * 2014 2126 3356 * 6194 58
+ 0 * * * * * * 5768 0 0
+
+V 59 5240 * * * * * * 1713 * 3602 * * * * * * 7008 790 * * 59
+ 0 * * * * * * 5768 0 0
+
+V 60 * 4639 * 4067 7422 * * 2652 * 1031 5635 * * 6416 * * 4829 2484 * * 60
+ 0 * * * * * * 5768 0 0
+
+M 61 * 4141 * * 5720 * * 2157 * 2029 1964 * * * * * * 2329 * * 61
+ 0 * * * * * * 5768 0 0
+
+H 62 * * * * * * 3588 * 1339 * 6991 2431 * 3962 2860 4895 4543 * * 4329 62
+ 80 6190 4639 1585 585 * * 5768 1048 0
+
+N 63 2639 * 1907 4072 * 4441 * * * * * 3282 3789 4035 * 2326 * 4974 * * 63
+ 33 * 5466 0 * 0 * 5699 1110 1217
+
+E 64 4241 * 2548 1787 * 2757 4848 * 5764 * * 4855 2834 6417 5740 3644 * * * * 64
+ 570 * 1615 * * 0 * 5762 0 1037
+
+A 65 4024 * 2161 2514 * 2510 * * 3594 * * 5162 4351 4725 * 5258 4507 3370 * * 65
+ 298 3372 3471 0 * 3529 131 4958 1304 2581
+
+A 66 2091 * * * * 4959 * 4482 * 4018 * 6014 3349 * * 2235 2291 3378 * * 66
+ 0 * * * * 0 * 4838 0 2655
+
+G 67 * * 1706 3898 * 2727 7367 * 3078 * * 2515 * 5186 5257 3033 * * * * 67
+ 0 * * * * * * 5768 0 0
+
+T 68 5292 * * 3033 5899 3339 * * 2255 * * 4246 * 4472 3953 2177 2798 * * * 68
+ 0 * * * * * * 5768 0 0
+
+Y 69 3240 * 3669 * 5841 * 4275 6308 4694 4141 * 3198 2286 7408 5037 6161 4070 6207 * 2314 69
+ 59 * 4639 * * * * 5768 0 0
+
+S 70 4795 * 4135 3224 5673 5075 * 4334 * * * * 3231 5458 * 1691 * 5679 2285 4740 70
+ 551 1655 * 1422 674 0 * 5716 2463 1110
+
+V 71 3781 * * * 4395 * * 2481 * 4938 * * * * * * * 686 * 4433 71
+ 0 * * * * * * 5768 0 0
+
+Y 72 1595 5758 * * * 1640 * * * * 6190 * * * * * * * * 1662 72
+ 0 * * * * * * 5768 0 0
+
+M 73 * * * * 5776 * * 2065 3253 1443 3633 * * * 3574 5758 4774 4306 * * 73
+ 0 * * * * * * 5768 0 0
+
+I 74 6812 * * * * * * 529 * 4031 * * * * * * * 2078 * * 74
+ 0 * * * * * * 5768 0 0
+
+Q 75 * 2932 * 2967 * * 2185 5184 2916 6308 5516 4196 * 2961 4334 5633 3913 * * 7042 75
+ 0 * * * * * * 5768 0 0
+
+E 76 6529 * 2465 1135 * 4379 * * 2922 * * * * 3709 4320 5127 * * * 5816 76
+ 52 4829 * 2456 290 * * 5768 1091 0
+
+L 77 * * * * 2337 * * 676 * 3495 6363 * * * 5816 * * 4122 * * 77
+ 346 2871 3706 0 * * * 5768 1504 0
+
+R 78 * * 4235 2760 6844 * 5092 * 2874 3728 * * * 4569 1587 3001 4597 6914 * * 78
+ 0 * * 0 * 0 * 5746 1278 1278
+
+L 79 3655 * 5335 2626 3287 7569 4443 3274 4829 1744 * * 5679 4659 * 5267 7367 6050 5758 5776 79
+ 14 6706 * 0 * * * 5768 1000 0
+
+N 80 4560 * 2508 3522 * 2272 5298 6161 4316 * 6050 1673 * 7118 6690 * 6991 4486 * * 80
+ 115 * 3706 * * * * 5768 0 0
+
+T 81 5850 7314 3452 2732 * 4003 7628 3642 6537 4967 5723 5119 * * 7082 4865 1400 3721 * * 81
+ 1185 * 836 * * * 0 5746 0 1278
+
+L 82 3961 * * * * 3000 * * 6057 1571 2958 * 3222 * 2253 6225 * * * * 82
+ 74 4316 * 1275 769 251 2646 4018 1089 3472
+
+N 83 5124 * 2769 3892 * 3501 * * 4523 5872 * 1469 3704 6501 * 3090 5542 5609 * * 83
+ 20 * 6158 * * 1866 462 5647 0 1402
+
+N 84 7319 * 3679 3377 * 5510 4351 * 3873 * * 1258 5826 3851 4239 5001 4068 5812 * 6203 84
+ 249 * 2658 * * 2685 244 5731 0 1338
+
+V 85 5200 * 2910 4275 2676 4742 5959 4986 * 4195 * 4985 5216 * * 4766 3498 2833 * 2574 85
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+NAME 71fdde7383f09a65b56a391c1db52e35
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+FILE 71fdde7383f09a65b56a391c1db52e35
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:48:26 2013
+LENG 94 match states, 94 columns in multiple alignment
+FILT 102 out of 383 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEECCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCCCEEEEEECCEEEEEEEEEECCCEEEEEEEEECCCCEEEEEECCCCCCC
+>ss_conf PSIPRED confidence values
+9973988998999999999999876375886399999997652543258999657899999999489779999997078928999801789998
+>Consensus
+GgwxxidvxxxvqxxaxfAvxexNkxxxxxxlxfxkVvxaxxxxxxxxxxQvVaGxnYxLxixaxxxxyxaxVxexpwxxxxxLxsFxxxxxxx
+>71fdde7383f09a65b56a391c1db52e35
+GEWEIIDIGPFTQNLGKFAVDEENKIGQYGRLTFNKVIRPCMKKTIYENEREIKGYEYQLYVYASDKLFRADISEDYKTRGRKLLRFNGPVPPP
+>gi|224158457|ref|XP_002337975.1| predicted protein [Populus trichocarpa]gi|224160549|ref|XP_002338224.1| predicted protein [Populus trichocarpa]gi|222870101|gb|EEF07232.1| predicted protein [Populus trichocarpa]gi|222871368|gb|EEF08499.1| predicted protein [Populus trichocarpa]
+GGWTPIkNMNdTQAIEIAEFAITENNKQA-SSNLELDSIVKGL-------ERDAGDNKNYQLVLTVKGGKadeqYEADVNV--SGNLKALILFVP-L---
+>gi|15225164|ref|NP_180758.1| cysteine proteinase inhibitor 2 [Arabidopsis thaliana]gi|125991828|sp|Q8L5T9.2|CYT2_ARATH RecName: Full=Cysteine proteinase inhibitor 2; Short=AtCYS-2; Flags: Precursorgi|4263720|gb|AAD15406.1| putative cysteine proteinase inhibitor B (cystatin B) [Arabidopsis thaliana]gi|110738361|dbj|BAF01107.1| putative cysteine proteinase inhibitor B [Arabidopsis thaliana]gi|330253521|gb|AEC08615.1| cysteine proteinase inhibitor 2 [Arabidopsis thaliana]
+GGKSGVpNIRtnREIQQLGRYCVEQFNQQA-qneqgnigsiaktdtaiSNPLQFSRVVSA--------QKQVVAGLKYYLRIEVTQPngstrMFDSVVVI
+QPWLHSKQLLGFTP-VVSP
+>gi|242039791|ref|XP_002467290.1| hypothetical protein SORBIDRAFT_01g023010 [Sorghum bicolor]gi|241921144|gb|EER94288.1| hypothetical protein SORBIDRAFT_01g023010 [Sorghum bicolor]
+-SYTKQeDVSsDFIKQVGKFAVNVYRLAH-MIPMNYLSTSKC--------WSSPAGgga-NNYWMVLSATNYtgtagSYVSTVWGIPGSesKTWKLLTF-
+------
+>gi|241159543|ref|XP_002408587.1| cystatin, putative [Ixodes scapularis]gi|215494370|gb|EEC04011.1| cystatin, putative [Ixodes scapularis]
+GVWRKHhpDVDPRYKEWAHFAISSQ---V-EDRTNFDtlmTLISV--------ESQVIAGVDYKLKMKVAESncvigvdsysrerchlkvdapymICTAL
+VNYMPWEHKTSLKSYNC-----
+>gi|296200364|ref|XP_002747566.1| PREDICTED: cystatin-S-like [Callithrix jacchus]
+GGIHDADLSdEWVQRALHFAISKYNKAT-KDAYYRRllRVLRA--------REQTVAGTNYFFDVEIgrttctksqPNLdtcPfreqpelqkkqfCSFQI
+YEVPWEDRMSLVKSR------
+>gi|2665886|gb|AAB95324.1| cystatin-1 [Haemonchus contortus]
+GGLTDQSTDdPEFMEQAWKAATKVNEEaN-DGDYYMipTKVLSA--------KTQVVSGVMFTSKVLFeesfckkgdvpvdqlkaSNcapkeGgkrvIYE
+ISVLLQPWVKSEQVG---------
+>gi|28900876|ref|NP_800531.1| hypothetical protein VPA1021 [Vibrio parahaemolyticus RIMD 2210633]gi|28809322|dbj|BAC62364.1| hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]
+GGWNEFDATPDAQKAMAFVLKQMDTLS-----SFKQILTV--------HAQIVSGVNYAIEFEMDDGSiWNTIVYR-------------------
+>gi|123480843|ref|XP_001323421.1| Clan IH, family I25, phytocystatin-like peptidase inhibitor [Trichomonas vaginalis G3]gi|121906286|gb|EAY11198.1| Clan IH, family I25, phytocystatin-like peptidase inhibitor [Trichomonas vaginalis G3]
+GGVKPANVDdEHVIQAFKDAVALANQKN-GTNLEFVELITA--------TQQVVSGFIFEGVVKTNDGDYKAKIWCKPGNTEKELQSFE------
+>gi|73991007|ref|XP_848363.1| PREDICTED: similar to cystatin 11 isoform 1 precursor [Canis familiaris]
+-----VSASdPYVTTTMQYLSDDFNKKS-NDKYNFRivRLLKV--------QKQITDHMEFHVNME-------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * 5599 * * 101 * * * * * 5908 * 5804 6299 * * * * * 1
+ 0 * * * * * * 5332 0 0
+
+E 2 4210 * * 3767 5843 772 * * 3596 * * 6191 5976 5523 5079 4040 * 4472 * * 2
+ 15 6614 * 0 * * * 5921 1000 0
+
+W 3 5235 * * 6304 3779 * * 4364 6461 3722 * * 3557 6658 6504 6927 * 5654 889 3672 3
+ 32 5490 * 2278 333 * * 6050 1090 0
+
+E 4 5307 * * 3388 4906 7120 5103 3426 3638 * 5443 4824 * 6420 3728 2884 2078 3541 7328 5247 4
+ 26 5817 * 1585 585 * * 6064 1055 0
+
+I 5 4862 * 2785 3600 * 6535 * 4227 3028 6507 * 4496 1645 5507 5184 5860 3714 4904 * * 5
+ 0 * * * * * * 6078 0 0
+
+I 6 2631 * 6515 * 6241 6498 5280 1350 3989 4751 5352 6471 * 4304 4616 5030 * 2970 * * 6
+ 769 1275 * 172 3157 * * 6013 3026 0
+
+D 7 5648 * 886 5052 * 5892 6502 * 5539 * * 2056 4746 * * 3842 6400 * * * 7
+ 26 5822 * 0 * * * 6020 1036 0
+
+I 8 4204 * * 5523 6736 * 6700 2473 6658 3851 4086 * 3330 6956 * 7068 4042 1282 * * 8
+ 73 5271 5413 0 * * * 6020 1064 0
+
+G 9 5192 * 2806 5033 * 3786 6475 6558 4305 6763 * 1851 * 4316 6528 2176 3551 * * * 9
+ 2861 214 * 109 3787 0 * 5998 4645 1053
+
+P 10 5133 * 4295 3459 * 5519 5455 * 2952 4424 * 4596 1280 5317 5017 4324 4631 6668 * * 10
+ 24 5927 * 0 * * 0 5996 1033 1000
+
+F 11 4514 5455 3377 2043 3335 4344 3137 * 3838 4549 * 4791 6810 4346 5357 4711 * 4652 7103 5958 11
+ 15 6636 * 1000 1000 0 * 5996 1052 1000
+
+T 12 4510 * * * 6269 * * 2110 * 4656 6596 * * * * 5671 3748 1164 * 3045 12
+ 0 * * * * * * 5925 0 0
+
+Q 13 5215 * 4800 4619 * * 5713 3203 2839 3479 5378 6466 * 1304 4249 * * 4432 * * 13
+ 0 * * * * * * 5939 0 0
+
+N 14 4335 * 3581 1786 * 6017 * * 2576 6487 * 3756 * 2618 4239 4561 5119 6611 * 6467 14
+ 0 * * * * * * 5939 0 0
+
+L 15 2155 6662 * * 5764 * 5792 3439 * 1580 5954 * * 5548 6494 * 4942 2473 5353 5893 15
+ 0 * * * * * * 5939 0 0
+
+G 16 940 * * * 5679 2120 * 5959 6593 3218 5465 * * * * 6597 6475 4293 * * 16
+ 0 * * * * * * 5919 0 0
+
+K 17 4776 6316 4944 3736 6799 * 3229 6564 2069 5424 6857 3766 6360 3897 2563 6747 4266 * 3974 * 17
+ 16 * 6494 * * * * 5933 0 0
+
+F 18 6068 * 5101 * 830 * 4738 5300 4613 4950 6628 * * * 4967 6355 5758 6614 3267 3825 18
+ 0 * * * * 0 * 5919 0 1000
+
+A 19 311 7050 * * 6467 5472 * 6360 * 5650 * * 6657 * * 5095 4935 4356 * * 19
+ 0 * * * * * * 5933 0 0
+
+V 20 3760 * * * * 6549 * 3105 * 3290 3782 6297 * * * * 3915 875 * * 20
+ 15 6583 * 1000 1000 * * 5920 1000 0
+
+D 21 3244 * 2804 3407 * 5863 7262 5199 3369 4842 6387 5128 6647 4432 5002 2676 2956 4694 6222 6803 21
+ 0 * * * * * * 5920 0 0
+
+E 22 3731 * 5655 1146 * 5409 7137 5386 3739 5686 5825 * * 3915 5224 3391 5277 3792 * * 22
+ 24 * 5930 * * * * 5920 0 0
+
+E 23 6669 * * 3464 2877 6689 2394 3721 * * 5174 5108 * 4021 5482 4859 6130 4463 6068 2071 23
+ 51 6481 5395 1000 1000 * 0 5927 1001 1011
+
+N 24 4620 * 4328 * * 5496 * * 6393 * * 559 6829 6453 5270 3021 7162 5616 * * 24
+ 29 * 5668 * * * 0 5880 0 1144
+
+K 25 4039 * 5253 4905 6395 4723 * * 1242 4785 4906 3871 * 3680 3611 4967 5119 4896 6077 * 25
+ 11 * 7034 * * 792 1243 5850 0 1253
+
+I 26 3128 5778 5594 4695 * 4491 * 3801 2489 4234 5465 4258 * 2246 3785 4096 5263 5807 * * 26
+ 89 4338 6561 1507 626 648 1466 5879 1283 1148
+
+G 27 2983 * * 6533 6671 3197 3532 6940 6557 6687 5371 3101 6148 3642 5467 1930 3922 4541 * * 27
+ 2008 * 413 * * * 0 5921 0 1065
+
+Q 28 3426 * * * * 2916 3613 * * * * 2793 3693 2568 3461 4174 2678 * * * 28
+ 67 4464 * 3861 103 173 3149 4018 1124 4489
+
+Y 29 4356 * 4464 3552 * 2593 5751 * 3349 6201 6182 1718 5838 5979 5544 4036 6061 * * 3714 29
+ 0 * * * * 1399 688 5682 0 1433
+
+G 30 3567 6691 1565 6409 * 2438 5375 6201 5678 6528 * 4596 * * 6382 3122 3908 5549 6648 4737 30
+ 14 6668 * 1000 1000 1587 584 5877 1000 1249
+
+R 31 4500 * 4835 4394 6143 3038 5040 4351 3144 3994 5413 3695 3278 6814 2950 3424 5177 5703 * * 31
+ 28 5691 * 1000 1000 * 0 5875 1042 1147
+
+L 32 5903 6543 * 5831 4103 * 5500 5208 6603 929 5023 5205 * * * 6526 5022 4537 * 2559 32
+ 16 6543 * 1000 1000 0 * 5875 1000 1147
+
+T 33 5343 5001 * 3601 4687 * 4431 5886 2393 3307 6370 3995 5875 3939 4386 4696 3099 4783 * 3801 33
+ 17 6437 * 1000 1000 * * 5928 1000 0
+
+F 34 * 6914 * 6953 1311 * 4857 6437 * 2477 4967 6531 6370 * 5638 5252 * 5322 * 2128 34
+ 216 2844 * 1000 1000 * * 5928 1783 0
+
+N 35 4959 * 3176 4248 * 5723 7185 3160 3756 4102 * 3290 * 4349 4384 3854 4388 2507 * 4552 35
+ 201 2942 * 1120 889 * * 5928 1683 0
+
+K 36 4480 6496 * 3185 * 5036 5938 6554 1561 * * 4803 * 4511 2542 3538 3756 * * 5254 36
+ 0 * * * * * * 5928 0 0
+
+V 37 * * * * * * * 2160 * 3625 6671 6836 * * * 6230 3737 765 * * 37
+ 17 6375 * 1585 585 * * 5928 1036 0
+
+I 38 6539 * 6109 5400 5423 * 4600 2215 5604 2434 5985 5166 * * * 4124 5289 1768 * 4465 38
+ 0 * * * * * * 5928 0 0
+
+R 39 5130 6761 5889 2469 * 4516 5752 * 1901 * 5783 3716 * 4659 3379 2360 6643 * * * 39
+ 64 * 4530 * * * * 5928 0 0
+
+P 40 1257 5011 * * * 1893 * 4502 * 5008 6490 * 4450 * * 6890 * 2828 * * 40
+ 2773 * 228 * * * 0 6014 0 1114
+
+C 41 * 1054 * * * * * * * 2568 * * * * * * * * 1516 * 41
+ 266 * 2568 * * * 0 2866 0 5002
+
+M 42 * * * * 2134 * * * * * 1816 * * * * * * 1035 * * 42
+ 323 * 2317 * * * 0 2578 0 5046
+
+K 43 * * * * * * * * 1527 * 1732 1506 * * * * * * * * 43
+ 0 * * * * 5728 27 2270 0 5099
+
+K 44 * * 2092 * * * * * 386 * * * * * * * * * * * 44
+ 0 * * * * 6241 19 2658 0 5041
+
+T 45 * * * * * * * * * 962 * * * * * * 1935 2152 * * 45
+ 354 * 2199 * * 4692 57 2756 0 5002
+
+I 46 * * * * * * * 735 * 2016 * * * * * * * * 2718 * 46
+ 0 * * * * * 0 2862 0 4965
+
+Y 47 * * * 2016 * * * * * 2214 * * * * * 2786 * * * 1350 47
+ 0 * * * * * 0 2862 0 4965
+
+E 48 * 2718 * 2058 * * * * * * * 2786 * * * * * 1111 * * 48
+ 0 * * * * 66 4476 2862 0 4965
+
+N 49 6112 * * 1635 * 6599 7351 * 3091 4708 6281 4266 6755 2626 3511 4582 3803 6596 4838 6793 49
+ 36 * 5361 * * 1296 755 5918 0 1175
+
+E 50 5718 * * 2758 6632 5442 * * 2700 5763 5570 * * 3577 4607 2566 2247 3473 * 6338 50
+ 0 * * * * 1206 820 5878 0 1186
+
+R 51 * * 6185 5664 * * * 6467 5618 5380 6466 5603 * 424 3558 6273 7022 5687 * 6852 51
+ 15 6636 * 3322 152 0 * 5969 1002 1079
+
+E 52 4706 * * 4548 6132 4222 5307 3148 * 3404 6483 4960 4391 6479 * * 4106 1126 * * 52
+ 40 5187 * 1278 767 * 0 6081 1132 1002
+
+I 53 4300 6588 * 6132 * 4916 5035 4335 6836 5831 * * * 4859 * 5656 4072 603 * 6269 53
+ 14 6701 * 0 * * 0 6081 1001 1002
+
+K 54 1447 * 3674 4626 * 4064 * 6483 3870 6852 * 3638 * 6900 5980 2235 5049 7012 6458 * 54
+ 108 3796 * 677 1416 * 0 6081 1335 1002
+
+G 55 6050 * * * * 308 5698 5508 5952 * * 3780 5843 * 6579 5691 * * * * 55
+ 0 * * * * 606 1543 5982 0 1122
+
+Y 56 * * 6464 7106 5794 * * 2963 4017 3277 2550 4948 * 5980 6173 6900 2621 2539 * 3406 56
+ 17 6458 * 0 * * 0 6081 1013 1002
+
+E 57 6773 * 4005 3420 * * * 4494 2409 4794 4464 1051 * 7608 6726 * 6132 6701 * * 57
+ 21 6132 * 0 * * 0 6081 1015 1002
+
+Y 58 * * * * 3341 * 5304 6599 * * * * * * * 6173 6966 5303 6500 309 58
+ 0 * * * * * 0 6081 0 1002
+
+Q 59 5247 * 7541 4282 5562 * 3963 4376 2785 4945 5228 5644 * 3088 1994 5402 5136 6308 5362 3298 59
+ 23 5980 * 2775 228 0 * 6081 1088 1002
+
+L 60 * * * * 3395 5088 * 2851 5991 815 3764 * * * * 6313 * 4816 * 5006 60
+ 0 * * * * * * 6094 0 0
+
+Y 61 6997 * 4140 3199 6999 * 3769 3993 3372 5134 7119 4992 * 5953 6176 5584 1861 2790 * 4378 61
+ 0 * * * * * * 6094 0 0
+
+V 62 6704 * * * 3986 * * 1786 * 1922 4194 * * 5991 * * 6610 1771 * * 62
+ 0 * * * * * * 6094 0 0
+
+Y 63 4599 * 3721 1932 * * 5991 * 2274 4318 * 5912 * 4259 4276 3853 3990 4478 * 4301 63
+ 156 3288 * 1878 458 * * 6094 1501 0
+
+A 64 1316 * 6601 6842 5118 4125 * 3714 5927 3786 4883 * * * * * 3659 2316 * 6139 64
+ 183 3070 * 3482 135 * 0 6206 1554 1000
+
+S 65 2565 5144 5660 4578 * 5171 5915 4818 3055 5662 7197 4042 6209 5866 6765 2296 2758 4378 * 6129 65
+ 35 6559 6233 2000 415 * 0 6206 1000 1000
+
+D 66 6872 * 1594 3778 * 3697 6589 * 5307 6856 * 2689 3794 4131 3452 3768 6741 7058 * * 66
+ 286 2549 6830 3597 124 1336 728 6189 1825 1073
+
+K 67 3674 5651 5467 5701 4906 1506 * 6417 3539 4668 * 7281 3993 5060 4622 3852 4048 5291 5070 6301 67
+ 1603 576 * 2877 211 0 * 6164 3991 1096
+
+L 68 6491 * 4342 4856 6522 4012 6691 4007 3488 2846 5780 3898 3626 3762 5153 3596 2994 4440 * 6689 68
+ 751 1301 * 2249 341 * * 6181 3014 0
+
+F 69 6857 1886 * * 3251 7391 6250 * * * 6202 * * * * * * 6704 5251 870 69
+ 0 * * * * * * 6181 0 0
+
+R 70 7204 * 2970 1967 * 5836 4469 5787 3302 * * 4194 5610 3449 4232 5379 3261 4296 * 5133 70
+ 0 * * * * * * 6181 0 0
+
+A 71 805 5000 * * 3563 * * 4425 * 5245 6490 * * * * 4669 4892 2692 * * 71
+ 20 6547 8287 1000 1000 * * 6181 1000 0
+
+D 72 6487 * 3809 3451 5397 * 6161 3345 3451 3953 * * * 4344 4912 6067 3372 1597 * 6729 72
+ 0 * * * * * 0 6181 0 1000
+
+I 73 6411 * * * * * * 1956 * 4929 * * * * * * * 519 * * 73
+ 0 * * * * * 0 6181 0 1000
+
+S 74 6348 * * * 2922 6748 4822 5694 * 3721 * 4132 * * 5433 4605 * 5354 1366 2455 74
+ 42 5111 * 0 * * 0 6161 1079 1000
+
+E 75 6274 5688 3441 1330 * 3662 6614 5614 6284 6062 * 6382 * 6298 4764 3718 4841 2904 6681 5344 75
+ 76 * 4278 * * 0 * 6161 0 1000
+
+D 76 6533 * 4068 4084 * * 4959 3103 2013 6261 5470 6766 6800 2522 2911 6148 6109 3557 * * 76
+ 58 * 4663 * * 466 1857 6050 0 1219
+
+Y 77 4704 5411 5366 3946 4943 5947 * * 5394 3602 6056 * 1057 6077 * 3281 6115 5523 * 4482 77
+ 225 3146 5006 1038 963 0 * 6050 1456 1234
+
+K 78 * * 5999 * 6537 2985 6222 * 4177 3703 * 6666 * 6036 5520 4316 5562 * 811 6188 78
+ 21 * 6098 * * 0 * 6070 0 1091
+
+T 79 4956 * 6188 2181 * 4728 * 5032 4850 2666 5178 3785 5584 4447 6397 3117 2611 6029 * * 79
+ 37 5315 * 1000 1000 * 0 6096 1059 1013
+
+R 80 6899 * 4030 5087 * 4684 3263 * 2581 * * 1517 5016 4996 3924 5806 3816 * 6557 6188 80
+ 52 * 4820 * * 0 * 6096 0 1013
+
+G 81 * 6179 4611 3830 2789 3681 5708 3926 3443 5999 6823 5399 * 6337 3484 3417 2466 4297 * * 81
+ 34 5416 * 0 * * 0 6082 1052 1152
+
+R 82 * * * 4663 3686 * * 2913 2368 4353 4465 6179 * 6530 2262 7014 3330 6337 3373 6257 82
+ 0 * * * * 632 1495 6082 0 1152
+
+K 83 6026 * * 2224 * 6176 * 4909 1630 * * 4210 * 3106 4663 2838 5494 6172 6075 * 83
+ 45 5017 * 0 * * 0 6122 1079 1015
+
+L 84 * * * * 4365 * * 4547 * 599 5029 * * * * * 6239 2288 * * 84
+ 0 * * * * * 0 6110 0 1015
+
+L 85 6364 * * 3583 * 5995 * 2695 4380 2487 5078 6117 5552 4363 4724 3832 2371 3657 6222 * 85
+ 23 5959 * 2807 222 * 0 6110 1012 1015
+
+R 86 5142 * 6202 2822 6273 5464 * * 3514 5125 * 4794 * * 3524 1009 6113 6020 * 6023 86
+ 0 * * * * * 0 5956 0 1015
+
+F 87 * * * * 506 * 6066 4919 * 4218 5943 4687 * * * 4477 6295 * * 3618 87
+ 0 * * * * * 0 5934 0 1015
+
+N 88 4969 * 4447 3081 * * * * 1895 3791 * 2980 * 5016 4265 3882 3036 3975 * * 88
+ 66 * 4485 * * * 0 5837 0 1015
+
+G 89 4413 3818 * 3729 * 3409 * * 4942 4312 * * 961 4420 4838 * 4868 * * * 89
+ 2259 * 338 * * 0 * 4750 0 1183
+
+P 90 * * 2221 * * * * * 2166 * * * 829 * * * * * * * 90
+ 348 2221 * 3459 138 0 * 2104 1015 1668
+
+V 91 1706 * * * * * * 4126 * 2453 * 4141 * * * * * 1334 * * 91
+ 194 2987 * 1000 1000 * * 3472 1000 0
+
+P 92 * * * * * * 2774 * * * * 2714 1893 * 2918 2827 * 2654 * * 92
+ 0 * * * * * * 2529 0 0
+
+P 93 * * * * * * * * * * * * 1220 * * 809 * * * * 93
+ 471 1843 * 1000 1000 * * 1880 1015 0
+
+P 94 * * * * * * * * * * * * 0 * * * * * * * 94
+ 0 * * 0 * * * 1609 0 0
+
+//
+�HHsearch 1.5
+NAME 74210cc330abf78ec4c1fa3592d2152d
+FAM
+FILE 74210cc330abf78ec4c1fa3592d2152d
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:23:49 2013
+LENG 223 match states, 223 columns in multiple alignment
+FILT 138 out of 1103 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEECCCCCCCEEEEEECCCEEEEEEEEECCEEEECHHHCCCCCEEEECCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCEEEEEECCCCCCCCCE
+EEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCEEEEEEEEEECHHHHHHHCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCEEEEEEEECCCCCCC
+CCCEEEEEHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9999899987888699997698699999980999998989977863899742102335787479998899818887777776868999988877678835
+7778687777899889999857647888777723279999971689966642588886749974178998657789788399989999999706788888
+98639999899799999997439
+>Consensus
+ixxgxxxxxxxxPwxvxxxxxxxxCxGtlIsxxxVLTaaxCxxxxxxvxxgxxxxxxxxxxxxxxxvxxxxxhpxxxxxxxxxDiAllxLxxxxxxxxxx
+xpiclxxxxxxxxxxxxxxgxgxxxxxxxxxxxxlxxxxxxxxxxxxCxxxxxxxxxxxxxCxxxxxxxxxxcxgdsGxplxxxxxlxGixsxxxxcxxx
+xxxxxxxxvxxxxxwIxxxixxx
+>74210cc330abf78ec4c1fa3592d2152d
+IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRV
+ASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQK
+NKPGVYTKVCNYVSWIKQTIASN
+>gi|118790260|ref|XP_001231107.1| AGAP004700-PA [Anopheles gambiae str. PEST]gi|116122431|gb|EAU76241.1| AGAP004700-PA [Anopheles gambiae str. PEST]
+----------------------YFCSAVFISADFLLAPAMCLKlmqpvddhpsSHMFVLIEAEHVFYYEGG--RRYINKIFYHPKLEEEPVYHNLAVVKL
+RNPIrEt-VmanGQSIVACLWSEIKLRNNKVYLGEWFKYHP---EQNPAFRWLDVPVITRKECREELSKNkviipefdrgVAETQLCVKDKKNSTmiEFC
+EPRSSGPLFMTLgntvYVVGMPTVHIdDCNV--QIEVFNQVSSFLDWIEAIV---
+>gi|17511021|ref|NP_491910.1| TRYpsin-like Protease family member (try-7) [Caenorhabditis elegans]gi|2088690|gb|AAB54144.1| Trypsin-like protease protein 7 [Caenorhabditis elegans]
+VYNGRDASQSEAPWSVFTYlyskdeQSATTCTGTIVSPRHILIATHCFAgqnrdGSWNLIEDTFDRSNCKDDDYVITNQEFLKRVEFLSnkkgisrypek
+itlvhactkrtanrtkkippQYYTDDFAIVHLYEELTFSSNVQSVCVADDETQPNDKLSLEYFGfglnppsDINQNGVDNTGQLRYEKIEVFRSHPMEIY
+F--------FQARDITDKTVACvvslkililnktqaslnislKGDSGGGAIADVkgkkTIIGVLSQTScqkRRGGNETMELYSSVGFYKNQI-------
+>gi|189240061|ref|XP_001808986.1| PREDICTED: hypothetical protein [Tribolium castaneum]gi|270011741|gb|EFA08189.1| hypothetical protein TcasGA2_TC005816 [Tribolium castaneum]
+--NGERVPPGYYSYAVIFKlmkepkshlfnNSDFFeslaiCSGTVLNRRWVVTKASPIAYYKTKLYRVMVQPDGSQASNTYKVESVLLHPNHFPGDITTD
+VALVRVARDFQFALDLRNANLGFPvMPLNQTACKMPVWSFFFVDNSNSSKIMEKGEISLtVVTTGC--------HTDFLCLK-PNNSKAPCSFNIGMPII
+CNTVLTAVY-FGNettgGCNG-QLPEMVTALRADTPFLE------
+>gi|187735175|ref|YP_001877287.1| 2-alkenal reductase [Akkermansia muciniphila ATCC BAA-835]gi|187425227|gb|ACD04506.1| 2-alkenal reductase [Akkermansia muciniphila ATCC BAA-835]
+------------PWNTGRY-QGGIGTGFLIGENAFMTNAHVVSNAERIYISMY-----GDSRKIPARVKFIAH--------DADLALLEADDPR-PFKGI
+RPFEFSkN-LPHLEDEVRVIGYPIGGNRLSVTRGVVSRIDFTTYAHPRNTEHLTIQVDAAIN------------PGNSGGPVLMGNKVIGVA--------
+------------------------
+>gi|195112812|ref|XP_002000966.1| GI10530 [Drosophila mojavensis]gi|193917560|gb|EDW16427.1| GI10530 [Drosophila mojavensis]
+-------------HLVYLRfNYNIICSGIVVNNRTVLTVTSCLDRKEPPKIIVHFTD-----GTAQTASSSSPSSDYTMSSGSNLLSFLHLEKPLD-QEF
+DTPPPFCTQAVRPQDNVMQLNWDKNYSR-------PIPRFVPQMPLDQCQTLNRDarMLAPAVHCVEN-TQYTDECIRSYGLPYVWKGAFCGMNINGHNC
+SVPSNADVYVRLLREKRLISKMLRT-
+>gi|42521718|ref|NP_967098.1| hypothetical protein Bd0072 [Bdellovibrio bacteriovorus HD100]gi|39574248|emb|CAE77752.1| hypothetical protein predicted by Glimmer/Critica [Bdellovibrio bacteriovorus HD100]
+------------------------CTVTLVSDNCVVTVGACALdrdyVEFNVPVSVAGVAQKSSLEDRYYVEKGTERHKADG--IGHQWAVLRLKPNEVT
+GKNAGAVqgfyRMATKKSQNNDPIRVVSYGYALND--LYdikrgdmpansnpdq-mHFAQQVSHGKLV----KAGIF--LIPEII-----EHDADTSYGS
+WGAPVINEKtnELVGINTHG-GCRAQyvvkagaRY---------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+A 221 3649 * 4784 3677 6055 3017 * * 2098 * * 2390 5803 4840 3533 4325 6031 * 4697 * 221
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+N 223 * * 2268 * * * 2371 * 3825 * * 1121 * * 3862 * * * * * 223
+ 0 * * 0 * * * 6021 0 0
+
+//
+�HHsearch 1.5
+NAME 757d964661b62316dff0960e2a4a87ea
+FAM
+FILE 757d964661b62316dff0960e2a4a87ea
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:41:44 2013
+LENG 201 match states, 201 columns in multiple alignment
+FILT 134 out of 974 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
+HHHHHCCCCCCEEEEEEEECCCCCCCCCEEEEECCCEEEEECCCCCEEEEEEEHHHEEEEEECCCEEEEEECCCCCEEEEEECHHHHHHHHHHHHHHHHH
+C
+>ss_conf PSIPRED confidence values
+9988699998999999999999998398889999999999999999957998433561220188867988877668999999999811389999999999
+9998578778689998870368877760799987875999838996068896279917887359889999836765399984559999999999999984
+9
+>Consensus
+xxxxxxxxdxxxxxlxyxQxxxdvlxgxxxxxxxxxxxLaAlxxqxxxGdxxxxxxxxxxxxxxxxxPxxxxxxxxxxxixxxxxxlxgxsxxxAxxxyL
+xxxxxxpxyGxxxfxvxxxxxgxxxxxxxxLgIxxxGIxxxxxxxxxxlxxxxxxxIxxxxxxxxxxxixxxxxxxxxxxxxtxxxxxixxlixxyxxxx
+x
+>757d964661b62316dff0960e2a4a87ea
+SDQNVDSRDPVQLNLLYVQARDDILNGSHPVSFDKACEFAGYQCQIQFGPHNEQKHKPGFLELKDFLPKEYIKQKGERKIFMAHKNCGNMSEIEAKVRYV
+KLARSLKTYGVSFFLVKEKMKGKNKLVPRLLGITKECVMRVDEKTKEVIQEWSLTNIKRWAASPKSFTLDFGDYQDGYYSVQTTEGEQIAQLIAGYIDII
+L
+>gi|72124671|ref|XP_790458.1| PREDICTED: similar to myosin regulatory light chain interacting protein [Strongylocentrotus purpuratus]gi|115963894|ref|XP_001177677.1| PREDICTED: similar to myosin regulatory light chain interacting protein [Strongylocentrotus purpuratus]
+------------RHLFFHDAKLLVKEEKIKAALKDAARLAALFTQAEKGDFgASN--DVELLagYFPQFADSE----EFKVTAQAEYARLRSMKVEHALL
+SLLREICEMDSYGLNTFTAKTCS-GQ----LCEVGVGAHGILVTNIETQD-CVKIPLSSVKRLSVEKRDCQMHYelddGHNfttdkmeltlhtkeiaegl
+yrsiteKVEFFTSETVSEPVKDQFVRD------
+>gi|47215134|emb|CAG02558.1| unnamed protein product [Tetraodon nigroviridis]
+--------NELYVSMHYNQVLPDYLKALLSIVpqgkaseqqLQQIARLAALQHRAKDSIYLPTV-----REAQECVPPPFYSKQNpqlwLNVTTQHMQHV
+QPLNPHQARAQFLGLVSAFPMFGSSFFYIQSCS-SASIQAPCVLAVNLNGLHFLNKDTHEAVVHFPLKEIqSTRTQRPtsgssyPYVDIMIGDLLNqRIT
+QLQLEQGLELCRVIAMHVENML
+>gi|195118260|ref|XP_002003658.1| GI21679 [Drosophila mojavensis]gi|193914233|gb|EDW13100.1| GI21679 [Drosophila mojavensis]
+--------DETSRHNYYLQLRHNVLQRELPrdHADQALVMLAGYALQADLGDAPTIaaaaeetheeqaatagtsrngrstgmtttlpkirkrlssynerm
+lrlstyvtstsqtatkreaapacpvpsNSSTDYFRMEDYLPATLHTDWAKSELRACHREHKGLAQAEAELMYIQQACSLhETINAHTFRMRLAK-SEVGV
+GSAWFVIYAKGIKILGSGAGAEPATFLWPHITKLSFERKKFEIRSGESRITLYAASDEKNKLLLTLCKDTHQ---
+>gi|324502376|gb|ADY41046.1| Pleckstriny domain-containing family H member 1 [Ascaris suum]
+-----SSETPAERLFLVHRMANEIVAGRIPMSNELAEELAAVYAQMHYGDIG-dSITDEQLRtVTISYFPAKMLDVGCertlRLNIQSHWTQLRGTSPAD
+CVRMILVVLRKWRFFGAHITEARMKMRNDE---RIFIALNDQGVHLLTVRQLDVIRSFPYHRLVSFGGYHNDFMLTVDRilppeaHPeetareRLTFSMP
+PRAIDQLTCHLAEYIR---
+>gi|241998718|ref|XP_002434002.1| focal adhesion kinase, putative [Ixodes scapularis]gi|215495761|gb|EEC05402.1| focal adhesion kinase, putative [Ixodes scapularis]
+-----YEKDPVLFAYFYKQVQSDFLVKCNDIDQDLAIHLCCLEIRRFWKDMTHAalDKKSNYelIekeiGLHKFLPANVITSNKvgllFCWISNAKVACS
+YYCHNTELFdksKLYGSFSIRLTFLFFSSLCLFQT-GWS--VPVELVVNQElGIGYLTDRKGLTNHIANFQQVQSIQtiv-NDasp-KpvLQLKIaGASE
+vrfPFLFPIpWAITGFSFLRLI--WGAEF-
+>gi|145541975|ref|XP_001456675.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124424488|emb|CAK89278.1| unnamed protein product [Paramecium tetraurelia]
+------YQDQVRMQYILLQFFEEIRELKFLLNREKLFLYIAFYLIIKRQEVK-------HENISKYLKSEIFDQIEphrwEVEVKRYITqinsQLLQL-E
+TEkkSMVylcqyqflknIYYEKEATMNIYKLEVHRELQAA-FSKLKVpDikgnIYIGLSQAKISLLTPLDKKVIQEIQYQEIDNIQSFPNKLVIRTKsnI
+P-EKGWKFITFQSYEIKMLINFYKEL--
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+I 149 6572 5253 * 5056 4041 6962 6088 2547 4861 1409 6108 * 6036 5539 5397 4834 4556 3482 7520 5619 149
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+N 156 4513 7062 2819 2084 * 5718 3877 * 4437 5993 6135 3385 * 4426 3105 3245 5237 5837 * * 156
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+I 157 * 5454 * * 4314 * * 975 * 2861 4295 * 6677 * 6522 * 6202 2429 * 6713 157
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+W 160 5118 * 6843 * 3119 * 6726 3220 6727 2259 6031 * * * 7031 * 4921 2213 2236 5131 160
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+
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+T 183 3662 5409 6339 6825 * 7146 6394 4335 5540 5340 5505 5678 5513 5484 6614 2420 1229 4259 * * 183
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+E 187 3586 * 4969 2485 5796 6574 5707 5558 2173 5421 * 5623 5339 3939 3238 3821 * 5539 6104 3853 187
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+
+Q 188 3855 * 3197 2105 * * 6330 6281 4139 3470 6253 4714 * 3667 3601 5582 5766 3676 * 3517 188
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+I 189 4335 * * * 4851 * * 912 6272 2902 3324 * * 6037 * * 5524 3309 * * 189
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+Q 191 3969 5162 3086 3423 * 6194 4254 6318 3339 3536 5085 4829 * 3563 3670 2355 * 6614 * * 191
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+L 192 5339 * * * 3255 * 4765 3886 5118 767 4886 * * * 6356 6513 4402 4947 * 6257 192
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+I 193 * 2410 * * 4113 * * 1441 * 2453 6348 * * 6002 * 6235 6289 2987 * 5430 193
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+A 194 3043 * 4672 4608 * 3831 6443 3984 3613 6724 6302 5031 6209 3797 2702 3293 3890 3369 * 6191 194
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+
+G 195 3456 * 2621 2725 4917 2769 5031 6005 5223 6376 * 6065 * 3468 4928 3193 4200 * * 5145 195
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+Y 196 * * * * 3987 * 5137 * * 4047 * 4543 * 4182 5931 4898 5781 4777 6204 662 196
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+I 197 5805 4692 * * 4868 5869 2386 1927 5666 3847 3199 * * 5163 5900 3975 4935 3951 5758 5994 197
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+D 198 3805 * 3798 2837 4429 4680 4539 5604 3586 * 5696 3208 * 3259 3640 3956 3454 * * 5928 198
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+
+I 200 * * * * 3834 * * 1803 * 2141 3005 * * * * * * 2868 * 2688 200
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+L 201 * * * * * * * 2727 * 856 * * * * * 2712 * 2799 * * 201
+ 0 * * 0 * * * 3966 0 0
+
+//
+�HHsearch 1.5
+NAME 75f1ddc04ebf9d5bc247ed264936c742
+FAM
+FILE 75f1ddc04ebf9d5bc247ed264936c742
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 11:56:49 2013
+LENG 168 match states, 168 columns in multiple alignment
+FILT 142 out of 811 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCEEEEECCCCHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCEEEEEEEECCCCCCCCCCHHHHHCCHHHHHHHHHHCC
+CCEEEECCHHHHHHHHCCCCCCCCCCCCCCCCCEEEEECCCCHHHHCCHHHHHHHHHHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9887569999899996799987885696246870169999997499965589889966887798988774347876121777777422888999999759
+98999849899998836666402665443488308995689957717999999999999998653379
+>Consensus
+xxppxxxxxxxvLilGxxPxxxsxxxgxyYxxxxNxFWxiLxxxglxxxxxxxxxxxxLxxxxixlxdvvxRxxxxxxxxxxxexxxxxxxlxxxixxxx
+pkxIxxxGxxaxxxxxgxxkxxxgxxxxxxxxxxxxvlPStSpaxxxxxxxkxxxwxxlxxxxxxxxx
+>75f1ddc04ebf9d5bc247ed264936c742
+MVEDILAPGLRVVFCGINPGLSSAGTGFPFAHPANRFWKVIYQAGFTDRQLKPQEAQHLLDYRCGVTKLVDRPTVQANEVSKQELHAGGRKLIEKIEDYQ
+PQALAILGKQAYEQGFSQRGAQWGKQTLTIGSTQIWVLPNPSGLSRVSLEKLVEAYRELDQALVVRGR
+>gi|294951287|ref|XP_002786911.1| conserved hypothetical protein [Perkinsus marinus ATCC 50983]gi|239901489|gb|EER18707.1| conserved hypothetical protein [Perkinsus marinus ATCC 50983]
+-FPPSIGDSPRVLILGSAPCEMSLEKGQFYGNPRNHFWAVMAYAmdDPTfPMLDFEARCSVLHSRGIALWNICdvfTRYKSSDATLHCEEYT----DIAG
+LLVEHpTIGYILCNGSASYDCMLKydlaaRLEVSTGLQPTPLSlatqargaaqavDLPvILKLPSTSPANAMadPVGTKGKVWKEKlQEAL-----
+>gi|326565388|gb|EGE15565.1| G:T/U mismatch-specific DNA glycosylase [Moraxella catarrhalis 103P14B1]
+-LPPFTPPNACVMMLGSFPPPPERwAMPFYYPNYNNDMWRILGLVFFDDAKrfidstnktFDQDAiEQFLTKTGIAIGDTAEqviRQKDNASDQFLQIVT
+P--ADIEKTLKQLpRCHAFITTGKKATEVLCqqfTSQKiPNIGEQVQlLIAnrRIDLYRLPSSSRAYPLAIDKKADFYRKVFETLGV---
+>gi|307106992|gb|EFN55236.1| hypothetical protein CHLNCDRAFT_134530 [Chlorella variabilis]
+-----GDAPLRLVIVGHNPSEHAWASSHFYSNPTNWFWRILRDTGIAPPAAisGAADDGKMPAvAGVGFTDVGSgAPGTDSSQFTAQDFEAWRPAFYQRM
+ATqarrasaaigctcgaCgAPCIVAFSGKRQFQELFaGaagggrgRskgaavaqaapaaagaagpplgegavaaaaapqqqqqqraptlqarrpRRVDTG
+RQwvlPEGWplpLDTEVWVMTSTSGAAPMTRQQRLAPWQALAERL-----
+>gi|325474169|gb|EGC77357.1| hypothetical protein HMPREF9353_01707 [Treponema denticola F0402]
+---AYVLENTNTLILGTFPGKKFTdpnkendKEDWYYGTDRNEFWALIEYAlGCKRNSlqTKNEKQKFLTEHKIGITDIIKKARRrqnnnLDINLNVIEI
+T----NLDFIIDKCkDIHTIILTSKDMYTRFFIpyyVKKYNaiFKedknKEPEtheekgkkiniyyyTFKGRPIRVVPLHSPARKNvSIKIKKALYKY--
+--------
+>gi|296444847|ref|ZP_06886809.1| Uracil-DNA glycosylase superfamily [Methylosinus trichosporium OB3b]gi|296257515|gb|EFH04580.1| Uracil-DNA glycosylase superfamily [Methylosinus trichosporium OB3b]
+------APGAPLMVLDFAPGEEDERSGEAFVGAEARLLDkMLKAIGQKR-------------ESAYLAYATPwRP-PGARELNAGEVTALQPFLRRHVEL
+AAPKILLILGDYAARAALGATDvakLRGQWFDYDAGASRPRALLASSLDNLLkTPALKRRAWRDLRA-------
+>gi|323452034|gb|EGB07909.1| hypothetical protein AURANDRAFT_64500 [Aureococcus anophagefferens]
+----------HTLILSTSSCSTDTFAGEYYARVDNAFWYIAGLRlGLTPERTmlgklnpannktahkipsnyaaafveehpkadYAQQCAALTGAGFGLW
+TVLSRCSVpdGHDKITAANSE--ANAIRALCEERGVtRVVLAEGTKCEQAFalFnedwlksglltlgpmdrlpggparfKQKKFDAVRGGAAAGGVELTV
+CISTQNAVKGLYADKRADWMR----------
+>gi|148269551|ref|YP_001244011.1| phage SPO1 DNA polymerase-like protein [Thermotoga petrophila RKU-1]gi|170288227|ref|YP_001738465.1| phage SPO1 DNA polymerase-like protein [Thermotoga sp. RQ2]gi|281411730|ref|YP_003345809.1| phage SPO1 DNA polymerase-related protein [Thermotoga naphthophila RKU-10]gi|147735095|gb|ABQ46435.1| phage SPO1 DNA polymerase-related protein [Thermotoga petrophila RKU-1]gi|170175730|gb|ACB08782.1| phage SPO1 DNA polymerase-related protein [Thermotoga sp. RQ2]gi|281372833|gb|ADA66395.1| phage SPO1 DNA polymerase-related protein [Thermotoga naphthophila RKU-10]
+------NLDTRIVFVGEGPGEEEDKTGRPFVGRAGMLLTELLrESGIRRE-------------DVYICNVVKCRPPNNRTPTPEEQAACGHFLLAQIEII
+NPDVIVALGATALSFLMdGKK-VSITKIRGNpIDwLAGKKVIPTFHPSYLLrNRsnELRKIVLEDIE--------
+>gi|255321596|ref|ZP_05362754.1| uracil-DNA glycosylase family protein [Campylobacter showae RM3277]gi|255301452|gb|EET80711.1| uracil-DNA glycosylase family protein [Campylobacter showae RM3277]
+------DKSAKVVFVFDAPNTAEDASGEFLAGDD-KFLqNLNELAGLKK-------------DEIYVTSLLKcK-P-AAKVPTNA-YELCEPYFSAEARL
+VAPKLIVALGEEVFYKMiKQSAqSFEtiRG-NI--MKFKHSALLATYSPTVVAkNPSKKELFFSDL---------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * 1908 2810 2772 1170 * * * * * * * * * 1
+ 0 * * * * * * 3012 0 0
+
+V 2 * * * * 1498 * * 5175 * 1128 5891 * * * * * * 2799 * * 2
+ 0 * * * * * * 6114 0 0
+
+E 3 4399 6435 3218 3207 6684 5510 6245 * 3571 * * 5020 943 * 6682 4806 * * * * 3
+ 44 5044 * 1093 913 * * 6711 1134 0
+
+D 4 4043 * 1727 * 6774 4649 * * * * * * 915 6362 * * 5388 * * 5509 4
+ 0 * * * * * * 6677 0 0
+
+I 5 6415 * * 6657 2913 * 5144 1692 * 2840 5318 5132 * * 5566 5721 * 2545 6446 3447 5
+ 0 * * * * * * 6732 0 0
+
+L 6 5928 6961 * 5980 3940 4271 7019 2121 * 1646 * * * * * 6745 5044 2618 5916 3911 6
+ 0 * * * * * * 6833 0 0
+
+A 7 3392 5974 2069 4960 5016 4962 5628 * 4542 5396 * 2724 2748 5727 4552 3574 6194 6787 * * 7
+ 23 5991 * 1000 1000 * * 7639 1048 0
+
+P 8 3552 * 4235 2532 * 5259 4374 * 2904 4524 * 5914 2392 4944 4093 3601 6327 5464 * 5534 8
+ 0 * * * * * * 7724 0 0
+
+G 9 7112 * 2409 3039 * 2854 4408 * 3978 * * 2121 4896 5636 4084 3861 5470 * * * 9
+ 0 * * * * * * 7724 0 0
+
+L 10 1763 4642 * * * * * 6000 * 2009 6711 * 3554 * * 2256 3572 6251 * * 10
+ 0 * * * * * * 7725 0 0
+
+R 11 5135 5852 2858 3893 * 7577 5063 6034 2199 5944 * 4717 5054 7271 1871 4720 4311 7144 7143 6142 11
+ 0 * * * * * * 7787 0 0
+
+V 12 4388 7221 * * * * 7359 1726 5640 2203 * * * * * 6738 4529 1527 * * 12
+ 0 * * * * * * 7787 0 0
+
+V 13 5231 * * * 5144 * * 4288 * 710 2708 * * * * * * 3052 6788 * 13
+ 0 * * * * * * 7787 0 0
+
+F 14 * * * * 1777 * * 1072 * 3097 4665 * * * * * * 3711 * * 14
+ 0 * * * * * * 7787 0 0
+
+C 15 * 3744 * * 7318 * * 2672 * 1143 6631 * * * * * 7023 1778 * * 15
+ 0 * * * * * * 7787 0 0
+
+G 16 5272 * 4647 6475 6529 188 * * * * * * * * * 5414 6558 * * * 16
+ 0 * * * * * * 7787 0 0
+
+I 17 7390 * 4632 2983 4287 * 4795 3143 6163 4054 * 5396 * * * 1978 2021 * * 5126 17
+ 0 * * * * * * 7787 0 0
+
+N 18 2383 * 4826 * 2257 6230 6490 5464 5898 3544 3101 2142 * 6902 * 5006 5246 * * 7597 18
+ 16 6486 * 3170 170 * * 7787 1027 0
+
+P 19 5270 * * * * * * * * * * * 104 * * 5252 * 5855 * * 19
+ 0 * * * * * * 7787 0 0
+
+G 20 4727 5581 5584 5458 * 1259 6433 * 6321 * * 6529 3899 * * 1477 6738 6735 * * 20
+ 0 * * * * * * 7787 0 0
+
+L 21 4007 * 4900 3149 5062 5284 7195 3848 3955 2922 6760 6479 3117 5488 4162 5449 3460 2963 * 7075 21
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+R 157 4428 6501 4824 4651 * 6022 4998 5408 2615 4803 5437 3339 * 3124 2069 3728 6270 5491 6313 * 157
+ 28 5720 * 434 1944 * * 7623 1110 0
+
+E 158 3415 * 1904 2380 7188 5461 6201 4986 3345 6083 * 6779 6335 3705 4388 5078 6144 4372 7009 6240 158
+ 19 6286 * 1748 510 * * 7610 1086 0
+
+L 159 3580 * * 7022 3374 6834 * 2750 5201 1051 4346 * * 7057 6945 * 6120 4269 * 6168 159
+ 18 6351 * 1680 540 * * 7528 1207 0
+
+D 160 2643 6993 5644 6315 3438 4923 6632 4400 2688 2181 5957 * * 3295 3840 6363 6024 6954 6638 7031 160
+ 21 6136 * 1585 585 * * 7153 1000 0
+
+Q 161 3919 * 3615 1902 6038 4273 * 5974 3022 5997 * 4127 4129 3307 4327 4260 4451 * * * 161
+ 145 3389 * 2407 301 * * 6538 1225 0
+
+A 162 1940 * 5135 * 2874 4422 5069 3680 4003 3637 5271 * 5613 5347 4132 * 3486 * * 4059 162
+ 0 * * * * * * 5804 0 0
+
+L 163 2632 5345 * * 4222 * * 4076 * 985 4765 * * * * 4908 * 2990 * * 163
+ 0 * * * * * * 5540 0 0
+
+V 164 * * 4479 3311 * 1513 * * 4169 4084 4424 * * 4129 3307 2925 * 4234 * * 164
+ 126 3577 * 0 * * * 4631 1000 0
+
+V 165 3185 * * * * 3367 * 2477 * 2523 * 4195 * * * * * 1377 * * 165
+ 0 * * * * * * 3685 0 0
+
+R 166 * * * * * * * * * * * * * * 1000 1000 * * * * 166
+ 0 * * * * * * 1475 0 0
+
+G 167 * * * * * 0 * * * * * * * * * * * * * * 167
+ 0 * * * * * * 1475 0 0
+
+R 168 * * * * * * * * * * * * * * 0 * * * * * 168
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 79b1bbcf6f43d0235bc61bef7593bdbe
+FAM
+FILE 79b1bbcf6f43d0235bc61bef7593bdbe
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:20:58 2013
+LENG 178 match states, 178 columns in multiple alignment
+FILT 116 out of 250 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHH
+HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9730599999999999999983677777788999997319999999999999998299999999852889874899999999997379998999999999
+999999999984885689999999999999989999998798989999969971889999899998886431023578
+>Consensus
+xxxxxxxxtxxLxxdYIxyrlxxxgxxxxxxxxxxpxxxxxxxxLrxxgdelexxxxxxfxxxxxxLxitxxxxxxxFxxVaxelFxdginWGRIvaLxx
+FxgxLaxxxxxxxxxxxvxxIxxwxxxylxexlxxWIxxxGGWxxxxxxfxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+>79b1bbcf6f43d0235bc61bef7593bdbe
+ATPASAPDTRALVADFVGYKLRQKGYVCGAGPGEGPAADPLHQAMRAAGDEFETRFRRTFSDLAAQLHVTPGSAQQRFTQVSDELFQGGPNWGRLVAFFV
+FGAALCAESVNKEMEVLVGQVQEWMVAYLETRLADWIHSSGGWAEFTALYGDGALEEARRLREGNWASVRLEHHHHHH
+>gi|30851239|gb|AAH52690.1| Bcl2l10 protein [Mus musculus]
+-------RTRRLLSDYIFFCAREPD------TPEPPPTSVEAALLRSVTRQIQQEHQEFFSSFCE----S--rgNRLELVKQMADKLLSkdQDFSWSQLV
+MLLAFAGTLMNQGPymavkq----krdlgnrvi---VTRDCCLIVNFLYNLLMgrrhrARLEALG--gwDGFCRFFK-----------------------
+----
+>gi|312377925|gb|EFR24635.1| hypothetical protein AND_10635 [Anopheles darlingi]
+----VIQQGKRLCGEYIRARLKRSGLLNRkilqrlrnsivpdgasAGIgsvGGgsgmmliagggGAVVREAFPILHGMGIELERMHPRLYTNVSRQISne
+pwgelTEPDTVGYLLHIVAKDLFKTGVTWGKVISLFAIVGGLAVDCVRQDHTDYLQQLIEGTTDVIEEDLAGWLVERGGWLGLQDHVYPQPAEITLTGWL
+TIT------------
+>gi|47213719|emb|CAF95150.1| unnamed protein product [Tetraodon nigroviridis]
+-----DSDTRQLVSRLMADVTGISRAQWR-------ESR-ALATTKRVVGDLMEKHRYTYRGMINKLFMEDRVgDVSFVGAVAKSTFEDGNtNWGRVASL
+LAFAAVVAQYLNDHGQRDCVEQVAQEISTYLLTDQRDWLIKNNAWDGFVEFFQVPDPESTVRT-----------------
+>gi|9188120|emb|CAB97205.1| BHP1 protein [Suberites domuncula]
+-------QSACLSYHLTYYLLNQGGIKLNGYAGNGRTShtrnrltndkkfREAISTLESSCKQMKSKYQQEIEGLVKTLDISDTQLYTNFQHAANSLMDG
+DIRWGRIAVLFFFTSVLAKRLHKDGHSHQISSLIGWLTTFLNDNATSWILENGGWAAIKDSV----------------------------
+>gi|125812975|ref|XP_001343654.1| PREDICTED: apoptosis regulator BAX-like [Danio rerio]
+----------------------------------DPSHKDAIECMVRIANEMEGNE--ELQGMLNSALLNPT--LEHYILVVNGTFSDVtLSWGSVVALF
+YVACRFVVKAAEINSVDLVRSIINWTMPFIRKtCILTWIREQGGWGAIRSYFGTPT------------------------
+>gi|308497734|ref|XP_003111054.1| CRE-CED-9 protein [Caenorhabditis remanei]gi|308242934|gb|EFO86886.1| CRE-CED-9 protein [Caenorhabditis remanei]
+----------GFVVrnlkkyfripkflkaDYFTYRIEQSGLDWYDAPALPDGVQDEFKMMRSLATIFEKKHTEELENCSEQLLAVPKLTFHLYQEVAKFF
+DRsigpghCSMSYGHLIGLISFGGMVAAKMMGTaELQGQVRNLLLYTSLFIKTRIRqCWKEHDRSWAGFMAL----------------------------
+-
+>gi|194382608|dbj|BAG64474.1| unnamed protein product [Homo sapiens]
+---QVAQDTEEVFRSYVFYRHQQEQEAEGVAAPADPemvtlplqPSStmgQVGRQLAIIGDDINRRYDSEFQTMLQHLQPTAENAYEYFTKIATRYP---
+-----------------------------------------------------------------------------------------
+>gi|311256133|ref|XP_003126516.1| PREDICTED: apoptosis facilitator Bcl-2-like protein 14-like [Sus scrofa]
+----------------------------------------IVELLKYSGDQLERELKKDSILMTS---FQDGLSYSVFKTITDQFLRGVDTRGEsEVKAQ
+SFKAALAIDAMAKLTtiDnHPMNRVLGFGTKYLKENFSPWVQQHGGWEKVLG------------------------------
+>gi|4590358|gb|AAD26543.1|AF120456_1 Bcl-2 homolog [Papiine herpesvirus 1]gi|9802029|gb|AAF99596.1| BHRF1 [Papiine herpesvirus 1]
+----------------------------------------------ALLEQIIVQNEDAFAETLDRFLLNTEDLDLDFSRVFAEIFHnEDPTLGRGLAWL
+AWCMHACRTlCGDTNCPYYVVDLAvRGMLE-ASEGLDGWIGQH-gGWPAVLR------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 0 * * * * * * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+T 2 * * * * * * * * * * * * * * * * 0 * * * 2
+ 0 * * * * * * 1000 0 0
+
+P 3 * * * * * * * * * * * * 0 * * * * * * * 3
+ 0 * * * * * * 1748 0 0
+
+A 4 1804 * * * * * * * * * * * * 487 * * * * * * 4
+ 0 * * * * * * 2527 0 0
+
+S 5 * * * * * * * 2419 * * * * * * * 2421 * 675 * * 5
+ 0 * * * * * * 3325 0 0
+
+A 6 1494 * 2856 * * 3049 * 2848 * * * * * * * * 3236 2827 * * 6
+ 0 * * * * * * 3981 0 0
+
+P 7 * * 3598 2027 * * 4331 4131 * * 4187 * 4803 2683 4142 3322 * * 4229 3198 7
+ 0 * * * * * * 5598 0 0
+
+D 8 * * 2305 2723 * * 5157 * * * * * * 1312 3785 3928 4608 * * 4785 8
+ 0 * * * * * * 5977 0 0
+
+T 9 3032 * * * 5826 3002 * 4028 * * * 3708 * * * 2789 1383 4429 * 5450 9
+ 0 * * * * * * 6621 0 0
+
+R 10 3260 5442 * 2840 5427 * * * 2795 5460 * 5907 * 4188 1469 5553 4391 * * 4606 10
+ 0 * * * * * * 6740 0 0
+
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+
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+ 0 * * * * * * 6821 0 0
+
+V 13 2261 2640 * * 4305 5728 * 4790 * 2921 * * * * * 5381 5895 1621 * 5193 13
+ 0 * * * * * * 6821 0 0
+
+A 14 4210 5934 5780 2587 * 4121 * 5712 3313 4547 4216 4084 * 4172 3227 4467 3670 3862 * 4123 14
+ 30 5583 * 3907 100 * * 6874 1004 0
+
+D 15 * * 725 3699 4961 * 4540 * 5131 * * 5284 * 4103 5485 3910 5448 * * 5747 15
+ 0 * * * * * * 6874 0 0
+
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+ 0 * * * * * * 6874 0 0
+
+V 17 * * * * 3548 * * 967 * 2444 5485 * * * * 5747 4968 2773 * * 17
+ 0 * * * * * * 6874 0 0
+
+G 18 4543 5566 3766 4088 4032 4310 4249 * 4727 4184 * 4228 5747 3097 2822 3398 4068 4695 * 5419 18
+ 124 * 3605 * * * * 6874 0 0
+
+Y 19 4667 * 4385 3900 3566 4787 3394 * 5968 5367 * * * * * 4652 5257 * 6035 975 19
+ 0 * * * * 1808 485 6771 0 1269
+
+K 20 * 4008 * 5207 * * 5669 * 1910 4385 * * * 3861 1312 * * 3244 * * 20
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+
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+
+R 22 4375 * * 4320 5521 3076 5617 * 3255 5843 * 4186 * 2551 1859 3335 5757 * * * 22
+ 0 * * * * * 0 6835 0 1242
+
+Q 23 5687 * 5394 3577 * 5521 5597 4306 2461 3885 * 5872 * 1944 2475 4252 5553 * * * 23
+ 53 5617 6017 2000 415 * 0 6835 1000 1242
+
+K 24 * * 3918 2693 * 4707 5180 * 3612 * * 3163 3206 4406 3151 1990 * * * * 24
+ 127 * 3572 * * * 0 6812 0 1293
+
+G 25 5223 * 5677 * 5736 961 * 4504 5528 * * 2993 7511 5285 3285 4482 5126 5466 * * 25
+ 220 5223 3124 0 * * 0 6752 1000 1561
+
+Y 26 5013 * 5391 4060 3275 * 6031 2714 * 1772 4153 4922 * * 5236 5284 5188 5207 * 2993 26
+ 194 3337 5207 1663 547 1497 631 6530 1223 1933
+
+V 27 3762 6103 5361 3149 4175 4335 3765 4264 3855 3134 * * 4483 3463 4255 4380 4403 3679 * * 27
+ 70 5494 5308 1585 585 3862 103 6659 1003 1664
+
+C 28 7495 2235 5384 3749 * 6651 4259 4415 5089 3598 * 3915 * 5168 3341 5708 4751 5015 2452 * 28
+ 117 5426 4199 4322 74 * 0 6622 1000 1687
+
+G 29 3250 6200 4205 4600 5395 2432 * * 4609 * * 5062 3848 * 2520 3203 4425 4091 * 4375 29
+ 683 3318 1853 3499 134 * 0 6517 1351 1857
+
+A 30 2744 5497 3916 4130 * 2261 * 4827 2972 5126 * * * * 3980 * 3240 3265 * 4967 30
+ 181 3081 * 3692 116 1426 672 5933 1199 2615
+
+G 31 3699 4246 4186 3889 5816 2607 * * 3957 3548 6035 * 5603 4437 3725 3329 4234 5472 5688 3968 31
+ 153 4408 4231 2003 414 964 1037 6544 1056 2027
+
+P 32 3379 * 6170 3483 * 6269 5713 4669 6026 5589 * 3014 1677 * 5478 4881 2769 4228 * * 32
+ 148 4438 4291 1074 930 1870 461 6812 1184 1681
+
+G 33 3467 * 4228 6280 * 2536 * * 3407 4120 5960 * 2519 4793 3596 4052 5445 3660 5556 5250 33
+ 193 3467 4856 4118 86 1594 580 6856 1239 1648
+
+E 34 3472 5913 5336 2909 5200 4155 * 6027 5949 2427 5238 4750 4180 3270 4782 4517 3558 * 5233 5602 34
+ 342 2898 3705 2589 262 1644 556 6930 1560 1580
+
+G 35 4190 3930 2462 4665 * 2295 * 4882 5879 3786 * 5723 3035 5634 5732 3757 5127 5412 * 5295 35
+ 86 4694 5682 2398 303 1322 737 6913 1078 1676
+
+P 36 4135 * 5447 4756 * * 6046 6197 * 4566 5662 4380 749 5689 4629 3742 * 6065 * * 36
+ 149 5015 3896 2655 249 901 1106 6910 1192 1479
+
+A 37 2490 * 5250 3798 5803 3819 * * 4787 6083 * 4855 2466 4431 4179 3580 3325 3580 * * 37
+ 96 4581 5476 1803 487 2631 254 6948 1147 1428
+
+A 38 3450 5825 4302 4893 * * 4899 3580 5124 6365 6421 5806 2769 3719 5684 2502 3188 3463 * * 38
+ 158 3660 5351 2676 245 1355 715 6805 1325 1420
+
+D 39 6188 * 3920 3828 * * 4929 5993 3444 * * 3393 5977 3514 2722 2296 3126 4607 * * 39
+ 121 4975 4355 1032 968 3140 174 6891 1209 1317
+
+P 40 2751 4862 3793 2723 * 5784 * 6391 2648 * * 5947 2213 6763 3452 6270 4663 5721 * * 40
+ 95 3967 * 1823 479 796 1238 6936 1215 1501
+
+L 41 2610 * * 3494 * * 6299 3327 6527 2356 * 5316 6556 * 5357 4424 4028 1938 * * 41
+ 31 * 5557 2484 284 507 1755 7116 1032 1176
+
+H 42 1796 * * * 4203 4342 4033 4313 5548 3672 * 4728 5681 5345 * 2760 6830 3027 * 4787 42
+ 80 4657 6143 1787 493 1265 776 7117 1158 1105
+
+Q 43 2675 5704 5514 2541 7073 5171 5348 6165 4812 3968 * 4715 4028 3767 2805 4012 5497 4503 * 6249 43
+ 0 * * * * 779 1262 7211 0 1105
+
+A 44 3320 3966 6386 3646 * 6295 6008 5609 4837 3338 3869 4590 * 5660 4602 4037 2218 3125 * * 44
+ 39 5216 * 3122 176 0 * 7224 1127 1003
+
+M 45 * * * * * * * 3760 * 568 2842 * * * * * 6224 3546 * 6261 45
+ 0 * * * * * * 7231 0 0
+
+R 46 3269 * 5216 6487 5106 5392 4566 5047 3376 3918 5598 * * 4607 1044 6296 * 6489 * * 46
+ 0 * * * * * * 7227 0 0
+
+A 47 3937 5479 5256 3823 5665 5510 4113 4895 2890 6203 7275 4917 * 3674 2275 3320 4482 5119 6651 5274 47
+ 28 5720 * 1803 487 * * 7366 1043 0
+
+A 48 3025 6304 * * 6817 * 5910 2283 * 1954 4218 6260 * 6477 * 4230 5576 2163 * * 48
+ 0 * * * * * 0 7363 0 1000
+
+G 49 2167 3760 * * * 1267 5921 * 6189 5022 * * * 6413 * 3550 5462 3221 * * 49
+ 20 6190 * 1000 1000 * 0 7364 1000 1000
+
+D 50 3807 * 1316 4121 * 3932 * 6675 6574 4226 * 3501 * 4652 4847 3693 4024 5993 * 6276 50
+ 0 * * * * * 0 7376 0 1000
+
+E 51 5288 * 2912 1017 * 4656 * 3590 7168 5911 * 6583 * 2906 5407 5357 6729 * * * 51
+ 18 6319 * 0 * 0 * 7376 1006 1000
+
+F 52 5329 * * * 2459 * * 2399 * 1184 3606 * * * * * 6206 4123 * 6579 52
+ 0 * * * * * * 7389 0 0
+
+E 53 * * 3438 1126 6622 * * 4253 5453 3084 5299 4283 * 3674 5311 4938 * 4908 * * 53
+ 0 * * * * * * 7389 0 0
+
+T 54 3982 6868 3915 2658 * 4893 * 4917 3124 5934 6532 4829 6328 3248 2272 3599 5174 5341 * * 54
+ 40 * 5203 * * * * 7389 0 0
+
+R 55 3567 5863 5217 4294 * * * 5041 1904 4178 3330 3594 * 4053 2419 5254 6375 * * * 55
+ 89 4587 5757 1889 454 * 0 7372 1193 1089
+
+F 56 * 6293 6168 4424 3470 5928 1893 6325 * 3849 6138 3626 * 5449 4813 6194 6498 6771 * 1829 56
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+
+R 57 4589 * 4186 2731 * 4705 6715 6653 3405 * * 6067 2423 3338 2627 3191 5106 * * * 57
+ 26 6563 7157 1585 585 1190 832 7322 1000 1114
+
+R 58 4368 * 3001 3163 6649 4326 3895 3433 4455 4876 * 5342 3577 3782 2963 4678 5469 * * 4485 58
+ 16 6480 * 1000 1000 428 1961 7404 1000 1069
+
+T 59 3432 6505 4931 2659 2734 * 5395 5553 5543 2416 5948 6368 5574 4824 4987 4901 3260 4405 * * 59
+ 50 4873 * 725 1340 0 * 7441 1115 1000
+
+F 60 6558 6577 * 6331 1102 * * 3685 6300 2290 6477 * * * 6631 6350 * 4910 * 2848 60
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+
+S 61 3690 7493 3864 2899 * 5205 4796 5433 3866 5642 * 3128 5405 3343 2644 3491 4463 6891 * * 61
+ 13 * 6793 * * * 0 7439 0 1000
+
+D 62 5896 6200 2625 3911 * 3263 4227 6448 4717 4317 * 2672 5531 4453 3124 3238 4684 * * * 62
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+
+L 63 4450 4398 5725 * 4318 5905 * 3176 * 2237 1803 * * * 6420 6236 5035 3126 5138 6225 63
+ 30 * 5618 * * 940 1062 7439 0 1032
+
+A 64 2901 2884 4596 5682 6846 4776 * 3299 * 2885 5949 * 4696 6265 4809 2683 4942 3644 5970 * 64
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+
+A 65 5087 * 3374 2790 * 6864 4773 * 3162 4977 * 2707 5428 3296 2956 3613 5086 5458 * * 65
+ 208 4337 3563 1807 486 * 0 7359 1250 1230
+
+Q 66 5037 * 4755 4171 * 5314 4213 5185 3347 5113 4244 5715 * 2093 2638 3433 4749 4914 * 6216 66
+ 109 4098 6126 241 2698 3807 107 7187 1197 1875
+
+L 67 5245 * * * 3700 * * 3248 * 791 4068 * * 5960 5872 * 6355 3872 5500 5785 67
+ 65 5374 5660 3809 107 2371 310 7199 1069 1853
+
+H 68 5779 6019 2187 3998 6423 3458 3885 5695 5561 3608 * 2738 4590 3801 5706 4118 4986 5655 * * 68
+ 102 4708 5046 2398 304 1732 517 7189 1207 1821
+
+V 69 4461 7014 5782 6042 4186 4392 * 1884 5846 2359 5072 * 4857 * 4565 6742 5100 2632 * 5553 69
+ 104 4376 5548 919 1086 653 1457 7231 1406 1689
+
+T 70 5022 6183 3392 3864 * 6502 5899 * 5907 * * 3160 6695 4412 5288 2332 1781 4295 * 6331 70
+ 71 6509 4760 0 * 539 1682 7315 1000 1337
+
+P 71 4024 * 3606 3242 6784 5883 7363 6869 3770 4185 * 5890 1734 5763 4155 4071 3696 4561 * 6544 71
+ 72 5425 5284 1938 436 2650 250 7328 1154 1320
+
+G 72 4995 6467 2273 2543 7131 3453 4939 7157 5340 4973 6368 4797 5335 5503 3590 3125 3665 * * 6286 72
+ 80 5331 5119 1633 561 843 1176 7316 1121 1391
+
+S 73 3874 5593 4046 6892 5364 6766 5041 4710 4655 3741 5844 2598 6639 5236 6041 3151 2137 4283 * * 73
+ 63 5036 6370 672 1424 2296 328 7348 1174 1300
+
+A 74 1673 6470 4444 3956 * 4974 * 4887 5962 3660 * 5068 3907 * 5242 3552 3630 3120 * * 74
+ 131 3529 * 1107 900 0 * 7342 1487 1310
+
+Q 75 6346 3795 4672 4667 3797 4109 4277 5215 3981 3553 6486 * 7182 3588 3813 5792 6818 4282 6617 2189 75
+ 15 6563 * 2322 322 * * 7427 1000 0
+
+Q 76 4949 * 3395 2278 * 4597 5817 5603 4074 5079 * 7455 4021 3447 3504 2600 4014 6011 * 6895 76
+ 82 5758 4776 611 1535 * * 7427 1105 0
+
+R 77 3511 * 4489 5528 4364 * 5735 4606 4311 3204 4786 4558 * 5631 4149 3943 2401 2740 * 5677 77
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+
+F 78 6264 6777 * * 668 * * 4471 * 3292 6661 * * * * * * 3783 * 3073 78
+ 16 6529 * 0 * * 0 7392 1000 1173
+
+T 79 4164 * * 5366 4082 4609 5331 4170 3315 3381 4594 3752 * 3485 4807 3255 3782 3673 5818 5117 79
+ 0 * * * * 0 * 7445 0 1173
+
+Q 80 3223 7006 4229 2998 * 3594 6963 4977 4077 6894 * 4001 * 3561 3227 3025 3062 6454 * 6870 80
+ 15 6636 * 0 * * * 7595 1000 0
+
+V 81 5598 7001 * * 5163 6068 * 1972 * 3490 4267 * * * * 6877 5138 1011 * * 81
+ 0 * * * * * * 7595 0 0
+
+S 82 1322 4973 * 6663 4849 4027 * 6618 * 3560 3484 * * 7023 6639 4530 4284 2691 6553 * 82
+ 0 * * * * * * 7595 0 0
+
+D 83 4573 * 2488 2798 * 4870 5166 6037 3498 5411 5992 3405 * 3744 2936 4652 3782 6869 * 6609 83
+ 15 * 6622 * * * * 7595 0 0
+
+E 84 4997 * 4682 1347 6412 4397 5087 * 3953 6309 * 4033 * 3243 3805 3467 5540 5588 * * 84
+ 0 * * * * 0 * 7584 0 1000
+
+L 85 * * * 6787 4054 * 6162 2319 6761 1450 3226 6112 * * * * 4236 2612 * 8204 85
+ 0 * * * * * * 7594 0 0
+
+F 86 * * 5364 7273 632 5486 * 4750 * 2936 5940 6064 6124 * * * 5373 4214 6583 * 86
+ 96 3953 * 1476 643 * * 7594 1410 0
+
+Q 87 3724 6200 3999 2736 * 4447 4135 6905 3679 6305 6306 4323 * 3803 2975 2423 4645 6893 * * 87
+ 311 2441 6638 1189 833 * * 7592 2101 0
+
+G 88 7440 5042 1127 4111 * 2610 * * 5296 6842 7090 3767 5201 5300 6287 4079 4475 * * * 88
+ 96 3955 * 3697 116 0 * 7588 1310 1000
+
+G 89 * 4905 4084 4313 * 1039 5647 * 4410 6600 * 3982 4880 4003 * 3949 6151 4184 * * 89
+ 387 2160 6457 829 1194 * * 7592 2460 0
+
+P 90 * 4784 5279 * 3730 * 6600 1517 4746 3075 4103 6782 3699 * * * 5472 2715 6800 5735 90
+ 57 4680 * 0 * 0 * 7548 1286 1062
+
+N 91 5580 * * * * 5179 5035 * 6865 6753 * 964 6103 6647 5143 2979 2326 6459 * * 91
+ 0 * * * * * * 7567 0 0
+
+W 92 * 5545 * * 6587 * * 6557 * 4901 * * 6459 * 4206 * * 5330 347 4392 92
+ 0 * * * * * * 7567 0 0
+
+G 93 4174 * * 4378 * 427 * * 6623 * * * 6575 * * 3359 6647 6695 * 6064 93
+ 16 6459 * 3170 170 * * 7567 1000 0
+
+R 94 6147 * * 5337 * * 4572 * 3241 6575 * * * 5390 439 5886 6103 6645 * * 94
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+
+L 95 4811 6066 * 5337 * 6299 * 1095 * 3201 * * * * * * * 1578 * * 95
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+
+V 96 2569 5801 * * * * * 2326 * 2749 6748 * * * * 6936 5608 1227 * * 96
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+
+A 97 1304 6615 * * 6647 3768 * 6861 5337 5379 5750 * * * * 2375 3384 2869 * * 97
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+ 59 * 4642 * * 0 * 7226 0 1000
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+ 0 * * * * 603 1549 7385 0 1145
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+//
+�HHsearch 1.5
+NAME 79cba631d7059d8c2467baa2b9e42370
+FAM
+FILE 79cba631d7059d8c2467baa2b9e42370
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:20:42 2013
+LENG 77 match states, 77 columns in multiple alignment
+FILT 173 out of 1097 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+98887776330133188985887888875552566377643210234446667135327778999866677888788
+>Consensus
+xxxxxxxxxxkxxlCxxxxxxgxCxxGxxCxfxHxxxxxxxxxxxxxxxxxxCxxfxxxGxCxxGxxCxfxHxxxex
+>79cba631d7059d8c2467baa2b9e42370
+GSHMTTSSRYKTELCRTYSESGRCRYGAKCQFAHGLGELRQANRHPKYKTELCHKFKLQGRCPYGSRCHFIHNPTED
+>gi|255724312|ref|XP_002547085.1| hypothetical protein CTRG_01391 [Candida tropicalis MYA-3404]gi|240134976|gb|EER34530.1| hypothetical protein CTRG_01391 [Candida tropicalis MYA-3404]
+--------KDTIKLCASLIDPedEsvVCSAgGaENCKFHHDVVSYL-ESKPEDIE-GVCPVFEAIGYCPSGIKCRWLKS----
+>gi|124088676|ref|XP_001347192.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|50057581|emb|CAH03565.1| hypothetical protein PTMB.368c [Paramecium tetraurelia]
+-----NEEKKKTEICKNFLFKGSCKYQENVQIIKisVHSPMETTNQeIEYLRMRTSKQSHArtiislelapmdqgVNTCTRKQRTR-LNGG---
+>gi|302851829|ref|XP_002957437.1| hypothetical protein VOLCADRAFT_98560 [Volvox carteri f. nagariensis]gi|300257241|gb|EFJ41492.1| hypothetical protein VOLCADRAFT_98560 [Volvox carteri f. nagariensis]
+----------AANTPQPIAGRPDVPRDpwktvvvKNVPWAAGEEEIA------GFFAQAGqvvnvwrgtnnrdgrvqafthVQFETREGAERALQlhnCD
+FngrqvfvePSTAGT-
+>gi|303286099|ref|XP_003062339.1| predicted protein [Micromonas pusilla CCMP1545]gi|226455856|gb|EEH53158.1| predicted protein [Micromonas pusilla CCMP1545]
+----------RARLAANIDRRP----------LQGDTDKT------VYVRNLG------------------------
+>gi|116192477|ref|XP_001222051.1| hypothetical protein CHGG_05956 [Chaetomium globosum CBS 148.51]gi|88181869|gb|EAQ89337.1| hypothetical protein CHGG_05956 [Chaetomium globosum CBS 148.51]
+-----------DLGAGQLTP------GFSGRQSGAVKK-----------VNMpCKQFSMTGNIISSTD----------
+>gi|322699105|gb|EFY90869.1| CCCH zinc finger protein [Metarhizium acridum CQMa 102]
+-----------LQPCKTFSTTGN-------RYFQMDRT-----------SALSK---RDSPETRGWLWVYTNDDT--
+>gi|61675708|ref|NP_035876.2| probable E3 ubiquitin-protein ligase makorin-3 [Mus musculus]gi|341940956|sp|Q60764.2|MKRN3_MOUSE RecName: Full=Probable E3 ubiquitin-protein ligase makorin-3; AltName: Full=Zinc finger protein 127gi|32452060|gb|AAH54771.1| Makorin, ring finger protein, 3 [Mus musculus]gi|74147940|dbj|BAE22320.1| unnamed protein product [Mus musculus]
+--------WTKQILCRYYL-HGQCKEGDNCRYSHDLSGRRR--------SRGGQ-DAQPRASADRGPKMATRWE---
+>gi|328856795|gb|EGG05915.1| hypothetical protein MELLADRAFT_29924 [Melampsora larici-populina 98AG31]
+--------LHAKTVCKHWL-RGLCKKGNSCEFLHEYNLRTMPecwffgkygfcsngdecmylHVDERMRVLEC-MDYRRGFCSKGPTCSQKHIR---
+>gi|156101764|ref|XP_001616575.1| hypothetical protein [Plasmodium vivax SaI-1]gi|148805449|gb|EDL46848.1| hypothetical protein, conserved [Plasmodium vivax]
+--SLIKKQFFKTKMCPFQKNKNYCLNESNCHYAHSIDELKPM--PDLRNTKLC-DYVKKKIPCRDENCKFAHDID--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 0 * * * * * * * * * * * * * * 1
+ 356 2195 * 3170 170 * * 2605 1106 0
+
+S 2 * * * * * * * * * * * * * * * 0 * * * * 2
+ 0 * * * * * * 3010 0 0
+
+H 3 2964 * * * * 3954 2336 * * 3214 * 3744 3164 * * 1665 * * * * 3
+ 0 * * * * * * 3825 0 0
+
+M 4 4662 3879 * 4256 * * * 4014 * * 2482 * 1308 3960 * 2931 * * * * 4
+ 0 * * * * * * 5118 0 0
+
+T 5 * * * 3975 4719 3900 4922 4857 * 4416 * 4457 2418 3868 4815 4679 2544 2557 * * 5
+ 0 * * * * * * 5846 0 0
+
+T 6 3800 * 4159 4102 4783 4213 * * 2969 * 5463 2392 * * 3137 3305 2801 * * 5359 6
+ 0 * * * * * * 6319 0 0
+
+S 7 6552 * 4636 3459 * 4742 3486 * 3382 4657 * 2461 2561 5925 5390 2582 5750 5718 * * 7
+ 15 6552 * 1000 1000 * * 6733 1106 0
+
+S 8 3050 * 5103 4041 4987 4669 6204 5340 4270 4404 6037 4068 3814 3712 3588 2437 5790 4152 * 5902 8
+ 0 * * 1000 1000 * * 7225 1000 0
+
+R 9 5830 * 4675 5087 3667 6747 4056 * 2128 4089 6632 3149 4638 6417 2470 4454 6667 * 4969 4808 9
+ 0 * * * * * * 7532 0 0
+
+Y 10 5448 * 4054 4966 3227 6800 5551 * 3726 3996 * 5854 3755 5675 3899 5181 4148 5778 5743 1686 10
+ 14 6731 * 0 * * * 7728 1000 0
+
+K 11 3951 * 5460 4120 6131 4128 7192 7126 1063 6909 * 5294 5881 5471 3340 3495 5417 * * 7208 11
+ 19 * 6260 * * * * 8082 0 0
+
+T 12 3673 * 5573 4228 * 5182 5998 4654 3338 4895 6004 5029 5223 3843 3667 3462 1936 4448 * 6310 12
+ 10 7229 * 0 * * 0 8237 1021 1124
+
+E 13 4625 * 5332 2966 * 4892 6540 4174 2808 4222 4596 4259 4033 3525 2845 * 3593 4415 * * 13
+ 0 * * * * 1631 563 8242 0 1216
+
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+ 9 7272 * 887 1123 0 * 8300 1090 1124
+
+C 15 5309 136 * * * * * 6606 * * * 7283 5958 * 6391 * * * 5637 * 15
+ 7 7732 * 2000 415 * * 8341 1000 0
+
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+ 0 * * * * * * 8341 0 0
+
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+ 0 * * 3585 126 * * 8341 1017 0
+
+Y 18 5843 * * * 1463 * 7124 3862 6861 3845 6216 6408 6248 7330 * * 6570 3753 3441 2033 18
+ 30 * 5614 * * * * 8341 0 0
+
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+ 610 7662 1557 2585 263 738 1320 8331 1000 1158
+
+E 20 4643 6729 4421 4700 4729 4326 7021 4791 3033 4251 6956 4849 5570 3461 2548 3352 2972 * * 6901 20
+ 213 3445 4462 2287 331 56 4726 8264 1609 4616
+
+S 21 4177 * 6350 4854 5716 3187 3358 6280 3102 6188 * 2983 4238 4438 3809 4238 2542 * * 7188 21
+ 33 5480 * 3305 154 1292 757 8256 1251 1527
+
+G 22 5924 * 4981 4061 7023 685 7291 * 3404 * * 5171 5109 6396 4181 5948 5552 * * * 22
+ 73 4542 7280 2506 279 2026 406 8267 1358 1287
+
+R 23 4773 5848 4679 3939 4364 3852 4311 4605 3515 4855 * 4296 5419 4730 3194 2933 4729 3887 7428 4403 23
+ 41 7193 5575 1585 585 * 0 8212 1000 1383
+
+C 24 * 117 6813 * * * * * * * * 6909 * * * * 5648 5204 6187 * 24
+ 0 * * * * * 0 8150 0 1623
+
+R 25 4051 * 5664 5088 5090 7227 5414 5310 2789 4494 6077 4247 2751 4309 2516 3714 3702 6040 * 7106 25
+ 0 * * * * 2816 221 8150 0 1623
+
+Y 26 4637 * 6029 4041 3009 * 4605 5893 3174 4260 5708 3577 * 5744 2832 6473 6408 5187 5674 2275 26
+ 78 6393 4608 0 * 1232 800 8145 1091 1528
+
+G 27 5298 * 4544 4981 * 409 * * 5309 * * 5053 * 5113 5103 5835 * 5963 * * 27
+ 36 5360 * 2401 303 745 1310 8208 1171 1771
+
+A 28 4323 * 1590 3035 4965 5366 6180 6403 4067 5739 6388 3761 4090 5816 6467 3082 6404 6286 * 5687 28
+ 8 7482 * 1000 1000 * 0 8225 1000 1277
+
+K 29 3025 * 3862 4470 * 5206 6300 * 2800 5051 6301 2522 * 3936 2744 3099 4979 * * * 29
+ 8 7444 * 0 * * 0 8225 1000 1277
+
+C 30 6447 146 * * * 5594 * * * * 5739 * * * 6835 * * 4777 * * 30
+ 0 * * * * 1101 906 8225 0 1277
+
+Q 31 5546 * 5151 4288 6607 5039 3881 5845 2409 4464 * 5147 3472 4284 2247 3849 3862 7554 6726 7277 31
+ 17 * 6447 * * * 0 8273 0 1116
+
+F 32 7267 7541 6995 * 870 * 7638 5909 6689 4832 * 7371 * 5835 * 6499 * 7918 4378 1838 32
+ 10 * 7119 * * 2027 406 8240 0 1308
+
+A 33 1871 6845 6391 4776 6265 6127 5344 4689 5362 3079 7188 5493 6994 5055 5355 1824 6607 5249 * 5278 33
+ 6 * 7962 * * * 0 8253 0 1303
+
+H 34 5847 * 6719 * * 6037 160 * 5908 * * 5591 * 5716 7331 * * * * * 34
+ 24 5908 * 1000 1000 * 0 8255 1088 1355
+
+G 35 4898 5721 2090 4367 * 2365 6662 5207 4692 6208 6263 3459 3968 5379 7431 3345 5048 4193 * * 35
+ 26 * 5796 * * * 0 8255 0 1355
+
+L 36 4792 6823 3848 2902 6112 5123 5666 3473 4048 2748 6983 * 3461 4728 4405 4537 5473 3256 6549 5318 36
+ 15 6588 * 2545 271 2389 306 8260 1119 1587
+
+G 37 4040 7376 3359 2427 5090 4990 5530 5952 3078 5643 6621 4820 4012 4195 4201 3304 4245 4569 * * 37
+ 36 5342 * 2276 334 2545 271 8254 1428 1464
+
+E 38 3267 8492 3539 1661 * 4019 6722 7120 3045 5927 6421 5675 3927 5802 5502 3675 5278 6054 6070 7926 38
+ 139 4233 4688 2386 306 * 0 8265 1497 1375
+
+L 39 4431 5217 5246 5389 3419 5700 5336 4130 5336 2632 3985 5401 5703 3742 3984 4208 4525 4829 7622 3133 39
+ 64 4897 6667 2416 299 * 0 8135 1385 1842
+
+R 40 4087 6925 * 4378 5350 7260 5688 4320 3251 2937 4132 5884 5748 4382 1937 4542 5192 4778 5294 6078 40
+ 227 4444 3324 2525 275 * 0 8128 1410 1966
+
+Q 41 3048 * 4865 4426 4396 5194 5522 6256 3148 5103 4789 3614 4042 4223 3823 2980 3747 5085 * 6234 41
+ 109 5449 4324 3134 174 3420 141 7888 1189 2945
+
+A 42 2637 7253 4751 3786 7436 6350 4561 3896 4262 4565 4843 4381 3538 4719 4874 3532 3200 4226 * 6447 42
+ 567 2806 2459 3466 137 4169 82 7811 2210 3143
+
+N 43 3632 6945 4895 3860 * 5253 4159 5534 3533 4616 6159 2371 2760 4178 * 3732 4407 5462 * 5474 43
+ 620 1772 4147 4409 70 3967 95 7647 3102 4296
+
+R 44 4802 * 2795 4422 6697 6263 4781 5937 2641 4814 5064 5331 4827 4173 2473 4832 5314 3543 * 5029 44
+ 369 2210 6697 3176 169 1607 574 7662 2456 4523
+
+H 45 7648 6504 3678 4426 5035 4669 3949 4309 2703 4443 * 3263 2354 5185 4052 5260 5169 5263 * 7089 45
+ 218 2882 7718 3223 163 2061 395 7849 2108 3584
+
+P 46 3991 6087 4718 2873 * 4877 6070 6602 5365 7225 * 5311 1348 4759 4995 3123 5463 5368 * 6664 46
+ 151 3329 * 2694 242 2132 374 7892 1899 3063
+
+K 47 4069 * 3404 4288 4611 4981 4926 4568 2576 3889 6884 4313 4270 4386 3040 4849 5140 5182 * 4599 47
+ 95 4087 7586 2443 293 3508 133 8050 1559 2624
+
+Y 48 5329 7174 2980 3991 3658 5508 6250 5459 5372 3515 6038 6067 4695 4997 4479 4261 5303 3703 4993 2327 48
+ 140 4706 4212 371 2142 2099 384 8082 1318 2624
+
+K 49 5811 * 3983 4962 5216 4089 6385 3953 1992 4126 7026 5943 5752 3784 2463 4395 4583 5507 * 6914 49
+ 182 3132 7814 3232 162 82 4183 8035 2005 2726
+
+T 50 3480 * 7491 4259 4986 3785 6372 4741 4082 5773 5489 6638 4383 4911 4309 3006 1819 4550 * 7114 50
+ 41 5174 * 1220 809 0 * 8308 1220 1079
+
+E 51 4033 * 5504 5034 4742 4172 6152 4525 2543 4794 5296 4380 4193 3633 2887 4241 3899 4322 7580 6754 51
+ 18 6353 * 0 * * * 8299 1061 0
+
+L 52 4176 7195 5283 4563 7345 5572 * 2995 5347 2313 3641 7441 2908 5441 4442 4900 5464 2819 * 7535 52
+ 26 5835 * 524 1715 * * 8299 1147 0
+
+C 53 * 235 * * * 4766 * * * * * * 4892 7347 5850 5063 7207 * 6592 6709 53
+ 295 5956 2567 4392 70 * * 8299 1102 0
+
+H 54 5575 4221 5379 7355 5102 6349 5731 5239 2201 7053 7380 4533 2131 4724 3139 * 4119 4142 * 4626 54
+ 102 * 3869 * * 59 4648 8331 0 2858
+
+K 55 5374 * 3448 5490 3325 * 4196 5554 2901 4872 5341 3020 6734 3789 3762 3797 5639 4279 6937 3981 55
+ 78 6157 4704 2585 263 585 1586 8150 1095 1656
+
+F 56 6371 * 5279 * 1253 * 7963 6290 * 4039 6826 5702 * * * 5282 6986 4706 3537 1843 56
+ 149 * 3351 * * 3428 141 8197 0 1628
+
+K 57 3813 * 5011 3217 3527 6003 3218 4407 4452 3700 4295 5035 5404 3808 5751 4092 4725 5804 5730 3599 57
+ 91 5872 4506 0 * 380 2112 8128 1132 2534
+
+L 58 2891 * 4261 4118 5539 6416 * 5100 3598 2796 5241 4931 7236 2970 3751 4091 3261 5070 7367 * 58
+ 106 4227 5831 2684 244 471 1845 8235 1439 1857
+
+Q 59 4132 * 4992 7393 5303 4102 4742 6154 3398 4101 5104 4288 4528 3324 3374 3555 3027 4816 7529 4355 59
+ 8 7495 * 1000 1000 2927 203 8236 1000 1474
+
+G 60 5723 7325 6345 4976 7253 531 7205 * 5064 * 6673 3886 * 5311 4724 4592 6954 7582 * * 60
+ 59 4959 6945 2168 363 1534 611 8235 1387 1404
+
+R 61 4752 6642 5104 5012 3278 3626 5153 5081 3299 5453 5252 3982 5620 4886 4156 3890 3849 4653 6553 2840 61
+ 9 7276 * 1000 1000 985 1015 8277 1021 1320
+
+C 62 5394 137 * 6134 * * * 6175 * 6003 * 6958 * * * 6028 * * * * 62
+ 6 8019 * 0 * * 0 8257 1001 1124
+
+P 63 4278 6178 7416 4265 6511 6003 5133 4859 2573 5973 7442 5768 2151 5341 2544 4906 3855 4900 7369 5975 63
+ 20 * 6151 * * * 0 8257 0 1124
+
+Y 64 4101 * 4653 5165 2695 6976 5092 * 4082 5368 5180 2709 * 4962 2485 4549 * 7391 * 2650 64
+ 40 7064 5649 0 * 1014 986 8265 1009 1313
+
+G 65 4493 * 6105 4918 * 409 6843 7534 5350 6929 * 6208 * * 5268 4254 * * 5946 * 65
+ 8 7476 * 0 * 926 1078 8251 1000 1337
+
+S 66 3940 * 2591 3686 7208 4273 * 4314 4472 3483 6725 4972 3785 4051 4776 3559 5489 3756 4965 5374 66
+ 18 7492 7255 0 * * 0 8256 1024 1124
+
+R 67 3856 6072 4315 4759 5637 5560 5406 * 2660 4815 5180 2868 6039 4883 2689 3475 3790 5207 * 6342 67
+ 43 5082 * 2059 396 * 0 8300 1211 1192
+
+C 68 * 127 * * * * * * 5944 5999 * * * * 6557 * 5851 * 6084 6691 68
+ 0 * * * * * 0 8271 0 1192
+
+H 69 4487 * 4800 6021 4966 7239 4826 7386 3579 5282 4301 4968 3542 3585 1540 4937 4700 5052 5797 * 69
+ 25 * 5851 * * 435 1942 8271 0 1192
+
+F 70 5910 6987 7509 7568 877 * 5035 5964 * 4466 5731 5896 * 7134 6136 * * * 5899 1974 70
+ 37 5291 * 2665 248 0 * 8247 1155 1156
+
+I 71 1988 5211 4616 5979 7318 4775 4966 5262 3909 2895 5396 5799 5246 6548 4860 2957 5013 4096 6666 5566 71
+ 10 7156 * 0 * * * 8303 1000 0
+
+H 72 6949 * 6540 * * 4198 381 * 5163 * 6969 4968 * * 5900 3756 * * * * 72
+ 0 * * * * 0 * 8253 0 1000
+
+N 73 4642 * 2658 4078 5706 2632 5652 4724 6062 7342 6970 6479 3731 6497 5578 2798 3144 3609 5838 * 73
+ 19 6275 * 716 1353 * * 8203 1073 0
+
+P 74 3769 * 3354 2763 6098 4603 4756 4536 4157 3923 5764 5018 3742 5941 3559 4152 5087 3413 7235 6353 74
+ 17 6410 * 1585 585 0 * 8140 1000 1000
+
+T 75 3518 6443 3383 3012 * 3886 * 6703 6331 5280 * 3700 3870 3479 4588 3392 2781 5620 6680 5748 75
+ 0 * * * * * * 7742 0 0
+
+E 76 5321 * 4361 627 * * * * 5166 * * 4211 5668 3829 * 5303 3613 * * * 76
+ 0 * * * * * * 6738 0 0
+
+D 77 * * 915 2386 * * * * * * * * * 1845 * * * * * * 77
+ 0 * * 0 * * * 4019 0 0
+
+//
+�HHsearch 1.5
+NAME 7aa7e6eee43e1aae66ded2fce9550a54
+FAM
+FILE 7aa7e6eee43e1aae66ded2fce9550a54
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 11:59:39 2013
+LENG 67 match states, 67 columns in multiple alignment
+FILT 101 out of 249 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCEEEEEEEEEEEEEEEEECCCC
+>ss_conf PSIPRED confidence values
+9689999987998899999999999874013970999999999899797799999999999988889
+>Consensus
+VxKviElvgsSxxSxeDAixxAixxAxkTlxnixxxeVxxxxVxdgxixxxxyqvxlkVxFxxexxx
+>7aa7e6eee43e1aae66ded2fce9550a54
+VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVWAEVVDQGVEIGAVEERTYQTEVQVAFELDGSQ
+>gi|89900230|ref|YP_522701.1| hypothetical protein Rfer_1437 [Rhodoferax ferrireducens T118]gi|89344967|gb|ABD69170.1| protein of unknown function DUF1458 [Rhodoferax ferrireducens T118]
+VAKVIEVSATSKISFEDAINQGITRACDTVSNVRgaWIKEQKVSIEDGRI--SAYRVNMQVTFVLGGD-
+>gi|332704415|ref|ZP_08424503.1| protein of unknown function DUF1458 [Desulfovibrio africanus str. Walvis Bay]gi|332554564|gb|EGJ51608.1| protein of unknown function DUF1458 [Desulfovibrio africanus str. Walvis Bay]
+VVKTIEIIAQSEKGFEDAVRTAVSEVAKSVRNIVSVWIKefEAKVENNQV--TVFRVTTKISFMVE---
+>gi|300311709|ref|YP_003775801.1| hypothetical protein Hsero_2394 [Herbaspirillum seropedicae SmR1]gi|300074494|gb|ADJ63893.1| hypothetical protein Hsero_2394 [Herbaspirillum seropedicae SmR1]
+TIEVIEVLAESDSSWRQAAQNAVHGAAVKIHNLRSLYVSdmEAVVADNKI--TRYRINAKISFLVD---
+>gi|297204099|ref|ZP_06921496.1| conserved hypothetical protein [Streptomyces sviceus ATCC 29083]gi|197714765|gb|EDY58799.1| conserved hypothetical protein [Streptomyces sviceus ATCC 29083]
+TYRVTEIVGTSPDGVDQAIRNGISRASQTLRNLDWFEVTqvRGQIEDGQI--LHWQVGLKVGFRLDES-
+>gi|78189964|ref|YP_380302.1| hypothetical protein Cag_2011 [Chlorobium chlorochromatii CaD3]gi|78172163|gb|ABB29259.1| conserved hypothetical protein [Chlorobium chlorochromatii CaD3]
+IYKKVEMVGSSPNSIEDAINNAVAKAAETMHSIRWVEVAetRCHVENQKV--AYFQVTVKIGATLEE--
+>gi|256752056|ref|ZP_05492924.1| protein of unknown function DUF1458 [Thermoanaerobacter ethanolicus CCSD1]gi|320115951|ref|YP_004186110.1| hypothetical protein Thebr_1151 [Thermoanaerobacter brockii subsp. finnii Ako-1]gi|256749066|gb|EEU62102.1| protein of unknown function DUF1458 [Thermoanaerobacter ethanolicus CCSD1]gi|319929042|gb|ADV79727.1| protein of unknown function DUF1458 [Thermoanaerobacter brockii subsp. finnii Ako-1]
+VVKVLNVVGDSTVSWEDAIHKAVEEAAKSIDNISGIEVVnqTANVKNGKI--VEYKANIQIAYRADK--
+>gi|330508936|ref|YP_004385364.1| hypothetical protein MCON_3276 [Methanosaeta concilii GP6]gi|328929744|gb|AEB69546.1| Protein of unknown function (DUF1458) [Methanosaeta concilii GP6]
+VYRAIELVGSSPIGWEDAAKNAIDTAHKSIWNLRIARVAelDAKLdEKGNI--ILYRIKLRISLKYED--
+>gi|284165347|ref|YP_003403626.1| hypothetical protein Htur_2070 [Haloterrigena turkmenica DSM 5511]gi|284015002|gb|ADB60953.1| protein of unknown function DUF1458 [Haloterrigena turkmenica DSM 5511]
+--EIVELVGNSTESWEDAVQNAMDAADETIDHVSGVEIEseRIDREGRET--ERYVVTLEASIVPE---
+>gi|258654236|ref|YP_003203392.1| hypothetical protein Namu_4114 [Nakamurella multipartita DSM 44233]gi|258557461|gb|ACV80403.1| protein of unknown function DUF1458 [Nakamurella multipartita DSM 44233]
+VQKAIDLSGSG-ETIQDAVSEALDRARETLEGITRFEVKDItGIVDGPH--TAYQVEIRVWFTV----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 6549 * * * 4934 * * 2627 * 6753 * * * 5881 * * 2965 643 * * 1
+ 0 * * * * * * 4280 0 0
+
+F 2 2468 * * 6328 3529 * * 5328 * 3652 * * * 5413 * * * 2388 * 1318 2
+ 0 * * * * * * 4314 0 0
+
+K 3 6603 * * 4815 * 6790 * * 373 * * 6022 6708 6397 2879 * * * * * 3
+ 0 * * * * * * 4345 0 0
+
+K 4 4931 * * * 5312 * 5253 2469 2463 4534 7149 6035 * * * 6740 5681 1121 * * 4
+ 0 * * * * * * 4345 0 0
+
+V 5 6000 * * * * * * 1093 * 3768 * * * * * 4721 2778 1952 * * 5
+ 0 * * * * * * 4345 0 0
+
+L 6 5957 * 3503 340 * * * * * 5276 * 6670 * 6093 * * 4179 * * * 6
+ 0 * * * * * * 4372 0 0
+
+L 7 5060 * * * 5503 * * 1866 * 1251 5111 * * * * * 5943 2264 * * 7
+ 0 * * * * * * 4390 0 0
+
+T 8 * * * * * * * 2274 * 3342 * 6846 * * * 3355 2723 1226 * 6749 8
+ 0 * * * * * * 4390 0 0
+
+G 9 1896 5968 * * * 653 * * * * * * * * * 3658 * * * * 9
+ 0 * * * * * * 4390 0 0
+
+T 10 6446 * 4933 2881 5503 * * 5483 * 6777 6645 4092 * 4424 6048 1707 1643 6693 * * 10
+ 0 * * * * * * 4390 0 0
+
+S 11 * * * * * 4841 * * * * * * * * * 51 * * * * 11
+ 51 * 4841 * * * * 4390 0 0
+
+E 12 5277 * 2643 2437 * * * * 3517 * * 4417 2009 4868 5854 4024 2983 7082 * * 12
+ 0 * * * * 0 * 4347 0 1095
+
+E 13 * * 3708 2035 * * 6600 4768 2046 * * 3711 * 4769 6693 3552 3397 3516 * * 13
+ 0 * * * * * * 4390 0 0
+
+S 14 6720 * * * * 2567 * * * * * 4707 * * * 393 5515 * * * 14
+ 0 * * * * * * 4390 0 0
+
+F 15 * * * * 1744 * * 2330 * 5426 7136 * * 6772 * 4733 7023 3608 1616 6698 15
+ 0 * * * * * * 4390 0 0
+
+T 16 7078 * 1792 857 * * * * 4944 * * 7112 * 4496 6038 5913 4805 * * * 16
+ 0 * * * * * * 4390 0 0
+
+A 17 3170 * 521 3711 * * 6533 * 4892 * * 6377 * 4079 * * * * * * 17
+ 0 * * * * * * 4390 0 0
+
+A 18 0 * * * * * * * * * * * * * * * * * * * 18
+ 0 * * * * * * 4390 0 0
+
+A 19 2051 * * * 5968 * * 1515 * 6294 * * * * * * 4656 1555 * * 19
+ 0 * * * * * * 4390 0 0
+
+D 20 4307 * 3471 3414 * * 6679 * 2430 6034 * 3912 * 1901 2675 4433 5804 * * * 20
+ 0 * * * * * * 4390 0 0
+
+D 21 3844 * 4412 4053 * 5763 5060 * 3498 * * 1264 * 3916 6611 3836 4027 4008 * * 21
+ 0 * * * * * * 4390 0 0
+
+A 22 401 * * * * 2407 * * * * * * * * * * 4494 6656 * * 22
+ 0 * * * * * * 4390 0 0
+
+I 23 * * * * 5599 * * 1236 * 2695 5091 * * * 5060 * * 1552 * * 23
+ 0 * * * * * * 4390 0 0
+
+D 24 2455 * 2935 2291 * 6034 4048 6590 2901 * * 5497 * 4784 4177 3733 4817 5035 7023 * 24
+ 0 * * * * * * 4390 0 0
+
+R 25 4773 * 6062 2269 * 5220 4573 * 2851 * * * * 4601 1390 6640 3492 6388 * * 25
+ 0 * * * * * * 4390 0 0
+
+A 26 256 7043 * * * 5060 * 6057 * * * * * * * * 5757 3450 * * 26
+ 0 * * * * * * 4390 0 0
+
+E 27 2191 5854 4898 5295 * 3093 4932 * * * * 3364 * 5341 4395 1653 4047 7153 * * 27
+ 32 * 5503 * * * * 4390 0 0
+
+D 28 5410 * 4553 2456 * * * * 1045 * * 4483 * 3178 3862 6018 6360 6023 * * 28
+ 24 5899 * 2322 322 * 0 4364 1021 1051
+
+T 29 * * 6405 * * * * * 4443 * * * * * * 1936 555 * * * 29
+ 19 * 6276 * * * 0 4364 0 1051
+
+L 30 * * * * * * 6402 2280 5889 1164 4191 * * * * * * 1919 * * 30
+ 0 * * * * * 0 4346 0 1122
+
+D 31 6745 * 2805 3841 * 5187 3326 * 2446 6962 * 5328 6371 * 1548 4439 5364 * 6674 * 31
+ 0 * * * * 840 1180 4346 0 1122
+
+N 32 * * 3198 5874 * 2891 2974 * 4726 * * 885 * 6600 * 6741 * * * 6252 32
+ 0 * * * * 0 * 4373 0 1032
+
+V 33 * * * * * * * 1306 * 2066 3555 * 5503 * * * * 2002 * * 33
+ 0 * * * * * * 4390 0 0
+
+V 34 5904 7184 3026 3305 * * 6855 * 3112 * 5968 * * 3636 2007 3666 2793 4828 * 5341 34
+ 115 3711 * 1000 1000 * * 4390 1257 0
+
+W 35 6428 * * * 6650 2276 5503 4498 * * * * * 6262 5515 2539 * 4089 1185 * 35
+ 0 * * * * * * 4390 0 0
+
+A 36 2152 * * * 1601 6440 * 2832 * 4780 6446 * * * * * * 2026 * * 36
+ 0 * * * * * * 4390 0 0
+
+E 37 * * * 848 * * * * 4060 * * 4384 * 4301 4574 5749 6792 * 3200 3217 37
+ 118 * 3667 * * * * 4390 0 0
+
+V 38 * * 5541 4085 * * * 2532 * * 6705 * * * * * 6588 460 * * 38
+ 0 * * 0 * 0 * 4423 1260 1260
+
+V 39 4409 * 4279 5304 * * * 4585 2203 4911 6650 3995 * 3102 6977 5314 2864 2278 * 5787 39
+ 2557 269 * 980 1020 * * 4390 3725 0
+
+D 40 6913 * 2586 2751 * * * * 2919 * * 4505 * 5937 1614 4896 3014 * * * 40
+ 0 * * * * * * 4390 0 0
+
+Q 41 2047 5155 * * 5341 1805 * 4045 * 4212 4423 * * 5295 * 6303 6072 2286 * * 41
+ 153 3313 * 0 * * * 4390 1344 0
+
+G 42 5442 6760 3456 4230 * 2868 2464 4523 4210 * 6304 3236 * 4364 5220 4136 3719 3810 * 6755 42
+ 0 * * * * 0 * 4423 0 1260
+
+V 43 4734 * * * * * * 1944 * 3388 6440 * * * 5907 5503 * 845 * * 43
+ 102 3876 * 0 * * * 4390 1226 0
+
+E 44 4430 * 3228 1447 * 5387 * * 2942 6303 * 4471 * 4071 5048 4490 4318 3574 * * 44
+ 0 * * * * * * 4390 0 0
+
+I 45 6645 * 1081 3645 * 3301 6428 5295 4758 5341 * 2700 6118 5060 * 5836 * 5538 * * 45
+ 32 5495 * 0 * * * 4390 1061 0
+
+G 46 5067 * 4304 6969 * 668 * * 5341 * * 2615 * 5962 4691 4655 * * * * 46
+ 11 7040 * 0 * * * 4390 1000 0
+
+A 47 3703 * 5015 3383 * 4975 6015 * 1444 6992 6693 3513 5515 3336 3257 5130 * 6172 * 6880 47
+ 0 * * * * * * 4390 0 0
+
+V 48 * * * 6303 6880 * 5515 1246 * 4025 * * 5633 * * 4778 5907 1320 * * 48
+ 3803 * 107 * * * * 4390 0 0
+
+E 49 1607 * 1574 1574 * * * * * * * * * * * * * * * * 49
+ 0 * * * * 5343 36 1494 0 3989
+
+E 50 * * 942 1060 * * * * * * * * * * * * * * * * 50
+ 0 * * * * 62 4568 1948 0 3929
+
+R 51 2692 * 4221 4454 7004 5015 * 4479 4034 5578 5290 5397 5326 4714 3720 3825 2533 2747 * * 51
+ 0 * * * * 0 * 4368 0 1111
+
+T 52 3094 * 5819 2128 * 5201 2430 * 3432 5781 * 6262 * 6698 3450 4275 3739 5865 * 4186 52
+ 0 * * * * * * 4390 0 0
+
+Y 53 * * * * 2587 * * * * * * * * * * * * 6698 2743 568 53
+ 0 * * * * * * 4390 0 0
+
+Q 54 * * * * * 4753 5412 * 3352 5943 * * * 1209 1442 * * 5348 * * 54
+ 0 * * * * * * 4390 0 0
+
+T 55 2481 5208 * * * * * 3942 * 6590 6377 * * * * 5060 4503 661 * * 55
+ 118 * 3667 * * * * 4390 0 0
+
+E 56 6824 * 4399 3655 * 4866 4292 6064 3749 * * 2087 * * 3294 5507 2033 3540 * * 56
+ 0 * * * * * 0 4423 0 1260
+
+V 57 3335 4013 * * * * * 3819 * 1360 3187 * * * * * 6504 1956 * * 57
+ 0 * * 1000 1000 0 * 4423 1260 1260
+
+Q 58 5390 * * 2709 * * 6852 6057 848 7035 6986 5278 * 3772 3799 5546 4780 * * * 58
+ 0 * * * * * * 4390 0 0
+
+V 59 5197 * * * * * * 1684 * 3162 * 5029 * * * * * 946 * * 59
+ 0 * * * * * * 4364 0 0
+
+A 60 2371 6060 * * * 1996 * 5385 * * * * * * * 1655 2515 * 5358 * 60
+ 0 * * * * * * 4381 0 0
+
+F 61 6379 * * * 220 * * 5460 * 5600 6565 * * * * * * 5890 * 4096 61
+ 0 * * * * * * 4381 0 0
+
+E 62 4707 * * 2879 * 6921 6141 4710 2810 3358 6467 * 6609 * 2343 5831 2759 2826 * * 62
+ 0 * * * * * * 4381 0 0
+
+L 63 6389 * 5097 5849 6666 * 5866 3173 6422 1384 5791 * 4229 * 5890 * * 1997 * 3835 63
+ 22 6025 * 1000 1000 * * 4381 1010 0
+
+D 64 3852 * 1943 1347 * 5669 4732 * 3861 * * 4800 * 3813 5560 * 6585 6301 * * 64
+ 61 4593 * 552 1653 * * 4302 1036 0
+
+G 65 4903 * 1038 2964 * 3236 * * 4834 * * 4527 4490 5843 4963 3778 * * * * 65
+ 899 1108 * 1854 467 * * 3811 1189 0
+
+S 66 2671 * 2155 3263 * 2016 * * * * * * * * * 1905 * * * * 66
+ 0 * * * * * * 2682 0 0
+
+Q 67 * * * * * * * * * * * * * 0 * * * * * * 67
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 7bf67dbec14c0ea001ff88bc73dd7396
+FAM
+FILE 7bf67dbec14c0ea001ff88bc73dd7396
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:27:42 2013
+LENG 229 match states, 229 columns in multiple alignment
+FILT 167 out of 236 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEEECCCCCCCCCCCCCCCEEEHHEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCEECCCCCCCCCEECCCCCCCCCCCCCCCHHH
+HHHHCCCCCEEEECCEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCEEEECCCCCC
+CCCCCCCCCCCHHHHHHHCCEEEEEECCC
+>ss_conf PSIPRED confidence values
+9734899996257874777999974531013234651467888989887422125645786257799984155567874200256888887778868778
+5524351625043367589841676478899986322321647878347887778776888631146246771588899987636887406763268765
+43477441223210020231604866039
+>Consensus
+xxxxgxlxtxHSQtxxiPxCpxgxxxLwxGySllxxxgxxxxxgQdLGxxGSClxxFstmPfxxCxxxxvCxyasrndxSyWLstxxxxpxxmxpxxxxx
+ixxyISRCxVCexxxxxiaxHSQtxxiPxCPxGxxxLWxGYSflmxtgxgxxgxGQxLgspGSCLxxFrtxPFieCxgxgxCxyxsnxxSfWLstxxxxx
+xfxxPxxxxlxxxxixxxISRCxVCxxxx
+>7bf67dbec14c0ea001ff88bc73dd7396
+SVDHGFLVTRHSQTTDDPQCPPGTKILYHGYSLLYVQGNERAHGQDLGTAGSCLRKFSTMPFLFCNINNVCNFASRNDYSYWLSTPEPMPMSMAPITGEN
+IRPFISRCAVCEAPAMVMAVHSQTIQIPQCPTGWSSLWIGYSFVMHTSAGAEGSGQALASPGSCLEEFRSAPFIECHGRGTCNYYANAYSFWLATIERSE
+MFKKPTPSTLKAGELRTHVSRCQVCMRRT
+>gi|261408017|ref|YP_003244258.1| collagen triple helix repeat-containing protein [Paenibacillus sp. Y412MC10]gi|261284480|gb|ACX66451.1| collagen triple helix repeat protein [Paenibacillus sp. Y412MC10]
+---GVTGATGATGE-------TGVTGATGATGAIGVTGATGTTGETgvTGATGATGTTGAATGATGVRGNRSNRINSNRSYR------------------
+----------------------------------------------------------------------------------------------------
+-------------------------------
+>gi|76154243|gb|AAX25734.2| SJCHGC06113 protein [Schistosoma japonicum]
+----------------------------------------------------------------------------------------------------
+--------------SILFARHYQTpfVen--LTCPGGTNKLFTGYSYVMGGGV-DDLVSMDLGTPSSCLSKFSSLPMTQCERDTTCQS--smrH--erSY
+WLATL--VPRSEQP----IPVNQTADQIARCVVCEA--
+>gi|260825417|ref|XP_002607663.1| hypothetical protein BRAFLDRAFT_84648 [Branchiostoma floridae]gi|229293011|gb|EEN63673.1| hypothetical protein BRAFLDRAFT_84648 [Branchiostoma floridae]
+----------------------------------------------------------------------------------------------------
+--------------AILTVIHSQTKDIPECPCGLTEVYNGYSLV-ELTGSNFDPDQDLGSTRSCLPYFSVS-pVTVC-g-GKVCT-EQpT---qktLWLT
+S-gEALPTSQ------hVTDDVLASAVSRCTLC----
+>gi|313230516|emb|CBY18732.1| unnamed protein product [Oikopleura dioica]
+----------------------------------------------------------------------------------------------------
+--------------GFVVTRHSQSTFVPKCPAGSMKLWDGYSLAGIRT-PAGDIAQDMGGSGSCLPNVSLEPAKSCR-KGSCK--SmTKLTSWLGIGDSP
+PTGPNP----VC--DVKAFISRCSVCEV--
+>gi|26348681|dbj|BAC37980.1| unnamed protein product [Mus musculus]
+----------------------------------------------------------------------------------------------------
+-----------VAHGFLITRHSQTTEAPQCPRGTVHIYEGFSLLYVQ-GNKRAHGQDLGTAGSCLRRFSTMPFMFCNINNVCNFAsRNDYSYWLSTPEPM
+PMN----MEPLKGQSIQPFISRCAVCEA--
+>gi|318087214|gb|ADV40199.1| putative glycine-rich secreted cement protein [Latrodectus hesperus]
+-----NVIAVHSQSLSIPNCPRGWDSLWIGYSFAMHTAAgAEGGGQSLSSAGSCLEDFRATPFIECNGgKGTCHYFA-SKYSFWLTSIEDDEQFERPAsv
+tlk-ANDLRSRVSRCNVCVKNTNV----------------------------------------------------------------------------
+------------------------------------
+>gi|340380057|ref|XP_003388540.1| PREDICTED: mucin-19-like [Amphimedon queenslandica]
+------LIAKVYQNESglqqedgheqgDLAFNLENQSLY---I--YVNAttalraCSDFIPGPPGSPGE--RGLRGKPGSKGDKGASGLPGLKGEpgprg
+RPGKMGPQGPTGP--GGMKGEKGNEGMKGDQGLKGAA--------GKKGIPGPVGMKG-FPGSMGQKGEK-GNQGARGRSGKPGPIGEKGDTGPpgLNGT
+TGSiG-------------------------------------------------
+>gi|261408017|ref|YP_003244258.1| collagen triple helix repeat-containing protein [Paenibacillus sp. Y412MC10]gi|261284480|gb|ACX66451.1| collagen triple helix repeat protein [Paenibacillus sp. Y412MC10]
+----------------------------------------------------------------------------------------------------
+----------------GATGATGE-------TGVTGATGATGAIGVTGAT-GTTGETgvTGATGATGTTGAATGATGVRGNRSNRINSnRSYR-------
+--------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+
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+
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+
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+
+H 218 4307 * 6725 6295 3721 * 3943 6150 3964 5781 6708 5354 * 5420 2133 4171 * 7028 * 1550 218
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+R 221 * * * * * * * * 3983 6054 * * * * 118 * * * * * 221
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+C 225 6760 72 * * * * 6000 * * * * * * * 5405 * * * * * 225
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+R 227 2093 * * 5972 * 6316 5493 * 2110 4964 6094 5645 * * 2394 4644 3533 3509 6361 * 227
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+
+R 228 4431 * 5719 * * 4896 4478 5405 3399 5082 6584 2074 5005 5034 2613 3391 3492 6116 * 4773 228
+ 0 * * 4158 83 * * 2962 1069 0
+
+T 229 * * 4368 6308 3921 4754 * * 6011 3611 4478 5168 4198 3847 3065 2838 2013 4849 * * 229
+ 0 * * 0 * * * 2923 0 0
+
+//
+�HHsearch 1.5
+NAME 7cff8b05889041a6d059231e4f4bc281
+FAM
+FILE 7cff8b05889041a6d059231e4f4bc281
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:50:46 2013
+LENG 193 match states, 193 columns in multiple alignment
+FILT 135 out of 327 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCEEEEEEECCCEEEEECCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEECCCEEEEECCCCCEEEECCCCCEEEEEEEECCCCE
+EEEEEEEECCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEEEECCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCEECCCEECCCCCCC
+>ss_conf PSIPRED confidence values
+9876566787752017289999858858998799859774389980346999991388899998136528999899988870235740489999846976
+899988604888885179999989988117767999850358731079885527885543664877677887786232232187076877889
+>Consensus
+xxxxxxxxxxxxxlxgxxxqLYcrxgxxLqIxxdGxVxGtxdxxsxxsxleixsvxxgxVxIrgvxsxxYLcMNxxGkLyxsxxxsxeCxFxExxxeNxY
+xtYxSxxyxxxxxxrxwYlalnkxGkxrxGxrtkxxxxsshFLprxvxxxxxrxpxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+>7cff8b05889041a6d059231e4f4bc281
+GSKKRRRRRPEPQLKGIVTKLYSRQGYHLQLQADGTIDGTKDEDSTYTLFNLIPVGLRVVAIQGVQTKLYLAMNSEGYLYTSELFTPECKFKESVFENYY
+VTYSSMIYRQQQSGRGWYLGLNKEGEIMKGNHVKKNKPAAHFLPKPLKVAMYKEPSLHDLTEFSRSGSGTPTKSRSVSGVLNGGKSMSHNEST
+>gi|28071267|dbj|BAC55965.1| fibroblast growth factor 8/17/18 isoform 2 [Ciona savignyi]
+---------------------------RVQILGK-RVNAKGVRGNKYSKMAILSTSFggR-IMIQGVETGRVLCMNRKGRLvgkvLRRAKHDLKCQFNDL
+MMPNLFDYFTNVAH------PKWYVAFNSHGRPKKGPTTKLGQVETMFLKRPIETFGY-----------------------------------------
+>gi|56692781|ref|YP_164239.1| hypothetical protein ORF144R [Singapore grouper iridovirus]gi|42517493|gb|AAS18159.1| unknown [Singapore grouper iridovirus]
+------------------KILYCKTNFMLEVNGTA-VSGGTDKQSQTAKLTLKSVRAGQIVIKGSI-GGYVCMDRNGAVSAKTTYvQSDCVFNETLLPNN
+YNSYSAAEHLNPETRANMHLAIDKAGKVRSGKRTAKTDNSAQWLVL------------------------------------------------
+>gi|221110175|ref|XP_002166704.1| PREDICTED: similar to fibroblast growth factor 1B, partial [Hydra magnipapillata]
+-----------------LIYARRRNGMNLGII-NKKVAGMKKDNDINGLFEIQSYATSIVMLRHFATENYIAINEKGEIIVTPSKNDECLFYHYMEENGY
+VTFASVKYYI-NEHYDLFLNLKANGKVRDVRRTAPGQTSSQFILIP-----------------------------------------------
+>gi|170589121|ref|XP_001899322.1| Fibroblast growth factor family protein [Brugia malayi]gi|158593535|gb|EDP32130.1| Fibroblast growth factor family protein [Brugia malayi]
+-----------------VWQLYSRcSSAFVQIFLKhANARGQQFNH-CLTDLLMHADNEGRIRIENALTGKFICFNKRQRLAIrSDGMDDKCLFREQLTS
+SGYTMFQSA-WK-----QNLFLGFNRKGKFQDPSQINTKRRCFLFIKLLREVKSTR----------------------------------------
+>gi|20069930|ref|NP_613134.1| fibroblast growth factor FGF [Mamestra configurata NPV-A]gi|20043324|gb|AAM09159.1| fibroblast growth factor FGF [Mamestra configurata NPV-A]gi|33331762|gb|AAQ11070.1| FGF [Mamestra configurata NPV-A]
+-------------------QIFI-NHHLLRMNLDGIVNGTQTGESSETVWHRISQSDG-ILLRSSLYCNYACINECGYGYSALIPNNECLWTEQYDEHNY
+R-FINKKFG----NRTAYLSINLEGKLKRTVLL------------------------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 421 * * * * * 2883 * * * 3089 * * * * 1
+ 0 * * * * * * 1544 0 0
+
+S 2 * * * * * 997 * * * 3056 * * * * 2883 2040 * * * * 2
+ 0 * * * * * * 1544 0 0
+
+K 3 * * * * * * * * 2944 * * * * * 201 * * * * * 3
+ 0 * * * * * * 1544 0 0
+
+K 4 * * * * * 3143 * * 681 * * * 2751 * 3126 * * * * * 4
+ 452 1895 * 0 * * * 1544 1063 0
+
+R 5 * * * * * 3126 * * * * * * * 2883 415 * * * * * 5
+ 0 * * * * * * 1544 0 0
+
+R 6 * * * * * * * * 3723 * * 3724 1957 2487 1277 * * * * * 6
+ 533 1695 * 0 * * * 2130 1197 0
+
+R 7 3645 * 3841 4786 * * 3772 * 2740 5299 * 3098 * * 1733 * 2755 * * * 7
+ 0 * * 0 * 0 * 3165 1054 1054
+
+R 8 4136 5384 * * * 3662 * * 1753 * * 4064 4299 * 2422 4226 3663 3135 * * 8
+ 0 * * * * * * 3175 0 0
+
+R 9 2936 * 4328 5600 * 3742 * 4725 * * * 3088 * 4273 1932 3392 3216 4262 * * 9
+ 0 * * * * * * 3509 0 0
+
+P 10 5646 * 3534 3128 * 4565 * * 2861 * * * 2109 2765 4963 3100 3800 * * * 10
+ 0 * * * * * * 3509 0 0
+
+E 11 * * 6061 1309 3311 * * * * 2813 * 3845 * 4002 4078 4738 * * * 3190 11
+ 0 * * * * * * 3926 0 0
+
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+ 54 * 4767 * * * * 4033 0 0
+
+Q 13 * * * * * * 1711 * * * * 4113 * 1059 4230 * * 3962 * 4662 13
+ 0 * * * * 0 * 3996 0 1000
+
+L 14 * * * * 4209 * * 2092 * 623 * * * * * * * * * 4013 14
+ 0 * * * * * * 4033 0 0
+
+K 15 * * 4281 3451 4482 * * * 981 4938 * 4153 * 4849 * * 2765 4835 * * 15
+ 0 * * * * * * 4098 0 0
+
+G 16 3817 4528 * * * 392 * * * 4432 * * 4764 4625 * * * * * * 16
+ 0 * * * * * * 4281 0 0
+
+I 17 3882 * 3778 * * * 5235 1481 * 4738 * 4817 5072 4655 3675 * 3245 2754 * * 17
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+H 158 4276 3997 * 3006 * * 914 * * * * * 2984 4589 * * * * * 3996 158
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+
+D 159 * * 1148 1912 * * 3316 * * * * * 3604 * 3843 5033 * * * * 159
+ 117 3687 * 0 * * * 3770 1120 0
+
+L 160 * * * * 1839 * * 2489 * 1890 * * * * * * 3230 2591 * * 160
+ 39 * 5239 * * * * 3625 0 0
+
+T 161 2849 * 5329 4291 2186 2197 * 4160 * 3927 * * 3882 * * * 2663 * * * 161
+ 0 * * * * 0 * 3244 0 1069
+
+E 162 4269 * * 784 * 2778 * * * * * * * * * 2566 * 4248 * * 162
+ 220 2825 * 1235 798 * * 2793 1283 0
+
+F 163 3764 * * 3755 4771 * 3652 * * * * * 3222 1794 3081 2893 3511 * * * 163
+ 0 * * * * * 0 2805 0 1043
+
+S 164 * * 2893 * * * * * 4831 * * * 4683 * * 550 * 3207 * * 164
+ 0 * * * * 0 * 2805 0 1043
+
+R 165 * * * * * 4926 * * * 2459 * * 1510 * 1334 * * 4737 * * 165
+ 0 * * * * * * 2793 0 0
+
+S 166 * * * * * * * * 2024 2928 * * 3961 * 1927 1758 * * * * 166
+ 214 5425 3127 0 * * * 2793 1062 0
+
+G 167 2700 * * * * 4376 * * * * * 4634 4049 * * 769 * 3178 * * 167
+ 134 3497 * 0 * * 0 2370 1028 1165
+
+S 168 * * * * * 3418 * * * * 2570 * 2868 * 4571 839 * * * * 168
+ 0 * * * * * 0 2298 0 1235
+
+G 169 * * * 2731 * 1599 * * * * * * * * 4159 2539 * 1779 * * 169
+ 0 * * * * * 0 2257 0 1235
+
+T 170 * * * * * 2479 * * * * * * 4238 * * 2782 1084 2731 * * 170
+ 0 * * * * * 0 2257 0 1235
+
+P 171 * * 2539 * * * * * * * * * 562 2731 * * * * * * 171
+ 0 * * 0 * 613 1530 2257 1028 1235
+
+T 172 * * * * * * 2882 * * * * * * * * 911 1588 * * * 172
+ 986 * 1014 * * * 0 2218 0 1054
+
+K 173 * * * * * * * * 816 * * * * 1942 2543 * * * * * 173
+ 0 * * * * * 0 1735 0 1555
+
+S 174 * * * * * 1942 * * 2543 * * * * * * 816 * * * * 174
+ 0 * * * * * 0 1735 0 1555
+
+R 175 * * 2543 * * * * * * * * * * * 1224 * 1321 * * * 175
+ 0 * * 3170 170 2659 249 1735 1054 1555
+
+S 176 * * * * * * * * * * * * 2315 * * 542 3155 * * * 176
+ 0 * * * * 1471 646 1808 0 1463
+
+V 177 1683 * * * * 3012 * * * * * * * * * 1458 * 2318 * * 177
+ 545 1669 * 3131 175 * 0 1883 1125 1283
+
+S 178 * * * 2804 * * * * * * * * * * * 543 2551 * * * 178
+ 0 * * * * * 0 1763 0 1352
+
+G 179 1967 * * 2551 * 2625 * * * * * * 2804 * * * 1898 * * * 179
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+
+V 180 2551 * * 1898 * * * 1967 * * * * * * * * * 1711 * * 180
+ 543 1672 * 1021 979 0 * 1763 1174 1352
+
+L 181 * * * * 2646 * * * * 1975 1105 * * * * * * 3047 * * 181
+ 0 * * * * * * 1890 0 0
+
+N 182 * * * * * * * * * * * 298 * * * 3927 3047 * * * 182
+ 0 * * * * * * 1890 0 0
+
+G 183 * * * * * 215 * * * * * * * * * 3785 3927 * * * 183
+ 186 3047 * 2000 415 * * 1890 1028 0
+
+G 184 * * * * * 478 * * * * * * * * 3756 2265 * * * * 184
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+
+K 185 * * * 3658 * * * * 119 * * * * * * * * * * * 185
+ 0 * * * * * * 1822 0 0
+
+S 186 3542 * * 3391 * * * * * * * * 1729 * 3370 2932 * 1789 * * 186
+ 177 3118 * 0 * * * 1563 1045 0
+
+M 187 2861 * * * * * * * * 3170 2769 * * * * * * 726 * * 187
+ 0 * * 2700 241 * * 1518 1065 0
+
+S 188 * * * * * 2861 * * * * * 715 * * * 2769 3233 * * * 188
+ 0 * * * * * * 1518 0 0
+
+H 189 * * * * * * 2769 * 1599 * * * * 1232 3358 * * * * * 189
+ 129 * 3543 * * * * 1518 0 0
+
+N 190 * * 1039 * * * * * * * * 2682 2942 * * 2135 * * * * 190
+ 0 * * * * 0 * 1529 0 1016
+
+E 191 * * 3365 2639 * * * * 1978 * * * * * * 1034 * * * * 191
+ 0 * * * * * * 1514 0 0
+
+S 192 * * * * * * * * * * * * * * * 1957 430 * * * 192
+ 604 1547 * 2199 354 * * 1514 1146 0
+
+T 193 * * * * * * * * * * * * * * * 1073 930 * * * 193
+ 0 * * 0 * * * 1548 0 0
+
+//
+�HHsearch 1.5
+NAME 7d7b394238d3b3e35f1bbacceedade0b
+FAM
+FILE 7d7b394238d3b3e35f1bbacceedade0b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:07:45 2013
+LENG 212 match states, 212 columns in multiple alignment
+FILT 177 out of 1181 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEECCCCCCCCCCEECCCCCCCCCEEEECCCCCEEEECCCEEEEEEEECCCCCEEEEEEEEECCEEEEEEEEEEEECCCCCEEEEEEEECCCCCCCC
+CCEEEEEEEECCCCEEEEEEECCCCCCCCEEEECCCCCCCCEEEEEEEEECCEEEEEECCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCE
+EEEEEEEEEECC
+>ss_conf PSIPRED confidence values
+9836961799974567884797788305777086677990899899999946899737899998230312599999994699964999996035677999
+7629999983269778899976998996459758999877819999999599899999999999968999999749999997278765568887999985
+999999999869
+>Consensus
+xxxfxDeFxxldxxxWxxxxxwxxxxxxxxxxxxxnvxvxxxGxLxlxxxxxxgxxxxsgxixsxxxxxyGxxEarxkxxxxxgxxxafwlxxxxxxxxx
+xxEIDiExxgxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxHxYxxxWxxxxixfyvDgxxvxxxxxxxpxxpxxlxlnxxxxxxxxxwxgxxxxxxxx
+xxxVDxVrvyxx
+>7d7b394238d3b3e35f1bbacceedade0b
+GSVFWEPLSYFNPSTWEKADGYSNGGVFNCTWRANNVNFTNDGKLKLGLTSSAYNKFDCAEYRSTNIYGYGLYEVSMKPAKNTGIVSSFFTYTGPAHGTQ
+WDEIDIEFLGKDTTKVQFNYYTNGVGGHEKVISLGFDASKGFHTYAFDWQPGYIKWYVDGVLKHTATANIPSTPGKIMMNLWNGTGVDDWLGSYNGANPL
+YAEYDWVKYTSN
+>gi|109897132|ref|YP_660387.1| glycoside hydrolase family protein [Pseudoalteromonas atlantica T6c]gi|109699413|gb|ABG39333.1| glycoside hydrolase, family 16 [Pseudoalteromonas atlantica T6c]
+--QFTDEFDGqiLDTQRWHPTnPGWKGREPTF--FHKDNTRLEG-GELVMSINQHgdtelpEGYTHSSGFIKTKERVLYGYFESEAKLMDA-PWVSGFWL
+TMG--TKEWWTEIDIqENCPCVDGqrhDINSNLHVfrSpkEHGNvkkhfsDSKKYYHPDEIQKDYHVWGLEWNEDVIRFFIDGFMFREVENTHWHQPLTI
+NVNNES----NKWFNALPdDnRTDEEYRVKYVRVWQ-
+>gi|90021040|ref|YP_526867.1| thiol oxidoreductase-like protein [Saccharophagus degradans 2-40]gi|89950640|gb|ABD80655.1| putative retaining b-glycosidase [Saccharophagus degradans 2-40]
+--IFEENFNTLNSDRWNVIegdgcqygpnlCGWGNQELQYYQD--SNVTIEDvpgePGnkAVVFEARNETvnGSAFTSGKIDSEDgiAIKYGMIEFRLRV
+PNmGVGYWPAVWMLGTSTESWPSkGEIDMMEMGHRAQgmadagHPGTNlnNYTAanaifyaeAAcvPENPTcaAMTAWQtdnayvsqtSMGERFVIYRTY
+WTDTQLRFTVIdnGVEYDMyddpitIGEEatELQQPFYLLANLAVGGNFTDA-STPAevtAQLPGKMYLDYIRVYQL
+>gi|170727005|ref|YP_001761031.1| hydrolase [Shewanella woodyi ATCC 51908]gi|169812352|gb|ACA86936.1| hydrolase (secreted protein) [Shewanella woodyi ATCC 51908]
+--IMFDDFNYINlaqaeENGWMARTETGHPGIKGATWWSEGVSFhpdpLNYSnqVMRISSKTDGTPaNTRQTQVCHKRKYHEGTYAARVYFndkpqygPD
+GDGIVETFYAISPlASPLDPAySEMDFEYLANGgwgeGDhALFaTSWETfQLKpwtPVNA--YDATRNSLQGWNTLVLQVSDNKLRYFINGELFAEHgSE
+VYPEVAMSINFNLWFIP---------------------------
+>gi|152967800|ref|YP_001363584.1| hypothetical protein Krad_3857 [Kineococcus radiotolerans SRS30216]gi|151362317|gb|ABS05320.1| conserved hypothetical protein [Kineococcus radiotolerans SRS30216]
+--------------------------------------------------------------------REGQVDVRVTASLDRGCMLAVWLVGTEHEsPG
+DSGEVCVcEIDADAVGetstRVRTGVKAHHDPrlrTEVTEVVVPVGA-GQAHWWSARWNASGVVVACDERVVFTSA-QHVRGPQQLMVDLFEVV------
+APgPAGEYPKTAVVHAVRGS--
+>gi|154296949|ref|XP_001548903.1| hypothetical protein BC1G_12563 [Botryotinia fuckeliana B05.10]gi|150843090|gb|EDN18283.1| hypothetical protein BC1G_12563 [Botryotinia fuckeliana B05.10]
+------------------------------------TKVIG-NQVYMGVDNTTvlsdkVNGkRNSIWVNLFMSF---LMV--FLlVISRtCLVVivePGL
+vsanrfasWTIRN---GdGPYg-EMDIlEGSNDIT-----------------------------------------------------------------
+----------------------------------
+>gi|255692839|ref|ZP_05416514.1| conserved hypothetical protein [Bacteroides finegoldii DSM 17565]gi|260621401|gb|EEX44272.1| conserved hypothetical protein [Bacteroides finegoldii DSM 17565]
+------------------------------------AQVTNEGELNICV--GVegt--NYGTAAIHcckslaqmwaQNVtRIYPGmRIEVKVRLGGnRTG
+FVPMIEVKNPSTATtskEAKQSICIlKNVsGTAITqSVRGETIS-D----VKSVvtAIP--KVEDYNIYWMELVDENtIKLGINGSTTLevsKdMLNSWP
+ftkastgtsvgAKGLYLIMRwdLFGesntiSPDlPAGWDTELKsidptkyATEGPRMIIDWIRFYV-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 0 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+S 2 * * * * * 1676 * * * * * * 2498 * * 971 * * * * 2
+ 281 2498 * 0 * * * 3035 1011 0
+
+V 3 3115 6437 4064 4988 * * 6795 3443 5828 3419 6730 4972 6882 4749 6688 4594 3216 1797 * 4787 3
+ 0 * * * * * * 7936 0 0
+
+F 4 * * * * 960 * * 6327 6690 3518 4397 * * * * * * 4822 1862 5764 4
+ 0 * * * * * * 8056 0 0
+
+W 5 4077 6527 4778 2812 3822 5299 4082 7007 4993 6988 5631 4560 * 3745 4065 2045 6839 4047 4918 7087 5
+ 0 * * * * * * 8149 0 0
+
+E 6 6538 * 351 2649 6799 * * * * * * * 6422 6748 * 7096 6887 * * * 6
+ 0 * * * * * * 8136 0 0
+
+P 7 * * 1842 1155 * 5862 6737 * * * * 3274 5833 5011 * 4580 4274 * * * 7
+ 0 * * * * * * 8136 0 0
+
+L 8 * 6566 * * 72 * * * * 5982 * * * * * * * 6340 6670 * 8
+ 0 * * * * * * 8162 0 0
+
+S 9 4828 * 1547 3941 * 5864 5686 * 6094 * * 1542 * * 5668 3806 3802 * * * 9
+ 775 1266 * 1216 812 * * 8174 4482 0
+
+Y 10 3492 * 3942 4844 * 2431 6756 * 4132 7047 * 4457 7108 3907 5306 2336 2945 5879 * 4006 10
+ 376 2177 6919 1886 455 * * 8174 3053 0
+
+F 11 5875 * * 6813 4089 5889 6659 2713 5854 1318 7101 7063 2515 * * 6746 5243 3721 6730 7147 11
+ 79 4238 * 1325 735 * 0 8157 1449 1000
+
+N 12 5843 * 952 4492 6984 5207 * 5427 6701 5236 * 1977 * 5338 6949 5136 * 6436 * * 12
+ 148 3608 6000 1919 443 0 * 8186 1865 1000
+
+P 13 4171 * 3794 3649 * 4594 * 7112 5803 4076 5794 4875 3243 4747 4703 3150 1789 7159 6031 6760 13
+ 10 7159 * 2807 222 * 0 8191 1000 1114
+
+S 14 2680 * 3352 5039 * 4885 5414 * 3730 6645 6928 3819 5436 3929 6649 2018 2854 6655 * * 14
+ 10 7158 * 1000 1000 * 0 8279 1000 1114
+
+T 15 5884 6989 4882 5255 5376 4994 5865 4958 1537 4906 6905 2776 6644 6116 3115 6875 6150 3777 * 4553 15
+ 0 * * * * * 0 8415 0 1114
+
+W 16 * * * * 5275 * * * * * * * * * * * * * 38 * 16
+ 12 * 6944 * * * 0 8415 0 1114
+
+E 17 4597 * 4593 4252 5413 4599 5247 3883 3865 4213 7054 2613 * 3559 3896 4013 3043 4663 * 4733 17
+ 110 4189 5759 766 1280 * 0 8400 1532 1214
+
+K 18 3825 5745 5009 6786 4165 4888 4419 3495 3743 3920 6982 * 4042 5457 4515 5654 4584 2611 * 2790 18
+ 97 4547 5498 1518 620 2105 382 8360 1494 1430
+
+A 19 4024 6047 4832 3035 7025 3582 4950 4377 5037 3804 5002 4389 5125 4586 3374 3803 4155 4361 5281 4485 19
+ 485 2008 4754 1602 576 1934 438 8361 3380 1553
+
+D 20 5385 6860 2385 4379 6725 3882 4927 6097 4580 5016 6545 3140 3324 5125 4617 3286 3776 5735 * 4547 20
+ 699 1973 2952 2123 376 2907 206 8333 3360 1767
+
+G 21 4916 * 4131 4751 4981 1197 5383 5370 4595 6928 * 3618 3990 5210 5348 3744 5713 * * 5854 21
+ 156 3800 5017 1233 799 862 1152 8308 1643 2867
+
+Y 22 6681 6881 4339 7120 3502 4803 5226 7313 7143 3869 5829 7190 7332 6970 6896 5409 6068 6876 890 4089 22
+ 393 2570 3838 998 1002 1938 436 8521 2673 2116
+
+S 23 4535 7037 4051 6792 5921 1927 4427 5244 4270 5877 * 4247 4679 5878 4101 3170 4796 3847 5959 4083 23
+ 99 4643 5238 1515 621 726 1338 8506 1352 2508
+
+N 24 3476 * 5062 6734 * 2461 5260 * 4693 5578 5675 1612 3731 5849 * 4296 3611 * * 4996 24
+ 36 6112 6660 1322 737 1685 538 8536 1075 1820
+
+G 25 5345 * 4281 6767 * 1642 6035 6764 5015 6623 * 2884 3803 3901 3115 4013 5045 5270 6044 7382 25
+ 40 5541 7382 1000 1000 1907 447 8536 1147 1648
+
+G 26 4699 7545 3909 1814 5301 3408 6051 * 5066 6009 6129 4732 4898 3530 4933 3009 4697 4987 7160 5705 26
+ 124 6772 3770 0 * 2943 201 8558 1003 1522
+
+V 27 3890 5811 4882 4959 4683 4665 5508 4328 5248 2901 5112 4891 2369 4161 3791 4587 5295 4113 5578 6904 27
+ 154 6680 3450 1290 759 1838 474 8462 1132 2211
+
+F 28 * 6799 * 3384 3347 4178 7037 5355 3888 5359 5368 5382 5074 1787 4143 4647 5800 4181 * 3635 28
+ 96 6964 4146 2322 322 1960 429 8383 1000 2867
+
+N 29 3765 4059 3845 4849 3973 4660 4328 5868 5428 3693 5731 3390 5865 4660 5176 3739 3580 5853 6007 3301 29
+ 143 7203 3511 1000 1000 1252 785 8352 1000 2861
+
+C 30 3518 3428 * 6926 4065 4032 5299 4450 6714 5472 5353 4106 5382 * 6580 5044 3770 5502 5200 1655 30
+ 271 5749 2714 2995 193 1597 579 8429 1111 2845
+
+T 31 5244 * 4683 6640 5898 5188 5104 4283 5188 2920 6878 3906 5126 4879 4749 3536 2178 2986 * 4964 31
+ 126 4840 4361 1842 472 2072 392 8344 1253 3574
+
+W 32 4355 * 2651 * 2264 5986 6767 6836 5900 4639 6721 3628 5054 * 4414 4987 4946 5077 2510 4144 32
+ 148 3998 4841 2303 327 371 2141 8564 1548 3410
+
+R 33 4119 6046 2545 4736 * 3415 6996 6053 4850 4571 6990 3686 6419 4915 3732 2315 3946 4799 * 5822 33
+ 39 6038 6444 0 * 442 1923 8702 1085 1906
+
+A 34 2716 * 5223 3823 * 3523 4621 6144 3508 7488 * 4704 1865 4600 4114 4483 5124 * * 5063 34
+ 51 5316 6699 2810 222 0 * 8764 1238 1349
+
+N 35 4021 * 2236 2414 * 3637 * * 3642 7362 7090 3668 6539 4574 4357 2957 5251 7517 7208 5854 35
+ 52 4818 * 1531 613 * 0 8697 1431 1021
+
+N 36 3536 5248 4693 7371 * 6296 5092 * 6918 6507 7110 744 5882 4257 6241 4899 5774 5742 * 5372 36
+ 0 * * * * * 0 8697 0 1021
+
+V 37 2948 6243 * 7608 5950 * 6259 3251 * 4991 6319 7062 5780 6127 * 4172 3760 1078 7054 5425 37
+ 26 5819 * 1312 744 0 * 8686 1177 1021
+
+N 38 5453 6901 4444 3832 3787 5790 5785 5685 3697 5780 * 4620 7427 4464 3460 2616 2635 4595 4824 4446 38
+ 17 7427 7388 1585 585 * * 8727 1000 0
+
+F 39 4538 * 7609 5106 3451 7431 6954 2526 6279 3721 6169 6785 7074 5385 * 6955 4886 1226 * 4992 39
+ 49 6202 5650 725 1341 0 * 8710 1100 1000
+
+T 40 4563 6966 3009 2645 * 4110 6283 5862 3501 5586 * 4514 6780 4930 4788 2362 3441 4220 7273 * 40
+ 28 5719 * 0 * 704 1373 8688 1194 1208
+
+N 41 4440 * 1703 4096 * 2260 7387 * 4106 7080 * 2675 4669 4782 7283 4681 5960 7118 * 7138 41
+ 1659 4697 633 1658 550 * 0 8706 1460 1025
+
+D 42 4836 * 1566 3156 * 3943 4799 * 6345 5576 * 3231 4338 3327 * 3225 5781 * * * 42
+ 86 4104 * 1643 557 18 6361 7819 1218 6879
+
+G 43 * * 5086 6554 * 227 * * 7279 * * 4517 * * 6995 6446 5532 6826 * 7525 43
+ 143 3774 5568 748 1305 * 0 8695 1940 1025
+
+K 44 3348 6408 4859 4579 5541 5759 4797 4637 3576 4386 4703 2465 * 4754 4051 4700 3915 3711 * 3882 44
+ 77 4260 * 1311 744 0 * 8702 1745 1410
+
+L 45 3845 * * * * * * 5216 * 437 4562 7438 * * * 5075 * 3782 * 6122 45
+ 20 7325 6995 1585 585 * * 8698 1008 0
+
+K 46 5258 7434 5178 4794 * 7550 3651 4214 3160 5718 7435 4710 * 4396 2742 4062 3841 2115 6443 5524 46
+ 0 * * * * 0 * 8675 0 1032
+
+L 47 * 6082 * * 5179 * * 1517 * 1012 3762 * * * * 7265 * 4955 * * 47
+ 0 * * * * * * 8698 0 0
+
+G 48 5078 * 7125 3409 6984 5625 5194 4298 2767 5291 7674 4608 * 4089 3245 3045 2454 4190 6126 7088 48
+ 30 6139 7309 0 * * * 8698 1107 0
+
+L 49 1722 7519 * * 6473 4494 * 2987 * 2708 4839 5680 4604 7155 * 6326 3298 3108 7449 5779 49
+ 26 5829 * 1452 656 * 0 8692 1178 1006
+
+T 50 5007 6050 3439 4529 5169 5197 5439 4227 3258 7162 * 4186 5677 4095 2407 3978 3250 4500 5525 5699 50
+ 93 4003 * 1704 529 * 0 8692 1836 1006
+
+S 51 3873 * 5195 4058 5583 5041 5812 7147 2331 5796 7144 3697 4174 4148 2838 3740 5089 4466 6423 4196 51
+ 165 3399 6245 1739 514 0 * 8693 2291 1109
+
+S 52 4200 * 2825 2603 6148 4336 5693 6983 3948 5632 6520 3263 3504 4068 5014 3639 3867 7103 * 6140 52
+ 366 2411 4802 2883 210 * 0 8708 3335 1117
+
+A 53 3476 7177 3641 4715 * 3109 6379 6958 5688 6340 6943 3404 3282 4488 5565 2207 3009 7532 * * 53
+ 1097 1109 3856 2789 226 2158 366 8643 5699 1703
+
+Y 54 3892 * 3701 4734 * 1072 4900 * 5456 * * 3706 7586 4854 * 3653 4637 5516 * 5154 54
+ 679 1569 4706 2622 256 2083 388 8566 4630 2449
+
+N 55 4766 * 5175 4172 4500 2626 4549 5558 2944 5785 * 4891 4355 5821 3210 4802 3766 4400 6759 3513 55
+ 39 6097 6386 1369 706 1487 637 8588 1291 2543
+
+K 56 4437 * 3535 4780 6829 4584 5247 5673 3442 5043 7429 3190 2687 4233 4017 4176 3453 4885 5114 5839 56
+ 39 6565 5985 503 1764 791 1244 8638 1107 2139
+
+F 57 7506 * 7146 * 3076 4786 4845 4053 6150 4522 5612 5717 5380 * 5889 * 5711 3435 2645 1607 57
+ 17 7440 7459 2585 263 970 1030 8640 1007 1641
+
+D 58 3791 7153 3661 4907 * 6132 5826 4654 5300 4396 5669 5568 * 5521 4064 2871 1799 4172 7290 4167 58
+ 53 5246 6655 597 1562 1309 746 8680 1269 1351
+
+C 59 3469 3637 * * 6164 2425 6205 6861 6802 * * 5523 * 7260 * 1259 2996 5235 * * 59
+ 22 6062 * 618 1522 0 * 8705 1140 1321
+
+A 60 1678 6350 5472 * * 1091 * 7766 5406 * * * 5393 * * 3482 5387 5789 * * 60
+ 0 * * * * * * 8715 0 0
+
+E 61 3260 5731 7024 2629 5095 3521 6290 4961 4863 4651 4463 5570 * 6618 2319 4016 5069 5000 5058 4566 61
+ 0 * * * * * * 8739 0 0
+
+Y 62 6397 7034 7542 7442 4095 * * 1621 * 1963 5482 7518 * * * * * 1856 * 5314 62
+ 35 5734 7682 2910 206 * * 8739 1198 0
+
+R 63 3940 * 4369 3697 5205 5031 4175 4645 4878 6233 5831 4507 * 3234 3661 2876 3187 3724 * 4628 63
+ 46 5008 * 3938 97 * 0 8741 1357 1000
+
+S 64 5576 * * * 7102 5141 7097 * * 4709 * 5864 5657 6788 6932 1124 1421 * 7343 7581 64
+ 21 7539 6815 2322 322 0 * 8741 1000 1000
+
+T 65 4716 * 6331 4132 7745 5065 6077 6316 2095 4137 7775 3633 5812 3637 2840 4612 3738 3914 6635 5361 65
+ 133 3617 7246 1750 509 0 * 8718 2113 1021
+
+N 66 3328 * 3930 3473 3646 3014 5066 6242 4058 7308 7739 3161 * 3912 3353 3919 4288 7258 7234 5618 66
+ 258 2610 * 1241 793 0 * 8733 3183 1004
+
+I 67 3129 6399 4689 5073 5341 5362 6465 5550 2713 4962 5882 4430 5335 4650 3398 3138 2845 7281 7034 4336 67
+ 295 2489 7186 1099 907 0 * 8738 3382 1000
+
+Y 68 6271 * 7547 7084 1293 5622 6246 3343 6008 3019 5007 6300 7773 4587 6213 7321 5872 4256 5256 3475 68
+ 248 2771 6454 1382 698 0 * 8728 3018 1014
+
+G 69 5342 * 5350 4693 6314 2983 6443 7170 2655 3376 6145 5101 5324 3121 3164 4199 3102 5529 7192 7535 69
+ 41 5170 * 2163 365 * 0 8741 1329 1129
+
+Y 70 5750 6331 * 5235 3386 5002 4008 * 5492 7163 * 4961 4414 6060 7249 5230 5046 5397 6533 910 70
+ 36 5751 7401 1839 473 * 0 8748 1250 1129
+
+G 71 5099 6060 7252 * 7179 209 * 7532 * * 7259 * 5196 * * 6261 6207 7508 * 7427 71
+ 118 3669 * 511 1745 826 1198 8730 2180 1362
+
+L 72 7232 7109 * * 5272 7109 7880 * 2962 5271 4818 5263 * 5152 2043 4066 3360 4705 7439 1938 72
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+Y 201 3715 * 3749 2988 5458 * 7348 5415 3801 * 6247 7350 6266 4505 4195 3065 2398 4596 6022 3288 201
+ 0 * * * * * 0 8557 0 1051
+
+A 202 3738 * * 5389 2920 6023 6099 5420 7117 2757 1465 7112 * 7032 * 5633 4837 3904 * 4021 202
+ 0 * * * * 0 * 8557 0 1051
+
+E 203 * * 3839 2463 5429 6985 5824 5322 3895 3256 7301 5369 7118 3480 4134 4840 4156 3611 5616 2994 203
+ 0 * * * * * * 8578 0 0
+
+Y 204 6155 * * * 4502 * * 1695 * 5044 * * * * * 6617 6793 917 * 4215 204
+ 0 * * * * * * 8578 0 0
+
+D 205 5501 * 529 4177 * 5211 5150 * 3964 * * 5347 * 5667 4475 7311 6061 * * * 205
+ 0 * * * * * * 8570 0 0
+
+W 206 7049 6597 5149 7121 5448 * 5682 * 6631 * * 5486 * 6967 5035 3988 7037 * 1467 1318 206
+ 0 * * * * * * 8567 0 0
+
+V 207 6845 5803 * * 3315 * * 1976 * 3862 * * * * * * 6593 911 * 6978 207
+ 0 * * * * * * 8553 0 0
+
+K 208 4343 * * 4166 * 6040 6232 6564 2790 5340 * 5598 * 5751 848 4131 5519 7380 * 7157 208
+ 0 * * * * * * 8525 0 0
+
+Y 209 3628 4916 * 6888 3465 5124 4767 3242 * 4576 6060 * * 6128 * * 4701 1204 6349 4058 209
+ 0 * * * * * * 8482 0 0
+
+T 210 6815 * 6869 5415 4080 * * 6332 * 6483 * * * * 5832 4882 2985 5029 2635 980 210
+ 0 * * * * * * 8262 0 0
+
+S 211 3626 * 5620 4172 * * 6495 5433 2947 * * 5557 3001 1851 3264 3287 4335 * * * 211
+ 0 * * * * * * 8033 0 0
+
+N 212 * * * * 3433 * * * * 1243 3596 4240 2097 5143 5033 5177 * * * 5110 212
+ 0 * * 0 * * * 6466 0 0
+
+//
+�HHsearch 1.5
+NAME 7ec67cbbd85f59718803563580f1731b
+FAM
+FILE 7ec67cbbd85f59718803563580f1731b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:07:18 2013
+LENG 190 match states, 190 columns in multiple alignment
+FILT 120 out of 1646 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCEEEEEEECCCCHHHHHHHHHHHCCCCEEEEEEEC
+CCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9413099999999974787667618999999999899999999668876546744630799998999999985698244556677662257689999857
+755768899999999997650379978999987105663499999999731222102233114685299996788979999999999749
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxixlxGxxxxGKStlixxlxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDxxgxxxxxxxxxxxxxxxdxxixvxdx
+xxxxxxxxxxxxxxxxxxxxxxxxxxxiivxnKxDxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxSaxxxxxixxlxxxlxxxx
+>7ec67cbbd85f59718803563580f1731b
+MAGWDIFGWFRDVLASLGLWNKHGKLLFLGLDNAGKTTLLHMLKNDRLATLQPTWHPTSEELAIGNIKFTTFDLGGHIQARRLWKDYFPEVNGIVFLVDA
+ADPERFDEARVELDALFNIAELKDVPFVILGNKIDAPNAVSEAELRSALGLLNTTGSQRIEGQRPVEVFMCSVVMRNGYLEAFQWLSQYI
+>gi|328699670|ref|XP_001952428.2| PREDICTED: mitochondrial Rho GTPase-like [Acyrthosiphon pisum]
+---------------------------VIGSKGSGKSTICKRHVKTAK------IDNCFEdaeDI----TSVNRVQVYGQDKYLVLkeiktisenhLTKK
+DIKCDVVCLVFDSSQSCSFEYSAHVYLKYYQS---RNIPVLIVANDKGRPLmkqdyILQPDQFCKQNRLS-------------SPYIFINSNEG---KKL
+YSNLA---
+>gi|290971748|ref|XP_002668642.1| rab family small GTPase [Naegleria gruberi]gi|284082126|gb|EFC35898.1| rab family small GTPase [Naegleria gruberi]
+------------------LNtnKANFKLCITGPGGSGIHSFIHRYLNDVFYdQYDYSIDDIfYKTILFNErkVELEIWETGFRStDYYLFLESKLKGARG
+YIVLLPIHADVDkYGVFERIIKSIVYMHDDESVPLLIGITQIDKLETNSslnldqvKQKVTDIMNVY---------SCLDFEIVETSSKSNINIHTVIE-
+-----
+>gi|6690690|gb|AAF24258.1| UreG [Rhodobacter sphaeroides]
+---------------------DPCAWGSAARWAPARRPSTEKLCAALAHRCSMAVITNDIytredaealmraqvlpaerirgvetgaapytairedasin
+laavadlRRTFPDLDLILIESGGDNLAATFSPEL---ADLTIYVIDTAAGQ-------------DIPRKRGPGLarsdLLVVNKIDLAPhvGVDLARLEA
+DTQAA----------RGQRPYVMARMRAGVGVEAIVAFLEREG
+>gi|260810141|ref|XP_002599862.1| hypothetical protein BRAFLDRAFT_127644 [Branchiostoma floridae]gi|229285145|gb|EEN55874.1| hypothetical protein BRAFLDRAFT_127644 [Branchiostoma floridae]
+-------------------EKTNISIVVIGHVNSGKSNTTGHLiykcggidkrniekyereaaearfneiqqELSAcIKKVGYDPGTVAFVPVSAQHGDN
+MVEPSGNMPWYKGWSiernegngSGTTLlealdsilppqrpTDKPLRLPLADVynfrpggmgtmpvGRVetgILKPGmevtfapagltaevepvdikhES
+VPEALPGDTVGInfKNADVSVKELwrgcvagdSKNDppkeAVSFD--AEELSACiKKVGYD----PGTVAFVPVSAQHGDNMVE---------
+>gi|296089292|emb|CBI39064.3| unnamed protein product [Vitis vinifera]
+---------IAKTLRAMPvVDLETPTLCLVGAPNVGKSSLVRVLSTGKPEVcnyPFTTRGILMGHIAFNYRHFQVTDTPGLLNRHDDERNNLekltlavl
+sHLPTAILYVHDLSGECGTSPSDQFFIYKEIRERFSDHLWIDVVSKCDLLQespiifntEDVSADNPELARYQ---------KMGPEGAIHVSVKNEAAL
+NQLKGRVHELL
+>gi|14595136|dbj|BAB61872.1| Picchu-236-X [synthetic construct]
+------------------LDMAGNfdseersswywgrlsrqeavallqgqrhGVFLVRDSSTSPGDYVLSVSENSRVsHYIINSSGPRpPVPPSPAqppp
+gvspSRLRI----GDQEFDSLPALL-----EFYKIHYLDTTTLIEPVSR---------SRQGSGVILRQEEAEYVRAL----------------------
+----------------------------
+>gi|238852571|ref|ZP_04642981.1| ribosome small subunit-dependent GTPase A [Lactobacillus gasseri 202-4]gi|238834717|gb|EEQ26944.1| ribosome small subunit-dependent GTPase A [Lactobacillus gasseri 202-4]
+-----------------------------------------------------------------------------PRTNEIGRPAVANVSRVLLVISA
+VEPD---FSLELLDRYLTFFAWKNVGVVIYLSKADITpTEKlkAIKCKLDYY------------QKIGYSvFEDAEE----LERQLPTMIQKDQ
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * 1046 955 * * * * * * * * * 1
+ 0 * * * * * * 1747 0 0
+
+A 2 0 * * * * * * * * * * * * * * * * * * * 2
+ 0 * * * * * * 2344 0 0
+
+G 3 2052 * * * * 398 * * * * * * * * * * * * * * 3
+ 0 * * * * * * 2951 0 0
+
+W 4 * * * * * * * * * 1788 1254 * * * * * 2839 * 2724 * 4
+ 0 * * * * * * 4192 0 0
+
+D 5 * * 1829 3329 * 3546 * * 3578 * * 3470 * * * 1476 * * * * 5
+ 0 * * * * * * 5339 0 0
+
+I 6 * * * * 2497 * * 2435 * 1324 4200 * * 4094 * * * 3984 * 4009 6
+ 0 * * * * * * 6487 0 0
+
+F 7 3159 * 3289 * 2060 * * 3178 * 2446 * * * * * 3295 * 3272 * 4427 7
+ 0 * * * * * * 6963 0 0
+
+G 8 * * 2374 4399 * 2746 * * 3421 * * 3629 * 4377 3192 2109 4410 * * * 8
+ 0 * * * * * * 7112 0 0
+
+W 9 * 4454 4075 * 2869 * * 4252 4369 2768 * * * * * 2106 4318 3451 4430 3469 9
+ 0 * * * * * * 7112 0 0
+
+F 10 2475 * * * 2292 * * 3627 * 2547 3773 * * * 4590 4451 3524 * 4625 3716 10
+ 60 * 4625 * * * * 7428 0 0
+
+R 11 3558 * * 3954 4833 * 4900 * 3536 3686 4624 4531 * 2959 3286 2779 * 4631 4572 3736 11
+ 0 * * * * * 0 7605 0 1027
+
+D 12 * * 5060 3720 * 5051 5039 4929 2517 3107 * 4846 * 3949 2303 3831 3815 3910 * * 12
+ 106 3818 * 2711 239 * 0 8025 1214 1027
+
+V 13 4845 * 4859 4879 2817 * 4983 3415 * 2116 4978 4812 * * 4083 4864 4129 2734 5027 * 13
+ 0 * * * * * 0 8321 0 1027
+
+L 14 3616 5022 * * 2991 * * 5132 3940 1797 3435 * * * 4612 * 3685 3232 * 3989 14
+ 0 * * * * 0 * 8509 0 1027
+
+A 15 3262 * 2560 4124 * 4675 5023 * 2903 5046 * 5107 4910 3073 3557 2763 * 5533 * * 15
+ 92 * 4015 * * * * 8573 0 0
+
+S 16 4143 5086 * 5027 * 3635 4622 * 3346 5124 * 3411 5489 3472 3987 1580 5002 * * * 16
+ 0 * * * * * 0 8433 0 1412
+
+L 17 4191 3998 * 4010 4805 * * 3118 5067 1411 5033 * 5071 4920 * 4826 * 2886 * * 17
+ 300 * 2415 * * 0 * 8463 0 1412
+
+G 18 5003 * 3378 3295 * 3000 * 4802 5150 * * 2866 2730 5006 4823 2319 * * * 5213 18
+ 221 3136 5148 794 1240 1521 618 8477 1713 2188
+
+L 19 4301 * * 5307 3844 5298 5012 2813 * 1734 2971 * * 5311 4384 * 5353 3320 * 5071 19
+ 73 4337 * 1416 677 2406 302 8943 1497 1955
+
+W 20 3305 * 3239 3708 * 4540 * 3091 4504 3428 * 3854 5466 * 4388 2703 3214 * 5772 * 20
+ 0 * * * * 427 1966 9011 0 1747
+
+N 21 5483 * 5853 4422 * 5076 4760 3959 3561 5269 3611 3089 3177 3126 4365 6186 3701 3709 * 4966 21
+ 29 5664 * 1000 1000 * 0 9719 1038 1049
+
+K 22 3599 * 6046 4005 * 6059 4115 4521 2863 * * 4096 2286 3850 2890 3732 5067 * * 6211 22
+ 0 * * * * * 0 9974 0 1049
+
+H 23 6468 5272 4644 3656 4833 3588 4348 5119 2995 5393 6286 4740 3162 4309 3592 3507 3122 * * * 23
+ 19 6283 * 2322 322 * 0 10116 1027 1049
+
+G 24 5469 * 6232 6262 3035 3518 * 3577 4278 2790 4738 4158 3683 6219 6235 5268 4672 3385 6562 3437 24
+ 28 5682 * 4807 52 0 * 10146 1093 1049
+
+K 25 4620 5480 4562 5639 * 5070 4275 5367 2232 6571 * 3004 * 4903 2259 4856 3450 4250 * * 25
+ 89 4372 6404 0 * * * 10332 1784 0
+
+L 26 5528 3747 * * 3593 * 6532 1207 * 2877 6548 * * * * 6137 6669 2439 * 5523 26
+ 83 4158 * 333 2278 0 * 10351 1721 1002
+
+L 27 2928 4237 * * 4454 2744 * 3024 * 2460 5557 6497 * 6252 * 4326 4985 2489 * 6509 27
+ 0 * * * * * * 10444 0 0
+
+F 28 6118 * * * 2594 5824 * 2058 * 1710 4701 * * * * * * 2352 * 5494 28
+ 0 * * * * * * 10368 0 0
+
+L 29 4120 4233 6337 * 6586 6318 * 2207 * 2524 3719 * 6329 5860 6711 4732 3613 2202 * 6405 29
+ 0 * * * * * * 10561 0 0
+
+G 30 6252 * * * * 133 * * * * * * * * 5277 4880 * 6065 * * 30
+ 0 * * * * * * 10567 0 0
+
+L 31 4280 * 2978 4029 5072 5997 3775 * 3627 4569 5144 3960 2406 5113 3975 3953 4758 5296 * 5792 31
+ 0 * * * * * * 10567 0 0
+
+D 32 4206 6757 5889 3229 5639 4105 6716 4658 5239 6947 6065 4063 2615 5090 4448 2567 3471 3799 * 7105 32
+ 0 * * * * * * 10567 0 0
+
+N 33 3905 6279 3490 5857 * 1287 6618 * 3986 5580 * 2728 7300 4626 4990 3631 * * * * 33
+ 0 * * * * * * 10567 0 0
+
+A 34 2465 3286 6279 * * * 4868 4727 * 5440 * 5198 * * 5636 1773 3979 2287 * * 34
+ 24 * 5902 * * * * 10567 0 0
+
+G 35 5301 * 5372 * * 148 * * * * * * * 5870 * 5983 * 6068 * * 35
+ 0 * * * * 862 1152 10403 0 1198
+
+K 36 * * * 6337 * * * 6014 198 * * * 5984 5428 5044 * 6175 * * 5863 36
+ 0 * * 1000 1000 0 * 10555 1000 1000
+
+T 37 * * 6094 6604 * 5992 * * 5709 * * * * 5168 5448 1091 1311 * 5872 * 37
+ 15 * 6590 * * * * 10567 0 0
+
+T 38 3555 4879 5257 5262 6609 6744 6336 6266 * 4332 * 5212 * 6083 6271 1832 1401 6581 * 6724 38
+ 0 * * 0 * 0 * 10555 1000 1000
+
+L 39 4542 * * * 3013 * * 3138 * 1017 4969 6424 * * * 5230 4260 3854 * 4887 39
+ 0 * * * * * * 10651 0 0
+
+L 40 3917 3700 * * 3534 4673 * 1895 * 2471 5213 * * 5434 5340 6628 6874 2406 * * 40
+ 17 * 6408 * * * * 10651 0 0
+
+H 41 3878 6710 4521 4388 6441 5226 5454 6979 2712 4590 7135 2276 5901 3612 2893 4020 5585 * * 4686 41
+ 0 * * * * 0 * 10639 0 1009
+
+M 42 2999 5432 * 6956 5092 5131 5769 4227 3027 4401 7135 4761 * 3476 2250 3657 4496 4558 5896 5858 42
+ 0 * * * * * * 10651 0 0
+
+L 43 6005 7239 * * 2297 * 5770 2783 * 1529 5587 * 6442 * 5918 6464 5175 3340 5759 4080 43
+ 13 6753 * 5285 37 * * 10651 1030 0
+
+K 44 4187 3748 5770 5041 3414 6618 5591 4532 4470 2816 5959 4977 6408 6584 4192 3291 3073 3389 5284 * 44
+ 184 3060 * 2248 341 * * 10651 3220 0
+
+N 45 4037 * 4395 3489 5930 2128 5327 6071 3805 4178 * 4105 6767 3399 4464 4744 3817 * 5271 4348 45
+ 191 5146 3387 3209 165 * * 10526 1443 0
+
+D 46 4651 6598 3724 3892 * 3114 5005 6738 2801 4919 * 2895 * 3837 3748 3798 4691 4553 * 4566 46
+ 44 5679 6613 668 1432 3945 97 10477 1202 2862
+
+R 47 4377 5503 3286 3355 4915 4610 6507 5067 2805 4034 5060 4362 4576 4249 4460 3362 5335 4532 * 5230 47
+ 44 * 5056 0 * 2783 227 10482 1000 3034
+
+L 48 3985 * 4506 5822 2567 4191 5444 4013 4241 3200 4483 5404 3598 * 4770 4210 4268 4608 * 3826 48
+ 189 3268 5700 4334 73 2378 308 10470 2978 3179
+
+A 49 3790 6734 4624 4328 5701 * 5806 3716 4483 3751 4951 3724 3089 5781 3832 2850 5057 3474 * 5432 49
+ 447 1909 * 664 1438 3943 97 10515 4986 3042
+
+T 50 4428 * 3359 3570 * 4768 4906 3583 5126 4975 5985 3746 3351 3645 4225 3227 4059 4068 * 6683 50
+ 149 3348 * 1977 423 3331 151 10514 2623 3072
+
+L 51 5905 6480 4737 4512 6350 3738 3785 6238 3810 3696 * 4959 4116 5636 4971 4318 3338 3213 * 2551 51
+ 74 4604 6810 1003 997 * 0 10525 1743 2870
+
+Q 52 4342 * 4086 3468 4334 2936 5707 3475 3970 6645 6681 6636 4032 4242 5942 2373 5590 4592 * 4922 52
+ 29 6574 6769 1000 1000 * 0 10464 1000 3184
+
+P 53 3196 6381 4252 4060 6281 6784 4573 3762 5780 5665 * * 1991 4865 5391 3340 2965 4199 * * 53
+ 194 2990 * 3700 115 223 2802 10461 3021 3362
+
+T 54 4812 * 4853 4664 5434 4347 6020 4019 4140 4439 6653 4613 5062 4528 5212 3646 1520 4092 * * 54
+ 17 6427 * 1000 1000 * 0 10645 1046 1211
+
+W 55 5050 7057 5598 4899 4880 4626 5030 2663 5245 2476 4502 4192 3768 * 4634 3878 4138 4158 7183 4684 55
+ 23 5971 * 1156 859 948 1054 10645 1290 1211
+
+H 56 4536 6924 3531 3471 4961 2145 7196 4704 3437 5714 * 4783 5837 4195 4344 3332 4262 5464 * 5290 56
+ 116 3695 * 1532 612 0 * 10675 2521 1000
+
+P 57 4404 4788 5166 3725 3700 4526 7100 3067 5753 4228 5338 4460 3326 4923 5902 5167 3928 3293 * 3658 57
+ 0 * * * * * * 10689 0 0
+
+T 58 4378 4482 2947 3947 5678 5694 6882 4916 4103 5298 * 3777 4493 3728 5848 3742 2592 4762 * 4036 58
+ 85 4316 7161 2565 267 * * 10689 1901 0
+
+S 59 4081 6824 6773 3471 3911 4516 5948 3577 5187 5922 6008 4593 * 4092 3483 3065 3300 3337 6890 4468 59
+ 160 3255 * 1034 967 * 0 10680 2978 1000
+
+E 60 4480 5633 4617 3673 5277 2349 5048 5768 3072 4304 * 4381 5595 4190 5162 4123 3440 4227 * 5548 60
+ 93 5113 4893 4973 47 * 0 10680 1531 1000
+
+E 61 4856 6591 3683 4256 5697 6972 4061 3674 3159 4201 6706 5496 3921 5439 3403 3654 3268 3764 * 5583 61
+ 23 * 5989 * * * 0 10592 0 1652
+
+L 62 4615 6622 6641 4745 3575 5155 * 2441 5280 2639 3795 5840 5344 * 5281 6563 5360 2433 6718 4323 62
+ 27 6605 6973 3187 168 1854 467 10713 1373 2001
+
+A 63 4427 6788 4300 2507 6816 5362 5538 4165 3839 4103 * 4843 4879 4380 3813 3721 3286 4285 * 4021 63
+ 24 5912 * 671 1428 1925 441 10504 1192 1846
+
+I 64 4269 5779 * 5581 3187 6288 5225 2704 6683 3407 4870 4107 * 5926 6254 3992 5236 2890 4148 3326 64
+ 151 3514 6383 3166 170 2145 370 10563 2609 1798
+
+G 65 4575 6717 2351 4084 6675 3106 4635 6476 3957 4917 * 3672 3890 3839 4853 3783 5142 6633 * 4130 65
+ 104 3850 * 1937 437 644 1474 10520 2381 1810
+
+N 66 3944 * 2839 3462 5647 2186 4515 * 4233 6837 * 3098 6930 * 4677 3050 4588 5943 6694 7186 66
+ 850 1235 5624 2018 409 1093 913 10598 7132 1174
+
+I 67 4490 4753 5234 3997 3698 5822 4668 3015 5388 3573 6484 6757 6383 7328 3611 3892 4475 2808 * 3508 67
+ 45 6003 6019 4524 64 944 1059 10534 1113 1581
+
+K 68 4465 5178 3621 3818 * 5637 5528 4585 2709 4667 * 3827 3960 3570 3255 5180 4557 4177 5616 5075 68
+ 135 3480 * 4412 69 * 0 10540 2672 1445
+
+F 69 4622 4942 5576 5659 2757 * 6666 2743 5650 2211 4766 6612 6975 6621 6256 6764 5969 2646 7369 3759 69
+ 34 7015 5983 0 * 851 1166 10531 1004 1603
+
+T 70 5494 5816 6989 3347 6757 6305 4638 4127 4815 3397 4822 3575 6666 3245 4904 3929 2943 3009 * 5937 70
+ 0 * * * * * 0 10658 0 1560
+
+T 71 5150 5793 6666 5598 2739 6305 * 2030 6762 2182 4772 * 5900 5019 5662 * 4836 3218 * 4642 71
+ 58 * 4672 * * * 0 10658 0 1560
+
+F 72 4331 5794 * 4648 4850 6942 * 2507 6710 3755 5992 6662 6383 * 5154 * 4404 2608 2070 3739 72
+ 30 5600 * 1400 687 2866 213 10507 1247 2237
+
+D 73 * * 676 3146 6750 4540 6787 6857 * * * 4414 * 5263 4780 4971 4994 * * 5767 73
+ 54 4757 * 1739 514 1033 967 10438 1738 2052
+
+L 74 4295 4733 5040 6980 4109 6825 * 3096 * 2487 6612 * * * 5542 3987 1659 4025 6876 5072 74
+ 25 6964 6779 4087 87 1924 441 10576 1000 1459
+
+G 75 3167 6917 5023 5170 5812 2253 6659 5824 5037 * 6893 4799 1741 * 5052 3389 5061 4750 * * 75
+ 14 6727 * 2585 263 1146 867 10594 1000 1440
+
+G 76 5200 * 5088 4682 5775 791 5938 6086 4775 5281 * 5259 6786 6891 6743 3812 5144 5222 * 4802 76
+ 111 3898 7132 2153 367 * 0 10667 2292 1155
+
+H 77 4389 * 3408 3943 3499 4453 3598 3844 5659 4581 * 4596 5350 2530 * 3833 5944 4082 * 4043 77
+ 65 4907 6583 3149 173 694 1389 10658 1580 1317
+
+I 78 4825 5699 3052 2448 6889 3894 5395 4514 4930 4707 6087 3785 3774 4383 3847 4390 4329 5326 6538 5923 78
+ 163 3354 6823 2497 281 * 0 10684 2844 1200
+
+Q 79 3850 * 2708 2835 7146 4736 5677 5960 3243 5277 * 4941 4583 4352 2836 3709 4505 6354 6392 5804 79
+ 96 4148 6957 3448 139 1894 452 10667 2333 1539
+
+A 80 4447 * 5872 5508 2483 5152 4255 3902 * 2675 4569 4699 4338 4911 6519 4428 4448 5141 6780 2961 80
+ 39 5215 * 2617 257 * 0 11556 1332 1513
+
+R 81 3665 * 3003 3707 5359 5853 5945 4852 3725 3585 4810 4625 4768 5295 2888 4389 4120 4001 * 5195 81
+ 59 4644 * 847 1171 400 2047 11556 1602 1513
+
+R 82 3537 5798 4992 3536 4609 4246 5528 6192 3822 5294 7200 3948 4149 3828 4085 2655 3274 5954 * 5847 82
+ 25 * 5882 * * * 0 11594 0 1000
+
+L 83 3622 4749 7145 3929 5061 5590 7420 4122 3844 2610 3722 5006 7084 3710 6728 3771 3779 3860 * 4432 83
+ 82 5149 5191 1883 456 539 1682 11554 1417 1358
+
+W 84 4564 * 4232 4939 4745 5208 4871 3420 * 3115 5390 3923 5587 5842 3345 4646 3645 3710 3486 4250 84
+ 44 5065 * 3025 189 943 1059 11554 1392 1571
+
+K 85 3561 6949 3999 3381 4647 5807 5254 4637 3319 4768 * 5198 2727 3915 3532 3472 5636 5189 * 5723 85
+ 31 6069 7304 1538 609 * 0 11571 1172 1176
+
+D 86 3411 6769 3337 3693 6883 4580 5144 5283 3981 3846 5264 3615 4763 4011 4362 3209 3779 4403 * * 86
+ 127 3920 5794 913 1092 * 0 11550 2148 1371
+
+Y 87 3296 4525 * 5620 2844 4922 5538 3099 5734 2525 5271 * 7494 4017 6857 4593 4807 4842 * 3089 87
+ 97 5313 4650 1951 432 2321 322 11528 1362 1773
+
+F 88 4153 6990 * 4340 2751 5562 * 2855 5893 2385 4816 * * 4351 5030 4439 4716 3599 6257 3727 88
+ 241 2764 7276 2686 244 * 0 11471 3546 2524
+
+P 89 4593 6592 5221 3321 5158 4210 4772 5888 2788 5337 6686 4820 3428 3860 2833 3348 5261 4481 * * 89
+ 43 5092 * 2000 415 3450 138 11486 1338 2687
+
+E 90 4978 * 3833 3156 6399 3352 4479 4700 3345 3759 6407 2900 * 4106 4085 4117 4593 5697 6794 5036 90
+ 0 * * * * 975 1026 11496 0 2529
+
+V 91 2375 3478 5228 4870 5207 5061 * 4137 5606 3202 4920 6553 4033 * 6763 3236 3885 3127 6470 * 91
+ 22 6050 * 5209 40 2243 342 11523 1113 1687
+
+N 92 4541 * 1375 4442 4519 4707 3507 6440 5067 5154 * 3651 * 4173 4837 4076 4685 6601 * 6989 92
+ 27 5768 * 3955 96 469 1848 11511 1187 1506
+
+G 93 2676 4192 * 5719 4962 2423 * 3141 5632 3541 4795 5812 6329 6843 5047 5145 4893 2677 * 6917 93
+ 0 * * * * * 0 11568 0 1000
+
+I 94 3065 4945 * 4878 3273 6958 5514 2217 * 2636 5904 * * * 5642 4764 4765 2725 * 4533 94
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+
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+
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+
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+
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+
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+C 171 4530 3304 7059 * 5144 4184 7109 2437 * 3905 4715 6325 * * 6307 5582 2489 2111 * 6330 171
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+ 28 5699 * 753 1299 497 1778 10432 1431 1480
+
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+ 63 5431 5669 3138 174 0 * 10474 1177 1001
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+G 178 4541 * 4209 * * 1262 6642 * 4650 * * 2343 6530 3614 5666 3602 4876 6575 * * 178
+ 30 5582 * 1510 624 1197 826 10480 1142 1211
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+Y 179 4995 6621 5241 * 4438 6649 6705 1821 5479 2680 4094 7086 4926 * * 5584 6688 1909 * 6753 179
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+E 181 4272 * 2771 1503 * 5022 * 6550 4520 4300 * 4459 5239 4288 4003 4533 4043 5398 * * 181
+ 0 * * * * * * 10387 0 0
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+A 182 2948 6289 * 6656 4882 4230 6292 3633 * 1428 4997 * 5640 * 6560 6279 4072 2846 5508 * 182
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+
+F 183 6323 6115 * 5623 1899 6439 * 3615 3831 2149 3702 * 6105 5317 4555 5563 6586 4321 5568 4879 183
+ 0 * * * * * 0 10379 0 1000
+
+Q 184 3069 * 3171 2543 * 4967 * * 3596 4215 6454 3523 * 3985 4118 3859 3581 4414 * 6490 184
+ 0 * * * * * 0 10354 0 1000
+
+W 185 2861 * 4660 3698 4384 3833 5320 5742 2954 4169 6352 6609 5720 5124 5339 4446 4668 4920 2990 4049 185
+ 0 * * * * * 0 10298 0 1000
+
+L 186 6354 6371 * * 6731 * * 2050 * 1134 3656 * * * * 6527 6279 2589 * * 186
+ 0 * * * * * 0 10267 0 1000
+
+S 187 2843 4416 5019 3305 6100 4770 * 2938 4794 3484 6395 * * * 4047 3123 4687 3131 6546 5391 187
+ 0 * * * * * 0 10180 0 1000
+
+Q 188 3987 * 2970 2982 * 5203 5328 * 2581 5318 * 3477 * 2880 3505 4263 4052 * 6327 * 188
+ 0 * * 2585 263 0 * 10114 1000 1000
+
+Y 189 3237 5828 5392 5102 3457 * 4710 4432 3429 2710 4094 4435 * 3595 3414 4684 * 5927 * 3935 189
+ 0 * * * * * * 9902 0 0
+
+I 190 * * * * 3526 * * 1857 * 1549 * * * * 5789 5646 5090 2132 * * 190
+ 0 * * 0 * * * 9404 0 0
+
+//
+�HHsearch 1.5
+NAME 81e79b5741c9fbdcdbbebf2c8b14e32c
+FAM
+FILE 81e79b5741c9fbdcdbbebf2c8b14e32c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:06:51 2013
+LENG 163 match states, 163 columns in multiple alignment
+FILT 142 out of 1148 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCEEEEEEECCEEEEEEEEEEECCCCEEEEEEEEECHHHCCCCHHHHHHHHHHH
+HHHHCCCCEEEEECCCHHHHHHHHCCCEEEEEECCCEEECEECCCCCEEEEEEECCCCCCCCC
+>ss_conf PSIPRED confidence values
+9799992788998999999999999764367668999999863689858999998998999999999279988999999997888489899999999999
+999869969999348379999998899999674463120403189976999998899988679
+>Consensus
+xxxxxxxxxxxxxxxxxxlxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxvGxxxxxxxxxxxxxxixxxxvxxxxrxxGxgxxllxxxxx
+xxxxxxxxxxxxxxxnxxxxxyxxxGfxxxxxxxxxxxxxxxxxxxxxxxmxxxlxxxxxxxx
+>81e79b5741c9fbdcdbbebf2c8b14e32c
+LLDFDILTNDGTHRNMKLLIDLKNIFSRQLPKMPKEYIVKLVFDRHHESMVILKNKQKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKD
+HMQKQNIEYLLTYADNFAIGYFKKQGFTKEHRMPQEKWKGYIKDYDGGTLMECYIHPYVDYGR
+>gi|328907443|gb|EGG27209.1| acetyltransferase, GNAT family [Propionibacterium humerusii P08]
+--------------------QVYDDWASdpevtrflTWPTHSsvdvsravVGPWVDSY--eDPGTFNWGIELieDGTLIGQTSV-VKEDLT-VGLvnVGY
+VVGRRWWGKGYCTEALVAVMNYLFAvAEANKveASHDPANvASGRVMEKAGMVAEGLRRA----SCLSGsmIRVQLYHGM----------
+>gi|320156268|ref|YP_004188647.1| acetyltransferase [Vibrio vulnificus MO6-24/O]gi|319931580|gb|ADV86444.1| predicted acetyltransferase [Vibrio vulnificus MO6-24/O]
+--KFEHKKVEPSNIDFQSLVGELNSSLTQITSDSgESSFASDAFDSSKDGCIVVYLNNVAVACGVFRYHEN-EVCELKRMYSN----KSGAGSYLLKHLE
+CYAVSKGYRKaiLSTRRVNsKAVSFYERNSYSES------SAYGKYVGVKRSICLSKVLVT------
+>gi|302526259|ref|ZP_07278601.1| predicted protein [Streptomyces sp. AA4]gi|302435154|gb|EFL06970.1| predicted protein [Streptomyces sp. AA4]
+EIAFLPPSAAeDTALVALLTDLVNTVYAKAEAGLWAGSADRTNAGEmaglvRAGEIAVARIDGTVVGSVRIQRLAE-DLGEFGLLAASPEVRGAGIGRAL
+VEFAESCCRAQGCTRmqleLLVPreWTHPSkeflAQWYGRLGYQVVeTSTIDGPHPELAPLlatPCDFLIWHKDL--------
+>gi|168701123|ref|ZP_02733400.1| hypothetical protein GobsU_16469 [Gemmata obscuriglobus UQM 2246]
+------------------FSMLRKRYETQVMRaaGVPSWWHECvWGTLDPVEFrMVDKLASGFIAArALVWELEGygwrwgFPSAGVLDIQVRSDLRRLG
+LAKLLLSQILRFLQDQFFGICEVQapAADpALVGLCRSVTLDH----------------------------------
+>gi|290954852|ref|YP_003486034.1| acetyltransferase [Streptomyces scabiei 87.22]gi|260644378|emb|CBG67463.1| putative acetyltransferase [Streptomyces scabiei 87.22]
+----------------------------------RTEKEQRVRESRTHASLVF-AGDDCLGWCQFGSPAElpeikrerryekdltvLPDWRITCFFTGKG
+LRKRGVAHAALEGALTQISRNGGGTVEGYPeethgrtlsgSFlhtGPMAV-----fenhgFTRTRPISP-----------HRWVV----tltvDP-----
+-
+>gi|301165969|emb|CBW25543.1| hypothetical protein BMS_0636 [Bacteriovorax marinus SJ]
+--HWRCMNTVIEHAKLTDVNELLSLYLSvygedyplDIG-TKRSVMEEALNHPEENHWYVMRcTdSNQIIVSGIIQIERENLIGKLSGVAVHDEYRKHGL
+ATGFIGHVVNEVLKEKkLvNSIYATARTiShsSQTMLMKNGFIPLGFFPNCRRIKTYETlallaiFADGVLEKRKVPTVVP---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+L 1 3147 * 3165 2136 * 3235 * * 3300 3207 * 2107 * * * * * * * * 1
+ 0 * * * * * * 5162 0 0
+
+L 2 * * * * 3954 * * 1618 * 1578 4843 * 4907 * * 5057 * 3979 * 3144 2
+ 0 * * * * * * 8544 0 0
+
+D 3 5160 * 4278 3488 * * 3975 3613 4143 5192 5177 * * 2940 2869 3211 2564 * * 5049 3
+ 37 5309 * 1000 1000 * * 9132 1000 0
+
+F 4 5237 * * * 1686 * 4457 1882 * 2679 * * * * * * * 3440 5302 3793 4
+ 0 * * * * * * 9532 0 0
+
+D 5 * 5437 3114 3186 5378 * * 5539 3115 5553 5363 * * 4023 1532 5521 3929 4314 * * 5
+ 0 * * * * * * 9532 0 0
+
+I 6 5625 5357 5680 4508 3814 * 4540 2389 4029 4615 * * 2663 5608 2918 5451 3930 4043 * 5329 6
+ 0 * * * * * * 9604 0 0
+
+L 7 4022 * * 5592 3551 5537 * 3080 4545 2099 4551 5457 4022 * * * 5232 1929 * * 7
+ 0 * * * * * * 9681 0 0
+
+T 8 3372 5649 3727 3668 * 5582 4670 * 3550 5690 * 3538 * * 4698 2441 1968 * * * 8
+ 27 * 5774 * * * * 9822 0 0
+
+N 9 3424 * 3396 3310 5747 * * 4097 3145 4179 * 1766 * * 4188 * 3687 4668 * * 9
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+K 139 3982 * 5591 3655 4102 4452 4022 3923 2409 4086 5637 5602 5572 5665 3071 4113 * 4013 * 4721 139
+ 0 * * * * 267 2567 9548 0 4435
+
+G 140 5052 * 3709 3225 6061 2473 3596 * 4008 5020 * 3030 4445 * 2808 4937 5070 4563 * * 140
+ 0 * * * * * 0 10074 0 1550
+
+Y 141 5755 * 4855 4241 2607 5825 * 3840 4776 2961 4749 * 5534 * 4410 6065 5555 6072 4793 1813 141
+ 0 * * * * * 0 9803 0 1550
+
+I 142 4726 * 5212 * 3501 * 5774 3843 6024 2977 5693 * * 5768 5684 4735 * 3213 4774 1405 142
+ 55 * 4749 * * 915 1090 9760 0 1550
+
+K 143 4864 * 4515 3168 5763 3177 4947 * 2659 4121 5641 3845 3756 3912 3605 3957 5694 5881 * 5611 143
+ 89 5723 4604 1585 585 * 0 9676 1005 1518
+
+D 144 4604 * 2601 3259 * 3405 * 5665 3649 4416 * 2982 3449 3704 * 4024 4566 5568 * 5094 144
+ 1218 956 4194 1792 491 530 1701 9543 4656 1865
+
+Y 145 * * 4588 5440 3453 1725 5896 * 4571 5677 5567 3400 3597 * 4537 4720 * 4612 4640 3283 145
+ 26 5829 * 2000 415 1004 997 9502 1135 1925
+
+D 146 4477 4629 3291 2122 5481 3745 4619 5644 4567 4571 4576 3299 5657 5867 4514 4127 5876 5647 5481 * 146
+ 29 5643 * 1585 585 978 1022 9507 1005 1394
+
+G 147 4658 * 1675 5489 * 2395 5697 * 5643 5417 * 3472 2939 5734 4630 6049 * 5813 * 4068 147
+ 0 * * * * * 0 9439 0 1112
+
+G 148 2439 4564 4567 3518 4425 2967 4454 * 4682 3883 * 4963 * * 5560 2965 5355 3445 * 5692 148
+ 33 * 5463 * * * 0 9296 0 1112
+
+T 149 4387 * * * 4594 * * 2458 * 2293 5810 5362 * * 4581 5759 3464 2634 4438 3006 149
+ 35 5383 * 0 * * 0 9249 1000 1282
+
+L 150 5680 5569 4523 * 3432 * 4727 2719 5322 1863 * 5810 4437 * 4077 * 4372 3184 * 4264 150
+ 0 * * 1000 1000 0 * 9249 1005 1282
+
+M 151 5930 5751 * 5293 4530 * 5411 4362 * 1919 1302 * * * * * 5403 5718 5315 3532 151
+ 0 * * * * * * 9330 0 0
+
+E 152 4371 4895 * 2269 * * 4340 5307 3621 3910 5528 * * 4497 3215 3101 * 2945 5513 4436 152
+ 0 * * * * * * 9105 0 0
+
+C 153 * 3814 * * 5123 * 5358 4470 1819 1776 * * * * 2887 * * 5570 3793 5210 153
+ 80 5095 5331 0 * * * 9014 1103 0
+
+Y 154 4356 * 3526 * * 5256 4154 5289 2601 4053 5580 4219 3699 5382 3024 * 4285 4215 3347 5087 154
+ 0 * * * * * 0 8734 0 1053
+
+I 155 * * * * * 5028 4835 2742 * 871 4743 * 4978 * 3839 * 4010 4758 * * 155
+ 59 * 4649 * * * 0 8374 0 1053
+
+H 156 4366 4454 2869 * 4342 4583 2582 * 3425 * * 4622 4213 4247 3492 4567 3416 4443 * * 156
+ 0 * * * * 0 * 7306 0 1219
+
+P 157 3473 * 2363 4485 * * * * 3271 * * * 1531 4160 * * 3255 4044 * * 157
+ 0 * * * * * * 7124 0 0
+
+Y 158 3796 * 4106 2320 * * * * 2437 * * 3023 * 2960 * 3603 * 3714 * 3737 158
+ 0 * * * * * * 6311 0 0
+
+V 159 3669 * * 3724 3752 * * 2662 * 2581 * * 2627 * 3538 * * 2333 * * 159
+ 0 * * * * * * 5625 0 0
+
+D 160 * * 2384 3536 3274 * 3509 * * * * * 2373 3506 * 3532 2613 * * * 160
+ 0 * * * * * * 5355 0 0
+
+Y 161 * * * 2907 2849 * * * * * * * * * 2842 * * 2914 * 1134 161
+ 0 * * * * * * 4037 0 0
+
+G 162 * * * * * 1989 * * * 1426 * * * * * * 2389 2434 * * 162
+ 0 * * * * * * 3260 0 0
+
+R 163 2487 * 2389 * * * * * * * * * * * 665 * * * * * 163
+ 0 * * 0 * * * 3260 0 0
+
+//
+�HHsearch 1.5
+NAME 8237cebaaa25ac6a2b0d49c9d5837da5
+FAM
+FILE 8237cebaaa25ac6a2b0d49c9d5837da5
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:52:06 2013
+LENG 188 match states, 188 columns in multiple alignment
+FILT 83 out of 85 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEECCCCEEECCHHHHHCCCCCCCCC
+CCCEECCCCEECCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCC
+>ss_conf PSIPRED confidence values
+9965414557703789992798677767613388999999998378762456775152368420340105678808356978556899970798885688
+9857674896647899876116876789997662348533554468762420344668964337765677765899985365556688
+>Consensus
+xxxxxxxxxxxxxLxliAlNxPxxGdlgGixGADxxCxxqAraaGlxgTfRAfLSsxxqdlxxiVxxxDRxxxPxvNlkGevLfxswxxlfxxxxxxxxx
+xxxIxsfngxdVltdxxwPqKxvWhGSxxxGxxxxdxxCxxWxsxxxxxxGxAsxlxxxxllxqxxxsCxxxxivLCiExxxxxxxxx
+>8237cebaaa25ac6a2b0d49c9d5837da5
+APLAHTHQDFQPVLHLVALNTPLSGGMRGIRGADFQCFQQARAVGLSGTFRAFLSSRLQDLYSIVRRADRGSVPIVNLKDEVLSPSWDSLFSGSQGQLQP
+GARIFSFDGRDVLRHPAWPQKSVWHGSDPSGRRLMESYCETWRTETTGATGQASSLLSGRLLEQKAASCHNSYIVLCIENSFMTSFSK
+>gi|328709259|ref|XP_003243912.1| PREDICTED: hypothetical protein LOC100573836 [Acyrthosiphon pisum]
+-----------KMLRIAALNEPYTGNMHGVQSVDYSCYRQSQRAGLHGAFKAFLSSRINNLKTIVHESDRD-LPVVNIKGDVLFNSWKDIFSENGAFISQ
+QPRIYSFSGKNVLTDFTWPQKTIWHGSDMSGDSAVDGNCDAWNSESSDKRGLGSSLTpksdrQAKLLDQDSaFDCRNFFVVLCVEI--------
+>gi|268566099|ref|XP_002639634.1| C. briggsae CBR-CLE-1 protein [Caenorhabditis briggsae]
+---------KDRVIHMIALSQPFAGNIHGLRGADLQCYREARASGYTTTFRAMLSSNVQDLVKIVHSVDHD-TPVVNIAGHHLFASWRSFVNG--AKINQ
+HARLFSFDRHDVLNDSRWPDKRVWHGSKEGGIR-ADQYCDGWRRSDASITSLAGQIYSNTTIFQSSgpSTCENKLVILCVENM-------
+>gi|313229600|emb|CBY18415.1| unnamed protein product [Oikopleura dioica]
+----------GKRIRLVALDVPMSGLTHGVRGLDHRCYNAARSSRLRGTFRGFVSAVVQDINTIVRRSERYDYPICNSKDELLFNSWNELFSDESNkGAL
+YGKSIYSFSGRDILTDRRWPNKSIWTGSTPDGRRNPSKYCDGWRSANSNNVGLSSNLSAG-LLNQQVSKCSERKVILCVENAA------
+>gi|149584137|ref|XP_001519691.1| PREDICTED: similar to type XVIII collagen alpha 1 chain, partial [Ornithorhynchus anatinus]
+---------LSPQLRLVALNAPLPGHLGGLRGADLQCHQQAREAGLYGTFRALLAASGQRLASLVHRADRV-LPIVNLQGQRLARTWESLLESKTRRAhG
+LRAPIYTFDDRAVLEDPLWTQKAAWIGPSQKDSPGPQGTCQDWRMG-SGVQGLAALLDEREFPRVASLDCAESLAVLCIEIAFP-----
+>gi|76152955|gb|AAX24626.2| SJCHGC06390 protein [Schistosoma japonicum]
+-----------KKLYLIAQNEPLRGDLKhgdRITGAhagsIFACQ---RAANLKGLGRAFyplLSTDMFNMDYVVPPTYRYGVPLVNLYGEVLFDDFMSL
+V---EGRSRPQAKILNFDGADIADDIVAP--CIWIGQKPIylngdYEYAAQSKCRNWQSTYPGENGF---------------------------------
+---
+>gi|149920904|ref|ZP_01909366.1| putative lipoprotein [Plesiocystis pacifica SIR-1]gi|149818303|gb|EDM77756.1| putative lipoprotein [Plesiocystis pacifica SIR-1]
+------------------TSEDFSGDLGGLTGADAACQQLAEAAGLTGDYLAWLSASPlsapasrfvQsnALYRLV-------------DGTPVAANWGD
+LVDDT---LAAAINMDEFG------ATVGP-HRVWTNTSSSGHYDTSSTCLGWHSED--GTGRAGHTNEVdKnWTSHAFHPCSFSAKLYCVQ--------
+-
+>gi|121606464|ref|YP_983793.1| hypothetical protein Pnap_3576 [Polaromonas naphthalenivorans CJ2]gi|120595433|gb|ABM38872.1| conserved hypothetical protein [Polaromonas naphthalenivorans CJ2]
+-----------------------GADLGGLAGADAYCQTLAASANAGGkNWRAYLSAPASGASPAVNARERIgRGPWQNARGVVVATSVDNLHSADNQ-L
+TKQNsltekgEVVsgrgdAVNMHDMLT-----------GSTADGRLDTsapDTTCGGWTQSG--------------------------------------
+----
+>gi|24213395|ref|NP_710876.1| hypothetical protein LA_0695 [Leptospira interrogans serovar Lai str. 56601]gi|24194153|gb|AAN47894.1| LenA [Leptospira interrogans serovar Lai str. 56601]gi|86753692|gb|ABD15102.1| LenA [Leptospira interrogans serovar Pomona]
+---------------FIATNngAGYNGNLGGISGADAKCA-AAKSSSLTGAYKALIVDGPTG-RQVISALDGS----VDKKDWVLYSNKQYRRSDGTtIT
+FTTNAnSIVIdnlQNGID-----SGAQKFFWNGLGNNvGfLWEPLSNCNNWNSADGLITGQAGNTTelqADItpegAFTVDNHACNTNLNLLCVE-----
+----
+>gi|307823103|ref|ZP_07653333.1| conserved hypothetical protein [Methylobacter tundripaludum SV96]gi|307735878|gb|EFO06725.1| conserved hypothetical protein [Methylobacter tundripaludum SV96]
+-----------------------GAELGGLAGADAHCQKLAEAAGSVNkTWHAYLSTQAADGQPVINARDRIgSGPWHNAKGAEVAKNIAHLHGNTLela
+rlgNNLSRTTV-LTEKNETVNGAGDKPnQHDILTGSQPDGTAftdAADHTCKNYTrSAED----------------------------------------
+-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 1000 * * * * * * * * * * * * * * 1000 * * * * 1
+ 0 * * * * * * 1118 0 0
+
+P 2 * * * * * * * * * * * * 0 * * * * * * * 2
+ 0 * * * * * * 1487 0 0
+
+L 3 2730 * * * * * 3982 1881 * 2613 3225 * 2396 * * * 4214 * * * 3
+ 0 * * * * * * 2121 0 0
+
+A 4 1560 * * * 3563 * * 4360 * 4402 * * 2758 * * 2694 4619 2865 * * 4
+ 0 * * * * * * 2194 0 0
+
+H 5 * * * * * * 492 4402 * * * 4048 3524 * * 3410 * * * * 5
+ 0 * * * * * * 2194 0 0
+
+T 6 3410 * * * * * * * * * 4048 * * * * 1926 1083 3181 * * 6
+ 0 * * * * * * 2194 0 0
+
+H 7 * * 3524 * 2801 * 1063 * 4048 3490 * 3410 * * * 4402 * * * * 7
+ 0 * * * * * * 2194 0 0
+
+Q 8 * * * * * * 2174 * * * * 3671 * 2020 4956 4304 2901 2567 * 3884 8
+ 820 4481 1364 2408 301 * * 2384 1081 0
+
+D 9 2743 * 1620 2495 * * * * 3841 3964 * 2617 * 4293 * * * * * * 9
+ 295 4293 2901 2807 222 0 * 2553 1000 1282
+
+F 10 5376 * 4569 3942 2343 4461 * * 2391 3864 * * * * 4420 2304 3923 * 4968 5660 10
+ 65 4506 * 0 * 851 1166 2967 1029 1064
+
+Q 11 5595 * 2743 * 5257 2041 * 4118 4760 * 5543 4300 * 2370 4369 3457 5082 4977 * * 11
+ 0 * * * * * 0 3085 0 1005
+
+P 12 5929 * * 5445 * * 5422 * 2303 5282 4998 * 1264 4491 2879 6157 4663 5191 * * 12
+ 0 * * * * * 0 3218 0 1005
+
+V 13 2150 * * * * 4207 * * 4095 * 3961 5377 * 2599 3612 3178 5900 2325 * * 13
+ 20 6204 * 3700 115 0 * 3219 1000 1005
+
+L 14 * * * * * * * 3105 * 178 * * * * * * * * * * 14
+ 0 * * * * * * 3270 0 0
+
+H 15 * * * * * * 823 * * * * * * * 1401 * * * * 4154 15
+ 0 * * * * * * 3270 0 0
+
+L 16 * * * * 2924 * * 5504 * 827 2098 * * * * * * 4347 * * 16
+ 0 * * * * * * 3617 0 0
+
+V 17 2241 * * * * 6327 * 1272 * * * * * * * * * 1558 * 5487 17
+ 0 * * * * * * 3617 0 0
+
+A 18 0 * * * * * * * * * * * * * * * * * * * 18
+ 0 * * * * * * 3617 0 0
+
+L 19 * * * * * * * * * 362 * * * 4432 * * 2512 * * * 19
+ 0 * * * * * * 3732 0 0
+
+N 20 * * 4930 * * * * * * * * 225 * * * 3163 * * * * 20
+ 191 3011 * 1000 1000 * * 3732 1238 0
+
+T 21 2023 * 5875 1755 3940 5715 * * * 6466 6691 6321 * 3482 * 3915 3495 4098 * 5650 21
+ 0 * * * * * * 3732 0 0
+
+P 22 5802 * 4285 * * 3011 * * * * * * 310 * * * * * * * 22
+ 0 * * * * * * 3732 0 0
+
+L 23 * * * * 2418 * 5101 6087 * 1655 3486 * * 3813 * 4664 * 5072 * 2172 23
+ 0 * * * * * * 3732 0 0
+
+S 24 4041 * 5001 * * 1846 * * 6738 * * 3374 5308 * 3877 1967 2960 5169 5750 * 24
+ 0 * * * * * * 4277 0 0
+
+G 25 2852 * * * * 265 * * * * * * * * 5101 * * * * * 25
+ 18 6346 * 2585 263 * * 4329 1005 0
+
+G 26 6375 * 1195 6018 * 5175 5383 * * 5438 * 1339 * * 5681 4438 * * * * 26
+ 40 * 5197 * * * * 4329 0 0
+
+M 27 * * * * 4784 * * 4085 * 926 1629 * * * * * 4571 6270 * * 27
+ 0 * * * * * 0 4282 0 1034
+
+R 28 * * * * * 1052 2777 * 4307 * * 5642 * 3506 2665 5785 5396 * * 6200 28
+ 120 4704 4599 1585 585 * 0 4282 1073 1034
+
+G 29 * * * * * 89 * * * * * * * * 4723 5491 * * * * 29
+ 0 * * * * 1834 475 4314 0 1230
+
+I 30 * * * * * * * 1205 * 1288 * * 5388 * * 5241 * 3235 * * 30
+ 0 * * * * * 0 4360 0 1154
+
+R 31 2127 5241 5388 4348 * 5640 * * 5740 * * * * 4627 1358 3290 3592 5857 * * 31
+ 0 * * * * * 0 4360 0 1154
+
+G 32 5388 * * * * 180 * * * * * * * * 5242 3901 * * * * 32
+ 0 * * * * 0 * 4360 0 1154
+
+A 33 193 * * * * * * 7090 * 5487 * * * * * 5275 * 3841 * * 33
+ 54 4771 * 2000 415 * * 4351 1073 0
+
+D 34 * * 132 * * * * 4771 * * * * * * * 4293 * * * * 34
+ 0 * * * * * * 4351 0 0
+
+F 35 1623 * * 5275 2058 * 4926 * 5489 3341 5709 4544 * 5312 3602 * * * * 3542 35
+ 0 * * * * * * 4351 0 0
+
+Q 36 2393 * * * 6718 * 2029 * 3311 4125 5054 * * 2286 4673 5326 4529 * * 4201 36
+ 0 * * * * * * 4351 0 0
+
+C 37 * 38 * * * * * * * * * * 5275 * * * * * * * 37
+ 0 * * * * * * 4351 0 0
+
+F 38 3137 * * * 2411 6221 4038 * * * * 6024 * 1909 5312 * 4382 * * 1894 38
+ 191 * 3010 * * * * 4351 0 0
+
+Q 39 4960 * 5488 3602 * * 6197 * 3408 6455 * 4609 5150 1948 2318 3952 2881 6070 * * 39
+ 0 * * * * 493 1788 3991 0 1350
+
+Q 40 3136 * * 4329 * * * * * 1541 * * * 1101 5226 * * * * * 40
+ 0 * * * * * 0 4267 0 1073
+
+A 41 138 * * * * 5283 * * * * * * * * 5226 4677 * * * * 41
+ 0 * * * * 0 * 4267 0 1073
+
+R 42 3750 * * 2938 * 6499 * * 3860 * * 5100 * 2724 1165 3970 5330 * * * 42
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+
+A 43 1099 * 5709 3594 * 5695 * * 5598 7085 * 5694 3936 3995 3150 3169 6292 * * * 43
+ 0 * * * * * * 4351 0 0
+
+V 44 753 * * * * 6221 * 5028 5275 5312 4997 * * * 6525 2871 6292 3059 * * 44
+ 0 * * * * * * 4351 0 0
+
+G 45 * * * * * 369 * * * * * 3232 * * 5487 3872 5126 * * * 45
+ 53 4794 * 1789 493 * * 4351 1060 0
+
+L 46 2528 * * * 4917 6266 * 4741 5265 883 5666 * * * * 3855 * 5067 5686 4763 46
+ 0 * * 0 * 0 * 4324 1010 1010
+
+S 47 4074 * * * * 2474 4888 * 3260 3936 7092 6302 5472 6369 3113 4370 1826 6035 * 4600 47
+ 0 * * * * * * 4351 0 0
+
+G 48 4781 * * * * 700 * * * 5275 * 3540 5472 6629 5126 3994 3711 4794 * * 48
+ 531 1700 * 37 5317 * * 4351 1824 0
+
+T 49 4545 * 5328 * * 5312 * 4531 * 4771 * 4487 * * * 6790 385 7000 * * 49
+ 16 6486 * 2322 322 * * 4351 1000 0
+
+F 50 * * * * 1185 4771 * * * * * * * * * * * * 1700 2211 50
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+
+R 51 6790 * * * * * 3558 * 2994 5328 * * * 5312 453 * * * * * 51
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+
+A 52 70 * * * * 5487 * * * * * * 5312 * * * * * * * 52
+ 0 * * * * * * 4351 0 0
+
+F 53 * * * * 944 * * * * 3168 4782 * * * * * * * 5328 1700 53
+ 54 4771 * 1585 585 * * 4351 1073 0
+
+L 54 * * * * * * * 5074 * 130 * * * * * * * 4148 * * 54
+ 0 * * * * * * 4351 0 0
+
+S 55 3673 * * * * * * * * * * * * * * 272 3966 5074 * * 55
+ 0 * * * * * * 4351 0 0
+
+S 56 2705 * 4100 * * * 5312 * * * * 6616 * 6492 * 1187 1725 * * * 56
+ 0 * * * * * * 4351 0 0
+
+R 57 6616 * 3935 * * 5074 2827 * 4599 * 5100 4428 5168 2382 1847 3378 6718 4887 * * 57
+ 0 * * * * * * 4351 0 0
+
+L 58 2456 * 4180 4250 * 3951 * 4801 * 2373 4771 * 4196 5126 5472 5246 4098 2401 * * 58
+ 36 5328 * 3170 170 * * 4351 1077 0
+
+Q 59 3445 * 6499 3437 4771 * * * * 4821 6629 6250 * 1001 4579 4821 3039 6492 * * 59
+ 178 5328 3450 1000 1000 * * 4351 1077 0
+
+D 60 5211 * 1135 5213 * 2607 5640 * 6016 * * 2119 * * 5204 * 5553 6307 * * 60
+ 151 6451 3503 0 * * 0 4219 1000 1251
+
+L 61 3861 * * * * 2316 * 4095 * 881 4569 5449 * * * * * 3969 * * 61
+ 0 * * * * 444 1916 4051 0 1476
+
+Y 62 4271 * 2765 6272 * 6310 6360 * 2834 4783 * 4169 * 3063 2544 4181 * 4151 * 2958 62
+ 0 * * * * * 0 4330 0 1098
+
+S 63 5214 * 4041 5076 * * 4237 * 4044 * * * 2509 4538 3460 1781 2937 * * 4728 63
+ 16 * 6536 * * 1991 418 4330 0 1098
+
+I 64 2087 * * * * 5207 * 1418 * 3703 * * 5442 * 4857 6328 * 2207 * * 64
+ 0 * * 0 * 1798 489 4335 1000 1105
+
+V 65 * * * * * * * 2625 * * * * * 6707 * * * 272 * * 65
+ 147 * 3369 * * 0 * 4333 0 1063
+
+R 66 * * 5566 * 5040 * 2743 * 5049 * * 1986 4699 * 1522 3240 * * * 5382 66
+ 0 * * * * 1465 649 4206 0 1283
+
+R 67 1454 * * 6192 * * 5307 5404 3140 6366 * * 3077 * 2212 3799 * 5074 * 6494 67
+ 0 * * * * * 0 4251 0 1167
+
+A 68 2012 * * 5055 * 3064 * 6241 6661 4551 * 5027 6039 * 1766 3710 3615 4691 * * 68
+ 0 * * * * 1221 809 4251 0 1167
+
+D 69 * * 392 3219 5457 4566 * * * * * * * * * 6259 * * * 4252 69
+ 46 * 4988 * * * 0 4306 0 1077
+
+R 70 * * 6411 * 5257 3464 6314 * 6491 * * * * 5676 338 * * * 6603 5212 70
+ 12 * 6951 * * * 0 4251 0 1167
+
+G 71 5154 * 2856 3611 5753 5671 6957 1712 6325 6737 * 4667 * 6367 5049 2722 4928 5322 * 3513 71
+ 1113 2180 1658 0 * 963 1038 4254 1524 1202
+
+S 72 4960 * 3801 5618 * 2317 5140 * 3032 * * 2619 * 5162 4352 2482 3240 * * * 72
+ 197 3261 5439 0 * 698 1382 3826 1235 2067
+
+V 73 * * * * 5439 1510 * 5091 * 1758 6759 * * * * * 3896 2477 * 4475 73
+ 0 * * * * 2317 323 4013 0 1452
+
+P 74 * * * * * * * * * * * * 42 6171 * * 6105 * * * 74
+ 0 * * * * * 0 4024 0 1355
+
+I 75 * * * * * * * 1491 * 4578 * * * * * * * 1967 1529 * 75
+ 0 * * * * 510 1748 4024 0 1355
+
+V 76 6459 5470 * * 6724 * 3415 5158 6465 * * * * 4575 5377 4599 3073 890 * 4117 76
+ 0 * * * * * 0 4306 0 1077
+
+N 77 * * 5036 * * * * * * * * 135 * * 5069 5093 * * * * 77
+ 0 * * * * * 0 4306 0 1077
+
+L 78 1738 * * * * * * 3904 5036 1132 * * * * * 5470 3958 4071 * * 78
+ 0 * * * * 0 * 4306 0 1077
+
+K 79 4167 * 5328 * * * * * 1042 * * 5394 * 5004 1675 * * 5100 * 4771 79
+ 0 * * * * * * 4351 0 0
+
+D 80 * * 2046 * * 488 * * 7394 * * 5065 * 6821 * * * * * * 80
+ 0 * * * * * * 4340 0 0
+
+E 81 4348 * 3086 1260 * * 4793 * 6806 * * * * 3366 * * 5323 2625 3532 * 81
+ 0 * * * * * * 4340 0 0
+
+V 82 * * * 4363 * * 4793 3899 4407 3234 4885 * 5323 5095 4236 * 4959 939 * * 82
+ 0 * * * * * * 4340 0 0
+
+L 83 7394 * * * * * * 2340 * 692 5466 * * * * * * 2691 * * 83
+ 0 * * * * * * 4340 0 0
+
+S 84 1413 * * * 1019 * * * * * * * * * * 4927 * * * 3346 84
+ 0 * * * * * * 4340 0 0
+
+P 85 4210 * 2975 * * 6288 * * 2699 * * 2350 2655 6614 3281 3084 4230 6282 * * 85
+ 0 * * * * * * 4340 0 0
+
+S 86 * * 2212 * * 6407 * * * * * 1907 * * * 1220 3707 * * * 86
+ 0 * * * * * * 4340 0 0
+
+W 87 * * * * 4768 * * 5236 3529 4287 * * * * * * * 2105 820 * 87
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+
+D 88 2794 * 2449 2749 * 5319 * * 3931 * 4174 2997 * 3529 4075 3861 5462 6031 * * 88
+ 0 * * * * * * 4340 0 0
+
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+N 180 2548 * * * * * * 3626 * * * 734 * * * * 3390 4285 * * 180
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+ 86 4110 * 2322 322 0 * 2712 1005 1016
+
+T 184 4532 * 4217 * * 4875 * * 4112 * * 3751 4864 4759 * 3289 828 * * * 184
+ 0 * * * * * * 2535 0 0
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+S 187 * * * * * 4153 3557 * 2230 3195 * * * 2907 2060 2614 * * * * 187
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+K 188 * * * * * 3235 * * 468 * * * * * 2552 * * * * * 188
+ 0 * * 0 * * * 2105 0 0
+
+//
+�HHsearch 1.5
+NAME 84792f9cbc9eb5adabb41b1a904360bb
+FAM
+FILE 84792f9cbc9eb5adabb41b1a904360bb
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:17:16 2013
+LENG 51 match states, 51 columns in multiple alignment
+FILT 100 out of 113 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+987788867666888880999999999999999999999999999999819
+>Consensus
+MaehxxxxxxxxxgxMDxxxhexTyxgFixxxkxgtixxxxxllxlaifxx
+>84792f9cbc9eb5adabb41b1a904360bb
+MADHSHPAHGHVAGSMDITQQEKTFAGFVRMVTWAAVVIVAALIFLALANA
+>gi|126740567|ref|ZP_01756254.1| hypothetical protein RSK20926_04347 [Roseobacter sp. SK209-2-6]gi|126718368|gb|EBA15083.1| hypothetical protein RSK20926_04347 [Roseobacter sp. SK209-2-6]
+---------------MDTSVQEQTYEGFIKFSTRFCIFLVFVALFLAVFAT
+>gi|158422053|ref|YP_001523345.1| hypothetical protein AZC_0429 [Azorhizobium caulinodans ORS 571]gi|158328942|dbj|BAF86427.1| conserved hypothetical protein [Azorhizobium caulinodans ORS 571]
+MSEHGAIEYAT-ADGNDYAEHKRTYELFTALTKWGTVAVAALMVIMWFTL-
+>gi|337264849|ref|YP_004608904.1| aa3 type cytochrome c oxidase subunit IV [Mesorhizobium opportunistum WSM2075]gi|336025159|gb|AEH84810.1| aa3 type cytochrome c oxidase subunit IV [Mesorhizobium opportunistum WSM2075]
+MADHTPSGPVELGAKMDYAEHDRTYAGFLMLAKYGSLFCGAILLAMA----
+>gi|92117331|ref|YP_577060.1| hypothetical protein Nham_1786 [Nitrobacter hamburgensis X14]gi|91800225|gb|ABE62600.1| hypothetical protein Nham_1786 [Nitrobacter hamburgensis X14]
+MSDHSEMIFTT-ADGMDYPAHEQQFKTFVKIGMIATATVATIVVLMAIFIG
+>gi|296444936|ref|ZP_06886898.1| aa3 type cytochrome c oxidase subunit IV [Methylosinus trichosporium OB3b]gi|296257604|gb|EFH04669.1| aa3 type cytochrome c oxidase subunit IV [Methylosinus trichosporium OB3b]
+MGEHHK-----VASSAEFAEHEATYKGFLTLLKVSTAACVVTLLLLFFFV-
+>gi|254295291|ref|YP_003061314.1| aa3 type cytochrome C oxidase subunit IV [Hirschia baltica ATCC 49814]gi|254043822|gb|ACT60617.1| aa3 type cytochrome c oxidase subunit IV [Hirschia baltica ATCC 49814]
+--------GEYVRGQMDVKSQTATYSGFLKVTAWTSLLLTLILGY------
+>gi|83859915|ref|ZP_00953435.1| hypothetical protein OA2633_07939 [Oceanicaulis alexandrii HTCC2633]gi|83852274|gb|EAP90128.1| hypothetical protein OA2633_07939 [Oceanicaulis alexandrii HTCC2633]
+--------EEYIRGDMDISEHKASFDGFIGVSVYSTLVIVTTLLC------
+>gi|197106565|ref|YP_002131942.1| hypothetical protein PHZ_c3104 [Phenylobacterium zucineum HLK1]gi|196479985|gb|ACG79513.1| conserved hypothetical protein [Phenylobacterium zucineum HLK1]
+------PASDYHRGEMDIAEQRSTYHLVMLMTKWGSLYTAALILLLTM---
+>gi|220920257|ref|YP_002495558.1| hypothetical protein Mnod_0210 [Methylobacterium nodulans ORS 2060]gi|219944863|gb|ACL55255.1| conserved hypothetical protein [Methylobacterium nodulans ORS 2060]
+MASSNHASNDAYGPSMDGDTHEATYRGFVRFVEIATTVVVCWILSLGI---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 4850 * * * * * * * * * 51 * * * * * * * * * 1
+ 0 * * * * * * 4126 0 0
+
+A 2 559 * * * * 4859 4850 * * * * * * * * 1987 * * * * 2
+ 72 4369 * 704 1373 * * 4126 1099 0
+
+D 3 * * 1269 1172 * * * * 4333 * * 5313 * * * 3917 * * * * 3
+ 0 * * * * * * 4132 0 0
+
+H 4 * * 4628 * 5884 * 460 * 6081 * * 5034 * 5960 * 4017 3937 * * 5187 4
+ 0 * * * * * * 4132 0 0
+
+S 5 5449 * 5262 4470 * 3621 2463 * 1776 * 5960 4155 4852 6571 4554 2581 5375 * * * 5
+ 265 * 2577 * * * * 4132 0 0
+
+H 6 4264 * 5856 2447 * 3591 1352 * 4562 5790 * * 3684 5924 * * 3085 * * * 6
+ 898 * 1110 * * 270 2549 3953 0 1377
+
+P 7 4217 * * 4444 * * * 2413 * 3467 4981 * 2408 * * 3200 2678 2868 * * 7
+ 0 * * * * * 0 3706 0 2095
+
+A 8 1636 * * 3295 * 2246 * 5019 * 5559 5940 * * * * 4231 4492 2326 * * 8
+ 0 * * * * * 0 3707 0 2095
+
+H 9 * * * 3824 5589 2467 5099 * * * * 4853 2471 5151 * 3448 5195 * * 1571 9
+ 0 * * * * * 0 4251 0 2095
+
+G 10 2597 * 1870 3956 * 5130 5295 5667 * 5160 * * * * * 2595 3197 3054 * * 10
+ 0 * * * * * 0 4264 0 2095
+
+H 11 3968 * * 2157 * * 5130 5582 * * * 5160 6313 6476 * * 1784 * * 1642 11
+ 604 * 1548 * * 2542 272 4264 0 2095
+
+V 12 4367 * * * * * 2822 3783 * 4206 * * * 5227 * * 2179 1684 * 3004 12
+ 0 * * * * 1021 979 4026 0 2623
+
+A 13 1400 * * * * 1918 4888 * 5241 * * * 5791 * 2240 3913 * * * * 13
+ 0 * * * * 0 * 4379 0 1844
+
+G 14 2681 * 3351 3312 * 993 * * * * * * 3443 * * 4297 * * * * 14
+ 0 * * * * * * 4546 0 0
+
+S 15 3529 * 3958 1945 * 2346 * * 5371 * * 4856 3795 5797 * 2722 3592 * 6712 * 15
+ 0 * * * * * * 4559 0 0
+
+M 16 4483 * * * * * * * * * 198 3584 * * * * * * * * 16
+ 0 * * * * * * 4562 0 0
+
+D 17 * * 205 5463 * * * * 6152 * * 4026 * 6143 * * 5614 * * * 17
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+
+I 18 6333 6676 * 6366 5463 5860 * 1459 * * * * * * * 4918 4104 4262 5504 1334 18
+ 0 * * * * * * 4562 0 0
+
+T 19 2018 * 4724 4066 * * 4188 * 3188 * * 6143 2677 6209 4822 2931 2923 6849 * * 19
+ 0 * * * * * * 4562 0 0
+
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+
+Q 21 * * * * * * 889 * * * * * * 1120 * * * * * * 21
+ 0 * * * * * 0 4529 0 1072
+
+E 22 4220 * 6059 636 * * 6478 * 4387 5515 * 5597 * 4071 4766 4794 4528 6552 * * 22
+ 0 * * * * 0 * 4529 0 1072
+
+K 23 2610 * 5615 4742 * 4233 6207 * 1856 * * 4568 * 2403 2916 4388 6610 * 6196 * 23
+ 0 * * * * * * 4562 0 0
+
+T 24 5281 * * * * * * * * * * * * 5485 * 5380 108 * * * 24
+ 0 * * * * * * 4562 0 0
+
+F 25 * * * * 1739 * * * * * * * * * * * * * 4349 618 25
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+
+A 26 2894 * 2218 2865 * 5522 3675 * 2951 * * 3126 * 6281 3988 3865 6426 6249 * * 26
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+
+G 27 3790 * 5435 * 4921 854 * * * 2683 5199 5925 * 6661 6281 3702 5694 * * * 27
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+
+F 28 * * * * 54 * * * * * * * * * * * * 5585 * 5949 28
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+
+V 29 4762 * * * * 5382 * 1683 * 2232 2710 * * 5614 * * 5407 2198 * * 29
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+
+R 30 2833 * 4855 * * 4048 * * 1488 4525 6087 4289 * * 3093 4014 3357 * 5504 * 30
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+
+M 31 4074 * * * 1923 4537 * 4426 * 1532 2997 * * * * * * 4346 4183 6362 31
+ 0 * * * * * * 4562 0 0
+
+V 32 3318 * * * 6559 3488 * 5716 * 3762 4421 * * * * 2641 1753 2296 * * 32
+ 0 * * * * * * 4562 0 0
+
+T 33 5238 * * 4582 * * * 4197 1024 5338 4600 * * * 6649 5434 2012 4693 * * 33
+ 0 * * * * * * 4562 0 0
+
+W 34 * * * * 5504 * * 2601 4971 * * * * * 2845 * * 3270 1417 2608 34
+ 0 * * * * * * 4562 0 0
+
+A 35 3813 * * * 3750 1009 * 5042 * 4608 * * * * * 3026 3152 4295 * * 35
+ 0 * * * * * * 4562 0 0
+
+A 36 2747 4012 * * * 4225 * 4584 * 5402 * * * * * 2125 1492 3547 * * 36
+ 0 * * * * * * 4562 0 0
+
+V 37 2734 * * * * 5465 * 1960 * 2040 4846 * * * * 4802 5860 2215 * 5402 37
+ 0 * * * * * * 4562 0 0
+
+V 38 1448 * * * 4070 4790 * 2581 * 3432 * 6013 * * * 5466 3683 2823 * 5585 38
+ 0 * * * * * * 4562 0 0
+
+I 39 3607 3884 * * * * * 1974 * 3025 6426 6306 * * * 2789 4143 2016 * * 39
+ 0 * * * * * * 4562 0 0
+
+V 40 1535 6462 * * 4775 6087 * 2054 * 3931 * * * * * 6209 5823 1973 * * 40
+ 0 * * * * * * 4562 0 0
+
+A 41 1954 3283 * * 4274 4352 * 3924 * 3581 6059 5947 * * * * 3420 1919 * * 41
+ 0 * * * * * * 4562 0 0
+
+A 42 4800 * * * 3551 6168 * 2060 * 1953 * * * * * 5425 3480 2237 4582 * 42
+ 0 * * * * * * 4562 0 0
+
+L 43 3753 6735 * * * 5103 * 3322 * 913 4319 * * * * * 6827 2341 * * 43
+ 0 * * * * * * 4562 0 0
+
+I 44 3282 * * * * 4936 * 2043 * 1433 * * * * * 5562 5126 2311 * * 44
+ 0 * * * * * * 4562 0 0
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+F 45 2748 4617 * * 1729 5904 * 4966 * 1584 * * * * * 5091 6578 4830 6791 4557 45
+ 0 * * * * * * 4562 0 0
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+L 46 6304 * * * 4496 6248 * 4233 * 1057 1416 * * * * * * 5539 * * 46
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+
+A 47 696 * * * 5308 4932 * 3823 5507 * 6195 * * * * * 2917 5170 5237 4985 47
+ 0 * * * * * * 4447 0 0
+
+L 48 6145 * * * 3420 * * 1119 * 1980 3839 * * * * * * 3201 * * 48
+ 0 * * * * * * 4429 0 0
+
+A 49 4551 6155 * * 641 * * 3645 * 4200 * * * * * * 4692 2954 * * 49
+ 0 * * * * * * 4004 0 0
+
+N 50 2710 * * * * 3679 * 3796 * 1386 * 2068 * * 5648 * 5820 4704 * * 50
+ 0 * * * * * * 3946 0 0
+
+A 51 2144 * * * * 1613 * 5673 * * * * * * 4340 3275 2007 5282 * * 51
+ 0 * * 0 * * * 3288 0 0
+
+//
+�HHsearch 1.5
+NAME 86ed36c2fe7938800e5622d9b4acb515
+FAM
+FILE 86ed36c2fe7938800e5622d9b4acb515
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:36:43 2013
+LENG 234 match states, 234 columns in multiple alignment
+FILT 112 out of 117 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCEECCCCEEEEEEECCCCCEEEEEEEECCHHHHHHCCCCCEEEEEEECCCEEECC
+CCCCCEEEECCEEECCCCCCCCCCCCCEEEEECCCCEEECCEEEEEECCEEEEEEEHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCEEEEECC
+CCCCCCHHHHHHHHCCCCEEECCCCEEEEEEECC
+>ss_conf PSIPRED confidence values
+9845699596895325416733489999975659957998130453208886899866056786889999966889997536896589999713303125
+7778689978799679763476654545999889720864415998476887875437999999987453368987777312289999899988999886
+6899788887665416975875044799999569
+>Consensus
+xxxxxxxxxxxxlxxxsxxxxxxxxnLkxyYxxxxxxexxNvxxxxxxxxxxlxfxxxxxxxxxxxxlxvxxxxxxxxxkfkxkxVDIFgvxyxxxcxxx
+xxxxxxxxyGGVTkxnxxxxdxxkxixinvxxdgxxxxxxxxxixxxKkxVTlQELDfKlRkxLixxxxLYxxxxxxsxxxxGxIxxxxkdgxxxtxDLx
+xxxxxxxxxxLxxYxdNktIdsxxxhIdVxLxxx
+>86ed36c2fe7938800e5622d9b4acb515
+MSEKSEEINEKDLRKKSELQGTALGNLKQIYYYNEKAKTENKESHDQFRQHTILFKGFFTDHSWYNDLLVRFDSKDIVDKYKGKKVDLYGAYAGYQCAGG
+TPNKTACMYGGVTLHDNNRLTEEKKVPINLWLDGKQNTVPLETVKTNKKNVTVQELDLQARRYLQEKYNLYNSDVFDGKVQRGLIVFHTSTEPSVNYDLF
+GAQGQYSNTLLRIYRDNKTINSENMHIDIYLYTS
+>gi|21282488|ref|NP_645576.1| enterotoxin type C precursor [Staphylococcus aureus subsp. aureus MW2]gi|21203925|dbj|BAB94624.1| ENTEROTOXIN TYPE C PRECURSOR [Staphylococcus aureus subsp. aureus MW2]
+--ESQPDPTPDELHKSSEF-TGTMGNMKYLYD-DHYVSATKVKSVDKFLAHDLIYNISDKKLKNYDKVKTELLNEDLAKKYKDEVVDVYGSNYYVNCYFs
+SKDnvgkvtGGKTCMYGGITKHEGNHFDNgnl-QNVLIRVYENKRNTISF--EVQTDKKSVTAQELDIKARNFLINKKNLYEFNS--SPYETGYIKFIEN
+NGNTFWYDMMPAPGdkFDQSKYLMMYNDNKTVDSKRVKIEVHlttk----
+>gi|34536505|dbj|BAC87686.1| exotoxin G variant 5 [Streptococcus dysgalactiae subsp. equisimilis]gi|34536507|dbj|BAC87687.1| exotoxin G variant 6 [Streptococcus dysgalactiae subsp. equisimilis]
+---------------------------RFAYD-VTPLEYENVE-ITFVTTNNIH--I---NTGQKKSGCVLYVDSivslGITDNFiKGDKVDVFGLPYNF
+-----SSPNVDNIYGGVVKHSDdK---LQSLQFVGiLNQDGEETSLPSYTILIKHKQFTLQEFDFKIRKFLMETYSIYDS-E--SRYISGSFFLATKDSK
+HYEVDLFNKDDkLlDRNRFFKRYRDNKVFNSEEiSHFDIYLKT-
+>gi|225871304|ref|YP_002747251.1| exotoxin H precursor [Streptococcus equi subsp. equi 4047]gi|8117875|gb|AAF72809.1|AF186180_3 SeeH [Streptococcus equi]gi|225700708|emb|CAW95321.1| exotoxin H precursor [Streptococcus equi subsp. equi 4047]
+------------------YNTTNRHNLESLYKHdSNLIEADSIKnSPDIVTSHMLKYSVKD------KNLSVFFEKDWISQEFKDKEVDIYALSAQEACE
+--CPGKRYEAFGGITLTNSE---KkEIKVPINVWDKSKQHPPMF--ITVNKPKVTAQEVDIKVRKLLIKKYDIYNNRE--QKYSKGTVTLDLNSGKDIVF
+DLYYFGNGDFNSMLKIYSNNERIDSTQFHVDVS----
+>gi|71903885|ref|YP_280688.1| exotoxin type K precursor [Streptococcus pyogenes MGAS6180]gi|94990809|ref|YP_598909.1| exotoxin type C precursor [Streptococcus pyogenes MGAS10270]gi|71802980|gb|AAX72333.1| exotoxin type K precursor [Streptococcus pyogenes MGAS6180]gi|94544317|gb|ABF34365.1| Exotoxin type C precursor [Streptococcus pyogenes MGAS10270]
+--------------------DEILDNrrLKEIYN-KEIIEKNNIS-INAKQGTQLIFNTDEnTTVWndnTFKKVISSNLSPSQERMFnVGDHVNIFAIVk
+sYHVVCK----EQFNYSDGGIIKTSDV-KPEEKAIYINIFGEKELRTlTAKDKITFKNNIVTLQEIDVRLRKSLMgdSKIKLYEY-D--SLYKKGFWDIH
+YKDGGIRHTNLFTYPD---------YTDNETIDMSKvSHFDVHLNE-
+>gi|253730779|ref|ZP_04864944.1| superantigen family protein [Staphylococcus aureus subsp. aureus USA300_TCH959]gi|253725492|gb|EES94221.1| superantigen family protein [Staphylococcus aureus subsp. aureus USA300_TCH959]
+----------------------DKEALYRYYT-GKTMEMKNISALKH-GKNNLRFK----FRGIKI--QVLLPGND-KSKFQQRsyeGLDVFFVQEKR--
+---DKHDIFYTVGGVIQNNKTS-GVVSAPILNISKeKGEDAFVKGYPYYIKKEKITLKELDYKLRKHLIEKYGLYKTIS-----KDGRVKISLKDGSFYN
+LDLRS--------KLKFKYMGEVIESKQiKDIEVNLK--
+>gi|224475929|ref|YP_002633535.1| superantigen-like protein [Staphylococcus carnosus subsp. carnosus TM300]gi|222420536|emb|CAL27350.1| similar to exotoxin [Staphylococcus carnosus subsp. carnosus TM300]
+---------------------NQADELKKYYS-QTPEIFSNKKLT-QVeegSDKGKIYVKI--QSSWGAFINVIGnQSWGNVNKLRGKQVDVFGIKDKPT
+S------QYWWAYteyftGGVTPAANP---SAPVYPIKVTvKKNAHVKSSfdIKAFETRKDKITLKELDFQIRKALINNNNLYSN-----GQNTGTVQIT
+-TKDNQlFTFDLN---KRLENERANVYVDGK----------------
+>gi|22219371|pdb|1M4V|A Chain A, Crystal Structure Of Set3, A Superantigen-Like Protein From Staphylococcus Aureusgi|22219372|pdb|1M4V|B Chain B, Crystal Structure Of Set3, A Superantigen-Like Protein From Staphylococcus Aureus
+--------------------TKDIFDLRDYYS-GASKELKNVTG--YRYSKGgkhyLIFD----KHQKFTRIQIFGKDIERLKTRKNPGLDIFVVKEAE-
+----NRNGTVFSYGGVTKKNQGaYYDYLN--APKFVIkkeVDAGVYTHVKRHYIYKEEVSLKELDFKLRQYLIQNFDLYKKFP-----KDSKIKVIMKDG
+GYYTFELNKK--------LQPHRMSDVIDGRNiEKMEANI---
+>gi|261263454|gb|ACX55067.1| exotoxin I [Streptococcus dysgalactiae subsp. equisimilis]
+---------------------------------------------GPPFSGSLFYKNIP-YGNSSIELKVELNSVEKANFFSGKRVDIFTLEYSPPC---
+NSNIKKNSYGGITLS-------------------------------------------------------------------------------------
+----------------------------------
+>gi|166409297|dbj|BAG06666.1| enterotoxin T [Staphylococcus aureus]
+------------------------EGLKDFYS-KKIDVYTNKK-INEKDKY----SV-DIEVDNYV-YRINTLDDKILNQFkVGDYVDAWGHIINN----
+----KPigkvIKFYDGdISKHSP--LDKPTNIsyRINLFKEQKQTEVTPEkELEIGNRYLTMKQIDYRIKSYLVKKQQLYTE------FYNGKIEISMLD
+GKKHFIDLS---T--------YYYdpSNFTLDYTKiSHFDIYM---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+S 2 * * * * * * * * * * * * * * * 0 * * * * 2
+ 0 * * * * * * 1000 0 0
+
+E 3 * * 3056 1477 3571 * * 3823 * * * 2433 * * * 2470 * * * * 3
+ 0 * * * * * * 2999 0 0
+
+K 4 2360 3995 * * * * 4200 4198 2416 * * 4436 * * * 2099 3857 3358 * * 4
+ 0 * * * * * * 3201 0 0
+
+S 5 3618 * * 3584 * * * * 4224 * * 2798 * 1621 * 2139 3545 * * * 5
+ 0 * * * * * * 3326 0 0
+
+E 6 3589 * * 2037 4608 3934 * * * 4486 * 3249 2190 4041 * 3618 4168 * * * 6
+ 0 * * * * * * 3326 0 0
+
+E 7 3618 * 1104 2581 * * * * * * * 3228 * 4608 4168 4411 4805 * * * 7
+ 0 * * * * * * 3326 0 0
+
+I 8 * * * 4626 * * * 2049 * * * * 768 * * * 4608 3480 * * 8
+ 69 * 4411 * * * * 3326 0 0
+
+N 9 * * 3671 3529 * * * * 1748 * * 2150 * * 3334 3527 2990 * * * 9
+ 576 1602 * 291 2454 * 0 3273 1534 1026
+
+E 10 * * * 2811 * * * 2181 * 3742 * * 831 * * * * * * * 10
+ 0 * * 0 * 0 * 2893 1013 1534
+
+K 11 * * 2640 1663 * 4307 * * 2396 * * * * * * 1820 * * * * 11
+ 0 * * * * * * 3426 0 0
+
+D 12 * * 1435 2157 * * * * * * * 4890 * 1994 * 3680 4534 * * * 12
+ 0 * * * * * * 3426 0 0
+
+L 13 * * * * * * * * * 0 * * * * * * * * * * 13
+ 0 * * * * * * 3426 0 0
+
+R 14 * 3682 * * * * 1248 * 3679 * * 1982 * 3595 3520 * * * * * 14
+ 0 * * * * * * 3426 0 0
+
+K 15 * * 4026 * * * 3135 * 686 * * 4534 * * 2643 * * * * * 15
+ 575 * 1605 * * * * 3426 0 0
+
+K 16 2904 * * * * * * * 1504 * * * * * * 1390 * 2920 * * 16
+ 0 * * * * * 0 3076 0 1534
+
+S 17 * * * * * * * * * * * 3852 * * * 104 * * * * 17
+ 241 * 2702 * * 0 * 3076 0 1534
+
+E 18 * * 3156 1774 * * * * 1319 * * * * 3220 * 3521 * * * * 18
+ 645 1472 * 1000 1000 0 * 3350 1534 1167
+
+L 19 * * * * 2343 * * * * 958 * * * * * * * 3778 * 2216 19
+ 841 3432 1518 0 * * * 3578 1101 0
+
+Q 20 * * 1601 * * * * * 3504 * * 2020 * 2672 * 3408 3564 * * * 20
+ 1353 717 * 0 * 0 * 3127 1680 1604
+
+G 21 * * 1942 * * 3815 * * 3186 * * * 4691 * * 2695 1867 3451 * * 21
+ 0 * * * * 0 * 4239 0 1534
+
+T 22 4952 * * 4896 5088 2532 * 4078 2157 3720 * 4745 * 3966 * 5808 2098 * * 5668 22
+ 0 * * 3459 138 * * 5203 1000 0
+
+A 23 2308 * 2628 4851 * * * 5375 4648 4257 * 2223 * 4986 5088 4616 3224 4673 * 5426 23
+ 96 5039 4890 1959 429 * * 5598 1094 0
+
+L 24 4998 * * * 4673 * * 2706 5214 1878 3223 * 4989 * 5434 4813 3036 3135 5809 5246 24
+ 0 * * * * * 0 5587 0 1259
+
+G 25 4433 * 3473 4017 4489 3216 3897 5164 3150 4852 * 3020 * 3036 6908 3652 5877 5726 * 4700 25
+ 0 * * * * * 0 5737 0 1259
+
+N 26 5423 * 2781 2910 * 5226 * 5429 4685 * 5644 1007 5734 6283 * 4530 5890 * * * 26
+ 83 4153 * 1000 1000 0 * 5725 1187 1259
+
+L 27 4378 * * * * * * 3586 * 414 4182 * * * * * * 4652 * 5416 27
+ 0 * * * * * * 5819 0 0
+
+K 28 * * 6246 5061 * * 4310 3808 1447 5493 6337 5221 * * 1835 4971 5117 * 6164 4266 28
+ 0 * * * * * * 5992 0 0
+
+Q 29 4649 6328 2916 3521 3874 4888 4017 * 3251 6104 6466 2861 * 4418 4311 4206 5715 5430 * 3289 29
+ 10 7185 * 1585 585 * * 5992 1000 0
+
+I 30 4132 * 5235 * 3254 * 5853 3155 * 2723 * 6617 * 5672 * 4271 6905 * * 1182 30
+ 66 * 4474 * * * * 5992 0 0
+
+Y 31 * * * * 5335 * * * * * 5521 * * * * * * * * 69 31
+ 0 * * * * * 0 5905 0 1259
+
+Y 32 4103 * 3623 5034 5614 5064 * 5324 3899 * 5041 2735 * * 5521 1969 2332 * * 4988 32
+ 1987 * 419 * * * 0 5905 0 1259
+
+Y 33 * * 3258 * 4766 * 2085 * 2951 * * 3464 * 4500 * 2601 3217 * * 3530 33
+ 838 1454 3725 0 * 172 3154 3261 1484 4279
+
+N 34 * * 4029 6765 * 2432 6320 4352 2575 * * 3840 * 2671 3830 3586 5802 4540 * 3765 34
+ 0 * * * * * 0 5795 0 1916
+
+E 35 4961 * 2892 3037 * * 5255 5802 3096 6619 * 3611 2235 5399 3799 6463 2847 * * * 35
+ 48 4919 * 1115 893 0 * 5795 1959 1916
+
+K 36 6319 * * * 3473 4903 3634 3377 4927 4675 * * 2154 6537 * 2180 3921 4979 * 4025 36
+ 0 * * * * * * 5992 0 0
+
+A 37 5005 6150 5410 3871 2465 6633 * 2718 4265 2989 6001 * * * * * 3670 2397 * 4114 37
+ 0 * * * * * * 5992 0 0
+
+K 38 7055 * 2501 1480 * * * 3519 3929 * * 3729 * 6466 * 3614 3777 3985 * * 38
+ 0 * * * * * * 5992 0 0
+
+T 39 3967 * * 4171 2951 4282 3518 5111 3367 2360 5348 * 6961 * 5693 5695 5455 6123 * 2446 39
+ 0 * * * * * * 5992 0 0
+
+E 40 * * 5843 2376 * * 6683 5257 1811 * * 5184 * 4283 4964 2549 2681 5001 * * 40
+ 0 * * * * * * 5992 0 0
+
+N 41 * * 4631 * * 3998 * 6225 4200 * * 380 6246 * * 4395 * * * * 41
+ 0 * * * * * * 5992 0 0
+
+K 42 * 5196 * 6072 * * * 2227 1980 4470 5943 * * 7471 5808 6806 5400 1422 * * 42
+ 0 * * * * * * 5992 0 0
+
+E 43 * * 5097 3677 * 6254 * 3673 2019 6246 6633 3915 5001 * 4933 2619 2699 5312 4088 * 43
+ 285 5843 2627 0 * * * 5992 1038 0
+
+S 44 4461 * 4726 * * 1603 * 5166 * 3162 * 3818 5412 * * 2293 3136 4802 * * 44
+ 47 * 4977 * * 0 * 5611 0 1740
+
+H 45 * * 4688 4874 6122 5255 6021 2551 3738 4022 * 4175 5811 5185 * 4717 3441 3630 4563 2250 45
+ 191 7089 3101 1000 1000 * 0 5987 1000 1094
+
+D 46 5994 * 1869 3835 * 3890 6499 4120 3430 * * 2754 * * 3560 4992 3525 4695 * 5518 46
+ 13 6775 * 1000 1000 172 3154 5621 1000 1699
+
+Q 47 5934 * * 2893 3620 4819 5610 4479 3297 5294 * 5095 5799 1863 4171 4417 5687 * * 3381 47
+ 544 2668 2675 1449 658 * 0 5943 1752 1033
+
+F 48 * * 5360 6509 2381 6860 5779 4880 2510 2690 * 4504 3919 6551 4224 4487 6543 3278 * 4361 48
+ 58 5686 5647 1585 585 155 3294 5827 1008 1772
+
+R 49 * * 4562 4654 5774 2447 * 4701 3511 1700 * 5294 6998 5885 4415 5357 3066 * * 4590 49
+ 0 * * * * 0 * 5919 0 1116
+
+Q 50 3996 * 2715 4041 4832 3017 * * 3087 * * 3946 5977 4220 7354 2149 3902 * 7619 6650 50
+ 72 6239 4832 2322 322 * * 5997 1010 0
+
+H 51 * * 4594 * 4760 5774 1721 6966 2707 * * 1859 6373 * 6002 6860 3444 * * 4829 51
+ 180 * 3089 * * * 0 5959 0 1144
+
+T 52 * * 1928 6550 5684 2540 5694 * 4924 5949 5714 3831 * 2928 6583 5602 3088 3969 * 4898 52
+ 68 4439 * 1265 776 514 1738 5860 1144 1684
+
+I 53 5690 * * * 4798 * * 3595 4646 929 3824 5222 * * * 5608 4541 2880 * * 53
+ 144 * 3398 * * * 0 5897 0 1236
+
+L 54 * * 6111 3707 7110 * 4453 1458 5120 3228 * 3091 * 6307 4145 * 3885 3967 * 4700 54
+ 121 * 3638 * * * 0 5836 0 1806
+
+F 55 * * * * 989 * 4296 4427 * 7115 4205 5899 * * * * * 3212 * 2234 55
+ 0 * * * * 2092 386 5663 0 2122
+
+K 56 4159 6269 3891 * 7185 5940 * 2868 2897 5095 5975 2647 3869 * 5548 3044 4543 3941 5395 5533 56
+ 929 4175 1254 2500 281 1440 663 5803 1828 1860
+
+G 57 4140 * * 4331 * 4807 * 1522 3994 * * 3304 * * * 5357 2466 2833 * * 57
+ 639 * 1482 * * 2190 357 5078 0 3338
+
+F 58 * * 4505 * 2896 * * 2966 3341 2760 * 3033 * 3342 5191 3484 4059 4328 * * 58
+ 1311 3540 969 1182 839 3758 111 4553 1173 3587
+
+F 59 * * 1153 2603 2995 3516 4129 * 4016 * * * 4217 * * * * * * * 59
+ 523 2505 2966 0 * 3999 93 4278 1187 4286
+
+T 60 * * * * * 2388 * 3727 4679 4584 * 4079 * * * 3157 1055 * * * 60
+ 244 * 2684 * * 318 2338 3912 0 4213
+
+D 61 * * 3023 3853 5662 5669 * 5956 1967 5025 * 3468 3959 2918 5619 4060 5197 5157 * 4535 61
+ 0 * * * * 4038 91 5751 0 1948
+
+H 62 * * 3736 5117 * 3253 2980 4708 5269 4048 * 3595 * 4628 3609 3611 3853 2703 * 5055 62
+ 151 3663 5599 0 * 142 3415 5799 1283 1890
+
+S 63 5303 * 3166 * * 3215 7216 5871 3527 4143 5243 3387 4082 3863 5125 2808 5860 5054 3694 4554 63
+ 97 3941 * 1315 742 * 0 5937 1269 1102
+
+W 64 * * 4233 3496 6042 4273 6066 6816 3210 * 4952 2815 * 2312 * 3752 3817 * 2966 6563 64
+ 13 * 6842 * * 1291 758 5937 0 1102
+
+Y 65 5664 * 5651 * 2937 4905 6272 6045 3120 5119 * 3718 * 4110 * 3705 4970 4324 * 1590 65
+ 0 * * * * 0 * 5950 0 1100
+
+N 66 4707 * 3184 5923 5379 6475 5253 3677 2771 * * 2098 * * 4530 3601 3679 4630 * 3811 66
+ 488 * 1802 * * * * 5997 0 0
+
+D 67 6394 * 1911 3846 4748 5682 3472 4633 2889 5156 * 4239 * 4093 4564 3452 4749 * * 5632 67
+ 0 * * * * 2768 229 5627 0 2389
+
+L 68 5650 * * 5901 5261 5776 * 2540 4849 1361 * * * * * * * 1874 * 4312 68
+ 132 * 3517 * * 0 * 5753 0 2192
+
+L 69 * 5075 4223 * 5860 * * 3793 1814 3738 * 3651 * 3082 2835 4498 4913 5401 * 5102 69
+ 64 * 4533 * * * 0 5922 0 1259
+
+V 70 5031 * 5904 * * * * 2668 * 3398 * * * * * 3143 2608 1240 * * 70
+ 0 * * * * 1303 749 5855 0 1467
+
+R 71 4460 * 5954 1643 2690 5639 * 6223 4995 4110 * 4358 * 4402 6062 3392 3965 5737 5228 5341 71
+ 0 * * * * * 0 5922 0 1259
+
+F 72 * * * * 1771 3030 * 4559 * 1406 6655 4311 * * * 4828 5334 * * 4494 72
+ 127 3565 * 0 * * 0 5922 1343 1259
+
+D 73 4996 * 4850 2839 5802 5954 6759 3696 3072 2509 * 3115 5577 4890 * 4804 4688 3110 * 5737 73
+ 0 * * * * * 0 5922 0 1259
+
+S 74 * * 2969 5215 * 2023 5884 * 5761 * * 2115 * * * 1705 5246 * * * 74
+ 0 * * * * * 0 5922 0 1259
+
+K 75 5707 * 3617 3854 5634 * * 6545 1939 * * 4002 3949 5092 6800 2338 4542 4732 3399 * 75
+ 147 3365 * 2076 390 * 0 5901 1426 1259
+
+D 76 3810 * 1507 2151 6675 3131 * * 4438 6213 * 6500 * * * 3696 6106 * 5769 4409 76
+ 445 * 1914 * * * 0 5901 0 1259
+
+I 77 4271 * 4734 4535 * * * 2301 3702 2511 3563 3129 * 4516 4774 * 3892 4688 * 5213 77
+ 0 * * * * 308 2378 5523 0 2463
+
+V 78 2122 * 6431 3767 5745 6953 6781 3235 2631 3733 * 7378 * * 6680 3036 3832 3624 * 5829 78
+ 0 * * * * * 0 5901 0 1259
+
+D 79 5119 * 2736 3594 * 4987 * * 2640 5851 * 2048 * 3249 4253 3684 4273 * * * 79
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+ 0 * * * * * * 4916 0 0
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+T 233 * * * 2328 * * * * 2523 * * 5063 * * * 3642 952 * * * 233
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+S 234 * * 3731 * * * * * 1496 * * 3600 * 3672 * 1731 3211 * * * 234
+ 0 * * 0 * * * 2540 0 0
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+//
+�HHsearch 1.5
+NAME 88117153c423d8f3cd1f072dcda24597
+FAM
+FILE 88117153c423d8f3cd1f072dcda24597
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:00:03 2013
+LENG 123 match states, 123 columns in multiple alignment
+FILT 138 out of 594 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEECCEEEECCCCCHHHHHHHHHHH
+HHHHHHHHCCCCHHHCCCCCCCC
+>ss_conf PSIPRED confidence values
+9899999999885899887999627867678998982632668888438899997028998645688647656899868937889999969999999799
+99999996888887727982469
+>Consensus
+xlxqlxxMixxxxxxxxxxxxyxxYGCxCgxgGxGxPvDxiDxcCxxhxxCyxcxxxxxxCxxxxxxxxxxxYxxxxxxxxixCxxxxxxCxxxlCeCDx
+xxAxclxxxxynxxxxxxxxxxC
+>88117153c423d8f3cd1f072dcda24597
+ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDR
+NAAICFSKVPYNKEHKNLDKKNC
+>gi|321469432|gb|EFX80412.1| putative phospholipase A2 [Daphnia pulex]
+DIFHLYN-MMSCT-tQC-DPLSYKGYGCYCGFLGSGLTVDAIDRCCKKHDFCYGA----TPCRHQS-LIYFVPYKWKCNGGHPYCVTGYgqmkagDICAH
+HLCECDRQFAECIRHYPCPAKKTTCPSN--
+>gi|313239766|emb|CBY14648.1| unnamed protein product [Oikopleura dioica]
+--LQMKIVILFMQK-NKFLGKYCFYGCWCFPrgagnnGGFGQPVDNIDKSCREYSTCYNCIYNqnigSQRCPE----NTADRYQIGgfvdrFGQVQIFCT
+DPWGTCNRSRCECDRDLAMKLRQHepEWNMQYHH------
+>gi|313241201|emb|CBY33484.1| unnamed protein product [Oikopleura dioica]
+---QLMQLMQFYTLdETFDADKYWNYGCNCMIhgdrplsdMGTGPGVDRLDRKCREYKLCQQCARAqhGDMCIGEFIsyrRPRTrtILNDLGVEETHKVC
+RDAPDTCERALCECDLQFAKDHAKVslvAFDPAHHN------
+>gi|313220609|emb|CBY31456.1| unnamed protein product [Oikopleura dioica]gi|313226182|emb|CBY21325.1| unnamed protein product [Oikopleura dioica]
+-LRQFRRLYTFYLVGyRLRPAHLVQYGCWCFPRgqlimGYGQPIDGIDATCRNHQLCLNCVGLdtNYECN-----PHTQPYRVYgqiyQNGRRLMCKDPP
+GSCAWLACQCDVNMVTTSIiESlkGYKPRFWMYDPGRC
+>gi|313232232|emb|CBY09341.1| unnamed protein product [Oikopleura dioica]
+-------------------TKYTSYGCYCWAkgtsniedlg--AGSAnVDWNDKACTDLYRCYACVNIDYGKK-YTELSYDAIFSTDvDGNRKIDCSGAA
+QSDGEHICQCDAAFAERIAFN--------------
+>gi|313234547|emb|CBY10504.1| unnamed protein product [Oikopleura dioica]
+--------------------RMNNYGCHCWPdypqienlSGQGASLDGIDSSCHKLQDCHACLKQeygAEDCD-----PVHTRYKARLIDGEILCLNKss
+gKQACKRNLCECDKKFSSEFSLSfgSWSSEY--------
+>gi|313212373|emb|CBY36361.1| unnamed protein product [Oikopleura dioica]
+------KLVQHFT--SIDIEKLQDYGCA-GRGyfdstepAVGLPVDEIDRSFIWWKKCIKCAQSEYSAYDLEynHFDYREFYEFDF--DSEICGG-SETV
+EHAICQCDKSFAKRLIDLTENNDFHNYDTDSC
+>gi|313232459|emb|CBY24127.1| unnamed protein product [Oikopleura dioica]
+SILQFHLNFEYGF-GAYSAADLLSYGCWCDLEnphRHGKPVDDVDKLCHKHFRCHRCVSMdsSYACS-----PN-VQYELTFDtaTQSHFCAASnTDLCE
+MEACLCDLELITQMVRQ--------------
+>gi|313225706|emb|CBY07180.1| unnamed protein product [Oikopleura dioica]
+-------------------YEFHNYGCYCVApsdtkKMRGRPVDEIDRKLVAkfplvknthfvtpvHFLTTDAIRKQ---W----GFSILIYRYKItkts
+SGNRIECTNAADTCAYASCMCDKGLAEDLGTLlmngvKVNSTYREHDGEK-
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 6585 0 0
+
+S 107 1627 7085 6060 5155 5096 3529 6319 4066 3688 4937 7138 6186 6444 4692 3486 3798 4622 5213 6647 5823 107
+ 36 5334 * 706 1370 * * 6559 1147 0
+
+K 108 3577 * 2946 3424 * 5586 5461 * 2816 4537 * 4085 7063 3481 2163 4688 4710 * * 6883 108
+ 34 6203 6701 1000 1000 * * 6537 1058 0
+
+V 109 2568 * 6808 4644 5276 6654 3883 4883 5116 4263 5642 2975 * 4370 5904 3047 4698 3377 * 3380 109
+ 1109 898 * 1289 759 0 * 6574 3869 1006
+
+P 110 4414 * 4002 3501 * 5718 5139 5590 3715 5673 5933 6724 2362 5105 5047 2781 2649 4214 * * 110
+ 85 4122 * 924 1081 * * 6483 1341 0
+
+Y 111 * 5850 * 6212 2198 * 6987 5899 6732 6607 6154 * 5936 * * * * 5126 3367 860 111
+ 0 * * * * * * 6483 0 0
+
+N 112 5336 * 2710 3978 * 6957 5760 7446 5704 * * 888 3993 6072 5921 4459 6813 5751 * * 112
+ 8 7590 * 0 * * * 6465 1000 0
+
+K 113 4292 5541 4161 3275 6883 6700 6008 5808 2781 3919 5278 3964 2945 6799 4471 3528 4251 3875 6958 5970 113
+ 0 * * * * * * 6402 0 0
+
+E 114 3177 * 3451 3322 * 4421 5408 * 2065 5239 * 3460 * 4738 3864 3665 3930 6570 * 6590 114
+ 0 * * * * * * 6426 0 0
+
+H 115 * * * * 2638 * 3142 5984 5672 3495 6240 3176 * 4535 * * * * * 1201 115
+ 0 * * * * * * 6416 0 0
+
+K 116 4990 * 4935 4445 4058 6616 2302 6874 2960 3683 5082 5347 6059 5156 2876 5333 5449 5659 4322 4289 116
+ 0 * * * * * * 6374 0 0
+
+N 117 4985 * 3770 4938 3849 3203 3798 5589 7072 3738 4207 2405 6069 4988 5028 3334 6026 5825 * 4126 117
+ 0 * * * * * * 6250 0 0
+
+L 118 5015 5748 * 5994 2410 5897 4734 3722 * 2797 4713 6247 5602 6052 * * * 3918 6373 1702 118
+ 32 * 5503 * * * * 6127 0 0
+
+D 119 6299 * 1343 * 4891 4895 * * 5374 5875 * 3576 2432 6270 5829 3411 6025 * 4239 5464 119
+ 0 * * 0 * 0 * 6143 1019 1019
+
+K 120 4158 * 5848 4996 * 4457 * 5972 2412 * * 4388 4333 3762 3035 2884 2635 5806 * 4700 120
+ 0 * * * * * * 6030 0 0
+
+K 121 6096 5948 3342 3090 4916 3822 * 5716 2996 4817 * 3170 4714 4321 4803 2802 3457 * * * 121
+ 107 4163 6003 0 * * * 5870 1082 0
+
+N 122 * * * 3693 5383 * * 4398 1848 2712 5621 4803 * * 3013 3221 3703 5262 * 5022 122
+ 268 2560 * 0 * 0 * 5473 1441 1000
+
+C 123 4883 50 * * * * * * * * * * * * * * * * * * 123
+ 0 * * 0 * * * 5348 0 0
+
+//
+�HHsearch 1.5
+NAME 8e30ca516d2b86076f51d1316fab39ad
+FAM
+FILE 8e30ca516d2b86076f51d1316fab39ad
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 15:03:45 2013
+LENG 244 match states, 244 columns in multiple alignment
+FILT 114 out of 1070 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCCCCEEECCCCCEEEEECCCEEEEECCCHHHHHHHHHHHHHHHHHHHHH
+HCCCCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCCCEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
+HHCCCCCCCEEEEEEECCCCCCCCCEEECCHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9863447775478998364778787677519659999979999999846556686463377444999769899998356899999999999999987886
+2998999999999999999986213678743899999995799947999948998787135998677599999999874239999999999999999998
+53567899589999965643789888993999999999997449
+>Consensus
+xxxxxdxxxxxfxpxGxlxQxeyaxxavxxGxtxigixxxdgvviaxdxxxxxxxxxxxxxxxKixxIxxxixxxxsGxxxDxxxlxxxxxxxxxxxxxx
+xxxxxxxxxlaxxlxxxxxxxxxxxxxrPxxxxxivaGxdxxxxpxLyxidxxGxxxxxxxxaxGxgxxxaxxxLexxxxxxxsxxeaxxlxxxxlxxxx
+xrdxxxxxxixvxiixxxxxxxxgxxxxxxxxxixxxxxxxxxx
+>8e30ca516d2b86076f51d1316fab39ad
+GSRRYDSRTTIFSPEGRLYQVEYALESISHAGTAIGIMASDGIVLAAERKVTSTLLEQDTSTEKLYKLNDKIAVAVAGLTADAEILINTARIHAQNYLKT
+YNEDIPVEILVRRLSDIKQGYTQHGGLRPFGVSFIYAGYDDRYGYQLYTSNPSGNYTGWKAISVGANTSAAQTLLQMDYKDDMKVDDAIELALKTLSKTT
+DSSALTYDRLEFATIRKGANDGEVYQKIFKPQEIKDILVKTGIT
+>gi|291226741|ref|XP_002733349.1| PREDICTED: proteasome beta 9 subunit isoform 1 proprotein-like [Saccoglossus kowalevskii]
+----------R-LKMDKFPV-PFPDitKPVQTGTTIMATEFNDGVVIGGDTRTTSGTIITHKVSDKITEITDSIYCARSGSLADTQALADIIKYYMDMYR
+YYIDTNPMVSVvakQFQSLSYTWRDK--------IQAGLIVAGWDSVNCGQVYSIPMGGACVRQHVTISGSGSSYISGYIDAYYHNQMTKNECMNFTTNA
+ISLAIARDGGSGGVIRLAVITKD----GVERKVILGNHLPCFYDG----
+>gi|195037993|ref|XP_001990445.1| GH19348 [Drosophila grimshawi]gi|193894641|gb|EDV93507.1| GH19348 [Drosophila grimshawi]
+-----------------------------CNGSIIAMHGKDCVAIAV------KGGNINDSNKNLYKLGARLYLGLTGRLADILMAYKHLILRKNIFELE
+KNRELLPKELTLILSQLL--Y----AHRlvPFQIEAVIVGMDPDTlEPHICSLGMIGYPNVtKDFVVAGHRHGPLLGLCKSLWRPSLNPSQLYDTIGQTM
+IQFCTSYISVGCGVDICLIEK---------------------------
+>gi|335282239|ref|XP_003354003.1| PREDICTED: LOW QUALITY PROTEIN: proteasome subunit beta type-5-like [Sus scrofa]
+---------------------------MLHHTTILAFKILLGVIVAADSWDMAVAYIASQTVKNVIEISLYLLATGAVGAVN----crf---LAQQXXIY
+ELQNKGCISVAAASKLLANMVYQYKGM----GLSMGTMICVWGK----rgpGLYYMDSEGNWIWGVDFSVGSRSVHAY--gfM--GYSYDLE-vERAYDM
+ASQATYXASXSDAYSGGLVNLYHVW-----E--DgWIQSSSDNVAYLH---ykyS--
+>gi|194765170|ref|XP_001964700.1| GF23325 [Drosophila ananassae]gi|190614972|gb|EDV30496.1| GF23325 [Drosophila ananassae]
+----------------------HSTAAITTGSSVIGIRFDKGVMMAADTLVSYGSLaRY-QNMERIFMINNNILFGGCGDFADIQSIIRGIEQKIVeDQC
+NGDDIEMKPKALGQWMTRVL--YDRRTQMNPLLVDVVLGGLDvQ-GKPYLANVDLRGRSHDDFVIATGFARHLTIPFIRSAKPkdRDFNMDEAHEMIKRS
+MQILYYRDTRNNSQYTLGVCSP-----KN-CGIEGPYQVAEN-------
+>gi|341876605|gb|EGT32540.1| hypothetical protein CAEBREN_25994 [Caenorhabditis brenneri]gi|341877137|gb|EGT33072.1| hypothetical protein CAEBREN_23993 [Caenorhabditis brenneri]
+----------------------------MAGMhFLVGISTENYVILAADKATfAYGAILADSENDKEYRLGKKLTMMCIGEEGDVAQFGDWTKRNLQLYS
+VRNGYEVSPACAHHFVRRSIAEGLRS--QDHYTVDVLIGGYDDKEeKAFLGSVDYLANgLAQQPYLFRGFCGRFCYAIMDREYKKDMSEADGLALMNKCI
+GEAKRRFVANIPGYKVVIIDK-----NG-YRKLD--------------
+>gi|328543397|ref|YP_004303506.1| peptidase, T1 family [Polymorphum gilvum SL003B-26A1]gi|326413142|gb|ADZ70205.1| Peptidase, T1 family [Polymorphum gilvum SL003B-26A1]
+------------------------------MTYCVGLKLDRGLVFAADTRTNAGVDNI-ATFKKLKIWEKPgervFALMSSGNLAITQSVVSILSEQIAs
+hSNKGPtLMSVDTLFQAARVVGSAVrEVRALDGeaLaasAENFYVTFIFGGQIMGEEPRLFQIYSAGNFIEatddTMFFQIGE-HKYGKPILDRVTRHDM
+RLGEAAKMALLSFDSTLRSNLSVGMPIDLLLYNT---------------------------
+>gi|162606210|ref|XP_001713620.1| 26s proteasome SU A6 [Guillardia theta]gi|13794540|gb|AAK39915.1|AF165818_123 26s proteasome SU A6 [Guillardia theta]
+-------NQTLFDSDGKILQLEFALKIPNQGKMIFSFKSINHSYIISEiheKKTNN------KFFNRFYSIDNNIGLGISGIFFDAKKIFNFCVELNIKI
+KQAFKNFCSVEYISKKISEAFSNNTLKINQRPYAINVFIIGFSD-KGPIIFEISTDGLMTYKKTCLSGSSINSYTKELFSIIKndKKMLNDEIFMIsFYQ
+CIKKSEK--NSSNQIFSLSILGK-----KTKFTILN-KIVDRFYTK----
+>gi|114705646|ref|ZP_01438549.1| hypothetical protein FP2506_14309 [Fulvimarina pelagi HTCC2506]gi|114538492|gb|EAU41613.1| hypothetical protein FP2506_14309 [Fulvimarina pelagi HTCC2506]
+-------------------------------TVVLAVVCRDGVVIGSDSQITDKGRDMTYPADKLHPLGELAAWGGSGARSVLADVKRRFDENSAaiLDA
+PDIGRALQEQvlpilrhHYETFIPDVPGE---AGGG-TPAAYVMAAGWRN-GEPWILEITPSGMighYANIGFHAIGSGAPMAQQanSLLSHFHlTKRSL
+RFGCAAVLRVLQ-ALDLTsSSVGGPFNLCRIDA-----EG-AHHLDKDEIEVVSDIV---
+>gi|340788739|ref|YP_004754204.1| 20S proteasome subunits A and B [Collimonas fungivorans Ter331]gi|340554006|gb|AEK63381.1| 20S proteasome, A and B subunits [Collimonas fungivorans Ter331]
+------------HPTGQ---LAYRWRAIM--TTCVVVKKNGQIAIASDSLVTFGdtrLSHAYEVNNKIFQIGE-SYITLAGTAAHFPVMRKLLTAMGEEC
+RLNSRDEVfdTFSKVHTILKDQYFLNTKEDEDDPYESsqiTSLVA--NP-YG--IFGVYSYREVFSfDRFWGIGSGRNFALGAMYAVYDKDVSAQH---I
+AEVGIHAGVEFDKSSAMPLRIHSFEM---------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 0 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+S 2 * * 3477 3350 * 3511 * * * 3484 * * 3431 3352 2560 1864 * * * * 2
+ 0 * * * * * * 3948 0 0
+
+R 3 4213 * 4050 * * 4104 * * 2680 4133 * 3264 * * 3264 2243 2781 * * 4335 3
+ 0 * * * * * * 4969 0 0
+
+R 4 3711 * 3856 3696 * 2203 * * 3492 4758 4701 3116 4577 4839 3234 3937 * 4951 * * 4
+ 0 * * 1585 585 * * 5647 1046 0
+
+Y 5 * 4759 4878 * 3712 * 4113 4823 * * * 4930 * * * 4971 4105 * 4523 753 5
+ 0 * * * * * * 5919 0 0
+
+D 6 4302 * 747 3888 * * * * 4124 * * * * 5164 * 3392 4905 5009 * 4613 6
+ 0 * * * * * * 5998 0 0
+
+S 7 4700 * 4101 * 4068 * * * 4992 2236 * 3170 4971 5406 2559 2679 3590 * * 5348 7
+ 0 * * 0 * * * 6119 1037 0
+
+R 8 4413 * 2720 4037 4496 * 5335 * 5329 5026 * 3430 3363 * 4260 1772 5165 5021 * 5512 8
+ 35 * 5382 3999 93 * * 6276 1154 0
+
+T 9 3620 5035 * * * * * 3151 * 2158 * 5743 2514 4946 5352 5258 3838 3070 * 3543 9
+ 32 * 5489 * * * 0 6499 0 1000
+
+T 10 4370 5333 4900 * * 4041 * * * 4157 * 2568 * * 5319 3848 962 * * * 10
+ 0 * * * * 0 * 6476 0 1110
+
+I 11 5531 * * * 4501 * * 1901 4034 3696 3697 4478 4437 * 5014 4130 2421 3550 * * 11
+ 89 * 4058 * * * * 6752 0 0
+
+F 12 * * * * 666 * * * * * * * * * * * * 3806 4427 1991 12
+ 0 * * * * 0 * 6594 0 1190
+
+S 13 3300 * 3938 4543 * 3398 4807 * * 5078 * 3901 * * 5006 1248 3171 * * * 13
+ 0 * * * * * * 6918 0 0
+
+P 14 5820 * * 5708 * * 5550 * 5078 * * 5429 570 5531 * 3425 4324 4301 * * 14
+ 38 5269 * 0 * * * 6918 1046 0
+
+E 15 5514 * 1591 1626 * 5460 * * 5626 * 5078 5726 * 3871 * 3885 3400 * * * 15
+ 63 4543 * 0 * * * 6918 1124 0
+
+G 16 * * 5109 5916 5009 158 * * * * 5214 * * * * * * * * * 16
+ 0 * * * * * * 6886 0 0
+
+R 17 5916 * 5760 * * * 4770 5009 2281 * * 3922 * 4040 1297 3124 5516 * * 5571 17
+ 80 * 4210 * * * * 6886 0 0
+
+L 18 * * * * 5038 * * 2206 * 1139 4562 5948 * * 5146 * 4250 2648 * * 18
+ 41 * 5146 * * * 0 6743 0 1185
+
+Y 19 * * 4508 4525 2723 4326 4485 5341 4609 2142 * 5796 3670 * 4130 5863 4495 * * 2651 19
+ 35 5393 * 0 * * 0 6790 1000 1335
+
+Q 20 * * * 5482 * * * * * 5604 * * 5175 244 * 5213 * 4106 * * 20
+ 49 * 4903 * * 1519 619 6790 0 1335
+
+V 21 * 5476 * * * 5472 * 2351 5408 1868 * 5470 4878 * * 4412 * 1482 * * 21
+ 0 * * * * 1412 680 6797 0 1354
+
+E 22 4961 * 3175 746 * * 4985 * 4613 5028 * * 4995 5268 * 4424 4746 5895 * * 22
+ 0 * * 2322 322 1004 996 7051 1006 1174
+
+Y 23 * 6018 5662 * 3390 * 5356 5162 * 4604 * 5658 5633 * 3735 5459 * * * 648 23
+ 0 * * 2585 263 0 * 7270 1021 1021
+
+A 24 728 * * * 5278 4063 * 4523 5457 * 5201 * 5229 5598 5101 3569 5830 4681 * * 24
+ 0 * * * * * * 7299 0 0
+
+L 25 4051 * 5697 * 3494 4866 5764 5205 3971 2128 3087 5393 * 3350 4823 3713 4774 4364 5436 * 25
+ 146 4390 4365 1661 548 * * 7860 1305 0
+
+E 26 4299 * 3751 2253 * 4970 * 4799 1885 * 5745 3573 * 3955 3001 5654 6103 * * * 26
+ 0 * * * * * 0 7894 0 1223
+
+S 27 1046 4776 * 5885 5804 5560 * 4704 5597 4997 * 5427 2866 5954 5638 3663 5061 5197 * * 27
+ 58 5721 5597 1843 471 706 1370 7925 1153 1223
+
+I 28 3196 * * 6343 6098 * * 2480 * 4807 4352 5531 4526 5889 * 3210 4594 1548 * 5225 28
+ 19 6287 * 0 * 889 1121 8239 1000 1167
+
+S 29 4747 6087 3460 4000 6534 * * 4593 2711 4242 3571 2509 5312 4676 * 3855 3747 4809 * 4901 29
+ 85 4641 5866 2115 379 0 * 8406 1280 1006
+
+H 30 3620 6143 6370 6379 4372 6333 4468 5309 2927 3910 6239 2379 * 3930 3451 4361 2962 * * 6412 30
+ 0 * * * * * 0 8480 0 1032
+
+A 31 3703 * * 5991 * 618 * * * * 4610 6236 * 6547 6592 2689 6347 6247 * * 31
+ 24 5914 * 2361 312 0 * 8663 1099 1032
+
+G 32 5965 6725 5378 6570 6453 2301 5586 * 5085 4994 6481 3645 5118 * 4907 2765 1648 5352 * * 32
+ 60 4626 * 0 * * * 8833 1350 0
+
+T 33 3822 6888 * * 4672 * 6311 4626 * 3381 6226 5420 3841 * * 2540 1422 4135 * 5381 33
+ 0 * * * * * * 8909 0 0
+
+A 34 3158 3405 * * * * * 2150 * 3123 5640 * 6507 * * 3588 3165 2176 * 7288 34
+ 0 * * * * * * 8909 0 0
+
+I 35 4421 * * * 4914 * * 1583 * 2373 5184 * 6507 * * * * 1495 * * 35
+ 12 * 6888 * * * * 8909 0 0
+
+G 36 1409 6712 * * 6254 1068 * * * * * * * * * 4911 5103 4021 * * 36
+ 0 * * 0 * 0 * 8903 1000 1000
+
+I 37 3689 * * * 4048 * * 1534 * 2212 3982 * * * * 6283 6678 2283 * 6727 37
+ 0 * * * * * * 8929 0 0
+
+M 38 3923 5771 * 4676 * * 6549 4612 1635 4540 5810 * * 3661 2736 4036 4118 3403 * * 38
+ 9 7262 * 4392 70 * * 8929 1000 0
+
+A 39 4220 3331 6283 * 3441 2290 5711 6845 5022 4874 * 4428 * * 6901 3189 3277 5217 6768 2824 39
+ 0 * * * * * * 8929 0 0
+
+S 40 4331 * 3219 3950 * 4407 5485 6276 1860 * * 2577 5778 5933 3420 3429 5503 6657 * * 40
+ 0 * * * * * * 8953 0 0
+
+D 41 5517 * 1138 4098 * 3285 5192 * 3630 * * 3223 6835 5805 5950 4054 4489 * * * 41
+ 50 6406 5499 0 * * * 8953 1027 0
+
+G 42 5571 3861 * 6763 3037 875 5037 * 5291 6891 * 6880 * 6303 6875 4359 5808 5733 * 4197 42
+ 0 * * * * 0 * 8906 0 1154
+
+I 43 3011 5683 * * 6526 6555 * 1961 * 3696 6560 * * * * 5082 5607 1184 * * 43
+ 16 * 6525 * * * * 8953 0 0
+
+V 44 3677 5049 * * 6786 * * 1980 * 2739 4822 * * * 6518 * 6445 1360 * 4965 44
+ 0 * * * * 0 * 8934 0 1029
+
+L 45 5841 * * * 3157 * * 1752 * 1566 3598 * * * * * * 2706 * * 45
+ 34 5440 * 2416 299 * * 8953 1158 0
+
+A 46 915 5134 * * 5607 2830 * 4033 * 4215 5841 6332 * * * 5520 6345 3305 * * 46
+ 27 * 5757 * * * * 8953 0 0
+
+A 47 1894 4112 6504 * 6765 3161 * 4855 6407 5267 * * * 6546 * 2267 2914 3397 * 5455 47
+ 83 6504 4469 572 1612 799 1234 8902 1157 1126
+
+E 48 5960 * 891 2479 6440 * 4604 * 5526 4720 5746 5475 5928 4442 6737 5786 * 6957 * 6149 48
+ 36 6194 6550 792 1243 636 1487 8827 1317 1548
+
+R 49 * 6850 6525 6281 * 3948 * 4573 2264 3944 6081 4067 6765 6772 3557 2512 2199 5887 * * 49
+ 43 6759 5637 5170 41 * 0 8895 1004 1282
+
+K 50 4308 6643 5431 5778 5378 6492 6207 5621 2694 4262 6519 5008 4490 3075 1873 3974 4042 5640 * * 50
+ 10 7234 * 1000 1000 * 0 8875 1000 1534
+
+V 51 2948 5699 * 6127 4974 5829 5663 2924 4537 3075 5576 5588 5698 4691 5551 3910 2855 2753 * * 51
+ 102 5123 4661 470 1846 2624 255 8875 1221 1534
+
+T 52 4322 5788 * 4841 5601 4197 4377 4689 * 5738 * 3212 4194 5640 6631 2216 1981 4514 * 6486 52
+ 168 3480 5613 1916 444 * 0 8794 1974 1909
+
+S 53 4204 6012 4590 4396 5402 3665 5086 * 5577 4536 4227 3052 4806 4203 4479 2445 4048 * * 3437 53
+ 58 5339 6103 277 2518 2303 327 8771 1292 2133
+
+T 54 * * 4606 4081 7001 1472 * 6697 2691 5839 * 4060 3623 5025 6491 2936 5416 * * 6316 54
+ 78 4925 5679 2451 291 * 0 8767 1387 2040
+
+L 55 3637 * * 5006 4643 4287 6610 3436 6428 1881 3745 4077 * 6805 6496 3414 4616 3543 * 4748 55
+ 58 5336 6111 0 * 1843 472 8703 1347 2314
+
+L 56 4005 * 4844 5749 4656 5617 * 2964 * 2547 3839 5337 5586 4764 4726 3193 4270 4291 * 3026 56
+ 218 3892 3778 2100 383 2974 196 8741 1701 2080
+
+E 57 5657 * 3376 3248 4436 5053 6110 2208 3587 5078 * 3757 5891 6402 3952 4016 5105 3545 * 6087 57
+ 126 5276 4118 0 * 2551 270 8665 1232 2767
+
+Q 58 3224 * 4377 4794 4594 6821 6527 4734 4705 3739 4210 4625 3560 5278 5500 3061 3433 3272 * 4215 58
+ 1144 5488 929 1330 732 * 0 8606 1134 2997
+
+D 59 4609 5557 3101 * * * 4374 * 2286 5420 5310 3184 * 5339 4399 2229 3787 * * 4279 59
+ 72 4370 * 1539 608 209 2889 7296 1201 6538
+
+T 60 5212 5612 3261 3471 6754 4782 5988 6290 2780 * * 4081 4630 4103 2914 2784 4209 6469 * 4739 60
+ 49 * 4901 0 * 519 1728 8815 1150 1987
+
+S 61 4454 * 2869 4235 5470 5935 5087 5976 5214 5052 6361 2266 4040 6528 5461 2544 4340 4003 * 5293 61
+ 0 * * 2661 248 1288 760 8830 1185 1627
+
+T 62 3533 4438 5568 4233 3301 4185 5841 4774 * 4859 5039 3739 7262 3292 * 4307 4934 2446 * 3887 62
+ 12 * 6968 * * 595 1566 8869 0 1323
+
+E 63 * 6930 2933 2865 * * 5257 * 3171 6409 6723 2982 3804 3654 4231 2969 3920 5937 6506 6245 63
+ 0 * * 0 * 0 * 8926 1000 1116
+
+K 64 * * 6301 5306 5924 * 5015 * 715 5604 6449 4838 * * 2418 5023 5605 * * * 64
+ 0 * * * * * * 8954 0 0
+
+L 65 * 5636 * 6672 3763 * 5897 1171 6826 2649 4933 * * 6685 * * 5079 2357 * * 65
+ 0 * * * * * * 8954 0 0
+
+Y 66 4363 6393 6702 6154 1760 * 3419 3839 * 4161 5117 6389 * 4967 4187 5015 4254 4149 6863 2995 66
+ 12 6904 * 3459 138 * * 8967 1002 0
+
+K 67 3992 6455 4456 2954 6306 6641 5569 4402 2606 4758 * 4169 3481 4241 3785 4120 4400 4454 * 4730 67
+ 53 * 4783 * * * * 8967 0 0
+
+L 68 5812 * * * 5387 * 6473 1287 * 1819 * * * * * * * 2028 * 6852 68
+ 28 5681 * 351 2213 0 * 8908 1383 1370
+
+N 69 5381 5855 2005 6646 6641 2954 4951 * 4992 5823 * 2776 6521 4846 5180 2724 4056 * * 4367 69
+ 15 * 6588 * * * * 8967 0 0
+
+D 70 5149 * 1861 2875 * 3700 6466 6514 2908 * * 3200 3273 6633 7237 3801 5210 * * * 70
+ 88 4677 5637 393 2068 0 * 8840 1388 1030
+
+K 71 6253 6677 4547 6069 6780 5652 2731 6891 2674 5013 6841 2143 * 4132 3532 4847 4370 5600 * 4023 71
+ 79 4237 * 2739 234 0 * 8841 1535 1194
+
+I 72 4373 5539 * * 5515 5801 6745 1485 4648 3110 3694 * * * 7194 4080 3839 2690 * * 72
+ 46 * 5007 * * * * 8906 0 0
+
+A 73 3322 5359 * * 5690 2054 * 3638 * 2213 4710 * * * * * 4584 3482 4769 3140 73
+ 0 * * * * 0 * 8822 0 1298
+
+V 74 4017 2578 * * 4197 4585 * 2343 * 2615 3021 * * * * 6506 6931 3057 5035 5564 74
+ 0 * * * * * * 8906 0 0
+
+A 75 2022 3564 * * 6772 1810 6374 4000 * 4662 4912 * * * * 4581 3089 3873 * * 75
+ 12 6882 * 2000 415 * * 8906 1000 0
+
+V 76 3194 4325 * * 2585 3692 * 3051 * 4017 3645 * * * 5251 3433 3755 3408 6350 4834 76
+ 0 * * * * * * 8906 0 0
+
+A 77 2132 * 6685 * * 4463 6783 4540 * 6840 * 4915 5531 * * 1287 2835 4286 * * 77
+ 0 * * * * * * 8906 0 0
+
+G 78 * * * * * 55 * * * * * * * * 6206 6526 6296 * * * 78
+ 16 * 6490 * * * * 8906 0 0
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+ 17 * 6386 * * * * 8883 0 0
+
+F 212 6703 * * * 4480 * * 1788 * 2286 3705 * * * * * 6537 1509 * 6340 212
+ 14 * 6725 0 * 0 * 8846 1016 1016
+
+A 213 2555 3099 6174 4830 4169 2587 6291 6519 3812 3699 6759 5957 * * 6923 4058 4166 4700 5003 4284 213
+ 18 * 6367 0 * 0 * 8864 1000 1000
+
+T 214 * 6633 * 5236 5397 * 5605 1823 4071 3357 8613 * * * 4911 6261 3508 2166 3920 4218 214
+ 20 6213 * 1036 964 0 * 8846 1181 1016
+
+I 215 4309 5100 * * 4689 * * 1833 * 2331 6900 * * * * * 4733 1739 * 4146 215
+ 74 5120 5577 0 * 0 * 8829 1253 1033
+
+R 216 4480 6444 2551 4098 6162 3206 6717 * 3969 5580 * 5663 6913 * 3564 3101 2131 * * 4620 216
+ 464 6631 1917 0 * 0 * 8823 1000 1136
+
+K 217 3531 * 4666 4086 4876 6438 6563 6251 1802 3734 4844 4231 4425 5208 3105 4712 6101 4229 * * 217
+ 1001 5869 1049 3000 193 * 0 8448 1000 3722
+
+G 218 3378 * 1675 1863 * 3842 * * 4680 4922 4518 * * 4564 * 4798 4260 * * * 218
+ 1549 * 603 * * * 0 6539 0 5463
+
+A 219 2893 * 1751 * * 2885 * * 2795 * * * * * 2682 * 2909 * * * 219
+ 514 * 1738 * * * 0 3706 0 6352
+
+N 220 * * 2357 2377 * 2370 * * * * * 2304 * 2208 * * * * * * 220
+ 0 * * * * 5655 29 2949 0 6489
+
+D 221 2423 * 1641 * * * * * * * * 2567 1626 * * * * * * * 221
+ 252 2643 * 4087 87 637 1486 3322 1000 6422
+
+G 222 3352 * * 3407 5300 3434 * * 2283 * * 3510 4482 5731 5577 3404 2516 5448 * 5652 222
+ 122 4459 4809 0 * 305 2392 7514 1159 3462
+
+E 223 4935 * 2650 2993 * 2794 * 6422 3618 * * 2175 5568 2870 5894 5084 * 5682 * * 223
+ 117 6260 3940 523 1718 1007 993 8145 1143 1671
+
+V 224 * * * 3645 * 946 * 5670 3698 * * 4936 3963 4836 4553 6033 4790 4021 * 5892 224
+ 851 * 1166 1810 484 673 1424 8123 1163 1938
+
+Y 225 5226 * 3585 3323 * 3401 5071 4294 2617 4224 5420 5032 3741 5010 3657 * 3648 4221 * 5285 225
+ 0 * * * * 65 4512 7346 0 4005
+
+Q 226 3750 5052 * * 1667 * 4322 3660 * 3413 * * * 6052 5017 5245 4125 2846 4078 5072 226
+ 65 5102 6045 635 1489 * 0 8168 1140 1033
+
+K 227 * 4956 4513 3209 6250 * 3196 5929 1826 5012 6128 5917 * 5042 2255 6064 4386 5027 * * 227
+ 0 * * * * 1055 947 8149 0 1185
+
+I 228 * 6242 6096 6152 4008 * 3663 1931 2779 3526 * * * 4655 3764 * 4619 3221 * 4033 228
+ 26 5795 * 0 * * 0 8168 1023 1033
+
+F 229 6258 * 6187 3517 3001 4407 6338 3440 6173 1523 4925 4941 * * * * * 3178 5939 4180 229
+ 68 4444 * 2220 349 * 0 8168 1246 1033
+
+K 230 4149 * 3199 3610 5888 3691 * * 4485 5896 * 3311 2356 6047 5226 2874 3224 5986 * * 230
+ 32 * 5507 * * 0 * 8086 0 1033
+
+P 231 4319 * 4296 2679 4369 3830 5190 6002 3073 5018 5660 3952 2611 5866 6039 3787 4375 5931 * 6160 231
+ 0 * * * * 0 * 7982 0 1033
+
+Q 232 4218 * 2901 2053 6133 4998 4984 6000 3042 5954 6080 3293 5675 4968 * 4208 6166 6084 * 3475 232
+ 55 * 4740 * * * * 8044 0 0
+
+E 233 5512 * 3169 1317 5964 * 5778 3686 4080 4202 * 5893 * 5377 3883 5920 4941 4023 5591 * 233
+ 27 5769 * 4459 67 * 0 7921 1021 1154
+
+I 234 * * * 4782 4241 * * 1486 * 3258 * 5973 * * 4322 5574 5948 1531 * * 234
+ 0 * * 1000 1000 0 * 7848 1154 1154
+
+K 235 4219 * 2556 2215 5842 4076 5800 4913 3257 6212 * 3875 4270 4701 4093 3354 * * * * 235
+ 56 5604 5823 1585 585 * * 7938 1021 0
+
+D 236 3352 4605 3110 2142 5799 5812 * 4611 3709 5854 5415 4130 3673 3987 5269 5646 4601 4681 * * 236
+ 0 * * 0 * 0 * 7603 1021 1021
+
+I 237 5052 5489 * * 2331 * 5778 2604 * 2148 5634 4222 * * * * * 2520 * 3436 237
+ 0 * * * * * * 7344 0 0
+
+L 238 5312 * * * 3003 * 4416 2846 5432 1469 * * * * 4390 3425 * 5091 5062 3649 238
+ 0 * * * * * * 7192 0 0
+
+V 239 4140 * 2708 2203 * 3554 * * 3588 5109 * * * 4124 3987 3549 3999 4266 * 4173 239
+ 0 * * * * * * 7032 0 0
+
+K 240 5079 * 5117 5142 * 4044 * 4184 2606 * 5186 3906 * 4085 3687 2768 3054 2884 * * 240
+ 0 * * * * * * 6958 0 0
+
+T 241 3402 * * * 5105 * * 1949 * 3185 4788 * * * 4825 4903 3855 2168 * 3175 241
+ 0 * * * * * * 6481 0 0
+
+G 242 1807 * 3784 1937 * 2633 * * 2773 * * * 3779 * * * * * * * 242
+ 391 2073 * 1000 1000 * * 4701 1013 0
+
+I 243 * * * * 2049 * * 1958 1988 * * * * * * * * 2006 * * 243
+ 0 * * * * * * 2507 0 0
+
+T 244 * * * * * * * * * * * * * * * * 0 * * * 244
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 8fd273e25da1bf193a2bf90e2bc9fef0
+FAM
+FILE 8fd273e25da1bf193a2bf90e2bc9fef0
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:12:17 2013
+LENG 63 match states, 63 columns in multiple alignment
+FILT 7 out of 9 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 1.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEEEEECCCEEEEEEECCHHHHHHHHHHHHHHHHHHCCEEEEEECCCCEEEEEEECCC
+>ss_conf PSIPRED confidence values
+938999999807947878860307888799999999878657806999617926999996679
+>Consensus
+evtikanlifaxgxtqtaefkgtfeeataeayxyadxlxkxngextxdxxdxgxtlnikfagk
+>8fd273e25da1bf193a2bf90e2bc9fef0
+EVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALLAKVNGEWTADLEDGGNHMNIKFAGK
+>gi|159164775|pdb|2PTL|A Chain A, Three-Dimensional Solution Structure Of An Immunoglobulin Light Chain-Binding Domain Of Protein L. Comparison With The Igg-Binding Domains Of Protein G
+EVTIKANLIFANGSTQTAEFKGTFEKATSEAYAYADTLKKDNGEYTVDVADKGYTLNIKFAG-
+>gi|261824459|pdb|2KAC|A Chain A, Nmr Solution Structure Of Kx6e Protl Mutant
+EVTIKANLIFANGSTQTAEFEGTFEEATSEAYAYADTLEEDNGEWTVDVADEGYTLNIEFAG-
+>gi|150674|gb|AAA67503.1| protein L [Finegoldia magna]gi|745058|prf||2015385A protein L
+EVTIKVNLIFADGKIQTAEFKGTFEEATAKAYAYANLLAKENGEYTADLEDGGNTINIKFAGK
+>gi|322065|pir||A45063 immunoglobulin-binding protein LG - Peptostreptococcus magnusgi|261706|gb|AAA03280.1| protein LG [Finegoldia magna]
+EVTIKANLIYADGKTQTAEFKGTFAEATAEAYRYADLLAKENGKYTADLEDGGYTINIRFAGK
+>gi|297588180|ref|ZP_06946824.1| probable protein L precursor [Finegoldia magna ATCC 53516]gi|297574869|gb|EFH93589.1| probable protein L precursor [Finegoldia magna ATCC 53516]
+EVTIKANLIYADGKTQTAEFKGTFEEATAEAYRYADLLAKENGKYTVDVADKGYTLNIKFAGK
+>gi|18655716|pdb|1KH0|A Chain A, Accurate Computer Base Design Of A New Backbone Conformation In The Second Turn Of Protein Lgi|18655717|pdb|1KH0|B Chain B, Accurate Computer Base Design Of A New Backbone Conformation In The Second Turn Of Protein L
+EVTIKANLIFANGSTQTAEFKGTKEKALSEVLAYADTLKKDNGEWTIDkrVTNGVIILNIKFAG-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+E 1 * * * 0 * * * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1417 0 0
+
+V 2 * * * * * * * * * * * * * * * * * 0 * * 2
+ 0 * * * * * * 1417 0 0
+
+T 3 * * * * * * * * * * * * * * * * 0 * * * 3
+ 0 * * * * * * 1417 0 0
+
+I 4 * * * * * * * 0 * * * * * * * * * * * * 4
+ 0 * * * * * * 1417 0 0
+
+K 5 * * * * * * * * 0 * * * * * * * * * * * 5
+ 0 * * * * * * 1417 0 0
+
+V 6 476 * * * * * * * * * * * * * * * * 1831 * * 6
+ 0 * * * * * * 1417 0 0
+
+N 7 * * * * * * * * * * * 0 * * * * * * * * 7
+ 0 * * * * * * 1417 0 0
+
+L 8 * * * * * * * * * 0 * * * * * * * * * * 8
+ 0 * * * * * * 1417 0 0
+
+I 9 * * * * * * * 0 * * * * * * * * * * * * 9
+ 0 * * * * * * 1417 0 0
+
+F 10 * * * * 440 * * * * * * * * * * * * * * 1928 10
+ 0 * * * * * * 1417 0 0
+
+A 11 0 * * * * * * * * * * * * * * * * * * * 11
+ 0 * * * * * * 1417 0 0
+
+D 12 * * 879 * * * * * * * * 1133 * * * * * * * * 12
+ 0 * * * * * * 1417 0 0
+
+G 13 * * * * * 0 * * * * * * * * * * * * * * 13
+ 0 * * * * * * 1417 0 0
+
+K 14 * * * * * * * * 879 * * * * * * 1133 * * * * 14
+ 0 * * * * * * 1417 0 0
+
+I 15 * * * * * * * 1831 * * * * * * * * 476 * * * 15
+ 0 * * * * * * 1417 0 0
+
+Q 16 * * * * * * * * * * * * * 0 * * * * * * 16
+ 0 * * * * * * 1417 0 0
+
+T 17 * * * * * * * * * * * * * * * * 0 * * * 17
+ 0 * * * * * * 1417 0 0
+
+A 18 0 * * * * * * * * * * * * * * * * * * * 18
+ 0 * * * * * * 1417 0 0
+
+E 19 * * * 0 * * * * * * * * * * * * * * * * 19
+ 0 * * * * * * 1417 0 0
+
+F 20 * * * * 0 * * * * * * * * * * * * * * * 20
+ 0 * * * * * * 1417 0 0
+
+K 21 * * * 2757 * * * * 231 * * * * * * * * * * * 21
+ 0 * * * * * * 1417 0 0
+
+G 22 * * * * * 0 * * * * * * * * * * * * * * 22
+ 0 * * * * * * 1417 0 0
+
+T 23 * * * * * * * * * * * * * * * * 0 * * * 23
+ 0 * * * * * * 1417 0 0
+
+F 24 * * * * 289 * * * 2461 * * * * * * * * * * * 24
+ 0 * * * * * * 1417 0 0
+
+E 25 2865 * * 213 * * * * * * * * * * * * * * * * 25
+ 0 * * * * * * 1417 0 0
+
+E 26 * * * 532 * * * * 1698 * * * * * * * * * * * 26
+ 0 * * * * * * 1417 0 0
+
+A 27 0 * * * * * * * * * * * * * * * * * * * 27
+ 0 * * * * * * 1417 0 0
+
+T 28 * * * * * * * * * 2461 * * * * * * 289 * * * 28
+ 0 * * * * * * 1417 0 0
+
+A 29 879 * * * * * * * * * * * * * * 1133 * * * * 29
+ 0 * * * * * * 1417 0 0
+
+E 30 * * * 214 * * * * 2858 * * * * * * * * * * * 30
+ 0 * * * * * * 1417 0 0
+
+A 31 289 * * * * * * * * * * * * * * * * 2461 * * 31
+ 0 * * * * * * 1417 0 0
+
+Y 32 * * * * * * * * * 2461 * * * * * * * * * 289 32
+ 0 * * * * * * 1417 0 0
+
+R 33 751 * * * * * * * * * * * * * 1300 * * * * * 33
+ 0 * * * * * * 1417 0 0
+
+Y 34 * * * * * * * * * * * * * * * * * * * 0 34
+ 0 * * * * * * 1417 0 0
+
+A 35 0 * * * * * * * * * * * * * * * * * * * 35
+ 0 * * * * * * 1417 0 0
+
+A 36 2805 * 476 * * * * * * * * 2858 * * * * * * * * 36
+ 0 * * * * * * 1417 0 0
+
+L 37 * * * * * * * * * 879 * * * * * * 1133 * * * 37
+ 0 * * * * * * 1417 0 0
+
+L 38 * * * * * * * * * 0 * * * * * * * * * * 38
+ 0 * * * * * * 1417 0 0
+
+A 39 879 * * 2757 * * * * 1698 * * * * * * * * * * * 39
+ 0 * * * * * * 1417 0 0
+
+K 40 * * * 2757 * * * * 231 * * * * * * * * * * * 40
+ 0 * * * * * * 1417 0 0
+
+V 41 * * 1133 1319 * * * * * * * * * * * * * 2805 * * 41
+ 0 * * * * * * 1417 0 0
+
+N 42 * * * * * * * * * * * 0 * * * * * * * * 42
+ 0 * * * * * * 1417 0 0
+
+G 43 * * * * * 0 * * * * * * * * * * * * * * 43
+ 0 * * * * * * 1417 0 0
+
+E 44 * * * 440 * * * * 1928 * * * * * * * * * * * 44
+ 0 * * * * * * 1417 0 0
+
+W 45 * * * * * * * * * * * * * * * * * * 1081 923 45
+ 0 * * * * * * 1417 0 0
+
+T 46 * * * * * * * * * * * * * * * * 0 * * * 46
+ 0 * * * * * * 1417 0 0
+
+A 47 1257 * * * * * * 2461 * * * * * * * * * 1322 * * 47
+ 0 * * * * * * 1417 0 0
+
+D 48 * * 0 * * * * * * * * * * * * * * * * * 48
+ 289 2461 * 1000 1000 * * 1417 1016 0
+
+L 49 * * * * * * * * * 1257 * * * * * * * 782 * * 49
+ 0 * * * * * * 1417 0 0
+
+E 50 1322 * * 1257 * * * * * * * * * * * * 2461 * * * 50
+ 0 * * * * * * 1417 0 0
+
+D 51 * * 289 * * * * * * * * 2461 * * * * * * * * 51
+ 0 * * * * * * 1417 0 0
+
+G 52 * * * 2757 * 737 * * 1988 * * * * * * * * * * * 52
+ 0 * * * * * * 1417 0 0
+
+G 53 * * * * * 289 * * * * * * * * * * * 2461 * * 53
+ 0 * * * * * * 1417 0 0
+
+N 54 * * * * * * * 2461 * * * 1831 * * * * * * * 896 54
+ 0 * * * * * * 1417 0 0
+
+H 55 * * * * * * 2805 2461 * * * * * * * * 567 * * * 55
+ 0 * * * * * * 1417 0 0
+
+M 56 * * * * * * * 1861 * 782 2805 * * * * * * * * * 56
+ 0 * * * * * * 1417 0 0
+
+N 57 * * * * * * * * * * * 0 * * * * * * * * 57
+ 0 * * * * * * 1417 0 0
+
+I 58 * * * * * * * 0 * * * * * * * * * * * * 58
+ 0 * * * * * * 1417 0 0
+
+K 59 * * * 2757 * * * * 484 * * * * * 2865 * * * * * 59
+ 0 * * * * * * 1417 0 0
+
+F 60 * * * * 0 * * * * * * * * * * * * * * * 60
+ 0 * * * * * * 1417 0 0
+
+A 61 0 * * * * * * * * * * * * * * * * * * * 61
+ 0 * * * * * * 1417 0 0
+
+G 62 * * * * * 0 * * * * * * * * * * * * * * 62
+ 0 * * * * * * 1417 0 0
+
+K 63 * * * * * * * * 0 * * * * * * * * * * * 63
+ 0 * * 0 * * * 1205 0 0
+
+//
+�HHsearch 1.5
+NAME 91ee985382113129d3975a1aa1210405
+FAM
+FILE 91ee985382113129d3975a1aa1210405
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:16:49 2013
+LENG 211 match states, 211 columns in multiple alignment
+FILT 130 out of 1316 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEECCCCEEEECCCCEEEEEEECCCCCCEEEEEEECCCCCCEEEEEECCCCCCCCCCCEEEECCCCEEEEEEECCCHHHCEEEEEEEEECCCCEEEE
+EEEEEEEEEEEEEEEEECCCCEEEECCCEEEEEEEECCCCCCCCEEEEEECCEECCCCCCEEEEEEECCCCCEEEEEEEEECCCCHHHCCEEEEEEECCC
+CCCCEEEEEEC
+>ss_conf PSIPRED confidence values
+9499965983899789989999997478997799999589987279997046447676762687426870589991343111849999998178731410
+2899999730044589718850662397099999971688986189999899784577520111476289848888999983488776928999999089
+88338999709
+>Consensus
+xxxvxxxxxxxxxxxGxxvxLxCxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLxIxxxxxxDxgxYxCxvxxxxxxxxxx
+xxxlxvxxxxxxpxvxxxxxxxxxxxgxxxxlxCxxxxxxpxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxsxLxixxxxxxdxgxyxCxvxxxx
+xxxxxxxxxxx
+>91ee985382113129d3975a1aa1210405
+DIKMTQSPSSMYASLGERVTITCKASQDINSYLNWFQQKPGKSPKTLIYRTNRLVDGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGS
+GTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
+LSSPVTKSFNR
+>gi|281349765|gb|EFB25349.1| hypothetical protein PANDA_021873 [Ailuropoda melanoleuca]
+--SVSQMKNQVTLSERAFLIVNHSFAANKsappfsgvFSVLVKLCSCPENH----KRKCDGSNKG----FEATnEEKTTFPWEKLSVPMADMAVCHCA--
+----------------------------------------------------------------------------------------------------
+--------------------
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+----------------------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne--DLRSWTAADMAAQN-----------------tqr
+kweaagvaeqw----RAYLEGECLEWLRRYLEKGK------------------et--LQ----
+>gi|62464905|gb|AAX83161.1| immunoglobulin heavy chain variable region [Aotus nancymaae]
+---------------GDPVPHLRCLWLLhRQ------willeldpPAPKGRG--WSGldisivwWVHql-qrlpQES-----sh---YFsrHVQEPVLVE
+---------A------------------------------------------------------------------------------------------
+-------------------------------------
+>gi|301609249|ref|XP_002934188.1| PREDICTED: vascular cell adhesion protein 1-like [Xenopus (Silurana) tropicalis]
+NTRLTITPS-ELVRQGDRVIIQCMSEAFPAPTLILKRKTERGQVELE--------------------TTSGEYIITSVTVKHSGTYTCESVNpvgnevae
+lhvtvqvppqnttvlvkpsknvtegdtvtitcethsttlptillkkvcagnstvqqaengtftlhnvtrndtgtyvlsiiNEAGNTTEVIEinvqvppkn
+trltitpselvregdhviphavppqnttvlvkpskn--------------------VTEGDTVTITCETHSTTHPTILLKKVCAGNSTVQQA--------
+-ENGTF------TLHNVTRNDTGTYMVSIINEAGNT--------
+>gi|26367762|dbj|BAB26738.2| unnamed protein product [Mus musculus]
+---FITPIFDFRIPENSSAVFKCSVIGIPPPEVRWYKEYMCIEPDD-------------TKYVISEEKGSHSLRIQDVGPSDCATYRCRALNSAGEAICR
+GfltmgdsqvsavatrtSKVTLSSQkeelvlrsryadsffefqvvDGPPRFIKGISDCHAPLGTAAYFQCLVRGSPRP--TVSWYKDGKLVQGSRFSAEE
+SGIGFHNLF-------ITGLVKGDEGEYSCVATNNS-----------
+>gi|209732526|gb|ACI67132.1| Butyrophilin subfamily 1 member A1 precursor [Salmo salar]
+-FEVLGPTDPIVAVAGDDIILPCYLKPNISAedmTVDWLNLDFKDSrvyryqnHRIIRDYQIPYYRGRTSLFEEELWRGNTSLKLTRVQGTDEGRYKCFI
+KAK-SWYDDFTIQVLVKAVGSKPVVS-----IEGHREGGMGLLCESEGWHPEP-ELAWLDSKGVHLSAG--PPETHRDFKGFYRVKQHVIVQETD---TN
+RFTCRVQQSRINEKMETEV--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+D 1 * * 1804 3068 * * * * 4186 * * 4067 3894 2506 * 2532 * * * 3976 1
+ 0 * * * * * * 6548 0 0
+
+I 2 3569 * 5145 * 3407 * 5215 2961 * 2010 5567 * 5438 4426 4847 4244 5150 2447 * * 2
+ 0 * * * * * * 8793 0 0
+
+K 3 4828 * 5347 4015 4710 5805 6360 4815 3762 5763 5760 5807 * 2349 5730 2688 2675 3313 * 5749 3
+ 27 5749 * 6256 19 * * 9380 1186 0
+
+M 4 6087 * * * 2988 5841 * 2335 5736 2495 5177 * 5969 5891 * * 5807 1505 5899 * 4
+ 0 * * 0 * * * 9786 1000 0
+
+T 5 5302 * 4635 3612 * 4572 5033 3190 4713 3696 * 4688 6045 4359 4081 3302 2293 3786 * 6016 5
+ 0 * * * * * * 9994 0 0
+
+Q 6 4166 * * 3263 * 4548 6416 3771 4692 5017 6089 5107 4158 2088 3782 4225 5239 2687 * * 6
+ 128 * 3555 * * * * 10035 0 0
+
+S 7 4019 * 5147 3392 6276 4601 6205 5041 4160 6420 6291 5199 2411 5052 3588 2476 3325 5143 * * 7
+ 11 * 7066 * * 0 * 10044 0 2034
+
+P 8 3567 * 5477 4918 6193 4913 5829 * 4091 6325 * 5520 1249 3761 5375 3472 4052 5493 * 6445 8
+ 20 * 6193 0 * 0 * 10238 1006 1006
+
+S 9 3521 * 4496 3068 * 4214 6379 * 3454 6519 5516 4525 3267 6498 3352 2698 4061 4100 * 5026 9
+ 42 6429 5875 0 * * 0 10291 1011 1024
+
+S 10 5399 * 5699 3522 5480 3977 4970 4285 4999 3188 * 3777 3245 4624 5189 2608 3937 4061 * 5367 10
+ 0 * * * * 0 * 10359 0 1408
+
+M 11 4025 * 5952 4129 5527 * 6512 3120 5080 2780 6774 * 5130 3630 4669 6704 4567 1670 * 5746 11
+ 0 * * * * * * 10509 0 0
+
+Y 12 5024 * 4256 2985 4664 6279 7056 4674 5196 3959 6145 4774 5861 3728 4822 3146 2498 3577 6776 4701 12
+ 0 * * * * * * 10603 0 0
+
+A 13 2401 6930 * 5243 6843 3965 6670 3462 4561 3089 6465 * 6581 6735 5802 5009 5054 1588 * * 13
+ 0 * * * * * * 10611 0 0
+
+S 14 4218 * 4805 4566 4154 6882 5046 4844 4197 2887 4602 5528 5354 3759 2872 3866 4274 3822 5693 4619 14
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+
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+
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+
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+Q 155 5335 7200 4022 6139 5758 6822 7288 2854 5927 2015 4666 4920 * 5163 5010 4478 3920 2221 * * 155
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+
+T 172 4778 6557 5707 5205 6860 4902 * 5681 3858 2753 5611 3526 6625 5915 3601 3114 2205 4122 * 5533 172
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+
+Y 173 4439 6688 * 4340 2555 6638 4798 4147 * 4102 * 4282 6551 4014 4729 3866 5491 4156 6134 2052 173
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+C 194 7044 160 6649 * 6635 7128 * * * 5228 6774 * * 7086 * * * 5212 * * 194
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+
+E 195 3707 5910 6647 2652 5147 6801 5316 4433 3843 4974 5991 7062 * 4020 2907 3848 3397 2784 * * 195
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+
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+ 29 6691 6567 368 2153 0 * 10409 1454 1733
+
+H 198 6343 * 6806 5492 4632 5617 1919 6498 6883 5786 5578 1413 * 4974 5465 3578 5521 * * 4747 198
+ 47 6441 5602 3907 100 0 * 10446 1011 1026
+
+Q 199 4207 * 4853 2613 6821 3921 6380 4783 2821 5576 6518 5302 2782 3870 4550 3923 4868 4878 * 4828 199
+ 0 * * * * * 0 10225 0 1308
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+G 200 2577 * 3764 3219 * 3266 4381 5478 6446 3794 * 3384 4183 4830 4914 3005 * 4967 * 5818 200
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+S 203 3356 * 5143 2688 5897 5682 * 4886 3556 4771 * 4424 5052 4267 3775 2527 4263 3570 * 5993 203
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+
+P 204 4745 5852 5745 5044 * * 4171 * 4929 5652 * 3723 1747 4244 3711 3232 2849 4631 * * 204
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+
+V 205 3915 5774 5969 4265 4200 4934 6395 3184 3812 2541 6028 6060 * 5708 * 3650 4875 2207 * 5993 205
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+
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+ 53 4785 * 1582 587 * * 9513 1207 0
+
+K 207 2823 5722 5614 5907 5607 5683 4647 3982 2770 4521 * 5848 * 4723 2998 4849 3111 2852 * * 207
+ 0 * * * * * * 9483 0 0
+
+S 208 * * 5611 3908 4912 * 4811 4894 4988 * * 2305 6294 5920 4833 2324 1851 4818 * * 208
+ 0 * * * * * * 9483 0 0
+
+F 209 6248 5601 * * 2562 * * 2163 6147 2449 5653 * * * 5654 * 4029 2383 6151 3845 209
+ 0 * * * * * * 9411 0 0
+
+N 210 * * 5068 * * 5596 5271 * 3912 * * 1907 * * 2912 2115 2535 4201 * * 210
+ 0 * * * * * * 8262 0 0
+
+R 211 * * * * * * * * 2515 * 3177 * 3287 3223 1308 * * * 3308 * 211
+ 0 * * 0 * * * 5040 0 0
+
+//
+�HHsearch 1.5
+NAME 9287755aa6aa27583da6be3b2408bfcc
+FAM
+FILE 9287755aa6aa27583da6be3b2408bfcc
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:18:36 2013
+LENG 146 match states, 146 columns in multiple alignment
+FILT 107 out of 1086 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH
+HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9999999999999998855677999999999998978888762334568388874389999999999999999998476389999999998787619998
+9999999999999998734049999999999999999999987648
+>Consensus
+mxLsxxxxxxixxsWxxvxxxxxgxxxxxxlfxxxPxxkxxFxxxxxxxxxxxlxxxxxxxxhxxxxxxxlxxxixxlxxlxxxlxxlgxxHxxxxgvxx
+xxxxxxxxxlxxxlxxxlgxxxxxxxxxAWxxxxxxixxxmxxxxx
+>9287755aa6aa27583da6be3b2408bfcc
+VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
+ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
+>gi|454407|gb|AAA33018.1| hemoglobin [Casuarina glauca]gi|454920|emb|CAA54775.1| haemoglobin [Casuarina glauca]
+MALTEKQEALLKQSWEVLKqnIPAHSLRLFALILEAAPESKYVFSFLKDS---NEIpENNPKLKAHAAVIFKTICESATELRQkghAVWDNNTlkrLGSI
+HLKN-KITDPHFEVMKGALLGTIKEAIKENWSDEMGCAWTEAYNQLVATIKAEM-
+>gi|114799562|ref|YP_759630.1| globin domain-containing protein [Hyphomonas neptunium ATCC 15444]gi|114739736|gb|ABI77861.1| globin domain protein [Hyphomonas neptunium ATCC 15444]
+--------I-ILSTFERAaqACADPAPLIYARLFELRPDFKPLFDMD----------TDGGVRGS--MLETCFEAILGVIEGassQRVIISAARFSHGG-
+YGVVDEEFDIMFASIRDVFRDLLGARWTGTEEAQWAILLKEIAAis-------
+>gi|321473021|gb|EFX83989.1| hypothetical protein DAPPUDRAFT_223071 [Daphnia pulex]
+-SFSQKDVDVIVNTWNTLKRrGDFAPKVFIRYFKAKPESQKMFPAFANVPI-TELPTNHDFLNSAYTCITSLNYLIPYLKFdHPERCPAFP-KHLkDKYN
+A--VDLKKLGSIWMTAMQEEMGNAFTNDVRDVWKKAVMAVIEYA-----
+>gi|110319969|emb|CAJ44467.1| haemoglobin type 2 [Biomphalaria glabrata]
+-GPTANDRKALDSSWRKLRSgaggrKNAGTNLVLWMLSNVPNMRSQFSKFDANQPDSVLKENTEFLNQVDRILGGIESLVNTVNDpvaLKAAIDKLADAH
+LSmPSRIGLDFFGPLQQNIAQYIQQELGVSADSDESKAWPDLFAAYNLVLKE---
+>gi|20270894|gb|AAM18464.1|AF461710_1 myoglobin [Clonorchis sinensis]gi|23344091|gb|AAN28366.1| 17 kDa myoglobin [Clonorchis sinensis]
+-PLSKDEVDaLFEELNPLVSTteqrTEFGKAVYMALFSAYPEYIQLFTKMQGLTK-DNVEASEGIKYYGQTFADSILEMLQCASDdgkLEAVLEKSGKEH
+IT-RNVTKQQFLSAEEVFIKHFSGVLT---KEENKQSMERFLKHIVPKVAGF--
+>gi|339256778|ref|XP_003370265.1| putative globin [Trichinella spiralis]gi|316965561|gb|EFV50254.1| putative globin [Trichinella spiralis]
+-KFTDEEVELLARTWKKDDFDwlyRIGTDIYTCVFQLAPELKVFFPYVTECEKkNQSWESSKGFRTQALRFVQILGMAVEKTESrmkdddshLHHRLYKL
+GETHRRfaLKGFTPTHWKGFVIAVRVAMRRAVeaMPNLTPAecetAIEAWDKLSRYVVHRMEEGY-
+>gi|88813510|ref|ZP_01128744.1| hypothetical protein NB231_06775 [Nitrococcus mobilis Nb-231]gi|88789223|gb|EAR20356.1| hypothetical protein NB231_06775 [Nitrococcus mobilis Nb-231]
+---------LFNDSYERCidnpNPPGFLQRFYKVFLSSSEEVAEKFKNT-DF------------EKQTRVLKASLYYLMLScngSPEAMAHLRRIACLHS
+rkQ-LDIRPELYDLWLASLLQAAREYD-PRFDQQTETAWRQVLSHGIDFMKSRY-
+>gi|195427633|ref|XP_002061881.1| GK17234 [Drosophila willistoni]gi|194157966|gb|EDW72867.1| GK17234 [Drosophila willistoni]
+--FSLTEKVALRQAFDLIKPfrRKMGKDIFYTYLVQHEDVIDIFRKNGDldek---------inLTALHKHAQTMMRTIHFVVNKgld-DMpsFHMMAHD
+IVNIHVD-HWVPKAHVQLLGLAIRDYVLNVMSNRCSESLISGFDKVLN-----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 * * * * * * * 3695 * * 477 * 3844 * * * * 2894 * * 1
+ 0 * * * * * * 5465 0 0
+
+H 2 4212 5857 4689 6101 * 3092 4108 5650 3484 * * 3997 2361 * 4118 2462 4270 4544 * * 2
+ 0 * * * * * * 7886 0 0
+
+L 3 * * * * 3156 * * 4451 * 507 3882 * * * * * * 4157 6116 * 3
+ 0 * * * * * * 8397 0 0
+
+T 4 6361 * 4464 * * * 6303 * 5324 * * 3779 6105 6149 * 1260 1442 5814 * * 4
+ 0 * * * * * * 8428 0 0
+
+P 5 2600 6113 2810 3571 * 5187 5845 5482 3418 4799 5150 6472 2753 4699 5464 3718 6037 5046 * 5225 5
+ 0 * * * * * * 8481 0 0
+
+E 6 2566 6575 3311 2771 * 5362 4634 4295 2729 6645 * 4711 6491 4350 4165 3383 5442 6622 * 6180 6
+ 0 * * * * * * 8590 0 0
+
+E 7 4651 * 2219 1770 * * 5509 * 5499 6364 * 5055 * 1569 * * 5113 * * * 7
+ 0 * * * * * * 8702 0 0
+
+K 8 4625 * * 5543 5058 * 6428 2435 2129 3772 6832 * * 4920 2338 * 5069 3243 5602 6165 8
+ 0 * * * * * * 8694 0 0
+
+S 9 3220 * 3302 2685 4869 6796 4805 4224 2635 4926 * 5428 * 3157 3998 4691 6315 5745 * 4591 9
+ 38 6249 6298 0 * * * 8785 1043 0
+
+A 10 2627 * 4933 5755 6857 6552 5685 3626 4691 1420 5735 4714 * 5656 * * 3530 3451 * * 10
+ 0 * * * * 0 * 8926 0 1036
+
+V 11 4816 * * * 4267 * * 1694 * 2188 5056 * * * * * 5496 1637 * 6577 11
+ 0 * * * * * * 8950 0 0
+
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+ 0 * * * * * * 8950 0 0
+
+A 13 3560 * 2471 3386 * 4574 5704 * 3308 6597 * 3262 * 3103 4240 2511 6858 * * 6777 13
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+
+L 14 3055 * 5345 * 6447 * 5241 5616 * 4911 * * * 5660 * 1152 2088 4517 6075 * 14
+ 0 * * * * * * 8950 0 0
+
+W 15 5545 * * * 3394 * * 5602 * 5674 6620 6359 * * * * * 5701 432 4054 15
+ 0 * * * * * * 8950 0 0
+
+G 16 2423 6492 4049 3028 6277 4066 * 6205 3128 * * 2986 3861 4279 4363 3833 4488 6775 * * 16
+ 0 * * * * * * 8950 0 0
+
+K 17 3069 * * 5653 * 5081 6726 4446 2634 3593 5913 4542 4281 3465 2936 4044 4239 3701 * 6738 17
+ 33 5471 * 2103 382 * * 8950 1227 0
+
+V 18 3376 4389 6366 * 4798 * * 2022 7041 2373 5044 6277 6996 6959 6482 6597 * 1834 * * 18
+ 711 1361 * 972 1028 * * 8950 5639 0
+
+N 19 5180 6867 3206 3680 5121 4577 5245 6942 2519 5204 * 2754 5733 4452 3383 3614 5209 5583 * 4942 19
+ 467 1854 * 1308 746 * * 8950 4503 0
+
+V 20 3635 4923 4791 4749 6366 3499 4850 5262 2703 4909 5071 5202 2693 5944 4225 3922 5341 4376 6305 4950 20
+ 490 1795 * 1325 735 * * 8950 4644 0
+
+D 21 3758 * 2482 3182 * 3849 6420 * 4531 5682 * 3585 4598 3573 3549 4528 3487 3910 * * 21
+ 115 3704 * 2189 357 * * 8961 2046 0
+
+E 22 4314 * 3244 2342 6319 4274 6883 6438 3446 4468 6662 5464 6309 3455 3164 4605 3504 4360 * * 22
+ 38 5280 * 1249 788 * * 8961 1326 0
+
+V 23 3649 6501 * * 2325 * 3784 2952 * 3008 5260 3774 6743 6210 * * 4390 2800 6453 4089 23
+ 48 5295 7062 3066 183 * * 8961 1254 0
+
+G 24 3035 5528 6862 6595 3934 939 6449 6476 * 5574 6259 * 6820 * * 4377 5053 3395 * 6457 24
+ 0 * * * * * 0 8964 0 1000
+
+G 25 4466 6479 3943 3863 6531 6744 7135 4166 3846 3785 5083 4066 4588 3419 3440 3521 3391 3540 * * 25
+ 0 * * * * 0 * 8940 0 1000
+
+E 26 3284 6325 3517 2766 5605 5723 4648 3742 3470 3971 * 3791 * 4074 4284 4164 3811 5827 * 6078 26
+ 19 6249 * 1585 585 * * 8937 1061 0
+
+A 27 4638 5285 * * 1784 * * 2255 * 2363 3784 * * * * 5455 * 2791 * * 27
+ 0 * * * * * * 8937 0 0
+
+L 28 6487 * * * 1378 * * * * 2414 4774 * * * * * * 5698 6739 1510 28
+ 0 * * * * * * 8937 0 0
+
+G 29 3465 * 5081 4031 4604 4796 4961 3354 3678 3067 4704 4855 * 4168 3457 4172 3753 4806 * 5096 29
+ 0 * * * * * * 8957 0 0
+
+R 30 3807 6391 6874 5615 6621 5655 4907 5143 2964 3978 6784 3250 * 4512 1711 5553 4087 5510 6458 5183 30
+ 0 * * * * * * 8957 0 0
+
+L 31 * * * * 2020 * * 3527 * 1165 4175 * * * * * * 4285 4863 3647 31
+ 0 * * * * * * 8961 0 0
+
+L 32 * 5422 * 5476 666 * * 4017 * 2367 6349 6452 * 5934 * * 6347 * 5949 * 32
+ 0 * * * * * * 8961 0 0
+
+V 33 3775 * 4751 2143 5485 7038 5872 * 2845 5326 6695 3050 * 3672 5052 3858 3101 5172 * * 33
+ 0 * * * * * * 8961 0 0
+
+V 34 2826 6849 3529 3111 * * 5056 4459 2852 3385 4698 4268 * 5208 3259 4646 4057 5954 * * 34
+ 12 * 6890 * * * * 8961 0 0
+
+Y 35 3310 4873 3367 4755 3817 6898 2551 6456 4423 7011 6910 3277 * 5729 5551 4489 5408 5679 6852 2579 35
+ 0 * * * * 0 * 8962 0 1000
+
+P 36 5799 * 6347 5140 * 5979 * 6603 5577 6447 * * 327 5708 6798 6089 * 6168 * 5101 36
+ 11 * 7107 * * * * 8961 0 0
+
+W 37 4452 * 2227 1889 6485 4309 5098 6954 5532 5647 5561 4619 * 3619 4074 4000 5883 5040 5809 * 37
+ 0 * * 0 * 0 * 8970 1000 1000
+
+T 38 3250 5572 5640 5573 3920 6812 * 3525 * 2674 4323 4881 * * 6712 3594 3219 3140 6532 3233 38
+ 0 * * * * * * 8961 0 0
+
+Q 39 6497 * * 4703 * * 5797 4076 1654 3795 5696 * 5674 2861 2072 5687 6347 5017 * 7255 39
+ 0 * * * * * * 8961 0 0
+
+R 40 2912 * 3171 3407 * 5735 5681 6005 3098 4496 * 3832 4428 4175 4142 2767 5060 5585 * 5609 40
+ 15 6627 * 0 * * * 8961 1009 0
+
+F 41 4284 * * 5956 3085 * 5049 3268 3473 2084 3169 6890 6879 5485 5753 6849 6506 3880 * 3348 41
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+
+F 42 * * * * 138 * 6347 * * 6465 6447 * * * * * * * 4964 5378 42
+ 58 * 4659 * * * * 8961 0 0
+
+E 43 4847 * 5119 4704 6494 3028 4502 * 2811 6228 6806 4607 2267 4557 5326 3523 3783 4099 * 5558 43
+ 67 * 4469 * * 569 1618 8910 0 1539
+
+S 44 4885 * 4125 4303 5671 3278 4481 5751 2622 4993 5589 4733 4950 3365 3734 3373 4863 4362 6550 5310 44
+ 346 4202 2655 722 1345 383 2099 8921 1673 1804
+
+F 45 4134 * 5381 6032 1327 6681 6830 5044 6601 3064 4366 6244 * * 6559 4700 3777 3450 6316 4688 45
+ 424 6140 2057 1585 585 3042 187 8740 1061 3406
+
+G 46 3862 * 4186 3825 * 2640 * * 2019 * * * 5688 4404 2994 3361 4290 4111 * * 46
+ 85 5612 4754 0 * 635 1489 8296 1046 5404
+
+D 47 4411 * 1727 4058 6465 2605 3616 6411 4011 * * 2699 * * * 4058 4451 * * * 47
+ 36 6135 6632 1000 1000 * 0 8763 1038 3183
+
+L 48 * 5131 4532 6740 3275 6401 5309 3500 3152 2294 3660 4737 6404 5423 5208 6470 5535 2812 * 5665 48
+ 518 6148 1798 2322 322 1645 556 8763 1291 3312
+
+S 49 4323 5901 3207 3597 5167 5892 * * 3734 4696 * 5644 2494 4975 5885 1759 4985 6548 * * 49
+ 405 5798 2140 1000 1000 1894 452 8456 1061 5435
+
+T 50 4836 * 5034 3553 5609 5999 6025 3950 3006 5999 * 4073 2627 4911 5509 3235 2665 5812 5703 6003 50
+ 663 3853 1740 1141 872 1535 610 8390 1534 5825
+
+P 51 3271 * 3575 3644 5985 6084 * 5842 3171 2663 5632 3408 3658 4277 4841 * 5614 3507 * 5199 51
+ 184 * 3059 * * 1955 430 8273 0 6123
+
+D 52 2506 * 1629 3129 5548 3681 * * 5120 * 5882 5721 5667 3565 * 4156 4503 * * 5801 52
+ 22 6058 * 2585 263 3035 188 8241 1000 5746
+
+A 53 3460 * 2647 1605 * 5875 * * 6184 6204 5635 3336 * 3479 5209 3125 * 6155 * 6410 53
+ 111 * 3754 * * * 0 8307 0 5328
+
+V 54 * 5670 6122 * * * * 2589 * 1097 3663 5491 * 5838 5510 * 5765 2831 5776 6086 54
+ 25 * 5883 * * 3316 153 8187 0 5745
+
+M 55 3320 5600 * 3121 6401 * * 3843 2814 3410 5157 4761 3268 2988 3509 5018 * 4922 * * 55
+ 51 5813 5905 1000 1000 1772 500 8254 1011 5505
+
+G 56 3274 * 3408 3868 4951 3641 * * 3494 * * 3398 * 4464 3809 2614 3382 * 6486 4300 56
+ 0 * * * * 2572 266 8538 0 4577
+
+N 57 4383 6690 2309 6215 * 6377 * 5473 * 5315 5303 2144 4990 * * 1632 4439 5993 * * 57
+ 21 * 6104 * * 3167 170 8573 0 4076
+
+P 58 2879 6002 5253 3560 6043 4516 3898 6396 4190 * * 4408 1933 5010 4292 3411 4731 6389 * 6608 58
+ 12 6959 * 0 * 1341 724 8725 1000 3918
+
+K 59 3237 6078 3503 2794 4918 3677 6497 * 2968 4816 6379 4990 * 3534 3100 3935 * 5467 6312 6153 59
+ 15 * 6568 * * 2716 238 8826 0 2849
+
+V 60 6223 * * 6651 1606 * * 3072 6666 1939 3510 5351 * * * 6336 * 3335 6756 5286 60
+ 22 6025 * 1585 585 844 1176 8846 1046 2703
+
+K 61 4712 6268 6445 3362 6548 4666 3667 5082 2702 3793 6888 3842 * 3862 2365 4710 4877 6666 * 4926 61
+ 0 * * * * 1874 460 8934 0 1713
+
+A 62 2137 * 4959 4931 5826 3240 4297 5535 3891 4009 * 4053 * 5737 2859 4225 4395 5778 * 4436 62
+ 32 * 5496 * * * 0 8936 0 1482
+
+H 63 * * * * 6554 * 864 6628 5291 5638 5991 * * 1623 6653 6477 * 6633 * 6305 63
+ 25 * 5837 * * 1586 584 8900 0 1822
+
+G 64 1541 3759 * 6943 4978 2631 * 4410 6846 6744 5469 * 5529 * 4851 3537 4050 3633 * 6624 64
+ 17 * 6406 * * 1644 556 8911 0 1779
+
+K 65 3242 6823 4193 4780 5237 5090 7001 3973 2953 2995 4960 4639 * 5577 3108 3968 4166 4112 * 5276 65
+ 19 * 6266 * * 382 2103 8875 0 1676
+
+K 66 3221 6250 * * * 5753 5688 4039 3043 4858 4029 4762 * 4389 2067 3948 3195 4126 * 6738 66
+ 36 5353 * 1585 585 1113 895 8882 1269 1268
+
+V 67 * 6558 * * 1991 * * 2717 * 2238 5501 * * * * 6302 * 1714 * 4877 67
+ 16 * 6487 * * 0 * 8910 0 1069
+
+L 68 2879 5092 * 6704 3728 3909 * 3433 5733 2578 2815 * * 4970 6973 4297 4740 3482 5281 5740 68
+ 0 * * * * * 0 8927 0 1022
+
+G 69 3435 6086 3761 2910 * 3483 5271 * 3555 4645 5132 3217 * 4366 3669 4231 3409 7191 * 5148 69
+ 18 6335 * 3000 193 0 * 8927 1069 1022
+
+A 70 1877 * * 6523 3824 3354 * 4504 6841 3158 4265 * * 5140 5008 2800 4167 4055 * 6295 70
+ 0 * * * * * 0 8910 0 1069
+
+F 71 * * * * 3559 * * 1964 * 1322 4301 * * * * * * 2265 * * 71
+ 17 6448 * 1585 585 * 0 8910 1034 1069
+
+S 72 3679 * 2148 3385 * 2756 4282 6529 6586 4834 5609 3126 6324 4913 6703 4422 3964 4887 * 6650 72
+ 46 4983 * 3014 191 * 0 8910 1362 1069
+
+D 73 4186 5708 3708 3348 4305 5840 6234 4572 4024 4491 4205 3622 * 5660 4773 2816 3792 4478 6118 4142 73
+ 0 * * * * * 0 8910 0 1069
+
+G 74 3003 4714 * * 3201 4179 * 2360 * 2475 5022 6448 * 5628 * 6703 4894 2680 5694 5827 74
+ 91 4035 * 1870 461 * 0 8910 1861 1069
+
+L 75 4133 5422 * 6485 5723 * * 1518 * 3354 4280 6345 * 6573 * 6577 * 1574 * 5504 75
+ 47 4949 * 2400 303 * 0 8910 1386 1069
+
+A 76 4872 * 2337 2799 * 4191 5712 * 3266 6711 4838 3222 5565 4907 4031 3509 4671 4605 6486 * 76
+ 28 5709 * 2000 415 * 0 8910 1149 1069
+
+H 77 3966 4980 4972 3845 5755 4553 3741 * 3953 4253 6672 2235 6486 4504 4031 3022 4361 5705 * 5616 77
+ 110 4012 6485 1457 653 * 0 8910 1876 1069
+
+L 78 4616 * 5223 6252 5779 6663 * 3624 5022 1239 4040 6651 3680 6740 6310 4106 5568 3902 * 4688 78
+ 75 4301 * 1819 481 1113 895 8882 1713 1268
+
+D 79 4775 6324 1462 2788 6672 2997 5059 6573 4155 * 7039 3930 * 5397 5726 4080 5201 6723 * * 79
+ 77 4496 7017 1575 590 0 * 8910 1596 1069
+
+N 80 5154 * 1792 3611 4992 5566 6783 6334 3973 5708 6689 2067 4386 4603 6583 4054 5183 6788 * * 80
+ 1093 936 6897 1673 543 * 0 8933 6657 1017
+
+L 81 4428 5719 6233 * 2704 * 4683 3809 * 1356 4418 6263 4366 * * 6489 5225 3052 * * 81
+ 34 5417 * 3911 99 * 0 8934 1211 1176
+
+K 82 3386 * 3703 3047 * 5773 4412 4633 4427 4590 4815 5361 5171 3249 3883 3305 4699 3149 * * 82
+ 18 6325 * 0 * * 0 8934 1061 1176
+
+G 83 2610 6680 3652 2976 5565 3328 5352 6325 3397 4776 6951 5644 4684 4805 4955 3466 3855 4795 * * 83
+ 15 6560 * 2000 415 1096 910 8934 1012 1176
+
+T 84 3268 * * 4299 3800 4850 4376 4109 5786 3000 3428 5600 6851 4509 5474 4406 4013 3331 * 3434 84
+ 26 5826 * 1585 585 0 * 8933 1145 1017
+
+F 85 4928 4631 6713 * 3632 7027 * 2853 * 1195 4760 * * * * 4744 * 2561 6655 * 85
+ 44 5044 * 1848 470 * * 8945 1393 0
+
+A 86 2934 6051 3885 3491 5571 5707 6518 5395 3007 5908 5378 3762 4660 3885 3313 4837 3837 4381 * 5451 86
+ 40 5210 * 1585 585 * * 8945 1282 0
+
+T 87 3950 * 3399 3775 6040 5795 5149 * 2461 5034 6264 5913 4910 3688 2945 3433 4593 5115 6729 4283 87
+ 19 6264 * 1585 585 * * 8945 1046 0
+
+L 88 5526 * * 6756 4078 * * 2620 * 1099 3807 4561 * 5757 * 6388 5086 3896 * 4656 88
+ 66 4484 * 967 1034 * * 8945 1579 0
+
+S 89 2386 5795 * 6912 * 992 6979 5708 5721 5834 6626 4660 6563 * 5414 4575 4661 4582 * 6770 89
+ 28 6839 6563 1000 1000 * * 8945 1000 0
+
+E 90 2950 * 5142 3216 * 4924 4450 7022 2844 4329 5181 5165 6290 3379 2737 4524 4098 4969 * 6495 90
+ 8 * 7484 * * 0 * 8931 0 1015
+
+L 91 3695 * 4162 4893 * 5797 6307 4103 3074 3667 5075 4160 6705 4340 2434 3706 3342 4570 * * 91
+ 0 * * * * 0 * 8961 0 1000
+
+H 92 * * * * * 5839 70 * * * * * * 6500 * 5708 * * * * 92
+ 16 6509 * 0 * * * 8945 1016 0
+
+C 93 2464 6785 5627 6626 5295 5825 4305 4333 3083 4452 * 4979 6509 7032 3138 4175 3806 2797 5690 5773 93
+ 135 3834 5711 1058 944 * * 8945 2024 0
+
+D 94 3909 5486 3767 4183 4415 3799 5781 * 2648 5773 5384 3505 4126 5477 3342 4155 3401 5884 * 6690 94
+ 1953 3437 623 563 1630 * 0 8938 2269 1168
+
+K 95 4374 * 4846 4843 * 4079 * 5117 1989 5025 5143 3877 * 4053 2888 * 3709 3120 * 5140 95
+ 399 2926 3186 1416 677 42 5120 7430 1593 7497
+
+L 96 6706 5712 * * 3471 * 4308 5861 4588 2747 3907 5591 5483 5902 2043 4638 * 4905 5583 2649 96
+ 0 * * * * 0 * 8912 0 1770
+
+H 97 5696 6802 4915 * * 1088 4174 * 3369 * * 3238 5083 4085 3458 5029 * * * * 97
+ 90 4044 * 2065 394 * * 8945 1826 0
+
+V 98 3730 6349 * * 3392 * * 1992 * 2679 4201 * 6503 * * * * 1539 * * 98
+ 42 5795 6563 0 * * * 8945 1149 0
+
+D 99 4656 4380 3611 3332 * 3537 6451 6481 3452 5034 * 4047 3816 4585 4281 4252 2291 6707 * 6730 99
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+
+P 100 3028 * 4503 4554 6313 4184 6720 5638 3917 4972 6692 6891 1598 4297 4109 3319 5779 5652 * * 100
+ 0 * * * * 0 * 8931 0 1015
+
+E 101 3770 * 3121 2057 6756 4687 4452 4973 3189 * 6876 5067 5002 3474 5262 3922 5049 4200 * * 101
+ 0 * * * * * * 8945 0 0
+
+N 102 5535 * 3288 * 5124 * 2079 6549 6997 3312 3631 4845 * 3458 7000 5698 6509 5033 5770 2337 102
+ 0 * * * * * * 8945 0 0
+
+F 103 6335 * * * 1324 * * 3425 * 3101 4925 6674 * * * * * 4472 2930 2647 103
+ 0 * * * * * * 8945 0 0
+
+R 104 3908 * 2654 2402 * 3579 * 6759 3201 3999 6599 3416 5528 4278 4437 6783 4770 4895 6627 6915 104
+ 15 6580 * 2322 322 * * 8933 1012 0
+
+L 105 3182 * 4133 3659 5158 5675 5292 3832 4473 2936 4321 3739 4558 4423 6627 6380 3829 3280 5990 6723 105
+ 15 6599 * 0 * * * 8933 1026 0
+
+L 106 3853 * * * 1708 * * 3405 * 2195 2958 * * * * * * 3172 4072 6281 106
+ 0 * * * * * * 8933 0 0
+
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+ 26 * 5780 * * * * 8933 0 0
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+ 14 * 6649 * * 1058 944 8936 0 1167
+
+H 116 3777 6308 3124 2005 * 5574 6738 * 3527 5465 * 4256 6478 3529 4096 3234 4107 5423 * 6100 116
+ 73 * 4336 * * 0 * 8939 0 1167
+
+H 117 3382 4462 5141 4230 5595 4646 3767 4035 3887 4030 5604 4771 * 4875 4923 4945 4312 2790 4981 3837 117
+ 142 6292 3627 0 * 1290 759 8904 1006 1651
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+F 118 5182 3829 3459 6191 3798 5943 6582 5453 * 1270 4491 5004 6066 5401 * 6595 6260 3931 5433 4832 118
+ 278 4341 2987 3311 153 465 1860 8813 1590 2501
+
+G 119 5272 6150 6691 4466 * 837 4968 5504 4435 * 6198 * 3567 4382 4794 4924 6070 6043 * * 119
+ 107 6712 4020 0 * 669 1431 8731 1005 3127
+
+K 120 3919 * 2861 4446 * 4277 6456 6534 3058 5519 * 4266 2749 4458 4012 3787 3789 4008 * 5678 120
+ 31 6305 6832 1000 1000 966 1034 8836 1020 2549
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+E 121 3097 4506 3494 3390 6005 3373 5204 * 3448 5604 6447 3837 6649 3273 3847 3545 5134 5317 * * 121
+ 88 4083 * 1877 458 1050 952 8881 1825 1842
+
+F 122 4804 5101 * 6848 1877 * * 4846 6626 3016 4643 6563 5522 6572 4314 4334 6477 4683 2561 3585 122
+ 82 4917 5513 1721 522 505 1759 8910 1373 1369
+
+T 123 5801 6459 2120 5734 6704 5643 5726 * 4883 * * 2857 6666 * 6403 2699 1658 6805 * * 123
+ 14 6745 * 2807 222 1719 522 8924 1000 1356
+
+P 124 2546 * 3183 2823 5596 4161 4467 * 3947 6770 6319 5572 2863 4794 3996 3443 5648 * * * 124
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+
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+ 12 * 6913 * * * 0 8905 0 1636
+
+Q 127 3954 * 4215 2131 * 5185 5330 4143 2833 4776 4929 5559 5578 3705 3581 6712 4825 3514 * * 127
+ 0 * * * * 0 * 8904 0 1765
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+A 128 2853 * 2801 2907 6709 4356 5454 5736 2861 4719 6135 4952 6897 3638 5604 4148 3522 6664 * * 128
+ 0 * * * * * * 8933 0 0
+
+A 129 548 * * 5808 * 4422 * 4661 * 5016 * * * * 6530 3365 6679 4229 6600 * 129
+ 13 6783 * 1585 585 * * 8933 1000 0
+
+Y 130 5513 * * * 4161 * * * * 4589 4921 * * * * * * * 314 4524 130
+ 0 * * * * * * 8933 0 0
+
+Q 131 3848 * 3739 3776 6599 5033 6649 4525 3067 4747 4925 3535 * 3906 2693 4064 3581 6247 5313 6683 131
+ 0 * * * * * * 8933 0 0
+
+K 132 3499 5311 3694 3735 5516 5033 6456 4606 1778 4606 6679 4784 * 5513 3495 4712 5007 3826 * * 132
+ 0 * * * * * * 8933 0 0
+
+V 133 2765 4179 * * 3091 5291 * 3458 * 1883 4092 * * 6599 * 5082 3972 2940 * * 133
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+
+V 134 6297 * * * 2046 5720 * 3111 * 2126 3572 5138 * * 6775 5569 5720 3696 4686 3271 134
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+
+G 136 4005 5424 * 5616 2155 4934 4797 3910 * 3860 6965 4387 5349 6554 4687 4318 3966 2659 * 3986 136
+ 0 * * * * * 0 8815 0 1000
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+V 137 5068 6084 * * 3644 4270 * 1538 * 3025 3626 * * * * * * 1910 6763 * 137
+ 0 * * 1585 585 0 * 8817 1000 1000
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+A 138 2437 3914 6633 * 5524 4878 * 2559 6606 3047 5574 5717 * 5721 4938 4382 3731 2871 * 5025 138
+ 0 * * * * * * 8808 0 0
+
+N 139 3396 6410 2414 2924 6372 3826 4850 6659 3808 6165 * 3043 4821 5068 5548 4029 3973 * 6630 5754 139
+ 0 * * * * * * 8829 0 0
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+A 140 3009 6223 5606 4647 6093 3941 4376 3934 4139 3066 5556 6439 6332 4921 3697 4751 3580 3398 * 4023 140
+ 0 * * * * * * 8790 0 0
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+L 141 5287 * * * 4103 * 6516 2147 * 1975 1494 * * * * * * 3834 * * 141
+ 0 * * * * * * 8790 0 0
+
+A 142 3411 6732 6533 3816 6626 4618 6385 4444 1807 4028 4378 * 6349 5166 4061 3447 3831 4356 * * 142
+ 0 * * * * * * 8637 0 0
+
+H 143 3026 * 3934 2617 * 3889 3540 5688 4410 * * 4180 * 4396 2934 3222 4178 4924 * * 143
+ 0 * * * * * * 8382 0 0
+
+K 144 2955 * * 3277 4863 1007 5078 * 3554 4809 * * * * * 3549 * * * * 144
+ 0 * * * * * * 7481 0 0
+
+Y 145 4769 3889 * * 2321 * * * * 4741 4481 * * * * 4549 * * 4293 944 145
+ 0 * * * * * * 6750 0 0
+
+H 146 * * * * * * 1917 * 444 * * * * * * * * * * * 146
+ 0 * * 0 * * * 2630 0 0
+
+//
+�HHsearch 1.5
+NAME 9343cd2395312266b68b016d74fb3c86
+FAM
+FILE 9343cd2395312266b68b016d74fb3c86
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:15:32 2013
+LENG 84 match states, 84 columns in multiple alignment
+FILT 131 out of 989 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEECCCCHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCCHHHHHHHHCCC
+>ss_conf PSIPRED confidence values
+976366032078899989868989999879899899999999972998379997884899538999879999389998853559
+>Consensus
+xxxvixxpxxTEKsxxxxexxnxyxFxVxxxanKxxIKxavexlfxVkVxxVnTxxxxxxxKKAxVxLxxgxxaxxxaxxxgxx
+>9343cd2395312266b68b016d74fb3c86
+SWDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGEKKAVVRLSEDDDAQEVASRIGVF
+>gi|162606070|ref|XP_001713550.1| 60S ribosomal protein L23A [Guillardia theta]gi|13794470|gb|AAK39845.1|AF165818_53 60S ribosomal protein L23A [Guillardia theta]
+IYKQLIYPVTSESAMKKIQTSNTLTFLVEPMNNKNSLKKIISKLFKVKTIKINSLISMNGKKKIFVKLGPEHDALDVANKIGYI
+>gi|116515257|ref|YP_802886.1| 50S ribosomal protein L23 [Buchnera aphidicola str. Cc (Cinara cedri)]gi|58384690|gb|AAW72705.1| 50S ribosomal protein L23 [Buchnera aphidicola (Cinara cedri)]gi|116257111|gb|ABJ90793.1| 50S ribosomal protein L23 [Buchnera aphidicola str. Cc (Cinara cedri)]
+-LKIILSAHVSDKTSDNMKRNNTVVLKVLKNSKKYEIKLAIEKFFKVRVYKINTLIVKgkrkrqknkickfSNWKKAYVILHTGQ------------
+>gi|58617354|ref|YP_196553.1| 50S ribosomal protein L23 [Ehrlichia ruminantium str. Gardel]gi|58416966|emb|CAI28079.1| 50S ribosomal protein L23 [Ehrlichia ruminantium str. Gardel]
+-FSIIHSSIITEKAVLLNEKFNKYAVYVSGDADKKTIKKAFKVVFGLDVVRINILNQKgkkkyfkgiighrKDRKKVYFSLLKDQ------------
+>gi|281339576|gb|EFB15160.1| hypothetical protein PANDA_018218 [Ailuropoda melanoleuca]
+--PIIKFSL----TIKKMENNSTLVFTVDAKANNPQIKHSLKKLHDIDVAEVNTLVRPEEAQEAYTKLVSD------------y-
+>gi|251772492|gb|EES53058.1| Ribosomal protein L25/L23 [Leptospirillum ferrodiazotrophum]
+ISDVLIRPILSEKSDRVREKNSVYLFHVYKKANKIQIQKAIESIFNVKVESVRTVVRKgkakrigivkgslPDRKRAYITLKDGFK-LDI-------
+>gi|49574623|ref|NP_848102.2| ribosomal protein L23 [Adiantum capillus-veneris]gi|68566046|sp|Q85FI0.2|RK23_ADICA RecName: Full=50S ribosomal protein L23, chloroplasticgi|48476034|gb|AAP29433.2| ribosomal protein L23 [Adiantum capillus-veneris]
+--DKLKNQVITGKSIRLLQQ-NQYTFQVDLKLTKTGMKDWIERFFDVKVEGINSSRMTskngkkknklnityVSYKKMIVRLKKNYF-IPL-------
+>gi|268680585|ref|YP_003305016.1| 50S ribosomal protein L23 [Sulfurospirillum deleyianum DSM 6946]gi|268618616|gb|ACZ12981.1| 50S ribosomal protein L23 [Sulfurospirillum deleyianum DSM 6946]
+----IKAILYTEKSLSLQEN-GTVVIQTSVRMTKNGLKEVLKQYFGFTPIKINSLRVMgkvkkfkgiegkrNDFKKFYVQLPEGAKL----------
+>gi|225709724|gb|ACO10708.1| Probable mitochondrial 39S ribosomal protein L23 [Caligus rogercresseyi]gi|225711026|gb|ACO11359.1| Probable mitochondrial 39S ribosomal protein L23 [Caligus rogercresseyi]
+---------------------NVIKFHVSPEMSRLDAKSYLEKIYGLPVMDVHSfhpsqKIKVsrlksdilykkegHEFKVIYAVLPKDFS---------
+--
+>gi|159478154|ref|XP_001697169.1| mitochondrial ribosomal protein L23 [Chlamydomonas reinhardtii]gi|158274643|gb|EDP00424.1| mitochondrial ribosomal protein L23 [Chlamydomonas reinhardtii]
+----ICFPNITLQMMKLTPEQmdqvketgwlREVAFKTTPDVTKLEIAAFLQSVYGMNVERVSTINYLgrrrlaisrngkrlwwreDDWKKAYVIFRPP-
+------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 2748 5674 5951 5583 4824 * 2851 3537 * 2417 4787 6009 2800 * * 3463 5755 5885 * 5277 1
+ 0 * * * * * * 4629 0 0
+
+W 2 4165 6405 6551 5327 2703 * 4115 3921 6446 3881 * 6231 * 5484 4415 5214 4329 5147 6177 1560 2
+ 75 5341 5264 224 2800 * * 4985 1161 0
+
+D 3 5506 * 1490 4347 * 4377 * 5646 3371 * * 3505 5710 3728 4016 3152 4927 * * 5770 3
+ 34 5440 * 0 * * 0 5257 1058 1055
+
+V 4 * 6563 6103 6804 7261 4577 * 1806 5332 3817 * 6426 7107 4558 * 6240 4396 1409 * 4748 4
+ 91 4380 6240 1360 712 * 0 5300 1216 1055
+
+I 5 * * * * 4654 * * 979 * 1786 6506 * * * * 6346 5545 3083 * * 5
+ 13 6808 * 1000 1000 1531 613 5350 1000 1109
+
+K 6 6294 5989 * 5590 5236 * 5841 2190 1599 3182 6498 * 5930 4445 3807 5559 * 3618 * * 6
+ 0 * * * * * 0 5377 0 1055
+
+H 7 4048 * 5341 5145 5443 5851 4585 4642 2676 5446 4986 4334 * 4173 2764 2847 5658 6368 * 2938 7
+ 0 * * * * * 0 5400 0 1055
+
+P 8 4372 * * * 5942 4674 6575 4982 * 4948 * * 479 5070 6494 5140 * 4843 * * 8
+ 0 * * * * * 0 5400 0 1055
+
+H 9 * * * * 5019 * 3700 2268 5626 1987 6395 6013 * 5801 5533 6261 * 1877 6221 4427 9
+ 34 5443 * 1505 627 * 0 5419 1073 1055
+
+V 10 5709 * * * 4389 * 6097 2135 7035 2321 7476 5198 6486 6543 * 4456 3436 1909 * 5374 10
+ 31 6801 6347 0 * * 0 5430 1000 1055
+
+T 11 5328 * * * * 6760 * 6052 * * * 4900 6072 * * 2149 563 * * * 11
+ 0 * * * * * 0 5462 0 1116
+
+E 12 * * 3170 395 6568 6652 * * 6344 5294 * * * 5790 5222 5912 6864 * * * 12
+ 0 * * * * 1425 672 5525 0 1116
+
+K 13 5516 6088 * 5541 * * 7223 * 405 * * 6361 6168 5194 4141 3833 * * * * 13
+ 36 * 5323 * * * 0 5569 0 1055
+
+A 14 1901 * * * * 5136 * 5948 6849 * 5035 5041 * * * 1389 2256 6011 * 6456 14
+ 29 6771 6583 1000 1000 922 1083 5512 1000 1169
+
+M 15 5352 6475 7042 5664 5756 5582 * 3685 6666 4161 2465 4391 * 5016 6897 3389 2012 4171 * 3521 15
+ 0 * * * * * 0 5593 0 1126
+
+N 16 3933 * 4821 5682 5142 4332 5649 5201 2649 3747 3429 3776 * 4079 2737 4432 4338 4535 * 7186 16
+ 31 5546 * 2325 321 1289 759 5593 1134 1126
+
+D 17 4650 * 5415 5790 5693 4986 5999 4378 2779 1271 3772 5204 6289 4335 6361 5806 5306 6213 * 6309 17
+ 46 4983 * 0 * * 0 5608 1107 1055
+
+M 18 3462 * 7040 4908 4568 5895 * 2686 5260 2492 3231 5095 5755 4421 4037 4266 3439 4504 * * 18
+ 13 6836 * 0 * * 0 5608 1000 1055
+
+D 19 4688 * 3651 878 * 4605 * * 4831 5794 6826 6762 5513 3620 7218 3959 5064 7453 * 6033 19
+ 77 5231 5307 2651 250 * 0 5608 1084 1055
+
+F 20 5349 * 3487 3053 6946 4973 7631 6291 2302 6316 5674 2488 * 3353 3727 3731 5176 * * 5765 20
+ 945 * 1058 * * 1521 618 5595 0 1215
+
+Q 21 4705 * 3783 2289 3550 6510 4149 4756 4823 6254 * 2332 5066 4388 5835 4266 4209 * * 4430 21
+ 33 5483 * 3322 152 93 3999 5110 1015 3315
+
+N 22 6589 * 4641 7222 * 2991 6501 * 3448 * * 844 5887 7421 3910 4113 6578 * * * 22
+ 63 4540 * 2371 310 0 * 5764 1267 1121
+
+K 23 5900 6949 7460 4621 * * 5116 6599 2136 5855 * 6535 7763 2378 3718 5452 2347 2979 6906 7257 23
+ 0 * * * * * * 5815 0 0
+
+L 24 6569 * * * 5215 * * 2856 6495 2226 5115 * * * * * * 3042 6751 1184 24
+ 31 5562 * 0 * * * 5917 1067 0
+
+Q 25 3658 5275 * 5588 5806 5292 * 4708 * 5326 5507 * 6958 4243 * 3905 1528 1912 * 7521 25
+ 26 * 5806 * * * * 5917 0 0
+
+F 26 * * * * 349 * * 4781 * 3383 * * * * * 4797 * 4717 * 6841 26
+ 0 * * * * 0 * 5872 0 1055
+
+A 27 5047 * 3826 3614 6495 * 5857 2347 2771 3850 6914 4440 * 3909 3915 5729 4428 4041 5932 4404 27
+ 16 6495 * 0 * * * 5917 1006 0
+
+V 28 4486 4722 * * * * * 4362 * * * * * * * 6304 3811 349 * * 28
+ 0 * * * * * * 5917 0 0
+
+D 29 3227 * 1555 3698 6243 5256 4129 6922 6542 6180 * 3633 4576 5488 5030 3042 6009 5692 * 6085 29
+ 0 * * * * * * 5917 0 0
+
+D 30 3841 5507 7004 5498 * 5745 * 3816 2800 3969 4055 5473 2228 * 2935 4164 7281 3440 * * 30
+ 0 * * * * * * 5917 0 0
+
+R 31 5811 7221 2902 4054 * 4616 5308 * 1762 * 6580 2935 * 5393 2759 3584 5909 * 6980 * 31
+ 0 * * * * * * 5917 0 0
+
+A 32 819 * * * 6996 * * * * 3283 3337 6580 5796 * * 3591 5426 3878 * 5573 32
+ 0 * * * * * * 5917 0 0
+
+S 33 6338 * 5039 * * 4624 7281 * 5493 * * 1352 6851 * 6282 2557 1714 * * * 33
+ 0 * * * * * * 5917 0 0
+
+K 34 * * * * * * * * 107 * * * * * 3803 * * * * * 34
+ 0 * * * * * * 5917 0 0
+
+G 35 4739 5562 6613 5688 6950 5980 3965 3643 3605 3423 * 4785 2616 4738 3810 7112 2275 6771 6569 5229 35
+ 0 * * * * * * 5917 0 0
+
+E 36 7460 * 2970 1645 6980 5941 5806 7312 4286 4634 5937 5370 * 1678 * 5124 6749 7040 * 6901 36
+ 0 * * * * * * 5917 0 0
+
+V 37 * * * * 6520 * * 469 * 4301 5961 6670 * * * 6741 * 2470 * * 37
+ 0 * * * * * * 5917 0 0
+
+A 38 3749 * * * 6217 6587 * 6561 503 * * * * 4258 3096 5954 * * * * 38
+ 14 * 6670 * * * * 5917 0 0
+
+D 39 3252 * 4036 2868 * * 5868 6122 2982 4456 6041 3453 * 2421 3124 4373 5965 6154 * 7112 39
+ 0 * * * * * 0 5917 0 1032
+
+A 40 900 6756 5859 4274 4761 * * 4551 * 4137 * * * * 5748 4647 6927 5044 4661 3144 40
+ 0 * * * * 0 * 5917 0 1032
+
+V 41 * * * * 3154 * * 1804 * 2396 5941 * * * * * * 1340 * * 41
+ 0 * * * * * * 5917 0 0
+
+E 42 6451 * * 812 7131 6741 * * 2463 6997 6509 5047 * 3996 4501 5060 4826 * * * 42
+ 0 * * * * * * 5917 0 0
+
+E 43 3505 * 5113 3271 6273 * 6914 6243 1714 4215 6078 4260 * 3218 4380 3611 4538 5458 * 5945 43
+ 0 * * * * * * 5917 0 0
+
+Q 44 3931 * * * 3918 * * 2505 5610 1396 3901 6224 * 5022 4971 6217 6751 3686 5872 5008 44
+ 36 * 5362 * * * * 5917 0 0
+
+Y 45 * 4583 * * 1017 * * * * 5289 6916 * 5621 * * 5748 * * 5744 1425 45
+ 12 6956 * 1585 585 1144 869 5731 1002 1109
+
+D 46 * * 2031 4104 * 1924 * * 3127 * * 2120 * 4949 5204 5071 * * * * 46
+ 49 4915 * 482 1815 * 0 5867 1164 1038
+
+V 47 5265 6894 * 6626 5531 7273 * 3748 6676 4370 6833 * * 5276 * 6504 3287 645 * 7101 47
+ 0 * * * * 0 * 5867 0 1038
+
+T 48 5902 * 3277 3819 7270 6771 6851 * 1324 6217 * 3893 4068 5432 3758 4573 3601 5405 * * 48
+ 0 * * * * * * 5917 0 0
+
+V 49 5833 * * * * * * 3976 * 6338 * * 3279 * * 5872 5294 394 * * 49
+ 0 * * * * * * 5917 0 0
+
+E 50 2872 * 4915 2737 * * 6304 3829 2795 3368 * 4738 * 6772 4841 5607 3720 2778 * 4940 50
+ 0 * * * * * * 5917 0 0
+
+Q 51 3612 * 3552 3973 * 3931 * * 1596 * * 3744 * 5146 3284 2579 * * * * 51
+ 0 * * * * * * 5913 0 0
+
+V 52 5603 5831 * * * * * 2552 * 5910 5871 * * * * * 6846 417 * * 52
+ 0 * * * * * * 5913 0 0
+
+N 53 5801 5764 * * * * 5344 6594 6995 * 6561 630 * 5547 2491 5188 4970 * 7445 * 53
+ 0 * * * * * * 5913 0 0
+
+T 54 * * * * * * * 4274 6271 6580 6108 5523 * * * 2951 561 3614 * * 54
+ 24 * 5907 * * * * 5903 0 0
+
+Q 55 4441 4860 * * * * 3687 3160 5587 1628 3436 * * 4168 4295 4054 * 3392 * 5003 55
+ 0 * * 0 * 0 * 5901 1023 1097
+
+N 56 * 6834 * * 6367 * 5794 1598 5309 5442 6063 1713 * * 2687 6193 6111 3828 6847 * 56
+ 73 5725 5049 3807 107 * * 5903 1105 0
+
+T 57 4901 6318 6347 * 5818 7039 * 5121 4638 3935 3908 5737 4863 3870 3058 3979 2920 2207 * 4016 57
+ 13 6774 * 0 * 583 1590 5919 1002 1136
+
+M 58 4137 * 5790 4318 5437 5836 7407 5925 2382 3777 3766 6926 1865 4178 4227 4459 5142 6847 * * 58
+ 1382 748 5583 3817 106 0 * 5926 3809 1013
+
+D 59 3232 * 4027 4705 * 4221 6245 * 2731 7586 5557 3498 2766 7145 4142 2740 4184 6965 5464 6010 59
+ 138 4238 4720 3416 142 1059 944 5923 1297 1100
+
+G 60 4559 7345 2160 5088 6161 1814 5397 * 3830 * * 3671 * 7046 3935 3352 6077 * 5470 5703 60
+ 62 6999 4870 0 * 359 2182 5793 1023 1299
+
+E 61 7188 * 6421 3702 3156 5312 * 6933 4454 4481 5788 5079 * 6842 2912 6670 3808 5854 2586 2222 61
+ 50 4883 * 3456 138 0 * 5907 1130 1320
+
+K 62 * * * 4648 * 5621 * * 191 * * 6253 * * 4301 * * * * * 62
+ 0 * * * * * * 5940 0 0
+
+K 63 * * * 5517 6484 * 6379 5466 464 6384 * * * * 2751 * * 4726 * 6777 63
+ 0 * * * * * * 5940 0 0
+
+A 64 531 6839 * * 5783 5542 5668 4953 * * 3633 * 5835 * 6996 * * 3301 * * 64
+ 0 * * * * * * 5834 0 0
+
+V 65 * * 5835 * 3018 * * 1469 * * 4293 * * * 6896 6415 4933 3607 * 1681 65
+ 26 * 5823 * * * * 5834 0 0
+
+V 66 5436 * * * 4341 * 5388 1854 * 5601 * * * * * * 5711 768 * * 66
+ 30 5611 * 3310 153 0 * 5792 1156 1055
+
+R 67 * * 6941 5117 * * 7152 5905 2472 5652 6776 * 5818 4030 2880 3464 1461 4562 * 5707 67
+ 0 * * * * * * 5834 0 0
+
+L 68 * * * * 3326 * * 4892 * 502 5748 * * * * 5652 5528 3319 * * 68
+ 16 * 6521 * * * * 5834 0 0
+
+S 69 2266 * 4145 3830 * 5873 5617 * 2275 6614 6001 5604 3097 4379 3859 4359 4926 4640 * 5695 69
+ 45 6910 5485 0 * * 0 5813 1000 1030
+
+E 70 3244 * 3136 2148 6808 5854 5775 7026 3084 4966 * 5184 2964 5165 4586 3462 5182 6722 * * 70
+ 17 * 6453 * * * 0 5714 0 1144
+
+D 71 6007 * 3067 2880 * 1108 6102 * 6178 6420 * 4442 4122 * 5828 4315 5070 5372 * * 71
+ 0 * * * * 0 * 5694 0 1198
+
+D 72 5866 * 2661 3400 6211 4440 4122 4799 4278 5736 * 4792 7022 2509 6750 5358 7216 4109 * 2405 72
+ 9 7325 * 1000 1000 * * 5558 1000 0
+
+D 73 4658 * 2846 3941 5636 * 4747 5092 2366 7045 * 4497 5547 4715 4125 2430 3478 4983 * * 73
+ 636 * 1488 * * * * 5508 0 0
+
+A 74 528 * 4287 * * * * 2602 * 3887 * * * * * * 5451 * * * 74
+ 0 * * * * 0 * 4787 0 2032
+
+Q 75 * * 5786 3354 4895 * * 1323 5455 1976 4292 * * 6147 4668 4185 * 6129 * * 75
+ 0 * * * * * * 4952 0 0
+
+E 76 4372 * 1276 2086 * * * * 4291 * * 4931 3400 5857 4902 5786 4980 5373 * * 76
+ 0 * * * * * * 4952 0 0
+
+V 77 4406 * * * 3228 * * 1747 * 2651 * * * * * 5373 4958 1981 * 3657 77
+ 48 4929 * 0 * * * 4952 1007 0
+
+A 78 564 * * * 4172 3760 * * * 3165 * * 5076 * * * 5086 * * 5402 78
+ 44 * 5045 * * * * 4420 0 0
+
+S 79 4227 * * 4843 * 5252 * * 4851 4771 3543 2114 * * * 1808 2473 4969 * * 79
+ 0 * * 0 * 0 * 4193 1022 1022
+
+R 80 4584 * * 3756 * * * * 1116 * * * * 3484 1752 4771 * * * * 80
+ 0 * * * * * * 4126 0 0
+
+I 81 3618 * * * * * * 1540 * 1132 3544 * * * * * * 4942 * * 81
+ 0 * * * * * * 4055 0 0
+
+G 82 * * * * * 196 * * 4595 * * 4458 * * * 4648 * * * * 82
+ 0 * * * * * * 3995 0 0
+
+V 83 3789 * * * 3142 * * 1359 * 2391 4653 * * * 4648 * * 3167 * 4541 83
+ 0 * * * * * * 3995 0 0
+
+F 84 4814 * * * 2245 * * 1275 * 2506 3680 * * * * * * 3535 * * 84
+ 0 * * 0 * * * 3919 0 0
+
+//
+�HHsearch 1.5
+NAME 93a4e2eb4447ccb72cf9476930f1f5df
+FAM
+FILE 93a4e2eb4447ccb72cf9476930f1f5df
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:33:27 2013
+LENG 148 match states, 148 columns in multiple alignment
+FILT 106 out of 1062 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCC
+CHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCEECHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9899999999997779999486999999999807888899999999998287889954799999999988654300231269999999998676899958
+799999999983799999999999998577899818099999998649
+>Consensus
+xxxxxxxxxFxxxDxxxxgxixxxexxxxlxxxxxxxxxxxxxxlxxxxxdxxxxxxixxxefxxxxxxxxxxxxxxxxxxxxxxxxxfxxxDxxxxgxI
+xxxelxxxxxxxxxxxxxxxxxxxxxxxxxxxxgxixxxefxxxlxxx
+>93a4e2eb4447ccb72cf9476930f1f5df
+SATRANKDIFTLFDKKGQGAIAKDSLGDYLRAIGYNPTNQLVQDIINADSSLRDASSLTLDQITGLIEVNEKELDATTKAKTEDFVKAFQVFDKESTGKV
+SVGDLRYMLTGLGEKLTDAEVDELLKGVEVDSNGEIDYKKFIEDVLRQ
+>gi|335293094|ref|XP_001928795.2| PREDICTED: EF-hand domain-containing protein 1 [Sus scrofa]
+------------------------------------RRDTPALELDS-PQGRPKPrkGPKGVGGQ-----------------------------------
+--------------------------------------------------
+>gi|255084932|ref|XP_002504897.1| predicted protein [Micromonas sp. RCC299]gi|226520166|gb|ACO66155.1| predicted protein [Micromonas sp. RCC299]
+--SEALRVVFHALDGDDSGSIEIEEVLHLATGMCQTMSEDDARAWFQ-EMDKDGDATVDEAEYLEAMLKLTDDLSpqqfehrvkdllartnkevtdprwy
+yhcennreyleaevvpllesglnemmraieaerlrvasgkdwdedghvppdwrpmrplqflgeylrensrtmvrkreeearlaaeaaakaeylnrtFDEM
+DREQKLRYSFDKIDGDGNGALDFDELVFVCRKINPGKGVEEARMQLSWMDKDGDGQVDQDEYVNAILE-
+>gi|74189848|dbj|BAE24569.1| unnamed protein product [Mus musculus]
+--IAASTNRGKDLIGVQNLLKKHQALQAEIAGHEPRIkavt-----------------------------------------------------------
+----------------------------------------------------
+>gi|270012781|gb|EFA09229.1| stem cell tumour protein [Tribolium castaneum]
+-LRDQWRQFFDKYDPEGFGEIPWGDLISAMSDPEFrhRVGTGKREILLE-KARSATTPAITFQDFVNVMTGK----------------------------
+--------------------------------------------------
+>gi|340500330|gb|EGR27218.1| protein kinase domain protein [Ichthyophthirius multifiliis]
+-----INSYLDDNNNNNTinkDFINEDQFYQLLLSIDNRIAKDDSNYLFQ-NIihqlqseqtitssNNQNEKQISIQLFKMILNEQ-------NYIEIEQ
+ktiqifnslkgifkhknfdLNFIYSNYNDESKEILNQQKFQQILKILNIDLQKYEINCVFEIFDKKKNGIVTYQQFYQILNEL
+>gi|281202106|gb|EFA76311.1| phosphoinositide-specific phospholipase C [Polysphondylium pallidum PN500]
+SLDNEMGFVMREFNSFGKDSLNRDEIKKLLERLNYTTSSEMLARMMA-MVDRNDDCNLDFVEFSDLLK---------YLRSRPEIKMIFERYSSDSAQHL
+TIPQMIRFFKEEQqEDWKESDCIALITKYNHEELPHILFEQLEDYIVSD
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 3510 * 3490 1637 * 4260 * * * * * * 4190 3354 * 2031 4255 * * * 1
+ 0 * * * * * * 7021 0 0
+
+A 2 2946 * 4219 2307 5681 * 4106 5190 4069 5070 * 5118 * 2041 3049 5184 * * * * 2
+ 0 * * * * * * 8538 0 0
+
+T 3 4803 * 5682 3351 5616 5758 * 2285 4232 2303 4690 4811 4710 4723 6620 4524 5525 3287 5747 * 3
+ 0 * * * * * * 9520 0 0
+
+R 4 3224 * 4562 3011 * 6096 6025 4980 2864 4951 * 3994 6129 3887 2581 2554 6251 * * * 4
+ 0 * * * * * * 9951 0 0
+
+A 5 4079 5439 3468 2230 * * 4932 5007 3636 5133 6064 6180 * 3634 2591 4520 4321 5240 * 4439 5
+ 0 * * * * * * 9980 0 0
+
+N 6 3721 5425 * * 2488 * * 2371 5322 1805 5461 6065 * * * 6815 4954 3445 4647 7020 6
+ 39 5242 * 938 1065 * * 10388 1260 0
+
+K 7 3885 7022 * 3582 4760 5621 4564 4440 2663 4202 6255 5519 6602 3193 2524 4030 5725 5826 6224 4513 7
+ 0 * * 0 * * * 10475 1005 0
+
+D 8 4210 6374 2802 2969 5123 6778 5588 5392 2809 5437 4783 4288 6011 3679 3142 4011 5049 5156 * * 8
+ 25 * 5892 * * * * 10531 0 0
+
+I 9 2856 4987 5683 4733 4891 7193 6358 2321 5448 3346 3975 6684 * 4635 4264 5574 4681 2820 5519 6614 9
+ 0 * * * * * 0 10539 0 1106
+
+F 10 6584 4680 * * 561 6970 * 5174 * 3756 5771 * * * * 6521 * 6000 5412 3402 10
+ 18 6298 * 0 * 0 * 10539 1020 1106
+
+T 11 3488 6676 4101 4045 6440 4537 6361 6644 2849 4340 4853 2910 * 3836 3326 3680 5336 5066 * 4399 11
+ 12 * 6926 2585 263 * * 10620 1000 0
+
+L 12 3489 5569 4601 3251 4883 6647 4874 4120 2999 2822 3652 4281 * 4307 5067 5811 6503 4313 * 4289 12
+ 13 6833 * 0 * 0 * 10618 1000 1000
+
+F 13 4243 5478 6472 * 1921 * 5602 4204 6791 2169 4566 6655 * 5516 6788 6836 5331 4022 6410 2707 13
+ 60 6393 5112 2807 222 * * 10634 1000 0
+
+D 14 4298 6452 652 4504 * 5184 6524 6972 4681 * * 3812 7212 6528 5079 4954 * 5557 * * 14
+ 13 6855 * 3700 115 0 * 10602 1000 1470
+
+K 15 3841 6613 4158 3616 5568 7038 * 5708 2624 4256 * 4964 3836 4907 3280 3161 3519 4143 6069 6482 15
+ 16 * 6466 * * * * 10657 0 0
+
+K 16 5138 6802 1587 2798 6828 3668 6341 6639 4884 5423 6844 2841 5831 5526 6055 4052 4681 5864 * * 16
+ 85 5625 4748 2075 391 0 * 10633 1190 1042
+
+G 17 5414 * 4352 4886 5408 2317 3598 6625 2393 4963 6380 3632 4298 3601 5148 4554 5471 * 5622 6067 17
+ 31 5556 * 1530 613 882 1128 10611 1477 1645
+
+Q 18 * 6418 2233 4642 * 4916 * 5462 3121 5189 6536 2940 * 5033 5371 2669 2810 4585 * * 18
+ 54 5346 6333 832 1190 0 * 10662 1316 1179
+
+G 19 6731 5582 3857 4659 * 822 5105 * 5599 7042 5834 3535 * 5438 5389 4548 5867 5885 * 6541 19
+ 65 5008 6295 786 1251 * 0 10647 1466 1023
+
+A 20 6319 6631 6787 3613 3987 4276 4245 4133 3282 4775 4413 4417 6542 6010 2948 5195 3503 3853 6648 3669 20
+ 0 * * * * 0 * 10624 0 1285
+
+I 21 5137 * * * 4751 * * 1581 7048 1650 3405 * 7349 * * * 6524 2619 * * 21
+ 0 * * * * * * 10688 0 0
+
+A 22 4983 5587 2582 4343 * 5066 * * 7048 5855 * 2906 3980 4759 5136 1969 2953 6893 * 5537 22
+ 15 6590 * 1000 1000 * * 10688 1001 0
+
+K 23 4723 5384 6559 4380 3402 4102 5487 2962 3200 3614 4873 * 4135 4151 3925 4405 5152 4257 6874 4787 23
+ 0 * * * * * * 10688 0 0
+
+D 24 3600 * 2893 2747 4658 * 5406 5651 3068 5521 * 3558 4522 3529 5046 3719 4837 5704 * 4862 24
+ 0 * * * * * * 10688 0 0
+
+S 25 5803 * 2858 1312 * 5776 5480 * 4470 5997 * 3864 * 2735 6766 4606 4040 6633 * * 25
+ 17 * 6437 * * * * 10688 0 0
+
+L 26 5079 5558 * * 1433 * * 3420 * 1652 4051 * * * * * * 3722 * 5002 26
+ 38 6073 6505 1000 1000 0 * 10681 1106 1028
+
+G 27 4223 4267 5738 4683 5670 4506 5071 4576 3061 3251 6545 6230 5066 3209 2705 4813 5644 4145 * 4343 27
+ 28 5693 * 1000 1000 * 0 10668 1243 1025
+
+D 28 3571 6173 4331 2584 5468 6757 6719 5599 3418 4077 5160 3222 * 4036 4171 3117 5703 4511 * 4615 28
+ 54 6387 5341 3322 152 * 0 10668 1011 1025
+
+Y 29 2888 4845 * 7035 2915 4164 * 2794 * 2193 4977 * * * 4126 6743 4332 3897 5453 4911 29
+ 25 5868 * 0 * 415 2001 10626 1421 1675
+
+L 30 4288 6658 * * 3529 * 6447 3188 6420 1199 4134 * 6557 6092 5567 5773 5729 3519 7042 4364 30
+ 106 4616 5063 612 1532 0 * 10677 1868 1003
+
+R 31 4214 5685 4139 3620 * 4053 6399 5413 3537 3535 6284 4197 5013 3379 2622 4239 5119 5548 4656 5575 31
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+
+//
+�HHsearch 1.5
+NAME 98b5ff80a113b7bb28949a2a5cd20879
+FAM
+FILE 98b5ff80a113b7bb28949a2a5cd20879
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:35:45 2013
+LENG 121 match states, 121 columns in multiple alignment
+FILT 30 out of 32 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 1.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCEECCCCEEEECCCEEEEEECCCCCCCCEEEECCCCCCEEEEEEEECCEECCCEEEEEEECCCCCCCEEEEEEEECCCCCCCCCEEEEEEEE
+CCCEECCCCCEEEEEEEEECC
+>ss_conf PSIPRED confidence values
+9842725550234630130443024761640212425640001563045653000002033266444037610787999742148312289568876796
+498388988616600088639
+>Consensus
+dgtcxntnsqisxnsxcvxstxtnCyidNSQxxxxttCtxSqyxxaxvxxSttTnCxIdNSQvxtTTCTxSqYxgxxitsSTTTxxxIsgxxxxxttCTi
+TxgxxxpxxaCxISgCtlxax
+>98b5ff80a113b7bb28949a2a5cd20879
+DGTCVNTNSQITANSQCVKSTATNCYIDNSQLVDTSICTRSQYSDANVKKSVTTDCNIDKSQVYLTTCTGSQYNGIYIRSSTTTGTSISGPGCSISTCTI
+TRGVATPAAACKISGCSLSAM
+>gi|11181763|gb|AAF86610.1| antifreeze protein isoform 10 precursor [Choristoneura fumiferana]
+DGSCVNTNSQVSENSWCVRSTLTFCNIDNSQL-ESTTCTRSQYNGAYVVSSRTTNCNIRNSQLHTTTCTNSQYDGVYITSSTTTNTRISGPACSISRCTI
+TRGVAAPSAACRISGCTLRA-
+>gi|11225528|gb|AAG33033.1| PR-S/thermal hysteresis protein fusion protein [synthetic construct]
+DGSCTNTNSQLSANSKCEKSTLTNCYVDKS-------------------------------EVYGTTCTGSRFDGVTITTSTSTGSRISGPGCKISTCII
+TGGVPAPSAACKISGCTFSA-
+>gi|57635206|gb|AAW52736.1| antifreeze protein AFP Cr32 [Choristoneura rosaceana]
+---------QISENSRCVNSTANNCYIDNSQV-DTTTCTRSRYINANVMISTTTDCSISNSQVLISTCTNSQFSGIYMTTSTIRDSRISGP---------
+---------------------
+>gi|57635194|gb|AAW52730.1| antifreeze protein AFP Cc5 [Choristoneura conflictana]
+---------QI-TNSRCFKSTATNCYIDNSQL-DTTTCTNSQYNNAYVVISTTTNSIIDYSQVYSTTCTNSHYNGVHITSSTTTNTRITGP---------
+---------------------
+>gi|57635212|gb|AAW52739.1| antifreeze protein AFP Cc9 [Choristoneura conflictana]
+---------HIT-NSECVTSTLTNCNLVNS-------------------------------QVDTTTCTNSEYKDAHISTATTTGTRIA-----------
+---------------------
+>gi|11181765|gb|AAF86611.1| antifreeze protein isoform 501 precursor [Choristoneura fumiferana]
+------------------------CVNTNSQITANSQCVKSTA----------TNCYIDNSQLvDTs-ICTRSQYSDANVKKSVTTDCNIDKSQVYLTTC
+TgsqyngiyirssTTTGTSISGPGCSISTCTI---
+>gi|11181767|gb|AAF86612.1| antifreeze protein isoform 104 precursor [Choristoneura fumiferana]
+------------------------CRNTNSQISANSLCASSTL----------TNCYIDDSQLESTTCTRSQYNGAYVVSSRTTNCNIRNSQVHTTTCTn
+sqyeegvyitssTTTNTRVTGIACSVSSCTI---
+>gi|57635206|gb|AAW52736.1| antifreeze protein AFP Cr32 [Choristoneura rosaceana]
+-------------------------------------------------NSTANNCYIDNSQVDTTTCTRSRYINANVMISTTTDCSISNSQVLISTCT-
+---------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+D 1 * * 0 * * * * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1443 0 0
+
+G 2 * * * * * 0 * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1443 0 0
+
+T 3 * * * * * * * * * * * * * * * 1612 571 * * * 3
+ 0 * * * * * * 1443 0 0
+
+C 4 * 0 * * * * * * * * * * * * * * * * * * 4
+ 0 * * * * * * 1443 0 0
+
+V 5 * * * * * * * * * * * * * * 1625 * 1957 1258 * * 5
+ 0 * * * * * * 1443 0 0
+
+N 6 * * * * * * * * 3014 * * 191 * * * * * * * * 6
+ 0 * * * * * * 1443 0 0
+
+T 7 * * * * * * * * * * * * * * * * 0 * * * 7
+ 0 * * * * * * 1443 0 0
+
+N 8 * * * * * * * * * * * 0 * * * * * * * * 8
+ 0 * * * * * * 1443 0 0
+
+S 9 * * * * * * * * * * * * * * * 0 * * * * 9
+ 0 * * * * * * 1443 0 0
+
+Q 10 * * * * * * 4561 * * * * * * 228 * * * * 5377 3652 10
+ 0 * * * * * * 1761 0 0
+
+I 11 * * * * * * * 240 * 4590 * * * * * * * 3160 * * 11
+ 96 * 3954 * * * * 1761 0 0
+
+T 12 * * * * * * * * * * * * * * * 423 1976 * * * 12
+ 242 * 2697 * * 0 * 1752 0 1000
+
+A 13 1514 * * 2469 * * * * * * * * 4923 3843 2870 3899 2618 * * * 13
+ 0 * * * * 0 * 1713 0 1091
+
+N 14 * * * * * * * * * * * 93 * * * * * * * 3998 14
+ 0 * * * * * * 1761 0 0
+
+S 15 * * * * * * * * * * * * * * * 0 * * * * 15
+ 0 * * * * * * 1761 0 0
+
+Q 16 * * * 4561 * * * * 3663 3995 * * * 1549 1277 * * * 4025 * 16
+ 0 * * * * * * 1761 0 0
+
+C 17 * 0 * * * * * * * * * * * * * * * * * * 17
+ 0 * * * * * * 1761 0 0
+
+V 18 3995 * * 4590 2796 * * * * * * 3946 * * * * * 542 * * 18
+ 0 * * * * * * 1761 0 0
+
+K 19 * * * * * * * * 1643 * * 2841 * * 1803 2813 3166 * * * 19
+ 0 * * * * * * 1761 0 0
+
+S 20 * * * * * * * * * * * * * * * 0 * * * * 20
+ 0 * * * * * * 1761 0 0
+
+T 21 * * * * * * * * * * * * * * * * 55 4741 * * 21
+ 0 * * * * * * 1761 0 0
+
+A 22 1388 * * * * * * * * 1177 * * 4741 * * * * 2855 * * 22
+ 0 * * * * * * 1761 0 0
+
+T 23 * * * * * * * * * * * 3290 * * * * 156 * * * 23
+ 0 * * * * * * 1761 0 0
+
+N 24 * * * * 4025 * * * * * * 91 * * * * * * * * 24
+ 0 * * * * * * 1761 0 0
+
+C 25 * 101 * * * * * * * * * * * * * 3881 * * * * 25
+ 0 * * * * * * 2033 0 0
+
+Y 26 * * * * * * * * * * * 2544 * * 3938 * * 2802 * 690 26
+ 0 * * * * * * 2033 0 0
+
+I 27 * * * * * * * 848 * 3131 * 2261 * * * * * 3040 * * 27
+ 0 * * * * * * 2033 0 0
+
+D 28 * * 631 * * * * * * * * 3881 * * 6005 * 2261 4005 * * 28
+ 0 * * * * * * 2033 0 0
+
+N 29 * * 4223 * * * * * 4992 * * 165 * * * 5442 * * * * 29
+ 0 * * * * * * 2033 0 0
+
+S 30 * * * * * * * * * * * * * * * 0 * * * * 30
+ 330 * 2292 * * * * 2033 0 0
+
+Q 31 * * * * * * * * * * * * * 0 * * * * * * 31
+ 0 * * * * * 0 1976 0 1242
+
+L 32 * * * * * * * 1993 * 1195 * * * * * * * 1680 * * 32
+ 1521 * 618 * * * 0 1976 0 1242
+
+V 33 * * * * * * * * * * * * * * * 1385 2180 1335 * * 33
+ 0 * * * * 880 1131 1620 0 1559
+
+D 34 2399 * 1049 1902 * 4072 * * * * * * * * * * * * * * 34
+ 0 * * * * * 0 1976 0 1242
+
+T 35 3636 * 4072 * * * * * * * * 1937 * * * 2352 1311 * * * 35
+ 0 * * * * * 0 1976 0 1242
+
+S 36 * * * * * * * * * * * * * * * 1521 618 * * * 36
+ 0 * * * * * 0 1976 0 1242
+
+I 37 * * * * * * * 3517 * 3662 * * * 3177 * * 618 * 3803 * 37
+ 0 * * * * * 0 1976 0 1242
+
+C 38 * 0 * * * * * * * * * * * * * * * * * * 38
+ 0 * * * * * 0 1976 0 1242
+
+T 39 3662 * * * * * * * * * * * * * * * 437 2456 * * 39
+ 0 * * * * * 0 1976 0 1242
+
+R 40 * * * * * 2438 * * 3177 * * 2667 * * 1338 2719 * * * * 40
+ 0 * * * * * 0 1976 0 1242
+
+S 41 * * * * * * * * * * * * * * * 0 * * * * 41
+ 0 * * * * * 0 1976 0 1242
+
+Q 42 * * * * * * * * * * * * * 656 3264 * 1937 * * * 42
+ 0 * * * * * 0 1976 0 1242
+
+Y 43 3177 * * * * * * * * 2731 * * * * * * * * * 437 43
+ 437 * 1937 * * * 0 1976 0 1242
+
+S 44 * * * * * * * 2952 * * * 597 * * * 2255 * * * * 44
+ 0 * * * * * 0 1631 0 1397
+
+D 45 * * 2970 * * 1103 * * * * * 1689 * * * 3370 * * * * 45
+ 0 * * * * * 0 1631 0 1397
+
+A 46 0 * * * * * * * * * * * * * * * * * * * 46
+ 0 * * * * * 0 1631 0 1397
+
+N 47 * * * * * * 3207 * * * * 731 * * * * * * * 1790 47
+ 0 * * * * * 0 1631 0 1397
+
+V 48 * * * * * * * 3595 * * * * * * * * * 125 * * 48
+ 0 * * * * * 0 1631 0 1397
+
+K 49 * * * * * * * * 2970 * 778 * * * * * * 1790 * * 49
+ 0 * * * * * 0 1631 0 1397
+
+K 50 * * * * * * * 2205 2100 * * 3755 * * 3086 2666 2319 * * * 50
+ 0 * * * * * 0 2087 0 1397
+
+S 51 4203 * * * * * * * * * * * * * * 218 3540 * * * 51
+ 0 * * * * * 0 2087 0 1397
+
+V 52 * * * * * * * * * * * * * * 3322 * 343 3163 * * 52
+ 0 * * * * * 0 2087 0 1397
+
+T 53 2049 * * * * * * * * 3981 * * * * * * 799 3054 * * 53
+ 0 * * * * 1454 655 2087 0 1397
+
+T 54 * * * * * * * * * * * 4023 * * * * 92 * * * 54
+ 0 * * * * * 0 2146 0 1242
+
+D 55 * * 2741 * 4758 * * * * * * 367 * * * * 4714 * * * 55
+ 0 * * * * * 0 2146 0 1242
+
+C 56 * 163 * * * * * * * * * * * * * 3229 * * * * 56
+ 0 * * * * * 0 2146 0 1242
+
+N 57 * * * * * * * 4146 * * * 1321 * * * 3328 * * * 1172 57
+ 0 * * * * * 0 2146 0 1242
+
+I 58 * * * * * * * 80 * * * * * * * * * 4205 * * 58
+ 0 * * * * * 0 2146 0 1242
+
+D 59 * * 897 * * * * * * * * 3397 * * 1897 3328 * * * * 59
+ 0 * * * * * 0 2146 0 1242
+
+K 60 * * 4802 * * * * * 4320 * * 285 * * * * 4757 * * 4146 60
+ 0 * * * * * 0 2146 0 1242
+
+S 61 * * * * * * * * * * * * * * * 0 * * * * 61
+ 0 * * * * 0 * 2146 0 1242
+
+Q 62 * * 5487 3976 * * * * * * * * * 190 * * * * * 4740 62
+ 0 * * * * * * 2184 0 0
+
+V 63 * * * * * * * 4670 * 1864 * * * * * * * 544 * * 63
+ 71 4374 * 0 * * * 2184 1026 0
+
+Y 64 * * 1583 3379 3824 5048 3972 * * 3558 * * * * * 5487 * * * 1745 64
+ 0 * * * * * * 2184 0 0
+
+L 65 4595 * 3921 * * 3976 * 3558 * 4653 * * * * 4843 2202 1145 * * * 65
+ 71 4374 * 0 * * * 2184 1026 0
+
+T 66 * * * * * * * * * * * 4566 * * * 3488 203 * * * 66
+ 0 * * * * 0 * 2124 0 1026
+
+T 67 * * * * * * * 4374 * * * * 4740 * * * 129 * * * 67
+ 0 * * * * * * 2184 0 0
+
+C 68 * 0 * * * * * * * * * * * * * * * * * * 68
+ 0 * * * * * * 2184 0 0
+
+T 69 * * * * * * * * * * * * * * * * 0 * * * 69
+ 0 * * * * * * 2184 0 0
+
+G 70 * * * * * 2124 * * * * * 981 * * 2663 3539 5633 * * * 70
+ 0 * * * * * * 2184 0 0
+
+S 71 * * * * * * * * * * * * * * * 0 * * * * 71
+ 0 * * * * * * 2184 0 0
+
+Q 72 * * * 4812 * * 4524 * * * * * * 372 2751 * * * * * 72
+ 0 * * * * * * 2184 0 0
+
+Y 73 * * * * 3044 * * * * * * * * * * * * * * 186 73
+ 55 4730 * 0 * * * 2184 1019 0
+
+N 74 * * 1937 4730 * * * 4383 4812 * * 1268 * * * 2578 4843 * * * 74
+ 0 * * * * * * 2184 0 0
+
+G 75 * * 3577 * * 459 * * * * * 2833 * * * 4364 * * * * 75
+ 0 * * * * * * 2184 0 0
+
+I 76 1154 * * * * * * 1949 * * * * * * * * * 1778 * * 76
+ 0 * * * * * * 2184 0 0
+
+Y 77 * * * * * * 2322 * * * * 2008 * * 4880 * 4783 * * 1055 77
+ 0 * * * * * * 2184 0 0
+
+I 78 * * * * * * * 810 * * 3558 * * * * * * 1537 * * 78
+ 0 * * * * * * 2184 0 0
+
+R 79 * * * * * * * * 4374 * 2048 * * * 4653 4812 887 3412 * * 79
+ 0 * * * * * * 2184 0 0
+
+S 80 * * * * * * * 3041 4374 * * * * * * 1300 1237 * * * 80
+ 0 * * * * * * 2184 0 0
+
+S 81 3837 * * * * * * * * * * * * * * 268 3329 * * * 81
+ 0 * * * * * * 2184 0 0
+
+T 82 * * * * * * * * * * * * * * 4017 * 225 3598 * * 82
+ 0 * * * * * * 2184 0 0
+
+T 83 * * * * * * * 3558 * * * * * * * 4783 186 * * * 83
+ 0 * * * * * * 2184 0 0
+
+T 84 * * * * * * * * * * * * * * 3558 * 128 * * * 84
+ 0 * * * * * * 2184 0 0
+
+G 85 * * 2466 * * 1734 * * * * * 1062 * * * * 4670 * * * 85
+ 0 * * * * * * 2184 0 0
+
+T 86 * 1507 * * * * * * * * * * * * * 1842 1437 * * * 86
+ 0 * * * * * * 2184 0 0
+
+S 87 * * * * * * 4843 4959 * * * 1719 * * 959 3122 * * * * 87
+ 0 * * * * * * 2184 0 0
+
+I 88 5200 * * * * * * 97 * * * * * * * * * 4730 * * 88
+ 0 * * * * * * 2184 0 0
+
+S 89 4747 * 3593 * * * * * * * * 4550 * * 2140 975 3300 * * * 89
+ 0 * * * * * * 2172 0 0
+
+G 90 * * * * * 857 * * 4096 * * 1711 * * * * 4545 * * 4608 90
+ 0 * * * * * * 2183 0 0
+
+P 91 * * * * * * * 4345 * * * * 991 * * 1159 * * * * 91
+ 0 * * * * * * 2183 0 0
+
+G 92 2862 * * * * 1991 * * * * * * * 893 * * * * * 3789 92
+ 0 * * * * * * 2109 0 0
+
+C 93 * 1362 * * * * * * * 2989 * * * * * * * 1044 * * 93
+ 0 * * * * * * 2109 0 0
+
+S 94 * * * * 3746 * 3337 * 3682 3893 * * * * * 1964 4189 * * 1434 94
+ 0 * * * * * * 2109 0 0
+
+I 95 * * * * * * * 1398 * 3836 * * * * 3746 3100 1824 3703 * * 95
+ 0 * * * * * * 2109 0 0
+
+S 96 * * * * * * * * * * * 4036 * * * 1132 1051 * * * 96
+ 0 * * * * * * 2109 0 0
+
+T 97 * * * * * * 4511 * * * * * 3789 * 4041 2926 532 * * * 97
+ 0 * * * * * * 2109 0 0
+
+C 98 * 0 * * * * * * * * * * * * * * * * * * 98
+ 0 * * * * * * 2109 0 0
+
+T 99 * * * * * * * 3682 * * * * * * * * 117 * * * 99
+ 520 1724 * 3626 122 * * 2109 1126 0
+
+I 100 * * * * * * * 692 * * * * * * * * 1393 * * * 100
+ 0 * * * * * * 1927 0 0
+
+T 101 * * * * * * * * * * * * * * * * 0 * * * 101
+ 0 * * * * * * 1927 0 0
+
+R 102 * * * * * 2712 * * * * * * * * 1100 * 1393 * * * 102
+ 0 * * * * * * 1927 0 0
+
+G 103 * * * * * 390 * * * * * 2076 * * * * * * * * 103
+ 0 * * * * * * 1927 0 0
+
+V 104 * * * * * * * * * * * * * * * 3999 1393 845 * * 104
+ 0 * * * * * * 1927 0 0
+
+A 105 1597 * * * * * * * * * * * 2712 * 2076 2799 * 2879 * * 105
+ 0 * * * * * * 1927 0 0
+
+T 106 1587 * * * * * * 1969 * * * * * * * * 1804 2995 * * 106
+ 0 * * * * * * 1927 0 0
+
+P 107 * * * * * * * * * * * * 692 * * 1969 2995 * * * 107
+ 0 * * * * * * 1927 0 0
+
+A 108 2231 * * * * 1393 * * * * * * * * * 1300 * * * * 108
+ 0 * * * * * * 1927 0 0
+
+A 109 1249 * * * * * * 2995 * * * 2879 1653 * * * * * * * 109
+ 0 * * * * * * 1927 0 0
+
+A 110 343 * * * * 2799 * * * * * * 3881 * * * * * * * 110
+ 0 * * * * * * 1927 0 0
+
+C 111 * 0 * * * * * * * * * * * * * * * * * * 111
+ 0 * * * * * * 1927 0 0
+
+K 112 * * * * * * * * 1748 * * * * * 1637 1393 * * * * 112
+ 0 * * * * * * 1927 0 0
+
+I 113 * * * * * * * 193 * * * * * * * * * 2995 * * 113
+ 0 * * * * * * 1927 0 0
+
+S 114 * * * * * * * * * * * * * * * 0 * * * * 114
+ 0 * * * * * * 1927 0 0
+
+G 115 * * * * * 692 * * * * * * * * 3162 2995 2799 * * * 115
+ 0 * * * * * * 1927 0 0
+
+C 116 * 0 * * * * * * * * * * * * * * * * * * 116
+ 0 * * * * * * 1927 0 0
+
+S 117 * * * * * * * 2879 * * * * * * * 2733 487 * * * 117
+ 0 * * * * * * 1927 0 0
+
+L 118 * * * * 3561 * * 1393 * 904 * * * * * * * * * * 118
+ 0 * * * * * * 1927 0 0
+
+S 119 * * * * * * * * * * * * * * 950 1051 * * * * 119
+ 0 * * * * * * 1443 0 0
+
+A 120 0 * * * * * * * * * * * * * * * * * * * 120
+ 0 * * * * * * 1443 0 0
+
+M 121 * * * * * * * * * * 0 * * * * * * * * * 121
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 9ac9d2aa5d496091f1a6d71517f29360
+FAM
+FILE 9ac9d2aa5d496091f1a6d71517f29360
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:13:50 2013
+LENG 92 match states, 92 columns in multiple alignment
+FILT 110 out of 170 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCEECCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCEEEECCCEEEEEEECC
+>ss_conf PSIPRED confidence values
+98786140428677897566999961687571015567787637806697387456768874417999997225801321561673788659
+>Consensus
+mkiPKxxxtyCpxCxkHtxHkVxxykkgKxsxxaxgxRryxRxkqxGygGqxkpixxxaKxTKKixLrxxCxxCxxxxxxxxxRxkkfElxe
+>9ac9d2aa5d496091f1a6d71517f29360
+MQMPRRFNTYCPHCNEHQEHEVEKVRSGRQTGMKWIDRQRERNSGIGNDGKFSKVPGGDKPTKKTDLKYRCGECGKAHLREGWRAGRLEFQE
+>gi|118353575|ref|XP_001010053.1| Ribosomal protein L44 containing protein [Tetrahymena thermophila]gi|89291820|gb|EAR89808.1| Ribosomal protein L44 containing protein [Tetrahymena thermophila SB210]
+VQVPKTRKTYCKKCNSHTNHKVSQYKKSKESTHAQGRRRYDM-KQSGFGGQTKPIFRKkAKTTKKVALKFDCTTCKTKRVIPIKRCKTIVFMD
+>gi|41614978|ref|NP_963476.1| hypothetical protein NEQ183 [Nanoarchaeum equitans Kin4-M]gi|40068702|gb|AAR39037.1| NEQ183 [Nanoarchaeum equitans Kin4-M]
+MKIPSMIKTYCPYCKRHTIHIVKQVRPStKKSVLSAGKRRMERNtVGKGNHGRYSRRPitqwkrVGvKGGSKRIDLRLVCEECGKAIIKTLPRTKKFEIV
+P
+>gi|167043979|gb|ABZ08666.1| putative ribosomal protein L44 [uncultured marine crenarchaeote HF4000_APKG3J11]
+VNIPKEINRFCPKCNKHTIQKVSIYKAGKRRGTAAGERRHAL-RKKGYGGQKFPKLAKpAKTTKKVVQIFTCPECKKKTDKRGIRIRKFELVA
+>gi|118431044|ref|NP_147229.2| 50S ribosomal protein L44e [Aeropyrum pernix K1]gi|150421648|sp|Q9YF00.2|RL44_AERPE RecName: Full=50S ribosomal protein L44Egi|116062370|dbj|BAA79396.2| 50S ribosomal protein L44e [Aeropyrum pernix K1]
+MKFPKRIRTYCPRCNTHTEHRVAQYRAGKRRAMALGERRYRR-KQEGYGSQRRPEQKRfAKVTKKQVLVITCTVCGRKRPFLGIRLKRLELVD
+>gi|150402908|ref|YP_001330202.1| 50S ribosomal protein L44e [Methanococcus maripaludis C7]gi|150033938|gb|ABR66051.1| Ribosomal protein L44E [Methanococcus maripaludis C7]
+MKMKKKMNRYCPYCKKHTAHTVERAKKRKASELKWGQRQFRR-VTAGYGGYPRPLPGGAKPIKKLDLRYKCSECGKMHTRSNggFRARMFELIE
+>gi|170291146|ref|YP_001737962.1| 50S ribosomal protein L44E [Candidatus Korarchaeum cryptofilum OPF8]gi|170175226|gb|ACB08279.1| Ribosomal protein L44E [Candidatus Korarchaeum cryptofilum OPF8]
+MQVPEKINTYCPRCKKHTSHKVSLYKAGRARKLSWGQRQLER-KRRGYGGEPRGMLRRkAKTTKKVLLVLTCEECGRKVMRNLGRLAKVEIQR
+>gi|339756369|gb|EGQ39952.1| ribosomal protein L44E [Candidatus Nanosalinarum sp. J07AB56]
+VKIPKEQNRYCSDCDTYTEHTVKETTNARASPFKKKDRKRERKINKGYGGFPYEDPAhrsrgRkNPISEKKDLCYTCKDCGTAYKPqNQIRTAKLEIE-
+>gi|290559500|gb|EFD92830.1| Ribosomal protein L44E [Candidatus Parvarchaeum acidophilus ARMAN-5]
+MKLPTQVKRYCKFCKEHTLQKVVQVKGGHRGTLTAGSRRKGWNLEHGYGSTPYPMFEhakrlGik--q-SKRIDLRYKCTKCGKMTTQkRGVKAKKLEI-
+-
+>gi|332222714|ref|XP_003260515.1| PREDICTED: 60S ribosomal protein L36a-like [Nomascus leucogenys]
+ANVPKTHRTFCNKYGKRQSHKMTQNEMGKDSLYAQGKKCYKR-KPSGYCGQTEPIFRKkAKTTKKIVLRLECIEpnCRSTKVLAVKRCKDFELG-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 4055 * * * * * * * * 5933 1007 * * * * * * 1231 * * 1
+ 0 * * * * * * 3937 0 0
+
+Q 2 6268 * * 5011 * * 5146 * 1125 * * 1462 * 4219 4814 * 6472 7437 * * 2
+ 0 * * * * * * 3934 0 0
+
+M 3 5679 * * * 4064 * 6171 1645 6503 5843 2113 * * * * * * 2022 * 3621 3
+ 0 * * * * * * 3934 0 0
+
+P 4 * * * * 6268 * * * 5214 * * * 77 6393 * * * * * * 4
+ 0 * * * * * * 3934 0 0
+
+R 5 4962 * * 6246 * 6695 * * 416 * * * * * 3179 4395 5218 6503 * * 5
+ 0 * * * * * * 3934 0 0
+
+R 6 7359 * * 2600 5939 * * 6520 2207 5604 5672 4090 * 3854 3340 4907 2240 3770 * * 6
+ 0 * * * * * * 3934 0 0
+
+F 7 6268 * * 6996 2832 * 3600 2326 3375 5073 4405 * * 3897 2313 * * 3241 * 6718 7
+ 0 * * * * * * 3934 0 0
+
+N 8 6269 * * 6754 * * * 7082 1787 * 4216 2101 * 4711 1683 * 5977 5151 * * 8
+ 0 * * * * * * 3935 0 0
+
+T 9 4007 * * * 6184 * 6073 6785 4712 * 4923 5755 * * 2794 5194 646 * * * 9
+ 0 * * * * * * 3935 0 0
+
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+Q 91 * * * 4253 * 1433 * 5201 5085 6216 6898 6798 * 3695 * 6081 3098 1831 * * 91
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+E 92 4509 * 3522 643 * 4084 * 4751 * * * * 4771 * 4350 5542 5302 * * * 92
+ 0 * * 0 * * * 3550 0 0
+
+//
+�HHsearch 1.5
+NAME 9b972e307eb0d9de3734ffdbf33ed781
+FAM
+FILE 9b972e307eb0d9de3734ffdbf33ed781
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:09:45 2013
+LENG 245 match states, 245 columns in multiple alignment
+FILT 163 out of 1103 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEEEEEEECCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCHHHCCCCCCCCCCCEEEEEHHEEEHHHCCCCCCCCCCCCEEEECC
+CCEEEEHHEEECCCCEEEEECCCCCCCCEEEEECCCCCEEEEEEECCCCCCHHHHHHHHCHHHHHHHHHHCCCEEEEEECCCEEEEEEEEHHHHHHHCCC
+CCCCCCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCHHHEECCC
+>ss_conf PSIPRED confidence values
+9089998788880899608999999998717546799899999999999761485101265667997432305232762133476775563043377179
+9642330000025520267515546773899974679789999967988879999987179899999985663169998257899841005999975697
+411478667677789995813178999999889830413001039
+>Consensus
+xxxlxxanxlxvxxxxxlxxxfxxxxxxxxxxvdFxxxxxxxxINxwvxxxTxgxIxxxxxxxlxxxtxlxlxnaxxfxxxWxxxFxxxxtxxxxFxxxx
+gxxxxvxmMxxxxxxxxyxxxxxlxxxxxxveLpyxxxxsmxiilPxxxxxlxxlxxxlxxxxlxxxxxxxxxxxvxlxlPkFxixxxxdLxxxLxxlGi
+xxxFxxxadxsxisxxxxxvxxvxhxxxixvxExGtxaxaxtxxx
+>9b972e307eb0d9de3734ffdbf33ed781
+DISFKSMNKVYGRYSAVFKDSFLRKIGDNFQTVDFTDSRTVDAINKSVDIFTEGKINPLLDEPLSPDTSLLAISAVYFKAKWLMPFEKEFTSDYPFYVSP
+TEMVDVSMMSMYGEAFNHASVKESFGNFSIIELPYVGDTSMVVILPDNIDGLESIEQNLTDTNFKKWSDSMDAMFIDVHIPKFKVTGSYNLVDALVKLGL
+TEVFGSTGDYSNMSNSDVSVDAMIHKTYIDVNEEYTEAAAATSAL
+>gi|226342890|ref|NP_001139707.1| serine protease inhibitor 15 [Bombyx mori]gi|195972032|gb|ACG61178.1| serpin-15 [Bombyx mori]
+--------NVYADEDNKFCKAFTQSYYKTFGGktrlVDYSDPvGAAKEINNEVKEEGSGRFKSLIsSKMIKEGAGLNFVSTYEQTIIYDDKFIFKKNVTI
+KFKS--GRKVtNVPGIAG-EGIVKYADLKDF--DAKSYELVGERgLCSYLILVPNKPDGLLGLLDKLRSpTAFGEILERGEEVCAKISILYRDLIAKVDL
+GKSARESNyLEGAFQEGgLQLRGVSQNcnNTYISSVLHEVSLKS--------------
+>gi|226342920|ref|NP_001139722.1| serine protease inhibitor 31 [Bombyx mori]gi|195972064|gb|ACG61194.1| serpin-31 [Bombyx mori]
+--------RLYlVDESIKISDDWLNFAKNYCGLtiraVPMKrNPQlTAVII--------REAISSFLP-SLNFKGDSVLLDSLDYKGLWNEAFPETRIFR
+EPFHDNSGNVIgAVDMMRT-RKRIKMTYDHTL--KATIAEIPVGHnaQYRFIFAM---GDGITEALASADIDTLIELLTNLNDTrvPIEIAIPRFIIVSE
+LDVRTLLESIGVESLWTDPMATGNITSPPASPSTFIQRVTATIKNRG----------
+>gi|308493168|ref|XP_003108774.1| hypothetical protein CRE_10956 [Caenorhabditis remanei]gi|308248514|gb|EFO92466.1| hypothetical protein CRE_10956 [Caenorhabditis remanei]
+---------------------------------------------------------------------EMIVNSINYNPIFDEMIHTFFHSKRTFYSTE
+SSPQTMGFMEW-GAHqHHF---------WKMISFECtaeKKYVNVKTF-------------SIlNGTIF----------YFQIALPTFNINAETDLASFM
+KSIGIEK------ELYDIiSEKtYRNIPSFVHKSQFELTYQK----------
+>gi|320012766|gb|ADW07616.1| proteinase inhibitor I4 serpin [Streptomyces flavogriseus ATCC 33331]
+---LGAALGLWSRSTLPVEPAWLDQLPAEAHGhLT-GDPvRDQVHLDTWAANRTQGQIDTM-PITVNDETLLVLASALTLRTDWIRSFTPGGMEAGtgPW
+R-----DMNLAGLHR-TTRLlnrvGVVDTEAG--PLTELQIIGTHGIDVHLYLgtPEASagqvltAAVGALHNRRAMvpgDHlphgtpgpglsVTRVLSV
+DGESVLRVSTVPFTVTSHHDLLNHHDLFGLGTATDTsQGHFPGISAKPLAVQAAAQAMTATFGARGFRSAAATAF-
+>gi|18568304|gb|AAL76022.1|AF466599_1 putative serpin [Aedes aegypti]
+---ISVETRLYYDKSIG---NARSVLtAKSLKPigTSFSDKrAFCEKVNSWIRNAPIKGTDNLVrDYDLNNETQAFVAGALSI--YWNTQLKS-STDQKG
+FQ---G--ENVKFLEG-SISAGYAKLDNL--KVEVVELISDKvdGVKLWLIMPDRASSIKDFNDQLSVESIRQIENGLTaqKVDVSLALPMVTIEYNSQ-
+------------------------------------------------------
+>gi|2393891|gb|AAC58237.1| serpin [Fowlpox virus]
+--------VLLIKRCYNINEKFIKDSNTIYNTdvLEFYNVrQIPRIMNKWIRSRSNNKITDIG-CHIYDNTKSIIAEAMFFTMKHESIFGSTRKDTITFY
+KYDGTSLPVEAIHA--------------------------------------------------------------------------------------
+------------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+D 1 * * 561 * * 1635 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 2166 0 0
+
+I 2 4782 4757 * * * 4687 * 3337 4962 5044 3956 4882 * 4856 5056 3788 3819 1899 * 2717 2
+ 50 4882 * 543 1673 * * 6578 1118 0
+
+S 3 5924 * 3601 3306 5965 4032 * 3932 3552 5138 5861 6321 5438 3111 3487 3395 2925 4466 * 6156 3
+ 23 6004 * 612 1532 * * 7554 1255 0
+
+F 4 * * * * 3427 * * 2555 * 1201 4301 * 5654 * * * 4245 2870 6599 4994 4
+ 12 6891 * 1593 581 * * 8405 1233 0
+
+K 5 4132 * 4875 4693 6693 5029 4023 5989 2393 4044 7002 4229 * 3961 3119 3287 3933 4108 6514 5361 5
+ 0 * * * * 0 * 8516 0 1013
+
+S 6 4068 * 6946 7053 4328 * 5648 2634 * 2394 2860 5909 6831 6100 7075 3507 3043 3292 * 7158 6
+ 14 6691 * 1000 1000 * * 8604 1003 0
+
+M 7 1127 5886 7125 6993 7032 3357 * 4642 4632 4401 7101 6029 7031 5918 4397 3927 4186 4004 * * 7
+ 0 * * * * * * 8657 0 0
+
+N 8 4893 5548 5253 * 6061 5583 * * * 5177 * 1229 6734 7168 * 2140 3242 4048 * 5710 8
+ 0 * * * * * * 8657 0 0
+
+K 9 2810 * 6192 7029 4984 2657 6212 7209 3160 4631 6560 5249 * 5177 2395 2816 5642 4321 7184 * 9
+ 22 7041 7116 1000 1000 * * 8798 1009 0
+
+V 10 4673 * * * 4241 * * 1931 * 1318 4462 7141 * * 7143 7119 * 2555 * 7062 10
+ 0 * * * * 979 1022 8797 0 1131
+
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+ 23 7055 6929 0 * 0 * 8824 1003 1009
+
+G 12 3330 7287 * * 5408 5577 5538 3271 7114 2748 5625 * 6333 7167 * 5168 3284 1542 * 4186 12
+ 10 7206 * 2000 415 0 * 8819 1000 1020
+
+R 13 3583 7096 2006 3444 * 4849 5364 6041 4451 5507 6431 4126 6000 3483 3156 3094 7168 * * 5946 13
+ 9 * 7273 * * * * 8830 0 0
+
+Y 14 4231 * 3923 3016 * 4756 * 6694 2454 6920 6523 3661 3707 3381 3151 3631 4313 * * 6191 14
+ 0 * * * * * 0 8831 0 1013
+
+S 15 4392 6391 3124 4079 7222 2297 6096 * 3773 4821 * 3329 4946 5124 3752 3135 3831 7211 7069 * 15
+ 64 5399 5656 1585 585 * 0 8831 1213 1013
+
+A 16 4902 6922 6013 5179 2894 7074 6236 3142 7140 1866 6045 6433 6071 6261 4905 4273 4521 3662 * 3280 16
+ 109 4308 5507 1286 762 0 * 8829 1568 1325
+
+V 17 6908 6868 4540 3365 * 4099 6197 6908 2930 5357 7182 3999 2794 3891 3364 3714 3643 3940 * 7046 17
+ 44 6061 6043 2224 347 0 * 8824 1082 1209
+
+F 18 4589 * * * 3090 * * 2285 * 1486 6906 * 4035 * * 6864 5347 2683 7138 6215 18
+ 11 * 7052 * * * 0 8764 0 1122
+
+K 19 4031 6465 3812 4234 7148 7269 4610 7409 2437 3498 6067 3318 6673 4237 3549 2730 5366 5005 * * 19
+ 12 6906 * 3700 115 * 0 8734 1017 1236
+
+D 20 4763 * 3052 2913 * 4572 5580 * 4383 * 7189 7114 1731 3523 7317 3914 3658 5317 * 5667 20
+ 8 * 7516 * * 1603 576 8734 0 1236
+
+S 21 2963 5680 3318 2448 6845 3986 5157 * 3918 * 7306 4060 5048 3963 5497 3081 3697 6830 * 5977 21
+ 10 7222 * 936 1067 613 1530 8763 1086 1228
+
+F 22 5964 * * * 780 * * 5686 * 4728 5565 * 6941 * * 7498 4745 7327 4638 2146 22
+ 21 * 6113 * * 0 * 8840 0 1008
+
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+ 22 6065 * 742 1315 968 1033 8763 1251 1122
+
+R 24 4050 * 2729 2997 * 6215 5796 * 2857 4986 * 4358 6205 3157 3817 3133 3933 5519 6610 7490 24
+ 0 * * * * 947 1055 8763 0 1126
+
+K 25 3778 7402 4150 5216 4508 4647 6964 4487 3832 2666 5435 4433 6927 3496 4396 4022 3234 3673 * 6192 25
+ 32 7246 6048 0 * * 0 8768 1013 1004
+
+I 26 2197 6046 * * 4144 5953 * 2985 * 1841 4110 6632 * 7109 * 3737 4815 3450 * 6444 26
+ 43 6086 6083 0 * 959 1042 8785 1241 1361
+
+G 27 2621 * 6189 3296 7188 5069 6124 5528 2762 6134 6967 3819 6438 2964 3146 3334 6827 5502 * 5264 27
+ 11 * 7079 * * 423 1977 8786 0 1332
+
+D 28 3952 7406 3269 3555 * 4142 5560 6958 2881 5134 * 3334 * 3463 3235 3708 3636 5096 * 6908 28
+ 11 7063 * 1585 585 1087 918 8804 1017 1105
+
+N 29 4470 7352 3808 4693 3057 7158 5069 3721 5024 3424 4847 4279 * 6084 4794 4383 3918 4725 4472 2756 29
+ 27 7321 6353 0 * * 0 8806 1013 1004
+
+F 30 4279 5430 5215 6906 1900 4787 5812 6248 * 3641 6643 7095 6226 7218 6026 7048 7125 7052 * 1323 30
+ 39 * 5212 3000 193 1022 979 8796 1004 1332
+
+Q 31 4803 * 3915 4816 5444 2361 3445 4710 3796 5998 5011 2517 4118 4584 5035 4743 5259 6150 * 6157 31
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+L 245 * * * * 2581 * * 1591 * 998 * * * * * * * * * * 245
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+
+//
+�HHsearch 1.5
+NAME 9c68b86897cc76a533b3376c5680b606
+FAM
+FILE 9c68b86897cc76a533b3376c5680b606
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:24:46 2013
+LENG 130 match states, 130 columns in multiple alignment
+FILT 63 out of 65 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEEECCCCEEEEEECCCCEEEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEEEEEEECCCCEEEEEEE
+EEEECCCCCCHHHEEECCCCCEECCCCCCC
+>ss_conf PSIPRED confidence values
+9445608999668999999978998899998877545788520022431376436558988739999995667777676989899876099234999899
+998225574557719678867885350469
+>Consensus
+xxcxlxGxWxNelGSxmxIxxxxxGxixGxYxTxvxxxxxxxxxxGxxxxxpxxgxxxxxxxtfxFsVxWxxxxxxxxStTxWtGqcxxxxxexlxTxWx
+lxxxxxxxdxWxatxvGxDxFtrxxxxxxx
+>9c68b86897cc76a533b3376c5680b606
+AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPGRGDSVGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWL
+LTSGTTEANAWKSTLVGHDTFTKVKPSAAS
+>gi|76809171|ref|YP_333887.1| putative exported avidin family protein [Burkholderia pseudomallei 1710b]gi|167719107|ref|ZP_02402343.1| putative exported avidin family protein [Burkholderia pseudomallei DM98]gi|167815293|ref|ZP_02446973.1| putative exported avidin family protein [Burkholderia pseudomallei 91]gi|167845243|ref|ZP_02470751.1| putative exported avidin family protein [Burkholderia pseudomallei B7210]gi|167902241|ref|ZP_02489446.1| putative exported avidin family protein [Burkholderia pseudomallei NCTC 13177]gi|76578624|gb|ABA48099.1| putative exported avidin family protein [Burkholderia pseudomallei 1710b]
+-----IGSWLNELGSTMtIASISGTGAITGTYVSPSGTTGQTFSLSGWFYAAPPANNGLDQVTLVTFSVNWNNTAARYNSITTWSGLCQitNN-VPTITA
+LYYYSNAF-AQYSWKHVNVGQDIFHPIAP----
+>gi|62909782|emb|CAI84979.1| single chain avidin precursor [synthetic construct]
+-KCSLTGKWTNDLGSNMTIGAvNSRGEFTGTYITAVTATSNE------IKESPLHGTqntinkrtqptfgftvnwkfseggsgsgsgsGSgRTQPTFGFT
+VNWK----FSESTTVFTGQCFIDrnGKEVLKTMWLLRSSVnDIGDDWKATRVGINIFTRLRTQ---
+>gi|163759983|ref|ZP_02167067.1| hypothetical conserved protein [Hoeflea phototrophica DFL-43]gi|162282941|gb|EDQ33228.1| hypothetical conserved protein [Hoeflea phototrophica DFL-43]
+------SNWVNQSGSVAQFvftpsptQPQTY-EVSGNYINnaqGTGCKGTPYPLSGAYYS---------GNQIISFSVVWSNASANCQSATGWTGYFdFS
+GSQAVLKTDWNLAFYSGST---PAIQQGQDDFMQSVAT---
+>gi|115893467|ref|XP_001199294.1| PREDICTED: similar to fibropellin Ia [Strongylocentrotus purpuratus]gi|115930644|ref|XP_001178415.1| PREDICTED: similar to fibropellin Ia [Strongylocentrotus purpuratus]
+--------------------------endvdecasfpclngaicsnQENQFVC-------------------tcVLG-----------------------
+----WTGiNCQi-DIDECASDPCQNGAL--CSDlINRYECQCLPGWTgvNYigeltrdsdm------
+>gi|115893457|ref|XP_781372.2| PREDICTED: similar to fibrosurfin [Strongylocentrotus purpuratus]gi|115930654|ref|XP_001178907.1| PREDICTED: similar to fibrosurfin [Strongylocentrotus purpuratus]
+-YCDLEGVWYNELNDRITITGTTTGMLLGDYKDSVELLTG------YSAATVVVGYaNrNCDFPSFGFVVTRDN----GLSTTSWSGQCHlCDGEEVLYT
+TWTNTQRVtTCAEVKRATLIGQDKWTRYQQST--
+>gi|90423149|ref|YP_531519.1| avidin/streptavidin [Rhodopseudomonas palustris BisB18]gi|90105163|gb|ABD87200.1| Avidin/streptavidin [Rhodopseudomonas palustris BisB18]
+-QAQVSWTWTNQYGSVLAITTynQSNGAITGTYTNKAAgscDDGKPQAAAGWLAA-------GNTGSAISFSVNFA----GCSSTTVWTGQLNSN--AGF
+QGLWLLSLAE--PVAWNGISAGADTFTFSS-----
+>gi|256395584|ref|YP_003117148.1| hypothetical protein Caci_6456 [Catenulispora acidiphila DSM 44928]gi|256361810|gb|ACU75307.1| conserved hypothetical protein [Catenulispora acidiphila DSM 44928]
+----WVGTWHNQYGSRLTITDESDHRIQGSFRTALGDSAFA----G--EEAEISGIHQGECITFNFSTS----SATGESICSFTGLLR---EGKLQTLWH
+VVSDSavKppapgeqaqlMKLPwAHAVLTNADTFTRD------
+>gi|73539298|ref|YP_299665.1| hypothetical protein Reut_B5476 [Ralstonia eutropha JMP134]gi|72122635|gb|AAZ64821.1| hypothetical protein Reut_B5476 [Ralstonia eutropha JMP134]
+---SIAGTWRNEYGSLMTLSVgDgvAPGALRGLYRSSTGSVGS-YLVAG-FAAAQAVS--LDHGQPVALSICWHSLGGeQadpsWQWTSGLSGQLSvVDG
+EEVLTLSHL------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 860 * * * * * * * 1155 * * * * * * * * * * * 1
+ 0 * * * * * * 1523 0 0
+
+E 2 * * * 1897 * * * * 3821 * * * 3753 2751 3517 3626 * * * 1890 2
+ 0 * * * * * * 3427 0 0
+
+A 3 2729 483 * * * * * * * * * * * * * 2902 * * * * 3
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+
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+ 0 * * * * 0 * 4702 0 1007
+
+I 5 * * * * 4791 * * 2708 * 828 5368 * 5261 * * * * 3230 3462 * 5
+ 0 * * 4459 67 * * 5185 1000 0
+
+T 6 5089 * 4318 3269 * * 5583 4000 5083 4775 * 4383 * 3634 * 2620 1928 3139 * * 6
+ 0 * * * * * * 5276 0 0
+
+G 7 * * * * * 165 * * * * * * * * * 3836 * * 4716 * 7
+ 0 * * * * * * 5441 0 0
+
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+
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+
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+
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+
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+
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+
+S 15 * * 3124 * * * * * * * * * * * * 220 5218 * * * 15
+ 0 * * * * * * 5534 0 0
+
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+ 0 * * * * * * 5534 0 0
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+//
+�HHsearch 1.5
+NAME 9c7b8409c5da2a6bc10d796287eb4c1f
+FAM
+FILE 9c7b8409c5da2a6bc10d796287eb4c1f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:25:45 2013
+LENG 160 match states, 160 columns in multiple alignment
+FILT 139 out of 1041 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEECCCCCCHHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHCCHHHCCEEEECCCHHHHHHHCCCCEEEEEECCCCCCCHHCCCCCCEEEEEC
+CCCCCCCHHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9899996898866499999999984981999779977856799999836725540589829999999972598899997478853110056899999989
+997798999998657974999638999775369999999999999972555455676769
+>Consensus
+xxxvvldxvxxpxNvGxixRtaxxfGvxxvixxxxxxxxxxxxxxrxsxgaxxxxxixxxxxxxxxlxxlkxxxvxxxxxxxxxxlxxxxxxxxxxlvxG
+xExxGlsxxxlxxxxxdxxvxIPxxgxxxSLNvsxAxaIxlyexxrqxxxxxxxxxxxxx
+>9c7b8409c5da2a6bc10d796287eb4c1f
+MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFG
+PETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNLPEVK
+>gi|335036871|ref|ZP_08530186.1| RNA methylase [Agrobacterium sp. ATCC 31749]gi|333791695|gb|EGL63077.1| RNA methylase [Agrobacterium sp. ATCC 31749]
+--VLVGCGISNHDNLGAMFRNAAAFYADAVLLDETCCDPLYRKALRVSVGSVLSVPYHRGGGAVEMLERLSeeGFAIWGLSPDGKTeI-RDI-Prs-ERM
+ALVIGTEGEGLPQSVLSRF--QT-ARIAQSPQLDSLNAGTASGLALYQMAG--------------
+>gi|242280259|ref|YP_002992388.1| tRNA guanosine-2'-O-methyltransferase [Desulfovibrio salexigens DSM 2638]gi|242123153|gb|ACS80849.1| tRNA guanosine-2'-O-methyltransferase [Desulfovibrio salexigens DSM 2638]
+-FTLIIDNVWDPHNVSAILRSCDAFGIyGIHLYYTVSqWPE---LAKKSSASGKKWVERTKHTDPVKMVGGLRdqGYQVLRTGFsETARPLMDFDLSKPS
+AVILSNEHSGTAPELAELV--PDEVYIPMQGMIQSFNVSVAAALILYHGFSQRFAKGMYDNPS--
+>gi|218282592|ref|ZP_03488830.1| hypothetical protein EUBIFOR_01412 [Eubacterium biforme DSM 3989]gi|218216463|gb|EEC90001.1| hypothetical protein EUBIFOR_01412 [Eubacterium biforme DSM 3989]
+-FLCYIDGVEDPYNLGSISRTLYASGCDAMILPKRDWSFAEQTILKASAGAYEKLPIYFVDADEELVNYCKKnnLPILCAHRKDAVGLYDYTFESDFCLC
+LGGALRGLSSTITAAS--KQNIVVEYGRDfRNALDSASAAAVFSFEILRQKKV----------
+>gi|254780904|ref|YP_003065317.1| tRNA/rRNA methyltransferase [Candidatus Liberibacter asiaticus str. psy62]gi|254040581|gb|ACT57377.1| tRNA/rRNA methyltransferase [Candidatus Liberibacter asiaticus str. psy62]
+--VIILVDPQLGENIGMVARAMWNFNLtQLRLVNPRDGWP-SEKARSSSANADCVIdSVRVFSNLKEAIADL--HFIYATTARNRNnfkSVLAPkeaaiV
+LnerifsGQNVGIIFGRERWGLTNEEIALS--NAIISFPVNPLFPSLNISQAVLLMVWECMENSI-----------
+>gi|198452347|ref|XP_001358733.2| GA15007 [Drosophila pseudoobscura pseudoobscura]gi|198131892|gb|EAL27876.2| GA15007 [Drosophila pseudoobscura pseudoobscura]
+---VVASLIDKLPNLGGLARTCEVLGVQTLALGNKAQA-GKSDFTNLSMTAEKTLNIIELkpSCIAAFLMekQMEGFRVVGAEQTAhSVSFANFKFPKKC
+VLLLGHEKHGIPADLIGFL--DYAVEIPQFGVVRSLNVHVTGSLFIWEYCKQHFF----------
+>gi|71405533|ref|XP_805376.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]gi|70868764|gb|EAN83525.1| hypothetical protein, conserved [Trypanosoma cruzi]
+--ILVLDNVDDPGLLGTLLRTAAGFHYDAIITTNHCADIYDHRVVRSARGAHFQKAVPIYTlkeeDGDNVYGMLNhivqrnNmSTVCFTPIDDDTektnt
+gkapnvvlsssvahagtfereALSEYchrCFttegTKGQLLIAGPNHKR--NSLRRW---SKRITGPVTqlllDEVTQTDSLVALSVVIHAL-RPHG---
+--------
+>gi|294901665|ref|XP_002777464.1| hypothetical protein Pmar_PMAR024217 [Perkinsus marinus ATCC 50983]gi|239885101|gb|EER09280.1| hypothetical protein Pmar_PMAR024217 [Perkinsus marinus ATCC 50983]
+--LIMLDGVKYPGNAGNVLSNAGKLGCSAVLLGRSRrsSQPYQQDFALSALcsssTVRrGGIPLVLNVHCVDTIHLLREeyaYRVILIENKEvavdhGLP
+FIDLSceasaraeIsTPRVLFVGGGELEGVGPLIPKVA--DAILSIPTVFdHHHSYNVCTAMTLVMFERYRF-------------
+>gi|167630255|ref|YP_001680754.1| hypothetical protein HM1_2187 [Heliobacterium modesticaldum Ice1]gi|167592995|gb|ABZ84743.1| conserved hypothetical protein [Heliobacterium modesticaldum Ice1]
+----------------DISRSATTYDVAgYFVIHPHQAQQRlVGEIlryWMEGYGaeynpdrreALERL--KVTATLEEAMAVIEEkegrrPKIITTDAR
+TYdnsVGYRQMRerfvaEEGPWLLLFGT-GFGMEREMMLQA--DYIL-YPVWgrGSYNHLSVRAAAAIILDRLL---------------
+>gi|302348084|ref|YP_003815722.1| RecB-family nuclease-like protein [Acidilobus saccharovorans 345-15]gi|302328496|gb|ADL18691.1| RecB-family nuclease-like protein [Acidilobus saccharovorans 345-15]
+-VIPVIHNTSSVQRLVDMARIVLSMNIdLLVATKVYGAAaqSGIAEAFRLLLKA--GKGLVVLPELKDAVETYDGTQVFLVDKEHAAELVDPLsgdftag
+SNSPLMLVFNGSDAPFSPQELSLG---KPIYIKGlSYRAGST---AEASLLLYGILR--------------
+#
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+ 32 5505 * 1585 585 750 1302 7919 1142 1283
+
+R 129 4885 * 2467 2228 4861 3677 5698 7508 5204 * 5788 3466 3475 5207 3755 4686 4234 6919 * 7079 129
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+
+S 130 5760 4635 * 5470 * 7046 5913 6881 * * * * 5571 5796 7153 298 * 5234 * * 130
+ 47 4978 * 1455 655 * * 7963 1248 0
+
+M 131 6455 * * * 4288 * 7091 4477 * 647 3367 * * * * * 4805 4411 * 3899 131
+ 101 * 3882 * * * * 7963 0 0
+
+N 132 * * 4258 * * * * * * * * 225 6841 * * 3744 6848 * * * 132
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+
+L 133 3460 * * * * * * 4715 * 2083 * * 6500 * * 4809 6467 794 * * 133
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+
+N 135 2675 5806 * * * 4201 4692 3887 * * 4087 4222 * 3288 * 4531 3955 1546 * * 135
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+
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+
+V 137 1434 5311 * * 6163 3145 6682 * * 3679 5570 * * * * 4336 2896 2435 * * 137
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+
+A 138 1409 7125 * * * 1991 * * * 5927 6704 4712 7163 6035 * 2182 4422 6477 * * 138
+ 0 * * 1000 1000 0 * 7929 1061 1061
+
+V 139 6320 * * * * * * 960 * 2719 4059 * * * * * * 1935 * * 139
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+
+T 140 2939 4690 * * 4024 6332 * 3143 * 2070 4276 * * * * 6124 3622 2051 * 5862 140
+ 0 * * * * * * 7968 0 0
+
+V 141 3913 5102 * * 5219 * * 3119 * 868 3003 * * 7156 * 5923 5877 4344 * * 141
+ 19 6272 * 1000 1000 * * 7968 1109 0
+
+Y 142 3703 6874 5901 5538 2983 7023 2900 * * * 7022 6669 * 5209 7070 3984 * 6580 3874 1271 142
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+
+E 143 4094 5992 3723 1288 * 6487 3327 * 4277 5349 6189 5339 * 4589 3755 4785 5177 7108 7214 5530 143
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+
+A 144 3118 4672 * * 3599 5854 * 3101 * 1822 4139 * 7195 * 3868 7040 5234 4408 3598 4310 144
+ 90 5583 4661 1247 789 * * 7910 1109 0
+
+W 145 3935 5356 6154 * 3031 6853 4764 3464 3851 3073 5099 5411 * 5533 3767 3872 4050 3996 4143 4213 145
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+R 146 4370 6722 * 3814 * 5722 5259 5811 2791 * 5000 5514 6747 4384 1115 4434 6687 6668 * 5272 146
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+
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+
+L 148 5414 * 6243 6467 4721 4399 3130 5004 3332 3951 6195 3574 5275 3376 2247 6003 4749 5339 5385 5295 148
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+
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+
+G 152 4095 * 3913 2913 * 1806 * * * * * 4018 2978 * * 2284 4001 * * * 152
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+V 154 * * 2951 * 2952 * * * * * * * * * * * * 1938 * 1058 154
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+
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+L 156 * * * * * * * * 3007 1734 * 2868 * * 2795 * * 1767 * * 156
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+P 157 * * * * * * 1548 * * * * * 970 * 2762 * * * * * 157
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+E 158 * * * 1000 * * * * * * * * * 2000 * 2000 * * * * 158
+ 0 * * * * * * 2762 0 0
+
+V 159 * * * * * * * * * * * * * * * * * 0 * * 159
+ 0 * * * * * * 1000 0 0
+
+K 160 * * * * * * * * 0 * * * * * * * * * * * 160
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME 9f519c37964061e00a9e9906f774552e
+FAM
+FILE 9f519c37964061e00a9e9906f774552e
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:27:18 2013
+LENG 79 match states, 79 columns in multiple alignment
+FILT 111 out of 161 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCEECCCCCCCCEEEEEEECCHHHHHHCCCCCCCCHHHHHHHCCCCCCCEEEEEECCCCCCEEEEECCCCCCCCC
+>ss_conf PSIPRED confidence values
+9857757567723886279999839999975786766499999660500068848988808997289870468989999
+>Consensus
+mxxxxixYSxkYxDdxyeYRhViLpkexxkxvpkxxLlsExEWRxLGIqqSxGWxHyxxhxpEphiLlFRRpxxxxxxx
+>9f519c37964061e00a9e9906f774552e
+MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFRRPLPKKPKK
+>gi|118375604|ref|XP_001020986.1| Cyclin-dependent kinase regulatory subunit family protein [Tetrahymena thermophila]gi|89302753|gb|EAS00741.1| Cyclin-dependent kinase regulatory subunit family protein [Tetrahymena thermophila SB210]
+MP-KFpkeIEYSDTYNDDAYFYRNVRLPQDLYKKIPKGKIMTEDVWRSLGIKSSKGWQHFYVYKPEPFIIMLRKPVNFQN--
+>gi|145478429|ref|XP_001425237.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124392306|emb|CAK57839.1| unnamed protein product [Paramecium tetraurelia]
+--------SQDFEDDTHIYRIIRLGRESVRLMQEFKwekkLLKEEEWRRLRVYQRRGWLHYAIFEKEPYVLLFKRKITKNK--
+>gi|326427105|gb|EGD72675.1| hypothetical protein PTSG_04406 [Salpingoeca sp. ATCC 50818]
+--SSGIVYVERHRDDQFQYRTVILPGEMGQGLPLHRALTEKECRRLGIRQSKGWTHCLIRKKDPNSLLFRRKLD-----
+>gi|71034137|ref|XP_766710.1| hypothetical protein [Theileria parva strain Muguga]gi|68353667|gb|EAN34427.1| hypothetical protein TP01_1189 [Theileria parva]
+---NNIQYSPKITHSNCQIRCVTLPREHPVLVGgldgyGTRLLSESEWRKLGIKMSKGWTHSGYSPYESHILIFQL--------
+>gi|221485644|gb|EEE23925.1| conserved hypothetical protein [Toxoplasma gondii GT1]
+---GDVYYSPRYSDERYTYRHVILSRGVRKeaeklasTMP-DGLLTEDMFiHCLGIALSPGWTHFMCFNRKLKELILRRPREDDN--
+>gi|294881882|ref|XP_002769521.1| hypothetical protein Pmar_PMAR003251 [Perkinsus marinus ATCC 50983]gi|239873027|gb|EER02239.1| hypothetical protein Pmar_PMAR003251 [Perkinsus marinus ATCC 50983]
+---DENEYSDKYMDDTYEYRHVILNKPTYRMLQrsvrgysASTILEENEWRV----------------------------------
+>gi|221054734|ref|XP_002258506.1| hypothetical protein, conserved in Plasmodium species [Plasmodium knowlesi strain H]gi|193808575|emb|CAQ39278.1| hypothetical protein, conserved in Plasmodium species [Plasmodium knowlesi strain H]
+---GPVCYSALYRDDKYVYRHIILSDNVRQyaesKVRKtNAFLTEHCIvNELQIDIGKGWKHFMIYDGKIRELILRKVLTA----
+>gi|237841603|ref|XP_002370099.1| hypothetical protein TGME49_023120 [Toxoplasma gondii ME49]gi|211967763|gb|EEB02959.1| hypothetical protein TGME49_023120 [Toxoplasma gondii ME49]
+-------HSLKYEDNEYEYKDVTLTKKydlyreQLKKNPR-KFIDEDYmYNVLQLQQTPGWEQYYIY-------------------
+>gi|288817839|ref|YP_003432186.1| hypothetical protein HTH_0521 [Hydrogenobacter thermophilus TK-6]gi|288787238|dbj|BAI68985.1| hypothetical protein HTH_0521 [Hydrogenobacter thermophilus TK-6]
+----------RCEFDLFYYRHLWLTPYL-----------------LAVQQVKGWVLYEVLKYEPNLLIVRE--------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * 3885 101 * * * * * * * * * 1
+ 344 3359 3126 1220 809 * * 2691 1084 0
+
+S 2 3705 6294 * * 6110 * 5668 * * 6172 6021 * 1950 4798 * 1503 4072 6016 * 3003 2
+ 988 2392 1713 613 1531 260 2601 2795 1170 1133
+
+H 3 2520 * * * * 4186 3388 5881 6094 * 4711 * 2288 3721 4595 2253 5600 4237 * * 3
+ 131 3522 * 1080 924 124 3600 2669 1069 1347
+
+K 4 6461 7712 2418 3323 * 2598 7953 * 2957 * * 2640 4721 5265 3898 3422 6163 * * * 4
+ 106 6143 4133 0 * 0 * 3513 1016 1004
+
+Q 5 5579 * 2634 2910 5465 4161 4932 * 3561 7351 * 3188 4629 2310 4039 4645 5055 * * * 5
+ 41 5165 * 2347 316 0 * 3439 1159 1107
+
+I 6 * * * * 4761 * * 568 * * 7494 4432 4681 * * * 4991 2695 6412 * 6
+ 0 * * 0 * * * 3569 1010 0
+
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+ 0 * * * * * * 3578 0 0
+
+Y 8 * * * 5058 * * 4907 * * * * * * 4884 * * * * * 148 8
+ 0 * * * * * * 3641 0 0
+
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+ 0 * * * * * * 3683 0 0
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ 0 * * * * * * 3738 0 0
+
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+
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+
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+ 26 5829 * 2807 222 * 0 3776 1018 1014
+
+K 26 6126 * 5266 4439 * 5284 6176 * 1127 5492 * * 3101 4136 2581 5119 6181 6527 * * 26
+ 0 * * * * * 0 3781 0 1014
+
+D 27 4024 * 2293 1286 * 4366 7037 * 4213 * * 4870 4051 4027 6846 6658 * 6802 * 5015 27
+ 78 4248 * 2906 207 * 0 3781 1124 1014
+
+I 28 4170 * * * 6434 * 4659 2280 * 1752 2569 * * 5040 * 5494 6038 3247 5081 5706 28
+ 45 * 5015 * * * 0 3781 0 1014
+
+A 29 1945 5735 * * 5561 4368 * 4869 * 2929 * * 5088 4401 3690 2986 7357 2602 * 4830 29
+ 8 * 7586 * * * 0 3713 0 1118
+
+K 30 6775 * 5480 3796 * 5634 6956 * 1095 * 4774 4666 * 3041 2725 6406 6627 5083 * * 30
+ 148 3362 * 2331 320 * 0 3717 1214 1132
+
+L 31 3777 * * 6298 6529 4943 5160 7315 2355 1772 4456 4997 5179 3327 4175 5615 4316 7490 * 6294 31
+ 0 * * * * * 0 3717 0 1132
+
+V 32 7056 * 7502 * 7311 6472 5838 1748 * 2306 3871 5016 * * * * * 1545 * 6630 32
+ 102 3870 * 2896 208 * 0 3717 1146 1132
+
+P 33 6831 * * * * 5063 * * * 6069 5896 5069 435 4638 4309 4016 7004 * * * 33
+ 185 3347 5491 2237 344 2332 319 3710 1280 1181
+
+K 34 5969 * 7389 3439 6598 3902 * 6823 1106 5187 * 4851 4704 4843 2854 5668 4578 * * * 34
+ 250 3102 4558 2496 281 741 1316 3650 1254 1264
+
+T 35 6550 7592 2499 6349 5435 2409 4949 6015 3895 * * 3265 6840 6549 4118 3209 2521 7604 * * 35
+ 100 4178 6447 3170 170 869 1144 3669 1140 1202
+
+H 36 4461 * * 6180 4919 4113 2179 * 2696 * * * 6488 5551 1494 * 5304 5268 * 4789 36
+ 103 3865 * 2573 265 1810 484 3723 1201 1118
+
+L 37 5288 5918 * * 3339 * * 3887 * 463 * * * * 5535 * 7212 6165 * 5406 37
+ 15 * 6579 * * * 0 3723 0 1077
+
+M 38 6958 * 6495 * * * * 5053 * 848 1340 * * * * * * * * * 38
+ 5 8041 * 1585 585 2277 333 3713 1000 1104
+
+S 39 4581 * 4861 5061 * * 6666 * 4607 7435 * 7035 5945 7277 4607 1366 1510 * 5227 * 39
+ 0 * * * * * 0 3723 0 1077
+
+E 40 * * 5481 79 * * * * * * * * * * * * * 6873 * 5465 40
+ 0 * * * * * 0 3723 0 1077
+
+S 41 4184 * 2746 2375 5150 6884 3906 6648 3722 7867 5047 5362 5036 4240 5835 3175 3523 4908 * 5426 41
+ 0 * * * * * 0 3723 0 1077
+
+E 42 * 5219 6824 317 * * * * * 5535 5889 * * 3919 * * * 5210 * 5053 42
+ 121 3639 * 0 * * 0 3723 1195 1077
+
+W 43 * 4391 * * 4901 * * 3626 * 6287 * * * * * * * 5746 365 5053 43
+ 99 3914 * 0 * * 0 3723 1143 1077
+
+R 44 * * * 6287 * 7540 4217 5913 5775 * * 4134 * * 258 * * * * * 44
+ 24 5913 * 0 * * 0 3723 1018 1077
+
+N 45 4206 5889 5777 3732 * 2334 5775 * 3993 * 5979 2954 * 3509 3153 2790 5188 4683 * * 45
+ 27 5762 * 0 * 0 * 3723 1023 1077
+
+L 46 6012 * * * 4629 * * 2565 * 485 4747 * * * * * * * * 5411 46
+ 0 * * * * * * 3769 0 0
+
+G 47 5099 5950 * * * 189 * * * * * * * 4166 5505 * * * * * 47
+ 0 * * * * * * 3769 0 0
+
+V 48 5266 * * * * * * 965 * 4388 * * * * * * * 1306 * 6695 48
+ 0 * * * * * * 3769 0 0
+
+Q 49 5911 * 3791 6374 6441 * * * 3223 * * * * 787 3434 * 3534 * * 5505 49
+ 0 * * * * * * 3769 0 0
+
+Q 50 * * * * * * * 4494 * 3463 2279 * * 659 6745 5959 * * * * 50
+ 0 * * * * * * 3681 0 0
+
+S 51 * * 6386 5856 5332 4655 * * * * * 5190 * * 5461 351 4574 5055 * * 51
+ 0 * * * * * * 3684 0 0
+
+Q 52 7952 5516 6075 7262 * * 7131 * 2331 3023 6104 5737 2004 3210 2262 6526 6875 7537 * * 52
+ 0 * * * * * * 3684 0 0
+
+G 53 * * * 4438 * 119 * 5856 * * * 7100 * * * * * * * 6924 53
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+
+W 54 * * * * * * * 5856 * * * * * * * * * * 25 * 54
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+
+V 55 * * 5856 2256 * * 5538 3125 4872 4395 5982 * * 3404 5198 * 3832 1593 * 5949 55
+ 0 * * * * * * 3684 0 0
+
+H 56 * * * * * * 235 * * 5055 5922 4993 * 4649 4945 * * * * * 56
+ 0 * * * * * * 3684 0 0
+
+Y 57 * 5314 * * 2197 * * 5737 * * * * * * * 5154 * * 5516 539 57
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+
+M 58 3117 7362 4537 3154 * 3382 5470 * * 3214 1218 * * * * 5703 * * * 4382 58
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+
+I 59 * 5045 5736 6091 7903 * 5900 1536 6538 4876 6453 5031 * * 4028 5320 4551 2223 4988 3199 59
+ 0 * * * * * * 3668 0 0
+
+H 60 * * * * 2913 * 737 * * 4553 * * * * 5307 3632 * * 5736 3322 60
+ 7 7605 * 1000 1000 * * 3668 1000 0
+
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+ 0 * * * * * * 3685 0 0
+
+P 62 * * * 5721 * 4423 * * 3869 * * 4221 545 * 5840 6467 * * * 3348 62
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+
+E 63 * * 3832 382 * * * * 3690 5721 * * * * 4878 6673 * 5503 * * 63
+ 16 * 6467 * * * * 3685 0 0
+
+P 64 * * * 6351 * * * 5077 7384 3859 5851 5680 432 5184 4858 4535 * * * * 64
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+
+H 65 * 5980 5882 5329 5737 * 793 * 3801 * * 2955 * 7380 4413 * * * 5603 3788 65
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+
+I 66 * 6351 * 2855 * * * 770 * 5077 * * * * * 5270 * 2268 * * 66
+ 0 * * * * * 0 3685 0 1014
+
+L 67 * * * * 6633 * * 4653 * 140 6689 * * * * * 6351 5572 * * 67
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+
+L 68 * 5603 * * 4366 * * 2349 * 772 3374 6351 5572 * * * * 5680 * * 68
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+
+F 69 * * * * 409 * * * * 2441 * * * * * 4914 * 5077 * * 69
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+
+R 70 5468 * * * * * * * 3065 * * * 6353 4385 379 * * * 5118 * 70
+ 0 * * * * * 0 3685 0 1014
+
+R 71 * * * 5064 * * * * 3056 5132 * * 5981 6077 339 * * * * * 71
+ 50 5811 5971 1963 428 * 0 3687 1024 1014
+
+P 72 6025 * * 3962 * * * * 2993 5570 7434 * 620 7191 4875 5738 5916 4596 * * 72
+ 45 5412 7078 1704 529 968 1033 3579 1025 1058
+
+L 73 6812 7261 * * 6855 * 4687 3161 2701 1224 6008 6682 5545 5406 3484 * 7460 3680 * * 73
+ 0 * * 3322 152 611 1535 3596 1014 1036
+
+P 74 5714 * 2545 4818 * 2356 5945 * 4946 5144 * 3013 2863 6333 * 4589 2422 * * * 74
+ 13 6827 * 0 * * 0 3497 1000 1000
+
+K 75 3012 * 3351 6368 4025 3203 * * 2509 * 7172 4145 4279 6691 * 4979 2349 * * 3888 75
+ 206 3279 5062 2414 300 0 * 3425 1120 1000
+
+K 76 4168 * 1945 * * 4263 * 6367 3203 * * 2028 4191 3223 4167 4783 6273 * * * 76
+ 0 * * * * 0 * 3268 0 1033
+
+P 77 4042 5625 6190 5568 * 5427 * 3101 3717 4599 5635 2975 2147 4072 4207 4673 4026 4649 * * 77
+ 0 * * * * * * 3128 0 0
+
+K 78 * * * * * * * * 1579 * * * 1318 2300 * * 4027 * * * 78
+ 0 * * * * * * 2344 0 0
+
+K 79 2446 * * 2365 * * * * 1206 * * 2406 * * * * * * * * 79
+ 0 * * 0 * * * 2165 0 0
+
+//
+�HHsearch 1.5
+NAME a0a16d5fe9c52ade8dbd14d530daeeb8
+FAM
+FILE a0a16d5fe9c52ade8dbd14d530daeeb8
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 11:57:43 2013
+LENG 72 match states, 72 columns in multiple alignment
+FILT 103 out of 199 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCCCEEEEECC
+>ss_conf PSIPRED confidence values
+975568874755676268999983677567888675232999999999976098898897356513688519
+>Consensus
+xxxxxpxxxxxFEGxEKxLEIxfxxxxxxxxxxxxgLRxixrxxWxxxLxxvxCxIlSxxsnxxxDAYvLSE
+>a0a16d5fe9c52ade8dbd14d530daeeb8
+MEMDLPVSAIGFEGFEKRLEISFVEPGLFADPNGKGLRSLSKAQLDEILGPAECTIVDNLSNDYVDSYVLSE
+>gi|340054298|emb|CCC48594.1| putative S-adenosylmethionine decarboxylase [Trypanosoma vivax Y486]
+--ARFdPGPQPSFEGPEKRLEIIM---RFLEVTHVDGLHALDDKVWEEVVSAVNAKIVSKESNEHIRSYVLTE
+>gi|149618484|ref|XP_001514093.1| PREDICTED: hypothetical protein [Ornithorhynchus anatinus]
+--------------meKNHSYSVCLGtcnstvdRPF--ALQSV-ILGRGSSFEWDKLLENVHCLIISVTKTDKQEAYVLSE
+>gi|167623734|ref|YP_001674028.1| adenosylmethionine decarboxylase [Shewanella halifaxensis HAW-EB4]gi|167353756|gb|ABZ76369.1| Adenosylmethionine decarboxylase [Shewanella halifaxensis HAW-EB4]
+---------MFFEGSEKKIELQL-------NSSAVSLRSLPHSFWQQALSLAQAEILSSLSNSHCDAYVLSE
+>gi|196006337|ref|XP_002113035.1| hypothetical protein TRIADDRAFT_56768 [Trichoplax adhaerens]gi|190585076|gb|EDV25145.1| hypothetical protein TRIADDRAFT_56768 [Trichoplax adhaerens]
+------TQQAFFEGTEKLLEIWFASSDSTQstqDGRVHDLREISKDDWSELLTYANCSILSEVSSNDITAYLLSE
+>gi|331247566|ref|XP_003336411.1| S-adenosylmethionine decarboxylase [Puccinia graminis f. sp. tritici CRL 75-36-700-3]gi|309315401|gb|EFP91992.1| S-adenosylmethionine decarboxylase [Puccinia graminis f. sp. tritici CRL 75-36-700-3]
+-----PANGPPFEGPEKLLELWFAPSADqvpiAsnvgtragllrSGPKFTGLRTVNHPLWHAMLDQVKCKVLSVIESEHVDAFLLSE
+>gi|90408155|ref|ZP_01216324.1| S-adenosylmethionine decarboxylase proenzyme, putative [Psychromonas sp. CNPT3]gi|90310767|gb|EAS38883.1| S-adenosylmethionine decarboxylase proenzyme, putative [Psychromonas sp. CNPT3]
+---------MFYEGREKRLEIIT---------QGINLLDFPVDFWHAMVQQAGACILGEIKENNIKAFILSE
+>gi|119576475|gb|EAW56071.1| hCG17429, isoform CRA_a [Homo sapiens]
+-------AVHFSEGTEKRLEVWFSWQQPNANQGSGDLRTIPRSE----------------------------
+>gi|156081893|ref|XP_001608439.1| S-adenosylmethionine decarboxylase-ornithine decarboxylase [Plasmodium vivax SaI-1]gi|148801010|gb|EDL42415.1| S-adenosylmethionine decarboxylase-ornithine decarboxylase, putative [Plasmodium vivax]
+----------VFEGIEKRIVIKLRKECFEEKKNISSLFDISRELWEEKLKYIGCSIVSEIEEdvqapaeERCRVYLLSE
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 652 * * * * * * 1460 * * 1
+ 0 * * * * * * 1658 0 0
+
+E 2 1636 * * 1667 * * * * * * * 1460 * * * * * * * * 2
+ 0 * * * * * * 1658 0 0
+
+M 3 2756 * * 3443 * * * 3897 2488 * 2030 * * * * 2836 * 2947 * * 3
+ 0 * * * * * * 3017 0 0
+
+D 4 1780 * 2909 3076 * 3697 * * * * * 3443 * * 2145 * * 4012 * * 4
+ 154 * 3305 3459 138 * * 3017 1001 0
+
+L 5 4227 * * 3108 2197 2336 * * * 3231 * * * * 3037 3128 * * * 3800 5
+ 714 1550 4357 0 * 0 * 3031 1328 1000
+
+P 6 * * 3847 * * * * * * * * 3778 491 * * 3550 * 4045 * * 6
+ 0 * * * * * 0 3576 0 1000
+
+V 7 4295 * 2828 4525 * 3516 3533 * 4516 4673 2714 3533 5179 * * 4246 3681 3171 * * 7
+ 0 * * 4391 70 0 * 3942 1075 1000
+
+S 8 2558 * 5010 5494 * 3361 4067 * * * 4316 4411 5317 3035 * 1740 4194 * * 5534 8
+ 0 * * * * * * 4198 0 0
+
+A 9 3078 * 4251 4065 * 3203 5623 * 5892 * 5491 5729 3758 3591 * 3011 2116 3820 * * 9
+ 62 5173 6138 2893 209 * * 4342 1082 0
+
+I 10 4187 5398 3853 4360 6451 4974 3207 3311 * 6702 2471 3871 3382 5189 5768 3868 5345 * 5240 4980 10
+ 95 4260 6451 2585 263 0 * 4585 1127 1000
+
+G 11 2277 6039 * 6279 1543 2699 5403 6811 * * * 5336 4261 * * 3714 6251 4693 * 5011 11
+ 46 4988 * 2909 206 0 * 4623 1068 1023
+
+F 12 * * * * 130 * * * * * * * * * * 6583 * * * 3725 12
+ 0 * * * * * * 4631 0 0
+
+E 13 * * * 74 * * * * * * * * * * * 4320 * * * * 13
+ 0 * * * * * * 4631 0 0
+
+G 14 * * * * * 74 * * * * * 4320 * * * * * * * * 14
+ 0 * * 1000 1000 * * 4631 1088 0
+
+F 15 3341 4512 * * 3801 * * 5377 4940 * * * 1575 6366 5234 3298 3239 2950 * 5807 15
+ 0 * * * * * * 4730 0 0
+
+E 16 * * * 115 * * * * * * * 4940 * * * * * 4512 * * 16
+ 0 * * * * * * 4730 0 0
+
+K 17 * * * * * * 4940 * 115 * * * * * 4512 * * * * * 17
+ 0 * * * * * * 4730 0 0
+
+R 18 * * * * * * * 5001 2689 1324 * 6331 * * 1601 4940 4655 * * * 18
+ 0 * * * * * * 4730 0 0
+
+L 19 6907 * * * * * * 3012 * 430 5873 * 4512 * * * * 4974 * 4940 19
+ 0 * * * * * * 4730 0 0
+
+E 20 * * 4911 280 * * * * * * * * * 5764 * 3313 * 5377 * * 20
+ 0 * * * * * * 4730 0 0
+
+I 21 6878 * * * 6010 * * 950 * 2736 4512 * * * * * * 1918 * * 21
+ 0 * * * * * * 4730 0 0
+
+S 22 4302 4006 3589 4049 * 6285 * 3307 4557 6864 * * * 7176 4518 6085 4722 3488 1372 * 22
+ 0 * * * * * * 4730 0 0
+
+F 23 * * * * 614 * * 5764 * 3292 3826 * * * * * 5325 3056 6591 * 23
+ 563 * 1630 * * * * 4730 0 0
+
+V 24 2386 6079 4614 3539 4120 3690 4113 * 4297 6021 * * 4149 6643 3443 3171 4966 5014 5305 4313 24
+ 194 3349 5169 3378 146 4230 79 4330 1255 2310
+
+E 25 4247 * 4396 2586 * 4580 * 5488 3865 4848 * 6417 1845 * 3048 3129 * * 5061 6559 25
+ 157 6559 3435 0 * * 0 4339 1000 2303
+
+P 26 5869 * 5924 4103 * 4812 4569 4789 4101 * * 4877 2022 4351 6678 1865 3986 4075 * * 26
+ 143 5168 3906 1000 1000 1640 558 4273 1024 2511
+
+G 27 3212 4036 3399 6462 4606 4883 6309 * 5185 5294 6717 5227 2864 4742 3065 2458 6482 5071 * 5005 27
+ 490 3541 2306 2274 334 * 0 4389 1169 2180
+
+L 28 6037 * 4129 3440 2757 4427 5906 2878 5993 3182 * * 3051 * 5403 3072 5708 4024 * 5749 28
+ 605 3887 1862 1608 574 4649 59 4191 1093 2705
+
+F 29 4325 * 4290 3791 2075 4290 5616 * 5419 2268 * 5773 3617 * * 5403 3240 5065 * 5178 29
+ 283 2795 4888 2183 359 1848 469 3976 1172 3061
+
+A 30 2691 * 3439 2587 * 2774 * 5226 3332 * * 4026 4055 5045 5962 2772 * * * * 30
+ 193 3471 4846 1600 578 346 2229 4291 1158 2568
+
+D 31 4200 5669 2893 3008 * 4318 * 7096 3532 4847 * 3175 3964 6185 6609 2539 4315 3893 * * 31
+ 30 7124 6239 3585 126 2478 285 4638 1000 1394
+
+P 32 3886 5316 5953 4118 5687 2844 6699 4084 3507 4332 7101 6813 2855 3905 6102 3798 3215 4536 * 6612 32
+ 195 3261 5513 2058 396 161 3245 4651 1465 1370
+
+N 33 3705 6603 4833 3487 * 3132 3353 * 3422 4214 * 3191 3805 5128 4574 3395 3592 * * * 33
+ 179 3096 * 2534 273 1555 600 4716 1475 1087
+
+G 34 3302 6113 4103 3644 5213 2569 5905 5034 4065 6798 6570 3454 4207 5752 4069 3351 6014 3795 6063 * 34
+ 70 * 4397 * * * 0 4726 0 1043
+
+K 35 4651 5450 4553 3804 5798 3804 6796 4896 3200 4283 3705 4713 4525 4224 2828 3616 4697 4669 * 5733 35
+ 23 * 5980 1000 1000 174 3136 4631 1043 1229
+
+G 36 * * 2770 6655 * 1006 * 4943 5982 * * 3794 * * * 2386 4879 * * * 36
+ 69 4412 * 462 1869 1845 470 4716 1171 1069
+
+L 37 5101 5513 * * * * * * * 76 * * * * * * * * * * 37
+ 0 * * * * * 0 4715 0 1038
+
+R 38 * * * * 5374 4946 5397 * 4741 3680 6429 5872 * * 367 * * * * * 38
+ 0 * * * * * 0 4715 0 1038
+
+S 39 2294 6690 3815 3412 * 6679 7082 * 3911 4211 * 3900 * 4275 4025 2237 4058 4993 * * 39
+ 44 5068 * 0 * 0 * 4715 1067 1038
+
+L 40 6188 * * * 5355 4949 4716 1303 * 1647 * * * * 5996 * * 2725 * * 40
+ 0 * * * * * * 4731 0 0
+
+S 41 6647 * 3487 4913 * 2915 * * 5447 * * 5392 1479 * 6295 2242 3246 * * * 41
+ 0 * * * * * * 4731 0 0
+
+K 42 4662 * 3264 5575 5955 7124 5237 6872 3235 3972 5050 * * 5231 1221 4576 7037 4744 * 4861 42
+ 8 7484 * 0 * * * 4732 1000 0
+
+A 43 2867 6795 2209 2118 4445 4791 6339 * 5671 * * 5166 5378 4684 * 2675 5510 * 5387 * 43
+ 0 * * * * * * 4732 0 0
+
+Q 44 5043 * 4135 3040 2770 6162 * 5912 3239 4951 5705 * * 2714 5619 5142 3544 2685 * 6128 44
+ 0 * * * * * * 4732 0 0
+
+L 45 * * * * * * * 4461 * 2081 * * * * * * * 6376 521 6747 45
+ 0 * * * * * * 4728 0 0
+
+D 46 6078 7229 1488 2191 * * 4341 5973 4733 * * * * 2968 5313 4383 6176 3646 * 7463 46
+ 0 * * * * * * 4728 0 0
+
+E 47 3234 * 3644 2035 * 4249 * 6726 3017 5254 7463 4473 * 3965 4282 3508 3793 4980 * * 47
+ 0 * * * * * * 4728 0 0
+
+I 48 4942 6571 * * 5851 6672 * 1937 5375 2047 1961 * * * * * * 2780 * * 48
+ 0 * * * * * * 4727 0 0
+
+L 49 6280 5511 * * * * * 6147 * 447 5040 * * * * * * 2418 * * 49
+ 0 * * * * * * 4727 0 0
+
+G 50 2882 7017 2188 3203 * 4133 * * 2178 * * 4486 * 4817 4315 4409 3774 * * * 50
+ 0 * * * * * * 4727 0 0
+
+P 51 3090 4814 6701 4157 7875 * 5038 3681 5116 2041 6107 4394 3385 3910 5511 3274 7069 7098 * 4945 51
+ 0 * * * * * * 4727 0 0
+
+A 52 1217 5079 * * * 6334 * 4299 * 6242 * * * * * 5281 * 1190 * * 52
+ 0 * * * * * * 4727 0 0
+
+E 53 6978 4338 3367 2926 * 3996 3448 * 2493 * * 2527 * 3524 3350 5397 * * * * 53
+ 0 * * * * * * 4727 0 0
+
+C 54 2338 389 * * * 5374 * * * * * * * * * * 6116 * * * 54
+ 0 * * * * * * 4727 0 0
+
+T 55 6519 4774 5866 1915 6504 * 4883 * 2341 4288 * * * 4515 5870 4046 2137 6013 6311 * 55
+ 0 * * * * * * 4727 0 0
+
+I 56 * * * * * * * 311 * * * * * * * * * 2368 * * 56
+ 0 * * * * * * 4727 0 0
+
+V 57 * 6011 * 5143 * * * 2376 * 1110 * * * * * * * 1735 * * 57
+ 0 * * * * * * 4727 0 0
+
+D 58 5918 * 4002 6411 * 4994 4930 * * * * 5758 * * 6011 302 * * * * 58
+ 0 * * * * * * 4727 0 0
+
+N 59 4981 6280 * 3200 4824 * 4621 4935 2843 6286 4195 6983 * 3633 4152 2595 4523 2641 * 5871 59
+ 0 * * * * * * 4727 0 0
+
+L 60 5641 6166 * 3645 5405 * * 2106 3103 2411 4355 6685 * 6411 5240 4502 3286 3601 * * 60
+ 0 * * * * * * 4727 0 0
+
+S 61 4524 5245 * 3344 6147 5220 4794 * 2734 6311 * 5705 * 6706 3599 1160 4919 * * * 61
+ 23 6011 * 0 * * * 4727 1021 0
+
+N 62 6468 * 6666 4243 * 3934 5877 * * 5008 * 928 * * * 2915 2694 * * * 62
+ 35 5375 * 2807 222 * * 4727 1047 0
+
+D 63 3920 * 1663 1786 * 4812 5801 * 3996 * * 4743 5190 4337 6848 4118 5578 6571 * * 63
+ 0 * * * * * * 4727 0 0
+
+Y 64 4510 6138 2562 3573 4377 * 2603 7027 3001 5689 * 5270 * 3899 4768 4537 5448 5409 * 3255 64
+ 0 * * * * * * 4727 0 0
+
+V 65 5932 2687 * * 3509 * * 2580 * 2383 2862 * * 3910 * 5758 6742 2897 * 6011 65
+ 0 * * * * * * 4727 0 0
+
+D 66 * * 466 4336 * * 6925 6578 5216 * * 6011 * * 3382 * 4511 5296 * * 66
+ 0 * * * * * * 4727 0 0
+
+S 67 595 6439 * * * * * * * * * * * * * 1725 * 5375 * * 67
+ 0 * * * * * * 4727 0 0
+
+Y 68 * * * * 3127 * * * * 6177 * * * * * * * * * 198 68
+ 0 * * * * * * 4727 0 0
+
+V 69 * * * * * * * 3498 * 1256 * * * * * * * 1021 * * 69
+ 0 * * * * * * 4727 0 0
+
+L 70 * * * * * * * 5374 * 35 * * * * * * * * * * 70
+ 0 * * * * * * 4727 0 0
+
+S 71 * * * * * * * * * * * * * * * 71 4382 * * * 71
+ 0 * * * * * * 4727 0 0
+
+E 72 4608 * * 60 * * * * * * * * * * * * * * * * 72
+ 0 * * 0 * * * 4727 0 0
+
+//
+�HHsearch 1.5
+NAME a1369bdee466c1364c07095750be3efc
+FAM
+FILE a1369bdee466c1364c07095750be3efc
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:14:51 2013
+LENG 85 match states, 85 columns in multiple alignment
+FILT 148 out of 1020 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCCCEEHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9999976646897377624385100667999999854266600067874112126553015426899999279999975403688
+>Consensus
+xxxxxxxCxVCxxxxxgxxygvxsCxaCxxFFrRxvxxxxxxxCxxxxxCxixxxxrxxCxxCRxxKClxvGMxxxxvxxxrxxx
+>a1369bdee466c1364c07095750be3efc
+GSFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRG
+>gi|148694040|gb|EDL25987.1| nuclear receptor subfamily 2, group E, member 3, isoform CRA_a [Mus musculus]gi|148694041|gb|EDL25988.1| nuclear receptor subfamily 2, group E, member 3, isoform CRA_a [Mus musculus]
+------------------------------------------------TKMVSGGHGEVGKAGEKMASLPRGRcvcvlslpAFQAVQNERQPR
+>gi|20663783|pdb|1H9U|A Chain A, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic Agonist Lg100268gi|20663784|pdb|1H9U|B Chain B, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic Agonist Lg100268gi|20663785|pdb|1H9U|C Chain C, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic Agonist Lg100268gi|20663786|pdb|1H9U|D Chain D, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic Agonist Lg100268
+-----------------------------MPVDRILEAELAVEQKSDQGV---------------EGPGGTGGSGSS--------
+>gi|268576120|ref|XP_002643040.1| Hypothetical protein CBG22952 [Caenorhabditis briggsae]gi|187021410|emb|CAP39479.1| hypothetical protein CBG_22952 [Caenorhabditis briggsae AF16]
+----PVVneCPVCRGqngKAVQFFYGGYACLACVSFFRRHYNVDP-KPCLTGGNCNPE---GRKCPSCRLKNIRSAGMIHT---------
+>gi|341888135|gb|EGT44070.1| hypothetical protein CAEBREN_05825 [Caenorhabditis brenneri]
+-------CIIC--LEDSN-iLTQGICSKCFMFFR-rVVNEKRMRRCVSPCEEK-RVGSPSFCRYCRLQKILDAGIIIeDHITW-----
+>gi|308496399|ref|XP_003110387.1| hypothetical protein CRE_05779 [Caenorhabditis remanei]gi|308243728|gb|EFO87680.1| hypothetical protein CRE_05779 [Caenorhabditis remanei]
+----IEKCQVCGFEGHGYHFGAFTCRACAAFFRRCHLAAttEHRKCRNKYsTCVPNRNGKWFCKKCRFDRCNKLGMSSANIQYDRD--
+>gi|309356070|emb|CAP37680.2| hypothetical protein CBG_20720 [Caenorhabditis briggsae AF16]
+-DNTVPLCTVCGDVANGKRYGTWACLGCIVFFRRTVLRKMKYKCQREERCEVTVaiQIRDVIGPRKPKSGSTVSQNRSSA-------
+>gi|341902990|gb|EGT58925.1| hypothetical protein CAEBREN_14389 [Caenorhabditis brenneri]
+--------MI-c-VDGHAFLY--------SLFIepK--raLLTKkFRK--HcqYDG--CCtdfSGEKSPPCKSCRMKKCIRMGMNSQS--------
+>gi|268560284|ref|XP_002638018.1| Hypothetical protein CBG04845 [Caenorhabditis briggsae]
+-------CVLCGNHTLLHRYGPVTCSMCNTFFRGAISGNVVlGKCLSGCFRRKVFDFKIMCRGCKLGRCLASGMDPKKI-------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 587 * * * * * * * * * 1580 * * * * 1
+ 0 * * * * * * 2084 0 0
+
+S 2 * * 3598 3440 * * * * * * * 4267 4518 * 4406 659 * 4340 * * 2
+ 0 * * * * * * 4410 0 0
+
+F 3 2498 * * 4865 2999 5372 4992 3763 * 3349 5066 3201 3996 * 4997 3205 4826 5035 5086 * 3
+ 0 * * * * * * 5230 0 0
+
+T 4 3572 * 5629 3593 * 5442 5163 * * 6155 * 4900 5003 3665 5712 1992 2539 2955 * 4925 4
+ 0 * * * * * * 5689 0 0
+
+K 5 6265 6294 3275 6103 4812 4930 4423 5145 3337 3854 * 3334 3195 3240 3947 4579 5008 3840 5432 * 5
+ 16 6517 * 3070 183 * * 5971 1222 0
+
+H 6 4568 * 5949 3274 * 3692 6456 4880 2388 5545 4091 5302 3031 4295 3870 3603 4015 5330 * 6892 6
+ 87 4336 6804 2904 207 * * 6199 1312 0
+
+I 7 5437 * 5187 4558 5350 5797 5862 3063 3798 2693 4684 3637 2867 5042 5334 4511 4287 3514 * 7151 7
+ 84 4964 5333 3079 182 0 * 6361 1134 1000
+
+C 8 * 140 5700 * * * * * * 6109 * * * * 6200 * * * * 4471 8
+ 51 5700 5997 5672 29 * 0 6549 1047 1086
+
+A 9 3334 7246 6883 3418 4491 6124 7295 5444 3453 3422 5314 6976 4132 3421 3460 3487 4220 3529 6674 7405 9
+ 0 * * * * * 0 6568 0 1169
+
+I 10 * * * * * * * 1951 * 5681 6404 * * 5726 5676 * 5499 643 * 6739 10
+ 8 * 7441 1585 585 576 1603 6568 1011 1169
+
+C 11 * 133 * * 6311 5533 * * * 5465 * 5810 * * * 6237 * * * * 11
+ 32 * 5513 0 * * 0 6579 1000 1059
+
+G 12 * * 4269 3810 5981 1221 5829 * 5030 5290 6110 4422 7412 3514 3872 3963 6756 5613 * 4582 12
+ 40 6101 6254 0 * 1209 818 6532 1044 1210
+
+D 13 3699 7785 1854 4320 * 3669 6807 * 3622 6660 6678 3494 7214 4090 3173 3903 5872 4377 * 7321 13
+ 67 5680 5285 943 1059 1790 493 6548 1070 1208
+
+R 14 6095 6677 4687 3817 * 6445 4488 5349 3079 3802 6723 5337 2604 4178 3142 3465 4433 4021 * 5081 14
+ 129 3549 * 1521 618 1137 875 6553 1680 1296
+
+S 15 1677 6371 6954 4834 * 3834 7590 6242 3663 5398 5442 5392 4582 * 5402 2339 3867 4736 * 5324 15
+ 22 6076 * 514 1738 2102 383 6601 1070 1137
+
+S 16 4361 5992 4535 6091 6422 5477 3681 4196 5624 3946 4923 3107 5267 4844 4521 2395 3100 5028 6094 5601 16
+ 32 5525 * 1000 1000 0 * 6664 1101 1092
+
+G 17 3870 5483 5119 4237 * 1131 * 7037 4643 4103 6170 5520 5837 5690 4457 3451 5036 5941 * 6831 17
+ 63 4775 7367 0 * * * 6771 1234 0
+
+K 18 7714 4936 * 6159 3046 6339 4909 3496 3450 3972 5850 3698 5075 6052 4521 3974 4811 4410 7100 2310 18
+ 95 6096 4339 0 * * 0 6769 1046 1011
+
+H 19 4776 6453 6947 6370 5280 6686 1251 5315 4356 4732 * 2789 * * 3194 4520 4464 * * 5524 19
+ 46 6702 5522 247 2670 351 2212 6663 1308 1382
+
+Y 20 5805 7187 6062 * 1782 * 5728 5680 * 5834 * 6367 * 6231 6421 4656 5898 5261 5229 1097 20
+ 32 * 5498 * * 658 1449 6723 0 1204
+
+G 21 6195 5060 5037 5538 * 646 * * 4598 * * 4055 6784 4681 5200 4099 5611 6680 * * 21
+ 22 6024 * 2322 322 * 0 6716 1051 1208
+
+V 22 2080 5580 5530 * 6550 4344 6019 4937 5472 * 5695 7051 5461 5380 6957 4861 4128 1261 * * 22
+ 28 * 5695 * * * 0 6716 0 1208
+
+Y 23 4169 * 4586 5420 3653 5795 7270 3495 6239 2893 5662 4482 3651 5111 4005 3776 5022 3216 4418 4460 23
+ 34 7309 5866 1000 1000 645 1473 6675 1000 1322
+
+S 24 2682 3380 * * * 6529 6754 4700 * 4387 6674 * 5720 7042 6750 1684 2244 3956 * 6731 24
+ 34 6318 6529 2449 292 259 2607 6720 1052 1196
+
+C 25 5456 216 * * * * * * * 5748 * 6767 * * 5522 5360 * 6000 5988 6546 25
+ 0 * * * * * 0 6766 0 1059
+
+E 26 5497 5734 4244 2580 6072 4261 6723 7401 3493 4023 7628 2539 5104 6533 2820 3353 6579 5769 7271 6099 26
+ 41 5143 * 2425 297 642 1478 6766 1158 1059
+
+G 27 1286 6205 5243 7468 6625 2162 * * 4942 6781 6834 5139 4565 * 5976 2809 5010 * * * 27
+ 9 * 7380 * * * 0 6779 0 1000
+
+C 28 6683 196 * 5987 * * * * * 5699 * * 6208 5848 * 6424 6593 5536 * 7020 28
+ 0 * * * * 1403 686 6776 0 1053
+
+K 29 2440 6575 5895 * 6637 5026 * 5432 1514 6601 5740 5301 * 3891 3468 4328 4557 4095 * 6457 29
+ 28 5708 * 2701 241 * 0 6793 1094 1011
+
+G 30 2257 6727 7252 4703 6875 3208 6148 5235 4843 4820 2832 5375 6243 5580 6638 3237 3598 3333 * 6348 30
+ 0 * * * * * 0 6859 0 1011
+
+F 31 7333 * * * 202 * 6243 * * * * * 6091 * 6875 5241 * 4694 * 5442 31
+ 0 * * * * * 0 6859 0 1011
+
+F 32 * * * * 295 * 6098 4917 * 5936 * * 6700 * * 6697 * 5661 6256 3861 32
+ 7 7665 * 1000 1000 * 0 6859 1000 1011
+
+K 33 5918 6462 5267 7470 7333 5721 7391 * 3567 5512 6381 5986 * 5046 723 3972 5254 4720 * 6443 33
+ 65 * 4511 * * * 0 6859 0 1011
+
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+
+T 35 3000 4812 * 7003 7476 5673 4442 4184 4976 6234 5311 4518 * 7514 6522 2479 1819 3862 * 4523 35
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+
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+
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+ 101 4630 5214 1277 768 * 0 6860 1350 1109
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+K 38 4189 * 6256 3635 5325 3252 7536 7250 2316 3831 4880 3796 4943 4790 3873 2937 4752 5642 * 6941 38
+ 23 5991 * 595 1565 1966 426 6884 1088 1321
+
+D 39 6672 * 3990 3493 6113 4346 6503 6814 2147 6142 * 2361 5044 3606 4299 3958 4922 4817 7036 5922 39
+ 80 4398 7222 528 1705 2432 296 6819 1329 1225
+
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+ 89 5086 5054 2919 205 2564 267 6814 1168 1220
+
+T 41 4205 * 4250 4003 5155 6022 4724 3759 2682 5276 4385 3998 3661 4275 3850 4411 3784 4131 * 7186 41
+ 212 2944 7266 995 1005 2969 197 6777 2016 1395
+
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+ 17 * 6422 3953 96 2878 211 6783 1011 1440
+
+T 43 5569 6408 4550 3497 7128 6043 6130 5054 2220 4998 5988 4819 4589 3958 3807 4739 3416 2722 * 6352 43
+ 81 4954 5502 415 2000 1436 665 6774 1172 1458
+
+C 44 5778 247 6831 6720 * * * * 5143 * * 7341 * 6061 6123 4900 * * 7028 5991 44
+ 91 6555 4316 0 * 2088 387 6758 1026 1430
+
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+
+D 46 4077 4188 5469 4554 3904 4005 4649 6525 2709 7528 * 4911 5601 5180 2374 3591 3808 * * 4215 46
+ 144 4210 4618 597 1562 * 0 6786 1323 1464
+
+N 47 6217 * 3574 3765 6722 2863 4677 5066 4104 5479 5859 2312 4804 4447 4735 4101 3062 8108 * 6246 47
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+
+K 48 7608 4441 5454 4342 * 2044 5037 7069 2708 * * 2308 7206 3702 3791 4523 * 6236 5734 6632 48
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+
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+ 26 6785 6810 1793 491 2386 306 6681 1018 2009
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+ 111 5537 4247 860 1156 1244 791 6722 1107 1925
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+ 9 7394 * 698 1382 1045 957 6794 1053 1861
+
+N 58 4394 5253 4162 4830 5337 6513 4569 4771 3124 3904 4828 2953 4100 4218 3608 4205 4711 5255 7303 4161 58
+ 97 4370 5915 3705 115 766 1279 6808 1451 1428
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+C 60 * 187 6396 * * 6276 * 5931 * 5548 6549 * * * 6943 6520 6166 6003 * * 60
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+C 68 * 288 * * * 5981 * 5839 * 6822 5517 * 6103 * * 4671 * 4366 * 6110 68
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+ 0 * * 3000 193 0 * 7016 1011 1011
+
+A 70 3691 * 2962 2246 * 6023 5629 * 3108 4748 6096 3716 6305 3540 3421 3899 4636 * * 7748 70
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+M 71 2274 * * 6464 6230 6934 * 3727 4853 3842 4520 * * 5821 4315 3715 5099 1508 * 6378 71
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+G 72 * * 7009 6980 * 121 6881 6207 * * * * * 6546 * 5933 * 5972 * * 72
+ 19 * 6243 * * * 0 7156 0 1022
+
+M 73 5943 * * * * 5995 * 5793 * 4076 264 6330 * 5893 6097 6146 * * * * 73
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+K 74 5226 6178 3578 5159 7426 5214 6846 4262 2982 4526 6789 2794 * 4813 3149 2896 3165 4761 * * 74
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+ 79 4234 * 4003 93 1225 805 6870 1319 1101
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+A 77 1884 7210 4545 4368 5264 5088 6267 5454 3893 5575 6829 3836 5129 6081 5534 2750 4728 3895 6980 4432 77
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+V 78 5575 * * 5713 3279 * * 2785 4238 3785 * 6315 * * 5124 5263 4887 1069 * 6857 78
+ 11 7097 * 1585 585 * 0 6615 1000 1000
+
+Q 79 6666 * 6598 3785 6316 4632 5344 6595 3318 4592 7019 5697 * 1443 2518 5346 4626 5407 * 5679 79
+ 0 * * * * * 0 6446 0 1000
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+E 80 3892 6052 4698 3891 3739 4971 5472 7025 4749 6655 4773 3053 3780 5871 3747 2898 3262 * 4657 5154 80
+ 0 * * * * 0 * 6324 0 1000
+
+E 81 6527 * 2179 2732 5439 3760 6483 6002 2797 4096 * 3185 5208 * 3430 4845 * * * 5198 81
+ 52 4829 * 1000 1000 * * 5920 1058 0
+
+R 82 4355 * 4934 5312 5990 * * 5689 2947 5016 * 6178 * 5557 771 3708 * * * * 82
+ 0 * * * * * * 5948 0 0
+
+Q 83 5618 * 2596 3535 5365 * * 3847 3852 3976 4675 3191 * 2344 4878 * 3951 4988 * 5291 83
+ 0 * * * * * * 5321 0 0
+
+R 84 * * * 4391 * 4441 4391 * 3035 3165 * * 3082 * 1370 3658 * 4609 * * 84
+ 221 2815 * 2322 322 * * 4535 1069 0
+
+G 85 * * * * * 1366 * * * * * 2268 * * 1684 * 3426 * * * 85
+ 0 * * 0 * * * 3632 0 0
+
+//
+�HHsearch 1.5
+NAME a1cf9299e65402da85fa1134c4159419
+FAM
+FILE a1cf9299e65402da85fa1134c4159419
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:17:17 2013
+LENG 209 match states, 209 columns in multiple alignment
+FILT 135 out of 1311 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEECCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHCCCCCCCCEEEECCEEEECHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
+HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHCCHHHHHHHHHHHCCHHHHHHHCCCCCCC
+CCCCCCCCC
+>ss_conf PSIPRED confidence values
+9769995699814999999999849987799845122476878721878888889889987655999999999844469999999999999999999999
+9999998535587899999999999999999998546899722789998999999999999997181021107899999999984899999870355455
+125787779
+>Consensus
+xxxxLyxxxxsxxxxxvxxxlxxxgixxxxxxvxxxxxxxxxxxxxxpxxxvPxLxxxxxxlxesxxIxxyLxxxxxlxpxxxxxxxxxxxxxxxxxxlx
+xxxxxxxxxxxxxxxxxxxxxxxxxlxxlexxLxxxxxxxxxlxGxxxtxaDxxxxxxlxxxxxxxxxxxxxxpxlxxwxxxixxxpxxxxxxxxxxxxx
+xxxxxxxxx
+>a1cf9299e65402da85fa1134c4159419
+PPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASCLYGQLPKFQDGDLTLYQSNTILRHLGRTLGLYGKDQQEAALVDMVNDGVEDLR
+CKYISLIYTNYEAGKDDYVKALPGQLKPFETLLSQNQGGKTFIVADQISFADYNLLDLLLIHEVLAPGCLDAFPLLSAYVGRLSARPKLKAFLASPEYVN
+LPINGNGKQ
+>gi|226288896|gb|EEH44408.1| glutathione S-transferase [Paracoccidioides brasiliensis Pb18]
+--LTIHHLH-SSQSERIPWLCEELNIPYELKTYKRDPiFAPPEYKALHPSGAAPVIQDTlptndggsdaepqTLILAESCACVEYISHK-yGngrLFLps
+THKDYATFLYWFHWANGTFQPLLGrlltVETimssiggggggnsnsrsetQNQtlgSNPLIALWSGRRQRALRMLDNRF-KKrdegGEEATWLAGEEFTA
+ADIIVVFSLTTFRNW-YrYSLQEYKGILGYLQRIGGREGYR-rAMAQVDPEMTLA------
+>gi|242006743|ref|XP_002424206.1| methionine-tRNA synthetase, putative [Pediculus humanus corporis]gi|212507555|gb|EEB11468.1| methionine-tRNA synthetase, putative [Pediculus humanus corporis]
+--MKVLTNENNINSLKIVISSKITKKSIHVLTNSIEK---LNLKS---PKTIPQLVlDSGVHIFSSNASSKFLFPP------SVEHnSCVNYYLDVEATV
+IQPLIATF--SG-KVSDKNKKSFE-EILNQCNNDLI----SKKFLCGNEITVSDVSIWcalyPIFTD-TK-FNDILLNKDSLKKWFEFIFKLPEVQESLK
+LCNI-----------
+>gi|340039913|gb|EGR00886.1| glutaredoxin, GrxB family [Vibrio cholerae HCUF01]
+-------------------MAGMLNIPLDVITLDYDDDQT--TNQIIGSKQVPLLIkESGEALAESLDIIQFLLESVNSS-ETAQPAQATLDWQRSAFLP
+LQKIgYPRWsnmnlpefktasaqqaWrVKKETtelhfesllkDTSQIALQVQACIDAVKPLLK----LHSYQHV--ALIDEAIIFSILRGFFSAPE--IQ
+WDSEVRDWMVSVSQKTQVRL------------------
+>gi|255079028|ref|XP_002503094.1| predicted protein [Micromonas sp. RCC299]gi|226518360|gb|ACO64352.1| predicted protein [Micromonas sp. RCC299]
+--PVAYIAPTCPFAHKAWLALVEKEVDFEMRAVDLND-KQPDMIAaygvASPdagsVAKVPILIHDGVAMIESALCATYVAEAFkssgaDLLPATPAEQY
+KVGLWCETFA-VGPPFFRALRATSQSDVDSALDDLRSVLRKCERCLEIaqtttgrdkGQSDGPFVLGAKYSMAEVLTSTMLPRLsvalghyRGFRLhAAV
+EemGLHRLARWMDASMDRPSMRQTLGEVGR-----------
+>gi|170579264|ref|XP_001894752.1| Metaxin 2 [Brugia malayi]gi|158598526|gb|EDP36401.1| Metaxin 2, putative [Brugia malayi]
+---ALLYEY--ADCVAVQTLLKMANLPVRLEER-----PNAEF--MSPTGKVPFLKLQSFLVSEFLPVVDFLAKRNVKLSAGLTDLERGDMhaHMALFDD
+ILKNVEMYVMWMDkrnysqvtkcrygsvylfplnlilprvkwrevnnyltavdwkSKSQECVMDLADRCFKSMSSKL----DHNEYFFGDSPTELDALAF
+GHFYTILTTELPNmelkncLRRYSNLTEFCQRIDK------------------------
+>gi|151967130|gb|ABS19445.1| multivalent antigen sj97-23 [synthetic construct]
+ATLGTGMRCLKSCVFILNIICllcslvligagAYVEVKFSQYEANLhKVWQAAPIAI--------------IVVGVVILIVSF-------LGCCGAIKEN
+VCMLYMyafflivlLIAELVAAIVAVVYkdkiDDeINTLMTGALENPNEEITATMDKIqtsfhcCGVkgpddykgnvpasckEGQEVYVQGCLSVFSAFL
+KRNLIIVACVAFGVCFFQLLSIViacCLGQRIHDYQNV--------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+P 1 2615 * * * * * * * 4246 * 4276 * 751 * * 2852 * * * * 1
+ 0 * * * * * * 6861 0 0
+
+P 2 3520 * 3739 3009 * * 5442 5369 2607 4573 4885 5539 3851 3423 * 3114 3307 5265 * * 2
+ 29 5639 * 2000 415 * * 8750 1137 0
+
+Y 3 5356 * * * 4353 6401 * 2298 * 2212 3124 5077 3309 * 6210 6290 5392 4569 * 2660 3
+ 19 6290 * 0 * * * 9795 1005 0
+
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+ 0 * * * * * * 9906 0 0
+
+V 5 * * * 6337 3685 * * 3569 * 535 5486 * * * * * 5025 3798 * 6543 5
+ 0 * * * * * * 9947 0 0
+
+V 6 * * * * 3082 4619 3266 3907 5376 4025 * * * * 5670 6690 5325 3636 5789 1210 6
+ 0 * * * * * * 9974 0 0
+
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+
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+
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+
+V 10 3266 6642 3655 * 3135 4488 4198 3161 * 3896 5649 5721 3718 4862 4082 4607 4496 4216 4524 5395 10
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+
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+
+G 12 3515 * 6554 5906 5763 2278 6035 4957 6943 4523 * 4907 1348 5782 * 4093 5307 4907 * * 12
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+
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+
+C 14 2537 2408 * * * 2903 6758 * 6632 * * 6592 6106 * * 1952 3643 3025 * * 14
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+
+A 15 3341 6118 6684 3016 4734 6654 3696 4738 5702 3450 4112 6558 6541 3125 2717 5342 5810 5059 4521 5732 15
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+
+A 16 2970 6016 * * 5292 5480 6657 4123 2286 4120 5282 * 5798 6695 1902 3798 5042 4156 * * 16
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+
+L 17 2887 4191 * * 7033 * * 2289 * 2922 6726 * 4565 * * 4239 4513 1655 * * 17
+ 0 * * * * * * 10248 0 0
+
+R 18 4433 6363 * 4685 5258 6731 4292 4158 4286 2901 5275 5458 6559 4396 1468 6752 5494 5975 5248 4915 18
+ 15 6566 * 0 * * * 10260 1042 0
+
+M 19 3133 5900 * * 4428 6632 * 2604 * 2025 2960 * * * 6561 5583 3984 3789 3873 4696 19
+ 0 * * * * * * 10244 0 0
+
+L 20 1770 4717 * * 3736 7092 * 4636 * 2260 3647 * * 6375 6582 6865 4606 2943 6167 4596 20
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+
+L 21 2875 4323 * * 3907 6585 * 3727 * 780 4557 * * * * * * 4779 * * 21
+ 33 6167 6795 3459 138 * * 10291 1149 0
+
+A 22 2624 6817 4453 2403 5035 4469 4243 5270 2900 4358 * 4142 * 4635 4152 5527 5268 6991 4960 5945 22
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+
+D 23 2958 5910 4890 2041 4700 6712 4438 5080 * 2451 3828 6538 * 6797 5402 * 6887 5098 4569 3685 23
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+
+Q 24 2489 4981 * * 5212 5317 5351 5883 2177 2428 5388 5808 6541 5370 5264 3796 4737 4739 6799 5007 24
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+
+G 25 5408 6795 3631 3709 * 1073 * * 4625 * * 2600 * 4362 4263 5126 * * * * 25
+ 24 7199 6662 1585 585 * * 10291 1269 0
+
+Q 26 4216 * 5816 * 5474 * * 2004 6742 1823 6834 * 5667 4639 6086 6106 5637 2018 * * 26
+ 43 5074 * 712 1360 * 0 10266 1705 1062
+
+S 27 4104 * 2960 3090 * 5188 6008 6980 4104 * 6353 4299 1547 5823 4139 4282 4921 6074 * 6985 27
+ 11 7037 * 1000 1000 * 0 10243 1000 1492
+
+W 28 6989 6039 5952 6575 2030 * 3940 4765 6628 3768 6823 * * * * 6549 5599 3225 4323 1631 28
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+
+K 29 6361 7010 2797 1842 * 5850 5846 6655 3154 * * 4377 * 4506 3126 4427 3229 4963 * 6881 29
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+
+E 30 4801 * 2945 3417 3788 6652 5328 2816 6953 2688 * 5810 * 5424 5958 5117 3485 3121 6069 5439 30
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+
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+
+V 32 4602 5957 5055 3196 3885 6794 5512 4337 5043 3456 5358 4572 3202 5364 3125 4609 3594 4225 7042 4833 32
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+
+V 33 3784 4725 * 5427 3596 6200 5789 2590 * 2948 4990 6900 * 6955 4938 6830 5015 1753 * 4665 33
+ 202 4895 3361 2730 236 * 0 10266 1676 1062
+
+T 34 4020 5782 1917 3859 5631 4290 4690 6900 4635 5682 * 3322 4129 5689 4072 4023 3425 5817 * * 34
+ 280 6740 2583 0 * 2935 202 10133 1076 2814
+
+V 35 5494 6178 5483 5281 2890 4454 * 3570 5600 2322 3664 6363 3125 5580 3496 5526 6430 5506 6885 4274 35
+ 352 2464 4816 1452 656 3206 166 9923 3432 4873
+
+E 36 3475 6387 2938 3556 5609 2990 5255 4843 3422 6778 * 3852 3406 6664 4534 4463 3947 4444 * * 36
+ 301 2488 6625 1007 993 833 1189 9943 3279 4860
+
+T 37 4202 * 2591 2345 5729 4532 7076 5110 4253 5769 6755 3607 4069 3871 4405 5281 4133 4247 * 6397 37
+ 287 4533 2864 465 1859 4061 89 10126 1636 3081
+
+W 38 5320 * 4388 6450 3532 5579 3745 3704 3988 3691 5579 3850 3758 3972 * 4467 4684 5781 2606 5494 38
+ 194 6453 3131 0 * 766 1279 9949 1005 4714
+
+Q 39 3529 * 4822 4255 5036 * 5051 6741 2412 4388 * 4317 2829 3515 3091 4246 4347 * * 5484 39
+ 319 3055 3677 456 1884 1047 955 10022 2617 4015
+
+E 40 3867 * 3860 2834 5002 3471 * 6532 3512 5757 6781 3807 2861 7042 5171 2720 3867 * * 6621 40
+ 90 * 4050 * * 2709 239 10056 0 3871
+
+G 41 2681 6887 3348 2796 * 3544 * 6300 3837 6506 * 5315 1805 5263 * 5427 5513 4989 * * 41
+ 57 4690 * 1850 469 1725 520 9986 1681 4228
+
+S 42 3040 * 2537 1992 6889 4409 6537 6801 4657 5787 * 6654 4494 5153 * 3727 3579 6742 3820 * 42
+ 150 3478 6848 3325 152 695 1387 10092 2416 3342
+
+L 43 7052 6674 7015 4812 2462 6708 5777 3874 * 2160 6757 6537 5072 5694 4964 4864 4441 3642 5960 2641 43
+ 120 5279 4211 1577 589 1523 617 10197 1312 2071
+
+K 44 3415 5884 4052 5042 5802 5802 6687 3275 2978 2296 6899 4784 * 4230 3426 3743 6684 4848 6794 * 44
+ 43 5102 * 1349 719 790 1246 10208 1361 2559
+
+A 45 3291 * 3437 3397 4885 4547 6800 6130 2750 4335 * 3829 4071 3775 3383 3827 5403 5670 * * 45
+ 99 4880 4946 1115 893 1344 723 10259 1530 1599
+
+S 46 5621 7116 5189 4580 4509 3918 6740 2656 4116 2284 4377 4800 5096 5504 4744 4930 4320 3622 6575 6060 46
+ 125 4378 4849 2806 223 2899 208 10163 1707 1960
+
+C 47 4046 7040 4430 5740 4311 5410 4064 4050 5334 4162 * 1581 6581 5840 * 2788 4282 6963 7097 5774 47
+ 67 4455 * 561 1635 1022 979 10127 1689 2404
+
+L 48 3980 * 5691 4896 6880 3457 4916 * 5321 4651 6815 5900 951 7083 4746 5299 6839 4308 * 6164 48
+ 67 5337 5599 1167 850 1154 861 10188 1379 1662
+
+Y 49 4741 7161 5995 6137 3039 4907 4957 * 3613 2502 4669 4506 5998 4558 4121 3929 3339 4877 6555 3791 49
+ 14 * 6711 * * * 0 10187 0 1699
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+
+//
+�HHsearch 1.5
+NAME a251ab96460cc372677a195a346bdc79
+FAM
+FILE a251ab96460cc372677a195a346bdc79
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:15:00 2013
+LENG 96 match states, 96 columns in multiple alignment
+FILT 101 out of 175 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHHHHHCCCEEEEEEEECHHHCCCCCCEEEECCEEEEEECCCCCCCCCEEEECCEEEEEEEEEEEEEECCCCEEEEEEEEECCEEEEEECC
+>ss_conf PSIPRED confidence values
+941469963514874656999841217998763998884999853276699987996416799999999997258988999999773356517688
+>Consensus
+xxxxxxxvxxxaxCxPrxxxVxixxexpxxxxxxyxPxCvxvxRCxGCCxxexlxCxPtxtxxvxxxvxxxxxxxxxxxxxvxxxxHxxCxCxxkx
+>a251ab96460cc372677a195a346bdc79
+MVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRAGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKAECRPKK
+>gi|41057195|ref|NP_957909.1| ORF132 vascular endothelial growth factor-like protein [Orf virus]gi|41018752|gb|AAR98357.1| ORF132 vascular endothelial growth factor-like protein [Orf virus]
+-TNDWVRTLDKSGCRPRDTVVYLGDEYPENTNLQYNPRCVTVKRCSGCCNGEGQICTAVETRNTTVVVSVTSVSSSSgansgvsnNLQRISLTEHTKCDC
+IGRT
+>gi|62421239|gb|AAX82359.1| vascular endothelial growth factor-like protein [Orange-spotted grouper iridovirus]
+------ESILESSCQPRPTKVQLSG------YDMYIPACAYVPRCGGCCSgDEATTCRPTATSTVNVTAYKLVFHETH-QVVVSVVTHTACACKFK-
+>gi|340710875|ref|XP_003394009.1| PREDICTED: hypothetical protein LOC100647889 [Bombus terrestris]
+---------KQANCEPSPTVVPTYQR--NDPSIIYFPRCTRVKRCTGCCGSELLSCQPKEIETRNFEIMLAKLTAQGrfeyqGKQIVPIDEHIRCGCD--
+-
+>gi|340719499|ref|XP_003398190.1| PREDICTED: vascular endothelial growth factor A-A-like [Bombus terrestris]
+--------FRCSMPQPRAIPVAELLTVGPSPDEVFYPASTVLTRCKgaGCCPDPKQICAPIETRNVSLVFMVkhtIDRQRDRHHEVIHALEHTKCGCVHK
+-
+>gi|47218000|emb|CAG11405.1| unnamed protein product [Tetraodon nigroviridis]
+------EEAVPALCKTRTVIYEIPrsQVDPTSANFLIWPPCVEVKRCTGCCNTSNMRCHPSRKHYRTVKVAKVEYVkRKPKlkEVFVRLEDHLECMCTS-
+-
+>gi|221110330|ref|XP_002160342.1| PREDICTED: similar to vascular endothelial growth factor [Hydra magnipapillata]
+---------DSPSCQLMQKFEQIPKSKT--DSFIFFPSCIKVNRCSGCCNTDVMECVALTNSSHFIDVYKVPTNGRPYLYRVSYFNDESCGCQ---
+>gi|198416765|ref|XP_002128012.1| PREDICTED: hypothetical protein [Ciona intestinalis]
+--------LRSTKCAVREEIVDIRDIHPHLPpDVLLLPSCILIRKCSGCCQNSRHVCKPTAIYVTRVEVSQQHVvRRRLDYITLNFTHHDECECMS--
+>gi|91081701|ref|XP_970909.1| PREDICTED: similar to Pvf3 CG34378-PD [Tribolium castaneum]gi|270006461|gb|EFA02909.1| PDGF- and VEGF-related factor 3 [Tribolium castaneum]
+-----AKVRQEGQCRkPLPKVISVQSEHPDPS-KTYTPHCTILHRCAddtGCCANHTTRCGPKTQVLVHLYFYAKTLGvPGTKVEKLTFYNHTECACIEK
+-
+>gi|335293493|ref|XP_003129048.2| PREDICTED: platelet-derived growth factor C-like [Sus scrofa]
+------EEVRLYSCTPRNFSVSIREELK-RTDTIFWPGCLLVKRCGGncaCCMHTCneCQCVPSKVTKKYHEVLQLRPKTGVrglhkSLTDVALEHHEEC
+DCV---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+ 0 * * * * * * 5798 0 0
+
+K 89 3150 * * 1815 * 4768 5082 * 2459 5980 * 7131 * 3722 2921 3532 5144 6718 * * 89
+ 17 6430 * 1000 1000 * * 5803 1007 0
+
+A 90 5808 61 * * * * * * * * * * * * 5395 * * * * * 90
+ 0 * * * * * * 5803 0 0
+
+E 91 3345 * 3807 1550 * 3842 3968 6819 2549 * 6541 * * 4542 4544 5057 4990 5858 * * 91
+ 0 * * * * * * 5803 0 0
+
+C 92 * 0 * * * * * * * * * * * * * * * * * * 92
+ 29 5632 * 1585 585 * * 5803 1064 0
+
+R 93 6457 * 3949 4082 6579 5524 * 4704 4552 5982 4488 * * 2530 1638 5265 6276 2663 * * 93
+ 0 * * 0 * 0 * 5725 1064 1064
+
+P 94 5754 3162 5582 3285 4304 4947 4744 5550 4855 4794 6220 5628 1580 6223 * 2824 * * 6467 * 94
+ 0 * * * * * * 5198 0 0
+
+K 95 * * * * * * * 4621 648 5818 * * * 5719 1814 * * * * * 95
+ 0 * * * * * * 4804 0 0
+
+K 96 * * 3185 * 4111 * * * 1413 4715 * 4281 2992 * 3574 4685 4389 * * 3817 96
+ 0 * * 0 * * * 3576 0 0
+
+//
+�HHsearch 1.5
+NAME a44d747376cfd87bd0f30749697bc63b
+FAM
+FILE a44d747376cfd87bd0f30749697bc63b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:20:24 2013
+LENG 202 match states, 202 columns in multiple alignment
+FILT 138 out of 1781 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEECCCEEEEECCCCEEEEEEECCCCCCEEEEEEECCCCCCEEEEEECCCCCCCCCCCCEEEEEECCCCEEEEEECCCCHHHCCCEEEEECCCCCCCC
+CCCEEEECCCCCCCCCCCCEEEECCCCCCEEEEEEECCCCCCCEEEEECCCCCCCCCCCEEEEECCCCEEEEEEEECCCCEEEEEEEECCCCCCCCCCCC
+CC
+>ss_conf PSIPRED confidence values
+9089479718997999799999974789946999992799984499995254345677882799984489747888756887567659999806887530
+0010000122454200000145315544207899972669886799978985302443066550367679967973489849999995998715778788
+89
+>Consensus
+xxvxqxpxxxxxxxGxxvxLxCxxsxxxxxxixWxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxxLxIxxxxxxDxgxYxCxvxxxxxxxx
+xxxxxxlxvxxxxxxxxpxvxxxxxxxxxxxlxCxxxxxxPxxxvxWxxxxxxxxxxxxxxxxxxxxxlxlxxxxxxxxxxytCxvxhxxxxxxxxxxxx
+xx
+>a44d747376cfd87bd0f30749697bc63b
+QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQLLLKYYSGDPVVQGVNGFEAEFSKSNSSFHLRKASVHWSDSAVYFCAVSGFASALT
+FGSGTKVIVLPYIQNPEPAVYALKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDATVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETNATYPSSDV
+PC
+>gi|54779581|gb|AAV39959.1| immunoglobulin mu heavy chain [Homo sapiens]
+------SDPGLVKPSETLSLTCTVSGGSIssYYWSWIRQPPGKvtGVDWVYLLQWE-hQlqPLPQ-ESSHHISRHVQEPVlpEAELCDRCGHGRVLLC--
+eRcrlDivvvvAAGfDWFdPWGQGTLVTVSS---------------------------------------------------------------------
+----------------------
+>gi|293353800|ref|XP_002728296.1| PREDICTED: rCG64189-like [Rattus norvegicus]
+-FLDDTKDGLFSRIRGFntsptRKPQCKSQTRPCTTVLWVTQWQ-----------------KP-QGELSTNREATGGLAAEKLPLRSSD---FTTAF---
+----------------------------------------------------------------------------------------------------
+-------
+>gi|115497936|ref|NP_001068678.1| poliovirus receptor-related 2 [Bos taurus]gi|109658349|gb|AAI18435.1| Poliovirus receptor-related 2 (herpesvirus entry mediator B) [Bos taurus]gi|296477435|gb|DAA19550.1| poliovirus receptor-related 2 [Bos taurus]
+DVRVQVAAEVRGNLGDTVELPCHLlpSAPEirVSQVTWLRLDAPEGKQNVAIFHPQYGrsfpSPKpgK-ERLSFVN-TapssgagqgselEVRDATLSLR
+GLTVEDEGNYTCE------FATFPKGtsrgvTWLRVIAQPQNHAEKQEVTFNLDPVPVARCVSAGGRPPARVSWlspLDGEAKETQGSGPLPGTVTVTsr
+YTVTPLSEADGVKVICKVEHESFqePKLLP------
+>gi|53987930|gb|AAV28078.1| immunoglobulin delta heavy chain [Salmo trutta]
+-KIVR-PSDSDLWGSNNATLLCLVSGFFPSDVIVNWEKAGSRLPFSRYSSIPSVlYAGS-STYSMN-------SRLIVPRSEWDQNSNYSCAVRHESSER
+PI-THTIENVFGSVTPSASTATLL---QGPSELVCLVLGFSPsDINITWlLDNVTELWNNNTSTTYRAPGGKfgirshlSLAHQDWTPGAVYTCRVTHTT
+Q-----------
+>gi|30268720|gb|AAP29471.1|AF387763_1 costimulatory molecule B7.1 [Meriones unguiculatus]gi|37903876|gb|AAO38852.1| costimulatory molecule B7.1 [Meriones unguiculatus]
+--------QVFKSVNEKVSLSCGYNFSFdeLAIHRIYWQKDDRKMVLSISSGDKKVwPEYQ-NRTLCDISNN---FSLMILGLLPSDRGTYECVVqkkER
+GVYLLRHLNSVELSIRAD--FPVPNITQFGNQSADmKTIICETSGGFPEPRSLWLESGRELRGINTTVSQDPESELYavSSKLDFNatYNRSIVCSVAYG
+K------------
+>gi|341890725|gb|EGT46660.1| CBN-ZIG-2 protein [Caenorhabditis brenneri]
+-RIAQGLEDMKAAPGEHITLHCMVLSTPSSVFHW--EHNGIRVQEDSNVNIHERMMNI-GKEVVG--DGTISSFYTIPCVNANSTGIYKCIAF--NGHGT
+VESSAKVTVegkptecVSN-DKTAPKIITITGIRlqengRVATLNCRAD---KPAKFEWTFKGKPIDMNDGRFSVLSYGDLVISNISWSDMGDFTCYARN
+K-------------
+>gi|301791774|ref|XP_002930855.1| PREDICTED: signal-regulatory protein beta-1 isoform 3-like [Ailuropoda melanoleuca]
+-----SGPAARASPEQTVSFTCESHGFSprNITLRWFK----NGNELAASQTTVDAEGHG-TSYNIS---SMTRLVLAPGDVRSQV--------------
+PLHPqpnprSGPQLLLCAVSVPPTLEVSQQPVAGDQVNVTCQVTKFYPrHLQLTWLENGNVSRTEmasMASNLIENKDGTFnwtswllVKSSTHREDVVL
+TCQVQHDRQ-----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+Q 1 * * 3282 3467 * * * 3550 * * * * 3462 858 * * * 3663 * * 1
+ 0 * * * * * * 4956 0 0
+
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+ 0 * * * * * * 8957 0 0
+
+V 3 * * * * 3458 * * 2317 * 2166 3716 * 5964 * 5843 * 5930 1476 * * 3
+ 0 * * 2585 263 * * 9375 1036 0
+
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+ 29 6538 6803 0 * * * 9482 1000 0
+
+Q 5 4960 * 4928 3977 6114 6181 5190 5413 4691 4560 * * 4180 1190 4338 4436 6090 3394 * 6317 5
+ 226 * 2784 * * * 0 9702 0 1000
+
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+
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+
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+
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+
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+ 21 6117 * 2431 296 0 * 10312 1479 1188
+
+V 12 2218 5647 * * 6849 4569 * 3999 3771 4921 4983 6810 6705 * 6661 4500 3387 1677 * 4918 12
+ 9 7395 * 0 * * * 10371 1000 0
+
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+
+E 14 4789 * 4824 2237 * 5544 * 4169 4338 2682 7202 6743 3045 5110 4774 3822 4838 2992 * * 14
+ 0 * * 0 * * 0 10407 1000 1000
+
+G 15 * * 4497 6860 * 464 6642 * 5718 6552 * 4267 * 4916 4720 5164 5653 6399 * * 15
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+
+A 16 4734 * 2968 2241 * 3060 7085 6822 3702 5325 6438 4559 6355 3264 5902 2747 4343 * * * 16
+ 0 * * * * 919 1086 10550 0 1159
+
+S 17 6788 5889 3265 5327 6875 5143 5583 * 4241 6880 * 3197 3178 4802 4633 2001 2819 4687 * * 17
+ 46 5639 6444 2322 322 * 0 10525 1225 1000
+
+L 18 1702 * * 5932 6214 5051 7087 3741 * 4352 6865 * * 7339 6893 5261 4251 1365 * 6425 18
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+
+Q 19 5308 * 5824 4166 6138 * 5675 3734 4127 5001 6032 3822 6133 4453 4305 2868 1743 3965 * 7008 19
+ 0 * * * * 846 1172 10509 0 1179
+
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+ 0 * * * * * 0 10553 0 1000
+
+R 21 4972 7037 5929 5107 5532 4496 4893 5738 5335 4112 6938 3127 2701 5404 3621 2891 2851 4512 * 6008 21
+ 0 * * 2807 222 0 * 10553 1000 1000
+
+C 22 5648 151 * * 5450 * * * * * * * 6816 * 6442 5956 7037 6352 * * 22
+ 30 6857 6366 0 * * * 10554 1003 0
+
+K 23 6287 * 3876 3579 6979 4144 4003 4943 3814 4568 6012 3937 7065 4141 3157 3155 3191 4033 7041 6033 23
+ 39 5669 7141 1029 972 0 * 10577 1477 1152
+
+Y 24 2985 5432 * 6419 3172 4871 6857 3242 6850 2998 * 6859 * 6644 * 3957 4181 2181 * 3525 24
+ 48 7027 5307 1000 1000 0 * 10592 1040 1000
+
+S 25 5091 * 5134 3266 5327 5853 5140 5801 4013 4774 7006 4698 4129 5391 4267 1661 2786 * * 6548 25
+ 56 4726 * 1523 617 0 * 10519 1686 1314
+
+Y 26 5460 7145 3126 4032 6032 2258 5092 5379 5323 5328 5255 3644 3637 4241 5323 3544 4366 5243 * 4579 26
+ 37 6321 6292 1000 1000 * * 10554 1039 0
+
+S 27 4338 5843 4480 4346 3864 4136 5029 3937 3872 4167 6724 4897 3404 5929 4476 3022 4357 3543 * 4751 27
+ 49 6928 5302 1797 489 1086 919 10578 1127 1159
+
+A 28 4947 6859 4811 4897 5267 3410 4957 6766 4478 4210 * 3836 2387 3654 5831 3450 3733 3838 6351 5480 28
+ 1083 1052 4448 1484 638 451 1898 10538 6895 1466
+
+T 29 4001 4840 3621 3463 4672 3294 6537 6012 5169 3594 7035 3785 4421 4762 4562 3129 4288 3794 * 6801 29
+ 126 3894 5907 1337 727 585 1585 10448 1868 2091
+
+P 30 4091 * 4207 5326 4881 4444 4175 3530 5030 3728 6520 4010 2823 4646 4848 3793 4058 4441 6939 4080 30
+ 73 4584 7064 775 1267 588 1579 10464 1489 1803
+
+Y 31 4586 * 4318 4325 5321 5551 4706 4056 7035 3914 6699 3443 5930 4199 4512 3403 2794 4196 5935 3136 31
+ 18 6362 * 749 1305 610 1537 10551 1314 1329
+
+L 32 5940 6365 * * 3751 4997 7001 1848 5990 2602 4292 * * 6843 6333 * 6327 1810 5936 6179 32
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+
+F 33 4229 6327 6746 4397 3355 5983 3799 4832 5088 3700 * 4842 * 4287 3045 3193 3130 4990 * 3500 33
+ 17 * 6448 * * 0 * 10525 0 1007
+
+W 34 * * * * 5244 * * 5443 * 4520 * * * * * 6077 * 4632 260 5892 34
+ 86 4557 6045 748 1305 * 0 10492 1526 1008
+
+Y 35 * 5962 * 5094 2232 * 5279 4001 3785 3429 * 6552 * 5168 4531 4806 4611 3974 5829 2008 35
+ 74 5973 4887 2169 363 * 0 10470 1153 1322
+
+V 36 5964 * 5808 * 4504 * 4201 5859 2484 4688 5598 6173 6068 2891 1693 5385 5937 5448 4033 6054 36
+ 168 5842 3438 1155 860 1857 466 10401 1129 2014
+
+Q 37 4174 6112 3492 3800 5840 4856 6007 * 3345 5330 * 5034 4846 1532 5072 4328 4711 4645 * 6643 37
+ 163 * 3229 1000 1000 1900 450 10383 1000 3310
+
+Y 38 4860 * 3604 5084 5625 3664 4603 5124 2532 4387 6580 4017 5303 4354 3608 3339 3543 5734 6687 5470 38
+ 92 6718 4265 0 * 3553 128 10234 1000 4241
+
+P 39 4526 6711 3427 3486 4587 3580 6676 6354 4931 4231 * 3669 2087 4315 6694 3842 4068 5713 * 6756 39
+ 79 * 4225 * * 1259 780 10236 0 4671
+
+R 40 5533 * 3566 3734 6400 1563 5409 * 3852 6609 * 3475 5267 6713 3866 3713 4722 5075 5772 6749 40
+ 0 * * 1585 585 1990 418 10319 1000 3992
+
+Q 41 5234 * 4271 3343 6864 3940 6653 6089 3142 6093 * 4242 3853 2682 4352 2601 3863 4778 * * 41
+ 42 7182 5497 1585 585 3244 161 10356 1000 3305
+
+G 42 3424 * 7100 3618 * 2578 5589 4930 3790 4133 6520 3578 3493 5886 5008 3019 3554 5166 * * 42
+ 132 4888 4216 1092 913 4083 88 10378 1338 3408
+
+L 43 5438 5771 6693 6314 4551 6800 * 3445 5271 2983 5745 4414 1738 4333 5415 5166 4428 2966 * * 43
+ 71 6813 4677 1585 585 2976 196 10266 1000 3920
+
+Q 44 5035 * 4197 3010 * 4042 6773 3696 3183 * * 5898 6401 2771 4369 3301 3467 3592 6078 5607 44
+ 22 * 6069 1312 744 1316 741 10205 1152 4124
+
+L 45 4808 6722 5809 4383 2877 5315 7261 4085 5234 2344 6570 5904 5400 5454 3524 4406 4611 3470 4805 3961 45
+ 42 * 5138 * * 2487 283 10301 0 3199
+
+L 46 5800 5637 7175 4686 5426 6762 6581 2742 * 1653 4467 4713 5289 5115 6936 4476 5287 2917 5522 4830 46
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+
+L 47 3090 5834 4326 4199 4979 5188 * 2218 5085 2696 * 6355 * 5717 5755 3927 4853 3559 * 3879 47
+ 51 6150 5610 0 * * 0 10302 1014 3215
+
+K 48 4423 6835 4497 6656 3342 5281 4531 3632 4351 4770 7039 5854 5492 5401 3928 3613 3046 5015 5804 2570 48
+ 38 6883 5812 1000 1000 4342 73 10330 1001 3589
+
+Y 49 5119 5420 5574 4574 3475 3433 4405 3765 4388 3631 5834 4848 4168 6724 4255 3525 3216 4354 * 4641 49
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+Y 50 4165 * 3325 5313 3792 3677 3610 5046 4210 4132 6375 3153 * 5274 * 3209 3374 5217 * 3967 50
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+
+S 51 4301 * 3378 4426 4999 3270 4327 6396 3625 4677 7025 3150 4928 6629 4568 2941 3634 5225 4811 6478 51
+ 85 5713 4709 615 1527 2819 220 10332 1131 3964
+
+G 52 3239 6315 4198 3731 6332 3706 5273 5818 3505 4511 * 3228 4745 4373 4492 3159 4265 3722 * 6544 52
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+
+D 53 4077 * 3913 5485 5435 3174 4669 5723 3656 4645 7232 3815 4121 3754 4096 3076 3510 5230 * 4649 53
+ 119 7294 3781 521 1722 3248 160 10253 1125 4265
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+ 1158 915 5530 1672 543 2258 338 10081 6632 4738
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+V 55 4424 6816 3208 3117 4455 3193 6664 5066 5018 4698 6667 4707 3182 3572 4973 5166 4057 4210 * 4613 55
+ 37 5287 * 0 * 2814 221 10269 1245 4277
+
+V 56 3670 * 4156 3097 4893 4417 5641 4806 3750 3504 5549 5868 4856 3993 5249 3752 4775 2805 * 4886 56
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+
+G 58 4011 6427 3488 4130 6436 2932 4570 * 2945 6367 4878 2999 5534 3833 4129 3256 5213 * * 6180 58
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+
+V 59 * * * * 2495 3804 * 4060 * 2788 * * * * 4010 * 4046 2515 * 2008 59
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+
+N 60 3057 * 2903 3324 6780 2215 4919 * 4217 6697 * 3818 4335 5136 5532 3119 5008 6864 * * 60
+ 57 5353 6102 1976 423 2407 301 10490 1380 1573
+
+G 61 6073 5566 4938 5707 * 4408 6751 5832 3103 6827 6539 4980 5720 3802 1189 4340 4361 5791 * 5308 61
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+
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+ 0 * * 0 * 1345 722 10440 1000 1810
+
+E 63 4418 * 6107 4480 4584 * 5448 5700 3675 4073 6145 6060 5350 3349 3974 1893 3022 4485 6745 6558 63
+ 45 5840 6253 1297 754 * 0 10493 1125 1437
+
+A 64 3463 5212 5856 6332 4371 3542 5417 2922 6909 2554 4161 5420 5445 5508 5693 4345 4580 2808 * 7117 64
+ 41 6976 5626 1585 585 2783 227 10529 1027 1762
+
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+
+F 66 4592 * 3894 3916 4140 2822 4850 4499 3944 3590 6415 5431 5529 4700 2997 4443 4235 4050 5627 * 66
+ 148 * 3355 * * 4869 50 10001 0 5842
+
+S 67 * * 2117 4602 6791 5544 4637 5760 3984 3924 * 2945 4550 4485 3707 3551 3825 4687 * 5526 67
+ 294 4509 2832 0 * 630 1499 9868 1287 6327
+
+K 68 4362 * 4147 4040 5695 3510 4833 5124 3253 3429 * 3548 3231 5854 4119 3461 3878 4644 * * 68
+ 117 3858 6803 1559 598 1291 758 10196 1949 4414
+
+S 69 3783 * 3085 4183 5365 3776 5489 * 3693 3775 * 3585 6621 4350 4666 2379 3916 4880 * 6628 69
+ 138 5314 3913 611 1534 3010 191 10250 1449 3265
+
+N 70 4248 * 5484 3473 * 2583 5560 6425 3585 4582 5866 3325 4760 3435 3891 3545 3571 5817 6796 * 70
+ 243 6545 2795 1000 1000 3745 112 10208 1005 3936
+
+S 71 5612 5811 3773 6515 * 2462 4731 6322 3804 6426 4882 3150 6562 4056 3229 3679 3433 4047 * 7012 71
+ 60 4624 * 822 1203 3704 115 10189 1453 5479
+
+S 72 4541 * 3497 4386 4526 4535 * 4372 4362 3958 * 3324 6642 4265 3947 2431 3481 4065 * 6440 72
+ 90 5053 5056 1019 981 646 1471 10250 1447 5215
+
+F 73 2836 4175 * 6612 2934 4375 5619 5570 5135 3974 6021 5578 6838 7109 5067 2748 6919 3534 5114 2972 73
+ 42 5598 6904 0 * 229 2771 10677 1307 3080
+
+H 74 4129 * 5968 4754 5711 6722 4510 3994 5100 7776 5319 3955 5786 4383 4368 2024 2423 4113 * 5230 74
+ 51 5681 6037 1281 765 523 1717 10645 1149 1354
+
+L 75 4854 6562 * * 5014 * * 4034 * 422 5117 * 7151 6609 6741 * * 4242 * 6916 75
+ 11 7004 * 0 * 504 1762 10713 1159 1370
+
+R 76 5037 * 6132 3289 7486 5420 4271 4307 3616 4393 5511 5133 6350 3798 3147 3563 2432 4665 5685 5935 76
+ 21 * 6103 * * 0 * 10661 0 1000
+
+K 77 * * 7217 * 6284 6986 * 912 5045 2252 5148 6346 6950 * * * * 2974 6017 6689 77
+ 0 * * * * 892 1117 10791 0 1166
+
+A 78 4684 4875 5829 5422 6718 5844 4382 5973 3125 3795 7224 4015 3240 3305 3947 2587 3509 6162 * * 78
+ 0 * * * * * 0 10778 0 1000
+
+S 79 2974 6716 3066 4470 * 3164 6494 * 3571 5244 7070 2445 4949 4258 4089 3204 6205 * * 6821 79
+ 0 * * * * * 0 10778 0 1000
+
+V 80 2484 * 6823 6964 5084 5674 5850 3947 6757 2069 6235 * 5144 7201 * 4377 5730 1736 6628 * 80
+ 0 * * * * * 0 10778 0 1000
+
+H 81 4554 * 5017 2839 6114 4040 4663 6621 3789 5965 * 5886 7009 2591 2874 3686 2845 6953 6351 6750 81
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+
+W 82 3761 * 6770 3566 5952 6061 * 5199 4207 2544 5887 6970 3119 4787 3937 3777 4213 3555 3502 7182 82
+ 23 6883 7037 0 * * 0 10675 1000 1000
+
+S 83 4101 7021 3636 2049 6563 4934 6933 6998 3878 5188 * 4460 * 4298 3924 2393 3925 4688 * * 83
+ 0 * * * * * 0 10770 0 1148
+
+D 84 5156 * 542 4158 * 5765 4067 * 5897 6693 6609 5753 * 5557 5282 4997 * 6943 * 6694 84
+ 41 6488 5897 2000 415 * 0 10770 1064 1148
+
+S 85 2393 5508 5468 2783 * 3679 5861 6883 5048 5793 5365 4339 * 5049 4556 2292 3402 5465 * * 85
+ 29 6346 7039 0 * 2090 386 10770 1037 1508
+
+A 86 2548 6218 5312 6963 * 806 6783 * 4693 6573 * 5794 6613 6717 6346 4062 5255 5976 * * 86
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+
+V 87 7244 6976 4949 4485 4902 5248 5145 4073 4879 2707 4579 4271 * 5049 5035 4595 2193 2947 6001 6143 87
+ 40 5193 * 1316 741 1113 895 10753 1681 1677
+
+Y 88 * 6395 * * 3087 6688 5938 5732 * 5476 * * * * * 6590 * * 6492 355 88
+ 19 6975 7589 0 * 1614 571 10662 1001 1296
+
+F 89 5890 * 5667 3675 3148 * 5794 4014 5283 3915 6648 6955 * 6347 3524 3516 2563 4947 4937 2631 89
+ 0 * * 3700 115 639 1482 10671 1000 1318
+
+C 90 6622 198 * * 5948 * * * 6713 4551 * * * * 6580 6718 5582 6839 * * 90
+ 41 5428 7736 771 1272 * 0 10778 1371 1009
+
+A 91 2734 6315 7114 3399 4808 4313 6707 4301 4211 3972 4525 4971 * 3385 4331 3819 3676 3608 * 5708 91
+ 24 * 5949 * * * 0 10777 0 1162
+
+V 92 2583 4883 * 6860 4034 7311 6065 3184 5394 3822 * 6357 6689 6189 5351 3733 7392 1505 * 6601 92
+ 369 3042 3265 886 1124 2212 351 10776 3314 1531
+
+S 93 5286 6433 3112 3689 5481 4281 6213 3638 3807 4743 4550 3979 * 4516 4309 2879 4326 4929 4994 4540 93
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+
+//
+�HHsearch 1.5
+NAME a4ffb81039c95ec205e15ab0095774e5
+FAM
+FILE a4ffb81039c95ec205e15ab0095774e5
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:42:11 2013
+LENG 103 match states, 103 columns in multiple alignment
+FILT 4 out of 6 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 1.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHHHHHHHCCEEEEHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHEEEECCCCCCCEEEEE
+ECC
+>ss_conf PSIPRED confidence values
+9844889998751433254557898888863676069999942896799966872002433507999888899999842434241353489976121555
+059
+>Consensus
+xpqnitxlcxeyxntqiyxlnxxixsyteslagkremviisfxngatfqvevpgsqhxxsqkxxxermkdtlrxayxtxxkixklcvwnnktpnsiaaix
+xxn
+>a4ffb81039c95ec205e15ab0095774e5
+TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAIS
+MAN
+>gi|23263340|dbj|BAC16524.1| ECXB [Escherichia coli]
+TPQNITDLCNEYQNTMIYSLNKEIATYTESLAGKREMVIISFSNGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKISKLCAWTNKSPNSIAAIE
+LSN
+>gi|23263337|dbj|BAC16522.1| CFXB [Citrobacter freundii]
+APQNITELCSEYHNTQIYELNKEIKTYTESLAGYREMVIISFANGATFQVEVPGSQHLESQKRPLERMKDTLRAAYFTGIKVSKLCVWNNKTPNSIAAIE
+LSN
+>gi|224796281|gb|ACN62546.1| CFaB/LTB fusion protein [synthetic construct]
+APQSITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTETKIDKLCVWNNKTPNSIAAIS
+MEN
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 1019 * * * * * * * * * * * * * * * 981 * * * 1
+ 0 * * * * * * 1310 0 0
+
+P 2 * * * * * * * * * * * * 0 * * * * * * * 2
+ 0 * * * * * * 1310 0 0
+
+Q 3 * * * * * * * * * * * * * 0 * * * * * * 3
+ 0 * * * * * * 1310 0 0
+
+N 4 * * * * * * * * * * * 421 * * * 1981 * * * * 4
+ 0 * * * * * * 1310 0 0
+
+I 5 * * * * * * * 0 * * * * * * * * * * * * 5
+ 0 * * * * * * 1310 0 0
+
+T 6 * * * * * * * * * * * * * * * * 0 * * * 6
+ 0 * * * * * * 1310 0 0
+
+D 7 * * 981 1019 * * * * * * * * * * * * * * * * 7
+ 0 * * * * * * 1310 0 0
+
+L 8 * * * * * * * * * 0 * * * * * * * * * * 8
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+
+C 9 * 0 * * * * * * * * * * * * * * * * * * 9
+ 0 * * * * * * 1310 0 0
+
+A 10 1981 * * * * * * * * * * 1981 * * * 1019 * * * * 10
+ 0 * * * * * * 1310 0 0
+
+E 11 * * * 0 * * * * * * * * * * * * * * * * 11
+ 0 * * * * * * 1310 0 0
+
+Y 12 * * * * * * * * * * * * * * * * * * * 0 12
+ 0 * * * * * * 1310 0 0
+
+H 13 * * * * * * 1019 * * * * * * 1981 1981 * * * * * 13
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+
+N 14 * * * * * * * * * * * 0 * * * * * * * * 14
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+
+T 15 * * * * * * * * * * * * * * * * 0 * * * 15
+ 0 * * * * * * 1310 0 0
+
+Q 16 * * * * * * * * * * 1981 * * 421 * * * * * * 16
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+
+I 17 * * * * * * * 0 * * * * * * * * * * * * 17
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+
+H 18 * * * * * * 1981 * * * * * * * * * * * * 421 18
+ 0 * * * * * * 1310 0 0
+
+T 19 * * * 2057 * * * * * * * * * * * 1981 981 * * * 19
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+
+L 20 * * * * * * * 1981 * 421 * * * * * * * * * * 20
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+
+N 21 * * * * * * * * * * * 0 * * * * * * * * 21
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+
+D 22 * * 981 * * * * * 1019 * * * * * * * * * * * 22
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+
+K 23 * * * 1019 * * * * 981 * * * * * * * * * * * 23
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+
+I 24 * * * * * * * 0 * * * * * * * * * * * * 24
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+
+F 25 1981 * * * 1981 * * * 2057 1981 * * * * * * * * * * 25
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+
+S 26 * * * * * * * * * * * * * * * 981 1019 * * * 26
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+
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+
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+
+E 29 * * * 0 * * * * * * * * * * * * * * * * 29
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+
+S 30 * * * * * * * * * * * * * * * 0 * * * * 30
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+
+L 31 * * * * * * * * * 421 1981 * * * * * * * * * 31
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+
+A 32 0 * * * * * * * * * * * * * * * * * * * 32
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+G 33 * * * * * 0 * * * * * * * * * * * * * * 33
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+
+K 34 * * * * * * * * 396 * * * * * * * * * * 2057 34
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+M 37 * * * * * * * * * * 0 * * * * * * * * * 37
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+A 38 1981 * * * * * * * * * * * * * * * * 421 * * 38
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+
+T 41 * * * * * * * * * * * * * * * 1019 981 * * * 41
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+
+F 42 * * * * 0 * * * * * * * * * * * * * * * 42
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+
+K 43 2057 * * * * * * * 981 * * * * * * 1981 * * * * 43
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+
+N 44 * * * * * * * * * * * 421 * * * 1981 * * * * 44
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+G 45 * * * * * 0 * * * * * * * * * * * * * * 45
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+A 46 0 * * * * * * * * * * * * * * * * * * * 46
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+Q 49 * * * * * * * * * * * * * 0 * * * * * * 49
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+Q 61 * * * * * * * * * * * * * 0 * * * * * * 61
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+K 62 * * * * * * * * 0 * * * * * * * * * * * 62
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+K 63 * * * * * * * * 981 * * * * * 1019 * * * * * 63
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+A 64 981 * * * * * * * * * * * 1019 * * * * * * * 64
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+I 65 * * * * * * * 981 * 1019 * * * * * * * * * * 65
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+E 66 * * * 0 * * * * * * * * * * * * * * * * 66
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+R 67 * * * * * * * * * * * * * * 0 * * * * * 67
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+M 68 * * * * * * * * * * 0 * * * * * * * * * 68
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+E 79 * * * 981 * 1019 * * * * * * * * * * * * * * 79
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+A 80 1981 * * * * * * 1019 * * * * * * * * 1981 * * * 80
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+K 81 * * * * * * * * 0 * * * * * * * * * * * 81
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+V 82 * * * * * * * 981 * * * * * * * * * 1019 * * 82
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+E 83 * * 1981 1981 * * * * * * * * * * * 1019 * * * * 83
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+L 85 * * * * * * * * * 0 * * * * * * * * * * 85
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+C 86 * 0 * * * * * * * * * * * * * * * * * * 86
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+V 87 1981 * * * * * * * * * * * * * * * * 421 * * 87
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+N 90 * * * * * * * * * * * 0 * * * * * * * * 90
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+K 91 * * * * * * * * 0 * * * * * * * * * * * 91
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+T 92 * * * * * * * * * * * * * * * 1981 421 * * * 92
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+P 93 * * * * * * * * * * * * 0 * * * * * * * 93
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+H 94 * * * * * * 1981 * * * * 421 * * * * * * * * 94
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+A 95 1981 * * * * * * * * * * * * * * 421 * * * * 95
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+I 96 * * * * * * * 0 * * * * * * * * * * * * 96
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+I 99 * * * * * * * 0 * * * * * * * * * * * * 99
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+
+S 100 * * * 1019 * * * * * * * * * * * 981 * * * * 100
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+M 101 * * * * * * * * * 1019 981 * * * * * * * * * 101
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+
+A 102 1981 * * 1981 * * * * * * * * * * * 1019 * * * * 102
+ 0 * * * * * * 1310 0 0
+
+N 103 * * * * * * * * * * * 0 * * * * * * * * 103
+ 0 * * 0 * * * 1310 0 0
+
+//
+�HHsearch 1.5
+NAME a58e5f77fe5c98ba022ce3bec19b5c22
+FAM
+FILE a58e5f77fe5c98ba022ce3bec19b5c22
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:13:32 2013
+LENG 105 match states, 105 columns in multiple alignment
+FILT 130 out of 1048 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHCCCCCCCEEEEEECCEEEEEECCCCHHHHHHH
+HHHHC
+>ss_conf PSIPRED confidence values
+9799528889999998518981999998899857999999999999987897899997787899999849985228999989979999758997999999
+99759
+>Consensus
+xxxxxxxxxxxxxxlxxxxxxxxvvxfxxxxcxxCxxxxxxxxxxxxxxxxixxxxvxxdxxxxxxxxxxvxxxPxxxxxxxgxxxxxxxgxxxxxlxxx
+lxxxl
+>a58e5f77fe5c98ba022ce3bec19b5c22
+MVKQIESKTAFQEALDAAGDKLVVVDFSATWCGPAKMIKPFFHSLSEKYSNVIFLEVDVDDAQDVASEAEVKATPTFQFFKKGQKVGEFSGANKEKLEAT
+INELV
+>gi|304384645|ref|ZP_07366991.1| thioredoxin-disulfide reductase [Pediococcus acidilactici DSM 20284]gi|304328839|gb|EFL96059.1| thioredoxin-disulfide reductase [Pediococcus acidilactici DSM 20284]
+----LTEEKQLAQILNDF-DAKVAFIFFNPYESQDIDQATKFEN---ALVEkYKVYRQDVSHQTVLFNQLKLNHTVVAALYEHGQL-------tkIINSi
+EELEK----
+>gi|118386291|ref|XP_001026265.1| hypothetical protein TTHERM_01367670 [Tetrahymena thermophila]gi|89308032|gb|EAS06020.1| hypothetical protein TTHERM_01367670 [Tetrahymena thermophila SB210]
+--VAVVSSLNFIKLVQKtKETTktVQVLHFYKMNDGHSTRIAKEVDSLANQYRGiFQFGAVNCGEEPTICEKEKITQFPTVRVYpPLPLPSIDIEVPads
+LVsNDILKLASRYI
+>gi|32491289|ref|NP_871543.1| hypothetical protein WGLp540 [Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis]gi|25166496|dbj|BAC24686.1| grxC [Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis]
+-----------------------VEIYIKSTCSFCVKAKNLLKQNNIKFKEIFVEN-STANLSKMIKRSKKTTVPQIFI--NKVHIG---GYEDLIIFLK
+KN---
+>gi|152967281|ref|YP_001363065.1| alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Kineococcus radiotolerans SRS30216]gi|151361798|gb|ABS04801.1| alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen [Kineococcus radiotolerans SRS30216]
+---PgavVPDQHGERLPLRELWAqGPALLVLVpAAFSTHCTAELGALAFEIERFDAagVQLAALSCDPvtslrawgedrvypfpllsdfwpHGAVSRALG
+AFdedlgvAQRLSLLVVDGTVRWSLRGDLGapRSLKRHLAAL-
+>gi|116694462|ref|YP_728673.1| hypothetical protein H16_B0511 [Ralstonia eutropha H16]gi|113528961|emb|CAJ95308.1| conserved hypothetical protein [Ralstonia eutropha H16]
+--------ASAAQLAASQQGKPFVLVVWSLDCVYCKRNFDTIGKLRAQHPNLRVVTLATDNpdaLPQVQQLLQRVRLT--------RNAWVFGHEPQERL
+RYAVD---
+>gi|325281368|ref|YP_004253910.1| Thioredoxin domain-containing protein [Odoribacter splanchnicus DSM 20712]gi|324313177|gb|ADY33730.1| Thioredoxin domain-containing protein [Odoribacter splanchnicus DSM 20712]
+-MKYIYSFEEALKKARE-VNKPIFVNCFADWAVPCHGMNQLVfsdQQFADWMDRhFVNLFIDIttNEGRPLATKYNTLQMAHYIVLdQDGNLIYRIVGGH
+QlPEFQELLAKSL
+>gi|195052497|ref|XP_001993310.1| GH13139 [Drosophila grimshawi]gi|193900369|gb|EDV99235.1| GH13139 [Drosophila grimshawi]
+-VKELSD-DNFEHLTQASTGattGDWFIFFYSAECVLCQRLYAVWEAVGGTLRRkINVARMNSLTAGmGTAQRLKIAEAPEFVFLRLGKLYRYPLKDyTP
+KAFIEFVED--
+>gi|269119723|ref|YP_003307900.1| NADH dehydrogenase [Sebaldella termitidis ATCC 33386]gi|268613601|gb|ACZ07969.1| NADH dehydrogenase [Sebaldella termitidis ATCC 33386]
+-----NIVKQLKGFFDKITEDIKIISF--lSESDKSKELDSFLNEVADISDSIKYESYMFGSNNKLEELYGIKReTAFTIVK-NNEkTGINFFGIPGgHE
+FNSFVLAIL
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 3634 * * * * * * * 3675 3596 585 3444 * * * * * * * * 1
+ 122 3629 * 2807 222 * * 5913 1069 0
+
+V 2 4434 * * 4524 4033 * 5380 2828 * 2621 2130 * * 5401 * 5414 * 2145 * 5629 2
+ 30 5595 * 1000 1000 * * 9128 1015 0
+
+K 3 * * 5732 3972 * * 4966 1883 3477 4261 * * * 2987 4251 4883 3696 2582 * 5983 3
+ 0 * * * * * * 9559 0 0
+
+Q 4 3865 * 3445 1829 6137 5225 6173 * 3610 * 6322 4015 5265 4250 4035 4690 3589 3823 * 6071 4
+ 25 5873 * 3398 144 * * 9932 1227 0
+
+I 5 4577 * * 4282 4034 * * 2217 * 1687 4240 * * 5219 * * 5409 2206 * * 5
+ 19 6254 * 0 * * * 10110 1015 0
+
+E 6 5376 * 6306 4106 6447 6106 5247 3821 3978 4022 * 3020 5266 3792 5485 3207 2241 3624 * 6338 6
+ 18 * 6372 * * * * 10166 0 0
+
+S 7 4837 5602 2241 3658 * 4257 * 5536 5620 6452 * 2585 5599 5693 * 2644 2629 * 5655 * 7
+ 44 * 5071 * * 0 * 10452 0 1017
+
+K 8 4697 * 3444 3146 4364 4052 5559 4076 3571 3255 6781 5898 3242 4962 5013 4101 4299 4587 4917 * 8
+ 16 6544 * 0 * 0 * 10452 1002 1355
+
+T 9 3156 * 2711 2567 * 4470 5706 6745 2741 3900 * 3868 4792 4746 4726 4226 4927 6608 * * 9
+ 0 * * * * * * 10586 0 0
+
+A 10 3891 * 2665 2608 5165 3010 5983 * 6452 5130 5774 3458 * 3378 5199 4269 3294 6860 * 6960 10
+ 23 5998 * 0 * * * 10676 1196 0
+
+F 11 4075 * 6732 5134 1958 * 6486 3629 4213 2511 6708 * 5791 4893 7009 6538 5296 4058 4750 3040 11
+ 16 * 6528 * * * * 10676 0 0
+
+Q 12 3295 * 2915 2563 5697 6054 4380 4790 4064 4714 6552 3548 5244 3498 4040 4614 4701 5117 * * 12
+ 13 6804 * 2000 415 0 * 10624 1002 1030
+
+E 13 3849 * 3041 2985 6563 5798 4638 4704 2582 4805 6614 4565 * 3165 4730 4080 4327 5406 * 4686 13
+ 13 * 6821 * * * * 10681 0 0
+
+A 14 3130 * 5124 5284 3722 4905 4740 3549 3909 3042 5720 5823 7017 4241 4036 3806 4045 3172 * 6618 14
+ 0 * * * * * 0 10705 0 1010
+
+L 15 4477 * 6917 6969 5993 * * 2491 5799 1356 3603 6533 * 5760 6033 5249 5219 2769 * 6630 15
+ 38 5255 * 715 1356 * 0 10710 1466 1010
+
+D 16 2387 * 3793 3748 5693 4547 6857 5825 2872 3389 5837 4268 * 3855 4208 3397 4532 * * 6489 16
+ 448 5216 2060 490 1797 * 0 10710 1399 1010
+
+A 17 3028 * 3069 2528 * 5726 5505 6405 3453 6605 * 3385 5079 2928 4784 3398 5071 * * 6275 17
+ 214 3378 4591 592 1571 2141 371 10448 2414 5282
+
+A 18 3482 5700 4957 6219 3718 4820 5766 3779 3674 3469 6382 4028 3940 5597 6811 2695 4416 5060 6736 3925 18
+ 239 6583 2814 0 * 337 2263 10526 1000 4947
+
+G 19 3583 * 4158 3344 6619 3899 6684 * 2435 5535 * 3282 4432 3899 3662 3261 4331 5689 * * 19
+ 13 6753 * 4248 78 0 * 10677 1000 4013
+
+D 20 4687 * 3708 3646 * 2208 * * 3097 5904 * 2712 3678 4210 5252 3666 4376 5887 * * 20
+ 34 5986 7105 961 1040 * * 10761 1158 0
+
+K 21 5347 * 3630 3263 6863 5120 * * 1659 * * 4282 4327 3868 3193 4073 5441 5004 * 4511 21
+ 62 5981 5270 1000 1000 0 * 10751 1166 1000
+
+L 22 4892 5869 4902 6924 5194 5745 4512 3961 3591 2888 5826 4976 2526 5185 5897 7034 3966 3023 6030 4101 22
+ 0 * * 0 * 549 1660 10739 1092 1481
+
+V 23 3527 6690 5914 5730 6070 6003 6578 3145 3863 3398 * 4410 * 6951 * 4769 3081 1733 6070 5329 23
+ 39 5211 * 0 * 0 * 10737 1415 1024
+
+V 24 4545 5334 * * 3335 * 6628 2427 * 1868 5057 * * * * 6978 5850 1859 6878 5400 24
+ 0 * * * * * * 10797 0 0
+
+V 25 4359 * * 6007 5298 * * 2216 5912 1796 5922 * * * * 5981 6998 1648 * 5002 25
+ 0 * * * * * * 10788 0 0
+
+D 26 3985 6876 4269 5002 2976 5322 4262 3934 7049 2682 4479 4084 * 4682 6080 5336 6068 4006 * 2710 26
+ 0 * * * * * * 10801 0 0
+
+F 27 5445 4980 * * 974 5967 * 3234 6707 3663 6816 6752 * * 6967 * 6654 4174 5251 3213 27
+ 23 * 5999 * * * * 10801 0 0
+
+S 28 4474 * 6739 * 2887 3667 4402 6028 5787 4902 * 6655 * * 6750 3650 3205 4397 2948 2100 28
+ 125 3587 * 1174 844 * 0 10774 2782 1198
+
+A 29 2513 6874 3828 4198 5399 3733 6715 5300 4419 4625 5254 4982 * 4245 4040 2357 3945 5967 7169 5973 29
+ 26 5808 * 1586 585 0 * 10774 1582 1198
+
+T 30 3491 * 3025 3030 6596 6029 5351 7276 4866 5018 7007 4385 2529 4840 5953 3313 3535 4237 7089 5888 30
+ 23 6760 7264 1000 1000 * * 10801 1069 0
+
+W 31 5781 7092 3356 4386 4669 3346 5415 5408 7041 * 6937 3334 6963 7052 4720 3416 3900 5916 1943 4699 31
+ 24 6739 7105 0 * 0 * 10797 1069 1000
+
+C 32 5568 653 4447 5809 6722 7261 6660 * 5395 5472 * 5411 * 6937 6694 3142 4838 6978 * 6721 32
+ 0 * * * * * 0 10788 0 1000
+
+G 33 3300 7087 4585 3758 5440 2867 4730 4939 3785 4041 * 7040 2283 5609 4947 3887 5513 4402 * 6788 33
+ 0 * * * * * 0 10788 0 1000
+
+P 34 4483 * 4107 3794 4215 4287 3847 5213 4207 4662 4911 5246 3058 4575 6722 4076 4923 4536 7077 2679 34
+ 11 7064 * 4248 78 0 * 10788 1000 1000
+
+A 35 5581 532 5807 7097 6956 5458 7264 7089 7108 * 6813 * * * * 2573 6997 7077 * 5778 35
+ 0 * * * * * * 10801 0 0
+
+K 36 3790 * 4459 3984 6752 7049 4042 4119 2770 4401 5126 5059 4737 3256 2852 4934 4646 4160 7009 6115 36
+ 0 * * * * * * 10801 0 0
+
+M 37 3140 6791 3821 3585 7108 4374 5459 3928 3194 5010 4468 4430 5948 3559 3287 4965 4785 4349 6300 6148 37
+ 0 * * * * * * 10801 0 0
+
+I 38 2670 6813 5938 3709 2734 * * 3486 6816 2392 3645 4683 * 4117 5899 7001 5184 4117 * 5949 38
+ 0 * * * * * * 10801 0 0
+
+K 39 3300 5364 4355 3930 5957 4980 4893 4941 3748 3187 3497 4962 * 4638 3474 3543 5183 4500 * 4232 39
+ 24 * 5944 * * * * 10801 0 0
+
+P 40 4727 * 4270 3538 * 6958 5961 5779 2946 4671 6033 5145 1868 3613 3449 3977 4738 5566 * * 40
+ 23 6958 7053 0 * 0 * 10786 1000 1199
+
+F 41 3165 7200 5384 3241 4450 5207 4851 4486 4165 3669 5784 5171 * 3760 5292 4611 3271 2930 * 4487 41
+ 21 6105 * 966 1035 * 0 10779 1196 1015
+
+F 42 4743 * * * 2504 * * 2940 * 1540 4523 * * * * 6979 5097 3113 4232 3993 42
+ 107 3968 7100 1737 514 * 0 10779 2405 1015
+
+H 43 4747 * 3512 2529 * 4676 5676 5185 3220 4934 5018 3393 4571 3534 3964 3542 5039 4878 7189 * 43
+ 10 7149 * 634 1492 0 * 10775 1182 1183
+
+S 44 3369 * 3547 2530 * 5422 6146 * 2973 4959 4969 3738 5501 3294 3988 3724 4738 4945 6960 * 44
+ 37 7036 5797 1585 585 * * 10801 1000 0
+
+L 45 3284 * 6690 5448 3682 * * 2902 6791 1556 4509 5471 6913 5403 6966 * 5964 2831 4918 6976 45
+ 25 6736 7048 1000 1000 * 0 10759 1023 1263
+
+S 46 1669 * 6957 4303 5537 4644 7170 3877 4791 3832 4748 7189 4184 4485 5491 3063 * 5044 * 3880 46
+ 11 * 7045 * * * 0 10745 0 1461
+
+E 47 3075 6938 3157 3140 * 4676 5868 5402 3089 5171 6823 3359 4914 3636 3725 3696 4870 7080 * 6912 47
+ 0 * * 0 * 409 2018 10739 1000 1618
+
+K 48 3571 * 3203 2944 * 5453 5003 4609 2612 3583 5027 4402 5557 3773 5337 3729 4399 * 6952 7059 48
+ 51 5196 7077 1727 519 * 0 10788 1431 1012
+
+Y 49 5246 6033 * 7033 2866 6957 3797 4371 7156 2646 4984 4183 * 5790 6800 4165 4469 3489 5340 2395 49
+ 53 6063 5553 1574 591 991 1009 10784 1205 1217
+
+S 50 3835 * 3483 3351 * 4033 5326 * 3047 * * 4665 2672 4098 3549 3571 3944 4735 * 6863 50
+ 78 4240 * 1498 630 0 * 10787 2092 1496
+
+N 51 3964 * 2703 3427 5962 3067 4611 6980 3028 7097 * 2767 4467 4615 4505 3936 6028 7000 6679 * 51
+ 1448 658 * 783 1255 * * 10801 9166 0
+
+V 52 3694 5517 * 5422 3618 6767 * 1898 5866 2463 7072 7077 * * * 5933 3865 2460 6046 5412 52
+ 12 * 6925 * * * * 10801 0 0
+
+I 53 4391 6288 3645 3540 5036 5361 4511 6363 2940 4257 5815 4564 6969 4737 3839 4759 3150 3050 * 4860 53
+ 0 * * * * 0 * 10785 0 1012
+
+F 54 5116 5270 * * 1656 * 5290 2855 * 3228 5495 6102 7216 * 5842 5300 * 2478 4800 4169 54
+ 104 4534 5238 5765 27 * * 10801 1854 0
+
+L 55 3437 5323 * 4721 4745 4870 5792 2948 4660 2850 4961 5869 * 6729 5029 * 4904 2899 * 2392 55
+ 23 6944 7026 2000 415 * 0 10768 1000 1500
+
+E 56 3826 6954 6199 4097 4629 3681 6748 4594 3564 4025 4151 5018 4549 4439 3540 3718 4233 3660 5302 4689 56
+ 11 * 7082 * * 385 2095 10764 0 1676
+
+V 57 3932 5867 * * 6196 7091 * 2037 * 2430 4031 * * 5695 5943 6979 5996 1697 * 4697 57
+ 10 * 7192 * * 1090 915 10791 0 1198
+
+D 58 5964 6078 1584 3577 5852 5408 5419 7042 7377 * 6956 2328 5000 5580 6883 2974 4695 5683 * 5578 58
+ 77 5068 5492 5107 42 * 0 10775 1593 1207
+
+V 59 3164 4106 5277 6609 4493 4594 7165 2997 5184 3121 6875 6667 6764 5869 4888 3442 3980 2519 * 5291 59
+ 101 4273 5997 3186 168 2319 323 10767 2191 1765
+
+D 60 6070 * 1356 2732 6893 4202 6809 * 5320 4584 * 3499 5284 5895 6726 3094 5430 * * 5324 60
+ 116 4003 6076 3096 179 620 1518 10757 2302 1925
+
+D 61 4792 * 2832 2985 * 5332 4462 4917 3182 4460 5998 3716 5985 3834 4263 3792 3635 4973 6779 6073 61
+ 225 2794 * 4098 87 1981 421 10751 3936 1568
+
+A 62 3735 6870 3370 3656 4730 3803 3079 5429 5026 4029 * 2753 5418 4982 5962 4178 4941 4274 7032 5014 62
+ 50 5232 7083 2261 337 1683 538 10760 1610 1380
+
+Q 63 4266 6763 3893 3860 4785 3482 5490 6802 4109 4232 5337 3783 2379 4034 3760 4285 4628 6826 * 6724 63
+ 119 4015 5848 3176 169 0 * 10776 2195 1384
+
+D 64 3482 * 3372 2277 6693 4151 5358 4917 3514 5022 6948 4826 3905 4766 4107 3742 4325 5709 * 5871 64
+ 23 6004 * 3993 94 * 0 10779 1163 1387
+
+V 65 4437 6003 5254 4401 3333 7188 * 2656 5452 2002 4699 6074 6903 * 5449 7057 3833 2908 5915 6026 65
+ 12 * 6970 * * 1444 661 10779 0 1387
+
+A 66 2137 3629 6974 4995 3343 4464 * 3405 6669 3742 4387 5893 5539 6038 4949 4354 7060 3392 5155 5955 66
+ 19 6262 * 2150 368 594 1567 10791 1148 1362
+
+S 67 3704 * 3403 3108 * 5363 * 5444 2302 5559 5786 4164 5974 3760 3390 3623 3830 7184 6939 5967 67
+ 36 6629 6094 1000 1000 * 0 10797 1049 1000
+
+E 68 3547 * 4702 3339 5800 6910 * 4673 2752 4452 5870 4116 5725 3135 2900 4974 3237 6863 * 5075 68
+ 42 5597 6930 3580 126 1594 581 10774 1324 1376
+
+A 69 4035 * 5346 4706 2172 * 5454 5137 4972 2653 4874 7053 6879 4996 6765 * 5628 6068 6018 1884 69
+ 47 4959 * 2144 370 569 1617 10773 1593 1381
+
+E 70 4437 * 3366 4009 * 1900 6629 5781 3124 5961 6906 3127 4903 4287 4919 3977 4616 * 6103 6900 70
+ 42 5603 6886 0 * * 0 10797 1297 1000
+
+V 71 4142 5798 7192 5498 5983 6099 * 1864 * 3354 7139 4657 4223 5915 6044 6868 4652 1751 7091 6846 71
+ 51 5222 6945 2884 210 950 1052 10779 1443 1198
+
+K 72 3977 6899 5029 3098 3762 4542 4164 * 3530 4437 4929 4523 4703 4080 4138 3706 2994 4546 * * 72
+ 123 3921 5982 3418 142 1007 993 10782 2413 1182
+
+A 73 3198 6964 5012 4662 4909 2735 4640 4859 4460 4959 5963 5272 5897 5407 4331 2212 4000 4656 * 5211 73
+ 81 4741 5848 2243 342 1540 608 10769 1741 1406
+
+T 74 4446 6017 * 5854 3847 7042 6051 3340 5931 2372 5901 7020 5189 6563 * 6682 2919 2153 6652 3614 74
+ 0 * * * * 958 1043 10738 0 1609
+
+P 75 5319 * * 6703 * 6591 6897 * 7189 5251 * * 228 * 5407 6791 5881 6646 * * 75
+ 52 4827 * 825 1199 932 1071 10775 1625 1203
+
+T 76 3457 5000 5802 5404 4532 6041 4683 7039 5966 4728 4920 6852 * 4688 6190 2982 1605 3622 6922 4699 76
+ 11 * 7068 * * 0 * 10797 0 1000
+
+F 77 4047 * * 6732 2703 6695 * 3050 * 1856 4826 6895 6984 * 6765 5809 3553 2660 5931 4988 77
+ 23 * 5989 * * 0 * 10788 0 1012
+
+Q 78 4267 7037 * 6056 3355 6382 5651 2747 5093 2481 4629 * * 4802 5405 * 5655 2250 5915 3445 78
+ 0 * * * * 755 1295 10785 0 1286
+
+F 79 4150 5849 * * 2452 6967 5449 2415 7034 2407 5371 * * 7028 6620 4722 * 2413 6101 4418 79
+ 93 6954 4205 2585 263 * 0 10783 1010 1004
+
+F 80 5587 6557 6652 5315 2544 5279 6920 2634 6776 2569 6865 5381 * * 6835 5439 5906 3584 6600 2220 80
+ 580 1720 5184 169 3178 2994 194 10753 6226 2289
+
+K 81 3441 * 4638 2820 6903 3958 4838 5026 2485 5906 * 3884 4643 4101 3337 5075 5859 4343 * 5003 81
+ 36 5902 6984 1000 1000 322 2320 10718 1192 2672
+
+K 82 5581 * 1943 3302 7006 3739 4932 * 3139 4918 7057 2333 5463 5867 4227 4960 5943 6966 * * 82
+ 25 6799 6932 1461 651 603 1549 10786 1211 1372
+
+G 83 4338 6523 4376 5557 6216 1005 7004 * 5007 6842 6693 3597 4805 4727 4489 4213 5016 * * 5994 83
+ 16 6523 * 3000 193 976 1024 10779 1037 1189
+
+Q 84 6068 * 3674 3359 7000 4988 5562 7255 2862 5937 6981 2852 5878 2977 3115 3857 3661 4861 * * 84
+ 56 4705 * 789 1247 * 0 10784 1684 1000
+
+K 85 5066 6691 * 2915 4537 5578 6931 3104 3769 3011 4521 5935 3828 * 3920 5707 5323 2535 7139 5519 85
+ 50 7073 5248 2000 415 * 0 10784 1000 1000
+
+V 86 4932 * 5054 5734 5158 4572 * 2787 5017 3112 4172 5964 4985 5281 4343 4650 3975 2093 * 4607 86
+ 63 5237 5954 445 1915 2242 343 10733 1400 1678
+
+G 87 3245 5771 3225 3523 4624 4102 4145 4019 3225 4071 6880 4919 4730 4851 6123 7070 4942 4373 5865 3939 87
+ 34 5444 * 2819 221 2034 404 10742 1350 1845
+
+E 88 3968 * 4983 3866 6950 4206 * 4028 3927 5286 5974 4185 6682 3660 2123 4144 4709 3138 * 5420 88
+ 36 6961 5910 0 * 501 1770 10757 1030 1601
+
+F 89 4748 5892 4233 4385 2824 5163 3393 3414 4402 3638 5391 7268 6128 7060 5015 4600 6968 3954 5406 2849 89
+ 22 6051 * 1886 455 * 0 10736 1229 1453
+
+S 90 4297 6874 4727 3849 3995 4633 5084 3326 4961 4453 6873 4768 5416 4842 4732 3459 3374 2707 6860 4917 90
+ 54 5138 6876 1000 1000 650 1463 10736 1413 1453
+
+G 91 3691 * 3644 4000 5337 1079 5985 * 4353 5396 * 4430 7129 5017 6086 5246 5909 5282 * 5281 91
+ 23 5984 * 940 1063 * 0 10737 1191 1234
+
+A 92 3883 6872 5911 3942 4171 5883 * 3789 5380 3336 5963 4310 3076 4923 4412 3530 4241 3536 6815 3744 92
+ 195 3080 6902 595 1565 0 * 10703 3460 1234
+
+N 93 4369 * 3356 4821 6020 4886 5268 5244 3858 3697 4709 3149 3724 6997 4097 2903 3818 4583 * 4982 93
+ 50 4886 * 1233 799 0 * 10729 1623 1000
+
+K 94 3685 6868 4362 3506 5774 4461 5855 4562 4242 7015 7131 5024 2193 5943 4418 3127 3599 4278 * 5314 94
+ 1158 857 * 198 2965 * 0 10725 8419 1032
+
+E 95 3883 * 3044 1995 7144 4889 5205 6065 3594 5924 5393 3666 4356 4600 4919 3515 4182 6682 * * 95
+ 0 * * * * * 0 10713 0 1032
+
+K 96 3919 * 2882 2468 5206 6051 5283 6959 3558 4799 5946 3857 6682 3081 5487 3706 3763 5255 * 6825 96
+ 28 5698 * 1024 976 0 * 10713 1452 1032
+
+L 97 4559 * * 6547 3286 6758 * 1896 * 1528 4595 * 5784 * * 7123 5664 3462 5271 5899 97
+ 12 6906 * 0 * * * 10711 1000 0
+
+E 98 4861 6946 4565 2780 5507 6849 4758 4149 3071 2993 5080 5045 * 3637 4196 4078 4606 3743 7043 5399 98
+ 0 * * * * * * 10698 0 0
+
+A 99 3229 * 3697 2660 * 5763 5957 5195 3350 4620 6598 3104 5923 3628 4392 3925 3511 6661 * 5474 99
+ 0 * * * * * * 10698 0 0
+
+T 100 2976 6619 * 4481 2633 * 5977 4031 4056 2514 4735 6991 * 5066 5578 5860 5137 3874 3617 4241 100
+ 0 * * * * * * 10694 0 0
+
+I 101 4038 * * * 5022 * * 1888 5773 1456 6156 * * * 6704 6867 5871 2450 * 5431 101
+ 39 5214 * 642 1478 * * 10692 1376 0
+
+N 102 3505 * 2611 2485 * 5869 4866 * 3499 4466 * 4082 * 4274 3420 3363 4171 5713 * 6862 102
+ 0 * * * * * * 10554 0 0
+
+E 103 3020 * 3856 3299 4834 5624 5502 5673 2467 5024 * 4029 * 3239 3037 3963 5446 6526 * 6578 103
+ 0 * * * * * * 10508 0 0
+
+L 104 2893 6076 * 6395 3855 * 4047 2862 5294 2139 * 4678 * 5450 4720 4787 5209 3606 * 3763 104
+ 0 * * * * * * 10312 0 0
+
+V 105 4723 * * * 4610 * * 2662 5690 925 4036 * * * * 5551 * 4745 5600 3697 105
+ 0 * * 0 * * * 9481 0 0
+
+//
+�HHsearch 1.5
+NAME a7297e082b04c39b5ed5edf7a5889375
+FAM
+FILE a7297e082b04c39b5ed5edf7a5889375
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:31:46 2013
+LENG 228 match states, 228 columns in multiple alignment
+FILT 130 out of 1369 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEECCCCCCEECCCCCCCEEEEECCCCCEEEEEECCCCCCCCEEEEEEEEC
+CCCCCCCCCEEEEEEEECCCCCCCEEECCCCCCCCCCCEEEEEEEECCCCCCCEEEEECCCCCCCCCCCEEEEECCCCEEEEEEEEEECCCCCCCEEEEE
+EEECCCCEEEEEEEEECCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9289586858997899899999964888888679999928999828999995368850215666873899853778713799825740026679999970
+6874412212677786112125413414874200379858999994465799769998898435763110358629978999999995145579779999
+9948898679999920679899898999
+>Consensus
+xxxxxxpxxxxvxxGxxvtLxCxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxsLxIxxvxxxDxGxYxCxvxx
+xxxxxxxxxxxxlxVxxxxxxxpxvxxxxxxxxxxxgxxxxlxCxxxxxxPxxxxvxWxxxxxxxxxxxxxxxxxxgxxxxxsxlxixxxxxdxgxyxCx
+vxxxxxxxxxxxxxxxxxxxxxxxxxxx
+>a7297e082b04c39b5ed5edf7a5889375
+QVQLQQPGAELVKPGASVKLSCKASGYTFTSSWINWVKQRPGQGLEWIGNVYPGSSSTNYNEKFKNKATLTVDTSSSTAYMQLSSLTSDDSAFYYCVRKD
+YSWFPYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCN
+VAHPASSTKVDKKIEPRGPTIKPCPPCK
+>gi|2707433|gb|AAB92274.1| T-cell receptor gamma chain Vg2-Jg1 [Gallus gallus]
+---------ITMSRVNT-DLKCHFKdfSGNFDNTVIHWYQQKENKAPVRMIYFTSG--RTKVNESFQRhRYRIQTIPTQRLCTLTIRNVIPDDAATYYCA
+YWDprRILLQSFRLWYKAHCIRQRKFSTREL---------------------------------------------------------------------
+---------------------------------
+>gi|149632037|ref|XP_001512632.1| PREDICTED: similar to T cell receptor gamma chain [Ornithorhynchus anatinus]
+---------------------------------------------------------------------------STVSGVKYFGTGTKLVVTGFKHCaL
+QsGAYIKVFGSGTKLIVENTtpqln-----DPIQFYPTSLERKqQNTETYVCLFKDFFPDVIRMHWKEEgsdKILESQ-QSDPLPVNGKYWQMSWLTVKK
+SPP-GKIYRLIYKHEK-t-GPAGKEE--------------
+>gi|334323375|ref|XP_001366403.2| PREDICTED: butyrophilin subfamily 2 member A2-like [Monodelphis domestica]
+QFTVVAPAKPLlVMVGEDAILHCHLFPKKNAEQmEVRWFRSQFSPAIY--VYKDGKNRDEEQMEEYRSRTTFMRDNiKDGSVALKIHNVTAFENGRYHCY
+FQEG---RSYDEAFIDLKVASMGSDPLIEI-----TGYEYGWIQLECTSAGWYPQP-RVEWrnLSEETIPSLEENLVPSEDGLFIVKLSVNITDHT--VV
+SVFCSIQNSLLSQELLAMMSIPE----------
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+--------------------------------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne--DLRSWTAADMAAQN----------
+----tqrkweaagvaeqw----RAYlEGECLEWLRRYLEKGK-----------------et--LQ--raEPs-SQSTIP-----
+>gi|190340181|gb|AAI62589.1| Mcam protein [Danio rerio]
+--------------KGQAKISCTYT-LTEEAKMIIWFtkLPGKDQNRKRFYYSENQT--eiIDQNHEYAERIKVSHS-----YDteeergsvvLILDDVQ
+LTDEREFICMVHSvLN--DVGEGRTHLKIY--NSPSLPVIERE-----htgisvsETEPSKVAQCKVDDGYPRP-NITWyKGSfpldPSDGEVKILESVT
+VkpSGLFRVESELHIKVKKEDeGAHFYCEVKYLMLGKARMTESSR------------
+>gi|189235128|ref|XP_972469.2| PREDICTED: similar to sticks and stones CG33141-PA [Tribolium castaneum]
+---VATSENVVVNPNEDATLSCTADGNPLSDDTITWKR---DDFPDFD-----------------ARtSVMYDK--NGTSYLRITDVTRDDLGNFQCIVN
+NG-----VGNVTTKEVMLIVKHKPEIDQHPalLKFASDAGDTGRVVCRSQAS--PLAKYKWarSGAPITANTTGkyYTTYRQiDALTSESVLFITHVTSS
+DYGNYECVARNELGFATASPRLEVTSAPDTP-----
+>gi|317419334|emb|CBN81371.1| MAM domain-containing glycosylphosphatidylinositol anchor protein 1 [Dicentrarchus labrax]
+------PSEIVASPNTNATLPCNVT------FPLSVTGDKIDKSLIKVSWISNGSDIASFSEaatQIKEGFSWDTSDFvNGDFSLTVLRAGLDLQGLYKC
+TVGYNFTMLQYRNVTLSILASPTLSIPQLWVVLETESHLK-------CHADGFYPPPVYFSWtRDGQVIQPPYDVEGEQSpDGYYMAVGNLTFYPSREDq
+NVTFGCKVSHNGSYQELDFQLN-------------
+>gi|301618640|ref|XP_002938728.1| PREDICTED: tapasin-like [Xenopus (Silurana) tropicalis]
+------SATLYARLGHPLAVPCGFWRGQQSRFAVEWRHRALGDGSVLYAYDGRLDRIEEIFQGCEMNFSTL--HSHGNASLLVDKVAVSDHGTFLCTIYL
+P--YIRAQRDMQLEVT----ALPVVTFLPDPLFARPGEEITLSCEVSRFHPLEISVDLlvrfpgDSQfSVLPGVSLSTHTLNkDGTFSLTASLSITASPE
+RhGARYFCKVRHVSAPEGITRS---------------
+>gi|297303273|ref|XP_001086428.2| PREDICTED: matrix-remodeling-associated protein 5 [Macaca mulatta]
+---------ITAMAGHTISLNCSAA----------------GSPTPSLVWVLPNG------TDLQSGQQLQRFYHKADGMLHISGLSSVDAGAYRCVARN
+A-----AGHTERLVSLKVGLKPEANKQYHNLVSIINGETLKLPCTPPGA-GQG-RFSW---TLPNSMRLEGPQA-LGRISLLdnGTLEVREASVfDRGTY
+VCRm-ET-------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+Q 1 4197 * 2731 2488 * 3196 * * * * * * 4116 1563 * 4138 4197 * * * 1
+ 0 * * * * * * 6919 0 0
+
+V 2 * * * 5263 3572 5117 * 4282 5376 1908 5169 4976 * 5023 * 3730 * 1619 * 5177 2
+ 0 * * * * * * 8451 0 0
+
+Q 3 5203 * 5408 5648 5386 4623 5329 5529 2736 3670 * * * 3198 4664 3604 3828 2062 * 4347 3
+ 0 * * * * * * 8853 0 0
+
+L 4 4892 * * * 4681 * * 3205 5839 1588 4962 * 5972 5907 5887 4335 3421 2034 * * 4
+ 50 4864 * 2613 258 * * 9200 1172 0
+
+Q 5 4970 * 5181 3557 * 6840 5922 5181 5286 3872 * 4268 * 2876 4878 3023 2215 2754 * * 5
+ 0 * * * * * * 9398 0 0
+
+Q 6 3180 * 5806 4636 * 4926 6292 5065 3213 4171 * 5144 4453 2347 4366 3592 3535 3259 * * 6
+ 93 3999 * 0 * * * 9486 1497 0
+
+P 7 5034 * 6103 4522 6383 6089 5141 * 5848 5367 * 4403 828 5902 5939 3438 3666 * * * 7
+ 82 4176 * 0 * * * 9782 1481 0
+
+G 8 2981 * 4280 3313 * 3455 * 6347 3730 4668 * 5258 2836 4832 5366 2820 3373 5294 * 6167 8
+ 51 4842 * 425 1969 * * 9816 1245 0
+
+A 9 3699 * 3606 3656 5236 6324 6393 6220 4330 3932 * 3657 5377 3367 5493 2255 3517 3996 * * 9
+ 33 6646 6321 0 * * * 9797 1000 0
+
+E 10 5437 * * 3671 * 6326 6742 2791 4953 2164 4897 * 5371 4374 6308 4688 4198 1969 * 6763 10
+ 0 * * * * * 0 9968 0 1001
+
+L 11 5031 6140 3991 3413 5439 * * 4242 4415 4840 5557 6148 5631 6762 3794 2576 2727 2741 * 4810 11
+ 47 4951 * 0 * 0 * 10029 1306 1001
+
+V 12 2443 * * * 6622 3455 * 3833 5011 3709 4484 * 6472 5567 5335 4493 5731 1514 * 5508 12
+ 0 * * * * * * 10124 0 0
+
+K 13 4346 * 6913 4184 5114 6194 6523 6658 3088 3746 4112 5829 5715 2887 3376 3184 3854 3492 5042 7025 13
+ 0 * * * * * * 10111 0 0
+
+P 14 3923 * 5489 1932 * 6743 * 5145 4201 3134 6810 * 3092 5341 3790 4488 4085 3531 * 5022 14
+ 0 * * * * * * 10227 0 0
+
+G 15 * * 5915 5536 6859 365 * * 4381 * * 4422 * 4655 * 4895 * 6820 * * 15
+ 0 * * * * * * 10144 0 0
+
+A 16 4610 6743 3057 2421 * 3030 5806 * 3352 5694 * 4549 * 2916 5281 3127 4042 6779 * * 16
+ 0 * * * * * * 10119 0 0
+
+S 17 4818 5709 3361 4542 * * 5671 * 4799 5707 * 3777 3036 4059 5158 2323 2245 4765 * * 17
+ 13 * 6848 * * * * 10145 0 0
+
+V 18 2039 * * * 4518 6031 * 4353 * 3189 4216 * * * * 6148 5260 1200 * 6682 18
+ 0 * * * * 0 * 10144 0 1000
+
+K 19 5244 * 6873 4859 5877 6705 * 3439 4386 4523 * 5028 5524 4553 4255 3267 1478 3571 * 5260 19
+ 0 * * * * * * 10159 0 0
+
+L 20 6820 * * * 3509 * * 2950 6753 617 4161 * * * * * * 4138 * * 20
+ 0 * * * * * * 10159 0 0
+
+S 21 7139 * 3689 5402 5777 5464 5158 5890 5204 4009 5274 3576 2373 4935 3485 3020 2955 4656 * * 21
+ 0 * * * * * * 10159 0 0
+
+C 22 5935 85 * * 6926 6416 * * 6753 * * * * * * 6415 * * * * 22
+ 12 6924 * 0 * * * 10159 1000 0
+
+K 23 4723 * 4432 4524 5383 4090 3972 5993 3147 4724 * 3966 4215 4849 3279 2754 3399 4761 * 5386 23
+ 21 6933 7248 1000 1000 * * 10159 1000 0
+
+A 24 3140 * * * 2985 6661 6546 3269 6687 2657 * 6911 4602 5811 * 4829 4985 2375 * 2827 24
+ 91 4881 5208 1350 719 * 0 10160 1435 1000
+
+S 25 6841 * 3225 3270 5709 4373 6694 6776 4166 5045 * 3549 3647 4135 5735 2910 2386 6283 6637 5627 25
+ 181 3890 4303 1356 714 572 1610 10126 2085 1456
+
+G 26 3870 6689 4378 4110 * 1635 5489 6562 5856 5214 5756 3513 3695 5710 3767 4030 4653 5738 * 5550 26
+ 159 6664 3405 0 * 814 1213 10206 1000 1899
+
+Y 27 5139 * 5564 4117 3246 3615 3734 6451 4358 3964 5697 5225 3405 4270 6420 3291 3610 4288 * 3896 27
+ 87 * 4089 * * 122 3623 9982 0 2721
+
+T 28 4530 6496 3626 3928 5956 4788 * * 3329 4073 * 5142 2424 5016 3717 2927 3548 5096 * 5652 28
+ 195 6581 3107 1000 1000 1869 462 10207 1001 1865
+
+F 29 4050 5566 4181 3277 5079 4252 4864 5661 6363 3527 * 4776 2840 5637 4756 3704 4606 3966 * 3182 29
+ 389 5157 2262 1424 673 2568 266 10010 1233 3522
+
+T 30 4504 * 2913 4603 6456 3163 6463 6353 4627 4520 * 4380 3477 4454 3589 3299 2918 5257 * 5341 30
+ 114 4323 5263 850 1168 3140 174 9854 1489 5661
+
+S 31 * * 2230 3904 * 3971 3848 4758 4690 3553 * 4094 3947 4024 4007 3688 5082 3803 * * 31
+ 234 2983 5444 616 1524 277 2517 9713 2352 5456
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+E 215 * * 3809 2355 * * 5672 4896 4311 4517 * 2686 5825 3460 2782 3075 4668 5744 * * 215
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+P 223 * * * * * * * 3318 * * * * 391 * * 2864 * * * * 223
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+C 224 * 1039 * * * * * * * * * * * * * 2783 2387 2499 * * 224
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+P 226 2708 2499 2801 * * * * * * * * * 1391 * * * 2783 * * * 226
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+C 227 * 592 * * * * * * * * * * 1572 * * * * * * * 227
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+K 228 * * * * * * * * 791 * 1244 * * * * * * * * * 228
+ 0 * * 0 * * * 1589 0 0
+
+//
+�HHsearch 1.5
+NAME a7d85b5797fc7c87d5f26fc1eaa87af7
+FAM
+FILE a7d85b5797fc7c87d5f26fc1eaa87af7
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:10:44 2013
+LENG 151 match states, 151 columns in multiple alignment
+FILT 104 out of 109 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
+HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9976431478716743512248999999999999873266755313688789646775404799999999998725444354452333066479999999
+985871588845629999999999998760789999889999999999709
+>Consensus
+xxxxxxxxxxxCxlxxxxxqxxxixxxxxxixxxxqxxDxxxxvrLLxxxllxxxkxxxxCxxxxxlLxFYLexVxxpxaxxxxpxixxxvssLaxlxxx
+LxxCxxxxxcexxxxxvxxikxxfxkLxxxgxxKAiGELDiLlxwiexxcx
+>a7d85b5797fc7c87d5f26fc1eaa87af7
+QGGAAAPISSHCRLDKSNFQQPYITNRTFMLAKEASLADNNTDVRLIGEKLFHGVSMSERCYLMKQVLNFTLEEVLFPQSDRFQPYMQEVVPFLARLSNR
+LSTCHIEGDDLHIQRNVQKLKDTVKKLGESGEIKAIGELDLLFMSLRNACI
+>gi|78127838|gb|ABB22222.1| Ov2.5 [Ovine herpesvirus 2]
+--ERVLPLRGNCKLLL---QDTVIPNLLYSMrsifqdIKPYFQGKDSLNNLLLSGQLLEDLQSPIGCDALSEMIQFYLEEVM-PQAEIHHPKHKNSVMQL
+GEtlhtLISQLQECTALFPCKHKSLGAQKIKEEVSKLGQYGIIKAVAEFDIFINYMES---
+>gi|335295319|ref|XP_003357467.1| PREDICTED: interleukin-24-like [Sus scrofa]
+----------PCRVEGIVLQELW--EAFWDMKDVVQAQDNITNVRLLRKEVLQNVSEAESCYLIHSLLKFYLNTIFKNYREKAvKFRILRSFSTLANnfv
+vIMSKLQPSqenEMFPISENARRRFLLFQREFKQLDrEVALTKAFGEMDILLTWMETF--
+>gi|194354137|gb|ACF54622.1| interleukin 10 [Larimichthys crocea]
+------------------------------------------------------FKTPFACHAINSILDFYLATVL-PGAlagvTEDTKSMKPHMESIQq
+ifdQLKNDVTACRHYFHCKNQFD-ITNLNSTYTQMQSKGLFKAVGELE-----------
+>gi|293341320|ref|XP_001058779.2| PREDICTED: rCG46376-like [Rattus norvegicus]gi|293352718|ref|XP_001060482.2| PREDICTED: interleukin 19 [Rattus norvegicus]gi|149058680|gb|EDM09837.1| rCG46376 [Rattus norvegicus]
+------------------------------IRRTLQTKDTFKNVTILStLENLRSIKPVDVCCVTNNLLTFYRDRVFKDHQE-TSLEVVRRISRIANsfl
+hMQKTLEQCvHRQCHCsQEATNATRTIHDNYNQLEvSSAALKSLGELNIFLAWIDR---
+>gi|7542405|gb|AAF63435.1|AF202534_1 interleukin-10-like protein [Cercopithecine herpesvirus 5]
+-------------------------------RETLQTKDTVYYVSLFHEQLLQEMLSPVGCRVTNELMQHYLDGVL-PRAfhcgyDNTtLNALHFLSSSL
+STLYQHMLKCP-ALACTGQTPAWTQFLDTEHKLDpWKGTVKATAEMDLLLNYLETF--
+>gi|282174062|ref|YP_003358164.1| ORF25 [Anguillid herpesvirus 1]gi|281308905|gb|ADA57788.1| ORF25 [Anguillid herpesvirus 1]
+----------------------------------------------------EHLHGPESCSVIDELITHHTKCVI-PAANEEeGADL-LSLDTLQvale
+NVKGLLANCQEEFGCKPPFS-MRDYKKQYRQLNkekNAGMIKAMGELGMLFNGIEE---
+>gi|212549595|ref|NP_001131083.1| interleukin 22 [Xenopus (Silurana) tropicalis]gi|156148266|gb|ABU54058.1| interleukin-26 [Xenopus (Silurana) tropicalis]
+--------------------------------KELFPKDNITDIQFLTEELKQDFMAQKNCNLRNNFLSFYIKTFLekPPVQEKA-KKL-KIIQDLMVIQ
+DMLLHCKKS-HCDHKETGIKsltELKIKIRQINgNKVLWKAISEMDTLLEWIYE---
+>gi|40555956|ref|NP_955041.1| CNPV018 IL-10-like protein [Canarypox virus]gi|40233781|gb|AAR83364.1| CNPV018 IL-10-like protein [Canarypox virus]
+------------------------------------GRDNDLSYMLLQ-GVRETHKKPCGCYVLYLLLSFYRKTIRDTIQSNKHASINAELTNLAvsvlS
+LEDLLDACGITCN-PKKDSLLKRIEEYMKEHGDDAIYKLIGEIEFLFQAIER---
+>gi|66472836|ref|NP_001018628.1| interleukin 22 [Danio rerio]gi|56044561|dbj|BAD72867.1| interleukin 22 [Danio rerio]gi|169154277|emb|CAQ13398.1| novel protein similar to interleukin 22 (il22) [Danio rerio]
+--------------------------------DTARNEDD-HETRLLPYFSHDMLQEEGSCCINARILKYYVNHVL-ESDEHtdmKYPMIRNVREGLHRV
+EQELQnHCKHDYS-SH--PLVKQFKRNYHAsaiMDlAAARNKAIGETNTLYHYLFESCT
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 2501 0 0
+
+G 2 * * * 3705 * 1367 * * 2036 * * * 2679 2880 * * * * * * 2
+ 0 * * * * * * 2501 0 0
+
+G 3 4003 * * 1870 * 919 * * * * * * * 2887 * * * * * * 3
+ 0 * * * * * * 2918 0 0
+
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+
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+
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+
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+
+S 9 * * * * * 3508 * * * * * 2112 * * 2086 1536 3316 * * * 9
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+
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+ 0 * * * * * * 3304 0 0
+
+H 11 2623 * * * * * 2666 * * * * 2443 2683 3731 3316 2602 * * * * 11
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+
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+
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+
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+
+N 18 * * 1892 * 3450 * * * * * * 1042 * * * * * 2704 * * 18
+ 0 * * * * * 0 3322 0 1478
+
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+ 52 * 4813 * * 285 2482 3322 0 1478
+
+Q 20 * * * 2740 * * * * * 2935 * * * 475 * * * * * * 20
+ 95 * 3971 * * 0 * 3948 0 1111
+
+Q 21 * * 3443 1862 * * * * 4142 3618 3908 * 4209 1795 * * 5263 4064 * * 21
+ 260 * 2600 * * * 0 4088 0 1041
+
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+ 0 * * * * 1732 517 4018 0 1276
+
+Y 23 * * * 2399 2965 4414 * * 4657 * * 3702 * * * * * 3452 3594 1536 23
+ 125 * 3594 * * 0 * 4153 0 1176
+
+I 24 * * * * * * * 437 * 2847 3033 * * * * * * * * * 24
+ 0 * * * * * 0 4347 0 1091
+
+T 25 * * * 3470 5341 * * 4534 2597 * * 4269 3580 4358 1872 * 3508 5323 3234 * 25
+ 0 * * * * 0 * 4347 0 1091
+
+N 26 4544 * 5042 2679 * * * * 3051 * * 933 * 3594 * 4528 * * * * 26
+ 0 * * * * * * 4375 0 0
+
+R 27 2762 4492 * 3680 * 2848 5387 4058 * 3331 * 4227 * * 2146 3549 * 5459 * 5619 27
+ 0 * * * * * * 4375 0 0
+
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+ 0 * * * * * * 4430 0 0
+
+F 29 * * * * 1667 * * * * 3140 * * * 3584 * 2593 4590 * 2735 2934 29
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+
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+
+L 31 * * * * * * * 1487 * 1817 2898 * * * * * * 2150 * * 31
+ 85 4132 * 2585 263 * * 4731 1083 0
+
+A 32 1581 * * * * * * 4335 1576 * * * * 5609 2353 4872 * 5042 * * 32
+ 0 * * * * * * 4945 0 0
+
+K 33 4497 * 2424 2925 * 5260 4003 * 1992 * * 2889 * 3565 3929 * 6303 * * * 33
+ 0 * * * * * * 5203 0 0
+
+E 34 2341 * * 2521 * * 4851 5652 5158 5955 5547 5459 4649 3467 6150 3906 2238 4333 * 6269 34
+ 0 * * * * * * 5453 0 0
+
+A 35 1641 * * * 4590 * * 3026 * 3456 4361 * * * * 4963 3661 2092 * 5073 35
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+
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+
+A 38 2983 * 5242 2390 * 4247 * * 2140 5919 4003 6287 * 3511 3849 3225 5563 * * * 38
+ 0 * * * * * * 5780 0 0
+
+D 39 * * 264 * * * * * 3558 * * 4779 * 5323 5563 * * * * * 39
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+
+N 40 * 5932 1934 3436 * 5157 6363 * 4584 * * 2329 4822 5986 4466 4646 2549 4593 * * 40
+ 41 * 5161 * * * * 5810 0 0
+
+N 41 6401 * 1969 3385 3759 * 6077 1861 5776 6705 7144 3855 * 3247 * 5324 * 4691 * * 41
+ 17 6381 * 1000 1000 0 * 6051 1000 1065
+
+T 42 * * * 6092 * * 4551 3903 3061 1932 4246 * 5025 4238 5294 * 1767 * * 4709 42
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+
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+ 0 * * 0 * * * 3390 0 0
+
+//
+�HHsearch 1.5
+NAME a9670fd5e42b822d83bb9b8a9eda5dc0
+FAM
+FILE a9670fd5e42b822d83bb9b8a9eda5dc0
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:21:05 2013
+LENG 143 match states, 143 columns in multiple alignment
+FILT 106 out of 692 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCEEEEECCCCCEEEEEEEEECCCCEEEEEECCCCEEEEEEECCCEEEEEECCCCEEEEEEECCCCCEEEEEEECCHHHHH
+HHHHCCCCCCCCEECCCCCCCCCCCCCEEECCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9886657632101325676743467759898899999996899769999799999999950221137996599999998603779889799977999999
+9998599942218144523677877517864788640142339
+>Consensus
+pxxxxxgxknxxxxxxxxxxxxxexxxpxexexxgxVxxxlGnxxfxVxxxdGxxxlaxIpGKmRKrIwIxxGDxVlVexxxxdxxKgxIvxRyxxxqvk
+xLxkxgxxpxxfxxxexxxxxxxxxxxxxxxxxxxxxxxxxxx
+>a9670fd5e42b822d83bb9b8a9eda5dc0
+PKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVILKYNADEAR
+SLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI
+>gi|170291061|ref|YP_001737877.1| S1 IF1 family protein [Candidatus Korarchaeum cryptofilum OPF8]gi|170175141|gb|ACB08194.1| S1 IF1 family protein [Candidatus Korarchaeum cryptofilum OPF8]
+-----KRKEDREEVERSLDAEMEELLPADELEIFGRVLEPLGKGHFRVECIDNLIRICRVRGKLRgRRAWIKRGDIVLISLWPFQRTKGDIVVRYDRQQV
+EWLIEKGYIPR-dWATleeg-----------------------------
+>gi|20138737|sp|Q9HP87.2|IF1A2_HALSA RecName: Full=Translation initiation factor 1A 2; Short=aIF-1A 2
+---------------MSDESGRRNLRMPNDDEVFAVVKRHDGGNHVTLQCEDGKERMGRIPGRMKYRTWINEGDVVLAEPWDWQDEKANVEWRYSDQDAD
+QLREEGHIE----------------------------------
+>gi|198427951|ref|XP_002130036.1| PREDICTED: similar to eukaryotic translation initiation factor 1A domain containing [Ciona intestinalis]
+----ATKRKHVIKEVLEN------FSMPAPDQTIVKVLGNSGSNLHEVITPSGERFLASLPVKFRKNIWIKRGDYVITEP---iIeGDrvKGEIVRILYA
+QHIKEIKICKMWPKEFE------------------------------
+>gi|115450283|ref|NP_001048742.1| Os03g0114200 [Oryza sativa Japonica Group]gi|27476090|gb|AAO17021.1| Hypothetical protein [Oryza sativa Japonica Group]gi|108705834|gb|ABF93629.1| LOC496359 protein, putative, expressed [Oryza sativa Japonica Group]gi|113547213|dbj|BAF10656.1| Os03g0114200 [Oryza sativa Japonica Group]gi|125542126|gb|EAY88265.1| hypothetical protein OsI_09718 [Oryza sativa Indica Group]gi|215765975|dbj|BAG98203.1| unnamed protein product [Oryza sativa Japonica Group]gi|222624072|gb|EEE58204.1| hypothetical protein OsJ_09157 [Oryza sativa Japonica Group]
+----KAGRKNLRRACSEG------AVTLGEGESIMQVLALRGSNVIEVMDAKGVKSLALFPAKFQKSFWIKNGNFVVVDAsgRDQalEsGSkiACVVSQV
+LFHDQVRAMEKSEEWPAIFKS-----------------------------
+>gi|303285654|ref|XP_003062117.1| predicted protein [Micromonas pusilla CCMP1545]gi|226456528|gb|EEH53829.1| predicted protein [Micromonas pusilla CCMP1545]
+----------------------ELCPELNDGDAVCRVVELRGGNQVQVEKPDASTTLIRIPSKFSKVLWVRKGSHVLAHFEEDATSdaanggargskvTG
+ELLRVLYAEQIKELRRARpeAWPERFG------------------------------
+>gi|332250254|ref|XP_003274267.1| PREDICTED: probable RNA-binding protein EIF1AD-like [Nomascus leucogenys]
+---------------------LGEHIVPSDQQQIVRVKRQP--SLGDRTTSYGFGF------PYCKQaclpfLFLPTGDFLIVDPIEEGeKVKAEISFVL
+CKDHVRSLQKEGFWPEGFS------------------------------
+>gi|322511287|gb|ADX06597.1| putative eukaryotic translation initiation factor eIF-1A [Organic Lake phycodnavirus]gi|322511357|gb|ADX06665.1| putative eukaryotic translation initiation factor eIF-1A [Organic Lake phycodnavirus]
+--------------------TTNKLRLSnDEDELYAVVTKMLGNSQCHVVTLHGQTLLCIIRkkftGKHKHQHFLKSGSWVLVGLRNWEtiqsDkmAKCD
+LLECYSENDKQTICKQSDLNVETLIQE---------------------------
+>gi|310831445|ref|YP_003970088.1| hypothetical protein crov455 [Cafeteria roenbergensis virus BV-PW1]gi|309386629|gb|ADO67489.1| hypothetical protein crov455 [Cafeteria roenbergensis virus BV-PW1]
+PGQKQKGKKNVRRTKT-----RFELIEPSKGQLIAEVEDTHGGYPPRFSCktVDGDIIIAPIQGSIMkgpKRVLVKKDNLVLLVPIDFTTGKEgttsyYI
+HHVYTSEDRHQLEKKGFLEKKDKISDA--------------------------
+>gi|330819201|ref|YP_004348063.1| Translation initiation factor IF-1 [Burkholderia gladioli BSR3]gi|327371196|gb|AEA62551.1| Translation initiation factor IF-1 [Burkholderia gladioli BSR3]
+------------------------------LELDGVVDEVLPDSRYRVTLENGAVVGAYASGRLKKnHIRILAGDRVRLEMSMYDLTKGRINYRHKDERA
+--------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+P 1 * * * * * * * * * * * * 0 * * * * * * * 1
+ 0 * * * * * * 2762 0 0
+
+K 2 2794 * * * * 2313 * * 612 * * * * * * * * * * * 2
+ 0 * * * * * * 2762 0 0
+
+N 3 * * * * * * * * 2794 * * 612 * 2313 * * * * * * 3
+ 0 * * * * * * 2762 0 0
+
+K 4 * * * * * * * * 572 * 2258 * 3079 * * * * * * * 4
+ 0 * * * * * * 3023 0 0
+
+G 5 3602 * * * * 1288 * * 2230 * * * * 3223 * 2411 * * * * 5
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+//
+�HHsearch 1.5
+NAME aa7797cb86715b5f00dd396459cdd380
+FAM
+FILE aa7797cb86715b5f00dd396459cdd380
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:26:11 2013
+LENG 191 match states, 191 columns in multiple alignment
+FILT 154 out of 304 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCCEEECCEEEECCCEEEEEEEEEEE
+EECCCCCCCCCCCEEEEEEEEECCCCCCCHHHHHCCCCCCCCCCCCCCEEEEEECCEEEECCCCEEEEEECCCCCEECCCCCEEEEEEEEC
+>ss_conf PSIPRED confidence values
+9467777765552033146898755467898379998068756654476554333378735786547887522158589899999753709999999999
+6325886555687028999997789886236762567775079887351677660238925999999997895507118997199999929
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxkpaaHLxgxxxxxxxxxxxxxxxxxxxxxxxlxWxxxxxgxaxxxgxxxxxgxLxVxxxGlYyVYSQVxF
+xxxxxxxxxxxxxxxlxhxvxxxxxxxxxxxLlxxxxtxcxsxxxxxxxxsxyxGgvfxLxxGDxLxVxvsxxxxvxxxxxxTfFGxfxlx
+>aa7797cb86715b5f00dd396459cdd380
+MILRTSEETISTVQEKQQNISPLVRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYF
+RFQEEIKENTKNDKQMVQYIYKYTSYPAPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG
+>gi|47225327|emb|CAG09827.1| unnamed protein product [Tetraodon nigroviridis]
+-------------------------ENPTCKKFCHLEICNLKECKTKPPKS--FNVSAANYLQWDIQ---HSFLRDIGYyHNVWLTVQQSGDYYVYSRVT
+FSKGD-------PRVPLASMIKMrKNeTDKEEKTVMQAYCSLTdQSGTQIPQLCTATQGEVVTLESGNQLSVWVQDLSLVDYEEGATTFGMYKL-
+>gi|310788577|gb|ADP24261.1| tumor necrosis factor alpha [Haliotis diversicolor]
+---------------------------NLLKPVAYLTGLDFDGRIE---SE-----NDTFVRNWVPFVahGGRQLMsNGMRYDHGSIIVPTPGVYAVESH
+VKFYTENNR--RRETEIDFHHSIMRYNAiKQTSQPALADIMSENKNdvIEGGCLEYSSNIHGLLELNAGDQLIVKVSHLKPLQHDRDWHYFGLYMV-
+>gi|197210937|gb|ACH48393.1| Eda [Maylandia zebra]
+-----------------------------QPAVVHLQGQETT---IQVR-EDLS---QGILKNWKMVS-IHHRVFKMHSRTGQLEVLLDGVYFIYSQVev
+YYLNFTD----------IASY--D--VMVDSSPFLRCTCSIET---GQRKFNTCYTAGVSPLRAGQKIYIRIAHEYtLINMTNHTTFLGSVRLG
+>gi|115719327|ref|XP_001204312.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]gi|115801769|ref|XP_799917.2| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
+-------------------------MRQEGEPSAHVVPLISPNAQQNNNFY--P---TSAWFVWTDQV--NRISHaTIPLSNtgKFLLAPHSGYYFIYSQ
+VTLES--CNND--SDTDGRGHSLYVKTTcgRDTEQELTYTVTTPY-NRNLGCTYDTGYIGGVYYLEQHDHVGVKPYvppgsMRSRIFLKLSNSYFGMILI
+S
+>gi|198413177|ref|XP_002126703.1| PREDICTED: similar to tumor necrosis factor [Ciona intestinalis]
+------------------------------------------------------------VVVWEHAN-GAGTTsrKGFDVSGGNITVNSEGVYYMYLHT
+TFRTN---GNPRTRSRRISHKvLVNNS----PIELLGEKRDLGEDDT----IQTLDSLMTYVLEKENRLTIELEKPDYMSVstNPSETYFGIFKL-
+>gi|68534978|ref|NP_001020390.1| tumor necrosis factor receptor superfamily member 8 [Sus scrofa]gi|61338439|gb|AAX43996.1| tumor necrosis factor ligand superfamily member 8 [Sus scrofa]
+------------------------------------------------------------KLSWNKDG----IIHGVRYHDGNLVIQFPGWYFIICQLQF
+LVKCPEH-SV--DLKLELLINENVKK-------QTLVTVCESGVQTkSIYQNLSQFLLEHLQVNTTISVNVDKFQYVNTNTfpLENVLSIFL--
+>gi|83921653|ref|NP_001033075.1| tumor necrosis factor beta [Takifugu rubripes]gi|66391027|dbj|BAD98729.1| tumor necrosis factor beta [Takifugu rubripes]
+------------------------------------------------------------NRSWQEFH-S----g-gscSFVHHEGSIHCRKNSLYFLYA
+QVAFTKHASQT--RSKS----VILVRNPaDdKS-l-RKLAEGTF----PPTTE---GSVWVANVVRLKEDDTISINITGEVlS-----DITLWGAFEL-
+>gi|115496536|ref|NP_001070075.1| tumor necrosis factor ligand superfamily member 12 [Danio rerio]gi|115313437|gb|AAI24496.1| Zgc:153941 [Danio rerio]gi|158253868|gb|AAI54256.1| Zgc:153941 [Danio rerio]gi|305678684|gb|ADM64322.1| tumor necrosis factor superfamily member 12 [Danio rerio]
+---------------------------NGRKVASHFEITSDS--F--QKVGN-----EGVIKGWTEEQ--LNMSRAVNYnsETGTFRVERSGVYFVYCQV
+HFNEN------------QSQYVKLEVSIPKGPLLqcIEGYGTTPASGSHRFHFlKPCQVSGLLRLNKGTELK-AVTGASFSLQTSGKHYFGLFKVN
+>gi|157822647|ref|NP_001100348.1| CD70 antigen [Rattus norvegicus]gi|149028135|gb|EDL83573.1| similar to Tumor necrosis factor ligand superfamily member 7 (CD27 ligand) (CD27-L) (CD70 antigen) [Rattus norvegicus]
+-----------------------------------------------------------LTLRWGAGPaLGRSFTHGPGLEKGNLRIHQDGIYRLHIQVT
+LAN--CSSSGSAlqHRASLVVGICS--PAVHIISLLRRrFGQDCTVSLQ----------RLTPLARGDVLCSNLTQPLLPSRNADETFFGVQ---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 3538 * * 2544 * * * 2639 * * 3107 * * * * 2947 * 1573 * * 1
+ 0 * * * * * * 3196 0 0
+
+I 2 * * * * * * * 3079 * 2458 2301 * * * * * 1573 2639 * * 2
+ 0 * * * * * * 3196 0 0
+
+L 3 2681 * 3746 2641 3777 * * * * 1687 * * * 3197 * 3098 * * * * 3
+ 167 3197 * 4248 78 * * 3196 1013 0
+
+R 4 * * 3408 * * * * * 2018 * * 2452 * 3615 2025 2747 * * * * 4
+ 0 * * * * * 0 2969 0 1013
+
+T 5 * * * * * * 2764 1902 * * * 3293 * * 2059 3897 2506 * * * 5
+ 0 * * * * * 0 2969 0 1013
+
+S 6 * * * * 2018 * * 2697 * 2381 * * * * 3810 4167 * * * 1837 6
+ 0 * * * * * 0 3187 0 1013
+
+E 7 * * * 1558 * * * * 3468 3810 * * * 1538 * 2697 * * * * 7
+ 0 * * * * * 0 3187 0 1013
+
+E 8 * * 3161 2414 3468 * * * 1129 * * * * * 2708 * * * * * 8
+ 0 * * * * * 0 3187 0 1013
+
+T 9 * * 3810 1270 * * 3655 * * * * 4042 * 3740 * 4014 2075 * * * 9
+ 0 * * * * * 0 3187 0 1013
+
+I 10 2714 * * * * * * 1217 * * * 3468 * * * 4014 2697 3173 * * 10
+ 1360 712 * 787 1251 * 0 3187 1773 1013
+
+S 11 * * 3173 3655 * 3468 3740 * 3623 * * 3565 * * * 1062 * * * * 11
+ 119 * 3655 * * * 0 3187 0 1013
+
+T 12 1411 * * 2267 * * * * * * 3410 * * * 3916 * 2597 3464 * * 12
+ 0 * * * * * 0 3104 0 1118
+
+V 13 2385 * * * * * * 3948 * 1858 3464 * * * * * 3738 1726 * * 13
+ 151 3334 * 1000 1000 755 1295 3104 1048 1118
+
+Q 14 * * * 2824 * 3810 * * 4133 * * 4042 3314 4167 1241 3468 * * * * 14
+ 0 * * * * * 0 3187 0 1013
+
+E 15 * * 2175 1496 * 4140 * * * * * * * 4242 2904 3796 4051 4369 * * 15
+ 0 * * * * * 0 3432 0 1013
+
+K 16 * * * 2693 * * 4051 * 1242 * * * * 4399 * 3060 2958 3912 * * 16
+ 78 4245 * 1000 1000 * 0 3432 1036 1013
+
+Q 17 * * * * * * * 3896 4369 2413 4071 * 3003 2090 4399 2446 * 4421 * * 17
+ 0 * * * * * 0 3432 0 1013
+
+Q 18 * * * 4245 3912 * * 1768 * 2689 * * * 2744 * 3235 3104 * * 4051 18
+ 99 * 3912 * * * 0 3432 0 1013
+
+N 19 * * * * * 1701 4192 * * 4276 * 1991 3740 * 3149 3511 * 4077 * * 19
+ 0 * * * * 755 1295 3356 0 1118
+
+I 20 * * * * * * 4220 1814 * 2424 * * 3912 4203 * 4140 2382 3235 * * 20
+ 0 * * 2895 208 * 0 3432 1073 1013
+
+S 21 * * * 4526 * * * * * 2044 * 3095 2172 4538 * 3323 2599 * * 3896 21
+ 0 * * * * * 0 3703 0 1013
+
+P 22 4279 * 4059 4086 * 4223 4538 * 4207 * * 4517 1107 * 4050 4526 * * 3896 * 22
+ 0 * * * * * 0 3703 0 1013
+
+L 23 2599 * * * * * 3347 * 4526 2650 * 3075 2777 * * 2743 4050 4068 * * 23
+ 396 3896 2533 1000 1000 * 0 3703 1095 1013
+
+V 24 3242 3650 * 2836 * * * * * 2379 * 3823 1961 * * 4321 4227 4285 * * 24
+ 598 1559 * 1832 476 0 * 3297 1344 1317
+
+R 25 * * * 3249 * 4770 * 3936 2507 * * * * 2840 1664 4162 3690 5136 * * 25
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+
+E 26 3354 * 3748 2428 5369 2291 * 4801 4894 5140 4271 3585 5251 4077 * 3825 5362 * * * 26
+ 275 2525 * 1048 953 1563 596 5152 1611 1140
+
+R 27 3503 * 5560 4624 4504 4702 4298 5897 2931 4989 5666 5100 6170 5623 2253 2511 3856 * * * 27
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+
+G 28 * * 5592 3203 * 3529 * 5469 4095 * 5564 2442 3177 3511 5668 2444 5140 4612 5218 * 28
+ 0 * * * * * 0 6457 0 1073
+
+P 29 4514 5501 5125 3465 * 4158 5547 4396 4913 3719 6585 2885 3253 * 4422 3270 2794 6686 * 5270 29
+ 48 4945 * 647 1468 0 * 6664 1400 1073
+
+Q 30 2704 5658 4310 5050 6073 3829 4932 5366 5981 3499 5252 4427 3309 3179 3586 3517 5352 7009 * 6296 30
+ 0 * * * * * * 6823 0 0
+
+R 31 * * * 4934 6204 6125 6915 5940 1161 4969 * 4649 3305 4478 2637 4729 6191 5170 6680 * 31
+ 37 5321 * 4144 84 * * 6844 1083 0
+
+V 32 2968 * * * 5162 6552 * 3099 4673 5530 * * 1140 * 7032 3706 * 3328 * 5772 32
+ 0 * * * * * * 6844 0 0
+
+A 33 969 * * * 4027 4376 5932 * * 6268 5616 * * * 5767 3075 5717 2524 * * 33
+ 0 * * * * * * 6844 0 0
+
+A 34 627 4726 * * * * * 2707 * 6071 * * * * * 5967 5341 3235 * * 34
+ 0 * * * * * * 6844 0 0
+
+H 35 5932 * * * * * 91 * * * * * * 6006 * * * * * 5107 35
+ 0 * * * * * * 6844 0 0
+
+I 36 6695 * * * 3853 * * 4058 * 655 5932 * * * * * * 2253 * * 36
+ 0 * * * * * * 6844 0 0
+
+T 37 4969 * * 2946 * * 6623 2501 * * * * 6194 4165 * 4056 1390 2831 * * 37
+ 119 3654 * 1386 696 * * 6844 1569 0
+
+G 38 3248 * 4598 * 6798 587 * 3991 * 4977 * * 5070 5919 * 5703 5744 * * * 38
+ 79 4543 6604 610 1537 * 0 6851 1207 1108
+
+T 39 3183 4891 3442 4406 6299 5881 5883 3854 3569 4010 * 3148 6696 4322 4078 2830 4862 5713 * 5097 39
+ 292 4338 2900 0 * * 0 6842 1222 1159
+
+R 40 4110 7173 4460 4272 7016 4152 6899 4458 4293 5152 * 3144 2903 4829 4486 3506 3678 5906 5587 3176 40
+ 58 * 4677 * * 3424 141 6825 0 1913
+
+G 41 5659 * 4111 3747 4511 3319 5288 5505 4982 3808 5567 2671 6563 6576 4260 2109 3956 7486 * * 41
+ 71 6595 4738 0 * * 0 6783 1048 1968
+
+R 42 3844 * 4959 3407 * 6174 6301 * 3365 4526 * 5854 2684 3222 3160 2400 5746 4758 * * 42
+ 470 3614 2349 631 1498 2792 225 6750 1293 2105
+
+S 43 4315 * 3894 3246 * 2947 * 5542 4030 5011 * 3459 6387 3105 3926 2943 3942 6857 * 4470 43
+ 648 5037 1594 943 1059 2268 336 6234 1063 2754
+
+N 44 4064 4731 4284 5090 5732 3357 5730 4955 4285 4389 5677 3236 4682 * 4990 3575 2912 3358 * 4480 44
+ 183 * 3072 * * 2757 231 5832 0 3275
+
+T 45 3829 * 4352 * 3078 3325 5947 3121 3946 2978 4577 * 5796 4109 * 3822 3303 * * 4330 45
+ 226 5395 3043 2240 343 2120 377 5828 1167 3172
+
+L 46 3492 * * 4556 5558 5256 * 3812 * 4628 4122 4317 2438 4371 * 2608 2524 5005 * * 46
+ 263 * 2585 * * 3139 174 6069 0 2932
+
+S 47 5379 * 4214 4079 5233 5358 4929 * 3846 2163 5138 3907 3441 3270 5827 2817 4796 * * * 47
+ 189 * 3027 * * 3116 177 5977 0 3157
+
+S 48 2926 * 5671 5685 * 6080 3890 2766 * 3605 4450 3178 3996 3773 4419 4066 4613 3672 * * 48
+ 47 * 4957 * * 3851 104 5963 0 3201
+
+P 49 5095 * 4642 2972 * 5596 5871 6167 2356 5918 * 3200 1553 5026 4554 * 5898 * * * 49
+ 276 5662 2695 1000 1000 1500 629 6082 1024 3134
+
+N 50 4672 6830 4526 4904 4206 6237 5555 5549 4221 6085 * 3291 5983 3993 3408 2034 4347 2961 * * 50
+ 318 3346 3330 1843 471 3811 107 6250 1421 2755
+
+S 51 * * * 3226 4749 2330 * 5515 * 4437 4679 5458 4389 4650 3388 2112 5741 5470 * 3807 51
+ 544 * 1670 * * 5052 44 6193 0 2923
+
+K 52 3121 * 2555 4689 4524 5366 4769 * 2733 * * 3432 2405 * * 3839 5358 * 4457 * 52
+ 475 * 1833 * * 5354 36 5609 0 3564
+
+N 53 * * 4665 3360 * 2468 * * * 1172 * 4553 3926 * 4685 * * * * 3453 53
+ 209 5248 3200 2322 322 3280 157 4960 1036 3930
+
+E 54 * * 5164 5703 3251 3598 3071 * 4022 * * 4566 3374 3192 2316 2880 * * * * 54
+ 261 * 2593 * * * 0 5270 0 3761
+
+K 55 * * * * * 2842 * * 2259 * * 2976 * 1327 2991 * * * * * 55
+ 77 * 4263 * * * 0 4743 0 3956
+
+A 56 4341 * * 4875 4654 5423 4250 * 5660 * * 5118 4637 * 4384 1947 4609 1779 * 3786 56
+ 86 * 4107 * * 2900 207 4605 0 3997
+
+L 57 * 2698 4695 * * 4261 4991 5814 5126 2586 4836 2540 3602 5519 4390 4334 5263 4086 * 5858 57
+ 183 * 3070 * * 1002 998 5363 0 3718
+
+G 58 5122 * 4299 4623 * 1469 5319 5581 3665 * 5479 5462 * 4810 3033 4341 3294 6338 * 5199 58
+ 194 * 2988 * * 2365 311 6522 0 2605
+
+R 59 3999 * 3991 4196 5468 2685 3191 * 4301 5879 * 3570 6056 3310 4138 4044 3603 5282 * 4672 59
+ 41 * 5154 * * 1610 573 6488 0 2661
+
+K 60 4615 6172 6830 5181 5811 3656 7077 5897 2139 6151 * 3422 2874 5321 4505 3238 3659 3999 * * 60
+ 270 5130 2816 1953 431 932 1071 6796 1069 2214
+
+I 61 4655 * * 6257 6419 6550 5348 2707 3805 2762 5514 5780 * 4109 5479 4191 3495 2223 6100 4815 61
+ 38 6518 6029 0 * 206 2913 7403 1000 2121
+
+N 62 * * 6772 6810 4265 5166 7522 4674 4821 1147 6293 4386 * 4983 3585 5797 4307 3226 6243 7267 62
+ 0 * * * * 494 1785 7512 0 1186
+
+S 63 4850 7359 4161 3190 5914 5067 3888 6103 5046 4450 6637 3433 4792 3279 3398 2846 4204 4744 7436 5947 63
+ 0 * * * * 0 * 7539 0 1012
+
+W 64 * * * * * * * * * 6060 * * * * * * * * 22 * 64
+ 0 * * * * * * 7549 0 0
+
+E 65 4133 * 3806 1946 5198 5415 6080 5762 3610 5733 5494 4017 * 4086 3627 5709 3853 3529 * 5125 65
+ 0 * * * * * * 7549 0 0
+
+S 66 4193 6882 3622 3220 * 4042 3953 5749 3616 6173 5963 3586 3296 4096 5165 3263 3732 4927 7152 8792 66
+ 47 6887 5403 1000 1000 * * 7549 1000 0
+
+S 67 4473 * 2517 4656 4298 3485 5609 6616 3367 7573 4693 3440 6091 3544 4595 3395 3846 5957 * 6124 67
+ 25 * 5859 * * 653 1457 7519 0 1085
+
+R 68 5195 * 3726 4806 6930 3298 3806 7030 4767 4004 7110 4533 4319 2965 3502 3507 3752 3901 7465 5522 68
+ 2448 3945 412 738 1320 * 0 7521 1393 1126
+
+S 69 2424 * 5699 * 3244 3518 * * 3477 3960 * * 3144 4678 4027 3177 * 4558 * 3627 69
+ 478 4511 2071 1000 1000 427 1965 5734 1016 5247
+
+G 70 5021 * 2595 3852 * 821 * 5616 * 5607 6187 5986 * * 6670 4809 4591 6505 * * 70
+ 172 6394 3311 1585 585 495 1784 7059 1006 2735
+
+H 71 4198 * 5161 4315 * 5254 3304 7464 4662 2675 7189 3437 4539 3060 3180 5943 5486 6375 4021 4225 71
+ 0 * * * * 830 1193 7309 0 2135
+
+S 72 1338 6189 4801 5110 6946 4053 6577 6544 6662 7080 * 6540 4408 5168 6639 1856 5884 5889 * 6226 72
+ 23 6801 7124 2000 415 667 1433 7431 1000 1484
+
+F 73 * * * 6392 1394 5739 3104 4604 6001 3053 5596 4328 4917 7148 5139 4276 3787 7194 6246 6338 73
+ 39 5717 6967 692 1393 1176 843 7559 1059 1188
+
+L 74 4831 4440 5905 6968 5934 5795 * 4014 6123 1702 3575 7009 6210 5667 * 4019 2498 3240 * 7196 74
+ 342 2243 * 293 2444 * 0 7579 2433 1150
+
+S 75 5649 5705 4470 4750 5760 4688 3114 * 3487 * 6824 3178 5783 2653 3212 2612 5661 6014 * 6215 75
+ 372 2137 * 632 1495 0 * 7593 2515 1150
+
+N 76 4599 * 3852 5139 7057 1248 4031 * 4429 5343 * 2765 6488 6247 5260 4175 5273 * * 5544 76
+ 148 3363 * 370 2145 * * 7679 1653 0
+
+L 77 6259 * * * 1980 * * 3108 6906 2567 2168 * 5891 * * * 6317 2534 * 5999 77
+ 12 6878 * 1585 585 * * 7652 1004 0
+
+H 78 4876 * 5258 3273 * 4351 4081 6296 2738 6550 6921 4335 5887 3801 2997 3246 2918 4454 * * 78
+ 0 * * * * * * 7681 0 0
+
+L 79 5042 6635 * 6892 3129 6945 5161 4848 * 1580 5668 7348 7065 * * 5377 6879 4083 * 1705 79
+ 185 3054 * 281 2497 * * 7681 1816 0
+
+R 80 7012 * 3073 3487 7038 6272 3306 5915 3204 5013 5591 4286 5833 4293 2971 2905 4133 4386 * * 80
+ 62 4860 6991 557 1642 * * 7693 1257 0
+
+N 81 4926 * 1843 3360 * 3321 5989 * 4663 * * 1738 * 6513 5694 4350 4657 6514 7365 * 81
+ 22 6071 * 704 1373 0 * 7688 1062 1006
+
+G 82 7465 * 5664 5357 * 861 4679 * 4589 * * 2580 * 5025 4417 6954 4705 6605 * 5835 82
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+
+E 83 5379 * 7091 2541 5516 3816 4601 7442 3065 5650 * 3879 * 3509 3566 2725 4830 4635 6591 4632 83
+ 9 7275 * 0 * 0 * 7681 1000 1000
+
+L 84 7061 * * * 5818 * * 1747 * 687 * * * * * * * 4171 * * 84
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+
+V 85 4931 * * 3494 * * 5009 2802 3906 3644 6521 * * 4358 3416 7111 2654 2134 * 6626 85
+ 11 7061 * 1000 1000 * * 7693 1024 0
+
+I 86 5575 5832 * * * * * 1369 * 5022 * * * * 7061 * 7419 915 * * 86
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+
+H 87 6593 * 6442 4138 7073 6244 3811 7041 4388 3817 * 3462 1502 3320 3913 6780 4740 5304 7020 6233 87
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+
+E 88 5333 7755 4993 2308 5795 6399 4742 * 3300 4794 7453 7591 * 2342 3019 3614 3716 4532 * * 88
+ 0 * * * * * * 7693 0 0
+
+K 89 3552 * 2838 3325 * 4781 * * 4912 * 7338 5032 2611 5956 * 2317 2409 * * * 89
+ 0 * * * * * * 7693 0 0
+
+G 90 7031 * * * * 29 * * * * * * * * * 6363 * * * * 90
+ 0 * * * * * * 7693 0 0
+
+F 91 * * 4830 * 3240 * * 3306 5670 1450 * * * 5709 5090 * 3818 3027 5795 3157 91
+ 0 * * * * * * 7693 0 0
+
+Y 92 * * * * 5517 * * * * * * * * * * * * * * 32 92
+ 0 * * * * * * 7693 0 0
+
+Y 93 5847 * * * 1409 * 5765 6953 6289 3144 * 5910 * * 5938 6188 6644 * 6031 1390 93
+ 0 * * * * * * 7693 0 0
+
+I 94 * * * * 6626 * * 1543 * 2904 6634 * * * * * * 991 * * 94
+ 0 * * * * * * 7693 0 0
+
+Y 95 * * * 6723 4537 * 5938 5293 * * * * * * * 6289 * * * 164 95
+ 0 * * * * * * 7693 0 0
+
+S 96 2418 3535 * * * 5166 * 4896 * 4515 6399 6991 7061 * * 866 4818 6626 * * 96
+ 0 * * * * * * 7693 0 0
+
+Q 97 * * * * 5778 * 3149 * 3715 * * 5205 * 447 5295 7191 * * * * 97
+ 6 * 7964 * * * * 7693 0 0
+
+T 98 3757 * * * * * * 2663 * 2606 5341 * * * * 6668 3509 1054 * * 98
+ 33 5453 * 1000 1000 * 0 7698 1166 1000
+
+Y 99 5129 4083 6447 6036 6462 4383 4518 6893 5139 3530 6974 5047 * 4250 * 2932 2267 4444 * 2442 99
+ 0 * * * * * 0 7698 0 1000
+
+F 100 * * * * 680 * * 6754 * 3360 * * 6893 * * * 6864 5815 * 2094 100
+ 32 6634 6407 0 * * 0 7698 1037 1000
+
+R 101 4571 4563 6035 5088 5682 * 4311 5279 3853 3813 6474 4458 * 5277 1629 3662 4412 5873 * 3539 101
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+
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+ 82 6171 4597 0 * 767 1278 7644 1046 1407
+
+Q 103 * * 4356 3683 5984 5119 3728 6535 3697 4356 7386 3304 3817 3959 3622 2955 3240 4506 * 6167 103
+ 217 * 2837 * * * 0 7634 0 1434
+
+E 104 3814 2891 4165 3396 7546 4114 3220 7079 4210 5835 6144 5111 5396 5957 4309 3140 3280 5072 * 6115 104
+ 116 5301 4271 4091 87 2576 265 7449 1109 2384
+
+E 105 5468 2428 2983 6023 * 4142 5979 5730 4278 4501 * 3967 3376 5346 * 3182 3804 5314 6601 4042 105
+ 171 * 3164 * * 2517 277 7481 0 2532
+
+I 106 4568 6606 3977 3691 * 3136 4550 5424 4115 5628 * 3902 3499 4839 4216 2160 4339 6039 * 5921 106
+ 320 5696 2475 436 1938 5034 45 7401 1043 2941
+
+K 107 4227 5917 4310 3141 6155 2317 5309 4666 4662 6492 * 2643 3359 * 5791 3424 4586 5266 * * 107
+ 658 2950 2079 2504 280 3711 115 7191 2171 3744
+
+E 108 3798 4593 2509 3169 * 2092 5700 * 4633 * 4748 3743 6247 * 5596 2966 6699 6223 * 6797 108
+ 360 3473 2938 1479 641 1991 418 6741 1350 4356
+
+N 109 3529 6057 3216 2376 5489 5352 4947 6544 3873 4201 * 5081 3650 7403 2930 4173 5902 6376 6094 4628 109
+ 42 7199 5525 0 * 2354 314 6915 1000 3981
+
+T 110 4189 * 4904 2854 * 4890 5205 3261 3616 4620 4065 * 4421 4373 2811 3785 3973 4248 * * 110
+ 366 3161 3157 1738 514 3196 167 7111 1442 3533
+
+K 111 3628 6851 4198 4997 * 2366 5553 5194 4283 6399 * 4207 4489 4995 3694 2584 3603 4506 5763 * 111
+ 328 2509 5164 939 1064 1180 840 7006 2018 3674
+
+N 112 4281 * 2836 3759 5796 4782 5277 * 3153 6148 5248 2699 4418 5294 3602 3175 4010 5631 * * 112
+ 13 6849 * 1567 594 1042 960 7245 1253 2694
+
+D 113 4768 * 4112 3782 5849 2427 5332 5120 5189 5324 * 3145 3296 5667 4806 3206 3216 4991 * 7422 113
+ 173 4966 3631 1494 632 2582 264 7504 1159 1889
+
+K 114 3395 5336 3602 4325 4723 7169 4352 4261 3420 2770 * 5334 4341 4188 3775 5905 3750 3859 * * 114
+ 189 3277 5657 1398 688 1187 834 7415 1630 2215
+
+Q 115 4521 * 5738 4645 5908 5253 3374 4286 4691 4043 6228 * 2479 2898 4640 3718 3409 4775 * 4877 115
+ 21 * 6128 0 * 479 1823 7479 1000 1883
+
+M 116 6469 * * * 2719 * * 3291 6594 1313 3159 * 6578 6739 5380 6637 5090 3412 * 4937 116
+ 7 7604 * 1000 1000 2868 213 7591 1000 1356
+
+V 117 3986 * 6899 5616 * 3383 5341 3993 6126 3313 4818 6962 6107 5047 6358 2028 2900 2940 * * 117
+ 20 * 6194 * * 1143 870 7569 0 1300
+
+Q 118 5273 * * * 6489 * 1307 7028 * 3747 5434 4825 7864 2210 6358 3656 7000 3462 * 6988 118
+ 6 7864 * 1585 585 2425 297 7615 1000 1240
+
+Y 119 4674 3624 5543 4786 7281 4336 7016 5125 4316 5172 5480 5482 * 5057 3503 3558 3324 3493 6941 2272 119
+ 77 4788 5998 0 * 779 1261 7623 1199 1185
+
+I 120 * * * * 6423 * * 1699 7196 2333 5113 * * * * * 3541 1473 * * 120
+ 41 6150 6151 1556 599 * 0 7605 1070 1185
+
+Y 121 7792 4521 * 6881 4092 7077 5100 4946 4042 4445 4417 3755 * 4924 4922 3710 3655 3477 4123 2188 121
+ 49 * 4902 * * 887 1122 7595 0 1285
+
+K 122 * * 5218 5824 * 6976 4228 5806 1786 3451 5114 5573 * 6987 1912 4208 5008 4237 6637 5431 122
+ 524 2258 3385 637 1487 1757 506 7599 2560 1355
+
+Y 123 4517 * 4613 5199 5379 6703 4885 6495 2969 4925 5969 3385 5555 7554 2811 3362 4628 3759 5735 2858 123
+ 64 4870 6786 0 * 1966 427 7471 1177 1976
+
+T 124 4063 * 4476 5280 * 3383 5244 4743 6341 5418 * 3206 5259 5615 4529 2279 2286 3945 * * 124
+ 536 1780 5716 492 1791 1683 539 7445 2769 1775
+
+S 125 3893 * 3291 * 7507 4888 * * 3443 5124 * 3840 2849 4322 5604 1692 5140 4844 * 5744 125
+ 482 1898 6015 229 2768 1913 445 7570 2957 1644
+
+Y 126 5194 6268 4636 5233 3857 5834 6912 4704 3524 4076 4955 4091 5868 4717 4344 3969 6530 4971 * 1682 126
+ 159 3892 4751 568 1621 3424 141 7549 1447 1560
+
+P 127 4336 * 4096 3795 7024 2345 * * 5432 5056 5575 5102 2170 4287 3946 3964 4502 3929 * * 127
+ 43 * 5095 * * * 0 7476 0 1776
+
+A 128 4117 6644 3712 2726 5245 4446 5207 5624 3524 6470 * 4850 4895 3369 4345 3195 3017 4854 * 7506 128
+ 57 6269 5285 1440 663 3113 177 7421 1128 1970
+
+P 129 6007 5961 3468 2192 * 6435 4832 5446 3141 * * 4762 2109 5346 5760 3571 5633 5339 7265 5108 129
+ 21 * 6097 * * 2473 287 7449 0 2064
+
+I 130 3906 * 5698 3402 * * 6370 2288 3703 3797 5307 6890 6441 3758 3846 5056 3536 2932 * 5805 130
+ 75 6413 4675 1585 585 2554 269 7463 1014 1955
+
+L 131 6287 * 4987 3224 5484 * * 3765 5292 2413 6946 4800 3163 5027 4866 3384 2827 3607 * * 131
+ 22 7150 6917 2322 322 2766 229 7417 1000 2028
+
+L 132 5755 * * * 4783 * * 3722 6762 321 7048 * 7112 * * 6850 * 4784 * * 132
+ 40 6472 5978 1000 1000 4164 83 7446 1017 1928
+
+M 133 4871 * * 6348 5090 * * 4474 * 1217 1519 * * 6008 * 5719 4947 4915 * * 133
+ 26 * 5822 * * 1861 464 7438 0 1966
+
+K 134 5066 6912 * 2810 * 4866 7495 5669 1917 6457 * 4713 * 3385 3233 2939 4174 4613 * 5904 134
+ 11 * 7064 * * 2919 205 7530 0 1801
+
+S 135 2345 4302 4321 6572 * 2225 6538 * 6583 5815 * 3728 * * 5293 1900 3835 * * * 135
+ 51 5736 5982 0 * 3675 118 7543 1068 1740
+
+A 136 2828 * * * 3938 3569 5611 3449 3900 3491 5407 5326 * 3928 5444 4736 3632 2603 * 5526 136
+ 22 6045 * 0 * 3971 95 7541 1043 1810
+
+R 137 5642 5192 7501 3830 6304 3777 5051 6831 2503 * 4526 4931 6428 5031 1968 3346 4859 4555 * 5234 137
+ 71 5357 5404 479 1824 1459 652 7550 1109 1757
+
+N 138 6105 6885 6545 4892 * 6564 6467 7483 6872 4886 6674 4467 5068 5850 * 1773 1190 * * 5080 138
+ 16 6464 * 0 * 1695 533 7557 1014 1624
+
+S 139 3679 * 5839 5139 6187 4964 4216 4555 3388 3765 4761 5678 3584 4373 4504 3743 3465 2745 * 5769 139
+ 121 6339 3875 0 * * 0 7603 1016 1419
+
+C 140 * 1054 * 4150 5207 4537 7167 5078 6270 * * 4166 5124 5726 4768 4248 4037 5237 * 4008 140
+ 283 4563 2883 1435 666 2507 279 7484 1372 1916
+
+W 141 4935 4478 6730 3216 6003 4513 4655 * 4465 * 6949 * 4558 3106 4343 3324 3479 4469 2321 6606 141
+ 250 3465 3861 2336 318 1479 641 7319 1474 2601
+
+S 142 2909 * 4698 6261 * 3957 4683 6258 4809 7058 6550 3587 3840 5169 * 1518 3798 4735 * 7484 142
+ 125 5078 4226 831 1192 2110 380 7360 1190 2453
+
+K 143 4045 * 4189 4892 * 2816 5198 4478 3358 5224 5406 4951 3706 5166 3359 3582 2960 4958 * 6595 143
+ 97 4916 4978 1353 717 1942 435 7338 1190 2452
+
+D 144 4714 * 2894 2997 * 3291 4994 6462 4437 5085 6642 2828 4277 5953 4459 3312 3466 5248 * * 144
+ 294 4945 2721 1449 658 1367 708 7409 1177 2266
+
+A 145 3369 6205 5489 4758 * 3280 4613 6529 3846 5301 * 3957 3512 2974 4271 2548 4425 4958 * * 145
+ 168 4310 4066 1839 473 2051 398 7299 1216 2666
+
+E 146 4866 * 5465 2128 6629 3251 5677 4780 3438 5704 5331 4331 5985 3647 4516 3580 3583 4302 * * 146
+ 313 2966 3894 734 1327 1436 666 7347 1757 2581
+
+Y 147 4456 3588 5693 4832 3452 6061 7687 6840 4491 4536 5684 4753 3050 5541 5151 4315 5277 4268 3973 2390 147
+ 162 3752 4979 1801 488 3319 152 7397 1616 2364
+
+G 148 3979 * 4809 5127 * 1915 4204 5603 4193 5558 6124 4108 4233 5592 5181 6378 4487 5442 2300 * 148
+ 180 4369 3864 1317 740 778 1263 7367 1292 2430
+
+L 149 4987 7632 * 5669 2675 6544 6161 4436 5204 2501 5182 6689 5151 5106 5214 3931 4964 5237 3443 2514 149
+ 56 4713 * 0 * 967 1033 7434 1233 2063
+
+Y 150 6045 4497 4570 3831 5694 5586 3761 7420 4193 6603 * 3044 * 2779 3441 5729 5097 5670 * 2206 150
+ 131 3529 * 0 * * 0 7536 1547 1507
+
+S 151 3775 5257 6875 * * 5902 7142 6755 7475 * * 4409 4225 6364 * 1256 1634 * * * 151
+ 0 * * * * 2611 258 7536 0 1507
+
+I 152 4714 2402 * * * 4745 * 2162 6596 3020 5543 5198 * 7213 6336 2394 7670 3117 * * 152
+ 0 * * * * 806 1224 7532 0 1417
+
+Y 153 6919 * 5132 6410 2182 5251 3462 * * 6575 * 4904 6864 4748 5921 5286 6564 * 6324 1123 153
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+
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+
+G 155 2322 * * 6243 5200 708 5156 * * 5606 * 5940 * * * 3827 6355 * * * 155
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+
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+I 157 3850 * 6441 * 5977 5769 * 3405 * 1848 5344 6756 6579 7055 * * 4114 1310 * * 157
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+
+E 162 1928 * 7348 2783 * 5200 * * 2489 * 6078 6268 4682 3491 3582 3879 4624 4931 * * 162
+ 11 7035 * 0 * * * 7692 1000 0
+
+N 163 6218 * 3769 4270 * 688 5061 * 5729 5937 6574 3212 * 5573 5643 * * 7064 * 6864 163
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+D 164 4741 * 578 3193 * * 6037 * * * * 4246 * 4529 * 4723 5221 7055 * * 164
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+
+R 165 5122 * * 2934 * 6827 4440 6060 2701 6619 5993 4857 * 3862 2012 3735 3527 3998 6037 * 165
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+ 40 5187 * 162 3235 0 * 7622 1295 1149
+
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+ 146 3378 * 1162 854 * * 7692 1686 0
+
+N 172 4709 * 2411 4677 6150 3615 3262 * 4425 5456 5075 2693 6804 4631 3858 3897 4540 6078 * 4723 172
+ 57 5402 6036 924 1081 0 * 7666 1282 1122
+
+E 173 3698 7075 * 3876 4841 5413 5290 3651 4520 2724 6563 * 1808 5887 4731 3763 5617 4495 * * 173
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+
+H 174 4374 5559 3133 3948 * 5086 3924 * 4318 5493 6513 3870 3988 3807 4075 2244 3917 6340 6234 6949 174
+ 217 2839 * 274 2530 0 * 7681 2004 1000
+
+L 175 4196 * 7293 4730 4164 7022 4283 4447 4397 2073 4001 5832 5838 4297 4084 4296 5383 4485 6570 3081 175
+ 110 4040 6340 696 1386 * * 7692 1410 0
+
+I 176 6247 * 6261 6564 5331 * 7020 2535 * 1850 4881 * 5364 6749 * 5090 6106 1634 6478 4801 176
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+
+D 177 5497 8472 2032 3505 4587 6137 4625 6031 4440 3760 * 3362 * 4575 3986 2846 * 6189 7039 4379 177
+ 54 6693 5220 1585 585 1000 1000 7611 1016 1131
+
+M 178 5031 6631 5025 * 3340 5627 4734 5670 6871 2712 2881 4525 3933 6068 4271 5386 3252 4175 * 3384 178
+ 134 3628 6971 461 1870 1766 502 7617 1484 1236
+
+D 179 3327 * 2068 3052 5004 4150 5981 * 5859 6345 * 3145 7181 4119 4983 3350 4161 5985 * 5082 179
+ 0 * * * * 1141 871 7645 0 1197
+
+H 180 3848 * 4923 2653 6922 3819 3577 * 3948 6787 5846 4529 2376 3963 4121 3854 5296 5282 * 7270 180
+ 110 3764 * 556 1644 563 1631 7622 1528 1082
+
+E 181 3970 * 2461 2784 * 2422 4018 7061 7890 5714 * 4318 5053 5512 5805 2976 3729 7013 * * 181
+ 14 6661 * 421 1982 0 * 7659 1075 1000
+
+A 182 2841 * 4312 3026 6443 4016 * 5643 2266 5565 6981 4249 * 5535 4111 3217 3976 6861 5834 5170 182
+ 54 4766 * 0 * * * 7693 1213 0
+
+S 183 7103 7334 * * * * 5214 7421 6914 7485 * 2791 * * * 2240 891 4493 * * 183
+ 17 6422 * 2322 322 * * 7693 1023 0
+
+F 184 * * * * 1034 * 6750 5696 * 5661 * * * * * 6350 6599 4215 5807 1439 184
+ 0 * * * * * * 7693 0 0
+
+F 185 * * * * 267 * * 6967 * 3311 5873 * * * * * 6420 * 4991 * 185
+ 0 * * * * * * 7653 0 0
+
+G 186 * * * 7045 * 76 * * * * * * * * * 5724 * 6238 6420 * 186
+ 0 * * * * * * 7653 0 0
+
+A 187 1579 * * * 6992 * * 3490 * 2058 3411 7045 * * * 6965 5045 2408 * * 187
+ 6 7846 * 1000 1000 * * 7653 1000 0
+
+F 188 * * * * 985 * 4574 2626 * 4922 5269 * * 5888 * * 6966 3504 * 3072 188
+ 0 * * * * 0 * 7660 0 1000
+
+L 189 3153 * * 4909 5151 7574 * * 1648 2556 2376 * * 5644 3148 7295 * * * * 189
+ 0 * * * * * * 7592 0 0
+
+V 190 * * * * 5897 * * 2229 * 1118 5208 * * 5886 * * * 1987 * 6255 190
+ 0 * * * * * * 7454 0 0
+
+G 191 3172 * 3643 * * 1666 * * * 5251 * 3667 * * * 1429 * 5848 * * 191
+ 0 * * 0 * * * 6019 0 0
+
+//
+�HHsearch 1.5
+NAME abf7361a887c4e53ac97adc19e64234b
+FAM
+FILE abf7361a887c4e53ac97adc19e64234b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:15:45 2013
+LENG 220 match states, 220 columns in multiple alignment
+FILT 120 out of 1461 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEECCCCCCEEECCCCCCCEEEEECCCCCEEEEEECCCCHHHCEEEEEEE
+ECCCCCCCCCCCEEEEEEEEEEEEEEEEEECCCCCEECCCCEEEEEEEECCCCCCCEEEEECCCCCCCCCEEEEEEECCCCEEEEEEEEEEECCCCCCEE
+EEEEEECCCCEEEEEECCCC
+>ss_conf PSIPRED confidence values
+9089787878996899899998963888888579999947999847999997315788604356667517998527897579998347764674999998
+5598861101412677787500001312642875211059769999996676899759998998315772000127629968999999996234689769
+99999089729999953799
+>Consensus
+xvxlxxxxxxxxxxGxxvtLxCxxxxxxxxxxxvxWxkxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxsLxIxxvxxxDxGxYxCxv
+xxxxxxxxxxxxxxxlxvxxxxxxxpxvxxxxxxxxxxxgxxxxlxCxxxxxxPxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxSxLxixxxxxdxxxy
+tCxvxxxxxxxxxxxxxxxp
+>abf7361a887c4e53ac97adc19e64234b
+EVKVEESGGGLVQPGGSMKLSCVASGFTFSNYWMEWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTR
+GGAVGAMDYWGQGTSVTVSSATTTAPSVYPLVPGCSDTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTV
+ICNVAHPASKVDLIKEPSGP
+>gi|62464905|gb|AAX83161.1| immunoglobulin heavy chain variable region [Aotus nancymaae]
+--------------GDPVPHLRCLWLLHRQ-------willeldpPAPKGRG--WSGldisivwWVHQ-L-QRLPQES-----sh---YFSRHVQEPVLV
+E---------AE-LCDRR----------------------------------------------------------------------------------
+-------------------------------------
+>gi|50428758|gb|AAT77091.1| anti-HCC scFv antibody [synthetic construct]
+EIVMTQTPLsSPVTLGQPASISFRSSQS-LVHsdgNtYLSWLQQRPGQPPRLL--IY-----KVSNRFSGGPRQIQ--WQwGQGQIFTLKNQQGWKLRMS
+GFITARKLHN--FRvgTFGPRDQAGNRRAAA---------------------------------------------------------------------
+----------------------------
+>gi|207200|gb|AAA42213.1| T-cell receptor beta chain precursor [Rattus norvegicus]
+---VIQSPRHLVKgKEQKARMQCTPI---KEHSYVYWYYKKLGEDLKFLVyFQN----TDIIDKTDMIKKIISAEC-FT-NKTCTIeIKSSKLTDSAVYY
+CASSQGGQgsqNTLFFGXGTRLSVLE--------------------------------------------------------------------------
+--------------------------
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+-----------------------------------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne--DLRSWTAADMAAQN-------
+-----tqrkweaagvaeqw---RAYL--EGECLEWLRRYLEKG--K-------------et--LQ--raEPs-SQ
+>gi|221330930|ref|NP_001137898.1| CG42256, isoform F [Drosophila melanogaster]gi|220902492|gb|ACL83253.1| CG42256, isoform F [Drosophila melanogaster]
+--------------------vaknpaaeikytallqvKGSVLAYPS--QKLN-TEHK-KRKPHKYRshllskl---------------------------
+-kLSQCSLTLAA----slkp----FI--------------------------------------------------------------------------
+-------------------------------------------------
+>gi|38382894|gb|AAH62459.1| BTNL9 protein [Homo sapiens]gi|119574109|gb|EAW53724.1| butyrophilin-like 9, isoform CRA_a [Homo sapiens]
+--VLGPEYPILALVGEEVEFPCHLWPQLDAqQMEIRWFRSQTFNVVHLY--QE--QQELPGRQMPAFRNRTKLVKDDiAYGSVVLQLHSIIPSDKGTYGC
+RFHSD----NFSGEALWELEVAGLGSDPHLSLEGF-----KEGGIQLRLRSSGWYPKP-KVQWrDHQGQCLPPEFEAIVWDaQDLFSLETSVVVRAGAL-
+-SNVSVSIQNLLLSQKKELVVQIA
+>gi|312373456|gb|EFR21197.1| hypothetical protein AND_17411 [Anopheles darlingi]
+------KPVMDAVEGQSFSVMCNATGKPV--PEFQWIKQGTQQNAADL-------------------DRFSVN----AITGQLDISKVEQQDHDSYACIA
+RNPAG---QSESVMKPNVL----IRPKIIELINITVS-EDTEAVFVCKAFGRPEPEITFRRygtleeysIGLQVSDDRIQLEQSVDVDKGESVGTLRISK
+VTTtDDGLYECIARNRGDvafkagHITVEYSPI--
+>gi|260841781|ref|XP_002614089.1| hypothetical protein BRAFLDRAFT_67325 [Branchiostoma floridae]gi|229299479|gb|EEN70098.1| hypothetical protein BRAFLDRAFT_67325 [Branchiostoma floridae]
+SISLTLPKSVNTIVGDPITLPATYQT-QRRVISVVWNKLNPQDSEKRIPVFSYFPLLGSTESFGTYSGRAELAGK-----ASIKIDATTVQDEGKYVLTV
+-------TVDGLPPEEgFVTVNMMVPPVVDVGPANPYVTAsGRSASLTCAVKDARPNITSLYWEKDGVRVDNLRFDTKYSGGNIQSPNLLIRHVTRGDAG
+RYKCVADH--------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+E 1 4274 * 2751 2674 * 4487 3310 * 4256 4428 * 4538 4666 1868 * 4554 * * * * 1
+ 0 * * * * * * 6959 0 0
+
+V 2 * * * * 3437 4874 * 3332 * 3170 * 4720 * 5222 * 4955 4933 999 * 4923 2
+ 0 * * * * * * 7971 0 0
+
+K 3 4577 * 3666 4213 4472 4484 * 5398 3840 * * 5395 * 3385 4075 3345 3339 2078 * 5100 3
+ 0 * * * * * * 8567 0 0
+
+V 4 4495 * * * 4494 * * 5370 5619 1234 4381 * 5365 * * * 3913 1722 * * 4
+ 0 * * * * * * 8876 0 0
+
+E 5 5427 * * 3311 * 5757 5615 4608 5600 5355 4468 * * 2252 * 3291 1690 3575 * * 5
+ 32 * 5494 * * * * 8974 0 0
+
+E 6 3460 * 5342 4016 * 5502 4591 5503 4663 4596 * * 2989 2245 3625 4126 4079 3038 * * 6
+ 113 3736 * 336 2267 0 * 8935 1502 1015
+
+S 7 4156 * 4849 3591 5784 4077 * 5740 5716 4525 * 6046 1267 4626 5854 3847 3437 5854 * * 7
+ 27 * 5740 * * * * 8967 0 0
+
+G 8 * * 4824 3451 * 2327 * 5669 4162 5761 * 5804 1961 4399 3836 2898 4827 5754 * * 8
+ 0 * * 0 * 0 * 9051 1011 1011
+
+G 9 3924 * 3987 3946 4780 5854 4440 4875 5133 4233 5790 2966 3260 4820 * 2412 3938 4275 * * 9
+ 26 5808 * 0 * * * 9164 1055 0
+
+G 10 5082 * * 5121 * 6079 5052 3646 4551 2607 4513 5901 5076 3956 6081 4441 5244 1538 * 5391 10
+ 22 6074 * 1585 585 * * 9433 1022 0
+
+L 11 4011 * 4560 4058 5147 * 6184 3253 6084 4236 * 4322 4693 4725 3655 3001 2635 3311 * 5144 11
+ 40 5179 * 0 * * * 9624 1232 0
+
+V 12 2417 * * 5161 5362 4285 * 4059 4705 4359 5125 * * 6401 4751 4253 4102 1527 * 5221 12
+ 0 * * * * * * 9743 0 0
+
+Q 13 3316 * 6770 3823 * 4375 4861 4351 3154 3111 5211 4502 3738 3694 5147 4658 3996 3234 * * 13
+ 15 6597 * 0 * * * 9770 1000 0
+
+P 14 3265 * * 1667 6301 * * 6727 3949 2981 6364 * 3807 * 4182 3970 4341 3668 * 4752 14
+ 0 * * * * 0 * 9967 0 1000
+
+G 15 6557 * 5191 3898 * 562 * * 6676 6541 * 3696 * 5046 6429 4423 5483 6808 * * 15
+ 15 * 6557 * * * * 10142 0 0
+
+G 16 5837 * 2695 2269 * 2593 5758 * 3972 5594 * 4470 * 3004 4939 3364 5084 5443 * * 16
+ 17 6401 * 0 * 0 * 10265 1010 1007
+
+S 17 4352 5602 3083 4238 * * 6445 * 4804 * 6726 3828 3350 6656 5145 2117 2096 5589 * 6520 17
+ 13 * 6782 * * * * 10291 0 0
+
+M 18 2120 6570 * 6896 5500 * * 3477 * 3916 4010 * 6579 * * * 4905 1099 * * 18
+ 0 * * * * 0 * 10178 0 1000
+
+K 19 5660 * 6878 3413 * 6557 6545 3945 4769 4533 5892 4838 5160 4360 4033 3071 1413 5180 * * 19
+ 0 * * * * * * 10193 0 0
+
+L 20 * * * * 3708 * 6578 3147 * 588 4037 * * * * * * 3756 * * 20
+ 0 * * * * * * 10193 0 0
+
+S 21 7180 * 4220 4174 6843 4684 4838 7048 4542 4760 5647 3512 2343 5236 3909 3024 2752 5280 5706 * 21
+ 0 * * * * * * 10193 0 0
+
+C 22 5164 148 * * 6614 * * 6551 * * * * 6578 * * 6634 6641 6728 6804 * 22
+ 42 5806 6523 568 1620 * * 10193 1189 0
+
+V 23 4195 * 4432 4047 * 5564 3957 6712 3544 3785 6563 3387 4080 5270 3512 3395 2888 3890 * 6831 23
+ 46 4989 * 738 1320 * 0 10296 1371 1015
+
+A 24 2973 6838 * * 3119 * 6031 3494 6508 3185 * 5875 3879 6771 * 4781 4069 2472 * 2704 24
+ 163 3838 4761 484 1811 * 0 10296 2044 1015
+
+S 25 4321 * 3319 4463 6762 4378 4344 6502 4119 6452 * 3748 3138 4291 4778 2498 2693 6552 * * 25
+ 118 4454 4917 1146 868 1239 795 10140 1755 1715
+
+G 26 4551 * 4129 4064 6424 1735 * 5693 5056 4512 * 3554 3266 4310 5518 3539 3889 6509 * 6765 26
+ 90 * 4051 * * 1584 585 10112 0 1917
+
+F 27 4626 * 4252 4656 3111 4685 4041 6431 3473 4809 * 5720 3476 4449 4754 2890 3967 6394 * 3154 27
+ 81 5678 4826 1585 585 201 2940 10065 1153 2609
+
+T 28 * 6608 3307 4308 4337 4017 5601 5196 3710 6452 6664 5028 2597 4699 4395 2930 3871 4370 * 4283 28
+ 182 6440 3227 0 * 984 1017 10121 1003 1676
+
+F 29 4601 4306 5004 4494 4012 5586 5406 4204 4032 3201 6572 * 2537 4210 4015 3508 5246 4295 6515 5195 29
+ 421 4309 2303 651 1462 4092 87 10250 1624 3136
+
+S 30 3911 * 2862 3859 * 3625 5112 * 3483 5225 6395 3881 4161 4606 4310 3176 3048 5214 * 6037 30
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+K 160 5006 * 4224 4390 6068 5688 4977 5415 4089 5025 5783 4350 7577 4241 3253 2749 2370 4805 * 3635 160
+ 11 * 6982 * * 0 * 10194 0 1000
+
+W 161 * 7577 * * 6766 * * * * 5411 * * * * 5776 5927 * * 128 6344 161
+ 1890 550 4408 1125 885 * 0 10158 8232 1105
+
+N 162 5617 * 2907 3985 6750 3981 5591 6509 2306 5012 6502 2898 6457 5177 3409 3709 5637 6626 * 4045 162
+ 32 5515 * 1535 611 * 0 10020 1181 1902
+
+Y 163 5350 * 3379 3755 6362 1687 5731 * 3740 5593 * 2622 6587 6642 4505 3453 5722 6638 6581 6574 163
+ 66 4863 6601 395 2061 * 0 10020 1393 1902
+
+G 164 3858 * 3034 3220 * 1783 5661 6574 4502 6502 7823 4008 6415 4409 3546 4212 4270 6833 * * 164
+ 36 5337 * 1327 734 2837 217 10005 1184 2071
+
+A 165 3048 * 3976 2810 6834 3539 * 4601 3271 4030 5702 4299 4209 4489 3873 3963 5492 4353 * * 165
+ 91 * 4027 * * 1340 725 10012 0 1905
+
+L 166 6260 6793 4701 3625 5175 7460 * 2400 6325 2362 4442 6587 5742 * 4209 4274 4472 2549 5503 6671 166
+ 112 6195 4036 2807 222 * 0 9924 1018 2509
+
+S 167 5680 * 4075 4184 5425 5285 * 3798 4643 3084 4962 4854 3473 4977 3818 3154 3059 3585 6330 * 167
+ 33 5477 * 1302 750 3831 105 9834 1203 3350
+
+S 168 4742 6277 3812 3429 * 4303 4853 3743 4191 3345 5383 3830 4176 3953 4887 3168 4445 5006 6184 5476 168
+ 13 6753 * 1000 1000 * 0 9793 1000 3195
+
+G 169 3799 5467 2692 3949 6384 2457 4556 4678 * * * 4920 4607 5301 5514 3264 2970 4883 * 5423 169
+ 75 4309 * 1052 949 1915 444 9793 1580 3195
+
+V 170 4673 * 4049 4153 3934 4719 6306 3687 5714 3248 6275 4418 4684 4252 6412 3619 3716 2471 * 5292 170
+ 57 * 4681 * * 1178 842 9936 0 2624
+
+R 171 4610 * 5639 4227 4922 4865 3583 3799 3994 3920 4784 4301 4566 4661 4299 3500 3070 3696 * 5065 171
+ 96 5581 4528 2198 355 2145 370 9929 1187 2414
+
+T 172 4933 * 4055 4413 * 5467 5766 6314 3968 4562 5070 2997 4391 3309 3902 3376 2314 6373 * 5620 172
+ 16 6495 * 0 * 3684 117 9912 1000 2699
+
+V 173 4592 * 3934 5105 2904 4382 5774 4390 3954 3632 * 5627 5621 5599 6802 2456 3135 4089 6475 4831 173
+ 37 6036 6599 3000 193 284 2485 9919 1109 2566
+
+S 174 4766 * 4966 3147 5530 4043 5546 5174 5619 4123 6581 5541 2649 5509 4555 2676 2863 5700 7076 4926 174
+ 46 6645 5563 1000 1000 * 0 10034 1000 1343
+
+S 175 4162 * 4743 4184 5846 3663 4261 4217 5550 4688 4617 4889 3955 3373 5146 2882 3204 4300 * 5024 175
+ 35 6479 6312 1585 585 1382 699 10003 1014 1708
+
+V 176 4874 * 4507 3348 4734 4438 4369 3549 3949 4522 5496 4008 4209 5011 4200 3932 4561 2684 * 6553 176
+ 49 6079 5744 0 * 1251 786 9987 1109 1762
+
+L 177 * 6433 3915 3633 5561 5088 5597 5578 3296 3115 5560 3762 4540 3820 2956 3626 4704 4497 * 5016 177
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+
+Q 178 3827 5209 3971 2864 * 4285 6330 4161 3989 4125 5369 3147 4258 3494 4580 4844 4330 4437 * 6540 178
+ 770 1273 * 965 1036 575 1606 9764 5829 3502
+
+S 179 4094 * 1924 3160 * 2996 * 6163 6433 6135 5727 3030 5020 5431 5594 2958 4897 5465 * * 179
+ 50 5464 6472 0 * * 0 10004 1241 1788
+
+G 180 5194 * 3066 3913 7028 1310 6397 * 4383 6126 * 3804 5060 5812 5597 3268 5296 5475 6657 * 180
+ 34 5413 * 0 * * 0 9982 1224 1967
+
+F 181 * * 3932 5109 5599 5529 * 5115 3164 2624 5704 4618 * 4577 3711 3443 2157 4195 * 6420 181
+ 189 3470 4953 828 1195 * 0 9982 2363 1967
+
+Y 182 4812 5818 5677 5736 2223 5454 4420 4908 6765 3656 * * 5623 5464 6761 4837 4915 4204 6769 1648 182
+ 31 6337 6761 3907 100 1752 508 9918 1000 2492
+
+S 183 4605 * 4391 3688 6588 6649 4777 * 4598 4054 6412 3781 5738 4002 5223 1820 2610 5043 * 7487 183
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+
+L 184 3756 5550 6551 6640 6431 3958 5407 3047 4561 3200 3858 * 5525 * 4074 3991 3092 2718 5057 * 184
+ 77 * 4258 * * 3184 168 9935 0 2343
+
+S 185 5119 6437 5485 6695 4468 5566 4618 5555 5553 5996 5554 6436 4806 4628 4365 2307 1992 3538 6330 4241 185
+ 22 6019 * 1000 1000 2641 252 9868 1044 2934
+
+S 186 3403 5300 6495 * 6450 4419 * 6732 5662 4553 6732 4024 * * * 718 4983 6565 * 5805 186
+ 33 5472 * 1311 745 * 0 9900 1156 2626
+
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+ 101 3880 * 2325 321 234 2740 9900 1882 2626
+
+V 188 4984 * * 6646 4022 6655 6542 3753 * 695 7508 * 6891 5849 * * 5261 3400 * 4962 188
+ 0 * * * * * 0 10044 0 1105
+
+T 189 5897 * 5253 3809 * 5020 5482 3190 3932 3234 6683 3716 6534 5617 3945 4113 2149 4014 * 5375 189
+ 13 6814 * 2322 322 * 0 10044 1038 1105
+
+V 190 6872 * * * 3645 6542 * 1803 * 1638 * * * * 4985 * 6734 2481 5614 4247 190
+ 27 5749 * 0 * * 0 10044 1178 1105
+
+P 191 6382 * 4315 4979 * 6639 4144 * 4419 4130 5471 3656 3475 3749 3544 2957 2360 4056 * * 191
+ 0 * * * * * 0 10030 0 1105
+
+S 192 3121 * 4273 4535 5546 6428 5865 4059 4454 3902 6654 3847 2552 5036 4098 4036 3501 3838 6720 * 192
+ 0 * * * * * 0 10003 0 1105
+
+S 193 3831 5726 4763 4250 6479 4223 6244 6724 4239 4316 6880 4631 6436 3873 5013 2746 2421 3369 6553 5159 193
+ 38 * 5273 * * * 0 10003 0 1105
+
+T 194 3779 * 3586 3248 * 3807 6384 5350 3329 3155 * * 4946 3777 3050 3103 4937 4940 * 6475 194
+ 125 * 3596 * * 2078 390 9980 0 1654
+
+W 195 4082 6517 5048 3226 5768 5402 4418 5359 5696 2082 * 6481 4905 4788 3595 4241 4920 4430 3078 6631 195
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+
+P 196 5612 * 1228 3551 * * 3979 * 4254 6389 6483 3469 3956 * 3627 4903 4630 * * 5732 196
+ 385 2232 5545 370 2143 342 2245 9925 3833 2136
+
+S 197 3495 * 2525 6646 * 2828 3784 6542 4666 * * 2967 5553 6389 6449 2358 4161 5024 * 6681 197
+ 414 2005 * 57 4682 1926 441 9973 4511 1504
+
+Q 198 2813 * 4208 4279 * 1457 * * 3036 * 4777 5003 * 4930 4993 4658 4191 5471 * 5861 198
+ 15 * 6552 * * * 0 9987 0 1326
+
+T 199 5771 * 4394 3906 6475 6553 6911 5066 4644 4410 5732 3593 4890 5788 4594 3303 2018 2681 5548 * 199
+ 110 3770 * 0 * 1975 423 9973 2028 1496
+
+V 200 * * * * 2722 * 6419 4489 * 3057 * * * * * * * 2866 5666 957 200
+ 14 * 6742 * * 822 1203 9987 0 1326
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+I 201 5900 * 6908 4945 5525 * 6252 5110 2971 5269 7007 6809 * 4534 3692 3010 1482 5386 5549 4048 201
+ 0 * * * * 926 1078 10019 0 1238
+
+C 202 * 17 * * * * * 6398 * * * * * * * * * * * * 202
+ 0 * * * * * 0 10036 0 1015
+
+N 203 3630 6598 * 2803 * 6420 6478 3275 3919 5027 4967 5270 * 2785 3548 3999 4343 3146 * 5086 203
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+
+V 204 1543 * * 6134 4878 * * 3947 * 4675 * * 6303 * * 5595 6662 1116 * * 204
+ 0 * * * * * * 9930 0 0
+
+A 205 3844 * 3490 4163 6533 5423 6413 6418 4366 5329 * 4016 6587 3897 3607 2145 2356 6389 * * 205
+ 0 * * * * * * 9867 0 0
+
+H 206 * 6699 * * 4937 * 1327 * 6777 6394 * 1729 * 3452 6402 4379 5315 6409 * 4375 206
+ 33 6317 6645 1000 1000 * * 9851 1000 0
+
+P 207 5306 5939 3766 3098 6380 3436 * 6435 3133 6112 * 4665 3236 3783 3781 2868 4398 6786 * 4669 207
+ 0 * * * * * 0 9678 0 1105
+
+A 208 2880 * 6090 4707 5412 2264 * 6199 6032 4588 6490 3943 5017 4690 4814 2084 * 4496 5992 4969 208
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+
+S 209 5782 * 5955 4906 4779 1871 * 4680 4341 2898 6027 4379 5882 3804 5086 3137 3947 4644 * * 209
+ 1294 756 * 1878 458 * 0 9245 5642 1105
+
+K 210 3891 * 5700 4620 5605 4141 4281 6219 4269 6591 * 5737 2437 4601 4247 2607 2741 4126 * * 210
+ 0 * * * * 0 * 9056 0 1105
+
+V 211 2999 * * * 4305 4688 * 2560 4227 2562 * 6126 5844 * 6020 4760 5132 1833 * * 211
+ 0 * * * * * * 9008 0 0
+
+D 212 5913 * 2911 2135 6054 * 4829 4966 4714 * 5659 3768 6060 3730 4250 2902 3349 5713 * 6015 212
+ 46 6126 5894 3000 193 * * 9008 1000 0
+
+L 213 4714 * * 6009 6024 5799 3969 4361 2275 3588 5984 5602 * 4842 3851 4826 3700 2158 * 4881 213
+ 0 * * * * * 0 8984 0 1015
+
+I 214 4816 * * 3739 5594 5696 * 5868 5619 4304 * 3224 4469 4277 4040 2240 2082 4918 5968 * 214
+ 0 * * * * * 0 8984 0 1015
+
+K 215 * * * * 3763 * * 1822 5828 2620 4250 * * 4594 * 4292 4754 2154 6021 4604 215
+ 0 * * * * * 0 8887 0 1015
+
+E 216 4523 * 5233 3091 5286 * * * 2760 * * 3330 2842 * 2970 3002 3068 * * 5125 216
+ 56 4727 * 0 * 0 * 8502 1016 1015
+
+P 217 4947 * * 4691 4705 4638 * 3624 3145 3576 * * 1413 4875 4854 4847 * 3419 * * 217
+ 0 * * * * * * 7397 0 0
+
+S 218 3669 * 4831 3023 * * 4503 3704 4718 * * * 3696 * 3950 1577 2974 * * * 218
+ 0 * * * * * * 7238 0 0
+
+G 219 3294 * 3404 * * 2672 4255 4474 4196 * * * 4474 * 3084 2403 4513 4464 * 4222 219
+ 0 * * * * * * 6742 0 0
+
+P 220 3922 * * 3930 * * * * 3840 * * * 324 * * * * * * * 220
+ 0 * * 0 * * * 5814 0 0
+
+//
+�HHsearch 1.5
+NAME ae209f299335d3708222d92bc2697502
+FAM
+FILE ae209f299335d3708222d92bc2697502
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:22:48 2013
+LENG 116 match states, 116 columns in multiple alignment
+FILT 101 out of 375 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCEEECCCCEEEEECCCCEEEEEEECCCCCEEEEEEECCCCCEEEECCCEEEECCCCEEEEEEEECCCCCCCCEEEEEEEECCCCCCCHHHHH
+HCCCCCCEEEEEEECC
+>ss_conf PSIPRED confidence values
+9855454315603998579988899799999979998599999927998789738636988999799999978999888889999999999986999996
+2589786099999729
+>Consensus
+xxxxxxxxxxxxxxpxxxxfxxxggxxxlxLxNxsxxrvaFKVKtTxnxxyrVrPxxGxIePgxsxxIxIxxxxgxxkxDKflixxxxxxxxxxdxxxxw
+kxxxpxgxxxixlxax
+>ae209f299335d3708222d92bc2697502
+MGHHHHHHSMINVDPPTGNYPATGGNSTHNITSESDSRLAFKVKSSNNEHYRVRPVYGFVDAKGKSKLDINRLPGPPKEDKIVIQYAEVPAEETDPMAPF
+KAGAQQGEIIVKLIAA
+>gi|115533618|ref|NP_491051.3| hypothetical protein W03D8.5 [Caenorhabditis elegans]gi|90568079|gb|ABD94094.1| Hypothetical protein W03D8.5 [Caenorhabditis elegans]
+-------------PPGQLLFTPDECQEKLTITNTHDKKIMYKLKLSDNIAFQLNPVFGVLEPGKSVDVAVTHRKSEPMEGKLIIVNSLLTGDEDKVKELF
+KQITkPTGdSVHVKLI--
+>gi|193207282|ref|NP_506565.2| hypothetical protein C15H11.1 [Caenorhabditis elegans]gi|169402782|emb|CAB02735.2| C. elegans protein C15H11.1, partially confirmed by transcript evidence [Caenorhabditis elegans]
+------------------------QKTILKITNQSEMKQAFKVKCTRNDLFRIKPSTGILDYNQTLTVILVYRGGQETvpiDRQHFGVYHIpAPENCTC-
+EGAWAEhyGPPQGEHKLRVV--
+>gi|17534907|ref|NP_495146.1| hypothetical protein K05F1.9 [Caenorhabditis elegans]gi|868179|gb|AAA68716.1| Hypothetical protein K05F1.9 [Caenorhabditis elegans]
+---------------TTVTFTNPKlGdevtIASLNLTNPTKDRYAFKIKCTSNQLFKIKSPVGYINPEESLTIPVYHYPATVIpenNKHyFVVYYIKAAn
+tvKEKIPVRDLWKAAaSSEGTRRVFI---
+>gi|313240732|emb|CBY33049.1| unnamed protein product [Oikopleura dioica]
+------------------------SasKSKQLHPKGNFENARF-FTKNAKKRYCVRPNTGVIEPYQSKEIKIALQPGDINqRHKFMIQSIVYPKNytdfn
+te--ELQRIWSSKSNnk-----------
+>gi|70994708|ref|XP_752131.1| integral ER membrane protein Scs2 [Aspergillus fumigatus Af293]gi|66849765|gb|EAL90093.1| integral ER membrane protein Scs2, putative [Aspergillus fumigatus Af293]
+--------------------------EILHLSNTNSEPVVFKVfSKCAPRKvayhdrtltsLCVLGQNNRSEAllrsaqlrtdrtrqecgcprlihilkl
+vlqplmGVLISRTVLLQAMkeePapdAKcKDKFLVQTVAVTGDMefSNVSSIF----------------
+>gi|145499313|ref|XP_001435642.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|74830029|emb|CAI38987.1| VAMP-associated protein 3-1 [Paramecium tetraurelia]gi|124402776|emb|CAK68245.1| unnamed protein product [Paramecium tetraurelia]
+----------------ILEFMAEEnrfAHAQLTLQNLQSQPVAFKIKTTVPQMFQVKPSVGFIEADRSTIVEISTTQ-AIGqdqklDAKFQINACFRDSN
+EQDLNQFWRSRD------------
+>gi|145545552|ref|XP_001458460.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124426280|emb|CAK91063.1| unnamed protein product [Paramecium tetraurelia]
+----------------SLQFQEGQlNQLKFKITNVSDVPITFRIRCNNNTNYKLDHYMGLIHSHQDFENNIQNFEAAdLKlpGDQLEIQYAEFLDPLQDL
+KDFWKSTQSQDHVMIPI---
+>gi|340716611|ref|XP_003396790.1| PREDICTED: motile sperm domain-containing protein 2-like [Bombus terrestris]
+---------------DAFIFNKVGNeiSGTITIKNITlDKPLSYKVKTTSPGKFKVRLSSGVLLPQEQRTISVVVQQEHnmrspFHVDKFLVMCLPLKDp
+naSAQELAVLWKSEKPAEEHK------
+>gi|268568010|ref|XP_002640135.1| Hypothetical protein CBG12634 [Caenorhabditis briggsae]
+-----------------------MTCNELTLKNHSKFAVLFKVKCTSNKRIKIEDCSEILRPGNQTSVPI-KLVDNIDGDSLYVIYTLVGKQWhderMSA
+FRCWErakkQDVPTKCVSIRIK--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+G 2 * * * * * 0 * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1000 0 0
+
+H 3 * * * * * * 0 * * * * * * * * * * * * * 3
+ 0 * * * * * * 1000 0 0
+
+H 4 * * * * * * 0 * * * * * * * * * * * * * 4
+ 0 * * * * * * 1000 0 0
+
+H 5 * * * * * * 0 * * * * * * * * * * * * * 5
+ 0 * * * * * * 1000 0 0
+
+H 6 * * * * * * 0 * * * * * * * * * * * * * 6
+ 0 * * * * * * 1000 0 0
+
+H 7 * * * * * * 0 * * * * * * * * * * * * * 7
+ 0 * * * * * * 1000 0 0
+
+H 8 * * * * * * 0 * * * * * * * * * * * * * 8
+ 0 * * * * * * 1000 0 0
+
+S 9 * * * * * * * * * * * * * * * 0 * * * * 9
+ 0 * * * * * * 1000 0 0
+
+M 10 * * * * * * * * * * 0 * * * * * * * * * 10
+ 0 * * * * * * 1000 0 0
+
+I 11 * * * * * * * 0 * * * * * * * * * * * * 11
+ 0 * * * * * * 1000 0 0
+
+N 12 1589 * * * * * * * * * * 1545 * * * 1623 * * * * 12
+ 0 * * * * * * 1771 0 0
+
+V 13 2435 * 2668 * * * * 2153 * 3161 * * * * * * * 1639 * * 13
+ 0 * * * * * * 3178 0 0
+
+D 14 * * 1697 3341 * * * 3847 * * * * 1416 3460 * * * 4116 * * 14
+ 0 * * * * * * 4398 0 0
+
+P 15 * * * * 4400 4370 * * 4121 * * 4201 573 4060 4049 * * * * * 15
+ 0 * * * * * * 4671 0 0
+
+P 16 5342 * 3474 2975 * 3544 4681 * 3384 * * 3466 2326 5150 3528 5220 3834 4796 * * 16
+ 0 * * * * * * 5349 0 0
+
+T 17 2802 * 5453 2950 4376 * * 3785 2863 * * * 5585 5460 * 3283 2691 3373 * 4366 17
+ 31 5550 * 4524 64 * * 5873 1000 0
+
+G 18 2899 3060 * * * 5780 * 2446 * 1476 * * * * * * * 2434 * * 18
+ 0 * * * * * * 5883 0 0
+
+N 19 5430 * 5415 2521 * * 5731 4760 4422 4707 * 3998 3134 2800 3807 4375 2471 5763 * * 19
+ 0 * * * * * * 5971 0 0
+
+Y 20 * * * * 625 * * 2845 * 4570 * * * * * * * 4160 4135 4124 20
+ 30 * 5602 * * * * 6010 0 0
+
+P 21 4061 5590 5437 * * * * 4623 3470 4513 5390 3621 2496 3284 4331 3702 2757 4809 5248 * 21
+ 63 4549 * 1585 585 * 0 6034 1041 1000
+
+A 22 2143 3506 4445 4403 3991 * * 5924 4156 3495 * 4363 4192 4387 4591 4472 4233 4157 * 5549 22
+ 70 4409 * 549 1660 0 * 6034 1065 1000
+
+T 23 3654 * 4311 3056 5779 4326 * 3773 4708 4113 * 4907 4028 4576 * 2445 2568 5391 * * 23
+ 56 4713 * 0 * * * 6055 1107 0
+
+G 24 * * 4521 2746 * 901 * 4907 4405 5433 * 5580 * 4685 * 3519 5563 * * * 24
+ 421 2124 5392 953 1048 * * 6131 1647 0
+
+G 25 3794 5202 * * * 1115 * 4522 5294 4361 5624 3407 * 5698 * 2835 4921 6126 * * 25
+ 121 3635 * 1280 765 * 0 6350 1256 1027
+
+N 26 5268 5707 6805 4494 4758 * 5090 4831 3090 4171 5300 6787 * 2967 6502 2604 2240 4256 * 5302 26
+ 31 5554 * 1674 542 * 0 6486 1067 1027
+
+S 27 2707 3623 * 4163 * 4552 * 4927 3695 5013 * 5881 * 4021 4020 2346 3577 3244 * * 27
+ 0 * * * * * 0 6568 0 1107
+
+T 28 * 6882 5142 3927 5506 * 4545 3909 2761 4319 6224 4392 5914 5535 4126 3229 2041 4715 * 5361 28
+ 0 * * 1000 1000 1123 887 6589 1013 1107
+
+H 29 5450 * * * 3723 * 2714 2973 * 1413 4906 * * 5581 * * * 2382 * * 29
+ 0 * * * * * 0 6614 0 1027
+
+N 30 6782 * 6287 4634 6687 5741 4032 4893 2110 4435 4332 4615 * 5306 4717 5072 1992 3501 * 6211 30
+ 0 * * * * 0 * 6628 0 1027
+
+I 31 * * * * 4913 * 5604 1769 * 990 6276 * * * 5481 * 6696 3262 * * 31
+ 0 * * * * * * 6646 0 0
+
+T 32 5398 * * 3903 5154 * 4553 3359 2358 6921 6522 5052 5604 5180 3982 3470 2379 3913 * 4769 32
+ 0 * * * * * * 6646 0 0
+
+S 33 4722 * * * * * * * 5604 * 5789 169 * * * 4875 * * * * 33
+ 0 * * * * * * 6646 0 0
+
+E 34 5263 * 3947 4855 6140 5049 4635 3170 6220 4294 * 4372 2417 5418 5986 4425 2218 3677 * * 34
+ 45 * 5037 * * * * 6646 0 0
+
+S 35 4876 5579 5328 * * 3380 5807 * 6187 6476 * 3630 * 5047 * 1539 1734 * 6271 6293 35
+ 23 6003 * 0 * 1834 475 6585 1085 1102
+
+D 36 3806 * 2445 3777 5538 4564 * 5147 2951 6502 5489 3272 4744 4576 5948 3470 3104 6395 * * 36
+ 37 5294 * 0 * * 0 6588 1066 1055
+
+S 37 4273 5457 4039 2528 4902 6974 4982 * 2803 4403 6315 3416 * 3981 3676 3816 4939 3992 * 6217 37
+ 10 7182 * 0 * * 0 6588 1000 1055
+
+R 38 4054 * 6063 * 6601 * 4828 5761 3259 * 6668 4435 2465 * 1288 5805 4076 5714 * 6199 38
+ 0 * * * * * 0 6588 0 1055
+
+L 39 5538 * * * 5109 * * 2080 5887 2446 4712 * * 3217 6694 * * 1720 * 4219 39
+ 0 * * * * 0 * 6588 0 1055
+
+A 40 919 4373 * * * * * 3676 * 4505 3643 * * * 5605 4096 3460 4549 * 6953 40
+ 0 * * * * * * 6659 0 0
+
+F 41 * 6263 * * 710 * * 3895 * 4269 6363 * * * 5791 6008 * 5107 * 2461 41
+ 57 5791 5605 1585 585 * * 6659 1031 0
+
+K 42 * * * * * * * * 135 * 6249 * * * 3919 * 6599 * * * 42
+ 51 5358 6599 2563 267 0 * 6610 1067 1037
+
+V 43 * * * * 4902 * * 1489 * 4060 4391 * * 5468 * * * 1059 * * 43
+ 54 4768 * 2109 381 * 0 6649 1132 1004
+
+K 44 * * * 5781 * * * * 456 * * 5468 * 5790 2646 5583 4988 * * * 44
+ 31 5552 * 0 * * 0 6649 1038 1004
+
+S 45 6281 1664 * * * * 5468 6559 4592 4932 * * * 5552 * 3349 1306 4636 * * 45
+ 0 * * * * * 0 6649 0 1004
+
+S 46 * 4568 * * * 6126 * 5781 6008 * * 3821 * * 5980 1942 829 * * * 46
+ 48 5781 6126 1000 1000 * 0 6649 1031 1004
+
+N 47 2253 6305 2442 * * 5534 5942 5756 6296 * * 2025 * 5980 6326 2374 4431 6486 * * 47
+ 54 5265 6542 1590 582 912 1094 6627 1105 1085
+
+N 48 4320 * * * * * * 6320 5596 5273 * 1226 1457 * * 5053 4943 5583 * 6003 48
+ 0 * * * * 865 1149 6637 0 1091
+
+E 49 6126 * 2701 2752 5672 6933 5720 4432 2386 4708 6141 3665 * 4448 3907 4414 3511 6882 * 6359 49
+ 33 * 5468 * * * 0 6649 0 1004
+
+H 50 5038 6436 6835 4517 4667 5572 6032 4244 2478 2309 3108 3906 * 5425 3359 5046 6542 4281 * * 50
+ 32 5505 * 3322 152 * 0 6591 1038 1126
+
+Y 51 * * * * 1313 * 5513 5640 * 5505 * * * * * 5933 * * * 951 51
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+A 116 822 * * * * * * * * * * 2184 * * * * 2223 * * * 116
+ 0 * * 0 * * * 2184 0 0
+
+//
+�HHsearch 1.5
+NAME af5e37f6170ad6dd671732b9beb56903
+FAM
+FILE af5e37f6170ad6dd671732b9beb56903
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:30:34 2013
+LENG 215 match states, 215 columns in multiple alignment
+FILT 130 out of 1360 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCEEEECCCCEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEEEECCCCCEEECCCCCCCEEEEECCCCCCEEEEEECCCCCCCCEEEEEEEC
+CCCCEEEEEEEEEEEEEECCCCCEEECCCCCEECCCCEEEEEEEEECCCCCCEEEEECCCCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCCCEEEEEE
+EECCCCEEEEEEECC
+>ss_conf PSIPRED confidence values
+9299488858996899799999965788888789999927999827999995278840325766772588404788806898823300356208998864
+9853366667777864101465123058741112799699999984656998599988996857731024571799699999999953346898799999
+938987589999539
+>Consensus
+xxxxxxpxxxxxxxGxxvxLxCxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxxLxixxvxxxDxgxYxCxvxx
+xxxxxxxxxxxlxvxxxxxxxpxxxxxxxxxxxxxgxxxxlxCxxxxxxPxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxsxlxixxxxxxxxxytCxv
+xxxxxxxxxxxxlxx
+>af5e37f6170ad6dd671732b9beb56903
+QVQLQQSGAELVKPGASVKLSCKASGYTFTSYWMQWVKQRPGQGLEWIGEIDPSDSYTNYNQKFKGKATLTVDTSSSTAYMQLSSLTSEDSAVYYCANLR
+GYFDYWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSV
+AHPASSTTVDKKLEP
+>gi|326674722|ref|XP_689309.4| PREDICTED: poliovirus receptor-related protein 2-like [Danio rerio]
+-QHVRVEPEVVSFPGQTVTLRCQFPNPGDTqLTQVSWIFERTDTERTNIAVFHPNFGVNYPTTSPvSGRVTFVSNPpTLDNPSIQIKDVKMTDEGRYICE
+-----YATYPSGNEqgvssLVMLAKPKNTATTVTVSAGKTPVI----VARCESSNGRP-AATITWSTALNGNVTTPKKTDNPDNTVSIQSVYMLaPQPED
+NGKDISCIVSHRTMAQPETFPMK-
+>gi|145408204|gb|ABP65664.1| MHC class I antigen [Sus scrofa]
+----------------------------------------------------------------------------------------------------
+-------------------------------------htyqwmygcylgpdglflrgysqfgydgadyvalne--DLRSWTAADMAAQI-----------
+--skrkweaadeaerm--RSYL--QGRCVEWLQKYLEMGK-----------------dt--------
+>gi|2114481|gb|AAC02653.1| butyrophilin [Homo sapiens]
+-IVVGPTDPILATVGENTTLRCHLSPEKNAEDmEVRWFRSQFSPAVFVY--KGGRERTEEQMEEYRGRTTFVSKDiSRGSVALVIHNITAQGNGTYRCYF
+QEG-RSYDEAILHLVVAERLGSKPLISMRGHEDGG-----IRLECISRGWYPKPL-TVWrdPYGGVAPALKEVSMPDADGLFMVTTAVIIRDKS--VRNM
+SCSINNTLLGQKKESVI--
+>gi|17542472|ref|NP_499896.1| hypothetical protein T21D12.9 [Caenorhabditis elegans]gi|14670183|gb|AAK72063.1|AF016687_10 Small protein 10, isoform a, confirmed by transcript evidence [Caenorhabditis elegans]
+---VRQPVEVSTLIGEKARFTCNVYGASP--LSIEWRVMENGQPRVLVqdsATFLSINRTAVVNGTFDERELAAAE-------LLLDNVAMTDNSEYQCV
+ARNR----FGSDFSTHVKLQVYQAPKFTYTPEDMPLLVGQTAKFLCAATGT-PRPE-IKWafEQIPFPAAEARRLYVTPndDHIYIM----NVTKED--Q
+GAYTCHATNVAG----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
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+
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+
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+
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+G 26 4060 * 3252 5750 * 1784 4660 6526 5243 5671 * 3576 4232 4373 4435 3344 5225 3981 6710 * 26
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+
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+
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+
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+
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+
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+
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+
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+
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+ 147 * 3364 * * 1794 491 10837 0 1980
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+
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+ 149 3544 6361 385 2095 * 0 10737 2308 2534
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+G 49 2345 5377 * 6187 3632 4819 6173 4204 6052 2555 5011 * 4583 4529 6323 3158 4513 3641 5745 6298 49
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+M 180 3489 6502 6510 5356 5658 4954 * 3737 4159 2753 3958 6441 * 6504 4063 3688 4402 2233 5614 5142 180
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+
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+
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+
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+ 0 * * 1585 585 0 * 10505 1000 1000
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+C 198 * 92 6685 * * 6406 * 6743 * * * * * * * * * 5014 * * 198
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+H 202 6536 * 5612 6256 * * 1235 * * 6717 6097 1477 6557 5155 * 4660 5271 * * 4529 202
+ 0 * * * * 0 * 9822 0 1000
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+P 203 3436 * 4831 2074 * 3645 5497 6375 3329 4846 * 5554 3294 4543 4053 3729 4536 4921 6841 * 203
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+S 206 * * 4934 2691 * 4369 5116 * 3563 5016 * 5013 2709 3477 5879 2473 3811 4057 * 5834 206
+ 0 * * * * 3305 154 9418 0 2328
+
+T 207 2583 * 5966 3258 5916 4577 4981 5144 3769 5721 * 3995 6009 3971 5123 3058 2699 4535 * 6157 207
+ 0 * * 1000 1000 0 * 9418 1040 2185
+
+T 208 5427 * 4543 3203 5336 3495 6372 * 3971 * 6203 5280 2242 4571 3975 3614 3060 3680 * * 208
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+
+V 209 2880 5187 6244 5332 * 5144 6245 3185 3868 2405 6332 6113 * * 6053 4568 3850 2079 * * 209
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+
+L 213 5955 * * * 2716 * * 1877 6175 1389 6051 * * 5964 * * 5878 3112 * * 213
+ 31 5550 * 3322 152 * * 9244 1000 0
+
+E 214 3546 * 4660 2541 * 5347 5469 * 4525 * * 2974 3895 4486 2891 3481 3235 * * 4551 214
+ 0 * * * * * * 8626 0 0
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+P 215 * * * * * * * * 3030 2328 * * 996 * 4095 4119 4034 * * * 215
+ 0 * * 0 * * * 6369 0 0
+
+//
+�HHsearch 1.5
+NAME af828e69a5f2d0fd42a2a213e09eb64f
+FAM
+FILE af828e69a5f2d0fd42a2a213e09eb64f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:17:01 2013
+LENG 141 match states, 141 columns in multiple alignment
+FILT 122 out of 1049 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCHHHHHH
+HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9699999999999999986088899999999999895699876344677567988999999999999999832147889999999888852999899999
+99999999998836249999999999999999999987639
+>Consensus
+xLtxxxxxxixxsWxxixxxxxxxgxxxxxxlfxxxPxxxxxFxxxxxxxxxxxxxxhxxxxxxxlxxxixxldxxxxxxxxlxxxHxxxxgvxxxxfxx
+xxxxlxxxlxxxlgxxxxxxxxxAWxxxxxxixxxxxxxyx
+>af828e69a5f2d0fd42a2a213e09eb64f
+VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL
+LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
+>gi|83699633|gb|ABC40722.1| leghemoglobin 6 [Sesbania rostrata]
+-FTESQEALVTSSYETFKQNASDLSVLFYTFILEKAPGAKNLFSFLKDSdgvpKDNPNLKAHAAKVFELVVDSAVQLRTKGAVviaDANLGPVHV-QKGV
+TDAHFVVVKEALLKTVKEATGAKWSDELSNAWEVAYDELAAAIKKAM-
+>gi|291238614|ref|XP_002739227.1| PREDICTED: Globin D, coelomic, putative-like [Saccoglossus kowalevskii]
+-LTKEQKDTLIQTWQNLHADLERIGMLMFMGLFEHNPEIKEFFVGADsrdMKteelRYNEKLQEHGIRVMGLVEKIISSMGfedeKIDQMVVDLGKRHL-
+GYDVHIPFIDLFGRQFVFAIKPTLHTHWTANVEEAWTQLFKYIGYLMRYGYH
+>gi|50897135|dbj|BAD34601.1| hemoglobin chain I [Calyptogena kaikoi]
+-VSASDIKNVQDTWTKLYDQWeAVHASKFYNKLFKDNEDISEAFVKAGT-GSGIAMKRQALVFGAILQEFVENLSDPTALSLKIKGLcatHK-TRGItNM
+ELFAFALADLVAYMGTT--ISFTAAQKTSWTAVNDVILHQMSSY--
+>gi|255724342|ref|XP_002547100.1| predicted protein [Candida tropicalis MYA-3404]gi|240134991|gb|EER34545.1| predicted protein [Candida tropicalis MYA-3404]
+-LSPFEIDQIQSSWNRIS-NKNNFYNELYLNLIEKNPNLGEIFNHDE-----SVITHHAKTFGDCFNFVVSNIENVEIIeefiYSFVQENQR-FSQMSTK
+YLEPMGNSLILTLKQFLRSYSTSVLELTWVKVYVYFANSI-----
+>gi|311279880|ref|YP_003942111.1| hypothetical protein Entcl_2577 [Enterobacter cloacae SCF1]gi|308749075|gb|ADO48827.1| hypothetical protein Entcl_2577 [Enterobacter cloacae SCF1]
+-------ELFNNSYARILPgdKGDRFFTHFYTLFTKSTDDETSAH------------svarrLEKQKIiyktf-FYmlsvanth-------IVA---DYL
+VKITRESNpQNLNLPPSAYALWRRAVLQTVRDLD-PECDEEIITAWAIVLAPGLEFMRR---
+>gi|159461074|gb|ABW96608.1| hemoglobin F2 [Fasciola hepatica]
+-LTQTQIDSiLADLAHHTDttEHITEMGVSIYKTLFAAHPEYISYFSKLqGLTKdnvgQSEGIRYYGRTLGEELIRLLKAASNPsvlEERIVQGAKDHK-
+ARPVTKDQFTGAAPIFIKFFQGLL---KKQEDKDAIEKFLLHVMQAIAAK--
+>gi|237756266|ref|ZP_04584824.1| conserved hypothetical protein [Sulfurihydrogenibium yellowstonense SS-5]gi|237691567|gb|EEP60617.1| conserved hypothetical protein [Sulfurihydrogenibium yellowstonense SS-5]
+-FTQEDVERIKKLKPILEKYLDEFISKFYFFIS-RFPDYNQFLKN-------EDlFKRHKSELKNWFLDLFsGNYDENYfSRLYKIGEVHV-NIGLPTHY
+VNAafnfVRRFIIEKIDAEIQDRNErNLYVTSIGKLIDINLDVLTLAYR
+>gi|324521693|gb|ADY47909.1| Unknown [Ascaris suum]
+--------RIQQCFKAA---RPPIGQQILKRACILRSEMRLFLAHLP----DDMVDELAIDLYTFISNCVENIDDPDRVNALARAFgeqHAalCSLGFRP
+DYFAPIADAAIAECVRLDGgAHKRCETLLAWSQLIAAMFTGVRDGY-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 * 4317 4489 * * 4524 3412 * * * * * 1330 * * 2340 4659 2910 * * 1
+ 54 4766 * 3702 115 * * 6177 1162 0
+
+L 2 * * * * 4095 6278 * 3378 * 669 3672 * * * * * 6481 3838 4512 * 2
+ 0 * * * * * * 8702 0 0
+
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+ 0 * * * * * * 8769 0 0
+
+P 4 2603 6496 3224 2675 * 4046 5589 5594 4994 5835 5357 5208 3326 4268 4426 3438 5096 5991 * 5444 4
+ 0 * * * * * * 8878 0 0
+
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+ 0 * * * * * * 8902 0 0
+
+D 6 5926 * 1860 2102 * * 5661 6612 6672 6649 5931 5123 * 1605 * 5823 4879 * * * 6
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+
+K 7 4971 6730 * 4213 6361 * 5232 2445 2133 3449 5887 * * 4488 2594 * 6624 3207 5855 * 7
+ 0 * * * * * * 9059 0 0
+
+T 8 2896 * 3360 2879 4960 6171 5604 4737 2711 5651 * 5734 * 3073 3980 4062 4984 5695 * 4510 8
+ 15 * 6614 * * * * 9168 0 0
+
+N 9 2612 * 4861 4696 * 6859 6259 3047 4803 1818 6902 3669 * 5643 6306 6660 3622 3626 * 6717 9
+ 33 5480 * 358 2185 0 * 9276 1385 1017
+
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+
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+
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+
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+
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+
+V 17 3444 5181 * 6069 4552 7030 * 2260 * 1995 3942 6560 6930 6234 6562 6660 5743 2189 * * 17
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+
+G 18 3268 6613 4827 3656 4009 4774 5276 5866 2489 4598 4732 6660 6103 5106 3595 3134 4181 5611 5233 5611 18
+ 161 3932 4649 659 1447 2337 318 9183 1962 2418
+
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+ 63 4861 6965 796 1238 177 3116 9126 1382 2764
+
+H 20 4378 6568 2524 3915 6575 4312 3801 5299 3489 5187 * 2256 5758 4907 3952 4979 6907 5714 6145 5171 20
+ 51 5746 5972 1412 680 818 1209 9253 1162 1263
+
+A 21 4101 6819 4991 4572 5807 3017 5624 4869 2861 3016 4877 4392 4304 4894 4651 3654 * 4334 5066 4729 21
+ 180 3195 6956 2346 316 700 1379 9280 2704 1315
+
+G 22 3634 * 2936 2631 6735 4642 5576 5313 4202 5045 6056 4147 3453 3510 4897 4444 4603 3880 * 6957 22
+ 51 4845 * 1573 591 700 1379 9292 1464 1316
+
+E 23 2744 * 3680 2180 * 3840 4395 * 4801 5357 6868 4536 5223 3532 3947 3940 4493 4832 * * 23
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+
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+
+G 25 2553 5232 * 7083 4664 1038 6588 5699 * 4688 * * 7198 * * 4814 4044 3355 * * 25
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+
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+
+E 27 3058 6602 3410 3410 5877 4985 4941 3987 2839 4024 6941 4026 * 4685 3994 4731 3782 4542 * 6436 27
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+
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+
+L 29 6562 * * * 1399 * 5631 * * 2714 4267 * * * * 5979 6050 6605 * 1537 29
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+
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+
+R 31 4086 5477 6055 4885 5979 5159 4533 5966 2451 4245 7131 3332 * 5750 1760 6007 5022 6792 5696 4784 31
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+
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+
+F 33 4996 * * * 739 * * 4392 * 2376 4688 * * 5193 * * 6559 4558 6651 * 33
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+
+L 34 3599 * 4547 2332 * * 6668 6423 2415 4973 5919 3899 * 3530 4368 3460 3313 5308 * * 34
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+
+S 35 2762 6943 3977 3260 * 6947 4184 7185 2884 3622 4791 5027 * 4160 3355 3664 3809 6476 * 6991 35
+ 10 * 7222 * * * 0 9250 0 1154
+
+F 36 3707 5620 3187 4923 3052 * 2941 6608 3797 6114 7263 2828 * 6876 3745 4410 5391 5937 * 3392 36
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+
+P 37 5043 * 4685 4570 5986 6017 7091 6526 * 6808 * * 460 5650 5792 4618 5811 7185 * * 37
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+
+T 38 3838 * 2287 1800 * 4654 4856 * 5238 5685 6821 5176 * 3730 4184 3625 5483 5339 6476 6431 38
+ 0 * * * * * 0 9250 0 1154
+
+T 39 3172 7040 6564 6564 3982 6931 5960 3171 * 2560 4071 5176 * * * 3722 2942 3319 6733 3481 39
+ 0 * * * * * 0 9250 0 1154
+
+K 40 4114 * * 4391 * 6052 5261 4455 1987 3316 * 6526 5986 2547 2353 5831 5790 5775 * 6987 40
+ 0 * * * * * 0 9250 0 1154
+
+T 41 3016 6274 3279 3271 * 6431 5980 6244 3375 5545 * 3028 3630 4623 4124 3649 3461 5986 * 6526 41
+ 0 * * * * * 0 9250 0 1154
+
+Y 42 3938 * * * 3446 * 4962 3618 3135 2319 2790 * 5179 7244 5894 6943 5986 4209 * 2820 42
+ 16 * 6526 * * 0 * 9250 0 1154
+
+F 43 * * * * 226 * 6509 5252 * 4391 * * * * * * * * 5720 4595 43
+ 16 * 6510 * * * 0 9315 0 1046
+
+P 44 4789 * 3921 4855 * 3389 4152 * 2952 * * 3917 2139 6893 4947 3126 3830 4499 * 5708 44
+ 128 * 3559 * * * 0 9253 0 1269
+
+H 45 4598 * 3667 3655 4289 3455 4890 5914 2665 5216 5295 5130 5990 4405 2922 3873 4252 4925 6732 6446 45
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+
+F 46 4045 * 5331 6037 1313 * 6823 4481 6323 3011 4391 * * 6574 4956 4329 4215 3999 6217 4761 46
+ 1080 1231 3305 182 3077 * 0 8802 5415 5058
+
+D 47 4694 * 1723 4743 * 2971 4742 * 3055 5329 * 2797 * * 4561 4080 3930 * * * 47
+ 355 3238 3160 314 2353 * 0 8524 2184 5784
+
+L 48 4477 * 4177 6470 4508 3627 6172 3565 4087 1945 5321 6171 * * * 6362 4716 2114 * 5229 48
+ 298 2560 5899 1132 879 4154 83 8234 2783 6402
+
+S 49 4573 * 3174 4396 * 5131 5044 * 3096 5035 * 3518 2220 5077 6109 2892 3604 6070 * 6009 49
+ 1426 671 * 2018 409 4006 93 8227 6059 6284
+
+H 50 3186 5771 3920 4110 6232 5983 5308 4640 2819 4116 4840 * 2632 6005 3448 3493 4372 6216 * * 50
+ 385 2093 * 2245 342 3840 104 8352 3328 6067
+
+G 51 3032 * 3215 4367 * 3910 5265 * 3533 * * 3306 * 3999 5216 2680 2922 5374 5934 5399 51
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+
+S 52 5256 6694 3158 5782 * 4721 4643 5228 * 6477 * 1570 6159 * * 1696 4088 * * * 52
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+
+A 53 2849 * 4264 3109 6342 4143 5834 6408 4044 4566 6530 4283 1783 6773 5239 4327 4534 6544 * * 53
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+
+Q 54 3587 * 2275 3006 7150 3872 6877 5234 3202 6096 * 4160 5948 4187 3574 4242 4249 5283 * 6651 54
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+
+V 55 5411 * 6125 6626 1691 6867 * 3644 6906 2108 2801 * * 7112 6645 6550 6006 3375 * 5043 55
+ 0 * * 2322 322 728 1336 9244 1062 1692
+
+K 56 3420 6600 4336 3122 * 5678 4281 5444 2420 3836 * 4682 * 3577 2701 3700 5787 * * 6717 56
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+
+G 57 2475 6332 5066 3346 5921 3707 4419 6614 3296 4233 * 4093 * 4601 2888 4203 5186 6037 6979 4852 57
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+H 58 6959 6143 * * * * 1155 5779 5529 3738 6495 * * 1627 5525 5949 * 6283 * 5140 58
+ 24 * 5893 * * * 0 9294 0 1276
+
+G 59 1878 4622 * 5939 6125 2629 7078 5379 3976 5359 6558 6038 5200 5344 4714 3132 4248 3423 * * 59
+ 15 6595 * 2322 322 1366 709 9273 1017 1579
+
+K 60 3726 5692 5097 3239 6517 4534 7247 3574 3355 3194 4902 5797 * 4730 3235 4930 3530 3641 * 5412 60
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+
+K 61 4202 * * * 6785 7000 4943 4055 2827 3934 3817 4797 * 3673 2344 4203 3142 3831 * 6685 61
+ 60 4615 * 2085 388 * 0 9303 1683 1000
+
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+
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+ 15 6588 * 3000 193 0 * 9303 1062 1000
+
+A 65 2330 4795 * 6757 4715 3352 * 3994 5940 3174 4733 * * 6007 4348 2961 3518 3975 4724 6574 65
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+
+L 66 * * * * 3539 * * 2499 * 1122 4726 * * * * * 6919 2296 * 5173 66
+ 15 6621 * 4087 87 * 0 9280 1034 1062
+
+T 67 4220 5829 2061 3091 * 3242 5406 5482 5765 5083 6637 3177 * 4258 5585 4016 3845 5012 * 5958 67
+ 0 * * * * * 0 9280 0 1062
+
+N 68 3707 5885 3375 3084 3779 6916 5466 5113 3292 4581 7147 3902 6300 5899 4491 4066 3631 4892 5504 3803 68
+ 0 * * * * * 0 9280 0 1062
+
+A 69 2454 4601 * * 3653 4389 * 2148 * 2811 4386 * * * * 5415 4407 2781 6757 7013 69
+ 0 * * * * * 0 9280 0 1062
+
+V 70 4111 5757 * 6828 4576 * * 1626 * 3032 3866 * * * 6637 * * 1581 * 6190 70
+ 79 4237 * 0 * * 0 9280 1930 1062
+
+A 71 4288 6906 2975 3174 * 3061 6890 6971 3049 4289 6638 3703 5307 4052 4152 3491 4482 4970 * * 71
+ 63 4543 * 1362 711 0 * 9280 1643 1062
+
+H 72 2996 5510 * 5075 5309 4273 3407 5009 3992 4455 5214 2411 5496 4814 4637 3140 6664 4552 * 4897 72
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+
+V 73 4216 5920 4999 6135 4593 * 6167 3725 5530 1087 3686 6849 5919 * 6624 * 6902 3352 * 4589 73
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+
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+
+D 75 5882 * 1617 3201 5364 4874 4188 * 3530 * 6731 2400 6855 4948 4626 4722 5462 7076 * * 75
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+
+M 76 3443 6867 4710 3896 5786 4437 4981 4331 4287 2272 5059 5733 2585 5418 4846 4499 5839 4500 * 6565 76
+ 31 6291 6833 1585 585 * 0 9227 1075 1591
+
+P 77 4447 6496 2517 2484 7172 3772 5811 6844 3558 4671 5641 6159 4600 4340 4392 3338 5347 5626 * 4547 77
+ 162 3237 * 940 1062 276 2522 9222 2759 1752
+
+N 78 3640 * 4791 2836 6883 4105 6778 5175 3266 3565 6186 4348 6840 4263 4848 3278 3329 3778 * 5806 78
+ 100 4013 7593 1031 970 0 * 9330 2062 1000
+
+A 79 4517 * * 5750 3398 4906 5908 3326 4250 1879 4047 6966 5086 5335 6005 5339 4658 3064 * 4423 79
+ 326 2305 * 1970 425 0 * 9304 4065 1000
+
+L 80 4257 4044 5502 5399 4131 * 6902 3534 4573 1710 4610 5843 * 6864 4891 5145 * 2560 5961 5187 80
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+S 81 2843 6111 4033 4397 * * 4998 4349 2768 4164 5305 5260 3356 3896 3881 3871 3939 4755 * * 81
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+
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+
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+
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+
+L 86 6767 * 6954 4750 4321 * 6537 3854 3811 1578 5742 4371 6860 6772 3096 3902 4100 3794 * 6598 86
+ 494 1786 * 1529 614 0 * 9311 5150 1096
+
+H 87 5874 * * 6490 * 4271 302 * 5316 * * 6060 6969 6724 6557 6591 * * * 5044 87
+ 50 6788 5316 1000 1000 * * 9305 1014 0
+
+A 88 2517 6027 5196 5342 * 5378 4623 4874 3187 3629 * 5749 * 4730 2865 4024 4231 2927 6693 5692 88
+ 2384 2859 576 708 1367 0 * 9272 3209 1306
+
+H 89 4359 5056 4105 3058 4063 * 5376 * 3335 * 4469 4413 5359 2938 2843 * 2730 5444 * * 89
+ 165 3208 * 1260 780 0 * 7838 1450 7934
+
+K 90 3028 6922 4197 4876 5820 3250 4133 6985 2217 7017 7199 3576 4344 4790 3776 4570 4452 5312 * 6940 90
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+
+L 91 4254 * 7176 6347 3548 * 5323 4468 4984 2951 4226 7017 5797 6063 2134 5551 * 4798 6676 2166 91
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+
+R 92 7236 6902 4927 * * 1006 6042 6557 3718 6624 * 3070 4409 5539 3713 3865 * 6673 * * 92
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+V 93 4030 6167 * 6490 3826 6702 * 1976 * 3229 4332 * 5628 5390 * * * 1399 * * 93
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+
+D 94 4673 6607 3722 4187 * 3347 4404 * 3086 5999 7170 3581 3517 5077 4056 4281 2344 6014 * 6715 94
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+
+P 95 3132 * 4327 5309 6607 4481 4781 4148 4159 4421 6066 7227 1768 3987 3833 3918 6715 4784 * * 95
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+
+V 96 3403 * 2896 1975 7179 4381 4077 6097 3311 5419 * * 5403 3796 4452 4215 4850 5368 * 6670 96
+ 0 * * * * * 0 9294 0 1013
+
+N 97 4708 * 3226 5427 5944 * 2000 6295 * 3847 4493 6169 * 3234 5813 5311 7222 5903 5903 2087 97
+ 0 * * 0 * 0 * 9294 1013 1013
+
+F 98 6622 * * * 1294 * * 3755 * 2646 5618 * 6490 * * * 6770 4110 3387 2699 98
+ 0 * * * * * * 9305 0 0
+
+K 99 3221 * 2391 2731 * 4310 * 5632 3321 5187 6961 3512 4650 3780 5179 5356 4800 5880 5229 6200 99
+ 15 6642 * 2322 322 * * 9330 1017 0
+
+L 100 3031 * 3357 4153 5857 5468 5337 3907 4417 2873 5343 3936 3803 4730 5978 4579 3995 3568 * 7585 100
+ 77 4263 * 2000 415 * * 9330 1930 0
+
+L 101 4244 * * * 2029 6974 * 3231 * 1949 2951 * * * * 6298 * 2842 4406 * 101
+ 15 * 6583 * * * * 9330 0 0
+
+S 102 3584 5556 * 4058 5891 1925 * 5359 3524 3858 * * 6183 4420 2868 3073 7024 4928 6654 6951 102
+ 0 * * * * * 0 9315 0 1028
+
+H 103 3641 * 3105 2059 * 4535 6128 6682 5283 6759 * 4194 4064 4389 3229 3133 4588 5535 6910 7099 103
+ 0 * * * * * 0 9315 0 1028
+
+C 104 1715 3904 6670 * 5247 6668 * 3053 * 4730 6280 7144 4525 5169 * 2935 6261 2707 6060 5551 104
+ 0 * * * * * 0 9315 0 1028
+
+L 105 5629 6336 * * 2144 * * 2949 * 1171 4659 * * * * * 6487 3741 5295 5907 105
+ 0 * * * * 0 * 9315 0 1028
+
+L 106 4875 7010 5720 5505 6678 7160 4954 2707 5521 1667 4144 * 5525 4778 5110 * 4398 2660 6670 5696 106
+ 0 * * * * * * 9330 0 0
+
+V 107 2825 5656 3085 2840 4529 4457 4998 6773 3764 5056 6949 6716 5599 4048 4245 4131 3660 5152 5990 5874 107
+ 0 * * * * * * 9302 0 0
+
+T 108 2195 6842 * 5589 4229 5863 5792 5564 5102 4629 4423 * * * 6331 5219 1878 2634 * 4214 108
+ 0 * * * * * * 9302 0 0
+
+L 109 4563 6302 * * 2845 * * 2533 * 1412 3211 * * * * * * 2744 * * 109
+ 43 6331 5865 1585 585 * * 9302 1104 0
+
+A 110 3615 5283 5384 2771 5160 4395 5805 6156 2954 * * 5374 5100 3093 2606 3443 4738 5525 * * 110
+ 12 * 6916 * * 1039 962 9278 0 1157
+
+A 111 3318 6597 3206 1880 * 5735 4554 * 3453 * * 4548 5770 2874 6025 3853 4391 5962 * 6510 111
+ 38 5271 * 1405 684 0 * 9284 1315 1147
+
+H 112 3092 4414 * 3950 6891 5170 3527 4619 3924 3455 5961 5052 * 4961 4063 5110 4156 2804 4800 4377 112
+ 100 * 3900 * * * * 9302 0 0
+
+L 113 5416 4418 3958 * 4173 5696 5799 4218 6267 1146 4120 5154 * 5321 * 5563 5781 3680 6842 5846 113
+ 265 * 2573 * * 1951 432 9256 0 2053
+
+P 114 5156 * 6361 4246 * 766 6656 * 3743 * * 6354 3010 4318 * 4739 * 6576 * * 114
+ 124 5012 4275 722 1344 918 1087 8974 1315 4183
+
+A 115 3415 * 2610 4004 * 3837 * 6458 3506 6647 * 3642 3318 5408 3971 3367 3938 4700 5841 6062 115
+ 17 6430 * 0 * 567 1622 9157 1013 3218
+
+E 116 3275 5246 2832 3087 * 3360 4023 * 3097 * * 4876 6328 3878 3439 3391 5759 7114 * 6834 116
+ 184 3321 5675 896 1113 538 1685 9227 2691 1850
+
+F 117 4404 5229 * * 1865 * 6146 3960 4835 3251 4859 6843 5466 * 5733 5750 * 4981 2353 3286 117
+ 19 6279 * 4907 49 * 0 9253 1104 1497
+
+T 118 5470 * 2324 6788 6801 5489 4860 * 5813 * * 2901 7246 5069 4936 2734 1627 6925 * * 118
+ 146 3778 5436 750 1302 961 1040 9253 2220 1497
+
+P 119 2619 6228 2432 3314 6463 4709 5662 5692 4042 6741 6521 4942 3390 3814 4573 4050 4078 7008 * * 119
+ 47 * 4952 * * 2408 301 9279 0 1587
+
+A 120 3491 * 2716 1703 * 4363 6609 5452 3843 * * 5202 6927 3684 5139 3243 5108 5367 * * 120
+ 0 * * * * * 0 9247 0 1993
+
+V 121 3007 6493 5137 4215 5899 * 6756 2988 * 2794 4948 6187 * 3826 * 4713 2653 2702 * 5744 121
+ 0 * * * * 1533 612 9247 0 1993
+
+H 122 3569 * 4083 2130 6138 5250 5986 4651 3001 3767 5149 * 5773 4147 3471 5940 4634 3571 * * 122
+ 0 * * * * 0 * 9255 0 1609
+
+A 123 2765 * 2944 2519 * 4045 6910 6828 3894 5590 4899 3988 * 5008 3933 3433 4201 4547 * * 123
+ 11 7083 * 1585 585 * * 9295 1000 0
+
+S 124 685 * * 5879 * 5736 * 4878 * 4541 6040 * 7091 6908 6841 3641 4122 3648 6897 * 124
+ 12 6936 * 3000 193 * * 9295 1007 0
+
+L 125 5103 * 6902 * 4079 * * * * 4359 5594 * * * * * * 5482 405 4154 125
+ 0 * * * * * * 9295 0 0
+
+D 126 3776 * 3152 3644 * 4972 4587 4863 2983 4901 5598 3793 * 5395 2668 3864 3474 5344 6711 * 126
+ 0 * * * * * * 9295 0 0
+
+K 127 4100 * 4145 4040 6889 4588 5617 4013 1719 5573 5833 5822 * 3705 3551 4191 4434 3857 * * 127
+ 0 * * * * * * 9281 0 0
+
+F 128 2149 4304 * * 3469 5294 * 3955 * 1921 4142 * * * * 6161 3749 2999 * 6720 128
+ 0 * * * * * * 9281 0 0
+
+L 129 6539 * * * 2008 6636 * 3206 * 1932 3733 6674 * * * 6655 5390 3979 4947 2781 129
+ 0 * * * * * * 9281 0 0
+
+A 130 3625 * 2501 4444 * 3350 * * 3303 5782 6985 4268 6520 4162 3371 2798 3845 4887 6886 * 130
+ 13 * 6834 * * * * 9281 0 0
+
+S 131 3894 * 5996 4327 2395 6137 5128 3523 6839 3128 5998 5332 5058 6887 4302 4904 5648 2918 * 3197 131
+ 0 * * * * * 0 9238 0 1021
+
+V 132 5189 5875 * * 3525 5029 * 1600 * 2489 4488 6287 * * * 4771 5104 2324 7109 * 132
+ 0 * * 1585 585 0 * 9221 1021 1021
+
+S 133 2265 3966 6814 5075 4820 3953 * 2946 6619 2930 6093 5305 * 5237 6907 4195 4063 3494 * 4635 133
+ 0 * * * * * * 9189 0 0
+
+T 134 2909 6481 2146 3716 * 3915 5617 5816 3404 7009 * 3195 6814 4607 5944 3753 3854 6212 * 6076 134
+ 13 6809 * 1000 1000 * * 9189 1000 0
+
+V 135 3353 5467 5852 6776 5535 4029 5098 3198 4910 3302 4875 5868 6375 4317 3710 4690 3620 2845 * 4370 135
+ 0 * * * * * * 9098 0 0
+
+L 136 6436 * * * 4350 * 6711 1781 * 1611 1853 * * * * * * 4845 * * 136
+ 0 * * * * * * 9009 0 0
+
+T 137 3327 6309 4852 5333 5432 3753 * 3088 2642 3805 6276 6566 6296 4919 3313 3208 4713 3931 * * 137
+ 0 * * * * * * 8801 0 0
+
+S 138 3418 * 4805 2988 5191 4581 3873 4664 4311 4580 * 6331 5725 3621 4107 2135 5152 5003 * 5803 138
+ 0 * * * * * * 8512 0 0
+
+K 139 2789 * * 4151 * 1669 * * 3121 4246 5170 * * 4125 5359 3173 4648 * * 4144 139
+ 0 * * * * * * 8000 0 0
+
+Y 140 * 4668 * * 4735 * * * * 4848 3901 * * 4618 * * * 5331 4551 488 140
+ 0 * * * * * * 7277 0 0
+
+R 141 * * * * * * 3200 * 1309 * * * * * 1863 * * 3435 * 3058 141
+ 0 * * 0 * * * 4773 0 0
+
+//
+�HHsearch 1.5
+NAME b056b4c4d9017a19c3095e4c72f67a47
+FAM
+FILE b056b4c4d9017a19c3095e4c72f67a47
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:52:42 2013
+LENG 194 match states, 194 columns in multiple alignment
+FILT 116 out of 1318 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHC
+CCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9988557999997988887179999999999999852668978999998892279876777668999999998450579997399999999999875540
+4778996299998379988980559999999987899899999588433435899999997288986499749999999999999998513388
+>Consensus
+CxxxxxdivxllDxSxSmxxxxxxxxkxxxxxxxxxxxxxxxxvxlvxfxxxxxxxxxlxxxxxxxxxxxxixxxxxxxgxtxxxxalxxaxxxxxxxxx
+xxrxxxxxxiiliTDGxxxxxxxxxxxxxxxxxxxxixvxxigxgxxxxxxxxxxxlxxiaxxxxxxxxxxxxxxxxlxxxxxxixxxicxxxx
+>b056b4c4d9017a19c3095e4c72f67a47
+CPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVRELFNITN
+GARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREKIFCIGS
+>gi|260837234|ref|XP_002613610.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]gi|229298996|gb|EEN69619.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]
+--------LYPYGSySGGYPPSNMEKTMG-PGNYRVPLVagGETITIGSIKKTEETSPseslsaekQAVVAAQDTRECTMSSITiySEERLRGTKKTYSG
+NGWLPRDPSWV-----VDSAGPAWVDSNGVTWEDV--------------VTVDNVQSGDQ------RQVFGGFQGKARYWKLVITQTYTGWQPYVRE---
+-------
+>gi|317505805|ref|ZP_07963650.1| von Willebrand factor type A domain-containing protein [Segniliparus rugosus ATCC BAA-974]gi|316255887|gb|EFV15112.1| von Willebrand factor type A domain-containing protein [Segniliparus rugosus ATCC BAA-974]
+-AKNQATVILLLDISESMRAtdvkpSRVEAARAAAIKFVDGM-APTVQLGVVTFAGNAQPLVRPSTD--HETAKKVIDQMIrpdKLEKQTATGEGIYTAL
+QQIEtiAGalGGKNHA-PPARIVLVSDGKETVpdDLNAPrgaYAAARTAKEKHVPVCTVAFGTKAGKitldnqvdevPVDLESLKKISDLSNSPgnscRF
+FPAESQGELAQIYQSLNEDI-----
+>gi|82913384|ref|XP_728622.1| micronemal protein WARP [Plasmodium yoelii yoelii str. 17XNL]gi|23485067|gb|EAA20187.1| micronemal protein WARP [Plasmodium yoelii yoelii]
+C-DNYYDITLIVENSSFIQKDYWMKgTIPFLESMVRNARvsKDKAHMAIILFAGRQDLIVPFTDELSQdkEKLIDKIRTLNDAATDsnTLYVYALEYAFE
+KVIFGE-GTRSDAPKVAVLFYYGFDYgSNTSLIPDVVEDYKQNNIKLIIVGIALG-----NKQNAFILADCKSDGDCPNLilEPWDYVIRAAEQVKGKIC
+N---
+>gi|149173297|ref|ZP_01851928.1| hypothetical protein PM8797T_28944 [Planctomyces maris DSM 8797]gi|148848103|gb|EDL62435.1| hypothetical protein PM8797T_28944 [Planctomyces maris DSM 8797]
+-------LAIILHTCEFPEGNTWGKRIT-----KQAIKvlGAQDEVGVLVYdfMDGEKWLFKLMPAGDYEKMVPKINGAQ-IGDMPSFANTMQLGLNGLI
+KSDA-----STKHMIIISDGDPQ-PPT--PQLIGQFLKNKVSVSMVAIfphGGE-----DISKMRDIAGVTGGR-YYFPSDPNQLPSIF-----------
+-
+>gi|171684709|ref|XP_001907296.1| hypothetical protein [Podospora anserina S mat+]gi|170942315|emb|CAP67967.1| unnamed protein product [Podospora anserina S mat+]
+-PSSKPEIVFVCDRSGSMGdGKRIPNLQTALHLFLKSL-PLGVKFNICSFGSHWDFMFpEGSRTYDASSLAHATQYVNSISanyGGTEMRMPLQDTFKR-
+------RYKDMDLEVFMLTDGEIWDQQQVFGMINTHVAESegAIRVFSLGIGNDV----SHALIEGIAQAGNGFSQSVADDESMNSKVIRMLKASL----
+-
+>gi|212634224|ref|YP_002310749.1| TPR domain-containing protein [Shewanella piezotolerans WP3]gi|212555708|gb|ACJ28162.1| TPR repeat protein [Shewanella piezotolerans WP3]
+-------LVIALDLSPSMQERQhgiehLTRAKLAITTLLQQ--GSARPISLVAFSGSSHQVLPASEQLALlTLYLGYLSPDIMPVEGDDIDSLVSVISAM
+P------ETEEFGVDLLIFSDGFtGGSELSSLVDRLKA----QVVFAALTt--EAE----EVARKFGYAVISSGSLIETP--DRLLAKVASLEKR-----
+--
+>gi|119486146|ref|ZP_01620206.1| von Willebrand factor, type A [Lyngbya sp. PCC 8106]gi|119456637|gb|EAW37766.1| von Willebrand factor, type A [Lyngbya sp. PCC 8106]
+------SYTIVIARSGVSRD-qHhpwfneWIDAQASLIDLAKKCQeFDPEGLTIYEASSY------LKKYPKAtVSRFADLLQ-ENNrscvtnIIDINVV
+EAVADILNHYFERKENHQtkp-KG-EIIVVVLDKHGI-D-giGDLQQLIIKSshqmdyaEELGITFIQVG------------------------------
+---------------------
+>gi|227498725|ref|ZP_03928867.1| conserved hypothetical protein [Acidaminococcus sp. D21]gi|226904179|gb|EEH90097.1| conserved hypothetical protein [Acidaminococcus sp. D21]
+---------IMLDASASRG-EYQRVIAAQAYVIAEALRACGIPYQIYSFCTlrGYTVMTLYQSYEEKKKSTSVFS--YCATGWNRDGLALRGARVLM---
+---GDlTDAKKILVMLTDASPNDDHPlytgkgalsqheyrderavdDTAAEAASLRRDGVRIVGLINDEIA----GSmEDAQKIFG----KDLVRVKTLD
+KMAESVGKALCHQ-----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+C 1 * 0 * * * * * * * * * * * * * * * * * * 1
+ 639 4263 1710 0 * * * 6636 1009 0
+
+P 2 4708 * * 4795 4856 * * 3785 4920 * * 4903 1731 3273 3520 3371 2947 4879 * * 2
+ 44 * 5047 * * 0 * 7806 0 1988
+
+Q 3 * * 2844 3107 5430 4374 4585 * 3469 5424 * 4006 5533 3456 3848 3054 3264 4351 * * 3
+ 40 * 5195 * * 0 * 8697 0 1000
+
+E 4 3240 5840 6033 3154 * 2206 * * 3363 4827 5809 4288 5735 2909 3850 5388 4263 5908 * 5881 4
+ 0 * * * * * 0 9090 0 1055
+
+D 5 3653 * 4595 4088 * 3632 4264 5897 3198 4576 6376 4977 2364 3630 5394 3876 4532 6267 6227 4659 5
+ 19 6224 * 1000 1000 0 * 9446 1000 1055
+
+S 6 2983 * * * 3995 6153 6571 2764 5349 2397 3791 * 6156 5340 4330 6462 3799 2573 * 6301 6
+ 0 * * * * * * 9583 0 0
+
+D 7 4896 * 643 3845 * 5335 4848 * 6559 * * 4533 6407 6540 4683 4874 5343 6463 * 6434 7
+ 0 * * * * * * 9704 0 0
+
+I 8 5473 6667 * * 5145 * * 1652 * 2073 4406 * * * * * 4534 1879 * 5547 8
+ 0 * * * * * * 10083 0 0
+
+A 9 3029 6820 * * 5076 5664 6766 2869 * 3161 5225 * * * * 5711 3930 1429 6842 3838 9
+ 0 * * * * * * 10185 0 0
+
+F 10 5926 * * * 1449 6882 * 2381 * 1879 6979 * * * * 6223 5697 3693 6441 6011 10
+ 0 * * * * * * 10236 0 0
+
+L 11 2866 5040 * * * * * 2758 * 1442 6622 6767 6011 * * 6223 6772 1949 * * 11
+ 0 * * * * * * 10236 0 0
+
+I 12 5804 6803 * * 4120 6640 * 1972 * 1616 4550 * * * 6628 6608 6924 2214 6223 5375 12
+ 0 * * * * * * 10236 0 0
+
+D 13 6750 * 352 4000 * 5417 5320 * * * 6643 5092 * 5282 * 5814 6226 * * * 13
+ 0 * * * * * * 10245 0 0
+
+G 14 3145 5864 4185 4446 6711 3902 6713 3796 5118 5865 5151 4889 6916 4873 4519 2892 2815 3105 * 5375 14
+ 36 6022 6734 0 * * * 10245 1149 0
+
+S 15 5440 6630 5883 * * 5273 * * * 5627 * 5131 * * 6893 384 3312 * * * 15
+ 0 * * * * 0 * 10231 0 1018
+
+G 16 3315 * 4504 3404 6724 1611 6903 6701 5263 4827 * 5178 5162 4975 4630 3028 4866 4931 6824 5746 16
+ 14 * 6713 * * * * 10245 0 0
+
+S 17 4085 * 5298 6888 5224 3727 6809 5755 4780 6722 * 5656 5503 6879 5947 752 4508 5721 * 6897 17
+ 27 * 5768 * * 0 * 10226 0 1004
+
+I 18 4841 6204 6761 * * 6840 * 3052 * 4414 1035 6059 6613 5222 * 4735 4663 2904 * 6013 18
+ 52 5122 7188 3241 161 * 0 10237 1390 1206
+
+I 19 3089 * 3720 4645 * 2710 * 5826 4608 4433 6707 6709 4934 4033 3286 2663 4309 5033 * 4198 19
+ 278 * 2511 * * 1754 507 10289 0 1373
+
+P 20 3509 * 3938 2801 4930 2410 6499 6812 5557 4517 5485 4317 3698 3573 6642 4742 4748 4862 6449 4896 20
+ 32 * 5504 * * 219 2828 9994 0 4274
+
+H 21 3552 * 3300 3155 5770 4558 4941 6702 4287 6785 6536 3636 4719 3453 4169 3120 4709 4352 6533 4363 21
+ 97 3937 * 2442 293 1402 686 10177 2311 1765
+
+D 22 5158 * 2550 3293 5777 3606 4896 5800 3820 5184 4810 3147 5867 4377 5086 3423 3563 5753 * 6750 22
+ 237 2926 5651 2815 221 1353 717 10203 3406 1411
+
+F 23 6634 * * 5683 1999 6336 5193 3508 5670 2957 3964 5746 5820 5156 6435 4685 * 5217 2682 3597 23
+ 42 5106 * 1031 970 917 1088 10203 1412 1584
+
+R 24 4415 * 2517 3030 * 4856 5887 5246 4005 4369 5851 4188 5756 3487 3736 4468 3145 5752 * 4801 24
+ 42 5129 * 889 1120 * 0 10236 1430 1176
+
+R 25 2651 * 4201 4754 5166 7001 6728 3765 3237 3788 5270 5918 5210 3950 3349 4579 4554 4619 6784 3542 25
+ 36 5353 * 1775 498 1023 977 10236 1528 1176
+
+M 26 2221 * * 5146 4605 5810 * 3415 5152 3397 2933 5671 * 4487 5527 5850 3910 2538 * 6844 26
+ 25 * 5843 * * * 0 10245 0 1000
+
+K 27 4533 * 5183 6876 * * 5530 3426 1436 3822 6004 5714 6712 3574 2853 4660 6930 5295 6825 5870 27
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+ 18 6321 * 2000 415 0 * 10106 1017 2191
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+
+I 181 3781 6726 * 5416 3206 * 6281 2112 5485 2684 3926 6392 * 5120 4405 4609 4982 3493 6704 4672 181
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+L 185 6340 6567 * * 3357 6563 * 1683 * 1854 3641 * * 6373 * 6118 6508 2614 * * 185
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+E 187 5128 * 2640 2917 6130 3846 5256 * 3270 6047 6265 3708 * 3066 3331 4356 4258 5198 * 6236 187
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+
+K 188 3898 6035 5177 3139 6430 4170 * 6010 2971 5314 6206 4122 * 3818 2611 5133 3340 4157 6446 4615 188
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+I 192 4711 * 4377 * * * 4545 1929 4306 2875 4446 4388 * * * 4536 4466 2062 * * 192
+ 143 3410 * 0 * * * 7069 1073 0
+
+G 193 2687 * 2482 2604 * 1608 * * * 3587 * * * * * 3475 * * * * 193
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+S 194 * * * * * * * * * * * * * * * 0 * * * * 194
+ 0 * * 0 * * * 3455 0 0
+
+//
+�HHsearch 1.5
+NAME b3693168b9f04cd2db237b30b4be5176
+FAM
+FILE b3693168b9f04cd2db237b30b4be5176
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:48:59 2013
+LENG 176 match states, 176 columns in multiple alignment
+FILT 130 out of 1041 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHH
+HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9725554254999999999999999999999999999850387807899999999999999999999999986997747667777667769999999999
+9999999999999999998859999999999999999999999999999999984799976118997487506899
+>Consensus
+xxxxxrxxxxxxvxxxLnxxlxxexxaxxxYxxxaxxxxxxxxxxxxlxxxfxxxaxeexxhaxxlaexixxlGgxpxxxxixxxxxxxxxxxxexlxxx
+lxxExxxxxxxxxlxxxaxxxxDxxtxxxlxxxxixeqxxxxxxlxxxlxxlxxxxxxxxxxxxxxxDxxlxxxxx
+>b3693168b9f04cd2db237b30b4be5176
+MVSQVRQNYHSDCEAAVNRMLNLELYASYTYSSMYAFFDRDDVALHNVAEFFKEHSHEEREHAEKFMKYQNKRGGRVVLQDIKKPERDEWGNTLEAMQAA
+LQLEKTVNQALLDLHKLATDKVDPHLCDFLESEYLEEQVKDIKRIGDFITNLKRLGLPENGMGEYLFDKHSVKESS
+>gi|156933508|ref|YP_001437424.1| hypothetical protein ESA_01328 [Cronobacter sakazakii ATCC BAA-894]gi|156531762|gb|ABU76588.1| hypothetical protein ESA_01328 [Cronobacter sakazakii ATCC BAA-894]gi|333956802|gb|EGL74437.1| hypothetical protein CSE899_00345 [Cronobacter sakazakii E899]
+------------VVQKLNAQMNQEFYASNLCLYYSDWCAQQ--SLNGSATVLRQQAQHNVTQMMRLFDYLKQTGANPVVGALKSV-KPDCSSLEAIFHQM
+QDELGGRHAALARLMSEAQAARDDAMLAMLGE-FEQELRQDEALLATILNELTQARQ--AGLC-------------
+>gi|319789636|ref|YP_004151269.1| Ferritin Dps family protein [Thermovibrio ammonificans HB-1]gi|317114138|gb|ADU96628.1| Ferritin Dps family protein [Thermovibrio ammonificans HB-1]
+----------DKIVELLNRALADEWLAYYQYWIGSKVVK--GPMKSAVEAELVQHAADELRHADMLVMRILELGGTPILTPKrwfeltncgyDAP-EDP-
+-FVRRILEQNIKGEQCAIEVYNQIISFTK-DIDPVTYNLAVQ-IMTDEMEHEEDLQSLLEDLEnlKFLR-------------------
+>gi|110004363|emb|CAK98701.1| hypothetical ferritin protein [Spiroplasma citri]
+---------TKDIEKDLQHYIDEHIKMQFFCYNLSSAA--DKLGFPGFSHYFQVQAQDEVLHQRRIMNFVLDRDGHYQIKNIAEE-YKDIKNIIELMETY
+QTKRAYFAELTNKLAQHANTVGDLVTYKFYDW-FIIDFYEELAEVKDIIEWIKMSNN-----NYYEIDRKMG----
+>gi|260590733|ref|ZP_05856191.1| rubrerythrin [Prevotella veroralis F0319]gi|260537335|gb|EEX19952.1| rubrerythrin [Prevotella veroralis F0319]
+----------TGLEKFIEAVAMSKAMGVMNYYSLALMAEEQ--GLPEeLAKCFRELADRESVHAGFYATLNA------------K--LPS--DVFQMMEN
+MQKGELGAGKFLQPLADKLRELGREDVALQIEE-YIRQELHHGEILGELLAKYKK----------------------
+>gi|340755444|ref|ZP_08692131.1| ferritin [Fusobacterium sp. D12]gi|313687436|gb|EFS24271.1| ferritin [Fusobacterium sp. D12]
+------------------------------------------QQFMSIHSFTESQYDTYFGYYDDVAEALKMQGQRPLvrMkdylavTSIQEL-EDKNFS
+PCEVLSIVKADLEEMNQLAKEIRELAGEEDDFAVSNMMED-HIAANKKQLWFIDSMTK--------------------------
+>gi|116627595|ref|YP_820214.1| peroxide resistance protein,non-heme iron-containing ferritin [Streptococcus thermophilus LMD-9]gi|116100872|gb|ABJ66018.1| DNA-binding ferritin-like protein (oxidative damage protectant) [Streptococcus thermophilus LMD-9]
+------------TKAVLNQAVADLSV-AASIVHQVHWYM-RGPGFLYLHPKMDELMDSLNSHLDKISERLITIGGEPYstLVefssnsGLTET-TGTF-D
+QpmSDRIQLLVDIYKYLSVLFQVGLDITDEEGDVPSNDIFTD-AKSEIDKTIWMLTAELG--------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 2382 0 0
+
+V 2 * * * * * 1173 * * * * * * * * * 1829 * 1862 * * 2
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+
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+
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+
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+ 0 * * * * * * 4258 0 0
+
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+
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+
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+
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+
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+
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+
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+
+Y 29 4583 * 4207 5506 3908 4625 3621 5105 * 3403 5260 3810 * 3772 * 3841 3838 4660 * 2183 29
+ 0 * * * * 0 * 9487 0 1331
+
+T 30 4741 * 5761 5023 4054 * 4405 3730 5943 2361 4768 5854 * 2234 4642 4742 3828 4031 5904 5182 30
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+
+Y 31 5145 5569 * * 4650 * 5240 6480 4126 5140 6577 5764 * 5219 * * 6555 5281 * 524 31
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+
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+
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+
+A 36 2658 5688 6757 5242 4295 5743 2366 5201 3602 4356 5874 5938 * 6557 4438 3337 4737 4362 5328 3956 36
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+
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+
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+
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+
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+
+V 43 4550 6232 5562 3256 5910 * 4479 3899 3098 3657 6889 4986 3305 6907 4181 4713 4804 3571 3383 4837 43
+ 0 * * * * 495 1783 9602 0 2853
+
+A 44 4845 5860 3509 4355 6788 1910 4116 * 4840 6890 5966 2662 * 3775 6051 3299 4682 7139 * 5303 44
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+ 13 6788 * 0 * * * 9767 1026 0
+
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+
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+
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+F 52 * 5359 * * 1312 * * 5248 * 1683 3615 * * 6923 * 5786 4949 5832 6364 3939 52
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+K 53 5389 * 2774 2311 7162 7128 6781 6538 3279 3859 7025 4594 * 3100 2546 5835 * 5191 * 4617 53
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+
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+H 57 3401 * 2458 2707 * 7090 5379 4230 4160 3607 5674 3846 7183 3374 4712 4261 4557 6449 6522 * 57
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+
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+Y 69 6892 * * 6860 3683 * 4146 5340 4092 3504 4959 * * 6813 1428 * * * 5931 2010 69
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+N 71 5008 5780 7090 * 6149 4405 * 4297 4036 2038 5861 4134 * 4888 3046 6086 3122 2906 6944 5237 71
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+R 73 6994 7118 6682 * 5165 * * 4610 5876 1113 5124 4877 * 5053 1864 6839 5954 4851 * * 73
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+S 176 * * * * * * * * * * * * * * * 0 * * * * 176
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME b49b9cb98eb527401c12984cc1a2e18d
+FAM
+FILE b49b9cb98eb527401c12984cc1a2e18d
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:04:07 2013
+LENG 181 match states, 181 columns in multiple alignment
+FILT 157 out of 1390 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCEEEEEECCEEEEEEEEEECCCCCCCCCCCEEEEEEEEECHHHCCCCHHHHHH
+HHHHHHHCCCEEEEEECCCHHHHHHHHHCCCEEEEEEEEEEECCCEECCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9787379998998898788899999999987367889999998604887999999999999999963555566788779999999988883798999999
+999998647869999459989999999889999515702560088043233199999857776789887536686877779
+>Consensus
+xxxxxxxirxxxxxdxxxxxxxxixxlxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxivGxxxxxxxxxxxxxxxxxxxxixxxxVxxxxrgxGigxxLl
+xxxxxxxxxxxxlxxxxxnxxaxxxyxkxGfxxxxxxxxxxxxxxxxxxxxxxxmxxxlxxxxxxxxxxxxxxxxxxxxxx
+>b49b9cb98eb527401c12984cc1a2e18d
+MHTQVHTARLVHTADLDSETRQDIRQMVTGAFAGDFTETDWEHTLGGMHALIWHHGAIIAHAAVIQRRLIYRGNALRCGYVEGVAVRADWRGQRLVSALL
+DAVEQVMRGAYQLGALSSSARARRLYASRGWLPWHGPTSVLAPTGPVRTPDDDGTVFVLPIDISLDTSAELMCDWRAGDVW
+>gi|301059854|ref|ZP_07200746.1| acetyltransferase, GNAT family [delta proteobacterium NaphS2]gi|300446066|gb|EFK09939.1| acetyltransferase, GNAT family [delta proteobacterium NaphS2]
+-----------------------M-EIWEKKgDYLDpkrsneierAYIAKLEIEMKNGnCiaWVIEDKESVVASGAVtFISLVpNPSDLSSKVAYLHSMY
+TEKSYRNKKCAQQIIQKAIGLCAsQGVKRIMLNASDAGQPVYQKIGFRSAPDTM-------------------------------------------
+>gi|188501574|gb|ACD54701.1| GCN5-related N-acetyltransferase-like protein [Adineta vaga]
+-----FVLRNATDSDNVS-----LAKLNqqtffetyVNDYSTRytksdiknyfnssVSPESFAKTISDPkqAtwiIEDRTNGKFAAFAnagpckMTLPEI
+EK----GK-DGEIYRLYVLRHYQDDKLGETLMNVSLSwLEKqyPgrPIWLGVWKENLKAQEFHKQYNFKKVGERFY--QIGEYK--RPSFIMKKESS---
+------------------
+>gi|218677147|ref|YP_002395966.1| putative acetyltransferase [Vibrio splendidus LGP32]gi|218325415|emb|CAV27533.1| putative acetyltransferase [Vibrio splendidus LGP32]
+---mtieeENIQFQLVSNLEFEELFACVKQGLFihvDSVFgwDDDFQRQRLLNEYNPSwFHWVYLGKQRVGLVCF--------KPYDNAYHVHLLIISHQ
+YQDQSIGKKVMSriHEKAHQEqrnQVTLSSFRSN-TRAISFYQSLSYRVVD----------------------------------------------
+>gi|171915043|ref|ZP_02930513.1| putative acetyltransferase [Verrucomicrobium spinosum DSM 4136]
+LTSARLLLRPLHPGDAEA-----LCAYRslPEVAryqswesfGPDDAARLIEAQRTAQPdvpgtwfqlaFVETATGRVIGDCGLHCLQE-----DGRQME
+MG-ITLSPQYQGRGYATEAVECVLHYLFGtlhkhRVLASTDALNHRAAALFRRLGFRQEAHLVESLWFKGQW--GSEYLFALLKREWEASHSQKNLD---
+------
+>gi|120436347|ref|YP_862033.1| hypothetical protein GFO_2001 [Gramella forsetii KT0803]gi|117578497|emb|CAL66966.1| hypothetical protein GFO_2001 [Gramella forsetii KT0803]
+-----MEIKEADLNDIPE-----IVEVLKASLGEEqleLSEKVWRYKhIDNPFgssviLIAKEDNKIVGVRAFMRWQWQHGDKKYHALRAVDTATHPNHQ
+GKGIFKKLTLRAVDFSRsNDDNFIFNTPNEQSRPGYLKMGWEQVGNIQVGLRPSLSFLKFKKKQKFYKINKNISNSEIKELCTKW------
+>gi|256825653|ref|YP_003149613.1| acetyltransferase (GNAT) family protein [Kytococcus sedentarius DSM 20547]gi|256689046|gb|ACV06848.1| acetyltransferase (GNAT) family protein [Kytococcus sedentarius DSM 20547]
+------HLRKPVaae---TPA-----MTRLLaahQERVLGKasAAWADVDDRVLGR-gaefrfhRIAQDAdgq--ARGWVNVNDRAV---HR----vmid
+vyldpal-------Vagevd-----gadAAAVWDALFAWGRAAAIRmawrrgvsetVLDSSPYEADEFTRERLAAAGFHK--------------------
+----------------------------
+>gi|268610629|ref|ZP_06144356.1| hypothetical protein RflaF_14177 [Ruminococcus flavefaciens FD-1]
+-----FNCRILTRDEIASVYNAFMKQDFPSD--ELKPLSMITRSLDKGEyfcYGIFSGDKLCGYAYFVSI----IMDEKQYCLLDYFAILSDLRGQGTGS
+EFLHLLREELKnaEMVICESEDPVGTSgdeldirqrrIAFYLRNHFIDTGVKAEI---------FGVNYVLLELDSGRKHSEA-------------
+>gi|83945228|ref|ZP_00957577.1| hypothetical protein OA2633_00635 [Oceanicaulis alexandrii HTCC2633]gi|83851398|gb|EAP89254.1| hypothetical protein OA2633_00635 [Oceanicaulis alexandrii HTCC2633]
+-----------NLEDMQRIAVVRALVYMAEQDCP-YDEEFDGNDLAgATHFLGEAGGEPLGCLRIRW------FADF--AKIERVCVRKGHRSGRVARQM
+MTEAMEIIRrKGYRKFVGHVQEHLIPYWKRYGFIHREHRGVFVF-SDRA--YAE--MEGRPAPHPQalHIDTDPLILDRPEGD--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * 2075 * 2618 1417 4203 * * * 4185 * 3105 * * 1
+ 0 * * * * * * 7082 0 0
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+H 135 3473 7059 3661 3340 * 1453 4721 6147 4560 6498 6771 5751 4421 6095 4762 4013 6166 5043 6096 7129 135
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+S 139 3763 6876 4250 3388 5674 3378 3873 6573 4279 5703 * 3871 4010 5439 4770 3774 5366 3526 5061 3317 139
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+ 186 3050 * 1307 747 6241 19 6374 1148 7949
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+ 0 * * * * 821 1205 8128 0 1204
+
+D 166 2701 * 1656 3779 * 3774 4764 4635 4768 3158 * * 4737 * * 3062 * * * * 166
+ 56 4719 * 1585 585 * 0 8116 1013 1003
+
+T 167 * * 2407 2278 * 4625 * 3752 * 3779 * * 3115 * 4626 4714 3127 3811 4719 * 167
+ 67 4454 * 3000 193 * 0 8039 1015 1003
+
+S 168 3449 4458 2492 4584 * * * 3357 2441 4617 * * * 4428 4589 2870 3378 * * * 168
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+E 170 3395 * * 2359 * 4344 * 4548 2393 4527 * 3385 2388 * * 3358 * * * * 170
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+L 171 * * * * * 4170 * 4365 * 1072 4151 * * 4169 * * * 1964 4260 * 171
+ 0 * * * * * * 7081 0 0
+
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+C 173 3883 2294 * * 3840 * 4052 * 3898 2876 * 4019 4037 3872 3903 * 3754 3988 * * 173
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+G 178 * * * * * 0 * * * * * * * * * * * * * * 178
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+D 179 * * 0 * * * * * * * * * * * * * * * * * 179
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+W 181 * * * * * * * * * * * * * * * * * * 0 * 181
+ 0 * * 0 * * * 1665 0 0
+
+//
+�HHsearch 1.5
+NAME b5e4c6287793467d8b047e64ec6f935b
+FAM
+FILE b5e4c6287793467d8b047e64ec6f935b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:24:59 2013
+LENG 57 match states, 57 columns in multiple alignment
+FILT 167 out of 1145 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEECCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEEEEHHHEEECC
+>ss_conf PSIPRED confidence values
+999995354899988325669999999884489959999579978987875689987
+>Consensus
+xxxxaxxxxxxxxxxxlxxxxgdxixvxxxxxxxwxxxxxxxgxxgxxPxxxvxxxx
+>b5e4c6287793467d8b047e64ec6f935b
+CYVRALFDFNGNDEEDLPFKKGDILRIRDKPEEQWWNAEDSEGKRGMIPVPYVEKYG
+>gi|149638364|ref|XP_001515583.1| PREDICTED: similar to BMX non-receptor tyrosine kinase [Ornithorhynchus anatinus]
+--AVEEWDSESKRNSEVQPNISNLYALKHE-SPDEWPVKTKQSNENFllesqpnrifkcqraskiswfVRRKGEEE--
+>gi|302414846|ref|XP_003005255.1| AbpA [Verticillium albo-atrum VaMs.102]gi|261356324|gb|EEY18752.1| AbpA [Verticillium albo-atrum VaMs.102]
+--QELREANIPAAQPPAGAQAGGQRALIHSARANtsptlkWstrtggWAPTRrARAASSLATTSSSSRT-
+>gi|32565949|ref|NP_502695.2| Lateral Signaling Target family member (lst-4) [Caenorhabditis elegans]gi|24817571|emb|CAA19487.2| C. elegans protein Y37A1B.2b, confirmed by transcript evidence [Caenorhabditis elegans]
+--LRKAVENYPtPPGGSSEDAHRQLLerrrkQMLRrHTCSTLIKQDTSASPHKMKPpilmeeedEQHSTGK-
+>gi|55648067|ref|XP_512320.1| PREDICTED: cdc42-interacting protein 4 isoform 6 [Pan troglodytes]
+--CVAIYHFEDlGPPPPPSQGPARALSLWPrVKTSVlWKKTKGTAGP-GSGGKREAR---
+>gi|47226831|emb|CAG06673.1| unnamed protein product [Tetraodon nigroviridis]
+-LPPVSANPLGSGEvhGDSGLREGRSPGGVRQERR-----RGPaDPRRR-----------
+>gi|50309763|ref|XP_454894.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]gi|49644029|emb|CAG99981.1| KLLA0E20879p [Kluyveromyces lactis]
+-LFICITEYSKRMDDELDMRPGDKIQVVTDDgsyNDGWYFGKNLrTQEEGLYPKVFTQVI-
+>gi|328776214|ref|XP_393399.3| PREDICTED: tyrosine-protein kinase CSK [Apis mellifera]
+------------MTTHSNVTTPNITSHMNtGSTPVILTSNVTNPSNPAALS--VNP--
+>gi|47205035|emb|CAG14497.1| unnamed protein product [Tetraodon nigroviridis]
+-----------------------------lTgGvttfvalydyesrtasdlsfrkgerlqivnntegDWWLARSLTTGESGYIPSNYVAPS--
+>gi|125805800|ref|XP_694393.2| PREDICTED: myosin-VIIa [Danio rerio]
+-YAVAIQD-lsRqgASSALAIFWQGSHIAELQTrrcAVYHkGWRIFSRRrVDKSKeredksnwgsflRCNSDSA----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+C 1 4843 2231 4543 * 2855 5214 * 3839 * 4592 5620 * * * 2083 * * 2675 * 5650 1
+ 64 6018 5147 0 * * * 7500 1000 0
+
+Y 2 6502 * * 6792 3800 * 3757 4218 4297 3042 4826 * 5927 4115 2204 6167 4710 4733 6060 2499 2
+ 30 6963 6281 3492 134 0 * 8669 1161 1059
+
+V 3 2195 2831 7015 6698 3693 4540 * 5480 7223 3604 6105 5670 6729 6490 6527 4695 6974 2528 7213 3324 3
+ 33 5954 7222 0 * * 0 9900 1217 1053
+
+R 4 4957 * * 3760 7547 5073 7480 3700 2841 4236 6848 7542 6800 4571 1828 5834 4006 2743 7010 * 4
+ 8 7565 * 6426 17 * 0 9953 1000 1204
+
+A 5 1059 5228 6733 5367 * 4511 * 6065 4521 4755 6338 * 5096 * 5219 4819 4449 2638 * 6616 5
+ 33 7072 6023 3585 126 * 0 10021 1006 1204
+
+L 6 5260 * 6678 5055 5886 * * 2628 4306 1564 3907 5793 5790 4479 4126 4686 4016 4187 * 7358 6
+ 0 * * * * * 0 10002 0 1504
+
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+
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+
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+
+N 10 4759 6540 3482 2744 * 4456 4856 4384 3625 5238 7352 5536 5801 3964 3629 3401 3270 4199 * 4849 10
+ 49 4907 * 607 1542 1371 705 10051 1483 1346
+
+G 11 1939 7045 4981 5826 * 2626 * 7145 4228 * * 5898 2363 5928 6276 2775 4288 5947 * 7364 11
+ 80 4404 7268 307 2383 529 1703 10089 1816 1359
+
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+ 55 5447 6078 349 2220 1266 776 10094 1329 1127
+
+D 13 4099 7109 3206 4044 5607 3401 4438 6858 3736 7477 5345 3297 3827 4966 4517 3029 4384 6639 6087 4405 13
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+
+E 14 3352 7153 3322 3257 * 3707 6593 7043 5460 6580 6047 3944 2371 4080 4199 3856 3564 5501 * * 14
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+
+E 15 5173 6002 2204 3869 * 2425 4556 7034 3690 5058 7389 4683 4096 5314 4277 3793 4117 6392 7510 * 15
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+
+D 16 4717 * 3041 1576 5776 4069 5010 * 7236 4633 5840 5631 3626 4445 4602 3956 4525 5367 * 6449 16
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+
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+
+P 18 3261 7091 4503 3944 5730 4006 5507 7042 4548 7124 6549 4080 4311 4802 5096 1690 3453 5421 6832 * 18
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+
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+
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+ 22 7619 6665 1000 1000 * 0 10176 1000 1322
+
+K 21 3039 6560 5724 2991 5528 6254 5944 4428 2333 5209 6129 5894 3390 4742 3610 3885 4712 4369 * * 21
+ 38 5923 6698 2553 270 2022 408 10150 1224 1514
+
+G 22 5681 5752 3940 5425 * 819 6259 * 4915 5149 * 3396 5558 5536 4444 4573 7261 * * * 22
+ 26 6348 7517 3013 191 579 1597 10166 1156 1559
+
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+ 19 6254 * 1283 764 * 0 10205 1141 1221
+
+I 24 4162 5521 6693 4345 4685 7154 5194 2763 4318 3000 5430 6761 6269 4562 3547 3922 4690 2642 * 5076 24
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+L 25 4936 7521 * * 3860 5710 6663 2080 * 2078 5856 * 5286 7406 4958 * 6529 2038 6584 4475 25
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+
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+ 23 6724 7342 0 * 2323 322 10148 1084 1471
+
+I 27 5840 7157 5453 7135 7110 6415 5376 2587 * 2237 4867 5991 5017 4775 6662 6661 7089 1417 * 7619 27
+ 31 6146 7135 0 * * 0 10135 1176 1497
+
+R 28 4320 5724 5667 5345 4853 5292 4513 3314 5055 2008 6019 5996 5122 4886 4690 4798 3887 3014 5820 5261 28
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+
+D 29 5064 6972 4226 2711 6644 3857 3934 5810 3309 5744 * 3986 4361 3545 3326 3250 5389 4799 * 6373 29
+ 351 2211 * 743 1313 1673 543 10138 4903 1629
+
+K 30 4584 6692 3725 2884 * 3851 5673 4850 2519 4981 5219 5302 5433 4113 3401 4508 3619 4854 6248 7165 30
+ 152 4804 3964 2487 283 * 0 10197 1669 1395
+
+P 31 4721 5775 3005 3529 7466 3318 5024 4543 4655 3984 6551 4562 4779 5294 4979 2891 3401 3979 * 6556 31
+ 123 4856 4413 4236 79 532 1698 10055 1614 2634
+
+E 32 5920 4655 2384 2904 5613 3710 4921 * 4421 6068 7197 3239 5353 5191 3663 3771 3687 7278 6253 6236 32
+ 28 5692 * 2445 293 620 1517 10146 1253 2442
+
+E 33 3807 6690 2795 3095 6575 3343 5159 5035 3809 5922 * 4002 3936 5606 4185 2812 4915 7347 7276 6507 33
+ 207 3291 4995 1192 830 1539 609 10163 2983 1446
+
+Q 34 5031 7504 3014 3411 * 1398 5090 6099 5324 5083 6916 3706 6163 7667 5228 4512 4954 4690 7292 5916 34
+ 67 4736 7045 2749 232 1508 625 10144 1663 1907
+
+W 35 7547 * * 6643 4125 4532 7024 6466 6016 4435 6182 * * 5375 6433 4706 6446 4967 669 4529 35
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+
+W 36 4876 6190 5548 * 4114 5481 7617 4174 5694 3189 5171 6833 5996 7269 5713 5984 5947 4048 1395 3173 36
+ 42 5671 6738 2529 275 1823 479 10046 1278 1823
+
+N 37 4468 * 5553 4301 4226 5696 6352 4351 2933 2751 5489 5774 4236 4403 3076 4431 5231 5938 4272 3860 37
+ 21 6924 7282 5392 35 1504 627 10031 1050 1755
+
+A 38 3368 3650 6399 7290 6324 1503 * 5070 5572 * 6754 * 5654 5407 5623 4587 4616 2097 * * 38
+ 55 5904 5603 1850 469 1259 780 10162 1219 1572
+
+E 39 4990 7592 4676 3247 5184 6138 5114 6679 2956 5109 7517 5866 6665 4337 2132 3931 3163 3947 7177 5526 39
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+
+D 40 4365 6804 3647 4376 6808 4234 4364 5161 4043 3941 * 2221 * * 3138 3204 4174 4366 * 6679 40
+ 58 4656 * 1448 659 253 2634 9817 1510 5036
+
+S 41 3589 4759 4845 4077 7347 4971 5131 4412 3516 2405 6023 6559 4393 4866 4809 3872 3998 3481 * 4959 41
+ 456 1884 * 375 2126 2958 199 10103 5316 1695
+
+E 42 4048 6933 3107 3550 5760 2816 4989 * 3953 6241 7163 3423 4702 5961 3615 3990 3076 4565 * * 42
+ 88 4210 7541 1444 661 * 0 10076 1960 1592
+
+G 43 5734 5474 4369 4373 * 1163 5382 * 3840 6410 6899 4173 5324 4468 4871 3371 6047 6431 * 5769 43
+ 9 7397 * 2322 322 2024 407 10043 1000 1708
+
+K 44 4393 5610 4928 3043 6185 4805 4760 4660 2423 5084 6004 5013 5338 3509 3242 3262 4672 5182 * * 44
+ 31 6987 6258 1000 1000 2036 403 9997 1051 1507
+
+R 45 4188 7487 6391 2555 5583 5853 5747 4721 3420 3765 7350 5320 4113 4911 3657 3195 3682 3744 6361 5618 45
+ 50 4870 * 3026 189 703 1374 9941 1519 1593
+
+G 46 4332 7199 6189 5187 5953 642 * 7193 4083 * * 5658 4739 * 4626 4167 * 7255 * 5673 46
+ 95 4542 5584 2665 248 * 0 10026 1670 1151
+
+M 47 4354 7421 6212 6597 3133 6459 5002 3640 5875 2457 5385 7248 5108 * 5046 3648 5848 4718 2774 3129 47
+ 51 5143 7258 4167 83 2056 397 9946 1408 1572
+
+I 48 4003 5518 6440 * 1879 6224 * 2872 5642 3183 7131 * 4903 * * 5123 6391 1984 * 5779 48
+ 26 5829 * 2100 383 1332 731 9986 1339 1528
+
+P 49 5682 * 5640 5844 5944 5708 5456 * 6306 5096 * 5644 487 5973 5763 4465 5991 7561 * 6778 49
+ 34 5444 * 2080 389 481 1818 9977 1424 1270
+
+V 50 2332 7102 7612 4104 5872 3967 6500 5547 3275 4011 7449 5075 6408 4382 5154 2459 3734 3917 * 7444 50
+ 36 7080 5857 1000 1000 * 0 10005 1000 1000
+
+P 51 3782 * 4073 4569 * 4377 * 7199 4217 7044 * 2312 4201 3794 4349 2234 3436 7300 * 5565 51
+ 10 7191 * 2585 263 * 0 9829 1009 1342
+
+Y 52 5717 4344 7262 6206 2461 5627 3814 4587 6339 4505 6162 4416 5890 5552 5670 3668 * 5301 5497 1757 52
+ 42 5133 * 2462 289 395 2062 9791 1491 1342
+
+V 53 4350 5816 * 6284 5624 5952 * 2923 * 2181 6391 * 7211 6710 7020 3960 4999 1388 6806 6797 53
+ 32 5493 * 537 1687 * 0 9778 1229 1000
+
+E 54 4130 5992 4731 1846 * 7335 4812 7082 2843 4715 7379 5418 5979 3655 3556 4169 3973 5113 6637 5892 54
+ 39 5230 * 0 * 655 1454 9610 1377 1180
+
+K 55 4717 5660 4318 2359 5496 5311 7194 3583 4327 3791 7044 5000 2519 5621 4373 5021 6082 3412 * 5963 55
+ 43 5085 * 3791 108 1202 823 9403 1248 1130
+
+Y 56 5205 6676 6733 4956 4129 * 6787 2379 5519 1904 5898 * * 5899 6626 6722 4526 2184 * 4121 56
+ 159 3260 * 1488 636 0 * 8854 1391 1015
+
+G 57 3355 * 3883 * * 1363 5333 5416 * * * 3828 5211 5416 5467 2295 4316 * * * 57
+ 0 * * 0 * * * 7155 0 0
+
+//
+�HHsearch 1.5
+NAME b6a8572284504b5d762ee82f90b16d91
+FAM
+FILE b6a8572284504b5d762ee82f90b16d91
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:04:18 2013
+LENG 109 match states, 109 columns in multiple alignment
+FILT 151 out of 1109 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEECCCCEECCCCEEEECCEEEEEECCCCEEEEECCEEEEECCCCCCCCCCEEEECCCCCEEEECCCCCEEEECCCCCCCCCEEEEEECCCCEEEECCC
+EEECCCCCC
+>ss_conf PSIPRED confidence values
+9890699783899989989999999669989998099899977873588752699958986999979997898567779997689999089859995898
+043798488
+>Consensus
+xxxlxxgxxLxxgxxLxsgxxxlxxxxdgnlvlxxxxxxvWxsxxxxxxxxxxlxlxxxGnLvlxdxxxxxiWxSxtxxxxxxxxlxlxxdGnlvlyxxx
+xWxSxxxxx
+>b6a8572284504b5d762ee82f90b16d91
+DNILYSGETLSTGEFLNYGSFVFIMQEDCNLVLYDVDKPIWATNTGGLSRSCFLSMQTDGNLVVYNPSNKPIWASNTGGQNGNYVCILQKDRNVVIYGTD
+RWATGTHTG
+>gi|224099309|ref|XP_002334494.1| predicted protein [Populus trichocarpa]gi|222872794|gb|EEF09925.1| predicted protein [Populus trichocarpa]
+------------------TGSKAVLTANRGISLTDPqGRELWRSETIIGVV-AYGAMTDKGNFVLQDRVSDKLWESfknpadtllpsqvldrgmtlssrq
+sENNFSMGRFQLKLTDDGNLELATinlpsDytnePYYKSGTDG-
+>gi|302760705|ref|XP_002963775.1| hypothetical protein SELMODRAFT_405198 [Selaginella moellendorffii]gi|300169043|gb|EFJ35646.1| hypothetical protein SELMODRAFT_405198 [Selaginella moellendorffii]
+-----QGSTLPKGNSLISpsTEFRLSMEAGCDLVVRSshSgeiMRRIF----HGRDQACVLSLWTNGVLMVTGLQ-GSAGRRKRAMDaSFCSMHGEKEQH
+EARNECEhekaNYllyWRRSN---
+>gi|302765240|ref|XP_002966041.1| S-receptor kinase 1 [Selaginella moellendorffii]gi|300166855|gb|EFJ33461.1| S-receptor kinase 1 [Selaginella moellendorffii]
+------------------ANARLQLTAQGLF----VsDGAQLITIANVPSVAS-AELQDNGNFVVISSSGS--WQSFdvptdtlltgqliqgnkdilrsg
+sfSLylnqNSIGLKSYAVPE--------SnsqSYWDvqrspTSSN--
+>gi|224057535|ref|XP_002299255.1| predicted protein [Populus trichocarpa]gi|222846513|gb|EEE84060.1| predicted protein [Populus trichocarpa]
+-DTLLPTQIMEKGGILSsrlsetnfsQGRFQFRLIPDGNAVLNTInlptgfpYEAYFWSKTVD-snssNAGYQVVFNESGYLYVLRANNTreaLTL-GRV
+VPaTENYHRATLHFDGVFVLY------------
+>gi|125551438|gb|EAY97147.1| hypothetical protein OsI_19069 [Oryza sativa Indica Group]
+-NQLKSGNTLTph--SYITSpsGDFAFGFLAiESelsySsqFILalwFNlkvaessQQKVVWFAAEESSgsavtvQQQAVLSISANQLSLSnAGNGVVWK
+NQ---NPNQrFGSLVEITDNGNVKFLGDDgktIWES-----
+>gi|302789784|ref|XP_002976660.1| hypothetical protein SELMODRAFT_72392 [Selaginella moellendorffii]gi|300155698|gb|EFJ22329.1| hypothetical protein SELMODRAFT_72392 [Selaginella moellendorffii]
+-----------------------------------------------VGENATLQFTTDGELKVEED-GDVVWSTKTANR-GVRWLCMSNRATIMLLDES
+gsnvIWQSS----
+>gi|255550026|ref|XP_002516064.1| Serine/threonine-protein kinase PBS1, putative [Ricinus communis]gi|223544969|gb|EEF46484.1| Serine/threonine-protein kinase PBS1, putative [Ricinus communis]
+-RTILQGGELKYDQELVSadGMFKLKFGtvgESGESsdsYLgiwYNyieEKFPVWVANRDTPifGNSGILTVDSQGNLKILRDKGRSIVLYSVQKAIYNA
+IATLEDTGNFILRELNsngsikqvLWQSF----
+>gi|225461213|ref|XP_002280379.1| PREDICTED: hypothetical protein [Vitis vinifera]
+--------------------GVLRVTHQGILVVVNGInRILWNSNSSRSAQNPNAQLLESGNLVMKNGNDsdpeNFLWQSfdypcdtllpgmklgrntvt
+gldwylsswksADDPSKGNFTYGIDPSGlpQLVLRNGLavKFRAGPW--
+>gi|15227459|ref|NP_181720.1| curculin-like mannose-binding lectin fand PAN domain-containing protein [Arabidopsis thaliana]gi|75319139|sp|P93756.1|SD31_ARATH RecName: Full=G-type lectin S-receptor-like serine/threonine-protein kinase SD3-1; AltName: Full=S-domain-3 (SD3) receptor kinase 1; Short=SD3-1; Flags: Precursorgi|1871193|gb|AAB63553.1| putative receptor-like protein kinase [Arabidopsis thaliana]gi|20196890|gb|AAM14823.1| putative receptor-like protein kinase [Arabidopsis thaliana]gi|330254951|gb|AEC10045.1| curculin-like mannose-binding lectin fand PAN domain-containing protein [Arabidopsis thaliana]
+--TLLPNQKFPAFEMLRAasensrsSYYSLHLEDSGRLELRwESNITFWSSGNEvvkkkkK-KKNIGAVLTSEGALFLEDQDLmRPVWSVFGEDHndTVK
+FrFLRLDRDGNLRMYS-----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
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+V 36 3537 * 4261 4896 4824 2625 5646 * 4053 5224 6980 3526 4577 4174 4384 3200 4075 3538 * 5083 36
+ 814 1232 7556 1350 719 325 2311 8728 5317 1973
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+D 37 4749 6453 3615 5594 * 2362 5965 5613 3651 7380 6676 2908 6217 3522 3735 3427 4693 4594 5785 5458 37
+ 117 3680 * 1404 685 2079 390 8744 1861 1695
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+K 38 4240 * 4691 4675 5826 4190 4785 5265 3161 5838 * 3771 * 4894 2774 3476 2619 4191 * 4486 38
+ 49 4903 * 1647 555 605 1546 8752 1376 1638
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+P 39 3200 5282 6880 4074 5847 4877 7175 3591 5317 4920 * 5126 2768 4218 4702 5019 3777 2261 6592 6996 39
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+I 40 5133 * 6722 6397 5249 6277 6631 2554 4786 2763 5425 5636 6693 5886 5236 5737 4564 1720 * 3540 40
+ 47 5387 6888 1077 927 1076 928 8812 1222 1178
+
+W 41 * * 7013 * 4620 * * 6686 5781 7342 * 6616 * 6604 * 7209 * 6364 260 4529 41
+ 22 * 6029 * * * 0 8809 0 1154
+
+A 42 2777 4948 7011 5561 6462 5328 7451 5117 5330 * 5737 4860 6026 3512 4019 2111 3021 3697 5283 5517 42
+ 79 5862 4794 787 1250 * 0 8777 1261 1422
+
+T 43 2273 * * * 7090 4758 * 6071 5682 6091 * 4750 4262 6699 * 1486 2328 5276 6970 6496 43
+ 42 5117 * 1724 520 2402 303 8770 1389 1969
+
+N 44 4341 * 3261 4294 6857 2975 4884 5966 3643 5076 6418 1886 4008 5737 7394 4935 4435 4678 6994 7620 44
+ 37 7187 5744 1660 549 3265 159 8721 1085 1893
+
+T 45 3370 * 4881 5178 * 4416 5352 5091 7013 5217 6137 4764 5097 6756 2948 3460 1689 3865 6991 6676 45
+ 150 4379 4311 1614 571 278 2513 8747 1592 2072
+
+G 46 3086 5299 2959 4118 4432 3488 6010 4551 5064 4638 * 3767 5176 5766 4995 3273 4099 6168 4815 4476 46
+ 199 3304 5167 1016 984 1658 550 8743 2175 1727
+
+G 47 4514 7436 4350 4814 5794 2176 4989 5718 4902 7157 6909 2761 4027 4280 4821 3284 4139 4101 * 6164 47
+ 117 4621 4746 562 1631 1577 589 8742 1421 1749
+
+L 48 4610 6432 4618 4561 6972 4490 5896 4357 3048 4573 5985 4846 2733 4219 3714 3322 3934 4199 7211 5269 48
+ 478 2098 4371 1486 637 1460 652 8724 3621 2100
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+ 181 4860 3580 1003 997 341 2249 8776 1382 2519
+
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+M 56 6063 * * * 2827 * * 2902 * 974 3969 6596 * 5558 * * * 3609 * 5393 56
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+T 58 4556 * 2192 3483 6641 4274 6003 7132 4990 5175 6786 3097 3600 4259 6093 3172 3348 5560 * * 58
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+
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+
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+ 121 3635 * 956 1046 459 1876 8783 2018 2152
+
+K 70 4344 * 4524 4602 6256 3233 * 5669 3103 4846 4951 3581 6357 3917 3724 2737 4033 3675 * 5911 70
+ 116 3814 7366 1506 626 * 0 8883 1925 1259
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+P 71 3217 5494 7568 5054 5563 6804 7289 3081 6325 3743 5574 5057 3095 6132 5392 4221 3646 2221 5431 5992 71
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+I 72 4275 * * 5671 5686 7120 * 2109 5164 1933 6515 6895 5935 5910 6072 5390 4528 2288 7266 4835 72
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+W 73 * * * * 3814 6700 * 5608 6114 5642 6884 5369 * * * 6094 6758 6699 379 5099 73
+ 13 * 6791 * * 1110 898 8765 0 1430
+
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+ 139 4591 4321 179 3100 1852 468 8865 1660 1296
+
+S 75 4421 * * * * 5793 * 5141 5550 5126 * 4933 6357 7431 6643 805 2261 7620 * 6654 75
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+
+N 76 4534 * 3740 4507 2936 2476 6118 5257 4266 * 6535 2871 3539 5520 4627 3500 5284 5935 6812 * 76
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+
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+ 111 3925 6975 3433 140 841 1178 8501 1677 1897
+
+G 78 3387 7227 2479 * 4442 3764 4736 6986 5605 4030 5919 3021 5990 4428 6540 3066 4115 4675 * 4549 78
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+ 246 3208 4358 405 2031 1202 823 8504 2325 1476
+
+N 81 3622 * 5390 3742 * 2793 6712 4804 4056 6816 5271 4492 3250 4490 4465 2671 3637 4243 * 7364 81
+ 330 2900 3826 1533 612 506 1758 8481 2826 1971
+
+G 82 4296 6819 6025 4845 4755 1273 5825 5440 5486 5419 * 3969 3949 5928 6240 3774 5902 3965 * 4613 82
+ 143 4946 4007 1387 695 565 1626 8375 1592 1991
+
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+ 16 6471 * 3000 193 0 * 8565 1015 1328
+
+C 86 2173 6461 6723 * 4373 7027 6012 4453 * 1052 5120 * * * * * 4815 4205 6578 5099 86
+ 16 * 6507 * * * * 8599 0 0
+
+I 87 4237 6516 6897 4097 5179 4285 5150 3410 3889 6159 6562 6017 * 4311 3632 3863 2695 2319 * 7379 87
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+
+L 88 6485 * * 6012 4912 * * 2837 * 1189 2726 5737 6913 7565 * 6650 5931 2720 * * 88
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+
+Q 89 5816 * 2953 3343 * 5981 5122 * 4867 2891 * 4146 7119 1796 4213 4459 3853 5590 * * 89
+ 26 5828 * 2088 387 * * 8595 1131 0
+
+K 90 4764 * 1410 3591 6747 5382 5392 7072 5584 6693 6872 2977 3167 5552 4613 4659 4958 5852 * 6544 90
+ 32 7085 6113 0 * * 0 8586 1000 1007
+
+D 91 5259 * 1225 5658 * 6872 6805 6732 5824 5572 6677 3193 * 5970 5329 2604 3175 * * 5292 91
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+
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+
+N 93 5836 * 3916 4787 7070 7248 5476 5627 4755 4887 5803 982 * 4242 5009 4555 5292 4635 5624 5977 93
+ 85 4131 * 1449 658 882 1128 8601 1726 1098
+
+V 94 4756 6909 * * 2452 6636 * 3354 * 1052 4710 * 5556 * * * 5996 3355 * 6805 94
+ 32 5533 * 1000 1000 * 0 8610 1232 1000
+
+V 95 5630 5540 5617 5226 4462 5324 * 3965 5268 5422 5438 5524 * 4313 3510 5024 5011 1155 * 4887 95
+ 0 * * * * * 0 8610 0 1000
+
+I 96 6140 * 6703 * 4844 5896 6073 2588 * 1131 4675 5975 * 5026 * * 5979 2606 * 5570 96
+ 0 * * * * * 0 8610 0 1000
+
+Y 97 5084 * * 5117 3721 5534 6214 4451 5189 3518 5918 5828 * 5901 3745 6203 5120 5031 5086 1176 97
+ 175 3228 7044 1250 787 * 0 8599 2176 1000
+
+G 98 4060 5861 2184 5577 5595 2596 5864 6879 4804 6843 5506 2802 5479 5486 5226 3209 4815 6745 5210 6838 98
+ 178 3309 6041 1721 522 0 * 8357 1965 1227
+
+T 99 3364 * 4529 3383 * 3687 5312 6709 4190 5465 6152 3487 3453 4343 4158 2461 3939 5529 * 7495 99
+ 572 1649 6905 1953 431 * 0 8302 3553 1057
+
+D 100 3298 * 3239 4145 * 4302 * 5468 3451 4994 * 3547 3058 4584 4181 3486 4615 3219 * * 100
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+
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+
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+
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+
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+
+G 105 4027 * 3640 4099 3529 1757 6079 * 4976 * * 2940 4375 * 6060 3006 6191 * 5794 5552 105
+ 0 * * 0 * * * 7466 1000 0
+
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+ 0 * * * * * * 7066 0 0
+
+H 107 3527 * 4346 5585 3848 5480 4912 * 5391 * * 2893 5507 5498 * 2790 4430 4434 1971 5423 107
+ 0 * * * * * * 6723 0 0
+
+T 108 3987 * 3056 * * 3967 * 4196 1826 4436 * 3278 * 3139 4194 * 3338 * * * 108
+ 240 2706 * 1585 585 * * 5232 1073 0
+
+G 109 * * * * * 236 * * * * * * 2730 * * * * * * * 109
+ 0 * * 0 * * * 3200 0 0
+
+//
+�HHsearch 1.5
+NAME b903b162c87715ee7384e2af499c16cd
+FAM
+FILE b903b162c87715ee7384e2af499c16cd
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:31:15 2013
+LENG 99 match states, 99 columns in multiple alignment
+FILT 137 out of 1099 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEECCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCEECCCEEECCEEECCCCCEEEEEEEEECCCCCCEEEEEEECCCCCCCEEEECCCCC
+>ss_conf PSIPRED confidence values
+941999999736853479818999996575089889999889959677580656888999799999999745469989999998878976899726899
+>Consensus
+xxxxPxvxvxxxxxxxxxxxxxLxCxaxgfxPxxixvxWxxxgxxxxxxxxxxxxxxxxgtyxxxsxlxvxxxxxxxyxCxvxhxxxxxxxxxxxxxxx
+>b903b162c87715ee7384e2af499c16cd
+IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+-S----------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne---DLRSWTAADMAAQN---------------tqrkweaagvaeqw
+----RAYLEGECLEWLRRYLEKGK---------------et--LQ--raE---
+>gi|82407640|pdb|1ZVO|C Chain C, Semi-Extended Solution Structure Of Human Myeloma Immunoglobulin D Determined By Constrained X-Ray Scatteringgi|82407641|pdb|1ZVO|D Chain D, Semi-Extended Solution Structure Of Human Myeloma Immunoglobulin D Determined By Constrained X-Ray Scattering
+--I--------------------------FR-------WPESPKAQAsSVPTAQPQAEGSLAKATTAPATTRNTGrggEEKKKEKEKE------------
+---
+>gi|145559665|gb|ABP73658.1| MHC class I antigen [Sus scrofa]
+----LKTLR-GYYNQSEAG-SHTYQWMYGCYlgPDGLFLcgysQFGYDGADYvALNEDLRSWTAADMAAQISKRKWEAADEAERMRSYLQGrcvEWLQKY
+LemgkdTLQHAD--
+>gi|291165399|gb|ADD81220.1| immunoglobulin light chain [Larimichthys crocea]
+--TAPTLTVLPPSSEQLqQGKATLMCLANKGFPSDWSLSWKVDSSSSIs-weESRSPVVLEKDGLYSWSSTLRLDADQwrkVDSVTCEATQGSQ-TSLSQ
+TLR---
+>gi|16555266|gb|AAL23601.1| MHC class I antigen [Papio anubis]
+-EPSSQSTI-PIVGIIAGL-VLLGTVVTGAAVAAVM--------------WRRKSSDR-----------------------------------------
+>gi|66864114|dbj|BAD99230.1| immunoglobulin mu heavy chain [Takifugu rubripes]
+-------SLFPLIQCGsgtG-TMVTLGCLAADFTPSDLTYTWRkDGVD-LKDFIQYP-PTMNGNFYTkisqiqVkRQDWDGSPNftCAATHSTGNLWTPF
+TRPKE-------
+>gi|194376438|dbj|BAG62978.1| unnamed protein product [Homo sapiens]
+----PSVFLFPPKPKDtlmISRTPEVTCVVVDVshEDPEVQFKWYVDGVEVHNAKTKLREEQYNSTFRVVSVLTVLHQDwlnGKEYKCKVSNKALPAPIE
+KT-----
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+P 72 3178 * 5463 4202 7081 5407 5093 * 2968 4595 * 6563 2463 4587 3924 2859 3890 5673 4558 5940 72
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+M 99 * * * * * * * * * 1146 1805 * * * * * * 1932 * * 99
+ 0 * * 0 * * * 2405 0 0
+
+//
+�HHsearch 1.5
+NAME b94e58bdb4361ef7c1237e2f79e9939a
+FAM
+FILE b94e58bdb4361ef7c1237e2f79e9939a
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:39:46 2013
+LENG 131 match states, 131 columns in multiple alignment
+FILT 70 out of 72 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCEEECCCEECCCEECCCCCCCCCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHCCCCCCCCHHHHHCCCCEEEEEE
+EEHHHCCCCEEEECCEEECCCCCCCHHCCCC
+>ss_conf PSIPRED confidence values
+9999945744473877745265788789978689999866984788899999999998319999998489889999779999898899718831699885
+2222048825761047882854112001488
+>Consensus
+pRxxPGvvtGxGxxvxxxWlxxaxxxxGapIPxqIAdkLrGrxFxsFdxFRxafWxeVsxDpeLxxQFxxxNxxxmkxGxAPxaxxxexvGxrxkxelHH
+xxxIxxGGxVYdlDNLxixTPkxHixihxxx
+>b94e58bdb4361ef7c1237e2f79e9939a
+MRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHH
+EKPISQNGGVYDMDNISVVTPKRHIDIHRGK
+>gi|339489891|ref|YP_004704419.1| HNH endonuclease:S-type Pyocin [Pseudomonas putida S16]gi|338840734|gb|AEJ15539.1| HNH endonuclease:S-type Pyocin [Pseudomonas putida S16]
+PRNLPGVASGNGVITPDRVLDAATTAAGAPIPAKIAERLRGRRFARFDRLKEAIWMEIATDEVFSRHIMPAILDDMRRGLAPFAKRDQRVGKRVKLEIHH
+KHEIAKGGAVYDFDNLVFMTPQVHINHHRG-
+>gi|300938507|ref|ZP_07153246.1| type VI secretion system effector, Hcp1 family [Escherichia coli MS 21-1]gi|300456530|gb|EFK20023.1| type VI secretion system effector, Hcp1 family [Escherichia coli MS 21-1]
+PRKLPGVVTGRGVPLspGTRWLGmsVSNNGNGAPIPAHIADKLRGREFKTFDEFREALWLEVSQDPELIAQFSSGNQTRIKQGLTQKHHLKvGIMALKks
+lKNSRYIIVLQLNMAAAYTILIIYELLPPdytmRFTTGDKY--
+>gi|311033214|ref|ZP_07711304.1| YeeF [Bacillus sp. m3-13]
+-RHTPGVATTNKVSNAKVIMRGTDGNAGV-VPKEVADRLKGKSFKNFDAFRSEFWKTVSTS-SYAGEFSSANIKRMEKGFAPIAPKSQHYGKQKSYVLHH
+LTPINHGGGVYDIDNLLIVSPRLHQDIL---
+>gi|167035534|ref|YP_001670765.1| S-type pyocin [Pseudomonas putida GB-1]gi|166862022|gb|ABZ00430.1| S-type pyocin [Pseudomonas putida GB-1]
+---------------------------ASHLPEFIIQKLAGRTFHSFDHFSQSFWLAIAEDPIYSQQFIPAQLNRLKKGWPPRAPFHETAKGLRSYQLCH
+LNPPEWGGLMYDAENLRIMSA----------
+>gi|167036364|ref|YP_001671595.1| S-type pyocin domain-containing protein [Pseudomonas putida GB-1]gi|166862852|gb|ABZ01260.1| S-type Pyocin domain protein [Pseudomonas putida GB-1]
+----TGVVSGNGQVAGADWWPANGAAAGVAMPVQVGNQLRGRLFTGMPAFESAVWRAIAAEQGLLGQFDEVNQRRIIRGFPPVAPRASWSGARHEFELRH
+VGAVDVGSGLYNLDQLRIHTPAD--------
+>gi|300724110|ref|YP_003713427.1| hypothetical protein XNC1_3257 [Xenorhabdus nematophila ATCC 19061]gi|297630644|emb|CBJ91309.1| hypothetical protein XNC1_3257 [Xenorhabdus nematophila ATCC 19061]
+--------------------------------------------TPLDKFREDIWRAVEKDPTLKQNLKtKANKKAIEKGKAPFVRKKDQVGGRKKLELH
+HIAAIL--------------------------
+>gi|238786554|ref|ZP_04630416.1| klebicin D activity protein [Yersinia bercovieri ATCC 43970]gi|238712540|gb|EEQ04690.1| klebicin D activity protein [Yersinia bercovieri ATCC 43970]
+-----------------------------------------------------------------GQFNIVNKVEMINYRAPYPPAIEKVGGRKKYEIHH
+IKFIKMGVK----------------------
+>gi|108806970|ref|YP_650886.1| hypothetical protein YPA_0973 [Yersinia pestis Antiqua]gi|108778883|gb|ABG12941.1| conserved hypothetical protein [Yersinia pestis Antiqua]
+---------------------------------------------QFRGMRSKFLKSISDNPEVKKRFDSATLADLANGKAPK-----------GWDVHH
+KLPLDDSGT-NDVGNLVLI------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * 2533 4428 5476 * 452 * 5191 * * * * * 1
+ 0 * * * * * * 3313 0 0
+
+R 2 * * * * * * * * * * * * * * 0 * * * * * 2
+ 0 * * * * * * 3440 0 0
+
+N 3 * * 1976 4737 * * 4280 * 2626 4697 * 2054 * 5661 * 3129 * * * 3621 3
+ 0 * * * * * * 3440 0 0
+
+K 4 * * 4126 2489 * * * 3129 2980 2342 3786 5590 * 4193 * 4522 3258 5041 * * 4
+ 0 * * * * * * 3440 0 0
+
+P 5 4378 * * * * * * * * * * * 209 * * 4884 4234 * * * 5
+ 0 * * * * * * 3562 0 0
+
+G 6 * 5879 * * * 25 * * * * * * * * * * * * * * 6
+ 0 * * * * * * 3562 0 0
+
+K 7 4774 * * 6275 * * * 4141 3092 * * * * 5642 * * 1978 992 * * 7
+ 0 * * * * * * 3562 0 0
+
+A 8 1309 * * * * * * 4992 * * * * * * * 5086 * 901 * * 8
+ 0 * * * * * * 3562 0 0
+
+T 9 * * * * * * * * * * * * * * * 1378 701 * * * 9
+ 0 * * * * * * 3562 0 0
+
+G 10 * * * * * 224 * * * * * * * * * 3127 5093 * * * 10
+ 0 * * * * * * 3562 0 0
+
+K 11 * * * * 5421 * 3711 4908 2177 * * 2407 * 3937 3261 3208 5886 4095 * 3264 11
+ 0 * * * * * * 3562 0 0
+
+G 12 * * * * 3590 224 * 4992 5093 * * * * * * * * * * * 12
+ 125 3590 * 1820 480 * * 3562 1147 0
+
+K 13 5086 * * 1710 * * * * 3251 4604 * 4142 * 1890 * * 5886 2511 * * 13
+ 46 4992 * 2322 322 * * 3562 1018 0
+
+P 14 3533 * 3572 5974 * 4604 * 4256 3826 * * 4381 2154 3804 2986 4197 4242 3800 * * 14
+ 62 4577 * 1585 585 * * 3562 1048 0
+
+V 15 4234 * * 4992 * * * 2790 * 2750 * 5093 * * * * 3092 1072 * * 15
+ 200 2948 * 1000 1000 * * 3562 1247 0
+
+N 16 4566 * * 4947 5034 1629 * * * * * 4403 4868 3590 * 2165 2443 * * * 16
+ 0 * * * * * * 3562 0 0
+
+N 17 3203 * 2469 * * 1362 * * 2862 * * 3768 * * * 5789 3429 * * * 17
+ 28 5711 * 1000 1000 * * 3562 1000 0
+
+K 18 * * 4234 * * 4573 * 2513 2585 4884 * 2988 5711 * 2610 4828 3475 3394 * * 18
+ 0 * * * * * * 3562 0 0
+
+W 19 * * * * * * * 5093 * 3590 * * * * * * * 4868 229 * 19
+ 0 * * * * * * 3562 0 0
+
+L 20 * * * * 4897 * * * * 466 2634 * * * 5100 * * * 4258 * 20
+ 0 * * * * * * 3563 0 0
+
+N 21 2403 * 2397 5809 * 2372 * * 3552 * * 5197 4258 * 3587 3638 * * * 3613 21
+ 164 3217 * 1000 1000 * * 3563 1206 0
+
+N 22 2636 * 2998 4204 * 1709 5495 * 4589 6035 * 3375 * 5770 * 5760 5738 3024 * * 22
+ 0 * * * * * * 3563 0 0
+
+A 23 943 * 4599 * * * * * 4195 * * 4258 4764 * 4250 3034 3054 * * * 23
+ 26 * 5809 * * * * 3563 0 0
+
+G 24 3604 * 5079 * * 1289 5299 * * * * 2497 * * 5482 3187 2794 * * * 24
+ 0 * * 2322 322 * 0 3556 1000 1000
+
+K 25 2777 * * 4867 * 3732 * * 2434 * * 3240 * 3150 3283 3109 3030 * * * 25
+ 194 * 2991 1000 1000 0 * 3566 1000 1000
+
+D 26 2699 * 2726 3973 * 1257 * * * 4863 * 3748 * 5648 * 3575 * * * * 26
+ 0 * * * * 0 * 3427 0 1258
+
+L 27 2876 * 4242 2989 * * * 3287 * 2398 3898 2432 * 3661 * 4025 * * * * 27
+ 0 * * * * * * 3578 0 0
+
+G 28 3891 * * * * 217 * * * * * * 4320 * * 5480 * * * * 28
+ 0 * * * * * * 3706 0 0
+
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+ 183 * 3072 * * * * 3645 0 0
+
+P 30 3545 * * * * * 4117 * 5501 * * * 332 * * 4626 * * * * 30
+ 0 * * * * 0 * 3479 0 1327
+
+V 31 * * * * 5497 * * 447 * 4348 4410 * * * * * * 2753 * * 31
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+
+P 32 * * * * * * * * * * * * 0 * * * * * * * 32
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+
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+
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+
+I 35 * * * * * * * 335 * * * * * * * * * 2271 * * 35
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+
+A 36 307 * * * * 4410 * 4348 * * * * * * 3655 * * 5963 * * 36
+ 0 * * * * * * 3645 0 0
+
+N 37 * * 584 2694 * * * * * * * 2954 * 4348 * * * * * * 37
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+
+K 38 * * * * * * * * 565 5452 * * * 2407 3438 5615 * * * * 38
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+
+L 39 * * * * * * * * * 25 5845 * * * * * * * * * 39
+ 0 * * * * * * 3623 0 0
+
+R 40 4330 * * * * * * 5022 4720 * * 5676 * * 368 4681 * 4377 * * 40
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+
+D 41 * * 4061 * * 146 * * * * * * * * * 4771 * * * * 41
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+
+K 42 * * * * * 5439 * * 1794 * * * * 4974 652 * * 5624 * * 42
+ 0 * * * * * * 3637 0 0
+
+E 43 6089 * * 1419 * * * * 3975 4439 * 6000 4422 * 2416 2943 3217 * 6123 * 43
+ 0 * * * * * * 3637 0 0
+
+F 44 * * * * 52 * * * * * * * * * * * * * * 4828 44
+ 0 * * * * * * 3637 0 0
+
+K 45 3639 * 5591 * * 3799 4360 * 2063 * * 2929 * * 3911 2108 3479 * * 5662 45
+ 0 * * * * * * 3650 0 0
+
+S 46 * * 4509 * * 4503 5122 * * * * 2137 6030 4316 5043 1203 2993 * * * 46
+ 0 * * * * * * 3711 0 0
+
+F 47 * * * * 136 * * * * 6030 4503 * * * * * * * 5023 * 47
+ 0 * * * * * * 3711 0 0
+
+D 48 5167 * 460 * * 4181 * * * 5712 * 6224 4186 * 3288 * * * * * 48
+ 0 * * * * * * 3686 0 0
+
+D 49 2553 * 2124 2408 * 4997 3693 * 3350 * * * * 6195 3539 3414 * * 6425 * 49
+ 0 * * * * * * 3686 0 0
+
+F 50 * * * * 282 * * * * 3140 4997 * * 5778 * 6077 * * * * 50
+ 0 * * * * * * 3686 0 0
+
+R 51 * 6179 * 4529 * * * * 5054 * * * * * 290 3724 5712 * * * 51
+ 0 * * * * * * 3686 0 0
+
+K 52 3715 * 5712 1495 * * * * 2281 * * * * 4371 2736 2779 * * * * 52
+ 0 * * 0 * * * 3686 1000 0
+
+K 53 675 * 5051 3301 * 5077 * * 3953 * * * * 4306 * 4071 5225 6523 * * 53
+ 0 * * * * * * 3712 0 0
+
+F 54 * * * * 614 * * 3249 * 2614 * * * * * * 5341 4222 * * 54
+ 0 * * * * * * 3712 0 0
+
+W 55 * * * * * * * * * 4983 * * * * * * * * 46 * 55
+ 0 * * * * * * 3712 0 0
+
+E 56 4531 * * 3865 * * * 4797 1467 1956 3711 * * 4772 3646 * 5303 * * 6116 56
+ 0 * * * * * * 3876 0 0
+
+E 57 1676 6001 5763 1013 * * * * * * * * * * * 4865 3612 4593 * * 57
+ 0 * * * * * * 3876 0 0
+
+V 58 5797 * * * * * * 2496 * 6302 5126 * * * * * * 389 * * 58
+ 0 * * * * * * 4021 0 0
+
+S 59 1322 * * 5772 * 2612 * * * * * * 6285 * * 1303 * * * * 59
+ 98 * 3930 * * * * 4021 0 0
+
+K 60 3500 * 3098 3235 * * 5292 * 2188 * * 2328 * 2719 6132 5308 4234 * * * 60
+ 0 * * * * 0 * 4033 0 1193
+
+D 61 * 5419 340 3964 * * * * * * * 4269 * * * 6201 6148 * * 4545 61
+ 41 * 5146 * * * * 4021 0 0
+
+P 62 * * * 4912 * * * * * 5128 * * 536 3823 * 2769 5000 * * * 62
+ 0 * * 0 * 0 * 4014 1000 1072
+
+E 63 3709 * 3774 991 * 4549 * 4609 4880 * * 5933 * * 5797 3587 4608 3816 * * 63
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+
+L 64 5801 * * * 4951 * * 5702 * 402 * * * * * * * 4220 * 3057 64
+ 0 * * * * * * 4021 0 0
+
+S 65 2962 * * * 6269 4951 * 2627 3841 3169 5295 * * * * 1374 * 3791 * * 65
+ 0 * * * * * * 4073 0 0
+
+K 66 2660 * * 3250 * 2767 * * 1732 * * 4631 * 3334 3433 4498 6350 * * * 66
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+
+Q 67 * * 6359 3741 * 5867 4158 * * * * 3993 * 476 4608 * * * * 5858 67
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+
+F 68 * * * * 205 * * 4987 * 3311 * * * * * * * * * * 68
+ 0 * * * * * * 4147 0 0
+
+S 69 * * 2877 * * 4323 * 3441 2556 * 4987 2632 * * 6144 1826 4367 * * 6115 69
+ 29 5669 * 0 * * * 4147 1010 0
+
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+
+N 71 1983 * 4514 * 6234 2369 4413 6252 * 4787 4344 3787 * 4186 4168 3275 * 3952 * * 71
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+
+N 72 * * 5014 * * * * 5027 * * * 406 * 4784 * 3224 4627 * * * 72
+ 0 * * * * * * 4199 0 0
+
+N 73 4779 * * * * * * 2819 2923 1750 6032 5229 * 1972 3753 * * 5532 * * 73
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+
+D 74 3423 * 4570 3310 5232 3853 * 5437 3535 6252 5454 3681 * 5062 3963 3588 2241 4696 * 5832 74
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+
+R 75 6063 * 3384 3978 5087 * * 5423 * 2542 * 3398 * 5927 1248 4802 6232 6414 6979 * 75
+ 0 * * * * * * 4199 0 0
+
+M 76 * * * * * * * 1518 * 3345 1128 * * * * * 6862 3532 * * 76
+ 0 * * * * * * 4388 0 0
+
+K 77 4043 * * 5125 * 6551 * 4407 982 5155 5634 * 6567 6628 2878 2944 6418 * * * 77
+ 20 6218 * 0 * * * 4352 1025 0
+
+V 78 5137 * 3994 3945 * 5263 6774 * 2259 4837 6416 2383 * 2169 3326 5924 * 5450 * * 78
+ 0 * * * * * * 4352 0 0
+
+G 79 * * * * * 129 * * 4853 * * * * * 5359 6353 * * * 6145 79
+ 0 * * * * * * 4352 0 0
+
+K 80 * * * * 3369 5043 * * 1765 1963 * 4155 * * 2745 * 5992 * 4862 3906 80
+ 0 * * * * * * 4352 0 0
+
+A 81 744 * * * * * * 4629 * * * * 3892 * * 2463 3364 5898 * * 81
+ 0 * * * * * * 4352 0 0
+
+P 82 4315 * * * * * * * * * * * 259 3759 * 4635 * * * * 82
+ 0 * * * * * * 4352 0 0
+
+K 83 6453 * * * 2291 * 4839 4534 2040 6379 * * * * 3353 4966 4656 4482 6302 2159 83
+ 78 * 4244 * * * * 4352 0 0
+
+T 84 1243 * * * * * 3635 * * * * * 3429 * * 3633 3033 2312 * * 84
+ 0 * * * * 2741 234 4273 0 1142
+
+R 85 5698 * 5111 * 6554 * 3636 3873 3524 5111 * 6766 1369 * 1932 * * 5795 * * 85
+ 0 * * * * * 0 4272 0 1114
+
+T 86 3978 * 6168 3195 3368 6295 * 5308 2507 2346 * 6839 3706 * 3105 4091 5420 5482 * * 86
+ 0 * * * * * 0 4272 0 1114
+
+Q 87 3254 5695 4216 3003 * * 4518 4319 3021 4772 * 4909 5284 4845 3872 2187 4495 5821 * * 87
+ 270 2647 6511 0 * * 0 4183 1328 1114
+
+D 88 * * 1966 1345 * 3417 5240 * * * * * * 2945 * 4873 * * 4247 6177 88
+ 0 * * * * * 0 4183 0 1142
+
+V 89 5817 * * * * * 2646 3651 3758 * * * * 1827 2841 3916 3812 6385 4151 4578 89
+ 0 * * * * * 0 4183 0 1142
+
+S 90 2848 * 5684 * * 6406 6132 3958 * 5139 3651 * * * 6388 4439 * 1244 * 2617 90
+ 20 6158 * 0 * * 0 4183 1000 1142
+
+G 91 3651 * * * * 272 * * 4513 6132 * 5328 * * * 6741 * * * * 91
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+
+K 92 4414 * 6614 4577 * 1692 * * 1756 3651 * 5207 3658 6202 5012 3948 * * * * 92
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+
+R 93 * * * * * * 4229 * 2404 4066 * 5155 * 4434 726 * * 5712 * * 93
+ 230 2765 * 1928 440 1362 711 4145 1328 1191
+
+T 94 * * 5333 3307 * 5247 4477 4572 1756 5325 * 5192 * 4402 3599 5716 3596 2590 6075 * 94
+ 15 6607 * 2296 329 0 * 4190 1026 1098
+
+S 95 6461 * * 4354 * 4418 * * 1318 * * 3713 6454 5086 3793 2567 3740 4087 * * 95
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+F 96 * * * * 1351 * 4766 4381 * 4107 * * * * * 3713 6598 6317 5070 1572 96
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+
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+
+H 100 * * * * * * 110 3773 * * * * * * * * * * * * 100
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+
+E 101 * 5999 4613 5291 6207 * * 3250 1939 3560 * 4681 * * 5648 5124 * 1449 * * 101
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+
+K 102 6032 * 3899 3633 * 4418 3969 3841 2357 3265 * 3513 * 3251 * * 4957 2915 * * 102
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+
+P 103 2624 * * 2641 4715 * 5708 * 6151 4732 * * 1572 3281 4863 5528 5365 * 5349 5356 103
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+
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+
+Q 106 * 6098 2931 3002 * * 4169 * 3137 * 3533 3548 5983 2937 4396 5125 * 4835 4588 3488 106
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+
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+
+G 108 3786 * * * * 187 * * * * * * * * * 4835 * 6171 * * 108
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+G 109 1670 * 2979 2557 * 2583 * * 4779 4588 6157 5385 * * * 4051 4447 * * * 109
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+
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+ 0 * * * * 0 * 4056 0 1070
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+
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+
+V 119 4727 * * * * * 4111 4275 * 2434 2407 4367 * * 5043 * 3150 1798 * * 119
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+
+T 120 * * * * * * * * * * * * 3824 * * 3006 313 * * * 120
+ 0 * * * * * * 3902 0 0
+
+P 121 4391 * * * * * * * * * * * 70 * * * * * * * 121
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+K 122 4380 * * * * * * * 642 5505 * * * 4958 2067 * * * * 5751 122
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+
+H 124 * * * * * * 155 * * * * * * * * * 3842 * * 4964 124
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+I 125 * * 3583 * * 5092 * 783 5417 * * 5452 * 3267 * 5505 3561 4344 * * 125
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+//
+�HHsearch 1.5
+NAME ba17a05f924bfd8ff94a6c5d73635b4a
+FAM
+FILE ba17a05f924bfd8ff94a6c5d73635b4a
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:21:28 2013
+LENG 207 match states, 207 columns in multiple alignment
+FILT 121 out of 1261 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCEEEEEEEEEECCEEEEEEEEEECCCCCEEEEEEECCCCEEEEEEEECCCEEEEEEEECCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHHHCC
+CCEEEEEEEEEEECCCCCEEEEEEEEEEECCCCCCCCCCCCCCEEEEEEEEHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHH
+HHHHCCC
+>ss_conf PSIPRED confidence values
+9988737954699997888999999999799979878998249999999993799899999743788898198657552889989999999999998799
+6503489899994489750799999999747765556788540479999889998878767884547999999999998737566888899987775145
+4543159
+>Consensus
+xxxxxxxxxxxxxvxxxxxxxxxxxxxxxxxgxxxxxxxxxxxxxvxvvvxxxxgxvlLxrxxrxxxxxxxwxxPgGxvxexxEsxxxaAxRElxEEtGl
+xxxxxxxxxxxxxxxxxxxxxxxxfxxxxxxxxxxxxxxxexExxxxxwvxxxelxxxxxxgxxxxxxxxxaxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+xxxxxxx
+>ba17a05f924bfd8ff94a6c5d73635b4a
+MAEHDFETISSETLHTGAIFALRRDQVRMPGGGIVTREVVEHFGAVAIVAMDDNGNIPMVYQYRHTYGRRLWELPAGLLDVAGEPPHLTAARELREEVGL
+QASTWQVLVDLDTAPGFSDESVRVYLATGLREVGRPEAHHEEADMTMGWYPIAEAARRVLRGEIVNSIAIAGVLAVHAVTTGFAQPRPLDTEWIDRPTAF
+AARRAER
+>gi|110639472|ref|YP_679681.1| oxidative damage repair protein [Cytophaga hutchinsonii ATCC 33406]gi|110282153|gb|ABG60339.1| mutator protein; oxidative damage repair protein [Cytophaga hutchinsonii ATCC 33406]
+-------------------------------------------AVVCAVIKQ-QDSYFIAQRSAKMKMPLKWEFPGGKV-EKGETNAQAIMREMKEEFDV
+NVEVIQEHPFYLHQYPNFILQLSPMEVEITSGKLTL---KEH--ANYRWVAVKDLFTYD-----------------------------------------
+-------
+>gi|156371508|ref|XP_001628805.1| predicted protein [Nematostella vectensis]gi|156215791|gb|EDO36742.1| predicted protein [Nematostella vectensis]
+---------KVVPCENSRFIQPSRVVFN-QNGRQRAWDYITEHDDVACLMFNTTrQAFVLVKQFRPAIYmhnnralhntkhgidgtlvksedpktealad
+ptsGITYELCAGIID-QNISLVKLMKQEMLEECGYDVpeNKIERVTSFRAGVGSTGAVQTIFYAEVTDEmivTgAGGGNLQEGERIEVYYLPLDKSKEFV
+FNESLAKPaALLFAFLWYF------------------------------
+>gi|304311751|ref|YP_003811349.1| predicted NUDIX hydrolase [gamma proteobacterium HdN1]gi|301797484|emb|CBL45704.1| predicted NUDIX hydrolase [gamma proteobacterium HdN1]
+------------------------------------------PSSTVVLLRDTRRgiKVLLLRRNSKIAYGGSWVFPGGRI-DPDEiaktdhnalqAAKL
+AAVRETHEEAGITLEQEKLVyFSHWTTPVIRPKRFsTWFFMAPVS-EKKVEI-DGGEIHDFEWHTPESALQAQNQGSIElpppTFVTLTQLSRFGSTTQA
+LEHFAAQPPLE--------------
+>gi|262200404|ref|YP_003271612.1| NUDIX hydrolase [Gordonia bronchialis DSM 43247]gi|262083751|gb|ACY19719.1| NUDIX hydrolase [Gordonia bronchialis DSM 43247]
+---------------------------------------------IAVLTVQS-g---GLQVVVQ-----hdasGRAALPGRFV-RERRTVEETVREVLE
+LKLGLSPDHIRPhlLAVFSDpdrDPRGWT-ISIAHAVAIPAGDLTD---VV-gE--LVPVTPDGRLASgerLLYD-------------------------
+---------------------
+>gi|339018605|ref|ZP_08644736.1| DNA glycosylase A/G-specific MutY [Acetobacter tropicalis NBRC 101654]gi|338752283|dbj|GAA08040.1| DNA glycosylase A/G-specific MutY [Acetobacter tropicalis NBRC 101654]
+--------------------------------------------GAHFLVIDAAGQVLLRKRPEKGLLAAMTELPGTPW-RTEPW-----STEeALTHAP
+VQTEWQD-CGMVKHVFTHFTLQVTVYAAHIsrfSNQAVQE----------GFLAPATGVDAL--------------------------------------
+-----------
+>gi|260655139|ref|ZP_05860627.1| conserved hypothetical protein [Jonquetella anthropi E3_33 E1]gi|260630061|gb|EEX48255.1| conserved hypothetical protein [Jonquetella anthropi E3_33 E1]
+---------------------------------------------ITTVIIYYNGQVLV--NTTNTTESRQYELITCDA-DVEEIGQVALKIVLGKVIDD
+TINDIKKFKIEEETRDDSQVTVQYFIYEPQNETILK---DNSD---VKWLACDNLDQ-------------------------------------------
+-------
+>gi|288923038|ref|ZP_06417192.1| NUDIX hydrolase [Frankia sp. EUN1f]gi|288345621|gb|EFC79996.1| NUDIX hydrolase [Frankia sp. EUN1f]
+------------------------------------------------VFLTLGNRVVVANHR----GQPWFFLLGERV-APGEGVEQVLHRVLRRTAGF
+EVRALDFVGGMerhETGRGTgheaAHEIDVLFAGAVPRYAEFG---SRVDEVDLVTVERSDLHRV-----------------------------------
+--------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * 2383 714 * * * * * * 2333 * * 1
+ 0 * * * * * * 3269 0 0
+
+A 2 501 * * * * * * * * * * * * * * 2797 2741 * * * 2
+ 0 * * * * * * 4087 0 0
+
+E 3 * * * 1939 * * 3556 * * * * 3305 3531 * 1801 3605 3359 * * * 3
+ 115 3703 * 0 * * * 5107 1035 0
+
+H 4 * * * 2005 * * 2453 * 2624 * 4091 * * 3791 3013 3340 * 4250 * * 4
+ 82 * 4180 5044 44 * * 5985 1023 0
+
+D 5 4681 * 1980 * * 4421 * 4313 2690 * * * 2667 * 2975 4532 3525 4611 * * 5
+ 44 5048 * 1585 585 0 * 6635 1035 1000
+
+F 6 4781 * * 4303 3086 4437 * 3562 * 4686 * * 3905 4438 * * * 3751 1620 3146 6
+ 0 * * * * * * 6824 0 0
+
+E 7 * * 4833 2320 * 4926 * 3973 1959 3226 * * * 4102 4838 4647 2832 5042 * * 7
+ 0 * * * * * * 7099 0 0
+
+T 8 * 3601 4972 5021 * * * 2188 * 2618 * * * * 3876 4583 2104 2940 * * 8
+ 0 * * * * * * 7294 0 0
+
+I 9 4583 * * 4913 4888 4705 5135 2654 3983 2464 4770 5103 * * 3889 * 3510 2321 * * 9
+ 0 * * * * * * 7294 0 0
+
+S 10 3240 * * 2145 * 3043 5120 * 3494 4857 5005 3130 * * 5144 2649 4021 * * * 10
+ 0 * * * * * * 7485 0 0
+
+S 11 3834 5218 3502 2785 * * 3471 5163 * 5025 5120 * 5144 3857 2506 2772 3789 * * * 11
+ 0 * * * * * * 7485 0 0
+
+E 12 * * 5115 1935 5255 5446 4030 5597 2685 * * * * 4174 2278 3343 4920 * * 5062 12
+ 0 * * * * * * 7610 0 0
+
+T 13 5255 * 3085 3941 5219 * 3397 3943 4109 3979 * * 4065 4920 5313 4121 2501 3263 * 5237 13
+ 0 * * 3459 138 * * 7610 1000 0
+
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+
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+ 0 * * * * * * 7773 0 0
+
+T 16 3509 * 5263 2597 * * 5282 * 2491 * * 5233 4061 3755 3094 2807 3752 5478 * * 16
+ 0 * * * * * * 7773 0 0
+
+G 17 3649 5130 3850 * 5101 1362 * * * * * 2578 * * 5352 2961 3577 * * * 17
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+
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+
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+
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+
+A 21 4527 5440 3046 4133 * 5290 4323 * 2823 4970 * 4444 5137 4372 2853 2975 3385 5453 * * 21
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+
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+ 0 * * * * * * 8000 0 0
+
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+ 0 * * * * * * 8199 0 0
+
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+
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+ 0 * * * * * * 8223 0 0
+
+Q 26 3234 5745 2537 3587 * 5643 4086 * 2614 5659 5434 4547 * 5633 3629 4566 3164 5761 5758 * 26
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+
+V 27 4026 4024 * * 3482 * * 2976 * 2392 5408 * * * * 5387 * 1874 4253 3361 27
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+
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+
+M 29 4542 * 3957 * 2430 5582 * 3782 5357 2252 4379 4020 5731 * 4024 3396 5265 4390 * 5612 29
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+
+P 30 4437 * 3845 3950 5373 4707 5940 * 3527 5603 * 5609 1586 4084 4951 3158 4109 * * 5741 30
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+
+G 31 3759 6059 1945 5714 * 3735 6264 * 4142 5912 * 2493 4748 3749 4682 3873 3742 * * * 31
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+
+G 32 5705 * 6111 3842 6049 938 4881 * 4054 * * 4248 * 5933 5881 3210 4258 5713 * * 32
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+
+G 33 4628 * 5860 3325 5732 3872 4853 5903 2259 5675 * * 5710 3472 2459 3300 4944 5066 * 5598 33
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+
+I 34 3842 6085 * 2361 5957 * 5773 3813 3632 5473 * * 5994 3999 3411 3524 2872 3674 * 4720 34
+ 108 4241 5702 0 * 704 1373 8574 1260 1179
+
+V 35 3366 * 5998 3369 4304 5882 * 3892 4192 3125 4822 5516 4713 4217 3315 3465 * 3167 5903 5784 35
+ 51 4854 * 749 1304 0 * 8693 1224 1099
+
+T 36 5920 * 3505 3630 * 4606 5819 4622 6213 3839 5712 3458 3034 3805 4081 3400 4038 3963 4948 5872 36
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+
+R 37 5681 * 4398 * 3119 5910 * * 4199 5016 * 4996 4406 5024 1876 5559 5872 4966 4100 2282 37
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+
+E 38 4769 * 2664 2172 4600 3412 5177 5342 5978 5762 5793 5013 6223 * 4545 3721 4450 * 4554 3435 38
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+
+V 39 4244 5212 * 5801 4991 6135 6132 4341 4242 3925 5923 5988 * 3908 4246 4315 4203 1932 4398 3202 39
+ 0 * * * * * 0 8942 0 1010
+
+V 40 3625 4427 * 6135 4481 * * 2942 5963 2937 6091 5198 3801 5811 * 5502 5026 1921 5904 3803 40
+ 55 4734 * 2326 321 0 * 8942 1280 1010
+
+E 41 6107 * 2957 2577 6000 2568 5172 6174 5242 3880 * 5216 3876 4996 3009 3987 4176 * * * 41
+ 54 5308 6432 2178 360 * * 9000 1143 0
+
+H 42 5079 * * 4149 4645 4567 3043 * 4538 4637 * 4040 5101 4258 2011 3940 4205 4423 * 3818 42
+ 122 3625 * 2232 345 * 0 9045 1604 1040
+
+F 43 5340 4950 3983 * 5361 3885 3832 6294 4200 5092 * 3118 2196 6166 3435 6409 4685 3233 * 5365 43
+ 244 2682 * 1610 572 0 * 9058 2213 1040
+
+G 44 3706 4996 3034 6304 5206 2599 4698 6128 4364 4666 * 4482 3278 5444 3593 3456 4718 4585 * * 44
+ 62 4579 * 2396 304 * * 9122 1289 0
+
+A 45 1714 5142 6744 5735 4984 2855 6215 5003 6449 6793 * 6705 5788 * 5597 2869 3602 3387 6797 4979 45
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+
+V 46 2959 4511 * 5790 4725 5300 * 4552 6566 4618 5873 * * * 6554 4425 4299 1062 6538 4734 46
+ 0 * * * * * * 9807 0 0
+
+A 47 2650 4205 4484 5683 * 3145 5484 4380 * 3803 3329 5861 6331 * 4641 4199 3472 3028 6520 5653 47
+ 0 * * * * * * 9810 0 0
+
+I 48 3031 4437 * 6883 5003 4243 * 2108 6747 3278 4212 * * * 6468 5115 5145 1924 6839 * 48
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+
+V 49 3550 4941 6664 * 3192 6889 * 2376 * 2529 4043 * 5875 6553 * 6702 * 2096 5840 4677 49
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+
+A 50 3360 5331 * * 5264 5606 6438 2288 * 2705 6593 * 2814 6663 5570 6585 5718 2131 6991 6326 50
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+
+M 51 5465 * 5120 4305 2946 6316 6558 2654 4699 2894 4872 7063 * 5278 3341 5957 4431 3274 5575 4055 51
+ 134 4085 5060 2128 375 * 0 9827 1625 1178
+
+D 52 5667 6659 1911 4321 5591 * 5131 4746 4282 5830 6199 2660 6822 4853 3328 4110 3985 4934 7227 5397 52
+ 184 4984 3507 1866 462 823 1202 9729 1216 1607
+
+D 53 4100 * 4181 2219 * 3737 5252 4885 3500 5100 * 4691 3262 5467 3786 3547 4597 4973 * 5481 53
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+N 54 4108 6912 2465 2772 6952 3642 4219 6770 3730 5818 6543 2915 5223 4069 4041 * 4680 5303 * 7066 54
+ 230 3092 5067 189 3026 0 * 9853 2689 1275
+
+G 55 5611 5727 2886 4047 * 1334 6471 6905 3980 6814 * 3465 6023 7062 4500 4792 4265 * 6554 5648 55
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+
+N 56 4354 * 4750 2501 * 4914 4766 * 2402 5647 * 4607 * 2836 2656 5985 4039 * 6924 4895 56
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+I 57 5466 5710 6836 5938 3667 * * 2610 5288 2680 5679 * * 5901 7155 * 5391 1424 6915 4034 57
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+
+M 59 4638 5418 * 6679 4049 * 6901 2919 * 1044 3818 * * * * * 6070 2786 * 6630 59
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+V 60 3898 5274 6693 5125 * 4201 6130 2570 6767 2724 5672 * 6379 4653 4414 5715 3766 2048 * 5750 60
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+
+Y 61 5830 6645 6765 3925 * 5785 4749 6427 2098 4704 * 5442 6109 3718 1680 4579 5809 4719 5737 5919 61
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+
+Q 62 5161 6852 * 3734 6760 5754 4454 5818 4596 6642 5941 4738 * 2027 1637 3801 5207 5917 * 6673 62
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+
+Y 63 3385 * 4782 5018 3325 6671 6011 5614 3473 3783 * 5082 3485 4772 3841 3751 4004 5698 6970 2839 63
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+ 77 6607 4578 1585 585 2775 228 9793 1000 2168
+
+H 65 3696 * 4201 4330 6836 4315 3639 5641 3401 4199 6811 4863 2810 5152 4537 3384 4531 4842 6909 3816 65
+ 26 5784 * 1614 571 1902 449 9788 1163 2419
+
+T 66 3262 * 4348 3766 * 2219 5709 6397 3396 6069 5141 4805 2317 6918 5172 3649 5098 * 7023 * 66
+ 538 3173 2320 1552 602 2750 232 9815 2055 2032
+
+Y 67 4311 6279 5507 4638 4830 4733 5462 3049 4947 2846 4708 4148 4004 * 4601 3547 3301 4633 5336 4775 67
+ 148 4585 4163 2090 386 1137 875 9585 1396 4201
+
+G 68 5205 5564 4195 3734 4754 2680 4333 5852 3896 4466 6671 3677 4834 3997 4825 3645 5925 * 3929 3911 68
+ 96 5296 4689 3577 126 1504 627 9828 1501 3368
+
+R 69 3040 * 3883 3375 * 3008 5704 * 3571 5684 * 5333 2454 4838 3385 3729 5581 4926 * * 69
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+
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+ 61 4979 6688 305 2390 319 2334 9840 1353 2787
+
+L 71 4666 4766 4011 4284 4637 4317 5481 * 4508 2563 3834 * * 3854 4311 3879 3878 3908 5767 3756 71
+ 58 4982 6990 1513 622 301 2407 9962 1328 1380
+
+W 72 * * 5633 * 3834 6614 * 4114 * 2687 5013 * * * 6859 * 5231 5409 1068 3062 72
+ 40 5176 * 709 1365 937 1066 9958 1200 1056
+
+E 73 3249 5665 3537 2158 4594 3654 * 7193 5078 4944 5688 4851 * 4576 4858 3486 3784 4320 * 4929 73
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+
+L 74 5802 5039 * * 1831 5394 * 3544 * 1564 4871 7188 4528 7015 * 5676 4669 4170 5947 * 74
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+
+P 75 4257 5331 * 6681 5821 * * 4342 * 4473 5775 * 614 * * 5311 5577 3585 * * 75
+ 26 6801 6839 4755 54 * * 10031 1000 0
+
+A 76 2274 5953 * 7057 * 1137 * * 3357 5858 * 5622 * 5248 4506 4107 4962 6673 6721 * 76
+ 54 4778 * 1640 558 * 0 10018 1419 1000
+
+G 77 5589 6569 * 5281 5475 260 * * 5828 6721 * * * * * 5239 6388 6834 * 6466 77
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+
+L 78 3677 5908 5695 * 3625 3147 2834 5511 2907 4170 5299 6732 6388 4862 3132 4472 5746 4779 6855 4764 78
+ 14 6653 * 3459 138 * 0 10018 1018 1000
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+
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+
+A 82 3047 6792 4494 3733 5358 4344 4441 4821 3665 4269 * 4178 1975 6838 6580 4653 4805 4249 7012 * 82
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+
+G 83 4440 * 2243 3198 * 1457 5879 * 5142 7074 * 3308 * 6479 5046 4207 6514 6741 * * 83
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+
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+
+P 86 3021 6610 5388 * 4608 5738 6780 3643 6621 2079 5724 5232 2401 7028 5196 4315 4733 3944 * 5358 86
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+
+H 87 3902 7055 4428 1860 4502 4669 4028 4878 5233 3017 6589 * 5821 5155 3629 5392 5280 4362 7109 4947 87
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+
+L 88 3330 * 2633 1990 6056 4894 6617 6980 4340 4746 * 5328 * 2705 * 5092 4240 3763 * * 88
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+
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+
+A 90 784 6621 * * 6860 4902 * 3842 * 2514 5432 * * * * * * 3336 * * 90
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+
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+
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+
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+
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+
+E 96 5975 * 5667 366 * 6860 6702 * 4709 5676 6839 * 6697 5762 4968 5464 6436 6707 * * 96
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+
+E 97 7112 6624 6878 391 * 6535 6439 5462 4840 6658 * * * 4971 5185 5868 6854 5173 * 6821 97
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+
+V 98 2705 4680 * * 5222 6455 * 3929 * 2482 4902 * * * * 4274 1401 4033 * * 98
+ 0 * * * * * * 10031 0 0
+
+G 99 5902 * 4205 7074 * 452 5674 * * * 5924 4340 6439 5939 5923 4877 5210 * * * 99
+ 12 6897 * 1000 1000 * * 10031 1000 0
+
+L 100 4572 * 5642 * 4379 * * 2353 6455 1730 7022 6897 * 6040 6861 6795 * 2478 5495 2935 100
+ 21 6112 * 2000 415 * * 10031 1125 0
+
+Q 101 3830 * 3179 2945 6535 5103 4756 5217 3127 5237 * 4283 4315 3779 3448 4342 3698 4261 * * 101
+ 32 5524 * 1000 1000 * * 10031 1203 0
+
+A 102 3059 4475 5766 4358 * 3450 6469 3230 5073 3424 6897 5825 3933 * 4879 4292 4459 2227 * * 102
+ 77 5182 5375 962 1039 * * 10031 1205 0
+
+S 103 3866 6728 3395 2852 * 3184 5978 4979 3797 4860 * 4667 6617 3988 3435 3503 4093 4239 * 5667 103
+ 100 4618 5247 540 1680 * 0 10003 1503 1200
+
+T 104 3312 * 3557 3368 6929 7001 4183 3925 5238 4282 6714 4186 3863 3936 5907 3516 4229 3261 6407 5030 104
+ 46 5423 6933 2531 274 605 1546 9948 1217 1541
+
+W 105 5343 * 4947 4168 4132 4316 5645 3139 4136 2519 5392 7135 5328 4410 6948 5238 4987 2713 3729 5765 105
+ 12 6968 * 1585 585 0 * 9958 1000 1246
+
+Q 106 3725 7029 3215 3664 6615 7129 4618 3894 3764 6039 5838 6455 4933 3349 4115 3118 3817 3558 * 5184 106
+ 66 6799 4816 0 * * * 10031 1098 0
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+V 107 5090 * * 3920 4009 5333 4285 4386 4331 2534 5323 4207 3640 4369 4817 5171 4333 3460 6016 3852 107
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+
+D 110 4519 6631 3733 3314 5965 3664 5672 4189 4286 4176 6399 4319 3953 4889 4548 3442 2989 4468 * 5135 110
+ 108 4008 6603 2668 247 256 2621 9952 1822 1667
+
+L 111 5150 * * 4713 3041 5861 4497 2944 5685 3119 4886 6822 5809 4926 7013 4318 4531 2996 4482 3039 111
+ 152 3326 * 1656 551 764 1282 10003 2049 1193
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+D 112 4068 * 4497 3492 3487 4134 4499 4207 5766 4818 6000 7012 6275 5424 3126 4876 3620 4626 4806 2805 112
+ 55 5263 6449 1225 806 0 * 10024 1176 1003
+
+T 113 3860 6738 3711 3736 4804 4307 3705 4414 5816 4689 6056 5150 3126 5548 4528 3308 3793 4477 6025 4379 113
+ 118 4160 5482 1754 507 0 * 9955 1594 1015
+
+A 114 4085 * 3453 4104 4887 4486 5336 4312 4516 6834 6613 3395 4873 4260 4378 2885 3142 4351 5975 4949 114
+ 66 4907 6428 2068 393 * 0 9990 1279 1168
+
+P 115 3789 * 5090 3633 3947 4249 4795 5968 6013 4575 * 3822 1931 6647 3452 4752 5218 4562 * 4314 115
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+
+G 116 3783 6872 4146 4075 5241 2076 5099 6666 3978 4934 * 3856 5028 5321 4968 2983 3848 6398 5790 5532 116
+ 61 4602 * 3202 166 2243 342 9954 1323 1343
+
+F 117 3473 5911 4938 5080 3553 3987 3538 3766 4596 4816 5734 4614 5480 4867 3772 4498 4038 4066 5655 3792 117
+ 312 3132 3633 1952 431 1905 448 9954 2565 1245
+
+S 118 4023 4637 4798 4514 3870 3787 5199 3926 4826 5235 4738 4604 4924 5306 3941 2738 4000 4087 5029 5701 118
+ 70 4391 * 2495 282 3628 122 9910 1471 2239
+
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+ 88 5080 5064 3222 163 2885 210 9914 1193 2136
+
+E 120 4845 5728 6943 2321 5950 4428 4490 5107 4206 3857 5511 3394 5531 3895 4840 4176 4781 3320 5103 5876 120
+ 26 5781 * 2162 365 271 2545 9876 1225 2232
+
+S 121 4921 6728 5002 4851 4664 5877 4233 3865 3453 3206 4614 5797 5001 4329 3055 4956 3769 3476 6693 4365 121
+ 0 * * * * 0 * 10018 0 1118
+
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+
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+
+G 129 3330 4713 3053 4317 5158 7074 7001 3225 4324 3670 6741 4776 3692 * 4630 5867 4685 2702 6657 5067 129
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+V 133 3052 6723 3763 3009 4250 4967 * 5084 3654 3699 6424 4161 6052 4224 * 3676 4009 2998 * * 133
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+G 134 3879 * 3218 3477 4486 4248 4995 4129 4587 2895 * 4225 3273 4354 5265 3686 5267 4741 * * 134
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+
+R 135 4206 6696 3844 2858 6021 5478 5160 4315 3463 3803 * 5835 3951 3955 4082 3875 3221 4045 * 6867 135
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+P 136 4356 6739 5190 5142 5226 3546 6620 4620 4291 3354 * 4854 2629 3280 6107 4018 3734 3301 6135 7004 136
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+
+E 137 5237 4793 3436 3434 * 4591 3949 5078 3513 4311 5177 3290 4329 * 2856 4802 4247 3787 * * 137
+ 202 3137 5894 1710 526 2052 398 8758 1942 5803
+
+A 138 5302 5848 3488 5081 4415 3951 * 4877 5293 1847 * 6387 3648 5315 4487 6079 3815 4198 5212 4038 138
+ 723 * 1342 * * 2478 285 9041 0 4995
+
+H 139 3328 * 2565 2964 * 3883 4244 4755 4174 4666 * 5558 3120 5919 4059 4096 4081 * * 5608 139
+ 0 * * * * 115 3708 8594 0 6268
+
+H 140 3854 6923 2031 3826 * 3701 4947 5334 4836 4280 5935 3416 4466 4082 5830 3630 4753 4751 * * 140
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+
+E 141 4921 5725 2403 1650 6551 3872 5090 6838 4599 6349 * 5246 4384 5370 4802 3968 4887 5690 * 5757 141
+ 189 6087 3208 692 1392 * 0 9899 1084 1322
+
+E 142 3684 6632 3163 2698 * 2895 3950 4818 6100 4359 6536 4404 4338 5305 6631 4513 3402 4473 6572 6417 142
+ 87 * 4092 0 * 1838 473 9660 1015 2508
+
+A 143 4369 * 3747 865 5453 4377 4873 5796 5794 6919 6560 * * 4308 5039 * 4992 5062 6534 6045 143
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+D 144 4638 5818 3517 4394 3813 4744 4298 2641 5537 4715 * 4625 4634 5066 * 3591 4237 2658 6568 6345 144
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+
+M 145 4312 6526 4314 3527 5493 4272 4368 2817 4588 3591 4210 5161 6583 3801 3915 3987 4320 4144 * 6280 145
+ 13 * 6780 * * 357 2189 9672 0 3010
+
+T 146 4237 * 2871 1786 6558 3840 5087 6736 4102 6954 * 4367 6431 4239 3661 4174 3855 7036 * 6551 146
+ 45 6636 5579 0 * 0 * 9916 1004 1470
+
+M 147 3524 5970 * * 3068 4569 5230 3323 * 3083 4908 6808 5731 7037 5373 4593 3823 2186 4954 4868 147
+ 12 * 6906 * * 930 1074 9964 0 1097
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+
+W 149 6661 * * 4896 4063 6686 5716 5581 4994 3158 * * 7135 6493 4469 * 4921 4989 844 5741 149
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+Y 150 4481 6767 * 6824 2395 * 6675 2735 * 2377 4693 * * 6832 5927 * 6635 2012 7049 3940 150
+ 11 7067 * 0 * * * 10003 1000 0
+
+P 151 4457 * 2937 4589 * * 5820 * 4587 5797 * 4624 2117 7036 4910 2294 2402 * * * 151
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+I 152 3581 5129 * 4376 4588 * * 2823 4230 2775 3960 * 2784 7067 3948 6931 * 3295 5965 4334 152
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+A 153 3703 * 1893 1954 * 5778 6794 * 3890 * 7163 3749 4737 4819 5173 3802 4789 6465 * * 153
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+E 154 3479 * 2853 1655 5621 5438 4816 * 4249 6051 5971 5142 * 3188 4169 4435 4576 6644 * * 154
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+ 0 * * * * * * 9997 0 0
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+A 156 4290 5773 3908 4181 5162 4387 6695 4623 3862 2963 4326 6995 2797 6956 3383 4350 4734 3923 6948 5659 156
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+L 160 3357 * 3865 3795 3491 6431 5391 6300 3177 2757 4410 4826 4803 5011 4133 4142 3895 6450 6303 6360 160
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+R 161 3282 * 2943 3594 6520 5255 4003 * 4882 6446 * 3212 4090 4682 3157 2821 4692 6140 * 5186 161
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+G 162 6133 * 4838 3919 4937 1212 5751 5909 5127 6007 * 5113 3476 4445 4111 5042 4305 * 5773 5696 162
+ 0 * * * * 1135 877 8886 0 1398
+
+E 163 4149 * 2947 2481 4874 4454 5746 5185 3411 5900 6322 4856 6009 4026 3839 3718 4402 5012 4856 5999 163
+ 25 * 5867 * * 1531 613 8982 0 1160
+
+I 164 6186 5641 5913 * 3369 5898 4923 1806 * 2730 2769 5908 4393 * 6137 * 5908 3671 * 4443 164
+ 0 * * * * * 0 8984 0 1285
+
+V 165 4441 6208 4296 4176 * 5838 * 5042 3410 3444 4817 4386 3945 3386 3037 3835 3107 4367 * * 165
+ 71 5058 5822 2000 415 876 1136 8863 1218 1285
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+N 166 * 4082 2226 2924 * 4233 5722 6023 4076 3510 5722 3543 4715 3592 * 4894 4434 5766 * 4764 166
+ 56 5661 5746 1000 1000 * 0 8767 1000 1185
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+S 167 2251 * 5501 5773 5508 2823 * 5922 5463 3412 4889 4686 3797 4639 5924 4788 4343 2889 5982 5983 167
+ 52 4831 * 740 1317 2111 380 8719 1303 1407
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+I 168 5611 5537 4608 * 5870 5786 5987 3888 3362 1837 5026 * 6125 4766 3155 2642 4294 5955 * * 168
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+A 171 1441 4491 * * * 3494 * 4678 5703 3892 5742 5287 * 5320 5183 3733 3233 3408 * * 171
+ 33 * 5473 * * * 0 8218 0 1060
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+G 172 1085 * * 4409 * 4469 5392 5262 * 2558 * * * * 3703 4461 3869 5256 * * 172
+ 0 * * * * 912 1094 8161 0 1226
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+V 173 3913 * * * 3752 * 5268 2884 * 1466 4344 * * 5374 5556 5201 * 3447 3029 * 173
+ 0 * * * * 0 * 8058 0 1038
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+L 174 3631 5499 4544 * 4030 5509 * * * 1915 4336 4072 5173 4395 * 4256 3328 5435 5037 3106 174
+ 0 * * * * * * 8025 0 0
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+A 175 2184 5259 5094 * 4937 * * 4133 4994 1973 5635 * * 5370 3317 * * 3937 3831 3864 175
+ 0 * * * * * * 7818 0 0
+
+V 176 2120 * * * 3092 4025 * 3025 * 2849 5135 * * * * * * 3588 3359 3052 176
+ 49 4905 * 0 * * * 7663 1009 0
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+H 177 5032 * 3234 2852 * 3791 2752 4741 * 3687 4954 4602 4884 4999 2845 * * 4931 4650 4697 177
+ 114 4826 4619 0 * * * 7270 1043 0
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+A 178 2947 * * 4914 * 4521 4768 * 2237 2486 4688 4558 * * 3045 3582 3636 * * * 178
+ 0 * * * * 0 * 6854 0 1000
+
+V 179 2594 * * * * 4620 2845 * * 2205 * * * * 4439 * 4325 2537 4841 2895 179
+ 0 * * * * * * 6790 0 0
+
+T 180 * * * 3340 * * * * 2393 1931 4437 * * * 1675 4449 4522 * * * 180
+ 155 * 3299 * * * * 6681 0 0
+
+T 181 4629 * 4354 1548 * 4172 * 4394 3363 4105 * * * * 3182 * 2733 4326 * * 181
+ 449 1902 * 0 * 0 * 6417 1595 1458
+
+G 182 2220 * 3737 * * 762 * * * * * 4124 * * * * * 3981 * * 182
+ 118 * 3670 * * * * 6067 0 0
+
+F 183 * * * * 1718 * 3532 3872 * 3915 * 3773 3782 * 3700 * * 2555 3608 * 183
+ 0 * * * * * 0 5508 0 1067
+
+A 184 2740 * 2166 2847 3592 * * * * 2049 * * 3848 * 3404 * * * * * 184
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+
+Q 185 2541 * 3757 * * 2602 * * 3317 3554 * 3416 * 3616 * 2733 * * 3671 * 185
+ 0 * * * * * 0 5281 0 1067
+
+P 186 2541 * * 3754 * * * * 3317 1335 * * 2539 * * * * 3554 * * 186
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+R 187 3305 * * * * * * * * 3187 * * 3466 * 1013 3403 * * * 3205 187
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+
+P 188 * 3376 * * * * * * * * * 3654 860 3700 * 3508 * 3207 * * 188
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+L 189 3207 3426 * 1886 3700 3458 3376 * * 3435 * * 3444 * * * 3654 * * * 189
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+ 0 * * * * * * 5104 0 0
+
+T 191 1804 * * * * * 3235 * * * * * 3475 * * 2133 2319 3490 * * 191
+ 0 * * * * * * 4838 0 0
+
+E 192 3172 * 3095 3124 * * * * 2935 * * * 1636 3198 * * * * * 3385 192
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+
+W 193 * * * * * 2805 * * * * * * * 2986 2630 * * * 1277 2677 193
+ 337 * 2264 * * * * 3953 0 0
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+I 194 * * * * * * * 1953 * * * * 1057 * * * * 1937 * * 194
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+D 195 * * 2034 * * 2012 * * * * * * * * 1985 * * 1970 * * 195
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+R 196 2012 * * * * * * * 1970 * * * * * 2034 * 1985 * * * 196
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+
+P 197 * * * * * * * * * * * * 0 * * * * * * * 197
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+T 198 1985 * * * 1970 2012 * * * * * * * * * * 2034 * * * 198
+ 0 * * * * * * 2936 0 0
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+A 199 2034 * * * * * * * 1985 * * * * * 991 * * * * * 199
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+A 201 0 * * * * * * * * * * * * * * * * * * * 201
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+R 207 * * * * * * * * * * * * * * 0 * * * * * 207
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME ba48b3cd7ebd29a9e2e367a37ac501cf
+FAM
+FILE ba48b3cd7ebd29a9e2e367a37ac501cf
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:45:49 2013
+LENG 110 match states, 110 columns in multiple alignment
+FILT 149 out of 1021 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEECCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCEEEEECCCEEEEECCHHHHHHHHHHHHHCCCCCHHEE
+ECCCCCCCCC
+>ss_conf PSIPRED confidence values
+9976999908989788667644553899999999999877559997399999345765267988999529979960799999999999986699554405
+1377878779
+>Consensus
+xxxxxIxVCxxxrxxgxxxxxCxxxGxxxlxxxlxxxlxxxxglxxxvxvxxxxClgxCxxgPxVxIxpxxxxyxxvtxxxvxxilxxxlxxgxxvxxxx
+xxxxxxxxxx
+>ba48b3cd7ebd29a9e2e367a37ac501cf
+AEFKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGSMNACMMGPVVVVYPDGVWYGQVKPEDVDEIVEKHLKGGEPVERLV
+ISKGKPPGMF
+>gi|51244535|ref|YP_064419.1| NADP-reducing hydrogenase, 51 kDa subunit [Desulfotalea psychrophila LSv54]gi|50875572|emb|CAG35412.1| probable NADP-reducing hydrogenase, 51 kDa subunit [Desulfotalea psychrophila LSv54]
+---TVIYIGAA-----T---CGRSAGALKTKKAFETELAKQ-NVK--AEIVEVGCFGPCYTEPLICIArPgkTKLFFQNVDGERAEELVTGYLqTGEIPR
+DYLFAAV-------
+>gi|335048061|ref|ZP_08541081.1| protein HymB [Parvimonas sp. oral taxon 110 str. F0139]gi|333757861|gb|EGL35419.1| protein HymB [Parvimonas sp. oral taxon 110 str. F0139]
+---------------------------------------------------------------------------MGYIENLDKIKNKKypeMLE-IKSQ
+DEKYi-V-------
+>gi|338811198|ref|ZP_08623428.1| NADH dehydrogenase (ubiquinone) 24 kDa subunit [Acetonema longum DSM 6540]gi|337276809|gb|EGO65216.1| NADH dehydrogenase (ubiquinone) 24 kDa subunit [Acetonema longum DSM 6540]
+--------------------ACHIKGSYNVLNSLQQLREEY-GLADQVEINAIFCLNHCTEAVSVQID--DGAVHSVSGSTARDFFIKNILP--------
+----------
+>gi|325281878|ref|YP_004254420.1| hypothetical protein Odosp_3281 [Odoribacter splanchnicus DSM 20712]gi|324313687|gb|ADY34240.1| hypothetical protein Odosp_3281 [Odoribacter splanchnicus DSM 20712]
+--------------------SCYSRGNNVHLEVIKKYIAEN-HLEAEISFSGHLCEELCSSGPILRID--EKVYKEVNLSGLYKILQEEFPI--------
+----------
+>gi|38637753|ref|NP_942727.1| NAD-reducing hydrogenase diaphorase moiety large subunit [Ralstonia eutropha H16]gi|123467|sp|P22317.1|HOXF_RALEH RecName: Full=NAD-reducing hydrogenase hoxS subunit alphagi|141947|gb|AAC06140.1| NAD-reducing hydrogenase [Ralstonia eutropha H16]gi|32527091|gb|AAP85841.1| NAD-reducing hydrogenase diaphorase moiety large subunit [Ralstonia eutropha H16]
+-GKYRIYLCNS-----V---IAKINGYQAVREALERETGIRFGEtdpNGMFGLFDTPCIGLSDQEPAMLID--KVVFTRLRPGKITDIIAQ-LKQGRSPA
+EI-----------
+>gi|114771712|ref|ZP_01449116.1| formate dehydrogenase, beta subunit [alpha proteobacterium HTCC2255]gi|114547784|gb|EAU50674.1| formate dehydrogenase, beta subunit [alpha proteobacterium HTCC2255]
+-DEeippsLTIRVCDS-----L---SCELAGAQDLLFKLGEKYNGggK------VRVVRAPCMGRCDTAPTLEIG--HNHIDNANEEKVEKAIIT-KDFH
+PKIPNY-----------
+>gi|85857988|ref|YP_460190.1| NADH-quinone oxidoreductase chain F [Syntrophus aciditrophicus SB]gi|85721079|gb|ABC76022.1| NADH-quinone oxidoreductase chain F [Syntrophus aciditrophicus SB]
+----RyhLQVDTN-----I---PATLMgageILDHLEKTLNIRAGET-TPDGLFTLSEVECLASCGTCPVIQVN--DVYYENMTREKVDSLLDS-LRKG-
+----------------
+>gi|17230086|ref|NP_486634.1| hypothetical protein alr2594 [Nostoc sp. PCC 7120]gi|17131687|dbj|BAB74293.1| alr2594 [Nostoc sp. PCC 7120]
+-TKHTLFVCKSCHRSSEELAENQPCDGSILLDKITSLYSEK-FATEELEIQSVGCLWACSRGCVVALSsPEKptYLLVDLPPdaENASALLE--------
+---------------
+>gi|163749625|ref|ZP_02156872.1| precorrin methylase [Shewanella benthica KT99]gi|161330735|gb|EDQ01672.1| precorrin methylase [Shewanella benthica KT99]
+--LYQLIVCEGG--------RCEIPGQAGLAHRIRGLLKES-GFskgVNRIKVTRSHCLGCCRKLVPMVIYQgksqtrisenHALWLQkvdRLTDEQWQQ
+VFH-SLVEDSSVKACLRA--------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 1840 * * * * * * * 2679 * * * 2471 3541 * * * 1745 * * 1
+ 0 * * * * * * 3600 0 0
+
+E 2 2663 * 4177 2993 * 1331 * * * * * * 3676 * * 2683 * 5068 * * 2
+ 0 * * * * * * 5414 0 0
+
+F 3 3794 * 3678 3283 5616 4392 4871 * 2043 5660 * 5828 * 5232 1886 * 3885 * * * 3
+ 51 4852 * 2303 327 * * 7113 1483 0
+
+K 4 3576 * 6191 4903 4171 5666 2329 4005 3057 3940 * 5155 4795 5648 4129 4628 5316 4881 * 3231 4
+ 139 3449 * 0 * * * 7560 1576 0
+
+H 5 5507 5485 7288 4138 6902 * 2710 4640 3252 4155 5548 * * 3482 2876 6138 2857 3442 * 4688 5
+ 75 4297 * 1318 740 * * 7983 1478 0
+
+V 6 6381 7045 * * 5452 * * 1416 * 2171 * * * 6358 * * * 1520 * * 6
+ 0 * * * * * * 8048 0 0
+
+F 7 5381 5759 * 6095 2525 5657 4788 4356 4198 2134 5925 * * 4122 3567 4070 4441 4284 5806 4353 7
+ 0 * * * * * * 8048 0 0
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+//
+�HHsearch 1.5
+NAME bbd36c9292c799cc4a4733df8189699f
+FAM
+FILE bbd36c9292c799cc4a4733df8189699f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:48:50 2013
+LENG 184 match states, 184 columns in multiple alignment
+FILT 113 out of 1318 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCEEEEEEECCCEEEEEEECCCCCEEEEEEEEEECCCCCCEEEEEECCCCCEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCCEEE
+EECCCCEEEEEEECCCCCCCEEEEEEEECCCCCCEEEEEECCCCCEEEECCCCCCCEEEEEEEEEECCCCCCCCCCCEEEEEEC
+>ss_conf PSIPRED confidence values
+9898840499980499799999799998139999999899998269999379836899838889988999999993898788515477606899953199
+963799699999489987457999999689997218999668846999908899988999999996997267878848999889
+>Consensus
+xlxxPxxlxxxxxxxxxixlxWxxxxxxxxxyxvxxxxxxxxxxxxxxxxxxxxxxxxixxLxpxtxYxxxvxaxxxxxxxxxxxxxxxxxxxxPxxlxx
+xxxxxxxixlxWxxxxxxxxxYxvxxxxxxxxxxxxxxxxxxxxxxxxxxxLxpxxxYxxxVxaxxxxgxxxxxxxxxxxxxxT
+>bbd36c9292c799cc4a4733df8189699f
+GLDSPTGFDSSDITANSFTVHWVAPRAPITGYIIRHHAEHSVGRPRQDRVPPSRNSITLTNLNPGTEYVVSIIAVNGREESPPLIGQQATVSDIPRDLEV
+IASTPTSLLISWEPPAVSVRYYRITYGETGGNSPVQEFTVPGSKSTATINNIKPGADYTITLYAVTGRGDSPASSKPVSINYKT
+>gi|242004913|ref|XP_002423320.1| conserved hypothetical protein [Pediculus humanus corporis]gi|212506339|gb|EEB10582.1| conserved hypothetical protein [Pediculus humanus corporis]
+-IPSPPEIILQALNSSEIEVRWNLPSkeIKVIGYKIFYRKQNSS-QVGPIIVPADTKKYIVAGLEPETWYEITVLGFTSEDDGETGVSfmhtlsnvgssn
+kmmsEFPSIPEPPVSLEAEPISSRAINLTWSISQQatpgliNIKHFTICFNPVQNSLDKNAVvrCVKSLENKILISGLNPHTLYEFKVRSHNSNEKYSAF
+SQTI------
+>gi|14861868|ref|NP_149090.1| receptor-type tyrosine-protein phosphatase V precursor [Rattus norvegicus]gi|2499757|sp|Q64612.1|PTPRV_RAT RecName: Full=Receptor-type tyrosine-protein phosphatase V; Short=R-PTP-V; AltName: Full=Embryonic stem cell protein-tyrosine phosphatase; Short=ES cell phosphatase; AltName: Full=Osteotesticular protein-tyrosine phosphatase; Short=OST-PTP; Flags: Precursorgi|725329|gb|AAA63911.1| protein tyrosine phosphatase [Rattus norvegicus]
+--GPLLSVNVSSHGkSTSLFLSWVAAELGGFDYALSLRSVNSSGSPEGQQlqAHTNESGFEFHGLVPGSRYQLKLTVLRPCWQNVTITLTARTAPTVVRG
+LQLHSAGSpARLEASWSDAPGDQDSYQLLLYHLESQTLACNVSVSPDTLSYSFGDLLPGTQYVLEVITWAGSLH--------------
+>gi|317048328|ref|YP_004115976.1| hypothetical protein Pat9b_2108 [Pantoea sp. At-9b]gi|316949945|gb|ADU69420.1| Protein of unknown function DUF1983 [Pantoea sp. At-9b]
+-----------venltiintNSETVQVTAKWETATtTKKLTFELTVYTEAGTVVKSYET---EAFTYDFYGLDAG-SYTLGVRGRNSNGMKgAETQVSLV
+iGAPSAPTFIQWT-PGIFSADIVPVMNVTatTDTSFEFWYTgEVQASSVASVEDEAQflgRASQWTLHGLKADTTYYMYVRTKNAFGVSAFVE-------
+--
+>gi|326203258|ref|ZP_08193123.1| S-layer domain-containing protein [Clostridium papyrosolvens DSM 2782]gi|325986516|gb|EGD47347.1| S-layer domain-containing protein [Clostridium papyrosolvens DSM 2782]
+-LSPPANLSFNIISKTEVELTWDDTSSMEAGFIVEKKIGLLSQWYQISQLEPNVTKYNDKWISSTEPTFYRIKAFDRSTAVSYSNEVQLSLdaPEVPSNL
+QTSVLSTNDVKLSWKDNSSTEEGFIIEAKQLY---LFREIgRVDSNVTTFIYHDAIPGRTMTYRIRAVKGLVQSNPSNEVATVTLV-
+>gi|297570154|ref|YP_003691498.1| hypothetical protein DaAHT2_2214 [Desulfurivibrio alkaliphilus AHT2]gi|296926069|gb|ADH86879.1| conserved hypothetical protein [Desulfurivibrio alkaliphilus AHT2]
+---APRALAAEA-GDRVVELRWQPPREIPAlPaevsaelrYQLYRSRDGKDF--TALATT-AELHHLDREVVGGRTYYYRVRAMAVLGetrvAGPVGATV
+SVtardlTPPTAPLLEAAVP-VREGVRLLWEMPDDrRIAEFIVLRRLPGEDEGREIGRQRAPALSHLDRHPPAEADvWYYRLVAVDVEGNRSE-PGNELR
+FRR-
+>gi|301627360|ref|XP_002942842.1| PREDICTED: interferon alpha/beta receptor 1-like [Xenopus (Silurana) tropicalis]
+GRPYPENVTM-EALNTNYMLKWDWdysQHPNVTfsve----NNSEIWPGKWNQVQGcENISRRNCDVSgI-YIYGKYNFRVAASLDNNNRTLSRAlrfnp
+EKDTVIGPPSNVStel---YGT-KLHVNVLKVEAFhnddlknycDWEYNLIYWKDSa-S---DReeKTLNEKVGRFTI-EVEASTTYCLTVRVV------
+-------------
+>gi|194207920|ref|XP_001501538.2| PREDICTED: ephrin type-B receptor 2 [Equus caballus]
+---GTFKANQGDEACAHCPIN-SRTTsegATNCVCRNGYYRADLD--PldmpcttipsapQAVISSVNETSLMLEWTPPRDSggredLVYNIICKSCgSG
+RG--------------------------------------------------------------------------------------------------
+-----
+>gi|338710274|ref|XP_001917456.2| PREDICTED: myosin-binding protein C, fast-type-like [Equus caballus]
+--DPPEAVRVTSVGEDWAVLVWEPPKydggqplteqpkirlprhlretyvrkvGEHLNLVIPFQGKPRPQVVWTKGgAPVDTSRVHVRTSDFDTVFFVRE
+AARSDSGEYELSVQienmkdtatiriRVVEKAGPPEHVMVKEVWGTNALVEWQPPKDdgnsEITGYLVQKADKKTMEW-FTVYEHNRHTCCTVSDLIMGN
+EYYFRVYSENFCGLS-------------
+>gi|89891172|ref|ZP_01202679.1| extracellular ribonuclease [Flavobacteria bacterium BBFL7]gi|89516484|gb|EAS19144.1| extracellular ribonuclease [Flavobacteria bacterium BBFL7]
+----------------------------------------------------------------------------------------SGTlfPTLSgty
+VDINGNTIVDAGDEIQYTYDIANigTTTlYNLR--------ATAPLGTFNPGNQVAslAAGQSlnnPFGTFTYVLTAADATNSCGCITNQLLLA---
+#
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+I 124 5420 * * * 5623 6571 * 1856 6521 2086 5590 7004 * * * 6728 5723 1610 * 4697 124
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+
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+ 144 5556 3765 4803 53 1744 511 10846 1279 1515
+
+Y 126 5874 6465 7115 * 3425 * 6492 3387 5203 2842 6609 * * 5586 4502 5412 6575 3403 3714 1652 126
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+E 128 4267 * 4153 2470 6605 4109 * 5088 4271 4881 * 3673 3716 5696 3665 3353 3696 3873 5497 6655 128
+ 57 5014 7025 4108 86 3033 188 10799 1428 2335
+
+T 129 3880 * 4236 3147 4275 4148 5472 4924 3472 4677 5943 3459 4347 4049 4616 4439 3619 3937 6601 6289 129
+ 45 5595 6631 532 1698 1974 424 10804 1251 2317
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+G 130 4118 6686 2450 3487 6530 2861 5012 6436 4529 6585 5752 3756 5747 4592 5159 3107 3731 4848 * 6789 130
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+G 131 3447 6463 4650 3344 5420 2776 5501 5046 4088 5258 6594 4151 5279 4677 4399 2622 3748 5213 * 6750 131
+ 65 5375 5665 1843 471 1349 719 10775 1684 2490
+
+N 132 3741 6537 3230 3901 5032 4108 6636 5561 4063 5117 * 3064 4981 4740 4217 2700 3474 4804 * 6605 132
+ 326 3807 2937 1618 569 3060 184 10798 2385 2421
+
+S 133 5119 6435 3016 2734 5543 3104 6417 4960 3290 6351 6485 4842 4550 6439 4586 2709 4783 5237 5578 6491 133
+ 89 5330 4825 2192 356 770 1274 10636 1240 4503
+
+P 134 3487 5497 3479 4497 4638 4312 6555 4337 4263 3871 5561 5083 4024 * 4346 3786 3970 4989 3308 4224 134
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+V 135 3757 * 4132 4217 6597 4947 6322 4265 3935 3315 * 4976 3904 4546 4643 2898 3143 4130 4778 5658 135
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+Q 136 4320 6439 4696 3927 5638 4704 5913 4351 3360 3979 * 5002 4380 3038 3560 3574 3890 4027 4558 6917 136
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+E 137 4450 4431 4647 3158 6816 5643 * 3458 3678 3381 6632 3532 5153 5415 5526 4239 5135 3171 5647 3648 137
+ 13 6823 * 1585 585 1568 593 10843 1000 2052
+
+F 138 4728 6894 5741 4993 3989 4728 6611 3207 4214 3462 5584 5160 6501 5519 3822 4124 4185 2645 5757 3369 138
+ 107 4608 5034 321 2324 2026 407 10859 1672 1639
+
+T 139 5095 * 4724 3364 4617 5921 5547 4490 3651 4460 * 3089 3788 5813 3862 3319 3411 3557 * 4975 139
+ 29 6506 6821 1982 421 994 1007 10818 1226 2071
+
+V 140 3436 5689 4620 4292 4448 5204 6686 2703 6575 2712 5238 4611 6812 6555 5742 4444 3401 2841 * 6457 140
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+
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+K 144 3530 7439 4432 3262 6787 3416 5800 4364 3743 5661 * 4539 5031 3179 4246 3154 3502 4684 6671 7106 144
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+A 147 3604 4040 * 5551 2502 5588 5101 4711 * 4063 * 6883 * 6634 6554 5723 4650 3021 4420 1981 147
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+ 25 5841 * 1000 1000 * 0 10884 1293 1000
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+G 155 5591 * 3626 4576 4392 1708 5607 * 5908 3639 6391 2481 7733 * 4705 3887 4816 7108 6526 5064 155
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+
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+G 167 3235 6818 3219 3593 6592 3691 5446 * 3209 6762 * 3870 4509 6612 4096 2819 4276 6481 5401 4122 167
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+G 169 4876 6351 4012 5461 5766 884 6329 5524 6487 5748 * 4334 5489 5345 5356 4434 5464 4469 * 6683 169
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+
+S 175 4527 5963 4360 3137 5090 3524 4976 5005 5048 * 6077 6180 2939 6053 6060 1949 3417 6018 * 6424 175
+ 0 * * * * 0 * 10190 0 2262
+
+K 176 4253 6437 3607 3285 * 4708 5069 4908 3832 4148 * 4286 4541 4657 4200 2910 3488 3548 5867 6604 176
+ 0 * * * * * * 10239 0 0
+
+P 177 3074 * 5095 4017 5075 5827 * 4436 4402 5123 * * 2796 4007 5851 2702 3309 3974 * 3661 177
+ 0 * * * * * * 10106 0 0
+
+V 178 3427 5103 * 4858 4509 4936 5905 2783 3715 2442 5209 5859 6058 5115 5853 5997 * 2254 6175 * 178
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+ 0 * * * * * * 10001 0 0
+
+I 180 3041 4811 * * 4892 * * 2349 * 3868 4316 * 4699 * 5822 4823 3512 1758 * 5696 180
+ 0 * * * * * * 9860 0 0
+
+N 181 4011 * 3809 5316 4546 * * 5511 2757 * * 2260 5526 5335 4584 2525 2660 * * * 181
+ 0 * * * * * * 9387 0 0
+
+Y 182 2518 * * * 1236 4044 5279 3114 * * * * * * * 4983 4313 5114 * 3505 182
+ 0 * * * * * * 8703 0 0
+
+K 183 * * * 3739 * * * 3760 2875 4797 * * 4683 * 2583 2283 2103 4834 * * 183
+ 0 * * * * * * 8287 0 0
+
+T 184 * * * * * * * * * * * * * * * * 0 * * * 184
+ 0 * * 0 * * * 7166 0 0
+
+//
+�HHsearch 1.5
+NAME bc4ef49e84c894acd9a656db73d52eeb
+FAM
+FILE bc4ef49e84c894acd9a656db73d52eeb
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:58:09 2013
+LENG 108 match states, 108 columns in multiple alignment
+FILT 129 out of 629 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
+CCCCCCCC
+>ss_conf PSIPRED confidence values
+9788887652687755788886657789716424575332675563332455455888698989999999604555666786478999999999972202
+26886779
+>Consensus
+xxCxxxxxyRtxDGsCNNlxxpxxGxaxxxxxRllpxxYxDGixxprxxxxxxxxxgxxlPxpRxVSxxlxxxxxxxxxxxxxxtxxxxxwgQfixHDix
+xtxxxxxx
+>bc4ef49e84c894acd9a656db73d52eeb
+VTCPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLD
+FTPEPAAR
+>gi|241709425|ref|XP_002412033.1| peroxinectin, putative [Ixodes scapularis]gi|215505064|gb|EEC14558.1| peroxinectin, putative [Ixodes scapularis]
+-GCDFSYPFRYPDGSCNNQNHTDWGNAGSCMRKLLRPDYGDMVGEPR-----VASDGGPLPPPRVVSYTVHP--P-LEASSPKMTQLGVLFGQFITHDVS
+qiLRSGT---
+>gi|322798709|gb|EFZ20307.1| hypothetical protein SINV_07073 [Solenopsis invicta]
+-------------------------------------MSALGISRPRQSV-----GTHSLPAPSDIVSHVLQSSPKI-RSHEGLTSLSGVWSELVLQDIA
+ATVR----
+>gi|328875443|gb|EGG23807.1| peroxinectin [Dictyostelium fasciculatum]
+-PFTNgeSTEWRSYDGSNNNLINPNQGEIYEPFIRVA---------QQQFFNPDDYP-TLSIPLSREVSNIVCDQQ-SPVPSKELLSDMFNMWGQFLIHN
+MAHAL-----
+>gi|332028340|gb|EGI68387.1| Dual oxidase [Acromyrmex echinatior]
+------RPPARSIAPLCAIAWAFWAVLpvetDSRLIRKVPAAYSDGVYTMA---------GQDRPSPRKLSDLFMQGDD-GLPSVKNRTALFAFFGQLVT
+SEIIMA------
+>gi|313230135|emb|CBY07839.1| unnamed protein product [Oikopleura dioica]
+-KCD--PRLHTFDGTCNHPQN--KGSVLTPYIRWAPANYCNDRDTDRC-----SEHKRPLKNPRHISLF--GQRMNTMETNRFHTRFMIDWGQFLTHNIM
+QTPDL---
+>gi|195451388|ref|XP_002072896.1| GK13444 [Drosophila willistoni]gi|194168981|gb|EDW83882.1| GK13444 [Drosophila willistoni]
+-----------LKGQCENLLQsRRDG--HYAFRRLLDRHYKNGFHKMY--------DDDDLPGAWPISMALYEhvP-GSVppEDQNESPNLCLVQWAQFI
+EHDLSKPVSQS--
+>gi|296411466|ref|XP_002835452.1| hypothetical protein [Tuber melanosporum Mel28]gi|295629235|emb|CAZ79609.1| unnamed protein product [Tuber melanosporum]
+-----EFSYRQADGGYNNIMYPQLGRAGSAYARSVKPM---------------TKMPGAPPDAYTLFDRIFSRGpnDEHFREHDnNVSSMLFYTATIIIH
+DLFRT------
+>gi|302658402|ref|XP_003020905.1| hypothetical protein TRV_04981 [Trichophyton verrucosum HKI 0517]gi|291184775|gb|EFE40287.1| hypothetical protein TRV_04981 [Trichophyton verrucosum HKI 0517]
+-----------------------LGLLGRGMQRLFSQN------LY---------NRSTFQTRGFFlirswperdLNHTLAR-SLVCYSISLQSSFMIFL
+--IPSKDLFKT------
+>gi|30249221|ref|NP_841291.1| oxygenase [Nitrosomonas europaea ATCC 19718]gi|30180540|emb|CAD85149.1| putative oxygenase [Nitrosomonas europaea ATCC 19718]
+------IRFRTVTGICNDIYNPLMGSTHQIFARNVQfdTTFPDlGLDEMAR-NRHGDRLGLLKPDPQVISRKLFTRtqsqPDKcrnddElsgdlekfacd
+YKKAPALNVLAAFWIQFMTHDW---------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 * * * * * * * 2856 * * * * 1909 * 3568 * * 968 * * 1
+ 0 * * * * * * 3432 0 0
+
+T 2 6170 * 4539 3721 * 5747 5823 3741 3595 5199 * * 2762 4220 4293 2695 2478 4055 * * 2
+ 19 6225 * 1000 1000 * * 5623 1000 0
+
+C 3 * 104 * * 4969 * * * * * * * * 6187 * 5381 * * * * 3
+ 98 4363 5848 1066 936 * * 5670 1104 0
+
+P 4 4874 6190 1328 5317 5969 5148 5768 5271 6099 * * 3954 2161 4686 4680 * 4501 6008 * * 4
+ 448 5768 2009 1585 585 0 * 5668 1000 1000
+
+E 5 3063 * 3385 3116 3243 * 4277 * 5428 * * 3543 1843 5793 5395 3957 * 5786 * * 5
+ 351 2746 3905 1324 736 251 2645 5179 1370 1769
+
+Q 6 3469 * 4712 4847 6310 * 4099 4986 4619 6148 * 3143 2985 4978 3290 2786 3046 * * 4641 6
+ 15 6643 * 0 * 0 * 5922 1000 1278
+
+D 7 3234 * 4861 5749 4352 4403 5029 5485 5265 3218 6539 4074 6042 4018 5893 2420 3919 4977 5840 3441 7
+ 86 4298 7109 1101 905 * * 6589 1261 0
+
+K 8 * 6609 5654 3289 * 4286 5687 * 2012 6896 5543 5366 2945 4909 2473 4571 4278 4502 6180 * 8
+ 0 * * * * 0 * 6758 0 1000
+
+Y 9 4985 6577 * 6293 2830 * * 5211 * 5319 * 5736 5023 * 6661 6600 7119 4764 6175 678 9
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+
+R 10 5528 * * 6684 * * 5650 5895 * 6710 * * 4331 4577 286 * * * * 6577 10
+ 0 * * * * * * 6733 0 0
+
+T 11 5245 * 4614 5633 * 6684 6638 * 7062 5538 * 6345 5522 4253 3244 1789 1457 6661 * 6903 11
+ 10 * 7117 * * * * 6733 0 0
+
+I 12 3508 * * 5752 2878 * 4449 2617 * 2870 5093 * 3953 5919 * 4551 5396 4218 * 2462 12
+ 0 * * * * 0 * 6853 0 1000
+
+T 13 * * 570 6879 * 6784 * 6176 5743 5485 * 3848 5920 * 5523 3955 3612 * * * 13
+ 0 * * * * * * 6849 0 0
+
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+ 0 * * * * * * 6849 0 0
+
+M 15 5012 * * 5215 5728 6709 5451 4768 4112 6302 5426 * 6176 5248 4356 1477 2726 4345 3827 4602 15
+ 0 * * * * * * 6849 0 0
+
+C 16 * 553 6083 * 4883 3560 * * * 6176 * 4897 * * 5720 5118 * * * 3478 16
+ 0 * * * * * * 6849 0 0
+
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+ 0 * * * * * * 6849 0 0
+
+N 18 5132 * 4568 6684 * 6589 3932 5819 * * * 378 * * 6489 4909 * * 6366 * 18
+ 27 6885 6589 1585 585 * * 6859 1028 0
+
+R 19 6644 * * 4628 5245 * 6842 3238 4675 1222 5343 * 3163 6952 4322 * 6004 2936 * * 19
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+
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+
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+ 91 5006 5052 0 * * * 6859 1187 0
+
+P 22 4368 * 4742 5260 * 5860 5465 7135 5997 6277 * 6733 627 6517 5641 4163 5035 4704 * * 22
+ 12 6930 * 0 * * 0 6801 1000 1161
+
+T 23 5183 * 4063 3303 5448 5931 4824 7212 6700 2805 6084 3585 * 4903 3821 2553 2934 5967 6333 4464 23
+ 32 5493 * 1273 770 0 * 6801 1098 1161
+
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+
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+ 32 * 5496 * * 0 * 6922 0 1016
+
+A 26 2128 6396 * 5345 * 6682 * 5036 3015 5913 4882 4347 * 4230 3641 1987 4624 5090 * 6007 26
+ 16 * 6542 * * * 0 6876 0 1104
+
+S 27 1205 * * * * * * 4861 5389 4571 * * 4011 5419 5092 2479 3913 3246 * * 27
+ 19 6235 * 2000 415 0 * 6856 1035 1187
+
+N 28 * * 3209 * 4568 1537 4471 6361 6463 3627 4295 2560 * 7164 6939 5167 6018 5870 * 4067 28
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+
+R 29 4108 * 6714 3479 * * 5596 6266 * 5605 4001 5305 * 3516 3759 2373 1677 5899 * 5875 29
+ 29 6943 6416 0 * 0 * 6870 1000 1154
+
+A 30 2636 5950 5842 6081 4964 5933 5660 4687 7418 5696 * 5852 1380 3847 3012 5278 5276 6358 * * 30
+ 17 6380 * 0 * * 0 6927 1036 1075
+
+F 31 * * * 7115 1423 * 7018 6887 6393 2193 3224 7312 * 7455 * * * 6730 * 2031 31
+ 0 * * 1000 1000 0 * 6927 1075 1075
+
+V 32 3216 * 5493 4318 * 3121 6998 3664 3156 3416 7265 5235 5034 3482 2838 4410 4970 4939 * 6971 32
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+
+R 33 * * * * * * 6766 6251 5192 * * 6385 * 5268 162 5750 * * * * 33
+ 0 * * * * * * 6936 0 0
+
+W 34 6587 * 5676 5407 4690 * 7050 3504 6299 1292 4098 3367 6777 6452 4704 4645 7079 4582 4279 4795 34
+ 44 5740 6450 0 * * * 6950 1085 0
+
+L 35 3533 * * * 3570 5432 * 3672 7045 1276 4036 * * 6786 * 5789 4324 2727 6758 6775 35
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+
+P 36 3755 * 4052 5752 5104 4480 * * 4336 5595 * 5335 1061 4579 4482 4406 4133 6938 * * 36
+ 54 5267 6567 863 1151 * 0 6918 1148 1191
+
+A 37 1757 * * 7157 * * 6346 5628 * 4975 * 4556 1278 5908 4645 3789 4575 7170 * * 37
+ 35 * 5396 * * * 0 6899 0 1275
+
+E 38 2844 4873 3171 3477 6284 6022 4050 6212 5035 5993 5077 3345 * 4760 4414 3068 5421 3392 * 5165 38
+ 115 5750 4105 0 * 3018 190 6825 1077 1474
+
+Y 39 6554 6674 * * 3810 * * 7231 6519 7273 6191 * * * * 4880 * 5412 * 299 39
+ 30 * 5624 2322 322 2764 230 6677 1075 1860
+
+E 40 2009 4422 3115 2640 7279 3906 6628 6630 4415 7259 7314 5380 5547 5286 5451 2887 4747 * * 6703 40
+ 0 * * * * * 0 6638 0 1854
+
+D 41 6630 * 386 5658 6003 4859 6694 * * 6846 * 3377 * * 6285 * 7370 7004 * 6178 41
+ 107 4564 5113 417 1995 * 0 6638 1240 1854
+
+G 42 5249 * 4548 5236 6115 499 * * 6268 * 6824 4257 5354 6980 5345 5978 * 6649 * 5285 42
+ 0 * * 1326 734 * 0 6620 1211 2093
+
+F 43 5438 * 4748 5768 2980 * * 1734 7305 3859 6102 6324 5373 * 4284 4864 * 1971 6830 5795 43
+ 95 * 3969 * * * 0 6618 0 2093
+
+S 44 4116 * 3456 4616 4795 3621 4965 6643 5338 * 7252 3705 * 3991 5606 1730 4424 6585 6044 3539 44
+ 11 7051 * 2458 290 1443 661 6717 1191 2507
+
+L 45 3180 * 4186 2105 * 6599 6679 6447 3600 3789 6744 * 6595 3487 5749 3019 3051 4489 * * 45
+ 54 6381 5338 2000 415 1947 433 6886 1020 1962
+
+P 46 4627 * 5445 4840 5280 * * 3952 * 4572 4176 6096 830 6241 6102 4686 7274 5161 * 4808 46
+ 119 7369 3773 1000 1000 3555 128 6970 1000 1878
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+
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+K 54 2472 * 4758 * * 3113 5819 * 3682 4660 4609 6556 6100 5605 4616 1782 3751 5716 * 5611 54
+ 98 5069 4794 3724 114 2941 201 5876 1052 4231
+
+R 55 4724 * * 4992 6051 4198 6642 5669 3374 4704 * 6714 4515 4765 3392 2453 3850 2416 * 3796 55
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+
+G 57 * * 4325 5161 * 790 * * 5111 * * 3125 4773 5566 5289 5421 3999 6340 5731 * 57
+ 94 4432 5887 3177 169 1086 919 6764 1250 2243
+
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+ 55 7407 4993 4700 57 1413 679 6974 1000 1764
+
+P 59 2830 * 3316 3018 * 4786 5712 6653 5229 3821 5624 4838 2267 6952 5977 4325 3912 4737 6399 5634 59
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+A 61 6211 * * * 7055 * * * 5978 5504 * * 152 5896 * 7125 * 6813 * 6949 61
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+V 66 5572 * * 6669 5945 * * 1474 * 2753 6759 * 6969 * * * 6587 1262 * * 66
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+
+S 67 3702 * * 6374 4586 * * 4918 * 5945 4603 6308 * 5830 5670 587 4842 5503 * 7276 67
+ 26 * 5800 * * * 0 7043 0 1025
+
+N 68 4084 * 3929 4578 7272 * * 5085 5770 3175 4900 1909 * 5920 3158 3809 3057 4851 * 6148 68
+ 11 * 7005 0 * 553 1651 7029 1075 1222
+
+E 69 3127 6534 4724 4082 6018 6447 5392 3963 3336 3420 5435 4932 * 4035 4025 4358 2999 3308 * 5847 69
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+
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+R 72 3235 * 3527 4999 6974 3522 4604 6988 3047 5225 * 3698 4853 4482 3172 3034 3935 5793 6480 * 72
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+F 73 3568 * 3762 4348 3861 3296 4430 5594 5846 5866 * * 4171 2653 2917 4501 3768 4155 * * 73
+ 339 4808 2525 2638 253 4676 58 7009 1090 4121
+
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+ 317 4140 2834 414 2004 592 1571 6259 1165 4573
+
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+ 460 6714 1923 0 * 610 1537 6919 1000 2863
+
+D 76 3783 * 2374 3563 * 3540 5730 6829 4203 3962 * 4397 4521 5606 4551 2853 3466 5953 * 5752 76
+ 195 4015 3954 1067 936 350 2213 6839 1309 3130
+
+Q 77 3649 * 3979 3442 5317 2927 5700 4709 4223 4242 5278 3774 4341 4356 5117 3542 4372 3764 * 6531 77
+ 139 4578 4324 2544 271 1516 621 6886 1220 1880
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+L 78 4844 5796 3100 3740 3100 5255 4708 4007 4837 3297 5523 4212 4100 5577 5072 4130 5266 3517 * 5611 78
+ 90 4584 5723 0 * 661 1444 6906 1216 1951
+
+T 79 4689 * 3777 4192 4939 7534 * 4179 3241 4252 * 5980 3032 5694 3536 3919 3138 3360 6839 4248 79
+ 100 4569 5323 0 * 570 1615 7005 1296 1467
+
+P 80 4600 5943 5280 3821 4759 6048 4985 5370 5221 5136 7322 3302 2295 5463 4361 2360 4253 5523 * 4998 80
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+D 81 3347 * 2193 4373 6702 5414 2631 5870 3904 6013 * 4080 3826 6573 5580 3513 4927 4421 * 6306 81
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+F 88 3257 * * * 2539 4233 5971 3955 * 1927 3547 5850 * * * 4898 4255 2857 * * 88
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+M 89 2371 5984 * * 4373 4607 * 3591 * 5270 1889 4850 5579 * * 6174 3842 2964 4574 6231 89
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+L 95 6430 * * * 6356 * * 1485 * 2104 3351 6097 5941 5379 * 6897 6681 2215 * * 95
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+D 98 * * 199 4079 * 5263 * * * * * 5481 * * * * 5560 * * * 98
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+
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+
+T 102 3136 * * * * 4712 * 4263 * 4734 5012 6452 5534 * 6636 3169 989 4062 * 6714 102
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+P 103 2918 * * 6795 6639 3941 * * 5414 4602 5204 * 1226 5752 7141 4350 4477 2788 * * 103
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+E 104 3786 6386 2850 3367 5340 3748 5784 4673 5350 6449 4574 4785 5580 3502 6082 3033 4951 2934 * * 104
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+P 105 5128 * 3406 5746 3976 6072 5381 6354 5224 5541 5959 3803 4476 4030 4230 1709 3962 4107 * 5624 105
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+A 106 4034 * * 4684 * * * 4932 3268 3944 * * 2083 * 4989 1895 3088 4487 * * 106
+ 0 * * * * * * 5543 0 0
+
+A 107 1671 * * * * * * * * 3672 2214 * * * * 1351 * * * * 107
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+
+R 108 * * * * * * * 1093 2347 * 2746 * * * 2431 * * * * * 108
+ 0 * * 0 * * * 2897 0 0
+
+//
+�HHsearch 1.5
+NAME bdf48b24c3f0fdeaa0d9654593ea6f0d
+FAM
+FILE bdf48b24c3f0fdeaa0d9654593ea6f0d
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:06:10 2013
+LENG 164 match states, 164 columns in multiple alignment
+FILT 116 out of 1158 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEEEEEEEECCEECCEEEEEEECCCCHHHHHHHHHHHCCCCCCEECCCEEEEEECCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEE
+EECCCCCCCCEEEEEECCCCCCCCCCEEEEEEEECHHHHHHHHHCCCCCCCCCCCEEEEEEEEC
+>ss_conf PSIPRED confidence values
+9987899999999995552999997776937999999985137784136988899777926881763578888887546753255443104688749998
+2269998456699991687224898358999870799999998568889989455799981609
+>Consensus
+xxxxxvxxdixixxtxxGxixixLxxxxaPxxxxxFxxlxxxxxgxxYxgxxfxrvxxxxxiqxGxxxxxxxxxxxsxxxxxxxxexxxxxxxxxGxlsx
+xxxxxxxxxsxFfIxlxxxxxldxxxxvfGxVxxGxxvlxxIxxxxxxxgxPxxxixIxxcgxl
+>bdf48b24c3f0fdeaa0d9654593ea6f0d
+MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSM
+ANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQL
+>gi|254584676|ref|XP_002497906.1| ZYRO0F16214p [Zygosaccharomyces rouxii]gi|238940799|emb|CAR28973.1| ZYRO0F16214p [Zygosaccharomyces rouxii]
+---------------TAGDIIVDLKYKQYEIESYNFLKLCKCN---FYQNQCFYNLHKDQSVQFGNPLLG-YEDRKELrlKNTSVEgiTsepvksrllka
+teSPDRSGKALKGSLGnvvvqKQESGQELIGSQVIISlAEhGLDATNA--IYFGDViQTSWSTLDKIERfAVDDTQRPIEDIRI------
+>gi|85374706|ref|YP_458768.1| peptidyl-prolyl cis-trans isomerase [Erythrobacter litoralis HTCC2594]gi|84787789|gb|ABC63971.1| peptidyl-prolyl cis-trans isomerase [Erythrobacter litoralis HTCC2594]
+-----LVMTLAPpdrgpgqaSaEGNTREVVIQLMPApFSQGWVSNIRTLAR--AGW-YDGISVNRVQDNYVVQWGDPnydnpeaegeakplpeglkvmge
+eeysangrilsqltvsnlvakerlePGADwIAPDVSEVGDEYSDLVGFQRgwpvasglsnnsaqtwpiHC-YGMVGVGRGySPDTGsGAELYTVIGHAPr
+HLDRNIALVGRIIAGMEHLSSLPRGKGALGfyaadeidkrTPIVSIRVAS----
+>gi|328865705|gb|EGG14091.1| phosphoglycerate/bisphosphoglycerate mutase [Dictyostelium fasciculatum]
+--------------TSKGGIIVELYRDKARLSCERFTNQI--EVGR-YQDTIIHRIVKNLFIQCGRYSINSSSLDNSLMNNNDSSsnsnnddsitsftst
+stttsiydnnnnnnntqptslnssstilnqlyvdssdddeleqeqqqddivyisdnkesnltnskkesssskqqelldkdqfkrlikenNDNGLSFNERG
+LVAMGSYN------QIIFTLDACGALNRKYPIIGRVHpSTMQMLCILESTPTnESNCPIDPIFLTN----
+>gi|156839035|ref|XP_001643213.1| hypothetical protein Kpol_457p6 [Vanderwaltozyma polyspora DSM 70294]gi|156113813|gb|EDO15355.1| hypothetical protein Kpol_457p6 [Vanderwaltozyma polyspora DSM 70294]
+--------------TSKGNLNVELWAKECPIASKLFIETC--LSKF-WVGSSLGEFgedGSKLYIDFDGDTKF---------KDSIAMEsNSRLLFNREG
+LLGW-----DIDAGLWFVTTSEKC-DGKRKILIGKIV-------------------------------
+>gi|309366416|emb|CAR98339.1| hypothetical protein CBG_27914 [Caenorhabditis briggsae AF16]
+----RIIFDVVSGNLMMGRIIIMLSN-FEPELRKHFYKMADGNRtNRSFSGTIFHRKTNKFIEGGVLTSSNDTSTVESLYTTKPVNNPKFYSKY--VMIA
+NRNIHDDYRGTRFLITTSPLLHCDQDHIPLGTIVCGREIFDQIAELPcDQDGKFLSTLSI------
+>gi|321456758|gb|EFX67858.1| hypothetical protein DAPPUDRAFT_330682 [Daphnia pulex]
+----KCYFRMNINGVMSERIIVQLEKAKAPIMCAKFIEMCTKKDG--YKGSKIYKTIKGesVFCSSGWFHTYDLDQRCDVFTADKSDVAEQRGSM-RFQI
+KKSENGIAQVSTEFNVILANRPRHHRSTSVFAQIIEGLTVFDQISGMDMKQNR----VIFAECGV-
+>gi|159482122|ref|XP_001699122.1| hypothetical protein CHLREDRAFT_193502 [Chlamydomonas reinhardtii]gi|158273185|gb|EDO98977.1| predicted protein [Chlamydomonas reinhardtii]
+---------------EMGDVVVKLLPDLAPASVRELRRMAALLAleGTGCDGCKLYRSEVNFLVQGVIRHPGAYVATPRRPNPP------QKKMMERGLA
+CWAGGM---GGPDWFVNLIDQSGFGDDHLCWGKI-DDMSLLDAIVKLPTK----------------
+>gi|308813275|ref|XP_003083944.1| peptidyl-prolyl cis-trans isomerase TLP38, chloroplast / thylakoid lumen PPIase of 38 kDa / cyclophilin / rotamase (ISS) [Ostreococcus tauri]gi|116055826|emb|CAL57911.1| peptidyl-prolyl cis-trans isomerase TLP38, chloroplast / thylakoid lumen PPIase of 38 kDa / cyclophilin / rotamase (ISS) [Ostreococcus tauri]
+--------------LNEATLEITVDGYNAPLTAGNFVDNVR--RGV-YRNAPMRRSET--AILGGASN--pDAPSVPleikasdafdPSYRFPLDvqnGE
+aIPSIPLSINGSVAMARS-sdGQSDKDQFFVYLFDkrsaglggLSFEEGEFSVFGYVTKGEEYLGSI----------------------
+>gi|342181197|emb|CCC90675.1| putative RNA-binding protein [Trypanosoma congolense IL3000]
+-PRPIVTAAVLIE-TSVGTFVVDLYGADCPAATGELVNLCRCK---YFNGCIATEVIPDSvlifshpveALQQQTFASLLDMgGMRHLPLRDGTLdatst
+rqavyaewkrmrrhvarpqdgakgavgaenvefvirpplEAPGTIRY-SGLLLLevpqvesgATTVCHPLKMRLLITLSNrhLDYLEGQFIVVGEVREGC
+DVVEKMRAAPhrrltTSSGittRPSRLVRIKHTTVL
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 2120 0 0
+
+V 2 * * * * * 3092 * 2696 3075 * * * 2380 * * 2833 * 1851 * * 2
+ 0 * * * * * * 3322 0 0
+
+N 3 * * * * 4693 * * * 3754 * * 1296 * * 2222 3264 3027 * * 4681 3
+ 178 3106 * 0 * * * 5803 1348 0
+
+P 4 4773 * 4927 * * * 4567 * 3350 4945 * * 1126 3175 3345 3464 * * * * 4
+ 0 * * * * * * 6353 0 0
+
+T 5 * 5133 * 5349 * * 4364 2892 2714 4185 5131 5315 * 5118 2348 5366 4021 3792 * 3065 5
+ 0 * * * * * * 6936 0 0
+
+V 6 3223 3777 * * 5146 * * 2633 * 4194 * * 5586 * * * 5243 1194 * 3448 6
+ 0 * * * * * * 7153 0 0
+
+F 7 * * * 5556 1798 * * 5268 * 5458 * 5664 * * 5367 3889 4158 4026 * 1274 7
+ 0 * * * * * * 7160 0 0
+
+F 8 5099 * * * 1689 * * 3697 * 1712 2458 * 5081 5480 * * 5482 5508 * * 8
+ 0 * * * * * * 7196 0 0
+
+D 9 5099 * 869 3657 5236 * 4326 * 5544 * * * 5590 4814 5001 * 3398 3974 * * 9
+ 67 * 4468 * * * * 7196 0 0
+
+I 10 * 5549 * * 3596 * * 1256 5667 3198 4195 * 5639 * * * * 1869 * * 10
+ 66 5328 5654 0 * * 0 7353 1045 1116
+
+A 11 1914 * * 2583 * 3666 * 5548 3423 5228 * 5110 * 5173 * 3187 3774 3211 * * 11
+ 0 * * * * * 0 7335 0 1235
+
+V 12 * * * 5013 5430 * * 1516 4498 4305 5839 * 5285 * 4750 3635 4556 1746 * * 12
+ 75 4312 * 2336 318 * 0 7432 1179 1235
+
+D 13 4452 * 2534 2807 4650 3204 * 4913 5967 3478 * 2455 5771 * 5553 4141 5795 4818 * 5690 13
+ 195 3274 5427 563 1630 * 0 7463 1557 1235
+
+G 14 6167 * 3476 2795 * 2003 5272 * 4895 5323 * 2951 6295 5882 3391 4269 3564 5185 * * 14
+ 40 5182 * 949 1053 371 2141 7624 1116 1410
+
+E 15 4594 6352 6466 4103 * 4310 * 4856 3712 4877 * 4832 * 4424 4234 5227 1087 4348 * * 15
+ 36 5326 * 1958 429 0 * 8021 1158 1004
+
+P 16 5204 * 4277 4155 4640 5684 * 5595 5108 4670 5313 2799 3143 5084 5863 2313 2727 5793 * 5826 16
+ 0 * * * * * * 8346 0 0
+
+L 17 3207 6810 6675 4094 4793 5484 5956 3696 2788 2401 4556 * 6696 4649 5745 4732 5540 3280 * 4160 17
+ 0 * * * * * * 8361 0 0
+
+G 18 5777 * * 5739 * 160 6375 * 6709 * * * * 5929 5594 * * 6710 * * 18
+ 26 6386 7464 0 * * * 8318 1042 0
+
+R 19 6333 6471 2410 4362 6774 6601 * 7151 4215 5295 * 3925 4601 6119 1822 3842 3269 4159 * * 19
+ 0 * * * * 0 * 8333 0 1000
+
+V 20 * * * * 2743 * * 1424 * 2310 3950 * * * * * * 2241 * * 20
+ 0 * * * * * * 8337 0 0
+
+S 21 6749 * 4304 3907 * 5250 * 2866 4201 4061 * 4601 6588 5016 4647 3920 3055 1887 * 5913 21
+ 0 * * * * * * 8337 0 0
+
+F 22 4032 7079 * * 3060 * * 1071 * 3498 5075 * * * * * * 2203 * * 22
+ 0 * * * * * * 8337 0 0
+
+E 23 6690 * 2868 1587 * 3312 6352 4247 5002 5272 5732 * * 2855 4520 6860 4797 4251 * * 23
+ 16 * 6464 * * * * 8337 0 0
+
+L 24 6610 * * * 5774 * * 4137 * 377 5379 * * * * 6666 * 3174 * * 24
+ 31 6417 6672 2807 222 * 0 8307 1040 1023
+
+F 25 4382 * 3160 5554 2137 * 5238 * 5575 3685 6480 5366 * * 4471 4837 * * 3924 1811 25
+ 0 * * * * 879 1132 8286 0 1140
+
+A 26 3507 5258 3758 4929 * 2569 7044 * 4593 5787 * 3456 2779 * 3258 4276 3588 4762 * 5031 26
+ 72 5890 4974 636 1487 * 0 8319 1095 1000
+
+D 27 4518 * 1536 2557 * * 5195 * 3066 * * 4393 * 5209 4652 3902 4245 * 6674 4292 27
+ 85 5595 4768 0 * 300 2413 8308 1137 1398
+
+K 28 3174 6305 4251 2699 4373 5068 5009 4150 3425 3142 6789 6006 * 4482 6927 4700 5195 3375 4685 5667 28
+ 14 6745 * 0 * 0 * 8316 1000 1449
+
+V 29 1258 3038 * 4732 4869 * 6918 6011 6470 4785 6753 * * 6798 6514 2994 4121 3431 * 6370 29
+ 36 5961 6837 0 * * * 8340 1194 0
+
+P 30 4602 6796 6458 5638 6779 * 6745 * 5954 * * 7027 323 6501 5669 * 5104 6442 7473 * 30
+ 0 * * * * * 0 8330 0 1000
+
+K 31 3568 4229 4967 4384 * 5326 5786 3917 2725 2603 4596 3291 * 4187 3779 5794 5808 4629 * 6674 31
+ 0 * * * * * 0 8330 0 1000
+
+T 32 2727 * * 4995 6395 3370 4295 5026 * 4472 4415 6833 6734 5862 * 2953 1851 4427 6501 4791 32
+ 0 * * * * 0 * 8330 0 1000
+
+A 33 2217 2958 * * * 4858 6746 * * 6455 * * * 6989 4229 3442 3598 1453 * * 33
+ 0 * * * * * * 8340 0 0
+
+E 34 3113 * 2943 2882 5969 4503 5881 6912 3775 4228 5791 3700 * 3506 3050 4291 5502 * * 5055 34
+ 16 6460 * 0 * * * 8340 1040 0
+
+N 35 4976 7515 * 3629 5640 6687 4096 5682 5053 4807 * 1340 * 5660 3177 4294 4962 4936 6954 4075 35
+ 0 * * * * * * 8340 0 0
+
+F 36 * * * * 255 * * 4524 * 3846 5803 * * * * * * 5526 * 6740 36
+ 0 * * * * * * 8340 0 0
+
+R 37 4311 5635 6365 4630 6514 5917 4929 2737 4096 1832 5462 * * 5351 4247 7258 4757 2888 6837 4637 37
+ 0 * * * * * * 8340 0 0
+
+A 38 3829 * 3357 3257 5635 5898 4155 * 3047 6945 7489 3777 * 3132 2821 3453 4294 6980 * 5574 38
+ 56 5007 7122 475 1834 * * 8340 1296 0
+
+L 39 4166 * 7200 7075 4894 * 5818 5061 * 866 3667 4210 6453 6655 3775 6603 5871 * 6440 4874 39
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+//
+�HHsearch 1.5
+NAME be74be0e66ca7b4603630a5a17fef2a4
+FAM
+FILE be74be0e66ca7b4603630a5a17fef2a4
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:00:02 2013
+LENG 61 match states, 61 columns in multiple alignment
+FILT 101 out of 263 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEECCCCCCCCCCEECCCCCEEEEEEECCCCCEEEECCCCCCCCCCCEEEEECCCCCCCC
+>ss_conf PSIPRED confidence values
+9746388878980249778317889986689888846467989889868997498676788
+>Consensus
+xxCxxxxxxxxxxxxtCgxxxCykxxxxxxxgxxixrGCtCPxxxxxxxvxCCxTxDxCNx
+>be74be0e66ca7b4603630a5a17fef2a4
+TMCYSHTTTSRAILTNCGENSCYRKSRRHPPKMVLGRGCGCPPGDDNLEVKCCTSPDKCNY
+>gi|82134454|sp|Q8JFX7.1|NX14_BUNMU RecName: Full=Muscarinic toxin BM14; Flags: Precursorgi|21388237|emb|CAD18848.1| muscarinic toxin-like protein [Bungarus multicinctus]
+-MCNMCVRPYPFMSSCCpeGQDRCYKSYWVNENGKQKkyhgkypvilERGCvtACTGPGSGSiynLYTCCPT-NRCGS
+>gi|162145668|gb|ABX82866.1| three finger toxin V [Walterinnesia aegyptia]
+-TCLICPKKYCNQVHTCrnGENLCIKTFYEGNlLGKQFKRGCaaTCPEARPREIVECCSR-DKCNH
+>gi|25452897|sp|P79688.1|CXH_BUNMU RecName: Full=Cardiotoxin homolog TA-ctx-like; Flags: Precursorgi|1813889|emb|CAA71820.1| cardiotoxin-like protein [Bungarus multicinctus]
+-TCFNDDLTNPKTTELCrhSVYFCFKNSRIAGGVERMQRGCslTCPDIKYnGKYIYCCTR-DNCNA
+>gi|331691435|gb|AED89560.1| putative three finger toxin precursor [Micrurus altirostris]
+-IC---DDSNIPSERTpkrCqgGYNICYKINFPTPgYELLQIKGCaaRCPTNPRFPKAECCAT-DNCI-
+>gi|82199672|sp|Q69CJ8.1|TXW1H_OPHHA RecName: Full=Weak toxin DE-1 homolog 1; Short=WTX DE-1 homolog 1; Flags: Precursorgi|38049479|gb|AAR10442.1| weak toxin DE-1-like protein [Ophiophagus hannah]
+-ICLKQEPFQPETTTTCpeGEDACYNLFWSDHSEIKIEMGCGCPKTEPYTNLYCCKI-DSCNK
+>gi|156485220|gb|ABU68471.1| 3FTx-Tel1 [Telescopus dhara]
+-KCHSCTGRLCITFQNCpdA-QACSQMWKdSDMLKLNVVKGCatNCTLPGPGQQILYCTK-DYCN-
+>gi|166215732|sp|A7X3S2.1|NXAC3_TRIBI RecName: Full=Toxin 3FTx-Tri3; Flags: Precursorgi|156485234|gb|ABU68478.1| 3FTx-Tri3 [Trimorphodon biscutatus]
+--------PPFPLGLYTvsHVKSCGGHLSSIGQCgeDWVVKGCakTCPTAGPGERVKCCYS-PRCNK
+>gi|41017457|sp|P60236.1|NXM14_DENAN RecName: Full=Muscarinic m1-toxin4
+-TCVKSNSIWFITSENCpaGQNLCFKRWQyISPRMYDF--------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 * * * * * * * * * * * * * * * * 0 * * * 1
+ 0 * * * * * * 1000 0 0
+
+M 2 * * 5626 5011 6174 * * 1804 2362 5380 4345 4912 * 5606 6954 6116 1876 4961 * * 2
+ 0 * * * * * * 5724 0 0
+
+C 3 * 31 * * * * * * * * * 5563 * * * * * * * * 3
+ 446 2166 4546 539 1682 * * 5721 2196 0
+
+Y 4 * 5952 5409 * 3158 * 2977 * 4392 2878 5101 4632 * * 4401 5664 * 4121 * 1541 4
+ 0 * * * * * 0 5379 0 1990
+
+S 5 * * * 5892 * * * 4756 2767 5132 5372 2104 * 3982 * 2298 2310 5449 * 5450 5
+ 0 * * * * 3730 113 5379 0 1990
+
+H 6 6516 1799 3511 6461 5956 4604 2810 * 5204 4468 * * * 3400 4783 4264 3427 5731 5414 6378 6
+ 34 * 5414 * * 3384 145 5394 0 1915
+
+T 7 * * 2896 3927 6222 6329 4863 5962 3364 5689 4805 4483 2617 4355 4188 4756 3062 5398 * 3654 7
+ 145 * 3385 * * * 0 5413 0 1949
+
+T 8 5234 * 4749 4439 4957 2607 * * 5827 3884 6057 5640 5007 * 5269 1802 2638 6444 * 4120 8
+ 252 4996 2956 0 * 711 1361 5390 1077 2347
+
+T 9 5023 6013 6381 5532 6362 6672 6218 3552 4782 3211 5190 3735 3241 5438 5266 3308 2654 3890 6311 4109 9
+ 243 2789 6590 1503 628 3289 156 5762 1680 1987
+
+S 10 * * 4293 5836 3557 4626 * 5078 4700 3014 7131 3424 4734 3426 3753 3823 3388 3935 6088 3994 10
+ 0 * * * * 979 1021 5835 0 1976
+
+R 11 4869 2008 4268 * 4229 4032 * 5114 * 6569 5809 5346 1819 * 3599 4081 6160 6470 6657 6835 11
+ 18 * 6372 * * 641 1479 5852 0 1464
+
+A 12 4247 * 4455 3447 3120 4850 5540 3859 3246 4188 5848 4444 3034 5107 4226 4275 6524 3856 * 6597 12
+ 22 6049 * 2314 324 1022 979 5826 1078 1202
+
+I 13 5209 * 4848 5021 5635 4274 5673 3369 3271 4393 5626 4491 * 4678 5293 3755 1554 6102 * 6707 13
+ 19 * 6237 * * * 0 5852 0 1072
+
+L 14 6551 * 6585 4768 3844 5089 5326 5234 5853 3496 * * 3717 * * 2129 1747 4844 6403 4776 14
+ 0 * * * * * 0 5837 0 1156
+
+T 15 6050 * 5878 1682 6408 7109 5144 5742 2541 5554 6329 6585 * 3318 4484 5608 3310 3389 6320 * 15
+ 51 * 4850 * * 1374 703 5837 0 1156
+
+N 16 6481 5172 5204 5665 4998 * 7100 4907 4994 4441 6423 3507 4984 5083 4395 4907 1135 4432 * 5528 16
+ 42 5114 * 1109 899 711 1362 5806 1106 1282
+
+C 17 * 67 * * * * * * * * * * * * * * 5556 5356 * * 17
+ 4343 73 * 928 1075 0 * 5852 5401 1072
+
+G 18 3930 * 4492 3890 * 699 4868 * 6692 * * 5488 * 5477 * 3745 * 6503 5504 6605 18
+ 64 * 4532 * * 0 * 5872 0 1189
+
+E 19 * * 6748 1713 6471 5333 5034 6548 3596 5434 4694 5717 * 1789 4494 5190 6703 4455 * 5127 19
+ 17 * 6407 * * 0 * 5794 0 1199
+
+N 20 * * 2676 4570 6816 5678 * 5481 2896 * * 1670 6875 5103 4377 4614 2902 * * 4588 20
+ 38 * 5253 * * 0 * 5873 0 1008
+
+S 21 4238 * * * 3833 * 6869 2381 4739 2080 5325 5988 * 5539 5655 3522 2739 3826 * 6257 21
+ 0 * * * * 0 * 5830 0 1113
+
+C 22 5409 34 * * * * * * * * * * * * * * * * * * 22
+ 0 * * * * * * 5886 0 0
+
+Y 23 6674 6756 * 4976 1976 5581 * 6450 * 5658 * * * 6696 * 5110 * 5134 * 796 23
+ 0 * * * * * * 5886 0 0
+
+R 24 6562 5658 * 4282 * 5581 * 3978 1050 5481 5572 5044 * 3953 4316 5882 2923 6203 * * 24
+ 40 7403 5544 0 * * * 5886 1000 0
+
+K 25 * * * 3607 6356 * 5531 5954 2043 3655 3182 3828 5650 5489 3046 4761 4161 4727 6738 4009 25
+ 15 * 6603 * * 1903 449 5879 0 1086
+
+S 26 3574 * 6794 * 3524 * * 4295 4244 4986 7240 5955 6619 * 4949 2565 2436 5017 2926 3275 26
+ 199 5449 3238 2032 405 530 1702 5887 1143 1107
+
+R 27 * 7043 * 5523 3692 * 4800 3629 4440 4716 5536 4965 6737 5004 4357 4623 5457 3462 1384 6344 27
+ 249 2771 6390 1402 686 2959 199 5722 1779 1633
+
+R 28 4953 3682 5785 5393 * 4598 6639 3890 4315 5907 5370 5977 3212 6612 2651 3232 3031 3933 6156 4773 28
+ 0 * * * * 650 1462 5722 0 1606
+
+H 29 3536 * 2823 3452 5805 3736 4772 4678 4340 6716 6648 3387 3913 5509 5181 4428 2956 4406 * 6707 29
+ 86 4465 6282 1786 494 2110 380 5822 1221 1185
+
+P 30 3606 * 4756 5283 3816 2696 3368 3972 4356 3623 4895 6368 3990 5857 4718 3696 4048 5673 * 5783 30
+ 585 2724 2456 187 3043 225 2793 5835 1833 1208
+
+P 31 * * 5519 * 4831 3426 5455 6404 4065 4150 6082 3372 3748 4801 1505 3685 5110 * * 5740 31
+ 22 * 6075 0 * 3738 112 5621 1000 2100
+
+K 32 6317 5295 5900 3777 5087 856 6504 * 3796 4881 6158 * * 6323 5202 4692 6541 4298 * 5680 32
+ 202 3099 6137 1777 498 185 3054 5790 2321 2081
+
+M 33 6859 * 4493 4012 4395 5601 * 4088 2996 3460 3815 5787 4232 6654 3608 6028 2859 4099 6045 3629 33
+ 72 4361 * 1940 435 1634 561 5863 1308 1166
+
+V 34 * * 4102 4535 6026 6578 * 3023 3307 4508 * 4838 5533 4172 1772 * 5940 3427 3774 5835 34
+ 0 * * * * 1921 442 5843 0 1205
+
+L 35 4874 * * * 3816 * 5451 1457 5636 3711 6558 * 5689 5726 * 5092 3984 2224 6587 4465 35
+ 73 4660 6700 2473 287 808 1221 5835 1174 1134
+
+G 36 4568 * 4310 1741 6835 4931 6408 3997 3561 4106 5124 7403 * 6558 3976 3866 4165 3102 * * 36
+ 15 6590 * 1000 1000 1323 736 5853 1000 1078
+
+R 37 * * * * 6766 6539 * * 2627 3858 4290 * * 4734 700 * * * 5167 5868 37
+ 7 * 7627 * * * 0 5874 0 1021
+
+G 38 5777 * * 6575 * 168 6071 * * * * * * 5869 5235 * 6487 * * 6464 38
+ 0 * * * * 557 1642 5868 0 1062
+
+C 39 * 0 * * * * * * * * * * * * * * * * * * 39
+ 1988 419 * 1000 1000 0 * 5883 4683 1000
+
+G 40 3319 * * 5872 * 2469 * 5093 5136 * 6505 4151 * * 5118 2781 1377 5806 * * 40
+ 112 3745 * 1000 1000 * * 5885 1386 0
+
+C 41 * 0 * * * * * * * * * * * * * * * * * * 41
+ 0 * * * * * 0 5857 0 1085
+
+P 42 5033 * * * 6195 6767 4935 5833 * 5856 * * 350 * * 5746 3891 * * 6844 42
+ 0 * * * * 0 * 5863 0 1085
+
+P 43 * * 5022 3152 * 4670 * 3834 2106 4361 * 5040 3660 4602 4648 3851 2430 6356 6816 * 43
+ 11 7096 * 0 * * * 5885 1000 0
+
+G 44 2576 * * 5196 5394 2843 * 6585 5030 5294 5409 4911 2381 4874 4693 3953 4296 2950 * 6814 44
+ 50 * 4874 * * * * 5889 0 0
+
+D 45 3871 * 4788 3085 * 3183 * 5162 2032 5719 5157 4392 4522 4620 3876 3490 5246 5530 6506 * 45
+ 151 * 3330 * * * 0 5844 0 1169
+
+D 46 4479 * 4849 4540 * 4755 6739 4567 4612 4823 * 4710 1492 6116 3493 3591 5406 4639 5692 4328 46
+ 333 2637 4470 426 1967 * 0 5620 1773 1763
+
+N 47 * * 3895 5482 4812 1246 4933 * 5373 4002 5919 3373 4980 * 3322 * 6047 6040 * 4088 47
+ 12 6908 * 0 * 2151 368 5600 1000 1988
+
+L 48 * * 3882 1851 7036 6527 * 3344 3254 3587 6892 6066 4608 5181 4948 5489 5800 2889 6715 4612 48
+ 165 3891 4609 815 1212 108 3791 5620 1302 1763
+
+E 49 * 6539 4721 3551 5502 5675 6214 4004 2839 5538 6660 3912 * 3827 3957 3768 3518 4765 * 2485 49
+ 10 * 7231 * * * 0 5819 0 1213
+
+V 50 5836 * 5751 * 6718 * 6590 1871 * 3568 5317 6024 6143 * 5644 6014 5258 1271 * 4163 50
+ 14 * 6706 * * 1635 560 5816 0 1253
+
+K 51 5631 6772 6777 3307 4992 * 4389 5157 2322 3442 5584 3688 * 4945 5381 6915 3116 3380 * 3526 51
+ 8 7563 * 0 * 0 * 5821 1000 1207
+
+C 52 * 90 * * * * * * * * * * * * * * * * * 4045 52
+ 0 * * * * * * 5889 0 0
+
+C 53 * 35 * * * * * * * * * * * * 5365 * * * * * 53
+ 0 * * * * * * 5889 0 0
+
+T 54 3330 * 6017 5053 5779 6000 * * 3185 6639 5867 4376 5610 5443 4687 1834 2170 6564 * 4628 54
+ 0 * * * * * * 5889 0 0
+
+S 55 * * * 5870 * 5158 * 4978 3921 * * * * * 3352 3094 681 * * 5779 55
+ 5268 * 38 * * * * 5889 0 0
+
+P 56 * * * * * * * * * * * * 0 * * * * * * * 56
+ 0 * * * * 0 * 1000 0 5433
+
+D 57 * * 268 6633 * 6355 * * * * * 4052 4312 5776 * 5779 * * * * 57
+ 0 * * * * * * 5889 0 0
+
+K 58 6488 * 4922 4419 6070 5777 * * 1608 3545 6655 1996 * * 2753 5753 6576 * * 5360 58
+ 7 * 7626 * * * * 5895 0 0
+
+C 59 * 36 * * * * * * * * * * * * 5352 * * * * * 59
+ 0 * * 0 * 0 * 5892 1000 1000
+
+N 60 * * 6532 * * 4663 * 5116 * * * 139 * * * * 6278 * * * 60
+ 13 6754 * 0 * * * 5895 1000 0
+
+Y 61 3867 * 4891 5795 * 4907 3907 4140 1978 3486 5039 3248 * 5336 4015 3644 * 6187 * 3966 61
+ 0 * * 0 * * * 5443 0 0
+
+//
+�HHsearch 1.5
+NAME c12ad1255bc3ed843ae21de938ab5f62
+FAM
+FILE c12ad1255bc3ed843ae21de938ab5f62
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:17:02 2013
+LENG 157 match states, 157 columns in multiple alignment
+FILT 206 out of 1461 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 11.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCEEEEEEECCEEEEEEEEEECCCCCCEEEEEEEEECHHHCCCCHHHHHHHHHHHHHHHC
+CCCEEEEEECCCCHHHHHHHHHCCCEEECCCCCCCCCEEEECCCCCCCCEEEEEEEC
+>ss_conf PSIPRED confidence values
+9199999999999999999975266108999999986178965999999998999999996158997799999999788857979999999999999987
+998999998369989999999879999742234444304410136998589999969
+>Consensus
+xixirxxxxxdxxxixxlxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxvGxxxxxxxxxxxxxxxixxxxvxxxxrxxGigxxllxxxxxxxxxx
+xxxxxxxxxxxxnxxxxxxyxxxGfxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxl
+>c12ad1255bc3ed843ae21de938ab5f62
+HMDIRTITSSDYEMVTSVLNEWWGGRQLKEKLPRLFFEHFQDTSFITSEHNSMTGFLIGFQSQSDPETAYIHFSGVHPDFRKMQIGKQLYDVFIETVKQR
+GCTRVKCVTSPVNKVSIAYHTKLGFDIEKGTKTVNGISVFANYDGPGQDRVLFVKNI
+>gi|288940219|ref|YP_003442459.1| acetyltransferase [Allochromatium vinosum DSM 180]gi|288895591|gb|ADC61427.1| acetyltransferase [Allochromatium vinosum DSM 180]
+-IQLKIAGSSEIDEVLKLHYRYQIDSIAKEDKSDGFVTTsftkdqmvdliNk-ENGLFIAK-kgGAVVAYVMAASWEFwsawpmfafminelpnleyKGQ
+MLSVENsyqygpICIDKSVRGTGVLEAIFEFAKNKMSER-YPILVTFVNKANERSYQAHKRKlGLDVIH-------------QFEfNSNSYYEMACK-
+>gi|256825653|ref|YP_003149613.1| acetyltransferase (GNAT) family protein [Kytococcus sedentarius DSM 20547]gi|256689046|gb|ACV06848.1| acetyltransferase (GNAT) family protein [Kytococcus sedentarius DSM 20547]
+-WHLRKPVaae---TPAMTRLLAAHQervlgkasaAWADVDDRVLGR--gAEFRFHRIAQDAdgq---ARGWVNVNDRAVHR----vmidvyldpal---
+--Vagevd-----gadAAAVWDALFAWGRAAAIRMAWRRgvsetvLDSSPYEADEFTRERLAAAGFHKE-----------------------------
+>gi|328866934|gb|EGG15317.1| hypothetical protein DFA_10151 [Dictyostelium fasciculatum]
+-LLLEPFtfdatkalnqeEDEEWETIEELAGDakvamttqFIPHPyPTGASKSWIASqqkawSTGTDMTLAIKLIeqgptkSKIIGVISiMSDIY--NGT
+NILKlGYWIGSPYWNNGYATEASLVIVDFVFNTlNISCLWASCMSHNIGSERVFQKIGMKYQY---------SQPLVIRgQPIDCKFYNITK
+>gi|324502796|gb|ADY41227.1| Protein NCOAT [Ascaris suum]
+---mkcaiplslncytI-----------------rpykdedekelrtfydasedr-f---avegsilndtkeERFFDRTIGPFVSLss-PRTAFVAVDNi
+gttskr--IAA--ivSAAlnaksfaekfrrqyipkvrskyamyaeiekeqgisgedverlWQCQREE--isdweppNLSDyfydqfpsqvdIRYRSVTQD
+AVAVRRLIYVTAVALSFNGSNG----ffvvLQSSETEKIDF-------------------------------------ycklglvtlkevglpeeillmg
+hsL
+>gi|284030371|ref|YP_003380302.1| GCN5-related N-acetyltransferase [Kribbella flavida DSM 17836]gi|283809664|gb|ADB31503.1| GCN5-related N-acetyltransferase [Kribbella flavida DSM 17836]
+TASINDAPKDDLD----IEDDEFTPERLRAYEHAQLMHDRSLYRVIARHrgTGELAGHSTITVERERPHIGEQADTAVSRNHRGHRLGALVKTGMLLWMR
+EAepALSQLDTWNAESNDHMIGINEQLGYRVVA---------RAMAY--------------
+>gi|333030862|ref|ZP_08458923.1| hypothetical protein Bcop_1750 [Bacteroides coprosuis DSM 18011]gi|332741459|gb|EGJ71941.1| hypothetical protein Bcop_1750 [Bacteroides coprosuis DSM 18011]
+--------------------------------------------FELKINDTTAIVEYILTP---QGVVFMTHTEIPNSLESDEVIPVLMEESLQEIKRK
+EHVVFPMC-------------------------------------------------
+>gi|221114075|ref|XP_002160156.1| PREDICTED: hypothetical protein [Hydra magnipapillata]
+-VQTAIATLNDVDDILECINDAFMEyaffkkpeyhQKFTRENVTSMLLQKDSVFILAYNneicehfKNKVVGTIFLHWitttetyvlendsIAKVTLIGK
+FSSLSVPPKYANQGFGKALVSSAEKYLCQEVFNTIQhttlsasdsnkkkqfgvlmeLKAINFRKDLLSWYEKQGYQFISEIRQLDAAFTRRLLEDKDVYF
+ILMRKIL
+>gi|163849368|ref|YP_001637412.1| hypothetical protein Caur_3846 [Chloroflexus aurantiacus J-10-fl]gi|222527365|ref|YP_002571836.1| hypothetical protein Chy400_4155 [Chloroflexus sp. Y-400-fl]gi|163670657|gb|ABY37023.1| hypothetical protein Caur_3846 [Chloroflexus aurantiacus J-10-fl]gi|222451244|gb|ACM55510.1| conserved hypothetical protein [Chloroflexus sp. Y-400-fl]
+--AAQRLSADMRADLAALhSAtagwQSWHPDG--------------GPAFGVVAtTGQLQAIAA--TCFATRDVIEIGWAMQPAAVPA---LQGCIGALT
+QLCFGL-ASRVYLFVEAGDDEIVTGCRHLGF--------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+H 1 * * 2798 4450 * * 2841 * 2393 * 4264 1589 3380 * * * * * * * 1
+ 0 * * * * * * 7761 0 0
+
+M 2 6263 6752 * * 3173 * 6854 2029 * 2095 2429 * 6164 * * * 6220 3110 6918 4573 2
+ 10 7113 * 2825 219 * * 11503 1103 0
+
+D 3 4646 * 4141 3132 7473 7426 4815 3168 3105 4678 5179 4465 7331 3937 3735 4415 2792 4587 7283 5878 3
+ 41 5166 * 1197 827 * * 11632 1693 0
+
+I 4 6542 6408 * 7444 3538 * * 1596 5658 1989 5378 * 7550 * * 7210 5484 2623 7369 4153 4
+ 0 * * * * * * 11669 0 0
+
+R 5 4316 6512 5616 4235 * 7324 5205 4676 2966 5145 7506 6276 * 4768 1209 4710 4807 4017 * 6242 5
+ 15 7793 7467 0 * * * 11715 1000 0
+
+T 6 4807 7514 4624 3776 5533 7717 6608 4584 3416 3638 7491 4475 2037 4115 3809 4434 4251 4637 7646 5284 6
+ 26 6298 7617 535 1690 * 0 11695 1151 1025
+
+I 7 2045 5525 7699 5991 3368 6200 7069 2844 * 2216 4783 * 4587 7579 * 6436 6482 3583 5958 4735 7
+ 39 5219 * 451 1896 935 1068 11709 1513 1197
+
+T 8 4688 7212 3896 3010 7594 5027 6773 7493 3766 4481 * 4009 5468 3894 4169 2993 2260 4256 * * 8
+ 17 6453 * 1051 951 * 0 11718 1171 1025
+
+S 9 3466 * 3715 2654 * 6753 5167 4148 3477 3801 * 4274 2995 5123 4541 4329 4792 3889 * 5857 9
+ 61 4785 7585 1862 464 1025 975 11700 1709 1188
+
+S 10 3413 7566 2888 2538 * 5070 6033 5881 3746 5658 6507 3772 5663 3769 4632 3182 3578 6792 5914 * 10
+ 29 5653 * 0 * 1166 851 11700 1349 1161
+
+D 11 5703 * 928 2854 6103 5684 4235 * 7774 5481 * 5237 7558 4090 5493 6318 5529 6582 6373 4901 11
+ 21 6818 7400 1000 1000 0 * 11742 1120 1030
+
+Y 12 2834 5298 6127 4505 3323 6302 6756 3381 4527 2379 5884 7598 6563 7456 4624 5099 6494 3254 4907 3940 12
+ 20 6160 * 2141 371 0 * 11747 1256 1022
+
+E 13 3322 * 2766 2892 5956 4617 6566 6447 3661 4151 6884 5451 2783 3733 4521 4174 5505 5273 * 7493 13
+ 9 * 7278 * * * * 11758 0 0
+
+M 14 2887 7649 3180 2877 5791 4831 6456 4722 4167 3902 5629 5781 5329 3300 3982 3755 5025 4783 6714 6699 14
+ 8 7522 * 1585 585 * 0 11749 1000 1058
+
+V 15 4316 5663 7533 6043 4201 7437 * 2038 * 1834 4265 7481 * * * * 7581 2455 4970 4377 15
+ 15 6609 * 0 * * 0 11759 1218 1058
+
+T 16 3300 5043 7530 4207 4294 5334 4779 3743 4626 2794 4072 4550 6573 4884 4316 4675 4640 3778 4999 4135 16
+ 8 7550 * 3000 193 * 0 11768 1003 1058
+
+S 17 3152 7454 3000 2436 * 5394 5142 7814 3342 5438 7618 4669 5807 3965 2983 4042 4650 5098 * 6468 17
+ 0 * * * * 0 * 11768 0 1058
+
+V 18 5314 5872 6540 6670 3291 6638 6666 2711 7544 1437 4498 * 6617 6626 7683 5279 6518 3610 3874 4983 18
+ 0 * * * * * * 11781 0 0
+
+L 19 3851 6174 5337 4173 3267 5216 4872 3934 5571 2607 4769 5409 7618 4708 4248 6786 5859 3595 3821 3553 19
+ 7 * 7676 * * * * 11781 0 0
+
+N 20 4256 7573 4283 4358 5524 4528 4417 4897 3335 4646 6427 2639 5329 3725 3613 3832 4729 4165 6682 5061 20
+ 39 5934 6644 2082 389 * 0 11778 1301 1000
+
+E 21 3804 * 3045 2550 6848 6257 5245 6732 3596 4335 6041 3998 6648 3037 4121 3393 4838 6197 7269 5088 21
+ 51 5328 6625 2912 206 539 1682 11766 1514 1235
+
+W 22 3051 4230 5938 3595 5640 4483 5317 4028 * 3701 6089 4221 4722 5307 4853 3750 4007 3187 4393 4683 22
+ 284 2484 * 2558 268 1327 734 11767 4975 1253
+
+W 23 4182 6061 5232 5079 2268 4822 5044 4328 6085 3725 4300 5827 6547 5069 5327 4921 5338 4892 2656 3709 23
+ 283 2642 5805 2934 202 0 * 11769 4445 1100
+
+G 24 3853 6443 3678 3786 7085 2898 6584 6580 5226 5307 6369 4867 2654 3861 4242 3268 4020 4554 * 5688 24
+ 64 5305 5781 769 1275 876 1136 11781 1476 1377
+
+G 25 5139 * 3382 2640 5331 4127 3791 5092 4182 4811 6016 4775 3287 4040 3901 4182 4715 4720 6445 5946 25
+ 663 1440 * 3111 177 664 1438 11772 7408 1574
+
+R 26 3410 * 3267 3094 6064 3402 4168 6626 4643 4771 4944 5592 3339 4322 3951 4054 5093 4539 6818 5329 26
+ 37 5611 7769 2147 369 919 1086 11771 1377 1132
+
+Q 27 3629 7547 3587 3498 5691 4106 7357 4729 5664 4509 5770 4232 3237 3607 4279 3900 3355 5253 7747 4309 27
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+ 0 * * * * * * 10475 0 0
+
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+ 0 * * * * * * 10045 0 0
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+I 157 * 5984 * * 5012 4690 * 2564 5884 761 5831 5947 5875 * * * 5890 4299 * 5656 157
+ 0 * * 0 * * * 9753 0 0
+
+//
+�HHsearch 1.5
+NAME c2c32c13af9575e387657a5ea9736806
+FAM
+FILE c2c32c13af9575e387657a5ea9736806
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:19:22 2013
+LENG 135 match states, 135 columns in multiple alignment
+FILT 130 out of 509 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCEE
+EEEECCHHHHHHHCCCEECCCCHHHHHHHHHCCCC
+>ss_conf PSIPRED confidence values
+9865557565798999855564457678888898878856588652157788774476654567458999999999873021142999999986355678
+62347648888751820146320999998647689
+>Consensus
+aRtkxtaxkxxxxkaprkxxxxkxxxxxxxxxxxxxkxxrxrpgtxalrEIrxyQkstxlLIxKlpFxrLVrEIxxxxxxxxrxqxxAlxaLQeAaExxL
+vxlfexaxxxaxHakRvTlxxkDxxlxxxirxxxx
+>c2c32c13af9575e387657a5ea9736806
+ARTKQTARKSTGGKAPRKQLVTKAAKKCAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYL
+VALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
+>gi|290998115|ref|XP_002681626.1| histone H3 [Naegleria gruberi]gi|284095251|gb|EFC48882.1| histone H3 [Naegleria gruberi]
+--------------------------------------EKRKRKQRWLQEIRKYQKSTRNLIPRASLIRLIKQVTAELSEKIpyirqlagegaiRWRKDA
+LAALHSAAEDFLHEFLTLSNYATLHAKRVTLMGRDLKLVQNINREH-
+>gi|309354883|emb|CAP39585.2| hypothetical protein CBG_23442 [Caenorhabditis briggsae AF16]
+ARTKQTARKSTGGKAQESSWPPRLPANRP------QLPEESRSHIVTAQEPSLFVRSD---VTRSPLSSLSAS-CHS--SVLFVRSPRISRLTFASNLPL
+SWLFK------------------------------
+>gi|119175703|ref|XP_001240035.1| predicted protein [Coccidioides immitis RS]
+--------------------------------------QNWKASTCTIKEICHFQSSIKLILLVALFQQLVQEITLSChqEHEYYWQHTAIESLQKAAEV
+ILCALFECKSLLAmaptiilsnigfviamVHHKCVTVNTNNMKLIL-------
+>gi|115388761|ref|XP_001211886.1| predicted protein [Aspergillus terreus NIH2624]gi|114195970|gb|EAU37670.1| predicted protein [Aspergillus terreus NIH2624]
+ARTSQTARKRTGPPRPRNT------TH-------DFTDHSNKTYTVVDPFQRRCP--NPHVITKLSIHLY-------SLGPLQPspeaigqellKSNDII
+DWANARNWWprvdVYSPLDSIEACIEHHRREKTFRK-------------
+>gi|195124333|ref|XP_002006648.1| GI21176 [Drosophila mojavensis]gi|193911716|gb|EDW10583.1| GI21176 [Drosophila mojavensis]
+---------------------------------------PFRRAQKFKREVRLLQRTPNFMIPRISFGRVVREIMLErcdCEPHFRITMGALEALQTATE
+MFLTQRFQDSYMMTMHRQRVTLELRDMALMAFICK---
+>gi|239613301|gb|EEQ90288.1| predicted protein [Ajellomyces dermatitidis ER-3]
+--------------------------------------------CKSLHEICFYQKSENFIFLKIIFTHLVCEIDEK---NHQFQYSILNTIQVTAEFTL
+ITLFKYNIKIITYYSHITLTVRDIQLMINIA----
+>gi|327409929|ref|YP_004347349.1| histone H3-like protein [Lausannevirus]gi|326785103|gb|AEA07237.1| histone H3-like protein [Lausannevirus]
+----------------------------------------------NMQEIRKQQRQTCMIIPKARFRDIAKEIVDRELEGVRLSEKALDLLQLIVESLT
+VRLLEKAVALTLEAQKDRVTGRSIEAIFKI-----
+>gi|308503172|ref|XP_003113770.1| hypothetical protein CRE_26460 [Caenorhabditis remanei]gi|308263729|gb|EFP07682.1| hypothetical protein CRE_26460 [Caenorhabditis remanei]
+--------------------------------------RKQKRQSKIYREIVYEKMSTKFAIPPEDFRDVVDEIMEEEFPDHQIETGAIMALQHESEMML
+TKMMCLASHLADYADRETLRKKDIDFLKF------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+
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+
+L 109 3588 * * 4197 * * 5611 3804 3854 1283 4145 6911 5279 5776 3789 4858 4762 5553 7095 6790 109
+ 57 5511 5914 0 * * * 5318 1032 0
+
+C 110 3652 1103 * * 6146 5969 * 3893 * 2449 4967 7023 * * * 4873 4988 4021 * 7048 110
+ 0 * * * * * 0 5288 0 1023
+
+A 111 905 5029 * * * * * 3495 * * 4269 * * * * 3433 2495 5339 * * 111
+ 51 4859 * 3008 192 * 0 5288 1080 1023
+
+I 112 4238 * 5597 3837 5497 * 5186 2094 4916 2406 4916 4760 5382 4743 4878 5226 3703 4750 * 4483 112
+ 0 * * * * * 0 5288 0 1023
+
+H 113 6525 * * 5666 4910 * 406 * 6778 * 6021 7087 * * 4524 4710 * 6299 * 4182 113
+ 0 * * * * * 0 5288 0 1023
+
+A 114 1011 4313 6299 * * 2982 3705 * * * * * * 6565 3513 3879 4370 * * 5433 114
+ 0 * * * * * 0 5288 0 1023
+
+K 115 6504 * 5208 * * 3762 4688 6517 1134 * * 3544 5482 4192 2578 4248 * * * * 115
+ 0 * * * * * 0 5174 0 1023
+
+R 116 * 5223 * * * * 5420 6517 5639 6740 * * * 5798 231 4652 * * * * 116
+ 33 5482 * 1585 585 * 0 5174 1032 1023
+
+V 117 5030 6661 4949 3009 * * * 3081 4610 4215 5607 * * * * * 5198 883 * * 117
+ 0 * * * * * 0 5174 0 1023
+
+T 118 * * * * * * * 5148 3612 5103 6779 * 5734 * 4303 * 354 * * * 118
+ 0 * * * * * 0 5123 0 1023
+
+I 119 5580 * * * * * * 1490 * 1247 * * * * * * 4882 2573 * * 119
+ 0 * * * * * 0 5123 0 1023
+
+M 120 6475 * 6335 4083 3208 * 7450 6823 3850 5367 1608 4066 * 3926 4470 6018 2578 * * 5686 120
+ 0 * * * * 0 * 5123 0 1023
+
+P 121 3389 * 5189 4944 * 5126 * 6075 3747 4303 * 7514 1794 5261 3468 3920 4205 2781 * * 121
+ 22 6075 * 4322 74 * * 5164 1014 0
+
+K 122 6466 * 4162 4344 * 6969 * * 1162 * * 6259 6366 6064 1806 5368 3958 6156 * * 122
+ 0 * * * * * * 5125 0 0
+
+D 123 * * 135 * * * 5495 * * * * 4402 * * * 5637 * * * * 123
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+
+I 124 6576 * * * 5216 * * 1509 * 2939 1623 * * * * 6713 5063 3180 7271 * 124
+ 0 * * * * * * 4826 0 0
+
+Q 125 3966 6096 5101 3623 * * 5455 5350 2479 4242 * 4887 5495 1512 3285 * * * 7169 6011 125
+ 0 * * * * * * 4826 0 0
+
+L 126 3835 * 6008 * 4097 * * 5107 * 407 6539 * * * * 5495 5134 6495 * * 126
+ 10 7186 * 1000 1000 * * 4826 1000 0
+
+A 127 1352 5979 * * * * 6435 3904 * 5006 3650 * * * * 5926 5247 1756 4757 5178 127
+ 0 * * * * * * 4826 0 0
+
+R 128 3839 * 7759 6495 4473 * * 4901 3562 2547 3724 6809 5495 4266 1691 4780 5395 4755 * 6096 128
+ 0 * * * * * * 4826 0 0
+
+R 129 6507 6998 6488 5165 3887 4197 5122 6254 3207 4174 5270 4525 * 5307 1060 6295 * * * 5177 129
+ 0 * * * * * * 4758 0 0
+
+I 130 5941 6419 * * 4320 * * 963 * 1515 5143 * * * * * * 5597 * 6608 130
+ 0 * * * * * * 4679 0 0
+
+R 131 4623 5996 5519 * 5562 4170 5328 * 3934 4710 5981 6114 * 5566 716 4144 * * * * 131
+ 34 7164 5918 2000 415 * * 4374 1000 0
+
+G 132 5989 * 4532 4783 * 762 6418 * 3982 5449 * 4176 * 4386 3687 5997 * * * 5582 132
+ 31 6416 6683 1000 1000 0 * 4010 1000 1002
+
+E 133 5034 * 2844 1650 * 6084 5241 3230 5101 3779 5890 4628 7255 4583 3172 * 6604 6085 * 5623 133
+ 0 * * 0 * * 0 3957 1000 1000
+
+R 134 * * 4455 3690 5261 3608 4195 4948 4936 4223 6030 3997 4786 3356 2283 4001 6319 3672 6775 5996 134
+ 0 * * * * 0 * 3609 0 1000
+
+A 135 2376 * 3808 4547 3985 3656 5433 2627 * 4869 4986 4912 5308 4164 5265 4754 3845 * * 4240 135
+ 0 * * 0 * * * 3656 0 0
+
+//
+�HHsearch 1.5
+NAME c5753ae3727f4c7fc5433d2395780f60
+FAM
+FILE c5753ae3727f4c7fc5433d2395780f60
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:38:21 2013
+LENG 115 match states, 115 columns in multiple alignment
+FILT 131 out of 1126 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCEEECCCCCCEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEE
+ECCHHHEEECCEECC
+>ss_conf PSIPRED confidence values
+9889999758888789999999999999997939165999998787889689899659999999708999999999999999999986939210999999
+989899478889886
+>Consensus
+MPxixixtnxxxxxxxxxlxxxxxxxxxxxlxkpxxxixvxxxxxxxxxxxgxxxpxxxvxixxxxxxxxexxxxxxxxixxxlxxxlgixxxxixixxx
+exxxxxwgxxGxtxx
+>c5753ae3727f4c7fc5433d2395780f60
+MPMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYY
+DMNAASVGWNNSTFA
+>gi|224543411|ref|ZP_03683950.1| hypothetical protein CATMIT_02614 [Catenibacterium mitsuokai DSM 15897]gi|224523666|gb|EEF92771.1| hypothetical protein CATMIT_02614 [Catenibacterium mitsuokai DSM 15897]
+MPYLALRTNKTLTLSQEvELKTTVGKLITMFPGESVDTFMIHIEDNQLIYFKGQEANCMMITLYLKGHYTDEQKEQFVAELTKALVKITKIPASNQYVTI
+SEFE--KWGHGGVYE-
+>gi|291545105|emb|CBL18214.1| hypothetical protein RUM_22010 [Ruminococcus sp. 18P13]
+MPICQLKTNYPMDAAArEALLLDTATTAAELLNKPLAAVMAMLD-PCDMRMNGTDDTVFFAEFRYV--LPPEfsKekqafLDRFADRMLALFRQHTGVDP
+HRIYMQFTEMAREsAWKY------
+>gi|55380103|ref|YP_137952.1| tautomerase [Haloarcula marismortui ATCC 43049]gi|55232828|gb|AAV48246.1| tautomerase [Haloarcula marismortui ATCC 43049]
+MPLLQFDIARTLSdAAKTSLAERVTEFYTTEMATTAGHVAVTIRErdPTEMHLGRaVDGPLLFLDAEIRRGRSIDRKRAFALATMEYAAEELDIPDENMK
+VVFTEHPGSAM--------
+>gi|194290744|ref|YP_002006651.1| hypothetical protein RALTA_A2657 [Cupriavidus taiwanensis LMG 19424]gi|193224579|emb|CAQ70590.1| Conserved hypothetical protein; Putative 4-oxalocrotonate tautomerase COG1942 [Cupriavidus taiwanensis LMG 19424]
+MPHIVLHLAGQPDADlTRRSARAIADLTERVLGKQRDVIAVTVQYIphDSWIIADAPlseqgRNAFHLDISVTDETNTKaEKAQFIAAVFEAMSGLLGNL
+HPVSYVHVIDARAAAYGYGGRT--
+>gi|226953011|ref|ZP_03823475.1| transglutaminase-like protein [Acinetobacter sp. ATCC 27244]gi|226836240|gb|EEH68623.1| transglutaminase-like protein [Acinetobacter sp. ATCC 27244]
+MSQIKIYALNQtISQFRPRLSEAIHQALVTSLAYPIEKKFQRFIpmEPENFVYPdDRSDHYVIIEISMFEGRSIEAKQKLIQTIFSNIQNLCDISPQDIE
+ITIFETPKNHWGIRGKN--
+>gi|284042957|ref|YP_003393297.1| 4-oxalocrotonate tautomerase [Conexibacter woesei DSM 14684]gi|283947178|gb|ADB49922.1| 4-oxalocrotonate tautomerase [Conexibacter woesei DSM 14684]
+MPVMDVTYPVGaLTDAArATLVEELTTVLLRAERAPDteffrnvTWVYLHELPGEAVLSAGRpvTAPTFRVDVTVpAGALSDRRKQELVGEATRRVLDAA
+GLTQEhalRVMVLIRDVPEGNWGAAGTVI-
+>gi|322437161|ref|YP_004219373.1| 4-oxalocrotonate tautomerase [Acidobacterium sp. MP5ACTX9]gi|321164888|gb|ADW70593.1| 4-oxalocrotonate tautomerase [Acidobacterium sp. MP5ACTX9]
+MPFARIDLAKGKTPEyRATVADVVYDGIVNVLKAPEGdrFMIIGEHAPDNFVFDPnflniKrTPDLIILQVTStVG-NTKEQKLAFFRHMADELNRRLNV
+RREDVFISLVFVDRDDWSFGN----
+>gi|71282624|ref|YP_270060.1| hypothetical protein CPS_3384 [Colwellia psychrerythraea 34H]gi|71148364|gb|AAZ28837.1| hypothetical protein CPS_3384 [Colwellia psychrerythraea 34H]
+-----------------EAVEKITHSMLKHHGLLGNTVMtpnitahVSVLPKNSTFSGGEEFSGVWMEWKvpSFAFASRDIQLAHFADATEIIRALSggK
+QPIEHIYSNVIHTVDGSWNFNGIAM-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 8472 0 0
+
+P 2 5766 * * * * * * * * * * * 140 5490 * 4738 * 6141 * * 2
+ 19 * 6287 * * * * 8463 0 0
+
+M 3 * 4383 * 6533 2498 * 4796 2654 6189 2554 4291 5274 * 5932 6414 5878 3940 3082 * 3643 3
+ 0 * * * * 0 * 8483 0 1025
+
+F 4 3250 4349 * * 5692 * * 1655 * 2145 6302 * * * * * 5319 2105 * 6310 4
+ 0 * * * * * * 8506 0 0
+
+I 5 5041 * 4888 3317 * * 4089 4100 3566 4369 4959 3103 * 3272 2961 4196 3330 4606 * 6625 5
+ 0 * * * * * * 8506 0 0
+
+V 6 5027 5575 * * 3422 * * 1419 * 2365 4974 * * * * 6551 4819 2259 * * 6
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+
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+ 0 * * * * * * 8506 0 0
+
+T 8 4428 6221 * 6262 * 4642 6062 4027 * 2577 6399 * * * * 4389 1278 2657 * 6302 8
+ 54 4778 * 0 * * * 8506 1316 0
+
+N 9 4688 * 6456 5070 * 5697 * 5371 5655 4028 * 1147 3356 4831 4228 3836 4414 5014 * 6652 9
+ 0 * * * * * * 8506 0 0
+
+V 10 4512 * * 3678 6435 4421 4221 4883 3483 3036 6583 6016 6399 3795 4756 4473 4186 1924 * 6551 10
+ 140 6823 3584 0 * * * 8506 1017 0
+
+P 11 4480 * 3808 5133 6524 2738 * 4753 2799 * * 4071 2880 3471 4433 2836 4999 6555 * * 11
+ 383 2268 5309 352 2207 0 * 8604 3619 1797
+
+R 12 2920 * 5146 5559 4452 6442 4793 3290 3902 2754 4637 6712 4243 * 3547 4065 4071 4002 6180 5370 12
+ 71 6506 4762 0 * 925 1079 8443 1030 1225
+
+A 13 3439 6412 2927 4246 * 4314 * * 6655 5602 * 4921 3583 5507 5547 2125 2229 5692 * 6742 13
+ 45 5018 * 0 * 1276 768 8463 1286 1570
+
+S 14 3166 * 2357 3394 * * * * 3469 5077 * * 3615 3317 3201 3765 5386 3471 * * 14
+ 31 * 5568 * * 0 * 8467 0 1287
+
+V 15 3280 6448 2816 1947 4261 * * 3838 5028 4772 * 6508 6063 4768 4750 4427 5092 3067 * * 15
+ 379 2195 6282 0 * 0 * 8489 3323 1187
+
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+
+D 17 3128 * 2968 3073 6592 * 6265 6639 2255 5011 * 4510 5472 3402 3768 4035 4821 4863 * * 17
+ 212 2871 * 0 * * * 8518 2615 0
+
+G 18 3080 * 3427 2577 * 3534 6489 5084 3236 * * 4006 6652 3872 4053 3539 3303 * * * 18
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+
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+ 0 * * * * * * 8548 0 0
+
+L 20 2607 6648 6488 4260 4710 5054 5570 3385 4359 2146 4062 5020 * 5568 5238 4065 * 3254 * * 20
+ 0 * * * * * * 8551 0 0
+
+S 21 4000 * 2965 2940 * 6488 5881 6663 2562 6541 6460 6141 6525 4056 2963 3575 3607 3830 * * 21
+ 0 * * * * * * 8551 0 0
+
+E 22 2858 7064 3599 2153 * 3476 * 5495 3357 4923 * 4871 * 5174 3328 3834 4868 5577 5807 * 22
+ 0 * * * * * * 8551 0 0
+
+L 23 3221 6484 * * 3675 * * 2268 * 1580 * * * * * 5129 4036 2646 * 6384 23
+ 0 * * * * * * 8551 0 0
+
+T 24 3334 5464 * 5350 6326 4104 3311 6636 6141 6668 6602 6511 * * * 1905 1876 5618 * 3895 24
+ 13 * 6753 * * * * 8551 0 0
+
+Q 25 3850 6415 3024 2188 6699 6347 4638 7274 3285 5859 6378 3804 * 3537 3255 4140 5635 5979 * 5572 25
+ 0 * * * * 0 * 8547 0 1022
+
+Q 26 1627 4385 * 5740 4390 5582 5492 3529 6082 2368 5778 * * 6827 5690 6619 5798 2846 * 6619 26
+ 0 * * * * * * 8551 0 0
+
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+
+A 28 1850 4206 * 4947 * 4755 5764 4307 6136 4088 * 6385 6705 * 4190 2191 5137 3138 * 5664 28
+ 0 * * * * 0 * 8541 0 1026
+
+Q 29 3993 * 3223 1705 6691 6497 6489 4717 3077 4791 6727 5654 * 3951 3895 4595 3549 6524 * * 29
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+
+A 30 2686 6110 5728 3713 6521 6248 6597 2884 6081 3461 5776 4725 * * 5031 3937 3474 2352 5522 * 30
+ 0 * * * * * * 8551 0 0
+
+T 31 5709 6848 * 4700 3037 * 6717 3871 * 1284 2892 * 4402 * * 6525 3940 6141 * 4289 31
+ 0 * * * * * * 8551 0 0
+
+G 32 4125 6373 3429 4087 * 1426 4982 * 3255 * * 3263 5828 3689 5578 5559 5781 6559 * * 32
+ 0 * * * * * * 8551 0 0
+
+K 33 3749 6413 5828 * 6511 * * 3932 1195 5060 4381 6539 * * 3714 5516 4959 2747 * 6035 33
+ 10 * 7227 * * * * 8551 0 0
+
+P 34 6501 * 3943 4538 * 4976 * * 5759 * * 5030 714 6238 4702 3250 4898 * * * 34
+ 0 * * * * * 0 8653 0 1000
+
+P 35 3728 * 4291 1649 * 5032 * 4087 3418 4749 4310 5924 3313 4018 5289 4632 5149 6475 * * 35
+ 54 4774 * 2807 222 0 * 8653 1350 1000
+
+Q 36 3972 6164 2501 2393 * 4305 5916 5438 3601 6869 6539 3713 5806 5719 4269 3010 3911 * 7035 * 36
+ 120 3773 7300 1000 1000 * * 8551 1811 0
+
+Y 37 4359 6613 3718 4973 3428 4918 4304 5695 3503 4040 * 5124 * 5978 3295 3880 6691 4174 3932 2803 37
+ 0 * * * * * 0 8559 0 1043
+
+I 38 5482 5536 * * 4028 * 5550 1753 6034 3617 4499 6246 * 3679 5489 6110 4504 1923 * * 38
+ 0 * * * * * 0 8559 0 1043
+
+A 39 3679 4684 6407 6394 3050 * 5417 4131 * 3829 2145 5119 * 6324 4556 4483 3413 3349 6513 5053 39
+ 30 5615 * 2807 222 * 0 8559 1305 1043
+
+V 40 5030 6738 * * * 6363 * 2622 * 3628 4744 5823 * 4187 * 5467 3972 976 * * 40
+ 0 * * * * * 0 8559 0 1043
+
+H 41 4051 6964 5066 4334 5623 5449 3251 3728 7280 3250 4378 4621 * 3779 3626 4138 2906 4048 6394 6395 41
+ 34 5407 * 1585 585 0 * 8559 1199 1043
+
+V 42 5310 * * 4253 3229 6753 * 2200 * 2191 6792 * 6248 * 6532 6239 * 1981 6110 4161 42
+ 117 3679 * 1000 1000 * * 8551 1844 0
+
+V 43 * * 3312 3163 * * 3252 4168 4125 3252 5935 3972 * 3472 3792 3702 4013 4073 * 5367 43
+ 99 4174 6558 1000 1000 * * 8551 1559 0
+
+P 44 4074 5301 2483 2858 * 4311 4346 * 5789 6622 * * 2189 5380 6420 4817 3184 5418 * 4416 44
+ 76 4829 5966 1000 1000 0 * 8804 1307 1036
+
+D 45 2848 * 3021 3742 * 2716 6461 5726 5405 5931 * 2869 3043 4304 4735 3906 6563 6467 * 7449 45
+ 129 3862 5921 1397 689 0 * 8810 1746 1076
+
+Q 46 3409 5011 4323 3392 * 3612 4696 4864 4405 4378 6744 4866 4473 2828 5554 4177 3876 3608 * 5421 46
+ 75 * 4300 * * 0 * 8716 0 1115
+
+L 47 4043 4409 3421 4532 5563 3689 3763 4891 5457 6741 6229 3917 3665 3610 2996 3833 4372 7079 6290 6229 47
+ 0 * * * * 0 * 8687 0 1523
+
+M 48 4813 6241 * * 2790 6442 * 2389 * 2459 1835 6168 * * * * 7622 4069 3979 * 48
+ 134 3897 5524 2051 398 * * 8780 1718 0
+
+A 49 3791 4307 6490 * 4145 4460 4296 3402 * 3517 6654 * * 6491 4525 3325 3032 3294 6225 2949 49
+ 18 * 6304 * * * 0 8923 0 1368
+
+F 50 4530 * * * 1679 * 4832 3344 6497 3076 4739 * 6247 * 2813 4333 * 4074 5568 4101 50
+ 21 6086 * 1000 1000 480 1822 8900 1049 1531
+
+G 51 3042 5210 5573 6824 7118 1197 6125 * 6667 5845 5766 4817 3166 3996 5003 4204 6350 * * 6503 51
+ 38 5253 * 0 * * 0 8736 1194 1060
+
+G 52 3690 6296 3576 6338 5456 833 * * 5582 4319 * 5499 6301 * 3662 5605 5385 * * * 52
+ 325 2404 6315 1649 554 * 0 8736 3040 1060
+
+S 53 4853 * 4254 3146 * 6345 6349 * 4093 4568 * 3733 * 4949 2979 2013 2735 4562 * * 53
+ 192 3002 * 311 2367 1094 912 8719 2519 1227
+
+S 54 4799 6383 2708 3534 4892 4807 5524 6432 5269 5404 * 3755 2967 6645 6125 2713 2660 6360 * 6476 54
+ 151 3468 6812 2385 306 * 0 8736 1903 1060
+
+E 55 3288 * 2132 2263 * 4488 * 6541 4219 4209 * 4859 5310 4450 3698 5358 5018 4051 * * 55
+ 127 3567 * 684 1405 1269 773 8731 1924 1194
+
+P 56 4143 * 3258 4006 6406 4924 5378 * 5450 5003 * 3363 1116 6618 6358 5384 4352 * * * 56
+ 0 * * 0 * 0 * 8737 1060 1060
+
+C 57 2352 2718 * * 4484 4241 5734 5749 6272 3277 4320 * 6950 6338 6626 4133 3993 3220 5401 3844 57
+ 0 * * * * * * 8910 0 0
+
+A 58 1588 4076 * * 4860 4066 * 3732 * 4518 4724 * 4206 * * 6375 3723 2452 * 4947 58
+ 19 * 6290 * * * * 8897 0 0
+
+L 59 6388 6388 6384 * 2284 6887 4822 3064 * 2990 3733 6931 * 4794 4636 5887 5195 3494 5528 2687 59
+ 0 * * * * 0 * 8886 0 1060
+
+C 60 4085 5053 * * 4410 5643 * 2152 * 2802 3728 * 6106 * * * 6784 1519 * 5179 60
+ 0 * * * * * * 8917 0 0
+
+S 61 6878 * 3878 1920 5647 * 4035 6538 4941 6159 5642 3117 * 3548 3789 3203 3534 4922 * * 61
+ 0 * * * * * * 8917 0 0
+
+L 62 4682 4698 * * 5125 * * 1525 * 2518 5300 * * 6202 * * 6545 1634 * * 62
+ 29 * 5661 * * * * 8917 0 0
+
+H 63 4375 5029 4183 3355 5076 * 5329 4890 2513 5859 * 4543 * 4000 3529 3992 2675 3936 * 6518 63
+ 88 4292 6939 915 1090 0 * 8914 1587 1234
+
+S 64 3405 4734 * * 5938 5739 * 3395 * 2609 4040 4750 * * 5269 2060 4091 3221 5264 5762 64
+ 145 3686 5808 0 * 0 * 8913 2245 1000
+
+I 65 3678 * * * 3576 6902 * 2073 7130 3291 4378 6327 6458 7198 4214 3864 3200 3607 5201 3979 65
+ 31 * 5572 * * 902 1106 8909 0 1160
+
+G 66 3375 6617 4555 3453 6056 1446 7117 * 5117 6481 * 3824 3590 6462 4178 4309 5333 5437 6414 * 66
+ 207 3733 4095 388 2086 1600 577 8871 1928 1317
+
+K 67 4527 * 5423 4245 * 1248 * 5983 4069 4469 5750 4035 5129 4712 5893 4451 5008 3677 6681 6501 67
+ 58 5161 6450 283 2488 0 * 8902 1230 2335
+
+I 68 5909 * 6637 5982 3348 5374 6611 3310 6095 2436 4556 6863 5054 * 1823 4658 3878 4553 * 6560 68
+ 0 * * * * * 0 8906 0 1029
+
+G 69 4036 * 2923 6935 * 3032 6041 * 4715 7101 * 3387 4123 4984 6917 2176 2370 6862 * * 69
+ 18 6334 * 0 * * 0 8906 1115 1029
+
+G 70 3348 * 3725 3876 6915 5489 5567 4070 4183 3991 * 5176 2483 4433 3414 5233 3545 4218 * 5946 70
+ 19 6259 * 0 * 0 * 8933 1053 1029
+
+A 71 3293 * 2862 1402 5577 5232 * 5724 3845 5833 * 5716 5626 5718 5433 3486 4347 6856 * * 71
+ 148 3357 * 162 3238 * * 8949 2201 0
+
+Q 72 3324 * 5246 3004 6947 6046 5911 5514 4185 3428 5774 4756 * 1940 4368 5289 3489 4299 * 6678 72
+ 28 6586 6879 2322 322 * * 8949 1036 0
+
+N 73 6445 6400 6791 6564 5455 * * 4880 1509 4564 * 2091 4917 5601 3200 6637 3883 5930 * 6042 73
+ 38 5250 * 1534 611 0 * 8949 1278 1030
+
+R 74 3866 5750 4417 2899 * 5125 6670 6833 2586 4481 * 6802 5957 3440 2033 4859 5005 4438 * * 74
+ 0 * * * * * * 8949 0 0
+
+S 75 2523 * 4286 2581 * 4359 5977 6718 2562 4725 6571 4012 * 3687 3238 4633 5692 6551 * * 75
+ 0 * * * * * * 8949 0 0
+
+Y 76 5556 6534 * * 2676 6211 4237 3431 6628 1616 4268 5737 * * 5283 6621 5911 4762 5481 2906 76
+ 0 * * * * * * 8949 0 0
+
+S 77 2135 4987 5950 * 4574 4686 * 2726 * 6534 5791 6046 * * * 2433 3419 3242 * 3960 77
+ 20 * 6211 * * * * 8949 0 0
+
+K 78 2235 * 4767 3649 * 4580 6069 5593 1941 4868 * 6792 6538 4161 3655 3709 4821 4963 * * 78
+ 0 * * * * * 0 8891 0 1043
+
+L 79 2101 * 4625 2408 6633 4310 6397 6833 2865 3646 5680 5604 6756 5825 3469 6836 4710 4816 * * 79
+ 0 * * * * * 0 8891 0 1043
+
+L 80 3841 * * * 3237 * * 1438 * 1883 4821 * * * * * 5702 3049 * 6872 80
+ 0 * * * * 0 * 8891 0 1043
+
+C 81 3402 3862 * 5992 3100 6751 4754 5663 6545 5165 4640 5922 * 5112 * 3339 1675 3836 * 4962 81
+ 11 * 7056 * * * * 8949 0 0
+
+G 82 3138 5517 2108 2128 * 6135 5925 * 3623 * * 5347 5594 4993 3066 4223 4564 * * * 82
+ 15 6584 * 0 * 0 * 8949 1021 1023
+
+L 83 2778 * 7233 4045 2707 * 5952 3343 6769 2374 5720 5049 6417 7004 4758 4479 4508 4256 * 3829 83
+ 11 * 7037 * * * * 8949 0 0
+
+L 84 4011 5819 * * 3637 * * 2475 * 1422 3664 * * * * 5026 4489 3100 * 5947 84
+ 28 5704 * 1036 965 0 * 8952 1199 1018
+
+A 85 2316 5782 6832 3002 * 6155 3802 * 3749 5075 5629 5812 * 3368 4915 3309 3831 3499 * 5062 85
+ 0 * * * * * * 8949 0 0
+
+E 86 3211 * 4037 1938 * 5264 * * 2613 * * 3844 5922 3292 3425 4996 3879 * * * 86
+ 11 * 7052 * * * * 8949 0 0
+
+R 87 3128 6826 4943 2391 6988 6997 4446 3893 3674 4441 * 4725 7027 4194 5017 5189 3594 2990 6559 5460 87
+ 0 * * * * 0 * 8948 0 1000
+
+L 88 3455 4729 * * 3717 6850 * 5305 * 699 5844 * 5487 * 6945 5751 4095 6875 * 6432 88
+ 54 4772 * 820 1206 * * 8949 1435 0
+
+R 89 4666 * 3394 4739 * 1124 4698 * 3420 6871 * 3540 5751 5987 5082 4415 6763 6211 * 6779 89
+ 0 * * * * * * 8949 0 0
+
+I 90 4341 4644 * * 6856 5708 5911 1685 4737 2689 * 5112 * * * 5439 5349 1916 * 5564 90
+ 0 * * * * * * 8949 0 0
+
+S 91 4401 * 3086 3311 * 4459 6046 * 4609 4887 * 4596 1499 4572 4702 3380 5205 * * * 91
+ 34 6628 6211 0 * * * 8949 1028 0
+
+P 92 3457 * 5191 4847 * 4092 5168 4719 3306 4131 * 6691 1516 3932 3882 4245 6682 * * 6777 92
+ 12 6898 * 0 * * 0 8891 1000 1043
+
+D 93 4317 * 2214 1949 * 4603 5743 6499 6990 6487 * 3112 5714 3358 6591 3683 4804 6633 * 5712 93
+ 36 5343 * 1585 585 * 0 8891 1350 1043
+
+R 94 3756 * 2953 6811 * 6108 4918 * 5223 5125 7107 3423 6712 4342 1408 3490 5080 5865 * 6260 94
+ 0 * * * * 0 * 8891 0 1043
+
+V 95 6633 4366 * * 4108 4633 * 1516 * 4386 5331 6545 * * * 5191 3517 1827 6192 * 95
+ 0 * * * * * * 8949 0 0
+
+Y 96 * 6587 5922 5840 3238 6850 5415 4571 5094 3973 4360 5594 * * 3595 5259 3669 3167 5022 1818 96
+ 15 6569 * 0 * * * 8949 1021 0
+
+I 97 * 6660 * * 4569 6430 * 1244 * 3441 4424 * * * * 5303 4628 1691 * * 97
+ 0 * * * * * * 8917 0 0
+
+N 98 4915 6809 6034 4490 4620 5617 4648 3697 3855 2988 5058 2875 * 4246 4851 3854 4301 3097 * 4853 98
+ 0 * * * * * * 8917 0 0
+
+Y 99 6554 5987 * * 1346 * * 2236 * 2924 5312 * * 6607 * * * 3595 * 3081 99
+ 0 * * * * * * 8917 0 0
+
+Y 100 4962 * 3861 3069 4700 6174 3456 4500 4416 4516 * 4189 * 3940 3701 5575 3047 3304 7038 4212 100
+ 0 * * * * * * 8917 0 0
+
+D 101 5544 7045 2431 1413 5811 5931 5560 6570 * * * 3631 3260 5087 4819 4894 4861 5263 * * 101
+ 0 * * * * * * 8917 0 0
+
+M 102 4073 7158 * 5455 6511 6172 4757 2512 6031 2464 4032 3702 5592 4995 5404 7011 4248 2361 * 6881 102
+ 0 * * * * * * 8716 0 0
+
+N 103 5020 * 2752 2963 * 4470 5819 6763 4283 6041 * 4864 1976 5626 4616 3306 4127 5051 * 5975 103
+ 118 6151 3948 2000 415 * * 8683 1023 0
+
+A 104 2321 * 3594 4673 * 4511 5714 * 3328 4033 5642 6951 2399 6664 3408 4074 4398 5881 * 6834 104
+ 0 * * * * * 0 8546 0 1793
+
+A 105 3601 5300 3416 1964 * 3022 3732 6851 4780 5959 * 5867 5454 5000 6062 3762 3939 6789 4558 7343 105
+ 17 6416 * 0 * 0 * 8546 1036 1793
+
+S 106 3644 5414 2638 3922 6006 4282 3621 6288 * 4950 4553 1977 * 4360 5407 4585 4643 6179 * 6370 106
+ 0 * * * * * * 8656 0 0
+
+V 107 5485 6002 * 6152 3627 * * 2990 * 5511 4703 5761 * * 5863 * 5106 3426 1124 3957 107
+ 27 6995 6529 0 * * * 8642 1000 0
+
+G 108 2119 * 6417 * * 922 * * 6537 6679 7075 5415 * 5965 6080 3136 * 6264 * 5562 108
+ 0 * * * * * 0 8593 0 1026
+
+W 109 4430 5771 * 5872 2507 5889 6694 2796 3838 4240 5657 4907 * * 5176 5097 3574 3625 3819 3279 109
+ 0 * * * * 0 * 8579 0 1026
+
+N 110 3546 * 3207 * * 1629 6673 6057 3567 5845 * 2461 6459 4583 4498 3996 * * 6108 * 110
+ 0 * * * * * * 8579 0 0
+
+N 111 7024 6082 3866 5811 * 436 5675 * 6430 6921 * 4407 * 6370 5498 6287 7002 * * 6542 111
+ 46 6138 5842 1000 1000 * * 8544 1017 0
+
+S 112 5195 * 5399 4582 * 3318 4822 5800 2774 * 4546 6212 5191 5718 3030 3443 2430 3532 * 5754 112
+ 19 6277 * 0 * 0 * 8461 1037 1083
+
+T 113 4490 * * * 5561 * 5506 4339 5915 2073 * 4473 5401 6205 * 4806 1123 4982 * * 113
+ 0 * * * * * * 8123 0 0
+
+F 114 5010 * * * 1838 * 4998 2558 5601 2571 3666 5670 * * * 5343 * 3518 5321 3964 114
+ 175 3130 * 2193 356 * * 7664 1269 0
+
+A 115 1203 * 4883 4922 * 3071 4400 * 2902 * * * 4798 4613 * 3039 * * * * 115
+ 0 * * 0 * * * 6264 0 0
+
+//
+�HHsearch 1.5
+NAME c582c9c4daca574c1be2935ee4ecc45f
+FAM
+FILE c582c9c4daca574c1be2935ee4ecc45f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:25:17 2013
+LENG 53 match states, 53 columns in multiple alignment
+FILT 117 out of 808 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCEEEECCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCC
+>ss_conf PSIPRED confidence values
+99867688467768999999999999990999999999999999873367899
+>Consensus
+xxxmxkxxxxxlRipxelxxxlxxxAxxxgxSlnxxIxxxlxxxlxxxxxxxx
+>c582c9c4daca574c1be2935ee4ecc45f
+MKGMSKMPQFNLRWPREVLDLVRKVAEENGMSVNSYIYQLVMESFKKEGRIGA
+>gi|303241486|ref|ZP_07327988.1| conserved hypothetical protein [Acetivibrio cellulolyticus CD2]gi|302590995|gb|EFL60741.1| conserved hypothetical protein [Acetivibrio cellulolyticus CD2]
+---MAEKKTVLLRLNPKTWEELSCWAEDEFRSINGQIEYILHDAIQKRKKA--
+>gi|159028551|emb|CAO87359.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
+------MK-LSTNIPDVLYQQIETLANKQNIPVEQLVTMALSAQI--------
+>gi|260662424|ref|ZP_05863319.1| conserved hypothetical protein [Lactobacillus fermentum 28-3-CHN]gi|260553115|gb|EEX26058.1| conserved hypothetical protein [Lactobacillus fermentum 28-3-CHN]
+---------mvshqLTISLDEDAFRALEKRAQSERRPLEEVAASLLTTASKVP-----
+>gi|331698714|ref|YP_004334953.1| hypothetical protein Psed_4962 [Pseudonocardia dioxanivorans CB1190]gi|326953403|gb|AEA27100.1| hypothetical protein Psed_4962 [Pseudonocardia dioxanivorans CB1190]
+-------SRINFRPPESLKARIEEAAGREGLSVNAWLVRAATTALEA------
+>gi|291619469|ref|YP_003522211.1| hypothetical Protein PANA_3916 [Pantoea ananatis LMG 20103]gi|291154499|gb|ADD79083.1| Hypothetical Protein PANA_3916 [Pantoea ananatis LMG 20103]
+----GKSPTFQIRINPELREQLDQEAAKDQTTLANWFKELARDELKRRG----
+>gi|153869106|ref|ZP_01998794.1| HicB family protein [Beggiatoa sp. PS]gi|152074343|gb|EDN71207.1| HicB family protein [Beggiatoa sp. PS]
+-------DQIMVPVSPEIHRNLVIQAIKSGVSLNKLAMAKLSQ----------
+>gi|163868137|ref|YP_001609341.1| hypothetical protein Btr_0949 [Bartonella tribocorum CIP 105476]gi|161017788|emb|CAK01346.1| hypothetical protein BT_0949 [Bartonella tribocorum CIP 105476]
+-----KEASMNIRLPQALMKALKEKAKNQAIPYTRYVRHLIEQDLRKSH----
+>gi|197262440|ref|ZP_03162514.1| putative ABC-type transporter [Salmonella enterica subsp. enterica serovar Saintpaul str. SARA23]gi|200388356|ref|ZP_03214968.1| putative ABC-type transporter [Salmonella enterica subsp. enterica serovar Virchow str. SL491]gi|205357922|ref|ZP_02574237.2| putative ABC-type transporter [Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. CVM23701]gi|197240695|gb|EDY23315.1| putative ABC-type transporter [Salmonella enterica subsp. enterica serovar Saintpaul str. SARA23]gi|199605454|gb|EDZ03999.1| putative ABC-type transporter [Salmonella enterica subsp. enterica serovar Virchow str. SL491]gi|205328748|gb|EDZ15512.1| putative ABC-type transporter [Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. CVM23701]
+----ESNERLSLRVSTDAKKLIVRAAAIQQTNLTDFVVSNILP----------
+>gi|342899959|ref|ZP_08721781.1| hypothetical protein SmacN1_00909 [Streptococcus macacae NCTC 11558]
+-------VPTSVRLSDELNEKLTLWTNSHNISKSEFIAQVLAEKLEDLSDI--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 2715 0 0
+
+K 2 2849 * * * * * * * 1474 2449 * * * 2572 * * 2738 * * * 2
+ 0 * * * * * * 3026 0 0
+
+G 3 2681 * * * * 1740 * * 2070 * * * * 2683 2728 * * * * * 3
+ 0 * * * * * * 3293 0 0
+
+M 4 4022 * * * * 4505 * * * * 251 * * * * * * 4205 * * 4
+ 0 * * * * * * 4586 0 0
+
+S 5 3726 * 3488 3027 * 3264 * * 2713 5105 * 5031 3515 5499 5486 2515 3804 5802 * * 5
+ 0 * * * * * * 6512 0 0
+
+K 6 * * 4597 3290 * 4826 * 5414 1297 * * 3472 4459 3568 4669 3582 4378 * * * 6
+ 81 * 4196 * * * * 6646 0 0
+
+M 7 5985 * 2996 4219 * * 5608 3918 3876 4407 2501 3302 4768 4323 5253 3974 2912 5985 * * 7
+ 0 * * * * * 0 6825 0 1398
+
+P 8 3094 * 4073 3188 * 4015 6473 4907 2628 * * 5271 3793 5315 3886 3151 3780 4223 * 5988 8
+ 28 * 5689 * * 0 * 7140 0 1398
+
+Q 9 5427 * 5791 5242 * 6407 5388 7185 3045 * 6154 5110 4061 2517 2458 3226 2513 6838 * 5787 9
+ 12 6914 * 2037 403 0 * 7167 1074 1011
+
+F 10 6190 * * * 2297 * * 2303 4680 2007 3962 * * * * 6858 3833 3540 * 3980 10
+ 0 * * * * * * 7239 0 0
+
+N 11 4925 * 5080 6801 * 5895 4344 5398 6088 4768 4756 2755 5175 3423 5407 3080 1727 5056 * 7083 11
+ 0 * * * * * * 7239 0 0
+
+L 12 4817 * * * 4014 * * 1961 * 1293 6151 * * * * * 6211 2251 * * 12
+ 0 * * * * * * 7239 0 0
+
+R 13 * * * 5505 * * 5248 * 3788 * * 5008 6205 5510 401 6579 4475 * * * 13
+ 80 4220 * 0 * * * 7239 1311 0
+
+W 14 * 5830 * * 4612 * * 1449 * 1741 3743 * 5904 * * * 4640 3018 6706 6445 14
+ 0 * * * * * * 7239 0 0
+
+P 15 6137 * 2921 5901 * 4667 5932 * 7095 6806 * 4433 1145 5828 5817 2695 3706 * * * 15
+ 0 * * * * * * 7239 0 0
+
+R 16 3660 5719 2772 2716 * 6813 4976 * 3977 5181 6836 5061 1849 5170 4476 4213 5127 * * * 16
+ 0 * * * * * * 7239 0 0
+
+E 17 4185 * 2456 1312 7421 4172 5606 6872 4231 6269 * * 6764 5814 5811 3319 5989 5571 6230 6940 17
+ 0 * * * * * * 7239 0 0
+
+V 18 4952 * 6619 5213 * * * 3481 4463 919 3842 6762 * 4974 6771 5311 4531 3675 * * 18
+ 0 * * * * * * 7239 0 0
+
+L 19 6248 * 4107 6167 4503 7271 2092 5779 1775 3816 5359 6285 * 5781 3721 6894 * 5058 6430 3896 19
+ 0 * * * * * * 7239 0 0
+
+D 20 2986 * 4006 1940 * 6890 * * 2789 5687 * 4608 6122 3663 2705 4228 4739 * * * 20
+ 0 * * * * * * 7239 0 0
+
+L 21 3080 * 4470 3307 * * 5830 5043 2355 3252 4423 6205 * 3636 3003 4589 4876 6098 4984 * 21
+ 21 6122 * 0 * * * 7239 1018 0
+
+V 22 3630 * * * 4857 * * 2075 * 1092 4200 * * * * * * 3163 * 6354 22
+ 0 * * * * * * 7239 0 0
+
+R 23 3148 * 5030 2200 6725 * * 6051 2515 5276 5280 4737 * 4579 3402 4221 3758 3532 * * 23
+ 0 * * * * * * 7239 0 0
+
+K 24 3594 6430 5947 2276 5986 6821 5836 3880 2802 5790 4255 5200 * 3450 3015 5968 5511 4698 * 4637 24
+ 0 * * * * * * 7239 0 0
+
+V 25 1804 6794 * 4516 6354 * 5896 3758 3892 2827 5567 5812 * 4766 3406 6176 * 3557 4461 4813 25
+ 0 * * * * * * 7239 0 0
+
+A 26 155 * * * * * * * 6122 * 5625 * * 6445 * 4545 6285 * * * 26
+ 0 * * * * * * 7239 0 0
+
+E 27 2531 * 4804 2397 6616 5845 * 6205 2084 4801 6794 4491 * 3324 4046 4377 6142 6362 * * 27
+ 0 * * * * * * 7239 0 0
+
+E 28 3739 * 4686 2980 4982 * 5830 4306 2587 3594 5329 4034 * 3642 3340 3839 6936 5707 * 4364 28
+ 21 6122 * 2000 415 * * 7239 1018 0
+
+N 29 3755 6339 2960 2157 4979 * 3819 6750 4280 5937 7112 2659 * 3654 5460 3420 5639 * * * 29
+ 0 * * * * * 0 7204 0 1018
+
+G 30 6612 6186 4266 5523 5339 1110 3787 * 4581 7168 6274 2691 * 4619 4048 5361 * * * * 30
+ 33 5482 * 0 * * 0 7204 1087 1018
+
+M 31 6644 6227 * 5636 * * * 2557 3666 4355 4095 6634 6700 4746 1840 6270 3254 2772 * * 31
+ 0 * * * * * 0 7204 0 1018
+
+S 32 5177 * 6122 * * * * * 5013 * * 5766 3999 * * 498 2855 * * * 32
+ 0 * * * * 0 * 7204 0 1018
+
+V 33 6030 * * 6445 4091 * * 2748 4108 1571 3203 * * 5895 5828 6133 5168 2600 * 5567 33
+ 0 * * * * * * 7239 0 0
+
+N 34 3696 * 4435 4610 * * 6133 * * * * 891 * 5846 * 2628 3282 * * * 34
+ 0 * * * * * * 7239 0 0
+
+S 35 2576 * 3738 3496 * 4509 * * 3053 6230 * 3301 * 2450 5083 3187 4674 6725 6803 6717 35
+ 0 * * * * * * 7239 0 0
+
+Y 36 4339 * * 3001 2221 * * 5298 * 2241 5739 * * 4334 * * 4725 5075 2893 3268 36
+ 0 * * * * * * 7239 0 0
+
+I 37 4460 4909 * * 5684 * * 1098 * 3025 4493 * * * * * * 1974 * 6275 37
+ 0 * * * * * * 7239 0 0
+
+Y 38 4181 5070 5231 2727 5828 * * 3366 3594 2641 5595 4489 * 4771 4104 5373 4830 2729 * 6706 38
+ 0 * * * * * * 7239 0 0
+
+Q 39 3655 * 5123 2631 4690 5338 4362 7031 4514 4620 4874 4421 * 3027 3684 3252 4161 5003 * 4237 39
+ 22 6057 * 2585 263 * * 7237 1021 0
+
+L 40 1566 6570 * * * * 6481 2989 4754 2007 6074 6281 * 6284 3704 5902 6043 3926 * 6183 40
+ 0 * * * * * * 7264 0 0
+
+V 41 3610 5550 * * 5936 6116 * 2080 * 1381 6884 * * * * 4933 5261 2487 * * 41
+ 86 4103 * 1319 739 * * 7264 1474 0
+
+M 42 3307 * 4149 2584 7124 * 6418 4235 4196 3652 4550 7067 * 4240 3269 3399 3573 3995 * 5545 42
+ 0 * * * * * * 7210 0 0
+
+E 43 3397 6385 3185 1745 * * 5792 * 3016 6010 * 4776 5078 3281 3571 5103 4739 6976 * * 43
+ 0 * * * * * * 7125 0 0
+
+S 44 2468 * 3947 3109 5342 6615 6618 * 2771 5457 * 5683 * 3525 5470 2826 4560 * 6637 3297 44
+ 22 6044 * 0 * * * 6828 1002 0
+
+F 45 3760 5997 * * 3288 * * 2877 * 1388 4346 * * * 6302 4972 6005 2869 6256 5032 45
+ 17 * 6413 * * * * 6840 0 0
+
+K 46 * 4903 3753 1569 * 3066 * * 2676 * * 4793 6306 3927 3129 4304 * * * * 46
+ 0 * * * * 0 * 6613 0 1000
+
+K 47 3429 * 3714 3643 * 4133 4791 6311 2658 4697 * 4832 5102 3507 2511 3995 5987 4573 * * 47
+ 0 * * * * * * 6609 0 0
+
+E 48 4320 * 4691 1500 5659 * 5938 * 3398 4550 * 5845 3281 3832 3467 3964 4682 * * * 48
+ 0 * * * * * * 6282 0 0
+
+G 49 5500 * 4193 5179 * 1928 3564 4978 3378 * * 3331 * 5300 4327 2993 5175 4188 * 4737 49
+ 0 * * * * * * 6031 0 0
+
+R 50 * * 2200 3957 4270 * * * 3125 * * * 4292 * 2178 3331 * * * 2473 50
+ 0 * * * * * * 4949 0 0
+
+I 51 4006 * * * * * * 1473 3005 2083 * * * * * * * 2205 * * 51
+ 0 * * * * * * 4949 0 0
+
+G 52 * * * * * 1556 * * * * * * 1556 1645 * * * * * * 52
+ 0 * * * * * * 2163 0 0
+
+A 53 0 * * * * * * * * * * * * * * * * * * * 53
+ 0 * * 0 * * * 1624 0 0
+
+//
+�HHsearch 1.5
+NAME c5863f5030b5a39b990f9179f7f8cfae
+FAM
+FILE c5863f5030b5a39b990f9179f7f8cfae
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:56:09 2013
+LENG 134 match states, 134 columns in multiple alignment
+FILT 107 out of 511 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEEEECCCHHHHHHHCCCCHHHHHHHHCCCCEEEEEECCCEEEEEEEECCCCEEEEEECCCEEEEECCCCCCCEEEEEEEEECCEEEEEEECC
+CCCEEEEEEEECCEEEEEEEECCEEEEEEEEECC
+>ss_conf PSIPRED confidence values
+9742189999974598999988399899999886289889999929989999960785389999879648876148999799999999599999999699
+8868999999999999999999999999999749
+>Consensus
+xxxxxGxwklxxseNxdexLxxxGvxxxxrkxxxxxxpxxeixxxgdxxxixxxxxxxtxxxxfxlGxefeexxxxxxgxxxkxxxxxegxklvxxxxxx
+xxxxxxxrxixxxxlxxtxxxxxvxxxrxyxrxx
+>c5863f5030b5a39b990f9179f7f8cfae
+PVDFNGYWKMLSNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDDRKCMTTVSWDGDKLQCVQKGE
+KEGRGWTQWIEGDELHLEMRAEGVTCKQVFKKVH
+>gi|399472|sp|P31417.3|FABP2_MANSE RecName: Full=Fatty acid-binding protein 2; Short=FABP 2gi|159512|gb|AAA29314.1| fatty acid binding protein 2 [Manduca sexta]
+-SYLGKVYSLVKQENFDGFLKSAGLSDDKIQALVSDKPTQKMEANGDSYSITSTGIGGERTVSFKSGVEFDDVI--GAGESVKSMYTVDGNVVTHVVKGD
+AGVATFKKEYNGDDLVVTITSSNWDGVARrYYKA-
+>gi|307178371|gb|EFN67116.1| hypothetical protein EAG_12099 [Camponotus floridanus]
+---VVGKYQYITSENLDEFLKDINKSEFSGILKSALTVEVQV-NDDQSFTVTITNPERSVTNTFKLGEVYDEWFPSQK-VPFKSVATKHDLGFQSETSLS
+pdlKLIRIYEFTGTQLIAVSAVFNTEECNNSYLI---
+>gi|310693845|gb|ADP05225.1| fatty acid-binding protein 1 [Eriocheir sinensis]
+-MSIAGKYVLSGNEKYADWLSAVGIPADLAAKLEAAKPSLDVTQSGNDIVIKTTAGDKNFTNTITLGKESQA--TLPGGIEYTVKLTLSGTTLNGTWDFg
+GKTG-TATVEFTADGVTQTMIYNNIASKRIYSRQ-
+>gi|107051720|gb|ABF83552.1| fatty acid binding protein [Branchiostoma belcheri tsingtauense]
+--VDKfcGTWKHgSHSDNYLQMMEKFGMSAEMLKKIQESTFPMNASLVGDKLTFKVEFEGKTYENNFTLGVEGEEE--DATsGKKRKVTYTIEGDHLVSV
+YPDpdgKVTSRVCRHFDDDDTIHTDIKAGDVEAWTKSKRC-
+>gi|242020766|ref|XP_002430822.1| fatty acid-binding protein, putative [Pediculus humanus corporis]gi|212516025|gb|EEB18084.1| fatty acid-binding protein, putative [Pediculus humanus corporis]
+---YTKTYRLIKSDNYDAFLREVGAGPLKRKQEVRERPTIQLRQYGNDYVLTMASEHQTKNVKFRPSEKFVQE--GYDGNYVQTIMSFENgNILVEMQMG
+AKPVTILREFFVNGVMEM-MMCEKTVCCRVYSS--
+>gi|308493489|ref|XP_003108934.1| hypothetical protein CRE_11771 [Caenorhabditis remanei]gi|308247491|gb|EFO91443.1| hypothetical protein CRE_11771 [Caenorhabditis remanei]
+--AIIGKWKPISSENLEDYFKVSNLSEICELAWEHGIVC--YEMKDGDLHAHTQLYNKKlNATVLEVGQKNQNK----N-G--TMDCHVENNSLNSIYF-
+seEKELWKVERFIESGQLVIINKREQLQwCKRTYERVE
+>gi|221091788|ref|XP_002161777.1| PREDICTED: hypothetical protein [Hydra magnipapillata]gi|221107985|ref|XP_002167566.1| PREDICTED: hypothetical protein [Hydra magnipapillata]
+--DMVGTWRLESRDpTFNDFLVCRQTRYLLRTIMTTFSADFEYSLSEDKslLTKKTISSFNTNMYPMSTAHDFVPE-KTLSGKPEiGRIFETSGRKVIQE
+MryKSDdSIAAIMEHQVIDGKLHVKLKCENVVCNEIYRRI-
+>gi|325188594|emb|CCA23127.1| conserved hypothetical protein [Albugo laibachii Nc14]
+--NLSGRWSLDRndSDSTNDYLEAMGLPLIARQAADKLDLMVIINQTPGDFVITRRTRIFSETKHLKLGQEVILK---------NNIISIAGDAsqIKTt
+TQlTAYRGLLMDIRSLDeKGRMKVELTLvlpdkPPVTIQRYFKK--
+>gi|313230106|emb|CBY07810.1| unnamed protein product [Oikopleura dioica]
+--EMIGRWQEKSKSNVPEYIDAEEGPYFYQIFAKKMKADIEYEMvAKNVFRSTFyVSWMPPLKYPLRLDMPYEHEN--PTGDAVVSEARfrVEfNDIFVV
+T-KGGHEGTtTTRIQIVNEDLILTSTMleKNVLCERVYTRK-
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
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+FAM
+FILE c5af58a62688d809a1a0747990141890
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:08:47 2013
+LENG 62 match states, 62 columns in multiple alignment
+FILT 102 out of 698 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+96178999988999999999999999999767999888778999999999999999998738
+>Consensus
+xxxxxrRxxxnxrERxRxxxiNxafxxLrxxiPxxxxxklsKxxiLrxAixYIxxLxxxLxx
+>c5af58a62688d809a1a0747990141890
+TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLRD
+>gi|308487455|ref|XP_003105923.1| CRE-HLH-10 protein [Caenorhabditis remanei]gi|308254979|gb|EFO98931.1| CRE-HLH-10 protein [Caenorhabditis remanei]
+---TSRRVEANARERNRVQQLSRMFDELRVILPVEAEMKISKLSTLKVASAYIGYLGAIMKD
+>gi|194216475|ref|XP_001917290.1| PREDICTED: LOW QUALITY PROTEIN: oligodendrocyte transcription factor 3-like [Equus caballus]
+----QLRLKnIGEGSETSMKQLELATgKDIARSVIYphGXxXXXXXXXXXXXXARNYILMLTSSLE-
+>gi|71020467|ref|XP_760464.1| hypothetical protein UM04317.1 [Ustilago maydis 521]gi|46100369|gb|EAK85602.1| hypothetical protein UM04317.1 [Ustilago maydis 521]
+-VNANRRVAHLLSEQKRRESINTGFEDLRQAIPACRDGQDSKATILKRALEYIRELEEVVE-
+>gi|213972574|ref|NP_001135435.1| extra macrochaetae [Nasonia vitripennis]
+--------------------VAAYLGKLRDLVPDMPrSRKLSKLEVIQHVIRYICELETTLEK
+>gi|74214926|dbj|BAE33463.1| unnamed protein product [Mus musculus]
+---GERRTTHNIIEKRYRSSINDKIIELKDLVMG-TDAKMHKSGVLRKAIDYIKYLQQV---
+>gi|111119871|gb|AAN76139.2| c-myc [Todirostrum cinereum]
+SEENDKRRTHNVLERQRRNELKLSFFALRDQIPeVANNEKAPKVVILKKATEYVLSIQS----
+>gi|156555495|ref|XP_001604081.1| PREDICTED: similar to daughterless [Nasonia vitripennis]
+--EKERRQANNARERIRIRDINEALKELgRMCMAhMKSEKPQTKLGILNMAVEVIMALEQQVRE
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 * * * * * * * * * * * * * * * 1554 601 * * * 1
+ 0 * * * * * * 2111 0 0
+
+T 2 * * * 3139 * * * * * * * * * * * 2673 1478 1432 * * 2
+ 0 * * * * * * 3637 0 0
+
+N 3 3692 * 2928 2847 * 5161 * * 3734 5302 * 3354 5245 4936 * 1965 3662 4976 * * 3
+ 0 * * * * * * 4941 0 0
+
+A 4 3454 * 5362 5252 5686 4853 * 4504 2581 * 3945 3909 3477 4804 3776 3362 4751 3285 * 5275 4
+ 0 * * * * * * 5188 0 0
+
+D 5 2976 * 3150 2496 * 5854 5201 5226 2523 * 5999 5853 * 2733 4199 4210 6135 5458 * 6806 5
+ 0 * * * * * * 5519 0 0
+
+R 6 * * 6550 6601 * * 6442 4806 2255 3463 * 5482 6209 3198 1356 5020 5512 * * 4529 6
+ 15 6624 * 0 * * * 5666 1000 0
+
+R 7 * * * * * * 6097 * 3442 * * * 6268 5391 223 * * * * * 7
+ 0 * * * * * * 5739 0 0
+
+K 8 3964 * * 3735 5857 * * 4188 3544 2402 5765 4747 6656 3670 3582 2776 4072 3632 * * 8
+ 37 * 5294 * * * * 5747 0 0
+
+A 9 1717 * * 3923 4975 6432 6446 * 2723 3776 * 4078 6324 4632 3914 5394 2970 5597 * * 9
+ 54 4765 * 0 * 0 * 5728 1197 1073
+
+A 10 1314 * * * * * 1788 4049 5000 * * 4362 * * 3631 4879 4576 * * 6433 10
+ 0 * * * * * * 5745 0 0
+
+T 11 3656 5607 * * * 4837 * 5071 5777 6610 * 609 * * 6095 3633 4154 * * * 11
+ 0 * * * * * * 5751 0 0
+
+M 12 1983 * 4068 2805 6206 5615 * 3812 3791 3920 5005 6357 * 4228 5347 4841 5050 3125 * * 12
+ 0 * * * * * * 5756 0 0
+
+R 13 5288 6515 * * 6564 5031 5705 3546 3496 4420 5172 5369 * 6898 935 4209 5195 * 6686 6980 13
+ 17 6416 * 3170 170 * * 5845 1000 0
+
+E 14 * * * 82 * * * * 5323 * * * * * * 5044 * * * * 14
+ 0 * * * * * * 5807 0 0
+
+R 15 * 6545 5995 5044 * * 5355 * 3140 * * * * 3767 479 * 6126 * * * 15
+ 23 5995 * 3000 193 * * 5807 1029 0
+
+R 16 * * 3997 3441 * 6625 6168 3843 2996 4475 7026 3289 * 3130 2060 5148 3995 6944 5785 * 16
+ 0 * * * * * * 5807 0 0
+
+R 17 * * * * * * 5781 * 6126 * * * * * 210 4154 * * * 4422 17
+ 0 * * * * * * 5807 0 0
+
+L 18 5080 5592 * * * * * 3905 6486 3997 2206 5269 * 5319 1678 6655 5539 2548 * 5242 18
+ 0 * * * * * * 5821 0 0
+
+S 19 4696 7026 4135 3998 * 5976 3287 * 2718 4671 * 4935 * 2388 2995 3312 5115 5388 * 5506 19
+ 0 * * * * * * 5821 0 0
+
+K 20 4045 6503 3569 3021 6533 4738 4260 6444 3006 5894 6737 2986 * 3825 4126 3381 4202 4211 * * 20
+ 0 * * * * * * 5887 0 0
+
+V 21 * * * * 4593 * 6277 1288 * 1723 3046 * * * * 6759 * 3596 * 5620 21
+ 0 * * * * * * 5905 0 0
+
+N 22 5639 * 5639 5143 * 7266 6632 7061 3326 * * 603 * * 3951 4194 5044 * * * 22
+ 0 * * * * * * 5905 0 0
+
+E 23 3952 * 2867 2771 * 4931 5944 * 2798 3061 5554 4678 * 3623 5182 3544 3842 6099 * * 23
+ 0 * * * * * * 5905 0 0
+
+A 24 1171 4933 * 4569 * 3056 6741 * 4084 6073 4232 6473 * 6653 3743 4028 4510 * * 5424 24
+ 0 * * * * * * 5905 0 0
+
+F 25 * * * * 787 * * 3593 * 2670 5563 * * * * * 5143 6303 * 3079 25
+ 41 5143 * 0 * * * 5902 1123 0
+
+E 26 3129 * 2255 2315 5326 4900 6639 4778 3617 5063 5015 4505 * 3983 6737 4169 * 4441 * 6685 26
+ 0 * * * * * * 5902 0 0
+
+T 27 2977 5214 3610 2638 5981 4853 * 4727 3849 4604 5581 5436 6494 * 3416 3839 3462 3713 * 5706 27
+ 0 * * * * * * 5902 0 0
+
+L 28 * * * * * * * 4661 * 79 * * * * * * * 6172 * * 28
+ 48 4935 * 0 * * * 5902 1125 0
+
+K 29 4424 * * 5820 * 5842 * 6260 2005 * * * * 3508 888 * 6583 * * 5855 29
+ 0 * * * * * * 5902 0 0
+
+R 30 4159 6633 2866 3281 * 4619 5428 7069 3011 5664 4880 4166 * 3530 2905 2694 6112 * * * 30
+ 11 6983 * 1585 585 * * 5902 1000 0
+
+S 31 3253 4132 * 5193 * 6983 3161 5281 3888 1955 4295 6579 * 5113 4305 4213 5523 3482 * 4890 31
+ 0 * * * * * * 5902 0 0
+
+T 32 * * * * * * * 1605 * 1495 4143 * 6240 * * * 5369 2169 * * 32
+ 73 4345 * 673 1424 * * 5902 1289 0
+
+S 33 5132 5599 * * * * * 5143 6595 5506 6767 6108 390 * 6653 4068 5466 6469 * * 33
+ 152 3495 6469 0 * * * 5902 1583 0
+
+S 34 4182 6866 4164 5562 4064 4443 4548 4169 3813 4968 5590 3275 4997 5388 5134 3555 3249 3712 6189 3963 34
+ 398 2332 4554 1966 427 0 * 5908 2171 1010
+
+N 35 5311 4257 4450 4645 4330 3354 4968 5035 5760 2481 6620 4266 2726 6739 5697 3995 5838 3852 * 4718 35
+ 287 2806 4736 663 1441 1229 802 5872 1773 1189
+
+P 36 3477 * 6490 4780 4933 3587 5415 * 4413 * * 5245 1614 3115 4165 4119 4166 6171 * 5331 36
+ 394 2125 6640 1766 502 0 * 5734 2410 1292
+
+N 37 6693 * 2168 2886 * 2672 5456 6020 5825 5987 * 2997 5549 5244 4317 3875 4030 4278 * * 37
+ 98 4315 6028 0 * 0 * 5714 1211 1059
+
+Q 38 5168 * 4006 3489 * 5282 * 5315 1626 6229 * 6548 * 3011 3028 4136 3592 6638 * 5291 38
+ 55 4743 * 420 1985 0 * 5789 1187 1000
+
+R 39 5685 * 5371 3889 * * * * 878 * * 5669 5053 4176 2228 6472 6069 * * * 39
+ 50 4863 * 2346 316 * * 5788 1122 0
+
+L 40 3717 * 6961 * 5603 * 6432 4142 6092 1119 3722 * 3791 5155 5814 4423 6559 3430 6917 * 40
+ 0 * * * * * * 5788 0 0
+
+P 41 3658 * 4311 * * * 4935 * 5809 * * 5609 3734 * 6073 771 3019 * * * 41
+ 40 5488 7584 0 * * * 5788 1061 0
+
+K 42 * * * * * * * 6067 410 * * 5195 6492 5110 3278 * 4757 6605 * 6071 42
+ 0 * * * * * 0 5789 0 1000
+
+V 43 2581 5918 * 6211 6492 5253 6830 1955 5311 2558 6227 6902 6067 * * 4142 5335 2548 6957 7210 43
+ 0 * * * * * 0 5789 0 1000
+
+E 44 3112 * 3550 1869 * 3933 6071 5166 3903 5281 5633 5952 * 3748 7029 3258 4472 4593 * 6067 44
+ 0 * * * * * 0 5789 0 1000
+
+I 45 6241 * 5918 * 5283 * 6016 1216 6466 4852 6963 * * * * 6941 1697 2965 * * 45
+ 0 * * * * * 0 5789 0 1000
+
+L 46 6016 * * * * * * 3655 * 226 * 6466 * * * * * 4690 * * 46
+ 0 * * * * * 0 5789 0 1000
+
+R 47 * * 5719 5106 * 6662 6248 * 2319 4422 * 4281 * 2905 1342 4209 4760 * 6439 * 47
+ 0 * * * * * 0 5700 0 1000
+
+N 48 4657 6430 5304 3598 5709 4541 5759 4565 2869 2004 3957 4840 * 5732 3630 3684 * 5991 * 4660 48
+ 0 * * * * * 0 5700 0 1000
+
+A 49 283 * * * * * * * * * * * * * 5807 4094 4659 4010 * * 49
+ 0 * * * * 0 * 5824 0 1000
+
+I 50 3603 6363 * * * * 6481 1076 5109 3872 4620 5830 * * 4564 5375 3102 3612 * * 50
+ 0 * * * * * * 5888 0 0
+
+R 51 3980 5983 3432 2064 * 4682 5692 * 3112 4645 6512 3000 * 4511 4516 3804 4549 5129 6854 * 51
+ 0 * * * * * * 5888 0 0
+
+Y 52 * 6127 * * 5951 * 4668 * * 4423 * * * * 5613 * * 5673 6772 261 52
+ 25 5835 * 0 * * * 5888 1027 0
+
+I 53 * 5951 * * * * * 177 * 5242 5812 * * * * * * 4188 * * 53
+ 0 * * * * * * 5888 0 0
+
+E 54 3888 6642 5078 3912 * 3618 4640 6357 2871 3597 4929 3653 5270 2853 3113 4825 5245 6919 6481 * 54
+ 0 * * * * * * 5888 0 0
+
+G 55 4454 * 4962 3920 3757 4982 3003 5455 4153 4341 4302 6522 * 3920 5956 3922 3252 5371 * 2655 55
+ 0 * * * * * * 5888 0 0
+
+L 56 * * * * * * * 5407 * 170 3840 * * * * 5829 * * * * 56
+ 0 * * * * * * 5796 0 0
+
+Q 57 6931 * 4971 2786 * 4589 6053 5544 4652 4620 6206 4725 * 1539 4696 3661 2802 * * * 57
+ 0 * * * * * * 5781 0 0
+
+A 58 3756 6878 2731 2693 * 4568 5194 * 2948 4761 5582 4161 * 3026 4558 3867 4677 6856 5794 * 58
+ 0 * * * * * * 5770 0 0
+
+L 59 5130 4979 5853 6435 5116 * 5121 3412 3685 2446 3491 * * 3902 4766 4305 3744 2556 * 6608 59
+ 0 * * * * * * 5509 0 0
+
+L 60 * * * * * * * 3586 * 487 5835 * * * * * * 2429 * * 60
+ 0 * * * * * * 5462 0 0
+
+R 61 4237 * 3549 2076 * 5759 4649 * 4911 * 5196 3277 * 2360 2552 5477 * 6101 * * 61
+ 0 * * * * * * 5410 0 0
+
+D 62 * * 1626 2802 * 1790 4990 * 4538 * * * * * * 4261 3098 * * * 62
+ 0 * * 0 * * * 4908 0 0
+
+//
+�HHsearch 1.5
+NAME c5d10a25f4692ab6cc7c072c5ac3efcd
+FAM
+FILE c5d10a25f4692ab6cc7c072c5ac3efcd
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:31:27 2013
+LENG 235 match states, 235 columns in multiple alignment
+FILT 183 out of 1906 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEECCCCCCCCCCCCHHHHHHHHHHEEECCCCCCCCCCEEEEHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCCEEE
+EEEECCCCCCCCCHHHHHHHHCCCCCCEEEEECCCCCCCCEEEEEEEEHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCCHHHHHHHHHHCCCCCCCE
+EEEEEECCCCCCCCCHHHCCCCEEEEECHHHHCCC
+>ss_conf PSIPRED confidence values
+9700217661413674759999998522758999999981599747864899999999999999988615698799998047769999999984999899
+9950578764101244444405553433998357678999999996471030999999999998699399999999866765899997542012479868
+99999464461108610337970999856853269
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxgxpxyxdxxxlxxdpxxxxxlxxxlaxxxxxxxxxxdxIvxvxxxGxxlAxxlAxxlxxpxxx
+irkxxxxxxxxxxxxxxrxxxxxxxxxxxxxxxxxxxxgxxVlLVDDvitTGxTlxxaxxxLxxxGaxxvxvxvlxxxxxxxgxxxlxxxxxxxxxgvxx
+xslxxxxxxxxxxxxxcxxxxxxxxxxxxxxxxxx
+>c5d10a25f4692ab6cc7c072c5ac3efcd
+MSLKEIGPNSLLLEDSHSLSQLLKKNYRWYSPIFSPRNVPRFADVSSITESPETLKAIRDFLVERYRTMSPAPTHILGFDARGFLFGPMIAVELGIPFVL
+MRKADKNAGLLIRSEPYEKEYKEAAPEVMTIRHGSIGKNSRVVLIDDVLATGGTALSGLQLVEASGAEVVEMVSILTIPFLKAAERIHSTAGGRYKNVRF
+IGLLSEDVLTEANCGDLNDYTGPRVLSCSDLLVNQ
+>gi|335437281|ref|ZP_08560063.1| adenine phosphoribosyltransferase [Halorhabdus tiamatea SARL4B]gi|334896411|gb|EGM34562.1| adenine phosphoribosyltransferase [Halorhabdus tiamatea SARL4B]
+--------------RET-LAAEIESRIDRD-EE-------GYVDNTAVVFDQSLLDLVAGVAAETFEL--ERPDVVLTAATDGITIAGAMARHFDVPVAY
+AKKS-RETGV----SEFVEARqrltpG--IEITYSLPASALEDGDDVLLVDDFVRSGNTQALLLELADRAGATVSGVFTLIAVGEDG-LASVRQS-----
+TDAPVVAFTTLS----------------------------
+>gi|319891753|ref|YP_004148628.1| ComF operon protein C [Staphylococcus pseudintermedius HKU10-03]gi|317161449|gb|ADV04992.1| ComF operon protein C [Staphylococcus pseudintermedius HKU10-03]gi|323465078|gb|ADX77231.1| competence protein F, putative [Staphylococcus pseudintermedius ED99]
+----------------------------------------------KFLNDVALAKVFAYYIRVkLVK---D--ELIVPMPssqdhdlQRTFNPVQTILH
+HLKLPYVAClKMRPRSKQFALS-RSERYAV----DNPIYFDSDISLENKSILLIDDIYTTGHTAHCAGNVLLQQKVRKLSMLTFAR--------------
+--------------------------------------------
+>gi|315924848|ref|ZP_07921065.1| orotate phosphoribosyltransferase [Pseudoramibacter alactolyticus ATCC 23263]gi|315621747|gb|EFV01711.1| orotate phosphoribosyltransferase [Pseudoramibacter alactolyticus ATCC 23263]
+------------------------SKVLTF-GDFITkSGrkTPYFVN-TGNYKTSEQIAKLGQYYAACIKNHLDGIDFLYGPAYKGIPLVITAAASLyrd
+hhvTIPYCFNRKEAK-------------DHG--EGGHI-I-GYRPQNGDTAMIVEDVITAGTSVKETVPLLKSlaEDVKVARLIISVDRMEKGdGgKTAI
+EEI--ADRFGIATTPIVTVKEIVA--CLHNREVDGRVVI---------
+>gi|217033895|ref|ZP_03439319.1| hypothetical protein HP9810_870g27 [Helicobacter pylori 98-10]gi|216943658|gb|EEC23103.1| hypothetical protein HP9810_870g27 [Helicobacter pylori 98-10]
+----------------------------------------AYSEIEELIKSKYvligsrILPLLSQkagaEFVKILQE--KgltTPLYGIAIDdkiKSFY
+SHSAALLKGFCQGNLkptYgrLRANNTISYAGKS-LEFRANNP----RDFTFKG---DENLDYFLLDDIITTGTTLKEALKYLKNLNIKAHFAIALCSAD
+--------------------------------------------------------
+>gi|309357838|emb|CAP35094.2| hypothetical protein CBG_17449 [Caenorhabditis briggsae AF16]
+-------------------------------------------------------------------------AIIVAKSPGVMNKATSYADRLRLGVAV
+IHGEQKdeeesgledgrqsPPpnvTS---------------YDflpaqeskqkpPLTVV-GDV-GGRIAIMVDDIIDDAQSFVAAAEVLKARGAYKIYVI
+ATHGVLSSMPPLFSKPPRSQsfspetiRKRKPTLFQVIVTNTVPHDlQKmR-CHK---IKTVDVSLMIC--
+>gi|333374604|ref|ZP_08466444.1| purine/pyrimidine phosphoribosyltransferase [Kingella kingae ATCC 23330]gi|332975242|gb|EGK12142.1| purine/pyrimidine phosphoribosyltransferase [Kingella kingae ATCC 23330]
+------------------------------------------------------IHHTVKKIAEQIQASGIQYDAMIAIGGGGFIPARMLRSFVDVPIYA
+VTTAYYLDESG---SGETADEI-QKVQWIDPIPEK-IVGKNILVVDEVDDSRVTAEFVLRELQKENFTEVGFAVIHNKIKE-KRGVIPE-------GVHY
+YAGLEVQ----------------------------
+>gi|339249839|ref|XP_003373907.1| hypoxanthine-guanine phosphoribosyltransferase [Trichinella spiralis]gi|316969883|gb|EFV53918.1| hypoxanthine-guanine phosphoribosyltransferase [Trichinella spiralis]
+----------------------------------------FKPFLDRVLIPFNLIDERISALADMLHQKYlDEDLVLVCVLKGAFRFFSSLYDKLVRirn
+nctgNLyyDFVRLQ-----------SYVDTKS---TGvvQVCMFKpS--FRRKHIVIVEDIVESGKTLEKLNSLVESYEPLSVRYVTLLTKR--------
+------------------------------------------------
+>gi|313905981|ref|ZP_07839335.1| conserved hypothetical protein [Eubacterium cellulosolvens 6]gi|313469165|gb|EFR64513.1| conserved hypothetical protein [Eubacterium cellulosolvens 6]
+-----------------------------------------------------MFHALGKKVGEACDG----VGLVIGFAETATAVGMAVAEEMSDDCIY
+IHTTReLVPEENDW-VEFCEEHSHAVEQKLSGSHldQWIKSCKSIVFVDDEISTGKTLINIVSRLKEQypEieEKRLVAASIINRVSEVNEQKMRD----
+--YGLECVSLLKLEE---------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1565 0 0
+
+S 2 * * * * * * * * * * * * * * * 0 * * * * 2
+ 0 * * * * * * 1565 0 0
+
+L 3 * * * * * * * * * 925 * * * * 1079 * * * * * 3
+ 0 * * * * * * 1565 0 0
+
+K 4 * * * * * * * * 925 * * * * * * * * * * 1079 4
+ 0 * * * * * * 1565 0 0
+
+E 5 * * 1079 925 * * * * * * * * * * * * * * * * 5
+ 0 * * * * * * 1565 0 0
+
+I 6 1079 * * * * * * 925 * * * * * * * * * * * * 6
+ 925 1079 * 2322 322 * * 1565 1266 0
+
+G 7 * * * * * 925 1079 * * * * * * * * * * * * * 7
+ 0 * * * * * * 1565 0 0
+
+P 8 * * * * * * * * * * * * 0 * * * * * * * 8
+ 0 * * * * * * 1565 0 0
+
+N 9 * * * * * * 1671 * 1523 * * 1565 * * * * * * * * 9
+ 0 * * * * * * 2152 0 0
+
+S 10 * * * * * * 1671 * 1523 * * * * * * 1565 * * * * 10
+ 0 * * * * * * 2152 0 0
+
+L 11 * * * * 1671 * * * * 1565 * * * * * * * * * 1523 11
+ 0 * * * * * * 2152 0 0
+
+L 12 * * * * 1924 * * 2073 * 1945 * * * * * * 2065 * * * 12
+ 0 * * * * * * 2603 0 0
+
+L 13 * * * * * * * * * 0 * * * * * * * * * * 13
+ 0 * * * * * * 2603 0 0
+
+E 14 1069 * * 1945 * * * * * * * * 1924 * * * * * * * 14
+ 0 * * * * * * 2603 0 0
+
+D 15 3447 * 2034 * * * * * * 1366 * 3489 3469 * 3370 * * * * * 15
+ 0 * * * * * * 3920 0 0
+
+S 16 * * 3489 3499 * * * * 2486 3083 3574 * * * * 1568 3256 * * * 16
+ 0 * * * * * * 4083 0 0
+
+H 17 * * * 2656 * * 1692 3998 * 3698 * 3461 * 3590 * * 2694 3966 * * 17
+ 123 * 3614 * * * * 4231 0 0
+
+S 18 * * 1658 1775 3584 * * * * * * * 3265 * * 2297 * * * * 18
+ 0 * * * * 0 * 4077 0 1022
+
+L 19 * * 3348 * * * * 2775 * 719 3774 * * * * * * * * 3732 19
+ 109 3774 * 2000 415 * * 4360 1003 0
+
+S 20 2060 * 4055 * 3362 3956 * * * 3553 * * * * * 2641 3801 3779 3682 3831 20
+ 0 * * * * * 0 4337 0 1003
+
+Q 21 3719 * 2813 3801 * * * * 2005 * * 3831 * 3298 * * 3362 3779 * 3074 21
+ 0 * * * * * 0 4337 0 1003
+
+L 22 * * * 2060 2685 * * * 3779 1745 * * * * 3362 * * 2877 * * 22
+ 96 3956 * 2276 334 0 * 4337 1079 1003
+
+L 23 * * * * 4078 * * 2380 * 684 4040 * * * * * * 3934 * * 23
+ 0 * * * * * * 4661 0 0
+
+K 24 2910 * * 4160 * 3922 3816 3092 2368 2562 * * * * 2368 * * * * * 24
+ 0 * * * * * * 4863 0 0
+
+K 25 3051 * 3324 1983 * * * * 2959 * * 3057 * * 4284 3084 3203 * * * 25
+ 0 * * * * * * 5034 0 0
+
+N 26 4241 * * * * 4298 * * 3243 2844 3928 2538 4144 3917 2049 4349 * * * * 26
+ 0 * * * * * * 5185 0 0
+
+Y 27 4137 * * * 2894 * * 1558 * 4358 * * * * * * * 1689 * 3183 27
+ 78 * 4246 * * * * 5384 0 0
+
+R 28 4399 * 3427 3661 4196 * * 4460 4412 4209 * * * 3873 1345 * 4121 4054 * * 28
+ 0 * * * * * 0 5368 0 1266
+
+W 29 4087 * * * * * * 4409 3420 4196 * 4412 * 4333 2857 * 3518 3494 1575 * 29
+ 70 4409 * 2000 415 0 * 5368 1031 1266
+
+Y 30 4988 * 3385 3899 2033 * * 3630 4716 * * * * * * * * 2217 * 2136 30
+ 3388 * 145 * * * * 5742 0 0
+
+S 31 * * * * * * * * * * * * * * * 0 * * * * 31
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+G 166 4623 7339 5322 4598 * 682 6208 * 4122 7212 * 4008 4730 6428 6309 4835 6028 * * 6464 166
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+Q 235 * * * * * * * * * * * * * 0 * * * * * * 235
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+
+//
+�HHsearch 1.5
+NAME c73204c4134fbbb074a65e8410643b7c
+FAM
+FILE c73204c4134fbbb074a65e8410643b7c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:56:51 2013
+LENG 137 match states, 137 columns in multiple alignment
+FILT 111 out of 1145 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHH
+HCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9775687665448888657588377999999999871986489888778766654576631575547799999999663202452110145777768500
+1024699999999999999975777789998886659
+>Consensus
+xxxxxxxxxxxxxxxxxxxxxxxxxxxxGxxLfxxxCaxCHxxxxxxxxPxlxxxxxxlxxxxxxrxxxxxlxxxlxxpxxxxgxxxxxxxxxxxxMpxx
+xxxxxxLsxeexxxIxxYlxxxxxxxxxxxxxxxxxx
+>c73204c4134fbbb074a65e8410643b7c
+AELTPEVLTVPLNSEGKTITLTEKQYLEGKRLFQYACASCHVGGITKTNPSLDLRTETLALATPPRDNIEGLVDYMKNPTTYDGEQEIAEVHPSLRSADI
+FPKMRNLTEKDLVAIAGHILVEPKILGDKWGGGKVYY
+>gi|194333943|ref|YP_002015803.1| cytochrome c class I [Prosthecochloris aestuarii DSM 271]gi|194311761|gb|ACF46156.1| cytochrome c class I [Prosthecochloris aestuarii DSM 271]
+------------------------ATPDGEAIFNRSCSVCHSVNPPPkSAPPVIPLANRYHMQFQTKeQGVAAMADFLEKPDVA-----KA-LdPRAVSR
+FGLMPLIP-LTDEERKAVSEWFWDQYNpaK-GGGRGFGG---
+>gi|117926827|ref|YP_867444.1| cytochrome C, class I [Magnetococcus sp. MC-1]gi|117610583|gb|ABK46038.1| cytochrome c, class I [Magnetococcus sp. MC-1]
+----------------TVVGFAGSAHAADDAV--MnKCRACHTweaGKKGKQGPNLFGIVGSAAGSNAdfkyNkssvlPdvgakgvvWDAALIDEYLQDP
+TKFLQR-VLGDAKAKSKM--TFK----LKGaDKADEraaIIEFLSNN---------------
+>gi|32473911|ref|NP_866905.1| hypothetical protein RB5806 [Rhodopirellula baltica SH 1]gi|32444448|emb|CAD74446.1| hypothetical protein-transmembrane prediction [Rhodopirellula baltica SH 1]
+----------------------DGDTVNGKAVFTKHCQTCHQLHGEGslVGPQLDGaisrSVERLlEDvVLPDRNIDQAFRtqslllddgrvlvgliasq
+ddevIRLTTSDGKTqdvRVDNVEarQASQRSLMPANLSE--LMTERELVDLMAYLKSSSGN------------
+>gi|118474682|ref|YP_892589.1| ubiquinol--cytochrome c reductase, cytochrome c1 subunit [Campylobacter fetus subsp. fetus 82-40]gi|118413908|gb|ABK82328.1| ubiquinol--Cytochrome c reductase, cytochrome c1 subunit [Campylobacter fetus subsp. fetus 82-40]gi|342328059|gb|EGU24543.1| ubiquinol--cytochrome c reductase, cytochrome c1 subunit [Campylobacter fetus subsp. venerealis NCTC 10354]
+----------------NSIDLAKGSAKTGEELIAAAgCNACHGIKSANMPAPMDDKtASESFGVAPPDlsdigylYDGKFLAALIKDPVLALKLSHKfSD
+EQPF-PMTP-FMGAGGDLNQEIADLVAYFKSI---------------
+>gi|291280072|ref|YP_003496907.1| cytochrome c family protein [Deferribacter desulfuricans SSM1]gi|290754774|dbj|BAI81151.1| cytochrome c family protein [Deferribacter desulfuricans SSM1]
+-----------------------YPADYGRNTWKKNCRlAC-HDGSKTG-VP-KLAPNS--------KTQQQWENVFA-qnrkyIYEM---------HK-
+---GVD-fS---H-lSEKDWNMIKLFVIQHAYD------------
+>gi|317405587|gb|EFV85888.1| alcohol dehydrogenase cytochrome c subunit [Achromobacter xylosoxidans C54]
+------------------SLLAGRYDSRGAVIYMEHCVICHRADGQGMprifpalagNSAIFA------------QNPQSIIQITLE-----GGGMPAnd
+HDTMAFAMPR-FN---HLSDQDITDVINFIRT----------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 0 * * * * * * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+E 2 * * * 0 * * * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1598 0 0
+
+L 3 * * * * * * * * * 844 * * * * * * * * 1174 * 3
+ 0 * * * * * * 1598 0 0
+
+T 4 2037 * 2128 2229 * * * * * * * * * * * * 1670 * * * 4
+ 0 * * * * * * 2530 0 0
+
+P 5 * * * 1082 * * * 2229 * * * * 1670 * * * * * * * 5
+ 0 * * * * * * 2530 0 0
+
+E 6 2296 * * 719 * * * * * * * * * * * * 2406 * * * 6
+ 0 * * * * * * 2869 0 0
+
+V 7 * * 1736 * * * * * * * * * 1624 * * 2777 * 2123 * * 7
+ 0 * * * * * * 3167 0 0
+
+L 8 * * * * * * * 3220 3077 2573 * * * 3101 2057 3008 * 3000 * * 8
+ 0 * * * * * * 3656 0 0
+
+T 9 3348 * * * * * 3253 * 3399 * * * 3349 * 3328 1424 2925 * * * 9
+ 0 * * * * * * 4117 0 0
+
+V 10 3473 * * * * * * 1967 * 3633 * * * * * * 3657 1320 * 3417 10
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+
+P 11 * * * * * * * 3414 * * * * 843 3417 3387 2649 * * * * 11
+ 0 * * * * * * 4266 0 0
+
+L 12 3858 * * * * 3763 * 2222 * 1796 * * * * * 3863 4006 3040 3286 * 12
+ 103 * 3863 * * * * 4909 0 0
+
+N 13 1941 * 2766 3601 * 3368 * * * * * 3638 3841 * * * 3982 2959 3812 * 13
+ 94 3982 * 2807 222 * 0 4947 1085 1099
+
+S 14 2931 * * 2804 * 2277 * * 2479 * * 3812 4079 * * 2771 3982 * * * 14
+ 0 * * * * * 0 4947 0 1099
+
+E 15 4316 3439 2893 2514 * 3085 * * 3286 * * 4502 4127 * 3843 3235 4314 * * * 15
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+
+G 16 4884 * 4670 * * 1155 * 3561 * 3238 * 3522 4316 * * 4697 3702 4858 * * 16
+ 0 * * * * 504 1762 6369 0 1612
+
+K 17 2571 * 3216 3256 * 3633 * 5155 4324 5017 * 3152 3469 5389 5418 5412 3528 3844 * * 17
+ 47 4957 * 3170 170 * 0 7359 1062 1100
+
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+ 100 3894 * 0 * * 0 7554 1113 1100
+
+I 19 2536 * 5823 4477 * 4281 5639 2709 4497 4119 * * 3591 5585 5724 4185 * 2198 * 4534 19
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+
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+ 24 5905 * 2807 222 * 0 7989 1000 1100
+
+L 21 3047 * 4789 * 2806 5904 5637 4821 5593 2204 3978 5788 4941 5594 * 4617 3475 4727 5555 3936 21
+ 0 * * * * * 0 8151 0 1100
+
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+ 72 * 4362 * * * 0 8339 0 1100
+
+E 23 2722 * 3962 3559 6130 3354 * 6226 3492 6442 5955 3222 2887 6186 6605 3538 3728 5074 * * 23
+ 78 4645 6276 675 1420 716 1354 8937 1182 1436
+
+K 24 2393 * 3223 2980 6271 2528 6647 6484 4071 4148 * 6498 3829 4542 5561 4206 5823 4836 * * 24
+ 15 6589 * 1000 1000 * 0 9184 1032 1199
+
+Q 25 3291 * 2311 3353 5338 6660 6852 5306 4726 3713 * 3480 3654 4022 5138 3731 4652 5090 * 6330 25
+ 80 5860 4763 3138 174 0 * 9459 1173 1199
+
+Y 26 2150 * 5418 4708 5696 3816 5760 3560 5305 2767 5535 6901 4041 4372 6025 5733 5209 3122 6572 5523 26
+ 38 5267 * 1160 856 817 1209 9501 1244 1289
+
+L 27 2076 * 4412 2868 * * 5033 6421 3601 4624 6364 6629 5310 4084 4022 3376 3738 3910 * 6960 27
+ 63 4539 * 1772 500 0 * 9555 1303 1057
+
+E 28 2728 * 3918 3271 * 6803 6382 6962 2927 5587 5825 5751 4788 3443 2529 4035 3909 5345 6914 * 28
+ 28 5708 * 1336 728 * * 9577 1082 0
+
+G 29 3949 * 5762 6833 * 251 * 5667 * 6760 * 6560 6778 * 6850 6593 * * * * 29
+ 13 * 6833 * * * * 9596 0 0
+
+K 30 3370 * 4280 2658 5556 7074 * * 2098 5854 * 5430 5415 2775 2775 4617 * 6946 6925 5807 30
+ 0 * * * * 0 * 9587 0 1000
+
+R 31 2869 * 4460 2952 5332 5683 6677 4583 3745 3675 * 5057 * 2824 3284 5103 3829 4725 6493 5842 31
+ 25 * 5880 * * * * 9598 0 0
+
+L 32 4025 * * 6479 * * 6826 2550 * 1096 4736 6873 * 5682 6704 6435 5915 2500 * * 32
+ 31 6435 6664 2000 415 0 * 9590 1017 1103
+
+F 33 3600 * * * 1204 * * 4838 6682 5311 6633 * * * 7048 6757 6826 3521 4650 1994 33
+ 40 5931 6524 0 * * 0 9586 1052 1000
+
+Q 34 2654 * 4338 2710 5511 6112 5595 5909 3625 4423 * 4474 * 3140 3764 4390 3441 4398 6616 6958 34
+ 28 * 5703 * * 0 * 9566 0 1099
+
+Y 35 3545 * 4332 4230 6933 3897 * 4628 2963 5617 5815 3889 6936 3175 2835 3952 3059 6790 * 6781 35
+ 244 2685 * 1886 455 0 * 9572 2638 1071
+
+A 36 3427 * 5599 4967 5160 4862 2845 4876 3864 6026 * 2300 6865 4100 4129 3917 4533 5691 6029 3975 36
+ 141 3430 * 204 2926 * * 9598 2075 0
+
+C 37 * 24 * * * * 5925 * * * * * * * * * * * * * 37
+ 0 * * * * * * 9598 0 0
+
+A 38 1657 * * * 5518 3000 6850 4405 5325 3843 4619 6323 * 6637 4103 2973 3873 3870 * * 38
+ 0 * * * * * * 9598 0 0
+
+S 39 2069 * 5839 5998 6208 3355 5654 6862 4309 5463 5816 5269 4488 4389 4801 2440 3569 3875 * 7117 39
+ 12 * 6929 * * * * 9598 0 0
+
+C 40 * 38 * * 6370 * * * * * * * * * * 6158 * * * * 40
+ 0 * * 0 * 0 * 9586 1000 1000
+
+H 41 5925 * * * * * 24 * * * * * * * * * * * * * 41
+ 87 5630 4716 0 * * * 9598 1080 0
+
+V 42 3299 6415 5858 6897 6527 1875 * * 5266 5629 5220 4550 5560 4218 3679 2884 3296 4200 * 5869 42
+ 30 6598 6636 916 1089 383 2101 9562 1120 1309
+
+G 43 3890 * 4076 4229 5291 4225 5869 3125 5266 2673 4506 5308 2997 7178 7004 5272 4473 3249 6757 4973 43
+ 52 4826 * 1606 574 0 * 9595 1496 1119
+
+G 44 4545 * 2626 3364 6932 2345 5543 5766 4110 5234 6786 3130 4462 5524 4851 4016 4628 6994 * 4894 44
+ 68 5111 5857 1060 942 * * 9598 1200 0
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+
+//
+�HHsearch 1.5
+NAME c737dfcd8b440f4a80b15ef9f3c3a806
+FAM
+FILE c737dfcd8b440f4a80b15ef9f3c3a806
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:12:26 2013
+LENG 100 match states, 100 columns in multiple alignment
+FILT 129 out of 1069 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCEEEEECCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCEECCCEECCCEEECCCCCEEEEEEEEECCCCCCEEEEEEECCCCCCCEEEECCCCC
+>ss_conf PSIPRED confidence values
+9865999999787822379848999998166588889899889913345451427878998599999999834469989999997888956899815899
+>Consensus
+xxxxxPxvxxxxxxxxxxxxxxtlxCxxxxfxPxxixvxWxxxgxxxxxxxxxxxxxxxxxxysxxsxlxxxxxxxxxxtCxvxhxxxxxpxxxxxxxxx
+>c737dfcd8b440f4a80b15ef9f3c3a806
+MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+--seagS----------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne---DLRSWTAADMAAQN---------------tqrkweaag
+vaeqw----RAYLEGECLEWLRRYLEKGK---------------et--LQ--raE---
+>gi|82407640|pdb|1ZVO|C Chain C, Semi-Extended Solution Structure Of Human Myeloma Immunoglobulin D Determined By Constrained X-Ray Scatteringgi|82407641|pdb|1ZVO|D Chain D, Semi-Extended Solution Structure Of Human Myeloma Immunoglobulin D Determined By Constrained X-Ray Scattering
+------------------------------FR-------WPESPKAQaSSVPTAQPQAEGSLAKATTAPATTRNTgrgGEEKKKEKEKE-----------
+----
+>gi|291165393|gb|ADD81217.1| immunoglobulin light chain [Larimichthys crocea]
+--DTAPTLTVLPPSSEQLQqGKATLMCLANKGFPSDWSLAWKVDSSSSiSwEESRSPVVLEKDGLYSWSSTLRLDADQwrkVDSVTCEATQGSQ-TPRSE
+TL----
+>gi|145559665|gb|ABP73658.1| MHC class I antigen [Sus scrofa]
+----GLKTLR-GYYNQSEAG-SHTYQWMYGCYlgPDGLFLcgysQFGYDGADYvALNEDLRSWTAADMAAQISKRKWEAADEAERMRSYLQGrcvEWLQK
+YLemgkdTLQHAD--
+>gi|148691350|gb|EDL23297.1| histocompatibility 2, M region locus 9, isoform CRA_a [Mus musculus]
+--TDPPEPTI-PFLPM----IIALVlgALLMGSVMTFLI---------------WKRRTRG---------------------------------------
+--
+>gi|16754812|emb|CAC82793.1| immunoglobulin heavy chain constant region [Lepus capensis]
+----GPSVFIFPPKPKDtLmiSLTPEVTCVVVDVSQddPEVQFTWYINNEQVytARPPLR--EQQFNSTIRVVSTLPIVHQdwlRGKEFKCKVHNKALPS
+PIE-------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 3066 0 0
+
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+ 0 * * 2000 415 * * 5676 1081 0
+
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+
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+
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+
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+
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+
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+ 0 * * * * * 0 9176 0 1646
+
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+
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+
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+
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+
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+
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+S 29 3921 * 5682 3373 5436 6895 6040 * 3994 4915 * 4346 6835 3764 3843 2194 2985 4301 6886 3833 29
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+G 30 5675 6809 2278 5457 * 1286 6085 * 4919 8546 * 2853 6047 5357 4712 4108 6975 * * * 30
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+H 32 5149 * 5239 5402 2766 7162 6138 5692 3833 4983 5795 4480 4845 6625 4640 2825 4809 5245 5901 1918 32
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+P 33 6597 * 6821 6078 * 5756 * 6281 5077 4868 * * 355 7666 5815 4844 5816 6200 * * 33
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+I 36 3620 * 5783 * * 6418 5978 1680 * 2674 5955 5326 4488 * * * 4424 2125 6848 4875 36
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+
+E 37 3830 * 4464 3128 4851 6909 3845 * 3407 6015 5491 3576 * 3907 4379 3219 2673 4877 * 5124 37
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+
+V 38 * * * * 2697 * * 2050 * 2663 5456 * * * * * 5174 1405 * 5761 38
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+
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+
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+ 101 3890 * 2627 255 1863 464 9481 1933 2036
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+K 42 3926 5829 5362 3638 * 6915 5316 5051 2150 4292 6938 4775 6454 4097 2464 5333 6087 3466 5844 5110 42
+ 38 5894 6766 2392 305 973 1028 9484 1480 1725
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+G 44 6056 * 3605 3723 * 1172 6968 * 4596 * * 3226 4357 5121 4441 4339 5258 5164 * * 44
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+I 47 6202 * 4977 5208 6918 6650 5394 3084 4264 1901 6159 7190 5380 3738 5643 3973 4455 2539 * 5223 47
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+K 49 3542 * 2920 3615 * 2386 5752 5903 4054 4404 * 4558 5457 5522 5717 3056 3104 5394 * * 49
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+H 52 4789 * 3551 4461 5276 4635 5197 5340 4043 4698 * 4461 3722 3275 5883 3375 2611 4990 6247 3842 52
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+S 53 4117 * * 4371 3931 3094 4946 5994 6858 3722 * 4083 4266 7067 6045 2704 2362 5131 * 3864 53
+ 143 4709 4157 1281 765 629 1500 9375 1587 1881
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+D 54 3828 5876 3253 3133 5968 4352 * 5483 3933 4698 * 4662 3210 4178 4266 3200 3966 4562 * 4944 54
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+
+L 55 4562 5808 * 4938 5568 5970 4909 3216 5495 3672 4751 4413 2363 * 6853 3914 3892 2723 * 4148 55
+ 0 * * 0 * 393 2070 9257 1000 2996
+
+S 56 3934 * * 3683 7048 7026 6907 4324 3920 3231 4751 5383 3841 3782 3215 3361 3781 3690 4857 5851 56
+ 100 5077 4739 693 1391 * 0 9492 1327 1411
+
+F 57 3778 4785 5755 3332 5949 3992 5967 4454 3938 3204 * 5975 2568 4300 3584 4930 4059 5231 * 5609 57
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+
+S 58 3522 6912 3438 3343 * 4065 4871 6469 5501 5308 5821 2658 4561 3922 4758 2916 4342 5834 6173 5226 58
+ 61 5372 5833 2030 405 881 1130 9525 1285 1101
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+K 59 3113 * 5015 2934 6649 2648 6123 6934 3512 5608 6926 4098 3767 3561 4770 3418 4513 5963 * 7024 59
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+ 76 6860 4545 727 1337 446 1912 9379 1225 1950
+
+W 61 5406 * 5683 4840 8126 1265 5112 * 3295 4776 5565 4125 6263 6171 5089 3628 4225 6867 4612 5920 61
+ 160 3995 4568 254 2629 689 1396 9485 1947 1881
+
+S 62 4996 6786 6328 4883 5776 4262 5503 * 4199 3216 5825 5192 6926 5302 4306 2505 1736 4424 * 7209 62
+ 45 6875 5504 0 * 1093 913 9461 1000 1975
+
+F 63 4391 4189 * 5985 1939 5927 5113 6675 5020 6697 * 5862 * 6823 * * 4556 6050 4441 1337 63
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+L 65 3020 6109 * 6379 5283 * * 3432 4098 3593 3854 * 5450 4132 6431 3125 2743 2735 5991 * 65
+ 26 5791 * 0 * 637 1487 9440 1118 2098
+
+L 66 6936 5963 6728 5988 4107 6224 4101 6899 6044 3151 7241 6011 5892 5206 3961 2399 2728 3339 3798 4530 66
+ 0 * * * * * 0 9490 0 1314
+
+Y 67 4083 6728 6827 7358 * 7277 4318 5852 4568 4273 * 6643 5892 5159 5574 1091 3861 3058 * 6077 67
+ 39 6976 5757 1000 1000 1678 541 9490 1000 1314
+
+Y 68 4436 * 4851 4661 4573 * 4754 2980 4726 4259 5325 6817 5191 4098 3566 3615 3310 3770 4925 3456 68
+ 11 7004 * 0 * 967 1034 9460 1036 1498
+
+T 69 4745 5168 * 7712 4809 6125 6119 3820 5613 1154 5248 * 5476 * 4167 5169 4789 3048 5808 5803 69
+ 19 6260 * 2322 322 * 0 9498 1096 1170
+
+E 70 4357 * 4413 3169 * 6939 5231 4774 3974 3747 4850 3748 3872 6090 3419 3776 2750 5514 5596 4883 70
+ 41 * 5152 * * * 0 9461 0 1411
+
+F 71 4226 * * 5550 3458 5755 * 2297 6993 2409 4925 * 6806 6594 * 4499 4551 1923 * 6227 71
+ 32 5529 * 1585 585 2551 270 9336 1172 1864
+
+T 72 3400 5948 3933 4754 5981 5626 6891 6749 3739 4802 6598 3967 3004 4748 4653 2800 2928 3815 * * 72
+ 12 6916 * 0 * * 0 9359 1000 1698
+
+P 73 2877 7046 * 3737 4689 5967 4618 * 3191 3464 7047 6440 2513 5051 3949 3128 4604 6964 5322 6970 73
+ 137 3465 * 1860 465 * 0 9359 2338 1698
+
+T 74 4291 * 2766 2651 * 3584 6650 5751 3793 5885 6413 3956 7060 3178 4765 2925 4045 7154 6437 * 74
+ 472 1954 5580 1859 465 616 1525 9359 4524 1698
+
+E 75 5268 5231 2750 2189 * 4572 5107 * 4096 4764 * 4075 4674 3290 5035 2895 5642 6478 * 5941 75
+ 532 1803 5527 1487 637 2823 220 9334 4811 1696
+
+K 76 3191 * 3847 2688 6675 1817 5136 4911 4428 6191 * 4102 5657 5573 4939 4627 4160 * 7206 6009 76
+ 36 5323 * 1606 575 * 0 9234 1281 1961
+
+D 77 3143 * 3231 3334 * 2817 5095 6750 3022 4698 6922 4715 * 4804 4434 3560 3681 5403 * 5365 77
+ 22 6048 * 1748 510 2694 242 9234 1166 1961
+
+E 78 6054 * 5925 2506 * 5445 5697 5836 3231 3833 5420 4099 5757 5071 3591 3346 2483 3922 * * 78
+ 68 4903 6340 1042 959 1979 422 9248 1444 1798
+
+Y 79 * 5624 * * 2031 * 4561 3984 6368 4108 4587 * * * 6855 6113 6034 3392 6546 1421 79
+ 25 5870 * 967 1034 3209 165 9286 1121 1980
+
+A 80 5172 * 5672 6987 * 6746 6471 4341 2935 6115 4798 6775 * 4760 4492 2282 1689 4284 * 4786 80
+ 49 4911 * 1453 656 1078 926 9304 1370 1865
+
+C 81 * 287 * 6602 * 5907 * 5748 * 6343 * * * 6649 5903 4837 5793 5354 * 5781 81
+ 0 * * * * 2417 299 9417 0 1519
+
+R 82 5097 5883 7174 2562 5847 5798 4736 4621 4064 6015 4640 5573 6100 3089 3143 5020 3640 2877 * 4826 82
+ 0 * * * * * 0 9401 0 1397
+
+V 83 2589 6187 * 5606 4439 4840 * 4338 * 4740 5158 5798 5883 * 6644 5497 6480 977 * 5867 83
+ 58 5572 5784 4644 59 * 0 9401 1159 1397
+
+N 84 4870 * 4403 3006 5218 7045 5430 5038 2660 5290 * 4657 5946 2986 3820 3237 3587 4923 * 4408 84
+ 0 * * 0 * 2798 224 9311 1000 1713
+
+H 85 6862 * 6132 5698 * 4070 804 6331 6804 4692 * 3127 5210 6944 5654 4759 6543 * 5728 5083 85
+ 85 4396 6714 2604 259 * 0 9239 1514 1594
+
+V 86 3862 * 4567 2284 6320 4458 * 4862 3030 5314 * 4115 3441 5766 3679 3906 4201 4435 5485 6983 86
+ 73 4769 6338 2211 351 1528 614 9113 1663 1751
+
+T 87 2391 * 4212 4499 6834 2378 6840 * 4741 4836 * 4348 4599 * 5303 2144 4257 6680 5321 * 87
+ 22 6037 * 0 * 2216 350 9068 1172 1605
+
+L 88 4917 * 6898 * 4130 3552 * 6477 4649 1347 6396 3938 5595 5148 5435 2934 4892 5204 7015 5424 88
+ 64 4522 * 2421 298 697 1384 9030 1442 1448
+
+S 89 4875 * 4137 3398 * 3836 4616 6291 3443 4794 * 3540 3202 4198 5143 3099 3196 4073 * * 89
+ 193 2998 * 1465 649 * 0 9028 2238 1081
+
+Q 90 3533 * 5044 3046 * 6262 6092 5816 3297 5803 5427 3215 4817 3085 3905 3249 3254 4796 * * 90
+ 0 * * 1000 1000 * 0 8741 1081 1081
+
+P 91 4874 * 3724 3795 4470 * * * 3707 4981 * 5179 1121 6434 * 4011 3835 * * 4894 91
+ 0 * * * * * 0 8734 0 1081
+
+K 92 4425 * * * 5016 * 4942 2526 3635 1576 4153 5897 * 3823 5905 * 4846 3457 * 6112 92
+ 53 4780 * 2322 322 0 * 8587 1213 1081
+
+I 93 5429 * 5167 4092 * 5344 * 3380 3807 3938 6257 6018 6063 4877 2769 3338 2093 3728 * * 93
+ 22 6032 * 2322 322 * * 8576 1000 0
+
+V 94 3381 * * 4192 4663 5191 * 3578 3186 2204 * * * 3909 4177 6061 4047 3054 * 4209 94
+ 27 * 5759 * * * * 8431 0 0
+
+K 95 * * 5471 4735 5256 4542 3895 5342 3566 * 4503 3641 4501 4028 3574 2479 2965 5650 * 4225 95
+ 0 * * * * * 0 8191 0 1081
+
+W 96 4676 * * * 2743 * 4170 5207 * 2962 * * 5155 * 4943 5207 * 3498 1332 5199 96
+ 0 * * 1000 1000 0 * 7388 1081 1081
+
+D 97 3935 * 2971 2448 * 3203 * * 2639 * * 3277 * * 4795 4046 3657 3724 * * 97
+ 0 * * * * * * 6949 0 0
+
+R 98 * * 3587 4579 * 4295 4721 * 4058 * * * 945 * 3353 * 4178 4226 * * 98
+ 0 * * * * * * 6220 0 0
+
+D 99 * * 3652 2520 * * 3515 * * * * * 1830 3785 * 2197 3529 * * * 99
+ 0 * * * * * * 4690 0 0
+
+M 100 * * * * * * * * * 844 1175 * * * * * * * * * 100
+ 0 * * 0 * * * 2653 0 0
+
+//
+�HHsearch 1.5
+NAME cb13cb2555c5bacde1dc168618e48f3f
+FAM
+FILE cb13cb2555c5bacde1dc168618e48f3f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:33:53 2013
+LENG 183 match states, 183 columns in multiple alignment
+FILT 143 out of 1887 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHCCCCEEEEEEECCCCHH
+HHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCC
+>ss_conf PSIPRED confidence values
+9137999999852899833999999999999999999965887544785434789999677789999757717678999998603999999998997311
+68899999999986244899789999882155423899999999887654269708999668896999999999998675179
+>Consensus
+xxxxxxxxxxxxxxxxxxxxixvxGxxxxGKstlixxlxxxxxxxxxxtxxxxxxxxxxxxxxxxxxDxxgxxxxxxxxxxxxxxxdxxixvxdxxxxxs
+xxxxxxxxxxxxxxxxxxxxxxivvxnKxDlxxxxxxxxxxxxxxxxxxxxxxxxxxxxSaxxxxxixxxxxxixxxxxxxxx
+>cb13cb2555c5bacde1dc168618e48f3f
+MGNIFSSMFDKLWGSNKELRILILGLDGAGKTTILYRLQIGEVVTTKPTIGFNVETLSYKNLKLNVWDLGGQTSIRPYWRCYYADTAAVIFVVDSTDKDR
+MSTASKELHLMLQEEELQDAALLVFANKQDQPGALSASEVSKELNLVELKDRSWSIVASSAIKGEGITEGLDWLIDVIKEEQL
+>gi|300121709|emb|CBK22284.2| unnamed protein product [Blastocystis hominis]
+--------------KDNNIRIIVVGDAAVGKTSIISTFVSDRFAENVDPVLcevVIPGECTTNHCSLTIVDSSSIEEDHDITCEQIRLADVVMIVYSLDK
+PHSLESVTTKWIPLVIDIGGPQKPIVVVGNKIDLEKnpssMNSNTHLREHSESILSQYPNVDcCMECSAKSRQNLTQVFYAAQRTV-----
+>gi|14595136|dbj|BAB61872.1| Picchu-236-X [synthetic construct]
+--------------DMAGNfdseersswywgrlsrqeavallqgqrhGVFLVRDSSTSPGDYVLSVSENSRVsHYIINSSgPRPPVPPSPaqPppgvspS
+RLRI----GDQEFDSLPALL-----EFYKIHYLDTTTLIEPVSR---------SRQGSGVILRQEEAEY-------------------------------
+---------------------
+>gi|288553110|ref|YP_003425045.1| GTPase RsgA [Bacillus pseudofirmus OF4]gi|288544270|gb|ADC48153.1| ribosome-associated GTPase [Bacillus pseudofirmus OF4]
+------------------------------------------------------------------------DRKNELVRPPISNIDQALLVFSAKEPDF
+---SPLLLDRFLVHIEANNIKPVIIISKVDLLLPNELAEIKEYQKQY--EAIGYTVILTTNQNQSSnqtneMVEILSCIKDQV-----
+>gi|326674986|ref|XP_001337060.4| PREDICTED: GTPase IMAP family member 8-like [Danio rerio]
+-----------------sEFSLVLLGYGEAGKSSAGNTILGRPafgs-----gRTYQCVQRHGEVGGQKVSIIDTPGWwkhlpiqqtpelnkEQITQSAS
+LSTSGPPAFILVTRAD--CSFKEQERKALEDHLNLFGSSVwdHSLVLFTFGDLIGGRAIEQHIEWEGealrwlVDRCGNRYHVFNNKA---kgeSQQVRG
+LLEKIQEMTVANK-
+>gi|169621003|ref|XP_001803912.1| hypothetical protein SNOG_13705 [Phaeosphaeria nodorum SN15]gi|160704153|gb|EAT78729.2| hypothetical protein SNOG_13705 [Phaeosphaeria nodorum SN15]
+--------------------------------------------------------------------------MSISLIHQVtQTSHGAVCILDG----
+-VAGVEAQTEKVWLQSGQYNIPRIIFVNKLDRVGA-------------------------------------------------
+>gi|118366321|ref|XP_001016379.1| hypothetical protein TTHERM_00128980 [Tetrahymena thermophila]gi|89298146|gb|EAR96134.1| hypothetical protein TTHERM_00128980 [Tetrahymena thermophila SB210]
+--------------KKKIINVLVDGSPKSGKSQLISKLSEYCLHEGYDYMErylknCSEVMIQNEQVTVIFYENSNHQ-YLKEESEFNIQFHIYLLLFDV
+NNQDSFEISIKQYNQYSSK--LKSSLKFLIASKCDLSNmsiviqkninnlqylsQITTEDIEQFLvessriylndqQEQFAQQNGFSIFAVSSATKRNVQ
+TLKFKLAQAAYNLGL
+>gi|27383230|ref|NP_774759.1| ABC transporter ATP-binding protein [Bradyrhizobium japonicum USDA 110]gi|27356404|dbj|BAC53384.1| ABC transporter ATP-binding protein [Bradyrhizobium japonicum USDA 110]
+-------------------VVALIGPSGSGKSTLLRCVNL----LVTPDGGS----VRVGDTRFQFGEGAKlpdvktLARFRATTGMVFQH-FNLFPHMT
+TLQNVmegPV----------------------------------------------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * 1946 717 * * * * 2921 * * * * 1
+ 0 * * * * * * 4567 0 0
+
+G 2 * * 3515 3407 * 1165 3386 * 3526 * * 3434 3363 * * * * * * * 2
+ 0 * * * * * * 5462 0 0
+
+N 3 3639 * * * 3633 3839 2728 * 3685 * * 2134 * 3387 3671 3778 3927 * * * 3
+ 0 * * * * * * 5919 0 0
+
+I 4 3778 3671 * 3839 * * * 2104 * 2461 * * * 2690 3633 3685 * 4290 * * 4
+ 0 * * * * * * 5919 0 0
+
+F 5 3212 * * * 1452 * 3708 3020 * 2576 3291 * * * * 4136 * * * * 5
+ 0 * * * * * * 6445 0 0
+
+S 6 * * * 4164 * * * * 1917 * * * * 4206 2549 2015 2721 4179 * * 6
+ 0 * * * * * * 6941 0 0
+
+S 7 * * 4348 * * 3559 * * 2010 3613 * 2448 * 2988 3351 4575 * * 4662 4402 7
+ 0 * * * * * * 7268 0 0
+
+M 8 4435 * 4551 * 2607 * * 2536 4399 1550 4659 * * * * 3924 * * 3645 * 8
+ 0 * * * * * * 7388 0 0
+
+F 9 * 4603 * * 3202 * * 2715 * 2112 4750 4698 4746 4710 3730 4738 * 2587 * 4787 9
+ 0 * * * * * * 7761 0 0
+
+D 10 * * 3014 3948 4845 * * * 3502 * * 2244 * 3306 2086 3228 4882 * * * 10
+ 105 4775 4882 1000 1000 * * 8086 1046 0
+
+K 11 4873 * * 4651 * 3408 * * 2443 * * 4927 * 3901 3857 1898 2491 * * 4924 11
+ 0 * * * * * 0 8057 0 1059
+
+L 12 4821 * * * 4882 3577 4651 3841 2547 1451 * * 4830 4918 4914 * * 4896 4873 5001 12
+ 0 * * * * 0 * 8057 0 1059
+
+W 13 3879 * * 4971 1599 * 5145 3400 3085 4021 * 5068 5009 5018 5024 3499 5088 * 5203 * 13
+ 0 * * * * * * 8271 0 0
+
+G 14 5145 * 2547 3446 5046 3050 * 4912 5036 * * 4083 4034 4038 2972 5184 3341 4067 * * 14
+ 1438 4020 813 594 1566 * * 8271 1310 0
+
+S 15 4056 * 2708 2099 4931 * * * 3029 4263 * 3424 4132 4962 4955 3938 4822 * * 5017 15
+ 47 4964 * 1000 1000 218 2832 8692 1000 4288
+
+N 16 4105 * 4427 3276 * 4297 4346 * 2733 4905 3487 4143 3986 4535 3445 3448 4592 4992 * * 16
+ 0 * * * * 1450 658 9711 0 1388
+
+K 17 4142 6232 6233 4238 * 4935 4132 4776 2364 6178 5959 3168 3336 6139 3143 4603 3689 5252 * 5019 17
+ 0 * * 5644 29 * 0 10267 1205 1183
+
+E 18 6227 * 3867 3928 * 4396 5335 3951 3109 4155 * 3622 3473 4987 3404 4858 2960 3772 * 6641 18
+ 0 * * * * 0 * 10504 0 1183
+
+L 19 5093 6298 * * 3215 6379 6368 2386 6576 2195 5535 6051 3906 * 4400 5422 * 2632 * 3823 19
+ 36 5342 * 4131 85 * * 10541 1303 0
+
+R 20 4848 5793 5332 5137 6318 5864 4147 6632 1754 6653 6768 2802 * 4857 2589 5927 3794 4612 * 6839 20
+ 51 5402 6493 3869 102 * * 10240 1182 0
+
+I 21 5877 5757 * * 4725 6761 * 1491 * 2659 5237 * 7016 * * 4870 6596 1665 * 6780 21
+ 0 * * * * * 0 10496 0 1011
+
+L 22 2383 4002 * * 4254 3269 7010 3205 * 2434 5406 5572 * * * 4888 5142 2460 * * 22
+ 0 * * * * * 0 10512 0 1011
+
+I 23 5753 * * * 3139 6884 * 2696 * 1743 5053 6694 * * * 5955 5737 1591 * * 23
+ 15 6581 * 4000 93 * 0 10450 1038 1011
+
+L 24 3416 6048 6658 * 4342 * * 2472 6764 2113 3760 * * * * 4540 4413 2014 * * 24
+ 0 * * * * * 0 10463 0 1011
+
+G 25 5148 * * 6559 * 147 * 6918 * * * * * * 6083 6367 6233 6726 * * 25
+ 0 * * * * 0 * 10476 0 1011
+
+L 26 4354 6831 2608 3558 4581 6563 3590 6633 3993 3692 5881 4129 3614 4908 4437 3315 4127 * * 6077 26
+ 15 6619 * 3170 170 * * 10485 1038 0
+
+D 27 4188 5369 4165 4098 5539 4727 * * 4167 4505 * 5210 2071 3867 4115 3029 4027 3783 * * 27
+ 0 * * * * * * 10485 0 0
+
+G 28 3794 6932 3789 4555 * 1598 6961 * 4054 6734 * 2245 6771 4664 4353 3634 6998 * * * 28
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+ 264 2579 * 999 1001 952 1050 11532 3955 1463
+
+I 156 4541 4762 6928 6574 2958 * 5792 2320 5970 2738 6580 6756 4334 * * 5326 * 2553 6766 3122 156
+ 12 6928 * 2585 263 1229 803 11519 1030 1134
+
+V 157 4575 * * 6615 2781 * 4486 1989 5709 3141 4934 6835 * 5693 6779 5186 5933 2567 * 3461 157
+ 21 6099 * 535 1690 0 * 11549 1119 1000
+
+A 158 4184 6593 4815 2207 4133 5699 4961 6040 3493 3503 6196 5406 3080 3719 5304 4930 4908 5800 * 4597 158
+ 21 6124 * 1585 585 * * 11560 1183 0
+
+S 159 4170 2671 * * 7043 5351 6797 3151 * 3735 4589 5959 6717 5860 6542 5101 2294 2231 6860 6833 159
+ 21 6141 * 0 * * * 11560 1085 0
+
+S 160 6115 5329 4450 6797 7460 6107 * 4809 6948 6673 * 3669 7013 6863 6542 686 3623 5397 * * 160
+ 23 5973 * 2310 325 * * 11560 1167 0
+
+A 161 1353 4396 7188 5285 * 4195 4646 4983 6906 5758 6508 5483 5790 7040 6837 2582 3937 3886 * 6964 161
+ 32 5496 * 3092 180 * * 11564 1332 0
+
+I 162 4093 * 4776 4703 5344 5437 4499 7168 1998 3124 6043 4799 * 3851 3213 4885 3734 4971 * 4899 162
+ 22 7164 6992 3322 152 * 0 11559 1011 1000
+
+K 163 4951 * 2948 3084 6798 4431 4172 * 3558 4928 5804 3465 7043 4932 4529 3520 2513 6590 * 5221 163
+ 41 6646 5819 2322 322 885 1125 11548 1001 1106
+
+G 164 5046 5710 4596 5114 6633 1550 5922 5762 3550 5315 5732 2540 4125 6009 4324 4954 5752 6792 * 6631 164
+ 39 5240 * 2050 399 0 * 11500 1394 1326
+
+E 165 4335 * 4162 2740 5163 4774 5194 3643 3602 4275 5265 3903 6998 5049 4509 3634 5403 3742 5873 3872 165
+ 25 5853 * 2224 347 * * 11535 1178 0
+
+G 166 5333 * 4017 7057 * 1369 4870 5964 6063 6091 * 2097 6589 4176 6615 3505 4868 * * 7174 166
+ 33 5460 * 1805 486 * * 11535 1364 0
+
+I 167 6799 4335 6613 * 4852 * 5843 1691 5515 2751 3744 * 5722 6691 5924 5364 5933 2066 * * 167
+ 0 * * * * * * 11533 0 0
+
+T 168 4037 * 2726 2835 5708 6972 4858 6789 3274 4509 5785 3356 4722 3816 4233 4012 4844 5163 6997 5684 168
+ 13 6854 * 2000 415 * * 11520 1000 0
+
+E 169 5079 6853 4472 1602 * 5421 6703 5987 3518 3477 6664 3384 * 3603 3955 4795 4470 5166 * * 169
+ 0 * * * * * * 11434 0 0
+
+G 170 3113 5698 * 6730 5760 5167 7049 2417 * 1712 5056 * 5618 7029 5573 5628 3822 2969 6424 * 170
+ 0 * * * * * * 11346 0 0
+
+L 171 5460 6762 6053 5021 1908 6946 6654 3171 3842 2476 4095 5807 5758 * 5123 5924 * 3844 4588 5264 171
+ 0 * * * * * * 11346 0 0
+
+D 172 3611 * 2712 2452 6791 6705 6797 5223 3540 6577 5718 3985 6135 3796 3752 3581 4149 5656 * 5074 172
+ 0 * * * * * * 11307 0 0
+
+W 173 3266 7386 4225 3669 4274 6615 6596 5827 3340 4052 4755 5505 7080 3757 4290 3707 4634 3907 4391 3534 173
+ 0 * * * * * * 10665 0 0
+
+L 174 3567 5882 * * 4942 * * 1324 * 1553 4787 * * * * 5619 6736 4058 * * 174
+ 0 * * * * * * 10665 0 0
+
+I 175 3447 4605 5809 4697 5609 4213 6836 3063 3553 2674 5759 6960 * 3920 4199 5021 4742 2842 * 6439 175
+ 0 * * * * * * 10588 0 0
+
+D 176 3782 * 3781 2928 * 5856 4691 * 2826 6476 * 3591 * 3038 3128 3330 3760 * * 5479 176
+ 0 * * * * * * 10577 0 0
+
+V 177 3393 * 6883 4506 6572 6293 4806 3944 2394 2621 5405 6355 6590 3524 4941 4254 3980 4239 * 4599 177
+ 0 * * * * * * 10176 0 0
+
+I 178 3218 5484 * 5341 3520 * 6423 2222 * 2090 6323 * * 6343 5977 6434 5321 2349 * 5376 178
+ 15 6613 * 0 * * * 10137 1000 0
+
+K 179 3665 * 4182 3378 5250 * 5985 * 3022 3418 6104 * 2964 6127 3864 3820 3902 3953 6375 3815 179
+ 0 * * * * * * 9833 0 0
+
+E 180 4452 * 3507 2425 * 4227 5076 4295 2876 3875 * 4109 6034 3998 3917 3678 5977 5139 * 5844 180
+ 0 * * * * * * 9710 0 0
+
+E 181 4671 * 5597 4837 4973 5501 4800 4866 3445 3690 * 3240 3581 4765 2338 3013 4592 * 5478 * 181
+ 0 * * * * * * 9198 0 0
+
+Q 182 4442 * 5448 3174 5278 5553 4055 * 3224 * * 3765 3328 2380 2950 * 3516 5385 * * 182
+ 0 * * * * * * 8957 0 0
+
+L 183 * * * * * 4341 * 3546 * 853 4297 * * * 2773 * * 4329 * 3951 183
+ 0 * * 0 * * * 7139 0 0
+
+//
+�HHsearch 1.5
+NAME cbc92a8a85651bd2fb2a8622778ceaf5
+FAM
+FILE cbc92a8a85651bd2fb2a8622778ceaf5
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:36:36 2013
+LENG 208 match states, 208 columns in multiple alignment
+FILT 128 out of 1149 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCHHHHH
+HHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHCC
+CCCCCCCC
+>ss_conf PSIPRED confidence values
+9999997655688871599999798988868999999999999995667899858999997794469865777678999999998754379984229999
+9999999862257789971999994799876503659999999998799899999488259999999982789981899599999999999999997166
+99999988
+>Consensus
+xxxxxpxxxxxcxxxxDivfllDxSxSmxxxxxxxxxxxxxxxxxxxxxxxxxxrvxvvxfsxxxxxxxxlxxxxxxxxxxxxixxlxxxggxxtxxxxa
+lxxxxxxxxxxxxrxxxxxxiiliTDGxxxxxxxxxxxxxxxxlxxxgixvxavgxgxxxxxxxLxxiaxxxxxxxxxxxxxxxxLxxxxxxixxxiCxx
+xxxxxxxx
+>cbc92a8a85651bd2fb2a8622778ceaf5
+DISEPPLHDFYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMEQLRISQKWVRVAVVEYHDGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEV
+LKYTLFQIFSKIDRPEASRIALLLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSSVDELEQQRDEIVSYLCDL
+APEAPPPT
+>gi|260837234|ref|XP_002613610.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]gi|229298996|gb|EEN69619.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]
+------------------LYPYGSySGGYPPSNMEKTMG-PGNYRVPLVAGGETITIGSIKKTEETSPseslsaekQAVVAAQDTRECTMSSITiySEER
+LRGT-KKTYSGNGWLPRDP---SWVVDSAGPAWVDSNGVTWED----V-----------VTVDNVQSGDQ--RQVFGGFQ--GKARywKLVITQTYTGWQ
+PYVRE----------------
+>gi|67677889|gb|AAH97100.1| Cfb protein [Danio rerio]
+------------GGKLDIYIAVDASDSIDPKDFDKAKKIIKTLIEKISYYEVSPNYEILMFATDVDQIVKMRDFKTNekArnivKVFEDLDNFNYDKkgd
+RTGTNIAKLYLKILDSMSLEQVQNkedflQTQHVIIVFTDGQAnmggnPKPKVDLIKNLViknNASRENKLDLYVFGVGKDVKKEDMNGLVSEKKdERHF
+FKLPDLDEVQNTFDLMLDdstvvGLCGMQQN-----
+>gi|308473880|ref|XP_003099163.1| CRE-CLEC-65 protein [Caenorhabditis remanei]gi|308267636|gb|EFP11589.1| CRE-CLEC-65 protein [Caenorhabditis remanei]
+------VSDRRCGSdvtrlWLDVVIIVDNCSIMNLNLVYETISGLFNKN--LQIGtgytdPRSTRVGFITYNYNATDVADFYKLQSWADLDSQIQRLKMT
+PlarTTLSKMDTALYAA-INMINstAGFRDNYKKMVIVFTSVHgSYQ--KNPPKDVSKILKARGIPVVTVNTGSSSDTqSYLKNIA---SDNMAYAMADG
+NATQEILKAMTDT------------
+>gi|254410148|ref|ZP_05023928.1| Vault protein inter-alpha-trypsin [Microcoleus chthonoplastes PCC 7420]gi|196183184|gb|EDX78168.1| Vault protein inter-alpha-trypsin [Microcoleus chthonoplastes PCC 7420]
+---IPAlDYRPDQIFPKDVVFLMDTSGSQQGAPLHKCQELMRRFIQGLN---PDDTFTILDFSNAVRHLSQTPLANTPENRELAINYINQLHaSGATEML
+SGIRAA----INVPAPEGRLRSVVLLSDGYIGNEN-RILAEVQQELKPGNR-LYSFGAGSSVNRFLLNRIAEIGR-GICRIIRHDEPTEKVVENFFRSI-
+----------
+>gi|224012469|ref|XP_002294887.1| predicted protein [Thalassiosira pseudonana CCMP1335]gi|220969326|gb|EED87667.1| predicted protein [Thalassiosira pseudonana CCMP1335]
+------------------------------NNFRDMVEFAKSMITSLAALQSNQSYSVVQFATNATLVSLLTSS---IETLEVMDKMAYSGGLT-NHAAA
+I-SACQETLAQSPTGDRKNLLLLITDGDPSLpelAAKEAASQAAAEAKEAGTLIISVMISSLFKPATLDYMREISSHGAVFNVSGFQDLASLQQSLLEEV
+-----------
+>gi|254776136|ref|ZP_05217652.1| chelatase [Mycobacterium avium subsp. avium ATCC 25291]
+-----------------VIFVVDASGSMAaRDRdgggqrcHAVAAARRLSAPRQG----RRDHVPATAGAAA-VAAHLLGAHRRAAAGPLRHRRQD-AAG
+RR-AAGR----ARADRPGEGPRpGAPRP-----RGGAHrrpghrrpgsvGPQPDRRGPAGRRGRGRGGGGLRNV--------------------------
+----------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+D 1 * * 0 * * * * * * * * * * * * * * * * * 1
+ 0 * * * * * * 2329 0 0
+
+I 2 * * 3141 2992 * * * 1942 * 3016 1983 * * * * * * 3011 * * 2
+ 190 3016 * 3807 107 * * 4427 1000 0
+
+S 3 * * 3820 * * * * * * * 3795 * 756 * 3775 3918 * 3983 * 3999 3
+ 0 * * * * * * 5927 0 0
+
+E 4 * * 3124 1440 * * * * * * * * 1625 * 3862 4027 * 3999 * * 4
+ 0 * * * * * * 6131 0 0
+
+P 5 * * * 4243 4125 * * * * 3468 * * 948 3212 4117 4075 4150 * * * 5
+ 0 * * * * * * 6412 0 0
+
+P 6 * * 4421 * * * 4423 * 4423 4387 * * 404 * * 4143 * * * * 6
+ 72 4352 * 0 * * * 6816 1024 0
+
+L 7 3816 2273 * * * * * 3515 4582 3019 * * * * 3649 4636 2967 2491 4513 * 7
+ 0 * * * * * * 7026 0 0
+
+H 8 4636 4476 4652 * 2785 * 2639 4608 4897 4808 * 3805 * 4912 * 3003 4947 3059 * 3696 8
+ 228 2775 * 3347 149 * * 7255 1582 0
+
+D 9 3980 4277 2474 * * 4978 5006 4998 3079 * * 4006 5029 5206 5468 2243 5070 3656 * 5075 9
+ 39 * 5232 * * * * 7597 0 0
+
+F 10 3287 5160 4352 3518 4177 * * 5127 * 2327 * 5133 2842 3505 3961 4208 * 4319 * 5286 10
+ 38 * 5257 * * * 0 7733 0 1000
+
+Y 11 3719 * 5397 * 3793 4318 * 3881 4387 2850 * 3870 3326 3887 3392 4348 4385 * * 3384 11
+ 0 * * * * 1042 959 8066 0 1142
+
+C 12 5603 711 * 5786 * 5624 * * 4617 * * 4617 4543 3675 4440 4077 * * * 5496 12
+ 26 5786 * 0 * 0 * 8376 1000 1000
+
+S 13 5140 * 3866 3478 4788 5717 6113 6233 3372 6116 * 4479 4196 3916 4064 2180 3229 4366 * 5783 13
+ 275 2525 * 806 1224 0 * 8669 2474 1000
+
+R 14 3417 6360 6623 3293 6409 3363 * 5149 3237 4828 6206 3539 4051 3920 3885 3638 5405 3411 * 6377 14
+ 91 4360 6346 1702 530 * * 8978 1464 0
+
+L 15 3691 * 4573 5098 5088 4096 6765 6722 3136 6762 6295 4525 2073 4548 4390 3698 5575 4656 4447 4208 15
+ 15 6604 * 2000 415 0 * 9224 1000 1005
+
+L 16 2609 * * * 5641 6475 * 3259 5115 2364 3456 6849 5627 4248 4655 5910 5121 2432 * 4867 16
+ 0 * * * * * * 9334 0 0
+
+D 17 5019 * 605 3815 * * 4589 * 6691 * * 3655 5961 6876 5186 6017 6365 5045 * * 17
+ 15 6564 * 1000 1000 * * 9419 1019 0
+
+L 18 6672 * * 7015 4981 * 6801 1696 * 2190 4123 * * * * 7417 4643 1800 7081 5934 18
+ 0 * * * * * * 9575 0 0
+
+V 19 2977 4552 * * 5244 4863 * 3002 * 3413 4683 * * 6661 * 4980 5423 1361 * 4109 19
+ 0 * * * * * * 9667 0 0
+
+F 20 6677 * * * 1239 * * 2290 * 2127 7058 * * * * * 6696 3780 * 4536 20
+ 0 * * * * * * 9667 0 0
+
+L 21 3198 5245 * * 5884 6065 * 2913 * 1368 5375 6710 5978 * * * * 1927 * * 21
+ 8 * 7447 * * * * 9667 0 0
+
+L 22 7081 4340 * * 4463 * * 1859 * 1526 4537 6853 * * * * * 2403 * 4868 22
+ 0 * * * * * 0 9665 0 1000
+
+D 23 * * 224 4224 * 5976 5212 * * * * 6533 6549 * * 5279 * * * * 23
+ 16 * 6533 * * * 0 9665 0 1000
+
+G 24 3045 6805 4904 4691 6896 3087 * 4940 5997 6010 5189 3589 * 5928 4408 2452 3035 2952 * * 24
+ 23 5953 * 0 * 766 1280 9643 1143 1181
+
+S 25 6761 6696 * * * * 6549 * * * * * * * * 143 4204 6533 * * 25
+ 11 * 7027 * * * 0 9665 0 1000
+
+S 26 4111 * 3116 3566 * 1421 6756 6316 * 5991 6663 4477 * 5466 4273 2728 4773 * * 6096 26
+ 35 * 5363 * * * 0 9660 0 1127
+
+R 27 4616 * 4630 * 5905 4233 6830 6600 5191 6732 5894 5319 6676 * 4361 624 4791 6979 * * 27
+ 25 * 5888 * * 1272 771 9606 0 1604
+
+L 28 6645 * 5352 * * 6667 * 2411 6758 3784 1292 * * 5744 * 6008 6454 2265 * 5383 28
+ 60 4912 7065 3145 173 1538 609 9609 1572 1617
+
+S 29 3696 6801 3770 4997 6994 2332 5591 6652 4047 6674 * 4463 4823 4897 3715 2233 3764 5822 * 7080 29
+ 238 4052 3447 922 1082 2169 363 9607 1926 1500
+
+E 30 3308 * 3761 3204 6900 2590 5010 5889 5388 4712 5821 3868 3196 3494 4636 3948 5841 6873 6852 6846 30
+ 87 4464 6237 3157 172 410 2016 9536 1706 2795
+
+A 31 3281 * 3560 2968 6708 3711 5363 5984 4343 4774 5890 4133 5958 4426 4646 2685 4079 4215 * 5173 31
+ 43 5893 6303 3272 158 875 1137 9656 1153 1601
+
+E 32 4108 * 3001 3152 4724 3463 5158 6147 3533 5259 6015 2918 4971 4505 3979 4176 4356 6682 * 5608 32
+ 91 4030 * 2375 309 1690 535 9587 1938 1533
+
+F 33 7199 * * * 1638 5399 6462 3830 7312 2466 4187 * 6001 5280 4888 5977 5852 4160 3199 4289 33
+ 25 5847 * 2098 384 1406 684 9627 1306 1323
+
+E 34 4314 * 3310 2298 6950 4139 7047 5366 3774 4532 7009 4709 4650 3206 3289 4584 4314 5692 * 5334 34
+ 11 7101 * 0 * * 0 9649 1000 1144
+
+V 35 3591 * 4951 3632 7049 5815 4011 3816 2557 3126 4476 7400 6462 4041 3878 4641 4722 4314 * 4575 35
+ 54 5005 7400 2388 306 0 * 9649 1686 1144
+
+L 36 2523 6919 * 4318 6136 5700 5629 3157 6984 2908 3052 * * 4321 * 4236 4038 2620 * 6210 36
+ 39 6330 6158 0 * * 0 9665 1159 1000
+
+K 37 4631 * 5131 6744 * * * 3470 1654 3430 4979 4161 * 4117 2807 4617 5757 4108 * 6000 37
+ 11 * 7056 * * 612 1532 9662 0 1245
+
+A 38 3269 * 2570 3509 6011 4201 6971 5340 3402 6642 6344 3967 5357 3963 4266 3784 2997 * * 5762 38
+ 23 * 5972 * * 1038 963 9661 0 1115
+
+F 39 2720 5803 6498 5042 1423 4793 * 4842 5478 3667 6769 5676 6846 7082 6434 4414 5734 4028 5773 4571 39
+ 38 * 5258 * * 550 1658 9579 0 1281
+
+V 40 2394 5437 * * 5897 7019 * 2233 * 2315 4417 * 5879 * 6333 * 3668 2368 * * 40
+ 0 * * * * 799 1234 9589 0 1511
+
+V 41 3140 * 5346 3457 5203 4864 6943 6000 2466 3361 5413 4635 5465 4546 3329 3669 5311 3737 * * 41
+ 0 * * * * * 0 9656 0 1131
+
+D 42 3364 * 2984 3900 6868 5407 4912 * 3252 4872 5589 2693 * 3044 4054 3334 5278 7019 * 6003 42
+ 0 * * 2577 265 1047 954 9656 1131 1131
+
+M 43 3456 * * * 2706 6990 * 2383 6688 1825 4136 * * * * 4860 5878 2838 * 5974 43
+ 0 * * * * * 0 9658 0 1000
+
+M 44 4171 * * * 4375 4341 6550 2304 7208 2252 4240 5752 6478 6631 5974 4713 4518 2233 * 6172 44
+ 50 5355 6688 0 * * 0 9658 1269 1000
+
+E 45 4497 6878 2567 2834 * 4758 6961 4944 3350 5129 * 3620 5748 3723 3266 3711 4010 5964 * * 45
+ 55 5639 5822 0 * * 0 9645 1197 1163
+
+Q 46 4503 5925 4400 4121 6472 4781 4234 4526 3629 4159 5497 4303 4187 2938 4285 2768 3994 * * 4855 46
+ 55 * 4744 * * 1096 910 9577 0 1519
+
+L 47 6662 6607 * 6930 2124 5587 * 3323 5018 1525 4884 5926 * * * 5034 5008 3528 * 4481 47
+ 56 6941 5054 0 * * 0 9589 1000 1873
+
+R 48 3415 * 3427 4018 * 3613 7013 * 3627 5304 5969 3297 4052 4221 4115 3460 3448 4145 * 5184 48
+ 482 3986 2178 162 3239 2470 287 9589 1929 2362
+
+I 49 5038 * 5008 5528 4061 5533 6101 1983 5970 2498 4469 5540 4747 5641 * 3916 4400 3340 * 4695 49
+ 50 5452 6521 1840 473 3394 144 9185 1132 5149
+
+S 50 3910 * 4033 5249 6190 2110 6397 5443 5073 * * 4315 5202 3993 3540 2556 3696 4987 * 5000 50
+ 432 2318 4099 1610 572 2192 356 9206 3430 4929
+
+Q 51 4444 * 3779 3902 5604 3368 6917 * 3464 4981 * 3308 2646 3844 4296 3659 4339 4147 * * 51
+ 76 4276 * 1637 560 578 1599 9383 1553 4732
+
+K 52 4078 * 2700 3870 6997 3908 4738 6871 3443 4996 * 3172 4817 3781 4777 3750 3864 4874 * 4569 52
+ 41 6883 5655 1188 833 661 1444 9642 1153 2360
+
+W 53 4057 * 2907 4659 5320 2971 4750 6716 4615 4903 5657 3166 7085 3959 3422 4310 3518 4929 7090 5679 53
+ 39 5239 * 1533 612 682 1409 9687 1307 1742
+
+V 54 3254 * 2894 5174 5927 5081 6769 3625 * 5651 5391 6956 6893 5602 5389 3496 2163 2538 6970 * 54
+ 0 * * * * 855 1161 9694 0 1190
+
+R 55 6630 * 4876 5460 5911 6006 3554 * 3274 6765 7032 4006 * 3125 1285 4754 4697 * * 4929 55
+ 12 6970 * 1585 585 * 0 9724 1000 1000
+
+V 56 3894 * * * 3134 6185 * 2295 * 3322 4975 * * * * 5923 7471 1383 * 3965 56
+ 47 5319 7223 1757 506 962 1039 9715 1282 1145
+
+A 57 1853 4960 * 6779 5836 1475 * 6078 * 6661 5952 4593 6495 7007 * 2617 4981 * * 6823 57
+ 0 * * 2000 415 1146 868 9718 1000 1168
+
+V 58 3337 * * * 3933 6715 * 2231 * 2027 4126 6884 * * * 5969 7114 1895 * 6665 58
+ 24 5946 * 1924 441 0 * 9728 1137 1021
+
+V 59 3418 5931 6998 * 4915 5102 * 2423 * 2548 5059 * * 5198 7040 4743 4573 1818 6659 5332 59
+ 0 * * * * * * 9736 0 0
+
+E 60 3571 * 7032 4595 5312 4757 4671 4172 3474 3808 7105 4927 6989 3163 4638 3367 2282 4773 * 6714 60
+ 0 * * * * * * 9736 0 0
+
+Y 61 6141 * 6663 6869 1266 5147 * 6030 5976 5251 6744 6811 * * * * * 5041 5780 1326 61
+ 27 * 5748 * * * * 9736 0 0
+
+H 62 3097 * 3692 * * 2232 5496 6654 4924 6853 * 3677 * * 5691 1542 3840 * 6867 * 62
+ 14 6688 * 0 * * 0 9711 1020 1177
+
+D 63 4421 6060 2415 3604 5344 3150 4633 * * * * 3694 6853 5942 6024 2041 3251 * 6901 5867 63
+ 37 6636 6016 2585 263 862 1153 9711 1058 1177
+
+G 64 4762 * 3739 3140 5003 4647 4306 6018 3565 5358 * 4049 7187 4744 3573 2579 3040 * 5239 5334 64
+ 111 4909 4608 3196 167 * 0 9711 1462 1279
+
+S 65 2294 * 6740 6689 * 4376 6850 4345 * 5069 6578 4590 3008 6811 * 2961 3259 2414 * 4816 65
+ 98 3923 * 2031 405 585 1585 9582 2212 2032
+
+H 66 4598 6708 4306 2946 5710 * 3966 4572 3390 6042 * 4050 * 3489 3147 3875 3382 4184 6846 4540 66
+ 15 6591 * 1585 585 524 1715 9725 1010 1255
+
+A 67 3800 * 4936 2883 4972 7004 6151 3544 5283 3789 5947 5826 3792 6055 5357 4962 3222 2351 4901 6899 67
+ 37 5303 * 2532 274 * 0 9742 1317 1000
+
+Y 68 3928 6948 6024 3080 4846 5017 4519 3021 4610 3670 7143 4425 5812 4083 4883 4886 4988 2588 6003 5106 68
+ 76 4734 6177 2163 365 * 0 9756 1571 1000
+
+I 69 3464 5626 * * 2050 5066 5728 3427 * 2642 5348 6909 7033 5002 4864 3540 5967 3338 5893 5501 69
+ 0 * * * * * 0 9758 0 1240
+
+G 70 4258 6953 2734 5209 7232 3410 4733 5833 3822 5224 * 4108 2093 5284 4635 3930 4407 4718 * * 70
+ 12 6950 * 1000 1000 * 0 9758 1000 1240
+
+L 71 6741 5895 * 6795 2218 6989 * 5616 6749 1233 5732 5850 4380 6879 * 4409 4617 4636 6125 4270 71
+ 38 5912 6749 1958 429 0 * 9758 1157 1240
+
+K 72 4405 * 3604 4945 * 3274 6010 5229 4635 7071 7124 2708 4940 5301 4427 3059 2422 4448 * 5166 72
+ 36 * 5332 * * * 0 9741 0 1076
+
+D 73 3285 * 2331 3706 5454 4748 6078 * 3763 4865 * 4100 3967 3759 3875 4377 3540 6879 5878 6017 73
+ 163 3519 5671 554 1650 * 0 9702 2539 1602
+
+R 74 4118 * 4655 4557 2833 4297 5854 3708 * 4189 6827 4614 4803 5004 7136 3628 3514 3670 6001 2899 74
+ 170 5378 3526 1696 533 1047 955 9665 1368 1920
+
+K 75 4244 5649 3709 4441 4581 4747 5453 6673 2933 * 6984 2897 5190 4764 3824 3219 4047 5515 * 3389 75
+ 58 5862 5501 890 1120 2591 262 9611 1153 2848
+
+R 76 5909 * 2593 4640 * 5433 6629 * 4757 6104 * 2354 6773 4669 4467 1941 3010 * * 5727 76
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+
+//
+�HHsearch 1.5
+NAME cbf4a79de0130a2230da880af29a77c4
+FAM
+FILE cbf4a79de0130a2230da880af29a77c4
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 14:26:52 2013
+LENG 195 match states, 195 columns in multiple alignment
+FILT 115 out of 1145 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.9
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHH
+HHHHHHCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9977677888873699999798888866999999999999986266896899999889227987677767899999999835267999639999999999
+98655415778986199999279978981669999999987899899999688433424899999998287985499759999999999999729
+>Consensus
+xxxxxxxxxxxxxdivxllDxSxSmxxxxxxxxkxxxxxxxxxlxxxxxxvxvvxfxxxxxxxxxlxxxxxxxxxxxxixxlxxxxgxtxxxxalxxaxx
+xxxxxxxxxrxxxxxxivliTDGxxxxxxxxxxxxxxxxxxxxixvxxvxxgxxxxxxxxxxxlxxiaxxxxxxxxxxxxxxxxlxxxxxxixxx
+>cbf4a79de0130a2230da880af29a77c4
+GSEALRGSPQEDSDIAFLIDGSGSIIPHDFRRMKEFVSTVMEQLKKSKTLFSLMQYSEEFRIHFTFKEFQNNPNPRSLVKPITQLLGRTHTATGIRKVVR
+ELFNITNGARKNAFKILVVITDGEKFGDPLGYEDVIPEADREGVIRYVIGVGDAFRSEKSRQELNTIASKPPRDHVFQVNNFEALKTIQNQLREK
+>gi|260837234|ref|XP_002613610.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]gi|229298996|gb|EEN69619.1| hypothetical protein BRAFLDRAFT_127098 [Branchiostoma floridae]
+---------------LYPYGSySGGYPPSNMEKTMG-PGNYRVPLVagGETITIGSIKKTEETSPseslsaekQAVVAAQDTRECTMSSITiySEERLRG
+TKKTYSGNGWLPRDPSWV-----VDSAGPAWVDSNGVTWEDV--------------VTVDNVQSGDQ------RQVFGGFQGKARYWKLVITQTYTGWQP
+YVRE----
+>gi|75055238|sp|Q5RER0.1|ITIH5_PONAB RecName: Full=Inter-alpha-trypsin inhibitor heavy chain H5; Short=ITI heavy chain H5; Short=ITI-HC5; Short=Inter-alpha-inhibitor heavy chain 5; Flags: Precursorgi|55725936|emb|CAH89747.1| hypothetical protein [Pongo abelii]
+---APKDLPPLPKNVVFVLDSSASMVG---TKLRQTKDALFTILHdlRPQDHFSIIGFSNRIKVWKDHF-DISHSRQHQGwqsvhSPYVAH---wrhrhQ
+RGLAEGHQAPQQVRGPQWHW---RPERVPHCLPDG--weahGrgdAHPQDPQQHPRGRPRPSLHLH-IGIGNDV----DFRLLEKLS-------------
+--------------
+>gi|320105837|ref|YP_004181427.1| VWFA-like domain-containing protein [Terriglobus saanensis SP1PR4]gi|319924358|gb|ADV81433.1| VWFA-related domain-containing protein [Terriglobus saanensis SP1PR4]
+---------RQPVSILVVMQTGGAGQ-RQFEYYRN-VPTLLDAMGgSAKHETAVMTFDSAPEDLFPFVSNPA--RLKQAFTHPHAGDHGAAVLDAVNYAI
+DLFKGKPAGTR----RIILLLSQPQDHGSKVHAEEVVRRLGENNITIFSVSFSPE------KTWLKD-----------------------------
+>gi|94967802|ref|YP_589850.1| hypothetical protein Acid345_0771 [Candidatus Koribacter versatilis Ellin345]gi|94549852|gb|ABF39776.1| hypothetical protein Acid345_0771 [Candidatus Koribacter versatilis Ellin345]
+---TVQSGSELPLRLGVLVDTSTKAHGDAYAAALHAISNFVQGAMlEQNVRVFFVPFANKT----DMSAFMSKDDLAHYQLKIS-KGDGAALYDAIVGAC
+KERMAVE--ETHPARRVLVVISNGEDNQSRFTYQQAIAAAQSAGVVIFTVNTGSGGSGDHGEVRLREFSDQTGGI-IFPGSNPGTISRPFEAISDQ
+>gi|163792343|ref|ZP_02186320.1| hypothetical protein BAL199_15888 [alpha proteobacterium BAL199]gi|159182048|gb|EDP66557.1| hypothetical protein BAL199_15888 [alpha proteobacterium BAL199]
+-----------DLELVLAVDSSASVDYSEFSLQLEGLALAFRDPElaatisagiHGVIAVTLMEWSSIGRQEvalpwTRIATTADASAFADAIDRSpRQL
+QtGATSISSAIEFANGLFAGN---GFEGVRRVIDLSGDGYNNQGE-PLDITRADVLATGTTINALAIENQVLGLTEYFEQQLIGG--VAAFAMRATDYRD
+Y----------
+>gi|84386024|ref|ZP_00989054.1| transporter [Vibrio splendidus 12B01]gi|84379340|gb|EAP96193.1| transporter [Vibrio splendidus 12B01]
+GPTwQQQPSPffEDNSELVIALDVSDSMNKTDIqpSRLERAKQKINQLVElRGDAKTGLVIYGGSAHVAMPVTKDKELtRYFLDVLDGSLLPDNESKPAS
+VLKPT-LELISQAK-----APSTVLILTDKTNDEAIEEFTKAF-EQQQHQVIVWAMGENpqsGGNGTAGltetQLASLSQLAQAGHGNMVSFTHDASDVE
+AVYQSIQNN
+>gi|242278087|ref|YP_002990216.1| OmpA/MotB domain protein [Desulfovibrio salexigens DSM 2638]gi|242120981|gb|ACS78677.1| OmpA/MotB domain protein [Desulfovibrio salexigens DSM 2638]
+---AESRIVlkPKVDAFAYFVDTSPSMsqtydstGNPKIIAGLNALKRLNNVVPELGYDSALYAMP--DFATYSPKSMFTRAAMAKGIASVPSdlpfF-Q
+STPIGTGFSDL-NGVVKNWGG-----KFAVIFVSDGLTNsgRNPALVVSDMAKTYGDRFCLHIISVADTA---RGKANLKRLAS----------------
+----------
+>gi|238924634|ref|YP_002938150.1| hypothetical protein EUBREC_2277 [Eubacterium rectale ATCC 33656]gi|238876309|gb|ACR76016.1| Hypothetical protein EUBREC_2277 [Eubacterium rectale ATCC 33656]
+----EVETPGFSVD--ILMDASSSRKQMQ-QKIAAQAYVLSKSLTNCGIPVQIYSYCSirGYTVMHIFKEYDDYGVEDELFH--FVAAGNNRDGLALRAA
+SHLM------ELsPKPKKLLFMFSDASPQDDQIagegafykdreytdalavkDTVNEVQRLKNHGIDVIGIFMGSAH----DSELATKIFG----RSLVK
+IKSINEFADAVGRVLNE
+>gi|307720601|ref|YP_003891741.1| hypothetical protein Saut_0680 [Sulfurimonas autotrophica DSM 16294]gi|306978694|gb|ADN08729.1| protein of unknown function DUF58 [Sulfurimonas autotrophica DSM 16294]
+----------RELNVVIASMLNGSVYFGSKRFKQDVIAEITAMLSfstiKNGDLLSSYIFSDKMESFLKPSKKLFSvHKSTDEILNFDPLNKKADYKVLA
+DTLF---------KRLKRKSLIVIVGDFF---EIPDFKVl------AKKHEVVAVIVRDR-------LEET-----------------------------
+-
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 3106 * * * * 825 * * * * * * * * 3272 * 3327 3102 * * 1
+ 0 * * * * * * 4733 0 0
+
+S 2 * * * * * * * * 3153 * 4138 4085 755 * * 3118 3963 * * * 2
+ 0 * * * * * * 6604 0 0
+
+E 3 3483 * * 2860 * 3510 * 4536 4420 * * * 1516 * * 3334 4213 4435 4429 * 3
+ 80 4213 * 0 * * * 7121 1074 0
+
+A 4 2659 4860 * 4938 * 3545 4741 4948 4009 3907 * * * 3875 4861 2510 2463 * * 5018 4
+ 0 * * * * * * 7949 0 0
+
+L 5 4201 5306 5521 3951 4534 * 5254 4380 5440 3734 * 4291 4215 3277 * 3797 4277 1931 5353 * 5
+ 39 5221 * 1000 1000 * * 8435 1031 0
+
+R 6 4414 * 4034 4586 * * * * 3057 * * 4574 2965 2523 3158 3279 4247 3075 * * 6
+ 68 4441 * 1329 732 * * 8640 1260 0
+
+G 7 4262 * 4488 2457 * 2872 5657 5722 3496 4778 5972 4176 4218 4303 4763 3226 4762 5791 5924 5059 7
+ 0 * * * * * * 8870 0 0
+
+S 8 5022 1065 * 5836 4858 4798 * 4863 * 4275 4165 4882 4866 5742 5747 3839 4869 4271 * * 8
+ 350 6016 2322 1000 1000 * * 9000 1000 0
+
+P 9 5599 * 3649 3480 4790 5480 * * 4078 4026 * 5777 1873 3802 * 3304 3505 3668 * * 9
+ 375 2126 * 820 1205 643 1476 8767 2865 2886
+
+Q 10 3888 * 6012 2827 * 4158 6139 * 3705 4441 4508 4067 4359 3688 3170 2565 4081 6164 * * 10
+ 141 3429 * 926 1078 357 2189 9239 1996 1607
+
+E 11 3461 6131 5224 3668 4787 2220 * 5487 3199 3640 6103 6254 4727 3546 4250 4986 4694 4225 * * 11
+ 18 6368 * 0 * 0 * 9670 1000 1000
+
+D 12 3656 * 3569 4427 6475 3418 6467 * 4516 3923 * 3966 2474 4473 5104 3706 3561 5521 5381 4683 12
+ 13 6750 * 2000 415 * * 9801 1000 0
+
+S 13 2599 * 6459 * 3720 5464 6334 3318 4225 2790 3547 6206 6205 * 4222 4544 3551 3536 * 4895 13
+ 0 * * * * * * 9859 0 0
+
+D 14 4618 * 971 3774 6708 6905 4570 * * 6904 * 3454 5470 4993 3932 5053 4127 6725 * * 14
+ 27 * 5733 * * * * 9944 0 0
+
+I 15 5604 6612 * 6587 4203 * 6765 1786 * 2136 4562 * * * 6573 * 5104 1858 * 5639 15
+ 0 * * * * * 0 10087 0 1201
+
+A 16 3100 6042 * * 4999 5225 * 3036 * 2997 4129 * * * 6861 5310 4237 1642 6638 3496 16
+ 14 6681 * 2322 322 0 * 10199 1028 1201
+
+F 17 6677 * * * 1567 * * 2456 * 1757 6988 * * * * 6158 6485 3365 6622 4863 17
+ 14 6678 * 0 * * * 10269 1008 0
+
+L 18 3728 4733 * * 6779 * * 2989 * 1184 5639 6867 6028 * * 6146 6565 2040 * * 18
+ 0 * * 0 * 0 * 10241 1008 1008
+
+I 19 5279 * * * 5005 6577 * 2141 * 1380 4244 * 6749 * * 6415 * 2253 6158 5379 19
+ 0 * * * * * * 10269 0 0
+
+D 20 6710 * 259 5095 * 6059 5234 * * * 6415 5878 * 5208 * 6151 6158 * * * 20
+ 0 * * * * * * 10269 0 0
+
+G 21 3348 5249 4761 3654 4788 3367 * 4104 4804 5511 6798 6709 * 5136 4619 3058 2653 3068 * 5366 21
+ 34 6059 6882 0 * * * 10269 1147 0
+
+S 22 5397 6875 6678 * * 6722 * * * * * 5625 * * * 278 3276 * * * 22
+ 0 * * * * 0 * 10262 0 1001
+
+G 23 3256 * 4297 4020 6945 1475 * 6785 5190 6000 * 5645 6695 5802 3691 2941 3992 5106 * 5977 23
+ 25 * 5839 * * * * 10269 0 0
+
+S 24 4024 6783 4790 * * 4868 6766 6689 5333 5770 6789 6775 6151 6870 5577 619 4138 6566 * 5880 24
+ 27 6774 6769 0 * 978 1023 10239 1185 1183
+
+I 25 4218 6151 * 6730 * 6716 6777 3027 * 3639 1087 5708 * * 5879 5280 4521 3187 * 6038 25
+ 67 4790 6779 3271 158 * 0 10242 1568 1210
+
+I 26 3383 * 3708 4288 * 2980 6690 5815 3784 4013 * 5255 5356 3514 3779 2806 4430 4377 * 4668 26
+ 231 6530 2866 2000 415 * 0 10243 1015 1409
+
+P 27 3563 * 3730 2990 5263 2320 6674 5661 5001 4473 6466 5088 3001 3955 * 3679 5574 5080 6376 6475 27
+ 62 6932 4881 2322 322 253 2637 10038 1000 3865
+
+H 28 3287 * 3680 3273 * 3567 5167 * 3807 5481 5277 3322 5689 3569 4319 3461 4337 4473 * 4470 28
+ 111 3756 * 1440 663 1748 510 10186 2469 1943
+
+D 29 4338 * 2509 3276 6685 3908 6742 6906 4468 4160 6563 3159 4692 3924 3456 3863 4936 6754 * 4397 29
+ 197 4214 3758 2444 293 2187 358 10206 1866 1617
+
+F 30 6629 * * 5074 2340 7055 6736 2962 6308 2608 4139 * 5006 * 4885 5124 5738 4542 2643 3864 30
+ 87 4097 * 1905 448 0 * 10093 1976 2814
+
+R 31 3785 * 2795 2707 * 4550 * 5355 3714 4525 5931 4446 4854 3716 3879 3612 3546 7023 * 5184 31
+ 36 5886 6994 1345 722 * * 10292 1195 0
+
+R 32 2711 6797 3616 5363 6436 4727 5266 4969 3005 3714 5092 5796 6895 3619 2984 4404 5086 4973 6737 4537 32
+ 25 5891 * 3715 114 * 0 10281 1222 1000
+
+M 33 2261 * * 4470 6878 6737 5842 3350 4055 3061 3394 6894 * 4785 6940 5234 3532 2774 * 5280 33
+ 14 * 6740 * * * 0 10281 0 1000
+
+K 34 4275 * 5152 6095 6583 6708 6627 3605 1517 4373 5530 5835 * 3714 2641 5202 4484 5109 6683 6761 34
+ 29 6609 6713 2000 415 0 * 10276 1001 1206
+
+E 35 2815 * 2557 3724 6624 3797 5140 6848 3824 4745 * 3674 5906 3358 3785 3943 4845 6515 6718 * 35
+ 81 * 4188 * * * 0 10271 0 1006
+
+F 36 1985 6722 5672 5635 2463 5602 * 5105 5578 3254 5813 6720 6820 5833 4994 5184 3771 3558 4871 4775 36
+ 12 6925 * 2322 322 206 2909 10103 1000 2101
+
+V 37 2542 6980 * * 4745 7147 * 2684 5503 2129 4495 6754 6080 * 5764 5859 4539 2602 6164 4507 37
+ 0 * * * * * 0 10275 0 1000
+
+S 38 3109 6943 3565 3751 4730 5365 6960 4396 3087 3785 5268 4591 5010 3490 3804 4245 5105 4933 6701 5254 38
+ 15 6567 * 0 * * 0 10275 1027 1000
+
+T 39 3226 * 3486 3294 5895 3764 6877 5804 3436 4416 5336 3250 6860 3722 4592 3830 3867 4938 * 5743 39
+ 0 * * * * * 0 10275 0 1000
+
+V 40 3521 * * * 2856 6730 * 2500 6399 1721 3691 6567 * * 6164 * 4890 3126 * 5429 40
+ 0 * * * * 0 * 10275 0 1000
+
+M 41 2843 * * 6768 4350 * * 2766 * 2404 4358 5852 * 7273 5359 3884 3577 2331 * 5697 41
+ 10 7222 * 0 * * * 10292 1000 0
+
+E 42 3916 * 3131 2851 6775 4570 * 6838 2794 4444 6897 4485 5664 3937 3340 3494 4371 4131 * * 42
+ 21 * 6115 * * * * 10292 0 0
+
+Q 43 3135 * 4510 4850 6728 3630 5317 5067 2996 3931 6432 6605 5499 3218 3152 2909 5337 4911 * 5922 43
+ 79 4902 5676 1805 487 * 0 10280 1543 1158
+
+L 44 4096 6720 * 6968 2268 * * 3845 * 1240 3861 * * 6743 6756 4539 6898 5112 * 4166 44
+ 38 * 5278 * * * 0 10268 0 1566
+
+K 45 3736 5548 3193 4284 5776 3326 4804 6701 3992 5097 5225 4062 4246 3623 4812 3484 3980 4271 7039 5701 45
+ 2354 444 3846 1874 460 439 1931 10244 8805 2098
+
+K 46 4115 5649 3836 3284 * 3009 5777 5094 4060 4227 5776 3932 2727 4469 3241 4371 5616 6615 * * 46
+ 12 6899 * 1000 1000 0 * 10251 1000 2541
+
+S 47 3668 5922 2786 3492 * 5030 5405 6876 3903 4820 6722 3622 2730 3825 5146 3146 6754 5263 * 5840 47
+ 52 6615 5314 2000 415 * * 10298 1028 0
+
+K 48 4172 * 3276 4959 * 2665 5191 5662 3295 5339 5482 3384 5188 3565 4368 3355 4567 5209 7112 5312 48
+ 14 * 6712 * * * 0 10278 0 1389
+
+T 49 3483 7030 2345 4650 5927 4993 5305 2934 6970 4409 6624 * 5819 * 6726 4021 2742 2930 6586 5862 49
+ 0 * * * * 0 * 10258 0 1582
+
+L 50 4734 * 4437 3972 6042 5247 4003 6776 3591 4233 5746 4117 5223 2921 1933 5363 4640 6529 * 5012 50
+ 0 * * * * * * 10298 0 0
+
+F 51 4134 * * * 3025 * * 2546 * 2869 5224 * * * * 5213 4446 1418 * 4714 51
+ 0 * * * * * * 10298 0 0
+
+S 52 1907 5898 6410 4546 6750 1682 6904 * 6529 * * 4608 5867 5922 * 2665 4023 6855 * 5674 52
+ 14 6712 * 1585 585 * * 10298 1008 0
+
+L 53 4824 6523 * * 3807 6604 * 2306 * 2078 4523 * * * * 4821 5596 1585 * * 53
+ 0 * * * * * 0 10271 0 1008
+
+M 54 4619 6697 * 5618 5115 5836 * 2429 * 3175 4245 5742 * 6693 5431 5010 4485 1809 4594 3648 54
+ 0 * * * * * 0 10271 0 1008
+
+Q 55 4293 * 5850 5013 3760 3117 5718 4200 4678 4120 5907 4917 5724 4608 4450 3248 2247 3831 * * 55
+ 12 * 6949 * * 0 * 10271 0 1008
+
+Y 56 6754 * * * 973 6797 5694 * 6082 4751 * 6844 * * * * * 5254 5643 1531 56
+ 13 6846 * 0 * 0 * 10284 1000 1000
+
+S 57 2859 5922 3711 5932 * 2180 5548 * * 6841 5721 3002 * 6720 5283 1871 4592 * * 6902 57
+ 24 7030 6812 5585 30 * * 10298 1016 0
+
+E 58 4103 * 2525 4138 * 3556 4598 * 5792 7010 5662 3731 5757 4597 4489 2075 3140 * * 6809 58
+ 152 3325 * 2528 275 992 1008 10281 2988 1224
+
+E 59 5841 * 3566 2669 6710 3589 3853 5274 3311 6846 6900 4158 4437 4478 3628 3136 3744 * 5716 * 59
+ 95 4770 5192 1980 422 0 * 10287 1634 1014
+
+F 60 2317 * 5887 5685 5026 4075 6812 4063 4814 4760 6417 5000 3436 6598 * 3394 3354 2769 6692 4764 60
+ 99 4426 5668 1673 543 613 1531 10257 1783 1378
+
+R 61 4626 6892 5356 3120 4758 5191 4262 5078 3362 5846 6740 3529 5779 4061 2702 3989 3884 4338 * 4541 61
+ 14 6665 * 1585 585 * 0 10238 1008 1414
+
+I 62 3882 * 3854 3115 * 5575 6712 3841 5189 3385 5821 5895 3502 4976 5109 5125 3222 2416 6806 6883 62
+ 22 6026 * 3000 193 * 0 10238 1147 1414
+
+H 63 4211 * 4247 3541 4636 5130 5173 4280 5935 2675 4803 7085 4071 4116 5437 5151 5299 2419 5557 4599 63
+ 156 3416 6780 2103 382 1620 568 10238 2741 1414
+
+F 64 3474 7257 * * 2357 6463 5694 3958 5437 3234 4311 * 5265 5313 5957 3812 4723 2677 4775 3958 64
+ 25 5861 * 1727 519 527 1708 10255 1368 1397
+
+T 65 4738 6805 3349 5441 * 4795 4519 4923 3669 4495 5925 3806 2159 6063 4062 3298 4358 5303 5991 5743 65
+ 37 5302 * 2070 392 * 0 10299 1362 1000
+
+F 66 5263 5034 * 6845 2975 5798 6356 4127 5140 1408 4824 * 3967 6749 6669 5215 6810 3654 5234 4192 66
+ 50 4868 * 2129 374 0 * 10299 1518 1000
+
+K 67 3723 * 3547 5798 5522 2984 6900 6776 4713 4792 * 3816 4202 4713 4127 3157 2467 4436 * 5577 67
+ 84 4884 5444 811 1218 * * 10298 1546 0
+
+E 68 3878 * 3144 3843 6623 3793 6855 6884 3548 4878 * 3850 3944 3762 3990 3290 3045 5867 6928 6560 68
+ 43 * 5100 * * 890 1119 10237 0 1278
+
+F 69 4078 * 2811 5281 3098 4495 4822 4003 5006 4078 6851 3954 3617 5319 4989 5177 5757 4628 7009 3086 69
+ 41 5580 7158 2159 366 * 0 10240 1193 1648
+
+Q 70 5785 6809 3714 3984 4890 4616 5703 4592 2740 4679 4553 3960 4173 5308 3970 3583 3384 6682 6574 4087 70
+ 54 5148 6905 763 1283 1287 761 10251 1391 1817
+
+N 71 4171 6985 2718 4138 5053 * 5783 * 4514 5261 5718 2782 6655 5251 4430 2083 3097 6646 * * 71
+ 147 * 3369 * * 357 2190 10283 0 1579
+
+N 72 3977 6529 3574 4035 5790 5761 4302 3459 3220 3632 6781 4805 4008 4404 3732 4469 4378 4157 * 4804 72
+ 404 2700 3472 1279 767 3699 116 10179 3495 2861
+
+P 73 3221 * 3167 3617 * 4588 5380 6429 2948 6481 5487 3974 5089 3656 4251 3269 3783 4665 * 5723 73
+ 25 6754 6949 3807 107 0 * 10054 1013 4083
+
+N 74 3707 6083 3133 2729 5101 4858 * 6787 3542 5359 5190 4136 6585 3462 3582 4293 3912 4128 * 5848 74
+ 12 6901 * 0 * * 0 10292 1005 1000
+
+P 75 3402 6949 6690 6828 3164 5331 6893 3340 5913 1856 4189 5942 7008 5526 5454 6439 4626 2654 * 6930 75
+ 0 * * * * * 0 10292 0 1000
+
+R 76 3197 * 4475 3827 5886 6621 6337 4386 2943 2617 4575 4941 * 4836 3427 4147 4851 3754 * 5182 76
+ 62 4906 6804 2135 373 * 0 10292 1522 1000
+
+S 77 3150 * 2834 3001 6710 4444 5276 6929 3731 5357 7066 3802 * 3265 3872 3009 5114 * 5729 6701 77
+ 0 * * * * * 0 10283 0 1194
+
+L 78 2132 5871 4828 4153 4919 4923 5722 3420 3266 3334 6860 * * 5658 3694 4078 4262 5172 * 4754 78
+ 32 6330 6763 2322 322 0 * 10283 1061 1194
+
+V 79 4103 5382 * * 3667 6966 * 2061 * 1848 4235 * * 5549 6896 5203 5285 2722 6589 5960 79
+ 25 5891 * 1000 1000 * 0 10278 1177 1034
+
+K 80 3857 6887 2631 3580 * 4841 6823 6635 3656 4174 5734 3138 5692 3967 3449 2855 4527 * * * 80
+ 46 6073 5902 1000 1000 * 0 10278 1147 1034
+
+P 81 3274 * 4013 4154 6738 4245 4543 * 3505 5864 5636 3201 4332 3969 3174 3638 4275 5828 * 3932 81
+ 72 5638 5128 2046 400 * 0 10248 1205 1425
+
+I 82 5626 * * 4916 4044 6959 7125 2100 6640 1736 2969 6584 6696 5753 * * 4176 3587 * 5474 82
+ 185 4227 3896 2650 250 0 * 10208 1905 1997
+
+T 83 4268 6721 3683 3197 6711 4796 4160 5524 3292 6570 5723 3498 3240 5749 4183 3578 3569 4876 * 5218 83
+ 184 5906 3280 1000 1000 0 * 10243 1185 2227
+
+Q 84 3895 6787 4074 5718 4444 4669 5467 5818 3815 4420 4397 4038 3364 4419 3238 4050 4202 5186 6710 3441 84
+ 479 2071 4483 2589 262 0 * 10131 4722 2821
+
+L 85 3761 6642 4862 5007 4188 4413 6887 4922 3992 3097 4737 5660 2560 5063 4852 3632 3425 4217 6815 * 85
+ 58 5202 6364 1611 572 417 1996 10186 1395 1800
+
+L 86 4417 6572 3179 4266 6995 1762 6621 * 4891 5186 * 3469 6708 5066 4229 3365 3633 6699 * 4796 86
+ 51 4846 * 1335 728 1060 943 10225 1534 1296
+
+G 87 4341 6520 4878 5200 * 1174 6759 6751 4082 4978 6729 5283 4217 5260 5310 3279 4148 5919 6628 * 87
+ 119 3660 * 670 1429 0 * 10257 2737 1061
+
+R 88 3816 * 4058 4914 6843 1573 6918 6598 4606 5265 5973 3371 4880 4542 4555 3765 4377 7210 5620 5346 88
+ 111 3751 * 770 1273 * * 10298 2379 0
+
+T 89 3304 6820 5964 5191 6831 5809 * 4874 6085 6956 6898 3899 4535 * 4459 2754 1218 5583 * * 89
+ 50 4868 * 1406 683 * * 10298 1574 0
+
+H 90 3578 7152 2651 5229 5250 4108 4702 6843 4913 5976 7039 2212 3727 6653 3323 3458 * * * 4539 90
+ 0 * * * * * * 10298 0 0
+
+T 91 3890 * 5363 * 4559 * * 2148 * 1795 3859 * 5776 * * 5434 3037 4231 6903 4099 91
+ 12 6903 * 4392 70 * * 10298 1000 0
+
+A 92 3517 5007 3988 5368 5344 1753 4789 6918 5623 3891 * 4131 6676 4726 6882 3193 4894 6776 5774 4125 92
+ 0 * * * * * * 10298 0 0
+
+T 93 2698 6615 3418 3124 6876 4837 4832 7039 4167 3771 6814 5903 4641 4350 3448 3618 4077 5174 * 4733 93
+ 0 * * * * * * 10298 0 0
+
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+N 181 * * 1919 3918 6323 3120 5096 * 4471 6487 6340 2370 * * 5544 2792 3561 * * * 181
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+F 182 3063 * 5411 4425 2357 4160 * 3846 5132 4839 4262 6173 3739 6072 * 4144 6432 3456 4461 3927 182
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+E 183 3457 * 1921 3156 * 4718 6633 6302 4769 4425 6223 4617 6266 4538 4336 3225 3360 * 6432 6250 183
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+A 184 2708 * 2637 2115 6231 5055 * 6168 6214 4348 5307 4615 6327 4101 * 3004 4004 6429 * * 184
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+K 186 3686 * 3805 4511 6278 * 6224 5097 3826 3676 * 3889 3347 3384 2720 3211 5273 4624 * 6059 186
+ 19 6261 * 0 * * * 9451 1000 0
+
+T 187 5289 * 2621 3203 * 3621 * * 3834 4923 5982 2927 5496 4160 3735 3070 4179 5076 * 6121 187
+ 0 * * * * * * 9423 0 0
+
+I 188 2934 5986 * * 4898 6113 5980 2346 4974 2419 4395 4470 5928 5978 4047 * 6030 3031 * 4291 188
+ 28 5683 * 0 * * * 9279 1022 0
+
+Q 189 6016 * * * 2087 5878 * 3364 5929 2771 3986 * * 4454 4632 6048 4983 2025 * 5034 189
+ 0 * * * * * * 9172 0 0
+
+N 190 4287 * 3014 3293 * 2892 * * 3105 4938 5987 3227 4966 3932 2730 4277 * * * 5870 190
+ 0 * * * * * * 9130 0 0
+
+Q 191 3446 * 4362 2785 * 4313 4972 * 3205 3842 * 5068 4918 2318 3391 3955 5014 * * * 191
+ 0 * * * * * * 9130 0 0
+
+L 192 * * * * 5548 * * 1149 * 1651 3161 * * * * 5437 5570 4230 * * 192
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+
+R 193 3856 * * 4255 4300 4423 * 3572 3324 2768 4267 4315 * 3723 5513 4240 3855 2959 * * 193
+ 0 * * * * * * 8358 0 0
+
+E 194 4931 * 2423 2328 4889 5163 * * 2952 5138 4813 4041 * 3423 * 3158 4045 * * * 194
+ 0 * * * * * * 7792 0 0
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+K 195 * * * 2869 * * * * 1230 * * 3944 * 2705 3185 * 4184 4221 * * 195
+ 0 * * 0 * * * 6715 0 0
+
+//
+�HHsearch 1.5
+NAME cd06863eb01c4bcc5ae9b1817480cf17
+FAM
+FILE cd06863eb01c4bcc5ae9b1817480cf17
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:16:27 2013
+LENG 226 match states, 226 columns in multiple alignment
+FILT 129 out of 1445 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEECCCCCCEECCCCCCCEEEEECCCCEEEEEEECCCCCCCCCEEEEEEEE
+CCCCCCCCCCEEEECCCCCCCEEEECCCEEEEEEECCCCCCCCCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCEEECCEECCCCEEEEEEEEEECCCC
+CCCEEEEEEEECCCCEEEEEEEEECC
+>ss_conf PSIPRED confidence values
+9389675888996899899998963788888669999968999958999995368841106766762699841543168899826680218369999973
+6766545332055315421000000000024567428631202474299999767887997499988995247720100065399789999999941336
+79879999995898878999996088
+>Consensus
+xxxxxxpxxxxvxxGxxvxLxCxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxxLxIxxvxxxDxGxYxCxxxx
+xxxxxxxxxxxxxxxxxxxxlxVxxxxxxxPxvxxxxxxxxxxxgxxxxlxCxxxxxxPxxxxvxWxxgxxxxxxxxxxxxxxxxxxxxxsxlxixxxxx
+dxxxyxCxvxxxxxxxxxxxxixxxx
+>cd06863eb01c4bcc5ae9b1817480cf17
+DVQLVESGGGLVQPGGSRKLSCAASGFTFMRFGMHWVRQAPEKGLEWVAYISSGSSTIYYADTVKGRFTISRDNPKNTLFLQMTSLRSEDTALYYCARSG
+GIERYDGTYYVMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPR
+PSETVTCNVAHPASSTKVDKKIVPRD
+>gi|293338546|gb|ADE43520.1| anti-2,4,6-trinitrotoluene scFv antibody 6-3 [synthetic construct]
+----------------------------------------------------------------------------------------------------
+------------------------------mgQVQLVQSGAEVKKPGA--SVEGLLQDF-----------------------------------------
+----------------------------
+>gi|33569904|gb|AAQ21854.1| immunoglobulin kappa chain variable region [Homo sapiens]
+----------lAVSLGERATINCKSSQSVLYSSnnkn-------------yllgtsrnqdSLLSCSF-----TGHLPGNPGSLTDSVaAGLGQISLSP--
+----------------------------------------------------------------------------------------------------
+------------------------------------------
+>gi|326674722|ref|XP_689309.4| PREDICTED: poliovirus receptor-related protein 2-like [Danio rerio]
+-QHVRVEPEVVSFPGQTVTLRCQFPNPGDTqLTQVSWIFERTDTERTNIAVFHPNFGVNYPTTSPvSGRVTFVSNPpTLDNPSIQIKDVKMTDEGRYICE
+--------------YATYPSGNEqgvssLVMLAKPKNTATTVTVSAGKTPVI----VARCESSNGRP-AATITW--STALNGNVTTPKKTDnpDNTVSIQ
+SVYMLAPQPEDnGKDISCIVSHRTMAQPETFPMK---
+>gi|168985092|emb|CAQ09233.1| major histocompatibility complex, class I, C [Homo sapiens]
+----------------------------------------------------------------------------------------------------
+-----------------------------HPKTHVTHHP---VSDHEASRR-WNLpevgscggAFWrRAEIHVPCaARGAARAPHPE-------------
+------------------------------------
+>gi|17570629|ref|NP_510069.1| 2 (Zwei) IG-domain protein family member (zig-2) [Caenorhabditis elegans]gi|18104589|gb|AAL59607.1|AF456249_1 secreted 2-immunoglobulin-domain protein ZIG-2 [Caenorhabditis elegans]gi|3877044|emb|CAA92170.1| C. elegans protein F42F12.2, confirmed by transcript evidence [Caenorhabditis elegans]
+---------SNVTFGEKFVLSCGA--NGAPLPSIYWELNGMR--------IQGEETSNVYENILNdGKQVSN--AAMVSSHYRIPCATARNSGAYKCIID
+NG----------LTKLEHVAKVFVGGnktncalNDNGAPFISMTVDFRLEISNNAVALSC----RSETATEWSW-------HKGEQLLTNDGERYQMFPS
+gdLIIRNISWSDmGEYNCTARNHFGETTAITFLYP--
+>gi|149597420|ref|XP_001520231.1| PREDICTED: similar to butyrophilin [Ornithorhynchus anatinus]
+--VIGPAEPVLALEGGDTEMPCHLNPKESAeFMEVRWFR----SRPSNIVHLYDNREELFREQMEEyqGRTELVRDaMDYGSVAVRLLNVRVSDEGNYHC
+SFYDG------------NTVDRAPLELQVvGSTAQCSIFMEHFSWIS-----LILDLFP-DWIPDlfPI-LQMrelsEGGVNIKCPKSYGIGHTCTMFSL
+ddifgnfisaplfptaLSLMVALGVTLPV--LGLIIAGglyLIWKQNMDIEK----
+>gi|221330930|ref|NP_001137898.1| CG42256, isoform F [Drosophila melanogaster]gi|220902492|gb|ACL83253.1| CG42256, isoform F [Drosophila melanogaster]
+--------------------vaknpaaeikytallqvKGSVLAYPS--QKLN-TEHKKRKPHKYRSHLL-----------SKL-----kLSQ----CSLT
+LAA----slkp----FI-----------------------------------------------------------------------------------
+------------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+D 1 4203 * 2592 2606 * * 4156 * * * * * 3315 1510 * 4147 4277 * * * 1
+ 0 * * * * * * 6193 0 0
+
+V 2 * * * * 4777 4882 * 4878 * 1598 * 4613 * * * 3945 * 1122 * * 2
+ 0 * * * * * * 7304 0 0
+
+Q 3 5405 * 4255 4309 4467 4481 * 5481 2811 * * * * 3013 4319 4428 2793 2144 * 5169 3
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+K 217 5083 * 5046 3154 5093 3953 3677 6202 3917 6010 * 4392 2583 3697 4413 3467 3865 3989 * * 217
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+D 219 5414 * 3742 3231 * * 5879 6168 4180 5018 * 4512 4755 3536 3823 2972 2205 3586 * 6268 219
+ 0 * * * * 0 * 8542 0 1000
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+K 220 3756 5940 * 5968 6021 5879 5160 2668 3850 3885 * 5901 * 2792 4143 6284 3257 2409 * 6016 220
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+
+K 221 6246 * 5234 3284 4518 5924 4399 6159 2884 * * 3628 4244 4501 3783 2724 2721 5046 * 5883 221
+ 0 * * * * * * 8477 0 0
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+I 222 5652 * * * 3405 * * 1811 * 1760 4344 * * 5755 * 4252 * 2432 * * 222
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+R 225 3054 * 3237 3687 * * * * 1504 * * * 3143 * 2813 * 3513 * * * 225
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+D 226 * * 1726 * * * * * 2746 * * 3021 1748 * * 2969 * * * * 226
+ 0 * * 0 * * * 3825 0 0
+
+//
+�HHsearch 1.5
+NAME ced02dc66c62cb64fc91194b87a4189c
+FAM
+FILE ced02dc66c62cb64fc91194b87a4189c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:27:33 2013
+LENG 101 match states, 101 columns in multiple alignment
+FILT 103 out of 1324 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHHHHHHHHHHHHHCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
+C
+>ss_conf PSIPRED confidence values
+9770899999999999997043899897769999999999868760689999999999998667999818299999999999999999998770469888
+9
+>Consensus
+xxxxxxxxxxxlxxxFxxxdxxdxxxgxlxxxelxxxlxxxxxxxxxxxxxxxxxxxxxxxxdxxxdgxIxfxEFxxxlxxxxxxxxxxxxxxxxxxxxx
+x
+>ced02dc66c62cb64fc91194b87a4189c
+MACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQKLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQPRK
+K
+>gi|323456850|gb|EGB12716.1| hypothetical protein AURANDRAFT_18505 [Aureococcus anophagefferens]
+-------GIVALARNFRIAD-RDRS-GALREVEFERSVKN-----SQSGLDSSDISALFAYFDADRSGEVDYDEFLAAIRGPPNARRQA-----------
+-
+>gi|168054523|ref|XP_001779680.1| predicted protein [Physcomitrella patens subsp. patens]gi|162668878|gb|EDQ55476.1| predicted protein [Physcomitrella patens subsp. patens]
+-----VKRTksgivsqalnapctihcseAELEAAFKVFD-ANGD-GRICITELGKVLGS-----LSGCevTEQELQLIMNDVD-KNQDGFISLEQFKAAN
+KTLTshlaDNEtpkEDSIREA--------
+>gi|341876965|gb|EGT32900.1| hypothetical protein CAEBREN_17400 [Caenorhabditis brenneri]
+-----SLTSEQwkdLGDRFQTiCH-TTQE-GSLKREEIQEAFKI-----LGLDIPTYELRPLLDrAFgakeI------MDVKDVVQLYVKIRE-------
+----------
+>gi|195121290|ref|XP_002005153.1| GI20321 [Drosophila mojavensis]gi|193910221|gb|EDW09088.1| GI20321 [Drosophila mojavensis]
+----SKELINELRLIYDKHD-VNRT-GKIDIRQLYQIMFD-----VGYAPTEGEVHEFMAEADEDDSSYIGFDAFIKMLAPKlnEMFSEENLGK------
+---
+>gi|66808853|ref|XP_638149.1| EF-hand domain-containing protein [Dictyostelium discoideum AX4]gi|74996819|sp|Q54MZ4.1|MCFB_DICDI RecName: Full=Mitochondrial substrate carrier family protein Bgi|60466585|gb|EAL64637.1| EF-hand domain-containing protein [Dictyostelium discoideum AX4]
+------------------------------MSNNNNNNNN-----NNNNNNNNNN----NNNNNNNNDKNNNNNIDSSIK--------------------
+-
+>gi|145507732|ref|XP_001439821.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124407016|emb|CAK72424.1| unnamed protein product [Paramecium tetraurelia]
+----------RIWGLFKQFDID--NKNYITTMDVRRAFER-----RGKSLSTVKINTMFKEISLDSQDRIDFQRFQDIMLADslkSQ-------------
+----
+>gi|51889273|emb|CAH04268.1| protein kinase C activity reporter protein [synthetic construct]
+----------------lgmdelyksgamepkriregylvkkgsvfntwkpmwvvlledgiefykkksdnspkgmiplkgstltspcqdfgkrmfvfkitt
+tkqqdhffqaafleerDAWV-RDinkaikciEG-GQKfarksTRRSIRLPETI------------------dlgalylsmkdtekgIKELNLEKDKK-if
+nhcfTGN-------cvidwlvS--------------------
+>gi|297562741|ref|YP_003681715.1| signal transduction protein with EFhand domain [Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111]gi|296847189|gb|ADH69209.1| putative signal transduction protein with EFhand domain [Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111]
+----VHASYQMLWLELLRH-GSPAQ-ARLDRDAFVAAMHAASEDR----SR---fnmtegvAEAVFDLLDTDDGGSISEAEYVRYAEVLGA---------
+--------
+>gi|148235622|ref|NP_001079452.1| calpain 8 [Xenopus laevis]gi|27503196|gb|AAH42349.1| Capn8-a protein [Xenopus laevis]
+-LDPSNVQVESeIEDILNELEQKKME---MSAEDLRINLSRILSKkkdIKSDGFSLTTCKEMINLFDTDLTGKLNCKEFRPLWIKL--------------
+-----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 655 1454 * 2322 322 * * 2265 1285 0
+
+A 2 2701 * * 3978 * 3311 * * * * 1892 2661 1975 * * * * * * * 2
+ 0 * * * * * * 4946 0 0
+
+C 3 4361 4024 3900 * * * * * * * * 3964 2408 * 3060 2463 1893 * * * 3
+ 0 * * * * * * 5759 0 0
+
+P 4 4680 * 2205 2699 * * * * 4571 * * * 3312 3015 2970 3264 * 3443 * * 4
+ 139 3443 * 2163 365 * * 6437 1183 0
+
+L 5 3886 * 4037 * 4697 * * 3914 5207 1514 5014 3995 * 5362 4859 3391 3849 3791 * * 5
+ 45 5040 * 0 * * * 7722 1000 0
+
+E 6 2972 * 3583 1723 * 5676 * * * 4045 3895 4448 5169 3636 3749 5475 * 5240 5592 4619 6
+ 22 * 6046 0 * * 0 8507 1067 1000
+
+K 7 3595 * 3102 2884 5562 * 4622 * 2676 5528 * 4731 * 3021 3125 4236 4633 4143 * * 7
+ 0 * * * * * 0 8795 0 1219
+
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+
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+
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+
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+
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+
+//
+�HHsearch 1.5
+NAME cf096ff6881b75de1c34ab8525847a53
+FAM
+FILE cf096ff6881b75de1c34ab8525847a53
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:03:46 2013
+LENG 68 match states, 68 columns in multiple alignment
+FILT 5 out of 7 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 1.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCEECHHHHEEECCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+91156889988888987699999871898753577888602686666334778601052101013469
+>Consensus
+xxxxxexeRqkxxeiExxksxxxRxfGxAxxddkxaxxyaxFDxxdxrvQxAEFYRFnDxxxnkxGYF
+>cf096ff6881b75de1c34ab8525847a53
+MEQLTKNQRKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQPAEFYRFHDAEVNTFGYF
+>gi|71843046|gb|AAZ49227.1| gpB [Enterobacteria phage WA11]
+--PDIEAERKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRVQPAEFYRFHDAEVNTFGYF
+>gi|89888610|ref|YP_512370.1| gpB [Enterobacteria phage ID2 Moscow/ID/2001]gi|71842743|gb|AAZ48950.1| gpB [Enterobacteria phage ID2 Moscow/ID/2001]
+--QHLEAERQERATIEAGKEICRRRFGGATCDDQSAKIHAQFDPSNRSVQPAEFYRFNDNEINKYGYF
+>gi|242346744|ref|YP_002985206.1| internal scaffolding protein gpB [Enterobacteria phage St-1]gi|240129555|gb|ACS44788.1| internal scaffolding protein gpB [Enterobacteria phage St-1]
+--SDSERERQKAIDLEHRRAAFARHFGCAPGSEKHVENYSSFDEKDTRVQLAEFYRFNDGHLKKWGYF
+>gi|71842809|gb|AAZ49010.1| gpB [Enterobacteria phage NC28]
+--SDSERERQKAIELEHRRSAFARHYGCAPASEKYVEKYPSFDEKDTRIQLAEFYRFNDGHLKKWGYF
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 1000 0 0
+
+E 2 * * * 0 * * * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1000 0 0
+
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+
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+ 0 * * * * * * 1804 0 0
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+D 46 * * 382 * * * * * * * * 2106 * * * * * * * * 46
+ 0 * * * * * * 1804 0 0
+
+W 47 * * * * * * * * * * * * * * 2106 * 1297 * 1471 * 47
+ 0 * * * * * * 1804 0 0
+
+R 48 * * * * * * * * * * * * * * 382 2106 * * * * 48
+ 0 * * * * * * 1804 0 0
+
+I 49 * * * * * * * 1351 * * * * * * * * * 718 * * 49
+ 0 * * * * * * 1804 0 0
+
+Q 50 * * * * * * * * * * * * * 0 * * * * * * 50
+ 0 * * * * * * 1804 0 0
+
+P 51 * * * * * * * * * 1297 * * 754 * * * * * * * 51
+ 0 * * * * * * 1804 0 0
+
+A 52 0 * * * * * * * * * * * * * * * * * * * 52
+ 0 * * * * * * 1804 0 0
+
+E 53 * * * 0 * * * * * * * * * * * * * * * * 53
+ 0 * * * * * * 1804 0 0
+
+F 54 * * * * 0 * * * * * * * * * * * * * * * 54
+ 0 * * * * * * 1804 0 0
+
+Y 55 * * * * * * * * * * * * * * * * * * * 0 55
+ 0 * * * * * * 1804 0 0
+
+R 56 * * * * * * * * * * * * * * 0 * * * * * 56
+ 0 * * * * * * 1804 0 0
+
+F 57 * * * * 0 * * * * * * * * * * * * * * * 57
+ 0 * * * * * * 1804 0 0
+
+H 58 * * * * * * 1471 * * * * 646 * * * * * * * * 58
+ 0 * * * * * * 1804 0 0
+
+D 59 * * 0 * * * * * * * * * * * * * * * * * 59
+ 0 * * * * * * 1804 0 0
+
+A 60 1471 * * * * 1297 * * * * * 2106 * * * * * * * * 60
+ 0 * * * * * * 1804 0 0
+
+E 61 * * * 754 * * 1297 * * * * * * * * * * * * * 61
+ 0 * * * * * * 1804 0 0
+
+V 62 * * * * * * * 2106 * 1297 * * * * * * * 1471 * * 62
+ 0 * * * * * * 1804 0 0
+
+N 63 * * * * * * * * 1297 * * 754 * * * * * * * * 63
+ 0 * * * * * * 1804 0 0
+
+T 64 * * * * * * * * 646 * * * * * * * 1471 * * * 64
+ 0 * * * * * * 1804 0 0
+
+F 65 * * * * 1471 * * * * * * * * * * * * * 1297 2106 65
+ 0 * * * * * * 1804 0 0
+
+G 66 * * * * * 0 * * * * * * * * * * * * * * 66
+ 0 * * * * * * 1804 0 0
+
+Y 67 * * * * * * * * * * * * * * * * * * * 0 67
+ 0 * * * * * * 1804 0 0
+
+F 68 * * * * 0 * * * * * * * * * * * * * * * 68
+ 0 * * 0 * * * 1804 0 0
+
+//
+�HHsearch 1.5
+NAME cfe750d45ad9ea874e03be9e47fe8331
+FAM
+FILE cfe750d45ad9ea874e03be9e47fe8331
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:42:40 2013
+LENG 71 match states, 71 columns in multiple alignment
+FILT 140 out of 808 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEECCCCCCCCHHHHHHHHHHHCCCCCCCCHHHCEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+99871442479982989999999999658975566554122478965799999999999657663657789
+>Consensus
+mxxxixGDxNxDGxvxxxDxxxxxxxlxgxxxxxxxxxaDvnxdgxixxxDxxxlxxxxlgxxxxxpxxxx
+>cfe750d45ad9ea874e03be9e47fe8331
+MSTKLYGDVNDDGKVNSTDAVALKRYVLRSGISINTDNADLNEDGRVNSTDLGILKRYILKEIDTLPYKNG
+>gi|317055743|ref|YP_004104210.1| cellulose 1,4-beta-cellobiosidase [Ruminococcus albus 7]gi|315448012|gb|ADU21576.1| Cellulose 1,4-beta-cellobiosidase [Ruminococcus albus 7]
+--GKDIGKENNGGDAEPAEKSTYDEEKADKNKAENKtkksasdddentdantkenikagSDSKILFIGLIAGAVIILVVATEIFIYKMtkLKMQnqnke-
+-
+>gi|317055204|ref|YP_004103671.1| mannan endo-1,4-beta-mannosidase [Ruminococcus albus 7]gi|315447473|gb|ADU21037.1| Mannan endo-1,4-beta-mannosidase [Ruminococcus albus 7]
+-PQEITYPTNIKANYSQQyhQVQFVWDKVKGAdKYGIAVylaGKWRVQTSN-ITTNSYVTPKNLTPGMTYKVAIA--
+>gi|317055945|ref|YP_004104412.1| fibronectin type III domain-containing protein [Ruminococcus albus 7]gi|315448214|gb|ADU21778.1| Fibronectin type III domain protein [Ruminococcus albus 7]
+--QFVWDKLYGADKYGIAVY-LAGKWRVQ-TTNITTNSyvtpKNLTPGmsyrvAIAARVNGVWSTTEAINNAVTVTVR--
+>gi|317055737|ref|YP_004104204.1| spore coat protein CotH [Ruminococcus albus 7]gi|315448006|gb|ADU21570.1| Spore coat protein CotH [Ruminococcus albus 7]
+-PTNIKVNYNTQyhqiqfvwDKVQGADKYGIAVYLAGKW-RVQ--TSSITTNSFVTPKNLTPGMSYKVAV---------
+>gi|160893736|ref|ZP_02074520.1| hypothetical protein CLOL250_01290 [Clostridium sp. L2-50]gi|156864721|gb|EDO58152.1| hypothetical protein CLOL250_01290 [Clostridium sp. L2-50]
+---IIFGDVTGDGVINALDLLKIQKHIIGASSlkGAFLQAANIKRSGGLSALDLLKVQKFLMGAA--------
+>gi|299136675|ref|ZP_07029858.1| glycoside hydrolase family 2 sugar binding [Acidobacterium sp. MP5ACTX8]gi|298601190|gb|EFI57345.1| glycoside hydrolase family 2 sugar binding [Acidobacterium sp. MP5ACTX8]
+-------------------------MWFATTASDSEstgePMSNTSSRR-----EFLAAAAVAAAGLPAILC---
+>gi|119960824|ref|YP_949129.1| FG-GAP repeat-containing protein [Arthrobacter aurescens TC1]gi|119947683|gb|ABM06594.1| FG-GAP repeat domain protein [Arthrobacter aurescens TC1]
+----------------------MKRSKHGSGrptaalhqrrcsLAYPskcsYRSTRSRAWKAVPLAASASLAAAAIALTG-VP----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 3297 0 0
+
+S 2 * * 4615 * * 5342 * * 5031 * * 2108 1073 * * 2980 4740 4946 * * 2
+ 0 * * 0 * * * 5583 1000 0
+
+T 3 5077 * 5036 3130 * 2858 * * 4542 * * 3761 3386 3224 * 4644 1900 4553 * 5811 3
+ 24 5927 * 1000 1000 * * 7011 1017 0
+
+K 4 3587 * 5880 3870 3782 3715 * 3037 4444 4982 6653 5260 3958 6454 4701 4185 4541 2679 * 3664 4
+ 17 6428 * 1802 488 * * 7320 1016 0
+
+L 5 4660 * 5039 * 6820 5728 7263 1687 4395 2588 4919 5159 6742 6986 6845 7101 4181 2275 * 6009 5
+ 0 * * * * 0 * 7322 0 1000
+
+Y 6 3711 5617 * 6829 6161 * * 3185 2776 2810 6045 7152 4429 * 3338 6016 3800 7402 4349 2538 6
+ 0 * * * * * * 7351 0 0
+
+G 7 4838 * 5193 * * 242 * * * * * 5627 5460 * * * * 5494 * 5227 7
+ 0 * * 1000 1000 * * 7362 1005 0
+
+D 8 * * 321 5610 * * * 5534 4049 * * 3831 5212 * * * * * * * 8
+ 30 * 5610 * * * * 7377 0 0
+
+V 9 2969 6605 * 5597 6060 * * 2682 * 2228 * 7045 * * * 4327 4303 1729 5430 5372 9
+ 0 * * * * * 0 7292 0 1155
+
+N 10 * * 2686 * * * * * * 7124 * 445 * * * * 4021 6329 * 5114 10
+ 0 * * * * * 0 7290 0 1155
+
+D 11 3303 3761 4014 4481 4812 1428 * 5067 6193 4793 6676 3709 * 6106 4543 4533 5030 * * 6170 11
+ 0 * * * * * 0 7290 0 1155
+
+D 12 4690 * 563 6119 * 3733 * * 5153 * * 3655 * 5381 * 4496 7388 * * 6289 12
+ 35 5381 * 3000 193 * 0 7304 1117 1155
+
+G 13 4826 * 3883 5858 * 524 * * 5512 * * 4406 * 5585 5429 4774 4851 * * * 13
+ 9 * 7361 * * * 0 7304 0 1155
+
+K 14 4765 6728 4892 3483 6328 7212 6665 4188 1926 5256 5759 4009 * 4779 3962 3596 4306 2882 * 7097 14
+ 0 * * * * 2114 379 7306 0 1223
+
+V 15 4439 * * * 4176 5471 * 2030 * 3965 * * * * 7000 * 4709 1213 * 3478 15
+ 0 * * * * 0 * 7304 0 1155
+
+N 16 5607 * 1783 4109 * 4427 * * 5849 6902 * 1790 * 4568 6874 3412 3002 * * * 16
+ 0 * * * * * * 7390 0 0
+
+S 17 3350 * 6412 6259 6213 3554 * 2914 * 4032 3980 * 4729 4805 6260 2397 5217 2402 6796 5651 17
+ 0 * * * * * * 7390 0 0
+
+T 18 1992 * 6940 6203 5138 4318 5651 3820 4510 2862 4782 4080 * 4612 4968 3639 3899 4525 * 5868 18
+ 38 5255 * 1000 1000 * * 7390 1144 0
+
+D 19 * * 293 4196 * * * * * 6342 * * * 4145 * * 4879 5232 * * 19
+ 0 * * * * * * 7390 0 0
+
+A 20 2564 6911 * 7335 3741 * * 3217 3972 1977 6350 * * 7102 6206 5859 5232 2653 * 3637 20
+ 48 7301 5232 2000 415 * * 7390 1000 0
+
+V 21 2447 7506 5917 4751 7137 5708 * 3699 7497 4599 4855 7361 6506 4233 5153 4229 2794 2024 * 5008 21
+ 0 * * * * 0 * 7230 0 1149
+
+A 22 3662 6940 7633 5844 4216 4846 6781 3589 5466 1746 3938 7057 * 5229 4894 * 3738 4261 6393 3097 22
+ 18 6320 * 1585 585 * * 7390 1055 0
+
+L 23 3442 5817 * * 4889 6786 * 2407 5646 1764 2894 * * * * 6812 4736 3274 * 4056 23
+ 62 4577 * 2249 341 * * 7454 1348 0
+
+K 24 2960 6781 4852 5089 7207 4257 6523 6291 2597 4448 4484 3989 * 2770 2795 4886 5894 7279 5181 5534 24
+ 0 * * * * 0 * 7368 0 1155
+
+R 25 4346 7193 3402 4122 * 5993 * * 1900 5780 5115 3397 * 2955 2892 4280 6852 4860 * 6939 25
+ 24 7003 6801 1000 1000 * * 7454 1000 0
+
+Y 26 4519 * 6906 5104 5512 4670 3231 4433 4724 5801 5116 4889 * 6396 6530 4639 7194 4958 3804 1275 26
+ 32 * 5496 * * 0 * 7522 0 1007
+
+V 27 5473 6992 5749 * 4943 5284 * 2202 4816 1453 4638 7112 * * 4857 4705 * 2994 6357 5902 27
+ 40 7286 5599 1000 1000 * 0 7408 1000 1125
+
+L 28 2673 5246 * 7129 5712 6831 4522 3348 4035 1805 5038 4078 5592 6290 6335 4243 5194 3843 * 7044 28
+ 25 6597 7207 666 1436 2610 258 7407 1021 1315
+
+R 29 3804 * 3686 4669 * 1194 * 7262 3709 * 7443 3161 * 4307 4981 4158 6113 6091 * 7234 29
+ 110 * 3769 * * * 0 7413 0 1325
+
+S 30 3770 * 4864 5141 6872 3387 * 3627 2013 3667 6035 3997 3605 6828 5464 4108 4718 4787 6107 6134 30
+ 157 3527 5913 658 1449 1051 950 7165 1612 1954
+
+G 31 4137 6176 4334 3910 5657 3206 * 3643 2972 4378 5738 4298 4171 5734 4573 3705 3225 4849 5310 * 31
+ 351 2599 4291 1561 597 2238 344 7340 2337 1615
+
+I 32 4044 * 3439 3604 6046 4900 7099 3993 3052 5451 7096 4151 3776 4605 6307 3412 3023 5396 * 3800 32
+ 339 2468 5113 905 1101 1147 867 7190 2385 1976
+
+S 33 3154 * 3305 3420 6284 3110 6907 5358 4725 4325 * 3229 3247 7034 4380 3637 3583 6321 * * 33
+ 136 4441 4505 1578 588 1963 428 7272 1422 1848
+
+I 34 3602 * 5202 3107 2921 * * 2007 4670 2892 5471 * 6740 6983 7000 5306 5975 3498 * 4557 34
+ 74 4554 7070 1461 651 2172 362 7249 1267 1992
+
+N 35 3538 6987 3281 5161 6112 5439 * 5522 4511 5025 7134 2770 3529 3264 6091 3449 2634 6849 7038 6233 35
+ 680 1693 3912 2240 343 635 1489 7262 3479 1823
+
+T 36 3653 6946 5339 3973 4373 7141 * 4449 3458 2722 4935 5648 5167 6236 4690 5711 2837 3991 3604 4520 36
+ 183 3073 * 3407 143 933 1070 7275 1885 1774
+
+D 37 3927 * 4099 3251 6132 4439 6225 4062 2219 3925 4984 5043 4275 4375 4960 4819 5213 4419 6824 4484 37
+ 38 5545 7710 1923 442 1142 871 7338 1147 1340
+
+N 38 1550 4882 4932 6561 5917 6845 * 4637 4459 4991 5814 2957 7114 5143 5201 2971 4325 5209 * 5306 38
+ 58 4670 * 2930 203 2391 305 7447 1484 1208
+
+A 39 807 5504 * * 5677 2938 * * 4308 7127 5065 * * * 6341 3377 5740 7273 4841 * 39
+ 9 7345 * 1000 1000 2648 251 7450 1000 1198
+
+D 40 * * 341 * * * * * 5689 * * 3763 * * 4093 5377 6315 * 5480 * 40
+ 0 * * * * * 0 7446 0 1155
+
+L 41 3766 4470 * * 4841 6964 * 2427 * 2544 4442 * * 6315 * 6316 5863 1455 5156 * 41
+ 0 * * * * * 0 7446 0 1155
+
+N 42 * 5308 2522 5156 7217 * 7090 5389 4436 5248 * 1037 * 5204 5329 6366 3833 5393 * 5911 42
+ 18 6344 * 1000 1000 0 * 7446 1042 1155
+
+E 43 3612 6423 4188 4376 5723 2034 7446 5675 3520 5857 4972 4398 4981 3452 4431 4682 4063 7037 7312 4342 43
+ 8 * 7513 * * * * 7531 0 0
+
+D 44 * * 786 7140 * 4873 6863 4964 * * * 2629 5631 * 5703 3435 * 4942 6342 * 44
+ 77 4667 6343 1938 436 0 * 7531 1318 1000
+
+G 45 3482 * 5077 6447 * 703 * * 5018 6563 * 3366 6359 * 5312 4274 5170 * * * 45
+ 78 6129 4710 0 * * 0 7499 1075 1070
+
+R 46 3617 * 4688 3981 4071 4155 * 4154 2620 4480 6834 6281 5373 4934 4120 3253 3822 3076 * 7167 46
+ 75 5114 5538 0 * 1306 748 7270 1237 1454
+
+V 47 4221 7028 * * 4624 * * 1190 * 3688 * * 5441 * 6318 6559 5542 1668 * * 47
+ 18 6315 * 2807 222 * 0 7344 1042 1465
+
+N 48 3810 * 1461 6560 * * * * * 7215 * 1847 5292 6766 6901 4853 2377 * * * 48
+ 18 * 6318 * * * 0 7344 0 1465
+
+S 49 2917 * 6296 5896 * 3620 * 2728 5762 5141 4054 4387 4732 7078 4538 3162 3657 2619 6770 * 49
+ 0 * * 1585 585 872 1141 7310 1155 1613
+
+T 50 2466 * 4686 4446 3481 4296 * 3293 3439 3513 5312 4168 * 6071 5143 4413 3978 4442 * 4986 50
+ 0 * * * * 856 1160 7430 0 1244
+
+D 51 4888 * 342 5754 * * * * 6855 6359 * 4310 * * * 5258 5674 4575 * * 51
+ 0 * * * * * 0 7499 0 1070
+
+L 52 3314 6428 * 5846 3124 5204 * 3368 6822 1788 6021 5483 * * 5488 3926 * 2894 * 3779 52
+ 0 * * * * * 0 7499 0 1070
+
+G 53 2644 7240 5608 5803 * 4615 * 2886 5101 3983 5746 6338 5674 6520 6194 4065 2614 2288 * 5411 53
+ 0 * * * * * 0 7499 0 1070
+
+I 54 3170 * 7216 4182 5300 7396 6576 3388 3738 2104 4969 * 5424 4296 5723 4687 3831 4900 4862 3640 54
+ 0 * * * * * 0 7499 0 1070
+
+L 55 6370 * * * 5996 5424 7251 1796 * 1398 3425 * 4366 6844 * 5204 7410 3450 * * 55
+ 39 5224 * 1357 714 * 0 7499 1219 1070
+
+K 56 3152 6948 7356 5278 7223 7283 6775 4309 2436 4913 4379 5856 * 2629 2712 4394 3971 4693 5483 7674 56
+ 0 * * * * * 0 7499 0 1070
+
+R 57 3385 * 3763 6209 7115 5407 * * 1838 5369 7496 3584 * 3288 2541 3920 4234 * * * 57
+ 0 * * * * * 0 7496 0 1070
+
+Y 58 4643 * 5960 4603 2987 6354 5549 3639 4893 2906 4558 6401 * 5843 5672 5679 5014 5364 * 1601 58
+ 0 * * * * * 0 7498 0 1070
+
+I 59 3469 6287 7382 4597 5942 * * 1993 4337 1890 6118 7071 * 7012 * 7488 4903 2787 * 4342 59
+ 0 * * * * * 0 7503 0 1070
+
+L 60 3436 7040 4916 * 6658 7135 7185 2800 5057 1353 4413 7069 5207 7046 6833 5105 5541 3148 7145 6678 60
+ 7 * 7646 * * * 0 7494 0 1070
+
+K 61 3900 6647 5425 5356 4525 1112 4326 * 3315 * * 3451 * 7262 4306 5518 6278 4807 * * 61
+ 30 7455 6097 0 * 0 * 7493 1000 1121
+
+E 62 4378 6897 6189 4257 6042 5060 * 3082 3405 3149 3717 4277 5325 5222 3622 4298 4737 2824 7019 6773 62
+ 23 5971 * 1070 933 0 * 7552 1044 1056
+
+I 63 3057 5558 4951 4486 * 6657 * 1675 5557 4051 5323 * * 6702 5016 6467 2885 3757 * 3460 63
+ 15 * 6621 * * * 0 7372 0 1000
+
+D 64 3812 * 3321 3580 * 4682 6451 5594 2427 6354 * 4893 4040 5524 4942 3036 3400 4050 * 4316 64
+ 113 4611 4863 1000 1000 1076 928 7321 1149 1049
+
+T 65 4230 * 3256 2972 6238 * 4662 6078 2432 4607 4927 * * 6246 4999 2321 2908 6634 * * 65
+ 165 3206 * 1000 1000 0 * 7104 1461 1275
+
+L 66 6049 * * 5230 1443 * * 4138 * 1378 * * * * * * 6325 2987 * 6621 66
+ 23 5958 * 2322 322 * * 7174 1009 0
+
+P 67 3868 * 5741 5976 * 4581 * * 3966 5368 * 5138 794 * * 4581 3329 5606 * * 67
+ 0 * * * * * * 7164 0 0
+
+Y 68 3499 5004 4916 4271 * 3761 * 3366 2745 5814 4661 5620 4892 * * 4918 5792 1895 * 4497 68
+ 55 4744 * 1354 716 * * 6944 1040 0
+
+K 69 3676 * * 2946 * 3413 * * 2230 * * 3963 * 2382 3508 3573 4130 * * * 69
+ 375 2128 * 2322 322 * * 6560 1103 0
+
+N 70 * * * * * 1661 * * * * * 885 * * * * 2812 * * * 70
+ 0 * * * * * * 2919 0 0
+
+G 71 * * * * * 0 * * * * * * * * * * * * * * 71
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME d3011fec8513a3e2267bf4e15e08704b
+FAM
+FILE d3011fec8513a3e2267bf4e15e08704b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:05:26 2013
+LENG 166 match states, 166 columns in multiple alignment
+FILT 117 out of 1051 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCHHHHCEEEEEEEEECCCCCHHCCCCCEEEEEEEEEECCCEEEEEEEEEECCEEEEEEEEEEECCCCCEEEEEEECCEEEEEEECC
+CCCEEEEEEEECCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCCHHHEEECCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9888888875788896893758899999528962000387047899999977996999999710982999999999758895899985084899999869
+998999999645899567899999789999999999999999984999899699887785877899
+>Consensus
+cxxxxxxxxxxxxfdxxkxxGxWyxiaxaxxxxxxxxxxxxxxxxxxxxxxxxxxlxvxxxxxxxxxcxxxxxxxxxxxxxgxxxxxxxgxxxxxvlxtD
+YxxyaixxxxxxxxxxxxxxxxlxsRxxxxxxxxxxxfxxxxxxxglxxxxixxxxxxxxCxxxxx
+>d3011fec8513a3e2267bf4e15e08704b
+CVHAEEASSTGRNFNVEKINGEWHTIILASDKREKIEDNGNFRLFLEQIHVLENSLVLKFHTVRDEECSELSMVADKTEKAGEYSVTYDGFNTFTIPKTD
+YDNFLMAHLINEKDGETFQLMGLYGREPDLSSDIKERFAQLCEEHGILRENIIDLSNANRCLQARE
+>gi|55958592|emb|CAI17198.1| progestagen-associated endometrial protein [Homo sapiens]
+----MDIPQTKQ----------------------DLElPKAPLRVHITSLLPTPEdNLEIVLHRWENNSCVEKKVLGEKTENPKKFKINCKASGAPQL--
+------SWKPQGPRTDPASS-T----ARVLVEDDEIMQGFIRAFRPLPRHLWYLLDLKQMEE------
+>gi|291241284|ref|XP_002740541.1| PREDICTED: apolipoprotein D-like [Saccoglossus kowalevskii]
+------TVVVQPDFNVDKYTGSWYEIE-----RFPASFESGLKCNNATYWLKQDgTIGVINSgIdIVTGERTSVEGNAWVPdpNVPAKLKVKFRWwvpAG
+DYWVLRTDYNTYSVVYSCDdFMFgFIKMEFAWILSRDRILNTGTLTDIKRDIQDRGIDISNFLS-TDQIGCDA---
+>gi|254468024|ref|ZP_05081430.1| lipocalin family protein [beta proteobacterium KB13]gi|207086834|gb|EDZ64117.1| lipocalin family protein [beta proteobacterium KB13]
+SGCAtngLPKIEPVEKISLDNFMGDWYVLAHIPA---LIEKN-AFNA-VESYSFNSaDqVIETTFTfNKGAldGPEKIYKPKGFVIPgtNNAVWGMQfiw
+piKAQYVIAYI-DEGY-ENTIVARDK----RD--YLWFMSRTTDLPTEKKQWIYKKTSELGYDGDMLRFVPHN--------
+>gi|285019342|ref|YP_003377053.1| lipocalin precursor [Xanthomonas albilineans GPE PC73]gi|283474560|emb|CBA17061.1| putative lipocalin precursor protein [Xanthomonas albilineans]
+PASTvrakspgPEQEAARPPIDLQRFMGRWYVIA-HIPY--FA-ERGHVAS-SDEYTLKDnGKI--avRY-Q-YRKGf-DEPLKEITSRATvnEGTGN-r
+RwttwffavLPTK-yRILEVAPDY-SWALIDYP------GRDLAWVFARSPDMSHKQYRELVDKMDhKYGIN----tdklLR------------
+>gi|47226724|emb|CAG07883.1| unnamed protein product [Tetraodon nigroviridis]
+----DDMVKPYIPLDPKAVFGKWVYVMGAGDPDPYHRALGSIKSSWVELSPTSdVqTVTLRWGDYLFNQCALGEVNATLSG----TTVTFQKNlseHRGH
+LLQTRANS--LLWTDSFrNVDVTGRFVMQFTRTGTTDPELVRLFKEQIACLHFPEN-FHsYDGTTELCPEASP
+>gi|260893984|emb|CAP10680.1| lipocalin homologue [Deinagkistrodon acutus]
+CVVQANEKKPFQNFDCSKMARNWILRVIVTNCSHFENMIRGIKACPVSFVKKSqENMEMIMDMFTPQGCQIIKVNLTW--VNGAIVATcGDGvEKTVEDV
+RINKNT--M-YTSaRVRGKEQCKVATLAAKDIADIQPDLEDFTRFVNGVGLEGKKIYVLPTEDICPRS--
+>gi|270046182|dbj|BAI50821.1| unnamed protein product [Triatoma dimidiata]
+------NPEPLDGFSASNfFSGTWYVSHVK---------SVTSPTVCQTFTTSqEDnKLITEYVFGKGGkdiivRCEA-----EK-KKNILLTFSckNSQ
+CrtflTVFTVMDTNYDNYAEFYKCVIfTSGSKA-DIYLVIKRESGNEQIPEK----AKSLNLQK-----------------
+>gi|270046234|dbj|BAI50847.1| unnamed protein product [Triatoma dimidiata]
+------GYKPMENFDSTRyLQITtpLYSTQA-KPKSN----YTVCREFRSIKKsgdkvdtNIHGYYKDrgkiFNYE---LLCSTTWE---S-FNKGQYLS
+VcevlKDTdvegplissfEQHMSVIHTDYDSYAILYiCISDESGIEENVVVLE-KDPGASNE---AVTTALRNNDMDLTEFF-PWNYAYCQN---
+>gi|156602033|gb|ABU86907.1| Apom [Ornithorhynchus anatinus]
+----------------RTYLGYWHFIAGSAPTPDPLATFDPVDNILFHLVPGsTPlELYLRASIrMKNGLCVPREWTYLLAK--GTTNLRIEGRpnMKTE
+LFSAPCAESIIL-K---ETGQDYERFLMYSRSPAPPARCVNDFQALVSCWNF-T-LLQTPRQQDACMLT--
+#
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+R 126 * * 6540 * * * * * 3206 * * 5983 5652 * 302 6228 6591 * * 6579 126
+ 0 * * * * * 0 9716 0 1019
+
+E 127 5214 * 2679 3950 6681 4077 * * 3622 * * 4079 5816 4282 3749 2393 2389 5796 * * 127
+ 11 * 6980 * * * 0 9716 0 1019
+
+P 128 5123 * 5171 5183 6632 5464 * 5486 3982 3325 6522 5706 1747 4800 2523 3994 4023 5804 5789 * 128
+ 40 * 5176 1000 1000 1127 883 9700 1019 1185
+
+D 129 4592 * 3189 2470 * 5332 4716 5302 3942 3537 5788 4782 5986 3528 6893 3839 2907 4049 * * 129
+ 68 6923 4735 0 * 1047 955 9663 1431 1572
+
+L 130 3524 * 4279 4985 5808 4532 6868 3582 * 1856 4410 5490 2981 * 6919 5655 4370 2964 * * 130
+ 15 * 6624 * * 221 2816 9601 0 2147
+
+S 131 4759 * 2823 2668 * 6586 * 5568 5189 7002 * 3761 3349 5459 5749 1945 3153 * * 6350 131
+ 28 5724 * 1000 1000 0 * 9697 1383 1192
+
+S 132 3716 * 2630 2720 6632 4032 6789 * 4024 5547 6900 4315 2712 2918 6572 5339 4289 5832 * * 132
+ 0 * * * * * * 9725 0 0
+
+D 133 2658 * 2293 2296 * 4276 7030 6809 3369 * 6875 5721 4207 3893 6818 3903 5315 6626 * 6806 133
+ 87 * 4103 * * * * 9725 0 0
+
+I 134 2134 6522 4845 4339 5228 5560 6203 3255 5839 3246 5051 6836 6851 4057 6663 5121 3768 2867 6477 5644 134
+ 81 4202 * 894 1115 * 0 9587 1769 1997
+
+K 135 5689 6935 6469 6595 4522 * * 2755 2878 2050 3115 5732 4892 * 4155 * 5671 4412 5539 3848 135
+ 12 * 6884 * * * 0 9587 0 1997
+
+E 136 2740 * 3635 1791 6714 5028 5752 * 2859 * * 4112 6910 3814 4434 4711 4811 6835 5777 * 136
+ 13 * 6835 * * 440 1926 9583 0 2148
+
+R 137 3229 * 3978 2663 6543 4867 5179 5806 2331 5248 4424 5145 * 3807 2887 5841 5615 * * 4753 137
+ 0 * * 0 * 488 1801 9693 1240 1404
+
+F 138 2812 4985 * * 1231 * * 3828 * 2952 5282 * * * * * 6714 3356 * 3888 138
+ 12 * 6971 * * * 0 9723 0 1000
+
+A 139 4506 6565 5320 3033 4316 * 4733 6734 2864 2831 4719 6637 * 4236 3414 5651 3640 3573 * 4505 139
+ 0 * * 0 * 891 1118 9706 1019 1188
+
+Q 140 3069 5740 3379 2873 * 4988 * * 2468 6923 4787 4237 * 4281 4132 3024 4238 * * 4821 140
+ 0 * * * * * 0 9699 0 1000
+
+L 141 3215 * 7027 6846 3141 * 6560 3778 3423 2364 * * * 4372 3005 6949 4934 3317 5775 4076 141
+ 14 6677 * 0 * * 0 9699 1044 1000
+
+C 142 2142 4038 * * 4089 5283 * 3759 * 1975 5631 * * * * 3979 3943 2808 * 6879 142
+ 21 7214 6969 0 * * 0 9699 1000 1000
+
+E 143 4046 6551 3814 2781 * 5095 * 5177 2478 4499 * 4934 4744 3994 2794 3586 4538 6853 6571 6793 143
+ 25 5852 * 573 1609 * 0 9682 1131 1188
+
+E 144 2773 4183 3536 3004 6908 4432 5229 5732 2906 5218 * 4370 6728 4507 3684 3253 4902 6737 * * 144
+ 0 * * 1000 1000 * 0 9682 1019 1188
+
+H 145 4809 * * 5012 4558 6908 5149 4138 4317 1780 4253 3860 6798 3390 4150 * 5246 4380 * 3323 145
+ 24 5943 * 1000 1000 * 0 9682 1133 1188
+
+G 146 6835 5209 4802 5678 * 688 5649 5180 4525 * * 3788 5291 5119 4842 5940 6598 6798 * * 146
+ 28 5714 * 433 1947 891 1118 9682 1381 1188
+
+I 147 * * 5883 * 2481 * * 2414 * 1580 4329 * * * 6734 6791 * 3213 * 3240 147
+ 12 * 6907 * * * 0 9699 0 1000
+
+L 148 6604 * 2165 3537 * 5752 4544 * 4192 4029 * 4378 3234 4723 4829 2587 3979 5145 * 5820 148
+ 61 * 4592 * * * 0 9682 0 1212
+
+R 149 6514 * 3549 2741 5105 6305 * 4255 4309 3014 4729 4779 3811 6036 4638 3424 3215 3971 * 5620 149
+ 32 * 5489 * * 2943 201 9617 0 2064
+
+E 150 4139 * 2566 2586 5847 4244 5291 * 3848 5537 * 4318 5395 4086 5636 2601 3766 * 5656 6625 150
+ 92 * 4018 * * 1947 433 9532 0 2264
+
+N 151 4952 * 3146 4730 4586 6522 4190 5481 2481 5089 5010 2785 6328 3703 3267 4492 6720 6611 * 4459 151
+ 0 * * 2585 263 1279 766 9470 1019 2878
+
+I 152 6607 * * * 2833 * 6457 1852 * 1870 4131 * * 5683 * 6875 5621 2747 6834 5356 152
+ 30 6580 6669 2149 369 1196 828 9564 1815 2090
+
+I 153 5708 * * 3764 3790 * 5413 2635 4596 3714 6368 5646 * 4359 3365 4248 4060 2323 5658 5442 153
+ 246 * 2674 0 * 350 2216 9581 1044 1717
+
+D 154 * * 3564 5557 2680 * 3971 4202 4472 3954 4600 3810 5370 4939 4068 5012 3838 3902 4594 3789 154
+ 32 6374 6687 0 * 97 3942 9290 1000 3482
+
+L 155 5023 * 4990 6691 4366 * * 3529 4434 2344 6141 6399 2591 5201 5782 4665 2901 3160 6826 5767 155
+ 89 5758 4607 0 * 1217 811 9600 1131 1168
+
+S 156 4640 * 4897 3882 4777 5284 6644 5376 5133 6485 6490 4093 2368 3983 3363 3326 3174 4655 6021 4911 156
+ 19 6283 * 0 * 338 2260 9509 1016 1743
+
+N 157 * * 4288 4253 6447 * 4114 5981 2852 6499 * 3019 4686 2096 3872 3152 4153 5667 * 6789 157
+ 16 6461 * 0 * * 0 9580 1013 1019
+
+A 158 4737 * 3255 3863 * 4063 5747 6521 3883 5670 6510 4554 3883 2856 4185 3695 2816 4569 * 4778 158
+ 116 3940 6386 699 1381 1023 977 9473 1916 1210
+
+N 159 3353 * 1737 2226 5460 3194 * 5484 4371 6545 6306 4279 * 6289 4403 6352 6435 5211 * * 159
+ 51 6285 5501 0 * 1744 511 9416 1000 1406
+
+R 160 3066 6417 3512 3111 5298 5186 5956 5069 4172 4855 6098 4255 4271 3280 3792 4843 3286 * * 4461 160
+ 0 * * * * 0 * 9159 0 1518
+
+C 161 * 114 * 5982 * * * * * * * * 6019 6037 * * * 6150 6009 * 161
+ 71 5019 5842 1601 577 * * 9092 1191 0
+
+L 162 3513 * 3891 4439 * 4714 5765 5006 4438 4072 * 4511 2120 3358 * 3427 4019 3918 * 6231 162
+ 0 * * * * * 0 8925 0 1057
+
+Q 163 3753 * 3876 3035 4505 3708 3135 5536 * 5404 5509 3482 3161 3753 4481 4659 4670 5785 * 5886 163
+ 0 * * * * * 0 8504 0 1057
+
+A 164 1227 * 2760 2280 * * * * * 4604 * * * * * 2489 * * * * 164
+ 154 3303 * 0 * 0 * 6896 1021 1057
+
+R 165 * * 2440 * * 3437 * * 3041 * * * * * 732 * * * * * 165
+ 213 2864 * 0 * * * 4798 1000 0
+
+E 166 2606 * * 2491 * 2735 * * * * * * 2785 1463 * * * * * * 166
+ 0 * * 0 * * * 3537 0 0
+
+//
+�HHsearch 1.5
+NAME d330d1598fd712b741ae1a07a1797d37
+FAM
+FILE d330d1598fd712b741ae1a07a1797d37
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:02:53 2013
+LENG 192 match states, 192 columns in multiple alignment
+FILT 167 out of 1196 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCEEEEEEEEECCCCCEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEECCCHHHHHCCCCCCCCCCEEEEECCCCCCCCCCCCEEEECCHHHHH
+HHHCCCCCEEEECCHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHCEEEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEEEC
+>ss_conf PSIPRED confidence values
+9986099999999588847379977876878999999997178754557879984008765230147889997999958897655789969989999999
+97478997999887999999974899789999999533366656324389983447998888611234555543442468921899999979
+>Consensus
+xxxxxxxxlixAxsldGxIgxxgxlpWxxxxdxxxfxxxxxxxxxxxxxxxvvmGRxTyexxxxxxxpxxxrxxiVvSxxxxxxxxxxxxxxxxxxxxxi
+xxxxxxxxixViGGxxlxxxxlxxxlvDelxltiipxxxxxxxxGdxxfpxxxxxxxlxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+>d330d1598fd712b741ae1a07a1797d37
+MLKPNVAIIVAALKPALGIGYKGKMPWRLRKEIRYFKDVTTRTTKPNTRNAVIMGRKTWESIPQKFRPLPDRLNIILSRSYENEIIDDNIIHASSIESSL
+NLVSDVERVFIIGGAEIYNELINNSLVSHLLITEIEHPSPESIEMDTFLKFPLESWTKQPKSELQKFVGDTVLEDDIKEGDFTYNYTLWTRK
+>gi|330723554|gb|AEC45924.1| dihydrofolate reductase [Mycoplasma hyorhinis MCLD]
+-------MIISilAMGKNNLIGKGDDLPWYVKEDFDFYREQTK-------HHDILVGKNTFFTLPKS---LQKWSKIYIVSddkNFN-Y-ENENVKTINN
+FSNLIKEyQNHpSKHLFVSGGYTLYKSII--NKCDQLIISFIKGE----HSGDIFLNElKWEKFE-----------------------------------
+>gi|308177537|ref|YP_003916943.1| RibD domain-containing protein [Arthrobacter arilaitensis Re117]gi|307745000|emb|CBT75972.1| RibD domain-containing protein [Arthrobacter arilaitensis Re117]
+-------IFDAAVSLNGYLADEnHGLQWLfdvpGAQEPDP-DLL------PKNVGVHVEGANTYKWLIDneqlmenpHKWQEyyPGVTTYVFTSRDLPIP
+DGADVRLVNgPVAKFLPEIrgtAGLKNIWVLGGGELLGQFLDAGAIDILALTIAPVA----LaRGTELLPRniGSERLELVQAHK---------------
+--------------
+>gi|298245066|ref|ZP_06968872.1| bifunctional deaminase-reductase domain protein [Ktedonobacter racemifer DSM 44963]gi|297552547|gb|EFH86412.1| bifunctional deaminase-reductase domain protein [Ktedonobacter racemifer DSM 44963]
+---------LEFVTLDGVIQaPGgPEEDtsggfayggWvapYDDDVAGTVMDKQMNL-----PFDLLLGRKTFEIWAP-FWPqhadgwpgVMSATKYVAS
+NSMTS-SEWQPSVFLgGDIAEKVSKLkhQPGPDLHVYGSANLLQTLMKHDLVDAFWLKIFPLT----LgSGKRLFTDgTiPAAFKVTESQV---------
+--------------------
+>gi|300783227|ref|YP_003763518.1| hypothetical protein AMED_1302 [Amycolatopsis mediterranei U32]gi|299792741|gb|ADJ43116.1| conserved hypothetical protein [Amycolatopsis mediterranei U32]gi|340524608|gb|AEK39813.1| hypothetical protein RAM_06605 [Amycolatopsis mediterranei S699]
+-------VASFCMSLDGFVaRPDDSvgplFDWYqagdvevpmagypitfrvAPASAEYLSTFLDSVR----HSAFVCGRRVFEYTHGwGGRPPGGGAAFV
+VTHRPPPaGWPAGNlapFTFCADVTSAIEQAKaaGDGTV-GVSGPSIAQQCLRLGLLDEVRIDLVPVL----LgTGVRYFE-------------------
+-----------------------
+>gi|281421474|ref|ZP_06252473.1| riboflavin biosynthesis protein RibD [Prevotella copri DSM 18205]gi|281404546|gb|EFB35226.1| riboflavin biosynthesis protein RibD [Prevotella copri DSM 18205]
+-HQRPYIILKWAQTANGFLDNGGR-GMAISSP---FTKMLSHK-LRAENDAILIGRVTDERDhSQlnvRDWSGKDPMRLVIDRHHPCFEGLDFsRGKTEV
+LQQIMQYlyNNKVQSLIVEGGAITHQAFLDAGLWDEIRAETllstsVENS----VTSGTPAPMLPHNVRLISH---------------------------
+----
+>gi|284052809|ref|ZP_06383019.1| riboflavin-specific deaminase [Arthrospira platensis str. Paraca]gi|291566856|dbj|BAI89128.1| putative riboflavin-specific deaminase [Arthrospira platensis NIES-39]
+--TRPHTTVILAMSADGKIADLMRSPARfgSNADIIHLERQIAQ------ADAVLFGNGTLAAYGTVLrvsstELLGdrekngkppQPVQIVCSASGKIN
+ptlkffqQPVPKWLLTTFlggqpwkrfsdhFDQVIvaddsngvitwsealQQlrDRDIQRLAVLGGGQLVASLMAHHAIDEFHLTVCP------------
+--------------------------------------------
+>gi|84494757|ref|ZP_00993876.1| hypothetical protein JNB_08164 [Janibacter sp. HTCC2649]gi|84384250|gb|EAQ00130.1| hypothetical protein JNB_08164 [Janibacter sp. HTCC2649]
+--GRLRYGVIISL--DGYArDASGSFAWARPDHdLhSFINEKERD------VRTYIYGRGLWETMR--YWQnpprGEvnapehdefatiwqGADKVIVST
+TLE-PPTEPRTQLWDtLDVDRLAALVgdASTDV-SIGGPTLAADALRAGLVDEITAYVMPHV----AgGGLPWLPD------------------------
+-----------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 2633 0 0
+
+L 2 * * * * * * 2564 * * 2667 2839 * * * * 1971 2727 2970 * * 2
+ 0 * * * * * * 3841 0 0
+
+K 3 * 4093 3943 4205 * 2609 * * 3166 4222 * * * 3790 2765 2578 3234 * * * 3
+ 0 * * * * * * 5567 0 0
+
+P 4 2891 * 4367 * 4502 4209 4440 * * * * 4433 2100 * 1742 4620 4231 * * * 4
+ 0 * * * * * * 5794 0 0
+
+N 5 * * * 4790 * 4539 3659 4562 3506 2826 * 3651 1860 3603 * * 4301 3603 * * 5
+ 204 4301 3619 1585 585 * * 5990 1026 0
+
+V 6 * * * 4578 3006 * 3405 3024 4685 3668 * * * 3532 4442 3555 3346 3010 * 4088 6
+ 0 * * * * 0 * 5970 0 1107
+
+A 7 4778 5380 5536 * 6059 * * 2219 5900 1989 6517 5967 * 5618 * 3838 3625 3025 * 3346 7
+ 20 6181 * 1000 1000 * * 7106 1049 0
+
+I 8 5189 6396 * 6448 6354 4397 5925 2173 3159 3983 * 4701 * * 4043 2990 2711 3779 * 5292 8
+ 104 5331 4481 0 * * * 7623 1110 0
+
+I 9 3148 5456 * * 4575 6760 * 2730 * 1437 4573 * * 6160 * 5665 5080 3277 * 3561 9
+ 15 6560 * 1000 1000 0 * 8033 1015 1253
+
+V 10 6980 6922 5041 * 3824 6986 4705 1588 5612 4982 4927 4130 * 5451 * 4806 5239 2704 5185 3384 10
+ 0 * * * * * * 8309 0 0
+
+A 11 2229 * 7147 5251 4342 6018 * 3300 * 3377 4022 5657 * 5898 * 7254 5245 1853 4143 5247 11
+ 32 6118 7006 621 1516 * * 8309 1109 0
+
+A 12 635 4762 6224 * 4043 5308 5841 6945 * 7372 6816 4617 7031 7334 * 4033 4991 4954 * * 12
+ 0 * * * * * 0 8303 0 1034
+
+L 13 3119 5667 * 5394 6635 6552 * 2692 5768 3621 3090 * * 4436 7223 5397 3233 2076 * 5124 13
+ 43 * 5077 0 * 0 * 8357 1034 1034
+
+K 14 3285 6057 2743 * * 4502 * * 7239 6108 * 6180 * 7371 7131 1233 2282 6657 * * 14
+ 55 5282 6405 3881 101 * 0 8365 1261 1206
+
+P 15 3285 * 4366 3663 7068 6597 * 4529 4298 1385 7164 5463 4785 5284 4322 4437 * 3517 * * 15
+ 37 5316 * 498 1777 0 * 8353 1329 1322
+
+A 16 5247 * 965 6492 * 5317 5096 * 4595 * * 1901 * 5588 5130 5909 7171 7181 * 7151 16
+ 30 5977 7644 945 1057 * * 8426 1087 0
+
+L 17 * * 7783 6838 4464 605 5387 6637 6693 4502 6156 3525 * 5544 4326 7142 * * 6381 7633 17
+ 10 7168 * 553 1652 0 * 8427 1043 1000
+
+G 18 3240 5257 * 5194 2380 3008 5488 4717 4415 3848 7416 6493 * 6550 6742 7075 7253 3086 7495 2528 18
+ 16 * 6493 * * * * 8424 0 0
+
+I 19 4470 5400 * * 3620 7243 6222 749 * 3451 5571 * * * * * 5559 3400 * 7266 19
+ 212 2873 * 290 2458 * 0 8442 2077 1032
+
+G 20 2119 * 3414 4397 * 1068 * * * 5957 * * 6858 5994 7025 4018 4584 * * * 20
+ 212 2940 7229 728 1335 * 0 8442 2089 1032
+
+Y 21 3955 7429 3597 5994 5035 4761 4207 5483 2925 3665 * 4181 2775 4374 3412 4674 4966 5963 * 4432 21
+ 95 3971 * 453 1891 * 0 8388 1472 1181
+
+K 22 3727 * 2380 4043 * 2940 5182 7447 3909 5589 6352 2451 4864 4900 4524 4663 4344 5796 7043 * 22
+ 136 3704 6228 0 * * 0 8388 1584 1181
+
+G 23 5111 * 3020 5222 * 1251 4473 6887 5558 * 5878 2561 4753 4694 7023 5154 6788 7157 * 6368 23
+ 83 5651 4799 1053 949 2601 260 8382 1100 1288
+
+K 24 4745 * 2561 3413 7003 2819 * 7187 2714 * * 4228 5652 4059 3870 3021 4917 6012 5864 * 24
+ 170 3456 5663 2437 294 1896 451 8335 1644 1519
+
+M 25 7491 * 5096 5378 4188 4860 5431 2989 5670 1414 2993 5419 6137 7324 * 5522 4842 4045 * 5556 25
+ 0 * * * * 281 2500 8328 0 1533
+
+P 26 3986 * 2546 5468 6700 5029 * 6706 5590 3764 * 7103 1243 5103 5470 3681 4899 7445 * * 26
+ 170 3869 4551 1862 464 0 * 8492 1534 1038
+
+W 27 5486 7205 * * 3420 * 6861 * * 4933 4885 * 6688 5773 * 6509 * 5131 508 4986 27
+ 225 3048 5421 796 1237 * 0 8429 1943 1300
+
+R 28 4314 7236 6209 5201 4448 4037 2762 5089 4076 2718 4611 4928 4357 4466 3464 3804 6327 4980 * 4904 28
+ 607 1738 4515 1518 620 0 * 8367 3465 1716
+
+L 29 4780 5127 4604 4088 3250 5120 5749 2949 5823 2275 4846 4898 5210 6068 * 3533 5639 4149 5594 4831 29
+ 112 4310 5381 1719 523 650 1463 8466 1570 1291
+
+R 30 4339 * 2908 3628 7018 5022 * 5858 2663 6179 7270 4421 1785 5456 4604 4241 5151 5591 * * 30
+ 104 4157 6180 1024 976 1585 585 8434 1506 1284
+
+K 31 3016 7141 2541 1708 * 3576 6985 * 3979 * * 5541 5226 4256 6663 4207 4534 5135 * * 31
+ 94 4171 7011 2054 398 2742 234 8434 1385 1311
+
+E 32 4799 * 1024 2006 7192 5505 5622 7120 7235 5332 * 5995 4428 6542 * 5603 4871 6961 * * 32
+ 124 4050 5501 1047 955 2705 240 8435 1508 1312
+
+I 33 3778 6151 6203 7432 3458 4428 5369 4733 4748 2032 2682 * 6092 4760 5336 4858 5094 3650 5621 5896 33
+ 73 4334 * 1386 696 2321 322 8380 1496 1451
+
+R 34 2577 * 3513 3471 6086 3694 4710 4933 3149 4811 6129 5009 5492 3220 3929 4436 4576 6101 * * 34
+ 37 6035 6625 602 1552 * 0 8408 1060 1348
+
+Y 35 4294 * 4795 4536 2525 5632 2694 7662 5284 5045 5721 4494 7162 4636 3500 * 5284 4625 4720 2667 35
+ 69 6380 4859 0 * 273 2537 8412 1034 1439
+
+F 36 7080 6633 7025 7225 1045 6368 5160 4462 6970 3296 5388 5657 * * 7194 7290 5108 4255 5330 2997 36
+ 62 4570 * 1998 416 771 1272 8486 1300 1304
+
+K 37 3429 * 5367 3435 5560 7233 7442 4342 2401 3879 4763 7335 6206 4859 2706 3866 4306 4489 6700 4934 37
+ 53 5101 7130 1894 452 * 0 8484 1234 1086
+
+D 38 3114 7509 3029 2597 5202 5379 5591 7206 3436 5502 * 3588 * 3212 4003 4474 4026 5131 * 6692 38
+ 19 6284 * 0 * * 0 8474 1047 1146
+
+V 39 3960 * 4725 3840 3744 7010 5266 3506 4791 2260 4481 5464 6289 4088 4118 6131 3257 4599 * 5059 39
+ 102 7451 4002 1000 1000 1694 533 8474 1000 1146
+
+T 40 4994 7312 5039 5127 4623 7360 * 3485 5319 3281 3887 7022 * 5136 5127 4681 1484 4205 6056 4596 40
+ 45 * 5028 * * 2002 414 8443 0 1582
+
+T 41 2941 * 3984 3808 * 6895 6005 4646 3905 2730 4116 5338 * 4535 5161 3836 2633 5847 7015 4512 41
+ 253 7335 2695 2585 263 * 0 8435 1045 1658
+
+R 42 3720 6186 5202 3816 5492 1997 5122 * 4434 5012 * 2638 * 4230 3410 3672 4713 6821 * * 42
+ 814 * 1213 * * * 0 8224 0 2943
+
+T 43 2645 * 5058 5183 4338 6242 3895 4355 3888 4069 * 3808 5243 4205 4218 4368 2627 4041 * * 43
+ 749 4382 1486 2795 224 * 0 7118 1159 5358
+
+T 44 4260 4222 * 4319 * * 5554 5263 3285 4210 * 3584 1745 * 3971 4382 4320 3899 5074 * 44
+ 1328 4623 834 3170 170 4563 62 6383 1121 6071
+
+K 45 4712 * 2587 4056 * 4319 * * 3514 3026 4588 3654 4580 4637 * 2434 3526 * * * 45
+ 252 * 2643 * * 4630 59 5184 0 6569
+
+P 46 3589 * * 4660 4180 5018 * 4557 4727 2857 * * 1410 * 3957 3593 * 4338 * * 46
+ 402 2040 * 3448 139 3704 115 5662 1653 6557
+
+N 47 2299 * 5643 2687 * 3576 * 5626 2630 * * 3285 * 5048 3166 4193 4741 5675 * * 47
+ 27 5756 * 1000 1000 3111 177 6897 1034 6291
+
+T 48 4465 5957 3730 3381 * 3680 6007 * 2928 4395 * 4168 * 4386 3700 2586 3146 6135 5607 * 48
+ 56 * 4704 * * 1408 682 7340 0 5887
+
+R 49 2575 6299 * 6271 4504 6980 5139 2310 4509 5996 4424 5436 4893 5460 5190 4311 4761 2311 * 5469 49
+ 10 7154 * 711 1361 384 2098 7860 1104 4605
+
+N 50 5170 6852 1542 6243 6143 2272 3761 7155 4216 * * 2875 7386 5691 6323 4144 5603 * * * 50
+ 9 7348 * 3000 193 2426 297 8682 1000 1965
+
+A 51 1616 4436 5196 * 7014 5991 6109 4149 7615 4177 7102 5222 5041 6655 * 5604 2545 2660 7286 6078 51
+ 8 7430 * 2807 222 154 3306 8689 1007 1781
+
+V 52 4566 5284 * 6887 4327 7246 4545 2030 * 2461 4768 7284 * 7070 * 6372 5861 1775 * 5275 52
+ 0 * * * * * 0 8722 0 1018
+
+I 53 6887 * * * 7145 * * 1721 * 1742 5200 * * * 6639 * * 1535 * * 53
+ 0 * * * * * 0 8722 0 1018
+
+M 54 5537 7285 * 6234 3382 7171 7236 3943 * 2814 1121 * * 6707 * 5551 7529 3846 5577 4171 54
+ 0 * * 4322 74 0 * 8722 1018 1018
+
+G 55 6391 * 6701 * * 66 * * * * * * * * * 6214 * * * 6667 55
+ 0 * * * * * * 8734 0 0
+
+R 56 3043 6639 * * * 7537 6214 * 4273 6422 7749 6580 * 7108 641 4442 5284 6141 5940 5595 56
+ 0 * * * * * * 8734 0 0
+
+K 57 5253 * * 6299 * 4865 4531 * 1800 6818 * 2703 6701 7107 2136 4441 3866 4026 * 6213 57
+ 25 * 5881 * * * * 8734 0 0
+
+T 58 5781 5771 * * * 6190 6206 7188 * 4919 4661 * * * * 3409 416 6236 * * 58
+ 0 * * * * * 0 8691 0 1105
+
+W 59 5967 * 6514 * 1976 * 7364 5956 * 4703 6355 * * * * 6932 * 5896 2812 1063 59
+ 12 6874 * 0 * 867 1147 8691 1003 1105
+
+E 60 4670 * 2632 1255 5712 5852 5822 7772 4694 4413 7401 4639 6602 3866 4003 7073 4783 7589 * * 60
+ 37 5655 7579 1403 685 * 0 8725 1100 1008
+
+S 61 3331 * 4707 4376 7380 3679 5342 5276 5650 3807 3987 6179 7082 4244 5409 1935 4466 4137 5321 4675 61
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+�HHsearch 1.5
+NAME d5222617b3ccb99da7e3ec0bb92c4cb5
+FAM
+FILE d5222617b3ccb99da7e3ec0bb92c4cb5
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:03:46 2013
+LENG 147 match states, 147 columns in multiple alignment
+FILT 138 out of 1740 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCC
+CHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9899999999999977899994879999999998578888999999999864345768857599999999998722422268999999998675899838
+69999999999489999999999998647899909399999998639
+>Consensus
+xxxxxxxxxxxFxxxdxxxxgxixxxexxxxlxxlxxxxxxxxxxxlxxxxxxxxxxxgxixxxefxxxlxxxxxxxxxxxxxxxxxxfxxxDxxxxgxI
+xxxelxxxlxxxgxxxxxxxxxxxxxxxxxxxgxixxxefxxxxxxx
+>d5222617b3ccb99da7e3ec0bb92c4cb5
+SKAAADDFKEAFLLFDRTGDAKITASQVGDIARALGQNPTNAEINKILGNPSKEEMNAAAITFEEFLPMLQAAANNKDQGTFEDFVEGLRVFDKEGNGTV
+MGAELRHVLATLGEKMTEEEVEELMKGQEDSNGCINYEAFVKHIMSV
+>gi|125532611|gb|EAY79176.1| hypothetical protein OsI_34285 [Oryza sativa Indica Group]
+TEDELIYIRAQYNLLEPsSTDGRLCIENFRMALLQnSTDAMKESRALDILNALEPL--AYRRMDFEEFRAATISPYQLEALsRWEEIAGTAFEYFEQEGN
+RPITIEELAQVPTVSPKKQpqkklpqmgaegrKCRSVFYFCRTmVRRhfivlrtinkcfQYPRLSLIpGNLEMLNT-
+>gi|312380158|gb|EFR26239.1| hypothetical protein AND_07834 [Anopheles darlingi]
+-----RKVCFGLSKTPVPRKVVPPSKLLVLLLDRCRRPIVRSSSQ-------------------------------------------------------
+-----------------------------------------------
+>gi|145501910|ref|XP_001436935.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124404080|emb|CAK69538.1| unnamed protein product [Paramecium tetraurelia]
+-------LLKIFKFFDLTNQGFLKKQDFLKAIAKSGVtITEQEFAEKLWSHYSDG--V--QLNYKDFINRVVIKDSYQEdfsesriiASPLESLRakiql
+kgalgllnlaISLP-------NQFNCQQLQDYLRRQDID-----IEGLHQLfNGE---FMSQANLIGLIK--
+>gi|307187651|gb|EFN72623.1| EF-hand domain-containing family member C2 [Camponotus floridanus]
+-QPVYNEFIQMY--appkDTKDDIQILEYGKFKEALHQYlGDKITEHEIITIAR--yySSHE-KI-eHk-S-rEYVRQLLHTE-lYRFLWHDLDRL---k
+edL-----hhwdkDRTGFLPR-----------eslytilrgcrVPV--dvELLNSMLDHLcKAEDg---------------
+>gi|32394789|gb|AAN08425.1| phospholipase C-delta1 [Misgurnus mizolepis]
+-------IYSCMRKSDKDFDKKMSPKELKSFLQSINIEVDDDYAKILFEKCDTS--KSGFIEGKEIERFYKILTHRE------EIDVIYGEYAKTG-SLM
+STTDLLNFLLKEQKDsaSQTD-ALQLIDKyELDEDAKakqlMTKDGFLMYLHQ-
+>gi|258593894|emb|CBE70235.1| putative signal transduction protein with EFhand domain [NC10 bacterium 'Dutch sediment']
+VQSMQQFKERMFSRIDSDGSGGVDKTEFSDLAKKMSEmSGSSPNVEDVYSKYDAN--GDGALSADELNSFMKD--NAPAPPPMNgpmegrgmqgRLEGLF
+SKIDTDTDGGISKSEFGVFAENIRErKGDSIDGDKVFSVyDTDGDGSLSADELNSFMKDN
+>gi|332227145|ref|XP_003262752.1| PREDICTED: calpain-14 isoform 2 [Nomascus leucogenys]
+-EDQNERQNEFFTKFFEKYP-EINAVQLQNLLNQMTWSslgsrqpfFSLEACQGILALLDLN--ASGTMSIQEFRDLWKQL---------KLSQKVFHKQ
+D-HGSGYLNWEQLHAAMREAGIMLSDDVCQLMLIRYGGPRLQMDFVSFVHLMLR-
+>gi|281211821|gb|EFA85983.1| hypothetical protein PPL_01216 [Polysphondylium pallidum PN500]
+------------------------------------------------------------------------------TAAAAAATSSNNNNNSEsnaes
+gEQSPLLHSEHQHLpvdVK-gIGL-------------------------------K-
+>gi|168033621|ref|XP_001769313.1| predicted protein [Physcomitrella patens subsp. patens]gi|162679419|gb|EDQ65867.1| predicted protein [Physcomitrella patens subsp. patens]
+--------QQVYRYFDRTNSGCISFRQYAVGIAYVSShLRFKEAVVAAYNFCGGE--ENDLPDEPTLLRSLRVLIPSVSK---QQVKmivfwavpALCAQ
+LTNHEEVDVEVyeftcidgtqvlastdncslygrftcf---------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+S 1 * * * * * * * * 5023 * 4945 3041 3966 4713 * 1315 1684 * * * 1
+ 0 * * * * * * 8079 0 0
+
+K 2 3735 * 2830 2468 * * * * 2688 5654 5925 * 3197 2820 4774 3601 5511 5609 * * 2
+ 0 * * * * * * 9128 0 0
+
+A 3 4935 * 2370 1944 5741 * * * 4072 3777 * 6105 4573 3231 3539 3963 5893 4927 * * 3
+ 0 * * * * * * 9588 0 0
+
+A 4 3741 * 4045 2337 * * 3466 * 3836 4915 5126 4405 * 1722 3953 * * 5080 * * 4
+ 0 * * * * * * 9781 0 0
+
+A 5 4696 * * 4053 * * * 2298 3146 2207 5229 6451 5199 4664 3952 4634 4796 3395 6213 6162 5
+ 0 * * * * * * 9826 0 0
+
+D 6 3239 * 3201 2808 * * * 4282 2593 4912 * 4522 6280 3169 2930 4173 6452 6288 * 6191 6
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+
+D 7 3400 * 3852 1899 6454 * 6486 5274 3038 4850 6619 4556 * 4929 3746 4221 3953 5466 * 4006 7
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+
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+
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+ 36 5330 * 3164 171 * * 10648 1319 0
+
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+
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+
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+
+T 18 5356 * 1930 2978 7025 4360 3985 * 4730 4238 6982 2722 4628 4074 6768 3881 4655 * * * 18
+ 89 4917 5216 0 * 0 * 10779 1533 1000
+
+G 19 5812 * 3344 4740 * 2207 4242 * 2980 6234 * 2577 4005 3792 3839 6141 5153 7198 * 5986 19
+ 35 5904 7171 2567 267 934 1069 10770 1205 1464
+
+D 20 4179 * 2294 4060 * 4152 4991 * 4249 5881 7052 2704 5664 * 6881 2470 2863 5920 * * 20
+ 50 6037 5706 0 * 566 1624 10781 1181 1277
+
+A 21 6869 * 4232 3537 6803 878 5409 * 4602 6838 * 3877 * 4757 4394 4993 6880 7769 * 5138 21
+ 64 5222 5893 0 * 580 1596 10753 1448 1388
+
+K 22 6847 6853 6071 3502 4303 5075 5041 3931 3173 3538 5432 5624 * 4703 3330 4449 3758 3576 6770 3154 22
+ 13 6846 * 2221 348 533 1694 10756 1190 1407
+
+I 23 5868 * * * 5492 * * 1608 6703 1645 4348 * 7793 * * 6876 5937 2153 * * 23
+ 0 * * * * * 0 10803 0 1002
+
+T 24 * 5344 2264 4357 * 4991 * 6790 4918 * * 2863 4336 * 4377 2498 2103 * * * 24
+ 0 * * * * * 0 10803 0 1002
+
+A 25 3759 * 5005 4551 3049 6843 7253 3249 3019 3491 4661 5984 4621 5195 3903 5159 4428 3742 4950 5207 25
+ 0 * * * * 0 * 10803 0 1002
+
+S 26 4649 7247 4063 2062 4599 6237 5859 5784 3587 6250 5964 5069 7060 3462 3354 3092 4553 4359 * 5831 26
+ 0 * * * * * * 10807 0 0
+
+Q 27 7279 * 2419 1476 * 6904 6709 * 4554 4363 * 3677 7055 2939 4710 4880 4527 7274 * * 27
+ 0 * * * * * * 11011 0 0
+
+V 28 5511 5074 * * 1620 * 6839 3285 7191 1823 5005 * * 6893 * * * 3230 6959 3878 28
+ 45 7081 5442 2000 415 * * 11014 1005 0
+
+G 29 3827 7224 5011 4066 5520 4232 5102 4674 3492 3551 7133 4439 4987 3530 2656 5320 5358 3622 * 4211 29
+ 25 * 5856 * * 1559 598 10997 0 1384
+
+D 30 3481 * 3164 3118 5267 6866 4983 5531 3847 4094 4873 4431 * 3513 3362 3699 3831 4629 * 6062 30
+ 48 5415 6798 0 * 1795 490 10969 1355 1641
+
+I 31 2895 5004 * * 3140 3684 * 3309 * 2230 4540 6049 * * 4421 5483 4497 2923 6738 5934 31
+ 35 6989 5940 1335 728 890 1119 10833 1265 1621
+
+A 32 4055 5472 * * 3655 5882 6639 2782 * 1220 4066 7168 6486 5374 * 5921 * 3774 * 4478 32
+ 71 4639 7009 0 * 0 * 10963 1708 1565
+
+R 33 5478 6190 4557 3497 6230 5165 5428 5331 2918 4307 5431 4527 4595 3626 2544 3214 4550 6236 5913 5644 33
+ 31 7282 6064 0 * * 0 11004 1000 1016
+
+A 34 3160 5168 4733 3203 7274 4552 4898 3875 3524 3974 5925 5910 * 3532 4054 3018 4134 4813 * 5880 34
+ 46 5426 6998 0 * 1450 658 10978 1422 1404
+
+L 35 5367 4921 * 6500 3741 5398 5447 3099 5547 1516 3757 5383 * 5758 5445 4790 5443 3596 7047 4884 35
+ 203 3121 5932 1470 646 1776 498 10993 3174 1418
+
+G 36 4621 6994 4056 4661 5111 1443 6284 6335 5009 4395 6915 3775 5509 4160 4302 3670 4449 5868 * * 36
+ 93 5459 4663 774 1268 * 0 10983 1307 1621
+
+Q 37 4633 4383 4387 4051 3504 5934 5766 3808 4311 2711 4702 4801 4403 5358 4320 4782 5026 3354 6717 4796 37
+ 166 3438 5934 962 1039 665 1438 10922 2803 2486
+
+N 38 3652 6935 3056 4062 5654 4744 7012 4488 3125 5850 6087 3079 2952 4499 4993 3695 4924 5545 * 5557 38
+ 112 3908 6993 2171 362 1149 865 10937 2414 1809
+
+P 39 4441 7023 4228 4925 3489 5484 * 3705 4963 2545 4178 4971 2717 * 4864 4682 4455 3661 7255 5334 39
+ 34 5420 * 1519 619 0 * 10947 1714 1525
+
+T 40 5886 * 3238 7303 4415 5089 * 5112 3769 5016 5104 3912 3588 6070 5255 2098 2526 5741 * 5994 40
+ 35 6950 6002 5807 26 * * 10999 1036 0
+
+N 41 4229 6303 3083 2877 5473 6022 6108 4826 3913 3433 6851 4387 4201 4215 3934 3630 4037 5942 6945 4754 41
+ 19 7043 7441 1000 1000 888 1122 10979 1000 1178
+
+A 42 3899 * 2841 2165 5103 5432 6191 7336 3854 4468 5291 5167 3748 3800 4405 4299 3955 5520 * * 42
+ 12 6868 * 4087 87 0 * 10997 1000 1135
+
+E 43 4877 * 3195 1961 5186 * 5495 5254 4493 3437 4643 5773 7102 3018 4482 5290 4895 4692 5899 4679 43
+ 25 6829 6881 1585 585 * * 10999 1023 0
+
+I 44 2816 6126 * 5935 4829 7105 * 2271 6843 1890 4137 * * * 6700 4719 5940 2983 6109 4735 44
+ 0 * * * * 0 * 11017 0 1039
+
+N 45 3743 6188 4392 2938 5210 6956 5388 4473 3356 4059 5453 4054 * 3100 3391 4064 4770 4056 * 5629 45
+ 22 6063 * 1585 585 * * 10999 1188 0
+
+K 46 3457 4637 3394 2779 6329 4742 6342 5385 2870 4559 * 5296 * 3567 3240 3957 4449 6858 6101 6199 46
+ 0 * * * * * * 10987 0 0
+
+I 47 4719 * * 5621 4578 6987 5515 2494 5231 1564 3338 * 7085 * * 5340 4484 3267 6249 4832 47
+ 0 * * * * * * 10987 0 0
+
+L 48 4269 6121 * 4932 1971 * * 3609 5020 2499 4198 7075 5460 6101 5973 5339 5091 3110 5475 4352 48
+ 90 4243 6974 2561 268 * * 10987 2132 0
+
+G 49 3353 5479 3646 3818 4362 5082 4611 5008 2604 4498 5552 4314 6003 3689 3723 3534 5654 6928 * 6045 49
+ 47 5360 6958 2807 222 * 0 10969 1370 1035
+
+N 50 3548 6974 5340 2954 4269 5634 4610 4852 4482 4094 4137 4277 * 4319 3037 3091 4712 4526 * 5466 50
+ 111 5000 4544 1000 1000 * 0 10965 1546 1222
+
+P 51 3852 4417 5880 5883 2896 6056 4552 4225 4954 2366 4508 6023 5861 6025 5594 7240 5003 3850 6160 2791 51
+ 323 7367 2361 2807 222 2710 239 10955 1000 2238
+
+S 52 4812 * 1348 4055 4258 3604 * 6675 5064 5727 5001 4277 4053 4627 4582 4482 6450 6996 * 5107 52
+ 148 4246 4489 2421 298 721 1346 10669 1726 5344
+
+K 53 3521 4473 5397 4102 4383 4457 4797 4123 3588 3734 * 4846 3465 4487 4205 3624 3924 4043 6808 * 53
+ 112 5265 4364 1195 828 1530 613 10885 1518 3610
+
+E 54 5902 * 1711 3107 5727 3985 5830 6925 3898 5698 * 3162 5643 4998 4659 3585 3911 7126 * 6975 54
+ 1151 6933 885 4700 57 * 0 10905 1000 3595
+
+E 55 4317 5697 4011 2904 4109 4679 * 4774 3210 5925 5673 5633 4038 5587 3725 3125 3556 4644 5570 5715 55
+ 208 4549 3447 0 * 4748 55 9480 1357 9018
+
+M 56 5546 * 2171 3534 * 5690 * * 4699 4819 3757 2090 * 4522 4589 4692 3929 4071 5702 * 56
+ 151 3329 * 2781 227 251 2646 9366 1696 9151
+
+N 57 3994 5035 4153 3965 7015 2450 4566 * 3271 5357 * 3195 4286 3660 3637 3971 4581 * * * 57
+ 90 4543 5806 1658 550 228 2773 10889 1810 3075
+
+A 58 4920 * 2015 4036 6935 3824 6158 4799 4326 6048 * 2968 5452 4129 5420 2855 4222 5351 * 5848 58
+ 31 6206 6965 3245 161 1961 428 10993 1178 1527
+
+A 59 4781 6915 3462 3610 6823 1182 * 7199 5051 6958 6134 3635 5842 6020 4154 3953 5482 6792 * 6920 59
+ 44 5359 7388 2377 308 * 0 10963 1373 1683
+
+A 60 5128 5174 5006 4474 5261 4401 4511 4630 2543 3966 4646 4478 * 3911 4013 3310 3485 5023 * 4638 60
+ 29 5629 * 1585 585 414 2004 10909 1225 2160
+
+I 61 5045 7014 5998 * 4749 * * 1541 5030 2068 3527 * 5785 * * 6875 6993 2513 * * 61
+ 0 * * * * 979 1021 11000 0 1168
+
+T 62 5514 7018 2070 3998 * 4202 5381 * 4876 6834 * 3047 6909 5137 4980 2470 2612 7212 * 6924 62
+ 21 7167 7124 0 * * 0 10977 1000 1000
+
+F 63 5552 7028 7357 5110 1757 * * 5501 5054 2348 6029 * 6862 6819 4000 * 5899 4215 4126 2571 63
+ 0 * * 1445 660 0 * 10966 1217 1217
+
+E 64 3600 * 3540 2320 6849 6690 6208 7218 2810 7277 5361 3694 4287 4346 4636 3748 3924 4675 * 5507 64
+ 0 * * * * * * 10987 0 0
+
+E 65 4549 * 2596 1386 7421 4727 7062 7046 4699 6125 6994 4036 7015 3189 6849 4423 4700 6669 * 6958 65
+ 68 6867 4745 4644 59 * * 10987 1000 0
+
+F 66 7203 6985 * * 674 * * 5100 * 2648 5468 * * * * * 6981 4387 4724 4220 66
+ 35 5382 * 1628 564 0 * 10793 1620 1817
+
+L 67 3738 4799 * 4814 6108 * 6029 3360 4542 2157 3931 6213 * 4802 4418 4008 5110 2662 * 4363 67
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+
+P 68 3440 7029 3326 3436 6000 5576 4243 5717 3737 4907 5522 4695 5446 3957 3659 3514 3567 4278 * 4608 68
+ 50 5805 5920 2513 278 970 1030 10989 1203 1226
+
+M 69 2944 6139 7118 5808 2725 4190 4779 3322 4974 2286 5437 6646 * 5635 * 4505 4090 4490 7053 4522 69
+ 22 6036 * 2308 325 576 1604 10955 1158 1421
+
+L 70 5014 4290 * 7158 3523 6928 5488 3024 * 1444 3660 * 7262 6027 6006 6966 5354 3112 6305 5281 70
+ 52 4829 * 4034 91 0 * 10973 1706 1018
+
+Q 71 3356 4563 4666 3584 5374 5219 4286 5039 2932 3594 5698 4820 6071 3746 3942 3377 4207 6704 * 5527 71
+ 0 * * * * * * 10987 0 0
+
+A 72 3434 5984 3931 3783 5101 5044 5391 4325 3557 3606 4891 3914 5121 6023 3710 3449 4241 4104 * 5056 72
+ 28 * 5678 * * * * 10987 0 0
+
+A 73 5087 6106 5583 4160 3364 6108 5308 3877 3899 2437 4496 7024 6785 3807 3996 4504 4802 3700 4836 4817 73
+ 205 6099 3086 2014 410 1475 643 10967 1157 1326
+
+A 74 3549 4570 4872 4945 4045 4344 4675 3633 4584 2298 3886 5060 5696 5930 4165 4511 5008 5019 6918 5146 74
+ 244 3455 3952 3319 152 2489 283 10856 2720 3784
+
+N 75 4821 * 4564 3394 4589 4123 4186 5193 2987 4876 * 4089 5328 3916 3564 2802 3955 6776 * 4864 75
+ 177 3494 5212 4699 57 3759 111 10787 2491 4405
+
+N 76 3855 6688 5822 2990 5572 3727 4863 3811 3293 3892 5398 3890 5165 4336 4037 3911 3918 5866 * 5217 76
+ 105 5073 4622 2741 234 2158 366 10752 1371 4568
+
+K 77 5966 5260 4351 3490 7074 4287 5518 5837 3923 3645 5694 3587 3693 5686 3399 3025 4150 3739 * 5166 77
+ 270 4307 3060 2882 210 1321 738 10807 2106 4459
+
+D 78 5006 6712 2850 3209 5649 5254 6926 6785 4242 3346 * 3076 3541 4040 3992 3016 5142 6904 * 6712 78
+ 304 5881 2531 2908 206 4842 51 10690 1365 4943
+
+Q 79 4189 * 4239 3427 6469 5340 5510 5536 2993 3246 * 4207 4082 3526 3897 4654 3856 4416 * 3921 79
+ 269 5260 2798 419 1988 2738 234 10078 1485 6814
+
+G 80 3310 * 2922 3924 * 4088 4733 4457 4850 3338 * 4157 4438 4845 4677 2976 3791 5414 * 5214 80
+ 126 3771 6557 2675 246 1630 563 10082 1905 7301
+
+T 81 3933 * 3831 3669 4658 4983 4508 3649 3875 3614 6542 4126 5011 5619 3438 3697 3508 4603 6129 6822 81
+ 59 5682 5623 2190 357 5339 36 10342 1222 5900
+
+F 82 6778 * 4320 2398 4279 4939 5371 4443 3692 3272 5067 5005 6723 4341 3189 4056 4876 4613 * 4280 82
+ 57 5089 6694 2959 199 409 2018 10318 1328 6008
+
+E 83 3534 * 2779 1977 6960 5361 5664 6911 3693 5083 5396 4014 4107 4127 4766 5521 4333 5350 * 6251 83
+ 49 5334 6911 3696 116 531 1699 10919 1373 2623
+
+D 84 4019 7054 3240 2270 4590 6217 5458 4311 3046 3870 5646 4596 6953 4084 4911 4519 4385 5983 6856 5472 84
+ 115 3897 6728 4398 70 2071 392 10960 2448 1578
+
+F 85 3611 6075 * 6961 3133 * 7152 2564 6753 1587 4486 6045 6681 5665 6906 4663 4994 3903 6142 6194 85
+ 32 * 5507 1585 585 749 1304 10934 1046 1782
+
+V 86 4709 * 3332 2797 6993 5813 5724 3692 2912 3960 5156 4833 * 4115 2896 4568 4129 4724 * 7108 86
+ 34 6904 6041 3000 193 * 0 10934 1006 1773
+
+E 87 3411 6589 3834 3333 5455 6889 * 4274 3587 3780 6283 4073 5382 3461 3743 3945 4894 3512 6006 5395 87
+ 11 7035 * 1256 783 268 2561 10881 1372 2107
+
+G 88 1930 5403 * 5565 4716 6168 6108 2665 5013 2491 4270 6170 6844 5508 5667 4376 5006 4151 6938 * 88
+ 13 6851 * 2807 222 * 0 10978 1064 1046
+
+L 89 6147 4499 * * 689 6698 6917 4588 * 3463 4757 * * * * 6364 * 5937 5921 3482 89
+ 13 6841 * 5248 38 * 0 10978 1017 1046
+
+R 90 4030 7119 3506 3370 * 7350 4560 6724 2805 4508 6195 3626 6497 3169 2634 4249 4447 5884 * 6882 90
+ 67 4676 7264 1747 510 * 0 10978 1808 1046
+
+V 91 3237 5895 6207 3562 4724 6990 * 3786 3746 2803 3894 4679 6489 4001 4570 3834 5510 3426 6705 5253 91
+ 0 * * 0 * 0 * 10972 1046 1272
+
+F 92 5088 4851 6671 * 1706 7159 6300 3211 5402 2340 4778 5693 * 6946 6506 5879 * 4081 7252 3142 92
+ 39 7316 5601 2322 322 * * 10999 1000 0
+
+D 93 4131 6908 576 4674 * 4877 * * 6849 * * 5032 6489 5791 5936 5048 4241 6204 * 6767 93
+ 9 * 7377 * * 533 1694 10986 0 1289
+
+K 94 4117 * 5884 4627 6975 4801 4945 4879 2654 3440 5343 4634 4520 4410 3552 3744 3271 3891 7039 5078 94
+ 75 5521 5118 2344 317 0 * 11000 1349 1145
+
+E 95 4354 5879 1627 3421 * 4907 6921 6948 4790 5237 7049 2631 4665 4114 4447 3960 5142 * * * 95
+ 0 * * * * 0 * 10985 0 1729
+
+G 96 5156 7268 4034 4096 5365 2245 5070 5721 2787 * 6691 3254 5969 3213 3959 3555 5082 * * * 96
+ 48 5936 5921 1544 606 * * 10999 1210 0
+
+N 97 3929 5772 2209 4386 6125 5634 6810 * 3430 5732 6684 2925 6959 5083 4469 2387 4090 6159 * 6783 97
+ 22 7001 7121 2807 222 0 * 10959 1005 1198
+
+G 98 * 5796 3883 4275 * 844 5768 * 4194 6972 5998 4278 6240 5397 4088 4680 6111 6940 * * 98
+ 73 5129 5576 3323 152 * 0 10994 1526 1000
+
+T 99 4171 4168 5418 3985 3271 7125 5015 6242 3106 4269 5810 4679 4965 4478 4432 5253 3104 4422 7011 3288 99
+ 72 4686 6627 0 * 748 1305 10925 1760 1767
+
+V 100 5292 * * * 5555 6836 * 1270 6770 2324 4874 * * * * * * 1846 * 6870 100
+ 0 * * * * 1921 442 10919 0 1441
+
+M 101 5331 5441 2816 3499 6857 4917 5870 7781 5213 4926 7079 3749 4891 6271 4514 2381 2250 7013 * 5942 101
+ 11 7051 * 1585 585 * 0 10953 1007 1279
+
+G 102 3389 5306 6674 4375 4141 5515 5098 4372 2750 2966 6061 6998 5392 6108 3128 3768 4960 4209 7122 4435 102
+ 12 6925 * 3846 104 1023 977 10953 1232 1279
+
+A 103 3596 7021 2889 2060 6882 4570 4622 6780 4126 7061 6856 3880 6311 3459 4752 3046 4990 * * * 103
+ 0 * * * * * 0 10918 0 1054
+
+E 104 6259 * 2274 1375 6976 5036 6929 5970 4294 6838 6827 4407 * 3516 5172 4876 5650 4999 7194 6780 104
+ 14 6716 * 1585 585 * 0 10918 1023 1054
+
+L 105 6123 * * * 1684 * 7889 3261 * 1384 4561 * 7152 * * * 6838 3616 7365 4752 105
+ 11 7049 * 2000 415 0 * 10918 1016 1054
+
+R 106 5069 6150 4822 3807 4794 4563 5065 3251 2658 4026 5502 5053 * 4224 2938 4616 5287 3331 * 6134 106
+ 9 * 7265 * * * * 10972 0 0
+
+H 107 3813 7023 3059 3720 6043 * 4726 5010 2936 5200 5802 3686 * 3363 3932 3299 3632 7174 7004 5150 107
+ 0 * * * * * 0 10965 0 1046
+
+V 108 2560 6036 * 6849 3031 4436 * 2485 7107 2858 4267 7286 * 6271 * 5787 4680 2982 6117 4477 108
+ 18 7772 6959 1289 759 0 * 10965 1226 1046
+
+L 109 4575 5078 * * 3087 7094 6995 3617 * 1332 3062 * 6580 5885 * 5181 5271 3430 6095 6826 109
+ 61 4587 * 1561 597 * 0 10937 1714 1004
+
+A 110 5971 4676 4762 4195 7060 4219 4899 6107 2340 5502 5494 4470 6048 3016 3061 3219 3598 6837 * * 110
+ 15 * 6559 * * 0 * 10637 0 1004
+
+T 111 4141 6020 3553 3338 7131 5050 4925 5447 3232 3670 6044 3681 5197 5209 4323 3420 3248 4723 * 4977 111
+ 31 5550 * 1151 864 965 1036 10623 1501 1172
+
+L 112 3446 * 6948 5331 2945 7139 5413 3619 * 2297 3911 5431 * 4007 4958 3800 4986 3680 7113 4123 112
+ 323 3008 3714 1847 470 * 0 10621 3250 1000
+
+G 113 4411 5850 5330 4552 5190 961 6667 6622 4351 5108 * 4222 4054 5192 4466 4547 * * * * 113
+ 211 3305 4846 1280 765 678 1415 10340 2701 2623
+
+E 114 6757 6793 4561 2448 4202 6720 5114 3648 3936 2769 5331 3929 4123 3895 5816 5931 5793 3789 * 4965 114
+ 111 4318 5401 770 1273 2033 404 10474 1825 2221
+
+K 115 5407 6913 3981 3667 5871 3262 4379 * 3004 4526 5835 3332 3308 3981 3469 4463 5913 4448 * 6731 115
+ 120 3642 * 2426 297 1062 940 10467 2319 2405
+
+M 116 4639 * 6866 5340 3445 6866 6695 3086 6737 1744 3682 6881 3934 6238 6740 4829 4612 3620 5271 4914 116
+ 41 5590 7070 3053 185 1353 716 10500 1238 1675
+
+T 117 4318 5225 3014 4750 * 5878 * 7078 3795 4832 7079 3532 3329 5293 5841 2250 2792 4656 * * 117
+ 73 4615 6839 2621 256 * 0 10515 1707 1492
+
+E 118 4541 6309 2523 2085 5672 5322 6558 5304 4088 5747 * 3874 3565 5312 4764 4109 4550 4469 * 5939 118
+ 26 5815 * 970 1031 * 0 10497 1171 1693
+
+E 119 3274 6949 2964 2216 * 5194 6636 6619 3846 5282 * 4797 5040 3560 4486 2711 6616 5301 6898 6669 119
+ 14 6689 * 0 * 1002 998 10491 1192 1852
+
+E 120 5219 * 2560 1640 * 6906 4822 4079 4313 4013 * 5281 * 3364 5018 5079 4335 5813 6763 7005 120
+ 39 5719 7058 2729 236 601 1553 10517 1192 1347
+
+V 121 2774 7162 5840 * 4135 5332 * 2383 6858 2300 5336 * 6012 5868 5903 5414 6908 2365 * 4499 121
+ 0 * * * * 1069 934 10538 0 1165
+
+E 122 4662 5766 2882 2703 6338 6903 4857 5348 3446 4934 7102 3602 6787 3715 2876 4807 4428 4710 * 5859 122
+ 29 6753 6559 0 * * 0 10541 1027 1000
+
+E 123 3683 * 3727 2440 5875 4574 6717 4494 3738 4353 6677 4336 6825 4119 4229 3557 3623 5926 5863 4417 123
+ 25 5854 * 2070 393 866 1148 10502 1400 1220
+
+L 124 4863 6804 * 5763 3319 6794 6028 2382 5822 1795 3047 6791 * 7045 6914 5990 5167 3297 * 5333 124
+ 23 7030 6993 3170 170 * 0 10559 1000 1000
+
+M 125 5843 4811 * 6736 1882 * 6563 2483 6781 2191 3662 * * 6803 5819 6933 4784 4349 5308 5365 125
+ 89 4579 5781 2005 414 846 1173 10518 1931 1226
+
+K 126 3822 6748 3321 4020 7132 5331 5332 6740 2230 4028 7020 3784 * 3178 3570 3401 5280 6226 * 6793 126
+ 49 5252 7067 995 1005 * 0 10509 1350 1366
+
+G 127 3466 5228 4344 3145 3915 4514 5143 3752 3894 3821 4004 6963 * 3578 3312 4269 5076 5956 6682 7004 127
+ 1468 647 * 70 4407 421 1982 10507 8586 1526
+
+Q 128 3586 5172 1325 4905 4808 3380 6002 5817 6812 4547 * 4413 6907 5284 5234 5825 5912 4200 * 4524 128
+ 102 4291 5875 699 1380 * 0 10520 2059 1226
+
+E 129 4877 6889 4049 3979 5864 3679 6687 4022 2983 3073 5240 5960 4273 4738 3708 3887 3831 3898 6863 * 129
+ 63 4543 * 230 2765 2364 312 10515 1760 1758
+
+D 130 5726 * 1827 3601 5828 4878 6814 6653 3882 * 6547 2084 6620 5800 4752 4201 4281 4539 * 5806 130
+ 68 4741 6824 2282 332 384 2096 10526 1817 1582
+
+S 131 6889 5837 4169 2995 * 2113 6918 * 3112 4464 5894 3505 4947 4021 3330 4027 6935 5839 * 7086 131
+ 52 5276 6756 724 1342 893 1115 10546 1363 1211
+
+N 132 4261 6730 1631 3310 5884 5829 5989 * 4076 5180 * 3074 5268 4421 * 3261 4036 6900 * 6309 132
+ 25 5881 * 1680 540 976 1025 10527 1225 1187
+
+G 133 4858 * 3664 4904 * 1083 5195 7076 3700 6956 5346 3845 4392 * 4930 5309 4501 7016 * 6690 133
+ 50 5346 6725 2610 258 * 0 10520 1533 1226
+
+C 134 4115 5307 5862 4292 4436 4802 4761 4970 2778 4857 5240 5871 6915 3304 3389 4312 2899 4372 * 4782 134
+ 53 4784 * 787 1250 519 1727 10508 1770 1414
+
+I 135 6706 * 6825 6610 3871 * 6807 1624 6595 2133 4413 * * 6989 * * * 1855 * * 135
+ 29 5651 * 585 1585 * 0 10536 1226 1000
+
+N 136 5305 5317 2582 4833 * 6016 4957 6911 6007 5812 * 2971 5917 5819 4623 1790 2757 5739 * * 136
+ 0 * * * * * 0 10536 0 1000
+
+Y 137 5904 6793 * 7070 2200 6882 5737 4620 3449 2818 6739 6912 6715 6593 4418 6933 * 5328 3848 1938 137
+ 0 * * * * * 0 10536 0 1000
+
+E 138 4128 6525 2257 2616 6053 4890 4871 6319 3687 5852 7031 3454 5890 4106 4874 4241 3995 4787 * 6738 138
+ 18 6319 * 0 * * 0 10536 1075 1000
+
+A 139 4952 * 2335 1177 * 4188 * * 3555 7044 * 6851 * 3933 5958 4838 5158 6874 * 5801 139
+ 0 * * * * * 0 10536 0 1000
+
+F 140 6923 * 6595 * 689 * * 4931 * 2647 4904 6319 * * * * * 6745 5145 3552 140
+ 0 * * * * * 0 10536 0 1000
+
+V 141 3702 4887 6862 5714 5138 6579 5321 2750 3657 2122 4823 5325 * 4528 4839 5841 4474 3369 6078 5180 141
+ 13 * 6852 * * * 0 10479 0 1000
+
+K 142 2686 5832 3416 3789 6816 5124 4743 5924 3547 7058 6924 3161 * 4228 3972 2433 4802 * * 5753 142
+ 13 6826 * 2000 415 980 1020 10470 1010 1186
+
+H 143 2872 4712 5638 5855 2620 5750 4769 4165 4787 2974 3889 6734 * 5644 4405 5253 4636 3567 5293 5052 143
+ 0 * * * * * 0 10414 0 1000
+
+I 144 4678 5639 * * 3542 * * 2965 6434 1615 2923 * 6414 * * 4996 6662 2651 5245 5754 144
+ 0 * * * * * 0 10358 0 1000
+
+M 145 4019 5370 * 5266 4686 6162 * 4721 3026 2543 3812 5053 * 4462 3346 4020 2870 4797 6402 6394 145
+ 0 * * * * 0 * 10071 0 1000
+
+S 146 4287 * 3948 3162 5841 5039 4883 * 2900 5769 5988 3375 6017 4571 3022 2522 4710 5899 * 5919 146
+ 0 * * * * * * 9740 0 0
+
+V 147 4253 * 4318 * * 4269 * * * * * 1532 4400 3325 * 2285 * 3346 * 4350 147
+ 0 * * 0 * * * 7169 0 0
+
+//
+�HHsearch 1.5
+NAME d7be13700ed7588ca7b576ccd24889ab
+FAM
+FILE d7be13700ed7588ca7b576ccd24889ab
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:17:03 2013
+LENG 175 match states, 175 columns in multiple alignment
+FILT 117 out of 1090 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
+CCCCCEEEEEEEEEECCCHHHHHHHHHHCCCEEEEEEECCHHHHCCCCCEEECCCCCCCCCCEEEEEEEECCCCC
+>ss_conf PSIPRED confidence values
+9872335548856887557777439999999999999998569987659999986500458999889878999999998199575455576355774556
+877641454207990787999999998569989999814503323577466578888885897999998568898
+>Consensus
+lPxxxDxrxxxxixxvxdQgxcgxCwAfaxxxxxexxxxxxxxxxxxlSxxxlxxcxxxxxxxxcxggxxxxaxxxxxxxxGxxxexxxpyxxxxxxcxx
+xxxxxxxxixxxxxixxxxxxikxxlxxxGPVxxxxxvxxxxfxxyxxgvxxxxxxxxxxxxHaVxIvGxgxxgx
+>d7be13700ed7588ca7b576ccd24889ab
+APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKY
+NPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFEST
+>gi|288560029|ref|YP_003423515.1| adhesin-like protein with cysteine protease domain [Methanobrevibacter ruminantium M1]gi|288542739|gb|ADC46623.1| adhesin-like protein with cysteine protease domain [Methanobrevibacter ruminantium M1]
+LPSHFDARDWGWTTSAKIQGDNTDCWAFASISSLETSFAKASGVLYNLSQNYLQKLQLKyfySGDKRNsLTGFSYSGPGYALSWYGVLPV-DNGYDDRGM
+IADTDLEDERIHVQDVLFIDTgrddAVELIKWAILKYGAVTVQRGINGPYGELPTEGDDIAI---MSHGTHFISLIGWDD---
+>gi|170028894|ref|XP_001842329.1| conserved hypothetical protein [Culex quinquefasciatus]gi|167879379|gb|EDS42762.1| conserved hypothetical protein [Culex quinquefasciatus]
+IPTSFDARTRwpncPSIALIPNQGCCNSSAFQIPAAVITDRACIRSNGtsTRTYSAYDALACCTDCpfsQLFKCAGGDPLKVWNYWATT-GLVSDSCMPF
+SLSPlclgFNCPLLCApgYagsiVGDRKKGLKvvTVAPYVDAIQSEIILNGPVEASFDL-YLDFVHLKqSQVYNSRS-GPNLGRQSVKIIGWGVE--
+>gi|326787377|dbj|BAK08431.1| putative papain-like cysteine prorease [Plasmodium simiovale]
+----------SCVSKieAGDQGDCATSWLFASKVHLETIKCMKGHDHVASSALYVANCSNKEAKDMCHAPsNPLEFLNTMEETKFLPAESDLPYSYKavN
+NVCPEPKShwqnlwanvklldpqNepNSVSTKGYTAYQSdhfngNMnafiKLVKSEVMSKGSVIAYVKAD-ELMGYDLNGKKVLSLCGGETPNLAVNIVG
+YGN---
+>gi|89890478|ref|ZP_01201988.1| putative cysteine protease [Flavobacteria bacterium BBFL7]gi|89517393|gb|EAS20050.1| putative cysteine protease [Flavobacteria bacterium BBFL7]
+LPAVYDLGF--LMPAPRSQGAQGSCVSWATHYYLATYMDNIRNDSIISSIQEIMSPSFAfnqikasDGSNNCFGSTIAQNLDLLINT-GALPLSEFSYND
+--TTCAPQPDmiqlanTRNNLISSYENIGpytflePttqesliasSLNEVKSALFDNRPVIVSMLTD-EAFGRHrNEDVFTVSEINeaTVRGCHAMTIVG
+YNDD--
+>gi|285018828|ref|YP_003376539.1| cysteine protease [Xanthomonas albilineans GPE PC73]gi|283474046|emb|CBA16547.1| putative cysteine protease protein [Xanthomonas albilineans]
+PPENADLTQW-AIKP-SDQKQLGACASFATARTLAGWYANFTKQSvNLFAPMYLYTQV----NDGQDNGSTMeAPLDVALKQ-GIDTKADYFQGDydwRT
+KPTKHEranARNYKQPF-HYQMIYNnwgdnspvdsqaLIEQIKLAIANGTPVVIGFNV-RAGFDSLNqdHDIDYDNH-SKILDGHEVIALGYDKDG-
+>gi|339445227|ref|YP_004711231.1| hypothetical protein EGYY_16900 [Eggerthella sp. YY7918]gi|338904979|dbj|BAK44830.1| hypothetical protein EGYY_16900 [Eggerthella sp. YY7918]
+FPSKYSLVDEGVVTPVKLQNPWGTCWSFGGTAAAEVSLLSELGltydeTQLDLSELHtawmantplsdgssqdgegIHTTSSDDATVLSQSGFPFTLTSV
+YSSGIGPVPESVAPYKNKaekkeeiatpsgpipvwyskEGDWSVDQSLRfeqLYQLEESSILPSpaergaGVEAMKRELMQGRAVDIAFCS-DQTSTYIN
+NTTWSHYTYEEKPINHSVCVVGWDDN--
+>gi|297833374|ref|XP_002884569.1| hypothetical protein ARALYDRAFT_896743 [Arabidopsis lyrata subsp. lyrata]gi|297330409|gb|EFH60828.1| hypothetical protein ARALYDRAFT_896743 [Arabidopsis lyrata subsp. lyrata]
+-----DWRLiVDLLGPIIEQRE-AICWAIVLARLIEAMYNIWIGdskCFLRISVDDLVSKIKAE-DDDKEITTLNRCIKVIELE-GIKKVP---------
+TTSHANRDKIKTIKWVIDTNEaaDRNFIQTKLEI-SPVGIIIDI-DDEFSALREGFYKVrdvPRTGKTVSRHALMILGRG----
+>gi|118579734|ref|YP_900984.1| peptidase C1A, papain [Pelobacter propionicus DSM 2379]gi|118502444|gb|ABK98926.1| peptidase C1A, papain [Pelobacter propionicus DSM 2379]
+-PDRIDYRDRVYNPPlvclpeqypspefienhladytrkhklILNQGKEGACTGFGLAAVINYLLWKEcleagkdgGRsvsRIARVSPRMLYHMARIYDe
+wpGEDYEGSSCRGAMKGWHRH-GICTEQFWPYKTKFvpPKEGWQQDAARRPLGAYYRINKdSIADMQAAIREVGAIYVSASV-HKGWSLGASSTLPMIPF
+TTEVaGGHAFAITGYTTRG-
+>gi|297846494|ref|XP_002891128.1| hypothetical protein ARALYDRAFT_336538 [Arabidopsis lyrata subsp. lyrata]gi|297336970|gb|EFH67387.1| hypothetical protein ARALYDRAFT_336538 [Arabidopsis lyrata subsp. lyrata]
+------WETeeiKDIVGPVRDQKQHLLCWAYAASDLVSAQRILRqwENDYYPLCPHYLCRFVHPgwlgkdekaEPGHFCYRCSIKDALKHIKKE-GIPRE
+INSVFECSsDSRSRDPIPRGHGEVKSIRTLEDTLEAALKELPL-QPIGADLIV-FSDLWKSGRNIYHGPKSigSKFEGYHAVIIVG------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 5000 * 5750 * 3403 * * 3155 * 610 * * 5949 * * * * 4625 * 4993 1
+ 39 5233 * 2000 415 * * 8015 1133 0
+
+P 2 5895 * 5725 * * * * 6003 5610 * * * 197 * * 4857 * 5533 * * 2
+ 0 * * * * * * 8193 0 0
+
+R 3 3495 * 2874 3163 * * * * 3930 4706 6174 4562 3639 5248 4781 2009 3604 6189 * 5985 3
+ 29 * 5658 * * * * 8372 0 0
+
+S 4 4781 * 5278 4227 4562 * 5270 6147 3410 6129 5319 3507 * 4870 3612 1845 3369 4340 * 4635 4
+ 0 * * * * 0 * 8587 0 1081
+
+V 5 4320 * * * 1535 * * 4664 6210 4464 4711 * * * * * 6062 2794 2989 2448 5
+ 0 * * * * * * 8593 0 0
+
+D 6 6401 * 443 * * 6256 * * 6135 6109 * 3755 * * * 2983 6636 * * * 6
+ 19 6263 * 2000 415 * * 8681 1025 0
+
+W 7 3511 * * * 4207 6256 6301 5324 * 2036 6227 6369 6345 * * 3826 * 5536 1303 5135 7
+ 0 * * * * * * 8736 0 0
+
+R 8 4771 6552 6450 6358 * 4057 * * 3755 6176 * 6290 6340 4995 722 3694 5146 6269 * * 8
+ 0 * * * * * * 8736 0 0
+
+E 9 5045 * 1731 2712 6447 * 5307 6575 3645 5387 6459 3164 5309 5465 6518 3856 3872 5497 6380 6421 9
+ 404 3168 2908 1553 601 * * 8750 2351 0
+
+K 10 * 6236 5213 3371 6621 6309 3484 * 2311 3899 * 4305 4666 4641 4593 3934 5415 3271 4042 4115 10
+ 786 1716 3115 1497 631 3433 140 8552 4055 2657
+
+G 11 4216 * 3242 * * 1452 5247 * * * * 2604 5360 6269 4577 3413 3990 4862 * 6178 11
+ 78 5231 5260 3106 178 327 2302 8502 1147 3714
+
+Y 12 4210 3529 6225 * 4191 6614 6739 2904 4524 2798 4844 6560 * 5424 6625 5445 6564 2886 4915 2557 12
+ 0 * * * * 252 2644 8873 0 1820
+
+V 13 5602 4288 6598 * 4075 * 6605 1825 * 3006 3683 5406 * 6588 * 5324 4274 1982 * * 13
+ 35 * 5381 * * 0 * 8912 0 1000
+
+T 14 4729 * 6472 5071 6642 2703 * 6478 6683 5616 * * 2562 * 6592 2293 1762 4726 * * 14
+ 28 5723 * 1000 1000 0 * 8964 1122 1212
+
+P 15 3910 * 3794 3220 * 5719 4913 6701 4084 6566 6889 4881 1201 6545 5041 4040 5527 5525 * * 15
+ 139 4228 4702 2830 219 * * 8994 1741 0
+
+V 16 3429 * * 6349 5284 6718 * 2145 * 4630 6198 5044 3303 6632 * 6545 * 1227 * * 16
+ 0 * * * * 0 * 8956 0 1505
+
+K 17 5772 * * 4801 4354 4459 6793 3568 1765 4313 5136 6726 5651 5766 2328 4306 6468 5298 5650 5009 17
+ 39 7040 5693 0 * * * 9062 1000 0
+
+N 18 6619 6671 1065 5532 * * 4953 6563 6268 6605 * 1981 4823 6349 6866 3785 6261 6703 * 6721 18
+ 35 5389 * 3375 146 * 0 9073 1272 1202
+
+Q 19 * * 5468 6268 * * 6741 5861 * * * * 6071 147 * * * 5658 * * 19
+ 107 3813 * 1246 790 * 0 9073 1991 1202
+
+G 20 3767 * 6493 5545 * 897 * 7089 3893 6823 5998 4741 6843 4517 5145 4742 4786 6099 * 4279 20
+ 27 6756 6757 0 * 0 * 9114 1000 1202
+
+Q 21 4069 6708 3415 4190 6504 4660 5654 6520 3813 4151 6863 3026 3868 3928 4789 2538 4973 6372 6565 4473 21
+ 32 * 5496 * * * 0 9119 0 1006
+
+C 22 5458 1013 * 4922 5087 5150 4781 * * 3691 * 5695 * 4832 3909 4858 4329 5306 5725 5167 22
+ 29 5635 * 601 1554 546 1666 9089 1195 1383
+
+G 23 3818 5145 5193 4750 * 877 5320 6710 5654 5517 * 3732 5093 * * 3641 5788 * * 6297 23
+ 0 * * * * * 0 9141 0 1006
+
+S 24 3704 4770 4286 * 6650 3669 * 4562 * 3167 * 4319 * * 6625 1700 2547 4519 * 6583 24
+ 44 * 5051 * * * 0 9141 0 1006
+
+C 25 6720 422 * * * 5543 * 6350 * 6085 * 5536 * * 6741 2679 * 6809 * * 25
+ 0 * * * * * 0 9024 0 1526
+
+W 26 4245 * * * 6642 * * 6510 * 5501 * * * * 5327 5251 4442 3602 675 3344 26
+ 13 6749 * 2000 415 * 0 9024 1000 1526
+
+A 27 674 6512 6742 * 5734 4994 * 5063 * 4786 * 7499 5727 * 6090 3463 5054 3881 * 6837 27
+ 13 * 6816 * * * 0 9033 0 1526
+
+F 28 * 6700 * 5789 1108 * 4763 2963 * 6078 5750 5001 5733 5844 * 6908 6775 4141 4350 3068 28
+ 0 * * * * 909 1098 9025 0 1674
+
+S 29 866 * * 5817 * 3492 * 5690 6154 * * * * * * 2237 4380 4293 * * 29
+ 14 6649 * 4170 82 * 0 9123 1039 1233
+
+A 30 2042 * 5714 * 5048 3914 6154 3869 * 3767 6795 * 5240 * * 2622 2813 2983 5731 * 30
+ 0 * * * * * 0 9123 0 1233
+
+T 31 2210 5623 * * 6667 4755 6702 4120 4445 3372 5865 6686 * * 6777 3252 2116 2883 * * 31
+ 0 * * * * * 0 9123 0 1233
+
+G 32 2161 * 3463 3795 6959 3197 5290 * 4232 5884 6587 4537 * 4701 4687 2715 4025 6794 * 4399 32
+ 0 * * * * 0 * 9123 0 1233
+
+A 33 1923 5728 * * * 4630 4868 3870 * 2835 3415 * * * * 3057 3684 2911 * 6722 33
+ 0 * * * * * * 9155 0 0
+
+L 34 3472 6897 * * 3685 5766 5582 2257 * 1633 3948 * * * 6813 * 6652 2917 6669 5218 34
+ 26 * 5834 * * * * 9155 0 0
+
+E 35 3748 6182 * 875 6592 4539 * 6521 * * 6886 4704 * 4096 5031 3358 4086 * * 6646 35
+ 12 * 6906 * * * 0 9132 0 1193
+
+G 36 2516 6310 3223 * 5546 4127 6850 3996 6808 5754 5107 6266 6322 * * 2127 2525 5696 * 4279 36
+ 0 * * * * 1347 720 9130 0 1374
+
+Q 37 2956 * 6022 5945 6744 4799 5744 4569 5070 3308 5130 4524 * 4595 2429 3051 4165 5263 4943 3863 37
+ 54 7166 5071 1000 1000 * 0 9152 1000 1163
+
+M 38 4306 * * 7497 3360 5807 * 3246 6765 1825 3751 5229 * 5182 3919 * * 3627 5689 2869 38
+ 39 5956 6595 3170 170 1596 579 9091 1103 1698
+
+F 39 2468 2849 6665 5637 6212 4482 6843 4375 3416 3213 4568 4455 5558 * 3661 4791 5458 5203 5610 4667 39
+ 74 5052 5662 980 1020 1095 911 9083 1404 1587
+
+R 40 5280 * * 6266 * 4734 6838 1804 2450 3811 3843 4504 * 6674 3238 4767 6553 3502 * 6787 40
+ 25 6838 6894 658 1449 1115 894 9073 1181 1578
+
+K 41 3123 6774 4803 3636 5828 4833 5103 6683 2565 3864 6255 3983 * 2967 3427 4073 4707 6080 5568 * 41
+ 124 3690 7744 1895 452 461 1871 9102 2136 1390
+
+T 42 5787 6704 5824 4871 7169 2476 4875 6421 3762 4427 * 3532 6657 5000 4416 2805 2330 5854 * 4877 42
+ 145 3651 5947 1653 552 0 * 9149 2242 1122
+
+G 43 5196 * 5696 4762 5803 1912 4702 5137 3518 4121 * 2754 5220 4233 3747 3773 * 6529 * 4852 43
+ 457 1882 * 1495 632 658 1448 9145 4838 1147
+
+R 44 3905 6434 3746 3343 * 3177 5552 5234 3038 * 5257 3982 5264 3106 3486 5013 3925 4756 6194 * 44
+ 213 3074 5745 1995 417 0 * 9162 2857 1000
+
+L 45 4092 6687 3340 4036 4135 5114 4596 3981 4751 3434 5771 4456 4162 5092 4048 4171 4200 3856 6786 4202 45
+ 105 3831 * 2190 357 0 * 9181 2413 1351
+
+I 46 4762 * 4718 5830 3970 * 5596 2880 5986 3398 6829 4793 3893 7184 4260 7205 3256 2482 5988 3334 46
+ 23 5977 * 1000 1000 * * 9156 1119 0
+
+S 47 4816 * 2207 4784 5510 7241 4940 4833 3065 4305 7019 3584 3622 4685 3748 4293 3939 5276 * 5822 47
+ 76 4278 * 1326 734 * * 9156 1770 0
+
+L 48 4966 * * * 2364 5563 * 4058 * 1009 6750 * 6539 * 5852 5248 * 4072 * 3786 48
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+//
+�HHsearch 1.5
+NAME d973556a2b119e22f373f42b3ee50271
+FAM
+FILE d973556a2b119e22f373f42b3ee50271
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:01:59 2013
+LENG 205 match states, 205 columns in multiple alignment
+FILT 126 out of 1058 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCEECCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCH
+HHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCCEEEEEEECCHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHH
+HHHHC
+>ss_conf PSIPRED confidence values
+9864667122799999902354757999999999979999999999999988753004765789874199856668899999999961787889987889
+9999999880899999999999997478774799999589992899952688874566987589886524675888655789999999986599999999
+99539
+>Consensus
+xxxxxxxxxxlpxLpyxxxxLxpxiSxxxlxxHxxxhxxxyVxxLNxxxxxlxxxxxxxxxxxixxxxxxixxxaxxxxNHxxfxxxLxpxxxxxxxpxx
+xLxxxIxxxFGSxexfkxxfxxxaxxxxGsGWxwLvxxxxxxxLxixxtxnxxxpxxxxxxPlLxlDvwEHAYyldYxnxrxxYixxxwxxinWxxvxxr
+xxxxx
+>d973556a2b119e22f373f42b3ee50271
+MNDLEKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSG
+KLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKR
+FEDIL
+>gi|153955389|ref|YP_001396154.1| superoxide dismutase [Clostridium kluyveri DSM 555]gi|219855805|ref|YP_002472927.1| hypothetical protein CKR_2462 [Clostridium kluyveri NBRC 12016]gi|146348247|gb|EDK34783.1| Sod [Clostridium kluyveri DSM 555]gi|219569529|dbj|BAH07513.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
+---------NMKPEVFNF-NSVKGISQRQLNEHYK-LYVGYVNILNQiwntDYTPQNYTDSNP-TYSkMRSLKLGETYALNGVKLHNLYFKNMT---GGN
+TTPHGPVLNSIINQFSSYDNFLSYLTNVGLS--MRGWAILSIDSLDNKFHIIGSDLHDKGSVWISYPILVMDVYEHAYFMDFGTNKKEYISTFIKNINWT
+VVNKRFQK--
+>gi|302697213|ref|XP_003038285.1| hypothetical protein SCHCODRAFT_43770 [Schizophyllum commune H4-8]gi|300111982|gb|EFJ03383.1| hypothetical protein SCHCODRAFT_43770 [Schizophyllum commune H4-8]
+-----RALHTVRPLPYSVeEGLGRFMPPQALKTVAVDYLGGLVERLNNEIRDTELENKK--LVDvIIGAAQqenqvLAFNYGSLALNTSFFLRQLYSETH
+ERsmsy-----DLRTAIRTQYGSLAQLKSAFMGAASGMFSSGFLWLVSDS-RGNMGIVPTFGPGTLLIRsrshlaasdadfkrprsilddvdadsnpidv
+gipaqaalsdkltalnyGdvLYPLLCVPIYEHAWMsAGFGVwGREEWLRHMWSVVDWAAVSQNY----
+>gi|50547305|ref|XP_501122.1| YALI0B20086p [Yarrowia lipolytica]gi|49646988|emb|CAG83375.1| YALI0B20086p [Yarrowia lipolytica]
+---LGRALHTMPAYSGlgsqaAPTQINKFLSAETVKSAWFEHQHEMLERVNEGLAsseELEGLDLQSLALEtCNRSEDALHHFASGAFANDFFFKGVAST
+VkPGevsepidayhglyvsprdpdyqtvmpalatGetpawgNHPgtDDALYDLILTSFGTVEAFREHLLTKAESIFGNGYTWLVLSKHSGRLHLVNTYNN
+GF-IQkkgtnsaelaaeaaakraveadeakalaelqaeaqnkklnaleekllknkiykmevakqmrqaqpkilHDLKPLLNVNVWQHMWLNDYGAfGKRK
+YLDNFWEKIDWNVVKGRLQ---
+>gi|71402548|ref|XP_804176.1| superoxide dismutase [Trypanosoma cruzi strain CL Brener]gi|70867006|gb|EAN82325.1| superoxide dismutase, putative [Trypanosoma cruzi]
+------GFFSRPRLNYPVaSGIPAFISRRQFDVQYNIFHHDAVATLNRHTLgtSLEGHS-----LEtVIRRAsfdatqAAVHTAAAEHFNYCFFYKSLRP
+--WG-TAVPKQLREAFQLQYGrdgSVdvvEEVKRLFTVVVLSHQeRCGWVYLVWT--GKQFDVVEFPHGACPIGSDLIPLLAINVHEGAYSLDYGpSGLE
+QYAQNYFRACNWFLAERYYLQA-
+>gi|164688120|ref|ZP_02212148.1| hypothetical protein CLOBAR_01765 [Clostridium bartlettii DSM 16795]gi|164602533|gb|EDQ95998.1| hypothetical protein CLOBAR_01765 [Clostridium bartlettii DSM 16795]
+------------KLNYNFYDLNDFINSNELKYSYC-QYGAYLDNLNHILKDYKEFKDAS--LKdLLTNLDsmpdeialKVKINASNALNYEYFFNNLSS-
+-E-KTFAKGKILKEINNSFSSFDNFKKEFEKIALN-SNSDWIFLALNS-QNKLYLTTSKEVSSPVIYKDKIILCLNLDKEIY-----SNREQIIHNFLNY
+VDWNIANKNYN---
+>gi|294948608|ref|XP_002785805.1| superoxide dismutase, putative [Perkinsus marinus ATCC 50983]gi|239899913|gb|EER17601.1| superoxide dismutase, putative [Perkinsus marinus ATCC 50983]
+-----------FDVPFStYANFFPLVQPKALSYHYRSICGRDTARFNTGLRQLSLLPNlpthvrhMGFdallyfcEYEnILSEEiplplcDKLVYYGNSY
+IYHEIYFNCLRA--TGMyddfEEPlsleSSLLVQDITNAFGGMKELFEELLEAALSLDGYGWVWLLSLP-EG-LSVITSQDYDGIHGDQIYAIFNIDLWE
+HAYIESHGANVEAYIKAWWGAVDWNKLDVQY----
+>gi|261884240|ref|ZP_06008279.1| superoxide dismutase(Fe) [Campylobacter fetus subsp. venerealis str. Azul-94]
+-----------RHSPFNP-ATNAVVSEQTCNYHYGKHHQSYVNNLSNLIKgtDFEGAD----LFEILtHSEGAIFNNAAQIDTHDFYWDCIAA-------
+----------------------------------------------------------------------------------------------------
+--------
+>gi|342180748|emb|CCC90224.1| conserved hypothetical protein [Trypanosoma congolense IL3000]
+-----------------------------------------------------------------CLSHRAHFLASEDFCHSLVKRCTRRV--ACPVP-A
+EWKGIVSRQFASEAALEAELVFRAANRREAGWTWLVYDNqrpEEQRLVVVNMPGNRTPLLLGLWPLGVVDMTDKAVV-----------------------
+--------
+>gi|167569530|ref|ZP_02362404.1| manganese and iron superoxide dismutase [Burkholderia oklahomensis C6786]
+---------QMKALSCDP-AQLPDLSERLIVGHYEHNSGGAVKRLNAITDQLAGIAPGSTPVFvPNGLKREELVAANSMILHEIHFENLGA--S--RSID
+RTPEAAIKRDFGSVDRWRDECR------------------------------------------------------------------------------
+------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 0 * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+N 2 * * * * * * * * * * * 0 * * * * * * * * 2
+ 0 * * * * * * 1000 0 0
+
+D 3 * * 0 * * * * * * * * * * * * * * * * * 3
+ 0 * * * * * * 1548 0 0
+
+L 4 * * * * * * * * * 1195 2861 * * 2754 * * 2779 2926 * * 4
+ 0 * * * * * * 3227 0 0
+
+E 5 2322 * * 3175 * 3516 * * 2708 * * * 3120 3954 3633 3025 3928 * * * 5
+ 62 * 4567 * * * * 4124 0 0
+
+K 6 5305 * * * * 5523 * 5334 4072 5170 3598 * * 4192 956 4317 5075 3767 * 4842 6
+ 32 5493 * 2807 222 * 0 5223 1000 1000
+
+K 7 3708 6360 5796 5350 6010 2304 * * 4915 3842 3526 5414 4606 * * 2420 3047 6082 * 3757 7
+ 65 4502 * 2792 225 * 0 5798 1098 1000
+
+F 8 2893 * 6667 3933 4055 6491 * 3560 3581 3850 4438 5575 3502 6683 * 3421 3441 4017 * 3866 8
+ 19 6251 * 732 1329 0 * 6102 1302 1000
+
+Y 9 4151 * * * 1817 6203 2070 6147 5744 5082 * * * 6923 * * * 4576 * 1758 9
+ 12 6915 * 0 * * * 6161 1000 0
+
+E 10 4239 * 6279 3075 6698 * 5147 5405 3259 5948 * 6925 4657 4660 4031 2655 2069 4101 * 5093 10
+ 0 * * * * * * 6215 0 0
+
+L 11 4974 6404 * * 5769 * * 3656 * 990 3969 * 4028 4823 4551 5696 6203 3068 * * 11
+ 16 6473 * 1000 1000 * * 6253 1000 0
+
+P 12 4911 * * 5543 5969 5894 * 5750 4267 5254 5776 7330 721 5823 4353 * 4122 4352 * 6397 12
+ 0 * * * * * * 6358 0 0
+
+E 13 4028 * 3369 2657 * 6713 * * 2734 * * 5571 1687 5858 4659 4653 3688 5817 * * 13
+ 7 7731 * 1000 1000 * * 6365 1000 0
+
+L 14 * * * * 6086 * * 4709 6243 393 5699 5839 4766 * * 6633 5395 4414 * 5811 14
+ 45 6315 5775 1585 585 * * 6394 1007 0
+
+P 15 3913 * 3640 4502 * 4796 6481 6316 3555 5528 6580 4530 1112 5946 * 3183 * * * * 15
+ 42 5963 6282 0 * 1011 989 6554 1125 1071
+
+Y 16 * 5490 * 5481 2398 6281 4783 6375 6089 4672 * 4440 * * 5366 * 5913 * 5543 884 16
+ 72 5085 5691 2470 287 * 0 6549 1127 1097
+
+P 17 2414 * 2398 3982 * 4365 5165 * 4561 4387 * 2779 3625 5813 4542 3667 5229 * * * 17
+ 113 3910 6837 1104 903 370 2143 6534 1428 1234
+
+Y 18 3738 * 6527 4817 3216 * * 5573 3920 4249 6676 5351 3374 4168 5761 5338 * 3300 * 1735 18
+ 333 2531 4905 1303 750 0 * 6561 2099 1066
+
+D 19 3794 * 2004 4077 * 5518 5023 * 2974 * * 2684 6779 4501 3619 4116 4129 * 6430 5460 19
+ 13 6778 * 0 * 240 2707 6528 1000 1188
+
+A 20 1569 * 3046 4017 6671 2111 * * 4642 6872 * 4180 * 6299 5675 3783 6497 5708 * * 20
+ 17 6447 * 2322 322 * 0 6578 1017 1000
+
+L 21 6863 5383 * 6279 3722 6540 * 3585 6671 622 6087 7125 * * * 6388 6597 4262 * 5116 21
+ 0 * * * * * 0 6578 0 1000
+
+E 22 3403 * 4489 1283 6122 4600 * * 4235 3294 5857 3797 3788 5929 * 4290 * 6597 * * 22
+ 203 3695 4211 2400 303 * 0 6578 1464 1000
+
+P 23 3906 * 4391 6557 * 3117 6367 * 3601 * 6294 5264 730 7087 * 5938 * * * * 23
+ 0 * * * * 0 * 6487 0 1350
+
+H 24 4501 * 5368 6477 2304 2508 3968 4755 6661 2673 * 7235 * 6740 * 6582 6084 3377 * 2868 24
+ 12 6864 * 0 * * * 6616 1007 0
+
+I 25 * * * * 2911 * * 1151 * 1935 4164 * * * * * * 4161 * 4524 25
+ 0 * * * * * * 6628 0 0
+
+S 26 6914 7395 2558 7043 * * * * * * 6066 4688 6373 6215 * 606 3796 * * * 26
+ 0 * * * * * * 6668 0 0
+
+R 27 2351 * 4032 2393 * 4708 * * 4157 6040 * 4867 2663 4977 3730 3113 5157 * * * 27
+ 11 * 6991 * * * * 6668 0 0
+
+E 28 3679 * 4628 2215 * * 7043 * 2596 6441 5932 3549 * 2458 2728 6040 6588 7111 * 6156 28
+ 0 * * * * * 0 6647 0 1002
+
+Q 29 3219 * * 5081 * 3253 * 3015 * 3672 * 6423 * 2838 * 5152 1552 4820 * * 29
+ 0 * * 1000 1000 0 * 6647 1002 1002
+
+L 30 6967 * * * 3013 * * 2502 * 1574 2329 6827 * * * 6021 * 3178 * 5509 30
+ 11 * 6991 * * * * 6668 0 0
+
+T 31 6160 * 2801 2178 6019 5985 * 6562 2631 5684 6681 3178 * 3899 3243 4275 4692 * * 5998 31
+ 17 6380 * 1000 1000 * 0 6647 1020 1002
+
+I 32 4482 6757 5377 4621 3348 6376 * 3278 * 2359 5038 5528 * 4851 * 4188 3062 3095 6190 3627 32
+ 0 * * * * * 0 6676 0 1002
+
+H 33 3221 * 6431 * * * 467 6671 * 4696 * 6049 * 5255 * 4911 6478 5419 * * 33
+ 5 8283 * 1585 585 * 0 6673 1000 1002
+
+H 34 5427 * * * 3488 * 1700 * * 4909 6972 * * * 6567 5118 * 7079 2496 1668 34
+ 131 * 3525 * * * 0 6678 0 1035
+
+Q 35 6476 6094 2721 3569 3766 2843 4675 6373 4117 5308 * 3917 * 4405 5477 3224 3333 4348 * * 35
+ 96 6381 4259 1000 1000 218 2836 6467 1031 1650
+
+K 36 5696 * 3590 3551 6126 3729 * 4938 1396 * 7102 4194 * 4032 4323 5477 4462 4107 * 6473 36
+ 0 * * 2585 263 0 * 6607 1002 1349
+
+H 37 * * * * 4763 * 883 4328 * 2911 * 4658 * 6160 4688 6600 6738 7021 5007 3520 37
+ 9 * 7270 * * * * 6687 0 0
+
+H 38 6404 5561 * 6766 7059 6089 1244 * * 4719 * * * 2311 6082 6735 7037 5622 * 2173 38
+ 15 * 6570 0 * 0 * 6664 1000 1000
+
+Q 39 3269 * 5749 4641 * 3324 5429 6942 2520 6491 * 5317 6954 1788 3775 4059 4964 4915 * * 39
+ 0 * * * * 0 * 6832 0 1007
+
+A 40 2378 * 4437 6404 5609 1548 5171 7125 7064 6353 6724 4932 7174 5166 5526 4881 3033 6338 5989 4332 40
+ 0 * * * * * * 6840 0 0
+
+Y 41 3664 5413 5507 * 6748 * 6615 6392 7125 3155 5279 * * * * 6630 * 4570 * 629 41
+ 23 6748 7276 2585 263 * * 6840 1000 0
+
+V 42 4768 5514 * * 6216 * * 2759 * 3010 6065 * * * * * 3781 834 * 7070 42
+ 11 * 7033 * * * 0 6838 0 1000
+
+D 43 3363 * 2023 3628 * 6978 * 6970 2953 * * 2066 * 4631 7238 4522 3653 5507 * * 43
+ 0 * * 0 * 924 1080 6829 1002 1065
+
+G 44 4775 6793 5868 5229 * 4129 * 6670 2161 6635 5938 1699 * 4460 2756 5011 4032 * * * 44
+ 11 * 6982 * * * 0 6838 0 1000
+
+A 45 3426 * * * 4348 * * 6251 * 637 6201 * * * 6868 6411 3601 4629 * 4471 45
+ 9 * 7374 * * * 0 6835 0 1060
+
+N 46 * 6377 * 7196 * 6933 7574 * 5701 6366 * 253 * 6785 6301 7215 4076 6739 * * 46
+ 24 * 5945 * * * 0 6833 0 1112
+
+A 47 2590 * 3409 2726 * 6468 5484 5665 2795 4196 5058 4406 * 3859 4479 4120 3680 * 6615 * 47
+ 30 5590 * 1609 573 1201 823 6816 1152 1249
+
+L 48 1967 6785 7126 4886 7579 5003 4302 3300 6871 1726 7056 6739 6741 6805 5424 5323 4564 3858 * * 48
+ 30 6026 7569 2139 372 * 0 6833 1049 1112
+
+L 49 4829 6822 5599 3953 6720 * 5777 4189 5967 1578 6022 4843 * 5185 4647 6530 2827 2851 6457 5807 49
+ 73 5113 5594 1945 434 2420 298 6837 1159 1153
+
+R 50 2700 * 4443 2210 * 4446 7182 * 2656 4631 6440 4345 5995 4115 3756 3627 5619 5445 * * 50
+ 667 1434 * 1155 860 1272 771 6805 3405 1324
+
+K 51 4431 * 3485 2651 * 3260 7332 7312 2502 5759 5621 5360 4160 2770 4830 3714 5436 7730 * 7213 51
+ 154 4297 4318 1423 673 * 0 6805 1354 1163
+
+L 52 6492 6890 7250 * 3658 6337 6246 3715 6812 1231 4562 4882 * 7364 6634 5314 3679 6204 4839 3134 52
+ 64 4761 7226 866 1148 682 1408 6777 1191 1534
+
+D 53 2875 7396 4251 2062 6908 4322 6761 7720 3462 6432 * 4960 4200 3723 4002 3672 5295 6044 * 4402 53
+ 79 4703 6047 1183 838 2257 339 6805 1216 1221
+
+E 54 4034 * 3199 2395 5356 2753 5966 6226 3873 5204 * 3778 5045 4103 6999 3324 5168 5760 7301 5592 54
+ 204 3420 4693 1063 940 * 0 6643 1618 1286
+
+A 55 2900 * 4432 4476 5571 5183 5192 5385 3193 2509 3818 5366 6374 4937 3502 3986 5983 5784 6874 4153 55
+ 44 5720 6530 1571 592 2085 388 6588 1079 1559
+
+R 56 4688 7303 3630 4551 5099 5653 5288 5741 5169 4074 * 4205 3575 5818 3045 1873 3662 6160 * 6980 56
+ 974 6306 1064 1585 585 * 0 6717 1031 1485
+
+E 57 2807 * 2434 3813 5753 4398 * * 3937 3617 * 4634 3973 3737 3787 3463 4965 6171 * * 57
+ 214 4477 3428 2230 346 5253 38 6223 1094 4338
+
+S 58 2525 * 3898 4000 * 5650 * 4803 3602 4889 5088 3281 4596 3669 4377 3895 2808 * * 6102 58
+ 37 * 5295 * * * 0 5859 0 4465
+
+D 59 3498 * 4262 4317 * 1832 * * 5612 * * 3025 3496 4739 * 2214 5379 5692 * * 59
+ 1860 4729 542 3139 174 4406 70 5854 1203 4519
+
+T 60 4178 * * * 3763 4061 * 4068 2721 3695 * 3451 * 4277 * 3176 3043 3925 * 3611 60
+ 708 1367 * 1585 585 1401 686 4851 1499 5689
+
+D 61 4030 * 2547 4138 5286 4885 5668 4682 * 3953 * 3100 3428 5779 * 2978 3905 3520 * 5673 61
+ 152 3325 * 1248 788 113 3734 6463 1320 4287
+
+V 62 4588 * 6081 5946 3329 5140 6460 2882 7113 1518 6370 5008 5045 7417 6298 5473 * 3205 7311 3904 62
+ 33 5452 * 1644 556 2140 371 6787 1107 1241
+
+D 63 3869 6295 3679 1855 6193 5610 5217 5962 4507 4665 5529 3934 4650 4350 6108 3495 3205 7402 * 6588 63
+ 2433 296 * 419 1989 1803 487 6796 5564 1171
+
+I 64 5641 6311 7250 7483 4376 * 5528 1762 * 2145 4035 6662 * 4392 5613 * 5892 2911 * 3722 64
+ 9 7370 * 4165 83 * 0 6804 1047 1103
+
+K 65 4260 7370 7224 5668 5570 6351 5887 2290 4070 2021 5988 4312 * 6542 3689 4548 5552 2874 * * 65
+ 0 * * * * * 0 6804 0 1103
+
+A 66 2952 5573 5597 4527 5704 3444 4938 6394 3292 4829 5711 4209 * 3814 3683 2724 3572 4826 * * 66
+ 32 7500 5912 0 * * 0 6920 1000 1103
+
+A 67 4440 * 4623 3480 6712 5845 5361 5397 4884 2019 5766 3449 * 5031 4407 3880 3584 3484 5953 5401 67
+ 8 * 7431 * * 2082 389 6913 0 1239
+
+L 68 2689 * * 3917 6018 5163 * 4277 2750 2609 * 6146 5556 3881 4857 2776 4101 5719 * 6610 68
+ 289 2794 4746 2438 294 2561 268 6931 2029 1215
+
+K 69 3246 * 3483 5386 7268 4000 3762 6485 2755 6809 5966 4093 5037 4791 2638 3321 4965 5708 * 5857 69
+ 1030 971 * 2529 274 300 2412 6921 4349 1498
+
+E 70 2490 * 3687 3642 5800 3636 4610 * 3317 4829 5595 4532 4415 5318 3288 4211 4425 4303 * * 70
+ 50 4862 * 1834 475 2390 305 6916 1206 1266
+
+L 71 4026 * 7281 3362 4433 * 6644 2061 * 2224 4443 * * 5541 * * 3992 2360 * * 71
+ 56 4725 * 229 2768 733 1327 6918 1233 1203
+
+S 72 4826 * * * 1805 4386 3291 4097 3708 4375 6365 6420 6510 5039 3282 4430 4710 4750 * 4169 72
+ 15 6561 * 1000 1000 * 0 6858 1016 1041
+
+F 73 * 7053 7511 5734 2286 * 4204 5010 4859 6183 6490 1292 * 4995 * 5026 4658 4953 5799 4101 73
+ 8 * 7584 * * * 0 6858 0 1041
+
+H 74 3287 5369 * 4331 4551 5383 5175 * * 3966 6007 1333 * 4450 6655 5233 5057 * * 2830 74
+ 0 * * * * 0 * 6865 0 1084
+
+V 75 1018 7155 7221 * 5122 2183 * 6446 * 3181 6824 * * * * 5996 5183 4658 * 5048 75
+ 0 * * * * * * 6890 0 0
+
+G 76 2654 6095 4653 * * 1361 * * * * 6492 3265 * * * 1983 5087 * * * 76
+ 0 * * * * * * 6890 0 0
+
+G 77 4808 * * 3766 * 1226 4938 * * 5505 4206 4526 * 2213 * 3603 * * 6252 * 77
+ 0 * * * * * * 6890 0 0
+
+Y 78 2453 6714 5529 * 5219 6637 2025 3566 * 4145 3705 * * 6934 * 5532 5258 2606 * 3929 78
+ 58 * 4657 * * * * 6890 0 0
+
+V 79 7302 * 7251 * 2903 * 3925 2825 4045 2863 * * * * 6761 4969 6071 3360 2895 2639 79
+ 11 * 7094 * * 0 * 6948 0 1245
+
+L 80 6548 6295 * * * * * 6278 * 2173 6437 574 * * * 5039 6018 * * 6274 80
+ 0 * * * * 0 * 6885 0 1000
+
+H 81 * * * * * * 519 * * 3900 * 2607 * 5641 * * * * * 4290 81
+ 0 * * * * * * 6889 0 0
+
+L 82 4245 4498 4572 2128 * 7527 3485 4895 5630 7241 * 3625 * 4332 5437 2459 3115 6934 * 5818 82
+ 17 * 6449 * * * * 6889 0 0
+
+F 83 5985 * * * 1576 * 7083 3233 * 1604 4704 * * 6890 6322 * * 4752 6332 3364 83
+ 0 * * * * * 0 6876 0 1040
+
+F 84 6529 * * * 955 * 6407 6274 * 5403 * * * * * * * 4865 6264 1405 84
+ 0 * * * * * 0 6876 0 1040
+
+W 85 * * * * 1275 * * * 6282 3629 * 6446 * * 5995 * * 6333 1218 5398 85
+ 10 * 7218 * * * 0 6876 0 1040
+
+G 86 3539 6723 3490 2132 * 5331 5702 * 2980 4781 * 3287 5306 3777 4635 3380 4986 7423 * 7432 86
+ 0 * * * * 660 1446 6871 0 1103
+
+N 87 5744 2890 * 6649 7055 3458 * 3960 * * 6064 1715 * 3923 * 2555 3800 4624 7426 * 87
+ 19 6278 * 1585 585 * 0 6885 1041 1000
+
+M 88 * * * * 5075 * * 2861 * 818 2187 * * * 6278 * 6295 5628 * * 88
+ 54 4765 * 680 1412 0 * 6885 1291 1000
+
+G 89 2363 4782 5360 * * 3055 * 6308 3480 6355 * 5615 * 4729 3421 2222 3056 5369 * * 89
+ 45 * 5038 * * * * 6889 0 0
+
+P 90 4180 * 5736 5229 7227 2805 * * 4513 7325 * 4384 889 6096 6278 4277 4944 * * * 90
+ 1604 6491 600 1000 1000 * 0 6863 1016 1205
+
+A 91 2606 * * 5080 * * * * 2944 4803 * 4509 2988 3249 5103 3041 2819 3777 * * 91
+ 373 3465 2865 0 * 6252 19 5837 1172 5135
+
+D 92 * * 2916 3810 * 3102 * * 3251 * 5389 5872 3004 * 4731 2064 3421 4686 * * 92
+ 224 2800 * 1332 730 93 4009 5283 1308 5321
+
+E 93 5432 * 3230 3613 6976 3205 4885 * 3741 * * 2303 4148 4099 3668 3466 4876 6402 5339 7326 93
+ 264 5120 2853 685 1403 912 1094 6835 1148 1392
+
+C 94 2917 6248 5829 6741 * 1361 7019 * 4016 6415 6652 4109 5327 5287 6823 2841 5271 4132 * 7111 94
+ 469 2816 2886 2494 282 301 2409 6807 2030 2268
+
+G 95 4927 5987 * 3732 6581 1490 * 6632 3624 * 6180 4629 4067 3739 5792 2998 3980 7371 * 5876 95
+ 234 3399 4191 2392 305 1264 777 6785 1656 2085
+
+G 96 4472 * 5179 4349 * 1803 * 6153 4547 4648 * 3233 6183 4999 4211 4095 2540 4791 * 5435 96
+ 134 3826 5777 1806 486 0 * 6548 1653 2077
+
+E 97 3432 * 4874 2393 5263 5542 5128 4655 3250 6039 5347 4321 4403 3414 4977 4558 3381 4299 * 6626 97
+ 103 4087 6628 886 1124 0 * 6884 1478 1071
+
+P 98 4106 5423 5393 * * 7078 * 3519 5805 4837 4583 * 807 5125 * 4104 * 4404 * * 98
+ 183 4015 4123 1162 854 * 0 6879 1409 1005
+
+S 99 4520 * 3783 3881 7158 3500 * 4748 3900 5817 * 4187 3006 6298 5242 1936 3701 5954 * 5277 99
+ 110 4101 6067 2938 202 881 1129 6640 1345 1512
+
+G 100 3461 7234 3737 5141 * 1465 * * 4768 7276 6035 5042 2751 4457 4009 4308 4936 6797 * * 100
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+
+//
+�HHsearch 1.5
+NAME da9c94dd81bbb9286cd73b3d2469179c
+FAM
+FILE da9c94dd81bbb9286cd73b3d2469179c
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:41:31 2013
+LENG 117 match states, 117 columns in multiple alignment
+FILT 107 out of 163 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCHHHHHHHHHHHHHHHHHHCCEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCCCCCHHHHCEEEEEEEECCCCCCCCC
+CCCCCHHHHHHHHCCCC
+>ss_conf PSIPRED confidence values
+9866677889999999999999983987897899999999999998998398779874799707666437702168467670915587677644467674
+34238999999870369
+>Consensus
+xxxxxxxxxxxexxxxxxekxaexxGyxlNpDxexxxxvxxGLxxnkxxyGxxxCPCRxxgdkexdxxxxdiiCPCxxixexGxChCxLfvxxexxxxxx
+xxxixxxxxxxxxxxxx
+>da9c94dd81bbb9286cd73b3d2469179c
+TSSDTQNNKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCPCRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGD
+AQDIPMETLEEVKASMA
+>gi|298676070|ref|YP_003727820.1| hypothetical protein Metev_2198 [Methanohalobium evestigatum Z-7303]gi|298289058|gb|ADI75024.1| conserved hypothetical protein [Methanohalobium evestigatum Z-7303]
+---SSEarTERRKNKLRELFTRVVDPLGYKFSPDEELVDFLLEQEVMTEREKGAPYCPCQALPGNREEDMKLV--CPCIPFNRKhfdimKRCWCGLFVHK
+DVTDPDKLEQISPKELEkmEKE----
+>gi|294495625|ref|YP_003542118.1| ferredoxin thioredoxin reductase subunit beta [Methanohalophilus mahii DSM 5219]gi|292666624|gb|ADE36473.1| ferredoxin thioredoxin reductase beta chain [Methanohalophilus mahii DSM 5219]
+---QE---DKVKT-KNWVTKYAQKKGYKLNPDPEMLDLVIEGLANNKIKYGKGYCPCRIPSGDEKEDRKI--ICPCIYHEDEiatdGSCHCDLFFQKvDD
+EKK---EEQQNDSED-------
+>gi|206890211|ref|YP_002249669.1| rubredoxin [Thermodesulfovibrio yellowstonii DSM 11347]gi|206742149|gb|ACI21206.1| rubredoxin [Thermodesulfovibrio yellowstonii DSM 11347]
+------PEKLYEVL----DRYAKSKGLELNKDKNFVFELLKGLLKNEERYGYRSCPCRLASGDKQRDADI--ICPCVysidDIKEYGRCYCGLYVTEEYN
+QGKIEERIVPERRKK------
+>gi|302038852|ref|YP_003799174.1| putative ferredoxin-thioredoxin reductase, catalytic subunit [Candidatus Nitrospira defluvii]gi|300606916|emb|CBK43249.1| putative Ferredoxin-thioredoxin reductase, catalytic subunit [Candidatus Nitrospira defluvii]
+---AEPSKESLDKMWKYVKGFAEKSGTAMHPNEAVTNAVVLGLAAHVDELGKPLCPCNFYPDKQAEAKLRRWMCACDEMQIYKYCHCLLFVREDG-----
+-----------------
+>gi|88602537|ref|YP_502715.1| hypothetical protein Mhun_1252 [Methanospirillum hungatei JF-1]gi|88187999|gb|ABD40996.1| conserved hypothetical protein [Methanospirillum hungatei JF-1]
+----------TeEEIRSWALEYSRSHGWVLNPDEKQTNAVIKGLSRNSEKHGERYCPCRIRsGDKEKDKA---IICPCVYhvheLEQAGHCTCNFFYDPE
+-----------------------
+>gi|91774293|ref|YP_566985.1| hypothetical protein Mbur_2384 [Methanococcoides burtonii DSM 6242]gi|91713308|gb|ABE53235.1| Hypothetical protein Mbur_2384 [Methanococcoides burtonii DSM 6242]
+----------EEEFYNRSKKNAETTGYRLNPDYDVITIAVKGICNNKREYGEWYCFCQKRtGDVEKDKK---IICPCAArsrdVEMRGSCKCGLYIK---
+----------------------
+>gi|149195059|ref|ZP_01872151.1| Rhodanese-like protein [Caminibacter mediatlanticus TB-2]gi|149134772|gb|EDM23256.1| Rhodanese-like protein [Caminibacter mediatlanticus TB-2]
+---------EFLKTEKFAHRVINQFNWKFNPNEEIVERVLKGLTNNKILYGKRFCPCFPVEkRNGKYVSSDDRICPCPQaiekeIPEDGVCHCGIFCNEE
+YVKNE------------------
+>gi|152991978|ref|YP_001357699.1| hypothetical protein SUN_0382 [Sulfurovum sp. NBC37-1]gi|151423839|dbj|BAF71342.1| hypothetical protein [Sulfurovum sp. NBC37-1]
+-----------KKQQRWMEKYCEQNGYTINPSWMMATNLKSNLCEMEETFGKRYCPCFEPsGDKELDKK---MMCPCDYvedeIKEYGTCHCALFGPADL
+SK--------------------
+>gi|334340537|ref|YP_004545517.1| hypothetical protein Desru_1975 [Desulfotomaculum ruminis DSM 2154]gi|334091891|gb|AEG60231.1| hypothetical protein Desru_1975 [Desulfotomaculum ruminis DSM 2154]
+-----------EEIEQRIEAFAKLRGFVFNEDRGM---VLEGLMEKKKQFGDFFCPCKFDNI--P-----ENICPCLEtrkgfVRKEGRCHCGLFN----
+----------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 * * * * * * * * * * * * * * * * 0 * * * 1
+ 0 * * * * * * 1000 0 0
+
+S 2 * * * * * 1582 * * * * * * * * * 587 * * * * 2
+ 0 * * * * * * 1462 0 0
+
+S 3 * * * * * * * * 2044 * * * * * 2061 949 * * * * 3
+ 0 * * * * * * 1536 0 0
+
+D 4 3806 * 1932 4956 * * * * 4507 5430 5001 4298 4573 3074 * 2221 3890 4561 * * 4
+ 152 * 3325 * * * * 3581 0 0
+
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+ 0 * * 0 * * * 1466 0 0
+
+//
+�HHsearch 1.5
+NAME db724bcc82eacb181edae3af47403f31
+FAM
+FILE db724bcc82eacb181edae3af47403f31
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:16:31 2013
+LENG 52 match states, 52 columns in multiple alignment
+FILT 100 out of 110 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCHHHCCCCCCEEEEEEEEECCCCHHHHHHHHHHHCCCCCEEEEEEC
+>ss_conf PSIPRED confidence values
+9853021000003687899997762588647789999997797641659839
+>Consensus
+mxxxxxxxxxxxxxPxkxfitxGxgxxxtxLxaFdxALxdAgIxnxNLVxVS
+>db724bcc82eacb181edae3af47403f31
+MNAEINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRIS
+>gi|212224474|ref|YP_002307710.1| pyruvoyl-dependent arginine decarboxylase [Thermococcus onnurineus NA1]gi|212009431|gb|ACJ16813.1| pyruvoyl-dependent arginine decarboxylase [Thermococcus onnurineus NA1]
+MYNRLIrekgKEEVgMsWTTPKRAFIGAATAEGGTKLNAFDNALLKLGIGNVNLVKLS
+>gi|188585514|ref|YP_001917059.1| Pyruvoyl-dependent arginine decarboxylase [Natranaerobius thermophilus JW/NM-WN-LF]gi|179350201|gb|ACB84471.1| Pyruvoyl-dependent arginine decarboxylase [Natranaerobius thermophilus JW/NM-WN-LF]
+-----------LKTLKYFKLVTGTGEGNTSLTAFDKALLNAEVGNFNLLKVT
+>gi|291575308|gb|ADE10233.1| pyruvoyl-dependent arginine decarboxylase [Actinoplanes liguriensis]
+---------------DQIPVVRAIGRGTTSLSAFHDALVTMECGFYNLVRLS
+>gi|229819355|ref|YP_002880881.1| Pyruvoyl-dependent arginine decarboxylase [Beutenbergia cavernae DSM 12333]gi|229565268|gb|ACQ79119.1| Pyruvoyl-dependent arginine decarboxylase [Beutenbergia cavernae DSM 12333]
+---------------PTIRISTGTGSGRTTLSAFDAALRSAGVADFNLLRLS
+>gi|76802875|ref|YP_330970.1| hypothetical protein NP4484A [Natronomonas pharaonis DSM 2160]gi|76558740|emb|CAI50333.1| conserved hypothetical protein [Natronomonas pharaonis DSM 2160]
+---------------GRIRIVWGTATAPTAMASYDAALAAANVHNYNLVAVS
+>gi|52549420|gb|AAU83269.1| conserved hypothetical protein [uncultured archaeon GZfos27B6]
+-------------IPDAFFVTSGAGMDFEQANAFDLALHDAGISECNLVEVS
+>gi|302341587|ref|YP_003806116.1| arginine decarboxylase, pyruvoyl-dependent [Desulfarculus baarsii DSM 2075]gi|301638200|gb|ADK83522.1| arginine decarboxylase, pyruvoyl-dependent [Desulfarculus baarsii DSM 2075]
+------------LVPKYIYLTKGKGEHKEKLASFEAALRDAGIAAQNIVEVS
+>gi|119719781|ref|YP_920276.1| pyruvoyl-dependent arginine decarboxylase [Thermofilum pendens Hrk 5]gi|119524901|gb|ABL78273.1| arginine decarboxylase [Thermofilum pendens Hrk 5]
+-------------LPKKYFVTKGKGLSnVSPLMAFNNALREAGIHQLNLVPVS
+>gi|34540667|ref|NP_905146.1| hypothetical protein PG0903 [Porphyromonas gingivalis W83]gi|188994902|ref|YP_001929154.1| hypothetical protein PGN_1038 [Porphyromonas gingivalis ATCC 33277]gi|334146632|ref|YP_004509559.1| hypothetical protein PGTDC60_0831 [Porphyromonas gingivalis TDC60]gi|34396981|gb|AAQ66045.1| conserved hypothetical protein [Porphyromonas gingivalis W83]gi|188594582|dbj|BAG33557.1| conserved hypothetical protein [Porphyromonas gingivalis ATCC 33277]gi|333803786|dbj|BAK24993.1| hypothetical protein PGTDC60_0831 [Porphyromonas gingivalis TDC60]
+-------------IPNTFFITKGSGESDLELHagSYHMALFDAGISDFNIMTYS
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * 3129 175 * * * * * * * * * 1
+ 0 * * * * * * 1967 0 0
+
+N 2 * * 3244 * * * * * 3268 * * 1210 * 2943 * * * * * 2131 2
+ 0 * * * * * * 1967 0 0
+
+A 3 3191 * 3140 * * * * * 3394 * * 1583 * * * 2943 2197 * * * 3
+ 0 * * * * * * 1967 0 0
+
+E 4 * * 3129 2289 * * * * 3244 * * 3140 * * 2131 2097 * * * * 4
+ 0 * * * * * * 1967 0 0
+
+I 5 2097 * * * * * * 1653 * 1545 * * * * * 3244 * * * * 5
+ 384 * 2097 * * * * 1967 0 0
+
+N 6 * 2700 * * * * * 1923 * * * 2804 * * * 1187 * * * * 6
+ 780 1260 * 2241 343 * 0 1818 1167 1114
+
+P 7 * 2725 * * * * * * 1923 * * * 773 * * * * * * * 7
+ 0 * * * * 0 * 1818 0 1114
+
+L 8 * * * 2247 * * * 782 * 3466 3092 * * * * * * * * * 8
+ 0 * * * * * * 1865 0 0
+
+H 9 * * * 2247 * * 573 3092 * * * * * * * * * * * * 9
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+
+A 10 3015 * * * * * * * * * 1677 3836 * * * 1397 * 3135 * * 10
+ 552 1654 * 0 * * * 2081 1129 0
+
+Y 11 * * * * * * * 3775 * * 608 * 2216 * * * * * * 4173 11
+ 126 3577 * 0 * * * 2335 1138 0
+
+F 12 * * * * 1749 * * * * 806 * * * * * * * * 3632 4328 12
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+
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+//
+�HHsearch 1.5
+NAME dbea14172bdf1965e97ce49c46d0fd07
+FAM
+FILE dbea14172bdf1965e97ce49c46d0fd07
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:22:59 2013
+LENG 133 match states, 133 columns in multiple alignment
+FILT 102 out of 457 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCEEEEEEEECCCCEEEEEEEEEECCCCEEECCCCCCCCCCCCCEEEEECCCCCEEEEEEEEEECCCCCEEEEEEEEEECCCEEECCCCCC
+CCEEEEECCCCEEEEEEEECCCCEEEEEEEEEC
+>ss_conf PSIPRED confidence values
+9765138998739999999489989999999947997998654588788973179996799978999999996878945999999998997231664889
+929998569999999999817858999999989
+>Consensus
+GxxxddgxxxxixxIxixxxxxxxIxxiqxxYxxxgxxxxxxxxGxxxxgxxxxxxxlxxxxEyItxvsGxxgxxxxxxxIxsLxFxTnkxxxxxfGxxx
+GxxFxxxxxxxxivGFxGrsgxxldsiGvyxxx
+>dbea14172bdf1965e97ce49c46d0fd07
+GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTS
+GTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL
+>gi|53791723|dbj|BAD53318.1| hypothetical protein [Oryza sativa Japonica Group]
+------------DLISVQIKSKDTIDHLTFTYkdtKGNQQT---V-SWGG------------------tmgddhlaevSGSVGPFpsqkq----------
+ACTVNSLTFVTS-EGRRGgp--wgkrgkddkDFKVPVGKGRIVGFYARADVFISAIGFYIR-
+>gi|242048128|ref|XP_002461810.1| hypothetical protein SORBIDRAFT_02g008430 [Sorghum bicolor]gi|241925187|gb|EER98331.1| hypothetical protein SORBIDRAFT_02g008430 [Sorghum bicolor]
+-SLWEMeGKSQRLENVTIY--HIGAVEGIQFSYvDEDGQIRTTGTWGRVHpSPLYKTEIKFG-PSEFVKQITGAARH---GGWLSQFKIVTSHKTYGPFG
+VDAGaPSFSYTVReDELVVGFFANADTFVQSIGVCT--
+>gi|15224348|ref|NP_181902.1| jacalin-like lectin domain-containing protein [Arabidopsis thaliana]gi|2281096|gb|AAB64032.1| hypothetical protein [Arabidopsis thaliana]gi|52354293|gb|AAU44467.1| hypothetical protein AT2G43740 [Arabidopsis thaliana]gi|330255220|gb|AEC10314.1| jacalin-like lectin domain-containing protein [Arabidopsis thaliana]
+-LEWEEKGRNMISSIYVAF-DKDTINSIQFSYCQNGGHVVSKKYGMSDaqkqkygsyNGRFHVMfvfalvtddhvktnlcniqVRLN-DDEFVTGLSAIY
+L----CKGITNLNIHTNQGKHGPICDRysSsknimdNYKVEIdvKIRDRrEFGGFFGSFDNygTLTSIGIYVC-
+>gi|38347662|emb|CAE04702.2| OSJNBa0041M06.4 [Oryza sativa Japonica Group]
+----KEGvN----------Y-FICGVPG-----hCAAGMKL--RVVADE-FP-SADTK------------------------------------------
+-----------------------------------
+>gi|294659253|ref|XP_461608.2| DEHA2G01562p [Debaryomyces hansenii CBS767]gi|199433820|emb|CAG90055.2| DEHA2G01562p [Debaryomyces hansenii]
+----------KVTKVRVY--HGGALDGVRFYFNSsdngetKNAPkvplrnylhkltnkssdssenRnssqgvnpKVVTIGHE-KS-HYSDYDIG-PGEYI
+TKFHIRNG-----AWIDAIQIETNTgKKSPMFGNPNGghlSTLESPGQGFHVIGMYGYVGSWLDGLGIIY--
+>gi|328835778|dbj|BAK19070.1| PL-toxin I [Plotosus lineatus]
+---TNNGS--TVRKIWVWA-AGWQIKSMKIWL-TDGREQ---QFGNP-AGN-HSEFEFQ-DGECMTSLSLWG-N-GAGTRLGAIKFKTNRSrEFfahmTD
+WG--LKTEYPIDVGSGICVGVTGSAGSDIDCLGFMF--
+>gi|301122501|ref|XP_002908977.1| conserved hypothetical protein [Phytophthora infestans T30-4]gi|262099739|gb|EEY57791.1| conserved hypothetical protein [Phytophthora infestans T30-4]
+GNEFSDQasvaAGQSIGSITIRA--GERVDGISLEVtaPKAAT----FSHGGS-GG-KANTLTLA-KEEYITSMEAHWGEKKGRTRIFYLSFGTSAGNTV
+AAGSQTESKNTVTAPkGFQLGGFFGQDGNEIDKLGAI---
+>gi|313231270|emb|CBY08385.1| unnamed protein product [Oikopleura dioica]
+GSKWSDVQykSRPVRRIVLW--CGAFLDAIKVDYDIKlGI--GSQKHGTG-RDHQRENVHIH-QGDHVQQITGKTCDFYGQVILTEIRIHTEQgRVHGPF
+GSYNepereLMPFTVGGPHCRLQYLDGK--------------
+>gi|145490355|ref|XP_001431178.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124398281|emb|CAK63780.1| unnamed protein product [Paramecium tetraurelia]
+GDDFDDGMIDKITRVKIQY-NKQNIVAIGIFYEQRQIYK-DHNFCAN-SLskfyfyVWEEEFVIE-KDDYLQQVTGTYD----GMYITSLQFVTYNGQSM
+HFKAsCLGESFNIEN-------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 4066 * * * * 89 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 6155 0 0
+
+K 2 5424 * 2639 5723 * 5118 5668 5703 3031 5420 6250 2958 * 4911 4811 2112 3361 4492 * * 2
+ 0 * * * * * * 6342 0 0
+
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+
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+ 42 * 5116 * * * * 6696 0 0
+
+D 5 5440 * 1097 2965 * * * * 6850 6061 * 4390 * * * 2437 3495 5894 5665 * 5
+ 0 * * * * 1035 965 6721 0 1062
+
+D 6 * * 838 3149 5708 * 4949 3947 * 4966 4254 5369 * 6068 * 4459 * * * 4562 6
+ 53 4804 * 0 * 0 * 6721 1097 1000
+
+G 7 * * 3796 5924 * 989 * 4589 4514 * * 3151 * 5537 3877 * 4449 3748 * * 7
+ 493 1789 * 1184 837 * * 6726 2564 0
+
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+
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+
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+ 0 * * * * 492 1792 6840 0 1351
+
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+ 18 6346 * 0 * * 0 7201 1000 1033
+
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+
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+
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+
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+
+L 17 6688 * * * 3888 6355 * 1411 * 2961 4477 6506 * * * * * 1513 * * 17
+ 39 * 5241 * * * 0 7292 0 1241
+
+S 18 4535 7217 6439 6253 5171 4305 3930 * 4219 6405 * 5039 * 4609 2849 2938 2654 * 3282 3137 18
+ 374 5658 2260 595 1565 267 2564 7238 1085 1472
+
+Y 19 3859 * 4897 5522 3502 5435 3976 2965 6131 3222 * 6495 * 5193 * 3688 5068 2934 6491 2612 19
+ 1694 6223 562 1000 1000 * 0 7035 1004 2721
+
+N 20 * 4602 * * 3196 4505 3849 4449 4613 * * 3421 * * 1913 4495 * 4798 2813 3875 20
+ 0 * * * * 444 1916 5148 0 6069
+
+K 21 4123 5108 2715 * 7395 2784 2788 * 5282 6243 * 3366 6197 5548 * 2223 4758 * * 4531 21
+ 17 6404 * 2322 322 64 4529 7313 1000 2715
+
+E 22 4430 * 3710 4484 6456 1214 * 5001 4247 4657 * 4488 4915 5900 6898 3122 5494 5753 6924 * 22
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+
+T 23 3642 6085 2596 3461 5916 3452 6036 * 4661 4944 5405 3409 * 4629 6277 3094 3689 5061 4853 5412 23
+ 43 5086 * 550 1658 0 * 7328 1270 1000
+
+A 24 2677 4792 6316 5565 4380 3240 5258 3872 5786 5418 6198 4623 * 5329 3348 5000 3698 3093 * 3621 24
+ 25 6613 7100 2000 415 * * 7328 1000 0
+
+I 25 * * * * 6407 * * 1267 * 2276 * * 6376 * * * 5785 1627 * 6341 25
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+
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+
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+
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+
+Y 32 * 6252 * 5719 3275 * * 6249 * 4117 * * * * * 5005 6110 5342 6549 488 32
+ 814 1462 3875 392 2070 1155 860 7291 3982 1480
+
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+
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+
+N 35 2938 6845 2099 6151 * 3211 * * 4508 6035 * 2432 * 4777 4578 3585 3988 6404 * 5363 35
+ 83 6192 4576 0 * 1276 769 7151 1011 2115
+
+G 36 5224 6475 4950 4886 * 583 * 5897 5274 * * 3795 6334 5186 * 4105 6003 * * * 36
+ 126 3782 6475 1336 728 3229 163 7208 1654 2012
+
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+ 90 6431 4358 1336 728 2640 252 7218 1082 1987
+
+P 38 4893 * 6312 4134 5481 4276 5320 3499 5350 4513 6181 3783 2845 6356 3337 3374 3622 3596 * 4510 38
+ 187 5352 3369 4321 74 1289 759 7146 1077 2201
+
+Y 39 4996 * * 3471 3283 * 4191 2934 4210 3556 * * 6324 4970 3335 5138 4850 2346 * 4384 39
+ 402 3741 2570 1443 662 1690 535 7105 1572 2464
+
+V 40 4825 6261 * 3810 * 5091 6586 5353 3858 4362 * 5982 5196 4311 5184 3210 2295 3375 2920 4743 40
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+
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+
+Q 42 3136 * 4283 3884 6033 2307 5354 6240 5023 4674 * 4993 3163 4065 3953 4349 4448 3644 * * 42
+ 74 * 4318 * * 483 1813 7013 0 2641
+
+N 43 4026 4396 5447 4355 6687 6227 5683 4168 2705 3095 5554 4751 3737 3732 3559 4402 4635 4650 * 5063 43
+ 57 5101 6662 1892 453 662 1441 7169 1146 1830
+
+H 44 * * * * 3143 6340 1457 5735 5164 3780 6348 6741 5323 * 4101 6133 * 4528 2832 3511 44
+ 0 * * * * 364 2164 7246 0 1353
+
+K 45 5985 6367 * * * 138 * * 6345 * * 6047 * * * 6309 * * 5415 * 45
+ 44 5477 7029 0 * * 0 7316 1115 1003
+
+S 46 4720 * 4033 5249 * 1217 6711 6579 4380 6291 6236 4833 6367 6473 4958 2920 3396 5629 6322 * 46
+ 30 * 5620 * * * 0 7323 0 1091
+
+F 47 3838 6234 4634 4333 6270 3454 5479 6499 4422 4847 6558 3043 4309 5350 3246 2833 3334 4748 * 5731 47
+ 1916 * 444 * * 2179 360 7301 0 1296
+
+I 48 4450 * 2923 * * 3121 4750 3632 4602 4233 * * 3986 * 3431 3491 * 3701 3013 4329 48
+ 859 1477 3483 2196 355 90 4051 5668 1873 5998
+
+T 49 3685 5800 5750 6801 5079 1467 * 6491 4555 6895 * 4077 5442 5185 4549 3179 2820 6788 * 6655 49
+ 139 4393 4491 785 1253 2054 397 7249 1310 1545
+
+G 50 5323 5879 5018 * 5284 595 6260 4458 * 4250 * 7124 5972 6512 5553 4208 6860 6599 * * 50
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+
+F 51 3884 * 3413 4814 5889 4301 4795 3579 4990 3933 * 3363 6021 * 4899 2542 2993 4698 5881 5670 51
+ 345 4681 2525 2077 390 100 3906 6855 1136 3928
+
+T 52 4912 * 4568 3237 6066 3943 6565 * 3031 5310 5461 3259 5033 3361 3459 2845 4168 6080 6141 6542 52
+ 36 6351 6314 0 * 293 2442 7147 1001 2141
+
+P 53 4058 6251 7050 2822 4208 6536 3928 6184 4400 4225 6707 * 3076 4138 4321 3373 3278 4749 * 4039 53
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+K 55 5172 * 4657 1584 * 5742 6157 3982 3429 * 4811 4870 5167 5461 6556 4060 2355 5391 * * 55
+ 64 4978 6452 2837 217 1477 642 7305 1291 1141
+
+I 56 5031 * 6727 6499 2049 * 6944 2005 7570 2978 4891 * * * * * 6377 2199 * 4202 56
+ 18 6370 * 1000 1000 * 0 7293 1026 1157
+
+S 57 5143 5641 3918 2874 5354 * 6471 5020 3989 3830 6386 4105 6407 5049 3916 3863 2861 2971 6863 5133 57
+ 13 6779 * 1000 1000 1322 737 7283 1003 1157
+
+L 58 6154 6717 * * 2650 * * 2485 6935 1023 5090 * * * * * * 3200 * * 58
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+F 60 5048 4792 4765 * 2938 5109 3996 * * 4988 * * * 5101 * 4874 4734 4151 4286 1201 60
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+
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+ 29 6369 7007 2161 365 817 1209 7185 1194 1673
+
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+
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+
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+V 68 4593 * * * 3975 6165 * 1779 * 3868 3216 * 6158 * * 6199 * 1373 * * 68
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+
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+ 0 * * * * 1785 495 7298 0 1287
+
+T 72 3981 5222 * * 3028 4864 5681 4968 5454 5022 * 5764 * 5516 6165 4880 3051 3012 6481 1718 72
+ 94 6199 4339 2322 322 * 0 7316 1055 1176
+
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+
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+ 446 4666 2143 1273 770 3183 168 6872 1190 3323
+
+V 75 5256 4745 5584 5661 2764 5994 6231 3523 4144 4138 * 5141 6192 5982 5901 4178 3706 4069 5954 2076 75
+ 1281 1209 2681 1239 795 3263 159 6436 3267 4236
+
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+
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+
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+ 0 * * * * 1397 689 6766 0 3714
+
+V 79 3279 6108 3282 4300 6818 4897 4849 6323 4937 3826 6057 3415 3922 5721 4843 4680 2744 3188 * 6710 79
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+
+V 80 4038 5830 6328 6050 5210 3148 4428 3869 5532 3721 6492 * * 6465 2557 6181 3784 2595 3997 4837 80
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+
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+
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+ 0 * * * * 642 1477 7295 0 1141
+
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+
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+
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+
+F 86 6184 * * * 556 * * 2507 * 3581 6494 * * * * * * 4822 * * 86
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+
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+ 12 6898 * 2462 289 0 * 7335 1070 1000
+
+T 88 * * * * 6446 * * * * 5365 * * * * * 3792 165 * * * 88
+ 0 * * * * * * 7334 0 0
+
+N 89 * * 4328 5467 * 6800 6409 * 5822 5484 * 887 * 6626 * 2065 4581 * * 4826 89
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+
+K 90 5027 * 4479 5512 * 6795 4943 * 1359 3154 4931 4277 * 3083 4697 * 4096 5223 * 4932 90
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+
+K 91 4686 * 4828 * 5159 1711 * * 3067 * * 3652 * 3725 2015 5315 4806 6675 * * 91
+ 83 4157 * 0 * 0 * 7322 1503 1075
+
+T 92 4119 * 5498 4212 * * * * 3537 * * 4599 6273 4081 2371 3483 1700 3709 * * 92
+ 50 4889 * 0 * * * 7334 1241 0
+
+Y 93 * 6469 * 6337 3539 * 3680 4684 * 4512 * 5736 6479 6866 6679 2012 3427 5420 6924 1696 93
+ 49 4911 * 1267 775 * * 7297 1223 0
+
+G 94 5644 * 5056 4364 4918 1262 4594 * 5043 3520 6373 4975 3490 6688 * 3759 5560 4186 * * 94
+ 58 * 4671 * * * * 7297 0 0
+
+P 95 4078 * 5334 4446 4744 5150 6265 4989 4789 5893 4981 6754 1222 6817 4347 4520 3885 4411 6676 6453 95
+ 29 5649 * 1304 749 0 * 7245 1172 1321
+
+Y 96 5297 4397 * 6212 1246 4931 * 4498 6282 5343 5544 5490 6267 * * * * 4878 4515 2040 96
+ 36 * 5342 * * * * 7286 0 0
+
+G 97 * 6170 * * * 122 * * 6318 * * * * 5706 6323 5431 * * * * 97
+ 148 3991 4859 0 * 738 1320 7238 1460 1136
+
+V 98 4497 4626 4307 4988 5486 3426 * 4504 3863 4970 * 2826 6326 4359 4564 3248 2722 4977 * 4643 98
+ 140 3431 * 1136 875 * 0 7184 1755 1315
+
+T 99 3270 6284 3991 3588 5273 3166 * * 3595 5574 4773 3953 3328 5736 5131 3646 3488 4560 5308 6416 99
+ 158 3266 * 598 1559 368 2149 7184 1834 1315
+
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+
+G 101 4286 * * 5016 * 542 5421 * 5020 6458 6554 4825 6477 5985 6732 4374 5399 * 6484 * 101
+ 184 3064 * 1261 779 * 0 7242 2023 1149
+
+T 102 5136 * 4352 3795 * 4851 5558 * 3753 * 4933 4035 5658 3945 4173 3414 1635 4142 * 6136 102
+ 90 4390 6302 2296 328 0 * 7242 1571 1149
+
+P 103 3840 * 4013 4177 6289 * 5202 5301 2969 * * 4380 2110 4407 4176 3274 3568 6600 * 4654 103
+ 50 * 4865 * * * 0 7276 0 1020
+
+F 104 * * * * 317 * * 6718 * 5031 * 5469 * * * 5552 5643 6158 6293 3907 104
+ 11 * 7063 0 * 251 2646 7242 1035 1347
+
+N 105 6163 5196 5025 2983 * * 5312 4872 4806 4876 * 3564 6068 5747 4571 1712 3502 3200 * 6656 105
+ 32 * 5498 0 * 876 1135 7285 1000 1059
+
+L 106 3651 6591 * 4337 3689 * 6100 2434 6305 2125 * * 5664 * * 4310 4209 2824 6232 3996 106
+ 139 3808 5595 248 2662 1227 804 7263 1576 1184
+
+P 107 4858 * 4579 4073 * 4363 6095 6172 3420 * 6615 5174 1424 3776 * 4600 2933 6768 * 5123 107
+ 209 4712 3371 0 * 932 1072 7261 1223 1257
+
+I 108 2671 * * 5195 5970 4105 * 3663 6406 2755 4432 5251 6376 6679 * 3519 5238 1878 6277 6686 108
+ 190 5525 3300 0 * 1335 729 7207 1077 1925
+
+E 109 3357 * 5423 2944 * 3841 * 6136 3893 4690 6446 3391 2150 4019 4280 5225 5881 5069 * 4634 109
+ 173 3146 * 546 1666 386 2089 7111 1806 2284
+
+N 110 4119 * 2292 4135 * 1802 5430 6870 4196 6047 * 3201 4576 5694 * 3643 5568 6303 * 6739 110
+ 122 3625 * 467 1853 597 1561 7200 1635 1246
+
+G 111 5707 4396 5042 4175 5544 1359 3793 * 5042 5389 * 4138 6792 5436 4468 3616 6939 5672 5329 4589 111
+ 361 2175 * 82 4179 0 * 7240 2763 1019
+
+L 112 4202 5536 6322 3750 * 4610 4166 4469 2697 5432 * 4999 * 3101 3403 3065 3810 3998 * 5480 112
+ 49 4915 * 1048 954 * * 7260 1221 0
+
+I 113 * 6043 * * 3233 * * 1239 * 2469 * * * * * * 6245 1938 * * 113
+ 23 6857 7092 2322 322 * * 7260 1000 0
+
+V 114 3644 * * * 6443 4128 6894 3166 5524 3648 6287 * * 5608 * 3752 * 937 * * 114
+ 0 * * * * * 0 7259 0 1000
+
+G 115 4453 * * * 6305 263 * * * * * * * 6707 5986 4329 * * * 4904 115
+ 23 5986 * 459 1877 0 * 7259 1131 1000
+
+F 116 4436 * * * 336 * * 4105 * 4128 5754 * * * * * * 5175 * * 116
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+
+K 117 5286 6500 5039 6375 1477 5072 2583 * 6277 4608 * 6721 * 6320 5400 4190 5386 6136 5358 2756 117
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+
+G 118 3843 * * * * 181 * 5680 * * 6316 * * * * * * 5969 * * 118
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+
+S 119 6609 * 6673 * 4543 6267 5075 * 3829 5784 * 3910 * 5300 1114 2470 5172 6230 * 5043 119
+ 33 5452 * 0 * * 0 7219 1091 1035
+
+I 120 1675 3612 5468 4948 5527 6813 * 6207 * * * * * 6518 * 1691 3910 4080 * 4068 120
+ 17 6457 * 1114 894 0 * 7194 1130 1035
+
+G 121 4332 * 2817 6765 * 954 * 6199 6469 * * 5422 * 4980 6151 2866 4269 * * * 121
+ 118 3665 * 339 2254 * * 7215 1603 0
+
+Y 122 3863 4776 2389 4621 * 4637 6637 * 5225 5338 * 3574 4785 4276 * 2623 4386 4928 4077 3516 122
+ 94 4233 6630 353 2203 * * 7215 1363 0
+
+W 123 4558 4446 4812 3916 3179 4197 5002 4477 6249 3396 * 6719 * 5745 4122 4873 5345 4699 4234 2154 123
+ 0 * * * * * 0 7217 0 1019
+
+L 124 6620 6347 * * 5508 * * 2037 * 1138 5647 * 6633 6252 * * 6538 2297 * * 124
+ 0 * * * * * 0 7217 0 1019
+
+D 125 6862 * 955 4889 * 6530 4796 6693 5509 * * 2982 * 4990 4588 4242 4403 4937 * 5019 125
+ 0 * * * * 0 * 7217 0 1019
+
+Y 126 1512 5975 * * 6060 3556 * * 4480 6630 * 5521 * 3925 5382 1641 4926 * * 6218 126
+ 0 * * * * * * 7215 0 0
+
+F 127 * * * * 3356 * * 939 * 1878 * * 6630 * * * * 3901 5696 6332 127
+ 0 * * * * * * 7215 0 0
+
+S 128 5092 * 5913 6266 * 229 * * * * * * * 6253 6808 4670 * * 6310 6151 128
+ 0 * * * * * * 7215 0 0
+
+M 129 2601 * * 6531 2337 6973 * 3017 * 4285 5250 * * * 5473 * 6332 1499 * 5125 129
+ 0 * * * * * * 7215 0 0
+
+Y 130 4594 6417 * * 4834 * 3591 3439 * 4869 5897 5633 * * 5920 * 5317 3893 * 845 130
+ 16 6474 * 0 * * * 7094 1003 0
+
+L 131 * * * * 2405 * * 3352 * 2719 4707 6060 * * * 6149 4348 2062 4072 2776 131
+ 27 5777 * 2322 322 0 * 6918 1000 1003
+
+S 132 2888 4040 5770 3821 * 4965 4672 * 3079 3697 5348 5989 4584 4795 2750 3345 6269 4242 * 5842 132
+ 0 * * * * * * 6211 0 0
+
+L 133 * * * * * * * * * 558 * * * * * * * 1640 * * 133
+ 0 * * 0 * * * 2015 0 0
+
+//
+�HHsearch 1.5
+NAME dea447cd63c9d8c162d6bcafb1cbb851
+FAM
+FILE dea447cd63c9d8c162d6bcafb1cbb851
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:33:24 2013
+LENG 197 match states, 197 columns in multiple alignment
+FILT 114 out of 165 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEEEECCCEECCEEEEECCEEEEECCCCCCCCCEEECCCCCCCCCCHHHHHHHHHCCCEEEEEEECCEEEEEECCCCCEEEECCCCCCCCCCCC
+CCEEEECCCCEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9811799998449767152895099899927636888985675447788988899999985477289999899899997689988982897774126887
+8618858998699817699999999985048876566200037999997677998787884558838999918699999999975599889788789
+>Consensus
+xxxWcxIxYyExxxrVGexfxxxxxxvxIDGfxdxxxxxrfcLgxlxnxxRxxxxxxxRxxIGxGvxLxxxxgxVxxxnxsxxxIFVqSxxxnxxxxxxx
+xtVxKvxpgxxxkvFdxxxfxxxlxxxxxxxxxxxxxlxxxcxiRISFvKGWGxxYxRqxitxxPCWiEixlxxplxxldxvlxxmxxpxxxxxsxx
+>dea447cd63c9d8c162d6bcafb1cbb851
+PAFWCSISYYELNQRVGETFHASQPSMTVDGFTDPSNSERFCLGLLSNVNRNAAVELTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHP
+ATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSIRCSSVS
+>gi|308489650|ref|XP_003107018.1| CRE-DAF-3 protein [Caenorhabditis remanei]gi|308252906|gb|EFO96858.1| CRE-DAF-3 protein [Caenorhabditis remanei]
+--RWGVVSYYEEGDCYIER-ECYRGNFHIDSgFI--ISEQRLSLGLIQNPSRSTMAFKIRKAMIDGIRFSYKtDGSVWLQNNMRLPIFVTSGYLDdQCPG
+IRVNKVHKLYGHAKVKVFGFTRVKQIIRdrlyskqmaRLYLQqnGNrnpmFEVYhripliaiqrearvttdSLVKYCCVKVSFGKGFGDAYPeRPIVSQC
+PVWLELKINSAFDYMDAILNDLEN---------
+>gi|308455180|ref|XP_003090150.1| hypothetical protein CRE_23794 [Caenorhabditis remanei]gi|308266234|gb|EFP10187.1| hypothetical protein CRE_23794 [Caenorhabditis remanei]
+-GYWCSVQlndcktmvsWREINLikaylksfQKGKPFLTRNMEFVVDSLETSVVSddKRMALmGLpMSEKGKHNSI---KTSFKDGIKVYCTGGTVKVSV
+LSDVTIFVQSPFWNHANGQDLAAVTRLGSnqprPVIFTVFDFEQFKTHLERAKQHPPTdEMNeFLQSICGFNVSVSKGFGPDYGNRTIFETCCWLSIKFT
+DPLLLFDKYYRQYRLAPDEINS--
+>gi|312377233|gb|EFR24116.1| hypothetical protein AND_11529 [Anopheles darlingi]
+-EIWAKVIVFERNRRVAKAY-ARAPVLTINGSDDGFDGmsdgsfsspvaefpwandvekwlmmseglthqvhslyssavptghglsisrslrvtaalrwd
+pgilgvtkvqrpfvrsvvmFPIGLCGFDNPMRDHKTDEVKRHVGQGVKIKMDdAGNILIRRYSKSNVYVKSTASQpNEETAIGADILKLPGQAiesekIV
+KLFDMKKFQSNVNRELRRAYPDRRRLETQCLSAIAFVKS------ENDILDCPMWVLIINVVAMDMLKSKLppgkssalgiiftskYQMNSPYDVTKSV-
+>gi|221125810|ref|XP_002162815.1| PREDICTED: hypothetical protein [Hydra magnipapillata]
+-SGWCRVDCYERQHHVAT-FRMDEPVICIDGIHPVSDKHRISFAGLPTRSEDLKVLKVKSCIGKGVQLHQDErQNLWATRLGKNPIFVRGHTLCPELVK-
+--LNGKLTQGVPMKVLDTSAFKEYMKKECeTSGL--VdDELRDKIMsrlkVCMSFIKD------TVVDEETPCWFEVWLI--------------------
+----
+>gi|313232554|emb|CBY19224.1| unnamed protein product [Oikopleura dioica]
+--DWARVSFYQKKMKRGPDFIARSRSFTIDGMTGPRCtSTRMPLGIRTLGLRgCPDTDRLLETVGHGIVIENKENCVLLRNISPVSVYVKSCQID-----
+--STPIRIPAAHEVDLFFYDEFSRSIAER--NTLADLWQLREHCTLFISFGLCWGSStVQVESVDGLPCWLKLDLQHCWRELNVAVEQ------------
+>gi|167517705|ref|XP_001743193.1| hypothetical protein [Monosiga brevicollis MX1]gi|163778292|gb|EDQ91907.1| predicted protein [Monosiga brevicollis MX1]
+---VASITYHERDSPLAQFY-LNQPIFNISCFRPVEDNtTTVSLSDIDNPCRDSRTEKIRRFIGSGLQVSIRRKCLYVTRLSRNPVFLKNYQSPStvSDS
+ILLRENGELPDGAEVCLFDYQVFSKEIARMPAE------LALKMATVSLAFVRT------GEFDDKIPCWIRIRMGDALRM-------------------
+>gi|313217634|emb|CBY38686.1| unnamed protein product [Oikopleura dioica]gi|313218130|emb|CBY41437.1| unnamed protein product [Oikopleura dioica]gi|313231875|emb|CBY08987.1| unnamed protein product [Oikopleura dioica]
+-KPWCNVSVYECNNKIevystaktqlGVEYKVADanryaKKEAMKG-KNATQSDVFDLSSISNVNRSTDTWDLLEKLQRGLTLVYDREKRIVSChnNcKN
+LKIYVLSYLMNVECGKHEQSLIQVGPGASRVVYDGYQLAKTIEG-VNSTT--QNDLQKwalisqyanyFTVFRISFQP-WGPEYTKKRLTDCDLWLEIFM
+REYLDWINQIEHH------------
+>gi|71985803|ref|NP_492746.2| Temporarily Assigned Gene name family member (tag-68) [Caenorhabditis elegans]gi|38422270|emb|CAB70215.2| C. elegans protein F37D6.6, confirmed by transcript evidence [Caenorhabditis elegans]gi|38422275|emb|CAB70221.2| C. elegans protein F37D6.6, confirmed by transcript evidence [Caenorhabditis elegans]
+-RSWAKMTRYERKEQIGDTVWLHGPFAAV-GVLSKSvhDAQLECSpWDLKNEV---SFALIRQadPIG-----STNPEDVWLYNSGTRPLFL-SMTPNVS
+ST--KDTLRRLSPGYCIRVHRGEVSASAPASERTKVrRPSKDPALAQQNLVISVGKGWGPNYSRLYLTDIPCRYEVSF----------------------
+---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+P 1 3983 * 3654 * * 6008 * * * * * * 597 4643 4374 5535 4649 5014 * * 1
+ 24 5925 * 1585 585 * * 3920 1000 0
+
+A 2 3769 * 3073 2660 * 3435 * * 2793 7673 7008 5200 4041 3478 4028 3001 5158 * 6922 * 2
+ 16 6513 * 1463 650 * * 5555 1053 0
+
+F 3 3588 5462 5333 4741 4140 4530 3189 3037 6471 * * 3441 3671 6134 6251 4294 3947 4113 * 3087 3
+ 0 * * * * * * 5907 0 0
+
+W 4 * * * * * * * * * 6212 * * * * * * * 5834 67 6143 4
+ 0 * * * * * * 5970 0 0
+
+C 5 1982 735 * * * 3672 * 6038 * 4246 * * * * * * * * * * 5
+ 0 * * * * * * 5970 0 0
+
+S 6 5077 * 7863 * * 5467 4467 * 2301 * 7048 3695 * 4014 4124 1664 2975 4863 * 6143 6
+ 8 * 7539 * * * * 5970 0 0
+
+I 7 6981 * * * * * * 1198 6138 2821 5660 * * * * * * 1393 * * 7
+ 0 * * * * * 0 5967 0 1000
+
+S 8 1443 7852 5734 * 5292 5650 6576 3094 * 4409 * * * 3325 * 2799 4031 4525 * 4611 8
+ 29 5664 * 3170 170 * 0 5967 1076 1000
+
+Y 9 * 5766 * * 4325 * * 6088 * 4640 * * * * 4984 * 5825 3719 5670 450 9
+ 0 * * * * * 0 5990 0 1000
+
+Y 10 * * * * 2714 * 4480 * * 6541 4199 5703 * 6158 5670 * * * 2030 1185 10
+ 0 * * 2000 415 0 * 5990 1000 1000
+
+E 11 5954 * * 119 * * * * 5240 * * * * 4773 * * * * * * 11
+ 18 * 6354 * * * * 5992 0 0
+
+L 12 * 5472 * 3113 4679 5006 4693 5664 3491 1325 5243 * * 6214 2922 5930 6156 6143 * 5114 12
+ 21 6143 * 0 * 0 * 5970 1023 1034
+
+N 13 4287 4985 2957 6652 * 2824 5198 5954 4093 * * 1615 * 5767 3268 4817 4290 * * * 13
+ 0 * * * * * * 5992 0 0
+
+Q 14 5729 * 4899 3190 * 6917 4029 7307 4616 4359 5717 3812 * 2993 3421 3071 2433 4075 * * 14
+ 75 4748 6181 2640 252 * * 5992 1182 0
+
+R 15 * 4515 * * 5230 * 4496 * 3217 * 6486 * 5137 2674 897 4495 * * * * 15
+ 0 * * * * 0 * 5968 0 1025
+
+V 16 5831 * * * * * * 2239 5671 3498 5142 * * 6599 4802 * * 798 * 6307 16
+ 33 5476 * 3322 152 * * 5992 1079 0
+
+G 17 2805 * 5292 * * 420 * 6307 5831 * 5954 * * 6181 * 6448 * 6354 * * 17
+ 0 * * * * * * 5992 0 0
+
+E 18 5063 * 3698 1315 * * * * 2651 6354 * * 3683 4597 2815 6229 5767 5220 * * 18
+ 67 6358 4899 0 * * * 5992 1045 0
+
+T 19 2459 6412 5640 5413 4229 * 6273 4824 4403 2508 4586 * 3808 4731 4560 7263 2502 4140 * 7543 19
+ 70 * 4391 0 * 0 * 5891 1045 1243
+
+F 20 5256 * * 6653 738 6734 * * * * * * * * * * * 4696 4986 1811 20
+ 202 * 2935 * * 0 * 5910 0 1239
+
+H 21 4656 6756 4638 3906 5412 * 2612 4126 2299 5444 * 5844 3331 3784 4353 4715 5096 4911 5519 6259 21
+ 0 * * * * 0 * 5634 0 1690
+
+A 22 1821 3755 * * 4964 4104 * 5016 * 3204 5767 * * * * 4783 3827 1795 * * 22
+ 151 3334 * 1000 1000 * * 5992 1541 0
+
+S 23 5186 6053 4937 4094 5745 4767 3431 6911 4157 6448 * 4544 6539 4206 2123 2346 4113 7071 6652 4907 23
+ 71 4384 * 976 1024 * * 5992 1245 0
+
+Q 24 3559 6215 4463 3820 7318 3757 4158 5212 4013 7625 6857 3812 5992 3149 3280 2772 4449 5203 * 5339 24
+ 33 5476 * 2322 322 * * 5992 1079 0
+
+P 25 5388 * 4336 5590 * 4130 4851 6701 4218 5589 5671 4118 1473 4122 3989 3731 3370 * * * 25
+ 44 5320 7572 1683 539 * * 5992 1088 0
+
+S 26 4027 5560 5187 4655 4086 * 4191 4989 4641 * * 4472 5330 6129 6533 1950 2512 3093 6572 6906 26
+ 0 * * 0 * 0 * 5990 1000 1000
+
+M 27 4137 4966 * 5476 3078 * * 2761 * 2748 8206 * * * * * 6246 1164 * 6512 27
+ 8 * 7572 * * * * 5992 0 0
+
+T 28 4052 5226 6923 * 5746 * 4056 2681 4661 3692 * 2631 * 6071 5751 4653 2072 4104 6049 7056 28
+ 24 5939 * 3700 115 * 0 5990 1034 1000
+
+V 29 * * * * * * * 955 * 6129 5474 * * * * * * 1160 * * 29
+ 367 * 2153 * * * 0 5990 0 1000
+
+D 30 * * 368 5521 * 5658 5599 * 5125 * * 3707 * * * 4805 * * * 5522 30
+ 0 * * * * 2711 239 5680 0 2291
+
+G 31 4857 4669 * 5599 * 310 * * * * * 4793 * * * 3997 * * * * 31
+ 192 4133 3889 0 * 52 4824 5800 1239 2098
+
+F 32 6064 * * * 1023 3479 7099 5716 * 3869 5628 * * * 6251 2821 6493 5613 * 3290 32
+ 71 6275 4829 1858 466 514 1737 5875 1057 1309
+
+T 33 6169 5379 3573 4414 6510 6644 4996 3798 4773 4478 6384 5160 * 4204 4968 5913 1606 3501 6553 4175 33
+ 157 4356 4204 868 1145 628 1503 5926 1291 1254
+
+D 34 3465 6998 1101 3968 * 4280 6198 * * 6166 * 3490 4753 5123 5953 3629 5560 5679 * * 34
+ 40 5821 6707 3822 106 * 0 5879 1043 1389
+
+P 35 4689 * * 4843 * 2754 6202 * 5592 3311 * * 1231 4729 6197 4032 5793 3831 * 5947 35
+ 34 * 5445 * * 403 2037 5879 0 1475
+
+S 36 4640 5489 * 4828 3175 5588 5601 4935 * 6744 * 4957 2644 6006 4381 1436 4670 5246 * 5857 36
+ 47 4954 * 1000 1000 515 1736 5982 1161 1208
+
+N 37 5348 5713 1872 4379 * 3451 4871 7462 5299 4052 * 3281 * 4062 4702 3807 3741 4160 * 6066 37
+ 260 2876 5126 1584 585 0 * 5992 1815 1022
+
+S 38 4538 6636 5122 3751 * 1591 * 5460 4619 * * 3162 3929 4956 5510 2637 5358 4975 * * 38
+ 423 1976 * 2206 352 2225 347 5961 2561 1112
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+ 0 * * * * * * 4648 0 0
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+ 0 * * * * * 0 4030 0 1000
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+C 193 * 1462 * * * * * 1604 * * 3989 * 4091 * * * 3570 3288 * * 193
+ 45 5027 * 1000 1000 0 * 4017 1057 1000
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+S 194 * * 4068 * * 3337 4123 * 3996 * * 3114 * * * 931 3619 * * * 194
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+ 0 * * 0 * * * 2962 0 0
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+//
+�HHsearch 1.5
+NAME deee1e6a65f0898c57dcde00fc15c870
+FAM
+FILE deee1e6a65f0898c57dcde00fc15c870
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:16:44 2013
+LENG 126 match states, 126 columns in multiple alignment
+FILT 111 out of 624 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 5.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEECCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCC
+CCCCCCCCCCCCCCCCHHHCCCCCCC
+>ss_conf PSIPRED confidence values
+9377366689975679788624465699999999990999451107499999999999984436321789999999799999864354328852997798
+76727765567764420112444689
+>Consensus
+mvxixxxxlxxxkxvxxaLxxIxGIGxxxAxxIcxxlgixxxxxxxxLxxxqixxlxxxlxxxxxixxdLxxxxxxxIxrlxxIxsyRGxRHxxGLPVRG
+QRTxTNarTxkxxxxxxxxxxxxxxx
+>deee1e6a65f0898c57dcde00fc15c870
+MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRG
+QRTRTNARTRKGPRKTVAGKKKAPRK
+>gi|225680884|gb|EEH19168.1| 40S ribosomal protein S13 [Paracoccidioides brasiliensis Pb03]
+------------------------------------marFYVHETAKIGDLGNKQILSLTAALSE-MKIENDLRRQILDDIQRLKDIGTVRACGPILvag
+pAASMRGlvslvfpfaDGYTLQNKT-----aiklnrldrrlgikgpr------------
+>gi|290559361|gb|EFD92694.1| ribosomal protein S13 [Candidatus Parvarchaeum acidophilus ARMAN-5]
+IVRIADTDLDGSKAVKDLLRSIPGISFSYSNALMKVLNIPKGKKLQDLDEKELNTLKEALSDPfkYkiphwlfnwrrddetgldyhLLSNDLRSKTTMRI
+QKIKTSRSYRGYRHSFNYKLRGQKVKSrganvHGRV-----------------
+>gi|15790213|ref|NP_280037.1| 30S ribosomal protein S13P [Halobacterium sp. NRC-1]gi|169235942|ref|YP_001689142.1| 30S ribosomal protein S13P [Halobacterium salinarum R1]gi|13124533|sp|Q9V2W4.1|RS13_HALSA RecName: Full=30S ribosomal protein S13P; AltName: Full=HS13gi|6172227|dbj|BAA85895.1| ribosomal protein HS13 [Halobacterium salinarum]gi|10580671|gb|AAG19517.1| 30S ribosomal protein S13P [Halobacterium sp. NRC-1]gi|167727008|emb|CAP13794.1| ribosomal protein S13 [Halobacterium salinarum R1]
+FVRIGQTDLDGTKTVERALAELGGVGRRVARIVADEAGVDRTATMGGLEDDAIESVTDAVDSFtEHapawlanrqndfytgenqhiTGTDVELTRDQDi-
+NRMRMIR-sYKGIRHER-gQKVRGQRTKSTGRTE----------------
+>gi|27661504|ref|XP_232915.1| PREDICTED: ribosomal protein S18-like [Rattus norvegicus]gi|109476520|ref|XP_001058861.1| PREDICTED: ribosomal protein S18-like [Rattus norvegicus]
+-LQVLNTNIDEQQETAFAITATKGAEQRYAHVVLRKAGIDLTKMAGELTEDKVERVITIMQNPrqYEipqkgvrdgrcsqvPANGLDNKLREELERLKKI
+RAHRGLRHFWGLHVHCQLTMSHG--CRGYTVGASKKKR----
+>gi|7525003|ref|NP_050101.1| ribosomal protein S13 [Dictyostelium discoideum]gi|74833664|sp|O21038.1|RT13_DICDI RecName: Full=Ribosomal protein S13, mitochondrialgi|2627258|dbj|BAA23575.1| ribosomal protein S13 [Dictyostelium discoideum]gi|4958906|dbj|BAA78083.1| ribosomal protein S13 [Dictyostelium discoideum]
+----GKIELNNEKQIIGELkKKIKGVNFHIAQKVIMLSGNVASIKGNKLIQSEEKQIVDILQRFkglYSHNYGLKEEALAKIRRIEN--VYRYIRVRQGY
+PVRG-RTKSNANTVKRQ-------------
+>gi|187764102|ref|YP_001876551.1| ribosomal protein S13 [Dictyostelium fasciculatum]gi|160688810|gb|ABX45225.1| ribosomal protein S13 [Dictyostelium fasciculatum]
+--------LNKRKKVLFEIkKKIAGMGESMTKRLCSMCGFLPMTYVSKISTKGGLRLMRIYKS-FKGLSDYSYYvyrKRFNQRRS-KERAYRSQRFTKGY
+PV-SQRTRTNGKIAS---------------
+>gi|72161465|ref|YP_289122.1| hypothetical protein Tfu_1061 [Thermobifida fusca YX]gi|71915197|gb|AAZ55099.1| conserved hypothetical protein [Thermobifida fusca YX]
+--------VIGKMKVSALLESLPGVGKVRAKQIMERLNIAESRRIRGLGANQRAALESEFG---------------------------------------
+--------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 5243 0 0
+
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+ 21 6092 * 0 * * * 5443 1053 0
+
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+ 13 6790 * 3478 136 * * 5464 1061 0
+
+I 4 5319 * * * 5578 * * 802 * 2857 3993 6656 * * * * 5973 2701 * * 4
+ 0 * * * * * * 5464 0 0
+
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+ 0 * * * * * * 5530 0 0
+
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+
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+ 15 6627 * 1357 714 * * 5530 1062 0
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+ 0 * * * * 0 * 5696 0 1077
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+
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+ 0 * * * * * * 5777 0 0
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+ 53 4789 * 717 1353 0 * 5810 1153 1200
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+ 146 3381 * 0 * * * 5889 1496 0
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+ 0 * * * * 0 * 6006 0 1077
+
+Y 21 3671 * 4272 4260 * 4415 6823 * 2094 * 5587 4078 * 3392 3434 2873 5181 6932 * 3515 21
+ 0 * * * * * * 6072 0 0
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+ 0 * * * * * * 6072 0 0
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+ 0 * * * * * * 6072 0 0
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+ 12 6889 * 2000 415 * * 6072 1000 0
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+
+E 35 3197 6951 3362 3535 * * 5604 * 2532 3808 5526 3439 7008 5096 2900 3425 * 5354 * 4960 35
+ 0 * * * * * * 6072 0 0
+
+K 36 3968 * 4563 4098 6007 7333 * 4346 1978 3922 5793 5700 * 3962 2412 4549 5971 3640 * 5931 36
+ 0 * * 1585 585 * * 6072 1099 0
+
+T 37 2549 3813 * * 3602 * * 4518 * 1304 5113 7285 * * * 4297 3703 4740 6935 5766 37
+ 20 6167 * 1000 1000 * * 6122 1025 0
+
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+
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+ 24 * 5946 * * * * 6122 0 0
+
+P 41 4308 * 4787 4191 6721 4420 * 4934 3340 3853 * 4862 1365 * 4759 3856 5426 4891 * 5943 41
+ 12 6910 * 4248 78 0 * 6101 1000 1094
+
+A 42 5082 * 3558 4586 4659 4806 4772 * 3773 4410 5808 2109 5893 5694 4333 2874 3179 * 5077 * 42
+ 0 * * * * * * 6122 0 0
+
+T 43 2907 3989 7339 4835 6990 * * 3863 2381 2923 3820 * * 5892 3566 4619 3242 5360 * 5707 43
+ 52 4824 * 916 1089 * * 6122 1186 0
+
+R 44 6873 * * 6505 6605 5181 6082 5466 1754 5055 5691 5061 4506 4924 1709 5775 3502 * 6288 5199 44
+ 13 * 6780 * * * * 6122 0 0
+
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+ 0 * * * * 0 * 6111 0 1000
+
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+ 35 6664 6167 0 * * * 6122 1000 0
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+ 12 * 6894 * * 0 * 6087 0 1025
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+ 0 * * * * * 0 6116 0 1006
+
+E 50 4247 * 2085 2390 5661 6982 * 6080 3504 5510 * 3449 3593 4059 5110 4846 4563 6469 * 5916 50
+ 15 6625 * 2000 415 * 0 6116 1000 1006
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+ 519 3251 2344 3665 118 2735 235 6022 1510 1271
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+T 63 * * 3743 5701 3229 * 5170 5779 3913 5576 * 2098 2198 4610 5400 3865 5692 * * 4015 63
+ 802 1230 * 1650 553 195 2985 5743 2695 2440
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+ 246 2676 * 4286 76 2395 304 6025 1762 1191
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+K 65 6746 6080 4702 4288 4366 4445 6890 4865 3032 2268 4989 4306 3919 5997 5812 4316 3516 3481 6587 * 65
+ 197 2972 * 4249 78 * 0 6030 1641 1144
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+ 9 7271 * 2585 263 * 0 6030 1000 1144
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+ 22 6057 * 2000 415 * 0 6030 1010 1144
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+ 23 5994 * 0 * * 0 6030 1031 1144
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+ 0 * * * * * 0 6030 0 1144
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+L 81 5128 * 6859 4233 5370 5544 6579 4313 3707 872 3214 * * 6859 * 5174 7147 * * 5101 81
+ 29 * 5668 * * * 0 6030 0 1144
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+ 11 7089 * 0 * 1570 593 5970 1000 1246
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+ 33 * 5487 * * * 0 6030 0 1144
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+ 0 * * 0 * 1260 780 5981 1077 1267
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+ 42 6304 5974 1000 1000 617 1523 6015 1010 1132
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+C 86 3272 2400 * 6557 * * 6070 * * 4721 6568 4788 * 6327 6560 1189 3260 5019 * * 86
+ 0 * * 3775 109 793 1242 6057 1098 1098
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+Y 87 * * * 6485 6332 * 5131 4471 6593 4286 * 5661 * * 6065 6959 * 4271 3617 588 87
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+ 0 * * 1585 585 0 * 6062 1006 1006
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+L 90 * 4405 * * 3616 * * 2355 4996 2118 5038 * * 5766 3723 4948 6460 2937 5228 3499 90
+ 0 * * * * * * 6070 0 0
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+ 98 5454 4552 2000 415 * * 6070 1099 0
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+//
+�HHsearch 1.5
+NAME e0ba85cb42b528cdde934e6e751de9b2
+FAM
+FILE e0ba85cb42b528cdde934e6e751de9b2
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:02:24 2013
+LENG 138 match states, 138 columns in multiple alignment
+FILT 249 out of 1276 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEEEEHHHCCCCCCCCCCCCCEEECCEEEEEECCCCCHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCEEEEEEECCCCCCEEECCCCCCCCCC
+CCCCCCCCCCEEEEECCCCEEECCCCCCEEEEEEEECC
+>ss_conf PSIPRED confidence values
+9513545001101676789999998997999999977753999999999974998946579999999997245789877854889976977998046566
+57899999886999789828865788876748987459
+>Consensus
+xxxlxxxxxxxxxxxxxxxxCpxxwxxxxxxCyxxxxxxxxwxxAxxxCxxxgxxLaxixxxxexxxixxxxxxxWiGlxxxxxxxxwxwxdgxxxxxxx
+wxxxxpxxxxCxxxxxxxxwxxxxCxxxxxxICexxxv
+>e0ba85cb42b528cdde934e6e751de9b2
+MNSLFNQEVQIPLTESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNL
+LTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRTV
+>gi|260832614|ref|XP_002611252.1| hypothetical protein BRAFLDRAFT_119658 [Branchiostoma floridae]gi|229296623|gb|EEN67262.1| hypothetical protein BRAFLDRAFT_119658 [Branchiostoma floridae]
+------------------PyKCDQ--------CdYSATQKGNLDQHRTNPTGE-------------KTYLCGYRtaGRSYLSLHMRTHTGEKPFkCDECD
+YSvAKKCEESHKAkhtdAKRYKCvecgYRTAymshlSVHMRTHTVWPF---------
+>gi|149637003|ref|XP_001508495.1| PREDICTED: similar to polycystic kidney disease 1-like 2 [Ornithorhynchus anatinus]
+------------------SPRPRARRDRGPPRRPLLVTGMTFAmlPGNATRGGPYGRSAVFRRPRAElrstpgPCRERpAGprAAACPGLSARirgsrgS
+VARPGpgvcggtTWLDESNTSYSNW---PEdpSPAArCGYLDqqSGYRWVaTENCSQELGFICEFE--
+>gi|341894061|gb|EGT49996.1| hypothetical protein CAEBREN_20633 [Caenorhabditis brenneri]
+VAARFDSSSSESCEdshshshgshshehgggggRGANRGCERGWRRFNrpsgGWCIKVAQGQFSQAQAESKCQVEGGTLSGLQDTNEISYITSAalrlfp
+erTGSLWVGAKRTpacssspisascNAMNSFTWTDGSTSGTAgfQWNKNQPDNahsktQQCVVLLASSTqvvtdsWtwntnqlDDVRCVNPggsqqrivR
+GYVCGKRA-
+>gi|268554055|ref|XP_002635015.1| Hypothetical protein CBG13558 [Caenorhabditis briggsae]gi|187028583|emb|CAP32339.1| CBR-CLEC-172 protein [Caenorhabditis briggsae AF16]
+ISQLILVSLMISLATSK--SCLAPASYILGSCFTFINTPMSFWEANSYCEYHSnnawSYLALVESPEQSIWLAKSAtmftsENYWIGVYRPSVIDNFRTI
+LNRYLTFQYFANINPSMNYAVGRKSDGKWETRPEEERFPFVCSYK--
+>gi|241594910|ref|XP_002404410.1| attractin, putative [Ixodes scapularis]gi|215500403|gb|EEC09897.1| attractin, putative [Ixodes scapularis]
+--------------------VGQEGREPAQACQETGLRTGRWMASKRRCLrgRLVNGTQGLVDARENQTDvDQCQQSEssncdkLHNCHACHTEF-HCgW
+QNDHRCYtfVRESAPGMIpGfyLGVSEWL------------------------
+>gi|341874183|gb|EGT30118.1| CBN-CLEC-265 protein [Caenorhabditis brenneri]
+--SAFLLIATVFHSSLAA-SCPTGTKLYNSKCYAALGMDMTRDKALAYCKKTygsYAVLATPLTYAENNFVTEQVQlhanwHTWLEF---VADGTYIVgD
+DGKPPVYTNFAVGEPfsvSVGYCITIGMNGYWYAQPCADSHSALCEFALY
+>gi|260816259|ref|XP_002602889.1| hypothetical protein BRAFLDRAFT_98109 [Branchiostoma floridae]gi|229288202|gb|EEN58901.1| hypothetical protein BRAFLDRAFT_98109 [Branchiostoma floridae]
+----------------------AGRDRR--------ATMSRLVSAGIACWLL---IVTGWGYSFFPMRYLLVlklssgAKLL-----LL--EVTVWP---
+-VVF--FLKNKSVIlGRSHHL------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 6945 0 0
+
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+ 0 * * * * * * 7401 0 0
+
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+
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+ 41 5172 * 1952 431 698 1382 9488 1473 1657
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+C 32 5485 343 7816 4746 7150 * 6994 7299 * 8082 * 7079 * 7803 5388 5857 6256 6116 6796 4912 32
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+Y 33 * * * * 2653 * 5322 4914 7335 3727 7800 * * 6352 5920 7456 7816 4997 7029 692 33
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+D 37 3967 * 4181 3846 5068 4274 4986 5305 3747 4426 5850 3241 3885 4314 4295 3612 3002 4489 * 6809 37
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+E 38 5077 * 2707 2917 5301 4245 6288 5091 3430 5917 6521 4114 5311 3502 4785 3970 3284 4455 * 5329 38
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+S 39 3476 * 6906 4047 6689 4248 5744 4922 2660 4302 5290 4760 3142 3735 4373 3653 3530 4977 6879 6270 39
+ 0 * * * * * * 9673 0 0
+
+K 40 3320 7309 6286 4215 5375 4480 5787 6037 3076 2363 3245 6171 6972 4992 3818 3968 4760 4121 * 5396 40
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+W 42 5748 * 6680 6614 2633 5892 4072 6243 7995 5365 7949 7895 * 6155 4592 6856 * 6029 1159 2767 42
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+E 44 3485 * 2285 2139 * 3675 5900 6279 3948 4897 6279 4339 6429 4150 5802 4529 4342 6233 6733 6850 44
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+S 45 371 5893 * 7795 6520 4867 7572 7280 * 7332 6014 * 7327 7725 6689 3613 6986 7035 * 6823 45
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+Q 46 4151 * 4802 3174 5437 6390 5890 5653 3057 4320 6195 4291 6849 2793 2755 4261 5022 3690 7440 5435 46
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+A 47 3290 7170 3862 3343 4866 5719 6431 4740 3988 5294 5502 3303 8477 3302 3254 3356 4133 5372 * 5540 47
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+C 49 8237 88 * * * 6730 * * * * * * * * 6202 6823 5975 * * 6944 49
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+Q 65 3731 * 4780 4657 4389 5543 4395 5532 4791 3126 4882 2449 6019 2730 3967 4611 5860 5819 6958 5131 65
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+S 73 3348 * 3489 3825 5575 3049 6053 7134 3675 5257 * 3547 5654 3691 4066 3341 3584 4951 * 5889 73
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+Y 74 4001 6007 3425 3333 4231 4258 4685 6222 4095 5079 8169 3990 4277 4998 3850 3048 3948 6259 6293 4221 74
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+H 75 4095 7797 7551 6372 2368 6403 6077 3389 * 3721 5731 6020 6046 7871 7052 5474 4456 2911 5252 2061 75
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+ 75 4853 5972 1338 726 2252 340 9619 1744 1440
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+N 99 5151 6934 4113 4417 4371 4288 5195 4854 4129 3922 7679 3543 4739 3990 4223 2734 2840 5196 6771 8163 99
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+ 47 5655 6345 2432 296 * 0 9611 1325 1605
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+ 26 5820 * 4192 81 1781 496 9584 1243 1826
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+I 103 4030 6592 4049 4365 6760 4544 6215 4201 4352 4695 7046 4094 2400 5434 4294 2938 3815 4639 6597 5046 103
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+ 81 4643 6122 1899 450 1375 702 9575 1678 2244
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+ 147 3364 * 2254 339 2774 228 9597 2675 1490
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+ 0 * * * * 0 * 9410 0 1082
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+I 132 4772 * * * 4532 * * 1080 * 3073 5287 * * * * 5946 8013 1850 * 7550 132
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+ 0 * * * * * * 9433 0 0
+
+M 134 5671 * * 1263 7561 5609 7990 * 2873 6806 4498 7163 * 2031 5942 4739 5736 * * 5638 134
+ 12 7633 8261 0 * * * 9416 1000 0
+
+Q 135 5026 * * 5037 3468 7387 5156 4468 1865 5007 4539 7437 * 3946 2760 4621 4887 3786 * 4175 135
+ 19 6288 * 2793 225 0 * 9415 1093 1000
+
+R 136 4746 * 3658 3445 6468 5718 5318 7262 3006 5584 6973 3587 2201 4851 3257 5439 3767 5855 7034 6047 136
+ 0 * * * * * * 9303 0 0
+
+T 137 1505 6755 6817 * 6289 * 6500 2887 5706 2598 4691 * 4103 * 6751 5427 4246 3264 * * 137
+ 0 * * * * * * 9055 0 0
+
+V 138 * * * * 3641 * * 3003 * 2701 * * 4690 * * * 4627 831 * * 138
+ 0 * * 0 * * * 6875 0 0
+
+//
+�HHsearch 1.5
+NAME e130d30836eaf714deba0688836fbaec
+FAM
+FILE e130d30836eaf714deba0688836fbaec
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:18:57 2013
+LENG 230 match states, 230 columns in multiple alignment
+FILT 134 out of 1359 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEECCCCCEEECCCCCCCEEEECCCCCCEEEEEECCCCCCCCEEEEEEEEC
+CCCCCCEECCCCEEEEEEECCCCCCEEEECCCCCEEECCCEEEEEEEECCCCCCCEEEEECCCCCCCCCCEEEEEECCCCEEEEEEEEEEECCCCCCEEE
+EEEEECCCCEEEEEEECCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9299488858996799889998961788889789999907999817999994378840205665762567305887617899625731445899999954
+9876401125515877862244575388608753010697489999965767997599988984157732025684599789999999951204798799
+999948998789999906768999698999
+>Consensus
+xxxxxxpxxxxxxxGxxvxLxCxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxxLxIxxxxxxDxgxYxCxvxx
+xxxxxxxxxxxxxxlxvxxxxxxxpxvxxxxxxxxxxxgxxxxlxCxxxxxxPxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxsxLxixxxxxxxgxyx
+Cxvxxxxxxxxxxxxlxxxxxxxxxxxxxx
+>e130d30836eaf714deba0688836fbaec
+QVQLQQPGAELVKPGASVKLSCKASGYTFTSNWINWVKQRPGQGLEWIGNIYPGSGYTNYNERFKSKATLTVDTSSSTAYMQLSSLTSDDSAVYYCARKH
+YFYDGVVYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTSGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSIT
+CNVAHPASSTKVDKKIEPRGPTIKPCPPCK
+>gi|94732089|emb|CAK03669.1| novel immune-type receptor 5, allele 2 [Danio rerio]
+---LQLHELEQVESEVKKPLYCLVQNQLVRNEHrLYWFSHGSEEsPPGFI--------HIygNSSKSCVGSSESDCLSPTCMYNLPMKRSRSSKMEMHYC
+ALATC---GQALFGNVSKLNPDAVGSPKI-----------------------------------------------------------------------
+----------------------------------
+>gi|168985092|emb|CAQ09233.1| major histocompatibility complex, class I, C [Homo sapiens]
+----------------------------------------------------------------------------------------------------
+-----------------------HPKTHVTHHPVSD---HEASRR-WNLpevgscggAFWrRAEIHVPCaaRGAARAPHPE-------------------
+-----------------------------------------
+>gi|194039786|ref|XP_001927231.1| PREDICTED: butyrophilin subfamily 1 member A1-like [Sus scrofa]
+HFDVIGPPEPIlAVVGEDAELPCRLSPNVSAERmELRWFRKKVSPAVFVR--REGREQAGEQMPEYRGRVtLVEDDIAAGHVAVRIQGVKASDDGEYRCF
+FRQ-----DENYEEAIVHLKVAALGSDPQIHM-----EVQESGEIQLECTSMGWYPEP-WVQWrtPKGEEFPSMSESKSPNEEGLFTVAASVIIRDPS--
+VKNVSCYVRNLLLGQEKEVEIS-------------
+>gi|18858393|ref|NP_571075.1| CD166 antigen homolog A precursor [Danio rerio]gi|2497299|sp|Q90460.1|C166A_DANRE RecName: Full=CD166 antigen homolog A; AltName: Full=Activated leukocyte cell adhesion molecule A; AltName: Full=DM-GRASP homolog; AltName: Full=Neurolin; AltName: CD_antigen=CD166; Flags: Precursorgi|452158|gb|AAA50024.1| transmembrane glycoprotein [Danio rerio]
+--------------GETIEVPCNngNN-KPDGLIFTKWKYAKDDGSPGDLLIKQAQKDDPtvSAMDGYKTRVSIAAN-----SSLLIAQGSLTDQRVFTC
+MVVSST----NLEEFSVEVKVH--KKPSAPVIKNKVKELENGKLTQLGECVVESANPAA-DLIWmkNNQALVDDgktiiITSDVTKDPvTGLSSTSSRLQ
+YTARKEDvASQFTCVAKHVTGPNQV---STP------------
+>gi|332257155|ref|XP_003277679.1| PREDICTED: poliovirus receptor-related protein 2-like [Nomascus leucogenys]
+SGRPPAPARTPSNLtfraGEAEHLPRPPPAPrAPSRVSPSWLAPPTPTPYTSDS-LEETLTPPFCISLTTtPILL------nptahptpacLSPSP----
+---------------------FLGFP---------RRKAKPENQAEAQKVTFSQDPTTVALCISKEGRP-PARISWLSSLDWEAKETQVSGTLAGTVTVT
+SRFTLVPSGRaDGVTVTCKVEHES-----------------------
+>gi|213982747|ref|NP_001135545.1| v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog [Xenopus (Silurana) tropicalis]gi|195539639|gb|AAI68021.1| Unknown (protein for MGC:185004) [Xenopus (Silurana) tropicalis]
+--------------------------------------------------------------------------------ITIKMVQVSFDGCYVCTGNQ
+SG---TVKKSSTFSIHVKPEPKKEPTIFLTKSRQLVKTGEPFEVTCTVMDV-FSTVKAQWLDARDmEsTERANFLPTR-IFSL--NLTLKSDGVLFSeSR
+TFTCQAENAIGQVNATFTLD-------------
+>gi|327265502|ref|XP_003217547.1| PREDICTED: macrophage colony-stimulating factor 1 receptor-like [Anolis carolinensis]
+--------------------------------------------------------------------------------IRLRRVGMDDNGWYKCRALV
+QG---Q-------WVQ-------SPKIGLIVKGFIIFYYIFTYFFVTAHCI-VLAFGSY-----CKCHIKLELSFK-----------------------I
+CILTK----KQSALIKT-------------
+>gi|11990448|dbj|BAB19782.1| vascular cell adhesion molecule-1 6D variant lacking D7 [Bos taurus]
+-VEISPGPQIAAQVGDSVVLTCDVRDCES--PSFSWRTLIDsplNGNVRSE---------------------------GSKSTLTLSPVSFENEHFYLCT
+VMCGQ--KKLEKRIQVKPYSFPSnpeiemsGplvsgnpvtvscrvpnvypsdqleielfkgesimmnktfskdvskkaletkslektfipttedignvlv
+clarlpidemefelkqrqstqtlyvnvAPRDTTILVSPSSILEEGSSVNMTCSSNGLPAPKILWSRqlSNGD------LQPISE-NATL------SFMST
+KMEDsGIYVCEGINQVGTSRKEVNL--------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+ 0 * * * * * * 6658 0 0
+
+V 2 4916 * * * 4920 3965 * 3036 * 2270 * 3975 5216 * * 5089 5523 1326 * * 2
+ 0 * * * * * * 8426 0 0
+
+Q 3 5599 * 4373 4058 5479 4001 * 5575 3416 5669 5572 * * 4521 3953 3229 3556 1840 * 4274 3
+ 0 * * * * * * 8966 0 0
+
+L 4 4850 * * * 4674 * * 3230 5352 1634 3889 * 4135 5107 5870 5757 4311 2098 * * 4
+ 59 4648 * 2206 352 * * 9713 1326 0
+
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+ 19 6285 * 0 * * * 10095 1000 0
+
+Q 6 3197 * 5927 5141 * 4224 5208 4697 4323 4479 * 5164 3285 2325 4031 3374 3789 4038 6450 * 6
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+
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+
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+ 17 6451 * 0 * * * 10239 1000 0
+
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+
+E 10 4789 * 6441 3490 6125 4644 6306 3225 4821 2330 4406 * 5502 3799 6373 4686 5355 2067 * * 10
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+
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+
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+
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+
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+ 30 5580 * 1350 719 * * 10599 1238 0
+
+G 15 5980 * 6795 3792 7206 487 5791 * 4961 * * 4242 * 5946 5625 5822 6989 6843 * 6806 15
+ 0 * * * * * * 10759 0 0
+
+A 16 5355 7114 2782 2399 * 2356 6693 7190 3339 6628 5969 4518 * 3678 4879 3637 4226 7170 * * 16
+ 0 * * * * * * 10804 0 0
+
+S 17 4178 6637 3307 3734 5806 6714 6914 7094 4780 5798 * 4149 3159 4579 5364 2334 2430 4547 * * 17
+ 34 7044 5984 1000 1000 * * 10824 1000 0
+
+V 18 2080 * * 6706 5811 5913 * 3353 6694 3333 5246 * 6709 * * 5646 5205 1218 * * 18
+ 15 6629 * 0 * 0 * 10851 1000 1142
+
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+ 0 * * * * * * 10876 0 0
+
+L 20 * * * * 3227 * 7225 2456 7133 776 4400 * 7094 7037 * * 7116 4862 * 6783 20
+ 0 * * * * * * 10876 0 0
+
+S 21 6012 * 4161 3809 5493 4380 5961 6677 5281 4457 5874 3582 2661 4543 3467 2989 2820 5042 * * 21
+ 0 * * * * * * 10876 0 0
+
+C 22 5828 130 * * 5283 * * * 7133 6726 * * * * 5939 6661 * * * * 22
+ 0 * * * * * * 10876 0 0
+
+K 23 4247 7225 4008 3488 4917 4158 4736 6041 3579 4270 6334 3466 4306 5436 3822 2885 3780 4554 * 6159 23
+ 23 5957 * 1764 503 * * 10876 1123 0
+
+A 24 3175 * * 6726 3092 6762 6493 3409 * 2939 7159 5996 4549 5995 * 4517 4370 2180 * 3013 24
+ 127 4323 4861 1306 748 * * 10876 1732 0
+
+S 25 5371 * 3397 3760 5877 4310 5311 5304 3855 4715 7128 4198 4525 5861 4119 2588 2469 4969 7157 5934 25
+ 151 4461 4211 1377 702 2140 371 10828 1654 1540
+
+G 26 4596 6977 3772 3773 * 1616 * * 4992 4575 * 3836 3740 3818 5684 3705 4866 5073 * 5115 26
+ 92 * 4021 * * 2364 312 10777 0 2537
+
+Y 27 3954 6103 5766 5726 3317 4078 4781 5150 3899 3647 6845 4637 3829 3926 4730 2864 4161 5869 * 3651 27
+ 118 4725 4618 0 * 288 2464 10749 1495 3279
+
+T 28 4039 6675 4063 3338 5631 4245 5333 7045 3918 4982 5843 4342 2980 4722 5021 3133 3182 3815 * 6625 28
+ 143 6734 3561 1000 1000 1735 515 10805 1000 1965
+
+F 29 3948 4475 4122 4157 5769 5065 6713 4930 4592 3506 * 4815 2356 5522 3877 3308 4822 4056 * 4660 29
+ 376 4760 2379 1466 648 2322 322 10754 1406 3095
+
+T 30 3499 * 2933 4711 * 3003 6359 * 3606 4268 6624 4926 4058 4616 4400 3012 3390 4710 * 5458 30
+ 158 4439 4115 866 1148 3355 148 10691 1436 5489
+
+S 31 4092 * 2411 4121 6496 3202 4335 6531 4840 3832 * 3760 3673 4173 4681 4156 4697 4145 * 6297 31
+ 233 2849 6574 936 1067 275 2527 10547 2651 5701
+
+N 32 4391 * 4715 3704 4488 4376 6795 3785 5310 3515 5790 3886 2999 4916 5265 3808 4119 3344 * 4229 32
+ 220 2915 6794 208 2899 762 1285 10793 3331 2054
+
+W 33 3728 * 6059 5202 5943 5851 6575 4337 5508 5692 4615 5277 6716 3689 4423 2495 2486 3440 5785 3625 33
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+ 42 5741 6672 589 1576 1377 702 10384 1129 2028
+
+G 163 6106 * 3808 3774 * 1726 5764 5221 3169 5811 * 3575 4941 3822 4391 3925 5086 4866 * * 163
+ 45 5586 6655 1445 660 955 1047 10397 1215 1746
+
+S 164 4394 * 3563 2742 6323 3839 * * 3549 4391 5231 3559 3915 4159 3859 3755 3695 4355 * * 164
+ 165 5167 3644 0 * 1075 929 10562 1305 1413
+
+L 165 5485 5834 4548 3008 5115 6397 * 2969 4332 2193 6520 4354 5731 6774 4356 4946 4336 2860 * * 165
+ 30 6531 6695 2807 222 * 0 10422 1000 2576
+
+S 166 6160 * 4044 3241 6349 * 5546 3823 4103 3147 6863 3864 3070 5017 4454 2978 3666 4164 6667 * 166
+ 43 5857 6397 1695 533 2526 275 10463 1144 2705
+
+S 167 4474 6779 3517 3116 5017 6706 6650 5087 4613 3332 5604 3753 3253 5614 5125 3364 3428 5704 6415 4222 167
+ 15 6633 * 0 * * 0 10503 1007 2556
+
+G 168 3327 * 2744 3742 * 2467 5191 5073 6675 5498 * 4090 6380 4245 5009 2956 3499 6397 * 5453 168
+ 86 4638 5801 1312 744 1581 587 10160 1394 2710
+
+V 169 4233 * 4253 3662 * 4487 4568 3599 4431 5000 5567 4072 4571 4452 4677 3114 3682 2669 * 6585 169
+ 48 5385 6787 2610 258 2303 327 10476 1198 2424
+
+H 170 4434 * 4928 3725 5062 3894 4601 4111 3693 5613 5063 4572 4926 3534 4695 3263 3231 4617 * 3835 170
+ 110 4772 4752 1428 670 1149 865 10546 1500 2262
+
+T 171 3926 * 6799 4051 * 5568 5904 6769 4248 4807 6429 2707 4457 4286 4618 3001 2173 4674 * 4596 171
+ 41 5591 7059 590 1575 * 0 10485 1192 2342
+
+F 172 4758 * 4332 4691 3543 4317 5133 4257 5251 3978 5734 4757 5465 4622 3517 2637 3193 4344 * 4558 172
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+
+P 173 4462 * 4519 4084 6812 3936 6947 5022 4265 4428 * 4654 2478 4228 4110 3186 2981 4543 6097 5964 173
+ 12 * 6881 * * 2585 263 10564 0 1716
+
+A 174 4511 * 4353 3604 5237 3253 4765 4808 4863 4333 6553 6436 3258 4091 4331 3093 3510 3716 * 5574 174
+ 67 4472 * 2013 411 1494 633 10556 1719 1714
+
+V 175 4573 * 4685 4266 4834 4154 5645 4023 3681 3849 6737 4746 3830 4638 4664 3019 4007 2676 * 6892 175
+ 50 5278 6859 728 1335 * 0 10575 1251 1553
+
+L 176 6311 6412 4008 3839 5319 4919 4049 4465 4041 2858 5563 5520 4926 3774 3299 4065 3897 4435 5743 4687 176
+ 269 6609 2646 0 * 2551 270 10567 1002 1697
+
+Q 177 4853 6364 3893 2889 * 4272 4246 5565 3876 4043 * 3084 3555 3489 6529 3842 3686 4862 * 6403 177
+ 986 1051 6350 913 1093 522 1719 10145 6390 4122
+
+S 178 5036 * 1886 3877 * 2860 * * 4638 4945 * 3011 4614 6550 4740 2811 4489 5608 * * 178
+ 0 * * * * 2411 300 10311 0 2265
+
+D 179 5794 * 3076 3753 5847 1361 5630 * 4127 5846 6476 3281 * 6375 4442 4085 4586 6828 * 7337 179
+ 223 3167 4981 1343 723 1447 659 10330 2696 2010
+
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+Y 181 6608 * 6536 5130 1891 * 5476 4349 6277 4083 6742 6285 4976 5026 5647 4064 5187 4629 6319 1773 181
+ 38 * 5282 * * 1220 809 10289 0 2332
+
+T 182 5634 * 4190 4424 5667 6516 4539 6853 5739 5760 4094 3400 6585 4426 5232 2199 1875 5627 6431 * 182
+ 33 6280 6633 4170 82 * 0 10301 1075 2175
+
+L 183 3888 * 6300 5299 5349 4608 6381 3516 4514 3015 3742 6781 * 4724 4656 4327 3256 2233 6467 5502 183
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+
+S 184 4413 * * * 4165 6604 4763 4941 4999 3917 5425 4015 5028 4590 5532 2522 2225 3869 4232 4984 184
+ 34 6201 6725 1000 1000 * 0 10362 1023 2988
+
+S 185 4105 4476 * 4823 * 3836 * 5083 4610 4830 5060 5652 6461 6542 6170 862 4802 6135 * * 185
+ 0 * * * * 4194 81 10360 0 3098
+
+S 186 5325 6738 5328 3815 6487 * 4645 4276 4558 3774 5135 4529 * 4455 3020 3003 3216 3159 4855 4967 186
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+
+V 187 5623 * * 6598 4985 4913 6644 3797 * 704 * 6735 * * * 5735 4776 3527 * 4120 187
+ 0 * * * * 418 1991 10366 0 1910
+
+T 188 5168 * 4881 4124 * 6530 * 3729 4373 3334 4894 3930 6573 5691 3072 2999 2472 3710 * 5837 188
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+
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+
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+ 0 * * * * * 0 10423 0 1107
+
+S 191 3384 * 4070 3901 5674 * 5947 4580 3714 4282 5095 3659 3112 5046 3673 2988 4964 3615 * * 191
+ 0 * * * * * 0 10423 0 1107
+
+S 192 3474 5184 4791 3528 6637 4728 5828 4764 4652 5119 7573 4689 5505 4179 4135 2558 2643 3628 * * 192
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+
+T 193 4269 7835 3368 2666 6790 4147 5701 6491 3227 4370 * 5772 4235 4224 3872 3468 3557 4463 6166 6573 193
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+
+W 194 4222 6380 4646 3177 4899 5529 5598 4747 5778 2653 5552 * 4933 5015 3463 3163 5715 4555 2996 5683 194
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+
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+ 304 2394 * 105 3832 1043 959 10321 3929 2202
+
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+I 199 * * * * 2951 * 5659 3305 * 3868 * * * * * * * 3011 * 844 199
+ 0 * * * * 0 * 10423 0 1107
+
+T 200 * * 7215 4518 5140 * 5841 4358 3182 5794 4691 * * 5152 3941 2908 1532 5636 6356 3580 200
+ 0 * * * * * * 10457 0 0
+
+C 201 * 37 * * * 6709 * * * * * * * * * * * 6003 * * 201
+ 30 5589 * 0 * * * 10457 1231 0
+
+N 202 3659 * * 2689 7328 * 5666 4089 4556 4412 5329 5013 6819 3807 3248 3719 3876 2485 6999 5663 202
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+
+V 203 1829 * * 6349 5710 5864 * 3784 * 4626 * * * * * 5076 6365 957 * * 203
+ 0 * * * * * * 10465 0 0
+
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+ 0 * * * * * * 10489 0 0
+
+H 205 * * * 6431 6417 6508 1296 * 6703 * 6236 1572 * 4656 * 4381 4847 6219 * 3983 205
+ 15 * 6593 * * * * 10459 0 0
+
+P 206 3439 4751 4031 2166 * 3518 * 6375 3726 5196 * 5360 3232 4934 3660 3851 4336 5443 * * 206
+ 54 4754 * 1835 475 * 0 10343 1410 1107
+
+A 207 2320 * 4326 5458 4940 2518 5283 * 4504 3746 5062 3753 * 5980 5426 2787 4550 4826 * 6693 207
+ 54 5429 6185 0 * * 0 10234 1316 1107
+
+S 208 5269 * 6131 5266 6314 1612 * 5223 4816 1972 5402 4098 6484 4680 6160 3385 5469 * * 6306 208
+ 98 4242 6314 1826 478 * 0 9817 1527 1270
+
+S 209 * * 4140 3093 * 4542 6403 6045 3933 * 6638 4505 2359 3486 3878 2982 3058 5246 6437 * 209
+ 84 4976 5350 0 * 1127 884 9739 1213 1775
+
+T 210 2622 * 4175 3312 6324 5365 6461 6141 4600 * * 3795 4472 4114 4637 2726 2342 6101 * * 210
+ 0 * * * * 850 1168 9457 0 1754
+
+K 211 5087 * 3589 3994 6155 4199 5419 5627 3283 4138 * 4537 2268 3344 3895 4603 4227 4568 * * 211
+ 32 5490 * 1000 1000 0 * 9492 1139 1247
+
+V 212 3370 6170 5298 6350 4485 6015 5336 2892 3532 2022 6206 6335 * * 4486 4488 5905 2693 6278 * 212
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+
+D 213 4550 * 4105 3035 * * 5788 4507 3969 6136 * 3191 4585 * 4653 3014 2386 3335 * 4969 213
+ 0 * * * * * 0 9331 0 1000
+
+K 214 3791 5950 * * 5050 * 5027 2873 3447 2848 5801 * * 3099 5027 4978 3909 2184 * * 214
+ 0 * * * * * 0 9269 0 1000
+
+K 215 6227 * * 2678 * 5964 4412 4890 3029 * 5919 3729 4146 3656 3997 3140 2526 6129 * 5687 215
+ 0 * * * * 0 * 9269 0 1000
+
+I 216 4940 * * * 3774 * 6091 2754 5661 1277 5899 * 6039 4788 * 5667 4743 2654 6060 * 216
+ 0 * * * * * * 9058 0 0
+
+E 217 * * 3804 2806 5774 4547 5607 4565 3687 3174 * 2766 * * * 2276 3533 4906 * * 217
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+P 218 5774 4706 5085 5069 * 3978 * 4901 3975 3237 * 4751 2278 * 3950 * 2918 2829 4777 * 218
+ 0 * * * * * * 7841 0 0
+
+R 219 3599 * 4835 3127 4385 4539 * 3671 * 4210 * 4550 * * 2140 2436 4190 4820 * * 219
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+
+G 220 * * * 2538 * 4471 * * 3605 3634 * * 4301 2164 5473 2504 2764 * * * 220
+ 0 * * * * * * 7085 0 0
+
+P 221 * 1346 * 4230 * * 4297 * 4318 * * * 2460 * * 2697 3987 4230 * * 221
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+
+T 222 * * 3607 * 3648 * * * 3089 * * * 2073 * * 2841 2272 2873 * * 222
+ 345 2234 * 3473 136 * * 5709 1600 0
+
+I 223 * 2576 2275 * * 3341 * 3348 * * * 3651 3294 * * 2590 * 3622 * * 223
+ 0 * * * * 0 * 5074 0 1052
+
+K 224 * * * * * * * * 1761 * * 3753 1096 * * 2616 * * * * 224
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+
+P 225 * * * 2679 * * * * * * * * 464 * * 3070 * * * * 225
+ 490 1795 * 1359 712 0 * 4716 1343 1107
+
+C 226 * 935 * * * * * * * * * * * * * * 1656 2647 * * 226
+ 0 * * * * * * 3770 0 0
+
+P 227 * * 3167 * * * 2647 * * * * * 741 * * * 2936 * * * 227
+ 260 2601 * 1585 585 * * 3770 1097 0
+
+P 228 * 2567 2655 * * * * * * * * * 1437 * * * 2814 2635 * * 228
+ 0 * * * * * * 3621 0 0
+
+C 229 * 294 * * * * * * * * * * 2442 * * * * * * * 229
+ 0 * * * * * * 3621 0 0
+
+K 230 * * * * * * * * 528 * * 1705 * * * * * * * * 230
+ 0 * * 0 * * * 2240 0 0
+
+//
+�HHsearch 1.5
+NAME e28b3a1dbc0f15f5e8575e6ca4f6ea00
+FAM
+FILE e28b3a1dbc0f15f5e8575e6ca4f6ea00
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:33:30 2013
+LENG 174 match states, 174 columns in multiple alignment
+FILT 179 out of 1574 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEEEEEECCEEEEEEEEECCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH
+HHCCCCCCEEEHHHHHHHHCCCHHHHHHHHHHCCCCEECCCEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCCC
+>ss_conf PSIPRED confidence values
+9689999989959999999479758999813827899888999999975176550414865999999999999974898888767254763779999999
+83189997486999999979889999999840998713367378889997788865999999999708675689
+>Consensus
+xxxyxxxxxxxxxxxlxxxtxxglxxlxfxxdxxxxxxxxxxxxxxlxxxxxxxxxxxxxxxxxxxxxxxlxxYfxgxxxxxxlxlxxxtxfqxxvxxxl
+xxxipxGxxxtYxxiAxxxgxxxraVgxaxxxnpxxxxiPcHRVvxxxGxxxyxxgxxxkxxlLxxEgxxxxxx
+>e28b3a1dbc0f15f5e8575e6ca4f6ea00
+MLSVEKFRVGERVVWIGVIFSGRVQGIAFAFDRGTLMKRIHDLAEHLGKRGVSISLDVQPSDYPEKVFKVLIGELDNASFLRELSFEGVTPFEKKVYEWL
+TKNVKRGSVITYGDLAKALNTSPRAVGGAMKRNPYPIVVPCHRVVAHDGIGYYSSGIEEKKFLLEIEGVKEWTS
+>gi|159901119|ref|YP_001547366.1| methylated-DNA--protein-cysteine methyltransferase [Herpetosiphon aurantiacus DSM 785]gi|159894158|gb|ABX07238.1| methylated-DNA--protein-cysteine methyltransferase [Herpetosiphon aurantiacus DSM 785]
+--------------------SEGLLLASFADDDsellAELTEA------Yperlllyrsnt----------------LLDQAFYQYQAYFSGQRQQFALP
+IAwHGSAQQQAIWQQIIQ-IPFGQQWSYQQLAQTLPTPyqaAHAINQALRHNPLALIIPCHRLSNSPqGLGYYRWGrVRQQQ---LCDRE-----
+>gi|322384642|ref|ZP_08058320.1| O6-methylguanine-DNA methyltransferase-like protein [Paenibacillus larvae subsp. larvae B-3650]gi|321150527|gb|EFX44008.1| O6-methylguanine-DNA methyltransferase-like protein [Paenibacillus larvae subsp. larvae B-3650]
+-----HLNRGNWNLHLAAT----SKGLCYVESGDSS---WEGLQRWAEMRLPHSQLKRD-DNRMNRYKEQFIQYLERERSdFTfPLDLH-GTPFQLTVWK
+ALQE-LSYASTYAYSDIAELIRRPgaARAVGAAIGANPVLIAIPCHRVIGKNRtLTGYRGGLKMKTDLLQLEKSRS---
+>gi|339449054|ref|ZP_08652610.1| methylated-DNA/protein-cysteine methyltransferase [Lactobacillus fructivorans KCTC 3543]
+-----SV-hVNGDKIFFTI-DD---HGLNFVSsPGQ-gV-SQ---LL--DfyTNDH---FEYAKNSERSLLYRKTIKNYLRGKSTdLDlPI--dfmsY-G
+SDEGRLIWNEIAQ-IPFGELVTVSDLAD--QSGlgPDKVELAISKSPIWLVLPLHRVTDRNGrYP-YRTGDTTRDFLVDLE-------
+>gi|302547238|ref|ZP_07299580.1| ADA regulatory protein [Streptomyces hygroscopicus ATCC 53653]gi|302464856|gb|EFL27949.1| ADA regulatory protein [Streptomyces himastatinicus ATCC 53653]
+----------------------GIc-SVLTGDQL--pgDALtgDAEAaLVGRLRKRfPKA-HLIRag--REFDD-RVAAAVRQSEPPRLgRdLPLNIR-V
+TAMSERLRKALRE-TPSEPSVQTR-------------------------------------------------------------
+>gi|90417471|ref|ZP_01225394.1| O6-methylguanine-DNA methyltransferase [marine gamma proteobacterium HTCC2207]gi|90330712|gb|EAS45991.1| O6-methylguanine-DNA methyltransferase [marine gamma proteobacterium HTCC2207]
+-------------------TPRGICQVTFSNGLPliAFVSN-------LQRLLPEAKLLRTEPEPIAVFESIFS-rN-KPI----DktLNLHlFALPTHT
+NVWRILLA-TDPGTLTDHIAIAKAVGRRksTLATHNAITSNPIAFFIPSHRAVDPEGhVGDYRWGVTRKHTMHAWECAT----
+>gi|262375845|ref|ZP_06069077.1| methylated DNA-protein cysteine methyltransferase [Acinetobacter lwoffii SH145]gi|262309448|gb|EEY90579.1| methylated DNA-protein cysteine methyltransferase [Acinetobacter lwoffii SH145]
+--------------------------------------------------------------------------------------SANQEMTEMILVVV
+NQ-IPYAKVATYGQIARLAGLPkhARLVGRVLSHLESDTNIPWYRVINAQAKISL-KQLDEhgqniQQQKLMQEGI-----
+>gi|153952539|ref|YP_001398247.1| methylated-DNA--protein-cysteine methyltransferase [Campylobacter jejuni subsp. doylei 269.97]gi|152939985|gb|ABS44726.1| methylated-DNA--protein-cysteine methyltransferase [Campylobacter jejuni subsp. doylei 269.97]
+-------------------YKIPLCYLSLHSDGKFLTGVdFCDN-----------KRSEKNCSLLDLAKYELDLYFTHKLKkFSvPVLV-QGTDFESKVY
+KALMK-IPYGKIATYKDIAEKkivklCTDTktQIRI------------------------------------------------
+>gi|313127164|ref|YP_004037434.1| methylated DNA-protein cysteine methyltransferase [Halogeometricum borinquense DSM 11551]gi|312293529|gb|ADQ67989.1| methylated DNA-protein cysteine methyltransferase [Halogeometricum borinquense DSM 11551]
+-----------------------------------------------------------------PILDRVFAYLDGDEDhFDDAPVAlTVPTDHRRVLD
+AVRN-IPYGETIALRRVIRMAGMdPededdVATARSALRENPVPLFIPDHRVDD--APGAIPEAVAR--RLRQVESA-----
+>gi|336393345|ref|ZP_08574744.1| hypothetical protein LcortK3_11535 [Lactobacillus coryniformis subsp. torquens KCTC 3535]
+VIYYRRHNLAGHTYYLGA-TAQGLCFVGSWA--QTL-AE-------LQSFYPLAELRPATT-QTEAAATELAQYLNGQRRkFTiPLAWPQATPLQQAV--
+----------------------------------------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * 2254 * * 1087 * * 2744 * * * 2553 * * 1
+ 0 * * * * * * 3290 0 0
+
+L 2 * * * * 3181 * * 1483 * 911 * * * * * * * * * * 2
+ 0 * * * * * * 4174 0 0
+
+S 3 * * * 3185 * * 3799 * 3037 * * 2714 * * * 3166 3800 * * 1471 3
+ 0 * * * * * * 4792 0 0
+
+V 4 * * * * * * * * * * * * * * * * * 2175 * 361 4
+ 0 * * * * * * 4792 0 0
+
+E 5 * * 1496 1722 * * * * * * * 3750 * * 2430 3598 * * * * 5
+ 0 * * * * * * 4792 0 0
+
+K 6 * * * * 4657 * 4573 3654 2504 4729 * 3761 * 3822 3506 2444 2540 * * 4770 6
+ 0 * * * * * * 5969 0 0
+
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+ 137 * 3466 * * * * 5969 0 0
+
+R 8 * * * 4497 * * * * 3794 * * 2754 2795 2560 3158 3553 2513 4341 * * 8
+ 0 * * 0 * 0 * 5729 1083 1083
+
+V 9 * * * * 2264 * 3025 1898 * 3197 * * * * 4622 4609 * 2252 * * 9
+ 0 * * * * * * 6013 0 0
+
+G 10 4731 * 3121 * * 2450 * * 3261 2861 * 2665 3591 4816 4732 3669 * 5056 * * 10
+ 0 * * 3170 170 * * 6013 1003 0
+
+E 11 4638 * 2733 3995 * 2141 4621 4668 * * * 2010 3813 4746 * 4626 * * 4545 * 11
+ 59 4638 * 1585 585 * * 6121 1012 0
+
+R 12 * * 4544 * * 2224 3435 * 3458 * 4855 * * 3642 2811 3807 5182 * 2297 * 12
+ 0 * * * * * * 6273 0 0
+
+V 13 3492 * * 3928 3849 * 4473 5076 3619 * * 3364 3874 4552 * 2895 2172 4168 * * 13
+ 0 * * * * * * 6368 0 0
+
+V 14 * * * * 3263 * * 1703 * 2436 * * * * * * * 2895 3784 2345 14
+ 0 * * * * * * 6682 0 0
+
+W 15 4622 * * 5218 4008 4053 4036 * * 2769 * * * * * 3234 3864 * 2784 1825 15
+ 0 * * * * * * 6682 0 0
+
+I 16 3862 * * * 3059 * * 2097 * 1575 * * * * 4965 * * 2253 * * 16
+ 0 * * * * * * 7551 0 0
+
+G 17 1546 * * * 3102 3224 5141 4085 * 3156 * * * 5209 * 4260 3860 3530 * * 17
+ 0 * * * * * * 7551 0 0
+
+V 18 2271 5518 * 3878 * 5316 * 3010 5182 4073 5216 * * * 5252 4289 3846 1894 * 5391 18
+ 973 * 1028 * * * * 7551 0 0
+
+I 19 2753 * * 4163 3284 * * 2993 * 4003 * * * * * * 2094 1884 * * 19
+ 287 * 2470 0 * 0 * 4730 1039 2212
+
+F 20 4982 6108 3541 4888 4075 6563 5407 5350 * * 6569 5552 * 6542 6173 2221 1759 6074 4570 3428 20
+ 62 4570 * 1139 873 * 0 7880 1116 1172
+
+S 21 3915 * 1983 2148 * 4274 5026 * 4589 * * 4114 3831 4478 3580 3941 6705 * * * 21
+ 174 5740 3395 2955 199 * 0 7969 1016 1172
+
+G 22 5569 * 3124 3412 * 2973 4564 5619 3342 * 6699 6538 5219 5321 2385 2775 3799 * * * 22
+ 37 5290 * 0 * 4603 61 7894 1070 1700
+
+R 23 3154 * * 4968 6456 1185 * * 3185 * * * 3031 5231 4940 4795 4224 6757 * 6143 23
+ 32 5509 * 0 * 1749 509 8038 1023 1671
+
+V 24 6534 * 5650 * * * * 1900 * 1371 * * 6652 * * 6496 4010 2111 * * 24
+ 90 4052 * 0 * 0 * 8075 1179 1463
+
+Q 25 4202 2528 6393 5473 4713 2560 5088 4175 4516 3686 * 5832 * 4220 4746 6814 5257 3099 * 3971 25
+ 12 6923 * 0 * 0 * 8034 1004 1179
+
+G 26 2597 4318 5511 6613 4129 2343 5958 * 4395 4191 5952 4579 6930 4688 3085 4180 5354 6279 7373 4095 26
+ 76 6402 4672 0 * * * 8194 1004 0
+
+I 27 5849 4829 * * 5611 * * 1921 * 1386 4699 5968 * * * 5450 6349 2391 * * 27
+ 12 * 6972 * * * 0 8194 0 1134
+
+A 28 2712 5207 4477 3512 * 4469 * 3916 6851 3494 5111 4989 * 4701 * 3002 2962 3700 6424 4710 28
+ 33 5473 * 1958 429 0 * 8190 1077 1165
+
+F 29 6294 6891 6484 * 1361 6417 * 3764 5829 2559 5960 * 5281 6809 5293 5693 5363 4848 4134 3409 29
+ 83 5010 5315 1033 968 * * 8193 1131 0
+
+A 30 2329 * 6478 4255 6759 2817 5063 4494 * 3911 * 5518 4423 5295 * 2829 3665 3071 7602 6992 30
+ 278 4292 3011 1438 665 1517 620 8110 1205 1122
+
+F 31 3006 5107 2035 4616 5444 3150 6531 5399 * 4267 * 4208 5053 5333 5686 2762 3971 * * * 31
+ 161 3855 4765 0 * 264 2579 8045 1305 1582
+
+D 32 4757 * 1710 2896 * 4310 5800 6839 4650 5099 * 3182 4273 4251 4630 4052 5158 7039 * 5252 32
+ 167 6954 3303 0 * 2952 200 8136 1000 1263
+
+R 33 4623 5751 3304 3009 6250 1957 5607 * 3902 4412 6277 4878 3293 * 3607 4445 5342 * * 6823 33
+ 189 6921 3130 2000 415 485 1808 8149 1004 1651
+
+G 34 2858 * 2866 3894 * 4060 4464 3739 3810 4077 * 5415 3724 3687 4631 5734 6587 3982 5770 5722 34
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+E 167 * * 3858 121 * * * * 6460 * * * * * * * * * * * 167
+ 15 7303 7872 3585 126 1998 416 5883 1012 1150
+
+G 168 3942 5382 * 6492 * 973 7044 * 3363 * 7393 6229 * 3721 3732 3913 4355 * * * 168
+ 119 3715 8479 1933 438 1261 779 5870 1400 1159
+
+V 169 2885 5584 5175 5157 5175 5316 4635 2651 6116 4874 * 4768 6228 4149 5836 4515 4496 2055 5982 5736 169
+ 73 4720 6449 982 1018 1404 685 5842 1203 1115
+
+K 170 2928 5190 4144 3375 * 5325 5079 4225 3573 2897 5131 4435 4833 5940 3940 5187 4325 3946 * 5134 170
+ 0 * * * * 0 * 5742 0 1140
+
+E 171 4157 * 4027 2983 4104 1398 * * * * * * * * * 2061 3665 * * * 171
+ 0 * * * * * * 4181 0 0
+
+W 172 * * * * * * * * * 2108 * * * * * * * 2224 852 * 172
+ 0 * * * * * * 2081 0 0
+
+T 173 * * * * * * * * * * 2108 * 1200 * * * 1587 * * * 173
+ 0 * * * * * * 2081 0 0
+
+S 174 * * * * * * * * * * * * * * * 0 * * * * 174
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME e2e8d293c6308e03168e6291d88b3e9e
+FAM
+FILE e2e8d293c6308e03168e6291d88b3e9e
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:04:27 2013
+LENG 50 match states, 50 columns in multiple alignment
+FILT 45 out of 47 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 4.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+98666661547899999999898731677888410023762301014789
+>Consensus
+xxmxxxSiqDRTxEFxsivxsxqkrxaxxxxxxrqxllxxxxxxxxxxxx
+>e2e8d293c6308e03168e6291d88b3e9e
+GAMAGMNIKDRTSEFQQSVLSYKKRNKNFREQQRERLQEKESENFANNTT
+>gi|149244238|ref|XP_001526662.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL YB-4239]gi|146449056|gb|EDK43312.1| conserved hypothetical protein [Lodderomyces elongisporus NRRL YB-4239]
+---MSVSIQNRTIEFQQCVNTYEKINRKQQQQQqAQQAQHHGSG-------
+>gi|339467499|gb|EGP82602.1| hypothetical protein MYCGRDRAFT_101897 [Mycosphaerella graminicola IPO323]
+--TTHASIQDRTPEFRSILTAAQKSLARQRKPGaPITSQQSQPL-------
+>gi|299756116|ref|XP_001829105.2| integral membrane protein sed5 [Coprinopsis cinerea okayama7#130]gi|298411529|gb|EAU92740.2| integral membrane protein sed5 [Coprinopsis cinerea okayama7#130]
+--M--TSFQDRTTEFRTCVESIRSRSAPGARAEaKQRLLHQPNG-------
+>gi|238505886|ref|XP_002384145.1| ER-Golgi SNARE complex subunit (Sed5), putative [Aspergillus flavus NRRL3357]gi|220690259|gb|EED46609.1| ER-Golgi SNARE complex subunit (Sed5), putative [Aspergillus flavus NRRL3357]
+--MTGPSIQDRTGEFHAILGQAQKRVATNKVGSqRQALLSDSQRRQANG--
+>gi|328772031|gb|EGF82070.1| hypothetical protein BATDEDRAFT_18965 [Batrachochytrium dendrobatidis JAM81]
+-----MVGKNRTNEFLAVVESCLSRDAGIHRQQ-----------------
+>gi|299471589|emb|CBN79451.1| Soluble NSF Attachment Protein (SNAP) Receptor (SNARE) [Ectocarpus siliculosus]
+-----MTDRTDDFRLIAAALPPQPRRASPHPPK-----------------
+>gi|224112555|ref|XP_002316227.1| predicted protein [Populus trichocarpa]gi|222865267|gb|EEF02398.1| predicted protein [Populus trichocarpa]
+---TTTKYRDRTAEFHSITQTLKKIggIAPVHQNK-----------------
+>gi|255549032|ref|XP_002515572.1| syntaxin, putative [Ricinus communis]gi|223545516|gb|EEF47021.1| syntaxin, putative [Ricinus communis]
+---GKSSYRDRTQEFLSVVERLKKSFSSANNAA-----------------
+>gi|320165357|gb|EFW42256.1| syntaxin 5A [Capsaspora owczarzaki ATCC 30864]
+---ALISAKDRTKEFLSAVATAQRTSAAASALP-----------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 0 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+A 2 0 * * * * * * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1000 0 0
+
+M 3 2562 * * * * * * * * * 438 * * * * * 3432 * * * 3
+ 280 3591 3421 1000 1000 * * 3260 1077 0
+
+A 4 1769 * * * * 3664 * * * * 2024 * * 4285 * * 2191 3165 * * 4
+ 77 * 4274 * * * 0 4277 0 1000
+
+G 5 2826 * * * * 3341 5338 * 4172 4765 5841 2937 2454 5311 * 3531 3681 3022 * * 5
+ 256 * 2623 * * 0 * 4239 0 1089
+
+M 6 2158 * * * 4388 * * 4165 * * 2142 * 4061 * * 3140 2201 4184 * * 6
+ 38 * 5267 * * 2570 266 4676 0 1329
+
+N 7 3885 * * * * * * * 4627 * * 3750 3847 * 5142 873 2969 4440 * * 7
+ 0 * * * * 0 * 4736 0 1355
+
+I 8 5037 5279 3098 * 3696 4648 * 1010 * 4578 * * * * * * * 4029 * 3182 8
+ 45 5023 * 2322 322 * * 4881 1007 0
+
+K 9 * * * * * * * * 2176 * 4665 4047 * 1444 1684 * * * * * 9
+ 0 * * * * * * 4827 0 0
+
+D 10 * * 475 * * * * * * * * 2676 * * * * 3009 * * * 10
+ 0 * * * * * * 4827 0 0
+
+R 11 * * 3009 * * * * * * * * * * * 191 * * * * * 11
+ 0 * * * * * * 4827 0 0
+
+T 12 * * 3009 * * * * * * * * * * * * 4744 254 * * * 12
+ 0 * * * * * * 4827 0 0
+
+S 13 3794 * 6232 4814 2595 5194 5544 4215 5132 4744 * 3118 3536 4146 * 2766 3427 5230 * 5602 13
+ 0 * * * * * * 4827 0 0
+
+E 14 * * * 191 * * * * * * * * * * 3009 * * * * * 14
+ 0 * * * * * * 4827 0 0
+
+F 15 * * * * 191 * * * * 3009 * * * * * * * * * * 15
+ 0 * * * * * * 4827 0 0
+
+Q 16 * * * * * * 3440 3009 3678 2787 * 5404 * 1843 1952 * * * * * 16
+ 0 * * * * * * 4827 0 0
+
+Q 17 1677 * * * * 5082 5325 * * * * * * 1970 * 1702 3833 * * * 17
+ 0 * * * * * * 4827 0 0
+
+S 18 2292 2473 * * * * * 1648 * 5082 * * * * * 3029 * 2790 * * 18
+ 0 * * * * * * 4827 0 0
+
+V 19 2275 * * * * * * 4584 * 2320 * * * * * * 4824 954 * * 19
+ 0 * * * * * * 4827 0 0
+
+L 20 2279 * 5445 2044 * 3664 * * * 2132 * 5081 * 4013 * 3440 4726 * * * 20
+ 0 * * * * * * 4827 0 0
+
+S 21 3732 * * * * * 5404 * * * * * 3009 2407 3319 1766 2672 4744 * * 21
+ 0 * * * * * * 4827 0 0
+
+Y 22 1445 4616 * * 4530 * 4744 3152 * 2883 * * 3009 * * * * * * 2846 22
+ 0 * * * * * * 4827 0 0
+
+K 23 4339 * 3887 5081 * * * * 2024 4616 * * * 1220 2862 * * * * * 23
+ 0 * * * * * * 4827 0 0
+
+K 24 * * * * * * * * 1061 * * * 3009 * 1909 2940 * * * * 24
+ 0 * * * * * * 4827 0 0
+
+R 25 * * * * * * 3860 3488 4741 4530 * * * 4028 802 3682 5132 * * 5652 25
+ 108 3788 * 1000 1000 * * 4827 1103 0
+
+N 26 4831 * 4616 * 3726 * 5230 4824 * 3174 5379 2499 5344 3152 3009 3299 4665 4370 * 5367 26
+ 65 * 4511 * * * * 4827 0 0
+
+K 27 921 * * * * 5372 * * 2531 * * 6028 5399 * 4297 3124 4554 5184 * * 27
+ 93 3999 * 1210 817 0 * 4785 1125 1042
+
+N 28 3723 * * * 5344 4616 * * 2892 * * 4041 3005 3416 4728 1702 3734 5325 * * 28
+ 137 * 3466 * * * * 4827 0 0
+
+F 29 2982 * * * 5349 5295 * 3927 * 4095 * 3260 2840 3276 * 1852 4706 4769 * * 29
+ 68 * 4440 * * * 0 4816 0 1235
+
+R 30 3693 * 5474 5244 * * 2319 * 1672 * * 3685 5818 4038 3728 3253 5450 * * * 30
+ 0 * * * * 1107 900 4765 0 1408
+
+E 31 2407 * * 5209 * * * 5431 2930 * * 4602 2525 3387 3909 4040 3600 3188 * * 31
+ 0 * * * * * 0 4728 0 1185
+
+Q 32 3593 * 5781 * * 2340 5009 * * 4968 * 3995 2303 2371 * 3180 4395 5509 * * 32
+ 0 * * * * 1616 570 4728 0 1185
+
+Q 33 2498 * * 2976 * 3347 * * 2448 5024 * 5300 4058 2971 * 2714 * 5781 * * 33
+ 1776 498 * 204 2924 0 * 4775 2428 1099
+
+R 34 4397 * * * * * * * 2253 * * 2627 3583 3960 1207 * * * * * 34
+ 99 * 3909 * * * * 4089 0 0
+
+E 35 4044 * 4432 3501 * 4667 * 4628 * * * * 4559 855 4112 3802 * * * * 35
+ 0 * * * * * 0 3805 0 1042
+
+R 36 3324 * * * * * * * 2943 4998 * * 4705 4391 2391 2071 2879 * 4044 5173 36
+ 0 * * * * 0 * 3805 0 1042
+
+L 37 3552 * * * 5159 * * * * 837 * 4435 4822 2971 * 4688 4862 4486 * * 37
+ 0 * * * * * * 4089 0 0
+
+Q 38 5065 * * * * * * * * 679 * * * 2237 4435 * 4557 4486 * * 38
+ 0 * * * * * * 4089 0 0
+
+E 39 4168 * 3601 2994 * 4764 3418 * 4435 4486 * 2828 * 4688 4924 2913 2557 * * * 39
+ 0 * * * * * * 4089 0 0
+
+K 40 5303 * 2442 * * 3772 4056 * 3104 * * 3690 2437 4225 * 3059 3245 * * * 40
+ 0 * * * * * * 3817 0 0
+
+E 41 2029 * 4615 2829 * 3386 * * * * * 4105 4000 3442 4530 2919 4292 * * 4695 41
+ 0 * * * * * * 3780 0 0
+
+S 42 3140 * * 4811 * * * * * * * 3967 4016 1471 3654 2085 4343 * * * 42
+ 0 * * * * * * 3834 0 0
+
+E 43 * * * 3592 * 2549 * * 3242 3904 * * 2783 3057 1961 4281 * * * * 43
+ 0 * * * * * * 3671 0 0
+
+N 44 * * * * * * 1707 * * * * 1480 * * 1577 * * * * * 44
+ 0 * * * * * * 1993 0 0
+
+F 45 1707 * * * 1480 * * * * * * * * 1577 * * * * * * 45
+ 0 * * * * * * 1993 0 0
+
+A 46 0 * * * * * * * * * * * * * * * * * * * 46
+ 0 * * * * * * 1620 0 0
+
+N 47 * * * * * * * * * * * 0 * * * * * * * * 47
+ 0 * * * * * * 1620 0 0
+
+N 48 * * * * * 1000 * * * * * 1000 * * * * * * * * 48
+ 0 * * * * * * 1620 0 0
+
+T 49 * * * * * * * * * * * * * * * * 0 * * * 49
+ 0 * * * * * * 1000 0 0
+
+T 50 * * * * * * * * * * * * * * * * 0 * * * 50
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME e3d87649b2f1632f153be8830af2c4ce
+FAM
+FILE e3d87649b2f1632f153be8830af2c4ce
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:14:59 2013
+LENG 125 match states, 125 columns in multiple alignment
+FILT 107 out of 1506 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEEEEECCHHHHHHHHHHCCCEEEECCCCEEEEEECCEEEEEEECCCCCCCCCEEEEEEEECCHHHHHHHHHHCCCEEEECCCCCCCCCEECCCCC
+EEEEEECCCCCEEEEEECCCCCCCC
+>ss_conf PSIPRED confidence values
+9829999991999999999998699899637999999959989999958888888861599999699999999999889968732443225862547961
+9999998999999999878878999
+>Consensus
+xxxxxxxlxvxdxxxxxxfYxxlGxxxxxxxxxxxxxxxxxxxlxlxxxxxxxxxxxxxxixxxvxdxxxxxxxlxxxGxxxxxxxxxxxxxxxxxxxgx
+xxxxxxDpxGxxieixxxxxxxxxx
+>e3d87649b2f1632f153be8830af2c4ce
+TDQATPNLPSRDFDSTAAFYERLGFGIVFRDAGWMILQRGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAPELQEWGG
+TMAALVDPDGTLLRLIQNELLAGIS
+>gi|333371105|ref|ZP_08463067.1| glyoxalase [Desmospora sp. 8437]gi|332976549|gb|EGK13390.1| glyoxalase [Desmospora sp. 8437]
+--SLSPYFVVNGAQRFVDLIKnLFNATELRRydrPDgtiMHVELRIDDTVIMVGDsSEQFPAN--HLLIHVYVPDVDEVFSRALELECVP-------VEE
+PKEsEGDPDRRGTFKDFAGNIWSVATQGK-----
+>gi|194016689|ref|ZP_03055302.1| lactoylglutathione lyase [Bacillus pumilus ATCC 7061]gi|194011295|gb|EDW20864.1| lactoylglutathione lyase [Bacillus pumilus ATCC 7061]
+-----IAIAVFSIKNTSRILQQlFNWHFSDIreipEQEikASFASLDHVHIELIEPMSGSsKLhtfltkrgEGLHHIALKSGDIQADLNRLDHFGVELLQ
+------QSAQIGASGKRIAFIspKETSGVLFELCEpLK------
+>gi|254466122|ref|ZP_05079533.1| glyoxalase/bleomycin resistance protein/dioxygenase [Rhodobacterales bacterium Y4I]gi|206687030|gb|EDZ47512.1| glyoxalase/bleomycin resistance protein/dioxygenase [Rhodobacterales bacterium Y4I]
+-----TTVGAGDIARGTVLFRvpaSp-GYAVEEG-PAGLRYTlpANpGQppalpDYYVkPPFGGrPAs-AGNGSMTAFEERtqkQVREPHAAALLAGGSD
+E--G---QPGfRADYGPLFYVGYLRGAQGNKIAHFS--------
+>gi|254787661|ref|YP_003075090.1| glyoxalase family protein [Teredinibacter turnerae T7901]gi|237686487|gb|ACR13751.1| glyoxalase family protein [Teredinibacter turnerae T7901]
+---FHVHLSVDNLATNIEFYSRlFGAQAHKIKSDYAKWLIEDlrLIFAISSRGD---RPGLNHFGVQALSdedLAVLRTRAINaNEGTFVD-------EA
+DaRCCYAKsDKHWVSDPQGIPWEHFYTR------
+>gi|239928418|ref|ZP_04685371.1| glyoxalase/bleomycin resistance protein/dioxygenase [Streptomyces ghanaensis ATCC 14672]gi|291436745|ref|ZP_06576135.1| glyoxalase/bleomycin resistance protein/dioxygenase [Streptomyces ghanaensis ATCC 14672]gi|291339640|gb|EFE66596.1| glyoxalase/bleomycin resistance protein/dioxygenase [Streptomyces ghanaensis ATCC 14672]
+-----VLQVVSDRARYESLFLDvLGFRLSdhidlapN---LaATFLHCNRrhHSFAFTPkVA---GRPLgVGHFMLEVTdldVIGRAMEHIEDEPHRLL-
+-----KTFGRHSNDRMVSFYLLTPSDVGLEFG---------
+>gi|291435257|ref|ZP_06574647.1| bphC [Streptomyces ghanaensis ATCC 14672]gi|291338152|gb|EFE65108.1| bphC [Streptomyces ghanaensis ATCC 14672]
+-----------DLEVMEKFLTAFGMVKAEgSDDRTLYMRGTgtQHHIHVTRKA---DKQRFVGASIEVAGYDDLVELAAKQGsSPV---------RESTE
+PGGGHEVSMTMPDGIEIRAIWGRRkAEPIP
+>gi|172036226|ref|YP_001802727.1| 4-hydroxyphenylpyruvate dioxygenase [Cyanothece sp. ATCC 51142]gi|171697680|gb|ACB50661.1| 4-hydroxyphenylpyruvate dioxygenase [Cyanothece sp. ATCC 51142]
+-------WYVKNADYWKKWFInVMGFHAIagghNDHTYTEIVKTGskdyPIIFVISSPLSPQSPVAkfleihppgVADIAFRVNNLKACLEKIKNLGTVI
+-------QEPMKEkkYTNGYLQWSKIISQTGLIH-----------
+>gi|224826541|ref|ZP_03699642.1| Glyoxalase/bleomycin resistance protein/dioxygenase [Lutiella nitroferrum 2002]gi|224601142|gb|EEG07324.1| Glyoxalase/bleomycin resistance protein/dioxygenase [Lutiella nitroferrum 2002]
+-------VRVTDTTKAIEWYQRvLGLTPDpryrhmqDEPHGVTMVANPSSTVRLALCEDAESSTAIGAVAFVVSgqEFMEWIDQLAGERVTNREGQTIAR
+DSVYDHHFFCS-LSFVDPFGNAFEVVSYD------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+T 1 * * * * * * * * * * * * 1643 * * * 557 * * * 1
+ 0 * * * * * * 2280 0 0
+
+D 2 2749 * 895 * * * * * * * * 2591 * * * * 2763 * * * 2
+ 0 * * * * * * 3733 0 0
+
+Q 3 3922 * * * * * 2144 * * * 2990 * 4119 2776 2316 3095 4044 * * * 3
+ 98 3922 * 0 * * * 6009 1038 0
+
+A 4 3039 4578 * * 3837 4930 * 1720 * 4118 4750 4934 5033 4694 * 4886 4765 2618 * * 4
+ 0 * * * * * * 7579 0 0
+
+T 5 5110 * * * 3422 5399 2292 3424 4201 * 4446 5598 * 4647 4504 4254 2638 3466 * 4374 5
+ 54 * 4754 * * * * 8543 0 0
+
+P 6 4136 6239 * * 4151 6055 * 2336 * 3721 5867 * 2869 6192 * 5021 3252 1830 * * 6
+ 19 * 6236 * * * 0 9930 0 1177
+
+N 7 2868 5246 6540 3745 3752 2956 4145 3981 4830 4379 4858 3467 * 5293 6432 4333 4839 3558 * 6183 7
+ 0 * * 0 * 0 * 10245 1058 1433
+
+L 8 * * * * 2929 * * 2347 * 1677 4686 * * 6455 5464 * 6825 2353 5769 3973 8
+ 0 * * 1000 1000 * * 10403 1000 0
+
+P 9 3495 6420 4901 4832 4137 4265 5670 5133 5860 4874 4718 4648 2993 5181 3424 4655 4341 4565 5054 2867 9
+ 14 6700 * 0 * * * 10412 1000 0
+
+S 10 3710 4185 * * 6414 5528 * 5022 * * * * * 6749 * 3223 2251 1125 6533 6825 10
+ 30 5605 * 516 1735 * * 10474 1253 0
+
+R 11 3550 * 3320 3568 5834 4620 4771 * 2798 6567 * 3464 3340 5707 4129 3289 3547 5192 * * 11
+ 34 5434 * 1000 1000 0 * 10429 1334 1058
+
+D 12 5153 * 1113 5271 * 5252 6555 * 4357 6340 * 1951 * 4564 4705 4425 * * * * 12
+ 0 * * * * * * 10443 0 0
+
+F 13 3339 * 6419 5606 4220 * * 2788 * 1959 3741 * 3501 6941 5011 4842 5527 2902 * 5597 13
+ 0 * * * * * * 10443 0 0
+
+D 14 3011 * 2386 2284 * 4750 5675 6556 3136 5658 6384 5675 4693 2810 5741 * 5693 5182 * * 14
+ 15 6552 * 0 * * * 10495 1058 0
+
+S 15 2250 6458 4964 2548 * 5121 6527 6794 2805 5195 * 5224 6556 4634 3119 4391 3906 5185 * 5518 15
+ 0 * * * * * * 10495 0 0
+
+T 16 1735 * 6780 4687 6923 4292 6371 6571 6552 3730 4010 6714 * 5271 * 2578 3045 4484 4477 6962 16
+ 0 * * * * * * 10495 0 0
+
+A 17 3025 5994 6344 4729 5551 6710 5698 3084 3610 3381 5123 * * 5911 2998 4240 4009 2474 * * 17
+ 0 * * * * * * 10495 0 0
+
+A 18 2444 * 3016 2829 * * * 5609 3269 * 6630 3550 5792 4397 3650 3751 4338 4272 6448 * 18
+ 12 6881 * 2000 415 * * 10495 1000 0
+
+F 19 6544 * 6677 6857 786 * 5311 5899 * 4010 6565 * * 5821 5305 6745 * 5763 3062 3541 19
+ 0 * * * * * 0 10483 0 1000
+
+Y 20 * * * * 2926 6390 5718 * * 3200 6476 * * * * 6677 * 6568 3379 734 20
+ 42 5674 6754 0 * * 0 10483 1176 1000
+
+E 21 3839 * 5094 2581 * 4145 6678 4286 3329 6645 6438 6839 5557 3378 3545 4318 2607 4101 6534 * 21
+ 869 1144 * 281 2501 959 1042 10471 6862 1178
+
+R 22 4023 6491 4137 3592 5591 5700 6616 4026 2831 4656 6603 4688 * 3591 4019 4047 4048 2546 * 6642 22
+ 855 1196 6544 80 4205 * 0 10483 6897 1000
+
+L 23 * * 6513 * 1825 * * 3957 * 1117 3146 * * * * 6732 * 5036 6545 5800 23
+ 12 6916 * 0 * 1085 920 10391 1000 1627
+
+G 24 5941 * 4338 4454 * 468 6946 * 5789 * * 3803 * 4769 6876 5464 * * * * 24
+ 0 * * 1000 1000 774 1268 10437 1058 1242
+
+F 25 3393 5498 * 6699 1472 4937 * 5276 * 2458 4312 * 6876 * 6880 * 5919 3933 3779 4324 25
+ 16 * 6545 * * * 0 10481 0 1000
+
+G 26 6286 6352 4375 2749 6802 4651 4746 * 3272 * 6462 5363 4079 3687 2723 4659 3386 3324 * 5088 26
+ 21 * 6106 0 * 774 1268 10436 1058 1242
+
+I 27 3985 6674 6696 3219 4453 6036 * 3507 4130 2688 6651 5541 3212 6568 5047 5716 4815 2404 * 5298 27
+ 58 5119 6536 1279 767 * 0 10465 1380 1312
+
+V 28 3398 6423 3709 3923 5657 4679 6650 3119 3910 5729 5024 6755 6523 6381 5293 3808 3853 2431 5177 4652 28
+ 242 2694 * 2004 414 1495 632 10426 3737 1712
+
+F 29 4676 * 3301 3118 3328 4286 4176 5691 5765 4485 6559 4248 4405 6597 3289 3934 4362 5784 4250 4387 29
+ 215 3016 6088 1418 676 1549 603 10442 3489 1396
+
+R 30 4318 6840 3434 2861 6858 3553 5608 5569 3841 5656 6494 5241 5243 4829 2790 3162 4743 5036 6760 4226 30
+ 293 2548 6270 1451 657 1135 876 10446 4185 1517
+
+D 31 4461 * 2882 3108 4502 3397 4246 6884 4039 5561 5614 4580 4282 3873 5168 3471 3837 5043 * 5608 31
+ 314 2353 * 2959 199 0 * 10422 4232 1436
+
+A 32 4426 * 3013 3637 6606 2627 4996 * 4216 4850 5101 4005 3085 4389 5183 4147 3779 4528 * * 32
+ 295 2579 5817 2078 390 0 * 10478 3845 1128
+
+G 33 4018 * 2912 3485 5430 2833 * 5266 4533 5613 6394 2941 5489 5067 3502 4341 4617 4403 6976 4831 33
+ 165 3208 * 1822 480 * 0 10478 2829 1148
+
+W 34 3123 5218 6605 4502 3087 5403 3801 4680 5795 3916 4747 * * 6661 * 4016 3852 5013 3485 2564 34
+ 69 4427 * 1977 423 0 * 10478 1924 1148
+
+M 35 2042 5972 6882 4415 5530 5886 5954 4167 5522 2523 5911 * * * 4774 3762 4164 2669 5097 6537 35
+ 112 3745 * 1002 998 * * 10494 2302 0
+
+I 36 4553 6674 4664 4456 3553 4432 4273 3565 5857 3589 4675 6585 7437 4428 4241 4358 4095 3918 4078 3221 36
+ 0 * * * * * * 10494 0 0
+
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+Y 87 * * 3790 3901 * 2256 3684 * * 2739 * 3745 * * 2826 * 3855 * * 2846 87
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+Q 96 3819 6748 4474 3383 5126 3547 4902 5824 4477 4091 4596 6810 3511 3514 3629 5743 4300 4741 5541 3728 96
+ 109 4545 5060 1674 542 1512 623 10380 2040 2368
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+G 99 4534 6605 4025 4846 5116 976 6562 6586 4130 6260 6629 3563 * 6639 5023 4882 5668 4920 * * 99
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+T 101 5463 * 5686 4637 4622 4827 7052 6733 2999 3327 5669 4543 5867 5238 2381 4692 3824 4319 4912 3191 101
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+ 0 * * * * 0 * 10466 0 1058
+
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+L 115 5763 6419 * 6459 2672 6803 6209 1669 * 2557 4928 * 5023 * * * 6594 2415 * 4904 115
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+ 17 6431 * 0 * * * 10310 1000 0
+
+Q 117 2967 5450 6456 2224 * 6809 5591 6349 5370 * * 6191 * 2445 5293 3241 2746 4903 4787 6592 117
+ 19 6249 * 0 * * * 10094 1000 0
+
+N 118 5275 * 3488 3794 3928 3497 4594 6052 4559 3872 6026 3863 2864 4606 4228 5314 5210 4163 * 3887 118
+ 0 * * * * * * 9800 0 0
+
+E 119 3421 * 3041 3688 4624 4171 3990 4180 3736 3434 5603 4758 4406 5934 4331 3937 4691 4291 * * 119
+ 31 5544 * 2000 415 * * 9417 1000 0
+
+L 120 4200 * 3195 3371 * 2988 4502 * 4313 3021 * * 3663 5396 4500 4354 2530 * * 5206 120
+ 1003 997 * 0 * * * 8716 1660 0
+
+L 121 2095 * * * * * * * * 891 * * 2142 * * * * * * * 121
+ 0 * * * * * * 2864 0 0
+
+A 122 1541 * * 1677 * * * * * * * * 1541 * * * * * * * 122
+ 0 * * * * * * 2399 0 0
+
+G 123 * * * * * 541 * * * * * * 1677 * * * * * * * 123
+ 0 * * * * * * 2399 0 0
+
+I 124 * * * * * * * 607 * * * * * * 1541 * * * * * 124
+ 0 * * * * * * 2399 0 0
+
+S 125 * * * * * * * * * * * * 1160 * * 856 * * * * 125
+ 0 * * 0 * * * 1711 0 0
+
+//
+�HHsearch 1.5
+NAME e44a004fd43907d485810413e310dc01
+FAM
+FILE e44a004fd43907d485810413e310dc01
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:56:25 2013
+LENG 124 match states, 124 columns in multiple alignment
+FILT 40 out of 42 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCCCCCCHHHCCCCCCCEECCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
+EEEECCCCCCCEEEEEEEEEEECC
+>ss_conf PSIPRED confidence values
+9865554889898652403010022684773658885466998855774167871589999667998304558752255023788566640056777846
+787537998757778777787159
+>Consensus
+xxxxxkxxpxxxDxxsCdYWRyCaiDGxlCsccGGsxtsCPPGTexSpxsWvGtCxNPxDgkxYlIsYnDCCGkxxcgxcxCxxxexexPxYrpxxxNDi
+xWCxgxxsxxxxYhCtxaxivGxA
+>e44a004fd43907d485810413e310dc01
+VDPRAKWQPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDI
+IWCFGAEDDAMTYHCTISPIVGKA
+>gi|312141802|ref|YP_004009138.1| methylamine dehydrogenase maua [Rhodococcus equi 103S]gi|325672940|ref|ZP_08152634.1| methylamine dehydrogenase small subunit [Rhodococcus equi ATCC 33707]gi|311891141|emb|CBH50460.1| putative methylamine dehydrogenase MauA [Rhodococcus equi 103S]gi|325556193|gb|EGD25861.1| methylamine dehydrogenase small subunit [Rhodococcus equi ATCC 33707]
+-----------KDPAECEYWRWCNMDGTSCAa-CnGGGVTTCAPGSKPGAEFWVGCCTNPDTGKTYLIAYYDCCGAPSCSNAFCGEPDMQAIMYNPVsgs
+---ydqEIIWCVSDES--QSYTCTMAPIIGED
+>gi|254516233|ref|ZP_05128293.1| methylamine dehydrogenase light chain [gamma proteobacterium NOR5-3]gi|219675955|gb|EED32321.1| methylamine dehydrogenase light chain [gamma proteobacterium NOR5-3]
+-----------GDNQSCDYWRYCAFSGQICSCCGGSMTQCPPGSETASVAWVGTCHNPLDGQDYLISYNDCCGKSACGRCGCHRSEGDRPVYFPSKSNSI
+LWCFGSNS--HAYHCTLARVVGKA
+>gi|326387252|ref|ZP_08208862.1| putative methylamine dehydrogenase light chain precursor [Novosphingobium nitrogenifigens DSM 19370]gi|326208433|gb|EGD59240.1| putative methylamine dehydrogenase light chain precursor [Novosphingobium nitrogenifigens DSM 19370]
+-----------SDDTKCNYWRYCAIDGALCTCCGGGIHTCPPGAEPSPVSWVGTCINPEDGKAYLIAYRDCCGKSFCNKCNCNGSDRETQIYTPQLNNDI
+IWCFGTQS--MEYHCSTAVLVGAA
+>gi|119898548|ref|YP_933761.1| methylamine dehydrogenase, L chain [Azoarcus sp. BH72]gi|119670961|emb|CAL94874.1| probable methylamine dehydrogenase, L chain [Azoarcus sp. BH72]
+-------AAKKagGkapTDEDCEYWRYCAQDGYLCNCCGGTASSCPPGTEASKVSWIGTCHNPEDGKDYLISYNDCCGKTACGRCFCNTNEREMPGYRMG
+LHNDINWCMANDS--TMFHCTMATVVGLA
+>gi|167644528|ref|YP_001682191.1| amine dehydrogenase [Caulobacter sp. K31]gi|167346958|gb|ABZ69693.1| Amine dehydrogenase [Caulobacter sp. K31]
+-------VADDpGDPTSCDYWRYCAIDGFLCSCCGGSVSTCPPGTEMSPITWIGTCTNPSDGRAYVISYNDCCGTSSCGQCSCHRSEGDRPQVRPQSNND
+YNWCLGTES--SIYHCSAAAIIGVA
+>gi|238796082|ref|ZP_04639593.1| Aralkylamine dehydrogenase light chain [Yersinia mollaretii ATCC 43969]gi|238720027|gb|EEQ11832.1| Aralkylamine dehydrogenase light chain [Yersinia mollaretii ATCC 43969]
+-------KPa---DVNECNYWRYCALDGNLCSSSGGSITTCPVGTETSKTSWVGTCRNPHDNKNYLVSYNDCCGKTTVANSVnCFNNQGERPGYRMGLHN
+DINWCMANTN--KGYHCTVATLVGIA
+>gi|335421103|ref|ZP_08552131.1| amine dehydrogenase [Salinisphaera shabanensis E1L3A]gi|334892933|gb|EGM31159.1| amine dehydrogenase [Salinisphaera shabanensis E1L3A]
+-------PGtpGDpGDPQSCDYWRYCSVDGFLCTCCGGTINACPPGTDVSEVTWVGTCHNPADGRDYVIAYNDCCGKQACGQCACNRNDSEQPLYRPFNN
+NDINWCLGAEH--LTYNCTIATIRDVA
+>gi|189220011|ref|YP_001940651.1| methylamine dehydrogenase, L chain [Methylacidiphilum infernorum V4]gi|189186869|gb|ACD84054.1| Methylamine dehydrogenase, L chain [Methylacidiphilum infernorum V4]
+----GKEPPASNDPaTSCSYWRYCSLDGFLCSCCGGGATACPPGTFPSPTHWVGSCRNPEDGKHYLVSYRDCCGKGYCGRCYCRQTDAkEMPVYQLLRNN
+DTIWCFGAPN--MIYHCTGAAVLAPA
+>gi|330503791|ref|YP_004380660.1| amine dehydrogenase [Pseudomonas mendocina NK-01]gi|328918077|gb|AEB58908.1| amine dehydrogenase [Pseudomonas mendocina NK-01]
+------------------------------------------------------------------------------------HDSEEPLYQPNNDNDV
+NWCLAAKS--HIYHCTASIIRGVA
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 * * * * * 1591 * * * * * * * * * * * 582 * * 1
+ 0 * * * * * * 1190 0 0
+
+D 2 * * 0 * * * * * * * * * * * * * * * * * 2
+ 0 * * * * * * 1190 0 0
+
+P 3 * * * * * * * * * * * * 0 * * * * * * * 3
+ 0 * * * * * * 1190 0 0
+
+R 4 * * * * * * * * * * * * * * 0 * * * * * 4
+ 0 * * * * * * 1190 0 0
+
+A 5 1129 * * * * 882 * * * * * * * * * * * * * * 5
+ 0 * * * * * * 1513 0 0
+
+K 6 * * * * * * * * 0 * * * * * * * * * * * 6
+ 0 * * * * * * 1513 0 0
+
+W 7 * * * 1628 * * * * * * * * * * * * * * 564 * 7
+ 0 * * * * * * 1513 0 0
+
+Q 8 2074 * * * * * * * 1958 * * * 2920 1683 * * * 4020 * * 8
+ 0 * * * * * * 2241 0 0
+
+P 9 2943 * * * * 4108 * * * * * * 300 * * * * * * * 9
+ 782 1256 * 1327 734 * * 2241 1211 0
+
+Q 10 3626 * 3935 * * 1763 * * 3717 * * * * 1236 * * * 4100 * * 10
+ 0 * * * * * 0 2185 0 1000
+
+D 11 3899 * 1086 2060 * * * * 3717 * * * * * * 3626 3942 * * * 11
+ 1683 682 3942 168 3186 * 0 2185 1308 1000
+
+N 12 4994 * 3205 5040 * 1170 * * 2352 * * 2672 * * * 4949 * * * * 12
+ 93 3998 * 3838 105 0 * 2535 1102 1032
+
+D 13 * * 90 4985 * * * * * * * * * * * * 5124 * * * 13
+ 49 * 4890 * * * * 2546 0 0
+
+I 14 * * 2817 5295 * * * 3661 * * * 4911 909 5350 4575 * * 3042 * * 14
+ 53 4806 * 0 * 0 * 2533 1023 1005
+
+Q 15 3477 * * 5179 * * * * 5467 4244 * 3165 * 1977 * 5484 1254 * * * 15
+ 0 * * * * * * 2548 0 0
+
+A 16 2503 * 5179 3347 * * * * 3591 * * * * 4332 * 900 5092 * * * 16
+ 0 * * * * * * 2548 0 0
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+
+//
+�HHsearch 1.5
+NAME e69e1ac0a4b2554df25f2c2183b0fba0
+FAM
+FILE e69e1ac0a4b2554df25f2c2183b0fba0
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 13:00:49 2013
+LENG 248 match states, 248 columns in multiple alignment
+FILT 178 out of 1119 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHHHCCCCEEEECCCEECCCCCCCCCCCHHHHHHCCCCEEEECCHHHHH
+HHCCCHHHHHHHHHHHHHCCCEEEEEECCCHHHHHCCCHHHHHHHHHHHHHCCHHHHCCEEEEECCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
+CCCEEEEECCCCCCCCHHHHHHCCCCCEEEECHHHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9987089997521689999999999998621244697699988788899999973147879833223036899736157999998699999978788755
+5078789999999999978998999908878998665559999999999851414436359998787761799999989999999999999998517100
+466059981766802299997078999899713847789999999859
+>Consensus
+mmrxxxixxNwKmnxxxxxxxxxxxxxxxxxxxxxxxxvxvxPpxxxLxxxxxxxxxxixigAQnxxxxxxGaxTGevSxxmLxdxGxxxviiGHSERRx
+xfxEtdxxixxKvxxalxxgLxpIlCvGExxexxxxgxxxxvxxxQlxxxlxxxxxxxxxiIAYEPvWAIGtGxxaxxexixxxxxxIRxxlxxxxxxxx
+xxxvxILYGGSVxxxNxxxlxxxxxiDGxLVGxaslxxxFxxiixxxx
+>e69e1ac0a4b2554df25f2c2183b0fba0
+MARKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRK
+YFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQ
+ANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM
+>gi|340708258|pdb|3S6D|A Chain A, Crystal Structure Of A Putative Triosephosphate Isomerase From Coccidioides Immitis
+--PKTLLIISLKMYFTPSRTIDYIQGLLEPRNDiirqenRSRLLLALIPDFLTIYPCSEAIKefesnlaapqdadtpPPLLLGAQDCFWDSLGPYTGEIS
+PVCLRDMNVSIVELGHAERRAIFGETDQQVARKAAAAADQGLIPLVCIGEVSTlgpivSEAIGRAVGECEAQIRPVLEALPRDAPVIFAYEPVWAIGKPQ
+PARVDHVGAVVSGIRSVIERI-DRHRKGEVRILYGGSAGPGLWGPGGLGKEVDGMFLGRFAHDiEGVRKVVRE--
+>gi|261368205|ref|ZP_05981088.1| triose-phosphate isomerase [Subdoligranulum variabile DSM 15176]gi|282569711|gb|EFB75246.1| triose-phosphate isomerase [Subdoligranulum variabile DSM 15176]
+----------------------------------SEVEFAAYLPEAHLLSAAAARKpgCPLQLGCQGVYRAdtavggNFGAFTTNRPASAAKALGCESVL
+IGHCEERNDKmgilAEagvtgteasraVNRLLNQEIRCAVARGMTVLYCIGEKSEEQD--AWQQVLGEQLSLGLEGV-DKSKVVIAYEPVWSIGPGKTPa
+DKPYITKIARFVKEQT---------GGMDVVYGGGLKSDNAAMLASIPEIDGGLIaltrfsGEIGFYpEEYLEIIRLY-
+>gi|170017749|ref|YP_001728668.1| triosephosphate isomerase [Leuconostoc citreum KM20]gi|169804606|gb|ACA83224.1| Triosephosphate isomerase [Leuconostoc citreum KM20]
+-----ICIVNFKSLMCYKKQLQWLQDIEQLP---LNFKLLVAPTLPEHNTY-----QNYEIIAQNISLAQ--RTVGEMSANVLKALDIRYAFVGHLERRK
+LLNETTDIIHERLANCLNNDMIPIICLGMHS-------GPDLVIRELKSILKNIDfMGQRIIVAYESLRSTQSNSSAySYVEMEAVYLKLNQYLSELVKN
+SNLASYSLVMGGHITAEG-ISVARKIGYDGVLIGDRYQEvSAFQPIIE---
+>gi|258614850|ref|ZP_05712620.1| triosephosphate isomerase [Enterococcus faecium DO]
+--RKPIIAGNWKMNKTASEAKEFAEAVKNKIPS-NDKVdsVIGSPALFLQELMTSAEGTELKISAQNCYWENSGAFTGETSPAALADLGVH---------
+----------------------------------------------------------------------------------------------------
+--------------------------------------------------
+>gi|20095100|ref|NP_614947.1| triosephosphate isomerase [Methanopyrus kandleri AV19]gi|22096220|sp|Q8TUT9.1|TPIS_METKA RecName: Full=Triosephosphate isomerase; Short=TIM; AltName: Full=Triose-phosphate isomerasegi|19888388|gb|AAM02877.1| Triosephosphate isomerase [Methanopyrus kandleri AV19]
+----PPVIVNFKAYSeaVGENALRLARVAAEVSEE-TGVEVGICPPHVDLRDVVREVGDEVTVLAQAVDAAEPGGRTGHVTPEMVVEAGADGTLLNHSER
+RMLLEDLKD----VCRACINEGLLTIVCASDALAAR--------------AAG----ALSPHAVAVEPPELIGTGtpvSKADPEVVERSVEVVKEV----
+-----SEETAVLCGAGITDGSDVRAAVELGADGVLVASGVVL-----------
+>gi|312870562|ref|ZP_07730679.1| conserved hypothetical protein [Lactobacillus oris PB013-T2-3]gi|311093922|gb|EFQ52249.1| conserved hypothetical protein [Lactobacillus oris PB013-T2-3]
+-----------------------------------------------------------------------------------------LTLLDHSSR--
+-------ELNHQLQTTLQGSQQPVLKLDEG-DLRLTPVdFAYLLSRRLANVLAGVsrAAVARLVIVYSPSWA-GEcRLPADAQRIRIAHRQIRDLLRIIY
+DQETAGQVQIIYGGFVFEEELADVLCDSNVDGVLMN----------------
+>gi|312887118|ref|ZP_07746722.1| triosephosphate isomerase [Mucilaginibacter paludis DSM 18603]gi|311300430|gb|EFQ77495.1| triosephosphate isomerase [Mucilaginibacter paludis DSM 18603]
+-MRNKVIAANWNMNDSYLKGLALFSEMLKLVHEeVkGNREIIICPPFIHLHVFGQLSKnhSRISIGAQNAHQSDSDA-----------------------
+----------------------------------------------------------------------------------------------------
+----------------------------------------------------
+>gi|262401201|gb|ACY66503.1| triose phosphate isomerase [Scylla paramamosain]
+-SKRFFVIGNWKMNVDKARIDGIVKMMTAASLS-KHTEVVVGCPSCYLE---------------------------------------------------
+----------------------------------------------------------------------------------------------------
+------------------------------------------------
+>gi|337294138|emb|CCB92123.1| putative uncharacterized protein [Waddlia chondrophila 2032/99]
+-----------------------------------QTEWLFALPFSLTSEISSF--PQVSCGAWNLSFAKTGAFTQEVHFSMLRERGASFVILGDRMSRR
+HLDVSDREINVWLLKALERGLSVVV--GLTD----QG----DLYEQIQGVLEGIEpkHLEKVrILLYAG--SLGWNLEDEAEKIAERAKNLRNVLSSLYD
+-DVSRTIKILIEISHFSDDPFAYLSHSSIDGISLSASAIK-----------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * 4279 * 253 * 4085 * * * * 4314 * * 1
+ 848 2013 2347 579 1598 * * 3956 1167 0
+
+A 2 4188 * * * * 5255 6581 4766 3832 4718 806 6128 6460 4868 5298 4482 5603 5123 * 6367 2
+ 377 2715 3685 959 1042 0 * 5187 1591 1120
+
+R 3 5310 * 5553 5470 * 6626 * 6848 2282 5875 3429 5667 6253 5464 1056 4925 5189 * * * 3
+ 101 6445 4151 0 * 376 2124 5497 1000 1296
+
+K 4 6803 * * 4344 * 6712 8637 5846 1333 6716 4662 4628 5656 3453 2256 4807 4009 7016 * * 4
+ 99 5667 4420 2702 241 1531 613 5583 1045 1295
+
+Y 5 5613 * * * 5010 * 6563 4985 2238 3898 4613 5792 1405 6967 3790 6102 4241 6466 * 4978 5
+ 57 5323 6159 622 1514 403 2036 6117 1121 1372
+
+F 6 * * * 7123 2629 * 5605 1924 7286 1943 4479 * 7282 * * 7253 4896 3801 4140 4039 6
+ 63 4808 7126 818 1208 0 * 6336 1247 1133
+
+V 7 6351 6291 * * 3490 * * 1323 * 2541 5979 * * * * * 6256 1809 * * 7
+ 7 * 7768 * * 940 1063 6351 0 1043
+
+A 8 2199 * * 6631 4997 2957 * 1785 * 3968 5081 * 6346 5649 * 6916 7710 2448 * * 8
+ 0 * * 0 * 0 * 6363 1000 1028
+
+A 9 2089 6575 * * 5402 1409 * 3528 * 5217 6499 5894 6355 * * 5553 4432 2910 * * 9
+ 25 5885 * 539 1681 * * 6359 1093 0
+
+N 10 * * * * * 5269 * * * * 6782 164 * * * 4060 6355 * * * 10
+ 0 * * * * * * 6359 0 0
+
+W 11 * 6858 * * 2838 * * * * 2909 5413 6351 4856 * * * 5380 * 713 6145 11
+ 42 5602 6964 962 1039 * * 6393 1095 0
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+//
+�HHsearch 1.5
+NAME e8936c77146e6b67b02efb57e9f7dba3
+FAM
+FILE e8936c77146e6b67b02efb57e9f7dba3
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:30:24 2013
+LENG 158 match states, 158 columns in multiple alignment
+FILT 179 out of 719 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCEEEECCCCCEEEHHHHHHCCCCEEEEECCCCCEEEEEEEEEEEECCCEEEEEEEECCCCEEEEECCCEEEECCCCEEHHHCCCCCEEEECCC
+CCCCHHCCCHHHHHCCCCCCEEEEEEEEEECCCCEEEEEEECCCCEEEECCEEEECCC
+>ss_conf PSIPRED confidence values
+9775889799977899199999963047978999828899899999999998597589999978998999978981996788799799789999984577
+7761000223233102566189999996685971699859779765999999986459
+>Consensus
+sgCxxxdTxVxxxdxGxxxxIxelxxxxxxxVxsxdxxxxxxxxxxvxxxxxxxxxxxxxIxtxxGxxixxTxxHxxxtxxgwxxaxxLxxGDxixxxxx
+xxxxxxxxxxxxxxxxxxxxxxxxvxxixxxxxxxVYdlxVxxxhxfxangxlVHNsi
+>e8936c77146e6b67b02efb57e9f7dba3
+SGAISGDSLISLASTGKRVSIKDLLDEKDFEIWAINEQTMKLESAKVSRVFMTGKKLVYILKTRLGRTIKATANHRFLTIDGWKRLDELSLKEHIALPRK
+LESSSLQLSPEIEKLSQSDISWDSIVSITETGVEEVFDLTVPGPHNFVANDIIVHASI
+>gi|341582094|ref|YP_004762586.1| MCM2/3/5 family DNA replication licensing factor [Thermococcus sp. 4557]gi|340809752|gb|AEK72909.1| MCM2/3/5 family DNA replication licensing factor [Thermococcus sp. 4557]
+----------------DIGSIQ-YSQGIEYSPYlgeSLSAEDGKIKNAPLSRVWrLKAPKELVKVRTITGKELTLTPETKLLTIQngepIWKEAKSLSEG
+DYVATLRKLTV-----------EERGVPILELLKDLDDl----IVYEIkdQVKGLIEEALKELHISKR-
+>gi|298245511|ref|ZP_06969317.1| SpoVR family protein [Ktedonobacter racemifer DSM 44963]gi|297552992|gb|EFH86857.1| SpoVR family protein [Ktedonobacter racemifer DSM 44963]
+-ACLVGESLVL-TEHG-LLRYDELhkrLAEGQS-I---QVASGERQCDVv-SDRHIQRNARTIRLRTRRGLILEGAEGHKLSVGPgQWMELKDVRVGQRI
+PL-------------------------------------------------------------
+>gi|297191963|ref|ZP_06909361.1| YD repeat-containing protein [Streptomyces pristinaespiralis ATCC 25486]gi|197723321|gb|EDY67229.1| YD repeat-containing protein [Streptomyces pristinaespiralis ATCC 25486]
+--SFLPGSLVLMAD-GSKKKIEDVG--LGDKVEVTDPKTGENSDREVVRTIvTEDDKDFVTLTVSTgsGaAELVSTVTHPFWVEsaQAWVDAGDLEPGMD
+LRTADGDQ--------------------VELTALDFfEKRQRTHDLTVAGIHAYFvfAGaePVLVHNmdlnC-
+>gi|126179195|ref|YP_001047160.1| MCM family protein [Methanoculleus marisnigri JR1]gi|125861989|gb|ABN57178.1| intein [Methanoculleus marisnigri JR1]
+----------------------------DMGIAAVDEM-DKMQKEDRSALHEameqQCYDDETEVLTESGWKLfrdvtaddrvatlsadgrleyappsnf
+vaseydgemyyvksrqvdlAVTPNHRMYVNlnrraDEWEgfrliRMDELPIHKRMRfkknaawTGErhethWIPpvvkfanqnaegkltDPitvgmddwl
+eflgyflsEgsvqrhhqtgvpyrviisqtnpesaetirqclerlpfrfsydgknfsinakqlaehLApfgkchekyVPDYAKSLPPEQIgilldalmlgd
+gyinkttgvsiYTTSSRRLADDvtelllkkglsgnvylrreagtvaanprggtstathDifqVTFIRDgqnepnintngkqhIEKRPYkgtiYCLEVPNH
+TLYvrrsgipvwcgNSI
+>gi|309790378|ref|ZP_07684943.1| deoxycytidine triphosphate deaminase [Oscillochloris trichoides DG6]gi|308227570|gb|EFO81233.1| deoxycytidine triphosphate deaminase [Oscillochloris trichoides DG6]
+-RCFSADTRVALVD-GTAPTLEEMARRADngelFWGYSIGPNG-RLIVSLLEQPRYIGRDSLLEVTLDNGEKINCTPDHIFLMRDGREtSADQLRPGDSL
+MPLyRDYhrgyemvyqPLngflnpthrladewntrygiyPDVpgthrhhkdmnRrnnnpWNiErmeasaHIRLhnnvihaFKGIAVRNHKVTAIRSlPGT
+HDVYCLTVPEAGNFALEaGVFVHNC-
+>gi|147898419|ref|NP_001079262.1| indian hedgehog protein precursor [Xenopus laevis]gi|6016351|sp|Q91612.1|IHH_XENLA RecName: Full=Indian hedgehog protein; Short=IHH; AltName: Full=Banded hedgehog protein; AltName: Full=X-BHH; Contains: RecName: Full=Indian hedgehog protein N-product; Contains: RecName: Full=Indian hedgehog protein C-product; Flags: Precursorgi|1147832|gb|AAA85165.1| banded hedgehog protein [Xenopus laevis]
+-GCFPGEALATLES-GEKIPVSQLS--PGLRVLAMDNS-GRPTYSDFLSFLdhsPKEEHMFQVIKTqDPHRRLFLTPAHLIFVSDNYStpasefqavFAS
+SVRPGQYILVSN-----------------------------------------------------------
+>gi|115374273|ref|ZP_01461558.1| hypothetical protein STIAU_0597 [Stigmatella aurantiaca DW4/3-1]gi|310818165|ref|YP_003950523.1| fibronectin type III domain-containing protein [Stigmatella aurantiaca DW4/3-1]gi|115368694|gb|EAU67644.1| hypothetical protein STIAU_0597 [Stigmatella aurantiaca DW4/3-1]gi|309391237|gb|ADO68696.1| Fibronectin type III domain protein [Stigmatella aurantiaca DW4/3-1]
+-----------MLHDGTELPAEML--RPGMRVLTMLEDGAEGGVYEVVHVGRHS-SARVKVVTVDGRVVVVTPNHRWRTCErGWVRSDELVRGDTIDG--
+--------------------FAPSRVARVEPFDSGEVIKISVDVARTFIVKGLLAHN--
+>gi|115380366|ref|ZP_01467366.1| putative cell surface protein [Stigmatella aurantiaca DW4/3-1]gi|310822206|ref|YP_003954564.1| hypothetical protein STAUR_4959 [Stigmatella aurantiaca DW4/3-1]gi|115362632|gb|EAU61867.1| putative cell surface protein [Stigmatella aurantiaca DW4/3-1]gi|309395278|gb|ADO72737.1| uncharacterized protein [Stigmatella aurantiaca DW4/3-1]
+ASCYTPEQKIRFPE-GD-VAIVEAVAGMKKNVVTLTPDssldAIALQTNKtysYTAEFRDTEHPIVNLLMASGGKLTVTKEHPLINSEGRlVTAQTVKVG
+DELV--------------------KVDGSFDPIVRVEHTTHfGKVYNLRpdtdDRVSNILVAEGYLVGSS-
+#
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+
+S 127 3796 * 4805 2958 7112 3426 * * 3418 * * 3522 * 4009 3492 1812 5812 5104 * * 127
+ 0 * * * * 2122 377 7939 0 1413
+
+I 128 4557 6772 6486 * * * 7290 1100 5148 2943 5989 5291 * * 6173 6365 5131 2250 * * 128
+ 26 5802 * 442 1922 2734 235 7976 1084 1302
+
+T 129 4019 * 3554 1663 7557 5255 6452 5763 3987 7202 6672 4726 5672 * 3444 3207 4057 5155 6412 4682 129
+ 68 7006 4697 1585 585 * 0 7975 1000 1246
+
+E 130 3918 4481 3844 2888 5205 5869 4836 3970 5144 5441 4864 4773 3233 4840 4229 3849 4884 5576 * 3319 130
+ 314 2408 7146 847 1171 3370 147 7890 2407 1593
+
+T 131 4256 * 3504 4559 5360 4632 6707 3197 4762 2544 6194 6771 3131 5840 * 4519 3534 3207 * 4932 131
+ 154 3436 6827 4182 82 2748 232 7867 1605 1716
+
+G 132 5098 5784 4232 3418 6330 1320 7831 * 4198 * 6718 4036 3887 5407 4608 4337 4548 * * 4677 132
+ 160 3256 * 1125 885 * 0 7861 1734 1691
+
+V 133 5567 * 6268 2727 6342 6729 4077 5934 3259 3689 * 5949 4059 5006 4281 4514 3564 2880 * 3149 133
+ 319 2334 * 452 1894 2393 305 7861 2701 1691
+
+E 134 4167 * 3872 2325 6166 3269 3869 4874 3755 * * 6633 5991 3004 4112 4995 3447 4298 * * 134
+ 131 3636 7236 204 2925 2277 333 7858 1566 1549
+
+E 135 5482 * 2719 3510 4598 * 4630 4381 3301 6005 4644 4379 3689 4585 3609 * 3459 * 5647 3457 135
+ 10 7148 * 0 * 2096 384 7878 1000 1557
+
+V 136 4706 6759 * * * * * 3860 * 4485 4600 * * * * 5923 2924 623 * * 136
+ 0 * * * * 1823 479 7905 0 1412
+
+F 137 * 5461 * * 2819 * 6800 6149 * 6352 6853 * * * 4587 * 7305 6194 7070 469 137
+ 0 * * * * * 0 7913 0 1276
+
+D 138 * 6290 923 6307 * 7681 5323 * 5806 * * 1613 * * 7206 4150 6714 * * * 138
+ 61 4587 * 3738 112 * 0 7913 1271 1276
+
+L 139 6010 * * * 3140 * * 1957 * 863 7741 * 6300 * * * * 4430 * * 139
+ 37 5320 * 630 1499 2001 415 7897 1162 1389
+
+T 140 4809 7058 4868 2017 7499 6181 6351 5169 5662 * 5354 7013 * 3541 4368 2979 2036 5477 5090 7067 140
+ 38 6919 5802 2000 415 * 0 7911 1046 1274
+
+V 141 5307 6666 6800 6865 6698 * * 2857 5963 3253 4514 * * * * * 4695 746 * * 141
+ 18 * 6363 * * 1519 619 7926 0 1458
+
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+P 144 3691 * 4526 5867 5591 3939 4742 6374 6259 3278 * 2858 4249 * * 3489 2472 6015 * 2887 144
+ 212 2998 6456 868 1145 573 1609 7911 1976 1274
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+H 145 6867 6689 6307 4254 6642 4841 744 6289 5354 6819 6892 4129 6376 5424 5346 5038 5752 6694 * 4494 145
+ 15 * 6642 * * 1217 811 7861 0 1125
+
+N 146 3845 3924 6249 6282 5775 6451 * 6849 * 4487 * 1334 6749 6003 5355 3899 2238 5849 6713 8054 146
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+ 104 3841 * 784 1254 * 0 7967 1501 1189
+
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+ 156 3290 * 1176 844 821 1205 7857 1945 1189
+
+N 150 6251 6913 4969 3491 6876 2503 * * 5560 * 7030 998 5025 4487 6892 4843 6045 6694 * * 150
+ 154 3302 * 968 1032 * 0 7882 1761 1038
+
+D 151 5155 * 3544 3870 * 736 6986 * 5731 * * 3610 5349 7243 4861 4536 * * * * 151
+ 53 4787 * 1766 502 * 0 7885 1206 1038
+
+I 152 4492 * * * 2588 6305 5021 2153 * 2152 * * * * * 5180 6478 2141 6858 5518 152
+ 29 6171 7338 1000 1000 * 0 7885 1041 1038
+
+I 153 5898 * * * 4501 * 6275 2108 6709 1544 4360 * * * * * 5268 2139 5130 6447 153
+ 0 * * * * * 0 7877 0 1178
+
+V 154 3659 * * * * * * 4464 * 3555 * * 6677 * * 3719 4430 603 * * 154
+ 62 4563 * 750 1303 * 0 7877 1270 1178
+
+H 155 5916 6481 * 7256 * 5249 212 * * * * * * * * 4545 * * * 4923 155
+ 74 4320 * 3319 152 0 * 7595 1276 1178
+
+A 156 5698 * * 5582 * 6858 * * 6017 * * 135 * 6171 * 6462 * * * * 156
+ 21 6143 * 3823 106 * * 7609 1051 0
+
+S 157 3787 2580 4544 5886 * 6436 * * 4907 * 5266 * * * 5734 1324 2242 * * * 157
+ 64 4522 * 1000 1000 * * 7407 1000 0
+
+I 158 * * * * 3004 * * 272 * 4413 * * * * * * * * * * 158
+ 0 * * 0 * * * 5033 0 0
+
+//
+�HHsearch 1.5
+NAME eb17077e5768f21bb26c456637a41be1
+FAM
+FILE eb17077e5768f21bb26c456637a41be1
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:16:11 2013
+LENG 247 match states, 247 columns in multiple alignment
+FILT 110 out of 183 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.5
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCEEEEEEECCCCCEEEEEEECCCEEEEEEEECCEEEEECCCCHHHHCCCCCCCCC
+CEEECCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHH
+HHCCCCCCCCCCCEEECCCCCEEEEEEHHHHHHHHHHHHHEECCCCC
+>ss_conf PSIPRED confidence values
+9489847997464999999999984758868996730899888877899999838999899999879779999998998899479963540056789987
+3588879999899998738870036408999999999996699179999999999996636662999999996521377898899999965999999999
+85389987689623654899889996678878866406433055779
+>Consensus
+xvxfxxxxatxxxYxxFIxxLRxxlxxxxxxxgiPvlxxxxxxxxrxxxVxLxxxxxxxvtLaixxxnlYvvGfxxxxxxyxFxdxxxxxxxxxlfpxxx
+xxxxLxfxgsYxxLxxxagxxrxxixLGxxxLxxAixxLxxxxxxxxArxLlvxIqMvsEAaRFxxIxxxvxxxxxxxxxpxxxxxsLexnWxxlSxxIx
+xxxxxxgxfxxpvxlxxxxxxxxxvxxvxxxxxxxxxxlxxxxxxxx
+>eb17077e5768f21bb26c456637a41be1
+DVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAM
+RKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQ
+IASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA
+>gi|132576|sp|P24476.2|RIP0_DIACA RecName: Full=Antiviral protein DAP-30; AltName: Full=Dianthin 30; AltName: Full=Ribosome-inactivating protein; AltName: Full=rRNA N-glycosidase; Flags: Precursor
+AYTLNLANPSASQYSSFLDQIRNNVRDTSLIYGgtdVAVIGAPSTT-DKFLRLNFQGP-RGTVSLGLRRENLYVVAYLAMDnanvnRAYYFknQITSA--
+ELTALFPEVvvaN-QKQLEYGEDYQAIEKNAKITtgdqsRKELGLGINLLITMIDGVNKKvrVVKDEARFLLIAIQMTAEAARFRYIQNLVTKNFPNKFD
+SENKVIQFQVSWSKISTAIFG-DCKNGVFNKDYDF--------------------------------
+>gi|204307504|gb|ACI00278.1| trig7 [Hordeum vulgare]
+TATFNVQASSAD-YATFIAGIRNKLRNPAHfSHNRPVLPPvePNVPPSKWFHVVLKASPTSAgLTLAIRADNIYLEGFKSSDGTW-W------ELTPGLI
+PGAT---YVGFGGTYRDLLGDTD-KLTNVALGRQQLADAVTALHGRtkadkasgPKQQQAReAVTTLVLMVNEATRFQTVSGFVAGLLHpKavekkSGKI
+GNEMNAQVNGWQDLSAALL--KTDVkpppgkspAKF-API-------EKMGMRTAEQAANTLGILLFVEV----
+>gi|256783605|ref|ZP_05522036.1| secreted protein [Streptomyces lividans TK24]gi|289767488|ref|ZP_06526866.1| secreted protein [Streptomyces lividans TK24]gi|289697687|gb|EFD65116.1| secreted protein [Streptomyces lividans TK24]
+-----------PHYRSVVQQLRR--GAGHLIHGNNIYETmGQGQNAGLVALNLYNADwVHQTTLYFNASNLYLVGFKSRtGQAYLFSDASA-NAREEVgr
+eVRGAP-VTTLPFAGSYTSLVNTlPGAETEPTTIGIYAIQTNMEALARTpNpaaatgayRGSIARAMLIMIGAFAEAARFPMFRDHFEAAFRRfanpSVV
+VTPTMQALRTAWGQMSRWVQ--QLVSGPPPTPAVFG-------------------------------
+>gi|295701322|ref|YP_003610323.1| ribosome-inactivating protein [Burkholderia sp. CCGE1002]gi|295441645|gb|ADG20812.1| ribosome-inactivating protein [Burkholderia sp. CCGE1002]
+--EFSVDFTSPQKYVQSLGAIRAAMGDAMSLTNIPGnkilyqLRPDASNIVEGVTIEIIGvgrnnsPSNRDVRFVINPSDLYLTGFIVGRIFYRFSDFSD
+T-ASGRVQVNAPRhlvdfTIDMTVDSSYLSLARSAGVSADRTDLSIDrySLMKGYrdliNHVSSTrtINGAEARALLSYATVLSEAVRFRSIQGNFASTa
+LgDDAFTP--YRLSLEDsnrttRWDRLSDEIR--KAHYGAI----KIATHGAAPILLANVRD-----------------
+>gi|242071645|ref|XP_002451099.1| hypothetical protein SORBIDRAFT_05g024110 [Sorghum bicolor]gi|241936942|gb|EES10087.1| hypothetical protein SORBIDRAFT_05g024110 [Sorghum bicolor]
+----------------------------------------------------------------------------------------------------
+----------------------------VEDLDEAISSLSLFptgnaTEEDVSRGLAACDAMVAAAATFLYVERRMSAGMWDgnGVSNDGSLRRLQESRP
+DLSAAVQ--DSYQGAFAAPVALQRSNGERVLVDNMRRAVP--------------
+>gi|254385328|ref|ZP_05000657.1| hypothetical protein SSAG_05020 [Streptomyces sp. Mg1]gi|194344202|gb|EDX25168.1| hypothetical protein SSAG_05020 [Streptomyces sp. Mg1]
+PVSFSVAHASVGDYRLLASSIRSRAALA---QCLPGRAGNEEVSARYLPVRIQLR-GLFielfIELRTQNSVLRITGFRNTFENW---QAPPEGRFRHVr
+davaPPGVHHAEALSFEGEVPALEAAAEVGRTGLSLGRRPMMKAVMWLHRNtDPKCTALGMLVLGEMLCEAASSPVLAQEMSRIW---------------
+---------------------------------------------------------
+>gi|157108298|ref|XP_001650164.1| hypothetical protein AaeL_AAEL005004 [Aedes aegypti]gi|108879337|gb|EAT43562.1| hypothetical protein AaeL_AAEL005004 [Aedes aegypti]
+----------DRAYLGFIQNLISALTESDEVYGnIKVTKRK----DGITKVTLKDS-STnsQVGFIYRNRDLYIVGLVVGTTFYIDKEVYDGlgkkipTT
+WKgVINAAN--TVSLSNPFSYNQILPS----GEGTVLQIGKLGDSLTHLTKIgDtSKrsqIMTQHLGPFVVAFSEAIRFPVVAREIQGAIRKatgtvSLs
+knlvrplslgHPSertsnhvFTMYSLLLNWSKLSDRVP-----------------------------------------------
+>gi|77553788|gb|ABA96584.1| Ribosome inactivating protein [Oryza sativa Japonica Group]
+---IDVTDPTQGGYTTALNSIRERDQEraGQnTFHGVAIT--S--LNKQWRRINLVHQDRPTVSLLIDESNGYLVGFRRGDGtWMHFNDQE-----LPNV
+PGTEQrvpGIPIQLSSSYMNLIKD--NERPYFSVGRQSLRHSYFVLLNYDaevdlrsamMKRQRKALTQLIILFCEAARIRPVLEFISEAMSTeDTTPlD
+ETLWTWIKNWSTLSRFA------------------------------------------------
+>gi|47496961|dbj|BAD20031.1| hypothetical protein [Oryza sativa Japonica Group]gi|47497865|dbj|BAD20039.1| hypothetical protein [Oryza sativa Japonica Group]
+-------RGTKNTYASLVSSIVTRITTRAMatVEGKPVCGPSG-----YFEIILFPkpgtqfaakHANGRVRLLFNYQNLYLVAFKVQGKWHKFKDLTPK
+IA-----PDYASikrkkhceAKNLPFESNYGVRGMAANLaqLkvSRQTPLQIYKML----SLYDPehnagmvRLSDLQKMLFKTCAVFPEVFRFPLLKKR
+VVYLMgktaDEESTVGEQHTDLFQNWGDCCMALR--MGR-QAFTPMADL--------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+D 1 * * 2471 * * * * 4512 4252 5215 * 2839 2995 * * 3715 1494 * * * 1
+ 0 * * * * * * 5016 0 0
+
+V 2 4547 * 5748 6092 4453 * * 2629 * 4498 * * 5599 * * 5628 * 663 * * 2
+ 0 * * * * * * 5373 0 0
+
+S 3 * * * 3275 6479 5714 * 5959 5182 5748 * 3600 5648 * 3639 1720 1736 5820 * * 3
+ 104 * 3840 * * * * 5741 0 0
+
+F 4 * 5524 * * 448 * * 5119 * 2601 * * * * 5867 * * * 5815 5900 4
+ 0 * * 0 * 0 * 5911 1268 1268
+
+R 5 5268 * 2016 4514 * * 5215 * 4823 * * 2311 * * 5358 2231 2696 * * 5178 5
+ 0 * * * * * * 5971 0 0
+
+L 6 6382 5387 * * * * * 4076 * 1560 6350 * 5640 5856 * * 2473 1642 * 6019 6
+ 22 * 6019 * * * * 5971 0 0
+
+S 7 2800 * 2716 3354 * 3373 5080 6459 4284 5142 * * 5922 3860 * 2792 3585 3714 * * 7
+ 120 5800 4016 0 * 0 * 5971 1011 1012
+
+G 8 5146 * 4219 5379 4084 2103 4552 * 4155 6291 * 3629 5424 6064 3446 2885 3098 * * 5173 8
+ 34 5424 * 483 1814 0 * 6032 1102 1174
+
+A 9 1233 6488 6086 6024 5966 3934 * 6339 4852 4430 * * 3827 * * 2951 3464 5419 * 4478 9
+ 13 * 6787 * * * * 6215 0 0
+
+T 10 6186 * 3010 5462 * 4170 * * 5059 * * 4705 * * 5819 2841 876 6229 * * 10
+ 20 * 6163 * * * 0 6274 0 1000
+
+S 11 2760 5498 4263 3661 * 3576 * 5072 3372 * * * 3265 4278 3956 2843 6595 3488 5728 6469 11
+ 53 5261 6646 575 1605 0 * 6453 1073 1064
+
+S 12 3353 * 3198 3817 * 3056 * 5798 2860 5765 * 3669 5785 3206 4777 3129 4795 * * 4801 12
+ 31 * 5550 * * * 0 6643 0 1000
+
+S 13 4280 * 3763 4701 * 4089 5770 5628 3166 * * 3847 4957 6614 4858 2159 2128 5123 * * 13
+ 0 * * * * 0 * 6634 0 1132
+
+Y 14 * * * * 4590 * * * * * * 5628 * * * * * * * 92 14
+ 0 * * * * * * 6673 0 0
+
+G 15 3418 * 6237 4204 6560 4386 * 5877 3935 4598 * 3559 6439 5429 2726 2393 2805 4250 * * 15
+ 0 * * * * * * 6691 0 0
+
+V 16 4208 * 2444 4974 * 5099 6863 * 4650 3635 * 4123 6439 4033 5360 2340 2332 5533 * * 16
+ 0 * * * * * * 6691 0 0
+
+F 17 5816 * 6230 * 489 * * 5642 * 3022 * * * * * 4550 * 4263 * 5752 17
+ 0 * * * * * * 6691 0 0
+
+I 18 5865 * * * * * * 889 * 1859 4104 * * * * 5642 4975 4127 * * 18
+ 0 * * * * * * 6691 0 0
+
+S 19 3641 * 3755 3397 * 4115 * 6076 2939 * * 3021 * 3398 3868 3347 2738 6234 * * 19
+ 0 * * * * * * 6676 0 0
+
+N 20 3337 * 3606 3339 * 4406 * * 3467 5269 * 2785 * 4111 4067 2083 4895 5358 * * 20
+ 0 * * * * * * 6676 0 0
+
+L 21 * * * 6242 4861 * * 2038 * 766 5351 * * * * * * 3620 6062 * 21
+ 0 * * * * * * 6676 0 0
+
+R 22 * * * * * 5829 * 4431 5643 * * * * 5507 223 * 5890 5598 * * 22
+ 0 * * * * * * 6676 0 0
+
+K 23 3585 * 2483 2874 * 4300 * 6561 3196 * * 2776 * 6827 4904 3366 3337 4421 * * 23
+ 68 * 4434 * * * * 6676 0 0
+
+A 24 2292 6187 4612 3617 6490 5369 6841 5363 3347 4221 * 4351 * 3036 2359 5909 4471 6398 * * 24
+ 0 * * * * 1570 593 6605 0 1221
+
+L 25 3281 * 5789 * 5495 * * 3696 * 963 5177 * * * * * * 2064 * * 25
+ 77 5605 4995 0 * 0 * 6614 1086 1122
+
+P 26 2226 * * 3968 * 3215 * 5432 2895 6018 * * 4372 4247 4566 3402 2672 4414 * * 26
+ 0 * * * * 0 * 6667 0 1150
+
+N 27 5160 * 2411 3227 4977 3959 5831 4829 4146 4630 * 3642 6730 5318 4166 2852 3311 5508 * * 27
+ 143 4602 4232 2042 401 * * 6679 1149 0
+
+E 28 3077 * 5035 4998 * 1809 4373 * 3530 * * 4782 2528 5264 4808 4016 4918 * 5807 6041 28
+ 103 4796 4921 566 1624 0 * 6603 1161 1258
+
+R 29 3180 * 4207 5385 * 3626 4792 * 5095 4755 5964 4026 3320 4519 4042 3307 2396 6905 * 4412 29
+ 146 3657 5901 1532 612 * 0 6594 1367 1136
+
+K 30 * * 4528 2617 5258 * 3909 4944 3721 2815 4834 4278 3991 5406 4729 4083 4185 3564 * 4602 30
+ 718 1535 4413 746 1309 2083 388 6554 2805 1302
+
+L 31 3529 4699 * 6837 4026 * 5363 3281 5063 3959 6821 * 4603 6472 4193 2000 * 2386 * 5263 31
+ 128 3554 * 1299 752 0 * 6701 1870 1548
+
+Y 32 4066 3690 4974 3581 6950 5442 1821 * 6624 4978 * 4057 6706 4234 * 5234 4757 6349 * 2375 32
+ 60 4617 * 816 1211 * * 6805 1183 0
+
+D 33 * 5219 3330 4591 * 992 * * 6962 6818 * 2371 * 6668 * 4499 4605 6318 * 6451 33
+ 197 2968 * 1008 992 * * 6805 1793 0
+
+I 34 * * * * 5513 * 5650 856 4879 2618 4991 5912 * * 3791 6349 5255 4321 * * 34
+ 20 6213 * 1000 1000 * * 6805 1003 0
+
+P 35 5009 * * * 6190 5899 * 6474 4086 5547 * 5174 579 5675 4330 5577 6890 5418 * 5163 35
+ 12 * 6956 * * * * 6805 0 0
+
+L 36 4546 * * * 6633 4490 * 3323 5566 3036 3617 * * * 4794 * 5739 934 * * 36
+ 21 6125 * 2585 263 * 0 6802 1019 1000
+
+L 37 6460 4315 * * 6247 6178 * 3306 * 776 4171 * * * 5933 5948 3205 6255 * 5906 37
+ 107 4820 4795 1169 849 0 * 6802 1298 1000
+
+R 38 2857 * 4654 5355 * 4921 6339 * 3132 5561 * 4857 2059 6455 2087 4933 5744 4748 * 7076 38
+ 22 6026 * 0 * * 0 6763 1017 1190
+
+S 39 3514 * 4875 4696 * 4330 6830 5413 3582 4551 * 4197 2150 4479 4159 2884 3612 4888 * * 39
+ 737 1322 * 1131 880 0 * 6763 3461 1190
+
+S 40 4692 * 4171 5001 * 4118 5483 * 5416 * * 4251 1960 3822 5218 2888 2245 5792 * * 40
+ 194 6763 3101 0 * * * 6807 1000 0
+
+L 41 3332 * 4924 3992 6514 4625 * 4416 6040 3374 * 5156 3525 4899 * 4789 2603 2108 * 6170 41
+ 229 5758 2966 0 * 3283 156 6550 1023 1689
+
+P 42 3230 * 3638 3159 * 3880 * 6326 5150 4877 6940 3896 2623 4050 5620 2807 4564 4618 * 6125 42
+ 417 4359 2305 258 2610 1972 424 6409 1251 2335
+
+G 43 4012 * 2840 3887 * 3781 * 3619 5370 4733 * 3927 3231 3690 * 3344 3269 3990 * * 43
+ 110 4740 4797 1575 590 710 1363 6188 1085 2857
+
+S 44 4282 6271 3443 4992 * 4239 * 6032 4771 4458 * 3327 1575 5131 7196 2717 5092 6667 * * 44
+ 35 5916 7026 1000 1000 661 1444 6564 1017 1875
+
+Q 45 2465 * 3213 3467 6431 5595 * * 4149 * 6242 3641 3415 2682 3551 4331 5480 5421 6927 * 45
+ 0 * * * * 2724 237 6800 0 1338
+
+R 46 4431 6980 5191 4226 * 3041 * 5945 2860 6386 * 4970 6435 4194 1389 4825 4547 * 6797 6563 46
+ 22 * 6048 * * 0 * 6843 0 1276
+
+Y 47 * * * * 1565 5201 6931 4733 * 3464 * 6453 * 6218 * 5421 * * 2321 1998 47
+ 19 6264 * 0 * 0 * 6867 1003 1029
+
+A 48 4597 * 5058 * 3117 * 6826 2255 5860 2160 5903 6612 * 7189 5064 6981 4521 2064 * * 48
+ 29 6463 6840 1000 1000 * * 6902 1008 0
+
+L 49 5230 * 5114 5867 4814 * 4037 5020 4189 1497 4533 5430 4837 6198 4175 5560 4214 4365 * 3367 49
+ 0 * * 0 * 0 * 6886 1008 1080
+
+I 50 4095 * * * 6816 6886 * 2034 * 3566 6292 * 5020 * * 5892 5210 977 * * 50
+ 12 * 6905 * * * * 6942 0 0
+
+H 51 4672 * 2901 2511 * 6180 4254 3529 3840 * * 3199 6722 4302 3078 6324 3758 4187 * * 51
+ 0 * * * * 0 * 6940 0 1002
+
+L 52 * * * * 5553 * * 3734 * 402 5376 * * 6919 6295 6592 * 3749 * 5872 52
+ 0 * * * * * * 6942 0 0
+
+T 53 6592 * 5344 4267 4116 * 6689 3449 2957 6130 * 7210 5872 3519 4432 3320 2448 2743 * 5578 53
+ 23 * 5967 * * * * 6942 0 0
+
+N 54 2767 6632 4606 5894 4598 2391 4703 * 6508 4588 * 1957 4153 * * 3903 4584 5279 7186 7118 54
+ 560 2986 2356 2095 385 0 * 6946 1819 1066
+
+Y 55 4774 * 5116 4212 6628 3452 4688 5237 4086 5200 6640 4324 4343 4634 3138 2477 6831 5405 4110 3400 55
+ 330 3796 2917 690 1395 129 3552 6766 1710 2383
+
+A 56 3012 * 2247 3907 * 2474 * * 5127 6690 * 3212 4648 6493 4431 3574 4044 5028 * * 56
+ 70 4640 7044 903 1104 0 * 6626 1279 1840
+
+D 57 3909 5868 2966 3750 * 2121 6751 * 4560 7079 7097 2923 5857 4389 4274 5344 3227 5573 * 5893 57
+ 82 5069 5290 2417 299 0 * 6948 1170 1000
+
+E 58 5140 * 2611 3550 * 3221 4344 5453 3552 4994 6064 3934 6143 3658 3033 4861 3687 5743 * * 58
+ 50 5382 6662 1327 734 0 * 6923 1176 1235
+
+T 59 4361 * 5581 3326 5255 6696 * 6301 3913 7016 * 4866 4352 3778 3899 2628 2048 5074 4878 5837 59
+ 64 4534 * 1536 610 0 * 6932 1257 1012
+
+I 60 3418 * * * 6683 * * 1751 * 4738 6606 * * * * 5828 2805 1354 * * 60
+ 0 * * * * * * 6944 0 0
+
+S 61 5071 * * 4409 * 6066 * 5146 5079 6650 4820 7001 5138 5424 3534 3159 920 5740 * * 61
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+
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+
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+
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+
+N 245 1625 1730 * * * * * * * * * 2148 * * 2750 * * * * * 245
+ 0 * * * * * * 2605 0 0
+
+M 246 * * * * * * * 2845 * * 3014 * * * * 1170 3106 2502 * * 246
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+
+//
+�HHsearch 1.5
+NAME eb75493f078d95ea52db97600717baa3
+FAM
+FILE eb75493f078d95ea52db97600717baa3
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:04:12 2013
+LENG 129 match states, 129 columns in multiple alignment
+FILT 3 out of 5 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 1.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEEECCCCCCEEEEECCCCCHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEEEEEECCCEEEEEECCEECCHHHHHHHHCCEEEEEEEECCCC
+HHHHHHHHHHHHCCCCCCHHHHHHCCCCC
+>ss_conf PSIPRED confidence values
+9862189999369856469951244303889862476030248888877155666506899962501356537785428998864165266567860761
+89999997776416985067786435779
+>Consensus
+asnxxxfvlvdnggtgxvtvxpxxxangvaewisxnsrsqaykvtxsxrxsxaxxrkytikxevpkvxtqvxxgvelpvaawrsyxxmeltipifatxdd
+xxxixkalxgxfkxgnpixxaiaaxsgxy
+>eb75493f078d95ea52db97600717baa3
+ASNFTQFVLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVDLPVAAWRSYLNMELTIPIFATNSD
+CELIVKAMQGLLKDGNPIPSAIAANSGIY
+>gi|435743|gb|AAC60713.1| alpha-atrial natriuretic factor/coat protein [synthetic construct]
+ASNFEEFVLVDNGGTGDVKVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSANNRKYTVKVEVPKVATQVQGGVELPVAAWRSYMNMELTIPVFATNDD
+CALIVKALQGTFKTGNPIATAIAANSGIY
+>gi|83642763|dbj|BAE54359.1| coat protein [Enterobacteria phage SD]
+---matLRSFVLVDNGGTGNVTVVPVSNANGVAEWLSNNSRSQAYRVTASYRASGADKRKYTIKLEVPKIVTQVVNGVELPISAWKAYASIDLTIPIFAA
+TDDVTTISKSLAGLFKVGNPIADAISSQSGFY
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
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+
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+ 0 * * * * * * 1102 0 0
+
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+ 0 * * 1585 585 * * 1102 1013 0
+
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+
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+
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+
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+
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+
+Q 109 1420 * * * * * * * * * * * * 675 * * * * * * 109
+ 0 * * * * * * 1355 0 0
+
+G 110 * * * * * 0 * * * * * * * * * * * * * * 110
+ 0 * * * * * * 1355 0 0
+
+L 111 * * * * * * * * * 540 * * * * * * 1680 * * * 111
+ 0 * * * * * * 1355 0 0
+
+L 112 * * * * 544 * * * * 1670 * * * * * * * * * * 112
+ 0 * * * * * * 1355 0 0
+
+K 113 * * * * * * * * 0 * * * * * * * * * * * 113
+ 0 * * * * * * 1355 0 0
+
+D 114 * * 1670 * * * * * * * * * * * * * 1680 1420 * * 114
+ 0 * * * * * * 1355 0 0
+
+G 115 * * * * * 0 * * * * * * * * * * * * * * 115
+ 0 * * * * * * 1355 0 0
+
+N 116 * * * * * * * * * * * 0 * * * * * * * * 116
+ 0 * * * * * * 1355 0 0
+
+P 117 * * * * * * * * * * * * 0 * * * * * * * 117
+ 0 * * * * * * 1355 0 0
+
+I 118 * * * * * * * 0 * * * * * * * * * * * * 118
+ 0 * * * * * * 1355 0 0
+
+P 119 544 * * * * * * * * * * * 1670 * * * * * * * 119
+ 0 * * * * * * 1355 0 0
+
+S 120 * * 1420 * * * * * * * * * * * * 1670 1680 * * * 120
+ 0 * * * * * * 1355 0 0
+
+A 121 0 * * * * * * * * * * * * * * * * * * * 121
+ 0 * * * * * * 1355 0 0
+
+I 122 * * * * * * * 0 * * * * * * * * * * * * 122
+ 0 * * * * * * 1355 0 0
+
+A 123 675 * * * * * * * * * * * * * * 1420 * * * * 123
+ 0 * * * * * * 1355 0 0
+
+A 124 675 * * * * * * * * * * * * * * 1420 * * * * 124
+ 0 * * * * * * 1355 0 0
+
+N 125 * * * * * * * * * * * 675 * 1420 * * * * * * 125
+ 0 * * * * * * 1355 0 0
+
+S 126 * * * * * * * * * * * * * * * 0 * * * * 126
+ 0 * * * * * * 1355 0 0
+
+G 127 * * * * * 0 * * * * * * * * * * * * * * 127
+ 0 * * * * * * 1355 0 0
+
+I 128 * * * * 1420 * * 675 * * * * * * * * * * * * 128
+ 0 * * * * * * 1355 0 0
+
+Y 129 * * * * * * * * * * * * * * * * * * * 0 129
+ 0 * * 0 * * * 1355 0 0
+
+//
+�HHsearch 1.5
+NAME ec6d5b33f2ae17f54335ee8fce56e790
+FAM
+FILE ec6d5b33f2ae17f54335ee8fce56e790
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:34:29 2013
+LENG 83 match states, 83 columns in multiple alignment
+FILT 101 out of 1081 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.8
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCEECCCHHHHHHHHCCCEEEEEECCCEEEEEEEEEECCCCEEEEEEEEEEECCCEEEECCEEEEECCEEEEEEC
+>ss_conf PSIPRED confidence values
+97543566536144649999987799899999499599999999868752898438999569818796689994998999969
+>Consensus
+xxxxxmxxxxxxxxxpxxxLxxxxxkxVxVxlxxgxxxxGxLxxxDxxmNlvLxdxxexxxxxxxxxlxxvxIRGxxIxxIxx
+>ec6d5b33f2ae17f54335ee8fce56e790
+GSVIDVSSQRVNVQRPLDALGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELEDGEVTRRLGTVLIRGDNIVYISP
+>gi|145524719|ref|XP_001448187.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|124415720|emb|CAK80790.1| unnamed protein product [Paramecium tetraurelia]
+--------------GYQADLNKYFGKRLKIKLNAKRTIIGTVIGFDIFMNLDKEQKIKIIciqalsnVTDQLVDIGQAIVRGNSIIM---
+>gi|327352187|gb|EGE81044.1| small nuclear ribonucleoprotein Sm D2 [Ajellomyces dermatitidis ATCC 18188]
+-------------SGPLSILQTATRshAQVLISCRNNRKLLARVKAFDRHCNMVLENVKEMWTEkpkggkgkgvNKDRFVSKMYVQTNTCLLA--
+>gi|254567285|ref|XP_002490753.1| Core Sm protein Sm D3 [Pichia pastoris GS115]gi|238030549|emb|CAY68473.1| Core Sm protein Sm D3 [Pichia pastoris GS115]
+-------------SIPVKLLNEAQGHIISAELTSGESYRGKLVESEDSMNIQLKDVTLTAQDGKVSHMEQIFIRGSQIRFFS-
+>gi|15920525|ref|NP_376194.1| hypothetical protein ST0326 [Sulfolobus tokodaii str. 7]gi|342306150|dbj|BAK54239.1| archaeal Sm protein [Sulfolobus tokodaii str. 7]
+----------------ATELNSLLDKAIVVRLINNKIYYGTLSSYElSPFILTLTNAKDN----DNNTYYKVILNGNSITEI--
+>gi|254585839|ref|XP_002498487.1| ZYRO0G11462p [Zygosaccharomyces rouxii]gi|238941381|emb|CAR29554.1| ZYRO0G11462p [Zygosaccharomyces rouxii]
+-----------------PLLKDYLHRRVLVITTAGDCIVATLEGFDKNTNVVISDVVDRCTLRPM--AMAQAVRGSEIVAMG-
+>gi|307105968|gb|EFN54215.1| hypothetical protein CHLNCDRAFT_24936 [Chlorella variabilis]
+--------------LFYSYFKTLVGKEVTVELKNDLAITGTLHSVDQYLNIKLNNIRVVNEQKypHMLSVRACFVRGSVVRYVQ-
+>gi|121710344|ref|XP_001272788.1| LSM domain protein [Aspergillus clavatus NRRL 1]gi|119400938|gb|EAW11362.1| LSM domain protein [Aspergillus clavatus NRRL 1]
+---------------AVRYLESLIGQTLRVHATDTRMFVGTFKCTDAERNIILGNTYEYRFpsssaikdaaaktndgeevvapperrniklDMTSRFIGL
+VVVPSQHITKI--
+>gi|307186087|gb|EFN71819.1| U7 snRNA-associated Sm-like protein LSm10 [Camponotus floridanus]
+----------HFLYNSLSILLKAVEKqRTIIDLRNEASIFGIVEQTDAYMNVVMRDCVFTDPREDSFKFDMFFVQARNIRCV--
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 0 * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1000 0 0
+
+S 2 * * * * * * * * * * * * * * * 0 * * * * 2
+ 0 * * * * * * 1000 0 0
+
+V 3 * * * * * * * * * * * * * * * * * 0 * * 3
+ 0 * * * * * * 1000 0 0
+
+I 4 * * * * * * * 0 * * * * * * * * * * * * 4
+ 0 * * * * * * 1000 0 0
+
+D 5 * * 1000 * * * * * * * * 1000 * * * * * * * * 5
+ 0 * * * * * * 1578 0 0
+
+V 6 * * * * * * * * * * 127 * * * * * * 3569 * * 6
+ 0 * * * * * * 3901 0 0
+
+S 7 1363 * * * * * * * * * * * * * * 950 3414 * * * 7
+ 277 2517 * 0 * * * 3901 1111 0
+
+S 8 2466 * 2351 * * * * * 2508 * * 3303 * * * 3569 2439 3696 * * 8
+ 659 1448 * 305 2393 * * 3901 1343 0
+
+Q 9 * * * * * 4075 * * 2992 * * * 3806 1188 3194 3917 2952 * * * 9
+ 99 3919 * 1000 1000 * * 4680 1003 0
+
+R 10 * * * * * 3060 * * 1484 * * * * * 2131 3915 2133 * * * 10
+ 370 3013 3291 1585 585 * * 4785 1235 0
+
+V 11 2558 4003 4130 * * * 3870 * 3388 4145 * 4447 4249 3177 * 4183 3061 4538 * 3981 11
+ 0 * * 0 * * 0 5080 1000 1104
+
+N 12 3607 4628 4414 * 4303 * * 4367 5114 * 2635 3128 * 2994 * 2674 3199 * * 4787 12
+ 0 * * * * 0 * 5542 0 1104
+
+V 13 4753 * * * * 4986 * 3659 * 3348 5126 3503 3106 3850 3975 4687 2684 2369 * * 13
+ 88 * 4084 * * * * 6094 0 0
+
+Q 14 * 4622 5553 2522 5594 3545 4347 3761 4116 3629 4361 5677 * 4477 * 3214 3617 3935 * 5132 14
+ 54 6088 5502 1000 1000 0 * 6574 1000 1115
+
+R 15 4179 5838 4446 3396 * 3102 * 3693 4972 3147 * 2577 5738 4829 6402 3428 3575 5802 * 5657 15
+ 0 * * * * 0 * 6829 0 1012
+
+P 16 3677 * * * 5235 * 5906 6199 6166 4801 * 5263 708 6058 5559 3805 5006 * 5698 5726 16
+ 24 * 5941 * * * * 7026 0 0
+
+L 17 6331 * * 4760 5037 * * 2427 4237 1866 4152 5049 6075 4925 3795 3770 5270 4045 * 4611 17
+ 18 6331 * 1000 1000 0 * 7171 1054 1000
+
+D 18 3533 * 3179 3008 6202 6505 * 4953 3653 6071 * 3822 3553 4168 3773 2750 3961 5833 * 6321 18
+ 16 6519 * 0 * * * 7396 1000 0
+
+A 19 4993 * 4392 3746 2429 5683 * 3904 3823 2154 5937 6072 * 6545 6129 4266 5144 3622 * 4026 19
+ 0 * * * * * * 7520 0 0
+
+L 20 * * * 6535 4294 * * 3360 * 507 4484 * * * * * * 3646 * 6338 20
+ 0 * * * * * * 7572 0 0
+
+G 21 4358 * 4546 3145 4890 5212 5072 5812 3294 3564 4289 3660 5569 3365 3116 4359 4698 5332 * 5330 21
+ 0 * * * * * * 7587 0 0
+
+N 22 4097 * 4086 3162 * 4270 6744 6418 2782 5325 5557 2642 * 3005 3855 3162 4611 * * * 22
+ 42 6014 6277 2537 273 * * 7596 1048 0
+
+S 23 3206 3716 5811 6316 3147 6318 5690 5528 * 1965 4331 6977 * * * 3395 5679 4838 5021 3004 23
+ 35 5372 * 1932 438 * 0 7566 1092 1012
+
+L 24 6276 * * 5070 6363 6597 * 2282 4234 1957 3882 6546 5870 4743 4675 * 5167 2332 5655 * 24
+ 67 4471 * 1000 1000 0 * 7583 1345 1012
+
+N 25 6749 * 2546 4816 * 1362 5055 6556 5497 6610 * 2398 6542 4352 5063 4969 6579 * * * 25
+ 52 4813 * 1000 1000 * * 7620 1210 0
+
+S 26 5479 5479 6297 3676 * 5512 4128 * 1502 * 6744 4914 * 4897 3322 3281 3632 5421 * 4350 26
+ 47 4962 * 406 2027 * * 7620 1224 0
+
+P 27 * * * 4113 * * 4988 4611 2327 5673 * 4151 3049 3827 2314 4190 3451 4449 * 6632 27
+ 10 7125 * 1000 1000 * * 7620 1000 0
+
+V 28 6338 * * * 6235 * 5820 2150 * 3456 4516 * * * * * 3956 944 * 6363 28
+ 0 * * * * * * 7620 0 0
+
+I 29 * 4928 5753 4894 7084 * 4332 3708 4007 3037 4755 5293 * 4879 3029 2996 2910 3667 6955 4917 29
+ 0 * * * * * * 7620 0 0
+
+I 30 * 4253 * * * 5878 * 1706 * 3978 * * * * * * 6236 870 * * 30
+ 32 5504 * 1000 1000 * * 7628 1088 0
+
+K 31 5937 6560 4251 2027 5653 * 4472 3666 2743 4049 6582 4740 * 5310 4159 5368 3853 4365 4745 6220 31
+ 0 * * * * * * 7628 0 0
+
+L 32 4985 5208 * * 5633 * * 5305 * 796 3657 * 6285 6518 * * 2326 7048 * 6636 32
+ 15 * 6560 * * * * 7628 0 0
+
+K 33 5068 6408 4945 * 7113 * 5897 5470 1970 5519 * 3374 * 5132 2228 3606 3561 3510 * 6766 33
+ 16 * 6508 1000 1000 0 * 7617 1012 1012
+
+G 34 4487 * 1669 4409 5538 3762 5105 5717 6553 * * 1722 * * 6213 4347 4722 * 5332 6457 34
+ 63 4889 6818 2000 415 0 * 7619 1212 1003
+
+D 35 4890 * 3297 3577 * 1007 * * 5546 * * 2575 6279 5565 5293 4856 * * * * 35
+ 51 4844 * 659 1447 0 * 7626 1263 1000
+
+R 36 5114 * 5635 3592 * 6220 5397 5006 3088 4177 5292 4943 * 5212 1751 3528 3295 4747 * 5719 36
+ 19 6285 * 1000 1000 * * 7628 1027 0
+
+E 37 5263 6699 6792 2349 4975 * 5513 3966 3560 4616 6946 4927 * 4892 5747 4273 2474 2955 * 4017 37
+ 10 7141 * 1000 1000 * * 7628 1000 0
+
+F 38 4597 5069 * * 2808 * 6343 2331 * 2173 * * * * * 6677 5473 3109 * 2286 38
+ 0 * * * * * * 7628 0 0
+
+R 39 * * 6966 2884 5523 * 3942 3286 4113 4265 * 3607 * 3962 2840 3960 3297 3244 * * 39
+ 18 * 6308 * * * * 7628 0 0
+
+G 40 5423 * * 6042 * 57 * * * * * * * * * * * * * * 40
+ 0 * * * * 0 * 7591 0 1012
+
+V 41 6290 * 6883 5628 4598 * 5135 2921 3095 3656 5477 5517 * 4770 3679 4717 1948 3626 * 5435 41
+ 0 * * * * * * 7628 0 0
+
+L 42 * 6285 * * 3882 * * 3127 * 608 * * 7284 * * 6414 5755 3157 * * 42
+ 0 * * * * * * 7628 0 0
+
+K 43 5904 6905 5504 3521 6764 6582 5936 3165 3259 3245 4225 5624 * 4039 3584 4226 4282 2679 * 5087 43
+ 0 * * * * * * 7628 0 0
+
+S 44 2215 3541 5748 4671 6556 1978 6606 * 6445 5878 6220 4070 * 5732 5866 2555 4579 7168 * 6675 44
+ 0 * * * * * * 7628 0 0
+
+F 45 4906 4624 * * 1815 * * 2928 6883 3837 * 6854 * * 6078 6581 3479 2311 * 3226 45
+ 0 * * * * * * 7628 0 0
+
+D 46 * * 278 3383 * 5878 5589 * * * * 6084 * * * 6209 * 6219 * * 46
+ 69 5687 5188 0 * * * 7628 1059 0
+
+L 47 3807 * 3038 3464 * 3661 6610 5637 3043 7320 6413 3759 4004 3103 3655 3573 6994 4517 * * 47
+ 0 * * * * * 0 7579 0 1129
+
+H 48 4420 6196 4439 * 2476 6937 3078 * * 4716 * 3124 6430 4225 4155 5467 4713 6576 5163 2223 48
+ 26 5814 * 1000 1000 * 0 7579 1038 1129
+
+M 49 5545 3761 * * 3375 4745 * 6682 6534 2816 1374 * 5814 4778 * 4926 4657 4136 4670 * 49
+ 0 * * * * * 0 7579 0 1129
+
+N 50 * * 5478 5814 * 6206 * 6430 * * * 132 * * * 5501 * * * * 50
+ 0 * * * * * 0 7579 0 1129
+
+L 51 * 5591 * * 4776 * * 1937 * 1608 2621 * * * * * 4915 2664 * * 51
+ 0 * * * * 916 1089 7579 0 1129
+
+V 52 4820 4680 6371 * 6704 * 5490 2956 4924 3520 5024 6080 * 4808 6330 4547 4213 1236 * 5805 52
+ 0 * * * * 0 * 7591 0 1012
+
+L 53 * * 6078 * 5139 * * 3766 5433 431 3384 * * * * * * 6614 * 6308 53
+ 18 6343 * 1000 1000 * * 7628 1011 0
+
+N 54 4442 6454 3283 2346 6833 4293 * * 2878 6582 * 4775 * 5207 3560 3020 3258 4265 * 6854 54
+ 18 6343 * 1585 585 * * 7628 1011 0
+
+D 55 6526 6535 1482 3144 * 6341 4808 * 3884 * * 2188 6300 3909 * 3818 6645 6400 * * 55
+ 0 * * * * * 0 7600 0 1011
+
+A 56 1893 2571 5181 5698 6400 6229 * 6839 5370 6404 6447 6355 * * * 5797 3247 1802 6373 * 56
+ 17 * 6404 * * * 0 7600 0 1011
+
+E 57 * 6597 3528 3404 4575 * 4955 3258 3251 6514 6954 5717 * 4729 4732 3896 2625 2994 6514 4454 57
+ 15 * 6630 * * * 0 7580 0 1103
+
+E 58 6516 5469 3844 1158 5562 6238 * 3776 4829 4352 5558 6333 * 4735 4501 * 5463 3722 * 4523 58
+ 28 * 5717 * * * 0 7570 0 1187
+
+L 59 * 6885 4677 4045 3958 6791 6623 4360 3926 3828 4730 6243 * 4589 3131 3999 2361 3671 6401 3849 59
+ 86 7100 4305 1000 1000 1583 586 7548 1000 1324
+
+E 60 5036 * 3401 4242 4428 5528 4991 2685 4065 4402 6574 5567 6586 4102 3716 4136 3687 4363 3928 4849 60
+ 383 2249 5470 1798 489 1988 419 7523 2580 1598
+
+D 61 3934 * 2858 3389 6559 5020 5429 6079 2761 5272 5260 4508 4534 5274 3520 4067 3292 5500 * 4706 61
+ 295 2437 * 3073 182 1961 428 7498 2331 1603
+
+G 62 4093 * 2652 3485 * 1929 6492 6220 4172 6402 6467 3615 5333 6023 4890 3373 4412 * 6272 6026 62
+ 300 2500 6472 3200 166 2347 316 7528 2223 1429
+
+E 63 4709 6282 5088 2674 * 2631 5154 5169 3425 6481 4501 3392 5371 3575 5072 4505 3761 5368 6804 6267 63
+ 212 2872 * 2081 389 265 2573 7536 1949 1407
+
+V 64 4917 6183 4080 2432 5075 4123 4019 * 2896 4632 6677 4328 * 3530 4229 3709 4094 6032 6213 5497 64
+ 62 5067 6344 692 1392 * 0 7588 1178 1096
+
+T 65 5248 * 4392 4833 4763 5612 6134 3601 2965 4623 5415 5383 3232 4480 3621 3591 3258 3307 * * 65
+ 14 * 6669 * * * 0 7563 0 1189
+
+R 66 5003 6702 5519 3604 5741 4505 4566 4087 3589 4370 * 4354 6426 * 1941 4108 3995 3316 5811 * 66
+ 20 6187 * 1000 1000 892 1117 7565 1007 1271
+
+R 67 5136 * 5308 3905 4147 5377 3747 4942 2868 4541 * 4373 3880 5482 3702 3296 4033 4403 * 3529 67
+ 16 * 6538 * * 1012 988 7619 0 1076
+
+L 68 4817 6645 * 4591 3803 6789 6766 2601 5572 1593 4008 6343 6767 * 6878 5136 * 3301 6416 3792 68
+ 18 * 6307 * * 0 * 7610 0 1076
+
+G 69 4998 * 3572 4732 * 1554 6521 * 5307 6398 6572 4018 2635 4230 4333 3175 * * * 6443 69
+ 0 * * * * 0 * 7598 0 1011
+
+T 70 4986 5272 4613 3094 5844 * 6656 5524 3774 2272 3737 4499 * 3774 3665 4074 4065 4304 * 6101 70
+ 0 * * * * * * 7551 0 0
+
+V 71 4200 3224 * 6682 5087 * 6739 2389 * 2956 3686 * * * 6385 5479 5869 1782 * 4310 71
+ 15 6571 * 0 * * * 7551 1000 0
+
+L 72 5844 * * * 1629 * 6812 3704 * 2062 3498 6101 * * * 4544 5254 2921 * 5060 72
+ 0 * * * * * * 7551 0 0
+
+I 73 * 5632 * * 5659 * * 1267 * 2117 5663 * * * * * * 1765 * * 73
+ 0 * * * * * * 7551 0 0
+
+R 74 * 6452 * * * * 4948 * 2851 * 6351 4148 3527 4956 782 5266 6360 6605 * * 74
+ 0 * * * * * * 7550 0 0
+
+G 75 4984 5296 * * * 230 * * 6360 6518 * * * * 5195 4648 * * * * 75
+ 0 * * * * * * 7550 0 0
+
+D 76 4675 6683 2484 3047 * 5576 5212 6644 4210 * * 2034 6525 6299 4861 2470 4444 6517 * * 76
+ 0 * * * * * * 7550 0 0
+
+N 77 6335 5314 5395 4267 6463 6691 4014 * 5497 5684 5936 1796 6506 3063 5281 2399 3955 5456 * 5333 77
+ 19 6222 * 0 * * * 7547 1007 0
+
+I 78 * * * * * * * 1052 6222 4838 6278 * * * * * 5449 1206 * * 78
+ 0 * * * * * * 7547 0 0
+
+V 79 4825 5495 * 5051 5857 5903 * 3098 3654 3490 6302 6492 * 5632 2581 4012 3951 2047 * 6211 79
+ 0 * * * * * * 7522 0 0
+
+Y 80 4986 5510 6289 4233 3152 6454 6787 6503 4854 2426 3333 5787 * 6036 * 3067 4621 4409 6719 2584 80
+ 0 * * * * * * 7512 0 0
+
+I 81 6337 5460 * * 4205 * * 1185 * 3320 4853 * * * * * * 1629 6266 * 81
+ 0 * * * * * * 7488 0 0
+
+S 82 5498 5210 * 3548 5334 4476 4338 3241 4454 5548 * * * 3154 2934 2388 3060 5699 * * 82
+ 0 * * * * * * 6533 0 0
+
+P 83 4048 * * 4033 * * * * 3590 3881 * * 726 * * 4135 3917 * * * 83
+ 0 * * 0 * * * 4687 0 0
+
+//
+�HHsearch 1.5
+NAME ee520d2fc85e5b54c5cab5b1125d8c3b
+FAM
+FILE ee520d2fc85e5b54c5cab5b1125d8c3b
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:18:01 2013
+LENG 249 match states, 249 columns in multiple alignment
+FILT 126 out of 1136 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CHHHHHHHHHHCCCEEEEECCCCCHHHCCCCCCCCCCHHHCCCHHHHCCHHHHHCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEEEECC
+CHHHHHCCCCCEEEECCCCCEEEECCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHH
+HHCCCEEEEECCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHHCCCCCC
+>ss_conf PSIPRED confidence values
+9689999998599889998876145328997678872444169998707886750999999999999988602799999999999997099659998430
+2266664887679944750001876789763368874267798773467756675887689799999999999985499999989997657699999999
+8679869998699878885420999488999999999999764185159
+>Consensus
+xxxxxxxxlxxaxxivixxGAGiSxxsGipxfrxxxxxxxxxxxxxxxxxxxxxxxpxxxxxxxxxxxxxxxxxxPnxxHxxLxxLxxxxxxxxviTqNi
+DxLxxxAGxxxvxelHGxxxxxxCxxCxxxxxxxxxxxxxxxpxCxxCggxlrpxvvxfgexxxxxxxxxaxxxxxxxdlxlvlGtslxvxpxxxlxxxx
+xxxxxxxixiNxxxxxxxxxxxxxixxxxxxxlxxlxxxxxxxxxxxxx
+>ee520d2fc85e5b54c5cab5b1125d8c3b
+MDEKLLKTIAESKYLVALTGAGVAAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNV
+DDLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADVIIVAGTSAVVQPAASLPLIV
+KQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALSLKLN
+>gi|306827305|ref|ZP_07460592.1| SIR2 family protein [Streptococcus pyogenes ATCC 10782]gi|304430452|gb|EFM33474.1| SIR2 family protein [Streptococcus pyogenes ATCC 10782]
+--EQLAQLIKEADTLVVGIGAGMSAADGFTYIgprfETAfPDFIAKYQFLDMLQASLFdFEDWQEYWAFQSRFVALNYlDQPVGQSYLDLKEILETK-DY
+HIITTNADNAFWVAgYdPHNIFHIQGEYGLWQCSQhCHqQTYKDDTVIRqmiaeqknmkvPGqLIPHCPECEAPFEINKRNEEKgMVEDADFHAQKARYE
+aflsehkeGKVLYLEIGvghtTpQFIKHPFWKRVSE--NPNALFVTLNHKHYRIPLsirRQSLELTEHIAQLISATKTIY---------
+>gi|259485388|tpe|CBF82370.1| TPA: conserved hypothetical protein [Aspergillus nidulans FGSC A4]
+--KTARSWLEQADYLIISAGAGLSAATGL-DYTSTD-LFANYfpaflplGLRRLYDVFGFSgwKSPAQKWGYYFHHLNMVKTWPKSPLYASLLEITSrFG
+PRCFVRTSNADGLFLANGfhPSRISTPQGQYAYLQCFaKCKReaVFPSAPFLtaalpfldsqtqlltDESKIPRCRYCSGELTLCVRggdYFNDSPFqgQ
+ErEYArfleHVSSEIeqGRSAVILELGVGMNTpsvlrWHNEELVEES-NGGSRLIRAGFDAAGcvpWRlaeEGVAVGVAGELNAVVDLLRG---------
+--
+>gi|71279737|ref|YP_269579.1| hypothetical protein CPS_2874 [Colwellia psychrerythraea 34H]gi|71145477|gb|AAZ25950.1| putative membrane protein [Colwellia psychrerythraea 34H]
+-----------AKQCVAITGSGIRKG-TLPDY--PSGQWLDPkVPItsyTLAEFKASKRCRYLYWKASYDYYQQALTINKNNIDEQLDYLLNHY-LSGLF
+TETVDSLFNTE-QHPVYECYGSIKRLYCLDCAKQQAWPPIPLwSQRDLHCQHCSGLLKPQILAADENIDSECYQALQKNMMECGCLLVIGVPTITPVVSM
+IIENANANKIPIIFIGTIPFGYfVEEKDVQLTGDIAHWLAEING-----------
+>gi|290978128|ref|XP_002671788.1| Sir2 NAD-dependent protein deacetylase [Naegleria gruberi]gi|284085360|gb|EFC39044.1| Sir2 NAD-dependent protein deacetylase [Naegleria gruberi]
+--EKAAQLIYNSKYLLITCGAGFSKDSGLAVYKDIasNPIYQEknLTYHDLARPVStFETEQEllDYYGFWVNCAQSYLNTPSHSGYQILKDWKQLlysk
+keiqkefnekqieilsasqwwkenckiASNMFIYSSNVDNHFSRYFeKEEIYNIHGHALNWQCGNhCNEDCVWNFtkqLQniiiNqetlqidneKLKELK
+CEKCQHASMPNVLMFGDLGQyirnteEEdryiAWECSVETFSKesstkfPFIILELGCGLTVPSVRRENECVLldCDESYLIRVNLGQEELDTihnvdli
+pmknDRILNIKNGCQDALHRIHQHLLK-------
+>gi|125973113|ref|YP_001037023.1| hypothetical protein Cthe_0595 [Clostridium thermocellum ATCC 27405]gi|256003907|ref|ZP_05428893.1| hypothetical protein ClothDRAFT_3012 [Clostridium thermocellum DSM 2360]gi|281417305|ref|ZP_06248325.1| hypothetical protein Cther_1977 [Clostridium thermocellum JW20]gi|125713338|gb|ABN51830.1| hypothetical protein Cthe_0595 [Clostridium thermocellum ATCC 27405]gi|255992035|gb|EEU02131.1| hypothetical protein ClothDRAFT_3012 [Clostridium thermocellum DSM 2360]gi|281408707|gb|EFB38965.1| hypothetical protein Cther_1977 [Clostridium thermocellum JW20]gi|316940661|gb|ADU74695.1| hypothetical protein Clo1313_1634 [Clostridium thermocellum DSM 1313]
+-------------------------------------------------------------------------TYSKEVEKLIRFFIEnrl--EYTGFLV
+LNWDTVLEKYisaiapkaiidycnggryltedlrfeekrdgkRKVEILKVHGSCNWLYCDNCRilindtvsrvpnirkvgfkksdfklfdemkkvtdkvf
+f------------EDVRCFICGDIVSAHIAtqsyrkSFRTNsFP-SIWDKAEDMLTNSEKWVFIGYSLPQadYEFKHLLKicehk---lghkkDRRlsid
+----VVlfd--SETTAM-------------------------------
+>gi|37526595|ref|NP_929939.1| hypothetical protein plu2704 [Photorhabdus luminescens subsp. laumondii TTO1]gi|36786027|emb|CAE15078.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii TTO1]
+-----------QGHVVFFCGAGISLAkAKLPNFFQLaQKVIDLLGTTNdSQARQLYDFlnkglkdkegnevalpsyaStlisTDRIfslleqeFETNLIE
+KTVAQVlkpsdTVDTSAHKLLLDLATTseG-RVQLITTNFDRLFNDCSlTeipcflppnlpdlskneliDGLVYLHGR--snsdY---------------
+----------------------------------------------------------------------------------------------------
+-------------
+>gi|333913474|ref|YP_004487206.1| hypothetical protein DelCs14_1828 [Delftia sp. Cs1-4]gi|333743674|gb|AEF88851.1| hypothetical protein DelCs14_1828 [Delftia sp. Cs1-4]
+---------------MWFLGAGASAAAGIPTagdmiweFKqklfvSQRraspemvadlsaPSVRQ-HLQSHIDSTSsLpaEGAPNEYSVIFEkvfpaeaD
+RRAYldakLSGAKPSYGHMALAALMKADHTRIVWTTNFDPLVADAcakvfdgtGALTSVAFGVgPEIARKAMA---------------------------
+------------------------------------------------------------------------------------------------
+>gi|69245855|ref|ZP_00603672.1| conserved hypothetical protein [Enterococcus faecium DO]gi|257882009|ref|ZP_05661662.1| conserved hypothetical protein [Enterococcus faecium 1,231,502]gi|258615570|ref|ZP_05713340.1| hypothetical protein EfaeD_07652 [Enterococcus faecium DO]gi|293563462|ref|ZP_06677910.1| USG protein [Enterococcus faecium E1162]gi|294620826|ref|ZP_06700030.1| USG protein [Enterococcus faecium U0317]gi|314947730|ref|ZP_07851137.1| conserved hypothetical protein [Enterococcus faecium TX0082]gi|68195557|gb|EAN09999.1| conserved hypothetical protein [Enterococcus faecium DO]gi|257817667|gb|EEV44995.1| conserved hypothetical protein [Enterococcus faecium 1,231,502]gi|291599611|gb|EFF30624.1| USG protein [Enterococcus faecium U0317]gi|291604464|gb|EFF33950.1| USG protein [Enterococcus faecium E1162]gi|313645710|gb|EFS10290.1| conserved hypothetical protein [Enterococcus faecium TX0082]
+------------GNAAIFAGAGLSMSQGYVSWPELlNDPATEigLDSkkeTDLVTLAQYYKNenggsRGILNQILMDN--FGEELEISENHRILASL---
+-PIETYWTTNYDHLIEKSIreayknpqvkknytqlattnpnvDTIVYKMHGDIDDVS-------------------------------------------
+-----------------------------------------------------------------------------------
+>gi|84686801|ref|ZP_01014688.1| hypothetical protein 1099457000266_RB2654_22528 [Maritimibacter alkaliphilus HTCC2654]gi|84665232|gb|EAQ11711.1| hypothetical protein RB2654_22528 [Rhodobacterales bacterium HTCC2654]
+-------------------------------mvkFKwclendrSIDdptvtraSYWPWLLKQHWFDQdknlaDLYpsavkhllnvSEDRRQ---FFKALI
+--NPAVDPREGYLGLAEILHQRWVTTILTTNFDECLQKAKNmvgrphqitsiktasdlvmfsssprdPQLIYLHGSVDHYT-------------------
+----------------------------------------------------------------------------------------------------
+-------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * * 567 * * * * * * 1621 * * 1
+ 0 * * * * * * 2162 0 0
+
+D 2 * * 1032 * * * * * * 1908 * * 2032 * * * * * * * 2
+ 0 * * * * * * 2820 0 0
+
+E 3 3555 * 3071 1774 * 4619 * * 3005 * 5279 5287 * 5341 2812 3802 5148 5648 * * 3
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+
+K 4 4424 * 3096 3319 6028 * 6096 5883 2296 * * 5128 6045 2643 2503 5858 3765 6085 * * 4
+ 44 6045 6085 2018 409 * * 7368 1078 0
+
+L 5 2014 6342 * 5961 3748 6349 * 3734 * 1233 * * * * * * 6017 3307 * 5637 5
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+
+L 6 1847 * 4904 5080 * 6286 6242 3303 3186 3522 4463 * * 4432 3143 * 5965 3324 * 6165 6
+ 0 * * * * * 0 7545 0 1000
+
+K 7 4639 6236 2909 1799 * 5008 5318 * 3570 5981 * 4184 * 3313 3623 3651 4605 6333 * * 7
+ 23 * 5992 1585 585 * 0 7577 1000 1000
+
+T 8 3481 6582 * 6133 4127 * 6624 3427 4119 1777 3459 * * 4371 5151 5589 4754 4750 3136 * 8
+ 45 5020 * 2864 213 873 1140 7612 1257 1109
+
+I 9 5155 4928 * * 4875 * 6555 1527 6283 1080 6562 * * * * * * 4292 * * 9
+ 0 * * * * * 0 7556 0 1000
+
+A 10 3123 * 4130 3123 * 6035 5238 * 2177 3942 * 4122 * 3117 2686 * 4885 * * 5421 10
+ 15 6554 * 1338 727 0 * 7574 1079 1000
+
+E 11 4239 * 3614 2252 * 4573 * 6983 3400 6674 * 3178 6313 2927 3393 3876 3810 * * 6410 11
+ 78 5249 5260 1392 692 * * 7569 1150 0
+
+S 12 1226 5352 5376 * * 4586 4417 5203 4727 * * 5146 4960 4648 6982 1999 * * * 6345 12
+ 106 3824 * 2084 388 0 * 7640 1503 1127
+
+K 13 6605 * 2170 3297 * 3115 4954 * 2179 * * 4071 4396 3984 3575 5734 5360 * * * 13
+ 35 5385 * 1367 708 * * 7876 1190 0
+
+Y 14 2952 4464 6727 4964 5280 5984 3622 * 2966 4489 * 2676 6793 3956 2980 4822 4773 6468 * 4353 14
+ 10 7155 * 1000 1000 * * 7892 1000 0
+
+L 15 4023 4800 * * 4554 6476 * 1983 * 1983 6207 * 5223 * * * 3530 2211 * * 15
+ 12 * 6923 * * * * 7898 0 0
+
+V 16 3843 6103 * * 6100 6368 * 2787 * 2008 4988 * * * * 6073 4698 1342 * 5944 16
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+
+A 17 3255 5270 * * 3040 * * 1778 * 3036 6105 * * * * * * 1868 4453 * 17
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+
+L 18 5269 * * 6412 2105 2815 4611 2833 * 1898 6607 * * * * 4891 4806 4301 * 7011 18
+ 8 * 7452 * * * * 7940 0 0
+
+T 19 2397 4117 * * * 4628 * 3517 * 3377 * * * * * 3092 1495 4149 * * 19
+ 0 * * 0 * 0 * 7939 1000 1000
+
+G 20 5315 * * * * 120 * * * * * * * * * 4192 * * * * 20
+ 0 * * * * * * 7940 0 0
+
+A 21 426 6412 * * * 6511 * * 5899 * * 3551 5207 * 6063 3651 6758 * * * 21
+ 0 * * * * * * 7940 0 0
+
+G 22 5899 * * 5042 * 108 * * * * * * * * 6660 * 6036 * * * 22
+ 0 * * * * * * 7940 0 0
+
+V 23 4294 5299 * * 4419 * * 1624 * 1769 3283 * * * * * 4374 3210 * * 23
+ 0 * * * * * * 7940 0 0
+
+A 24 4385 * 6307 * * 6180 * * * 6893 * * * * 5136 265 5203 6141 * 6021 24
+ 0 * * * * * * 7940 0 0
+
+A 25 1746 * * * 6791 * 7042 3952 3837 5322 4500 6248 * 4751 5595 5337 2318 2501 * 6870 25
+ 15 6572 * 1000 1000 * * 7940 1000 0
+
+E 26 1838 6476 3035 2528 * 4109 7452 * 6572 7134 6304 5400 4324 5352 * 2363 5201 * * * 26
+ 35 6530 6213 0 * * * 7940 1000 0
+
+S 27 2005 5610 5266 4041 * 4776 * * * 7191 * * * 5212 6010 1011 5011 5024 * * 27
+ 54 * 4763 * * 0 * 7902 0 1026
+
+G 28 * * 6099 * * 154 * * 5616 * * 4807 * * * * 6111 5959 * * 28
+ 0 * * * * 694 1388 7845 0 1305
+
+I 29 7116 5864 * * 4491 6328 * 1243 * 1606 5167 * * * * * * 3568 * 4165 29
+ 39 * 5243 * * * 0 7896 0 1050
+
+P 30 5002 * 4167 * * * 6472 5942 6733 * 6107 3342 653 6881 5769 4375 5622 4984 * * 30
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+
+T 31 4689 6911 1518 5947 4813 * 6560 5257 5888 4347 6244 4536 5593 * * 4696 1889 5215 6224 5427 31
+ 173 3228 7316 2405 302 382 2103 7876 1993 1321
+
+F 32 6727 * * * 891 6481 * 5361 * 4429 4996 * * * * 6716 * 7006 3499 2107 32
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+
+R 33 4154 * 6552 3321 6485 6664 6392 * 3210 * 6464 5003 6636 6665 996 4122 4387 6446 6427 * 33
+ 106 3960 7182 2504 280 * 0 7914 1569 1306
+
+G 34 5415 * 3005 3227 * 2025 6415 * 3347 5757 * 5312 * 4442 6383 2080 4548 * * 6864 34
+ 0 * * 2322 322 620 1517 7919 1000 1405
+
+K 35 3184 6653 3813 3907 * 6200 5625 4738 4261 2719 5096 4422 2874 4068 5762 3497 4635 5408 * 5369 35
+ 565 1674 6564 926 1078 0 * 7954 3691 1073
+
+D 36 5695 * 2507 3899 5880 2362 4595 * 4408 * * 2564 6601 3749 3894 3770 5981 5623 * 7114 36
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+
+G 37 4165 * 2473 3586 * 1350 * * 5132 6830 * * 3236 5223 7109 4459 7088 5518 * 4772 37
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+
+L 38 4837 * 5716 5811 2991 * 6067 2488 6014 1969 5432 6935 6653 6218 5364 5250 4918 2839 7128 4235 38
+ 29 7113 6270 0 * * 0 7942 1006 1091
+
+W 39 3740 * * 5891 4100 6507 * 3862 5662 4549 5444 7116 6955 6289 4889 4953 * 3973 1674 2227 39
+ 0 * * 1585 585 1729 518 7916 1000 1224
+
+N 40 3439 * 3343 3139 6964 5887 * 5764 2752 4861 6752 3993 5792 3421 3246 3649 3422 7016 * * 40
+ 160 3975 4604 1980 422 1237 796 7918 1733 1124
+
+R 41 4148 * 3644 3249 6398 4126 * 5485 2346 4875 * 3253 * 3915 2546 6132 5152 5476 5112 * 41
+ 366 2873 3514 2027 406 1543 606 7894 2275 1529
+
+Y 42 5006 * * 5869 3141 * 4543 4486 5912 2878 5754 5756 4592 5798 4556 5134 5132 4217 * 1521 42
+ 344 2348 6000 2935 202 350 2215 7812 3019 2203
+
+R 43 4745 * 2414 4645 7027 2604 4371 5893 4352 6840 * 3557 4218 3821 3971 3404 4860 5096 * 6853 43
+ 97 4192 6609 1003 997 1775 499 7883 1578 1343
+
+P 44 3307 5910 5403 6486 3472 5944 6664 3703 4724 3297 4723 5551 2003 6906 6563 5067 4155 3830 * 5006 44
+ 133 4274 4786 2121 377 1584 586 7910 1425 1414
+
+E 45 4371 * 4157 2505 5269 * 4208 3682 3300 4816 5858 4560 6375 3860 3166 3613 4385 5225 7175 6749 45
+ 85 4573 6047 1179 841 1129 882 7916 1321 1725
+
+E 46 3600 * 2501 2562 * 5033 6861 6960 3983 5158 6080 3957 5749 4737 4128 3326 3200 6776 * 5446 46
+ 129 3869 5875 2179 360 2885 210 7886 1724 1606
+
+L 47 4297 * * * 3699 7005 5414 2512 6750 2061 3285 * 5920 5657 5819 4602 5289 3019 5224 4539 47
+ 22 7321 6764 0 * 2438 294 7868 1000 1717
+
+A 48 2576 4823 6127 5221 2309 5204 6796 4092 4889 2496 5572 6763 * 5324 5977 4266 5024 4622 6429 4561 48
+ 58 5733 5610 2000 415 2090 386 7900 1076 1769
+
+N 49 3779 * 2557 2343 * * 7112 5643 5379 6223 * 3518 * 3734 5679 2686 2750 * * 6722 49
+ 51 6631 5332 2807 222 2980 196 7883 1000 1757
+
+P 50 2951 * 5733 6049 3835 2940 5423 4039 6094 3948 5576 6717 2715 6851 3636 3709 4398 4756 7313 4890 50
+ 58 5119 6512 1916 444 * 0 7840 1225 1894
+
+Q 51 3722 6423 3054 4061 4518 5785 5104 5722 3681 4601 4167 5385 5160 4217 4769 3234 3266 3711 6872 6641 51
+ 55 6292 5357 2000 415 1785 494 7820 1000 1997
+
+A 52 3028 5716 5371 6369 2633 3362 7257 * * 3442 4599 5420 * 4224 4546 3364 3881 4911 4686 3899 52
+ 155 3837 4963 285 2479 1981 422 7851 1595 1981
+
+F 53 * * 5777 7045 1320 6991 5344 6252 6201 2903 4513 * 5719 6550 5476 5433 5467 4512 5036 2602 53
+ 523 1838 5359 1289 760 297 2427 7838 3339 2003
+
+A 54 4534 * 4808 3478 3874 6909 5003 6195 3575 4008 * 4113 4893 3823 3011 3741 4764 4314 5611 3390 54
+ 57 4679 * 2718 238 1757 506 7882 1369 1355
+
+K 55 4326 * 4056 2691 6532 4134 4610 6500 3664 5661 6290 4196 4563 4601 2703 4092 3170 5767 5365 * 55
+ 55 4751 * 3027 189 * 0 7910 1268 1219
+
+D 56 4218 5337 1977 4459 5877 6506 4510 5898 4768 6349 * 2651 * 4292 3872 3544 3519 6441 * 5543 56
+ 145 3541 6678 1353 717 * 0 7910 1803 1219
+
+P 57 4905 * * 4108 6871 6984 * 5989 3814 4068 6824 * 1107 5333 2985 4925 4549 * 5418 5486 57
+ 38 5778 6984 2551 270 1000 1000 7906 1157 1320
+
+E 58 3175 * 3320 1907 * 4686 7041 6785 3278 5290 6973 4777 6910 3752 3798 5341 4115 5115 7346 5494 58
+ 94 5219 4796 5233 39 * 0 7925 1229 1215
+
+K 59 5252 * 4738 2217 6359 6308 6801 4596 3773 2954 5421 6012 4624 3379 3765 3946 6100 3703 * 4693 59
+ 57 6246 5303 0 * 3445 139 7926 1029 1739
+
+V 60 4317 5382 * * 2279 * 6202 4125 3556 3879 6816 6804 * 4332 6485 6249 5359 2781 6713 2153 60
+ 48 5431 6683 2343 317 3483 135 7875 1204 1970
+
+W 61 4787 * * 6905 3832 6615 4356 6435 6833 4070 7120 5030 * 6842 6445 5315 5655 5243 1236 2378 61
+ 0 * * * * 3693 116 7871 0 1958
+
+K 62 2332 * 4350 2581 * 3022 5709 * 3331 6289 5394 4039 * 3426 4783 3980 4978 5522 * * 62
+ 28 6577 6795 2322 322 2141 371 7866 1000 1880
+
+W 63 4472 7002 * 5679 1545 * 7343 4404 5047 4056 4294 * * 5689 3744 6896 6457 3934 3790 2850 63
+ 10 * 7128 * * * 0 7893 0 1771
+
+Y 64 4288 5997 5618 5718 2410 6715 4650 4611 7025 3442 4695 5678 * 5424 * 4488 5488 5160 3340 2055 64
+ 47 6678 5496 2585 263 3151 172 7878 1000 1876
+
+A 65 2896 7034 6527 2734 5784 4330 6033 5698 3341 4250 6603 4237 * * 2667 3265 4855 4402 6070 5521 65
+ 103 4164 6252 2670 247 2038 403 7893 1421 2013
+
+W 66 3854 * 3007 3035 6647 5596 5398 4340 3209 5967 6744 4246 6907 3961 2789 4300 4977 5594 4730 4780 66
+ 41 7033 5637 0 * 3642 120 7886 1000 1932
+
+R 67 5427 6522 5864 3598 4069 4961 4914 3560 4772 2555 4260 4899 * 5666 2061 6237 6414 6505 7020 4037 67
+ 150 3856 5082 1872 460 913 1092 7894 1829 2117
+
+M 68 3839 * * 5589 3649 7219 5826 2429 4752 2852 5270 * 6831 5409 2408 4626 5346 4459 5404 3984 68
+ 233 5084 3064 2121 377 2175 361 7849 1174 1758
+
+E 69 3612 6155 3426 3579 * 5927 4250 5867 3220 4181 6596 3888 4350 3239 3110 4803 4655 7040 6760 4724 69
+ 58 4655 * 1606 575 372 2136 7646 1363 2771
+
+K 70 4761 6473 4352 4164 3832 4468 * 5215 5755 2564 4322 3653 5415 4476 4277 4524 3828 4664 6444 3280 70
+ 361 2398 4985 1215 813 761 1287 7878 2743 1485
+
+V 71 3738 4046 6998 7077 3866 4775 6847 2801 4849 3144 4558 4663 5119 5318 4437 6904 3426 3750 6278 3763 71
+ 41 5589 7077 327 2303 679 1413 7855 1228 1533
+
+F 72 4204 * 4898 3877 3827 5019 5323 4107 4235 3065 * 4582 3923 3739 3408 3682 4742 5930 5471 4150 72
+ 121 3639 * 426 1967 714 1357 7922 1750 1233
+
+N 73 4619 * 2657 2951 7451 3661 4816 5880 3374 4692 6448 3376 6053 4769 3591 4099 4480 5088 * 5383 73
+ 58 4669 * 2162 365 * 0 7891 1322 1151
+
+A 74 1507 5137 7483 5556 5779 4972 6991 4552 3452 3805 6442 5872 5848 5161 6624 4913 3809 3876 4996 4591 74
+ 9 7337 * 0 * 0 * 8900 1000 1151
+
+Q 75 4361 * 6705 2516 6072 6367 5732 6684 1983 4473 * 5030 3326 3555 4237 4331 4780 4894 * 5302 75
+ 0 * * * * * * 8934 0 0
+
+P 76 4548 * 5965 5712 7399 6454 * 4551 5591 5836 * * 520 6432 * 5344 5003 4468 * 6137 76
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+
+N 77 5435 7168 5396 * * 3925 4224 6521 6083 6539 6562 1414 5013 * 5326 2417 2689 * * 7310 77
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+
+K 78 2961 * 4282 3038 5861 * 6068 5422 3646 3759 * 4766 2591 4429 3406 4586 5150 5407 6014 4762 78
+ 33 6609 6310 1000 1000 * * 8944 1017 0
+
+A 79 1936 * 6525 6431 5273 2386 7117 4128 * 3686 * 5805 5077 6430 * 4138 2984 3236 6863 * 79
+ 16 6525 * 1000 1000 782 1256 8938 1004 1132
+
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+
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+
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+
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+
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+
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+
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+
+R 88 4256 6531 3329 2991 * 4134 4426 6347 2235 5994 * 4117 5825 3145 4130 4065 3997 * * * 88
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+ 131 4056 5226 2879 211 2787 226 8825 1716 2194
+
+G 90 5341 5667 4532 4902 5878 1513 7319 * 2694 5700 5518 3433 6794 5975 4403 5024 5541 4933 7173 4239 90
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+
+V 91 6418 * 6661 5548 6773 4156 5145 4435 2297 3329 * * 3154 4263 2950 4130 5356 4669 5500 3688 91
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+
+L 92 * * 2922 4073 7064 4415 * 2714 5222 2312 * 3794 4598 5600 4244 4253 4527 3622 * 6682 92
+ 33 6817 6197 476 1832 1218 810 9040 1149 1379
+
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+ 9 7266 * 0 * 2369 310 9034 1018 1379
+
+C 94 5475 5922 7208 * 2066 3689 4156 4680 5964 3795 5719 5944 6086 5609 2651 4823 3091 4898 6262 5278 94
+ 0 * * * * 1787 494 9031 0 1286
+
+L 95 5141 5358 * 7217 4963 * 5114 1800 * 2874 7000 5319 * * * * 6445 1343 * 5848 95
+ 0 * * * * * 0 9030 0 1173
+
+I 96 5214 * * 6476 4436 * 6816 1764 6830 2430 5792 * * * 6787 * * 2108 4061 3337 96
+ 0 * * * * * 0 9030 0 1173
+
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+
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+
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+
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+
+D 101 * * 124 5017 6424 6526 * * * * * 5741 * * * * * * * 6594 101
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+M 233 6593 5529 * * 2954 * * 3447 * 878 4291 * * * * 5493 * 3122 6062 * 233
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+
+D 234 3239 6580 4493 2529 * 4823 4518 * 4067 4262 * 4999 2219 4846 3368 3865 6472 5834 * * 234
+ 42 6825 5675 782 1257 0 * 8334 1099 1024
+
+E 235 3836 6635 3463 2740 6274 5038 4843 5077 2518 4316 5265 4500 5490 3877 3407 * 4852 5371 * 4904 235
+ 21 6109 * 1093 912 0 * 7820 1124 1098
+
+L 236 4535 * * * 6402 * * 2516 * 923 3598 * * * * * 6259 3231 5294 6037 236
+ 54 5395 6264 969 1032 * * 8350 1180 0
+
+V 237 2962 4192 4776 5105 6022 6982 5037 3833 4639 2315 4301 5897 * 4238 3928 5080 * 2695 * 5963 237
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+
+R 238 3152 5660 3113 3409 * 3633 * * 2807 * * 3557 6402 3399 2771 4414 4790 6222 * * 238
+ 82 4857 5598 1871 461 * * 7482 1066 0
+
+H 239 3000 * 4748 3141 * * 4122 3810 3996 3031 5504 5477 4717 2854 3308 5618 4455 5446 * * 239
+ 30 5627 * 0 * * 0 7041 1000 1000
+
+V 240 * 5431 5610 * 4307 * * 3066 * 1279 3096 5174 * * 5574 4933 5297 3349 * 4256 240
+ 86 4111 * 1585 585 0 * 6772 1002 1000
+
+R 241 * * * * * 1978 * 3265 3263 2498 4233 * 4261 * 3282 3390 4122 * * * 241
+ 0 * * * * * * 5127 0 0
+
+K 242 * * * 1983 * 3051 * * 1892 * * * 2940 2141 * * * * * * 242
+ 0 * * * * * * 3931 0 0
+
+A 243 2668 * * 1516 * * 2841 * 2631 2382 * * * * * * * * * * 243
+ 0 * * * * * * 3192 0 0
+
+L 244 2841 * * * * * * 2631 * 2668 2382 * * * * 2584 * * * 2450 244
+ 575 1605 * 3000 193 * * 3192 1005 0
+
+S 245 * * 1024 * * * * * * * * * * * * 976 * * * * 245
+ 0 * * * * * * 1610 0 0
+
+L 246 * * * * * * * * * 0 * * * * * * * * * * 246
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+
+K 247 * * * * * * * * 0 * * * * * * * * * * * 247
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+
+L 248 * * * * * * * * * 0 * * * * * * * * * * 248
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+N 249 * * * * * * * * * * * 0 * * * * * * * * 249
+ 0 * * 0 * * * 1000 0 0
+
+//
+�HHsearch 1.5
+NAME f038453661ad6048b85e5011b6e6296a
+FAM
+FILE f038453661ad6048b85e5011b6e6296a
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:31:50 2013
+LENG 243 match states, 243 columns in multiple alignment
+FILT 229 out of 1408 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.4
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCEEEEEEECCCEEEEEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCCCCEEECCCCCCCCCCEE
+EEEEECCCEEEEEECCEEEEEECCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHCCCHHHHHH
+HHCCCCCCCCCCCCCCEEEECCEEEEEECCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9346893778999845212239999999159994089899851687677889887688998234488677689969989877873366179986568199
+9999928979999999999998443268999872699997627774446888876698589998999995789987222988744557652899999986
+3563636543456675698899999997788832421068899
+>Consensus
+xxxxxxxtsxxixSxxxxxyGxxEaRiKxpxxxGxxxAfwlxxxxxxxxxxxxxxEIDIExxGxxxxxxxtnxxxxxxgxxxxxexxxxxxxdxxxxfHt
+YxieWxpxxIxfyVDgxxvxxxxxxxxxxxxxpmxlixnlwxxxxxxxxGxxdxxxxPxxmxVDyVrvyxxxxxxxxxcxxxxxxxxxxxxxxnxxxxxx
+xxxxxxxnxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+>f038453661ad6048b85e5011b6e6296a
+MVSAKDFSGAELYTLEEVQYGKFEARMKMAAASGTVSSMFLYQNGSEIADGRPWVEVDIEVLGKNPGSFQSNIITGKAGAQKTSEKHHAVSPAADQAFHT
+YGLEWTPNYVRWTVDGQEVRKTEGGQVSNLTGTQGLRFNLWSSESAAWVGQFDESKLPLFQFINWVKVYKYTPGQGEGGSDFTLDWTDNFDTFDGSRWGK
+GDWTFDGNRVDLTDKNIYSRDGMLILALTRKGQESFNGQVPRD
+>gi|14330336|emb|CAC40809.1| Xet3 protein [Festuca pratensis]
+----SNSSGSMIRSKRQFIFGTVSTWIQASSRAtlarhrhNILP---ILG-------GDNHDEIDFEFLGNETGqpyTLHTNVYADGVGN---KEMQFVP
+WFDPTGGYHKYTISWTPCMIVWYVDDLPIRVFRNYRqSNgvAFPtsRPMYAYSSIWSADDWATQGGrvkTDWTHAPFVANYHGIDLDiceCYGGDCIY--
+-GCAGAYGQPYcGGLTDEQRWKMQWV--QERYRIYDYCVDYKDGKV-------------------
+>gi|331270344|ref|YP_004396836.1| putative endo-1,3(4)-beta-glucanase [Clostridium botulinum BKT015925]gi|329126894|gb|AEB76839.1| putative endo-1,3(4)-beta-glucanase [Clostridium botulinum BKT015925]
+MKNGKPYSSTsgNVSTQGiaFWKYGRIDVRAKIPMEMGMWPAIWMMPEANPYG-WPNDGEIDImEALGSEKNIVYGTLHTGNIDDpknhtRTSTGVTYKL
+qKGTLADDYHIYSVIWKEKSFEFLIDNKSIGKINSwpskfkvTDirtgkekvldpafPDPFNKPFYLILNLGV--GGGWGGEPNTTTswgDKTKMFVDYV
+RVYQKDN----------------------------------------------------------------------
+>gi|58266734|ref|XP_570523.1| hypothetical protein [Cryptococcus neoformans var. neoformans JEC21]gi|134110300|ref|XP_776206.1| hypothetical protein CNBD0270 [Cryptococcus neoformans var. neoformans B-3501A]gi|50258876|gb|EAL21559.1| hypothetical protein CNBD0270 [Cryptococcus neoformans var. neoformans B-3501A]gi|57226756|gb|AAW43216.1| conserved hypothetical protein [Cryptococcus neoformans var. neoformans JEC21]
+-----------------------------------------------------------------------------------------------GGFGV
+YGFEYFSNpedrdsgHITWVANGEKSWTMYPAAVGAvesmgigqrliSEEPMAMIINFGMS---ESFQSVDFNhlITPMEMLVDYIRVYQRSEG-KVGCD
+PKdrpTAAYienhLNAYSNPNLTTWEDAGYTIPKNS----------------------------------
+>gi|46138213|ref|XP_390797.1| hypothetical protein FG10621.1 [Gibberella zeae PH-1]
+-------VASEFDSIDRFQFLSIRFMGRVRGAPGACMAMFTYVPAKEIKD---VQEADMEILTREDHDrVHyTNHPGySATELF-PKAtRNITLPDgLKW
+NEWVEHRLDWTPTQSIWYANGIEAANISFQ---VPRDPSLLIFNSWGD-GGVWTQNMTTGQ-EAYMELQWLQMvYN------------------------
+-------------------------------------------------
+>gi|302915076|ref|XP_003051349.1| hypothetical protein NECHADRAFT_80733 [Nectria haematococca mpVI 77-13-4]gi|256732287|gb|EEU45636.1| hypothetical protein NECHADRAFT_80733 [Nectria haematococca mpVI 77-13-4]
+-----HYLSGAIHAKSTFtvvaGGGYdVKAEFIAPVDRGTWPAFWLNAA-------SGWpPEIDVaEWKGSG--KISFNTFNTSSE-----VTALDVDYP
+EPTQWHSVRAELRDengvdVRVKFFLDDREVTTQYGRE--YIGKGLRLIINY------QTEGSSgsPGPTTPTTFQIRNVEVISY---------------
+---------------------------------------------------------
+>gi|294054542|ref|YP_003548200.1| glycoside hydrolase family 16 [Coraliomargarita akajimensis DSM 45221]gi|293613875|gb|ADE54030.1| glycoside hydrolase family 16 [Coraliomargarita akajimensis DSM 45221]
+---GELYSGATIISNQKFTHGYIEARTR--LDW-VDGHFWPT----------FWMNEYRaDGSANE---fdimeynhwstYPTQSHHFP------KKEGV
+TTVpsNASVNEWHVWGVLWTENEITFYVDgikqfSSERPQVA------ATDLLPLVFSC----SPNLNKNPARTGQYPRFFVDWVRVWQG----------
+--------------------------------------------------------------
+>gi|298372310|ref|ZP_06982300.1| hypothetical protein HMPREF0156_00351 [Bacteroidetes oral taxon 274 str. F0058]gi|298275214|gb|EFI16765.1| hypothetical protein HMPREF0156_00351 [Bacteroidetes oral taxon 274 str. F0058]
+-----EFTSDVVNGYNlaKEEYCGIRVKMRCTG--NVNHAFWLTSGS-------KLPHINVaLIKGK-------TIEVGvHDArGDYY-YTTVT-GI-NP
+SKYYIYSIYQKNGYLIWRINNIEVFRTRNI---IAELRFSPCFSSFIP------ADKvDA--TEGQLDIAWVEVYK------------------------
+-------------------------------------------------
+>gi|328886601|emb|CCA59840.1| hypothetical protein SVEN_6554 [Streptomyces venezuelae ATCC 10712]
+---------AEVHTGVrKFKNGTYAARVRLADtptsgpdGDHLVQSFFTINDLTaPMA--DDYAEYDFEYLPNGgwgePANvLYTTSWETFRPDPWEAVN
+QHTEARTSQAGWHDLVLTIDDTALVYYLDGKEFARHDAR--YLPERPMSIHFNQWL---IDLTGQISTAPRAYEEQVDYVLHV-----------------
+---------------------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * * * 1074 930 * * * * * * * * * 1
+ 0 * * * * * * 1642 0 0
+
+V 2 * * * * * * * * * * * * * * * * 730 1333 * * 2
+ 0 * * * * * * 2435 0 0
+
+S 3 * * * * * * * 1560 * 3520 * 1785 * 2286 * 3671 * * * * 3
+ 0 * * * * * * 4034 0 0
+
+A 4 2563 * 4939 5055 * 1557 * * * * * 3730 * * 4786 2542 3177 * * 4865 4
+ 0 * * * * * * 5981 0 0
+
+K 5 5339 * 2611 3923 6106 4064 * * 2291 5813 * 4711 5193 * 2776 3544 3992 * * 3487 5
+ 0 * * * * * * 7336 0 0
+
+D 6 4319 * 3945 4215 * 4988 4663 * 3689 5333 * 2390 2420 3344 4070 5733 4179 * 5197 5584 6
+ 0 * * * * * * 7962 0 0
+
+F 7 6111 * 6050 7131 2235 5183 6769 4227 6702 4891 * 6266 * * 4871 4671 7044 3940 3113 1545 7
+ 0 * * * * * * 8125 0 0
+
+S 8 4260 * 4947 5521 * 5931 * 5028 4426 3924 6784 5389 6788 6172 4037 2495 1490 5270 * 4108 8
+ 9 * 7360 * * * * 8221 0 0
+
+G 9 3618 5718 * * * 1456 * * * * * 5552 * * * 1220 3760 6560 * * 9
+ 11 7088 * 0 * 0 * 8292 1049 1000
+
+A 10 1600 4836 5857 * * 1408 * 7624 * * 7312 * 6557 * * 2596 4737 5961 * * 10
+ 0 * * * * * * 8374 0 0
+
+E 11 3120 5323 * 2683 5415 2190 7031 5671 4451 5948 5072 5083 * * 2721 4532 5330 4780 4777 5610 11
+ 9 * 7318 * * * * 8399 0 0
+
+L 12 5440 * * * 2839 * * 1589 * 1938 4590 * * * 7240 * * 2478 * 5950 12
+ 10 * 7240 * * * 0 8389 0 1000
+
+Y 13 3719 * 4091 3428 5837 5046 4205 4354 4211 6321 5515 4341 * 3249 3423 3658 2919 4608 * 4924 13
+ 0 * * * * * 0 8391 0 1043
+
+T 14 6571 * * * * 4963 6954 * * 7595 * * * * * 786 1530 * 6977 6678 14
+ 21 6110 * 2407 302 * 0 8391 1043 1043
+
+L 15 3759 * 4968 5120 6261 5132 5951 5050 1779 4424 7238 3339 7191 3455 3127 5346 4142 6438 7068 5551 15
+ 225 2795 * 1275 769 * 0 8391 2019 1043
+
+E 16 3992 * 3468 3250 3649 3230 4555 * 3413 5040 7595 3184 * 3695 3808 4577 4722 5550 * 5406 16
+ 340 2252 * 1075 929 0 * 8391 2437 1043
+
+E 17 3464 6973 3300 3928 5600 4901 6533 6072 2784 6029 6732 4756 6341 4140 3798 2731 3407 7038 * 4209 17
+ 98 3928 * 978 1022 * * 8443 1371 0
+
+V 18 5280 * * 6194 1574 * * 3374 6318 4237 7125 7063 4772 4079 5829 6021 5442 3472 4490 2629 18
+ 62 4756 7622 1658 550 * * 8533 1207 0
+
+Q 19 5562 * 6428 5555 5553 3755 4484 5627 2778 2823 5683 5088 5945 2918 3507 3835 3249 5734 7378 6262 19
+ 40 5651 7035 1590 582 * 0 8668 1086 1028
+
+Y 20 5509 * * 5511 3165 5528 3862 6886 5562 6462 * 5275 4785 6416 5688 4138 5864 6175 6418 942 20
+ 13 6856 * 0 * * 0 8657 1010 1080
+
+G 21 5137 6938 * * * 179 * * * 6818 7117 6888 5685 * * 5781 6745 8047 7669 * 21
+ 132 3600 7734 715 1355 476 1832 8633 1571 1137
+
+K 22 7492 7310 * 7607 3915 6473 5829 7214 3080 4630 4972 6483 * 4579 2140 3633 5458 5355 7754 1845 22
+ 89 4064 * 239 2712 1338 726 8677 1378 1038
+
+F 23 5854 * * * 1750 * * 2518 * 4084 4351 7494 * 7262 * * 5795 2432 3908 3049 23
+ 5 * 8241 * * * 0 8675 0 1004
+
+E 24 5650 * 5195 741 * 4608 8260 * 5342 * * 5864 * 5317 3946 3326 4466 5284 * 7015 24
+ 11 7626 8573 1585 585 * 0 8679 1000 1032
+
+A 25 1331 5214 * 6882 4441 7039 * 3036 * 6604 3149 * * * * 4209 3831 2873 7040 * 25
+ 0 * * 1000 1000 2474 286 8724 1000 1108
+
+R 26 4924 7640 7837 4107 * 7363 8193 7211 3241 5215 6091 7254 * 5660 848 3594 4725 6495 6315 6669 26
+ 0 * * * * 0 * 8719 0 1080
+
+M 27 2098 6100 * * 3775 * * 1757 * 3361 2795 * * * * 7397 6581 2998 * * 27
+ 10 7218 * 1000 1000 * * 8674 1008 0
+
+K 28 5832 * 7370 6147 * * * 6518 856 6496 7462 7024 * 3977 1930 5572 6044 * 7572 7145 28
+ 15 * 6581 * * * * 8674 0 0
+
+M 29 2889 6204 * * 3865 4927 6278 3747 * 1810 2903 * 4302 7354 7145 5923 4575 3225 6113 * 29
+ 17 6414 * 2191 357 * 0 8638 1031 1031
+
+A 30 2804 * 5234 7017 * 5544 6175 5400 7002 5205 5192 4933 1312 5493 5534 3218 4068 4409 * 6966 30
+ 61 5714 5480 1596 580 0 * 8637 1125 1031
+
+A 31 3360 6345 3418 3887 7230 3767 6291 8624 3473 4604 7401 3231 3039 4778 3871 4021 4393 4781 7585 6280 31
+ 686 1478 5686 1317 740 0 * 8694 3532 1103
+
+A 32 3420 7856 3977 4319 * 2279 4518 5347 5549 5020 7260 5748 5724 5474 4412 2577 3316 4030 * 5690 32
+ 68 5478 5415 549 1659 1749 510 8630 1176 1107
+
+S 33 2148 8577 3429 4244 5647 5173 7828 6300 4298 6692 6765 5295 2685 4793 3843 3521 3682 5545 6534 7035 33
+ 88 7842 4196 2807 222 0 * 8574 1043 1216
+
+G 34 5341 * 6924 6178 * 348 6339 * * 4881 * 5283 7137 * 6267 4474 6985 * 5451 * 34
+ 9 7359 * 1000 1000 0 * 8619 1001 1329
+
+T 35 3720 6113 7374 7486 4214 6139 7215 3119 * 2920 3840 5490 * * 7266 3774 2548 2332 6231 5553 35
+ 6 * 7895 * * * * 8673 0 0
+
+V 36 5613 4327 5573 6876 3756 5791 7175 4167 * 4826 6112 4538 * 5658 7558 4488 5133 1917 2015 4557 36
+ 13 8592 7290 1585 585 * 0 8676 1028 1000
+
+S 37 4261 4945 7142 * 6126 5101 4989 * 6824 6829 5234 4853 1529 7109 * 2627 2439 4449 * 6833 37
+ 6 * 7923 * * 782 1258 8673 0 1045
+
+S 38 812 * * 6988 7371 3576 6581 * * 6336 6877 5458 6981 7224 * 2749 3382 6158 7535 * 38
+ 0 * * * * 1739 514 8675 0 1082
+
+M 39 6322 * * * 843 * 7225 2787 * 3296 4430 * 7227 8129 * * 6191 4574 5416 4616 39
+ 15 6574 * 2309 325 * 0 8672 1086 1043
+
+F 40 * * * 5801 2589 6123 6908 6358 * 4783 5680 * * * 7017 * * 5371 840 2894 40
+ 15 * 6568 * * 0 * 8672 0 1043
+
+L 41 4189 * * * 5050 5879 * 5086 * 1243 2546 * 5865 * * 5196 2549 4963 5196 * 41
+ 15 7621 7527 0 * * 0 8672 1000 1052
+
+Y 42 5781 7783 7013 6203 4333 7372 5924 3591 5039 2964 3667 5060 * 4219 4812 3213 3978 4554 4318 2473 42
+ 76 6137 4740 1000 1000 1536 610 8671 1047 1095
+
+Q 43 4148 6903 5019 5818 5702 2719 6270 * 5578 * * 2833 2767 6499 4678 2086 4227 * 6997 4395 43
+ 73 5528 5162 1226 805 2927 203 8664 1116 1311
+
+N 44 3374 * 2570 4003 * 3342 5017 6782 4409 6519 6925 2882 4872 3621 5329 3841 3636 7179 * 4841 44
+ 309 5022 2627 1717 523 1305 748 8613 1331 1597
+
+G 45 4711 * 2187 3237 5464 2584 7002 6909 4751 6733 6941 3361 3156 5478 5083 5373 4287 * * 4672 45
+ 601 3716 1918 606 1543 2101 383 8437 1758 2477
+
+S 46 4391 * 3265 3952 6662 3361 6201 7312 4794 7256 6021 4031 3283 5186 * 2387 3035 4215 5969 5370 46
+ 679 3933 1690 512 1744 3411 142 8264 1320 3612
+
+E 47 4656 5740 2710 3403 6660 6052 4716 5235 4034 5199 * 3146 3595 3791 * 4096 4473 5257 4993 3515 47
+ 400 4630 2308 1229 802 2167 363 7855 1102 4548
+
+I 48 4444 6428 4900 5037 3668 5340 * 3287 5158 3492 3651 6560 3647 5774 * 4339 5396 3094 * 2497 48
+ 321 5339 2517 967 1034 2512 278 8047 1044 4347
+
+A 49 3006 * 3812 3238 5073 1867 6217 * 3840 5407 * 6386 4254 4117 4727 3843 4296 * 7089 * 49
+ 203 5524 3188 1585 585 3634 121 8221 1113 4344
+
+D 50 4593 * 2287 3981 6554 3996 5730 * 4219 6097 * 2856 4845 3211 5408 3058 4188 6018 6305 5480 50
+ 561 3975 1950 1015 985 2614 257 8153 1179 4476
+
+G 51 5351 * 4838 5273 5878 1843 6100 * 5256 * * 3843 3993 4828 6155 5232 5071 * 1671 5268 51
+ 155 3292 * 1439 664 584 1587 7917 1296 4737
+
+R 52 3801 6693 3231 4297 * 2933 7850 4671 3681 5302 6934 4246 2293 5913 7569 4368 3638 4237 * 6084 52
+ 73 5007 5765 2061 395 770 1274 8529 1131 2488
+
+P 53 3806 6019 3973 4508 3920 2943 5633 5693 3162 5652 * 3935 3687 4963 4126 4012 3470 5225 6536 5949 53
+ 41 5663 6936 684 1406 1037 964 8602 1139 1724
+
+W 54 4990 4673 5368 5604 5637 3951 2413 6644 5800 4669 * 3708 6884 6207 4614 3424 7332 4456 2156 4793 54
+ 277 2539 8662 1350 719 592 1571 8652 2115 1405
+
+V 55 4707 5737 2256 4796 5667 2164 5851 5151 7133 5995 6540 4310 3456 3846 4632 5762 4268 4649 * 6148 55
+ 20 6186 * 1809 485 0 * 8680 1045 1182
+
+E 56 7109 7028 * 183 * 7213 5266 * * 7080 * 6651 7040 5357 6739 6279 * * * * 56
+ 0 * * * * * * 8697 0 0
+
+V 57 6893 * * 6652 4901 * * 783 * 2946 4109 7357 * 7141 * * 7319 3127 5806 5175 57
+ 7 * 7751 * * * * 8695 0 0
+
+D 58 5325 5216 245 * * 7832 * 7027 7331 7108 * 4699 * 6916 6266 6872 * * * 6601 58
+ 0 * * * * * 0 8703 0 1017
+
+I 59 6483 * * * 2379 * 6531 1162 * 3813 4223 7192 * * 6601 7154 7125 2669 6501 6105 59
+ 1195 829 * 0 * 0 * 8703 4681 1017
+
+E 60 * 7314 6350 282 * 7349 * * 5899 4774 5668 * * 5471 5914 6532 5893 * * 6268 60
+ 45 5459 6916 489 1799 * * 8695 1131 0
+
+V 61 4812 7370 * 5692 2073 4662 4301 3399 6520 3606 6029 3758 * 6261 * 4287 4365 3726 4123 3501 61
+ 107 4466 5265 542 1676 * 0 8678 1275 1010
+
+L 62 4874 6040 5261 * 4457 5201 6170 4118 4118 1732 4649 5512 5657 4858 3941 4629 5243 3663 7399 3492 62
+ 17 7611 7203 2585 263 708 1367 8646 1000 1207
+
+G 63 3973 7008 6057 * * 711 * * 4899 * 5735 4406 4982 4553 7289 3682 5247 5755 * * 63
+ 94 4893 5086 1911 446 0 * 8664 1235 1105
+
+K 64 4734 * 3693 4398 5748 3200 4168 6365 3413 6164 * 1999 5588 4279 3932 4007 4644 5328 7226 6275 64
+ 93 5024 4991 965 1036 339 2255 8634 1343 1170
+
+N 65 3822 6899 2534 3209 7305 3928 5581 5842 4821 5444 * 3065 5070 4864 3599 4354 4298 3978 * 4568 65
+ 284 2848 4647 1859 465 1428 670 8589 2186 1329
+
+P 66 4370 * 4202 5973 5261 3884 * 5925 4071 5244 7417 4034 1572 5364 5136 3889 3265 4203 * 8208 66
+ 113 4098 5888 2753 232 * 0 8582 1328 1499
+
+G 67 4888 * 2902 5434 7166 2129 5245 * 4014 6847 5743 2849 6043 5400 4665 4564 3334 7149 5940 3713 67
+ 142 3899 5222 1672 543 1616 570 8550 1473 1608
+
+S 68 4177 * 5417 3931 5538 4833 4137 4016 3418 4392 6729 4015 6275 2977 3545 5375 2531 4964 7075 7400 68
+ 674 1530 5208 1653 552 388 2084 8465 3618 1579
+
+F 69 4035 * 7458 * 4382 * 5628 2965 * 2033 4311 5339 5741 * * 6110 7208 2579 3353 3151 69
+ 41 5686 6907 2501 280 2866 213 8742 1088 1291
+
+Q 70 5245 * 6162 4832 5351 4719 2579 5636 6100 5098 6944 3575 5514 1799 4905 4228 4757 5614 4883 4280 70
+ 42 5108 * 1281 765 1171 847 8721 1149 1316
+
+S 71 3870 * 7212 6040 3906 4233 6263 6217 7428 4388 5219 4782 6289 6531 * 2385 1389 5098 * 5615 71
+ 29 7070 6358 0 * 352 2208 8631 1000 1156
+
+N 72 3839 6896 5530 6140 6933 4133 4903 7314 * 5612 * 977 * 4842 * 4378 2729 7381 * 6295 72
+ 65 4715 7400 2447 292 653 1458 8712 1241 1074
+
+I 73 4548 7275 * 4748 4162 7086 4466 2459 * 3134 5643 7308 7453 6329 * 4546 3912 2136 6322 3113 73
+ 20 6215 * 1000 1000 0 * 8680 1045 1035
+
+I 74 5821 7255 * 5949 2314 * 1484 4073 6839 5379 * 6281 6074 * 6368 7215 5539 5748 4104 2607 74
+ 88 4920 5246 1525 616 * * 8676 1184 0
+
+T 75 3378 6286 5219 5666 3667 4271 4729 5629 7819 3809 5769 5170 4202 7832 5365 4234 2894 3365 3822 3385 75
+ 82 4334 7467 1211 816 457 1880 8525 1387 1147
+
+G 76 4082 * 3829 4783 4660 1926 4499 7577 4754 5767 6843 2583 4918 4536 4964 4901 4169 6250 4779 7932 76
+ 174 3335 6120 1409 682 835 1187 8654 1657 1047
+
+K 77 4289 5694 4605 3712 6082 1710 5013 6149 3504 7690 * 4015 4547 6356 5111 3315 3929 5211 6898 7293 77
+ 152 3971 4783 1987 419 0 * 8653 1423 1101
+
+A 78 3901 * 4013 5590 5779 3701 5329 4648 3409 5768 * 3628 3852 3560 5058 3196 4914 3606 4209 4853 78
+ 157 4351 4212 1132 879 1824 479 8608 1350 1385
+
+G 79 3536 7268 4015 4356 * 1331 5018 * 7171 5829 * 3565 4212 4381 5066 4910 4128 5548 6966 7054 79
+ 353 2867 3647 1092 913 3023 189 8494 1846 1771
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+D 211 * * 1414 * * 4290 * * * * * 2619 * * 3870 * 2718 4171 * 2890 211
+ 0 * * * * * 0 4532 0 1271
+
+L 212 * * * * 1425 2384 * 3325 * 2912 * * * * * * * * 3730 2967 212
+ 241 * 2701 * * 0 * 4012 0 1271
+
+T 213 2422 * * 4073 * 2484 * * * * * * * * 3851 4121 1967 * * 2376 213
+ 280 * 2505 * * * 0 3943 0 1127
+
+D 214 * * 1724 2584 * * * * 3690 * * * 1142 * * * * * * * 214
+ 0 * * * * 211 2881 3698 0 1430
+
+K 215 * * 2914 3103 * 1622 * * 4034 4121 * 2951 * * * 3700 * * * 3305 215
+ 0 * * * * * 0 4081 0 1018
+
+N 216 4267 3305 4308 * * * * * * * * 1242 * 2945 3751 2560 * * * * 216
+ 0 * * * * * 0 4081 0 1018
+
+I 217 1575 * * * * * * 2857 * * 3929 * * * * * 3751 1372 * * 217
+ 0 * * * * * 0 4081 0 1018
+
+Y 218 2635 * 2583 3301 * 3751 * 3952 4002 4300 * * * * * * 2895 3022 * 4034 218
+ 0 * * * * 0 * 4081 0 1018
+
+S 219 * * * * 3883 * * 2669 * * * * * * * 4154 3144 975 * 3366 219
+ 159 3264 * 2322 322 * * 4141 1147 0
+
+R 220 * * 4358 3013 * * * 4009 1292 * * 4089 * * 2642 2858 * * * * 220
+ 0 * * * * * * 4141 0 0
+
+D 221 * * 908 3999 * 3264 * * * * * 1991 * 4358 * * * * * * 221
+ 0 * * * * * * 4141 0 0
+
+G 222 * * 4009 * * 351 * * 3264 * * 4333 * * * * * * * * 222
+ 0 * * * * * * 4141 0 0
+
+M 223 2709 * * * * * 4009 2493 2683 * 3241 * * 3215 * * 4257 2928 * 4200 223
+ 0 * * * * * * 4141 0 0
+
+L 224 2709 4028 * * 3834 * * 3187 * 1181 3883 * * * * * * 3366 * * 224
+ 0 * * * * * * 4141 0 0
+
+I 225 * * * * * * * 4002 2002 * * 3921 * * 2353 * 3658 1527 * * 225
+ 0 * * * * * * 3864 0 0
+
+L 226 * * * * 3737 * * 1824 * 780 * * * * * * * 4055 * * 226
+ 0 * * * * * * 3864 0 0
+
+A 227 1150 * 3921 * * 3929 * 3894 3871 * * * * * * 4055 2172 * * * 227
+ 0 * * * * * * 3864 0 0
+
+L 228 * * * * * * * 2034 * 780 * * * * * 4236 4201 3921 * * 228
+ 0 * * * * * * 3864 0 0
+
+T 229 4055 * 2338 4201 * 4223 * * 2783 4236 * * * * * 4038 1415 * * * 229
+ 0 * * * * * * 3864 0 0
+
+R 230 2861 * 4134 * * * * * 1798 * * 4084 * 2513 2956 3583 * * * 3809 230
+ 0 * * * * * * 3786 0 0
+
+K 231 * * * 788 * 2924 * * 3893 * * * 2852 * * * 3583 * * * 231
+ 0 * * * * * * 3786 0 0
+
+G 232 * * 3293 * * 441 * * * * * 3798 * * * * * 3479 * * 232
+ 0 * * * * * * 3588 0 0
+
+Q 233 3668 * 1174 * * * * * * * * 3547 * 2508 * 3797 2788 * * * 233
+ 0 * * * * * * 3419 0 0
+
+E 234 * * * 673 * * * * * * * * * 3797 * * 2635 2838 * * 234
+ 0 * * * * * * 3419 0 0
+
+S 235 * * 2581 * * 1628 * 3451 * 3417 * 3228 * * * 2975 3467 * * * 235
+ 0 * * * * * * 3032 0 0
+
+F 236 * * * * 2102 * * * * * * * * * * * * * * 383 236
+ 0 * * * * * * 3032 0 0
+
+N 237 3467 * * * * * * * * * * 2102 * * * 1124 2200 * * * 237
+ 0 * * * * * * 3032 0 0
+
+G 238 * * * * * 1150 * 3417 * * * * * * * * 3228 1519 * * 238
+ 0 * * * * * * 3032 0 0
+
+Q 239 * * * * * * * * * * * * * 564 * * 1628 * * * 239
+ 0 * * * * * * 3032 0 0
+
+V 240 * * * * * * * * * 1834 * * 963 * * * * 2277 * * 240
+ 0 * * * * * * 2350 0 0
+
+P 241 * * * * * * * * * * * * 0 * * * * * * * 241
+ 0 * * * * * * 1797 0 0
+
+R 242 2123 * * * * * * * * 2038 * * * * 1763 * * 2106 * * 242
+ 0 * * * * * * 1797 0 0
+
+D 243 * * 0 * * * * * * * * * * * * * * * * * 243
+ 0 * * 0 * * * 1797 0 0
+
+//
+�HHsearch 1.5
+NAME f10edaeff439be4afbba7757c8cac254
+FAM
+FILE f10edaeff439be4afbba7757c8cac254
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:38:56 2013
+LENG 64 match states, 64 columns in multiple alignment
+FILT 114 out of 272 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCHHHCCCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCEEEEEECCCCCEEEECCCCC
+>ss_conf PSIPRED confidence values
+9877687796999999999988899838997399841677789979999899995986089689
+>Consensus
+xxsWPELVGxxxxxAxxxIxxdxpxxxvxvlxxgxxvtxDfxxxRVxvxvdxxgxVxxxxPxvG
+>f10edaeff439be4afbba7757c8cac254
+LKSFPEVVGKTVDQAREYFTLHYPQYNVYFLPEGSPVTLDLRYNRVRVFYNPGTNVVNHVPHVG
+>gi|41053029|dbj|BAD07960.1| hypothetical protein [Oryza sativa Japonica Group]gi|125537886|gb|EAY84281.1| hypothetical protein OsI_05660 [Oryza sativa Indica Group]gi|125580633|gb|EAZ21564.1| hypothetical protein OsJ_05192 [Oryza sativa Japonica Group]
+-VRWAEVLGELAPLAVTQISNDRPDVAVEVLlrDAAAVVSPEFNPKRVRVFVDNNFIVVK-VPVIS
+>gi|186528913|ref|NP_199170.2| Serine protease inhibitor, potato inhibitor I-type family protein [Arabidopsis thaliana]gi|332007600|gb|AED94983.1| Serine protease inhibitor, potato inhibitor I-type family protein [Arabidopsis thaliana]
+-SSWPELVGRRGEEVKEIIDRENTKVTAKIISENAVVLAVVICDRVYVRVNDQGIVTR-TPI--
+>gi|87198879|ref|YP_496136.1| hypothetical protein Saro_0857 [Novosphingobium aromaticivorans DSM 12444]gi|87134560|gb|ABD25302.1| conserved hypothetical protein [Novosphingobium aromaticivorans DSM 12444]
+------HLGQKATGELGVELLRQTAARVlRWVPPRTAVTMDYRADRVTVGYDDDYTIVR------
+>gi|238498650|ref|XP_002380560.1| conserved hypothetical protein [Aspergillus flavus NRRL3357]gi|317155796|ref|XP_001825378.2| hypothetical protein AOR_1_770074 [Aspergillus oryzae RIB40]gi|220693834|gb|EED50179.1| conserved hypothetical protein [Aspergillus flavus NRRL3357]
+-----KLAGKTITEGTsdvtSFAKKDLPQS-HRIVKPGDMMTMDYKPERLNVHLDEQGTVHD------
+>gi|195657573|gb|ACG48254.1| hypothetical protein [Zea mays]
+-QTWPDLVGYAVVDAVNIIRQDNPNItEVRVLPPDgVPSPLQDGAIRVCIYNDivnGQAVVVNPAPYIG
+>gi|168066728|ref|XP_001785285.1| predicted protein [Physcomitrella patens subsp. patens]gi|162663119|gb|EDQ49902.1| predicted protein [Physcomitrella patens subsp. patens]
+--GWPDLAGLDCVAGMNSIKQDYLGVTIVYGPKGFMHIQDFQKDRVWVDINPDGTIAA-IPAIG
+>gi|254418094|ref|ZP_05031818.1| hypothetical protein BBAL3_404 [Brevundimonas sp. BAL3]gi|196184271|gb|EDX79247.1| hypothetical protein BBAL3_404 [Brevundimonas sp. BAL3]
+--------------------------NRRVTCTTCPVSQDYSAYRLNIFYNADtGIIEQ------
+>gi|325926183|ref|ZP_08187541.1| hypothetical protein XPE_1507 [Xanthomonas perforans 91-118]gi|325543365|gb|EGD14790.1| hypothetical protein XPE_1507 [Xanthomonas perforans 91-118]
+-----SLVGQPLTDAVGEQARSDAGAkSVRVLKPGQMTTMEFNGERLNLEVDAKNVITS------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+L 1 * * * * * * * * * 913 * * * * * * * 1093 * * 1
+ 0 * * * * * * 1459 0 0
+
+K 2 * * 4825 6191 * 6383 * * 3748 * 6012 4534 5377 2482 6238 2143 1631 * 5547 5723 2
+ 0 * * * * * * 4669 0 0
+
+S 3 3511 6297 * 3055 6024 3940 6034 * 5130 * * 6066 5304 * 5877 1038 3175 * * * 3
+ 0 * * * * * * 4938 0 0
+
+F 4 * * * * 4786 * * * * * * * * * * * * * 53 * 4
+ 0 * * * * * * 4935 0 0
+
+P 5 4150 * * * * * * * 5759 * * * 256 4678 * 5008 5833 * * * 5
+ 0 * * * * * * 5377 0 0
+
+E 6 6254 * 3342 557 * 5436 * * 3342 * * 6318 5619 6060 * 5283 * 6246 * * 6
+ 0 * * * * * * 6019 0 0
+
+V 7 4665 5041 * * 3822 * 6122 6844 * 597 5954 * * * * 6155 * 3064 6641 6004 7
+ 0 * * * * * * 6327 0 0
+
+V 8 4232 * * * * * * 3480 4801 3271 4881 * * 5685 * * 4776 671 * * 8
+ 0 * * * * * * 6365 0 0
+
+G 9 * * * * * 0 * * * * * * * * * * * * * * 9
+ 0 * * * * * * 6365 0 0
+
+K 10 4985 * 6374 4266 6925 * 5391 5285 1673 4325 5106 6581 * 3025 4294 5223 4477 3229 3718 6002 10
+ 0 * * * * * * 6365 0 0
+
+T 11 4628 6447 3166 * 6447 * 5942 * 3459 * 5481 3396 2293 5342 5247 2896 2410 5437 * * 11
+ 0 * * * * * * 6365 0 0
+
+V 12 1755 5971 * 5771 4951 2108 * 4074 6725 4075 4668 6845 * 5840 6533 6126 6334 3176 * 3982 12
+ 0 * * * * * * 6365 0 0
+
+D 13 5099 * 3036 1918 4561 5723 5611 6654 5493 4211 6586 5472 * 5282 5172 3736 2346 4102 * * 13
+ 86 * 4114 * * * * 6365 0 0
+
+Q 14 3219 * 2429 1807 6623 5372 5878 6821 5083 4434 6806 5928 5731 3850 * 4485 5776 4331 * 4083 14
+ 12 6957 * 0 * 0 * 6344 1000 1346
+
+A 15 513 6528 5391 3892 * 4727 * * * * * 6552 * 6151 6508 4039 5375 4686 * * 15
+ 46 * 5007 * * * * 6365 0 0
+
+R 16 3744 * * 3920 * 6002 * 4374 1841 3611 4576 6300 * * 4339 4241 3765 2424 * 5819 16
+ 106 3823 * 2057 396 0 * 6301 1332 1109
+
+E 17 2923 4845 4613 2321 * 3795 5820 5765 3278 3664 5006 4986 5461 4398 4740 4515 4157 4952 * * 17
+ 0 * * * * * * 6365 0 0
+
+Y 18 3393 * * 3773 3904 6547 7276 2450 3086 5195 6537 * 6348 3824 4716 5453 3120 2990 6528 6222 18
+ 0 * * * * * * 6365 0 0
+
+F 19 4183 5621 5063 4943 6222 * * 580 6622 6547 * * 6915 4168 5567 5034 6348 5001 * * 19
+ 0 * * * * * * 6365 0 0
+
+T 20 3613 * 6640 2549 * * 6586 4118 1987 2362 5552 6665 * 4753 4201 5057 5123 5273 6022 * 20
+ 29 * 5636 * * * * 6365 0 0
+
+L 21 3686 * 4527 3765 5005 5813 4440 * 2829 4098 6178 7151 * 2945 2020 3806 4957 6608 * * 21
+ 0 * * * * 0 * 6359 0 1082
+
+H 22 4210 * 1485 1535 6535 * 6227 6884 4031 6340 * * 5601 5461 5571 4913 5109 6516 * * 22
+ 20 6200 * 0 * * * 6377 1028 0
+
+Y 23 3790 5664 4797 4256 * 5031 7028 * 4197 3912 4418 2002 * 4757 2083 * 5396 * 6551 4142 23
+ 100 6543 4145 2807 222 * * 6377 1005 0
+
+P 24 3719 * * 5159 * 4610 * * * 5099 6437 * 835 5896 4720 2665 4924 6875 * * 24
+ 16 6463 * 3907 100 * 0 6354 1005 1346
+
+Q 25 5154 * 1931 3765 * 1958 * 5014 3655 6399 * 3825 6517 4960 5733 3560 * * * 4669 25
+ 28 5707 * 0 * * 0 6354 1032 1346
+
+Y 26 2091 5600 6358 6832 6836 5038 * 4481 4634 3039 6446 6548 * 6188 6886 4368 5782 1503 * 6151 26
+ 453 2321 3849 97 3949 0 * 6439 2194 1346
+
+N 27 4817 * 3905 3786 * 6943 5788 4069 3404 5046 6985 2996 4789 3207 3245 5204 3016 3948 * 5968 27
+ 0 * * * * 0 * 6297 0 1332
+
+V 28 2601 * 7096 * 5093 6226 4708 2181 * 6159 5191 * 6550 * 6390 5871 5181 1376 * 4941 28
+ 132 3682 6693 0 * * * 6352 1516 0
+
+Y 29 6156 * 5508 3432 * * * 2899 4540 5094 5711 5417 6240 4027 1327 * 5818 3114 * 5948 29
+ 11 7087 * 0 * 0 * 6361 1118 1065
+
+F 30 6875 * * * 3507 * 6600 2313 6638 4102 * 6880 7195 * * * 4680 1058 4943 4143 30
+ 0 * * * * * * 6352 0 0
+
+L 31 * * * * 5569 4426 5934 2165 6578 1410 5285 * * 6706 5047 5965 6317 2445 6840 5647 31
+ 0 * * * * * * 6406 0 0
+
+P 32 4690 5106 5649 5609 4924 4123 5733 6020 3017 4349 * * 1602 5337 3066 4413 4522 6390 6717 6772 32
+ 0 * * * * * * 6406 0 0
+
+E 33 4368 * 4982 2708 * 5649 7142 * 4070 4372 * 5492 1507 3970 6743 5328 4957 3495 5653 5700 33
+ 0 * * * * * * 6406 0 0
+
+G 34 * * 2387 5965 * 925 5347 * * 6598 * 3066 * 6407 5243 5008 4557 * * * 34
+ 40 5836 6715 0 * * * 6406 1071 0
+
+S 35 4043 4227 2866 4891 6241 7066 5748 * * * 4108 * * 2783 5840 2007 2644 4437 * * 35
+ 0 * * 0 * 0 * 6415 1065 1065
+
+P 36 2226 * * * 5391 5231 * 3588 5751 4224 3137 5618 2081 * 5154 5274 4576 3408 * 5634 36
+ 73 4775 6285 1170 848 * * 6406 1138 0
+
+V 37 3087 * 6587 5323 5880 * 6244 4404 5127 4787 3459 * 4963 6459 4987 4582 5227 1199 5363 6571 37
+ 13 6789 * 629 1502 0 * 6379 1104 1028
+
+T 38 6504 * * * * * 7381 4511 * 5837 * 6020 2424 * 6285 4052 695 5844 * 6407 38
+ 0 * * * * * * 6406 0 0
+
+L 39 3611 6532 4955 4883 * 5764 7541 * 3428 3358 1638 * 3092 4382 4218 6284 3959 * * 6706 39
+ 23 5954 * 0 * * * 6406 1128 0
+
+D 40 5965 * 647 2853 * 4009 * 4982 * * * 4103 * 5836 * * * 5326 * 6329 40
+ 0 * * * * * * 6406 0 0
+
+L 41 * * 5836 * 1330 * 4341 5326 5982 4454 6594 5844 6285 * * * 5845 5837 6966 1451 41
+ 0 * * * * * * 6406 0 0
+
+R 42 * 4235 3244 6189 5965 5836 * 6135 6014 7233 * 2404 * 4685 1331 4687 * 3416 * * 42
+ 33 5447 * 3217 164 * * 6406 1072 0
+
+Y 43 3259 2348 6107 3451 6766 6155 * 3786 6252 4995 5931 4605 1856 6444 7372 4743 4410 6971 * 6730 43
+ 0 * * * * * * 6406 0 0
+
+N 44 5312 7222 1728 3400 6547 4596 5686 5836 4519 5087 7096 2019 5125 5243 4935 4959 5444 * * 6317 44
+ 0 * * * * * * 6406 0 0
+
+R 45 * * * * * * * * * * * * * * 0 * * * * * 45
+ 0 * * * * * * 6406 0 0
+
+V 46 * * * * * * * 4238 * 2004 6014 * * * * * * 552 * * 46
+ 0 * * * * * * 6406 0 0
+
+R 47 5649 5121 6578 6717 3978 * * 3732 * 5009 * 2021 * * 1710 6067 3692 4483 4343 5427 47
+ 23 * 5975 * * * * 6406 0 0
+
+V 48 6029 * * * 4903 * * 1958 * 2036 * * * * * * * 1152 * * 48
+ 14 * 6693 * * 0 * 6352 0 1028
+
+F 49 4932 * 5502 4499 1846 6791 5007 3451 5327 5110 5763 5492 * 5724 4175 4908 5787 3896 3749 2949 49
+ 0 * * 0 * * 0 6415 1065 1065
+
+Y 50 6926 * 6221 * 4892 6107 5059 3168 6829 3239 6880 5211 * * * * 4094 980 * 3774 50
+ 28 5699 * 1763 504 * 0 6415 1176 1065
+
+N 51 6182 * 754 4704 * 4083 * * 6776 * * 2172 5818 6833 * 6870 5065 * * * 51
+ 75 4561 6949 1613 571 0 * 6415 1192 1065
+
+P 52 3082 5152 2464 2494 6516 3386 * 6219 4111 6805 * 4912 3754 4742 6474 3562 4193 * 6279 * 52
+ 101 4942 4844 1071 932 * 0 6403 1155 1000
+
+G 53 4183 6097 2347 3847 * 4085 7233 * 4155 3963 * 2409 * 4272 5199 3398 3888 4862 * 6112 53
+ 110 4011 6447 1388 694 * 0 6396 1264 1371
+
+T 54 4302 * 3722 5203 * 973 6358 5604 * 4440 5358 3249 * 5736 5702 4662 4585 * * 6716 54
+ 15 6627 * 487 1805 1639 559 6375 1089 1570
+
+N 55 6462 * 6178 5953 * * * 2141 3203 4744 6046 3342 4511 5681 3157 6627 2980 2644 * * 55
+ 40 5186 * 0 * 0 * 6394 1146 1371
+
+V 56 * * * * * * * 1746 * * * * * 5653 * * * 552 * * 56
+ 0 * * * * * * 6384 0 0
+
+V 57 2268 * * 3995 * * 7076 4361 4750 4887 5360 5294 * 5118 4729 3438 2700 2059 * * 57
+ 0 * * * * * * 6384 0 0
+
+N 58 3715 * 3718 3701 6379 5269 5806 6271 3581 6619 * 3794 * 3026 1968 3932 4843 5475 * 4834 58
+ 4009 * 93 * * * * 6381 0 0
+
+H 59 * * * * * * 1591 * * * * * 1523 * 1643 * * * * * 59
+ 0 * * * * 0 * 2019 0 4199
+
+V 60 3407 6457 * 4862 * * * 2821 * 5843 * 6223 3777 * * * 1814 1598 * * 60
+ 0 * * * * * * 4818 0 0
+
+P 61 * * * * * * * * * * * * 20 * * 6152 * * * * 61
+ 0 * * * * * * 4818 0 0
+
+H 62 4606 * * * * * 3109 4647 3413 * 3690 * * 5013 2470 3231 3586 2295 * 5220 62
+ 32 * 5490 * * * * 4818 0 0
+
+V 63 5125 * * * * * * 1260 * * 4959 * * * 4504 * * 1067 * * 63
+ 0 * * 0 * 0 * 4829 1065 1065
+
+G 64 5666 * * * 5604 111 * * * * 6066 * * * * * 5733 * * * 64
+ 0 * * 0 * * * 4755 0 0
+
+//
+�HHsearch 1.5
+NAME f22915668ca1cb3ce6b2cdc5b2a8d88f
+FAM
+FILE f22915668ca1cb3ce6b2cdc5b2a8d88f
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:26:53 2013
+LENG 111 match states, 111 columns in multiple alignment
+FILT 114 out of 267 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.2
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCHHHHHHHEECCCCCHHHHHHHHHHCCCCCCCCCCEEEEECCCHHHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCEEEECCCCC
+CEEECCCCCCC
+>ss_conf PSIPRED confidence values
+9568889850388980247999998578658988647889758989999985999887731698288689876258798986212123343899852999
+75887557796
+>Consensus
+xxxxxFxxqHvxxxxxxyCnxxMxxrxxxxxxxCKxxNTFIHxxxxxVxavCxxxxcxNxxSxxxxxxTxCxlxxxxxpxCxYxxxxxxxxixVaCxxxx
+PVHxdxxxxxx
+>f22915668ca1cb3ce6b2cdc5b2a8d88f
+ENWATFQQKHIINTPIINCNTIMDNNIYIVGGQCKRVNTFIISSATTVKAICTGVINMNVLSTTRFQLNTCTRTSITPRPCPYSSRTETNYICVKCENQY
+PVHFAGIGRCP
+>gi|326918746|ref|XP_003205649.1| PREDICTED: ribonuclease CL2-like [Meleagris gallopavo]
+-RYEKFLRQHVdyprtlGLMGHRYCGVMLARRQVTApGRPCKPSNTFVHAPAEDLVATCT-RPADSmgfHSTSTTMDITACRLRGgDTRPPCNYRARQLH
+HHVRVSCLDGLPVHLAGT----
+>gi|312597298|pdb|3LJE|A Chain A, The X-Ray Structure Of Zebrafish Rnase5
+PRYQKFLRQHVDaDMSVQKCDRAMSIKKITagTGNDCKEVNTFIQATKDRITTVCGDAgTPVnNlFKSNQPFPVVTCKLKSgNRRPNCQYRGTSSTRYIV
+LGCDKGWPVHYDE-----
+>gi|126277985|ref|XP_001379355.1| PREDICTED: ribonuclease pancreatic-like [Monodelphis domestica]
+-RIQRFWRFHVDnpkslipGGNTKYCTVMIRRRQISERGKCKRENTFIHAMAGAILDVCKAQsvkACKVgrkncHTSDHSFKQTLCVLQGfGYYPNCAYV
+SFPKFKKISLACTGLprVPVYVDP-----
+>gi|148710333|gb|EDL42279.1| mCG1042736 [Mus musculus]
+-ASQWFATQHITYKANLQCNVEMQAINMHR-PRCKGLNTFLHTSFINVVGVCGNPsglpApsqkfytepihnstyprcddamlvvnryrprckdvdtfrh
+tsfanvcvcghpsgfCKehksaNcHNSSSQVPIIVCNLTTpGrTYTQCRYQMKGSVKYYRVACENrtpwdspiypVVPVHLHGT----
+>gi|291403447|ref|XP_002717916.1| PREDICTED: hypothetical protein [Oryctolagus cuniculus]
+--------------LYRECNTLMAEKVKESNRSCITQYIFIHEEPKTVKAVCSSPavACEfmkgKcHKSPRPFDLTFCKLSKpGQlTPHCNYHTFVLEKH
+IFITCNDQ------------
+>gi|297459463|ref|XP_001249610.2| PREDICTED: ribonuclease, RNase A family, 4-like isoform 1 [Bos taurus]gi|297459467|ref|XP_002700563.1| PREDICTED: ribonuclease, RNase A family, 4-like [Bos taurus]gi|297479281|ref|XP_002690777.1| PREDICTED: ribonuclease, RNase A family, 4-like [Bos taurus]gi|296483458|gb|DAA25573.1| ribonuclease, RNase A family, 4-like [Bos taurus]
+--------------HKYYCDLMMKARGLATDQSCKKNKTFVHSVSPGTRGLCEGPavTCRkmsevyNcHL--IIFKVTQCNLYPeAVPPHCYYEGVTFQM
+DVRIVCVGKRPIHLDE-----
+>gi|38605204|sp|Q7YRH2.1|RNAS9_MACNE RecName: Full=Ribonuclease-like protein 9; Flags: Precursorgi|33243445|gb|AAQ01504.1| LOC122650 [Macaca nemestrina]
+-------------YHRDYCNEEIMRKNVYHKQRCVTEHYFLLMQYDELEKICYNRfvPCKNgvrkcNRSKGLVEGVYCNLTEaFKIPRCKYKSFYRRGYV
+LITCAWqneihkLIPHTIND-----
+>gi|300872939|gb|ADK39282.1| RNase-Cwar1 [Celestus warreni]
+-DFEYFQKHHVDfpkpgtWNDDVYCRMILYKRCI--GF-GLEWTYIIHATEEQLKAICTVDgKRLTgaYRNLTPLPLASCydT-----NNDYAFHGESLT
+GIFEVQCKDGLPVTFLK-----
+>gi|149568755|ref|XP_001515593.1| PREDICTED: similar to ribonuclease 13 [Ornithorhynchus anatinus]
+--ARTFRLMHIDfprsefaPGFRGYCNGLMAYVRAQReSWQCPEKHFVLHAPAATVRAICAHTdsFCEDfgefcTRSHKPLPVTTCARTPgLPPSVCRYN
+ATVHvqSHRVWLLCSS-------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+E 1 2910 * 5201 3357 * 4771 4946 5278 * * * * 4320 1575 4064 3464 4058 * * 4290 1
+ 0 * * * * * * 4534 0 0
+
+N 2 3692 * 2787 6109 * 5579 * * 5800 6117 5481 3269 4212 5121 1866 2978 3809 * 5130 * 2
+ 17 * 6411 * * * * 5418 0 0
+
+W 3 2479 * * 6590 3031 5419 * 4629 * * * * * * * 4120 5256 6549 2580 1464 3
+ 0 * * * * * 0 5546 0 1000
+
+A 4 4168 * 5707 2463 * * 6056 4567 2958 4868 6812 4112 * 1567 4250 4204 6296 * * * 4
+ 34 * 5438 * * * 0 6040 0 1000
+
+T 5 6083 * 3574 * * 6827 3937 * 2082 * 6651 4224 5969 6618 4131 4166 2988 6589 2200 4858 5
+ 0 * * 0 * 481 1819 5804 1098 1162
+
+F 6 * * * * 20 * * * * * * * * * * * * 6212 * * 6
+ 0 * * * * * 0 6044 0 1000
+
+Q 7 4162 * 7287 2748 * 7274 * 5641 3258 1853 6078 * * 2288 3706 6059 * 6063 5821 4748 7
+ 34 * 5441 * * * 0 6044 0 1000
+
+Q 8 5324 * 6928 4051 * * * 2300 3037 4705 5849 4446 * 4770 1803 * 2674 * * * 8
+ 0 * * 1273 770 0 * 5807 1162 1162
+
+K 9 * * * 5162 5858 * 4278 6106 2293 3557 5760 * * 941 4366 * 6381 * * * 9
+ 46 5472 6865 0 * * * 6073 1098 0
+
+H 10 * * 6970 * * * 102 * * * * 5927 6729 * 5345 * * * * 6692 10
+ 17 6410 * 0 * 481 1819 5852 1015 1162
+
+I 11 * * * * * * * 1660 * 3400 3410 * * * 5644 7102 6052 1426 * 3637 11
+ 716 2343 2364 2082 389 0 * 5848 2151 1000
+
+I 12 5614 * 1184 5381 5493 3786 5603 5830 5150 * * 5134 6149 5777 5415 4299 3077 5415 * 3691 12
+ 1158 858 * 2182 359 516 1733 5887 3397 2298
+
+N 13 5719 * 3815 3803 6393 2596 * * 4261 5991 * 2155 3856 3707 4810 3168 5975 6690 4550 7013 13
+ 27 6690 6809 1915 444 1556 600 6009 1074 1596
+
+T 14 4338 * 5608 7030 6555 2676 7064 5972 5349 5848 2998 3016 3946 5527 4529 2760 3588 4087 6728 6349 14
+ 28 * 5707 1335 728 757 1292 6021 1302 1485
+
+P 15 3485 * 2360 * 4204 4123 4501 6572 5004 5642 * 3240 4644 6298 4044 2909 3004 5538 * * 15
+ 0 * * * * 759 1289 6580 0 1290
+
+I 16 5136 7287 2822 4500 * 5669 4116 4999 3830 6874 * 2732 2924 6182 4395 3616 4427 4719 * 3600 16
+ 25 5857 * 1000 1000 1178 841 6458 1076 1080
+
+I 17 5748 * 3669 4376 5503 4064 5737 3284 4533 4099 * 5081 3446 3316 2773 5321 3787 3844 * 6099 17
+ 0 * * * * * 0 6463 0 1015
+
+N 18 6152 * 4177 5697 6349 6776 * 7408 3866 6534 * 3513 6218 3362 3608 6640 6973 * * 982 18
+ 0 * * * * 0 * 6463 0 1015
+
+C 19 * 0 * * * * * * * * * * * * * * * * * * 19
+ 0 * * * * * * 6481 0 0
+
+N 20 7063 * 2567 5316 7129 6473 * * 4404 * * 827 * 6548 5006 5176 3601 * * 5843 20
+ 0 * * * * * * 6481 0 0
+
+T 21 3943 * 3778 4076 * 3973 4786 5090 4146 3763 5006 4310 7110 3464 4202 3664 3008 3232 * * 21
+ 0 * * * * * * 6481 0 0
+
+I 22 2451 6860 * 2600 * * * 3555 5322 3417 1734 * * 6845 * 6856 4037 4035 * * 22
+ 0 * * * * * * 6481 0 0
+
+M 23 * * * * * * * 3195 * 3365 397 * * * 6550 * * 5402 * * 23
+ 13 6841 * 1000 1000 * * 6481 1000 0
+
+D 24 3462 7494 5630 5005 * 4898 5903 5693 2410 4779 5036 5768 6653 3699 1837 3663 * 4942 * 5006 24
+ 20 6174 * 0 * * * 6481 1024 0
+
+N 25 4176 6482 5588 4353 * 3992 5214 4800 3259 5219 4956 4300 7068 4238 1969 5576 5457 3564 * 3650 25
+ 57 4695 * 0 * * * 6481 1200 0
+
+N 26 5085 * * * * * * 3413 2922 5023 * 4773 5287 6796 1042 * 6587 2771 * * 26
+ 29 * 5653 * * * * 6481 0 0
+
+I 27 6636 4955 6720 5562 * 2599 5538 4524 3706 3633 6531 1455 * 3879 4180 6763 * 5692 6329 * 27
+ 16 6465 * 1177 842 0 * 6588 1173 1098
+
+Y 28 6109 * * * 3776 5220 7388 2217 3298 2859 2616 3733 * 5093 4215 * * 3895 * 4779 28
+ 119 * 3654 * * * 0 6472 0 1009
+
+I 29 5405 * * 4850 4751 * 3357 4442 4628 4657 * 3997 * 5319 5426 4819 1693 6216 5371 2414 29
+ 112 4478 5078 1600 577 3355 148 6349 1246 1686
+
+V 30 5560 * 4928 3289 5318 6400 5288 5027 3406 * * 3393 4286 3315 3382 3659 2633 4175 * 5833 30
+ 1312 3773 932 219 2831 1888 454 6364 1390 1870
+
+G 31 * * 2752 5369 * 2511 4046 * 2500 * * 2904 4416 * 2971 3230 * * * * 31
+ 33 5460 * 1000 1000 522 1719 6129 1026 4348
+
+G 32 6120 * 6293 6522 3937 1798 5183 * 4299 6236 6735 3167 4111 3128 3101 4807 5195 * 4476 * 32
+ 76 * 4276 * * 202 2933 6395 0 2145
+
+Q 33 * 6583 4596 6598 4935 6771 4044 7105 3565 7223 * 3470 3591 3504 2055 3470 4498 4678 5962 4463 33
+ 84 4149 * 1232 800 691 1394 6304 1309 1369
+
+C 34 * 78 * * * 4748 * * * * * * * * * * * * * 6045 34
+ 22 6045 * 0 * 0 * 6441 1037 1101
+
+K 35 * * * 6646 * * * 5016 468 4220 6945 * 4238 6161 5967 * 5850 4529 * 5016 35
+ 0 * * * * * * 6481 0 0
+
+R 36 5265 * 2950 2930 5774 5312 7116 * 2858 6172 * 4252 2280 4733 3461 4938 4640 5051 * 5553 36
+ 0 * * * * * * 6481 0 0
+
+V 37 5005 * * 2979 4999 * 4949 2930 3362 3355 5619 6114 * 3297 4100 5776 3989 2785 5006 * 37
+ 0 * * * * * * 6481 0 0
+
+N 38 * * 6938 6161 * * 2815 * 5410 * * 446 * * 5974 * 5006 * * 5016 38
+ 0 * * * * * * 6481 0 0
+
+T 39 6641 * * * 4423 * * 5760 6161 * * 6359 * * * 5049 420 6641 * 3171 39
+ 10 * 7116 * * * * 6481 0 0
+
+F 40 * * * * 238 * * 4007 * * * * * * * * 6190 4658 * 4773 40
+ 20 * 6158 * * * 0 6476 0 1000
+
+I 41 6024 * * * * * * 904 * 1870 * * * * 6890 * * 2570 * * 41
+ 0 * * * * * 0 6455 0 1102
+
+I 42 * * * * 5609 4981 558 5623 5500 3851 * 7060 * 4385 5811 * * 4629 * 4521 42
+ 0 * * * * * 0 6455 0 1102
+
+S 43 2016 * 3609 1953 * 3981 * * * * 4667 6872 * 7187 6891 3430 2571 5327 * * 43
+ 0 * * * * * 0 6455 0 1102
+
+S 44 6712 * 3785 5561 * 6478 6998 6539 * 5627 6207 3188 2397 6573 4392 2077 2220 5404 * * 44
+ 0 * * * * * 0 6455 0 1102
+
+A 45 3926 * 4537 3765 2252 5319 7143 4796 3562 3395 * 6475 2728 6070 7123 4950 6690 * 5163 3243 45
+ 65 4916 6478 461 1870 * 0 6455 1180 1102
+
+T 46 2441 * 3839 2863 * 3498 6105 7224 3371 * * 4287 3710 4717 3551 3764 4900 6504 4915 * 46
+ 0 * * * * 1696 532 6439 0 1177
+
+T 47 4799 * 2486 3187 7421 4879 6048 7268 3713 6827 * 2471 5161 3635 4941 3681 3416 5770 * 5802 47
+ 0 * * 3000 193 1381 699 6455 1000 1102
+
+V 48 7074 * * * * * * 1825 * 2618 * * * * * * 6095 908 * * 48
+ 0 * * * * * 0 6460 0 1037
+
+K 49 3328 6891 5824 4971 * * 6218 6317 1916 4231 5488 4567 * 2910 3265 5941 4095 3037 * * 49
+ 0 * * * * * 0 6460 0 1037
+
+A 50 1226 * 3983 5006 * 3719 6437 * 3346 7580 * 4298 5800 6879 4213 3715 3922 6181 * * 50
+ 0 * * * * * 0 6451 0 1037
+
+I 51 3995 * * * 4284 * * 1735 * 3102 5544 * * * * 6728 3635 1483 * * 51
+ 0 * * * * * 0 6451 0 1037
+
+C 52 * 0 * * * * * * * * * * * * * * * * * * 52
+ 16 * 6541 * * * 0 6451 0 1037
+
+T 53 4794 * 4723 5113 4826 2310 5876 5523 3697 5178 * 3461 * 5022 3243 3503 2965 7693 6553 4112 53
+ 178 3597 4901 124 3598 1250 787 6442 1591 1113
+
+G 54 6114 * 5312 5005 * 2276 4814 * 4383 5017 5731 2691 5109 3577 3754 4328 3238 4830 5847 4662 54
+ 39 5242 * 386 2091 2233 345 6509 1166 1256
+
+V 55 3251 * 4845 4375 * 3182 7244 3588 4063 4638 * 4575 1994 4967 4116 4275 4134 5590 * * 55
+ 4684 57 * 897 1111 757 1292 6522 5811 1188
+
+I 56 2795 5540 5185 5093 4013 4563 * 3856 4124 5725 * 3606 3492 3675 6016 5524 2434 5855 * 4672 56
+ 26 7311 6414 5781 26 * 0 6530 1000 1466
+
+N 57 4950 822 * 6702 * 4774 * * 4622 6682 * 5216 3385 5439 3602 4164 5531 * * * 57
+ 9 * 7404 752 1299 1362 711 6516 1173 1538
+
+M 58 7022 * 3755 3963 6550 * 7172 * 1471 4112 5352 4764 4169 4815 3815 5012 3766 5138 * 4024 58
+ 863 1187 6550 1880 457 1555 600 6531 3608 1342
+
+N 59 7339 * 3616 * 5349 4600 * * 4122 6669 * 609 * 6560 5377 5032 4512 6107 * * 59
+ 3196 167 * 1294 756 306 2385 6526 5503 1358
+
+V 60 * 6405 * 6584 4374 * 1347 5966 6640 * 6476 4589 6772 * 2907 * 3963 3229 6716 2890 60
+ 14 * 6716 * * 0 * 6573 0 1015
+
+L 61 5968 5521 4169 5411 * 5544 5392 3769 3147 3057 5790 4077 * 2879 2394 5019 3799 6145 * 6487 61
+ 53 5585 6025 0 * * 0 6577 1098 1000
+
+S 62 * * * * * 5233 5457 * * * * 4940 * * 5521 297 3607 * * * 62
+ 33 * 5471 * * 1011 989 6542 0 1262
+
+T 63 5281 6810 6128 3667 * 4749 5052 6929 3352 4696 4885 3475 3808 4632 3742 2224 3000 7433 * 7603 63
+ 0 * * * * 0 * 6509 0 1238
+
+T 64 4528 * 3985 3850 7171 4063 5256 6035 3728 6295 5300 3882 * 3452 4018 2134 3374 4507 * 6239 64
+ 0 * * * * * * 6584 0 0
+
+R 65 5038 * 6345 5313 * 6218 6424 4850 3341 3924 * * 1761 3353 3238 3205 4081 4875 * 7102 65
+ 0 * * * * * * 6584 0 0
+
+F 66 * * * * 1255 * * 3197 * 2984 3344 * * * * * 5886 2120 * * 66
+ 0 * * * * * * 6584 0 0
+
+Q 67 5844 * 3569 4019 7171 5816 4841 * 2964 * * 4873 1851 3893 3590 2964 4997 * * 5175 67
+ 0 * * * * * * 6584 0 0
+
+L 68 6392 * * * 6170 3669 * 2547 6309 1708 3689 * * 6172 * * 4716 1856 * * 68
+ 0 * * * * * * 6584 0 0
+
+N 69 4377 * * * 6628 * * 3551 * 6591 * 5629 5663 * * 5329 633 2876 * * 69
+ 30 * 5606 * * * * 6584 0 0
+
+T 70 6434 * 2249 4331 5297 * 4624 3277 5623 4088 6102 5244 * 4285 4897 4950 2638 3697 * 3570 70
+ 0 * * * * * 0 6589 0 1098
+
+C 71 * 0 * * * * * * * * * * * * * * * * * * 71
+ 63 4950 6635 1000 1000 0 * 6589 1309 1098
+
+T 72 6071 * 5571 4282 6335 * 6267 5063 2668 4461 * 2362 * 4513 2563 3892 3117 4148 * 6962 72
+ 112 * 3748 * * * 0 6575 0 1007
+
+R 73 5520 * * 4122 6767 * 3063 5338 6070 676 * 6680 * 6255 3872 * * 4834 * * 73
+ 76 * 4276 0 * 1917 444 6393 1098 1541
+
+T 74 5125 * 5266 4759 * * 6472 2941 3152 6618 4735 5401 * 4667 3502 4530 1460 4973 * 5904 74
+ 18 6354 * 0 * * 0 6279 1009 1839
+
+S 75 5120 6358 6618 4017 * 1786 6344 * 3308 * * 4653 4593 6354 3964 2014 3938 * * 6193 75
+ 4669 192 3555 125 3594 * 0 6279 5248 1839
+
+I 76 3335 * 4891 3748 6245 3244 * 4769 4233 5847 * 6695 4862 3954 4845 1688 3304 6386 * * 76
+ 223 4488 3343 992 1008 683 1407 6077 1312 2411
+
+T 77 4519 * * 6333 * * * 6500 2485 6616 6222 4548 3283 3023 2306 4053 2664 5777 6989 5985 77
+ 249 2658 * 0 * 93 3996 6278 1823 2058
+
+P 78 6084 6087 6034 * 5671 6784 3123 4316 4441 6247 4174 4351 2717 * 3434 4517 4929 5123 * 2010 78
+ 0 * * * * * 0 6575 0 1007
+
+R 79 * * 5546 * * 7551 * 6191 4693 5651 * 4949 740 * 4479 3644 3299 4524 * * 79
+ 0 * * 2000 415 0 * 6575 1007 1007
+
+P 80 5640 * 2385 * * 6055 4493 * 5879 7514 * 1852 2377 3888 4976 4115 4507 6073 * 5553 80
+ 0 * * * * * * 6585 0 0
+
+C 81 * 79 * * * 5550 * * * * * * * * * * * * * 4955 81
+ 10 * 7195 * * * * 6585 0 0
+
+P 82 3375 * 4460 4022 * 6506 3985 4635 2747 * 5059 4174 4492 4076 2080 4484 5313 6623 * 5177 82
+ 0 * * * * * 0 6320 0 1000
+
+Y 83 * * * * 4224 * * * * * * * * * * * * * * 79 83
+ 15 6615 * 1000 1000 * 0 6320 1015 1000
+
+S 84 5365 * 4309 3741 5495 7112 3703 * 2227 5513 * 3330 * 3590 2313 3679 4910 6181 * * 84
+ 0 * * 1585 585 0 * 6320 1000 1000
+
+S 85 3523 * 4074 4475 * 2176 6905 5290 4940 4386 6259 6156 6594 4107 * 2961 2066 * * 6583 85
+ 0 * * * * * * 6585 0 0
+
+R 86 6318 * 4375 4269 3789 7093 6580 3612 3251 6957 6180 4317 * 6533 4340 3037 1785 4213 * 6335 86
+ 16 6490 * 0 * * * 6585 1009 0
+
+T 87 4071 * 5715 4953 * 4419 6001 5392 3726 3891 6558 4480 3117 3302 4108 3160 3825 3801 * 3722 87
+ 0 * * 0 * 0 * 6573 1009 1009
+
+E 88 3760 * 4100 4764 4759 4216 6073 5876 3284 3188 4899 7097 4898 3495 3613 2803 3442 5959 * * 88
+ 22 6073 * 1000 1000 * * 6585 1036 0
+
+T 89 * * 5541 3337 4589 * 5425 4819 5315 6680 4832 2636 4410 3858 4588 3805 2026 5318 6867 4636 89
+ 23 5972 * 0 * * * 6585 1076 0
+
+N 90 4945 * 6032 5364 * 2234 4406 * 2107 * 5156 3787 * 3934 2118 5248 6211 * * * 90
+ 22 * 6019 * * * * 6585 0 0
+
+Y 91 6247 6636 5100 * 2471 6633 3478 3997 3577 4906 * 5474 5526 5417 3287 3870 4982 4205 * 2614 91
+ 0 * * * * * 0 6590 0 1056
+
+I 92 6366 * * * 3398 * * 1120 * 4458 * * 4882 * * 6946 * 2538 * 2529 92
+ 0 * * * * * 0 6590 0 1056
+
+C 93 6884 3101 6950 4949 5473 * * 2283 4654 3705 * 5449 * * 3306 6161 3674 2183 6055 4698 93
+ 0 * * * * * 0 6590 0 1056
+
+V 94 * * * * * * * 1755 * 2983 6391 * * * * * * 823 * * 94
+ 0 * * * * * 0 6297 0 1056
+
+K 95 1218 * * 6574 * 4069 * * 4274 3475 * * * 4975 6062 4672 2002 5456 * * 95
+ 0 * * * * * 0 6297 0 1056
+
+C 96 * 0 * * * * * * * * * * * * * * * * * * 96
+ 0 * * * * * 0 6297 0 1056
+
+E 97 5571 * 2527 1626 * 6277 5935 6426 4330 6483 6626 3175 * 4109 3846 4302 6166 4133 6664 * 97
+ 0 * * * * * 0 6297 0 1056
+
+N 98 * * 2945 5002 * 2217 5152 * 4341 * * 2207 2898 5725 3958 6142 * * 3346 * 98
+ 654 1455 * 3106 178 1035 966 6297 3202 1056
+
+Q 99 6735 * 5612 4227 4104 2253 * 4302 3896 2414 * 2956 * 4666 6140 * 5622 3048 6655 6692 99
+ 124 3606 * 1000 1000 * 0 6137 1464 1000
+
+Y 100 4911 * * * 4831 5217 * 3471 4481 2247 * * 6507 5669 4913 * * 1543 3545 3913 100
+ 0 * * * * * 0 6030 0 1000
+
+P 101 * * * * * * * * * 5940 * * 40 * * 6507 * * * * 101
+ 0 * * * * 0 * 6030 0 1000
+
+V 102 4938 4963 4478 * * * 6230 3983 * * * 4941 * * * * 5427 400 * * 102
+ 0 * * * * * * 6009 0 0
+
+H 103 5235 * * 6623 * * 334 * * 6435 * 6150 6527 * * 6268 4021 * * 4078 103
+ 25 * 5867 * * * * 6009 0 0
+
+F 104 * * * * 1438 * * 3916 * 1579 * * * * * * * 3734 5783 2872 104
+ 0 * * 0 * 0 * 6045 1056 1056
+
+A 105 3643 * 925 4390 * 5150 4502 5800 6947 4953 * 4271 * 4121 5239 * * 4047 * 5734 105
+ 26 5789 * 1585 585 * * 6042 1056 0
+
+G 106 3980 * 3646 2972 * 1720 * * 2741 5586 * 4396 5839 5321 3432 4164 6712 * 7093 * 106
+ 0 * * * * * * 5891 0 0
+
+I 107 * * 3427 5031 * 4405 * 2885 5937 4853 * 6154 * * * 2845 1998 2693 * 3562 107
+ 0 * * * * * * 5280 0 0
+
+G 108 * * * * * 0 * * * * * * * * * * * * * * 108
+ 0 * * * * * * 2239 0 0
+
+R 109 * * * * * * * * 1350 * * * * * 2231 1341 * * * * 109
+ 0 * * * * * * 2239 0 0
+
+C 110 * 0 * * * * * * * * * * * * * * * * * * 110
+ 0 * * * * * * 2239 0 0
+
+P 111 * * * * * * * * * * * * 0 * * * * * * * 111
+ 0 * * 0 * * * 1452 0 0
+
+//
+�HHsearch 1.5
+NAME f2a896c08302b679f64cd8e52af94835
+FAM
+FILE f2a896c08302b679f64cd8e52af94835
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:20:02 2013
+LENG 81 match states, 81 columns in multiple alignment
+FILT 43 out of 45 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 3.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCC
+>ss_conf PSIPRED confidence values
+964430474569999999999999999828989989999999843701777523556773210899999999898886029
+>Consensus
+xxrdxklgKisxexyxxqkvEILxALrkLGexLtxeExxFLxxxxxxxxsxFekVsxxxxxxgxxxxvlaxaxsqvxxxxx
+>f2a896c08302b679f64cd8e52af94835
+MNREGAPGKSPEEMYIQQKVRVLLMLRKMGSNLTASEEEFLRTYAGVVNSQLSQLPPHSIDQGAEDVVMAFSRSETEDRRQ
+>gi|242008131|ref|XP_002424866.1| conserved hypothetical protein [Pediculus humanus corporis]gi|212508416|gb|EEB12128.1| conserved hypothetical protein [Pediculus humanus corporis]
+-ERDFKLGQISEQQFNKCKKEFLTALKQLNENLNDEEIKFLNgNKSVSNNALFEKVTE-ESDKV--EAVVKQVAKEA-----
+>gi|154421834|ref|XP_001583930.1| leucine zipper protein [Trichomonas vaginalis G3]gi|121918174|gb|EAY22944.1| leucine zipper protein, putative [Trichomonas vaginalis G3]
+-KEAWHLKSITKQMYEEKAVEILTALQSLGESLSNEDAAFLKTQMSAKFSEFEESSN-SVNQAQQKSLIDKFGSEA-----
+>gi|340727909|ref|XP_003402276.1| PREDICTED: protein LZIC-like [Bombus terrestris]
+-DCGVKLGKLSKEVSDHQRAEILNALRQLGEKLEPQELQLLEklMLSNIDTTSYVQVPD-NVEKG--RMAMAVLHYST-----
+>gi|221106519|ref|XP_002158224.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
+-QLGISSGKLCGVFYQQQIVEILSALKKLGEVLTHSEEEYLRKNASAKLYQFSNVSE-TIG----DSLLKVVHKEV-----
+>gi|328874161|gb|EGG22527.1| Zinc finger protein [Dictyostelium fasciculatum]
+IQRDVKLAKISKDSYIDQSIEILYALKKLGFAISPEEENFLEQHKSRVMGDFEKVSG-NIGQGTKDNLMSNAATQIQK---
+>gi|124088302|ref|XP_001347044.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|145474481|ref|XP_001423263.1| hypothetical protein [Paramecium tetraurelia strain d4-2]gi|50057433|emb|CAH03417.1| hypothetical protein PTMB.219b [Paramecium tetraurelia]gi|124390323|emb|CAK55865.1| unnamed protein product [Paramecium tetraurelia]
+-DQDYTLQRINQAQYVKETLNCLNQLQDIGIPFTQQEINFINSN--TGKDNFV-IKQ-DNVQG--KTLLKSAEQQL-----
+>gi|308803242|ref|XP_003078934.1| leucine zipper and ICAT homologous domain protein (ISS) [Ostreococcus tauri]gi|116057387|emb|CAL51814.1| leucine zipper and ICAT homologous domain protein (ISS) [Ostreococcus tauri]
+-ERDAQLGKMTAEGAKTERVEVLTALKKLGAPLEDGELEFLRAHMTAGLADFVEek---------------------------
+>gi|170579733|ref|XP_001894960.1| leucine zipper and CTNNBIP1 domain containing [Brugia malayi]gi|158598270|gb|EDP36198.1| leucine zipper and CTNNBIP1 domain containing, putative [Brugia malayi]
+----HRLRKISDEIYEAKKLEILHALYKLNDHLSDEERSIIEAASRISDFQFELASNH-----------------------
+>gi|71998596|ref|NP_001022497.1| hypothetical protein ZK1248.19 [Caenorhabditis elegans]gi|33621047|gb|AAQ23126.1| Hypothetical protein ZK1248.19 [Caenorhabditis elegans]
+-----RSQKMPKQGYLERKFEILMALRRLEETLTEDERKFLSD--------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * * * * 949 * * 1053 * * * * * * * * * 1
+ 0 * * * * * * 2537 0 0
+
+N 2 5151 * 1644 2184 * * * * 3915 * * 3476 * 1859 * * * * * * 2
+ 0 * * * * * * 3922 0 0
+
+R 3 * 5291 * 4342 * * * * 5196 4658 * * * 3221 550 * 4605 * * 5219 3
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+
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+//
+�HHsearch 1.5
+NAME f2afa8933c4998c89a5c39f692e949bb
+FAM
+FILE f2afa8933c4998c89a5c39f692e949bb
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:13:42 2013
+LENG 203 match states, 203 columns in multiple alignment
+FILT 142 out of 1066 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCH
+HHHHHHHHHHCCHHHHHHHHHHHHHHCCCCEEEEEEECCCCCEEEEECCCCCCCCCCCCEEEEEEECCHHHHHHHHCCCHHHHHHHHHHHCCHHHHHHHH
+HCC
+>ss_conf PSIPRED confidence values
+9987379999990246364699999999998999999999999971688760898899998861626788998764488999999999637889999988
+9999999871899999999999987467872899998599998888516789976668752798742056869886456999999999865999999999
+639
+>Consensus
+xxxxxlpxLpyxxxxLepxiSxxxlxxHxxxhxxxyvxxlNxxxxxxxxxxxxxxxxiixxxxxxxxxlxxxxxxxaxxxxNHxxfxxxLxpxxxxxpxx
+xLxxxIxxxFGSxdxfkxxfxxxAxxxxGsGWxwLvxxxxxxLxixxtxnxxxpxxxxxxPlLxiDvwEHAYyldYxnxrxxYvxxxwxxinWxxvxxrx
+xxx
+>f2afa8933c4998c89a5c39f692e949bb
+PYPFKLPDLGYPYEALEPHIDAKTMEIHHQKHHGAYVTNLNAALEKYPYLHGVEVEVLLRHLAALPQDIQTAVRNNGGGHLNHSLFWRLLTPGGAKEPVG
+ELKKAIDEQFGGFQALKEKLTQAAMGRFGSGWAWLVKDPFGKLHVLSTPNQDNPVMEGFTPIVGIDVWEHAYYLKYQNRRADYLQAIWNVLNWDVAEEFF
+KKA
+>gi|220922215|ref|YP_002497517.1| manganese and iron superoxide dismutase [Methylobacterium nodulans ORS 2060]gi|219946822|gb|ACL57214.1| manganese and iron superoxide dismutase [Methylobacterium nodulans ORS 2060]
+-MPYAIKPLGCDPARIK-GMSERLIVSHYENNYGGAVKRLNLIEEQLAGLDYETTPGF-----V-INGLKREQLIAMNSMILHELFFGGLGQES--EPGP
+VLRKAIARNFGSFERWRSEFIAMGKALaGGSGWVLLSWSPrDGQLVNQWAADHAHTLA-GGVPILALDMYEHSYHIDYGARAATYVDTFMQAIRWENADR
+LFFDL
+>gi|338197129|gb|EGO89303.1| Fe/Mn family superoxide dismutase [Clostridium botulinum C str. Stockholm]
+-----------------KGMTSKQLDEHY-KLYLGYINKINEIDKMSKN-----sqfysgS------NPTY-STMRSlKMGetYSLDGVILHQYYFQNIT
+NSN--dYISDKLINIICTQWGCLDNFLSYLKEV-CL-AMRGWAVVCFDPLtSLLRITGSdLHDYGPIW-CSYPILVIDVYEHAYFMDFGTNRAKYIDVMF
+KNLNWKVISSRFNK-
+>gi|50285897|ref|XP_445377.1| hypothetical protein [Candida glabrata CBS 138]gi|49524681|emb|CAG58283.1| unnamed protein product [Candida glabrata]
+---HVVPKLPNGQelsrRGIPKVLSKDGFDLVWSQQQGYVCDKLTLATAGTS-LESYLPFHILLKTAKNQH--QSHIFNLASAAHNNHLFIENILPVTee
+GsalsetNKPSRLLEARLVDSFgHGWDQVKEEMVKSATDnVIGEGWLFLVENSNKELHILTIQNNGTPYyfprnqlfdMnsAirpeeyqhtksvkelvdk
+AselgkkvddwTMPLICVNLWDHAYLADYGvQNRAKYVRNVLDNLNWSVVNNRLF--
+>gi|336373225|gb|EGO01563.1| hypothetical protein SERLA73DRAFT_103425 [Serpula lacrymans var. lacrymans S7.3]
+---HSRKELPYKVEEgLGNFLPPNALKVVAEEYQQGLLDRLNDEVRGTA-EDKMTVAQIVLSTSQSYE--KAMAFNYASLALNNSFFLDNLKPPPpradn
+pgelgnhEGHLNGTYLHsAFRSQMGSLEHFKSSFCAAATGMAGTGYVWLVTDRSGSLAYFPTFAAGTLLvrsrrqvyddkysvlgegspsptdpqsatlg
+stptspvsglarappslnpsspsrtlhtspvsridtagagpsvysagtnepdapnatfrdirSLGEvlIPLFCVSVHEHCWMSaGYGVwGKEAWLKEFWS
+VLDWEKVVKAYTKF
+>gi|322493666|emb|CBZ28956.1| putative superoxide dismutase [Leishmania mexicana MHOM/GT/2001/U1103]
+---FYLPRIDYDVGQgVAPLMSRKQFDVQYHVFHKAAVDRLNAHTLGSE-LEGHNLNVVIRNSS-FDA-SRAVIHAAASEHFNYCFWYRSLRPW-GTAVP
+ARLKEELQLQYSqngTagaVEEVQRLFTVAALSQQSaGGWVYLVWT-GKTFDVIPFDHGTCPIGSDLIPLLALNTHESARCYDYPLAaedeegdeVERFV
+RNFFKTCNWRLVEHYFLQ-
+>gi|164688120|ref|ZP_02212148.1| hypothetical protein CLOBAR_01765 [Clostridium bartlettii DSM 16795]gi|164602533|gb|EDQ95998.1| hypothetical protein CLOBAR_01765 [Clostridium bartlettii DSM 16795]
+-------KLNYNFYDLNDFINSNELKYSYCQ-YGAYLDNLNHILKDYKEFKDASLKDLLTNLDSMPDEIALKVKINASNALNYEYFFNNLSSE-KTFAKG
+KILKEINNSFSSFDNFKKEFEKIALNS-NSDWIFLALNSQNKLYLTTSKEVSSPVIYKDKIILCLNLDKEI----YS-NREQIIHNFLNYVDWNIANKNY
+NS-
+>gi|255714643|ref|XP_002553603.1| KLTH0E02684p [Lachancea thermotolerans]gi|238934985|emb|CAR23166.1| KLTH0E02684p [Lachancea thermotolerans]
+--SYIAPSLEHLArgKGVRGLFSEKGLQTAWFDRADFYTENLNKYMGQSE---EKPLENIVYENAKSAS--KRDIFNNASMLYNLRFALSCLRANDLPsv
+tekpgpqsllaTPSlelkfsndprdngnEKLSAALASSFGSLVEFRSLLLNSNRAISGDGFTWLVARKvqsmhhesvisgTvefDWLYVLNTYNAGSPFN
+fnrvghmsdlkkqlsklqtveetpssnpfqmksveearetesyrdITYVPLLAIDASPKAWITDYGVfGKDLYLERVWESIEWNVVEQRL---
+>gi|340053388|emb|CCC47677.1| conserved hypothetical protein, fragment [Trypanosoma vivax Y486]
+--------------------------------------------------------------------LKRRVNFIASEDFSRKFEEECMRS-SSAVP-S
+EWRNVVTQQFGAMEVLETELVKRAISRREPGWTWLVYDGRrcvdQRLVGMNLPANQTPLTHGLWPLAAVNMTEGALV-----------------------
+-------
+>gi|291412421|ref|XP_002722485.1| PREDICTED: MHC class I-like family A1-like, partial [Oryctolagus cuniculus]
+--------------------------------------------------------------------SGGLLRLGAGGEVECESFLIP-TPHSCFSST-
+----------------------------------------------------------------------------------------------------
+---
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+P 1 * * * * * * * * * * * * 0 * * * * * * * 1
+ 0 * * * * * * 2123 0 0
+
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+ 136 4004 5178 684 1405 * * 5099 1113 0
+
+P 3 2989 * 6677 4486 6387 5314 * 5150 3138 * 3041 5610 2961 4763 6374 2709 3359 4578 * 5094 3
+ 65 5193 5914 1397 689 0 * 5887 1329 1000
+
+F 4 3789 * 6372 * 1837 6617 2179 5514 5276 5637 * * * * * * * 4596 * 1759 4
+ 49 4913 * 1150 864 * 0 6284 1130 1021
+
+K 5 3745 * 6468 3149 6869 5128 4826 5059 3667 5843 * 6347 5121 4762 4025 2621 2188 3951 * 5892 5
+ 0 * * * * 924 1080 6267 0 1096
+
+L 6 6026 * * * 6167 * * 3500 6856 945 4286 * 4237 4369 4603 5821 5246 3103 * * 6
+ 16 6543 * 1000 1000 0 * 6347 1002 1012
+
+P 7 4997 * * 6705 5986 6878 * 4502 3521 5304 5642 * 760 6853 4425 * 4065 4557 * 6586 7
+ 11 * 6992 * * * * 6378 0 0
+
+D 8 4371 * 2572 3137 * 6528 * * 2496 * * 5587 1969 * 4477 4243 3308 7209 * * 8
+ 0 * * * * 0 * 6407 0 1000
+
+L 9 * * * 6629 6309 6513 7672 4604 5342 332 5592 * 5100 * * 6955 * 4538 * * 9
+ 0 * * * * * * 6461 0 0
+
+G 10 4143 * 3901 4611 * 4948 * 6620 3944 5471 6440 4778 897 5957 6513 3722 7008 6629 * * 10
+ 14 6670 * 0 * * * 6461 1005 0
+
+Y 11 6405 6579 * 6407 2336 * 5308 * 6198 5090 * 4303 * 6377 6438 6817 6750 * 5151 788 11
+ 85 5000 5254 2000 415 * * 6461 1148 0
+
+P 12 2344 * 2445 4330 * 3335 5432 * 4612 4458 * 2625 4103 5567 6762 3325 * 6555 * * 12
+ 105 4022 6852 1558 598 1616 569 6455 1328 1120
+
+Y 13 4531 * 5813 4679 3434 * 7255 6393 3921 3561 6945 5612 3829 4556 4785 6400 5189 3690 * 1541 13
+ 274 3016 4348 1787 493 0 * 6458 1734 1119
+
+E 14 3667 * 2151 3569 * 5229 5316 * 3266 * * 2405 5569 5118 4016 3654 4029 * * 6063 14
+ 50 4873 * 778 1263 182 3079 6408 1151 1264
+
+A 15 1459 * 3131 3656 7137 2356 * 6302 4638 5735 * 4138 * 5382 5763 3846 * * * * 15
+ 107 3800 * 747 1307 * 0 6518 1431 1000
+
+L 16 6925 4994 * * 4807 6302 * 3177 * 587 5324 7071 * * 6629 5568 6883 4462 * 5783 16
+ 0 * * * * * 0 6518 0 1000
+
+E 17 4032 * 4891 1160 6183 4748 * * 4418 3682 5004 3995 3558 * 7170 4271 5260 5781 * * 17
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+
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+ 0 * * * * 0 * 6575 0 1297
+
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+ 17 6436 * 0 * * * 6634 1027 0
+
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+ 0 * * * * * * 6666 0 0
+
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+ 0 * * * * * * 6692 0 0
+
+A 22 2600 * 4367 2239 * 4039 6466 * 3968 5838 * 4766 2961 4541 3624 3352 4877 * * * 22
+ 11 * 7088 * * * * 6692 0 0
+
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+ 0 * * * * * 0 6664 0 1004
+
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+ 0 * * 1000 1000 0 * 6664 1004 1004
+
+M 25 7137 * * * 2891 * * 2840 * 1521 2320 6340 * * * 5968 * 3205 * 4919 25
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+
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+
+I 27 4648 6940 6621 4030 3552 * 7595 3344 * 2004 5588 4365 7036 5909 7616 4799 3056 3483 6228 3561 27
+ 0 * * * * * 0 6717 0 1004
+
+H 28 3271 * * * * 6606 455 * * 4582 * 5987 * 5210 * 5514 6454 4688 * * 28
+ 11 * 7049 * * * 0 6717 0 1004
+
+H 29 5545 * * * 3576 * 1562 * * 4898 * * * * 6767 5728 * 5980 2314 1849 29
+ 77 * 4274 * * 1101 906 6717 0 1064
+
+Q 30 5611 6212 2752 3571 3861 2923 5324 6598 4366 4786 * 3838 * 4692 5281 3185 2923 5238 * 6627 30
+ 105 6445 4095 1000 1000 227 2781 6585 1047 1397
+
+K 31 5961 * 3541 3426 5005 3837 * 5607 1304 * 5816 5088 * 3858 4116 4971 5336 4732 * 6596 31
+ 35 * 5365 2181 359 0 * 6611 1044 1443
+
+H 32 * * * * 4854 * 828 4646 6627 2934 * 5185 * 5069 5014 * 6667 7039 4999 3568 32
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+A 203 1115 5285 * 5239 3330 3554 * 3084 5770 3571 * * * * * 4036 * 5627 * * 203
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+
+//
+�HHsearch 1.5
+NAME f431126caeda0da6cffa83c7e49df465
+FAM
+FILE f431126caeda0da6cffa83c7e49df465
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:15:21 2013
+LENG 217 match states, 217 columns in multiple alignment
+FILT 137 out of 1430 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCEEEECCCCEEEEEEECCCCCCCCEEEEEEECCCCCCEEEEEEEECCCCCCCEECCCCCCCEEEEECCCCCCEEEEECCCCCCCCCEEEEEE
+ECCCCCEEECCCEEEEEEEECCCCCCEEECCCCCEEECCCEEEEEEEECCCCCCCEEEEECCCCCCCCCCEEEEEECCCCEEEEEEEEEEECCCCCCEEE
+EEEEECCCCEEEEEEEC
+>ss_conf PSIPRED confidence values
+9189777978996799799999961788888679999958999848999997215788603266557617999516898168998245523474489999
+5488721653425788875102476213158740132284699999963656998699989984157731145572599689999999950005898799
+99993898874899969
+>Consensus
+xxxxxxpxxxxxxxGxxvxLxCxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxxxLxIxxxxxxDxgxYxCxv
+xxxxxxxxxxxxxxlxvxxxxxxxpxvxxxxxxxxxxxgxxxxlxCxxxxxxPxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxsxLxixxxxxdxgxyx
+Cxvxxxxxxxxxxxxxx
+>f431126caeda0da6cffa83c7e49df465
+EVKLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKADGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCTR
+DPYGPAAYWGQGTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVT
+CSVAHPASSTTVDKKLE
+>gi|338724447|ref|XP_003364946.1| PREDICTED: hypothetical protein LOC100629784 [Equus caballus]
+DTKVTQrPGHLVKGKEQKAKMTCVP---IKAHIHVYWYRRKLEGEFEFLVYLQ---NNDVIDKIEGFDQQFSAQCPK-NASCSLEIKSTEPGDSALYFCA
+SSESTvLNDTFDKSEVAYV---GPVDAKIYQMPAFLLTGVEQDVTLEC----------------------------------------------------
+-------------------
+>gi|168985006|emb|CAQ10833.1| major histocompatibility complex, class I, C [Homo sapiens]
+----------------------------------------------------------------------------------------------------
+-----------------------HPKTHVTHHL---VSDHEASRR-WNLpevgscggAFWrRAEIHVPCaaRGAAGAPHPE-------------------
+----------------------------
+>gi|341890830|gb|EGT46765.1| hypothetical protein CAEBREN_12792 [Caenorhabditis brenneri]
+---------VVLPSGHALRLECSAYSAPT--GSIQWTFEG--------VVIS--GSDKTNRTENEFNkEALVSE--SMSVLSELHIDCPQ---SGRYTCS
+ATNSFdtitaQATVRIEGHHRHCHPTK--GPKISQYSDMRLELNGNTASVWCD--S-SNQDVSWSWstRSDGEITTDDHY-LVK-D-nE------LIIKN
+VSWNDtKSYFCQASNSYGSVTRE----
+>gi|221330930|ref|NP_001137898.1| CG42256, isoform F [Drosophila melanogaster]gi|220902492|gb|ACL83253.1| CG42256, isoform F [Drosophila melanogaster]
+--------------------vaknpaaeikytallqvKGSVLAYPS--QKLN-TEHK-KRKPHKYRshllskl---------------------------
+-kLSQCSLTLAA----slkp----FI--------------------------------------------------------------------------
+----------------------------------------------
+>gi|149597420|ref|XP_001520231.1| PREDICTED: similar to butyrophilin [Ornithorhynchus anatinus]
+--VIGPAEPVLALEGGDTEMPCHLNPKESAEFmEVRWFRSR----PSNIVHLY--DNREELFREQmeEYQGRTELVRDAmDYGSVAVRLLNVRVSDEGNY
+HCSFYDG----NTVDRAPLELQVvGSTAQCSIFMEHFSWIS-----LILDLFP-DWIPDlfPI-LQMrelsEGGVNIKCPKSYGIGHTCTMFSLddifgn
+fisaplfptaLSLMVALGVT--LPVLGLIIAGglyLIWKQNMDIEK-
+>gi|259089625|gb|ACV91668.1| RT02067p [Drosophila melanogaster]
+---------LRVLVNSSAQIKCDVGSSQADDkvLLVVWYK---NNLPIYSYDTRGAHAGTPSHWRDEevLEDRAVFRTH--KEPAELIINPVKEKDAGNF
+RCRVD-------FKLSqtrnsnVNLEV---VVPPTQPIIFNERRLRIDSragpyeegGSLEVTCVVYGGSPPPT-VIWlMNGQLQNSVVDYTYDGAiNSK
+LVV---RNLSRIHQ-HAVYTCQASNFHKKYVATN-IT
+>gi|335300333|ref|XP_003358857.1| PREDICTED: OX-2 membrane glycoprotein-like [Sus scrofa]
+----VVTQDVRERLNTPASLRCSLQN-PQEVLIVTWQKIKAVS-PENMITFS---KNHGVVVQPAYKDKINITQLGLMN-STITFWNTTLEDEGCYKCL-
+-----FNTFGAGKISGIACLTLSvQPTVSLHYKLSED----QLNITCSANAR-PAPM-ISW--KISGSGIENSTEILVhpNGTTSVTSILQIKDPKSQvG
+KEVICQVLHLGTVTDYRETV-
+#
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+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
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+
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+
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+K 67 4990 * 3621 3863 6240 4472 6277 * 2424 5128 6515 3418 3413 4066 4118 3258 4173 5254 * 5031 67
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+G 68 4393 * 3409 3063 * 1997 5572 * 3934 6466 6576 3567 4153 4850 5099 2897 5118 * 6330 * 68
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+
+T 200 * * 5694 4731 5578 5419 6583 3583 3850 5699 5913 6613 * 4129 3742 2762 1827 4726 6436 3664 200
+ 0 * * 1585 585 1631 563 10187 1000 1341
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+C 201 * 42 * * * 6969 * 6876 * * * * * * * * * * * 6358 201
+ 0 * * * * * 0 10185 0 1179
+
+S 202 5087 5327 * 3143 5790 6879 5780 3933 3918 4383 5552 4984 * 3184 3630 4185 3157 2558 5785 6744 202
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+
+V 203 1423 * * * 4601 6604 * 3836 * 6270 7227 * * 6563 * 5844 5554 1195 * * 203
+ 22 6019 * 0 * 0 * 9826 1143 1179
+
+A 204 3908 * 3820 2894 * 4374 6693 5767 3172 * 6386 4764 * 3591 3577 2519 3136 5925 6761 6462 204
+ 38 5264 * 705 1371 * * 9813 1277 0
+
+H 205 * 6123 6212 * 6310 5038 1336 6429 6573 6591 * 1510 * 5074 5992 4335 4830 * * 5711 205
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+
+P 206 4967 * 5509 2337 * 3811 6328 5461 3791 6066 * 3893 2808 4768 3751 2834 5468 4071 * 6489 206
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+A 207 2102 * 4455 4879 5165 2540 * 4786 6675 4339 * 5159 * 4668 4590 2531 3986 4905 6161 * 207
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+
+S 208 3330 * 5007 * 6235 1702 * 4676 * 1984 5327 5936 * 5293 * 3207 4388 5533 * 6313 208
+ 34 5425 * 557 1642 0 * 9409 1145 1014
+
+S 209 4974 * 4734 2545 * 4213 4747 * 2934 6403 * 5259 2675 4223 5111 3076 3499 4640 6245 * 209
+ 171 6029 3371 0 * 0 * 9331 1021 1000
+
+T 210 3130 * 5895 2861 6106 4630 5886 * 3632 5504 5559 3773 * 4356 4317 3124 2515 3762 * * 210
+ 0 * * * * * 0 9111 0 1949
+
+T 211 3888 * 3598 3610 4198 5080 6238 * 6000 6007 * 2864 2066 4980 3704 3711 3945 6198 * * 211
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+
+V 212 3142 6019 5610 * 6386 4997 6130 2321 4495 2536 6191 6020 * 6219 * 3386 4059 2615 * 6070 212
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+
+D 213 4762 * 3856 2704 * 5750 * 4524 * 5744 5887 3902 * 3654 3949 2911 2092 3958 * * 213
+ 22 * 6019 * * * * 9062 0 0
+
+K 214 1935 5662 * 5765 * 5761 5693 3515 3450 4298 5580 5570 5347 4101 2841 4746 4690 3434 * * 214
+ 0 * * * * 0 * 8830 0 1000
+
+K 215 5525 * 5733 3693 4106 5665 5788 * 3230 5762 5616 2670 * 4191 3564 2848 2583 5497 * 5923 215
+ 77 4258 * 3718 114 * * 8836 1282 0
+
+L 216 5535 * * * 2708 * * 2596 * 1464 4503 * * 5484 * * 5424 2266 * * 216
+ 0 * * * * * * 8557 0 0
+
+E 217 * * 4905 2059 * * 4794 4942 * 4720 * 3779 4619 4810 3635 * 1656 3772 * * 217
+ 0 * * 0 * * * 7368 0 0
+
+//
+�HHsearch 1.5
+NAME f56a6e550ea46518bc972010f973cfbd
+FAM
+FILE f56a6e550ea46518bc972010f973cfbd
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:05:14 2013
+LENG 216 match states, 216 columns in multiple alignment
+FILT 138 out of 1345 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 10.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCEEEECCCCEEEEEEECCCCCCCCCEEEEEEECCCCCCEEEEEECCCCCCCCCCCEEEEECCCEEEEEECCCCHHHCCEEEEEEECCCCCEE
+ECCCEEEEEEEEEEEEEEEEEECCCEEEECCCEEEEEEEECCCCCCCCEEEEEECCEECCCCCCEEEEEECCCCCEEEEEEEEECCCCHHHCEEEEEEEE
+ECCCCEEEEEEHHHCC
+>ss_conf PSIPRED confidence values
+9299889978997999799999970788788708999990799983799970564466678737986069816999856776558689999980788347
+6362689999731012469981786068649849999998357799819999999999867752014577289858888999981278775908999999
+1897589998355089
+>Consensus
+pxxxxxxxxxxxxxGxxvxLxCxxxxxxxxxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxrxxxxxxxxxxxLxixxvxxxDxGxYxCxvxxxxxxxx
+xxxxxxlxvxxxxxxxpxvxxxxxxxxxxxxxxxxlxCxxxxxxpxxxxvxWxxxxxxxxxxxxxxxxxxxxxxxxxxxsxLxixxxxxxdxgxytCxvx
+xxxxxxxxxxxxxxxx
+>f56a6e550ea46518bc972010f973cfbd
+PSALTQPPSASGSLGQSVTISCTGTSSDVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFV
+FGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVT
+HEGSTVEKTVAPTECS
+>gi|326703679|gb|AEA06491.1| MHC class I antigen [Macaca mulatta]
+----------------------------------------------------------------------------------------------------
+--------------------------------htiqtmygcdlgpdgrllrgyeqyaydgrdyfalne--DLRSWTAADMAAQN----------------
+tqrkweaagvaeqw----RAYLEGECLEWLRRYLEKGK------------------et--LQ------
+>gi|332257155|ref|XP_003277679.1| PREDICTED: poliovirus receptor-related protein 2-like [Nomascus leucogenys]
+--GRPPaPARTPSNLtfraGEAEHLPRPPPAPrAPSR-VSPSWLAPPTPTPYTSDS-LEETLTPPFCiSltttpillnptAHPTPACLSPSP--------
+---------------FLGFP-----RRKAKPENQAEAQKVTFSQDPTT----VALCISKEGRPPA-RISWLSslDWEAKETQVSGTL-----AGTVTVTS
+RFTLVPSGRADGVTVTCKVEHES-------------
+>gi|296246053|gb|ADH03430.1| variable region-containing chitin-binding protein 3 [Branchiostoma floridae]
+-MTVRTtHTEVEVHAGGTVELPCAYQLANDTQPPVISWLKG-AAPDRSTKVFKGNYnwqgeglgfvesdSYKESFGDFLGRasvANLAAPTLRLTHVHPQ
+DGGRYWCQVAQWSIRTEFGLDAKsvvLKVTGH--TPSnNVHVSTAEVVQVDEGnDITMTCPCTNCAN---ANvTWYTGPtffenyetgtyqplaNKNQFG
+ITWFSSEIAGRASFSGARNLVIRAAKITDAGRVWCELATGQSELDADRS-----
+>gi|149597420|ref|XP_001520231.1| PREDICTED: similar to butyrophilin [Ornithorhynchus anatinus]
+--VIGPAEPVLALEGGDTEMPCHLNPKESAEFMEVRWFRSRPS--NIVHLYDNReelfrEQMEEYQGRTELVRDamdYGSVAVRLLNVRVSDEGNYHCSF
+YDGN---TVDRAPLELQVVGSTAQCSIFMEHFSW-----ISLILDLFP-DWIPDlfP-ILQMRelSeGGVNIKC--PKSYGIGHTCTMFSLddifgnfis
+aplfptaLSLMVALGVT---LPVLGLIIAGglyLIWKQNMDIE-----
+>gi|47211727|emb|CAF92525.1| unnamed protein product [Tetraodon nigroviridis]
+--DVTVsQSSVQVARGQAAILPCSFTTSAALNNLNIIWMViplSNANQPEQVPKHNNGrtkNPQPTNPNtwvRvniFTHTHTHTHTHTHTHTHTHTHTHT
+HTHTLVALGS-----VPgplncsiRHLFRK-VN-SPSDCPVLgvcASGL----CVPALLVCMCDVPI-FP-SVSWLRSESwFVAT-----PQIGCPD---
+QIQGTVTLKNISTSTSGLYQCTSSN---------------
+>gi|327265502|ref|XP_003217547.1| PREDICTED: macrophage colony-stimulating factor 1 receptor-like [Anolis carolinensis]
+--------------------------------------------------------------------------IRLRRVGMDDNGWYKCRALVQG-Q--
+-----WVQ-------SPKIGLIVKGFIIFYYIFTYFFVTAHCIVL-AFGSY-----CK----CHIKLELSFK-----------------------ICILT
+K----KQSAL------
+>gi|170588355|ref|XP_001898939.1| Immunoglobulin I-set domain containing protein [Brugia malayi]gi|158593152|gb|EDP31747.1| Immunoglobulin I-set domain containing protein [Brugia malayi]
+-------EDNNIYEKDHLELICILPLN-d-D--FDVVWMRDDV-qLAY---------------PERHVTIYSQKFITTLDDISSNESGNYECIAKSKN-T
+Hiyrs---YTLHIKINVVVAPHIVGTEEEYEHLAKYGEKAELVCPIEGEPEP--LYRWLKNGIEYNg-YGSLT-------------KKIDFPRVLVEDKA
+TYTCVAKNRAGSQQ---------
+>gi|313240002|emb|CBY32362.1| unnamed protein product [Oikopleura dioica]
+------PDTECVPNNGKLVFE---avvANEA----LGTKWFR--NGQEIT------------SqNTHFKIEQRGRTRKLIIENANLMDDGLFEIRAGEEK
+------SSCEVHV-----LEAPTAVTKGFEDLQLveGEDAKFTA----TLsTAHGRFKILKDGIEFGLNDN--QTVTRDG----AVVNFEIKKISKSDAG
+FYE--------------------
+>gi|3702284|gb|AAC62834.1| PTPsigma [AA 524- 1926] [Homo sapiens]
+------------VPGQPMNLRAEARSE-TS--ITLSWSP--P-RQE-------------SIIKYELLfrEGDHGREV---------GRTFDPTTSYVVED
+LK--PNTEYAFRLAARSPqglG------AFTPVVRQRT-----------------------LQSKPSAPPQDVK--------------------------
+-CVS-----------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+P 1 4431 * * * * * 4054 * 3123 * * * 361 * * * * * * * 1
+ 0 * * * * * * 6585 0 0
+
+S 2 4359 * 5238 * 3750 5070 * 2435 5195 3112 5135 * 3388 * * 3809 3785 2319 * 5349 2
+ 0 * * * * * * 8887 0 0
+
+A 3 4716 * 5264 3035 4756 * 5976 4193 3664 4705 5755 5509 * 3291 4626 4324 3971 2048 5804 4945 3
+ 0 * * 2807 222 * * 9515 1000 0
+
+L 4 5108 * * * 4364 5752 * 2793 * 1775 * * 6018 * * 4973 4040 1695 5996 4839 4
+ 24 * 5917 * * * * 10015 0 0
+
+T 5 6043 * 6327 2981 6005 4299 4949 4350 5173 3173 5762 5008 5885 5232 4318 3475 2032 3614 * * 5
+ 0 * * * * 0 * 10005 0 1037
+
+Q 6 4565 * 6224 5269 * 6151 * 5910 3304 4071 * * 3075 1369 5040 3576 3816 4803 * * 6
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+
+P 7 4863 * 4050 3625 * 6318 5476 4815 4691 5391 * 4489 1366 4334 * 3417 4094 4133 * * 7
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+
+P 8 3718 * 3772 3389 6605 3180 6429 6627 5497 * * 4645 2153 4218 4176 3194 3536 6433 * 6647 8
+ 14 6737 * 0 * * * 10563 1000 0
+
+S 9 4603 * 4126 3551 6569 4990 4509 4584 5013 4640 6574 3781 3077 5117 5604 2432 3348 4123 5950 6739 9
+ 0 * * * * * * 10651 0 0
+
+A 10 4786 * * 3931 4944 5594 6615 3713 6810 2468 4999 * 5576 3520 5180 6574 4648 1590 * 5694 10
+ 92 4021 * 0 * * * 10684 1886 0
+
+S 11 5219 * 4445 3357 5012 6613 6796 4442 5099 3365 5136 5792 6589 4561 3732 2771 2408 3699 * 5598 11
+ 0 * * * * * * 10724 0 0
+
+G 12 2135 7146 * 6784 5175 4005 * 3923 5851 2637 6798 * 6769 5795 5742 6587 4535 1715 * 6767 12
+ 12 * 6969 * * * * 10970 0 0
+
+S 13 3846 * 4910 5085 4376 5154 4795 3992 3723 2937 6667 5385 4554 3856 4374 2877 4109 3930 5984 5868 13
+ 13 * 6851 * * 0 * 11004 0 1000
+
+L 14 3485 * 5877 1932 5775 5334 6997 5357 4285 3501 6939 5886 3565 5406 4802 3968 4826 3026 6895 5844 14
+ 11 7068 * 1585 585 * 0 10910 1000 1037
+
+G 15 * * 6808 3957 * 598 6758 * 5954 6790 * 3433 6214 5915 4770 3965 * * * 6913 15
+ 0 * * * * * 0 11059 0 1037
+
+Q 16 4837 6994 2172 2529 6805 2707 5429 6918 4344 6738 * 4631 * 3718 4663 3119 4962 7202 * * 16
+ 0 * * * * * 0 11102 0 1037
+
+S 17 4797 5774 3048 5431 6088 * 5952 * 3664 * * 3073 3238 4436 4639 2362 2548 6033 * * 17
+ 0 * * * * 0 * 11102 0 1037
+
+V 18 2186 * * 7746 5055 7021 * 3365 7246 2655 5210 * 6813 * * 5361 4763 1427 * 7322 18
+ 0 * * * * * * 11143 0 0
+
+T 19 5014 * * 3336 6108 6868 5988 3745 4991 3677 6194 3950 4574 5061 4193 3914 1868 3680 * 5400 19
+ 0 * * * * * * 11143 0 0
+
+I 20 6808 * * * 3077 * 7936 3185 7021 708 3778 * * * * 6981 * 4109 * * 20
+ 0 * * * * * * 11143 0 0
+
+S 21 4763 * 4663 3744 5991 4280 5004 5316 5057 6353 5432 3594 2860 5412 3313 3153 2734 5063 6936 6093 21
+ 12 * 6948 * * * * 11143 0 0
+
+C 22 4437 258 * * 6869 * 7322 5394 7016 5422 * * * * 7928 6346 * 4981 * * 22
+ 0 * * * * * 0 11130 0 1019
+
+T 23 4979 7928 4173 4093 4464 4890 4537 4422 3712 3743 7061 3568 4423 3973 4366 3512 3447 3600 * 5799 23
+ 11 7063 * 0 * * 0 11130 1000 1019
+
+G 24 2461 7014 7066 7001 3171 5762 6984 3421 * 3777 5861 5250 6007 7016 6869 5018 5901 2098 * 2888 24
+ 34 6020 7001 1585 585 0 * 11130 1342 1019
+
+T 25 3886 * 4008 4430 6165 4001 4650 6039 3787 5890 5996 4365 4618 4416 4065 2093 3323 5456 5730 5994 25
+ 76 5837 4873 2296 328 * 0 11134 1164 1001
+
+S 26 4975 6903 3927 4427 6877 1892 7100 6914 5962 3266 6991 4043 3839 4602 6077 3104 3655 5202 * 5892 26
+ 49 * 4891 0 * 1603 576 10976 1000 1845
+
+S 27 4097 6835 4279 3456 2870 3974 * 5272 5670 3834 5846 3839 3699 5524 5972 3056 3910 4967 6065 4696 27
+ 200 6965 3042 1585 585 891 1117 10924 1000 2246
+
+D 28 4489 * 3242 4053 4411 5752 4051 5623 3686 3806 5863 3469 3885 4725 5182 3128 4381 4430 5782 5222 28
+ 75 7154 4511 3000 193 413 2008 10920 1072 3779
+
+V 29 4795 5126 4029 4366 5337 5298 * 4541 4396 3031 5979 4728 2329 5877 6413 3312 4331 3632 * 4314 29
+ 209 * 2890 * * 3498 134 11061 0 2513
+
+G 30 3129 * 4415 3289 * 4127 * 6660 3221 3959 * 4409 4743 4242 4471 3239 3104 3783 * 5600 30
+ 421 5720 2093 551 1655 4760 54 10986 1141 4723
+
+G 31 4804 6939 2808 3664 6117 4010 4741 6355 3532 4799 6257 3506 3510 4291 3975 3306 4576 5282 * 6199 31
+ 1250 6180 821 1000 1000 5385 35 10447 1045 7087
+
+Y 32 4051 5387 4155 3312 3990 3583 4013 * 5270 4174 5125 3384 3945 5242 * 4273 4979 3527 * 3584 32
+ 432 2286 4215 525 1714 86 4119 8678 2015 9516
+
+N 33 3694 * 6997 4991 4456 6040 4693 3528 3928 2805 4734 4643 2841 5925 5830 4667 3742 3755 6821 4631 33
+ 11 * 7020 * * 1194 829 10943 0 2145
+
+Y 34 3643 * 4921 3448 * 5405 4999 4896 4378 3992 5471 3703 6888 3860 3825 2979 3098 3760 6846 5465 34
+ 11 7095 * 1259 781 721 1347 11104 1157 1757
+
+V 35 6168 6928 * 6989 3358 5852 5906 2555 5874 2733 6050 7713 * * * 6094 6080 1375 5228 4668 35
+ 0 * * * * * 0 11130 0 1196
+
+S 36 4708 * 4957 4336 3647 7146 5466 5812 3526 5015 7007 4548 * 4158 3531 2768 2549 4267 * 3790 36
+ 12 * 6924 * * * 0 11130 0 1196
+
+W 37 * 6795 * * 6436 * * 5931 7229 6055 7058 * * 6826 5813 6954 6845 5380 223 6684 37
+ 34 6047 6912 609 1539 * 0 11102 1232 1439
+
+Y 38 6014 5858 6860 5004 2773 5934 4947 4484 4106 3062 4874 4704 * 5408 4639 4775 3895 4325 5910 2297 38
+ 11 * 7015 3000 193 1836 474 11098 1047 1619
+
+Q 39 6968 6151 5029 5979 4624 4936 6014 5884 1928 4070 5365 4961 5383 5514 2164 4801 * 3557 5394 4895 39
+ 455 4357 2175 1674 543 2064 394 11098 1866 1589
+
+Q 40 4878 * 4291 4049 * 3262 4033 5650 4382 5080 6315 4555 5693 2233 6550 2941 5619 3280 * 4631 40
+ 50 * 4879 * * 4879 50 10842 0 5388
+
+H 41 4024 6842 2832 6562 * 3711 4351 * 3092 4485 6864 3864 4521 6604 3662 3275 3295 4572 * 4873 41
+ 137 5132 4016 2369 310 364 2166 10793 1285 5599
+
+A 42 3779 6785 3002 4253 5716 4459 4797 5235 3970 4583 6817 3273 2677 4395 6902 3329 4753 4410 * * 42
+ 137 3749 5955 982 1019 1233 800 11047 2232 3077
+
+G 43 3665 * 3158 4364 6931 1652 5305 * 3456 6743 * 3889 4852 4287 4855 3848 4520 7075 * * 43
+ 68 5420 5477 719 1350 1572 591 11059 1324 2651
+
+K 44 4041 6035 3891 2797 6959 3544 6867 5958 2928 5353 * 3975 4312 3324 4508 3597 4504 4460 6859 * 44
+ 193 5400 3300 0 * 2271 335 11011 1328 2481
+
+A 45 3511 6701 4392 3183 * 3325 5928 4811 3627 3854 4125 3913 3452 5265 4514 4202 4071 4803 * 6877 45
+ 108 4070 6329 1062 941 1236 797 10963 1885 3935
+
+P 46 4481 6709 4335 4315 4619 7186 * 3537 5978 2223 6755 4682 2643 4121 5301 4038 3952 3935 * * 46
+ 142 5904 3693 1329 732 2132 374 11008 1162 3135
+
+K 47 4453 * 3628 2809 * 4669 4718 3351 3651 5283 5797 3837 5233 3602 3592 4019 3973 4474 * * 47
+ 156 * 3287 * * 3198 167 11006 0 4000
+
+V 48 5031 * 6890 4756 3496 6872 * 4136 4699 2758 5713 4545 5622 5258 3949 4033 3458 2802 4259 3995 48
+ 155 * 3298 * * * 0 10771 0 5190
+
+I 49 4001 6653 5452 4559 4585 4873 5305 2628 3721 2452 4903 * 4322 * * 5197 5492 2561 6125 5371 49
+ 69 4421 * 1679 540 4047 90 10555 1652 6240
+
+I 50 3288 5513 6363 6586 4553 3987 5510 2616 4502 3151 5481 5070 6878 5029 5722 3574 4568 2947 * 4655 50
+ 181 5821 3323 2292 329 5130 42 10508 1211 6008
+
+Y 51 4359 6645 3831 * 3160 5634 4327 4989 5614 4409 * 6434 5511 5422 4217 3146 4160 4161 4206 2318 51
+ 65 5676 5348 649 1464 * 0 10817 1200 6774
+
+E 52 * 6464 4011 4153 4894 3647 4821 4197 2941 3974 * 4004 4263 5399 4490 4090 3477 3542 * 4151 52
+ 79 4225 * 1199 825 4676 58 10740 1596 6933
+
+V 53 5600 6263 3572 4497 5497 3599 4548 5708 3857 4732 6590 3463 4488 5318 3936 3641 3030 4094 6298 4185 53
+ 60 4613 * 888 1121 5444 34 10774 1667 6777
+
+N 54 5435 * 3269 5414 * 2643 4534 6517 4483 5443 * 3568 4041 4898 4207 2344 3583 5002 5412 * 54
+ 729 1464 4871 1941 435 5216 39 10318 5391 6793
+
+K 55 4906 * 4009 3559 * 3810 6050 5304 3419 3499 6456 3316 5324 3738 4793 3561 3610 4470 * 3909 55
+ 17 6455 * 3700 115 3650 120 10734 1019 6923
+
+R 56 4187 * 5632 4250 4846 4239 4888 4460 4810 3419 5368 3941 4647 3643 4677 3429 4892 3336 * 3289 56
+ 16 * 6497 * * 2600 260 10797 0 6600
+
+P 57 3742 6486 4401 3413 6848 3592 4897 6622 5471 4594 5156 4460 3799 3522 5096 3124 3959 3672 4931 5523 57
+ 25 * 5880 * * 2588 262 10524 0 6002
+
+S 58 4947 * 4291 3064 5116 3788 4747 4379 3449 4793 6664 4299 3186 4571 4032 3335 3467 5684 * * 58
+ 92 5038 5007 1040 961 5150 41 10796 1360 5579
+
+G 59 4970 6761 4615 2603 * 2604 6770 5425 4576 6418 6432 3918 4069 3766 5600 2766 4518 3629 * * 59
+ 48 6556 5508 0 * 602 1551 10768 1000 5779
+
+V 60 3780 * 4578 6016 2648 4840 5765 3859 5015 3662 6948 5091 4777 5030 5278 3768 4231 3936 6918 2760 60
+ 35 6966 5946 1000 1000 2203 353 11070 1000 3194
+
+P 61 3618 * 3999 4857 5771 4336 7009 6093 3691 4214 4624 3602 2614 4653 3541 3783 3951 5226 * 5379 61
+ 73 4342 * 756 1293 1449 658 11053 1764 3077
+
+D 62 4838 * 3107 3324 6979 2597 4678 7361 4162 4339 * 3626 3945 4173 4921 3419 4179 5980 6808 5823 62
+ 65 4784 6958 1629 563 * 0 11089 1794 2309
+
+R 63 5372 * 5007 4614 6022 4077 6166 4632 3451 5779 6779 4435 5927 6758 1216 3940 5819 4654 6070 5929 63
+ 151 3589 5952 817 1209 1655 551 11064 2505 2507
+
+F 64 4006 7346 5408 4120 2175 7028 5938 3508 5934 3406 7119 6864 6749 4982 6861 5410 4242 3005 6282 2972 64
+ 24 7014 6861 1000 1000 1529 614 11076 1000 2494
+
+S 65 5417 7170 5298 3638 6034 4670 4302 4936 3717 5356 6967 3608 5030 3352 4442 2713 2809 4558 6950 6027 65
+ 81 6884 4435 2585 263 2598 260 11212 1000 2142
+
+G 66 3556 6789 4225 5346 4929 3051 4390 3545 4483 2789 5295 4061 5958 6146 5959 4602 4790 3163 5840 6209 66
+ 50 * 4864 * * 3360 148 11135 0 3019
+
+S 67 5361 * 3398 3603 5605 4046 * 4370 4247 4380 6800 4127 5667 4401 3284 2915 3173 3943 * 5382 67
+ 539 1977 4110 1232 800 * 0 11031 5066 3429
+
+K 68 4463 * 3865 3905 5188 3213 4224 4099 3492 3665 6783 4387 4191 3894 3678 4224 4638 4504 * 6678 68
+ 43 6867 5566 2386 306 2651 250 10960 1356 4315
+
+S 69 5613 * 3063 3090 * 5323 6642 5836 3859 4269 * 3840 4808 3996 4516 2374 3854 5280 6576 4085 69
+ 354 2605 4227 825 1200 439 1931 11020 3608 4240
+
+G 70 4564 * 3943 3783 6978 2613 5127 * 4217 3929 6922 3197 4627 5003 3809 3467 3599 5027 * 4769 70
+ 85 5214 5052 738 1321 1923 442 11093 1334 2847
+
+N 71 4357 5847 3832 5571 5904 2417 4653 * 3492 4853 * 2829 * 4482 4323 3668 3397 4103 * 6938 71
+ 83 4737 5748 1760 505 3892 101 11125 1695 2933
+
+T 72 4447 * 2895 4149 5346 3996 4076 5383 3737 6040 4785 3664 5479 5059 5735 2806 3328 4908 * 4630 72
+ 97 4302 6147 1154 861 2263 337 11046 1897 3306
+
+A 73 3095 5292 * * 3250 3734 5279 6860 * 3951 * 5893 5882 5343 4922 2208 3978 4646 4941 2897 73
+ 34 6043 6912 2000 415 1249 788 11083 1162 3133
+
+S 74 5239 * 4334 4441 5284 * 3903 4189 5934 5143 6215 4477 6043 4160 3982 1718 3024 4339 * 5902 74
+ 11 6987 * 1000 1000 2007 413 11111 1000 2378
+
+L 75 * 6961 * * 4337 * 6858 3743 * 552 4806 * * 5840 * 7036 5799 3580 7235 6913 75
+ 9 * 7363 * * 2842 217 11253 0 2011
+
+T 76 5484 * 5904 5055 * 6913 4181 4403 4323 3508 7043 3777 5456 3609 3202 3069 2400 4209 * 5286 76
+ 17 * 6439 * * 2296 329 11245 0 2022
+
+V 77 * * * * 5004 * * 1090 5412 1800 3983 6865 6999 * * 7047 5799 3588 * * 77
+ 0 * * * * * 0 11119 0 2141
+
+S 78 4113 6867 3798 4452 5977 6999 4294 5454 3262 3566 * 4955 3243 5422 3349 3443 2932 7112 6013 5329 78
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+V 206 3728 * 4071 3416 4363 * 5208 4136 5340 2796 * 5092 6112 3626 * 3815 3708 2338 * * 206
+ 20 6191 * 0 * * * 9882 1000 0
+
+E 207 4479 * 3905 3016 * 6214 * 4392 3028 6104 * 3437 4070 3087 3025 3538 3508 * * * 207
+ 25 5874 * 0 * * * 9854 1022 0
+
+K 208 4078 * 5087 4420 * 5814 4467 4445 2053 3494 4715 * * 4419 2702 4170 5087 3482 6249 * 208
+ 0 * * * * * * 9854 0 0
+
+T 209 4668 5157 4605 5016 6093 5769 5212 * * 5050 * 2955 * 5005 3443 2145 1943 4957 * * 209
+ 0 * * * * * * 9807 0 0
+
+V 210 3398 * * 5726 2877 * * 3096 4918 2779 4029 * * * 5702 5946 3513 2063 * 5024 210
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+
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+ 80 * 4209 * * * * 9255 0 0
+
+P 212 4129 * * 4104 * * * 4020 1994 3216 * * 4073 * 2124 * 3950 4474 3922 * 212
+ 0 * * * * 0 * 6368 0 1036
+
+T 213 3902 * * 2997 * * * * * 4066 * * 2011 * 3156 1878 3111 * * * 213
+ 127 3565 * 0 * * * 6338 1015 0
+
+E 214 * * * 1302 * * * * 2497 2545 * * * 2570 * * * 3690 * * 214
+ 0 * * * * * * 5514 0 0
+
+C 215 * 460 * * * 2898 * * * * * * * * 2846 * * * * * 215
+ 0 * * * * * * 4372 0 0
+
+S 216 * * * * * * * * * * * * * * * 394 2065 * * * 216
+ 0 * * 0 * * * 2847 0 0
+
+//
+�HHsearch 1.5
+NAME f72d3b0c4bbb6e49ce2af6496d1b71a0
+FAM
+FILE f72d3b0c4bbb6e49ce2af6496d1b71a0
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:03:08 2013
+LENG 218 match states, 218 columns in multiple alignment
+FILT 130 out of 1347 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCEEEEECCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCHHHHHCCCCCCCCEEEECCEEEECHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
+HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHCHHHHHHHHHHHCCHHHHHHHHHCCCCC
+CCCCCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+9469993799804999999999859997799846664111257778851988888789889989876699999999867989999999999999999999
+9999999887301279999999999999999999986439802689999999999999999998472111118899999999984899999987476776
+776774454588788998
+>Consensus
+MxxxLxxxxxspxxxxvrxxLxxxxixxxxxxvxxxxxxxxxxxxxxxxxpxxxvPxLxxxgxxlxeSxaIxxyLxxxxxlxxxxxxxxaxxxxxxxxxx
+xlxxxxxxxxxxxxxxxxxxxxxxxlxxxlxxlexxlxxxxylxGxxxtxaDxxxxxxlxxxxxxxxxxxxxxpxlxxxxxxxxxxpxxxxxxxxxxxxx
+xxxxxxxxxxxxxxxxxx
+>f72d3b0c4bbb6e49ce2af6496d1b71a0
+MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVL
+DIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIA
+WPLQGWQATFGGGDHPPK
+>gi|151967108|gb|ABS19434.1| multivalent antigen sjFABP-97 [synthetic construct]
+MSSFLGKWKLSE------------SHNFDA--VMSKLGVSWATRQIG------------------NTVTPTVTF-----------TMDGDTMTML----T
+ESTFKNLSVTFkfGEEFDEKTSDGRSVKSVVTKDSESKI-----TQTQKDSKNTTVIVREIVGDTMKTTVTVDDVTAIR-------NYKR----------
+--------------------
+>gi|145240759|ref|XP_001393026.1| hypothetical protein ANI_1_2296074 [Aspergillus niger CBS 513.88]gi|134077550|emb|CAK96694.1| unnamed protein product [Aspergillus niger]
+-----------------AIALEALNTPYNVKLWEFGndREKgV---KGEVFLRINENgrVPALEDpnTGVVSWESGACMNYVRRVYDKenflGPKGsEQD
+IVDFEKweyfllstlgpmTGQTNWYRHYNGTKNEDALQ------RYSAQTERCYGVLEGQLKKSggQSVLPGRITAVDYHFEPWVREYDFAGLS-LEKYP
+LITQWLRVMTGRKEVQQAYiKI-----------------------
+>gi|336366382|gb|EGN94729.1| hypothetical protein SERLA73DRAFT_143587 [Serpula lacrymans var. lacrymans S7.3]gi|336379053|gb|EGO20209.1| hypothetical protein SERLADRAFT_400352 [Serpula lacrymans var. lacrymans S7.9]
+--LWTVP--GMRQAIVIRSVAALAGLQLDLPEYKHF--EDNKKPEFTAKFPHGKIPALETADGFkLFEGAPIARYLSTLApnsNLLGTNDQEAALVDQWV
+HFAESeISTPNDIMWQmlngylTPYNKPIHNTLAERQLRAINTLETVLATRTFLVTERITLADIVVASSFQRAVGLaiDASARAKLPNTIRHFETLANQP
+KLKEIFGETTYVEKAA---------------
+>gi|254282669|ref|ZP_04957637.1| glutathione S-transferase, N-terminal domain [gamma proteobacterium NOR51-B]gi|219678872|gb|EED35221.1| glutathione S-transferase, N-terminal domain [gamma proteobacterium NOR51-B]
+--LKLINAGPSPFGRKVMVALHEKSIPFKVEWDIPWH----KDTVVTVHNPLQQLPILIaDDGETVFESSYILEWIDTRFPeppLTPSDPEARLEMGRFR
+VLSVGIMDALVRTNFEVSrPlehqsQEWVQRHIRKINGGLAELDREIQDRNFVVGNELTLGDIEVGCVLGqldFIAENIPPlkeffaehvpWRSDCKYLS
+RYADRLCQRPSFVAS--------------------------
+>gi|294892437|ref|XP_002774063.1| conserved hypothetical protein [Perkinsus marinus ATCC 50983]gi|239879267|gb|EER05879.1| conserved hypothetical protein [Perkinsus marinus ATCC 50983]
+--VNIYQYEICPYCNKVKAFLDWQQVPYKTMDVNPLTKGE---IRFS--KDYRKVPIAFIDGVQVNDSAEIIKKLVEVLGrenvtkQMQDA-EISKWVDW
+TDNKLAVLLFPnLTrtfgesfeafgyimnipHMWlPMKmvnrllggwamwmANDKIRKKydiddEREDLLKCIDEwTLDlAARGGKFHGGPSPDLADVAV
+YGCIRSLEGFTThhWLLRNHTDLLAWYNRMFR---------------------------------
+>gi|340914821|gb|EGS18162.1| hypothetical protein CTHT_0061770 [Chaetomium thermophilum var. thermophilum DSM 1495]
+MVYRLYITNknYSSWSLRVWLLMRQLDIPFIEEFRPMISGT-FSQPQWKEFSPVARVPCLhVLPDnphtdsepLILWDSLSITTFLSLSHPekpIYPSSP
+QALAWslsaVAEMHSSFTSLRDHLAMNIGVRVQlsYPLPAGVVNDLQRLNTLWTEGLTrfGGPWLVGKEFSAVDAFYAPVALRLRTYVGLEEEFFSReAK
+GWVERVLGLESVREWVR------------------------
+>gi|124266174|ref|YP_001020178.1| hypothetical protein Mpe_A0981 [Methylibium petroleiphilum PM1]gi|124258949|gb|ABM93943.1| hypothetical protein Mpe_A0981 [Methylibium petroleiphilum PM1]
+----------GPWSEAAKAILHVKKLAHVKVRqelLG-------SNLPLIRWTAQATAPVAVWNGEPPRSTWIEQLYLFEWLApepaLIPRDVDERMLMf
+glaneifgengfvwNRRHLMVRDFSGPDQPpeiresfrFLGRKygCGDAAAAAAPARCAEVMGLLADRLRSQRergsrYCVGASLTALDLYAACAYALVS
+PLPQDLCAMTPLFRAVYT-------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+M 1 * * * * 4827 * * * * 3588 182 * * * * * * * * * 1
+ 0 * * * * * * 7232 0 0
+
+S 2 3501 * 4651 4537 * * * * 3311 * 4631 * 3561 * * 1371 2945 3531 * * 2
+ 766 1280 * 866 1148 * * 7717 2544 0
+
+P 3 5003 * * * 4412 6030 5449 3148 6083 3019 2503 5717 2866 * * 5951 3851 3692 * 2865 3
+ 73 4346 * 502 1768 * * 9665 1397 0
+
+I 4 * 6073 * 3507 6111 * 6086 3928 2323 4058 4578 5164 * 4549 3358 5948 1847 5308 * 6273 4
+ 42 5112 * 0 * * * 9788 1219 0
+
+L 5 * * * 6002 4817 * * 3200 6282 477 5299 * * * * 6336 4926 4719 * * 5
+ 0 * * * * * * 9827 0 0
+
+G 6 * * * * 3155 3936 4245 3505 5155 4046 * * * * 5428 6309 4359 3193 6297 1372 6
+ 35 6474 6300 0 * * * 9820 1000 0
+
+Y 7 5540 6261 5509 6285 6285 2396 5230 5368 5069 4071 5825 5213 * 4365 * 4778 3035 5380 5338 1798 7
+ 19 * 6285 * * 0 * 9803 0 1004
+
+W 8 6201 6411 5451 6216 2282 5211 4029 6119 * 3759 6488 4750 * 5287 4177 3533 3263 5542 3378 3073 8
+ 49 5568 6382 2807 222 * 0 9824 1107 1007
+
+K 9 4348 5875 2334 3580 5370 6163 6479 6414 3894 5347 * 4040 2173 4751 4859 3851 6433 5515 6043 5212 9
+ 181 3783 4462 206 2908 0 * 9850 1751 1156
+
+I 10 3097 * 5426 * 3364 3679 3707 3160 * 3408 4872 4970 4288 6483 6443 5234 4357 3390 5430 3877 10
+ 0 * * * * 0 * 9916 0 1530
+
+K 11 6191 3164 4874 * * 4949 4932 * 4769 6693 5386 3796 5024 6383 3786 1090 5437 6401 * 6220 11
+ 0 * * * * * * 10040 0 0
+
+G 12 3627 * * 4976 * 2435 6473 5048 * 4560 * 5115 1133 6580 * 4196 4152 6343 * * 12
+ 45 * 5034 * * * 0 10090 0 1069
+
+L 13 4943 4247 5345 4449 2696 6586 5648 6276 4776 5040 * 3466 4736 6626 2886 6570 5704 5476 4293 2298 13
+ 15 6586 * 0 * 1448 659 10057 1000 1589
+
+V 14 2478 2592 * * 6793 3281 6768 * 6341 * * 6561 6563 * * 1938 3064 3065 * * 14
+ 0 * * * * 1043 959 10106 0 1317
+
+Q 15 3844 6616 6723 2568 4576 * 4746 6520 6679 2965 4582 5002 6423 2987 2409 * 4694 5197 4989 5825 15
+ 53 4780 * 1867 462 * 0 10162 1490 1083
+
+P 16 3112 5619 * * 5128 6635 6596 4869 1983 4384 4915 * 4687 5011 2031 4520 7079 3620 * * 16
+ 0 * * * * * 0 10227 0 1083
+
+T 17 2640 4283 * * * * * 2396 * 3076 6399 * 5804 * * 4088 5708 1427 * * 17
+ 0 * * * * * 0 10247 0 1083
+
+R 18 5735 4935 6951 4381 6740 6818 5984 4831 4168 2678 5774 6189 6343 4540 1329 6861 5764 5661 4531 4791 18
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+
+L 19 2701 7250 * * 4242 * 7095 2812 * 2028 2808 * * 6650 6392 6322 3797 3870 4443 5140 19
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+
+L 20 2052 4780 * * 3721 5182 5702 3230 * 2268 4836 * * 6322 6565 5869 3662 3147 * 5743 20
+ 17 6392 * 1585 585 * 0 10353 1051 1083
+
+L 21 2643 4561 * * 4181 6392 * 4300 * 688 4665 * * * * * * 5664 * * 21
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+
+E 22 2486 6126 4477 2655 5064 4763 4218 5763 3449 3748 6826 4478 * 4916 3003 6046 4749 5830 6745 7008 22
+ 0 * * * * * 0 10352 0 1237
+
+Y 23 3302 6483 4164 2264 4205 * 3702 5111 7068 2713 4188 * * 4874 5229 * * 4388 5204 3145 23
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+
+L 24 2517 4205 * * 5951 5812 6672 * 2047 2516 5915 5336 6385 4099 6781 3673 5106 4996 6662 4606 24
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+
+E 25 6848 6914 3831 3347 * 1375 5829 * 3353 6665 * 2708 * 4176 4253 4549 * * * * 25
+ 43 5769 6532 2768 229 * 0 10382 1236 1000
+
+E 26 4021 6623 6875 6929 5244 * 6494 2000 6870 1861 5860 7062 5628 3967 * 6955 5438 2320 * * 26
+ 34 5404 * 1315 741 1325 735 10349 1495 1233
+
+K 27 4221 * 2643 3728 * 6914 5604 6757 3439 6706 6307 4679 1612 4920 4516 3621 5283 * * 6900 27
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+
+Y 28 * 6698 5745 * 1921 6707 5214 4472 * 4278 5285 * * 7114 * 6418 5614 3252 4395 1486 28
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+
+E 29 4138 * 3335 1807 * 5903 * 4441 3184 * 6886 4444 * 4107 4005 4956 2847 4658 * * 29
+ 0 * * * * * 0 10365 0 1074
+
+E 30 4567 * 3207 3105 5118 5719 5286 3582 5166 3117 6496 4852 * 5125 5384 4773 3067 3128 5911 4378 30
+ 45 * 5026 * * * 0 10370 0 1074
+
+H 31 5757 6994 5989 3180 5383 5221 4422 2988 2787 6005 6603 5597 * 4838 4951 4456 3793 2064 * 6862 31
+ 26 * 5814 * * 2416 299 10270 0 1744
+
+L 32 4191 * 3693 2931 4322 5320 5382 5349 4904 3917 6830 4803 3048 * 3112 6839 4404 3657 4599 4158 32
+ 44 6623 5655 1585 585 1052 950 10243 1002 1873
+
+Y 33 3977 5784 * 5877 4017 5820 4675 2274 5536 2840 5239 5930 6802 * 6858 6871 * 1807 6550 4343 33
+ 41 6925 5646 0 * 1444 661 10322 1000 1692
+
+E 34 3500 5892 2130 3486 * 3331 4934 * 3995 5377 5690 3471 4243 5639 6289 4205 3737 5834 * 5954 34
+ 103 * 3862 * * 2497 281 10321 0 1692
+
+R 35 4964 5523 4606 4288 3416 4147 * 4171 4687 2817 4067 5166 3053 * 4721 4152 4107 4095 6565 4706 35
+ 177 5172 3513 2786 226 3694 116 10258 1289 2776
+
+D 36 4031 6468 3135 4532 5704 3502 4437 4986 4575 3398 4142 4342 3562 4787 5793 3858 4726 4831 5179 4874 36
+ 605 3391 2015 564 1627 4311 75 10119 2200 3717
+
+E 37 3261 6428 3047 3516 6250 4990 * 4076 3698 4829 * 3083 4162 6453 3603 4292 3339 5210 6054 * 37
+ 369 4685 2422 4269 77 4430 69 9743 1276 5904
+
+G 38 5956 * 4033 4308 * 1650 5476 3927 3004 5964 4772 4290 4296 5933 3539 4926 * 6035 5696 5933 38
+ 168 6102 3392 0 * 2571 266 9450 1000 6802
+
+D 39 3437 * 2909 1666 4934 4406 * * 3831 5946 * 4886 3341 4876 5053 4920 5022 4939 * * 39
+ 329 4271 2718 2069 393 1679 540 9540 1334 6546
+
+K 40 4539 * 3773 2661 6053 5030 2739 * 6247 5036 6124 3406 4576 3144 4689 3753 4096 4801 * 6001 40
+ 877 5100 1229 2240 343 1687 537 9754 1127 6094
+
+W 41 * * * 5943 3494 4630 4571 4746 4727 3392 3779 5843 4211 4724 4193 4545 * 5753 1708 4716 41
+ 315 4556 2702 0 * 705 1372 9426 1187 7388
+
+R 42 2904 * 5157 4764 4631 4492 4539 6356 3007 3191 5374 3578 4053 4266 4386 3741 5253 5173 6700 5546 42
+ 36 * 5337 * * 1689 535 9884 0 5042
+
+N 43 3602 * 3943 4494 * 4969 * * 3618 4491 * 3138 3426 4251 4258 2341 3384 4444 * * 43
+ 0 * * * * 1413 679 10003 0 4225
+
+K 44 2372 6537 3786 2790 * 5335 5854 6442 3980 3467 5647 5736 2173 5184 5026 6379 6562 5657 * 6567 44
+ 55 6904 5115 1549 603 3388 145 10177 1207 3114
+
+K 45 4054 * 2852 2191 6556 4844 5643 5787 2909 6829 6482 6795 4395 4021 3988 3365 5026 6673 5216 * 45
+ 32 * 5505 * * 1867 462 10181 0 3247
+
+F 46 4693 * 6709 5060 2638 5704 5642 3921 6552 2435 5740 6362 4336 * 4576 5062 4665 3893 5677 2459 46
+ 47 6440 5618 0 * 1579 588 10172 1000 2938
+
+E 47 3372 * 4413 4086 5690 4103 5780 4700 3200 2280 6815 4976 6589 4648 3405 4055 4353 4205 * * 47
+ 219 4684 3292 279 2509 1107 901 10241 1528 2560
+
+L 48 3307 * 4095 3383 4579 4057 6518 6109 2311 4522 6550 4642 5505 3481 3344 4445 5622 4816 * 6670 48
+ 169 3746 4789 854 1163 2535 273 10088 2173 3295
+
+G 49 5581 5693 5082 4987 5103 4643 * 2260 4303 2118 6688 5582 5595 4958 5253 5133 4520 3008 6444 5493 49
+ 29 6615 6702 3700 115 1398 688 10023 1000 3390
+
+L 50 3397 6361 4995 6573 5095 3981 4230 5686 4623 4794 6876 1812 6625 5089 6438 2733 3833 5299 6910 6589 50
+ 46 5599 6502 2807 222 1044 958 10132 1189 2637
+
+E 51 4974 * 4984 4420 5756 4374 6666 5748 * 4553 5955 6847 791 5674 4159 4710 6725 6668 * 5925 51
+ 29 5642 * 2415 300 2678 245 10234 1215 1961
+
+F 52 5199 6893 * 6790 2568 4724 5239 5791 4569 2414 4638 3988 6669 4236 4445 3886 4324 4187 6351 3684 52
+ 28 5719 * 1675 542 * 0 10231 1146 2014
+
+P 53 4017 4647 5148 3825 * 1285 4954 * 3534 5784 5186 6940 3777 * 4724 4670 5212 5659 * 5636 53
+ 52 4831 * 2503 280 1123 887 10231 1416 2014
+
+N 54 4323 * 6881 4894 * 5678 4641 6858 2094 4079 6623 3893 * 2697 3267 4019 3375 4585 * 6517 54
+ 77 4582 6652 606 1544 * 0 10326 1681 1489
+
+L 55 5211 6727 6334 * 5779 6892 6503 2649 * 1933 4982 * 5174 5765 * 5138 4469 1625 * 5903 55
+ 11 * 6982 * * * 0 10311 0 1670
+
+P 56 4859 * * * * * * * * 6843 * * 122 * * 5168 * 6671 * * 56
+ 73 4351 * 1743 512 * 0 10303 1680 1798
+
+Y 57 2811 4181 * * 4342 6031 * 3467 5658 3636 4919 * * 6859 6509 5163 2979 1870 6909 4112 57
+ 67 4460 * 0 * 2759 231 10353 1670 1798
+
+Y 58 4830 * * * 3803 6373 * 2727 5720 780 4896 * * * * * * 4049 6810 5283 58
+ 287 2471 * 813 1215 2623 256 10382 3834 1661
+
+I 59 5351 * 6182 2623 4741 6913 5967 3939 3851 3373 5432 6955 * 4507 4368 7094 3494 1961 6363 5800 59
+ 190 3017 * 260 2599 * 0 10397 2907 1531
+
+D 60 4602 * 1649 3606 4707 4545 4427 4270 * 4220 7301 4214 4497 5823 5346 3889 4479 4643 5878 6875 60
+ 87 4101 * 1034 967 1894 452 10397 1908 1531
+
+G 61 5865 6546 2019 3965 * 2328 4743 6757 3458 * 5970 2952 4594 4347 5916 4805 5220 * * 6672 61
+ 82 4185 * 2695 242 * 0 10424 1861 1347
+
+D 62 4908 * 2371 3606 * 1138 6688 * 5925 6543 * 3873 5933 4725 7017 6763 4284 6764 * * 62
+ 207 2906 * 2421 298 955 1046 10424 3555 1347
+
+V 63 4836 * 4638 3184 4427 4398 6702 4102 3427 3394 6202 5031 5405 4466 3896 4391 3408 3195 * 4892 63
+ 91 4515 5830 887 1123 * 0 10480 1665 1083
+
+K 64 3720 6148 * 4793 5252 5714 6769 3551 4013 4983 * 5147 3758 4571 3852 4147 3217 2170 6712 4995 64
+ 41 5966 6369 0 * 773 1269 10445 1165 1431
+
+L 65 6786 6640 * * 4788 * 6959 2344 5709 1262 4619 6404 6713 6744 6705 5041 6555 2574 * 6191 65
+ 11 6984 * 3807 107 1137 875 10467 1000 1380
+
+T 66 3245 4998 6945 * 3059 3790 5305 4373 5813 6746 5171 4195 4981 5257 5825 3587 2469 4719 4385 4191 66
+ 0 * * * * * 0 10510 0 1133
+
+Q 67 6709 * 1976 1464 * 3319 6879 * 6783 * 6762 6197 5583 3198 * 4010 5756 6374 * 6573 67
+ 0 * * * * * 0 10510 0 1133
+
+S 68 4267 5850 5468 5679 * 7245 6985 6688 6758 5490 5415 5552 5769 6118 5364 839 2909 4678 * * 68
+ 11 * 7071 * * 0 * 10510 0 1133
+
+M 69 3090 6710 5247 4689 5405 4544 6583 4411 5465 3376 4302 3450 4764 4943 3699 3927 3824 3857 5183 4518 69
+ 8 7559 * 1585 585 * 0 10527 1000 1000
+
+A 70 1295 6606 3830 4499 6857 6092 6774 4390 5210 3651 * 6784 3989 5768 * 3960 6146 3156 * * 70
+ 0 * * * * * 0 10522 0 1111
+
+I 71 4826 6690 * 5236 6708 * * 403 * 3929 5133 * * * * 6656 6647 4361 * * 71
+ 0 * * * * * 0 10527 0 1111
+
+I 72 2677 3633 6976 5923 5008 * * 3509 * 1951 3558 6969 5448 5927 5525 4894 4677 3059 * 6123 72
+ 0 * * * * 1061 941 10619 0 1111
+
+R 73 4012 * 3970 2623 * 5327 5848 4241 4370 3807 5403 5772 * 3250 2282 4532 5003 5342 6043 5056 73
+ 0 * * * * * 0 10722 0 1000
+
+Y 74 5453 * 7479 7502 2934 * 3102 6881 5324 6117 6283 6984 * 5189 6001 * 6669 5265 5001 889 74
+ 32 * 5506 * * * 0 10722 0 1000
+
+I 75 4912 6916 * * 4054 * * 2597 * 707 5994 * * * * * 6570 3404 * * 75
+ 12 6884 * 1000 1000 * 0 10620 1004 1487
+
+A 76 2433 5502 2694 2797 6744 3287 5842 4225 7062 4289 * 3784 * 5677 6629 3986 4934 4495 * 6570 76
+ 12 * 6881 * * * 0 10620 0 1487
+
+D 77 2932 * 2997 2072 6866 6816 6917 6952 4303 4091 * 4814 7033 3882 2979 3217 6548 * * 7236 77
+ 0 * * * * * 0 10607 0 1627
+
+K 78 4676 5053 4924 3184 * * 5276 4298 2319 3580 5846 5256 5858 3995 3403 4158 3751 4309 6721 5728 78
+ 86 4647 5800 1626 565 2465 288 10607 1535 1627
+
+H 79 3887 5794 6937 5973 2411 4501 3039 5889 5338 3226 * 4867 * 6550 7071 4481 4994 4164 * 2296 79
+ 269 2553 * 2162 365 2868 213 10586 3982 1844
+
+N 80 4072 * 3288 4985 * 1998 4943 * 4677 6124 * 4464 1926 5638 5178 3953 4938 7008 * 6775 80
+ 1075 1056 4496 1861 465 * 0 10595 7102 1712
+
+M 81 5715 6677 4204 5525 3345 4788 5372 4266 4901 1142 4863 * 5948 6642 5261 4863 6792 4557 5307 * 81
+ 128 3557 * 1456 654 1677 541 10311 2241 2551
+
+L 82 4506 * 4585 6006 3764 4980 4735 3631 4561 2386 3759 7538 4819 6074 4451 5848 4918 3887 6869 2840 82
+ 59 4642 * 770 1274 1873 460 10568 1595 2182
+
+G 83 3366 * 3720 * 7055 2070 * 5834 5778 5939 * 6535 1394 5180 6716 4161 4957 7063 * 7551 83
+ 168 3427 5868 1101 906 * 0 10592 2765 1832
+
+G 84 3184 5535 3600 3127 5839 4013 * 5009 2922 3107 5385 7380 5008 5428 3619 3617 4475 5580 * * 84
+ 49 4905 * 377 2121 2088 387 10458 1470 2140
+
+C 85 3828 5623 1750 5854 5761 3103 * 5905 4794 5209 * 3143 4903 5725 6254 3071 3999 5648 * * 85
+ 184 3450 5156 2175 361 2060 395 10484 2462 1848
+
+P 86 3361 6804 4275 4317 6929 4432 5308 5465 7111 3703 6748 3764 2077 4149 4955 3150 5836 4354 6969 6664 86
+ 93 4679 5407 2642 252 285 2482 10484 1768 2134
+
+K 87 2650 * 4435 3302 4931 5096 6684 3960 4799 3961 4665 4344 3936 3462 5920 4533 4793 3996 5372 5079 87
+ 47 4956 * 4077 88 723 1342 10715 1402 1484
+
+E 88 3459 * 2729 2233 7134 4374 4962 4261 3773 4419 5429 5336 4850 3438 4756 5857 5447 4883 * * 88
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+//
+�HHsearch 1.5
+NAME f7a5e37dc7250be9dd8e0efc7b40d3b7
+FAM
+FILE f7a5e37dc7250be9dd8e0efc7b40d3b7
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 11:56:32 2013
+LENG 93 match states, 93 columns in multiple alignment
+FILT 106 out of 642 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 7.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
+>ss_conf PSIPRED confidence values
+986899999999999998389999898998999999987026675467633155302557876844877628865988999988887787789
+>Consensus
+xxxCxxvxxxLxpClxyxxgxxxxPxxxCCxxvxxlxxxaxxxxdrxxxClCxxxxxxxxxxixxxxaxxLPxxCxvxxpxpixxxxdCxxix
+>f7a5e37dc7250be9dd8e0efc7b40d3b7
+AISCGQVASAIAPCISYARGQGSGPSAGCCSGVRSLNNAARTTADRRAACNCLKNAAAGVSGLNAGNAASIPSKCGVSIPYTISTSTDCSRVN
+>gi|224133474|ref|XP_002328051.1| predicted protein [Populus trichocarpa]gi|222837460|gb|EEE75839.1| predicted protein [Populus trichocarpa]
+--KCEPVFEYFPYCLDFLTGYYNKPSKRCCDHIYKLNRLAKRGLGAQLICWCIEYMVRGTEpQIRADRISELPTKCQTHLSFPISEWKDCNTyslLS
+>gi|222619541|gb|EEE55673.1| hypothetical protein OsJ_04081 [Oryza sativa Japonica Group]
+-----QVALKLAPCAAGHAEPARRGAAQLLRAGAQHRA--------NPKCLCavMLSNTARSAGVKPAVAMTIPKGWAIaNRP-------------
+>gi|4154350|gb|AAD04945.1| lipid transfer protein [Pinus radiata]
+AIECSDVLSRPVHCLSYFVTPRAtlTPTSACCRESEEVLGMANSMGAKEDLCNCFVGLIRGFR-PNPNKIEGLLSSCALQLFFPIDPVTalpDCTQIQ
+>gi|11120788|gb|AAG30968.1|AC012396_4 hypothetical protein [Arabidopsis thaliana]gi|12323696|gb|AAG51810.1|AC079676_5 lipid transfer protein, putative; 26937-27275 [Arabidopsis thaliana]
+---LTACLQKLLPCQPYIHSLNPPPPPSCCGPMKEIVEK-------DAPCLCIAFnNPEVLKalNLTKENALLLPKACGVNPDV--S---LCSKI-
+>gi|52076890|dbj|BAD45903.1| hypothetical protein [Oryza sativa Japonica Group]
+---CLTPLLSMMSCADYLTNSSaQTPPGTCCEGFKSLVST-------APICLChgINGDLSKFlPlPVDMMKMMTLPNTCGATVPLQ-----------
+>gi|77551590|gb|ABA94387.1| Protease inhibitor/seed storage/LTP family protein [Oryza sativa Japonica Group]
+--YCRDSLSGLLACRDFMFGGAAAASPACCAAYSAAFD-------ADPFCLCYIADgvYGRSTgyDVNVTHALEIPVSCGLATP-PIE---------
+>gi|255540483|ref|XP_002511306.1| hypothetical protein RCOM_1508440 [Ricinus communis]gi|223550421|gb|EEF51908.1| hypothetical protein RCOM_1508440 [Ricinus communis]
+-PSCIFISSNLHSCSdvlrlGFLIG---KPSPQCCRGIRFIKEA-ALIFGVPKACHCVRNCAnthifrrhntqklsgslkagapisNKAPDFNGDIFIQL
+QKKCRVDLGFGLDQNIPCLIIK
+>gi|9758178|dbj|BAB08563.1| unnamed protein product [Arabidopsis thaliana]
+---CNINANHLEKCRPAVIGDNPPSPiKECCELLQAAN----------LKCICrFKSVLPVL-AVYPSKVQALLSKCGLtTIP-------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 1267 * 3855 5603 * 3494 * * * 3768 4715 * 4331 3809 4931 4809 3251 * * * 1
+ 145 3388 * 1916 444 * * 5511 1258 0
+
+I 2 3056 * 5220 5543 * * * 2338 * 3081 * 4404 2743 * * * 4182 2155 * 4672 2
+ 63 4551 * 3258 159 * * 6138 1131 0
+
+S 3 3720 * 2331 3618 * * 4365 5967 4152 * 5057 4991 3869 6370 * 2264 2718 * * 5568 3
+ 0 * * * * * * 6550 0 0
+
+C 4 * 72 6113 * * * * * * 6102 * * * * * 5655 * * * * 4
+ 0 * * * * * * 6959 0 0
+
+G 5 3293 * 5167 3814 6775 3078 * 4362 6713 5787 5622 3625 5435 5094 4023 2175 2943 5133 * * 5
+ 19 * 6285 * * * * 6959 0 0
+
+Q 6 3591 * 2672 3902 5594 4861 * 5636 4900 * 4543 3634 3738 3398 * 3794 2692 3956 * * 6
+ 0 * * * * * 0 7050 0 1063
+
+V 7 2892 5020 3941 5292 * * * 3152 6224 5668 6423 4669 5050 5142 6751 4363 4837 1336 * * 7
+ 18 * 6352 * * * 0 7090 0 1063
+
+A 8 2829 * 5049 6404 3721 5864 6228 3802 5468 2467 6439 5107 5793 3764 6469 5639 3762 2753 5797 4955 8
+ 0 * * 1585 585 0 * 7086 1063 1178
+
+S 9 3356 * 4902 5383 6367 4502 * 4044 6494 3951 4456 2903 4983 4525 4598 2669 3022 4198 * 5518 9
+ 24 5899 * 0 * * * 7285 1062 0
+
+A 10 3614 * 3245 4876 * 4015 5620 6588 2731 3971 5237 3619 6896 3257 5179 3419 3711 * 6619 4533 10
+ 0 * * * * * * 7288 0 0
+
+I 11 5818 * * * 3670 * * 4136 * 603 3948 * 5821 * * * * 3354 * 6917 11
+ 15 * 6611 * * * * 7343 0 0
+
+A 12 2664 * 6298 4837 5642 6138 5770 3878 4827 3334 3807 4666 4914 5316 6513 2780 2995 3713 * 6335 12
+ 0 * * * * * 0 7329 0 1063
+
+P 13 3768 * 3444 5238 6607 5624 5810 * 6772 6582 * 5188 948 4961 * 3081 5852 6638 * 5905 13
+ 29 5653 * 539 1681 0 * 7329 1249 1063
+
+C 14 * 0 * * * * * * * * * * * * * * * * * * 14
+ 48 6072 5826 1585 585 * * 7347 1027 0
+
+I 15 2910 * * * 5512 5992 * 3315 5894 1380 4119 * * 4890 4346 5257 * 2903 * 5180 15
+ 27 5772 * 1482 639 0 * 7330 1310 1131
+
+S 16 3093 * 3112 4767 * 3024 * * 5958 6641 5893 3998 1905 5272 5765 2761 5014 6353 * * 16
+ 9 7315 * 1398 688 * * 7286 1070 0
+
+Y 17 2547 * * * 1803 4951 * * * * * * * 5867 * 5758 6471 6509 * 1145 17
+ 0 * * * * * * 7286 0 0
+
+A 18 2695 6735 * * 4565 4525 4982 3528 * 1689 4969 * * * * 5467 5737 2007 * * 18
+ 0 * * * * * * 7303 0 0
+
+R 19 3689 * * 5120 5732 4957 5737 3633 4885 4451 5377 4887 * 3550 4474 3243 1884 3865 5942 6145 19
+ 98 4174 6603 965 1036 * * 7303 1452 0
+
+G 20 5418 * 3912 4577 * 990 5888 6825 5553 6480 * 4169 5120 4821 5088 3776 4338 5262 * 6814 20
+ 737 4781 1459 1392 692 0 * 7288 1243 1063
+
+Q 21 3737 * 3949 5650 * 3645 4408 5573 3319 4741 5945 3308 2808 4215 5383 3042 3798 * * 5409 21
+ 114 3718 * 417 1994 156 3288 6866 1349 3818
+
+G 22 2570 * 4667 4310 5543 2348 6392 7014 3649 * 6678 3449 5153 6522 4062 3795 3393 4636 * 5891 22
+ 62 5586 5570 0 * 784 1255 7231 1108 1337
+
+S 23 2526 * 4594 4072 * 3607 5886 6465 3717 * * 4864 3274 4738 4051 2957 3581 3699 * 6127 23
+ 107 4034 6574 1186 835 0 * 7273 1455 1271
+
+G 24 2512 * 5389 5172 * 4100 5987 6116 2973 5850 * 4352 3199 3852 4293 3571 3038 4448 * 6638 24
+ 183 3163 7113 908 1098 0 * 7288 2013 1063
+
+P 25 4678 * * 6658 * 4659 * 6350 4315 4539 * * 573 * * 4152 6641 3890 * * 25
+ 42 5135 * 0 * 0 * 7316 1176 1000
+
+S 26 4122 * 4681 * * 4202 5857 6577 * 5818 * 6818 1567 * * 1867 2527 6678 * * 26
+ 220 3134 5190 649 1465 0 * 7265 2059 1034
+
+A 27 2418 * 3966 4254 * 4381 * * 2601 5714 * 5088 2830 3876 6416 2791 4524 6115 * 6319 27
+ 15 6633 * 0 * 2105 382 7289 1189 1284
+
+G 28 2798 * 3226 3445 * 5228 * 5202 4699 6009 6712 7067 3761 2850 4262 2610 3715 5150 * * 28
+ 71 4742 6524 0 * 0 * 7298 1265 1198
+
+C 29 * 47 * * * * * * * 4977 * * * * * * * * * * 29
+ 0 * * 0 * 0 * 7288 1063 1063
+
+C 30 * 46 * * * * * * * 4982 * * * * * * * * * * 30
+ 0 * * * * * * 7303 0 0
+
+S 31 3273 * 3159 4077 * 4076 5989 5877 5167 5497 * 3534 5564 3897 2798 2769 3437 6847 * 5871 31
+ 0 * * * * * * 7303 0 0
+
+G 32 2065 * 5982 4422 * 1514 5942 6483 * 6802 6489 5641 4190 4224 * 3389 6839 4278 5896 * 32
+ 24 * 5896 * * * * 7303 0 0
+
+V 33 4604 * * * 4107 4974 * 2138 * 2147 4472 * * * * 5808 7078 1578 * 6502 33
+ 0 * * * * * 0 7234 0 1062
+
+R 34 3124 * 5175 3569 * 4503 5694 6727 1975 * 6937 4471 * 3792 2177 4179 5157 * * 5933 34
+ 15 * 6576 * * * 0 7234 0 1062
+
+S 35 3556 * 3398 3822 5854 3949 4945 * 3051 * 6307 4357 * 3461 3964 2758 3554 4876 6496 5662 35
+ 12 6932 * 1000 1000 697 1385 7217 1019 1156
+
+L 36 3072 * * * 3761 6864 4969 3143 * 1421 4552 * * * * 6937 5182 2387 * 6553 36
+ 12 * 6937 * * * 0 7284 0 1003
+
+N 37 3995 * 3523 6871 4862 4419 6811 5376 3496 3104 6824 2480 * 7268 3505 3723 6827 3331 * 4153 37
+ 159 * 3263 * * 1112 896 7283 0 1114
+
+N 38 2245 * 3937 3439 * 3784 6709 6018 3332 5638 * 3501 6286 3487 3826 3222 4425 * * * 38
+ 402 * 2039 * * 2939 202 7218 0 2042
+
+A 39 3039 * 6261 4407 4694 4211 6030 4311 4647 3359 3249 5053 5843 4324 5465 3154 3608 4939 * 3833 39
+ 657 * 1452 * * * 0 6967 0 3491
+
+A 40 948 4425 * * 5122 * * * * * * * 5514 * 4910 3810 5455 2368 * 3982 40
+ 41 5168 * 3322 152 4866 50 5836 1036 4974
+
+R 41 4020 * 3237 5053 * 4918 * 5271 1176 * * 4953 3812 5216 6026 3462 4603 * * 5444 41
+ 0 * * * * 4954 47 5929 0 4871
+
+T 42 5684 * 3407 * * 5709 * * 5215 5023 * 3191 * * 3702 2496 1269 * * 5008 42
+ 71 4371 * 0 * 5174 41 6016 1138 4776
+
+T 43 3847 * * * 5440 3587 * 5130 2118 * 5091 * 3651 5579 2911 3629 2847 4325 * 4921 43
+ 50 6550 5425 0 * * 0 6263 1000 4695
+
+A 44 3363 * 3010 3516 5037 3006 5545 4377 3298 5108 * 3954 3027 5303 * 4718 5583 4742 * 5189 44
+ 30 * 5609 * * 3459 138 6039 0 4733
+
+D 45 3472 * 1205 2707 * 3026 * 5484 4361 4477 * 5340 * 4682 5596 * * * * * 45
+ 0 * * * * 1960 429 6576 0 4510
+
+R 46 3842 * 4604 * * 5626 * 6118 3013 * * 4098 4690 5823 1218 3585 3618 5551 * * 46
+ 41 6063 6239 0 * 603 1550 6943 1033 3750
+
+R 47 4391 * 3918 3683 * 4640 5240 4136 3491 * 6499 3399 5028 2380 2457 4256 * 4931 * * 47
+ 0 * * * * 300 2415 7214 0 2065
+
+A 48 2347 * 4354 4291 6691 5630 6386 4883 4482 3137 6812 6180 2021 5093 4601 4721 5818 4285 6128 6872 48
+ 0 * * * * 0 * 7287 0 1136
+
+A 49 2584 * 5304 4428 6507 5368 * 2902 3645 2718 5452 5149 3920 4895 * 4497 4176 3181 * * 49
+ 0 * * * * * * 7302 0 0
+
+C 50 * 0 * * * * * * * * * * * * * * * * * * 50
+ 0 * * * * * * 7302 0 0
+
+N 51 6214 * * 4257 4239 7157 4798 4988 4236 1204 7125 3702 * 4508 3495 4740 6612 4677 5949 * 51
+ 28 5689 * 2322 322 * * 7302 1058 0
+
+C 52 * 0 * * * * * * * * * * * * * * * * * * 52
+ 602 1551 * 1081 923 * * 7302 3698 0
+
+L 53 4418 * * * 3546 6892 * 2544 6318 1570 3575 * 5689 5967 4434 5038 5339 3760 * 4509 53
+ 64 4918 6605 821 1204 * * 7302 1242 0
+
+K 54 4248 * 6787 3126 5881 6662 5508 5241 2003 3037 5500 4228 * 4019 4721 4011 3923 4199 * 5665 54
+ 58 5853 5519 504 1763 * 0 7287 1107 1063
+
+N 55 3756 * 3458 4572 4785 3331 5180 6148 3896 5695 7163 3162 * 4125 5105 2598 3867 4035 * 5091 55
+ 106 3820 * 921 1084 0 * 7251 1733 1299
+
+A 56 2333 5882 3829 3551 5992 5507 * 4322 5252 3731 4767 4220 4144 5156 5236 3422 4384 4125 6974 4979 56
+ 90 5226 4890 1217 811 * * 7302 1176 0
+
+A 57 2036 * 4675 * 5148 3375 6144 4155 6793 2945 3609 7130 4606 6626 6826 4556 3652 3746 * 4733 57
+ 218 2834 * 2196 355 0 * 7250 2289 1286
+
+A 58 2266 * 7286 4418 5680 4027 * 5206 3758 4271 6049 3695 3375 5855 4528 3410 3723 3898 * 5707 58
+ 106 4427 5367 1682 539 * * 7302 1348 0
+
+G 59 4295 * 4760 5009 6062 3019 7120 6387 3408 5441 6635 4527 3476 3777 2504 2900 4641 4971 * 6948 59
+ 76 5893 4861 0 * * 0 7291 1071 1218
+
+V 60 3424 5657 6630 * 2440 * 5516 3095 6340 2829 4771 4991 6664 4852 * 3711 4295 3916 * 3403 60
+ 410 4937 2220 299 2417 2055 397 7215 1204 1501
+
+S 61 3062 6020 5706 5004 5302 3502 6481 5541 3194 6486 * 3543 2002 3790 5470 3862 5265 * * 5458 61
+ 858 1899 2471 561 1635 327 2300 7067 2699 3054
+
+G 62 4241 * 4367 6161 * 1193 4730 * 4287 * * 3227 3429 5154 5499 3944 5394 5649 * * 62
+ 64 4529 * 1270 773 176 3124 7065 1284 2799
+
+L 63 5221 * 6869 * 3938 * * 1625 * 2546 * * 5800 * 6628 4581 5041 1813 * 5705 63
+ 0 * * * * * 0 7278 0 1300
+
+N 64 5510 * 2092 6293 * * * 5436 3493 4852 * 1614 6170 4595 4244 4132 5141 4562 * 5522 64
+ 12 * 6874 * * 1344 722 7278 0 1300
+
+A 65 3175 * 4446 4948 3896 4737 6451 5576 5957 2881 4143 5284 2076 6998 5010 6071 5031 3657 * 4680 65
+ 0 * * * * * 0 7285 0 1225
+
+G 66 3257 * 3161 4513 6659 4588 7028 * 3528 6175 6177 3656 4448 5747 4485 2708 2222 6586 * * 66
+ 0 * * 2474 286 353 2203 7285 1147 1225
+
+N 67 3270 * 5935 7227 5149 * 6486 5132 2397 3062 7097 3955 6200 4293 1988 6804 5150 3834 * * 67
+ 0 * * * * * 0 7299 0 1000
+
+A 68 845 6706 * * 4522 6766 * 2831 * 3474 5628 * * 6924 * 5308 * 3370 * * 68
+ 24 * 5896 * * 0 * 7299 0 1000
+
+A 69 2759 * 5921 4646 6769 * * 3453 4650 2438 3242 5070 6919 3347 4349 3300 5109 4340 * * 69
+ 35 6173 6660 1000 1000 0 * 7234 1036 1062
+
+S 70 2318 * 4500 3604 * 3491 6715 * 4027 4347 5215 3851 * 2900 6016 3535 3117 5887 * * 70
+ 26 6998 6598 0 * 0 * 7293 1000 1000
+
+I 71 * * * * 6664 * * 2274 * 554 4577 * * * * * 5678 4611 * * 71
+ 0 * * 0 * 0 * 7287 1063 1063
+
+P 72 5112 * * * * 5719 * * * 5244 * * 303 5882 5689 3665 * * * * 72
+ 0 * * * * * * 7302 0 0
+
+S 73 3425 * 4246 4421 * 2572 6677 5965 2070 6042 * 5340 * 4407 3833 2717 4654 5248 * * 73
+ 0 * * * * * * 7302 0 0
+
+K 74 2946 * 5024 3817 6164 4982 5725 6006 2030 3037 * 4494 * 4850 3100 3996 4775 5217 * * 74
+ 0 * * * * * * 7302 0 0
+
+C 75 * 95 * 5689 * * * * * * 6318 * * * * * * * 4982 * 75
+ 0 * * * * * * 7302 0 0
+
+G 76 4348 * 6077 * * 1273 3983 * 3315 * * 2497 * 4945 3717 4160 * 5882 * * 76
+ 14 * 6724 * * * * 7302 0 0
+
+V 77 3753 6312 * 7033 5225 * * 2455 * 1882 5749 5773 6720 * 6858 5700 4647 1724 * 6937 77
+ 161 3361 6914 320 2329 0 * 7289 1740 1000
+
+S 78 4280 * 3481 6298 * 5306 3663 6577 2849 4782 6901 3051 3417 4058 5427 3318 3224 4537 * * 78
+ 36 6785 6025 1000 1000 * 0 7314 1019 1000
+
+I 79 5398 5511 * * 3561 * 6113 2694 * 2049 5913 3830 5751 6150 4553 4271 3386 3006 * 5331 79
+ 39 5228 * 2494 282 0 * 7281 1152 1129
+
+P 80 4512 * 5631 * 3982 2985 5760 * 6262 5139 * 4721 1065 * 5250 3125 5079 * * * 80
+ 163 5293 3624 619 1520 * * 7154 1124 0
+
+Y 81 3888 6190 * * 1482 * * 5388 5031 3306 6338 6006 3804 * 5666 4660 * 3662 5989 2720 81
+ 87 4718 5594 633 1493 0 * 6960 1136 1440
+
+T 82 6053 * * 4988 * 4592 * 5814 3103 6612 * 4173 946 5054 * 6318 2903 * 5904 * 82
+ 28 5720 * 0 * 933 1070 6646 1023 1148
+
+I 83 4747 5677 * * 4003 * * 985 5883 4111 4417 * 6016 * * 6418 5635 2578 5700 5635 83
+ 0 * * * * 0 * 6572 0 1022
+
+S 84 4721 * 2662 5221 * 4400 * 3896 5470 * * 3600 4876 * 5713 1529 2984 * * 4977 84
+ 155 5472 3657 0 * * * 6624 1024 0
+
+T 85 4308 * 4504 4127 * 5107 4245 * * 4155 * 5447 1459 4098 3831 4551 3607 3830 * * 85
+ 0 * * * * * 0 6093 0 1267
+
+S 86 4410 * 3139 * * 4167 4924 * 3219 * * 1982 5689 5846 5326 2186 4409 4933 5109 * 86
+ 0 * * * * * 0 6093 0 1267
+
+T 87 5466 * * * 2490 * 4983 2683 5109 * 3031 4434 * * * * 1784 3385 * 5137 87
+ 142 3415 * 717 1353 0 * 6093 1351 1267
+
+D 88 * * 608 * * * * * 5728 5191 5613 2790 5043 5466 * 5276 4218 * * * 88
+ 64 4528 * 2256 339 * * 6221 1119 0
+
+C 89 * 0 * * * * * * * * * * * * * * * * * * 89
+ 0 * * * * * * 6221 0 0
+
+S 90 * 5201 2993 4760 * * * * 4549 4907 * 2648 5584 * 5191 1171 3601 * * * 90
+ 0 * * * * * * 5961 0 0
+
+R 91 * * * * 4154 * * 4874 1748 * * 4403 * 4078 3400 2852 1876 * * * 91
+ 148 3720 5537 2191 357 * * 5905 1233 0
+
+V 92 5153 * * * 5230 * * 995 * 2982 * * * * * * * 1658 * * 92
+ 70 4397 * 0 * 0 * 5711 1078 1000
+
+N 93 5115 * * * * 5007 4164 * 2024 4992 * 3232 2564 2572 * 2940 4925 * * * 93
+ 0 * * 0 * * * 5395 0 0
+
+//
+�HHsearch 1.5
+NAME f82cb3c7c161ae904b70948cfd869920
+FAM
+FILE f82cb3c7c161ae904b70948cfd869920
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:49:08 2013
+LENG 144 match states, 144 columns in multiple alignment
+FILT 138 out of 1115 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEECCEEECCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHH
+HHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9987350688678787455419999987997999899888632234687279996357888765899999999999999746998999879999759999
+99999999098999999999987886688999999999999739
+>Consensus
+xxxpxxIxxxlyxgxxxxxxxxxxlxxxgixxvixlxxxxxxxxxxxxxxxxxxixxxdxxxxxxxxxxxxxxxxixxxxxxxxxvlvHCxxGxxRsxxx
+xxxylxxxxxxxxxxaxxxvxxxrpxxxxxxxxxxxLxxxxxxl
+>f82cb3c7c161ae904b70948cfd869920
+ASFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLFENAGEFKYKQIPISDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTV
+TVAYLMQKLNLSMNDAYDIVKMKKSNISPNFNFMGQLLDFERTL
+>gi|163744309|ref|ZP_02151669.1| hypothetical protein OIHEL45_01960 [Oceanibulbus indolifex HEL-45]gi|161381127|gb|EDQ05536.1| hypothetical protein OIHEL45_01960 [Oceanibulbus indolifex HEL-45]
+-----TIDPTHNVALfTPDAKALEQAASAGMKTVINFRAADEKGGLSpdEErlvaeklGLNYLHHPVTPDTLGP-----ETVDEFRRSLDDLPQPVFLHC
+ASGK-RAGAMTLMALAADKGWDGDTALQEGKTRGID-LTEEKIGQFVKSYADR-
+>gi|335298243|ref|XP_003131846.2| PREDICTED: protein phosphatase Slingshot homolog 2, partial [Sus scrofa]
+-------------------------------------------------------------------------------eklSEHNHAFSFLC-------
+FRRLLLFSQRAAQAGSTHAISSTTPHAASTR---GYERRAWAFPVCV
+>gi|167646706|ref|YP_001684369.1| hypothetical protein Caul_2744 [Caulobacter sp. K31]gi|167349136|gb|ABZ71871.1| conserved hypothetical protein [Caulobacter sp. K31]
+---------mTLLVCPL--SQVETARTLHRPSHLVSLLSPtsaakaWPEADAN---ETCLRLAFHDVVEAregltpPDAALVARLLDFAARWDAAQ-PLL
+VHCWAGVSRStAAAFIIACQYAPERPERHIAQALRAAAPYATPNPLMVS---------
+>gi|302819053|ref|XP_002991198.1| hypothetical protein SELMODRAFT_161459 [Selaginella moellendorffii]gi|300141026|gb|EFJ07742.1| hypothetical protein SELMODRAFT_161459 [Selaginella moellendorffii]
+------VEYDLTRSGVVHQLNFPFLERLNLRTVLYLSQDEPSqqflSFLDEQGIHFrrTHQSsSTt-AAETTGSLSEAQVLSALEVILRpENYPLHVMCK
+QGRNTTGTV-IGCLRKLQRWNLTSIFE--------------------------
+>gi|257215044|emb|CAZ68050.1| protein-tyrosine phosphatase alpha [Danio rerio]
+-------------GNIRVSvEDTMILVDYTIRKFCIQQVGDvsgkKPQRLV---TQFHFTSWPDFGVPFTPIGMLKFLKKVKNCNPQyAGPIVVHCSAGV
+GRTGTFIVIDAMLDMMGAerKVDVFGFVTRIRAQ------------------
+>gi|170115154|ref|XP_001888772.1| predicted protein [Laccaria bicolor S238N-H82]gi|164636248|gb|EDR00545.1| predicted protein [Laccaria bicolor S238N-H82]
+----------------------------ta-YIVLTss--HTTPRnnvnc---------LYIPLHHERKkkGDTpy--lfTTILPSSLAFIKSRlr--LL
+TvkSVCIaipk--ndSDARDVAVGIMLVVLQLLFddhgelldgasvqlpatKQTIRTRLEWVIASVPDVNPSRTMLKRVNEF----
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 1513 * * * * * * * * * 1072 * 2524 * * * * * * * 1
+ 0 * * * * * * 3763 0 0
+
+S 2 * * * * * * * * * * 3019 3217 * * * 630 3022 * * * 2
+ 0 * * 0 * * * 4672 1042 0
+
+F 3 * * 4973 4566 2380 * 4337 * * 2640 * 4580 * 5168 3406 * 4609 * 2978 2380 3
+ 0 * * * * * * 7060 0 0
+
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+M 134 5245 * * 4113 4835 6321 6394 3591 4059 2235 3310 * * 4254 3133 6495 6193 3475 4603 3681 134
+ 0 * * * * 845 1174 9603 0 1148
+
+G 135 3886 * 4025 2934 6359 4292 5538 5440 2848 5419 6403 3739 5135 3648 2541 6094 4705 * * 4312 135
+ 19 6273 * 2000 415 * 0 9624 1016 1000
+
+Q 136 3899 * 5873 4690 3882 5233 5382 6146 4227 4763 5212 5031 * 1888 4708 3474 4776 4215 4172 4248 136
+ 65 4504 * 2027 406 * 0 9317 1397 1000
+
+L 137 4426 * * 4673 6253 * * 4187 * 527 * 5859 * * 5941 * * 3073 * * 137
+ 0 * * * * 0 * 9271 0 1000
+
+L 138 3153 * 4354 2917 5985 6157 6240 6467 4159 2975 4514 6330 * 2891 3093 4553 * 4249 5320 4630 138
+ 28 5711 * 0 * * * 9307 1054 0
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+D 139 3004 * 3042 2765 5753 5201 * 4726 3242 4614 * 4330 * 3737 3737 3544 4032 6028 * 6069 139
+ 0 * * * * * * 8977 0 0
+
+F 140 5787 6288 * * 2230 * * 4772 * 3004 5768 5665 5494 * * * * 5142 2439 1636 140
+ 0 * * * * * * 8939 0 0
+
+E 141 3472 * 3164 1505 * 4220 * 5530 5365 4723 5143 4568 4439 4740 4161 4617 4726 5646 * * 141
+ 0 * * * * * * 8689 0 0
+
+R 142 3883 * 3761 3786 * * * * 3216 4382 * 3224 * 2748 2295 3240 5378 4616 * * 142
+ 0 * * * * * * 8021 0 0
+
+T 143 5017 5360 4770 4062 * * 3113 3019 2693 4950 5251 5247 * 3718 3441 2723 4319 * * * 143
+ 0 * * * * * * 7479 0 0
+
+L 144 * * * * * * * 4246 * 288 * * * * * * 4389 3630 * * 144
+ 0 * * 0 * * * 6413 0 0
+
+//
+�HHsearch 1.5
+NAME f9eb38ef6943149426b564b15c282045
+FAM
+FILE f9eb38ef6943149426b564b15c282045
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:13:29 2013
+LENG 213 match states, 213 columns in multiple alignment
+FILT 215 out of 1347 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.0
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEEEECCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEECCCCCCCCCCCEECCCHHHHHHHHHHHHHCCCHHHHHHCCEEEEEECC
+CCCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCCHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCCCHHHHHCCCCC
+CEEEEEEEEECCC
+>ss_conf PSIPRED confidence values
+9807999999999998605655667753477747999999999972888774167877543322258989999999999848986785320606899604
+8655579999963657897389998797499998613441389530189999999999999998678869999999856322432122463455301268
+5899999987499
+>Consensus
+xNxMxVxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxllxxxxlcnxaxxxxxxxxxxxxxxxxxGxptExALlxxxxxxxxxxxxxxxxxxxxxxxpF
+xsxrKxmxxvxxxxxxxxxxxxxxxKGApexilxxcxxxxxxgxxxxlxxxxxxxixxxxxxxaxxGlRvLaxAxkxxxxxxxxxxxxxxxxxxxxxexx
+LxflGlvgixDPp
+>f9eb38ef6943149426b564b15c282045
+QNPMTVAHMWFDNQIHEADTTENQSGVSFDKTSATWFALSRIAGLCNRAVFQANQENLPILKRAVAGDASESALLKCIEVCCGSVMEMREKYTKIVEIPF
+NSTNKYQLSIHKNPNASEPKHLLVMKGAPERILDRCSSILLHGKEQPLDEELKDAFQNAYLELGGLGERVLGFCHLLLPDEQFPEGFQFDTDEVNFPVDN
+LCFVGLISMIDPP
+>gi|326426562|gb|EGD72132.1| calcium-transporting ATPase type 2C member 1 [Salpingoeca sp. ATCC 50818]
+ANKMVAKVVYDaaHDIHAQVT------GSGYQFSGrvmlgdrpvsintpaattvaaaaaaTANTSTLPMITITPTATAPA-SAP-------SPSSSAAAA
+AVKTASS-AV-EGAAVAPFASVIEAAVLCNNA--EVhTDGTlIG--QptE-VmarLcvclcvcvcvcvcvcvcvcvcvcVCVCVCVCVRVAMCvaVCPMC
+DGRCCSLFATLSPLLTTiTAAAITNTA-----------T-D------------------VFIFTpGLVAIADQP
+>gi|288941070|ref|YP_003443310.1| HAD superfamily ATPase [Allochromatium vinosum DSM 180]gi|288896442|gb|ADC62278.1| ATPase, P-type (transporting), HAD superfamily, subfamily IC [Allochromatium vinosum DSM 180]
+LNRLAISDLVDpVSGAsmdtpd--------------GRRG-----LLEAALIASELRPAtsqEAGAPCW--S----GDPLDVALAAYHAEQIGPPERLLA
+ETRR--HFPFDLARRREAGVFAEGD--E--ILFAIKGAWESLRPLIGQIQDGAGQHHVADDQTLAVCDRAVhRLSSQGRRVIAVAARRLERLP-----DP
+KApeESL---ERGLVLRGLIALDDPI
+>gi|255581776|ref|XP_002531689.1| cation-transporting atpase plant, putative [Ricinus communis]gi|223528665|gb|EEF30680.1| cation-transporting atpase plant, putative [Ricinus communis]
+CNQMEVNE-fFIGEENMNDdeVC-----------ETSpvVLEALGQGIGAStlvT---------GGsvrPI-----------------ddllaawAKsRW
+GANMELSDQ-cFSV-lDHGILESNKNCSRVVIKKNG--DDegILHLHLKGDASTILNFCSHYYNtKWEVH-aIKDQRR-d-FEQVIENMESRGLTAIAYA
+CKQME-T----------------tksra--EhLHLLALVG-l--K-
+>gi|239630295|ref|ZP_04673326.1| cadmium-/manganese-transporting P-type ATPase [Lactobacillus paracasei subsp. paracasei 8700:2]gi|239527907|gb|EEQ66908.1| cadmium-/manganese-transporting P-type ATPase [Lactobacillus paracasei subsp. paracasei 8700:2]
+------------------------------------ETVRAYSAFACDQQ---------------HPSVIDQAILTFTSNNHVE------A-TLSNFTPF
+TAETGYASATITI----ADRLLKVRLGSLKVLQSRDP-----------------ESPKLP-PLALDAGRSVAVSIN-----------------------E
+-HLVGVYILEDTI
+>gi|255565063|ref|XP_002523524.1| H(\+)-transporting atpase plant/fungi plasma membrane type, putative [Ricinus communis]gi|223537231|gb|EEF38863.1| H(\+)-transporting atpase plant/fungi plasma membrane type, putative [Ricinus communis]
+-----------------------------------------------------------------------------------------DADKETVVLLA
+ARASRTENQDAIDasivgmlS---DPKSAQLSLTLTTMVTGTDAA----------KGHLSKKPHEIIDNFADRGLRSLGVARQTIPEKT--------KES
+---AGTPWEFVGLLPLFDPP
+>gi|340054218|emb|CCC48513.1| putative phospholipid-translocating P-type ATPase (flippase), fragment [Trypanosoma vivax Y486]
+QNVMELLHVTIGDKRFSLHEC---EGEasKVDENEEDVLQFGRVLSLCNTVEVASDPardtDrlgAQPYGEhsGTvvyQAASPDEAALCCGAGKLSVrlt
+HReqtratlmvKGIVESWFIHYVFPFSSELKTMGIVVEREG--TGLIYYFVKGADDRIAEMSTVEsrddvSTNGVGKAGDTETFEFIGSELKHYATRGLR
+TLLIAQKRLSRDDLNHflsQiraAEllLTnrQEKLgeirRDMESGVRILGATAIEDK-
+>gi|340504230|gb|EGR30692.1| hypothetical protein IMG5_125530 [Ichthyophthirius multifiliis]
+----------------------------------------------------------------------------------------------YKVNQN
+NYEVMEGKKFRELIGGiaYDNPYAQNIEDRGEAKIFNFDIFKkIVKELKILARSTPDDKYMLVTGLIQ--ITNDAPALKKADVG-FAMGiagTEVAKEAA
+GIILLDDNFVSIVtackygrNIYDSI
+>gi|154286582|ref|XP_001544086.1| cation-transporting ATPase 4 [Ajellomyces capsulatus NAm1]gi|150407727|gb|EDN03268.1| cation-transporting ATPase 4 [Ajellomyces capsulatus NAm1]
+--------------------------------------------------------------------------------------------AIFCTEPF
+RIPYAGRIDIACFDK--T-GTLTG--------EDLLVD----------------------------GIAGLTLGHASAKTDKhGAhtDITPVEKVA---N
+ETTLVLA---------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+Q 1 4415 5646 * 2244 * 5792 * 7130 2529 4521 4232 * * 1991 4879 4930 3607 7248 * 5658 1
+ 0 * * * * * * 9141 0 0
+
+N 2 * * * * * 2978 * * 4642 * * 374 5036 * 5824 7277 7149 * * * 2
+ 16 7035 8140 3585 126 * * 9171 1025 0
+
+P 3 5295 7072 6245 2800 * * 4355 5021 1907 5142 5975 4929 6504 3131 2578 4975 5163 5250 * 6920 3
+ 0 * * * * * 0 9170 0 1000
+
+M 4 6035 * * * 5323 * * 5107 7242 3050 399 * 6217 5809 * 7639 * * 6827 * 4
+ 19 7242 7313 2322 322 * 0 9170 1002 1000
+
+T 5 5040 7466 7757 3883 6082 6574 5720 4713 3598 * * 5849 * 4475 3573 2765 1632 3428 * 5824 5
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+
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+
+A 7 3420 7424 5397 4876 7523 4955 5145 6087 3112 7010 6482 5440 * 6050 3208 2859 2723 2380 * * 7
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+
+H 8 3783 5681 3141 2674 * 4936 4325 6519 2698 * 7116 4395 * 3665 3064 4155 4740 4769 * 7183 8
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+
+M 9 4375 3836 7432 * 3558 4032 * 2143 * 2121 4155 * 5570 * * 7417 * 2631 6286 5934 9
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+
+W 10 4283 4624 6419 * 2674 7131 7353 3807 * 3886 7415 5833 7482 * 5949 4313 4807 2943 2319 2992 10
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+
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+
+D 12 3395 * 3498 3725 4651 2329 5312 5439 5009 4249 7781 3131 3697 6162 * 3357 6439 5608 6761 5534 12
+ 65 5454 5565 1497 631 * 0 9101 1241 1651
+
+N 13 5347 * 2340 3159 7159 1719 7169 * 4510 4390 6799 3774 5463 5440 7573 3648 5341 5690 * * 13
+ 75 5724 4981 1313 743 3407 143 9077 1162 1932
+
+Q 14 4083 7143 4687 3286 6695 3090 5271 4961 3153 6284 * 3841 * 3219 3422 3575 3794 4528 * 6335 14
+ 52 * 4809 3170 170 2933 203 9073 1000 2245
+
+I 15 4571 * 4752 4169 5181 6431 4881 3319 3999 3215 5929 4159 5634 4483 3655 3781 3461 3529 6153 4613 15
+ 96 4916 5011 2088 387 3941 97 9017 1368 2567
+
+H 16 4556 6235 6304 4281 2632 * 5036 3491 4849 3517 5040 5522 7167 4771 6815 6301 6380 3816 5289 1992 16
+ 126 3802 6394 1826 478 2384 307 8977 1834 3014
+
+E 17 3824 * 3282 3444 5785 3405 5188 4796 2970 4804 * 4230 5092 4011 4634 3672 3635 6229 * 4713 17
+ 95 4730 5266 732 1330 3723 114 8995 1387 2782
+
+A 18 3343 6973 4597 3973 4608 3843 * 3738 4999 3254 * 4113 4832 7397 * 3440 4782 2202 * 5493 18
+ 344 3845 2813 1742 513 3780 109 8957 1797 3021
+
+D 19 3700 * 2778 3106 * 4134 6574 * 3244 6261 6092 3524 5381 4085 4300 3614 2904 5990 * 6826 19
+ 151 4428 4239 3585 126 3039 187 8840 1477 4219
+
+T 20 4400 7105 3439 3519 5581 1979 5265 5030 4310 3953 5048 5031 5338 4071 4400 4366 4466 5938 * 5849 20
+ 142 5997 3681 529 1703 3947 97 8758 1078 4323
+
+T 21 3283 6542 5560 3020 4454 4587 * 5700 3900 3300 * 4546 5287 * 4824 2794 2988 4120 * 4806 21
+ 111 5054 4517 3850 104 4454 67 8692 1341 4730
+
+E 22 4248 5567 3338 3255 6696 2739 5632 * 3685 5472 6122 4582 3781 4848 4202 3863 4031 3869 * 5233 22
+ 443 2428 3667 912 1094 5606 30 8639 2575 4858
+
+N 23 4387 * 3051 3685 4884 5743 5061 5420 3962 5665 5594 4751 3926 3947 4646 3742 3520 4069 * 3130 23
+ 283 3093 4035 1642 557 5260 38 8538 1953 5251
+
+Q 24 3551 * 4054 3867 6424 5498 4560 4600 3325 4697 4622 3980 3342 4029 4945 4132 3034 4510 * 6539 24
+ 300 2745 4691 1758 506 2233 345 8437 2174 5479
+
+S 25 5716 5937 3488 2875 * 4525 3972 6052 3365 3880 6756 4356 2922 4147 6552 4139 3538 4546 * 6752 25
+ 319 3112 3595 1091 914 3886 101 8520 2127 4965
+
+G 26 4893 * 3839 4842 7016 1207 7112 5204 4276 4707 6100 4048 5166 5326 6554 4142 4285 4585 * 6875 26
+ 179 3595 4870 1944 434 3247 161 8507 1722 5223
+
+V 27 3794 * 4710 2529 6922 4847 5226 4210 3260 4246 * 4210 3903 3954 4170 2858 5037 5252 * * 27
+ 154 3701 5362 3808 107 2983 195 8626 1809 5120
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+S 28 4074 * 3454 3610 4840 3923 5332 3031 4244 4896 7770 3838 4027 3951 6495 2762 4591 5338 * 6979 28
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+
+F 29 4729 * 5015 5303 3650 5957 4889 4079 3984 2992 4974 5007 4389 5654 6157 4539 4319 4259 5720 2186 29
+ 532 2119 3680 2957 199 1936 437 8742 3090 4749
+
+D 30 2875 * 2921 2959 6983 3511 5881 5013 4618 5715 * 3223 4696 3806 4902 3244 7043 5130 * 7061 30
+ 173 3953 4363 1758 506 2370 310 8818 1720 4527
+
+K 31 4024 6943 5424 3909 4537 5411 6626 3624 3502 3194 7295 5518 2573 4138 5060 3776 4015 3893 * * 31
+ 378 2503 4215 2030 405 1623 567 8816 2923 4305
+
+T 32 3907 * 3155 3785 6089 4400 5579 5024 4650 3494 5914 3925 3921 3650 4250 2840 4371 5511 * 5998 32
+ 196 3958 3995 2626 255 1678 541 8900 1765 3870
+
+S 33 4063 * 2789 3754 * 2704 5271 7010 4277 4985 7416 3351 3893 4521 4467 3403 4275 6018 6840 5588 33
+ 236 2911 5793 3293 155 1435 666 8929 2689 3600
+
+A 34 3006 6903 3691 2270 7475 4373 5045 5615 3225 7157 * 5137 3799 3838 7465 3649 3766 5604 * 6135 34
+ 113 3939 6639 1994 417 1506 626 9039 1753 3220
+
+T 35 3425 * 3285 3640 * 4447 5437 4784 4413 3642 6376 4008 3543 5247 4792 2930 3785 4409 * 5746 35
+ 91 4191 7232 2635 253 2540 272 9105 1716 2653
+
+W 36 4012 * 6581 4126 3129 7423 5955 3463 5272 1894 6211 5094 5614 7423 4573 4030 5058 3340 5749 5121 36
+ 77 5038 5529 3918 99 1725 520 9196 1510 2449
+
+F 37 4455 7318 3664 2946 7557 4526 5135 4759 3393 3590 7318 5358 4578 3566 3047 4102 4239 4737 6936 6334 37
+ 45 5367 7311 1930 439 1680 540 9069 1251 2379
+
+A 38 3730 7212 3356 2456 6416 6210 6096 3826 4596 2759 4542 4891 * 3653 3781 4455 5371 4856 7524 * 38
+ 22 6659 7590 945 1058 1157 858 9059 1177 2042
+
+L 39 4460 6711 * * 3070 7544 * 3047 6485 1070 4690 * 7524 * * 6394 4497 3396 * 5881 39
+ 15 7736 7500 0 * 2713 239 9101 1002 1629
+
+S 40 3766 5310 * 6525 4543 5312 6502 3443 6788 1352 4289 7535 6214 6200 4475 4997 5433 3395 6283 5183 40
+ 24 7273 6641 0 * 1257 782 9115 1028 1617
+
+R 41 3599 6648 4638 2844 6206 5233 5659 5332 3391 3065 5339 4366 6330 3780 3052 5627 3482 5719 7494 6038 41
+ 47 4951 * 1820 481 659 1448 9134 1493 1514
+
+I 42 2045 3788 * * 5557 3036 6000 2920 * 4249 6412 4200 * 6239 7477 3408 5377 3104 7651 5852 42
+ 53 5436 6294 1958 429 * 0 9158 1362 1134
+
+A 43 2004 4529 * * 6168 3159 * 2555 * 2748 3800 6589 * * * 3061 5598 4835 * 7716 43
+ 8 * 7468 * * * 0 9119 0 1599
+
+G 44 2078 4350 7657 7953 5557 3527 7552 4129 * 3749 5144 5631 * 7250 7564 2826 3996 2608 7663 5201 44
+ 20 6214 * 4551 63 1555 600 9110 1136 1695
+
+L 45 4872 5489 7324 5532 5318 5781 7486 3047 6043 1033 4732 6387 * 6281 7656 5030 4866 3621 6942 5611 45
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+C 46 2606 1018 7356 7192 * * 7311 6754 7611 * * 2408 * * 7449 3744 4902 7365 * * 46
+ 44 6492 5703 999 1001 * 0 9135 1118 1786
+
+N 47 7425 4372 7540 5843 * * 3348 7387 7275 6614 7414 1297 5787 5565 * 2208 2903 * * * 47
+ 65 6532 4918 1437 665 1250 787 9097 1261 2104
+
+R 48 4726 * 2536 3514 * 5819 7475 * 4522 6567 6713 2315 6439 5066 5334 2804 2438 6155 * 7257 48
+ 23 7613 6535 1000 1000 2086 388 9082 1000 2167
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+A 49 1352 4804 5521 7679 5916 4522 6637 5091 6699 4273 8085 7331 6155 6102 6432 2512 4472 3264 * 6604 49
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+V 50 4443 6496 5456 3539 5967 5649 5557 4090 3987 5413 4894 3985 6585 3516 3537 3330 3080 3471 * 4534 50
+ 179 3766 4534 2629 254 4189 81 8998 1972 2947
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+F 51 4277 7603 7072 5564 2869 * * 2455 4862 2402 5705 5540 4638 5519 5441 4416 6293 2987 6301 4385 51
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+Q 52 4554 6148 3369 2525 5069 6555 6519 4128 3326 4792 7243 4570 5518 3936 4580 4002 4694 3044 * 5136 52
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+A 53 4221 * 3607 3186 4976 5257 4823 5832 3748 5030 * 3837 3280 4005 4632 3580 3802 4041 7237 4635 53
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+N 54 4654 6179 2201 3101 * 2761 7055 4958 4474 5706 * 3489 4161 4783 5176 3739 4425 5501 * 6880 54
+ 112 4524 4992 3018 190 1332 730 8759 1386 5828
+
+Q 55 4691 * 3253 3164 7389 3432 * 6481 3763 6277 6518 2855 4664 3155 4391 3417 3756 5761 7135 7223 55
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+E 56 4023 * 3039 2832 7388 2520 4601 4996 3883 5207 5746 3346 6438 4935 4496 4296 4418 5778 * 7082 56
+ 433 3386 2612 2391 305 2755 231 9053 2319 4123
+
+N 57 3824 * 3096 3267 6291 2342 5121 * 3713 5299 * 3391 5334 4042 4436 4416 4190 5051 6738 * 57
+ 628 5435 1601 1002 998 2092 386 9020 1191 5256
+
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+
+P 59 5362 * 3875 3832 * 3915 6066 4279 3482 4515 * 5151 1510 5078 4908 4353 5163 * 5257 5266 59
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+
+I 60 4488 * 3986 4143 5393 5253 5534 2983 4435 4631 * 5315 3881 * 3773 4275 4962 2643 * 2825 60
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+
+L 61 3753 * 4199 4761 5664 3576 3817 4894 4209 3206 4030 4825 3907 * * 2603 4736 4001 4786 * 61
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+
+K 62 3858 * 3513 2664 * 4542 5634 4320 3285 4718 6616 5021 5741 2762 4066 3907 4992 4595 * 5285 62
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+
+R 63 5894 6058 5221 4118 4565 4397 7230 5204 3514 4598 4813 5120 4615 4199 3565 4769 5336 3325 2950 3369 63
+ 174 4851 3660 2533 274 1942 435 8602 1321 5645
+
+A 64 4491 7131 4293 2676 6722 3957 4496 3943 3744 5573 6787 5649 5409 3961 3956 5994 3619 2866 * 4421 64
+ 44 5068 * 1393 691 1727 519 8690 1566 5232
+
+V 65 4005 7013 7295 6001 4061 6260 6489 2234 6442 3261 5072 5954 4504 3968 4446 3955 4982 3228 6322 3635 65
+ 48 5196 7480 219 2827 1374 703 8879 1372 4204
+
+A 66 3624 * 5821 5126 4402 3907 5534 2938 3830 4153 * 4394 5701 4461 4558 3037 5217 2707 * 5409 66
+ 91 4032 * 1728 519 437 1937 9059 1986 3178
+
+G 67 5273 * 5901 5168 5814 449 * 7560 5542 6725 * 6828 5573 5526 7455 4527 5460 5971 * 8039 67
+ 68 4572 8009 286 2473 2429 296 9202 1678 1564
+
+D 68 * * 1541 4388 * 6757 * 7191 * 6948 7455 1866 6510 6135 7312 1991 5550 * * * 68
+ 23 6419 7912 0 * 942 1060 9209 1094 1542
+
+A 69 2693 7801 7049 5311 * 7842 5953 5441 3538 5080 6415 6137 1036 4907 5778 4159 6241 6110 * * 69
+ 0 * * 0 * 1952 431 9219 1016 1323
+
+S 70 6483 * 3232 5664 6276 * * 3735 7105 3461 3720 6386 * * 6839 4059 1121 4423 * 6211 70
+ 0 * * * * * 0 9229 0 1217
+
+E 71 5405 * 1450 768 * 7474 * * * 7337 * * * * * 6440 * * * * 71
+ 20 7472 7003 0 * * 0 9229 1018 1217
+
+S 72 3184 3836 * 4688 * 3562 * 3055 3828 3701 5620 4812 * 3896 3970 5094 4866 2560 * 6834 72
+ 0 * * 0 * 2618 256 9212 1000 1402
+
+A 73 374 5046 * 6756 * 5117 * 6741 * 7984 6848 * 6670 7929 7669 3697 4992 7735 * 7336 73
+ 0 * * 1000 1000 1952 431 9219 1016 1323
+
+L 74 5364 7795 * * 4117 * * 2358 * 820 4013 * * * * 7591 6122 3969 * 7217 74
+ 13 6850 * 2807 222 1612 572 9229 1150 1217
+
+L 75 5292 7408 7861 7638 3907 * 5970 2834 5989 1251 4644 6810 7341 6145 5327 5540 6304 2712 * 5679 75
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+K 76 3938 6352 3871 3106 * 5264 5485 6023 2600 4019 6300 4471 8543 3788 3148 4227 4346 3401 * 7725 76
+ 16 6464 * 2177 361 2270 335 9229 1287 1277
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+C 77 2548 5744 * 6966 1789 4296 7880 5545 5869 2558 5394 6205 * 7388 * 5760 4686 5742 5295 3256 77
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+
+I 78 1347 4112 7419 * 5333 3559 7371 4260 * 2943 6158 * 7567 * 5134 3958 5410 3577 * 5263 78
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+V 80 4270 5748 4154 2977 5208 5104 5256 5521 2298 4294 5321 4073 7271 4698 3721 3619 4555 6144 5253 5754 80
+ 102 5822 4296 1434 667 332 2282 9090 1198 3461
+
+C 81 3465 4644 5459 4931 3887 5043 6685 4305 3454 2634 4263 3866 5887 4019 5362 3996 4920 4591 7680 4727 81
+ 79 5550 4957 1205 820 1372 705 9125 1268 2216
+
+C 82 4319 6138 6626 4381 5301 1424 5377 4076 4838 3468 5521 4447 6229 5425 6115 4599 4406 4885 7615 5332 82
+ 194 4321 3718 2572 266 2220 349 9153 1903 2248
+
+G 83 4335 6295 6478 4550 3394 2595 6720 3111 4507 3458 5280 5307 5683 5613 6644 5281 4189 3461 7735 3540 83
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+I 210 4897 * 5266 2373 5570 8023 7332 3590 4454 3867 3591 5774 7122 3463 3346 3932 6232 3942 * 3685 210
+ 0 * * * * 1004 996 9311 0 1117
+
+D 211 * 5344 240 4391 * 6608 6837 * * * * 4704 * * 7105 5922 * * * * 211
+ 0 * * * * 0 * 9227 0 1013
+
+P 212 5810 * 4572 4820 * * 6534 5485 5133 6430 * 6537 483 4252 7158 4611 * * * 7638 212
+ 0 * * * * * * 9132 0 0
+
+P 213 5071 * * 6708 * * 7202 3119 * 2954 * * 717 * * 6958 * 3422 * * 213
+ 0 * * 0 * * * 8623 0 0
+
+//
+�HHsearch 1.5
+NAME fb5bff21f8955d17ec9c9ef42e3fe2a1
+FAM
+FILE fb5bff21f8955d17ec9c9ef42e3fe2a1
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:06:41 2013
+LENG 104 match states, 104 columns in multiple alignment
+FILT 27 out of 29 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 1.6
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCHHHHCCCCHHHHEEEEEEEEHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCHHHCCCCCCCCHHHHHHHHHHCCCCCC
+CCCC
+>ss_conf PSIPRED confidence values
+9877660477777270012111578884447998861288899984110010078999999988629989981333004875151999999999199930
+2119
+>Consensus
+xxWngxyixPYaEhGkKseqVKKitvsIPxkVLkiLTdERTRRQvnnLRHATNSELLCEAFLHAfTGQPLPxDxDlxKdxxdxiPxxxkxxmxxxGixxx
+xxxx
+>fb5bff21f8955d17ec9c9ef42e3fe2a1
+AEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRKVNNLRHATNSELLCEAFLHAFTGQPLPDDADLRKERSDEIPEAAKEIMREMGINPE
+TWEY
+>gi|33151854|ref|NP_873207.1| transcriptional repressor protein MetJ [Haemophilus ducreyi 35000HP]gi|41017323|sp|Q7VN90.1|METJ_HAEDU RecName: Full=Met repressor; AltName: Full=Met regulon regulatory protein metJgi|33148075|gb|AAP95596.1| met repressor [Haemophilus ducreyi 35000HP]
+INWSGKYISPYAEHGKKSKQVKKITVSIPIKVLEILTNERTRRQINNLRHATNSELLCEAFLHAFTGQPLPADEDLMKERYDEIPEKAKSRMRDLGIDPD
+EWQY
+>gi|336317341|ref|ZP_08572197.1| transcriptional regulator of met regulon [Rheinheimera sp. A13L]gi|335878274|gb|EGM76217.1| transcriptional regulator of met regulon [Rheinheimera sp. A13L]
+AKWNGEYVHPYAEHGKKSEQVKKITVSIPLNVLKVLTDERTRRQVNNLRHATNSELLCEAFLHAFTGQPLPADEDLRKDNPHQIPVEVRNILTSMGKPIP
+VIQeA
+>gi|332142907|ref|YP_004428645.1| transcriptional repressor protein MetJ [Alteromonas macleodii str. 'Deep ecotype']gi|332143048|ref|YP_004428786.1| transcriptional repressor protein MetJ [Alteromonas macleodii str. 'Deep ecotype']gi|327552929|gb|AEA99647.1| transcriptional repressor protein MetJ [Alteromonas macleodii str. 'Deep ecotype']gi|327553070|gb|AEA99788.1| transcriptional repressor protein MetJ [Alteromonas macleodii str. 'Deep ecotype']
+AEWNGKYIHPYAEHGKKSEQVKKVTVSIPINVLKALTDERTRRQINNLRHATNSELLCEAFLHAFTGQPLPNDDDLRKDNPNRVPAEARRIMEEMGIDPS
+FENnV
+>gi|71280244|ref|YP_267212.1| transcriptional repressor protein MetJ [Colwellia psychrerythraea 34H]gi|71145984|gb|AAZ26457.1| met repressor [Colwellia psychrerythraea 34H]
+AQWNEEYINPYAEHGKKSEQVKKITVSIPLRVLKVLTDERTRRQVNNLRHATNSELLCEAFLHAFTGQPLPDDEDLAKDNNEKLPASVRRLLEAKGItDF
+SAYEvE
+>gi|336123089|ref|YP_004565137.1| Met repressor [Vibrio anguillarum 775]gi|335340812|gb|AEH32095.1| Met repressor [Vibrio anguillarum 775]
+ADWNGEYISPYAEHGKKSEQVKKITVSIPLKVLKVLTDERTRRQINNLRHATNSELLCEAFLHAYTGQPLPTDEDLRKDRPDDIPTEAKALMTAMGIEFE
+AYDdeeV
+>gi|85711529|ref|ZP_01042587.1| transcriptional repressor protein MetJ [Idiomarina baltica OS145]gi|85694681|gb|EAQ32621.1| transcriptional repressor protein MetJ [Idiomarina baltica OS145]
+K-WNGDYIYPYAEHGRKSEQVKKVTVSIPTRVLKVLTDERTRRQVKNLRHATNSELLCEAFLHAFTGQPLPTDTDLEKTNPNKIPKAVREELEARGLPIP
+ADDeL
+>gi|336452140|ref|ZP_08622572.1| transcriptional regulator of met regulon [Idiomarina sp. A28L]gi|336280956|gb|EGN74241.1| transcriptional regulator of met regulon [Idiomarina sp. A28L]
+E-WDGEYIYPYAEHGKKSTQVKKITVSIPVNVLKVLTDERTRRQVANLRHATNSELLCEAFLHAFTGQPLPDDEDLRKDNPHKMPKAVREYLDTH--NIP
+YSEdD
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 774 * * 4292 * * * 4475 4277 * * * * * * * 2116 4764 * * 1
+ 156 * 3285 * * * * 1625 0 0
+
+E 2 4605 * 2167 1776 * * * * 1961 * * 3371 * 3461 * * * * * * 2
+ 59 4641 * 1585 585 0 * 1546 1000 1037
+
+W 3 * * * * * * * * * * * * * * * * * * 0 * 3
+ 0 * * * * * * 1586 0 0
+
+S 4 * * 2404 * * * * * * * * 578 * * * 2824 * * * * 4
+ 0 * * * * * * 1586 0 0
+
+G 5 * * * 4574 * 62 * * * * * * * * * * * * * * 5
+ 0 * * * * * * 1586 0 0
+
+E 6 * * 2737 967 * * * * 2092 * * 4090 * 4468 * * * * * * 6
+ 0 * * * * * * 1586 0 0
+
+Y 7 * * * * 4090 * * * * * * * * * * * * * * 87 7
+ 0 * * * * * * 1586 0 0
+
+I 8 * * * * * * * 110 * * * * * * * * * 3764 * * 8
+ 0 * * * * * * 1586 0 0
+
+S 9 * * * * * * 2482 * * * * 2880 * * * 758 * * * 3415 9
+ 0 * * * * * * 1586 0 0
+
+P 10 * * * * * * * * * * * * 0 * * * * * * * 10
+ 0 * * * * * * 1586 0 0
+
+Y 11 * * * * * * * * * * * * * * * * * * * 0 11
+ 0 * * * * * * 1586 0 0
+
+A 12 87 * * * * * * * * * * * * * * * * 4090 * * 12
+ 0 * * * * * * 1586 0 0
+
+E 13 * * * 0 * * * * * * * * * * * * * * * * 13
+ 0 * * * * * * 1586 0 0
+
+H 14 * * * * * * 67 * * * * * * 4468 * * * * * * 14
+ 0 * * * * * * 1586 0 0
+
+G 15 * * * * * 0 * * * * * * * * * * * * * * 15
+ 0 * * * * * * 1586 0 0
+
+K 16 * * * 4090 * * * * 160 * * * * * 4436 * * * * * 16
+ 0 * * * * * * 1586 0 0
+
+K 17 * * * * * * * * 0 * * * * * * * * * * * 17
+ 0 * * * * * * 1586 0 0
+
+S 18 * * * * * * * * 3413 * * 2853 * * * 381 * * * * 18
+ 0 * * * * * * 1586 0 0
+
+E 19 * * 4090 234 * * * * 4531 * * * * * * * 4396 * * * 19
+ 0 * * * * * * 1586 0 0
+
+Q 20 * * * * * * * * 4090 * * * * 87 * * * * * * 20
+ 0 * * * * * * 1586 0 0
+
+V 21 * * * * * * * * * * * * * * * * * 0 * * 21
+ 0 * * * * * * 1586 0 0
+
+K 22 * * * * * * * * 0 * * * * * * * * * * * 22
+ 0 * * * * * * 1586 0 0
+
+K 23 * * * * * * * * 0 * * * * * * * * * * * 23
+ 0 * * * * * * 1586 0 0
+
+I 24 * * * * * * * 341 * 5564 * * * * * * * 2402 * * 24
+ 0 * * * * * * 1586 0 0
+
+T 25 * * * * * * * * * * * * * * 5564 * 31 * * * 25
+ 0 * * * * * * 1586 0 0
+
+V 26 * * * * 5564 * * * * * * * * * * * * 31 * * 26
+ 0 * * * * * * 1586 0 0
+
+S 27 * 4479 * * * * * * * * * * * * * 66 * * * * 27
+ 0 * * * * * * 1646 0 0
+
+I 28 * * * * * * * 0 * * * * * * * * * * * * 28
+ 0 * * * * * * 1646 0 0
+
+P 29 * * * * * * * * * * * * 0 * * * * * * * 29
+ 0 * * * * * * 1646 0 0
+
+L 30 * * * * 4162 * * 2037 * 946 * * * * * * 2910 4371 * * 30
+ 0 * * * * * * 1646 0 0
+
+K 31 * * * * * * * * 613 * * 2344 * * 3424 4162 * * * * 31
+ 0 * * * * * * 1646 0 0
+
+V 32 * * * * * * * * * * * * * * * * * 0 * * 32
+ 0 * * * * * * 1646 0 0
+
+L 33 * * * * * * * * * 0 * * * * * * * * * * 33
+ 0 * * * * * * 1646 0 0
+
+K 34 * * * 2567 * * * * 267 * * * * * * * * * * * 34
+ 0 * * * * * * 1646 0 0
+
+I 35 4805 * * * * * * 1013 * * * * * * * * * 1093 * * 35
+ 0 * * * * * * 1646 0 0
+
+L 36 * * * * * * * * * 0 * * * * * * * * * * 36
+ 0 * * * * * * 1646 0 0
+
+T 37 * * * * * * * * * * * * * * * * 0 * * * 37
+ 0 * * * * * * 1646 0 0
+
+D 38 * * 267 * * * * * * * * 2567 * * * * * * * * 38
+ 0 * * * * * * 1646 0 0
+
+E 39 * * * 0 * * * * * * * * * * * * * * * * 39
+ 0 * * * * * * 1646 0 0
+
+R 40 * * * * * * * * * * * * * * 0 * * * * * 40
+ 0 * * * * * * 1646 0 0
+
+T 41 * * * * * * * * * * * * * * * * 0 * * * 41
+ 0 * * * * * * 1646 0 0
+
+R 42 * * * * * * * * * * * * * * 0 * * * * * 42
+ 0 * * * * * * 1646 0 0
+
+R 43 * * * * * * * * * * * * * * 0 * * * * * 43
+ 0 * * * * * * 1646 0 0
+
+K 44 * * * * * * * * 4766 * * * * 54 * * * * * * 44
+ 0 * * * * * * 1646 0 0
+
+V 45 * * * * * * * 1390 * 4418 * * * * * * * 807 * * 45
+ 0 * * * * * * 1646 0 0
+
+N 46 4371 * * * * 3817 * * 2878 * * 501 * * 4718 * * * * * 46
+ 0 * * * * * * 1646 0 0
+
+N 47 * * * * * * * * * * * 69 * * * 4418 * * * * 47
+ 0 * * * * * * 1646 0 0
+
+L 48 * * * * * * * * * 57 * * * 4684 * * * * * * 48
+ 0 * * * * * * 1646 0 0
+
+R 49 * * * * * * * * * * * * * * 0 * * * * * 49
+ 0 * * * * * * 1646 0 0
+
+H 50 * * * * * * 0 * * * * * * * * * * * * * 50
+ 0 * * * * * * 1646 0 0
+
+A 51 0 * * * * * * * * * * * * * * * * * * * 51
+ 0 * * * * * * 1646 0 0
+
+T 52 * * * * * * * * * * * * * * * * 0 * * * 52
+ 0 * * * * * * 1646 0 0
+
+N 53 * * * * * * * * * * * 0 * * * * * * * * 53
+ 0 * * * * * * 1646 0 0
+
+S 54 * * * * * * * * * * * * * * * 0 * * * * 54
+ 0 * * * * * * 1646 0 0
+
+E 55 * * * 0 * * * * * * * * * * * * * * * * 55
+ 0 * * * * * * 1646 0 0
+
+L 56 * * * * * * * * * 27 5747 * * * * * * * * * 56
+ 0 * * * * * * 1646 0 0
+
+L 57 * * * * * * * * * 0 * * * * * * * * * * 57
+ 0 * * * * * * 1646 0 0
+
+C 58 * 0 * * * * * * * * * * * * * * * * * * 58
+ 0 * * * * * * 1646 0 0
+
+E 59 * * * 0 * * * * * * * * * * * * * * * * 59
+ 0 * * * * * * 1646 0 0
+
+A 60 0 * * * * * * * * * * * * * * * * * * * 60
+ 0 * * * * * * 1646 0 0
+
+F 61 * * * * 0 * * * * * * * * * * * * * * * 61
+ 0 * * * * * * 1646 0 0
+
+L 62 * * * * * * * * * 0 * * * * * * * * * * 62
+ 0 * * * * * * 1646 0 0
+
+H 63 * * * * * * 0 * * * * * * * * * * * * * 63
+ 0 * * * * * * 1646 0 0
+
+A 64 0 * * * * * * * * * * * * * * * * * * * 64
+ 0 * * * * * * 1646 0 0
+
+F 65 * * * * 691 * * * * * * * * * * * * * * 1394 65
+ 0 * * * * * * 1646 0 0
+
+T 66 * * * * * * * * * * * * * * * * 0 * * * 66
+ 0 * * * * * * 1646 0 0
+
+G 67 * * * * * 0 * * * * * * * * * * * * * * 67
+ 0 * * * * * * 1646 0 0
+
+Q 68 * * * * * * * * * * * * * 0 * * * * * * 68
+ 0 * * * * * * 1646 0 0
+
+P 69 * * * * * * * * * * * * 0 * * * * * * * 69
+ 0 * * * * * * 1646 0 0
+
+L 70 * * * * * * * * * 0 * * * * * * * * * * 70
+ 0 * * * * * * 1646 0 0
+
+P 71 * * * * * * * * * * * * 0 * * * * * * * 71
+ 0 * * * * * * 1646 0 0
+
+D 72 2664 4820 2971 4679 * * * * * * * 1859 * 4839 * * 1601 * * * 72
+ 0 * * * * * * 1646 0 0
+
+D 73 * * 59 * * * * * * * * 4652 * * * * * * * * 73
+ 0 * * * * * * 1646 0 0
+
+A 74 3645 * 1239 1580 * 4679 * * * * * 3740 * * * * 4381 * * * 74
+ 0 * * * * * * 1646 0 0
+
+D 75 * * 0 * * * * * * * * * * * * * * * * * 75
+ 0 * * * * * * 1646 0 0
+
+L 76 * * * * * * * 3751 * 111 * * * * * * * * * * 76
+ 0 * * * * * * 1646 0 0
+
+R 77 4508 * 4679 4381 * 4707 * * 4697 4753 2985 * * 4784 935 3845 * * * * 77
+ 0 * * * * * * 1646 0 0
+
+K 78 * * * * * * * * 0 * * * * * * * * * * * 78
+ 0 * * * * * * 1646 0 0
+
+E 79 * * 707 1934 * 4697 * * * * * 4679 * * * * 4381 * * * 79
+ 0 * * * * * * 1646 0 0
+
+R 80 * 4733 * * * * 4820 * 2789 * * 1634 * 3759 1522 * * * * 4715 80
+ 0 * * * * * * 1646 0 0
+
+S 81 3784 * 3448 * * * 4753 4844 4697 * * 2921 1252 * * 2934 * * * 4559 81
+ 0 * * * * * * 1646 0 0
+
+D 82 * * 647 3689 * * 3527 * * * * 2662 * * * * 4679 * * * 82
+ 0 * * * * * * 1646 0 0
+
+E 83 4733 * 3855 1934 * 3201 * * 2529 * * 4707 * 4680 3185 3795 4845 * * 4175 83
+ 0 * * * * * * 1646 0 0
+
+I 84 * * * * * * * 645 * 3616 4388 * * * * * * 2114 * * 84
+ 0 * * * * * * 1646 0 0
+
+P 85 * * * * * * * * * * * * 0 * * * * * * * 85
+ 0 * * * * * * 1686 0 0
+
+E 86 1837 * * 1544 * * * * 3263 4628 * * * 4453 * 3157 4917 4580 * * 86
+ 0 * * * * * * 1686 0 0
+
+A 87 2021 * 3574 1001 * * * * 4480 * * * * * * 2999 * * * * 87
+ 0 * * * * * * 1686 0 0
+
+A 88 794 * * * * * * * * * * * * * * * * 1240 * * 88
+ 0 * * * * * * 1686 0 0
+
+K 89 * * * * * * * * 913 4702 * * * 4628 1357 * * * * * 89
+ 0 * * * * * * 1686 0 0
+
+E 90 2374 * * 2823 * * * 4453 3148 * * 3632 * 3648 2075 4480 * 3952 * * 90
+ 0 * * * * * * 1686 0 0
+
+I 91 * * * 4257 * * * 1687 4585 1531 3764 * * 4640 4480 * * 4686 * 4269 91
+ 0 * * * * * * 1686 0 0
+
+M 92 * * * * * * * * * 2382 307 * * * * * * * * * 92
+ 0 * * * * * * 1686 0 0
+
+R 93 4628 * 2953 1799 * * * * 3638 4640 * * * 3738 2113 4585 3739 * * * 93
+ 0 * * * * * * 1686 0 0
+
+E 94 1820 * 3467 1134 * * * * 4650 * * * * 4747 * 4580 4269 * * * 94
+ 0 * * * * * * 1686 0 0
+
+M 95 * * * * * * 4222 * 4384 1300 1192 * * * 4188 * * * * * 95
+ 79 * 4222 * * * * 1676 0 0
+
+G 96 * * * * * 0 * * * * * * * * * * * * * * 96
+ 0 * * * * * 0 1652 0 1007
+
+I 97 * * * * * * * 816 2911 2123 * * * * * * * 3847 * * 97
+ 76 4287 * 0 * 0 * 1652 1002 1007
+
+N 98 4683 * 1841 2084 * * * * * * * 1919 2833 * * * 4597 * * * 98
+ 0 * * * * * * 1676 0 0
+
+P 99 4583 * * * 3003 * * 1666 * * * * 1637 * * * * 4688 3100 4597 99
+ 0 * * * * * * 1676 0 0
+
+E 100 * * 1846 1317 * * * * * * * 4561 2390 * * 3518 * * * * 100
+ 0 * * * * * * 1676 0 0
+
+T 101 2786 * 2577 2916 4579 * * 4607 4512 * * 3563 * * * 2900 3194 4465 * 4182 101
+ 0 * * * * * * 1669 0 0
+
+W 102 * * 4114 2954 4604 * * 3504 * 3034 * * * * * 4182 * 4627 1776 2521 102
+ 64 4534 * 1000 1000 * * 1669 1000 0
+
+E 103 * * 2193 1075 * * * * * * * 2992 * 2468 * * * * * * 103
+ 1382 699 * 368 2150 * * 1669 1261 0
+
+Y 104 3795 * 3687 2218 * * * * * 3568 * * * * * * * 2942 * 1248 104
+ 0 * * 0 * * * 1637 0 0
+
+//
+�HHsearch 1.5
+NAME fc94ceafa368716b735a0cc814095abc
+FAM
+FILE fc94ceafa368716b735a0cc814095abc
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:35:38 2013
+LENG 170 match states, 170 columns in multiple alignment
+FILT 132 out of 1139 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 8.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCCCEEEECC
+CCCCCCCCCCCCCCEEEEHHHHHHHCCCCCCCCCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC
+>ss_conf PSIPRED confidence values
+9216889878898888999278887688999999999999997068843899347777579987524678865556765504665548888465088645
+3210236776620101145553755178868999762167035786776888999999999985889899
+>Consensus
+xxxxxxxxxWxxxxityxxxxxxxxxxxxxxxxxvxxAxxxWxxxxxlxFxxxxxxxadixixxxxxxxxxxxxxxgxxxxlaxaxxpxxxxxgxixxxx
+xxxxxxxxxxxxxxxxxxxHElGHaLGLxHxxxxxsvMxxxxxxxxxxxxxlxxxDixxixxlYgxxxxx
+>fc94ceafa368716b735a0cc814095abc
+YSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDE
+DERWTDGSSLGINFLYAATHELGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGKRSNS
+>gi|73955226|ref|XP_854613.1| PREDICTED: similar to Interstitial collagenase precursor (Matrix metalloproteinase-1) (MMP-1) (Fibroblast collagenase) [Canis familiaris]
+----------------YNLKTGTNKSVRQRNDSLVAEKLKQMQAFFGLKVTGKVnTDTLNLMKQPRCGC-PmwlSTSSLMGANGT-THIrYIY-------
+-------------FGDVLLSQKDIDAPRHSMRL-HSKCFCVTSLPT--------------SLDFRTFIYAlvHSKN-
+>gi|116334127|ref|YP_795654.1| Zn-dependent protease [Lactobacillus brevis ATCC 367]gi|116099474|gb|ABJ64623.1| Predicted Zn-dependent protease [Lactobacillus brevis ATCC 367]
+------TAaktpswgSWDDTTITYKTENTSS-----YYQSIWKNAVKRWNKVGVVKLKAATTGeKADITLTSSAS-LSTQGG--KLAGYTNYSYYKKSG-
+NDQI-VSAKSTLNRSllSKYDytkNQRTNVATHEIGHALGLSHSASKKSVMYASDRY-----ASIDYQDKVALNNAYNN----
+>gi|104783199|ref|YP_609697.1| hypothetical protein PSEEN4224 [Pseudomonas entomophila L48]gi|95112186|emb|CAK16913.1| hypothetical protein PSEEN4224 [Pseudomonas entomophila L48]
+------------RVLKVAFLGSP----DEFLKSEIFRTASQWLlrsgANLSLALTWDNDSQAQIKVRTGRTLP-RNESCAGTDALAM----PAE----TM
+NLNV-------EPGDATFEHVVLHEFGHALGAEHE---------------------------------------
+>gi|302865602|ref|YP_003834239.1| peptidase M7 snapalysin [Micromonospora aurantiaca ATCC 27029]gi|315502150|ref|YP_004081037.1| peptidase m7 snapalysin [Micromonospora sp. L5]gi|302568461|gb|ADL44663.1| peptidase M7 snapalysin [Micromonospora aurantiaca ATCC 27029]gi|315408769|gb|ADU06886.1| peptidase M7 snapalysin [Micromonospora sp. L5]
+------------RNVCYNIS------QAGPFANTAVQAAAIWNnYTNNINMAQCG---snlrITY---TYg------GGSYAQRTSL-------G---NG
+RVVIDYYQ------AQQYSPLRIMTHEIGHILGLpDNYNGNCAiLMSGGSAGTSCTNPYPSSTEAARVDSLFGfaA----
+>gi|310820673|ref|YP_003953031.1| hypothetical protein STAUR_3414 [Stigmatella aurantiaca DW4/3-1]gi|309393745|gb|ADO71204.1| conserved uncharacterized protein [Stigmatella aurantiaca DW4/3-1]
+-------LFWTVPRITWNQSTLGnPGTqpAGSEF-EAVRRSFQSWQDVFsscgNITFEEGPrvadrdvgyvsKgENRNL-VLFRTRQCTvgSvvpaedpc
+weddvcGNVydcWSNGNETIAVTLttyDENTGiiYDSDIELNAVVfSFTTADgprctppltqgCVATDIQNTMTHEIGHLVGLDHTDAPNSTMNPRAPPG
+ETSKRTIDAGSRAFVCESY------
+>gi|339482545|ref|YP_004694331.1| chitinase C [Nitrosomonas sp. Is79A3]gi|338804690|gb|AEJ00932.1| chitinase C; ChiC [Nitrosomonas sp. Is79A3]
+-------AKWAGNNYTVRASSV--GFPVGSWRDALSSVITHWNGNpSNLSYGVVW-DEPGVAAN-----NNENETwWEANNGSnigtyPAvtytw---FN
+SsCNIkEADVIFNNSVAYHYTTsktslwpYGGasRPFQTTAMHEFGHAGGLAHTANTYNIMGQDWTHIHAngstAMAYSGEDANSGLVAVYGLW---
+>gi|119570361|gb|EAW49976.1| tolloid-like 2, isoform CRA_b [Homo sapiens]
+-------SSPDTTAMDTGTKEA---G-KGSQRAIFKQAMRHWEKHTCVTFIERTDEESFIV--FSYRTCG-CCSYVGRRGGGPQAISI------------
+--------GKNCDKFGIVAHELGHVVGFWHEHtrpDRDqhvTIIRENIQPGQEYNFlKMEAGEVSSLGETY------
+>gi|195386972|ref|XP_002052178.1| GJ23077 [Drosophila virilis]gi|194148635|gb|EDW64333.1| GJ23077 [Drosophila virilis]
+------TRHWPNATVYYKIDE---QFSA-AQIQHIELGMRRLELVSCIRFLPASEETV------------------------------------------
+----------------------------------------------------------------------
+#
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+G 123 4891 * * 6893 * 214 * 5979 * 4962 5993 * * 7673 5618 7198 * * * * 123
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+
+H 124 * * * * * * 35 * * * * * * 5393 * * * * * * 124
+ 12 * 6893 * * * 0 9301 0 1021
+
+S 125 1346 5688 * 6730 4672 5338 * 3648 * 3835 6217 6575 * 6323 * 3633 3002 3141 6833 * 125
+ 29 6711 6575 0 * * 0 9306 1030 1260
+
+L 126 6649 * * * 4120 6747 * 3122 * 620 3341 * * * * * * 4346 6690 * 126
+ 0 * * * * 430 1957 9284 0 1455
+
+G 127 * * 6736 * * 57 * * * * * 6832 * * 5618 * * * * * 127
+ 0 * * * * * 0 9301 0 1021
+
+M 128 5458 6829 * * 2823 * 6382 3943 * 511 5082 * 6705 * * * * 6760 * * 128
+ 89 4667 5619 0 * * 0 9301 1533 1021
+
+G 129 3263 * 2845 4177 5602 2801 6873 6982 3172 4958 5792 5264 5088 7057 3135 3762 4612 6923 4486 6017 129
+ 0 * * * * 551 1656 9209 0 1347
+
+H 130 * * 4900 5733 * 7116 235 * * * * 5774 * * 6984 5247 4698 * * * 130
+ 46 4981 * 1947 433 * 0 9301 1374 1021
+
+S 131 4909 6893 5399 2739 6770 6057 * 5524 6117 5790 6842 4544 2774 5454 5166 1880 3021 4342 * 6185 131
+ 250 3000 4867 4850 51 0 * 9301 2704 1021
+
+S 132 3898 * 2754 5989 4352 3124 3534 * 4788 * 6012 3608 3663 5019 4878 3545 4756 6566 5168 3638 132
+ 77 4269 * 4298 75 0 * 9025 1700 1497
+
+D 133 3477 4330 1501 3511 4622 4260 5863 * 6539 6719 * 3128 6806 4538 6807 5448 7195 4397 * 4767 133
+ 79 4235 * 2530 274 * * 9026 1687 0
+
+P 134 4343 6718 4454 3612 5006 5888 * 6872 3586 6499 * 4556 2252 4409 3234 3430 4021 5755 * 3569 134
+ 42 5129 * 2564 267 * * 9012 1246 0
+
+N 135 3570 4121 2794 4387 6738 2591 4322 6752 5921 5063 7026 2872 7164 5867 6857 3964 4360 4778 * 4081 135
+ 164 3485 5801 2814 221 * * 9012 2179 0
+
+A 136 3072 * 2990 * * 5762 * * * 6387 * 4472 4499 6364 6559 1019 3906 4245 * * 136
+ 106 3819 * 1847 470 * 0 8969 1831 1172
+
+V 137 5113 * * 6926 * 6553 * 2062 * 2704 6705 6980 6567 6783 * 5615 3622 1305 5995 * 137
+ 28 5682 * 3363 147 1008 992 8966 1166 1172
+
+M 138 5499 * 7017 * * 4668 * 4839 * 4044 338 * * 6458 * 5426 * * * 6726 138
+ 143 3669 6011 0 * 0 * 8976 1981 1021
+
+Y 139 4258 * 5296 6616 4280 4581 4010 6481 5503 3809 * 3569 6723 5881 4431 3058 4562 * 6700 1630 139
+ 100 4651 5216 1263 778 * 0 8980 1405 1098
+
+P 140 3115 * 6602 4151 5096 3931 * 5575 5215 * * * 1310 4248 5724 3663 5873 6436 * 3430 140
+ 27 6537 6981 1000 1000 273 2534 8935 1019 1570
+
+T 141 4716 4817 3952 4779 3222 4394 5731 4470 4631 6004 5044 3440 6542 4148 3745 3095 3702 5121 * 3965 141
+ 79 5141 5328 3212 165 1173 845 8952 1285 1146
+
+Y 142 3934 4819 4640 6613 3274 3855 6640 3480 6302 3370 6429 4253 5917 5334 * 4346 3826 * 4724 2291 142
+ 80 4215 * 1617 569 * 0 8878 1499 1349
+
+G 143 3425 6692 3366 5536 * 3617 * 6417 3029 4237 6792 3463 5027 3527 4299 3525 3751 3857 * 6397 143
+ 201 3875 4014 2432 296 1644 556 8780 1663 1349
+
+N 144 4564 * 3866 4574 4693 1911 4683 * 6423 6585 * 4304 2732 * 4397 3335 5334 * 6564 3342 144
+ 361 3478 2925 2620 256 * 0 8646 1896 1926
+
+G 145 3650 * 3908 3843 5353 2687 6343 4418 5297 4107 * 3602 5242 4282 5089 3291 3774 3785 * 5361 145
+ 421 3740 2490 1464 649 3435 140 8493 1696 3181
+
+D 146 4449 * 2192 4027 6135 3652 4699 6155 5778 5249 * 2978 * 3466 * 5700 2827 3808 5806 5943 146
+ 264 3200 4101 2177 361 2129 374 8116 1749 4263
+
+P 147 3728 4527 5189 5045 * 4514 4974 3669 5846 4273 * 6182 3096 4476 4304 2957 2435 5013 6313 5912 147
+ 278 2993 4332 1966 427 1117 892 8186 1941 3954
+
+Q 148 4087 * 5452 4238 * 4076 4699 6492 4366 * 6356 3196 4762 4758 2942 3450 3626 4726 4640 2917 148
+ 166 5109 3653 2691 243 753 1299 8488 1162 3057
+
+N 149 4425 5180 3613 * * 3926 * * 2659 3996 6011 2707 3745 4841 3797 3614 4224 4111 6133 * 149
+ 283 6179 2608 2322 322 835 1186 8473 1005 2511
+
+F 150 3301 * 4667 * 2974 5972 6293 4245 6089 3163 5050 6205 3922 4826 3441 4023 3870 3898 5455 3894 150
+ 123 3610 * 1346 721 366 2157 8461 1844 3138
+
+K 151 6564 * 4512 4042 * 3552 4995 5336 3677 * 5527 4586 5483 4995 3398 3385 2188 3668 6385 4390 151
+ 34 5424 * 1684 538 1240 794 8746 1133 1433
+
+L 152 5477 * * 6603 2661 * * 2439 * 1332 4048 * 3625 * * 6140 * 5135 5518 5542 152
+ 13 6782 * 4907 49 * 0 8730 1000 1197
+
+S 153 4655 * 4277 4954 * 3417 5550 * 5011 * 3516 4597 5033 3784 * 1756 2438 5795 * * 153
+ 61 4598 * 3233 162 * 0 8730 1455 1197
+
+Q 154 2665 * 3525 3150 5319 4855 * 5290 4862 4196 6751 4974 3320 3084 5539 4142 4181 3933 * 6542 154
+ 0 * * * * * 0 8722 0 1347
+
+D 155 3510 6677 2320 5271 6522 3061 6305 5356 5498 3980 6676 3353 6515 5578 5459 3251 5028 4863 * 3462 155
+ 0 * * * * 551 1656 8722 0 1347
+
+D 156 5156 * 272 3738 * * * * 6414 * * * * 6245 * 4513 * * * * 156
+ 0 * * * * * 0 8836 0 1021
+
+I 157 5666 * 6450 6661 * * * 1385 3228 3155 5711 4747 * 5662 3125 6406 * 2795 * 6573 157
+ 0 * * * * * 0 8817 0 1021
+
+K 158 2233 6314 3420 3416 6550 6270 5856 6374 3739 3883 6358 4230 * 4535 3925 3130 4348 5035 * 5398 158
+ 0 * * * * * 0 8817 0 1021
+
+G 159 1723 * 6310 4997 4827 2057 * * 5476 6041 * 4357 * 6666 4468 3765 3289 5497 5122 6726 159
+ 13 6811 * 2322 322 * 0 8693 1000 1021
+
+I 160 3766 * * * 6556 * * 1740 * 1525 4483 * * * 5412 5705 * 2620 * 5720 160
+ 0 * * * * * 0 8728 0 1021
+
+Q 161 4410 4473 5549 4904 * 5463 5212 6153 3084 6617 * 3457 * 1804 2515 4893 4734 4728 * * 161
+ 0 * * * * * 0 8611 0 1021
+
+K 162 2586 5413 6614 4129 3689 5545 5369 5586 2806 4332 6180 6463 * 4689 4210 4229 4943 * 4572 2642 162
+ 0 * * * * * 0 8611 0 1021
+
+L 163 4568 * * 5334 4492 * * 2495 5214 1075 3665 5366 * * 5494 6326 6560 4290 * 6597 163
+ 0 * * * * * 0 8611 0 1021
+
+Y 164 * * * * 4689 * 6392 * * * * * * 5619 * * * * 4383 183 164
+ 0 * * * * 0 * 8561 0 1021
+
+G 165 3418 * 6268 6230 * 924 * * 5042 * * 3656 2731 4656 5045 5460 * * * * 165
+ 50 4876 * 1000 1000 * * 8388 1197 0
+
+K 166 2584 4283 3729 3989 * 4017 4945 6325 5221 3951 * 4317 5147 4891 3459 3152 3726 4208 * * 166
+ 0 * * * * * * 8310 0 0
+
+R 167 4310 5327 * 5296 * * 5058 * 3766 * * 2033 2554 4378 3164 2379 * * 5096 * 167
+ 0 * * * * * * 7524 0 0
+
+S 168 3680 * 3772 4728 * 4823 * * 2937 * 2548 3702 3643 3274 * 2928 4383 * * 4855 168
+ 0 * * * * * * 6689 0 0
+
+N 169 * * * * * 2462 * * * * * 616 * * * 2591 * * * * 169
+ 0 * * * * * * 3517 0 0
+
+S 170 * * * * * * * * * * * * * * * 0 * * * * 170
+ 0 * * 0 * * * 1574 0 0
+
+//
+�HHsearch 1.5
+NAME fdfbd67ee8a6a80e1c49419316279395
+FAM
+FILE fdfbd67ee8a6a80e1c49419316279395
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:10:23 2013
+LENG 236 match states, 236 columns in multiple alignment
+FILT 231 out of 1040 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 6.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCEEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCEEEEEEECCCEEEEEEEECCCCCEEEEEEECCCCCCEEEEEEECHHHHCCCCEEEEEEECCCCC
+CCCCEEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCEEECCCEEECCCCCEEEECCCCCCCCCCCEEEEEECCCEEEECCCCCEEEEEEEEEEEEEE
+CCCCCCCEEEEEECCCCCCCCCCCCCCEEEEECCCC
+>ss_conf PSIPRED confidence values
+9868999975864775679999879998389645640763371896899999980787699999944899872688772268939765799999605886
+3343688999998746445535541678838988886776990753981498299863368966026468998378878586999761268999999953
+799998669999767888889888766562325899
+>Consensus
+xnxxvAVEFDTxxnxxxxDpxxnHvgIxvnsxxSxxxxxxxlxxGxxxxxxIxYdxxxxxLxVxlxxxxxxxxxlsxxxdLxxxlxxxxxvGFSasTGxx
+xxxhxIlswxFxsxxxlxxxaxxxxxxFxfxxFxxxxxxlxxxGxAxixxxgxlxLTxxxxxxxxxxxxGraxyxxPvxlxdxxxxxaSFsTxFxFxIxx
+xxxxxgdGlAFxlapxxxxxpxxsxgxxLGLxnxxx
+>fdfbd67ee8a6a80e1c49419316279395
+ADTIVAVELDTYPNTDIGDPSYQHIGINIKSIRSKATTRWDVQNGKVGTAHISYNSVAKRLSAVVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLY
+KETNTILSWSFTSKLKSNSTADAQSLHFTFNQFSQSPKDLILQGDASTDSDGNLQLTRVSNGSPQSDSVGRALYYAPVHIWDKSAVVASFDATFTFLIKS
+PDREIADGIAFFIANTDSSIPHGSGGRLLGLFPDAN
+>gi|255572597|ref|XP_002527232.1| kinase, putative [Ricinus communis]gi|223533408|gb|EEF35158.1| kinase, putative [Ricinus communis]
+----------------------------------------------------------------------------------------------------
+-----------------LLPPSTTSVSFQKTRFDPSDTSIIYEGGATP-SVGSIEF-------------------N------------------------
+----------------------------------S-
+>gi|242082227|ref|XP_002445882.1| hypothetical protein SORBIDRAFT_07g027410 [Sorghum bicolor]gi|241942232|gb|EES15377.1| hypothetical protein SORBIDRAFT_07g027410 [Sorghum bicolor]
+----------------------------------------------------------------------------------------------------
+------------------QEpgqlQPLEVATYNYTSFQEgnskEQRELAFSREARI-YKGAIQVSPDTaNVGSYqDimvNKSGSVLLQRRFTMWShvdvd
+ggGGGngsatsrvQVVSFNSTFSINVFHlpDSSpRPGEGLTFVVA-PSRDePPPGSYGGYLGLTN---
+>gi|297820310|ref|XP_002878038.1| hypothetical protein ARALYDRAFT_906979 [Arabidopsis lyrata subsp. lyrata]gi|297323876|gb|EFH54297.1| hypothetical protein ARALYDRAFT_906979 [Arabidopsis lyrata subsp. lyrata]
+----------------------------------------------------------------------------------------------------
+----------------------SLTHDFSFVGFKK-AsPNLIITGVAEIAATGAIRLTT---DTQR--VIGHAFYSLPIRFKPIgVNRALSFSTSFAIAM
+VPEFvTLGGHGLAFAITPTP-DLRGSLPSQYLGLLNSSR
+>gi|115452011|ref|NP_001049606.1| Os03g0258000 [Oryza sativa Japonica Group]gi|113548077|dbj|BAF11520.1| Os03g0258000 [Oryza sativa Japonica Group]
+SNHVFAVELDTVLSPELHDIDSNHVGIDVNSLQFIQSHTAgyyddstgafmnlTLISRKAMQVWVDYNGQAMVLNVTLAPLGvskPKKPLLPTGLDLSRV
+VEDIAYIGFSSATGlSI-AYHYVLGWSFSLNG--------------------------------------------------------------------
+-----------------------------------------------------
+>gi|255579110|ref|XP_002530403.1| carbohydrate binding protein, putative [Ricinus communis]gi|223530052|gb|EEF31973.1| carbohydrate binding protein, putative [Ricinus communis]
+--GYLGIEFGYSRDGN----DGNSTKILV--LIRVNNEPLghvWTERGQRMKAWIDYDASSKRIEIRINELNGkRpyDPFAAYALDLSKMWSDnEAFVVL
+GSNDgGNPSGTCNVYSWRFRLRKV----------------------------------------------------------------------------
+--------------------------------------------
+>gi|125562917|gb|EAZ08297.1| hypothetical protein OsI_30549 [Oryza sativa Indica Group]
+-----SLPLELTFDASRNLVSASSAGVDVDG---NSTAAVDLRNGNEVGSWVVYDASLARLEVFVSHASLRppTPALAADAdSIAARFAEFMFVGFevts
+SSGNGSSDGGFLIQSWTFQTSG------------------------------------------------------------------------------
+-------------------------------------------
+>gi|125605283|gb|EAZ44319.1| hypothetical protein OsJ_28941 [Oryza sativa Japonica Group]
+----------------------------------------------------------------------------------------------------
+----------------------ASTLSYNFSdpqSFTS--GDLHFEGDAYLG-DTSVVLAKKGTGE-VNPKAGRILYKQPCPSLEQhHRRGNELHHHL-L
+LPHE----RRTGRAGILPH---------------------
+>gi|91215870|ref|ZP_01252839.1| hypothetical protein P700755_15086 [Psychroflexus torquis ATCC 700755]gi|91185847|gb|EAS72221.1| hypothetical protein P700755_15086 [Psychroflexus torquis ATCC 700755]
+----LTIEFDTFQNADFGDPAGDHISIMRNGNPnhnlSTNLaGPvlaidtnPDIEDGIAHDVRIEWDASTNTLSVFFDCLL--R--LTFTDNVKDTiFsg
+DNSVFFGFVGSTGGDTNIHEVCFnrVSFVDNLQ-------------------------------------------------------------------
+-----------------------------------------------------
+>gi|300175644|emb|CBK20955.2| unnamed protein product [Blastocystis hominis]
+----FAIAFSTFKNKEFAryhrDIA-----LYVGDGNTGAFIQdkdhtgCyaryrfhekrqDFSVDNYAVVKIGYSEITGMVRVAIDEKNTGnyHICIHE
+HIDLPAGWWRKATIGISATTGQLADNHDILSVET------------------------------------------------------------------
+-----------------------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+A 1 2008 * 3559 3653 5542 * * * 4047 5345 * 5166 5539 4210 * 1633 * 4944 * 5485 1
+ 33 5465 * 0 * * * 5117 1000 0
+
+D 2 3444 * 3254 * 6256 6647 * 4841 6209 * * 896 5555 * 6596 3210 5151 6244 * 6204 2
+ 42 * 5112 * * * * 5832 0 0
+
+T 3 6382 * * 5565 * 3325 2406 * 4016 * * 4214 3552 2760 2123 4039 4660 * * * 3
+ 0 * * * * 1735 515 6225 0 1078
+
+I 4 5800 6671 * * 2619 5662 * 3092 6657 3250 5282 * * 6711 6070 2177 3008 2910 * 5121 4
+ 0 * * 1000 1000 0 * 6449 1043 1043
+
+V 5 6737 * * * 2720 * * 2677 * 2526 * * * * * 6084 * 1017 * * 5
+ 12 6957 * 1000 1000 * * 6515 1000 0
+
+A 6 386 6871 * * 5436 4269 6091 * * 6202 6948 6427 * * * 4103 5112 6863 7016 * 6
+ 21 6128 * 1585 585 * * 6593 1018 0
+
+V 7 * 6542 * * 5674 * * 2051 * 3941 6427 * * * 6128 * * 650 * * 7
+ 0 * * * * * * 6593 0 0
+
+E 8 4712 * * 224 * 5432 * * 4701 * * * 5366 * * * * 5672 * * 8
+ 24 5921 * 1705 529 * * 6593 1030 0
+
+L 9 * * * * 309 * * 5012 * 3149 * * * * * * * 5001 * 5806 9
+ 17 * 6445 * * * 0 6593 0 1000
+
+D 10 * * 243 5349 * 5843 5865 * 6321 6742 * 6583 * * 6123 5284 * 5417 * * 10
+ 0 * * * * 2067 394 6585 0 1068
+
+T 11 6282 * 5097 6503 * * 6126 3959 * 4991 * 4904 * * * 4407 498 5029 * 5845 11
+ 25 * 5854 1000 1000 0 * 6586 1043 1043
+
+Y 12 5027 6854 * * 1759 5025 3737 6711 * 5408 7520 6407 5509 7087 4826 4025 6529 3654 3907 2144 12
+ 130 5064 4146 1343 723 888 1122 6591 1085 1039
+
+P 13 5213 * 7161 5705 4077 5089 5261 6008 1978 4355 5810 4759 3682 2931 3171 4029 6074 6685 6036 4721 13
+ 53 6020 5600 1000 1000 1570 593 6541 1021 1286
+
+N 14 6019 * 2443 6330 6650 5156 * * 6428 6745 * 710 * 5856 * 4178 4773 * * 6793 14
+ 216 6711 2948 2322 322 2470 287 6517 1000 1256
+
+T 15 2812 * 2870 4649 4594 3906 6771 6775 3620 7124 * 4118 2678 6733 6426 3626 3881 3942 * 5853 15
+ 440 5213 2085 620 1517 1898 451 6413 1125 1710
+
+D 16 4023 * 2586 1827 5659 2848 5137 * 4353 * * 4025 4973 6496 4938 4031 4667 5922 * * 16
+ 871 3360 1491 763 1284 1905 448 6289 1332 2238
+
+I 17 * 4785 * 6046 1918 5813 6182 3928 5532 3147 5169 4296 4924 5303 5753 5672 4297 3872 5681 2852 17
+ 59 5704 5571 0 * 461 1870 6097 1003 2781
+
+G 18 4268 * 3500 6084 4768 2922 * 4873 4917 5364 * 2276 * 6797 3788 4556 6473 * 2144 5883 18
+ 99 3920 * 1156 859 1947 433 6419 1196 1577
+
+D 19 6673 * 383 3983 * 5721 * * 7077 6370 * 4817 * 5356 6073 5183 * * * 5705 19
+ 11 7077 * 1000 1000 3589 125 6446 1000 1422
+
+P 20 5689 * 5582 4806 * * 6973 2865 * 5014 * 5355 720 6594 * 5255 4771 4531 * * 20
+ 29 6509 6760 1000 1000 458 1878 6466 1003 1384
+
+S 21 4837 * 2535 5446 6775 5246 7196 5039 4998 * * 1969 4305 5967 4753 2392 4648 4926 * 4534 21
+ 236 3236 4485 1059 943 1984 420 6581 1430 1118
+
+Y 22 4015 5334 2732 5049 5784 1841 * 5981 6838 * 4664 3487 5651 * 6761 3324 4381 5324 7158 3772 22
+ 56 4718 * 0 * 670 1429 6496 1093 1339
+
+Q 23 6541 5742 2767 6227 * 6694 6234 * 6712 * * 967 4246 4399 5347 3305 4631 * * * 23
+ 0 * * * * * 0 6537 0 1103
+
+H 24 * 5499 * * * * 299 * * 6806 * 6101 6340 6691 4686 4262 6471 6895 * 6777 24
+ 36 * 5342 * * * 0 6537 0 1103
+
+I 25 4013 * * * * * * 1305 6721 4459 6062 * * * * * 5690 1172 * * 25
+ 0 * * * * * 0 6498 0 1194
+
+G 26 3055 * 6537 6658 * 633 * * 5690 6370 * * * * 5752 2727 6271 * * * 26
+ 0 * * * * 1944 434 6498 0 1194
+
+I 27 6607 * * 6178 5785 * * 717 * 2713 * * * * * * * 2460 * 6024 27
+ 0 * * * * * 0 6546 0 1134
+
+N 28 6770 * 1303 6845 6379 5602 4736 * 6282 3675 5113 2080 * 3400 6178 * * 6996 * 4884 28
+ 19 6282 * 1000 1000 * 0 6546 1012 1134
+
+I 29 5254 6751 7032 6024 6732 6687 * 2121 5143 2958 6683 4794 * 6225 5620 5334 3094 1671 * * 29
+ 61 5483 5702 1770 501 914 1091 6546 1051 1134
+
+K 30 6948 6883 3719 6287 * 3312 * 7359 5236 * * 720 5506 * 3585 5669 5101 * * * 30
+ 51 4845 * 2030 405 * 0 6542 1104 1108
+
+S 31 * 5903 5029 * 6549 1667 6710 * 6468 * * 4012 * 6523 4771 1186 4126 * * * 31
+ 86 6156 4510 1106 901 1161 855 6542 1035 1108
+
+I 32 4601 * * 6761 5166 6032 * 2438 5290 2705 3191 4730 5582 6752 4399 3991 4538 2235 * * 32
+ 90 4199 7321 410 2016 1671 544 6492 1167 1220
+
+R 33 5272 * 4397 3361 6896 6788 6549 3609 2961 4911 * 3294 6595 4929 2959 3566 3896 3119 * 5860 33
+ 122 3924 6033 2072 392 * 0 6508 1218 1165
+
+S 34 6410 * 6093 * * * 5738 * 4454 6699 6736 5075 3607 6525 5797 508 4876 6317 * * 34
+ 11 7039 * 1000 1000 750 1302 6418 1000 1223
+
+K 35 4121 6209 4712 5688 5445 4610 5816 3743 4433 3287 6008 3031 * * 5070 3978 3826 2061 * 5313 35
+ 28 5709 * 1954 431 2067 394 6586 1040 1068
+
+A 36 2240 * 6487 4947 7021 4884 4657 6154 2679 6765 * 3387 5587 5292 4596 3163 3501 3956 * 4778 36
+ 59 4869 7468 2946 200 * 0 6587 1216 1043
+
+T 37 4228 * 5864 * 5494 * 4362 5216 7064 5965 * 2976 6667 4864 4905 2168 2140 4010 * 3440 37
+ 221 2813 * 2724 237 2067 394 6586 1547 1068
+
+T 38 3150 5882 6562 3265 7045 4729 4830 4592 3324 5220 5940 5174 6807 4627 4276 3441 3394 2953 * 4447 38
+ 157 3363 7387 2319 323 0 * 6587 1333 1043
+
+R 39 3782 5180 4197 5404 * 5821 5645 6372 7049 6936 * 3444 2141 4962 4598 2222 3901 4627 * 4562 39
+ 290 2458 * 2383 307 * 0 6596 1694 1000
+
+W 40 3487 4416 * * 3826 4855 6799 4183 * 1946 6864 * 4661 * 6796 6041 4365 3351 2354 5583 40
+ 952 1050 * 2334 319 611 1534 6601 2812 1033
+
+D 41 5357 6529 2085 6540 4938 4502 6751 6061 4544 * 6629 2797 5551 5634 4389 2456 3750 4890 5852 5402 41
+ 174 3230 7158 2675 246 * 0 6596 1404 1000
+
+V 42 * * * * 2909 * * 2753 6843 1207 3424 * 6849 * 7314 3841 4834 3975 * * 42
+ 51 4860 * 2219 349 * 0 6593 1093 1016
+
+Q 43 3517 6715 4019 3668 6284 5807 4387 4360 3078 4404 7261 2949 5695 5380 4209 3005 4356 4205 6819 * 43
+ 47 6190 5757 1349 719 870 1142 6593 1017 1016
+
+N 44 4081 * 2092 5475 * 4965 * 5548 5150 7555 * 1790 7077 6964 4993 2201 5652 6077 * 6824 44
+ 106 4084 6415 716 1354 297 2424 6572 1212 1095
+
+G 45 5073 * 4778 6348 6747 455 * 6931 6114 * 6932 3947 7311 7002 4635 6426 6344 * 6854 * 45
+ 51 6841 5282 1000 1000 * 0 6589 1003 1068
+
+K 46 3943 * 3590 2817 6645 3864 7051 4436 2418 6111 5932 3150 * 4309 4346 4007 4499 4912 * 7002 46
+ 22 6836 7328 0 * 779 1261 6574 1000 1214
+
+V 47 4477 * 3631 3883 6989 5619 * 3391 4355 4242 6209 4001 3273 4387 3316 4989 3191 3557 * 5167 47
+ 8 * 7546 * * 2275 334 6597 0 1095
+
+G 48 3780 7049 * * 3916 5567 2602 3371 4510 3730 2972 4949 * 6652 5767 7189 4277 3131 4678 4267 48
+ 12 6873 * 2803 223 2438 294 6599 1020 1096
+
+T 49 4983 * 3679 4196 4551 4756 4343 4520 3212 5499 * 2995 * 3409 4392 4182 3214 4426 6847 4382 49
+ 0 * * * * * 0 6539 0 1071
+
+A 50 1519 4059 * * 6113 * * 7103 * 4515 * 6380 * 6518 * 3767 7583 1238 * * 50
+ 26 * 5824 * * * 0 6539 0 1071
+
+H 51 5887 * 6212 4778 6633 7126 4610 6104 3759 4656 6621 * 6746 5097 2331 4820 4572 5781 1348 6487 51
+ 0 * * * * 1374 703 6595 0 1140
+
+I 52 * * * * 5351 * * 457 * 5455 5582 * * * * * * 2298 * * 52
+ 0 * * * * * 0 6539 0 1071
+
+S 53 5294 * 1967 2530 * 5584 * 4457 5123 5556 * 4019 * 6925 3914 3189 3125 3861 * * 53
+ 0 * * * * * 0 6539 0 1071
+
+Y 54 * * * * 3276 * * 5459 * * * * * * * * * * 4830 253 54
+ 0 * * * * * 0 6539 0 1071
+
+N 55 7042 * 1214 3940 * * 7004 4974 5640 * 6911 2050 * 6543 4726 3367 6148 5758 * 6851 55
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+ 0 * * * * * 0 6611 0 1107
+
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+ 27 5731 * 0 * * 0 6611 1038 1107
+
+A 192 3534 * * * * * 5522 * * * * * * * * 3145 407 5342 * * 192
+ 16 * 6499 * * * 0 6611 0 1107
+
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+ 0 * * * * * 0 6436 0 1157
+
+F 194 * * * * 131 * 5756 5668 * 4659 * * * * * * * 6835 * * 194
+ 40 * 5203 * * 1369 706 6436 0 1157
+
+T 195 4590 * * 4360 6233 * * 4311 6909 4960 6430 5191 * 4686 * 1690 2536 2026 * * 195
+ 0 * * 2702 241 544 1670 6473 1040 1218
+
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+ 13 6805 * 0 * 668 1432 6722 1003 1043
+
+L 197 2305 6619 7237 * 5592 5343 * 3735 4151 4835 * 3134 * 4469 4724 2389 3754 3343 6873 * 197
+ 0 * * * * * 0 6722 0 1000
+
+I 198 6476 5218 * * 5147 * * 550 * 4132 3819 * 5552 * * * 7050 3412 * * 198
+ 54 4771 * 1068 935 * 0 6722 1128 1000
+
+K 199 4214 * 3667 4705 4472 6917 4638 5353 4636 4669 * 3452 5261 4379 3758 4116 2520 3266 * 4158 199
+ 93 4447 5944 495 1783 * 0 6722 1147 1000
+
+S 200 3605 5671 6754 4774 6609 3835 5744 6203 4811 6832 6305 3828 1823 5180 3884 2826 3600 6513 * * 200
+ 319 2563 5090 124 3607 768 1277 6733 1828 1157
+
+P 201 5373 * 4271 4143 5786 4384 5500 3936 3131 4089 * 2916 3130 4005 5249 3557 4287 4595 6724 5736 201
+ 232 2868 6428 1137 875 2051 398 6448 1537 1172
+
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+
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+
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+ 118 3896 6465 227 2781 1148 866 6340 1238 1411
+
+I 205 4360 5666 5084 5070 4877 2178 5126 4930 4302 5687 7004 6542 2831 4651 3889 3237 4643 * * 3770 205
+ 30 5604 * 0 * 157 3282 6493 1041 1251
+
+A 206 2047 * 5141 * * 703 * 5050 * * * * * 7155 5552 4799 6652 * * 6473 206
+ 35 * 5386 * * * 0 6722 0 1000
+
+D 207 * 4972 1190 3152 5111 4220 2578 * * * * 4418 5733 5520 * 5478 5547 * * 4792 207
+ 13 6789 * 0 * 355 2196 6666 1003 1099
+
+G 208 5748 * 7264 * * 67 * * * * * * * * 6476 * * 6810 * * 208
+ 16 * 6543 * * * 0 6722 0 1000
+
+I 209 * * * * 2724 * * 2685 * 1231 2140 * * * 5548 * * * 5744 * 209
+ 0 * * * * * 0 6722 0 1043
+
+A 210 612 5810 6154 6573 * * * 6635 * 5744 * * * * * 4277 3141 3470 * 5678 210
+ 28 5678 * 2000 415 * 0 6722 1038 1043
+
+F 211 * * 5678 * 152 5548 * * 6154 4838 * * * * * 6621 * * * * 211
+ 0 * * * * 668 1432 6722 0 1043
+
+F 212 4458 * * * 1296 * * 3587 * 3214 * 6492 * * * 6901 3724 2140 * 4871 212
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+
+I 213 * * * * 4932 * * 1655 * 1079 4367 * * * * * * 2965 * * 213
+ 0 * * 0 * 1710 526 6717 1001 1090
+
+A 214 1263 6564 * 4955 6996 4203 * 6484 6814 6864 6575 6696 5516 5295 * 2353 3453 3395 * * 214
+ 70 6858 4701 1000 1000 * 0 6691 1011 1051
+
+N 215 4441 * * * * 4109 5497 * * * * 4586 690 * * 2485 4897 * * * 215
+ 105 4930 4750 0 * 655 1454 6646 1088 1204
+
+T 216 4532 * 4751 4631 4987 5021 4584 6845 5813 4518 5601 3946 3280 6734 6506 2611 2893 3327 5727 3652 216
+ 218 6749 2935 0 * 190 3020 6350 1000 1204
+
+D 217 4294 * 2388 6859 * 2680 6898 * 3350 5376 5487 2991 3095 6446 4289 3310 4866 * * * 217
+ 380 * 2112 * * 183 3072 6327 0 1530
+
+S 218 3499 * 5575 5641 4831 6437 6072 6747 4015 4608 * 5318 4301 * 6185 1683 2104 * * 3981 218
+ 37 * 5292 * * 226 2786 6135 0 1852
+
+S 219 4878 * 3245 3875 6202 4189 * * 3878 6496 6109 2860 5066 2695 3613 3595 3676 4401 * 5768 219
+ 173 4663 3770 0 * 1833 475 6317 1110 1194
+
+I 220 5359 * * * 3568 7025 * 2328 * 1383 5018 6109 3391 6489 5756 4747 6398 3616 * * 220
+ 81 5447 4981 0 * 960 1041 6291 1044 1391
+
+P 221 4996 * 5474 4886 * 4008 5577 * 5007 6661 5590 4813 915 5086 6813 3085 4909 6353 * * 221
+ 134 * 3500 * * 913 1093 6260 0 1301
+
+H 222 3062 * 3745 4431 * 3017 5599 5402 3907 5096 * 5681 2522 4158 4852 3707 3794 4703 * 5364 222
+ 95 5918 4407 0 * 927 1077 6204 1038 1431
+
+G 223 2013 6466 3983 5444 * 2059 6050 * 4541 6210 6685 2701 * * 4474 4460 4477 5491 * 5506 223
+ 42 5864 6415 0 * 103 3861 6293 1037 1391
+
+S 224 4286 * 4721 6840 4701 3821 6776 5114 5561 3608 5293 4687 5490 5567 5459 1163 4966 5721 6366 6415 224
+ 35 6454 6330 0 * 1501 629 6205 1003 1073
+
+G 225 2465 6064 6384 5051 * 3491 5046 6527 4592 5036 6547 4889 2777 * 6693 2790 3503 5112 6102 3580 225
+ 53 5098 7207 0 * 430 1957 6204 1092 1078
+
+G 226 5037 6437 4432 4680 * 752 * 6415 * 6180 * 4060 6599 * 6893 3283 4340 * * 5464 226
+ 31 * 5572 1585 585 819 1207 6192 1001 1031
+
+R 227 5566 * * 5178 * 1074 5968 6885 6666 * 6856 5737 4430 1974 4603 4277 6408 6761 * * 227
+ 37 5297 * 0 * 1755 507 6172 1061 1077
+
+L 228 5022 4683 6475 5924 2720 4969 4928 * * 3898 * 3836 * * * 5230 5670 5922 3521 1326 228
+ 0 * * * * * 0 6163 0 1043
+
+L 229 * * * * 3870 * * 4742 * 206 5797 * * * * * * * * 6712 229
+ 0 * * * * * 0 6163 0 1043
+
+G 230 4549 * * * * 119 * * * * * 5480 * * * 6151 * * * * 230
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+L 231 * * * * 4588 * * 3347 * 348 * * * * * * * 3996 6383 * 231
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+
+F 232 4435 * * * 1187 * * 4297 * 2444 5043 * 4970 7031 * * 3167 3340 * * 232
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+
+P 233 4841 * 3486 4164 * 5687 * * 5436 * 6497 795 4402 * 6077 3605 4439 * * * 233
+ 0 * * * * * 0 6073 0 1101
+
+D 234 3514 * 4351 3304 6492 3657 * 5209 3953 6293 * 3587 2868 4741 3338 3147 4068 5455 * 5994 234
+ 129 3547 * 0 * 660 1445 5983 1158 1101
+
+A 235 3110 5115 5062 4233 * 4027 6008 5885 4364 * * 4710 5498 5968 5343 1630 2281 * * * 235
+ 0 * * * * 0 * 5734 0 1013
+
+N 236 * * 2568 * * * * * 3995 * * 722 * * * * 2622 * * * 236
+ 0 * * 0 * * * 4327 0 0
+
+//
+�HHsearch 1.5
+NAME ff5c81bfb664296a11b43497a69645cc
+FAM
+FILE ff5c81bfb664296a11b43497a69645cc
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 12:34:34 2013
+LENG 198 match states, 198 columns in multiple alignment
+FILT 10 out of 12 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 2.7
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCCCEEEEEEEECCCCEEEEECCEEEEEEEEEEECCCCEEEEEECCEEEEEEEEECCCHHHHCCCCCCCCCCCCCEEECCCCCCCEEEEECCCCCCCCC
+CCCEEEEECCCCCCCCCCCCCCCEEEEECCCCCCCCEEEECCCCEEEEECCEEHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCHHHHHHHHCCCCCC
+>ss_conf PSIPRED confidence values
+9766646688841144137987996999987899649988999856759999998757412300456546677882260447856568870578410110
+49769998889888986833897898865788756257988898197242387889456545999757676874573353218678999874177689
+>Consensus
+xxxxNxvxVxGssxGSGgvftxxgxxvvvTAsHVlxxxxaxvxxvxxxrxxltFkxxGDyaeaxxxxxxxxGxxPxxxxaxxxxGrAYwxxxxGvexgxi
+gxxxxxxfTxxGDSGSPViexGxliGVHTGSnxxGxGxvTtxxGxtxxxxxvkLSemxxhyxGPxvxxxxklpxxiixDvxxVpxxLaxllxxxxxxe
+>ff5c81bfb664296a11b43497a69645cc
+KARGNVGFVAGSSYGTGSVWTRNNEVVVLTASHVVGRANMATLKIGDAMLTLTFKKNGDFAEAVTTQSELPGNWPQLHFAQPTTGPASWCTATGDEEGLL
+SGEVCLAWTTSGDSGSAVVQGDAVVGVHTGSNTSGVAYVTTPSGKLLGADTVTLSSLSKHFTGPLTSIPKDIPDNIIADVDAVPRSLAMLIDGLSNRE
+>gi|330895434|gb|AEC48046.1| polyprotein [Simian hemorrhagic fever virus]
+--ATNTRRICGEKVGVCGVFQRGVDHIIITASHVLGNGDVGVVEIEGQRREVTFKKTGDFAvGNITG---LKGAYPTYREAPNHIGRAYWLCANGVESGF
+VGTDGCVVYTGPGDSGSPVVtPSGDLIGIHTGSDTFGCGAISKSDGHVI-VGPVKLSEMARYYAGPLQKTPTKMPRNVVGDCENVPLTLARVIAD-----
+>gi|330895463|gb|AEC48058.1| polyprotein [Simian hemorrhagic fever virus]
+--TDNAVGVFGTSVGSGGLFNRNGKTIVVTASHVIGDRNEGYVDLAGIRTRVQFVKKGDFAEGEID---VPGTYPDFKPVTNYVGRAYWLCQNGVEAGFI
+APTGCVVFTGPGDSGSPIItPDGSFIGVHTGSDAKGCGAFTTISGETV-HGVVPLSVIAPHYDG-V-sTTVKHLPKNVVADVTTVPHSLANILEK-----
+>gi|62511096|sp|Q9WJB2.2|RPOA_PRRSR RecName: Full=Replicase polyprotein 1ab; AltName: Full=ORF1ab polyprotein; Contains: RecName: Full=Nsp1; Contains: RecName: Full=Nsp1-alpha papain-like cysteine proteinase; AltName: Full=PCP1-alpha; Contains: RecName: Full=Nsp1-beta papain-like cysteine proteinase; AltName: Full=PCP1-beta; Contains: RecName: Full=Nsp2 cysteine proteinase; AltName: Full=CP2; Short=CP; Contains: RecName: Full=Non-structural protein 3; Short=Nsp3; Contains: RecName: Full=3C-like serine proteinase; Short=3CLSP; AltName: Full=Nsp4; Contains: RecName: Full=Non-structural protein 5-6-7; Short=Nsp5-6-7; Contains: RecName: Full=Non-structural protein 8; Short=Nsp8; Contains: RecName: Full=RNA-directed RNA polymerase; Short=Pol; Short=RdRp; AltName: Full=Nsp9; Contains: RecName: Full=Helicase; Short=Hel; AltName: Full=Nsp10; Contains: RecName: Full=Non-structural protein 11; Short=Nsp11; Contains: RecName: Full=Non-structural protein 12; Short=Nsp12
+KPSLNTVNVIGSSMGSGGVFTIDGKVKCVTAAHVLTGNSARVSGVGFNQ-MLDFDVKGDF--AIADCPNWQGAAPKTQFCTDGwTGRAYWLTSSGVEPGV
+IGKGFAFCFTACGDSGSPVItEAGELVGVHTGSNKQGGGIVTRPSGQFCNVAPIKLSELSEFFAGPKVPLGDvKVGSHIIKDISEVPSDLCALLAAKPEL
+E
+>gi|302393818|sp|Q04561.3|RPOA_PRRSL RecName: Full=Replicase polyprotein 1ab; AltName: Full=ORF1ab polyprotein; Contains: RecName: Full=Nsp1; Contains: RecName: Full=Nsp1-alpha papain-like cysteine proteinase; AltName: Full=PCP1-alpha; Contains: RecName: Full=Nsp1-beta papain-like cysteine proteinase; AltName: Full=PCP1-beta; Contains: RecName: Full=Nsp2 cysteine proteinase; AltName: Full=CP2; Short=CP; Contains: RecName: Full=Non-structural protein 3; Short=Nsp3; Contains: RecName: Full=3C-like serine proteinase; Short=3CLSP; AltName: Full=Nsp4; Contains: RecName: Full=Non-structural protein 5-6-7; Short=Nsp5-6-7; Contains: RecName: Full=Non-structural protein 8; Short=Nsp8; Contains: RecName: Full=RNA-directed RNA polymerase; Short=Pol; Short=RdRp; AltName: Full=Nsp9; Contains: RecName: Full=Helicase; Short=Hel; AltName: Full=Nsp10; Contains: RecName: Full=Non-structural protein 11; Short=Nsp11; Contains: RecName: Full=Non-structural protein 12; Short=Nsp12
+KPCLNTVNVVGSSLGSGGVFTIDGRRTVVTAAHVLNGDTARVTGDSYNR-MHTFKTNGDY--AWSHADDWQGVAPVVKVAK-GyRGRAYWQTSTGVEPGI
+IGEGFAFCFTNCGDSGSPVIsESGDLIGIHTGSNKLGSGLVTTPEGETCTIKETKLSDLSRHFAGPSVPLGDiKLSPAIIPDVTSIPSDLASLLASVPVV
+E
+>gi|62510944|sp|Q06502.2|RPOA_LDVC RecName: Full=Replicase polyprotein 1ab; AltName: Full=ORF1ab polyprotein; Contains: RecName: Full=Nsp1-alpha papain-like cysteine proteinase; AltName: Full=PCP1-alpha; Contains: RecName: Full=Nsp1-beta papain-like cysteine proteinase; AltName: Full=PCP1-beta; Contains: RecName: Full=Nsp2 cysteine proteinase; AltName: Full=CP2; Short=CP; Contains: RecName: Full=Non-structural protein 3; Short=Nsp3; Contains: RecName: Full=3C-like serine proteinase; Short=3CLSP; AltName: Full=Nsp4; Contains: RecName: Full=Non-structural protein 5-6-7; Short=Nsp5-6-7; Contains: RecName: Full=Non-structural protein 8; Short=Nsp8; Contains: RecName: Full=RNA-directed RNA polymerase; Short=Pol; Short=RdRp; AltName: Full=Nsp9; Contains: RecName: Full=Helicase; Short=Hel; AltName: Full=Nsp10; Contains: RecName: Full=Non-structural protein 11; Short=Nsp11; Contains: RecName: Full=Non-structural protein 12; Short=Nsp12
+GCAKNVVSVFGSASGSGGVFTINGNPVVVTASHLLSDGKARVSCVGFSQ-CLDFKCAGDY--AFARVANWKGDAPKAELSH--rRGRAYCSPLVGLSLDL
+LGKNSAFCFTKCGDSGSPVVdEDGNLLGIHTGSNKRGSGMVTTHGGKTLGMANVKLSEMCPHYSGPGVPVSTvKLPKHLVVDVETVSSDLVAVVESLPAL
+E
+>gi|123432666|ref|YP_001008394.1| polyprotein 1ab [Lactate dehydrogenase-elevating virus]gi|62510951|sp|Q83017.2|RPOA_LDVP RecName: Full=Replicase polyprotein 1ab; AltName: Full=ORF1ab polyprotein; Contains: RecName: Full=Nsp1-alpha papain-like cysteine proteinase; AltName: Full=PCP1-alpha; Contains: RecName: Full=Nsp1-beta papain-like cysteine proteinase; AltName: Full=PCP1-beta; Contains: RecName: Full=Nsp2 cysteine proteinase; AltName: Full=CP2; Short=CP; Contains: RecName: Full=Non-structural protein 3; Short=Nsp3; Contains: RecName: Full=3C-like serine proteinase; Short=3CLSP; AltName: Full=Nsp4; Contains: RecName: Full=Non-structural protein 5-6-7; Short=Nsp5-6-7; Contains: RecName: Full=Non-structural protein 8; Short=Nsp8; Contains: RecName: Full=RNA-directed RNA polymerase; Short=Pol; Short=RdRp; AltName: Full=Nsp9; Contains: RecName: Full=Helicase; Short=Hel; AltName: Full=Nsp10; Contains: RecName: Full=Non-structural protein 11; Short=Nsp11; Contains: RecName: Full=Non-structural protein 12; Short=Nsp12
+GCAKNVVSVFGSASGSGGVFTIHGNPVVVTATHLLSDGKARVSCVGFSQ-CLTFKSVGDY--AFARVAEWKGDAPKVELSD--rRGRAYCSPQVEWSLVL
+LGPNTAFCFTKCGDSGSPVVdEDGNLIGVHTGSNKRGSGMITTHNGKTLGMSNVKLSEMCQHYGGSGVPVSTvRLPKHLIVDVEAVASDLVAVVESLPTP
+E
+>gi|262358357|gb|ACY56797.1| replicase polyprotein 1a [Porcine reproductive and respiratory syndrome virus]
+KPCLNTVNVVGSSLGSGGVFIIDGRKTIITATHVLNGDTARVTSDSYNR-MHTFRANGDY--AWSYADDWQGVAPAVKVAK-SyRGRAYWQTSSGVEPGV
+IGEGFALCFTNCGDSGSPVIsETGDLVGVHTGSNKLGSGLVTTPEGETCSIKETRLSDLSRYFAGPNVPLGDiKLSPAIIPDVTFVPSDLASLLASVPVV
+E
+>gi|62510949|sp|Q68772.3|RPOA_SHFV RecName: Full=Replicase polyprotein 1ab; AltName: Full=ORF1ab polyprotein; Contains: RecName: Full=Nsp1-alpha papain-like cysteine proteinase; AltName: Full=PCP1-alpha; Contains: RecName: Full=Nsp1-beta papain-like cysteine proteinase; AltName: Full=PCP1-beta; Contains: RecName: Full=Nsp2 cysteine proteinase; AltName: Full=CP2; Short=CP; Contains: RecName: Full=Non-structural protein 3; Short=Nsp3; Contains: RecName: Full=3C-like serine proteinase; Short=3CLSP; AltName: Full=Nsp4; Contains: RecName: Full=Non-structural protein 5-6-7; Short=Nsp5-6-7; Contains: RecName: Full=Non-structural protein 8; Short=Nsp8; Contains: RecName: Full=RNA-directed RNA polymerase; Short=Pol; Short=RdRp; AltName: Full=Nsp9; Contains: RecName: Full=Helicase; Short=Hel; AltName: Full=Nsp10; Contains: RecName: Full=Non-structural protein 11; Short=Nsp11; Contains: RecName: Full=Non-structural protein 12; Short=Nsp12
+---SNSVSVYGVTCGSGGLFSDGNNTVCLTATHVCGNNKAVVDYQGT-RYEAVFTTKGDYASAVVP---IPGAFPPLKFAPQSyTGRAYWYANTGVETGF
+VGTTGCLVFSGPGDSGSPIItPDGLIVGVHTGSDSKGSGAYTTPNGLTV-SGPLSLKEMGAHYEGPIVDVPTRLPRNVHNDTKSVPQPLARLLESSIN--
+>gi|22299180|ref|NP_682427.1| hypothetical protein tlr1637 [Thermosynechococcus elongatus BP-1]gi|22295362|dbj|BAC09189.1| tlr1637 [Thermosynechococcus elongatus BP-1]
+------------SHGSGILLQRHGNTyVILTAYHVIEKGGQYtVKTVDGQRYavrpssirrlpsvdlaTLEIESNRDYtlatlgnsGEAVEGMPVFVAGF
+PAQEASV--LGGIYQFTEGRLtanASRPIQDGYALVYSNptlPGMSGGPVLdENGRLIGIHGS-------------------------------------
+-------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+K 1 * * * * * 1744 * * 512 * * * * * * * * * * * 1
+ 0 * * * * * * 2090 0 0
+
+A 2 1942 1744 * * * * * * * * * * 1180 * * * * * * * 2
+ 0 * * * * * * 2090 0 0
+
+R 3 1453 2359 * * * * * * * * * * * * 2533 3074 2753 * * * 3
+ 0 * * * * * * 2537 0 0
+
+G 4 * * 3016 * * 2700 * * 2400 1847 * * * * * 3012 2930 * * * 4
+ 0 * * * * * * 2658 0 0
+
+N 5 * * * * * * * * * * * 0 * * * * * * * * 5
+ 0 * * * * * * 2658 0 0
+
+V 6 3016 * * * * * * * * * * * * * * 3012 1289 1542 * * 6
+ 0 * * * * * * 2658 0 0
+
+G 7 * * * * * 2700 * * * * * * * * 2930 * * 484 * * 7
+ 0 * * * * * * 2658 0 0
+
+F 8 * * * * 2700 3016 * * * * * 1847 * * 2930 1674 * * * * 8
+ 0 * * * * * * 2658 0 0
+
+V 9 * * * * * * * 2930 * * * * * * * * * 203 * * 9
+ 0 * * * * * * 2658 0 0
+
+A 10 2700 2930 * * 1675 * * 3251 * * * * * * * * * 2533 * 3012 10
+ 0 * * * * * * 2658 0 0
+
+G 11 * * * * * 0 * * * * * * * * * * * * * * 11
+ 0 * * * * * * 2658 0 0
+
+S 12 * * * 2930 * * * * * * * * * * * 687 3016 3012 * * 12
+ 0 * * * * * * 2658 0 0
+
+S 13 2571 * * * * * * * 3071 * * * * * * 733 3169 * * * 13
+ 0 * * * * * * 2811 0 0
+
+Y 14 * 3169 * * * * 3356 * * 2685 3381 * * * * 2571 * 2114 * 2833 14
+ 0 * * * * * * 2811 0 0
+
+G 15 * * * * * 0 * * * * * * * * * * * * * * 15
+ 0 * * * * * * 2811 0 0
+
+T 16 * * * * * * * * * * * * * * * 433 2833 3071 * * 16
+ 0 * * * * * * 2811 0 0
+
+G 17 * 3071 * * * 183 * * * * * * * * * * * * * * 17
+ 0 * * * * * * 2811 0 0
+
+S 18 * * * * * 392 * 3356 * * * * * * * 2833 * * * * 18
+ 0 * * * * * * 2811 0 0
+
+V 19 * * * * * * * * * 1639 * * * * * * * 558 * * 19
+ 0 * * * * * * 2811 0 0
+
+W 20 * * * * 392 * * * * 3356 * * * * * * * * 2833 * 20
+ 0 * * * * * * 2811 0 0
+
+T 21 * * * * * * * 3667 * * * 3157 * 2207 * 3169 1055 * * * 21
+ 0 * * * * * * 2811 0 0
+
+R 22 * * 3169 * * * * 1252 * * * * * * 1092 * * * * * 22
+ 0 * * * * * * 2811 0 0
+
+N 23 * * 1992 * * 2119 2449 * * * * 1576 * * * * * * * * 23
+ 0 * * * * * * 2811 0 0
+
+N 24 * * * * * 668 * * * * * 1991 * * * * * 3071 * * 24
+ 0 * * * * * * 2811 0 0
+
+E 25 * * 3071 2833 * * * * 2265 * * 1407 * * 2685 * * * * * 25
+ 0 * * * * * * 2811 0 0
+
+V 26 * * * * * * 3071 * 3667 * * * 2571 * 3704 * 1639 2081 * * 26
+ 148 3356 * 0 * * * 2811 1068 0
+
+V 27 * * * * * * * 2114 3381 * * * * * * * 2685 950 * * 27
+ 0 * * * * * * 2811 0 0
+
+V 28 * 2271 * * * * * 1759 * * * * * * * * * 1007 * * 28
+ 0 * * * * * * 2811 0 0
+
+L 29 * * * * * * * 2339 * 1518 * * * * * * * 1142 * * 29
+ 0 * * * * * * 2811 0 0
+
+T 30 * * * * * * * * * * * * * * * * 0 * * * 30
+ 0 * * * * * * 2811 0 0
+
+A 31 0 * * * * * * * * * * * * * * * * * * * 31
+ 0 * * * * * * 2811 0 0
+
+S 32 2534 * * * * * * * * * * * * * * 1138 1861 * * 3356 32
+ 0 * * * * * * 2811 0 0
+
+H 33 * * * * * * 0 * * * * * * * * * * * * * 33
+ 0 * * * * * * 2811 0 0
+
+V 34 * * * * * * * * * 2571 * * * * * * * 266 * * 34
+ 0 * * * * * * 2811 0 0
+
+V 35 * 3169 * * * * * 2253 * 892 * * * * * * * 2833 * * 35
+ 0 * * * * * * 2811 0 0
+
+G 36 * * * 3356 * 1051 * * * * * 2685 * * * 2571 3381 * * * 36
+ 0 * * * * * * 2811 0 0
+
+R 37 * * 1834 * * 1992 * * 3356 * * 2119 * * 2833 * * * * * 37
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\ No newline at end of file
diff --git a/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db.index b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db.index
new file mode 100644
index 0000000000000000000000000000000000000000..c0afc6b812ba3c42cac91d69ced8a6b4be1c1127
--- /dev/null
+++ b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db.index
@@ -0,0 +1,200 @@
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diff --git a/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db.index.sizes b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db.index.sizes
new file mode 100644
index 0000000000000000000000000000000000000000..08839f6bb296e888d311d8ea2f35f7ff82dd3f2d
--- /dev/null
+++ b/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb_hhm_db.index.sizes
@@ -0,0 +1 @@
+200
diff --git a/modules/bindings/tests/testfiles/test.hhr b/modules/bindings/tests/testfiles/test.hhr
new file mode 100644
index 0000000000000000000000000000000000000000..ff9f05a8dc7f32ad9db367374a967388f8865453
--- /dev/null
+++ b/modules/bindings/tests/testfiles/test.hhr
@@ -0,0 +1,101 @@
+Query Test
+Match_columns 141
+No_of_seqs 253 out of 255
+Neff 9.4
+Searched_HMMs 5
+Date Mon Aug 31 16:45:45 2015
+Command /import/bc2/apps/HH-suite/2.0.16-goolf-1.4.10/bin/hhblits -cpu 1 -n 1 -e 0.001 -Z 10000 -B 10000 -i /import/bc2/home/schwede/bienert/git/ost_newenv.git/modules/bindings/tests/testfiles/testali.a3m -o /scratch/tmp9E5dor/testali_cpu1_n1.hhr -d /import/bc2/home/schwede/bienert/git/ost_newenv.git/modules/bindings/tests/testfiles/hhblitsdb/hhblitsdb
+
+ No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
+ 1 3e7b90809bd446a538f9eb1a1ca0e5 100.0 2.7E-42 6.9E-45 222.3 16.4 140 1-141 1-147 (153)
+ 2 af828e69a5f2d0fd42a2a213e09eb6 100.0 1.5E-41 3.9E-44 215.7 17.2 141 1-141 1-141 (141)
+ 3 9287755aa6aa27583da6be3b2408bf 100.0 3.8E-41 9.7E-44 215.1 16.5 138 1-141 2-146 (146)
+ 4 e69e1ac0a4b2554df25f2c2183b0fb 0.6 64 0.16 12.6 2.6 21 93-113 176-196 (248)
+
+No 1
+>3e7b90809bd446a538f9eb1a1ca0e551
+Probab=100.00 E-value=2.7e-42 Score=222.30 Aligned_cols=140 Identities=26% Similarity=0.420 Sum_probs=135.4
+
+Q ss_pred CCCHHHHHHHHHHHHHHhcCchhHHHHHHHHHHhhCccccccCCCC-CC-C----CCChhHHHHHHHHHHHHHHHHhccC
+Q Test 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DL-S----HGSAQVKGHGKKVADALTNAVAHVD 74 (141)
+Q Consensus 1 ~lt~~~~~~i~~sW~~v~~~~~~~g~~~f~~lf~~~P~~~~~F~~~-~~-~----~~~~~~~~h~~~v~~~l~~~i~~ld 74 (141)
+ |||++|+++|++||+.+.++.+++|..||.+||+.+|+++.+|+.| ++ + .+|+.|++|+.+|+++|+.+|+++|
+T Consensus 1 ~lt~~e~~~i~~sW~~v~~~~~~~g~~~f~~lF~~~P~~~~~F~~f~~~~~~~~l~~~~~~~~h~~~v~~~l~~~i~~ld 80 (153)
+T 3e7b90809bd446 1 VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKG 80 (153)
+T ss_pred CcCHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHCccHHhhCccccccCcHHHHhcCHHHHHHHHHHHHHHHHHHHhhh
+Confidence 7999999999999999998889999999999999999999999999 77 4 6999999999999999999999999
+
+
+Q ss_pred CHHHHHHHHHHHHhhh-cCCCHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHhhcC
+Q Test 75 DMPNALSALSDLHAHK-LRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR 141 (141)
+Q Consensus 75 ~~~~~l~~l~~~H~~~-~gv~~~~f~~~~~~l~~~l~~~lg~~~~~~~~~AW~~~~~~i~~~m~~~~~ 141 (141)
+ |++..+..||++|. . +||+|+||+.|+++|+++|++.+|+.||++++.||.+++++|++.|.++|+
+T Consensus 81 ~~~~~l~~lg~~H~-~~~gv~~~~f~~~~~~l~~~l~~~lg~~~t~~~~~AW~~~~~~i~~~~~~~~~ 147 (153)
+T 3e7b90809bd446 81 HHEAELKPLAQSHA-TKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYK 147 (153)
+T ss_pred hhHHHHHHHHHHHH-HHcCCCHHHHHHHHHHHHHHHHHHccccCCHHHHHHHHHHHHHHHHHHHHHHH
+Confidence 99999999999999 8 999999999999999999999999999999999999999999999999884
+
+
+No 2
+>af828e69a5f2d0fd42a2a213e09eb64f
+Probab=100.00 E-value=1.5e-41 Score=215.69 Aligned_cols=141 Identities=100% Similarity=1.413 Sum_probs=135.4
+
+Q ss_pred CCCHHHHHHHHHHHHHHhcCchhHHHHHHHHHHhhCccccccCCCCCCCCCChhHHHHHHHHHHHHHHHHhccCCHHHHH
+Q Test 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNAL 80 (141)
+Q Consensus 1 ~lt~~~~~~i~~sW~~v~~~~~~~g~~~f~~lf~~~P~~~~~F~~~~~~~~~~~~~~h~~~v~~~l~~~i~~ld~~~~~l 80 (141)
+ |||++|+++|++||+.+.++.+++|..||.+||+.+|+++++|+.|+++++||+|++|+.+|+++|+.+|+++||++.++
+T Consensus 1 ~Lt~~~~~~i~~sW~~i~~~~~~~g~~~~~~lf~~~P~~~~~F~~~~~~~~~~~~~~h~~~~~~~l~~~i~~ld~~~~~~ 80 (141)
+T af828e69a5f2d0 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNAL 80 (141)
+T ss_pred CcCHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHChhHHHHcccccCCccCHHHHHHHHHHHHHHHHHHHhhccHHHHH
+Confidence 79999999999999999888899999999999999999999999986667899999999999999999999999999999
+
+
+Q ss_pred HHHHHHHhhhcCCCHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHhhcC
+Q Test 81 SALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR 141 (141)
+Q Consensus 81 ~~l~~~H~~~~gv~~~~f~~~~~~l~~~l~~~lg~~~~~~~~~AW~~~~~~i~~~m~~~~~ 141 (141)
+ ..|++.|.+++||+|+||+.++++|+.+|++.+|++||+++++||++++++|++.|.++|+
+T Consensus 81 ~~l~~~H~~~~gv~~~~f~~~~~~l~~~l~~~lg~~~~~~~~~AW~~~~~~i~~~~~~~y~ 141 (141)
+T af828e69a5f2d0 81 SALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR 141 (141)
+T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHccccCCHHHHHHHHHHHHHHHHHHHHhcC
+Confidence 9999999636999999999999999999999999999999999999999999999999996
+
+
+No 3
+>9287755aa6aa27583da6be3b2408bfcc
+Probab=100.00 E-value=3.8e-41 Score=215.11 Aligned_cols=138 Identities=45% Similarity=0.799 Sum_probs=133.1
+
+Q ss_pred CCCHHHHHHHHHHHHHHhcCchhHHHHHHHHHHhhCccccccCCCC-CCC-----CCChhHHHHHHHHHHHHHHHHhccC
+Q Test 1 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-----HGSAQVKGHGKKVADALTNAVAHVD 74 (141)
+Q Consensus 1 ~lt~~~~~~i~~sW~~v~~~~~~~g~~~f~~lf~~~P~~~~~F~~~-~~~-----~~~~~~~~h~~~v~~~l~~~i~~ld 74 (141)
+ +||++|+++|++||+.+. .+++|..||.+||+.+|+++.+|+.| +++ ++|+.+++|+.+|+++|+.+|+++|
+T Consensus 2 ~Ls~~~~~~i~~sW~~v~--~~~~g~~~~~~lf~~~P~~k~~F~~~~~~~~~~~l~~~~~~~~h~~~~~~~l~~~i~~l~ 79 (146)
+T 9287755aa6aa27 2 HLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLD 79 (146)
+T ss_pred CCCHHHHHHHHHHHHHhh--hHHHHHHHHHHHHHHCHHHHHHcccccccCcHHHHhcCHHHHHHHHHHHHHHHHHHHhHh
+Confidence 699999999999999995 68999999999999999999999999 774 5899999999999999999999999
+
+
+Q ss_pred CHHHHHHHHHHHHhhh-cCCCHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHhhcC
+Q Test 75 DMPNALSALSDLHAHK-LRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR 141 (141)
+Q Consensus 75 ~~~~~l~~l~~~H~~~-~gv~~~~f~~~~~~l~~~l~~~lg~~~~~~~~~AW~~~~~~i~~~m~~~~~ 141 (141)
+ ++...+..||+.|. . +||+|+||+.++++|++++++.+|++||+++++||++++++|++.|++||+
+T Consensus 80 ~l~~~l~~lg~~H~-~~~gv~~~~~~~~~~~l~~~l~~~lg~~~~~~~~~AW~~~~~~i~~~m~~~~~ 146 (146)
+T 9287755aa6aa27 80 NLKGTFATLSELHC-DKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH 146 (146)
+T ss_pred hHHHHHHHHHHHHH-HhcCCCHHHHHHHHHHHHHHHHHHccccCCHHHHHHHHHHHHHHHHHHHHhcC
+Confidence 99999999999999 8 999999999999999999999999999999999999999999999999996
+
+
+No 4
+>e69e1ac0a4b2554df25f2c2183b0fba0
+Probab=0.56 E-value=64 Score=12.63 Aligned_cols=21 Identities=10% Similarity=0.105 Sum_probs=13.9
+
+Q ss_pred CCHHHHHHHHHHHHHHHHHhc
+Q Test 93 VDPVNFKLLSHCLLVTLAAHL 113 (141)
+Q Consensus 93 v~~~~f~~~~~~l~~~l~~~l 113 (141)
+ .+|++.+.+-+.+-+.+.+..
+T Consensus 176 a~~e~i~~~~~~IR~~l~~~~ 196 (248)
+T e69e1ac0a4b255 176 ATPEQAQLVHKEIRKIVKDTC 196 (248)
+T ss_pred CCHHHHHHHHHHHHHHHHHhc
+Confidence 467777777776666665543
+
+
+Done!
diff --git a/modules/bindings/tests/testfiles/test.hmm b/modules/bindings/tests/testfiles/test.hmm
new file mode 100644
index 0000000000000000000000000000000000000000..d1cf2e521e6e678cf864e1308128d4b1620cd29b
--- /dev/null
+++ b/modules/bindings/tests/testfiles/test.hmm
@@ -0,0 +1,469 @@
+HHsearch 1.5
+NAME Test
+FAM
+FILE test
+COM /import/bc2/apps/HH-suite/2.0.16-goolf-1.4.10/bin/hhmake -i ../modules/bindings/tests/testfiles/testali.a3m -o test.hmm
+DATE Mon Aug 31 11:37:41 2015
+LENG 141 match states, 141 columns in multiple alignment
+FILT 112 out of 255 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 9.3
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHHH
+HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+9999999999999988733915579999999986394411239877888888567889999999999987354777899999998876502999898998
+89999999997536679989999999999999999984329
+>Consensus
+xltxxxxxxixxsWxxvxxxxxxxgxxxxxxlfxxxPxxxxxFxxxxxxxxxxxxxxhxxxvxxxlxxxixxldxxxxxlxxlxxxHxxxxgvxxxxxxx
+xxxxlxxxlxxxxgxxxxxxxxxAWxxxxxxixxxmxxxyx
+>Test
+VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL
+LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
+>gi|1170183|sp|P42511.1|LGB_CANLI RecName: Full=Leghemoglobingi|495289|gb|AAA18503.1| leghemoglobin [Canavalia lineata]
+-FSEKQESLVKSSWEAFKQNVPHHSAVFYTLILEKAPAAQNMFSFLSNGvdPNNPKLKAHAEKVFKMTVDSAVQLRAKGEVvlaDPTLGSVHV-QKGVLD
+PHFLVVKEALLKTFKEAVGDKWNDELGNAWEVAYDELAAAIKKAM-
+>gi|88813510|ref|ZP_01128744.1| hypothetical protein NB231_06775 [Nitrococcus mobilis Nb-231]gi|88789223|gb|EAR20356.1| hypothetical protein NB231_06775 [Nitrococcus mobilis Nb-231]
+--------LFNDSYERCIDnpNPPGFLQRFYKVFLSSSEEVAEKFKNT-------DFEKQTRVLKASLYYLMLScNGspEAMAHLRRIACLHSrKQLDIR
+PELYDLWLASLLQAAREYD-PRFDQQTETAWRQVLSHGIDFMKSRY-
+>gi|336324532|ref|YP_004604499.1| hypothetical protein Flexsi_2317 [Flexistipes sinusarabici DSM 4947]gi|336108113|gb|AEI15931.1| hypothetical protein Flexsi_2317 [Flexistipes sinusarabici DSM 4947]
+-VKESDLKELGSIWEQMSKYSDEFTTDMSAFVV-KNFKLPETYST-------EITDEYKAMLGKLYERVLsGRFNNDYvSFLIKFSEFNL-AYSINQEMV
+NSlisyARSWIHEKIFQNIPDDFQrKGILMMFHKIMDITGDIIISTYY
+>gi|289549194|ref|YP_003474182.1| hypothetical protein Thal_1426 [Thermocrinis albus DSM 14484]gi|289182811|gb|ADC90055.1| conserved hypothetical protein [Thermocrinis albus DSM 14484]
+-WTAEDEENLRSLSHLVPSWVEEFLES---------------IRK-------DEhDERCFQSIREWLIATFsGPHDERYvRKIHNMLQEHL-KAGCTLHH
+LQVllssVREFLLDKLTAQLGYSHQrDSLFRSVEKTLDLSLSIMLLSQK
+>gi|341887822|gb|EGT43757.1| CBN-GLB-25 protein [Caenorhabditis brenneri]
+----RDFFTLKNWWKSVDRKRVEASTYMFSRYLNDFPENKAFYAKLkNVnAqtvdmnCSDPGFEAMAAQYLKVFDDVITAveekPGDVQSacdRLSAVGK
+MHR-AkvSGagMESSMFQNMEEPFIQMVKYILQDRFNEKAEMLYRKFFQFCLKYLLEGF-
+>gi|17567933|ref|NP_509614.1| GLoBin family member (glb-17) [Caenorhabditis elegans]gi|3877381|emb|CAA86423.1| C. elegans protein F49E2.4a, partially confirmed by transcript evidence [Caenorhabditis elegans]
+-ITDEEVTAIRDVWRRA--KTDNVGKKILQTLIEKRPKFAEYFGIQsESlDiralNQSKEFHLQAHRIQNFLDTAVGSLGFcpissVFDMAHRIGQIHF-
+YRGVNfgADNWLVFKKVTVDQVTtgttdsskekedtnsngtangkvdtdaSLIPiadinNVYSGencLARLGWNKLMTVIVREMKRGFL
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+V 1 4902 4723 * * * 3431 3746 * 3837 * 5128 4860 1870 4923 4832 2670 5280 3268 * * 1
+ 44 5066 * 2000 415 * * 6988 1000 0
+
+L 2 * * * * 3118 6092 * 3501 * 792 3848 * * * * * 6569 3621 4536 * 2
+ 0 * * * * * * 8826 0 0
+
+S 3 6516 * 6204 * * * 6508 * 5652 * * 3368 6238 6481 5972 1433 1325 4717 * * 3
+ 0 * * * * * * 8861 0 0
+
+P 4 3037 6170 2764 2586 * 4445 6630 5465 3966 4811 6242 * 2872 4851 4994 3922 5028 4835 * 5338 4
+ 0 * * * * * * 8912 0 0
+
+A 5 2684 * 3384 2457 * 5021 6212 3905 2685 * * 5386 4978 3661 4250 3499 * * * 5368 5
+ 0 * * * * * * 8946 0 0
+
+D 6 6353 * 1855 1840 * * 5446 6208 6634 6380 * 5599 * 1624 * * 5141 * * * 6
+ 0 * * * * * * 8971 0 0
+
+K 7 4798 6591 * 4398 5308 * 5441 2820 2041 3610 * * * 4776 2557 * 5226 2971 5746 6354 7
+ 0 * * * * * * 9237 0 0
+
+T 8 2935 * 3662 2847 5479 6921 5604 5134 2313 5429 * 5576 6602 3209 4105 4257 5027 5543 * 4469 8
+ 17 * 6376 * * * * 9250 0 0
+
+N 9 2579 * 5088 4363 7129 5773 5485 3082 5829 1592 * 3594 * 6552 5667 * 3839 4146 * * 9
+ 18 6337 * 0 * 0 * 9395 1049 1017
+
+V 10 4999 * * * 5673 * * 1706 * 1684 5250 * * * * * 5697 1807 * * 10
+ 0 * * * * * * 9429 0 0
+
+K 11 4282 * 5528 4776 * 5343 4720 5849 2459 3699 * 4481 * 2703 1771 * 4969 5148 * * 11
+ 14 * 6686 * * * * 9429 0 0
+
+A 12 3354 * 3142 3008 6297 4668 5790 * 3319 * * 3482 * 3477 3812 2383 4628 * * 6427 12
+ 0 * * * * * 0 9415 0 1016
+
+A 13 3828 6340 5053 * 6520 * 5571 4774 * 4054 6421 5620 * 6689 * 1162 2255 4380 6356 * 13
+ 0 * * * * * 0 9415 0 1016
+
+W 14 5645 * * 6340 3125 6297 * 5166 * 5527 6671 * * * * 6085 * 4853 528 4709 14
+ 0 * * * * 0 * 9415 0 1016
+
+G 15 2813 6632 3972 2769 6609 4325 5523 6552 3445 7078 * 3444 3587 4198 4054 3274 4552 6711 * * 15
+ 0 * * * * * * 9429 0 0
+
+K 16 3244 * 7059 5967 5867 5117 5470 3398 2698 3402 5964 4598 4890 4009 3205 4184 4203 3652 * 6878 16
+ 29 5643 * 1000 1000 * * 9429 1188 0
+
+V 17 3752 5102 6678 * 4196 * * 2157 * 2304 3643 6616 7131 5873 5614 * 6685 1938 * * 17
+ 179 4214 3998 1249 788 * * 9438 1879 0
+
+G 18 3766 7049 4191 3306 4893 5031 5890 4759 2692 4858 4741 4350 6086 4777 3462 3210 5010 5578 5230 4618 18
+ 258 4118 3235 850 1168 2935 202 9332 1827 2044
+
+A 19 2910 6335 3373 3864 * 4053 5684 6256 2601 6505 6772 * 2997 3506 4283 3488 4498 6210 * * 19
+ 153 4100 4568 861 1154 1073 931 9175 1747 3490
+
+H 20 5751 * 2174 4627 5269 3790 3644 5356 3245 4600 6471 2595 6360 4665 4498 5610 6922 5517 6021 4989 20
+ 36 5355 * 1361 711 224 2795 9237 1215 2928
+
+A 21 3777 * 4702 5615 5098 3888 5184 4467 2604 3226 5230 5612 3495 5298 5134 3728 4896 4066 5079 4665 21
+ 127 3718 6923 1356 715 * 0 9433 2200 1153
+
+G 22 3783 * 2784 2705 * 4650 5552 5227 4274 5447 7004 3897 3644 3149 4627 5558 3491 4379 * * 22
+ 77 4258 * 1618 569 1040 961 9433 1771 1462
+
+E 23 3350 * 4160 1900 6504 3768 5221 5756 3864 5644 * 4326 5764 3864 3823 4167 3951 4980 * * 23
+ 0 * * * * 0 * 9433 0 1153
+
+Y 24 3321 5664 6994 * 2411 * 3896 3008 * 3301 5362 3574 5612 5695 * 6063 4739 3024 6603 4118 24
+ 0 * * * * * * 9438 0 0
+
+G 25 2802 6446 6086 6979 4990 939 6603 * 6452 4925 6462 * * * * 4419 3930 3627 * 6587 25
+ 11 7014 * 3000 193 * * 9438 1000 0
+
+A 26 4114 6525 3406 4022 6462 6773 7035 4099 4022 3408 5885 4860 5762 3508 4219 3212 3042 3433 * * 26
+ 30 5622 * 2937 202 * * 9438 1210 0
+
+E 27 3127 6446 3489 2993 6462 4760 4961 3759 3026 4286 6553 3721 * 4443 4235 4442 4065 5164 * 6398 27
+ 36 6586 6152 1585 585 * * 9438 1020 0
+
+A 28 4205 5115 * * 1764 * * 1998 * 2780 3482 * * * * 6551 5856 3196 * * 28
+ 0 * * * * * 0 9386 0 1125
+
+L 29 6513 * * * 1447 * 6474 * * 2521 4310 * * * * 5926 6576 5836 * 1548 29
+ 0 * * * * * 0 9386 0 1125
+
+E 30 3434 * 4076 3517 5038 4990 6344 3346 3022 3127 5363 5843 * 4437 3637 3947 4034 4966 * 5350 30
+ 25 5856 * 4708 56 * 0 9386 1133 1125
+
+R 31 4323 5020 5945 5130 5249 4881 5219 5126 2755 5624 6862 3533 * 4858 1655 5731 4423 5553 5225 5059 31
+ 17 6448 * 3000 193 * 0 9386 1027 1125
+
+M 32 6350 6363 * * 2354 * * 3639 * 1171 3502 * * * * * 6646 3751 5575 4011 32
+ 0 * * * * * 0 9385 0 1125
+
+F 33 4975 5448 * 6460 806 * 6457 4755 * 2246 4801 6653 * 5535 * * * 5304 6634 * 33
+ 63 * 4558 * * * 0 9385 0 1125
+
+L 34 3330 * 4459 2124 6279 * * 6307 2936 5248 6733 3786 * 3717 4110 3393 3021 6810 * * 34
+ 0 * * * * 463 1864 9210 0 1899
+
+S 35 3265 6883 3754 3319 * * 4232 4216 2663 3422 4454 4935 * 4498 3486 3684 4464 6359 * 7001 35
+ 11 * 6977 * * * 0 9370 0 1125
+
+F 36 3681 5226 3589 5133 3735 * 2930 6706 4746 6808 7014 2549 * 6741 3944 3809 6926 5219 * 2624 36
+ 0 * * * * 1509 624 9372 0 1290
+
+P 37 4986 * 5115 4223 5927 * 7096 6485 6673 6374 * * 436 6653 6640 4663 6452 7068 * 6396 37
+ 0 * * * * * 0 9370 0 1125
+
+T 38 4121 * 2286 1986 6452 4323 5194 * 4763 4981 5558 4418 * 3947 4459 3563 5740 5505 6359 6382 38
+ 0 * * * * * 0 9370 0 1125
+
+T 39 3830 5004 5876 6920 3804 * * 3285 * 2396 3829 4439 * * 6396 4376 3128 3070 6728 3479 39
+ 0 * * * * * 0 9370 0 1125
+
+K 40 3900 * * 4772 * 6585 6577 4535 1889 3687 7155 6485 5927 2702 2176 6725 5604 4764 * 6907 40
+ 0 * * * * * 0 9370 0 1125
+
+T 41 3167 6352 3656 2806 * 6382 * 6071 3638 4801 * 3544 3741 4601 4568 2980 3329 5659 * 5566 41
+ 0 * * * * * 0 9370 0 1125
+
+Y 42 4364 * * * 3174 * 5228 3511 3000 2456 3190 * 5102 5173 5836 6883 5927 4155 * 2698 42
+ 16 * 6485 * * 0 * 9370 0 1125
+
+F 43 * * * * 246 * * 5224 * 4507 6379 * * * * * * * 5256 4381 43
+ 10 * 7184 * * * 0 9401 0 1043
+
+P 44 4754 * 4359 5788 * 2876 4688 * 2799 6449 6923 4035 2580 5187 4618 2987 3796 4858 * 5126 44
+ 109 * 3782 * * 1241 794 9408 0 1207
+
+H 45 5622 * 4692 4241 4747 3520 4388 5590 2472 5594 5876 4333 6840 3521 3268 3820 3778 4462 6729 5086 45
+ 391 4616 2347 808 1222 1276 769 9335 1555 2381
+
+F 46 3811 * 4827 6187 1414 * 6356 4681 * 2998 4009 6484 * 6302 5610 4757 3975 3846 6233 4701 46
+ 1690 694 3802 168 3184 2346 316 8928 6906 4656
+
+D 47 4386 * 2057 3487 6402 2414 5438 6412 3777 5797 * 2720 * * 5362 3532 4838 * * * 47
+ 154 4874 3903 668 1431 2398 304 8904 1339 4866
+
+L 48 5399 5312 5218 6425 3694 * 5533 3883 3008 2047 4152 4211 5535 5471 5267 6292 4881 2824 * 6453 48
+ 649 1736 4017 728 1335 3441 139 8868 4629 4852
+
+S 49 4111 * 2584 3942 * 3932 * 6227 3198 5172 * 4699 2673 6486 * 2461 3700 6133 * 6014 49
+ 2314 398 4643 2006 413 3053 185 8706 7555 5415
+
+H 50 3304 5840 5887 4083 * 6033 6349 4019 2787 3248 5537 4987 3434 3713 3001 4216 4297 6096 * * 50
+ 144 3397 * 2052 398 2150 368 8593 1972 5743
+
+G 51 3203 * 4126 4322 4568 4310 5421 6652 3509 * * 3292 * 3435 4660 2294 3364 * 6538 5352 51
+ 17 * 6406 * * 2982 195 8806 0 4926
+
+S 52 4926 * 2610 5957 6054 4934 5615 5282 * 6116 5459 2048 5331 6426 * 1753 4137 5358 * * 52
+ 40 6184 6230 0 * 1179 840 8884 1019 4639
+
+A 53 3151 6250 4282 3262 6379 4708 5344 6550 3599 5403 * 4056 1811 5822 5681 3521 4385 * * 6695 53
+ 32 * 5505 * * 809 1220 9252 0 3358
+
+Q 54 3272 6501 2954 3304 5184 3754 6710 5916 3189 5161 6483 4640 6937 3604 3367 4097 5050 4900 6449 5818 54
+ 52 5219 6838 0 * 1914 445 9350 1345 2329
+
+V 55 4774 * 6129 6543 1648 * * 3404 6782 2188 3177 6501 * 7125 * 6464 5940 3247 7038 5206 55
+ 17 6412 * 1585 585 1400 687 9371 1034 2105
+
+K 56 4547 6450 4826 3392 6778 4288 3868 5920 2492 4206 * 3967 * 3419 2528 4083 4767 * * 6439 56
+ 0 * * * * 2419 299 9408 0 1638
+
+G 57 2498 6326 4830 3699 6126 3564 4391 6455 3628 4032 * 4135 * 4569 2909 3988 5293 5168 6982 4576 57
+ 13 * 6764 * * * 0 9409 0 1489
+
+H 58 * 6139 * * 6684 * 996 6794 5468 3712 5198 * * 1884 6385 * 6552 6930 * 4729 58
+ 29 * 5661 * * 1345 722 9399 0 1658
+
+G 59 1803 3789 * 5385 4751 2668 * 4963 3928 5346 5644 6561 5795 * 5702 3572 4341 3334 * * 59
+ 45 6461 5670 2322 322 1331 731 9386 1026 1703
+
+K 60 3321 * 4508 3694 5494 4634 5614 4104 3050 3060 5705 4853 * 5546 3433 3896 3865 3555 * 6899 60
+ 0 * * * * * 0 9373 0 1725
+
+K 61 3583 6435 * * * 6348 5334 4178 3011 4667 4294 5401 * 4071 2050 3323 3082 4474 * 6552 61
+ 23 5978 * 1948 433 1276 768 9373 1141 1725
+
+V 62 * * * * 2188 * * 2332 * 2231 4254 * * * * 6458 * 1817 * 5556 62
+ 0 * * * * * 0 9400 0 1360
+
+A 63 3024 5675 * * 3641 4182 * 3882 6728 2272 2976 * * 4538 5387 4379 4689 2957 6802 5695 63
+ 0 * * * * 1399 688 9400 0 1360
+
+D 64 3620 5444 3823 2550 * 3549 6368 5829 3590 5078 4771 2909 * 3419 4088 4856 4307 6818 * 6561 64
+ 0 * * * * 0 * 9413 0 1157
+
+A 65 2125 7471 * 6757 3747 3442 * 3967 6897 3201 4810 * * 5315 4596 3331 4021 3466 4732 5873 65
+ 0 * * * * * * 9425 0 0
+
+L 66 * * * * 3355 * * 2277 * 1220 4234 * * * * * 6747 2506 * 5147 66
+ 0 * * * * * * 9425 0 0
+
+T 67 4311 6893 2064 3008 * 3252 5124 5509 5767 5354 6946 3170 6577 5063 7471 3539 3962 4385 * 5970 67
+ 15 6577 * 4087 87 * * 9425 1026 0
+
+N 68 3853 5810 3461 3687 4231 6957 5929 5040 3138 4178 5125 3398 6385 5637 3872 3730 3686 4723 6734 4527 68
+ 0 * * * * * * 9425 0 0
+
+A 69 2441 4834 * * 3592 4566 * 2487 * 2497 4156 * * * * 4757 5515 2723 5847 5944 69
+ 0 * * * * * * 9425 0 0
+
+V 70 3525 6577 * 6712 4514 * * 1706 * 3068 3883 * * * * 6582 7000 1607 * 6734 70
+ 119 3653 * 1455 654 * * 9425 2384 0
+
+A 71 5064 * 2849 2879 * 3033 6671 7035 2885 5820 5752 3334 * 4104 4531 3594 4114 4538 * * 71
+ 0 * * * * * * 9425 0 0
+
+H 72 3303 5864 6509 4452 5012 4870 3777 7424 3852 4273 * 2147 6168 5259 4084 2692 5257 5211 * 5197 72
+ 134 3659 6712 1063 940 * * 9425 2296 0
+
+V 73 4636 5878 5223 7414 4601 * 6163 3414 5247 1190 3608 5815 4657 6413 6554 6715 5771 4219 * 4235 73
+ 78 4477 7016 1162 854 0 * 9407 1719 1017
+
+D 74 4768 6566 1212 3047 7415 2771 4798 * 5855 * * 3860 5825 5147 6739 4783 5808 5949 * * 74
+ 53 4796 * 1419 676 * 0 9420 1539 1000
+
+D 75 5762 * 1745 3181 5154 5798 4732 7290 3956 * * 2023 5600 4593 5057 3924 6112 * * * 75
+ 437 1936 * 1771 500 0 * 9420 5056 1000
+
+M 76 3688 5873 4573 4433 4131 5321 5376 3747 5098 2138 4329 6629 2939 5831 4880 4485 5310 3870 * * 76
+ 75 4577 6809 3105 178 * * 9425 1618 0
+
+P 77 3472 * 2824 2430 6643 4570 4761 5087 3852 5196 5823 5195 5987 4604 4777 3475 4449 4268 * 4565 77
+ 191 3014 * 1129 882 0 * 9423 3111 1000
+
+N 78 3011 6705 5148 2566 6803 3870 5281 5499 3196 4604 * 3946 6938 4641 4631 3122 3756 4552 * 6810 78
+ 298 2552 5956 1515 621 * * 9425 3846 0
+
+A 79 4608 * 7007 4521 3615 6807 5161 3323 4104 2120 3735 * 5803 5213 5554 5307 4067 3026 6590 4579 79
+ 118 3669 * 1585 585 1327 734 9394 2275 1166
+
+L 80 3910 5469 6730 * 4155 * 6840 2978 4771 1214 5212 * * * 5892 5102 * 2822 6013 6369 80
+ 16 6504 * 1585 585 * 0 9396 1034 1027
+
+S 81 3296 5856 4282 3929 * 7176 5375 4848 3074 4103 4710 3665 3918 3900 3580 3919 3900 4861 * 5658 81
+ 10 7165 * 1585 585 0 * 9396 1000 1027
+
+A 82 3086 * 3970 3012 5082 5555 5099 * 2717 5590 6493 4744 5296 3978 3132 4027 4907 4884 * 4018 82
+ 16 6493 * 1585 585 * * 9425 1034 0
+
+L 83 5506 * * 5582 4278 * * 2353 6629 1214 3367 5309 * 5909 * * 5703 3474 * 5594 83
+ 39 5728 6946 964 1036 * * 9425 1202 0
+
+S 84 2425 6934 6726 4893 6474 1402 5848 5149 4967 5032 6696 4990 * * 5016 3413 5621 3671 * * 84
+ 18 * 6368 * * 0 * 9417 0 1000
+
+D 85 3383 6738 4279 3223 * 4928 4406 5576 2558 5762 5491 4850 6609 2917 3220 4318 4813 5456 * 4983 85
+ 0 * * * * * 0 9394 0 1104
+
+L 86 5137 * 4741 5525 5227 6588 5537 4235 3117 2440 6469 5111 6869 6932 2666 3655 3429 3280 * 6455 86
+ 213 2866 * 1575 590 0 * 9394 3228 1104
+
+H 87 6572 * * 6375 * 4357 199 * * * * 5999 * 6635 * 6827 * * * 5428 87
+ 0 * * * * * * 9425 0 0
+
+A 88 2536 5409 5241 5839 4449 6901 4839 4587 3189 3695 * * * 5716 2844 3759 5394 2563 6760 6933 88
+ 2833 3693 354 993 1007 * * 9425 2252 0
+
+H 89 3653 4336 4648 2658 4500 * 4668 * 3460 * 4432 4473 * 4645 2592 * 2314 * * * 89
+ 243 2689 * 1342 724 33 5457 6878 1372 8628
+
+K 90 3245 6569 3874 4460 4623 3462 4748 6728 2677 7032 7070 3613 4250 4325 3054 4788 4190 6026 * 6630 90
+ 190 3018 * 1057 945 887 1123 9407 3174 1184
+
+L 91 4651 6412 6999 6310 3825 * 4785 4982 4859 2718 4337 5843 5254 7080 2127 4342 * 5106 * 2357 91
+ 41 5147 * 1566 594 0 * 9417 1396 1000
+
+R 92 7168 6861 4335 * * 1066 5440 * 3466 * * 3614 4710 3926 3791 3915 * 6708 6650 * 92
+ 81 4197 * 1980 422 * * 9425 1852 0
+
+V 93 3931 5328 * 6375 3487 * * 2053 * 2934 4200 * 5625 7016 * * * 1498 * * 93
+ 37 5318 * 0 * * * 9425 1329 0
+
+D 94 4978 4977 3150 3462 * 3628 5313 6635 3195 6154 * 3582 4013 4785 4057 4744 2339 5883 * * 94
+ 14 6649 * 1000 1000 * * 9425 1013 0
+
+P 95 3278 * 5392 4650 6577 3743 5203 4254 4638 4148 5353 7015 1745 4551 4383 3355 5961 4752 * * 95
+ 0 * * * * * * 9425 0 0
+
+V 96 3394 * 2750 2017 5660 4495 3971 6886 3221 6884 * 6717 4786 3759 4525 5090 4454 5704 * * 96
+ 0 * * * * * * 9422 0 0
+
+N 97 5724 * 3940 5910 5162 6932 2092 5646 * 3207 3795 4874 * 3471 5643 4971 6958 5068 5845 2344 97
+ 0 * * * * * * 9422 0 0
+
+F 98 6475 * * * 1307 * * 3813 * 2920 4421 * 6373 * * * * 4065 3106 2769 98
+ 0 * * * * * * 9422 0 0
+
+K 99 3914 * 2607 2496 * 4023 * 6309 3632 4316 7028 3079 4361 3664 4409 5812 5375 5734 5774 7048 99
+ 28 5709 * 1891 453 * * 9422 1183 0
+
+L 100 3161 * 3858 3687 5860 5865 7073 3889 4782 2651 4676 3771 3910 4228 6768 4876 5044 3183 7133 6187 100
+ 79 4228 * 2000 415 * * 9422 1899 0
+
+L 101 4122 * * * 1907 5923 * 3571 * 2043 3166 * * * * 6380 * 2556 5126 6586 101
+ 0 * * * * * * 9422 0 0
+
+S 102 3126 5159 * 5608 4902 2054 * 4760 3130 3563 * * 6074 4562 3068 3393 6951 5626 6677 5854 102
+ 14 6703 * 0 * * * 9422 1001 0
+
+H 103 4334 6647 3394 1978 * 4922 5248 6683 4142 * * 3906 4034 4216 3483 3319 4771 4652 6581 7014 103
+ 0 * * * * * * 9422 0 0
+
+C 104 1778 3778 6741 6929 5236 7023 * 3278 * 4710 7016 5479 4616 4791 * 3173 5247 2625 5996 5603 104
+ 0 * * * * * * 9422 0 0
+
+L 105 5621 6309 * * 2189 * * 2758 * 1279 4319 * * * * 6485 5503 3675 6703 5896 105
+ 0 * * * * * * 9422 0 0
+
+L 106 5473 * 6745 7014 5661 5805 5318 2556 6570 1822 4304 * 5916 5041 4968 * 3881 2267 6706 5674 106
+ 0 * * * * * * 9422 0 0
+
+V 107 3532 6453 3000 2256 4324 4080 5346 6742 4229 5357 6669 5862 5884 3840 4053 3584 5271 5792 5867 5126 107
+ 0 * * * * * * 9333 0 0
+
+T 108 2621 5571 * 5083 4792 6906 5683 6379 5068 4262 4327 6664 * 6594 5498 4086 2272 2650 * 3164 108
+ 0 * * * * * * 9333 0 0
+
+L 109 4799 5432 * * 2921 * * 2063 * 1621 3054 * * * * * 6379 3158 * * 109
+ 44 6313 5862 1585 585 * * 9333 1087 0
+
+A 110 3297 6683 6811 2783 5105 3885 6948 5301 2965 5385 * 4866 5373 3327 2914 3685 4264 4987 * * 110
+ 15 6579 * 4755 54 1003 997 9317 1013 1151
+
+A 111 3161 6557 3409 2200 6771 5939 5522 * 3422 6532 * 3963 5218 3375 4458 3182 4550 5862 * 6444 111
+ 69 6749 4735 1585 585 0 * 9322 1001 1000
+
+H 112 3212 4845 * 4212 6614 5101 3751 4477 3410 3622 5667 5284 * 4282 3977 5539 4239 2674 6496 3900 112
+ 106 7095 3972 0 * 0 * 9373 1000 1550
+
+L 113 5352 4370 4151 6426 3697 4849 5735 3928 6239 1367 4703 5713 * 4978 * 5419 5779 3506 6311 5022 113
+ 338 4663 2563 3331 151 1148 866 9264 1542 1963
+
+P 114 4150 6214 * 4713 * 846 5704 * 3411 * 6380 * 3024 5434 6387 4673 * 6232 * * 114
+ 132 4508 4521 1381 699 955 1047 9189 1503 4041
+
+A 115 3346 6541 2812 4965 * 3710 * 6588 3643 5091 * 3795 3178 4954 4391 3369 4013 3804 6361 6025 115
+ 37 6250 6344 1000 1000 784 1254 9234 1046 3127
+
+E 116 3538 5000 3160 3933 7119 3548 3929 * 3088 * * 3738 5601 3780 3312 3338 5708 5001 * 6490 116
+ 109 4272 5565 1382 698 1136 876 9259 1751 2035
+
+F 117 4176 6733 6850 * 2041 * 5346 3977 5248 3220 4773 6686 5750 * 5409 4261 * 4766 2478 3251 117
+ 33 5457 * 4186 82 1585 585 9288 1269 1855
+
+T 118 4877 * 2285 5727 6561 5936 5528 * 4717 * * 2982 6963 5020 5257 2534 1781 * * * 118
+ 108 3962 6961 778 1263 914 1092 9370 2036 1521
+
+P 119 2598 6300 2734 3577 6487 4057 4620 6920 4271 5586 6422 6112 3023 3673 4332 3496 5083 * * * 119
+ 54 6552 5246 1585 585 1590 582 9389 1013 1317
+
+A 120 3202 * 2745 1904 7038 4944 * 5417 3954 5569 * 4802 6905 3208 5671 3297 4594 6546 * * 120
+ 27 6614 6959 2000 415 * 0 9358 1002 1644
+
+V 121 2588 5448 5835 5246 6759 7629 5903 3111 * 2828 5053 6329 * 3963 6445 4939 2516 2789 * 6770 121
+ 0 * * * * 2611 258 9353 0 1798
+
+H 122 3479 * 4791 2168 6135 5731 6829 4176 2729 3657 5544 6606 6646 3768 3705 * 4199 3678 * * 122
+ 0 * * * * 0 * 9358 0 1644
+
+A 123 2950 * 3385 2361 * 3932 5625 6791 3549 4564 4793 4781 * 4136 3611 3995 3994 5567 * * 123
+ 12 6919 * 1585 585 * * 9333 1000 0
+
+S 124 723 * * 5756 * 4665 * 4527 * 5009 5975 * * * 6677 2836 4178 4975 6759 * 124
+ 11 7016 * 3000 193 * * 9333 1000 0
+
+L 125 5652 * * * 3969 * * * * 4262 5034 * * * * * * 5441 357 5057 125
+ 0 * * * * * * 9333 0 0
+
+D 126 3795 * 3376 3576 * 4559 4916 4510 2934 4630 4979 3787 * 5121 2700 3799 3591 6011 * * 126
+ 0 * * * * * * 9333 0 0
+
+K 127 4016 5519 3926 3827 6541 4812 5734 5779 1446 4315 * 5253 * 4143 4090 4792 4130 4484 * * 127
+ 0 * * * * * * 9333 0 0
+
+F 128 2344 4789 * * 2941 5045 * 3311 * 2003 4114 * * * * 6723 3978 3095 * 6878 128
+ 0 * * * * * * 9333 0 0
+
+L 129 6609 * * * 2250 5799 * 3505 * 1874 3431 5201 * * * 6680 5175 4267 4290 2832 129
+ 14 6744 * 0 * * * 9333 1000 0
+
+A 130 3258 * 2255 4171 * 3221 6959 * 3195 6778 6451 4511 6603 3967 3964 3035 3992 6604 6943 * 130
+ 13 * 6817 * * * * 9333 0 0
+
+S 131 4190 5659 5971 4777 2794 5404 4955 3447 6769 3536 7272 4262 6646 6623 4517 4415 4363 2877 * 2923 131
+ 10 7123 * 2000 415 * 0 9285 1000 1008
+
+V 132 5083 5828 * * 3010 5659 * 1725 * 2647 4814 6283 * * * 5279 4723 2137 7068 * 132
+ 0 * * 1585 585 0 * 9292 1008 1008
+
+S 133 2672 4251 6697 5449 3979 3897 * 2654 * 3468 5786 5251 * 5726 4839 4137 4138 2908 * 4907 133
+ 15 * 6571 * * * * 9247 0 0
+
+T 134 3243 6371 2143 3708 5671 4046 5018 5781 3728 5029 * 3580 5706 5260 4948 3907 3732 5983 * 5323 134
+ 17 6406 * 0 * 0 * 9232 1014 1001
+
+V 135 3056 6531 5849 4454 5747 4093 4646 3281 5097 3438 4550 * 6534 4346 3835 4945 3719 2842 * 4513 135
+ 0 * * * * * * 9223 0 0
+
+L 136 6586 * * * 4363 * 6711 1952 * 1675 1668 * * 6652 * * * 4824 * * 136
+ 15 6620 * 2000 415 * * 9187 1000 0
+
+T 137 3670 5671 5754 4564 4270 3863 * 3988 2197 3366 6501 7328 * 5195 3530 3698 4215 3638 * * 137
+ 0 * * * * * * 9145 0 0
+
+S 138 3032 * 4301 2873 6167 4852 4000 6243 4509 4502 * 5055 * 3868 4323 2107 5376 4017 * 6410 138
+ 20 6167 * 2000 415 * * 9050 1002 0
+
+K 139 2586 * * 3753 5978 1483 5001 6010 3707 5050 * * * 4364 5940 3818 4317 * * 4435 139
+ 0 * * * * * * 8790 0 0
+
+Y 140 4354 5611 * * 2745 5871 * 4830 * 4204 3239 * * 4680 * 5736 * 6341 5561 1066 140
+ 0 * * * * * * 8524 0 0
+
+R 141 3833 * 4287 3877 * * 4777 * 1861 3758 * * * 4873 2285 3881 * 4747 * 3635 141
+ 0 * * 0 * * * 7263 0 0
+
+//
diff --git a/modules/bindings/tests/testfiles/test.seq219 b/modules/bindings/tests/testfiles/test.seq219
new file mode 100644
index 0000000000000000000000000000000000000000..52b76eda49f227d4aa7c14f77ba719a48a3bfc25
--- /dev/null
+++ b/modules/bindings/tests/testfiles/test.seq219
@@ -0,0 +1,3 @@
+>Test
+�EM��{���X��NJ��X����������dn��EG���$�����+��~����h����S��^���C���X��~܍������<���%�����X����[��
+����E���d��ׄ��[�����F#�m��X���\���f�
diff --git a/modules/bindings/tests/testfiles/testali.a3m b/modules/bindings/tests/testfiles/testali.a3m
new file mode 100644
index 0000000000000000000000000000000000000000..3e2dd453dd151db297723936ebec391d489da2d5
--- /dev/null
+++ b/modules/bindings/tests/testfiles/testali.a3m
@@ -0,0 +1,510 @@
+>ss_pred PSIPRED predicted secondary structure
+CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
+>ss_conf PSIPRED confidence values
+999999999999998873391557999999998639441123987788888856788999999999998735477789999999887650299989899889999999997536679989999999999999999984329
+>Test
+VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
+>gi|118595805|sp|P02185.2|MYG_PHYCA RecName: Full=Myoglobingi|49259352|pdb|1UFP|A Chain A, Crystal Structure Of An Artificial Metalloprotein:fe(Iii)(3, 3'-Me2-Salophen)APO-Wild Type Myoglobingi|145579858|pdb|2JHO|A Chain A, Cyanomet Sperm Whale Myoglobin At 1.4a Resolutiongi|151567563|pdb|2EB8|A Chain A, Crystal Structure Of Cu(Ii)(Sal-Phe)APO-Myoglobingi|151567564|pdb|2EB9|A Chain A, Crystal Structure Of Cu(Ii)(Sal-Leu)APO-Myoglobingi|228311816|pdb|2W6W|A Chain A, Crystal Structure Of Recombinant Sperm Whale Myoglobin Under 1atm Of Xenongi|113374037|dbj|BAF03579.1| myoglobin [Physeter catodon]
+VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFkHLKTeaemkASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYK
+>gi|118595767|sp|P14398.2|MYG_GALJA RecName: Full=Myoglobin
+-----NWDKVNSVWSAVEQNITAIGQNILLRLFEQYPESEDYFPKLkN-KSlgelkDTADIKAQADTVLRALGNIVKKKGDHSQPVKALAATHITTHKIPPHYFTKITTIAVGVLSEMYPSEMNAQAQAAFSGAFKNICSDIEKEYK
+>gi|47226106|emb|CAG04480.1| unnamed protein product [Tetraodon nigroviridis]
+VWTDQERAIIDNIFSNL--DYEDVGSKALIRCLIVYPWTQRYFSSFgNLYnaeaiRNNPNVAKHGVTVLHGLDRALKNMDNIKEEYKKLS--ERAALREAARRPRQLCSLTA-----------------------------------
+>gi|5139299|gb|AAD40480.1|AF157494_1 hemoglobin [Myxine glutinosa]
+-TTEGERAAVRASWAVLMKDYEHAGVQILDKFFKANPAAKPFFTKMKdLhtlEdlASSADARWHVERIIQAVNFAVINIEDrekLSNKFVKLSQDHIEEFHVtDPQYFMILSQTILDEVEKRN---------GGlsgegksgWHKVMTIICKMLKSKY-
+>gi|74922327|sp|Q7SID0.1|GLBF1_EPTBU RecName: Full=Globin-F1gi|18655670|pdb|1IT2|A Chain A, Hagfish Deoxy Hemoglobingi|18655671|pdb|1IT2|B Chain B, Hagfish Deoxy Hemoglobingi|18655672|pdb|1IT3|A Chain A, Hagfish Co Ligand Hemoglobingi|18655673|pdb|1IT3|B Chain B, Hagfish Co Ligand Hemoglobingi|18655674|pdb|1IT3|C Chain C, Hagfish Co Ligand Hemoglobingi|18655675|pdb|1IT3|D Chain D, Hagfish Co Ligand Hemoglobin
+-LTDGDKKAINKIWPKIYKEYEQYSLNILLRFLKCFPQAQASFPKFS-tkkSnlEQDPEVKHQAVVIFNKVNEIINSMDNqeeIIKSLKDLSQKHKTVFKVDSIWFKELSSIFVSTI-DGG---------AEFEKLFSIICILLRSAY-
+>gi|157880060|pdb|1SCT|A Chain A, Scapharca Tetrameric Hemoglobin, Co-Stategi|157880061|pdb|1SCT|C Chain C, Scapharca Tetrameric Hemoglobin, Co-Stategi|157880062|pdb|1SCT|E Chain E, Scapharca Tetrameric Hemoglobin, Co-Stategi|157880063|pdb|1SCT|G Chain G, Scapharca Tetrameric Hemoglobin, Co-State
+CGSEAIKANLRRSWGVLSADIEATGLMLMSNLFTLRPDTKTYFTRLGDvqkGKANSKLRGHAITLTYALNNFVDSLDDPSRLKCVVEKFAVNHInrKISGDAFGAIVEPMKETLKARMGNYYSDDVAGAWAALVGVVQA-------
+>gi|29692328|gb|AAO89499.1| hemoglobin II [Phacoides pectinatus]gi|197726107|gb|ACH73203.1| hemoglobin II [Phacoides pectinatus]
+-LTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSlFGGLTlaqlqDNPKMKAQSLVFCNGMSSFVDHLDDNDmlvVLIQKMAKLHN-NRGIRASDLRTAYDILIHYMEDH--NHMVGGAKDAWEVFVGFICKTLG----
+>gi|2055266|dbj|BAA19794.1| myoglobin [Aplysia juliana]
+-LSAADAGLLAQSWAPVFANSAANGDSFLVALFTQFPESANFFNDFKGKSladiqASPKLRDVSSRIFARLNEFVSNAADAGkmgSMLQQFATEHA-GFGVGSAQFQNVRSMFPGFVASL--SAPAG--DAAWNSLFGLIISALQ----
+>gi|74096493|ref|NP_001027700.1| globin [Ciona intestinalis]gi|34364572|emb|CAD68147.1| globin [Ciona intestinalis]
+-LTSEQVVLLRSSWQTIGKLGms-NVGLAVLHRLFNDVPETLPFFHSVLSPtqqteievlksnakvvrhasRVGL-----------SIDKIINLLDNGEELVKYLLFLgqvHV-KRSIPRKYFSAMGPVLLSVISAVLEKDLDAPVMQAWATAYGVIEQGI-----
+>gi|54027379|ref|YP_121621.1| hypothetical protein nfa54050 [Nocardia farcinica IFM 10152]gi|54018887|dbj|BAD60257.1| putative flavohemoprotein [Nocardia farcinica IFM 10152]
+--DSRSVALIRTTFKAVAADDagpDELARTFYAILFTDHPQIRDFFP--------AAMDVQRDRLVKAISYALDRLEEPDKLLPFLAQLGRdhRKYGVRREHYAAVADSLKAAVRRCAGTEmWTDEVDRAWDEGLALISDAMI----
+>gi|153873469|ref|ZP_02002042.1| Globin [Beggiatoa sp. PS]gi|152070062|gb|EDN67955.1| Globin [Beggiatoa sp. PS]
+-----NTELIGQSWDKLAGKHEEMVATFYDRFFDKFPHYRKFFPE--------SMEHQLKRMAETIALLARVTHETEVTHPHLVKVgsrHT-GYCLAREDLDNFKTIFVQVVGEYCGDDWNQEYQESWTEAFE--qhiIPYMMH---
+>gi|215764931|dbj|BAG86629.1| globin [Samia cynthia ricini]
+-LTRREIYAVQKSWAPVFANSIPNGAELLRRLFQTFPETKEFFKMIrKLPdeeyIQNPQFRAHVINLMTSLNLAVNNLNQPEVVaamMNKLGESHK-RRQIKERHFGDLKQVIVTMFIEVL--HLDGDTLTAWDKTVTFWYKHI-----
+>gi|340716694|ref|XP_003396830.1| PREDICTED: cytoglobin-2-like isoform 1 [Bombus terrestris]gi|340716696|ref|XP_003396831.1| PREDICTED: cytoglobin-2-like isoform 2 [Bombus terrestris]
+-LTNKEKRIIRETWGVLRANSVKVGVDIMISYFKRFPQHHRAFPPFkDIPaddlLDNKKFHAHCQGIMSTLNDAIDALDDVDLMnaiLHTTGKRHG-RRGQGRQEFIDLKGVVLDAMRGAFGSKFTTEVEVAWDKAIDVLFSKI-----
+>gi|307167439|gb|EFN61015.1| Globin [Camponotus floridanus]
+-MTEKQKRLVQNTWAIARKDEVSAGVAIMIALFKQYPEYQKQFKPFkDVPidelPKNKRFQAHCVNIISAISKLIEQMCDPELMqatLINLIEKHK-NRGQTQEQFENLRQLLAKLFPSLFGKQYTQEAEEAWKKLLDLMYSVI-----
+>gi|254463896|ref|ZP_05077307.1| globin [Rhodobacterales bacterium Y4I]gi|206684804|gb|EDZ45286.1| globin [Rhodobacterales bacterium Y4I]
+-MTDAELEQLRESYSKLKDEAVRDPAFFYDALFRHAPELRQLFRE--------DLEGQGMKFMTTLGVILAKLGDESAVDPHFQELgrkHA-SLGVQISHFAPMEEALVDSLRNALEDDFTPELEALWRRAFEEISARMIQ---
+>gi|15613621|ref|NP_241924.1| nitric oxide dioxygenase [Bacillus halodurans C-125]gi|52000645|sp|Q9RC40.1|HMP_BACHD RecName: Full=Flavohemoprotein; AltName: Full=Flavohemoglobin; AltName: Full=Hemoglobin-like protein; AltName: Full=Nitric oxide dioxygenase; Short=NO oxygenase; Short=NODgi|5822815|dbj|BAA83959.1| HMP [Bacillus halodurans]gi|10173673|dbj|BAB04777.1| flavohemoglobin [Bacillus halodurans C-125]
+TLSQETKQIVKATVPILAEHGEAITKHFYKRMFSHHPELLNIFNQ-----THQKQGRQPQALANSIYAAAEHIDNLEAILPVVSRIahkHR-SLNIKPEQYPIVGENLLAAMREVLGDAASDDVLEAWREAYELIADVFIQ---
+>gi|241959586|ref|XP_002422512.1| flavohemoprotein, putative; hemoglobin-like protein, putative; nitric oxide oxidoreductase, putative [Candida dubliniensis CD36]gi|223645857|emb|CAX40520.1| flavohemoprotein, putative [Candida dubliniensis CD36]
+PLTRSERKIIKDSIPILEYLDIQFGEKFFKRLVKRFPEYKPYFNE-----THLTLLRQPRSFHHCLLEFARNIDDLRPMKDFIMKIaskHV-ARQVSPDQYRVFGQILIGVMVDQFPKEfVDEEFVEAWTMAFRILANILI----
+>gi|254425852|ref|ZP_05039569.1| Globin domain protein [Synechococcus sp. PCC 7335]gi|196188275|gb|EDX83240.1| Globin domain protein [Synechococcus sp. PCC 7335]
+-LAVRQVELVQRSFAKVEPISEQVGKLFYEHLFETRPDFKPLFSS-------TDMETQQRKLMMTLATAVEGLRHPEEIISKVQALgrsHQ-GYGVKAEDYEAIGATLLWTLKEKLGDDFTPEVKRAWEVAFQFLSKIMIN---
+>gi|342859152|ref|ZP_08715806.1| hypothetical protein MCOL_09748 [Mycobacterium colombiense CECT 3035]gi|342133393|gb|EGT86596.1| hypothetical protein MCOL_09748 [Mycobacterium colombiense CECT 3035]
+---ADALRVLRDAFAPGaadsAGDPGGLVHRFYTHWFALDGSVRDLFP--------PEMAAQRLAFGHALHWVYGELvaRRAQEPVAFLAQLgrdHR-KYGVLPHHYDTLRRALLATLRTHLGAAWTDAVDEAATQSLNLITGVMSG---
+>gi|183980669|ref|YP_001848960.1| monooxygenase [Mycobacterium marinum M]gi|183173995|gb|ACC39105.1| monooxygenase [Mycobacterium marinum M]
+---RDALRVLRDAFAPQpdldhKTQSSELVRSFYTNWFSLDSSVRDLFP--------PEMSGQRAAFTRALHWVYSELvaQRAEEPIAFLAQLgrdHR-KYGVQPTQYETLRRALQTTLRSHLGSSWTDSVARAAEQSLNLIVGVMSG---
+>gi|120401655|ref|YP_951484.1| oxidoreductase FAD-binding subunit [Mycobacterium vanbaalenii PYR-1]gi|119954473|gb|ABM11478.1| Oxidoreductase FAD-binding domain protein [Mycobacterium vanbaalenii PYR-1]
+---RESMRILRDALDL-DLGSEALIGDFHTRWFAADLSARDLFP--------PDLEKQRQVFAQALCWLCDELiaQRAEEPVAFLAQLgrdHR-KYGVTQSHYATLQDALLTTLRKALVEQWDRRLAEAVDDVVQLVVGVMSG---
+>gi|119368204|sp|P15161.2|GLB1_PARCH RecName: Full=Globin-1; AltName: Full=Globin I
+-LTLAQKKIVRKTWHQLMRNKTSFVTDLFIRIFAYDPAAQNKFPQMaGMSAsqlrSSRQMQAHAIRVSSIMSEYIEELDSdiLPELLATLARTHD-LNKVGPAHYDLFAKVLMEALQAELGSDFNQKTRDSWAKAFSIVQAVLLVK--
+>gi|340378768|ref|XP_003387899.1| PREDICTED: neuroglobin-like [Amphimedon queenslandica]
+SLTSAQVALIESTWKVVKKDLQGAGNIMFLKLFQIDVSVRDKFPFRDVpyEelEDSESFLKHSLQVMETIDLAITLLlgGEMEKLVEALVDLgmaHA-MQGLKPEDFDHVGEALVHALGVALGKEFNDEAKKAWTLLYSVVTAKMKEGLK
+>gi|241146860|ref|XP_002405154.1| cytoglobin-1, putative [Ixodes scapularis]gi|215493696|gb|EEC03337.1| cytoglobin-1, putative [Ixodes scapularis]
+PLTARQIFSISKSWKAIARAMEPTGIEMFVRLFQEKEDLLDLFEKFqALRtkesqRESMELAQHASVVMTTLDEGINALDNLDYFMsylHNAGRLHY-KIKGfKKEYFWHIEGPFLAAVSDTLGDRYTDNIENIYKITIRFILQTLIE---
+>gi|327360040|emb|CBL51562.1| globin [Branchiostoma floridae]
+PLDAWQRFYLQKSWKTVARKSDQAARTVFLRMLQDNPGLRQKWPRIsLLTeeeiPTSPYIKFLGERIFDCLDYIIDNLGDLDHVIselTKLGRQHS-DMNVmTPEDVWAIEAAFLAGVQECLEDRFTIKYEEIYSRFIVFVIETMVI---
+>gi|255642839|gb|ACU21602.1| extracellular tetra-domain globin [Branchipolynoe seepensis]
+-ISSEQKAAIKTSWAGA--NLQAAGTGFYVHLAADAPAAYAVFN-LGANPHGAKAQAQGLKVMQFVDDCVKSLDDMAAVRDKLEVLahrHT-GYPAKKEYFGPGKACFLAGLADALGAKFTAEAKAAWATFYDIIAISLCQ---
+>gi|327360034|emb|CBL51559.1| globin [Branchiostoma floridae]
+SLSAADKKAVADSWAKMSkPSFQDAGERVFLKLLKK-DSTKAMFKKFkDIPrdrlAGNAALRDHGGKVVQALDDFIKGLDGsGHETVRNVGRIHK-AAGMTNDNINLMKPILLELLDEV-G--CG-DAKAAWDKLWNLFMTVHG----
+>gi|313502|emb|CAA23729.1| leghemoglobin [Glycine max]
+-FTEKQEALVNSSFEAFKANLPHHSVVFFNSILEKAPAAKNMFSFLGDAvdPKNPKLAGHAEKLFGLVRDSAVQLQTKGLVvaDATLGPIHT-QKGVTDLQFAVVKEALLKTIKEAVGDKWSEELSNPWEVAYDEIAAAIKKAM-
+>gi|1170183|sp|P42511.1|LGB_CANLI RecName: Full=Leghemoglobingi|495289|gb|AAA18503.1| leghemoglobin [Canavalia lineata]
+-FSEKQESLVKSSWEAFKQNVPHHSAVFYTLILEKAPAAQNMFSFLSNGvdPNNPKLKAHAEKVFKMTVDSAVQLRAKGEVvlaDPTLGSVHV-QKGVLDPHFLVVKEALLKTFKEAVGDKWNDELGNAWEVAYDELAAAIKKAM-
+>gi|163742519|ref|ZP_02149905.1| putative flavohemoprotein [Phaeobacter gallaeciensis 2.10]gi|161384104|gb|EDQ08487.1| putative flavohemoprotein [Phaeobacter gallaeciensis 2.10]
+-VSADDRTLIHRSVESERMELDHFVPLFYTKFFETCPDVRTFFPN--------DMAGQHEKLLTSLTYIIEALDHpekLSAILKHQGERHR-AIRITDAHFDGFIYSFTSALAETLGPEWSEDTHSAWRVFLTDVALNMN----
+>gi|254474495|ref|ZP_05087881.1| Globin, putative [Ruegeria sp. R11]gi|214028738|gb|EEB69573.1| Globin, putative [Ruegeria sp. R11]
+-VAPADRDLILASVESQKMELDQFVSLFYAKFFERCPDTRPMFPH--------DMSLQEEKLLMSLTHIIEALEHpakLRLILLDQGERHK-ALQINDDHFAGFIDSFTGALKDTLQEDWSEETRQAWLRFLQYVAYQMG----
+>gi|121228|sp|P15447.2|GLB4_GLYDI RecName: Full=Globin, monomeric component M-IV; AltName: Full=GMH4gi|159149|gb|AAA29162.1| hemoglobin IV [Glycera dibranchiata]
+GLSAAQRQVVASTWKDIAgsDNGAGVGKECFTKFLSAHHDIAAVFG-F--SgASDPGVADLGAKVLAQIGVAVSHLGDEGKMVAEMKAVGVRhkGYgykHIKAEYFEPLGASLLSAMEHRIGGKMTAAAKDAWAAAYADISGALISG--
+>gi|195110175|ref|XP_001999657.1| GI24641 [Drosophila mojavensis]gi|193916251|gb|EDW15118.1| GI24641 [Drosophila mojavensis]
+-MNSDELAMIKKTWEIPVATPTDSGAAILTAFFNRFPSALEKFP-FrDVPleelPANARFRAHAGRIIRVFDESIRVLgqEGdqekLDEIWTKVAVNHI-PRRISKESYNQLRGVILETLTAVC--NLDDSQQETWTKLVDHVYSII-----
+>gi|62990081|emb|CAI56309.1| haemoglobin B2 chain [Arenicola marina]
+--TTEDRKEVQTLWSEIWSAQftgrrVQVAQAVFEDLFRRDPESKNLFKRVNVdDMNSPEFHAHCIRVVNGLDTVIGLLDDPDTLKSQLEHLaqqHKERDGIHKTHFDEMSHAFGAVMPQVS-SCFNP---DAWNRCFGSIATKIASL--
+>gi|13810245|emb|CAC37410.1| globin [Sabella spallanzanii]
+--SMEDRQEVLNAWEALWSAEytgrrVMIAQAAFQKLFEKAPDSKALFTRVNVdNIGSPQFRAHCIRVTNGFDTIINMAFDTDVLEELLTHLgnqHTKYQGMRAAYLTHFRESFAEILPQAI-PCFNT---AAWNRCITAMQDKIGAS--
+>gi|34447132|dbj|BAC84992.1| globin D2 precursor [Haemadipsa zeylanica]
+--SIEDIRDIQHDWQFTWGDAsldarIVFGQAVFKKLIELDSSVVEPLKGVHVeDPNSLTFKNHVLRVLNGLDNLINLFDEQGVLVSQLNHLsqqHKERAGVNAAHFKAFARAFIDVLEVSG-NCPNL---DAWKGCLAALGHRISLQ--
+>gi|299757081|emb|CBN88274.1| hemoglobin [Carcinus maenas]
+-LTLRHRTAIYRTWDLVRPNPKLHGINLFLTMFQEEPVLQTRFKGFaGKSieelKNSKRLAAHGTTVVMAITAMVDNLEDVSVLVELLKNTganHR-DRGVPKGDFELLAPVLVRFLKDNLGSAWSPVAEEAWTQAMKVINAVIFTSY-
+>gi|156405932|ref|XP_001640985.1| predicted protein [Nematostella vectensis]gi|156228122|gb|EDO48922.1| predicted protein [Nematostella vectensis]
+PLSVAQKYLVRETWETIEQHSKAVGKKTFLrmfymssidfiysvvmeskgskdirvlglelafddvknsyrtwRFFEMNPDYQKLFPEFaTLDqvelEQANALHGHAKRVMKAVENAVSAMDDAESFAAYLENLGARhkARALKPAYLDAMQVAYTDTIQDLLKTQWTDGTAEAWNKLFRFIADTMKHG--
+>gi|114765375|ref|ZP_01444490.1| probable bacterial hemoglobin [Pelagibaca bermudensis HTCC2601]gi|114542218|gb|EAU45248.1| probable bacterial hemoglobin [Roseovarius sp. HTCC2601]
+--DNATKQQVLSSALRLRLASSALTRDFYDRLFDRAPELRAMFPA--------DMSAQSDKLFDMVLVLVQSLDHLQMLVAEIEALgvrHH-EYGVTEEQYALVSEVLLDTLEHHV-ADWSEVDRKAWALLLGYVCDLMIT---
+>gi|67463862|pdb|1X46|A Chain A, Crystal Structure Of A Hemoglobin Component (Ta-Vii) From Tokunagayusurika Akamusigi|409321|gb|AAB27064.1| hemoglobin component VII [Tokunagayusurika akamusi=midges, 4th-instar larva, Peptide, 150 aa]
+DMEAGDIALVKSSWAQIHD----KEVDILYNFFKSYPASQAKFSAFagkDLEslKDTAPFALHATRIVSVINEAIALMGVaenrpaLKNVLKQQGINHK-GRGVTAAHFEEFETALEAFLESHA--SgYNAGTKKAWDSAFNNMYSVVFP---
+>gi|321471887|gb|EFX82859.1| hemoglobin [Daphnia pulex]
+-LDCFDHSIIRNTWDQAKKNG-EFAPQVLLRFIKAHPEYQQMFGKFaSVPHynllRNGDFLAQAYTISAGLNVVIQSLSSQELLAAQFNLLgsaYQ-PRGVTPAMFEEFSVILEQVLEETLGSTFNVEARKAWNKGMVAIIAGIS----
+>gi|259418086|ref|ZP_05742005.1| globin [Silicibacter sp. TrichCH4B]gi|259346992|gb|EEW58806.1| globin [Silicibacter sp. TrichCH4B]
+-LHQIDAQLVKGSFRQVFARKAALTDKFYEYLFLEMPDTKAMFTG--------DFSHQKEMFASVLAAGVRSLGQDAEllaLIDRLLLRHR-HLGLTSGHMYMAQRALLLAFREVMGPHLTAAEVSAWGAAIRRLCQTLAA---
+>gi|99082334|ref|YP_614488.1| globin [Ruegeria sp. TM1040]gi|99038614|gb|ABF65226.1| globin [Ruegeria sp. TM1040]
+-LRQIEVQLIKVSFNRVFAQKAALAEKFYHHLFLELPDAEVMFTR--------DFSHQTEMFARVLTTGMQSLGRDREmmvLVDDLLQRHK-HLGLTLDQMYTAQRALHLAFCEVMQAELTAAEVSAWDNAIGRLCRALAA---
+>gi|86137140|ref|ZP_01055718.1| globin domain protein [Roseobacter sp. MED193]gi|85826464|gb|EAQ46661.1| globin domain protein [Roseobacter sp. MED193]
+---------MRSSFPTIFARKAELADRFYSHLFVHLPEVESLFGD--------DFSKQKEMFAAMLTYCLKGVANSQSlpqARAGLVKVHA-RFNLGPREMELAGKAVMAALEDVLGNDLSTKQREIWEQAISGVMQLLLA---
+>gi|301122887|ref|XP_002909170.1| Nitric oxide dioxygenase (Pi-NOD1) [Phytophthora infestans T30-4]gi|262099932|gb|EEY57984.1| Nitric oxide dioxygenase (Pi-NOD1) [Phytophthora infestans T30-4]
+PMSAKTIAILKATAPVVQEHGTEITSTMYGTMFSEFPEVQNLFNMShhRVAgatKggAPPGVSRQATALANAVIGFAANCDQLGNLgdaVPRMVHKHV-SLDIRAKHYPIVGGCLLRAIKTVLGDAATDEIIDAWKEAYWFLADLLI----
+>gi|114799562|ref|YP_759630.1| globin domain-containing protein [Hyphomonas neptunium ATCC 15444]gi|114739736|gb|ABI77861.1| globin domain protein [Hyphomonas neptunium ATCC 15444]
+---------iILSTFERAAQACADPAPLIYARLFELRPDFKPLFDM----DTDGGVRGS--MLETCFEAILGVIEGASSQrVIISAARfsHG-GYGVVDEEFDIMFASIRDVFRDLLGARWTGTEEAQWAILLKEIAAis-------
+>gi|8101728|gb|AAF72633.1|AF258616_1 hemoglobin P polymer precursor [Parartemia zietziana]
+-ITDAEKQLVQESWELLKPDLMGLGQKVFGRIFTKNPEYQTLFTRvgFgDTplTqlMANPAYGAHLIKVMRSFDFVIQNLGKPKTLLAYLKNVGADhiARNVERRHLQAFSESLIPVMQNELKAKLKPEAVAAWRKGLDRIIGVID----
+>gi|4020136|gb|AAC96002.1| hemoglobin T1 polymer precursor [Artemia salina]
+-ITDAEKALVQESWDLLKPDLLGLGRKIFTKVFTKHPDYQILFTRtgFgDTplTklDDNPAFGTHIIKVMRAFDHVIQILGKPKTLMAYLRSVGADhiARNVERRHFQAFSNALIPVMQHELKAQLRPDAVAAWRKGLDRIIGIID----
+>gi|291238614|ref|XP_002739227.1| PREDICTED: Globin D, coelomic, putative-like [Saccoglossus kowalevskii]
+-LTKEQKDTLIQTWQNLHADLERIGMLMFMGLFEHNPEIKEFFVGADsrdMKteelRYNEKLQEHGIRVMGLVEKIISSMGfedeKIDQMVVDLGKRHL-GYDVHIPFIDLFGRQFVFAIKPTLHTHWTANVEEAWTQLFKYIGYLMRYGYH
+>gi|57914327|ref|XP_555006.1| AGAP008434-PA [Anopheles gambiae str. PEST]gi|55237255|gb|EAL39570.1| AGAP008434-PA [Anopheles gambiae str. PEST]gi|85813752|emb|CAJ65692.1| globin 2 [Anopheles gambiae]
+-LTASEKITLFSAWGLIRKDLDVHGRNVLLLLFHKHPRYIAYFD-FtDDPnaqslVDNKSLYDQAIHVFKAVGALIEyGFKDPVLFdatLRKITRRHK-DRPVYTEDILTIGEVLLNYLEQALGRQMSDSLPDAFWKLFQTIAGRFP----
+>gi|284041096|ref|YP_003391026.1| nitric oxide synthase NOS [Spirosoma linguale DSM 74]gi|283820389|gb|ADB42227.1| Nitric oxide synthase NOS [Spirosoma linguale DSM 74]
+-LTPDMIRQMRQIGDELSANARVIGTDFYHALFQTHPEIIPYFNR-------TDLDSLTEHLMLAIGFLVRSLDNGLDItheLRELSQIHT-NFSVPPDAYPKLVDPLLTVLRKHVP-GFGTEQEQAWVILLNRVTNVLR----
+>gi|254426005|ref|ZP_05039722.1| Nitric oxide synthase, oxygenase domain protein [Synechococcus sp. PCC 7335]gi|196188428|gb|EDX83393.1| Nitric oxide synthase, oxygenase domain protein [Synechococcus sp. PCC 7335]
+-LPPALVQKMADSWQYFAPRKNEMGVEFYQTLFERYPQVLPIFGR-------ADMDYLSTHLFQSLEFIFLCLAEGSTerLmkeLRHLGRLHG-NAGVPSFAYGAISEVMISMFEKYVP-GFDEQLKEAWQVLIARVSNVIK----
+>gi|312385086|gb|EFR29666.1| hypothetical protein AND_01190 [Anopheles darlingi]
+PLTAKQKYTMVASWKGISRAMETTGITMFIKLFEEHADLLNMFAKFrELKTkeeqaTSEELQEHANKVMNTLDEGIRGLDDLDTFFEFIHQVgasHRRIPGFKQEYFWRIEEPFLTAVSTTLGDRYTQNVEGIYKLTIKFIIETLVAGY-
+>gi|74934410|sp|Q8T7J9.1|GLB_YOLEI RecName: Full=Globingi|19880109|gb|AAM00251.1|AF361744_1 hemoglobin [Yoldia eightsi]
+SFSAAQVDTVRSNWCSMTADIDAAGYRIFELLFQRNPDYQSKFKAFkGLavSalKGNPNAEKHIRIVLGGLGRILGALNTpeLDVIYKEMASNHK-PRGVMKQQFKDMGQAIVTALSEiqsKSGGSFD---RATWEALFESVANGIG----
+>gi|321473288|gb|EFX84256.1| hypothetical protein DAPPUDRAFT_223072 [Daphnia pulex]
+SygggygggeknkftegssgtsplmniLSENDISVLVNSWHILKKR-SDFAPKVFMRYFKAKPEAQKLFSEFaNVSvtdlPNNHDFLNAAYSCISSLEFILPHLRFqHPERCPALTDLK-NKYSV--VDLKRFVPIWMAAMQEEMGNAYSNEVRDVWKKAFSAFTDY------
+>gi|321457980|gb|EFX69056.1| hypothetical protein DAPPUDRAFT_301206 [Daphnia pulex]
+-rsLSDSDINLIVSSWNFLKKRLSSFAPKVFIGYLEARTDSKKMFPDFaHVNiaelATNVEFRSRACNCVASLNYIIPHLKRsFPVlQCPALKNLK-TKYNQHiD--iLKSLGIIWVKAMQEELDKk-iFTDDVRVVWKKLFSVLKEH------
+>gi|50897135|dbj|BAD34601.1| hemoglobin chain I [Calyptogena kaikoi]
+-VSASDIKNVQDTWTKLYDQWeAVHASKFYNKLFKDNEDISEAFVKAGT-GSGIAMKRQALVFGAILQEFVENLSDPTALSLKIKGLcatHK-TRGItNMELFAFALADLVAYMGTT--ISFTAAQKTSWTAVNDVILHQMSSY--
+>gi|156392484|ref|XP_001636078.1| predicted protein [Nematostella vectensis]gi|156223178|gb|EDO44015.1| predicted protein [Nematostella vectensis]
+-MTYEQKYLIRETVDNRECVNEkdflawRYVCELAAIFLNMHPGLQTYFSEFKhIKIDNiNGSHGHPRRLLMAIDNAVTALGDSDSFSAYLVELGRrhhgMNFRPGPTHFNDLRKCFLSVIKEILATAslWDFQVEEAWNRLFDSITAMML----
+>gi|298705122|emb|CBJ28565.1| hemoglobin [Ectocarpus siliculosus]
+---------VKRNWAMISEGPETQGsfngastslvalyDTFFARLFLLEPSMRSMFGD--------NMIRQSKFLVGLVNIIVKMEDMLKQGLSPLYSFAdrSVAMGARPEHYEVIAEVLPIALEACAGEGvWTPDIAGAWRDVMSFA---------
+>gi|212659295|ref|NP_001129874.1| hypothetical protein Y57G11B.97 [Caenorhabditis elegans]gi|189309807|emb|CAQ58126.1| C. elegans protein Y57G11B.97, partially confirmed by transcript evidence [Caenorhabditis elegans]
+-ITERQKHIFTETFPVIFKEYKRNGLVLFAKYFSEFPHYKNIWPQFrTLQdsalLASNELANHCSVYMSGLKEIVEVMDDEEKLtyfMARIARSHV-KWNINKYHITNMLEGVDVVLQRSFGDKLTDEIVNAYHTLYDVIGNLLD----
+>gi|150866030|ref|XP_001385495.2| hypothetical protein PICST_32831 [Scheffersomyces stipitis CBS 6054]gi|149387286|gb|ABN67466.2| hypothetical protein PICST_32831 [Scheffersomyces stipitis CBS 6054]
+HLTTSEISLIRYTWNKMLLDDpiekqstfrnipgaypveqeipkhkqpatsaSSiasslFCRQFYDNLLMSKPDLEEMFP---------SIRHQAVQFAGVMAMTISQLEDLTlmdEYLMKLGKRHSRVLGIGSDHFELMGEVLILTFQERFGTRFTQELAVLWIRLYLYLANTL-----
+>gi|312115464|ref|YP_004013060.1| globin [Rhodomicrobium vannielii ATCC 17100]gi|311220593|gb|ADP71961.1| globin [Rhodomicrobium vannielii ATCC 17100]
+---PNQLAALREFFSNIESDLPEIVSLMYERFFEAVPEAASLFKG--------DFAAQQMQFTSMLRSTIAltrssqlwPVDAeaGRASLPEIEYLglrHA-CVGVQPEHFAAMKWALARTLAEMYPRDFDRDIEDALSFIFDVVARA------
+>gi|149247543|ref|XP_001528180.1| hypothetical protein LELG_00700 [Lodderomyces elongisporus NRRL YB-4239]gi|146448134|gb|EDK42522.1| hypothetical protein LELG_00700 [Lodderomyces elongisporus NRRL YB-4239]
+-LSPVELHNLRTSWSKT--NQKEFFDKLYPNLLDQNRSLRRIFNNDD-----FVVKHHLEIFADCLQFVISNVQDASLVdeflYQFVQENQR-FASMAVQYLEPMGNAFITTFKQVLNTSWTSVLELVWIKVFVFIANSI-----
+>gi|321471887|gb|EFX82859.1| hemoglobin [Daphnia pulex]
+-LTRPQIRNVQRSWESMKSGRNSLVSAIFIKLFKETPRVQKHFAKFaNVPvdslRGNGDYIQQVALVADRLDTLISAMDDQLQLlgnINYLKYTHA-KRSIPRKTWEDFARLLVELLPTR---GVSASDVESWKGVTTVLVNGIA----
+>gi|321477132|gb|EFX88091.1| hemoglobin [Daphnia pulex]
+-LSGHMIGDVQRSWENIRGGRNAMVSDIFIKLFKETPRIQKFFAKFaTVAadalPGNADYEKQVALVADRVDTIISALDDKLQLlgnINYMRYTHT-ARSIPRGAWDDFGRLLVQSLAAK---GVSSDDLDSWKSVLSVLVNGIS----
+>gi|321477133|gb|EFX88092.1| hemoglobin [Daphnia pulex]
+-LTPQQIKEVQRTWASMRSDRNSIVSAIFIELFRENPRSQKYFAKFaSLPleslTSNTDFNQQVALVANRLDTIISAMGDKLQLlgnINYMRYSHEQriysPRNAVRDRFEDFGRLLLDTLIAK---GIAGDDLDSWKSVLKIFIDGIA----
+>gi|56753437|gb|AAW24922.1| SJCHGC09035 protein [Schistosoma japonicum]
+-INDEQLLLLQSSWSIVKQHIEKIGVITFLGIFEQHSDFRDAFTEFRKrkfvdVKHDPAMQVHGLRVLSIVDKMITRLPktdDIELKLMTIGSKHC-RYVPTIGLISSVSDQLWGAIEPVLKeeGSWSDELAVTWKTVLDYLTKT------
+>gi|332532408|ref|ZP_08408286.1| hypothetical protein PH505_af00140 [Pseudoalteromonas haloplanktis ANT/505]gi|332038051|gb|EGI74498.1| hypothetical protein PH505_af00140 [Pseudoalteromonas haloplanktis ANT/505]
+------QSALLNNLTIIKPNFHAFTAKFHSKLAQSSIEMNYP--------TALQFNEKSFTLFCVLERIVKHLDKPASVAPFLAHHlmYLKKSGASHSDIALLSNAFYETLEEHLGKHFTTESQLAWKKALRYF---------
+>gi|308480175|ref|XP_003102295.1| CRE-GLB-30 protein [Caenorhabditis remanei]gi|308262221|gb|EFP06174.1| CRE-GLB-30 protein [Caenorhabditis remanei]
+HLTPIDREILNKSWAIVSKDMQQVAVNIFQMIFEQAPDAKLMFSFMmkDYkeDKKSNEFIFHAVRFLQVIESTMTHLDDPSqldAVFLNLGKIHAkheEQLGFSAHYWSVFKECVLFHFRKAMKahNKFSkhkemsfAEIDSaiiLWREVLRFIIDRMKVGY-
+>gi|311279880|ref|YP_003942111.1| hypothetical protein Entcl_2577 [Enterobacter cloacae SCF1]gi|308749075|gb|ADO48827.1| hypothetical protein Entcl_2577 [Enterobacter cloacae SCF1]
+-------ELFNNSYARILPgdKGDRFFTHFYTLFTKSTDDETSAH------------svarrLEKQKIiyktf-FYmlsvanth-------IVA---DYLVKITRESNpQNLNLPPSAYALWRRAVLQTVRDLD-PECDEEIITAWAIVLAPGLEFMRR---
+>gi|94501577|ref|ZP_01308094.1| hypothetical protein RED65_08344 [Oceanobacter sp. RED65]gi|94426260|gb|EAT11251.1| hypothetical protein RED65_08344 [Oceanobacter sp. RED65]
+-------DLVFQSFGRSC-NNPAFFEDFYDNFMSKSDQIRAMFKQT-------NMEAQRGLlrggIMWLVMHARGMPD---NKIRALGESHSrKHMNIHPSHYNDWVDALMATLHKHD-PEFNDHMESVWRETIRPSIDLIKSMY-
+>gi|62990085|emb|CAI56311.1| intracellular haemoglobin [Alvinella pompejana]
+----DNIAAVR-------GDVSTHAMNIFVEYFKKFPQHQNAFADYKgKDPeslkSLPKFKTHTTKVVSKLLDIVEKASDSGalqSNCTTLAKMPQ-HKGLNQQQFADLGAVLVPYLQKALGGACD---SAAWEQAYN-----------
+>gi|150865287|ref|XP_001384437.2| hypothetical protein PICST_67553 [Scheffersomyces stipitis CBS 6054]gi|149386543|gb|ABN66408.2| hypothetical protein PICST_67553 [Scheffersomyces stipitis CBS 6054]
+-LTASEIKAIQTSWERLQSSNrkhkDHFTSRLYSNLVRSHPQFKTIFDDS------SVLKEHSTLFGEILSFIVLYKHDPEILNDFMYQFiHEnQRfANVTVLYLEPMGESLIDTFKQWLGDSvFTNEFESVWIKTYVFVANSL-----
+>gi|294659323|ref|XP_461690.2| DEHA2G03322p [Debaryomyces hansenii CBS767]gi|199433874|emb|CAG90138.2| DEHA2G03322p [Debaryomyces hansenii]
+-LSGEDIQKLTTCWSGLQANNkyhkDDFITRLFSNLVAANPKLRKVFHSE------SIIAEQSTLFGDLLSFTMLYLDDECTLNQCMNAFlREnPKfVIVGPEYLEPMGSALIVTFRQWLGQGkFNDQIQSLWVQVYLYIANCL-----
+>gi|82655305|emb|CAI26300.1| hemoglobin [Biomphalaria glabrata]
+-LSDNDREAIDSSWKKLRSGAggrRNAGIKLVQWMLRTIPNMRDRFNKFDAKqsdaalQRDPEFLAQVDRILGGVESLVNNVDDPVALKAAIDRLadaHLsFDPRVGLDYFGPLQTYIHDYIEEALGVGADSDEAKGWTDLFAAFNKVLKE---
+>gi|122733|sp|P06148.2|HBF1_URECA RecName: Full=Hemoglobin F-Igi|162545|gb|AAA30331.1| F-I globin precursor [Urechis caupo]
+-LTTAQIKAIQDHWFLNiKGCLQAAADSIFFKYLTAYPGDLAFFHKFSsVPlyglRSNPAYKAQTLTVINYLDKVVDALGGNAGALmKAKVPSHD-AMGITPKHFGQL----LKLVGGVFQEEFSadPTTVAAWGDAAGVLVAAM-----
+>gi|339250872|ref|XP_003374421.1| putative myoglobin [Trichinella spiralis]gi|164521930|gb|ABY60753.1| unknown [Trichinella spiralis]gi|316969271|gb|EFV53396.1| putative myoglobin [Trichinella spiralis]
+------CDLIKEQWAKIE-INNENGGELYKWFFTEKPEFATYFQLDNVNPaeiaKTERFQALGKAFLERVKKLVNVCDDEKKLKSEVTILkneHD-PRNVGLDQLKQVRPILVKFLQSKTG--LTDQQTSAWDEMLKKFEA-------
+>gi|91224749|ref|ZP_01260009.1| hypothetical protein V12G01_01110 [Vibrio alginolyticus 12G01]gi|91190295|gb|EAS76564.1| hypothetical protein V12G01_01110 [Vibrio alginolyticus 12G01]
+--------VFNDSYERCT-SDQEFFDLFYKNLWSKSANFRQKFDGI-------DMHQQVRMLRGSIVFFMMADTstEAHKMVEKYGKKHAsADIGIEPQDFDVWLESLLETVRQCD-SGYDADVETAWRTCFKTGLEVMKQEC-
+>gi|88813510|ref|ZP_01128744.1| hypothetical protein NB231_06775 [Nitrococcus mobilis Nb-231]gi|88789223|gb|EAR20356.1| hypothetical protein NB231_06775 [Nitrococcus mobilis Nb-231]
+--------LFNDSYERCIDnpNPPGFLQRFYKVFLSSSEEVAEKFKNT-------DFEKQTRVLKASLYYLMLScNGspEAMAHLRRIACLHSrKQLDIRPELYDLWLASLLQAAREYD-PRFDQQTETAWRQVLSHGIDFMKSRY-
+>gi|312095861|ref|XP_003148491.1| globin family protein [Loa loa]gi|307756344|gb|EFO15578.1| globin family protein [Loa loa]
+-LSKSQRITIENSWKRATKsNaREQVGIQLFGRILTARPEMKHLFGLQKIPEgrlkYDPRFRRHAIVFTKSFDYIVKNVAykeKLEQHFQALGERHTmlQGRGFNPEYWDTFSDCMRQTVS-LWGRDKDHKTTNTWQMLISFVLQNMK----
+>gi|339234991|ref|XP_003379050.1| putative globin [Trichinella spiralis]gi|316978322|gb|EFV61323.1| putative globin [Trichinella spiralis]
+-LTKSQRQNVVRSWEKV-PNKRALGEEIYIQIFMHKPMLKSLFPFRTVPvdqlRNNALFTRQAAIFADFIDCVVGYLaiDNG-NLIMELSERvgvnHAlmTSVNFDPEWWVLFANSVLDCIRQYCEPQficlpisrhITRKIMIAWRILLKEVVDRMSEAF-
+>gi|212642107|ref|NP_001129775.1| GLoBin family member (glb-18) [Caenorhabditis elegans]gi|193248121|emb|CAQ76478.1| C. elegans protein F52A8.4b, confirmed by transcript evidence [Caenorhabditis elegans]
+----YEKELLRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPFIsKYqgDewKESKEFRSQALKFVQTLAQVVKNIYHMERTESFLymvGQKHV-KfadRGFKHEYWDIFQDAMEFALEHRLS---------------------------
+>gi|221117199|ref|XP_002161790.1| PREDICTED: similar to globin X [Hydra magnipapillata]
+PLSHSDIYALQGTWLKVKARWFEICTIAFERWLVADPEIRTLFKGLpdDLHSkdlmKHNSLKKHACMIEKTLDQVLLILDKKKEFvntLIELGKLHY-RLGANHKYTKGLALSLQCAVCQEV--DIDISEESAWDSLFRFMLGLL-----
+>gi|325180197|emb|CCA14598.1| conserved hypothetical protein [Albugo laibachii Nc14]
+----------------------------------NAPELKPVFKT----------SKHARNvvlqhIVGGLRTMLAHDVHIER-VRALTRTHL-QFGVKMEYFDLLGQAVIFSMRHCSGSHWSSEIEEAWRRLYGHCSVIL-----
+>gi|29841203|gb|AAP06216.1| similar to trematode hemoglobin from Paramphistomum Epiclitum [Schistosoma japonicum]
+-VTQSQVDHlITELEPHVDteAHKLELGLKVYECFLKDRPEYICKFSRLqGLDAsnvaQSEGIKYYARTFVAAFVPMIQAAANKcelDKLCLEEAILHR-TRPVDEKIFQDSLPIFIKIFNNLI---KDQQNKETMSKILTYTFTMIGSQ--
+>gi|308506641|ref|XP_003115503.1| CRE-GLB-25 protein [Caenorhabditis remanei]gi|308256038|gb|EFO99990.1| CRE-GLB-25 protein [Caenorhabditis remanei]
+-----DFFTLKNWWKTVDRKRVEASGYMFSKYLNDFPENKNFYPKLkNVNaatvdmsCSDPGFESMALQYLKIFDDVITAVEekpgDVQTAcdrLSAVGKMHRQKvSGMTATQFQNMEEPFIQMVKYILSDRFNEKAEMLYRKFFQFCLKYLLEG--
+>gi|268552639|ref|XP_002634302.1| Hypothetical protein CBG17640 [Caenorhabditis briggsae]
+-LSSDEMQAVRDSWKRA--KEREIGKHILQALIERKPQFKDYFGIHvDEKKddvfSCREFQLQSHRIQNFLDTAVSSL-----GFCPIGNIHQMAYRIGQIHF-------------------------------------------
+>gi|339237741|ref|XP_003380425.1| putative globin [Trichinella spiralis]gi|316976730|gb|EFV59959.1| putative globin [Trichinella spiralis]
+-LNPKEVILTRNVWAALKeKHQHLVGMEIFRQIFNRRPDLKSLFGVSALDtemaLNSTRLHRHTMIFQDVIDILMVNISNVDVnIADSLIDLgaqHWvlTKRGFDPAYWLIFGDVLFDLVENvtrKLPSR--KRSTNAWRKTIAFMLDCMQIGY-
+>gi|319789164|ref|YP_004150797.1| hypothetical protein Theam_0183 [Thermovibrio ammonificans HB-1]gi|317113666|gb|ADU96156.1| hypothetical protein Theam_0183 [Thermovibrio ammonificans HB-1]
+-IREKDVQNLRFLGNILLPYKKEFADAFYDNLM-KFEDIKEYIPE-------EKLQRLKTTIQEWYEKLFsGKYDSEYlLYLLRIAKVHV-EEGIPPHYIIVamnfVSRFCTRRIaefFAKKAREFfehyrkeqdvvcdparaeilegfvleevfeRmEDLTRSLRKILALNEDVLVSYYV
+>gi|301061358|ref|ZP_07202138.1| conserved hypothetical protein [delta proteobacterium NaphS2]gi|300444535|gb|EFK08520.1| conserved hypothetical protein [delta proteobacterium NaphS2]
+-FTDQDEVLLKKMAELFMPIHDRFADDFYRYLQ-EDDYTAGYFRT-------DAaVNRRKETILQWLNEILtSKYDNRLlIKLVRIGKIHV-KIGLDGHYVNAamgfIRRYFQEHLNQVVSEPAKrEIMIETLDKALDISLDIMTSSYR
+>gi|336324532|ref|YP_004604499.1| hypothetical protein Flexsi_2317 [Flexistipes sinusarabici DSM 4947]gi|336108113|gb|AEI15931.1| hypothetical protein Flexsi_2317 [Flexistipes sinusarabici DSM 4947]
+-VKESDLKELGSIWEQMSKYSDEFTTDMSAFVV-KNFKLPETYST-------EITDEYKAMLGKLYERVLsGRFNNDYvSFLIKFSEFNL-AYSINQEMVNSlisyARSWIHEKIFQNIPDDFQrKGILMMFHKIMDITGDIIISTYY
+>gi|289549194|ref|YP_003474182.1| hypothetical protein Thal_1426 [Thermocrinis albus DSM 14484]gi|289182811|gb|ADC90055.1| conserved hypothetical protein [Thermocrinis albus DSM 14484]
+-WTAEDEENLRSLSHLVPSWVEEFLES---------------IRK-------DEhDERCFQSIREWLIATFsGPHDERYvRKIHNMLQEHL-KAGCTLHHLQVllssVREFLLDKLTAQLGYSHQrDSLFRSVEKTLDLSLSIMLLSQK
+>gi|238638045|gb|AAZ82851.2| Hypothetical protein B0361.4 [Caenorhabditis elegans]
+--------RIQQCFKAA---KPSIGDAIMKRAAASRAEMRTMLSKMN----EKQIECLGKQMFELITDAVENADKSEKVLTHARQLggtYAslCPLGFRPDLFAPLADAAIAECVKLDGVHKRCETLSAWSQLFSALFTGVRDGY-
+>gi|17509143|ref|NP_492188.1| GLoBin family member (glb-26) [Caenorhabditis elegans]gi|3880027|emb|CAA99921.1| C. elegans protein T22C1.2, confirmed by transcript evidence [Caenorhabditis elegans]
+-LNSYQKSIVRNAWRHMSQKGPsNCGSTITRRMMARKSTIGDILDR-------STLDYHNLQIVEFLQKVMQSLDEPDKIsklCQEIGQKHA-KYrrskGMKIDYWDKLGEAITETIREYQGWKIHRESLRAATVLVSYVVDQLRFGY-
+>gi|320170061|gb|EFW46960.1| predicted protein [Capsaspora owczarzaki ATCC 30864]
+------HAVMMATWKEATdaDSGERVLNGFFTRLQVNDPQASHIYETAD-----ARMRK--VIIWSAVTKILDCLENPRSLrkeLKPLAQSHA-HMGVTPQMIDAFGTSLCAVLKEVLQEKYTTEVDVVWRRCFRLFAAQ------
+>gi|320164492|gb|EFW41391.1| predicted protein [Capsaspora owczarzaki ATCC 30864]
+------HAVLHASWVKATegDNGDAVLTGFLVRLQSNNPQATLIYERAD-----PRMRK--VIIWTAVSKILDCMQNPRSLrkeLKPLGQSHA-KMGVTGPMLDSFGVALRAVLKDVLKARYTTETDMVWRRCYRLFSVQ------
+>gi|170573273|ref|XP_001892405.1| hypothetical protein Bm1_04635 [Brugia malayi]gi|158602064|gb|EDP38764.1| hypothetical protein Bm1_04635 [Brugia malayi]
+-LSEIQQELIRQSWQTISAKlevnEQNFGFFVYRRVFEHNPLLKRAFHVeeYDLLDSIP--REHSifrqmRLFTNLIALAVRHDNELETeIAPAVFRYGQRHYKFAAEYFNegtvrLFCSQVVCAVADLLEVDIDPACMEAWIDMMRFIGCRL-----
+>gi|157278270|ref|NP_001098237.1| cytoglobin-1 [Oryzias latipes]gi|82122237|sp|Q575T0.1|CYGB1_ORYLA RecName: Full=Cytoglobin-1gi|62176936|emb|CAG25610.1| cytoglobin-1 [Oryzias latipes]
+PLTDKERVMIQDSWAKVYQNCDDAGVAILVRLFVNFPSSKQYFSQFkHIeDaeelEKSSQLRKHARRVMNAINTLVESLDNsdkVSSVLNAVGKAHA-IrHKVDPVYFKILSGVILEVLGEAYPQVMTAEVASAWTNLLAILCCSIKAVYE
+>gi|147903264|ref|NP_001089155.1| globin Y [Xenopus laevis]gi|62176948|emb|CAG25618.1| globin Y [Xenopus laevis]
+DLTAADIENINEIWCKIYANPEESGKTVVIRLFTTYPQTKVYFKNLkNIaTleemQVNPGIRAHGKRVMGALNQVIQNLNdwEvVSSALTHLAQRHQ-DvHKVGVNNFQLL-fLVILTIFKEALGADFTPEHCKSWEKLFSITYNFLDSCYT
+>gi|45360951|ref|NP_988859.1| hemoglobin subunit beta-1 [Xenopus (Silurana) tropicalis]gi|122524|sp|P07429.2|HBB1_XENTR RecName: Full=Hemoglobin subunit beta-1; AltName: Full=Beta-1-globin; AltName: Full=Hemoglobin beta-1 chaingi|213983|gb|AAA49659.1| beta globin protein [Xenopus (Silurana) tropicalis]gi|56971743|gb|AAH88022.1| beta globin [Xenopus (Silurana) tropicalis]
+NLTAKERQLITGTWSKI--CAKTLGKQALGSMLYTYPWTQRYFSSFgNLsSieaiFHNAAVATHGEKVLTSIGEAIKHMDDIKGYYAQLSKYHS-EtLHVDPYNFKRFCSCTIISMAQTLQEDFTPELQAAFEKLFAAIADALGKGYH
+>gi|4929993|pdb|1CH4|A Chain A, Module-Substituted Chimera Hemoglobin Beta-Alpha (F133v)gi|4929994|pdb|1CH4|B Chain B, Module-Substituted Chimera Hemoglobin Beta-Alpha (F133v)gi|4929995|pdb|1CH4|C Chain C, Module-Substituted Chimera Hemoglobin Beta-Alpha (F133v)gi|4929996|pdb|1CH4|D Chain D, Module-Substituted Chimera Hemoglobin Beta-Alpha (F133v)
+HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFgDLsTpdavMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHC-DkLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKVLASVSTVLTSKYR
+>gi|110825993|sp|P02209.2|GLB3_MYXGL RecName: Full=Globin-3; AltName: Full=Hemoglobin IIIgi|5924295|gb|AAD56539.1|AF184047_1 hemoglobin [Myxine glutinosa]
+-LSEGDKKAIRESWPQIYKNFEQNSLAVLLEFLKKFPKAQDSFPKFs--aKkshlEQDPAVKLQAEVIINAVNHTIGLMDKEAAmkkYLKDLSTKHS-TeFQVNPDMFKELSAVFVSTM-GGK---------AAYEKLFSIIATLLRSTY-
+>gi|118572332|sp|P0C227.1|GLB_NERAL RecName: Full=Globin; AltName: Full=Myoglobin
+-LSADQKAAIKSSWAAFAADITGNGSNVLVQFFKDYPGDQSYFKKFdGKKpdelKGDAQLATHASQVFGSLNNMIDSMDDPDKmvgLLCKNASDHI-PRGVRQQQYKELFSTLMNYMQSLpG-ANVAGDTKAAWDKALNAMANIIDAEQK
+>gi|154818214|gb|ABS87592.1| hemoglobin III [Phacoides pectinatus]gi|197320684|gb|ACH68470.1| hemoglobin III [Phacoides pectinatus]
+-LTGPQKAALKSSWSRFMDNAVTNGTNFYMDLFKAYPDTLTPFKSlFeDVSfnqmTDHPTMKAQALVFCNGMSSFVDNLDDHEVlvvLLQKMAKLHF-NRGIRIKELRDGYGVLLRYLED-H-CHVEGSTKNAWEDFIAYICRVQGDFMK
+>gi|121267|sp|P29287.1|GLB_BURLE RecName: Full=Globin; AltName: Full=Myoglobin
+-LSGAEADLLAKSWAPVFANKDANGDNFLIALFEAFPDSANFFGDFkGKSiadiRASPKLRSVSSRIVNRLNDFVGNAADAGKmagMLDQFSKEHV-GFGVGSQQFENVRSMFPGFVSS-V-AAPPAGADAAWGKLFGLIIDALKKAGK
+>gi|327360040|emb|CBL51562.1| globin [Branchiostoma floridae]
+---------LQKSWKTVARKSDQAARTVFLRMLQDNPGLRQKWPRIsLLtEeeiPTSPYIKFLGERIFDCLDYIIDNLGDLDHVISELTKLGR-QhSDMNV----------------------------------------------
+>gi|156390503|ref|XP_001635310.1| predicted protein [Nematostella vectensis]gi|156222402|gb|EDO43247.1| predicted protein [Nematostella vectensis]
+PLDAKETQLVRKTWAILGDRQVEVGKSLFLRFFEEHPTSKDLFPEFrNISnekiAESPALYGHARRVMKSVDNAVASieNVQvYSAYLYELGTRHQ-Tr-QLSEEQLKFMGGAFLFAMRLHLRKEWSRATSKAWEKIFSFMADAMMRGC-
+>gi|198424683|ref|XP_002119119.1| PREDICTED: hypothetical protein [Ciona intestinalis]
+PFTDEELKLLRNSWDEVKKLGmk-EVGLHIFTGLLNAAPSLRTLFYTIdLPdEeeltidvmrenkkvvahatRIAN-----------AISKFIKFLDQPEElekLLTSLGESHA-RRQVDPESFEYVAPVILSVIGGHLKLPSNSPTLQAWVKAYGVLRNGIVSAME
+>gi|316933010|ref|YP_004107992.1| globin [Rhodopseudomonas palustris DX-1]gi|315600724|gb|ADU43259.1| globin [Rhodopseudomonas palustris DX-1]
+SplatFSPADIHRVRTSFDLMWPRSTEMADQFYARLFEIAPDSRTLFRS--------DMTRMKDKFIQTLAVLVGSLDNLTGlyaVAGKLAVDHV-RYGVRPDHYAPVGEALLWSLGRQLAGFWDDDVEQSWRKVYAVISARMIGAAY
+>gi|37521141|ref|NP_924518.1| flavohemoprotein [Gloeobacter violaceus PCC 7421]gi|35212137|dbj|BAC89513.1| glr1572 [Gloeobacter violaceus PCC 7421]
+LmevtAMALQVKLLEQSFEGVKPNAHAFAASFYDNLFSDFPQTQALFAHS-------DMQAQQQKLLASLVLVVENLRQPQVlstALQDLGNRHA-GYGIVPEHYPMVGTSLLKTFETYLGDAWTPEVKQAWVDAYGAITGLMLTGAE
+>gi|307192580|gb|EFN75768.1| Globin [Harpegnathos saltator]
+-MSEKQKKLVQNTWAIVRKDDVSSGLAIMNAFFTRYPEYQDQFKSFkGIPfeelSKNKKFQAHCVSVIAGLSNVIDHIHNpelMEASLINLAERHK-NRGQTREHFQNLRYVLEDLIPSVFGKQYTQEVQEAWKKMFDYLFLILCQ---
+>gi|195054581|ref|XP_001994203.1| GH13816 [Drosophila grimshawi]gi|193896073|gb|EDV94939.1| GH13816 [Drosophila grimshawi]
+-MNNDEVQMIKKTWEIPVATPTDSGAAILTAFFNRHPSSLEKFP-FrDVPlaelPTNSRFRAHASRIIRVFDDSIRVLgqDDaeekLEEIWTKVAVNHI-PRQISKESYNNLKEVVLEVLTAAC--NLNESQVQSWTKLVNHVYDILFKSIN
+>gi|289741211|gb|ADD19353.1| hemoglobin-like flavoprotein [Glossina morsitans morsitans]
+-MNSDEVYEIKRTWEIPATTPTESGVAILIRFFTKYPSNLQKFSTFkDMTldelKNNPRFKAHANRIMKVFDDSIKTLDDncshLEEIWTKIAQSHF-NRQIEKQSFNELKEVILEVLVAAC--NLNDQQTEIWLKLLDFVYEIIFKTID
+>gi|83754459|pdb|2C0K|A Chain A, The Structure Of Hemoglobin From The Botfly Gasterophilus Intestinalisgi|83754460|pdb|2C0K|B Chain B, The Structure Of Hemoglobin From The Botfly Gasterophilus Intestinalisgi|3885490|gb|AAC80435.1| hemoglobin [Gasterophilus intestinalis]
+-MNSEEVNDIKRTWEVVAAKMTEAGVEMLKRYFKKYPHNLNHFPWFkEIPfddlPENARFKTHGTRILRQVDEGVKALsvDFgdkkFDDVWKKLAQTHH-EKKVERRSYNELKDIIIEVVCSCV--KLNEKQVHAYHKFFDRAYDIAFAEMA
+>gi|327360028|emb|CBL51556.1| globin [Branchiostoma floridae]
+SLSAADKKLVQESWDKVSkPSFADAGERVFLKLFRRNESTKAHFKKFkDIPsdqlAGQAVVRDHGEKVCKVLDDFIKGLDGsGDEAVKKVGRMHK-GLGMSNEQIDQMKGAIIEVLADA-G--F-GDAnyKGAWGKLWDRFMAVHR----
+>gi|336310636|ref|ZP_08565608.1| globin [Shewanella sp. HN-41]gi|335866366|gb|EGM71357.1| globin [Shewanella sp. HN-41]
+GLTEIEKEAITSSFSLINHQEQHFATIFYDCLFDMAPLIKPMFKRDrKLi----------EEHFYMIFCAAVDNIHHLDTirtILLELGARHR-NYGVKVLHFPIVKSALILAIQHELKGQSNASIENAWSHYYDVLAAIILEG--
+>gi|2155297|gb|AAB58934.1| globin XII [Chironomus thummi thummi]
+QFVEDQTEIIRASWNQVKH----NEVDILYSIFAANPDIQARFPQFaGKDlktlKSSSSFASHAGRIVGFFSKITELNPNdsgvsaAKTLINEVAASHK-GRGVSKAQFNAFRVSLTAYLADHV--TWNDNVAQAWEKGLDNVYFVLFSAF-
+>gi|2506460|sp|P02221.2|GLB1_CHITH RecName: Full=Globin CTT-I/CTT-IA; AltName: Full=Erythrocruorin; Flags: Precursorgi|540255|gb|AAA80189.1| hemoglobin I precursor [Chironomus thummi]
+GPSGDQIAAAKASWNTVKN----NQVDILYAVFKANPDIQTAFSQFaGKDldsiKGTPDFSKHAGRVVGLFSEVMDLLGNdantptILAKAKDFGKSHK-SR-ASPAQLDNFRKSLVVYLKGAT--KWDSAVESSWAPVLDFVFSTLKNEL-
+>gi|1805725|emb|CAA71646.1| globin Cpa 3-2 [Chironomus pallidivittatus]
+ALTADQISTVQASFDKVKG----DSVGILYAVFKADPSIQTKFTQFaGKDletiKGTTPFEAHANRIVGFFSKIISEL--pnIDADVDAFVATHK-PRSVTHDQLNNFRAGFVGYMKAHT--DYAGA-ESAWGATLDTFFGAIFAKM-
+>gi|291224997|ref|XP_002732490.1| PREDICTED: neuroglobin-like protein-like [Saccoglossus kowalevskii]
+-LTPSEAIAIQSTWLFVYEDKEENGVELFVKLFTEHPDYQALFGYLeGIvGieniKNVPFLRVHASHVLIYLNTMLESLNDgtiLVELLKTLGYTHV-GLNLTPEHFDALGPILISLLQEKGGDSFTPFAEKAWLKGWGVmksvIVGALENGYQ
+>gi|15080667|dbj|BAB62534.1| hemoglobin chain [Moina macrocopa]gi|15080672|dbj|BAB62537.1| hemoglobin chain [Moina macrocopa]
+-LSASDRAIIRKTWEQARKDG-DVAPQILFRFVKAHPEYQKLFRSFaSVPqdelLGNGNFLAQAYTILAGLNVVIQSLGSrelLANQLNALGGAHF-SRGATPVMFDEFGAIAMDVLAEELGSAFNAEAKAAWTTAVRGLNAGIVKTL-
+>gi|4589708|dbj|BAA76873.1| hemoglobin [Daphnia magna]gi|4589710|dbj|BAA76874.1| hemoglobin [Daphnia magna]gi|322229321|dbj|BAJ72728.1| 2-domain hemoglobin [Daphnia magna]
+-LSANERSLIRKTWDQAKKDG-DVAPQVLFRFIKAHPEYQKKFSKFaDVPqselLTNGNFLAQAYTILAGLNVVIQSLSSqelLANQLNVLGGAHQ-PRGVTPAMFEEFGVIVEQVLEEELGNGFSAEARQAWKHGIHALVAGVSKTL-
+>gi|321477133|gb|EFX88092.1| hemoglobin [Daphnia pulex]
+-LSTQERAIIRTTWNKARKDG-DVAPKLLFKFLKAYPEYQKKFSKFaDVPqsnlLSNGNFLAQAYTILAGLNVIVQSLSSqelMANQLNALGGAHQ-PRGVTTTILElkEFGVILIQVLEEEIGSAMTIDARQAWKNGIHELIGGLSQTL-
+>gi|121268|sp|P02214.1|GLB_BUSCA RecName: Full=Globin; AltName: Full=Myoglobin
+-LDGAQKTALKESWKVLGADGPtmmKNGSLLFGLLFKTYPDTKKHFKHFdDATfaamDTTGVGKAHGVAVFSGLGSMICSIDDddcVNGLAKKLSRNHL-ARGVSAADFKLLEAVFKEFLDEATQRKATDAQKDADGALLTMLIKA------
+>gi|162453361|ref|YP_001615728.1| flavohemoprotein [Sorangium cellulosum 'So ce 56']gi|161163943|emb|CAN95248.1| putative flavohemoprotein [Sorangium cellulosum 'So ce 56']
+------VGLLRESFELVIERAPNLTHRFYGILFSRYPQVKPLFGRNSQe--------QQEKMLTEALAAVIDRLEDASwleEKLMAMGAKHV-DYGVTDAMYPWVADALISAMAEVAAAEWSPAHQEAWTEALGAIASLMQRGAR
+>gi|34330143|dbj|BAC82446.1| hemoglobin, chain IIB [Macrobdella decora]
+--SIEDIRDVQHDWKFVWGDAsldarVVFGKAVFKKLQELDGSVVEPLKVVHVeDp-DSDEFKNHVLRVLNGLDNLINLFDEqgvLVSQLDHLAKQHK-ErPGVNASHFRAFAKAFLEVLEVS-GSCPNL---DAWRGCLYGLGVRITAQ--
+>gi|61680653|pdb|1YHU|D Chain D, Crystal Structure Of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly Of 24 Subunits.gi|61680657|pdb|1YHU|H Chain H, Crystal Structure Of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly Of 24 Subunits.gi|61680661|pdb|1YHU|L Chain L, Crystal Structure Of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly Of 24 Subunits.gi|61680665|pdb|1YHU|P Chain P, Crystal Structure Of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly Of 24 Subunits.gi|61680669|pdb|1YHU|T Chain T, Crystal Structure Of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly Of 24 Subunits.gi|61680673|pdb|1YHU|X Chain X, Crystal Structure Of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly Of 24 Subunits
+--TTEDRREMQLMWGNVWSAQftgrrIAIAQAVFKDLFANVPDAVGLFGAVKGdEv-NSNEFKAHCIRVVNGLDSSIGLLSDpatLNEQLSHLATQHK-ArSGVTKGGFSAIAQSFLRVMPQV-ASCFNP---DAWSRCFNRITTGMTEP--
+>gi|125661837|gb|ABN49927.1| hemoglobin [Myrica gale]
+-FSEDQEALVVKSWTVMKLNAGELALKFFLKIFEIAPTAQKLFSYLkDS-nvplERNSKLKSHATNVFMMTCEsAVQLrkAGKvtvTESSLKRIGDVHF-KLQVVDEHYEVTRFALLETIKEAVPEMWSPEMKNAWGEAYDQLVSAIKTEMK
+>gi|229500|prf||742505A hemoglobin zeta
+---------LKNAWGKISTDTTEIGTEALERLHLSFPTQK-LLSH-----GFAHVKAHGSKVAEALTSILGPVDSFKNAVGALSEVHA-Ki-------LRALSHCLGKSLZAHLYAZFTIGVBASLDKFLASVSTVLZSKYR
+>gi|255642835|gb|ACU21601.1| extracellular tetra-domain globin [Branchipolynoe seepensis]
+-VSDAQKAAIKASWAGA--DLQAAGTGFYVHLAAEAPAVYANF---NLg--ADPhgaKSQEQGLRVMKFVNQCVNSIDNMAIvqaKIDALAHRHM-SYNVKKSDFVPAKPCFLGALADALGGKFNADARAAWAGFYDIIAAGLST---
+>gi|326383372|ref|ZP_08205059.1| oxidoreductase FAD/NAD(P)-binding domain-containing protein [Gordonia neofelifaecis NRRL B-59395]gi|326197778|gb|EGD54965.1| oxidoreductase FAD/NAD(P)-binding domain-containing protein [Gordonia neofelifaecis NRRL B-59395]
+-MSEPEQPILA---RTRVLLAgdpDRFARNVFARMFAMRPSLREFFPA-E-------MGSLRSSFVDVLDHVLEAIEAPDghgelvEFLAQLGRDHR--kYGVVSEHYWLMYEALMSEFQFAFGRRWTPEVEETVGQAMLLTTGVMRG---
+>gi|115913844|ref|XP_001199205.1| PREDICTED: similar to polymeric globin [Strongylocentrotus purpuratus]gi|115965676|ref|XP_001197673.1| PREDICTED: similar to polymeric globin [Strongylocentrotus purpuratus]
+PLTSAQKELVKRTWQVLAPNPAKHGAVMFAKLLTRHPNVGKLFP-FgkeDLSyeqlLKHAQVQAHGKKVMEKVGDAVDGLDDLDLlvpILKELGGRHV-GYGVNKQLFEPVGEVLLETIKEALGDTFNEELRLAWTAVFKIISDTMSEPLN
+>gi|121399|sp|P23216.1|GLBP1_GLYDI RecName: Full=Globin, major polymeric component P1gi|9347|emb|CAA37995.1| globin P1 [Glycera dibranchiata]
+HLTADQVAALKASWPEVSagDGGAQLGLEMFTKYFHENPQMMFIFG-YsGR--TEalkhssk--LQHHGKVIIDQIGKAVAEMDNakqMAGTLHALGVRHK-GFgd-IRAEFFPALGMCLLDAMEEKVPG-----lNRTLWAAAYREISDACIAG--
+>gi|148908091|gb|ABR17163.1| unknown [Picea sitchensis]
+-FSEEQEALVKKSWNAMKPNAPQLGFKFFLRVFEIAPSAKRLFSFLqD-SdvpiEKNPKLKAHGLIVFKmTCESAVQLREKgtvtfSESNAKDMGKLHL-TYGVLDEHFDVVKFCLLETIKDAVPDIWSPEMKIAWDEAYTQLAEAIKSEMK
+>gi|170031919|ref|XP_001843831.1| globin 2 [Culex quinquefasciatus]gi|167871230|gb|EDS34613.1| globin 2 [Culex quinquefasciatus]
+-LTGKQKITLLSAWGLIKQDLDLHGRNIMLLIFREHPHFIPYFD-FsADpNntslSENRALQAHSLNLIMALGALIEYgLKTpkmFECTLAKLVKNHK-TRRVTSQDVKMFGEVILMYFAQVLGRQSASSLPTAFNRLIEQIAEAFEAA--
+>gi|229366652|gb|ACQ58306.1| Hemoglobin subunit alpha-D [Anoplopoma fimbria]
+MLSKKQKELIAEIWGRLTPVADDIGADALHRMFASYPGTKTYFSHLDIsP-RSAHMLSHGKKIVLANPARlpaPDRPDKLQGALARTSVRHQ-T---------------------------------------------------
+>gi|260827190|ref|XP_002608548.1| hypothetical protein BRAFLDRAFT_98914 [Branchiostoma floridae]gi|229293899|gb|EEN64558.1| hypothetical protein BRAFLDRAFT_98914 [Branchiostoma floridae]
+-LTPTQVRLLQQTWKVILLHKKQNGFLIFKILFTDYPMTKKLFKGIdKVDpeqyEKTTSMRAHVTRFINSFDSFMECLEDPEalkSLLYDTGKAHL-RHNTKPEHFDDLEVVMMKSLKAVLGLKFTESVEEAWRTAFAFFVVHLK----
+>gi|340356646|ref|ZP_08679288.1| nitric oxide dioxygenase [Sporosarcina newyorkensis 2681]gi|339620573|gb|EGQ25142.1| nitric oxide dioxygenase [Sporosarcina newyorkensis 2681]
+MLDQKTIHIIKSTVPVLEQHGKTITTVFYRNMFEAHPELLDIFN---H--ANQSQGRQQTALANTVYAAAQHIDDLGailPAVVQIAHKHV-SLGILPEHYPIVGEYLLGAIKEVLGDAATSEIIDAWAAAYGVIADAFIGleakMYD
+>gi|314933259|ref|ZP_07840624.1| putative flavohemoprotein [Staphylococcus caprae C87]gi|313653409|gb|EFS17166.1| putative flavohemoprotein [Staphylococcus caprae C87]
+MLTEKEKSIIKETVPVLQDKGEIITSHFYKRMFKQHPELKNMFN---Q--TNQQKGLQSTALAQSVLAAAVNIEHLEnimPVVKEIAYKHC-ALQVPPAGYDIVGENLIEAIKEVVGLDDDHEIIKTWKKAYQDIADVFISveqdIYS
+>gi|8101728|gb|AAF72633.1|AF258616_1 hemoglobin P polymer precursor [Parartemia zietziana]
+-LSEREVAVVKQTWNLVKPDLMGVGMRIFRSLFETFPAYRVVFPKFgDVPlnqlADIPAVGKHAIAVTAKLDQLIQTLDEPANlalLARQLGEDHI-VLQVNRPMFKNFGTVLVRLLENDLGQKFSNYASKAWHKAYNVITEYIEE---
+>gi|156405084|ref|XP_001640562.1| predicted protein [Nematostella vectensis]gi|156227697|gb|EDO48499.1| predicted protein [Nematostella vectensis]
+-LTERQIKLVQDTWRLLIPSQKKTAMIFYLKLFTLDPIFKEVFS-FHTeNegqlEQDERFLFQSRKFMEMINSAVDRLNDISllvMILKSLGEVHW-TkFKIKPEYYEPVGKALIYSISKGLGSLFNDEIGEAWQAMYDLMSGAMISGTK
+>gi|974720|dbj|BAA09964.1| two-domain chain of the polymeric hemoglobin (intracellular) [Barbatia lima]
+---SDNKSLIRETWEMIAGD-RKNGVELMALLFEMAPESKKEFRRLgDISpeniPNNRKLNGHGITLWYALTSFVDQLDNkndLEDLCRKFAVNHV-SRGVLNVKFGWIKEPLAELLRRKCGSRCEDRHINAWWKLIDVICAILEE---
+>gi|334704356|ref|ZP_08520222.1| globin [Aeromonas caviae Ae398]
+-MTFEQIELVQKAWGRVSALNNSYVQEVYEELFRLSPELRALFPPYqELPv----------AKVSDTLNTVITSLSQLDAlgfIIRDLGRRHQ-RFNVQPHQFALLKQALTQVLARRLGSGFTPALHS------------------
+>gi|255722886|ref|XP_002546377.1| conserved hypothetical protein [Candida tropicalis MYA-3404]gi|240130894|gb|EER30456.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
+PLTARQIEIIHQSIPILESLDIRLGEKFYKRVVRRYDNLKPYFN---ETntklLRQPRAFAY------TILMYAKYIEDLSplqELLNRIISRHI-GLQVKPEQYPLLGEVFIETMADLFPPGvADDEFKEAWATAYGNLSNMLieaeRVEYA
+>gi|62183620|gb|AAX73248.1| myoglobin [Ophelia bicornis]
+---------VADTWATVSADSHKHGVAFFLDFFAAHPNYQDFFPKLeGKSgsalKGDPNMQAQADAVMAAIGQCVAAGGDkgaLAGPLGALAKTHL-PRGIKSAYFKDAFDSFVAYLGKS-GV-----STDGWPAAIDTIMEVLTAELK
+>gi|333988983|ref|YP_004521597.1| monooxygenase [Mycobacterium sp. JDM601]gi|333484951|gb|AEF34343.1| monooxygenase [Mycobacterium sp. JDM601]
+-----ALQALRNAFAVADGGGDSFVGRLFTRWFGTDPSARDLFPA-DL-------TAIRVAFAQAMNWVYGELvaQraqEPVAFLAQLGRDHR--kYGVTQHHYGTMGRVLYAALRDELAEDWTAAVEDAARESLNLIIGVMGGA--
+>gi|221117935|ref|XP_002162062.1| PREDICTED: similar to neuroglobin [Hydra magnipapillata]gi|221123757|ref|XP_002164731.1| PREDICTED: similar to neuroglobin [Hydra magnipapillata]
+PLSGKEIETLKKSWTTAKQFWNEICTCAFSRWFSTYPEIQSKFGVYgDNlTmnevLASESLCIHIRKSVELIEIIIKKVDErheLSEYLIELGKLHH-KFGAEQKYATALGSSFVFAISQIC-PNIDMITEGAWDSLFKYIVTHIKLGIR
+>gi|321477127|gb|EFX88086.1| hypothetical protein DAPPUDRAFT_96311 [Daphnia pulex]
+-LTPHQIRDVQTSWENLRSDRNSLVSAIFIKIFKETPRAQKHFTKFaNVAvdslSGNADYEKQIALVADRLDTIISAMNDKlqlLGNINYMRYSHqP-PRAIPRERFEDFARVLLDVLVSK---GVSADDMDSWKGVLTVFVNGVS----
+>gi|322229318|dbj|BAJ72725.1| 2-domain hemoglobin [Daphnia magna]
+-LTPHQIQDVQRSWENVRNGRNALISSIFVKLFKETPRIQKHFAKFgSVAvdslAGNAEYEKQIALVADRLDTMISAMDDKlqlLGNINYMRYTHT-ERGIPRAPWEDFSRLLLDVLGSK---GVSTDDLDSWKGVLAVFVNGVS----
+>gi|255080446|ref|XP_002503803.1| predicted protein [Micromonas sp. RCC299]gi|226519070|gb|ACO65061.1| predicted protein [Micromonas sp. RCC299]
+-WTERKRLVIQSSWAALLsahgNDRMATGSKIFRKLFTGDTAVLRLFP-FrH-QartlFVSAPFKLHAKLFVDTMTELIANLHDLEKverDVRELGKRHL-TYGVQPAHFDAMGEALIAVLDEscHHPSDevtLDKEERDAWLGFWGFIAKET-----
+>gi|198419488|ref|XP_002119301.1| PREDICTED: hypothetical protein [Ciona intestinalis]
+PLTEIEIEGVQESWEKVSSgGPKTTGLILMEKLFNTYPASIAVFSHLgIPsKpdgaitvsdlASIGGVSNHAVSLASRIGKLVGLLNNeteLKESSTEVGRIHV-KYGVTSEHVDLLGSVLLSVISENQGLSNTSELIGWWSKTWNIIGNYVKTGL-
+>gi|154252910|ref|YP_001413734.1| globin [Parvibaculum lavamentivorans DS-1]gi|154156860|gb|ABS64077.1| globin [Parvibaculum lavamentivorans DS-1]
+--TEQEKQLIEKSIERVADVAGDPASHVYARLFAQQPEMEAMFV---LD-TDGNVRGHM--LSEALDCVFDFLGPRAYapvLIQSELTNHS-NLGVPPAVFATFFRVVMETFRELLGAEWTAETDAAWAKLLGEFDTTIAEHAE
+>gi|119474700|ref|ZP_01615053.1| hypothetical protein GP2143_12811 [marine gamma proteobacterium HTCC2143]gi|119450903|gb|EAW32136.1| hypothetical protein GP2143_12811 [marine gamma proteobacterium HTCC2143]
+--DQ-----IVSCLEQVGDRCKDPTALVYERLFSANPEMKPLFI---MD-GNDAVKGQM--LFQVLDGIIDFVGDRRYaetLFLSELINHD-IIGVPPRVFSTFFRTIMETFRDIMGADWTAEFDQAWAQLLSDLDEMIREKAE
+>gi|67463861|pdb|1X3K|A Chain A, Crystal Structure Of A Hemoglobin Component (Ta-V) From Tokunagayusurika Akamusigi|220702318|pdb|2ZWJ|A Chain A, Crystal Structure Of A Hemoglobin Component V From Propsilocerus Akamusi (Ph4.6 Coordinates)gi|288562877|pdb|3A5A|A Chain A, Crystal Structure Of A Hemoglobin Component V From Propsilocerus Akamusi (Ph5.6 Coordinates)gi|288562878|pdb|3A5B|A Chain A, Crystal Structure Of A Hemoglobin Component V From Propsilocerus Akamusi (Ph6.5 Coordinates)gi|288562879|pdb|3A5G|A Chain A, Crystal Structure Of A Hemoglobin Component V From Propsilocerus Akamusi (Ph7.0 Coordinates)gi|291463432|pdb|3A9M|A Chain A, Crystal Structure Of A Hemoglobin Component V From Propsilocerus Akamusi (Ph9.0 Coordinates)gi|330689360|pdb|3ARJ|A Chain A, Cl- Binding Hemoglobin Component V Form Propsilocerus Akamusi Under 500 Mm Nacl At Ph 4.6gi|330689361|pdb|3ARK|A Chain A, Cl- Binding Hemoglobin Component V Form Propsilocerus Akamusi Under 1 M Nacl At Ph 4.6gi|330689362|pdb|3ARL|A Chain A, Cl- Binding Hemoglobin Component V Form Propsilocerus Akamusi Under 500 Mm Nacl At Ph 5.5gi|409322|gb|AAB27065.1| hemoglobin component V [Tokunagayusurika akamusi=midges, 4th-instar larva, Peptide, 152 aa]
+-LSDSEEKLVRDAWAPIHGDLQGTANTVFYNYLKKYPSNQDKFETLkGHPldevKDTANFKLIAGRIFTIFDNCVKNVGNDKgfqKVIADMSGPHV-ARPITHGSYNDLRGVIYDSM--HL----DSTHGAAWNKMMDNFF--------
+>gi|290462305|gb|ADD24200.1| Non-symbiotic hemoglobin 2 [Lepeophtheirus salmonis]
+----------------------------------------------------KKLKRHGGIVMKALGKLVGFLETgkiiaIVNTIKGIANSHS-KRGVLVQQFTPICDILLKYLGEAFGDQLSNEGTATWKKFLDIFVSVINEAYD
+>gi|260950945|ref|XP_002619769.1| hypothetical protein CLUG_00928 [Clavispora lusitaniae ATCC 42720]gi|238847341|gb|EEQ36805.1| hypothetical protein CLUG_00928 [Clavispora lusitaniae ATCC 42720]
+-FSPKEIALVRYTWNRMLVDDAEPKIslpGAFARpkkmaqssLHASSTFCTQLYSNLlSMDpeleQAFPSLRHQAVSMAGVMSLAVNSLDNLsslDAYLEQLGKRHS-RiLGIEPFQFEMMGEALVQTFVQRFGSKFTQQLEVLWIKFYMYLANTLL----
+>gi|254463661|ref|ZP_05077072.1| globin domain protein [Rhodobacterales bacterium Y4I]gi|206684569|gb|EDZ45051.1| globin domain protein [Rhodobacterales bacterium Y4I]
+-MTPQEVQHVQQSFAGVFARKADLAERFYVHLFTRLPQARGMFRG-NFvKqkamL------------TEMIAACVRNLDDpatLAELSARLVQDHA-HLDLGARESEAAKRALIAALRDVLGPALDPETETAWASAISRVAGTMARH--
+>gi|326434457|gb|EGD80027.1| hypothetical protein PTSG_10302 [Salpingoeca sp. ATCC 50818]
+------MKITQESWAMVEREIPNWTDIFYDKMFS-DPNIAKLFP-F--SagdfKTNEKFQTHTQKVRDTMHTAMTSIREFEklgPVLKKMGERHA-DYGVIPEHSVNFKEAFLHTLKTGYGDKWNEDLDDAWNQCVDALLEP------
+>gi|51773697|emb|CAH23231.1| hemoglobin [Biomphalaria glabrata]
+-VSDDDRRALQSSWSRLQsqaGNKQEAGIKLVTWLFDNVPNMRDQFSKFnAHsSdealRANNEFLRQVDVIVGGLDSLINNVDNSDNfqaAIERLVDVHL-HmsPSVGLEYFGPLQQNIRSYIQNALGVAADSAEARSWTNLFTAFNEFLA----
+>gi|196001585|ref|XP_002110660.1| predicted protein [Trichoplax adhaerens]gi|190586611|gb|EDV26664.1| predicted protein [Trichoplax adhaerens]
+-------------------------------------------------dlIKDPLVRSHGLRFMKAIETMLEIEFDSNGcifLFSAIGNRHC-SYGIEADYLDYVPQAFRFMLTKALGNNYTDKIASVWDEILSHIIKAMQDKVR
+>gi|50897143|dbj|BAD34605.1| hemoglobin III [Calyptogena nautilei]
+-VTIADVKNVQTSWNSIKDKWEtDHGLNFYTTLFDDVPEIKSAFVKAgNK--TDYQVKGQAVRFGRMVTEWIDNLDNEEAlvaKINGMCATHR-TRGItNVDLFEVALGELVKYIAGK--TSFTKAQRESWAVVNGCIIQTMRNYF-
+>gi|122733|sp|P06148.2|HBF1_URECA RecName: Full=Hemoglobin F-Igi|162545|gb|AAA30331.1| F-I globin precursor [Urechis caupo]
+-LTTAQIKAIQDHWFLNIKGcLQAAADSIFFKYLTAYPGDLAFFHKFsSVPlyglRSNPAYKAQTLTVINYLDKVVDALGGNAGaLMKAKVPSHD-AMGITPKHFGQLLKLVGGVFQEEFSA--DPTTVAAWGDAAGVLVAAM-----
+>gi|256080649|ref|XP_002576591.1| globin X [Schistosoma mansoni]gi|238661865|emb|CAZ32828.1| globin X, putative [Schistosoma mansoni]
+-FTNEQLLLLQTSWSIVKQHIEKIGVITFLGIFEQHSDFRDAFTEFrKRKfvdiKHDPAMQVHGLRVLSVVDKLITRlpkTDDIEKQLMMIGSKHC-R-YVPTIAlVssvsDQLWGAIEPVLKEE--GLWSADLAVTWKSILDYLTRT------
+>gi|153876610|ref|ZP_02003843.1| bacterial hemoglobin [Beggiatoa sp. PS]gi|152066926|gb|EDN66157.1| bacterial hemoglobin [Beggiatoa sp. PS]
+-------FEIQSTYEKILPHLDEFSRLFYQQLFEIKPAFKILFRQTDLrIq------KQMVIRMIEVVVQGINNLENFMSIIQRIHQRHY-ELHLKPEDYRLAGQALVLSLEKYFGDEFTPTLKKIWLDFYESIVATM-----
+>gi|1707914|sp|P51536.1|GLBC_NIPBR RecName: Full=Globin, cuticular isoform; Flags: Precursorgi|309617|gb|AAA65540.1| globin [Nippostrongylus brasiliensis]
+------KKHTVESMKAvpVGRDKAQNGIDFYKFFFTHHKDLRKFFKGAeNFGaddvQKSKRFEKQGTALLLAVHVLANVYDNqavFHGFVRELMNRHE-KRGVDPKLWKIFFdDVWVPFLESK-GAKLSGDAKAAWKELNKNF---------
+>gi|121251|sp|P27613.1|GLBH_TRICO RecName: Full=Globin-like host-protective antigen; Flags: Precursorgi|161675|gb|AAA30102.1| globin-like, host-protective antigen [Trichostrongylus colubriformis]
+------RKDALSALDVvpLgsTPEKLENGREFYKYFFTNHQDLRKYFKGAeTFTaddiAKSDRFKKLGNQLLLSVHLAADTYDNemiFRAFVRDTIDRHV-DRGLDPKLWKEFWSIYQKFLESK-GKTLSADQKAAFDAIGTRF---------
+>gi|110825998|sp|P80721.2|GLB_PAREP RecName: Full=Globin-3; AltName: Full=Myoglobin
+--------------------IVETGLGAYHALFTAHPQYIIHFSRLeGHTienvMQSEGIKHYARTLTEAIVHMLKEIsndAEVKKIAAQYGKDHT-SRKVTKDEFMSGEPIFTKYFQNLVK---DAEGKAAVEKFLKHVFPMMAAE--
+>gi|196001583|ref|XP_002110659.1| hypothetical protein TRIADDRAFT_54901 [Trichoplax adhaerens]gi|190586610|gb|EDV26663.1| hypothetical protein TRIADDRAFT_54901 [Trichoplax adhaerens]
+-------------------------------LIKLSPATKIYFHGVDFeKrdsylAKNTFLRNHAARFMEAINVIIGQdMDIfsVESYFRVVGSKHH-SYNLKLEHVQDISDAFLEMARNALKKKFTKSTEAAWRSFFQMVTDAIKNG--
+>gi|339235287|ref|XP_003379198.1| putative globin [Trichinella spiralis]gi|316978174|gb|EFV61187.1| putative globin [Trichinella spiralis]
+PLTPRECFLLIQNWRAISRKMVDTGIRTFInnnvDLLELFPTVKQEIQS----npesFDTEILEYHAQRVMSVLDQAIHLIGDADSffnLLHLYADYHA-KkQLFSPDFFWEIEPALVDSIKETLGDRYTENMANIYPKVFKLILSTLVQFCR
+>gi|170589934|ref|XP_001899728.1| hypothetical protein Bm1_41355 [Brugia malayi]gi|158592854|gb|EDP31450.1| hypothetical protein Bm1_41355 [Brugia malayi]
+-LSLEDRKLLHETFNLFEKDLTTNGLRIFLqlalitkfiylfcmRTLSENPDYKYFWPQFrAIPdsslISSSVLRNFAHTYMNALKKIVESLNNEQmpyEVLQRISAKHA-RHNIQMHHMQKMIKPLLENVRRALG-RHDENAERAWETLFQTVG-AIVEHYK
+>gi|320164492|gb|EFW41391.1| predicted protein [Capsaspora owczarzaki ATCC 30864]
+---HETRDVIKSTWALAIQKQDEADvtpvatfvNVFFGKLFELCPETRLVFGQ-DLsL-QGKS----LSSVLTGMLEFVVHPKKLTTQVKSLAVKHV-GLGITPDMFDAFGAALVYTIKTRIGKVWSPQTERVWVDAYGGVNNIITQQMS
+>gi|341887822|gb|EGT43757.1| CBN-GLB-25 protein [Caenorhabditis brenneri]
+----RDFFTLKNWWKSVDRKRVEASTYMFSRYLNDFPENKAFYAKLkNVnAqtvdmnCSDPGFEAMAAQYLKVFDDVITAveekPGDVQSacdRLSAVGKMHR-AkvSGagMESSMFQNMEEPFIQMVKYILQDRFNEKAEMLYRKFFQFCLKYLLEGF-
+>gi|242007866|ref|XP_002424739.1| hypothetical protein Phum_PHUM149070 [Pediculus humanus corporis]gi|212508232|gb|EEB12001.1| hypothetical protein Phum_PHUM149070 [Pediculus humanus corporis]
+--------VVLNDWPKIRKNYKKIFIDSFINYFAENPNYKLLFPSFsNVSeddlPFNHCFRLHCFAVYKAINFLMSNwLGEyeedDSKILPVIGKTHF-DRGITLEMMNLYKHSIVYSCNNHLKPN--LKRKLSWQTVFDHIFDyYLGSAY-
+>gi|17567933|ref|NP_509614.1| GLoBin family member (glb-17) [Caenorhabditis elegans]gi|3877381|emb|CAA86423.1| C. elegans protein F49E2.4a, partially confirmed by transcript evidence [Caenorhabditis elegans]
+-ITDEEVTAIRDVWRRA--KTDNVGKKILQTLIEKRPKFAEYFGIQsESlDiralNQSKEFHLQAHRIQNFLDTAVGSLGFcpissVFDMAHRIGQIHF-YRGVNfgADNWLVFKKVTVDQVTtgttdsskekedtnsngtangkvdtdaSLIPiadinNVYSGencLARLGWNKLMTVIVREMKRGFL
+>gi|341890740|gb|EGT46675.1| CBN-GLB-13 protein [Caenorhabditis brenneri]
+-LTRRERILLEQSWRKTRKtGADHIGSKIFFMVLTAQPDIKAIFGL-eKIPtgrlKYDPRFRQHALVYTKTLDFVIRNLDYpgkLEVYFENLGKRHV-AmqgRGFEPGYWETFAECMTQAAVEWE-ANRQRPTLGAWRNLISCIISFMRRGFD
+>gi|339235297|ref|XP_003379203.1| putative WAP-type 'four-disulfide core' [Trichinella spiralis]gi|316978179|gb|EFV61192.1| putative WAP-type 'four-disulfide core' [Trichinella spiralis]
+-LSVYDKRLIEESWCALR-DKDEVAKQIFLRVLTSNEKIRTIFDLH-TcPddelEENSAFQRHVKSLSLFLSICADSlsvsPDRLVSIARSIGEKHV-NfRWvsFDAEYWLLMKCAMVEVISSKQRPKISHLVNTAWNSLLSFVIFEIKHSFL
+>gi|9664871|gb|AAF97245.1|AF284381_1 dehaloperoxidase A [Amphitrite ornata]
+----------------IRGDLRTYAQDIFLAFLNKYPDERRYFKNYvGKSdqelKSMAKFGDHTEKVFNLMMEVADRATDCvplASdanTLVQM-KQHS---SLTTGNFEKLFVALVEYMRA-SGQSFDS---QSWDRFGKNLVSALSSA--
+>gi|308487955|ref|XP_003106172.1| CRE-GLB-28 protein [Caenorhabditis remanei]gi|308254162|gb|EFO98114.1| CRE-GLB-28 protein [Caenorhabditis remanei]
+-LVPDHHKLIRKSWGRI--PKTQFGKAALEAFIRISEVNHSIFGD--KeT-----ENRHIKYFVDLVQSSVDNLEDLEAsvkpWLDLIGRGHS-DFKITGKHWENFAESLLNTATEWNGPGrRHKETVRAWMLMTSFLADRLAHASR
+>gi|307179623|gb|EFN67896.1| hypothetical protein EAG_07959 [Camponotus floridanus]
+-FSAEEYALVKKVWSGIEINPQFHGNACLRSFCEIYPQYVKFFTQEsKLh-lSFDTRITVKFSIIMETMGYLLldfnkrpKQLDRLVG---YIAMVHK-DMQLDEQDMRNFATSLFQYLSRTYPTQMTAQCQEAMSKFMDSVIKELFV---
+>gi|194745446|ref|XP_001955199.1| GF16359 [Drosophila ananassae]gi|190628236|gb|EDV43760.1| GF16359 [Drosophila ananassae]
+-FTLSERLALRQAWNIVRPFTRRYGQEIFFNYLNDAYLRISKFKHTkGN--YLHVLHNHFRGFLCFIGSLIEEQDPvmFQLMLNDNNMTHS-RCKVGAAFILELAQAMTDYILKVFEKVSSASLESGFRKIVD-----------
+>gi|312115464|ref|YP_004013060.1| globin [Rhodomicrobium vannielii ATCC 17100]gi|311220593|gb|ADP71961.1| globin [Rhodomicrobium vannielii ATCC 17100]
+---PNQLAALREFFSNIESDLPEIVSLMYERFFEAVPEAASLFKG-DFAaqqmQFTSMLRST-----IALTRSSQLwPVDAEAgraslpEIEYLGLRHA-CVGVQPEHFAAMKWALARTLAEMYPRDFDRDIEDALSFIFDVVARA------
+>gi|84684315|ref|ZP_01012217.1| flavohemoprotein-like protein [Maritimibacter alkaliphilus HTCC2654]gi|84668068|gb|EAQ14536.1| flavohemoprotein-like protein [Rhodobacterales bacterium HTCC2654]
+---------IRACLSDLYSVRIEFSRRFYDRFFEQVPEARRLFVHNqDK-qalML----YAAVAMTMRG----MESGRDLDGELIEFGKRHA-RLGVKQDMFPIFGSTFLETLIEYLPHHDHPKIAKAWWGGFT-----------
+>gi|255724342|ref|XP_002547100.1| predicted protein [Candida tropicalis MYA-3404]gi|240134991|gb|EER34545.1| predicted protein [Candida tropicalis MYA-3404]
+-LSPFEIDQIQSSWNRIS-NKNNFYNELYLNLIEKNPNLGEIFNH-----DESVITHHAKTFGDCFNFVVSNIENveiIEEFIYSFVQENQ-RfSQMSTKYLEPMGNSLILTLKQFLRSYSTSVLELTWVKVYVYFANSIL----
+>gi|339256778|ref|XP_003370265.1| putative globin [Trichinella spiralis]gi|316965561|gb|EFV50254.1| putative globin [Trichinella spiralis]
+-FTDEEVELLARTWKKDDFDwLYRIGTDIYTCVFQLAPELKVFFPYVtECeKknqswESSKGFRTQALRFVQILGMAVEKTesrmkDDdshLHHRLYKLGETHR-RFalkGFTPTHWKGF--VIAVRVAMrraveAM-PNLTPAecetAIEAWDKLSRYVVHRMEEGYF
+>gi|298705122|emb|CBJ28565.1| hemoglobin [Ectocarpus siliculosus]
+--------GVKRNWAMISEGPETQGSfngastslvalydTFFARLFLLEPSMRSMFGD-NM-iRQ--------SKFLVGLVNIIVKMEDmLKQGLSPLysfADRSV-AMGARPEHYEVIAEVLPIALEACAGEGvWTPDIAGAWRDVMSFAILAVV----
+>gi|312080149|ref|XP_003142477.1| hypothetical protein LOAG_06894 [Loa loa]gi|307762359|gb|EFO21593.1| hypothetical protein LOAG_06894 [Loa loa]
+SLTSAQIHLVRNIWRQVYvtKGPTVIGSTLLHGIFFKSKKIKDQFFKcpFpHQfPn-RDSFNNAHAKAIGEMLDKIVDNLENLEsvsGYLFSIGAIHA-NlvrRQVSREIWNLMAETFIDCTLDWgDKKGRTEASRKAWAFIIAFVIEKIKR---
+>9287755aa6aa27583da6be3b2408bfcc
+HLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFgDLStpdavMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHC-DkLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
+>gi|77917416|emb|CAG25614.2| cytoglobin-2 [Tetraodon nigroviridis]
+-LSDTEREMIRDAWGHVykN--CEDVGVSILIRFFVNFPSAKQYFSQFqDMEepeemERSSQLRHHACRVMNALNTVVENLHDpekVSSVLAVVGRAHA-VkHKVEPMYFKILSGVILEVLCEDFPEFFTADVQLVWSKLMATVYWHVTG---
+>gi|121270|sp|P09965.1|GLB_DOLAU RecName: Full=Globin; AltName: Full=Myoglobin
+ALSAAEAEVVAKSWGPVfaN--KDANGDNFLIALFEAYPDSPNFFADFkGK-siadiRASPKLRNVSSRIVSRLNEFVSSAADagkMAAMLDQFSKEHA-GFGVGSQQFQNVSAMFPGFVAS--IAAPPAGADAAWGKLFGLIIDAMK----
+>gi|156390503|ref|XP_001635310.1| predicted protein [Nematostella vectensis]gi|156222402|gb|EDO43247.1| predicted protein [Nematostella vectensis]
+PLDAKETQLVRKTWAILG--DRqvEVGKSLFLRFFEEHPTSKDLFPEFrNISnekiAESPALYGHARRVMKSVDNAVASIENVQVYSAYLYELGTRhQtRQLSEEQLKFMGGAFLFAMRLHLRKEWSRATSKAWEKIFSFMADAMMRG--
+>gi|156373757|ref|XP_001629477.1| predicted protein [Nematostella vectensis]gi|156216478|gb|EDO37414.1| predicted protein [Nematostella vectensis]
+PLSEAQKYLVRETWETIE--PQkqTVGKKAFLRFFDMNPDYQNLFPEFkSLSyeelQKANALHGHAKRVMKAVENAVMSIDDVMSFSAYLEELGRRhKtRALKPSYLEAMHGALMDTLRNLLQSQWTEETAEAWNKLFSFISTTMVRG--
+>gi|226304877|ref|YP_002764835.1| oxidoreductase [Rhodococcus erythropolis PR4]gi|226183992|dbj|BAH32096.1| putative oxidoreductase [Rhodococcus erythropolis PR4]
+SVDSQAISLVRSSFKSVAAVEdgpERLARTFYSILFARSPETREFFPA--------AMDVQRDRLVGAIAHVVERLDEsdaILEYLAQLGRDHR-KYGVTDEHYTAVGNALIEALETFGGAEmWTDEVDSAWRNALAIISAAMMD---
+>gi|111022476|ref|YP_705448.1| flavohemoprotein [Rhodococcus jostii RHA1]gi|110822006|gb|ABG97290.1| probable flavohemoprotein [Rhodococcus jostii RHA1]
+-MDSQAISLVRSSFKAIAAVPdgpQTLSRSFYALLFARYPDARDFFPA--------AMDAQRDRLISAVQYVIERLEEesgqILAYLAQLGRDHR-KYGIEDAHYVAVGNSLIAAVEQFPSTEpWTDELEQAWRDVLAVVAATMMD---
+>gi|119368208|sp|P80017.3|GLBD_CAUAR RecName: Full=Globin D, coelomic
+DLTPAEKDLIRSTWDQLmtH--RTGFVADVFIRIFHNDPTAQRKFPQMaGLSpaelRTSRQMHAHAIRVSALMTTYIDEMDTevLPELLATLTRTHD-KNHVGKKNYDLFGKVLMEAIKAELGVGFTKQVHDAWAKTFAIVQGVLITK--
+>gi|340378768|ref|XP_003387899.1| PREDICTED: neuroglobin-like [Amphimedon queenslandica]
+SLTSAQVALIESTWKVVK--KDLqgAGNIMFLKLFQIDVSVRDKFP-FrDV-pyeelEDSESFLKHSLQVMETIDLAITLLlgGemeKLVEALVDLGMAHA-MQGLKPEDFDHVGEALVHALGVALGKEFNDEAKKAWTLLYSVVTAKMKEGLK
+>gi|327360036|emb|CBL51560.1| globin [Branchiostoma floridae]
+ALSAAELATVKQAWAKLT--AssfEDAGEKVFLALLKD-PNIKANFKKFkDIPeaslPGNADMRAHGKKVCTVLDKFIKGDDG---AAKSTGTMHK-GLGMSNDQIGAMRGALVAVLNDA-G--E-GGAVPAWNKLFDHFMEVHKT---
+>gi|309274255|gb|ADO63769.1| hemoglobin [Branchinotogluma segonzaci]
+-VTAAQKAAIKDSWAGVD--LQVAGNAFYNQLQANAPDAYAVFN-Lg----SDSgKIAAQGLKVMTFIDGIVKGLDDMDGVkasIDTLGGRHT-SYGAKKVHFGPAGPCLLAALAEVCGGKFTPAAKDGWTALYGLISDGICA---
+>gi|321252935|ref|XP_003192569.1| flavohemoprotein (Hemoglobin-like protein) [Cryptococcus gattii WM276]gi|317459038|gb|ADV20782.1| Flavohemoprotein (Hemoglobin-like protein), putative [Cryptococcus gattii WM276]
+PLTEAQKDIIKSTAPVLEKHGVTITTHFYKNMILAHPELKDVFSES-----AQKLGHQPAALAAAVYAYalnIHDLTPMVPVVERIAHKHT-SLHITANQYGIVGKHLIQSIVDILGDAVTPEVADAWYNGYWNLAHIFIN---
+>gi|19639|emb|CAA32492.1| unnamed protein product [Medicago sativa]gi|166388|gb|AAA32657.1| leghemoglobin [Medicago sativa]
+SFTDKQEALVNSSWEAFKQNLPRYSVFFYTVILEKAPAAKGLFSFLkNS-aevQDSPQLQAHAEKVFGLVRDSAVQLRAtggVVLGDATLGAIHV-Rk-GVVDPHFVVVKEALLKTIKEAAGDKWSEELNTAWEVAYDALATAIKKAM-
+>gi|242247087|ref|NP_001156237.1| neuroglobin-like [Acyrthosiphon pisum]gi|239788583|dbj|BAH70964.1| ACYPI007228 [Acyrthosiphon pisum]
+SLSPLQISQLKDSWSVLaqD--PSQLASALVIRLFKENPEYQSLFKRLkNLSidelASNPQFMSHASKVGAALASTIDHLDKpeeLEKLLTNLGIKHK-KYGLSAKHFQVIGDVLIAMITEAIG-DSEPELLDLWKSSLTSVLSI------
+>gi|13810245|emb|CAC37410.1| globin [Sabella spallanzanii]
+--SMEDRQEVLNAWEALwS--AeytgrrVMIAQAAFQKLFEKAPDSKALFTRVNVDnIGSPQFRAHCIRVTNGFDTIINMAFDtdvLEELLTHLGNQHT-KyQGMRAAYLTHFRESFAEILPQA-IPCFNT---AAWNRCITAMQDKIGAS--
+>gi|241825972|ref|XP_002414692.1| cytoglobin-1, putative [Ixodes scapularis]gi|215508904|gb|EEC18357.1| cytoglobin-1, putative [Ixodes scapularis]
+GLSKRDTKLIRNSWSMLCKQHPKADQLIFKALFTKHPDFMALFQHFkDKDlgvvLSDPQFALHSSAIIQAFGTIIRSLDDPAGVVAlirKNATDHT-TrKGVQPSHFEAMLNVVLEVLQDKLGSRFKPEAITAWEKFIEV----------
+>gi|291238620|ref|XP_002739222.1| PREDICTED: Globin D, coelomic, putative-like [Saccoglossus kowalevskii]
+SLTDQHRVILLDSWKVIqeD--IAKVGVIMFMGLFETHPECKEVFMPFkELQgddlRWSSALKAHGLRVMAVIERVLARIDSdekIEEHLKALAKKHV-EYGANSDLVRLFGPQFIGSMKRQLHKSWSDEMQDAWTVLFDIIIYHMTT---
+>gi|322229316|dbj|BAJ72723.1| 2-domain hemoglobin [Daphnia magna]
+-LTANDRRIIRKTWDQAK--KdGDVPPQILFRFIKAHPEYQKMFKSFaDVPqaelLGNGNFLAQAYTILAGLNVVIQSLSSqelIANQINALGGAHK-PRGATPIMFEQFGAVTEEVLAEELGSSFNAEARQAWKNGMRALVTGIT----
+>gi|893363|dbj|BAA09588.1| hemoglobin (2 domain) [Barbatia lima]
+---PANKGLIRETWNIVA--GdRKNGVELMALLFEMAPDSKKEFRRLgDVSpaniPNNRKLNGHGITLWYALANFVDQLDNktdLEDVCRKFAVNHV-LRGVLDVKFAWIKEPLAELLKRKCGQRCTEKHVKAWWKLIDVVCAVLEEH--
+>gi|56405306|sp|P02226.2|GLB7A_CHITH RecName: Full=Globin CTT-VIIA; Flags: Precursorgi|2155293|gb|AAB58930.1| globin VIIA.1 [Chironomus thummi thummi]
+PLSADQAALVKSTWAQVR--NSEV--EILAAVFTAYPDIQARFPQFaGKDvasiKDTGAFATHAGRIVGFVSEIIALIGnesnapAVQTLVGQLAASHK-ARGISQAQFNEFRAGLVSYVSSNV--AWNAAAESAWTAGLDNIFGLLFA---
+>gi|13249109|gb|AAK16680.1|AF257469_1 globin chain a1 precursor [Eudistylia vancouveri]
+-----KRLKVKLQWAQSFGfenTREDFEDELFRNFFKRKPDAPEkFFTRVrGD-nIYSPEFRAFGMRVASGLDMVLSLSDDeaaFQAALAFLKAQHA-PLGIGAEFNLAFKEAVLDTVAAHVGRCFDK---DAWNACMEIIMTGIQS---
+>gi|121275|sp|P18202.1|GLB_TUBTU RecName: Full=Globin, extracellular monomeric
+-----QRFKVKHQWAEAFGtshHRLDFGLKLWNSIFRDAPEIRGLFKRVdGD-nAYSAEFEAHAERVLGGLDMTISLLDDqaaFDAQLAHLKSQHA-ERNIKADYYGVFVNELLAVLPDYLGTKLDF---KAWSECLGVITGAIHD---
+>gi|974720|dbj|BAA09964.1| two-domain chain of the polymeric hemoglobin (intracellular) [Barbatia lima]
+---PVNKSLIRQTWNMMA--GdSKNGVDLMALLFQIAPESKKEFTRLgDVSpeniPNNRKLNGHGITLWYALTSFVDQLDSpndLEDLCRKFAVNHV-ARGVLDVRFGWIKEPLAKLLRRNCGN-CDEAI-QAWWELIDVICAVVKE---
+>gi|74096499|ref|NP_001027701.1| globin [Ciona intestinalis]gi|34364574|emb|CAD89600.1| globin [Ciona intestinalis]
+--KRSDIINIQDSWNTLKGfGYETVGMLVLHRLFNDAPQTRYLFSQLSLSsnesftleqmRNNSRVVYHANRVARAVGRLVDLIElptNFTDHLVWLGQRHA-YHGVAPVNFDYMGPVLLETIKVNLELPSDSPTLSAWAKAYGVIKNGIK----
+>gi|342859152|ref|ZP_08715806.1| hypothetical protein MCOL_09748 [Mycobacterium colombiense CECT 3035]gi|342133393|gb|EGT86596.1| hypothetical protein MCOL_09748 [Mycobacterium colombiense CECT 3035]
+----DALRVLRDAFAPgaadsAgD--PGGLVHRFYTHWFALDGSVRDLFPP--------EMAAQRLAFGHALHWVYGELvarraQEPVAFLAQLGRDHR-KYGVLPHHYDTLRRALLATLRTHLGAAWTDAVDEAATQSLNLITGVMSG---
+>gi|183980669|ref|YP_001848960.1| monooxygenase [Mycobacterium marinum M]gi|183173995|gb|ACC39105.1| monooxygenase [Mycobacterium marinum M]
+----DALRVLRDAFAPqpdldhKtQ--SSELVRSFYTNWFSLDSSVRDLFPP--------EMSGQRAAFTRALHWVYSELvaqraEEPIAFLAQLGRDHR-KYGVQPTQYETLRRALQTTLRSHLGSSWTDSVARAAEQSLNLIVGVMSG---
+>gi|296167812|ref|ZP_06849998.1| oxidoreductase FAD-binding subunit [Mycobacterium parascrofulaceum ATCC BAA-614]gi|295897042|gb|EFG76662.1| oxidoreductase FAD-binding subunit [Mycobacterium parascrofulaceum ATCC BAA-614]
+----DALRVLRDAFAPdePgT--GNELVRRFYTHWFGLDVSVRDLFPP--------EMGAQRAAFAHALHYVYGELvaqraQEPVAFLAQLGRDHR-KYGVLPRHYDTLRRALLSTLRTSLGDSWTDSVAAAADQSLNLITGVMRG---
+>gi|196016934|ref|XP_002118316.1| hypothetical protein TRIADDRAFT_62364 [Trichoplax adhaerens]gi|190579092|gb|EDV19196.1| hypothetical protein TRIADDRAFT_62364 [Trichoplax adhaerens]
+-LNYQERQAIIDSWNAISTEKQKYGTILFLKLFELEPRVKSLFTIFdFNEplediIQSPHFRSHAMRFMQSLETGVlMGFDKesCDFLFKSLGSRHH-FYDLKSEFLDVIPECILHTIKKGCGNNWSNETADAWKIATKVLCELFRE---
+>gi|8101728|gb|AAF72633.1|AF258616_1 hemoglobin P polymer precursor [Parartemia zietziana]
+AFSAADIQAIQQTWALAK--PDLMgkGATVFRNLFNEHS-eYQPLFSNLvGY-evtalEGSPELNAHARNVMAQLDVFVRSLENsieLGRSLNQLGKDHV-PRKVNKIHFKEFAEDFVVLMKADLGEEFTPLAESAWKKVFDVMISTIEQG--
+>gi|56698153|ref|YP_168525.1| globin domain-containing protein [Ruegeria pomeroyi DSS-3]gi|56679890|gb|AAV96556.1| globin domain protein [Ruegeria pomeroyi DSS-3]
+-MKDEQIRLVQSSFARVfaR--KAELAERFYVHLFERLPDAKSLFRG-DFFaqke-----------MFATMLASTVRGMNDvqaFHTMGQALARSHA-RFNLRRDDLDKAAEALSAAFRDVFGDTLNAQEQEAWDVAMRRLTRMLAT---
+>gi|268561672|ref|XP_002638386.1| Hypothetical protein CBG18593 [Caenorhabditis briggsae]
+RLSDRQREILQKTFTSIEQDCVRNGLKIFVRLFAEYPRYKLIWPQFrAIPdsslMNAVELRRHASVYLKGLGKIIESMRDeeeLRKSMSRIALAHI-KWNVQRNHVIHMIEPVLEVVKECNGYQLDDETRQAWTVLYQVIANLIE----
+>gi|47115693|sp|Q7M416.1|GLB1_LIOJA RecName: Full=Globin-1; AltName: Full=Myoglobin Igi|298242|gb|AAB25285.1| myoglobin I [Liolophura japonica, Peptide, 145 aa]
+-ISADQAKALKDDIAVVaqN--PNGCGKALFIKMFEMNPGWVEKFPAWkGKSldeiKASDKITNHGGKVINELANWINNINSASGILKSQGTAHK-GRSIGIEYFENVLPVIDATFAQQMGGAYTAAMKDALKAAWtGVIVPGMKAGY-
+>gi|321473021|gb|EFX83989.1| hypothetical protein DAPPUDRAFT_223071 [Daphnia pulex]
+SFSQKDVDVIVNTWNTLK--RrGDFAPKVFIRYFKAKPESQKMFPAFaNVPitelPTNHDFLNSAYTCITSLNYLIPYLKFdHPERCPAFP-KHLKDkYNA--VDLKKLGSIWMTAMQEEMGNAFTNDVRDVWKKAVMAVIEYA-----
+>gi|153876610|ref|ZP_02003843.1| bacterial hemoglobin [Beggiatoa sp. PS]gi|152066926|gb|EDN66157.1| bacterial hemoglobin [Beggiatoa sp. PS]
+------IFEIQSTYEKIlpH--LDEFSRLFYQQLFEIKPAFKILFRQT-------DLRIQKQMVIRMIEvvvQGINNLENFMSIIQRIHQRHY-ELHLKPEDYRLAGQALVLSLEKYFGDEFTPTLKKIWLDFYESIVATM-----
+>gi|320170061|gb|EFW46960.1| predicted protein [Capsaspora owczarzaki ATCC 30864]
+---HETRDAIQSSWALAiQK-HDdhdvtpvaTFVNILFAKLFEVCPETRLVFGH-DMV-------RQGKSlssILTGMLEFVVHPKKLQSQVKRLAHMHV-GLGVTPDMFEAFGFSLLYTIRVRIGSAWNQQIERVWVDTYGGVSNILSQ---
+>gi|156392484|ref|XP_001636078.1| predicted protein [Nematostella vectensis]gi|156223178|gb|EDO44015.1| predicted protein [Nematostella vectensis]
+DMTYEQKYLIRETVDNRecvN--EkDflawRYVCELAAIFLNMHPGLQTYFSEFkHIKidniN---GSHGHPRRLLMAIDNAVTALGDsdsFSAYLVELGRRHH-GmnFRPGPTHFNDLRKCFLSVIKEILATAslWDFQVEEAWNRLFDSITAMMLR---
+>gi|149244943|ref|XP_001527010.1| hypothetical protein LELG_01839 [Lodderomyces elongisporus NRRL YB-4239]gi|146449404|gb|EDK43660.1| hypothetical protein LELG_01839 [Lodderomyces elongisporus NRRL YB-4239]
+NLSQHEIDMVRYTWNKML--MedksnrpNrmpgqfpDLgftpitetpncssvslslfCRQLYMNLLARDPELEKMFPSIkHQSi----S----FAGVMTLIVSQLENLSVLQSYFTSLAKKHS-RvLGIEPPQFELMGEALIQTFKERFGNQFTLELEILWIKVFLFLANSLM----
+>gi|50897135|dbj|BAD34601.1| hemoglobin chain I [Calyptogena kaikoi]
+-VSASDIKNVQDTWTKLY--DqweAVHASKFYNKLFKDNEDISEAFVKAgTG--SGIAMKRQALVFGAILQEFVENLSDptaLSLKIKGLCATHK-Tr-GItNMELFAFALADLVAYMGTT--ISFTAAQKTSWTAVNDVILHQMSS---
+>gi|18029239|gb|AAL56426.1|AF370721_1 cuticle globin [Syngamus trachea]
+------KKHVVDSLVNVplG--NDQTGKDFYKYFFTNHPDLRKYFKGFeTF-taddvQKSEKFRTLGNAFILAIHIVANTYDNepvFRAYVRDNIARHV-ERGLEPSLWKDFWKIWTAFLESK-GTTLSADDKAAWEALRD-----------
+>gi|326430027|gb|EGD75597.1| hypothetical protein PTSG_06664 [Salpingoeca sp. ATCC 50818]
+RLDMEQLKIALGSWTAVVELVPTWHEVFFAELFQAHPETERLLYSSDKSk--S-WNERHMARVGKSVGDVIKSLsnyDDVIEHLTALGTRHA-RYGLHVDQLDLFINAFLWTLGAGLGDSWDHSVKKAWMHVLPFILSPLKS---
+>gi|303271567|ref|XP_003055145.1| predicted protein [Micromonas pusilla CCMP1545]gi|226463119|gb|EEH60397.1| predicted protein [Micromonas pusilla CCMP1545]
+-WQKRKKRFVRQSWQAAceNApcGVDGVGDELLRRFFASHPGFVQLF-NFr---rarlLNSAAWRLHARSVARAIDDFVvvatagadpssSSFDNgawrrTKTALRELGGRHL-VaYKVTPAHYDAFGRALLATVEATArggggggdgggdggggdggGdGGFDRETLAAWTETWEGMRELM-----
+>gi|321477128|gb|EFX88087.1| hypothetical protein DAPPUDRAFT_230332 [Daphnia pulex]
+KLTPHQIHDVQRSWENIR--AnrNSLISAIFVKLFKETPRVQKHFVKFaNVAvdslSGNADYEKQIALVADRLDTIISAMDDklqLLGNINYMRYTHqP-PRAIPRQTFEDFARLLIDGLSAS---GVSGDDMDSWKGVLTIFVNGVS----
+>gi|241950916|ref|XP_002418180.1| conserved hypothetical protein [Candida dubliniensis CD36]gi|223641519|emb|CAX43480.1| conserved hypothetical protein [Candida dubliniensis CD36]
+SLNKIELNQIKSSWSKIN--PKEFYPELYENLFELNPQLRSIFNND-----DSVINYHCDIFGDLFNFIINNIEDdllLNEFLYQFvNENQR-FSSMISQYLEPMGNALIQTFKNELSGQFTSVLELIWIKIFVFVANLLL----
+>gi|82655305|emb|CAI26300.1| hemoglobin [Biomphalaria glabrata]
+GLSDNDREAIDSSWKKLR--SgaggrRNAGIKLVQWMLRTIPNMRDRFNKFdAKQsdaalQRDPEFLAQVDRILGGVESLVNNVDDpvaLKAAIDRLADAHL-SfdPRVGLDYFGPLQTYIHDYIEEALGVGADSDEAKGWTDLFAAFNKVLKE---
+>gi|47230183|emb|CAG10597.1| unnamed protein product [Tetraodon nigroviridis]
+KLSSKDKELIRGSWDSLGKNKVPHGVILFSRLFELDPELLNLFHYTtNCGstqdcLSSPEFLEHVTKVSETVPgeppprlhaeprsvipgDACDRRCSqppgrppLpgglfaqpgakasgsgsqttvvccmIHTVQLFRHLHI-FvHRkkkttcfftcllVCFGLLQMVGESLLYMLQCSLGQAYTASLRQAWLNMYSVVVASMSRGW-
+>gi|312094877|ref|XP_003148174.1| hypothetical protein LOAG_12613 [Loa loa]gi|307756662|gb|EFO15896.1| hypothetical protein LOAG_12613 [Loa loa]
+-----------------------------FRLFSDFPEYKQIWPQFrGIPdsliITANEVKGHGLVYMAGLKSIIDNIKNeekLVKTISKITLAHL-KWHICKDHIMNmLKEVIVILQAD--PHCQGRDVEEAWFTLFDVIGNLV-----
+>gi|20270894|gb|AAM18464.1|AF461710_1 myoglobin [Clonorchis sinensis]gi|23344091|gb|AAN28366.1| 17 kDa myoglobin [Clonorchis sinensis]
+PLSKDEVDaLFEELNPLVS--TteqrTEFGKAVYMALFSAYPEYIQLFTKMqGLTkdnvEASEGIKYYGQTFADSILEMLQCASDdgkLEAVLEKSGKEHI-TRNVTKQQFLSAEEVFIKHFSGVLT---KEENKQSMERFLKHIVPKVAGF--
+>gi|341884590|gb|EGT40525.1| CBN-GLB-28 protein [Caenorhabditis brenneri]
+CLSIEQQKIIKQSWNRIP--KAQFGRAVLNTFINTEGVGHNIFVDR--Dt-----KERHVRQIVDLVQSCVEHLDNLQTGVkpwlDLIGRGHA-NFRITGKHWENFAEALVTTASEWNGPGrRHKETGKAWLIMTSFLADRLAHA--
+>gi|17570331|ref|NP_510537.1| GLoBin family member (glb-28) [Caenorhabditis elegans]gi|6425266|emb|CAB60330.1| C. elegans protein Y15E3A.2, partially confirmed by transcript evidence [Caenorhabditis elegans]
+TISPEHQKLIKRSWNRIP--KAQFGRASLEAFITAAQVTHAIFVDK--Et-----ENRHVKYFVDLVQSCVDNLENLETGVkpwlDLIGRGHA-NFKITGKHWEKFGESLLTTATEWNGPGrRHKETVKAWMVMSSFLADRLAHA--
+>gi|339256778|ref|XP_003370265.1| putative globin [Trichinella spiralis]gi|316965561|gb|EFV50254.1| putative globin [Trichinella spiralis]
+KFTDEEVELLARTWKKDD--FDwlyRIGTDIYTCVFQLAPELKVFFPYVtECEkknqswESSKGFRTQALRFVQILGMAVEKTESrmkdddshLHHRLYKLGETHR-RfalKGFTPTHWKGFVIAVRVAMRRAVeaMPNLTPAecetAIEAWDKLSRYVVHRMEEGY-
+>gi|260903027|ref|ZP_05911422.1| conserved hypothetical protein [Vibrio parahaemolyticus AQ4037]gi|308108400|gb|EFO45940.1| conserved hypothetical protein [Vibrio parahaemolyticus AQ4037]gi|328470864|gb|EGF41775.1| hypothetical protein VP10329_08707 [Vibrio parahaemolyticus 10329]
+--------VFNDSYERCvL--SEHFFERFYAKFWSKGESFRQKFEGVDM-------QKQVRMLKGSIVFFMMTdtSSDARKMMEKYGKKHGIgNIGVKPEDIDIWFESLLETVQECD-YEYNSDVEKAWRACFKSGLEIMKREC-
+>gi|254786906|ref|YP_003074335.1| hypothetical protein TERTU_2953 [Teredinibacter turnerae T7901]gi|237685129|gb|ACR12393.1| conserved hypothetical protein [Teredinibacter turnerae T7901]
+--------LFNDSFEKCL--HGRystFFERFYRNFEQRQPEVRRMFQGTDV-------QRRYDMFEESILILVDYsaNGTASENLERLATLHT-SKGATPEMFDEWMDALIQTLREVD-PQFDDNAEFAWRDILSTGLEYLKNSA-
+>gi|90409683|ref|ZP_01217700.1| hypothetical protein P3TCK_02931 [Photobacterium profundum 3TCK]gi|90329036|gb|EAS45293.1| hypothetical protein P3TCK_02931 [Photobacterium profundum 3TCK]
+--------LYQASYQRCmG--NDDFLPLFYSLFINADIAIKDMFGSTDK-------EQQILTLKASLAMLQPAqdLITHEQLIKSIALRHK-KMNIAPHLFNVWFDCLMQAVKQYD-PQYNEDLHTIWREQLDFGIKLMTKES-
+>gi|339234991|ref|XP_003379050.1| putative globin [Trichinella spiralis]gi|316978322|gb|EFV61323.1| putative globin [Trichinella spiralis]
+-LTKSQRQNVVRSWEKVpN--KRALGEEIYIQIFMHKPMLKSLFP-FrTVPvdqlRNNALFTRQAAIFADFIDCVvgylaIDNGNLIMELSERVGVNHA-LmtsVNFDPEWWVLFANSVLDCIRQYCEPQFiclpisrhiTRKIMIAWRILLKEVVDRMSEAF-
+>gi|289208690|ref|YP_003460756.1| globin [Thioalkalivibrio sp. K90mix]gi|288944321|gb|ADC72020.1| globin [Thioalkalivibrio sp. K90mix]
+-------D-VHQSYGRCrR--AGDFVTRFYEHFLQADPRVKAAFGSTDFSqq---KRALGQA--ISTAISYAEGE-SFVASTMERMGQVHS-RegrVPVEPDLYPIWLDCMVRTAAEID-PRWEPRLEERWRGAMQPAIDLFVRLY-
+>gi|339237741|ref|XP_003380425.1| putative globin [Trichinella spiralis]gi|316976730|gb|EFV59959.1| putative globin [Trichinella spiralis]
+VLNPKEVILTRNVWAALK--EkhqHLVGMEIFRQIFNRRPDLKSLFGV-sALDtemal-NSTRLHRHTMIFQDVIdilMVNISNVDvNIADSLIDLGAQHWVlTkRGFDPAYWLIFGDVLFDLVENVTRKLPsRKRSTNAWRKTIAFMLDCMQIGY-
+>gi|119470819|ref|ZP_01613430.1| hypothetical protein ATW7_05751 [Alteromonadales bacterium TW-7]gi|119446046|gb|EAW27325.1| hypothetical protein ATW7_05751 [Alteromonadales bacterium TW-7]
+----------------------------------------------------------SYILYCTLERIIKNIDNPSSVAPFLSH-HLQflKkLNIQQSDIKPLTDIFYVTLVEHLGRFFNEESHLAWRKVLTYF---------
+>gi|268557836|ref|XP_002636908.1| Hypothetical protein CBG09371 [Caenorhabditis briggsae]
+-IVDDDFELARAHWIQLQK-SNKQGLAirgCFLTMLEKYPQVRPIWG-FgKRiegriDetwkpelVEDFYFRHHCASLQAALNMIIQNKDDrngMRRMLNEMGAHHF-FYDACEPHFEVFQDCLLESMRLVLngGDALDDEIEHSWICLLQTIRLHMGE---
+>gi|170573273|ref|XP_001892405.1| hypothetical protein Bm1_04635 [Brugia malayi]gi|158602064|gb|EDP38764.1| hypothetical protein Bm1_04635 [Brugia malayi]
+-LSEIQQELIRQSWQTIS--AklevneQNFGFFVYRRVFEHNPLLKRAFHVeeYDL-ldsiPREHSIFRQMRLFTNLIALAVRHDNELETeiapAVFRYGQRHY---KFAAEYFNegtvrLFCSQVVCAVADLLEVDIDPACMEAWIDMMRFIGCRLLDG--
+>gi|308466646|ref|XP_003095575.1| CRE-GLB-8 protein [Caenorhabditis remanei]gi|308245099|gb|EFO89051.1| CRE-GLB-8 protein [Caenorhabditis remanei]
+PLTCAQIHLVRALWRQVYTtkGPTVIGASIYHRLCFKNLMVKEQMKQVELPpkfqNRDNFIKAHCKAVAELIDQVVENldhLDNVTNELMRIGRVHA-KvLRgeLTGKLWNTVAETIIDCTLE-WGDrrCRSETVRKAWALIVAFVIEKIKAG--
+>gi|198452804|ref|XP_002137542.1| GA26483 [Drosophila pseudoobscura pseudoobscura]gi|198132084|gb|EDY68100.1| GA26483 [Drosophila pseudoobscura pseudoobscura]
+-FTLCEKVALRQAWNLIR--PreRRFGQDVFYTFLNEWYWSISKFKKGeDI--NIALLHAHALTFIRFVGALINESDPimFQVMINENNQTHS-RCRVGADYIAMLGQALTDYILKVLDKVRSPSLEQGLQRIVE-----------
+>gi|195454050|ref|XP_002074063.1| GK14442 [Drosophila willistoni]gi|194170148|gb|EDW85049.1| GK14442 [Drosophila willistoni]
+-FTLSERLALKQAWNQIK--PkeRRLGQEVFYRFLNEHYFAMYTFQSNeKL--DLHSLHSHARNFVHFIGDLINESDPtmFQFMVHDINQIHN-CRHVPKHYIEMLLQALTDAILKDLHKMTCPTLENGLKRLVD-----------
+>gi|308071704|emb|CBX25204.1| C. elegans protein Y17G7B.6a, partially confirmed by transcript evidence [Caenorhabditis elegans]
+NLSVKQKKLLRQSFNAMN--SGgtflKLMEKIFRRLETKCPDMRSIFLTtaFvnSLSrerQTPPLVkteYDHCKCMVGIFERLIENLENINEQLTMirhYGEKHA-QmaeSGFTGAMIEQFGEISVFVIGSQDVVKFNHETVKAWRLLLACVTDEMKVGF-
+>gi|322493086|emb|CBZ28370.1| adenylate cyclase-like protein [Leishmania mexicana MHOM/GT/2001/U1103]
+--------TVEGTWRILEDegMVEQFGQQLYDELLTRNRRLRVHFYGV-------DIEEQSKSLLRMVGTAVHFYQKpqlTVDMFTKAGARHR-GYGVNAEVFVEMRNAFMRVFSKFVGTDVFQAAEEEWQKFWKYVLDLLVH---
+>gi|341888892|gb|EGT44827.1| CBN-GLB-12 protein [Caenorhabditis brenneri]
+-LNKKDRTLLRETWQRLDE-PkDIVGLIFLDIVNDIEPDLKKVFGV-DRApraamLKMPKFGGHILRfyeFMEQLTSMLGTSENLTGAwqlVRKTGRSHV-KqgfleqnqNQMEKNYFEVVINVFIERLIPYLtgeqelppaegkeqkkvrfAQNYtTSQITDVWKKFLNTVISQMTDSF-
+>gi|206994324|emb|CAR81336.1| C. elegans protein C06H2.5a, partially confirmed by transcript evidence [Caenorhabditis elegans]
+HLSPHQVQLLTSTWPRIK--TqSSLFTQVFKVLMQRSPVCREMFQKMsivgGFSsn-SVCDLNSHTKLLCELLDSLMTDLHQPAkIVLakcQDVGAAHV-NMNekCCGVVFDQLGEAFTELITKVECVRSKREAVKSWMCVISYMADSIKSGY-
diff --git a/modules/config/base.hh b/modules/config/base.hh
index 02bdc2b4c97929fedc6b5742ec59860c1e7190e6..2019437b5b47828492ec8de2422a77287d650092 100644
--- a/modules/config/base.hh
+++ b/modules/config/base.hh
@@ -19,7 +19,6 @@
#ifndef OST_BASE_HH
#define OST_BASE_HH
-#include <string>
#include <cmath>
#include <math.h>
#include <complex>
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index 3a9e4e6118867027b04db2bbf3eb3031878c44ed..661fa9db11019c805f6eb8d032aa06d8b50c9990 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -106,7 +106,7 @@ void export_Compound() {
.def("GetAtomSpecs", &Compound::GetAtomSpecs,
return_value_policy<copy_const_reference>())
.add_property("bond_specs", make_function(&Compound::GetBondSpecs,
- return_value_policy<copy_const_reference>()))
+ return_value_policy<copy_const_reference>()))
.add_property("atom_specs", make_function(&Compound::GetAtomSpecs,
return_value_policy<copy_const_reference>()))
.def("AddAtom", &Compound::AddAtom)
@@ -120,6 +120,12 @@ void export_Compound() {
&Compound::SetFormula)
.add_property("dialect", &Compound::GetDialectAsString,
&set_dialect)
+ .add_property("inchi",
+ make_function(&Compound::GetInchi,
+ return_value_policy<copy_const_reference>()))
+ .add_property("inchi_key",
+ make_function(&Compound::GetInchiKey,
+ return_value_policy<copy_const_reference>()))
;
class_<AtomSpec>("AtomSpec", no_init)
diff --git a/modules/conop/src/CMakeLists.txt b/modules/conop/src/CMakeLists.txt
index 3709e846aa244c06bc2fbca34e8e848fe95d8d22..0185618ea4a9ebb02d917393670ce3f401ed494c 100644
--- a/modules/conop/src/CMakeLists.txt
+++ b/modules/conop/src/CMakeLists.txt
@@ -43,9 +43,13 @@ endif(WIN32)
if (COMPOUND_LIB)
if (EXISTS "${COMPOUND_LIB}")
- copy_if_different("./" "${STAGE_DIR}/share/openstructure"
- "${COMPOUND_LIB}" "COMPOUND_LIB" ost_conop)
- install(FILES ${COMPOUND_LIB} DESTINATION "share/openstructure")
+ # this ensures that file is called 'compounds.chemlib' (as required)
+ set(TO "${STAGE_DIR}/share/openstructure/compounds.chemlib")
+ file(MAKE_DIRECTORY "${STAGE_DIR}/share/openstructure")
+ add_custom_command(TARGET "ost_conop" PRE_BUILD
+ DEPENDS "${COMPOUND_LIB}"
+ COMMAND ${CMAKE_COMMAND} -E copy_if_different ${COMPOUND_LIB} ${TO})
+ install(FILES ${TO} DESTINATION "share/openstructure")
else()
message(FATAL_ERROR "${COMPOUND_LIB} does not exist. \n"
"Pass -DCOMPOUND_LIB=NONE if you would like to build "
diff --git a/modules/conop/src/compound.hh b/modules/conop/src/compound.hh
index e06dde4c3b15964fd191c64de25a6f673dd19ad7..9e2547bbfbd44c689483d91a5c50cd22154fbf9f 100644
--- a/modules/conop/src/compound.hh
+++ b/modules/conop/src/compound.hh
@@ -98,6 +98,7 @@ struct DLLEXPORT_OST_CONOP AtomSpec {
return ordinal==rhs.ordinal && name==rhs.name && alt_name==rhs.alt_name &&
element==rhs.element && is_leaving==rhs.is_leaving &&
rhs.is_aromatic==rhs.is_aromatic;
+
}
bool operator!=(const AtomSpec& rhs) const {
return !this->operator==(rhs);
@@ -146,6 +147,8 @@ public:
tlc_(id),
formula_(),
name_(),
+ inchi_(),
+ inchi_key_(),
atom_specs_(),
bond_specs_(),
chem_class_(),
@@ -236,11 +239,19 @@ public:
const String& GetName() { return name_; }
void SetName(const String& name) { name_=name; }
-
+
void SetFormula(const String& formula) { formula_=formula; }
const String& GetFormula() { return formula_; }
-
+
+ void SetInchi(const String& inchi) { inchi_=inchi; }
+
+ const String& GetInchi() { return inchi_; }
+
+ void SetInchiKey(const String& inchikey) { inchi_key_=inchikey; }
+
+ const String& GetInchiKey() { return inchi_key_; }
+
const BondSpecList& GetBondSpecs() const {
return bond_specs_;
}
@@ -268,6 +279,8 @@ private:
String tlc_;
String formula_;
String name_;
+ String inchi_;
+ String inchi_key_;
AtomSpecList atom_specs_;
BondSpecList bond_specs_;
mol::ChemClass chem_class_;
diff --git a/modules/conop/src/compound_lib.cc b/modules/conop/src/compound_lib.cc
index 35c60e0c3fa133d9cc11165273d30e760dd77790..e2cf22263aa88071b425f686cd0d7a9666ef112c 100644
--- a/modules/conop/src/compound_lib.cc
+++ b/modules/conop/src/compound_lib.cc
@@ -49,7 +49,9 @@ const char* CREATE_CMD[]={
" formula VARCHAR(64) NOT NULL, "
" pdb_initial TIMESTAMP, "
" pdb_modified TIMESTAMP, "
-" name VARCHAR(256) "
+" name VARCHAR(256), "
+" inchi_code TEXT, "
+" inchi_key TEXT "
");",
" CREATE UNIQUE INDEX IF NOT EXISTS commpound_tlc_index ON chem_compounds "
" (tlc, dialect)",
@@ -85,8 +87,8 @@ const char* CREATE_CMD[]={
const char* INSERT_COMPOUND_STATEMENT="INSERT INTO chem_compounds "
-" (tlc, olc, dialect, chem_class, chem_type, formula, pdb_initial, pdb_modified, name) "
-" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?), ?)";
+" (tlc, olc, dialect, chem_class, chem_type, formula, pdb_initial, pdb_modified, name, inchi_code, inchi_key) "
+" VALUES (?, ?, ?, ?, ?, ?, DATE(?), DATE(?), ?, ?, ?)";
const char* INSERT_ATOM_STATEMENT="INSERT INTO atoms "
" (compound_id, name, alt_name, element, is_aromatic, stereo_conf, "
@@ -220,8 +222,16 @@ void CompoundLib::AddCompound(const CompoundPtr& compound)
Date modi_date=compound->GetModificationDate();
crea_date_str=crea_date.ToString();
modi_date_str=modi_date.ToString();
- sqlite3_bind_text(stmt, 7, crea_date_str.c_str(), crea_date_str.length(), NULL);
- sqlite3_bind_text(stmt, 8, modi_date_str.c_str(), modi_date_str.length(), NULL);
+ sqlite3_bind_text(stmt, 7, crea_date_str.c_str(), crea_date_str.length(),
+ NULL);
+ sqlite3_bind_text(stmt, 8, modi_date_str.c_str(), modi_date_str.length(),
+ NULL);
+ sqlite3_bind_text(stmt, 9, compound->GetName().c_str(),
+ compound->GetName().length(), NULL);
+ sqlite3_bind_text(stmt, 10, compound->GetInchi().c_str(),
+ compound->GetInchi().length(), NULL);
+ sqlite3_bind_text(stmt, 11, compound->GetInchiKey().c_str(),
+ compound->GetInchiKey().length(), NULL);
} else {
LOG_ERROR(sqlite3_errmsg(conn_));
sqlite3_finalize(stmt);
@@ -356,6 +366,12 @@ CompoundLibPtr CompoundLib::Load(const String& database, bool readonly)
static_cast<int>(aq.length()),
&stmt, NULL);
lib->name_available_ = retval==SQLITE_OK;
+ // check if InChIs are available
+ aq="SELECT inchi_code FROM chem_compounds LIMIT 1";
+ retval=sqlite3_prepare_v2(lib->conn_, aq.c_str(),
+ static_cast<int>(aq.length()),
+ &stmt, NULL);
+ lib->inchi_available_ = retval==SQLITE_OK;
lib->creation_date_ = lib->GetCreationDate();
lib->ost_version_used_ = lib->GetOSTVersionUsed();
@@ -422,12 +438,18 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
return i->second;
}
String query="SELECT id, tlc, olc, chem_class, dialect, formula";
+ int col_offset = 0;
if(chem_type_available_) {
query+=", chem_type";
+ col_offset+=1;
if(name_available_) {
query+=", name";
+ col_offset+=1;
}
}
+ if(inchi_available_) {
+ query+=", inchi_code, inchi_key";
+ }
query+=" FROM chem_compounds"
" WHERE tlc='"+id+"' AND dialect='"+String(1, char(dialect))+"'";
@@ -459,6 +481,16 @@ CompoundPtr CompoundLib::FindCompound(const String& id,
compound->SetName(name);
}
}
+ if (inchi_available_) {
+ const char* inchi_code=reinterpret_cast<const char*>(sqlite3_column_text(stmt, 6+col_offset));
+ if (inchi_code) {
+ compound->SetInchi(inchi_code);
+ }
+ const char* inchi_key=reinterpret_cast<const char*>(sqlite3_column_text(stmt, 6+col_offset+1));
+ if (inchi_key) {
+ compound->SetInchiKey(inchi_key);
+ }
+ }
// Load atoms and bonds
this->LoadAtomsFromDB(compound, pk);
this->LoadBondsFromDB(compound, pk);
@@ -482,6 +514,7 @@ CompoundLib::CompoundLib():
conn_(NULL),
chem_type_available_(false),
name_available_(),
+ inchi_available_(),
creation_date_(),
ost_version_used_()
{
diff --git a/modules/conop/src/compound_lib.hh b/modules/conop/src/compound_lib.hh
index fef48b1a766899cff3e4097fe68e70a0031291b8..8b6c444868de16503e4d2d37fd22297d467e3d3c 100644
--- a/modules/conop/src/compound_lib.hh
+++ b/modules/conop/src/compound_lib.hh
@@ -57,8 +57,9 @@ private:
private:
mutable CompoundMap compound_cache_;
sqlite3* conn_;
- bool chem_type_available_; // weather pdbx_type is available in db
- bool name_available_; // weather name is available in db
+ bool chem_type_available_; // wether pdbx_type is available in db
+ bool name_available_; // wether name is available in db
+ bool inchi_available_; //whether inchi is available in db
Date creation_date_;
String ost_version_used_;
};
diff --git a/modules/conop/src/diag.cc b/modules/conop/src/diag.cc
index 470673bf73f3c6bcb7acc0836839c25c7d740336..cf7147ede8fab30eca26dbf22dfe977b6350ed51 100644
--- a/modules/conop/src/diag.cc
+++ b/modules/conop/src/diag.cc
@@ -79,7 +79,7 @@ String Diag::Format(bool colored) const
char *end=NULL;
long int id=strtol(start, &end, 10);
assert(start!=end);
- assert(id>=0 && id<strings.size());
+ assert(id>=0 && static_cast<unsigned long>(id)<strings.size());
if (plural_s) {
if (ints_[args_[id].index]!=1) {
ss << "s";
diff --git a/modules/conop/src/nonstandard.hh b/modules/conop/src/nonstandard.hh
index 374694303e1d5d0f05626e7cc43d2f9c53139c5a..a57022def8ef7436889491c7ae6714c6e9a69d6e 100644
--- a/modules/conop/src/nonstandard.hh
+++ b/modules/conop/src/nonstandard.hh
@@ -31,9 +31,6 @@ namespace ost { namespace conop {
/// \brief copies all atom of src_res to dst_res, gets compound lib from builder
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the
-/// dst_residue is not a glycine, it will be inserted if in the dst should
-/// be one and in src it was not present
bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
@@ -41,16 +38,16 @@ bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
ost::mol::XCSEditor& edi);
/// \brief copies all atom of src_res to dst_res, requires a compound lib
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the
-/// dst_residue is not a glycine, it will be inserted if in the dst should
-/// be one and in src it was not present
bool DLLEXPORT_OST_CONOP CopyResidue(ost::mol::ResidueHandle src_res,
ost::mol::ResidueHandle dst_res,
ost::mol::XCSEditor& edi, CompoundLibPtr lib);
/// \brief copies all atom of src_res to dst_res
-/// \param has_cbeta will be set to true if the src_res has a cbeta and the
+/// \param src_res
+/// \param dst_res
+/// \param edi
+/// \param has_cbeta will be set to true if the src_res has a cbeta and the
/// dst_residue is not a glycine
bool DLLEXPORT_OST_CONOP CopyIdentical(ost::mol::ResidueHandle src_res,
ost::mol::ResidueHandle dst_res,
diff --git a/modules/conop/tests/CMakeLists.txt b/modules/conop/tests/CMakeLists.txt
index 29140807826e25e812d312371013f9ca96e2b3bd..a0c348ac5fb2337c3ed3a3e521c26e300d87404d 100644
--- a/modules/conop/tests/CMakeLists.txt
+++ b/modules/conop/tests/CMakeLists.txt
@@ -2,13 +2,15 @@ set(OST_CONOP_UNIT_TESTS
test_heuristic_conop.cc
tests.cc
test_rule_based_conop.cc
- helper.cc
- test_compound.py
+ helper.cc
test_cleanup.py
test_processor.py
test_nonstandard.py
)
+if (COMPOUND_LIB)
+ list(APPEND OST_CONOP_UNIT_TESTS test_compound.py)
+endif()
+
ost_unittest(MODULE conop
SOURCES "${OST_CONOP_UNIT_TESTS}")
-
diff --git a/modules/conop/tests/test_compound.py b/modules/conop/tests/test_compound.py
index 700f52b286d6e7f842cd004c2dffff6006603436..fd480a54bc95dcb4958d635038ec43dde1c2db7e 100644
--- a/modules/conop/tests/test_compound.py
+++ b/modules/conop/tests/test_compound.py
@@ -1,30 +1,40 @@
import unittest
+import os
+from ost import GetSharedDataPath, SetPrefixPath
from ost import mol
from ost import conop
+def setUpModule():
+ SetPrefixPath(os.path.abspath(os.path.join(conop.__path__[0], os.pardir,
+ os.pardir, os.pardir,
+ os.pardir, os.pardir)))
+ compound_lib_path = os.path.join(GetSharedDataPath(),
+ 'compounds.chemlib')
+ compound_lib = conop.CompoundLib.Load(compound_lib_path)
+ conop.SetDefaultLib(compound_lib)
+
class TestCompound(unittest.TestCase):
-
- def setUp(self):
- self.compound_lib=conop.GetDefaultLib()
+ def setUp(self):
+ self.compound_lib=conop.GetDefaultLib()
- def testFindCompound(self):
- compound=self.compound_lib.FindCompound('***')
- self.assertEqual(compound, None)
- compound=self.compound_lib.FindCompound('ALA')
- self.assertNotEqual(compound, None)
- self.assertEqual(compound.id, 'ALA')
- self.assertEqual(compound.three_letter_code, 'ALA')
- self.assertEqual(compound.one_letter_code, 'A')
- self.assertTrue(compound.IsPeptideLinking())
- self.assertEqual(compound.dialect, 'PDB')
- self.assertEqual(compound.formula, 'C3 H7 N O2')
- self.assertEqual(compound.chem_class, mol.L_PEPTIDE_LINKING)
+ def testFindCompound(self):
+ compound=self.compound_lib.FindCompound('***')
+ self.assertEqual(compound, None)
+ compound=self.compound_lib.FindCompound('ALA')
+ self.assertNotEqual(compound, None)
+ self.assertEqual(compound.id, 'ALA')
+ self.assertEqual(compound.three_letter_code, 'ALA')
+ self.assertEqual(compound.one_letter_code, 'A')
+ self.assertTrue(compound.IsPeptideLinking())
+ self.assertEqual(compound.dialect, 'PDB')
+ self.assertEqual(compound.formula, 'C3 H7 N O2')
+ self.assertEqual(compound.chem_class, mol.L_PEPTIDE_LINKING)
+ self.assertEqual(compound.inchi,
+ "1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1")
+ self.assertEqual(compound.inchi_key, "QNAYBMKLOCPYGJ-REOHCLBHSA-N")
if __name__=='__main__':
- if not conop.GetDefaultLib():
- print 'No compound library available. ignoring compound unit tests'
- else:
from ost import testutils
testutils.RunTests()
diff --git a/modules/doc/install.rst b/modules/doc/install.rst
index a0b36a3f12cfc3a305e8b5e553f16bdc824e07c8..76f6c465f02c47e1167e922a23a275f8a96a1354 100644
--- a/modules/doc/install.rst
+++ b/modules/doc/install.rst
@@ -28,8 +28,8 @@ Installing the Dependencies
OpenStructure uses a bunch of OpenSource libraries. If you haven't already installed them, please install them now! Where appropriate the minimally required version is given in parantheses.
* `CMake <http://cmake.org>`_ (2.6.4)
- * `Eigen2 <http://eigen.tuxfamily.org>`_ (2.0.6)
- * `Boost <http://boost.org>`_ (1.47)
+ * `Eigen3 <http://eigen.tuxfamily.org>`_ (3.2.0)
+ * `Boost <http://boost.org>`_ (1.53)
* `libpng <http://www.libpng.org>`_
* `Python <http://python.org>`_ (2.7)
* `Qt <http://qt-project.org/>`_ (4.5)
diff --git a/modules/doc/newmodule.rst b/modules/doc/newmodule.rst
index 03822cb7e4cfe57e7df4e7946d5961d8d1ed80e1..8c4864cb4e0145f4ce8916f1384e7a92bf13f391 100644
--- a/modules/doc/newmodule.rst
+++ b/modules/doc/newmodule.rst
@@ -160,7 +160,7 @@ The Testing Framework
The `tests` directory contains code for unit tests. The code is compiled and
executed when one invokes compilation using the 'make check' command. Tests are
run by means of the `Boost Unitests Library
-<http://www.boost.org/doc/libs/1_37_0/libs/test/doc/html/index.html>`_. Before coding the test routines, the required skeleton needs to be put in place.
+<http://www.boost.org/doc/libs/1_53_0/libs/test/doc/html/index.html>`_. Before coding the test routines, the required skeleton needs to be put in place.
The main code is put into 'tests.cc', which will become the test executable. There are only 3 lines required
@@ -224,7 +224,7 @@ The Python Wrapper
--------------------------------------------------------------------------------
Finally, the module API is exported to Python using the `Boost Python
-Library <http://www.boost.org/doc/libs/1_37_0/libs/python/doc/index.html>`_.
+Library <http://www.boost.org/doc/libs/1_53_0/libs/python/doc/index.html>`_.
In `mod/pymod`, the wrapper code for the classes in the new module is put into a
file named `wrap\_mod.cc`:
diff --git a/modules/geom/pymod/export_vec3.cc b/modules/geom/pymod/export_vec3.cc
index 0df8101549767a5c3a7af43bdde4bd33da3b9dd2..8adf113fcfd5fb1ae09fd6bbb097212489a65ab5 100644
--- a/modules/geom/pymod/export_vec3.cc
+++ b/modules/geom/pymod/export_vec3.cc
@@ -24,6 +24,7 @@
using namespace boost::python;
+
const Real Vec3_getitem(const geom::Vec3& v, int i) {
return v.At(i);
}
@@ -51,6 +52,11 @@ list vec3_data(const geom::Vec3& v)
return nrvo;
}
+boost::python::tuple wrap_FitCylinder(const geom::Vec3List& vl,const geom::Vec3& initial_direction) {
+ std::pair<geom::Line3,Real> pair=vl.FitCylinder(initial_direction);
+ return boost::python::make_tuple<geom::Line3,Real>(pair.first,pair.second);
+}
+
void export_Vec3()
{
using namespace geom;
@@ -114,6 +120,6 @@ void export_Vec3()
.add_property("inertia", &Vec3List::GetInertia)
.add_property("principal_axes", &Vec3List::GetPrincipalAxes)
.def("GetODRLine", &Vec3List::GetODRLine)
- .def("FitCylinder", &Vec3List::FitCylinder)
+ .def("FitCylinder", wrap_FitCylinder,(arg("direction initial guess")))
;
}
diff --git a/modules/geom/pymod/export_vecmat3_op.cc b/modules/geom/pymod/export_vecmat3_op.cc
index 5c06a2499ed7e2af0a5e73fe9ad5dd589b289a46..0cdc3e37358693f63215c0bb8fe05adf17b6617e 100644
--- a/modules/geom/pymod/export_vecmat3_op.cc
+++ b/modules/geom/pymod/export_vecmat3_op.cc
@@ -38,9 +38,13 @@ Real (*Mat3Comp)(const Mat3& m, unsigned int i, unsigned int j) = &Comp;
Real (*Mat3Minor)(const Mat3& m, unsigned int i, unsigned int j) = &Minor;
Vec3 (*Vec3Min)(const Vec3&, const Vec3&) = &Min;
Vec3 (*Vec3Max)(const Vec3&, const Vec3&) = &Max;
+Real (*Vec3SignedAngle)(const Vec3& v1, const Vec3& v2, const Vec3& v3) = &SignedAngle;
Real (*Vec3Distance2WithPBC)(const Vec3&, const Vec3&, const Vec3&) = &Distance2WithPBC;
Real (*Vec3DistanceWithPBC)(const Vec3&, const Vec3&, const Vec3&) = &DistanceWithPBC;
-
+Vec3 (*wrap_vec3_1)(const Vec3&, const Vec3&, const Vec3&) = &WrapVec3;
+Vec3 (*wrap_vec3_2)(const Vec3&, const Vec3&, const Vec3&, const Vec3&) = &WrapVec3;
+Vec3List (*wrap_vec3list1)(const Vec3List&, const Vec3&, const Vec3&) = &WrapVec3List;
+Vec3List (*wrap_vec3list2)(const Vec3List&, const Vec3&, const Vec3&, const Vec3&) = &WrapVec3List;
void export_VecMat3_op()
{
using namespace geom;
@@ -53,6 +57,7 @@ void export_VecMat3_op()
def("Distance",Vec3Distance);
def("Equal",Mat3Equal, (arg("m1"), arg("m2"), arg("epsilon")=EPSILON));
def("DihedralAngle", &DihedralAngle);
+ def("SignedAngle", Vec3SignedAngle, (arg("v1"), arg("v2"),arg("ref_normal")));
def("Dot",Mat3Dot);
def("Det",Mat3Det);
def("Cross",Vec3Cross);
@@ -70,6 +75,8 @@ void export_VecMat3_op()
def("MinDistance",MinDistance);
def("MinDistanceIndices",MinDistanceIndices);
def("MinDistanceWithPBC",MinDistanceWithPBC);
- def("WrapVec3",WrapVec3);
- def("WrapVec3List",WrapVec3List);
+ def("WrapVec3",wrap_vec3_1,(arg("vector"),arg("cell_center"),arg("cell_size")));
+ def("WrapVec3",wrap_vec3_2,(arg("vector"),arg("cell_center"),arg("cell_size"),arg("cell_angles")));
+ def("WrapVec3List",wrap_vec3list1,(arg("vector_list"),arg("cell_center"),arg("cell_size")));
+ def("WrapVec3List",wrap_vec3list2,(arg("vector_list"),arg("cell_center"),arg("cell_size"),arg("cell_angles")));
}
diff --git a/modules/geom/src/composite3.cc b/modules/geom/src/composite3.cc
index 3813fb668c31f0b52f7a03d5388de12857a45b1a..b2d795247fe3858c11fb2ee2262746aa9c495d1e 100644
--- a/modules/geom/src/composite3.cc
+++ b/modules/geom/src/composite3.cc
@@ -190,28 +190,28 @@ Real Rotation3::GetPhi() const
return GetRotationAngle()*
(q_.GetAxis().GetZ()/std::fabs(q_.GetAxis().GetZ()));
}else{
- return reduce_angle(M_PI-atan2(q_.GetAxis().GetX()*q_.GetAxis().GetZ()+
- q_.GetAxis().GetY()*q_.GetAngle(),
- q_.GetAxis().GetY()*q_.GetAxis().GetZ()-
- q_.GetAxis().GetX()*q_.GetAngle()));
+ return reduce_angle(M_PI-atan2(q_.x*q_.z+
+ q_.y*q_.w,
+ q_.y*q_.z-
+ q_.x*q_.w));
}
}
Real Rotation3::GetTheta() const
{
- return reduce_angle(acos(-q_.GetAxis().GetX()*q_.GetAxis().GetX()-
- q_.GetAxis().GetY()*q_.GetAxis().GetY()+
- q_.GetAxis().GetZ()*q_.GetAxis().GetZ()+
- q_.GetAngle()*q_.GetAngle()));
+ return reduce_angle(acos(-q_.x*q_.x-
+ q_.y*q_.y+
+ q_.z*q_.z+
+ q_.w*q_.w));
}
Real Rotation3::GetPsi() const
{
if(GetTheta()<EPSILON){
return 0.0;
}else{
- return reduce_angle(atan2(q_.GetAxis().GetX()*q_.GetAxis().GetZ()-
- q_.GetAxis().GetY()*q_.GetAngle(),
- q_.GetAxis().GetY()*q_.GetAxis().GetZ()+
- q_.GetAxis().GetX()*q_.GetAngle()));
+ return reduce_angle(atan2(q_.x*q_.z-
+ q_.y*q_.w,
+ q_.y*q_.z+
+ q_.x*q_.w));
}
}
@@ -302,7 +302,7 @@ Vec3 Rotation3::find_invariant_vector(Mat3 rot)
Real minors[9];
for(int i=2;i>=0;--i){
for(int j=2;j>=0;--j){
- minors[3*i+j]=Minor(rot,i,j);
+ minors[3*(2-i)+(2-j)]=Minor(rot,i,j);
}
}
Real* where = ::std::max_element(minors, minors+9);
@@ -328,7 +328,7 @@ Vec3 Rotation3::find_invariant_vector(Mat3 rot)
case 2:
result.SetX(1.0);
result.SetY(-minors[1]/det);
- result.SetZ(-minors[0]/det);
+ result.SetZ(minors[0]/det);
break;
case 3:
result.SetZ(1.0);
@@ -338,7 +338,7 @@ Vec3 Rotation3::find_invariant_vector(Mat3 rot)
case 4:
result.SetY(1.0);
result.SetX(-minors[5]/det);
- result.SetZ(-minors[4]/det);
+ result.SetZ(-minors[3]/det);
break;
case 5:
result.SetX(1.0);
diff --git a/modules/geom/src/vec3.cc b/modules/geom/src/vec3.cc
index 8909ce8b8648879741c01965ef13961614223e6b..a69b2682d7d53aaaf8970b165d068c1adb228988 100644
--- a/modules/geom/src/vec3.cc
+++ b/modules/geom/src/vec3.cc
@@ -60,7 +60,7 @@ Mat3 Vec3List::GetPrincipalAxes() const
Mat3 inertia=this->GetInertia();
EMat3 inertia_mat(inertia.Data());
- Eigen::SVD<EMat3> svd(inertia_mat);
+ Eigen::JacobiSVD<EMat3> svd(inertia_mat,Eigen::ComputeFullU);
EMat3 rot=svd.matrixU();
Mat3 axes(rot.data());
return axes;
@@ -91,76 +91,96 @@ Plane Vec3List::GetODRPlane() const
Vec3 normal=this->GetPrincipalAxes().GetRow(0);
return Plane(origin,normal);
}
-
-Line3 Vec3List::FitCylinder(const Vec3& initial_direction, const Vec3& center) const
-{
- Line3 axis=Line3(center,center+initial_direction), axis_old;
- Real radius,res_sum_old,res_sum,delta_0=0.01,prec=0.0000001,err,norm,delta;
- unsigned long n_step=1000, n_res=this->size();
- Vec3 v,gradient;
-
- radius=0.0;
- delta=delta_0;
- for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
- radius+=geom::Distance(axis,(*i));
- }
- radius/=Real(n_res);
- res_sum=0.0;
- for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
- Real r=Distance(axis,(*i))-radius;
- res_sum+=r*r;
- }
- unsigned long k=0;
- err=2.0*prec;
- while (err>prec && k<n_step) {
- res_sum_old=res_sum;
- axis_old=axis;
+
+std::pair<Line3, Real> Vec3List::FitCylinder(const Vec3& initial_direction) const
+ {
+ Vec3 center=this->GetCenter();
+ Line3 axis=Line3(center,center+initial_direction), axis_old;
+ Real radius,res_sum_old,res_sum,delta_0=0.01,prec=0.0000001,err,norm,delta;
+ unsigned long n_step=1000, n_res=this->size();
+ Vec3 v,gradient_dir,gradient_center;
+
radius=0.0;
- if (k>50) {
- delta=delta_0*50.0*50.0/(k*k);
- }
+ delta=delta_0;
for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
- radius+=Distance(axis,(*i));
+ radius+=geom::Distance(axis,(*i));
}
radius/=Real(n_res);
- for (int j=0; j!=3; ++j){
- res_sum=0.0;
- v=Vec3(0.0,0.0,0.0);
- v[j]=delta;
- axis=Line3(axis_old.GetOrigin(),axis_old.GetOrigin()+axis_old.GetDirection()+v);
+ res_sum=0.0;
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ Real r=Distance(axis,(*i))-radius;
+ res_sum+=r*r;
+ }
+ unsigned long k=0;
+ err=2.0*prec;
+ while (err>prec && k<n_step) {
+ res_sum_old=res_sum;
+ axis_old=axis;
+ //radius=0.0;
+ if (k>50) {
+ delta=delta_0*50.0*50.0/(k*k);
+ }
+ //for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ // radius+=Distance(axis,(*i));
+ //}
+ radius/=Real(n_res);
+ for (int j=0; j!=3; ++j){
+ res_sum=0.0;
+ v=Vec3(0.0,0.0,0.0);
+ v[j]=delta;
+ axis=Line3(axis_old.GetOrigin(),axis_old.GetOrigin()+axis_old.GetDirection()+v);
+ radius=0.0;
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ radius+=Distance(axis,(*i));
+ }
+ radius/=Real(n_res);
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ Real r=Distance(axis,(*i))-radius;
+ res_sum+=r*r;
+ }
+ gradient_dir[j]=(res_sum-res_sum_old)/delta;
+ }
+ norm=Dot(gradient_dir,gradient_dir);
+ if (norm>1.) {
+ gradient_dir=Normalize(gradient_dir);
+ }
+ for (int j=0; j!=3; ++j){
+ res_sum=0.0;
+ v=Vec3(0.0,0.0,0.0);
+ v[j]=delta;
+ axis=Line3(axis_old.GetOrigin()+v,axis_old.GetOrigin()+axis_old.GetDirection()+v);
+ radius=0.0;
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ radius+=Distance(axis,(*i));
+ }
+ radius/=Real(n_res);
+ for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
+ Real r=Distance(axis,(*i))-radius;
+ res_sum+=r*r;
+ }
+ gradient_center[j]=(res_sum-res_sum_old)/delta;
+ }
+ norm=Dot(gradient_center,gradient_center);
+ if (norm>1.) {
+ gradient_center=Normalize(gradient_center);
+ }
+ axis=Line3(axis_old.GetOrigin()-50*delta*gradient_center,axis_old.GetOrigin()-50*delta*gradient_center+axis_old.GetDirection()-delta*gradient_dir);
radius=0.0;
for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
radius+=Distance(axis,(*i));
}
radius/=Real(n_res);
+ res_sum=0.0;
for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
Real r=Distance(axis,(*i))-radius;
res_sum+=r*r;
}
- gradient[j]=(res_sum-res_sum_old)/delta;
- }
- norm=Dot(gradient,gradient);
- if (norm>1.) {
- gradient=Normalize(gradient);
+ err=fabs((res_sum-res_sum_old)/float(n_res));
+ k++;
}
- axis=Line3(axis_old.GetOrigin(),axis_old.GetOrigin()+axis_old.GetDirection()-delta*gradient);
- radius=0.0;
- for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
- radius+=Distance(axis,(*i));
+ if (err>prec) {
+ std::cout<<"axis fitting did not converge"<<std::endl;
}
- radius/=Real(n_res);
- res_sum=0.0;
- for (Vec3List::const_iterator i=this->begin(),e=this->end(); i!=e; ++i) {
- Real r=Distance(axis,(*i))-radius;
- res_sum+=r*r;
- }
- err=fabs((res_sum-res_sum_old)/float(n_res));
- k++;
+ return std::make_pair(axis,radius);
}
- if (err>prec) {
- std::cout<<"axis fitting did not converge"<<std::endl;
- }
- return axis;
-}
-
}
diff --git a/modules/geom/src/vec3.hh b/modules/geom/src/vec3.hh
index 58e63b89258294462a34e9ab28311ddde59a9670..47137476eb9aa8c2a9d6286de9da7954a97f269b 100644
--- a/modules/geom/src/vec3.hh
+++ b/modules/geom/src/vec3.hh
@@ -195,6 +195,10 @@ inline Vec3 operator/(Real d, const Vec3& v)
return nrvo;
}
+// The following operator is among other things used to write vector
+// data into info files. If its format is changed, the string to
+// vector type cast in item_type_cast.hh has to be changed
+// accordingly.
inline std::ostream& operator<<(std::ostream& os, const Vec3& v)
{
os << "[" << v.x << ", " << v.y << ", " << v.z << "]";
@@ -316,10 +320,13 @@ public:
Plane GetODRPlane() const;
//This function fits a cylinder to the positions in Vec3List
- //It takes as argument an initial guess for the direction and the geometric
- //center of the atoms. The center is not changed during optimisation as the
- //best fitting cylinder can be shown to have its axis pass through the geometric center
- Line3 FitCylinder(const Vec3& initial_direction, const Vec3& center) const;
+ //It takes as argument an initial guess for the direction.
+ //The center is set to the geometric centero of the atoms
+ //and is not changed during optimisation as the best fitting cylinder
+ //can be shown to have its axis pass through the geometric center
+ //It returns a pair containing a line3, giving the direction of the Cylinder
+ //and a Real containing the radius.
+ std::pair<Line3, Real> FitCylinder(const Vec3& initial_direction) const;
};
} // ns geom
diff --git a/modules/geom/src/vecmat3_op.cc b/modules/geom/src/vecmat3_op.cc
index 2653a081fc83a0bef9bb062d1f451d1a5996672c..3c5cbdea27e4da7b92180eb558856757aa5f535d 100644
--- a/modules/geom/src/vecmat3_op.cc
+++ b/modules/geom/src/vecmat3_op.cc
@@ -208,20 +208,20 @@ Real MinDistance(const Vec3List& l1, const Vec3List& l2)
return std::sqrt(min);
}
-Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec)
+Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& ucell_size)
{
// returns the minimal distance between two sets of points (Vec3List)
- // given the periodic boundary condition along x,y,z given in the basis_vec
+ // given the periodic boundary condition along x,y,z given in the ucell_size
if (l1.size()==0 || l2.size()==0){throw GeomException("cannot calculate minimal distance: empty Vec3List");}
Real min=Length2(*l1.begin()-*l2.begin());
Real d;
Vec3 v;
for (int i=0; i<3; i++) {
- basis_vec[i]=std::fabs(basis_vec[i]);
+ ucell_size[i]=std::fabs(ucell_size[i]);
}
for (Vec3List::const_iterator p1=l1.begin(),e1=l1.end(); p1!=e1; p1++) {
for (Vec3List::const_iterator p2=l2.begin(),e2=l2.end(); p2!=e2; p2++) {
- d=Distance2WithPBC(*p1, *p2, basis_vec);
+ d=Distance2WithPBC(*p1, *p2, ucell_size);
if (d<min) min=d;
}
}
@@ -250,26 +250,63 @@ std::vector<unsigned int> MinDistanceIndices(const Vec3List& l1, const Vec3List&
}
return il;
}
+
+Vec3List CalculateUnitCellVectors(const Vec3& ucell_size, const Vec3& ucell_angles){
+ // Calculates the unit cell vectors from their sizes and angles.
+ // The angles are given as Vec3(gamma,beta,alpha)
+ geom::Vec3List ucell_vec;
+ geom::Vec3 ucell_vec1,ucell_vec2,ucell_vec3;
+ Real cosa=cos(ucell_angles[2]),cosb=cos(ucell_angles[1]);
+ Real cosg=cos(ucell_angles[0]),sing=sin(ucell_angles[0]);
+ ucell_vec1=geom::Vec3(ucell_size[0],0,0);
+ ucell_vec2=ucell_size[1]*geom::Vec3(cosg,sing,0);
+ ucell_vec3=ucell_size[2]*geom::Vec3(cosb,(cosa-cosb*cosg)/sing,\
+ pow(1-(cosa*cosa+cosb*cosb-2.*cosa*cosb*cosg)/(sing*sing),0.5));
+ ucell_vec.push_back(ucell_vec1);
+ ucell_vec.push_back(ucell_vec2);
+ ucell_vec.push_back(ucell_vec3);
+ return ucell_vec;
+}
-Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec){
+Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& ucell_size){
Vec3 v;
Real r;
for (int i=0; i<3; i++) {
- r=(v1[i]-box_center[i])/basis_vec[i];
+ r=(v1[i]-box_center[i])/ucell_size[i];
r=(r > 0.0) ? std::floor(r + 0.5) : std::ceil(r - 0.5);
- v[i]=v1[i]-basis_vec[i]*r;
+ v[i]=v1[i]-ucell_size[i]*r;
}
return v;
}
-Vec3List WrapVec3List(const Vec3List& vl, const Vec3& box_center,const Vec3& basis_vec){
+Vec3List WrapVec3List(const Vec3List& vl, const Vec3& box_center,const Vec3& ucell_size){
Vec3List vl_out;
vl_out.reserve(vl_out.size());
for (Vec3List::const_iterator v1=vl.begin(),e=vl.end();v1!=e ; v1++) {
- vl_out.push_back(WrapVec3(*v1,box_center,basis_vec));
+ vl_out.push_back(WrapVec3(*v1,box_center,ucell_size));
}
return vl_out;
}
+Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& ucell_size,const Vec3& ucell_angles){
+ Vec3List vl=CalculateUnitCellVectors(ucell_size,ucell_angles);
+ Vec3 v=v1-box_center,v_wrapped=v1,r;
+ for (int i=0; i<3; i++) {
+ r[2-i]=v[2-i]/vl[2-i][2-i];
+ v=v-r[2-i]*vl[2-i];
+ r[2-i]=(r[2-i] > 0.0) ? std::floor(r[2-i] + 0.5) : std::ceil(r[2-i] - 0.5);
+ v_wrapped=v_wrapped-vl[2-i]*r[2-i];
+ }
+ return v_wrapped;
+}
+
+Vec3List WrapVec3List(const Vec3List& vl, const Vec3& box_center,const Vec3& ucell_size,const Vec3& ucell_angles){
+ Vec3List vl_out;
+ vl_out.reserve(vl_out.size());
+ for (Vec3List::const_iterator v1=vl.begin(),e=vl.end();v1!=e ; v1++) {
+ vl_out.push_back(WrapVec3(*v1,box_center,ucell_size,ucell_angles));
+ }
+ return vl_out;
+}
} // ns
diff --git a/modules/geom/src/vecmat3_op.hh b/modules/geom/src/vecmat3_op.hh
index b4a18d3cb965e4d30cec4820cca9abb38c592472..fbaaec161b20ba7ddc9112c89bda93295a2ec407 100644
--- a/modules/geom/src/vecmat3_op.hh
+++ b/modules/geom/src/vecmat3_op.hh
@@ -195,35 +195,39 @@ inline Real Distance(const Vec3& p1, const Vec3& p2)
}
-//! return the squared distance between two points with periodic boundaries in x,y,z given in basis_vec
-inline Real Distance2WithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_vec){
+//! return the squared distance between two points with periodic boundaries in x,y,z given in ucell_size
+inline Real Distance2WithPBC(const Vec3& v1, const Vec3& v2, const Vec3& ucell_size){
Vec3 v;
v=v1-v2;
for (int i=0; i<3; i++) {
- if (std::fabs(v[i])>basis_vec[i]/2.){
- v[i]=std::fabs(v[i])-basis_vec[i]*int(std::fabs(v[i])/basis_vec[i]+0.5);
+ if (std::fabs(v[i])>ucell_size[i]/2.){
+ v[i]=std::fabs(v[i])-ucell_size[i]*int(std::fabs(v[i])/ucell_size[i]+0.5);
}
}
return Length2(v);
}
-//! return the distance between two points with periodic boundaries in x,y,z given in basis_vec
-inline Real DistanceWithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_vec){
- return sqrt(Distance2WithPBC(v1, v2, basis_vec));
+//! return the distance between two points with periodic boundaries in x,y,z given in ucell_size
+inline Real DistanceWithPBC(const Vec3& v1, const Vec3& v2, const Vec3& ucell_size){
+ return sqrt(Distance2WithPBC(v1, v2, ucell_size));
}
//! returns the minimal distance between the points in two Vec3List
Real DLLEXPORT_OST_GEOM MinDistance(const Vec3List& l1, const Vec3List& l2);
//! returns the minimal distance between the points in two Vec3List
-// with periodic boundaries in x,y,z given in basis_vec
-Real DLLEXPORT_OST_GEOM MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec);
+// with periodic boundaries in x,y,z given in ucell_size
+Real DLLEXPORT_OST_GEOM MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& ucell_size);
//! returns the indices index1, index2 corresponding to the points in
//! the Vec3List l1 and l2 having the minimal distance.
std::vector<unsigned int> DLLEXPORT_OST_GEOM MinDistanceIndices(const Vec3List& l1, const Vec3List& l2);
-
+//! Calculates the Unit Cell Vectors from their sizes and angles (given as Vec3(gamma,beta,alpha)).
+Vec3List DLLEXPORT_OST_GEOM CalculateUnitCellVectors(const Vec3& ucell_size, const Vec3& ucell_angles);
//!wraps a vector in a box with periodic boundaries
-Vec3 DLLEXPORT_OST_GEOM WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec);
-//!wraps all the verctors in a Vec3List in a box with periodic boundaries
-Vec3List DLLEXPORT_OST_GEOM WrapVec3List(const Vec3List& vl,const Vec3& box_center,const Vec3& basis_vec);
-
+Vec3 DLLEXPORT_OST_GEOM WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& ucell_size);
+//!wraps all the vectors in a Vec3List in a box with periodic boundaries
+Vec3List DLLEXPORT_OST_GEOM WrapVec3List(const Vec3List& vl,const Vec3& box_center,const Vec3& ucell_size);
+//!wraps a vector in a non-rothogonal box with periodic boundaries
+Vec3 DLLEXPORT_OST_GEOM WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& ucell_size,const Vec3& ucell_angles);
+//!wraps all the vectors in a Vec3List in a non-rothogonal box with periodic boundaries
+Vec3List DLLEXPORT_OST_GEOM WrapVec3List(const Vec3List& vl,const Vec3& box_center,const Vec3& ucell_size,const Vec3& ucell_angles);
} // ns
diff --git a/modules/geom/tests/test_transform.cc b/modules/geom/tests/test_transform.cc
index ae27fd594b71432bfa271fbcf5fecce52c9e5594..8ac2ce97b579fe2e5c854c31b6a348e9e0a0910c 100644
--- a/modules/geom/tests/test_transform.cc
+++ b/modules/geom/tests/test_transform.cc
@@ -44,17 +44,6 @@ BOOST_AUTO_TEST_CASE(test_transform_essentials)
tf.SetTrans(tra);
tf.SetCenter(cen);
- Mat4 tmat =
- geom::Mat4(1.0,0.0,0.0,tra[0],
- 0.0,1.0,0.0,tra[1],
- 0.0,0.0,1.0,tra[2],
- 0.0,0.0,0.0,1.0) *
- geom::Mat4(rot) *
- geom::Mat4(1.0,0.0,0.0,-cen[0],
- 0.0,1.0,0.0,-cen[1],
- 0.0,0.0,1.0,-cen[2],
- 0.0,0.0,0.0,1.0);
-
BOOST_CHECK_EQUAL(tf.GetRot(), rot);
BOOST_CHECK_EQUAL(tf.GetCenter(), cen);
BOOST_CHECK_EQUAL(tf.GetTrans(), tra);
diff --git a/modules/gfx/pymod/__init__.py b/modules/gfx/pymod/__init__.py
index 7cb3cc51452eca9c2a1507b9e7b692e591ba2aa1..d1b59f1a7cd7e59807cd7d16b7c3ce5a68d623e8 100644
--- a/modules/gfx/pymod/__init__.py
+++ b/modules/gfx/pymod/__init__.py
@@ -407,3 +407,15 @@ def ColladaExporter(file,scale=1.0,to_origin=True):
e.to_origin=to_origin
return e
+def _go_get_vis(go):
+ return go.IsVisible()
+
+def _go_set_vis(go,flag):
+ if flag:
+ go.Show()
+ else:
+ go.Hide()
+
+GfxObj.visible=property(_go_get_vis,_go_set_vis)
+
+
diff --git a/modules/gfx/pymod/export_entity.cc b/modules/gfx/pymod/export_entity.cc
index d8ee109298405de304b4b7e178671b1f4388141f..0a3ca83624e815e57878fe8a92680d42e46912a6 100644
--- a/modules/gfx/pymod/export_entity.cc
+++ b/modules/gfx/pymod/export_entity.cc
@@ -236,6 +236,7 @@ void (Entity::*set_rm2)(RenderMode::Type)=&Entity::SetRenderMode;
void (Entity::*set_vis1)(const mol::EntityView&, bool)=&Entity::SetVisible;
void (Entity::*set_vis2)(const String&, bool)=&Entity::SetVisible;
+
RenderOptionsPtr ent_trace_opts(Entity* ent)
{
return ent->GetOptions(RenderMode::TRACE);
@@ -339,7 +340,6 @@ void export_Entity()
.def("SetBlurFactors",&Entity::SetBlurFactors)
.def("SetBlur",&Entity::SetBlur)
.def("GetBoundingBox",&Entity::GetBoundingBox)
- .add_property("bounding_box",&Entity::GetBoundingBox)
.def("SetSelection",&Entity::SetSelection)
.def("GetSelection",&Entity::GetSelection)
.add_property("selection", &Entity::GetSelection,
diff --git a/modules/gfx/pymod/export_map.cc b/modules/gfx/pymod/export_map.cc
index 6bfc908656f6f7f692a1a116556bd1ecc0d7e1b8..ea334ead8a8e3dc69808af841d26c1fee46d805a 100644
--- a/modules/gfx/pymod/export_map.cc
+++ b/modules/gfx/pymod/export_map.cc
@@ -47,6 +47,9 @@ void ms_color_by_04(MapSlab *s, const Color& c1, const Color& c2)
s->ColorBy(c1,c2);
}
+bool get_gds() {return MapIso::global_downsampling_flag;}
+void set_gds(bool f) {MapIso::global_downsampling_flag=f;}
+
} // anon ns
void export_Map()
@@ -82,6 +85,7 @@ void export_Map()
.def("SetColor", &MapIso::SetColor)
.def("GetColor", &MapIso::GetColor, return_value_policy<copy_const_reference>())
.def("SetDebugOctree", &MapIso::SetDebugOctree)
+ .add_static_property("global_downsampling_flag",get_gds,set_gds)
;
class_<MapSlab, bases<GfxObj>, boost::shared_ptr<MapSlab>,
diff --git a/modules/gfx/src/bitmap_io.cc b/modules/gfx/src/bitmap_io.cc
index ab42f9de5a67242ee9edf51a705c6cec4a078121..4245c32ec0b7b70daf17f56f73349b10cd39dfa8 100644
--- a/modules/gfx/src/bitmap_io.cc
+++ b/modules/gfx/src/bitmap_io.cc
@@ -114,7 +114,7 @@ Bitmap import_png(const String& filename)
int png_transforms;
png_bytep *row_pointers;
png_uint_32 row,column,chn;
- png_uint_32 width,height,bpp;
+ png_uint_32 width,height;
if((fp=fopen(filename.c_str(),"rb"))==NULL) {
LOG_ERROR("error opening " << filename);
@@ -158,8 +158,7 @@ Bitmap import_png(const String& filename)
width=(unsigned int)png_get_image_width(png_ptr, info_ptr);
height=(unsigned int)png_get_image_height(png_ptr, info_ptr);
- bpp=(unsigned int)png_get_bit_depth(png_ptr,info_ptr);
-
+
boost::shared_array<unsigned char> data(new unsigned char[width*height*channels]);
row_pointers = png_get_rows(png_ptr, info_ptr);
diff --git a/modules/gfx/src/entity.cc b/modules/gfx/src/entity.cc
index c14e4e16024055a383ae500611f58ae9d77e6f95..6b8468a249a469a4e256f62834d91ba74aae36d8 100644
--- a/modules/gfx/src/entity.cc
+++ b/modules/gfx/src/entity.cc
@@ -135,6 +135,10 @@ Entity::Entity(const String& name,
}
+Entity::~Entity()
+{
+}
+
impl::EntityRenderer* Entity::GetOrCreateRenderer(RenderMode::Type rm)
{
RendererMap::iterator rit = renderer_.find(rm);
@@ -186,11 +190,11 @@ void Entity::init(RenderMode::Type rm)
render_mode_=rm;
trace_.ResetView(this->GetView());
sel_=this->GetView().CreateEmptyView();
- impl::EntityRenderer* r=this->GetOrCreateRenderer(rm);
- if(!r) return;
- r->AddView(this->GetView());
- r->UpdateViews();
+ impl::EntityRenderer* renderer=this->GetOrCreateRenderer(rm);
+
+ renderer->AddView(this->GetView());
+ renderer->UpdateViews();
set_static_max_rad();
Rebuild();
@@ -297,13 +301,17 @@ bool Entity::UpdateIfNeeded() const
for (RendererMap::iterator i=renderer_.begin(),
e=renderer_.end(); i!=e; ++i) {
EntityRenderer* renderer =i->second;
- if (renderer->IsEnabled() && renderer->HasDataToRender()) {
- if (renderer->IsDirty()) {
- renderer->PrepareRendering();
- updated=true;
- }
- renderer->VA().SetOpacity(opacity_);
+ if (!renderer->IsEnabled())
+ continue;
+ renderer->UpdateViews();
+ if (!renderer->HasDataToRender())
+ continue;
+
+ if (renderer->IsDirty()) {
+ renderer->PrepareRendering();
+ updated=true;
}
+ renderer->VA().SetOpacity(opacity_);
}
if (updated) {
this->CacheBoundingBox();
@@ -1135,22 +1143,21 @@ bool Entity::GetSeqHack() const
void Entity::do_update_view() const
{
- // also signals an update in positions
- if (update_view_) {
- update_view_=false;
- cached_view_=qv_.GetEntityView();
- trace_.ResetView(cached_view_);
- for (RendererMap::iterator i=renderer_.begin(),
- e=renderer_.end(); i!=e; ++i) {
- impl::EntityRenderer* r=i->second;
- if (r->IsEnabled() && r->HasDataToRender()) {
- r->ClearViews();
- r->AddView(cached_view_);
- r->UpdateViews();
- r->FlagPositionsDirty();
- r->PrepareRendering();
- }
- }
+ if (!update_view_)
+ return;
+ update_view_=false;
+ cached_view_=qv_.GetEntityView();
+ trace_.ResetView(cached_view_);
+ for (RendererMap::iterator
+ i=renderer_.begin(), e=renderer_.end(); i!=e; ++i) {
+ impl::EntityRenderer* renderer=i->second;
+ if (!renderer->IsEnabled() || !renderer->HasDataToRender())
+ continue;
+ renderer->ClearViews();
+ renderer->AddView(cached_view_);
+ renderer->UpdateViews();
+ renderer->FlagPositionsDirty();
+ renderer->PrepareRendering();
}
}
diff --git a/modules/gfx/src/entity.hh b/modules/gfx/src/entity.hh
index a9687c81c6e5d2f7c8da4b3ac67210eb7285fc3d..9106e260769091b06aac55bc9f346514c73f5e8a 100644
--- a/modules/gfx/src/entity.hh
+++ b/modules/gfx/src/entity.hh
@@ -89,6 +89,7 @@ public:
Entity(const String& name,
RenderMode::Type m,
const mol::EntityView& ev);
+ virtual ~Entity();
virtual geom::AlignedCuboid GetBoundingBox(bool use_tf=false) const;
@@ -363,13 +364,13 @@ private:
/// \example load_and_display.py
///
-/// Shows how to display one \ref Entity "entity" with several render modes
+/// Shows how to display one \ref ost::gfx::Entity "entity" with several render modes
/// at once. The sidechains are displayed simple mode, whereas the backbone is
/// displayed with smooth lines.
/// \example rendermodes.py
///
-/// Shows how to switch between different \ref RenderMode "render modes" and
+/// Shows how to switch between different \ref ost::gfx::RenderMode "render modes" and
/// explains some of the rendermode parameters.
/// \sa \ref load_and_display.py "Loading and Displaying an Entity"
@@ -386,7 +387,7 @@ private:
/// \example color_by_property.py
///
-/// Color \ref Entity "graphical entity" by property using a gradient
+/// Color \ref ost::gfx::Entity "graphical entity" by property using a gradient
/// \sa \ref gradient.py "Gradient Example"
}} // ns
diff --git a/modules/gfx/src/entity_fw.hh b/modules/gfx/src/entity_fw.hh
index 5e00ae29cd7ffb15b3c67642cc176d341f6d1586..192ad391322da684abb6590365c8e2b89530ea56 100644
--- a/modules/gfx/src/entity_fw.hh
+++ b/modules/gfx/src/entity_fw.hh
@@ -20,11 +20,13 @@
#define OST_GFX_ENTITY_FW_HH
#include <boost/shared_ptr.hpp>
+#include <boost/weak_ptr.hpp>
namespace ost { namespace gfx {
class Entity;
typedef boost::shared_ptr<Entity> EntityP;
+typedef boost::weak_ptr<Entity> EntityW;
}}
diff --git a/modules/gfx/src/exporter.cc b/modules/gfx/src/exporter.cc
index 28dbd9b692365f4cfd1590d584a92a0ebbac7477..5100490c1d1ed852b9788f05d57ad3a05e38beaa 100644
--- a/modules/gfx/src/exporter.cc
+++ b/modules/gfx/src/exporter.cc
@@ -28,7 +28,6 @@ namespace ost { namespace gfx {
normal_tf_=geom::Mat3();
geom::Mat4 Tmat,Rmat,Smat,Cmat;
if(to_origin_) {
- geom::Vec3 trans=scene->GetTransform().GetTrans();
geom::Vec3 cen=scene->GetTransform().GetCenter();
vertex_tf_=geom::Mat4(scene->GetTransform().GetRot()) *
geom::Mat4(scale_, 0.0, 0.0, 0.0,
diff --git a/modules/gfx/src/gfx_node.cc b/modules/gfx/src/gfx_node.cc
index 59b44d162d991620c77bd58ad300f49f5d3fc8de..657068c9ef836eeb73db31a956fa627d1b1e321a 100644
--- a/modules/gfx/src/gfx_node.cc
+++ b/modules/gfx/src/gfx_node.cc
@@ -33,7 +33,8 @@ GfxNode::GfxNode(const String& name):
{}
GfxNode::~GfxNode()
-{}
+{
+}
GfxNode::GfxNode(const GfxNode& o) {}
diff --git a/modules/gfx/src/impl/backbone_trace.cc b/modules/gfx/src/impl/backbone_trace.cc
index efcd761a5304f9f6c03ffe5362d7ee976dda8d2e..da56ae1796004e52c4ceca18cc8e1df287035be5 100644
--- a/modules/gfx/src/impl/backbone_trace.cc
+++ b/modules/gfx/src/impl/backbone_trace.cc
@@ -123,13 +123,15 @@ private:
BackboneTrace::BackboneTrace():
view_(),
node_list_list_(),
- seq_hack_(false)
+ seq_hack_(false),
+ twist_hack_(false)
{}
BackboneTrace::BackboneTrace(const mol::EntityView& ent):
view_(ent),
node_list_list_(),
- seq_hack_(false)
+ seq_hack_(false),
+ twist_hack_(false)
{
Rebuild();
}
@@ -210,8 +212,6 @@ void BackboneTrace::PrepList(NodeEntryList& nelist) const
// start loop with the second residue
unsigned int i=1;
for(;i<nelist.size()-1;++i) {
- geom::Vec3 p10=p0-p1;
- geom::Vec3 p12=p2-p1;
dir=geom::Normalize(p2-p0);
e1->direction = dir;
orth=geom::Normalize(geom::Cross(dir,e1->normal));
diff --git a/modules/gfx/src/impl/cartoon_renderer.cc b/modules/gfx/src/impl/cartoon_renderer.cc
index f9eee510679686554c1f7bfac9fd6550f7e3f837..00894483df3e7c0e3433463810fb403a80a84a46 100644
--- a/modules/gfx/src/impl/cartoon_renderer.cc
+++ b/modules/gfx/src/impl/cartoon_renderer.cc
@@ -23,10 +23,7 @@
#include "cartoon_renderer.hh"
-#include <Eigen/Core>
-#include <Eigen/Array>
#include <Eigen/SVD>
-#include <Eigen/LU>
#include <ost/gfx/entity.hh>
#include <ost/gfx/impl/tabulated_trig.hh>
@@ -138,7 +135,7 @@ namespace {
A.row(i)=to_eigen(points[i]-cen);
}
- Eigen::SVD<EMatX> svd(A);
+ Eigen::JacobiSVD<EMatX> svd(A,Eigen::ComputeThinV);
EMatX V=svd.matrixV();
geom::Vec3 ax(V(0,0),V(1,0),V(2,0));
diff --git a/modules/gfx/src/impl/entity_detail.cc b/modules/gfx/src/impl/entity_detail.cc
index 407654cfcfa514cc379a240ac1a68bc6d131a077..7e7f65989bca37bfdbba9ef8c68e2208492cfec9 100644
--- a/modules/gfx/src/impl/entity_detail.cc
+++ b/modules/gfx/src/impl/entity_detail.cc
@@ -311,8 +311,6 @@ SplineEntryList Spline::Generate(const SplineEntryList& entry_list, int nsub, ui
sublist.at(0).direction=geom::Normalize(p1-p0);
unsigned int i=1;
for(;i<sublist.size()-1;++i) {
- geom::Vec3 p10 = p0-p1;
- geom::Vec3 p12 = p2-p1;
geom::Vec3 dir=geom::Normalize(p2-p0);
sublist.at(i).direction=dir;
geom::Vec3 orth=geom::Normalize(geom::Cross(dir,sublist[i].normal));
diff --git a/modules/gfx/src/map_iso.cc b/modules/gfx/src/map_iso.cc
index 7a2c5160c435badb6bd25267759c6fd9a119ebed..fdcf0a3fe95724e0d5082d144b25835fb2615378 100644
--- a/modules/gfx/src/map_iso.cc
+++ b/modules/gfx/src/map_iso.cc
@@ -59,6 +59,8 @@ namespace ost {
namespace gfx {
+bool MapIso::global_downsampling_flag=true;
+
MapIso::MapIso(const String& name, const img::MapHandle& mh,
float level, uint a):
GfxObj(name),
@@ -71,7 +73,6 @@ MapIso::MapIso(const String& name, const img::MapHandle& mh,
histogram_bin_count_(100),
level_(level),
normals_calculated_(false),
- alg_(a),
debug_octree_(false),
color_(1.0,1.0,1.0),
bb_(),
@@ -412,6 +413,7 @@ bool MapIso::IsDownsampledMapAvailable() const
img::ImageHandle MapIso::DownsampleMap(const img::ImageHandle& mh)
{
+ if(!MapIso::global_downsampling_flag) return mh;
uint downsampling_fact = compute_downsampling_fact(mh);
img:: ImageHandle ret_mh = mh;
if (downsampling_fact != 1) {
diff --git a/modules/gfx/src/map_iso.hh b/modules/gfx/src/map_iso.hh
index bb47a129c1d0b04d223387dba693fc89031b12a0..cee9025fa6e60598d3a08df3642cf7c4fff8781b 100644
--- a/modules/gfx/src/map_iso.hh
+++ b/modules/gfx/src/map_iso.hh
@@ -144,6 +144,8 @@ public:
/// \brief checks is the octree needs to be rebuilt
bool IfOctreeDirty() const;
+ static bool global_downsampling_flag;
+
protected:
void UpdateRenderParams();
void CalculateStat() const;
@@ -163,7 +165,6 @@ private:
int histogram_bin_count_;
float level_;
bool normals_calculated_;
- uint alg_;
float smoothf_;
float min_;
float max_;
diff --git a/modules/gfx/src/render_options/render_options.cc b/modules/gfx/src/render_options/render_options.cc
index 0c5597b33648663ad1afc18f853700cbceabe2a6..5d8e7a72c5a1c11c034d1c2ac4e4a83667d8070f 100644
--- a/modules/gfx/src/render_options/render_options.cc
+++ b/modules/gfx/src/render_options/render_options.cc
@@ -30,33 +30,31 @@ RenderOptions::RenderOptions(){}
bool RenderOptions::AddObserver(EntityP entity)
{
- if((std::find( this->observers_.begin(), this->observers_.end(), entity )) == this->observers_.end())
- {
- this->observers_.push_back( entity );
- return true;
+ for (EntityWObservers::const_iterator
+ i = observers_.begin(), e = observers_.end(); i != e; ++i) {
+ if (i->lock() == entity)
+ return false;
}
- return false;
+ observers_.push_back(entity);
+ return true;
}
bool RenderOptions::RemoveObserver(EntityP entity)
{
- EntityPObservers::iterator found = std::find( this->observers_.begin(), this->observers_.end(), entity);
- if( found != this->observers_.end() ){
-
- this->observers_.erase(found);
- return true;
+ for (EntityWObservers::iterator
+ i = observers_.begin(), e = observers_.end(); i != e; ++i) {
+ if (i->lock() == entity)
+ observers_.erase(i);
+ return true;
}
return false;
}
void RenderOptions::NotifyStateChange()
{
- InputEvent event = InputEvent(INPUT_DEVICE_MOUSE,INPUT_COMMAND_REBUILD,0);
- EntityPObservers::const_iterator observers_it = this->observers_.begin() ;
- while( observers_it != this->observers_.end() )
- {
- ( *observers_it )->OptionsChanged(this->GetRenderMode()) ;
- observers_it++;
+ for (EntityWObservers::iterator
+ i = observers_.begin(), e = observers_.end(); i != e; ++i) {
+ i->lock()->OptionsChanged(this->GetRenderMode());
}
}
diff --git a/modules/gfx/src/render_options/render_options.hh b/modules/gfx/src/render_options/render_options.hh
index 0c2515bdb6ec8aa830d7dca2023deeac0e310858..ce9dfc60209876eea3a142f08599022c86e041a2 100644
--- a/modules/gfx/src/render_options/render_options.hh
+++ b/modules/gfx/src/render_options/render_options.hh
@@ -51,8 +51,8 @@ public:
void NotifyStateChange();
private:
- typedef std::vector< EntityP > EntityPObservers;
- EntityPObservers observers_;
+ typedef std::vector< EntityW > EntityWObservers;
+ EntityWObservers observers_;
};
diff --git a/modules/gfx/src/scene.cc b/modules/gfx/src/scene.cc
index 5c96c47ad84bdbd9cc1198c0531f4669567e2a9a..5c1e9cbb7149115b219ceccc8e88698fa5e70e97 100644
--- a/modules/gfx/src/scene.cc
+++ b/modules/gfx/src/scene.cc
@@ -1058,7 +1058,7 @@ void Scene::Remove(const String& name)
if(fn.node) {
root_node_->Remove(name);
if(GfxObjP go = dyn_cast<GfxObj>(fn.node)) {
- this->NotifyObservers(bind(&SceneObserver::NodeRemoved, _1,go));
+ this->NotifyObservers(bind(&SceneObserver::NodeRemoved, _1, go));
}
}
}
diff --git a/modules/gfx/src/scene.hh b/modules/gfx/src/scene.hh
index 89717de74999e157aeae36443d60333a9e479018..53a935c10f8ff5d21e959f231646d27e8b26c242 100644
--- a/modules/gfx/src/scene.hh
+++ b/modules/gfx/src/scene.hh
@@ -298,7 +298,6 @@ class DLLEXPORT_OST_GFX Scene {
void Export(const String& fname, unsigned int w,
unsigned int h, bool transparent=false);
/// \brief export into bitmap, using multisample anti-aliasing
- /// \ref Scene::StartOfffscreenMode(unsigned int, unsigned int, int) for more detail
void Export(const String& fname, unsigned int w,
unsigned int h, int max_samples, bool transparent=false);
@@ -308,7 +307,7 @@ class DLLEXPORT_OST_GFX Scene {
/// \brief export scene into povray files named fname.pov and fname.inc
void ExportPov(const std::string& fname, const std::string& wdir=".");
- /// \rbrief export scene via exporter
+ /// \brief export scene via exporter
void Export(Exporter* ex) const;
//@}
diff --git a/modules/gfx/tests/test_ent_pov_export.cc b/modules/gfx/tests/test_ent_pov_export.cc
index b5c409f9628a110cdfb3f85880f29fb791c517a7..c7730806a1476ce02728b42bcc194c6353908b3d 100644
--- a/modules/gfx/tests/test_ent_pov_export.cc
+++ b/modules/gfx/tests/test_ent_pov_export.cc
@@ -22,7 +22,7 @@
*/
#include <fstream>
-#include <ost/io/load_entity.hh>
+#include <ost/io/mol/load_entity.hh>
#include <ost/gfx/scene.hh>
#include <ost/gfx/entity.hh>
diff --git a/modules/gui/pymod/CMakeLists.txt b/modules/gui/pymod/CMakeLists.txt
index 87a9c63374927f743fdc21d2c03d9d80a1235a3e..3c9e13e8a806730b0452a1b56828ab94a8121ac1 100644
--- a/modules/gui/pymod/CMakeLists.txt
+++ b/modules/gui/pymod/CMakeLists.txt
@@ -79,7 +79,7 @@ set(OST_GUI_PYMOD_MODULES
init_menubar.py
init_spacenav.py
init_splash.py
- traj.py
+ trajectory_viewer.py
helpwidget.py
table.py
gosty_startup.py
diff --git a/modules/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index 7848916906ee02d47ef8d685c1551051a4e7fd21..227a0db3b969c4cf6f2b8ee91085874cb0b8d9ca 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -16,12 +16,13 @@
# along with this library; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
+import ost.gui.trajectory_viewer
from _ost_gui import *
import sip
## \brief Opens a DataViewer
-# \sa \ref fft_li.py "View Fourier Transform Example" \sa \ref modulate_image.py "Modulate Image Example"
+# \sa \example fft_li.py "View Fourier Transform Example" \sa \ref modulate_image.py "Modulate Image Example"
def _close_event_override_(event):
print "close event"
def _set_data_override_(data):
diff --git a/modules/gui/pymod/data_viewer_proxy.cc b/modules/gui/pymod/data_viewer_proxy.cc
index 9ee1c099aff32fdf1be85223af69f5bd4c89499e..d4d418e1f378588c09dfed18f7541788df47b07a 100644
--- a/modules/gui/pymod/data_viewer_proxy.cc
+++ b/modules/gui/pymod/data_viewer_proxy.cc
@@ -22,9 +22,9 @@
Authors: Ansgar Philippsen, Andreas Schenk
*/
-#include <ost/message.hh>
#include "data_viewer_proxy.hh"
+#include <ost/message.hh>
namespace ost { namespace img { namespace gui {
@@ -154,6 +154,11 @@ void DataViewerProxy::ClearOverlays()
viewer()->ClearOverlays();
}
+void DataViewerProxy::ClearActiveOverlay()
+{
+ viewer()->ClearActiveOverlay();
+}
+
OverlayManagerPtr DataViewerProxy::GetOverlayManager() const
{
return viewer()->GetOverlayManager();
@@ -185,6 +190,10 @@ void DataViewerProxy::Hide()
viewer()->hide();
}
+object DataViewerProxy::GetButtonGroup()
+{
+ return ost::gui::get_py_qobject<QButtonGroup>(viewer()->GetButtonGroup());
+}
object DataViewerProxy::GetQObject(){
return ost::gui::get_py_qobject<DataViewer>(viewer());
diff --git a/modules/gui/pymod/data_viewer_proxy.hh b/modules/gui/pymod/data_viewer_proxy.hh
index 49e764b65e15271db14331f2772c2f64969ead1c..096485b406fa07b36082936fa0c966e9e862e155 100644
--- a/modules/gui/pymod/data_viewer_proxy.hh
+++ b/modules/gui/pymod/data_viewer_proxy.hh
@@ -83,6 +83,7 @@ public:
int AddOverlay(const OverlayPtr& ov, bool make_active=true);
OverlayManagerPtr GetOverlayManager() const;
void ClearOverlays();
+ void ClearActiveOverlay();
void AddDockWidget(QWidget* w, const QString& name, bool shown=true, int area=2);
void RemoveDockWidget(QWidget* w);
@@ -96,7 +97,7 @@ public:
//Vec3 GetClickedPosition();
void Hide();
-
+ object GetButtonGroup();
object GetQObject();
protected:
QPointer<DataViewer> viewer_ptr_;
diff --git a/modules/gui/pymod/export_data_viewer.cc b/modules/gui/pymod/export_data_viewer.cc
index e1b047d84cd09022b75a953bbeb25fdf631304d5..d5e03fe5e3888bd86c74ba531f5e01afdcc4c796 100644
--- a/modules/gui/pymod/export_data_viewer.cc
+++ b/modules/gui/pymod/export_data_viewer.cc
@@ -66,6 +66,7 @@ void export_data_viewer()
.def("Renormalize",&DataViewerProxy::Renormalize)
.def("AddOverlay",&DataViewerProxy::AddOverlay,o_AddOverlay())
.def("ClearOverlays",&DataViewerProxy::ClearOverlays)
+ .def("ClearActiveOverlay",&DataViewerProxy::ClearActiveOverlay)
.def("GetSelection",&DataViewerProxy::GetSelection)
.def("SetSelection",&DataViewerProxy::SetSelection)
.def("UpdateView",&DataViewerProxy::UpdateView)
@@ -99,6 +100,7 @@ void export_data_viewer()
.def("SetOffset", &DataViewerProxy::SetOffset)
.def("GetOffset", &DataViewerProxy::GetOffset)
.add_property("offset", &DataViewerProxy::GetOffset, &DataViewerProxy::SetOffset)
+ .def("GetButtonGroup", &DataViewerProxy::GetButtonGroup)
.def("GetQObject",&DataViewerProxy::GetQObject)
.add_property("qobject",&DataViewerProxy::GetQObject)
diff --git a/modules/gui/pymod/export_gosty.cc b/modules/gui/pymod/export_gosty.cc
index adc5594a8454dfb71042755a10c28e1818229e5d..ef7ee6777b43c63ad6c0e8ce0e296b6a0c73c48c 100644
--- a/modules/gui/pymod/export_gosty.cc
+++ b/modules/gui/pymod/export_gosty.cc
@@ -54,8 +54,11 @@ DataViewerProxyPtr app_create_data_viewer2(GostyApp* app, const ost::img::ImageH
{
return DataViewerProxyPtr(new DataViewerProxy(app->CreateDataViewer(d)));
}
+DataViewerProxyPtr app_create_data_viewer3(GostyApp* app, const ost::img::ImageHandle& d, const QString& name, int noparent)
+{
+ return DataViewerProxyPtr(new DataViewerProxy(app->CreateDataViewer(d,name,noparent)));
+}
#endif
-
}
void app_add_widget_to_app_a(GostyApp* app, const QString& ident,
@@ -115,6 +118,7 @@ void export_Gosty()
#if OST_IMG_ENABLED
.def("CreateDataViewer", &app_create_data_viewer1)
.def("CreateDataViewer", &app_create_data_viewer2)
+ .def("CreateDataViewer", &app_create_data_viewer3)
#endif
.def("ProcessEvents", &GostyApp::ProcessEvents)
.add_property("perspective",
diff --git a/modules/gui/pymod/traj.py b/modules/gui/pymod/traj.py
deleted file mode 100644
index 1fcb1c77959528cdda00f05140f89902d4c86863..0000000000000000000000000000000000000000
--- a/modules/gui/pymod/traj.py
+++ /dev/null
@@ -1,143 +0,0 @@
-#-------------------------------------------------------------------------------
-# This file is part of the OpenStructure project <www.openstructure.org>
-#
-# Copyright (C) 2008-2011 by the OpenStructure authors
-#
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation; either version 3.0 of the License, or (at your option)
-# any later version.
-# This library is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-#-------------------------------------------------------------------------------
-from PyQt4.QtCore import *
-from PyQt4.QtGui import *
-from ost import *
-
-class TrajWidget(QWidget):
- def __init__(self, traj=None, render_mode=gfx.SIMPLE, sel='', parent=None):
- QWidget.__init__(self, parent, Qt.Tool)
- self.render_mode=render_mode
- vb=QVBoxLayout()
- hb=QHBoxLayout()
- hb2=QHBoxLayout()
- self.selection=sel
- self.callback=None
- self._slider=QSlider(self)
- self._slider.setOrientation(Qt.Horizontal)
- self._speed_slider=QSlider(self)
- self._speed_slider.setOrientation(Qt.Horizontal)
- self._play=QToolButton(self)
- self._repeat=QCheckBox(self)
- self._frame=QLabel(self)
- self._frameNo=QLabel(self)
- self._frameEnd=QLabel(self)
- self._repeat.setText('Repeat')
- self._slider.setTracking(True)
- self._play.setText('Play')
- self._play.setCheckable(True)
- self._frame.setText('Frame: ')
- self._frameNo.setNum(0)
- self._frameNo.setAlignment(Qt.AlignRight)
- self._frameEnd.setText('/ '+ str(traj.GetFrameCount()-1))
- self._frameEnd.setAlignment(Qt.AlignLeft)
- self._speed_slider.setTracking(True)
- self._speed_slider.setRange(-1000,-1)
- self._speed_slider.value=-100
- hb.addWidget(self._play)
- hb.addWidget(self._repeat)
- hb2.addWidget(self._frame)
- hb2.addWidget(self._frameNo)
- hb2.addWidget(self._frameEnd)
- hb2.addWidget(self._speed_slider)
- self.setLayout(vb)
- vb.addLayout(hb)
- vb.addWidget(self._slider)
- vb.addLayout(hb2)
- self.traj=traj
- self.time=1
- QObject.connect(self._play, SIGNAL('toggled(bool)'),
- self._TogglePlay)
- QObject.connect(self._slider, SIGNAL('valueChanged(int)'),
- self._SliderValueChanged)
- QObject.connect(self._speed_slider,SIGNAL('valueChanged(int)'),self._SpeedSliderValChanged)
-
- def _SpeedSliderValChanged(self,speed_pos):
- self.time=-speed_pos
- if self._play.isChecked():
- self._TogglePlay(False)
- self._TogglePlay(True)
-
- def _SetTime(self,t):
- self.time=t
- self._speed_slider.setSliderPosition(-t)
- if self._play.isChecked():
- self._TogglePlay(False)
- self._TogglePlay(True)
-
- def _SliderValueChanged(self, pos):
- self.current_frame=pos
- self._traj.CopyFrame(self.current_frame)
- self.gfx_entity.UpdatePositions()
-
- def _GetCurrentFrame(self):
- return self._slider.sliderPosition()
-
- def _SetCurrentFrame(self, pos):
- if self._slider.maximum()<pos:
- if self._repeat.isChecked():
- pos=0
- else:
- pos=self._slider.maximum()
- self._slider.setSliderPosition(pos)
- self._frameNo.setNum(pos)
-
- current_frame=property(_GetCurrentFrame, _SetCurrentFrame)
-
- def timerEvent(self, event):
- self.gfx_entity.BlurSnapshot()
- self.current_frame+=1
- if self.callback:
- self.callback(self.gfx_entity)
- self.gfx_entity.UpdatePositions()
-
- def _TogglePlay(self, playing):
- if playing:
- self.timer_id_=self.startTimer(self.time)
- else:
- self.killTimer(self.timer_id_)
-
- def _SetTraj(self, traj):
- self._traj=traj
- if self._traj:
- ev=traj.GetEntity()
- self.gfx_entity=gfx.Entity("mol",self.render_mode,
- ev.Select(self.selection))
- gfx.Scene().Add(self.gfx_entity)
- gfx.Scene().CenterOn(self.gfx_entity)
- # enable the blur effect
- #self.gfx_entity.SetBlur(True)
- self._slider.setMinimum(0)
- self._slider.setMaximum(self._traj.GetFrameCount()-1)
- self._slider.setSliderPosition(0)
- else:
- if self._traj:
- del self._anim
- self._traj=None
- def _SetBlur(self, blur):
- self.gfx_entity.SetBlur(blur)
-
- def _GetBlur(self):
- return self.gfx_entity.GetBlur()
-
- def _GetTraj(self):
- return self._traj
-
- blur=property(_GetBlur, _SetBlur)
- traj=property(_GetTraj, _SetTraj)
diff --git a/modules/gui/pymod/trajectory_viewer.py b/modules/gui/pymod/trajectory_viewer.py
new file mode 100644
index 0000000000000000000000000000000000000000..0741f98fb10214f3add38c767d24a3d647293f4c
--- /dev/null
+++ b/modules/gui/pymod/trajectory_viewer.py
@@ -0,0 +1,357 @@
+"""
+This module defines a widget used for visualization of trajectories.
+
+"""
+
+__all__=('TrajWidget','SetTimeUnit','AddTrajectory','RemoveTrajectory','SetSpeed','ReleaseGfxEntity','FixGfxEntity')
+
+#-------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2011 by the OpenStructure authors
+#
+# This library is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3.0 of the License, or (at your option)
+# any later version.
+# This library is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this library; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+#-------------------------------------------------------------------------------
+#from PyQt4.QtCore import *
+#from PyQt4.QtGui import *
+import PyQt4 as _PyQt4
+from PyQt4.QtCore import Qt as _Qt
+from PyQt4.QtCore import QObject as _QObject
+from PyQt4.QtGui import QWidget as _QWidget
+from PyQt4.QtGui import QLabel as _QLabel
+from PyQt4.QtGui import QPushButton as _QPushButton
+from PyQt4.QtCore import SIGNAL as _SIGNAL
+from PyQt4.QtCore import QString as _QString
+import ost as _ost
+import math as _math
+
+
+class TrajWidget(_QWidget):
+ def __init__(self, trajlist=None, golist=None, parent=None,ref_index=0):
+ _QWidget.__init__(self, parent, _Qt.Tool)
+ self.setFocusPolicy(_Qt.ClickFocus)
+ self.ref_index_=ref_index
+ self.trajlist_=trajlist
+ self.golist_=golist
+ self.ehlist_=[go.GetView().handle for go in self.golist_]
+ self.index_dict={}
+ self.fix_dict={}
+ self.modifiers=None
+ for i,go in enumerate(self.golist_):
+ self.index_dict[go.name]=i
+ vb=_PyQt4.QtGui.QVBoxLayout()
+ hb=_PyQt4.QtGui.QHBoxLayout()
+ hb1=_PyQt4.QtGui.QHBoxLayout()
+ hb2=_PyQt4.QtGui.QHBoxLayout()
+ hb3=_PyQt4.QtGui.QHBoxLayout()
+ hb4=_PyQt4.QtGui.QHBoxLayout()
+ self.callback=None
+ self._slider=_PyQt4.QtGui.QSlider(self)
+ self._slider.setOrientation(_Qt.Horizontal)
+ self._speed_slider=_PyQt4.QtGui.QSlider(self)
+ self._speed_slider.setOrientation(_Qt.Horizontal)
+ self._speedLabel=_QLabel(self)
+ self._speedLabel.setText('Speed:')
+ self._speedLabel.setAlignment(_Qt.AlignLeft)
+ self._play=_PyQt4.QtGui.QToolButton(self)
+ self._repeat=_PyQt4.QtGui.QCheckBox(self)
+ self._frame=_QLabel(self)
+ self._frameNo=_QLabel(self)
+ self._frameEnd=_QLabel(self)
+ self._repeat.setText('Repeat')
+ self._slider.setTracking(True)
+ self._play.setText('Play')
+ self._play.setCheckable(True)
+ self._frame.setText('Frame: ')
+ self._frameNo.setNum(0)
+ self._frameNo.setAlignment(_Qt.AlignRight)
+ self._frameEnd.setAlignment(_Qt.AlignLeft)
+ self._timeLabel=_QLabel(self)
+ self._timeNo=_QLabel(self)
+ self._timeEnd=_QLabel(self)
+ self._timeUnit=_QLabel(self)
+ self._timeLabel.setText('Time: ')
+ self._timeNo.setNum(0)
+ self._timeNo.setAlignment(_Qt.AlignRight)
+ self._timeEnd.setAlignment(_Qt.AlignLeft)
+ self._timeUnit.setAlignment(_Qt.AlignLeft)
+ self._speed_slider.setTracking(True)
+ self._speed_slider_min=-50
+ self._speed_slider_max=-10
+ self._speed_slider.setRange(self._speed_slider_min,self._speed_slider_max)
+ self._right_arrow=_QPushButton(">")
+ self._right_arrow2=_QPushButton(">>")
+ self._right_end=_QPushButton(">|")
+ self._left_arrow=_QPushButton("<")
+ self._left_arrow2=_QPushButton("<<")
+ self._left_end=_QPushButton("|<")
+ self._align_selection=_PyQt4.QtGui.QLineEdit()
+ self._align=_QPushButton("Align")
+ self._align_label=_QLabel(self)
+ self._align_label.setText('Selection:')
+ self._ref_entity_selection=_PyQt4.QtGui.QComboBox()
+ for go in self.golist_:self._ref_entity_selection.addItem(go.name)
+ self._ref_entity_selection_label=_QLabel(self)
+ self._ref_entity_selection_label.setText('Ref. Entity:')
+ hb.addWidget(self._play)
+ hb.addWidget(self._repeat)
+ hb.addWidget(self._ref_entity_selection_label)
+ hb.addWidget(self._ref_entity_selection)
+ hb1.addWidget(self._left_end)
+ hb1.addWidget(self._left_arrow2)
+ hb1.addWidget(self._left_arrow)
+ hb1.addWidget(self._right_arrow)
+ hb1.addWidget(self._right_arrow2)
+ hb1.addWidget(self._right_end)
+ hb2.addWidget(self._frame)
+ hb2.addWidget(self._frameNo)
+ hb2.addWidget(self._frameEnd)
+ hb2.addWidget(self._timeLabel)
+ hb2.addWidget(self._timeNo)
+ hb2.addWidget(self._timeEnd)
+ hb2.addWidget(self._timeUnit)
+ hb3.addWidget(self._speedLabel)
+ hb3.addWidget(self._speed_slider)
+ hb4.addWidget(self._align_label)
+ hb4.addWidget(self._align_selection)
+ hb4.addWidget(self._align)
+ self.setLayout(vb)
+ vb.addLayout(hb)
+ vb.addLayout(hb1)
+ vb.addWidget(self._slider)
+ vb.addLayout(hb2)
+ vb.addLayout(hb3)
+ vb.addLayout(hb4)
+ self._SetSpeedSliderPos(self._speed_slider_min+0.5*(self._speed_slider_max-self._speed_slider_min))
+ _QObject.connect(self._play, _SIGNAL('toggled(bool)'),
+ self._TogglePlay)
+ _QObject.connect(self._slider, _SIGNAL('valueChanged(int)'),
+ self._SliderValueChanged)
+ _QObject.connect(self._speed_slider,_SIGNAL('valueChanged(int)'),self._SpeedSliderValChanged)
+ _QObject.connect(self._right_end,_SIGNAL('clicked()'),self._RightEndClicked)
+ _QObject.connect(self._right_arrow2,_SIGNAL('clicked()'),self._Right2Clicked)
+ _QObject.connect(self._right_arrow,_SIGNAL('clicked()'),self._RightClicked)
+ _QObject.connect(self._left_arrow2,_SIGNAL('clicked()'),self._Left2Clicked)
+ _QObject.connect(self._left_arrow,_SIGNAL('clicked()'),self._LeftClicked)
+ _QObject.connect(self._left_end,_SIGNAL('clicked()'),self._LeftEndClicked)
+ _QObject.connect(self._align, _SIGNAL('clicked()'), self._AlignClicked)
+ _QObject.connect(self._ref_entity_selection, _SIGNAL('currentIndexChanged(int)'), self._EntitySelected)
+ self._slider.setMinimum(0)
+ self.frame_number_=self.traj_.GetFrameCount()-1
+ self.timestep_=self.traj_.GetDelta()
+ self.SetTimeUnit('ns')
+ self.SetReferenceIndex(0)
+
+ def _p2u(self,u):
+ if u=="s":
+ return 1.0e-12
+ elif u=="ms":
+ return 1.0e-9
+ elif u=="us":
+ return 1.0e-6
+ elif u=="ns":
+ return 1.0e-3
+ elif u=="ps":
+ return 1.0
+ elif u=="fs":
+ return 1.0e3
+ raise RuntimeError("expected one of s,ms,us,ns,ps or fs for unit")
+
+ def SetTimeUnit(self,u):
+ self._time_prefactor=self._p2u(u)
+ self._timeEnd.setText('/ '+ str((self.frame_number_-1)*self.timestep_*self._time_prefactor))
+ self._timeNo.setNum(self.current_frame*self.timestep_*self._time_prefactor)
+ self._timeUnit.setText('['+u+']')
+
+ def _SetSpeedSliderPos(self,pos):
+ self._speed_slider.setSliderPosition(pos)
+ self._SpeedSliderValChanged(pos)
+
+ def _SpeedSliderValChanged(self,speed_pos):
+ self.time=_math.exp(-0.15*speed_pos)
+ if self._play.isChecked():
+ self._TogglePlay(False)
+ self._TogglePlay(True)
+
+ def _SetTime(self,t):
+ self.time=t
+ self._speed_slider.setSliderPosition(-1./0.15*_math.log(t))
+ if self._play.isChecked():
+ self._TogglePlay(False)
+ self._TogglePlay(True)
+
+
+ def _SliderValueChanged(self, pos):
+ self.current_frame=pos
+ for traj,go in zip(self.trajlist_,self.golist_):
+ if go.name in self.fix_dict:continue
+ traj.CopyFrame(self.current_frame)
+ go.UpdatePositions()
+
+ def _GetCurrentFrame(self):
+ return self._slider.sliderPosition()
+
+ def _SetCurrentFrame(self, pos):
+ if self._slider.maximum()<pos:
+ if self._repeat.isChecked():
+ pos=0
+ else:
+ pos=self._slider.maximum()
+ self._slider.setSliderPosition(pos)
+ self._frameNo.setNum(pos)
+ self._timeNo.setNum(pos*self.timestep_*self._time_prefactor)
+
+ current_frame=property(_GetCurrentFrame, _SetCurrentFrame)
+
+ def _GetReferenceTraj(self):
+ return self.trajlist_[self.ref_index_]
+ traj_=property(_GetReferenceTraj)
+
+ def timerEvent(self, event):
+ #if self.callback:
+ # self.callback(self.golist_)
+ self.current_frame+=1
+ for go in self.golist_:
+ if go.name in self.fix_dict:continue
+ go.BlurSnapshot()
+ go.UpdatePositions()
+
+ def _TogglePlay(self, playing):
+ if playing:
+ self.timer_id_=self.startTimer(self.time)
+ else:
+ self.killTimer(self.timer_id_)
+
+ def _LeftClicked(self):
+ if self.current_frame>0:
+ self.current_frame-=1
+
+ def _RightClicked(self):
+ if self.current_frame<self.frame_number_-1:
+ self.current_frame+=1
+
+ def _Left2Clicked(self):
+ if self.current_frame>=10:
+ self.current_frame-=10
+
+ def _Right2Clicked(self):
+ if self.current_frame<self.frame_number_-10:
+ self.current_frame+=10
+
+ def _LeftEndClicked(self):
+ if self.current_frame>0:
+ self.current_frame=0
+
+ def _RightEndClicked(self):
+ if self.current_frame<self.frame_number_-1:
+ self.current_frame=self.frame_number_-1
+
+ def _AlignClicked(self):
+ ref_eh=self.ehlist_[self.ref_index_]
+ ref_v=ref_eh.Select(str(self._align_selection.text()))
+ if ref_v.GetAtomCount()<=3:
+ print 'not enough atoms for alignment'
+ return
+ for i,t,eh in zip(range(len(self.trajlist_)),self.trajlist_,self.ehlist_):
+ t=_ost.mol.alg.SuperposeFrames(t,eh.Select(str(self._align_selection.text())),ref_v)
+ self.trajlist_[i]=t
+
+ def _SetBlur(self, blur):
+ for go in self.golist_:
+ go.SetBlur(blur)
+
+ def _GetBlur(self):
+ return self.gfx_entity.GetBlur()
+
+ blur=property(_GetBlur, _SetBlur)
+
+ def SetReferenceIndex(self,ref_index):
+ if type(ref_index)==type(''):
+ self.ref_index_=self.index_dict[ref_index]
+ else:
+ self.ref_index_=ref_index
+ self.frame_number_=self.traj_.GetFrameCount()
+ self.timestep_=self.traj_.GetDelta()
+ self._slider.setMaximum(self.frame_number_-1)
+ self._frameEnd.setText('/ '+ str(self.frame_number_-1))
+ self._timeEnd.setText('/ '+ str((self.frame_number_-1)*self.timestep_*self._time_prefactor))
+ self._ref_entity_selection.setCurrentIndex(self.ref_index_)
+
+ def _EntitySelected(self,index):
+ ref_index=self.index_dict[str(self._ref_entity_selection.currentText())]
+ self.SetReferenceIndex(ref_index)
+
+ def keyPressEvent(self, event):
+ key=event.key()
+ if event.modifiers()==_Qt.ControlModifier:
+ self.modifiers=event.modifiers()
+ if self.modifiers==_Qt.ControlModifier:
+ if key==_Qt.Key_Left:
+ self._Left2Clicked()
+ elif key==_Qt.Key_Right:
+ self._Right2Clicked()
+ else:
+ if key==_Qt.Key_Left:
+ self._LeftClicked()
+ elif key==_Qt.Key_Right:
+ self._RightClicked()
+ elif key==_Qt.Key_Space:
+ self._play.setChecked(not self._play.isChecked())
+ else:
+ _QWidget.keyPressEvent(self, event)
+
+ def keyReleaseEvent(self, event):
+ if event.key()==_Qt.Key_Control:
+ self.modifiers=None
+ else:
+ _QWidget.keyPressEvent(self, event)
+
+ def FixGfxEntity(self,index,frame_number=None):
+ if not frame_number:frame_number=self.current_frame
+ if type(index)==type(''):
+ self.fix_dict[index]=frame_number
+ i=self.index_dict[index]
+ else:
+ i=index
+ self.fix_dict[self.golist_[i].name]=frame_number
+ self.trajlist_[i].CopyFrame(frame_number)
+ self.golist_[i].UpdatePositions()
+
+ def ReleaseGfxEntity(self,index):
+ if type(index)==type(''):self.fix_dict.pop(index)
+ else:self.fix_dict.pop(self.golist_[index].name)
+
+ def AddTrajectory(self,traj,go):
+ self.trajlist_.append(traj)
+ self.golist_.append(go)
+ self.ehlist_.append(go.GetView().handle)
+ self.index_dict[go.name]=len(self.golist_)-1
+
+ def RemoveTrajectory(self,index):
+ if type(index)==type(''):
+ index=self.index_dict[index]
+ self.trajlist_.pop(index)
+ self.golist_.pop(index)
+ self.ehlist_.pop(index)
+
+ def SetSpeed(self,val):
+ #Value should be between 0 and 1
+ if not (val<=1. and val >=0.):
+ print 'Speed should be set between 0 and 1'
+ return
+ else:
+ val=self._speed_slider_min-val*(self._speed_slider_min-self._speed_slider_max)
+ self._SetSpeedSliderPos(val)
+ print val
+
diff --git a/modules/gui/pymod/wrap_gui.cc b/modules/gui/pymod/wrap_gui.cc
index a4474a6f861e427982f701581f852c2ea14c63bf..6e4baae550ea669ab9e9ee79781f1b2c86d4ea12 100644
--- a/modules/gui/pymod/wrap_gui.cc
+++ b/modules/gui/pymod/wrap_gui.cc
@@ -16,10 +16,10 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#include <iostream>
#include <boost/python.hpp>
#include <QString>
+#include <iostream>
#include <ost/config.hh>
#include <ost/gui/admin.hh>
using namespace boost::python;
diff --git a/modules/gui/src/data_viewer/data_viewer.cc b/modules/gui/src/data_viewer/data_viewer.cc
index 2c1966b4e7ccc73c973f3bafe67a67e310837416..5a75d518126e747a9ac98f8a9f1cf8314f90faf8 100644
--- a/modules/gui/src/data_viewer/data_viewer.cc
+++ b/modules/gui/src/data_viewer/data_viewer.cc
@@ -23,17 +23,17 @@
Authors: Ansgar Philippsen, Andreas Schenk, Jeff Lovelace
*/
+#include <ost/gui/gosty_app.hh>
#include <cassert>
#include <iostream>
//#include <cstring>
//#include <sstream>
-//#include <ost/img/io/io_manager.hh>
+//#include <ost/io/io_manager.hh>
#include <ost/message.hh>
//#include <ost/img/alg/fft.hh>
#include <ost/img/alg/norm.hh>
-#include <ost/gui/gosty_app.hh>
#include <ost/gui/dock_widget.hh>
#include <ost/gui/perspective.hh>
@@ -205,6 +205,11 @@ geom::Vec2 DataViewer::GetOffset() const
return panel_->GetOffset();
}
+QButtonGroup* DataViewer::GetButtonGroup(void)
+{
+ return ov_manager_gui_->GetButtonGroup();
+}
+
int DataViewer::AddOverlay(const OverlayPtr& ov, bool make_active)
{
int retval= ov_manager_->AddOverlay(ov,make_active);
@@ -217,6 +222,11 @@ void DataViewer::ClearOverlays()
ov_manager_->DeleteAllOverlays();
}
+void DataViewer::ClearActiveOverlay()
+{
+ ov_manager_->DeleteActiveOverlay();
+}
+
OverlayManagerPtr DataViewer::GetOverlayManager() const
{
return ov_manager_;
diff --git a/modules/gui/src/data_viewer/data_viewer.hh b/modules/gui/src/data_viewer/data_viewer.hh
index 902466a68c9b44ca0b7c4e1070b9dbf384de3c7d..ca6893edc34895fde6df19e2b1344ea11affcb98 100644
--- a/modules/gui/src/data_viewer/data_viewer.hh
+++ b/modules/gui/src/data_viewer/data_viewer.hh
@@ -95,6 +95,9 @@ public:
//! remove all overlays
void ClearOverlays();
+ //! remove the active overlay
+ void ClearActiveOverlay();
+
//! return the overlay manager for this viewer
OverlayManagerPtr GetOverlayManager() const;
@@ -142,6 +145,8 @@ public:
//! get image offset
geom::Vec2 GetOffset() const;
+ QButtonGroup* GetButtonGroup(void);
+
signals:
void released();
diff --git a/modules/gui/src/data_viewer/mask_overlay.cc b/modules/gui/src/data_viewer/mask_overlay.cc
index c0c0e6560344c59f75cb95031a1a372086aba0ad..dc18830debf329c45e6869def2f681b572e7952d 100644
--- a/modules/gui/src/data_viewer/mask_overlay.cc
+++ b/modules/gui/src/data_viewer/mask_overlay.cc
@@ -116,7 +116,7 @@ bool MaskOverlay::OnMouseEvent(QMouseEvent* e, DataViewerPanel* dvp,
new_poly_=geom::Polygon2();
add_mode_=true;
}
- new_poly_.AddNode(mousepos);
+ new_poly_.AddNode(mousepos-shift_);
} else {
if(active_>=0){
geom::Polygon2 pol=polygons_[active_];
diff --git a/modules/gui/src/data_viewer/overlay_manager.cc b/modules/gui/src/data_viewer/overlay_manager.cc
index a9bc950284806a530d92687412e398deb7edf3be..ac2a709fbff4888096c6877a08b919e3e1dbc93d 100644
--- a/modules/gui/src/data_viewer/overlay_manager.cc
+++ b/modules/gui/src/data_viewer/overlay_manager.cc
@@ -103,6 +103,18 @@ void OverlayManager::DeleteAllOverlays()
ov_list_.clear();
}
+void OverlayManager::DeleteActiveOverlay()
+{
+ OverlayList::iterator pos=find_ov(active_ov_);
+ if (pos!=ov_list_.end()) {
+ for(ObserverList::iterator xit=obs_list_.begin();xit!=obs_list_.end();++xit) {
+ (*xit)->OnRemoveOverlay(this, pos->id);
+ }
+ pos=ov_list_.erase(pos);
+ active_ov_.reset();
+ }
+
+}
void OverlayManager::ActivateOverlay(const String& name)
{
@@ -351,4 +363,15 @@ OverlayManager::OverlayList::iterator OverlayManager::find_ov(const String& name
return ov_list_.end();
}
+OverlayManager::OverlayList::iterator OverlayManager::find_ov(OverlayPtr anoverlay)
+{
+ for(OverlayList::iterator it=ov_list_.begin();it!=ov_list_.end();++it) {
+ if(anoverlay==it->ov) {
+ return it;
+ break;
+ }
+ }
+ return ov_list_.end();
+}
+
}}} //ns
diff --git a/modules/gui/src/data_viewer/overlay_manager.hh b/modules/gui/src/data_viewer/overlay_manager.hh
index d1e9736093b20134e17ed2e573a4e001d44b8bd8..2a3bb76573b3052656a0533ec3798dc377bff1e6 100644
--- a/modules/gui/src/data_viewer/overlay_manager.hh
+++ b/modules/gui/src/data_viewer/overlay_manager.hh
@@ -110,6 +110,8 @@ public:
void DeleteAllOverlays();
+ void DeleteActiveOverlay();
+
void OnDraw(QPainter& pnt, DataViewerPanel* dvp) const;
bool OnMouseEvent(QMouseEvent* e, DataViewerPanel* dvp, const QPoint& lastmouse) const;
@@ -138,6 +140,7 @@ private:
OverlayList::iterator find_ov(int id);
OverlayList::iterator find_ov(const String& name);
+ OverlayList::iterator find_ov(OverlayPtr anoverlay);
};
diff --git a/modules/gui/src/data_viewer/overlay_manager_gui.cc b/modules/gui/src/data_viewer/overlay_manager_gui.cc
index ba9d884cbd88b0f603c670a93dcfb995eb168177..69bb6a5dd91f740aec70fea1a4684fcbaed7a2da 100644
--- a/modules/gui/src/data_viewer/overlay_manager_gui.cc
+++ b/modules/gui/src/data_viewer/overlay_manager_gui.cc
@@ -209,6 +209,11 @@ void OverlayManagerGUI::OnEventMenu(QAction* e)
{
}
+QButtonGroup* OverlayManagerGUI::GetButtonGroup(void)
+{
+ return active_group_;
+}
+
void OverlayManagerGUI::UpdateView()
{
}
diff --git a/modules/gui/src/data_viewer/overlay_manager_gui.hh b/modules/gui/src/data_viewer/overlay_manager_gui.hh
index 437b0c3b72617d6ad2d213be3feadee2cf34997c..13ba39f87dedfcdeb5c78bdb5e633dd2ed7a77d6 100644
--- a/modules/gui/src/data_viewer/overlay_manager_gui.hh
+++ b/modules/gui/src/data_viewer/overlay_manager_gui.hh
@@ -120,6 +120,8 @@ public:
void OnEventMenuPopup(QAction* e);
void OnEventMenu(QAction* e);
+ QButtonGroup* GetButtonGroup(void);
+
public slots:
void SetInfoText(const QString& t);
diff --git a/modules/gui/src/file_loader.hh b/modules/gui/src/file_loader.hh
index 23419b613eb851fb9aeeec56ce8c9efe91701050..8e2e50758643ae67df2ea8f9d668f2e0128b7bde 100644
--- a/modules/gui/src/file_loader.hh
+++ b/modules/gui/src/file_loader.hh
@@ -26,11 +26,11 @@
#include <ost/gui/module_config.hh>
#include <ost/io/io_exception.hh>
-#include <ost/io/entity_io_handler.hh>
-#include <ost/io/sequence_io_handler.hh>
-#include <ost/io/surface_io_handler.hh>
+#include <ost/io/mol/entity_io_handler.hh>
+#include <ost/io/seq/sequence_io_handler.hh>
+#include <ost/io/mol/surface_io_handler.hh>
#if OST_IMG_ENABLED
-#include <ost/io/map_io_handler.hh>
+# include <ost/io/img/map_io_handler.hh>
#endif
#include <QString>
diff --git a/modules/gui/src/file_type_dialog.hh b/modules/gui/src/file_type_dialog.hh
index 4cd7746afb32d17f843b9d4680e07e5aaa2c8fd6..f1fe6ce5e5fc6e856b15c091b65d03e41309bda2 100644
--- a/modules/gui/src/file_type_dialog.hh
+++ b/modules/gui/src/file_type_dialog.hh
@@ -27,11 +27,11 @@
-#include <ost/io/entity_io_handler.hh>
-#include <ost/io/sequence_io_handler.hh>
-#include <ost/io/surface_io_handler.hh>
+#include <ost/io/mol/entity_io_handler.hh>
+#include <ost/io/seq/sequence_io_handler.hh>
+#include <ost/io/mol/surface_io_handler.hh>
#if OST_IMG_ENABLED
-#include <ost/io/map_io_handler.hh>
+#include <ost/io/img/map_io_handler.hh>
#endif
#include <QDialog>
diff --git a/modules/gui/src/gl_canvas.cc b/modules/gui/src/gl_canvas.cc
index f94bff0458c4fbfe746c489e424ebc467c9137d2..9e39789b90bbf9d57dbf04f1da02f8563de73215 100644
--- a/modules/gui/src/gl_canvas.cc
+++ b/modules/gui/src/gl_canvas.cc
@@ -16,11 +16,11 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+#include <ost/gui/python_shell/python_interpreter.hh>
#ifndef _MSC_VER
#include <sys/time.h>
#endif
-#include <ost/gui/python_shell/python_interpreter.hh>
#include "gl_canvas.hh"
#include "gl_win.hh"
diff --git a/modules/gui/src/gosty.cc b/modules/gui/src/gosty.cc
index a767d1b9f06f68b58fc66faee54d6de7c2f9d00a..b5275bb3e694c37359aad5eb2d5140544aae58f8 100644
--- a/modules/gui/src/gosty.cc
+++ b/modules/gui/src/gosty.cc
@@ -16,23 +16,23 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#include <utility>
-#include <vector>
-#include <signal.h>
-#include <iostream>
-#include <sstream>
-#include <ctime>
-#include <ost/gui/module_config.hh>
-#include <ost/log.hh>
-#include <ost/platform.hh>
#include <ost/gui/python_shell/text_logger.hh>
#include <ost/gui/python_shell/python_shell.hh>
#include <ost/gui/python_shell/python_interpreter.hh>
#include "gl_win.hh"
#include "widget_state_saver.hh"
#include "gosty.hh"
+#include <ost/log.hh>
+#include <ost/platform.hh>
+#include <ost/gui/module_config.hh>
+#include <utility>
+#include <vector>
+#include <signal.h>
+#include <iostream>
+#include <sstream>
+#include <ctime>
// must come last
#include <QApplication>
#include <QResource>
diff --git a/modules/gui/src/gosty_app.cc b/modules/gui/src/gosty_app.cc
index 66c612e94cb2484d17f51b8510d9276646298e81..949c764910e16d957ccec9bd1edba5e9c24b6ec5 100644
--- a/modules/gui/src/gosty_app.cc
+++ b/modules/gui/src/gosty_app.cc
@@ -109,20 +109,30 @@ SequenceViewer* GostyApp::GetSequenceViewer()
}
#if OST_IMG_ENABLED
-ost::img::gui::DataViewer* GostyApp::CreateDataViewer(const ost::img::ImageHandle& d, const QString& name)
+ost::img::gui::DataViewer* GostyApp::CreateDataViewer(const ost::img::ImageHandle& d, const QString& name, const int noparent)
{
- ost::img::gui::DataViewer* viewer=new ost::img::gui::DataViewer(main_,d,name);
- QMdiSubWindow* mdi=new QMdiSubWindow(this->GetPerspective()->GetMainArea());
- mdi->setWindowTitle(name);
- mdi->setWidget(viewer);
- mdi->setFocusProxy(viewer);
- viewer->setAttribute(Qt::WA_DeleteOnClose);
- mdi->setAttribute(Qt::WA_DeleteOnClose);
- viewer->setParent(mdi);
- this->GetPerspective()->GetMainArea()->addSubWindow(mdi);
- mdi->showMaximized();
- connect(viewer,SIGNAL(released()),mdi,SLOT(close()));
- return viewer;
+ ost::img::gui::DataViewer* viewer=NULL;
+ if (noparent)
+ {
+ viewer=new ost::img::gui::DataViewer(NULL,d,name);
+ }
+ else
+ {
+ viewer=new ost::img::gui::DataViewer(main_,d,name);
+ QMdiSubWindow* mdi=new QMdiSubWindow(this->GetPerspective()->GetMainArea());
+ mdi->setWindowTitle(name);
+ mdi->setWidget(viewer);
+ mdi->setFocusProxy(viewer);
+ viewer->setAttribute(Qt::WA_DeleteOnClose);
+ mdi->setAttribute(Qt::WA_DeleteOnClose);
+ viewer->setParent(mdi);
+ this->GetPerspective()->GetMainArea()->addSubWindow(mdi);
+ mdi->showMaximized();
+ connect(viewer,SIGNAL(released()),mdi,SLOT(close()));
+ }
+
+ return viewer;
+
}
#endif
diff --git a/modules/gui/src/gosty_app.hh b/modules/gui/src/gosty_app.hh
index a635c407ae9cd3e75570101b73aeb3948f0f5910..47b0f23fadfe151a262e25f39910b5da9eda1c24 100644
--- a/modules/gui/src/gosty_app.hh
+++ b/modules/gui/src/gosty_app.hh
@@ -25,8 +25,8 @@
#include <ost/config.hh>
-#include <ost/gui/module_config.hh>
#include <ost/gui/main.hh>
+#include <ost/gui/module_config.hh>
#include <ost/gui/widget_geom_handler.hh>
@@ -124,7 +124,7 @@ public:
#if OST_IMG_ENABLED
/// \brief create new DataViewer
///
- ost::img::gui::DataViewer* CreateDataViewer(const ost::img::ImageHandle& d, const QString& name="");
+ ost::img::gui::DataViewer* CreateDataViewer(const ost::img::ImageHandle& d, const QString& name="", const int noparent=0);
#endif
/// \brief give the application time to run the mainloop and process events
diff --git a/modules/gui/src/main.hh b/modules/gui/src/main.hh
index deee0797264437d5b47f041fe712fe8da19c9c88..86105fb96e78180d0b56c17058bf1348ea5ca26d 100644
--- a/modules/gui/src/main.hh
+++ b/modules/gui/src/main.hh
@@ -19,11 +19,11 @@
#ifndef OST_GUI_OST_MAIN_HH
#define OST_GUI_OST_MAIN_HH
-#include <map>
-#include <boost/shared_ptr.hpp>
-#include <ost/gui/module_config.hh>
#include <ost/gui/python_shell/text_logger.hh>
+#include <boost/shared_ptr.hpp>
+#include <ost/gui/module_config.hh>
+#include <map>
#include "widget_state_saver.hh"
diff --git a/modules/gui/src/panels/panel_bar_widget_holder.cc b/modules/gui/src/panels/panel_bar_widget_holder.cc
index a9789cb2abd90498be2a7798aeec8cb3d143c720..358f86eef565b82f586c3b1003b49f58a40e3ad4 100644
--- a/modules/gui/src/panels/panel_bar_widget_holder.cc
+++ b/modules/gui/src/panels/panel_bar_widget_holder.cc
@@ -16,7 +16,6 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#include <cassert>
#include <ost/gui/gosty_app.hh>
@@ -30,6 +29,7 @@
#include "panel_bar.hh"
#include "panel_bar_widget_holder.hh"
+#include <cassert>
#include <QApplication>
#include <QMenu>
#include <QHBoxLayout>
diff --git a/modules/gui/src/python_shell/gutter.cc b/modules/gui/src/python_shell/gutter.cc
index bb8cb98ee3748e8ecccc22396bc2a0725715127b..eed96f4573cc1b8ea35d5d5e51cd8de0ae1c257e 100644
--- a/modules/gui/src/python_shell/gutter.cc
+++ b/modules/gui/src/python_shell/gutter.cc
@@ -49,7 +49,7 @@ void Gutter::paintEvent(QPaintEvent* paint_event)
QPainter painter(this);
painter.setPen(QPen(Qt::black));
painter.fillRect(paint_event->rect(), QBrush(Qt::lightGray));
- for (GutterBlockList::const_iterator it=blocks.begin();
+ for (GutterBlockList::const_iterator it=blocks.begin();
it!=blocks.end(); ++it) {
if (it->type & BLOCKTYPE_ACTIVE) {
QColor green(Qt::green);
diff --git a/modules/gui/src/python_shell/python_completer.cc b/modules/gui/src/python_shell/python_completer.cc
index 9ec41df66d7a4e57fdf61a5a30809a5b3a596504..af7f93d380726b0d520f496645a2f519f2fd09b8 100644
--- a/modules/gui/src/python_shell/python_completer.cc
+++ b/modules/gui/src/python_shell/python_completer.cc
@@ -20,10 +20,10 @@
Authors: Marco Biasini, Andreas Schenk
*/
-#include <iostream>
#include "python_completer.hh"
#include "python_namespace_tree_model.hh"
+#include <iostream>
#include <QStringList>
diff --git a/modules/gui/src/python_shell/python_context_parser.hh b/modules/gui/src/python_shell/python_context_parser.hh
index ddc2c93ddd19b9bf65169fb062dac94a0999ba93..0e5df593f494fb57edb1c3dc188ca5e5b32533b6 100644
--- a/modules/gui/src/python_shell/python_context_parser.hh
+++ b/modules/gui/src/python_shell/python_context_parser.hh
@@ -23,10 +23,10 @@
Author: Marco Biasini
*/
+#include "python_tokenizer.hh"
#include <vector>
#include <iostream>
-#include "python_tokenizer.hh"
namespace ost { namespace gui {
diff --git a/modules/gui/src/python_shell/python_interpreter.hh b/modules/gui/src/python_shell/python_interpreter.hh
index 5f12d6bbde982697f00350bcf2a1160992000e73..3cbe055cbb6dc0afd060a19b1c54b495e4372bb2 100644
--- a/modules/gui/src/python_shell/python_interpreter.hh
+++ b/modules/gui/src/python_shell/python_interpreter.hh
@@ -27,14 +27,11 @@
#ifndef PYTHON_INTERPRETER_HH
#define PYTHON_INTERPRETER_HH
-#include <vector>
-#include <ost/gui/module_config.hh>
-
-#include <ost/gui/module_config.hh>
#include "python_interpreter_worker.hh"
#include "output_redirector.hh"
#include "main_thread_runner.hh"
+#include <ost/gui/module_config.hh>
#include <QQueue>
#include <QMetaType>
diff --git a/modules/gui/src/python_shell/python_interpreter_worker.cc b/modules/gui/src/python_shell/python_interpreter_worker.cc
index 68f38a247f0026555ee87ff9d12da4b41579c217..e75f484600f3b749756042783316ece6697991fb 100644
--- a/modules/gui/src/python_shell/python_interpreter_worker.cc
+++ b/modules/gui/src/python_shell/python_interpreter_worker.cc
@@ -1,3 +1,23 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+
#include "python_interpreter_worker.hh"
#include "python_interpreter.hh"
diff --git a/modules/gui/src/python_shell/python_interpreter_worker.hh b/modules/gui/src/python_shell/python_interpreter_worker.hh
index ed80f6fe78b308f1269a5a723bffe46883fbe35b..557604900e046dee0c46fec77550a4b1e2292ad4 100644
--- a/modules/gui/src/python_shell/python_interpreter_worker.hh
+++ b/modules/gui/src/python_shell/python_interpreter_worker.hh
@@ -1,14 +1,34 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+
#ifndef PYTHON_INTERPRETER_WORKER_HH
#define PYTHON_INTERPRETER_WORKER_HH
-#include <csignal>
-#include <utility>
// workaround for QTBUG-22829: https://bugreports.qt-project.org/browse/QTBUG-22829
#ifndef Q_MOC_RUN
#include <boost/python.hpp>
#include <boost/shared_ptr.hpp>
#endif
#include "output_redirector.hh"
+#include <csignal>
+#include <utility>
#include <QObject>
#include <QQueue>
diff --git a/modules/gui/src/python_shell/python_namespace_tree_item.cc b/modules/gui/src/python_shell/python_namespace_tree_item.cc
index b3e2960901f91b003c3fed8184f5d9e39a6313e6..5c59e235810eb61c730cc36b11989aa416c46901 100644
--- a/modules/gui/src/python_shell/python_namespace_tree_item.cc
+++ b/modules/gui/src/python_shell/python_namespace_tree_item.cc
@@ -17,9 +17,9 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+#include "python_namespace_tree_item.hh"
#include <ost/base.hh>
-#include "python_namespace_tree_item.hh"
@@ -107,13 +107,9 @@ void PythonNamespaceTreeItem::FetchMore()
continue;
}
bp::object child_namespace;
- bool found=false;
try{
String keystring=bp::extract<String>(keys[i]);
child_namespace=namespace_.attr(keystring.c_str());
- if (bp::len(dir(child_namespace))>0) {
- found=true;
- }
} catch(bp::error_already_set) {
PyErr_Clear();
}
diff --git a/modules/gui/src/python_shell/python_shell.cc b/modules/gui/src/python_shell/python_shell.cc
index cdd9c28c3315058b54bcfa4c9e1a206b4a20fcbc..b651747b8d522c10eb3b9514491c4997539ff627 100644
--- a/modules/gui/src/python_shell/python_shell.cc
+++ b/modules/gui/src/python_shell/python_shell.cc
@@ -21,11 +21,11 @@
Author: Marco Biasini
*/
+#include "python_shell_widget.hh"
+#include "python_shell.hh"
#include <ost/gui/gosty_app.hh>
#include <ost/gui/widget_registry.hh>
-#include "python_shell.hh"
-#include "python_shell_widget.hh"
#include <QVBoxLayout>
namespace ost { namespace gui {
diff --git a/modules/gui/src/python_shell/python_shell_fw.hh b/modules/gui/src/python_shell/python_shell_fw.hh
index d70eb83d841be3ab6e26fe941e81702c0bd41177..9abb7cae16532955fe0d1177fab66a4988b91492 100644
--- a/modules/gui/src/python_shell/python_shell_fw.hh
+++ b/modules/gui/src/python_shell/python_shell_fw.hh
@@ -23,7 +23,6 @@
Author: Andreas Schenk
*/
-#include <vector>
namespace ost { namespace gui {
// fw decl
@@ -51,7 +50,6 @@ struct GutterBlock{
BlockType type;
};
-typedef std::vector<GutterBlock> GutterBlockList;
}}//ns
diff --git a/modules/gui/src/python_shell/python_shell_widget.cc b/modules/gui/src/python_shell/python_shell_widget.cc
index 9adafdd7c764e8727f3a7dab0912c4b82347bbd3..9c816f5dcb6585bfba7af6ec202bae17e08ad75a 100644
--- a/modules/gui/src/python_shell/python_shell_widget.cc
+++ b/modules/gui/src/python_shell/python_shell_widget.cc
@@ -20,21 +20,20 @@
Authors: Marco Biasini, Andreas Schenk
*/
-#include <iostream>
#include "python_shell_widget.hh"
-
+#include "state_machine.hh"
+#include "state.hh"
#include "gutter.hh"
-
#include "string_literal_positions.hh"
-
#include "python_shell_text_document_layout.hh"
-
#include "python_completer.hh"
#include "path_completer.hh"
#include "transition.hh"
+#include <iostream>
+
#include <QApplication>
#include <QFontMetrics>
#include <QClipboard>
diff --git a/modules/gui/src/python_shell/python_shell_widget.hh b/modules/gui/src/python_shell/python_shell_widget.hh
index f2b2dbcedefc22696a6b5f1d7cf0b0f4753f0fdf..090272bbbd00e3b5155a917e2fc566c2c41cfc44 100644
--- a/modules/gui/src/python_shell/python_shell_widget.hh
+++ b/modules/gui/src/python_shell/python_shell_widget.hh
@@ -25,13 +25,11 @@
#define OST_GUI_PYTHON_SHELL_WIDGET_HH
-#include <ost/gui/module_config.hh>
#include "python_interpreter.hh"
#include "shell_history.hh"
#include "python_shell_fw.hh"
#include "python_syntax_highlighter.hh"
-#include "state_machine.hh"
-#include "state.hh"
+#include <ost/gui/module_config.hh>
#include <QPlainTextEdit>
#include <QHash>
@@ -41,7 +39,10 @@ namespace ost { namespace gui {
class Gutter;
class PythonCompleter;
class PathCompleter;
+class State;
+class StateMachine;
+typedef std::vector<GutterBlock> GutterBlockList;
class DLLEXPORT_OST_GUI PythonShellWidget : public QPlainTextEdit {
diff --git a/modules/gui/src/python_shell/python_syntax_highlighter.cc b/modules/gui/src/python_shell/python_syntax_highlighter.cc
index cca2c0b8b088550a007c4aacf7c6789961a279ad..72ab4be2a096a3cab15fc0849eff8fcbb42dbc6d 100644
--- a/modules/gui/src/python_shell/python_syntax_highlighter.cc
+++ b/modules/gui/src/python_shell/python_syntax_highlighter.cc
@@ -20,14 +20,13 @@
Authors: Marco Biasini, Andreas Schenk
*/
-#include <iostream>
#include "python_shell.hh"
#include "string_literal_positions.hh"
-
#include "python_syntax_highlighter.hh"
#include "python_context_parser.hh"
+#include <iostream>
#include <QDebug>
#include <QTextCursor>
diff --git a/modules/gui/src/python_shell/shell_history.hh b/modules/gui/src/python_shell/shell_history.hh
index 20e0405afe4aec3b1d17b7533b9750c0b50af57e..87e082af623c137959144216a5778698a545630d 100644
--- a/modules/gui/src/python_shell/shell_history.hh
+++ b/modules/gui/src/python_shell/shell_history.hh
@@ -22,8 +22,8 @@
Author: Andreas Schenk
*/
-#include <vector>
#include "python_shell_fw.hh"
+#include <vector>
#include <QString>
namespace ost { namespace gui {
diff --git a/modules/gui/src/python_shell/state.cc b/modules/gui/src/python_shell/state.cc
index 381fffff4d120cf891fa2b5e552258cdfafc5274..f5b7c522306c5f96df8b0817005f30f02a70800a 100644
--- a/modules/gui/src/python_shell/state.cc
+++ b/modules/gui/src/python_shell/state.cc
@@ -1,7 +1,26 @@
-#include <cassert>
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
#include "transition.hh"
#include "state.hh"
#include "state_machine.hh"
+#include <cassert>
namespace ost { namespace gui {
diff --git a/modules/gui/src/python_shell/state.hh b/modules/gui/src/python_shell/state.hh
index a6c05c36b3b6fc94db8498caf41a0fa71f90323f..679542078d8a17086c099b0dfa6e9df04173ae68 100644
--- a/modules/gui/src/python_shell/state.hh
+++ b/modules/gui/src/python_shell/state.hh
@@ -1,3 +1,22 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
#ifndef PYTHON_SHELL_STATE_HH
#define PYTHON_SHELL_STATE_HH
diff --git a/modules/gui/src/python_shell/state_machine.cc b/modules/gui/src/python_shell/state_machine.cc
index 9ce3f37bc85946686bcb1d34f3593b37789336ce..048ed68eb83a0bdd2324d451e7f4f6f7aea65ed2 100644
--- a/modules/gui/src/python_shell/state_machine.cc
+++ b/modules/gui/src/python_shell/state_machine.cc
@@ -1,3 +1,22 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
#include <QEvent>
#include <QKeyEvent>
#include <QMouseEvent>
diff --git a/modules/gui/src/python_shell/state_machine.hh b/modules/gui/src/python_shell/state_machine.hh
index ac265dfd91e898d3af9ef483de11076a846cafdb..8db26c10a64f521ab5e27021e78e4db391b7b245 100644
--- a/modules/gui/src/python_shell/state_machine.hh
+++ b/modules/gui/src/python_shell/state_machine.hh
@@ -1,3 +1,22 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
#ifndef PYTHON_SHELL_STATE_MACHINE_HH
#define PYTHON_SHELL_STATE_MACHINE_HH
diff --git a/modules/gui/src/python_shell/transition.cc b/modules/gui/src/python_shell/transition.cc
index b2a07eb6b724273523dbf78121b768f260977f12..9916657713fe9be0a0c56913cffaf5dc312b468c 100644
--- a/modules/gui/src/python_shell/transition.cc
+++ b/modules/gui/src/python_shell/transition.cc
@@ -1,7 +1,26 @@
-#include <cassert>
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
#include "python_shell_widget.hh"
#include "transition.hh"
#include "state.hh"
+#include <cassert>
#include <QKeyEvent>
#include <QMouseEvent>
diff --git a/modules/gui/src/python_shell/transition.hh b/modules/gui/src/python_shell/transition.hh
index a17b38ee5c55b85b2915651bb2b1e9e28020fae0..a3550f4280f8f186023f5750aeb7feee8fb5da92 100644
--- a/modules/gui/src/python_shell/transition.hh
+++ b/modules/gui/src/python_shell/transition.hh
@@ -1,12 +1,31 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
#ifndef PYTHON_SHELL_TRANSITION_HH
#define PYTHON_SHELL_TRANSITION_HH
-#include <utility>
#include <ost/gui/python_shell/python_interpreter.hh>
+#include "transition_guard.hh"
+#include <utility>
#include <QObject>
#include <QEvent>
-#include "transition_guard.hh"
//fw decl
class QKeyEvent;
class QMouseEvent;
diff --git a/modules/gui/src/python_shell/transition_guard.cc b/modules/gui/src/python_shell/transition_guard.cc
index 940d5bba15a96f7605ffa90348cf6f64933f9994..acf6ff2c95a35cef4b689c22a3c22822e82ff7c0 100644
--- a/modules/gui/src/python_shell/transition_guard.cc
+++ b/modules/gui/src/python_shell/transition_guard.cc
@@ -1,7 +1,27 @@
-#include <iostream>
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+
#include "transition_guard.hh"
#include "python_shell_widget.hh"
#include "shell_history.hh"
+#include <iostream>
namespace ost { namespace gui {
diff --git a/modules/gui/src/python_shell/transition_guard.hh b/modules/gui/src/python_shell/transition_guard.hh
index 5a2906481c36da41fc7ef1d5aefecfc853d76ad9..c3b20201a7d5f7a3b0e1c2d21c34f819a7294ac3 100644
--- a/modules/gui/src/python_shell/transition_guard.hh
+++ b/modules/gui/src/python_shell/transition_guard.hh
@@ -1,3 +1,22 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2014 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
#ifndef TRANSITION_GUARD_HH
#define TRANSITION_GUARD_HH
diff --git a/modules/gui/src/scene_menu.cc b/modules/gui/src/scene_menu.cc
index ef02a2aee2807a00034228fc451a2763d73bdde1..bedcf0df437f5feb57243056dbbebd2bd1ebd02e 100644
--- a/modules/gui/src/scene_menu.cc
+++ b/modules/gui/src/scene_menu.cc
@@ -16,9 +16,9 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+#include <ost/gui/gosty_app.hh>
#include <ost/dyn_cast.hh>
#include <ost/mol/view_op.hh>
-#include <ost/gui/gosty_app.hh>
#include <ost/gfx/scene.hh>
#include <ost/gfx/entity.hh>
diff --git a/modules/gui/src/scene_selection.cc b/modules/gui/src/scene_selection.cc
index 2faa79d6c09bbe1c5e3092126cf42a2acbe03bfb..be66a839918dcaa10d6f71db4bcc99ff989f89b6 100644
--- a/modules/gui/src/scene_selection.cc
+++ b/modules/gui/src/scene_selection.cc
@@ -103,6 +103,7 @@ void SceneSelection::CenterOnObjects() {
geom::AlignedCuboid pair = obj->GetBoundingBox();
min = geom::Min(min, pair.GetMin());
max = geom::Max(max, pair.GetMax());
+ std::cerr << obj->GetName() << " " << min << " " << max << std::endl;
changed=true;
}
}
diff --git a/modules/gui/src/scene_win/context_menu.cc b/modules/gui/src/scene_win/context_menu.cc
index 370800556aa052a3f11460a4c0578dfb2935c157..70a8c2bdcd088308fa5073fa6a8093df7fb9fbf6 100644
--- a/modules/gui/src/scene_win/context_menu.cc
+++ b/modules/gui/src/scene_win/context_menu.cc
@@ -199,16 +199,15 @@ void ContextMenu::ShowMenu(const QPoint& pos)
flags &= ~SINGLE;
}
QMenu* menu = new QMenu();
- QMapIterator<QAction*, ContextActionTypes> i(actions_);
+ QVectorIterator<std::pair<QAction*, ContextActionTypes> > i(actions_);
flags ^= NOT_VISIBLE;
flags ^= NOT_HIDDEN;
while (i.hasNext()) {
- i.next();
- if (i.value() == (i.value() & flags)){
- menu->addAction(i.key());
- }
+ const std::pair<QAction*, ContextActionTypes>& value = i.next();
+ if (value.second == (value.second & flags)){
+ menu->addAction(value.first);
+ }
}
-
if(! menu->actions().empty()){
menu->popup(pos);
}
@@ -216,7 +215,7 @@ void ContextMenu::ShowMenu(const QPoint& pos)
}
void ContextMenu::AddAction(QAction* action,ContextActionTypes type){
- actions_[action] = type;
+ actions_.push_back(std::make_pair(action, type));
}
void ContextMenu::AddView(){
diff --git a/modules/gui/src/scene_win/context_menu.hh b/modules/gui/src/scene_win/context_menu.hh
index c145164d7c3303ccca24d447497ffb465252070b..56ca0929a2693f65756584341463c24dfa09f26f 100644
--- a/modules/gui/src/scene_win/context_menu.hh
+++ b/modules/gui/src/scene_win/context_menu.hh
@@ -28,7 +28,7 @@
#include <ost/gui/scene_win/scene_win_model.hh>
#include <QFlags>
-#include <QMap>
+#include <QVector>
#include <QAbstractItemModel>
#include <QTreeView>
namespace ost { namespace gui {
@@ -53,6 +53,7 @@ enum ContextActionType
MAP_DSAMPLED_AVAIL=0x4000
#endif
};
+
Q_DECLARE_FLAGS(ContextActionTypes, ContextActionType)
@@ -73,7 +74,7 @@ private slots:
void DeleteView();
private:
- QMap<QAction*, ContextActionTypes> actions_;
+ QVector<std::pair<QAction*, ContextActionTypes> > actions_;
QTreeView* view_;
SceneWinModel* model_;
diff --git a/modules/gui/src/scene_win/entity_node.cc b/modules/gui/src/scene_win/entity_node.cc
index 02dc97c54f8396bc2e986b208c727a4a52144b43..1fa74f165a1318011fb6ede4708485723469fdc7 100644
--- a/modules/gui/src/scene_win/entity_node.cc
+++ b/modules/gui/src/scene_win/entity_node.cc
@@ -72,7 +72,9 @@ EntityNode::EntityNode(gfx::EntityP& entity, SceneNode* parent):
custom_view_ = new LabelNode("Custom Views", this);
model->AddNode(this, custom_view_);
- node = new EntityPartNode("Full View", entity, mol::QueryViewWrapper(entity->GetView()), this);
+ node = new EntityPartNode("Full View", entity,
+ mol::QueryViewWrapper(entity->GetView()),
+ this);
model->AddNode(this, node);
node = new CurrentSelectionNode(entity, this);
diff --git a/modules/gui/src/scene_win/gfx_scene_node.cc b/modules/gui/src/scene_win/gfx_scene_node.cc
index 2b7255f25c663152d5d6eb1e3a247b99bddf131b..ca06e19c844a54e5fc36bd75c627d0cd9d042d5c 100644
--- a/modules/gui/src/scene_win/gfx_scene_node.cc
+++ b/modules/gui/src/scene_win/gfx_scene_node.cc
@@ -25,12 +25,15 @@
#include <QFont>
namespace ost { namespace gui {
-GfxSceneNode::GfxSceneNode(gfx::GfxNodeP gfx_node, SceneNode* parent):SceneNode(parent),gfx_node_(gfx_node){}
+GfxSceneNode::GfxSceneNode(gfx::GfxNodeP gfx_node, SceneNode* parent):
+ SceneNode(parent), gfx_node_(gfx_node) { }
-GfxSceneNode::GfxSceneNode(gfx::GfxNodeP gfx_node, QObject* parent):SceneNode(parent),gfx_node_(gfx_node){}
+GfxSceneNode::GfxSceneNode(gfx::GfxNodeP gfx_node, QObject* parent):
+ SceneNode(parent), gfx_node_(gfx_node) { }
QVariant GfxSceneNode::GetData(int column, int role){
- if(column<0 || column > 2)return QVariant();
+ if (column<0 || column > 2)
+ return QVariant();
if (role==Qt::CheckStateRole && column==0) {
return QVariant(gfx_node_->IsVisible() ? Qt::Checked : Qt::Unchecked);
@@ -52,7 +55,8 @@ int GfxSceneNode::GetColumnCount() const{
return 2;
}
-bool GfxSceneNode::SetData(int column, const QVariant& value, int role){
+bool GfxSceneNode::SetData(int column, const QVariant& value, int role)
+{
if (column==0 && role == Qt::CheckStateRole) {
if (value.toBool()) {
this->GetParent()->SetData(0,value,Qt::CheckStateRole);
diff --git a/modules/gui/src/scene_win/label_node.cc b/modules/gui/src/scene_win/label_node.cc
index f6d2d72f549b124ca55395fbbe0f97489334ea4a..f71c832680aa5b0a8f601d61173b4f4aa6befbbe 100644
--- a/modules/gui/src/scene_win/label_node.cc
+++ b/modules/gui/src/scene_win/label_node.cc
@@ -52,7 +52,7 @@ bool LabelNode::SetData(int column, const QVariant& value, int role){
if (value.toBool()) {
this->GetParent()->SetData(0,value,Qt::CheckStateRole);
} else {
- for(int i = 0; i<this->GetChildCount(); i++){
+ for(int i = 0; i<this->children().size(); i++){
this->GetChild(i)->SetData(0,value,Qt::CheckStateRole);
}
}
diff --git a/modules/gui/src/scene_win/scene_node.cc b/modules/gui/src/scene_win/scene_node.cc
index 347b529a59f6d5ec8a03e3ca91fb91de231a455d..3e99b51ccfbdcef37d0ddaeaf08bd558ac8b6c43 100644
--- a/modules/gui/src/scene_win/scene_node.cc
+++ b/modules/gui/src/scene_win/scene_node.cc
@@ -29,56 +29,31 @@ SceneNode::SceneNode(QObject* parent):QObject(parent){
parent_ = NULL;
}
-SceneNode* SceneNode::GetParent() const{
- return parent_;
-}
-
-void SceneNode::AddChild(SceneNode* node){
- nodes_.append(node);
-}
-
-void SceneNode::RemoveChild(SceneNode* node){
- nodes_.removeAll(node);
-}
-
-int SceneNode::GetChildRow(const SceneNode* node) const{
- for(int i = 0; i < nodes_.size(); i++){
- if(nodes_[i] == node)return i;
+int SceneNode::GetChildRow(const SceneNode* node) const {
+ for(int i = 0; i < this->children().size(); i++){
+ if (this->children()[i] == node)
+ return i;
}
return -1;
}
-int SceneNode::GetChildCount() const{
- return nodes_.size();
+SceneNode::~SceneNode() {
}
int SceneNode::GetRow() const{
- if(parent_){
+ if (parent_) {
return parent_->GetChildRow(this);
}
return 0;
}
-bool SceneNode::IsParent(SceneNode* node) const{
- if(node == this)return true;
- for(int i = 0; i< nodes_.size(); i++){
- if(nodes_[i]==node){
- return true;
- }
- if(nodes_[i]->IsParent(node))
- return true;
- }
- return false;
-}
-
-SceneNode* SceneNode::GetChild(int row) const{
- if(row>=0 && row<nodes_.size()){
- return nodes_[row];
- }
- return NULL;
+SceneNode* SceneNode::GetChild(int row) const
+{
+ return dynamic_cast<SceneNode*>(this->children()[row]);
}
-QVariant SceneNode::GetData(int column, int role){
+QVariant SceneNode::GetData(int column, int role)
+{
return QVariant();
}
diff --git a/modules/gui/src/scene_win/scene_node.hh b/modules/gui/src/scene_win/scene_node.hh
index f701e67b5508d7b3486b8d0cb05dc912803a3258..6b183788d5e336f97e9e44e257e752d3f98905c0 100644
--- a/modules/gui/src/scene_win/scene_node.hh
+++ b/modules/gui/src/scene_win/scene_node.hh
@@ -39,13 +39,13 @@ class DLLEXPORT_OST_GUI SceneNode : public QObject {
public:
SceneNode(SceneNode* node_parent);
SceneNode(QObject* parent=0);
+ virtual ~SceneNode();
- SceneNode* GetParent() const;
- virtual void AddChild(SceneNode* node);
- virtual void RemoveChild(SceneNode* node);
- virtual bool IsParent(SceneNode* node) const;
+ SceneNode* GetParent() const { return dynamic_cast<SceneNode*>(this->parent()); }
+ void AddChild(SceneNode* node) {
+ node->setParent(this);
+ }
virtual SceneNode* GetChild(int row) const;
- virtual int GetChildCount() const;
virtual int GetChildRow(const SceneNode* node) const;
virtual int GetRow() const;
virtual QVariant GetData(int column, int role);
@@ -54,7 +54,6 @@ public:
virtual int GetColumnCount() const;
private:
SceneNode* parent_;
- SceneNodeList nodes_;
};
}}
diff --git a/modules/gui/src/scene_win/scene_win_model.cc b/modules/gui/src/scene_win/scene_win_model.cc
index 08cebc4491118b5656a74443be5a1c8aa1a29b7d..2acc15eb393a8abc7b55669caf08faa1b5235572 100644
--- a/modules/gui/src/scene_win/scene_win_model.cc
+++ b/modules/gui/src/scene_win/scene_win_model.cc
@@ -114,21 +114,23 @@ void SceneWinModel::Update()
QModelIndex SceneWinModel::index(int row, int col,
const QModelIndex& parent) const
{
+ if (!hasIndex(row, col, parent)){
+ return QModelIndex();
+ }
SceneNode* parent_node = GetItem(parent);
- SceneNode* child_node = parent_node->GetChild(row);
- if (child_node) {
- return createIndex(row, col, child_node);
- } else {
- return QModelIndex();
- }
+ if (parent_node->children().size() <= row)
+ return QModelIndex();
+ return createIndex(row, col, parent_node->GetChild(row));
}
QModelIndex SceneWinModel::parent(const QModelIndex& index) const
{
- if(!index.isValid())return QModelIndex();
-
+ if(!index.isValid())
+ return QModelIndex();
SceneNode* node = GetItem(index);
+ if (!node)
+ return QModelIndex();
assert(node);
SceneNode* parent_node = node->GetParent();
@@ -141,7 +143,7 @@ int SceneWinModel::rowCount(const QModelIndex& parent) const
{
SceneNode* parent_node = GetItem(parent);
- return parent_node->GetChildCount();
+ return parent_node->children().size();
}
int SceneWinModel::columnCount(const QModelIndex& parent) const
@@ -270,8 +272,8 @@ void SceneWinModel::SelectionChanged(const gfx::GfxObjP& obj,
void SceneWinModel::RenderModeChanged(const gfx::GfxNodeP& node)
{
- if(render_observers_.contains(node)){
- render_observers_[node]->RenderModeChanged();
+ if(render_observers_.contains(node.get())){
+ render_observers_[node.get()]->RenderModeChanged();
}
}
@@ -288,7 +290,7 @@ bool SceneWinModel::AddNode(SceneNode* parent, SceneNode* child)
{
QModelIndex parent_index=this->GetIndexOf(parent);
if(parent_index.isValid()){
- int row = parent->GetChildCount();
+ int row = parent->children().size();
this->beginInsertRows(parent_index,row,row);
parent->AddChild(child);
this->endInsertRows();
@@ -305,7 +307,7 @@ bool SceneWinModel::RemoveNode(SceneNode* node)
QModelIndex parent_index =this->GetIndexOf(parent);
int row = node->GetRow();
this->beginRemoveRows(parent_index,row,row);
- parent->RemoveChild(node);
+ delete node;
this->endRemoveRows();
return true;
}
@@ -315,13 +317,13 @@ bool SceneWinModel::RemoveNode(SceneNode* node)
void SceneWinModel::AttachRenderModeObserver(RenderModesNode* node)
{
- render_observers_.insert(node->GetGfxNode(),node);
+ render_observers_.insert(node->GetGfxNode().get(),node);
}
void SceneWinModel::DetachRenderModeObserver(RenderModesNode* node)
{
- if(render_observers_.contains(node->GetGfxNode())){
- render_observers_.remove(node->GetGfxNode());
+ if(render_observers_.contains(node->GetGfxNode().get())){
+ render_observers_.remove(node->GetGfxNode().get());
}
}
@@ -351,7 +353,7 @@ QModelIndex SceneWinModel::GetIndex(SceneNode* node, QModelIndex parent,
if(parent.isValid()){
SceneNode* parent_node =reinterpret_cast<SceneNode*>(parent.internalPointer());
if (parent_node == node) return parent;
- for (int i=parent_node->GetChildCount()-1; i>=0; --i) {
+ for (int i=parent_node->children().size()-1; i>=0; --i) {
SceneNode* child = parent_node->GetChild(i);
if(child == node){
if(column<child->GetColumnCount())
diff --git a/modules/gui/src/scene_win/scene_win_model.hh b/modules/gui/src/scene_win/scene_win_model.hh
index c476b16f2c1b14d8fa5fed73546a51cd172b2f38..3382331640b0e9b74166d784cb43be15095ee349 100644
--- a/modules/gui/src/scene_win/scene_win_model.hh
+++ b/modules/gui/src/scene_win/scene_win_model.hh
@@ -106,7 +106,7 @@ private:
SceneNode* root_node_;
SceneNode* scene_node_;
- QMap<gfx::GfxNodeP, RenderModesNode*> render_observers_;
+ QMap<gfx::GfxNode*, RenderModesNode*> render_observers_;
QMap<gfx::GfxNode*, SceneNode*> node_map_;
};
diff --git a/modules/gui/src/widget_geom_handler.cc b/modules/gui/src/widget_geom_handler.cc
index 431fd8ff1903a5e04f456528b1ab86640e3f58d2..efb6d752a83c802fd6339e1be26c338d9242f8d0 100644
--- a/modules/gui/src/widget_geom_handler.cc
+++ b/modules/gui/src/widget_geom_handler.cc
@@ -34,7 +34,6 @@ void WidgetGeomHandler::LoadGeom(const QString& prefix)
settings.beginGroup(prefix+this->objectName());
if (settings.contains("pos") && settings.contains("size")) {
QPoint pos = settings.value("pos").toPoint();
- QSize size = settings.value("size").toSize();
Qt::WindowStates state = Qt::WindowStates(settings.value("state").toInt());
widget_->move(pos);
widget_->setWindowState(state);
diff --git a/modules/img/alg/src/CMakeLists.txt b/modules/img/alg/src/CMakeLists.txt
index a49b80125f11de0531412e7fd2929577669aa647..5df3fd55852d08aad58d14147fdf1b7d7c9ec0da 100644
--- a/modules/img/alg/src/CMakeLists.txt
+++ b/modules/img/alg/src/CMakeLists.txt
@@ -59,7 +59,6 @@ gaussian.hh
gaussian_laplacian.hh
highest_peak_search_3d.hh
histogram.hh
-levenberg_marquardt.h
line_iterator.hh
local_sigma_threshold.hh
mask_image.hh
@@ -70,7 +69,6 @@ normalizer.hh
norm_linear.hh
norm_log.hh
norm_od.hh
-numeric.h
power_spectrum.hh
randomize.hh
smooth_mask_image.hh
diff --git a/modules/img/alg/src/dft.hh b/modules/img/alg/src/dft.hh
index 32dcf022ea747211bf6a69b78e6b7cc2a239dc0c..8265dcc102c961595c428ae2b65ebd6a3ab65cb4 100644
--- a/modules/img/alg/src/dft.hh
+++ b/modules/img/alg/src/dft.hh
@@ -30,7 +30,7 @@ namespace ost { namespace img { namespace alg {
/// \brief Computes Fourier Trasnform honoring the origin of the image
///
/// \sa \ref view_phase_diff.py "View Phase Diference Example"
-/// \sa \ref fft_li.py "View Fourier Transform Example"
+/// \sa \example fft_li.py "View Fourier Transform Example"
class DLLEXPORT_IMG_ALG DFT: public ConstModOPAlgorithm {
public:
DFT();
diff --git a/modules/img/alg/src/discrete_shrink.cc b/modules/img/alg/src/discrete_shrink.cc
index ba01ae54635d9c4bab555b1772f38f5c43b1129b..6aef59bcfa03c4c6bbd1332d1254916b73a3e465 100644
--- a/modules/img/alg/src/discrete_shrink.cc
+++ b/modules/img/alg/src/discrete_shrink.cc
@@ -49,7 +49,6 @@ void do_shrink(const ImageStateImpl<T,D>& isi, T& dest, const Extent& inner_ext)
T sum(0);
Real count=0.0;
for(ExtentIterator bit(inner_ext);!bit.AtEnd();++bit) {
- LOG_VERBOSE("inner extent point:" << Point(bit)<<","<<isi.GetExtent().Contains(Point(bit)));
sum+=isi.Value(bit);
count+=1.0;
}
diff --git a/modules/img/alg/src/fft.cc b/modules/img/alg/src/fft.cc
index 955f218346844dedbb6e816606664be9f864169b..61cc3199c645e37f8d17a9daab0b9fd8c286858d 100644
--- a/modules/img/alg/src/fft.cc
+++ b/modules/img/alg/src/fft.cc
@@ -267,6 +267,10 @@ ImageStateBasePtr FFTFnc::VisitState(const ImageStateImpl<T,D>& s) const
throw FFTException(ostr.str());
}
+// force explicit instantiation to make intel compiler happy
+template ImageStateBasePtr FFTFnc::VisitState<Real,FrequencyDomain>(const ImageStateImpl<Real,FrequencyDomain>& ) const;
+template ImageStateBasePtr FFTFnc::VisitState<unsigned short,SpatialDomain>(const ImageStateImpl<unsigned short,SpatialDomain>& ) const;
+
} //alg ns
template class TEMPLATE_DEF_EXPORT image_state::ImageStateConstModOPAlgorithm<alg::FFTFnc>;
diff --git a/modules/img/alg/src/levenberg_marquardt.h b/modules/img/alg/src/levenberg_marquardt.h
deleted file mode 100644
index f2e50c8c1be237b2ebc73a76f6244a079025a369..0000000000000000000000000000000000000000
--- a/modules/img/alg/src/levenberg_marquardt.h
+++ /dev/null
@@ -1,178 +0,0 @@
-// Copyright (c) 2007, 2008, 2009 libmv authors.
-//
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to
-// deal in the Software without restriction, including without limitation the
-// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-// sell copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-//
-// The above copyright notice and this permission notice shall be included in
-// all copies or substantial portions of the Software.
-//
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-// IN THE SOFTWARE.
-//
-// A simple implementation of levenberg marquardt.
-//
-// [1] K. Madsen, H. Nielsen, O. Tingleoff. Methods for Non-linear Least
-// Squares Problems.
-// http://www2.imm.dtu.dk/pubdb/views/edoc_download.php/3215/pdf/imm3215.pdf
-//
-// TODO(keir): Cite the Lourakis' dogleg paper.
-
-#ifndef LIBMV_NUMERIC_LEVENBERG_MARQUARDT_H
-#define LIBMV_NUMERIC_LEVENBERG_MARQUARDT_H
-
-#include <cmath>
-
-#include <ost/img/alg/numeric.h>
-
-namespace ost { namespace img { namespace alg {
-
-template<typename Function,
- typename Jacobian,
- typename Solver = Eigen::SVD<
- Matrix<typename Function::FMatrixType::RealScalar,
- Function::XMatrixType::RowsAtCompileTime,
- Function::XMatrixType::RowsAtCompileTime> > >
-class LevenbergMarquardt {
- public:
- typedef typename Function::XMatrixType::RealScalar Scalar;
- typedef typename Function::FMatrixType FVec;
- typedef typename Function::XMatrixType Parameters;
- typedef Matrix<typename Function::FMatrixType::RealScalar,
- Function::FMatrixType::RowsAtCompileTime,
- Function::XMatrixType::RowsAtCompileTime> JMatrixType;
- typedef Matrix<typename JMatrixType::RealScalar,
- JMatrixType::ColsAtCompileTime,
- JMatrixType::ColsAtCompileTime> AMatrixType;
-
- // TODO(keir): Some of these knobs can be derived from each other and
- // removed, instead of requiring the user to set them.
- enum Status {
- RUNNING,
- GRADIENT_TOO_SMALL, // eps > max(J'*f(x))
- RELATIVE_STEP_SIZE_TOO_SMALL, // eps > ||dx|| / ||x||
- ERROR_TOO_SMALL, // eps > ||f(x)||
- HIT_MAX_ITERATIONS,
- };
-
- LevenbergMarquardt(const Function &f)
- : f_(f), df_(f) {}
-
- struct SolverParameters {
- SolverParameters()
- : gradient_threshold(1e-20),
- relative_step_threshold(1e-20),
- error_threshold(1e-16),
- initial_scale_factor(1e-3),
- max_iterations(200) {}
- Scalar gradient_threshold; // eps > max(J'*f(x))
- Scalar relative_step_threshold; // eps > ||dx|| / ||x||
- Scalar error_threshold; // eps > ||f(x)||
- Scalar initial_scale_factor; // Initial u for solving normal equations.
- int max_iterations; // Maximum number of solver iterations.
- };
-
- struct Results {
- Scalar error_magnitude; // ||f(x)||
- Scalar gradient_magnitude; // ||J'f(x)||
- int iterations;
- Status status;
- };
-
- Status Update(const Parameters &x, const SolverParameters ¶ms,
- JMatrixType *J, AMatrixType *A, FVec *error, Parameters *g) {
- *J = df_(x);
- *A = (*J).transpose() * (*J);
- *error = -f_(x);
- *g = (*J).transpose() * *error;
- if (g->cwise().abs().maxCoeff() < params.gradient_threshold) {
- return GRADIENT_TOO_SMALL;
- } else if (error->norm() < params.error_threshold) {
- return ERROR_TOO_SMALL;
- }
- return RUNNING;
- }
-
- Results minimize(Parameters *x_and_min) {
- SolverParameters params;
- minimize(params, x_and_min);
- }
-
- Results minimize(const SolverParameters ¶ms, Parameters *x_and_min) {
- Parameters &x = *x_and_min;
- JMatrixType J;
- AMatrixType A;
- FVec error;
- Parameters g;
-
- Results results;
- results.status = Update(x, params, &J, &A, &error, &g);
-
- Scalar u = Scalar(params.initial_scale_factor*A.diagonal().maxCoeff());
- Scalar v = 2;
-
- Parameters dx, x_new;
- int i;
- for (i = 0; results.status == RUNNING && i < params.max_iterations; ++i) {
-// LOG(INFO) << "iteration: " << i;
-// LOG(INFO) << "||f(x)||: " << f_(x).norm();
-// LOG(INFO) << "max(g): " << g.cwise().abs().maxCoeff();
-// LOG(INFO) << "u: " << u;
-// LOG(INFO) << "v: " << v;
-
- AMatrixType A_augmented = A + u*AMatrixType::Identity(J.cols(), J.cols());
- Solver solver(A_augmented);
- bool solved = solver.solve(g, &dx);
-// if (!solved) LOG(ERROR) << "Failed to solve";
- if (solved && dx.norm() <= params.relative_step_threshold * x.norm()) {
- results.status = RELATIVE_STEP_SIZE_TOO_SMALL;
- break;
- }
- if (solved) {
- x_new = x + dx;
- // Rho is the ratio of the actual reduction in error to the reduction
- // in error that would be obtained if the problem was linear.
- // See [1] for details.
- Scalar rho((error.squaredNorm() - f_(x_new).squaredNorm())
- / dx.dot(u*dx + g));
- if (rho > 0) {
- // Accept the Gauss-Newton step because the linear model fits well.
- x = x_new;
- results.status = Update(x, params, &J, &A, &error, &g);
- Scalar tmp = Scalar(2*rho-1);
- u = u*std::max(Real(1/3.), 1 - (tmp*tmp*tmp));
- v = 2;
- continue;
- }
- }
- // Reject the update because either the normal equations failed to solve
- // or the local linear model was not good (rho < 0). Instead, increase u
- // to move closer to gradient descent.
- u *= v;
- v *= 2;
- }
- if (results.status == RUNNING) {
- results.status = HIT_MAX_ITERATIONS;
- }
- results.error_magnitude = error.norm();
- results.gradient_magnitude = g.norm();
- results.iterations = i;
- return results;
- }
-
- private:
- const Function &f_;
- Jacobian df_;
-};
-
-}}} // namespace mv
-
-#endif // LIBMV_NUMERIC_LEVENBERG_MARQUARDT_H
diff --git a/modules/img/alg/src/numeric.h b/modules/img/alg/src/numeric.h
deleted file mode 100644
index cbd5711c0884e8a3e54cde2cc4f95a4c8b66a87a..0000000000000000000000000000000000000000
--- a/modules/img/alg/src/numeric.h
+++ /dev/null
@@ -1,441 +0,0 @@
-// Copyright (c) 2007, 2008 libmv authors.
-//
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to
-// deal in the Software without restriction, including without limitation the
-// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-// sell copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-//
-// The above copyright notice and this permission notice shall be included in
-// all copies or substantial portions of the Software.
-//
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
-// IN THE SOFTWARE.
-//
-// Matrix and vector classes, based on Eigen2.
-//
-// Avoid using Eigen2 classes directly; instead typedef them here.
-
-#ifndef LIBMV_NUMERIC_NUMERIC_H
-#define LIBMV_NUMERIC_NUMERIC_H
-
-#include <Eigen/Array>
-#include <Eigen/Cholesky>
-#include <Eigen/Core>
-#include <Eigen/Geometry>
-#include <Eigen/LU>
-#include <Eigen/SVD>
-
-#include <ost/base.hh>
-
-#include <iostream>
-
-#if _WIN32 || __APPLE__
- void static sincos (Real x, Real *sinx, Real *cosx) {
- *sinx = sin(x);
- *cosx = cos(x);
- }
-#endif //_WIN32 || __APPLE__
-
-// #if _WIN32
- // inline long lround(double d) {
- // return (long)(d>0 ? d+0.5 : ceil(d-0.5));
- // }
- // inline int round(double d) {
- // return (d>0) ? int(d+0.5) : int(d-0.5);
- // }
- // typedef unsigned int uint;
-// #endif //_WIN32
-
-namespace ost { namespace img { namespace alg {
-
-typedef Eigen::MatrixXf Mat;
-typedef Eigen::VectorXf Vec;
-
-typedef Eigen::MatrixXf Matf;
-typedef Eigen::VectorXf Vecf;
-
-typedef Eigen::Matrix<unsigned int, Eigen::Dynamic, Eigen::Dynamic> Matu;
-typedef Eigen::Matrix<unsigned int, Eigen::Dynamic, 1> Vecu;
-
-typedef Eigen::Matrix<Real, 2, 2> Mat2;
-typedef Eigen::Matrix<Real, 2, 3> Mat23;
-typedef Eigen::Matrix<Real, 3, 3> Mat3;
-typedef Eigen::Matrix<Real, 3, 4> Mat34;
-typedef Eigen::Matrix<Real, 3, 5> Mat35;
-typedef Eigen::Matrix<Real, 4, 3> Mat43;
-typedef Eigen::Matrix<Real, 4, 4> Mat4;
-typedef Eigen::Matrix<Real, 4, 6> Mat46;
-typedef Eigen::Matrix<float, 2, 2> Mat2f;
-typedef Eigen::Matrix<float, 2, 3> Mat23f;
-typedef Eigen::Matrix<float, 3, 3> Mat3f;
-typedef Eigen::Matrix<float, 3, 4> Mat34f;
-typedef Eigen::Matrix<float, 3, 5> Mat35f;
-typedef Eigen::Matrix<float, 4, 3> Mat43f;
-typedef Eigen::Matrix<float, 4, 4> Mat4f;
-typedef Eigen::Matrix<float, 4, 6> Mat46f;
-
-typedef Eigen::Matrix<Real, 3, 3, Eigen::RowMajor> RMat3;
-
-typedef Eigen::Matrix<Real, 2, Eigen::Dynamic> Mat2X;
-typedef Eigen::Matrix<Real, 3, Eigen::Dynamic> Mat3X;
-typedef Eigen::Matrix<Real, 4, Eigen::Dynamic> Mat4X;
-typedef Eigen::Matrix<Real, Eigen::Dynamic, 2> MatX2;
-typedef Eigen::Matrix<Real, Eigen::Dynamic, 3> MatX3;
-typedef Eigen::Matrix<Real, Eigen::Dynamic, 4> MatX4;
-typedef Eigen::Matrix<Real, Eigen::Dynamic, 9> MatX9;
-
-typedef Eigen::Vector2f Vec2;
-typedef Eigen::Vector3f Vec3;
-typedef Eigen::Vector4f Vec4;
-typedef Eigen::Matrix<Real, 5, 1> Vec5;
-typedef Eigen::Matrix<Real, 6, 1> Vec6;
-typedef Eigen::Matrix<Real, 7, 1> Vec7;
-typedef Eigen::Matrix<Real, 8, 1> Vec8;
-typedef Eigen::Matrix<Real, 9, 1> Vec9;
-typedef Eigen::Matrix<Real, 10, 1> Vec10;
-typedef Eigen::Matrix<Real, 13, 1> Vec13;
-
-typedef Eigen::Vector2f Vec2f;
-typedef Eigen::Vector3f Vec3f;
-typedef Eigen::Vector4f Vec4f;
-
-typedef Eigen::VectorXi VecXi;
-
-typedef Eigen::Vector2i Vec2i;
-typedef Eigen::Vector3i Vec3i;
-typedef Eigen::Vector4i Vec4i;
-
-typedef Eigen::Matrix<float,
- Eigen::Dynamic,
- Eigen::Dynamic,
- Eigen::RowMajor> RMatf;
-
-using Eigen::Map;
-using Eigen::Dynamic;
-using Eigen::Matrix;
-
-// Find U, s, and VT such that
-//
-// A = U * diag(s) * VT
-//
-template <typename TMat, typename TVec>
-inline void SVD(TMat *A, Vec *s, Mat *U, Mat *VT) {
- assert(0);
-}
-
-// Solve the linear system Ax = 0 via SVD. Store the solution in x, such that
-// ||x|| = 1.0. Return the singluar value corresponding to the solution.
-// Destroys A and resizes x if necessary.
-// TODO(maclean): Take the SVD of the transpose instead of this zero padding.
-template <typename TMat, typename TVec>
-Real Nullspace(TMat *A, TVec *nullspace) {
- if (A->rows() >= A->cols()) {
- Eigen::SVD<TMat> svd(*A);
- (*nullspace) = svd.matrixV().col(A->cols()-1);
- return svd.singularValues()(A->cols()-1);
- }
- // Extend A with rows of zeros to make it square. It's a hack, but is
- // necessary until Eigen supports SVD with more columns than rows.
- Mat A_extended(A->cols(), A->cols());
- A_extended.block(A->rows(), 0, A->cols() - A->rows(), A->cols()).setZero();
- A_extended.block(0,0, A->rows(), A->cols()) = (*A);
- return Nullspace(&A_extended, nullspace);
-}
-
-// Solve the linear system Ax = 0 via SVD. Finds two solutions, x1 and x2, such
-// that x1 is the best solution and x2 is the next best solution (in the L2
-// norm sense). Store the solution in x1 and x2, such that ||x|| = 1.0. Return
-// the singluar value corresponding to the solution x1. Destroys A and resizes
-// x if necessary.
-template <typename TMat, typename TVec1, typename TVec2>
-Real Nullspace2(TMat *A, TVec1 *x1, TVec2 *x2) {
- if (A->rows() >= A->cols()) {
- Eigen::SVD<TMat> svd(*A);
- Mat V = svd.matrixV();
- *x1 = V.col(A->cols() - 1);
- *x2 = V.col(A->cols() - 2);
- return svd.singularValues()(A->cols()-1);
- }
- // Extend A with rows of zeros to make it square. It's a hack, but is
- // necessary until Eigen supports SVD with more columns than rows.
- Mat A_extended(A->cols(), A->cols());
- A_extended.block(A->rows(), 0, A->cols() - A->rows(), A->cols()).setZero();
- A_extended.block(0,0, A->rows(), A->cols()) = (*A);
- return Nullspace2(&A_extended, x1, x2);
-}
-
-// In place transpose for square matrices.
-template<class TA>
-inline void TransposeInPlace(TA *A) {
- *A = A->transpose().eval();
-}
-
-template<typename TVec>
-inline Real NormL1(const TVec &x) {
- return x.cwise().abs().sum();
-}
-
-template<typename TVec>
-inline Real NormL2(const TVec &x) {
- return x.norm();
-}
-
-template<typename TVec>
-inline Real NormLInfinity(const TVec &x) {
- return x.cwise().abs().maxCoeff();
-}
-
-template<typename TVec>
-inline Real DistanceL1(const TVec &x, const TVec &y) {
- return (x - y).cwise().abs().sum();
-}
-
-template<typename TVec>
-inline Real DistanceL2(const TVec &x, const TVec &y) {
- return (x - y).norm();
-}
-template<typename TVec>
-inline Real DistanceLInfinity(const TVec &x, const TVec &y) {
- return (x - y).cwise().abs().maxCoeff();
-}
-
-// Normalize a vector with the L1 norm, and return the norm before it was
-// normalized.
-template<typename TVec>
-inline Real NormalizeL1(TVec *x) {
- Real norm = NormL1(*x);
- *x /= norm;
- return norm;
-}
-
-// Normalize a vector with the L2 norm, and return the norm before it was
-// normalized.
-template<typename TVec>
-inline Real NormalizeL2(TVec *x) {
- Real norm = NormL2(*x);
- *x /= norm;
- return norm;
-}
-
-// Normalize a vector with the L^Infinity norm, and return the norm before it
-// was normalized.
-template<typename TVec>
-inline Real NormalizeLInfinity(TVec *x) {
- Real norm = NormLInfinity(*x);
- *x /= norm;
- return norm;
-}
-
-// Return the square of a number.
-template<typename T>
-inline T Square(T x) {
- return x * x;
-}
-
-Mat3 RotationAroundX(Real angle);
-Mat3 RotationAroundY(Real angle);
-Mat3 RotationAroundZ(Real angle);
-
-// Returns the rotation matrix of a rotation of angle |axis| around axis.
-// This is computed using the Rodrigues formula, see:
-// http://mathworld.wolfram.com/RodriguesRotationFormula.html
-Mat3 RotationRodrigues(const Vec3 &axis);
-
-// Make a rotation matrix such that center becomes the direction of the
-// positive z-axis, and y is oriented close to up.
-Mat3 LookAt(Vec3 center);
-
-// Return a diagonal matrix from a vector containg the diagonal values.
-template <typename TVec>
-inline Mat Diag(const TVec &x) {
- return x.asDiagonal();
-}
-
-template<typename TMat>
-inline Real FrobeniusNorm(const TMat &A) {
- return sqrt(A.cwise().abs2().sum());
-}
-
-template<typename TMat>
-inline Real FrobeniusDistance(const TMat &A, const TMat &B) {
- return FrobeniusNorm(A - B);
-}
-
-inline Vec3 CrossProduct(const Vec3 &x, const Vec3 &y) {
- return x.cross(y);
-}
-
-Mat3 CrossProductMatrix(const Vec3 &x);
-
-void MeanAndVarianceAlongRows(const Mat &A,
- Vec *mean_pointer,
- Vec *variance_pointer);
-
-#if _WIN32
- // TODO(bomboze): un-#if this for both platforms once tested under Windows
- /* This solution was extensively discussed here http://forum.kde.org/viewtopic.php?f=74&t=61940 */
- #define SUM_OR_DYNAMIC(x,y) (x==Eigen::Dynamic||y==Eigen::Dynamic)?Eigen::Dynamic:(x+y)
-
- template<typename Derived1, typename Derived2>
- struct hstack_return {
- typedef typename Derived1::Scalar Scalar;
- enum {
- RowsAtCompileTime = Derived1::RowsAtCompileTime,
- ColsAtCompileTime = SUM_OR_DYNAMIC(Derived1::ColsAtCompileTime, Derived2::ColsAtCompileTime),
- Options = Derived1::Flags&Eigen::RowMajorBit ? Eigen::RowMajor : 0,
- MaxRowsAtCompileTime = Derived1::MaxRowsAtCompileTime,
- MaxColsAtCompileTime = SUM_OR_DYNAMIC(Derived1::MaxColsAtCompileTime, Derived2::MaxColsAtCompileTime)
- };
- typedef Eigen::Matrix<Scalar,
- RowsAtCompileTime,
- ColsAtCompileTime,
- Options,
- MaxRowsAtCompileTime,
- MaxColsAtCompileTime> type;
- };
-
- template<typename Derived1, typename Derived2>
- typename hstack_return<Derived1,Derived2>::type
- HStack (const Eigen::MatrixBase<Derived1>& lhs, const Eigen::MatrixBase<Derived2>& rhs) {
- typename hstack_return<Derived1,Derived2>::type res;
- res.resize(lhs.rows(), lhs.cols()+rhs.cols());
- res << lhs, rhs;
- return res;
- };
-
-
- template<typename Derived1, typename Derived2>
- struct vstack_return {
- typedef typename Derived1::Scalar Scalar;
- enum {
- RowsAtCompileTime = SUM_OR_DYNAMIC(Derived1::RowsAtCompileTime, Derived2::RowsAtCompileTime),
- ColsAtCompileTime = Derived1::ColsAtCompileTime,
- Options = Derived1::Flags&Eigen::RowMajorBit ? Eigen::RowMajor : 0,
- MaxRowsAtCompileTime = SUM_OR_DYNAMIC(Derived1::MaxRowsAtCompileTime, Derived2::MaxRowsAtCompileTime),
- MaxColsAtCompileTime = Derived1::MaxColsAtCompileTime
- };
- typedef Eigen::Matrix<Scalar,
- RowsAtCompileTime,
- ColsAtCompileTime,
- Options,
- MaxRowsAtCompileTime,
- MaxColsAtCompileTime> type;
- };
-
- template<typename Derived1, typename Derived2>
- typename vstack_return<Derived1,Derived2>::type
- VStack (const Eigen::MatrixBase<Derived1>& lhs, const Eigen::MatrixBase<Derived2>& rhs) {
- typename vstack_return<Derived1,Derived2>::type res;
- res.resize(lhs.rows()+rhs.rows(), lhs.cols());
- res << lhs, rhs;
- return res;
- };
-
-
-#else //_WIN32
-
- // Since it is not possible to typedef privately here, use a macro.
- // Always take dynamic columns if either side is dynamic.
- #define COLS \
- ((ColsLeft == Eigen::Dynamic || ColsRight == Eigen::Dynamic) \
- ? Eigen::Dynamic : (ColsLeft + ColsRight))
-
- // Same as above, except that prefer fixed size if either is fixed.
- #define ROWS \
- ((RowsLeft == Eigen::Dynamic && RowsRight == Eigen::Dynamic) \
- ? Eigen::Dynamic \
- : ((RowsLeft == Eigen::Dynamic) \
- ? RowsRight \
- : RowsLeft \
- ) \
- )
-
- // TODO(keir): Add a static assert if both rows are at compiletime.
- template<typename T, int RowsLeft, int RowsRight, int ColsLeft, int ColsRight>
- Eigen::Matrix<T, ROWS, COLS>
- HStack(const Eigen::Matrix<T, RowsLeft, ColsLeft> &left,
- const Eigen::Matrix<T, RowsRight, ColsRight> &right) {
- assert(left.rows() == right.rows());
- int n = left.rows();
- int m1 = left.cols();
- int m2 = right.cols();
-
- Eigen::Matrix<T, ROWS, COLS> stacked(n, m1 + m2);
- stacked.block(0, 0, n, m1) = left;
- stacked.block(0, m1, n, m2) = right;
- return stacked;
- }
-
- // Reuse the above macros by swapping the order of Rows and Cols. Nasty, but
- // the duplication is worse.
- // TODO(keir): Add a static assert if both rows are at compiletime.
- // TODO(keir): Mail eigen list about making this work for general expressions
- // rather than only matrix types.
- template<typename T, int RowsLeft, int RowsRight, int ColsLeft, int ColsRight>
- Eigen::Matrix<T, COLS, ROWS>
- VStack(const Eigen::Matrix<T, ColsLeft, RowsLeft> &top,
- const Eigen::Matrix<T, ColsRight, RowsRight> &bottom) {
- assert(top.cols() == bottom.cols());
- int n1 = top.rows();
- int n2 = bottom.rows();
- int m = top.cols();
-
- Eigen::Matrix<T, COLS, ROWS> stacked(n1 + n2, m);
- stacked.block(0, 0, n1, m) = top;
- stacked.block(n1, 0, n2, m) = bottom;
- return stacked;
- }
- #undef COLS
- #undef ROWS
-#endif //_WIN32
-
-
-
-void HorizontalStack(const Mat &left, const Mat &right, Mat *stacked);
-
-template<typename TTop, typename TBot, typename TStacked>
-void VerticalStack(const TTop &top, const TBot &bottom, TStacked *stacked) {
- assert(top.cols() == bottom.cols());
- int n1 = top.rows();
- int n2 = bottom.rows();
- int m = top.cols();
-
- stacked->resize(n1 + n2, m);
- stacked->block(0, 0, n1, m) = top;
- stacked->block(n1, 0, n2, m) = bottom;
-}
-
-void MatrixColumn(const Mat &A, int i, Vec2 *v);
-void MatrixColumn(const Mat &A, int i, Vec3 *v);
-void MatrixColumn(const Mat &A, int i, Vec4 *v);
-
-template <typename TMat, typename TCols>
-TMat ExtractColumns(const TMat &A, const TCols &columns) {
- TMat compressed(A.rows(), columns.size());
- for (int i = 0; i < columns.size(); ++i) {
- compressed.col(i) = A.col(columns[i]);
- }
- return compressed;
-}
-
-template <typename TMat, typename TDest>
-void reshape(const TMat &a, int rows, int cols, TDest *b) {
- assert(a.rows()*a.cols() == rows*cols);
- b->resize(rows, cols);
- for (int i = 0; i < rows; i++) {
- for (int j = 0; j < cols; j++) {
- (*b)(i, j) = a[cols*i + j];
- }
- }
-}
-
-}}} // namespace mv
-
-#endif // LIBMV_NUMERIC_NUMERIC_H
diff --git a/modules/img/alg/src/stat_accumulator.hh b/modules/img/alg/src/stat_accumulator.hh
index 53399f8be99c0cb4e1a445b38aabfd7252bb4c41..cb4530eac56c0c133d58581359b19540d25c685d 100644
--- a/modules/img/alg/src/stat_accumulator.hh
+++ b/modules/img/alg/src/stat_accumulator.hh
@@ -20,183 +20,231 @@
#ifndef OST_STAT_ACCUMULATOR_HH
#define OST_STAT_ACCUMULATOR_HH
+#include <limits>
+#include <boost/math/special_functions/binomial.hpp>
#include <ost/base.hh>
#include <ost/message.hh>
#include <ost/img/alg/module_config.hh>
namespace ost { namespace img { namespace alg {
-template<unsigned int MAX_MOMENT=4>
+namespace {
+
+template<class D>
+struct MinMax{
+ static bool less_cmp_(const D& v1, const D& v2){return v1<v2;}
+};
+template<>
+struct MinMax<Complex>{
+ static bool less_cmp_(const Complex& v1, const Complex& v2){return abs(v1)<abs(v2);}
+};
+
+} //anon ns
+
+template<unsigned int MAX_MOMENT=4,typename DATATYPE=Real>
class StatAccumulator
{
public:
StatAccumulator():
- mean_(0.0),
sum_(0.0),
sum2_(0.0),
- m2_(0.0),
- m3_(0.0),
- m4_(0.0),
- n_(1)
- {}
-
- void operator()(Real val)
+ max_(-std::numeric_limits<DATATYPE>::max()),
+ min_(std::numeric_limits<DATATYPE>::max()),
+ m_(),
+ w_(0.0),
+ n_(0)
{
- Real delta,delta_n,delta_n2,term;
- if(MAX_MOMENT>0){
- delta = val - mean_;
- delta_n = delta / n_;
- }
- if(MAX_MOMENT>3){
- delta_n2 = delta_n * delta_n;
- }
- if(MAX_MOMENT>1){
- term = delta * delta_n * (n_-1);
- }
- if(MAX_MOMENT>3){
- m4_ += term * delta_n2 * (n_*n_ - 3*n_ + 3) + 6 * delta_n2 * m2_ - 4 * delta_n * m3_;
- }
- if(MAX_MOMENT>2){
- m3_ += term * delta_n * (n_ - 2) - 3 * delta_n * m2_;
- }
- if(MAX_MOMENT>1){
- m2_ += term;
+ for(unsigned int i=0;i<MAX_MOMENT;++i){
+ m_[i]=0.0;
}
+
+ }
+
+ StatAccumulator(DATATYPE val, Real w=1.0):
+ sum_(val),
+ sum2_(val*val),
+ max_(val),
+ min_(val),
+ m_(),
+ w_(w),
+ n_(1)
+ {
if(MAX_MOMENT>0){
- mean_ += delta_n;
+ m_[0]=val;
+ for(unsigned int i=1;i<MAX_MOMENT;++i){
+ m_[i]=0.0;
+ }
}
- n_+=1;
- sum_+=val;
- sum2_+=val*val;
}
- StatAccumulator<MAX_MOMENT> operator+(const StatAccumulator<MAX_MOMENT>& acc2) const
+ void operator()(DATATYPE val, Real w=1.0)
{
- StatAccumulator<MAX_MOMENT> acc(acc2);
+ *this+=StatAccumulator(val,w);
+ }
+
+ StatAccumulator<MAX_MOMENT,DATATYPE> operator+(const StatAccumulator<MAX_MOMENT,DATATYPE>& acc2) const
+ {
+ StatAccumulator<MAX_MOMENT,DATATYPE> acc(acc2);
acc+=*this;
return acc;
}
- StatAccumulator<MAX_MOMENT>& operator+=(const StatAccumulator<MAX_MOMENT>& acc)
+ StatAccumulator<MAX_MOMENT,DATATYPE>& operator+=(const StatAccumulator<MAX_MOMENT,DATATYPE>& acc)
{
- if(acc.n_==1){
+ if(0.0>=w_){
+ *this=acc;
return *this;
}
- if(n_==1){
- mean_=acc.mean_;
- sum_=acc.sum_;
- sum2_=acc.sum2_;
- m2_=acc.m2_;
- m3_=acc.m3_;
- m4_=acc.m4_;
- n_=acc.n_;
+ if(0.0>=acc.w_){
return *this;
}
- Real delta,delta_n,delta_n2,na,nanb;
- Real nb=acc.n_-1;
- if(MAX_MOMENT>0){
- na=n_-1;
- delta = acc.mean_ - mean_;
- delta_n = delta / (na+nb);
- }
- if(MAX_MOMENT>1){
- nanb=na*nb;
- }
- if(MAX_MOMENT>2){
- delta_n2 = delta_n * delta_n;
- }
- if(MAX_MOMENT>3){
- m4_+=acc.m4_+delta*delta_n*delta_n2*nanb*(na*na-nanb+nb*nb)+6.0*delta_n2*(na*na*acc.m2_+nb*nb*m2_)+4.0*delta_n*(na*acc.m3_-nb*m3_);
- }
- if(MAX_MOMENT>2){
- m3_+=acc.m3_+delta*delta_n2*nanb*(na-nb)+3.0*delta_n*(na*acc.m2_-nb*m2_);
- }
- if(MAX_MOMENT>1){
- m2_ += acc.m2_+delta*delta_n*nanb;
- }
- if(MAX_MOMENT>0){
- mean_ += nb*delta_n;
- }
+ n_+=acc.n_;
+ Real wn=w_+acc.w_;
+
sum_+=acc.sum_;
sum2_+=acc.sum2_;
- n_+=nb;
+ max_=std::max<DATATYPE>(max_,acc.max_,MinMax<DATATYPE>::less_cmp_);
+ min_=std::min<DATATYPE>(min_,acc.min_,MinMax<DATATYPE>::less_cmp_);
+ if(MAX_MOMENT>0){
+ DATATYPE delta=acc.m_[0]-m_[0];
+ DATATYPE delta_w=delta/wn;
+ if(MAX_MOMENT>2){
+ DATATYPE w1w2_delta_w=w_*acc.w_*delta_w;
+ DATATYPE w1w2_delta_wp=w1w2_delta_w*w1w2_delta_w;
+ Real iw2=1.0/acc.w_;
+ Real iw2pm1=iw2;
+ Real miw1=-1.0/w_;
+ Real miw1pm1=miw1;
+ DATATYPE mn[MAX_MOMENT]; // only MAX_MOMENT-2 values needed but overdimensioned to allow compilation for MAX_MOMENT==0 (even though it gets kicked out in the end by the dead code elimination)
+ for(unsigned int p=3;p<=MAX_MOMENT;++p){
+ w1w2_delta_wp*=w1w2_delta_w;
+ iw2pm1*=iw2;
+ miw1pm1*=miw1;
+ DATATYPE delta_wk=1.0;
+ DATATYPE s=0.0;
+ Real mw2k=1.0;
+ Real w1k=1.0;
+ for(unsigned int k=1;k<=p-2;++k){
+ w1k*=w_;
+ mw2k*=-acc.w_;
+ delta_wk*=delta_w;
+ s+=boost::math::binomial_coefficient<Real>(p, k)*(mw2k*m_[p-k-1]+w1k*acc.m_[p-k-1])*delta_wk;
+ }
+ mn[p-3]=acc.m_[p-1]+s+w1w2_delta_wp*(iw2pm1-miw1pm1);
+ }
+ for(unsigned int p=3;p<=MAX_MOMENT;++p){
+ m_[p-1]+=mn[p-3];
+ }
+ }
+ if(MAX_MOMENT>1){
+ m_[1]+=acc.m_[1]+delta_w*delta*acc.w_*w_;
+ }
+ m_[0]+=delta_w*acc.w_;
+ w_=wn;
+ }
return *this;
}
Real GetNumSamples() const
{
- return n_-1.0;
+ return n_;
+ }
+
+ DATATYPE GetMaximum() const
+ {
+ return max_;
+ }
+
+ DATATYPE GetMinimum() const
+ {
+ return min_;
+ }
+
+ Real GetWeight() const
+ {
+ return w_;
+ }
+
+ DATATYPE GetMoment(unsigned int i) const
+ {
+ if(1>i){
+ throw Error("Invalid moment.");
+ }
+ if(MAX_MOMENT<i){
+ throw Error("Moment was not calculated.");
+ }
+ return m_[i-1];
}
- Real GetMean() const
+ DATATYPE GetMean() const
{
if(MAX_MOMENT<1){
throw Error("Mean was not calculated.");
}
- return mean_;
+ return m_[0];
}
- Real GetSum() const
+ DATATYPE GetSum() const
{
return sum_;
}
- Real GetVariance() const
+ DATATYPE GetVariance() const
{
if(MAX_MOMENT<2){
throw Error("Variance was not calculated.");
}
- if(n_==1.0){
+ if(n_==0.0){
return 0.0;
}
- return m2_/(n_-1);
+ return m_[1]/(w_);
}
- Real GetStandardDeviation() const
+ DATATYPE GetStandardDeviation() const
{
return sqrt(GetVariance());
}
- Real GetRootMeanSquare() const
+ DATATYPE GetRootMeanSquare() const
{
- if(n_==1.0){
+ if(n_==0.0){
return 0.0;
}
- return sqrt(sum2_/(n_-1));
+ return sqrt(sum2_/(w_));
}
- Real GetSkewness() const
+ DATATYPE GetSkewness() const
{
if(MAX_MOMENT<3){
throw Error("Skewness was not calculated.");
}
- if(m2_<1e-20){
+ if(m_[1]<1e-20){
return 0.0;
}else{
- return m3_/sqrt(m2_*m2_*m2_);
+ return m_[2]/sqrt(m_[1]*m_[1]*m_[1]);
}
}
- Real GetKurtosis() const
+ DATATYPE GetKurtosis() const
{
if(MAX_MOMENT<4){
throw Error("Kurtosis was not calculated.");
}
- if(m2_<1e-20){
+ if(m_[1]<1e-20){
return 0.0;
}else{
- return ((n_-1)*m4_) / (m2_*m2_);
+ return w_*m_[3] / (m_[1]*m_[1]);
}
}
private:
- Real mean_;
- Real sum_;
- Real sum2_;
- Real m2_;
- Real m3_;
- Real m4_;
- Real n_;
+ DATATYPE sum_;
+ DATATYPE sum2_;
+ DATATYPE max_;
+ DATATYPE min_;
+ DATATYPE m_[MAX_MOMENT];
+ Real w_;
+ unsigned int n_;
};
}}} //ns
diff --git a/modules/img/alg/tests/test_stat.cc b/modules/img/alg/tests/test_stat.cc
index b736c6bd93d30aebbcc2eb05616e70c4d0d19f7e..7e202193f37dcc42a6929a777dc9e37a26c4fca0 100644
--- a/modules/img/alg/tests/test_stat.cc
+++ b/modules/img/alg/tests/test_stat.cc
@@ -86,6 +86,51 @@ void test() {
BOOST_CHECK_CLOSE(acc_c.GetStandardDeviation(),Real(2.58198889747),Real(0.0001));
BOOST_CHECK_CLOSE(acc_c.GetSkewness()+Real(0.5),Real(0.5),Real(0.0001));
BOOST_CHECK_CLOSE(acc_c.GetKurtosis(),Real(1.77),Real(0.0001));
+
+ // check accumulator template for restriction to lower order moments
+ StatAccumulator<3> acc4;
+ for(int u=0;u<3;++u) {
+ for(int v=0;v<3;++v) {
+ acc4(val[u][v]);
+ }
+ }
+ BOOST_CHECK_CLOSE(acc4.GetMean(),Real(5.0),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc4.GetStandardDeviation(),Real(2.58198889747),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc4.GetSkewness()+Real(0.5),Real(0.5),Real(0.0001));
+ BOOST_CHECK_THROW(acc4.GetKurtosis(),ost::Error);
+
+ StatAccumulator<2> acc5;
+ for(int u=0;u<3;++u) {
+ for(int v=0;v<3;++v) {
+ acc5(val[u][v]);
+ }
+ }
+ BOOST_CHECK_CLOSE(acc5.GetMean(),Real(5.0),Real(0.0001));
+ BOOST_CHECK_CLOSE(acc5.GetStandardDeviation(),Real(2.58198889747),Real(0.0001));
+ BOOST_CHECK_THROW(acc5.GetSkewness(),ost::Error);
+ BOOST_CHECK_THROW(acc5.GetKurtosis(),ost::Error);
+
+ StatAccumulator<1> acc6;
+ for(int u=0;u<3;++u) {
+ for(int v=0;v<3;++v) {
+ acc6(val[u][v]);
+ }
+ }
+ BOOST_CHECK_CLOSE(acc6.GetMean(),Real(5.0),Real(0.0001));
+ BOOST_CHECK_THROW(acc6.GetStandardDeviation(),ost::Error);
+ BOOST_CHECK_THROW(acc6.GetSkewness(),ost::Error);
+ BOOST_CHECK_THROW(acc6.GetKurtosis(),ost::Error);
+
+ StatAccumulator<0> acc7;
+ for(int u=0;u<3;++u) {
+ for(int v=0;v<3;++v) {
+ acc7(val[u][v]);
+ }
+ }
+ BOOST_CHECK_THROW(acc7.GetMean(),ost::Error);
+ BOOST_CHECK_THROW(acc7.GetStandardDeviation(),ost::Error);
+ BOOST_CHECK_THROW(acc7.GetSkewness(),ost::Error);
+ BOOST_CHECK_THROW(acc7.GetKurtosis(),ost::Error);
}
} // namespace
diff --git a/modules/img/base/src/image_state/binop.cc b/modules/img/base/src/image_state/binop.cc
index 16ff05ea217adc5a7f2e414a091902a27507dde4..dc3339aa2939b1f6b1974b0fceadc584eb7b93ab 100644
--- a/modules/img/base/src/image_state/binop.cc
+++ b/modules/img/base/src/image_state/binop.cc
@@ -103,7 +103,20 @@ template struct fnc_paste_ip<Word,SpatialDomain,Complex,HalfFrequencyDomain>;
template struct fnc_paste_ip<Real,FrequencyDomain,Complex,HalfFrequencyDomain>;
template struct fnc_paste_ip<Complex,FrequencyDomain,Complex,HalfFrequencyDomain>;
template struct fnc_paste_ip<Complex,HalfFrequencyDomain,Complex,HalfFrequencyDomain>;
-
+template struct fnc_paste_ip<Real,FrequencyDomain,Complex,SpatialDomain>;
+template struct fnc_paste_ip<Real,FrequencyDomain,unsigned short,SpatialDomain>;
+template struct fnc_paste_ip<Complex,FrequencyDomain,unsigned short,SpatialDomain>;
+template struct fnc_paste_ip<Complex,HalfFrequencyDomain,unsigned short,SpatialDomain>;
+template struct fnc_paste_ip<Complex,HalfFrequencyDomain,Real,SpatialDomain>;
+template struct fnc_paste_ip<Complex,HalfFrequencyDomain,Complex,SpatialDomain>;
+template struct fnc_paste_ip<Complex,FrequencyDomain,Complex,SpatialDomain>;
+template struct fnc_paste_ip<Complex,FrequencyDomain,Real,SpatialDomain>;
+template struct fnc_paste_ip<Real,FrequencyDomain,Real,SpatialDomain>;
+
+template struct fnc_add_ip<Real,SpatialDomain,Real,SpatialDomain>;
+template struct fnc_sub_ip<Real,SpatialDomain,Real,SpatialDomain>;
+template struct fnc_mul_ip<Real,SpatialDomain,Real,SpatialDomain>;
+template struct fnc_div_ip<Real,SpatialDomain,Real,SpatialDomain>;
}
template struct dispatch::binary_dispatch_ip<binop::fnc_add_ip>;
diff --git a/modules/img/base/src/image_state/image_state_visitor.hh b/modules/img/base/src/image_state/image_state_visitor.hh
index d1808be7bf9d4cec4871ba9247d9d5ede941dc94..64fdadb3f29cb2344f02b689bd113f80eeac48ab 100644
--- a/modules/img/base/src/image_state/image_state_visitor.hh
+++ b/modules/img/base/src/image_state/image_state_visitor.hh
@@ -197,8 +197,8 @@ public:
const P6& p6, \
const P7& p7, \
const P8& p8, \
- const P8& p9, \
- const P9& pa): \
+ const P9& p9, \
+ const PA& pa): \
FNC(p0,p1,p2,p3,p4,p5,p6,p7,p8,p9,pa) {} \
/* 12 params */ \
template <class P0, \
@@ -222,9 +222,9 @@ public:
const P6& p6, \
const P7& p7, \
const P8& p8, \
- const P8& p9, \
- const P8& pa, \
- const P9& pb): \
+ const P9& p9, \
+ const PA& pa, \
+ const PB& pb): \
FNC(p0,p1,p2,p3,p4,p5,p6,p7,p8,p9,pa,pb) {}
diff --git a/modules/img/base/tests/test_value_holder.cc b/modules/img/base/tests/test_value_holder.cc
index f5b09f938f0bd48ba09e0701631d10ab67f4e8c4..bd0cacbd6ba76084ea7933717ff47a308dc15136 100644
--- a/modules/img/base/tests/test_value_holder.cc
+++ b/modules/img/base/tests/test_value_holder.cc
@@ -91,8 +91,6 @@ test_suite* CreateValueHolderTest()
{
using namespace value_holder_test;
- typedef boost::mpl::vector<Real, Complex> values;
-
test_suite* ts=BOOST_TEST_SUITE("ValueHolder Test");
ts->add( BOOST_TEST_CASE(ReadWrite<Real>) );
diff --git a/modules/index.rst b/modules/index.rst
index f8b688fa05414f021b9efbb9150d6c25a244f907..f664be809700225a527c9c342483d6ed7c7b18e9 100644
--- a/modules/index.rst
+++ b/modules/index.rst
@@ -43,7 +43,7 @@ For Starters
Molecules
--------------------------------------------------------------------------------
-**Overview**: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>` | :doc:`queries <mol/base/query>` | :doc:`algorithms <mol/alg/molalg>`
+**Overview**: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>` | :doc:`queries <mol/base/query>` | :doc:`algorithms <mol/alg/molalg>` | :doc:`mm <mol/mm/molmm>`
**Trajectories**: :doc:`basics <mol/base/traj>` | :ref:`analysis <traj-analysis>`
@@ -96,7 +96,7 @@ Varia
**Datasets:** :doc:`tabular data <table>`
-**Supported File Formats:** :doc:`structure formats<io/structure_formats>` | :doc:`sequence formats <io/sequence_formats>` | :doc:`image formats <io/image_formats>`
+**Supported File Formats:** :doc:`structure formats<io/structure_formats>` | :doc:`sequence formats <io/sequence_formats>` | :doc:`sequence profile formats <io/sequence_profile_formats>` | :doc:`image formats <io/image_formats>`
**Users** :doc:`Reporting a problem <users>`
diff --git a/modules/info/src/item_type_cast.hh b/modules/info/src/item_type_cast.hh
index 33caf38679e92ebb10e1734118c953e5ef0254e4..0b364d575a31737eec8e0f6fa775d5b1a14956dd 100644
--- a/modules/info/src/item_type_cast.hh
+++ b/modules/info/src/item_type_cast.hh
@@ -99,7 +99,7 @@ template <> void set_new_type<IT_STRING,IT_BOOL>(EleImpl& item)
template <> void set_new_type<IT_STRING,IT_VECTOR>(EleImpl& item)
{
static String num("[-+]?[0-9]*\\.?[0-9]+([eE][-+]?[0-9]+)?");
- boost::regex expression("\\(("+num+"),("+num+"),("+num+")\\)");
+ boost::regex expression("\\[ *("+num+") *, *("+num+") *, *("+num+") *\\]");
boost::cmatch what;
if(boost::regex_match(item.GetStringRepr().c_str(), what, expression)) {
diff --git a/modules/io/doc/io.dox b/modules/io/doc/io.dox
index e89777217a2d449f1c91edbf0e4c52946fc22609..b266c977afdc96f07ecd37bdffb06d660e7038f6 100644
--- a/modules/io/doc/io.dox
+++ b/modules/io/doc/io.dox
@@ -6,7 +6,7 @@ namespace ost { namespace io {
The io module deals with input and output of \ref mol::EntityHandle "entities",
\ref seq::AlignmentHandle "multiple sequence alignments" and
-\ref iplt::ImageHandle "map data". Importers for common file formats such as PDB,
+\ref ost::img::ImageHandle "map data". Importers for common file formats such as PDB,
SDF, FASTA, CLUSTAL W, DX and the CHARMM files are available.
@@ -28,7 +28,7 @@ control over the exact loading behaviour.
Some of the file formats for molecules do not explicitly define bonds. The
IO handlers for these file formats make use of the conop module to infer
-connectivity information (see \ref ost::conop::Builder "Builder").
+connectivity information.
\subsection io_handler IO Handlers
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index 8d6cee55047692afa3ff20b6f1734fb5266c0e43..9b40234d5084fec0f9a8d58d8ab48bba5a0ef926 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -157,16 +157,49 @@ Loading sequence or alignment files
.. function:: LoadSequenceList(filename, format='auto')
- For a desription of how to use :func:`LoadSequenceList` please refer to
+ For a description of how to use :func:`LoadSequenceList` please refer to
:func:`LoadSequence`. For a list of file formats supported by
:func:`LoadSequenceList` see :doc:`sequence_formats`.
.. function:: LoadAlignment(filename, format='auto')
- For a desription of how to use :func:`LoadAlignment` please refer to
+ For a description of how to use :func:`LoadAlignment` please refer to
:func:`LoadSequence`. For a list of file formats supported by
:func:`LoadAlignment` see :doc:`sequence_formats`.
+
+.. function:: LoadSequenceProfile(filename, format='auto')
+
+ Load sequence profile data from disk. If format is set to 'auto', the function
+ guesses the filetype based on the extension of the file. Files ending in
+ '.hhm' (output of HHblits) and '.pssm' (ASCII Table (PSSM) output of PSI-BLAST
+ as generated with blastpgp and flag -Q) will automatically be loaded.
+
+ For files with non-standard extensions, the format can be set explicitly
+ specifying the `format` parameter.
+
+ .. code-block:: python
+
+ # recognizes hhm file by file extension
+ myprof = io.LoadSequenceProfile('myhmm.hhm')
+ # recognizes pssm file by file extension
+ myprof = io.LoadSequenceProfile('myprof.pssm')
+
+ # to override format
+ myprof = io.LoadSequenceProfile('myfile', format='hhm')
+ myprof = io.LoadSequenceProfile('myfile', format='pssm')
+
+ For a list of file formats supported by :func:`LoadSequenceProfile` see
+ :doc:`sequence_profile_formats`.
+
+ :rtype: :class:`~ost.seq.ProfileHandle`
+
+ :raises: :exc:`~ost.io.IOUnknownFormatException` if the format string supplied
+ is not recognized or the file format can not be detected based on the
+ file extension.
+ :exc:`~ost.io.IOException` if the import fails due to an erroneous or
+ inexistent file.
+
Saving Sequence Data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -247,7 +280,7 @@ Loading Density Maps
# recognizes mrc file by file extension
ent = io.LoadImage('file.mrc')
- # it is always possible to explicitely set the image format
+ # it is always possible to explicitly set the image format
# DAT file explicitly
ent = io.LoadImage('file', Dat())
diff --git a/modules/io/doc/sequence_profile_formats.rst b/modules/io/doc/sequence_profile_formats.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8c14c7d7f8ad7f5003d700d7edc060b48da119ec
--- /dev/null
+++ b/modules/io/doc/sequence_profile_formats.rst
@@ -0,0 +1,23 @@
+Supported Sequence Profile File Formats
+================================================================================
+
+HHblits output
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+ .hhm, .hhm.gz
+
+*Format Name*
+ hhm
+
+
+PSI-BLAST output
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+ASCII Table (PSSM) output of PSI-BLAST as generated with blastpgp and flag -Q.
+
+*Recognized File Extensions*
+ .pssm, .pssm.gz
+
+*Format Name*
+ pssm
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index b64e0d23d1be9eefc2c75833d49e90b70604b395..9d6536d9efd7ace2d39917cb26d507ae5c344419 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -210,7 +210,7 @@ except ImportError:
pass
## loads several images and puts them in an ImageList
- # \sa \ref fft_li.py "View Fourier Transform Example"
+ # \sa \example fft_li.py "View Fourier Transform Example"
def LoadImageList (files):
image_list=img.ImageList()
for file in files:
diff --git a/modules/io/pymod/export_map_io.cc b/modules/io/pymod/export_map_io.cc
index 4d49dad7f6f2e08de62a1fa39a65146d8cecd7bd..ab195ef2dc25f8323f27f08de82e31b4f8363980 100644
--- a/modules/io/pymod/export_map_io.cc
+++ b/modules/io/pymod/export_map_io.cc
@@ -112,8 +112,10 @@ void export_map_io()
.def("GetEndianessOnSave", &Spider::GetEndianessOnSave)
;
- class_<MRC, bases<ImageFormatBase> >("MRC", init<bool,Subformat,Endianess>
- ((arg("normalize_on_save") = false,arg("subformat")=MRC_AUTO_FORMAT,arg("endianess_on_save")=OST_LOCAL_ENDIAN)))
+ class_<MRC, bases<ImageFormatBase> >("MRC", init<bool,Subformat,Endianess,Format>
+ ((arg("normalize_on_save") = false,arg("subformat")=MRC_AUTO_FORMAT,arg("endianess_on_save")=OST_LOCAL_ENDIAN,arg("format")=OST_DEFAULT_FORMAT)))
+ .def("SetBitDepth", &MRC::SetBitDepth)
+ .def("GetBitDepth", &MRC::GetBitDepth)
.def("SetNormalizeOnSave", &MRC::SetNormalizeOnSave)
.def("GetNormalizeOnSave", &MRC::GetNormalizeOnSave)
.def("SetSubformat", &MRC::SetSubformat)
@@ -122,8 +124,8 @@ void export_map_io()
.def("GetEndianessOnSave", &MRC::GetEndianessOnSave)
;
- class_<CCP4, bases<MRC> >("CCP4", init<bool,Endianess>
- ((arg("normalize_on_save") = false,arg("endianess_on_save")=OST_LOCAL_ENDIAN)))
+ class_<CCP4, bases<MRC> >("CCP4", init<bool,Endianess,Format>
+ ((arg("normalize_on_save") = false,arg("endianess_on_save")=OST_LOCAL_ENDIAN,arg("format")=OST_DEFAULT_FORMAT)))
;
class_<DM3, bases<ImageFormatBase> >("DM3", init<>())
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
index 824d70340208f61ac9959cddcff4902833f1bed4..7c6a5b69750a362f01842ad13c52b555353b017a 100644
--- a/modules/io/pymod/export_mmcif_io.cc
+++ b/modules/io/pymod/export_mmcif_io.cc
@@ -99,7 +99,6 @@ void export_mmcif_io()
&MMCifInfoCitation::SetAuthorList)
;
- typedef std::vector<MMCifInfoCitation> MMCifInfoCitationList;
class_<std::vector<MMCifInfoCitation> >("MMCifInfoCitationList", init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoCitation> >())
;
@@ -124,7 +123,6 @@ void export_mmcif_io()
&MMCifInfoTransOp::SetMatrix)
;
- typedef std::vector<MMCifInfoTransOp> MMCifInfoTransOpList;
class_<std::vector<MMCifInfoTransOp> >("MMCifInfoTransOpList", init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoTransOp> >())
;
@@ -134,7 +132,6 @@ void export_mmcif_io()
.def(vector_indexing_suite<std::vector<MMCifInfoTransOpPtr>, true >())
;
- typedef std::vector<MMCifInfoTransOpPtrList > MMCifInfoTransOpPtrListList;
class_<std::vector<MMCifInfoTransOpPtrList > >("MMCifInfoTransOpPtrListList",
init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoTransOpPtrList >, true >())
@@ -228,7 +225,6 @@ void export_mmcif_io()
class_<MMCifInfoStructRefSeqDifs>("MMCifInfoStructRefSeqDifs", init<>())
.def(vector_indexing_suite<MMCifInfoStructRefSeqDifs, true>())
;
- typedef std::vector<MMCifInfoBioUnit> MMCifInfoBioUnitList;
class_<std::vector<MMCifInfoBioUnit> >("MMCifInfoBioUnitList", init<>())
.def(vector_indexing_suite<std::vector<MMCifInfoBioUnit> >())
;
diff --git a/modules/io/pymod/export_pdb_io.cc b/modules/io/pymod/export_pdb_io.cc
index 237b2918c4e0188c1af301d212e073195266d87f..752647f67fd2aa3652c09c1fbee4aa6db8189b40 100644
--- a/modules/io/pymod/export_pdb_io.cc
+++ b/modules/io/pymod/export_pdb_io.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2015 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
@@ -22,6 +22,8 @@ using namespace boost::python;
#include <ost/io/mol/io_profile.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/mol/pdb_writer.hh>
+#include <ost/io/mol/pdb_str.hh>
+
using namespace ost;
using namespace ost::io;
@@ -33,6 +35,9 @@ BOOST_PYTHON_FUNCTION_OVERLOADS(load_PDB_ov, LoadPDB, 1, 2)
void (PDBWriter::*write_a)(const mol::EntityHandle&)=&PDBWriter::Write;
void (PDBWriter::*write_b)(const mol::EntityView&)=&PDBWriter::Write;
+String (*pdb_str_a)(const mol::EntityHandle&, const IOProfile&)=&EntityToPDBString;
+String (*pdb_str_b)(const mol::EntityView&, const IOProfile&)=&EntityToPDBString;
+
void remove_profiles() {
IOProfileRegistry::RemoveProfiles();
}
@@ -88,6 +93,12 @@ void export_pdb_io()
&PDBWriter::SetWriteMultiModel)
.def("Write", write_b)
;
+ def("EntityToPDBStr", pdb_str_a,
+ (arg("entity"), arg("profile")=IOProfile()));
+ def("EntityToPDBStr", pdb_str_b,
+ (arg("entity"), arg("profile")=IOProfile()));
+
+ def("PDBStrToEntity", &PDBStringToEntity, (arg("pdb_string"),arg("profile")=IOProfile()));
// we need to make sure there are no pending references to Python objects
// tied to the IOProfileRegistry singleton. The destructor of
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index 1e2b5186906a5f94cd11526f9837aa74c6af5fca..6d16af3e91192a6b47c39a3f4d770e2be94cd260 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -99,6 +99,9 @@ BOOST_PYTHON_MODULE(_ost_io)
def("SequenceListFromString", &SequenceListFromString);
def("SequenceFromString", &SequenceFromString);
def("SaveAlignment", &SaveAlignment, arg("format")="auto");
+
+ def("LoadSequenceProfile", &LoadSequenceProfile, arg("format")="auto");
+
def("LoadSurface",LoadSurface,load_surface_ov());
def("LoadManagedSurface",LoadManagedSurface,load_msurface_ov());
diff --git a/modules/io/src/CMakeLists.txt b/modules/io/src/CMakeLists.txt
index 58470a33136c2b794668dc2b39effab39cd2f805..13d6e3c6adef7c8adbe30aa0494d2668ce7242d7 100644
--- a/modules/io/src/CMakeLists.txt
+++ b/modules/io/src/CMakeLists.txt
@@ -38,12 +38,18 @@ if (ENABLE_IMG)
foreach(fname ${OST_IO_IMG_SOURCES})
set(OST_IO_SOURCES ${OST_IO_SOURCES} img/${fname})
endforeach(fname ${OST_IO_IMG_SOURCES})
-
- foreach(fname ${OST_IO_IMG_HEADERS})
- set(OST_IO_HEADERS ${OST_IO_HEADERS} img/${fname})
- endforeach(fname ${OST_IO_IMG_HEADERS})
endif()
+####################################
+# Add headers in subfolders (additionally) to OST_IO_HEADERS.
+# In the end, we will have two copies (!) of each header in the subfolders.
+# One copy in ost/io/<SUB> and one in ost/io.
+
+# As it's silly to have duplicate headers, this behavior might be removed in the
+# future. So please always include the headers in the subfolders.
+# (e.g. use "#include <ost/io/mol/load_entity.hh>"
+# instead of #include <ost/io/load_entity.hh>)
+# For compatibility reasons, we keep it for now (dates back to 2010).
foreach(fname ${OST_IO_MOL_HEADERS})
set(OST_IO_HEADERS ${OST_IO_HEADERS} mol/${fname})
endforeach(fname ${OST_IO_MOL_HEADERS})
@@ -52,6 +58,12 @@ foreach(fname ${OST_IO_SEQ_HEADERS})
set(OST_IO_HEADERS ${OST_IO_HEADERS} seq/${fname})
endforeach(fname ${OST_IO_SEQ_HEADERS})
+if (ENABLE_IMG)
+ foreach(fname ${OST_IO_IMG_HEADERS})
+ set(OST_IO_HEADERS ${OST_IO_HEADERS} img/${fname})
+ endforeach(fname ${OST_IO_IMG_HEADERS})
+endif()
+####################################
set(OST_IO_DEPENDENCIES ost_base;ost_conop;ost_seq)
if (ENABLE_IMG)
diff --git a/modules/io/src/converting_streams.hh b/modules/io/src/converting_streams.hh
index fb6b3b82d103aee36cb298be7956dfb52269027a..b451769185cd823c7f66cd465242b935dfd24078 100644
--- a/modules/io/src/converting_streams.hh
+++ b/modules/io/src/converting_streams.hh
@@ -204,6 +204,10 @@ public:
{
return read_helper(value,n);
}
+ BinaryIStream& read(int8_t* value,std::streamsize n)
+ {
+ return read_helper(value,n);
+ }
BinaryIStream& read(int16_t* value,std::streamsize n)
{
return read_helper(value,n);
diff --git a/modules/io/src/img/map_io_dx_handler.cc b/modules/io/src/img/map_io_dx_handler.cc
index 4509d327d51187961802658a214d69c8b8bdf245..5ecaab90479a1f878a151ccf3af10e6f2da14bca 100644
--- a/modules/io/src/img/map_io_dx_handler.cc
+++ b/modules/io/src/img/map_io_dx_handler.cc
@@ -108,9 +108,11 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
}
String line;
- int u_size,v_size,w_size;
- Real x_orig=0, y_orig=0, z_orig=0;
- Real u_spacing=0, v_spacing=0, w_spacing=0;
+ int u_size=0,v_size=0,w_size=0;
+ Real x_orig=0.0, y_orig=0.0, z_orig=0.0;
+ Real u_spacing=1.0, v_spacing=1.0, w_spacing=1.0;
+ size_t delta_count=0;
+ Real deltas[][3]={{1.0,0.0,0.0},{0.0,1.0,0.0},{0.0,0.0,1.0}};
int num_gridpoints;
img::MapHandle mh2;
std::vector<String> tokens;
@@ -120,6 +122,7 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
}
// read gridpoints line
if (boost::iequals(line.substr(0,35), "object 1 class gridpositions counts")) {
+ LOG_DEBUG("DXImport: reading gridpoints line [" << line << "]");
boost::split(tokens, line, boost::is_any_of(" "), boost::token_compress_on);
int tokens_size = (int)tokens.size();
if(tokens_size < 3) {
@@ -137,6 +140,7 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
}
// read grid origin line
else if (boost::iequals(line.substr(0,6), "origin")) {
+ LOG_DEBUG("DXImport: reading origin line [" << line << "]");
boost::split(tokens, line, boost::is_any_of(" "), boost::token_compress_on);
int tokens_size = (int)tokens.size();
if(tokens_size < 3) {
@@ -154,42 +158,24 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
}
// read grid spacing line
else if (boost::iequals(line.substr(0,5), "delta")) {
- boost::split(tokens, line, boost::is_any_of(" "), boost::token_compress_on);
- int tokens_size = (int)tokens.size();
- if(tokens_size < 3) {
- String msg="Bad spacing line: Can't read spacing of grid points";
+ LOG_DEBUG("DXImport: reading delta line [" << line << "]");
+ boost::split(tokens, line, boost::is_any_of("\t "), boost::token_compress_on);
+ if(tokens.size() < 4) {
+ String msg="DXImport: expected delta line with 3 floats";
throw IOException(msg);
}
try {
- Real tmp;
- tmp = boost::lexical_cast<Real>(boost::trim_copy(tokens[tokens_size-3]));
- if(tmp != 0) {
- u_spacing=tmp;
- } else if(tmp == 0) {
- tmp = boost::lexical_cast<Real>(boost::trim_copy(tokens[tokens_size-2]));
- if(tmp != 0) {
- v_spacing=tmp;
- } else if(tmp == 0) {
- tmp = boost::lexical_cast<Real>(boost::trim_copy(tokens[tokens_size-1]));
- if(tmp != 0) {
- w_spacing=tmp;
- } else {
- String msg="Bad spacing line: Can't read spacing of grid points";
- throw IOException(msg);
- }
+ if(delta_count<3) {
+ for(size_t i=0;i<3;++i) {
+ deltas[delta_count][i] = boost::lexical_cast<Real>(tokens[i+1]);
}
+ ++delta_count;
}
} catch(boost::bad_lexical_cast&) {
- format fmer= format("Bad spacing line: Can't convert String of origin"
- " '%s' to Real constant.") % line;
+ format fmer= format("Bad spacing line: Can't convert String of delta"
+ " '%s' to Real constants.") % line;
throw IOException(fmer.str());
}
- // create map handle
- if(u_spacing != 0 && v_spacing != 0 && w_spacing != 0) {
- mh2 = CreateMap(img::Size(u_size,v_size,w_size));
- mh2.SetAbsoluteOrigin(geom::Vec3(x_orig, y_orig, z_orig));
- mh2.SetSpatialSampling(geom::Vec3(u_spacing,v_spacing,w_spacing));
- }
}
// read number of data points
if (boost::iequals(line.substr(0,25), "object 3 class array type")) {
@@ -207,6 +193,25 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
throw IOException(fmer.str());
}
+ // at this point enough info should be available to create map
+ if(u_size>1e5 || v_size>1e5 || w_size>1e5) {
+ format fmer=format("DXImport: nonsense mapsize read (%d %d %d)") % u_size % v_size % w_size;
+ throw IOException(fmer.str());
+ }
+ LOG_DEBUG("DXImport: creating map of size " << img::Size(u_size,v_size,w_size));
+ LOG_DEBUG(" at absolute origin " << geom::Vec3(x_orig, y_orig, z_orig));
+ mh2 = CreateMap(img::Size(u_size,v_size,w_size));
+ mh2.SetAbsoluteOrigin(geom::Vec3(x_orig, y_orig, z_orig));
+ if(delta_count==3) {
+ u_spacing=deltas[0][0];
+ v_spacing=deltas[1][1];
+ w_spacing=deltas[2][2];
+ LOG_DEBUG(" and spatial sampling " << geom::Vec3(u_spacing,v_spacing,w_spacing));
+ mh2.SetSpatialSampling(geom::Vec3(u_spacing,v_spacing,w_spacing));
+ }
+
+ // and read in the values
+ // TODO: this is glacially slow
Real value=0;
for(int i=0; i<num_gridpoints; i+=3) {
std::getline(infile,line);
@@ -226,6 +231,7 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
mh.Swap(mh2);
}
+
void MapIODxHandler::Export(const img::MapHandle& mh2,
const bf::path& loc,const ImageFormatBase& formatstruct) const
{
diff --git a/modules/io/src/img/map_io_mrc_handler.cc b/modules/io/src/img/map_io_mrc_handler.cc
index c80ec39aba853070679aefdfd7b890cd5b876de0..9d1740abbd6a1b0b20e463ee166514af472d477a 100644
--- a/modules/io/src/img/map_io_mrc_handler.cc
+++ b/modules/io/src/img/map_io_mrc_handler.cc
@@ -74,7 +74,7 @@ u v w x . . . d*c*b*a b c d 3
#include <ost/base.hh>
#include <ost/img/image_state.hh>
-#include <ost/img/alg/stat.hh>
+#include <ost/img/alg/stat_accumulator.hh>
#include <ost/img/alg/normalizer_factory.hh>
#include <ost/img/util.hh>
#include <ost/img/progress.hh>
@@ -94,13 +94,24 @@ namespace ost { namespace io {
String MRC::FORMAT_STRING = "defined_mrc";
-MRC::MRC(bool normalize_on_save, Subformat subformat,Endianess endianess_on_save):
+MRC::MRC(bool normalize_on_save, Subformat subformat,Endianess endianess_on_save, Format bit_depth):
ImageFormatBase(FORMAT_STRING),
subformat_(subformat),
normalize_on_save_(normalize_on_save),
- endianess_on_save_(endianess_on_save)
+ endianess_on_save_(endianess_on_save),
+ bit_depth_(bit_depth)
{
}
+Format MRC::GetBitDepth() const
+{
+ return bit_depth_;
+}
+
+void MRC::SetBitDepth (Format bitdepth)
+{
+ bit_depth_ = bitdepth;
+}
+
Endianess MRC::GetEndianessOnSave() const
{
@@ -132,8 +143,8 @@ void MRC::SetNormalizeOnSave(bool normalize_on_save)
normalize_on_save_ = normalize_on_save;
}
-CCP4::CCP4(bool normalize_on_save, Endianess endianess_on_save):
- MRC(normalize_on_save,MRC_NEW_FORMAT,endianess_on_save)
+CCP4::CCP4(bool normalize_on_save, Endianess endianess_on_save, Format bit_depth):
+ MRC(normalize_on_save,MRC_NEW_FORMAT,endianess_on_save,bit_depth)
{}
@@ -223,7 +234,7 @@ public:
label[i]=' ';
}
}
- header_base(const img::ConstImageHandle& im):
+ header_base(const img::ConstImageHandle& im, Format bit_depth):
nc(),
nr(static_cast<int>(im.GetExtent().GetSize().GetHeight())),
ns(static_cast<int>(im.GetExtent().GetSize().GetDepth())),
@@ -247,22 +258,55 @@ public:
{
if(im.GetType()==img::REAL){
nc=static_cast<int>(im.GetExtent().GetSize().GetWidth());
- mode=2;
+ switch(bit_depth){
+ case OST_BIT8_FORMAT:
+ mode=0;
+ break;
+ case OST_BIT16_FORMAT:
+ mode=1;
+ break;
+ case OST_FLOAT_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ mode=2;
+ break;
+ default:
+ throw(IOException("MRC/CCP4 export: Bit depth not supported."));
+ break;
+ }
x=im.GetExtent().GetSize().GetWidth()*im.GetSpatialSampling()[0];
y=im.GetExtent().GetSize().GetHeight()*im.GetSpatialSampling()[1];
z=im.GetExtent().GetSize().GetDepth()*im.GetSpatialSampling()[2];
}else{
nc=static_cast<int>(im.GetExtent().GetSize().GetWidth()/2 +1);
- mode=4;
+ switch(bit_depth){
+ case OST_BIT16_FORMAT:
+ mode=3;
+ break;
+ case OST_FLOAT_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ mode=4;
+ break;
+ default:
+ throw(IOException("MRC/CCP4 export: Bit depth not supported."));
+ break;
+ }
x=1.0;
y=1.0;
z=1.0;
}
- ost::img::alg::Stat stat;
- im.Apply(stat);
- amin=stat.GetMinimum();
- amax=stat.GetMaximum();
- amean=stat.GetMean();
+ ost::img::alg::StatAccumulator<1> acc;
+ if(im.GetType()==img::REAL) {
+ img::image_state::RealSpatialImageState *isr=dynamic_cast<img::image_state::RealSpatialImageState*>(im.ImageStatePtr().get());
+ if(! isr){
+ throw(IOException("MRC/CCP4 export: dynamic cast failed in header base."));
+ }
+ for(Real* ptr = isr->Data().GetData(); ptr<isr->Data().GetEnd(); ++ptr) {
+ acc(*ptr);
+ }
+ amin=acc.GetMinimum();
+ amax=acc.GetMaximum();
+ amean=acc.GetMean();
+ }
for(unsigned int i=0;i<800;++i)
{
label[i]=' ';
@@ -342,8 +386,8 @@ public:
yorigin(0.0)
{
}
- mrc_header(const img::ConstImageHandle& im):
- header_base(im),
+ mrc_header(const img::ConstImageHandle& im, Format bit_depth):
+ header_base(im,bit_depth),
xorigin(0.0), // todo determine origin
yorigin(0.0)
{
@@ -435,8 +479,8 @@ public:
arms()
{
}
- ccp4_header(const img::ConstImageHandle& im):
- header_base(im),
+ ccp4_header(const img::ConstImageHandle& im, Format bit_depth):
+ header_base(im,bit_depth),
lskflag(),
skwmat(),
skwtrn(),
@@ -703,15 +747,17 @@ void real_dumper(BinaryOStream<CONVERSIONTYPE>& f, header_base& header, const Co
char this_dummy; //create dummy variable to give to Progress as this
Progress::Instance().Register(&this_dummy,header.ns*header.nr,100);
for(int ss=0;ss<header.ns;++ss) {
+ std::vector<B> buffer(header.nr*header.nc);
pnt[maps]=header.nsstart+ss;
for(int sr=0;sr<header.nr;++sr) {
pnt[mapr]=header.nrstart+sr;
for(int sc=0;sc<header.nc;++sc) {
pnt[mapc]=header.ncstart+sc;
- f << static_cast<B>(norm.Convert(isr->Value(pnt)));
+ buffer[header.nc*sr+sc]=img::Val2Val<Real,B>(norm.Convert(isr->Value(pnt)));
}
Progress::Instance().AdvanceProgress(&this_dummy);
}
+ f.write(&buffer[0],header.nr*header.nc);
}
Progress::Instance().DeRegister(&this_dummy);
}
@@ -795,7 +841,7 @@ void import_helper(img::MapHandle& image, std::istream& in,const MRC& formatmrc)
} else {
throw IOException("internal error in MRC io: expected ComplexHalfFrequencyImageState");
}
- } else if (header.mode>=0 && header.mode<=2) {
+ } else if (header.mode==0 || header.mode==2 || header.mode==5 || header.mode==6 || header.mode==7) {
img::Size msize;
msize[header.mapc-1]=header.nc;
msize[header.mapr-1]=header.nr;
@@ -815,11 +861,15 @@ void import_helper(img::MapHandle& image, std::istream& in,const MRC& formatmrc)
LOG_INFO("resulting image extent: " << image.GetExtent());
if(img::image_state::RealSpatialImageState *rs=dynamic_cast<img::image_state::RealSpatialImageState*>(image.ImageStatePtr().get())) {
if(header.mode==0) {
- detail::real_filler<uchar,CONVERSIONTYPE>(*rs,f,header);
- } else if(header.mode==1) {
- detail::real_filler<unsigned short,CONVERSIONTYPE>(*rs,f,header);
+ detail::real_filler<int8_t,CONVERSIONTYPE>(*rs,f,header);
+ } else if(header.mode==1 || header.mode==5) {
+ detail::real_filler<int16_t,CONVERSIONTYPE>(*rs,f,header);
} else if(header.mode==2) {
detail::real_filler<float,CONVERSIONTYPE>(*rs,f,header);
+ } else if(header.mode==6) {
+ detail::real_filler<uint16_t,CONVERSIONTYPE>(*rs,f,header);
+ } else if(header.mode==7) {
+ detail::real_filler<int32_t,CONVERSIONTYPE>(*rs,f,header);
}
} else {
throw IOException("internal error in MRC/CCP4 io: expected RealSpatialImageState");
@@ -857,14 +907,39 @@ void export_helper(const img::MapHandle& image,
const MRC& formatmrc)
{
BinaryOStream<CONVERSIONTYPE> f(out);
- HEADER header(image);
+ HEADER header(image,formatmrc.GetBitDepth());
f << header;
if(image.GetType()==img::REAL) {
- detail::real_dumper<float,CONVERSIONTYPE>(f,header,image,formatmrc);
+ switch(formatmrc.GetBitDepth()){
+ case OST_BIT8_FORMAT:
+ detail::real_dumper<int8_t,CONVERSIONTYPE>(f,header,image,formatmrc);
+ break;
+ case OST_BIT16_FORMAT:
+ detail::real_dumper<int16_t,CONVERSIONTYPE>(f,header,image,formatmrc);
+ break;
+ case OST_FLOAT_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ detail::real_dumper<float,CONVERSIONTYPE>(f,header,image,formatmrc);
+ break;
+ default:
+ throw(IOException("MRC/CCP4 export: Bit depth not supported."));
+ break;
+ }
} else {
if(image.GetDomain()==img::HALF_FREQUENCY){
- detail::complex_dumper<float,CONVERSIONTYPE>(f,header,image,formatmrc);
+ switch(formatmrc.GetBitDepth()){
+ case OST_BIT16_FORMAT:
+ detail::complex_dumper<int16_t,CONVERSIONTYPE>(f,header,image,formatmrc);
+ break;
+ case OST_FLOAT_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ detail::complex_dumper<float,CONVERSIONTYPE>(f,header,image,formatmrc);
+ break;
+ default:
+ throw(IOException("MRC/CCP4 export: Bit depth not supported."));
+ break;
+ }
} else {
throw(IOException("MRC/CCP4 export: full complex export not supported."));
}
diff --git a/modules/io/src/img/map_io_mrc_handler.hh b/modules/io/src/img/map_io_mrc_handler.hh
index c12096b68ff711366e597118aea85f5e0550fc21..d8e2e9710dfa15eb688bd8594fb055923e3d1c11 100644
--- a/modules/io/src/img/map_io_mrc_handler.hh
+++ b/modules/io/src/img/map_io_mrc_handler.hh
@@ -28,7 +28,10 @@ class DLLEXPORT_OST_IO MRC: public ImageFormatBase
{
public:
- MRC(bool normalize_on_save = false, Subformat subformat = MRC_AUTO_FORMAT ,Endianess endianness_on_save = OST_LOCAL_ENDIAN);
+ MRC(bool normalize_on_save = false, Subformat subformat = MRC_AUTO_FORMAT ,Endianess endianness_on_save = OST_LOCAL_ENDIAN, Format bit_depth = OST_DEFAULT_FORMAT);
+
+ Format GetBitDepth() const;
+ void SetBitDepth ( Format bitdepth);
Endianess GetEndianessOnSave() const;
void SetEndianessOnSave(Endianess end);
@@ -46,12 +49,13 @@ class DLLEXPORT_OST_IO MRC: public ImageFormatBase
Subformat subformat_;
bool normalize_on_save_;
Endianess endianess_on_save_;
+ Format bit_depth_;
};
class DLLEXPORT_OST_IO CCP4: public MRC
{
public:
- CCP4(bool normalize_on_save = false, Endianess endianness_on_save = OST_LOCAL_ENDIAN);
+ CCP4(bool normalize_on_save = false, Endianess endianness_on_save = OST_LOCAL_ENDIAN, Format bit_depth = OST_DEFAULT_FORMAT);
};
typedef CCP4 MAP;
diff --git a/modules/io/src/img/map_io_png_handler.cc b/modules/io/src/img/map_io_png_handler.cc
index d77db114b4d20c72d026d10e3f6e2435a8737b06..61156a58b2121bb00b698455906a9733125f3907 100644
--- a/modules/io/src/img/map_io_png_handler.cc
+++ b/modules/io/src/img/map_io_png_handler.cc
@@ -111,7 +111,7 @@ void MapIOPngHandler::Import(img::MapHandle& image, std::istream& f,const ImageF
png_bytep *row_pointers;
png_uint_32 row,column;
png_byte *png_data;
- png_uint_32 width,height,bpp;
+ png_uint_32 width,height;
std::ostringstream mesg;
PNG form;
@@ -156,7 +156,6 @@ void MapIOPngHandler::Import(img::MapHandle& image, std::istream& f,const ImageF
width=(unsigned int)png_get_image_width(png_ptr, info_ptr);
height=(unsigned int)png_get_image_height(png_ptr, info_ptr);
- bpp=(unsigned int)png_get_bit_depth(png_ptr,info_ptr);
// TODO 16 bit greyscale
diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index 4be8a815e335f4c17ff75ad2f57241cffad24430..cd0ad364c112f65118498e292194cc1749f9e422 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -324,6 +324,7 @@ void MapIOTiffHandler::do_export(const img::MapHandle& image,TIFF* tfile,TIF& fo
TIFFSetField(tfile,TIFFTAG_YRESOLUTION,yreso);
TIFFSetField(tfile,TIFFTAG_PLANARCONFIG,1);
TIFFSetField(tfile,TIFFTAG_ORIENTATION,ORIENTATION_TOPLEFT);
+ TIFFSetField(tfile,TIFFTAG_PHOTOMETRIC,1); // 1=zero is black
if(image.GetDomain()!=img::SPATIAL){
throw IOException("Frequency export not implemented.");
}
diff --git a/modules/io/src/io_manager.cc b/modules/io/src/io_manager.cc
index 6edc7fe430dd928159152bed7ebea0bde53aeb44..cfd288c75ea302e8c6ece75af15593c92a74dad8 100644
--- a/modules/io/src/io_manager.cc
+++ b/modules/io/src/io_manager.cc
@@ -25,6 +25,8 @@
#include <ost/io/seq/fasta_io_handler.hh>
#include <ost/io/seq/pir_io_handler.hh>
#include <ost/io/seq/promod_io_handler.hh>
+#include <ost/io/seq/hhm_io_handler.hh>
+#include <ost/io/seq/pssm_io_handler.hh>
#include <ost/io/mol/surface_io_msms_handler.hh>
#include <ost/io/seq/clustal_io_handler.hh>
#if OST_IMG_ENABLED
@@ -50,10 +52,12 @@ IOManager::IOManager()
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOCRDHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOSDFHandlerFactory));
RegisterFactory(EntityIOHandlerFactoryBaseP(new EntityIOMAEHandlerFactory));
- RegisterFactory(SequenceIOHandlerFactoryBasePtr(new FastaIOHandlerFactory));
+ RegisterFactory(SequenceIOHandlerFactoryBasePtr(new FastaIOHandlerFactory));
RegisterFactory(SequenceIOHandlerFactoryBasePtr(new PirIOHandlerFactory));
- RegisterFactory(SequenceIOHandlerFactoryBasePtr(new ClustalIOHandlerFactory));
- RegisterFactory(SequenceIOHandlerFactoryBasePtr(new PromodIOHandlerFactory));
+ RegisterFactory(SequenceIOHandlerFactoryBasePtr(new ClustalIOHandlerFactory));
+ RegisterFactory(SequenceIOHandlerFactoryBasePtr(new PromodIOHandlerFactory));
+ RegisterFactory(ProfileIOHandlerFactoryBasePtr(new HhmIOHandlerFactory));
+ RegisterFactory(ProfileIOHandlerFactoryBasePtr(new PssmIOHandlerFactory));
RegisterFactory(SurfaceIOHandlerFactoryBasePtr(new SurfaceIOMSMSHandlerFactory));
#if OST_IMG_ENABLED
RegisterFactory(MapIOHandlerFactoryBasePtr(new MapIODxHandlerFactory));
@@ -103,7 +107,7 @@ EntityIOHandlerP IOManager::FindEntityExportHandler(const String& filename,
}
SequenceIOHandlerPtr IOManager::FindAlignmentImportHandler(const String& filename,
- const String& format) {
+ const String& format) {
for(AlignmentIOFList::const_iterator it=alignment_io_list_.begin();
it!=alignment_io_list_.end();++it) {
if( (*it)->ProvidesImport(filename,format)) {
@@ -114,7 +118,7 @@ SequenceIOHandlerPtr IOManager::FindAlignmentImportHandler(const String& filenam
}
SequenceIOHandlerPtr IOManager::FindAlignmentExportHandler(const String& filename,
- const String& format)
+ const String& format)
{
for(AlignmentIOFList::const_iterator it=alignment_io_list_.begin();
it!=alignment_io_list_.end();++it) {
@@ -125,6 +129,29 @@ SequenceIOHandlerPtr IOManager::FindAlignmentExportHandler(const String& filenam
throw IOUnknownFormatException("no suitable alignment io handler found for "+filename);
}
+ProfileIOHandlerPtr IOManager::FindProfileImportHandler(const String& filename,
+ const String& format) {
+ for(ProfileIOFList::const_iterator it=profile_io_list_.begin();
+ it!=profile_io_list_.end();++it) {
+ if( (*it)->ProvidesImport(filename,format)) {
+ return (*it)->Create();
+ }
+ }
+ throw IOUnknownFormatException("no suitable profile io handler found for "+filename);
+}
+
+ProfileIOHandlerPtr IOManager::FindProfileExportHandler(const String& filename,
+ const String& format)
+{
+ for(ProfileIOFList::const_iterator it=profile_io_list_.begin();
+ it!=profile_io_list_.end();++it) {
+ if( (*it)->ProvidesExport(filename,format)) {
+ return (*it)->Create();
+ }
+ }
+ throw IOUnknownFormatException("no suitable profile io handler found for "+filename);
+}
+
SurfaceIOHandlerPtr IOManager::FindSurfaceImportHandler(const String& filename,
const String& format)
{
@@ -267,6 +294,11 @@ void IOManager::RegisterFactory(const SequenceIOHandlerFactoryBasePtr& f)
alignment_io_list_.push_back(f);
}
+void IOManager::RegisterFactory(const ProfileIOHandlerFactoryBasePtr& f)
+{
+ profile_io_list_.push_back(f);
+}
+
void IOManager::RegisterFactory(const SurfaceIOHandlerFactoryBasePtr& f)
{
surface_io_list_.push_back(f);
@@ -282,6 +314,11 @@ const AlignmentIOFList& IOManager::GetAvailableAlignmentHandler() const
return alignment_io_list_;
}
+const ProfileIOFList& IOManager::GetAvailableProfileHandler() const
+{
+ return profile_io_list_;
+}
+
const SurfaceIOFList& IOManager::GetAvailableSurfaceHandler() const
{
return surface_io_list_;
diff --git a/modules/io/src/io_manager.hh b/modules/io/src/io_manager.hh
index bfebe32bdb476e41d5b69f675476509d9fab6881..18297af6d03fda77784aca5593c2d6a0d2f63012 100644
--- a/modules/io/src/io_manager.hh
+++ b/modules/io/src/io_manager.hh
@@ -26,6 +26,7 @@
#include <ost/io/mol/entity_io_handler.hh>
#include <ost/io/seq/sequence_io_handler.hh>
+#include <ost/io/seq/profile_io_handler.hh>
#include <ost/io/mol/surface_io_handler.hh>
#if OST_IMG_ENABLED
@@ -33,10 +34,12 @@
#endif
#include <ost/io/io_exception.hh>
+
namespace ost { namespace io {
typedef std::vector<EntityIOHandlerFactoryBaseP> EntityIOHFList;
typedef std::vector<SequenceIOHandlerFactoryBasePtr> AlignmentIOFList;
+typedef std::vector<ProfileIOHandlerFactoryBasePtr> ProfileIOFList;
typedef std::vector<SurfaceIOHandlerFactoryBasePtr> SurfaceIOFList;
#if OST_IMG_ENABLED
@@ -77,11 +80,17 @@ public:
/// \brief get sequence io handler that is able to import the given file.
/// \sa FindEntityImportHandler(filename)
SequenceIOHandlerPtr FindAlignmentImportHandler(const String& filename,
- const String& format="auto");
+ const String& format="auto");
SequenceIOHandlerPtr FindAlignmentExportHandler(const String& filename,
- const String& format="auto");
-
+ const String& format="auto");
+
+ ProfileIOHandlerPtr FindProfileImportHandler(const String& filename,
+ const String& format="auto");
+
+ ProfileIOHandlerPtr FindProfileExportHandler(const String& filename,
+ const String& format="auto");
+
SurfaceIOHandlerPtr FindSurfaceImportHandler(const String& filename,
const String& format="auto");
//@}
@@ -90,7 +99,10 @@ public:
void RegisterFactory(const EntityIOHandlerFactoryBaseP&);
/// \brief register aligment io handler factory
/// \sa adding_io_handler
- void RegisterFactory(const SequenceIOHandlerFactoryBasePtr&);
+ void RegisterFactory(const SequenceIOHandlerFactoryBasePtr&);
+ /// \brief register profile io handler factory
+ /// \sa adding_io_handler
+ void RegisterFactory(const ProfileIOHandlerFactoryBasePtr&);
/// \brief register surface io handler factory
/// \sa adding_io_handler
void RegisterFactory(const SurfaceIOHandlerFactoryBasePtr&);
@@ -101,6 +113,9 @@ public:
/// \brief Get a list with all available AlignmentHandler
const AlignmentIOFList& GetAvailableAlignmentHandler() const;
+ /// \brief Get a list with all available ProfileHandler
+ const ProfileIOFList& GetAvailableProfileHandler() const;
+
/// \brief Get a list with all available SurfaceHandler
const SurfaceIOFList& GetAvailableSurfaceHandler() const;
@@ -137,6 +152,7 @@ private:
EntityIOHFList entity_iohf_list_;
AlignmentIOFList alignment_io_list_;
+ ProfileIOFList profile_io_list_;
SurfaceIOFList surface_io_list_;
#if OST_IMG_ENABLED
diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index e7b729cb67c2361636103b86e1cb02f225db4c66..e0792e93ee64ec6038451cad5a283a5c5c12144c 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -19,6 +19,7 @@ dcd_io.cc
star_parser.cc
mmcif_reader.cc
mmcif_info.cc
+pdb_str.cc
PARENT_SCOPE
)
@@ -45,5 +46,6 @@ load_entity.hh
surface_io_handler.hh
load_surface.hh
surface_io_msms_handler.hh
+pdb_str.hh
PARENT_SCOPE
)
diff --git a/modules/io/src/mol/chemdict_parser.cc b/modules/io/src/mol/chemdict_parser.cc
index 654204dcd6591d31267b67bbde7b14ddabea19b4..47f7f6f2d369a9e446a4929ec6a914fa6aa179d4 100644
--- a/modules/io/src/mol/chemdict_parser.cc
+++ b/modules/io/src/mol/chemdict_parser.cc
@@ -38,6 +38,11 @@ bool ChemdictParser::OnBeginLoop(const StarLoopDesc& header)
indices_[ATOM_ID2]=header.GetIndex("atom_id_2");
indices_[BOND_ORDER]=header.GetIndex("value_order");
return true;
+ } else if (header.GetCategory()=="pdbx_chem_comp_descriptor") {
+ loop_type_=DESC_SPEC;
+ indices_[DESC_TYPE]=header.GetIndex("type");
+ indices_[DESC]=header.GetIndex("descriptor");
+ return true;
}
loop_type_=DONT_KNOW;
return false;
@@ -68,6 +73,19 @@ void ChemdictParser::OnDataRow(const StarLoopDesc& header,
std::swap(bond.atom_one, bond.atom_two);
}
compound_->AddBond(bond);
+ } else if (loop_type_==DESC_SPEC) {
+ if (columns[indices_[DESC_TYPE]] == StringRef("InChI", 5)) {
+ // for type InChi check prefix 'InChI='
+ if (columns[indices_[DESC]].substr(0, 6) != StringRef("InChI=", 6)) {
+ std::cout << "InChI problem: compound " << compound_->GetID()
+ << " has an InChI descriptor not starting with the "
+ "'InChI=' prefix." << std::endl;
+ return;
+ }
+ compound_->SetInchi(columns[indices_[DESC]].substr(6).str());
+ } else if (columns[indices_[DESC_TYPE]] == StringRef("InChIKey", 8)) {
+ compound_->SetInchiKey(columns[indices_[DESC]].str());
+ }
}
}
@@ -160,8 +178,12 @@ void ChemdictParser::InitTypeMap()
if (!tm_.empty())
return;
tm_["L-PEPTIDE COOH CARBOXY TERMINUS"]=mol::ChemClass(mol::ChemClass::L_PEPTIDE_LINKING);
- tm_["L-PEPTIDE NH3 AMINO TERMINUS"]=mol::ChemClass(mol::ChemClass::L_PEPTIDE_LINKING);
+ tm_["L-PEPTIDE NH3 AMINO TERMINUS"]=mol::ChemClass(mol::ChemClass::L_PEPTIDE_LINKING);
+ tm_["L-GAMMA-PEPTIDE, C-DELTA LINKING"]=mol::ChemClass(mol::ChemClass::L_PEPTIDE_LINKING);
+ tm_["L-BETA-PEPTIDE, C-GAMMA LINKING"]=mol::ChemClass(mol::ChemClass::L_PEPTIDE_LINKING);
tm_["D-PEPTIDE NH3 AMINO TERMINUS"]=mol::ChemClass(mol::ChemClass::D_PEPTIDE_LINKING);
+ tm_["D-BETA-PEPTIDE, C-GAMMA LINKING"]=mol::ChemClass(mol::ChemClass::D_PEPTIDE_LINKING);
+ tm_["D-GAMMA-PEPTIDE, C-DELTA LINKING"]=mol::ChemClass(mol::ChemClass::D_PEPTIDE_LINKING);
tm_["L-SACCHARIDE 1,4 AND 1,4 LINKING"]=mol::ChemClass(mol::ChemClass::L_SACCHARIDE);
tm_["D-SACCHARIDE 1,4 AND 1,4 LINKING"]=mol::ChemClass(mol::ChemClass::D_SACCHARIDE);
tm_["L-SACCHARIDE"]=mol::ChemClass(mol::ChemClass::L_SACCHARIDE);
@@ -182,6 +204,7 @@ void ChemdictParser::InitTypeMap()
tm_["PEPTIDE-LINKING"]=mol::ChemClass(mol::ChemClass::PEPTIDE_LINKING);
tm_["NON-POLYMER"]=mol::ChemClass(mol::ChemClass::NON_POLYMER);
tm_["RNA OH 3 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
+ tm_["RNA OH 5 PRIME TERMINUS"]=mol::ChemClass(mol::ChemClass::RNA_LINKING);
tm_["?"]=mol::ChemClass(mol::ChemClass::UNKNOWN);
tm_["WATER"]=mol::ChemClass(mol::ChemClass::WATER);
}
diff --git a/modules/io/src/mol/chemdict_parser.hh b/modules/io/src/mol/chemdict_parser.hh
index 51142744c37de1e419f39395db04edc926801982..16c968252faf07a0dc9ba3efcde81e9ef18d2dcc 100644
--- a/modules/io/src/mol/chemdict_parser.hh
+++ b/modules/io/src/mol/chemdict_parser.hh
@@ -34,6 +34,7 @@ namespace ost { namespace io {
typedef enum {
ATOM_SPEC,
BOND_SPEC,
+ DESC_SPEC,
DONT_KNOW
} LoopType;
@@ -77,7 +78,9 @@ private:
STEREO_CONF=6,
ATOM_ID1=0,
ATOM_ID2=1,
- BOND_ORDER=2
+ BOND_ORDER=2,
+ DESC_TYPE=0,
+ DESC=1
} PropIndex;
char last_;
int indices_[10];
diff --git a/modules/io/src/mol/entity_io_sdf_handler.cc b/modules/io/src/mol/entity_io_sdf_handler.cc
index 31ba544b0214906993ae1fced35ebf1cbd6feffb..e99933ec3044f97dbcc2715f66bb2a411a168e95 100644
--- a/modules/io/src/mol/entity_io_sdf_handler.cc
+++ b/modules/io/src/mol/entity_io_sdf_handler.cc
@@ -21,8 +21,8 @@
*/
#include <ost/log.hh>
-#include <ost/io/sdf_writer.hh>
-#include <ost/io/sdf_reader.hh>
+#include <ost/io/mol/sdf_writer.hh>
+#include <ost/io/mol/sdf_reader.hh>
#include "entity_io_sdf_handler.hh"
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index ca8da62036b5151ff38cbefe65645515be2b0851..8087e7e0718972ddc1343899af4d69696fda1f3e 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -180,7 +180,9 @@ public:
/// \brief Set the translational vector
///
- /// \param
+ /// \param x
+ /// \param y
+ /// \param z
void SetVector(Real x, Real y, Real z)
{
translation_.SetX(x);
@@ -194,7 +196,15 @@ public:
/// \brief Set the rotational matrix
///
- /// \param
+ /// \param i00
+ /// \param i01
+ /// \param i02
+ /// \param i10
+ /// \param i11
+ /// \param i12
+ /// \param i20
+ /// \param i21
+ /// \param i22
void SetMatrix(Real i00, Real i01, Real i02,
Real i10, Real i11, Real i12,
Real i20, Real i21, Real i22)
@@ -266,7 +276,7 @@ public:
/// \brief Set method details
///
- /// \param method details
+ /// \param method_details
void SetMethodDetails(String method_details) {
method_details_ = method_details;
}
@@ -435,7 +445,7 @@ public:
/// \brief Set the start page for a publication
///
- /// \param start
+ /// \param first
void SetPageFirst(String first) { page_first_ = first; }
/// \brief Get the start page of a publication
@@ -445,7 +455,7 @@ public:
/// \brief Set the end page for a publication
///
- /// \param end
+ /// \param last
void SetPageLast(String last) { page_last_ = last; }
/// \brief Get the last page of a publication
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 93807f921e50c1457dc3cf7d0cc890375900183f..3df667baf15fdcd215cef2c63cac5222c5b4232c 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -374,9 +374,9 @@ bool MMCifReader::ParseAtomIdent(const std::vector<StringRef>& columns,
return false;
}
- std::pair<bool, int> a_num = this->TryGetInt(columns[indices_[AS_ID]],
- "atom_site.id",
- profile_.fault_tolerant); // unit test
+ this->TryGetInt(columns[indices_[AS_ID]],
+ "atom_site.id",
+ profile_.fault_tolerant); // unit test
alt_loc = columns[indices_[LABEL_ALT_ID]][0];
res_name = columns[indices_[LABEL_COMP_ID]];
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 15cc727ad76d4a86b2952970bbfb3c4321fbb733..a8e35f52cf543ca6f744224d88723caef4d16b42 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -61,18 +61,22 @@ public:
/// \brief create a MMCifReader
///
/// \param stream input stream
+ /// \param ent_handle
+ /// \param profile
+
MMCifReader(std::istream& stream, mol::EntityHandle& ent_handle,
const IOProfile& profile);
/// \brief create a MMCifReader
///
/// \param filename input file
+ /// \param ent_handle
+ /// \param profile
MMCifReader(const String& filename, mol::EntityHandle& ent_handle,
const IOProfile& profile);
/// \brief Initialise the reader.
///
- /// \param loc Location of the file
void Init();
/// \brief Set up a fresh instance
@@ -193,8 +197,9 @@ protected:
/// \brief fetch values identifying atoms
///
/// \param[in] columns data row
- /// \param[out] chain_name takes atom_site.label_asym_id or, if
+ /// \param[out] auth_chain_name takes atom_site.label_asym_id or, if
/// auth_chain_id_ is set, atom_site.auth_asym_id as a chain name
+ /// \param[out] cif_chain_name
/// \param[out] res_name fetches atom_site.label_comp_id
/// \param[out] resnum gets atom_site.label_seq_id if available, consecutive
/// numbers, otherwise
diff --git a/modules/io/src/mol/pdb_str.cc b/modules/io/src/mol/pdb_str.cc
new file mode 100644
index 0000000000000000000000000000000000000000..7168dfb16fb3d8d304ae58b747d125668600883e
--- /dev/null
+++ b/modules/io/src/mol/pdb_str.cc
@@ -0,0 +1,48 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <sstream>
+#include <ost/io/mol/pdb_str.hh>
+#include <ost/io/mol/pdb_writer.hh>
+#include <ost/io/mol/pdb_reader.hh>
+
+namespace ost { namespace io {
+
+String EntityToPDBString(const mol::EntityHandle& ent, const IOProfile& profile) {
+ std::stringstream stream;
+ PDBWriter writer(stream, profile);
+ writer.Write(ent);
+ return stream.str();
+}
+
+String EntityToPDBString(const mol::EntityView& ent, const IOProfile& profile) {
+ std::stringstream stream;
+ PDBWriter writer(stream, profile);
+ writer.Write(ent);
+ return stream.str();
+}
+
+mol::EntityHandle PDBStringToEntity(const String& pdb, const IOProfile& profile) {
+ std::stringstream stream(pdb);
+ PDBReader reader(stream, profile);
+ mol::EntityHandle ent = mol::CreateEntity();
+ reader.Import(ent);
+ return ent;
+}
+
+}}
diff --git a/modules/io/src/mol/pdb_str.hh b/modules/io/src/mol/pdb_str.hh
new file mode 100644
index 0000000000000000000000000000000000000000..d376dce59dce243ac9783c09d2dad6b9ade24ad8
--- /dev/null
+++ b/modules/io/src/mol/pdb_str.hh
@@ -0,0 +1,41 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_IO_PDB_STR_HH
+#define OST_IO_PDB_STR_HH
+
+#include <ost/io/module_config.hh>
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/io/mol/io_profile.hh>
+
+namespace ost { namespace io {
+
+// Saves an entity to a string in PDB format.
+String DLLEXPORT_OST_IO
+EntityToPDBString(const mol::EntityHandle& ent, const IOProfile& profile=IOProfile());
+
+String DLLEXPORT_OST_IO
+EntityToPDBString(const mol::EntityView& ent, const IOProfile& profile=IOProfile());
+
+mol::EntityHandle DLLEXPORT_OST_IO
+PDBStringToEntity(const String& pdb, const IOProfile& profile=IOProfile());
+
+}}
+
+#endif
diff --git a/modules/io/src/mol/star_parser.hh b/modules/io/src/mol/star_parser.hh
index c5febf7fb3c2672c2381cdac72c178e9e93beb9a..53e170e72b6e7f2b0fdfe55b2679c72d10b5ad34 100644
--- a/modules/io/src/mol/star_parser.hh
+++ b/modules/io/src/mol/star_parser.hh
@@ -114,7 +114,7 @@ public:
/// \brief create a StarParser
///
/// \param stream input stream
- /// \param item_as_row if true, data-items are first gathered (identifier as
+ /// \param items_as_row if true, data-items are first gathered (identifier as
/// header, values as row) and then parsed like a loop
/// (OnBeginLoop(), OnDataRow(), OnEndLoop())
explicit StarParser(std::istream& stream, bool items_as_row=false);
diff --git a/modules/io/src/seq/CMakeLists.txt b/modules/io/src/seq/CMakeLists.txt
index 9dd14b52abbaf97d83967c2660e48e4438dfce76..605eb9546d40541406b64459ff02e6d82e65bff4 100644
--- a/modules/io/src/seq/CMakeLists.txt
+++ b/modules/io/src/seq/CMakeLists.txt
@@ -5,6 +5,8 @@ save.cc
fasta_io_handler.cc
pir_io_handler.cc
promod_io_handler.cc
+hhm_io_handler.cc
+pssm_io_handler.cc
PARENT_SCOPE
)
@@ -13,6 +15,9 @@ sequence_io_handler.hh
fasta_io_handler.hh
pir_io_handler.hh
promod_io_handler.hh
+profile_io_handler.hh
+hhm_io_handler.hh
+pssm_io_handler.hh
clustal_io_handler.hh
load.hh
save.hh
diff --git a/modules/io/src/seq/hhm_io_handler.cc b/modules/io/src/seq/hhm_io_handler.cc
new file mode 100644
index 0000000000000000000000000000000000000000..395c97bd1f48c0bb6bdc0829497f0846afaadb78
--- /dev/null
+++ b/modules/io/src/seq/hhm_io_handler.cc
@@ -0,0 +1,179 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello, Gabriel Studer
+ */
+
+#include "hhm_io_handler.hh"
+
+#include <boost/algorithm/string/predicate.hpp>
+#include <boost/filesystem/convenience.hpp>
+#include <boost/filesystem/fstream.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
+
+#include <ost/string_ref.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/io/io_utils.hh>
+
+namespace ost { namespace io {
+
+namespace {
+// reset pc with freqs in chunks[i+offset] (i in [0,20[)
+// checks for consistency of chunks and values read
+seq::ProfileColumn GetColumn(const std::vector<ost::StringRef>& chunks,
+ const uint offset, const char* olcs,
+ const String& exception) {
+ // check chunks size
+ if (chunks.size() < offset+20) {
+ throw IOException(exception);
+ }
+ // reset pc
+ seq::ProfileColumn pc; // all 0
+ for (uint i = 0; i < 20; ++i) {
+ if (chunks[i+offset] != ost::StringRef("*", 1)) {
+ std::pair<bool, int> pbi = chunks[i+offset].to_int();
+ if (!pbi.first) {
+ throw IOException(exception);
+ }
+ pc.SetFreq(olcs[i], pow(2.0, -0.001 * pbi.second));
+ }
+ }
+ return pc;
+}
+} // anon ns
+
+void HhmIOHandler::Import(seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc) {
+ // open it up
+ boost::iostreams::filtering_stream<boost::iostreams::input> in;
+ boost::filesystem::ifstream stream(loc);
+ if (!stream) {
+ throw IOException("Could not open " + loc.string());
+ }
+ // add unzip if necessary
+ if (boost::iequals(".gz", boost::filesystem::extension(loc))) {
+ in.push(boost::iostreams::gzip_decompressor());
+ }
+ in.push(stream);
+
+ // reset profile
+ prof.clear();
+
+ // tmp. storage
+ std::string line;
+ ost::StringRef sline;
+ std::string null_line;
+ char olcs[20];
+ std::vector<ost::StringRef> chunks;
+
+ // read line-by-line looking for NULL
+ bool null_found = false;
+ while (std::getline(in, line)) {
+ sline = ost::StringRef(line.c_str(), line.length());
+ if (sline.length()>4 &&
+ sline.substr(0, 5) == ost::StringRef("NULL ", 5)) {
+ null_line = line;
+ null_found = true;
+ break;
+ }
+ }
+ if (!null_found) {
+ throw IOException("No NULL found in file " + loc.string());
+ }
+
+ // read until we hit HMM, extract olcs, then skip 2 more lines
+ bool hmm_found = false;
+ while (std::getline(in, line)) {
+ sline = ost::StringRef(line.c_str(), line.length());
+ chunks = sline.split();
+ if (chunks[0] == ost::StringRef("HMM", 3)) {
+ // extract olcs
+ if (chunks.size() != 21) {
+ throw IOException("Badly formatted HMM line in " + loc.string());
+ }
+ for (uint i = 1; i < 21; ++i) {
+ if (chunks[i].length() != 1) {
+ throw IOException("Badly formatted HMM line in " + loc.string());
+ }
+ olcs[i-1] = chunks[i][0];
+ }
+ // skip 2 lines and get out
+ std::getline(in, line);
+ std::getline(in, line);
+ hmm_found = true;
+ break;
+ }
+ }
+ if (!hmm_found) {
+ throw IOException("No HMM found in file " + loc.string());
+ }
+
+ // set null model
+ chunks = ost::StringRef(null_line.c_str(), null_line.length()).split();
+ prof.SetNullModel(GetColumn(chunks, 1, olcs, "Badly formatted NULL line\n"
+ + null_line + "\n in " + loc.string()));
+
+ // set columns
+ String seqres;
+ while (std::getline(in, line)) {
+ sline = ost::StringRef(line.c_str(), line.length());
+ if (sline.trim().empty()) continue;
+ if (sline.trim() == ost::StringRef("//", 2)) break;
+ chunks = sline.split();
+ // one letter code
+ seqres += chunks[0][0];
+ // frequencies
+ prof.push_back(GetColumn(chunks, 2, olcs, "Badly formatted line\n"
+ + line + "\n in " + loc.string()));
+ // skip line (trans. matrix)
+ std::getline(in, line);
+ }
+ prof.SetSequence(seqres);
+}
+
+void HhmIOHandler::Export(const seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc) const {
+ throw IOException("Cannot write hhm files.");
+}
+
+bool HhmIOHandler::ProvidesImport(const boost::filesystem::path& loc,
+ const String& format) {
+ if (format=="auto") {
+ String match_suf_string = loc.string();
+ std::transform(match_suf_string.begin(), match_suf_string.end(),
+ match_suf_string.begin(), tolower);
+ if ( detail::FilenameEndsWith(match_suf_string,".hhm")
+ || detail::FilenameEndsWith(match_suf_string,".hhm.gz")) {
+ return true;
+ }
+ } else if (format == "hhm") {
+ return true;
+ }
+ return false;
+}
+
+bool HhmIOHandler::ProvidesExport(const boost::filesystem::path& loc,
+ const String& format) {
+ // no writers here
+ return false;
+}
+
+}}
diff --git a/modules/io/src/seq/hhm_io_handler.hh b/modules/io/src/seq/hhm_io_handler.hh
new file mode 100644
index 0000000000000000000000000000000000000000..a3acd275c1e7feff6ca57692efa2bbaddcc02532
--- /dev/null
+++ b/modules/io/src/seq/hhm_io_handler.hh
@@ -0,0 +1,52 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello
+ */
+
+#ifndef OST_HHM_IO_HANDLER_HH
+#define OST_HHM_IO_HANDLER_HH
+
+#include <ost/io/module_config.hh>
+#include "profile_io_handler.hh"
+
+namespace ost { namespace io {
+
+class DLLEXPORT_OST_IO HhmIOHandler : public ProfileIOHandler {
+public:
+ virtual void Import(seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc);
+ virtual void Export(const seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc) const;
+
+ static bool ProvidesImport(const boost::filesystem::path& loc,
+ const String& format="auto");
+ static bool ProvidesExport(const boost::filesystem::path& loc,
+ const String& format="auto");
+
+ static String GetFormatName() { return String("HHM"); }
+ static String GetFormatDescription() { return String("HHM output of HHblits"); }
+};
+
+typedef ProfileIOHandlerFactory<HhmIOHandler> HhmIOHandlerFactory;
+
+}}
+
+#endif
diff --git a/modules/io/src/seq/load.cc b/modules/io/src/seq/load.cc
index 896c5fa970ef5de0abc04565dbf972647c71bebc..9bca49efef18b341e107f0653ca1506af7e401ab 100644
--- a/modules/io/src/seq/load.cc
+++ b/modules/io/src/seq/load.cc
@@ -101,4 +101,14 @@ seq::SequenceHandle SequenceFromString(const String& data,
return get_one_seq(SequenceListFromString(data, format));
}
+seq::ProfileHandlePtr LoadSequenceProfile(const String& file_name,
+ const String& format)
+{
+ seq::ProfileHandlePtr prof(new seq::ProfileHandle);
+ IOManager& m = IOManager::Instance();
+ ProfileIOHandlerPtr prof_io = m.FindProfileImportHandler(file_name, format);
+ prof_io->Import(*prof, file_name);
+ return prof;
+}
+
}}
diff --git a/modules/io/src/seq/load.hh b/modules/io/src/seq/load.hh
index 485fef1d8ba525853cc1aeeffd5d08150b5a0bb2..a72cee4b297615fbf8900fc7bdf9df8e0285d810 100644
--- a/modules/io/src/seq/load.hh
+++ b/modules/io/src/seq/load.hh
@@ -26,8 +26,9 @@
#include <ost/io/module_config.hh>
#include <ost/seq/sequence_list.hh>
#include <ost/seq/alignment_handle.hh>
-namespace ost { namespace io {
+#include <ost/seq/profile_handle.hh>
+namespace ost { namespace io {
seq::AlignmentHandle DLLEXPORT_OST_IO
LoadAlignment(const String& file_name, const String& format="auto");
@@ -57,6 +58,9 @@ SequenceFromStream(std::istream& stream, const String& format);
seq::SequenceHandle DLLEXPORT_OST_IO
SequenceFromString(const String& data, const String& format);
+seq::ProfileHandlePtr DLLEXPORT_OST_IO
+LoadSequenceProfile(const String& file_name, const String& format="auto");
+
}}
#endif
diff --git a/modules/io/src/seq/profile_io_handler.hh b/modules/io/src/seq/profile_io_handler.hh
new file mode 100644
index 0000000000000000000000000000000000000000..783d697620164263cc71af8bddfc3bd029accd87
--- /dev/null
+++ b/modules/io/src/seq/profile_io_handler.hh
@@ -0,0 +1,93 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello
+ */
+
+#ifndef OST_IO_PROFILE_IO_HANDLER_HH
+#define OST_IO_PROFILE_IO_HANDLER_HH
+
+#include <boost/shared_ptr.hpp>
+#include <boost/filesystem/operations.hpp>
+
+#include <ost/io/module_config.hh>
+#include <ost/io/io_utils.hh>
+#include <ost/seq/profile_handle.hh>
+
+namespace ost { namespace io {
+
+//! pure abstract base class for profile io handlers
+class DLLEXPORT_OST_IO ProfileIOHandler {
+public:
+ virtual ~ProfileIOHandler() {}
+
+ virtual void Import(seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc) = 0;
+
+ virtual void Export(const seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc) const = 0;
+};
+
+typedef boost::shared_ptr<ProfileIOHandler> ProfileIOHandlerPtr;
+
+//! pure abstract base class for creation of a specfic io handler
+class DLLEXPORT_OST_IO ProfileIOHandlerFactoryBase {
+public:
+ virtual ~ProfileIOHandlerFactoryBase() {}
+ virtual bool ProvidesImport(const boost::filesystem::path& loc,
+ const String& format="auto") const = 0;
+ virtual bool ProvidesExport(const boost::filesystem::path& loc,
+ const String& format="auto") const = 0;
+ virtual ProfileIOHandlerPtr Create() const = 0;
+ virtual String GetFormatName() const =0;
+ virtual String GetFormatDescription() const =0;
+};
+
+typedef boost::shared_ptr<ProfileIOHandlerFactoryBase> ProfileIOHandlerFactoryBasePtr;
+
+template <class HANDLER>
+class ProfileIOHandlerFactory: public ProfileIOHandlerFactoryBase {
+ virtual bool ProvidesImport(const boost::filesystem::path& loc,
+ const String& format="auto") const {
+ return HANDLER::ProvidesImport(loc, format);
+ }
+
+ virtual bool ProvidesExport(const boost::filesystem::path& loc,
+ const String& format="auto") const {
+ return HANDLER::ProvidesExport(loc, format);
+ }
+
+ virtual ProfileIOHandlerPtr Create() const {
+ return ProfileIOHandlerPtr(new HANDLER);
+ }
+
+ virtual String GetFormatName() const {
+ return HANDLER::GetFormatName();
+ }
+
+ virtual String GetFormatDescription() const {
+ return HANDLER::GetFormatDescription();
+ }
+
+};
+
+}} // ns
+
+#endif
diff --git a/modules/io/src/seq/pssm_io_handler.cc b/modules/io/src/seq/pssm_io_handler.cc
new file mode 100644
index 0000000000000000000000000000000000000000..4b16ed6cb94cede54755a4c22ac95a56b6b9f0a3
--- /dev/null
+++ b/modules/io/src/seq/pssm_io_handler.cc
@@ -0,0 +1,147 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello
+ */
+
+#include "pssm_io_handler.hh"
+
+#include <boost/algorithm/string/predicate.hpp>
+#include <boost/filesystem/convenience.hpp>
+#include <boost/filesystem/fstream.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
+
+#include <ost/string_ref.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/io/io_utils.hh>
+
+namespace ost { namespace io {
+
+void PssmIOHandler::Import(seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc) {
+ // open it up
+ boost::iostreams::filtering_stream<boost::iostreams::input> in;
+ boost::filesystem::ifstream stream(loc);
+ if (!stream) {
+ throw IOException("Could not open " + loc.string());
+ }
+ // add unzip if necessary
+ if (boost::iequals(".gz", boost::filesystem::extension(loc))) {
+ in.push(boost::iostreams::gzip_decompressor());
+ }
+ in.push(stream);
+
+ // reset profile
+ prof.clear();
+
+ // set null model
+ prof.SetNullModel(seq::ProfileColumn::BLOSUMNullModel());
+
+ // tmp. storage
+ std::string line;
+ ost::StringRef sline;
+ char olcs[20];
+ std::vector<ost::StringRef> chunks;
+
+ // read line-by-line looking for table
+ // -> start = line with 40 1-char tokens
+ bool table_found = false;
+ while (std::getline(in, line)) {
+ sline = ost::StringRef(line.c_str(), line.length());
+ chunks = sline.split();
+ if (chunks.size() == 40) {
+ bool got_it = true;
+ for (uint i = 0; i < 40; ++i) {
+ if (chunks[i].length() != 1) {
+ got_it = false;
+ break;
+ }
+ if (i >= 20) {
+ olcs[i-20] = chunks[i][0];
+ }
+ }
+ if (got_it) {
+ table_found = true;
+ break;
+ }
+ }
+ }
+ if (!table_found) {
+ throw IOException("No ASCII table found in file " + loc.string());
+ }
+
+ // parse table (assume: index olc 20xscore 20xfreq)
+ String seqres;
+ while (std::getline(in, line)) {
+ sline = ost::StringRef(line.c_str(), line.length());
+ chunks = sline.split();
+ // stop if not enough entries
+ if (chunks.size() < 42) break;
+ // parse row (freq in % as integers)
+ seqres += chunks[1][0];
+ Real sum_freq = 0;
+ Real freqs[20];
+ for (uint i = 22; i < 42; ++i) {
+ std::pair<bool, int> pbi = chunks[i].to_int();
+ if (!pbi.first) {
+ throw IOException("Badly formatted line\n" + line + "\n in " + loc.string());
+ }
+ sum_freq += pbi.second;
+ freqs[i-22] = pbi.second;
+ }
+ // fill normalized frequencies
+ seq::ProfileColumn pc;
+ for (uint i = 0; i < 20; ++i) {
+ pc.SetFreq(olcs[i], freqs[i]/sum_freq);
+ }
+ prof.push_back(pc);
+ }
+ prof.SetSequence(seqres);
+}
+
+void PssmIOHandler::Export(const seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc) const {
+ throw IOException("Cannot write pssm files.");
+}
+
+bool PssmIOHandler::ProvidesImport(const boost::filesystem::path& loc,
+ const String& format) {
+ if (format=="auto") {
+ String match_suf_string = loc.string();
+ std::transform(match_suf_string.begin(), match_suf_string.end(),
+ match_suf_string.begin(), tolower);
+ if ( detail::FilenameEndsWith(match_suf_string,".pssm")
+ || detail::FilenameEndsWith(match_suf_string,".pssm.gz")) {
+ return true;
+ }
+ } else if (format == "pssm") {
+ return true;
+ }
+ return false;
+}
+
+bool PssmIOHandler::ProvidesExport(const boost::filesystem::path& loc,
+ const String& format) {
+ // no writers here
+ return false;
+}
+
+}}
diff --git a/modules/io/src/seq/pssm_io_handler.hh b/modules/io/src/seq/pssm_io_handler.hh
new file mode 100644
index 0000000000000000000000000000000000000000..87a00673bdab1f8ad242b43c3c6818b0f7b8e7a5
--- /dev/null
+++ b/modules/io/src/seq/pssm_io_handler.hh
@@ -0,0 +1,54 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello
+ */
+
+#ifndef OST_PSSM_IO_HANDLER_HH
+#define OST_PSSM_IO_HANDLER_HH
+
+#include <ost/io/module_config.hh>
+#include "profile_io_handler.hh"
+
+namespace ost { namespace io {
+
+class DLLEXPORT_OST_IO PssmIOHandler : public ProfileIOHandler {
+public:
+ virtual void Import(seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc);
+ virtual void Export(const seq::ProfileHandle& prof,
+ const boost::filesystem::path& loc) const;
+
+ static bool ProvidesImport(const boost::filesystem::path& loc,
+ const String& format="auto");
+ static bool ProvidesExport(const boost::filesystem::path& loc,
+ const String& format="auto");
+
+ static String GetFormatName() { return String("PSSM"); }
+ static String GetFormatDescription() {
+ return String("ASCII Table (PSSM) output of PSI-BLAST (flag -Q)");
+ }
+};
+
+typedef ProfileIOHandlerFactory<PssmIOHandler> PssmIOHandlerFactory;
+
+}}
+
+#endif
diff --git a/modules/io/tests/CMakeLists.txt b/modules/io/tests/CMakeLists.txt
index 64a31041525e12f4c1c0bc2ba906284b1a424a5e..0efbc1058f2112d8385017d3e63734b64cb80fe3 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -6,6 +6,7 @@ set(OST_IO_UNIT_TESTS
test_io_crd.cc
test_io_dcd.cc
test_io_sdf.cc
+ test_io_sequence_profile.cc
test_pir.cc
test_iomanager.cc
tests.cc
diff --git a/modules/io/tests/test_exceptions.cc b/modules/io/tests/test_exceptions.cc
index 2ed51ce3e61239424f4d3ce8b9ce2f77a3825b24..27d9ea661822b6d4879f6b47a1fc204194fa677f 100644
--- a/modules/io/tests/test_exceptions.cc
+++ b/modules/io/tests/test_exceptions.cc
@@ -25,7 +25,7 @@
#include <boost/test/unit_test.hpp>
#include <boost/test/auto_unit_test.hpp>
-#include <ost/io/load_map.hh>
+#include <ost/io/img/load_map.hh>
#include <ost/img/image.hh>
#include <ost/io/io_exception.hh>
diff --git a/modules/io/tests/test_io_crd.cc b/modules/io/tests/test_io_crd.cc
index b317e936bce58126c130f2260c318af8112a7422..4cde64f327c6a0bcd9710d0468db5399edc7f250 100644
--- a/modules/io/tests/test_io_crd.cc
+++ b/modules/io/tests/test_io_crd.cc
@@ -23,7 +23,7 @@
#include <ost/test_utils/compare_files.hh>
#include <ost/mol/mol.hh>
#include <ost/io/mol/entity_io_crd_handler.hh>
-#include <ost/io/save_entity.hh>
+#include <ost/io/mol/save_entity.hh>
using namespace ost;
using namespace ost::io;
diff --git a/modules/io/tests/test_io_dcd.cc b/modules/io/tests/test_io_dcd.cc
index 016555e696f569175ff066ffef96ed43abdddb52..fb95e6e83d3f161ebdbd1ae0e21f4a9e34a860ce 100644
--- a/modules/io/tests/test_io_dcd.cc
+++ b/modules/io/tests/test_io_dcd.cc
@@ -74,7 +74,7 @@ BOOST_AUTO_TEST_CASE(test_io_dcd_charmm_frames)
SaveCHARMMTraj(cg,"test_io_dcd_out.pdb","test_io_dcd_out.dcd");
mol::CoordGroupHandle cg2=LoadCHARMMTraj(eh,"test_io_dcd_out.dcd");
BOOST_CHECK_EQUAL(cg2.GetAtomCount(),natoms);
- BOOST_CHECK_EQUAL(cg2.GetFrameCount(),1);
+ BOOST_CHECK_EQUAL(cg2.GetFrameCount(),uint(1));
mol::CoordFramePtr cf2 = cg2.GetFrame(0);
BOOST_CHECK(geom::Distance(cf2->GetCellSize(),cell_size)<1e-6);
diff --git a/modules/io/tests/test_io_img.cc b/modules/io/tests/test_io_img.cc
index 78093264b4b204fd095152fff381ae0ac5419512..411201a97e167be7235c1aa9ab041c43e98c95c9 100644
--- a/modules/io/tests/test_io_img.cc
+++ b/modules/io/tests/test_io_img.cc
@@ -21,7 +21,7 @@
#include <boost/test/auto_unit_test.hpp>
#include <map>
-#include <ost/io/load_map.hh>
+#include <ost/io/img/load_map.hh>
#include <ost/img/image_factory.hh>
#include <ost/img/alg/randomize.hh>
#include <ost/io/img/map_io_df3_handler.hh>
diff --git a/modules/io/tests/test_io_pdb.cc b/modules/io/tests/test_io_pdb.cc
index 7d33d8bce38ecc45702b190cbb37439b2b94960d..ff4d3a8dbdfb70988274a0611802cc7413bded60 100644
--- a/modules/io/tests/test_io_pdb.cc
+++ b/modules/io/tests/test_io_pdb.cc
@@ -32,8 +32,8 @@ using boost::unit_test_framework::test_suite;
#include <ost/conop/heuristic.hh>
#include <ost/io/mol/entity_io_pdb_handler.hh>
-#include <ost/io/pdb_reader.hh>
-#include <ost/io/pdb_writer.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/io/mol/pdb_writer.hh>
#include <ost/log.hh>
#include <ost/io/io_exception.hh>
diff --git a/modules/io/tests/test_io_sdf.cc b/modules/io/tests/test_io_sdf.cc
index 289bdfea3a7a79247a762cb7a300eab4c6957910..c90b80b30f4efc571412222d4b7ca7e36fdf4f2c 100644
--- a/modules/io/tests/test_io_sdf.cc
+++ b/modules/io/tests/test_io_sdf.cc
@@ -27,7 +27,7 @@ using boost::unit_test_framework::test_suite;
#include <ost/test_utils/compare_files.hh>
#include <ost/mol/mol.hh>
#include <ost/io/mol/entity_io_sdf_handler.hh>
-#include <ost/io/save_entity.hh>
+#include <ost/io/mol/save_entity.hh>
#include <ost/io/io_exception.hh>
using namespace ost;
diff --git a/modules/io/tests/test_io_sequence_profile.cc b/modules/io/tests/test_io_sequence_profile.cc
new file mode 100644
index 0000000000000000000000000000000000000000..85d2dc60201ba74d6627b0ed45c1c3acad738448
--- /dev/null
+++ b/modules/io/tests/test_io_sequence_profile.cc
@@ -0,0 +1,261 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello, Gabriel Studer
+ */
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <iostream>
+
+#include <ost/seq/profile_handle.hh>
+#include <ost/io/seq/load.hh>
+#include <ost/io/seq/hhm_io_handler.hh>
+#include <ost/io/seq/pssm_io_handler.hh>
+
+using namespace ost::seq;
+using namespace ost::io;
+
+BOOST_AUTO_TEST_SUITE( io );
+
+// helper to compare profiles element by element (with delta)
+// delta given in % !
+template <typename T, typename T2>
+void compareProfiles(T& t, T2& t2, Real delta = 0) {
+ BOOST_REQUIRE_EQUAL(t.size(), t2.size());
+ BOOST_CHECK_EQUAL(t.GetSequence(), t2.GetSequence());
+ BOOST_CHECK_CLOSE(t.GetAverageEntropy(), t2.GetAverageEntropy(), delta*20);
+ const Real* f = t.GetNullModel().freqs_begin();
+ const Real* f2 = t2.GetNullModel().freqs_begin();
+ for (uint j = 0; j < 20; ++j) {
+ BOOST_CHECK_CLOSE(f[j], f2[j], delta);
+ }
+ uint N = t.size();
+ for (uint i = 0; i < N; ++i) {
+ f = t[i].freqs_begin();
+ f2 = t2[i].freqs_begin();
+ for (uint j = 0; j < 20; ++j) {
+ BOOST_CHECK_CLOSE(f[j], f2[j], delta);
+ }
+ }
+}
+
+BOOST_AUTO_TEST_CASE(hhm_loading)
+{
+ // check hhm factory
+ ProfileIOHandlerFactoryBasePtr fac(new HhmIOHandlerFactory);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test.hhm"), true);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test.hhm.gz"), true);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test.pssm"), false);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test.pssm.gz"), false);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test", "hhm"), true);
+ BOOST_CHECK_EQUAL(fac->ProvidesExport("test.hhm"), false);
+ BOOST_CHECK_EQUAL(fac->ProvidesExport("test.hhm.gz"), false);
+ BOOST_CHECK_EQUAL(fac->ProvidesExport("test", "hhm"), false);
+ ProfileIOHandlerPtr io_handler = fac->Create();
+
+ // load file
+ ProfileHandlePtr prof(new ProfileHandle);
+ io_handler->Import(*prof, "testfiles/test_hmm.hhm");
+ BOOST_CHECK_EQUAL(prof->size(), size_t(5));
+ BOOST_CHECK_EQUAL(prof->GetSequence(), "ETGSP");
+
+ // we first check, whether the null model has been read correctly
+ // and then randomly pick a column to check
+
+ ProfileColumn null_model = prof->GetNullModel();
+
+ String olc = "ACDEFGHIKLMNPQRSTVWY";
+
+ Real correct_aa_freqs[] = {pow(2.0,-0.001*3706), pow(2.0,-0.001*5728),
+ pow(2.0,-0.001*4211), pow(2.0,-0.001*4064),
+ pow(2.0,-0.001*4839), pow(2.0,-0.001*3729),
+ pow(2.0,-0.001*4763), pow(2.0,-0.001*4308),
+ pow(2.0,-0.001*4069), pow(2.0,-0.001*3323),
+ pow(2.0,-0.001*5509), pow(2.0,-0.001*4640),
+ pow(2.0,-0.001*4464), pow(2.0,-0.001*4937),
+ pow(2.0,-0.001*4285), pow(2.0,-0.001*4423),
+ pow(2.0,-0.001*3815), pow(2.0,-0.001*3783),
+ pow(2.0,-0.001*6325), pow(2.0,-0.001*4665)};
+
+ for (int i = 0; i < 20; ++i) {
+ BOOST_CHECK_CLOSE(null_model.GetFreq(olc[i]), correct_aa_freqs[i],
+ Real(1e-5));
+ }
+
+ // let's check, whether a particular column has been read correctly
+ ProfileColumn col = (*prof)[2];
+
+ memset(correct_aa_freqs, 0, 20*sizeof(Real));
+ correct_aa_freqs[0] = pow(2.0,-0.001*3676);
+ correct_aa_freqs[1] = pow(2.0,-0.001*2597);
+ correct_aa_freqs[5] = pow(2.0,-0.001*5359);
+ correct_aa_freqs[6] = pow(2.0,-0.001*3275);
+ correct_aa_freqs[11] = pow(2.0,-0.001*3292);
+ correct_aa_freqs[12] = pow(2.0,-0.001*5077);
+ correct_aa_freqs[13] = pow(2.0,-0.001*3826);
+ correct_aa_freqs[15] = pow(2.0,-0.001*2409);
+ correct_aa_freqs[16] = pow(2.0,-0.001*3733);
+ correct_aa_freqs[17] = pow(2.0,-0.001*4503);
+ correct_aa_freqs[19] = pow(2.0,-0.001*3070);
+
+ for(int i = 0; i < 20; ++i){
+ BOOST_CHECK_CLOSE(col.GetFreq(olc[i]), correct_aa_freqs[i], Real(1e-5));
+ }
+
+ // check, whether the entropy of the column above gets correctly calculated
+ Real entropy = 0.0;
+ entropy -= correct_aa_freqs[0] * log(correct_aa_freqs[0]);
+ entropy -= correct_aa_freqs[1] * log(correct_aa_freqs[1]);
+ entropy -= correct_aa_freqs[5] * log(correct_aa_freqs[5]);
+ entropy -= correct_aa_freqs[6] * log(correct_aa_freqs[6]);
+ entropy -= correct_aa_freqs[11] * log(correct_aa_freqs[11]);
+ entropy -= correct_aa_freqs[12] * log(correct_aa_freqs[12]);
+ entropy -= correct_aa_freqs[13] * log(correct_aa_freqs[13]);
+ entropy -= correct_aa_freqs[15] * log(correct_aa_freqs[15]);
+ entropy -= correct_aa_freqs[16] * log(correct_aa_freqs[16]);
+ entropy -= correct_aa_freqs[17] * log(correct_aa_freqs[17]);
+ entropy -= correct_aa_freqs[19] * log(correct_aa_freqs[19]);
+ BOOST_CHECK_CLOSE((*prof)[2].GetEntropy(), entropy, Real(1e-5));
+
+ // look at avg entropy...
+ BOOST_CHECK_CLOSE(prof->GetAverageEntropy(), 1.48704, Real(1e-2));
+
+ // reload with LoadSequenceProfile
+ ProfileHandlePtr prof2 = LoadSequenceProfile("testfiles/test_hmm.hhm");
+ BOOST_CHECK(*prof == *prof2);
+
+ // reload
+ io_handler->Import(*prof2, "testfiles/test_hmm.hhm");
+ BOOST_CHECK(*prof == *prof2);
+}
+
+BOOST_AUTO_TEST_CASE(pssm_loading)
+{
+ // check pssm factory
+ ProfileIOHandlerFactoryBasePtr fac(new PssmIOHandlerFactory);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test.hhm"), false);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test.hhm.gz"), false);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test.pssm"), true);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test.pssm.gz"), true);
+ BOOST_CHECK_EQUAL(fac->ProvidesImport("test", "pssm"), true);
+ BOOST_CHECK_EQUAL(fac->ProvidesExport("test.pssm"), false);
+ BOOST_CHECK_EQUAL(fac->ProvidesExport("test.pssm.gz"), false);
+ BOOST_CHECK_EQUAL(fac->ProvidesExport("test", "pssm"), false);
+ ProfileIOHandlerPtr io_handler = fac->Create();
+
+ // load file
+ ProfileHandlePtr prof(new ProfileHandle);
+ io_handler->Import(*prof, "testfiles/test_pssm.pssm");
+
+ // compare manually
+ ProfileHandle prof_pssm_ref;
+ prof_pssm_ref.SetSequence("RRSPP");
+ prof_pssm_ref.SetNullModel(ProfileColumn::BLOSUMNullModel());
+ ProfileColumn pc1, pc2, pc3, pc4, pc5;
+ pc1.SetFreq('R', 0.74);
+ pc1.SetFreq('Q', 0.01);
+ pc1.SetFreq('K', 0.25);
+
+ pc2.SetFreq('A', 0.02/0.99);
+ pc2.SetFreq('R', 0.61/0.99);
+ pc2.SetFreq('N', 0.03/0.99);
+ pc2.SetFreq('Q', 0.02/0.99);
+ pc2.SetFreq('E', 0.02/0.99);
+ pc2.SetFreq('G', 0.02/0.99);
+ pc2.SetFreq('H', 0.01/0.99);
+ pc2.SetFreq('I', 0.01/0.99);
+ pc2.SetFreq('L', 0.01/0.99);
+ pc2.SetFreq('K', 0.13/0.99);
+ pc2.SetFreq('P', 0.03/0.99);
+ pc2.SetFreq('S', 0.06/0.99);
+ pc2.SetFreq('T', 0.01/0.99);
+ pc2.SetFreq('V', 0.01/0.99);
+ pc3.SetFreq('A', 0.17/0.99);
+ pc3.SetFreq('R', 0.07/0.99);
+ pc3.SetFreq('N', 0.03/0.99);
+
+ pc3.SetFreq('A', 0.17);
+ pc3.SetFreq('R', 0.07);
+ pc3.SetFreq('N', 0.03);
+ pc3.SetFreq('D', 0.02);
+ pc3.SetFreq('C', 0.01);
+ pc3.SetFreq('Q', 0.03);
+ pc3.SetFreq('E', 0.02);
+ pc3.SetFreq('G', 0.03);
+ pc3.SetFreq('L', 0.02);
+ pc3.SetFreq('K', 0.04);
+ pc3.SetFreq('M', 0.01);
+ pc3.SetFreq('F', 0.01);
+ pc3.SetFreq('P', 0.06);
+ pc3.SetFreq('S', 0.37);
+ pc3.SetFreq('T', 0.08);
+ pc3.SetFreq('V', 0.03);
+
+ pc4.SetFreq('A', 0.11/0.98);
+ pc4.SetFreq('R', 0.06/0.98);
+ pc4.SetFreq('D', 0.01/0.98);
+ pc4.SetFreq('Q', 0.02/0.98);
+ pc4.SetFreq('E', 0.02/0.98);
+ pc4.SetFreq('I', 0.01/0.98);
+ pc4.SetFreq('L', 0.03/0.98);
+ pc4.SetFreq('K', 0.04/0.98);
+ pc4.SetFreq('F', 0.01/0.98);
+ pc4.SetFreq('P', 0.58/0.98);
+ pc4.SetFreq('S', 0.03/0.98);
+ pc4.SetFreq('T', 0.05/0.98);
+ pc4.SetFreq('V', 0.01/0.98);
+
+ pc5.SetFreq('A', 0.04);
+ pc5.SetFreq('R', 0.01);
+ pc5.SetFreq('N', 0.02);
+ pc5.SetFreq('D', 0.03);
+ pc5.SetFreq('Q', 0.02);
+ pc5.SetFreq('E', 0.03);
+ pc5.SetFreq('H', 0.01);
+ pc5.SetFreq('I', 0.01);
+ pc5.SetFreq('L', 0.04);
+ pc5.SetFreq('K', 0.05);
+ pc5.SetFreq('M', 0.01);
+ pc5.SetFreq('F', 0.01);
+ pc5.SetFreq('P', 0.63);
+ pc5.SetFreq('S', 0.03);
+ pc5.SetFreq('T', 0.02);
+ pc5.SetFreq('V', 0.04);
+
+ prof_pssm_ref.push_back(pc1);
+ prof_pssm_ref.push_back(pc2);
+ prof_pssm_ref.push_back(pc3);
+ prof_pssm_ref.push_back(pc4);
+ prof_pssm_ref.push_back(pc5);
+
+ compareProfiles(*prof, prof_pssm_ref, 1e-3);
+
+ // reload with LoadSequenceProfile
+ ProfileHandlePtr prof2 = LoadSequenceProfile("testfiles/test_pssm.pssm");
+ BOOST_CHECK(*prof == *prof2);
+
+ // reload
+ io_handler->Import(*prof2, "testfiles/test_pssm.pssm");
+ BOOST_CHECK(*prof == *prof2);
+}
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/test_mae_standalone.cc b/modules/io/tests/test_mae_standalone.cc
index 10395fb69d479d11a80be64f53ac2832f30b90c7..48d19c3da2ebf6f50a6591b8fe1c706673de0ccc 100644
--- a/modules/io/tests/test_mae_standalone.cc
+++ b/modules/io/tests/test_mae_standalone.cc
@@ -1,6 +1,6 @@
#include <ost/log.hh>
#include <ost/conop/conop.hh>
-#include <ost/io/entity_io_mae_handler.hh>
+#include <ost/io/mol/entity_io_mae_handler.hh>
using namespace ost;
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 3a1906df9ea7c8f7ffc0dae6f79fcc9a54b7972e..40f81cd8c441801df9412d60f9b562610b18498a 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -644,14 +644,14 @@ BOOST_AUTO_TEST_CASE(mmcif_struct_ref)
MMCifReader mmcif_p(s, eh, profile);
mmcif_p.Parse();
MMCifInfoStructRefs refs=mmcif_p.GetInfo().GetStructRefs();
- BOOST_CHECK_EQUAL(refs.size(), 1);
+ BOOST_CHECK_EQUAL(refs.size(), size_t(1));
MMCifInfoStructRefPtr sr1=refs[0];
BOOST_CHECK_EQUAL(sr1->GetDBName(), "UNP");
BOOST_CHECK_EQUAL(sr1->GetDBID(), "BLA2_BACCE");
BOOST_CHECK_EQUAL(sr1->GetDBAccess(), "P04190");
BOOST_CHECK_EQUAL(sr1->GetID(), "1");
MMCifInfoStructRefSeqs seqs=sr1->GetAlignedSeqs();
- BOOST_CHECK_EQUAL(seqs.size(), 2);
+ BOOST_CHECK_EQUAL(seqs.size(), size_t(2));
BOOST_CHECK_EQUAL(seqs[0]->GetID(), "1");
BOOST_CHECK_EQUAL(seqs[0]->GetChainName(), "A");
BOOST_CHECK_EQUAL(seqs[0]->GetSeqBegin(), 1);
@@ -665,7 +665,7 @@ BOOST_AUTO_TEST_CASE(mmcif_struct_ref)
BOOST_CHECK_EQUAL(seqs[1]->GetDBBegin(), 31);
BOOST_CHECK_EQUAL(seqs[1]->GetDBEnd(), 49);
MMCifInfoStructRefSeqDifs diffs=seqs[0]->GetDifs();
- BOOST_CHECK_EQUAL(diffs.size(), 1);
+ BOOST_CHECK_EQUAL(diffs.size(), size_t(1));
BOOST_CHECK_EQUAL(diffs[0]->GetSeqRNum(), 91);
BOOST_CHECK_EQUAL(diffs[0]->GetDetails(), "ENGINEERED MUTATION");
}
diff --git a/modules/io/tests/test_star_parser.cc b/modules/io/tests/test_star_parser.cc
index 4d611807830aabf0b7b24725a708f3f99d81af04..40cdf674f81a7da4a33f3dadab18f3330d338a75 100644
--- a/modules/io/tests/test_star_parser.cc
+++ b/modules/io/tests/test_star_parser.cc
@@ -137,19 +137,19 @@ public:
BOOST_CHECK_EQUAL(columns[0].size(), static_cast<size_t>(1));
++cur_char_;
BOOST_CHECK_EQUAL(columns[1][0], cur_char_);
- BOOST_CHECK_EQUAL(columns[1].size(), 1);
+ BOOST_CHECK_EQUAL(columns[1].size(), static_cast<size_t>(1));
++cur_char_;
BOOST_CHECK_EQUAL(columns[2][0], cur_char_);
- BOOST_CHECK_EQUAL(columns[2].size(), 1);
+ BOOST_CHECK_EQUAL(columns[2].size(), static_cast<size_t>(1));
++cur_char_;
BOOST_CHECK_EQUAL(columns[3][0], cur_char_);
- BOOST_CHECK_EQUAL(columns[3].size(), 1);
+ BOOST_CHECK_EQUAL(columns[3].size(), static_cast<size_t>(1));
++cur_char_;
BOOST_CHECK_EQUAL(columns[4][0], cur_char_);
- BOOST_CHECK_EQUAL(columns[4].size(), 1);
+ BOOST_CHECK_EQUAL(columns[4].size(), static_cast<size_t>(1));
++cur_char_;
BOOST_CHECK_EQUAL(columns[5][0], cur_char_);
- BOOST_CHECK_EQUAL(columns[5].size(), 1);
+ BOOST_CHECK_EQUAL(columns[5].size(), static_cast<size_t>(1));
++cur_char_;
}
diff --git a/modules/io/tests/testfiles/test_hmm.hhm b/modules/io/tests/testfiles/test_hmm.hhm
new file mode 100644
index 0000000000000000000000000000000000000000..1b9a665d1e1ce09e89efa6f38f1648a38bdbe529
--- /dev/null
+++ b/modules/io/tests/testfiles/test_hmm.hhm
@@ -0,0 +1,31 @@
+HHsearch 1.5
+I don't get parsed
+I don't get parsed
+I don't get parsed
+I don't get parsed
+I don't get parsed
+I don't get parsed
+I don't get parsed
+I don't get parsed
+I don't get parsed
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+E 1 1780 * * 497 * * * * * * * * * * * * * * * * 1
+ 0 * * * * * * 1610 0 0
+
+T 2 1615 * * * * 2652 * * * * * * * * * * 3992 1147 * * 2
+ 0 * * * * * * 2652 0 0
+
+G 3 3676 2597 * * * 5359 3275 * * * * 3292 5077 3826 * 2409 3733 4503 * 3070 3
+ 46 4979 * 2006 413 * * 3076 1097 0
+
+S 4 2579 * * * * * * * * 4320 * 4532 3895 4519 * 951 5140 3595 * * 4
+ 58 4660 * 2833 218 * * 3050 1146 0
+
+P 5 2585 * 4184 * * 2345 4748 * * * * * 2839 1766 5056 3635 * * * * 5
+ 0 * * * * * * 3036 0 0
+
+//
diff --git a/modules/io/tests/testfiles/test_pssm.pssm b/modules/io/tests/testfiles/test_pssm.pssm
new file mode 100644
index 0000000000000000000000000000000000000000..e3f72045cb33946a47d75db70ceb21dffedb3849
--- /dev/null
+++ b/modules/io/tests/testfiles/test_pssm.pssm
@@ -0,0 +1,14 @@
+
+Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
+ A R N D C Q E G H I L K M F P S T W Y V A R N D C Q E G H I L K M F P S T W Y V
+ 1 R -4 7 -3 -4 -7 -1 -3 -5 -3 -6 -5 4 -4 -6 -5 -4 -4 -6 -5 -6 0 74 0 0 0 1 0 0 0 0 0 25 0 0 0 0 0 0 0 0 1.96 0.65
+ 2 R -2 7 0 -4 -6 0 -1 -3 -1 -4 -4 2 -4 -6 -1 0 -3 -6 -5 -4 2 61 3 0 0 2 2 2 1 1 1 13 0 0 3 6 1 0 0 1 1.22 0.52
+ 3 S 2 1 0 -1 -2 0 -1 -1 -2 -4 -3 0 -2 -2 1 4 1 -5 -4 -2 17 7 3 2 1 3 2 3 0 0 2 4 1 1 6 37 8 0 0 3 0.42 0.31
+ 4 P 1 0 -5 -3 -6 -2 -3 -5 -3 -4 -3 -1 -5 -3 7 -1 0 -3 -6 -4 11 6 0 1 0 2 2 0 0 1 3 4 0 1 58 3 5 0 0 1 1.42 0.62
+ 5 P -1 -3 -2 -2 -7 -2 -2 -6 -3 -4 -2 0 -2 -4 7 -2 -2 -7 -6 -1 4 1 2 3 0 2 3 0 1 1 4 5 1 1 63 3 2 0 0 4 1.56 0.71
+
+ K Lambda
+Standard Ungapped 0.1342 0.3155
+Standard Gapped 0.0410 0.2670
+PSI Ungapped 0.1607 0.3175
+PSI Gapped 0.0492 0.2670
diff --git a/modules/mol/CMakeLists.txt b/modules/mol/CMakeLists.txt
index d417b44124dae1b87b844ec98109a7856b796e32..ac68189a49e54e7d4512519f238c88c4a30b6762 100644
--- a/modules/mol/CMakeLists.txt
+++ b/modules/mol/CMakeLists.txt
@@ -1,2 +1,5 @@
add_subdirectory(base)
add_subdirectory(alg)
+if (ENABLE_MM)
+ add_subdirectory(mm)
+endif()
diff --git a/modules/mol/alg/doc/lddt.rst b/modules/mol/alg/doc/lddt.rst
index 47e033501bce8acb1609573a2275866e950f6dec..3d3e862c3fbc61682eb880fe3e738365b8cb1501 100644
--- a/modules/mol/alg/doc/lddt.rst
+++ b/modules/mol/alg/doc/lddt.rst
@@ -2,9 +2,9 @@
lDDT
======
-------------
+-------------------------------------
Where can I find the lDDT executable?
-------------
+-------------------------------------
The lDDT executable can be found at <YOUR-OST-STAGE-DIR>/bin/
@@ -179,4 +179,4 @@ For example:
lddt -v 1 -f -p stereo_chemical_params.txt mdl1.pdb ref.pdb
WARNING: Verbosity levels 1 and 2 can generate a large amount of output text,
-especially with large structures and multiple models being evaluated.
\ No newline at end of file
+especially with large structures and multiple models being evaluated.
diff --git a/modules/mol/alg/pymod/CMakeLists.txt b/modules/mol/alg/pymod/CMakeLists.txt
index 000e754817bce15b4e118a6ad65de253d9af8763..7efbf88165105ae87c97d3b9aacd23e923e29060 100644
--- a/modules/mol/alg/pymod/CMakeLists.txt
+++ b/modules/mol/alg/pymod/CMakeLists.txt
@@ -4,6 +4,7 @@ set(OST_MOL_ALG_PYMOD_SOURCES
export_clash.cc
export_trajectory_analysis.cc
export_structure_analysis.cc
+ export_contact_overlap.cc
)
set(OST_MOL_ALG_PYMOD_MODULES
@@ -13,6 +14,7 @@ set(OST_MOL_ALG_PYMOD_MODULES
trajectory_analysis.py
structure_analysis.py
helix_kinks.py
+ hbond.py
)
if (ENABLE_IMG)
diff --git a/modules/mol/alg/pymod/__init__.py b/modules/mol/alg/pymod/__init__.py
index b8c09d51d67b99b606ddc9c99af55afe37823dd4..73d5bd802ce28765d309e65b7eed4f65374abdfb 100644
--- a/modules/mol/alg/pymod/__init__.py
+++ b/modules/mol/alg/pymod/__init__.py
@@ -4,6 +4,7 @@ from ost.mol.alg.superpose import *
import ost.mol.alg.trajectory_analysis
import ost.mol.alg.structure_analysis
import ost.mol.alg.helix_kinks
+import ost.mol.alg.hbond
# Fills a list of reference clashing distances from a file (requires a path to the file)
def FillClashingDistancesFromFile(filename):
diff --git a/modules/mol/alg/pymod/export_contact_overlap.cc b/modules/mol/alg/pymod/export_contact_overlap.cc
new file mode 100644
index 0000000000000000000000000000000000000000..0f7c56c5feda9f18ea71ff7c0860686e1e75f113
--- /dev/null
+++ b/modules/mol/alg/pymod/export_contact_overlap.cc
@@ -0,0 +1,102 @@
+#include <boost/python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+
+#include <ost/mol/alg/contact_overlap.hh>
+#include <ost/mol/alg/domain_find.hh>
+
+using namespace boost::python;
+using namespace ost;
+using namespace ost::mol::alg;
+
+SimilarityMatrix (*com_a)(const ost::seq::AlignmentHandle&,
+ Real, int, int)=&ContactOverlapMap;
+SimilarityMatrix (*com_b)(const ost::seq::AlignmentHandle&,
+ Real, OverlapMode, Real)=&ContactOverlapMap;
+SimilarityMatrix (*com_c)(const DistanceMatrix&, const DistanceMatrix&,
+ Real, OverlapMode, Real)=&ContactOverlapMap;
+
+void export_contact_overlap()
+{
+ class_<SimilarityMatrix>("SimilarityMatrix", init<int, Real>())
+ .def("Get", &SimilarityMatrix::Get,
+ return_value_policy<copy_const_reference>())
+ .def("Set", &SimilarityMatrix::Set)
+ .def("GetSize", &SimilarityMatrix::GetSize)
+ .add_property("size", &SimilarityMatrix::GetSize)
+ .def("AsImage", &SimilarityMatrix::AsImage)
+ .def("Save", &SimilarityMatrix::Save)
+ .def("Load", &SimilarityMatrix::Load).staticmethod("Load")
+ ;
+
+ class_<DistanceMatrix, DistanceMatrixPtr>("DistanceMatrix", no_init)
+ .def("Create", &DistanceMatrix::Create).staticmethod("Create")
+ .def("FromAln", &DistanceMatrix::FromAln,
+ (arg("aln"), arg("index")=1)).staticmethod("FromAln")
+ .def("Get", &DistanceMatrix::Get,
+ return_value_policy<copy_const_reference>())
+ .def("Set", &DistanceMatrix::Set)
+
+ .def("GetSize", &DistanceMatrix::GetSize)
+ .add_property("size", &DistanceMatrix::GetSize)
+ ;
+
+ enum_<OverlapMode>("OverlapMode")
+ .value("OM_RELATIVE", OM_RELATIVE)
+ .value("OM_ABSOLUTE", OM_ABSOLUTE)
+ .export_values()
+ ;
+
+ def("DomainsFromCOM", &DomainsFromCOM, (arg("idx_a")=-1, arg("idx_b")=-1));
+
+ def("ContactOverlap", &ContactOverlap, (arg("dist_mat_a"), arg("dist_mat_b"),
+ arg("tolerance")=0.1,
+ arg("mode")=OM_RELATIVE,
+ arg("max_dist")=1e6));
+ class_<ContactList>("ContactList", init<>())
+ .def(vector_indexing_suite<ContactList>())
+ ;
+
+ def("Contacts", &Contacts);
+ def("CalcContactNodeDegree", &CalcContactNodeDegree);
+ def("LocalDistanceTest", &LocalDistanceTest);
+ def("ContactOverlapMap", com_a);
+ def("ContactOverlapMap", com_b, (arg("mode")=OM_RELATIVE,
+ arg("max_dist")=1e6));
+ def("ContactOverlapMap", com_c, (arg("mode")=OM_RELATIVE,
+ arg("max_dist")=1e6));
+ class_<Domain>("Domain", no_init)
+ .def_readwrite("views", &Domain::views)
+ .def_readwrite("views", &Domain::views)
+ .def_readwrite("inter_s", &Domain::inter_s)
+ .def_readwrite("inter_d", &Domain::inter_d)
+ .def_readwrite("intra_s", &Domain::intra_s)
+ .def_readwrite("intra_d", &Domain::intra_d)
+ ;
+ class_<std::vector<Domain> >("DomainList", init<>())
+ .def(vector_indexing_suite<std::vector<Domain> >())
+ ;
+
+ class_<Domains, DomainsPtr>("Domains", no_init)
+ .def("FromCOM", Domains::FromCOM,
+ (arg("sim"), arg("aln"), arg("idx_a")=-1,
+ arg("idx_b")=-1)).staticmethod("FromCOM")
+ .def("FromAln", Domains::FromAln,
+ (arg("aln"), arg("tolerance")=1.5,
+ arg("radius")=1e6, arg("threshold")=0.5, arg("idx_a")=0, arg("idx_b")=1)).staticmethod("FromAln")
+ .def("FromDistMats", Domains::FromDistMats,
+ (arg("dmat_a"), arg("dmat_b"), arg("tolerance")=1.5,
+ arg("radius")=1e6, arg("threshold")=0.5,
+ arg("num_threads")=1,
+ arg("defined_only")=true,
+ arg("adj_map")=false)).staticmethod("FromDistMats")
+ .add_property("domains", make_function(&Domains::GetDomains,
+ return_value_policy<copy_const_reference>()))
+ .add_property("components", make_function(&Domains::GetComponents,
+ return_value_policy<copy_const_reference>()))
+ .add_property("adj_map", &Domains::GetAdjMap)
+ .add_property("num_free", &Domains::GetNumFreeResidues)
+ .add_property("free_d", &Domains::GetFreeD)
+ .add_property("free_s", &Domains::GetFreeS)
+ ;
+}
+
diff --git a/modules/mol/alg/pymod/export_structure_analysis.cc b/modules/mol/alg/pymod/export_structure_analysis.cc
index f9f58347d1313d30d7a6d71f20e9733c2df243bc..2714f5847ea4e40bd1ec5c63faec3ea317b57336 100644
--- a/modules/mol/alg/pymod/export_structure_analysis.cc
+++ b/modules/mol/alg/pymod/export_structure_analysis.cc
@@ -24,6 +24,9 @@ using namespace boost::python;
using namespace ost;
using namespace ost::mol::alg;
+std::vector< std::vector<Real> > (*pair_dist1)(const mol::EntityView&) = PariwiseDistanceMatrix;
+std::vector< std::vector<Real> > (*pair_dist2)(const mol::EntityView&,const mol::EntityView&) = PariwiseDistanceMatrix;
+
void export_StructureAnalysis()
{
def("GetPosListFromView",&GetPosListFromView, (arg("view")));
@@ -31,5 +34,9 @@ void export_StructureAnalysis()
def("CalculateAverageAgreementWithDensityMap",&CalculateAverageAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
def("CalculateAgreementWithDensityMap",&CalculateAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
#endif
- def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("basis_vec"),arg("group_res")=true));
+ def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("ucell_size"),arg("ucell_angles")=geom::Vec3(),arg("group_res")=true,arg("follow_bonds")=false));
+
+
+ def("PariwiseDistanceMatrix",pair_dist2,(arg("EntityView1"),arg("EntityView2")));
+ def("PariwiseDistanceMatrix",pair_dist1,(arg("EntityView")));
}
diff --git a/modules/mol/alg/pymod/export_svd_superpose.cc b/modules/mol/alg/pymod/export_svd_superpose.cc
index d5f942fe756731899f62c9d3ffd0d5a570355040..87e4cbbc76af199a357155261c729676528b7b29 100644
--- a/modules/mol/alg/pymod/export_svd_superpose.cc
+++ b/modules/mol/alg/pymod/export_svd_superpose.cc
@@ -35,9 +35,9 @@ using namespace ost::mol::alg;
void export_svdSuperPose()
{
SuperpositionResult (*sup1)(const mol::EntityView&,const mol::EntityView&,bool) = SuperposeSVD;
- SuperpositionResult (*sup2)(const std::vector<geom::Vec3>&,const std::vector<geom::Vec3>& ) = SuperposeSVD;
+ SuperpositionResult (*sup2)(const geom::Vec3List&,const geom::Vec3List& ) = SuperposeSVD;
SuperpositionResult (*sup3)(const mol::EntityView&,const mol::EntityView&, int, Real, bool) = IterativeSuperposeSVD;
- SuperpositionResult (*sup4)(const std::vector<geom::Vec3>&,const std::vector<geom::Vec3>&, int, Real) = IterativeSuperposeSVD;
+ SuperpositionResult (*sup4)(const geom::Vec3List&,const geom::Vec3List&, int, Real) = IterativeSuperposeSVD;
class_<SuperpositionResult>("SuperpositionResult", init<>())
.def_readwrite("ncycles", &SuperpositionResult::ncycles)
.def_readwrite("rmsd", &SuperpositionResult::rmsd)
diff --git a/modules/mol/alg/pymod/hbond.py b/modules/mol/alg/pymod/hbond.py
new file mode 100644
index 0000000000000000000000000000000000000000..33545bd2f5430aac82e65cbb9023bece29608634
--- /dev/null
+++ b/modules/mol/alg/pymod/hbond.py
@@ -0,0 +1,443 @@
+import ost as _ost
+import ost.geom as _geom
+
+"""
+Module written by Niklaus Johner (niklaus.johner@a3.epfl.ch) 2012
+
+This module is a flexible rewrite of HBPlus, allowing to calculate hbond
+conservation between different structures or over a trajectory.
+It uses customizable dictionaries to define donors and acceptors and can
+account for equivalent HBonds such as involving for example either oxygen atom
+of an Aspartic Acid.
+"""
+__all__=('HBondDonor','HBondAcceptor','BuildCHARMMHBondDonorAcceptorDict','AreHBonded','GetHbondDonorAcceptorList',\
+ 'GetHbondListFromDonorAcceptorLists','GetHbondListFromView','GetHbondListFromTraj','GetHbondListBetweenViews'\
+ 'CalculateHBondScore','AnalyzeHBondScore')
+
+
+class HBondableAtoms:
+ def __init__(self,donors=[],acceptors=[]):
+ self.donors=donors
+ self.acceptors=acceptors
+
+def BuildCHARMMHBondDonorAcceptorDict():
+ hb_da_dict={}
+ bb_donors=[['N','HN']]
+ bb_acceptors=[['O',['C']]]
+
+ #hydrophobic
+ hb_da_dict['ALA']=HBondableAtoms(bb_donors,bb_acceptors)
+ hb_da_dict['GLY']=HBondableAtoms(bb_donors,bb_acceptors)
+ hb_da_dict['ILE']=HBondableAtoms(bb_donors,bb_acceptors)
+ hb_da_dict['LEU']=HBondableAtoms(bb_donors,bb_acceptors)
+ hb_da_dict['PHE']=HBondableAtoms(bb_donors,bb_acceptors)
+ hb_da_dict['MET']=HBondableAtoms(bb_donors,bb_acceptors)
+ hb_da_dict['VAL']=HBondableAtoms(bb_donors,bb_acceptors)
+ #special case
+ hb_da_dict['PRO']=HBondableAtoms([],bb_acceptors)
+
+ #sidechain donors
+ ne=[['NE','HE']]
+ cz=[['NH1','HH11'],['NH1','HH12'],['NH2','HH21'],['NH2','HH22']]
+ hb_da_dict['ARG']=HBondableAtoms(bb_donors+ne+cz,bb_acceptors)
+ nz=[['NZ','HZ1'],['NZ','HZ2'],['NZ','HZ3']]
+ hb_da_dict['LYS']=HBondableAtoms(bb_donors+nz,bb_acceptors)
+ ne1=[['NE1','HE1']]
+ hb_da_dict['TRP']=HBondableAtoms(bb_donors+ne1,bb_acceptors)
+ sg=[['SG','HG1']]
+ hb_da_dict['CYS']=HBondableAtoms(bb_donors+sg,bb_acceptors)
+
+ #sidechain acceptors
+ od12=[['OD1',['CG']],['OD2',['CG']]]
+ hb_da_dict['ASP']=HBondableAtoms(bb_donors,bb_acceptors+od12)
+ oe12=[['OE1',['CD']],['OE2',['CD']]]
+ hb_da_dict['GLU']=HBondableAtoms(bb_donors,bb_acceptors+oe12)
+
+ #sidechain donor and acceptor
+ od1=[['OD1',['CG']]]
+ nd2=[['ND2','HD21'],['ND2','HD22']]
+ hb_da_dict['ASN']=HBondableAtoms(bb_donors+nd2,bb_acceptors+od1)
+ ne2=[['NE2','HE21'],['NE2','HE22']]
+ oe1=[['OE1',['CD']]]
+ hb_da_dict['GLN']=HBondableAtoms(bb_donors+ne2,bb_acceptors+oe1)
+ og_d=[['OG','HG1']]
+ og_a=[['OG',['CB']]]
+ hb_da_dict['SER']=HBondableAtoms(bb_donors+og_d,bb_acceptors+og_a)
+ og1_d=[['OG1','HG1']]
+ og1_a=[['OG1',['CB']]]
+ hb_da_dict['THR']=HBondableAtoms(bb_donors+og1_d,bb_acceptors+og1_a)
+ oh_d=[['OH','HH']]
+ oh_a=[['OH',['CZ']]]
+ hb_da_dict['TYR']=HBondableAtoms(bb_donors+oh_d,bb_acceptors+oh_a)
+ #histidine
+ nd1_d=[['ND1','HD1']]
+ ne2_a=[['NE2',['CD2','CE1']]]
+ hb_da_dict['HSD']=HBondableAtoms(bb_donors+nd1_d,bb_acceptors+ne2_a)
+ ne2_d=[['NE2','HE2']]
+ nd1_a=[['ND1',['CG','CE1']]]
+ hb_da_dict['HSE']=HBondableAtoms(bb_donors+ne2_d,bb_acceptors+nd1_a)
+ hb_da_dict['HSP']=HBondableAtoms(bb_donors+nd1_d+ne2_d,bb_acceptors)
+ #non-standard protonation state:
+ oe12=[['OE1',['CD']],['OE2',['CD']]]
+ oe2=[['OE2','HE2']]
+ hb_da_dict['GLUP']=HBondableAtoms(bb_donors+oe2,bb_acceptors+oe12)
+ od12=[['OD1',['CG']],['OD2',['CG']]]
+ od2=[['OD2','HD2']]
+ hb_da_dict['ASPP']=HBondableAtoms(bb_donors+od2,bb_acceptors+od12)
+ return hb_da_dict
+
+def BuildCHARMMHBondDonorEquivalenceDict():
+ donor_swap_dict={}
+ donor_swap_dict['ARG']=[[['NH1','HH11'],['NH1','HH12'],['NH2','HH21'],['NH2','HH22']]]
+ donor_swap_dict['ASN']=[[['ND2','HD21'],['ND2','HD22']]]
+ donor_swap_dict['GLN']=[[['NE2','HE21'],['NE2','HE22']]]
+ donor_swap_dict['LYS']=[[['NZ','HZ1'],['NZ','HZ2'],['NZ','HZ3']]]
+ return donor_swap_dict
+
+def BuildCHARMMHBondAcceptorEquivalenceDict():
+ acceptor_swap_dict={}
+ acceptor_swap_dict['ASP']=[[['OD1',['CG']],['OD2',['CG']]]]
+ acceptor_swap_dict['GLU']=[[['OE1',['CD']],['OE2',['CD']]]]
+ return acceptor_swap_dict
+
+def ListEquivalentDonors(donor,donor_swap_dict):
+ if not donor.heavy_atom.residue.name in donor_swap_dict:return [donor]
+ donor_list=[donor]
+ donor_atom_names=[donor.heavy_atom.name,donor.hydrogen.name]
+ res=donor.heavy_atom.residue
+ for equivalence_list in donor_swap_dict[donor.heavy_atom.residue.name]:
+ if not donor_atom_names in equivalence_list:continue
+ for atom_names in equivalence_list:
+ if atom_names==donor_atom_names:continue
+ else:donor_list.append(HBondDonor.FromResidue(res,atom_names[0],atom_names[1]))
+ return donor_list
+
+def ListEquivalentAcceptors(acceptor,acceptor_swap_dict):
+ if not acceptor.atom.residue.name in acceptor_swap_dict:return [acceptor]
+ acceptor_list=[acceptor]
+ acceptor_atom_names=[acceptor.atom.name,[a.name for a in acceptor.antecedent_list]]
+ res=acceptor.atom.residue
+ for equivalence_list in acceptor_swap_dict[acceptor.atom.residue.name]:
+ if not acceptor_atom_names in equivalence_list:continue
+ for atom_names in equivalence_list:
+ if atom_names==acceptor_atom_names:continue
+ else:acceptor_list.append(HBondAcceptor.FromResidue(res,atom_names[0],atom_names[1]))
+ return acceptor_list
+
+
+class HBondDonor:
+ def __init__(self,donor,hydrogen):
+ self.heavy_atom=donor
+ self.hydrogen=hydrogen
+ def __eq__(self,hbd):
+ if not isinstance(hbd,HBondDonor):return False
+ else:return self.heavy_atom==hbd.heavy_atom and self.hydrogen==hbd.hydrogen
+ def __hash__(self):
+ return hash((self.heavy_atom,self.hydrogen))
+ @classmethod
+ def FromResidue(cls,res,donor_name,hydrogen_name,verbose=True):
+ _donor=res.FindAtom(donor_name).handle
+ _hydrogen=res.FindAtom(hydrogen_name).handle
+ if not _donor.IsValid():
+ if verbose:print 'Could not find '+donor_name+' in residue '+str(res)
+ return
+ if not _hydrogen.IsValid():
+ if verbose:print 'Could not find '+hydrogen_name+' in residue '+str(res)
+ return
+ return cls(_donor,_hydrogen)
+
+ def IsHBondedTo(self,acceptor):
+ return AreHBonded(self,acceptor)
+
+
+class HBondAcceptor:
+ def __init__(self,acceptor,antecedent_list):
+ self.atom=acceptor
+ self.antecedent_list=antecedent_list
+ def __eq__(self,hba):
+ if not isinstance(hba,HBondAcceptor):return False
+ else:return self.atom==hba.atom
+ def __hash__(self):
+ return hash(self.atom)
+ @classmethod
+ def FromResidue(cls,res,acceptor_name,antecedent_name_list,verbose=True):
+ _acceptor=res.FindAtom(acceptor_name).handle
+ _antecedent_list=_ost.mol.AtomHandleList([res.FindAtom(name).handle for name in antecedent_name_list])
+ if not _acceptor.IsValid():
+ if verbose:print 'Could not find '+acceptor_name+' in residue '+str(res)
+ return
+ for i,a in enumerate(_antecedent_list):
+ if not a.IsValid():
+ if verbose:print 'Could not find '+antecedent_name_list[i]+' in residue '+str(res)
+ return
+ return cls(_acceptor,_antecedent_list)
+
+ def IsHBondedTo(self,donor):
+ return AreHBonded(donor,self)
+
+class HBond:
+ def __init__(self,donor,acceptor):
+ self.donor=donor
+ self.acceptor=acceptor
+ def __eq__(self,hb):
+ if not isinstance(hb,HBond):return False
+ else:return self.acceptor==hb.acceptor and self.donor==hb.donor
+ def __hash__(self):
+ return hash((self.donor,self.acceptor))
+ def IsFormed(self):return AreHBonded(self.donor,self.acceptor)
+ def DonorAcceptorDistance(self):return _geom.Distance(self.donor.heavy_atom.pos,self.acceptor.atom.pos)
+ def HydrogenAcceptorDistance(self):return _geom.Distance(self.donor.hydrogen.pos,self.acceptor.atom.pos)
+ def DonorHydrogenAcceptorAngle(self):
+ dp=self.donor.heavy_atom.pos;ap=self.acceptor.atom.pos;hp=self.donor.hydrogen.pos
+ return _geom.Angle(dp-hp,ap-hp)
+ def DonorAcceptorAcceptorAntecedentAngle(self):
+ dp=self.donor.heavy_atom.pos;ap=self.acceptor.atom.pos
+ a=min([_geom.Angle(aa.pos-ap,dp-ap) for aa in self.acceptor.antecedent_list])
+ return a
+ def HydrogenAcceptorAcceptorAntecedentAngle(self):
+ hp=self.donor.hydrogen.pos;ap=self.acceptor.atom.pos
+ a=min([_geom.Angle(aa.pos-ap,hp-ap) for aa in acceptor.antecedent_list])
+ return a
+
+
+def AreHBonded(donor,acceptor,da_dist=3.9,ha_dist=2.5,dha_angle=1.57,daaa_angle=1.57,haaa_angle=1.57):
+ """
+ determines if a donor/acceptor pair is hydrogen bonded or not
+ """
+ dp=donor.heavy_atom.pos
+ ap=acceptor.atom.pos
+ if _geom.Distance(dp,ap)>da_dist:return False
+ hp=donor.hydrogen.pos
+ if _geom.Distance(hp,ap)>ha_dist:return False
+ if _geom.Angle(dp-hp,ap-hp)<dha_angle:return False
+ a=min([_geom.Angle(aa.pos-ap,dp-ap) for aa in acceptor.antecedent_list])
+ if a<daaa_angle:return False
+ a=min([_geom.Angle(aa.pos-ap,hp-ap) for aa in acceptor.antecedent_list])
+ if a<haaa_angle:return False
+ return True
+
+def GetHbondDonorAcceptorList(eh,hbond_donor_acceptor_dict={},verbose=True):
+ """
+ returns a list of hydrogen-bond donors and acceptors from an Entity or EntityView.
+ It relies on atom names to determine the list of H-bond donors and acceptors.
+ These names are given in a dictionary, which defaults to CHARMM.
+ """
+ if not hbond_donor_acceptor_dict:
+ print 'Using default CHARMM atom namings'
+ hbond_donor_acceptor_dict=BuildCHARMMHBondDonorAcceptorDict()
+ donor_list=[]
+ acceptor_list=[]
+ for r in eh.residues:
+ if not r.name in hbond_donor_acceptor_dict:
+ print 'donors and acceptors for',r,'are not defined in the dictionary and will not be included'
+ continue
+ res_da_dict=hbond_donor_acceptor_dict[r.name]
+ for acceptor in res_da_dict.acceptors:
+ a=HBondAcceptor.FromResidue(r,acceptor[0],acceptor[1],verbose)
+ if not a==None:acceptor_list.append(a)
+ for donor in res_da_dict.donors:
+ d=HBondDonor.FromResidue(r,donor[0],donor[1],verbose)
+ if not d==None:donor_list.append(d)
+ return [donor_list,acceptor_list]
+
+
+def GetHbondListFromDonorAcceptorLists(donor_list,acceptor_list):
+ """
+ return a list of hydrogen bonds between donors and acceptors from
+ a list of donors and a list of acceptors.
+ """
+ hbond_list=[]
+ for donor in donor_list:
+ for acceptor in acceptor_list:
+ if AreHBonded(donor,acceptor):hbond_list.append(HBond(donor,acceptor))
+ return hbond_list
+
+def GetHbondListFromView(eh,hbond_donor_acceptor_dict={},verbose=True):
+ """
+ return a list of hydrogen bonds from an Entity or EntityView.
+ if no dictionary for the hbond donors and acceptors is specified
+ it will use the standard CHARMM names to determine them
+ """
+ [donor_list,acceptor_list]=GetHbondDonorAcceptorList(eh,hbond_donor_acceptor_dict,verbose)
+ hbond_list=[]
+ for donor in donor_list:
+ for acceptor in acceptor_list:
+ if AreHBonded(donor,acceptor):hbond_list.append(HBond(donor,acceptor))
+ return hbond_list
+
+def GetHbondListFromTraj(t,eh,cutoff=0.7,stride=1,swap=False,donor_swap_dict={},acceptor_swap_dict={},hbond_donor_acceptor_dict={},verbose=True):
+ """
+ return a list of hydrogen bonds from an Entity or EntityView that are
+ present in a fraction of the frames larger than *cutoff*.
+ if no dictionary for the hbond donors and acceptors is specified
+ it will use the standard CHARMM names to determine them
+ """
+ if swap:
+ if not donor_swap_dict:
+ print 'use of standard CHARMM HBond donor swap dictionary'
+ donor_swap_dict=BuildCHARMMHBondDonorEquivalenceDict()
+ if not acceptor_swap_dict:
+ print 'use of standard CHARMM HBond acceptor swap dictionary'
+ acceptor_swap_dict=BuildCHARMMHBondAcceptorEquivalenceDict()
+ [donor_list,acceptor_list]=GetHbondDonorAcceptorList(eh,hbond_donor_acceptor_dict,verbose)
+ hb_list=[]
+ hb_score=[]
+ nframes=0
+ for i in range(0,t.GetFrameCount(),stride):
+ t.CopyFrame(i)
+ nframes+=1
+ hbond_list=GetHbondListFromDonorAcceptorLists(donor_list,acceptor_list)
+ if swap:
+ hbond_list=GetEquivalentHBonds(hbond_list,eh,swap,donor_swap_dict,acceptor_swap_dict,verbose)
+ for hb in hbond_list:
+ if hb in hbond_list[hbond_list.index(hb)+1:]:hbond_list.pop(hbond_list.index(hb))
+ for hb in hbond_list:
+ if hb in hb_list:hb_score[hb_list.index(hb)]+=1
+ else:
+ hb_score.append(1)
+ hb_list.append(hb)
+ hbond_list=[]
+ hbond_score=[]
+ for hb,s in zip(hb_list,hb_score):
+ if s/float(nframes)>=cutoff:
+ if swap:hbond_list.append(list(hb)[0])
+ else:hbond_list.append(hb)
+ hbond_score.append(s/float(nframes))
+ return (hbond_list,hbond_score)
+
+def GetHbondListBetweenViews(eh1,eh2,hbond_donor_acceptor_dict={},verbose=True):
+ """
+ return the list of hydrogen bonds formed between two Entity or EntityView.
+ if no dictionary for the hbond donors and acceptors is specified
+ it will use the standard CHARMM names to determine them
+ """
+ [donor_list1,acceptor_list1]=GetHbondDonorAcceptorList(eh1,hbond_donor_acceptor_dict,verbose)
+ [donor_list2,acceptor_list2]=GetHbondDonorAcceptorList(eh2,hbond_donor_acceptor_dict,verbose)
+ hbond_list=[]
+ for donor in donor_list1:
+ for acceptor in acceptor_list2:
+ if AreHBonded(donor,acceptor):
+ hb=HBond(donor,acceptor)
+ if hb in hbond_list:continue
+ hbond_list.append(hb)
+ for donor in donor_list2:
+ for acceptor in acceptor_list1:
+ if AreHBonded(donor,acceptor):
+ hb=HBond(donor,acceptor)
+ if hb in hbond_list:continue
+ hbond_list.append(hb)
+ return hbond_list
+
+def GetEquivalentHBonds(ref_hbond_list,eh,swap=False,donor_swap_dict={},acceptor_swap_dict={},verbose=True):
+ hbond_list=[]
+ if not swap:
+ for hbond in ref_hbond_list:
+ res1=eh.FindResidue(hbond.donor.heavy_atom.chain.name,hbond.donor.heavy_atom.residue.number.num)
+ res2=eh.FindResidue(hbond.acceptor.atom.chain.name,hbond.acceptor.atom.residue.number.num)
+ donor=HBondDonor.FromResidue(res1,hbond.donor.heavy_atom.name,hbond.donor.hydrogen.name,verbose)
+ acceptor=HBondAcceptor.FromResidue(res2,hbond.acceptor.atom.name,[a.name for a in hbond.acceptor.antecedent_list],verbose)
+ hbond_list.append(set([HBond(donor,acceptor)]))
+ else:
+ if not donor_swap_dict:
+ print 'use of standard CHARMM HBond donor swap dictionary'
+ donor_swap_dict=BuildCHARMMHBondDonorEquivalenceDict()
+ if not acceptor_swap_dict:
+ print 'use of standard CHARMM HBond acceptor swap dictionary'
+ acceptor_swap_dict=BuildCHARMMHBondAcceptorEquivalenceDict()
+ for hbond in ref_hbond_list:
+ res1=eh.FindResidue(hbond.donor.heavy_atom.chain.name,hbond.donor.heavy_atom.residue.number.num)
+ res2=eh.FindResidue(hbond.acceptor.atom.chain.name,hbond.acceptor.atom.residue.number.num)
+ donor=HBondDonor.FromResidue(res1,hbond.donor.heavy_atom.name,hbond.donor.hydrogen.name,verbose)
+ acceptor=HBondAcceptor.FromResidue(res2,hbond.acceptor.atom.name,[a.name for a in hbond.acceptor.antecedent_list],verbose)
+ donor_list=ListEquivalentDonors(donor,donor_swap_dict)
+ acceptor_list=ListEquivalentAcceptors(acceptor,acceptor_swap_dict)
+ hbond_list.append(set([HBond(d,a) for d in donor_list for a in acceptor_list]))
+ return hbond_list
+
+
+def CalculateHBondScore(ref_eh,eh2,ref_eh2=None,hbond_donor_acceptor_dict={},swap=False,donor_swap_dict={},acceptor_swap_dict={},verbose=True):
+ """
+ Returns the fraction of H-bonds from ref_eh that are also present in eh2.
+ If ref_eh2 is specified, it uses as reference the Hbonds between ref_eh and ref_eh2.
+ This allows to look at H-bonds between specific parts of proteins or so.
+ Alternatively ref_eh can be a list of H-bonds.
+ This function relies on atom names to determine the list of H-bond donors and acceptors.
+ These names are given in a dictionary, which defaults to CHARMM.
+ If swap is set to True, a dictionary for equivalent donors and one for equivalent acceptors
+ (defaults to CHARMM) is used to check for equivalent HBonds in eh2.
+ If swap is set to True, if two equivalent hydrogen bonds are present in the reference entity
+ (for example both oxygens of ASP H-bonding the same atom), it suffices that on of these bonds is
+ present in eh2 for both of them to be counted as present in eh2.
+ """
+ if ref_eh2:hbond_list1=GetHbondListBetweenViews(ref_eh,ref_eh2,hbond_donor_acceptor_dict,verbose)
+ elif type(ref_eh)==list:hbond_list1=ref_eh
+ else:hbond_list1=GetHbondListFromView(ref_eh,hbond_donor_acceptor_dict,verbose)
+ nbonds=float(len(hbond_list1))
+ if nbonds==0:
+ print 'No HBonds in reference view'
+ return None
+ hbond_list2=GetEquivalentHBonds(hbond_list1,eh2,swap,donor_swap_dict,acceptor_swap_dict,verbose)
+ c=0
+ for hl in hbond_list2:
+ for hbond in hl:
+ if HBond(hbond.donor,hbond.acceptor).IsFormed():
+ c+=1
+ break
+ return c/float(len(hbond_list1))
+
+
+def AnalyzeHBondScore(ref_eh,t,eh2,ref_eh2=None,hbond_donor_acceptor_dict={},swap=False,donor_swap_dict={},acceptor_swap_dict={},first=0,last=-1,stride=1,verbose=True):
+ """
+ Returns the same score as CalculateHBondScore, but for a trajectory.
+ """
+ if swap:
+ if not donor_swap_dict:
+ print 'use of standard CHARMM HBond donor swap dictionary'
+ donor_swap_dict=BuildCHARMMHBondDonorEquivalenceDict()
+ if not acceptor_swap_dict:
+ print 'use of standard CHARMM HBond acceptor swap dictionary'
+ acceptor_swap_dict=BuildCHARMMHBondAcceptorEquivalenceDict()
+ if ref_eh2:hbond_list1=GetHbondListBetweenViews(ref_eh,ref_eh2,hbond_donor_acceptor_dict,verbose)
+ elif type(ref_eh)==list:hbond_list1=ref_eh
+ else:hbond_list1=GetHbondListFromView(ref_eh,hbond_donor_acceptor_dict,verbose)
+ nbonds=float(len(hbond_list1))
+ if nbonds==0:
+ print 'No HBonds in reference view'
+ return None
+ print 'number of hbonds in ref_eh:',nbonds
+ hbond_list2=GetEquivalentHBonds(hbond_list1,eh2,swap,donor_swap_dict,acceptor_swap_dict,verbose)
+ if last==-1:last=t.GetFrameCount()
+ score=FloatList()
+ for f in range(first,last,stride):
+ t.CopyFrame(f)
+ c=0
+ for hl in hbond_list2:
+ for hbond in hl:
+ if hbond.IsFormed():
+ c+=1
+ break
+ score.append(c/nbonds)
+ return score
+
+
+def GetHBondListIntersection(ref_hbond_list,ref_eh,hbond_list,swap=False,donor_swap_dict={},acceptor_swap_dict={}):
+ if swap:
+ if not donor_swap_dict:
+ print 'use of standard CHARMM HBond donor swap dictionary'
+ donor_swap_dict=BuildCHARMMHBondDonorEquivalenceDict()
+ if not acceptor_swap_dict:
+ print 'use of standard CHARMM HBond acceptor swap dictionary'
+ acceptor_swap_dict=BuildCHARMMHBondAcceptorEquivalenceDict()
+ hbond_list=GetEquivalentHBonds(hbond_list,ref_eh,swap,donor_swap_dict,acceptor_swap_dict)
+ ref_hbond_list=GetEquivalentHBonds(ref_hbond_list,ref_eh,swap,donor_swap_dict,acceptor_swap_dict)
+ out_hbond_list=[]
+ for hb in ref_hbond_list:
+ if hb in hbond_list:
+ out_hbond_list.append(hb)
+ return out_hbond_list
+
+
+
+
+
+
diff --git a/modules/mol/alg/pymod/helix_kinks.py b/modules/mol/alg/pymod/helix_kinks.py
index eac71f4777c854d9ef2e78625809538291cb44e4..3a45a20dc0264e56ef83a7177d7ad344ddd73fb2 100644
--- a/modules/mol/alg/pymod/helix_kinks.py
+++ b/modules/mol/alg/pymod/helix_kinks.py
@@ -77,7 +77,7 @@ def AnalyzeHelixKink(t,sele,proline=False):
"""
This function calculates the bend,wobble and face-shift angles
in an alpha-helix over a trajectory. The determination is more stable if
- there are at least 4 residues on each side (8 is even better) of the prolin around which
+ there are at least 4 residues on each side (8 is even better) of the proline around which
the helix is kinked. The selection should contain all residues in the correct
order and with no gaps and no missing C-alphas.
@@ -108,9 +108,9 @@ def AnalyzeHelixKink(t,sele,proline=False):
ca3_pos=ost.mol.alg.AnalyzeAtomPos(t,ca_3.GetHandle())
ca4_pos=ost.mol.alg.AnalyzeAtomPos(t,ca_4.GetHandle())
#Now we calculate the bend angle
- bend_angle=[]
- face_shift=[]
- wobble_angle=[]
+ bend_angle=ost.FloatList()
+ face_shift=ost.FloatList()
+ wobble_angle=ost.FloatList()
for i in range(n_frames):
bend_angle.append(__CalculateBendAngle(pre_proline_axis[i],post_proline_axis[i]))
face_shift.append(__CalculateFaceShift(pre_proline_axis[i],post_proline_axis[i],pre_proline_centers[i],post_proline_centers[i],proline_pos[i],ca3_pos[i],ca4_pos[i],bend_angle[i]))
@@ -154,4 +154,4 @@ def CalculateHelixKink(sele,proline=False):
-
\ No newline at end of file
+
diff --git a/modules/mol/alg/pymod/structure_analysis.py b/modules/mol/alg/pymod/structure_analysis.py
index 4a2cb0dae47a4717a34127a628306aec6e9fcb8b..75ae223e1203e6116bccc487341d00e7d52d80a0 100644
--- a/modules/mol/alg/pymod/structure_analysis.py
+++ b/modules/mol/alg/pymod/structure_analysis.py
@@ -150,7 +150,7 @@ def CalculateHelixAxis(sele1):
return
eh=sele1.GetHandle()
f=GetFrameFromEntity(eh)
- return f.FitCylinder(sele1)
+ return f.FitCylinder(sele1)[0]
def CalculateDistanceDifferenceMatrix(sele1,sele2):
@@ -180,10 +180,10 @@ def CalculateDistanceDifferenceMatrix(sele1,sele2):
n_atoms=sele1.GetAtomCount()
M=npy.zeros([n_atoms,n_atoms])
for i,a1 in enumerate(sele1.atoms):
- for j,a2 in enumerate(sele2.atoms):
+ for j,a2 in enumerate(sele1.atoms):
if i>=j:continue
- d1=geom.Distance(a1.pos,a2.pos)
- d2=geom.Distance(sele2.atoms[i].pos,sele2.atoms[j].pos)
+ d1=ost.geom.Distance(a1.pos,a2.pos)
+ d2=ost.geom.Distance(sele2.atoms[i].pos,sele2.atoms[j].pos)
M[i,j]=d2-d1
M[j,i]=d2-d1
return M
diff --git a/modules/mol/alg/pymod/trajectory_analysis.py b/modules/mol/alg/pymod/trajectory_analysis.py
index 709d6793fbca050994d06f3157488b02161eb596..2d71b5a4d533c8a14a066176311c2da99e5b84d5 100644
--- a/modules/mol/alg/pymod/trajectory_analysis.py
+++ b/modules/mol/alg/pymod/trajectory_analysis.py
@@ -55,7 +55,7 @@ def smooth(vec,n):
From here on the module needs numpy
"""
-def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1):
+def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1,align=True,align_sele=None):
"""
This function calculates a matrix M such that M[i,j] is the
RMSD (calculated on **sele**) between frames i and j of the trajectory **t**
@@ -73,14 +73,16 @@ def RMSD_Matrix_From_Traj(t,sele,first=0,last=-1):
:return: Returns a numpy N\ :subscript:`frames`\ xN\ :subscript:`frames` matrix,
where N\ :subscript:`frames` is the number of frames.
"""
+ if not align_sele:align_sele=sele
try:
import numpy as npy
if last==-1:last=t.GetFrameCount()
n_frames=last-first
rmsd_matrix=npy.identity(n_frames)
for i in range(n_frames):
- t=ost.mol.alg.SuperposeFrames(t,sele,begin=first,end=last,ref=i)
- eh=t.GetEntity()
+ if align:
+ t=ost.mol.alg.SuperposeFrames(t,align_sele,begin=first,end=last,ref=i)
+ eh=t.GetEntity()
t.CopyFrame(i)
rmsd_matrix[i,:]=ost.mol.alg.AnalyzeRMSD(t,sele,sele)
if i==0:
@@ -253,10 +255,35 @@ def AverageDistanceMatrixFromTraj(t,sele,first=0,last=-1):
M=npy.zeros([n_atoms,n_atoms])
for i,a1 in enumerate(sele.atoms):
for j,a2 in enumerate(sele.atoms):
+ if j>i:continue
d=ost.mol.alg.AnalyzeDistanceBetwAtoms(t,a1.GetHandle(),a2.GetHandle())[first:last]
M[i,j]=npy.mean(d)
M[j,i]=npy.mean(d)
return M
-
+def AnalyzeDistanceFluctuationMatrix(t,sele,first=0,last=-1):
+ try:
+ import numpy as npy
+ except ImportError:
+ LogError("Function needs numpy, but I could not import it.")
+ raise
+ n_atoms=sele.GetAtomCount()
+ M=npy.zeros([n_atoms,n_atoms])
+ for i,a1 in enumerate(sele.atoms):
+ for j,a2 in enumerate(sele.atoms):
+ if i>j:continue
+ d=ost.mol.alg.AnalyzeDistanceBetwAtoms(t,a1.GetHandle(),a2.GetHandle())[first:last]
+ M[j,i]=npy.std(d)
+ M[i,j]=npy.std(d)
+ return M
+
+def IterativeSuperposition(t,sele,threshold=1.0,initial_sele=None,iterations=5,ref_frame=0):
+ if initial_sele:current_sele=initial_sele
+ else: current_sele=sele
+ for i in range(iterations):
+ t=ost.mol.alg.SuperposeFrames(t,current_sele,ref=ref_frame)
+ al=[a for a in sele.atoms if ost.mol.alg.AnalyzeRMSF(t,ost.mol.CreateViewFromAtoms([a]))<threshold]
+ if len(al)==0:return
+ current_sele=ost.mol.CreateViewFromAtoms(al)
+ return current_sele
\ No newline at end of file
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 909f41d711b987afccd82319cbe10575ed7dca5f..acd951f1a6413536d26ef05c08d957f75c953ab1 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -27,9 +27,11 @@
#include <ost/mol/alg/filter_clashes.hh>
#include <ost/mol/alg/consistency_checks.hh>
#include <ost/mol/alg/pdbize.hh>
+#include <ost/mol/alg/contact_overlap.hh>
#include <ost/export_helper/pair_to_tuple_conv.hh>
#include <ost/export_helper/vec_to_list_conv.hh>
+
using namespace boost::python;
using namespace ost;
@@ -37,6 +39,7 @@ void export_svdSuperPose();
void export_TrajectoryAnalysis();
void export_StructureAnalysis();
void export_Clash();
+void export_contact_overlap();
#if OST_IMG_ENABLED
void export_entity_to_density();
#endif
@@ -105,6 +108,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
export_TrajectoryAnalysis();
export_StructureAnalysis();
export_Clash();
+ export_contact_overlap();
#if OST_IMG_ENABLED
export_entity_to_density();
#endif
@@ -120,8 +124,6 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
def("CreateDistanceList",&mol::alg::CreateDistanceList);
def("CreateDistanceListFromMultipleReferences",&create_distance_list_from_multiple_references);
- def("DistanceRMSDTest", &mol::alg::DistanceRMSDTest, (arg("sequence_separation")=0,arg("local_lddt_property_string")=""));
-
def("SuperposeFrames", superpose_frames1,
(arg("source"), arg("sel")=ost::mol::EntityView(), arg("begin")=0,
arg("end")=-1, arg("ref")=-1));
@@ -261,6 +263,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
.def(map_indexing_suite<mol::alg::GlobalRDMap,true>())
;
- def("DRMSD",&mol::alg::DRMSD);
+ def("DRMSD",&mol::alg::DRMSD,(arg("view"),arg("distance_list"),
+ arg("cap_distance")=5.0,arg("sequence_separation")=0));
}
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index b6a7f28922257cd548acd6355a0d8387a4a9f8d6..8f2038f96f4ab2dc03bcb9bd4624ca78a3f2003f 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -13,6 +13,11 @@ set(OST_MOL_ALG_HEADERS
structure_analysis.hh
consistency_checks.hh
pdbize.hh
+ adjacency_bitmap.hh
+ consistency_checks.hh
+ contact_overlap.hh
+ domain_find.hh
+ similarity_matrix.hh
)
set(OST_MOL_ALG_SOURCES
@@ -29,6 +34,11 @@ set(OST_MOL_ALG_SOURCES
structure_analysis.cc
consistency_checks.cc
pdbize.cc
+ adjacency_bitmap.cc
+ consistency_checks.cc
+ contact_overlap.cc
+ domain_find.cc
+ similarity_matrix.cc
)
set(MOL_ALG_DEPS ost_mol ost_seq)
@@ -44,7 +54,7 @@ if (ENABLE_IMG)
entity_to_density.cc
)
- set(MOL_ALG_DEPS ${MOL_ALG_DEPS} ost_img ost_img_alg)
+ set(MOL_ALG_DEPS ${MOL_ALG_DEPS} ost_img ost_img_alg ost_seq_alg)
endif()
executable(NAME lddt SOURCES lddt.cc
@@ -54,7 +64,7 @@ module(NAME mol_alg SOURCES ${OST_MOL_ALG_SOURCES}
HEADERS ${OST_MOL_ALG_HEADERS}
HEADER_OUTPUT_DIR ost/mol/alg
DEPENDS_ON ${MOL_ALG_DEPS}
- LINK ${BOOST_PROGRAM_OPTIONS})
+ LINK ${BOOST_PROGRAM_OPTIONS} ${BOOST_THREAD})
copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure"
"atom_scattering_properties.txt" "ATOM_SCATTERING_PROPS"
diff --git a/modules/mol/alg/src/adjacency_bitmap.cc b/modules/mol/alg/src/adjacency_bitmap.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e117e08645d8acad456df2b102a4650e57ea304c
--- /dev/null
+++ b/modules/mol/alg/src/adjacency_bitmap.cc
@@ -0,0 +1,105 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <ost/img/image_factory.hh>
+#include <ost/mol/atom_view.hh>
+#include <ost/mol/residue_view.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/residue_view.hh>
+#include "adjacency_bitmap.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+const uint8_t AdjacencyBitmap::NUMBER_OF_BITS_SET[] = {
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3,
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3,
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 2,
+ 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3,
+ 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3,
+ 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3,
+ 1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 3,
+ 2, 2, 2, 3, 2, 2, 2, 3, 2, 2, 2, 3, 3, 3, 3, 4
+};
+
+const uint8_t AdjacencyBitmap::NUMBER_OF_EDGES_SET[] = {
+ 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2,
+ 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2,
+ 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3,
+ 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3,
+ 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2,
+ 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2,
+ 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3,
+ 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3,
+ 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3,
+ 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3,
+ 2, 2, 3, 3, 2, 2, 3, 3, 3, 3, 4, 4, 3, 3, 4, 4,
+ 2, 2, 3, 3, 2, 2, 3, 3, 3, 3, 4, 4, 3, 3, 4, 4,
+ 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3,
+ 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 3, 3,
+ 2, 2, 3, 3, 2, 2, 3, 3, 3, 3, 4, 4, 3, 3, 4, 4,
+ 2, 2, 3, 3, 2, 2, 3, 3, 3, 3, 4, 4, 3, 3, 4, 4
+};
+
+OverlapResult AdjacencyBitmap::Overlap(size_t vert_i, size_t vert_j) const {
+ // To determine the union of the direct neighbors of vert_i and vert_j,
+ // we calculated the bitwise or of the edge_bits and combine it with
+ // the union of the defined bits. For that purpose, we will need a mask
+ // for the edge bits. In binary the mask looks like 0101010101.
+ uint64_t edge_mask = 0x5555555555555555;
+ uint64_t* pi = data_+storage_size_*vert_i;
+ uint64_t* ei = pi + storage_size_;
+ uint64_t* pj = data_+storage_size_*vert_j;
+ size_t nominator = 0;
+ size_t denominator = 0;
+ size_t edges_set = 0;
+ for (; pi != ei; ++pi, ++pj) {
+ uint64_t intersection_ij = *pi & *pj;
+ uint64_t union_ij = ((*pi | *pj) & edge_mask) | intersection_ij;
+ for (size_t i = 0; i < sizeof(uint64_t); ++i) {
+ nominator += NUMBER_OF_BITS_SET[(intersection_ij >> 8*i) & 0xff];
+ edges_set += NUMBER_OF_EDGES_SET[(intersection_ij >> 8*i) & 0xff];
+ denominator += NUMBER_OF_BITS_SET[(union_ij >> 8*i) & 0xff];
+ }
+ }
+ return OverlapResult(nominator, denominator, edges_set);
+}
+
+void AdjacencyBitmap::dump() const {
+
+ for (size_t i=0; i<this->size(); i+=10) {
+ for (size_t j=0;j<this->size(); j+=10) {
+ if (this->defined(i, j)) {
+ std::cout << (this->get(i, j) ? '*' : '.');
+ } else {
+ std::cout << 'u';
+ }
+ }
+ std::cout << std::endl;
+ }
+}
+
+}}}
+
diff --git a/modules/mol/alg/src/adjacency_bitmap.hh b/modules/mol/alg/src/adjacency_bitmap.hh
new file mode 100644
index 0000000000000000000000000000000000000000..69eee65f22f26d45244adab63611cbf75ea7d530
--- /dev/null
+++ b/modules/mol/alg/src/adjacency_bitmap.hh
@@ -0,0 +1,165 @@
+#ifndef OST_MOL_ALG_ADJACENCY_BITMAP_HH
+#define OST_MOL_ALG_ADJACENCY_BITMAP_HH
+
+#include <cstring>
+#include <boost/shared_ptr.hpp>
+#include <ost/img/image_handle.hh>
+#include <ost/tri_matrix.hh>
+#include <ost/seq/sequence_handle.hh>
+#include <ost/seq/alignment_handle.hh>
+#include "similarity_matrix.hh"
+#include "contact_overlap.hh"
+#include "module_config.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+
+struct OverlapResult {
+ OverlapResult(uint16_t nom, uint16_t denom, uint16_t def):
+ nominator(nom), denominator(denom), defined(def) {}
+ OverlapResult(): nominator(0), denominator(0), defined(0) {}
+ uint16_t nominator;
+ uint16_t denominator;
+ uint16_t defined;
+};
+
+// A highly optimized representation of the adjacency matrix
+class AdjacencyBitmap {
+public:
+ explicit AdjacencyBitmap(size_t n_vertices):
+ num_vertices_(n_vertices),
+ storage_size_(StorageSize(n_vertices))
+ {
+ data_ = static_cast<uint64_t*>(malloc(this->num_bytes()));
+ end_ = data_+storage_size_*num_vertices_;
+ memset(data_, 0, this->num_bytes());
+ }
+
+ AdjacencyBitmap(const DistanceMatrix& dmat_a,
+ const DistanceMatrix& dmat_b,
+ Real threshold, Real radius,
+ int start, int end):
+ num_vertices_(end-start),
+ storage_size_(StorageSize(end-start)),
+ data_(static_cast<uint64_t*>(malloc(this->num_bytes()))),
+ end_(data_+storage_size_*num_vertices_) {
+
+ for (int i = start; i < end; ++i) {
+ this->set(i-start, i-start, false, false);
+ for (int j = i+1; j < end; ++j) {
+ Real da = dmat_a.Get(i, j);
+ Real db = dmat_b.Get(i, j);
+ bool defined = da>=0 && db>=0 && (db < radius || da < radius);
+ bool agree = false;
+ if (defined) {
+ agree = std::abs(da-db)<threshold;
+ }
+ this->set(i-start, j-start, agree, defined);
+ this->set(j-start, i-start, agree, defined);
+ }
+ }
+ }
+
+ AdjacencyBitmap(const SimilarityMatrix& sim, Real threshold):
+ num_vertices_(sim.GetSize()),
+ storage_size_(StorageSize(sim.GetSize())),
+ data_(static_cast<uint64_t*>(malloc(this->num_bytes()))),
+ end_(data_+storage_size_*num_vertices_) {
+ memset(data_, 0, this->num_bytes());
+ for (int i = 0; i < sim.GetSize(); ++i) {
+ this->set(i, i, false, false);
+ for (int j = i+1; j < sim.GetSize(); ++j) {
+ this->set(i, j, sim.Get(i, j)>threshold, sim.Get(i, j)>=0.0);
+ this->set(j, i, sim.Get(i, j)>threshold, sim.Get(i, j)>=0.0);
+ }
+ }
+ }
+
+ AdjacencyBitmap(const AdjacencyBitmap& rhs):
+ num_vertices_(rhs.num_vertices_),
+ storage_size_(rhs.storage_size_),
+ data_(static_cast<uint64_t*>(malloc(this->num_bytes()))),
+ end_(data_+storage_size_*num_vertices_) {
+ memcpy(data_, rhs.data_, this->num_bytes());
+ }
+
+ ~AdjacencyBitmap() {
+ if (data_)
+ free(data_);
+ }
+
+ // calculates the overlap between the direct neighbours of vertex i
+ // and j using pure awesomeness and some bit trickery.
+ OverlapResult Overlap(size_t vert_i, size_t vert_j) const;
+
+ void set(size_t i, size_t j, bool val, bool defined=true) {
+ size_t byte_index = i*storage_size_ + j/(4*sizeof(uint64_t));
+ assert(byte_index < this->num_bytes());
+ size_t bit_index = (2*j) % BITS;
+ // the following two variables are required to force use of
+ // 64 bit integer for bit operations.
+ uint64_t one = 1;
+ uint64_t two = 2;
+ assert(bit_index < sizeof(uint64_t)*8);
+
+ if (val) {
+ data_[byte_index] |= (one << bit_index);
+ } else {
+ data_[byte_index] &= ~(one << bit_index);
+ }
+
+ if (defined) {
+ data_[byte_index] |= (two << bit_index);
+ } else {
+ data_[byte_index] &= ~(two << bit_index);
+ }
+ }
+
+ bool get(size_t i, size_t j) const {
+ uint64_t one = 1;
+ size_t byte_index = i*storage_size_ + j/(4*sizeof(uint64_t));
+ assert(byte_index < storage_size_*num_vertices_);
+ size_t bit_index = (2*j) % BITS;
+ assert(bit_index < sizeof(uint64_t)*8);
+ return data_[byte_index] & (one << bit_index);
+ }
+
+ bool defined(size_t i, size_t j) const {
+ uint64_t two = 2;
+ size_t byte_index = i*storage_size_ + j/(4*sizeof(uint64_t));
+ assert(byte_index < storage_size_*num_vertices_);
+ size_t bit_index = (2*j) % BITS;
+ assert(bit_index < sizeof(uint64_t)*8);
+ return data_[byte_index] & (two << bit_index);
+ }
+
+ size_t size() const {
+ return num_vertices_;
+ }
+
+ size_t num_bytes() const {
+ return storage_size_*num_vertices_*sizeof(uint64_t);
+ }
+ void dump() const;
+private:
+
+ AdjacencyBitmap();
+ AdjacencyBitmap& operator=(const AdjacencyBitmap&);
+
+ const static size_t BITS=sizeof(uint64_t)*8;
+ size_t num_vertices_;
+ size_t storage_size_;
+ uint64_t* data_;
+ uint64_t* end_;
+
+ static const uint8_t NUMBER_OF_BITS_SET[];
+ static const uint8_t NUMBER_OF_EDGES_SET[];
+ static size_t StorageSize(size_t verts) {
+ return verts/(4*sizeof(uint64_t)) + (verts % (sizeof(uint64_t)*4) ? 1 : 0);
+ }
+};
+
+
+}}}
+#endif
+
diff --git a/modules/mol/alg/src/contact_overlap.cc b/modules/mol/alg/src/contact_overlap.cc
new file mode 100644
index 0000000000000000000000000000000000000000..89246d9db9ca5c3d55664b024606c19208c727fa
--- /dev/null
+++ b/modules/mol/alg/src/contact_overlap.cc
@@ -0,0 +1,461 @@
+#include <ost/log.hh>
+#include <ost/mol/mol.hh>
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/alg/merge_pairwise_alignments.hh>
+#include "contact_overlap.hh"
+
+using namespace ost;
+using namespace ost::mol;
+using namespace ost::seq;
+
+namespace ost { namespace mol { namespace alg {
+
+ContactList Contacts(const ost::mol::EntityView& ent, Real min_dist,
+ Real max_dist)
+{
+ Real min_sqr=min_dist*min_dist;
+ Real max_sqr=max_dist*max_dist;
+ ContactList contacts;
+ ResidueViewList residues=ent.GetResidueList();
+ for (ResidueViewList::const_iterator
+ i=residues.begin(), e=residues.end(); i!=e; ++i) {
+ AtomView atom_a=i->FindAtom("CA");
+ if (!atom_a.IsValid()) {
+ continue;
+ }
+ for (ResidueViewList::const_iterator
+ j=i+1, e2=residues.end(); j!=e2; ++j) {
+ AtomView atom_b=j->FindAtom("CA");
+ if (!atom_b.IsValid()) {
+ continue;
+ }
+ Real d=geom::Length2(atom_a.GetPos()-atom_b.GetPos());
+ if (min_sqr<d && max_sqr>d) {
+ contacts.push_back(Contact(atom_a.GetHandle(), atom_b.GetHandle()));
+ }
+ }
+
+ }
+ return contacts;
+}
+
+namespace {
+
+struct AtomHashCmp {
+ bool operator()(const AtomHandle& a,
+ const AtomHandle& b) const {
+ return a.GetHashCode()<b.GetHashCode();
+ }
+};
+
+}
+
+void CalcContactNodeDegree(const ContactList& contacts)
+{
+ std::map<AtomHandle, int, AtomHashCmp> degrees;
+ for (ContactList::const_iterator
+ i=contacts.begin(), e=contacts.end(); i!=e; ++i) {
+ // yes, this is sane. upon first accessing a key, the value is initialised
+ // to 0 and *then* incremented.
+ degrees[i->atom_a]+=1;
+ degrees[i->atom_b]+=1;
+ }
+ for (std::map<AtomHandle, int>::iterator
+ i=degrees.begin(), e=degrees.end(); i!=e; ++i) {
+ AtomHandle atom=i->first;
+ atom.SetIntProp("degree", i->second);
+ }
+}
+
+Real Reward(Real ref_dist, Real obs_dist, Real tolerance,
+ OverlapMode mode=OM_RELATIVE) {
+ assert(ref_dist>0.0);
+ Real norm_diff=mode==OM_RELATIVE ?
+ std::abs((obs_dist-ref_dist)/sqrt(obs_dist+ref_dist)) :
+ std::abs(ref_dist-obs_dist);
+ if (norm_diff<tolerance*0.5) {
+ return 1.0;
+ }
+ Real one_over_tol=0.5/tolerance;
+ return std::max(0.0, 1.0-(norm_diff-tolerance*0.5)*one_over_tol);
+}
+
+Real LocalDistanceTest(const EntityView& mdl, const EntityView& ref,
+ Real max_dist, Real tolerance, bool only_complete)
+{
+ Real max_sqr=pow(max_dist+max_dist*tolerance, 2);
+ ContactList contacts;
+ ResidueViewList residues=ref.GetResidueList();
+ Real in_ref=0.0;
+ Real in_mdl=0.0;
+ for (ResidueViewList::const_iterator
+ i=residues.begin(), e=residues.end(); i!=e; ++i) {
+ AtomView atom_a=i->FindAtom("CA");
+ if (!atom_a.IsValid()) {
+ continue;
+ }
+ for (ResidueViewList::const_iterator
+ j=i+1, e2=residues.end(); j!=e2; ++j) {
+ AtomView atom_b=j->FindAtom("CA");
+ if (!atom_b.IsValid()) {
+ continue;
+ }
+ Real d=geom::Length2(atom_a.GetPos()-atom_b.GetPos());
+ if (max_sqr<d) {
+ continue;
+ }
+ if (!only_complete) {
+ in_ref+=1.0;
+ }
+
+ AtomView atom_c=mdl.FindAtom(atom_a.GetResidue().GetChain().GetName(),
+ atom_a.GetResidue().GetNumber(), "CA");
+ if (!atom_c.IsValid()) {
+ continue;
+ }
+ AtomView atom_d=mdl.FindAtom(atom_b.GetResidue().GetChain().GetName(),
+ atom_b.GetResidue().GetNumber(), "CA");
+ if (!atom_d.IsValid()) {
+ continue;
+ }
+ if (only_complete) {
+ in_ref+=1.0;
+ }
+ in_mdl+=Reward(sqrt(d), geom::Length(atom_c.GetPos()-atom_d.GetPos()),
+ tolerance);
+ }
+ }
+ if (in_ref==0.0) {
+ return 0.0;
+ }
+ return in_mdl/in_ref;
+}
+
+namespace {
+void calculate_com(const ost::seq::AlignmentHandle& target_tpl_aln,
+ Real tolerance, int idx_a, int idx_b,
+ SimilarityMatrix& overlap, OverlapMode mode,
+ Real max_dist)
+{
+ ConstSequenceHandle s1=target_tpl_aln.GetSequence(idx_a);
+ ConstSequenceHandle s2=target_tpl_aln.GetSequence(idx_b);
+ if (!(s1.HasAttachedView() && s2.HasAttachedView())) {
+ throw Error("Both sequences must have a view attached");
+ }
+ EntityView av=s1.GetAttachedView();
+ for (int x=0; x<s1.GetLength(); ++x) {
+ if (s1[x]=='-' || s2[x]=='-') {
+ continue;
+ }
+ ResidueView res_a=s1.GetResidue(x);
+ if (!res_a) {
+ continue;
+ }
+ AtomView ca_a=res_a.FindAtom("CA");
+ if (!ca_a) {
+ continue;
+ }
+ for (int y=x+1; y<s1.GetLength(); ++y) {
+ if (s1[y]=='-' || s2[y]=='-') {
+ continue;
+ }
+ ResidueView res_b=s1.GetResidue(y);
+ AtomView ca_b=res_b.FindAtom("CA");
+ if (!ca_b.IsValid()) {
+ continue;
+ }
+ ResidueView res_c=s2.GetResidue(x);
+ AtomView ca_c=res_c.FindAtom("CA");
+ if (!ca_c.IsValid()) {
+ continue;
+ }
+ ResidueView res_d=s2.GetResidue(y);
+ AtomView ca_d=res_d.FindAtom("CA");
+ if (!ca_d.IsValid()) {
+ continue;
+ }
+ Real da=geom::Length(ca_a.GetPos()-ca_b.GetPos());
+ Real db=geom::Length(ca_c.GetPos()-ca_d.GetPos());
+ if (da>max_dist && db>max_dist) {
+ continue;
+ }
+ Real reward=Reward(da, db, tolerance, mode);
+ if (overlap.Get(x, y)>=0) {
+ reward=std::min(reward, overlap.Get(x, y));
+ }
+ overlap.Set(x, y, reward);
+ }
+ }
+}
+
+}
+DistanceMatrixPtr DistanceMatrix::FromAln(const AlignmentHandle& aln,
+ int index) {
+ if (!aln.GetSequence(index).HasAttachedView()) {
+ throw Error("Sequence must have a view attached");
+ }
+ return DistanceMatrixPtr(new DistanceMatrix(aln, index));
+
+}
+
+DistanceMatrixPtr DistanceMatrix::Create(const ConstSequenceHandle& s)
+{
+ if (!s.HasAttachedView()) {
+ throw Error("Sequence must have a view attached");
+ }
+ return DistanceMatrixPtr(new DistanceMatrix(s));
+}
+
+SimilarityMatrix ContactOverlapMap(const DistanceMatrix& dmat1,
+ const DistanceMatrix& dmat2,
+ Real tolerance, OverlapMode mode,
+ Real max_dist)
+{
+ if (dmat1.GetSize()!=dmat2.GetSize()) {
+ throw Error("Distance matrices must have equal size");
+ }
+ SimilarityMatrix sim(dmat1.GetSize(), -1.0);
+ for (int i=0; i<dmat1.GetSize(); ++i) {
+ for (int j=i+1; j<dmat1.GetSize(); ++j) {
+ Real a=dmat1.Get(i, j);
+ Real b=dmat2.Get(i, j);
+ if ((a<0 || b<0.0) || (a>max_dist && a>max_dist)) {
+ continue;
+ }
+ sim(i, j)=Reward(a, b, tolerance, mode);
+ }
+ }
+ return sim;
+}
+
+DistanceMatrix::DistanceMatrix(const AlignmentHandle& a, int index):
+ ost::TriMatrix<Real>(a.GetSequence(0).GetGaplessString().size(), -1.0)
+{
+ EntityView av=a.GetSequence(index).GetAttachedView();
+ ConstSequenceHandle trg_seq = a.GetSequence(0);
+ ConstSequenceHandle tpl_seq = a.GetSequence(index);
+ for (int x=0; x<a.GetLength(); ++x) {
+ if (trg_seq[x]=='-' || tpl_seq[x]=='-') {
+ continue;
+ }
+ ResidueView res_a=tpl_seq.GetResidue(x);
+ if (!res_a) {
+ continue;
+ }
+ AtomView ca_a=res_a.FindAtom("CA");
+ if (!ca_a) {
+ continue;
+ }
+ for (int y=x; y<a.GetLength(); ++y) {
+ if (trg_seq[y]=='-' || tpl_seq[y] =='-') {
+ continue;
+ }
+ ResidueView res_b=tpl_seq.GetResidue(y);
+ if (!res_b.IsValid()) {
+ continue;
+ }
+ AtomView ca_b=res_b.FindAtom("CA");
+ if (!ca_b.IsValid()) {
+ continue;
+ }
+ this->Set(trg_seq.GetResidueIndex(x),
+ trg_seq.GetResidueIndex(y),
+ geom::Length(ca_a.GetPos()-ca_b.GetPos()));
+ }
+ }
+}
+
+DistanceMatrix::DistanceMatrix(const ConstSequenceHandle& s):
+ ost::TriMatrix<Real>(s.GetLength(), -1.0)
+{
+ EntityView av=s.GetAttachedView();
+ for (int x=0; x<s.GetLength(); ++x) {
+ if (s[x]=='-') {
+ continue;
+ }
+ ResidueView res_a=s.GetResidue(x);
+ if (!res_a) {
+ continue;
+ }
+ AtomView ca_a=res_a.FindAtom("CA");
+ if (!ca_a) {
+ continue;
+ }
+ for (int y=x; y<s.GetLength(); ++y) {
+ if (s[y]=='-') {
+ continue;
+ }
+ ResidueView res_b=s.GetResidue(y);
+ if (!res_b.IsValid()) {
+ continue;
+ }
+ AtomView ca_b=res_b.FindAtom("CA");
+ if (!ca_b.IsValid()) {
+ continue;
+ }
+ this->Set(x, y, geom::Length(ca_a.GetPos()-ca_b.GetPos()));
+ }
+ }
+}
+
+SimilarityMatrix ContactOverlapMap(const AlignmentHandle& target_tpl_aln,
+ Real tolerance, OverlapMode mode, Real max_dist)
+{
+ SimilarityMatrix overlap(target_tpl_aln.GetLength(), -1.0);
+ for (int i=1; i<target_tpl_aln.GetCount(); ++i) {
+ calculate_com(target_tpl_aln, tolerance, 0, i, overlap, mode, max_dist);
+ }
+ return overlap;
+}
+
+SimilarityMatrix ContactOverlapMap(const AlignmentHandle& target_tpl_aln,
+ Real tolerance,
+ int idx_a, int idx_b)
+{
+ SimilarityMatrix overlap(target_tpl_aln.GetLength(), -1.0);
+ calculate_com(target_tpl_aln, tolerance, idx_a, idx_b, overlap,
+ OM_ABSOLUTE, 1e6);
+ return overlap;
+}
+
+
+Real ContactOverlap(const DistanceMatrixPtr& lhs,
+ const DistanceMatrixPtr& rhs,
+ Real tolerance, OverlapMode mode,
+ Real dist_limit)
+{
+ Real nom=0.0, denom=0.0;
+ for (int i=0; i<lhs->GetSize(); ++i) {
+ for (int j=i+1; j<lhs->GetSize(); ++j) {
+ Real a=lhs->Get(i, j);
+ Real b=rhs->Get(i, j);
+ if (a>dist_limit && b>dist_limit) {
+ continue;
+ }
+ if (a>=0.0 && b>=0.0) {
+ denom+=1.0;
+ nom+=Reward(a, b, tolerance, mode);
+ }
+ }
+ }
+ return denom>0 ? nom/denom : 0.0;
+}
+
+int LabelComponents(const SimilarityMatrix& sim, std::vector<int>& components,
+ int x, int comp_id, Real tolerance)
+{
+ int count=1;
+ components[x]=comp_id;
+ for (int y=x+1; y<sim.GetSize(); ++y) {
+ if (sim.Get(x, y)<tolerance || components[y]>-1) {
+ continue;
+ }
+ count+=LabelComponents(sim, components, y, comp_id, tolerance);
+ }
+ return count;
+}
+
+
+//img::ImageHandle
+void DomainsFromCOM(const SimilarityMatrix& sim,
+ AlignmentHandle aln,
+ Real tolerance, int idx_a, int idx_b)
+{
+ const static int MAX_ITERATIONS=20;
+ const static Real EPSILON=1e-6;
+ SimilarityMatrix sim1=sim;
+ SimilarityMatrix sim2(sim1.GetSize(), 0.0);
+ SimilarityMatrix* sim1p=&sim1;
+ SimilarityMatrix* sim2p=&sim2;
+ img::ImageHandle im/*=img::CreateImage(img::Size(sim1.GetSize(),
+ sim1.GetSize(), MAX_ITERATIONS+1))*/;
+
+ /*for (int i=0; i<sim.GetSize(); ++i) {
+ for (int j=i+1; j<sim.GetSize(); ++j) {
+ im.SetReal(img::Point(i, j, MAX_ITERATIONS), sim1.Get(i, j));
+ }
+ }*/
+ // iteratively update similarity based on direct neighbours
+ int n=MAX_ITERATIONS;
+ std::vector<bool> fixed_residues(sim1.GetSize(), false);
+ Real last_error=0.0;
+ while (n>0) {
+ --n;
+ Real error=0.0;
+ for (int i=0; i<sim.GetSize(); ++i) {
+ /*if (fixed_residues[i]) {
+ continue;
+ }*/
+ fixed_residues[i]=true;
+ for (int j=i+1; j<sim.GetSize(); ++j) {
+ int nom=0, denom=0;
+ for (int k=0; k<sim.GetSize(); ++k) {
+ Real ik=sim1p->Get(i, k);
+ Real jk=sim1p->Get(j, k);
+ if (jk<0 || ik <0) {
+ continue;
+ }
+ if (ik>tolerance) {
+ denom+=1;
+ if (jk>tolerance) {
+ nom+=1;
+ }
+ } else if (jk>tolerance) {
+ denom+=1;
+ }
+ }
+ if (denom) {
+ Real newval=Real(nom)/denom;
+ if (!(newval>0.95 || newval<0.05)) {
+ fixed_residues[i]=false;
+ }
+ sim2p->Set(i, j, newval);
+ } else {
+ sim2p->Set(i, j, 0);
+ }
+ error+=std::abs(sim2p->Get(i, j)-sim1p->Get(i, j));
+ //sim.SetReal(img::Point(i, j, n), sim2p->Get(i, j));
+ }
+ }
+ error/=sim.GetSize()*(sim.GetSize()-1)/2;
+ std::swap(sim1p, sim2p);
+ if (std::abs(error-last_error)<EPSILON) {
+ break;
+ }
+ last_error=error;
+ }
+ // run connected component algorithm on similarity matrix to identify
+ // conserved domains.
+ std::vector<int> components(sim.GetSize(), -1);
+ int comp_id=0;
+ for (int i=0; i<sim.GetSize(); ++i) {
+ if (components[i]!=-1) {
+ continue;
+ }
+ if (LabelComponents(*sim2p, components, i, comp_id, tolerance)>1) {
+ comp_id+=1;
+ } {
+ components[i]=-1;
+ }
+ }
+
+ for (int i=0; i<aln.GetLength(); ++i) {
+ if (idx_a>=0 && idx_b>=0) {
+ if (ResidueView r=aln.GetResidue(idx_a, i)) {
+ r.SetIntProp("comp_id", components[i]);
+ }
+ if (ResidueView r=aln.GetResidue(idx_b, i)) {
+ r.SetIntProp("comp_id", components[i]);
+ }
+ } else {
+ for (int j=0; j<aln.GetCount(); ++j) {
+ if (ResidueView r=aln.GetResidue(j, i)) {
+ r.SetIntProp("comp_id", components[i]);
+ }
+ }
+ }
+
+ }
+}
+
+}}}
diff --git a/modules/mol/alg/src/contact_overlap.hh b/modules/mol/alg/src/contact_overlap.hh
new file mode 100644
index 0000000000000000000000000000000000000000..e7c470656e36fa5284207367fd4a592467a9bfe5
--- /dev/null
+++ b/modules/mol/alg/src/contact_overlap.hh
@@ -0,0 +1,108 @@
+#ifndef OST_MOL_ALG_CONTACT_HH
+#define OST_MOL_ALG_CONTACT_HH
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/mol/entity_view.hh>
+#include <ost/img/image.hh>
+#include <ost/seq/alignment_handle.hh>
+
+
+#include "module_config.hh"
+#include "similarity_matrix.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+struct Contact {
+ Contact(): atom_a(), atom_b() {}
+ Contact(ost::mol::AtomHandle a, ost::mol::AtomHandle b):
+ atom_a(a), atom_b(b)
+ { }
+ ost::mol::AtomHandle atom_a;
+ ost::mol::AtomHandle atom_b;
+
+ bool operator==(const Contact& rhs) const
+ {
+ return atom_a==rhs.atom_a && atom_b==rhs.atom_b;
+ }
+
+ bool operator!=(const Contact& rhs) const
+ {
+ return !this->operator==(rhs);
+ }
+};
+
+typedef std::vector<Contact> ContactList;
+
+/// \brief returns a a list of contacts between C-alpha atoms
+ContactList DLLEXPORT_OST_MOL_ALG
+Contacts(const ost::mol::EntityView& ent, Real min_dist,
+ Real max_dist);
+
+typedef enum {
+ OM_RELATIVE,
+ OM_ABSOLUTE
+} OverlapMode;
+/// \brief calculates and assigns the contact node degree as the int
+/// property 'degree' for each atom
+void DLLEXPORT_OST_MOL_ALG CalcContactNodeDegree(const ContactList& contacts);
+
+struct LDT {
+ Real ha;
+ Real ma;
+ Real la;
+};
+
+class DistanceMatrix;
+
+typedef boost::shared_ptr<DistanceMatrix> DistanceMatrixPtr;
+
+class DLLEXPORT_OST_MOL_ALG DistanceMatrix: public ost::TriMatrix<Real> {
+public:
+ static DistanceMatrixPtr Create(const ost::seq::ConstSequenceHandle& s);
+ static DistanceMatrixPtr FromAln(const ost::seq::AlignmentHandle& a,
+ int index=1);
+private:
+ DistanceMatrix(const ost::seq::ConstSequenceHandle& sequence);
+ DistanceMatrix(const ost::seq::AlignmentHandle& aln, int index);
+
+};
+
+
+Real DLLEXPORT_OST_MOL_ALG ContactOverlap(const DistanceMatrixPtr& lhs,
+ const DistanceMatrixPtr& rhs,
+ Real tolerance,
+ OverlapMode mode=OM_RELATIVE,
+ Real dist_limit=1e6);
+
+
+Real DLLEXPORT_OST_MOL_ALG
+LocalDistanceTest(const ost::mol::EntityView& mdl,
+ const ost::mol::EntityView& ref,
+ Real max_dist,
+ Real tolerance=0.02,
+ bool only_complete=false);
+
+SimilarityMatrix DLLEXPORT_OST_MOL_ALG
+ContactOverlapMap(const ost::seq::AlignmentHandle& target_tpl_aln,
+ Real tolerance, int idx_a, int idx_b);
+
+SimilarityMatrix DLLEXPORT_OST_MOL_ALG
+ContactOverlapMap(const ost::seq::AlignmentHandle& target_tpl_aln,
+ Real tolerance, OverlapMode mode=OM_RELATIVE,
+ Real max_dist=1e6);
+
+SimilarityMatrix DLLEXPORT_OST_MOL_ALG
+ContactOverlapMap(const DistanceMatrix& dmat1, const DistanceMatrix& dmat2,
+ Real tolerance, OverlapMode mode=OM_RELATIVE,
+ Real max_dist=1e6);
+
+
+//ost::img::ImageHandle
+void DLLEXPORT_OST_MOL_ALG
+DomainsFromCOM(const SimilarityMatrix& sim, ost::seq::AlignmentHandle aln,
+ Real tolerance, int idx_a=-1, int idx_b=-1);
+
+}}}
+
+#endif
diff --git a/modules/mol/alg/src/distance_rmsd_test.cc b/modules/mol/alg/src/distance_rmsd_test.cc
index 1411c1806f779563f621e17956443233a5a8202a..6bb500e36eb34a398272141a229807dfa81b3150 100644
--- a/modules/mol/alg/src/distance_rmsd_test.cc
+++ b/modules/mol/alg/src/distance_rmsd_test.cc
@@ -8,117 +8,176 @@ namespace ost { namespace mol { namespace alg {
namespace {
-std::pair<Real, long int> calc_rmsd(const ResidueRDMap& res_distance_list, const ResNum& rnum,
- ChainView mdl_chain, int sequence_separation, Real cap_distance,
- bool only_fixed, bool swap, std::vector<std::pair<Real, long int> >& local_rmsd_data_list, bool log )
-{
- std::pair<Real, long int> rmsd_data(0, 0);
- ResidueView mdl_res=mdl_chain.FindResidue(rnum);
- for (ResidueRDMap::const_iterator ai=res_distance_list.begin(); ai!=res_distance_list.end(); ++ai) {
- const UAtomIdentifiers& uais = ai->first;
- const std::pair <Real,Real>& values = ai->second;
- const UniqueAtomIdentifier& first_atom=uais.first;
- const UniqueAtomIdentifier& second_atom=uais.second;
- String name=swap ? SwappedName(first_atom.GetAtomName()) : first_atom.GetAtomName();
- AtomView av1=mdl_res ? mdl_res.FindAtom(name) : AtomView();
-
- if (only_fixed) {
- if (std::abs(first_atom.GetResNum().GetNum()-second_atom.GetResNum().GetNum())<=sequence_separation) {
- continue;
- }
- if (Swappable(second_atom.GetResidueName(), second_atom.GetAtomName())) {
- continue;
- }
- }
- if (!only_fixed) {
- if (first_atom.GetResNum().GetNum()<=(second_atom.GetResNum().GetNum()+sequence_separation)) {
- continue;
+
+Real calc_squared_diff(const std::vector<geom::Vec3>& pos_one,
+ const std::vector<geom::Vec3>& pos_two,
+ const std::vector<Real>& exp_dist,
+ Real cap){
+ //expect all all vectors to have the same length...
+ Real squared_diff = 0.0;
+ Real diff;
+ for(uint i = 0; i < pos_one.size(); ++i){
+ diff = std::min(std::abs(geom::Distance(pos_one[i],pos_two[i]) - exp_dist[i]),cap);
+ squared_diff += diff*diff;
+ }
+ return squared_diff;
+}
+
+void fill_residue_positions(const ResidueRDMap& res_dist_list, const ResidueView& res,
+ const ChainView& mdl_chain, Real cap_distance, int sequence_separation,
+ std::map<String,geom::Vec3>& positions){
+
+ AtomViewList atom_list = res.GetAtomList();
+ //let's already fill in the positions and check later on whether a swap is necessary
+ for(AtomViewList::const_iterator i = atom_list.begin();
+ i != atom_list.end(); ++i){
+ positions[i->GetName()] = i->GetPos();
+ }
+
+ String rname = res.GetName();
+ if(!(rname=="GLU" || rname=="ASP" || rname=="VAL" || rname=="TYR" ||
+ rname=="PHE" || rname=="LEU" || rname=="ARG")){
+ return; //no ambiguity check necessary for all other amino acids
+ }
+
+ std::map<String,geom::Vec3> original_positions;
+ std::map<String,geom::Vec3> swapped_positions;
+ AtomView atom;
+ for(AtomViewList::const_iterator i = atom_list.begin(); i !=atom_list.end(); ++i){
+ if(Swappable(rname,i->GetName())){
+ atom = res.FindAtom(SwappedName(i->GetName()));
+ if(atom){ //both atoms are valid => note, that only in this case a swap is possible
+ original_positions[i->GetName()] = i->GetPos();
+ swapped_positions[i->GetName()] = atom.GetPos();
}
}
- ResidueView rv2=mdl_chain.FindResidue(second_atom.GetResNum());
- rmsd_data.second+=1;
- int rindex2=0;
- int rindex1=mdl_res ? mdl_res.GetIndex() : -1;
- if (!only_fixed && rindex1!=-1)
- local_rmsd_data_list[rindex1].second+=1;
- if (!rv2) {
- rmsd_data.first+=(cap_distance*cap_distance);
- local_rmsd_data_list[rindex1].first+=(cap_distance*cap_distance);
- continue;
- }
- rindex2=rv2.GetIndex();
- if (!only_fixed)
- local_rmsd_data_list[rindex2].second+=1;
- AtomView av2=rv2.FindAtom(second_atom.GetAtomName());
- if (!(av1 && av2)) {
- rmsd_data.first+=(cap_distance*cap_distance);
- local_rmsd_data_list[rindex1].first+=(cap_distance*cap_distance);
- local_rmsd_data_list[rindex2].first+=(cap_distance*cap_distance);
- continue;
- }
- Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
- Real diff = mdl_dist-values.first;
- if (diff > cap_distance) {
- diff = cap_distance;
- }
- if (log) {
- LOG_VERBOSE("drmsd:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
- << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
- << mdl_dist << " " << values.first << " " << diff)
- }
- rmsd_data.first+=(diff*diff);
- if (!only_fixed) {
- local_rmsd_data_list[rindex1].first+=(diff*diff);
- local_rmsd_data_list[rindex2].first+=(diff*diff);
- }
}
- return rmsd_data;
-}
+ std::vector<geom::Vec3> or_positions;
+ std::vector<geom::Vec3> sw_positions;
+ std::vector<geom::Vec3> other_positions;
+ std::vector<Real> expected_dist;
+ ResidueView other_residue;
+
+ for(ResidueRDMap::const_iterator i = res_dist_list.begin();
+ i != res_dist_list.end(); ++i){
+ //check whether first atom is one of the swappables
+ const UniqueAtomIdentifier& first_atom = i->first.first;
+ if(original_positions.find(first_atom.GetAtomName()) == original_positions.end()) continue;
+ //we only check the second atom of the distance if it is NOT swappable
+ const UniqueAtomIdentifier& second_atom = i->first.second;
+ if(Swappable(second_atom.GetResidueName(),second_atom.GetAtomName())) continue;
+ //check whether other atom is valid and check the sequence separation
+ other_residue = mdl_chain.FindResidue(second_atom.GetResNum());
+ if(!other_residue) continue;
+ if(std::abs(res.GetNumber().GetNum() - other_residue.GetNumber().GetNum()) <= sequence_separation) continue;
+ atom = other_residue.FindAtom(second_atom.GetAtomName());
+ if(!atom) continue;
+
+ or_positions.push_back(original_positions[first_atom.GetAtomName()]);
+ sw_positions.push_back(swapped_positions[first_atom.GetAtomName()]);
+ expected_dist.push_back(i->second.first);
+ other_positions.push_back(atom.GetPos());
+ }
-void drmsdt_check_and_swap(const GlobalRDMap& glob_dist_list, const EntityView& mdl, int sequence_separation, Real cap_distance, std::vector<std::pair<Real, long int> > local_rmsd_data_list)
-{
- ChainView mdl_chain=mdl.GetChainList()[0];
- XCSEditor edi=mdl.GetHandle().EditXCS(BUFFERED_EDIT);
- for (GlobalRDMap::const_iterator i=glob_dist_list.begin(); i!=glob_dist_list.end(); ++i) {
- ResNum rnum = i->first;
- if (i->second.size()==0) {
- continue;
+ Real diff_orig = calc_squared_diff(or_positions,other_positions,expected_dist, cap_distance);
+ Real diff_swapped = calc_squared_diff(sw_positions,other_positions,expected_dist, cap_distance);
+ //finally swap the stuff if necessary
+ if(diff_swapped < diff_orig){
+ for(std::map<String,geom::Vec3>::iterator i = swapped_positions.begin();
+ i != swapped_positions.end(); ++i){
+ positions[i->first] = i->second;
}
- ResidueView mdl_res=mdl_chain.FindResidue(rnum);
- if (!mdl_res) {
- continue;
+ }
+}
+
+void fill_positions(const GlobalRDMap& glob_dist_list, const ChainView& mdl_chain,
+ Real cap_distance, int sequence_separation,
+ std::map<ResNum, std::map<String, geom::Vec3> >& positions){
+
+ ResidueView actual_res;
+ for(GlobalRDMap::const_iterator i = glob_dist_list.begin();
+ i != glob_dist_list.end(); ++i){
+ actual_res = mdl_chain.FindResidue(i->first);
+ if(actual_res){
+ std::map<String,geom::Vec3> residue_positions;
+ fill_residue_positions(i->second, actual_res, mdl_chain,
+ cap_distance, sequence_separation,
+ residue_positions);
+ if(!residue_positions.empty()) positions[i->first] = residue_positions;
}
- String rname = mdl_res.GetName();
- if (!(rname=="GLU" || rname=="ASP" || rname=="VAL" || rname=="TYR" ||
- rname=="PHE" || rname=="LEU" || rname=="ARG")) {
+ }
+}
+
+void fill_values(const GlobalRDMap& glob_dist_list,
+ const std::map<ResNum, std::map<String, geom::Vec3> >& positions,
+ Real cap_distance, int sequence_separation,
+ std::map<ResNum, std::pair<Real,long int> >& drmsd_values){
+
+ ResNum rnum_one, rnum_two;
+ std::vector<geom::Vec3> positions_one, positions_two;
+ std::vector<Real> expected_distances;
+ std::map<ResNum, std::map<String, geom::Vec3> >::const_iterator res_positions_one, res_positions_two;
+ std::map<String,geom::Vec3>::const_iterator pos_one, pos_two;
+ int penalties;
+ Real squared_diff;
+ int num_interactions;
+ Real squared_cap_distance = cap_distance * cap_distance;
+
+ for(GlobalRDMap::const_iterator i = glob_dist_list.begin();
+ i != glob_dist_list.end(); ++i){
+ rnum_one = i->first;
+ res_positions_one = positions.find(rnum_one);
+ if(res_positions_one == positions.end()){
+ //this residue is missing, so we give it the full penalty
+ drmsd_values[rnum_one] = std::make_pair(i->second.size()*squared_cap_distance,i->second.size());
continue;
}
- std::pair<long int, long int> ov1=calc_rmsd(i->second, rnum,mdl_chain, sequence_separation,
- cap_distance, true, false, local_rmsd_data_list,true);
-
- std::pair<long int, long int> ov2=calc_rmsd(i->second, rnum, mdl_chain, sequence_separation,
- cap_distance, true, true, local_rmsd_data_list,true);
-
- if (std::sqrt(ov1.first/static_cast<Real>(ov1.second))>(std::sqrt(ov2.first/static_cast<Real>(ov2.second)))) {
-
- AtomViewList atoms=mdl_res.GetAtomList();
- for (AtomViewList::iterator j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
- if (Swappable(rname, j->GetName())) {
- edi.RenameAtom(j->GetHandle(), SwappedName(j->GetName()));
- }
+ positions_one.clear();
+ positions_two.clear();
+ expected_distances.clear();
+ penalties = 0;
+
+ for(ResidueRDMap::const_iterator j = i->second.begin(); j != i->second.end(); ++j){
+ //check sequence separation
+ rnum_two = j->first.second.GetResNum();
+ if(std::abs(rnum_one.GetNum() - rnum_two.GetNum()) <= sequence_separation) continue;
+ //if residue is not present in the positions map, the positions are also missing in the
+ //model => penalty
+ res_positions_two = positions.find(rnum_two);
+ if(res_positions_two == positions.end()){
+ ++penalties;
+ continue;
}
+ //check whether both positions are present in the positions map
+ pos_one = res_positions_one->second.find(j->first.first.GetAtomName());
+ pos_two = res_positions_two->second.find(j->first.second.GetAtomName());
+ if(pos_one == res_positions_one->second.end() || pos_two == res_positions_two->second.end()){
+ ++penalties; //one of the atoms is missing
+ continue;
+ }
+ positions_one.push_back(pos_one->second);
+ positions_two.push_back(pos_two->second);
+ expected_distances.push_back(j->second.first);
+ }
+ squared_diff = calc_squared_diff(positions_one, positions_two,
+ expected_distances, cap_distance);
+ num_interactions = positions_one.size();
+ //add the penalty values
+ if(penalties > 0){
+ squared_diff += squared_cap_distance*penalties;
+ num_interactions += penalties;
}
+ drmsd_values[rnum_one] = std::make_pair(squared_diff,num_interactions);
}
}
-
-}
+}//ns
std::pair<Real,long int> DistanceRMSDTest(const EntityView& mdl, const GlobalRDMap& glob_dist_list,
- Real cap_distance, int sequence_separation, const String& local_drmsdt_property_string)
-{
+ Real cap_distance, int sequence_separation,
+ const String& local_drmsdt_property_string){
if (!mdl.GetResidueCount()) {
LOG_WARNING("model structures doesn't contain any residues");
return std::make_pair<long int,long int>(0,0);
@@ -127,53 +186,47 @@ std::pair<Real,long int> DistanceRMSDTest(const EntityView& mdl, const GlobalRDM
LOG_WARNING("global reference list is empty");
return std::make_pair<long int,long int>(0,0);
}
- std::vector<std::pair<Real, long int> > local_rmsd_data_list(mdl.GetResidueCount(), std::pair<Real, long int>(0, 0));
- drmsdt_check_and_swap(glob_dist_list,mdl,sequence_separation, cap_distance, local_rmsd_data_list);
+
+ //every residue gets a map of positions
+ std::map<ResNum, std::map<String, geom::Vec3> > positions;
+ //every residue will have a sum of squared distances and number of distances
+ std::map<ResNum, std::pair<Real,long int> > drmsd_values;
+ //currently we're only looking at the first chain
ChainView mdl_chain=mdl.GetChainList()[0];
- local_rmsd_data_list.clear();
- std::pair<Real, long int> total_ov(0, 0);
- for (GlobalRDMap::const_iterator i=glob_dist_list.begin(), e=glob_dist_list.end(); i!=e; ++i) {
- ResNum rn = i->first;
- if (i->second.size()!=0) {
- std::pair<Real, long int> ov1=calc_rmsd(i->second, rn, mdl_chain, sequence_separation, cap_distance, false, false, local_rmsd_data_list,true);
- total_ov.first+=ov1.first;
- total_ov.second+=ov1.second;
- }
- }
-
- for (GlobalRDMap::const_iterator i=glob_dist_list.begin(),
- e=glob_dist_list.end();i!=e; ++i) {
- ResNum rn = i->first;
- if(local_drmsdt_property_string!="") {
- ResidueView mdlr=mdl_chain.FindResidue(rn);
- if (mdlr.IsValid()) {
- int mdl_res_index =mdlr.GetIndex();
- Real local_rmsd=sqrt(local_rmsd_data_list[mdl_res_index].first/(static_cast<Real>(local_rmsd_data_list[mdl_res_index].second) ? static_cast<Real>(local_rmsd_data_list[mdl_res_index].second) : 1));
- mdlr.SetFloatProp(local_drmsdt_property_string, local_rmsd);
- mdlr.SetFloatProp(local_drmsdt_property_string+"_sum", local_rmsd_data_list[mdl_res_index].first);
- mdlr.SetIntProp(local_drmsdt_property_string+"_count", local_rmsd_data_list[mdl_res_index].second);
- }
+ fill_positions(glob_dist_list, mdl_chain, cap_distance,
+ sequence_separation,positions);
+ fill_values(glob_dist_list, positions, cap_distance,
+ sequence_separation, drmsd_values);
+
+ Real total_squared_diff = 0.0;
+ long int total_num_interactions = 0;
+ Real drmsd;
+ std::pair<Real, long int> residue_data;
+ ResidueView actual_residue;
+ for(GlobalRDMap::const_iterator i = glob_dist_list.begin();
+ i != glob_dist_list.end(); ++i){
+ residue_data = drmsd_values[i->first];
+ total_squared_diff += residue_data.first;
+ total_num_interactions += residue_data.second;
+ actual_residue = mdl_chain.FindResidue(i->first);
+ if(actual_residue){
+ drmsd = residue_data.second > 0 ? std::sqrt(residue_data.first/residue_data.second) : 0;
+ actual_residue.SetFloatProp(local_drmsdt_property_string, drmsd);
+ actual_residue.SetFloatProp(local_drmsdt_property_string+"_sum",residue_data.first);
+ actual_residue.SetFloatProp(local_drmsdt_property_string+"_count",residue_data.second);
}
}
- local_rmsd_data_list.clear();
- return std::make_pair<Real,long int>(total_ov.first,total_ov.second);
+ drmsd = total_num_interactions > 0 ? std::sqrt(total_squared_diff/total_num_interactions) : 0;
+ return std::make_pair(drmsd,total_num_interactions);
}
Real DRMSD(const EntityView& v, const GlobalRDMap& global_dist_list, Real cap_distance, int sequence_separation)
{
String label="localdrmsd";
- std::pair<Real,long int> total_ov=alg::DistanceRMSDTest(v, global_dist_list, cap_distance, sequence_separation, label);
-
- Real calcdrmsd = static_cast<Real>(total_ov.first)/(static_cast<Real>(total_ov.second) ? static_cast<Real>(total_ov.second) : 1);
-
- return std::sqrt(calcdrmsd);
+ std::pair<Real,long int> result=alg::DistanceRMSDTest(v, global_dist_list, cap_distance, sequence_separation, label);
+ return result.first;
}
-
-
-
-
-
-}}}
+}}} //ns
diff --git a/modules/mol/alg/src/distance_rmsd_test.hh b/modules/mol/alg/src/distance_rmsd_test.hh
index 12e4ec86646d7241aa6649f19b512f54cb95df17..bd583ed0210a8f3e276432ba5e75162d6f3ffc85 100644
--- a/modules/mol/alg/src/distance_rmsd_test.hh
+++ b/modules/mol/alg/src/distance_rmsd_test.hh
@@ -52,7 +52,7 @@ namespace ost { namespace mol { namespace alg {
/// If a string is provided as an argument to the function, residue-per-residue statistics are stored as
/// residue properties. Specifically, the local residue-based Distance RMSD score is stored in a float property
/// as the provided string, while the residue-based sum of squared distances and the number of distances checked
-/// are saved in two properties named <string>_sum (a float property) and <string>_count (an int property).
+/// are saved in two properties named [string]_sum (a float property) and [string]_count (an int property).
std::pair<Real,long int> DLLEXPORT_OST_MOL_ALG
DistanceRMSDTest(const EntityView& mdl,
const GlobalRDMap& glob_dist_list,
diff --git a/modules/mol/alg/src/domain_find.cc b/modules/mol/alg/src/domain_find.cc
new file mode 100644
index 0000000000000000000000000000000000000000..0d5d9ba6147f42521a8e38b4f33a6a16f336d4d5
--- /dev/null
+++ b/modules/mol/alg/src/domain_find.cc
@@ -0,0 +1,383 @@
+#include <boost/thread.hpp>
+
+#include <ost/img/image_factory.hh>
+#include <ost/mol/atom_view.hh>
+#include <ost/mol/residue_view.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/img/image_handle.hh>
+#include <ost/mol/residue_view.hh>
+#include <ost/seq/alignment_handle.hh>
+#include <ost/mol/alg/domain_find.hh>
+#include <ost/mol/alg/adjacency_bitmap.hh>
+
+using namespace ost::seq;
+using namespace ost::mol;
+using namespace ost::img;
+using namespace ost;
+
+namespace ost { namespace mol { namespace alg {
+
+int clear_component(const AdjacencyBitmap& bmap, std::vector<int>& components,
+ int x, int comp_id, int offset) {
+ int count=1;
+ components[offset+x]=-1;
+ for (size_t y=x+1; y<bmap.size(); ++y) {
+ if (components[offset+y]==comp_id && bmap.get(x, y) && bmap.defined(x, y)) {
+ count+=clear_component(bmap, components, y, comp_id, offset);
+ }
+ }
+ return count;
+}
+
+int label_component(const AdjacencyBitmap& bmap, std::vector<int>& components,
+ int x, int comp_id, int offset) {
+ int count=1;
+ components[offset+x]=comp_id;
+ for (size_t y=x+1; y<bmap.size(); ++y) {
+ if (components[offset+y]==-2 && bmap.get(x, y) && bmap.defined(x, y)) {
+ count+=label_component(bmap, components, y, comp_id, offset);
+ }
+ }
+ return count;
+}
+
+// use template to force generation of two loops, one without image update
+// and one with image update. we for sure don't want to have the image update
+// when running DomainFind in fast mode
+//
+// this is the single-threaded variant
+template <bool update_img>
+void update_edge_weights_st(AdjacencyBitmap* adj1p,
+ AdjacencyBitmap* adj2p,
+ img::ImageHandle& im,
+ int n, Real tolerance,
+ int offset) {
+ for (size_t i=0; i<adj1p->size(); ++i) {
+ for (size_t j=i+1; j<adj1p->size(); ++j) {
+ OverlapResult ov = adj1p->Overlap(i, j);
+ if (ov.defined>10) {
+ // fixme: avoid promotion to float. totally unneccessary.
+ Real set = (static_cast<Real>(ov.nominator)/
+ static_cast<Real>(ov.denominator ? ov.denominator : 1));
+ adj2p->set(i, j, set>=tolerance);
+ adj2p->set(j, i, set>=tolerance);
+ if (update_img) {
+ im.SetReal(img::Point(i+offset, j+offset, n), set);
+ im.SetReal(img::Point(j+offset, i+offset, n), set);
+ }
+ } else {
+ adj2p->set(i, j, false, false);
+ adj2p->set(j, i, false, false);
+ if (update_img) {
+ im.SetReal(img::Point(i+offset, j+offset, n), 0);
+ im.SetReal(img::Point(j+offset, i+offset, n), 0);
+ }
+ }
+ }
+ }
+}
+
+template <bool update_img>
+struct update_edge_weights_mt {
+
+ AdjacencyBitmap* adj1p;
+ AdjacencyBitmap* adj2p;
+ Real tolerance;
+ size_t start;
+ size_t end;
+
+ img::ImageHandle im;
+ int n;
+ int offset;
+ update_edge_weights_mt(AdjacencyBitmap* a1p, AdjacencyBitmap* a2p,
+ Real tol, size_t s, size_t e,
+ img::ImageHandle i, int nth,
+ int o):
+ adj1p(a1p), adj2p(a2p), tolerance(tol), start(s),
+ end(std::min(a1p->size(), e)), im(i), n(nth),
+ offset(o) {}
+
+ void operator()() {
+ for (size_t i=start; i<end; ++i) {
+ for (size_t j=0; j<adj1p->size(); ++j) {
+ if (i==j) continue;
+ OverlapResult ov = adj1p->Overlap(i, j);
+ if (ov.defined>10) {
+ // fixme: avoid promotion to float. totally unneccessary.
+ Real set = (static_cast<Real>(ov.nominator)/
+ static_cast<Real>(ov.denominator ? ov.denominator : 1));
+ adj2p->set(i, j, set>=tolerance);
+ if (update_img) {
+ im.SetReal(img::Point(i+offset, j+offset, n), set);
+ }
+ } else {
+ adj2p->set(i, j, false, false);
+ if (update_img) {
+ im.SetReal(img::Point(i+offset, j+offset, n), 0.0);
+ }
+ }
+ }
+ }
+ }
+};
+
+AdjacencyBitmap optimize_domains(AdjacencyBitmap adj1, Real tolerance,
+ img::ImageHandle& im,
+ bool update_img,
+ int num_threads,
+ int offset,
+ int full_size) {
+
+ const static int MAX_ITERATIONS=10;
+ AdjacencyBitmap adj2(adj1.size());
+
+ AdjacencyBitmap* adj1p=&adj1;
+ AdjacencyBitmap* adj2p=&adj2;
+ int n=MAX_ITERATIONS;
+ if (update_img) {
+ im = img::CreateImage(img::Size(full_size, full_size, n+1));
+ for (size_t i=0;i<adj1.size();++i) {
+ for (size_t j=0;j<adj1.size();++j) {
+ if (i==j) {
+ im.SetReal(img::Point(i+offset, j+offset, n), 0.0);
+ } else {
+ im.SetReal(img::Point(i+offset, j+offset, n),
+ adj1.get(i, j));
+ }
+ }
+ }
+ }
+
+ if (num_threads>1) {
+ while (n>0) {
+ --n;
+ boost::thread_group tg;
+ int rows_per_thread= ((adj1p->size()+1)/num_threads);
+ int adj_rows_per_thread = rows_per_thread;
+ if (int modulo = rows_per_thread % 64) {
+ adj_rows_per_thread = adj_rows_per_thread+64-modulo;
+ }
+ for (int i=0;i<num_threads;++i) {
+ if (size_t(i*adj_rows_per_thread) > adj1p->size()) {
+ continue;
+ }
+ if (update_img) {
+ tg.create_thread(update_edge_weights_mt<true>(adj1p, adj2p, tolerance,
+ (i+0)*adj_rows_per_thread,
+ (i+1)*adj_rows_per_thread,
+ im, n, offset));
+ } else {
+ tg.create_thread(update_edge_weights_mt<false>(adj1p, adj2p, tolerance,
+ (i+0)*adj_rows_per_thread,
+ (i+1)*adj_rows_per_thread,
+ im, n, offset));
+ }
+ }
+ tg.join_all();
+ std::swap(adj1p, adj2p);
+ }
+ return *adj1p;
+ }
+ while (n>0) {
+ --n;
+ if (update_img) {
+ update_edge_weights_st<true>(adj1p, adj2p, im, n, tolerance, offset);
+ } else {
+ update_edge_weights_st<false>(adj1p, adj2p, im, n, tolerance, offset);
+ }
+ std::swap(adj1p, adj2p);
+ }
+ return *adj1p;
+}
+
+void connected_components(const AdjacencyBitmap& adj_bitmap,
+ std::vector<int>& components, int offset) {
+ int comp_id=0;
+ for (int i=0; i<offset; ++i) {
+ components[i] = -1;
+ }
+ for (size_t i=0; i<adj_bitmap.size(); ++i) {
+ if (components[offset+i]!=-2) {
+ continue;
+ }
+ int count = label_component(adj_bitmap, components, i, comp_id, offset);
+ if (count>16) {
+ comp_id+=1;
+ } else {
+ clear_component(adj_bitmap, components, i, comp_id, offset);
+ }
+ }
+ for (size_t i=offset+adj_bitmap.size(); i<components.size(); ++i) {
+ components[i] = -1;
+ }
+}
+
+DomainsPtr Domains::FromAln(ost::seq::AlignmentHandle aln,
+ Real tolerance, Real radius, Real threshold,
+ int idx_a, int idx_b) {
+ SimilarityMatrix sim = ContactOverlapMap(aln, tolerance, OM_ABSOLUTE,
+ radius);
+ return Domains::FromCOM(sim, aln, threshold, idx_a, idx_b);
+}
+
+DomainsPtr Domains::FromCOM(const SimilarityMatrix& sim, AlignmentHandle aln,
+ Real tolerance, int idx_a, int idx_b)
+{
+ bool update_img = false;
+ AdjacencyBitmap adj1(sim, 0.5);
+ img::ImageHandle im;
+
+ AdjacencyBitmap final_adj(optimize_domains(adj1, tolerance, im,
+ update_img, 1, 0,
+ adj1.size()));
+
+ // identify connected components in the graph
+ std::vector<int> components(adj1.size(), -2);
+ connected_components(final_adj, components, 0);
+
+ DomainsMap domains_map;
+ if (idx_a>=0 && idx_b>=0) {
+ for (int i=0; i<aln.GetLength(); ++i) {
+ if (components[i]==-1) {
+ continue;
+ }
+ DomainsMap::iterator k = domains_map.find(components[i]);
+ if (k == domains_map.end()) {
+ std::pair<DomainsMap::iterator, bool> k2;
+ k2 = domains_map.insert(std::make_pair(components[i],
+ Domain(EntityViewList())));
+ k = k2.first;
+ k->second.views.push_back(aln.GetSequence(idx_a).GetAttachedView().CreateEmptyView());
+ k->second.views.push_back(aln.GetSequence(idx_b).GetAttachedView().CreateEmptyView());
+ }
+ if (ResidueView r=aln.GetResidue(idx_a, i)) {
+ k->second.views[0].AddResidue(r.GetHandle(), ViewAddFlag::INCLUDE_ALL);
+ }
+ if (ResidueView r=aln.GetResidue(idx_b, i)) {
+ k->second.views[1].AddResidue(r.GetHandle(), ViewAddFlag::INCLUDE_ALL);
+ }
+ }
+ }
+
+ int num_free = 0;
+
+ Real free_d = 0, free_s = 0;
+
+ for (size_t i=0; i<adj1.size(); ++i) {
+ if (components[i]==-1) {
+ num_free+=1;
+ }
+ for (size_t j=i+1; j<adj1.size(); ++j) {
+ if (!final_adj.defined(i, j)) {
+ continue;
+ }
+ if (components[i] == -1 || components[j] == -1) {
+ free_d+=1;
+ if (sim.Get(i, j)>=0)
+ free_s+=sim.Get(i, j);
+ continue;
+ }
+ Real s = sim.Get(i, j);
+ if (s<0) {
+ continue;
+ }
+ if (components[i] == components[j]) {
+ domains_map.find(components[i])->second.intra_s+= adj1.get(i, j);
+ domains_map.find(components[i])->second.intra_d+= 1;
+ } else {
+ domains_map.find(components[i])->second.inter_s+=adj1.get(i, j);
+ domains_map.find(components[i])->second.inter_d+= 1;
+ domains_map.find(components[j])->second.inter_s+= adj1.get(i, j);
+ domains_map.find(components[j])->second.inter_d+= 1;
+ }
+ }
+ }
+
+ DomainsPtr domains(new Domains);
+ for (DomainsMap::iterator i = domains_map.begin(),
+ e = domains_map.end(); i!=e; ++i) {
+ domains->domains_.push_back(i->second);
+ }
+ domains->num_free_ = num_free;
+ domains->components_ = components;
+ domains->free_d_ = free_d;
+ domains->free_s_ = free_s;
+ if (im.IsValid())
+ domains->adj_map_ = im;
+ return domains;
+}
+
+
+std::pair<int, int> get_defined_region(const DistanceMatrix& dmat_a,
+ const DistanceMatrix& dmat_b) {
+ int start = 0;
+ for (int i=0; i<dmat_a.GetSize(); ++i) {
+ if (dmat_a.Get(i, i)>=0.0 && dmat_b.Get(i, i)>=0.0) {
+ break;
+ }
+ start++;
+ }
+ if (start == dmat_a.GetSize()) {
+ // the two don't have an overlap
+ return std::make_pair(start, start);
+ }
+ int end = dmat_a.GetSize();
+ for (int i=dmat_a.GetSize()-1; i>=0; --i) {
+ if (dmat_a.Get(i, i)>=0.0 && dmat_b.Get(i, i)>=0.0) {
+ break;
+ }
+ end--;
+ }
+ return std::make_pair(start, end);
+}
+
+DomainsPtr Domains::FromDistMats(const DistanceMatrix& dmat_a,
+ const DistanceMatrix& dmat_b,
+ Real tolerance, Real radius,
+ Real threshold, int num_threads,
+ bool defined_only,
+ bool update_img)
+{
+ // for distance matrices derived from target-template alignments, C-
+ // and N-terminal regions of the distance map are undefined, since
+ // they are not covered in the alignment. To avoid doing a full-blown
+ // O(n^3) update on the full distance matrix, we first identify regions
+ // of the distance map which are defined and perform the update only on
+ // that part of the map.
+ std::pair<int, int> region(0, dmat_a.GetSize());
+ if (defined_only)
+ region = get_defined_region(dmat_a, dmat_b);
+
+ DomainsPtr domains(new Domains);
+
+ if (region.first == region.second) {
+ // there is no overlap whatsoever between the two distance matrices.
+ // all present residues will thus be assigned to the unassigned
+ // component (designated as -1).
+ domains->components_.resize(dmat_a.GetSize(), -1);
+ return domains;
+ }
+
+ // derive initial connectivity bitmap from the two distance matrices
+ AdjacencyBitmap adj1(dmat_a, dmat_b, tolerance, radius, region.first,
+ region.second);
+
+ img::ImageHandle im;
+
+ // optimize domains
+ AdjacencyBitmap final_adj(optimize_domains(adj1, threshold, im,
+ update_img, num_threads,
+ region.first,
+ dmat_a.GetSize()));
+ // identify connected components in the graph
+ std::vector<int> components(dmat_a.GetSize(), -2);
+ connected_components(final_adj, components, region.first);
+ domains->components_ = components;
+ if (im.IsValid())
+ domains->adj_map_ = im;
+ return domains;
+
+}
+
+}}}
+
diff --git a/modules/mol/alg/src/domain_find.hh b/modules/mol/alg/src/domain_find.hh
new file mode 100644
index 0000000000000000000000000000000000000000..f3ce2b0ddd19a8b0c3bc3af9362b74469da5fa41
--- /dev/null
+++ b/modules/mol/alg/src/domain_find.hh
@@ -0,0 +1,81 @@
+#ifndef OST_MOL_ALG_DOMAIN_FIND_HH
+#define OST_MOL_ALG_DOMAIN_FIND_HH
+
+#include <ost/seq/alignment_handle.hh>
+
+#include "module_config.hh"
+#include "contact_overlap.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+struct Domain {
+ Domain(const ost::mol::EntityViewList& v):
+ inter_s(0), inter_d(0), intra_s(0), intra_d(0), views(v) {}
+ Domain(): inter_s(0), inter_d(0), intra_s(0), intra_d(0) {}
+
+ Real inter_s;
+ Real inter_d;
+ Real intra_s;
+ Real intra_d;
+
+ bool operator==(const Domain& rhs) const {
+ return views==rhs.views && inter_s == rhs.inter_s &&
+ inter_d == rhs.inter_d && intra_s == rhs.intra_s &&
+ intra_d == rhs.intra_d;
+ }
+ ost::mol::EntityViewList views;
+};
+
+
+class Domains;
+
+typedef boost::shared_ptr<Domains> DomainsPtr;
+
+class DLLEXPORT_OST_MOL_ALG Domains {
+public:
+
+ static DomainsPtr FromAln(ost::seq::AlignmentHandle aln,
+ Real tolerance, Real radius, Real threshold,
+ int idx_a=-1, int idx_b=-1);
+
+ static DomainsPtr FromCOM(const SimilarityMatrix& sim,
+ ost::seq::AlignmentHandle aln,
+ Real tolerance, int idx_a=-1, int idx_b=-1);
+
+ // version of domain find which operates on two distances matrices
+ // we on purpose only return the connected components, since the
+ // distance matrices may not need to correpsond to an actual
+ // entity view.
+ static DomainsPtr FromDistMats(const DistanceMatrix& dmat_a,
+ const DistanceMatrix& dmat_b,
+ Real tolerance,
+ Real radius,
+ Real threshold,
+ int num_threads,
+ bool defined_only,
+ bool adj_map);
+ size_t GetNumFreeResidues() const { return num_free_; }
+
+ Real GetFreeD() const { return free_d_; }
+ Real GetFreeS() const { return free_s_; }
+
+ const std::vector<Domain>& GetDomains() const { return domains_; }
+ const std::vector<int>& GetComponents() const { return components_; }
+
+ ost::img::ImageHandle GetAdjMap() const { return adj_map_; }
+private:
+ Domains(): num_free_(0), free_s_(0), free_d_(0) {}
+ // holds the steps of the algorithm. mainly for debuggin purposes
+ ost::img::ImageHandle adj_map_;
+ int num_free_;
+ Real free_s_;
+ Real free_d_;
+ std::vector<Domain> domains_;
+ std::vector<int> components_;
+};
+
+typedef std::map<int, Domain> DomainsMap;
+
+}}}
+#endif
+
diff --git a/modules/mol/alg/src/lddt.cc b/modules/mol/alg/src/lddt.cc
index 2509a0af9371ef15d6ec18d9d744bc916340893d..90c6819dfb6974e902ca02ef908aad8492f8fac2 100644
--- a/modules/mol/alg/src/lddt.cc
+++ b/modules/mol/alg/src/lddt.cc
@@ -18,7 +18,9 @@
//------------------------------------------------------------------------------
#include <iomanip>
#if defined (_MSC_VER)
-#define BOOST_ALL_DYN_LINK 1
+ #define BOOST_ALL_DYN_LINK 1
+ #include <BaseTsd.h>
+ typedef SSIZE_T ssize_t;
#endif
#include <boost/program_options.hpp>
#include <boost/filesystem/fstream.hpp>
@@ -142,9 +144,13 @@ CompoundLibPtr load_compound_lib(const String& custom_path)
if (!_NSGetExecutablePath(result, &size)) {
exe_path=String(result);
}
- #else
- ssize_t count = readlink( "/proc/self/exe", result, 1024 );
- exe_path = std::string( result, (count > 0) ? count : 0 );
+ #else
+ #if defined (_MSC_VER)
+ // todo find exe path on Windows
+ #else
+ ssize_t count = readlink( "/proc/self/exe", result, 1024 );
+ exe_path = std::string( result, (count > 0) ? count : 0 );
+ #endif
#endif
if (exe_path.empty()) {
std::cerr << "Could not determine the path of the molck executable. Will only "
@@ -506,7 +512,6 @@ int main (int argc, char **argv)
ResNum rnum = ritv.GetNumber();
bool assessed = false;
String assessed_string="No";
- bool quality_problems = false;
String quality_problems_string="No";
Real lddt_local = -1;
String lddt_local_string="-";
@@ -519,12 +524,10 @@ int main (int argc, char **argv)
}
if (ritv.HasProp("stereo_chemical_violation_sidechain") ||
ritv.HasProp("steric_clash_sidechain")) {
- quality_problems = true;
quality_problems_string="Yes";
}
if (ritv.HasProp("stereo_chemical_violation_backbone") ||
ritv.HasProp("steric_clash_backbone")) {
- quality_problems = true;
quality_problems_string="Yes+";
}
diff --git a/modules/mol/alg/src/local_dist_diff_test.hh b/modules/mol/alg/src/local_dist_diff_test.hh
index f9013c97566e4edb261bb3ee4e0a2b8be90f53a4..9dd2f230617ac1b0b795ec6a7e467a80c1485655 100644
--- a/modules/mol/alg/src/local_dist_diff_test.hh
+++ b/modules/mol/alg/src/local_dist_diff_test.hh
@@ -45,7 +45,7 @@ namespace ost { namespace mol { namespace alg {
/// If a string is provided as an argument to the function, residue-per-residue statistics are stored as
/// residue properties. Specifically, the local residue-based lddt score is stored in a float property named
/// as the provided string, while the residue-based number of conserved and total distances are saved in two
-/// int properties named <string>_conserved and <string>_total.
+/// int properties named [string]_conserved and [string]_total.
std::pair<long int,long int> DLLEXPORT_OST_MOL_ALG
LocalDistDiffTest(const EntityView& mdl, const GlobalRDMap& dist_list,
std::vector<Real> cutoff_list, int sequence_separation = 0,
@@ -67,7 +67,7 @@ LocalDistDiffTest(const EntityView& mdl, const GlobalRDMap& dist_list,
/// If a string is provided as an argument to the function, residue-per-residue statistics are stored as
/// residue properties. Specifically, the local residue-based lddt score is stored in a float property named
/// as the provided string, while the residue-based number of conserved and total distances are saved in two
-/// int properties named <string>_conserved and <string>_total.
+/// int properties named [string]_conserved and [string]_total.
Real DLLEXPORT_OST_MOL_ALG LocalDistDiffTest(const EntityView& mdl,
const EntityView& target,
Real cutoff,
diff --git a/modules/mol/alg/src/pdbize.cc b/modules/mol/alg/src/pdbize.cc
index e99366831c01bf2f4c8e4b422a4d617c1722d654..e9265312c6f07be3752229ed4eb8348fb736df1a 100644
--- a/modules/mol/alg/src/pdbize.cc
+++ b/modules/mol/alg/src/pdbize.cc
@@ -29,9 +29,9 @@
namespace ost { namespace mol { namespace alg {
-DLLEXPORT const char* POLYPEPTIDE_CHAIN_NAMES="ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz";
-DLLEXPORT const char* LIGAND_CHAIN_NAME="_";
-DLLEXPORT const char* WATER_CHAIN_NAME="-";
+const char* POLYPEPTIDE_CHAIN_NAMES="ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz";
+const char* LIGAND_CHAIN_NAME="_";
+const char* WATER_CHAIN_NAME="-";
namespace {
diff --git a/modules/mol/alg/src/similarity_matrix.cc b/modules/mol/alg/src/similarity_matrix.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e44ef5f67d4ed4b8240c7a009320c3c85b65f62f
--- /dev/null
+++ b/modules/mol/alg/src/similarity_matrix.cc
@@ -0,0 +1,41 @@
+#include "similarity_matrix.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+
+ost::img::ImageHandle SimilarityMatrix::AsImage(bool full) const
+{
+ ost::img::Size img_size(this->GetSize(), this->GetSize());
+ ost::img::ImageHandle im=ost::img::CreateImage(img_size);
+ for (int i=0; i<this->GetSize(); ++i) {
+
+ for (int j=full ? 0 : i+1; j<this->GetSize(); ++j) {
+ im.SetReal(ost::img::Point(i, j), this->Get(i, j));
+ im.SetReal(ost::img::Point(j, i), this->Get(i, j));
+ }
+ }
+ return im;
+}
+
+SimilarityMatrix SimilarityMatrix::Load(const String& filename)
+{
+ std::ifstream istream(filename.c_str(), std::ios::binary);
+ size_t the_size;
+ istream.read(reinterpret_cast<char*>(&the_size), sizeof(size_t));
+ SimilarityMatrix sim(the_size);
+ istream.read(reinterpret_cast<char*>(&sim.Data().front()),
+ sizeof(Real)*sim.Data().size());
+ return sim;
+}
+
+void SimilarityMatrix::Save(const String& filename)
+{
+ std::ofstream of(filename.c_str(), std::ios::binary);
+ size_t the_size=this->GetSize();
+ of.write(reinterpret_cast<const char*>(&the_size), sizeof(size_t));
+ of.write(reinterpret_cast<const char*>(&this->Data().front()),
+ sizeof(Real)*this->Data().size());
+}
+
+}}}
+
diff --git a/modules/mol/alg/src/similarity_matrix.hh b/modules/mol/alg/src/similarity_matrix.hh
new file mode 100644
index 0000000000000000000000000000000000000000..f871485863d7299701bf69757263275e1dd7db1a
--- /dev/null
+++ b/modules/mol/alg/src/similarity_matrix.hh
@@ -0,0 +1,36 @@
+#ifndef OST_MOL_ALG_SIMILARITY_MATRIX_HH
+#define OST_MOL_ALG_SIMILARITY_MATRIX_HH
+
+#include <limits>
+#include <fstream>
+#include <ost/tri_matrix.hh>
+#include <ost/img/image.hh>
+#include "module_config.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+// triangular distance matrix
+class DLLEXPORT_OST_MOL_ALG SimilarityMatrix : public ost::TriMatrix<Real> {
+public:
+ /// \brief initialise similarity matrix with n datapoints.
+ ///
+ /// The distances are initialised with the default value
+ ///
+ /// \param n is the number of datapoints
+ /// \param def_val is the default similarity
+ SimilarityMatrix(int n, Real def_val=std::numeric_limits<Real>::min()):
+ ost::TriMatrix<Real>(n, def_val)
+ { }
+
+ ost::img::ImageHandle AsImage(bool full=false) const;
+
+ static SimilarityMatrix Load(const String& filename);
+
+ void Save(const String& filename);
+
+};
+
+}}}
+
+#endif
+
diff --git a/modules/mol/alg/src/structure_analysis.cc b/modules/mol/alg/src/structure_analysis.cc
index c2d02f0ad7fc7657fdce9523def4f1a5788fa09a..b561b0a7fb7d7607217190317c18d643aedd62ea 100644
--- a/modules/mol/alg/src/structure_analysis.cc
+++ b/modules/mol/alg/src/structure_analysis.cc
@@ -59,10 +59,42 @@ Real CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapH
}
return sum/float(vl.size());
}
+
+std::vector< std::vector<Real> > PariwiseDistanceMatrix(const EntityView& view1, const EntityView& view2){
+ std::vector< std::vector<Real> > dist_mat;
+ unsigned int n1=view1.GetAtomCount(),n2=view2.GetAtomCount();
+ dist_mat.resize(n1,std::vector<Real>(n2,0));
+ AtomViewList atoms1=view1.GetAtomList(),atoms2=view2.GetAtomList();
+ for (unsigned int i=0; i!=n1; ++i){
+ for (unsigned int j=0; j!=n2; ++j) {
+ dist_mat[i][j]=geom::Distance(atoms1[i].GetPos(),atoms2[j].GetPos());
+ }
+ }
+ return dist_mat;
+}
+std::vector< std::vector<Real> > PariwiseDistanceMatrix(const EntityView& view){
+ std::vector< std::vector<Real> > dist_mat;
+ unsigned int n=view.GetAtomCount();
+ //dist_mat.resize(n,std::vector<Real>(n,0));
+ AtomViewList atoms1=view.GetAtomList(),atoms2=view.GetAtomList();
+ for (unsigned int i=0; i!=n; ++i){
+ dist_mat.push_back(std::vector<Real>(n-i-1,0));
+ for (unsigned int j=i+1; j!=n; ++j) {
+ dist_mat[i][j-i-1]=geom::Distance(atoms1[i].GetPos(),atoms2[j].GetPos());
+ }
+ }
+ return dist_mat;
+}
+
+
#endif
-void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec, bool group_residues){
+void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 ucell_size, \
+ const geom::Vec3 ucell_angles, bool group_residues,bool follow_bonds){
mol::XCSEditor edi=eh.EditXCS(mol::BUFFERED_EDIT);
+ bool orthogonal;
+ if (ucell_angles==geom::Vec3()){ orthogonal=true; }
+ else { orthogonal=false; }
if (group_residues) {
geom::Vec3 cm,wrapped_cm,shift;
ResidueHandleList residues=eh.GetResidueList();
@@ -71,14 +103,43 @@ void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom:
ResidueHandle r=residues[i];
AtomHandleList atoms=r.GetAtomList();
geom::Vec3 ref_pos=atoms[0].GetPos();
- for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
- edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,basis_vec));
- }
+ if (follow_bonds) {
+ int natoms=r.GetAtomCount(),n=1,cycles=1;
+ AtomHandle a=atoms[0];
+ AtomHandleList wrapped_atoms;
+ wrapped_atoms.reserve(natoms);
+ wrapped_atoms.push_back(a);
+ while (n<natoms and cycles<natoms) {
+ ++cycles;
+ for (AtomHandleList::iterator a=wrapped_atoms.begin(), e=wrapped_atoms.end(); a!=e; ++a) {
+ AtomHandleList al=(*a).GetBondPartners();
+ ref_pos=(*a).GetPos();
+ for (AtomHandleList::iterator a2=al.begin(), e2=al.end(); a2!=e2; ++a2) {
+ if (std::find(wrapped_atoms.begin(),wrapped_atoms.end(), *a2) !=wrapped_atoms.end()){
+ continue;
+ } else {
+ ++n;
+ wrapped_atoms.push_back(*a2);
+ if (orthogonal) {
+ edi.SetAtomPos((*a2),geom::WrapVec3((*a2).GetPos(),ref_pos,ucell_size));
+ } else {
+ edi.SetAtomPos((*a2),geom::WrapVec3((*a2).GetPos(),ref_pos,ucell_size,ucell_angles));
+ }}}}}
+ } else {
+ if (orthogonal) {
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,ucell_size));
+ }}
+ else {
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,ucell_size,ucell_angles));
+ }}}
}
for (unsigned int i=0; i<n_residues; ++i) {
ResidueHandle r=residues[i];
cm=r.GetCenterOfMass();
- wrapped_cm=geom::WrapVec3(cm,cell_center,basis_vec);
+ if (orthogonal) {wrapped_cm=geom::WrapVec3(cm,cell_center,ucell_size);}
+ else {wrapped_cm=geom::WrapVec3(cm,cell_center,ucell_size,ucell_angles);}
if (wrapped_cm==cm) continue;
AtomHandleList atoms=r.GetAtomList();
unsigned int n_atoms=r.GetAtomCount();
@@ -90,9 +151,14 @@ void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom:
}
else {
AtomHandleList atoms=eh.GetAtomList();
- for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
- edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),cell_center,basis_vec));
- }
+ if (orthogonal){
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),cell_center,ucell_size));
+ }}
+ else {
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),cell_center,ucell_size,ucell_angles));
+ }}
}
}
diff --git a/modules/mol/alg/src/structure_analysis.hh b/modules/mol/alg/src/structure_analysis.hh
index 7ad8ad575cb0ebdb448e800748408f251fd69c49..2f450f6924fb9d0f50e558e2da1d54d1dce5606b 100644
--- a/modules/mol/alg/src/structure_analysis.hh
+++ b/modules/mol/alg/src/structure_analysis.hh
@@ -37,6 +37,8 @@ namespace ost { namespace mol { namespace alg {
std::vector<Real> DLLEXPORT_OST_MOL_ALG CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
Real DLLEXPORT_OST_MOL_ALG CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
#endif
- void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec, bool group_res=true);
+ void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 ucell_size, const geom::Vec3 ucell_angles=geom::Vec3(), bool group_res=true, bool follow_bond=true);
+ std::vector< std::vector<Real> > DLLEXPORT_OST_MOL_ALG PariwiseDistanceMatrix(const EntityView& view1, const EntityView& view2);
+ std::vector< std::vector<Real> > DLLEXPORT_OST_MOL_ALG PariwiseDistanceMatrix(const EntityView& view);
}}}//ns
#endif
diff --git a/modules/mol/alg/src/superpose_frames.cc b/modules/mol/alg/src/superpose_frames.cc
index f5cbba61073416b7c47dd05393c9104f4ee0b0b2..ef8ebe9216de6d6cbc69b918509e6c37d044367b 100644
--- a/modules/mol/alg/src/superpose_frames.cc
+++ b/modules/mol/alg/src/superpose_frames.cc
@@ -17,10 +17,7 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#include <Eigen/Core>
-#include <Eigen/Array>
-#include <Eigen/SVD>
-#include <Eigen/LU>
+#include <Eigen/Eigenvalues>
#include <ost/message.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/alg/superpose_frames.hh>
@@ -100,7 +97,7 @@ void AddSuperposedFrame(CoordGroupHandle& superposed, EMatX3& ref_mat,EMatX3& re
frame_center=frame_mat.rowwise().sum()/frame_mat.cols();
frame_centered=row_sub(frame_mat, frame_center);
//single value decomposition
- Eigen::SVD<EMat3> svd(frame_centered*ref_centered);
+ Eigen::JacobiSVD<EMat3> svd(frame_centered*ref_centered,Eigen::ComputeFullU | Eigen::ComputeFullV);
EMat3 matrixVT=svd.matrixV().transpose();
//determine rotation
Real detv=matrixVT.determinant();
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index fbc69cd1df4bf5a0c0b65709311bad34318cf735..89d6fcfdb50ef748af8c97c5a7a5041359efc8f7 100644
--- a/modules/mol/alg/src/svd_superpose.cc
+++ b/modules/mol/alg/src/svd_superpose.cc
@@ -21,10 +21,8 @@
#include <iostream>
#include <boost/bind.hpp>
-#include <Eigen/Core>
-#include <Eigen/Array>
#include <Eigen/SVD>
-#include <Eigen/LU>
+#include <Eigen/Geometry>
#include <ost/base.hh>
#include <ost/geom/vec3.hh>
@@ -94,7 +92,7 @@ Real calc_rmsd_for_ematx(const EMatX& atoms1,
const EMatX& atoms2,
const EMat4& transformation)
{
- EMatX transformed_atoms1 = EMatX::Zero(atoms1.rows(), 3);
+ EMatX transformed = EMatX::Zero(atoms1.rows(), 3);
EMatX vector = EMatX::Zero(4,1);
EMatX transformed_vector = EMatX::Zero(4,1);
@@ -103,17 +101,12 @@ Real calc_rmsd_for_ematx(const EMatX& atoms1,
for(int i=0;i<atoms1.rows();++i){
vector.block<3,1>(0,0)=atoms1.block<1,3>(i,0).transpose();
transformed_vector = transformation*vector;
- transformed_atoms1.block<1,3>(i,0)=transformed_vector.block<3,1>(0,0).transpose();
+ transformed.block<1,3>(i,0)=transformed_vector.block<3,1>(0,0).transpose();
}
- EMatX diff = EMatX::Zero(atoms1.rows(),atoms1.cols());
- EMatX squared_dist = EMatX::Zero(atoms1.rows(),1);
-
- diff = transformed_atoms1-atoms2;
- squared_dist = (diff.cwise()*diff).rowwise().sum();
-
- return sqrt(squared_dist.sum()/squared_dist.rows());
-
+ transformed = transformed - atoms2;
+ transformed = transformed.array()*transformed.array();
+ return sqrt(transformed.rowwise().sum().sum()/atoms1.rows());
}
Real CalculateRMSD(const mol::EntityView& ev1,
@@ -204,7 +197,8 @@ public:
EMatX TransformEMatX(const EMatX& mat, const EMat4& transformation) const;
- std::vector<int> CreateMatchingSubsets(const EMatX& atoms, const EMatX& atoms_ref, Real distance_threshold) const;
+ void CreateMatchingSubsets(std::vector<int>& matching_subset, const EMatX& atoms,
+ const EMatX& atoms_ref, Real distance_threshold) const;
SuperpositionResult IterativeMinimize(int ncycles, Real distance_threshold) const;
@@ -287,7 +281,7 @@ SuperpositionResult MeanSquareMinimizerImpl::IterativeMinimize(int max_cycles, R
for(;cycles<max_cycles;++cycles){
transformed_atoms = this->TransformEMatX(atoms1_, transformation_matrix);
- matching_indices = this->CreateMatchingSubsets(transformed_atoms, atoms2_, distance_threshold);
+ this->CreateMatchingSubsets(matching_indices, transformed_atoms, atoms2_, distance_threshold);
if(matching_indices.size()<3){
std::stringstream ss;
@@ -312,7 +306,7 @@ SuperpositionResult MeanSquareMinimizerImpl::IterativeMinimize(int max_cycles, R
diff = transformation_matrix_old-transformation_matrix;
- if(diff.cwise().abs().sum()<0.0001){
+ if(diff.array().abs().sum()<0.0001){
++cycles;
break;
}
@@ -348,24 +342,25 @@ EMatX MeanSquareMinimizerImpl::TransformEMatX(const EMatX& mat, const EMat4& tra
return transformed_mat;
}
-std::vector<int> MeanSquareMinimizerImpl::CreateMatchingSubsets(const EMatX& atoms, const EMatX& atoms_ref, Real distance_threshold) const{
+void MeanSquareMinimizerImpl::CreateMatchingSubsets(std::vector<int>& matching_subset,
+ const EMatX& atoms, const EMatX& atoms_ref,
+ Real distance_threshold) const{
- std::vector<int> return_vec;
+ matching_subset.clear();
EMatX diff = EMatX::Zero(atoms.rows(),atoms.cols());
EMatX dist = EMatX::Zero(atoms.rows(),1);
diff = atoms-atoms_ref;
- dist = (diff.cwise()*diff).rowwise().sum();
- dist = dist.cwise().sqrt();
+ dist = (diff.array()*diff.array()).rowwise().sum();
+
+ Real squared_dist_threshold = distance_threshold * distance_threshold;
for(int i=0; i<dist.rows(); ++i){
- if(dist(i,0) <= distance_threshold){
- return_vec.push_back(i);
+ if(dist(i,0) <= squared_dist_threshold){
+ matching_subset.push_back(i);
}
}
-
- return return_vec;
}
@@ -381,7 +376,7 @@ SuperpositionResult MeanSquareMinimizerImpl::Minimize(const EMatX& atoms, const
EMatX atoms_ref_shifted = MatrixShiftedBy(atoms_ref, avg_ref).transpose();
// determine rotational component
- Eigen::SVD<EMat3> svd(atoms_ref_shifted*atoms_shifted);
+ Eigen::JacobiSVD<EMat3> svd(atoms_ref_shifted*atoms_shifted,Eigen::ComputeFullU | Eigen::ComputeFullV);
EMatX matrixVT=svd.matrixV().transpose();
//determine rotation
@@ -469,8 +464,8 @@ SuperpositionResult SuperposeSVD(const mol::EntityView& ev1,
return result;
}
-SuperpositionResult SuperposeSVD(const std::vector<geom::Vec3>& pl1,
- const std::vector<geom::Vec3>& pl2)
+SuperpositionResult SuperposeSVD(const geom::Vec3List& pl1,
+ const geom::Vec3List& pl2)
{
MeanSquareMinimizer msm = MeanSquareMinimizer::FromPointLists(pl1, pl2);
SuperpositionResult result = msm.MinimizeOnce();
@@ -505,8 +500,8 @@ SuperpositionResult IterativeSuperposeSVD(const mol::EntityView& ev,
return result;
}
-SuperpositionResult IterativeSuperposeSVD(const std::vector<geom::Vec3>& pl1,
- const std::vector<geom::Vec3>& pl2,
+SuperpositionResult IterativeSuperposeSVD(const geom::Vec3List& pl1,
+ const geom::Vec3List& pl2,
int max_cycles,
Real distance_threshold){
diff --git a/modules/mol/alg/src/svd_superpose.hh b/modules/mol/alg/src/svd_superpose.hh
index 28ee7a0d4fea5312de3937416f6af63e6410a870..72719c2e66c5f49f7ae16917ef59be76f05c9334 100644
--- a/modules/mol/alg/src/svd_superpose.hh
+++ b/modules/mol/alg/src/svd_superpose.hh
@@ -92,8 +92,8 @@ SuperpositionResult DLLEXPORT_OST_MOL_ALG SuperposeSVD(const mol::EntityView& ev
bool apply_transform);
/// \brief superposes two pointlists
-SuperpositionResult DLLEXPORT_OST_MOL_ALG SuperposeSVD(const std::vector<geom::Vec3>& pl1,
- const std::vector<geom::Vec3>& pl2);
+SuperpositionResult DLLEXPORT_OST_MOL_ALG SuperposeSVD(const geom::Vec3List& pl1,
+ const geom::Vec3List& pl2);
/// \brief iterative superposition
SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD(const mol::EntityView& ev1,
@@ -103,8 +103,8 @@ SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD(const mol::Entit
bool apply_transform);
/// \brief iterative superposition of two point lists
-SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD(const std::vector<geom::Vec3>& pl1,
- const std::vector<geom::Vec3>& pl2,
+SuperpositionResult DLLEXPORT_OST_MOL_ALG IterativeSuperposeSVD(const geom::Vec3List& pl1,
+ const geom::Vec3List& pl2,
int max_cycles,
Real distance_threshold);
diff --git a/modules/mol/alg/src/trajectory_analysis.cc b/modules/mol/alg/src/trajectory_analysis.cc
index 96dd5fabb0599b77fb68fa4d9ca8dea94a8de313..359530f7cf63f18778acb40507c251df01a81567 100644
--- a/modules/mol/alg/src/trajectory_analysis.cc
+++ b/modules/mol/alg/src/trajectory_analysis.cc
@@ -242,6 +242,7 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
throw Error("EntityView is empty");
}
std::vector<unsigned long> indices_ca;
+ std::pair<geom::Line3, Real> cylinder;
geom::Line3 axis;
Real sign;
directions.reserve(ceil(traj.GetFrameCount()/float(stride)));
@@ -250,7 +251,8 @@ std::vector<Real> AnalyzeAromaticRingInteraction(const CoordGroupHandle& traj, c
unsigned int n_atoms=indices_ca.size();
for (size_t i=0; i<traj.GetFrameCount(); i+=stride) {
CoordFramePtr frame=traj.GetFrame(i);
- axis=frame->FitCylinder(indices_ca);
+ cylinder=frame->FitCylinder(indices_ca);
+ axis=cylinder.first;
sign=geom::Dot(axis.GetDirection(),(*frame)[indices_ca[n_atoms-1]]-axis.GetOrigin());
sign=sign/fabs(sign);
directions.push_back(sign*axis.GetDirection());
diff --git a/modules/mol/alg/tests/CMakeLists.txt b/modules/mol/alg/tests/CMakeLists.txt
index 8258cb3d1398734c19b1e1f73051444dc87711ab..10397c0d8e3414633ebd9a679a4d90a6fe289397 100644
--- a/modules/mol/alg/tests/CMakeLists.txt
+++ b/modules/mol/alg/tests/CMakeLists.txt
@@ -4,6 +4,7 @@ set(OST_MOL_ALG_UNIT_TESTS
test_consistency_checks.cc
test_pdbize.py
test_convenient_superpose.py
+ test_hbond.py
)
ost_unittest(MODULE mol_alg SOURCES "${OST_MOL_ALG_UNIT_TESTS}")
diff --git a/modules/mol/alg/tests/test_hbond.py b/modules/mol/alg/tests/test_hbond.py
new file mode 100644
index 0000000000000000000000000000000000000000..dfef424412c5557c34c5f1b9202616076b4ccd86
--- /dev/null
+++ b/modules/mol/alg/tests/test_hbond.py
@@ -0,0 +1,25 @@
+from ost import io,mol
+import unittest
+import os
+
+class TestHBond(unittest.TestCase):
+
+ def setUp(self):
+ p=io.IOProfile(dialect='CHARMM')
+ self.eh1=io.LoadPDB(os.path.join("testfiles","hbond1.pdb"),profile=p)
+ self.eh2=io.LoadPDB(os.path.join("testfiles","hbond2.pdb"),profile=p)
+ self.hb_da_dict=mol.alg.hbond.BuildCHARMMHBondDonorAcceptorDict()
+
+ def testHBondList(self):
+ hbl1=mol.alg.hbond.GetHbondListFromView(self.eh1.Select('cname=PROA'),self.hb_da_dict)
+ for hb in hbl1:self.assertTrue(hb.IsFormed())
+ hbl=mol.alg.hbond.GetHbondListBetweenViews(self.eh1,self.eh2,self.hb_da_dict)
+ self.assertEqual(len(hbl),1)
+
+ def testHBondScore(self):
+ self.assertEqual(mol.alg.hbond.CalculateHBondScore(self.eh1,self.eh2,hbond_donor_acceptor_dict=self.hb_da_dict),0.8)
+
+
+if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/mol/alg/tests/testfiles/hbond1.pdb b/modules/mol/alg/tests/testfiles/hbond1.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..657a7721657b735840bc71ccebfec1302dad8ae6
--- /dev/null
+++ b/modules/mol/alg/tests/testfiles/hbond1.pdb
@@ -0,0 +1,153 @@
+CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
+ATOM 1 N VAL X 365 11.618 5.729 5.041 1.00 0.00 PROA
+ATOM 2 HN VAL X 365 12.357 5.874 5.695 1.00 0.00 PROA
+ATOM 3 CA VAL X 365 11.817 4.614 4.057 1.00 0.00 PROA
+ATOM 4 HA VAL X 365 12.120 5.063 3.123 1.00 0.00 PROA
+ATOM 5 CB VAL X 365 12.880 3.638 4.555 1.00 0.00 PROA
+ATOM 6 HB VAL X 365 12.758 3.271 5.597 1.00 0.00 PROA
+ATOM 7 CG1 VAL X 365 12.923 2.493 3.581 1.00 0.00 PROA
+ATOM 8 HG11 VAL X 365 13.769 1.825 3.851 1.00 0.00 PROA
+ATOM 9 HG12 VAL X 365 13.253 2.820 2.572 1.00 0.00 PROA
+ATOM 10 HG13 VAL X 365 11.981 1.905 3.547 1.00 0.00 PROA
+ATOM 11 CG2 VAL X 365 14.252 4.368 4.370 1.00 0.00 PROA
+ATOM 12 HG21 VAL X 365 15.034 3.769 4.883 1.00 0.00 PROA
+ATOM 13 HG22 VAL X 365 14.264 5.327 4.931 1.00 0.00 PROA
+ATOM 14 HG23 VAL X 365 14.509 4.512 3.299 1.00 0.00 PROA
+ATOM 15 C VAL X 365 10.530 3.823 3.977 1.00 0.00 PROA
+ATOM 16 O VAL X 365 9.878 3.644 2.985 1.00 0.00 PROA
+ATOM 17 N VAL X 366 10.051 3.478 5.122 1.00 0.00 PROA
+ATOM 18 HN VAL X 366 10.696 3.723 5.842 1.00 0.00 PROA
+ATOM 19 CA VAL X 366 8.835 2.700 5.461 1.00 0.00 PROA
+ATOM 20 HA VAL X 366 8.796 1.776 4.904 1.00 0.00 PROA
+ATOM 21 CB VAL X 366 8.746 2.433 7.004 1.00 0.00 PROA
+ATOM 22 HB VAL X 366 9.106 3.359 7.502 1.00 0.00 PROA
+ATOM 23 CG1 VAL X 366 7.329 1.969 7.489 1.00 0.00 PROA
+ATOM 24 HG11 VAL X 366 7.144 0.966 7.048 1.00 0.00 PROA
+ATOM 25 HG12 VAL X 366 6.516 2.720 7.398 1.00 0.00 PROA
+ATOM 26 HG13 VAL X 366 7.439 1.826 8.585 1.00 0.00 PROA
+ATOM 27 CG2 VAL X 366 9.782 1.385 7.527 1.00 0.00 PROA
+ATOM 28 HG21 VAL X 366 10.802 1.644 7.170 1.00 0.00 PROA
+ATOM 29 HG22 VAL X 366 9.494 0.418 7.061 1.00 0.00 PROA
+ATOM 30 HG23 VAL X 366 9.859 1.344 8.635 1.00 0.00 PROA
+ATOM 31 C VAL X 366 7.586 3.380 4.923 1.00 0.00 PROA
+ATOM 32 O VAL X 366 6.625 2.754 4.429 1.00 0.00 PROA
+ATOM 33 N SER X 367 7.487 4.721 5.110 1.00 0.00 PROA
+ATOM 34 HN SER X 367 8.179 5.195 5.649 1.00 0.00 PROA
+ATOM 35 CA SER X 367 6.337 5.546 4.756 1.00 0.00 PROA
+ATOM 36 HA SER X 367 5.563 4.863 5.073 1.00 0.00 PROA
+ATOM 37 CB SER X 367 6.182 6.894 5.600 1.00 0.00 PROA
+ATOM 38 HB1 SER X 367 5.344 7.513 5.212 1.00 0.00 PROA
+ATOM 39 HB2 SER X 367 7.029 7.611 5.544 1.00 0.00 PROA
+ATOM 40 OG SER X 367 5.775 6.479 6.922 1.00 0.00 PROA
+ATOM 41 HG1 SER X 367 6.559 6.323 7.455 1.00 0.00 PROA
+ATOM 42 C SER X 367 6.198 5.925 3.285 1.00 0.00 PROA
+ATOM 43 O SER X 367 5.073 5.984 2.834 1.00 0.00 PROA
+ATOM 44 N MET X 368 7.342 6.011 2.516 1.00 0.00 PROA
+ATOM 45 HN MET X 368 8.222 5.956 2.983 1.00 0.00 PROA
+ATOM 46 CA MET X 368 7.428 6.146 1.069 1.00 0.00 PROA
+ATOM 47 HA MET X 368 6.557 6.750 0.862 1.00 0.00 PROA
+ATOM 48 CB MET X 368 8.820 6.736 0.716 1.00 0.00 PROA
+ATOM 49 HB1 MET X 368 8.940 6.324 -0.309 1.00 0.00 PROA
+ATOM 50 HB2 MET X 368 9.600 6.202 1.300 1.00 0.00 PROA
+ATOM 51 CG MET X 368 9.114 8.160 0.683 1.00 0.00 PROA
+ATOM 52 HG1 MET X 368 8.970 8.637 1.676 1.00 0.00 PROA
+ATOM 53 HG2 MET X 368 8.370 8.708 0.066 1.00 0.00 PROA
+ATOM 54 SD MET X 368 10.854 8.414 0.112 1.00 0.00 PROA
+ATOM 55 CE MET X 368 10.429 8.518 -1.623 1.00 0.00 PROA
+ATOM 56 HE1 MET X 368 9.988 7.542 -1.920 1.00 0.00 PROA
+ATOM 57 HE2 MET X 368 11.252 8.736 -2.337 1.00 0.00 PROA
+ATOM 58 HE3 MET X 368 9.589 9.226 -1.790 1.00 0.00 PROA
+ATOM 59 C MET X 368 7.275 4.776 0.395 1.00 0.00 PROA
+ATOM 60 O MET X 368 7.019 4.790 -0.788 1.00 0.00 PROA
+ATOM 61 N THR X 369 7.214 3.623 1.096 1.00 0.00 PROA
+ATOM 62 HN THR X 369 7.600 3.536 2.011 1.00 0.00 PROA
+ATOM 63 CA THR X 369 6.846 2.309 0.543 1.00 0.00 PROA
+ATOM 64 HA THR X 369 6.730 2.329 -0.531 1.00 0.00 PROA
+ATOM 65 CB THR X 369 7.907 1.155 0.795 1.00 0.00 PROA
+ATOM 66 HB THR X 369 7.533 0.164 0.462 1.00 0.00 PROA
+ATOM 67 OG1 THR X 369 8.262 1.067 2.193 1.00 0.00 PROA
+ATOM 68 HG1 THR X 369 9.002 1.674 2.272 1.00 0.00 PROA
+ATOM 69 CG2 THR X 369 9.178 1.518 0.004 1.00 0.00 PROA
+ATOM 70 HG21 THR X 369 9.671 2.472 0.289 1.00 0.00 PROA
+ATOM 71 HG22 THR X 369 8.889 1.546 -1.069 1.00 0.00 PROA
+ATOM 72 HG23 THR X 369 9.937 0.734 0.209 1.00 0.00 PROA
+ATOM 73 C THR X 369 5.462 1.772 0.950 1.00 0.00 PROA
+ATOM 74 O THR X 369 4.930 0.735 0.605 1.00 0.00 PROA
+ATOM 75 N THR X 370 4.854 2.524 1.837 1.00 0.00 PROA
+ATOM 76 HN THR X 370 5.428 3.274 2.153 1.00 0.00 PROA
+ATOM 77 CA THR X 370 3.475 2.307 2.319 1.00 0.00 PROA
+ATOM 78 HA THR X 370 3.360 3.216 2.891 1.00 0.00 PROA
+ATOM 79 CB THR X 370 2.240 2.301 1.374 1.00 0.00 PROA
+ATOM 80 HB THR X 370 1.254 2.317 1.885 1.00 0.00 PROA
+ATOM 81 OG1 THR X 370 2.242 1.131 0.613 1.00 0.00 PROA
+ATOM 82 HG1 THR X 370 3.158 1.140 0.326 1.00 0.00 PROA
+ATOM 83 CG2 THR X 370 2.369 3.574 0.385 1.00 0.00 PROA
+ATOM 84 HG21 THR X 370 3.203 3.523 -0.347 1.00 0.00 PROA
+ATOM 85 HG22 THR X 370 2.338 4.553 0.910 1.00 0.00 PROA
+ATOM 86 HG23 THR X 370 1.474 3.574 -0.273 1.00 0.00 PROA
+ATOM 87 C THR X 370 3.265 1.190 3.381 1.00 0.00 PROA
+ATOM 88 O THR X 370 2.139 0.782 3.712 1.00 0.00 PROA
+ATOM 89 N VAL X 371 4.303 0.659 4.032 1.00 0.00 PROA
+ATOM 90 HN VAL X 371 5.248 0.913 3.842 1.00 0.00 PROA
+ATOM 91 CA VAL X 371 4.174 -0.341 5.080 1.00 0.00 PROA
+ATOM 92 HA VAL X 371 3.441 -1.080 4.793 1.00 0.00 PROA
+ATOM 93 CB VAL X 371 5.481 -1.050 5.302 1.00 0.00 PROA
+ATOM 94 HB VAL X 371 6.237 -0.236 5.308 1.00 0.00 PROA
+ATOM 95 CG1 VAL X 371 5.466 -1.885 6.550 1.00 0.00 PROA
+ATOM 96 HG11 VAL X 371 6.411 -2.466 6.596 1.00 0.00 PROA
+ATOM 97 HG12 VAL X 371 4.716 -2.694 6.420 1.00 0.00 PROA
+ATOM 98 HG13 VAL X 371 5.106 -1.485 7.523 1.00 0.00 PROA
+ATOM 99 CG2 VAL X 371 5.853 -2.056 4.210 1.00 0.00 PROA
+ATOM 100 HG21 VAL X 371 6.761 -2.619 4.515 1.00 0.00 PROA
+ATOM 101 HG22 VAL X 371 6.035 -1.600 3.213 1.00 0.00 PROA
+ATOM 102 HG23 VAL X 371 5.121 -2.885 4.106 1.00 0.00 PROA
+ATOM 103 C VAL X 371 3.496 0.214 6.320 1.00 0.00 PROA
+ATOM 104 O VAL X 371 2.650 -0.424 6.942 1.00 0.00 PROA
+ATOM 105 N GLY X 372 3.947 1.347 6.802 1.00 0.00 PROA
+ATOM 106 HN GLY X 372 4.595 1.901 6.287 1.00 0.00 PROA
+ATOM 107 CA GLY X 372 3.520 1.972 8.032 1.00 0.00 PROA
+ATOM 108 HA1 GLY X 372 2.723 2.649 7.763 1.00 0.00 PROA
+ATOM 109 HA2 GLY X 372 4.361 2.574 8.344 1.00 0.00 PROA
+ATOM 110 C GLY X 372 3.136 1.234 9.276 1.00 0.00 PROA
+ATOM 111 O GLY X 372 1.970 1.231 9.629 1.00 0.00 PROA
+ATOM 112 N TYR X 373 4.173 0.790 9.993 1.00 0.00 PROA
+ATOM 113 HN TYR X 373 5.105 0.907 9.660 1.00 0.00 PROA
+ATOM 114 CA TYR X 373 4.103 0.124 11.289 1.00 0.00 PROA
+ATOM 115 HA TYR X 373 3.395 -0.690 11.244 1.00 0.00 PROA
+ATOM 116 CB TYR X 373 5.483 -0.396 11.768 1.00 0.00 PROA
+ATOM 117 HB1 TYR X 373 5.336 -1.033 12.666 1.00 0.00 PROA
+ATOM 118 HB2 TYR X 373 6.131 0.393 12.207 1.00 0.00 PROA
+ATOM 119 CG TYR X 373 6.167 -1.214 10.741 1.00 0.00 PROA
+ATOM 120 CD1 TYR X 373 7.308 -0.793 10.077 1.00 0.00 PROA
+ATOM 121 HD1 TYR X 373 7.643 0.203 10.326 1.00 0.00 PROA
+ATOM 122 CE1 TYR X 373 8.073 -1.689 9.309 1.00 0.00 PROA
+ATOM 123 HE1 TYR X 373 8.917 -1.335 8.734 1.00 0.00 PROA
+ATOM 124 CZ TYR X 373 7.697 -2.975 9.180 1.00 0.00 PROA
+ATOM 125 OH TYR X 373 8.377 -3.851 8.259 1.00 0.00 PROA
+ATOM 126 HH TYR X 373 7.688 -4.382 7.853 1.00 0.00 PROA
+ATOM 127 CD2 TYR X 373 5.680 -2.561 10.477 1.00 0.00 PROA
+ATOM 128 HD2 TYR X 373 4.788 -3.024 10.874 1.00 0.00 PROA
+ATOM 129 CE2 TYR X 373 6.480 -3.382 9.648 1.00 0.00 PROA
+ATOM 130 HE2 TYR X 373 6.226 -4.418 9.483 1.00 0.00 PROA
+ATOM 131 C TYR X 373 3.617 1.013 12.496 1.00 0.00 PROA
+ATOM 132 O TYR X 373 3.034 0.496 13.423 1.00 0.00 PROA
+ATOM 133 N GLY X 374 3.825 2.267 12.445 1.00 0.00 PROA
+ATOM 134 HN GLY X 374 4.376 2.631 11.698 1.00 0.00 PROA
+ATOM 135 CA GLY X 374 3.328 3.182 13.462 1.00 0.00 PROA
+ATOM 136 HA1 GLY X 374 2.305 2.898 13.661 1.00 0.00 PROA
+ATOM 137 HA2 GLY X 374 3.435 4.173 13.045 1.00 0.00 PROA
+ATOM 138 C GLY X 374 3.994 3.245 14.868 1.00 0.00 PROA
+ATOM 139 O GLY X 374 3.441 3.506 15.895 1.00 0.00 PROA
+ATOM 140 N ASP X 375 5.321 2.894 14.810 1.00 0.00 PROA
+ATOM 141 HN ASP X 375 5.795 2.561 13.998 1.00 0.00 PROA
+ATOM 142 CA ASP X 375 6.199 2.731 15.953 1.00 0.00 PROA
+ATOM 143 HA ASP X 375 5.607 2.484 16.822 1.00 0.00 PROA
+ATOM 144 CB ASP X 375 7.318 1.659 15.729 1.00 0.00 PROA
+ATOM 145 HB1 ASP X 375 6.916 0.639 15.553 1.00 0.00 PROA
+ATOM 146 HB2 ASP X 375 7.905 1.600 16.671 1.00 0.00 PROA
+ATOM 147 CG ASP X 375 8.095 1.992 14.492 1.00 0.00 PROA
+ATOM 148 OD1 ASP X 375 7.527 2.389 13.446 1.00 0.00 PROA
+ATOM 149 OD2 ASP X 375 9.333 1.825 14.541 1.00 0.00 PROA
+ATOM 150 C ASP X 375 6.890 4.164 16.143 1.00 0.00 PROA
+ATOM 151 O ASP X 375 7.375 4.508 17.268 1.00 0.00 PROA
+END
diff --git a/modules/mol/alg/tests/testfiles/hbond2.pdb b/modules/mol/alg/tests/testfiles/hbond2.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..2f1f7395b6721639c3137b8f54497e95ca636448
--- /dev/null
+++ b/modules/mol/alg/tests/testfiles/hbond2.pdb
@@ -0,0 +1,153 @@
+CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
+ATOM 152 N VAL X 365 -5.554 10.917 5.263 1.00 0.00 PROA
+ATOM 153 HN VAL X 365 -5.487 11.435 6.112 1.00 0.00 PROA
+ATOM 154 CA VAL X 365 -4.443 11.069 4.295 1.00 0.00 PROA
+ATOM 155 HA VAL X 365 -4.843 10.903 3.305 1.00 0.00 PROA
+ATOM 156 CB VAL X 365 -3.524 12.340 4.423 1.00 0.00 PROA
+ATOM 157 HB VAL X 365 -3.253 12.456 5.494 1.00 0.00 PROA
+ATOM 158 CG1 VAL X 365 -2.216 12.278 3.596 1.00 0.00 PROA
+ATOM 159 HG11 VAL X 365 -1.525 11.626 4.173 1.00 0.00 PROA
+ATOM 160 HG12 VAL X 365 -1.831 13.320 3.602 1.00 0.00 PROA
+ATOM 161 HG13 VAL X 365 -2.437 11.945 2.559 1.00 0.00 PROA
+ATOM 162 CG2 VAL X 365 -4.425 13.546 3.950 1.00 0.00 PROA
+ATOM 163 HG21 VAL X 365 -5.359 13.460 4.546 1.00 0.00 PROA
+ATOM 164 HG22 VAL X 365 -4.691 13.416 2.879 1.00 0.00 PROA
+ATOM 165 HG23 VAL X 365 -3.990 14.518 4.268 1.00 0.00 PROA
+ATOM 166 C VAL X 365 -3.585 9.847 4.444 1.00 0.00 PROA
+ATOM 167 O VAL X 365 -3.242 9.204 3.452 1.00 0.00 PROA
+ATOM 168 N VAL X 366 -3.285 9.472 5.670 1.00 0.00 PROA
+ATOM 169 HN VAL X 366 -3.775 9.952 6.394 1.00 0.00 PROA
+ATOM 170 CA VAL X 366 -2.467 8.371 5.951 1.00 0.00 PROA
+ATOM 171 HA VAL X 366 -1.507 8.470 5.466 1.00 0.00 PROA
+ATOM 172 CB VAL X 366 -2.075 8.398 7.434 1.00 0.00 PROA
+ATOM 173 HB VAL X 366 -3.000 8.654 7.994 1.00 0.00 PROA
+ATOM 174 CG1 VAL X 366 -1.681 7.006 7.930 1.00 0.00 PROA
+ATOM 175 HG11 VAL X 366 -1.042 6.384 7.268 1.00 0.00 PROA
+ATOM 176 HG12 VAL X 366 -2.625 6.443 8.094 1.00 0.00 PROA
+ATOM 177 HG13 VAL X 366 -1.257 7.106 8.952 1.00 0.00 PROA
+ATOM 178 CG2 VAL X 366 -0.899 9.358 7.612 1.00 0.00 PROA
+ATOM 179 HG21 VAL X 366 -1.114 10.376 7.223 1.00 0.00 PROA
+ATOM 180 HG22 VAL X 366 -0.054 8.930 7.031 1.00 0.00 PROA
+ATOM 181 HG23 VAL X 366 -0.616 9.392 8.686 1.00 0.00 PROA
+ATOM 182 C VAL X 366 -3.008 6.988 5.448 1.00 0.00 PROA
+ATOM 183 O VAL X 366 -2.313 6.111 4.893 1.00 0.00 PROA
+ATOM 184 N SER X 367 -4.332 6.886 5.581 1.00 0.00 PROA
+ATOM 185 HN SER X 367 -4.703 7.664 6.082 1.00 0.00 PROA
+ATOM 186 CA SER X 367 -5.141 5.772 5.060 1.00 0.00 PROA
+ATOM 187 HA SER X 367 -4.643 4.849 5.316 1.00 0.00 PROA
+ATOM 188 CB SER X 367 -6.518 5.685 5.729 1.00 0.00 PROA
+ATOM 189 HB1 SER X 367 -7.163 4.883 5.311 1.00 0.00 PROA
+ATOM 190 HB2 SER X 367 -7.072 6.633 5.560 1.00 0.00 PROA
+ATOM 191 OG SER X 367 -6.416 5.557 7.171 1.00 0.00 PROA
+ATOM 192 HG1 SER X 367 -5.984 6.307 7.585 1.00 0.00 PROA
+ATOM 193 C SER X 367 -5.415 5.859 3.562 1.00 0.00 PROA
+ATOM 194 O SER X 367 -5.270 4.884 2.894 1.00 0.00 PROA
+ATOM 195 N MET X 368 -5.730 7.029 2.940 1.00 0.00 PROA
+ATOM 196 HN MET X 368 -5.866 7.929 3.348 1.00 0.00 PROA
+ATOM 197 CA MET X 368 -5.795 7.114 1.519 1.00 0.00 PROA
+ATOM 198 HA MET X 368 -6.548 6.394 1.235 1.00 0.00 PROA
+ATOM 199 CB MET X 368 -6.380 8.511 1.170 1.00 0.00 PROA
+ATOM 200 HB1 MET X 368 -6.326 8.686 0.074 1.00 0.00 PROA
+ATOM 201 HB2 MET X 368 -5.876 9.300 1.768 1.00 0.00 PROA
+ATOM 202 CG MET X 368 -7.924 8.541 1.385 1.00 0.00 PROA
+ATOM 203 HG1 MET X 368 -8.032 8.383 2.479 1.00 0.00 PROA
+ATOM 204 HG2 MET X 368 -8.330 7.620 0.915 1.00 0.00 PROA
+ATOM 205 SD MET X 368 -8.865 9.874 0.776 1.00 0.00 PROA
+ATOM 206 CE MET X 368 -9.036 9.409 -0.929 1.00 0.00 PROA
+ATOM 207 HE1 MET X 368 -9.695 8.515 -0.956 1.00 0.00 PROA
+ATOM 208 HE2 MET X 368 -8.087 9.204 -1.470 1.00 0.00 PROA
+ATOM 209 HE3 MET X 368 -9.547 10.168 -1.559 1.00 0.00 PROA
+ATOM 210 C MET X 368 -4.566 6.781 0.700 1.00 0.00 PROA
+ATOM 211 O MET X 368 -4.593 6.129 -0.321 1.00 0.00 PROA
+ATOM 212 N THR X 369 -3.408 7.154 1.181 1.00 0.00 PROA
+ATOM 213 HN THR X 369 -3.323 7.498 2.112 1.00 0.00 PROA
+ATOM 214 CA THR X 369 -2.039 6.822 0.741 1.00 0.00 PROA
+ATOM 215 HA THR X 369 -2.031 7.105 -0.301 1.00 0.00 PROA
+ATOM 216 CB THR X 369 -0.913 7.602 1.451 1.00 0.00 PROA
+ATOM 217 HB THR X 369 0.129 7.288 1.229 1.00 0.00 PROA
+ATOM 218 OG1 THR X 369 -1.048 7.538 2.896 1.00 0.00 PROA
+ATOM 219 HG1 THR X 369 -1.786 8.110 3.119 1.00 0.00 PROA
+ATOM 220 CG2 THR X 369 -0.882 9.067 0.993 1.00 0.00 PROA
+ATOM 221 HG21 THR X 369 -0.022 9.636 1.405 1.00 0.00 PROA
+ATOM 222 HG22 THR X 369 -1.903 9.483 1.130 1.00 0.00 PROA
+ATOM 223 HG23 THR X 369 -0.623 9.074 -0.087 1.00 0.00 PROA
+ATOM 224 C THR X 369 -1.678 5.341 0.902 1.00 0.00 PROA
+ATOM 225 O THR X 369 -1.000 4.641 0.135 1.00 0.00 PROA
+ATOM 226 N THR X 370 -2.257 4.809 2.001 1.00 0.00 PROA
+ATOM 227 HN THR X 370 -2.900 5.255 2.619 1.00 0.00 PROA
+ATOM 228 CA THR X 370 -2.193 3.436 2.374 1.00 0.00 PROA
+ATOM 229 HA THR X 370 -3.085 3.344 2.976 1.00 0.00 PROA
+ATOM 230 CB THR X 370 -2.419 2.272 1.319 1.00 0.00 PROA
+ATOM 231 HB THR X 370 -2.680 1.365 1.904 1.00 0.00 PROA
+ATOM 232 OG1 THR X 370 -1.216 2.089 0.500 1.00 0.00 PROA
+ATOM 233 HG1 THR X 370 -1.051 3.016 0.312 1.00 0.00 PROA
+ATOM 234 CG2 THR X 370 -3.679 2.581 0.484 1.00 0.00 PROA
+ATOM 235 HG21 THR X 370 -3.498 3.399 -0.246 1.00 0.00 PROA
+ATOM 236 HG22 THR X 370 -4.289 3.016 1.304 1.00 0.00 PROA
+ATOM 237 HG23 THR X 370 -4.118 1.612 0.164 1.00 0.00 PROA
+ATOM 238 C THR X 370 -1.029 3.093 3.264 1.00 0.00 PROA
+ATOM 239 O THR X 370 -0.716 1.894 3.397 1.00 0.00 PROA
+ATOM 240 N VAL X 371 -0.363 4.083 3.837 1.00 0.00 PROA
+ATOM 241 HN VAL X 371 -0.669 4.976 3.515 1.00 0.00 PROA
+ATOM 242 CA VAL X 371 0.627 3.921 4.891 1.00 0.00 PROA
+ATOM 243 HA VAL X 371 1.450 3.259 4.667 1.00 0.00 PROA
+ATOM 244 CB VAL X 371 1.338 5.277 5.130 1.00 0.00 PROA
+ATOM 245 HB VAL X 371 0.594 6.103 5.108 1.00 0.00 PROA
+ATOM 246 CG1 VAL X 371 2.304 5.414 6.306 1.00 0.00 PROA
+ATOM 247 HG11 VAL X 371 3.003 4.559 6.434 1.00 0.00 PROA
+ATOM 248 HG12 VAL X 371 1.759 5.579 7.260 1.00 0.00 PROA
+ATOM 249 HG13 VAL X 371 2.814 6.399 6.357 1.00 0.00 PROA
+ATOM 250 CG2 VAL X 371 2.294 5.484 3.901 1.00 0.00 PROA
+ATOM 251 HG21 VAL X 371 3.148 4.775 3.948 1.00 0.00 PROA
+ATOM 252 HG22 VAL X 371 2.613 6.548 3.904 1.00 0.00 PROA
+ATOM 253 HG23 VAL X 371 1.822 5.394 2.899 1.00 0.00 PROA
+ATOM 254 C VAL X 371 0.037 3.426 6.191 1.00 0.00 PROA
+ATOM 255 O VAL X 371 0.538 2.690 7.003 1.00 0.00 PROA
+ATOM 256 N GLY X 372 -1.232 3.937 6.416 1.00 0.00 PROA
+ATOM 257 HN GLY X 372 -1.498 4.659 5.782 1.00 0.00 PROA
+ATOM 258 CA GLY X 372 -2.162 3.544 7.487 1.00 0.00 PROA
+ATOM 259 HA1 GLY X 372 -2.714 2.680 7.149 1.00 0.00 PROA
+ATOM 260 HA2 GLY X 372 -2.750 4.408 7.761 1.00 0.00 PROA
+ATOM 261 C GLY X 372 -1.600 3.218 8.845 1.00 0.00 PROA
+ATOM 262 O GLY X 372 -1.643 2.102 9.319 1.00 0.00 PROA
+ATOM 263 N TYR X 373 -1.031 4.202 9.564 1.00 0.00 PROA
+ATOM 264 HN TYR X 373 -1.181 5.155 9.311 1.00 0.00 PROA
+ATOM 265 CA TYR X 373 -0.306 3.990 10.850 1.00 0.00 PROA
+ATOM 266 HA TYR X 373 0.450 3.300 10.505 1.00 0.00 PROA
+ATOM 267 CB TYR X 373 0.222 5.228 11.603 1.00 0.00 PROA
+ATOM 268 HB1 TYR X 373 0.710 4.995 12.573 1.00 0.00 PROA
+ATOM 269 HB2 TYR X 373 -0.581 5.976 11.773 1.00 0.00 PROA
+ATOM 270 CG TYR X 373 1.290 5.928 10.866 1.00 0.00 PROA
+ATOM 271 CD1 TYR X 373 1.293 7.331 10.766 1.00 0.00 PROA
+ATOM 272 HD1 TYR X 373 0.456 7.864 11.191 1.00 0.00 PROA
+ATOM 273 CE1 TYR X 373 2.140 8.027 9.936 1.00 0.00 PROA
+ATOM 274 HE1 TYR X 373 1.928 9.084 9.870 1.00 0.00 PROA
+ATOM 275 CZ TYR X 373 3.187 7.395 9.338 1.00 0.00 PROA
+ATOM 276 OH TYR X 373 4.021 8.140 8.369 1.00 0.00 PROA
+ATOM 277 HH TYR X 373 4.637 7.538 7.945 1.00 0.00 PROA
+ATOM 278 CD2 TYR X 373 2.341 5.259 10.196 1.00 0.00 PROA
+ATOM 279 HD2 TYR X 373 2.410 4.189 10.323 1.00 0.00 PROA
+ATOM 280 CE2 TYR X 373 3.305 5.961 9.450 1.00 0.00 PROA
+ATOM 281 HE2 TYR X 373 4.168 5.521 8.972 1.00 0.00 PROA
+ATOM 282 C TYR X 373 -1.188 3.298 11.900 1.00 0.00 PROA
+ATOM 283 O TYR X 373 -0.739 2.394 12.589 1.00 0.00 PROA
+ATOM 284 N GLY X 374 -2.486 3.742 12.054 1.00 0.00 PROA
+ATOM 285 HN GLY X 374 -2.925 4.399 11.446 1.00 0.00 PROA
+ATOM 286 CA GLY X 374 -3.364 3.172 13.072 1.00 0.00 PROA
+ATOM 287 HA1 GLY X 374 -3.231 2.117 13.263 1.00 0.00 PROA
+ATOM 288 HA2 GLY X 374 -4.362 3.397 12.726 1.00 0.00 PROA
+ATOM 289 C GLY X 374 -3.137 3.860 14.374 1.00 0.00 PROA
+ATOM 290 O GLY X 374 -3.327 3.323 15.446 1.00 0.00 PROA
+ATOM 291 N ASP X 375 -2.716 5.132 14.258 1.00 0.00 PROA
+ATOM 292 HN ASP X 375 -2.592 5.517 13.347 1.00 0.00 PROA
+ATOM 293 CA ASP X 375 -2.706 6.055 15.382 1.00 0.00 PROA
+ATOM 294 HA ASP X 375 -2.052 5.529 16.061 1.00 0.00 PROA
+ATOM 295 CB ASP X 375 -1.922 7.358 15.033 1.00 0.00 PROA
+ATOM 296 HB1 ASP X 375 -0.878 7.053 14.806 1.00 0.00 PROA
+ATOM 297 HB2 ASP X 375 -1.902 8.008 15.933 1.00 0.00 PROA
+ATOM 298 CG ASP X 375 -2.464 8.125 13.886 1.00 0.00 PROA
+ATOM 299 OD1 ASP X 375 -3.290 7.631 13.085 1.00 0.00 PROA
+ATOM 300 OD2 ASP X 375 -1.993 9.254 13.689 1.00 0.00 PROA
+ATOM 301 C ASP X 375 -4.051 6.331 16.038 1.00 0.00 PROA
+ATOM 302 O ASP X 375 -4.171 6.341 17.271 1.00 0.00 PROA
+END
diff --git a/modules/mol/base/pymod/export_coord_frame.cc b/modules/mol/base/pymod/export_coord_frame.cc
index e3e269e7d7054817d18a3ae642c0e3065846186c..566f0a43c0c3562830401f339ea62865631d757f 100644
--- a/modules/mol/base/pymod/export_coord_frame.cc
+++ b/modules/mol/base/pymod/export_coord_frame.cc
@@ -43,7 +43,11 @@ Real (CoordFrame::*get_min_dist)(const mol::EntityView&, const mol::EntityView&)
Real (CoordFrame::*get_alpha)(const mol::EntityView&) const = &CoordFrame::GetAlphaHelixContent;
geom::Line3 (CoordFrame::*get_odr_line)(const mol::EntityView&) const = &CoordFrame::GetODRLine;
geom::Plane (CoordFrame::*get_odr_plane)(const mol::EntityView&) const = &CoordFrame::GetODRPlane;
-geom::Line3 (CoordFrame::*fit_cylinder)(const mol::EntityView&) const = &CoordFrame::FitCylinder;
+boost::python::tuple wrap_FitCylinder(const CoordFrame& f,const mol::EntityView& ev) {
+ std::pair<geom::Line3,Real> pair=f.FitCylinder(ev);
+ return boost::python::make_tuple<geom::Line3,Real>(pair.first,pair.second);
+}
+
// TODO: move to geom
geom::Line3 (CoordFrame::*get_odr_line2)() const = &geom::Vec3List::GetODRLine;
@@ -69,6 +73,7 @@ void export_CoordFrame()
.def("SetCellAngles",&CoordFrame::SetCellAngles)
.def("GetCellAngles",&CoordFrame::GetCellAngles)
.add_property("cell_angles",&CoordFrame::GetCellAngles,&CoordFrame::SetCellAngles)
+ .def("GetCellVectors",&CoordFrame::GetCellVectors)
.def("GetAtomPos", get_atom_pos)
.def("GetDistanceBetwAtoms", get_dist_atom)
.def("GetAngle", get_angle)
@@ -82,7 +87,7 @@ void export_CoordFrame()
.def("GetODRLine",get_odr_line)
.def("GetODRLine",get_odr_line2)
.def("GetAlphaHelixContent",get_alpha)
- .def("FitCylinder",fit_cylinder)
+ .def("FitCylinder",wrap_FitCylinder)
;
def("CreateCoordFrame",create_coord_frame1);
def("CreateCoordFrame",create_coord_frame2);
diff --git a/modules/mol/base/pymod/export_editors.cc b/modules/mol/base/pymod/export_editors.cc
index 6a659d286e095a8436dc338b9f9492f70e857f45..cd7b326fdbcc88581feb24e2af2deb838ff435b0 100644
--- a/modules/mol/base/pymod/export_editors.cc
+++ b/modules/mol/base/pymod/export_editors.cc
@@ -243,6 +243,8 @@ void export_Editors()
.def("DeleteResidue", &EditorBase::DeleteResidue)
.def("DeleteChain", &EditorBase::DeleteChain)
.def("DeleteAtom", &EditorBase::DeleteAtom)
+ .def("DeleteBond", &EditorBase::DeleteBond)
+ .def("DeleteBonds", &EditorBase::DeleteBonds)
.def("InsertResidueBefore", &EditorBase::InsertResidueBefore)
.def("InsertResidueAfter", &EditorBase::InsertResidueAfter)
.def("AppendResidue", append_a)
diff --git a/modules/mol/base/pymod/export_surface.cc b/modules/mol/base/pymod/export_surface.cc
index 874ab51d5c8b9c741a46eba69f47a9b0fdc35a4a..f569d3e403ba59adf4dd362ebcaf39abcd3b792a 100644
--- a/modules/mol/base/pymod/export_surface.cc
+++ b/modules/mol/base/pymod/export_surface.cc
@@ -49,6 +49,11 @@ void export_Surface()
.def_readwrite("Normal", &SurfaceVertex::normal)
.def_readwrite("Atom", &SurfaceVertex::atom)
;
+ class_<SurfaceTri>("SurfaceTri", init<>())
+ .def_readwrite("v0", &SurfaceTri::v0)
+ .def_readwrite("v1", &SurfaceTri::v1)
+ .def_readwrite("v2", &SurfaceTri::v2)
+ ;
class_<SurfaceTriIDList>("SurfaceTriIDList", init<>())
.def(vector_indexing_suite<SurfaceTriIDList>())
;
@@ -60,8 +65,9 @@ void export_Surface()
.def("Attach",attach2)
.def("GetVertexIDList", &SurfaceHandle::GetVertexIDList)
.def("GetTriIDList", &SurfaceHandle::GetTriIDList)
- .def("GetVertex", &SurfaceHandle::GetVertex)
- .def("FindWithin", &SurfaceHandle::FindWithin)
+ .def("GetVertex", &SurfaceHandle::GetVertex)
+ .def("GetTri", &SurfaceHandle::GetTri)
+ .def("FindWithin", &SurfaceHandle::FindWithin)
.def("Invert",&SurfaceHandle::Invert)
.def("IsValid",&SurfaceHandle::IsValid)
;
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 4ddc13f2f46cea4c19c0e0372bb313b936d51386..c3ec3777d53e836b43d16b9ddd7dfe83f2886226 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -33,10 +33,6 @@ namespace ost { namespace mol {
///
/// Groups common functionality for AtomView and AtomHandle.
///
-/// Most of the atom properties such as temperature factor, element, radius
-/// and charge can be accessed with #GetAtomProps() that returns an object of
-/// type AtomProp.
-///
/// Like \ref ResidueBase residues, \ref ChainBase "chains" and
/// \ref EntityBase "entities" atoms are generic property containers and may as
/// such store \ref generic_properties "custom properties".
diff --git a/modules/mol/base/src/bounding_box.cc b/modules/mol/base/src/bounding_box.cc
index 4b70f78172ecdfde25af3d612944823423b46138..85c40ed1acbb0832893da76f57af96815a3829cc 100644
--- a/modules/mol/base/src/bounding_box.cc
+++ b/modules/mol/base/src/bounding_box.cc
@@ -22,7 +22,7 @@
*/
#include <limits>
-#include <Eigen/QR>
+#include <Eigen/Eigenvalues>
#include <ost/mol/mol.hh>
#include <ost/mol/bounding_box.hh>
namespace ost { namespace mol {
diff --git a/modules/mol/base/src/coord_frame.cc b/modules/mol/base/src/coord_frame.cc
index 8ba7963054d04416b464e70f254f307a6082003d..49c294fcee0fc4ac784e79cd02935d4d4f66e2c6 100644
--- a/modules/mol/base/src/coord_frame.cc
+++ b/modules/mol/base/src/coord_frame.cc
@@ -48,6 +48,11 @@ namespace ost { namespace mol {
}
}
+ geom::Vec3List CoordFrame::GetCellVectors() const
+ {
+ return geom::CalculateUnitCellVectors(ucell_size_,ucell_angles_);
+ }
+
geom::Vec3 CoordFrame::GetAtomPos(const AtomHandle& atom) const
{
return this->GetAtomPos(atom.GetIndex());
@@ -230,7 +235,7 @@ namespace ost { namespace mol {
return this->GetODRPlane(indices);
}
- geom::Line3 CoordFrame::FitCylinder(std::vector<unsigned long>& indices_ca) const {
+ std::pair<geom::Line3, Real> CoordFrame::FitCylinder(std::vector<unsigned long>& indices_ca) const {
geom::Vec3List atoms_pos_list;
int n_atoms=indices_ca.size();
atoms_pos_list.reserve(n_atoms);
@@ -238,7 +243,7 @@ namespace ost { namespace mol {
atoms_pos_list.push_back((*this)[*i1]);
}
//Initial guess
- geom::Vec3 initial_axis=geom::Vec3(0.0,0.0,0.0),center=geom::Vec3(0.0,0.0,0.0);
+ geom::Vec3 initial_axis=geom::Vec3(0.0,0.0,0.0);
if (n_atoms<5) {
initial_axis=atoms_pos_list[n_atoms-1]-atoms_pos_list[0];
}
@@ -247,14 +252,10 @@ namespace ost { namespace mol {
initial_axis+=(*(i+4))-(*i);
}
}
- for (geom::Vec3List::const_iterator i=atoms_pos_list.begin(),e=atoms_pos_list.end(); i!=e; ++i) {
- center+=(*i);
- }
- center/=atoms_pos_list.size();
- return atoms_pos_list.FitCylinder(initial_axis,center);
+ return atoms_pos_list.FitCylinder(initial_axis);
}
- geom::Line3 CoordFrame::FitCylinder(const mol::EntityView& view1) const {
+ std::pair<geom::Line3, Real> CoordFrame::FitCylinder(const mol::EntityView& view1) const {
CheckHandleValidity(view1);
std::vector<unsigned long> indices_ca;
GetCaIndices(view1, indices_ca);
diff --git a/modules/mol/base/src/coord_frame.hh b/modules/mol/base/src/coord_frame.hh
index e624ebf87065849c87c169249f7994a892e1bf75..33d24d1d402999d3c0e24bc4afa0a587d047e377 100644
--- a/modules/mol/base/src/coord_frame.hh
+++ b/modules/mol/base/src/coord_frame.hh
@@ -77,7 +77,9 @@ public:
geom::Vec3 GetCellAngles() const {
return this->ucell_angles_;
}
-
+
+ geom::Vec3List GetCellVectors() const;
+
geom::Vec3 GetAtomPos(const AtomHandle& atom) const;
geom::Vec3 GetAtomPos(int atom_index) const;
Real GetDistanceBetwAtoms(const AtomHandle& a1, const AtomHandle& a2) const;
@@ -180,10 +182,10 @@ public:
It is assumed that we fit an alpha-helix and that the CA atoms are oredered sequentially
This is used for the initial guess of the helix axis
*/
- geom::Line3 FitCylinder(std::vector<unsigned long>& indices_ca) const;
+ std::pair<geom::Line3, Real> FitCylinder(std::vector<unsigned long>& indices_ca) const;
//! see FitCylinder(std::vector<unsigned long>&)
- geom::Line3 FitCylinder(const mol::EntityView& view1) const;
+ std::pair<geom::Line3, Real> FitCylinder(const mol::EntityView& view1) const;
/*!
Returns the percentage of residues in the EntityView (segment) that are in an alpha-helix
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 1edd38b4542f2b03be5d561c59b7f66a948d5e42..3ab9ec3dbf7077bf88c56a62aa582984833e0a70 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -146,7 +146,8 @@ void CoordGroupHandle::AddFrames(const CoordGroupHandle& cg)
throw IntegrityError("Atom number don't match");
}
for (size_t i=0; i<cg.GetFrameCount(); ++i) {
- source_->AddFrame(*cg.GetFrame(i));
+ CoordFramePtr p = cg.GetFrame(i);
+ source_->AddFrame(*p,p->GetCellSize(),p->GetCellAngles());
}
} else {
throw IntegrityError("Can't add frame to immutable CoordGroup");
@@ -256,7 +257,7 @@ CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected, int first,
j=indices.begin(), e2=indices.end(); j!=e2; ++j) {
vecs[j-indices.begin()]=(*frame)[*j];
}
- filtered_cg.AddFrame(vecs);
+ filtered_cg.AddFrame(vecs,(*frame).GetCellSize(),(*frame).GetCellAngles());
}
return filtered_cg;
}
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index c9ea57e4efef9f7e07a5f9e868220f50587d050b..754330d6c3b703809ee734e79e53f2afe58558bc 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -64,7 +64,7 @@ public:
/// \brief start time in ps, default 0.0
float GetStartTime() const;
- /// \rbrief set start time in ps
+ /// \brief set start time in ps
void SetStartTime(float t);
/// \brief assign positions to the given frame - order and count must match
diff --git a/modules/mol/base/src/editor_base.cc b/modules/mol/base/src/editor_base.cc
index 76e41f216e989e543d577a80e18527e2170febe3..364ea0be0bbbd07f44073d6e65b9723e1039e25f 100644
--- a/modules/mol/base/src/editor_base.cc
+++ b/modules/mol/base/src/editor_base.cc
@@ -193,6 +193,19 @@ void EditorBase::DeleteAtom(const AtomHandle& atom_handle)
atom_handle.GetResidue().Impl()->DeleteAtom(atom_handle.Impl());
}
+void EditorBase::DeleteBond(const BondHandle& bond)
+{
+ bond.GetFirst().Impl()->DeleteConnector(bond.Impl(),true);
+}
+
+void EditorBase::DeleteBonds(const BondHandleList& bond_list)
+{
+ for(BondHandleList::const_iterator i = bond_list.begin();
+ i != bond_list.end(); ++i){
+ i->GetFirst().Impl()->DeleteConnector(i->Impl(),true);
+ }
+}
+
void EditorBase::DeleteResidue(const ResidueHandle& residue_handle)
{
CheckHandleValidity(residue_handle);
diff --git a/modules/mol/base/src/editor_base.hh b/modules/mol/base/src/editor_base.hh
index 255390c29dc3f3e7e286ad5ea966748b75ab72b2..c45036072670958e5eeef9cadb9f23c6def955be 100644
--- a/modules/mol/base/src/editor_base.hh
+++ b/modules/mol/base/src/editor_base.hh
@@ -153,7 +153,11 @@ public:
/// algorithms as well as most builders in the conop module rely on proper
/// naming.
/// \param pos is the position of the atom in global coordinates
- AtomHandle InsertAtom(ResidueHandle residue, const String& name,
+ /// \param ele
+ /// \param occupancy
+ /// \param b_factor
+ /// \param is_hetatm
+ AtomHandle InsertAtom(ResidueHandle residue, const String& name,
const geom::Vec3& pos, const String& ele="",
Real occupancy=1.0, Real b_factor=0.0,
bool is_hetatm=false);
@@ -194,6 +198,8 @@ public:
/// Error will be thrown.
/// \param position
/// is the alternative position
+ /// \param occ
+ /// \param b_factor
/// \sa EditorBase::InsertAltAtom(), ResidueHandle
void AddAltAtomPos(const String& group, const AtomHandle& atom,
const geom::Vec3& position, Real occ=1.0,
@@ -248,6 +254,20 @@ public:
///
/// All associated torsions and bonds will be removed as well
void DeleteAtoms(const AtomHandleList& atoms);
+
+ /// \ brief Delete bond
+ ///
+ /// \param bond
+ /// Is the bond to remove. If no such bond exists, this method will
+ /// have no effect
+ void DeleteBond(const BondHandle& bond);
+
+ /// \ brief Delete a set of bond
+ ///
+ /// \param bonds
+ /// bonds to remove. If no such bonds exist, this method will
+ /// have no effect
+ void DeleteBonds(const BondHandleList& bonds);
/// \brief Add named torsion to entity
TorsionHandle AddTorsion(const String& name, const AtomHandle& a1,
@@ -287,7 +307,7 @@ public:
/// \brief renumber residues of one chain
///
- /// \param name
+ /// \param chain
/// All residues of this chain will be renumbered according to the
/// parameters start and keep_spacing
///
diff --git a/modules/mol/base/src/entity_base.hh b/modules/mol/base/src/entity_base.hh
index fb23974d1e346f51862c9ec998d92e7d80049c27..b00ac720e9847e18419786a929d5e869735b0724 100644
--- a/modules/mol/base/src/entity_base.hh
+++ b/modules/mol/base/src/entity_base.hh
@@ -41,7 +41,7 @@ public:
/// \brief Set entity name
///
- /// \param entity_name is the new entity name.
+ /// \param ent_name is the new entity name.
///
/// \sa EntityBase::GetName
void SetName(const String& ent_name);
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index 5cb26134bb181c3055bc73bed2a71ac23c0a45a4..cb0ab5f0f2f6d694daac83694df3dc3af10d83a1 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -250,11 +250,9 @@ public:
void FixTransform();
/// \brief get complete list of residues
- /// \sa #ResiduesBegin, #ResiduesEnd
ResidueHandleList GetResidueList() const;
/// \brief get complete list of atoms
- /// \sa #AtomsBegin, #AtomsEnd
AtomHandleList GetAtomList() const;
/// \brief get complete list of atom positions
diff --git a/modules/mol/base/src/impl/atom_impl.cc b/modules/mol/base/src/impl/atom_impl.cc
index 3a2b4d013f2c14e82f345e55241aa911d0809ffe..7bc585b14662360f400d241ca77e4a48ee8b1184 100644
--- a/modules/mol/base/src/impl/atom_impl.cc
+++ b/modules/mol/base/src/impl/atom_impl.cc
@@ -355,20 +355,29 @@ void AtomImpl::DeleteAllTorsions() {
EntityImplPtr e=this->GetEntity();
TorsionImplMap::iterator i;
std::vector<TorsionImplMap::iterator> t_rm_vec;
+ std::set<ResidueImpl*> involved_residues;
for (i=e->GetTorsionMap().begin(); i!=e->GetTorsionMap().end(); ++i) {
if (i->second->IsAtomInvolved(shared_from_this())) {
t_rm_vec.push_back(i);
+ involved_residues.insert(i->second->GetFirst()->GetResidue().get());
+ involved_residues.insert(i->second->GetSecond()->GetResidue().get());
+ involved_residues.insert(i->second->GetThird()->GetResidue().get());
+ involved_residues.insert(i->second->GetFourth()->GetResidue().get());
}
}
std::vector<TorsionImplMap::iterator>::iterator it_rm;
for (it_rm=t_rm_vec.begin(); it_rm!=t_rm_vec.end(); ++it_rm) {
e->GetTorsionMap().erase(*it_rm);
}
- TorsionImplList& l=this->GetResidue()->GetTorsionList();
- TorsionImplList::iterator j;
- j=std::remove_if(l.begin(), l.end(),
- bind(&TorsionImpl::IsAtomInvolved, _1, shared_from_this()));
- l.erase(j, l.end());
+
+ for(std::set<ResidueImpl*>::iterator i = involved_residues.begin();
+ i != involved_residues.end(); ++i){
+ TorsionImplList& l = (*i)->GetTorsionList();
+ TorsionImplList::iterator j;
+ j=std::remove_if(l.begin(), l.end(),
+ bind(&TorsionImpl::IsAtomInvolved, _1, shared_from_this()));
+ l.erase(j, l.end());
+ }
}
}}} // ns
diff --git a/modules/mol/base/src/impl/query_ast.cc b/modules/mol/base/src/impl/query_ast.cc
index ea96a485877b9c01226f4acdfa94e69c526fcb99..26e99bed2bfaca2a1d026f758cdd7a11b9c8d32f 100644
--- a/modules/mol/base/src/impl/query_ast.cc
+++ b/modules/mol/base/src/impl/query_ast.cc
@@ -199,7 +199,7 @@ void SelNode::Dump(int level) const{
String op = CompOPToString(op_);
switch(sel_.type) {
case Prop::STRING:
- std::cout << sel_.GetName()<< " " << op << " " << boost::get<String>(param_) << std::endl;
+ std::cout << sel_.GetName()<< " " << op << " " << boost::get<StringOrRegexParam>(param_).str() << std::endl;
break;
case Prop::FLOAT:
std::cout << sel_.GetName()<< " " << op << " " << boost::get<float>(param_) << std::endl;
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index 993683cb223aaf661704ce0c08c81d16f55f1bbf..30e174b24f80da16914b740e946f54c28f38e6ca 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -62,8 +62,6 @@ namespace ost { namespace mol {
/// amino acids, co-enzymes, water coordinated ions, drugs, solvents) as obtained
/// from the PDB.
///
-/// When loading an entity from file, the one-letter and chemical class of a
-/// residue are assigned by the \ref conop::Builder "default builder".
class DLLEXPORT_OST_MOL ResidueBase:
public GenericPropContainer<ResidueBase> {
public:
diff --git a/modules/mol/base/src/spatial_organizer.hh b/modules/mol/base/src/spatial_organizer.hh
index 8876473aa60ed477511029d00617401ff085a418..0e9dce74005141d9103453a806a475704d0ba2b2 100644
--- a/modules/mol/base/src/spatial_organizer.hh
+++ b/modules/mol/base/src/spatial_organizer.hh
@@ -117,7 +117,8 @@ public:
Real dist2=dist*dist;
Index imin = Index::Max(min_, gen_index(pos-VEC(dist,dist,dist)));
Index imax = Index::Min(max_, gen_index(pos+VEC(dist,dist,dist)));
- if ((imax.u-imin.u+1)*(imax.v-imin.v+1)*(imax.w-imin.w+1)>map_.size()) {
+ const size_t tmp = (imax.u-imin.u+1)*(imax.v-imin.v+1)*(imax.w-imin.w+1);
+ if (tmp > map_.size()) {
return this->has_within_all_buckets(pos, dist2);
}
for(int wc=imin.w;wc<=imax.w;++wc) {
diff --git a/modules/mol/base/src/view_op.hh b/modules/mol/base/src/view_op.hh
index 1774b289dc7689166f075500f2ee3c96026e3a35..dea7c29ab58f11f2f70c9c864554c69884592c89 100644
--- a/modules/mol/base/src/view_op.hh
+++ b/modules/mol/base/src/view_op.hh
@@ -73,7 +73,7 @@ EntityView DLLEXPORT_OST_MOL CreateViewFromAtomList(const AtomViewList& atoms);
/// \throw IntegrityError if trying to compare two views that do not point to
/// the same entity.
/// \return a pair of views. \c first contains the elements that are in \p view1,
-/// but not in \p view2, \second contains the elements that are in \p view2
+/// but not in \p view2, \c second contains the elements that are in \p view2
/// but not in \p view1
std::pair<EntityView, EntityView> DLLEXPORT_OST_MOL
CompareViews(const EntityView& view1, const EntityView& view2);
diff --git a/modules/mol/mm/CMakeLists.txt b/modules/mol/mm/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..4468b05a8c86e042baeebb9b56f19468d9f2e4b5
--- /dev/null
+++ b/modules/mol/mm/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_subdirectory(src)
+add_subdirectory(pymod)
+add_subdirectory(tests)
diff --git a/modules/mol/mm/doc/buildingblock.rst b/modules/mol/mm/doc/buildingblock.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c9dbcfd7d936986f5ed18ffa1a3905e852fe6918
--- /dev/null
+++ b/modules/mol/mm/doc/buildingblock.rst
@@ -0,0 +1,459 @@
+Blocks
+================================================================================
+
+.. currentmodule:: ost.mol
+
+The most basic type of residue description is the BuildingBlock. It contains
+information on atom names and their corresponding types, charges and
+optionally also their masses. Interactions for all particles can also
+be defined even though they are optional, except the bonds giving
+information about the connectivity.
+You often need to manipulate building blocks or
+the residues they refer to in an automated manner. That's where the
+BlockModifiers come in, with the GromacsBlockModifier as a specific
+implementation. As a special case there also exist HydrogenConstructors.
+
+
+The BuildingBlock Class
+--------------------------------------------------------------------------------
+
+.. class:: BuildingBlock
+
+ .. method:: Match(residue, [,match_connectivity=True])
+
+ Checks, whether the given residue matches the atom names in the
+ BuildingBlock. The connectivity gets checked optionally.
+
+ :param residue:
+ :param match_connectivity: If set to true, the function checks the bonds
+ in the residue with the defined bonds in the
+ BuildingBlock
+
+ :type residue: :class:`ResidueHandle`
+ :type match_connectivity: :class:`bool`
+
+ :returns: :class:`bool`
+
+ .. method:: Connect(residue, editor)
+
+ Connects atoms of **residue** based on the bond definitions of the
+ BuildingBlock.
+
+ :param residue: Residue to be connected
+ :param editor: Editor associated to the residue's entity
+
+ :type residue: :class:`ResidueHandle`
+ :type editor: :class:`XCSEditor`
+
+ :raises: :class:`RuntimeError` when required atom can not be found in
+ residue
+
+
+ .. method:: AddAtom(name, type, charge,[,mass = None])
+
+ :param name: Name of atom
+ :param type: Its corresponding forcefield type
+ :param charge: Its charge
+ :param mass: Its mass
+
+ :type name: :class:`str`
+ :type type: :class:`str`
+ :type charge: :class:`float`
+ :type mass: :class:`float`
+
+
+
+ .. method:: RemoveAtom(name)
+
+ Removes atom from BuildingBlock with all its associated values and
+ interactions
+
+ :param name: Name of atom to be removed
+
+ :type name: :class:`str`
+
+
+
+ .. method:: ReplaceAtom(name, new_name, new_type, new_charge, [,new_mass = None])
+
+ Replace given atom by resetting name, type, charge and mass. All interactions
+ containing that atom get adapted as well
+
+ :param name: Name of atom to be replaced
+ :param new_name: New name of atom
+ :param new_type: New type of atom
+ :param new_charge: New charge of atom
+ :param new_mass: New mass of atom
+
+ :type name: :class:`str`
+ :type new_name: :class:`str`
+ :type new_type: :class:`str`
+ :type new_charge: :class:`float`
+ :type new_mass: :class:`float`
+
+
+
+ .. method:: RemoveInteractionsToPrev()
+
+ Removes all interactions associated to an atom of a previous residues.
+ This gets indicated in the :class:`BuildingBlock` by an atom name prefixed by a *-*
+
+
+ .. method:: RemoveInteractionsToNext()
+
+ Removes all interactions associated to an atom of a next residues.
+ This gets indicated in the :class:`BuildingBlock` by an atom name prefixed by a *+*
+
+
+ .. method:: AddBond(bond, [,replace_existing = False])
+
+ :param bond: Bond to be added
+ :param replace_existing: Whether potentially already existing bond for the
+ same atoms should be replaced.
+
+ :type bond: :class:`Interaction`
+ :type replace_existing: :class:`bool`
+
+
+ .. method:: AddAngle(angle, [,replace_existing = False])
+
+ :param angle: Angle to be added
+ :param replace_existing: Whether a potentially already existing angle for the
+ same atoms should be replaced.
+
+ :type angle: :class:`Interaction`
+ :type replace_existing: :class:`bool`
+
+
+ .. method:: AddDihedral(dihedral, [,replace_existing = False])
+
+ :param dihedral: Dihedral to be added
+ :param replace_existing: Whether potentially already existing dihedral for the
+ same atoms should be replaced.
+
+ :type dihedral: :class:`Interaction`
+ :type replace_existing: :class:`bool`
+
+
+ .. method:: AddImproper(improper, [,replace_existing = False])
+
+ :param improper: Improper to be added
+ :param replace_existing: Whether potentially already existing improper for the
+ same atoms should be replaced.
+
+ :type improper: :class:`Interaction`
+ :type replace_existing: :class:`bool`
+
+
+ .. method:: AddExclusion(exclusion, [,replace_existing = False])
+
+ :param exclusion: Exclusion to be added
+ :param replace_existing: Whether potentially already existing Exclusion for the
+ same atoms should be replaced.
+
+ :type exclusion: :class:`Interaction`
+ :type replace_existing: :class:`bool`
+
+
+ .. method:: AddCMap(cmap, [,replace_existing = False])
+
+ :param cmap: CMap to be added
+ :param replace_existing: Whether potentially already existing cmap for the
+ same atoms should be replaced.
+
+ :type cmap: :class:`Interaction`
+ :type replace_existing: :class:`bool`
+
+
+ .. method:: AddConstraint(constraint, [,replace_existing = False])
+
+ :param constraint: Constraint to be added
+ :param replace_existing: Whether potentially already existing constraint for the
+ same atoms should be replaced.
+
+ :type constraint: :class:`Interaction`
+ :type replace_existing: :class:`bool`
+
+
+ .. method:: GetType(name)
+
+ Gets forcefield type from atom with given name
+
+ :param name: Name of atom you want the type from
+
+ :type name: :class:`str`
+
+ :returns: :class:`str`
+
+ :raises: :class:`RuntimeError` when atom can not be found in
+ BuildingBlock
+
+ .. method:: GetCharge(name)
+
+ Gets charge from atom with given name
+
+ :param name: Name of atom you want the charge from
+
+ :type name: :class:`str`
+
+ :returns: :class:`float`
+
+ :raises: :class:`RuntimeError` when atom can not be found in
+ BuildingBlock
+
+
+ .. method:: GetMass(name)
+
+ Gets mass from atom with given name
+
+ :param name: Name of atom you want the mass from
+
+ :type name: :class:`str`
+
+ :returns: :class:`float`
+
+ :raises: :class:`RuntimeError` when atom can not be found in
+ BuildingBlock
+
+ .. method:: GetAtoms()
+
+ :returns: :class:`list` of all atom names
+
+ .. method:: GetTypes()
+
+ :returns: :class:`list` of all atom types
+
+ .. method:: GetCharges()
+
+ :returns: :class:`list` of all charges
+
+ .. method:: GetMasses()
+
+ :returns: :class:`list` of all masses
+
+ .. method:: GetBonds()
+
+ :returns: :class:`list` of all bonds
+
+
+ .. method:: GetAngles()
+
+ :returns: :class:`list` of all angles
+
+
+ .. method:: GetDihedrals()
+
+ :returns: :class:`list` of all dihedrals
+
+
+ .. method:: GetImpropers()
+
+ :returns: :class:`list` of all impropers
+
+
+ .. method:: GetCMaps()
+
+ :returns: :class:`list` of all cmaps
+
+
+ .. method:: GetExclusions()
+
+ :returns: :class:`list` of all exlusions
+
+
+ .. method:: GetConstraints()
+
+ :returns: :class:`list` of all constraints
+
+Block Modifiers
+--------------------------------------------------------------------------------
+.. class:: BlockModifier
+
+ Basis class. Block modifiers are used to change building blocks or residues.
+ See :class:`GromacsBlockModifier` for a specific example.
+
+.. class:: GromacsBlockModifier
+
+ .. method:: ApplyOnBuildingBlock(block)
+
+ Applies all defined rules on the given :class:`BuildingBlock`
+
+ :param block: BuildingBlock to be modified
+ :type block: :class:`BuildingBlock`
+
+ .. method:: ApplyOnResidue(residue)
+
+ Applies all defined rules on the given :class:`ResidueHandle`
+
+ :param residue: Residue to be modified
+ :type residue: :class:`ResidueHandle`
+
+ .. method:: AddReplaceRule(name, new_name, new_type, new_charge)
+
+ Rule, that basically renames an atom and also resets its type and charge
+ in a :class:`BuildingBlock`. A simple renaming occurs in a :class:`ResidueHandle`.
+
+ :param name: Name of the atom to be changed
+ :param new_name: Its new name
+ :param new_type: Its new type
+ :param new_charge: Its new charge
+
+ :type name: :class:`str`
+ :type new_name: :class:`str`
+ :type new_type: :class:`str`
+ :type new_charge: :class:`float`
+
+ .. method:: AddAddRule(number, method, atom_names, anchors, type, charge)
+
+ A rule to add new atoms the Gromacs way, see
+ `Gromacs Manual <http://www.gromacs.org/Documentation/Manual>`_
+ for the exact definition of the parameters. A :class:`BuildingBlock`
+ gets modified by adding the new atom definitions and also the
+ corresponding bonds describing the connectivity. In case of
+ :class:`ResidueHandle` the new Atoms with connectivity get added with
+ their positions as defined by the Gromacs adding rule.
+
+ :param number: Number of atoms to be added
+ :param method: Gromacs adding rule
+ :param atom_names: Strings containing the new atom names
+ :param anchors: Strings containing atom names used as anchor
+ :param type: The type the atoms will have
+ :param charge: The charge the atoms will have
+
+ :type number: :class:`int`
+ :type method: :class:`int`
+ :type atom_names: :class:`list`
+ :type anchors: :class:`list`
+ :type type: :class:`str`
+ :type charge: :class:`float`
+
+ .. method:: AddDeleteAtom(name)
+
+ Defines an atom that has to be removed. In case of the
+ :class:`BuildingBlock` this removes this particular atom plus all
+ interactions connected to it, in case of :class:`ResidueHandle`, the
+ atom simply gets deleted.
+
+ :param name: Atom to be deleted
+
+ :type name: :class:`str`
+
+ .. method:: AddBond(bond)
+
+ Adds a bond, this only has effect on :class:`BuildingBlock`, not
+ on :class:`ResidueHandle` when the corresponding Apply function gets
+ called
+
+ :param bond: Bond to be added
+ :type bond: :class:`Interaction`
+
+ .. method:: AddAngle(angle)
+
+ Adds an angle, this only has effect on :class:`BuildingBlock`, not
+ on :class:`ResidueHandle` when the corresponding Apply function gets
+ called
+
+ :param angle: Angle to be added
+ :type angle: :class:`Interaction`
+
+ .. method:: AddDihedral(dihedral)
+
+ Adds a dihedral, this only has effect on :class:`BuildingBlock`, not
+ on :class:`ResidueHandle` when the corresponding Apply function gets
+ called
+
+ :param dihedral: Dihedral to be added
+ :type dihedral: :class:`Interaction`
+
+ .. method:: AddImproper(improper)
+
+ Adds an improper, this only has effect on :class:`BuildingBlock`, not
+ on :class:`ResidueHandle` when the corresponding Apply function gets
+ called
+
+ :param improper: Improper to be added
+ :type improper: :class:`Interaction`
+
+ .. method:: AddCMap(cmap)
+
+ Adds a cmap, this only has effect on :class:`BuildingBlock`, not
+ on :class:`ResidueHandle` when the corresponding Apply function gets
+ called
+
+ :param cmap: CMap to be added
+ :type cmap: :class:`Interaction`
+
+
+Hydrogen Constructors
+--------------------------------------------------------------------------------
+
+.. class:: HydrogenConstructor
+
+ Basis class. Hydrogen constructors are used to add hydrogens to residues.
+
+
+.. class:: GromacsHydrogenConstructor
+
+ The :class:`GromacsHydrogenConstructor` is the Gromacs way of adding
+ hydrogens to a structure.
+
+ .. method:: ApplyOnBuildingBlock(block)
+
+ Guess what it does: !!ABSOLUTELY NOTHING!! just there for consistency
+
+ :param block: Block that won't be changed at all!
+ Isn't that awesome?
+
+ :type block: :class:`BuildingBlock`
+
+ .. method:: ApplyOnResidue(residue)
+
+ Constructs hydrogens based on the defined hydrogen addition rules
+
+ :param residue: Residue to be modified
+
+ :type residue: :class:`ResidueHandle`
+
+ .. method:: AddHydrogenRule(number, method, hydrogen_names, anchors)
+
+ Adds a hydrogen building rule as defined in
+ `Gromacs Manual <http://www.gromacs.org/Documentation/Manual>`_
+
+ :param number: Number of hydrogens to be added
+ :param method: Gromacs adding rule
+ :param hydrogen_names: Strings containing the hydrogen names
+ :param anchors: Strings containing atom names used as anchor
+
+ :type number: :class:`int`
+ :type method: :class:`int`
+ :type hydrogen_names: :class:`list`
+ :type anchors: :class:`list`
+
+.. class:: HeuristicHydrogenConstructor(block)
+
+ As soon as we leave the well defined world of Gromacs residue definitions,
+ we have to find new ways for constructing hydrogens. The
+ :class:`HeuristicHydrogenConstructor` takes a :class:`BuildingBlock` at
+ initialization and builds heuristic rules to build hydrogens based on
+ the connecticity defined in the given block.
+
+ :param block: :class:`BuildingBlock` from which the connectivity
+ information for hydrogen construction is extracted
+
+ .. method:: ApplyOnBuildingBlock(block)
+
+ Guess what it does: !!ABSOLUTELY NOTHING!! Just there for consistency
+
+ :param block: Block that won't be changed at all!
+ Isn't that awesome?
+
+ :type block: :class:`BlockModifier`
+
+ .. method:: ApplyOnResidue(residue)
+
+ Constructs hydrogen based on heuristic rules
+
+ :param residue: Residue to be modified
+
+ :type residue: :class:`ResidueHandle`
+
diff --git a/modules/mol/mm/doc/forcefield.rst b/modules/mol/mm/doc/forcefield.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9c5754152381c0712e176100ffe0d42a8cbb4f3b
--- /dev/null
+++ b/modules/mol/mm/doc/forcefield.rst
@@ -0,0 +1,677 @@
+Forcefields
+================================================================================
+
+.. currentmodule:: ost.mol
+
+The forcefields are a dump for interactions with their parameters, but also
+for atom specific information or residue definitions in the form of a
+:class:`BuildingBlock`. Objects for modifying residues can be set in form of
+:class:`BlockModifier` or :class:`HydrogenConstructor`.
+They're also involved in dealing with the naming mess we're observing in the molecular mechanics
+community and contain definable renaming rules that can be applied on an
+:class:`EntityHandle` for renaming from e.g. PDB standard to the forcefield
+specific standard. The standard forcefields in OpenStructure are loaded from
+the files provided by Gromacs and the "standard" naming is therefore the same.
+This has implications for controlling the protonation states for histidine.
+If you e.g. want to enforce a d-protonated histidine you have to name
+it HISD. Further reading can be found in the
+`Gromacs Manual <http://www.gromacs.org/Documentation/Manual>`_
+
+Loading the standard forcefields provided by OpenStructure
+--------------------------------------------------------------------------------
+
+.. function:: LoadCHARMMForcefield()
+
+ Loads the CHARMM27 forcefield read from Gromacs
+
+ :returns: The loaded :class:`Forcefield`
+
+
+.. function:: LoadAMBERForcefield()
+
+ Loads the AMBER03 forcefield read from Gromacs
+
+ :returns: The loaded :class:`Forcefield`
+
+
+Reading forcefields
+--------------------------------------------------------------------------------
+The :class:`FFReader` object is rather experimental. It has nevertheless been
+thoroughly tested for loading the CHARMM and AMBER forcefields in the
+Gromacs format. The reader is capable of resolving the preprocessor statements
+as they are used in Gromacs.
+
+
+.. class:: FFReader(base_dir)
+
+ :param base_dir: Base path of the reader.
+ All loaded files must be defined relative to this base
+ path.
+
+ :type base_dir: :class:`str`
+
+ The :class:`FFReader` builds up a :class:`Forcefield`, that gets updated with
+ every call to the read functions. If the read files contain preprocessor
+ statements as they are used in Gromacs, they will be applied to all
+ subsequent lines read in. Parsed preprocessor statements are:
+ #include, #define, #ifdef, #ifndef, #else and #endif
+
+ .. method:: ReadGromacsForcefield()
+
+ Searches and reads the forcefield.itp and atomtypes.atp files
+ in the **base_dir** given at initialization. All atom specific
+ informations and bonded as well as nonbonded forces are read
+ this way.
+
+ .. method:: ReadResidueDatabase(basename)
+
+ Searches and reads all files belonging the the residue database
+ defined by **basename**. With *basename=aminoacids* this function
+ searches and reads all files in the **base_dir** matching *aminoacids.x*
+ where *x* is *.rtp .arn .hdb .n.tdb .c.tdb .vsd .r2b*.
+ Only the rtp file is mandatory, all others are neglected if not present.
+
+ :param basename: Basename of residue database to be loaded
+
+ :type basename: :class:`str`
+
+ .. method:: ReadITP(basename)
+
+ Searches and reads the itp file in the **base_dir**. *basename=amazing_ion*
+ would therefore load the file *amazing_ion.itp*
+
+ :param basename: Basename of itp file to be loaded
+
+ :type basename: :class:`str`
+
+ .. method:: SetForcefield(forcefield)
+
+ Resets reader internal forcefield. Everything read so far is lost,
+ except the already read preprocessor statements.
+
+ :param forcefield: Forcefield to be set
+
+ :type forcefield: :class:`Forcefield`
+
+ .. method:: GetForcefield()
+
+ Get the forcefield with everything read so far.
+
+ :returns: The reader internal :class:`Forcefield`
+
+
+
+
+ .. code-block:: python
+
+ path = "path_to_gromacs/share/top/charmm27.ff"
+ reader = FFReader(path)
+
+ #read in the data given in forcefield.itp and atomtypes.atp
+ reader.ReadGromacsForcefield()
+
+ #we also want to read several residue databases
+ reader.Read("aminoacids")
+ reader.Read("rna")
+ reader.Read("dna")
+
+ #ions and water are also nice to have, they're stored in itp files
+ reader.ReadITP("tip3p")
+ reader.ReadITP("ions")
+
+ #let's finally get the reader internal forcefield out
+ ff = reader.GetForcefield()
+
+ #there is also an amazing ion definition in some other directory
+ new_reader = FFReader("path/to/directory/with/itp/files")
+
+ #we want to modify the previously read forcefield
+ new_reader.SetForcefield(ff)
+
+ #and read the amazing ion definition from an itp file
+ #note, that any previously defined preprocessor statements
+ #from the previous reader are lost
+ new_reader.ReadITP("amazing_ion")
+
+ #the new forcefield finally contains everything we need, lets
+ #extract it and save it down
+ ff = new_reader.GetForcefield()
+ ff.Save("charmm_forcefield.dat")
+
+The Forcefield Class
+--------------------------------------------------------------------------------
+
+.. class:: Forcefield
+
+
+ .. method:: Save(filename)
+
+ Dumps forcefield into a binary file on disk
+
+ :param filename: Filename of the saved forcefield
+
+ :type filename: :class:`str`
+
+
+
+ .. method:: Load(filename)
+
+ reads in binary forcefield file
+
+ :param filename: Filename of the forcefield to be loaded
+
+ :type filename: :class:`str`
+
+ :returns: loaded :class:`Forcefield`
+
+ :raises: :class:`RuntimeError` when **filename** can't be found
+
+
+
+ .. method:: AddBond(bond)
+
+ :param bond: Bond to be added
+
+ :type bond: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no bond specific FuncType
+
+
+
+ .. method:: AddAngle(angle)
+
+ :param angle: Angle to be added
+
+ :type angle: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no angle specific FuncType
+
+
+ .. method:: AddDihedral(dihedral)
+
+ :param dihedral: Dihedral to be added
+
+ :type dihedral: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no dihedral specific FuncType
+
+
+ .. method:: AddImproper(improper)
+
+ :param improper: Improper to be added
+
+ :type improper: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no improper specific FuncType
+
+
+ .. method:: AddCMap(cmap)
+
+ :param cmap: CMap to be added
+
+ :type cmap: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no cmap specific FuncType
+
+
+ .. method:: AddImplicitGenborn(gb)
+
+ :param gb: GB to be added
+
+ :type gb: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no gb specific FuncType
+
+
+ .. method:: AddLJ(lj)
+
+ :param lj: LJ to be added
+
+ :type lj: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no lj specific FuncType
+
+
+ .. method:: AddLJPair(lj_pair)
+
+ :param lj_pair: LJPair to be added
+
+ :type lj_pair: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no lj_pair specific FuncType
+
+
+ .. method:: AddConstraint(constraint)
+
+ :param constraint: Constraint to be added
+
+ :type constraint: :class:`Interaction`
+
+ :raises: :class:`RuntimeError` when given interaction has
+ no constraint specific FuncType
+
+
+ .. method:: AddMass(type, mass)
+
+ :param type: Type of atom
+ :param mass: Its mass
+
+ :type type: :class:`str`
+ :type mass: :class:`float`
+
+ .. method:: SetFudgeLJ(factor)
+
+ :param factor: Factor with which the 1,4 Lennard Jones term
+ should be dampened
+
+ :type factor: :class:`float`
+
+
+ .. method:: SetFudgeQQ(factor)
+
+ :param factor: Factor with which the 1,4 electrostatic term
+ should be dampened
+
+ :type factor: :class:`float`
+
+
+ .. method:: SetGenPairs(gen_pairs)
+
+ :param gen_pairs: If set to false, all 1,4 interactions must be set
+ with AddLJPair. The Lorentz-Berthelot rule gets
+ used otherwise.
+
+ :type gen_pairs: :class:`bool`
+
+
+ .. method:: AddResidueRenamingRule(name, ff_main_name, ff_n_ter_name, ff_c_ter_name, ff_two_ter_name)
+
+ :param name: Original name of the residue
+ (e.g. PDB/Gromacs standard)
+ :param ff_main_name: Forcefield specific residue name
+ :param ff_n_ter_name: Forcefield specific name if the residue
+ is N-Terminal
+ :param ff_c_ter_name: Forcefield specific name if the residue
+ is C-Terminal
+ :param ff_two_ter_name: Forcefield specific name if the residue
+ is N- and C-Terminal
+
+ :type name: :class:`str`
+ :type ff_main_name: :class:`str`
+ :type ff_n_ter_name: :class:`str`
+ :type ff_c_ter_name: :class:`str`
+ :type ff_two_ter_name: :class:`str`
+
+
+
+ .. method:: AddAtomRenamingRule(res_name, old_atom_name, new_atom_name)
+
+ :param res_name: Forcefield specific name of the residue the
+ atom belongs to
+
+ :param old_atom_name: Atom name in PDB/Gromacs standard
+
+ :param new_atom_name: FF specific atom name
+
+ :type res_name: :class:`str`
+ :type old_atom_name: :class:`str`
+ :type new_atom_name: :class:`str`
+
+
+ .. method:: AddBuildingBlock(name, block)
+
+ :param name: Name of residue this :class:`BuildingBlock`
+ is supposed to be related to
+
+ :param block: BuildingBlock to be added
+
+ :type block: :class:`BuildingBlock`
+ :type name: :class:`str`
+
+
+ .. method:: AddHydrogenConstructor(name, h_constructor)
+
+ :param name: Name of residue this
+ :class:`HydrogenConstructor`
+ is supposed to be related to
+
+ :param h_constructor: HydrogenConstructor to be added
+
+ :type name: :class:`str`
+ :type h_constructor: :class:`HydrogenConstructor`
+
+
+ .. method:: AddBlockModifier(name, modifier)
+
+ :param name: Name of residue this
+ :class:`BlockModifier`
+ is supposed to be related to
+
+ :param modifier: BlockModifier to be added
+
+ :type name: :class:`str`
+ :type modifier: :class:`BlockModifier`
+
+
+ .. method:: SetStandardCTer(res_name, ter_name)
+
+ Setting a standard CTer influences the behaviour of the GetCTerModifier
+ function. If no specific block modifier is defined there, this is the
+ one that gets returned.
+
+ :param res_name: Forcefield specific residue name this block
+ modifier is supposed to be related to
+
+ :param ter_name: Name of the default c-terminal block
+ modifier for this residue
+
+ :type res_name: :class:`str`
+ :type ter_name: :class:`str`
+
+
+ .. method:: SetStandardNTer(res_name, ter_name)
+
+ Setting a standard NTer incluences the behaviour of the GetNTerModifier
+ function. If no specific block modifier is defined there, this is the
+ one that gets returned.
+
+ :param res_name: Forcefield specific residue name this block
+ modifier is supposed to be related to
+
+ :param ter_name: Name of the default n-terminal block
+ modifier for this residue
+
+ :type res_name: :class:`str`
+ :type ter_name: :class:`str`
+
+
+
+ .. method:: AssignFFSpecificNames(ent,[,reverse = False])
+
+ This function does the forcefield specific renaming magic. It takes
+ the given :class:`EntityHandle` and applies the rules set in
+ AddResidueRenamingRule and AddAtomRenamingRule.
+
+ :param ent: Entity to be renamed
+
+ :param reverse: If False, the function does the renaming
+ from PDB/Gromacs naming to the forcefield
+ specific naming.
+ If True, the opposite happens.
+
+ :type ent: :class:`EntityHandle`
+ :type reverse: :class:`bool`
+
+
+ .. method:: GetBond(type1, type2)
+
+ :param type1: Type of interacting particle 1
+ :param type2: Type of interacting particle 2
+
+ :type type1: :class:`str`
+ :type type2: :class:`str`
+
+ :returns: an :class:`Interaction` with a bond FuncType
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given types can be found
+
+
+ .. method:: GetAngle(type1, type2, type3)
+
+ :param type1: Type of interacting particle 1
+ :param type2: Type of interacting particle 2
+ :param type3: Type of interacting particle 3
+
+ :type type1: :class:`str`
+ :type type2: :class:`str`
+ :type type3: :class:`str`
+
+ :returns: an :class:`Interaction` with a angle FuncType
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given types can be found
+
+
+ .. method:: GetDihedrals(type1, type2, type3, type4)
+
+ Several dihedral definitions can be merged to one dihedral function.
+ This function therefore returns a list.
+ In a first step all dihedrals matching the given types are gathered
+ and returned.
+ If no dihedrals can be found, the search continues by including
+ wildcard characters in the atom types (X). All found dihedrals
+ matching with all possible combinations of wildcards are then gathered
+ and returned.
+
+ :param type1: Type of interacting particle 1
+ :param type2: Type of interacting particle 2
+ :param type3: Type of interacting particle 3
+ :param type4: Type of interacting particle 4
+
+ :type type1: :class:`str`
+ :type type2: :class:`str`
+ :type type3: :class:`str`
+ :type type4: :class:`str`
+
+ :returns: a :class:`list` of :class:`Interaction` objects with dihedral
+ FuncType matching given types
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given types can be found
+
+
+
+ .. method:: GetImpropers(type1, type2, type3, type4)
+
+ The same search strategy as in GetDihedrals is used to extract
+ the impropers.
+
+ :param type1: Type of interacting particle 1
+ :param type2: Type of interacting particle 2
+ :param type3: Type of interacting particle 3
+ :param type4: Type of interacting particle 4
+
+ :type type1: :class:`str`
+ :type type2: :class:`str`
+ :type type3: :class:`str`
+ :type type4: :class:`str`
+
+ :returns: a :class:`list` of :class:`Interaction` objects with improper
+ FuncType matching given types
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given types can be found
+
+
+ .. method:: GetCMap(type1, type2, type3, type4, type5)
+
+ :param type1: Type of interacting particle 1
+ :param type2: Type of interacting particle 2
+ :param type3: Type of interacting particle 3
+ :param type4: Type of interacting particle 4
+ :param type5: Type of interacting particle 5
+
+ :type type1: :class:`str`
+ :type type2: :class:`str`
+ :type type3: :class:`str`
+ :type type4: :class:`str`
+ :type type5: :class:`str`
+
+ :returns: an :class:`Interaction` with a cmap FuncType
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given types can be found
+
+
+ .. method:: GetImplicitGenborn(type)
+
+ :param type: Type of particle
+
+ :type type: :class:`str`
+
+ :returns: an :class:`Interaction` with a gb FuncType
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given type can be found
+
+
+ .. method:: GetLJ(type)
+
+ :param type: Type of particle
+
+ :type type: :class:`str`
+
+ :returns: an :class:`Interaction` with a lj FuncType
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given type can be found
+
+
+ .. method:: GetLJ(type1, type2,[,pair=False])
+
+ :param type1: Type of interacting particle 1
+ :param type2: Type of interacting particle 2
+ :param pair: If set to true, the interaction is
+ assumed to be a 1,4-interaction and
+ the set lj_pairs are first searched
+ for matches. In case of no success,
+ the function uses the Lorentz-Berthelot
+ rule to combine the sigma and epsilon
+ parameters.
+ If set to false, the Lorentz-Berthelot
+ rule is applied directly.
+
+ :type type1: :class:`str`
+ :type type2: :class:`str`
+ :type pair: :class:`bool`
+
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given types can be found
+ or when pair is true and no
+ appropriate lj_pair is set
+ despite gen_pair flag being false.
+
+
+ .. method:: GetConstraint(type1, type2)
+
+ :param type1: Type of interacting particle 1
+ :param type2: Type of interacting particle 2
+
+ :type type1: :class:`str`
+ :type type2: :class:`str`
+
+ :returns: an :class:`Interaction` with a constraint FuncType
+
+ :raises: :class:`RuntimeError` when no :class:`Interaction`
+ matching given types can be found
+
+
+ .. method:: GetMass(type)
+
+ :param type: Type of particle
+
+ :type type: :class:`str`
+
+ :returns: :class:`float` - the mass
+
+ :raises: :class:`RuntimeError` if no mass has been set for this
+ atom type
+
+
+ .. method:: GetFudgeLJ()
+
+ :returns: :class:`float` - Factor with which the 1,4 Lennard Jones
+ term should be dampened
+
+ .. method:: GetFudgeQQ()
+
+ :returns: :class:`float` - Factor with which the 1,4
+ electrostatic term should be dampened
+
+
+ .. method:: GetAtomType(res_name, atom_name)
+
+ :param res_name: Forcefield specific residue name
+
+ :param atom_name: Forcefield specific atom name belonging
+ to that residue
+
+ :type res_name: :class:`str`
+ :type atom_name: :class:`str`
+
+ :returns: :class:`str` - atom type
+
+ :raises: :class:`RuntimeError` if forcefield has no such
+ :class:`BuildingBlock` or when atom is not present
+ in that :class:`BuildingBlock`
+
+
+ .. method:: GetHydrogenConstructor(res_name)
+
+ :param res_name: Name of residue
+ :type res_name: :class:`str`
+
+ :returns: :class:`HydrogenConstructor` for this name, invalid if it can't
+ be found
+
+
+ .. method:: GetBuildingBlock(res_name)
+
+ :param res_name: Name of residue
+ :type res_name: :class:`str`
+
+ :returns: :class:`BuildingBlock` for this name, invalid if it can't be
+ found
+
+
+ .. method:: GetBlockModifier(res_name)
+
+ :param res_name: Name of residue
+ :type res_name: :class:`str`
+
+ :returns: :class:`BlockModifier` for this name, invalid if it can't
+ be found
+
+
+ .. method:: GetNTerModifier(res_name,[,ter_name=""])
+
+ :param res_name: Name of residue
+
+ :param ter_name: If not set, the ter_name
+ defined by SetStandardNTer gets used
+
+ :type res_name: :class:`str`
+ :type ter_name: :class:`str`
+
+
+ :returns: :class:`BlockModifier` for this name, invalid if it can't
+ be found
+
+
+ .. method:: GetCTerModifier(name,[,ter_name=""])
+
+ :param res_name: Name of residue
+
+ :param ter_name: If not set, the ter_name
+ defined by SetStandardCTer gets used
+
+ :type res_name: :class:`str`
+ :type ter_name: :class:`str`
+
+ :returns: :class:`BlockModifier` for this name, invalid if it can't
+ be found
+
+
+
+
+
diff --git a/modules/mol/mm/doc/integrators.rst b/modules/mol/mm/doc/integrators.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ed94d86955d0046806e872480146bf05a38393d3
--- /dev/null
+++ b/modules/mol/mm/doc/integrators.rst
@@ -0,0 +1,179 @@
+Integrators
+================================================================================
+
+.. currentmodule:: ost.mol
+
+.. class:: Integrator
+
+ The :class:`Integrator` are a wrapper around the integrators provided by OpenMM and
+ have to be attached to the :class:`Settings` when setting up a simulation.
+ They define the algorithm used to integrate the equations of motion of the system.
+
+
+
+Verlet Dynamics
+--------------------------------------------------------------------------------
+
+.. class:: VerletIntegrator(step_size)
+
+ Implementation of Verlet dynamics
+
+ :param step_size: Defining timestep in ps
+ :type step_size: :class:`float`
+
+
+.. class:: VariableVerletIntegrator(error_tol)
+
+ Implementation of Verlet dynamics with variable time steps
+
+ :param error_tol: Error tolerance
+ :type error_tol: :class:`float`
+
+ .. method:: GetErrorTolerance()
+
+ :returns: :class:`float`
+
+ .. method:: SetErrorTolerance(tol)
+
+ :param tol: Error tolerance
+ :type tol: :class:`float`
+
+
+Langevin Dynamics
+--------------------------------------------------------------------------------
+
+.. class:: LangevinIntegrator(temperature, friction_coeff, step_size)
+
+ Implementation of the Langevin dynamics
+
+ :param temperature: Temperature of heat bath in K
+ :param friction_coeff: Friction coefficient coupling the
+ system to the heat bath in 1/ps
+ :param step_size: Defining timestep in ps
+
+ :type temperature: :class:`float`
+ :type friction_coeff: :class:`float`
+ :type step_size: :class:`float`
+
+ .. method:: GetTemperature()
+
+ :returns: :class:`float` - the temperature in K
+
+ .. method:: SetTemperature(temperature)
+
+ :param temperature: Temperature in K
+ :type temperature: :class:`float`
+
+ .. method:: GetFriction()
+
+ :returns: :class:`float` - the friction in 1/ps
+
+ .. method:: SetFriction(friction)
+
+ :param friction: Friction in 1/ps
+ :type friction: :class:`float`
+
+ .. method:: GetRandomNumberSeed()
+
+ :returns: :class:`int`
+
+ .. method:: SetRandomNumberSeed(seed)
+
+ :param seed: Random number seed
+ :type seed: :class:`int`
+
+
+
+
+.. class:: VariableLangevinIntegrator(temperature, friction_coeff, error_tol)
+
+ Implementation of Langevin dynamics with variable time steps
+
+ :param temperature: Temperature of heat bath in K
+ :param friction_coeff: Friction coefficient coupling the
+ system to the heat bath in 1/ps
+ :param error_tol: Error tolerance
+
+ :type temperature: :class:`float`
+ :type friction_coeff: :class:`float`
+ :type error_tolerance: :class:`float`
+
+ .. method:: GetTemperature()
+
+ :returns: :class:`float` - the temperature in K
+
+ .. method:: SetTemperature(temperature)
+
+ :param temperature: Temperature in K
+ :type temperature: :class:`float`
+
+ .. method:: GetFriction()
+
+ :returns: :class:`float` - the friction in 1/ps
+
+ .. method:: SetFriction(friction)
+
+ :param friction: Friction in 1/ps
+ :type friction: :class:`float`
+
+ .. method:: GetRandomNumberSeed()
+
+ :returns: :class:`int`
+
+ .. method:: SetRandomNumberSeed(seed)
+
+ :param seed: Random number seed
+ :type seed: :class:`int`
+
+ .. method:: GetErrorTolerance()
+
+ :returns: :class:`float`
+
+ .. method:: SetErrorTolerance(tol)
+
+ :param tol: Error tolerance
+ :type tol: :class:`float`
+
+
+Brownian Dynamics
+--------------------------------------------------------------------------------
+
+.. class:: BrownianIntegrator(temperature, friction_coeff, step_size)
+
+ Implementation of Brownian dynamics
+
+ :param temperature: Temperature of heat bath in K
+ :param friction_coeff: Friction coefficient coupling the
+ system to the heat bath in 1/ps
+ :param step_size: Defining timestep in ps.
+
+ :type temperature: :class:`float`
+ :type friction_coeff: :class:`float`
+ :type step_size: :class:`float`
+
+ .. method:: GetTemperature()
+
+ :returns: :class:`float` - the temperature in K
+
+ .. method:: SetTemperature(temperature)
+
+ :param temperature: Temperature in K
+ :type temperature: :class:`float`
+
+ .. method:: GetFriction()
+
+ :returns: :class:`float` - the friction in 1/ps
+
+ .. method:: SetFriction(friction)
+
+ :param friction: Friction in 1/ps
+ :type friction: :class:`float`
+
+ .. method:: GetRandomNumberSeed()
+
+ :returns: :class:`int`
+
+ .. method:: SetRandomNumberSeed(seed)
+
+ :param seed: Random number seed
+ :type seed: :class:`int`
diff --git a/modules/mol/mm/doc/interaction.rst b/modules/mol/mm/doc/interaction.rst
new file mode 100644
index 0000000000000000000000000000000000000000..95d193e1a9e64b9e312590033bc3214d1b198fc9
--- /dev/null
+++ b/modules/mol/mm/doc/interaction.rst
@@ -0,0 +1,267 @@
+Interactions
+================================================================================
+
+.. currentmodule:: ost.mol
+
+The :class:`Interaction` object is intended to build a basic container that can
+be used
+in various scenarios. At the initialization a FuncType has to be defined.
+Whenever names, types or parameters are set, the number of parameters
+gets checked according to the FuncType. A name or type can also consist of
+a wildcard expressed as X.
+
+
+The FuncType enum
+--------------------------------------------------------------------------------
+
+Every Interaction is linked to one particular *FuncType* describing the types
+of interactions supported by OpenStructure. There are 15 possible values with
+Invalid defining an unknown interaction:
+
+ HarmonicBond, HarmonicAngle, UreyBradleyAngle, PeriodicDihedral,
+ PeriodicImproper, HarmonicImproper, CMap, LJ, LJPair, GBSA,
+ DistanceConstraint, Exclusion, HarmonicPositionRestraint,
+ HarmonicDistanceRestraint, Invalid
+
+The implementation guarantees that the parameter related to atom types,
+names, parameters are checked regarding their dimension (e.g. 3 atoms and 2
+parameters for a harmonic angle)
+
+
+Interaction Parametrization
+--------------------------------------------------------------------------------
+
+* HarmonicBond, Interacting Particles: 2, Num Parameters: 2
+
+ #. :class:`float` bond length in nm
+ #. :class:`float` force constant in kJ/mol/nm^2
+
+* HarmonicAngle, Interacting Particles: 3, Num Parameters: 2
+
+ #. :class:`float` angle in radians
+ #. :class:`float` force constant in kJ/mol/radian^2
+
+* UreyBradleyAngle, Interacting Particles: 3, Num Parameters: 4
+
+ #. :class:`float` angle in radians
+ #. :class:`float` angle force constant in kJ/mol/radian^2
+ #. :class:`float` bond length in nm
+ #. :class:`float` bond force constant in kJ/mol/nm^2
+
+* PeriodicDihedral, Interacting Particles: 4, Num Parameters: 3
+
+ #. :class:`int` multiplicity
+ #. :class:`float` phase in radians
+ #. :class:`float` force constant in kJ/mol/radian^2
+
+* PeriodicImproper, Interacting Particles: 4, Num Parameters: 3
+
+ #. :class:`int` multiplicity
+ #. :class:`float` phase in radians
+ #. :class:`float` force constant in kJ/mol/radian^2
+
+* HarmonicImproper, Interacting Particles: 4, Num Parameters: 2
+
+ #. :class:`float` angle in radians
+ #. :class:`float` force constant in kJ/mol/radian^2
+
+* CMap, Interacting Particles: 5, Num Parameters: n*n+1
+
+ #. :class:`list` of :class:`float` of size n*n+1, first value describes the dimension n of the cmap, the other n*n values describe the correction map in kJ/mol in the ordering (phi1,psi1),(phi1,psi2)... and torsion angles in [-pi,pi] (will be converted to the format OpenMM prefers)
+
+* LJ, Interacting Particles: 1, Num Parameters: 2
+
+ #. :class:`float` sigma in nm
+ #. :class:`float` epsilon in kJ/mol
+
+* LJPair, Interacting Particles: 2, Num Parameters: 2
+
+ #. :class:`float` sigma in nm
+ #. :class:`float` epsilon in kJ/mol
+
+* GBSA, Interacting Particles: 1, Num Parameters: 2
+
+ #. :class:`float` GBSA radius in nm
+ #. :class:`float` OBC scaling factor
+
+* DistanceConstraint, Interacting Particles: 2, Num Parameters: 1
+
+ #. :class:`float` constraint distance
+
+* Exclusion, Interacting Particles: 2, Num Parameters: 0
+
+* HarmonicPositionRestraint, Interacting Particles: 1, Num Parameters: 7
+
+ #. :class:`float` ref pos x
+ #. :class:`float` ref pos y
+ #. :class:`float` ref pos z
+ #. :class:`float` force constant
+ #. :class:`float` x_scale
+ #. :class:`float` y_scale
+ #. :class:`float` z_scale
+
+
+* HarmonicDistanceRestraint, Interacting Particles: 2, Num Parameters: 2
+
+ #. :class:`float` restraint length
+ #. :class:`float` force constant
+
+
+
+The Interaction Class
+--------------------------------------------------------------------------------
+
+.. class:: Interaction (func_type)
+
+ :param func_type: :class:`FuncType` defining a particular interaction
+
+
+ .. method:: SetTypes(types)
+
+ Sets the forcefield specific atom types.
+
+ :param types: Strings describing the force field specific atom types.
+ :type types: :class:`list`
+
+ :raises: :class:`RuntimeError` when size of input is not consistent with
+ the interactions functype
+
+
+ .. method:: SetNames(names)
+
+ Sets atom names
+
+ :param names: Strings describing the atom names
+ :type names: :class:`list`
+
+ :raises: :class:`RuntimeError` when size of input is not
+ consistent with the interactions functype
+
+
+ .. method:: SetParam(param)
+
+ Sets interaction specific parameters.
+
+ :param param: Float values .
+ :type param: :class:`list`
+
+ :raises: :class:`RuntimeError` when size of input is not consistent with
+ the interactions functype
+
+
+ .. method:: GetTypes()
+
+ Get previously set types
+
+ :returns: :class:`list`
+
+
+
+ .. method:: GetNames()
+
+ Get previously set names
+
+ :returns: :class:`list`
+
+
+ .. method:: GetParam()
+
+ Get previously set parameters
+
+ :returns: :class:`list`
+
+
+ .. method:: GetAtoms(residue)
+
+ Returns an :class:`AtomHandleList` containing the atoms in residue matching
+ the atom names of the interaction
+
+ :param residue: Residue from which atoms are extracted
+ :type residue: :class:`ResidueHandle`
+
+ :returns: :class:`AtomHandleList`
+
+ :raises: :class:`RuntimeError` when an atom cannot be found in
+ **residue**
+
+ .. method:: GetFuncType()
+
+ Returns the functype enum of the interaction
+
+ :returns: :class:`FuncType`
+
+
+ .. method:: ReplaceAtom(name, new_name, new_type)
+
+ Searches for given atom name. If found, this particular atom name
+ gets changed to new_name. If the atom types are set as well, the
+ associated atom type gets also reset to new_type.
+
+ :param name: Name of atom to be replaces
+ :param new_name: Its new name
+ :param new_type: Its new type
+
+ :type name: :class:`str`
+ :type new_name: :class:`str`
+ :type new_type: :class:`str`
+
+ :returns: :class:`bool` whether replacement was successful or not
+
+
+ .. method:: MatchTypes(atom_types)
+
+ Checks, whether the given types match the internal types. The match
+ can be "as is" or in reversed order
+
+ :param atom_types: Atom types to be matched
+ :type atom_types: :class:`list`
+ :returns: :class:`bool`
+
+
+ .. method:: MatchNames(atom_names)
+
+ Checks, whether the given names match the internal names. The match
+ can be "as is" or in reversed order
+
+ :param atom_names: Atom names to be matched
+ :type atom_names: :class:`list`
+ :returns: :class:`bool`
+
+
+ .. method:: HasName(name)
+
+ Checks, whether the given name is present in the internal names
+
+ :param name: Name to be checked
+ :type name: :class:`str`
+ :returns: :class:`bool`
+
+
+ .. method:: HasType(type)
+
+ Checks, whether the given type is present in the internal types
+
+ :param type: Type to be checked
+ :type type: :class:`str`
+ :returns: :class:`bool`
+
+
+ .. method:: IsParametrized()
+
+ Checks, whether the parameters have been set
+
+ :returns: :class:`bool`
+
+
+ .. method:: HasTypeWildcard()
+
+ Checks, whether one of the types is a wildcard ('X')
+
+ :returns: :class:`bool`
+
+
+ .. method:: HasNameWildcard()
+
+ Checks, whether one of the names is a wildcard ('X')
+
+ :returns: :class:`bool`
diff --git a/modules/mol/mm/doc/molmm.rst b/modules/mol/mm/doc/molmm.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f243b7dfb4869e7123ccb0757479745fc3a85b8b
--- /dev/null
+++ b/modules/mol/mm/doc/molmm.rst
@@ -0,0 +1,93 @@
+The mm Module
+================================================================================
+
+.. currentmodule:: ost.mol
+
+Introduction
+--------------------------------------------------------------------------------
+
+The mol.mm module provides a wrapper around the
+`OpenMM <http://openmm.org>`_ molecular mechanics library to provide
+basic molecular dynamics (MD) capabilities fully embedded into the OpenStructure universe.
+The heart of every simulation is the :class:`Topology` describing how the
+particles of an :class:`EntityHandle` interact. The :class:`Simulation` class connects the :class:`EntityHandle` with a :class:`Topology` and allows you to perform energy minimizations
+or move the simulation through time using an :class:`Integrator`.
+A :class:`Topology` can either be built from scratch by adding
+one interaction after the other or automatically using the
+:class:`TopologyCreator`. The process of :class:`Topology` building
+and setting up a :class:`Simulation` gets controlled with the :class:`Settings`.
+
+Latest Publication of `OpenMM <http://openmm.org>`_:
+P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, and V. S. Pande. "OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation." J. Chem. Theor. Comput. 9(1):461-469. (2013)
+
+
+
+
+Installation
+--------------------------------------------------------------------------------
+
+OpenStructure does not come by default with
+`OpenMM <http://openmm.org>`_ support.
+You have to install it as an additional dependency and
+recompile OpenStructure to dive into the amazing world of GPU accelerated
+molecular mechanics. Once installed, you have to pass cmake additional
+flags to allow compilation with OpenMM support. e.g.:
+
+ .. code-block:: bash
+
+ cmake . -DENABLE_MM=1 -DOPEN_MM_INCLUDE_DIR=/path/to/openmm/include
+ -DOPEN_MM_LIBRARY=/path/to/openmm/lib/libOpenMM.so
+ -DOPEN_MM_PLUGIN_DIR=/path/to/openmm/lib/plugins
+
+
+Setting up a simple simulation
+--------------------------------------------------------------------------------
+
+
+ .. code-block:: python
+
+ from ost.mol import mm
+
+ prot=io.LoadPDB('1crn',remote=True)
+
+ #set up the simulation
+ settings = mm.Settings()
+ settings.integrator = mm.LangevinIntegrator(310,1,0.002)
+ settings.forcefield = mm.LoadCHARMMForcefield()
+ sim = mm.Simulation(prot,settings)
+
+ #minimize it
+ sim.ApplySD(tolerance = 1.0, max_iterations = 200)
+
+ #create a trajectory observer and register it to the simulation
+ #every 10 steps, the actual positions will be written down to disk
+ observer = mm.TrajWriter(10,"example_traj.pdb","example_traj.dcd")
+ sim.Register(observer)
+
+ #run the simulation
+ sim.Steps(10000)
+
+ #Trajectory Observer needs to finalize, otherwise you might get a corrupt dcd file
+ observer.Finalize()
+
+
+Doing more sophisticated stuff
+--------------------------------------------------------------------------------
+
+You want to create your own :class:`BuildingBlock` to parameterize custom
+residues? Or even generate your own custom :class:`Forcefield`?
+Check out the mm dir in the examples/code_fragments directory.
+
+Documentation
+--------------------------------------------------------------------------------
+
+.. toctree::
+ interaction
+ buildingblock
+ forcefield
+ settings
+ topology
+ observers
+ integrators
+ simulation
+
diff --git a/modules/mol/mm/doc/observers.rst b/modules/mol/mm/doc/observers.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1aecc69fed3ff22253aef5f7a8ddfa8e31df1bbd
--- /dev/null
+++ b/modules/mol/mm/doc/observers.rst
@@ -0,0 +1,55 @@
+Observers
+================================================================================
+
+.. currentmodule:: ost.mol
+
+Observers can be registered to a :class:`Simulation` and get called at a
+defined interval.
+
+
+Trajectory observers
+--------------------------------------------------------------------------------
+
+.. class:: TrajObserver(rhythm)
+
+ Stores and updates the md trajectory produced by a :class:`Simulation`
+ in memory
+
+ :param rhythm: Frequency, at which the observer gets
+ notified by the simulation
+ :type rhythm: :class:`int`
+
+ .. method:: GetTraj()
+
+ Get current Trajectory
+
+ :returns: :class:`ost.mol.CoordGroupHandle`
+
+ .. method:: Rhythm()
+
+ :returns: :class:`int` calling rythm
+
+
+.. class:: TrajWriter(rythm, pdb_filename, dcd_filename)
+
+ Writes the MD trajectory produced by a :class:`Simulation` directly to
+ disk in dcd format
+
+ :param rythm: Frequency, at which the observer gets
+ notified by the simulation
+ :param pdb_filename: Name of produced pdb file
+ :param dcd_filename: Name of produced dcd file
+
+ :type rythm: :class:`int`
+ :type pdb_filename: :class:`str`
+ :type dcd_filename: :class:`str`
+
+ .. method:: Rhythm()
+
+ :returns: :class:`int` calling rhythm
+
+ .. method:: Finalize()
+
+ Obligatory function to be called after the last simulation step to
+ write missing information into the dcd header
+
diff --git a/modules/mol/mm/doc/settings.rst b/modules/mol/mm/doc/settings.rst
new file mode 100644
index 0000000000000000000000000000000000000000..648be8bcc11b04995057433bf2644eedc679a94d
--- /dev/null
+++ b/modules/mol/mm/doc/settings.rst
@@ -0,0 +1,277 @@
+The Molecular Mechanics Settings
+================================================================================
+
+.. currentmodule:: ost.mol
+
+The :class:`Settings` define all parameters to control the buildup of a
+:class:`Topology` in the :class:`TopologyCreator` and the final setup
+of the :class:`Simulation` object.
+
+.. class:: Settings
+
+ .. attribute:: add_bonds
+
+ Flag, whether bonds should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_angles
+
+ Flag, whether angles should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_dihedrals
+
+ Flag, whether dihedrals should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_impropers
+
+ Flag, whether impropers should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_cmaps
+
+ Flag, whether cmaps should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_exclusions
+
+ Flag, whether exclusions should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_nonbonded
+
+ Flag, whether nonbonded interactions should be parametrized
+ in :class:`TopologyCreator`. default: True
+
+ .. attribute:: add_gbsa
+
+ Flag, whether GBSA interactions should be parametrized
+ in :class:`TopologyCreator`. default: False
+
+ .. attribute:: constrain_hbonds
+
+ Flag, whether bonds involving hydrogens should be constrained
+ in :class:`TopologyCreator`. default: False
+
+ .. attribute:: constrain_bonds
+
+ Flag, whether all bonds should be constrained in
+ :class:`TopologyCreator`. default: False
+
+ .. attribute:: rigid_water
+
+ Flag, whether water molecules should be made rigid in
+ :class:`TopologyCreator`. This is achieved by adding
+ a distance constraint on the O-H bonds and an additional
+ one between the two hydrogens. default: False
+
+ .. attribute:: strict_interactions
+
+ Makes sure that an error is thrown when a particular interaction cannot
+ be parametrized with the given forcefield in the :class:`TopologyCreator`.
+ By setting it to False, these cases just get ignored. default: True
+
+ .. attribute:: ideal_bond_length_constraints
+
+ Flag, whether the ideal bond length from the :class:`Forcefield` should be
+ taken for distance constraints in the :class:`TopologyCreator`.
+ The actual distances from the :class:`EntityHandle` get taken otherwise.
+ default: True
+
+ .. attribute:: fix_heavy_atoms
+
+ Flag, whether all heavy atom positions (non hydrogens) should be fixed in
+ space in the :class:`TopologyCreator`. default: False
+
+ .. attribute:: kill_electrostatics
+
+ Flag, whether all charges should just be set to zero in the
+ :class:`TopologyCreator`. default: False
+
+ .. attribute:: generate_disulfid_bonds
+
+ Flag, whether disulfid bonds based on a simple geometric criterion
+ (SG-SG dist < 2.5A) should be built in :class:`TopologyCreator`.
+ default: True
+
+ .. attribute:: nonbonded_method
+
+ Nonbonded method set up at the creation of the :class:`Simulation`.
+ Must be one of mm.NoCutoff, mm.CutoffNonPeriodic, mm.CutoffPeriodic
+ mm.Ewald or mm.PME. default: mm.NoCutoff
+
+ .. attribute:: nonbonded_cutoff
+
+ Nonbonded cutoff set when simulation is set up. default: 10.0
+
+ .. attribute:: remove_cmm_motion
+
+ Whether a center of mass remover object should be attached to the
+ :class:`Simulation`. default: True
+
+ .. attribute:: cmm_frequency
+
+ Frequency regarding simulation steps when the cmm remover should be applied.
+ default: 1
+
+ .. attribute:: periodic_box_extent
+
+ :class:`ost.geom.Vec3` describing the X,Y and Z extents of the rectangular
+ simulation_box defined when setting up the :class:`Simulation`.
+ default: (0,0,0)
+
+ .. attribute:: init_temperature
+
+ Initial simulation velocities get set according to a Boltzman distribution
+ controlled by init_temperature(Kelvin). default: 0.0
+
+ .. attribute:: forcefield
+
+ :class:`Forcefield` that is used in :class:`TopologyCreator`. default: None
+
+ .. attribute:: termini_exceptions
+
+ Use termini other than the defaults set in the :class:`Forcefield` when
+ using :class:`TopologyCreator`. Has to be a :class:`TerminiExceptions`
+ object. default: None
+
+ .. attribute:: platform
+
+ Platform used by OpenMM to do the calculations. Must be one of mm.Reference,
+ mm.CPU, mm.CUDA or mm.OpenCL. If anything else than the reference platform
+ is used, the attribute openmm_plugin_directory has to be set accordingly.
+ default: mm.Reference
+
+ .. attribute:: reference_properties
+
+ :class:`dict` of OpenMM specific properties that can be set for the
+ reference platform.
+
+ .. attribute:: cpu_properties
+
+ :class:`dict` of OpenMM specific properties that can be set for the
+ cpu platform.
+
+ .. attribute:: opencl_properties
+
+ :class:`dict` of OpenMM specific properties that can be set for the
+ opencl platform.
+
+ .. attribute:: cuda_properties
+
+ :class:`dict` of OpenMM specific properties that can be set for the
+ cuda platform.
+
+ .. attribute:: add_thermostat
+
+ Flag, whether an Andersen thermostat should be attached when settings up
+ the :class:`Simulation`. default: False
+
+ .. attribute:: thermostat_temperature
+
+ Temperature for the Andersen thermostat in K. default: NaN
+
+ .. attribute:: thermostat_collision_frequency
+
+ Collision frequency of the Andersen thermostat in 1/ps. default: NaN
+
+ .. attribute:: add_barostat
+
+ Flag, whether an MonteCarlo barostat should be attached when setting up
+ the :class:`Simulation`. default: False
+
+ .. attribute:: barostat_temperature
+
+ Temperature for the MonteCarlo Barostat in K. default: NaN
+
+ .. attribute:: barostat_pressure
+
+ Pressure for the MonteCarlo Barostat in bar. default: NaN
+
+ .. attribute:: barostat_frequency
+
+ Frequency of the MonteCarlo Barostat. default: 25
+
+ .. attribute:: integrator
+
+ Integrator to move the simulation forward in time. OpenMM offers following
+ Integrators: :class:`VerletIntegrator`, :class:`BrownianIntegrator`,
+ :class:`LangevinIntegrator`, :class:`VariableVerletIntegrator` and
+ :class:`VariableLangevinIntegrator`. default: None
+
+ .. attribute:: solvent_dielectric
+
+ Solvent dielectric constant. This is used for the GBSA force when the
+ :class:`Simulation` gets set up. default: 78.3
+
+ .. attribute:: solute_dielectric
+
+ Solute dielectric constant. This is used for the GBSA force when the
+ :class:`Simulation` gets set up. default: 1.0
+
+ .. attribute:: reaction_field_dielecric
+
+ Sets the reaction field dielectric for the Nonbonded Force when setting
+ up the :class:`Simulation`. default: 78.3
+
+ .. attribute:: use_dispersion_correction
+
+ Flag, whether the dispersion correction should be used when setting
+ up the Nonbonded Force in the :class:`Simulation`. default: True
+
+ .. attribute:: keep_ff_specific_naming
+
+ When running through the :class:`TopologyCreator`, the given entity gets
+ renamed to the forcefield specific naming. If set to true, the naming
+ stays like that, if not the entity gets renamed to PDB standard.
+ default: True
+
+ .. attribute:: openmm_plugin_directory
+
+ Path where OpenMM specific plugins are searched. If you want
+ to use other platforms than Reference, this has to be set.
+ default: "/usr/local/openmm/lib/plugins"
+
+ .. attribute:: custom_plugin_directory
+
+ Path where custom plugins are searched for.
+ default: "/usr/local/openmm/lib/plugins"
+
+
+
+
+.. class:: TerminiExceptions
+
+ Can be used to define exceptions from the standard assignments
+ assigned in the :class:`Forcefield`.
+
+ .. method:: SetException(residue, exception_name)
+
+ :param residue: Residue for which the exception
+ should be set.
+ :param exception_name: Name of the
+ Blockmodifier in the forcefield that should be
+ applied in case of a termini
+
+ :type residue: :class:`ResidueHandle`
+ :type exception_name: :class:`str`
+
+ .. method:: HasException(residue)
+
+ :param residue: Residue that should be checked for
+ exceptions
+ :type residue: :class:`ResidueHandle`
+
+ :returns: :class:`bool` True if **residue** has an exception
+
+ .. method:: GetException(residue)
+
+ :param residue: Residue containing the exception
+ :type residue: :class:`ResidueHandle`
+
+ :raises: :class:`RuntimeError` if **residue** has no associated exception
+
+ :returns: :class:`str` describing the name of the Blockmodifier in
+ the forcefield that should be applied in case of a
+ terminal residue
diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst
new file mode 100644
index 0000000000000000000000000000000000000000..217c1cc7df013f3b0c427586e62144c1d681e6b9
--- /dev/null
+++ b/modules/mol/mm/doc/simulation.rst
@@ -0,0 +1,447 @@
+Simulation
+================================================================================
+
+.. currentmodule:: ost.mol
+
+The simulation finally connects a :class:`Topology` with an
+:class:`EntityHandle`. While applying minimization or
+md tasks, the current positions of the simulation object can be
+mapped back to the attached structure at any time.
+
+
+
+.. class:: Simulation(entity, settings)
+
+ First constructor that takes an :class:`ost.mol.EntityHandle` as an input
+ and automatically constructs an internal :class:`Topology` according
+ to the provided **settings**. Be aware, that the **entity** will be altered
+ depending on hydrogen/termini definitions in the :class:`Forcefield` attached
+ to the **settings**
+
+ :param entity: Entity from which a default
+ :class:`Topology` will be created according to the
+ **settings**
+ :param settings: Controls the parametrization of
+ the :class:`Simulation` and the buildup of the
+ internal :class:`Topology`
+
+ :type entity: :class:`EntityHandle`
+ :type settings: :class:`Settings`
+
+ :raises: :class:`RuntimeError` when construction of
+ :class:`Topology` fails
+
+.. class:: Simulation(topology,entity,settings)
+
+ Second constructor that takes a :class:`Topology`, a consistent
+ :class:`ost.mol.EntityHandle` and a :class:`Settings` as input.
+
+ :param topology: Topology to initialize the :class:`Simulation`
+ :param entity: Entity that is consistent with
+ the provided **topology**
+ :param settings: Controls the parametrization of
+ the :class:`Simulation`
+
+ :type topology: :class:`Topology`
+ :type entity: :class:`EntityHandle`
+ :type settings: :class:`Settings`
+
+ :raises: :class:`RuntimeException` when number of atoms in
+ **entity** is not equal the number of particles
+ in **topology**
+
+
+ .. method:: Save(filename, settings)
+
+ Dumps current status of the simulation with its connected **entity** onto
+ disk. All informations from the **entity** except plain chains, residues,
+ atoms and bonds are lost.
+
+ :param filename: Filename
+ :type filename: :class:`str`
+
+ .. method:: Load(filename)
+
+ Loads a dumped simulation from disk. You have to make sure, that the provided
+ settings are consistent with those from the saved simulation. Undefined
+ behaviour must be expected otherwise.
+
+ :param filename: Filename
+ :param settings: Settings to reparametrize loaded simulation
+
+ :type filename: :class:`str`
+ :type settings: :class:`Settings`
+
+ .. method:: ApplyLBFGS([tolerance=1.0,max_iterations=1000])
+
+ Run minimization using the Limited-memory Broyden–Fletcher–Goldfarb–Shanno
+ (L-BFGS) method.
+
+ :param tolerance: Tolerance describing abort criteria of minimization.
+ The tolerance is interpreted as the root mean square
+ value of all force components.
+ :param max_iterations: Maximum number of minimization iterations
+
+ :type tolerance: :class:`float`
+ :type max_iterations: :class:`int`
+
+
+ .. method:: ApplySD([tolerance=100,max_iterations=1000])
+
+ Run minimization using the steepest descend method.
+
+ :param tolerance: Tolerance describing abort criteria of minimization.
+ The tolerance is interpreted as the norm of the maximum
+ force acting onto the particles.
+ :param max_iterations: Maximum number of minimization iterations
+
+ :type tolerance: :class:`float`
+ :type max_iterations: :class:`int`
+
+ :returns: :class:`bool` whether tolerance has been reached
+
+ .. method:: Steps(steps)
+
+ Runs the simulation for **steps** number of steps.
+
+ :param steps: Number of steps to perform
+ :type steps: :class:`int`
+
+ .. method:: GetPositions([enforce_periodic_box = false, in_angstrom = true])
+
+ :param enforce_periodic_box: True if periodic box has to be enforced
+ :param in_angstrom: True if positions should be in Angstrom, they're in nm
+ otherwise
+
+ :type enforce_periodic_box: :class:`bool`
+ :type in_angstrom: :class:`bool`
+
+ :returns: A :class:`ost.geom.Vec3List` of all the positions of the atoms in the Entity.
+
+ .. method:: SetPositions(positions,[,in_angstrom = true])
+
+ :param positions: Positions to be set
+ :param in_angstrom: True if **positions** are in Angstrom, they're expected
+ to be in nm otherwise
+
+ :type positions: :class:`ost.geom.Vec3List`
+ :type in_angstrom: :class:`bool`
+
+ .. method:: UpdatePositions([enforce_periodic_box=false])
+
+ Sets the positions of the atoms in the :class:`EntityHandle` to the current positions of the simulation.
+
+ :param enforce_periodic_box: True if periodic box should be enforced
+ :type enforce_periodic_box: :class:`bool`
+
+ .. method:: GetVelocities()
+
+ :returns: A :class:`~ost.geom.Vec3List` of all the velocities of the atoms in the Entity.
+
+ .. method:: GetForces()
+
+ :returns: A :class:`~ost.geom.Vec3List` of all the resulting forces for each atom in the Entity.
+
+ .. method:: SetVelocities(velocities)
+
+ :param velocities: Velocities to be set
+ :type velocities: :class:`ost.geom.Vec3List`
+
+ .. method:: GetEntity()
+
+ :returns: :class:`EntityHandle` attached to the simulation
+
+ .. method:: GetEnergy()
+
+ :returns: :class:`float` *Potential + Kinetic* energy in kJ/mol of current
+ simulation state
+
+ .. method:: GetPotentialEnergy()
+
+ :returns: :class:`float` *Potential* energy in kJ/mol of current simulation
+ state
+
+ .. method:: GetKineticEnergy()
+
+ :returns: :class:`float` *Kinetic* energy in kJ/mol of current simulation
+ state
+
+ .. method:: GetTopology()
+
+ :returns: :class:`Topology` attached to the simulation
+
+ .. method:: GetPeriodicBoxExtents()
+
+ :returns: :class:`~ost.geom.Vec3` Extents of the periodic box
+
+ .. method:: SetPeriodicBoxExtents(vec)
+
+ :param vec: Periodic box extents in A
+ :type vec: :class:`ost.geom.Vec3`
+
+ .. method:: Register(observer)
+
+ Adds an observer to the simulation object. This can be used for example to write out the trajectory during the simulation.
+
+ :param observer: Observer to be attached
+ :type observer: :class:`Observer`
+
+ .. method:: AddPositionConstraint(index)
+
+ Fixes the position of the particle with index given in the argument.
+
+ :param index: Particle to be fixed
+ :type index: :class:`int`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
+
+ .. method:: AddPositionConstraints(indices)
+
+ Fixes the position of the atoms with the indices given in in the argument.
+
+ :param indices: Particles to be fixed
+ :type indices: :class:`list`
+
+ :raises: :class:`RuntimeError` when an index in **indices**
+ exceeds number of particles
+
+ .. method:: ResetPositionConstraints()
+
+ Removes all position constraints.
+
+ .. method:: ResetHarmonicBond(index, bond_length, force_constant)
+
+ Update of the harmonic bond parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Harmonic Bond to be reset
+ :param bond_length: New bond length in nm
+ :param force_constant: New force constant in kJ/mol/nm^2
+
+ :type index: :class:`int`
+ :type bond_length: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic bonds
+
+ .. method:: ResetHarmonicAngle()
+
+ Update of the harmonic angle parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Harmonic Angle to be reset
+ :param angle: New Angle in radians
+ :param force_constant: New force constant in kJ/mol/radian^2
+
+ :type index: :class:`int`
+ :type angle: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic angles
+
+ .. method:: ResetUreyBradleyAngle(index, angle, angle_force_constant, bond_length, bond_force_constant)
+
+ Update of the Urey-Bradley angle parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Urey-Bradley angle that has to be reset
+ :param angle: New angle in radians
+ :param angle_force_constant: New angle force constant kJ/mol/radian^2
+ :param bond_length: New bond length in nm
+ :param bond_force_constant: New bond force constant in kJ/mol/nm^2
+
+ :type index: :class:`int`
+ :type angle: :class:`float`
+ :type angle_force_constant: :class:`float`
+ :type bond_length: :class:`float`
+ :type bond_force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of urey-bradley angles
+
+ .. method:: ResetPeriodicDihedral(index, multiplicity, phase, force_constant)
+
+ Update of the periodic dihedral parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Periodic dihedral to be reset
+ :param multiplicity: New Multiplicity
+ :param phase: New phase in radians
+ :param force_constant: New force constant in kJ/mol/radian^2
+
+ :type index: :class:`int`
+ :type multiplicity: :class:`int`
+ :type phase: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of periodic dihedrals
+
+
+ .. method:: ResetPeriodicImproper(index, multiplicity, phase, force_constant)
+
+ Update of the periodic improper parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Periodic improper to be reset
+ :param multiplicity: New multiplicity
+ :param phase: New phase in radians
+ :param force_constant: New force constant kJ/mol/radian^2
+
+ :type index: :class:`int`
+ :type multiplicity: :class:`int`
+ :type phase: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of periodic impropers
+
+ .. method:: ResetHarmonicImproper(index, phase, force_constant)
+
+ Update of the harmonic improper parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Harmonic improper to be reset
+ :param phase: New phase in radians
+ :param force_constant: New force constant kJ/mol/radian^2
+
+ :type index: :class:`int`
+ :type phase: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic impropers
+
+ .. method:: ResetLJPair(index,sigma,epsilon)
+
+ Update of the LJ pair parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: LJ pair to be reset
+ :param sigma: New sigma in nm
+ :param epsilon: New epsilon in kJ/mol
+
+ :type index: :class:`int`
+ :type sigma: :class:`float`
+ :type epsilon: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of LJ pairs
+
+
+ .. method:: ResetDistanceConstraint(index, constraint_length)
+
+ Update of the distance constraint parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Distance constraint to be reset
+ :param constraint_length: New constraint length in nm
+
+ :type index: :class:`int`
+ :type constraint_length: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of distance constraints
+
+ .. method:: ResetHarmonicPositionRestraint(index,ref_position, force_constant,x_scale,y_scale,z_scale)
+
+ Update of the harmonic position restraint parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Harmonic position restraint to be reset
+ :param ref_position: New reference position in nm
+ :param force_constant: New force constant in kJ/mol/nm^2
+ :param x_scale: New x-scale
+ :param y_scale: New y-scale
+ :param z_scale: New z-scale
+
+ :type index: :class:`int`
+ :type ref_position: :class:`ost.geom.Vec3`
+ :type force_constant: :class:`float`
+ :type x_scale: :class:`float`
+ :type y_scale: :class:`float`
+ :type z_scale: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic position restraints
+
+ .. method:: ResetHarmonicDistanceRestraint(index, length, force_constant)
+
+ Update of the harmonic distance restraint parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Harmonic distance restraint to be reset
+ :param length: New restraint length in nm
+ :param force_constant: New force constant kJ/mol/nm^2
+
+ :type index: :class:`int`
+ :type length: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of harmonic distance restraints
+
+ .. method:: ResetLJ(index,sigma,epsilon)
+
+ Update of the lj parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: LJ to be reset
+ :param sigma: New sigma in nm
+ :param epsilon: New epsilon in kJ/mol
+
+ :type index: :class:`int`
+ :type sigma: :class:`float`
+ :type epsilon: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
+
+ .. method:: ResetGBSA(index,radius,scaling)
+
+ Update of the GBSA parameters in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: : GB to be reset
+ :param radius: New radius in nm
+ :param scaling: New OBC scaling
+
+ :type index: :class:`int`
+ :type radius: :class:`float`
+ :type scaling: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
+
+ .. method:: ResetCharge(index,charge)
+
+ Update of the charge in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Charge to be reset
+ :param charge: New Charge
+
+ :type index: :class:`int`
+ :type charge: :class:`float`
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
+
+
+ .. method:: ResetMass(index,mass)
+
+ Update of the mass in the simulation **and**
+ in the attached :class:`Topology`
+
+ :param index: Mass to be reset
+ :param mass: New mass
+
+ :type index: :class:`int`
+ :type mass: :class:`float`
+
+ :raises: :class:`RuntimeError` when **index** exceeds
+ number of particles
+
+
+
diff --git a/modules/mol/mm/doc/topology.rst b/modules/mol/mm/doc/topology.rst
new file mode 100644
index 0000000000000000000000000000000000000000..421be2fe9cf5d95ea3cd89352994f5e67bdcbbe6
--- /dev/null
+++ b/modules/mol/mm/doc/topology.rst
@@ -0,0 +1,1387 @@
+Topology
+================================================================================
+
+.. currentmodule:: ost.mol
+
+The :class:`Topology` object is an abstract representation of a protein
+structure or any combination of particles that interact with each other in
+some way. Being initialized with a list of masses representing the particles,
+the topology allows to define arbitrary forces between these particles. The
+:class:`Topology` gets internally translated to a molecular mechanics system
+as soon as a :class:`Simulation` is set up. To make setting up a
+:class:`Topology` more convenient, the :class:`TopologyCreator` class allows
+to create a :class:`Topology` based on an mm :class:`Settings` object,
+that should suffice for most needs.
+
+Automatically create topologies
+--------------------------------------------------------------------------------
+
+.. class:: TopologyCreator
+
+ .. method:: Create(entity, settings)
+
+ Creates a topology given an :class:`EntityHandle` and a :class:`Settings`
+ object. Note, that the :class:`EntityHandle` is passed by reference
+ and gets altered by rebuilding bonds, adding hydrogens and modification of
+ terminal residues based on the information given by the
+ :class:`Settings`/:class:`Forcefield`.
+ The Topology Creation process consists of:
+
+ #. Rename to the Gromacs standard
+
+ #. Kill all bonds
+
+ #. Build difulfide bonds if flag is set in **settings**
+
+ #. Rename residues/atoms to the standard defined in the forcefield
+
+ #. Extract the building blocks from the forcefield for every residue
+
+ #. Apply BlockModifiers on termini and reconstruct hydrogens with HydrogenConstructors
+
+ #. Reconnect based on the connectivity definitions in the building blocks
+
+ #. Check, whether the residues match with the building blocks
+
+ #. Extract bonds/angles etc. based on the flags in the **settings**
+
+ #. Impropers and CMaps get only extracted when they are defined in the :class:`BuildingBlock`
+
+ #. Add Parametrization from :class:`Forcefield` to the :class:`Topology`. Note, that you can override the :class:`Forcefield` parametrization if you add this particular :class:`Interaction` in a parameterized form in the :class:`BuildingBlock`
+
+ #. Rename entity back to PDB naming if flag is set accordingly in **settings**
+
+ :param entity: Entity for which to create :class:`Topology`
+ :param settings: Settings to control :class:`Topology` buildup
+
+ :type entity: :class:`ost.mol.EntityHandle`
+ :type settings: :class:`Settings`
+
+
+ :raises: :class:`RuntimeError` if settings has no
+ :class:`Forcefield` assigned
+
+ :raises: :class:`RuntimeError` if there is a residue with no
+ appropriate :class:`BuildingBlock` in the
+ :class:`Forcefield`
+
+ :raises: :class:`RuntimeError` if there is a
+ :class:`ResidueHandle` not matching the
+ :class:`BuildingBlock` definition in the
+ :class:`Forcefield`
+
+ :raises: :class:`RuntimeError` if there is an interaction
+ that has no parameters in the forcefield. This
+ :class:`RuntimeError` can be supressed by setting the
+ appropriate flag in the :class:`Settings` object.
+
+
+The Topology Class
+--------------------------------------------------------------------------------
+
+.. class:: Topology(masses)
+
+ :param masses: :class:`list` of the particles'masses
+
+ .. method:: Save(filename)
+
+ Dump Toplogy into binary file
+
+ :param filename: Name of file
+ :type filename: :class:`str`
+
+
+ .. method:: Load(filename)
+
+ Load binary topology from disk
+
+ :param filename: Name of file
+ :type filename: :class:`str`
+
+ :returns: loaded :class:`Topology`
+
+ :raises: :class:`RuntimeError` when file can't be found
+
+
+ .. method:: Merge(other)
+
+ Merges in another :class:`Topology` and adds all their particles and interactions.
+ Assuming the actual :class:`Topology` containing n particles, the indexing of the
+ other :class:`Topology` gets altered by adding n everywhere.
+
+ :param other: Topology to merge in
+ :type other: :class:`Topology`
+
+ :raises: :class:`RuntimeError` if fudge parameters are not consistent
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains charges but the **other** not
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains sigmas but the **other** not
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains epsilons but the **other** not
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains GBSA Radii but the **other** not
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains OBC scalings but the **other** not
+
+ .. method:: Merge(ent, other, other_ent)
+
+ Merges in another :class:`Topology` and adds all their particles and
+ interactions. Assuming the actual :class:`Topology` contains n particles,
+ the indexing of the other :class:`Topology` gets altered by adding n
+ everywhere. This version of the Merge function assumes the current topology
+ describes the :class:`EntityHandle` ent and the other :class:`Topology`
+ describes the :class:`EntityHandle` other_ent. During merging, all
+ chains, residues, atoms and bonds from **other_ent** are pulled into **ent** in
+ a way, that the current :class:`Topology` is consistent with the
+ :class:`EntityHandle` **ent**.
+
+ :param ent: Entity consistent with current topology
+ :param other: Topology to merge in
+ :param other_ent: Entity consistent with **other**
+
+ :type ent: :class:`ost.mol.EntityHandle`
+ :type other: :class:`Topology`
+ :type other_ent: :class:`ost.mol.EntityHandle`
+
+ :raises: :class:`RuntimeError` if fudge parameters are not consistent
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains charges but the other not
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains sigmas but the other not
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains epsilons but the other not
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains GBSA Radii but the other not
+
+ :raises: :class:`RuntimeError` if current :class:`Topology`
+ contains OBC scalings but the other not
+
+ :raises: :class:`RuntimeError` if the number of atoms in one
+ of the entities is not consistent with their related
+ topologies.
+
+ :raises: :class:`RuntimeError` other_ent contains a chain with
+ a name already present in **ent**.
+
+
+ .. method:: AddHarmonicBond(index_one, index_two, bond_length, force_constant)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param bond_length: Bond length in nm
+ :param force_constant: Force constant in kJ/mol/nm^2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type bond_length: :class:`float`
+ :type force_constant: :class:`float`
+
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+
+ .. method:: AddHarmonicAngle(index_one, index_two, index_three, angle,
+ force_constant)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param angle: Angle in radians
+ :param force_constant: Force constant in kJ/mol/radian^2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type angle: :class:`float`
+ :type force_constant: :class:`float`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: AddUreyBradleyAngle(index_one, index_two, index_three,
+ angle, angle_force_constant,
+ bond_length, bond_force_constant)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param angle: Angle in radians
+ :param angle_force_constant: Angle force constant kJ/mol/radian^2
+ :param bond_length: Bond length in nm
+ :param bond_force_constant: Bond force constant kJ/mol/nm^2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type angle: :class:`float`
+ :type angle_force_constant: :class:`float`
+ :type bond: :class:`float`
+ :type bond_force_constant: :class:`float`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: AddPeriodicDihedral(index_one, index_two, index_three, index_four,
+ multiplicity, phase, force_constant)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param index_four: Index of particle 4
+ :param multiplicity: Multiplicity
+ :param phase: Phase in radians
+ :param force_constant: Force constant in kJ/mol/radian^2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type index_four: :class:`int`
+ :type multiplicity: :class:`int`
+ :type phase: :class:`float`
+ :type force_constant: :class:`float`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: AddPeriodicImproper(index_one, index_two, index_three, index_four,
+ multiplicity, phase, force_constant)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param index_four: Index of particle 4
+ :param multiplicity: Multiplicity
+ :param phase: Phase in radians
+ :param force_constant: Force constant in kJ/mol/radian^2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type index_four: :class:`int`
+ :type multiplicity: :class:`int`
+ :type phase: :class:`float`
+ :type force_constant: :class:`float`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: AddHarmonicImproper(index_one, index_two, index_three, index_four,
+ angle, force_constant)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param index_four: Index of particle 4
+ :param angle: Angle in radians
+ :param force_constant: Force constant kJ/mol/radian^2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type index_four: :class:`int`
+ :type angle: :class:`float`
+ :type force_constant: :class:`float`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: AddCMap(index_one, index_two, index_three, index_four,
+ index_five, dimension, values)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param index_four: Index of particle 4
+ :param index_five: Index of particle 5
+ :param dimension: Dimension of CMap
+ :param values: Map of size
+ **dimension** * **dimension** describing the correction
+ map in kJ/mol. The values have to be ordered like
+ (phi1,psi1),(phi1,psi2)...(phi1,psin),
+ (phi2,psi1),(phi2,psi2)...(phi2,psin),
+ ...(phin,psin).
+ the range for phi and psi are [-pi,pi[
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type index_four: :class:`int`
+ :type index_five: :class:`int`
+ :type dimension: :class:`int`
+ :type values: :class:`list`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when size of values is not
+ **dimension** * **dimension** or index exceeds number of
+ particles.
+
+
+ .. method:: AddLJPair(index_one, index_two, sigma, epsilon)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param sigma: Sigma in nm
+ :param epsilon: Epsilon in kJ/mol
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type sigma: :class:`float`
+ :type epsiolon: :class:`float`
+
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles or when particular LJPair is already
+ parameterized
+
+
+ .. method:: AddDistanceConstraint(index_one, index_two, distance)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param distance: Constraint distance in nm
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type distance: :class:`float`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles or when particular distance constraint
+ is already parameterized
+
+
+ .. method:: AddExclusion(index_one, index_two)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles or when particular exclusion is already set
+
+
+ .. method:: AddPositionConstraint(index)
+
+ :param index: Index of particle to be constrained
+
+ :type index: :class:`int`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: AddHarmonicPositionRestraint(index, reference_pos, force_constant,
+ x_scale=1.0, y_scale=1.0, z_scale=1.0)
+
+ Adds a harmonic position restraint for a particle in the form:
+ force_constant*(x_scale*(x-x0)^2+y_scale*(y-y0)^2+z_scale*(z-z0)^2)
+
+ :param index: Index of particle to be constrained
+ :param reference_pos: Reference position in nm
+ :param force_constant: Force constant in kJ/mol/nm^2
+ :param x_scale: X-scale
+ :param y_scale: Y-scale
+ :param z_scale: Z-scale
+
+ :type index: :class:`int`
+ :type reference_pos: :class:`ost.geom.Vec3`
+ :type force_constant: :class:`float`
+ :type x_scale: :class:`float`
+ :type y_scale: :class:`float`
+ :type z_scale: :class:`float`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: AddHarmonicDistanceRestraint(index_one, index_two, length, force_constant)
+
+ Adds a force between two particles in the form:
+ force_constant * (b-b0)^2
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param length: Restraint length in nm
+ :param force_constant: Force constant in kJ/mol/nm^2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type length: :class:`float`
+ :type force_constant: :class:`float`
+
+ :returns: :class:`int` index of added interaction
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: ResetPositionConstraints()
+
+ Removes all position constraints
+
+
+ .. method:: ResetExclusions()
+
+ Removes all set exclusions
+
+
+ .. method:: SetSigmas(sigmas)
+
+ :param sigmas: Sigma parameters for all particles in nm
+
+ :type sigmas: :class:`list` (:class:`float`)
+
+ :raises: :class:`RuntimeError` when list size is inconsistent
+ with number of particles
+
+
+ .. method:: SetSigma(index, sigma)
+
+ :param index: Index of particle in nm
+ :param sigma: Sigma
+
+ :type index: :class:`int`
+ :type sigma: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: SetEpsilons(epsilons)
+
+ :param epsilons: Epsilon parameters for all particles in kJ/mol
+
+ :type epsilons: :class:`list` (:class:`float`)
+
+ :raises: :class:`RuntimeError` when list size is inconsistent
+ with number of particles
+
+
+ .. method:: SetEpsilon(index, epsilon)
+
+ :param index: Index of particle
+ :param epsilon: Epsilon in kJ/mol
+
+ :type index: :class:`int`
+ :type epsilon: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: SetGBSARadii(radii)
+
+ :param radii: GBSA radii for all particles in nm
+
+ :type radii: :class:`list` (:class:`float`)
+
+ :raises: :class:`RuntimeError` when list size is inconsistent
+ with number of particles
+
+
+ .. method:: SetGBSARadius(index, radius)
+
+ :param index: Index of particle
+ :param radius: GBSA radius in nm
+
+ :type index: :class:`int`
+ :type radius: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: SetOBCScalings(scalings)
+
+ :param scalings: OBC scaling factors for all particles
+
+ :type scalings: :class:`list` (:class:`float`)
+
+ :raises: :class:`RuntimeError` when list size is inconsistent
+ with number of particles
+
+
+ .. method:: SetOBCScaling(index, scaling)
+
+ :param index: Index of particle
+ :param scaling: OBC scaling factor
+
+ :type index: Index of particle
+ :type scaling: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: SetCharges(charges)
+
+ :param charges: Charges for all particles
+
+ :type charges: :class:`list` (:class:`float`)
+
+ :raises: :class:`RuntimeError` when list size is inconsistent
+ with number of particles
+
+
+ .. method:: SetCharge(index, charge)
+
+ :param index: Index of particle
+ :param charge: Charge
+
+ :type index: :class:`int`
+ :type charge: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+ .. method:: SetMasses(masses)
+
+ :param masses: Masses for all particles
+ :type masses: :class:`list` (:class:`float`)
+
+ :raises: :class:`RuntimeError` when list size is inconsistent
+ with number of particles
+
+
+ .. method:: SetMass(index, mass)
+
+ :param index: Index of particle
+ :param mass: Mass
+
+ :type index: :class:`int`
+ :type mass: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ particles
+
+
+ .. method:: SetFudgeQQ(fudge)
+
+ :param fudge: Dampening factor for electrostatic 1,4 interactions
+ :type fudge: :class:`float`
+
+ .. method:: SetFudgeLJ(fudge)
+
+ :param fudge: Dampening factor for LJ 1,4 interactions
+ :type fudge: :class:`float`
+
+
+ .. method:: GetHarmonicBondParameters(index)
+
+ :param index: Index of harmonic bond
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic bonds
+
+
+ .. method:: GetHarmonicAngleParameters(index)
+
+ :param index: Index of harmonic angle
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic angles
+
+ .. method:: GetUreyBradleyAngleParameters(index)
+
+ :param index: Index of Urey-Bradley angle
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set Urey-Bradley angles
+
+ .. method:: GetPeriodicDiheralParameters(index)
+
+ :param index: Index of periodic dihedral
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set periodic dihedrals
+
+ .. method:: GetPeriodicImproperParameters(index)
+
+ :param index: Index of periodic improper
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set periodic impropers
+
+ .. method:: GetHarmonicImproperParameters(index)
+
+ :param index: Index of harmonic improper
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic impropers
+
+
+ .. method:: GetCMapParameters(index)
+
+ :param index: Index of CMap
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set cmaps
+
+
+ .. method:: GetLJPairParameters(index)
+
+ :param index: Index of LJ pair
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set lj pairs
+
+
+ .. method:: GetDistanceConstraintParameters(index)
+
+ :param index: Index of distance constraint
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set distance constraints
+
+
+ .. method:: GetHarmonicPositionRestraintParameters(index)
+
+ :param index: Index of harmonic position restraint
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic position restraints
+
+
+ .. method:: GetHarmonicDistanceRestraintParameters(index)
+
+ :param index: Index of harmonic distance restraint
+ :type index: :class:`int`
+
+ :returns: :class:`tuple` containing the indices of the involved
+ particles and the set parameters
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic distance restraints
+
+
+ .. method:: SetHarmonicBondParameters(index, bond_length, force_constant)
+
+ Replaces existing parameters for particular interaction
+
+ :param index: Index of harmonic bond
+ :param bond_length: New bond length in nm
+ :param force_constant: New force constant in kJ/mol/nm^2
+
+ :type index: :class:`int`
+ :type bond_length: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic bonds
+
+
+ .. method:: SetHarmonicAngleParameters(index, angle, force_constant)
+
+ Replaces existing parameters for particular interaction
+
+ :param index: Index of harmonic angle
+ :param angle: New angle in radians
+ :param force_constant: New force constant kJ/mol/radian^2
+
+ :type index: :class:`int`
+ :type angle: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic angles
+
+ .. method:: SetUreyBradleyAngleParameters(index, angle, angle_force_constant,
+ bond_length, bond_force_constant)
+
+ Replaces existing parameters for particular interaction
+
+ :param index: Index of Urey-Bradley angle
+ :param angle: New angle in radians
+ :param angle_force_constant: New angle force constant in kJ/mol/radian^2
+ :param bond_length: New bond length in nm
+ :param bond_force_constant: New bond force constant in kJ/mol/nm^2
+
+ :type index: :class:`int`
+ :type angle: :class:`float`
+ :type angle_force_constant: :class:`float`
+ :type bond_length: :class:`float`
+ :type bond_force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set Urey-Bradley angles
+
+ .. method:: SetPeriodicDiheralParameters(index, multiplicity, phase, force_constant)
+
+ Replaces existing parameters for a particular interaction
+
+ :param index: Index of periodic dihedral
+ :param multiplicity: New periodicity
+ :param phase: New phase in radians
+ :param force_constant: New force constant in kJ/mol/radian^2
+
+ :type index: :class:`int`
+ :type multiplicity: :class:`int`
+ :type phase: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set periodic dihedrals
+
+ .. method:: SetPeriodicImproperParameters(index, multiplicity, phase, force_constant)
+
+ Replaces existing parameters for a particular interaction
+
+ :param index: Index of periodic improper
+ :param multiplicity: New multiplicity
+ :param phase: New phase in radians
+ :param force_constant: New force constant kJ/mol/radian^2
+
+ :type index: :class:`int`
+ :type multiplicity: :class:`int`
+ :type phase: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set periodic impropers
+
+ .. method:: SetHarmonicImproperParameters(index, angle, force_constant)
+
+ Replaces existing parameters for a particular interaction
+
+ :param index: Index of harmonic improper
+ :param angle: New angle in radians
+ :param force_constant: New force constant kJ/mol/radian^2
+
+ :type index: :class:`int`
+ :type angle: :class:`float`
+ :type force_constant: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic impropers
+
+
+ .. method:: SetCMapParameters(index, dimension, map)
+
+ Replaces existing parameters for a particular interaction
+
+ :param index: Index of CMap
+ :param dimension: New dimension
+ :param map: New CMap of format described in the AddCMap function.
+
+ :type index: :class:`int`
+ :type dimension: :class:`int`
+ :type map: :class:`list`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set cmaps or size of map is not dimension*dimension
+
+
+ .. method:: SetLJPairParameters(index, sigma, epsilon)
+
+ Replaces existing parameters for a particular interaction
+
+ :param index: Index of LJ pair
+ :param sigma: New sigma in nm
+ :param epsilon: New epsilon in kJ/mol
+
+ :type index: :class:`int`
+ :type sigma: :class:`float`
+ :type epsilon: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set lj pairs
+
+
+ .. method:: SetDistanceConstraintParameters(index, distance)
+
+ Replaces existing parameters for a particular interaction
+
+ :param index: Index of distance constraint
+ :param distance: New constraint distance in nm
+
+ :type index: :class:`int`
+ :type distance: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set distance constraints
+
+
+ .. method:: SetHarmonicPositionRestraintParameters(index, ref_position, k,[,
+ x_scale=1.0, y_scale=1.0, z_scale=1.0])
+
+ Replaces existing parameters for a particular interaction
+
+ :param index: Index of harmonic position constraint
+ :param ref_position: New reference position in nm
+ :param k: New force constant in kJ/mol/nm^2
+ :param x_scale: New x-scale
+ :param y_scale: New y-scale
+ :param z_scale: New z-scale
+
+ :type index: :class:`int`
+ :type ref_position: :class:`ost.geom.Vec3`
+ :type k: :class:`float`
+ :type x_scale: :class:`float`
+ :type y_scale: :class:`float`
+ :type z_scale: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic position restraints
+
+
+ .. method:: SetHarmonicDistanceRestraintParameters(index, length, k)
+
+ Replaces existing parameters for a particular interaction
+
+ :param index: Index of harmonic distance restraint
+ :param length: New restraint distance in nm
+ :param k: New force constant in kJ/mol/nm^2
+
+ :type index: :class:`int`
+ :type length: :class:`float`
+ :type k: :class:`float`
+
+ :raises: :class:`RuntimeError` when index exceeds number of
+ set harmonic distance restraints
+
+
+ .. method:: GetSigmas()
+
+ :returns: :class:`list` of :class:`float` with previously set
+ sigmas
+
+
+ .. method:: GetEpsilons()
+
+ :returns: :class:`list` of :class:`float` with previously set
+ epsilons
+
+
+ .. method:: GetGBSARadii()
+
+ :returns: :class:`list` of :class:`float` with previously set
+ GBSA radii
+
+
+ .. method:: GetOBCScalings()
+
+ :returns: :class:`list` of :class:`float` with previously set
+ OBC scalings
+
+
+ .. method:: GetCharges()
+
+ :returns: :class:`list` of :class:`float` with previously set
+ charges
+
+
+ .. method:: GetMasses()
+
+ :returns: :class:`list` of :class:`float` with previously set
+ masses
+
+
+ .. method:: GetSigma(particle_index)
+
+ :param particle_index: Index of particle
+ :type particle_index: :class:`int`
+
+ :returns: :class:`float`
+
+ :raises: :class:`RuntimeError` when particle_index exceeds
+ number of particles or sigmas have not been set
+
+
+ .. method:: GetEpsilon(particle_index)
+
+ :param particle_index: Index of particle
+ :type particle_index: :class:`int`
+
+ :returns: :class:`float`
+
+ :raises: :class:`RuntimeError` when particle_index exceeds
+ number of particles or epsilons have not been set
+
+
+
+ .. method:: GetGBSARadius(particle_index)
+
+ :param particle_index: Index of particle
+ :type particle_index: :class:`int`
+
+ :returns: :class:`float`
+
+ :raises: :class:`RuntimeError` when particle_index exceeds
+ number of particles or gbsa_radii have not been set
+
+
+ .. method:: GetOBCScaling(particle_index)
+
+ :param particle_index: Index of particle
+ :type particle_index: :class:`int`
+
+ :returns: :class:`float`
+
+ :raises: :class:`RuntimeError` when particle_index exceeds
+ number of particles or obc scalings have not been set
+
+
+ .. method:: GetCharge(particle_index)
+
+ :param particle_index: Index of particle
+ :type particle_index: :class:`float`
+
+ :returns: :class:`float`
+
+ :raises: :class:`RuntimeError` when particle_index exceeds
+ number of particles or charges have not been set
+
+
+ .. method:: GetMass(particle_index)
+
+ :param particle_index: Index of particle
+ :type particle_index: :class:`int`
+
+ :returns: :class:`float`
+
+ :raises: :class:`RuntimeError` when particle_index exceeds
+ number of particles
+
+
+ .. method:: GetHarmonicBondIndices(index_one, index_two)
+
+ :param index_one: Index of particle 1
+ :param index_one: Index of particle 2
+
+ :type index_one: :class:`int`
+ :type index_one: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of
+ all harmonic bonds acting on given particle pair
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetHarmonicAngleIndices(index_one, index_two, index_three)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
+ angles acting on given particles
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetUreyBradleyAngleIndices(index_one, index_two, index_three)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all
+ Urey-Bradley angles acting on given particles
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetPeriodicDihedralIndices(index_one, index_two, index_three,
+ index_four)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param index_four: Index of particle 4
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type index_four: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all periodic
+ dihedrals acting on given particles
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetPeriodicImpropersIndices(index_one, index_two, index_three,
+ index_four)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param index_four: Index of particle 4
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type index_four: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all periodic
+ impropers acting on given particles
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetHarmonicImpropersIndices(index_one, index_two, index_three,
+ index_four)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param index_four: Index of particle 4
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type index_four: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
+ impropers acting on given particles
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetCMapIndices(index_one, index_two, index_three,
+ index_four, index_five)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+ :param index_three: Index of particle 3
+ :param index_four: Index of particle 4
+ :param index_five: Index of particle 5
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+ :type index_three: :class:`int`
+ :type index_four: :class:`int`
+ :type index_five: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all cmaps
+ acting on given particles
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetLJPairIndex(index_one, index_two)
+
+ :param index_one: Index of particle 1
+ :param index_two: Index of particle 2
+
+ :type index_one: :class:`int`
+ :type index_two: :class:`int`
+
+ :returns: :class:`int` Index of LJPair acting on particles,
+ -1 if there is none
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetDistanceConstraintIndex(index_one, index_two)
+
+ :param index_one: Index of particle 1
+ :param index_one: Index of particle 2
+
+ :type index_one: :class:`int`
+ :type index_one: :class:`int`
+
+ :returns: :class:`int` - Index of distance constraint acting on
+ particles, -1 if there is none
+
+ :raises: :class:`RuntimeError` when an index exceeds
+ number of particles in topology
+
+
+ .. method:: GetHarmonicBondIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
+ bonds this particular particle is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetHarmonicAngleIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
+ angles this particular particle is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetUreyBradleyAngleIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all
+ Urey-Bradley angles this particular particle
+ is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetPeriodicDihedralIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all periodic
+ dihedrals this particular particle is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetPeriodicImproperIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all periodic
+ impropers this particular particle is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+ .. method:: GetHarmonicImproperIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
+ impropers this particular particle is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetCMapIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all cmaps
+ this particular particle is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetLJPairIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all LJ pairs
+ this particular particle is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetDistanceConstraintIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all distance
+ constraints this particular particle is involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetHarmonicPositionRestraintIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
+ position restraints this particular particle is
+ involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetHarmonicDistanceRestraintIndices(index)
+
+ :param index: Index of particle
+ :type index: :class:`int`
+
+ :returns: :class:`list` of :class:`int` - Indices of all harmonic
+ distance restraints this particular particle is
+ involved in
+
+ :raises: :class:`RuntimeError` when index exceeds
+ number of particles in topology
+
+
+ .. method:: GetNumParticles()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumHarmonicBonds()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumHarmonicAngles()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumUreyBradleyAngles()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumPeriodicDihedrals()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumPeriodicImpropers()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumHarmonicImpropers()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumCMaps()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumLJPairs()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumDistanceConstraints()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumPositionConstraints()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumHarmonicPositionRestraints()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumHarmonicDistanceRestraints()
+
+ :returns: :class:`int`
+
+
+ .. method:: GetNumExclusions()
+
+ :returns: :class:`int`
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/CMakeLists.txt b/modules/mol/mm/pymod/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3156429e1c24cf25b6c7685fd6507254a02e0f8f
--- /dev/null
+++ b/modules/mol/mm/pymod/CMakeLists.txt
@@ -0,0 +1,23 @@
+set(OST_MOL_MM_PYMOD_SOURCES
+ export_forcefield.cc
+ export_settings.cc
+ export_simulation.cc
+ export_openmm.cc
+ export_observers.cc
+ export_ff_reader.cc
+ export_interaction.cc
+ export_buildingblock.cc
+ export_block_modifiers.cc
+ export_topology.cc
+ export_modeller.cc
+ wrap_mol_mm.cc
+)
+
+set(OST_MOL_MM_PYMOD_MODULES
+ "__init__.py"
+)
+
+if (NOT ENABLE_STATIC)
+ pymod(NAME mol_mm OUTPUT_DIR ost/mol/mm CPP ${OST_MOL_MM_PYMOD_SOURCES}
+ PY ${OST_MOL_MM_PYMOD_MODULES})
+endif()
diff --git a/modules/mol/mm/pymod/__init__.py b/modules/mol/mm/pymod/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..5c1138cd0354113ea8d1744912a0cc0868202d2b
--- /dev/null
+++ b/modules/mol/mm/pymod/__init__.py
@@ -0,0 +1,9 @@
+import os.path
+from _ost_mol_mm import *
+import ost
+
+def LoadAMBERForcefield():
+ return Forcefield.Load(os.path.join(ost.GetSharedDataPath(),'forcefields','AMBER03.dat'))
+
+def LoadCHARMMForcefield():
+ return Forcefield.Load(os.path.join(ost.GetSharedDataPath(),'forcefields','CHARMM27.dat'))
diff --git a/modules/mol/mm/pymod/export_block_modifiers.cc b/modules/mol/mm/pymod/export_block_modifiers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..a6570e3aa5e342ae3724c54f827ec6b822e0d0c6
--- /dev/null
+++ b/modules/mol/mm/pymod/export_block_modifiers.cc
@@ -0,0 +1,100 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+#include <ost/mol/mm/heuristic_block_modifiers.hh>
+
+using namespace boost::python;
+
+namespace{
+
+template<typename T>
+std::vector<T> ListToVec(const boost::python::list& l){
+ std::vector<T> vec;
+ for (int i = 0; i < boost::python::len(l); ++i){
+ vec.push_back(boost::python::extract<T>(l[i]));
+ }
+ return vec;
+}
+
+void WrapAddAddRule(ost::mol::mm::GromacsBlockModifierPtr p,
+ int number, int method,
+ const boost::python::list& atom_names,
+ const boost::python::list& anchors,
+ const String& type, Real new_charge){
+ std::vector<String> v_atom_names = ListToVec<String>(atom_names);
+ std::vector<String> v_anchors = ListToVec<String>(anchors);
+
+ p->AddAddRule(number,method,v_atom_names,v_anchors,type,new_charge);
+
+}
+
+void WrapAddHydrogenRule(ost::mol::mm::GromacsHydrogenConstructorPtr p, int number, int method,
+ const boost::python::list& hydrogen_names,
+ const boost::python::list& anchors){
+ std::vector<String> v_hydrogen_names = ListToVec<String>(hydrogen_names);
+ std::vector<String> v_anchors = ListToVec<String>(anchors);
+ p->AddHydrogenRule(number,method,v_hydrogen_names,v_anchors);
+}
+
+
+}
+
+
+void export_BlockModifiers()
+{
+
+ class_<ost::mol::mm::HydrogenConstructor, boost::noncopyable>("HydrogenConstructor",no_init);
+ boost::python::register_ptr_to_python<ost::mol::mm::HydrogenConstructorPtr>();
+
+ class_<ost::mol::mm::BlockModifier, boost::noncopyable>("BlockModifier",no_init);
+ boost::python::register_ptr_to_python<ost::mol::mm::BlockModifierPtr>();
+
+ class_<ost::mol::mm::GromacsHydrogenConstructor, bases<ost::mol::mm::HydrogenConstructor> >("GromacsHydrogenConstructor", init<>())
+ .def("ApplyOnBuildingBlock",&ost::mol::mm::GromacsHydrogenConstructor::ApplyOnBuildingBlock,(arg("block")))
+ .def("ApplyOnResidue",&ost::mol::mm::GromacsHydrogenConstructor::ApplyOnResidue,(arg("residue"),arg("editor")))
+ .def("AddHydrogenRule",&WrapAddHydrogenRule,(arg("number"),arg("method"),arg("hydrogen_names"),arg("anchors")))
+ ;
+
+ class_<ost::mol::mm::GromacsBlockModifier, bases<ost::mol::mm::BlockModifier> >("GromacsBlockModifier", init<>())
+ .def("ApplyOnBuildingBlock",&ost::mol::mm::GromacsBlockModifier::ApplyOnBuildingBlock,(arg("block")))
+ .def("ApplyOnResidue",&ost::mol::mm::GromacsBlockModifier::ApplyOnResidue,(arg("residue"),arg("editor")))
+ .def("AddReplaceRule",&ost::mol::mm::GromacsBlockModifier::AddReplaceRule,(arg("name"),arg("new_name"),arg("new_type"),arg("new_charge")))
+ .def("AddAddRule",&WrapAddAddRule,(arg("number"),arg("method"),arg("atom_names"),arg("anchors"),arg("type"),arg("charge")))
+ .def("AddBond",&ost::mol::mm::GromacsBlockModifier::AddBond,(arg("bond")))
+ .def("AddAngle",&ost::mol::mm::GromacsBlockModifier::AddAngle,(arg("angle")))
+ .def("AddDihedral",&ost::mol::mm::GromacsBlockModifier::AddDihedral,(arg("dihedral")))
+ .def("AddImproper",&ost::mol::mm::GromacsBlockModifier::AddImproper,(arg("improper")))
+ .def("AddCMap",&ost::mol::mm::GromacsBlockModifier::AddCMap,(arg("cmap")))
+ .def("AddDeleteAtom",&ost::mol::mm::GromacsBlockModifier::AddDeleteAtom,(arg("name")))
+ ;
+
+ class_<ost::mol::mm::HeuristicHydrogenConstructor, bases<ost::mol::mm::HydrogenConstructor> >("HeuristicHydrogenConstructor", init<ost::mol::mm::BuildingBlockPtr>())
+ .def("ApplyOnBuildingBlock",&ost::mol::mm::HeuristicHydrogenConstructor::ApplyOnBuildingBlock,(arg("block")))
+ .def("ApplyOnResidue",&ost::mol::mm::HeuristicHydrogenConstructor::ApplyOnResidue,(arg("residue"),arg("editor")))
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::GromacsHydrogenConstructorPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::GromacsBlockModifierPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::HeuristicHydrogenConstructorPtr>();
+
+}
+
diff --git a/modules/mol/mm/pymod/export_buildingblock.cc b/modules/mol/mm/pymod/export_buildingblock.cc
new file mode 100644
index 0000000000000000000000000000000000000000..514b7919b86cc9462921ba8f5cc5073251660786
--- /dev/null
+++ b/modules/mol/mm/pymod/export_buildingblock.cc
@@ -0,0 +1,109 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <limits>
+#include <boost/python.hpp>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/log.hh>
+#include <vector>
+
+using namespace boost::python;
+
+namespace{
+
+template<typename T>
+boost::python::list VecToList(std::vector<T>& vec){
+ boost::python::list l;
+ for(typename std::vector<T>::iterator it=vec.begin();it!=vec.end();++it){
+ l.append(*it);
+ }
+ return l;
+}
+
+bool WrapMatch(ost::mol::mm::BuildingBlockPtr p, const ost::mol::ResidueHandle& res, bool match_connectivity){
+ String match_fail_info;
+ bool match = p->Match(res,match_connectivity,match_fail_info);
+ if(!match){
+ std::stringstream ss;
+ ss << "Residue "<< res.GetQualifiedName() << " does not match the building";
+ ss << "block. "<<match_fail_info;
+ LOG_INFO(ss.str());
+ }
+ return match;
+}
+
+boost::python::list WrapGetAtoms(ost::mol::mm::BuildingBlockPtr p){
+ std::vector<String> atoms = p->GetAtoms();
+ return VecToList<String>(atoms);
+}
+
+boost::python::list WrapGetTypes(ost::mol::mm::BuildingBlockPtr p){
+ std::vector<String> types = p->GetTypes();
+ return VecToList<String>(types);
+}
+
+boost::python::list WrapGetCharges(ost::mol::mm::BuildingBlockPtr p){
+ std::vector<Real> charges = p->GetCharges();
+ return VecToList<Real>(charges);
+}
+
+boost::python::list WrapGetMasses(ost::mol::mm::BuildingBlockPtr p){
+ std::vector<Real> masses = p->GetMasses();
+ return VecToList<Real>(masses);
+}
+
+
+}
+
+void export_Buildingblock()
+{
+ class_<ost::mol::mm::BuildingBlock>("BuildingBlock",init<>())
+ .def("Match",&WrapMatch,(arg("res"),arg("match_connectivity")=true))
+ .def("Connect",&ost::mol::mm::BuildingBlock::Connect,(arg("residue"),arg("xcs_editor")))
+ .def("GetAtoms",&WrapGetAtoms)
+ .def("GetTypes",&WrapGetTypes)
+ .def("GetCharges",&WrapGetCharges)
+ .def("GetMasses",&WrapGetMasses)
+ .def("GetType",&ost::mol::mm::BuildingBlock::GetType,(arg("name")))
+ .def("GetCharge",&ost::mol::mm::BuildingBlock::GetCharge,(arg("name")))
+ .def("GetMass",&ost::mol::mm::BuildingBlock::GetMass,(arg("name")))
+ .def("GetBonds",&ost::mol::mm::BuildingBlock::GetBonds)
+ .def("GetAngles",&ost::mol::mm::BuildingBlock::GetAngles)
+ .def("GetDihedrals",&ost::mol::mm::BuildingBlock::GetDihedrals)
+ .def("GetImpropers",&ost::mol::mm::BuildingBlock::GetImpropers)
+ .def("GetCMaps",&ost::mol::mm::BuildingBlock::GetCMaps)
+ .def("GetExclusions",&ost::mol::mm::BuildingBlock::GetExclusions)
+ .def("GetConstraints",&ost::mol::mm::BuildingBlock::GetConstraints)
+ .def("AddAtom",&ost::mol::mm::BuildingBlock::AddAtom,(arg("name"),arg("type"),arg("charge"),arg("mass")=std::numeric_limits<Real>::quiet_NaN()))
+ .def("AddBond",&ost::mol::mm::BuildingBlock::AddBond,(arg("bond"),arg("replace_existing")=false))
+ .def("AddAngle",&ost::mol::mm::BuildingBlock::AddAngle,(arg("angle"),arg("replace_existing")=false))
+ .def("AddDihedral",&ost::mol::mm::BuildingBlock::AddDihedral,(arg("dihedral"),arg("replace_existing")=false))
+ .def("AddImproper",&ost::mol::mm::BuildingBlock::AddImproper,(arg("improper"),arg("replace_existing")=false))
+ .def("AddExclusion",&ost::mol::mm::BuildingBlock::AddExclusion,(arg("exclusion"),arg("replace_existing")=false))
+ .def("AddCMap",&ost::mol::mm::BuildingBlock::AddCMap,(arg("cmap"),arg("replace_existing")=false))
+ .def("AddConstraint",&ost::mol::mm::BuildingBlock::AddConstraint,(arg("constraint"),arg("replace_existing")=false))
+ .def("RemoveAtom",&ost::mol::mm::BuildingBlock::RemoveAtom,(arg("name")))
+ .def("ReplaceAtom",&ost::mol::mm::BuildingBlock::ReplaceAtom,(arg("name"),arg("new_name"),arg("new_type"),arg("new_charge"),arg("new_mass")=std::numeric_limits<Real>::quiet_NaN()))
+ .def("RemoveInteractionsToNext",&ost::mol::mm::BuildingBlock::RemoveInteractionsToNext)
+ .def("RemoveInteractionsToPrev",&ost::mol::mm::BuildingBlock::RemoveInteractionsToPrev)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::BuildingBlockPtr>();
+
+}
diff --git a/modules/mol/mm/pymod/export_ff_reader.cc b/modules/mol/mm/pymod/export_ff_reader.cc
new file mode 100644
index 0000000000000000000000000000000000000000..b8a4fa6a894f9635a50d37c4b7c550941ecdd631
--- /dev/null
+++ b/modules/mol/mm/pymod/export_ff_reader.cc
@@ -0,0 +1,42 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <ost/mol/mm/ff_reader.hh>
+#include <ost/mol/residue_handle.hh>
+
+using namespace boost::python;
+using namespace ost::mol::mm;
+
+
+void export_FFReader()
+{
+ class_<ost::mol::mm::FFReader>("FFReader",init<String>())
+ .def("ReadGromacsForcefield",&ost::mol::mm::FFReader::ReadGromacsForcefield)
+ .def("SetPreprocessorDefinition",&ost::mol::mm::FFReader::SetPreprocessorDefinition,(arg("definition")))
+ .def("GetForcefield",&ost::mol::mm::FFReader::GetForcefield)
+ .def("SetForcefield",&ost::mol::mm::FFReader::SetForcefield,(arg("forcefield")))
+ .def("ReadResidueDatabase",&ost::mol::mm::FFReader::ReadResidueDatabase,(arg("basename")))
+ .def("ReadITP",&ost::mol::mm::FFReader::ReadITP,(arg("basename")))
+ .def("ReadCHARMMPRM",&ost::mol::mm::FFReader::ReadCHARMMPRM,(arg("basename")))
+ .def("ReadCHARMMRTF",&ost::mol::mm::FFReader::ReadCHARMMRTF,(arg("basename")))
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::FFReaderPtr>();
+}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_forcefield.cc b/modules/mol/mm/pymod/export_forcefield.cc
new file mode 100644
index 0000000000000000000000000000000000000000..096b6eef433b075dd3e47ab0d08791103f44a879
--- /dev/null
+++ b/modules/mol/mm/pymod/export_forcefield.cc
@@ -0,0 +1,93 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <boost/shared_ptr.hpp>
+#include <ost/mol/mm/forcefield.hh>
+
+using namespace boost::python;
+
+namespace{
+
+
+ ost::mol::mm::InteractionPtr GetLJOneType(ost::mol::mm::ForcefieldPtr p, String type){
+ return p->GetLJ(type);
+ }
+
+ ost::mol::mm::InteractionPtr GetLJTwoTypes(ost::mol::mm::ForcefieldPtr p, String type1, String type2, bool pair){
+ return p->GetLJ(type1,type2,pair);
+ }
+
+}
+
+
+void export_Forcefield()
+{
+
+ class_<ost::mol::mm::Forcefield>("Forcefield", init<>())
+ .def("Load",&ost::mol::mm::Forcefield::Load,(arg("filename"))).staticmethod("Load")
+ .def("Save",&ost::mol::mm::Forcefield::Save,(arg("filename")))
+ .def("GetBuildingBlock",&ost::mol::mm::Forcefield::GetBuildingBlock,(arg("name")))
+ .def("GetBlockModifier",&ost::mol::mm::Forcefield::GetBlockModifier,(arg("name")))
+ .def("GetAtomType",&ost::mol::mm::Forcefield::GetAtomType,(arg("res_name"),arg("atom_name")))
+ .def("GetHydrogenConstructor",&ost::mol::mm::Forcefield::GetHydrogenConstructor,(arg("name")))
+ .def("GetNTerModifier",&ost::mol::mm::Forcefield::GetNTerModifier,(arg("residue_name"),arg("ter_name")=""))
+ .def("GetCTerModifier",&ost::mol::mm::Forcefield::GetCTerModifier,(arg("residue_name"),arg("ter_name")=""))
+ .def("GetBond",&ost::mol::mm::Forcefield::GetBond,(arg("atom_type_1"),arg("atom_type_2")))
+ .def("GetAngle",&ost::mol::mm::Forcefield::GetAngle,(arg("atom_type_1"),arg("atom_type_2"),arg("atom_type_3")))
+ .def("GetDihedrals",&ost::mol::mm::Forcefield::GetDihedrals,(arg("atom_type_1"),arg("atom_type_2"),arg("atom_type_3"),arg("atom_type_4")))
+ .def("GetImpropers",&ost::mol::mm::Forcefield::GetImpropers,(arg("atom_type_1"),arg("atom_type_2"),arg("atom_type_3"),arg("atom_type_4")))
+ .def("GetCMap",&ost::mol::mm::Forcefield::GetCMap,(arg("atom_type_1"),arg("atom_type_2"),arg("atom_type_3"),arg("atom_type_4"),arg("atom_type_5")))
+ .def("GetImplicitGenborn",&ost::mol::mm::Forcefield::GetImplicitGenborn,(arg("atom_type")))
+ .def("GetLJ",&GetLJOneType,(arg("atom_type")))
+ .def("GetLJ",&GetLJTwoTypes,(arg("atom_type_1"),arg("atom_type_2")))
+ .def("GetConstraint",&ost::mol::mm::Forcefield::GetConstraint,(arg("atom_type_1"),arg("atom_type_2")))
+ .def("GetMass",&ost::mol::mm::Forcefield::GetMass,(arg("atom_type")))
+ .def("GetFudgeLJ",&ost::mol::mm::Forcefield::GetFudgeLJ)
+ .def("GetFudgeQQ",&ost::mol::mm::Forcefield::GetFudgeQQ)
+ .def("AddBuildingBlock",&ost::mol::mm::Forcefield::AddBuildingBlock,(arg("name"),arg("block")))
+ .def("AddBond",&ost::mol::mm::Forcefield::AddBond,(arg("bond")))
+ .def("AddAngle",&ost::mol::mm::Forcefield::AddAngle,(arg("angle")))
+ .def("AddDihedral",&ost::mol::mm::Forcefield::AddDihedral,(arg("dihedral")))
+ .def("AddImproper",&ost::mol::mm::Forcefield::AddImproper,(arg("improper")))
+ .def("AddCMap",&ost::mol::mm::Forcefield::AddCMap,(arg("cmap")))
+ .def("AddImplicitGenborn",&ost::mol::mm::Forcefield::AddImplicitGenborn,(arg("implicit_genborn")))
+ .def("AddLJ",&ost::mol::mm::Forcefield::AddLJ,(arg("lj")))
+ .def("AddLJPair",&ost::mol::mm::Forcefield::AddLJPair,(arg("lj_pair")))
+ .def("AddMass",&ost::mol::mm::Forcefield::AddMass,(arg("mass")))
+ .def("AddResidueRenamingRule",&ost::mol::mm::Forcefield::AddResidueRenamingRule,(arg("name"),arg("main_name"),arg("n_ter_name"),arg("c_ter_name"),arg("two_ter_name")))
+ .def("AddAtomRenamingRule",&ost::mol::mm::Forcefield::AddAtomRenamingRule,(arg("res_name"),arg("old_atom_name"),arg("new_atom_name")))
+ .def("AddHydrogenConstructor",&ost::mol::mm::Forcefield::AddHydrogenConstructor,(arg("name"),arg("hydrogen_constructor")))
+ .def("AddBlockModifier",&ost::mol::mm::Forcefield::AddBlockModifier,(arg("name"),arg("modifier")))
+ .def("SetStandardCTer",&ost::mol::mm::Forcefield::SetStandardCTer,(arg("res_name"),arg("ter_name")))
+ .def("SetStandardNTer",&ost::mol::mm::Forcefield::SetStandardNTer,(arg("res_name"),arg("ter_name")))
+ .def("SetFudgeLJ",&ost::mol::mm::Forcefield::SetFudgeLJ,(arg("fudge_factor")))
+ .def("SetFudgeQQ",&ost::mol::mm::Forcefield::SetFudgeQQ,(arg("fudge_factor")))
+ .def("SetGenPairs",&ost::mol::mm::Forcefield::SetGenPairs,(arg("set_gen_pairs_flag")))
+ .def("GetResidueRenamingMain",&ost::mol::mm::Forcefield::GetResidueRenamingMain,(arg("res_name")))
+ .def("GetResidueRenamingNTer",&ost::mol::mm::Forcefield::GetResidueRenamingNTer,(arg("res_name")))
+ .def("GetResidueRenamingCTer",&ost::mol::mm::Forcefield::GetResidueRenamingCTer,(arg("res_name")))
+ .def("GetResidueRenamingTwoTer",&ost::mol::mm::Forcefield::GetResidueRenamingTwoTer,(arg("res_name")))
+ .def("GetAtomRenaming",&ost::mol::mm::Forcefield::GetAtomRenaming,(arg("res_name"),arg("atom_name")))
+ .def("AssignFFSpecificNames",&ost::mol::mm::Forcefield::AssignFFSpecificNames,(arg("ent"),arg("reverse")=false))
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::ForcefieldPtr>();
+
+}
diff --git a/modules/mol/mm/pymod/export_index.cc b/modules/mol/mm/pymod/export_index.cc
new file mode 100644
index 0000000000000000000000000000000000000000..240f22f4b10c698d11377e49ae76888894aec78a
--- /dev/null
+++ b/modules/mol/mm/pymod/export_index.cc
@@ -0,0 +1,74 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <ost/mol/mm/index.hh>
+
+using namespace boost::python;
+
+namespace{
+
+template<typename T>
+int Get(T index, uint i){
+ return index[i];
+}
+
+template<typename T>
+void Set(T& index, uint i, uint v){
+ index[i] = v;
+}
+}
+
+void export_Index()
+{
+ class_<ost::mol::mm::Index<1> >("Index1", init<uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<1> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<1> >)
+ ;
+
+ class_<ost::mol::mm::Index<2> >("Index2", init<uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<2> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<2> >)
+ ;
+
+ class_<ost::mol::mm::Index<3> >("Index3", init<uint, uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<3> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<3> >)
+ ;
+
+ class_<ost::mol::mm::Index<4> >("Index4", init<uint, uint, uint,uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<4> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<4> >)
+ ;
+
+ class_<ost::mol::mm::Index<5> >("Index5", init<uint, uint, uint, uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<5> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<5> >)
+ ;
+
+ class_<ost::mol::mm::Index<6> >("Index6", init<uint, uint, uint, uint, uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<6> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<6> >)
+ ;
+
+ class_<ost::mol::mm::Index<7> >("Index7", init<uint, uint, uint, uint, uint, uint, uint>())
+ .def("__getitem__",Get<ost::mol::mm::Index<7> >)
+ .def("__setitem__",Set<ost::mol::mm::Index<7> >)
+ ;
+}
diff --git a/modules/mol/mm/pymod/export_interaction.cc b/modules/mol/mm/pymod/export_interaction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..57dc7a911b8fe67996fdc7355024265c8e370595
--- /dev/null
+++ b/modules/mol/mm/pymod/export_interaction.cc
@@ -0,0 +1,127 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+
+#include <ost/mol/mm/interaction.hh>
+
+#include <vector>
+
+using namespace boost::python;
+
+namespace{
+
+template<typename T>
+boost::python::list VecToList(std::vector<T>& vec){
+ boost::python::list l;
+ for(typename std::vector<T>::iterator it=vec.begin();it!=vec.end();++it){
+ l.append(*it);
+ }
+ return l;
+}
+
+template<typename T>
+std::vector<T> ListToVec(boost::python::list& l){
+ std::vector<T> vec;
+ for (int i = 0; i < boost::python::len(l); ++i){
+ vec.push_back(boost::python::extract<T>(l[i]));
+ }
+ return vec;
+}
+
+boost::python::list WrapGetNames(ost::mol::mm::InteractionPtr p){
+ std::vector<String> names = p->GetNames();
+ return VecToList<String>(names);
+}
+
+boost::python::list WrapGetTypes(ost::mol::mm::InteractionPtr p){
+ std::vector<String> types = p->GetTypes();
+ return VecToList<String>(types);
+}
+
+boost::python::list WrapGetParam(ost::mol::mm::InteractionPtr p){
+ std::vector<Real> param = p->GetParam();
+ return VecToList<Real>(param);
+}
+
+void WrapSetNames(ost::mol::mm::InteractionPtr p, boost::python::list l){
+ std::vector<String> names = ListToVec<String>(l);
+ p->SetNames(names);
+}
+
+void WrapSetTypes(ost::mol::mm::InteractionPtr p, boost::python::list l){
+ std::vector<String> types = ListToVec<String>(l);
+ p->SetTypes(types);
+}
+
+void WrapSetParam(ost::mol::mm::InteractionPtr p, boost::python::list l){
+ std::vector<Real> param = ListToVec<Real>(l);
+ p->SetParam(param);
+}
+
+}
+
+void export_Interaction()
+{
+
+ enum_<ost::mol::mm::FuncType>("FuncType")
+ .value("Invalid", ost::mol::mm::Invalid)
+ .value("HarmonicBond", ost::mol::mm::HarmonicBond)
+ .value("HarmonicAngle", ost::mol::mm::HarmonicAngle)
+ .value("UreyBradleyAngle", ost::mol::mm::UreyBradleyAngle)
+ .value("PeriodicDihedral", ost::mol::mm::PeriodicDihedral)
+ .value("PeriodicImproper", ost::mol::mm::PeriodicImproper)
+ .value("HarmonicImproper", ost::mol::mm::HarmonicImproper)
+ .value("CMap", ost::mol::mm::CMap)
+ .value("LJ", ost::mol::mm::LJ)
+ .value("LJPair", ost::mol::mm::LJPair)
+ .value("GBSA", ost::mol::mm::GBSA)
+ .value("DistanceConstraint", ost::mol::mm::DistanceConstraint)
+ .value("Exclusion", ost::mol::mm::Exclusion)
+ .value("HarmonicPositionRestraint", ost::mol::mm::HarmonicPositionRestraint)
+ .value("HarmonicDistanceRestraint", ost::mol::mm::HarmonicDistanceRestraint)
+ ;
+
+ class_<ost::mol::mm::Interaction>("Interaction",init<ost::mol::mm::FuncType>())
+ .def("SetTypes",&WrapSetTypes,(arg("types")))
+ .def("SetNames",&WrapSetNames,(arg("names")))
+ .def("SetParam",&WrapSetParam,(arg("parameters")))
+ .def("GetTypes",&WrapGetTypes)
+ .def("GetNames",&WrapGetNames)
+ .def("GetParam",&WrapGetParam)
+ .def("GetAtoms",&ost::mol::mm::Interaction::GetAtoms,(arg("residue")))
+ .def("GetFuncType",&ost::mol::mm::Interaction::GetFuncType)
+ .def("ReplaceAtom",&ost::mol::mm::Interaction::ReplaceAtom,(arg("name"),arg("new_name"),arg("new_type")))
+ .def("MatchTypes",&ost::mol::mm::Interaction::MatchTypes,(arg("types")))
+ .def("MatchNames",&ost::mol::mm::Interaction::MatchNames,(arg("names")))
+ .def("HasName",&ost::mol::mm::Interaction::HasName,(arg("name")))
+ .def("HasType",&ost::mol::mm::Interaction::HasType,(arg("type")))
+ .def("IsParametrized",&ost::mol::mm::Interaction::IsParametrized)
+ .def("HasTypeWildcard",&ost::mol::mm::Interaction::HasTypeWildcard)
+ .def("HasNameWildcard",&ost::mol::mm::Interaction::HasNameWildcard)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::InteractionPtr>();
+
+ class_<std::vector<ost::mol::mm::InteractionPtr> >("InteractionList", init<>())
+ .def(vector_indexing_suite<std::vector<ost::mol::mm::InteractionPtr>, true>())
+ ;
+
+}
diff --git a/modules/mol/mm/pymod/export_modeller.cc b/modules/mol/mm/pymod/export_modeller.cc
new file mode 100644
index 0000000000000000000000000000000000000000..c0f71609d11a1bc5f2b1a40cb98c9cababee0d00
--- /dev/null
+++ b/modules/mol/mm/pymod/export_modeller.cc
@@ -0,0 +1,36 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/modeller.hh>
+
+using namespace boost::python;
+
+
+void export_Modeller()
+{
+
+ class_<ost::mol::mm::Modeller>("MMModeller", no_init)
+ .def("GenerateDisulfidBonds",&ost::mol::mm::Modeller::GenerateDisulfidBonds,(arg("ent"))).staticmethod("GenerateDisulfidBonds")
+ .def("AssignPDBNaming",&ost::mol::mm::Modeller::AssignPDBNaming,(arg("ent"))).staticmethod("AssignPDBNaming")
+ .def("AssignGromacsNaming",&ost::mol::mm::Modeller::AssignGromacsNaming,(arg("ent"))).staticmethod("AssignGromacsNaming")
+ ;
+
+}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_observers.cc b/modules/mol/mm/pymod/export_observers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..47a0236125a4033bc8529d10c5107d62c290c1e0
--- /dev/null
+++ b/modules/mol/mm/pymod/export_observers.cc
@@ -0,0 +1,44 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <boost/shared_ptr.hpp>
+#include <ost/mol/mm/observer.hh>
+
+using namespace boost::python;
+
+
+void export_Observers()
+{
+
+ class_<ost::mol::mm::Observer, boost::noncopyable>("Observer", no_init);
+
+ class_<ost::mol::mm::TrajObserver, bases<ost::mol::mm::Observer> >("TrajObserver", init<int>())
+ .def("GetTraj", &ost::mol::mm::TrajObserver::GetTraj)
+ ;
+
+ //noncopyable, because TrajWriter contains a unique ofstream
+ class_<ost::mol::mm::TrajWriter, boost::noncopyable, bases<ost::mol::mm::Observer> >("TrajWriter", init<int, String, String>())
+ .def("Finalize", &ost::mol::mm::TrajWriter::Finalize)
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::ObserverPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::TrajObserverPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::TrajWriterPtr>();
+}
\ No newline at end of file
diff --git a/modules/mol/mm/pymod/export_openmm.cc b/modules/mol/mm/pymod/export_openmm.cc
new file mode 100644
index 0000000000000000000000000000000000000000..38a09d305b51edd0df5278644832633f2100498e
--- /dev/null
+++ b/modules/mol/mm/pymod/export_openmm.cc
@@ -0,0 +1,71 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <OpenMM.h>
+
+using namespace boost::python;
+
+
+
+void export_OpenMM()
+{
+
+ //we have to tell boost, that the Integrator class is around...
+ class_<OpenMM::Integrator, boost::noncopyable>("Integrator",no_init)
+ .def("GetConstraintTolerance",&OpenMM::Integrator::getConstraintTolerance)
+ .def("SetConstraintTolerance",&OpenMM::Integrator::setConstraintTolerance,(arg("tolerance")))
+ ;
+
+ class_<OpenMM::VerletIntegrator, bases<OpenMM::Integrator> >("VerletIntegrator", init<double>());
+
+ class_<OpenMM::BrownianIntegrator, bases<OpenMM::Integrator> >("BrownianIntegrator", init<double,double,double>())
+ .def("GetTemperature",&OpenMM::BrownianIntegrator::getTemperature)
+ .def("SetTemperature",&OpenMM::BrownianIntegrator::setTemperature,(arg("temperature")))
+ .def("GetFriction",&OpenMM::BrownianIntegrator::getFriction)
+ .def("SetFriction",&OpenMM::BrownianIntegrator::setFriction,(arg("friction")))
+ .def("GetRandomNumberSeed",&OpenMM::BrownianIntegrator::getRandomNumberSeed)
+ .def("SetRandomNumberSeed",&OpenMM::BrownianIntegrator::setRandomNumberSeed,(arg("seed")))
+ ;
+
+ class_<OpenMM::LangevinIntegrator, bases<OpenMM::Integrator> >("LangevinIntegrator", init<double,double,double>())
+ .def("GetTemperature",&OpenMM::LangevinIntegrator::getTemperature)
+ .def("SetTemperature",&OpenMM::LangevinIntegrator::setTemperature,(arg("temperature")))
+ .def("GetFriction",&OpenMM::LangevinIntegrator::getFriction)
+ .def("SetFriction",&OpenMM::LangevinIntegrator::setFriction,(arg("friction")))
+ .def("GetRandomNumberSeed",&OpenMM::LangevinIntegrator::getRandomNumberSeed)
+ .def("SetRandomNumberSeed",&OpenMM::LangevinIntegrator::setRandomNumberSeed,(arg("seed")))
+ ;
+
+ class_<OpenMM::VariableVerletIntegrator, bases<OpenMM::Integrator> >("VariableVerletIntegrator",init<double>())
+ .def("GetErrorTolerance", &OpenMM::VariableVerletIntegrator::getErrorTolerance)
+ .def("SetErrorTolerance", &OpenMM::VariableVerletIntegrator::setErrorTolerance,(arg("tolerance")))
+ ;
+
+ class_<OpenMM::VariableLangevinIntegrator, bases<OpenMM::Integrator> >("VaribaleLangevinIntegrator", init<double,double,double>())
+ .def("GetTemperature",&OpenMM::VariableLangevinIntegrator::getTemperature)
+ .def("SetTemperature",&OpenMM::VariableLangevinIntegrator::setTemperature,(arg("temperature")))
+ .def("GetFriction",&OpenMM::VariableLangevinIntegrator::getFriction)
+ .def("SetFriction",&OpenMM::VariableLangevinIntegrator::setFriction,(arg("friction")))
+ .def("GetRandomNumberSeed",&OpenMM::VariableLangevinIntegrator::getRandomNumberSeed)
+ .def("SetRandomNumberSeed",&OpenMM::VariableLangevinIntegrator::setRandomNumberSeed,(arg("seed")))
+ .def("GetErrorTolerance",&OpenMM::VariableLangevinIntegrator::getErrorTolerance)
+ .def("SetErrorTolerance",&OpenMM::VariableLangevinIntegrator::setErrorTolerance,(arg("tolerance")))
+ ;
+}
diff --git a/modules/mol/mm/pymod/export_settings.cc b/modules/mol/mm/pymod/export_settings.cc
new file mode 100644
index 0000000000000000000000000000000000000000..7e38401d68d3888b89e0cd9d021e07077b9b7c9b
--- /dev/null
+++ b/modules/mol/mm/pymod/export_settings.cc
@@ -0,0 +1,110 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <ost/mol/mm/settings.hh>
+#include <OpenMM.h> //for definition of Integrator
+#include <boost/python/suite/indexing/map_indexing_suite.hpp>
+
+using namespace boost::python;
+
+
+void export_Settings()
+{
+
+ enum_<ost::mol::mm::Platform>("Platform")
+ .value("Reference", ost::mol::mm::Reference)
+ .value("OpenCL", ost::mol::mm::OpenCL)
+ .value("CUDA", ost::mol::mm::CUDA)
+ .value("CPU", ost::mol::mm::CPU)
+ ;
+
+ enum_<ost::mol::mm::NonbondedMethod>("NonbondedMethod")
+ .value("NoCutoff", ost::mol::mm::NoCutoff)
+ .value("CutoffNonPeriodic", ost::mol::mm::CutoffNonPeriodic)
+ .value("CutoffPeriodic", ost::mol::mm::CutoffPeriodic)
+ .value("Ewald", ost::mol::mm::Ewald)
+ .value("PME", ost::mol::mm::PME)
+ ;
+
+ //export the termini exceptions object
+ class_<ost::mol::mm::TerminiExceptions>("TerminiExceptions",init<>())
+ .def("SetException", &ost::mol::mm::TerminiExceptions::SetException)
+ .def("HasException", &ost::mol::mm::TerminiExceptions::HasException)
+ .def("GetException", &ost::mol::mm::TerminiExceptions::GetException)
+ ;
+
+ //export the settings
+
+ class_<ost::mol::mm::Settings>("Settings",init<>())
+ .def_readwrite("add_bonds",&ost::mol::mm::Settings::add_bonds)
+ .def_readwrite("add_angles",&ost::mol::mm::Settings::add_angles)
+ .def_readwrite("add_dihedrals",&ost::mol::mm::Settings::add_dihedrals)
+ .def_readwrite("add_impropers",&ost::mol::mm::Settings::add_impropers)
+ .def_readwrite("add_cmaps",&ost::mol::mm::Settings::add_cmaps)
+ .def_readwrite("add_exclusions",&ost::mol::mm::Settings::add_exclusions)
+ .def_readwrite("add_nonbonded",&ost::mol::mm::Settings::add_nonbonded)
+ .def_readwrite("add_gbsa",&ost::mol::mm::Settings::add_gbsa)
+ .def_readwrite("constrain_hbonds",&ost::mol::mm::Settings::constrain_hbonds)
+ .def_readwrite("constrain_bonds",&ost::mol::mm::Settings::constrain_bonds)
+ .def_readwrite("rigid_water",&ost::mol::mm::Settings::rigid_water)
+ .def_readwrite("strict_interactions",&ost::mol::mm::Settings::strict_interactions)
+ .def_readwrite("ideal_bond_length_constraints",&ost::mol::mm::Settings::ideal_bond_length_constraints)
+ .def_readwrite("fix_heavy_atoms",&ost::mol::mm::Settings::fix_heavy_atoms)
+ .def_readwrite("kill_electrostatics",&ost::mol::mm::Settings::kill_electrostatics)
+ .def_readwrite("generate_disulfid_bonds",&ost::mol::mm::Settings::generate_disulfid_bonds)
+ .def_readwrite("nonbonded_method",&ost::mol::mm::Settings::nonbonded_method)
+ .def_readwrite("nonbonded_cutoff",&ost::mol::mm::Settings::nonbonded_cutoff)
+ .def_readwrite("remove_cmm_motion",&ost::mol::mm::Settings::remove_cmm_motion)
+ .def_readwrite("periodic_box_extents",&ost::mol::mm::Settings::periodic_box_extents)
+ .def_readwrite("init_temperature",&ost::mol::mm::Settings::init_temperature)
+ .def_readwrite("forcefield",&ost::mol::mm::Settings::forcefield)
+ .def_readwrite("termini_exceptions",&ost::mol::mm::Settings::termini_exceptions)
+ .def_readwrite("platform",&ost::mol::mm::Settings::platform)
+ .def_readwrite("reference_properties",&ost::mol::mm::Settings::reference_properties)
+ .def_readwrite("cpu_properties",&ost::mol::mm::Settings::cpu_properties)
+ .def_readwrite("cuda_properties",&ost::mol::mm::Settings::cuda_properties)
+ .def_readwrite("opencl_properties",&ost::mol::mm::Settings::opencl_properties)
+ .def_readwrite("add_thermostat",&ost::mol::mm::Settings::add_thermostat)
+ .def_readwrite("thermostat_temperature",&ost::mol::mm::Settings::thermostat_temperature)
+ .def_readwrite("thermostat_collision_frequency",&ost::mol::mm::Settings::thermostat_collision_frequency)
+ .def_readwrite("add_barostat",&ost::mol::mm::Settings::add_barostat)
+ .def_readwrite("barostat_temperature",&ost::mol::mm::Settings::barostat_temperature)
+ .def_readwrite("barostat_pressure",&ost::mol::mm::Settings::barostat_pressure)
+ .def_readwrite("barostat_frequency",&ost::mol::mm::Settings::barostat_frequency)
+ .def_readwrite("integrator",&ost::mol::mm::Settings::integrator)
+ .def_readwrite("solvent_dielectric",&ost::mol::mm::Settings::solvent_dielectric)
+ .def_readwrite("solute_dielectric",&ost::mol::mm::Settings::solute_dielectric)
+ .def_readwrite("reaction_field_dielectric",&ost::mol::mm::Settings::reaction_field_dielectric)
+ .def_readwrite("use_dispersion_correction",&ost::mol::mm::Settings::use_dispersion_correction)
+ .def_readwrite("keep_ff_specific_naming",&ost::mol::mm::Settings::keep_ff_specific_naming)
+ .def_readwrite("openmm_plugin_directory",&ost::mol::mm::Settings::openmm_plugin_directory)
+ .def_readwrite("custom_plugin_directory",&ost::mol::mm::Settings::custom_plugin_directory)
+
+ ;
+
+ class_<ost::mol::mm::PropertyMap>("PropertyMap", no_init)
+ .def(map_indexing_suite<ost::mol::mm::PropertyMap>())
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::SettingsPtr>();
+ boost::python::register_ptr_to_python<ost::mol::mm::TerminiExceptionsPtr>();
+
+}
+
diff --git a/modules/mol/mm/pymod/export_simulation.cc b/modules/mol/mm/pymod/export_simulation.cc
new file mode 100644
index 0000000000000000000000000000000000000000..a5d3cae349e83f51c84bc2f95c3b3b052b0b03d4
--- /dev/null
+++ b/modules/mol/mm/pymod/export_simulation.cc
@@ -0,0 +1,93 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <ost/mol/mm/simulation.hh>
+
+using namespace boost::python;
+
+
+
+namespace{
+
+
+template<typename T>
+std::vector<T> ListToVec(const boost::python::list& l){
+ std::vector<T> vec;
+
+ for (int i = 0; i < boost::python::len(l); ++i){
+ vec.push_back(boost::python::extract<T>(l[i]));
+ }
+ return vec;
+}
+
+void WrapAddPositionConstraints(ost::mol::mm::SimulationPtr p, const boost::python::list& l){
+ std::vector<uint> vec = ListToVec<uint>(l);
+ p->AddPositionConstraints(vec);
+}
+
+}
+
+
+void export_Simulation()
+{
+
+ class_<ost::mol::mm::Simulation>("Simulation",no_init)
+ .def(init<const ost::mol::EntityHandle, const ost::mol::mm::SettingsPtr>())
+ .def(init<const ost::mol::mm::TopologyPtr,const ost::mol::EntityHandle&,const ost::mol::mm::SettingsPtr>())
+ .def("Save",&ost::mol::mm::Simulation::Save,(arg("filename")))
+ .def("Load",&ost::mol::mm::Simulation::Load,(arg("filename"))).staticmethod("Load")
+ .def("Steps",&ost::mol::mm::Simulation::Steps,(arg("steps")))
+ .def("GetPositions",&ost::mol::mm::Simulation::GetPositions,(arg("enforce_periodic_box")=false, arg("in_angstrom")=true))
+ .def("GetVelocities",&ost::mol::mm::Simulation::GetVelocities)
+ .def("GetForces",&ost::mol::mm::Simulation::GetForces)
+ .def("SetPositions",&ost::mol::mm::Simulation::SetPositions,(arg("positions"),arg("in_angstrom")=true))
+ .def("SetVelocities",&ost::mol::mm::Simulation::SetVelocities)
+ .def("GetEntity",&ost::mol::mm::Simulation::GetEntity)
+ .def("ApplySD",&ost::mol::mm::Simulation::ApplySD, (arg("tolerance")=100.0,arg("max_iterations")=1000))
+ .def("ApplyLBFGS",&ost::mol::mm::Simulation::ApplyLBFGS,(arg("tolerance")=1.0,arg("max_iterations")=1000))
+ .def("GetEnergy",&ost::mol::mm::Simulation::GetEnergy)
+ .def("GetPotentialEnergy",&ost::mol::mm::Simulation::GetPotentialEnergy)
+ .def("GetKineticEnergy",&ost::mol::mm::Simulation::GetKineticEnergy)
+ .def("Register",&ost::mol::mm::Simulation::Register)
+ .def("UpdatePositions",&ost::mol::mm::Simulation::UpdatePositions, (arg("enforce_periodic_box")=false))
+ .def("GetTopology",&ost::mol::mm::Simulation::GetTopology)
+ .def("ResetHarmonicBond",&ost::mol::mm::Simulation::ResetHarmonicBond,(arg("bond_idx"),arg("bond_length"),arg("force_constant")))
+ .def("ResetHarmonicAngle",&ost::mol::mm::Simulation::ResetHarmonicAngle,(arg("angle_idx"),arg("angle"),arg("force_constant")))
+ .def("ResetUreyBradleyAngle",&ost::mol::mm::Simulation::ResetUreyBradleyAngle,(arg("angle_idx"),arg("angle"),arg("angle_force_constant"),arg("bond_length"),arg("bond_force_constant")))
+ .def("ResetPeriodicDihedral",&ost::mol::mm::Simulation::ResetPeriodicDihedral,(arg("dihedral_idx"),arg("multiplicity"),arg("phase"),arg("force_constant")))
+ .def("ResetPeriodicImproper",&ost::mol::mm::Simulation::ResetPeriodicImproper,(arg("improper_idx"),arg("multiplicity"),arg("phase"),arg("force_constant")))
+ .def("ResetHarmonicImproper",&ost::mol::mm::Simulation::ResetHarmonicImproper,(arg("improper_idx"),arg("phase"),arg("force_constant")))
+ .def("ResetLJPair",&ost::mol::mm::Simulation::ResetLJPair,(arg("ljpair_idx"),arg("sigma"),arg("epsilon")))
+ .def("ResetDistanceConstraint",&ost::mol::mm::Simulation::ResetDistanceConstraint,(arg("constraint_idx"),arg("length")))
+ .def("ResetHarmonicPositionRestraint",&ost::mol::mm::Simulation::ResetHarmonicPositionRestraint,(arg("restraint_idx"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
+ .def("ResetHarmonicDistanceRestraint",&ost::mol::mm::Simulation::ResetHarmonicDistanceRestraint,(arg("restraint_idx"),arg("length"),arg("force_constant")))
+ .def("ResetLJ",&ost::mol::mm::Simulation::ResetLJ,(arg("particle_idx"),arg("sigma"),arg("epsilon")))
+ .def("ResetGBSA",&ost::mol::mm::Simulation::ResetGBSA,(arg("particle_idx"),arg("radius"),arg("scaling")))
+ .def("ResetCharge",&ost::mol::mm::Simulation::ResetCharge,(arg("particle_idx"),arg("charge")))
+ .def("ResetMass",&ost::mol::mm::Simulation::ResetMass,(arg("particle_idx"),arg("mass")))
+ .def("AddPositionConstraint",&ost::mol::mm::Simulation::AddPositionConstraint,(arg("particle_idx")))
+ .def("AddPositionConstraints",&WrapAddPositionConstraints,(arg("particle_idx")))
+ .def("ResetPositionConstraints",&ost::mol::mm::Simulation::ResetPositionConstraints)
+ .def("GetPeriodicBoxExtents",&ost::mol::mm::Simulation::GetPeriodicBoxExtents)
+ .def("SetPeriodicBoxExtents",&ost::mol::mm::Simulation::SetPeriodicBoxExtents,(arg("extents")))
+ ;
+
+ boost::python::register_ptr_to_python<ost::mol::mm::SimulationPtr>();
+}
diff --git a/modules/mol/mm/pymod/export_topology.cc b/modules/mol/mm/pymod/export_topology.cc
new file mode 100644
index 0000000000000000000000000000000000000000..c104fbf8c7de6fbe8f85fd6b259193c7bb2f8a58
--- /dev/null
+++ b/modules/mol/mm/pymod/export_topology.cc
@@ -0,0 +1,506 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/topology_creator.hh>
+#include <ost/mol/entity_handle.hh>
+#include <vector>
+
+using namespace boost::python;
+namespace{
+
+ template<typename T>
+ int Get(T index, int i){
+ return index[i];
+ }
+
+ template<typename T>
+ void Set(T& index, int i, int v){
+ index[i] = v;
+ }
+
+ template<typename T>
+ std::vector<T> ListToVec(const boost::python::list& l){
+
+ std::vector<T> vec;
+ for (int i = 0; i < boost::python::len(l); ++i){
+ vec.push_back(boost::python::extract<T>(l[i]));
+ }
+ return vec;
+ }
+
+ template<typename T>
+ boost::python::list VecToList(std::vector<T>& vec){
+ boost::python::list l;
+ for(typename std::vector<T>::iterator it=vec.begin();it!=vec.end();++it){
+ l.append(*it);
+ }
+ return l;
+ }
+
+ ost::mol::mm::TopologyPtr WrapTopologyConstructor(const boost::python::list& masses_list){
+ std::vector<Real> masses_vector = ListToVec<Real>(masses_list);
+ ost::mol::mm::TopologyPtr p(new ost::mol::mm::Topology(masses_vector));
+ return p;
+ }
+
+ void WrapAddCMap(ost::mol::mm::TopologyPtr p, int index_one, int index_two, int index_three,
+ int index_four, int index_five, uint dimension, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->AddCMap(index_one,index_two,index_three,index_four,index_five,dimension,v);
+ }
+
+ void WrapSetSigmas(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetSigmas(v);
+ }
+
+ void WrapSetEpsilons(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetEpsilons(v);
+ }
+
+ void WrapSetGBSARadii(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetGBSARadii(v);
+ }
+
+ void WrapSetOBCScalings(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetOBCScalings(v);
+ }
+
+ void WrapSetCharges(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetCharges(v);
+ }
+
+ void WrapSetMasses(ost::mol::mm::TopologyPtr p, const boost::python::list& l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetMasses(v);
+ }
+
+
+ boost::python::list WrapGetSigmas(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetSigmas();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetEpsilons(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetEpsilons();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetGBSARadii(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetGBSARadii();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetOBCScalings(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetOBCScalings();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetCharges(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetCharges();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+ boost::python::list WrapGetMasses(ost::mol::mm::TopologyPtr p){
+ std::vector<Real> v = p->GetMasses();
+ boost::python::list l = VecToList<Real>(v);
+ return l;
+ }
+
+
+ boost::python::tuple WrapGetHarmonicBondParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2;
+ Real b,k;
+ p->GetHarmonicBondParameters(index,i1,i2,b,k);
+ return boost::python::make_tuple(i1,i2,b,k);
+ }
+
+ boost::python::tuple WrapGetHarmonicAngleParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3;
+ Real a,k;
+ p->GetHarmonicAngleParameters(index,i1,i2,i3,a,k);
+ return boost::python::make_tuple(i1,i2,i3,a,k);
+ }
+
+ boost::python::tuple WrapGetUreyBradleyAngleParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3;
+ Real a,a_k,b,b_k;
+ p->GetUreyBradleyAngleParameters(index,i1,i2,i3,a,a_k,b,b_k);
+ return boost::python::make_tuple(i1,i2,i3,a,a_k,b,b_k);
+ }
+
+ boost::python::tuple WrapGetPeriodicDihedralParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3,i4;
+ int m;
+ Real ph,k;
+ p->GetPeriodicDihedralParameters(index,i1,i2,i3,i4,m,ph,k);
+ return boost::python::make_tuple(i1,i2,i3,i4,m,ph,k);
+ }
+
+ boost::python::tuple WrapGetPeriodicImproperParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3,i4;
+ int m;
+ Real ph,k;
+ p->GetPeriodicImproperParameters(index,i1,i2,i3,i4,m,ph,k);
+ return boost::python::make_tuple(i1,i2,i3,i4,m,ph,k);
+ }
+
+ boost::python::tuple WrapGetHarmonicImproperParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2,i3,i4;
+ Real a,k;
+ p->GetHarmonicImproperParameters(index,i1,i2,i3,i4,a,k);
+ return boost::python::make_tuple(i1,i2,i3,i4,a,k);
+ }
+
+ boost::python::tuple WrapGetCMapParam(ost::mol::mm::TopologyPtr p, uint index){
+ std::vector<Real> map;
+ int dimension;
+ uint i1,i2,i3,i4,i5;
+ p->GetCMapParameters(index,i1,i2,i3,i4,i5,dimension,map);
+ boost::python::list l = VecToList<Real>(map);
+ return boost::python::make_tuple(i1,i2,i3,i4,i5,dimension,l);
+ }
+
+ boost::python::tuple WrapGetLJPairParam(ost::mol::mm::TopologyPtr p, uint index){
+ uint i1,i2;
+ Real s,e;
+ p->GetLJPairParameters(index,i1,i2,s,e);
+ return boost::python::make_tuple(i1,i2,s,e);
+ }
+
+ boost::python::tuple WrapGetDistanceConstraintParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2;
+ Real d;
+ p->GetDistanceConstraintParameters(index,i1,i2,d);
+ return boost::python::make_tuple(i1,i2,d);
+ }
+
+ boost::python::tuple WrapGetHarmonicPositionRestraintParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint atom_index;
+ geom::Vec3 ref_pos;
+ Real k;
+ Real x_scale, y_scale, z_scale;
+ p->GetHarmonicPositionRestraintParameters(index,atom_index,ref_pos,k,x_scale,y_scale,z_scale);
+ return boost::python::make_tuple(atom_index,ref_pos,k,x_scale,y_scale,z_scale);
+ }
+
+ boost::python::tuple WrapGetHarmonicDistanceRestraintParam(ost::mol::mm::TopologyPtr p,uint index){
+ uint i1,i2;
+ Real l,k;
+ p->GetHarmonicDistanceRestraintParameters(index,i1,i2,l,k);
+ return boost::python::make_tuple(i1,i2,l,k);
+ }
+
+ boost::python::tuple WrapGetFGMDHBondDonorParam(ost::mol::mm::TopologyPtr p, uint index){
+ uint i1, i2;
+ Real d,k_d,a,k_a,b,k_b;
+ p->GetFGMDHBondDonorParameters(index,i1,i2,d,k_d,a,k_a,b,k_b);
+ return boost::python::make_tuple(i1,i2,d,k_d,a,k_a,b,k_b);
+ }
+
+ boost::python::tuple WrapGetFGMDHBondAcceptorParam(ost::mol::mm::TopologyPtr p, uint index){
+ uint i1, i2;
+ p->GetFGMDHBondAcceptorParameters(index,i1,i2);
+ return boost::python::make_tuple(i1,i2);
+ }
+
+ void WrapSetCMapParameters(ost::mol::mm::TopologyPtr p, uint index, int dimension, boost::python::list l){
+ std::vector<Real> v = ListToVec<Real>(l);
+ p->SetCMapParameters(index,dimension,v);
+ }
+
+ boost::python::list GetHarmonicBondIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2){
+ std::vector<uint> return_vec = p->GetHarmonicBondIndices(i1,i2);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicBondIndicesSingleIndex(ost::mol::mm::TopologyPtr p, int i){
+ std::vector<uint> return_vec = p->GetHarmonicBondIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicAngleIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3){
+ std::vector<uint> return_vec = p->GetHarmonicAngleIndices(i1,i2,i3);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicAngleIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetHarmonicAngleIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetUreyBradleyAngleIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3){
+ std::vector<uint> return_vec = p->GetUreyBradleyAngleIndices(i1,i2,i3);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetUreyBradleyAngleIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetUreyBradleyAngleIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetPeriodicDihedralIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3, int i4){
+ std::vector<uint> return_vec = p->GetPeriodicDihedralIndices(i1,i2,i3,i4);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetPeriodicDihedralIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetPeriodicDihedralIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetPeriodicImproperIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3, uint i4){
+ std::vector<uint> return_vec = p->GetPeriodicImproperIndices(i1,i2,i3,i4);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetPeriodicImproperIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetPeriodicImproperIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicImproperIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3, uint i4){
+ std::vector<uint> return_vec = p->GetHarmonicImproperIndices(i1,i2,i3,i4);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicImproperIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetHarmonicImproperIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetCMapIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2, uint i3, uint i4, uint i5){
+ std::vector<uint> return_vec = p->GetCMapIndices(i1,i2,i3,i4,i5);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetCMapIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetCMapIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetLJPairIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetLJPairIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetDistanceConstraintIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetDistanceConstraintIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicDistanceRestraintIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2){
+ std::vector<uint> return_vec = p->GetHarmonicDistanceRestraintIndices(i1,i2);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicDistanceRestraintIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetHarmonicDistanceRestraintIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetFGMDHBondDonorIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2){
+ std::vector<uint> return_vec = p->GetFGMDHBondDonorIndices(i1,i2);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetFGMDHBondDonorIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetFGMDHBondDonorIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetHarmonicPositionRestraintIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetHarmonicPositionRestraintIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetFGMDHBondAcceptorIndices(ost::mol::mm::TopologyPtr p, uint i1, uint i2){
+ std::vector<uint> return_vec = p->GetFGMDHBondAcceptorIndices(i1,i2);
+ return VecToList<uint>(return_vec);
+ }
+
+ boost::python::list GetFGMDHBondAcceptorIndicesSingleIndex(ost::mol::mm::TopologyPtr p, uint i){
+ std::vector<uint> return_vec = p->GetFGMDHBondAcceptorIndices(i);
+ return VecToList<uint>(return_vec);
+ }
+
+
+ void MergeTop(ost::mol::mm::TopologyPtr top, ost::mol::mm::TopologyPtr other){
+ top->Merge(other);
+ }
+
+ void MergeTopEnt(ost::mol::mm::TopologyPtr top, ost::mol::EntityHandle& ent,
+ ost::mol::mm::TopologyPtr other, ost::mol::EntityHandle& other_ent){
+ top->Merge(ent,other,other_ent);
+ }
+}
+
+void export_Topology()
+{
+
+ class_<ost::mol::mm::TopologyCreator>("TopologyCreator",no_init)
+ .def("Create",&ost::mol::mm::TopologyCreator::Create).staticmethod("Create")
+ ;
+
+ class_<ost::mol::mm::Topology>("Topology",no_init)
+
+ .def("__init__",make_constructor(&WrapTopologyConstructor))
+ .def("Save",&ost::mol::mm::Topology::Save,(arg("filename")))
+ .def("Load",&ost::mol::mm::Topology::Load,(arg("filename"))).staticmethod("Load")
+
+ //interaction adding functions
+ .def("AddHarmonicBond",&ost::mol::mm::Topology::AddHarmonicBond,(arg("idx_one"),arg("idx_two"),arg("bond_length"),arg("force_constant")))
+ .def("AddHarmonicAngle",&ost::mol::mm::Topology::AddHarmonicAngle,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("angle"),arg("force_constant")))
+ .def("AddUreyBradleyAngle",&ost::mol::mm::Topology::AddUreyBradleyAngle,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("angle"),arg("angle_force_constant"),arg("bond_length"),arg("bond_force_constant")))
+ .def("AddPeriodicDihedral",&ost::mol::mm::Topology::AddPeriodicDihedral,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("idx_four"),arg("multiplicity"),arg("phase"),arg("force_constant")))
+ .def("AddPeriodicImproper",&ost::mol::mm::Topology::AddPeriodicImproper,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("idx_four"),arg("multiplicity"),arg("phase"),arg("force_constant")))
+ .def("AddHarmonicImproper",&ost::mol::mm::Topology::AddHarmonicImproper,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("idx_four"),arg("angle"),arg("force_constant")))
+ .def("AddCMap",&WrapAddCMap,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("idx_four"),arg("idx_five"),arg("dimension"),arg("map")))
+ .def("AddLJPair",&ost::mol::mm::Topology::AddLJPair,(arg("idx_one"),arg("idx_two"),arg("sigma"),arg("epsilon")))
+ .def("AddDistanceConstraint",&ost::mol::mm::Topology::AddDistanceConstraint,(arg("idx_one"),arg("idx_two"),arg("distance")))
+ .def("AddExclusion",&ost::mol::mm::Topology::AddExclusion,(arg("idx_one"),arg("idx_two")))
+ .def("AddPositionConstraint",&ost::mol::mm::Topology::AddPositionConstraint,(arg("idx")))
+ .def("ResetPositionConstraints",&ost::mol::mm::Topology::ResetPositionConstraints)
+ .def("ResetExclusions",&ost::mol::mm::Topology::ResetExclusions)
+ .def("AddHarmonicPositionRestraint",&ost::mol::mm::Topology::AddHarmonicPositionRestraint,(arg("idx"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
+ .def("AddHarmonicDistanceRestraint",&ost::mol::mm::Topology::AddHarmonicDistanceRestraint,(arg("idx_one"),arg("idx_two"),arg("length"),arg("force_constant")))
+ .def("AddFGMDHBondDonor",&ost::mol::mm::Topology::AddFGMDHBondDonor,(arg("idx_one"),arg("idx_two"),arg("length"),arg("k_length"),arg("alpha"),arg("k_alpha"),arg("beta"),arg("k_beta")))
+ .def("AddFGMDHBondAcceptor",&ost::mol::mm::Topology::AddFGMDHBondAcceptor,(arg("idx_one"),arg("idx_two")))
+
+ //single atom parameter getter and setter functions
+ .def("SetSigmas",&WrapSetSigmas,(arg("sigmas")))
+ .def("SetSigma",&ost::mol::mm::Topology::SetSigma,(arg("particle_idx"),arg("sigma")))
+ .def("SetEpsilons",&WrapSetEpsilons,(arg("epsilons")))
+ .def("SetEpsilon",&ost::mol::mm::Topology::SetEpsilon,(arg("particle_idx"),arg("epsilon")))
+ .def("SetGBSARadii",&WrapSetGBSARadii,(arg("gbsa_radii")))
+ .def("SetGBSARadius",&ost::mol::mm::Topology::SetGBSARadius,(arg("particle_idx"),arg("radius")))
+ .def("SetOBCScalings",&WrapSetOBCScalings,(arg("obc_scalings")))
+ .def("SetOBCScaling",&ost::mol::mm::Topology::SetOBCScaling,(arg("particle_idx"),arg("obc_scaling")))
+ .def("SetCharges",&WrapSetCharges,(arg("charges")))
+ .def("SetCharge",&ost::mol::mm::Topology::SetCharge,(arg("particle_idx"),arg("charge")))
+ .def("SetMasses",&WrapSetMasses,(arg("masses")))
+ .def("SetMass",&ost::mol::mm::Topology::SetMass,(arg("particle_idx"),arg("mass")))
+ .def("GetSigmas",&WrapGetSigmas)
+ .def("GetEpsilons",&WrapGetEpsilons)
+ .def("GetGBSARadii",&WrapGetGBSARadii)
+ .def("GetOBCScalings",&WrapGetOBCScalings)
+ .def("GetCharges",&WrapGetCharges)
+ .def("GetMasses",&WrapGetMasses)
+ .def("GetCharge",&ost::mol::mm::Topology::GetCharge,(arg("particle_idx")))
+ .def("GetMass",&ost::mol::mm::Topology::GetMass,(arg("particle_idx")))
+ .def("GetOBCScaling",&ost::mol::mm::Topology::GetOBCScaling,(arg("particle_idx")))
+ .def("GetGBSARadius",&ost::mol::mm::Topology::GetGBSARadius,(arg("particle_idx")))
+
+ //getter and setter functions for nonbonded fudge parameters
+ .def("SetFudgeLJ",&ost::mol::mm::Topology::SetFudgeLJ,(arg("fudge_param")))
+ .def("SetFudgeQQ",&ost::mol::mm::Topology::SetFudgeQQ,(arg("fudge_param")))
+ .def("GetFudgeLJ",&ost::mol::mm::Topology::GetFudgeLJ)
+ .def("GetFudgeQQ",&ost::mol::mm::Topology::GetFudgeQQ)
+
+ //getter functions for interaction parameters
+ .def("GetHarmonicBondParameters",&WrapGetHarmonicBondParam,(arg("interaction_idx")))
+ .def("GetHarmonicAngleParameters",&WrapGetHarmonicAngleParam,(arg("interaction_idx")))
+ .def("GetUreyBradleyAngleParameters",&WrapGetUreyBradleyAngleParam,(arg("interaction_idx")))
+ .def("GetPeriodicDihedralParameters",&WrapGetPeriodicDihedralParam,(arg("interaction_idx")))
+ .def("GetPeriodicImproperParameters",&WrapGetPeriodicImproperParam,(arg("interaction_idx")))
+ .def("GetHarmonicImproperParameters",&WrapGetHarmonicImproperParam,(arg("interaction_idx")))
+ .def("GetCMapParameters",&WrapGetCMapParam,(arg("interaction_idx")))
+ .def("GetLJPairParameters",&WrapGetLJPairParam,(arg("interaction_idx")))
+ .def("GetDistanceConstraintParameters",&WrapGetDistanceConstraintParam,(arg("interaction_idx")))
+ .def("GetHarmonicPositionRestraintParameters",&WrapGetHarmonicPositionRestraintParam,(arg("interaction_idx")))
+ .def("GetHarmonicDistanceRestraintParameters",&WrapGetHarmonicDistanceRestraintParam,(arg("interaction_idx")))
+ .def("GetFGMDHBondDonorParameters",&WrapGetFGMDHBondDonorParam,(arg("interaction_idx")))
+ .def("GetFGMDHBondAcceptorParameters",&WrapGetFGMDHBondAcceptorParam,(arg("interaction_idx")))
+
+ //setter functions for interaction parameters
+ .def("SetHarmonicBondParameters",&ost::mol::mm::Topology::SetHarmonicBondParameters,(arg("interaction_idx"),arg("bond_length"),arg("force_constant")))
+ .def("SetHarmonicAngleParameters",&ost::mol::mm::Topology::SetHarmonicAngleParameters,(arg("interaction_idx"),arg("angle"),arg("force_constant")))
+ .def("SetUreyBradleyAngleParameters",&ost::mol::mm::Topology::SetUreyBradleyAngleParameters,(arg("interaction_idx"),arg("angle"),arg("angle_force_constant"),arg("bond_length"),arg("bond_force_constant")))
+ .def("SetPeriodicDihedralParameters",&ost::mol::mm::Topology::SetPeriodicDihedralParameters,(arg("interaction_idx"),arg("multiplicity"),arg("phase"),arg("force_constant")))
+ .def("SetPeriodicImproperParameters",&ost::mol::mm::Topology::SetPeriodicImproperParameters,(arg("interaction_idx"),arg("multiplicity"),arg("phase"),arg("force_constant")))
+ .def("SetHarmonicImproperParameters",&ost::mol::mm::Topology::SetHarmonicImproperParameters,(arg("interaction_idx"),arg("angle"),arg("force_constant")))
+ .def("SetCMapParameters",&WrapSetCMapParameters,(arg("interaction_idx"),arg("map")))
+ .def("SetLJPairParameters",&ost::mol::mm::Topology::SetLJPairParameters,(arg("interaction_idx"),arg("sigma"),arg("epsilon")))
+ .def("SetDistanceConstraintParameters",&ost::mol::mm::Topology::SetDistanceConstraintParameters,(arg("interaction_idx"),arg("distance")))
+ .def("SetHarmonicPositionRestraintParameters",&ost::mol::mm::Topology::SetHarmonicPositionRestraintParameters,(arg("interaction_idx"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
+ .def("SetHarmonicDistanceRestraintParameters",&ost::mol::mm::Topology::SetHarmonicDistanceRestraintParameters,(arg("interaction_idx"),arg("length"),arg("force_constant")))
+ .def("SetFGMDHBondDonorParameters",&ost::mol::mm::Topology::SetFGMDHBondDonorParameters,(arg("interaction_idx"),arg("length"),arg("k_length"),arg("alpha"),arg("k_alpha"),arg("beta"),arg("k_beta")))
+
+ //functions to find interactions certain atoms are involved in
+ .def("GetHarmonicBondIndices",&GetHarmonicBondIndices,(arg("idx_one"),arg("idx_two")))
+ .def("GetHarmonicBondIndices",&GetHarmonicBondIndicesSingleIndex,(arg("idx")))
+ .def("GetHarmonicAngleIndices",&GetHarmonicAngleIndices,(arg("idx_one"),arg("idx_two"),arg("idx_three")))
+ .def("GetHarmonicAngleIndices",&GetHarmonicAngleIndicesSingleIndex,(arg("idx")))
+ .def("GetUreyBradleyAngleIndices",&GetUreyBradleyAngleIndices,(arg("idx_one"),arg("idx_two"),arg("idx_three")))
+ .def("GetUreyBradleyAngleIndices",&GetUreyBradleyAngleIndicesSingleIndex,(arg("idx")))
+ .def("GetPeriodicDihedralIndices",&GetPeriodicDihedralIndices,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("idx_four")))
+ .def("GetPeriodicDihedralIndices",&GetPeriodicDihedralIndicesSingleIndex,(arg("idx")))
+ .def("GetPeriodicImproperIndices",&GetPeriodicImproperIndices,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("idx_four")))
+ .def("GetPeriodicImproperIndices",&GetPeriodicImproperIndicesSingleIndex,(arg("idx")))
+ .def("GetHarmonicImproperIndices",&GetHarmonicImproperIndices,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("idx_four")))
+ .def("GetHarmonicImproperIndices",&GetHarmonicImproperIndicesSingleIndex,(arg("idx")))
+ .def("GetDistanceConstraintIndex",&ost::mol::mm::Topology::GetDistanceConstraintIndex,(arg("idx_one"),arg("idx_two")))
+ .def("GetDistanceConstraintIndices",&GetDistanceConstraintIndicesSingleIndex,(arg("idx")))
+ .def("GetCMapIndices",&GetCMapIndices,(arg("idx_one"),arg("idx_two"),arg("idx_three"),arg("idx_four"),arg("idx_five")))
+ .def("GetCMapIndices",&GetCMapIndicesSingleIndex,(arg("idx")))
+ .def("GetLJPairIndex",&ost::mol::mm::Topology::GetLJPairIndex,(arg("idx_one"),arg("idx_two")))
+ .def("GetLJPairIndices",&GetLJPairIndicesSingleIndex,(arg("idx")))
+ .def("GetHarmonicDistanceRestraintIndices",&GetHarmonicDistanceRestraintIndices,(arg("idx_one"),arg("idx_two")))
+ .def("GetHarmonicDistanceRestraintIndices",&GetHarmonicDistanceRestraintIndicesSingleIndex,(arg("idx")))
+ .def("GetHarmonicPositionRestraintIndices",&GetHarmonicPositionRestraintIndicesSingleIndex,(arg("idx")))
+ .def("GetFGMDHBondDonorIndices",&GetFGMDHBondDonorIndices,(arg("idx_one"),arg("idx_two")))
+ .def("GetFGMDHBondDonorIndices",&GetFGMDHBondDonorIndicesSingleIndex,(arg("idx")))
+ .def("GetFGMDHBondAcceptorIndices",&GetFGMDHBondAcceptorIndices,(arg("idx_one"),arg("idx_two")))
+ .def("GetFGMDHBondAcceptorIndices",&GetFGMDHBondAcceptorIndicesSingleIndex,(arg("idx")))
+
+
+ //functions to get amount of data in topology
+ .def("GetNumParticles",&ost::mol::mm::Topology::GetNumParticles)
+ .def("GetNumHarmonicBonds",&ost::mol::mm::Topology::GetNumHarmonicBonds)
+ .def("GetNumHarmonicAngles",&ost::mol::mm::Topology::GetNumHarmonicAngles)
+ .def("GetNumPeriodicDihedrals",&ost::mol::mm::Topology::GetNumPeriodicDihedrals)
+ .def("GetNumPeriodicImpropers",&ost::mol::mm::Topology::GetNumPeriodicImpropers)
+ .def("GetNumHarmonicImpropers",&ost::mol::mm::Topology::GetNumHarmonicImpropers)
+ .def("GetNumCMaps",&ost::mol::mm::Topology::GetNumCMaps)
+ .def("GetNumLJPairs",&ost::mol::mm::Topology::GetNumLJPairs)
+ .def("GetNumDistanceConstraints",&ost::mol::mm::Topology::GetNumDistanceConstraints)
+ .def("GetNumExclusions",&ost::mol::mm::Topology::GetNumExclusions)
+ .def("GetNumHarmonicPositionRestraints",&ost::mol::mm::Topology::GetNumHarmonicPositionRestraints)
+ .def("GetNumHarmonicDistanceRestraints",&ost::mol::mm::Topology::GetNumHarmonicDistanceRestraints)
+ .def("GetNumFGMDHBondDonors",&ost::mol::mm::Topology::GetNumFGMDHBondDonors)
+ .def("GetNumFGMDHBondAcceptors",&ost::mol::mm::Topology::GetNumFGMDHBondAcceptors)
+
+ .def("Merge",&MergeTop,(arg("other_topology")))
+ .def("Merge",&MergeTopEnt,(arg("ent"),arg("other_topology"),arg("other_ent")))
+ ;
+
+
+ boost::python::register_ptr_to_python<ost::mol::mm::TopologyPtr>();
+}
diff --git a/modules/mol/mm/pymod/wrap_mol_mm.cc b/modules/mol/mm/pymod/wrap_mol_mm.cc
new file mode 100644
index 0000000000000000000000000000000000000000..32e36e04b3bff7e01e4d50dda9a6c1a2f98a6173
--- /dev/null
+++ b/modules/mol/mm/pymod/wrap_mol_mm.cc
@@ -0,0 +1,52 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/python.hpp>
+
+
+using namespace boost::python;
+
+
+void export_Settings();
+void export_Simulation();
+void export_OpenMM();
+void export_Observers();
+void export_FFReader();
+void export_Interaction();
+void export_Buildingblock();
+void export_Forcefield();
+void export_BlockModifiers();
+void export_Topology();
+void export_Modeller();
+
+
+BOOST_PYTHON_MODULE(_ost_mol_mm)
+{
+ export_Forcefield();
+ export_Settings();
+ export_Simulation();
+ export_OpenMM();
+ export_Observers();
+ export_FFReader();
+ export_Interaction();
+ export_Buildingblock();
+ export_BlockModifiers();
+ export_Topology();
+ export_Modeller();
+}
diff --git a/modules/mol/mm/src/AMBER03.dat b/modules/mol/mm/src/AMBER03.dat
new file mode 100644
index 0000000000000000000000000000000000000000..69e7d22171f447229ce354d731773876fcba7bd4
Binary files /dev/null and b/modules/mol/mm/src/AMBER03.dat differ
diff --git a/modules/mol/mm/src/CHARMM27.dat b/modules/mol/mm/src/CHARMM27.dat
new file mode 100644
index 0000000000000000000000000000000000000000..9a9459fb0c9882ff4db05a70560389124a73f2e6
Binary files /dev/null and b/modules/mol/mm/src/CHARMM27.dat differ
diff --git a/modules/mol/mm/src/CMakeLists.txt b/modules/mol/mm/src/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f5d7ba62c87a26d480e10cd969fa0ac896f14c79
--- /dev/null
+++ b/modules/mol/mm/src/CMakeLists.txt
@@ -0,0 +1,64 @@
+set(OST_MOL_MM_HEADERS
+ forcefield.hh
+ ff_reader.hh
+ buildingblock.hh
+ block_modifiers.hh
+ gromacs_block_modifiers.hh
+ heuristic_block_modifiers.hh
+ interaction.hh
+ settings.hh
+ simulation.hh
+ modeller.hh
+ observer.hh
+ state_extractor.hh
+ system_creator.hh
+ topology_creator.hh
+ index.hh
+ topology.hh
+ steep.hh
+
+)
+
+set(OST_MOL_MM_SOURCES
+ forcefield.cc
+ ff_reader.cc
+ buildingblock.cc
+ gromacs_block_modifiers.cc
+ heuristic_block_modifiers.cc
+ interaction.cc
+ simulation.cc
+ modeller.cc
+ state_extractor.cc
+ observer.cc
+ system_creator.cc
+ topology_creator.cc
+ topology.cc
+ steep.cc
+)
+
+# create settings.hh as configurational header, needed to set the plugins path
+set(config_hh_generator "CMake")
+set(SETTINGS_HH_FILE "${CMAKE_CURRENT_SOURCE_DIR}/settings.hh")
+configure_file(settings.hh.in ${SETTINGS_HH_FILE})
+
+
+set(MOL_MM_DEPS ost_mol ost_io)
+
+
+module(NAME mol_mm SOURCES ${OST_MOL_MM_SOURCES}
+ HEADERS ${OST_MOL_MM_HEADERS}
+ HEADER_OUTPUT_DIR ost/mol/mm
+ DEPENDS_ON ${MOL_MM_DEPS}
+ LINK ${BOOST_PROGRAM_OPTIONS})
+
+target_link_libraries(ost_mol_mm ${OPEN_MM_LIBRARIES})
+
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/forcefields"
+ "AMBER03.dat" "AMBER_03_FORCEFIELD"
+ "ost_mol_mm")
+install(FILES "AMBER03.dat" DESTINATION "share/openstructure/forcefields/")
+
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/forcefields"
+ "CHARMM27.dat" "CHARMM_27_FORCEFIELD"
+ "ost_mol_mm")
+install(FILES "CHARMM27.dat" DESTINATION "share/openstructure/forcefields/")
diff --git a/modules/mol/mm/src/block_modifiers.hh b/modules/mol/mm/src/block_modifiers.hh
new file mode 100644
index 0000000000000000000000000000000000000000..4212e496bb65d5133816f019025369441ecc6ade
--- /dev/null
+++ b/modules/mol/mm/src/block_modifiers.hh
@@ -0,0 +1,78 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_BLOCK_MODIFIERS
+#define OST_MM_BLOCK_MODIFIERS
+
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <boost/shared_ptr.hpp>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/io/binary_data_source.hh>
+#include <ost/io/binary_data_sink.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+class HydrogenConstructor;
+class TerminiConstructor;
+class BlockModifier;
+
+typedef boost::shared_ptr<HydrogenConstructor> HydrogenConstructorPtr;
+typedef boost::shared_ptr<TerminiConstructor> TerminiConstructorPtr;
+typedef boost::shared_ptr<BlockModifier> BlockModifierPtr;
+
+typedef enum {
+ GromacsBlockModifiers,
+ HeuristicBlockModifiers
+} BlockModifierType;
+
+class HydrogenConstructor{
+public:
+ HydrogenConstructor() { }
+ virtual ~HydrogenConstructor() { }
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p) = 0;
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed) = 0;
+ virtual void OnSave(ost::io::BinaryDataSink& ds) = 0;
+ virtual BlockModifierType GetBlockModifierType() = 0;
+};
+
+class TerminiConstructor{
+public:
+ TerminiConstructor() { }
+ virtual ~TerminiConstructor() { }
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p) = 0;
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed) = 0;
+ virtual void OnSave(ost::io::BinaryDataSink& ds) = 0;
+ virtual BlockModifierType GetBlockModifierType() = 0;
+};
+
+class BlockModifier{
+public:
+ BlockModifier() { }
+ virtual ~BlockModifier() { }
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p) = 0;
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed) = 0;
+ virtual void OnSave(ost::io::BinaryDataSink& ds) = 0;
+ virtual BlockModifierType GetBlockModifierType() = 0;
+};
+
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/buildingblock.cc b/modules/mol/mm/src/buildingblock.cc
new file mode 100644
index 0000000000000000000000000000000000000000..2077880c7eb0e58c3096ec0f545197a43d966f3c
--- /dev/null
+++ b/modules/mol/mm/src/buildingblock.cc
@@ -0,0 +1,706 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/buildingblock.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+BuildingBlock::BuildingBlock(const BuildingBlock& block){
+
+ atoms_ = block.GetAtoms();
+ types_ = block.GetTypes();
+ charges_ = block.GetCharges();
+ masses_ = block.GetMasses();
+
+ //We have to force to create new interactions with new!!!
+ //There would be to danger to mess around with an interaction,
+ //that is associated with another building block.
+
+ std::vector<InteractionPtr> bonds = block.GetBonds();
+ std::vector<InteractionPtr> angles = block.GetAngles();
+ std::vector<InteractionPtr> dihedrals = block.GetDihedrals();
+ std::vector<InteractionPtr> impropers = block.GetImpropers();
+ std::vector<InteractionPtr> exclusions = block.GetExclusions();
+ std::vector<InteractionPtr> cmaps = block.GetCMaps();
+ std::vector<InteractionPtr> constraints = block.GetConstraints();
+
+ for(std::vector<InteractionPtr>::iterator i = bonds.begin();
+ i != bonds.end(); ++i){
+ bonds_.push_back(InteractionPtr(new Interaction(**i)));
+ }
+ for(std::vector<InteractionPtr>::iterator i = angles.begin();
+ i != angles.end(); ++i){
+ angles_.push_back(InteractionPtr(new Interaction(**i)));
+ }
+ for(std::vector<InteractionPtr>::iterator i = dihedrals.begin();
+ i != dihedrals.end(); ++i){
+ dihedrals_.push_back(InteractionPtr(new Interaction(**i)));
+ }
+ for(std::vector<InteractionPtr>::iterator i = impropers.begin();
+ i != impropers.end(); ++i){
+ impropers_.push_back(InteractionPtr(new Interaction(**i)));
+ }
+ for(std::vector<InteractionPtr>::iterator i = exclusions.begin();
+ i != exclusions.end(); ++i){
+ exclusions_.push_back(InteractionPtr(new Interaction(**i)));
+ }
+ for(std::vector<InteractionPtr>::iterator i = cmaps.begin();
+ i != cmaps.end(); ++i){
+ cmaps_.push_back(InteractionPtr(new Interaction(**i)));
+ }
+ for(std::vector<InteractionPtr>::iterator i = constraints.begin();
+ i != constraints.end(); ++i){
+ constraints_.push_back(InteractionPtr(new Interaction(**i)));
+ }
+}
+
+int BuildingBlock::GetAtomIndex(const String& atom_name) const{
+
+ uint ind = std::find(atoms_.begin(),atoms_.end(),atom_name) - atoms_.begin();
+
+ if(ind<atoms_.size()){
+ return ind;
+ }
+ return -1;
+}
+
+bool BuildingBlock::Match(const ost::mol::ResidueHandle& handle, bool match_connectivity, String& info) const{
+
+ //check for size
+ if(uint(handle.GetAtomCount()) != atoms_.size()){
+ std::stringstream ss;
+ ss << "Expected "<<atoms_.size()<<" atoms, got "<<handle.GetAtomCount();
+ info = ss.str();
+ return false;
+ }
+
+ //check for presence of particular atoms
+ for(std::vector<String>::const_iterator i = atoms_.begin(); i!=atoms_.end(); ++i){
+ if(!handle.FindAtom(*i).IsValid()){
+ std::stringstream ss;
+ ss << "Buildingblock has atom of name " << *i;
+ ss << ", which is not present in residue";
+ info = ss.str();
+ return false;
+ }
+ }
+
+ if(!match_connectivity) return true;
+
+ //check connectivity by extracting all unique bonds from handle,
+ //also bonds to other residues.
+ std::set<std::pair<String,String> > raw_bonds_handle;
+ std::vector<InteractionPtr> bonds_handle;
+ ost::mol::AtomHandleList atom_list = handle.GetAtomList();
+ ost::mol::ResidueHandle prev = handle.GetPrev();
+ ost::mol::ResidueHandle next = handle.GetNext();
+ ost::mol::AtomHandle atom_one;
+ ost::mol::AtomHandle atom_two;
+ String name_one;
+ String name_two;
+ std::vector<String> names;
+ names.push_back("");
+ names.push_back("");
+ ost::mol::BondHandleList bond_list;
+
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i != atom_list.end(); ++i){
+ bond_list = i->GetBondList();
+ for(ost::mol::BondHandleList::iterator j = bond_list.begin();
+ j != bond_list.end(); ++j){
+ atom_one = j->GetFirst();
+ atom_two = j->GetSecond();
+ name_one = atom_one.GetName();
+ name_two = atom_two.GetName();
+
+ if(atom_one.GetResidue() == prev) name_one = "-"+name_one;
+ else if(atom_one.GetResidue() == next) name_one = "+"+name_one;
+ else if(atom_one.GetResidue() != handle) continue; //in the building block
+ //there can only be atoms
+ //to previous or subsequent
+ //residues. So we don't check
+ //cases as they occur for example
+ //in disulfid bridges
+ if(atom_two.GetResidue() == prev) name_two = "-"+name_two;
+ else if(atom_two.GetResidue() == next) name_two = "+"+name_two;
+ else if(atom_two.GetResidue() != handle) continue; //dito
+
+ if(atom_one.GetIndex()<atom_two.GetIndex()) raw_bonds_handle.insert(std::make_pair(name_one,name_two));
+ else raw_bonds_handle.insert(std::make_pair(name_two,name_one));
+
+ }
+ }
+
+ for(std::set<std::pair<String,String> >::iterator i = raw_bonds_handle.begin();
+ i != raw_bonds_handle.end(); ++i){
+ InteractionPtr p(new Interaction(HarmonicBond));
+ names[0] = i->first;
+ names[1] = i->second;
+ p->SetNames(names);
+ bonds_handle.push_back(p);
+ }
+
+ bool found;
+ //let's first check for bonds
+ for(std::vector<InteractionPtr>::const_iterator i = bonds_.begin();
+ i!=bonds_.end(); ++i){
+ found = false;
+ for(std::vector<InteractionPtr>::iterator j = bonds_handle.begin();
+ j != bonds_handle.end(); ++j){
+ if((*j)->MatchNames((*i)->GetNames())){
+ found = true;
+ std::vector<String> names = (*j)->GetNames();
+ raw_bonds_handle.erase(std::make_pair(names[0],names[1]));
+ break;
+ }
+ }
+ if(!found){
+ std::stringstream ss;
+ std::vector<String> names_for_info = (*i)->GetNames();
+ ss << "Buildingblock defines bond between \"" <<names_for_info[0];
+ ss << "\" and \"" << names_for_info[1] << "\". Those atoms are not connected in your residue";
+ info = ss.str();
+ return false;
+ }
+ }
+ //If there is a distance constraint matching a remaining raw bond, we also
+ //remove it from raw bonds
+ for(std::vector<InteractionPtr>::const_iterator i = constraints_.begin();
+ i != constraints_.end(); ++i){
+ for(std::vector<InteractionPtr>::iterator j = bonds_handle.begin();
+ j != bonds_handle.end(); ++j){
+ if((*j)->MatchNames((*i)->GetNames())){
+ std::vector<String> names = (*j)->GetNames();
+ raw_bonds_handle.erase(std::make_pair(names[0],names[1]));
+ break;
+ }
+ }
+ }
+ //we finally check whether there is an additional internal bond in the
+ //residue. Note, that a remaining bond to another residue (starting with +/-)
+ //is not a criterium for failing the match procedure
+ for(std::set<std::pair<String,String> >::iterator i = raw_bonds_handle.begin();
+ i != raw_bonds_handle.end(); ++i){
+ if( i->first.at(0) == '+' || i->first.at(0) == '-') continue;
+ if( i->second.at(0) == '+' || i->second.at(0) == '-') continue;
+ std::stringstream ss;
+ ss << "Your residue has a bond between atoms of name \"" << i->first << "\" and \"";
+ ss << i->second << "\", which is not defined in the buildingblock";
+ info = ss.str();
+ return false;
+ }
+ return true;
+}
+
+void BuildingBlock::Connect(ost::mol::ResidueHandle& handle, ost::mol::XCSEditor& ed){
+
+ if(!handle.IsValid()) throw ost::Error("Invalid Residue encountered in connecting procedure!");
+
+ ost::mol::ResidueHandle prev = handle.GetPrev();
+ ost::mol::ResidueHandle next = handle.GetNext();
+
+ //Let's build the connectivity
+ ost::mol::AtomHandle atom1,atom2;
+ std::vector<String> names;
+ String name1, name2;
+
+
+ for(std::vector<InteractionPtr>::iterator i = bonds_.begin();
+ i != bonds_.end(); ++i){
+
+ names = (*i)->GetNames();
+ name1 = names[0];
+ name2 = names[1];
+
+ if(name1[0] == '-'){
+ if(!prev.IsValid()) throw ost::Error("Cannot access previous residue in connecting procedure!");
+ atom1 = prev.FindAtom(name1.substr(1));
+ }
+ else if(name1[0] == '+'){
+ if(!next.IsValid()) throw ost::Error("Cannot access next residue in connecting procedure!");
+ atom1 = next.FindAtom(name1.substr(1));
+ }
+ else{
+ atom1 = handle.FindAtom(name1);
+ }
+
+ if(name2[0] == '-'){
+ if(!prev.IsValid()) throw ost::Error("Cannot access previous residue in connecting procedure!");
+ atom2 = prev.FindAtom(name2.substr(1));
+ }
+ else if(name2[0] == '+'){
+ if(!next.IsValid()) throw ost::Error("Cannot access next residue in connecting procedure!");
+ atom2 = next.FindAtom(name2.substr(1));
+ }
+ else{
+ atom2 = handle.FindAtom(name2);
+ }
+
+ if(!atom1.IsValid() || !atom2.IsValid()) throw ost::Error("Could not find required atom in connecting procedure!");
+
+ ed.Connect(atom1,atom2);
+ }
+}
+
+String BuildingBlock::GetType(const String& name) const{
+ int index = this->GetAtomIndex(name);
+ if(index!=-1) return types_[index];
+ std::stringstream ss;
+ ss << "Could not find requested atom of name \""<<name;
+ ss << "\" in buildingblock!";
+ throw ost::Error(ss.str());
+}
+
+Real BuildingBlock::GetCharge(const String& name) const{
+ int index = this->GetAtomIndex(name);
+ if(index!=-1) return charges_[index];
+ std::stringstream ss;
+ ss << "Could not find requested atom of name \""<<name;
+ ss << "\" in buildingblock!";
+ throw ost::Error(ss.str());
+}
+
+Real BuildingBlock::GetMass(const String& name) const{
+ int index = this->GetAtomIndex(name);
+ if(index!=-1) return masses_[index];
+ std::stringstream ss;
+ ss << "Could not find requested atom of name \""<<name;
+ ss << "\" in buildingblock!";
+ throw ost::Error(ss.str());
+}
+
+
+void BuildingBlock::AddBond(InteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < bonds_.size(); ++i){
+ if(bonds_[i]->MatchNames(names)){
+ bonds_.erase(bonds_.begin() + i);
+ --i;
+ }
+ }
+ }
+ bonds_.push_back(p);
+}
+
+void BuildingBlock::AddAngle(InteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < angles_.size(); ++i){
+ if(angles_[i]->MatchNames(names)){
+ angles_.erase(angles_.begin() + i);
+ --i;
+ }
+ }
+ }
+ angles_.push_back(p);
+}
+
+void BuildingBlock::AddDihedral(InteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < dihedrals_.size(); ++i){
+ if(dihedrals_[i]->MatchNames(names)){
+ dihedrals_.erase(dihedrals_.begin() + i);
+ --i;
+ }
+ }
+ }
+ dihedrals_.push_back(p);
+}
+
+void BuildingBlock::AddImproper(InteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < impropers_.size(); ++i){
+ if(impropers_[i]->MatchNames(names)){
+ impropers_.erase(impropers_.begin() + i);
+ --i;
+ }
+ }
+ }
+ impropers_.push_back(p);
+}
+
+void BuildingBlock::AddExclusion(InteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < exclusions_.size(); ++i){
+ if(exclusions_[i]->MatchNames(names)){
+ exclusions_.erase(exclusions_.begin() + i);
+ --i;
+ }
+ }
+ }
+ exclusions_.push_back(p);
+}
+
+void BuildingBlock::AddCMap(InteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ if(cmaps_[i]->MatchNames(names)){
+ cmaps_.erase(cmaps_.begin() + i);
+ --i;
+ }
+ }
+ }
+ cmaps_.push_back(p);
+}
+
+void BuildingBlock::AddConstraint(InteractionPtr p, bool replace_existing){
+ this->CheckInteractionToAdd(p);
+ if(replace_existing){
+ std::vector<String> names = p->GetNames();
+ for(uint i = 0; i < constraints_.size(); ++i){
+ if(constraints_[i]->MatchNames(names)){
+ constraints_.erase(constraints_.begin() + i);
+ --i;
+ }
+ }
+ }
+ constraints_.push_back(p);
+}
+
+void BuildingBlock::RemoveAtom(const String& name){
+ int index = this->GetAtomIndex(name);
+ if(index != -1){
+ atoms_.erase(atoms_.begin()+index);
+ types_.erase(types_.begin()+index);
+ charges_.erase(charges_.begin()+index);
+ masses_.erase(masses_.begin()+index);
+ }
+
+ //All interactions, that contain this atom get deleted as well
+ //note, that we're looking at all interactions independently whether tere
+ //really is such an atom in the building block
+ for(uint i = 0; i < bonds_.size(); ++i){
+ if(bonds_[i]->HasName(name)){
+ bonds_.erase(bonds_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < angles_.size(); ++i){
+ if(angles_[i]->HasName(name)){
+ angles_.erase(angles_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < dihedrals_.size(); ++i){
+ if(dihedrals_[i]->HasName(name)){
+ dihedrals_.erase(dihedrals_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < impropers_.size(); ++i){
+ if(impropers_[i]->HasName(name)){
+ impropers_.erase(impropers_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < exclusions_.size(); ++i){
+ if(exclusions_[i]->HasName(name)){
+ exclusions_.erase(exclusions_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ if(cmaps_[i]->HasName(name)){
+ cmaps_.erase(cmaps_.begin()+i);
+ --i;
+ }
+ }
+ for(uint i = 0; i < constraints_.size(); ++i){
+ if(constraints_[i]->HasName(name)){
+ constraints_.erase(constraints_.begin()+i);
+ --i;
+ }
+ }
+}
+
+void BuildingBlock::ReplaceAtom(const String& name,const String& new_name,
+ const String& new_type, Real new_charge, Real new_mass){
+
+ int index = this->GetAtomIndex(name);
+ if(index != -1){
+ atoms_[index] = new_name;
+ types_[index] = new_type;
+ charges_[index] = new_charge;
+ masses_[index] = new_mass;
+
+ //we don't want to search every interaction associated with this
+ //atom, so we call the ReplaceAtom method for every interaction
+ //nothing will happen, if the atom of interest is not part of
+ //that interaction.
+
+ for(std::vector<InteractionPtr>::iterator i = bonds_.begin();
+ i!=bonds_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = angles_.begin();
+ i!=angles_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = dihedrals_.begin();
+ i!=dihedrals_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = impropers_.begin();
+ i!=impropers_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = exclusions_.begin();
+ i!=exclusions_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = cmaps_.begin();
+ i!=cmaps_.end(); ++i){
+ (*i)->ReplaceAtom(name, new_name, new_type);
+ }
+ }
+}
+
+void BuildingBlock::AddAtom(const String& name, const String& type, Real charge, Real mass){
+ if (std::find(atoms_.begin(),atoms_.end(),name) != atoms_.end()) return;
+ atoms_.push_back(name);
+ types_.push_back(type);
+ charges_.push_back(charge);
+ masses_.push_back(mass);
+}
+
+void BuildingBlock::RemoveInteractionsToPrev(){
+ std::vector<String> names;
+ bool has_prev_atom;
+
+ for(uint i = 0; i < bonds_.size(); ++i){
+ has_prev_atom = false;
+ names = bonds_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ bonds_.erase(bonds_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < angles_.size(); ++i){
+ has_prev_atom = false;
+ names = angles_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ angles_.erase(angles_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < dihedrals_.size(); ++i){
+ has_prev_atom = false;
+ names = dihedrals_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ dihedrals_.erase(dihedrals_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < impropers_.size(); ++i){
+ has_prev_atom = false;
+ names = impropers_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ impropers_.erase(impropers_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < exclusions_.size(); ++i){
+ has_prev_atom = false;
+ names = exclusions_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ exclusions_.erase(exclusions_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ has_prev_atom = false;
+ names = cmaps_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '-'){
+ has_prev_atom = true;
+ break;
+ }
+ }
+ if(has_prev_atom){
+ cmaps_.erase(cmaps_.begin()+i);
+ --i;
+ }
+ }
+}
+
+void BuildingBlock::RemoveInteractionsToNext(){
+ std::vector<String> names;
+ bool has_next_atom;
+
+ for(uint i = 0; i < bonds_.size(); ++i){
+ has_next_atom = false;
+ names = bonds_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ bonds_.erase(bonds_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < angles_.size(); ++i){
+ has_next_atom = false;
+ names = angles_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ angles_.erase(angles_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < dihedrals_.size(); ++i){
+ has_next_atom = false;
+ names = dihedrals_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ dihedrals_.erase(dihedrals_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < impropers_.size(); ++i){
+ has_next_atom = false;
+ names = impropers_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ impropers_.erase(impropers_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < exclusions_.size(); ++i){
+ has_next_atom = false;
+ names = exclusions_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ exclusions_.erase(exclusions_.begin()+i);
+ --i;
+ }
+ }
+
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ has_next_atom = false;
+ names = cmaps_[i]->GetNames();
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ if((*j)[0] == '+'){
+ has_next_atom = true;
+ break;
+ }
+ }
+ if(has_next_atom){
+ cmaps_.erase(cmaps_.begin()+i);
+ --i;
+ }
+ }
+}
+
+void BuildingBlock::CheckInteractionToAdd(InteractionPtr p) const{
+ if(p->GetNames().empty()){
+ throw ost::Error("Expect interaction to have names properly set!");
+ }
+}
+
+}}}//ns
diff --git a/modules/mol/mm/src/buildingblock.hh b/modules/mol/mm/src/buildingblock.hh
new file mode 100644
index 0000000000000000000000000000000000000000..aa28327d4b03f278665b3fe9d4ff9307d9298e40
--- /dev/null
+++ b/modules/mol/mm/src/buildingblock.hh
@@ -0,0 +1,267 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_BUILDING_BLOCK_HH
+#define OST_MM_BUILDING_BLOCK_HH
+
+#include <vector>
+#include <limits>
+#include <set>
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/mol/mm/interaction.hh>
+#include <ost/message.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/geom/vec3.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class BuildingBlock;
+typedef boost::shared_ptr<BuildingBlock> BuildingBlockPtr;
+
+class BuildingBlock{
+public:
+ BuildingBlock() { }
+
+ //copy constructor needs to be defined explicitely, since the forces
+ //have to be newly created
+ BuildingBlock(const BuildingBlock& block);
+
+ bool Match(const ost::mol::ResidueHandle& handle, bool match_connectivity, String& info) const;
+
+ void Connect(ost::mol::ResidueHandle& handle, ost::mol::XCSEditor& ed);
+
+ //getter functionality for all buildingblock members
+
+ std::vector<String> GetAtoms() const { return atoms_; }
+
+ std::vector<String> GetTypes() const { return types_; }
+
+ std::vector<Real> GetCharges() const { return charges_; }
+
+ std::vector<Real> GetMasses() const { return masses_; }
+
+ String GetType(const String& name) const;
+
+ Real GetCharge(const String& name) const;
+
+ Real GetMass(const String& name) const;
+
+ std::vector<InteractionPtr> GetBonds() const { return bonds_; }
+
+ std::vector<InteractionPtr> GetAngles() const { return angles_; }
+
+ std::vector<InteractionPtr> GetDihedrals() const { return dihedrals_; }
+
+ std::vector<InteractionPtr> GetImpropers() const { return impropers_; }
+
+ std::vector<InteractionPtr> GetCMaps() const { return cmaps_; }
+
+ std::vector<InteractionPtr> GetExclusions() const { return exclusions_; }
+
+ std::vector<InteractionPtr> GetConstraints() const { return constraints_;}
+
+ //Add data to building block
+
+ void AddAtom(const String& name, const String& type, Real charge, Real mass = std::numeric_limits<Real>::quiet_NaN());
+
+ void AddBond(InteractionPtr p, bool replace_existing = false);
+
+ void AddAngle(InteractionPtr p, bool replace_existing = false);
+
+ void AddDihedral(InteractionPtr p, bool replace_existing = false);
+
+ void AddImproper(InteractionPtr p, bool replace_existing = false);
+
+ void AddExclusion(InteractionPtr p, bool replace_existing = false);
+
+ void AddCMap(InteractionPtr p, bool replace_existing = false);
+
+ void AddConstraint(InteractionPtr p, bool replace_existing = false);
+
+ //modifiers
+
+ //removes atom and all interactions associated to it
+ void RemoveAtom(const String& name);
+
+ //replaces atom in all interactions
+ void ReplaceAtom(const String& name,const String& new_name,
+ const String& new_type, Real new_charge,
+ Real new_mass = std::numeric_limits<Real>::quiet_NaN());
+
+
+ //remove all interactions to previous or next residue
+ void RemoveInteractionsToPrev();
+
+ void RemoveInteractionsToNext();
+
+ template <typename DS>
+ void Serialize(DS& ds){
+ int num_atoms = atoms_.size();
+ ds & num_atoms;
+
+ if(ds.IsSource()){
+ atoms_ = std::vector<String>(num_atoms);
+ types_ = std::vector<String>(num_atoms);
+ charges_ = std::vector<Real>(num_atoms);
+ masses_ = std::vector<Real>(num_atoms);
+ }
+
+ for(int i = 0; i < num_atoms; ++i){
+ ds & atoms_[i];
+ ds & types_[i];
+ ds & charges_[i];
+ ds & masses_[i];
+ }
+
+ int num_bonds = bonds_.size();
+ int num_angles = angles_.size();
+ int num_dihedrals = dihedrals_.size();
+ int num_impropers = impropers_.size();
+ int num_exclusions = exclusions_.size();
+ int num_cmaps = cmaps_.size();
+ int num_constraints = constraints_.size();
+
+ ds & num_bonds;
+ ds & num_angles;
+ ds & num_dihedrals;
+ ds & num_impropers;
+ ds & num_exclusions;
+ ds & num_cmaps;
+ ds & num_constraints;
+
+ for(int i = 0; i < num_bonds; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ bonds_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = bonds_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(bonds_[i]);
+ }
+
+ for(int i = 0; i < num_angles; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ angles_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = angles_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(angles_[i]);
+ }
+
+ for(int i = 0; i < num_dihedrals; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ dihedrals_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = dihedrals_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(dihedrals_[i]);
+ }
+
+ for(int i = 0; i < num_impropers; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ impropers_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = impropers_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(impropers_[i]);
+ }
+
+ for(int i = 0; i < num_exclusions; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ exclusions_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = exclusions_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(exclusions_[i]);
+ }
+
+ for(int i = 0; i < num_cmaps; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ cmaps_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = cmaps_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(cmaps_[i]);
+ }
+
+ for(int i = 0; i < num_constraints; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ constraints_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = constraints_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(constraints_[i]);
+ }
+ }
+
+
+private:
+
+ int GetAtomIndex(const String& atom_name) const;
+ void CheckInteractionToAdd(InteractionPtr p) const;
+
+ std::vector<String> atoms_;
+ std::vector<String> types_;
+ std::vector<Real> charges_;
+ std::vector<Real> masses_;
+ std::vector<InteractionPtr> bonds_;
+ std::vector<InteractionPtr> angles_;
+ std::vector<InteractionPtr> dihedrals_;
+ std::vector<InteractionPtr> impropers_;
+ std::vector<InteractionPtr> exclusions_;
+ std::vector<InteractionPtr> cmaps_;
+ std::vector<InteractionPtr> constraints_;
+};
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/ff_reader.cc b/modules/mol/mm/src/ff_reader.cc
new file mode 100644
index 0000000000000000000000000000000000000000..dd14426c8f13145fdf66ee32e07c5d89130e18ce
--- /dev/null
+++ b/modules/mol/mm/src/ff_reader.cc
@@ -0,0 +1,2088 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/ff_reader.hh>
+
+
+namespace ost { namespace mol{ namespace mm {
+
+
+GromacsData::GromacsData(){
+ keyword_map_["atoms"] = 0;
+ keyword_map_["bonds"] = 1;
+ keyword_map_["angles"] = 2;
+ keyword_map_["impropers"] = 3;
+ keyword_map_["dihedrals"] = 4;
+ keyword_map_["exclusions"] = 5;
+ keyword_map_["cmap"] = 6;
+ keyword_map_["replace"] = 7;
+ keyword_map_["moleculetype"] = 8;
+ keyword_map_["add"] = 9;
+ keyword_map_["delete"] = 10;
+ keyword_map_["bondtypes"] = 11;
+ keyword_map_["constrainttypes"] = 12;
+ keyword_map_["angletypes"] = 13;
+ keyword_map_["dihedraltypes"] = 14;
+ keyword_map_["atomtypes"] = 15;
+ keyword_map_["implicit_genborn_params"] = 16;
+ keyword_map_["pairtypes"] = 17;
+ keyword_map_["nonbond_params"] = 18;
+ keyword_map_["defaults"] = 19;
+ keyword_map_["cmaptypes"] = 20;
+ keyword_map_["pairs"] = 21;
+ keyword_map_["settles"] = 22;
+
+
+ renaming_to_standard_["ILE"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["HOH"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["HO4"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["HO5"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["HEME"] = std::vector<std::pair<String,String> >();
+ renaming_to_standard_["protein"] = std::vector<std::pair<String,String> >();
+
+ renaming_to_standard_["ILE"].push_back(std::make_pair("CD1","CD"));
+ renaming_to_standard_["ILE"].push_back(std::make_pair("HD11","HD1"));
+ renaming_to_standard_["ILE"].push_back(std::make_pair("HD12","HD2"));
+ renaming_to_standard_["ILE"].push_back(std::make_pair("HD13","HD3"));
+
+ renaming_to_standard_["HOH"].push_back(std::make_pair("O","OW"));
+ renaming_to_standard_["HOH"].push_back(std::make_pair("OW1","OW"));
+ renaming_to_standard_["HO4"].push_back(std::make_pair("O","OW"));
+ renaming_to_standard_["HO4"].push_back(std::make_pair("OW1","OW"));
+ renaming_to_standard_["HO5"].push_back(std::make_pair("O","OW"));
+ renaming_to_standard_["HO5"].push_back(std::make_pair("OW1","OW"));
+
+ renaming_to_standard_["HEME"].push_back(std::make_pair("N_A","NA"));
+ renaming_to_standard_["HEME"].push_back(std::make_pair("N_B","NB"));
+ renaming_to_standard_["HEME"].push_back(std::make_pair("N_C","NC"));
+ renaming_to_standard_["HEME"].push_back(std::make_pair("N_D","ND"));
+
+ renaming_to_standard_["protein"].push_back(std::make_pair("O1","O"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("O2","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OT1","O"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OT2","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OT","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("O'","O"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("O''","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OC1","O"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("OC2","OXT"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("HN","H"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("HT1","H1"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("HT2","H2"));
+ renaming_to_standard_["protein"].push_back(std::make_pair("HT3","H3"));
+}
+
+int GromacsData::GetKeywordIndex(const String& keyword){
+ String lowercase_keyword = keyword;
+ boost::algorithm::to_lower(lowercase_keyword);
+ if(keyword_map_.find(lowercase_keyword) == keyword_map_.end()) return -1;
+ else return keyword_map_[lowercase_keyword];
+}
+
+String GromacsData::ConvertToStandard(const String& res_name, const String& atom_name){
+
+ if(renaming_to_standard_.find(res_name) == renaming_to_standard_.end()) return atom_name;
+ for(std::vector<std::pair<String,String> >::iterator i = renaming_to_standard_[res_name].begin();
+ i != renaming_to_standard_[res_name].end(); ++i){
+ if(i->first == atom_name) return i->second;
+ }
+ return atom_name;
+}
+
+bool GromacsData::ConversionExists(const String& res_name){
+ return renaming_to_standard_.find(res_name) != renaming_to_standard_.end();
+}
+
+GromacsDataPtr GromacsData::Instance(){
+ if(!instance_){
+ instance_ = GromacsDataPtr(new GromacsData);
+ }
+ return instance_;
+}
+
+GromacsDataPtr GromacsData::instance_ = GromacsDataPtr();
+
+CHARMMData::CHARMMData() {
+
+ keyword_map_["atoms"] = 0;
+ keyword_map_["bonds"] = 1;
+ keyword_map_["angles"] = 2;
+ keyword_map_["dihedrals"] = 3;
+ keyword_map_["improper"] = 4;
+ keyword_map_["cmap"] = 5;
+ keyword_map_["nonbonded"] = 6;
+ keyword_map_["hbond"] = 7;
+ keyword_map_["end"] = 8;
+ keyword_map_["mass"] = 9;
+ keyword_map_["decl"] = 10;
+ keyword_map_["defa"] = 11;
+ keyword_map_["auto"] = 12;
+ keyword_map_["resi"] = 13;
+ keyword_map_["pres"] = 14;
+ keyword_map_["atom"] = 15;
+ keyword_map_["group"] = 16;
+ keyword_map_["bond"] = 17;
+ keyword_map_["angle"] = 18;
+ keyword_map_["dihe"] = 19;
+ keyword_map_["impr"] = 20;
+ keyword_map_["donor"] = 21;
+ keyword_map_["acceptor"] = 22;
+ keyword_map_["ic"] = 23;
+ keyword_map_["patching"] = 24;
+ keyword_map_["print"] = 25;
+ keyword_map_["double"] = 26;
+}
+
+int CHARMMData::GetKeywordIndex(const String& keyword){
+ String lowercase_keyword = keyword;
+ boost::algorithm::to_lower(lowercase_keyword);
+ if(keyword_map_.find(lowercase_keyword) == keyword_map_.end()) return -1;
+ else return keyword_map_[lowercase_keyword];
+}
+
+
+CHARMMDataPtr CHARMMData::Instance(){
+ if(!instance_){
+ instance_ = CHARMMDataPtr(new CHARMMData);
+ }
+ return instance_;
+}
+
+CHARMMDataPtr CHARMMData::instance_ = CHARMMDataPtr();
+
+std::vector<std::vector<String> > MMPreprocessor::Process(const String& filename){
+
+ std::vector<std::vector<String> > file_content = this->ReadFile(filename);
+ std::vector<std::vector<String> > temp;
+ std::vector<std::vector<String> > return_file;
+
+ //we first resolve all include statements
+ String include_file_name;
+ for(uint i = 0; i<file_content.size(); ++i){
+ if(file_content[i][0] == "#include"){
+ if(file_content[i].size() != 2){
+ std::stringstream ss;
+ ss<<"Can only evaluate include statement in combination with a filename.";
+ ss<<"Also more stuff in the same line blows the thing up...";
+ throw ost::io::IOException(ss.str());
+ }
+ String include_filename = file_content[i][1].substr(1,file_content[i][1].size()-2);
+ temp = this->ReadFile(include_filename);
+ //directly delete the line with the
+ //include statement and fill in the full content
+ file_content.insert(file_content.erase(file_content.begin()+i), temp.begin(), temp.end());
+ }
+ }
+
+ //let's resolve all definitions
+ std::map<String,std::vector<String> >::iterator definitions_it;
+ for(uint i=0; i<file_content.size(); ++i){
+ //resolve definition
+ if(file_content[i][0] == "#define"){
+ if(file_content[i].size()==2){
+ defines_.insert(file_content[i][1]);
+ file_content.erase(file_content.begin()+i);
+ if(i == file_content.size()) break;
+ --i;
+ continue;
+ }
+ definitions_[file_content[i][1]] = std::vector<String>(file_content[i].begin()+2,file_content[i].end());
+ file_content.erase(file_content.begin()+i);
+ if(i == file_content.size()) break;
+ --i;
+ continue;
+ }
+ //resolve ifdef
+ if(file_content[i][0] == "#ifdef" || file_content[i][0] == "#ifndef"){
+ this->ResolveIFDEF(file_content,i);
+ --i;
+ continue;
+ }
+ //check whether a word in current line corresponds to a found definition
+ for(uint j = 0; j<file_content[i].size(); ++j){
+ definitions_it = definitions_.find(file_content[i][j]);
+ if(definitions_it!=definitions_.end()){
+ file_content[i].insert(file_content[i].erase(file_content[i].begin()+j),definitions_it->second.begin(),definitions_it->second.end());
+ }
+ }
+ }
+ return file_content;
+}
+
+void MMPreprocessor::ResolveIFDEF(std::vector<std::vector<String> >& file_content, int line_counter){
+
+ String ifdef_statement = file_content[line_counter][1];
+ bool logical_outcome;
+ if(file_content[line_counter][0] == "#ifdef"){
+ logical_outcome = defines_.find(ifdef_statement) != defines_.end();
+ }
+ else if(file_content[line_counter][0] == "#ifndef"){
+ logical_outcome = defines_.find(ifdef_statement) == defines_.end();
+ }
+ else{
+ throw ost::Error("Invalid preprocessor statement observed in ResolveIFDEF function!");
+ }
+
+ bool has_else = true;
+ uint else_position = line_counter+1;
+ while(true){
+ if(else_position >= file_content.size()){
+ throw ost::io::IOException("Invalid ifdef statement encountered!");
+ }
+ if(file_content[else_position][0] == "#ifdef" || file_content[else_position][0] == "#ifndef"){
+ this->ResolveIFDEF(file_content,else_position);
+ }
+ if(file_content[else_position][0] == "#else") break;
+ if(file_content[else_position][0] == "#endif"){
+ has_else = false;
+ break;
+ }
+ ++else_position;
+ }
+
+ uint endif_position = else_position+1;
+ while(true && has_else){
+ if(endif_position >= file_content.size()){
+ throw ost::io::IOException("Invalid ifdef statement encountered!");
+ }
+ if(file_content[endif_position][0] == "#ifdef" || file_content[endif_position][0] == "#ifndef"){
+ this->ResolveIFDEF(file_content,endif_position);
+ }
+ if(file_content[endif_position][0] == "#endif") break;
+ ++endif_position;
+ }
+
+ if(has_else){
+ if(logical_outcome){
+ //delete part after else
+ file_content.erase(file_content.begin()+else_position, file_content.begin()+endif_position+1);
+ file_content.erase(file_content.begin()+line_counter);
+ }
+ else{
+ //delete part before else
+ file_content.erase(file_content.begin()+line_counter,file_content.begin()+else_position+1);
+ file_content.erase(file_content.begin()+line_counter+(endif_position-else_position)-1);
+ }
+ }
+ else{
+ if(logical_outcome){//only delete ifdef and endif
+ file_content.erase(file_content.begin()+else_position);
+ file_content.erase(file_content.begin()+line_counter);
+ }
+ else{//it's not defined => delete whole block
+ file_content.erase(file_content.begin()+line_counter,file_content.begin()+else_position+1);
+ }
+ }
+}
+
+std::vector<std::vector<String> > MMPreprocessor::ReadFile(const String& filename){
+
+ boost::filesystem::path file_path = basepath_ / filename;
+ std::ifstream file;
+ file.open((file_path.string()).c_str());
+
+ if(!file){
+ std::stringstream ss;
+ ss<<"Could not read file. File '";
+ ss<<filename<<"' does not exist!";
+ throw ost::io::IOException(ss.str());
+ }
+
+ std::vector<String> file_content;
+ std::vector<std::vector<String> > split_file_content;
+ String string_line;
+ ost::StringRef stringref_line;
+ std::vector<ost::StringRef> data;
+ std::vector<String> fill_data;
+
+ while(file.good()){
+ std::getline(file,string_line);
+ file_content.push_back(string_line);
+ }
+
+ //splitting the stuff up. Everything in a line coming after an element starting
+ //with a colon or exclamation mark, is neglected. (wont neglect anything of:
+ //ab! c, but will neglect the second item of: ab !c)
+ for(std::vector<String>::iterator i = file_content.begin();
+ i!=file_content.end(); ++i){
+ stringref_line = ost::StringRef(i->c_str(),i->length());
+ data = stringref_line.split();
+ if(data.empty()) continue;
+ fill_data.clear();
+ for(std::vector<ost::StringRef>::iterator j = data.begin();
+ j!=data.end(); ++j){
+ //if(*(j->begin()) == ';' || *(j->begin()) == '*'){
+ if(*(j->begin()) == ';' || *(j->begin()) == '!'){
+ break;
+ }
+ fill_data.push_back(j->str());
+ }
+ if(fill_data.empty()) continue;
+ split_file_content.push_back(fill_data);
+ }
+
+ //handling linebreaks ("\")
+ for(uint i = 0; i != split_file_content.size(); ++i){
+ if(*split_file_content[i].back().rbegin() == '\\'){
+ if(i < split_file_content.size() - 1){
+ if(split_file_content[i].back() == "\\"){
+ split_file_content[i].pop_back();
+ }
+ else{
+ split_file_content[i].back() = split_file_content[i].back().substr(0,split_file_content[i].back().size()-1);
+ }
+ if(split_file_content[i].empty()){
+ throw io::IOException("Observed single linebreak (\\) in one line of input file!");
+ }
+ for(std::vector<String>::iterator j = split_file_content[i+1].begin();
+ j != split_file_content[i+1].end(); ++j){
+ split_file_content[i].push_back(*j);
+ }
+ split_file_content.erase(split_file_content.begin()+i+1);
+ --i;
+ }
+ }
+ }
+
+ return split_file_content;
+}
+
+FFReader::FFReader(const String& base_dir): preprocessor_(base_dir),
+ ff_(new Forcefield)
+{
+ for(int i = 0; i < 4; ++i){
+ ff_bonded_types_.push_back(Invalid);
+ bonded_types_.push_back(Invalid);
+ }
+}
+
+void FFReader::ReadGromacsForcefield(){
+
+ //read in the forcefield
+ if(!boost::filesystem::exists(preprocessor_.GetBasedir() / "forcefield.itp")){
+ throw io::IOException("directory must contain forcefield.itp file!");
+ }
+ if(!boost::filesystem::exists(preprocessor_.GetBasedir() / "atomtypes.atp")){
+ throw io::IOException("directory must contain atomtypes.atp file!");
+ }
+ std::vector<std::vector<String> > content = preprocessor_.Process("forcefield.itp");
+ this->ParseForcefield(content);
+ content = preprocessor_.Process("atomtypes.atp");
+ this->ParseAtomTypes(content);
+}
+
+void FFReader::ReadResidueDatabase(const String& basename){
+ std::vector<std::vector<String> > data = preprocessor_.Process(basename+".rtp");
+ this->ParseRTP(data);
+
+ try{
+ data = preprocessor_.Process(basename+".arn");
+ this->ParseARN(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".hdb");
+ this->ParseHDB(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".n.tdb");
+ this->ParseNTDB(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".c.tdb");
+ this->ParseCTDB(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".vsd");
+ this->ParseVSD(data);
+ }catch(ost::io::IOException e) { }
+
+ try{
+ data = preprocessor_.Process(basename+".r2b");
+ this->ParseRtoB(data);
+ }catch(ost::io::IOException e) { }
+}
+
+void FFReader::ReadCHARMMPRM(const String& filename){
+ std::vector<std::vector<String> > data = preprocessor_.Process(filename);
+ this->ParseCHARMMPRM(data);
+}
+
+void FFReader::ReadCHARMMRTF(const String& filename){
+ std::vector<std::vector<String> > data = preprocessor_.Process(filename);
+ this->ParseCHARMMRTF(data);
+}
+
+void FFReader::ParseForcefield(std::vector<std::vector<String> >& content){
+
+ int keyword_id = -1;
+ std::vector<String> current_line;
+
+ for(uint line_counter = 0; line_counter<content.size(); ++line_counter){
+ current_line = content[line_counter];
+ if(current_line[0] == "["){
+ keyword_id = GromacsData::Instance()->GetKeywordIndex(current_line[1]);
+ if(keyword_id == -1){
+ std::stringstream ss;
+ ss << "Unknown keyword '"<<current_line[1];
+ ss << "' in forcefield file."<<std::endl;
+ throw io::IOException(ss.str());
+ }
+ continue;
+ }
+
+ switch(keyword_id){
+ case 11:{
+ InteractionPtr bond = this->ParseBond(current_line,true);
+ ff_->AddBond(bond);
+ ff_bonded_types_[0] = bond->GetFuncType();
+ break;
+ }
+ case 12:{
+ InteractionPtr constraint = this->ParseConstraint(current_line,true);
+ ff_->AddConstraint(constraint);
+ break;
+ }
+ case 13:{
+ InteractionPtr angle = this->ParseAngle(current_line,true);
+ ff_->AddAngle(angle);
+ ff_bonded_types_[1] = angle->GetFuncType();
+ break;
+ }
+ case 14:{
+
+ InteractionPtr p = this->ParseDihedral(current_line,true);
+ FuncType functype = p->GetFuncType();
+
+ if(functype == PeriodicDihedral){
+ ff_->AddDihedral(p);
+ ff_bonded_types_[2] = functype;
+ }
+ else if(functype == PeriodicImproper || functype == HarmonicImproper){
+ ff_->AddImproper(p);
+ ff_bonded_types_[3] = functype;
+ }
+ break;
+ }
+ case 15:{
+ InteractionPtr lj = this->ParseLJ(current_line,true);
+ ff_->AddLJ(lj);
+ break;
+ }
+ case 16:{
+ InteractionPtr genborn = this->ParseGenborn(current_line,true);
+ ff_->AddImplicitGenborn(genborn);
+ break;
+ }
+ case 17:{
+ InteractionPtr lj_pair = this->ParseLJPair(current_line,true);
+ ff_->AddLJPair(lj_pair);
+ break;
+ }
+ case 18:{
+ std::stringstream ss;
+ ss << "Observerd nonbond_params in forcefield file. Only forcefields with ";
+ ss << "combining rules for sigma epsilon calculations are supported!"<<std::endl;
+ throw ost::Error(ss.str());
+ break;
+ }
+ case 19:{
+ bool gen_pairs;
+ Real fudge_lj, fudge_qq;
+ if(current_line[2] == "yes") gen_pairs = true;
+ else if(current_line[2] == "no") gen_pairs = false;
+ else throw io::IOException("Only \"yes\" and \"no\" are supported for gen_pairs parameter!");
+
+ fudge_lj = boost::lexical_cast<Real>(current_line[3]);
+ fudge_qq = boost::lexical_cast<Real>(current_line[4]);
+
+ ff_->SetGenPairs(gen_pairs);
+ ff_->SetFudgeLJ(fudge_lj);
+ ff_->SetFudgeQQ(fudge_qq);
+ break;
+ }
+ case 20:{
+ InteractionPtr cmap = this->ParseCMap(current_line,true);
+ ff_->AddCMap(cmap);
+ break;
+ }
+ default: break;
+ }
+ }
+}
+
+void FFReader::ParseAtomTypes(std::vector<std::vector<String> >& content){
+ for(std::vector<std::vector<String> >::iterator i = content.begin();
+ i!=content.end(); ++i){
+ ff_->AddMass((*i)[0],boost::lexical_cast<Real>((*i)[1]));
+ }
+}
+
+void FFReader::ParseRTP(std::vector<std::vector<String> >& content){
+
+ read_residues_.clear();
+
+ //we assume, that at the beginning is the keyword 'bondedtypes'
+ //we neglect anything before that...
+ uint line_counter = 0;
+ for(; line_counter<content.size(); ++line_counter){
+ if(content[line_counter].size()>1){
+ if(content[line_counter][1] == "bondedtypes"){
+ ++line_counter;
+ //we're interested in the next line
+ if(content[line_counter].size() < 4){
+ throw ost::Error("Error in parsing bondedtypes section of RTP file!");
+ }
+ int gromacs_functype;
+ //first element defines the bonds
+ gromacs_functype = boost::lexical_cast<int>(content[line_counter][0]);
+ if(gromacs_functype == 1){
+ bonded_types_[0] = HarmonicBond;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for bond in bondedtypes section of rtp file!";
+ throw ost::Error(ss.str());
+ }
+ //second element defines angle
+ gromacs_functype = boost::lexical_cast<int>(content[line_counter][1]);
+ if(gromacs_functype == 5) bonded_types_[1] = UreyBradleyAngle;
+ else if(gromacs_functype == 1) bonded_types_[1] = HarmonicAngle;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for angle in bondedtypes section of rtp file!";
+ throw ost::Error(ss.str());
+ }
+ //third element defines the dihedral
+ gromacs_functype = boost::lexical_cast<int>(content[line_counter][2]);
+ if(gromacs_functype == 9 || gromacs_functype == 1) bonded_types_[2] = PeriodicDihedral;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for dihedral in bondedtypes section of rtp file!";
+ throw ost::Error(ss.str());
+ }
+ //fourth elemend defines improper dihedral
+ gromacs_functype = boost::lexical_cast<int>(content[line_counter][3]);
+ if(gromacs_functype == 4) bonded_types_[3] = PeriodicImproper;
+ else if(gromacs_functype == 2) bonded_types_[3] = HarmonicImproper;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for dihedral!";
+ throw ost::Error(ss.str());
+ }
+ ++line_counter;
+ break;
+ }
+ }
+ }
+
+ //data for specific residue will be filled in here and passed
+ //in the residue_building block Parse function
+ std::vector<std::vector<String> > residue_data;
+ String residue_name;
+ for(; line_counter < content.size(); ++line_counter){
+ if(content[line_counter][0] == "["){
+ //I there is a keyword (start with [) not defined above,
+ //we assume, that it is a new residue
+ if(GromacsData::Instance()->GetKeywordIndex(content[line_counter][1]) == -1){
+ //parse the old residue and set new residue name
+ if(!residue_data.empty()){
+ ff_->AddBuildingBlock(residue_name, this->BlockFromRTP(residue_data));
+ read_residues_.push_back(residue_name);
+ }
+ residue_data.clear();
+ residue_name = content[line_counter][1];
+ continue;
+ }
+ }
+ residue_data.push_back(content[line_counter]);
+ }
+ //we probably missed the last residue
+ if(!residue_data.empty()){
+ ff_->AddBuildingBlock(residue_name, this->BlockFromRTP(residue_data));
+ read_residues_.push_back(residue_name);
+ }
+
+
+ //It could be, that certain bondedtypes in the forcefield are not defined yet,
+ //since all forces are defined in the building blocks...
+ //We assume, that the whole stuff is consistent across all forcefield and rtp
+ //files... If not, you'll get errors when setting up your system
+ for(int i = 0; i < 4; ++i){
+ if(ff_bonded_types_[i] == Invalid) ff_bonded_types_[i] = bonded_types_[i];
+ }
+
+}
+
+void FFReader::ParseARN(std::vector<std::vector<String> >& content){
+ String res_name, a_one, a_two;
+
+ for(std::vector<std::vector<String> >::iterator i = content.begin();
+ i!=content.end(); ++i){
+ res_name = (*i)[0];
+ a_one = (*i)[1];
+ a_two = (*i)[2];
+ if(res_name == "*"){
+ // * is wildcard... valid for all residues in the previously read rtp file
+ for(std::vector<String>::iterator j = read_residues_.begin();
+ j != read_residues_.end(); ++j){
+ ff_->AddAtomRenamingRule(*j,a_one,a_two);
+ }
+ }
+ else{
+ ff_->AddAtomRenamingRule(res_name, a_one, a_two);
+ }
+ }
+}
+
+void FFReader::ParseHDB(std::vector<std::vector<String> >& content){
+
+ std::vector<std::vector<String> > residue_data;
+ String residue_name;
+ for(uint line_counter = 0; line_counter<content.size(); ++line_counter){
+ if(content[line_counter].size() == 2){
+ if(!residue_data.empty()){
+ GromacsHydrogenConstructor* p = new GromacsHydrogenConstructor;
+ for(std::vector<std::vector<String> >::iterator i = residue_data.begin();
+ i != residue_data.end(); ++i){
+ this->ParseHydrogenRule(*i,*p);
+ }
+ ff_->AddHydrogenConstructor(residue_name,HydrogenConstructorPtr(p));
+ }
+ residue_data.clear();
+ residue_name = content[line_counter][0];
+ continue;
+ }
+ residue_data.push_back(content[line_counter]);
+ }
+ //we probably missed the last residue
+ if(!residue_data.empty()){
+ GromacsHydrogenConstructor* p = new GromacsHydrogenConstructor;
+ for(std::vector<std::vector<String> >::iterator i = residue_data.begin();
+ i != residue_data.end(); ++i){
+ this->ParseHydrogenRule(*i,*p);
+ }
+ ff_->AddHydrogenConstructor(residue_name,HydrogenConstructorPtr(p));
+ }
+}
+
+void FFReader::ParseHydrogenRule(const std::vector<String>& data,
+ GromacsHydrogenConstructor& constructor){
+
+ if(data.size() < 4){
+ throw ost::Error("Require at least four items when parsing hydrogen rule!");
+ }
+
+ int number = boost::lexical_cast<int>(data[0]);
+ int method = boost::lexical_cast<int>(data[1]);
+ String prefix = data[2];
+ std::vector<String> anchors;
+ std::vector<String> hydrogen_names;
+
+ for(uint i=3; i<data.size(); ++i){
+ anchors.push_back(data[i]);
+ }
+
+ switch(number){
+ case 1:{
+ hydrogen_names.push_back(prefix);
+ break;
+ }
+ case 2:{
+ hydrogen_names.push_back(prefix+"1");
+ hydrogen_names.push_back(prefix+"2");
+ break;
+ }
+ case 3:{
+ hydrogen_names.push_back(prefix+"1");
+ hydrogen_names.push_back(prefix+"2");
+ hydrogen_names.push_back(prefix+"3");
+ break;
+ }
+ default:{
+ break;
+ }
+ }
+
+ constructor.AddHydrogenRule(number,method,hydrogen_names, anchors);
+}
+
+
+void FFReader::ParseTerminiReplaceRule(const std::vector<String>& data,
+ GromacsBlockModifier& modifier){
+
+ String name;
+ String new_name;
+ String new_type;
+ Real new_charge;
+ if(data.size() == 5 && data.back() != "0"){
+ name = data[0];
+ new_name = data[1];
+ new_type = data[2];
+ new_charge = boost::lexical_cast<Real>(data[4]);
+ }
+ else{
+ name = data[0];
+ new_name = name;
+ new_type = data[1];
+ new_charge = boost::lexical_cast<Real>(data[3]);
+ }
+
+ modifier.AddReplaceRule(name, new_name, new_type, new_charge);
+ //we neglect the mass! This will be read from the forcefield itself!
+}
+
+void FFReader::ParseTerminiAddRule(const std::vector<String>& data1,
+ const std::vector<String>& data2,
+ GromacsBlockModifier& modifier){
+
+ int number = boost::lexical_cast<int>(data1[0]);
+ int method = boost::lexical_cast<int>(data1[1]);
+ String prefix = data1[2];
+
+ std::vector<String> anchors;
+ for(uint i = 3; i < data1.size(); ++i){
+ anchors.push_back(data1[i]);
+ }
+
+ String type = data2[0];
+ Real charge = boost::lexical_cast<Real>(data2[2]);
+ //we again neglect the masses...
+
+ std::vector<String> names;
+
+ switch(number){
+ case 1:{
+ names.push_back(prefix);
+ break;
+ }
+ case 2:{
+ names.push_back(prefix+"1");
+ names.push_back(prefix+"2");
+ break;
+ }
+ case 3:{
+ names.push_back(prefix+"1");
+ names.push_back(prefix+"2");
+ names.push_back(prefix+"3");
+ break;
+ }
+ default:{
+ std::stringstream ss;
+ ss<<"Can only add one, two or three atoms at one position.";
+ ss<<"The provided force field file seems to tell something different";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ modifier.AddAddRule(number, method, names, anchors, type, charge);
+
+}
+
+
+void FFReader::ParseNTDB(std::vector<std::vector<String> >& content){
+
+ //Besided general termini constructors, there are also residue
+ //specific constructors => custom constructors
+ std::vector<String> termini;
+ std::map<String,std::vector<String> > custom_termini;
+
+ std::vector<std::vector<String> > data;
+ String name;
+
+ for(uint line_counter = 0; line_counter < content.size(); ++line_counter){
+ if(content[line_counter][0] == "["){
+ //I there is a keyword (start with [) not defined above,
+ //we assume, that it is a new residue
+ if(GromacsData::Instance()->GetKeywordIndex(content[line_counter][1]) == -1){
+ //parse the old residue and set new residue name
+ if(!data.empty()){
+ BlockModifierPtr p = this->ParseBlockModifier(data);
+ ff_->AddBlockModifier(name,p);
+ size_t minus_pos = name.find("-");
+ if(minus_pos != String::npos && minus_pos < (name.size()-1)){
+ String a = name.substr(0,minus_pos);
+ if(custom_termini.find(a) == custom_termini.end()){
+ custom_termini[a] = std::vector<String>();
+ }
+ custom_termini[a].push_back(name);
+ }
+ else{
+ termini.push_back(name);
+ }
+ }
+ data.clear();
+ name = content[line_counter][1];
+ continue;
+ }
+ }
+ data.push_back(content[line_counter]);
+ }
+
+ if(!data.empty()){
+ BlockModifierPtr p = this->ParseBlockModifier(data);
+ ff_->AddBlockModifier(name,p);
+ size_t minus_pos = name.find("-");
+ if(minus_pos != String::npos && minus_pos < (name.size()-1)){
+ String a = name.substr(0,minus_pos);
+ if(custom_termini.find(a) == custom_termini.end()){
+ custom_termini[a] = std::vector<String>();
+ }
+ custom_termini[a].push_back(name);
+ }
+ else{
+ termini.push_back(name);
+ }
+ }
+
+ for(std::vector<String>::iterator i = read_residues_.begin();
+ i != read_residues_.end(); ++i){
+ if(custom_termini.find(*i) != custom_termini.end()){
+ if(!custom_termini[*i].empty()) ff_->SetStandardNTer(*i,custom_termini[*i][0]);
+ continue;
+ }
+ if(!termini.empty()) ff_->SetStandardNTer(*i,termini[0]);
+ }
+}
+
+void FFReader::ParseCTDB(std::vector<std::vector<String> >& content){
+
+ //Besided general termini constructors, there are also residue
+ //specific constructors => custom constructors
+ std::vector<String> termini;
+ std::map<String,std::vector<String> > custom_termini;
+
+ std::vector<std::vector<String> > data;
+ String name;
+
+ for(uint line_counter = 0; line_counter < content.size(); ++line_counter){
+ if(content[line_counter][0] == "["){
+ //I there is a keyword (start with [) not defined above,
+ //we assume, that it is a new residue
+ if(GromacsData::Instance()->GetKeywordIndex(content[line_counter][1]) == -1){
+ //parse the old residue and set new residue name
+ if(!data.empty()){
+ BlockModifierPtr p = this->ParseBlockModifier(data);
+ ff_->AddBlockModifier(name,p);
+ size_t minus_pos = name.find("-");
+ if(minus_pos != String::npos && minus_pos < (name.size()-1)){
+ String a = name.substr(0,minus_pos);
+ if(custom_termini.find(a) == custom_termini.end()){
+ custom_termini[a] = std::vector<String>();
+ }
+ custom_termini[a].push_back(name);
+ }
+ else{
+ termini.push_back(name);
+ }
+ }
+ data.clear();
+ name = content[line_counter][1];
+ continue;
+ }
+ }
+ data.push_back(content[line_counter]);
+ }
+
+ if(!data.empty()){
+ BlockModifierPtr p = this->ParseBlockModifier(data);
+ ff_->AddBlockModifier(name,p);
+ size_t minus_pos = name.find("-");
+ if(minus_pos != String::npos && minus_pos < (name.size()-1)){
+ String a = name.substr(0,minus_pos);
+ if(custom_termini.find(a) == custom_termini.end()){
+ custom_termini[a] = std::vector<String>();
+ }
+ custom_termini[a].push_back(name);
+ }
+ else{
+ termini.push_back(name);
+ }
+ }
+
+ for(std::vector<String>::iterator i = read_residues_.begin();
+ i != read_residues_.end(); ++i){
+ if(custom_termini.find(*i) != custom_termini.end()){
+ if(!custom_termini[*i].empty()) ff_->SetStandardCTer(*i,custom_termini[*i][0]);
+ continue;
+ }
+ if(!termini.empty()) ff_->SetStandardCTer(*i,termini[0]);
+ }
+}
+
+void FFReader::ParseVSD(std::vector<std::vector<String> >& content){
+
+}
+
+void FFReader::ParseRtoB(std::vector<std::vector<String> >& content){
+
+ //there are two versions of this file, either with two or five
+ //columns further instructions can be found in the gromacs manual
+
+ String res_name, main, n_ter, c_ter, two_ter;
+
+ for(std::vector<std::vector<String> >::iterator i = content.begin();
+ i != content.end(); ++i){
+ if((*i).size() == 2){
+ res_name = (*i)[0];
+ main = (*i)[1];
+ n_ter = main;
+ c_ter = main;
+ two_ter = main;
+ ff_->AddResidueRenamingRule(res_name,main,n_ter,c_ter,two_ter);
+ continue;
+ }
+ if((*i).size() == 5){
+ res_name = (*i)[0];
+ main = (*i)[1];
+ n_ter = (*i)[2];
+ c_ter = (*i)[3];
+ two_ter = (*i)[4];
+ ff_->AddResidueRenamingRule(res_name,main,n_ter,c_ter,two_ter);
+ continue;
+ }
+ throw io::IOException("Entries in r2b files must contain 2 or 5 columns");
+ }
+}
+
+void FFReader::ReadITP(const String& basename){
+ std::vector<std::vector<String> > content = preprocessor_.Process(basename + ".itp");
+ this->ParseITP(content);
+}
+
+void FFReader::ParseITP(std::vector<std::vector<String> >& content){
+
+ std::vector<std::vector<String> > residue_data;
+ String residue_name;
+ for(uint line_counter = 0; line_counter < content.size(); ++line_counter){
+ if(content[line_counter][0] == "["){
+ if(GromacsData::Instance()->GetKeywordIndex(content[line_counter][1]) == 8){
+ //parse the old residue and set new residue name
+ if(!residue_data.empty()){
+ BuildingBlockPtr p = this->BlockFromITP(residue_data);
+ ff_->AddBuildingBlock(residue_name, p);
+ }
+ residue_data.clear();
+ residue_name = content[++line_counter][0];
+ continue;
+ }
+ }
+ residue_data.push_back(content[line_counter]);
+ }
+ //we probably missed the last residue
+ if(!residue_data.empty()){
+ BuildingBlockPtr p = this->BlockFromITP(residue_data);
+ ff_->AddBuildingBlock(residue_name, p);
+ }
+}
+
+BuildingBlockPtr FFReader::BlockFromRTP(const std::vector<std::vector<String> >& data){
+
+ if(bonded_types_.size()<4){
+ std::stringstream ss;
+ ss << "There must be at least 4 parameters in the bondedtypes section of";
+ ss << ".rtp file";
+ throw io::IOException(ss.str());
+ }
+
+ if(data[0][1] != "atoms"){
+ std::stringstream ss;
+ ss << "Expect residue definition to start with the atom keyword!";
+ throw io::IOException(ss.str());
+ }
+
+ int keyword_index = 0;
+ BuildingBlockPtr p(new BuildingBlock);
+
+ for(uint i=1;i<data.size(); ++i){
+ if(data[i].size()>1){
+ if(data[i][0]=="["){
+ keyword_index = GromacsData::Instance()->GetKeywordIndex(data[i][1]);
+ continue;
+ }
+ }
+
+ switch(keyword_index){
+ case 0:{
+ p->AddAtom(data[i][0],
+ data[i][1],
+ boost::lexical_cast<Real>(data[i][2]));
+ break;
+ }
+ case 1:{
+ p->AddBond(this->ParseBond(data[i],false,bonded_types_[0]));
+ break;
+ }
+ case 2:{
+ p->AddAngle(this->ParseAngle(data[i],false,bonded_types_[1]));
+ break;
+ }
+ case 3:{
+ p->AddImproper(this->ParseDihedral(data[i],false,bonded_types_[3]));
+ break;
+ }
+ case 4:{
+ p->AddDihedral(this->ParseDihedral(data[i],false,bonded_types_[2]));
+ break;
+ }
+ case 5:{
+ p->AddExclusion(this->ParseExclusion(data[i],false));
+ break;
+ }
+ case 6:{
+ p->AddCMap(this->ParseCMap(data[i],false));
+ break;
+ }
+ default:{
+ std::stringstream ss;
+ ss << "Encountered invalid keyword while parsing rtp file: " << data[i-1][1];
+ throw ost::io::IOException(ss.str());
+ }
+ }
+ }
+ return p;
+}
+
+BuildingBlockPtr FFReader::BlockFromITP(const std::vector<std::vector<String> >& data){
+
+ int keyword_index;
+
+ if(data[0][1] != "atoms"){
+ std::stringstream ss;
+ ss << "Expect residue definition to start with the atom keyword!";
+ throw io::IOException(ss.str());
+ }
+
+ std::map<int,String> index_name_mapper;
+ keyword_index = 0;
+ BuildingBlockPtr p(new BuildingBlock);
+ std::vector<String> current_line;
+
+ for(uint i=1;i<data.size(); ++i){
+ if(data[i].size()>1){
+ if(data[i][0]=="["){
+ keyword_index = GromacsData::Instance()->GetKeywordIndex(data[i][1]);
+ continue;
+ }
+ }
+ current_line = data[i];
+ switch(keyword_index){
+ case 0:{
+ p->AddAtom(current_line[4],
+ current_line[1],
+ boost::lexical_cast<Real>(current_line[6]));
+ index_name_mapper[boost::lexical_cast<int>(current_line[0])] = current_line[4];
+ break;
+ }
+ case 1:{
+ current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ p->AddBond(this->ParseBond(current_line,false));
+ break;
+ }
+ case 2:{
+ current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ current_line[2] = index_name_mapper[boost::lexical_cast<int>(current_line[2])];
+ p->AddAngle(this->ParseAngle(current_line,false));
+ break;
+ }
+ case 4:{
+ //there must be a function type, otherwise we can't distinguish
+ //between dihedrals and impropers
+ current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ current_line[2] = index_name_mapper[boost::lexical_cast<int>(current_line[2])];
+ current_line[3] = index_name_mapper[boost::lexical_cast<int>(current_line[3])];
+
+ InteractionPtr int_ptr = this->ParseDihedral(current_line,false);
+ FuncType functype = int_ptr->GetFuncType();
+
+ if(functype == PeriodicDihedral){
+ p->AddDihedral(int_ptr);
+ }
+ else if(functype == PeriodicImproper || functype == HarmonicImproper){
+ p->AddImproper(int_ptr);
+ }
+ break;
+ }
+ case 5:{
+ //current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ //current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ //p->exclusions_.push_back(Interaction::ParseExclusion(current_line,false));
+ break;
+ }
+ case 6:{
+ current_line[0] = index_name_mapper[boost::lexical_cast<int>(current_line[0])];
+ current_line[1] = index_name_mapper[boost::lexical_cast<int>(current_line[1])];
+ current_line[2] = index_name_mapper[boost::lexical_cast<int>(current_line[2])];
+ current_line[3] = index_name_mapper[boost::lexical_cast<int>(current_line[3])];
+ current_line[4] = index_name_mapper[boost::lexical_cast<int>(current_line[4])];
+ p->AddCMap(this->ParseCMap(current_line,false));
+ break;
+ }
+ case 21:{
+ //we extract pairs manually...
+ break;
+ }
+ case 22:{
+ std::vector<String> block_atom_names = p->GetAtoms();
+ if(block_atom_names.size() < 3){
+ throw ost::Error("Molecule with settles keyword must contain at least 3 atoms!");
+ }
+ std::vector<Real> parameters;
+ std::vector<String> names;
+
+
+ InteractionPtr p1(new Interaction(DistanceConstraint));
+ InteractionPtr p2(new Interaction(DistanceConstraint));
+ InteractionPtr p3(new Interaction(DistanceConstraint));
+
+ //first constraint dist => O - H
+ parameters.push_back(boost::lexical_cast<Real>(current_line[2]));
+ names.push_back(block_atom_names[0]);
+ names.push_back(block_atom_names[1]);
+ p1->SetNames(names);
+ p1->SetParam(parameters);
+ p->AddConstraint(p1);
+
+ //second constraint dist => O - H
+ names[1] = block_atom_names[2];
+ p2->SetNames(names);
+ p2->SetParam(parameters);
+ p->AddConstraint(p2);
+
+ //third constraint dist => H - H
+ names[0] = block_atom_names[1];
+ parameters[0] = boost::lexical_cast<Real>(current_line[3]);
+ p3->SetNames(names);
+ p3->SetParam(parameters);
+ p->AddConstraint(p3);
+
+ break;
+ }
+ default:{
+ std::stringstream ss;
+ ss << "Encountered invalid keyword while parsing itp file: " << data[i-1][1];
+ throw ost::io::IOException(ss.str());
+ }
+ }
+ }
+ return p;
+}
+
+
+BlockModifierPtr FFReader::ParseBlockModifier(const std::vector<std::vector<String> >& data){
+
+
+ int keyword_index = -1;
+
+ if(data[0].size() > 0){
+ keyword_index = GromacsData::Instance()->GetKeywordIndex(data[0][1]);
+ if(keyword_index == -1){
+ throw ost::io::IOException("Expect termini data to start with a valid keyword!");
+ }
+ }
+
+ GromacsBlockModifier* p = new GromacsBlockModifier;
+
+ for(uint i = 1; i < data.size(); ++i){
+ if(data[i].size()>1){
+ if(data[i][0] == "["){
+ keyword_index = GromacsData::Instance()->GetKeywordIndex(data[i][1]);
+ continue;
+ }
+ }
+ switch(keyword_index){
+ case 7:{
+ this->ParseTerminiReplaceRule(data[i],*p);
+ break;
+ }
+ case 9:{
+ std::vector<String> line1 = data[i];
+ std::vector<String> line2 = data[++i];
+ this->ParseTerminiAddRule(line1, line2, *p);
+ break;
+ }
+ case 10:{
+ p->AddDeleteAtom(data[i][0]);
+ break;
+ }
+ case 1:{
+ p->AddBond(this->ParseBond(data[i],false,bonded_types_[0]));
+ break;
+ }
+ case 2:{
+ p->AddAngle(this->ParseAngle(data[i],false,bonded_types_[1]));
+ break;
+ }
+ case 4:{
+ p->AddDihedral(this->ParseDihedral(data[i],false,bonded_types_[2]));
+ break;
+ }
+ case 3:{
+ p->AddImproper(this->ParseDihedral(data[i],false,bonded_types_[3]));
+ break;
+ }
+ case 6:{
+ p->AddCMap(this->ParseCMap(data[i],false));
+ break;
+ }
+
+ default:{
+ std::stringstream ss;
+ ss << "Encountered invalid keyword while parsing termini: " << data[i-1][1];
+ throw ost::io::IOException(ss.str());
+ }
+ }
+ }
+
+ return BlockModifierPtr(p);
+}
+
+
+InteractionPtr FFReader::ParseBond(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 2){
+ throw ost::io::IOException("Require at least 2 arguments in parsing bond!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 2){
+ throw ost::Error("Error in determining bond function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[2]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing bond!");
+ }
+ if(gromacs_functype == 1){
+ functype = HarmonicBond;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for bond!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 3){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast bond parameters into real type!");
+ }
+ return p;
+}
+
+InteractionPtr FFReader::ParseAngle(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 3){
+ throw ost::io::IOException("Require at least 3 arguments in parsing angle!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 3){
+ throw ost::Error("Error in determining angle function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[3]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing angle!");
+ }
+ if(gromacs_functype == 5) functype = UreyBradleyAngle;
+ else if(gromacs_functype == 1) functype = HarmonicAngle;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for angle!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+ atom_definition.push_back(data[2]);
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 4){
+ std::vector<Real> parameters;
+ if(functype == UreyBradleyAngle){
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-4])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-3]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+
+ }
+ else{
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ }
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast angle parameters into real type!");
+ }
+ return p;
+}
+
+InteractionPtr FFReader::ParseDihedral(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+ if(data.size() < 4){
+ throw ost::io::IOException("Require at least 4 arguments in parsing dihedral/improper!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 4){
+ throw ost::Error("Error in determining angle function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[4]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing dihedral!");
+ }
+ if(gromacs_functype == 9 || gromacs_functype == 1) functype = PeriodicDihedral;
+ else if(gromacs_functype == 4) functype = PeriodicImproper;
+ else if(gromacs_functype == 2) functype = HarmonicImproper;
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for dihedral!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+ atom_definition.push_back(data[2]);
+ atom_definition.push_back(data[3]);
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 5){
+ std::vector<Real> parameters;
+ if(functype == HarmonicImproper){
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ }
+ else{
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-3])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ }
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast dihedral/improper parameters into real type!");
+ }
+ return p;
+}
+
+InteractionPtr FFReader::ParseCMap(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+ if(data.size() < 5){
+ throw ost::io::IOException("Require at least 5 arguments in parsing cmap!");
+ }
+
+ if(functype == Invalid){
+ functype = CMap; //well, there is only this possibility
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+ atom_definition.push_back(data[2]);
+ atom_definition.push_back(data[3]);
+ atom_definition.push_back(data[4]);
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ if(data.size() > 6){
+ uint a,b;
+ try{
+ a = boost::lexical_cast<uint>(data[6]);
+ b = boost::lexical_cast<uint>(data[7]);
+ }catch(std::exception& e){
+ throw ost::io::IOException("Failed to parse size of the cmap!");
+ }
+ if(a != b){
+ throw ost::io::IOException("Expect cmap to have equal extension into both dimensions!");
+ }
+
+ if((8+a*b) > data.size()){
+ throw ost::io::IOException("Expected more data to fill cmap!");
+ }
+ try{
+ std::vector<Real> parameters;
+ parameters.push_back(Real(a));
+ for(uint i = 0; i < a*a; ++i){
+ parameters.push_back(boost::lexical_cast<Real>(data[8+i]));
+ }
+ p->SetParam(parameters);
+ }catch(std::exception& e){
+ throw ost::io::IOException("Failed to cast cmap values into real type!");
+ }
+ }
+ return p;
+}
+
+
+InteractionPtr FFReader::ParseLJ(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 1){
+ throw ost::io::IOException("Require at least 1 arguments in parsing LJ!");
+ }
+
+ if(functype == Invalid){
+ functype = LJ; //well, there is only this possibility
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 2){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast atomtype parameters into real type!");
+ }
+ return p;
+}
+
+
+InteractionPtr FFReader::ParseLJPair(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 2){
+ throw ost::io::IOException("Require at least 2 arguments in parsing nonbonded parameters!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 2){
+ throw ost::Error("Error in determining LJ Pair function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[2]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing lj pair!");
+ }
+ if(gromacs_functype == 1){
+ functype = LJPair;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for LJ Pair!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 3){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-2]));
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast nonbonded parameters into real type!");
+ }
+ return p;
+}
+
+InteractionPtr FFReader::ParseConstraint(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 2){
+ throw ost::io::IOException("Require at least 2 arguments in parsing nonbonded parameters!");
+ }
+
+ if(functype == Invalid){
+ if(data.size() == 2){
+ throw ost::Error("Error in determining constraint function type!");
+ }
+ int gromacs_functype;
+ try{ gromacs_functype = boost::lexical_cast<int>(data[2]); } catch(std::exception& e){
+ throw ost::io::IOException("Could not cast function type into int while parsing constraint!");
+ }
+ if(gromacs_functype == 1 || gromacs_functype == 2){
+ functype = DistanceConstraint;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Not supported gromacs function type \""<<gromacs_functype<<"\"";
+ ss << " for constraint!";
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 3){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[data.size()-1]));
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast constraint parameters into real type!");
+ }
+ return p;
+}
+
+InteractionPtr FFReader::ParseGenborn(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+
+ if(data.size() < 1){
+ throw ost::io::IOException("Require at least 1 argument in parsing genborn parameters!");
+ }
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+
+ functype = GBSA; //bit hacky, I know, but there is only one type for gbsa anyway....
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ try{
+ if(data.size() > 1){
+ std::vector<Real> parameters;
+ parameters.push_back(boost::lexical_cast<Real>(data[4]));
+ parameters.push_back(boost::lexical_cast<Real>(data[5]));
+ p->SetParam(parameters);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast genborn parameters into real type!");
+ }
+ return p;
+}
+
+
+InteractionPtr FFReader::ParseExclusion(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype){
+
+ if(data.size() < 2){
+ throw ost::io::IOException("Require at least 2 argument in parsing exclusion parameters!");
+ }
+
+ functype = Exclusion; //bit hacky, I know, but there is only one type for exclusion anyway....
+
+ std::vector<String> atom_definition;
+ atom_definition.push_back(data[0]);
+ atom_definition.push_back(data[1]);
+
+ InteractionPtr p(new Interaction(functype));
+
+ if(type_definition) p->SetTypes(atom_definition);
+ else p->SetNames(atom_definition);
+
+ return p;
+}
+
+void FFReader::ParseCHARMMPRM(std::vector<std::vector<String> >& content){
+
+
+ int keyword_id = -1;
+ std::vector<String> current_line;
+
+ //will be used to calculate all pairwise 1,4 lj parameters later on
+ std::vector<String> lj_14_types;
+ std::vector<Real> lj_14_sigmas;
+ std::vector<Real> lj_14_epsilons;
+ std::vector<String> lj_types;
+ std::vector<Real> lj_sigmas;
+ std::vector<Real> lj_epsilons;
+
+ for(uint line_counter = 0; line_counter<content.size(); ++line_counter){
+ current_line = content[line_counter];
+ if(CHARMMData::Instance()->GetKeywordIndex(current_line[0]) != -1){
+ keyword_id = CHARMMData::Instance()->GetKeywordIndex(current_line[0]);
+ continue;
+ }
+
+ if(keyword_id == 8) break;
+
+ switch(keyword_id){
+ case 0:{ //atoms keyword
+ ff_->AddMass(current_line[2],boost::lexical_cast<Real>(current_line[3]));
+ break;
+ }
+ case 1:{ //bonds
+ InteractionPtr p(new Interaction(HarmonicBond));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ try{
+ parameters.push_back(0.1 * boost::lexical_cast<Real>(current_line[3]));
+ parameters.push_back(418.4*2 * boost::lexical_cast<Real>(current_line[2]));
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast bond parameters into real type!");
+ }
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddBond(p);
+ break;
+ }
+ case 2:{ //angles
+ InteractionPtr p(new Interaction(UreyBradleyAngle));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ types.push_back(current_line[2]);
+ try{
+ parameters.push_back(boost::lexical_cast<Real>(current_line[4])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(current_line[3])*4.184*2);
+ if(current_line.size() > 5){
+ parameters.push_back(boost::lexical_cast<Real>(current_line[6])*0.1);
+ parameters.push_back(boost::lexical_cast<Real>(current_line[5])*418.4*2);
+ }
+ else{
+ parameters.push_back(0.0);
+ parameters.push_back(0.0);
+ }
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast angle parameters into real type!");
+ }
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddAngle(p);
+ break;
+ }
+ case 3:{ //diherals
+ InteractionPtr p(new Interaction(PeriodicDihedral));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ types.push_back(current_line[2]);
+ types.push_back(current_line[3]);
+ try{
+ parameters.push_back(boost::lexical_cast<Real>(current_line[5]));
+ parameters.push_back(boost::lexical_cast<Real>(current_line[6])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(current_line[4])*4.184);
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast bond parameters into real type!");
+ }
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddDihedral(p);
+ break;
+ }
+ case 4:{ //improper
+ InteractionPtr p(new Interaction(HarmonicImproper));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ types.push_back(current_line[2]);
+ types.push_back(current_line[3]);
+ try{
+ parameters.push_back(boost::lexical_cast<Real>(current_line[6])/360*2*M_PI);
+ parameters.push_back(boost::lexical_cast<Real>(current_line[4])*4.184*2);
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast bond parameters into real type!");
+ }
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddImproper(p);
+ break;
+ }
+ case 5:{ //cmap
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ types.push_back(current_line[1]);
+ types.push_back(current_line[2]);
+ types.push_back(current_line[3]);
+ types.push_back(current_line[7]);
+ uint dim = boost::lexical_cast<uint>(current_line[8]);
+ parameters.push_back(Real(dim));
+
+ ++line_counter;
+
+ while(true){
+ if(line_counter >= content.size()){
+ throw ost::io::IOException("Not enough data to fill cmap!");
+ }
+ if(parameters.size() > dim*dim+1){
+ std::stringstream ss;
+ ss << "Expect cmap values to fit exactly into a grid with dim ";
+ ss << dim << " x " << dim;
+ throw ost::io::IOException(ss.str());
+ }
+ if(parameters.size() == dim*dim+1){
+ InteractionPtr p(new Interaction(CMap));
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddCMap(p);
+ --line_counter;
+ break;
+ }
+
+ for(std::vector<String>::iterator i = content[line_counter].begin();
+ i != content[line_counter].end(); ++i){
+ parameters.push_back(boost::lexical_cast<Real>(*i)*4.184);
+ }
+ ++line_counter;
+ }
+
+ break;
+ }
+ case 6:{ //nonbonded
+ if(current_line[0] == "cutnb") break;
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(current_line[0]);
+ try{
+ parameters.push_back(boost::lexical_cast<Real>(current_line[3])*0.1/(std::pow(2,1.0/6.0))*2);
+ parameters.push_back(std::abs(boost::lexical_cast<Real>(current_line[2])*4.184));
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast LJ parameters into real type!");
+ }
+ InteractionPtr p(new Interaction(LJ));
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddLJ(p);
+
+ if(current_line.size() >= 7){
+ try{
+ lj_14_types.push_back(current_line[0]);
+ lj_14_sigmas.push_back(boost::lexical_cast<Real>(current_line[6])*0.1/(std::pow(2,1.0/6.0))*2);
+ lj_14_epsilons.push_back(std::abs(boost::lexical_cast<Real>(current_line[5])*4.184));
+ }catch(std::exception& e){
+ throw ost::io::IOException("Could not cast LJ parameters into real type!");
+ }
+ }else{
+ lj_types.push_back(types[0]);
+ lj_sigmas.push_back(parameters[0]);
+ lj_epsilons.push_back(parameters[1]);
+ }
+
+ break;
+ }
+ case 7:{ //hbond
+ //we don't implement any things regarding hbonds in CHARMM
+ break;
+ }
+ }
+ }
+ //let's add all possible pairwise 1,4 interactions, where both interaction partners
+ //have explicitely defined 1,4 interactions
+ for(uint i = 0; i < lj_14_types.size(); ++i){
+ for(uint j = i; j < lj_14_types.size(); ++j){
+ InteractionPtr p(new Interaction(LJPair));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(lj_14_types[i]);
+ types.push_back(lj_14_types[j]);
+ parameters.push_back(0.5 * (lj_14_sigmas[i] + lj_14_sigmas[j]));
+ parameters.push_back(sqrt(lj_14_epsilons[i] * lj_14_epsilons[j]));
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddLJPair(p);
+ }
+ }
+ //let's add all pairwise 1,4 interactions, where only one partner has explicitely defined 1,4 interactions
+ for(uint i = 0; i < lj_14_types.size(); ++i){
+ for(uint j = 0; j < lj_types.size(); ++j){
+ InteractionPtr p(new Interaction(LJPair));
+ std::vector<String> types;
+ std::vector<Real> parameters;
+ types.push_back(lj_14_types[i]);
+ types.push_back(lj_types[j]);
+ parameters.push_back(0.5 * (lj_14_sigmas[i] + lj_sigmas[j]));
+ parameters.push_back(sqrt(lj_14_epsilons[i] * lj_epsilons[j]));
+ p->SetTypes(types);
+ p->SetParam(parameters);
+ ff_->AddLJPair(p);
+ }
+ }
+
+
+}
+
+void FFReader::ParseCHARMMRTF(std::vector<std::vector<String> >& content){
+
+ bool in_block = false;
+
+ BuildingBlockPtr actual_block;
+
+ String actual_block_name = "";
+
+ int keyword_id = -1;
+ std::vector<String> current_line;
+ bool line_read = false;
+
+ for(uint line_counter = 0; line_counter < content.size(); ++line_counter){
+ current_line = content[line_counter];
+ std::cerr<<current_line[0]<<std::endl;
+ if(CHARMMData::Instance()->GetKeywordIndex(current_line[0]) != -1){
+ keyword_id = CHARMMData::Instance()->GetKeywordIndex(current_line[0]);
+ }
+ if(keyword_id == -1) continue;
+
+
+
+ if(in_block){
+ line_read = false;
+ switch(keyword_id){
+ case 15:{ //atom
+ actual_block->AddAtom(current_line[1],current_line[2],boost::lexical_cast<Real>(current_line[3]));
+ line_read=true;
+ break;
+ }
+ case 16:{//group
+ line_read=true;
+ break;
+ }
+ case 17:{//bond
+ int num_bonds = (current_line.size()-1) / 2;
+ for(int i = 0; i < num_bonds; ++i){
+ InteractionPtr p(new Interaction(HarmonicBond));
+ std::vector<String> names;
+ names.push_back(current_line[i*2+1]);
+ names.push_back(current_line[i*2+2]);
+ p->SetNames(names);
+ actual_block->AddBond(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 18:{//angle
+ int num_angles = (current_line.size()-1) / 3;
+ for(int i = 0; i < num_angles; ++i){
+ InteractionPtr p(new Interaction(UreyBradleyAngle));
+ std::vector<String> names;
+ names.push_back(current_line[i*3+1]);
+ names.push_back(current_line[i*3+2]);
+ names.push_back(current_line[i*3+3]);
+ p->SetNames(names);
+ actual_block->AddAngle(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 19:{//dihedral
+ int num_dihedrals = (current_line.size()-1) / 4;
+ for(int i = 0; i < num_dihedrals; ++i){
+ InteractionPtr p(new Interaction(PeriodicDihedral));
+ std::vector<String> names;
+ names.push_back(current_line[i*4+1]);
+ names.push_back(current_line[i*4+2]);
+ names.push_back(current_line[i*4+3]);
+ names.push_back(current_line[i*4+4]);
+ p->SetNames(names);
+ actual_block->AddDihedral(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 20:{//improper
+ int num_impropers = (current_line.size()-1) / 4;
+ for(int i = 0; i < num_impropers; ++i){
+ InteractionPtr p(new Interaction(HarmonicImproper));
+ std::vector<String> names;
+ names.push_back(current_line[i*4+1]);
+ names.push_back(current_line[i*4+2]);
+ names.push_back(current_line[i*4+3]);
+ names.push_back(current_line[i*4+4]);
+ p->SetNames(names);
+ actual_block->AddImproper(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 5:{//cmap
+ int num_cmaps = (current_line.size()-1) / 8;
+ for(int i = 0; i < num_cmaps; ++i){
+ InteractionPtr p(new Interaction(CMap));
+ std::vector<String> names;
+ names.push_back(current_line[i*4+1]);
+ names.push_back(current_line[i*4+2]);
+ names.push_back(current_line[i*4+3]);
+ names.push_back(current_line[i*4+4]);
+ names.push_back(current_line[i*4+8]);
+ p->SetNames(names);
+ actual_block->AddCMap(p);
+ }
+ line_read=true;
+ break;
+ }
+ case 21:{ //donor
+ line_read=true;
+ break; //I don't think. that this will ever be read...
+ }
+ case 22:{//acceptor
+ line_read=true;
+ break; //I don't think. that this will ever be read...
+ }
+ case 23:{// ic
+ line_read=true;
+ break;
+ }
+ case 24:{ //patching
+ line_read=true;
+ break;
+ }
+ case 25:{ //print
+ line_read=true;
+ break;
+ }
+ case 26:{ //double =>basically a bond
+ int num_bonds = (current_line.size()-1) / 2;
+ for(int i = 0; i < num_bonds; ++i){
+ InteractionPtr p(new Interaction(HarmonicBond));
+ std::vector<String> names;
+ names.push_back(current_line[i*2+1]);
+ names.push_back(current_line[i*2+2]);
+ p->SetNames(names);
+ actual_block->AddBond(p);
+ }
+ line_read=true;
+ break;
+ }
+ }
+ }
+
+ if(line_read) continue;
+
+ switch(keyword_id){
+ case 9:{
+ try {ff_->AddMass(current_line[2],boost::lexical_cast<Real>(current_line[3]));}
+ catch(std::exception& e){
+ throw ost::io::IOException("Could not cast mass into real type!");
+ }
+ break;
+ }
+ case 10:{
+ break; //we don't read that for now....
+ }
+ case 11:{//we don't allow patches for now
+ break;
+ }
+ case 12:{
+ break; //we don't read that for now
+ }
+ case 13:{
+ //check, whether there is an "open block"
+ if(in_block){
+ ff_->AddBuildingBlock(actual_block_name,actual_block);
+ std::cerr<<"added building block: "<<actual_block_name<<std::endl;
+ }
+ actual_block_name = current_line[1];
+ actual_block = BuildingBlockPtr(new BuildingBlock);
+ in_block = true;
+ std::cerr<<actual_block_name<<std::endl;
+ break;
+ }
+ case 14:{
+ //check, whether there is an "open block"
+ if(in_block){
+ ff_->AddBuildingBlock(actual_block_name,actual_block);
+ in_block = false;
+ }
+ break;
+ }
+
+
+ }
+
+ }
+
+ //add last building block if necessary
+ if(in_block) ff_->AddBuildingBlock(actual_block_name,actual_block);
+
+}
+
+}}}
diff --git a/modules/mol/mm/src/ff_reader.hh b/modules/mol/mm/src/ff_reader.hh
new file mode 100644
index 0000000000000000000000000000000000000000..957e4457922c6a017c4a6983accc733a412f786f
--- /dev/null
+++ b/modules/mol/mm/src/ff_reader.hh
@@ -0,0 +1,213 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_FORCEFIELD_READER_HH
+#define OST_MM_FORCEFIELD_READER_HH
+
+#include <fstream>
+
+#include <boost/filesystem.hpp>
+#include <boost/algorithm/string.hpp>
+#include <boost/lexical_cast.hpp>
+#include <boost/unordered_map.hpp>
+
+#include <ost/base.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class GromacsData;
+class CHARMMData;
+class FFReader;
+typedef boost::shared_ptr<GromacsData> GromacsDataPtr;
+typedef boost::shared_ptr<FFReader> FFReaderPtr;
+typedef boost::shared_ptr<CHARMMData> CHARMMDataPtr;
+
+class GromacsData{
+public:
+ static GromacsDataPtr Instance();
+ int GetKeywordIndex(const String& keyword);
+ String ConvertToStandard(const String& res_name, const String& atom_name);
+ bool ConversionExists(const String& res_name);
+
+private:
+ GromacsData();
+ GromacsData(const GromacsData&);
+ GromacsDataPtr operator=(const GromacsDataPtr&);
+ static GromacsDataPtr instance_;
+ boost::unordered_map<String,int> keyword_map_;
+ boost::unordered_map<String, std::vector<std::pair<String,String> > > renaming_to_standard_;
+
+};
+
+class CHARMMData{
+public:
+ static CHARMMDataPtr Instance();
+ int GetKeywordIndex(const String& keyword);
+
+private:
+ CHARMMData();
+ CHARMMData(const CHARMMData&);
+ CHARMMDataPtr operator=(const CHARMMDataPtr&);
+ static CHARMMDataPtr instance_;
+ boost::unordered_map<String,int> keyword_map_;
+};
+
+class MMPreprocessor{
+
+public:
+
+ MMPreprocessor(const String& basepath): basepath_(basepath) { }
+
+ std::vector<std::vector<String> > Process(const String& filename);
+
+ void SetDefinition(const String& def) { defines_.insert(def); }
+
+ boost::filesystem::path GetBasedir() { return basepath_; }
+
+private:
+
+ //function, that can recursively resolve ifdef / ifndef statements
+ void ResolveIFDEF(std::vector<std::vector<String> >& file_content, int line_counter);
+
+ //simply reads a file, cuts it into pieces and removes comments marked by '*' and ';'
+ std::vector<std::vector<String> > ReadFile(const String& filename);
+
+ std::map<String,std::vector<String> > definitions_;
+ std::set<String> defines_;
+ boost::filesystem::path basepath_;
+};
+
+
+class FFReader {
+public:
+
+ FFReader(const String& base_dir);
+
+ void SetPreprocessorDefinition(const String& def) { preprocessor_.SetDefinition(def); }
+
+ void ReadGromacsForcefield();
+
+ ForcefieldPtr GetForcefield() { return ff_;}
+
+ void SetForcefield(ForcefieldPtr ff) { ff_ = ff; }
+
+ void ReadResidueDatabase(const String& basename);
+
+ void ReadITP(const String& basename);
+
+ void ReadCHARMMPRM(const String& basename);
+
+ void ReadCHARMMRTF(const String& basename);
+
+private:
+
+ InteractionPtr ParseBond(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ InteractionPtr ParseAngle(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ InteractionPtr ParseDihedral(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ InteractionPtr ParseCMap(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ InteractionPtr ParseLJ(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ InteractionPtr ParseLJPair(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ InteractionPtr ParseConstraint(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ InteractionPtr ParseGenborn(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ InteractionPtr ParseExclusion(const std::vector<String>& data,
+ bool type_definition,
+ FuncType functype = Invalid);
+
+ BuildingBlockPtr BlockFromRTP(const std::vector<std::vector<String> >& data);
+
+ BuildingBlockPtr BlockFromITP(const std::vector<std::vector<String> >& data);
+
+ TerminiConstructorPtr ParseTermini(const std::vector<std::vector<String> >& data);
+
+ BlockModifierPtr ParseBlockModifier(const std::vector<std::vector<String> >& data);
+
+ void ParseHydrogenRule(const std::vector<String>& data, GromacsHydrogenConstructor& constructor);
+
+ void ParseTerminiReplaceRule(const std::vector<String>& data, GromacsBlockModifier& constructor);
+
+ void ParseTerminiAddRule(const std::vector<String>& data1, const std::vector<String>& data2,
+ GromacsBlockModifier& constructor);
+
+ //Reader functions for the mandatory forcefield files
+ void ParseForcefield(std::vector<std::vector<String> >& content);
+ void ParseAtomTypes(std::vector<std::vector<String> >& content);
+
+ //Reader functions for CHARMM stuff
+ void ParseCHARMMPRM(std::vector<std::vector<String> >& content);
+
+ void ParseCHARMMRTF(std::vector<std::vector<String> >& content);
+
+ //Reader functions for all different residue database files
+ void ParseRTP(std::vector<std::vector<String> >& content);
+ void ParseARN(std::vector<std::vector<String> >& content);
+ void ParseHDB(std::vector<std::vector<String> >& content);
+ void ParseNTDB(std::vector<std::vector<String> >& content);
+ void ParseCTDB(std::vector<std::vector<String> >& content);
+ void ParseVSD(std::vector<std::vector<String> >& content);
+ void ParseRtoB(std::vector<std::vector<String> >& content);
+ //Reader function for single molecule itp files
+ void ParseITP(std::vector<std::vector<String> >& content);
+
+ boost::unordered_map<String, std::vector<std::pair<String,String> > > atom_renaming_ff_specific_;
+ boost::unordered_map<String, ResidueNamesPtr> res_renaming_ff_specific_;
+
+ std::vector<FuncType> ff_bonded_types_;
+
+ MMPreprocessor preprocessor_;
+ ForcefieldPtr ff_;
+
+ //following part is ugly...
+ //data that is read during the residue datababase parsing process gets stored in there
+ std::vector<FuncType> bonded_types_;
+ std::vector<String> read_residues_;
+};
+
+
+}}}//ns
+
+#endif
diff --git a/modules/mol/mm/src/forcefield.cc b/modules/mol/mm/src/forcefield.cc
new file mode 100644
index 0000000000000000000000000000000000000000..5e1b1ac7102f9fbb32841016a6a4d179078a146a
--- /dev/null
+++ b/modules/mol/mm/src/forcefield.cc
@@ -0,0 +1,1042 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/forcefield.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+ForcefieldPtr Forcefield::Load(const String& filename){
+
+
+ if (!boost::filesystem::exists(filename)) {
+ std::stringstream ss;
+ ss << "Could not open forcefield. File '"
+ << filename << "' does not exist";
+ throw ost::io::IOException(ss.str());
+ }
+
+ std::ifstream stream(filename.c_str(), std::ios_base::binary);
+ ost::io::BinaryDataSource ds(stream);
+ ForcefieldPtr ff_p(new Forcefield);
+
+ bool gen_pairs;
+ Real fudge_LJ;
+ Real fudge_QQ;
+ ds & gen_pairs;
+ ds & fudge_LJ;
+ ds & fudge_QQ;
+
+ ff_p->SetGenPairs(gen_pairs);
+ ff_p->SetFudgeLJ(fudge_LJ);
+ ff_p->SetFudgeQQ(fudge_QQ);
+
+ int num_atom_masses;
+ ds & num_atom_masses;
+
+ String atom_name;
+ Real mass;
+ for(int i = 0; i < num_atom_masses; ++i){
+ ds & atom_name;
+ ds & mass;
+ ff_p->AddMass(atom_name,mass);
+ }
+
+ int num_building_blocks;
+ ds & num_building_blocks;
+ String block_name;
+ for(int i = 0; i < num_building_blocks; ++i){
+ ds & block_name;
+ BuildingBlockPtr p(new BuildingBlock);
+ ds & *p;
+ ff_p->AddBuildingBlock(block_name,p);
+ }
+
+ int func_type;
+ int num_bonds;
+ ds & num_bonds;
+ for(int i = 0; i < num_bonds; ++i){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddBond(p);
+ }
+
+ int num_angles;
+ ds & num_angles;
+ for(int i = 0; i < num_angles; ++i){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddAngle(p);
+ }
+
+ int num_lj_pairs;
+ ds & num_lj_pairs;
+ for(int i = 0; i < num_lj_pairs; ++i){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddLJPair(p);
+ }
+
+ int num_constraints;
+ ds & num_constraints;
+ for(int i = 0; i < num_constraints; ++i){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddConstraint(p);
+ }
+
+ int num_cmaps;
+ ds & num_cmaps;
+ for(int i = 0; i < num_cmaps; ++i){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddCMap(p);
+ }
+
+ int num_genborn;
+ ds & num_genborn;
+ for(int i = 0; i < num_genborn; ++i){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddImplicitGenborn(p);
+ }
+
+ int num_ljs;
+ ds & num_ljs;
+ for(int i = 0; i < num_ljs; ++i){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddLJ(p);
+ }
+
+
+ int num_dihedrals;
+ ds & num_dihedrals;
+ int temp_num;
+ for(int i = 0; i < num_dihedrals; ++i){
+ ds & temp_num;
+ for(int j = 0; j < temp_num; ++j){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddDihedral(p);
+ }
+ }
+
+ int num_impropers;
+ ds & num_impropers;
+ for(int i = 0; i < num_impropers; ++i){
+ ds & temp_num;
+ for(int j = 0; j < temp_num; ++j){
+ ds & func_type;
+ InteractionPtr p(new Interaction(FuncType(func_type)));
+ ds & *p;
+ ff_p->AddImproper(p);
+ }
+ }
+
+ int num_atom_renamings;
+ ds & num_atom_renamings;
+ String res_name, old_name, new_name;
+ for(int i = 0; i < num_atom_renamings; ++i){
+ ds & res_name;
+ ds & temp_num;
+ for(int j = 0; j < temp_num; ++j){
+ ds & old_name;
+ ds & new_name;
+ ff_p->AddAtomRenamingRule(res_name,old_name,new_name);
+ }
+ }
+
+ int num_res_renaming;
+ ds & num_res_renaming;
+ for(int i = 0; i < num_res_renaming; ++i){
+ ds & res_name;
+ ResidueNamesPtr p(new ResidueNames);
+ ds & *p;
+ ff_p->AddResidueRenamingRule(res_name, p->main, p->nter, p->cter, p->twoter);
+ }
+
+ int num_hydrogen_constructors;
+ int block_modifier_type;
+ String block_modifier_name;
+ ds & num_hydrogen_constructors;
+ for(int i = 0; i < num_hydrogen_constructors; ++i){
+ ds & block_modifier_type;
+ ds & block_modifier_name;
+ switch(block_modifier_type){
+ case GromacsBlockModifiers:{
+ GromacsHydrogenConstructorPtr p(new GromacsHydrogenConstructor);
+ ds & *p;
+ ff_p->AddHydrogenConstructor(block_modifier_name,p);
+ break;
+ }
+ default:{
+ throw ost::Error("Invalid Block Modifier type encountered when loading hydrogen constructor!");
+ }
+
+ }
+ }
+
+ int num_block_modifiers;
+ ds & num_block_modifiers;
+ String modifier_name;
+
+ for(int i = 0; i < num_block_modifiers; ++i){
+ ds & block_modifier_type;
+ switch(block_modifier_type){
+ case GromacsBlockModifiers:{
+ GromacsBlockModifierPtr p(new GromacsBlockModifier);
+ ds & modifier_name;
+ ds & *p;
+ ff_p->AddBlockModifier(modifier_name,p);
+ break;
+ }
+ default:{
+ throw ost::Error("Invalid Block Modifier type encountered when loading!");
+ }
+ }
+
+ }
+
+ int num_standard_n_termini;
+ int num_standard_c_termini;
+
+ ds & num_standard_n_termini;
+ ds & num_standard_c_termini;
+
+ for(int i = 0; i < num_standard_n_termini; ++i){
+ ds & res_name;
+ ds & modifier_name;
+ ff_p->SetStandardNTer(res_name,modifier_name);
+ }
+
+ for(int i = 0; i < num_standard_c_termini; ++i){
+ ds & res_name;
+ ds & modifier_name;
+ ff_p->SetStandardCTer(res_name,modifier_name);
+ }
+
+ return ff_p;
+}
+
+void Forcefield::Save(const String& filename){
+ std::ofstream stream(filename.c_str(), std::ios_base::binary);
+ io::BinaryDataSink ds(stream);
+
+
+ ds & gen_pairs_;
+ ds & fudge_LJ_;
+ ds & fudge_QQ_;
+
+ int num_atom_masses = atom_masses_.size();
+ ds & num_atom_masses;
+ for(boost::unordered_map<String,Real>::iterator i = atom_masses_.begin();
+ i != atom_masses_.end(); ++i){
+ ds & i->first;
+ ds & i->second;
+ }
+
+ int num_building_blocks = building_blocks_.size();
+ ds & num_building_blocks;
+ for(boost::unordered_map<String,BuildingBlockPtr>::iterator i = building_blocks_.begin();
+ i != building_blocks_.end(); ++i){
+ ds & i->first;
+ ds & *(i->second);
+ }
+
+
+ int func_type;
+ int num_bonds = bonds_.size();
+ ds & num_bonds;
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = bonds_.begin();
+ i != bonds_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_angles = angles_.size();
+ ds & num_angles;
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = angles_.begin();
+ i != angles_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_lj_pairs = lj_14_pairs_.size();
+ ds & num_lj_pairs;
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = lj_14_pairs_.begin();
+ i != lj_14_pairs_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_constraints = constraints_.size();
+ ds & num_constraints;
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = constraints_.begin();
+ i != constraints_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_cmaps = cmaps_.size();
+ ds & num_cmaps;
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = cmaps_.begin();
+ i != cmaps_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_genborn = implicit_genborn_.size();
+ ds & num_genborn;
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = implicit_genborn_.begin();
+ i != implicit_genborn_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_ljs = ljs_.size();
+ ds & num_ljs;
+ for(boost::unordered_map<String,InteractionPtr>::iterator i = ljs_.begin();
+ i != ljs_.end(); ++i){
+ func_type = int(i->second->GetFuncType());
+ ds & func_type;
+ ds & *(i->second);
+ }
+
+ int num_dihedrals = dihedrals_.size();
+ int vector_size;
+ ds & num_dihedrals;
+ for(boost::unordered_map<String,std::vector<InteractionPtr> >::iterator i = dihedrals_.begin();
+ i != dihedrals_.end(); ++i){
+ vector_size = i->second.size();
+ ds & vector_size;
+ for(std::vector<InteractionPtr>::iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ func_type = int((*j)->GetFuncType());
+ ds & func_type;
+ ds & **j;
+ }
+ }
+
+ int num_impropers = improper_dihedrals_.size();
+ ds & num_impropers;
+ for(boost::unordered_map<String,std::vector<InteractionPtr> >::iterator i = improper_dihedrals_.begin();
+ i != improper_dihedrals_.end(); ++i){
+ vector_size = i->second.size();
+ ds & vector_size;
+ for(std::vector<InteractionPtr>::iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ func_type = int((*j)->GetFuncType());
+ ds & func_type;
+ ds & **j;
+ }
+ }
+
+
+ int num_atom_renamings = atom_renaming_ff_specific_.size();
+ ds & num_atom_renamings;
+ for(boost::unordered_map<String,std::vector<std::pair<String,String> > >::iterator i = atom_renaming_ff_specific_.begin();
+ i != atom_renaming_ff_specific_.end(); ++i){
+ ds & i->first;
+ vector_size = i->second.size();
+ ds & vector_size;
+ for(std::vector<std::pair<String,String> >::iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ ds & j->first;
+ ds & j->second;
+ }
+ }
+
+ int num_res_renaming = res_renaming_ff_specific_.size();
+ ds & num_res_renaming;
+ for(boost::unordered_map<String,ResidueNamesPtr>::iterator i = res_renaming_ff_specific_.begin();
+ i != res_renaming_ff_specific_.end(); ++i){
+ ds & i->first;
+ ds & *(i->second);
+ }
+
+ int num_hydrogen_constructors = hydrogen_constructors_.size();
+ ds & num_hydrogen_constructors;
+ for(boost::unordered_map<String,HydrogenConstructorPtr>::iterator i = hydrogen_constructors_.begin();
+ i != hydrogen_constructors_.end(); ++i){
+ func_type = int(i->second->GetBlockModifierType());
+ ds & func_type;
+ ds & i->first;
+ i->second->OnSave(ds);
+ }
+
+ int num_block_modifiers = block_modifiers_.size();
+ ds & num_block_modifiers;
+ for(boost::unordered_map<String,BlockModifierPtr>::iterator i = block_modifiers_.begin();
+ i != block_modifiers_.end(); ++i){
+ func_type = int(i->second->GetBlockModifierType());
+ ds & func_type;
+ ds & i->first;
+ i->second->OnSave(ds);
+ }
+
+ int num_standard_n_termini = standard_c_termini_.size();
+ int num_standard_c_termini = standard_n_termini_.size();
+ ds & num_standard_n_termini;
+ ds & num_standard_c_termini;
+
+ for(boost::unordered_map<String, String>::iterator i = standard_n_termini_.begin();
+ i != standard_n_termini_.end(); ++i){
+ ds & i->first;
+ ds & i->second;
+ }
+
+ for(boost::unordered_map<String, String>::iterator i = standard_c_termini_.begin();
+ i != standard_c_termini_.end(); ++i){
+ ds & i->first;
+ ds & i->second;
+ }
+
+}
+
+BuildingBlockPtr Forcefield::GetBuildingBlock(const String& name) const{
+ boost::unordered_map<String,BuildingBlockPtr>::const_iterator i = building_blocks_.find(name);
+ if(i == building_blocks_.end()){
+ std::stringstream ss;
+ ss << "Forcefield does not contain requested building block ";
+ ss << "\"" << name << "\"";
+ throw ost::Error(ss.str());
+ }
+ BuildingBlockPtr ff_p = i->second;
+ //let's create a new building block to avoid messing around with the
+ //force field building blocks
+ BuildingBlockPtr p(new BuildingBlock(*ff_p));
+ return p;
+}
+
+BlockModifierPtr Forcefield::GetBlockModifier(const String& modifier_name) const{
+ boost::unordered_map<String,BlockModifierPtr>::const_iterator i = block_modifiers_.find(modifier_name);
+ if(i == block_modifiers_.end()) return BlockModifierPtr();
+ return i->second;
+}
+
+String Forcefield::GetAtomType(const String& res_name, const String& atom_name) const{
+ BuildingBlockPtr block = this->GetBuildingBlock(res_name);
+ if(!block){
+ std::stringstream ss;
+ ss << "There is no building block for " << res_name;
+ ss << "in the forcefield!";
+ throw ost::Error(ss.str());
+ }
+ return block->GetType(atom_name);
+}
+
+HydrogenConstructorPtr Forcefield::GetHydrogenConstructor(const String& name) const{
+ boost::unordered_map<String,HydrogenConstructorPtr>::const_iterator i = hydrogen_constructors_.find(name);
+ if(i != hydrogen_constructors_.end()) return i->second;
+ return HydrogenConstructorPtr();
+}
+
+BlockModifierPtr Forcefield::GetNTerModifier(const String& res_name, const String& ter_name) const{
+ String temp = ter_name;
+ if(temp == ""){
+ boost::unordered_map<String,String>::const_iterator it = standard_n_termini_.find(res_name);
+ if(it != standard_n_termini_.end()) temp = it->second;
+ else return BlockModifierPtr();
+ }
+ return this->GetBlockModifier(temp);
+}
+
+BlockModifierPtr Forcefield::GetCTerModifier(const String& res_name, const String& ter_name) const{
+ String temp = ter_name;
+ if(temp == ""){
+ boost::unordered_map<String,String>::const_iterator it = standard_c_termini_.find(res_name);
+ if(it != standard_c_termini_.end()) temp = it->second;
+ else return BlockModifierPtr();
+ }
+ return this->GetBlockModifier(temp);
+}
+
+InteractionPtr Forcefield::GetBond(const String& type1, const String& type2) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
+ bonds_.find(this->AtomTypesToKeyword(types));
+ if(i != bonds_.end()) return i->second;
+ throw ost::Error("Forcefield does not contain bond for requested atom types!");
+}
+
+InteractionPtr Forcefield::GetAngle(const String& type1, const String& type2,
+ const String& type3) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ types.push_back(type3);
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
+ angles_.find(this->AtomTypesToKeyword(types));
+ if(i != angles_.end()) return i->second;
+ throw ost::Error("Forcefield does not contain angle for requested atom types!");
+}
+
+std::vector<InteractionPtr> Forcefield::GetDihedrals(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ types.push_back(type3);
+ types.push_back(type4);
+
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator i =
+ dihedrals_.find(this->AtomTypesToKeyword(types));
+
+ if(i != dihedrals_.end()) return i->second;
+
+ //if we reach this point, we have to look for all dihedrals with wildcards...
+ std::vector<InteractionPtr> dihedrals;
+ std::vector<String> types_with_wildcards;
+
+ //lets first check single wildcards
+ for(int i = 0; i < 4; ++i){
+ types_with_wildcards = types;
+ types_with_wildcards[i] = "X";
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator j =
+ dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(j != dihedrals_.end()) dihedrals.insert(dihedrals.end(),j->second.begin(),j->second.end());
+ }
+
+ //we check for two wildcards
+ for(int i = 0; i < 4; ++i){
+ for(int j = i+1; j < 4; ++j){
+ types_with_wildcards = types;
+ types_with_wildcards[i] = "X";
+ types_with_wildcards[j] = "X";
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator k =
+ dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(k != dihedrals_.end()) dihedrals.insert(dihedrals.end(),k->second.begin(),k->second.end());
+ }
+ }
+
+ //as stupid as it may sound, we also look for dihedrals with 3 wildcards
+ std::vector<String> all_wildcards;
+ for(int i = 0; i < 4; ++i){
+ all_wildcards.push_back("X");
+ }
+ for(int i = 0; i < 4; ++i){
+ types_with_wildcards = all_wildcards;
+ types_with_wildcards[i] = types[i];
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator j =
+ dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(j != dihedrals_.end()) dihedrals.insert(dihedrals.end(),j->second.begin(),j->second.end());
+ }
+
+ if(!dihedrals.empty()) return dihedrals;
+ throw ost::Error("Forcefield does not contain any dihedrals for requested atom types!");
+}
+
+std::vector<InteractionPtr> Forcefield::GetImpropers(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ types.push_back(type3);
+ types.push_back(type4);
+
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator i =
+ improper_dihedrals_.find(this->AtomTypesToKeyword(types));
+
+ if(i != improper_dihedrals_.end()) return i->second;
+
+ //if we reach this point, we have to look for all dihedrals with wildcards...
+ std::vector<InteractionPtr> impropers;
+ std::vector<String> types_with_wildcards;
+
+ //lets first check single wildcards
+ for(int i = 0; i < 4; ++i){
+ types_with_wildcards = types;
+ types_with_wildcards[i] = "X";
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator j =
+ improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(j != improper_dihedrals_.end()) impropers.insert(impropers.end(),j->second.begin(),j->second.end());
+ }
+
+ //we check for two wildcards
+ for(int i = 0; i < 4; ++i){
+ for(int j = i+1; j < 4; ++j){
+ types_with_wildcards = types;
+ types_with_wildcards[i] = "X";
+ types_with_wildcards[j] = "X";
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator k =
+ improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(k != improper_dihedrals_.end()) impropers.insert(impropers.end(),k->second.begin(),k->second.end());
+ }
+ }
+
+ //as stupid as it may sound, we also look for dihedrals with 3 wildcards
+ std::vector<String> all_wildcards;
+ for(int i = 0; i < 4; ++i){
+ all_wildcards.push_back("X");
+ }
+ for(int i = 0; i < 4; ++i){
+ types_with_wildcards = all_wildcards;
+ types_with_wildcards[i] = types[i];
+ boost::unordered_map<String,std::vector<InteractionPtr> >::const_iterator j =
+ improper_dihedrals_.find(this->AtomTypesToKeyword(types_with_wildcards));
+ if(j != improper_dihedrals_.end()) impropers.insert(impropers.end(),j->second.begin(),j->second.end());
+ }
+
+ if(!impropers.empty()) return impropers;
+
+ throw ost::Error("Forcefield does not contain any impropers for requested atom types!");
+}
+
+InteractionPtr Forcefield::GetCMap(const String& type1, const String& type2,
+ const String& type3, const String& type4,
+ const String& type5) const{
+
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ types.push_back(type3);
+ types.push_back(type4);
+ types.push_back(type5);
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
+ cmaps_.find(this->AtomTypesToKeyword(types,false));
+ if(i != cmaps_.end()) return i->second;
+
+ throw ost::Error("Forcefield does not contain cmap for requested atom types!");
+}
+
+InteractionPtr Forcefield::GetImplicitGenborn(const String& type) const{
+
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
+ implicit_genborn_.find(type);
+ if(i != implicit_genborn_.end()) return i->second;
+ throw ost::Error("Forcefield does not contain implicit genborn parameters for requested atom type!");
+}
+
+InteractionPtr Forcefield::GetLJ(const String& type) const{
+
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
+ ljs_.find(type);
+
+ if(i != ljs_.end()){
+ return i->second;
+ }
+ throw ost::Error("Forcefield does not contain lennard jones parameters for requested atom types!");
+}
+
+InteractionPtr Forcefield::GetLJ(const String& type1,
+ const String& type2,
+ bool pair) const{
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+
+ if(pair){
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
+ lj_14_pairs_.find(this->AtomTypesToKeyword(types));
+ if(i == lj_14_pairs_.end()){
+ if(!gen_pairs_){
+ std::stringstream ss;
+ ss << "was not able to find lj parameters between atoms of type ";
+ ss << type1 << " and " << type2 << " with gen_pairs ";
+ ss << "set to no!";
+ throw ost::Error(ss.str());
+ }
+ }
+ else{
+ return i->second;
+ }
+ }
+
+ InteractionPtr temp1, temp2;
+ temp1 = this->GetLJ(type1);
+ temp2 = this->GetLJ(type2);
+ if(temp1 && temp2){
+ InteractionPtr return_ptr(new Interaction(LJPair));
+ std::vector<Real> param1, param2, param;
+ param1 = temp1->GetParam();
+ param2 = temp2->GetParam();
+ param.push_back(0.5*(param1[0]+param2[0]));
+ param.push_back(sqrt(param1[1]*param2[1]));
+ return_ptr->SetTypes(types);
+ return_ptr->SetParam(param);
+ return return_ptr;
+ }
+
+ throw ost::Error("Forcefield does not contain lennard jones parameters for requested atom types!");
+
+}
+
+InteractionPtr Forcefield::GetConstraint(const String& type1,
+ const String& type2){
+ std::vector<String> types;
+ types.push_back(type1);
+ types.push_back(type2);
+ boost::unordered_map<String,InteractionPtr>::const_iterator i =
+ constraints_.find(this->AtomTypesToKeyword(types));
+ if(i != constraints_.end()) return i->second;
+ throw ost::Error("Forcefield does not contain constraint for requested atom types!");
+}
+
+Real Forcefield::GetMass(const String& atom_type) const{
+ boost::unordered_map<String,Real>::const_iterator it = atom_masses_.find(atom_type);
+ if(it == atom_masses_.end()){
+ std::stringstream ss;
+ ss << "There is no mass defined for atom of type " << atom_type;
+ throw ost::Error(ss.str());
+ }
+ return it->second;
+}
+
+void Forcefield::AddBond(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"BOND");
+ std::vector<String> types = p->GetTypes();
+ bonds_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddAngle(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"ANGLE");
+ std::vector<String> types = p->GetTypes();
+ angles_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddDihedral(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"DIHEDRAL");
+ std::vector<String> types = p->GetTypes();
+ String keyword = this->AtomTypesToKeyword(types);
+ if(dihedrals_.find(keyword) == dihedrals_.end()){
+ dihedrals_[keyword] = std::vector<InteractionPtr>();
+ }
+ dihedrals_[keyword].push_back(p);
+}
+
+void Forcefield::AddImproper(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"IMPROPER");
+ std::vector<String> types = p->GetTypes();
+ String keyword = this->AtomTypesToKeyword(types);
+ if(improper_dihedrals_.find(keyword) == improper_dihedrals_.end()){
+ improper_dihedrals_[keyword] = std::vector<InteractionPtr>();
+ }
+ improper_dihedrals_[keyword].push_back(p);
+}
+
+void Forcefield::AddCMap(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"CMAP");
+ std::vector<String> types = p->GetTypes();
+ cmaps_[this->AtomTypesToKeyword(types,false)] = p;
+}
+
+void Forcefield::AddImplicitGenborn(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"IMPLICIT_GENBORN");
+ std::vector<String> types = p->GetTypes();
+ implicit_genborn_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddLJ(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"LJ");
+ std::vector<String> types = p->GetTypes();
+ ljs_[types[0]] = p;
+}
+
+void Forcefield::AddLJPair(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"LJ_PAIR");
+ std::vector<String> types = p->GetTypes();
+ lj_14_pairs_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddConstraint(InteractionPtr p){
+ this->CheckInteractionToAdd(p,"CONSTRAINT");
+ std::vector<String> types = p->GetTypes();
+ constraints_[this->AtomTypesToKeyword(types)] = p;
+}
+
+void Forcefield::AddResidueRenamingRule(const String& name,
+ const String& ff_main_name,
+ const String& ff_n_ter_name,
+ const String& ff_c_ter_name,
+ const String& ff_two_ter_name){
+ ResidueNamesPtr p(new ResidueNames(ff_main_name,
+ ff_n_ter_name,
+ ff_c_ter_name,
+ ff_two_ter_name));
+ res_renaming_ff_specific_[name] = p;
+}
+
+void Forcefield::AddAtomRenamingRule(const String& res_name,
+ const String& old_atom_name,
+ const String& new_atom_name){
+ if(atom_renaming_ff_specific_.find(res_name) == atom_renaming_ff_specific_.end()){
+ std::vector<std::pair<String,String> > new_vec;
+ atom_renaming_ff_specific_[res_name] = new_vec;
+ }
+
+ atom_renaming_ff_specific_[res_name].push_back(std::make_pair(old_atom_name,new_atom_name));
+}
+
+String Forcefield::GetResidueRenamingMain(const String& name) const{
+ boost::unordered_map<String, ResidueNamesPtr>::const_iterator i = res_renaming_ff_specific_.find(name);
+ if(i == res_renaming_ff_specific_.end()){
+ return name;
+ }
+ return i->second->main;
+}
+
+String Forcefield::GetResidueRenamingNTer(const String& name) const{
+ boost::unordered_map<String, ResidueNamesPtr>::const_iterator i = res_renaming_ff_specific_.find(name);
+ if(i == res_renaming_ff_specific_.end()){
+ return name;
+ }
+ return i->second->nter;
+}
+
+
+String Forcefield::GetResidueRenamingCTer(const String& name) const{
+ boost::unordered_map<String, ResidueNamesPtr>::const_iterator i = res_renaming_ff_specific_.find(name);
+ if(i == res_renaming_ff_specific_.end()){
+ return name;
+ }
+ return i->second->cter;
+}
+
+String Forcefield::GetResidueRenamingTwoTer(const String& name) const{
+ boost::unordered_map<String, ResidueNamesPtr>::const_iterator i = res_renaming_ff_specific_.find(name);
+ if(i == res_renaming_ff_specific_.end()){
+ return name;
+ }
+ return i->second->twoter;
+}
+
+String Forcefield::GetAtomRenaming(const String& res_name, const String& atom_name) const{
+ boost::unordered_map<String,std::vector<std::pair<String,String> > >::const_iterator i = atom_renaming_ff_specific_.find(res_name);
+ if(i == atom_renaming_ff_specific_.end()) return atom_name;
+ for(std::vector<std::pair<String,String> >::const_iterator j = i->second.begin(), e = i->second.end();
+ j != e; ++j){
+ if(atom_name == j->first) return j->second;
+ }
+ return atom_name;
+}
+
+void Forcefield::AssignFFSpecificNames(ost::mol::EntityHandle& handle, bool reverse) const{
+
+ //the whole FF specific renaming procedure assumes a standard naming,
+ //in our case the gromacs defined standard naming
+
+ ost::mol::XCSEditor ed = handle.EditXCS();
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ ost::mol::AtomHandleList atom_list;
+ ost::mol::AtomHandle atom;
+ ost::mol::ResidueHandle residue;
+
+ if(!reverse){
+
+ ost::mol::ResidueHandle next,prev;
+ bool n_ter,c_ter;
+ //ost::mol::AtomHandle peptide_n,peptide_c,nucleotide_p,nucleotide_o;
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+
+ if(res_renaming_ff_specific_.find(i->GetName()) == res_renaming_ff_specific_.end()){
+ continue;
+ }
+
+ n_ter = false;
+ c_ter = false;
+
+ //peptide_n = i->FindAtom("N");
+ //nucleotide_p = i->FindAtom("P");
+
+ prev = i->GetPrev();
+ next = i->GetNext();
+
+ if(!prev.IsValid()){
+ n_ter = true;
+ }
+ //else{
+ //peptide_c = prev.FindAtom("C");
+ //nucleotide_o = prev.FindAtom("O3");
+
+ //if(!ost::mol::BondExists(peptide_n,peptide_c) && !ost::mol::BondExists(nucleotide_p,nucleotide_o)){
+ //n_ter = true;
+ //}
+ //}
+
+ if(!next.IsValid()){
+ c_ter = true;
+ }
+ //else{
+ //peptide_n = next.FindAtom("N");
+ //peptide_c = i->FindAtom("C");
+ //nucleotide_p = next.FindAtom("P");
+ //nucleotide_o = i->FindAtom("O3");
+
+ //if(!ost::mol::BondExists(peptide_n,peptide_c) && !ost::mol::BondExists(nucleotide_p,nucleotide_o)){
+ //c_ter = true;
+ //}
+ //}
+ if(c_ter && n_ter){
+ ed.RenameResidue(*i,res_renaming_ff_specific_.find(i->GetName())->second->twoter);
+ continue;
+ }
+ if(n_ter){
+ ed.RenameResidue(*i,res_renaming_ff_specific_.find(i->GetName())->second->nter);
+ continue;
+ }
+ if(c_ter){
+ ed.RenameResidue(*i,res_renaming_ff_specific_.find(i->GetName())->second->cter);
+ continue;
+ }
+ ed.RenameResidue(*i,res_renaming_ff_specific_.find(i->GetName())->second->main);
+ }
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();i!=res_list.end();++i){
+ boost::unordered_map<String,std::vector<std::pair<String,String> > >::const_iterator map_it = atom_renaming_ff_specific_.find(i->GetName());
+ if(map_it!=atom_renaming_ff_specific_.end()){
+ for(std::vector<std::pair<String,String> >::const_iterator j = map_it->second.begin();
+ j!=map_it->second.end();++j){
+ atom = i->FindAtom(j->first);
+ if(atom.IsValid()) ed.RenameAtom(atom,j->second);
+ }
+ }
+ }
+ return;
+ }
+
+ //it seems, that we have to do the reverse ff renaming => ff specific to gromacs standard
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();i!=res_list.end();++i){
+ boost::unordered_map<String,std::vector<std::pair<String,String> > >::const_iterator map_it = atom_renaming_ff_specific_.find(i->GetName());
+ if(map_it!=atom_renaming_ff_specific_.end()){
+ for(std::vector<std::pair<String,String> >::const_iterator j = map_it->second.begin();
+ j!=map_it->second.end();++j){
+ atom = i->FindAtom(j->second);
+ if(atom.IsValid()) ed.RenameAtom(atom,j->first);
+ }
+ }
+ }
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin(); i != res_list.end(); ++i){
+ for(boost::unordered_map<String,ResidueNamesPtr>::const_iterator j = res_renaming_ff_specific_.begin();
+ j != res_renaming_ff_specific_.end(); ++j){
+ if(j->second->Contains(i->GetName())){
+ ed.RenameResidue(*i,j->first);
+ break;
+ }
+ }
+ }
+}
+
+String Forcefield::AtomTypesToKeyword(std::vector<String>& types, bool allow_reordering) const{
+ bool revert = false;
+ int num_types = types.size();
+
+ int comparisons = num_types/2; //integer division => truncate
+ for(int i = 0; i < comparisons; ++i){
+ //note, that in case of equality the next iteration gets entered
+ if(types[i] < types[num_types - i - 1]) break;
+ else if(types[i] > types[num_types - i - 1]){
+ revert = true;
+ break;
+ }
+ }
+
+ if(revert && allow_reordering) std::reverse(types.begin(),types.end());
+ std::stringstream ss;
+ std::vector<String>::iterator i = types.begin();
+ ss << *i++;
+ for (; i != types.end(); ++i) {
+ ss << "_" << *i;
+ }
+ return ss.str();
+}
+
+void Forcefield::CheckInteractionToAdd(InteractionPtr p, const String& interaction_type) const{
+ bool valid = true;
+ if(p->GetTypes().empty()) valid = false;
+ if(!p->IsParametrized()) valid = false;
+ if(!valid){
+ throw ost::Error("Expect interaction to have types and parameters properly set!");
+ }
+ if(interaction_type == "BOND"){
+ if(p->GetFuncType() != HarmonicBond){
+ throw ost::Error("Invalid function type encountered when adding bond!");
+ } return;
+ }
+ if(interaction_type == "ANGLE"){
+ if(p->GetFuncType() != HarmonicAngle && p->GetFuncType() != UreyBradleyAngle){
+ throw ost::Error("Invalid function type encountered when adding angle!");
+ } return;
+ }
+ if(interaction_type == "DIHEDRAL"){
+ if(p->GetFuncType() != PeriodicDihedral){
+ throw ost::Error("Invalid function type encountered when adding dihedral!");
+ } return;
+ }
+ if(interaction_type == "IMPROPER"){
+ if(p->GetFuncType() != PeriodicImproper && p->GetFuncType() != HarmonicImproper){
+ throw ost::Error("Invalid function type encountered when adding improper!");
+ } return;
+ }
+ if(interaction_type == "CMAP"){
+ if(p->GetFuncType() != CMap){
+ throw ost::Error("Invalid function type encountered when adding cmap!");
+ } return;
+ }
+ if(interaction_type == "IMPLICIT_GENBORN"){
+ if(p->GetFuncType() != GBSA){
+ throw ost::Error("Invalid function type encountered when adding implicit genborn!");
+ } return;
+ }
+ if(interaction_type == "LJ"){
+ if(p->GetFuncType() != LJ){
+ throw ost::Error("Invalid function type encountered when adding lj!");
+ } return;
+ }
+ if(interaction_type == "LJ_PAIR"){
+ if(p->GetFuncType() != LJPair){
+ throw ost::Error("Invalid function type encountered when adding lj pair!");
+ } return;
+ }
+ if(interaction_type == "CONSTRAINT"){
+ if(p->GetFuncType() != DistanceConstraint){
+ throw ost::Error("Invalid function type encountered when adding constraint!");
+ } return;
+ }
+
+ std::stringstream ss;
+ ss << "Cannot validate added interaction of type "<< interaction_type << "!";
+ throw ost::Error(ss.str());
+
+}
+
+}}}//ns
diff --git a/modules/mol/mm/src/forcefield.hh b/modules/mol/mm/src/forcefield.hh
new file mode 100644
index 0000000000000000000000000000000000000000..3c65e37fea4673f5f7f4dba2dae582e3871ad269
--- /dev/null
+++ b/modules/mol/mm/src/forcefield.hh
@@ -0,0 +1,233 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_FORCE_FIELD_HH
+#define OST_MM_FORCE_FIELD_HH
+
+#include <vector>
+#include <algorithm>
+
+
+#include <boost/shared_ptr.hpp>
+#include <boost/unordered_map.hpp>
+
+#include <ost/message.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+namespace ost { namespace mol{ namespace mm{
+
+struct ResidueNames;
+class Forcefield;
+
+typedef boost::shared_ptr<ResidueNames> ResidueNamesPtr;
+typedef boost::shared_ptr<ost::mol::mm::Forcefield> ForcefieldPtr;
+
+struct ResidueNames{
+
+ ResidueNames() { };
+
+ ResidueNames(String a, String b, String c, String d):
+ main(a),nter(b),cter(c),twoter(d) { }
+
+ String main;
+ String nter;
+ String cter;
+ String twoter;
+
+ bool Contains(const String& name){
+ return name == main || name == nter || name == cter || name == twoter;
+ }
+
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & main;
+ ds & nter;
+ ds & cter;
+ ds & twoter;
+ }
+};
+
+
+class Forcefield {
+public:
+
+ Forcefield(): gen_pairs_(true), fudge_LJ_(1.0),fudge_QQ_(1.0) { }
+
+ static ForcefieldPtr Load(const String& filename);
+
+ void Save(const String& filename);
+
+ //Getter functions
+
+ BuildingBlockPtr GetBuildingBlock(const String& name) const;
+
+ BlockModifierPtr GetBlockModifier(const String& modifier_name) const;
+
+ String GetAtomType(const String& res_name, const String& atom_name) const;
+
+ HydrogenConstructorPtr GetHydrogenConstructor(const String& name) const;
+
+ BlockModifierPtr GetNTerModifier(const String& res_name, const String& ter_name = "") const;
+
+ BlockModifierPtr GetCTerModifier(const String& res_name, const String& ter_name = "") const;
+
+ InteractionPtr GetBond(const String& type1,
+ const String& type2) const;
+
+ InteractionPtr GetAngle(const String& type1,
+ const String& type2,
+ const String& type3) const;
+
+ std::vector<InteractionPtr> GetDihedrals(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4) const;
+
+ std::vector<InteractionPtr> GetImpropers(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4) const;
+
+ InteractionPtr GetCMap(const String& type1,
+ const String& type2,
+ const String& type3,
+ const String& type4,
+ const String& type5) const;
+
+ InteractionPtr GetImplicitGenborn(const String& type1) const;
+
+ InteractionPtr GetLJ(const String& type1,
+ const String& type2,
+ bool pair=false) const;
+
+ InteractionPtr GetLJ(const String& type) const;
+
+ InteractionPtr GetConstraint(const String& type1,
+ const String& type2);
+
+ Real GetMass(const String& type) const;
+
+ Real GetFudgeLJ() const { return fudge_LJ_; }
+
+ Real GetFudgeQQ() const { return fudge_QQ_; }
+
+ //functions to add interactions and settings
+
+ void AddBuildingBlock(const String& name, BuildingBlockPtr p) { building_blocks_[name] = p; }
+
+ void AddBond(InteractionPtr p);
+
+ void AddAngle(InteractionPtr p);
+
+ void AddDihedral(InteractionPtr p);
+
+ void AddImproper(InteractionPtr p);
+
+ void AddCMap(InteractionPtr p);
+
+ void AddImplicitGenborn(InteractionPtr p);
+
+ void AddLJ(InteractionPtr p);
+
+ void AddLJPair(InteractionPtr p);
+
+ void AddConstraint(InteractionPtr p);
+
+ void AddMass(const String& type, Real mass) { atom_masses_[type] = mass; }
+
+ void SetFudgeLJ(Real f_lj) { fudge_LJ_ = f_lj; }
+
+ void SetFudgeQQ(Real f_qq) { fudge_QQ_ = f_qq; }
+
+ void SetGenPairs(bool gen_pairs) { gen_pairs_ = gen_pairs; }
+
+ void AddResidueRenamingRule(const String& name,
+ const String& ff_main_name,
+ const String& ff_n_ter_name,
+ const String& ff_c_ter_name,
+ const String& ff_two_ter_name);
+
+ void AddAtomRenamingRule(const String& res_name,
+ const String& old_atom_name,
+ const String& new_atom_name);
+
+ String GetResidueRenamingMain(const String& name) const;
+
+ String GetResidueRenamingNTer(const String& name) const;
+
+ String GetResidueRenamingCTer(const String& name) const;
+
+ String GetResidueRenamingTwoTer(const String& name) const;
+
+ String GetAtomRenaming(const String& res_name, const String& atom_name) const;
+
+ void AddHydrogenConstructor(const String& residue_name, HydrogenConstructorPtr p){
+ hydrogen_constructors_[residue_name] = p;
+ }
+
+ void AddBlockModifier(const String& modifier_name,
+ BlockModifierPtr p) { block_modifiers_[modifier_name] = p; }
+
+ void SetStandardCTer(const String& res_name, const String& ter_name) { standard_c_termini_[res_name] = ter_name; }
+
+ void SetStandardNTer(const String& res_name, const String& ter_name) { standard_n_termini_[res_name] = ter_name; }
+
+
+ //Renaming to the forcefield specific names (residues/atoms)
+ void AssignFFSpecificNames(ost::mol::EntityHandle& handle, bool reverse=false) const;
+
+private:
+
+ String AtomTypesToKeyword(std::vector<String>& types, bool allow_reordering = true) const;
+ void CheckInteractionToAdd(InteractionPtr p, const String& interaction_type) const;
+
+ //this is all nonbonded stuff
+ bool gen_pairs_;
+ Real fudge_LJ_;
+ Real fudge_QQ_;
+
+ boost::unordered_map<String, Real> atom_masses_;
+ boost::unordered_map<String, BuildingBlockPtr> building_blocks_;
+ boost::unordered_map<String, BlockModifierPtr> block_modifiers_;
+
+ //the standard interactions
+ boost::unordered_map<String,InteractionPtr> bonds_;
+ boost::unordered_map<String,InteractionPtr> angles_;
+ boost::unordered_map<String,InteractionPtr> lj_14_pairs_;
+ boost::unordered_map<String,InteractionPtr> constraints_;
+ boost::unordered_map<String,InteractionPtr> cmaps_;
+ boost::unordered_map<String,InteractionPtr> implicit_genborn_;
+ boost::unordered_map<String,InteractionPtr> ljs_;
+ boost::unordered_map<String,std::vector<InteractionPtr> > dihedrals_;
+ boost::unordered_map<String,std::vector<InteractionPtr> > improper_dihedrals_;
+
+ boost::unordered_map<String, std::vector<std::pair<String,String> > > atom_renaming_ff_specific_;
+ boost::unordered_map<String, ResidueNamesPtr> res_renaming_ff_specific_;
+
+ boost::unordered_map<String, HydrogenConstructorPtr> hydrogen_constructors_;
+ boost::unordered_map<String, String> standard_n_termini_;
+ boost::unordered_map<String, String> standard_c_termini_;
+};
+
+}}}//ns
+
+#endif
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.cc b/modules/mol/mm/src/gromacs_block_modifiers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..b74b567ea03ff4c8f6737fb42e5ae79400927e32
--- /dev/null
+++ b/modules/mol/mm/src/gromacs_block_modifiers.cc
@@ -0,0 +1,487 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+namespace ost{ namespace mol{ namespace mm{
+
+std::vector<geom::Vec3> GromacsPositionRuleEvaluator::EvaluatePosRule(int rule,
+ int number,
+ const std::vector<geom::Vec3>& anchors){
+
+ std::vector<geom::Vec3> positions;
+
+ switch(rule){
+
+ case 1:{
+ geom::Vec3 i_j = geom::Normalize(anchors[0]-anchors[1]);
+ geom::Vec3 i_k = geom::Normalize(anchors[0]-anchors[2]);
+ geom::Vec3 temp = geom::Normalize(i_j+i_k);
+ positions.push_back(anchors[0]+temp);
+ break;
+ }
+
+ case 2:{
+ Real x = 0.333806859234;
+ Real y = 0.942641491092;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x*j_i+y*q);
+ break;
+ }
+
+ case 3:{
+ Real x = 0.5;
+ Real y = 0.866025403784;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x*j_i-y*q);
+ positions.push_back(i+x*j_i+y*q);
+ break;
+ }
+
+ case 4:{
+ Real x = 0.333313247568;
+ Real y = 0.942816142732;
+ Real z = 0.866025403784;
+
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ geom::Vec3 n1 = i+x*j_i+y*q;
+
+ geom::Vec3 temp = geom::Normalize(geom::Cross(j_i,n1-i));
+
+ geom::Vec3 n2 = i+x*j_i-0.5*q+z*temp;
+ geom::Vec3 n3 = i+x*j_i-0.5*q-z*temp;
+
+ positions.push_back(n1);
+ positions.push_back(n2);
+ if(number==3) positions.push_back(n3);
+ break;
+ }
+
+ case 5:{
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 i_j = geom::Normalize(i-anchors[1]);
+ geom::Vec3 i_k = geom::Normalize(i-anchors[2]);
+ geom::Vec3 i_l = geom::Normalize(i-anchors[3]);
+ geom::Vec3 temp = geom::Normalize(i_j+i_k+i_l);
+ positions.push_back(i+temp);
+ break;
+ }
+
+ case 6:{
+ Real x = 0.81649043092;
+ Real y = 0.577358966516;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 i_j = geom::Normalize(i-anchors[1]);
+ geom::Vec3 i_k = geom::Normalize(i-anchors[2]);
+ geom::Vec3 temp_one = geom::Normalize(i_j+i_k);
+ geom::Vec3 temp_two = geom::Normalize(geom::Cross(i_j,i_k));
+ positions.push_back(i+y*temp_one+x*temp_two);
+ positions.push_back(i+y*temp_one-x*temp_two);
+ break;
+ }
+
+ case 7:{
+ //not implemented yet, do nothing
+ break;
+ }
+
+ case 8:{
+ Real x = 1.36*0.522498564716;
+ Real y = 1.36*0.852640164354;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x*j_i-y*q);
+ positions.push_back(i+x*j_i+y*q);
+ break;
+ }
+
+ case 9:{
+ Real x1 = 1.23*0.51503807491;
+ Real x2 = 1.25*0.422618261741;
+ Real y1 = 1.23*0.857167300702;
+ Real y2 = 1.25*0.906307787037;
+
+ geom::Vec3 i = anchors[0];
+ geom::Vec3 j = anchors[1];
+ geom::Vec3 k = anchors[2];
+
+ geom::Vec3 j_i = geom::Normalize(i-j);
+ geom::Vec3 q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x1*j_i-y1*q);
+ positions.push_back(i+x2*j_i+y2*q);
+
+ //we have to construct a third position hanging at the second one...
+
+ Real x = 0.333806859234;
+ Real y = 0.942641491092;
+
+ std::vector<geom::Vec3> new_anchors;
+ new_anchors.push_back(positions[2]);
+ new_anchors.push_back(anchors[0]);
+ new_anchors.push_back(anchors[1]);
+
+ i = new_anchors[0];
+ j = new_anchors[1];
+ k = new_anchors[2];
+
+ j_i = geom::Normalize(i-j);
+ q = geom::Normalize(geom::Cross(geom::Cross(k-j,j_i),j_i));
+
+ positions.push_back(i+x*j_i+y*q);
+ break;
+ }
+
+ case 10:{
+ //not implemented yet, do nothing
+ break;
+ }
+
+ case 11:{
+ //not implemented yet, do nothing
+ break;
+ }
+
+ default:{
+ break;
+ }
+ }
+ return positions;
+}
+
+
+void GromacsHydrogenConstructor::ApplyOnBuildingBlock(BuildingBlockPtr p){
+ //we assume, that the hydrogens are already correct in the building block...
+}
+
+void GromacsHydrogenConstructor::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed){
+
+ if(!res.IsValid()) return;
+
+ int number;
+ int method;
+ String prefix;
+
+ std::vector<String> anchor_names;
+ ost::mol::AtomHandleList anchor_atoms;
+
+ std::vector<String> hydrogen_names;
+ std::vector<geom::Vec3> hydrogen_positions;
+ std::vector<geom::Vec3> anchor_positions;
+
+ for(uint a=0;a<add_number_.size();++a){
+
+ hydrogen_names = hydrogen_names_[a];
+
+ number = add_number_[a];
+ method = methods_[a];
+ anchor_names = anchor_atom_names_[a];
+
+ hydrogen_positions.clear();
+ anchor_positions.clear();
+ anchor_atoms.clear();
+
+ String atom_name;
+ ost::mol::ResidueHandle temp_res;
+ ost::mol::AtomHandle atom;
+ bool found_anchors = true;
+
+ for(std::vector<String>::iterator it = anchor_names.begin();it!=anchor_names.end();++it){
+
+ temp_res = res;
+ atom_name = *it;
+
+ if(atom_name[0] == '-'){
+ atom_name.erase(0,1);
+ temp_res = res.GetPrev();
+ if(!temp_res.IsValid()){
+ //happens in case of termini... In this case the adding definitions
+ //are taken from the termini database...
+ found_anchors = false;
+ break;
+ }
+ }
+ if(atom_name[0] == '+'){
+ atom_name.erase(0,1);
+ temp_res = res.GetNext();
+ if(!temp_res.IsValid()){
+ //happens in case of termini... In this case the adding definitions
+ //are taken from the termini database...
+ found_anchors = false;
+ break;
+ }
+ }
+
+ atom = temp_res.FindAtom(atom_name);
+ if(!atom.IsValid()){
+ std::stringstream ss;
+ ss << "cannot find required anchor atom " << atom_name << " in residue ";
+ ss << res.GetQualifiedName() << " to add hydrogen!";
+ throw ost::Error(ss.str());
+ }
+
+ anchor_atoms.push_back(atom);
+ anchor_positions.push_back(atom.GetPos());
+ }
+
+ if(!found_anchors){
+ continue;
+ }
+
+ hydrogen_positions = GromacsPositionRuleEvaluator::EvaluatePosRule(method,
+ number,
+ anchor_positions);
+
+ for(int b=0;b<number;++b){
+ //only add hydrogen if not already present!
+ atom = res.FindAtom(hydrogen_names[b]);
+ if(!atom.IsValid()) atom = ed.InsertAtom(res,hydrogen_names[b],hydrogen_positions[b],"H");
+ else ed.SetAtomPos(atom,hydrogen_positions[b]);
+ }
+ }
+}
+
+
+void GromacsHydrogenConstructor::AddHydrogenRule(uint number, int method,
+ const std::vector<String>& hydrogen_names,
+ const std::vector<String>& anchors){
+
+ if(number != hydrogen_names.size()){
+ std::stringstream ss;
+ ss << "Tried to add hydrogen rule to hydrogen constructor with add number ";
+ ss << number << ", but "<< hydrogen_names.size() << "hydrogen names";
+ }
+
+ hydrogen_names_.push_back(hydrogen_names);
+ add_number_.push_back(number);
+ methods_.push_back(method);
+ anchor_atom_names_.push_back(anchors);
+}
+
+void GromacsBlockModifier::AddReplaceRule(const String& name, const String& new_name,
+ const String& new_type, Real new_charge){
+ replace_old_atom_name_.push_back(name);
+ replace_new_atom_name_.push_back(new_name);
+ replace_new_atom_type_.push_back(new_type);
+ replace_new_charge_.push_back(new_charge);
+}
+
+void GromacsBlockModifier::AddAddRule(int number, int method,
+ const std::vector<String>& atom_names,
+ const std::vector<String>& anchors,
+ const String& type, Real charge){
+ add_add_number_.push_back(number);
+ add_methods_.push_back(method);
+ add_atom_names_.push_back(atom_names);
+ add_anchor_atom_names_.push_back(anchors);
+ add_atom_types_.push_back(type);
+ add_charges_.push_back(charge);
+}
+
+void GromacsBlockModifier::ApplyOnBuildingBlock(BuildingBlockPtr p){
+
+ //let's resolve the replace statement
+ for(uint i = 0; i < replace_old_atom_name_.size(); ++i){
+ p->ReplaceAtom(replace_old_atom_name_[i], replace_new_atom_name_[i],
+ replace_new_atom_type_[i], replace_new_charge_[i]);
+
+ }
+ //let's resolve the add statement
+ for(uint i = 0; i < add_add_number_.size(); ++i){
+ String type = add_atom_types_[i];
+ Real charge = add_charges_[i];
+ std::vector<String> anchor_atoms = add_anchor_atom_names_[i];
+ std::vector<String> names = add_atom_names_[i];
+
+ //let's add the stuff to the buildingblock
+ for(std::vector<String>::iterator j = names.begin();
+ j != names.end(); ++j){
+ p->AddAtom(*j,type,charge);
+ //the bond, that connects the newly added atom to its anchor is not necessarily
+ //defined. Let's add it here. Note, that nothing happens, if this specific bond
+ //is already part of the building block.
+ InteractionPtr b_p(new Interaction(p->GetBonds()[0]->GetFuncType()));
+ std::vector<String> bond_names;
+ std::vector<String> bond_types;
+ bond_names.push_back(anchor_atoms[0]);
+ bond_names.push_back(*j);
+ bond_types.push_back(p->GetType(anchor_atoms[0]));
+ bond_types.push_back(type);
+ b_p->SetNames(bond_names);
+ b_p->SetTypes(bond_types);
+ p->AddBond(b_p);
+ }
+ }
+
+ //let's resolve the delete statement
+ for(std::vector<String>::iterator i = delete_atom_names_.begin();
+ i != delete_atom_names_.end(); ++i){
+ p->RemoveAtom(*i);
+ }
+
+ //we simply add the new interactions to the building block
+ for(std::vector<InteractionPtr>::iterator i = bonds_.begin();
+ i != bonds_.end(); ++i){
+ p->AddBond(*i, true);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = angles_.begin();
+ i != angles_.end(); ++i){
+ p->AddAngle(*i, true);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = dihedrals_.begin();
+ i != dihedrals_.end(); ++i){
+ p->AddDihedral(*i, true);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = impropers_.begin();
+ i != impropers_.end(); ++i){
+ p->AddImproper(*i, true);
+ }
+
+ for(std::vector<InteractionPtr>::iterator i = cmaps_.begin();
+ i != cmaps_.end(); ++i){
+ p->AddCMap(*i, true);
+ }
+}
+
+void GromacsBlockModifier::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed){
+
+ //let's resolve the replace statement
+ for(uint i = 0; i < replace_old_atom_name_.size(); ++i){
+ ost::mol::AtomHandle at = res.FindAtom(replace_old_atom_name_[i]);
+ if(at.IsValid()){
+ ed.RenameAtom(at,replace_new_atom_name_[i]);
+ }
+ }
+
+
+ //let's resolve the add statement
+ for(uint i = 0; i < add_add_number_.size(); ++i){
+ int number = add_add_number_[i];
+ int method = add_methods_[i];
+ std::vector<String> anchor_names = add_anchor_atom_names_[i];
+ //String type = add_atom_types_[i];
+ std::vector<geom::Vec3> anchor_positions;
+ ost::mol::AtomHandleList anchor_atoms;
+ std::vector<String> names = add_atom_names_[i];
+
+ for(std::vector<String>::iterator j = anchor_names.begin();
+ j != anchor_names.end(); ++j){
+ ost::mol::AtomHandle at = res.FindAtom(*j);
+ if(!at.IsValid()){
+ std::stringstream ss;
+ ss << "Cannot find anchor atom required to construct termini";
+ ss << " in provided residue!";
+ throw ost::Error(ss.str());
+ }
+ anchor_positions.push_back(at.GetPos());
+ anchor_atoms.push_back(at);
+ }
+ std::vector<geom::Vec3> positions = GromacsPositionRuleEvaluator::EvaluatePosRule(method,
+ number,
+ anchor_positions);
+
+ String ele = "H";
+ if(method == 8 || method == 9){
+ ele = "O";
+ }
+ for(int j=0; j<number; ++j){
+ ost::mol::AtomHandle at = res.FindAtom(names[j]);
+ if(!at.IsValid()) at = ed.InsertAtom(res,names[j],positions[j],ele);
+ else ed.SetAtomPos(at,positions[j]);
+ ed.Connect(at, anchor_atoms[0]);
+ }
+ }
+ //let's resolve the delete statement
+ for(std::vector<String>::iterator i = delete_atom_names_.begin();
+ i != delete_atom_names_.end(); ++i){
+ ost::mol::AtomHandle at = res.FindAtom(*i);
+ if(at.IsValid()){
+ ed.DeleteAtom(at);
+ }
+ }
+}
+
+
+void GromacsBlockModifier::CheckInteractionToAdd(InteractionPtr p, const String& interaction_type) const{
+ if(p->GetNames().empty()) throw ost::Error("Expect interaction to have names properly set!");
+
+ if(interaction_type == "BOND"){
+ if(p->GetFuncType() != HarmonicBond){
+ throw ost::Error("Invalid function type encountered when adding bond!");
+ } return;
+ }
+ if(interaction_type == "ANGLE"){
+ if(p->GetFuncType() != HarmonicAngle && p->GetFuncType() != UreyBradleyAngle){
+ throw ost::Error("Invalid function type encountered when adding angle!");
+ } return;
+ }
+ if(interaction_type == "DIHEDRAL"){
+ if(p->GetFuncType() != PeriodicDihedral){
+ throw ost::Error("Invalid function type encountered when adding dihedral!");
+ } return;
+ }
+ if(interaction_type == "IMPROPER"){
+ if(p->GetFuncType() != PeriodicImproper && p->GetFuncType() != HarmonicImproper){
+ throw ost::Error("Invalid function type encountered when adding improper!");
+ } return;
+ }
+ if(interaction_type == "CMAP"){
+ if(p->GetFuncType() != CMap){
+ throw ost::Error("Invalid function type encountered when adding cmap!");
+ } return;
+ }
+
+ std::stringstream ss;
+ ss << "Cannot validate added interaction of type "<< interaction_type << "!";
+ throw ost::Error(ss.str());
+
+}
+
+}}}//ns
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.hh b/modules/mol/mm/src/gromacs_block_modifiers.hh
new file mode 100644
index 0000000000000000000000000000000000000000..af8fbbdc2ade9a8d9fcaf65d286fe68e3589c068
--- /dev/null
+++ b/modules/mol/mm/src/gromacs_block_modifiers.hh
@@ -0,0 +1,328 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_GROMCACS_BLOCK_MODIFIERS_HH
+#define OST_MM_GROMCACS_BLOCK_MODIFIERS_HH
+
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/message.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/buildingblock.hh>
+
+
+namespace ost{ namespace mol{ namespace mm{
+
+class GromacsHydrogenConstructor;
+class GromacsTerminiConstructor;
+class GromacsBlockModifier;
+
+typedef boost::shared_ptr<GromacsHydrogenConstructor> GromacsHydrogenConstructorPtr;
+typedef boost::shared_ptr<GromacsTerminiConstructor> GromacsTerminiConstructorPtr;
+typedef boost::shared_ptr<GromacsBlockModifier> GromacsBlockModifierPtr;
+
+class GromacsPositionRuleEvaluator{
+
+public:
+ static std::vector<geom::Vec3> EvaluatePosRule(int rule, int number,
+ const std::vector<geom::Vec3>& anchors);
+};
+
+class GromacsHydrogenConstructor : public HydrogenConstructor{
+
+public:
+
+ GromacsHydrogenConstructor() { }
+
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr);
+
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed);
+
+ void AddHydrogenRule(uint number, int method,
+ const std::vector<String>& hydrogen_names,
+ const std::vector<String>& anchors);
+
+ virtual void OnSave(ost::io::BinaryDataSink& ds) { ds << *this; }
+
+ virtual BlockModifierType GetBlockModifierType() { return GromacsBlockModifiers; }
+
+ template <typename DS>
+ void Serialize(DS& ds){
+ int num_hydrogen_add_rules = add_number_.size();
+ ds & num_hydrogen_add_rules;
+
+ if(ds.IsSource()){
+ add_number_ = std::vector<int>(num_hydrogen_add_rules);
+ methods_ = std::vector<int>(num_hydrogen_add_rules);
+ hydrogen_names_ = std::vector<std::vector<String> >(num_hydrogen_add_rules);
+ anchor_atom_names_ = std::vector<std::vector<String> >(num_hydrogen_add_rules);
+ }
+
+ for(int i = 0; i < num_hydrogen_add_rules; ++i){
+ ds & add_number_[i];
+ ds & methods_[i];
+ int num_hydrogen_names = hydrogen_names_[i].size();
+ int num_anchor_names = anchor_atom_names_[i].size();
+ ds & num_hydrogen_names;
+ ds & num_anchor_names;
+ if(ds.IsSource()){
+ hydrogen_names_[i] = std::vector<String>(num_hydrogen_names);
+ anchor_atom_names_[i] = std::vector<String>(num_anchor_names);
+ }
+
+ for(int j = 0; j < num_hydrogen_names; ++j){
+ ds & hydrogen_names_[i][j];
+ }
+ for(int j = 0; j < num_anchor_names; ++j){
+ ds & anchor_atom_names_[i][j];
+ }
+ }
+ }
+
+private:
+ std::vector<int> add_number_;
+ std::vector<int> methods_;
+ std::vector<std::vector<String> > hydrogen_names_;
+ std::vector<std::vector<String> > anchor_atom_names_;
+};
+
+
+class GromacsBlockModifier : public BlockModifier{
+
+public:
+
+ GromacsBlockModifier() { }
+
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p);
+
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed);
+
+ void AddReplaceRule(const String& name, const String& new_name,
+ const String& new_type, Real new_charge);
+
+ void AddAddRule(int number, int method,
+ const std::vector<String>& atom_names,
+ const std::vector<String>& anchors,
+ const String& type, Real charge);
+
+ void AddBond(InteractionPtr p) { this->CheckInteractionToAdd(p,"BOND");
+ bonds_.push_back(p); }
+
+ void AddAngle(InteractionPtr p) { this->CheckInteractionToAdd(p,"ANGLE");
+ angles_.push_back(p); }
+
+ void AddDihedral(InteractionPtr p) { this->CheckInteractionToAdd(p,"DIHEDRAL");
+ dihedrals_.push_back(p); }
+
+ void AddImproper(InteractionPtr p) { this->CheckInteractionToAdd(p,"IMPROPER");
+ impropers_.push_back(p); }
+
+ void AddCMap(InteractionPtr p) { this->CheckInteractionToAdd(p,"CMAP");
+ cmaps_.push_back(p); }
+
+ void AddDeleteAtom(const String& atom_name) { delete_atom_names_.push_back(atom_name); }
+
+ virtual void OnSave(ost::io::BinaryDataSink& ds) { ds << *this; }
+
+ virtual BlockModifierType GetBlockModifierType() { return GromacsBlockModifiers; }
+
+ template <typename DS>
+ void Serialize(DS& ds){
+
+ int num_bonds = bonds_.size();
+ int num_angles = angles_.size();
+ int num_dihedrals = dihedrals_.size();
+ int num_impropers = impropers_.size();
+ int num_cmaps = cmaps_.size();
+
+ ds & num_bonds;
+ ds & num_angles;
+ ds & num_dihedrals;
+ ds & num_impropers;
+ ds & num_cmaps;
+
+ for(int i = 0; i < num_bonds; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ bonds_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = bonds_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(bonds_[i]);
+ }
+
+ for(int i = 0; i < num_angles; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ angles_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = angles_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(angles_[i]);
+ }
+
+ for(int i = 0; i < num_dihedrals; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ dihedrals_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = dihedrals_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(dihedrals_[i]);
+ }
+
+ for(int i = 0; i < num_impropers; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ impropers_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = impropers_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(impropers_[i]);
+ }
+
+ for(int i = 0; i < num_cmaps; ++i){
+ int func_type;
+ if(ds.IsSource()){
+ ds & func_type;
+ cmaps_.push_back(InteractionPtr(new Interaction(FuncType(func_type))));
+ }
+ else{
+ func_type = cmaps_[i]->GetFuncType();
+ ds & func_type;
+ }
+ ds & *(cmaps_[i]);
+ }
+
+ int num_replace_atoms = replace_old_atom_name_.size();
+ ds & num_replace_atoms;
+
+ if(ds.IsSource()){
+ replace_old_atom_name_ = std::vector<String>(num_replace_atoms);
+ replace_new_atom_name_ = std::vector<String>(num_replace_atoms);
+ replace_new_atom_type_ = std::vector<String>(num_replace_atoms);
+ replace_new_charge_ = std::vector<Real>(num_replace_atoms);
+ }
+
+ for(int i = 0; i < num_replace_atoms; ++i){
+ ds & replace_old_atom_name_[i];
+ ds & replace_new_atom_name_[i];
+ ds & replace_new_atom_type_[i];
+ ds & replace_new_charge_[i];
+ }
+
+ int num_add_atoms = add_add_number_.size();
+ ds & num_add_atoms;
+
+ if(ds.IsSource()){
+ add_add_number_ = std::vector<int>(num_add_atoms);
+ add_methods_ = std::vector<int>(num_add_atoms);
+ add_atom_names_ = std::vector<std::vector<String> >(num_add_atoms);
+ add_anchor_atom_names_ = std::vector<std::vector<String> >(num_add_atoms);
+ add_atom_types_ = std::vector<String>(num_add_atoms);
+ add_charges_ = std::vector<Real>(num_add_atoms);
+ }
+
+ for(int i = 0; i < num_add_atoms; ++i){
+ ds & add_add_number_[i];
+ ds & add_methods_[i];
+ ds & add_atom_types_[i];
+ ds & add_charges_[i];
+ int num_add_atom_names = add_atom_names_[i].size();
+ int num_add_anchor_atom_names = add_anchor_atom_names_[i].size();
+ ds & num_add_atom_names;
+ ds & num_add_anchor_atom_names;
+ if(ds.IsSource()){
+ add_atom_names_[i] = std::vector<String>(num_add_atom_names);
+ add_anchor_atom_names_[i] = std::vector<String>(num_add_anchor_atom_names);
+ }
+ for(int j = 0; j < num_add_atom_names; ++j){
+ ds & add_atom_names_[i][j];
+ }
+ for(int j = 0; j < num_add_anchor_atom_names; ++j){
+ ds & add_anchor_atom_names_[i][j];
+ }
+ }
+
+ int num_delete_atoms = delete_atom_names_.size();
+ ds & num_delete_atoms;
+ if(ds.IsSource()){
+ delete_atom_names_ = std::vector<String>(num_delete_atoms);
+ }
+ for(int i = 0; i < num_delete_atoms; ++i){
+ ds & delete_atom_names_[i];
+ }
+ }
+
+private:
+
+ void CheckInteractionToAdd(InteractionPtr p, const String& interaction_type) const;
+
+ //Atoms, that will be added to the building block
+
+ //Interactions, that will be added to the building block
+ std::vector<InteractionPtr> bonds_;
+ std::vector<InteractionPtr> angles_;
+ std::vector<InteractionPtr> dihedrals_;
+ std::vector<InteractionPtr> impropers_;
+ std::vector<InteractionPtr> cmaps_;
+
+ //paramters we need for the replace statement
+ std::vector<String> replace_old_atom_name_;
+ std::vector<String> replace_new_atom_name_;
+ std::vector<String> replace_new_atom_type_;
+ std::vector<Real> replace_new_charge_;
+
+ //parameters we need for the add statement => gromacs dependent rules!
+ std::vector<int> add_add_number_;
+ std::vector<int> add_methods_;
+ std::vector<std::vector<String> > add_atom_names_;
+ std::vector<std::vector<String> > add_anchor_atom_names_;
+ std::vector<String> add_atom_types_;
+ std::vector<Real> add_charges_;
+
+ //parameters we need for the delete statement
+ std::vector<String> delete_atom_names_;
+};
+
+
+
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/heuristic_block_modifiers.cc b/modules/mol/mm/src/heuristic_block_modifiers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..09734d1dcf716d0f690f74dd7387f4fb3a20eab2
--- /dev/null
+++ b/modules/mol/mm/src/heuristic_block_modifiers.cc
@@ -0,0 +1,214 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/heuristic_block_modifiers.hh>
+#include <ost/geom/geom.hh>
+#include <math.h>
+
+namespace ost{ namespace mol{ namespace mm{
+
+
+void HeuristicHydrogenConstructor::ApplyOnBuildingBlock(BuildingBlockPtr p){
+ //we assume, that the hydrogens are already correct in the building block...
+}
+
+HeuristicHydrogenConstructor::HeuristicHydrogenConstructor(BuildingBlockPtr block){
+ std::vector<String> atom_names = block->GetAtoms();
+ std::vector<InteractionPtr> bonds = block->GetBonds();
+
+ for(std::vector<String>::iterator aname = atom_names.begin();
+ aname != atom_names.end(); ++aname){
+ if((*aname)[0] == 'H') continue; //it's a hydrogen
+
+ std::vector<String> antecedent_names, hydrogen_names;
+ String aname_other;
+
+ for (std::vector<InteractionPtr>::iterator i = bonds.begin() ;
+ i != bonds.end(); ++i){
+
+ std::vector<String> bond_names=(*i)->GetNames();
+
+ if (*aname!=bond_names[0] && *aname!=bond_names[1]) continue;//bond has nothing to do
+ //with current atom
+ if (*aname==bond_names[0]) aname_other=bond_names[1];
+ else aname_other=bond_names[0];
+
+ //check whether it's a hydrogen
+ if (aname_other[0] == 'H') {
+ hydrogen_names.push_back(aname_other);
+ }
+ else{
+ antecedent_names.push_back(aname_other);
+ }
+ }
+ if(!hydrogen_names.empty()){
+ if(antecedent_names.empty()){
+ std::stringstream ss;
+ ss << "Can only reconstruct hydrogens when at least one ";
+ ss << "antecedent atom is present!";
+ throw ost::Error(ss.str());
+ }
+ if(antecedent_names.size() + hydrogen_names.size() > 4){
+ std::stringstream ss;
+ ss << "Antecedent and hydrogen atoms sum up to more than four ";
+ ss << "around anchor atom "<<*aname<<". This is not possible with ";
+ ss << "the used block modifier implementation!";
+ throw ost::Error(ss.str());
+ }
+ anchor_atom_names_.push_back(*aname);
+ antecedent_names_.push_back(antecedent_names);
+ hydrogen_names_.push_back(hydrogen_names);
+ }
+ }
+}
+
+void HeuristicHydrogenConstructor::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& edi){
+
+ if(!res.IsValid()) return;
+
+ for(uint i = 0; i < anchor_atom_names_.size(); ++i){
+
+ ost::mol::AtomHandle anchor_atom = res.FindAtom(anchor_atom_names_[i]);
+ if(!anchor_atom.IsValid()){
+ std::stringstream ss;
+ ss << "Anchor atom of name " << anchor_atom_names_[i];
+ ss << " cannot be found in residue "<<res.GetQualifiedName()<<"!";
+ throw ost::Error(ss.str());
+ }
+
+ geom::Vec3List antecedent_positions;
+ for(std::vector<String>::iterator j = antecedent_names_[i].begin();
+ j != antecedent_names_[i].end(); ++j){
+ ost::mol::AtomHandle at = res.FindAtom(*j);
+ if(!at.IsValid()){
+ std::stringstream ss;
+ ss << "Cannot find required antecedent atom of name "<<*j;
+ ss << " in residue "<<res.GetQualifiedName()<<"!";
+ throw ost::Error(ss.str());
+ }
+ antecedent_positions.push_back(at.GetPos());
+ }
+
+ Real bond_length=1.08;
+ String ele(1,'H');
+ geom::Vec3 antecedents_cm=antecedent_positions.GetCenter();
+ geom::Vec3 pa=anchor_atom.GetPos();
+ geom::Vec3 v=geom::Normalize(pa-antecedents_cm);
+ geom::Vec3 n=geom::OrthogonalVector(v),direction=geom::Vec3(),hpos=geom::Vec3();
+ geom::Mat3 R=geom::Mat3();
+ Real bond_angle;
+ AtomHandle ha=mol::AtomHandle();
+
+ switch (hydrogen_names_[i].size()){
+ case 1:{
+ if (antecedent_names_[i].size()==1){
+ bond_angle=0.4*M_PI;
+ }
+ else {
+ bond_angle=0.0;
+ }
+ R=geom::AxisRotation(n,bond_angle);
+ direction=R*v;
+ hpos=pa+bond_length*direction;
+ ha = res.FindAtom(hydrogen_names_[i][0]);
+ if(!ha.IsValid()) ha=edi.InsertAtom(res,hydrogen_names_[i][0],hpos,ele);
+ else edi.SetAtomPos(ha,hpos);
+ break;
+ }
+ case 2:{
+ if (antecedent_names_[i].size()==1){
+ bond_angle=M_PI/3.;
+ }
+ else {
+ bond_angle = 0.4*M_PI;
+ n=geom::Normalize(antecedent_positions[0]-antecedent_positions[1]);
+ }
+
+ R=geom::AxisRotation(n,bond_angle);
+ direction=R*v;
+ hpos=pa+bond_length*direction;
+ ha = res.FindAtom(hydrogen_names_[i][0]);
+ if(!ha.IsValid()) ha=edi.InsertAtom(res,hydrogen_names_[i][0],hpos,ele);
+ else edi.SetAtomPos(ha,hpos);
+
+ R=geom::AxisRotation(v,M_PI);
+ direction=R*direction;
+ hpos=pa+bond_length*direction;
+ ha = res.FindAtom(hydrogen_names_[i][1]);
+ if(!ha.IsValid()) ha=edi.InsertAtom(res,hydrogen_names_[i][1],hpos,ele);
+ else edi.SetAtomPos(ha,hpos);
+
+ break;
+ }
+ case 3:{
+ bond_angle=0.4*M_PI;
+
+ R=geom::AxisRotation(n,bond_angle);
+ direction=R*v;
+ hpos=pa+bond_length*direction;
+ ha = res.FindAtom(hydrogen_names_[i][0]);
+ if(!ha.IsValid()) ha=edi.InsertAtom(res,hydrogen_names_[i][0],hpos,ele);
+ else edi.SetAtomPos(ha,hpos);
+
+ R=geom::AxisRotation(v,2.*M_PI/3.);
+ direction=R*direction;
+ hpos=pa+bond_length*direction;
+ ha = res.FindAtom(hydrogen_names_[i][1]);
+ if(!ha.IsValid()) ha=edi.InsertAtom(res,hydrogen_names_[i][1],hpos,ele);
+ else edi.SetAtomPos(ha,hpos);
+
+ direction=R*direction;
+ hpos=pa+bond_length*direction;
+ ha = res.FindAtom(hydrogen_names_[i][2]);
+ if(!ha.IsValid()) ha=edi.InsertAtom(res,hydrogen_names_[i][2],hpos,ele);
+ else edi.SetAtomPos(ha,hpos);
+ break;
+ }
+ }
+ }
+}
+
+void HeuristicBlockModifier::ApplyOnBuildingBlock(BuildingBlockPtr p){
+
+}
+
+void HeuristicBlockModifier::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed){
+
+}
+
+
+}}}//ns
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/modules/mol/mm/src/heuristic_block_modifiers.hh b/modules/mol/mm/src/heuristic_block_modifiers.hh
new file mode 100644
index 0000000000000000000000000000000000000000..facf818e52cf0290761cc1fd076c0f7fb62e617d
--- /dev/null
+++ b/modules/mol/mm/src/heuristic_block_modifiers.hh
@@ -0,0 +1,157 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_HEURISTIC_BLOCK_MODIFIERS_HH
+#define OST_MM_HEURISTIC_BLOCK_MODIFIERS_HH
+
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/message.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/buildingblock.hh>
+
+
+namespace ost{ namespace mol{ namespace mm{
+
+class HeuristicHydrogenConstructor;
+class HeuristicTerminiConstructor;
+class HeuristicBlockModifier;
+
+typedef boost::shared_ptr<HeuristicHydrogenConstructor> HeuristicHydrogenConstructorPtr;
+typedef boost::shared_ptr<HeuristicTerminiConstructor> HeuristicTerminiConstructorPtr;
+typedef boost::shared_ptr<HeuristicBlockModifier> HeuristicBlockModifierPtr;
+
+
+class HeuristicHydrogenConstructor : public HydrogenConstructor{
+
+public:
+
+ HeuristicHydrogenConstructor(BuildingBlockPtr block);
+
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr);
+
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed);
+
+ virtual void OnSave(ost::io::BinaryDataSink& ds) { ds << *this; }
+
+ virtual BlockModifierType GetBlockModifierType() { return HeuristicBlockModifiers; }
+
+ template <typename DS>
+
+ void Serialize(DS& ds){
+
+ if(ds.IsSource()){
+ int num_anchor_atoms = 0;
+ int num_antecendents = 0;
+ int num_hydrogens = 0;
+ String loaded_string;
+
+ ds & num_anchor_atoms;
+
+ for(int i = 0; i < num_anchor_atoms; ++i){
+ ds & num_antecendents;
+ ds & num_hydrogens;
+
+ ds & loaded_string;
+ anchor_atom_names_.push_back(loaded_string);
+
+ antecedent_names_.push_back(std::vector<String>());
+ for(int j = 0; j < num_antecendents; ++j){
+ ds & loaded_string;
+ antecedent_names_[i].push_back(loaded_string);
+ }
+
+ hydrogen_names_.push_back(std::vector<String>());
+ for(int j = 0; j < num_hydrogens; ++j){
+ ds & loaded_string;
+ hydrogen_names_[i].push_back(loaded_string);
+ }
+ }
+ }
+ else{
+ int num_anchor_atoms = anchor_atom_names_.size();
+ int num_antecendents = 0;
+ int num_hydrogens = 0;
+
+ ds & num_anchor_atoms;
+
+ for(int i = 0; i < num_anchor_atoms; ++i){
+
+ num_antecendents = antecedent_names_[i].size();
+ num_hydrogens = hydrogen_names_[i].size();
+ ds & num_antecendents;
+ ds & num_hydrogens;
+ ds & anchor_atom_names_[i];
+
+
+ for(std::vector<String>::iterator j = antecedent_names_[i].begin();
+ j != antecedent_names_[i].end(); ++j){
+ ds & *j;
+ }
+
+ for(std::vector<String>::iterator j = hydrogen_names_[i].begin();
+ j != hydrogen_names_[i].end(); ++j){
+ ds & *j;
+ }
+ }
+
+ }
+ }
+
+private:
+ std::vector<String> anchor_atom_names_;
+ std::vector<std::vector<String> > antecedent_names_;
+ std::vector<std::vector<String> > hydrogen_names_;
+};
+
+
+class HeuristicBlockModifier : public BlockModifier{
+
+public:
+
+ HeuristicBlockModifier() { }
+
+ virtual void ApplyOnBuildingBlock(BuildingBlockPtr p);
+
+ virtual void ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed);
+
+ virtual BlockModifierType GetBlockModifierType() { return HeuristicBlockModifiers; }
+
+ virtual void OnSave(ost::io::BinaryDataSink& ds) { ds << *this; }
+
+ template <typename DS>
+
+ void Serialize(DS& ds){
+
+ }
+
+};
+
+
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/index.hh b/modules/mol/mm/src/index.hh
new file mode 100644
index 0000000000000000000000000000000000000000..93e9d2311b48c39fc950f23f16aa68c7426172ba
--- /dev/null
+++ b/modules/mol/mm/src/index.hh
@@ -0,0 +1,241 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_INDEX_HH
+#define OST_MM_INDEX_HH
+
+/*
+ Author: Marco Biasini
+ */
+
+#include <algorithm>
+
+#include <cstring>
+
+namespace ost { namespace mol{ namespace mm{
+
+namespace impl {
+template <uint D>
+class IndexBase {
+public:
+ enum { Dimension = D };
+ IndexBase(const IndexBase& rhs) {
+ memcpy(data_, rhs.data_, sizeof(uint[D]));
+ }
+ IndexBase() {
+ memset(data_, 0, sizeof(uint[D]));
+ }
+
+ IndexBase& operator=(const IndexBase& rhs) {
+ memcpy(data_, rhs.data_, sizeof(uint[D]));
+ return *this;
+ }
+ uint operator[](uint idx) const {
+ assert(idx < D);
+ return data_[idx];
+ }
+ uint& operator[](uint idx) {
+ assert(idx < D);
+ return data_[idx];
+ }
+ //allows index to be inserted into set
+ inline bool operator < (const IndexBase<D>& rhs) const{
+ return std::lexicographical_compare(data_, data_+D, rhs.data_, rhs.data_+D);
+ }
+
+ inline bool operator==(const IndexBase<D>& rhs) const{
+ return std::equal(data_,data_+D,rhs.data_);
+ }
+
+ inline bool operator!=(const IndexBase<D>& rhs) const{
+ return !(*this == rhs);
+ }
+
+private:
+ uint data_[D];
+};
+
+} // namespace impl
+
+template <uint D>
+class Index;
+
+template <>
+class Index<1> : public impl::IndexBase<1> {
+public:
+ Index() : impl::IndexBase<1>() {}
+ Index(uint a) {
+ (*this)[0]=a;
+ }
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & (*this)[0];
+ }
+};
+template <>
+class Index<2> : public impl::IndexBase<2> {
+public:
+ Index() : impl::IndexBase<2>() {}
+ Index(uint a, uint b) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ }
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & (*this)[0];
+ ds & (*this)[1];
+ }
+};
+template <>
+class Index<3> : public impl::IndexBase<3> {
+public:
+ Index() : impl::IndexBase<3>() {}
+ Index(uint a, uint b, uint c) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ }
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & (*this)[0];
+ ds & (*this)[1];
+ ds & (*this)[2];
+ }
+};
+template <>
+class Index<4> : public impl::IndexBase<4> {
+public:
+ Index() : impl::IndexBase<4>() {}
+ Index(uint a, uint b, uint c, uint d) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ (*this)[3]=d;
+ }
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & (*this)[0];
+ ds & (*this)[1];
+ ds & (*this)[2];
+ ds & (*this)[3];
+ }
+};
+template <>
+class Index<5> : public impl::IndexBase<5> {
+public:
+ Index() : impl::IndexBase<5>() {}
+ Index(uint a, uint b, uint c, uint d, uint e) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ (*this)[3]=d;
+ (*this)[4]=e;
+ }
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & (*this)[0];
+ ds & (*this)[1];
+ ds & (*this)[2];
+ ds & (*this)[3];
+ ds & (*this)[4];
+ }
+};
+template <>
+class Index<6> : public impl::IndexBase<6> {
+public:
+ Index() : impl::IndexBase<6>() {}
+ Index(uint a, uint b, uint c, uint d, uint e, uint f) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ (*this)[3]=d;
+ (*this)[4]=e;
+ (*this)[5]=f;
+ }
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & (*this)[0];
+ ds & (*this)[1];
+ ds & (*this)[2];
+ ds & (*this)[3];
+ ds & (*this)[4];
+ ds & (*this)[5];
+ }
+};
+template <>
+class Index<7> : public impl::IndexBase<7> {
+public:
+ Index() : impl::IndexBase<7>() {}
+ Index(uint a, uint b, uint c, uint d, uint e, uint f, uint g) {
+ (*this)[0]=a;
+ (*this)[1]=b;
+ (*this)[2]=c;
+ (*this)[3]=d;
+ (*this)[4]=e;
+ (*this)[5]=f;
+ (*this)[6]=g;
+ }
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & (*this)[0];
+ ds & (*this)[1];
+ ds & (*this)[2];
+ ds & (*this)[3];
+ ds & (*this)[4];
+ ds & (*this)[5];
+ ds & (*this)[6];
+ }
+};
+template<uint D>
+class IndexIterator {
+public:
+ typedef Index<D> IndexType;
+ IndexIterator(const IndexType& s, const IndexType& e)
+ : start_(s), end_(e), current_(s) {
+
+ }
+
+ IndexIterator<D>& operator++() {
+ uint current_it=0;
+ while (++current_[current_it] > end_[current_it]) {
+ current_it++;
+ if (current_it < D) {
+ current_[current_it-1] = start_[current_it-1];
+ } else {
+ break;
+ }
+ }
+ return *this;
+ }
+ const IndexType& operator *() const {
+ return current_;
+ }
+ bool AtEnd() {
+ return current_[D-1] > end_[D-1];
+ }
+private:
+ IndexType start_;
+ IndexType end_;
+ IndexType current_;
+
+};
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/interaction.cc b/modules/mol/mm/src/interaction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..72f6ba8f01b54f5c33b2dd364bc204611f5b818a
--- /dev/null
+++ b/modules/mol/mm/src/interaction.cc
@@ -0,0 +1,213 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/interaction.hh>
+
+namespace ost { namespace mol{ namespace mm{
+
+Interaction::Interaction(FuncType func_type): func_type_(func_type),
+ set_parameters_(false),
+ has_type_wildcard_(false),
+ has_name_wildcard_(false){ }
+
+
+void Interaction::SetTypes(std::vector<String> types){
+ if(!this->CheckSetNamesTypes(types)){
+ throw ost::Error("Tried to set invalid number of types to interaction!");
+ }
+ atom_types_ = types;
+ if(std::find(atom_types_.begin(),atom_types_.end(),"X") != atom_types_.end()){
+ has_type_wildcard_ = true;
+ }
+ else has_type_wildcard_ = false;
+}
+
+void Interaction::SetNames(std::vector<String> names){
+ if(!this->CheckSetNamesTypes(names)){
+ throw ost::Error("Tried to set invalid number of names to interaction!");
+ }
+ atom_names_ = names;
+ if(std::find(atom_names_.begin(),atom_names_.end(),"X") != atom_names_.end()){
+ has_name_wildcard_ = true;
+ }
+ else has_name_wildcard_ = false;
+}
+
+void Interaction::SetParam(std::vector<Real>& parameters){
+ if(!this->CheckSetParam(parameters)){
+ throw ost::Error("Tried to set invalid number of parameters to interaction!");
+ }
+ parameters_ = parameters;
+ set_parameters_ = true;
+}
+
+ost::mol::AtomHandleList Interaction::GetAtoms(const ost::mol::ResidueHandle& res) const{
+
+ ost::mol::AtomHandleList return_list;
+ ost::mol::ResidueHandle prev = res.GetPrev();
+ ost::mol::ResidueHandle next = res.GetNext();
+ String atom_name;
+ ost::mol::AtomHandle atom;
+
+ for(std::vector<String>::const_iterator i = atom_names_.begin();
+ i != atom_names_.end(); ++i){
+ atom_name = (*i);
+ if(atom_name[0] == '+'){
+ atom_name = atom_name.substr(1);
+ if(!next.IsValid()){
+ throw ost::Error("Access to nonexistent next residue requested!");
+ }
+ atom = next.FindAtom(atom_name);
+ if(atom.IsValid()){
+ return_list.push_back(atom);
+ continue;
+ }
+ throw ost::Error("Could not find required atom "+*i+"!");
+ }
+ if(atom_name[0] == '-'){
+ atom_name = atom_name.substr(1);
+ if(!prev.IsValid()){
+ throw ost::Error("Access to nonexistent previous residue requested!");
+ }
+ atom = prev.FindAtom(atom_name);
+ if(atom.IsValid()){
+ return_list.push_back(atom);
+ continue;
+ }
+ throw ost::Error("Could not find required atom "+*i+"!");
+ }
+ atom = res.FindAtom(atom_name);
+ if(atom.IsValid()){
+ return_list.push_back(atom);
+ continue;
+ }
+ throw ost::Error("Could not find required atom "+*i+"!");
+ }
+
+ return return_list;
+}
+
+bool Interaction::MatchTypes(const std::vector<String>& atom_types) const {
+
+ if(atom_types_.size() == 0) return false;
+ if(atom_types.size() != atom_types_.size()) return false;
+
+ bool match = true;
+ bool reverse_match = true;
+
+ uint i,j;
+
+ for(i = 0, j = atom_types_.size()-1; i < atom_types_.size(); ++i,--j){
+ if((atom_types[i] != atom_types_[i]) && (atom_types_[i] != "X")) match = false;
+ if((atom_types[i] != atom_types_[j]) && (atom_types_[j] != "X")) reverse_match = false;
+ }
+
+ return match || reverse_match;
+}
+
+bool Interaction::MatchNames(const std::vector<String>& atom_names) const {
+
+ if(atom_names_.size() == 0) return false;
+ if(atom_names.size() != atom_names_.size()) return false;
+
+ bool match = true;
+ bool r_match = true;
+
+ uint i,j;
+
+ for(i = 0, j = atom_names_.size()-1; i < atom_names_.size(); ++i,--j){
+ if((atom_names[i] != atom_names_[i]) && (atom_names_[i] != "X")) match = false;
+ if((atom_names[i] != atom_names_[j]) && (atom_names_[j] != "X")) r_match = false;
+ }
+
+ return match || r_match;
+}
+
+bool Interaction::ReplaceAtom(const String& name, const String& new_name, const String& new_type){
+
+ for(uint i = 0; i < atom_names_.size(); ++i){
+ if(atom_names_[i] == name){
+ atom_names_[i] = new_name;
+ if(i < atom_types_.size()) atom_types_[i] = new_type;
+ //it could be, that wildcard stuff has changed
+ has_type_wildcard_ = std::find(atom_types_.begin(),atom_types_.end(),"X") != atom_types_.end();
+ has_name_wildcard_ = std::find(atom_names_.begin(),atom_names_.end(),"X") != atom_names_.end();
+ return true;
+ }
+ }
+ return false;
+}
+
+bool Interaction::HasName(const String& name) const{
+ return std::find(atom_names_.begin(),atom_names_.end(),name) != atom_names_.end();
+}
+
+bool Interaction::HasType(const String& type) const{
+ return std::find(atom_types_.begin(),atom_types_.end(),type) != atom_types_.end();
+}
+
+bool Interaction::CheckSetNamesTypes(std::vector<String>& types){
+
+ switch(func_type_){
+ case HarmonicBond: return types.size() == 2;
+ case HarmonicAngle: return types.size() == 3;
+ case UreyBradleyAngle: return types.size() == 3;
+ case PeriodicDihedral: return types.size() == 4;
+ case PeriodicImproper: return types.size() == 4;
+ case HarmonicImproper: return types.size() == 4;
+ case CMap: return types.size() == 5;
+ case LJ: return types.size() == 1;
+ case LJPair: return types.size() == 2;
+ case GBSA: return types.size() == 1;
+ case DistanceConstraint: return types.size() == 2;
+ case Exclusion: return types.size() == 2;
+ case HarmonicPositionRestraint: return types.size() == 1;
+ case HarmonicDistanceRestraint: return types.size() == 2;
+ default: return false;
+ }
+}
+
+bool Interaction::CheckSetParam(std::vector<Real>& param){
+
+ switch(func_type_){
+ case HarmonicBond: return param.size() == 2;
+ case HarmonicAngle: return param.size() == 2;
+ case UreyBradleyAngle: return param.size() == 4;
+ case PeriodicDihedral: return param.size() == 3;
+ case PeriodicImproper: return param.size() == 3;
+ case HarmonicImproper: return param.size() == 2;
+ case CMap:{
+ int num_param = param.size();
+ if(num_param < 1) return false;
+ int x = param[0];
+ return num_param == (x*x + 1);
+ }
+ case LJ: return param.size() == 2;
+ case LJPair: return param.size() == 2;
+ case GBSA: return param.size() == 2;
+ case DistanceConstraint: return param.size() == 1;
+ case Exclusion: return param.empty();
+ case HarmonicPositionRestraint: return param.size() == 7;
+ case HarmonicDistanceRestraint: return param.size() == 2;
+ default: return false;
+ }
+
+}
+
+}}} //ns
\ No newline at end of file
diff --git a/modules/mol/mm/src/interaction.hh b/modules/mol/mm/src/interaction.hh
new file mode 100644
index 0000000000000000000000000000000000000000..12762e244b1c608a795ef47421960a73fee37763
--- /dev/null
+++ b/modules/mol/mm/src/interaction.hh
@@ -0,0 +1,165 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_INTERACTION_HH
+#define OST_MM_INTERACTION_HH
+
+#include <vector>
+#include <fstream>
+
+#include <boost/shared_ptr.hpp>
+#include <boost/filesystem.hpp>
+
+#include <ost/io/binary_data_source.hh>
+#include <ost/io/binary_data_sink.hh>
+#include <ost/io/io_exception.hh>
+#include <ost/message.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/residue_handle.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class Interaction;
+typedef boost::shared_ptr<Interaction> InteractionPtr;
+
+enum FuncType{
+ Invalid,
+ HarmonicBond,
+ HarmonicAngle,
+ UreyBradleyAngle,
+ PeriodicDihedral,
+ PeriodicImproper,
+ HarmonicImproper,
+ CMap,
+ LJ,
+ LJPair,
+ GBSA,
+ DistanceConstraint,
+ Exclusion,
+ HarmonicPositionRestraint,
+ HarmonicDistanceRestraint
+};
+
+class Interaction{
+
+public:
+ Interaction(FuncType func_type);
+
+ void SetTypes(std::vector<String> types);
+
+ void SetNames(std::vector<String> names);
+
+ void SetParam(std::vector<Real>& parameters);
+
+ std::vector<String> GetTypes() const { return atom_types_; }
+
+ std::vector<String> GetNames() const { return atom_names_; }
+
+ std::vector<Real> GetParam() const { return parameters_; }
+
+ ost::mol::AtomHandleList GetAtoms(const ost::mol::ResidueHandle& res) const;
+
+ FuncType GetFuncType() const { return func_type_; }
+
+ bool ReplaceAtom(const String& name, const String& new_name, const String& new_type);
+
+ bool MatchTypes(const std::vector<String>& atom_types) const;
+
+ bool MatchNames(const std::vector<String>& atom_names) const;
+
+ bool HasName(const String& name) const;
+
+ bool HasType(const String& type) const;
+
+ bool IsParametrized() const { return set_parameters_; }
+
+ bool HasTypeWildcard() const { return has_type_wildcard_; }
+
+ bool HasNameWildcard() const { return has_name_wildcard_; }
+
+ template <typename DS>
+ void Serialize(DS& ds){
+ ds & set_parameters_;
+ ds & has_type_wildcard_;
+ ds & has_name_wildcard_;
+
+ if(ds.IsSource()){
+ int num_types = 0;
+ int num_names = 0;
+ int num_param = 0;
+ ds & num_types;
+ ds & num_names;
+ ds & num_param;
+ for(int i = 0; i < num_types; ++i){
+ String type;
+ ds & type;
+ atom_types_.push_back(type);
+ }
+ for(int i = 0; i < num_names; ++i){
+ String name;
+ ds & name;
+ atom_names_.push_back(name);
+ }
+ for(int i = 0; i < num_param; ++i){
+ Real param;
+ ds & param;
+ parameters_.push_back(param);
+ }
+ }
+ else{
+ int atom_types_size = atom_types_.size();
+ int atom_names_size = atom_names_.size();
+ int parameters_size = parameters_.size();
+ ds & atom_types_size;
+ ds & atom_names_size;
+ ds & parameters_size;
+
+ for(std::vector<String>::iterator i = atom_types_.begin();
+ i != atom_types_.end(); ++i){
+ ds & *i;
+ }
+ for(std::vector<String>::iterator i = atom_names_.begin();
+ i != atom_names_.end(); ++i){
+ ds & *i;
+ }
+ for(std::vector<Real>::iterator i = parameters_.begin();
+ i != parameters_.end(); ++i){
+ ds & *i;
+ }
+ }
+ }
+
+private:
+
+ bool CheckSetNamesTypes(std::vector<String>& types);
+ bool CheckSetParam(std::vector<Real>& param);
+
+ FuncType func_type_;
+ bool set_parameters_;
+ bool has_type_wildcard_;
+ bool has_name_wildcard_;
+ std::vector<Real> parameters_;
+ std::vector<String> atom_types_;
+ std::vector<String> atom_names_;
+};
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/modeller.cc b/modules/mol/mm/src/modeller.cc
new file mode 100644
index 0000000000000000000000000000000000000000..1a9da309452b9c0926fd3e1d27dff00dc6120f89
--- /dev/null
+++ b/modules/mol/mm/src/modeller.cc
@@ -0,0 +1,269 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/modeller.hh>
+
+namespace{
+
+bool IsCysteine(const ost::mol::ResidueHandle& res){
+ String res_name = res.GetName();
+ if(res_name[0] == 'C'){
+ if(res_name == "CYS" || res_name == "CYX" ||
+ res_name == "CYS2" || res_name == "CYM"){
+ return true;
+ }
+ }
+ return false;
+}
+
+bool BoundToSG(const ost::mol::AtomHandle& atom){
+ ost::mol::AtomHandleList bound_atoms = atom.GetBondPartners();
+ for(ost::mol::AtomHandleList::iterator i = bound_atoms.begin();
+ i != bound_atoms.end(); ++i){
+ if(i->GetResidue() == atom.GetResidue()) continue;
+ if(i->GetName() != "SG") continue;
+ if(IsCysteine(i->GetResidue())) return true;
+ }
+ return false;
+}
+
+}
+
+
+namespace ost{ namespace mol{ namespace mm{
+
+void Modeller::GenerateDisulfidBonds(ost::mol::EntityHandle& handle){
+
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ ost::mol::XCSEditor ed = handle.EditXCS();
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+
+ if(!IsCysteine(*i)) continue;
+ ost::mol::AtomHandle s = i->FindAtom("SG");
+ if(!s.IsValid()) continue;
+ if(BoundToSG(s)) continue; //it's already connected to another sulfur
+
+ //we have now a cysteine gamma-sulfur and can look around for potential
+ //disulfid bridges...
+ ost::mol::AtomHandleList in_reach = handle.FindWithin(s.GetPos(),2.5);
+ for(ost::mol::AtomHandleList::iterator j = in_reach.begin();
+ j != in_reach.end(); ++j){
+ if(j->GetResidue() != *i && j->GetName() == "SG" &&
+ IsCysteine(j->GetResidue())){
+ //the other atom is a gamma-sulfur as well!
+ if(BoundToSG(*j)) continue; //it's already connected to another sulfur
+ if(!ost::mol::BondExists(s,*j)){
+ ed.Connect(s,*j);
+ }
+ ed.RenameResidue(*i,"CYS2");
+ ed.RenameResidue(j->GetResidue(),"CYS2");
+ break; //sg can only be bound to one other sg
+ }
+ }
+ }
+}
+
+void Modeller::LowerPrecision(ost::mol::EntityHandle& handle){
+
+ ost::mol::AtomHandleList atom_list = handle.GetAtomList();
+ ost::mol::XCSEditor ed = handle.EditXCS(ost::mol::BUFFERED_EDIT);
+ geom::Vec3 pos;
+ geom::Vec3 truncated_pos;
+
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i != atom_list.end(); ++i){
+ pos = i->GetPos();
+ truncated_pos[0] = Real(round(pos[0]*100))/100;
+ truncated_pos[1] = Real(round(pos[1]*100))/100;
+ truncated_pos[2] = Real(round(pos[2]*100))/100;
+ ed.SetAtomPos(*i,truncated_pos);
+ }
+ ed.UpdateICS();
+}
+
+void Modeller::AssignPDBNaming(ost::mol::EntityHandle& handle){
+
+ std::map<String,String> gromacs_to_pdb;
+ gromacs_to_pdb["ARGN"] = "ARG";
+ gromacs_to_pdb["ASPH"] = "ASP";
+ gromacs_to_pdb["CYS2"] = "CYS";
+ gromacs_to_pdb["GLUH"] = "GLU";
+ gromacs_to_pdb["HISD"] = "HIS";
+ gromacs_to_pdb["HISE"] = "HIS";
+ gromacs_to_pdb["HISH"] = "HIS";
+ gromacs_to_pdb["HIS1"] = "HIS";
+ gromacs_to_pdb["LYSN"] = "LYS";
+ gromacs_to_pdb["HEME"] = "HEM";
+
+ ost::mol::XCSEditor ed = handle.EditXCS();
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ String res_name;
+ ost::mol::AtomHandle atom;
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ res_name = i->GetName();
+ if(gromacs_to_pdb.find(res_name) != gromacs_to_pdb.end()){
+ ed.RenameResidue(*i,gromacs_to_pdb[res_name]);
+ }
+ //this is nasty hardcoded stuff
+ //in case of ILE gromacs seems to define wrong standard naming
+ //we have to keep this wrong standard naming to remain consistent
+ //with the namings in the forcefields.
+ //to avoid errors in loading a pdb structure with these namings
+ //we have to hardcode a correct conversion
+ if(res_name == "ILE"){
+ atom = i->FindAtom("CD");
+ if(atom.IsValid()){
+ ed.RenameAtom(atom,"CD1");
+ }
+ atom = i->FindAtom("HD1");
+ if(atom.IsValid()){
+ ed.RenameAtom(atom,"HD11");
+ }
+ atom = i->FindAtom("HD2");
+ if(atom.IsValid()){
+ ed.RenameAtom(atom,"HD12");
+ }
+ atom = i->FindAtom("HD3");
+ if(atom.IsValid()){
+ ed.RenameAtom(atom,"HD13");
+ }
+ }
+ }
+}
+
+void Modeller::AssignGromacsNaming(ost::mol::EntityHandle& handle){
+
+ ost::mol::XCSEditor ed = handle.EditXCS();
+
+ //Let's first rename as much as possible to the gromacs standard
+ std::map<String,String> residue_renaming;
+
+ //a proper solution should be found for that (assign proper protonation)
+ residue_renaming["HIS"] = "HISE";
+ //this is awful....
+
+
+ residue_renaming["HID"] = "HISD";
+ residue_renaming["HIE"] = "HISE";
+ residue_renaming["HSP"] = "HISH";
+ residue_renaming["LSN"] = "LYSN";
+ residue_renaming["ASPP"] = "ASPH";
+ residue_renaming["GLUP"] = "GLUH";
+ residue_renaming["HOH"] = "SOL";
+ residue_renaming["TIP3"] = "SOL";
+ residue_renaming["HOH"] = "SOL";
+ residue_renaming["HEME"] = "HEM";
+ //following stuff are required to rename the charmm names that are different,
+ //as it for example comes from CHARMM GUI
+ residue_renaming["POT"] = "K";
+ residue_renaming["CLA"] = "CL";
+ residue_renaming["SOD"] = "NA";
+ residue_renaming["CAL"] = "CA";
+ residue_renaming["CES"] = "CS";
+ residue_renaming["ZN2"] = "ZN";
+
+ ost::mol::ResidueHandleList res_list = handle.GetResidueList();
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ if(residue_renaming.find(i->GetName()) != residue_renaming.end()){
+ ed.RenameResidue(*i,residue_renaming[i->GetName()]);
+ }
+ }
+
+ //this data is taken from the gromacs xlateat.dat file
+ std::map<String, std::map<String, String> > renaming_to_standard;
+ renaming_to_standard["ILE"] = std::map<String,String>();
+ renaming_to_standard["HOH"] = std::map<String,String>();
+ renaming_to_standard["HO4"] = std::map<String,String>();
+ renaming_to_standard["HO5"] = std::map<String,String>();
+ renaming_to_standard["HEME"] = std::map<String,String>();
+ renaming_to_standard["protein"] = std::map<String,String>();
+
+ renaming_to_standard["ILE"]["CD1"] = "CD";
+ renaming_to_standard["ILE"]["HD11"] = "HD1";
+ renaming_to_standard["ILE"]["HD12"] = "HD2";
+ renaming_to_standard["ILE"]["HD13"] = "HD3";
+
+ renaming_to_standard["SOL"]["O"] = "OW";
+ renaming_to_standard["SOL"]["OW1"] = "OW";
+ renaming_to_standard["SOL"]["OH2"] = "OW"; //specific for CHARMM-GUI
+ renaming_to_standard["SOL"]["H1"] = "HW1"; //specific for CHARMM-GUI
+ renaming_to_standard["SOL"]["H2"] = "HW2"; //specific for CHARMM-GUI
+
+ renaming_to_standard["HEM"]["N_A"] = "NA";
+ renaming_to_standard["HEM"]["N_B"] = "NB";
+ renaming_to_standard["HEM"]["N_C"] = "NC";
+ renaming_to_standard["HEM"]["N_D"] = "ND";
+
+ renaming_to_standard["protein"]["O1"] = "O";
+ renaming_to_standard["protein"]["O2"] = "OXT";
+ renaming_to_standard["protein"]["OT1"] = "O";
+ renaming_to_standard["protein"]["OT2"] = "OXT";
+ renaming_to_standard["protein"]["OT"] = "OXT";
+ renaming_to_standard["protein"]["O'"] = "O";
+ renaming_to_standard["protein"]["O''"] = "OXT";
+ renaming_to_standard["protein"]["OC1"] = "O";
+ renaming_to_standard["protein"]["OC2"] = "OXT";
+ renaming_to_standard["protein"]["HN"] = "H";
+ renaming_to_standard["protein"]["HT1"] = "H1";
+ renaming_to_standard["protein"]["HT2"] = "H2";
+ renaming_to_standard["protein"]["HT3"] = "H3";
+
+ //again CHARMM specific stuff
+ renaming_to_standard["K"]["POT"] = "K";
+ renaming_to_standard["CL"]["CLA"] = "CL";
+ renaming_to_standard["NA"]["SOD"] = "NA";
+ renaming_to_standard["CA"]["CAL"] = "CA";
+ renaming_to_standard["CS"]["CES"] = "CS";
+
+
+
+ //let's apply the explicit residue names definition of aboves weird data structure
+ ost::mol::AtomHandleList renaming_atom_list;
+ String res_name;
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ res_name = i->GetName();
+ if(renaming_to_standard.find(res_name) == renaming_to_standard.end()) continue;
+ renaming_atom_list = i->GetAtomList();
+ for(ost::mol::AtomHandleList::iterator j = renaming_atom_list.begin();
+ j != renaming_atom_list.end(); ++j){
+ if(renaming_to_standard[res_name].find(j->GetName()) == renaming_to_standard[res_name].end()) continue;
+ ed.RenameAtom(*j,renaming_to_standard[res_name][j->GetName()]);
+ }
+ }
+
+ //entries with of name protein have to be applied on all peptide residues
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ if(!i->IsPeptideLinking()) continue;
+ renaming_atom_list = i->GetAtomList();
+ for(ost::mol::AtomHandleList::iterator j = renaming_atom_list.begin();
+ j != renaming_atom_list.end(); ++j){
+ if(renaming_to_standard["protein"].find(j->GetName()) == renaming_to_standard["protein"].end()) continue;
+ ed.RenameAtom(*j,renaming_to_standard["protein"][j->GetName()]);
+ }
+ }
+}
+
+}}}
diff --git a/modules/mol/mm/src/modeller.hh b/modules/mol/mm/src/modeller.hh
new file mode 100644
index 0000000000000000000000000000000000000000..2ec09e194825a93ddbd36e988477b812c3dc0d45
--- /dev/null
+++ b/modules/mol/mm/src/modeller.hh
@@ -0,0 +1,73 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_MODELLER_HH
+#define OST_MM_MODELLER_HH
+
+
+#include <vector>
+#include <set>
+
+#include <ost/platform.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/geom/composite.hh>
+#include <ost/geom/transform.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/message.hh>
+#include <ost/mol/bounding_box.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/topology.hh>
+#include <ost/conop/heuristic.hh>
+#include <ost/mol/spatial_organizer.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class Modeller{
+public:
+
+ static void GenerateDisulfidBonds(ost::mol::EntityHandle& handle);
+
+ //may sound pretty stupid...
+ //But this is necessary if we want to compare our energies with
+ //the energies calculated by gromacs. When ost writes and entity
+ //down to disk, it uses 3 digits precision.
+ //If we feed this into gromacs, it also produces a topology
+ //with three digits precision. The problem is, that gromacs
+ //uses nm, therefore the precision gets lowered tenfold.
+ //To take care of that it is necessary to lower our precision...
+ static void LowerPrecision(ost::mol::EntityHandle& handle);
+
+ static void AssignPDBNaming(ost::mol::EntityHandle& handle);
+
+ static void AssignGromacsNaming(ost::mol::EntityHandle& handle);
+};
+
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/observer.cc b/modules/mol/mm/src/observer.cc
new file mode 100644
index 0000000000000000000000000000000000000000..0364715c42d4a3d551b99cb19bbe5b1ae891bbe3
--- /dev/null
+++ b/modules/mol/mm/src/observer.cc
@@ -0,0 +1,207 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/observer.hh>
+#include <OpenMM.h>
+
+namespace ost { namespace mol{ namespace mm{
+
+void TrajObserver::Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top,
+ ost::mol::EntityHandle& ent){
+
+ if(registered_){
+ throw ost::Error("Can register observer to only one simulation!");
+ }
+
+ registered_ = true;
+
+ context_ = c;
+ c_group_ = ost::mol::CreateCoordGroup(ent.GetAtomList());
+}
+
+void TrajObserver::Notify(){
+
+ geom::Vec3List positions;
+ StateExtractor::ExtractPositions(context_,positions,true);
+ c_group_.AddFrame(positions);
+}
+
+
+void TrajWriter::Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top,
+ ost::mol::EntityHandle& ent){
+
+ if(registered_){
+ throw ost::Error("Can register observer to only one simulation!");
+ }
+
+ registered_ = true;
+
+ context_ = c;
+ ost::io::IOProfile profile("CHARMM",false,false,false,false,false);
+ ost::io::PDBWriter writer(pdb_filename_, profile);
+ writer.Write(ent.GetAtomList());
+
+ stream_.open(dcd_filename_.c_str(), std::ios::binary);
+
+ x.resize(top->GetNumParticles());
+ y.resize(top->GetNumParticles());
+ z.resize(top->GetNumParticles());
+
+
+ // size of first header block in bytes
+ int32_t magic_number=84;
+ stream_.write(reinterpret_cast<char*>(&magic_number), 4);
+
+ // magic string
+ char crd[]={'C', 'O', 'R', 'D'};
+ stream_.write(crd, 4);
+
+ // icntrl[0], NSET, number of frames
+ // we don't know the number of frames yet, will be written
+ // when the finalize function is called.
+ int32_t zero=0;
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+
+ // icntrl[1], ISTART, starting timestep
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+
+ // icntrl[2], NSAVC, timesteps between DCD saves
+ int32_t one=1;
+ stream_.write(reinterpret_cast<char*>(&one), 4);
+
+ // icntrl[3] to icntrl[7], unused
+ for (int i=3; i<=7; ++i) {
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+ }
+
+ // icntrl[8], NAMNF, number of fixed atoms
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+
+ // icntrl[9], DELTA, timestep as float for CHARMM format
+ float delta=1.0;
+ stream_.write(reinterpret_cast<char*>(&delta), 4);
+
+ // icntrl[10], CHARMM format: ucell per frame
+ stream_.write(reinterpret_cast<char*>(&one), 4);
+
+ // icntrl[11] to icntrl[18], unused
+ for (int i=11; i<=18; ++i) {
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+ }
+
+ // icntrl[19], charmm version
+ int32_t charmm_version=24;
+ stream_.write(reinterpret_cast<char*>(&charmm_version), 4);
+ // bracket first header block
+ stream_.write(reinterpret_cast<char*>(&magic_number), 4);
+
+ // no titles in title block
+ int32_t four=4;
+ stream_.write(reinterpret_cast<char*>(&four), 4);
+ stream_.write(reinterpret_cast<char*>(&zero), 4);
+ stream_.write(reinterpret_cast<char*>(&four), 4);
+
+ // atom count block
+ stream_.write(reinterpret_cast<char*>(&four), 4);
+ int32_t atom_count=top->GetNumParticles();
+ stream_.write(reinterpret_cast<char*>(&atom_count), 4);
+ stream_.write(reinterpret_cast<char*>(&four), 4);
+}
+
+void TrajWriter::Notify(){
+
+ if(!registered_){
+ throw ost::Error("Trajectory writer is not registered to any simulation!");
+ }
+
+ if(!stream_){
+ throw ost::Error("Trajectory writer does not contain open filestream. Did you already call the finalize funciton before?");
+ }
+
+ geom::Vec3List positions;
+ StateExtractor::ExtractPositions(context_,positions,true,true);
+ OpenMM::State openmm_state = context_->getState(0); //create minimal state
+ //to only extract periodic
+ //box information
+ OpenMM::Vec3 ucell_a,ucell_b,ucell_c;
+
+ openmm_state.getPeriodicBoxVectors(ucell_a,ucell_b,ucell_c);
+
+ int32_t out_n=positions.size()*4;
+
+ // ucell
+ int32_t bsize=48; // ucell block size, 6 doubles
+
+ double a_length = 10 * sqrt(ucell_a.dot(ucell_a)); //directly transform
+ double b_length = 10 * sqrt(ucell_b.dot(ucell_b)); //stuff to Angstrom
+ double c_length = 10 * sqrt(ucell_c.dot(ucell_c));
+
+ //note, that following angles have a compatibility issue
+ //CHARMM seems to write out the cosines of the actual
+ //unit cell angles, while NAMD seems to write the angles itself...
+ //we stick with the CHARMM way of doing things
+
+ double alpha = ucell_b.dot(ucell_c)/(b_length*c_length);
+ double beta = ucell_c.dot(ucell_a)/(c_length*a_length);
+ double gamma = ucell_a.dot(ucell_b)/(a_length*b_length);
+
+ double ucell[]={a_length, alpha, b_length,
+ beta, gamma, c_length};
+
+ stream_.write(reinterpret_cast<char*>(&bsize),4);
+ stream_.write(reinterpret_cast<char*>(ucell),bsize);
+ stream_.write(reinterpret_cast<char*>(&bsize),4);
+
+ int k=0;
+ for (geom::Vec3List::iterator i=positions.begin();
+ i!=positions.end(); ++i, ++k) {
+ x[k]=float((*i)[0]);
+ y[k]=float((*i)[1]);
+ z[k]=float((*i)[2]);
+ }
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&x[0]), out_n);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&y[0]), out_n);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+ stream_.write(reinterpret_cast<char*>(&z[0]), out_n);
+ stream_.write(reinterpret_cast<char*>(&out_n), 4);
+
+ ++frames_;
+
+ stream_.seekp(8,std::ios_base::beg);
+ stream_.write(reinterpret_cast<char*>(&frames_),4);
+ stream_.seekp(0,std::ios_base::end);
+}
+
+void TrajWriter::Finalize(){
+ if(!registered_){
+ throw ost::Error("Trajectory writer is not registered to any simulation!");
+ }
+ if(!stream_){
+ throw ost::Error("Trajectory writer does not contain open filestream. Did you already call the finalize function before?");
+ }
+ stream_.close();
+}
+
+}}}// ns
diff --git a/modules/mol/mm/src/observer.hh b/modules/mol/mm/src/observer.hh
new file mode 100644
index 0000000000000000000000000000000000000000..d36229a9c4ef07177ca78c0d1787db1e0c3db899
--- /dev/null
+++ b/modules/mol/mm/src/observer.hh
@@ -0,0 +1,132 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_OBSERVER_HH
+#define OST_MM_OBSERVER_HH
+
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/io/mol/io_profile.hh>
+#include <ost/io/mol/pdb_writer.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/coord_frame.hh>
+#include <ost/mol/coord_group.hh>
+#include <ost/mol/mm/state_extractor.hh>
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/modeller.hh>
+
+namespace OpenMM{
+ class Context; //hacky way of telling the Context is around.
+ //will be included in source file to avoid
+ //dependencies on external libraries
+}
+
+namespace ost { namespace mol{ namespace mm{
+
+class Observer;
+class TrajObserver;
+class TrajWriter;
+typedef boost::shared_ptr<Observer> ObserverPtr;
+typedef boost::shared_ptr<TrajObserver> TrajObserverPtr;
+typedef boost::shared_ptr<TrajWriter> TrajWriterPtr;
+
+
+class Observer{
+public:
+
+ virtual void Notify() = 0;
+
+ virtual void Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top,
+ ost::mol::EntityHandle& ent) = 0;
+
+ virtual int Rhythm() = 0;
+
+};
+
+
+class TrajObserver : public Observer{
+
+public:
+
+ TrajObserver(int rhythm): rhythm_(rhythm), registered_(false) { }
+
+ void Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top,
+ ost::mol::EntityHandle& ent);
+
+ void Notify();
+
+ int Rhythm() { return rhythm_; }
+
+ CoordGroupHandle GetTraj() { return c_group_; }
+
+private:
+
+ ost::mol::CoordGroupHandle c_group_;
+ boost::shared_ptr<OpenMM::Context> context_;
+ int rhythm_;
+ bool registered_;
+};
+
+class TrajWriter : public Observer{
+
+//Note, that this code is highly redundant to the code in io/mol/dcd_io.hh!!!
+
+public:
+
+ TrajWriter(int rhythm, const String& pdb_filename, const String& dcd_filename): rhythm_(rhythm),
+ pdb_filename_(pdb_filename),
+ dcd_filename_(dcd_filename),
+ stream_(),
+ registered_(false),
+ frames_(0) { }
+
+ void Init(boost::shared_ptr<OpenMM::Context> c,
+ TopologyPtr top,
+ ost::mol::EntityHandle& ent);
+
+ void Notify();
+
+ int Rhythm() { return rhythm_; }
+
+ void Finalize();
+
+private:
+
+ TrajWriter(const TrajWriter& writer) { } //output filestream is unique!
+
+
+ boost::shared_ptr<OpenMM::Context> context_;
+ int rhythm_;
+ String pdb_filename_;
+ String dcd_filename_;
+ std::ofstream stream_;
+ bool registered_;
+ uint32_t frames_;
+ std::vector<float> x;
+ std::vector<float> y;
+ std::vector<float> z;
+};
+
+
+}}}//ns
+
+#endif
diff --git a/modules/mol/mm/src/settings.hh.in b/modules/mol/mm/src/settings.hh.in
new file mode 100644
index 0000000000000000000000000000000000000000..b3f5511a1d65f35e3f54bd8f4559549f3fdda4ba
--- /dev/null
+++ b/modules/mol/mm/src/settings.hh.in
@@ -0,0 +1,197 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_SETTINGS_HH
+#define OST_MM_SETTINGS_HH
+
+/*
+ DO NOT EDIT, automatically generated by @config_hh_generator@
+*/
+
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+#include <limits>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/mm/forcefield.hh>
+
+namespace OpenMM{
+ class Integrator;//hacky way of telling the Integrator us around
+ //will be included in source file to avoid
+ //dependencies on external libraries
+}
+
+namespace ost { namespace mol{ namespace mm{
+
+struct Settings;
+class TerminiExceptions;
+typedef boost::shared_ptr<Settings> SettingsPtr;
+typedef boost::shared_ptr<TerminiExceptions> TerminiExceptionsPtr;
+
+enum Platform{
+ Reference,
+ OpenCL,
+ CUDA,
+ CPU
+};
+
+enum NonbondedMethod{
+ NoCutoff,
+ CutoffNonPeriodic,
+ CutoffPeriodic,
+ Ewald,
+ PME
+};
+
+class TerminiExceptions{
+
+public:
+
+ TerminiExceptions(){ }
+
+ void SetException(const ost::mol::ResidueHandle& res, const String& exception_name){
+ exceptions_[res.GetHashCode()] = exception_name;
+ }
+
+ bool HasException(const ost::mol::ResidueHandle& res) const{
+ return exceptions_.find(res.GetHashCode()) != exceptions_.end();
+ }
+
+ String GetException(const ost::mol::ResidueHandle& res) const {
+ if(!this->HasException(res)){
+ std::stringstream ss;
+ ss<<"Tried to get termini exceptions of res "<<res<<" without defined exception!";
+ throw ost::Error(ss.str());
+ }
+ std::map<unsigned long, String>::const_iterator i = exceptions_.find(res.GetHashCode());
+ return i->second;
+ }
+private:
+ std::map<unsigned long, String> exceptions_;
+
+};
+
+typedef std::map<String,String> PropertyMap;
+
+struct Settings{
+
+ Settings(): add_bonds(true),
+ add_angles(true),
+ add_dihedrals(true),
+ add_impropers(true),
+ add_cmaps(true),
+ add_exclusions(true),
+ add_nonbonded(true),
+ add_gbsa(false),
+ constrain_hbonds(false),
+ constrain_bonds(false),
+ rigid_water(false),
+ strict_interactions(true),
+ ideal_bond_length_constraints(true),
+ fix_heavy_atoms(false),
+ kill_electrostatics(false),
+ generate_disulfid_bonds(true),
+ nonbonded_method(NoCutoff),
+ nonbonded_cutoff(10.0),
+ remove_cmm_motion(true),
+ cmm_frequency(1),
+ periodic_box_extents(0,0,0),
+ init_temperature(0.0),
+ forcefield(), //note, that we don't create an empty forcefield at this point =>force the user
+ //to assign a forcefield
+ termini_exceptions(new TerminiExceptions),
+ platform(Reference),
+ reference_properties(),
+ cpu_properties(),
+ opencl_properties(),
+ cuda_properties(),
+ add_thermostat(false),
+ thermostat_temperature(std::numeric_limits<Real>::quiet_NaN()),
+ thermostat_collision_frequency(std::numeric_limits<Real>::quiet_NaN()),
+ add_barostat(false),
+ barostat_temperature(std::numeric_limits<Real>::quiet_NaN()),
+ barostat_pressure(std::numeric_limits<Real>::quiet_NaN()),
+ barostat_frequency(25),
+ integrator(),
+ solvent_dielectric(78.3), //this is for GBSA
+ solute_dielectric(1.0), //this is for GBSA
+ reaction_field_dielectric(78.3),
+ use_dispersion_correction(true),
+ keep_ff_specific_naming(true),
+ openmm_plugin_directory("@OPEN_MM_PLUGIN_DIR@"),
+ custom_plugin_directory("@OPEN_MM_PLUGIN_DIR@")
+
+ { }
+
+ //
+ bool add_bonds;
+ bool add_angles;
+ bool add_dihedrals;
+ bool add_impropers;
+ bool add_cmaps;
+ bool add_exclusions;
+ bool add_nonbonded;
+ bool add_gbsa;
+ bool constrain_hbonds;
+ bool constrain_bonds;
+ bool rigid_water;
+ bool strict_interactions;
+ bool ideal_bond_length_constraints;
+ bool fix_heavy_atoms;
+ //set all charges to zero
+ bool kill_electrostatics;
+ //automatically generate disulfid bonds
+ bool generate_disulfid_bonds;
+ //see export_openmm.cc for all possibilities
+ NonbondedMethod nonbonded_method;
+ Real nonbonded_cutoff;
+ bool remove_cmm_motion;
+ int cmm_frequency;
+ //currently only boxes defined by base vectors are supported
+ geom::Vec3 periodic_box_extents;
+ //at the beginning of the simulation, the initial velociities are
+ //randomly set according to a boltzmann distribution
+ Real init_temperature;
+ ForcefieldPtr forcefield;
+ TerminiExceptionsPtr termini_exceptions;
+ Platform platform;
+ PropertyMap reference_properties;
+ PropertyMap cpu_properties;
+ PropertyMap opencl_properties;
+ PropertyMap cuda_properties;
+ bool add_thermostat;
+ Real thermostat_temperature;
+ Real thermostat_collision_frequency;
+ bool add_barostat;
+ Real barostat_temperature;
+ Real barostat_pressure;
+ int barostat_frequency;
+ boost::shared_ptr<OpenMM::Integrator> integrator;
+ Real solvent_dielectric;
+ Real solute_dielectric;
+ Real reaction_field_dielectric;
+ bool use_dispersion_correction;
+ bool keep_ff_specific_naming;
+ String openmm_plugin_directory;
+ String custom_plugin_directory;
+};
+
+}}} //namespace
+
+#endif
diff --git a/modules/mol/mm/src/simulation.cc b/modules/mol/mm/src/simulation.cc
new file mode 100644
index 0000000000000000000000000000000000000000..830b9bd5b6a1b14f92fdaf99248c95c279158dbb
--- /dev/null
+++ b/modules/mol/mm/src/simulation.cc
@@ -0,0 +1,870 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/simulation.hh>
+#include <OpenMM.h>
+
+namespace ost{ namespace mol{ namespace mm{
+
+Simulation::Simulation(const ost::mol::EntityHandle& handle,
+ const SettingsPtr settings){
+
+ //note, that ent_ will be "completed" inside this function!
+ //(hydrogens and shit)
+
+ ent_ = handle.Copy();
+ TopologyPtr top = TopologyCreator::Create(ent_,settings);
+ this->Init(top, settings);
+}
+
+Simulation::Simulation(const TopologyPtr top,
+ const ost::mol::EntityHandle& handle,
+ const SettingsPtr settings){
+
+ if(static_cast<uint>(handle.GetAtomCount()) != top->GetNumParticles()){
+ throw ost::Error("Number of atoms in entity must be consistent with number of particles in topology!");
+ }
+ ent_ = handle.Copy();
+ this->Init(top, settings);
+}
+
+void Simulation::Save(const String& filename){
+ std::ofstream stream(filename.c_str(), std::ios_base::binary);
+ io::BinaryDataSink ds(stream);
+ ds << *top_;
+ geom::Vec3List positions = this->GetPositions(false,false);
+ for(geom::Vec3List::iterator i = positions.begin();
+ i != positions.end(); ++i){
+ ds & (*i)[0];
+ ds & (*i)[1];
+ ds & (*i)[2];
+ }
+
+ uint num_chains;
+ uint num_residues;
+ uint num_atoms;
+ uint num_bonded_atoms;
+ Real bfac;
+ Real occ;
+ bool is_hetatm;
+ String chain_name;
+ String res_name;
+ int resnum_num;
+ char resnum_code;
+ String atom_name;
+ String atom_element;
+ uint atom_index;
+
+ num_chains = ent_.GetChainCount();
+ ds & num_chains;
+ ost::mol::ChainHandleList chain_list = ent_.GetChainList();
+ for(ost::mol::ChainHandleList::iterator i = chain_list.begin();
+ i != chain_list.end(); ++i){
+ chain_name = i->GetName();
+ num_residues = i->GetResidueCount();
+ ds & chain_name;
+ ds & num_residues;
+ ost::mol::ResidueHandleList res_list = i->GetResidueList();
+ for(ost::mol::ResidueHandleList::iterator j = res_list.begin();
+ j != res_list.end(); ++j){
+ res_name = j->GetKey();
+ resnum_num = j->GetNumber().GetNum();
+ resnum_code = j->GetNumber().GetInsCode();
+ num_atoms = j->GetAtomCount();
+ ds & res_name;
+ ds & resnum_num;
+ ds & resnum_code;
+ ds & num_atoms;
+ ost::mol::AtomHandleList atom_list = j->GetAtomList();
+ for(ost::mol::AtomHandleList::iterator k = atom_list.begin();
+ k != atom_list.end(); ++k){
+ atom_name = k->GetName();
+ atom_element = k->GetElement();
+ geom::Vec3 pos = k->GetPos();
+ bfac = k->GetBFactor();
+ occ = k->GetOccupancy();
+ is_hetatm = k->IsHetAtom();
+ ds & atom_name;
+ ds & atom_element;
+ ds & pos[0];
+ ds & pos[1];
+ ds & pos[2];
+ ds & bfac;
+ ds & occ;
+ ds & is_hetatm;
+ }
+ }
+ }
+
+ ost::mol::AtomHandleList atom_list = ent_.GetAtomList();
+ ost::mol::AtomHandleList bonded_atoms;
+
+ std::map<long,int> atom_indices;
+ int actual_index = 0;
+ for(ost::mol::AtomHandleList::const_iterator i = atom_list.begin(), e = atom_list.end();
+ i != e; ++i){
+ atom_indices[i->GetHashCode()] = actual_index;
+ ++actual_index;
+ }
+
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i != atom_list.end(); ++i){
+ bonded_atoms = i->GetBondPartners();
+ num_bonded_atoms = bonded_atoms.size();
+ ds & num_bonded_atoms;
+ for(ost::mol::AtomHandleList::iterator j = bonded_atoms.begin();
+ j != bonded_atoms.end(); ++j){
+ atom_index = atom_indices[j->GetHashCode()];
+ ds & atom_index;
+ }
+ }
+
+ context_->createCheckpoint(stream);
+}
+
+SimulationPtr Simulation::Load(const String& filename, SettingsPtr settings){
+ if (!boost::filesystem::exists(filename)) {
+ std::stringstream ss;
+ ss << "Could not open simulation File '"
+ << filename << "' does not exist";
+ throw ost::io::IOException(ss.str());
+ }
+
+ SimulationPtr sim_ptr(new Simulation);
+
+ std::ifstream stream(filename.c_str(), std::ios_base::binary);
+ io::BinaryDataSource ds(stream);
+ TopologyPtr top_p(new Topology);
+ ds >> *top_p;
+
+ sim_ptr->top_ = top_p;
+
+ sim_ptr->system_ = SystemCreator::Create(sim_ptr->top_,settings,
+ sim_ptr->system_force_mapper_);
+
+ sim_ptr->integrator_ = settings->integrator;
+
+ OpenMM::Platform::loadPluginsFromDirectory (settings->openmm_plugin_directory);
+ OpenMM::Platform* platform;
+
+ switch(settings->platform){
+ case Reference:{
+ platform = &OpenMM::Platform::getPlatformByName("Reference");
+ break;
+ }
+ case OpenCL:{
+ platform = &OpenMM::Platform::getPlatformByName("OpenCL");
+ break;
+ }
+ case CUDA:{
+ platform = &OpenMM::Platform::getPlatformByName("CUDA");
+ break;
+ }
+ case CPU:{
+ platform = &OpenMM::Platform::getPlatformByName("CPU");
+ break;
+ }
+ default:{
+ throw ost::Error("Invalid Platform when Loading simulation!");
+ }
+ }
+
+ sim_ptr->context_ = ContextPtr(new OpenMM::Context(*(sim_ptr->system_),
+ *(sim_ptr->integrator_),
+ *platform));
+
+ std::vector<OpenMM::Vec3> positions;
+ OpenMM::Vec3 open_mm_vec;
+ Real a,b,c;
+ for(int i = 0; i < sim_ptr->system_->getNumParticles(); ++i){
+ ds & a;
+ ds & b;
+ ds & c;
+ open_mm_vec[0] = a;
+ open_mm_vec[1] = b;
+ open_mm_vec[2] = c;
+ positions.push_back(open_mm_vec);
+ }
+ sim_ptr->context_->setPositions(positions);
+
+ uint num_chains;
+ uint num_residues;
+ uint num_atoms;
+ uint num_bonded_atoms;
+ Real x_pos;
+ Real y_pos;
+ Real z_pos;
+ Real bfac;
+ Real occ;
+ bool is_hetatm;
+ String chain_name;
+ String res_name;
+ int resnum_num;
+ char resnum_code;
+ String atom_name;
+ String atom_element;
+ uint atom_index;
+
+ ost::mol::EntityHandle ent = ost::mol::CreateEntity();
+ ost::mol::XCSEditor ed = ent.EditXCS();
+ ds & num_chains;
+ for(uint i = 0; i < num_chains; ++i){
+ ds & chain_name;
+ ds & num_residues;
+ ost::mol::ChainHandle chain = ed.InsertChain(chain_name);
+ for(uint j = 0; j < num_residues; ++j){
+ ds & res_name;
+ ds & resnum_num;
+ ds & resnum_code;
+ ds & num_atoms;
+ ost::mol::ResNum num(resnum_num,resnum_code);
+ ost::mol::ResidueHandle res = ed.AppendResidue(chain,res_name,num);
+ for(uint k = 0; k < num_atoms; ++k){
+ ds & atom_name;
+ ds & atom_element;
+ ds & x_pos;
+ ds & y_pos;
+ ds & z_pos;
+ ds & bfac;
+ ds & occ;
+ ds & is_hetatm;
+ geom::Vec3 pos(x_pos,y_pos,z_pos);
+ ed.InsertAtom(res,atom_name,pos,atom_element,occ,bfac,is_hetatm);
+ }
+ }
+ }
+ ost::mol::AtomHandleList atom_list = ent.GetAtomList();
+ for(uint i = 0; i < atom_list.size(); ++i){
+ ds & num_bonded_atoms;
+ for(uint j = 0; j < num_bonded_atoms; ++j){
+ ds & atom_index;
+ ed.Connect(atom_list[i],atom_list[atom_index]);
+ }
+ }
+
+ sim_ptr->ent_ = ent;
+
+ sim_ptr->context_->loadCheckpoint(stream);
+
+ return sim_ptr;
+}
+
+
+
+void Simulation::Init(const TopologyPtr top,
+ const SettingsPtr settings){
+
+
+ top_ = top;
+
+ if(!settings->integrator){
+ //user did not specify an integrator, so let's just use a standard integrator
+ settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.001));
+ }
+ integrator_ = settings->integrator;
+
+ system_ = SystemCreator::Create(top_,settings,system_force_mapper_);
+
+ //setting up the context, which combines the system with an integrator
+ //to proceed in time, but first we have to load the proper platform
+
+ OpenMM::Platform::loadPluginsFromDirectory (settings->openmm_plugin_directory);
+ OpenMM::Platform* platform;
+ std::map<String,String> context_properties;
+
+ switch(settings->platform){
+ case Reference:{
+ platform = &OpenMM::Platform::getPlatformByName("Reference");
+ for(PropertyMap::iterator i = settings->reference_properties.begin();
+ i != settings->reference_properties.end(); ++i){
+ context_properties[i->first] = i->second;
+ }
+ break;
+ }
+ case OpenCL:{
+ platform = &OpenMM::Platform::getPlatformByName("OpenCL");
+ for(PropertyMap::iterator i = settings->opencl_properties.begin();
+ i != settings->opencl_properties.end(); ++i){
+ context_properties[i->first] = i->second;
+ }
+ break;
+ }
+ case CUDA:{
+ platform = &OpenMM::Platform::getPlatformByName("CUDA");
+ for(PropertyMap::iterator i = settings->cuda_properties.begin();
+ i != settings->cuda_properties.end(); ++i){
+ context_properties[i->first] = i->second;
+ }
+ break;
+ }
+ case CPU:{
+ platform = &OpenMM::Platform::getPlatformByName("CPU");
+ for(PropertyMap::iterator i = settings->cpu_properties.begin();
+ i != settings->cpu_properties.end(); ++i){
+ context_properties[i->first] = i->second;
+ }
+ break;
+ }
+ default:{
+ throw ost::Error("Invalid platform encountered when settings up simualation!");
+ }
+ }
+
+ context_ = ContextPtr(new OpenMM::Context(*system_,*integrator_,*platform,context_properties));
+
+ ost::mol::AtomHandleList atom_list = ent_.GetAtomList();
+ std::vector<OpenMM::Vec3> positions;
+ geom::Vec3 ost_vec;
+ OpenMM::Vec3 open_mm_vec;
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i!=atom_list.end();++i){
+ ost_vec = i->GetPos();
+ open_mm_vec[0] = ost_vec[0]/10;
+ open_mm_vec[1] = ost_vec[1]/10;
+ open_mm_vec[2] = ost_vec[2]/10;
+ positions.push_back(open_mm_vec);
+ }
+
+ context_->setPositions(positions);
+
+ //make sure the context satisfies the distance constraints
+ context_->applyConstraints(0.00001);
+
+ if(settings->init_temperature > 0.0){
+ context_->setVelocitiesToTemperature(settings->init_temperature);
+ }
+}
+
+geom::Vec3List Simulation::GetPositions(bool enforce_periodic_box, bool in_angstrom){
+ geom::Vec3List return_vec;
+ StateExtractor::ExtractPositions(context_,return_vec, enforce_periodic_box, in_angstrom);
+ return return_vec;
+}
+
+geom::Vec3List Simulation::GetVelocities(){
+ geom::Vec3List return_vec;
+ StateExtractor::ExtractVelocities(context_, return_vec);
+ return return_vec;
+}
+
+geom::Vec3List Simulation::GetForces(){
+ geom::Vec3List return_vec;
+ StateExtractor::ExtractForces(context_, return_vec);
+ return return_vec;
+}
+
+void Simulation::SetPositions(const geom::Vec3List& positions, bool in_angstrom){
+ if(top_->GetNumParticles() != positions.size()){
+ throw ost::Error("Number of positions does not correspond to number of particles in topology!");
+ }
+ std::vector<OpenMM::Vec3> openmm_positions(top_->GetNumParticles());
+ OpenMM::Vec3* actual_pos = &openmm_positions[0];
+ if(in_angstrom){
+ for(geom::Vec3List::const_iterator i = positions.begin();
+ i != positions.end(); ++i){
+ (*actual_pos)[0] = (*i)[0]*0.1;
+ (*actual_pos)[1] = (*i)[1]*0.1;
+ (*actual_pos)[2] = (*i)[2]*0.1;
+ ++actual_pos;
+ }
+ }
+ else{
+ for(geom::Vec3List::const_iterator i = positions.begin();
+ i != positions.end(); ++i){
+ (*actual_pos)[0] = (*i)[0];
+ (*actual_pos)[1] = (*i)[1];
+ (*actual_pos)[2] = (*i)[2];
+ ++actual_pos;
+ }
+ }
+ context_->setPositions(openmm_positions);
+}
+
+void Simulation::SetVelocities(geom::Vec3List& velocities){
+ if(top_->GetNumParticles() != velocities.size()){
+ throw ost::Error("Number of velocities does not correspond to number of particles in topology!");
+ }
+ std::vector<OpenMM::Vec3> openmm_velocities(top_->GetNumParticles());
+ OpenMM::Vec3* actual_vel = &openmm_velocities[0];
+ for(geom::Vec3List::iterator i = velocities.begin();
+ i != velocities.end(); ++i){
+ (*actual_vel)[0] = (*i)[0];
+ (*actual_vel)[1] = (*i)[1];
+ (*actual_vel)[2] = (*i)[2];
+ ++actual_vel;
+ }
+ context_->setVelocities(openmm_velocities);
+}
+
+void Simulation::UpdatePositions(bool enforce_periodic_box){
+ if(top_->GetNumParticles() != static_cast<uint>(ent_.GetAtomCount())){
+ throw ost::Error("Num particles in topology and num atoms in entity are not consistent!");
+ }
+ geom::Vec3List positions = this->GetPositions(enforce_periodic_box, true);
+ ost::mol::XCSEditor ed = ent_.EditXCS(ost::mol::BUFFERED_EDIT);
+ ost::mol::AtomHandleList atom_list = ent_.GetAtomList();
+ ost::mol::AtomHandleList::iterator a = atom_list.begin();
+ ost::mol::AtomHandleList::iterator ae = atom_list.end();
+ geom::Vec3List::iterator v = positions.begin();
+ for(; a != ae; ++a, ++v){
+ ed.SetAtomPos(*a,*v);
+ }
+}
+
+bool Simulation::ApplySD(Real tolerance, int max_iterations){
+ return Steep::Minimize(*context_,tolerance, max_iterations);
+}
+
+void Simulation::ApplyLBFGS(Real tolerance, int max_iterations){
+ OpenMM::LocalEnergyMinimizer::minimize(*context_, tolerance, max_iterations);
+}
+
+void Simulation::Steps(int steps){
+
+ int time_to_next_notification;
+
+ while(steps > 0){
+ time_to_next_notification = this->TimeToNextNotification();
+ //we can just do the remaining steps and subtract them from
+ //time_to_notify_
+ if(steps < time_to_next_notification){
+ integrator_->step(steps);
+ for(std::vector<int>::iterator i = time_to_notify_.begin();
+ i != time_to_notify_.end(); ++i){
+ (*i) -= steps;
+ }
+ steps = 0;
+ }else{
+ integrator_->step(time_to_next_notification);
+ for(std::vector<int>::iterator i = time_to_notify_.begin();
+ i != time_to_notify_.end(); ++i){
+ (*i) -= time_to_next_notification;
+ }
+ for(uint i = 0; i < time_to_notify_.size(); ++i){
+ if(time_to_notify_[i] == 0){
+ observers_[i]->Notify();
+ time_to_notify_[i] = observers_[i]->Rhythm();
+ }
+ }
+ steps -= time_to_next_notification;
+ }
+ }
+}
+
+Real Simulation::GetEnergy(){
+ Real energy;
+ StateExtractor::ExtractEnergy(context_,energy);
+ return energy;
+}
+
+Real Simulation::GetKineticEnergy(){
+ Real energy;
+ StateExtractor::ExtractKineticEnergy(context_,energy);
+ return energy;
+}
+
+Real Simulation::GetPotentialEnergy(){
+ Real energy;
+ StateExtractor::ExtractPotentialEnergy(context_,energy);
+ return energy;
+}
+
+void Simulation::Register(ObserverPtr o){
+ observers_.push_back(o);
+ time_to_notify_.push_back(o->Rhythm());
+ o->Init(context_,top_,ent_);
+}
+
+int Simulation::TimeToNextNotification(){
+ if(observers_.empty()){
+ return std::numeric_limits<int>::max();
+ }
+ int minimal_time = std::numeric_limits<int>::max();
+ for(std::vector<int>::iterator i = time_to_notify_.begin();
+ i != time_to_notify_.end(); ++i){
+ if(*i < minimal_time){
+ minimal_time = *i;
+ }
+ }
+ return minimal_time;
+}
+
+void Simulation::ResetHarmonicBond(uint index, Real bond_length, Real force_constant){
+ if(system_force_mapper_.find(HarmonicBond) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic bond force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicBond];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::HarmonicBondForce* bond_force_ptr = reinterpret_cast<OpenMM::HarmonicBondForce*>(&force);
+ if(index >= uint(bond_force_ptr->getNumBonds())){
+ throw ost::Error("Provided bond index exceeds number of bonds!");
+ }
+ double dummy_one, dummy_two;
+ int particle1, particle2;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ bond_force_ptr->getBondParameters(index,particle1,particle2,dummy_one,dummy_two);
+ bond_force_ptr->setBondParameters(index,particle1,particle2,bond_length,force_constant);
+ bond_force_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicBondParameters(index,bond_length,force_constant);
+}
+
+void Simulation::ResetHarmonicAngle(uint index, Real angle, Real force_constant){
+ if(system_force_mapper_.find(HarmonicAngle) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic angle force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicAngle];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::HarmonicAngleForce* angle_force_ptr = reinterpret_cast<OpenMM::HarmonicAngleForce*>(&force);
+ if(index >= uint(angle_force_ptr->getNumAngles())){
+ throw ost::Error("Provided angle index exceeds number of angles!");
+ }
+ double dummy_one, dummy_two;
+ int particle1, particle2, particle3;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ angle_force_ptr->getAngleParameters(index,particle1,particle2,particle3,dummy_one,dummy_two);
+ angle_force_ptr->setAngleParameters(index,particle1,particle2,particle3,angle,force_constant);
+ angle_force_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicAngleParameters(index, angle, force_constant);
+}
+
+void Simulation::ResetUreyBradleyAngle(uint index, Real angle, Real angle_force_constant, Real bond_length, Real bond_force_constant){
+ if(system_force_mapper_.find(UreyBradleyAngle) == system_force_mapper_.end()){
+ throw ost::Error("There is no urey bradley angle force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[UreyBradleyAngle];
+ OpenMM::Force& angle_force = system_->getForce(force_index);
+ OpenMM::Force& bond_force = system_->getForce(force_index+1);
+
+ OpenMM::HarmonicAngleForce* angle_force_ptr = reinterpret_cast<OpenMM::HarmonicAngleForce*>(&angle_force);
+ OpenMM::HarmonicBondForce* bond_force_ptr = reinterpret_cast<OpenMM::HarmonicBondForce*>(&bond_force);
+ if(index >= uint(angle_force_ptr->getNumAngles())){
+ throw ost::Error("Provided angle index exceeds number of angles!");
+ }
+ double dummy_one, dummy_two;
+ int particle1, particle2, particle3;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ angle_force_ptr->getAngleParameters(index,particle1,particle2,particle3,dummy_one,dummy_two);
+ angle_force_ptr->setAngleParameters(index,particle1,particle2,particle3,angle,angle_force_constant);
+ bond_force_ptr->setBondParameters(index,particle1,particle3,bond_length,bond_force_constant);
+ angle_force_ptr->updateParametersInContext(*context_);
+ bond_force_ptr->updateParametersInContext(*context_);
+ top_->SetUreyBradleyAngleParameters(index,angle,angle_force_constant,bond_length,bond_force_constant);
+}
+
+void Simulation::ResetPeriodicDihedral(uint index, int multiplicity, Real phase, Real force_constant){
+ if(system_force_mapper_.find(PeriodicDihedral) == system_force_mapper_.end()){
+ throw ost::Error("There is no periodic dihedral force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[PeriodicDihedral];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::PeriodicTorsionForce* dihedral_force_ptr = reinterpret_cast<OpenMM::PeriodicTorsionForce*>(&force);
+ if(index >= uint(dihedral_force_ptr->getNumTorsions())){
+ throw ost::Error("Provided dihedral index exceeds number of dihedrals!");
+ }
+ int dummy_one;
+ double dummy_two, dummy_three;
+ int particle1, particle2, particle3, particle4;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ dihedral_force_ptr->getTorsionParameters(index,particle1,particle2,particle3,particle4,dummy_one,dummy_two,dummy_three);
+ dihedral_force_ptr->setTorsionParameters(index,particle1,particle2,particle3,particle4,multiplicity,phase,force_constant);
+ dihedral_force_ptr->updateParametersInContext(*context_);
+ top_->SetPeriodicDihedralParameters(index, multiplicity, phase, force_constant);
+}
+
+void Simulation::ResetPeriodicImproper(uint index, int multiplicity, Real phase, Real force_constant){
+ if(system_force_mapper_.find(PeriodicImproper) == system_force_mapper_.end()){
+ throw ost::Error("There is no periodic improper force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[PeriodicImproper];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::PeriodicTorsionForce* improper_ptr = reinterpret_cast<OpenMM::PeriodicTorsionForce*>(&force);
+ if(index >= uint(improper_ptr->getNumTorsions())){
+ throw ost::Error("Provided improper index exceeds number of impropers!");
+ }
+ int dummy_one;
+ double dummy_two, dummy_three;
+ int particle1, particle2, particle3, particle4;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ improper_ptr->getTorsionParameters(index,particle1,particle2,particle3,particle4,dummy_one,dummy_two,dummy_three);
+ improper_ptr->setTorsionParameters(index,particle1,particle2,particle3,particle4,multiplicity,phase,force_constant);
+ improper_ptr->updateParametersInContext(*context_);
+ top_->SetPeriodicImproperParameters(index, multiplicity, phase, force_constant);
+}
+
+void Simulation::ResetHarmonicImproper(uint index, Real phase, Real force_constant){
+ if(system_force_mapper_.find(HarmonicImproper) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic improper force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicImproper];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::CustomTorsionForce* improper_ptr = reinterpret_cast<OpenMM::CustomTorsionForce*>(&force);
+ if(index >= uint(improper_ptr->getNumTorsions())){
+ throw ost::Error("Provided improper index exceeds number of impropers!");
+ }
+ std::vector<double> parameters;
+ parameters.push_back(0.0);
+ parameters.push_back(0.0);
+ int particle1, particle2, particle3, particle4;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ improper_ptr->getTorsionParameters(index,particle1,particle2,particle3,particle4,parameters);
+ parameters[0] = phase;
+ parameters[1] = force_constant;
+ improper_ptr->setTorsionParameters(index,particle1,particle2,particle3,particle4,parameters);
+ improper_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicImproperParameters(index, phase, force_constant);
+}
+
+void Simulation::ResetLJPair(uint index, Real sigma, Real epsilon){
+ if(system_force_mapper_.find(LJ) == system_force_mapper_.end()){
+ throw ost::Error("There is no nonbonded force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[LJ];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::NonbondedForce* nonbonded_ptr = reinterpret_cast<OpenMM::NonbondedForce*>(&force);
+ if(index >= uint(nonbonded_ptr->getNumExceptions())){
+ throw ost::Error("Provided index exceeds number of defined pairs!");
+ }
+ double charge_prod, dummy_one, dummy_two;
+ int particle1, particle2;
+ //we know the parameters, but not the atom indices in the force object, we have to extract it from
+ //the force itself
+ nonbonded_ptr->getExceptionParameters(index,particle1,particle2,charge_prod,dummy_one,dummy_two);
+ nonbonded_ptr->setExceptionParameters(index,particle1,particle2,charge_prod,sigma,epsilon);
+ nonbonded_ptr->updateParametersInContext(*context_);
+ top_->SetLJPairParameters(index, sigma, epsilon);
+}
+
+void Simulation::ResetDistanceConstraint(uint index, Real constraint_length){
+ if(index >= uint(system_->getNumConstraints())){
+ throw ost::Error("Provided index exceeds number of defined constraints!");
+ }
+ double dummy;
+ int particle1, particle2;
+ system_->getConstraintParameters(index,particle1,particle2,dummy);
+ system_->setConstraintParameters(index,particle1,particle2,constraint_length);
+ context_->reinitialize();
+ top_->SetDistanceConstraintParameters(index, constraint_length);
+}
+
+void Simulation::AddPositionConstraint(uint index){
+ if(index >= top_->GetNumParticles()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ system_->setParticleMass(index,0.0);
+ context_->reinitialize();
+ top_->AddPositionConstraint(index);
+}
+
+void Simulation::AddPositionConstraints(const std::vector<uint>& index){
+
+ for(std::vector<uint>::const_iterator i = index.begin();
+ i != index.end(); ++i){
+ if(*i >= top_->GetNumParticles()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ system_->setParticleMass(*i,0.0);
+ top_->AddPositionConstraint(*i);
+ }
+ context_->reinitialize();
+}
+
+void Simulation::ResetPositionConstraints(){
+ std::vector<Real> original_masses = top_->GetMasses();
+ for(uint i = 0; i < original_masses.size(); ++i){
+ system_->setParticleMass(i,original_masses[i]);
+ }
+ top_->ResetPositionConstraints();
+ context_->reinitialize();
+}
+
+void Simulation::ResetHarmonicPositionRestraint(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale, Real y_scale, Real z_scale){
+ if(index >= uint(top_->GetNumHarmonicPositionRestraints())){
+ throw ost::Error("Provided index exceeds number of defined harmonic position restraints!");
+ }
+ if(system_force_mapper_.find(HarmonicPositionRestraint) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic position restraint in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicPositionRestraint];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::CustomExternalForce* restraint_ptr = reinterpret_cast<OpenMM::CustomExternalForce*>(&force);
+ if(index >= uint(restraint_ptr->getNumParticles())){
+ throw ost::Error("Provided index exceeds number of defined harmonic position restraints!");
+ }
+ int particle;
+ std::vector<double> parameters;
+ restraint_ptr->getParticleParameters(index,particle,parameters);
+ parameters[0] = ref_position[0];
+ parameters[1] = ref_position[1];
+ parameters[2] = ref_position[2];
+ parameters[3] = k;
+ parameters[4] = x_scale;
+ parameters[5] = y_scale;
+ parameters[6] = z_scale;
+ restraint_ptr->setParticleParameters(index,particle,parameters);
+ restraint_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicPositionRestraintParameters(index,ref_position,k,x_scale,y_scale,z_scale);
+}
+
+void Simulation::ResetHarmonicDistanceRestraint(uint index, Real length, Real force_constant){
+ if(index >= top_->GetNumHarmonicDistanceRestraints()){
+ throw ost::Error("Provided index exceeds number of defined harmonic distance restraints!");
+ }
+ if(system_force_mapper_.find(HarmonicDistanceRestraint) == system_force_mapper_.end()){
+ throw ost::Error("There is no harmonic distance restraint in the simulation!");
+ }
+ uint force_index = system_force_mapper_[HarmonicDistanceRestraint];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::HarmonicBondForce* restraint_ptr = reinterpret_cast<OpenMM::HarmonicBondForce*>(&force);
+ if(index >= uint(restraint_ptr->getNumBonds())){
+ throw ost::Error("Provided index exceeds number of defined harmonic distance restraints!");
+ }
+ int particle_one,particle_two;
+ double dummy_one, dummy_two;
+ restraint_ptr->getBondParameters(int(index),particle_one,particle_two,dummy_one,dummy_two);
+ restraint_ptr->setBondParameters(int(index),particle_one,particle_two,length,2*force_constant);
+ restraint_ptr->updateParametersInContext(*context_);
+ top_->SetHarmonicDistanceRestraintParameters(index,length,force_constant);
+}
+
+void Simulation::ResetLJ(uint index, Real sigma, Real epsilon){
+ if(index >= top_->GetNumParticles()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ if(system_force_mapper_.find(LJ) == system_force_mapper_.end()){
+ throw ost::Error("There is no nonbonded force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[LJ];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::NonbondedForce* nonbonded_ptr = reinterpret_cast<OpenMM::NonbondedForce*>(&force);
+
+ double charge, dummy_one, dummy_two;
+
+ nonbonded_ptr->getParticleParameters(index,charge,dummy_one,dummy_two);
+ nonbonded_ptr->setParticleParameters(index,charge,sigma,epsilon);
+ nonbonded_ptr->updateParametersInContext(*context_);
+ top_->SetSigma(index, sigma);
+ top_->SetEpsilon(index, epsilon);
+}
+
+void Simulation::ResetGBSA(uint index, Real radius, Real scaling){
+ if(index >= top_->GetNumParticles()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ if(system_force_mapper_.find(GBSA) == system_force_mapper_.end()){
+ throw ost::Error("There is no gbsa force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[GBSA];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::GBSAOBCForce* gbsa_ptr = reinterpret_cast<OpenMM::GBSAOBCForce*>(&force);
+
+ double charge, dummy_one, dummy_two;
+
+ gbsa_ptr->getParticleParameters(index,charge,dummy_one,dummy_two);
+ gbsa_ptr->setParticleParameters(index,charge,radius,scaling);
+ gbsa_ptr->updateParametersInContext(*context_);
+ top_->SetGBSARadius(index, radius);
+ top_->SetOBCScaling(index, scaling);
+}
+
+void Simulation::ResetCharge(uint index, Real charge){
+ if(index >= top_->GetNumParticles()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ if(system_force_mapper_.find(LJ) == system_force_mapper_.end()){
+ throw ost::Error("There is no nonbonded force in the simulation!");
+ }
+ uint force_index = system_force_mapper_[LJ];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::NonbondedForce* nonbonded_ptr = reinterpret_cast<OpenMM::NonbondedForce*>(&force);
+
+ double dummy, sigma, epsilon;
+
+ //first update the parameters of the single particle
+ nonbonded_ptr->getParticleParameters(index,dummy,sigma,epsilon);
+ nonbonded_ptr->setParticleParameters(index,charge,sigma,epsilon);
+
+ //the charge product has to be updated in the exceptions (1,4 interactions)
+ std::vector<uint> lj_pair_indices = top_->GetLJPairIndices(index);
+ Real old_charge = top_->GetCharge(index);
+ double charge_prod;
+ Real new_charge_prod;
+ int particle_one, particle_two;
+
+ for(std::vector<uint>::iterator i = lj_pair_indices.begin();
+ i != lj_pair_indices.end(); ++i){
+ nonbonded_ptr->getExceptionParameters(*i,particle_one,particle_two,charge_prod,sigma,epsilon);
+ new_charge_prod = charge_prod/old_charge*charge; // fudge_qq * q1 * q2
+ nonbonded_ptr->setExceptionParameters(*i,particle_one,particle_two,new_charge_prod,sigma,epsilon);
+ }
+
+ nonbonded_ptr->updateParametersInContext(*context_);
+ top_->SetCharge(index, charge);
+
+ //the charge also affects gbsa force...
+ if(system_force_mapper_.find(GBSA) != system_force_mapper_.end()){
+ force_index = system_force_mapper_[GBSA];
+ OpenMM::Force& force = system_->getForce(force_index);
+ OpenMM::GBSAOBCForce* gbsa_ptr = reinterpret_cast<OpenMM::GBSAOBCForce*>(&force);
+
+ double radius,scaling;
+
+ gbsa_ptr->getParticleParameters(index,dummy,radius,scaling);
+ gbsa_ptr->setParticleParameters(index,charge,radius,scaling);
+ gbsa_ptr->updateParametersInContext(*context_);
+ }
+}
+
+void Simulation::ResetMass(uint index, Real mass){
+ if(index >= top_->GetNumParticles()){
+ throw ost::Error("Provided index exceeds number of atoms!");
+ }
+ system_->setParticleMass(index,mass);
+ context_->reinitialize();
+ top_->SetMass(index,mass);
+}
+
+geom::Vec3 Simulation::GetPeriodicBoxExtents(){
+ geom::Vec3 vec;
+ OpenMM::Vec3 ucell_a, ucell_b, ucell_c;
+ OpenMM::State openmm_state = context_->getState(0); //create minimal state
+ //to only extract periodic
+ //box information
+ openmm_state.getPeriodicBoxVectors(ucell_a,ucell_b,ucell_c);
+ vec[0] = 10 * sqrt(ucell_a.dot(ucell_a));
+ vec[1] = 10 * sqrt(ucell_a.dot(ucell_b));
+ vec[2] = 10 * sqrt(ucell_a.dot(ucell_c));
+ return vec;
+}
+
+void Simulation::SetPeriodicBoxExtents(geom::Vec3& vec){
+ OpenMM::Vec3 ucell_a(vec[0]/10.0,0.0,0.0);
+ OpenMM::Vec3 ucell_b(0.0,vec[1]/10.0,0.0);
+ OpenMM::Vec3 ucell_c(0.0,0.0,vec[2]/10.0);
+ context_->setPeriodicBoxVectors(ucell_a,ucell_b,ucell_c);
+}
+
+}}}
+
diff --git a/modules/mol/mm/src/simulation.hh b/modules/mol/mm/src/simulation.hh
new file mode 100644
index 0000000000000000000000000000000000000000..9abe038bdf533ffcf788210198f18edf094617a1
--- /dev/null
+++ b/modules/mol/mm/src/simulation.hh
@@ -0,0 +1,160 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_SIMULATION_HH
+#define OST_MM_SIMULATION_HH
+
+#include <vector>
+#include <map>
+
+#include <ost/mol/mol.hh>
+#include <ost/mol/mm/system_creator.hh>
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/topology_creator.hh>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/modeller.hh>
+#include <ost/geom/vec3.hh>
+#include <ost/mol/mm/observer.hh>
+#include <ost/mol/mm/state_extractor.hh>
+#include <ost/mol/mm/steep.hh>
+
+#include <time.h>
+
+namespace OpenMM{
+ class Integrator;
+ class Context;//hacky way of telling the Context and Integrator
+ //are around.
+ //will be included in source file to avoid
+ //dependencies on external libraries
+}
+
+namespace ost { namespace mol{ namespace mm{
+
+class Simulation;
+
+typedef boost::shared_ptr<OpenMM::Integrator> IntegratorPtr;
+typedef boost::shared_ptr<OpenMM::Context> ContextPtr;
+typedef boost::shared_ptr<Simulation> SimulationPtr;
+
+class Simulation {
+
+public:
+
+ Simulation(const ost::mol::EntityHandle& handle,
+ const SettingsPtr settings);
+
+ Simulation(const ost::mol::mm::TopologyPtr top,
+ const ost::mol::EntityHandle& handle,
+ const SettingsPtr settings);
+
+ void Save(const String& filename);
+
+ static SimulationPtr Load(const String& filename, SettingsPtr settings);
+
+ ost::mol::EntityHandle GetEntity() { return ent_; }
+
+ geom::Vec3List GetPositions(bool enforce_periodic_box = false, bool in_angstrom = true);
+
+ geom::Vec3List GetVelocities();
+
+ geom::Vec3List GetForces();
+
+ void SetPositions(const geom::Vec3List& positions, bool in_angstrom = true);
+
+ void SetVelocities(geom::Vec3List& velocities);
+
+ void UpdatePositions(bool enforce_periodic_box = false);
+
+ bool ApplySD(Real tolerance = 100, int max_iterations = 1000);
+
+ void ApplyLBFGS(Real tolerance = 1, int max_iterations = 1000);
+
+ Real GetEnergy();
+
+ Real GetPotentialEnergy();
+
+ Real GetKineticEnergy();
+
+ TopologyPtr GetTopology() { return top_; }
+
+ void Steps(int steps);
+
+ void Register(ObserverPtr o);
+
+ void ResetHarmonicBond(uint index, Real bond_length, Real force_constant);
+
+ void ResetHarmonicAngle(uint index, Real angle, Real force_constant);
+
+ void ResetUreyBradleyAngle(uint index, Real angle, Real angle_force_constant, Real bond_length, Real bond_force_constant);
+
+ void ResetPeriodicDihedral(uint index, int multiplicity, Real phase, Real force_constant);
+
+ void ResetPeriodicImproper(uint index, int multiplicity, Real phase, Real force_constant);
+
+ void ResetHarmonicImproper(uint index, Real phase, Real force_constant);
+
+ void ResetLJPair(uint index, Real sigma, Real epsilon);
+
+ void ResetDistanceConstraint(uint index, Real constraint_length);
+
+ void ResetHarmonicPositionRestraint(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale = 1.0, Real y_scale = 1.0, Real z_scale = 1.0);
+
+ void ResetHarmonicDistanceRestraint(uint index, Real length, Real force_constant);
+
+ void ResetLJ(uint index, Real sigma, Real epsilon);
+
+ void ResetGBSA(uint index, Real radius, Real scaling);
+
+ void ResetCharge(uint index, Real charge);
+
+ void ResetMass(uint index, Real mass);
+
+ void AddPositionConstraint(uint index);
+
+ void AddPositionConstraints(const std::vector<uint>& index);
+
+ void ResetPositionConstraints();
+
+ geom::Vec3 GetPeriodicBoxExtents();
+
+ void SetPeriodicBoxExtents(geom::Vec3& vec);
+
+private:
+
+ Simulation() { } //hidden constructor...
+
+ void Init(const ost::mol::mm::TopologyPtr top,
+ const SettingsPtr settings);
+
+ int TimeToNextNotification();
+
+ SystemPtr system_;
+ IntegratorPtr integrator_;
+ ContextPtr context_;
+ TopologyPtr top_;
+ std::vector<ObserverPtr> observers_;
+ std::vector<int> time_to_notify_;
+ std::map<FuncType,uint> system_force_mapper_;
+ ost::mol::EntityHandle ent_;
+};
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/state_extractor.cc b/modules/mol/mm/src/state_extractor.cc
new file mode 100644
index 0000000000000000000000000000000000000000..478174f7f37cb9ac591094c5a0d0fab70807e34e
--- /dev/null
+++ b/modules/mol/mm/src/state_extractor.cc
@@ -0,0 +1,88 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/state_extractor.hh>
+#include <OpenMM.h>
+
+namespace ost { namespace mol{ namespace mm{
+
+void StateExtractor::ExtractPotentialEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy){
+
+ OpenMM::State s = context->getState(OpenMM::State::Energy);
+ energy = s.getPotentialEnergy();
+}
+
+void StateExtractor::ExtractKineticEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy){
+
+ OpenMM::State s = context->getState(OpenMM::State::Energy);
+ energy = s.getKineticEnergy();
+}
+
+void StateExtractor::ExtractEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy){
+
+ OpenMM::State s = context->getState(OpenMM::State::Energy);
+ energy = s.getKineticEnergy() + s.getPotentialEnergy();
+}
+
+void StateExtractor::ExtractPositions(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& positions, bool enforce_periodic_box,
+ bool in_angstrom){
+
+ positions.resize(context->getSystem().getNumParticles());
+ OpenMM::State s = context->getState(OpenMM::State::Positions, enforce_periodic_box);
+ const std::vector<OpenMM::Vec3>& p = s.getPositions();
+ int actual_index = 0;
+ for(std::vector<OpenMM::Vec3>::const_iterator i = p.begin(); i != p.end(); ++i){
+ positions[actual_index] = geom::Vec3((*i)[0],(*i)[1],(*i)[2]);
+ ++actual_index;
+ }
+ if(in_angstrom) positions*=10.0;
+}
+
+void StateExtractor::ExtractVelocities(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& velocities){
+
+ velocities.resize(context->getSystem().getNumParticles());
+ OpenMM::State s = context->getState(OpenMM::State::Velocities);
+ const std::vector<OpenMM::Vec3>& v = s.getVelocities();
+ int actual_index = 0;
+ for(std::vector<OpenMM::Vec3>::const_iterator i = v.begin(); i != v.end(); ++i){
+ velocities[actual_index] = geom::Vec3((*i)[0],(*i)[1],(*i)[2]);
+ ++actual_index;
+ }
+}
+
+void StateExtractor::ExtractForces(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& forces){
+
+ forces.resize(context->getSystem().getNumParticles());
+ OpenMM::State s = context->getState(OpenMM::State::Forces);
+ const std::vector<OpenMM::Vec3>& f = s.getForces();
+ int actual_index = 0;
+ for(std::vector<OpenMM::Vec3>::const_iterator i = f.begin(); i != f.end(); ++i){
+ forces[actual_index] = geom::Vec3((*i)[0],(*i)[1],(*i)[2]);
+ ++actual_index;
+ }
+}
+
+
+}}} //ns
diff --git a/modules/mol/mm/src/state_extractor.hh b/modules/mol/mm/src/state_extractor.hh
new file mode 100644
index 0000000000000000000000000000000000000000..38ecece645c0e343ce5812d3379ecbafa53a9290
--- /dev/null
+++ b/modules/mol/mm/src/state_extractor.hh
@@ -0,0 +1,66 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_STATE_EXTRACTOR_HH
+#define OST_MM_STATE_EXTRACTOR_HH
+
+#include <vector>
+
+#include <boost/shared_ptr.hpp>
+#include <ost/geom/vec3.hh>
+
+namespace OpenMM{
+ class Context; //hacky way of telling the Context is around.
+ //will be included in source file to avoid
+ //dependencies on external libraries
+
+}
+
+namespace ost { namespace mol{ namespace mm{
+
+class StateExtractor{
+
+public:
+
+ static void ExtractPotentialEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy);
+
+ static void ExtractKineticEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy);
+
+ static void ExtractEnergy(boost::shared_ptr<OpenMM::Context> context,
+ Real& energy);
+
+ static void ExtractPositions(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& positions,
+ bool enforce_periodic_box = false,
+ bool in_angstrom = true);
+
+ static void ExtractVelocities(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& velocities);
+
+ static void ExtractForces(boost::shared_ptr<OpenMM::Context> context,
+ geom::Vec3List& forces);
+
+};
+
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/steep.cc b/modules/mol/mm/src/steep.cc
new file mode 100644
index 0000000000000000000000000000000000000000..94d987d2c7ee8d568f51cb3a469a614ab0bfae72
--- /dev/null
+++ b/modules/mol/mm/src/steep.cc
@@ -0,0 +1,92 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/steep.hh>
+#include <OpenMM.h>
+
+namespace ost{ namespace mol{ namespace mm{
+
+bool Steep::Minimize(OpenMM::Context& context, double tolerance, uint max_iterations) {
+ const OpenMM::System& system = context.getSystem();
+ if(system.getNumConstraints() > 0){
+ throw ost::Error("Cannot handle constraints in steepest descent, use lbgfs instead!");
+ }
+ if( tolerance <= 0.0 ){
+ throw ost::Error("tolerance value must be greater 0.0!"); //also important to avoid zero division error when calculating normalization factor for forces
+ }
+
+ bool converged = false;
+
+ OpenMM::State state = context.getState(OpenMM::State::Energy | OpenMM::State::Forces | OpenMM::State::Positions);
+ std::vector<OpenMM::Vec3> positions = state.getPositions();
+ std::vector<OpenMM::Vec3> new_positions = positions;
+ std::vector<OpenMM::Vec3> normalized_forces = state.getForces();
+ double energy = state.getPotentialEnergy();
+ double h = 0.01;
+ double new_energy,max_length,factor;
+ bool normalize_forces = true;
+ std::vector<uint> non_zero_mass_particles;
+ for(int i = 0; i < system.getNumParticles(); ++i){
+ if(system.getParticleMass(i) != 0){
+ non_zero_mass_particles.push_back(i);
+ }
+ }
+ for(uint i = 0; i < max_iterations; ++i){
+ if(normalize_forces){
+ const std::vector<OpenMM::Vec3>& forces = state.getForces();
+ max_length = 0.0;
+ for(std::vector<uint>::iterator j = non_zero_mass_particles.begin();
+ j != non_zero_mass_particles.end(); ++j){
+ normalized_forces[*j] = forces[*j];
+ max_length = std::max(max_length,forces[*j].dot(forces[*j]));
+ }
+ max_length = sqrt(max_length);
+ if(max_length <= tolerance){
+ converged = true;
+ break;
+ }
+ factor = 1.0/max_length;
+ for(std::vector<uint>::iterator j = non_zero_mass_particles.begin();
+ j != non_zero_mass_particles.end(); ++j){
+ normalized_forces[*j] *= factor;
+ }
+ }
+ for(std::vector<uint>::iterator j = non_zero_mass_particles.begin();
+ j != non_zero_mass_particles.end(); ++j){
+ new_positions[*j] = positions[*j] + normalized_forces[*j] * h;
+ }
+ context.setPositions(new_positions);
+ //context.computeVirtualSites();
+ state = context.getState(OpenMM::State::Forces | OpenMM::State::Energy);
+ new_energy = state.getPotentialEnergy();
+ if(new_energy < energy){
+ std::swap(positions,new_positions);
+ energy = new_energy;
+ h *= 1.2;
+ normalize_forces = true;
+ }
+ else {
+ h *= 0.5;
+ normalize_forces = false;
+ }
+ }
+ context.setPositions(positions);
+ return converged;
+}
+}}}//ns
diff --git a/modules/mol/mm/src/steep.hh b/modules/mol/mm/src/steep.hh
new file mode 100644
index 0000000000000000000000000000000000000000..1d58267104a74be5ddece2b2c8c03bafd285c254
--- /dev/null
+++ b/modules/mol/mm/src/steep.hh
@@ -0,0 +1,49 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_STEEP_HH
+#define OST_MM_STEEP_HH
+
+#include <ost/base.hh>
+#include <cmath>
+#include <sstream>
+#include <vector>
+#include <iostream>
+#include <cstdio>
+#include <ctime>
+
+#include <ost/message.hh>
+
+namespace OpenMM{
+ class Context; //hacky way of telling the Context is around.
+ //will be included in source file to avoid
+ //dependencies on external libraries
+}
+
+namespace ost { namespace mol { namespace mm{
+
+
+class Steep {
+public:
+ static bool Minimize(OpenMM::Context& context, double tolerance = 100, uint maxIterations = 1000);
+};
+
+}}}
+
+#endif
diff --git a/modules/mol/mm/src/system_creator.cc b/modules/mol/mm/src/system_creator.cc
new file mode 100644
index 0000000000000000000000000000000000000000..2912a5dcab88240f5d0c254bcc4659aa3ba922af
--- /dev/null
+++ b/modules/mol/mm/src/system_creator.cc
@@ -0,0 +1,442 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/system_creator.hh>
+#include <OpenMM.h>
+
+namespace ost{ namespace mol{ namespace mm{
+
+SystemPtr SystemCreator::Create(const TopologyPtr top,
+ const SettingsPtr settings,
+ std::map<FuncType,uint>& mapper){
+
+ uint mapper_index = 0;
+
+ SystemPtr sys(new OpenMM::System);
+
+ //add particles to the system
+ std::vector<Real> masses = top->GetMasses();
+
+ //set masses of position constraints to zero
+ const std::vector<uint>& position_constraints = top->GetPositionConstraints();
+ if(!position_constraints.empty()){
+ for(std::vector<uint>::const_iterator i = position_constraints.begin();
+ i != position_constraints.end(); ++i){
+ masses[*i] = 0.0;
+ }
+ }
+
+ for(std::vector<Real>::iterator i = masses.begin(); i != masses.end(); ++i){
+ sys->addParticle(*i);
+ }
+
+ //parameters of all added interactions will temporarily be stored in here
+ std::vector<Real> parameters;
+
+ const std::vector<std::pair<Index<2>,std::vector<Real> > >& harmonic_bonds = top->GetHarmonicBonds();
+ if(!harmonic_bonds.empty()){
+ OpenMM::HarmonicBondForce& harmonic_bond_force = *new OpenMM::HarmonicBondForce();
+ sys->addForce(&harmonic_bond_force);
+ mapper[HarmonicBond] = mapper_index++;
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = harmonic_bonds.begin();
+ i != harmonic_bonds.end(); ++i){
+ harmonic_bond_force.addBond(i->first[0],i->first[1],i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& harmonic_angles = top->GetHarmonicAngles();
+ if(!harmonic_angles.empty()){
+ OpenMM::HarmonicAngleForce& harmonic_angle_force = *new OpenMM::HarmonicAngleForce();
+ sys->addForce(&harmonic_angle_force);
+ mapper[HarmonicAngle] = mapper_index++;
+ for(std::vector<std::pair<Index<3>,std::vector<Real> > >::const_iterator i = harmonic_angles.begin();
+ i != harmonic_angles.end(); ++i){
+ harmonic_angle_force.addAngle(i->first[0],i->first[1],i->first[2],
+ i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<3>,std::vector<Real> > >& urey_bradley_angles = top->GetUreyBradleyAngles();
+ if(!urey_bradley_angles.empty()){
+ //urey bradley is a mixture between a harmonic angle and harmonic bond term,
+ //that gets split up
+ OpenMM::HarmonicAngleForce& urey_angle_force = *new OpenMM::HarmonicAngleForce();
+ OpenMM::HarmonicBondForce& urey_bond_force = *new OpenMM::HarmonicBondForce();
+ sys->addForce(&urey_angle_force);
+ sys->addForce(&urey_bond_force);
+ mapper[UreyBradleyAngle] = mapper_index++;
+ ++mapper_index;
+ for(std::vector<std::pair<Index<3>,std::vector<Real> > >::const_iterator i = urey_bradley_angles.begin();
+ i != urey_bradley_angles.end(); ++i){
+ urey_angle_force.addAngle(i->first[0],i->first[1],i->first[2],
+ i->second[0],i->second[1]);
+ urey_bond_force.addBond(i->first[0],i->first[2],i->second[2],i->second[3]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>,std::vector<Real> > >& periodic_dihedrals = top->GetPeriodicDihedrals();
+ if(!periodic_dihedrals.empty()){
+ OpenMM::PeriodicTorsionForce& periodic_torsion_force = *new OpenMM::PeriodicTorsionForce();
+ sys->addForce(&periodic_torsion_force);
+ mapper[PeriodicDihedral] = mapper_index++;
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::const_iterator i = periodic_dihedrals.begin();
+ i != periodic_dihedrals.end(); ++i){
+ periodic_torsion_force.addTorsion(i->first[0],i->first[1],i->first[2],i->first[3],
+ i->second[0],i->second[1],i->second[2]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>,std::vector<Real> > >& periodic_impropers = top->GetPeriodicImpropers();
+ if(!periodic_impropers.empty()){
+ OpenMM::PeriodicTorsionForce& periodic_improper_force = *new OpenMM::PeriodicTorsionForce();
+ sys->addForce(&periodic_improper_force);
+ mapper[PeriodicImproper] = mapper_index++;
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::const_iterator i = periodic_impropers.begin();
+ i != periodic_impropers.end(); ++i){
+ periodic_improper_force.addTorsion(i->first[0],i->first[1],i->first[2],i->first[3],
+ i->second[0],i->second[1],i->second[2]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>,std::vector<Real> > >& harmonic_impropers = top->GetHarmonicImpropers();
+ if(!harmonic_impropers.empty()){
+ std::vector<double> custom_parameters;
+ custom_parameters.push_back(0.0);
+ custom_parameters.push_back(0.0);
+ OpenMM::CustomTorsionForce& harmonic_improper_force = *new OpenMM::CustomTorsionForce("0.5*k*(theta-b)^2");
+ harmonic_improper_force.addPerTorsionParameter("b");
+ harmonic_improper_force.addPerTorsionParameter("k");
+ sys->addForce(&harmonic_improper_force);
+ mapper[HarmonicImproper] = mapper_index++;
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::const_iterator i = harmonic_impropers.begin();
+ i != harmonic_impropers.end(); ++i){
+ custom_parameters[0] = i->second[0];
+ custom_parameters[1] = i->second[1];
+ harmonic_improper_force.addTorsion(i->first[0],i->first[1],i->first[2],i->first[3],
+ custom_parameters);
+ }
+ }
+
+ const std::vector<std::pair<Index<5>,std::vector<Real> > >& cmaps = top->GetCMaps();
+ if(!cmaps.empty()){
+ std::vector<std::vector<Real> > unique_cmap_parameters;
+ std::vector<Real> current_parameters;
+ std::vector<int> map_indices;
+ bool cmap_present;
+
+ for(std::vector<std::pair<Index<5>,std::vector<Real> > >::const_iterator i = cmaps.begin();
+ i != cmaps.end(); ++i){
+ cmap_present = false;
+ current_parameters = i->second;
+ for(uint j = 0; j < unique_cmap_parameters.size(); ++j){
+ if(current_parameters == unique_cmap_parameters[j]){
+ cmap_present = true;
+ map_indices.push_back(j);
+ break;
+ }
+ }
+ if(!cmap_present){
+ unique_cmap_parameters.push_back(current_parameters);
+ map_indices.push_back(unique_cmap_parameters.size()-1);
+ }
+ }
+
+ OpenMM::CMAPTorsionForce& cmap_force = *new OpenMM::CMAPTorsionForce();
+ sys->addForce(&cmap_force);
+ mapper[CMap] = mapper_index++;
+
+ for(std::vector<std::vector<Real> >::iterator u_cmap = unique_cmap_parameters.begin();
+ u_cmap != unique_cmap_parameters.end(); ++u_cmap){
+ uint size = sqrt(u_cmap->size());
+ if(size * size != u_cmap->size()){
+ throw ost::Error("Expect cmap to be quadratic!");
+ }
+
+ //in charmm/gromacs the cmap has the following order regarding angle bins:
+ //(phi1,psi1),(phi1,psi2)...
+ //openmm requires following order:
+ //(phi1,psi1),(phi2,psi1)...
+
+ //in charmm/gromacs the range of the angles in the map is [-180,180],[-pi,pi]
+ //respectively
+ //openmm requires the range to be [0,2pi], the map has to be shifted...
+
+ //=>we need basically two "transformation"
+
+ std::vector<double> transformed_map;
+ for(uint i = 0; i < size; ++i){
+ for(uint j = 0; j < size; ++j){
+ transformed_map.push_back((*u_cmap)[size*((j+size/2)%size) + ((i+size/2)%size)]);
+ }
+ }
+ cmap_force.addMap(size, transformed_map);
+ }
+
+ //add the cmaps
+ int atom1,atom2,atom3,atom4,atom5;
+ for(uint i = 0; i < cmaps.size(); ++i){
+ atom1 = cmaps[i].first[0];
+ atom2 = cmaps[i].first[1];
+ atom3 = cmaps[i].first[2];
+ atom4 = cmaps[i].first[3];
+ atom5 = cmaps[i].first[4];
+ cmap_force.addTorsion(map_indices[i],atom1,atom2,atom3,atom4,atom2,atom3,atom4,atom5);
+ }
+ }
+
+ const std::vector<std::pair<Index<1>,std::vector<Real> > >& harmonic_position_restraints = top->GetHarmonicPositionRestraints();
+ if(!harmonic_position_restraints.empty()){
+ OpenMM::CustomExternalForce& position_restraint_force = *new OpenMM::CustomExternalForce("k_force*(x_scale*(x-x0)^2+y_scale*(y-y0)^2+z_scale*(z-z0)^2)");
+ position_restraint_force.addPerParticleParameter("x0");
+ position_restraint_force.addPerParticleParameter("y0");
+ position_restraint_force.addPerParticleParameter("z0");
+ position_restraint_force.addPerParticleParameter("k_force");
+ position_restraint_force.addPerParticleParameter("x_scale");
+ position_restraint_force.addPerParticleParameter("y_scale");
+ position_restraint_force.addPerParticleParameter("z_scale");
+ sys->addForce(&position_restraint_force);
+ mapper[HarmonicPositionRestraint] = mapper_index++;
+ for(std::vector<std::pair<Index<1>,std::vector<Real> > >::const_iterator i = harmonic_position_restraints.begin();
+ i != harmonic_position_restraints.end(); ++i){
+ //stupid cast
+ std::vector<double> parameters;
+ for(std::vector<Real>::const_iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ parameters.push_back(*j);
+ }
+ position_restraint_force.addParticle(i->first[0], parameters);
+ }
+ }
+
+ const std::vector<std::pair<Index<2>,std::vector<Real> > > harmonic_distance_restraints = top->GetHarmonicDistanceRestraints();
+ if(!harmonic_distance_restraints.empty()){
+ OpenMM::HarmonicBondForce& harmonic_distance_restraint_force = *new OpenMM::HarmonicBondForce();
+ sys->addForce(&harmonic_distance_restraint_force);
+ mapper[HarmonicDistanceRestraint] = mapper_index++;
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = harmonic_distance_restraints.begin();
+ i != harmonic_distance_restraints.end(); ++i){
+ //note, that the restraint formula is k(b-b0)^2 instead of 1/2*k(b-b0)^2 => multiply by two!
+ harmonic_distance_restraint_force.addBond(i->first[0],i->first[1],i->second[0],2*i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<2>,std::vector<Real> > > fgmd_hbond_donors = top->GetFGMDHBondDonors();
+ const std::vector<Index<2> > fgmd_hbond_acceptors = top->GetFGMDHBondAcceptors();
+ if(!fgmd_hbond_donors.empty() && !fgmd_hbond_acceptors.empty()){
+ String distance_term = "k_length*(distance(a1,d1)-k_length)^2";
+ String alpha_term = "k_alpha*(angle(d2,d1,a1)-alpha)^2";
+ String beta_term = "k_beta*(angle(d1,a1,a2)-beta)^2";
+ String f = distance_term + "+" + alpha_term + "+" + beta_term;
+ OpenMM::CustomHbondForce& fgmd_hbond_force = *new OpenMM::CustomHbondForce(f);
+
+ fgmd_hbond_force.addPerDonorParameter("length");
+ fgmd_hbond_force.addPerDonorParameter("k_length");
+ fgmd_hbond_force.addPerDonorParameter("alpha");
+ fgmd_hbond_force.addPerDonorParameter("k_alpha");
+ fgmd_hbond_force.addPerDonorParameter("beta");
+ fgmd_hbond_force.addPerDonorParameter("k_beta");
+
+ fgmd_hbond_force.setCutoffDistance(3.0);
+ fgmd_hbond_force.setNonbondedMethod(OpenMM::CustomHbondForce::CutoffPeriodic);
+
+ switch(settings->nonbonded_method){
+ case NoCutoff:{
+ fgmd_hbond_force.setNonbondedMethod(OpenMM::CustomHbondForce::NoCutoff);
+ break;
+ }
+ case CutoffNonPeriodic:{
+ fgmd_hbond_force.setNonbondedMethod(OpenMM::CustomHbondForce::CutoffNonPeriodic);
+ break;
+ }
+ case CutoffPeriodic:{
+ fgmd_hbond_force.setNonbondedMethod(OpenMM::CustomHbondForce::CutoffPeriodic);
+ break;
+ }
+ case Ewald:{
+ fgmd_hbond_force.setNonbondedMethod(OpenMM::CustomHbondForce::CutoffPeriodic);
+ break;
+ }
+ case PME:{
+ fgmd_hbond_force.setNonbondedMethod(OpenMM::CustomHbondForce::CutoffPeriodic);
+ break;
+ }
+ }
+
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = fgmd_hbond_donors.begin();
+ i != fgmd_hbond_donors.end(); ++i){
+ //stupid cast
+ std::vector<double> parameters;
+ for(std::vector<Real>::const_iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ parameters.push_back(*j);
+ }
+ fgmd_hbond_force.addDonor(i->first[0],i->first[1],-1, parameters);
+ }
+ std::vector<double> dummy_vec;
+ for(std::vector<Index<2> >::const_iterator i = fgmd_hbond_acceptors.begin();
+ i != fgmd_hbond_acceptors.end(); ++i){
+ fgmd_hbond_force.addAcceptor((*i)[0],(*i)[1],-1,dummy_vec);
+ }
+ sys->addForce(&fgmd_hbond_force);
+ }
+
+ std::vector<Real> sigmas = top->GetSigmas();
+ std::vector<Real> epsilons = top->GetEpsilons();
+ std::vector<Real> charges = top->GetCharges();
+ if(!sigmas.empty() && !epsilons.empty() && !charges.empty()){
+ OpenMM::NonbondedForce& nonbonded_force = *new OpenMM::NonbondedForce();
+ switch(settings->nonbonded_method){
+ case NoCutoff:{
+ nonbonded_force.setNonbondedMethod(OpenMM::NonbondedForce::NoCutoff);
+ break;
+ }
+ case CutoffNonPeriodic:{
+ nonbonded_force.setNonbondedMethod(OpenMM::NonbondedForce::CutoffNonPeriodic);
+ break;
+ }
+ case CutoffPeriodic:{
+ nonbonded_force.setNonbondedMethod(OpenMM::NonbondedForce::CutoffPeriodic);
+ break;
+ }
+ case Ewald:{
+ nonbonded_force.setNonbondedMethod(OpenMM::NonbondedForce::Ewald);
+ break;
+ }
+ case PME:{
+ nonbonded_force.setNonbondedMethod(OpenMM::NonbondedForce::PME);
+ break;
+ }
+ }
+ //we can set the cutoff in any case, since it will have no effect when
+ //nonbonded method is NoCutoff
+ nonbonded_force.setCutoffDistance(settings->nonbonded_cutoff/10.0);
+ nonbonded_force.setReactionFieldDielectric(settings->reaction_field_dielectric);
+ nonbonded_force.setUseDispersionCorrection(settings->use_dispersion_correction);
+ sys->addForce(&nonbonded_force);
+ mapper[LJ] = mapper_index++;
+
+ //we first add all single particles to the force
+ for(uint i = 0; i < charges.size(); ++i){
+ nonbonded_force.addParticle(charges[i], sigmas[i], epsilons[i]);
+ }
+ //take care of the 1-4 interactions
+ const std::vector<std::pair<Index<2>,std::vector<Real> > >& lj_pairs = top->GetLJPairs();
+ if(!lj_pairs.empty()){
+ Real fudge_lj = top->GetFudgeLJ();
+ Real fudge_qq = top->GetFudgeQQ();
+ Real charge;
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = lj_pairs.begin();
+ i != lj_pairs.end(); ++i){
+ charge = fudge_qq * charges[i->first[0]] * charges[i->first[1]];
+ nonbonded_force.addException(i->first[0],i->first[1],charge,
+ i->second[0],fudge_lj*i->second[1]);
+ }
+ }
+ //take care of the exclusions
+ const std::vector<Index<2> >& exclusions = top->GetExclusions();
+ if(!exclusions.empty()){
+ for(std::vector<Index<2> >::const_iterator i = exclusions.begin(); i != exclusions.end(); ++i){
+ nonbonded_force.addException((*i)[0],(*i)[1],0.0,1.0,0.0);
+ }
+ }
+ }
+ std::vector<Real> gbsa_radii = top->GetGBSARadii();
+ std::vector<Real> gbsa_scaling = top->GetOBCScalings();
+ if(!gbsa_radii.empty() && !gbsa_scaling.empty()){
+ std::vector<Real> charges = top->GetCharges();
+ if(charges.empty())
+ throw ost::Error("GBSA force requires atom charges to be set!");
+ OpenMM::GBSAOBCForce& gbsa_force = *new OpenMM::GBSAOBCForce();
+ sys->addForce(&gbsa_force);
+ if(settings->nonbonded_method == NoCutoff){
+ gbsa_force.setNonbondedMethod(OpenMM::GBSAOBCForce::NoCutoff);
+ }
+ else if(settings->nonbonded_method == CutoffNonPeriodic){
+ gbsa_force.setNonbondedMethod(OpenMM::GBSAOBCForce::CutoffNonPeriodic);
+ }
+ else if(settings->nonbonded_method == CutoffPeriodic){
+ gbsa_force.setNonbondedMethod(OpenMM::GBSAOBCForce::CutoffPeriodic);
+ }
+ else{
+ throw ost::Error("Can only use Nonbonded methods NoCutoff, CutoffNonPeriodic,CutoffPeriodic when using GBSA");
+ }
+ mapper[GBSA] = mapper_index++;
+ gbsa_force.setCutoffDistance(settings->nonbonded_cutoff/10);
+ gbsa_force.setSolventDielectric(settings->solvent_dielectric);
+ gbsa_force.setSoluteDielectric(settings->solute_dielectric);
+ //it should be guaranteed from the topology object, that the vectors have the same size
+ for(uint i = 0; i < gbsa_radii.size(); ++i){
+ gbsa_force.addParticle(charges[i],
+ gbsa_radii[i],
+ gbsa_scaling[i]);
+ }
+ }
+ //set constraints
+ std::vector<std::pair<Index<2>,std::vector<Real> > > distance_constraints = top->GetDistanceConstraints();
+ if(!distance_constraints.empty()){
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::iterator i = distance_constraints.begin();
+ i != distance_constraints.end(); ++i){
+ sys->addConstraint(i->first[0],i->first[1],i->second[0]);
+ }
+ }
+ //set periodic box extents
+ if(geom::Length(settings->periodic_box_extents) > 0){
+ OpenMM::Vec3 x_vec(settings->periodic_box_extents[0]/10,0.0,0.0);
+ OpenMM::Vec3 y_vec(0.0,settings->periodic_box_extents[1]/10,0.0);
+ OpenMM::Vec3 z_vec(0.0,0.0,settings->periodic_box_extents[2]/10);
+ sys->setDefaultPeriodicBoxVectors(x_vec,y_vec,z_vec);
+ }
+ else if(settings->add_nonbonded &&
+ !(settings->nonbonded_method == NoCutoff ||
+ settings->nonbonded_method == CutoffNonPeriodic)){
+ throw ost::Error("Chosen nonbonded method requires to define the periodic box extents!");
+ }
+ //set the CMMMotion removing force if required
+ if(settings->remove_cmm_motion){
+ if(settings->cmm_frequency != settings->cmm_frequency){
+ throw ost::Error("Cannot set CMM Remover without valid cmm_frequency set!");
+ }
+ sys->addForce(new OpenMM::CMMotionRemover(settings->cmm_frequency));
+ }
+ if(settings->add_thermostat){
+ if(settings->thermostat_temperature != settings->thermostat_temperature ||
+ settings->thermostat_collision_frequency != settings->thermostat_collision_frequency){
+ throw ost::Error("Cannot set thermostat without defined temperature and collision frequency!");
+ }
+ OpenMM::AndersenThermostat& thermostat = *new OpenMM::AndersenThermostat(settings->thermostat_temperature,
+ settings->thermostat_collision_frequency);
+ sys->addForce(&thermostat);
+ }
+ if(settings->add_barostat){
+ if(geom::Length(settings->periodic_box_extents) == 0){
+ throw ost::Error("If you set a barostat, you also have to set nonzero periodic box extents!");
+ }
+ if(settings->barostat_temperature != settings->barostat_temperature ||
+ settings->barostat_pressure != settings->barostat_pressure ||
+ settings->barostat_frequency != settings->barostat_frequency){
+ throw ost::Error("Cannot set barostat without defined temperature, pressure, and frequency parameters!");
+ }
+ OpenMM::MonteCarloBarostat& barostat = *new OpenMM::MonteCarloBarostat(settings->barostat_pressure,
+ settings->barostat_temperature,
+ settings->barostat_frequency);
+ sys->addForce(&barostat);
+ }
+ return sys;
+}
+}}} //ns
diff --git a/modules/mol/mm/src/system_creator.hh b/modules/mol/mm/src/system_creator.hh
new file mode 100644
index 0000000000000000000000000000000000000000..274c9453b3c56e8bb928749f36fdb6e767f53949
--- /dev/null
+++ b/modules/mol/mm/src/system_creator.hh
@@ -0,0 +1,64 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_SYSTEM_CREATOR_HH
+#define OST_MM_SYSTEM_CREATOR_HH
+
+#include <vector>
+#include <map>
+#include <set>
+
+#include <ost/message.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/modeller.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/topology.hh>
+
+
+#include <time.h>
+
+
+namespace OpenMM{
+ class System; //hacky way of telling the System is around.
+ //will be included in source file to avoid
+ //dependencies on external libraries
+}
+
+namespace ost { namespace mol{ namespace mm{
+
+typedef boost::shared_ptr<OpenMM::System> SystemPtr;
+
+class SystemCreator {
+public:
+ static SystemPtr Create(const TopologyPtr top,
+ const SettingsPtr settings,
+ std::map<FuncType,uint>& mapper);
+
+};
+
+
+}}}//ns
+
+#endif
\ No newline at end of file
diff --git a/modules/mol/mm/src/topology.cc b/modules/mol/mm/src/topology.cc
new file mode 100644
index 0000000000000000000000000000000000000000..448e25490f6b8486b60f44b1e34bb55750d2fbcc
--- /dev/null
+++ b/modules/mol/mm/src/topology.cc
@@ -0,0 +1,1384 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/topology.hh>
+
+
+namespace ost{ namespace mol{ namespace mm{
+
+
+
+Topology::Topology(const std::vector<Real>& masses){
+ num_particles_ = masses.size();
+ atom_masses_ = masses;
+ fudge_lj_ = 1.0;
+ fudge_qq_ = 1.0;
+}
+
+TopologyPtr Topology::Load(const String& filename){
+
+ if (!boost::filesystem::exists(filename)) {
+ std::stringstream ss;
+ ss << "Could not open topology. File '"
+ << filename << "' does not exist";
+ throw ost::io::IOException(ss.str());
+ }
+
+ std::ifstream stream(filename.c_str(), std::ios_base::binary);
+ io::BinaryDataSource ds(stream);
+ TopologyPtr top_p(new Topology);
+ ds >> *top_p;
+ return top_p;
+}
+
+void Topology::Save(const String& filename){
+ std::ofstream stream(filename.c_str(), std::ios_base::binary);
+ io::BinaryDataSink ds(stream);
+ ds << *this;
+}
+
+uint Topology::AddHarmonicBond(uint index_one,
+ uint index_two,
+ Real bond_length,
+ Real force_constant){
+
+ if(index_one >= num_particles_ || index_two >= num_particles_){
+ throw ost::Error("Index of bond particle exceeds number of particles present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ std::vector<Real> parameters;
+ parameters.push_back(bond_length);
+ parameters.push_back(force_constant);
+ harmonic_bonds_.push_back(std::make_pair(index,parameters));
+ return harmonic_bonds_.size()-1;
+}
+
+uint Topology::AddHarmonicAngle(uint index_one,
+ uint index_two,
+ uint index_three,
+ Real angle,
+ Real force_constant){
+
+ if(uint(index_one) >= num_particles_ || uint(index_two) >= num_particles_ ||
+ uint(index_three) >= num_particles_){
+ throw ost::Error("Index of angle particle exceeds number of particles present in topology!");
+ }
+ Index<3> index(index_one,index_two,index_three);
+ std::vector<Real> parameters;
+ parameters.push_back(angle);
+ parameters.push_back(force_constant);
+ harmonic_angles_.push_back(std::make_pair(index,parameters));
+ return harmonic_angles_.size()-1;
+}
+
+uint Topology::AddUreyBradleyAngle(uint index_one,
+ uint index_two,
+ uint index_three,
+ Real angle,
+ Real angle_force_constant,
+ Real bond_length,
+ Real bond_force_constant){
+
+ if(index_one >= num_particles_ || index_two >= num_particles_ ||
+ index_three >= num_particles_){
+ throw ost::Error("Index of angle particle exceeds number of particles present in topology!");
+ }
+ Index<3> index(index_one,index_two,index_three);
+ std::vector<Real> parameters;
+ parameters.push_back(angle);
+ parameters.push_back(angle_force_constant);
+ parameters.push_back(bond_length);
+ parameters.push_back(bond_force_constant);
+ urey_bradley_angles_.push_back(std::make_pair(index,parameters));
+ return urey_bradley_angles_.size()-1;
+}
+
+uint Topology::AddPeriodicDihedral(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ int multiplicity,
+ Real phase,
+ Real force_constant){
+
+ if(index_one >= num_particles_ || index_two >= num_particles_||
+ index_three >= num_particles_ || index_four >= num_particles_){
+ throw ost::Error("Index of dihedral particle exceeds number of particles present in topology!");
+ }
+ Index<4> index(index_one,index_two,index_three,index_four);
+ std::vector<Real> parameters;
+ parameters.push_back(multiplicity);
+ parameters.push_back(phase);
+ parameters.push_back(force_constant);
+ periodic_dihedrals_.push_back(std::make_pair(index,parameters));
+ return periodic_dihedrals_.size()-1;
+}
+
+uint Topology::AddPeriodicImproper(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ int multiplicity,
+ Real phase,
+ Real force_constant){
+
+ if(index_one >= num_particles_ || index_two >= num_particles_||
+ index_three >= num_particles_ || index_four >= num_particles_){
+ throw ost::Error("Index of improper particle exceeds number of particles present in topology!");
+ }
+ Index<4> index(index_one,index_two,index_three,index_four);
+ std::vector<Real> parameters;
+ parameters.push_back(multiplicity);
+ parameters.push_back(phase);
+ parameters.push_back(force_constant);
+ periodic_impropers_.push_back(std::make_pair(index,parameters));
+ return periodic_impropers_.size()-1;
+}
+
+uint Topology::AddHarmonicImproper(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ Real angle,
+ Real force_constant){
+
+ if(index_one >= num_particles_ || index_two >= num_particles_||
+ index_three >= num_particles_ || index_four >= num_particles_){
+ throw ost::Error("Index of improper particle exceeds number of particles present in topology!");
+ }
+ Index<4> index(index_one,index_two,index_three,index_four);
+ std::vector<Real> parameters;
+ parameters.push_back(angle);
+ parameters.push_back(force_constant);
+ harmonic_impropers_.push_back(std::make_pair(index,parameters));
+ return harmonic_impropers_.size()-1;
+}
+
+uint Topology::AddCMap(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ uint index_five,
+ int dimension,
+ std::vector<Real> values){
+
+ if(index_one >= num_particles_ || index_two >= num_particles_ ||
+ index_three >= num_particles_ || index_four >= num_particles_ ||
+ index_five >= num_particles_){
+ throw ost::Error("Index of cmap particle exceeds number of particles present in topology!");
+ }
+ if(uint(dimension * dimension) != values.size()){
+ throw ost::Error("Dimension of CMap is inconsistent with its values!");
+ }
+ Index<5> index(index_one,index_two,index_three,index_four,index_five);
+ cmaps_.push_back(std::make_pair(index,values));
+ return cmaps_.size()-1;
+}
+
+uint Topology::AddLJPair(uint index_one,
+ uint index_two,
+ Real sigma,
+ Real epsilon){
+
+ if(index_one >= num_particles_ || index_two >= num_particles_){
+ throw ost::Error("Index of lj pair particle exceeds number of particles present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ if(added_lj_pairs_.find(index) != added_lj_pairs_.end() || added_lj_pairs_.find(reverse_index) != added_lj_pairs_.end()){
+ throw ost::Error("This particular lj 1,4-interaction is already parametrized!");
+ }
+ added_lj_pairs_.insert(index);
+ std::vector<Real> parameters;
+ parameters.push_back(sigma);
+ parameters.push_back(epsilon);
+ lj_pairs_.push_back(std::make_pair(index,parameters));
+ return lj_pairs_.size()-1;
+}
+
+uint Topology::AddExclusion(uint index_one,
+ uint index_two){
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ if(index_one >= num_particles_ || index_two >= num_particles_){
+ throw ost::Error("Index of exclusion particle exceeds number of particles present in topology!");
+ }
+ if(added_exclusions_.find(index) != added_exclusions_.end() || added_exclusions_.find(reverse_index) != added_exclusions_.end()){
+ throw ost::Error("This particular exclusion has already been set!");
+ }
+ added_exclusions_.insert(index);
+ exclusions_.push_back(index);
+ return exclusions_.size()-1;
+}
+
+uint Topology::AddDistanceConstraint(uint index_one,
+ uint index_two,
+ Real distance){
+
+ if(index_one >= num_particles_ || index_two >= num_particles_){
+ throw ost::Error("Index of distance constraint atom exceeds number of particles present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ if(added_distance_constraints_.find(index) != added_distance_constraints_.end() || added_distance_constraints_.find(reverse_index) != added_distance_constraints_.end()){
+ throw ost::Error("This particular distance constraint is already parametrized!");
+ }
+ added_distance_constraints_.insert(index);
+ std::vector<Real> parameters;
+ parameters.push_back(distance);
+ distance_constraints_.push_back(std::make_pair(index,parameters));
+ return distance_constraints_.size()-1;
+}
+
+void Topology::AddPositionConstraint(uint index){
+ if(index >= num_particles_){
+ throw ost::Error("Index of position constraint exceeds number of particles present in topology!");
+ }
+ std::vector<uint>::iterator it = std::find(position_constraints_.begin(),position_constraints_.end(),index);
+ if(it != position_constraints_.end()) return; //already present
+ position_constraints_.push_back(index);
+}
+
+uint Topology::AddHarmonicPositionRestraint(uint ind, const geom::Vec3& ref_position, Real k,
+ Real x_scale, Real y_scale, Real z_scale){
+ if(ind >= num_particles_){
+ throw ost::Error("Index of harmonic distance constraint exceeds number of particles present in topology!");
+ }
+ Index<1> index(ind);
+ std::vector<Real> parameters;
+ parameters.push_back(ref_position[0]);
+ parameters.push_back(ref_position[1]);
+ parameters.push_back(ref_position[2]);
+ parameters.push_back(k);
+ parameters.push_back(x_scale);
+ parameters.push_back(y_scale);
+ parameters.push_back(z_scale);
+
+ harmonic_position_restraints_.push_back(std::make_pair(index,parameters));
+ return harmonic_position_restraints_.size()-1;
+}
+
+uint Topology::AddHarmonicDistanceRestraint(uint index_one, uint index_two,
+ Real length, Real force_constant){
+ if(index_one >= num_particles_ || index_two >= num_particles_){
+ throw ost::Error("Index of distance restraint atom exceeds number of particles present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ std::vector<Real> parameters;
+ parameters.push_back(length);
+ parameters.push_back(force_constant);
+ harmonic_distance_restraints_.push_back(std::make_pair(index,parameters));
+ return harmonic_distance_restraints_.size()-1;
+}
+
+uint Topology::AddFGMDHBondDonor(uint index_one, uint index_two,
+ Real length, Real k_length, Real alpha,
+ Real k_alpha, Real beta, Real k_beta){
+ if(index_one >= num_particles_ || index_two >= num_particles_){
+ throw ost::Error("Index of fgmd hbond donor atom exceeds number of particles present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ std::vector<Real> parameters;
+ parameters.push_back(length);
+ parameters.push_back(k_length);
+ parameters.push_back(alpha);
+ parameters.push_back(k_alpha);
+ parameters.push_back(beta);
+ parameters.push_back(k_beta);
+ fgmd_hbond_donors_.push_back(std::make_pair(index,parameters));
+ return fgmd_hbond_donors_.size()-1;
+}
+
+uint Topology::AddFGMDHBondAcceptor(uint index_one, uint index_two){
+ if(index_one >= num_particles_ || index_two >= num_particles_){
+ throw ost::Error("Index of fgmd hbond acceptor atom exceeds number of particles present in topology!");
+ }
+ Index<2> index(index_one,index_two);
+ fgmd_hbond_acceptors_.push_back(index);
+ return fgmd_hbond_acceptors_.size()-1;
+}
+
+void Topology::SetSigmas(const std::vector<Real>& sigmas){
+ if(sigmas.size() != num_particles_){
+ throw ost::Error("Expect the same number of sigma parameters than particles!");
+ }
+ sigmas_ = sigmas;
+}
+
+void Topology::SetSigma(uint index, Real sigma){
+ if(sigmas_.empty()){
+ throw ost::Error("Modification of sigma parameter requires initial assignment of sigma parameters in globo!");
+ }
+ if(index >= num_particles_){
+ throw ost::Error("Given particle index exceeds number of available particles!");
+ }
+ sigmas_[index] = sigma;
+}
+
+void Topology::SetEpsilons(const std::vector<Real>& epsilons){
+ if(epsilons.size() != num_particles_){
+ throw ost::Error("Expect the same number of epsilon parameters than particles!");
+ }
+ epsilons_ = epsilons;
+}
+
+void Topology::SetEpsilon(uint index, Real epsilon){
+ if(epsilons_.empty()){
+ throw ost::Error("Modification of epsilon parameter requires initial assignment of epsilon parameters in globo!");
+ }
+ if(index >= num_particles_){
+ throw ost::Error("Given particle index exceeds number of available particles!");
+ }
+ epsilons_[index] = epsilon;
+}
+
+void Topology::SetGBSARadii(const std::vector<Real>& gbsa_radii){
+ if(gbsa_radii.size() != num_particles_){
+ throw ost::Error("Expect the same number of gbsa parameters than particles!");
+ }
+ gbsa_radii_ = gbsa_radii;
+}
+
+void Topology::SetGBSARadius(uint index, Real radius){
+ if(gbsa_radii_.empty()){
+ throw ost::Error("Modification of gbsa radius requires initial assignment of gbsa radii in globo!");
+ }
+ if(index >= num_particles_){
+ throw ost::Error("Given particle index exceeds number of available particles!");
+ }
+ gbsa_radii_[index] = radius;
+}
+
+void Topology::SetOBCScalings(const std::vector<Real>& obc_scaling){
+ if(obc_scaling.size() != num_particles_){
+ throw ost::Error("Expect the same number of gbsa parameters than particles!");
+ }
+ obc_scaling_ = obc_scaling;
+}
+
+void Topology::SetOBCScaling(uint index, Real scaling){
+ if(obc_scaling_.empty()){
+ throw ost::Error("Modification of obc scaling parameter requires initial assignment of obc scaling parameters in globo!");
+ }
+ if(index >= num_particles_){
+ throw ost::Error("Given particle index exceeds number of available particles!");
+ }
+ obc_scaling_[index] = scaling;
+}
+
+void Topology::SetCharges(const std::vector<Real>& charges){
+ if(charges.size() != num_particles_){
+ throw ost::Error("Expect the same number of charges than particles!");
+ }
+ charges_ = charges;
+}
+
+void Topology::SetCharge(uint index, Real charge){
+ if(charges_.empty()){
+ throw ost::Error("Modification of charge parameter requires initial assignment of charges in globo!");
+ }
+ if(index >= num_particles_){
+ throw ost::Error("Given particle index exceeds number of available particles!");
+ }
+ charges_[index] = charge;
+}
+
+void Topology::SetMasses(const std::vector<Real>& masses){
+ if(masses.size() != num_particles_){
+ throw ost::Error("Expect masses vector to have the same number of elements than particles in the topologies entity!");
+ }
+ atom_masses_ = masses;
+}
+
+void Topology::SetMass(uint index, Real mass){
+ if(atom_masses_.empty()){
+ throw ost::Error("Modification of mass parameter requires initial assignment of masses in globo!");
+ }
+ if(index >= num_particles_){
+ throw ost::Error("Given particle index exceeds number of available particles!");
+ }
+ atom_masses_[index] = mass;
+
+}
+
+
+void Topology::GetHarmonicBondParameters(uint index, uint& index_one, uint& index_two,
+ Real& bond_length, Real& force_constant) const{
+ if(index >= harmonic_bonds_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic bonds present in topology!");
+ }
+ bond_length = harmonic_bonds_[index].second[0];
+ force_constant = harmonic_bonds_[index].second[1];
+ index_one = harmonic_bonds_[index].first[0];
+ index_two = harmonic_bonds_[index].first[1];
+}
+
+void Topology::GetHarmonicAngleParameters(uint index, uint& index_one, uint& index_two, uint& index_three,
+ Real& angle, Real& force_constant) const{
+ if(index >= harmonic_angles_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic angles present in topology!");
+ }
+ angle = harmonic_angles_[index].second[0];
+ force_constant = harmonic_angles_[index].second[1];
+ index_one = harmonic_angles_[index].first[0];
+ index_two = harmonic_angles_[index].first[1];
+ index_three = harmonic_angles_[index].first[2];
+}
+
+void Topology::GetUreyBradleyAngleParameters(uint index, uint& index_one, uint& index_two, uint& index_three,
+ Real& angle, Real& angle_force_constant, Real& bond_length, Real& bond_force_constant) const{
+ if(index >= urey_bradley_angles_.size()){
+ throw ost::Error("Provided index exceeds number of urey_bradley angles present in topology!");
+ }
+ angle = urey_bradley_angles_[index].second[0];
+ angle_force_constant = urey_bradley_angles_[index].second[1];
+ bond_length = urey_bradley_angles_[index].second[2];
+ bond_force_constant = urey_bradley_angles_[index].second[3];
+ index_one = urey_bradley_angles_[index].first[0];
+ index_two = urey_bradley_angles_[index].first[1];
+ index_three = urey_bradley_angles_[index].first[2];
+}
+
+void Topology::GetPeriodicDihedralParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ int& multiplicity, Real& phase, Real& force_constant) const{
+ if(index >= periodic_dihedrals_.size()){
+ throw ost::Error("Provided index exceeds number of periodic dihedrals present in topology!");
+ }
+ multiplicity = int(periodic_dihedrals_[index].second[0]);
+ phase = periodic_dihedrals_[index].second[1];
+ force_constant = periodic_dihedrals_[index].second[2];
+ index_one = periodic_dihedrals_[index].first[0];
+ index_two = periodic_dihedrals_[index].first[1];
+ index_three = periodic_dihedrals_[index].first[2];
+ index_four = periodic_dihedrals_[index].first[3];
+}
+
+void Topology::GetPeriodicImproperParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ int& multiplicity, Real& phase, Real& force_constant) const{
+ if(index >= periodic_impropers_.size()){
+ throw ost::Error("Provided index exceeds number of periodic impropers present in topology!");
+ }
+ multiplicity = int(periodic_impropers_[index].second[0]);
+ phase = periodic_impropers_[index].second[1];
+ force_constant = periodic_impropers_[index].second[2];
+ index_one = periodic_impropers_[index].first[0];
+ index_two = periodic_impropers_[index].first[1];
+ index_three = periodic_impropers_[index].first[2];
+ index_four = periodic_impropers_[index].first[3];
+}
+
+void Topology::GetHarmonicImproperParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ Real& angle, Real& force_constant) const{
+ if(index >= harmonic_impropers_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic impropers present in topology!");
+ }
+ angle = harmonic_impropers_[index].second[0];
+ force_constant = harmonic_impropers_[index].second[1];
+ index_one = harmonic_impropers_[index].first[0];
+ index_two = harmonic_impropers_[index].first[1];
+ index_three = harmonic_impropers_[index].first[2];
+ index_four = harmonic_impropers_[index].first[3];
+}
+
+void Topology::GetCMapParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four, uint& index_five,
+ int& dimension, std::vector<Real>& map) const{
+ if(index >= cmaps_.size()){
+ throw ost::Error("Provided index exceeds number of cmaps present in topology!");
+ }
+ dimension = int(sqrt(cmaps_[index].second.size()));
+ map = cmaps_[index].second;
+ index_one = cmaps_[index].first[0];
+ index_two = cmaps_[index].first[1];
+ index_three = cmaps_[index].first[2];
+ index_four = cmaps_[index].first[3];
+ index_five = cmaps_[index].first[4];
+
+}
+
+void Topology::GetLJPairParameters(uint index, uint& index_one, uint& index_two,
+ Real& sigma, Real& epsilon) const{
+ if(index >= lj_pairs_.size()){
+ throw ost::Error("Provided index exceeds number of lj pairs present in topology!");
+ }
+ sigma = lj_pairs_[index].second[0];
+ epsilon = lj_pairs_[index].second[1];
+ index_one = lj_pairs_[index].first[0];
+ index_two = lj_pairs_[index].first[1];
+}
+
+void Topology::GetDistanceConstraintParameters(uint index, uint& index_one, uint& index_two,
+ Real& distance) const{
+ if(index >= distance_constraints_.size()){
+ throw ost::Error("Provided index exceeds number of distance_constraints present in topology!");
+ }
+ distance = distance_constraints_[index].second[0];
+ index_one = distance_constraints_[index].first[0];
+ index_two = distance_constraints_[index].first[1];
+}
+
+void Topology::GetHarmonicPositionRestraintParameters(uint index, uint& atom_index, geom::Vec3& ref_position,
+ Real& k, Real& x_scale, Real& y_scale, Real& z_scale) const{
+ if(index >= harmonic_position_restraints_.size()){
+ throw ost::Error("Provided index exceeds numnber of harmonic position constraints present in topology!");
+ }
+ atom_index = harmonic_position_restraints_[index].first[0];
+ ref_position[0] = harmonic_position_restraints_[index].second[0];
+ ref_position[1] = harmonic_position_restraints_[index].second[1];
+ ref_position[2] = harmonic_position_restraints_[index].second[2];
+ k = harmonic_position_restraints_[index].second[3];
+ x_scale = harmonic_position_restraints_[index].second[4];
+ y_scale = harmonic_position_restraints_[index].second[5];
+ z_scale = harmonic_position_restraints_[index].second[6];
+}
+
+void Topology::GetHarmonicDistanceRestraintParameters(uint index, uint& atom_one, uint& atom_two, Real& length,
+ Real& force_constant) const{
+ if(index >= harmonic_distance_restraints_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic distance restraints present in topology!");
+ }
+ atom_one = harmonic_distance_restraints_[index].first[0];
+ atom_two = harmonic_distance_restraints_[index].first[1];
+ length = harmonic_distance_restraints_[index].second[0];
+ force_constant = harmonic_distance_restraints_[index].second[1];
+}
+
+void Topology::GetFGMDHBondDonorParameters(uint index, uint& atom_one, uint& atom_two, Real& length,
+ Real& k_length, Real& alpha, Real& k_alpha,
+ Real& beta, Real& k_beta) const{
+ if(index >= fgmd_hbond_donors_.size()){
+ throw ost::Error("Provided index exceeds number of fgmd hbond donors present in topology!");
+ }
+ atom_one = harmonic_distance_restraints_[index].first[0];
+ atom_two = harmonic_distance_restraints_[index].first[1];
+ length = fgmd_hbond_donors_[index].second[0];
+ k_length = fgmd_hbond_donors_[index].second[1];
+ alpha = fgmd_hbond_donors_[index].second[2];
+ k_alpha = fgmd_hbond_donors_[index].second[3];
+ beta = fgmd_hbond_donors_[index].second[4];
+ k_beta = fgmd_hbond_donors_[index].second[5];
+}
+
+void Topology::GetFGMDHBondAcceptorParameters(uint index, uint& atom_one, uint& atom_two) const{
+ if(index >= fgmd_hbond_acceptors_.size()){
+ throw ost::Error("Provided index exceeds number of fgmd hbond acceptors present in topology!");
+ }
+ atom_one = fgmd_hbond_acceptors_[index][0];
+ atom_two = fgmd_hbond_acceptors_[index][1];
+}
+
+void Topology::SetHarmonicBondParameters(uint index, const Real bond_length, const Real force_constant){
+ if(index >= harmonic_bonds_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic bonds present in topology!");
+ }
+ harmonic_bonds_[index].second[0] = bond_length;
+ harmonic_bonds_[index].second[1] = force_constant;
+}
+
+void Topology::SetHarmonicAngleParameters(uint index, const Real angle, const Real force_constant){
+ if(index >= harmonic_angles_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic angles present in topology!");
+ }
+ harmonic_angles_[index].second[0] = angle;
+ harmonic_angles_[index].second[1] = force_constant;
+}
+
+void Topology::SetUreyBradleyAngleParameters(uint index, const Real angle, const Real angle_force_constant, const Real bond_length, const Real bond_force_constant){
+ if(index >= urey_bradley_angles_.size()){
+ throw ost::Error("Provided index exceeds number of urey_bradley angles present in topology!");
+ }
+ urey_bradley_angles_[index].second[0] = angle;
+ urey_bradley_angles_[index].second[1] = angle_force_constant;
+ urey_bradley_angles_[index].second[2] = bond_length;
+ urey_bradley_angles_[index].second[3] = bond_force_constant;
+}
+
+void Topology::SetPeriodicDihedralParameters(uint index, const int multiplicity, const Real phase, const Real force_constant){
+ if(index >= periodic_dihedrals_.size()){
+ throw ost::Error("Provided index exceeds number of periodic dihedrals present in topology!");
+ }
+ periodic_dihedrals_[index].second[0] = multiplicity;
+ periodic_dihedrals_[index].second[1] = phase;
+ periodic_dihedrals_[index].second[2] = force_constant;
+}
+
+void Topology::SetPeriodicImproperParameters(uint index, const int multiplicity, const Real phase, const Real force_constant){
+ if(index >= periodic_impropers_.size()){
+ throw ost::Error("Provided index exceeds number of periodic impropers present in topology!");
+ }
+ periodic_impropers_[index].second[0] = multiplicity;
+ periodic_impropers_[index].second[1] = phase;
+ periodic_impropers_[index].second[2] = force_constant;
+}
+
+void Topology::SetHarmonicImproperParameters(uint index, const Real angle, const Real force_constant){
+ if(index >= harmonic_impropers_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic impropers present in topology!");
+ }
+ harmonic_impropers_[index].second[0] = angle;
+ harmonic_impropers_[index].second[1] = force_constant;
+}
+
+void Topology::SetCMapParameters(uint index, const int dimension, const std::vector<Real>& map){
+ if(index >= cmaps_.size()){
+ throw ost::Error("Provided index exceeds number of cmaps present in topology!");
+ }
+ if(uint(dimension * dimension) != map.size()){
+ throw ost::Error("Provided dimension and map are inconsistent!");
+ }
+ cmaps_[index].second = map;
+}
+
+void Topology::SetLJPairParameters(uint index, const Real sigma, const Real epsilon){
+ if(index >= lj_pairs_.size()){
+ throw ost::Error("Provided index exceeds number of lj pairs present in topology!");
+ }
+ lj_pairs_[index].second[0] = sigma;
+ lj_pairs_[index].second[1] = epsilon;
+}
+
+void Topology::SetDistanceConstraintParameters(uint index, const Real distance){
+ if(index >= distance_constraints_.size()){
+ throw ost::Error("Provided index exceeds number of distance_constraints present in topology!");
+ }
+ distance_constraints_[index].second[0] = distance;
+}
+
+void Topology::SetHarmonicPositionRestraintParameters(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale, Real y_scale, Real z_scale){
+ if(index >= harmonic_position_restraints_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic position restraints present in topology!");
+ }
+ harmonic_position_restraints_[index].second[0] = ref_position[0];
+ harmonic_position_restraints_[index].second[1] = ref_position[1];
+ harmonic_position_restraints_[index].second[2] = ref_position[2];
+ harmonic_position_restraints_[index].second[3] = k;
+ harmonic_position_restraints_[index].second[4] = x_scale;
+ harmonic_position_restraints_[index].second[5] = y_scale;
+ harmonic_position_restraints_[index].second[6] = z_scale;
+}
+
+void Topology::SetHarmonicDistanceRestraintParameters(uint index, Real length,
+ Real force_constant){
+ if(index >= harmonic_distance_restraints_.size()){
+ throw ost::Error("Provided index exceeds number of harmonic distance restraints present in topology!");
+ }
+ harmonic_distance_restraints_[index].second[0] = length;
+ harmonic_distance_restraints_[index].second[1] = force_constant;
+}
+
+void Topology::SetFGMDHBondDonorParameters(uint index, Real length, Real k_length,
+ Real alpha, Real k_alpha, Real beta, Real k_beta){
+ if(index >= fgmd_hbond_donors_.size()){
+ throw ost::Error("Provided index exceeds number of fgmd donors present in topology!");
+ }
+ fgmd_hbond_donors_[index].second[0] = length;
+ fgmd_hbond_donors_[index].second[1] = k_length;
+ fgmd_hbond_donors_[index].second[2] = alpha;
+ fgmd_hbond_donors_[index].second[3] = k_alpha;
+ fgmd_hbond_donors_[index].second[4] = beta;
+ fgmd_hbond_donors_[index].second[5] = k_beta;
+}
+
+Real Topology::GetMass(uint index) const{
+ if(index >= num_particles_) throw ost::Error("Provided index exceeds number of particles present in topology!");
+ return atom_masses_[index];
+}
+
+Real Topology::GetSigma(uint index) const{
+ if(index >= num_particles_) throw ost::Error("Provided index exceeds number of particles present in topology!");
+ if(sigmas_.empty()) throw ost::Error("No sigmas set!");
+ return sigmas_[index];
+}
+
+Real Topology::GetEpsilon(uint index) const{
+ if(index >= num_particles_) throw ost::Error("Provided index exceeds number of particles present in topology!");
+ if(epsilons_.empty()) throw ost::Error("No epsilons set!");
+ return epsilons_[index];
+}
+
+Real Topology::GetGBSARadius(uint index) const{
+ if(index >= num_particles_) throw ost::Error("Provided index exceeds number of particles present in topology!");
+ if(gbsa_radii_.empty()) throw ost::Error("No gbsa radii set!");
+ return gbsa_radii_[index];
+}
+
+Real Topology::GetOBCScaling(uint index) const{
+ if(index >= num_particles_) throw ost::Error("Provided index exceeds number of particles present in topology!");
+ if(obc_scaling_.empty()) throw ost::Error("No obc scalings set!");
+ return obc_scaling_[index];
+}
+
+
+Real Topology::GetCharge(uint index) const{
+ if(index >= num_particles_) throw ost::Error("Provided index exceeds number of particles present in topology!");
+ if(charges_.empty()) throw ost::Error("No charges set!");
+ return charges_[index];
+}
+
+std::vector<uint> Topology::GetHarmonicBondIndices(uint index_one,
+ uint index_two) const{
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_bonds_.size(); ++i){
+ if(index == harmonic_bonds_[i].first || reverse_index == harmonic_bonds_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicAngleIndices(uint index_one,
+ uint index_two,
+ uint index_three) const{
+ Index<3> index(index_one,index_two,index_three);
+ Index<3> reverse_index(index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_angles_.size(); ++i){
+ if(index == harmonic_angles_[i].first || reverse_index == harmonic_angles_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetUreyBradleyAngleIndices(uint index_one,
+ uint index_two,
+ uint index_three) const{
+ Index<3> index(index_one,index_two,index_three);
+ Index<3> reverse_index(index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < urey_bradley_angles_.size(); ++i){
+ if(index == urey_bradley_angles_[i].first || reverse_index == urey_bradley_angles_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetPeriodicDihedralIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const{
+ Index<4> index(index_one,index_two,index_three,index_four);
+ Index<4> reverse_index(index_four,index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < periodic_dihedrals_.size(); ++i){
+ if(index == periodic_dihedrals_[i].first || reverse_index == periodic_dihedrals_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetPeriodicImproperIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const{
+ Index<4> index(index_one,index_two,index_three,index_four);
+ Index<4> reverse_index(index_four,index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < periodic_impropers_.size(); ++i){
+ if(index == periodic_impropers_[i].first || reverse_index == periodic_impropers_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicImproperIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const{
+ Index<4> index(index_one,index_two,index_three,index_four);
+ Index<4> reverse_index(index_four,index_three,index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_impropers_.size(); ++i){
+ if(index == harmonic_impropers_[i].first || reverse_index == harmonic_impropers_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetCMapIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ uint index_five) const{
+ //note, that in case of cmaps the order of the atoms matters
+ Index<5> index(index_one,index_two,index_three,index_four,index_five);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ if(index == cmaps_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+int Topology::GetLJPairIndex(uint index_one,
+ uint index_two) const{
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ for(uint i = 0; i < lj_pairs_.size(); ++i){
+ if(index == lj_pairs_[i].first || reverse_index == lj_pairs_[i].first){
+ return i;
+ }
+ }
+ return -1;
+}
+
+int Topology::GetDistanceConstraintIndex(uint index_one,
+ uint index_two) const{
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ for(uint i = 0; i < distance_constraints_.size(); ++i){
+ if(index == distance_constraints_[i].first || reverse_index == distance_constraints_[i].first){
+ return i;
+ }
+ }
+ return -1;
+}
+
+std::vector<uint> Topology::GetHarmonicPositionRestraintIndices(uint atom_index) const{
+ Index<1> index(atom_index);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_position_restraints_.size(); ++i){
+ if(index == harmonic_position_restraints_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicDistanceRestraintIndices(uint index_one, uint index_two) const{
+
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_distance_restraints_.size(); ++i){
+ if(index == harmonic_distance_restraints_[i].first || reverse_index == harmonic_distance_restraints_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetFGMDHBondDonorIndices(uint index_one, uint index_two) const{
+
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < fgmd_hbond_donors_.size(); ++i){
+ if(index == fgmd_hbond_donors_[i].first || reverse_index == fgmd_hbond_donors_[i].first){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetFGMDHBondAcceptorIndices(uint index_one, uint index_two) const{
+
+ Index<2> index(index_one,index_two);
+ Index<2> reverse_index(index_two,index_one);
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < fgmd_hbond_acceptors_.size(); ++i){
+ if(index == fgmd_hbond_acceptors_[i] || reverse_index == fgmd_hbond_acceptors_[i]){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicBondIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_bonds_.size(); ++i){
+ if(harmonic_bonds_[i].first[0] == atom_index || harmonic_bonds_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicAngleIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_angles_.size(); ++i){
+ if(harmonic_angles_[i].first[0] == atom_index || harmonic_angles_[i].first[1] == atom_index ||
+ harmonic_angles_[i].first[2] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetUreyBradleyAngleIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < urey_bradley_angles_.size(); ++i){
+ if(urey_bradley_angles_[i].first[0] == atom_index || urey_bradley_angles_[i].first[1] == atom_index ||
+ urey_bradley_angles_[i].first[2] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetPeriodicDihedralIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < periodic_dihedrals_.size(); ++i){
+ if(periodic_dihedrals_[i].first[0] == atom_index || periodic_dihedrals_[i].first[1] == atom_index ||
+ periodic_dihedrals_[i].first[2] == atom_index || periodic_dihedrals_[i].first[3] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetPeriodicImproperIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < periodic_impropers_.size(); ++i){
+ if(periodic_impropers_[i].first[0] == atom_index || periodic_impropers_[i].first[1] == atom_index ||
+ periodic_impropers_[i].first[2] == atom_index || periodic_impropers_[i].first[3] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicImproperIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_impropers_.size(); ++i){
+ if(harmonic_impropers_[i].first[0] == atom_index || harmonic_impropers_[i].first[1] == atom_index ||
+ harmonic_impropers_[i].first[2] == atom_index || harmonic_impropers_[i].first[3] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetCMapIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ if(cmaps_[i].first[0] == atom_index || cmaps_[i].first[1] == atom_index ||
+ cmaps_[i].first[2] == atom_index || cmaps_[i].first[3] == atom_index ||
+ cmaps_[i].first[4] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetLJPairIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < lj_pairs_.size(); ++i){
+ if(lj_pairs_[i].first[0] == atom_index || lj_pairs_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetDistanceConstraintIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < distance_constraints_.size(); ++i){
+ if(distance_constraints_[i].first[0] == atom_index || distance_constraints_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetHarmonicDistanceRestraintIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < harmonic_distance_restraints_.size(); ++i){
+ if(harmonic_distance_restraints_[i].first[0] == atom_index || harmonic_distance_restraints_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetFGMDHBondDonorIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < fgmd_hbond_donors_.size(); ++i){
+ if(fgmd_hbond_donors_[i].first[0] == atom_index || fgmd_hbond_donors_[i].first[1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+std::vector<uint> Topology::GetFGMDHBondAcceptorIndices(uint atom_index) const{
+ std::vector<uint> return_indices;
+ for(uint i = 0; i < fgmd_hbond_acceptors_.size(); ++i){
+ if(fgmd_hbond_acceptors_[i][0] == atom_index || fgmd_hbond_acceptors_[i][1] == atom_index){
+ return_indices.push_back(i);
+ }
+ }
+ return return_indices;
+}
+
+void Topology::Merge(ost::mol::EntityHandle& ent, TopologyPtr other,
+ const ost::mol::EntityHandle& other_ent){
+
+ this->CheckEntToAdd(ent,other,other_ent);
+ this->CheckTopToAdd(other);
+ this->MergeEnt(ent, other_ent);
+ this->MergeTop(other);
+}
+
+void Topology::Merge(TopologyPtr other){
+
+ this->CheckTopToAdd(other);
+ this->MergeTop(other);
+}
+
+void Topology::MergeTop(TopologyPtr other){
+
+ uint old_num_particles = num_particles_;
+ num_particles_ = num_particles_ + other->GetNumParticles();
+
+ //let's map over masses
+ atom_masses_.resize(old_num_particles + other->GetNumParticles());
+ memcpy(&atom_masses_[old_num_particles],&other->atom_masses_[0],other->GetNumParticles() * sizeof(Real));
+
+ //let's map over the other per atom parameters if they're defined in the destination topology
+ if(!charges_.empty()){
+ charges_.resize(old_num_particles + other->GetNumParticles());
+ memcpy(&charges_[old_num_particles],&other->charges_[0],other->GetNumParticles() * sizeof(Real));
+ }
+
+ if(!sigmas_.empty()){
+ sigmas_.resize(old_num_particles + other->GetNumParticles());
+ memcpy(&sigmas_[old_num_particles],&other->sigmas_[0],other->GetNumParticles() * sizeof(Real));
+ }
+
+ if(!epsilons_.empty()){
+ epsilons_.resize(old_num_particles + other->GetNumParticles());
+ memcpy(&epsilons_[old_num_particles],&other->epsilons_[0],other->GetNumParticles() * sizeof(Real));
+ }
+
+ if(!gbsa_radii_.empty()){
+ gbsa_radii_.resize(old_num_particles + other->GetNumParticles());
+ memcpy(&gbsa_radii_[old_num_particles],&other->gbsa_radii_[0],other->GetNumParticles() * sizeof(Real));
+ }
+
+ if(!obc_scaling_.empty()){
+ obc_scaling_.resize(old_num_particles + other->GetNumParticles());
+ memcpy(&obc_scaling_[old_num_particles],&other->obc_scaling_[0],other->GetNumParticles() * sizeof(Real));
+ }
+
+ //finally, all the interactions get mapped over
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& harmonic_bonds = other->GetHarmonicBonds();
+ if(!harmonic_bonds.empty()){
+ for(std::vector<std::pair<Index<2>, std::vector<Real> > >::const_iterator i = harmonic_bonds.begin();
+ i != harmonic_bonds.end(); ++i){
+ this->AddHarmonicBond(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& harmonic_angles = other->GetHarmonicAngles();
+ if(!harmonic_angles.empty()){
+ for(std::vector<std::pair<Index<3>, std::vector<Real> > >::const_iterator i = harmonic_angles.begin();
+ i != harmonic_angles.end(); ++i){
+ this->AddHarmonicAngle(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ old_num_particles + i->first[2],
+ i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& urey_bradley_angles = other->GetUreyBradleyAngles();
+ if(!urey_bradley_angles.empty()){
+ for(std::vector<std::pair<Index<3>, std::vector<Real> > >::const_iterator i = urey_bradley_angles.begin();
+ i != urey_bradley_angles.end(); ++i){
+ this->AddUreyBradleyAngle(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ old_num_particles + i->first[2],
+ i->second[0],i->second[1],
+ i->second[2],i->second[3]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& periodic_dihedrals = other->GetPeriodicDihedrals();
+ if(!periodic_dihedrals.empty()){
+ for(std::vector<std::pair<Index<4>, std::vector<Real> > >::const_iterator i = periodic_dihedrals.begin();
+ i != periodic_dihedrals.end(); ++i){
+ this->AddPeriodicDihedral(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ old_num_particles + i->first[2],
+ old_num_particles + i->first[3],
+ int(i->second[0]),i->second[1],i->second[2]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& periodic_impropers = other->GetPeriodicImpropers();
+ if(!periodic_impropers.empty()){
+ for(std::vector<std::pair<Index<4>, std::vector<Real> > >::const_iterator i = periodic_impropers.begin();
+ i != periodic_impropers.end(); ++i){
+ this->AddPeriodicImproper(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ old_num_particles + i->first[2],
+ old_num_particles + i->first[3],
+ int(i->second[0]),i->second[1],i->second[2]);
+ }
+ }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& harmonic_impropers = other->GetHarmonicImpropers();
+ if(!harmonic_impropers.empty()){
+ for(std::vector<std::pair<Index<4>, std::vector<Real> > >::const_iterator i = harmonic_impropers.begin();
+ i != harmonic_impropers.end(); ++i){
+ this->AddHarmonicImproper(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ old_num_particles + i->first[2],
+ old_num_particles + i->first[3],
+ i->second[0],i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<5>, std::vector<Real> > >& cmaps = other->GetCMaps();
+ if(!cmaps.empty()){
+ for(std::vector<std::pair<Index<5>, std::vector<Real> > >::const_iterator i = cmaps.begin();
+ i != cmaps.end(); ++i){
+ uint dimension = sqrt(i->second.size());
+ this->AddCMap(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ old_num_particles + i->first[2],
+ old_num_particles + i->first[3],
+ old_num_particles + i->first[4],
+ dimension,i->second);
+ }
+ }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& ljpairs = other->GetLJPairs();
+ if(!ljpairs.empty()){
+ for(std::vector<std::pair<Index<2>, std::vector<Real> > >::const_iterator i = ljpairs.begin();
+ i != ljpairs.end(); ++i){
+ this->AddLJPair(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ i->second[0],i->second[1]);
+ }
+ }
+
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& distance_constraints = other->GetDistanceConstraints();
+ if(!distance_constraints.empty()){
+ for(std::vector<std::pair<Index<2>, std::vector<Real> > >::const_iterator i = distance_constraints.begin();
+ i != distance_constraints.end(); ++i){
+ this->AddDistanceConstraint(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ i->second[0]);
+ }
+ }
+
+ const std::vector<Index<2> >& exclusions = other->GetExclusions();
+ if(!exclusions.empty()){
+ for(std::vector<Index<2> >::const_iterator i = exclusions.begin();
+ i != exclusions.end(); ++i){
+ this->AddExclusion(old_num_particles + (*i)[0],
+ old_num_particles + (*i)[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<1>,std::vector<Real> > >& harmonic_position_restraints = other->GetHarmonicPositionRestraints();
+ if(!harmonic_position_restraints.empty()){
+ for(std::vector<std::pair<Index<1>,std::vector<Real> > >::const_iterator i = harmonic_position_restraints.begin();
+ i != harmonic_position_restraints.end(); ++i){
+ geom::Vec3 ref_pos(i->second[0],i->second[1],i->second[2]);
+ this->AddHarmonicPositionRestraint(old_num_particles + i->first[0],
+ ref_pos,
+ i->second[3],
+ i->second[4],
+ i->second[5],
+ i->second[6]);
+ }
+ }
+
+ const std::vector<std::pair<Index<2>,std::vector<Real> > >& harmonic_distance_restraints = other->GetHarmonicDistanceRestraints();
+ if(!harmonic_distance_restraints.empty()){
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = harmonic_distance_restraints.begin();
+ i != harmonic_distance_restraints.end(); ++i){
+ this->AddHarmonicDistanceRestraint(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ i->second[0],
+ i->second[1]);
+ }
+ }
+
+ const std::vector<std::pair<Index<2>,std::vector<Real> > >& donors = other->GetFGMDHBondDonors();
+ if(!donors.empty()){
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::const_iterator i = donors.begin();
+ i != donors.end(); ++i){
+ this->AddFGMDHBondDonor(old_num_particles + i->first[0],
+ old_num_particles + i->first[1],
+ i->second[0],
+ i->second[1],
+ i->second[2],
+ i->second[3],
+ i->second[4],
+ i->second[5]);
+ }
+ }
+
+ const std::vector<Index<2> >& acceptors = other->GetFGMDHBondAcceptors();
+ if(!acceptors.empty()){
+ for(std::vector<Index<2> >::const_iterator i = acceptors.begin();
+ i != acceptors.end(); ++i){
+ this->AddFGMDHBondAcceptor(old_num_particles + (*i)[0],
+ old_num_particles + (*i)[1]);
+ }
+ }
+
+ const std::vector<uint>& position_constraints = other->GetPositionConstraints();
+ if(!position_constraints.empty()){
+ for(std::vector<uint>::const_iterator i = position_constraints.begin();
+ i != position_constraints.end(); ++i){
+ this->AddPositionConstraint(old_num_particles + (*i));
+ }
+ }
+
+ for(std::set<Index<2> >::iterator i = other->added_lj_pairs_.begin();
+ i != other->added_lj_pairs_.end(); ++i){
+ added_lj_pairs_.insert(Index<2>(old_num_particles + (*i)[0],
+ old_num_particles + (*i)[1]));
+ }
+
+ for(std::set<Index<2> >::iterator i = other->added_distance_constraints_.begin();
+ i != other->added_distance_constraints_.end(); ++i){
+ added_distance_constraints_.insert(Index<2>(old_num_particles + (*i)[0],
+ old_num_particles + (*i)[1]));
+ }
+
+ for(std::set<Index<2> >::iterator i = other->added_exclusions_.begin();
+ i != other->added_exclusions_.end(); ++i){
+ added_exclusions_.insert(Index<2>(old_num_particles + (*i)[0],
+ old_num_particles + (*i)[1]));
+ }
+
+
+
+}
+
+void Topology::MergeEnt(ost::mol::EntityHandle& ent, const ost::mol::EntityHandle& other_ent){
+
+ //mapper of hashcode from source atom to index in added_atom list
+ std::map<long,int> index_mapper;
+ ost::mol::AtomHandleList added_atoms;
+
+ ost::mol::ChainHandleList other_chains = other_ent.GetChainList();
+
+ //let's create an editor to copy over all chains, residues and atoms
+ //from the other topologies entity
+ ost::mol::XCSEditor ed = ent.EditXCS(ost::mol::BUFFERED_EDIT);
+ for(ost::mol::ChainHandleList::iterator i = other_chains.begin(),
+ e = other_chains.end(); i != e; ++i){
+ ost::mol::ResidueHandleList res_list = i->GetResidueList();
+ ost::mol::ChainHandle added_chain = ed.InsertChain(i->GetName());
+
+ for(ost::mol::ResidueHandleList::iterator j = res_list.begin();
+ j != res_list.end(); ++j){
+ ost::mol::AtomHandleList atom_list = j->GetAtomList();
+ ost::mol::ResidueHandle added_residue = ed.AppendResidue(added_chain,*j);
+
+ for(ost::mol::AtomHandleList::iterator k = atom_list.begin();
+ k != atom_list.end(); ++k){
+ index_mapper[k->GetHashCode()] = added_atoms.size();
+ added_atoms.push_back(ed.InsertAtom(added_residue,*k));
+ }
+ }
+ }
+
+ //let's rebuild the connectivity
+ ost::mol::BondHandleList bond_list = other_ent.GetBondList();
+ for(ost::mol::BondHandleList::iterator i = bond_list.begin();
+ i != bond_list.end(); ++i){
+ ed.Connect(added_atoms[index_mapper[i->GetFirst().GetHashCode()]],
+ added_atoms[index_mapper[i->GetSecond().GetHashCode()]]);
+ }
+ ed.UpdateICS();
+}
+
+
+void Topology::CheckTopToAdd(TopologyPtr other){
+
+ if(other->fudge_lj_ != fudge_lj_ || other->fudge_qq_ != fudge_qq_){
+ throw ost::Error("Expect the fudge parameters of source topology to consistent with the fudge parameters from the destination topology!");
+ }
+
+ if(!charges_.empty()){
+ if(other->charges_.empty()){
+ throw ost::Error("Cannot merge topology without charges into a topology with defined charges!");
+ }
+ }
+
+ if(!sigmas_.empty()){
+ if(other->sigmas_.empty()){
+ throw ost::Error("Cannot merge topology without lj sigmas into a topology with defined sigmas!");
+ }
+ }
+
+ if(!epsilons_.empty()){
+ if(other->epsilons_.empty()){
+ throw ost::Error("Cannot merge topology without lj epsilons into a topology with defined epsilons!");
+ }
+ }
+
+ if(!gbsa_radii_.empty()){
+ if(other->gbsa_radii_.empty()){
+ throw ost::Error("Cannot merge topology without gbsa radii into a topology with defined radii!");
+ }
+ }
+
+ if(!obc_scaling_.empty()){
+ if(other->obc_scaling_.empty()){
+ throw ost::Error("Cannot merge topology without obc scaling into a topology with defined scaling!");
+ }
+ }
+}
+
+void Topology::CheckEntToAdd(ost::mol::EntityHandle& ent, TopologyPtr other,
+ const ost::mol::EntityHandle& other_ent){
+
+ //check whether the particle numbers match
+ if(num_particles_ != static_cast<uint>(ent.GetAtomCount())){
+ throw ost::Error("Num Particles is not consistent with num atoms of provided ent!");
+ }
+
+ if(other->GetNumParticles() != static_cast<uint>(other_ent.GetAtomCount())){
+ throw ost::Error("Num Particles is not consistent with num atoms of provided other_ent!");
+ }
+
+ //check whether there is a chain from the new entity is already
+ //present in the actual entity
+ ost::mol::ChainHandleList other_chains = other_ent.GetChainList();
+ for(ost::mol::ChainHandleList::iterator i = other_chains.begin(),
+ e = other_chains.end(); i != e; ++i){
+ if(ent.FindChain(i->GetName()).IsValid()){
+ std::stringstream ss;
+ ss << "Chain with name \"" << i->GetName() << "\" from other topology";
+ ss << "is already present in destination topology!";
+ throw ost::Error(ss.str());
+ }
+ }
+}
+
+}}}//ns
diff --git a/modules/mol/mm/src/topology.hh b/modules/mol/mm/src/topology.hh
new file mode 100644
index 0000000000000000000000000000000000000000..e578e42001b8c7e56a9eef1a0aa0571b097ac8fc
--- /dev/null
+++ b/modules/mol/mm/src/topology.hh
@@ -0,0 +1,804 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_TOPOLOGY_HH
+#define OST_MM_TOPOLOGY_HH
+
+#include <vector>
+#include <map>
+#include <set>
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/message.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/mol/bond_handle.hh>
+#include <ost/mol/residue_prop.hh>
+
+#include <time.h>
+
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class Topology;
+typedef boost::shared_ptr<Topology> TopologyPtr;
+
+
+class Topology{
+
+public:
+
+ Topology(const std::vector<Real>& masses);
+
+ Topology() { } //should not be accessible from Python to avoid messing around
+ //with empty topology
+
+ static TopologyPtr Load(const String& filename);
+
+ void Save(const String& filename);
+
+ uint AddHarmonicBond(uint index_one,
+ uint index_two,
+ Real bond_length,
+ Real force_constant);
+
+ uint AddHarmonicAngle(uint index_one,
+ uint index_two,
+ uint index_three,
+ Real angle,
+ Real force_constant);
+
+ uint AddUreyBradleyAngle(uint index_one,
+ uint index_two,
+ uint index_three,
+ Real angle,
+ Real angle_force_constant,
+ Real bond_length,
+ Real bond_force_constant);
+
+ uint AddPeriodicDihedral(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ int multiplicity,
+ Real phase,
+ Real force_constant);
+
+ uint AddPeriodicImproper(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ int multiplicity,
+ Real phase,
+ Real force_constant);
+
+ uint AddHarmonicImproper(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ Real angle,
+ Real force_constant);
+
+ uint AddCMap(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ uint index_five,
+ int dimension,
+ std::vector<Real> values);
+
+ uint AddLJPair(uint index_one,
+ uint index_two,
+ Real sigma,
+ Real epsilon);
+
+
+ uint AddDistanceConstraint(uint index_one,
+ uint index_two,
+ Real distance);
+
+ uint AddExclusion(uint index_one,
+ uint index_two);
+
+ void AddPositionConstraint(uint index);
+
+ void ResetPositionConstraints() { position_constraints_.clear(); }
+
+ void ResetExclusions() { exclusions_.clear(); }
+
+ uint AddHarmonicPositionRestraint(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale = 1.0, Real y_scale = 1.0, Real z_scale = 1.0);
+
+ uint AddHarmonicDistanceRestraint(uint index_one, uint index_two,
+ Real length, Real force_constant);
+
+ uint AddFGMDHBondDonor(uint index_one, uint index_two,
+ Real length, Real k_length, Real alpha,
+ Real k_alpha, Real beta, Real k_beta);
+
+ uint AddFGMDHBondAcceptor(uint index_one, uint index_two);
+
+ //Single atom parameters are expected to be set at once...
+ void SetSigmas(const std::vector<Real>& sigmas);
+
+ void SetSigma(uint index, Real sigma);
+
+ void SetEpsilons(const std::vector<Real>& epsilons);
+
+ void SetEpsilon(uint index, Real epsilon);
+
+ void SetGBSARadii(const std::vector<Real>& gbsa_radii);
+
+ void SetGBSARadius(uint index, Real radius);
+
+ void SetOBCScalings(const std::vector<Real>& obc_scaling);
+
+ void SetOBCScaling(uint index, Real scaling);
+
+ void SetCharges(const std::vector<Real>& charges);
+
+ void SetCharge(uint index, Real charge);
+
+ void SetMasses(const std::vector<Real>& masses);
+
+ void SetMass(uint index, Real mass);
+
+ void SetFudgeQQ(Real fudge) { fudge_qq_ = fudge; }
+
+ void SetFudgeLJ(Real fudge) { fudge_lj_ = fudge;}
+
+
+ void GetHarmonicBondParameters(uint index, uint& index_one, uint& index_two,
+ Real& bond_length, Real& force_constant) const;
+
+ void GetHarmonicAngleParameters(uint index, uint& index_one, uint& index_two, uint& index_three,
+ Real& angle, Real& force_constant) const;
+
+ void GetUreyBradleyAngleParameters(uint index, uint& index_one, uint& index_two, uint& index_three,
+ Real& angle, Real& angle_force_constant, Real& bond_length, Real& bond_force_constant) const;
+
+ void GetPeriodicDihedralParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ int& multiplicity, Real& phase, Real& force_constant) const;
+
+ void GetPeriodicImproperParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ int& multiplicity, Real& phase, Real& force_constant) const;
+
+ void GetHarmonicImproperParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four,
+ Real& angle, Real& force_constant) const;
+
+ void GetCMapParameters(uint index, uint& index_one, uint& index_two, uint& index_three, uint& index_four, uint& index_five,
+ int& dimension, std::vector<Real>& map) const;
+
+ void GetLJPairParameters(uint index, uint& index_one, uint& index_two,
+ Real& sigma, Real& epsilon) const;
+
+ void GetDistanceConstraintParameters(uint index, uint& index_one, uint& index_two,
+ Real& distance) const;
+
+ void GetHarmonicPositionRestraintParameters(uint index, uint& atom_index, geom::Vec3& ref_position,
+ Real& k, Real& x_scale, Real& y_scale, Real& z_scale) const;
+
+ void GetHarmonicDistanceRestraintParameters(uint index, uint& atom_one, uint& atom_two, Real& length,
+ Real& force_constant) const;
+
+ void GetFGMDHBondDonorParameters(uint index, uint& index_one, uint& index_two,
+ Real& length, Real& k_length, Real& alpha,
+ Real& k_alpha, Real& beta, Real& k_beta) const;
+
+ void GetFGMDHBondAcceptorParameters(uint index, uint& index_one, uint& index_two) const;
+
+ void SetHarmonicBondParameters(uint index, const Real bond_length, const Real force_constant);
+
+ void SetHarmonicAngleParameters(uint index, const Real angle, const Real force_constant);
+
+ void SetUreyBradleyAngleParameters(uint index, const Real angle, const Real angle_force_constant,
+ const Real bond_length, const Real bond_force_constant);
+
+ void SetPeriodicDihedralParameters(uint index, const int multiplicity,
+ const Real phase, const Real force_constant);
+
+ void SetPeriodicImproperParameters(uint index, const int multiplicity, const Real phase,
+ const Real force_constant);
+
+ void SetHarmonicImproperParameters(uint index, const Real angle, const Real force_constant);
+
+ void SetCMapParameters(uint index, const int dimension, const std::vector<Real>& map);
+
+ void SetLJPairParameters(uint index, const Real sigma, const Real epsilon);
+
+ void SetDistanceConstraintParameters(uint index, const Real distance);
+
+ void SetHarmonicPositionRestraintParameters(uint index, const geom::Vec3& ref_position, Real k,
+ Real x_scale = 1.0, Real y_scale = 1.0, Real z_scale = 1.0);
+
+ void SetHarmonicDistanceRestraintParameters(uint index, Real length, Real force_constant);
+
+ void SetFGMDHBondDonorParameters(uint index, Real length, Real k_length,
+ Real alpha, Real k_alpha, Real beta,
+ Real k_beta);
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetHarmonicBonds() const { return harmonic_bonds_; }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& GetHarmonicAngles() const { return harmonic_angles_; }
+
+ const std::vector<std::pair<Index<3>, std::vector<Real> > >& GetUreyBradleyAngles() const { return urey_bradley_angles_; }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetPeriodicDihedrals() const { return periodic_dihedrals_; }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetPeriodicImpropers() const { return periodic_impropers_; }
+
+ const std::vector<std::pair<Index<4>, std::vector<Real> > >& GetHarmonicImpropers() const { return harmonic_impropers_; }
+
+ const std::vector<std::pair<Index<5>, std::vector<Real> > >& GetCMaps() const { return cmaps_; }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetLJPairs() const { return lj_pairs_; }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetDistanceConstraints() const { return distance_constraints_; }
+
+ const std::vector<std::pair<Index<1>, std::vector<Real> > >& GetHarmonicPositionRestraints() const { return harmonic_position_restraints_; }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetHarmonicDistanceRestraints() const{ return harmonic_distance_restraints_; }
+
+ const std::vector<Index<2> >& GetExclusions() const { return exclusions_; }
+
+ const std::vector<uint>& GetPositionConstraints() const { return position_constraints_; }
+
+ const std::vector<std::pair<Index<2>, std::vector<Real> > >& GetFGMDHBondDonors() const { return fgmd_hbond_donors_; }
+
+ const std::vector<Index<2> >& GetFGMDHBondAcceptors() const { return fgmd_hbond_acceptors_; }
+
+ std::vector<Real> GetSigmas() const { return sigmas_; }
+
+ std::vector<Real> GetEpsilons() const { return epsilons_; }
+
+ std::vector<Real> GetGBSARadii() const { return gbsa_radii_; }
+
+ std::vector<Real> GetOBCScalings() const { return obc_scaling_; }
+
+ std::vector<Real> GetCharges() const { return charges_; }
+
+ Real GetCharge(uint index) const;
+
+ Real GetMass(uint index) const;
+
+ Real GetSigma(uint index) const;
+
+ Real GetEpsilon(uint index) const;
+
+ Real GetGBSARadius(uint index) const;
+
+ Real GetOBCScaling(uint index) const;
+
+ std::vector<Real> GetMasses() const { return atom_masses_; }
+
+ Real GetFudgeQQ() const { return fudge_qq_; }
+
+ Real GetFudgeLJ() const { return fudge_lj_; }
+
+ std::vector<uint> GetHarmonicBondIndices(uint index_one,
+ uint index_two) const;
+
+ std::vector<uint> GetHarmonicAngleIndices(uint index_one,
+ uint index_two,
+ uint index_three) const;
+
+ std::vector<uint> GetUreyBradleyAngleIndices(uint index_one,
+ uint index_two,
+ uint index_three) const;
+
+ std::vector<uint> GetPeriodicDihedralIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const;
+
+ std::vector<uint> GetPeriodicImproperIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const;
+
+ std::vector<uint> GetHarmonicImproperIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four) const;
+
+ std::vector<uint> GetCMapIndices(uint index_one,
+ uint index_two,
+ uint index_three,
+ uint index_four,
+ uint index_five) const;
+
+ int GetLJPairIndex(uint index_one,
+ uint index_two) const;
+
+ int GetDistanceConstraintIndex(uint index_one,
+ uint index_two) const;
+
+
+
+ std::vector<uint> GetHarmonicDistanceRestraintIndices(uint index_one,
+ uint index_two) const;
+
+ std::vector<uint> GetFGMDHBondDonorIndices(uint index_one,
+ uint index_two) const;
+
+ std::vector<uint> GetFGMDHBondAcceptorIndices(uint index_one,
+ uint index_two) const;
+
+ std::vector<uint> GetHarmonicBondIndices(uint atom_index) const;
+
+ std::vector<uint> GetHarmonicAngleIndices(uint atom_index) const;
+
+ std::vector<uint> GetUreyBradleyAngleIndices(uint atom_index) const;
+
+ std::vector<uint> GetPeriodicDihedralIndices(uint atom_index) const;
+
+ std::vector<uint> GetPeriodicImproperIndices(uint atom_index) const;
+
+ std::vector<uint> GetHarmonicImproperIndices(uint atom_index) const;
+
+ std::vector<uint> GetCMapIndices(uint atom_index) const;
+
+ std::vector<uint> GetLJPairIndices(uint atom_index) const;
+
+ std::vector<uint> GetDistanceConstraintIndices(uint atom_index) const;
+
+ std::vector<uint> GetHarmonicPositionRestraintIndices(uint atom_index) const;
+
+ std::vector<uint> GetHarmonicDistanceRestraintIndices(uint atom_index) const;
+
+ std::vector<uint> GetFGMDHBondDonorIndices(uint atom_index) const;
+
+ std::vector<uint> GetFGMDHBondAcceptorIndices(uint atom_index) const;
+
+ uint GetNumParticles() { return num_particles_; }
+
+ uint GetNumHarmonicBonds() { return harmonic_bonds_.size(); }
+
+ uint GetNumHarmonicAngles() { return harmonic_angles_.size(); }
+
+ uint GetNumUreyBradleyAngles() { return urey_bradley_angles_.size(); }
+
+ uint GetNumPeriodicDihedrals() { return periodic_dihedrals_.size(); }
+
+ uint GetNumPeriodicImpropers() { return periodic_impropers_.size(); }
+
+ uint GetNumHarmonicImpropers() { return harmonic_impropers_.size(); }
+
+ uint GetNumCMaps() { return cmaps_.size(); }
+
+ uint GetNumLJPairs() { return lj_pairs_.size(); }
+
+ uint GetNumDistanceConstraints() { return distance_constraints_.size(); }
+
+ uint GetNumPositionConstraints() { return position_constraints_.size(); }
+
+ uint GetNumHarmonicPositionRestraints() { return harmonic_position_restraints_.size(); }
+
+ uint GetNumHarmonicDistanceRestraints() { return harmonic_distance_restraints_.size();}
+
+ uint GetNumExclusions() { return exclusions_.size(); }
+
+ uint GetNumFGMDHBondDonors() { return fgmd_hbond_donors_.size(); }
+
+ uint GetNumFGMDHBondAcceptors() { return fgmd_hbond_acceptors_.size(); }
+
+ void Merge(ost::mol::EntityHandle& ent, TopologyPtr other, const ost::mol::EntityHandle& other_ent);
+
+ void Merge(TopologyPtr other);
+
+ template <typename DS>
+ void Serialize(DS& ds){
+
+
+ uint num_items = 0;
+ Index<2> actual_index;
+
+ ds & num_particles_;
+ ds & fudge_qq_;
+ ds & fudge_lj_;
+
+ if(ds.IsSource()){
+ ds & num_items;
+ atom_masses_ = std::vector<Real>(num_items);
+ ds & num_items;
+ sigmas_ = std::vector<Real>(num_items);
+ ds & num_items;
+ epsilons_ = std::vector<Real>(num_items);
+ ds & num_items;
+ gbsa_radii_ = std::vector<Real>(num_items);
+ ds & num_items;
+ obc_scaling_ = std::vector<Real>(num_items);
+ ds & num_items;
+ charges_ = std::vector<Real>(num_items);
+ ds & num_items;
+ position_constraints_ = std::vector<uint>(num_items);
+ }
+ else{
+ num_items = atom_masses_.size();
+ ds & num_items;
+ num_items = sigmas_.size();
+ ds & num_items;
+ num_items = epsilons_.size();
+ ds & num_items;
+ num_items = gbsa_radii_.size();
+ ds & num_items;
+ num_items = obc_scaling_.size();
+ ds & num_items;
+ num_items = charges_.size();
+ ds & num_items;
+ num_items = position_constraints_.size();
+ ds & num_items;
+ }
+
+ for(std::vector<Real>::iterator i = atom_masses_.begin();
+ i != atom_masses_.end(); ++i){
+ ds & *i;
+ }
+
+ for(std::vector<Real>::iterator i = sigmas_.begin();
+ i != sigmas_.end(); ++i){
+ ds & *i;
+ }
+
+ for(std::vector<Real>::iterator i = epsilons_.begin();
+ i != epsilons_.end(); ++i){
+ ds & *i;
+ }
+
+ for(std::vector<Real>::iterator i = gbsa_radii_.begin();
+ i != gbsa_radii_.end(); ++i){
+ ds & *i;
+ }
+
+ for(std::vector<Real>::iterator i = obc_scaling_.begin();
+ i != obc_scaling_.end(); ++i){
+ ds & *i;
+ }
+
+ for(std::vector<Real>::iterator i = charges_.begin();
+ i != charges_.end(); ++i){
+ ds & *i;
+ }
+
+ for(std::vector<uint>::iterator i = position_constraints_.begin();
+ i != position_constraints_.end(); ++i){
+ ds & *i;
+ }
+
+ if(ds.IsSource()){
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ harmonic_bonds_.push_back(std::make_pair(Index<2>(),std::vector<Real>(2)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ harmonic_angles_.push_back(std::make_pair(Index<3>(),std::vector<Real>(2)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ urey_bradley_angles_.push_back(std::make_pair(Index<3>(),std::vector<Real>(4)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ periodic_dihedrals_.push_back(std::make_pair(Index<4>(),std::vector<Real>(3)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ periodic_impropers_.push_back(std::make_pair(Index<4>(),std::vector<Real>(3)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ harmonic_impropers_.push_back(std::make_pair(Index<4>(),std::vector<Real>(2)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ uint num_values = 0;
+ ds & num_values;
+ cmaps_.push_back(std::make_pair(Index<5>(),std::vector<Real>(num_values)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ lj_pairs_.push_back(std::make_pair(Index<2>(),std::vector<Real>(2)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ distance_constraints_.push_back(std::make_pair(Index<2>(),std::vector<Real>(1)));
+ }
+
+ ds & num_items;
+ exclusions_ = std::vector<Index<2> >(num_items);
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ harmonic_position_restraints_.push_back(std::make_pair(Index<1>(),std::vector<Real>(7)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ harmonic_distance_restraints_.push_back(std::make_pair(Index<2>(),std::vector<Real>(2)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ fgmd_hbond_donors_.push_back(std::make_pair(Index<2>(),std::vector<Real>(6)));
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ fgmd_hbond_acceptors_.push_back(Index<2>());
+ }
+ }
+ else{
+ num_items = harmonic_bonds_.size();
+ ds & num_items;
+ num_items = harmonic_angles_.size();
+ ds & num_items;
+ num_items = urey_bradley_angles_.size();
+ ds & num_items;
+ num_items = periodic_dihedrals_.size();
+ ds & num_items;
+ num_items = periodic_impropers_.size();
+ ds & num_items;
+ num_items = harmonic_impropers_.size();
+ ds & num_items;
+ num_items = cmaps_.size();
+ ds & num_items;
+ for(uint i = 0; i < cmaps_.size(); ++i){
+ num_items = cmaps_[i].second.size();
+ ds & num_items;
+ }
+ num_items = lj_pairs_.size();
+ ds & num_items;
+ num_items = distance_constraints_.size();
+ ds & num_items;
+ num_items = exclusions_.size();
+ ds & num_items;
+ num_items = harmonic_position_restraints_.size();
+ ds & num_items;
+ num_items = harmonic_distance_restraints_.size();
+ ds & num_items;
+ num_items = fgmd_hbond_donors_.size();
+ ds & num_items;
+ num_items = fgmd_hbond_acceptors_.size();
+ ds & num_items;
+ }
+
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::iterator i = harmonic_bonds_.begin();
+ i != harmonic_bonds_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ }
+
+ for(std::vector<std::pair<Index<3>,std::vector<Real> > >::iterator i = harmonic_angles_.begin();
+ i != harmonic_angles_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ }
+
+ for(std::vector<std::pair<Index<3>,std::vector<Real> > >::iterator i = urey_bradley_angles_.begin();
+ i != urey_bradley_angles_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ ds & i->second[2];
+ ds & i->second[3];
+ }
+
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::iterator i = periodic_dihedrals_.begin();
+ i != periodic_dihedrals_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ ds & i->second[2];
+ }
+
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::iterator i = periodic_impropers_.begin();
+ i != periodic_impropers_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ ds & i->second[2];
+ }
+
+ for(std::vector<std::pair<Index<4>,std::vector<Real> > >::iterator i = harmonic_impropers_.begin();
+ i != harmonic_impropers_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ }
+
+ for(std::vector<std::pair<Index<5>,std::vector<Real> > >::iterator i = cmaps_.begin();
+ i != cmaps_.end(); ++i){
+ ds & i->first;
+ for(std::vector<Real>::iterator j = i->second.begin();
+ j != i->second.end(); ++j){
+ ds & (*j);
+ }
+ }
+
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::iterator i = lj_pairs_.begin();
+ i != lj_pairs_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ }
+
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::iterator i = distance_constraints_.begin();
+ i != distance_constraints_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ }
+
+ for(std::vector<Index<2> >::iterator i = exclusions_.begin();
+ i != exclusions_.end(); ++i){
+ ds & (*i);
+ }
+
+ for(std::vector<std::pair<Index<1>,std::vector<Real> > >::iterator i = harmonic_position_restraints_.begin();
+ i != harmonic_position_restraints_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ ds & i->second[2];
+ ds & i->second[3];
+ ds & i->second[4];
+ ds & i->second[5];
+ ds & i->second[6];
+ }
+
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::iterator i = harmonic_distance_restraints_.begin();
+ i != harmonic_distance_restraints_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ }
+
+ for(std::vector<std::pair<Index<2>,std::vector<Real> > >::iterator i = fgmd_hbond_donors_.begin();
+ i != fgmd_hbond_donors_.end(); ++i){
+ ds & i->first;
+ ds & i->second[0];
+ ds & i->second[1];
+ ds & i->second[2];
+ ds & i->second[3];
+ ds & i->second[4];
+ ds & i->second[5];
+ }
+
+ for(std::vector<Index<2> >::iterator i = fgmd_hbond_acceptors_.begin();
+ i != fgmd_hbond_acceptors_.end(); ++i){
+ ds & (*i);
+ }
+
+ if(ds.IsSource()){
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ ds & actual_index;
+ added_lj_pairs_.insert(actual_index);
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ ds & actual_index;
+ added_distance_constraints_.insert(actual_index);
+ }
+
+ ds & num_items;
+ for(uint i = 0; i < num_items; ++i){
+ ds & actual_index;
+ added_exclusions_.insert(actual_index);
+ }
+ }
+ else{
+ num_items = added_lj_pairs_.size();
+ ds & num_items;
+ for(std::set<Index<2> >::iterator i = added_lj_pairs_.begin();
+ i != added_lj_pairs_.end(); ++i){
+ actual_index = *i;
+ ds & actual_index;
+ }
+ num_items = added_distance_constraints_.size();
+ ds & num_items;
+ for(std::set<Index<2> >::iterator i = added_distance_constraints_.begin();
+ i != added_distance_constraints_.end(); ++i){
+ actual_index = *i;
+ ds & actual_index;
+ }
+ num_items = added_exclusions_.size();
+ ds & num_items;
+ for(std::set<Index<2> >::iterator i = added_exclusions_.begin();
+ i != added_exclusions_.end(); ++i){
+ actual_index = *i;
+ ds & actual_index;
+ }
+ }
+ }
+
+private:
+
+ void MergeTop(TopologyPtr other);
+
+ void MergeEnt(ost::mol::EntityHandle& ent, const ost::mol::EntityHandle& other_ent);
+
+ void CheckTopToAdd(TopologyPtr other);
+
+ void CheckEntToAdd(ost::mol::EntityHandle& ent, TopologyPtr other,
+ const ost::mol::EntityHandle& other_ent);
+
+ uint num_particles_;
+
+ //fudge parameters for lj 1,4 pairs
+ Real fudge_qq_;
+ Real fudge_lj_;
+
+ //single atom parameters
+ std::vector<Real> atom_masses_;
+ std::vector<Real> sigmas_;
+ std::vector<Real> epsilons_;
+ std::vector<Real> gbsa_radii_;
+ std::vector<Real> obc_scaling_;
+ std::vector<Real> charges_;
+ std::vector<uint> position_constraints_;
+
+ //interactions with multiple atoms involved
+ std::vector<std::pair<Index<2>,std::vector<Real> > > harmonic_bonds_;
+ std::vector<std::pair<Index<3>,std::vector<Real> > > harmonic_angles_;
+ std::vector<std::pair<Index<3>,std::vector<Real> > > urey_bradley_angles_;
+ std::vector<std::pair<Index<4>,std::vector<Real> > > periodic_dihedrals_;
+ std::vector<std::pair<Index<4>,std::vector<Real> > > periodic_impropers_;
+ std::vector<std::pair<Index<4>,std::vector<Real> > > harmonic_impropers_;
+ std::vector<std::pair<Index<5>,std::vector<Real> > > cmaps_;
+ std::vector<std::pair<Index<2>,std::vector<Real> > > lj_pairs_;
+ std::vector<std::pair<Index<2>,std::vector<Real> > > distance_constraints_;
+ std::vector<Index<2> > exclusions_;
+ std::vector<std::pair<Index<1>,std::vector<Real> > > harmonic_position_restraints_;
+ std::vector<std::pair<Index<2>,std::vector<Real> > > harmonic_distance_restraints_;
+ std::vector<std::pair<Index<2>,std::vector<Real> > > fgmd_hbond_donors_;
+ std::vector<Index<2> > fgmd_hbond_acceptors_;
+
+ //the atoms of the interactions, that should be unique get tracked in here
+ //note, that this is waste of memory, needs better implementation
+ std::set<Index<2> > added_lj_pairs_;
+ std::set<Index<2> > added_distance_constraints_;
+ std::set<Index<2> > added_exclusions_;
+
+};
+
+
+}}} //ns
+
+#endif
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
new file mode 100644
index 0000000000000000000000000000000000000000..bb1c418f685ca488d13f564d77a7142cf649b71f
--- /dev/null
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -0,0 +1,980 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/mol/mm/topology_creator.hh>
+#include <ost/mol/mm/modeller.hh>
+
+namespace{
+
+int GetAtomIndex(uint residue_index,
+ ost::mol::ResidueHandleList& res_list,
+ std::map<long,int>& atom_indices,
+ const String& atom_name){
+
+ if(atom_name[0] == '+'){
+ ost::mol::ResidueHandle actual_res = res_list[residue_index];
+ ost::mol::ResidueHandle next_residue = actual_res.GetNext();
+ if(!next_residue){
+ throw ost::Error("Could not find required atom when settings up topology!");
+ }
+ String next_atom_name = atom_name.substr(1);
+ ost::mol::AtomHandle at = next_residue.FindAtom(next_atom_name);
+ if(!at.IsValid()){
+ throw ost::Error("Could not find required atom when settings up topology!");
+ }
+ return atom_indices[at.GetHashCode()];
+ }
+
+ if(atom_name[0] == '-'){
+ ost::mol::ResidueHandle actual_res = res_list[residue_index];
+ ost::mol::ResidueHandle prev_residue = actual_res.GetPrev();
+ if(!prev_residue){
+ throw ost::Error("Could not find required atom when settings up topology!");
+ }
+ String prev_atom_name = atom_name.substr(1);
+ ost::mol::AtomHandle at = prev_residue.FindAtom(prev_atom_name);
+ if(!at.IsValid()){
+ throw ost::Error("Could not find required atom when settings up topology!");
+ }
+ return atom_indices[at.GetHashCode()];
+ }
+
+ ost::mol::AtomHandle at = res_list[residue_index].FindAtom(atom_name);
+ if(!at.IsValid()){
+ throw ost::Error("Could not find required atom when settings up topology!");
+ }
+ return atom_indices[at.GetHashCode()];
+}
+
+
+
+
+
+
+}
+
+namespace ost{ namespace mol{ namespace mm{
+
+TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
+ const SettingsPtr settings){
+
+
+ ost::mol::ResidueHandleList res_list = ent.GetResidueList();
+ ost::mol::XCSEditor ed = ent.EditXCS(ost::mol::BUFFERED_EDIT);
+
+ //rename all the stuff to the gromacs naming...
+ Modeller::AssignGromacsNaming(ent);
+
+ //even if not reconnected yet, it gets assumed, that
+ //peptide or nucleotide bonds are correctly set in the input entity
+ //to allow the identification and tagging of terminal residues
+ //note, that only nucleotides or aminoacids are allowed to build termini...
+ //this should be enough for most needs
+
+ ost::mol::ResidueHandle next,prev;
+ bool n_ter,c_ter;
+ ost::mol::AtomHandle peptide_n,peptide_c,nucleotide_p,nucleotide_o;
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+
+ n_ter = false;
+ c_ter = false;
+
+ peptide_n = i->FindAtom("N");
+ nucleotide_p = i->FindAtom("P");
+
+ if(!peptide_n.IsValid() && !nucleotide_p.IsValid()) continue;
+ //in this case the residue is neither a peptide nor a nucleotide.
+ //There won't be a termini anyway...
+
+ prev = i->GetPrev();
+ next = i->GetNext();
+
+ if(!prev.IsValid()){
+ n_ter = true;
+ }
+ else{
+ peptide_c = prev.FindAtom("C");
+ nucleotide_o = prev.FindAtom("O3");
+
+ if(!ost::mol::BondExists(peptide_n,peptide_c) && !ost::mol::BondExists(nucleotide_p,nucleotide_o)){
+ n_ter = true;
+ }
+ }
+
+ if(!next.IsValid()){
+ c_ter = true;
+ }
+ else{
+ peptide_n = next.FindAtom("N");
+ peptide_c = i->FindAtom("C");
+ nucleotide_p = next.FindAtom("P");
+ nucleotide_o = i->FindAtom("O3");
+
+ if(!ost::mol::BondExists(peptide_n,peptide_c) && !ost::mol::BondExists(nucleotide_p,nucleotide_o)){
+ c_ter = true;
+ }
+ }
+
+ if(n_ter) i->SetBoolProp("n_ter",true);
+ if(c_ter) i->SetBoolProp("c_ter",true);
+ }
+
+
+ ForcefieldPtr ff = settings->forcefield;
+ if(!ff){
+ throw ost::Error("You have to assign a valid forcefield to the settings object when creating a topology!");
+ }
+ //The full parametrization procedure relies on the naming, that is force field specific
+
+ ost::mol::BondHandleList bond_list = ent.GetBondList();
+ ed.DeleteBonds(bond_list);
+ ed.UpdateICS();
+
+ if(settings->generate_disulfid_bonds){
+ Modeller::GenerateDisulfidBonds(ent);
+ }
+
+ ff->AssignFFSpecificNames(ent);
+
+ //we first generate the building blocks and directly construct hydrogens/termini and stuff
+ std::vector<BuildingBlockPtr> building_blocks;
+
+ for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
+ i != res_list.end(); ++i){
+ BuildingBlockPtr block = ff->GetBuildingBlock(i->GetName());
+ HydrogenConstructorPtr hc = ff->GetHydrogenConstructor(i->GetName());
+ if(hc){
+ hc->ApplyOnBuildingBlock(block);
+ hc->ApplyOnResidue(*i,ed);
+ }
+ //check for n terminus
+ if(i->HasProp("n_ter")){
+ String exception_name = "";
+ if(settings->termini_exceptions->HasException(*i)){
+ exception_name = settings->termini_exceptions->GetException(*i);
+ }
+ BlockModifierPtr bm = ff->GetNTerModifier(i->GetName(), exception_name);
+ if(bm){
+ bm->ApplyOnBuildingBlock(block);
+ bm->ApplyOnResidue(*i,ed);
+ block->RemoveInteractionsToPrev();
+ }
+ }
+ if(i->HasProp("c_ter")){
+ String exception_name = "";
+ if(settings->termini_exceptions->HasException(*i)){
+ exception_name = settings->termini_exceptions->GetException(*i);
+ }
+ BlockModifierPtr bm = ff->GetCTerModifier(i->GetName(), exception_name);
+ if(bm){
+ bm->ApplyOnBuildingBlock(block);
+ bm->ApplyOnResidue(*i,ed);
+ block->RemoveInteractionsToNext();
+ }
+ }
+ block->Connect(*i,ed);
+ building_blocks.push_back(block);
+ }
+
+ //The editor won't be needed anymore, let's update the internal coordinate system
+ ed.UpdateICS();
+
+
+ //check, whether all building blocks match now with the previously applied modifications
+ String match_fail_info;
+ for(unsigned int i = 0; i < building_blocks.size(); ++i){
+ if(!building_blocks[i]->Match(res_list[i], false, match_fail_info)){
+ std::stringstream ss;
+ ss << "Residue "<< res_list[i].GetQualifiedName() << " does not match the force field ";
+ ss << "definition. "<<match_fail_info;
+ throw ost::Error(ss.str());
+ }
+ }
+
+ std::vector<Real> initial_masses(ent.GetAtomCount());
+
+ TopologyPtr top = TopologyPtr(new Topology(initial_masses));
+
+ ost::mol::AtomHandleList atom_list = ent.GetAtomList();
+
+ std::map<long,int> atom_indices;
+ std::map<long,int> residue_indices;
+ int actual_index = 0;
+
+ for(ost::mol::AtomHandleList::const_iterator i = atom_list.begin(), e = atom_list.end();
+ i != e; ++i){
+ atom_indices[i->GetHashCode()] = actual_index;
+ ++actual_index;
+ }
+
+ actual_index = 0;
+ for(ost::mol::ResidueHandleList::const_iterator i = res_list.begin(), e = res_list.end();
+ i != e; ++i){
+ residue_indices[i->GetHashCode()] = actual_index;
+ ++actual_index;
+ }
+
+
+ //let's extract atom specific informations
+ //extract information about single atoms
+ std::vector<std::vector<uint> > bound_to;
+ std::vector<String> atom_types;
+ std::vector<Real> atom_charges;
+ std::vector<String> atom_names;
+ std::vector<Real> atom_masses;
+ std::vector<String> residue_names_of_atoms;
+ ost::mol::AtomHandleList bonded_atoms;
+ std::vector<uint> temp;
+ int residue_index;
+
+ //extract masses, types, charges and bondpartners
+
+ for(ost::mol::AtomHandleList::iterator i = atom_list.begin();
+ i!=atom_list.end();++i){
+ residue_index = residue_indices[i->GetResidue().GetHashCode()];
+ residue_names_of_atoms.push_back(i->GetResidue().GetName());
+ atom_types.push_back(building_blocks[residue_index]->GetType(i->GetName()));
+ atom_charges.push_back(building_blocks[residue_index]->GetCharge(i->GetName()));
+ atom_masses.push_back(ff->GetMass(atom_types.back()));
+ bonded_atoms = i->GetBondPartners();
+ temp.clear();
+ for(ost::mol::AtomHandleList::iterator j = bonded_atoms.begin();
+ j!=bonded_atoms.end();++j){
+ temp.push_back(atom_indices[j->GetHashCode()]);
+ }
+ bound_to.push_back(temp);
+ }
+
+ //let's set the proper masses
+ top->SetMasses(atom_masses);
+
+
+ //we simply set all charges to zero if we want to kill the electrostatics
+ if(settings->kill_electrostatics){
+ for(std::vector<Real>::iterator i = atom_charges.begin();
+ i != atom_charges.end(); ++i){
+ *i = 0;
+ }
+ }
+
+ top->SetCharges(atom_charges);
+
+ //the interaction read from the structure will be stored in here
+ std::set<Index<2> > bonds;
+ std::set<Index<3> > angles;
+ std::set<Index<4> > dihedrals;
+ std::set<Index<4> > impropers;
+ std::set<Index<5> > cmaps;
+ std::set<Index<2> > exclusions;
+ std::set<Index<2> > pairs_14;
+ std::set<Index<2> > distance_constraints;
+ //per atom parameters
+ std::vector<InteractionPtr> ljs;
+ std::vector<InteractionPtr> gbsa;
+ //extract all bonded interactions directly from the structure itself,
+ //except the impropers, cmaps and exclusions. Those two get read from the building
+ //blocks.
+ //Note, that the bonds build the basis to build angles and the angles
+ //build the basis to build dihedrals... so we have to extract bonds
+ //even when only dihedrals have to be added.
+ //Another special case is when nonbonded terms have to be added.
+ //They often exclude interactions originating from closely bonded
+ //atoms. We will use the bonds, angles and dihedrals later on to
+ //define these closely bonded atoms, so if nonbonded terms have to
+ //added, we also need to get the bonds, angles and dihedrals.
+ if(settings->add_bonds || settings->add_angles ||
+ settings->add_dihedrals || settings->add_nonbonded){
+ //build all bonds
+ for(uint i=0 ; i<bound_to.size() ;++i){
+ for(uint j = 0; j<bound_to[i].size(); ++j){
+ bonds.insert(Index<2>(std::min(i,bound_to[i][j]),std::max(i,bound_to[i][j])));
+ }
+ }
+ }
+ if(settings->add_angles || settings->add_dihedrals ||
+ settings->add_nonbonded){
+ //build all angles
+ for(std::set<Index<2> >::iterator i = bonds.begin();
+ i!=bonds.end();++i){
+ uint atom_1 = (*i)[0];
+ uint atom_2 = (*i)[1];
+
+ for(std::vector<uint>::iterator j = bound_to[atom_1].begin();
+ j!=bound_to[atom_1].end(); ++j){
+ if((*j) != atom_2){
+ angles.insert(Index<3>(std::min((*j),atom_2),atom_1,std::max((*j),atom_2)));
+ }
+ }
+ for(std::vector<uint>::iterator j = bound_to[atom_2].begin();
+ j!=bound_to[atom_2].end(); ++j){
+ if((*j) != atom_1){
+ angles.insert(Index<3>(std::min((*j),atom_1),atom_2,std::max((*j),atom_1)));
+ }
+ }
+ }
+ }
+ if(settings->add_dihedrals || settings->add_nonbonded){
+ //build all dihedrals
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i!=angles.end();++i){
+ uint atom_1 = (*i)[0];
+ uint atom_2 = (*i)[1];
+ uint atom_3 = (*i)[2];
+ for(std::vector<uint>::iterator j = bound_to[atom_1].begin();
+ j!=bound_to[atom_1].end();++j){
+ if((*j)!=atom_2){
+ if((*j)<atom_3) dihedrals.insert(Index<4>(*j,atom_1,atom_2,atom_3));
+ else dihedrals.insert(Index<4>(atom_3,atom_2,atom_1,*j));
+ }
+ }
+ for(std::vector<uint>::iterator j = bound_to[atom_3].begin();
+ j!=bound_to[atom_3].end();++j){
+ if((*j)!=atom_2){
+ if((*j)<atom_1) dihedrals.insert(Index<4>(*j,atom_3,atom_2,atom_1));
+ else dihedrals.insert(Index<4>(atom_1,atom_2,atom_3,*j));
+ }
+ }
+ }
+ }
+ //impropers exclusions and cmaps get read from residuetemplates!
+ std::vector<InteractionPtr> interaction_list;
+ std::vector<String> interaction_atom_names;
+
+ if(settings->add_impropers){
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetImpropers();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ interaction_atom_names = (*j)->GetNames();
+ Index<4> improper_index;
+ for(uint k = 0; k < 4; ++k){
+ improper_index[k] = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[k]);
+ }
+ impropers.insert(improper_index);
+ }
+ }
+ }
+
+ if(settings->add_cmaps){
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetCMaps();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ interaction_atom_names = (*j)->GetNames();
+ Index<5> cmap_index;
+ for(uint k = 0; k < 5; ++k){
+ cmap_index[k] = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[k]);
+ }
+ cmaps.insert(cmap_index);
+ }
+ }
+ }
+
+ if(settings->add_nonbonded && settings->add_exclusions){
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetExclusions();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
+ uint two = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[1]);
+ exclusions.insert(Index<2>(std::min(one,two),std::max(one,two)));
+ }
+ }
+ }
+ if(settings->add_nonbonded){
+
+ //find exclusions and excpetions based on connectivity
+ //add exclusions using previously extracted bonds => 1,2 interactions
+ for(std::set<Index<2> >::iterator i = bonds.begin();
+ i!=bonds.end(); ++i){
+ exclusions.insert(*i);
+ }
+ //add exclusions using previously extracted angles => 1,3 interactions
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i!=angles.end(); ++i){
+ exclusions.insert(Index<2>((*i)[0],(*i)[2]));
+ }
+ //add exclusions using previously extracted dihedrals => 1,4 interactions
+ for(std::set<Index<4> >::iterator i = dihedrals.begin();
+ i!=dihedrals.end(); ++i){
+ pairs_14.insert(Index<2>((*i)[0],(*i)[3]));
+ }
+
+ //remove all exclusions from the 1,4 interactions
+ for(std::set<Index<2> >::iterator i = exclusions.begin();
+ i != exclusions.end(); ++i){
+ pairs_14.erase(*i);
+ }
+ }
+
+ //we will need this goddamn variable in a lot of places...
+ std::vector<Real> parameters;
+
+
+ //add constraints from building blocks
+ //note, that the constraints are in some cases parametrized.
+ //If there is no constraint distance specified, the actual distance
+ //between the corresponding atoms is taken.
+ //if there are several constraints on the same atom pair,
+ //only the first is added to avoid contradicting constraints
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetConstraints();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
+ uint two = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[1]);
+ Index<2> index(std::min(one,two),std::max(one,two));
+ //we don't want contradicting constraints!
+ if(distance_constraints.find(index) != distance_constraints.end()) continue;
+ distance_constraints.insert(index);
+ Real distance;
+ if((*j)->IsParametrized()){
+ parameters = (*j)->GetParam();
+ distance = parameters[0];
+ }
+ else distance = geom::Distance(atom_list[one].GetPos(),atom_list[two].GetPos())/10;
+ top->AddDistanceConstraint(one,two,distance);
+ }
+ }
+
+ std::set<String> water_res_names;
+ water_res_names.insert("SOL");
+ water_res_names.insert("HOH");
+ water_res_names.insert("TIP3");
+
+ //add distance constrains given the corresponding settings
+ if(settings->constrain_bonds || settings->constrain_hbonds || settings->rigid_water){
+ for(std::set<Index<2> >::iterator i = bonds.begin();
+ i != bonds.end(); ++i){
+ if(settings->constrain_bonds){
+ if(distance_constraints.find(*i) != distance_constraints.end()) continue;
+ distance_constraints.insert(*i);
+ Real distance;
+ if(settings->ideal_bond_length_constraints){
+ InteractionPtr bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ parameters = bond_ptr->GetParam();
+ distance = parameters[0];
+ }
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[1]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[1],distance);
+ continue;
+ }
+ if(settings->constrain_hbonds){
+ if(atom_names[(*i)[0]][0] == 'H' || atom_names[(*i)[1]][0] == 'H'){
+ if(distance_constraints.find(*i) != distance_constraints.end()) continue;
+ distance_constraints.insert(*i);
+ Real distance;
+ if(settings->ideal_bond_length_constraints){
+ InteractionPtr bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ parameters = bond_ptr->GetParam();
+ distance = parameters[0];
+ }
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[1]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[1],distance);
+ continue;
+ }
+ }
+ if(settings->rigid_water){
+ if(water_res_names.find(residue_names_of_atoms[(*i)[0]]) != water_res_names.end() &&
+ water_res_names.find(residue_names_of_atoms[(*i)[1]]) != water_res_names.end()){
+ if(distance_constraints.find(*i) != distance_constraints.end()) continue;
+ distance_constraints.insert(*i);
+ Real distance;
+ if(settings->ideal_bond_length_constraints) distance = 0.09572; //OH bond length in water in CHARMM forcefield...
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[1]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[1],distance);
+ continue;
+ }
+ }
+ }
+ }
+
+ //set angle constraints given the corresponding settings
+ std::set<Index<3> > constrained_angles;
+ if(settings->rigid_water){
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i != angles.end(); ++i){
+ if(water_res_names.find(residue_names_of_atoms[(*i)[0]]) != water_res_names.end() &&
+ water_res_names.find(residue_names_of_atoms[(*i)[1]]) != water_res_names.end() &&
+ water_res_names.find(residue_names_of_atoms[(*i)[2]]) != water_res_names.end()){
+ //we only have to add the H-H distance constant, the O-H distance is already
+ //constrained above
+ Real distance;
+ if(settings->ideal_bond_length_constraints) distance = 0.15139; //HH distance taken from CHARMM
+ else distance = geom::Distance(atom_list[(*i)[0]].GetPos(),atom_list[(*i)[2]].GetPos())/10;
+ top->AddDistanceConstraint((*i)[0],(*i)[2],distance);
+ constrained_angles.insert(*i);
+ }
+ }
+ }
+
+ //remove all constraints from the bonds and angles
+ for(std::set<Index<2> >::iterator i = distance_constraints.begin();
+ i != distance_constraints.end(); ++i){
+ bonds.erase(*i);
+ }
+
+ for(std::set<Index<3> >::iterator i = constrained_angles.begin();
+ i!= constrained_angles.end(); ++i){
+ angles.erase(*i);
+ }
+
+
+ //the force definitions from the forcefield can be overwritten by parameters
+ //defined in the residue building blocks.
+ //We therefore check which forces have been defined in the building blocks
+ //and don't search them any more in the forcefield forces.
+ std::vector<String> types;
+ if(settings->add_bonds){
+ //handle bonds
+ for(uint i = 0; i < res_list.size(); ++i){
+ interaction_list = building_blocks[i]->GetBonds();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
+ uint two = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[1]);
+ Index<2> bond_index(std::min(one,two),std::max(one,two));
+ bonds.erase(bond_index);
+ //There are only harmonic bonds supported
+ parameters = (*j)->GetParam();
+ top->AddHarmonicBond(one,two,parameters[0],parameters[1]);
+ }
+ }
+ }
+ //add pointers of bond definitions, that are not already parametrized
+ //in the building blocks
+ for(std::set<Index<2> >::iterator i = bonds.begin();
+ i!=bonds.end(); ++i){
+
+ InteractionPtr bond_ptr;
+ try{
+ bond_ptr = ff->GetBond(atom_types[(*i)[0]],atom_types[(*i)[1]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize bond between: " << atom_list[(*i)[0]];
+ ss << " and "<<atom_list[(*i)[1]] << ". ";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+
+ parameters = bond_ptr->GetParam();
+ top->AddHarmonicBond((*i)[0],(*i)[1],parameters[0],parameters[1]);
+ }
+ }
+
+ if(settings->add_angles){
+ //handle angles
+ for(uint i = 0; i < res_list.size(); ++i){
+ interaction_list = building_blocks[i]->GetAngles();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
+ uint two = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[1]);
+ uint three = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[2]);
+ Index<3> angle_index(std::min(one,three),two,std::max(one,three));
+ if(angles.find(angle_index) == angles.end()){
+ std::stringstream ss;
+ ss << "Building block for residue " << res_list[i].GetQualifiedName();
+ ss << " defines angle, that doesn't exist!";
+ throw ost::Error(ss.str());
+ }
+ angles.erase(angle_index);
+ parameters = (*j)->GetParam();
+ switch((*j)->GetFuncType()){
+ case HarmonicAngle:{
+ top->AddHarmonicAngle(angle_index[0],angle_index[1],angle_index[2],
+ parameters[0], parameters[1]);
+ break;
+ }
+ case UreyBradleyAngle:{
+ top->AddUreyBradleyAngle(angle_index[0],angle_index[1],angle_index[2],
+ parameters[0], parameters[1], parameters[2],
+ parameters[3]);
+ break;
+ }
+ default:{
+ throw ost::Error("Observed unknown function type for angle interaction!");
+ }
+ }
+ }
+ }
+ }
+ //add pointers of angle definitions, that are not already parametrized
+ //in the building blocks
+ for(std::set<Index<3> >::iterator i = angles.begin();
+ i!=angles.end(); ++i){
+
+ InteractionPtr angle_ptr;
+ try{
+ angle_ptr = ff->GetAngle(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ atom_types[(*i)[2]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize angle between: " << atom_list[(*i)[0]];
+ ss << ", "<<atom_list[(*i)[1]] << " and " << atom_list[(*i)[2]] << ".";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+
+ parameters = angle_ptr->GetParam();
+ switch(angle_ptr->GetFuncType()){
+ case HarmonicAngle:{
+ top->AddHarmonicAngle((*i)[0],(*i)[1],(*i)[2],
+ parameters[0],parameters[1]);
+ break;
+ }
+ case UreyBradleyAngle:{
+ top->AddUreyBradleyAngle((*i)[0],(*i)[1],(*i)[2],
+ parameters[0],parameters[1],
+ parameters[2],parameters[3]);
+ break;
+ }
+ default:{
+ throw ost::Error("Observed invalid function type for angle interaction!");
+ }
+ }
+ }
+ }
+
+ if(settings->add_dihedrals){
+ //handle dihedrals
+ std::set<Index<4> > dihedrals_to_delete;
+ for(uint i = 0; i < res_list.size(); ++i){
+ interaction_list = building_blocks[i]->GetDihedrals();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ interaction_atom_names = (*j)->GetNames();
+ uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
+ uint two = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[1]);
+ uint three = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[2]);
+ uint four = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[3]);
+ Index<4> dihedral_index;
+ if(one<four){
+ dihedral_index[0] = one;
+ dihedral_index[1] = two;
+ dihedral_index[2] = three;
+ dihedral_index[3] = four;
+ }
+ else{
+ dihedral_index[0] = four;
+ dihedral_index[1] = three;
+ dihedral_index[2] = two;
+ dihedral_index[3] = one;
+ }
+ if(dihedrals.find(dihedral_index) == dihedrals.end()){
+ std::stringstream ss;
+ ss << "Building block for residue " << res_list[i].GetQualifiedName();
+ ss << "defines dihedral, that doesn't exist!";
+ throw ost::Error(ss.str());
+ }
+
+ dihedrals_to_delete.insert(dihedral_index);
+ //only periodic dihedrals are supported...
+ parameters = (*j)->GetParam();
+ top->AddPeriodicDihedral(one,two,three,four,
+ parameters[0],parameters[1],parameters[2]);
+ }
+ }
+ }
+
+ for(std::set<Index<4> >::iterator i = dihedrals_to_delete.begin();
+ i != dihedrals_to_delete.end(); ++i){
+ dihedrals.erase(*i);
+ }
+
+ //add pointers of dihedrals definitions, that are not already parametrized
+ //in the building blocks
+ for(std::set<Index<4> >::iterator i = dihedrals.begin();
+ i!=dihedrals.end(); ++i){
+
+ std::vector<InteractionPtr> dihedral_ptr;
+
+ try{
+ dihedral_ptr = ff->GetDihedrals(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ atom_types[(*i)[2]],
+ atom_types[(*i)[3]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize dihedral between: " << atom_list[(*i)[0]];
+ ss << ", "<<atom_list[(*i)[1]] << ", " << atom_list[(*i)[2]] << " and ";
+ ss << atom_list[(*i)[3]] << ".";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+
+ for(std::vector<InteractionPtr>::iterator j = dihedral_ptr.begin();
+ j != dihedral_ptr.end(); ++j){
+ parameters = (*j)->GetParam();
+ top->AddPeriodicDihedral((*i)[0],(*i)[1],(*i)[2],(*i)[3],
+ parameters[0],parameters[1],parameters[2]);
+ }
+ }
+ }
+
+ if(settings->add_impropers){
+ //handle impropers
+ std::set<Index<4> > impropers_to_delete;
+ for(uint i = 0; i < building_blocks.size(); ++i){
+ interaction_list = building_blocks[i]->GetImpropers();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ //we do not have to care about the ordering, since we extracted the
+ //impropers from the building block => they will have the same ordering
+ //anyway (or at least hopefully ;)
+ interaction_atom_names = (*j)->GetNames();
+ uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
+ uint two = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[1]);
+ uint three = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[2]);
+ uint four = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[3]);
+ Index<4> improper_index(one,two,three,four);
+ impropers_to_delete.insert(improper_index);
+ parameters = (*j)->GetParam();
+ switch((*j)->GetFuncType()){
+ case PeriodicImproper:{
+ top->AddPeriodicImproper(one,two,three,four,
+ parameters[0],parameters[1],parameters[2]);
+ break;
+ }
+ case HarmonicImproper:{
+ top->AddHarmonicImproper(one,two,three,four,
+ parameters[0],parameters[1]);
+ break;
+ }
+ default:{
+ throw ost::Error("Observed invalid function type when adding improper interaction!");
+ }
+ }
+ }
+ }
+ }
+
+ for(std::set<Index<4> >::iterator i = impropers_to_delete.begin();
+ i != impropers_to_delete.end(); ++i){
+ impropers.erase(*i);
+ }
+
+ //add pointers of improper definitions, that are not already parametrized
+ //in the building blocks
+
+ for(std::set<Index<4> >::iterator i = impropers.begin();
+ i!=impropers.end(); ++i){
+
+ std::vector<InteractionPtr> improper_ptr;
+
+ try{
+ improper_ptr = ff->GetImpropers(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ atom_types[(*i)[2]],
+ atom_types[(*i)[3]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize improper between: " << atom_list[(*i)[0]];
+ ss << ", "<<atom_list[(*i)[1]] << ", " << atom_list[(*i)[2]] << " and ";
+ ss << atom_list[(*i)[3]] << ".";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+
+ for(std::vector<InteractionPtr>::iterator j = improper_ptr.begin();
+ j != improper_ptr.end(); ++j){
+ parameters = (*j)->GetParam();
+ switch((*j)->GetFuncType()){
+ case PeriodicImproper:{
+ top->AddPeriodicImproper((*i)[0],(*i)[1],(*i)[2],(*i)[3],
+ parameters[0],parameters[1],parameters[2]);
+ break;
+ }
+ case HarmonicImproper:{
+ top->AddHarmonicImproper((*i)[0],(*i)[1],(*i)[2],(*i)[3],
+ parameters[0],parameters[1]);
+ break;
+ }
+ default:{
+ throw ost::Error("Observed invalid function type when adding improper interaction!");
+ }
+ }
+ }
+ }
+ }
+
+ if(settings->add_cmaps){
+ //handle cmaps
+ for(uint i = 0; i < res_list.size(); ++i){
+ interaction_list = building_blocks[i]->GetCMaps();
+ for(std::vector<InteractionPtr>::iterator j = interaction_list.begin();
+ j != interaction_list.end(); ++j){
+ if((*j)->IsParametrized()){
+ //we do not have to care about the ordering, since we extracted the
+ //cmaps from the building block => they will have the same ordering
+ //anyway
+ interaction_atom_names = (*j)->GetNames();
+ uint one = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[0]);
+ uint two = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[1]);
+ uint three = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[2]);
+ uint four = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[3]);
+ uint five = GetAtomIndex(i,res_list,atom_indices,interaction_atom_names[4]);
+ Index<5> cmap_index(one,two,three,four,five);
+ cmaps.erase(cmap_index);
+ parameters = (*j)->GetParam();
+ int dimension = int(parameters[0]);
+ parameters.erase(parameters.begin());
+ top->AddCMap(cmap_index[0],cmap_index[1],cmap_index[2],cmap_index[3],
+ cmap_index[4],dimension,parameters);
+ }
+ }
+ }
+
+ //add pointers of cmap definitions, that are not already parametrized
+ //in the building blocks
+ for(std::set<Index<5> >::iterator i = cmaps.begin();
+ i!=cmaps.end(); ++i){
+
+ InteractionPtr cmap_ptr;
+
+ try{
+ cmap_ptr = ff->GetCMap(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ atom_types[(*i)[2]],
+ atom_types[(*i)[3]],
+ atom_types[(*i)[4]]);
+ } catch(ost::Error& e){
+ if(settings->strict_interactions){
+ std::stringstream ss;
+ ss << "Failed to parametrize cmap between: " << atom_list[(*i)[0]];
+ ss << ", "<<atom_list[(*i)[1]] << ", " << atom_list[(*i)[2]] << ", ";
+ ss << atom_list[(*i)[3]] << " and " << atom_list[(*i)[4]] << ".";
+ ss << "To ignore these things, set strict_interactions in the settings";
+ ss << " object to False (not recommended).";
+ throw ost::Error(ss.str());
+ }
+ continue; // ignore it and continue with next interaction
+ }
+ parameters = cmap_ptr->GetParam();
+ int dimension = int(parameters[0]);
+ parameters.erase(parameters.begin());
+ top->AddCMap((*i)[0],(*i)[1],(*i)[2],(*i)[3],(*i)[4],dimension,parameters);
+ }
+ }
+
+ if(settings->add_nonbonded){
+
+ InteractionPtr lj_interaction;
+ std::vector<Real> sigmas;
+ std::vector<Real> epsilons;
+
+ for(std::vector<String>::iterator i = atom_types.begin();
+ i != atom_types.end(); ++i){
+ lj_interaction = ff->GetLJ(*i);
+ if(!lj_interaction){
+ std::stringstream ss;
+ ss << "Failed to find LJ parametrization for type \""<<*i<<"\"";
+ ss << " in given forcefield!";
+ throw ost::Error(ss.str());
+ }
+ parameters = lj_interaction->GetParam();
+ sigmas.push_back(parameters[0]);
+ epsilons.push_back(parameters[1]);
+ }
+ top->SetSigmas(sigmas);
+ top->SetEpsilons(epsilons);
+ //take care of the 1-4 interactions
+ for(std::set<Index<2> >::iterator i = pairs_14.begin();
+ i != pairs_14.end(); ++i){
+ //we can be sure, that the parameters are valid, since we found all single
+ //parameters. The forcefield can therefore build the new parametrization with
+ //the combination rules... Except: gen_pairs_ is set to no, but then an error
+ // is thrown anyway
+ lj_interaction = ff->GetLJ(atom_types[(*i)[0]],
+ atom_types[(*i)[1]],
+ true);
+ parameters = lj_interaction->GetParam();
+ top->AddLJPair((*i)[0],(*i)[1],parameters[0],parameters[1]);
+ }
+ //take care of the exclusions
+ for(std::set<Index<2> >::iterator i = exclusions.begin();
+ i != exclusions.end(); ++i){
+ top->AddExclusion((*i)[0],(*i)[1]);
+ }
+ }
+ if(settings->add_gbsa){
+ std::vector<Real> radii;
+ std::vector<Real> scaling;
+ for(uint i = 0; i < atom_list.size(); ++i){
+ InteractionPtr gbsa_ptr = ff->GetImplicitGenborn(atom_types[i]);
+ if(!gbsa_ptr){
+ std::stringstream ss;
+ ss << "Structure contains atom of type " << types[i] << " which is not";
+ ss << "parametrized in the forcefield!"<<std::endl;
+ throw ost::Error(ss.str());
+ }
+ parameters = gbsa_ptr->GetParam();
+ radii.push_back(parameters[0]);
+ scaling.push_back(parameters[1]);
+ }
+ top->SetGBSARadii(radii);
+ top->SetOBCScalings(scaling);
+ }
+
+ top->SetFudgeQQ(ff->GetFudgeQQ());
+ top->SetFudgeLJ(ff->GetFudgeLJ());
+
+ if(!settings->keep_ff_specific_naming){
+ //let's rename to the pdb standard!
+ //first, we rename to the gromacs standars...
+ ff->AssignFFSpecificNames(ent,true);
+ //still call the assign gromacs names function...
+ Modeller::AssignGromacsNaming(ent);
+ //let's finally do the renaming to PDB standard
+ Modeller::AssignPDBNaming(ent);
+ }
+
+
+ return top;
+
+}
+
+}}}//ns
diff --git a/modules/mol/mm/src/topology_creator.hh b/modules/mol/mm/src/topology_creator.hh
new file mode 100644
index 0000000000000000000000000000000000000000..026abdc5cd4ba660c1f63848bf49b39157f0f2d7
--- /dev/null
+++ b/modules/mol/mm/src/topology_creator.hh
@@ -0,0 +1,57 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#ifndef OST_MM_TOPOLOGY_CREATOR_HH
+#define OST_MM_TOPOLOGY_CREATOR_HH
+
+#include <vector>
+#include <map>
+#include <set>
+#include <math.h>
+
+#include <ost/message.hh>
+#include <ost/mol/entity_handle.hh>
+#include <ost/mol/residue_handle.hh>
+#include <ost/mol/atom_handle.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/block_modifiers.hh>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/modeller.hh>
+#include <ost/mol/mm/index.hh>
+#include <ost/mol/mm/topology.hh>
+
+
+namespace ost { namespace mol{ namespace mm{
+
+class TopologyCreator;
+typedef boost::shared_ptr<TopologyCreator> TopologyCreatorPtr;
+
+class TopologyCreator {
+public:
+ static TopologyPtr Create(ost::mol::EntityHandle& ent,
+ const SettingsPtr settings);
+
+};
+
+
+}}}//ns
+
+#endif
diff --git a/modules/mol/mm/tests/1CRN.pdb b/modules/mol/mm/tests/1CRN.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..13ca618d438ae60a55a8ce1c532cd23bf545e200
--- /dev/null
+++ b/modules/mol/mm/tests/1CRN.pdb
@@ -0,0 +1,329 @@
+ATOM 1 N THR A 1 17.047 14.099 3.625 1.00 13.79 N
+ATOM 2 CA THR A 1 16.967 12.784 4.338 1.00 10.80 C
+ATOM 3 C THR A 1 15.685 12.755 5.133 1.00 9.19 C
+ATOM 4 O THR A 1 15.268 13.825 5.594 1.00 9.85 O
+ATOM 5 CB THR A 1 18.170 12.703 5.337 1.00 13.02 C
+ATOM 6 OG1 THR A 1 19.334 12.829 4.463 1.00 15.06 O
+ATOM 7 CG2 THR A 1 18.150 11.546 6.304 1.00 14.23 C
+ATOM 8 N THR A 2 15.115 11.555 5.265 1.00 7.81 N
+ATOM 9 CA THR A 2 13.856 11.469 6.066 1.00 8.31 C
+ATOM 10 C THR A 2 14.164 10.785 7.379 1.00 5.80 C
+ATOM 11 O THR A 2 14.993 9.862 7.443 1.00 6.94 O
+ATOM 12 CB THR A 2 12.732 10.711 5.261 1.00 10.32 C
+ATOM 13 OG1 THR A 2 13.308 9.439 4.926 1.00 12.81 O
+ATOM 14 CG2 THR A 2 12.484 11.442 3.895 1.00 11.90 C
+ATOM 15 N CYS A 3 13.488 11.241 8.417 1.00 5.24 N
+ATOM 16 CA CYS A 3 13.660 10.707 9.787 1.00 5.39 C
+ATOM 17 C CYS A 3 12.269 10.431 10.323 1.00 4.45 C
+ATOM 18 O CYS A 3 11.393 11.308 10.185 1.00 6.54 O
+ATOM 19 CB CYS A 3 14.368 11.748 10.691 1.00 5.99 C
+ATOM 20 SG CYS A 3 15.885 12.426 10.016 1.00 7.01 S
+ATOM 21 N CYS A 4 12.019 9.272 10.928 1.00 3.90 N
+ATOM 22 CA CYS A 4 10.646 8.991 11.408 1.00 4.24 C
+ATOM 23 C CYS A 4 10.654 8.793 12.919 1.00 3.72 C
+ATOM 24 O CYS A 4 11.659 8.296 13.491 1.00 5.30 O
+ATOM 25 CB CYS A 4 10.057 7.752 10.682 1.00 4.41 C
+ATOM 26 SG CYS A 4 9.837 8.018 8.904 1.00 4.72 S
+ATOM 27 N PRO A 5 9.561 9.108 13.563 1.00 3.96 N
+ATOM 28 CA PRO A 5 9.448 9.034 15.012 1.00 4.25 C
+ATOM 29 C PRO A 5 9.288 7.670 15.606 1.00 4.96 C
+ATOM 30 O PRO A 5 9.490 7.519 16.819 1.00 7.44 O
+ATOM 31 CB PRO A 5 8.230 9.957 15.345 1.00 5.11 C
+ATOM 32 CG PRO A 5 7.338 9.786 14.114 1.00 5.24 C
+ATOM 33 CD PRO A 5 8.366 9.804 12.958 1.00 5.20 C
+ATOM 34 N SER A 6 8.875 6.686 14.796 1.00 4.83 N
+ATOM 35 CA SER A 6 8.673 5.314 15.279 1.00 4.45 C
+ATOM 36 C SER A 6 8.753 4.376 14.083 1.00 4.99 C
+ATOM 37 O SER A 6 8.726 4.858 12.923 1.00 4.61 O
+ATOM 38 CB SER A 6 7.340 5.121 15.996 1.00 5.05 C
+ATOM 39 OG SER A 6 6.274 5.220 15.031 1.00 6.39 O
+ATOM 40 N ILE A 7 8.881 3.075 14.358 1.00 4.94 N
+ATOM 41 CA ILE A 7 8.912 2.083 13.258 1.00 6.33 C
+ATOM 42 C ILE A 7 7.581 2.090 12.506 1.00 5.32 C
+ATOM 43 O ILE A 7 7.670 2.031 11.245 1.00 6.85 O
+ATOM 44 CB ILE A 7 9.207 0.677 13.924 1.00 8.43 C
+ATOM 45 CG1 ILE A 7 10.714 0.702 14.312 1.00 9.78 C
+ATOM 46 CG2 ILE A 7 8.811 -0.477 12.969 1.00 11.70 C
+ATOM 47 CD1 ILE A 7 11.185 -0.516 15.142 1.00 9.92 C
+ATOM 48 N VAL A 8 6.458 2.162 13.159 1.00 5.02 N
+ATOM 49 CA VAL A 8 5.145 2.209 12.453 1.00 6.93 C
+ATOM 50 C VAL A 8 5.115 3.379 11.461 1.00 5.39 C
+ATOM 51 O VAL A 8 4.664 3.268 10.343 1.00 6.30 O
+ATOM 52 CB VAL A 8 3.995 2.354 13.478 1.00 9.64 C
+ATOM 53 CG1 VAL A 8 2.716 2.891 12.869 1.00 13.85 C
+ATOM 54 CG2 VAL A 8 3.758 1.032 14.208 1.00 11.97 C
+ATOM 55 N ALA A 9 5.606 4.546 11.941 1.00 3.73 N
+ATOM 56 CA ALA A 9 5.598 5.767 11.082 1.00 3.56 C
+ATOM 57 C ALA A 9 6.441 5.527 9.850 1.00 4.13 C
+ATOM 58 O ALA A 9 6.052 5.933 8.744 1.00 4.36 O
+ATOM 59 CB ALA A 9 6.022 6.977 11.891 1.00 4.80 C
+ATOM 60 N ARG A 10 7.647 4.909 10.005 1.00 3.73 N
+ATOM 61 CA ARG A 10 8.496 4.609 8.837 1.00 3.38 C
+ATOM 62 C ARG A 10 7.798 3.609 7.876 1.00 3.47 C
+ATOM 63 O ARG A 10 7.878 3.778 6.651 1.00 4.67 O
+ATOM 64 CB ARG A 10 9.847 4.020 9.305 1.00 3.95 C
+ATOM 65 CG ARG A 10 10.752 3.607 8.149 1.00 4.55 C
+ATOM 66 CD ARG A 10 11.226 4.699 7.244 1.00 5.89 C
+ATOM 67 NE ARG A 10 12.143 5.571 8.035 1.00 6.20 N
+ATOM 68 CZ ARG A 10 12.758 6.609 7.443 1.00 7.52 C
+ATOM 69 NH1 ARG A 10 12.539 6.932 6.158 1.00 10.68 N
+ATOM 70 NH2 ARG A 10 13.601 7.322 8.202 1.00 9.48 N
+ATOM 71 N SER A 11 7.186 2.582 8.445 1.00 5.19 N
+ATOM 72 CA SER A 11 6.500 1.584 7.565 1.00 4.60 C
+ATOM 73 C SER A 11 5.382 2.313 6.773 1.00 4.84 C
+ATOM 74 O SER A 11 5.213 2.016 5.557 1.00 5.84 O
+ATOM 75 CB SER A 11 5.908 0.462 8.400 1.00 5.91 C
+ATOM 76 OG SER A 11 6.990 -0.272 9.012 1.00 8.38 O
+ATOM 77 N ASN A 12 4.648 3.182 7.446 1.00 3.54 N
+ATOM 78 CA ASN A 12 3.545 3.935 6.751 1.00 4.57 C
+ATOM 79 C ASN A 12 4.107 4.851 5.691 1.00 4.14 C
+ATOM 80 O ASN A 12 3.536 5.001 4.617 1.00 5.52 O
+ATOM 81 CB ASN A 12 2.663 4.677 7.748 1.00 6.42 C
+ATOM 82 CG ASN A 12 1.802 3.735 8.610 1.00 8.25 C
+ATOM 83 OD1 ASN A 12 1.567 2.613 8.165 1.00 12.72 O
+ATOM 84 ND2 ASN A 12 1.394 4.252 9.767 1.00 9.92 N
+ATOM 85 N PHE A 13 5.259 5.498 6.005 1.00 3.43 N
+ATOM 86 CA PHE A 13 5.929 6.358 5.055 1.00 3.49 C
+ATOM 87 C PHE A 13 6.304 5.578 3.799 1.00 3.40 C
+ATOM 88 O PHE A 13 6.136 6.072 2.653 1.00 4.07 O
+ATOM 89 CB PHE A 13 7.183 6.994 5.754 1.00 5.48 C
+ATOM 90 CG PHE A 13 7.884 8.006 4.883 1.00 5.57 C
+ATOM 91 CD1 PHE A 13 8.906 7.586 4.027 1.00 6.99 C
+ATOM 92 CD2 PHE A 13 7.532 9.373 4.983 1.00 6.52 C
+ATOM 93 CE1 PHE A 13 9.560 8.539 3.194 1.00 8.20 C
+ATOM 94 CE2 PHE A 13 8.176 10.281 4.145 1.00 6.34 C
+ATOM 95 CZ PHE A 13 9.141 9.845 3.292 1.00 6.84 C
+ATOM 96 N ASN A 14 6.900 4.390 3.989 1.00 3.64 N
+ATOM 97 CA ASN A 14 7.331 3.607 2.791 1.00 4.31 C
+ATOM 98 C ASN A 14 6.116 3.210 1.915 1.00 3.98 C
+ATOM 99 O ASN A 14 6.240 3.144 0.684 1.00 6.22 O
+ATOM 100 CB ASN A 14 8.145 2.404 3.240 1.00 5.81 C
+ATOM 101 CG ASN A 14 9.555 2.856 3.730 1.00 6.82 C
+ATOM 102 OD1 ASN A 14 10.013 3.895 3.323 1.00 9.43 O
+ATOM 103 ND2 ASN A 14 10.120 1.956 4.539 1.00 8.21 N
+ATOM 104 N VAL A 15 4.993 2.927 2.571 1.00 3.76 N
+ATOM 105 CA VAL A 15 3.782 2.599 1.742 1.00 3.98 C
+ATOM 106 C VAL A 15 3.296 3.871 1.004 1.00 3.80 C
+ATOM 107 O VAL A 15 2.947 3.817 -0.189 1.00 4.85 O
+ATOM 108 CB VAL A 15 2.698 1.953 2.608 1.00 4.71 C
+ATOM 109 CG1 VAL A 15 1.384 1.826 1.806 1.00 6.67 C
+ATOM 110 CG2 VAL A 15 3.174 0.533 3.005 1.00 6.26 C
+ATOM 111 N CYS A 16 3.321 4.987 1.720 1.00 3.79 N
+ATOM 112 CA CYS A 16 2.890 6.285 1.126 1.00 3.54 C
+ATOM 113 C CYS A 16 3.687 6.597 -0.111 1.00 3.48 C
+ATOM 114 O CYS A 16 3.200 7.147 -1.103 1.00 4.63 O
+ATOM 115 CB CYS A 16 3.039 7.369 2.240 1.00 4.58 C
+ATOM 116 SG CYS A 16 2.559 9.014 1.649 1.00 5.66 S
+ATOM 117 N ARG A 17 4.997 6.227 -0.100 1.00 3.99 N
+ATOM 118 CA ARG A 17 5.895 6.489 -1.213 1.00 3.83 C
+ATOM 119 C ARG A 17 5.738 5.560 -2.409 1.00 3.79 C
+ATOM 120 O ARG A 17 6.228 5.901 -3.507 1.00 5.39 O
+ATOM 121 CB ARG A 17 7.370 6.507 -0.731 1.00 4.11 C
+ATOM 122 CG ARG A 17 7.717 7.687 0.206 1.00 4.69 C
+ATOM 123 CD ARG A 17 7.949 8.947 -0.615 1.00 5.10 C
+ATOM 124 NE ARG A 17 9.212 8.856 -1.337 1.00 4.71 N
+ATOM 125 CZ ARG A 17 9.537 9.533 -2.431 1.00 5.28 C
+ATOM 126 NH1 ARG A 17 8.659 10.350 -3.032 1.00 6.67 N
+ATOM 127 NH2 ARG A 17 10.793 9.491 -2.899 1.00 6.41 N
+ATOM 128 N LEU A 18 5.051 4.411 -2.204 1.00 4.70 N
+ATOM 129 CA LEU A 18 4.933 3.431 -3.326 1.00 5.46 C
+ATOM 130 C LEU A 18 4.397 4.014 -4.620 1.00 5.13 C
+ATOM 131 O LEU A 18 4.988 3.755 -5.687 1.00 5.55 O
+ATOM 132 CB LEU A 18 4.196 2.184 -2.863 1.00 6.47 C
+ATOM 133 CG LEU A 18 4.960 1.178 -1.991 1.00 7.43 C
+ATOM 134 CD1 LEU A 18 3.907 0.097 -1.634 1.00 8.70 C
+ATOM 135 CD2 LEU A 18 6.129 0.606 -2.768 1.00 9.39 C
+ATOM 136 N PRO A 19 3.329 4.795 -4.543 1.00 4.28 N
+ATOM 137 CA PRO A 19 2.792 5.376 -5.797 1.00 5.38 C
+ATOM 138 C PRO A 19 3.573 6.540 -6.322 1.00 6.30 C
+ATOM 139 O PRO A 19 3.260 7.045 -7.422 1.00 9.62 O
+ATOM 140 CB PRO A 19 1.358 5.766 -5.472 1.00 5.87 C
+ATOM 141 CG PRO A 19 1.223 5.694 -3.993 1.00 6.47 C
+ATOM 142 CD PRO A 19 2.421 4.941 -3.408 1.00 6.45 C
+ATOM 143 N GLY A 20 4.565 7.047 -5.559 1.00 4.94 N
+ATOM 144 CA GLY A 20 5.366 8.191 -6.018 1.00 5.39 C
+ATOM 145 C GLY A 20 5.007 9.481 -5.280 1.00 5.03 C
+ATOM 146 O GLY A 20 5.535 10.510 -5.730 1.00 7.34 O
+ATOM 147 N THR A 21 4.181 9.438 -4.262 1.00 4.10 N
+ATOM 148 CA THR A 21 3.767 10.609 -3.513 1.00 3.94 C
+ATOM 149 C THR A 21 5.017 11.397 -3.042 1.00 3.96 C
+ATOM 150 O THR A 21 5.947 10.757 -2.523 1.00 5.82 O
+ATOM 151 CB THR A 21 2.992 10.188 -2.225 1.00 4.13 C
+ATOM 152 OG1 THR A 21 2.051 9.144 -2.623 1.00 5.45 O
+ATOM 153 CG2 THR A 21 2.260 11.349 -1.551 1.00 5.41 C
+ATOM 154 N PRO A 22 4.971 12.703 -3.176 1.00 5.04 N
+ATOM 155 CA PRO A 22 6.143 13.513 -2.696 1.00 4.69 C
+ATOM 156 C PRO A 22 6.400 13.233 -1.225 1.00 4.19 C
+ATOM 157 O PRO A 22 5.485 13.061 -0.382 1.00 4.47 O
+ATOM 158 CB PRO A 22 5.703 14.969 -2.920 1.00 7.12 C
+ATOM 159 CG PRO A 22 4.676 14.893 -3.996 1.00 7.03 C
+ATOM 160 CD PRO A 22 3.964 13.567 -3.811 1.00 4.90 C
+ATOM 161 N GLU A 23 7.728 13.297 -0.921 1.00 5.16 N
+ATOM 162 CA GLU A 23 8.114 13.103 0.500 1.00 5.31 C
+ATOM 163 C GLU A 23 7.427 14.073 1.410 1.00 4.11 C
+ATOM 164 O GLU A 23 7.036 13.682 2.540 1.00 5.11 O
+ATOM 165 CB GLU A 23 9.648 13.285 0.660 1.00 6.16 C
+ATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C
+ATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C
+ATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O
+ATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O
+ATOM 170 N ALA A 24 7.212 15.334 0.966 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.614 16.317 1.913 1.00 4.49 C
+ATOM 172 C ALA A 24 5.212 15.936 2.350 1.00 4.10 C
+ATOM 173 O ALA A 24 4.782 16.166 3.495 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.605 17.695 1.246 1.00 5.80 C
+ATOM 175 N ILE A 25 4.445 15.318 1.405 1.00 4.37 N
+ATOM 176 CA ILE A 25 3.074 14.894 1.756 1.00 5.44 C
+ATOM 177 C ILE A 25 3.085 13.643 2.645 1.00 4.32 C
+ATOM 178 O ILE A 25 2.315 13.523 3.578 1.00 4.72 O
+ATOM 179 CB ILE A 25 2.204 14.637 0.462 1.00 6.42 C
+ATOM 180 CG1 ILE A 25 1.815 16.048 -0.129 1.00 7.50 C
+ATOM 181 CG2 ILE A 25 0.903 13.864 0.811 1.00 7.65 C
+ATOM 182 CD1 ILE A 25 0.756 16.761 0.757 1.00 7.80 C
+ATOM 183 N CYS A 26 4.032 12.764 2.313 1.00 3.92 N
+ATOM 184 CA CYS A 26 4.180 11.549 3.187 1.00 4.37 C
+ATOM 185 C CYS A 26 4.632 11.944 4.596 1.00 3.95 C
+ATOM 186 O CYS A 26 4.227 11.252 5.547 1.00 4.74 O
+ATOM 187 CB CYS A 26 5.038 10.518 2.539 1.00 4.63 C
+ATOM 188 SG CYS A 26 4.349 9.794 1.022 1.00 5.61 S
+ATOM 189 N ALA A 27 5.408 13.012 4.694 1.00 3.89 N
+ATOM 190 CA ALA A 27 5.879 13.502 6.026 1.00 4.43 C
+ATOM 191 C ALA A 27 4.696 13.908 6.882 1.00 4.26 C
+ATOM 192 O ALA A 27 4.528 13.422 8.025 1.00 5.44 O
+ATOM 193 CB ALA A 27 6.880 14.615 5.830 1.00 5.36 C
+ATOM 194 N THR A 28 3.827 14.802 6.358 1.00 4.53 N
+ATOM 195 CA THR A 28 2.691 15.221 7.194 1.00 5.08 C
+ATOM 196 C THR A 28 1.672 14.132 7.434 1.00 4.62 C
+ATOM 197 O THR A 28 0.947 14.112 8.468 1.00 7.80 O
+ATOM 198 CB THR A 28 1.986 16.520 6.614 1.00 6.03 C
+ATOM 199 OG1 THR A 28 1.664 16.221 5.230 1.00 7.19 O
+ATOM 200 CG2 THR A 28 2.914 17.739 6.700 1.00 7.34 C
+ATOM 201 N TYR A 29 1.621 13.190 6.511 1.00 5.01 N
+ATOM 202 CA TYR A 29 0.715 12.045 6.657 1.00 6.60 C
+ATOM 203 C TYR A 29 1.125 11.125 7.815 1.00 4.92 C
+ATOM 204 O TYR A 29 0.286 10.632 8.545 1.00 7.13 O
+ATOM 205 CB TYR A 29 0.755 11.229 5.322 1.00 9.66 C
+ATOM 206 CG TYR A 29 -0.203 10.044 5.354 1.00 11.56 C
+ATOM 207 CD1 TYR A 29 -1.547 10.337 5.645 1.00 12.85 C
+ATOM 208 CD2 TYR A 29 0.193 8.750 5.100 1.00 14.44 C
+ATOM 209 CE1 TYR A 29 -2.496 9.329 5.673 1.00 16.61 C
+ATOM 210 CE2 TYR A 29 -0.801 7.705 5.156 1.00 17.11 C
+ATOM 211 CZ TYR A 29 -2.079 8.031 5.430 1.00 19.99 C
+ATOM 212 OH TYR A 29 -3.097 7.057 5.458 1.00 28.98 O
+ATOM 213 N THR A 30 2.470 10.984 7.995 1.00 5.31 N
+ATOM 214 CA THR A 30 2.986 9.994 8.950 1.00 5.70 C
+ATOM 215 C THR A 30 3.609 10.505 10.230 1.00 6.28 C
+ATOM 216 O THR A 30 3.766 9.715 11.186 1.00 8.77 O
+ATOM 217 CB THR A 30 4.076 9.103 8.225 1.00 6.55 C
+ATOM 218 OG1 THR A 30 5.125 10.027 7.824 1.00 6.57 O
+ATOM 219 CG2 THR A 30 3.493 8.324 7.035 1.00 7.29 C
+ATOM 220 N GLY A 31 3.984 11.764 10.241 1.00 4.99 N
+ATOM 221 CA GLY A 31 4.769 12.336 11.360 1.00 5.50 C
+ATOM 222 C GLY A 31 6.255 12.243 11.106 1.00 4.19 C
+ATOM 223 O GLY A 31 7.037 12.750 11.954 1.00 6.12 O
+ATOM 224 N CYS A 32 6.710 11.631 9.992 1.00 4.30 N
+ATOM 225 CA CYS A 32 8.140 11.694 9.635 1.00 4.89 C
+ATOM 226 C CYS A 32 8.500 13.141 9.206 1.00 5.50 C
+ATOM 227 O CYS A 32 7.581 13.949 8.944 1.00 5.82 O
+ATOM 228 CB CYS A 32 8.504 10.686 8.530 1.00 4.66 C
+ATOM 229 SG CYS A 32 8.048 8.987 8.881 1.00 5.33 S
+ATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N
+ATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C
+ATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C
+ATOM 233 O ILE A 33 11.971 13.583 7.552 1.00 7.19 O
+ATOM 234 CB ILE A 33 10.790 15.535 10.085 1.00 5.49 C
+ATOM 235 CG1 ILE A 33 12.059 14.803 10.671 1.00 6.85 C
+ATOM 236 CG2 ILE A 33 9.684 15.686 11.138 1.00 6.45 C
+ATOM 237 CD1 ILE A 33 12.733 15.676 11.781 1.00 8.94 C
+ATOM 238 N ILE A 34 11.490 15.773 7.038 1.00 5.52 N
+ATOM 239 CA ILE A 34 12.552 15.877 6.036 1.00 6.82 C
+ATOM 240 C ILE A 34 13.590 16.917 6.560 1.00 6.92 C
+ATOM 241 O ILE A 34 13.168 18.006 6.945 1.00 9.22 O
+ATOM 242 CB ILE A 34 11.987 16.360 4.681 1.00 8.11 C
+ATOM 243 CG1 ILE A 34 10.914 15.338 4.163 1.00 9.59 C
+ATOM 244 CG2 ILE A 34 13.131 16.517 3.629 1.00 9.73 C
+ATOM 245 CD1 ILE A 34 10.151 16.024 2.938 1.00 13.41 C
+ATOM 246 N ILE A 35 14.856 16.493 6.536 1.00 7.06 N
+ATOM 247 CA ILE A 35 15.930 17.454 6.941 1.00 7.52 C
+ATOM 248 C ILE A 35 16.913 17.550 5.819 1.00 6.63 C
+ATOM 249 O ILE A 35 17.097 16.660 4.970 1.00 7.90 O
+ATOM 250 CB ILE A 35 16.622 16.995 8.285 1.00 8.07 C
+ATOM 251 CG1 ILE A 35 17.360 15.651 8.067 1.00 9.41 C
+ATOM 252 CG2 ILE A 35 15.592 16.974 9.434 1.00 9.46 C
+ATOM 253 CD1 ILE A 35 18.298 15.206 9.219 1.00 9.85 C
+ATOM 254 N PRO A 36 17.664 18.669 5.806 1.00 8.07 N
+ATOM 255 CA PRO A 36 18.635 18.861 4.738 1.00 8.78 C
+ATOM 256 C PRO A 36 19.925 18.042 4.949 1.00 8.31 C
+ATOM 257 O PRO A 36 20.593 17.742 3.945 1.00 9.09 O
+ATOM 258 CB PRO A 36 18.945 20.364 4.783 1.00 9.67 C
+ATOM 259 CG PRO A 36 18.238 20.937 5.908 1.00 10.15 C
+ATOM 260 CD PRO A 36 17.371 19.900 6.596 1.00 9.53 C
+ATOM 261 N GLY A 37 20.172 17.730 6.217 1.00 8.48 N
+ATOM 262 CA GLY A 37 21.452 16.969 6.513 1.00 9.20 C
+ATOM 263 C GLY A 37 21.143 15.478 6.427 1.00 10.41 C
+ATOM 264 O GLY A 37 20.138 15.023 5.878 1.00 12.06 O
+ATOM 265 N ALA A 38 22.055 14.701 7.032 1.00 9.24 N
+ATOM 266 CA ALA A 38 22.019 13.242 7.020 1.00 9.24 C
+ATOM 267 C ALA A 38 21.944 12.628 8.396 1.00 9.60 C
+ATOM 268 O ALA A 38 21.869 11.387 8.435 1.00 13.65 O
+ATOM 269 CB ALA A 38 23.246 12.697 6.275 1.00 10.43 C
+ATOM 270 N THR A 39 21.894 13.435 9.436 1.00 8.70 N
+ATOM 271 CA THR A 39 21.936 12.911 10.809 1.00 9.46 C
+ATOM 272 C THR A 39 20.615 13.191 11.521 1.00 8.32 C
+ATOM 273 O THR A 39 20.357 14.317 11.948 1.00 9.89 O
+ATOM 274 CB THR A 39 23.131 13.601 11.593 1.00 10.72 C
+ATOM 275 OG1 THR A 39 24.284 13.401 10.709 1.00 11.66 O
+ATOM 276 CG2 THR A 39 23.340 12.935 12.962 1.00 11.81 C
+ATOM 277 N CYS A 40 19.827 12.110 11.642 1.00 7.64 N
+ATOM 278 CA CYS A 40 18.504 12.312 12.298 1.00 8.05 C
+ATOM 279 C CYS A 40 18.684 12.451 13.784 1.00 7.63 C
+ATOM 280 O CYS A 40 19.533 11.718 14.362 1.00 9.64 O
+ATOM 281 CB CYS A 40 17.582 11.117 11.996 1.00 7.80 C
+ATOM 282 SG CYS A 40 17.199 10.929 10.237 1.00 7.30 S
+ATOM 283 N PRO A 41 17.880 13.266 14.426 1.00 8.00 N
+ATOM 284 CA PRO A 41 17.924 13.421 15.877 1.00 8.96 C
+ATOM 285 C PRO A 41 17.392 12.206 16.594 1.00 9.06 C
+ATOM 286 O PRO A 41 16.652 11.368 16.033 1.00 8.82 O
+ATOM 287 CB PRO A 41 17.076 14.658 16.145 1.00 10.39 C
+ATOM 288 CG PRO A 41 16.098 14.689 14.997 1.00 10.99 C
+ATOM 289 CD PRO A 41 16.859 14.150 13.779 1.00 10.49 C
+ATOM 290 N GLY A 42 17.728 12.124 17.884 1.00 7.55 N
+ATOM 291 CA GLY A 42 17.334 10.956 18.691 1.00 8.00 C
+ATOM 292 C GLY A 42 15.875 10.688 18.871 1.00 7.22 C
+ATOM 293 O GLY A 42 15.434 9.550 19.166 1.00 8.41 O
+ATOM 294 N ASP A 43 15.036 11.747 18.715 1.00 5.54 N
+ATOM 295 CA ASP A 43 13.564 11.573 18.836 1.00 5.85 C
+ATOM 296 C ASP A 43 12.936 11.227 17.470 1.00 5.87 C
+ATOM 297 O ASP A 43 11.720 11.040 17.428 1.00 7.29 O
+ATOM 298 CB ASP A 43 12.933 12.737 19.580 1.00 6.72 C
+ATOM 299 CG ASP A 43 13.140 14.094 18.958 1.00 8.59 C
+ATOM 300 OD1 ASP A 43 14.109 14.303 18.212 1.00 9.59 O
+ATOM 301 OD2 ASP A 43 12.267 14.963 19.265 1.00 11.45 O
+ATOM 302 N TYR A 44 13.725 11.174 16.425 1.00 5.22 N
+ATOM 303 CA TYR A 44 13.257 10.745 15.081 1.00 5.56 C
+ATOM 304 C TYR A 44 14.275 9.687 14.612 1.00 4.61 C
+ATOM 305 O TYR A 44 14.930 9.862 13.568 1.00 6.04 O
+ATOM 306 CB TYR A 44 13.200 11.914 14.071 1.00 5.41 C
+ATOM 307 CG TYR A 44 12.000 12.819 14.399 1.00 5.34 C
+ATOM 308 CD1 TYR A 44 12.119 13.853 15.332 1.00 6.59 C
+ATOM 309 CD2 TYR A 44 10.775 12.617 13.762 1.00 5.94 C
+ATOM 310 CE1 TYR A 44 11.045 14.675 15.610 1.00 5.97 C
+ATOM 311 CE2 TYR A 44 9.676 13.433 14.048 1.00 5.17 C
+ATOM 312 CZ TYR A 44 9.802 14.456 14.996 1.00 5.96 C
+ATOM 313 OH TYR A 44 8.740 15.265 15.269 1.00 8.60 O
+ATOM 314 N ALA A 45 14.342 8.640 15.422 1.00 4.76 N
+ATOM 315 CA ALA A 45 15.445 7.667 15.246 1.00 5.89 C
+ATOM 316 C ALA A 45 15.171 6.533 14.280 1.00 6.67 C
+ATOM 317 O ALA A 45 16.093 5.705 14.039 1.00 7.56 O
+ATOM 318 CB ALA A 45 15.680 7.099 16.682 1.00 6.82 C
+ATOM 319 N ASN A 46 13.966 6.502 13.739 1.00 5.80 N
+ATOM 320 CA ASN A 46 13.512 5.395 12.878 1.00 6.15 C
+ATOM 321 C ASN A 46 13.311 5.853 11.455 1.00 6.61 C
+ATOM 322 O ASN A 46 13.733 6.929 11.026 1.00 7.18 O
+ATOM 323 CB ASN A 46 12.266 4.769 13.501 1.00 7.27 C
+ATOM 324 CG ASN A 46 12.538 4.304 14.922 1.00 7.98 C
+ATOM 325 OD1 ASN A 46 11.982 4.849 15.886 1.00 11.00 O
+ATOM 326 ND2 ASN A 46 13.407 3.298 15.015 1.00 10.32 N
+ATOM 327 OXT ASN A 46 12.703 4.973 10.746 1.00 7.86 O
+TER 328 ASN A 46
+END
diff --git a/modules/mol/mm/tests/AMBER03.dat b/modules/mol/mm/tests/AMBER03.dat
new file mode 100644
index 0000000000000000000000000000000000000000..69e7d22171f447229ce354d731773876fcba7bd4
Binary files /dev/null and b/modules/mol/mm/tests/AMBER03.dat differ
diff --git a/modules/mol/mm/tests/CHARMM27.dat b/modules/mol/mm/tests/CHARMM27.dat
new file mode 100644
index 0000000000000000000000000000000000000000..9a9459fb0c9882ff4db05a70560389124a73f2e6
Binary files /dev/null and b/modules/mol/mm/tests/CHARMM27.dat differ
diff --git a/modules/mol/mm/tests/CMakeLists.txt b/modules/mol/mm/tests/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..99f2c4575dbc77849567d5d9e08a0497dfc9118d
--- /dev/null
+++ b/modules/mol/mm/tests/CMakeLists.txt
@@ -0,0 +1,12 @@
+set(OST_MOL_MM_UNIT_TESTS
+ test_interaction.cc
+ test_block.cc
+ test_block_modifiers.cc
+ test_topology.cc
+ test_forcefield.cc
+ test_simulation.cc
+ tests.cc
+)
+
+ost_unittest(MODULE mol_mm SOURCES "${OST_MOL_MM_UNIT_TESTS}")
+
diff --git a/modules/mol/mm/tests/test.ff b/modules/mol/mm/tests/test.ff
new file mode 100644
index 0000000000000000000000000000000000000000..a9dfffe15ebe5915d3daba9c199e01cef5645e0c
Binary files /dev/null and b/modules/mol/mm/tests/test.ff differ
diff --git a/modules/mol/mm/tests/test_block.cc b/modules/mol/mm/tests/test_block.cc
new file mode 100644
index 0000000000000000000000000000000000000000..20aaf2a7328779ae52cf2c6e7b0626b3f94e78e7
--- /dev/null
+++ b/modules/mol/mm/tests/test_block.cc
@@ -0,0 +1,230 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mol.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+
+
+#include <ost/message.hh>
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_block_basics)
+{
+ BuildingBlock block = BuildingBlock();
+ block.AddAtom("A","a",0.5);
+ block.AddAtom("B","b",1.0);
+ InteractionPtr bond(new Interaction(HarmonicBond));
+ std::vector<String> names;
+ names.push_back("A");
+ names.push_back("B");
+ bond->SetNames(names);
+ block.AddBond(bond);
+ BOOST_CHECK_THROW(block.GetCharge("C"),ost::Error);
+ BOOST_CHECK_THROW(block.GetType("C"),ost::Error);
+ BOOST_CHECK(block.GetCharge("A") == 0.5);
+ BOOST_CHECK(block.GetType("A") == "a");
+ block.ReplaceAtom("A","X","x",42.0);
+ BOOST_CHECK(block.GetType("X") == "x");
+ BOOST_CHECK(block.GetCharge("X")==42.0);
+ BOOST_CHECK(block.GetAtoms().size() == 2);
+ std::vector<InteractionPtr> bonds = block.GetBonds();
+ BOOST_CHECK(bonds[0]->HasName("X"));
+ block.RemoveAtom("X");
+ BOOST_CHECK_THROW(block.GetType("X"),ost::Error);
+ BOOST_CHECK_NO_THROW(block.GetType("B"));
+ BOOST_CHECK(block.GetAtoms().size()==1);
+ BOOST_CHECK(block.GetCharges().size()==1);
+ BOOST_CHECK(block.GetBonds().size()==0);
+ std::vector<Real> param_one,param_two;
+ param_one.push_back(1.0);
+ param_one.push_back(1.0);
+ param_two.push_back(2.0);
+ param_two.push_back(2.0);
+ InteractionPtr bond_one(new Interaction(HarmonicBond));
+ InteractionPtr bond_two(new Interaction(HarmonicBond));
+ bond_one->SetNames(names);
+ bond_one->SetParam(param_one);
+ bond_two->SetNames(names);
+ bond_two->SetParam(param_two);
+ block.AddBond(bond_one);
+ BOOST_CHECK(block.GetBonds()[0]->GetParam() == param_one);
+ block.AddBond(bond_two,true);
+ BOOST_CHECK(block.GetBonds()[0]->GetParam() == param_two);
+ block.RemoveAtom("A");
+
+ names[0] = "-A";
+ bond_one->SetNames(names);
+ names[0] = "A";
+ names[1] = "+B";
+ bond_two->SetNames(names);
+ block.AddBond(bond_one);
+ block.AddBond(bond_two);
+ BOOST_CHECK(block.GetBonds().size() == 2);
+ block.RemoveInteractionsToPrev();
+ BOOST_CHECK(block.GetBonds().size() == 1);
+ BOOST_CHECK(block.GetBonds()[0]->HasName("+B"));
+ block.RemoveInteractionsToNext();
+ BOOST_CHECK(block.GetBonds().size() == 0);
+}
+
+BOOST_AUTO_TEST_CASE(test_connect)
+{
+ ost::mol::EntityHandle e = ost::mol::Builder()
+ .Chain("A")
+ .Residue("ONE")
+ .Atom("A",geom::Vec3(0,0,0))
+ .Atom("B",geom::Vec3(1,1,1))
+ .Residue("TWO")
+ .Atom("A",geom::Vec3(2,2,2))
+ .Atom("B",geom::Vec3(3,3,3))
+ .Residue("THREE")
+ .Atom("A",geom::Vec3(4,4,4))
+ .Atom("B",geom::Vec3(5,5,5));
+
+ ost::mol::XCSEditor ed = e.EditXCS();
+ ed.DeleteBonds(e.GetBondList());
+
+ BuildingBlock block = BuildingBlock();
+ block.AddAtom("A","a",0.0);
+ block.AddAtom("B","b",0.0);
+
+ InteractionPtr bond_one(new Interaction(HarmonicBond));
+ InteractionPtr bond_two(new Interaction(HarmonicBond));
+ InteractionPtr bond_three(new Interaction(HarmonicBond));
+ std::vector<String> two_string;
+ two_string.push_back("A");
+ two_string.push_back("B");
+ bond_one->SetNames(two_string);
+ two_string[0] = "-B";
+ two_string[1] = "A";
+ bond_two->SetNames(two_string);
+ two_string[0] = "B";
+ two_string[1] = "+A";
+ bond_three->SetNames(two_string);
+ block.AddBond(bond_one);
+ block.AddBond(bond_two);
+ block.AddBond(bond_three);
+
+ ost::mol::ResidueHandleList res_list = e.GetResidueList();
+ ost::mol::AtomHandleList atoms_one = res_list[0].GetAtomList();
+ ost::mol::AtomHandleList atoms_two = res_list[1].GetAtomList();
+ ost::mol::AtomHandleList atoms_three = res_list[2].GetAtomList();
+
+ block.Connect(res_list[1],ed);
+ BOOST_CHECK(ost::mol::BondExists(atoms_one[1],atoms_two[0]));
+ BOOST_CHECK(ost::mol::BondExists(atoms_two[0],atoms_two[1]));
+ BOOST_CHECK(ost::mol::BondExists(atoms_two[1],atoms_three[0]));
+
+ ed.DeleteBonds(e.GetBondList());
+
+ BOOST_CHECK_THROW(block.Connect(res_list[0],ed),ost::Error);
+ BOOST_CHECK_THROW(block.Connect(res_list[2],ed),ost::Error);
+
+ InteractionPtr bond_four(new Interaction(HarmonicBond));
+ two_string[1] = "X";
+ bond_four->SetNames(two_string);
+ block.AddBond(bond_four);
+
+ BOOST_CHECK_THROW(block.Connect(res_list[1],ed),ost::Error);
+}
+
+BOOST_AUTO_TEST_CASE(test_match)
+{
+
+ ost::mol::EntityHandle e = ost::mol::Builder()
+ .Chain("A")
+ .Residue("ONE")
+ .Atom("A",geom::Vec3(0,0,0))
+ .Atom("B",geom::Vec3(1,1,1))
+ .Residue("TWO")
+ .Atom("A",geom::Vec3(2,2,2))
+ .Atom("B",geom::Vec3(3,3,3))
+ .Residue("THREE")
+ .Atom("A",geom::Vec3(4,4,4))
+ .Atom("B",geom::Vec3(5,5,5))
+ .Residue("FOUR")
+ .Atom("A",geom::Vec3(6,6,6))
+ .Atom("B",geom::Vec3(7,7,7));
+
+ ost::mol::ResidueHandleList res_list = e.GetResidueList();
+ ost::mol::XCSEditor ed = e.EditXCS();
+
+ ed.Connect(res_list[0].FindAtom("A"),res_list[0].FindAtom("B"));
+ ed.Connect(res_list[0].FindAtom("B"),res_list[1].FindAtom("A"));
+ ed.Connect(res_list[1].FindAtom("A"),res_list[1].FindAtom("B"));
+ ed.Connect(res_list[1].FindAtom("B"),res_list[2].FindAtom("A"));
+ ed.Connect(res_list[2].FindAtom("A"),res_list[2].FindAtom("B"));
+ //ed.Connect(atoms_two[1],atoms_four[1]);
+
+ BuildingBlock block = BuildingBlock();
+ String info_string;
+ BOOST_CHECK(!block.Match(res_list[1],true,info_string));
+
+ block.AddAtom("A","a",0.0);
+ block.AddAtom("B","b",0.0);
+
+ BOOST_CHECK(!block.Match(res_list[1],true,info_string));
+
+ InteractionPtr bond_one(new Interaction(HarmonicBond));
+ InteractionPtr bond_two(new Interaction(HarmonicBond));
+ InteractionPtr bond_three(new Interaction(HarmonicBond));
+
+ std::vector<String> names_one;
+ names_one.push_back("A");
+ names_one.push_back("B");
+ std::vector<String> names_two;
+ names_two.push_back("-B");
+ names_two.push_back("A");
+ std::vector<String> names_three;
+ names_three.push_back("B");
+ names_three.push_back("+A");
+
+ bond_one->SetNames(names_one);
+ bond_two->SetNames(names_two);
+ bond_three->SetNames(names_three);
+
+ block.AddBond(bond_one);
+ BOOST_CHECK(block.Match(res_list[1],true,info_string));
+
+ block.AddBond(bond_two);
+ BOOST_CHECK(block.Match(res_list[1],true,info_string));
+
+ block.AddBond(bond_three);
+ BOOST_CHECK(block.Match(res_list[1],true,info_string));
+
+ //let's remove the central bond and replace it with a constraint
+
+ block.RemoveAtom("A");
+ block.AddAtom("A","a",0.0);
+ InteractionPtr constraint(new Interaction(DistanceConstraint));
+ constraint->SetNames(names_one);
+ BOOST_CHECK(!block.Match(res_list[1],true,info_string));
+ block.AddConstraint(constraint);
+ BOOST_CHECK(block.Match(res_list[1],true,info_string));
+}
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/mol/mm/tests/test_block_modifiers.cc b/modules/mol/mm/tests/test_block_modifiers.cc
new file mode 100644
index 0000000000000000000000000000000000000000..0c60dd268b4f06b02204c6eae8c075d650701685
--- /dev/null
+++ b/modules/mol/mm/tests/test_block_modifiers.cc
@@ -0,0 +1,103 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mol.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+
+
+#include <ost/message.hh>
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_gromacs_block_modifier_basics){
+
+ GromacsBlockModifier mod;
+
+ //let's create some interactions
+ InteractionPtr harmonic_bond(new Interaction(HarmonicBond));
+ InteractionPtr urey_bradley_angle(new Interaction(UreyBradleyAngle));
+ InteractionPtr harmonic_angle(new Interaction(HarmonicAngle));
+ InteractionPtr periodic_dihedral(new Interaction(PeriodicDihedral));
+ InteractionPtr periodic_improper(new Interaction(PeriodicImproper));
+ InteractionPtr harmonic_improper(new Interaction(HarmonicImproper));
+ InteractionPtr cmap(new Interaction(CMap));
+
+ //check whether error gets thrown, when names of interactions are not set
+ BOOST_CHECK_THROW(mod.AddBond(harmonic_bond),ost::Error);
+ BOOST_CHECK_THROW(mod.AddAngle(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(mod.AddDihedral(periodic_dihedral),ost::Error);
+ BOOST_CHECK_THROW(mod.AddImproper(periodic_improper),ost::Error);
+ BOOST_CHECK_THROW(mod.AddCMap(cmap),ost::Error);
+
+ std::vector<String> two_string, three_string, four_string, five_string;
+
+ two_string.push_back("one");
+ three_string.push_back("one");
+ four_string.push_back("one");
+ five_string.push_back("one");
+
+ two_string.push_back("two");
+ three_string.push_back("two");
+ four_string.push_back("two");
+ five_string.push_back("two");
+
+ three_string.push_back("three");
+ four_string.push_back("three");
+ five_string.push_back("three");
+
+ four_string.push_back("four");
+ five_string.push_back("four");
+
+ five_string.push_back("five");
+
+ harmonic_bond->SetNames(two_string);
+ harmonic_angle->SetNames(three_string);
+ urey_bradley_angle->SetNames(three_string);
+ periodic_dihedral->SetNames(four_string);
+ periodic_improper->SetNames(four_string);
+ harmonic_improper->SetNames(four_string);
+ cmap->SetNames(five_string);
+
+ BOOST_CHECK_NO_THROW(mod.AddBond(harmonic_bond));
+ BOOST_CHECK_NO_THROW(mod.AddAngle(harmonic_angle));
+ BOOST_CHECK_NO_THROW(mod.AddAngle(urey_bradley_angle));
+ BOOST_CHECK_NO_THROW(mod.AddDihedral(periodic_dihedral));
+ BOOST_CHECK_NO_THROW(mod.AddImproper(periodic_improper));
+ BOOST_CHECK_NO_THROW(mod.AddImproper(harmonic_improper));
+ BOOST_CHECK_NO_THROW(mod.AddCMap(cmap));
+
+ //check whether error get thrown when wrong interactions get added
+
+ BOOST_CHECK_THROW(mod.AddBond(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(mod.AddAngle(harmonic_bond),ost::Error);
+ BOOST_CHECK_THROW(mod.AddDihedral(harmonic_bond),ost::Error);
+ BOOST_CHECK_THROW(mod.AddImproper(periodic_dihedral),ost::Error);
+ BOOST_CHECK_THROW(mod.AddCMap(periodic_improper),ost::Error);
+
+}
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/mol/mm/tests/test_forcefield.cc b/modules/mol/mm/tests/test_forcefield.cc
new file mode 100644
index 0000000000000000000000000000000000000000..cda6b18df4a8c38e315aef5e3849642e083d0c18
--- /dev/null
+++ b/modules/mol/mm/tests/test_forcefield.cc
@@ -0,0 +1,290 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+#include <ost/message.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_forcefield_basics){
+ Forcefield ff;
+
+ //if a building block doesn't exist, it should throw an error
+ //this is not the case for hydrogen constructors and block modifiers
+ BOOST_CHECK_THROW(ff.GetBuildingBlock("IDoNotExist"),ost::Error);
+
+ //add some atom types
+ ff.AddMass("one",1.0);
+ ff.AddMass("two",2.0);
+ ff.AddMass("three",3.0);
+ ff.AddMass("four",4.0);
+ ff.AddMass("five",5.0);
+
+ BOOST_CHECK_THROW(ff.GetBond("one","two"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetAngle("one","two","three"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetDihedrals("one","two","three","four"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetImpropers("one","two","three","four"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetCMap("one","two","three","four","five"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetImplicitGenborn("one"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetLJ("one"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetLJ("one","two"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetConstraint("one","two"),ost::Error);
+ BOOST_CHECK_THROW(ff.GetMass("i_do_not_exist"),ost::Error);
+
+ //let's add some interactions
+ std::vector<String> one_string, two_string, three_string, four_string, five_string;
+ std::vector<Real> one_real, two_real, three_real, four_real, five_real;
+
+ one_string.push_back("one");
+ two_string.push_back("one");
+ three_string.push_back("one");
+ four_string.push_back("one");
+ five_string.push_back("one");
+
+ two_string.push_back("two");
+ three_string.push_back("two");
+ four_string.push_back("two");
+ five_string.push_back("two");
+
+ three_string.push_back("three");
+ four_string.push_back("three");
+ five_string.push_back("three");
+
+ four_string.push_back("four");
+ five_string.push_back("four");
+
+ five_string.push_back("five");
+
+
+ one_real.push_back(1.0);
+ two_real.push_back(1.0);
+ three_real.push_back(1.0);
+ four_real.push_back(1.0);
+ five_real.push_back(1.0);
+
+ two_real.push_back(2.0);
+ three_real.push_back(2.0);
+ four_real.push_back(2.0);
+ five_real.push_back(2.0);
+
+ three_real.push_back(3.0);
+ four_real.push_back(3.0);
+ five_real.push_back(3.0);
+
+ four_real.push_back(4.0);
+ five_real.push_back(4.0);
+
+ five_real.push_back(5.0);
+
+
+ InteractionPtr harmonic_bond(new Interaction(HarmonicBond));
+ InteractionPtr urey_bradley_angle(new Interaction(UreyBradleyAngle));
+ InteractionPtr harmonic_angle(new Interaction(HarmonicAngle));
+ InteractionPtr periodic_dihedral(new Interaction(PeriodicDihedral));
+ InteractionPtr periodic_improper(new Interaction(PeriodicImproper));
+ InteractionPtr harmonic_improper(new Interaction(HarmonicImproper));
+ InteractionPtr cmap(new Interaction(CMap));
+ InteractionPtr lj(new Interaction(LJ));
+ InteractionPtr lj_pair(new Interaction(LJPair));
+ InteractionPtr gbsa(new Interaction(GBSA));
+ InteractionPtr distance_constraint(new Interaction(DistanceConstraint));
+
+
+ //check whether errors get thrown when incorrectly parametrized interactions are added
+ BOOST_CHECK_THROW(ff.AddBond(harmonic_bond),ost::Error);
+ harmonic_bond->SetTypes(two_string);
+ BOOST_CHECK_THROW(ff.AddBond(harmonic_bond),ost::Error);
+ harmonic_angle->SetParam(two_real);
+ BOOST_CHECK_THROW(ff.AddAngle(harmonic_angle),ost::Error);
+ harmonic_bond->SetParam(two_real);
+ BOOST_CHECK_NO_THROW(ff.AddBond(harmonic_bond));
+ harmonic_angle->SetTypes(three_string);
+
+ //parametrize the rest
+ urey_bradley_angle->SetTypes(three_string);
+ urey_bradley_angle->SetParam(four_real);
+ periodic_dihedral->SetTypes(four_string);
+ periodic_dihedral->SetParam(three_real);
+ periodic_improper->SetTypes(four_string);
+ periodic_improper->SetParam(three_real);
+ harmonic_improper->SetTypes(four_string);
+ harmonic_improper->SetParam(two_real);
+ std::vector<Real> cmap_param = five_real;
+ cmap_param[0] = 2.0;
+ cmap->SetTypes(five_string);
+ cmap->SetParam(cmap_param);
+ lj->SetTypes(one_string);
+ lj->SetParam(two_real);
+ lj_pair->SetTypes(two_string);
+ lj_pair->SetParam(two_real);
+ gbsa->SetTypes(one_string);
+ gbsa->SetParam(two_real);
+ distance_constraint->SetTypes(two_string);
+ distance_constraint->SetParam(one_real);
+
+ //check whether errors get thrown when wrong interactions get added
+
+ BOOST_CHECK_THROW(ff.AddBond(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddAngle(harmonic_bond),ost::Error);
+ BOOST_CHECK_THROW(ff.AddDihedral(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddImproper(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddCMap(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddImplicitGenborn(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddLJ(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddLJPair(harmonic_angle),ost::Error);
+ BOOST_CHECK_THROW(ff.AddConstraint(harmonic_angle),ost::Error);
+
+ BOOST_CHECK_NO_THROW(ff.AddBond(harmonic_bond));
+ BOOST_CHECK_NO_THROW(ff.AddAngle(harmonic_angle));
+ BOOST_CHECK_NO_THROW(ff.AddDihedral(periodic_dihedral));
+ BOOST_CHECK_NO_THROW(ff.AddImproper(periodic_improper));
+ BOOST_CHECK_NO_THROW(ff.AddImproper(harmonic_improper));
+ BOOST_CHECK_NO_THROW(ff.AddCMap(cmap));
+ BOOST_CHECK_NO_THROW(ff.AddImplicitGenborn(gbsa));
+ BOOST_CHECK_NO_THROW(ff.AddLJ(lj));
+ BOOST_CHECK_NO_THROW(ff.AddLJPair(lj_pair));
+ BOOST_CHECK_NO_THROW(ff.AddConstraint(distance_constraint));
+
+
+ //add a building block
+ BuildingBlockPtr block(new BuildingBlock);
+ block->AddAtom("a","one",0.5);
+ block->AddAtom("b","two",1.0);
+ ff.AddBuildingBlock("im_so_sexy",block);
+
+ //add block modifier
+ BlockModifierPtr modifier(new GromacsBlockModifier);
+ ff.AddBlockModifier("el_modificator",modifier);
+
+ //add hydrogen constructor
+ HydrogenConstructorPtr hydrogen_constructor(new GromacsHydrogenConstructor);
+ ff.AddHydrogenConstructor("death_metal",hydrogen_constructor);
+
+ //add some renaming rules
+ ff.AddResidueRenamingRule("im_so_sexy","even_sexier","sexy_n","sexy_c","sexy_two");
+ ff.AddAtomRenamingRule("even_sexier","a","z");
+ ff.AddAtomRenamingRule("sexy_two","a","z");
+
+ //save and load it again, before we check parameters
+ ff.Save("test.ff");
+ ForcefieldPtr loaded_ff = Forcefield::Load("test.ff");
+
+
+ //check the parameters
+ BOOST_CHECK(loaded_ff->GetBond("one","two")->GetParam() == two_real);
+ BOOST_CHECK(loaded_ff->GetBond("two","one")->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetAngle("one","two","three")->GetParam() == two_real);
+ BOOST_CHECK(loaded_ff->GetAngle("three","two","one")->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetDihedrals("one","two","three","four")[0]->GetParam() == three_real);
+ BOOST_CHECK(loaded_ff->GetDihedrals("four","three","two","one")[0]->GetParam() == three_real);
+
+ BOOST_CHECK(loaded_ff->GetImpropers("one","two","three","four")[0]->GetParam() == three_real);
+ BOOST_CHECK(loaded_ff->GetImpropers("four","three","two","one")[0]->GetParam() == three_real);
+
+ BOOST_CHECK(loaded_ff->GetDihedrals("one","two","three","four")[0]->GetParam() == three_real);
+ BOOST_CHECK(loaded_ff->GetDihedrals("four","three","two","one")[0]->GetParam() == three_real);
+
+ BOOST_CHECK(loaded_ff->GetCMap("one","two","three","four","five")->GetParam() == cmap_param);
+ //cmaps are directional...
+ BOOST_CHECK_THROW(loaded_ff->GetCMap("five","four","three","two","one"),ost::Error);
+
+ BOOST_CHECK(loaded_ff->GetImplicitGenborn("one")->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetLJ("one","two",true)->GetParam() == two_real);
+ BOOST_CHECK(loaded_ff->GetLJ("two","one",true)->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetLJ("one")->GetParam() == two_real);
+
+ BOOST_CHECK(loaded_ff->GetConstraint("one","two")->GetParam() == one_real);
+ BOOST_CHECK(loaded_ff->GetConstraint("two","one")->GetParam() == one_real);
+
+ BOOST_CHECK(loaded_ff->GetMass("two") == 2.0);
+
+ BOOST_CHECK(loaded_ff->GetAtomType("im_so_sexy","a") == "one");
+
+ //check whether the modifiers are still there
+ BOOST_CHECK(loaded_ff->GetHydrogenConstructor("death_metal"));
+ BOOST_CHECK(loaded_ff->GetBlockModifier("el_modificator"));
+
+
+ //check the renaming stuff
+
+
+ ost::mol::EntityHandle new_ent = ost::mol::Builder()
+ .Chain("A")
+ .Residue("im_so_sexy")
+ .Atom("a",geom::Vec3(0,0,0))
+ .Atom("b",geom::Vec3(1,1,1))
+ .Residue("im_so_sexy")
+ .Atom("a",geom::Vec3(2,2,2))
+ .Atom("b",geom::Vec3(3,3,3))
+ .Residue("im_so_sexy")
+ .Atom("a",geom::Vec3(4,4,4))
+ .Atom("b",geom::Vec3(5,5,5));
+
+ ost::mol::XCSEditor ed = new_ent.EditXCS();
+
+
+ loaded_ff->AssignFFSpecificNames(new_ent);
+ ost::mol::ResidueHandleList res_list = new_ent.GetResidueList();
+ ost::mol::AtomHandleList atom_list = new_ent.GetAtomList();
+
+ BOOST_CHECK(res_list[0].GetName() == "sexy_n");
+ BOOST_CHECK(res_list[1].GetName() == "even_sexier");
+ BOOST_CHECK(res_list[2].GetName() == "sexy_c");
+ BOOST_CHECK(atom_list[2].GetName() == "z");
+
+ loaded_ff->AssignFFSpecificNames(new_ent,true);
+
+ BOOST_CHECK(res_list[0].GetName() == "im_so_sexy");
+ BOOST_CHECK(res_list[1].GetName() == "im_so_sexy");
+ BOOST_CHECK(res_list[2].GetName() == "im_so_sexy");
+ BOOST_CHECK(atom_list[2].GetName() == "a");
+
+ ost::mol::EntityHandle new_ent_two = ost::mol::Builder()
+ .Chain("A")
+ .Residue("im_so_sexy")
+ .Atom("a",geom::Vec3(0,0,0))
+ .Atom("b",geom::Vec3(1,1,1));
+
+ loaded_ff->AssignFFSpecificNames(new_ent_two);
+ res_list = new_ent_two.GetResidueList();
+ atom_list = new_ent_two.GetAtomList();
+ BOOST_CHECK(res_list[0].GetName() == "sexy_two");
+ BOOST_CHECK(atom_list[0].GetName() == "z");
+ loaded_ff->AssignFFSpecificNames(new_ent_two,true);
+ BOOST_CHECK(res_list[0].GetName() == "im_so_sexy");
+ BOOST_CHECK(atom_list[0].GetName() == "a");
+
+}
+
+BOOST_AUTO_TEST_SUITE_END();
\ No newline at end of file
diff --git a/modules/mol/mm/tests/test_interaction.cc b/modules/mol/mm/tests/test_interaction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..d021c5e711cfdc8b876b1d3a42a52310d8eb0db0
--- /dev/null
+++ b/modules/mol/mm/tests/test_interaction.cc
@@ -0,0 +1,292 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mol.hh>
+#include <ost/mol/builder.hh>
+
+#include <ost/message.hh>
+
+using namespace ost::mol::mm;
+
+
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_set_stuff)
+{
+ Interaction harmonic_bond = Interaction(HarmonicBond);
+ Interaction harmonic_angle = Interaction(HarmonicAngle);
+ Interaction urey_bradley = Interaction(UreyBradleyAngle);
+ Interaction periodic_dihedral = Interaction(PeriodicDihedral);
+ Interaction periodic_improper = Interaction(PeriodicImproper);
+ Interaction harmonic_improper = Interaction(HarmonicImproper);
+ Interaction cmap = Interaction(CMap);
+ Interaction lj = Interaction(LJ);
+ Interaction lj_pair = Interaction(LJPair);
+ Interaction gbsa = Interaction(GBSA);
+ Interaction distance_constraint = Interaction(DistanceConstraint);
+ Interaction exclusion = Interaction(Exclusion);
+ Interaction harmonic_distance_restraint = Interaction(HarmonicDistanceRestraint);
+ Interaction harmonic_position_restraint = Interaction(HarmonicPositionRestraint);
+
+ //std::vector<String> one_string, two_string, three_string, four_string, five_string;
+ //std::vector<Real> one_real, two_real, three_real, four_real, five_real, zero_real;
+
+ std::vector<Real> one_real(1);
+ std::vector<Real> two_real(2);
+ std::vector<Real> three_real(3);
+ std::vector<Real> four_real(4);
+ std::vector<Real> five_real(5);
+ std::vector<Real> seven_real(7);
+ std::vector<Real> zero_real(0);
+
+ std::vector<String> one_string(1);
+ std::vector<String> two_string(2);
+ std::vector<String> three_string(3);
+ std::vector<String> four_string(4);
+ std::vector<String> five_string(5);
+
+
+ BOOST_CHECK(!harmonic_bond.IsParametrized());
+
+ BOOST_CHECK_THROW(harmonic_bond.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_angle.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(urey_bradley.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(periodic_dihedral.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(periodic_improper.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_improper.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(cmap.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(lj.SetNames(two_string),ost::Error);
+ BOOST_CHECK_THROW(lj_pair.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(gbsa.SetNames(two_string),ost::Error);
+ BOOST_CHECK_THROW(distance_constraint.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(exclusion.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_distance_restraint.SetNames(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_position_restraint.SetNames(two_string),ost::Error);
+
+
+ BOOST_CHECK_THROW(harmonic_bond.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_angle.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(urey_bradley.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(periodic_dihedral.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(periodic_improper.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_improper.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(cmap.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(lj.SetTypes(two_string),ost::Error);
+ BOOST_CHECK_THROW(lj_pair.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(gbsa.SetTypes(two_string),ost::Error);
+ BOOST_CHECK_THROW(distance_constraint.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(exclusion.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_distance_restraint.SetTypes(one_string),ost::Error);
+ BOOST_CHECK_THROW(harmonic_position_restraint.SetTypes(two_string),ost::Error);
+
+ BOOST_CHECK_THROW(harmonic_bond.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(harmonic_angle.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(urey_bradley.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(periodic_dihedral.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(periodic_improper.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(harmonic_improper.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(cmap.SetParam(two_real),ost::Error);
+ BOOST_CHECK_THROW(lj.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(lj_pair.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(gbsa.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(distance_constraint.SetParam(two_real),ost::Error);
+ BOOST_CHECK_THROW(exclusion.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(harmonic_distance_restraint.SetParam(one_real),ost::Error);
+ BOOST_CHECK_THROW(harmonic_position_restraint.SetParam(one_real),ost::Error);
+
+
+
+ BOOST_CHECK_NO_THROW(harmonic_bond.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_angle.SetNames(three_string));
+ BOOST_CHECK_NO_THROW(urey_bradley.SetNames(three_string));
+ BOOST_CHECK_NO_THROW(periodic_dihedral.SetNames(four_string));
+ BOOST_CHECK_NO_THROW(periodic_improper.SetNames(four_string));
+ BOOST_CHECK_NO_THROW(harmonic_improper.SetNames(four_string));
+ BOOST_CHECK_NO_THROW(cmap.SetNames(five_string));
+ BOOST_CHECK_NO_THROW(lj.SetNames(one_string));
+ BOOST_CHECK_NO_THROW(lj_pair.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(gbsa.SetNames(one_string));
+ BOOST_CHECK_NO_THROW(distance_constraint.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(exclusion.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetNames(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetNames(one_string));
+
+
+ BOOST_CHECK_NO_THROW(harmonic_bond.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_angle.SetTypes(three_string));
+ BOOST_CHECK_NO_THROW(urey_bradley.SetTypes(three_string));
+ BOOST_CHECK_NO_THROW(periodic_dihedral.SetTypes(four_string));
+ BOOST_CHECK_NO_THROW(periodic_improper.SetTypes(four_string));
+ BOOST_CHECK_NO_THROW(harmonic_improper.SetTypes(four_string));
+ BOOST_CHECK_NO_THROW(cmap.SetTypes(five_string));
+ BOOST_CHECK_NO_THROW(lj.SetTypes(one_string));
+ BOOST_CHECK_NO_THROW(lj_pair.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(gbsa.SetTypes(one_string));
+ BOOST_CHECK_NO_THROW(distance_constraint.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(exclusion.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetTypes(two_string));
+ BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetTypes(one_string));
+
+ BOOST_CHECK_NO_THROW(harmonic_bond.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(harmonic_angle.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(urey_bradley.SetParam(four_real));
+ BOOST_CHECK_NO_THROW(periodic_dihedral.SetParam(three_real));
+ BOOST_CHECK_NO_THROW(periodic_improper.SetParam(three_real));
+ BOOST_CHECK_NO_THROW(harmonic_improper.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(lj.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(lj_pair.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(gbsa.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(distance_constraint.SetParam(one_real));
+ BOOST_CHECK_NO_THROW(exclusion.SetParam(zero_real));
+ BOOST_CHECK_NO_THROW(harmonic_distance_restraint.SetParam(two_real));
+ BOOST_CHECK_NO_THROW(harmonic_position_restraint.SetParam(seven_real));
+
+ std::vector<Real> valid_cmap_parameters;
+ valid_cmap_parameters.push_back(2.0);
+ valid_cmap_parameters.push_back(0.0);
+ valid_cmap_parameters.push_back(0.0);
+ valid_cmap_parameters.push_back(0.0);
+ valid_cmap_parameters.push_back(0.0);
+
+ BOOST_CHECK_NO_THROW(cmap.SetParam(valid_cmap_parameters));
+ BOOST_CHECK(harmonic_bond.IsParametrized());
+
+ Interaction new_bond = Interaction(HarmonicBond);
+ std::vector<String> with_wildcard, without_wildcard;
+ with_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+ with_wildcard.push_back("X");
+ without_wildcard.push_back("A");
+
+ //should be initialized with false
+ BOOST_CHECK(!new_bond.HasNameWildcard());
+ BOOST_CHECK(!new_bond.HasTypeWildcard());
+
+ new_bond.SetNames(without_wildcard);
+ new_bond.SetTypes(without_wildcard);
+ BOOST_CHECK(!new_bond.HasNameWildcard());
+ BOOST_CHECK(!new_bond.HasTypeWildcard());
+
+ new_bond.SetNames(with_wildcard);
+ new_bond.SetTypes(with_wildcard);
+ BOOST_CHECK(new_bond.HasNameWildcard());
+ BOOST_CHECK(new_bond.HasTypeWildcard());
+
+ //Check hasname/hastype
+ BOOST_CHECK(new_bond.HasType("A"));
+ BOOST_CHECK(!new_bond.HasType("B"));
+ BOOST_CHECK(new_bond.HasName("A"));
+ BOOST_CHECK(!new_bond.HasType("B"));
+
+}
+
+BOOST_AUTO_TEST_CASE(test_match_stuff)
+{
+ Interaction dihedral = Interaction(PeriodicDihedral);
+
+ std::vector<String> with_wildcard, without_wildcard;
+ with_wildcard.push_back("X");
+ with_wildcard.push_back("A");
+ with_wildcard.push_back("A");
+ with_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+ without_wildcard.push_back("A");
+
+ dihedral.SetTypes(with_wildcard);
+ BOOST_CHECK(dihedral.MatchTypes(with_wildcard));
+ BOOST_CHECK(dihedral.MatchTypes(without_wildcard));
+ dihedral.SetTypes(without_wildcard);
+ BOOST_CHECK(dihedral.MatchTypes(without_wildcard));
+ BOOST_CHECK(!dihedral.MatchTypes(with_wildcard));
+
+ dihedral.SetNames(with_wildcard);
+ BOOST_CHECK(dihedral.MatchNames(with_wildcard));
+ BOOST_CHECK(dihedral.MatchNames(without_wildcard));
+ dihedral.SetNames(without_wildcard);
+ BOOST_CHECK(dihedral.MatchNames(without_wildcard));
+ BOOST_CHECK(!dihedral.MatchNames(with_wildcard));
+
+}
+
+BOOST_AUTO_TEST_CASE(test_replace_atom){
+ Interaction bond = Interaction(HarmonicBond);
+ std::vector<String> strings;
+ strings.push_back("A");
+ strings.push_back("B");
+ bond.SetNames(strings);
+ bond.ReplaceAtom("A","X","X");
+ std::vector<String> new_names = bond.GetNames();
+ BOOST_CHECK(new_names != strings);
+ bond.SetTypes(strings);
+ bond.ReplaceAtom("X","A","X");
+ std::vector<String> new_types = bond.GetTypes();
+ BOOST_CHECK(new_types == new_names);
+
+}
+
+BOOST_AUTO_TEST_CASE(test_getatoms){
+ ost::mol::EntityHandle e = ost::mol::Builder()
+ .Chain("A")
+ .Residue("ONE")
+ .Atom("A",geom::Vec3(-5,-5,-5))
+ .Atom("B",geom::Vec3(-5, 5,-5))
+ .Residue("TWO")
+ .Atom("A",geom::Vec3(1,1,1))
+ .Atom("B",geom::Vec3(2,2,2))
+ .Residue("THREE")
+ .Atom("A",geom::Vec3(3,3,3))
+ .Atom("B",geom::Vec3(4,4,4));
+
+ ost::mol::ResidueHandleList res_list = e.GetResidueList();
+ ost::mol::AtomHandleList atom_list_one = res_list[0].GetAtomList();
+ ost::mol::AtomHandleList atom_list_two = res_list[1].GetAtomList();
+ ost::mol::AtomHandleList atom_list_three = res_list[2].GetAtomList();
+
+ Interaction bond = Interaction(HarmonicBond);
+ std::vector<String> strings;
+ strings.push_back("A");
+ strings.push_back("B");
+ bond.SetNames(strings);
+ ost::mol::AtomHandleList bond_atom_list = bond.GetAtoms(res_list[0]);
+ BOOST_CHECK(atom_list_one[0] == bond_atom_list[0]);
+ BOOST_CHECK(atom_list_one[1] == bond_atom_list[1]);
+ strings[1] = "X";
+ bond.SetNames(strings);
+ BOOST_CHECK_THROW(bond.GetAtoms(res_list[0]),ost::Error);
+ strings[0] = "-A";
+ strings[1] = "B";
+ bond.SetNames(strings);
+ BOOST_CHECK_THROW(bond.GetAtoms(res_list[0]),ost::Error);
+ bond_atom_list = bond.GetAtoms(res_list[1]);
+ BOOST_CHECK(bond_atom_list[0] == atom_list_one[0]);
+ BOOST_CHECK(bond_atom_list[1] == atom_list_two[1]);
+ strings[1]="+B";
+ bond.SetNames(strings);
+ BOOST_CHECK_THROW(bond.GetAtoms(res_list[2]),ost::Error);
+ bond_atom_list = bond.GetAtoms(res_list[1]);
+ BOOST_CHECK(bond_atom_list[0] == atom_list_one[0]);
+ BOOST_CHECK(bond_atom_list[1] == atom_list_three[1]);
+}
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/mol/mm/tests/test_simulation.cc b/modules/mol/mm/tests/test_simulation.cc
new file mode 100644
index 0000000000000000000000000000000000000000..cfe2b608136a315fd89aa72bf0685f2bcfc8c3ee
--- /dev/null
+++ b/modules/mol/mm/tests/test_simulation.cc
@@ -0,0 +1,182 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/mol/mm/interaction.hh>
+#include <ost/mol/mm/buildingblock.hh>
+#include <ost/mol/mm/gromacs_block_modifiers.hh>
+#include <ost/message.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/mol/mm/simulation.hh>
+#include <ost/mol/mm/topology.hh>
+#include <OpenMM.h>
+
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_simulation_basics){
+
+ String pdb_name = "1CRN.pdb";
+
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
+ processor->Process(test_ent);
+
+ SettingsPtr settings(new Settings);
+ ForcefieldPtr forcefield = Forcefield::Load("CHARMM27.dat");
+ settings->forcefield = forcefield;
+ settings->add_gbsa = true;
+
+ TopologyPtr top = TopologyCreator::Create(test_ent,settings);
+ //lets add interactions, that are not set when using charmm
+ top->AddHarmonicAngle(1,2,3,10.0,10.0);
+ top->AddPeriodicImproper(1,2,3,4,2,10.0,10.0);
+ top->AddDistanceConstraint(1,2,10.0);
+ top->AddHarmonicPositionRestraint(1,geom::Vec3(0.0,0.0,0.0),10.0);
+ top->AddHarmonicDistanceRestraint(1,2,10.0,10.0);
+
+ settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+
+ Simulation sim(top, test_ent, settings);
+
+
+ //we check, wether the reset functions have the desired effect on the topology
+ //we cannot really check the effect on the openmm system...
+ sim.ResetHarmonicBond(42,5.0,6.0);
+ sim.ResetHarmonicAngle(0,8.0,9.0);
+ sim.ResetUreyBradleyAngle(42,5.0,6.0,7.0,8.0);
+ sim.ResetPeriodicDihedral(42,4,5.0,6.0);
+ sim.ResetPeriodicImproper(0,5,8.0,9.0);
+ sim.ResetHarmonicImproper(42,5.0,6.0);
+ sim.ResetLJPair(42,5.0,6.0);
+ sim.ResetDistanceConstraint(0,10.0);
+ sim.ResetHarmonicPositionRestraint(0,geom::Vec3(1.0,1.0,1.0),5.0);
+ sim.ResetHarmonicDistanceRestraint(0,5.0,10.0);
+ sim.ResetLJ(42,2.0,3.0);
+ sim.ResetGBSA(42,5.0,6.0);
+ sim.ResetCharge(42,100.0);
+ sim.ResetMass(42,200.0);
+
+ uint ui1,ui2,ui3,ui4;
+ int i1;
+ Real r1,r2,r3,r4;
+ geom::Vec3 pos;
+
+
+ top->GetHarmonicBondParameters(42,ui1,ui2,r1,r2);
+ BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
+
+ top->GetHarmonicAngleParameters(0,ui1,ui2,ui3,r1,r2);
+ BOOST_CHECK(r1 == 8.0 && r2 == 9.0);
+
+ top->GetUreyBradleyAngleParameters(42,ui1,ui2,ui3,r1,r2,r3,r4);
+ BOOST_CHECK(r1 == 5.0 && r2 == 6.0 && r3 == 7.0 && r4 == 8.0);
+
+ top->GetPeriodicDihedralParameters(42,ui1,ui2,ui3,ui4,i1,r1,r2);
+ BOOST_CHECK(i1 == 4 && r1 == 5.0 && r2 == 6.0);
+
+ top->GetPeriodicImproperParameters(0,ui1,ui2,ui3,ui4,i1,r1,r2);
+ BOOST_CHECK(i1 == 5 && r1 == 8.0 && r2 == 9.0);
+
+ top->GetLJPairParameters(42,ui1,ui2,r1,r2);
+ BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
+
+ top->GetDistanceConstraintParameters(0,ui1,ui2,r1);
+ BOOST_CHECK(r1 == 10.0);
+
+ top->GetHarmonicPositionRestraintParameters(0, ui1, pos,r1, r2, r3, r3);
+ BOOST_CHECK(pos == geom::Vec3(1.0,1.0,1.0) && r1 == 5.0);
+
+ top->GetHarmonicDistanceRestraintParameters(0,ui1,ui2, r1, r2);
+ BOOST_CHECK(r1 == 5.0 && r2 == 10.0);
+
+ r1 = top->GetSigma(42);
+ r2 = top->GetEpsilon(42);
+ BOOST_CHECK(r1 == 2.0 && r2 == 3.0);
+
+ r1 = top->GetGBSARadius(42);
+ r2 = top->GetOBCScaling(42);
+ BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
+
+ r1 = top->GetCharge(42);
+ r2 = top->GetMass(42);
+ BOOST_CHECK(r1 == 100.0 && r2 == 200.0);
+}
+
+
+BOOST_AUTO_TEST_CASE(test_simulation_energy_calculations){
+
+
+ String pdb_name = "1CRN.pdb";
+
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
+ processor->Process(test_ent);
+
+ SettingsPtr settings(new Settings);
+ ForcefieldPtr forcefield = Forcefield::Load("CHARMM27.dat");
+ settings->forcefield = forcefield;
+
+ TopologyPtr top = TopologyCreator::Create(test_ent,settings);
+ //lets add interactions, that are not set when using charmm
+
+ settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
+
+ Simulation sim(top, test_ent,settings);
+
+ sim.ApplySD(1.0, 200);
+
+ //the energy values have been compared with the results from the
+ //CHARMM27 forcefield in gromacs
+
+ //differenecs in energy(kJ/mol):
+ //harmonic_bond: 0.00021344800001
+ //urey_bradley_angle: 0.00021319300003
+ //periodic_dihedral: 0.00018275799993
+ //harmonic_improper: 0.00001410630000
+ //cmap: 0.00192255100001
+ //nonbonded: 0.00204422999968
+
+ //You'll most likely get different results when repeating the comparison with gromacs
+ //this is because of the precision.
+ //Right now we have full real precision in the positions.
+ //When you write down the pdb, precision will be lowered to 3 digits.
+ //Another digit gets lost, when you create a gromacs topology...
+ //Gromacs writes down the positions using nm instead of A, but
+ //also has a precision of 3 digits.
+
+ BOOST_CHECK_CLOSE(sim.GetPotentialEnergy(), -2381.24, Real(1e-3));
+}
+
+
+
+BOOST_AUTO_TEST_SUITE_END();
\ No newline at end of file
diff --git a/modules/mol/mm/tests/test_topology.cc b/modules/mol/mm/tests/test_topology.cc
new file mode 100644
index 0000000000000000000000000000000000000000..d10bd05e6427ab64da9b54adb2fd076dd05370d6
--- /dev/null
+++ b/modules/mol/mm/tests/test_topology.cc
@@ -0,0 +1,598 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <ost/mol/mm/topology.hh>
+#include <ost/mol/mm/topology_creator.hh>
+#include <ost/mol/mm/settings.hh>
+#include <ost/mol/mm/forcefield.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/conop/heuristic.hh>
+#include <ost/message.hh>
+#include <ost/mol/builder.hh>
+#include <ost/mol/xcs_editor.hh>
+
+
+using namespace ost::mol::mm;
+
+BOOST_AUTO_TEST_SUITE( mol_mm );
+
+BOOST_AUTO_TEST_CASE(test_topology_basics){
+
+ String pdb_name = "1CRN.pdb";
+
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
+ processor->Process(test_ent);
+
+ //check initialisation without settings
+ std::vector<Real> zero_real(0);
+ std::vector<Real> lot_of_reals(test_ent.GetAtomCount());
+
+ TopologyPtr top(new Topology(lot_of_reals));
+
+ uint ui1(0), ui2(0), ui3(0), ui4(0), ui5(0);
+ int i1(0), i5(0);
+ Real r1(0.0), r2(0.0), r3(0.0), r4(0.0);
+ geom::Vec3 zero_vec(0.0,0.0,0.0);
+ geom::Vec3 test_vec(0.0,1.0,2.0);
+
+ //check wether errors geth thrown, when atom indices are too big
+ BOOST_CHECK_THROW(top->AddHarmonicBond(700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicBond(0,700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicAngle(700,1,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicAngle(1,700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicAngle(1,1,700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddUreyBradleyAngle(700,1,1,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->AddUreyBradleyAngle(1,700,1,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->AddUreyBradleyAngle(1,1,700,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicDihedral(700,1,1,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicDihedral(1,700,1,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicDihedral(1,1,700,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicDihedral(1,1,1,700,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicImproper(700,1,1,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicImproper(1,700,1,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicImproper(1,1,700,1,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddPeriodicImproper(1,1,1,700,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicImproper(700,1,1,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicImproper(1,700,1,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicImproper(1,1,700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicImproper(1,1,1,700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(700,1,1,1,1,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,700,1,1,1,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,1,700,1,1,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,1,1,700,1,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,1,1,1,700,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->AddCMap(1,1,1,1,1,0,lot_of_reals),ost::Error); //additionally checks error, when dimension and cmap are inconsistent
+ BOOST_CHECK_THROW(top->AddLJPair(1,700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddLJPair(700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddExclusion(1,700),ost::Error);
+ BOOST_CHECK_THROW(top->AddExclusion(700,1),ost::Error);
+ BOOST_CHECK_THROW(top->AddDistanceConstraint(1,700,r1),ost::Error);
+ BOOST_CHECK_THROW(top->AddDistanceConstraint(700,1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicPositionRestraint(700,zero_vec,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicDistanceRestraint(700,1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->AddHarmonicDistanceRestraint(1,700,r1,r2),ost::Error);
+
+ //check whether errors get thrown when single atom parameters are inconsistent with number of atoms in topology
+ BOOST_CHECK_THROW(top->SetSigmas(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetEpsilons(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetGBSARadii(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetOBCScalings(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetMasses(zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetCharges(zero_real),ost::Error);
+
+ //Single atom parameters are not allowed to be modified, without being set initially
+ BOOST_CHECK_THROW(top->SetSigma(1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetEpsilon(1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetGBSARadius(1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetOBCScaling(1,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetCharge(1,r1),ost::Error);
+
+ //Let's set the single atom parameters initially
+ top->SetSigmas(lot_of_reals);
+ top->SetEpsilons(lot_of_reals);
+ top->SetGBSARadii(lot_of_reals);
+ top->SetOBCScalings(lot_of_reals);
+ top->SetCharges(lot_of_reals);
+
+ //do the index checks for them
+ BOOST_CHECK_THROW(top->SetSigma(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetEpsilon(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetGBSARadius(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetOBCScaling(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetMass(1000,1.0),ost::Error);
+ BOOST_CHECK_THROW(top->SetCharge(1000,1.0),ost::Error);
+
+ //similar stupid checks for SetParameter functions
+ BOOST_CHECK_THROW(top->SetHarmonicBondParameters(700,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetHarmonicAngleParameters(3000,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetUreyBradleyAngleParameters(3000,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->SetPeriodicDihedralParameters(3000,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetPeriodicImproperParameters(3000,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetHarmonicImproperParameters(3000,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetCMapParameters(3000,0,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->SetLJPairParameters(3000,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->SetDistanceConstraintParameters(3000,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetHarmonicPositionRestraintParameters(3000,zero_vec,r1),ost::Error);
+ BOOST_CHECK_THROW(top->SetHarmonicDistanceRestraintParameters(3000,r1,r2),ost::Error);
+
+ BOOST_CHECK_THROW(top->GetHarmonicBondParameters(700,ui1,ui2,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetHarmonicAngleParameters(3000,ui1,ui2,ui3,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetUreyBradleyAngleParameters(3000,ui1,ui2,ui3,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->GetPeriodicDihedralParameters(3000,ui1,ui2,ui3,ui4,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetPeriodicImproperParameters(3000,ui1,ui2,ui3,ui4,i1,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetHarmonicImproperParameters(3000,ui1,ui2,ui3,ui4,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetCMapParameters(3000,ui1,ui2,ui3,ui4,ui5,i1,zero_real),ost::Error);
+ BOOST_CHECK_THROW(top->GetLJPairParameters(3000,ui1,ui2,r1,r2),ost::Error);
+ BOOST_CHECK_THROW(top->GetDistanceConstraintParameters(3000,ui1,ui2,r1),ost::Error);
+ BOOST_CHECK_THROW(top->GetHarmonicPositionRestraintParameters(3000,ui1,zero_vec,r1,r2,r3,r4),ost::Error);
+ BOOST_CHECK_THROW(top->GetHarmonicDistanceRestraintParameters(3000,ui1,ui2,r1,r2),ost::Error);
+
+ //let's add some interactions to the topology
+ for(int i = 0; i < 10; ++i){
+ top->AddHarmonicBond(0,1,r1,r2);
+ top->AddHarmonicAngle(0,1,2,r1,r2);
+ top->AddUreyBradleyAngle(0,1,2,r1,r2,r3,r4);
+ top->AddPeriodicDihedral(0,1,2,3,i1,r1,r2);
+ top->AddPeriodicImproper(0,1,2,3,i1,r1,r2);
+ top->AddHarmonicImproper(0,1,2,3,r1,r2);
+ top->AddCMap(0,1,2,3,4,i1,zero_real);
+ top->AddHarmonicPositionRestraint(0,zero_vec,r1,r2,r3,r4);
+ top->AddHarmonicDistanceRestraint(0,1,r1,r2);
+ }
+
+ //following interactions are unique for a pair of atoms
+ top->AddLJPair(0,1,r1,r2);
+ top->AddDistanceConstraint(0,1,r1);
+ top->AddExclusion(0,1);
+
+ //errors should be thrown, when previously added interactions are added again
+ BOOST_CHECK_THROW(top->AddLJPair(0,1,r1,r2), ost::Error);
+ BOOST_CHECK_THROW(top->AddDistanceConstraint(0,1,r1), ost::Error);
+ BOOST_CHECK_THROW(top->AddExclusion(0,1), ost::Error);
+ BOOST_CHECK_THROW(top->AddLJPair(1,0,r1,r2), ost::Error);
+ BOOST_CHECK_THROW(top->AddDistanceConstraint(1,0,r1), ost::Error);
+ BOOST_CHECK_THROW(top->AddExclusion(1,0), ost::Error);
+
+ //check set and get parameter stuff, but also the GetIndices functionality
+ std::vector<uint> ind1,ind2;
+ top->SetHarmonicBondParameters(0,0.5,15.0);
+ top->GetHarmonicBondParameters(0,ui1,ui2,r1,r2);
+ BOOST_CHECK(r1 == 0.5 && r2 == 15.0);
+ ind1 = top->GetHarmonicBondIndices(0,1);
+ ind2 = top->GetHarmonicBondIndices(1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetHarmonicBondIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicBondIndices(1).size() == 10);
+ BOOST_CHECK(top->GetHarmonicBondIndices(2).size() == 0);
+
+
+ top->SetHarmonicAngleParameters(0,1.0,10.0);
+ top->GetHarmonicAngleParameters(0,ui1,ui2,ui3,r1,r2);
+ BOOST_CHECK(r1 == 1.0 && r2 == 10.0);
+ ind1 = top->GetHarmonicAngleIndices(0,1,2);
+ ind2 = top->GetHarmonicAngleIndices(2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetHarmonicAngleIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicAngleIndices(1).size() == 10);
+ BOOST_CHECK(top->GetHarmonicAngleIndices(2).size() == 10);
+ BOOST_CHECK(top->GetHarmonicAngleIndices(3).size() == 0);
+
+ top->SetUreyBradleyAngleParameters(0,0.5,0.5,0.5,0.5);
+ top->GetUreyBradleyAngleParameters(0,ui1,ui2,ui3,r1,r2,r3,r4);
+ BOOST_CHECK( r1 == 0.5 && r2 == 0.5 && r3 == 0.5 && r3 == 0.5 );
+ ind1 = top->GetUreyBradleyAngleIndices(0,1,2);
+ ind2 = top->GetUreyBradleyAngleIndices(2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetUreyBradleyAngleIndices(0).size() == 10);
+ BOOST_CHECK(top->GetUreyBradleyAngleIndices(1).size() == 10);
+ BOOST_CHECK(top->GetUreyBradleyAngleIndices(2).size() == 10);
+ BOOST_CHECK(top->GetUreyBradleyAngleIndices(3).size() == 0);
+
+
+ top->SetPeriodicDihedralParameters(0,2,5.0,0.5);
+ top->GetPeriodicDihedralParameters(0,ui1,ui2,ui3,ui4,i1,r1,r2);
+ BOOST_CHECK( i5 == 0 && r1 == 5.0 && r2 == 0.5 );
+ ind1 = top->GetPeriodicDihedralIndices(0,1,2,3);
+ ind2 = top->GetPeriodicDihedralIndices(3,2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(0).size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(1).size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(2).size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(3).size() == 10);
+ BOOST_CHECK(top->GetPeriodicDihedralIndices(4).size() == 0);
+
+ top->SetPeriodicImproperParameters(6,2,2.0,1.0);
+ top->GetPeriodicImproperParameters(6,ui1,ui2,ui3,ui4,i1,r1,r2);
+ BOOST_CHECK( i5 == 0 && r1 == 2.0 && r2 == 1.0 );
+ ind1 = top->GetPeriodicImproperIndices(0,1,2,3);
+ ind2 = top->GetPeriodicImproperIndices(3,2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(0).size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(1).size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(2).size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(3).size() == 10);
+ BOOST_CHECK(top->GetPeriodicImproperIndices(4).size() == 0);
+
+ top->SetHarmonicImproperParameters(0,4.0,4.0);
+ top->GetHarmonicImproperParameters(0,ui1,ui2,ui3,ui4,r1,r2);
+ BOOST_CHECK(r1 == 4.0 && r2 == 4.0);
+ ind1 = top->GetHarmonicImproperIndices(0,1,2,3);
+ ind2 = top->GetHarmonicImproperIndices(3,2,1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(1).size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(2).size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(3).size() == 10);
+ BOOST_CHECK(top->GetHarmonicImproperIndices(4).size() == 0);
+
+ std::vector<Real> one_real(1);
+ one_real[0] = 42;
+ top->SetCMapParameters(0,1,one_real);
+ std::vector<Real> temp_real;
+ top->GetCMapParameters(0,ui1,ui2,ui3,ui4,ui5,i1,temp_real);
+ BOOST_CHECK( ui1 == 0 && temp_real.size() == 1 && temp_real[0] == 42);
+ ind1 = top->GetCMapIndices(0,1,2,3,4);
+ ind2 = top->GetCMapIndices(4,3,2,1,0);
+ BOOST_CHECK(ind1.size() == 10);
+ BOOST_CHECK(ind2.size() == 0); //cmaps are sensitive for the ordering!!
+ BOOST_CHECK(top->GetCMapIndices(0).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(1).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(2).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(3).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(4).size() == 10);
+ BOOST_CHECK(top->GetCMapIndices(5).size() == 0);
+
+ top->SetLJPairParameters(0,3.5,4.5);
+ top->GetLJPairParameters(0,ui1,ui2,r1,r2);
+ BOOST_CHECK( r1 == 3.5 && r2 == 4.5 );
+ i1 = top->GetLJPairIndex(0,1);
+ i5 = top->GetLJPairIndex(1,0);
+ BOOST_CHECK(i1 == i5 && i1 != -1);
+ BOOST_CHECK(top->GetLJPairIndices(0).size() == 1);
+ BOOST_CHECK(top->GetLJPairIndices(1).size() == 1);
+ BOOST_CHECK(top->GetLJPairIndices(2).size() == 0);
+
+ top->SetDistanceConstraintParameters(0,42.0);
+ top->GetDistanceConstraintParameters(0,ui1,ui2,r1);
+ BOOST_CHECK( r1 == 42.0 );
+ i1 = top->GetDistanceConstraintIndex(0,1);
+ i5 = top->GetDistanceConstraintIndex(1,0);
+ BOOST_CHECK(i1 == i5 && i1 != -1);
+
+ top->SetHarmonicPositionRestraintParameters(0,test_vec,3.0);
+ top->GetHarmonicPositionRestraintParameters(0,ui1,zero_vec,r1,r2,r3,r4);
+ BOOST_CHECK(zero_vec == test_vec);
+ BOOST_CHECK(r1 == 3.0);
+ BOOST_CHECK(r2 == 1.0); //should be the same for r3 and r4
+ //no reverse checking necessary
+ BOOST_CHECK(top->GetHarmonicPositionRestraintIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicPositionRestraintIndices(1).size() == 0);
+
+ top->SetHarmonicDistanceRestraintParameters(0,2.0,2.0);
+ top->GetHarmonicDistanceRestraintParameters(0,ui1,ui2,r1,r2);
+ BOOST_CHECK(r1 == 2.0 && r2 == 2.0);
+ ind1 = top->GetHarmonicDistanceRestraintIndices(0,1);
+ ind2 = top->GetHarmonicDistanceRestraintIndices(1,0);
+ BOOST_CHECK(ind1 == ind2 && ind1.size() == 10);
+ BOOST_CHECK(top->GetHarmonicDistanceRestraintIndices(0).size() == 10);
+ BOOST_CHECK(top->GetHarmonicDistanceRestraintIndices(1).size() == 10);
+ BOOST_CHECK(top->GetHarmonicDistanceRestraintIndices(2).size() == 0);
+
+ top->AddPositionConstraint(5);
+ BOOST_CHECK(top->GetNumPositionConstraints() == 1);
+ top->ResetPositionConstraints();
+ BOOST_CHECK(top->GetNumPositionConstraints() == 0);
+}
+
+BOOST_AUTO_TEST_CASE(test_topology_merge){
+
+ String pdb_name = "1CRN.pdb";
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ ost::mol::EntityHandle temp;
+
+ reader.Import(test_ent);
+
+ ForcefieldPtr ff = Forcefield::Load("CHARMM27.dat");
+ SettingsPtr settings = SettingsPtr(new Settings);
+ settings->add_gbsa = true;
+ settings->forcefield = ff;
+
+ ost::mol::EntityHandle new_ent = ost::mol::Builder()
+ .Chain("A")
+ .Residue("ONE")
+ .Atom("A",geom::Vec3(0,0,0))
+ .Atom("B",geom::Vec3(1,1,1))
+ .Residue("TWO")
+ .Atom("A",geom::Vec3(2,2,2))
+ .Atom("B",geom::Vec3(3,3,3))
+ .Residue("THREE")
+ .Atom("A",geom::Vec3(4,4,4))
+ .Atom("B",geom::Vec3(5,5,5));
+
+ //check whether error gets thrown when chain with same name is already present
+ std::vector<Real> real_vec(6);
+ TopologyPtr merge_top_one(new Topology(real_vec));
+ merge_top_one->SetCharges(real_vec);
+ merge_top_one->SetOBCScalings(real_vec);
+ merge_top_one->SetGBSARadii(real_vec);
+ merge_top_one->SetSigmas(real_vec);
+ merge_top_one->SetEpsilons(real_vec);
+ merge_top_one->SetFudgeQQ(1.0);
+ merge_top_one->SetFudgeLJ(1.0);
+ TopologyPtr top_one = TopologyCreator::Create(test_ent,settings);
+ temp = test_ent.Copy();
+ BOOST_CHECK_THROW(top_one->Merge(temp,merge_top_one,new_ent),ost::Error);
+ ost::mol::XCSEditor ed = new_ent.EditXCS();
+ ed.RenameChain(new_ent.GetChainList()[0],"B");
+ TopologyPtr merge_top_one_two(new Topology(real_vec)); // I know...
+ merge_top_one_two->SetCharges(real_vec);
+ merge_top_one_two->SetOBCScalings(real_vec);
+ merge_top_one_two->SetGBSARadii(real_vec);
+ merge_top_one_two->SetSigmas(real_vec);
+ merge_top_one_two->SetEpsilons(real_vec);
+ merge_top_one_two->SetFudgeQQ(1.0);
+ merge_top_one_two->SetFudgeLJ(1.0);
+ BOOST_CHECK_NO_THROW(top_one->Merge(temp,merge_top_one_two,new_ent));
+
+
+ //check whether error gets thrown, when fudge parameters are inconsistent
+ TopologyPtr merge_top_two(new Topology(real_vec));
+ merge_top_two->SetCharges(real_vec);
+ merge_top_two->SetOBCScalings(real_vec);
+ merge_top_two->SetGBSARadii(real_vec);
+ merge_top_two->SetSigmas(real_vec);
+ merge_top_two->SetEpsilons(real_vec);
+ merge_top_two->SetFudgeQQ(42.0);
+ merge_top_two->SetFudgeLJ(42.0);
+ TopologyPtr top_two = TopologyCreator::Create(test_ent,settings);
+ temp = test_ent.Copy();
+ BOOST_CHECK_THROW(top_two->Merge(temp,merge_top_two,new_ent),ost::Error);
+ merge_top_two->SetFudgeQQ(1.0);
+ merge_top_two->SetFudgeLJ(1.0);
+ BOOST_CHECK_NO_THROW(top_two->Merge(temp,merge_top_two,new_ent));
+
+
+ //check whether error gets thrown when charges are not set
+ TopologyPtr merge_top_three(new Topology(real_vec));
+ merge_top_three->SetOBCScalings(real_vec);
+ merge_top_three->SetGBSARadii(real_vec);
+ merge_top_three->SetSigmas(real_vec);
+ merge_top_three->SetEpsilons(real_vec);
+ merge_top_three->SetFudgeQQ(1.0);
+ merge_top_three->SetFudgeLJ(1.0);
+ TopologyPtr top_three = TopologyCreator::Create(test_ent,settings);
+ temp = test_ent.Copy();
+ BOOST_CHECK_THROW(top_three->Merge(temp,merge_top_three,new_ent),ost::Error);
+ TopologyPtr top_three_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_three->SetCharges(real_vec);
+ BOOST_CHECK_NO_THROW(top_three_two->Merge(temp,merge_top_three,new_ent));
+
+ //check whether error gets thrown when obc scaling factors are not set
+ TopologyPtr merge_top_four(new Topology(real_vec));
+ merge_top_four->SetCharges(real_vec);
+ merge_top_four->SetGBSARadii(real_vec);
+ merge_top_four->SetSigmas(real_vec);
+ merge_top_four->SetEpsilons(real_vec);
+ merge_top_four->SetFudgeQQ(1.0);
+ merge_top_four->SetFudgeLJ(1.0);
+ TopologyPtr top_four = TopologyCreator::Create(test_ent,settings);
+ temp = test_ent.Copy();
+ BOOST_CHECK_THROW(top_four->Merge(temp,merge_top_four,new_ent),ost::Error);
+ TopologyPtr top_four_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_four->SetOBCScalings(real_vec);
+ BOOST_CHECK_NO_THROW(top_four_two->Merge(temp,merge_top_four,new_ent));
+
+ //check whether error gets thrown when gbsa radii are not set
+ TopologyPtr merge_top_five(new Topology(real_vec));
+ merge_top_five->SetCharges(real_vec);
+ merge_top_five->SetOBCScalings(real_vec);
+ merge_top_five->SetSigmas(real_vec);
+ merge_top_five->SetEpsilons(real_vec);
+ merge_top_five->SetFudgeQQ(1.0);
+ merge_top_five->SetFudgeLJ(1.0);
+ TopologyPtr top_five = TopologyCreator::Create(test_ent,settings);
+ temp = test_ent.Copy();
+ BOOST_CHECK_THROW(top_five->Merge(temp,merge_top_five,new_ent),ost::Error);
+ TopologyPtr top_five_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_five->SetGBSARadii(real_vec);
+ BOOST_CHECK_NO_THROW(top_five_two->Merge(temp,merge_top_five,new_ent));
+
+ //check whether error gets thrown when sigmas are not set
+ TopologyPtr merge_top_six(new Topology(real_vec));
+ merge_top_six->SetCharges(real_vec);
+ merge_top_six->SetOBCScalings(real_vec);
+ merge_top_six->SetGBSARadii(real_vec);
+ merge_top_six->SetEpsilons(real_vec);
+ merge_top_six->SetFudgeQQ(1.0);
+ merge_top_six->SetFudgeLJ(1.0);
+ TopologyPtr top_six = TopologyCreator::Create(test_ent,settings);
+ temp = test_ent.Copy();
+ BOOST_CHECK_THROW(top_six->Merge(temp,merge_top_six,new_ent),ost::Error);
+ TopologyPtr top_six_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_six->SetSigmas(real_vec);
+ BOOST_CHECK_NO_THROW(top_six_two->Merge(temp,merge_top_six,new_ent));
+
+ //check whether error gets thrown when epsilons are not set
+ TopologyPtr merge_top_seven(new Topology(real_vec));
+ merge_top_seven->SetCharges(real_vec);
+ merge_top_seven->SetOBCScalings(real_vec);
+ merge_top_seven->SetGBSARadii(real_vec);
+ merge_top_seven->SetSigmas(real_vec);
+ merge_top_seven->SetFudgeQQ(1.0);
+ merge_top_seven->SetFudgeLJ(1.0);
+ TopologyPtr top_seven = TopologyCreator::Create(test_ent,settings);
+ temp = test_ent.Copy();
+ BOOST_CHECK_THROW(top_seven->Merge(temp,merge_top_seven,new_ent),ost::Error);
+ TopologyPtr top_seven_two = TopologyCreator::Create(test_ent,settings);
+ merge_top_seven->SetEpsilons(real_vec);
+ BOOST_CHECK_NO_THROW(top_seven_two->Merge(temp,merge_top_seven,new_ent));
+
+ TopologyPtr merge_top_eight(new Topology(real_vec));
+ merge_top_eight->SetCharges(real_vec);
+ merge_top_eight->SetOBCScalings(real_vec);
+ merge_top_eight->SetGBSARadii(real_vec);
+ merge_top_eight->SetSigmas(real_vec);
+ merge_top_eight->SetFudgeQQ(1.0);
+ merge_top_eight->SetFudgeLJ(1.0);
+ merge_top_eight->SetEpsilons(real_vec);
+
+ //let's add every possible interaction
+ merge_top_eight->AddHarmonicBond(0,1,42.0,42000.0);
+ merge_top_eight->AddHarmonicAngle(0,1,2,24.0,24000.0);
+ merge_top_eight->AddUreyBradleyAngle(1,2,3,1.0,2.0,3.0,4.0);
+ merge_top_eight->AddPeriodicDihedral(0,1,2,3,10,2.0,42.0);
+ merge_top_eight->AddPeriodicImproper(1,2,3,4,3,5.0,10.0);
+ merge_top_eight->AddHarmonicImproper(0,1,2,3,8.0,12.0);
+ std::vector<Real> cmap;
+ cmap.push_back(0.0);
+ cmap.push_back(1.0);
+ cmap.push_back(2.0);
+ cmap.push_back(3.0);
+ merge_top_eight->AddCMap(0,1,2,3,4,2,cmap);
+ merge_top_eight->AddLJPair(3,4,1.0,2.0);
+ merge_top_eight->AddDistanceConstraint(2,3,10.0);
+ merge_top_eight->AddExclusion(3,4);
+ merge_top_eight->AddPositionConstraint(2);
+ geom::Vec3 pos(1.0,2.0,3.0);
+ merge_top_eight->AddHarmonicPositionRestraint(2,pos,10.0,5.0,6.0,7.0);
+ merge_top_eight->AddHarmonicDistanceRestraint(1,2,10.0,1000.0);
+
+ TopologyPtr top_eight = TopologyCreator::Create(test_ent,settings);
+
+ uint num_harmonic_bonds = top_eight->GetNumHarmonicBonds();
+ uint num_harmonic_angles = top_eight->GetNumHarmonicAngles();
+ uint num_urey_bradley_angles = top_eight->GetNumUreyBradleyAngles();
+ uint num_periodic_dihedrals = top_eight->GetNumPeriodicDihedrals();
+ uint num_periodic_impropers = top_eight->GetNumPeriodicImpropers();
+ uint num_harmonic_impropers = top_eight->GetNumHarmonicImpropers();
+ uint num_cmaps = top_eight->GetNumCMaps();
+ uint num_lj_pairs = top_eight->GetNumLJPairs();
+ uint num_distance_constraints = top_eight->GetNumDistanceConstraints();
+ uint num_exclusions = top_eight->GetNumExclusions();
+ uint num_position_constraints = top_eight->GetNumPositionConstraints();
+ uint num_harmonic_position_restraints = top_eight->GetNumHarmonicPositionRestraints();
+ uint num_harmonic_distance_restraints = top_eight->GetNumHarmonicDistanceRestraints();
+
+ temp = test_ent.Copy();
+ top_eight->Merge(temp, merge_top_eight, new_ent);
+
+ BOOST_CHECK(top_eight->GetNumHarmonicBonds() == num_harmonic_bonds+1);
+ BOOST_CHECK(top_eight->GetNumHarmonicAngles() == num_harmonic_angles+1);
+ BOOST_CHECK(top_eight->GetNumUreyBradleyAngles() == num_urey_bradley_angles+1);
+ BOOST_CHECK(top_eight->GetNumPeriodicDihedrals() == num_periodic_dihedrals+1);
+ BOOST_CHECK(top_eight->GetNumPeriodicImpropers() == num_periodic_impropers+1);
+ BOOST_CHECK(top_eight->GetNumHarmonicImpropers() == num_harmonic_impropers+1);
+ BOOST_CHECK(top_eight->GetNumCMaps() == num_cmaps+1);
+ BOOST_CHECK(top_eight->GetNumLJPairs() == num_lj_pairs+1);
+ BOOST_CHECK(top_eight->GetNumDistanceConstraints() == num_distance_constraints+1);
+ BOOST_CHECK(top_eight->GetNumExclusions() == num_exclusions+1);
+ BOOST_CHECK(top_eight->GetNumPositionConstraints() == num_position_constraints+1);
+ BOOST_CHECK(top_eight->GetNumHarmonicPositionRestraints() == num_harmonic_position_restraints+1);
+ BOOST_CHECK(top_eight->GetNumHarmonicDistanceRestraints() == num_harmonic_distance_restraints+1);
+
+ uint atom_index_zero = 0 + test_ent.GetAtomCount();
+ uint atom_index_one = 1 + test_ent.GetAtomCount();
+ uint atom_index_two = 2 + test_ent.GetAtomCount();
+ uint atom_index_three = 3 + test_ent.GetAtomCount();
+ uint atom_index_four = 4 + test_ent.GetAtomCount();
+ //uint atom_index_five = 5 + test_ent.GetAtomCount();
+
+ //check whether the unique interactions are properly mapped
+ BOOST_CHECK_THROW(top_eight->AddExclusion(atom_index_three,atom_index_four),ost::Error);
+ BOOST_CHECK_THROW(top_eight->AddDistanceConstraint(atom_index_two,atom_index_three,10.0),ost::Error);
+ BOOST_CHECK_THROW(top_eight->AddLJPair(atom_index_three,atom_index_four,1.0,2.0),ost::Error);
+
+ //check whether the interactions are properly added (we do not check the correct parametrization at this point)
+
+ std::vector<uint> harmonic_bond_indices = top_eight->GetHarmonicBondIndices(atom_index_zero,atom_index_one);
+ std::vector<uint> harmonic_angle_indices = top_eight->GetHarmonicAngleIndices(atom_index_zero,atom_index_one,atom_index_two);
+ std::vector<uint> urey_bradley_angle_indices = top_eight->GetUreyBradleyAngleIndices(atom_index_one,atom_index_two,atom_index_three);
+ std::vector<uint> periodic_dihedral_indices = top_eight->GetPeriodicDihedralIndices(atom_index_zero,atom_index_one,atom_index_two,atom_index_three);
+ std::vector<uint> periodic_improper_indices = top_eight->GetPeriodicImproperIndices(atom_index_one,atom_index_two,atom_index_three,atom_index_four);
+ std::vector<uint> harmonic_improper_indices = top_eight->GetHarmonicImproperIndices(atom_index_zero,atom_index_one,atom_index_two,atom_index_three);
+ std::vector<uint> cmap_indices = top_eight->GetCMapIndices(atom_index_zero,atom_index_one,atom_index_two,atom_index_three,atom_index_four);
+ int lj_pair_index = top_eight->GetLJPairIndex(atom_index_three,atom_index_four);
+ int distance_constraint_index = top_eight->GetDistanceConstraintIndex(atom_index_two,atom_index_three);
+ std::vector<uint> harmonic_distance_restraint_indices = top_eight->GetHarmonicDistanceRestraintIndices(atom_index_one,atom_index_two);
+ std::vector<uint> harmonic_position_restraint_indices = top_eight->GetHarmonicPositionRestraintIndices(atom_index_two);
+
+ BOOST_CHECK(harmonic_bond_indices.size() == 1);
+ BOOST_CHECK(harmonic_angle_indices.size() == 1);
+ BOOST_CHECK(urey_bradley_angle_indices.size() == 1);
+ BOOST_CHECK(periodic_dihedral_indices.size() == 1);
+ BOOST_CHECK(periodic_improper_indices.size() == 1);
+ BOOST_CHECK(harmonic_improper_indices.size() == 1);
+ BOOST_CHECK(cmap_indices.size() == 1);
+ BOOST_CHECK(harmonic_distance_restraint_indices.size() == 1);
+ BOOST_CHECK(harmonic_position_restraint_indices.size() == 1);
+ BOOST_CHECK(lj_pair_index != -1);
+ BOOST_CHECK(distance_constraint_index != -1);
+
+
+ //let's finally check the parameters
+
+ uint ui0,ui1,ui2,ui3,ui4;
+ int i0;
+ Real r0,r1,r2,r3;
+ geom::Vec3 v0;
+
+ top_eight->GetHarmonicBondParameters(harmonic_bond_indices[0],ui0,ui1,r0,r1);
+ BOOST_CHECK(r0 = 42.0 && r1 == 42000.0);
+
+ top_eight->GetHarmonicAngleParameters(harmonic_angle_indices[0],ui0,ui1,ui2,r0,r1);
+ BOOST_CHECK(r0 == 24.0 && r1 == 24000.0);
+
+ top_eight->GetUreyBradleyAngleParameters(urey_bradley_angle_indices[0],ui0,ui1,ui2,r0,r1,r2,r3);
+ BOOST_CHECK(r0 == 1.0 && r1 == 2.0 && r2 == 3.0 && r3 == 4.0);
+
+ top_eight->GetPeriodicDihedralParameters(periodic_dihedral_indices[0],ui0,ui1,ui2,ui3,i0,r0,r1);
+ BOOST_CHECK(i0 == 10 && r0 == 2.0 && r1 == 42.0);
+
+ top_eight->GetPeriodicImproperParameters(periodic_improper_indices[0],ui0,ui1,ui2,ui3,i0,r0,r1);
+ BOOST_CHECK(i0 == 3 && r0 == 5.0 && r1 == 10.0);
+
+ top_eight->GetHarmonicImproperParameters(harmonic_improper_indices[0],ui0,ui1,ui2,ui3,r0,r1);
+ BOOST_CHECK(r0 == 8.0 && r1 == 12.0);
+
+ top_eight->GetCMapParameters(cmap_indices[0],ui0,ui1,ui2,ui3,ui4,i0,real_vec);
+ BOOST_CHECK(real_vec == cmap && i0 == 2);
+
+ top_eight->GetLJPairParameters(lj_pair_index,ui0,ui1,r0,r1);
+ BOOST_CHECK(r0 == 1.0 && r1 == 2.0);
+
+ top_eight->GetDistanceConstraintParameters(distance_constraint_index,ui0,ui1,r0);
+ BOOST_CHECK(r0 == 10.0);
+
+ top_eight->GetHarmonicPositionRestraintParameters(harmonic_position_restraint_indices[0],ui0,v0,r0,r1,r2,r3);
+ BOOST_CHECK(v0 == pos && r0 == 10.0 && r1 == 5.0 && r2 == 6.0 && r3 == 7.0);
+
+ top_eight->GetHarmonicDistanceRestraintParameters(harmonic_distance_restraint_indices[0],ui0,ui1,r0,r1);
+ BOOST_CHECK(r0 == 10.0 && r1 == 1000.0);
+
+}
+
+
+BOOST_AUTO_TEST_SUITE_END();
\ No newline at end of file
diff --git a/modules/mol/mm/tests/tests.cc b/modules/mol/mm/tests/tests.cc
new file mode 100644
index 0000000000000000000000000000000000000000..6a7e493fad5d292938130abacbe3c60511b5729e
--- /dev/null
+++ b/modules/mol/mm/tests/tests.cc
@@ -0,0 +1,25 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE ost_mol_base
+#define BOOST_AUTO_TEST_MAIN
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+
diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index a97895561a3564d00b3a13e65ecf9a02b3e1ca38..2137e5ab17b5d3cd1ba68715c6b050f4790c0f32 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -131,3 +131,162 @@
:returns: List of column entropies
+.. function:: SemiGlobalAlign(seq1, seq2, subst_weight, gap_open=-5, gap_ext=-2)
+
+ Performs a semi-global alignment of *seq1* and *seq2* and returns the best-
+ scoring alignment. The algorithm is Needleman/Wunsch same as GlobalAlign, but
+ without any gap penalty for starting or ending gaps. This is prefereble
+ whenever one of the sequences is significantly shorted than the other.
+ This make it also suitable for fragment assembly.
+
+ **Example:**
+
+ .. code-block:: python
+
+ seq_a=seq.CreateSequence('A', 'abcdefghijklmnok')
+ seq_b=seq.CreateSequence('B', 'cdehijk')
+ alns=seq.alg.GlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
+ print alns[0].ToString(80)
+ # >>> A abcdefghijklmnok
+ # >>> B --cde--hijk-----
+
+ :param seq1: A valid sequence
+ :type seq1: :class:`~ost.seq.ConstSequenceHandle`
+ :param seq2: A valid sequence
+ :type seq2: :class:`~ost.seq.ConstSequenceHandle`
+
+ :param subst_weigth: The substitution weights matrix
+ :type subst_weight: :class:`SubstWeightMatrix`
+ :param gap_open: The gap opening penalty. Must be a negative number
+ :param gap_ext: The gap extension penalty. Must be a negative number
+ :returns: best-scoring alignment of *seq1* and *seq2*.
+
+
+.. _contact-prediction:
+
+Contact Prediction
+--------------------------------------------------------------------------------
+
+This is a set of functions for predicting pairwise contacts from a multiple
+sequence alignment (MSA). The core method here is mutual information which uses
+coevolution to predict contacts. Mutual information is complemented by two other
+methods which score pairs of columns of a MSA from the likelyhood of certain
+amino acid pairs to form contacts (statistical potential) and the likelyhood
+of finding certain substitutions of aminio-acid pairs in columns of the MSA
+corresponding to interacting residues.
+
+.. class:: ContactPredictionScoreResult
+
+ Object containing the results form a contact prediction.
+
+ .. attribute:: matrix
+
+ An *NxN* :class:`~ost.FloatMatrix` where *N* is the length of the alignment.
+ The element *i,j* corresponds to the score of the corresponding
+ columns of the MSA. High scores correspond to high likelyhood of
+ a contact.
+
+ .. attribute:: sorted_indices
+
+ List of all indices pairs *i,j*, containing (N*N-1)/2 elements,
+ as the **matrix** is symmetrical and elements in the diagonal
+ are ignored. The indices are sorted from the pair most likely to form
+ a contact to the least likely one.
+
+ .. method:: GetScore(i,j)
+
+ returns **matrix(i,j)**
+
+ :param i: First index
+ :param j: Second index
+ :type i: :class:`int`
+ :type j: :class:`int`
+
+ .. method:: SetScore(i,j,score)
+
+ Sets **matrix(i,j)** to **score**
+
+ :param i: First index
+ :param j: Second index
+ :param score: The score
+ :type i: :class:`int`
+ :type j: :class:`int`
+ :type score: :class:`float`
+
+.. autofunction:: PredictContacts
+
+.. function:: CalculateMutualInformation(aln,weights=LoadConstantContactWeightMatrix(),
+ apc_correction=true,zpx_transformation=true,small_number_correction=0.05)
+
+ Calculates the mutual information (MI) from a multiple sequence alignemnt. Contributions of each pair of amino-acids are weighted using the matrix **weights** (weighted mutual information). The average product correction (**apc_correction**) correction and transformation into Z-scores (**zpx_transofrmation**) increase prediciton accuracy by reducing the effect of phylogeny and other noise sources. The small number correction reduces noise for alignments with small number of sequences of low diversity.
+
+ :param aln: The multiple sequences alignment
+ :type aln: :class:`~ost.seq.AlignmentHandle`
+ :param weights: The weight matrix
+ :type weights: :class`ContactWeightMatrix`
+ :param apc_correction: Whether to use the APC correction
+ :type apc_correction: :class:`bool`
+ :param zpx_transformation: Whether to transform the scores into Z-scores
+ :type zpx_transformation: :class:`bool`
+ :param small_number_correction: initial values for the probabilities of having a given pair of amino acids *p(a,b)*.
+ :type small_number_correction: :class:`float`
+
+.. function:: CalculateContactScore(aln,weights=LoadDefaultContactWeightMatrix())
+
+ Calculates the Contact Score (*CoSc*) from a multiple sequence alignment. For each pair of residues *(i,j)* (pair of columns in the MSA), *CoSc(i,j)* is the average over the values of the **weights** corresponding to the amino acid pairs in the columns.
+
+ :param aln: The multiple sequences alignment
+ :type aln: :class:`~ost.seq.AlignmentHandle`
+ :param weights: The contact weight matrix
+ :type weights: :class`ContactWeightMatrix`
+
+.. function:: CalculateContactSubstitutionScore(aln,ref_seq_index=0,
+ weights=LoadDefaultPairSubstWeightMatrix())
+
+ Calculates the Contact Substitution Score (*CoEvoSc*) from a multiple sequence alignment. For each pair of residues *(i,j)* (pair of columns in the MSA), *CoEvoSc(i,j)* is the average over the values of the **weights** corresponding to substituting the amino acid pair in the reference sequence (given by **ref_seq_index**) with all other pairs in columns *(i,j)* of the **aln**.
+
+ :param aln: The multiple sequences alignment
+ :type aln: :class:`~ost.seq.AlignmentHandle`
+ :param weights: The pair substitution weight matrix
+ :type weights: :class`ContactWeightMatrix`
+
+.. function:: LoadDefaultContactWeightMatrix()
+
+ :returns: *CPE*, a :class:`ContactWeightMatrix` that was calculated from a large (>15000) set of
+ high quality crystal structures as *CPE=log(CF(a,b)/NCF(a,b))* and then normalised so that all its elements are comprised between 0 and 1. *CF(a,b)* is the frequency of amino acids *a* and *b* for pairs of contacting residues and *NCF(a,b)* is the frequency of amino acids *a* and *b* for pairs of non-contacting residues. Apart from weights for the standard amino acids, this matrix gives a weight of 0 to all pairs for which at least one amino-acid is a gap.
+
+.. function:: LoadConstantContactWeightMatrix()
+
+ :returns: A :class:`ContactWeightMatrix`. This matrix gives a weight of one to all pairs of
+ standard amino-acids and a weight of 0 to pairs for which at least one amino-acid is a gap.
+
+.. function:: LoadDefaultPairSubstWeightMatrix()
+
+ :returns: *CRPE*, a :class:`PairSubstWeightMatrix` that was calculated from a large (>15000) set of
+ high quality crystal structures as *CRPE=log(CRF(ab->cd)/NCRF(ab->cd))* and then normalised so that all its elements are comprised between 0 and 1. *CRF(ab->cd)* is the frequency of replacement of a pair of amino acids *a* and *b* by a pair *c* and *d* in columns of the MSA corresponding to contacting residues and *NCRF(ab->cd)* is the frequency of replacement of a pair of amino acids *a* and *b* by a pair *c* and *d* in columns of the MSA corresponding to non-contacting residues. Apart from weights for the standard amino acids, this matrix gives a weight of 0 to all pair substitutions for which at least one amino-acid is a gap.
+
+
+.. class:: PairSubstWeightMatrix(weights, aa_list)
+
+ This class is used to associate a weight to any substitution from one amino-acid pair *(a,b)* to any other pair *(c,d)*.
+
+ .. attribute:: weights
+
+ A :class:`~ost.FloatMatrix4` of size *NxNxNxN*, where *N=len(aa_list)*
+
+ .. attribute:: aa_list
+
+ A :class:`CharList` of one letter codes of the amino acids for which weights are found in the **weights** matrix.
+
+.. class:: ContactWeightMatrix(weights, aa_list)
+
+ This class is used to associate a weight to any pair of amino-acids.
+
+ .. attribute:: weights
+
+ A :class:`~ost.FloatMatrix` of size *NxN*, where *N=len(aa_list)*
+
+ .. attribute:: aa_list
+
+ A :class:`CharList` of one letter codes of the amino acids for which weights are found in the **weights** matrix.
+
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 63e10f3565f5ade634e5d1a0f75f356ce2330e72..7eebf33878d565ecfcd09564daaf69f696c285f3 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -168,3 +168,37 @@ def AlignmentFromChainView(chain, handle_seq_name='handle',
s1.Append('-')
idx0+=1
return seq.CreateAlignment(s0, s1)
+
+def PredictContacts(ali):
+ """
+ Predicts contacts from a multiple sequence alignment using a combination
+ of Mutual Information (*MI*) and the Contact Substitution Score (*CoEvoSc*).
+ MI is calculated with the APC and small number corrections as well as with a
+ transformation into Z-scores. The *CoEvoSc* is calculated using the default
+ PairSubstWeightMatrix (see seq.alg.LoadDefaultPairSubstWeightMatrix).
+ The final score for a pair of columns *(i,j)* of **ali** is obtained from:
+
+ Sc(i,j)=MI(i,j)exp(CoEvoSc(i,j)) if *(i,j)* >=0
+
+ Sc(i,j)=MI(i,j)exp(1-CoEvoSc(i,j)) if *(i,j)* <0
+
+ :param ali: The multiple sequence alignment
+ :type ali: :class:`~ost.seq.AlignmentHandle`
+ """
+ import math
+ from ost import seq
+ if not type(ali)==type(seq.AlignmentHandle()):
+ print "Parameter should be an AlignmentHandle"
+ return
+ mi=CalculateMutualInformation(ali)
+ CoEvoSc=CalculateContactSubstitutionScore(ali)
+ ncol=ali.GetLength()
+ for i in range(ncol):
+ for j in range(ncol):
+ if mi.matrix[i][j]>=0:
+ mi.matrix[i][j]=mi.matrix[i][j]*(math.exp(CoEvoSc.matrix[i][j]))
+ else:
+ mi.matrix[i][j]=mi.matrix[i][j]*(math.exp(1.-CoEvoSc.matrix[i][j]))
+ mi.RefreshSortedIndices()
+ return mi
+
diff --git a/modules/seq/alg/pymod/mat.py b/modules/seq/alg/pymod/mat.py
index d500be8fd614befbaa84af003fe9e0c47042e1d9..f79bf8326891d5aa9bab92724a5cf781c97cde0a 100644
--- a/modules/seq/alg/pymod/mat.py
+++ b/modules/seq/alg/pymod/mat.py
@@ -1,125 +1,13 @@
from ost.seq.alg import SubstWeightMatrix
-def _InitMatrix(data):
- """
- Initialise a new substitution weight matrix with the weights in data. data
- must be a 24x24 array of ints.
- """
- mat=SubstWeightMatrix()
- # string of valid amino acid one letter codes
- chars='ABCDEFGHIKLMNPQRSTVWXYZ'
- for i, row in enumerate(data):
- for j, weight in enumerate(row):
- mat.SetWeight(chars[i], chars[j], weight)
+def _InitMatrix(preset_enum):
+ mat = SubstWeightMatrix()
+ mat.AssignPreset(preset_enum)
return mat
-_RAW_BLOSUM45_DATA=(
- ( 5, -1, -1, -2, -1, -2, 0, -2, -1, -1, -1, -1, -1, -1, -1, -2, 1, 0, 0, -2, 0, -2, -1),
- (-1, 4, -2, 5, 1, -3, -1, 0, -3, 0, -3, -2, 4, -2, 0, -1, 0, 0, -3, -4, -1, -2, 2),
- (-1, -2, 12, -3, -3, -2, -3, -3, -3, -3, -2, -2, -2, -4, -3, -3, -1, -1, -1, -5, -2, -3, -3),
- (-2, 5, -3, 7, 2, -4, -1, 0, -4, 0, -3, -3, 2, -1, 0, -1, 0, -1, -3, -4, -1, -2, 1),
- (-1, 1, -3, 2, 6, -3, -2, 0, -3, 1, -2, -2, 0, 0, 2, 0, 0, -1, -3, -3, -1, -2, 4),
- (-2, -3, -2, -4, -3, 8, -3, -2, 0, -3, 1, 0, -2, -3, -4, -2, -2, -1, 0, 1, -1, 3, -3),
- ( 0, -1, -3, -1, -2, -3, 7, -2, -4, -2, -3, -2, 0, -2, -2, -2, 0, -2, -3, -2, -1, -3, -2),
- (-2, 0, -3, 0, 0, -2, -2, 10, -3, -1, -2, 0, 1, -2, 1, 0, -1, -2, -3, -3, -1, 2, 0),
- (-1, -3, -3, -4, -3, 0, -4, -3, 5, -3, 2, 2, -2, -2, -2, -3, -2, -1, 3, -2, -1, 0, -3),
- (-1, 0, -3, 0, 1, -3, -2, -1, -3, 5, -3, -1, 0, -1, 1, 3, -1, -1, -2, -2, -1, -1, 1),
- (-1, -3, -2, -3, -2, 1, -3, -2, 2, -3, 5, 2, -3, -3, -2, -2, -3, -1, 1, -2, -1, 0, -2),
- (-1, -2, -2, -3, -2, 0, -2, 0, 2, -1, 2, 6, -2, -2, 0, -1, -2, -1, 1, -2, -1, 0, -1),
- (-1, 4, -2, 2, 0, -2, 0, 1, -2, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -1, -2, 0),
- (-1, -2, -4, -1, 0, -3, -2, -2, -2, -1, -3, -2, -2, 9, -1, -2, -1, -1, -3, -3, -1, -3, -1),
- (-1, 0, -3, 0, 2, -4, -2, 1, -2, 1, -2, 0, 0, -1, 6, 1, 0, -1, -3, -2, -1, -1, 4),
- (-2, -1, -3, -1, 0, -2, -2, 0, -3, 3, -2, -1, 0, -2, 1, 7, -1, -1, -2, -2, -1, -1, 0),
- ( 1, 0, -1, 0, 0, -2, 0, -1, -2, -1, -3, -2, 1, -1, 0, -1, 4, 2, -1, -4, 0, -2, 0),
- ( 0, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5, 0, -3, 0, -1, -1),
- ( 0, -3, -1, -3, -3, 0, -3, -3, 3, -2, 1, 1, -3, -3, -3, -2, -1, 0, 5, -3, -1, -1, -3),
- (-2, -4, -5, -4, -3, 1, -2, -3, -2, -2, -2, -2, -4, -3, -2, -2, -4, -3, -3, 15, -2, 3, -2),
- ( 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, -1, -2, -1, -1, -1),
- (-2, -2, -3, -2, -2, 3, -3, 2, 0, -1, 0, 0, -2, -3, -1, -1, -2, -1, -1, 3, -1, 8, -2),
- (-1, 2, -3, 1, 4, -3, -2, 0, -3, 1, -2, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 4),
-)
-
-_RAW_BLOSUM62_DATA=(
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- (-2, 4, -3, 4, 1, -3, -1, 0, -3, 0, -4, -3, 3, -2, 0, -1, 0, -1, -3, -4, -1, -3, 1),
- ( 0, -3, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2, -2, -3),
- (-2, 4, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -1, -3, 1),
- (-1, 1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -1, -2, 4),
- (-2, -3, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, -1, 3, -3),
- ( 0, -1, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -1, -3, -2),
- (-2, 0, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, -1, 2, 0),
- (-1, -3, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1, -1, -3),
- (-1, 0, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -1, -2, 1),
- (-1, -4, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1, -1, -3),
- (-1, -3, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1, -1, -1),
- (-2, 3, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -1, -2, 0),
- (-1, -2, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -2, -3, -1),
- (-1, 0, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1, -1, 3),
- (-1, -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -1, -2, 0),
- ( 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, 0, -2, 0),
- ( 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, 0, -2, -1),
- ( 0, -3, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1, -1, -2),
- (-3, -4, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, -2, 2, -3),
- ( 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, 0, 0, -1, -2, -1, -1, -1),
- (-2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, -1, 7, -2),
- (-1, 1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -1, 3, 0, 0, -1, -2, -3, -1, -2, 4),
-)
+BLOSUM45 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM45)
+BLOSUM62 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM62)
+BLOSUM80 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM80)
+BLOSUM100 = _InitMatrix(SubstWeightMatrix.Preset.BLOSUM100)
-_RAW_BLOSUM80_DATA=(
- ( 7, -3, -1, -3, -2, -4, 0, -3, -3, -1, -3, -2, -3, -1, -2, -3, 2, 0, -1, -5, -1, -4, -2),
- (-3, 6, -6, 6, 1, -6, -2, -1, -6, -1, -7, -5, 5, -4, -1, -2, 0, -1, -6, -8, -3, -5, 0),
- (-1, -6, 13, -7, -7, -4, -6, -7, -2, -6, -3, -3, -5, -6, -5, -6, -2, -2, -2, -5, -4, -5, -7),
- (-3, 6, -7, 10, 2, -6, -3, -2, -7, -2, -7, -6, 2, -3, -1, -3, -1, -2, -6, -8, -3, -6, 1),
- (-2, 1, -7, 2, 8, -6, -4, 0, -6, 1, -6, -4, -1, -2, 3, -1, -1, -2, -4, -6, -2, -5, 6),
- (-4, -6, -4, -6, -6, 10, -6, -2, -1, -5, 0, 0, -6, -6, -5, -5, -4, -4, -2, 0, -3, 4, -6),
- ( 0, -2, -6, -3, -4, -6, 9, -4, -7, -3, -7, -5, -1, -5, -4, -4, -1, -3, -6, -6, -3, -6, -4),
- (-3, -1, -7, -2, 0, -2, -4, 12, -6, -1, -5, -4, 1, -4, 1, 0, -2, -3, -5, -4, -2, 3, 0),
- (-3, -6, -2, -7, -6, -1, -7, -6, 7, -5, 2, 2, -6, -5, -5, -5, -4, -2, 4, -5, -2, -3, -6),
- (-1, -1, -6, -2, 1, -5, -3, -1, -5, 8, -4, -3, 0, -2, 2, 3, -1, -1, -4, -6, -2, -4, 1),
- (-3, -7, -3, -7, -6, 0, -7, -5, 2, -4, 6, 3, -6, -5, -4, -4, -4, -3, 1, -4, -2, -2, -5),
- (-2, -5, -3, -6, -4, 0, -5, -4, 2, -3, 3, 9, -4, -4, -1, -3, -3, -1, 1, -3, -2, -3, -3),
- (-3, 5, -5, 2, -1, -6, -1, 1, -6, 0, -6, -4, 9, -4, 0, -1, 1, 0, -5, -7, -2, -4, -1),
- (-1, -4, -6, -3, -2, -6, -5, -4, -5, -2, -5, -4, -4, 12, -3, -3, -2, -3, -4, -7, -3, -6, -2),
- (-2, -1, -5, -1, 3, -5, -4, 1, -5, 2, -4, -1, 0, -3, 9, 1, -1, -1, -4, -4, -2, -3, 5),
- (-3, -2, -6, -3, -1, -5, -4, 0, -5, 3, -4, -3, -1, -3, 1, 9, -2, -2, -4, -5, -2, -4, 0),
- ( 2, 0, -2, -1, -1, -4, -1, -2, -4, -1, -4, -3, 1, -2, -1, -2, 7, 2, -3, -6, -1, -3, -1),
- ( 0, -1, -2, -2, -2, -4, -3, -3, -2, -1, -3, -1, 0, -3, -1, -2, 2, 8, 0, -5, -1, -3, -2),
- (-1, -6, -2, -6, -4, -2, -6, -5, 4, -4, 1, 1, -5, -4, -4, -4, -3, 0, 7, -5, -2, -3, -4),
- (-5, -8, -5, -8, -6, 0, -6, -4, -5, -6, -4, -3, -7, -7, -4, -5, -6, -5, -5, 16, -5, 3, -5),
- (-1, -3, -4, -3, -2, -3, -3, -2, -2, -2, -2, -2, -2, -3, -2, -2, -1, -1, -2, -5, -2, -3, -1),
- (-4, -5, -5, -6, -5, 4, -6, 3, -3, -4, -2, -3, -4, -6, -3, -4, -3, -3, -3, 3, -3, 11, -4),
- (-2, 0, -7, 1, 6, -6, -4, 0, -6, 1, -5, -3, -1, -2, 5, 0, -1, -2, -4, -5, -1, -4, 6),
-)
-
-_RAW_BLOSUM100_DATA=(
- ( 8, -4, -2, -5, -3, -5, -1, -4, -4, -2, -4, -3, -4, -2, -2, -3, 1, -1, -2, -6, -2, -5, -2),
- (-4, 6, -7, 6, 0, -7, -3, -2, -8, -2, -8, -7, 5, -5, -2, -4, -1, -2, -7, -9, -4, -6, 0),
- (-2, -7, 14, -8, -9, -4, -7, -8, -3, -8, -5, -4, -5, -8, -7, -8, -3, -3, -3, -7, -5, -6, -8),
- (-5, 6, -8, 10, 2, -8, -4, -3, -8, -3, -8, -8, 1, -5, -2, -5, -2, -4, -8,-10, -4, -7, 0),
- (-3, 0, -9, 2, 10, -8, -6, -2, -7, 0, -7, -5, -2, -4, 2, -2, -2, -3, -5, -8, -3, -7, 7),
- (-5, -7, -4, -8, -8, 11, -8, -4, -2, -6, 0, -1, -7, -7, -6, -6, -5, -5, -3, 0, -4, 4, -7),
- (-1, -3, -7, -4, -6, -8, 9, -6, -9, -5, -8, -7, -2, -6, -5, -6, -2, -5, -8, -7, -4, -8, -5),
- (-4, -2, -8, -3, -2, -4, -6, 13, -7, -3, -6, -5, 0, -5, 1, -1, -3, -4, -7, -5, -4, 1, -1),
- (-4, -8, -3, -8, -7, -2, -9, -7, 8, -6, 2, 1, -7, -7, -6, -7, -5, -3, 4, -6, -3, -4, -7),
- (-2, -2, -8, -3, 0, -6, -5, -3, -6, 10, -6, -4, -1, -3, 2, 3, -2, -3, -5, -8, -3, -5, 0),
- (-4, -8, -5, -8, -7, 0, -8, -6, 2, -6, 8, 3, -7, -7, -5, -6, -6, -4, 0, -5, -3, -4, -6),
- (-3, -7, -4, -8, -5, -1, -7, -5, 1, -4, 3, 12, -5, -5, -2, -4, -4, -2, 0, -4, -3, -5, -4),
- (-4, 5, -5, 1, -2, -7, -2, 0, -7, -1, -7, -5, 11, -5, -1, -2, 0, -1, -7, -8, -3, -5, -2),
- (-2, -5, -8, -5, -4, -7, -6, -5, -7, -3, -7, -5, -5, 12, -4, -5, -3, -4, -6, -8, -4, -7, -4),
- (-2, -2, -7, -2, 2, -6, -5, 1, -6, 2, -5, -2, -1, -4, 11, 0, -2, -3, -5, -5, -2, -4, 5),
- (-3, -4, -8, -5, -2, -6, -6, -1, -7, 3, -6, -4, -2, -5, 0, 10, -3, -3, -6, -7, -3, -5, -1),
- ( 1, -1, -3, -2, -2, -5, -2, -3, -5, -2, -6, -4, 0, -3, -2, -3, 9, 2, -4, -7, -2, -5, -2),
- (-1, -2, -3, -4, -3, -5, -5, -4, -3, -3, -4, -2, -1, -4, -3, -3, 2, 9, -1, -7, -2, -5, -3),
- (-2, -7, -3, -8, -5, -3, -8, -7, 4, -5, 0, 0, -7, -6, -5, -6, -4, -1, 8, -5, -3, -5, -5),
- (-6, -9, -7, 10, -8, 0, -7, -5, -6, -8, -5, -4, -8, -8, -5, -7, -7, -7, -5, 17, -6, 2, -7),
- (-2, -4, -5, -4, -3, -4, -4, -4, -3, -3, -3, -3, -3, -4, -2, -3, -2, -2, -3, -6, -3, -4, -2),
- (-5, -6, -6, -7, -7, 4, -8, 1, -4, -5, -4, -5, -5, -7, -4, -5, -5, -5, -5, 2, -4, 12, -6),
- (-2, 0, -8, 0, 7, -7, -5, -1, -7, 0, -6, -4, -2, -4, 5, -1, -2, -3, -5, -7, -2, -6, 6),
-)
-
-BLOSUM45=_InitMatrix(_RAW_BLOSUM45_DATA)
-BLOSUM62=_InitMatrix(_RAW_BLOSUM62_DATA)
-BLOSUM80=_InitMatrix(_RAW_BLOSUM80_DATA)
-BLOSUM100=_InitMatrix(_RAW_BLOSUM100_DATA)
-
-__all__=['BLOSUM45','BLOSUM62','BLOSUM80','BLOSUM100']
\ No newline at end of file
+__all__=['BLOSUM45','BLOSUM62','BLOSUM80','BLOSUM100']
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index f22866761d38ac9c19fbe44b7f6d97cc41c27827..50f84ab9cd18235608c2db8e3e941656aeb6b791 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -21,12 +21,18 @@
#include <ost/seq/alg/merge_pairwise_alignments.hh>
#include <ost/seq/alg/sequence_identity.hh>
+#include <ost/seq/alg/sequence_similarity.hh>
#include <ost/seq/alg/ins_del.hh>
#include <ost/seq/alg/conservation.hh>
#include <ost/seq/alg/subst_weight_matrix.hh>
#include <ost/seq/alg/local_align.hh>
#include <ost/seq/alg/global_align.hh>
+#include <ost/seq/alg/semiglobal_align.hh>
#include <ost/seq/alg/entropy.hh>
+#include <ost/seq/alg/pair_subst_weight_matrix.hh>
+#include <ost/seq/alg/contact_weight_matrix.hh>
+#include <ost/seq/alg/contact_prediction_score.hh>
+
using namespace boost::python;
using namespace ost::seq;
using namespace ost::seq::alg;
@@ -38,27 +44,74 @@ BOOST_PYTHON_MODULE(_ost_seq_alg)
.value("LONGER_SEQUENCE", RefMode::LONGER_SEQUENCE)
.export_values()
;
+
def("SequenceIdentity", &SequenceIdentity,
(arg("ref_mode")=RefMode::ALIGNMENT, arg("seq_a")=0, arg("seq_b")=1));
+
+ def("SequenceSimilarity", &SequenceSimilarity,
+ (arg("aln"),arg("subst_weight"),arg("normalize")=false,
+ arg("seq_a")=0,arg("seq_b")=1));
+
class_<AlignedRegionList>("AlignedRegionList", init<>())
.def(vector_indexing_suite<AlignedRegionList>())
;
+
class_<InsDel>("InsDel", init<const AlignmentHandle&, int, int>())
.def(init<const AlignmentHandle&>())
.def("GetDeletions", &InsDel::GetDeletions)
.def("GetInsertions", &InsDel::GetInsertions)
;
- class_<SubstWeightMatrix, SubstWeightMatrixPtr>("SubstWeightMatrix", init<>())
- .def("GetWeight", &SubstWeightMatrix::GetWeight)
- .def("SetWeight", &SubstWeightMatrix::SetWeight)
- ;
def("MergePairwiseAlignments", &MergePairwiseAlignments);
def("Conservation", &Conservation, (arg("assign")=true, arg("prop_name")="cons", arg("ignore_gap")=false));
def("LocalAlign", &LocalAlign, (arg("seq1"), arg("seq2"),arg("subst_weight"),
arg("gap_open")=-5, arg("gap_ext")=-2));
def("GlobalAlign", &GlobalAlign,(arg("seq1"),arg("seq2"),arg("subst_weight"),
arg("gap_open")=-5, arg("gap_ext")=-2));
+ def("SemiGlobalAlign", &SemiGlobalAlign,(arg("seq1"),arg("seq2"),arg("subst_weight"),
+ arg("gap_open")=-5, arg("gap_ext")=-2));
def("ShannonEntropy", &ShannonEntropy, (arg("aln"), arg("ignore_gaps")=true));
+ class_<PairSubstWeightMatrix>("PairSubstWeightMatrix",init< std::vector <std::vector <std::vector <std::vector <Real> > > >,std::vector <char> >())
+ .def(init<>())
+ .def_readonly("weights",&PairSubstWeightMatrix::weights)
+ .def_readonly("aa_list",&PairSubstWeightMatrix::aa_list)
+ ;
+
+ class_<ContactWeightMatrix>("ContactWeightMatrix",init< std::vector <std::vector <Real> >,std::vector <char> >())
+ .def(init<>())
+ .def_readonly("weights",&ContactWeightMatrix::weights)
+ .def_readonly("aa_list",&ContactWeightMatrix::aa_list)
+ ;
+
+ class_<ContactPredictionScoreResult>("ContactPredictionScoreResult",no_init)
+ .def_readonly("matrix",&ContactPredictionScoreResult::matrix)
+ .def_readonly("sorted_indices",&ContactPredictionScoreResult::sorted_indices)
+ .def("RefreshSortedIndices",&ContactPredictionScoreResult::RefreshSortedIndices)
+ .def("GetScore",&ContactPredictionScoreResult::GetScore,(arg("i"),arg("j")))
+ .def("SetScore",&ContactPredictionScoreResult::SetScore,(arg("i"),arg("j"),arg("score")))
+ ;
+ def("CalculateMutualInformation", &CalculateMutualInformation,(arg("aln"),arg("w")=LoadConstantContactWeightMatrix(),
+ arg("apc_correction")=true,arg("zpx_transformation")=true,arg("small_number_correction")=0.05));
+ def("CalculateContactScore", &CalculateContactScore,(arg("aln"), arg("w")=LoadDefaultContactWeightMatrix()));
+ def("CalculateContactSubstitutionScore", &CalculateContactSubstitutionScore,(arg("aln"), arg("ref_seq_index")=0, arg("w")=LoadDefaultPairSubstWeightMatrix()));
+ def("LoadDefaultContactWeightMatrix",LoadDefaultContactWeightMatrix);
+ def("LoadConstantContactWeightMatrix",LoadConstantContactWeightMatrix);
+ def("LoadDefaultPairSubstWeightMatrix",LoadDefaultPairSubstWeightMatrix);
+
+ scope mat_scope = class_<SubstWeightMatrix, SubstWeightMatrixPtr>("SubstWeightMatrix", init<>())
+ .def("GetWeight", &SubstWeightMatrix::GetWeight)
+ .def("SetWeight", &SubstWeightMatrix::SetWeight)
+ .def("GetMinWeight", &SubstWeightMatrix::GetMinWeight)
+ .def("GetMaxWeight", &SubstWeightMatrix::GetMaxWeight)
+ .def("AssignPreset", &SubstWeightMatrix::AssignPreset)
+ ;
+
+ enum_<SubstWeightMatrix::Preset>("Preset")
+ .value("BLOSUM45", SubstWeightMatrix::BLOSUM45)
+ .value("BLOSUM62", SubstWeightMatrix::BLOSUM62)
+ .value("BLOSUM80", SubstWeightMatrix::BLOSUM80)
+ .value("BLOSUM100", SubstWeightMatrix::BLOSUM100)
+ ;
+
}
diff --git a/modules/seq/alg/src/CMakeLists.txt b/modules/seq/alg/src/CMakeLists.txt
index ea6284a98d46e553879c2f7266e8d6d27289e19b..7e969a6405fded0d522879d06a99ca86b2fb29b6 100644
--- a/modules/seq/alg/src/CMakeLists.txt
+++ b/modules/seq/alg/src/CMakeLists.txt
@@ -1,5 +1,6 @@
set(OST_SEQ_ALG_HEADERS
sequence_identity.hh
+sequence_similarity.hh
module_config.hh
ins_del.hh
subst_weight_matrix.hh
@@ -9,22 +10,30 @@ merge_pairwise_alignments.hh
conservation.hh
local_align.hh
global_align.hh
+semiglobal_align.hh
+pair_subst_weight_matrix.hh
+contact_weight_matrix.hh
+contact_prediction_score.hh
+data/default_pair_subst_weight_matrix.hh
+data/default_contact_weight_matrix.hh
)
set(OST_SEQ_ALG_SOURCES
merge_pairwise_alignments.cc
local_align.cc
global_align.cc
+semiglobal_align.cc
entropy.cc
sequence_identity.cc
+sequence_similarity.cc
ins_del.cc
conservation.cc
+contact_weight_matrix.cc
+subst_weight_matrix.cc
+pair_subst_weight_matrix.cc
+contact_prediction_score.cc
)
-if (ENABLE_INFO)
- list (APPEND OST_SEQ_ALG_SOURCES subst_weight_matrix.cc)
-endif()
-
module(NAME seq_alg HEADER_OUTPUT_DIR ost/seq/alg SOURCES ${OST_SEQ_ALG_SOURCES}
HEADERS ${OST_SEQ_ALG_HEADERS} DEPENDS_ON ost_seq)
diff --git a/modules/seq/alg/src/contact_prediction_score.cc b/modules/seq/alg/src/contact_prediction_score.cc
new file mode 100644
index 0000000000000000000000000000000000000000..c01653c2f08179e85aaec0fa039dd5933e32937d
--- /dev/null
+++ b/modules/seq/alg/src/contact_prediction_score.cc
@@ -0,0 +1,248 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/seq/aligned_column.hh>
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/alg/contact_prediction_score.hh>
+#include <math.h>
+
+namespace {
+ typedef std::pair<float, std::pair<int,int> > val_indices_pair;
+
+ bool pair_comparator ( const val_indices_pair& l, const val_indices_pair& r)
+ { return l.first > r.first; }
+}
+
+namespace ost { namespace seq { namespace alg {
+
+void ContactPredictionScoreResult::RefreshSortedIndices(){
+ int n_col=this->matrix.size();
+ std::vector <val_indices_pair> sorting_vec;
+ for (int col1=0; col1<n_col; ++col1) {
+ for (int col2=col1+1; col2<n_col; ++col2) {
+ std::pair <int,int> indices (col1,col2);
+ val_indices_pair vi (this->matrix[col1][col2],indices);
+ sorting_vec.push_back(vi);
+ }
+ }
+ std::sort(sorting_vec.begin(),sorting_vec.end(),pair_comparator);
+ int n_indices=sorting_vec.size();
+ std::vector <std::pair <int,int> > sorted_indices;
+ for (int i=0; i<n_indices; ++i) {
+ sorted_indices.push_back(sorting_vec[i].second);
+ }
+ this->sorted_indices=sorted_indices;
+}
+
+ContactPredictionScoreResult::ContactPredictionScoreResult(std::vector <std::vector <Real> > scores){
+ this->matrix=scores;
+ this->RefreshSortedIndices();
+}
+
+Real ContactPredictionScoreResult::GetScore(int i, int j){
+ return this->matrix[i][j];
+ }
+
+void ContactPredictionScoreResult::SetScore(int i, int j, Real score){
+ this->matrix[i][j]=score;
+ }
+
+
+ContactPredictionScoreResult CalculateContactSubstitutionScore(const AlignmentHandle& aln, int ref_seq_index, PairSubstWeightMatrix w){
+ int n_col=aln.GetLength();
+ int n_row=aln.GetCount();
+ //We transform the alignment in a list of ints
+ std::vector< std::vector <int> > ali(n_col, std::vector <int> (n_row) );
+ int naa=w.aa_list.size();
+ for (int i=0; i<n_col; ++i) {
+ for (int j=0; j<n_row; ++j) {
+ std::map<char,int>::iterator iter=w.aa_dict.find(aln[i][j]);
+ if (iter!=w.aa_dict.end()){
+ ali[i][j]=w.aa_dict[aln[i][j]];
+ }
+ else ali[i][j]=naa;
+ }
+ }
+ std::vector< std::vector <Real> > contact_subst_score(n_col, std::vector <Real> (n_col,0) );
+ for (int col1=0; col1<n_col; ++col1) {
+ std::vector<int> c1=ali[col1];
+ int i1=c1[ref_seq_index];
+ if (i1==naa){
+ for (int col2=col1+1; col2<n_col; ++col2) {
+ contact_subst_score[col1][col2]=0.0;
+ contact_subst_score[col2][col1]=0.0;
+ }
+ continue;
+ }
+ for (int col2=col1+1; col2<n_col; ++col2) {
+ std::vector<int> c2=ali[col2];
+ int i2=c2[ref_seq_index];
+ if (i2==naa){
+ contact_subst_score[col1][col2]=0.0;
+ contact_subst_score[col2][col1]=0.0;
+ continue;
+ }
+ Real score=0.0;
+ for (int i=0 ; i<n_row; ++i){
+ if (i==ref_seq_index) continue;
+ int i3=c1[i], i4=c2[i];
+ if (i3==naa || i4==naa){
+ score+=0.0;
+ continue;
+ }
+ score+=w.weights[i1][i2][i3][i4];
+ }
+ contact_subst_score[col1][col2]=score/(n_row-1.);
+ contact_subst_score[col2][col1]=score/(n_row-1.);
+ }
+ }
+ return ContactPredictionScoreResult(contact_subst_score);
+}
+
+ContactPredictionScoreResult CalculateContactScore(const AlignmentHandle& aln, ContactWeightMatrix weights){
+ int n_col=aln.GetLength();
+ int n_row=aln.GetCount();
+ //We transform the alignment in a list of ints
+ std::vector< std::vector <int> > ali(n_col, std::vector <int> (n_row) );
+ int naa=weights.aa_list.size();
+ for (int i=0; i<n_col; ++i) {
+ for (int j=0; j<n_row; ++j) {
+ std::map<char,int>::iterator iter=weights.aa_dict.find(aln[i][j]);
+ if (iter!=weights.aa_dict.end()){
+ ali[i][j]=weights.aa_dict[aln[i][j]];
+ }
+ else ali[i][j]=naa;
+ }
+ }
+
+ std::vector< std::vector <Real> > mi(n_col, std::vector <Real> (n_col,0) );
+
+ for (int col1=0; col1<n_col; ++col1) {
+ std::vector<int> c1=ali[col1];
+ for (int col2=col1+1; col2<n_col; ++col2) {
+ float score=0.0;
+ for (int i=0 ; i<n_row; ++i){
+ int aa1=c1[i];
+ int aa2=ali[col2][i];
+ if (aa1==naa || aa2==naa) continue;
+ score+=weights.weights[aa1][aa2];
+ }
+ mi[col1][col2]=score/n_row;
+ mi[col2][col1]=score/n_row;
+ }
+ }
+ return ContactPredictionScoreResult(mi);
+}
+
+
+ContactPredictionScoreResult CalculateMutualInformation(const AlignmentHandle& aln, ContactWeightMatrix weights,
+ bool apc_correction,bool zpx_transformation, float small_number_correction){
+ int n_col=aln.GetLength();
+ int n_row=aln.GetCount();
+ //We transform the alignment in a list of ints
+ std::vector< std::vector <int> > ali(n_col, std::vector <int> (n_row) );
+ int naa=weights.aa_list.size();
+ for (int i=0; i<n_col; ++i) {
+ for (int j=0; j<n_row; ++j) {
+ std::map<char,int>::iterator iter=weights.aa_dict.find(aln[i][j]);
+ if (iter!=weights.aa_dict.end()){
+ ali[i][j]=weights.aa_dict[aln[i][j]];
+ }
+ else ali[i][j]=naa;
+ }
+ }
+
+ std::vector< std::vector <Real> > mi(n_col, std::vector <Real> (n_col,0) );
+
+ for (int col1=0; col1<n_col; ++col1) {
+ std::vector<int> c1=ali[col1];
+ for (int col2=col1+1; col2<n_col; ++col2) {
+ std::vector<float> p1(naa,naa*small_number_correction),p2(naa,naa*small_number_correction);
+ std::vector<std::vector<float> > p12(naa, std::vector<float> (naa,small_number_correction));
+ for (int i=0 ; i<n_row; ++i){
+ int aa1=c1[i];
+ int aa2=ali[col2][i];
+ if (aa1==naa || aa2==naa) continue;
+ p1[aa1]++;
+ p2[aa2]++;
+ p12[aa1][aa2]++;
+ }
+ float n=naa*small_number_correction;
+ for (int aa1=0; aa1!=naa; ++aa1){
+ n+=p1[aa1];
+ }
+ float score=0.0;
+ for (int aa1=0; aa1!=naa; ++aa1){
+ if(p1[aa1]==0.0) continue;
+ for (int aa2=0; aa2!=naa; ++aa2){
+ if(p12[aa1][aa2]==0.0 || p2[aa2]==0.0) continue;
+ score+=weights.weights[aa1][aa2]*p12[aa1][aa2]/n*std::log(n*p12[aa1][aa2]/(p1[aa1]*p2[aa2]));
+ }
+ }
+ mi[col1][col2]=score;
+ mi[col2][col1]=score;
+ }
+ }
+ if (apc_correction==true){
+ float average_mi=0.;
+ std::vector <float> mi_col(n_col,0.);
+ for (int col1=0; col1<n_col; ++col1) {
+ for (int col2=0; col2<n_col; ++col2) {
+ average_mi+=mi[col1][col2];
+ mi_col[col1]+=mi[col1][col2];
+ }
+ }
+ for (int col1=0; col1<n_col; ++col1) {
+ for (int col2=col1+1; col2<n_col; ++col2) {
+ mi[col1][col2]-=mi_col[col1]*mi_col[col2]/average_mi;
+ mi[col2][col1]-=mi_col[col2]*mi_col[col1]/average_mi;
+ }
+ }
+ }
+ if (zpx_transformation==true){
+ std::vector <float> mi_col(n_col,0.);
+ for (int col1=0; col1<n_col; ++col1) {
+ for (int col2=0; col2<n_col; ++col2) {
+ mi_col[col1]+=mi[col1][col2];
+ }
+ }
+ for (int col1=0; col1<n_col; ++col1) {
+ mi_col[col1]/=n_col;
+ }
+ std::vector <float> mi_std_col(n_col,0.);
+ for (int col1=0; col1<n_col; ++col1) {
+ for (int col2=0; col2<n_col; ++col2) {
+ mi_std_col[col1]+=(mi[col1][col2]-mi_col[col1])*(mi[col1][col2]-mi_col[col1]);
+ }
+ }
+ for (int col1=0; col1<n_col; ++col1) {
+ mi_std_col[col1]=sqrt(mi_std_col[col1]/n_col);
+ }
+ for (int col1=0; col1<n_col; ++col1) {
+ for (int col2=col1+1; col2<n_col; ++col2) {
+ mi[col1][col2]=(mi[col1][col2]-mi_col[col1])/mi_std_col[col1]+(mi[col1][col2]-mi_col[col2])/mi_std_col[col2];
+ mi[col2][col1]=mi[col1][col2];
+ }
+ }
+ }
+ return ContactPredictionScoreResult(mi);
+}
+
+}}}
+
diff --git a/modules/seq/alg/src/contact_prediction_score.hh b/modules/seq/alg/src/contact_prediction_score.hh
new file mode 100644
index 0000000000000000000000000000000000000000..c88001e1dd250a1c04c67f8d6f4aebb6308b74ce
--- /dev/null
+++ b/modules/seq/alg/src/contact_prediction_score.hh
@@ -0,0 +1,57 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_SEQ_ALG_CONTACT_PREDICTION_SCORE_HH
+#define OST_SEQ_ALG_CONTACT_PREDICTION_SCORE_HH
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/alg/module_config.hh>
+#include <ost/seq/alg/pair_subst_weight_matrix.hh>
+#include <ost/seq/alg/contact_weight_matrix.hh>
+
+/*
+ Authors: Niklaus Johner
+ Functions and objects used to calculate different scores for predicting contacts
+ from a multiple sequence alignment (MSA). Several scores are available:
+ 1. Mutual information. The average product correction (apc_correction)
+ adds a correction term to account for common phylogenetic origin and inherent
+ entropy of each column. There is also a correction for small number of sequences
+ in the alignment and the possibility to use weighted mutual information.
+ 2. ContactScore. For each residue pair, this score calculates the average interaction
+ energy for the amino-acid pairs in the corresponding columns of the MSA
+ 3. ContactSubstitutionScore. For each residue pair, this score calculates
+ the average energy of the substitutions of amino-acid pairs in the corresponding
+ columns of the MSA.
+ */
+namespace ost { namespace seq { namespace alg {
+
+struct DLLEXPORT_OST_SEQ_ALG ContactPredictionScoreResult {
+ std::vector <std::vector <Real> > matrix;
+ std::vector <std::pair <int,int> > sorted_indices;
+ void SetScore(int i, int j, Real score);
+ Real GetScore(int i, int j);
+ void RefreshSortedIndices();
+ ContactPredictionScoreResult(std::vector <std::vector <Real> >);
+};
+
+ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG CalculateContactScore(const AlignmentHandle& aln, ContactWeightMatrix w=LoadDefaultContactWeightMatrix());
+ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG CalculateContactSubstitutionScore(const AlignmentHandle& aln, int ref_seq_index=0, PairSubstWeightMatrix w=LoadDefaultPairSubstWeightMatrix());
+ContactPredictionScoreResult DLLEXPORT_OST_SEQ_ALG CalculateMutualInformation(const AlignmentHandle& aln, ContactWeightMatrix w=LoadConstantContactWeightMatrix(),bool apc_correction=true,
+ bool zpx_transformation=true,float small_number_correction=0.05);
+
+}}}
+#endif
diff --git a/modules/seq/alg/src/contact_weight_matrix.cc b/modules/seq/alg/src/contact_weight_matrix.cc
new file mode 100644
index 0000000000000000000000000000000000000000..a8a18a5ebbf9d1319eda8995511f4e7f2af59dda
--- /dev/null
+++ b/modules/seq/alg/src/contact_weight_matrix.cc
@@ -0,0 +1,79 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <ost/info/info.hh>
+#include <ost/seq/alg/contact_weight_matrix.hh>
+#include <ost/seq/alg/default_contact_weight_matrix.hh>
+
+namespace {
+std::map<char,int> init_dict(std::vector <char> aal){
+ std::map<char,int> aa_dict;
+ const int aal_size = static_cast<int>(aal.size());
+ for (int i=0;i!=aal_size;++i){
+ aa_dict[aal[i]]=i;
+ }
+ return aa_dict;
+}
+}
+
+namespace ost { namespace seq { namespace alg {
+
+ContactWeightMatrix LoadConstantContactWeightMatrix(){
+ std::vector <std::vector<Real> > w(21, std::vector<Real>(21,1.0));
+ std::vector <char> aal(21);
+ for (int i=0;i!=21;i++){
+ aal[i]=RAW_CONTACT_WEIGHT_MATRIX_RES_LIST[i];
+ }
+ for (int i1=0;i1!=21;i1++){
+ w[20][i1]=0.0;
+ w[i1][20]=0.0;
+ }
+ return ContactWeightMatrix(w,aal);
+}
+
+ContactWeightMatrix LoadDefaultContactWeightMatrix(){
+ std::vector <std::vector<Real> > w(21, std::vector<Real>(21));
+ std::vector <char> aal(21);
+ for (int i=0;i!=21;i++){
+ aal[i]=RAW_CONTACT_WEIGHT_MATRIX_RES_LIST[i];
+ }
+ for (int i1=0;i1!=21;i1++){
+ for (int i2=0;i2!=21;i2++){
+ w[i1][i2]=RAW_CONTACT_WEIGHT_MATRIX[i1][i2];
+ }
+ }
+ return ContactWeightMatrix(w,aal);
+}
+
+ContactWeightMatrix::ContactWeightMatrix(){
+ std::vector <std::vector <Real> > w;
+ std::vector <char> aal;
+ this->aa_dict=init_dict(this->aa_list);
+ this->weights=w;
+}
+
+ContactWeightMatrix::ContactWeightMatrix(std::vector <std::vector <Real> > w,std::vector <char> aal){
+ this->aa_list=aal;
+ this->naa_=this->aa_list.size();
+ this->aa_dict=init_dict(this->aa_list);
+ this->weights=w;
+}
+
+
+}}}
+
diff --git a/modules/seq/alg/src/contact_weight_matrix.hh b/modules/seq/alg/src/contact_weight_matrix.hh
new file mode 100644
index 0000000000000000000000000000000000000000..2f89ece1f82e728cefe11ec9dba55547e71754a5
--- /dev/null
+++ b/modules/seq/alg/src/contact_weight_matrix.hh
@@ -0,0 +1,49 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_SEQ_CONTACT_WEIGHT_MATRIX_HH
+#define OST_SEQ_CONTACT_WEIGHT_MATRIX_HH
+
+#include <map>
+#include <ost/seq/alg/module_config.hh>
+
+/*
+ Author: Niklaus Johner
+ */
+namespace ost { namespace seq { namespace alg {
+
+
+/// \brief matrix to weight pairs of amino-acids.
+struct DLLEXPORT_OST_SEQ_ALG ContactWeightMatrix {
+ std::vector <std::vector <Real> > weights;
+ std::vector <char> aa_list;
+ std::map<char,int> aa_dict;
+ int naa_;
+
+ ContactWeightMatrix();
+ ContactWeightMatrix(std::vector <std::vector <Real> >,std::vector <char>);
+};
+
+/// \brief statistical potential matrix containing interaction pseudo energies
+ContactWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadDefaultContactWeightMatrix();
+/// \brief weight of 1 for all amino-acid pairs and 0 for gaps.
+ContactWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadConstantContactWeightMatrix();
+
+}}}
+
+#endif
\ No newline at end of file
diff --git a/modules/seq/alg/src/data/default_contact_weight_matrix.hh b/modules/seq/alg/src/data/default_contact_weight_matrix.hh
new file mode 100644
index 0000000000000000000000000000000000000000..4d1a78a60857313c2367684bd773b978e20ac656
--- /dev/null
+++ b/modules/seq/alg/src/data/default_contact_weight_matrix.hh
@@ -0,0 +1,29 @@
+namespace ost { namespace seq { namespace alg {
+
+char RAW_CONTACT_WEIGHT_MATRIX_RES_LIST[21]={'D', 'E', 'R', 'K', 'H', 'S', 'T', 'N', 'Q', 'G', 'P', 'Y', 'W', 'V', 'I', 'L', 'M', 'F', 'A', 'C','-'};
+
+Real RAW_CONTACT_WEIGHT_MATRIX[21][21]=
+ {
+ { 0.0168, 0.0000, 0.4730, 0.3602, 0.3627, 0.1650, 0.1716, 0.2177, 0.2272, 0.0770, 0.0733, 0.3501, 0.3262, 0.1228, 0.1393, 0.1263, 0.1792, 0.2105, 0.0757, 0.1801, 0.0000},
+ { 0.0000, 0.0676, 0.4996, 0.3966, 0.3357, 0.1594, 0.1866, 0.1958, 0.2390, 0.0333, 0.0945, 0.3699, 0.3719, 0.1753, 0.1948, 0.1866, 0.2057, 0.2506, 0.1179, 0.1688, 0.0000},
+ { 0.4730, 0.4996, 0.3499, 0.1961, 0.3666, 0.2970, 0.3204, 0.3266, 0.3599, 0.2218, 0.2777, 0.5060, 0.5262, 0.3196, 0.3532, 0.3577, 0.3560, 0.4251, 0.2489, 0.3517, 0.0000},
+ { 0.3602, 0.3966, 0.1961, 0.1128, 0.2100, 0.1731, 0.2061, 0.2093, 0.2493, 0.0799, 0.0802, 0.3928, 0.3725, 0.2150, 0.2331, 0.2226, 0.2164, 0.2845, 0.1383, 0.2104, 0.0000},
+ { 0.3627, 0.3357, 0.3666, 0.2100, 0.5496, 0.3269, 0.3494, 0.3122, 0.3180, 0.2106, 0.2629, 0.5362, 0.5588, 0.3475, 0.3754, 0.3618, 0.4193, 0.4679, 0.2361, 0.4789, 0.0000},
+ { 0.1650, 0.1594, 0.2970, 0.1731, 0.3269, 0.1866, 0.2143, 0.2210, 0.2315, 0.1203, 0.1250, 0.3501, 0.3960, 0.2381, 0.2586, 0.2358, 0.2758, 0.3335, 0.1628, 0.3010, 0.0000},
+ { 0.1716, 0.1866, 0.3204, 0.2061, 0.3494, 0.2143, 0.2894, 0.2553, 0.2783, 0.1418, 0.1529, 0.3962, 0.4310, 0.3452, 0.3660, 0.3237, 0.3417, 0.3951, 0.2073, 0.3458, 0.0000},
+ { 0.2177, 0.1958, 0.3266, 0.2093, 0.3122, 0.2210, 0.2553, 0.3119, 0.2868, 0.1666, 0.1810, 0.3706, 0.3994, 0.2195, 0.2391, 0.2168, 0.2834, 0.3160, 0.1618, 0.2983, 0.0000},
+ { 0.2272, 0.2390, 0.3599, 0.2493, 0.3180, 0.2315, 0.2783, 0.2868, 0.3159, 0.1473, 0.2187, 0.4208, 0.4769, 0.2727, 0.3014, 0.2989, 0.3234, 0.3733, 0.2010, 0.2982, 0.0000},
+ { 0.0770, 0.0333, 0.2218, 0.0799, 0.2106, 0.1203, 0.1418, 0.1666, 0.1473, 0.0990, 0.0727, 0.3054, 0.3354, 0.1831, 0.1984, 0.1959, 0.2488, 0.2887, 0.1321, 0.2889, 0.0000},
+ { 0.0733, 0.0945, 0.2777, 0.0802, 0.2629, 0.1250, 0.1529, 0.1810, 0.2187, 0.0727, 0.1358, 0.4454, 0.4871, 0.1879, 0.2176, 0.2163, 0.2738, 0.3492, 0.1143, 0.2611, 0.0000},
+ { 0.3501, 0.3699, 0.5060, 0.3928, 0.5362, 0.3501, 0.3962, 0.3706, 0.4208, 0.3054, 0.4454, 0.6013, 0.6686, 0.5248, 0.5702, 0.5625, 0.5797, 0.6506, 0.3876, 0.5335, 0.0000},
+ { 0.3262, 0.3719, 0.5262, 0.3725, 0.5588, 0.3960, 0.4310, 0.3994, 0.4769, 0.3354, 0.4871, 0.6686, 0.7438, 0.5554, 0.6133, 0.6157, 0.6450, 0.7208, 0.4170, 0.6399, 0.0000},
+ { 0.1228, 0.1753, 0.3196, 0.2150, 0.3475, 0.2381, 0.3452, 0.2195, 0.2727, 0.1831, 0.1879, 0.5248, 0.5554, 0.5436, 0.5726, 0.5340, 0.4934, 0.5834, 0.3537, 0.4786, 0.0000},
+ { 0.1393, 0.1948, 0.3532, 0.2331, 0.3754, 0.2586, 0.3660, 0.2391, 0.3014, 0.1984, 0.2176, 0.5702, 0.6133, 0.5726, 0.6365, 0.5952, 0.5478, 0.6388, 0.3921, 0.5096, 0.0000},
+ { 0.1263, 0.1866, 0.3577, 0.2226, 0.3618, 0.2358, 0.3237, 0.2168, 0.2989, 0.1959, 0.2163, 0.5625, 0.6157, 0.5340, 0.5952, 0.5835, 0.5272, 0.6279, 0.3691, 0.4760, 0.0000},
+ { 0.1792, 0.2057, 0.3560, 0.2164, 0.4193, 0.2758, 0.3417, 0.2834, 0.3234, 0.2488, 0.2738, 0.5797, 0.6450, 0.4934, 0.5478, 0.5272, 0.5920, 0.6433, 0.3527, 0.5070, 0.0000},
+ { 0.2105, 0.2506, 0.4251, 0.2845, 0.4679, 0.3335, 0.3951, 0.3160, 0.3733, 0.2887, 0.3492, 0.6506, 0.7208, 0.5834, 0.6388, 0.6279, 0.6433, 0.7323, 0.4201, 0.5920, 0.0000},
+ { 0.0757, 0.1179, 0.2489, 0.1383, 0.2361, 0.1628, 0.2073, 0.1618, 0.2010, 0.1321, 0.1143, 0.3876, 0.4170, 0.3537, 0.3921, 0.3691, 0.3527, 0.4201, 0.2846, 0.3407, 0.0000},
+ { 0.1801, 0.1688, 0.3517, 0.2104, 0.4789, 0.3010, 0.3458, 0.2983, 0.2982, 0.2889, 0.2611, 0.5335, 0.6399, 0.4786, 0.5096, 0.4760, 0.5070, 0.5920, 0.3407, 1.0000, 0.0000},
+ { 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0000}};
+
+}}}
\ No newline at end of file
diff --git a/modules/seq/alg/src/data/default_pair_subst_weight_matrix.hh b/modules/seq/alg/src/data/default_pair_subst_weight_matrix.hh
new file mode 100644
index 0000000000000000000000000000000000000000..3a70c16411dcba4918495dbaadecb03f8a45ede0
--- /dev/null
+++ b/modules/seq/alg/src/data/default_pair_subst_weight_matrix.hh
@@ -0,0 +1,8428 @@
+namespace ost { namespace seq { namespace alg {
+
+char RAW_PAIR_SUBST_WEIGHT_MATRIX_RES_LIST[20]={'D', 'E', 'R', 'K', 'H', 'S', 'T', 'N', 'Q', 'G', 'P', 'Y', 'W', 'V', 'I', 'L', 'M', 'F', 'A', 'C'};
+
+Real RAW_PAIR_SUBST_WEIGHT_MATRIX[20][20][20][20]=
+{
+ {
+ {
+ { 0.3946, 0.0767, 0.2169, 0.1598, 0.2375, 0.1478, 0.1355, 0.2275, 0.1232, 0.1301, 0.0470, 0.2061, 0.2077, 0.1068, 0.1105, 0.1023, 0.1537, 0.1704, 0.0907, 0.2600},
+ { 0.0767, 0.0936, 0.3070, 0.2443, 0.1934, 0.1282, 0.1267, 0.1462, 0.1775, 0.0579, 0.0906, 0.2395, 0.2447, 0.1376, 0.1701, 0.1637, 0.1780, 0.1779, 0.1470, 0.1205},
+ { 0.2169, 0.3070, 0.1979, 0.1333, 0.2066, 0.1524, 0.1761, 0.1629, 0.2002, 0.1169, 0.1507, 0.3009, 0.2986, 0.1987, 0.2281, 0.2454, 0.2326, 0.2553, 0.1780, 0.1676},
+ { 0.1598, 0.2443, 0.1333, 0.0783, 0.1264, 0.0984, 0.1113, 0.1044, 0.1439, 0.0472, 0.0770, 0.2276, 0.2353, 0.1534, 0.1595, 0.1665, 0.1338, 0.1574, 0.1389, 0.0774},
+ { 0.2375, 0.1934, 0.2066, 0.1264, 0.2565, 0.1530, 0.1797, 0.1929, 0.1882, 0.1248, 0.1312, 0.3419, 0.3212, 0.2031, 0.2193, 0.2195, 0.2268, 0.2908, 0.1313, 0.2378},
+ { 0.1478, 0.1282, 0.1524, 0.0984, 0.1530, 0.1084, 0.0972, 0.1268, 0.1252, 0.0652, 0.0714, 0.2062, 0.2082, 0.1216, 0.1260, 0.1195, 0.1399, 0.1851, 0.0920, 0.1321},
+ { 0.1355, 0.1267, 0.1761, 0.1113, 0.1797, 0.0972, 0.1410, 0.1448, 0.1532, 0.0628, 0.0789, 0.2101, 0.2033, 0.1615, 0.1677, 0.1611, 0.1743, 0.1978, 0.0889, 0.1827},
+ { 0.2275, 0.1462, 0.1629, 0.1044, 0.1929, 0.1268, 0.1448, 0.1989, 0.1619, 0.1006, 0.0950, 0.2348, 0.2226, 0.1580, 0.1560, 0.1467, 0.1614, 0.2111, 0.0944, 0.1807},
+ { 0.1232, 0.1775, 0.2002, 0.1439, 0.1882, 0.1252, 0.1532, 0.1619, 0.1923, 0.0675, 0.1242, 0.2350, 0.2928, 0.1639, 0.2071, 0.2061, 0.1934, 0.2321, 0.1390, 0.1423},
+ { 0.1301, 0.0579, 0.1169, 0.0472, 0.1248, 0.0652, 0.0628, 0.1006, 0.0675, 0.0302, 0.0468, 0.1724, 0.1769, 0.0774, 0.0912, 0.0889, 0.1383, 0.1436, 0.0526, 0.1400},
+ { 0.0470, 0.0906, 0.1507, 0.0770, 0.1312, 0.0714, 0.0789, 0.0950, 0.1242, 0.0468, 0.1052, 0.2498, 0.2692, 0.1065, 0.1261, 0.1501, 0.1642, 0.1973, 0.0948, 0.1295},
+ { 0.2061, 0.2395, 0.3009, 0.2276, 0.3419, 0.2062, 0.2101, 0.2348, 0.2350, 0.1724, 0.2498, 0.3973, 0.4283, 0.3044, 0.3235, 0.3245, 0.3386, 0.3973, 0.2060, 0.2737},
+ { 0.2077, 0.2447, 0.2986, 0.2353, 0.3212, 0.2082, 0.2033, 0.2226, 0.2928, 0.1769, 0.2692, 0.4283, 0.5221, 0.2768, 0.3582, 0.3248, 0.3763, 0.4262, 0.1858, 0.2921},
+ { 0.1068, 0.1376, 0.1987, 0.1534, 0.2031, 0.1216, 0.1615, 0.1580, 0.1639, 0.0774, 0.1065, 0.3044, 0.2768, 0.2283, 0.2561, 0.2378, 0.2470, 0.2773, 0.1281, 0.2128},
+ { 0.1105, 0.1701, 0.2281, 0.1595, 0.2193, 0.1260, 0.1677, 0.1560, 0.2071, 0.0912, 0.1261, 0.3235, 0.3582, 0.2561, 0.2970, 0.2720, 0.2779, 0.2990, 0.1477, 0.1899},
+ { 0.1023, 0.1637, 0.2454, 0.1665, 0.2195, 0.1195, 0.1611, 0.1467, 0.2061, 0.0889, 0.1501, 0.3245, 0.3248, 0.2378, 0.2720, 0.2724, 0.2617, 0.3145, 0.1435, 0.1863},
+ { 0.1537, 0.1780, 0.2326, 0.1338, 0.2268, 0.1399, 0.1743, 0.1614, 0.1934, 0.1383, 0.1642, 0.3386, 0.3763, 0.2470, 0.2779, 0.2617, 0.3295, 0.3392, 0.1559, 0.2691},
+ { 0.1704, 0.1779, 0.2553, 0.1574, 0.2908, 0.1851, 0.1978, 0.2111, 0.2321, 0.1436, 0.1973, 0.3973, 0.4262, 0.2773, 0.2990, 0.3145, 0.3392, 0.4093, 0.1737, 0.3043},
+ { 0.0907, 0.1470, 0.1780, 0.1389, 0.1313, 0.0920, 0.0889, 0.0944, 0.1390, 0.0526, 0.0948, 0.2060, 0.1858, 0.1281, 0.1477, 0.1435, 0.1559, 0.1737, 0.1735, 0.1164},
+ { 0.2600, 0.1205, 0.1676, 0.0774, 0.2378, 0.1321, 0.1827, 0.1807, 0.1423, 0.1400, 0.1295, 0.2737, 0.2921, 0.2128, 0.1899, 0.1863, 0.2691, 0.3043, 0.1164, 0.5576}},
+ {
+ { 0.0767, 0.2678, 0.2120, 0.1678, 0.1787, 0.1034, 0.1129, 0.1321, 0.1570, 0.0811, 0.0404, 0.1838, 0.2017, 0.1069, 0.1119, 0.1002, 0.1640, 0.1508, 0.0811, 0.1955},
+ { 0.2678, 0.1054, 0.2825, 0.2262, 0.2016, 0.1203, 0.1197, 0.1685, 0.1711, 0.0621, 0.0624, 0.2204, 0.2392, 0.1381, 0.1632, 0.1574, 0.1665, 0.1721, 0.1449, 0.1494},
+ { 0.2120, 0.2825, 0.1924, 0.1318, 0.1802, 0.1475, 0.1674, 0.1517, 0.1980, 0.1080, 0.1330, 0.2785, 0.2802, 0.1954, 0.2261, 0.2414, 0.2121, 0.2425, 0.1832, 0.1543},
+ { 0.1678, 0.2262, 0.1318, 0.0883, 0.1176, 0.1105, 0.1165, 0.1063, 0.1511, 0.0442, 0.0731, 0.2199, 0.2084, 0.1412, 0.1584, 0.1685, 0.1521, 0.1673, 0.1534, 0.0807},
+ { 0.1787, 0.2016, 0.1802, 0.1176, 0.2280, 0.1444, 0.1647, 0.1589, 0.1749, 0.1020, 0.1192, 0.2962, 0.3010, 0.1925, 0.2096, 0.2190, 0.2198, 0.2692, 0.1263, 0.2375},
+ { 0.1034, 0.1203, 0.1475, 0.1105, 0.1444, 0.1047, 0.0955, 0.1192, 0.1266, 0.0570, 0.0705, 0.1767, 0.1928, 0.1033, 0.1176, 0.1189, 0.1325, 0.1666, 0.0985, 0.1331},
+ { 0.1129, 0.1197, 0.1674, 0.1165, 0.1647, 0.0955, 0.1405, 0.1411, 0.1559, 0.0533, 0.0681, 0.2008, 0.2039, 0.1420, 0.1649, 0.1510, 0.1559, 0.1830, 0.0896, 0.1543},
+ { 0.1321, 0.1685, 0.1517, 0.1063, 0.1589, 0.1192, 0.1411, 0.1580, 0.1605, 0.0832, 0.0803, 0.2063, 0.2237, 0.1317, 0.1456, 0.1358, 0.1665, 0.1842, 0.0928, 0.1565},
+ { 0.1570, 0.1711, 0.1980, 0.1511, 0.1749, 0.1266, 0.1559, 0.1605, 0.1848, 0.0608, 0.1098, 0.2283, 0.2855, 0.1530, 0.1785, 0.1923, 0.2041, 0.2139, 0.1523, 0.1315},
+ { 0.0811, 0.0621, 0.1080, 0.0442, 0.1020, 0.0570, 0.0533, 0.0832, 0.0608, 0.0367, 0.0362, 0.1541, 0.1725, 0.0659, 0.0708, 0.0814, 0.1009, 0.1427, 0.0540, 0.1152},
+ { 0.0404, 0.0624, 0.1330, 0.0731, 0.1192, 0.0705, 0.0681, 0.0803, 0.1098, 0.0362, 0.0896, 0.2227, 0.2411, 0.0841, 0.1062, 0.1271, 0.1439, 0.1836, 0.1022, 0.1188},
+ { 0.1838, 0.2204, 0.2785, 0.2199, 0.2962, 0.1767, 0.2008, 0.2063, 0.2283, 0.1541, 0.2227, 0.3494, 0.3763, 0.2804, 0.3025, 0.3048, 0.3106, 0.3716, 0.1816, 0.2771},
+ { 0.2017, 0.2392, 0.2802, 0.2084, 0.3010, 0.1928, 0.2039, 0.2237, 0.2855, 0.1725, 0.2411, 0.3763, 0.4415, 0.2768, 0.3157, 0.3171, 0.3530, 0.3992, 0.1693, 0.2780},
+ { 0.1069, 0.1381, 0.1954, 0.1412, 0.1925, 0.1033, 0.1420, 0.1317, 0.1530, 0.0659, 0.0841, 0.2804, 0.2768, 0.2153, 0.2322, 0.2190, 0.2207, 0.2604, 0.1164, 0.1902},
+ { 0.1119, 0.1632, 0.2261, 0.1584, 0.2096, 0.1176, 0.1649, 0.1456, 0.1785, 0.0708, 0.1062, 0.3025, 0.3157, 0.2322, 0.2685, 0.2540, 0.2563, 0.2763, 0.1278, 0.2164},
+ { 0.1002, 0.1574, 0.2414, 0.1685, 0.2190, 0.1189, 0.1510, 0.1358, 0.1923, 0.0814, 0.1271, 0.3048, 0.3171, 0.2190, 0.2540, 0.2625, 0.2429, 0.2961, 0.1391, 0.1975},
+ { 0.1640, 0.1665, 0.2121, 0.1521, 0.2198, 0.1325, 0.1559, 0.1665, 0.2041, 0.1009, 0.1439, 0.3106, 0.3530, 0.2207, 0.2563, 0.2429, 0.2967, 0.3178, 0.1493, 0.2292},
+ { 0.1508, 0.1721, 0.2425, 0.1673, 0.2692, 0.1666, 0.1830, 0.1842, 0.2139, 0.1427, 0.1836, 0.3716, 0.3992, 0.2604, 0.2763, 0.2961, 0.3178, 0.3837, 0.1615, 0.2776},
+ { 0.0811, 0.1449, 0.1832, 0.1534, 0.1263, 0.0985, 0.0896, 0.0928, 0.1523, 0.0540, 0.1022, 0.1816, 0.1693, 0.1164, 0.1278, 0.1391, 0.1493, 0.1615, 0.1946, 0.1245},
+ { 0.1955, 0.1494, 0.1543, 0.0807, 0.2375, 0.1331, 0.1543, 0.1565, 0.1315, 0.1152, 0.1188, 0.2771, 0.2780, 0.1902, 0.2164, 0.1975, 0.2292, 0.2776, 0.1245, 0.4872}},
+ {
+ { 0.2169, 0.2120, 0.6034, 0.4640, 0.4383, 0.3423, 0.3546, 0.3720, 0.3446, 0.3165, 0.3039, 0.4002, 0.3828, 0.3411, 0.3429, 0.3310, 0.3454, 0.3518, 0.2985, 0.3974},
+ { 0.2120, 0.2867, 0.4742, 0.4725, 0.4235, 0.3550, 0.3690, 0.3582, 0.3830, 0.2935, 0.3277, 0.4341, 0.4470, 0.3783, 0.3905, 0.3969, 0.3984, 0.3947, 0.3754, 0.3676},
+ { 0.6034, 0.4742, 0.3299, 0.2733, 0.4110, 0.3682, 0.3819, 0.4045, 0.3830, 0.3381, 0.3371, 0.4630, 0.4740, 0.4045, 0.4204, 0.4272, 0.4281, 0.4432, 0.3634, 0.4371},
+ { 0.4640, 0.4725, 0.2733, 0.2947, 0.3765, 0.3533, 0.3722, 0.3651, 0.3827, 0.3171, 0.3095, 0.4546, 0.4405, 0.3884, 0.4029, 0.4046, 0.3918, 0.4050, 0.3669, 0.3682},
+ { 0.4383, 0.4235, 0.4110, 0.3765, 0.4836, 0.4087, 0.4429, 0.4062, 0.4188, 0.3680, 0.3849, 0.5283, 0.5278, 0.4589, 0.4643, 0.4622, 0.4690, 0.4881, 0.3856, 0.4683},
+ { 0.3423, 0.3550, 0.3682, 0.3533, 0.4087, 0.3621, 0.3606, 0.3702, 0.3799, 0.3232, 0.3385, 0.4147, 0.4242, 0.3716, 0.3776, 0.3750, 0.3895, 0.4049, 0.3502, 0.3933},
+ { 0.3546, 0.3690, 0.3819, 0.3722, 0.4429, 0.3606, 0.4151, 0.3876, 0.4089, 0.3219, 0.3413, 0.4311, 0.4408, 0.4104, 0.4225, 0.4019, 0.4122, 0.4258, 0.3544, 0.4072},
+ { 0.3720, 0.3582, 0.4045, 0.3651, 0.4062, 0.3702, 0.3876, 0.4177, 0.4064, 0.3456, 0.3499, 0.4283, 0.4415, 0.3869, 0.3921, 0.3866, 0.4132, 0.4194, 0.3477, 0.3989},
+ { 0.3446, 0.3830, 0.3830, 0.3827, 0.4188, 0.3799, 0.4089, 0.4064, 0.4196, 0.3312, 0.3679, 0.4531, 0.4953, 0.4082, 0.4306, 0.4379, 0.4484, 0.4455, 0.3900, 0.4087},
+ { 0.3165, 0.2935, 0.3381, 0.3171, 0.3680, 0.3232, 0.3219, 0.3456, 0.3312, 0.3217, 0.3383, 0.3757, 0.4075, 0.3443, 0.3430, 0.3445, 0.3648, 0.3861, 0.3290, 0.3776},
+ { 0.3039, 0.3277, 0.3371, 0.3095, 0.3849, 0.3385, 0.3413, 0.3499, 0.3679, 0.3383, 0.3615, 0.4539, 0.4686, 0.3578, 0.3671, 0.3783, 0.3991, 0.4190, 0.3639, 0.3888},
+ { 0.4002, 0.4341, 0.4630, 0.4546, 0.5283, 0.4147, 0.4311, 0.4283, 0.4531, 0.3757, 0.4539, 0.5511, 0.5747, 0.5125, 0.5406, 0.5321, 0.5502, 0.5565, 0.4284, 0.5173},
+ { 0.3828, 0.4470, 0.4740, 0.4405, 0.5278, 0.4242, 0.4408, 0.4415, 0.4953, 0.4075, 0.4686, 0.5747, 0.6162, 0.5012, 0.5444, 0.5252, 0.5718, 0.5896, 0.4245, 0.5293},
+ { 0.3411, 0.3783, 0.4045, 0.3884, 0.4589, 0.3716, 0.4104, 0.3869, 0.4082, 0.3443, 0.3578, 0.5125, 0.5012, 0.4653, 0.4791, 0.4695, 0.4758, 0.4915, 0.3864, 0.4493},
+ { 0.3429, 0.3905, 0.4204, 0.4029, 0.4643, 0.3776, 0.4225, 0.3921, 0.4306, 0.3430, 0.3671, 0.5406, 0.5444, 0.4791, 0.5146, 0.4970, 0.4883, 0.5077, 0.3951, 0.4574},
+ { 0.3310, 0.3969, 0.4272, 0.4046, 0.4622, 0.3750, 0.4019, 0.3866, 0.4379, 0.3445, 0.3783, 0.5321, 0.5252, 0.4695, 0.4970, 0.5054, 0.4944, 0.5127, 0.4053, 0.4430},
+ { 0.3454, 0.3984, 0.4281, 0.3918, 0.4690, 0.3895, 0.4122, 0.4132, 0.4484, 0.3648, 0.3991, 0.5502, 0.5718, 0.4758, 0.4883, 0.4944, 0.5392, 0.5375, 0.4082, 0.4838},
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+ { 0.3030, 0.3167, 0.3896, 0.3300, 0.4327, 0.4536, 0.4764, 0.4044, 0.4056, 0.4352, 0.4088, 0.5306, 0.5559, 0.5619, 0.5807, 0.5759, 0.5332, 0.5869, 0.5312, 0.4426},
+ { 0.3180, 0.3119, 0.3703, 0.3012, 0.4270, 0.4936, 0.5200, 0.4360, 0.4147, 0.4553, 0.4363, 0.5394, 0.5665, 0.5330, 0.5484, 0.5332, 0.5985, 0.5794, 0.4948, 0.5685},
+ { 0.3614, 0.3597, 0.4432, 0.3799, 0.4869, 0.4981, 0.5019, 0.4278, 0.4545, 0.5000, 0.4485, 0.5823, 0.6291, 0.5793, 0.5952, 0.5869, 0.5794, 0.6377, 0.5405, 0.5063},
+ { 0.2952, 0.2814, 0.3424, 0.2946, 0.3903, 0.4095, 0.4382, 0.3634, 0.3831, 0.4008, 0.3431, 0.4826, 0.4913, 0.5269, 0.5444, 0.5312, 0.4948, 0.5405, 0.4714, 0.3927},
+ { 0.2507, 0.2582, 0.3245, 0.2985, 0.4075, 0.3869, 0.4202, 0.3707, 0.4008, 0.3656, 0.2867, 0.4538, 0.4537, 0.4581, 0.4630, 0.4426, 0.5685, 0.5063, 0.3927, 0.5540}},
+ {
+ { 0.3043, 0.2776, 0.5036, 0.4466, 0.4385, 0.3462, 0.3693, 0.3801, 0.3566, 0.3245, 0.3174, 0.4436, 0.4388, 0.3377, 0.3372, 0.3303, 0.3695, 0.3414, 0.2945, 0.2741},
+ { 0.2776, 0.2890, 0.5457, 0.4461, 0.4523, 0.3476, 0.3509, 0.3945, 0.3816, 0.3082, 0.3253, 0.4634, 0.4765, 0.3561, 0.3767, 0.3638, 0.3797, 0.3657, 0.3100, 0.2817},
+ { 0.5036, 0.5457, 0.4106, 0.3423, 0.4377, 0.4036, 0.4126, 0.4075, 0.4512, 0.3748, 0.3964, 0.5011, 0.5360, 0.4106, 0.4285, 0.4254, 0.4403, 0.4348, 0.3804, 0.3321},
+ { 0.4466, 0.4461, 0.3423, 0.3043, 0.3676, 0.3403, 0.3535, 0.3435, 0.3722, 0.3160, 0.3044, 0.4665, 0.4700, 0.3676, 0.3859, 0.3739, 0.3847, 0.3789, 0.3126, 0.3176},
+ { 0.4385, 0.4523, 0.4377, 0.3676, 0.4921, 0.4972, 0.4942, 0.4386, 0.4371, 0.4152, 0.4422, 0.5217, 0.5646, 0.4629, 0.4795, 0.4609, 0.4899, 0.4855, 0.4199, 0.4630},
+ { 0.3462, 0.3476, 0.4036, 0.3403, 0.4972, 0.4402, 0.4555, 0.4408, 0.4217, 0.4151, 0.4092, 0.5170, 0.5216, 0.4646, 0.4720, 0.4546, 0.5040, 0.5030, 0.4194, 0.4281},
+ { 0.3693, 0.3509, 0.4126, 0.3535, 0.4942, 0.4555, 0.4800, 0.4626, 0.4527, 0.4258, 0.4085, 0.5181, 0.5321, 0.4992, 0.5098, 0.4952, 0.5100, 0.5250, 0.4486, 0.4089},
+ { 0.3801, 0.3945, 0.4075, 0.3435, 0.4386, 0.4408, 0.4626, 0.5185, 0.4635, 0.4107, 0.4068, 0.5062, 0.5251, 0.4114, 0.4402, 0.4231, 0.4801, 0.4686, 0.3755, 0.3676},
+ { 0.3566, 0.3816, 0.4512, 0.3722, 0.4371, 0.4217, 0.4527, 0.4635, 0.4438, 0.3855, 0.3847, 0.4837, 0.5249, 0.4167, 0.4294, 0.4186, 0.4703, 0.4479, 0.3725, 0.4034},
+ { 0.3245, 0.3082, 0.3748, 0.3160, 0.4152, 0.4151, 0.4258, 0.4107, 0.3855, 0.3889, 0.3696, 0.4727, 0.4903, 0.4377, 0.4532, 0.4417, 0.4902, 0.4462, 0.3965, 0.4031},
+ { 0.3174, 0.3253, 0.3964, 0.3044, 0.4422, 0.4092, 0.4085, 0.4068, 0.3847, 0.3696, 0.3614, 0.4955, 0.5316, 0.4108, 0.4428, 0.4313, 0.4721, 0.4470, 0.3684, 0.3517},
+ { 0.4436, 0.4634, 0.5011, 0.4665, 0.5217, 0.5170, 0.5181, 0.5062, 0.4837, 0.4727, 0.4955, 0.5283, 0.5796, 0.5676, 0.5726, 0.5699, 0.5779, 0.5713, 0.5131, 0.5366},
+ { 0.4388, 0.4765, 0.5360, 0.4700, 0.5646, 0.5216, 0.5321, 0.5251, 0.5249, 0.4903, 0.5316, 0.5796, 0.5895, 0.5813, 0.5876, 0.5966, 0.6442, 0.6094, 0.5218, 0.6071},
+ { 0.3377, 0.3561, 0.4106, 0.3676, 0.4629, 0.4646, 0.4992, 0.4114, 0.4167, 0.4377, 0.4108, 0.5676, 0.5813, 0.6098, 0.6214, 0.6009, 0.5909, 0.5965, 0.5343, 0.4507},
+ { 0.3372, 0.3767, 0.4285, 0.3859, 0.4795, 0.4720, 0.5098, 0.4402, 0.4294, 0.4532, 0.4428, 0.5726, 0.5876, 0.6214, 0.6469, 0.6321, 0.6120, 0.6059, 0.5553, 0.4666},
+ { 0.3303, 0.3638, 0.4254, 0.3739, 0.4609, 0.4546, 0.4952, 0.4231, 0.4186, 0.4417, 0.4313, 0.5699, 0.5966, 0.6009, 0.6321, 0.6256, 0.6120, 0.6030, 0.5410, 0.4329},
+ { 0.3695, 0.3797, 0.4403, 0.3847, 0.4899, 0.5040, 0.5100, 0.4801, 0.4703, 0.4902, 0.4721, 0.5779, 0.6442, 0.5909, 0.6120, 0.6120, 0.6691, 0.6332, 0.5408, 0.5063},
+ { 0.3414, 0.3657, 0.4348, 0.3789, 0.4855, 0.5030, 0.5250, 0.4686, 0.4479, 0.4462, 0.4470, 0.5713, 0.6094, 0.5965, 0.6059, 0.6030, 0.6332, 0.6219, 0.5580, 0.5766},
+ { 0.2945, 0.3100, 0.3804, 0.3126, 0.4199, 0.4194, 0.4486, 0.3755, 0.3725, 0.3965, 0.3684, 0.5131, 0.5218, 0.5343, 0.5553, 0.5410, 0.5408, 0.5580, 0.4776, 0.4069},
+ { 0.2741, 0.2817, 0.3321, 0.3176, 0.4630, 0.4281, 0.4089, 0.3676, 0.4034, 0.4031, 0.3517, 0.5366, 0.6071, 0.4507, 0.4666, 0.4329, 0.5063, 0.5766, 0.4069, 0.5547}},
+ {
+ { 0.1164, 0.1245, 0.3942, 0.3308, 0.2855, 0.2500, 0.2205, 0.2298, 0.2497, 0.2331, 0.2126, 0.3114, 0.2971, 0.1992, 0.1994, 0.1984, 0.2168, 0.2298, 0.1968, 0.1196},
+ { 0.1245, 0.1453, 0.4014, 0.3346, 0.2865, 0.1986, 0.2019, 0.2129, 0.2411, 0.1713, 0.1879, 0.3070, 0.3141, 0.1984, 0.2191, 0.2232, 0.2225, 0.2278, 0.1774, 0.1024},
+ { 0.3942, 0.4014, 0.2658, 0.2115, 0.3118, 0.2786, 0.2905, 0.2810, 0.3248, 0.2419, 0.2751, 0.3844, 0.4101, 0.3003, 0.3188, 0.3223, 0.3024, 0.3400, 0.2649, 0.2260},
+ { 0.3308, 0.3346, 0.2115, 0.1642, 0.2516, 0.2004, 0.2059, 0.2186, 0.2542, 0.1639, 0.1759, 0.3360, 0.3362, 0.2434, 0.2740, 0.2680, 0.2345, 0.2795, 0.2134, 0.1673},
+ { 0.2855, 0.2865, 0.3118, 0.2516, 0.3732, 0.3772, 0.3770, 0.3022, 0.2960, 0.3162, 0.3177, 0.4224, 0.4410, 0.3636, 0.3746, 0.3618, 0.3744, 0.4086, 0.3195, 0.2905},
+ { 0.2500, 0.1986, 0.2786, 0.2004, 0.3772, 0.4255, 0.4054, 0.3667, 0.2948, 0.3630, 0.3111, 0.3782, 0.3957, 0.3913, 0.3816, 0.3523, 0.3996, 0.3919, 0.3867, 0.4051},
+ { 0.2205, 0.2019, 0.2905, 0.2059, 0.3770, 0.4054, 0.4096, 0.3633, 0.2929, 0.3825, 0.3028, 0.3926, 0.4221, 0.4259, 0.4122, 0.4022, 0.4119, 0.4173, 0.4178, 0.3459},
+ { 0.2298, 0.2129, 0.2810, 0.2186, 0.3022, 0.3667, 0.3633, 0.3919, 0.2963, 0.3196, 0.2849, 0.3441, 0.3647, 0.3003, 0.3069, 0.2841, 0.3486, 0.3257, 0.3126, 0.2437},
+ { 0.2497, 0.2411, 0.3248, 0.2542, 0.2960, 0.2948, 0.2929, 0.2963, 0.3050, 0.2774, 0.2700, 0.3505, 0.3939, 0.2892, 0.3012, 0.3027, 0.3119, 0.3239, 0.2738, 0.2065},
+ { 0.2331, 0.1713, 0.2419, 0.1639, 0.3162, 0.3630, 0.3825, 0.3196, 0.2774, 0.3661, 0.2774, 0.3938, 0.4012, 0.4084, 0.4103, 0.3968, 0.4329, 0.4259, 0.3622, 0.3861},
+ { 0.2126, 0.1879, 0.2751, 0.1759, 0.3177, 0.3111, 0.3028, 0.2849, 0.2700, 0.2774, 0.2691, 0.3854, 0.3995, 0.2997, 0.3109, 0.2982, 0.3378, 0.3402, 0.2894, 0.2241},
+ { 0.3114, 0.3070, 0.3844, 0.3360, 0.4224, 0.3782, 0.3926, 0.3441, 0.3505, 0.3938, 0.3854, 0.4515, 0.5043, 0.4623, 0.4796, 0.4808, 0.4849, 0.5101, 0.4115, 0.3593},
+ { 0.2971, 0.3141, 0.4101, 0.3362, 0.4410, 0.3957, 0.4221, 0.3647, 0.3939, 0.4012, 0.3995, 0.5043, 0.5545, 0.4718, 0.4897, 0.4845, 0.5158, 0.5363, 0.3925, 0.3949},
+ { 0.1992, 0.1984, 0.3003, 0.2434, 0.3636, 0.3913, 0.4259, 0.3003, 0.2892, 0.4084, 0.2997, 0.4623, 0.4718, 0.5132, 0.5073, 0.4892, 0.4699, 0.4992, 0.4880, 0.3739},
+ { 0.1994, 0.2191, 0.3188, 0.2740, 0.3746, 0.3816, 0.4122, 0.3069, 0.3012, 0.4103, 0.3109, 0.4796, 0.4897, 0.5073, 0.5180, 0.5029, 0.4818, 0.5095, 0.4722, 0.3757},
+ { 0.1984, 0.2232, 0.3223, 0.2680, 0.3618, 0.3523, 0.4022, 0.2841, 0.3027, 0.3968, 0.2982, 0.4808, 0.4845, 0.4892, 0.5029, 0.4968, 0.4739, 0.5110, 0.4468, 0.3284},
+ { 0.2168, 0.2225, 0.3024, 0.2345, 0.3744, 0.3996, 0.4119, 0.3486, 0.3119, 0.4329, 0.3378, 0.4849, 0.5158, 0.4699, 0.4818, 0.4739, 0.5157, 0.5289, 0.4382, 0.3927},
+ { 0.2298, 0.2278, 0.3400, 0.2795, 0.4086, 0.3919, 0.4173, 0.3257, 0.3239, 0.4259, 0.3402, 0.5101, 0.5363, 0.4992, 0.5095, 0.5110, 0.5289, 0.5637, 0.4466, 0.4069},
+ { 0.1968, 0.1774, 0.2649, 0.2134, 0.3195, 0.3867, 0.4178, 0.3126, 0.2738, 0.3622, 0.2894, 0.4115, 0.3925, 0.4880, 0.4722, 0.4468, 0.4382, 0.4466, 0.4813, 0.4240},
+ { 0.1196, 0.1024, 0.2260, 0.1673, 0.2905, 0.4051, 0.3459, 0.2437, 0.2065, 0.3861, 0.2241, 0.3593, 0.3949, 0.3739, 0.3757, 0.3284, 0.3927, 0.4069, 0.4240, 0.5610}},
+ {
+ { 0.5576, 0.4872, 0.6751, 0.6186, 0.6043, 0.6988, 0.5087, 0.5541, 0.5007, 0.5095, 0.5010, 0.6443, 0.5837, 0.4842, 0.4796, 0.4428, 0.4863, 0.4943, 0.4682, 0.4716},
+ { 0.4872, 0.4355, 0.6210, 0.5882, 0.4915, 0.5239, 0.4839, 0.5193, 0.4696, 0.4339, 0.4659, 0.5851, 0.5479, 0.4440, 0.4655, 0.4519, 0.4541, 0.5060, 0.4049, 0.3941},
+ { 0.6751, 0.6210, 0.5115, 0.4685, 0.5183, 0.5183, 0.4984, 0.5660, 0.5393, 0.4858, 0.4708, 0.6174, 0.6264, 0.4873, 0.5167, 0.4851, 0.4879, 0.5407, 0.4780, 0.4809},
+ { 0.6186, 0.5882, 0.4685, 0.4798, 0.4852, 0.4608, 0.4801, 0.4636, 0.4885, 0.4455, 0.4174, 0.5886, 0.6033, 0.4688, 0.4893, 0.4554, 0.4419, 0.5087, 0.4106, 0.4135},
+ { 0.6043, 0.4915, 0.5183, 0.4852, 0.5638, 0.5621, 0.5683, 0.5448, 0.4733, 0.5594, 0.5122, 0.6493, 0.6697, 0.5255, 0.5431, 0.5280, 0.5239, 0.5843, 0.4761, 0.6040},
+ { 0.6988, 0.5239, 0.5183, 0.4608, 0.5621, 0.6484, 0.6257, 0.6260, 0.5391, 0.5733, 0.5322, 0.6282, 0.5714, 0.5640, 0.5456, 0.5436, 0.5726, 0.5793, 0.5641, 0.5583},
+ { 0.5087, 0.4839, 0.4984, 0.4801, 0.5683, 0.6257, 0.6347, 0.5907, 0.5420, 0.5796, 0.5215, 0.5757, 0.5660, 0.5744, 0.5532, 0.5467, 0.5565, 0.5916, 0.5740, 0.5264},
+ { 0.5541, 0.5193, 0.5660, 0.4636, 0.5448, 0.6260, 0.5907, 0.9297, 0.5739, 0.5496, 0.4530, 0.6211, 0.6329, 0.5113, 0.4971, 0.4862, 0.5594, 0.5267, 0.4971, 0.5172},
+ { 0.5007, 0.4696, 0.5393, 0.4885, 0.4733, 0.5391, 0.5420, 0.5739, 0.5614, 0.4997, 0.5237, 0.5929, 0.5385, 0.5009, 0.4868, 0.5032, 0.4601, 0.5682, 0.4742, 0.4609},
+ { 0.5095, 0.4339, 0.4858, 0.4455, 0.5594, 0.5733, 0.5796, 0.5496, 0.4997, 0.5619, 0.4700, 0.6679, 0.6625, 0.5770, 0.5889, 0.5694, 0.6394, 0.6768, 0.5168, 0.5276},
+ { 0.5010, 0.4659, 0.4708, 0.4174, 0.5122, 0.5322, 0.5215, 0.4530, 0.5237, 0.4700, 0.5480, 0.6617, 0.6654, 0.5119, 0.5154, 0.5148, 0.5814, 0.5710, 0.4937, 0.4487},
+ { 0.6443, 0.5851, 0.6174, 0.5886, 0.6493, 0.6282, 0.5757, 0.6211, 0.5929, 0.6679, 0.6617, 0.6735, 0.7111, 0.6100, 0.6196, 0.6298, 0.6529, 0.6867, 0.6173, 0.5084},
+ { 0.5837, 0.5479, 0.6264, 0.6033, 0.6697, 0.5714, 0.5660, 0.6329, 0.5385, 0.6625, 0.6654, 0.7111, 0.7990, 0.6185, 0.6440, 0.6333, 0.7068, 0.7255, 0.5503, 0.5665},
+ { 0.4842, 0.4440, 0.4873, 0.4688, 0.5255, 0.5640, 0.5744, 0.5113, 0.5009, 0.5770, 0.5119, 0.6100, 0.6185, 0.6443, 0.6155, 0.6028, 0.6053, 0.6361, 0.6682, 0.5100},
+ { 0.4796, 0.4655, 0.5167, 0.4893, 0.5431, 0.5456, 0.5532, 0.4971, 0.4868, 0.5889, 0.5154, 0.6196, 0.6440, 0.6155, 0.6305, 0.6193, 0.6149, 0.6376, 0.6320, 0.5124},
+ { 0.4428, 0.4519, 0.4851, 0.4554, 0.5280, 0.5436, 0.5467, 0.4862, 0.5032, 0.5694, 0.5148, 0.6298, 0.6333, 0.6028, 0.6193, 0.6572, 0.5979, 0.6393, 0.6081, 0.5019},
+ { 0.4863, 0.4541, 0.4879, 0.4419, 0.5239, 0.5726, 0.5565, 0.5594, 0.4601, 0.6394, 0.5814, 0.6529, 0.7068, 0.6053, 0.6149, 0.5979, 0.6577, 0.6766, 0.5992, 0.5540},
+ { 0.4943, 0.5060, 0.5407, 0.5087, 0.5843, 0.5793, 0.5916, 0.5267, 0.5682, 0.6768, 0.5710, 0.6867, 0.7255, 0.6361, 0.6376, 0.6393, 0.6766, 0.6936, 0.6394, 0.5547},
+ { 0.4682, 0.4049, 0.4780, 0.4106, 0.4761, 0.5641, 0.5740, 0.4971, 0.4742, 0.5168, 0.4937, 0.6173, 0.5503, 0.6682, 0.6320, 0.6081, 0.5992, 0.6394, 0.6387, 0.5610},
+ { 0.4716, 0.3941, 0.4809, 0.4135, 0.6040, 0.5583, 0.5264, 0.5172, 0.4609, 0.5276, 0.4487, 0.5084, 0.5665, 0.5100, 0.5124, 0.5019, 0.5540, 0.5547, 0.5610, 0.9228}}}};
+
+}}}
diff --git a/modules/seq/alg/src/merge_pairwise_alignments.hh b/modules/seq/alg/src/merge_pairwise_alignments.hh
index 6a825d2e036af65c03d191fee1064367fbd71a6e..04bc8832d4e6f40dc10084439a3d5bb38eb6a7f6 100644
--- a/modules/seq/alg/src/merge_pairwise_alignments.hh
+++ b/modules/seq/alg/src/merge_pairwise_alignments.hh
@@ -37,7 +37,7 @@ namespace ost { namespace seq { namespace alg {
/// The method does not produce the optimal multiple sequence alignemnt for all
/// the sequences.
///
-/// \param pairwise_alignments is a list of AlignmentHandles, each containing
+/// \param pairwise_alns is a list of AlignmentHandles, each containing
/// two sequences
/// \param ref_seq is the reference sequence. The reference sequence must not
/// contain any gaps.
diff --git a/modules/seq/alg/src/pair_subst_weight_matrix.cc b/modules/seq/alg/src/pair_subst_weight_matrix.cc
new file mode 100644
index 0000000000000000000000000000000000000000..4d0216428ba09c9cf1b288957dc0626df335ebe3
--- /dev/null
+++ b/modules/seq/alg/src/pair_subst_weight_matrix.cc
@@ -0,0 +1,72 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <ost/info/info.hh>
+#include <ost/seq/alg/pair_subst_weight_matrix.hh>
+#include <ost/seq/alg/default_pair_subst_weight_matrix.hh>
+#include <algorithm>
+
+namespace {
+
+std::map<char,int> init_dict(std::vector <char> aal){
+ std::map<char,int> aa_dict;
+ const int aal_size = static_cast<int>(aal.size());
+ for (int i=0;i!=aal_size;++i){
+ aa_dict[aal[i]]=i;
+ }
+ return aa_dict;
+}
+}
+
+namespace ost { namespace seq { namespace alg {
+
+PairSubstWeightMatrix LoadDefaultPairSubstWeightMatrix(){
+ std::vector <std::vector<std::vector<std::vector<Real> > > > w(20, std::vector<std::vector<std::vector<Real> > >(20,std::vector<std::vector<Real> >(20,std::vector<Real>(20))));
+ std::vector <char> aal(20);
+ for (int i=0;i!=20;i++){
+ aal[i]=RAW_PAIR_SUBST_WEIGHT_MATRIX_RES_LIST[i];
+ }
+ for (int i1=0;i1!=20;i1++){
+ for (int i2=0;i2!=20;i2++){
+ for (int i3=0;i3!=20;i3++){
+ for (int i4=0;i4!=20;i4++){
+ w[i1][i2][i3][i4]=RAW_PAIR_SUBST_WEIGHT_MATRIX[i1][i2][i3][i4];
+ }
+ }
+ }
+ }
+ return PairSubstWeightMatrix(w,aal);
+}
+
+
+PairSubstWeightMatrix::PairSubstWeightMatrix(){
+ std::vector <std::vector <std::vector <std::vector <Real> > > > w;
+ std::vector <char> aal;
+ this->aa_dict=init_dict(this->aa_list);
+ this->weights=w;
+}
+
+PairSubstWeightMatrix::PairSubstWeightMatrix(std::vector <std::vector <std::vector <std::vector <Real> > > > w,std::vector <char> aal){
+ this->aa_list=aal;
+ this->naa_=this->aa_list.size();
+ this->aa_dict=init_dict(this->aa_list);
+ this->weights=w;
+}
+
+
+}}}
diff --git a/modules/seq/alg/src/pair_subst_weight_matrix.hh b/modules/seq/alg/src/pair_subst_weight_matrix.hh
new file mode 100644
index 0000000000000000000000000000000000000000..174dfa4294e8d7a302a7149639a408499e580466
--- /dev/null
+++ b/modules/seq/alg/src/pair_subst_weight_matrix.hh
@@ -0,0 +1,47 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_SEQ_PAIR_SUBST_WEIGHT_MATRIX_HH
+#define OST_SEQ_PAIR_SUBST_WEIGHT_MATRIX_HH
+
+#include <map>
+#include <ost/seq/alg/module_config.hh>
+
+
+/*
+ Author: Niklaus Johner
+ */
+namespace ost { namespace seq { namespace alg {
+
+
+/// \brief position-independet pair substitution weight matrix
+struct DLLEXPORT_OST_SEQ_ALG PairSubstWeightMatrix {
+ std::vector <std::vector <std::vector <std::vector <Real> > > > weights;
+ std::vector <char> aa_list;
+ std::map <char,int> aa_dict;
+ int naa_;
+
+ PairSubstWeightMatrix();
+ PairSubstWeightMatrix(std::vector <std::vector <std::vector <std::vector <Real> > > >,std::vector <char>);
+};
+
+PairSubstWeightMatrix DLLEXPORT_OST_SEQ_ALG LoadDefaultPairSubstWeightMatrix();
+
+}}}
+
+#endif
\ No newline at end of file
diff --git a/modules/seq/alg/src/semiglobal_align.cc b/modules/seq/alg/src/semiglobal_align.cc
new file mode 100644
index 0000000000000000000000000000000000000000..4b89fd15cd1f21d0d56013138adb9c34d9fa06e6
--- /dev/null
+++ b/modules/seq/alg/src/semiglobal_align.cc
@@ -0,0 +1,103 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <ost/log.hh>
+#include "impl/align_impl.hh"
+#include "semiglobal_align.hh"
+
+namespace ost { namespace seq { namespace alg {
+
+void SemiTraceback(impl::AlnMat& mat, int max_i, int max_j,
+ const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2,
+ AlignmentList& alignments)
+{
+ int i = (max_i > 0 ? max_i-1 : 0);
+ int j = (max_j > 0 ? max_j-1 : 0);
+ String aln_str1;
+ String aln_str2;
+ while (i > 0 || j > 0) {
+ impl::SetRoute(mat, i, j, s1, s2, aln_str1, aln_str2);
+ }
+ impl::StoreStrAsAln(aln_str1, aln_str2, s1, s2, i, j, alignments);
+}
+
+AlignmentList SemiGlobalAlign(const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2,
+ alg::SubstWeightMatrixPtr& subst,
+ int gap_open,int gap_ext)
+{
+ impl::AlnMat mat(s1.GetLength()+1, s2.GetLength()+1);
+ // init first column of matrix no start gap penalty
+ if (mat.GetHeight() > 1) {
+ mat(0, 1).score = mat(0, 0).score;
+ mat(0, 1).from = impl::INS1;
+ }
+ for (int j = 2; j < mat.GetHeight(); ++j) {
+ mat(0, j).score = mat(0, j-1).score;
+ mat(0, j).from = impl::INS1;
+ }
+ // fill the alignment matrix
+ for (int i = 0; i < mat.GetWidth()-1; ++i) {
+ mat(i+1, 0).score = mat(i, 0).score;
+ mat(i+1, 0).from = impl::INS2;
+ for (int j = 0; j < mat.GetHeight()-1; ++j) {
+ char c1=s1[i];
+ char c2=s2[j];
+ short weight=subst->GetWeight(c1, c2);
+ int diag=weight+mat(i, j).score;
+ int ins1=mat(i+1, j).score
+ +(mat(i+1, j).from==impl::INS1 ? gap_ext : gap_open);
+ int ins2=mat(i, j+1).score
+ +(mat(i, j+1).from==impl::INS2 ? gap_ext : gap_open);
+ // ignore end gaps (if one of the two seqs is done)
+ if (j+1==mat.GetHeight()-1){
+ ins2=mat(i, j+1).score;
+ }
+ if (i+1==mat.GetWidth()-1){
+ ins1=mat(i+1, j).score;
+ }
+ if (diag>=ins1) {
+ if (diag>=ins2) {
+ mat(i+1, j+1).score=diag;
+ mat(i+1, j+1).from=impl::DIAG;
+ } else {
+ mat(i+1, j+1).score=ins2;
+ mat(i+1, j+1).from=impl::INS2;
+ }
+ } else if (ins1>ins2) {
+ mat(i+1, j+1).score=ins1;
+ mat(i+1, j+1).from=impl::INS1;
+ } else {
+ mat(i+1, j+1).score=ins2;
+ mat(i+1, j+1).from=impl::INS2;
+ }
+ }
+ }
+ // write traceback matrix in debug mode
+#if !defined(NDEBUG)
+ DbgWriteAlnMatrix(mat,s1, s2);
+#endif
+ AlignmentList alignments;
+ SemiTraceback(mat, mat.GetWidth(), mat.GetHeight(), s1, s2, alignments);
+ LOG_DEBUG(alignments.back().ToString(80));
+
+ return alignments;
+}
+
+}}}
diff --git a/modules/seq/alg/src/semiglobal_align.hh b/modules/seq/alg/src/semiglobal_align.hh
new file mode 100644
index 0000000000000000000000000000000000000000..6d1ca5002476b05ac10b013ee63dea0020e3cf4b
--- /dev/null
+++ b/modules/seq/alg/src/semiglobal_align.hh
@@ -0,0 +1,35 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_SEQ_ALG_SEMIGLOBAL_ALIGN_HH
+#define OST_SEQ_ALG_SEMIGLOBAL_ALIGN_HH
+
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/alg/subst_weight_matrix.hh>
+#include "module_config.hh"
+
+namespace ost { namespace seq { namespace alg {
+
+
+AlignmentList DLLEXPORT_OST_SEQ_ALG SemiGlobalAlign(const ConstSequenceHandle& s1,
+ const ConstSequenceHandle& s2,
+ SubstWeightMatrixPtr& subst,
+ int gap_open=-5,int gap_ext=-2);
+}}}
+
+#endif
diff --git a/modules/seq/alg/src/sequence_similarity.cc b/modules/seq/alg/src/sequence_similarity.cc
new file mode 100644
index 0000000000000000000000000000000000000000..67f2e063710830f508375a3dff3fe4245f7664b7
--- /dev/null
+++ b/modules/seq/alg/src/sequence_similarity.cc
@@ -0,0 +1,57 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+#include <ost/seq/aligned_column_iterator.hh>
+#include <ost/seq/alg/sequence_similarity.hh>
+
+
+namespace ost { namespace seq { namespace alg {
+
+Real SequenceSimilarity(const AlignmentHandle& aln, SubstWeightMatrixPtr subst,
+ bool normalize, int seq_a, int seq_b){
+ int non_gap_count=0;
+ int similarity_score = 0;
+
+ const String& sa=aln.GetSequence(seq_a).GetString();
+ const String& sb=aln.GetSequence(seq_b).GetString();
+
+ for (String::const_iterator
+ i=sa.begin(), e=sa.end(), j=sb.begin(); i!=e; ++i, ++j) {
+ if (!((*i)== '-' || (*j)=='-')) {
+ ++non_gap_count;
+ similarity_score += subst->GetWeight(*i,*j);
+ }
+ }
+
+ Real seq_sim = subst->GetMinWeight();
+
+ if(non_gap_count > 0){
+ seq_sim = static_cast<Real>(similarity_score)/non_gap_count;
+ }
+
+ if(normalize){
+ seq_sim -= subst->GetMinWeight();
+ Real weight_range = subst->GetMaxWeight() - subst->GetMinWeight();
+ if(weight_range > 0) seq_sim /= weight_range;
+ }
+
+ return seq_sim;
+}
+
+}}}
diff --git a/modules/seq/alg/src/sequence_similarity.hh b/modules/seq/alg/src/sequence_similarity.hh
new file mode 100644
index 0000000000000000000000000000000000000000..daaa09a7b54e819679b51113edc42c353e6ffe9a
--- /dev/null
+++ b/modules/seq/alg/src/sequence_similarity.hh
@@ -0,0 +1,39 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#ifndef OST_SEQ_SEQUENCE_SIMILARITY_HH
+#define OST_SEQ_SEQUENCE_SIMILARITY_HH
+
+#include <ost/seq/alg/module_config.hh>
+#include <ost/seq/alignment_handle.hh>
+#include <ost/seq/alg/subst_weight_matrix.hh>
+
+namespace ost { namespace seq { namespace alg {
+
+/// \brief calculate sequence similarity for two sequences in an alignment
+/// \param seq_a is the index of the first sequence
+/// \param seq_b is the index of the second sequence
+/// \param aln is the sequence alignment
+/// \return sequence similarity
+Real DLLEXPORT_OST_SEQ_ALG
+SequenceSimilarity(const AlignmentHandle& aln, SubstWeightMatrixPtr subst,
+ bool normalize=false, int seq_a=0, int seq_b=1);
+
+}}}
+
+#endif
diff --git a/modules/seq/alg/src/subst_weight_matrix.cc b/modules/seq/alg/src/subst_weight_matrix.cc
index 85851ce2c6689a99b1a311f615019b35a0296c76..d8102aa230cf7e4acb738f716e823e8ebb4ab884 100644
--- a/modules/seq/alg/src/subst_weight_matrix.cc
+++ b/modules/seq/alg/src/subst_weight_matrix.cc
@@ -1,7 +1,7 @@
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
-// Copyright (C) 2008-2011 by the OpenStructure authors
+// Copyright (C) 2008-2015 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
@@ -16,38 +16,155 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#include <ost/info/info.hh>
+
#include "subst_weight_matrix.hh"
+#include <iostream>
-namespace ost { namespace seq { namespace alg {
+namespace{
-SubstWeightMatrixPtr SubstWeightMatrixFromInfo(const info::InfoGroup& group)
-{
- SubstWeightMatrixPtr m(new SubstWeightMatrix);
- info::InfoItemList weights=group.GetItems("Weight");
- for (info::InfoItemList::iterator i=weights.begin(),
- e=weights.end(); i!=e; ++i) {
- info::InfoItem item=*i;
- String from=item.GetAttribute("From");
- String to=item.GetAttribute("To");
- m->SetWeight(from[0], to[0], item.AsInt());
+short RAW_BLOSUM45_DATA[23][23]={
+ { 5, -1, -1, -2, -1, -2, 0, -2, -1, -1, -1, -1, -1, -1, -1, -2, 1, 0, 0, -2, 0, -2, -1},
+ {-1, 4, -2, 5, 1, -3, -1, 0, -3, 0, -3, -2, 4, -2, 0, -1, 0, 0, -3, -4, -1, -2, 2},
+ {-1, -2, 12, -3, -3, -2, -3, -3, -3, -3, -2, -2, -2, -4, -3, -3, -1, -1, -1, -5, -2, -3, -3},
+ {-2, 5, -3, 7, 2, -4, -1, 0, -4, 0, -3, -3, 2, -1, 0, -1, 0, -1, -3, -4, -1, -2, 1},
+ {-1, 1, -3, 2, 6, -3, -2, 0, -3, 1, -2, -2, 0, 0, 2, 0, 0, -1, -3, -3, -1, -2, 4},
+ {-2, -3, -2, -4, -3, 8, -3, -2, 0, -3, 1, 0, -2, -3, -4, -2, -2, -1, 0, 1, -1, 3, -3},
+ { 0, -1, -3, -1, -2, -3, 7, -2, -4, -2, -3, -2, 0, -2, -2, -2, 0, -2, -3, -2, -1, -3, -2},
+ {-2, 0, -3, 0, 0, -2, -2, 10, -3, -1, -2, 0, 1, -2, 1, 0, -1, -2, -3, -3, -1, 2, 0},
+ {-1, -3, -3, -4, -3, 0, -4, -3, 5, -3, 2, 2, -2, -2, -2, -3, -2, -1, 3, -2, -1, 0, -3},
+ {-1, 0, -3, 0, 1, -3, -2, -1, -3, 5, -3, -1, 0, -1, 1, 3, -1, -1, -2, -2, -1, -1, 1},
+ {-1, -3, -2, -3, -2, 1, -3, -2, 2, -3, 5, 2, -3, -3, -2, -2, -3, -1, 1, -2, -1, 0, -2},
+ {-1, -2, -2, -3, -2, 0, -2, 0, 2, -1, 2, 6, -2, -2, 0, -1, -2, -1, 1, -2, -1, 0, -1},
+ {-1, 4, -2, 2, 0, -2, 0, 1, -2, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -1, -2, 0},
+ {-1, -2, -4, -1, 0, -3, -2, -2, -2, -1, -3, -2, -2, 9, -1, -2, -1, -1, -3, -3, -1, -3, -1},
+ {-1, 0, -3, 0, 2, -4, -2, 1, -2, 1, -2, 0, 0, -1, 6, 1, 0, -1, -3, -2, -1, -1, 4},
+ {-2, -1, -3, -1, 0, -2, -2, 0, -3, 3, -2, -1, 0, -2, 1, 7, -1, -1, -2, -2, -1, -1, 0},
+ { 1, 0, -1, 0, 0, -2, 0, -1, -2, -1, -3, -2, 1, -1, 0, -1, 4, 2, -1, -4, 0, -2, 0},
+ { 0, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5, 0, -3, 0, -1, -1},
+ { 0, -3, -1, -3, -3, 0, -3, -3, 3, -2, 1, 1, -3, -3, -3, -2, -1, 0, 5, -3, -1, -1, -3},
+ {-2, -4, -5, -4, -3, 1, -2, -3, -2, -2, -2, -2, -4, -3, -2, -2, -4, -3, -3, 15, -2, 3, -2},
+ { 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, -1, -2, -1, -1, -1},
+ {-2, -2, -3, -2, -2, 3, -3, 2, 0, -1, 0, 0, -2, -3, -1, -1, -2, -1, -1, 3, -1, 8, -2},
+ {-1, 2, -3, 1, 4, -3, -2, 0, -3, 1, -2, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 4},
+};
+
+short RAW_BLOSUM62_DATA[23][23]={
+ { 4, -2, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, 0, -2, -1},
+ {-2, 4, -3, 4, 1, -3, -1, 0, -3, 0, -4, -3, 3, -2, 0, -1, 0, -1, -3, -4, -1, -3, 1},
+ { 0, -3, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2, -2, -3},
+ {-2, 4, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -1, -3, 1},
+ {-1, 1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -1, -2, 4},
+ {-2, -3, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, -1, 3, -3},
+ { 0, -1, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -1, -3, -2},
+ {-2, 0, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, -1, 2, 0},
+ {-1, -3, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1, -1, -3},
+ {-1, 0, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -1, -2, 1},
+ {-1, -4, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1, -1, -3},
+ {-1, -3, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1, -1, -1},
+ {-2, 3, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -1, -2, 0},
+ {-1, -2, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -2, -3, -1},
+ {-1, 0, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1, -1, 3},
+ {-1, -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -1, -2, 0},
+ { 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, 0, -2, 0},
+ { 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, 0, -2, -1},
+ { 0, -3, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1, -1, -2},
+ {-3, -4, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, -2, 2, -3},
+ { 0, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, -1, -1, 0, 0, -1, -2, -1, -1, -1},
+ {-2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, -1, 7, -2},
+ {-1, 1, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -1, 3, 0, 0, -1, -2, -3, -1, -2, 4},
+};
+
+short RAW_BLOSUM80_DATA[23][23]={
+ { 7, -3, -1, -3, -2, -4, 0, -3, -3, -1, -3, -2, -3, -1, -2, -3, 2, 0, -1, -5, -1, -4, -2},
+ {-3, 6, -6, 6, 1, -6, -2, -1, -6, -1, -7, -5, 5, -4, -1, -2, 0, -1, -6, -8, -3, -5, 0},
+ {-1, -6, 13, -7, -7, -4, -6, -7, -2, -6, -3, -3, -5, -6, -5, -6, -2, -2, -2, -5, -4, -5, -7},
+ {-3, 6, -7, 10, 2, -6, -3, -2, -7, -2, -7, -6, 2, -3, -1, -3, -1, -2, -6, -8, -3, -6, 1},
+ {-2, 1, -7, 2, 8, -6, -4, 0, -6, 1, -6, -4, -1, -2, 3, -1, -1, -2, -4, -6, -2, -5, 6},
+ {-4, -6, -4, -6, -6, 10, -6, -2, -1, -5, 0, 0, -6, -6, -5, -5, -4, -4, -2, 0, -3, 4, -6},
+ { 0, -2, -6, -3, -4, -6, 9, -4, -7, -3, -7, -5, -1, -5, -4, -4, -1, -3, -6, -6, -3, -6, -4},
+ {-3, -1, -7, -2, 0, -2, -4, 12, -6, -1, -5, -4, 1, -4, 1, 0, -2, -3, -5, -4, -2, 3, 0},
+ {-3, -6, -2, -7, -6, -1, -7, -6, 7, -5, 2, 2, -6, -5, -5, -5, -4, -2, 4, -5, -2, -3, -6},
+ {-1, -1, -6, -2, 1, -5, -3, -1, -5, 8, -4, -3, 0, -2, 2, 3, -1, -1, -4, -6, -2, -4, 1},
+ {-3, -7, -3, -7, -6, 0, -7, -5, 2, -4, 6, 3, -6, -5, -4, -4, -4, -3, 1, -4, -2, -2, -5},
+ {-2, -5, -3, -6, -4, 0, -5, -4, 2, -3, 3, 9, -4, -4, -1, -3, -3, -1, 1, -3, -2, -3, -3},
+ {-3, 5, -5, 2, -1, -6, -1, 1, -6, 0, -6, -4, 9, -4, 0, -1, 1, 0, -5, -7, -2, -4, -1},
+ {-1, -4, -6, -3, -2, -6, -5, -4, -5, -2, -5, -4, -4, 12, -3, -3, -2, -3, -4, -7, -3, -6, -2},
+ {-2, -1, -5, -1, 3, -5, -4, 1, -5, 2, -4, -1, 0, -3, 9, 1, -1, -1, -4, -4, -2, -3, 5},
+ {-3, -2, -6, -3, -1, -5, -4, 0, -5, 3, -4, -3, -1, -3, 1, 9, -2, -2, -4, -5, -2, -4, 0},
+ { 2, 0, -2, -1, -1, -4, -1, -2, -4, -1, -4, -3, 1, -2, -1, -2, 7, 2, -3, -6, -1, -3, -1},
+ { 0, -1, -2, -2, -2, -4, -3, -3, -2, -1, -3, -1, 0, -3, -1, -2, 2, 8, 0, -5, -1, -3, -2},
+ {-1, -6, -2, -6, -4, -2, -6, -5, 4, -4, 1, 1, -5, -4, -4, -4, -3, 0, 7, -5, -2, -3, -4},
+ {-5, -8, -5, -8, -6, 0, -6, -4, -5, -6, -4, -3, -7, -7, -4, -5, -6, -5, -5, 16, -5, 3, -5},
+ {-1, -3, -4, -3, -2, -3, -3, -2, -2, -2, -2, -2, -2, -3, -2, -2, -1, -1, -2, -5, -2, -3, -1},
+ {-4, -5, -5, -6, -5, 4, -6, 3, -3, -4, -2, -3, -4, -6, -3, -4, -3, -3, -3, 3, -3, 11, -4},
+ {-2, 0, -7, 1, 6, -6, -4, 0, -6, 1, -5, -3, -1, -2, 5, 0, -1, -2, -4, -5, -1, -4, 6},
+};
+
+short RAW_BLOSUM100_DATA[23][23]={
+ { 8, -4, -2, -5, -3, -5, -1, -4, -4, -2, -4, -3, -4, -2, -2, -3, 1, -1, -2, -6, -2, -5, -2},
+ {-4, 6, -7, 6, 0, -7, -3, -2, -8, -2, -8, -7, 5, -5, -2, -4, -1, -2, -7, -9, -4, -6, 0},
+ {-2, -7, 14, -8, -9, -4, -7, -8, -3, -8, -5, -4, -5, -8, -7, -8, -3, -3, -3, -7, -5, -6, -8},
+ {-5, 6, -8, 10, 2, -8, -4, -3, -8, -3, -8, -8, 1, -5, -2, -5, -2, -4, -8,-10, -4, -7, 0},
+ {-3, 0, -9, 2, 10, -8, -6, -2, -7, 0, -7, -5, -2, -4, 2, -2, -2, -3, -5, -8, -3, -7, 7},
+ {-5, -7, -4, -8, -8, 11, -8, -4, -2, -6, 0, -1, -7, -7, -6, -6, -5, -5, -3, 0, -4, 4, -7},
+ {-1, -3, -7, -4, -6, -8, 9, -6, -9, -5, -8, -7, -2, -6, -5, -6, -2, -5, -8, -7, -4, -8, -5},
+ {-4, -2, -8, -3, -2, -4, -6, 13, -7, -3, -6, -5, 0, -5, 1, -1, -3, -4, -7, -5, -4, 1, -1},
+ {-4, -8, -3, -8, -7, -2, -9, -7, 8, -6, 2, 1, -7, -7, -6, -7, -5, -3, 4, -6, -3, -4, -7},
+ {-2, -2, -8, -3, 0, -6, -5, -3, -6, 10, -6, -4, -1, -3, 2, 3, -2, -3, -5, -8, -3, -5, 0},
+ {-4, -8, -5, -8, -7, 0, -8, -6, 2, -6, 8, 3, -7, -7, -5, -6, -6, -4, 0, -5, -3, -4, -6},
+ {-3, -7, -4, -8, -5, -1, -7, -5, 1, -4, 3, 12, -5, -5, -2, -4, -4, -2, 0, -4, -3, -5, -4},
+ {-4, 5, -5, 1, -2, -7, -2, 0, -7, -1, -7, -5, 11, -5, -1, -2, 0, -1, -7, -8, -3, -5, -2},
+ {-2, -5, -8, -5, -4, -7, -6, -5, -7, -3, -7, -5, -5, 12, -4, -5, -3, -4, -6, -8, -4, -7, -4},
+ {-2, -2, -7, -2, 2, -6, -5, 1, -6, 2, -5, -2, -1, -4, 11, 0, -2, -3, -5, -5, -2, -4, 5},
+ {-3, -4, -8, -5, -2, -6, -6, -1, -7, 3, -6, -4, -2, -5, 0, 10, -3, -3, -6, -7, -3, -5, -1},
+ { 1, -1, -3, -2, -2, -5, -2, -3, -5, -2, -6, -4, 0, -3, -2, -3, 9, 2, -4, -7, -2, -5, -2},
+ {-1, -2, -3, -4, -3, -5, -5, -4, -3, -3, -4, -2, -1, -4, -3, -3, 2, 9, -1, -7, -2, -5, -3},
+ {-2, -7, -3, -8, -5, -3, -8, -7, 4, -5, 0, 0, -7, -6, -5, -6, -4, -1, 8, -5, -3, -5, -5},
+ {-6, -9, -7, 10, -8, 0, -7, -5, -6, -8, -5, -4, -8, -8, -5, -7, -7, -7, -5, 17, -6, 2, -7},
+ {-2, -4, -5, -4, -3, -4, -4, -4, -3, -3, -3, -3, -3, -4, -2, -3, -2, -2, -3, -6, -3, -4, -2},
+ {-5, -6, -6, -7, -7, 4, -8, 1, -4, -5, -4, -5, -5, -7, -4, -5, -5, -5, -5, 2, -4, 12, -6},
+ {-2, 0, -8, 0, 7, -7, -5, -1, -7, 0, -6, -4, -2, -4, 5, -1, -2, -3, -5, -7, -2, -6, 6},
+};
+
+void FillData(ost::seq::alg::SubstWeightMatrix* subst, short (&data)[23][23]){
+ char chars[23] = {'A','B','C','D','E','F','G','H','I','K','L','M','N','P','Q',
+ 'R','S','T','V','W','X','Y','Z'};
+ for(uint i = 0; i < 23; ++i){
+ for(uint j = 0; j < 23; ++j){
+ subst->SetWeight(chars[i],chars[j],data[i][j]);
+ }
}
- return m;
}
-void SubstWeightMatrixToInfo(const SubstWeightMatrixPtr& subst_mat,
- info::InfoGroup& group)
+}
+
+namespace ost { namespace seq { namespace alg {
+
+void SubstWeightMatrix::AssignPreset(SubstWeightMatrix::Preset p)
{
- for (int i=0; i<SubstWeightMatrix::ALPHABET_SIZE; ++i) {
- for (int j=0; j<SubstWeightMatrix::ALPHABET_SIZE; ++j) {
- char from=char(i+'A');
- char to=char(j+'A');
- info::InfoItem item=group.CreateItem("Weight",
- subst_mat->GetWeight(from, to));
- item.SetAttribute("From", String(1, from));
- item.SetAttribute("To", String(1, to));
+ max_weight_ = 0;
+ min_weight_ = 0;
+ memset(weights_, 0, sizeof(WeightType)*ALPHABET_SIZE*ALPHABET_SIZE);
+
+ switch(p){
+ case BLOSUM45:{
+ FillData(this,RAW_BLOSUM45_DATA);
+ break;
+ }
+ case BLOSUM62:{
+ FillData(this,RAW_BLOSUM62_DATA);
+ break;
+ }
+ case BLOSUM80:{
+ FillData(this,RAW_BLOSUM80_DATA);
+ break;
+ }
+ case BLOSUM100:{
+ FillData(this,RAW_BLOSUM100_DATA);
+ break;
}
}
}
+
}}}
diff --git a/modules/seq/alg/src/subst_weight_matrix.hh b/modules/seq/alg/src/subst_weight_matrix.hh
index 97f0ef825cb45dda7e2572558b2917498e87a353..c3bb6d6057607b87969b1f7179614173f014b5da 100644
--- a/modules/seq/alg/src/subst_weight_matrix.hh
+++ b/modules/seq/alg/src/subst_weight_matrix.hh
@@ -23,9 +23,6 @@
#include <string.h>
#include <boost/shared_ptr.hpp>
#include <ost/config.hh>
-#if(OST_INFO_ENABLED)
-#include <ost/info/info_fw.hh>
-#endif
#include <ost/seq/alg/module_config.hh>
/*
@@ -43,14 +40,20 @@ class DLLEXPORT_OST_SEQ_ALG SubstWeightMatrix {
public:
typedef short WeightType;
const static int ALPHABET_SIZE='Z'-'A'+1;
+ enum Preset{BLOSUM45 = 0,
+ BLOSUM62 = 1,
+ BLOSUM80 = 2,
+ BLOSUM100 = 3};
/// \brief Initialize substitution matrix with zero.
///
/// In order to get a useful substitution weight matrix, use SetWeight().
/// Alternatively you may want to load the substitution from an info group.
- SubstWeightMatrix() {
+ SubstWeightMatrix():max_weight_(0),min_weight_(0) {
::memset(weights_, 0, sizeof(WeightType)*ALPHABET_SIZE*ALPHABET_SIZE);
}
+ void AssignPreset(Preset p);
+
/// \brief Get the substitution weight between two amino acids
///
/// If the amino acid single letter code is unknown (e.g. '?')
@@ -64,6 +67,12 @@ public:
return (i>=0 && i<ALPHABET_SIZE*ALPHABET_SIZE) ? weights_[i] : 0;
}
+ /// \brief Get the minimal substitution weight of the matrix
+ WeightType GetMinWeight() const { return min_weight_; }
+
+ /// \brief Get the maximal substitution weight of the matrix
+ WeightType GetMaxWeight() const { return max_weight_; }
+
/// \brief Set the substitution weight between two amino acids
///
/// The weight is only set if the amino acid single letter code
@@ -74,6 +83,8 @@ public:
int i=Index(aa_one, aa_two);
if (i>=0 && i<ALPHABET_SIZE*ALPHABET_SIZE) {
weights_[i]=weight;
+ min_weight_ = std::min(min_weight_,weight);
+ max_weight_ = std::max(max_weight_,weight);
}
}
}
@@ -88,17 +99,10 @@ private:
return (toupper(aa)>='A' && toupper(aa)<='Z');
}
WeightType weights_[ALPHABET_SIZE*ALPHABET_SIZE];
+ WeightType max_weight_;
+ WeightType min_weight_;
};
-#if(OST_INFO_ENABLED)
-SubstWeightMatrixPtr DLLEXPORT_OST_SEQ_ALG
-SubstWeightMatrixFromInfo(const info::InfoGroup& group);
-
-void DLLEXPORT_OST_SEQ_ALG
-SubstWeightMatrixToInfo(const SubstWeightMatrixPtr& subst_mat,
- info::InfoGroup& group);
-#endif
-
}}}
#endif
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 76b599790fd34347fcff9b518c3c72b8fb85811e..ca0e72988f5fb0e4e8e7841a405e7f1303541cd5 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -5,6 +5,7 @@ set(OST_SEQ_ALG_UNIT_TESTS
test_renumber.py
test_local_align.py
test_global_align.py
+ test_semiglobal_align.py
test_weight_matrix.py
test_aligntoseqres.py
)
diff --git a/modules/seq/alg/tests/test_semiglobal_align.py b/modules/seq/alg/tests/test_semiglobal_align.py
new file mode 100644
index 0000000000000000000000000000000000000000..e50198928edc146038187674163567ad0f7b460f
--- /dev/null
+++ b/modules/seq/alg/tests/test_semiglobal_align.py
@@ -0,0 +1,23 @@
+import unittest
+from ost import *
+from ost import settings
+from ost import seq
+from ost.bindings.clustalw import *
+
+class TestSemiGlobalAlign(unittest.TestCase):
+ def testSemiGlobalAlignment(self):
+ seq_a=seq.CreateSequence('A', 'abcdefghijklmnok')
+ seq_b=seq.CreateSequence('B', 'cdehijk')
+ alns=seq.alg.SemiGlobalAlign(seq_a, seq_b, seq.alg.BLOSUM62)
+ self.assertEqual(len(alns), 1)
+ self.assertEqual(alns[0].sequences[0].name, 'A')
+ self.assertEqual(alns[0].sequences[1].name, 'B')
+ self.assertEqual(str(alns[0].sequences[0]), 'abcdefghijklmnok')
+ self.assertEqual(str(alns[0].sequences[1]), '--cde--hijk-----')
+ self.assertEqual(alns[0].sequences[0].offset, 0)
+ self.assertEqual(alns[0].sequences[1].offset, 0)
+
+
+if __name__ == "__main__":
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/seq/base/doc/seq.rst b/modules/seq/base/doc/seq.rst
index 042f1d09c9811d0b7f42650576ec604cfa9d8fce..5022c0aba584d651d8e0d0d056e89cbc635468ff 100644
--- a/modules/seq/base/doc/seq.rst
+++ b/modules/seq/base/doc/seq.rst
@@ -30,7 +30,7 @@ Sequence Offset
When using sequences and structures together, often the start of the structure
and the beginning of the sequence do not fall together. In the following case,
-the alignment of sequences B and C only covers a subpart of structure A::
+the alignment of sequences B and C only covers a subsequence of structure A::
A acefghiklmnpqrstuvwy
B ghiklm
@@ -98,7 +98,8 @@ The SequenceHandle
Get residue index of character at given position. This method is the
inverse of :meth:`GetPos`. If the sequence contains a gap at that position,
- an :exc:`Error` is raised.
+ an :exc:`Error` is raised. Admires the
+ :ref:`sequence offset <sequence-offset>`.
.. code-block:: python
@@ -167,6 +168,10 @@ The SequenceHandle
Returns a string version of this sequence with all hyphens removed. Also
available as the property :attr:`gapless_string`.
+ .. method:: Normalise()
+
+ Remove '-' and '.' as gaps from the sequence and make it all upper case.
+ Works in place.
.. method:: SetName()
@@ -205,7 +210,7 @@ The SequenceHandle
Check whether the two sequences s1 and s2 match. This function performs are
case-insensitive comparison of the two sequences. The character 'X' is
- interpreted as a wildcard character that always matches the other sequence.
+ interpreted as a wild card character that always matches the other sequence.
The SequenceList
--------------------------------------------------------------------------------
@@ -220,7 +225,7 @@ The AlignmentHandle
--------------------------------------------------------------------------------
The :class:`AlignmentHandle` represents a list of aligned sequences. In
-constrast to :class:`SequenceList`, an alignment requires all sequences to be of
+contrast to :class:`SequenceList`, an alignment requires all sequences to be of
the same length. New instances of alignments are created with
:func:`CreateAlignment` and :func:`AlignmentFromSequenceList`.
@@ -432,3 +437,140 @@ an alignment:
Remove sequence at *index* from the alignment.
+
+Handling Sequence Profiles
+--------------------------------------------------------------------------------
+
+The :class:`ProfileHandle` provides a simple container for profiles for each
+residue. It mainly contains:
+
+- *N* :class:`ProfileColumn` objects (*N* = number of residues in sequence)
+ which each contains 20 amino acid frequencies
+- a :attr:`~ProfileHandle.sequence` (:class:`str`) of length *N*
+- a :attr:`~ProfileHandle.null_model` to use for this profile
+
+.. class:: ProfileColumn
+
+ .. method:: BLOSUMNullModel()
+
+ Static method, that returns a new :class:`ProfileColumn` with amino acid
+ frequencies given from the BLOSUM62 substitution matrix.
+
+ .. method:: GetFreq(aa)
+
+ :param aa: One letter code of standard amino acid
+ :type aa: :class:`str`
+
+ :returns: Frequency of aa
+
+ .. method:: SetFreq(aa,freq)
+
+ :param aa: One letter code of standard amino acid
+ :param freq: The frequency of the given amino acid
+ :type aa: :class:`str`
+ :type freq: :class:`float`
+
+ .. attribute:: entropy
+
+ Shannon entropy based on the columns amino acid frequencies
+
+
+.. class:: ProfileHandle
+
+ .. method:: __len__()
+
+ Returns the length of the sequence for which we have profile.
+
+ :rtype: :class:`int`
+
+ .. method:: AddColumn(col)
+
+ Appends column in the internal column list.
+
+ :param col: Column to add
+ :type col: :class:`ProfileColumn`
+
+ .. method:: Extract(from,to)
+
+ :param from: Col Idx to start from
+ :param to: End Idx, not included in sub-ProfileHandle
+
+ :type from: :class:`int`
+ :type to: :class:`int`
+
+ :returns: sub-profile as defined by given indices
+ (:attr:`null_model` is copied)
+ :rtype: :class:`ProfileHandle`
+
+ :raises: :exc:`~exceptions.Error` if if *to* <= *from* or
+ *to* > :meth:`__len__`.
+
+ .. method:: SetSequence(sequence)
+
+ Sets :attr:`sequence`.
+
+ .. method:: SetNullModel(null_model)
+
+ Sets :attr:`null_model`.
+
+ .. attribute:: sequence
+
+ Sequence for which we have this profile.
+ Note: user must enforce consistency between sequence length and number of
+ profile columns.
+
+ .. attribute:: columns
+
+ Iterable columns of the profile
+
+ .. attribute:: null_model
+
+ Null model of the profile
+
+ .. attribute:: avg_entropy
+
+ Average entropy of all the columns
+
+.. class:: ProfileDB
+
+ A simple database to gather :class:`ProfileHandle` objects. It is possible
+ to save them to disk in a compressed format with limited accuracy
+ (4 digits for each frequency).
+
+ .. method:: Save(filename)
+
+ :param filename: Name of file that will be generated on disk.
+ :type filename: :class:`str`
+
+ .. method:: Load(filename)
+
+ Static loading method
+
+ :param filename: Name of file from which the database should be loaded.
+ :type filename: :class:`str`
+ :returns: The loaded database
+
+ .. method:: AddProfile(name, prof)
+
+ :param name: Name of profile to be added
+ :param prof: Profile to be added
+
+ :type name: :class:`str`
+ :type prof: :class:`ProfileHandle`
+ :raises: :class:`Exception` when filename is longer than 255 characters.
+
+ .. method:: GetProfile(name)
+
+ :param name: Name of profile to be returned
+ :type name: :class:`str`
+ :returns: The requested :class:`ProfileHandle`
+ :raises: :class:`Exception` when no :class:`ProfileHandle` for **name** exists.
+
+ .. method:: Size()
+
+ :returns: Number of :class:`ProfileHandle` objects in the database
+
+ .. method:: GetNames()
+
+ :returns: A nonsorted list of the names of all :class:`ProfileHandle`
+ objects in the database
diff --git a/modules/seq/base/pymod/CMakeLists.txt b/modules/seq/base/pymod/CMakeLists.txt
index f2aac4ea51cb0cd57fed4d304199db0a420158fb..c40a805fa2dccb7feba2d4e35476d50a5e02a954 100644
--- a/modules/seq/base/pymod/CMakeLists.txt
+++ b/modules/seq/base/pymod/CMakeLists.txt
@@ -1,5 +1,6 @@
set(OST_SEQ_PYMOD_SOURCES
export_sequence.cc
+ export_profile_handle.cc
wrap_seq.cc
)
diff --git a/modules/seq/base/pymod/export_profile_handle.cc b/modules/seq/base/pymod/export_profile_handle.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e563960f424e448863bf17f7d52d10db8b2875e5
--- /dev/null
+++ b/modules/seq/base/pymod/export_profile_handle.cc
@@ -0,0 +1,82 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello, Gabriel Studer
+ */
+
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+#include <boost/python.hpp>
+#include <ost/seq/profile_handle.hh>
+
+using namespace ost::seq;
+using namespace boost::python;
+
+namespace {
+
+boost::python::list wrap_get_names(ProfileDBPtr db) {
+ std::vector<String> v_names = db->GetNames();
+ boost::python::list names;
+ for (std::vector<String>::iterator i = v_names.begin();
+ i != v_names.end(); ++i) {
+ names.append(*i);
+ }
+ return names;
+}
+
+} // anon ns
+
+void export_profile_handle()
+{
+ class_<ProfileColumn>("ProfileColumn", init<>())
+ .add_property("entropy", &ProfileColumn::GetEntropy)
+ .def("GetFreq", &ProfileColumn::GetFreq)
+ .def("SetFreq", &ProfileColumn::SetFreq)
+ .def("BLOSUMNullModel",
+ &ProfileColumn::BLOSUMNullModel).staticmethod("BLOSUMNullModel")
+ ;
+
+ class_<ProfileColumnList>("ProfileColumnList", init<>())
+ .def(vector_indexing_suite<ProfileColumnList>())
+ ;
+
+ class_<ProfileHandle, ProfileHandlePtr>("ProfileHandle", init<>())
+ .def("__len__",&ProfileHandle::size)
+ .def("AddColumn", &ProfileHandle::push_back)
+ .def("Extract", &ProfileHandle::Extract)
+ .def("SetNullModel", &ProfileHandle::SetNullModel)
+ .def("SetSequence", &ProfileHandle::SetSequence)
+ .add_property("null_model", make_function(&ProfileHandle::GetNullModel,
+ return_value_policy<copy_const_reference>()))
+ .add_property("columns",
+ make_function(&ProfileHandle::GetColumns,
+ return_value_policy<copy_const_reference>()))
+ .add_property("avg_entropy", &ProfileHandle::GetAverageEntropy)
+ .add_property("sequence", &ProfileHandle::GetSequence)
+ ;
+
+ class_<ProfileDB, ProfileDBPtr>("ProfileDB", init<>())
+ .def("Load", &ProfileDB::Load).staticmethod("Load")
+ .def("Save", &ProfileDB::Save)
+ .def("AddProfile", &ProfileDB::AddProfile)
+ .def("GetProfile", &ProfileDB::GetProfile)
+ .def("Size", &ProfileDB::size)
+ .def("GetNames",&wrap_get_names)
+ ;
+}
diff --git a/modules/seq/base/pymod/export_sequence.cc b/modules/seq/base/pymod/export_sequence.cc
index 6cdf081cd35740fa1f4a543ef341e37f3e0974f6..1919290e7f90f9cee97b19fcdcecccc007090c64 100644
--- a/modules/seq/base/pymod/export_sequence.cc
+++ b/modules/seq/base/pymod/export_sequence.cc
@@ -300,6 +300,7 @@ void export_sequence()
.def("AttachView", attach_two)
.def("Append", &SequenceHandle::Append)
.def("SetString", &SequenceHandle::SetString)
+ .def("Normalise", &SequenceHandle::Normalise)
.add_property("string",
make_function(&SequenceHandle::GetString,
return_value_policy<copy_const_reference>()),
diff --git a/modules/seq/base/pymod/wrap_seq.cc b/modules/seq/base/pymod/wrap_seq.cc
index c881dae0ab14a9678aabbacc575daba93bfcedd3..1dbc2ba17e65435db1480db4c8330d04718d1300 100644
--- a/modules/seq/base/pymod/wrap_seq.cc
+++ b/modules/seq/base/pymod/wrap_seq.cc
@@ -20,9 +20,10 @@
using namespace boost::python;
void export_sequence();
+void export_profile_handle();
BOOST_PYTHON_MODULE(_ost_seq)
{
export_sequence();
-
+ export_profile_handle();
}
diff --git a/modules/seq/base/src/CMakeLists.txt b/modules/seq/base/src/CMakeLists.txt
index 8ef75076e739e4cf90e01e97f5e9582f22cd67cf..ff359c8ad8dba949f3f0bfbf1aab122b973d4bd9 100644
--- a/modules/seq/base/src/CMakeLists.txt
+++ b/modules/seq/base/src/CMakeLists.txt
@@ -16,6 +16,7 @@ aligned_column.hh
aligned_column_iterator.hh
invalid_sequence.hh
views_from_sequences.hh
+profile_handle.hh
)
set(OST_SEQ_SOURCES
@@ -28,6 +29,7 @@ sequence_list.cc
alignment_handle.cc
sequence_op.cc
views_from_sequences.cc
+profile_handle.cc
)
if (ENABLE_INFO)
@@ -38,4 +40,5 @@ endif()
module(NAME seq SOURCES ${OST_SEQ_SOURCES}
HEADERS ${OST_SEQ_IMPL_HEADERS} IN_DIR impl
${OST_SEQ_HEADERS}
+ LINK ${BOOST_IOSTREAM_LIBRARIES}
DEPENDS_ON ost_mol ${INFO_DEPS})
\ No newline at end of file
diff --git a/modules/seq/base/src/impl/sequence_impl.cc b/modules/seq/base/src/impl/sequence_impl.cc
index 733eaf1b8e17f765581a4cb1e527beb2bf3483ef..9864fe8e5f375c3434b7050e5eca5d3ebd99da2d 100644
--- a/modules/seq/base/src/impl/sequence_impl.cc
+++ b/modules/seq/base/src/impl/sequence_impl.cc
@@ -331,6 +331,27 @@ void SequenceImpl::Replace(const String& str,int start, int end)
this->ShiftsFromSequence();
}
+void SequenceImpl::Normalise() {
+ const char gaps[]={'.', '-', '\0'};
+ bool is_gap;
+ String new_seq_string = "";
+ int n_gaps = sizeof(gaps) / sizeof(gaps[0]);
+ for (size_t i=0; i<seq_string_.length(); ++i) {
+ is_gap = false;
+ for (int j=0; j<n_gaps; ++j) {
+ if (seq_string_[i]==gaps[j]) {
+ is_gap = true;
+ break;
+ }
+ }
+ if (is_gap == false) {
+ new_seq_string = new_seq_string + char(toupper(seq_string_[i]));
+ }
+ }
+ seq_string_ = new_seq_string;
+ this->ShiftsFromSequence();
+}
+
void SequenceImpl::ShiftRegion(int start, int end, int amount)
{
if(start > end || start + amount < 0 || end + amount > this->GetLength()){
diff --git a/modules/seq/base/src/impl/sequence_impl.hh b/modules/seq/base/src/impl/sequence_impl.hh
index fecad2ca921599ecd85c58ee33e6c184bdbd5a52..ccb64b7754e9e20e2cd6683f612dbe533f86423e 100644
--- a/modules/seq/base/src/impl/sequence_impl.hh
+++ b/modules/seq/base/src/impl/sequence_impl.hh
@@ -81,6 +81,9 @@ public:
/// \brief Set sequence String
void SetString(const String& seq);
+ /// \brief Remove everything 'unusual' from sequence
+ void Normalise();
+
/// \brief replace substring starting from start to end
void Replace(const String& str,int start, int end);
diff --git a/modules/seq/base/src/profile_handle.cc b/modules/seq/base/src/profile_handle.cc
new file mode 100644
index 0000000000000000000000000000000000000000..0feebe958ba8aacaa9bdb690cc6c17d76a4e41c9
--- /dev/null
+++ b/modules/seq/base/src/profile_handle.cc
@@ -0,0 +1,220 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello, Gabriel Studer
+ */
+
+#include <fstream>
+#include <iostream>
+#include <ost/seq/profile_handle.hh>
+
+namespace ost { namespace seq{
+
+//////////////////////////////////////////////////////////////////////////////
+// ProfileColumn
+//////////////////////////////////////////////////////////////////////////////
+
+ProfileColumn ProfileColumn::BLOSUMNullModel() {
+ ProfileColumn col;
+
+ col.freq_[0] = 0.0732;
+ col.freq_[1] = 0.0250;
+ col.freq_[2] = 0.0542;
+ col.freq_[3] = 0.0547;
+ col.freq_[4] = 0.0447;
+ col.freq_[5] = 0.0751;
+ col.freq_[6] = 0.0261;
+ col.freq_[7] = 0.0700;
+ col.freq_[8] = 0.1011;
+ col.freq_[9] = 0.0584;
+ col.freq_[10] = 0.0246;
+ col.freq_[11] = 0.0463;
+ col.freq_[12] = 0.0351;
+ col.freq_[13] = 0.0326;
+ col.freq_[14] = 0.0484;
+ col.freq_[15] = 0.0573;
+ col.freq_[16] = 0.0505;
+ col.freq_[17] = 0.0758;
+ col.freq_[18] = 0.0124;
+ col.freq_[19] = 0.0345;
+
+ return col;
+}
+
+int ProfileColumn::GetIndex(char olc) {
+ if (olc == 'A') return 0;
+ if (olc >= 'C' && olc <= 'I') return (olc-'A') - 1;
+ if (olc >= 'K' && olc <= 'N') return (olc-'A') - 2;
+ if (olc >= 'P' && olc <= 'T') return (olc-'A') - 3;
+ if (olc == 'V' ) return 17;
+ if (olc == 'W' ) return 18;
+ if (olc == 'Y' ) return 19;
+ return -1;
+}
+
+Real ProfileColumn::GetFreq(char ch) const{
+ int idx = ProfileColumn::GetIndex(ch);
+ if (idx == -1) {
+ throw Error("Invalid One Letter Code observed when getting frequency in "
+ "ProfileColumn!");
+ }
+ return freq_[idx];
+}
+
+void ProfileColumn::SetFreq(char ch, Real freq){
+ int idx = ProfileColumn::GetIndex(ch);
+ if (idx == -1) {
+ throw Error("Invalid One Letter Code observed when setting frequency in "
+ "ProfileColumn!");
+ }
+ freq_[idx] = freq;
+}
+
+Real ProfileColumn::GetEntropy() const {
+ Real entropy = 0.0;
+ for (uint i = 0; i < 20; ++i) {
+ if (freq_[i] > 0.0) {
+ entropy -= log(freq_[i]) * freq_[i];
+ }
+ }
+ return entropy;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// ProfileHandle
+//////////////////////////////////////////////////////////////////////////////
+
+ProfileHandlePtr ProfileHandle::Extract(uint from, uint to){
+
+ if (to <= from) {
+ throw Error("Second index must be bigger than first one!");
+ }
+
+ if (to > this->size()) {
+ throw Error("Invalid index!");
+ }
+
+ ProfileHandlePtr return_prof(new ProfileHandle);
+ return_prof->SetNullModel(null_model_);
+ for(uint i = from; i < to; ++i){
+ return_prof->push_back(columns_[i]);
+ }
+ return_prof->SetSequence(seq_.substr(from, to-from));
+
+ return return_prof;
+}
+
+Real ProfileHandle::GetAverageEntropy() const {
+ Real n_eff = 0.0;
+ int n = 0;
+ for (std::vector<ProfileColumn>::const_iterator
+ i = this->columns_begin(), e = this->columns_end(); i != e; ++i) {
+ n += 1;
+ n_eff += i->GetEntropy();
+ }
+ return (n > 0) ? n_eff/n : 0.0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// ProfileDB
+//////////////////////////////////////////////////////////////////////////////
+
+void ProfileDB::Save(const String& filename) const{
+
+ std::ofstream out_stream(filename.c_str(), std::ios::binary);
+
+ //write out total size
+ uint32_t total_size = data_.size();
+ out_stream.write(reinterpret_cast<char*>(&total_size),4);
+
+ //write out the data elements
+ char string_size;
+ for (std::map<String, ProfileHandlePtr>::const_iterator i = data_.begin();
+ i != data_.end(); ++i){
+ string_size = static_cast<char>(i->first.size());
+ out_stream.write(reinterpret_cast<char*>(&string_size),1);
+ out_stream.write(i->first.c_str(),string_size);
+ out_stream << *i->second;
+ }
+ out_stream.close();
+}
+
+ProfileDBPtr ProfileDB::Load(const String& filename){
+
+ std::ifstream in_stream(filename.c_str(), std::ios::binary);
+ if (!in_stream){
+ std::stringstream ss;
+ ss << "the file '" << filename << "' does not exist.";
+ throw Error(ss.str());
+ }
+
+ ProfileDBPtr db(new ProfileDB);
+
+ //read in the total size
+ uint32_t total_size;
+ in_stream.read(reinterpret_cast<char*>(&total_size),4);
+
+ //read in the single profiles
+ char string_size;
+ for(uint i = 0; i < total_size; ++i){
+ in_stream.read(&string_size,1);
+ String name(string_size,'X');
+ in_stream.read(&name[0],string_size);
+ ProfileHandlePtr prof(new ProfileHandle);
+ in_stream >> *prof;
+ db->AddProfile(name, prof);
+ }
+
+ return db;
+}
+
+void ProfileDB::AddProfile(const String& name, ProfileHandlePtr prof) {
+ if (name.size() > 255) {
+ throw Error("Name of Profile must be smaller than 256!");
+ }
+ if (name.empty()) {
+ throw Error("Name must not be empty!");
+ }
+ data_[name] = prof;
+}
+
+ProfileHandlePtr ProfileDB::GetProfile(const String& name) const{
+ std::map<String,ProfileHandlePtr>::const_iterator i = data_.find(name);
+ if (i == data_.end()) {
+ std::stringstream ss;
+ ss << "Profile database does not contain an entry with name ";
+ ss << name << "!";
+ throw Error(ss.str());
+ }
+ return i->second;
+}
+
+std::vector<String> ProfileDB::GetNames() const{
+ std::vector<String> return_vec;
+ return_vec.reserve(this->size());
+ for (std::map<String, ProfileHandlePtr>::const_iterator i = data_.begin();
+ i != data_.end(); ++i){
+ return_vec.push_back(i->first);
+ }
+ return return_vec;
+}
+
+
+}} //ns
diff --git a/modules/seq/base/src/profile_handle.hh b/modules/seq/base/src/profile_handle.hh
new file mode 100644
index 0000000000000000000000000000000000000000..0d67f8c696a0995133473c2da7a979d8b84bd6bd
--- /dev/null
+++ b/modules/seq/base/src/profile_handle.hh
@@ -0,0 +1,250 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello, Gabriel Studer
+ */
+
+#ifndef OST_SEQ_PROFILE_HANDLE_HH
+#define OST_SEQ_PROFILE_HANDLE_HH
+
+#include <ost/base.hh>
+#include <ost/stdint.hh>
+#include <ost/message.hh>
+#include <ost/seq/module_config.hh>
+
+#include <string.h> // for memcpy, etc
+#include <vector>
+#include <map>
+#include <fstream>
+#include <boost/shared_ptr.hpp>
+
+namespace ost { namespace seq {
+
+class ProfileHandle;
+class ProfileColumn;
+class ProfileDB;
+typedef boost::shared_ptr<ProfileHandle> ProfileHandlePtr;
+typedef boost::shared_ptr<ProfileDB> ProfileDBPtr;
+typedef std::vector<ProfileColumn> ProfileColumnList;
+
+/// \brief Defines profile of 20 frequencies for one residue.
+///
+/// Frequencies are identified by the one-letter-code for that amino acid.
+/// (possible codes: ACDEFGHIKLMNPQRSTVWY)
+class DLLEXPORT_OST_SEQ ProfileColumn {
+public:
+
+ /// \brief Construct a profile with all frequencies set to 0.
+ ProfileColumn() {
+ memset(freq_, 0, sizeof(freq_));
+ }
+
+ ProfileColumn(const ProfileColumn& rhs) {
+ memcpy(freq_, rhs.freq_, sizeof(freq_));
+ }
+ ProfileColumn& operator= (const ProfileColumn& rhs) {
+ memcpy(freq_, rhs.freq_, sizeof(freq_));
+ return *this;
+ }
+
+ static ProfileColumn BLOSUMNullModel();
+
+ /// \brief Translate one-letter-code to index (0-indexing).
+ static int GetIndex(char ch);
+
+ Real GetFreq(char ch) const;
+
+ void SetFreq(char ch, Real freq);
+
+ bool operator==(const ProfileColumn& rhs) const {
+ return !memcmp(freq_, rhs.freq_, sizeof(freq_));
+ }
+ bool operator!=(const ProfileColumn& rhs) const { return !(rhs == (*this)); }
+
+ Real* freqs_begin() { return freq_; }
+ Real* freqs_end() { return freq_ + 20; }
+ const Real* freqs_begin() const { return freq_; }
+ const Real* freqs_end() const { return freq_ + 20; }
+
+ /// \brief Get entropy for this column.
+ Real GetEntropy() const;
+
+ // functions to feed streams with limited accuracy of internal data
+ // not intended for python export
+
+ friend std::ofstream& operator<<(std::ofstream& os, ProfileColumn& col) {
+ int16_t data[20];
+ //transform aa_freq
+ for (uint i = 0; i < 20; ++i) {
+ data[i] = static_cast<int16_t>(col.freq_[i]*10000);
+ }
+ os.write(reinterpret_cast<char*>(data), sizeof(data));
+ return os;
+ }
+
+ friend std::ifstream& operator>>(std::ifstream& is, ProfileColumn& col) {
+ int16_t data[20];
+ is.read(reinterpret_cast<char*>(data), sizeof(data));
+ //transform aa_freq
+ for (uint i = 0; i < 20; ++i) {
+ col.freq_[i] = data[i] * 0.0001;
+ }
+ return is;
+ }
+
+private:
+ Real freq_[20];
+};
+
+/// \brief Provides a profile for a sequence.
+///
+/// Properties:
+/// - consists of N ProfileColumn (N = #residues in sequence)
+/// - contains sequence (String) of length N
+/// - user must enforce consistency between sequence length and #columns
+/// - contains a null_model to use for this sequence
+class DLLEXPORT_OST_SEQ ProfileHandle {
+public:
+ /// \brief Constructs an empty profile handle (sequence = '', 0 columns).
+ ProfileHandle() {}
+
+ // uses compiler-generated copy- and assignment operators (work here!)
+
+ const std::vector<ProfileColumn>& GetColumns() const { return columns_; }
+
+ const ProfileColumn& GetNullModel() const { return null_model_; }
+
+ void SetNullModel(const ProfileColumn& null_model) { null_model_ = null_model; }
+
+ String GetSequence() const { return seq_; }
+
+ void SetSequence(const String& seq) { seq_ = seq; }
+
+ /// \brief Extract subset of profile for columns from until to-1 (0-indexing).
+ /// Null model is copied from this profile.
+ /// \throw Error if to <= from or to > size().
+ ProfileHandlePtr Extract(uint from, uint to);
+
+ /// \brief Compute average entropy over all columns.
+ Real GetAverageEntropy() const;
+
+ // some functions to make it behave like a vector
+
+ void clear() { seq_ = ""; columns_.clear(); }
+
+ size_t size() const { return columns_.size(); }
+
+ bool empty() const { return columns_.empty(); }
+
+ void push_back(const ProfileColumn& c) { columns_.push_back(c); }
+
+ ProfileColumn& operator[](size_t index) { return columns_[index]; }
+
+ const ProfileColumn& operator[](size_t index) const { return columns_[index]; }
+
+ ProfileColumn& at(size_t index) { return columns_.at(index); }
+
+ const ProfileColumn& at(size_t index) const { return columns_.at(index); }
+
+ bool operator==(const ProfileHandle& other) const {
+ return seq_ == other.seq_ &&
+ columns_ == other.columns_ &&
+ null_model_ == other.null_model_;
+ }
+
+ bool operator!=(const ProfileHandle& other) const { return !(other == (*this)); }
+
+ ProfileColumnList::const_iterator columns_end() const { return columns_.end(); }
+ ProfileColumnList::iterator columns_end() { return columns_.end(); }
+ ProfileColumnList::const_iterator columns_begin() const { return columns_.begin(); }
+ ProfileColumnList::iterator columns_begin() { return columns_.begin(); }
+
+ // functions to feed streams with limited accuracy of internal data
+ // not intended for python export
+
+ friend std::ofstream& operator<<(std::ofstream& os, ProfileHandle& prof) {
+ // null model
+ os << prof.null_model_;
+ // num. columns/residues
+ uint32_t size = prof.size();
+ os.write(reinterpret_cast<char*>(&size), sizeof(uint32_t));
+ // sequence
+ if (prof.seq_.length() != size) {
+ throw Error("ProfileHandle - Inconsistency between number of columns and "
+ " seq. length.");
+ }
+ os.write(prof.seq_.c_str(), size);
+ // columns
+ for(uint i = 0; i < size; ++i){
+ os << prof.columns_[i];
+ }
+
+ return os;
+ }
+
+ friend std::ifstream& operator>>(std::ifstream& is, ProfileHandle& prof) {
+ // null model
+ is >> prof.null_model_;
+ // num. columns/residues
+ uint32_t size;
+ is.read(reinterpret_cast<char*>(&size), sizeof(uint32_t));
+ // sequence
+ std::vector<char> tmp_buf(size);
+ is.read(&tmp_buf[0], size);
+ prof.seq_.assign(&tmp_buf[0], size);
+ // columns
+ prof.columns_.resize(size);
+ for(uint i = 0; i < size; ++i){
+ is >> prof.columns_[i];
+ }
+
+ return is;
+ }
+
+private:
+ String seq_;
+ ProfileColumn null_model_;
+ ProfileColumnList columns_;
+};
+
+/// \brief Contains a DB of profiles (identified by a unique name (String)).
+class DLLEXPORT_OST_SEQ ProfileDB {
+public:
+ /// \brief Saves all profiles in DB with limited accuracy of internal data.
+ /// Binary format with fixed-width integers (should be portable).
+ void Save(const String& filename) const;
+
+ static ProfileDBPtr Load(const String& filename);
+
+ void AddProfile(const String& name, ProfileHandlePtr prof);
+
+ ProfileHandlePtr GetProfile(const String& name) const;
+
+ size_t size() const { return data_.size(); }
+
+ std::vector<String> GetNames() const;
+
+private:
+ std::map<String, ProfileHandlePtr> data_;
+};
+
+}}
+
+#endif
diff --git a/modules/seq/base/src/sequence_handle.cc b/modules/seq/base/src/sequence_handle.cc
index 627ebdc36ee0501a7ff5fcf2926af7c199dae592..f57a624e7634410910b4b479debcd5db6b25a4cd 100644
--- a/modules/seq/base/src/sequence_handle.cc
+++ b/modules/seq/base/src/sequence_handle.cc
@@ -295,6 +295,11 @@ String SequenceHandle::GetGaplessString() const
return Impl()->GetGaplessString();
}
+void SequenceHandle::Normalise() {
+ this->CheckValidity();
+ Impl()->Normalise();
+}
+
int SequenceHandle::GetOffset() const
{
this->CheckValidity();
diff --git a/modules/seq/base/src/sequence_handle.hh b/modules/seq/base/src/sequence_handle.hh
index d7247cbd10abca25bdc9fc3c00b60dac7c6e9915..cf9aa732d1d2a85c154e0dd774790a724ac0e2b2 100644
--- a/modules/seq/base/src/sequence_handle.hh
+++ b/modules/seq/base/src/sequence_handle.hh
@@ -123,7 +123,7 @@ public:
bool HasAttachedView() const;
const String& GetRole() const;
-
+
bool operator==(const ConstSequenceHandle& rhs) const;
bool operator!=(const ConstSequenceHandle& rhs) const;
@@ -231,7 +231,11 @@ public:
/// \brief get attached view. may be an invalid entity view
/// \sa SequenceHandle::AttachView(const mol::EntityView&, const String&)
mol::EntityView GetAttachedView() const;
-
+
+ /// \brief remove '.', '-' as gaps and make sequence all-uppercase
+ /// Changes happen in place.
+ void Normalise();
+
/// \brief create copy sequence
/// The newly created sequence has the same attached view.
SequenceHandle Copy() const;
diff --git a/modules/seq/base/tests/CMakeLists.txt b/modules/seq/base/tests/CMakeLists.txt
index 645dba066e39c51c1fc0b9211228e8490ed85a07..c160c4b320d178ce1be2255ad2d4da20d2e5c09c 100644
--- a/modules/seq/base/tests/CMakeLists.txt
+++ b/modules/seq/base/tests/CMakeLists.txt
@@ -4,8 +4,8 @@ set(OST_SEQ_UNIT_TESTS
test_aligned_column.cc
test_aligned_region.cc
test_alignment.cc
+ test_profile.cc
tests.cc
)
ost_unittest(MODULE seq SOURCES "${OST_SEQ_UNIT_TESTS}")
-
diff --git a/modules/seq/base/tests/test_profile.cc b/modules/seq/base/tests/test_profile.cc
new file mode 100644
index 0000000000000000000000000000000000000000..ef2292bc74f0d981a0cf658a93b6c8ecf129bbec
--- /dev/null
+++ b/modules/seq/base/tests/test_profile.cc
@@ -0,0 +1,144 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2015 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+
+/*
+ Author: Gerardo Tauriello, Gabriel Studer
+ */
+
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+#include <iostream>
+
+#include <ost/seq/profile_handle.hh>
+#include <ost/io/seq/hhm_io_handler.hh>
+#include <ost/io/seq/pssm_io_handler.hh>
+
+using namespace ost::seq;
+
+
+BOOST_AUTO_TEST_SUITE( profile );
+
+
+BOOST_AUTO_TEST_CASE(profile_column)
+{
+ const char * olc = "ACDEFGHIKLMNPQRSTVWY";
+
+ // check empty column
+ ProfileColumn pc;
+ BOOST_CHECK_EQUAL(pc.GetEntropy(), Real(0));
+ Real* freq_ptr = pc.freqs_begin();
+ for (uint i = 0; i < 20; ++i) {
+ BOOST_CHECK_EQUAL(freq_ptr[i], Real(0));
+ BOOST_CHECK_EQUAL(pc.GetFreq(olc[i]), Real(0));
+ // check overwrite
+ const Real tst = Real(i)/Real(20);
+ pc.SetFreq(olc[i], tst);
+ BOOST_CHECK_EQUAL(pc.GetFreq(olc[i]), tst);
+ }
+
+ // check null model
+ ProfileColumn nm = ProfileColumn::BLOSUMNullModel();
+ BOOST_CHECK_GE(pc.GetEntropy(), Real(0));
+ Real sum_freq = 0;
+ freq_ptr = nm.freqs_begin();
+ for (uint i = 0; i < 20; ++i) {
+ BOOST_CHECK_GE(freq_ptr[i], Real(0));
+ sum_freq += freq_ptr[i];
+ }
+ BOOST_CHECK_CLOSE(sum_freq, Real(1), Real(1e-3));
+
+ // check assign/copy
+ ProfileColumn nm2(nm);
+ BOOST_CHECK(nm == nm2);
+ Real* freq_ptr2 = nm2.freqs_begin();
+ for (uint i = 0; i < 20; ++i) {
+ BOOST_CHECK_EQUAL(freq_ptr[i], freq_ptr2[i]);
+ }
+ pc = nm;
+ BOOST_CHECK(nm == pc);
+}
+
+BOOST_AUTO_TEST_CASE(profile_handle)
+{
+ // generate dummy
+ ProfileHandle prof;
+ BOOST_CHECK_EQUAL(prof.size(), size_t(0));
+ BOOST_CHECK_EQUAL(prof.GetSequence(), "");
+ prof.SetSequence("RRSPP");
+ ProfileColumn pc0 = ProfileColumn::BLOSUMNullModel();
+ prof.SetNullModel(pc0);
+ ProfileColumn pc1, pc2, pc3, pc4;
+ pc1.SetFreq('H', 0.74);
+ pc1.SetFreq('E', 0.01);
+ pc1.SetFreq('L', 0.25);
+ pc2.SetFreq('L', 1);
+ pc3.SetFreq('Y', 0.5);
+ pc3.SetFreq('E', 0.5);
+ pc4.SetFreq('A', 0.5);
+ pc4.SetFreq('H', 0.5);
+ prof.push_back(pc0);
+ prof.push_back(pc1);
+ prof.push_back(pc2);
+ prof.push_back(pc3);
+ prof.push_back(pc4);
+
+ // check components
+ BOOST_CHECK_EQUAL(prof.size(), size_t(5));
+ BOOST_CHECK(prof.GetNullModel() == pc0);
+ BOOST_CHECK_EQUAL(prof.GetSequence(), "RRSPP");
+
+ // check columns with different methods of getting the columns
+ BOOST_CHECK(prof[0] == pc0);
+ BOOST_CHECK(*(prof.columns_begin()+1) == pc1);
+ BOOST_CHECK(prof.GetColumns()[2] == pc2);
+ BOOST_CHECK(prof.at(3) == pc3);
+ BOOST_CHECK(*(prof.columns_end()-1) == pc4);
+
+ // check entropies
+ Real entropy1 = -0.74*log(0.74) - 0.01*log(0.01) - 0.25*log(0.25);
+ Real entropy2 = 0;
+ Real entropy3 = -log(0.5);
+ Real avg_entropy = (pc0.GetEntropy() + entropy1 + entropy2 + 2*entropy3)/5;
+ BOOST_CHECK_CLOSE(prof[1].GetEntropy(), entropy1, Real(1e-3));
+ BOOST_CHECK_CLOSE(prof[2].GetEntropy(), entropy2, Real(1e-3));
+ BOOST_CHECK_CLOSE(prof[3].GetEntropy(), entropy3, Real(1e-3));
+ BOOST_CHECK_CLOSE(prof.GetAverageEntropy(), avg_entropy, Real(1e-3));
+
+ // extract parts
+ ProfileHandlePtr pp = prof.Extract(1, 4);
+ avg_entropy = (entropy1 + entropy2 + entropy3)/3;
+ BOOST_CHECK_EQUAL(pp->size(), size_t(3));
+ BOOST_CHECK_EQUAL(pp->GetSequence(), "RSP");
+ BOOST_CHECK_CLOSE(pp->GetAverageEntropy(), avg_entropy, Real(1e-3));
+
+ pp = prof.Extract(0, 3);
+ avg_entropy = (pc0.GetEntropy() + entropy1 + entropy2)/3;
+ BOOST_CHECK_EQUAL(pp->size(), size_t(3));
+ BOOST_CHECK_EQUAL(pp->GetSequence(), "RRS");
+ BOOST_CHECK_CLOSE(pp->GetAverageEntropy(), avg_entropy, Real(1e-3));
+
+ pp = prof.Extract(3, 5);
+ BOOST_CHECK_EQUAL(pp->size(), size_t(2));
+ BOOST_CHECK_EQUAL(pp->GetSequence(), "PP");
+ BOOST_CHECK_CLOSE(pp->GetAverageEntropy(), entropy3, Real(1e-3));
+}
+
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/seq/base/tests/test_seq.py b/modules/seq/base/tests/test_seq.py
index bfd80d7bf70461211962f6b36c2c603584b4fe4c..f202fe522bf19367af6f9ca70c86837d41869cf1 100644
--- a/modules/seq/base/tests/test_seq.py
+++ b/modules/seq/base/tests/test_seq.py
@@ -175,6 +175,16 @@ class TestSeq(unittest.TestCase):
self.assertEqual(string_a, 'BDFH')
self.assertEqual(string_b, 'BDFH')
+ def testNormalise(self):
+ seq_a=seq.CreateSequence("A", "B-D-FGH")
+ self.assertEqual("B-D-FGH", seq_a.GetString())
+ seq_a.Normalise()
+ self.assertEqual("BDFGH", seq_a.GetString())
+ seq_a=seq.CreateSequence("A", "b.d-fgh")
+ self.assertEqual("b.d-fgh", seq_a.GetString())
+ seq_a.Normalise()
+ self.assertEqual("BDFGH", seq_a.GetString())
+
if __name__== '__main__':
from ost import testutils
testutils.RunTests()
diff --git a/modules/seq/base/tests/test_sequence.cc b/modules/seq/base/tests/test_sequence.cc
index 462747784933dcc25dd36689c3a0d0df5a5f2de2..309939db0d715aa4b8dce5256bac8176117bc07a 100644
--- a/modules/seq/base/tests/test_sequence.cc
+++ b/modules/seq/base/tests/test_sequence.cc
@@ -106,6 +106,26 @@ BOOST_AUTO_TEST_CASE(seq_string)
BOOST_CHECK_EQUAL(s.GetGaplessString(),"");
}
+BOOST_AUTO_TEST_CASE(seq_normalise)
+{
+ SequenceHandle s=CreateSequence("S1", "abfcdadeaf");
+ BOOST_CHECK_EQUAL(s.GetString(),"abfcdadeaf");
+ s.Normalise();
+ BOOST_CHECK_EQUAL(s.GetString(),"ABFCDADEAF");
+ s=CreateSequence("S1", ".afc..de.f");
+ BOOST_CHECK_EQUAL(s.GetString(),".afc..de.f");
+ s.Normalise();
+ BOOST_CHECK_EQUAL(s.GetString(),"AFCDEF");
+ s=CreateSequence("S1", "-afc--de-f");
+ BOOST_CHECK_EQUAL(s.GetString(),"-afc--de-f");
+ s.Normalise();
+ BOOST_CHECK_EQUAL(s.GetString(),"AFCDEF");
+ s=CreateSequence("S1", ".afc-.de-f");
+ BOOST_CHECK_EQUAL(s.GetString(),".afc-.de-f");
+ s.Normalise();
+ BOOST_CHECK_EQUAL(s.GetString(),"AFCDEF");
+}
+
BOOST_AUTO_TEST_CASE(seq_onelettercode)
{
SequenceHandle s=CreateSequence("S1", "abfcdadeaf");
diff --git a/scripts/ost_config.in b/scripts/ost_config.in
index f109f8b2d6188c65adb7c5157fc70b42692869d4..afce131f195b2f17c0198ac7439402916b15f4fb 100644
--- a/scripts/ost_config.in
+++ b/scripts/ost_config.in
@@ -53,6 +53,14 @@ if [ -n "$DNG_ATTACH_VALGRIND" ]; then
pyexec="`which valgrind`#--leak-check=full#$pyexec"
fi
+if [ -n "$DNG_ATTACH_VALGRIND_MASSIF" ]; then
+ if [ ! -x `which valgrind` ]; then
+ echo "Error: valgrind not found!"
+ exit
+ fi
+ pyexec="`which valgrind`#--tool=massif#$pyexec"
+fi
+
if [ -n "$DNG_PROFILE" ]; then
if [[ "$DNG_PROFILE" == "yep" ]]; then
echo "Profiling activated using yep"
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 09251bcfb6a29a38c36ba902498745bbf8ec23e5..2a445620212e97165e53b7f9bf3592ecd5a21387 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -10,6 +10,7 @@
#include <ost/conop/amino_acids.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/mol/pdb_writer.hh>
+#include <ost/io/mol/mmcif_reader.hh>
#include <ost/io/io_exception.hh>
#include <ost/conop/nonstandard.hh>
#if defined(__APPLE__)
@@ -26,15 +27,25 @@ namespace fs=boost::filesystem;
EntityHandle load_x(const String& file, const IOProfile& profile)
{
try {
- PDBReader reader(file, profile);
- if (reader.HasNext()) {
- EntityHandle ent=CreateEntity();
- reader.Import(ent);
+ EntityHandle ent = CreateEntity();
+ if(file.compare(file.length() - 6, 6, ".mmcif") == 0 ||
+ file.compare(file.length() - 4, 4, ".cif") == 0){
+ MMCifReader reader(file,ent,profile);
+ reader.Parse();
return ent;
}
- std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
+ //if its not mmcif, we assume the file to be in pdb format without even
+ //looking at the filename
+ else{
+ PDBReader reader(file, profile);
+ if (reader.HasNext()) {
+ reader.Import(ent);
+ return ent;
+ }
+ std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
<< "Are you sure this is a PDB file?" << std::endl;
- return EntityHandle();
+ return EntityHandle();
+ }
} catch (std::exception& e) {
std::cerr << "ERROR: " << e.what() << std::endl;
return EntityHandle();