Citrus Sinensis ID: 001843

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------101
Protein Sequence
MDAESSVSLLIVKLKTLFPAADEGATISSWTQKRVLKAIESLQLLIKNKKPCLDSSAGGEAADDEARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLRLRSLFSFGMNKFKRELEIRGSSSSSSSSYEHQQQLVEVNDTGPSFSPYQGGYSTHRSQQQRWARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTFGSVADIERVLGINVYVRMNQWSSSSQEDHY
Secondary Structure (PSIPRED)
ccccccEEEEEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHcEEEEEccccccHHHHHHHHHccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHcHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccEEEEEEEccccccHHHHHHHHcccccccccccccEEEEEcccccccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccEEEEEEEccccccHHHHHHHHHHccccccccEEEEEcccccHHcccccccccEEEcccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccHHHHHHHHHHcccHHHHHHHccccccccHHHHHHcccccccccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHcccEEEEEEcccccccEEEEcHHHHHHHHHHHHHHccEEEccccccccccccccccccEEEEEEEcccccccccccccccEEEEEEEcccccccccccHHHHHccccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccHHHHHccccccEEEEEEcccccHHHHHHHHHHHHccccccEEEEEEccccccccccccccccccEEEEEEEcccccccccccccccEEEEEEEcccccccccccccccccccEEEEEccEEEccEEEEcccccccccEEEEccccccccEEEcccccccccEEEEEcccccccccccccccccccEEEEEcccccccccccccccccccEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHcccccccccEcHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEccccccHHHHHHHHHHHcHHHHHHHHHHHHHHccHHHHHHHHHHHHHHccHcccHHHHHHHccHHHHHHHccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEEcccccccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHccccccccccEEEEEEccccEEEEEEcccccEEccccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHHccccHHHHHccHHHccHHHHHHEEEEEEccccccEcHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHccEEEEEcccccccEEEEEHHHHHHHHHHHHccccEEEEEEccccccccccccccccEEEEEEEEccccccccccccccccEEEEEccccccccccccccccccccccccccccEEEEEEccccccccccccccccccccEEEEcccccccccccccccccccEEEEEccccccccccccccccccEEEEcccccccccccccccccccccEEEEEEccccccccHHHHccccHccEEEEEcccccccccHHHHHHHHHccccccEEEEEcccccccccccccccccccEEEEccccccccccHHcccccccEEEEEEccccccccccHHcccccccEEEEccccHHcccccccccccccccEEEEcccccHccccccccccccccEEEEcccccHccccccccccccccEEEEccccHHccccccccccccccEEEccHHHccccccccc
Coil and Loop (DISEMBL)
MDAESSVSLLIVKLKTlfpaadegatisSWTQKRVLKAIESLQLLIKnkkpcldssaggeaadDEARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVttfpfssfenlRLRSLFSFGMNKFKRELeirgssssssssyEHQQQLVevndtgpsfspyqggysthrsQQQRWARISDYfcaedetdVLGLERQVKELLHVLipehhgindadvstkkivDGYEYArssgeeitelpipeqegggdalsneeeesgrcqssstttTTTQVIALIGkagsgkttLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKlcsftqcgkiiittsstedfveplgaafstlhvpglgkneSWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLlstkqpsyEEWSKVIERANGDNLVALCYQdlpaqvkpcilymglfpreyeipVRRLIHLWcaegfappdldliaSEEDLAEMYLEELVTRHMIQVIRWrldgspktccmpgvlydilrpkaedigflyhhhhpqrlnssakslPKFAVRRLAAnlgsnsfpysSLLSWRLHSYLvfdsrirgtpakQIGIILGKCISkrrlgmlkvldlegvykpmltnnnalgrlpfleylglrstfidslpdstpILFCLAtldvshtkvqrlpyafwpsrhlYLNWIFLATnvfrhpqfvkWETSLQTLWGLCikadevqsLDYFRRLTSLRKlglkcssttstSLKKEIIGAVLQLSELHSLKlicetpsylplleMAEHYKLQKLYlsghlppnsvigdrsfppnvVTLTLSQLrleydpmpilgRLRQLKILRLFggsytgeemscssgefpnLLVLKLWKLNRLRQWRikegampclrqleirscgylvpptglkhVTSSLREFLLtnmpstfgsvaDIERVLGINVYVRMnqwssssqedhy
Flexible Loop (DISEMBL)
MDAESSVSLLIVKLKTlfpaadegatisswtqKRVLKAIESLQLLIKNKKPCLDSSAGGEAADDEARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLRLRSLFSFGMNKFKRELEIRGSSSSSSSSYEHQQQLVEVNDTGPSFSPYQGGYSTHRSQQQRWARISDYFCAEDETDVLGLERQVKELLHVLipehhgindadvstkkIVDGYEYARssgeeitelpipeqEGGGDALSNEEEEsgrcqssstttttTQVIALigkagsgkttlarIVYNRvyvkrhftkrawvhipimSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSrirgtpakqigiilgkciskrrLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTslrklglkcssttstslkKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNsvigdrsfppNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTFGSVADIERVLGINVYVRmnqwssssqedhy
Low Complexity Region (SEG)
MDAESSVSLLIVKLKTLFPAADEGATISSWTQKRVLKAIESLQLLIKNKKPCLDSSAGGEAADDEARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLRLRSLFSFGMNKFKRELEIRGssssssssYEHQQQLVEVNDTGPSFSPYQGGYSTHRSQQQRWARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQsssttttttQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDglplrvvllagllSTKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRklglkcssttstslkkEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPnllvlklwklnrlrQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTFGSVADIERVLGINVYVRMNQWSSSSQEDHY
Disordered region (IsUnstruct)
*******SLLIVKLKTLFPAADEGATISSWTQKRVLKAIESLQLLIKNKKPCL************ARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLRLRSLFSFGMNKFK***********************************************RWARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEY*********************************************IALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFL******************FAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLG**************IIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTFGSVADIERVLGINVYVRMNQW*********
Disordered Region (DISOPRED)
*****SV**LIVKLKTLFPAADEGATISSWTQKRVLKAIESLQLLIKN***************DEARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLR*********NKF**E***************HQQQLVEVNDTGPSFSPYQGGYSTHRS**********YFCAEDETDVLGLERQVKELLHVLIPEHH************************************GGDALSNEEEESGRCQSSSTTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI**************ELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDL*****EEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHH**************AVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTF**********GINVYVRM************
Disordered Region (DISEMBL)
MDAESSVSLLIVKLKTLFPAADEGATISSWTQKRVLKAIESLQLLIKNKKPCLDSSAGGEAADDEARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLRLRSLFSFGMNKFKREL******************LVEVNDTGPSFSPYQ************WARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPE**************************TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTFGSVADIERVLGINVYVRMNQ**********
Disordered Region (DISPRO)
*****SVSLLIVKLKTLFPAADEGATISSWTQKRVLKAIESLQLLIKNKKPCLD******AADDEARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLRLRSLFSFGMNKFKRELEIRGSSSSSSSSYEHQQQLVEVNDTGPSFSPYQGGYSTHRSQQQRWARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVD**********************GGDALSNEEEESGRCQSSSTTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTFGSVADIERVLGINVYVRMNQWSSSS*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDAESSVSLLIVKLKTLFPAADEGATISSWTQKRVLKAIESLQLLIKNKKPCLDSSAGGEAADDEARFMQAFYSAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLRLRSLFSFGMNKFKRELEIRGSSSSSSSSYEHQQQLVEVNDTGPSFSPYQGGYSTHRSQQQRWARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTFGSVADIERVLGINVYVRMNQWSSSSQEDHY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	1007	2.2.26 [Sep-21-2011]
P0C8S1	906	Probable disease resistan	yes	no	0.720	0.801	0.282	4e-52
Q9FJB5	901	Disease resistance RPP8-l	no	no	0.662	0.740	0.275	3e-49
Q9XIF0	906	Putative disease resistan	no	no	0.652	0.725	0.273	6e-49
Q8W474	907	Probable disease resistan	no	no	0.633	0.703	0.285	1e-48
Q39214	926	Disease resistance protei	no	no	0.658	0.715	0.263	2e-47
Q8W4J9	908	Disease resistance protei	no	no	0.655	0.726	0.275	9e-46
Q9STE5	847	Putative disease resistan	no	no	0.613	0.729	0.291	2e-45
P0DI18	1049	Probable disease resistan	no	no	0.638	0.612	0.274	8e-45
P0DI17	1049	Probable disease resistan	no	no	0.638	0.612	0.274	8e-45
Q8W3K3	910	Putative disease resistan	no	no	0.640	0.708	0.272	1e-44

>sp|P0C8S1|RP8L2_ARATH Probable disease resistance RPP8-like protein 2 OS=Arabidopsis thaliana GN=RPP8L2 PE=1 SV=1

 Score =  207 bits (527), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 237/839 (28%), Positives = 379/839 (45%), Gaps = 113/839 (13%)

Query: 195 GLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALS 254
           G+++QV+ L   L+      +D +  TK+I +     +S G  I  +     +GGG +LS
Sbjct: 90  GIKKQVRTLACFLVDRRKFASDIEGITKRISEVIVGMQSLG--IQHIA----DGGGRSLS 143

Query: 255 NEEEESGRCQSSSTTT---------------------TTTQVIALIGKAGSGKTTLARIV 293
            +E +    Q+ S  +                      + QV+++ G  G GKTTLAR V
Sbjct: 144 LQERQREIRQTFSRNSESDLVGLDQSVEELVDHLVENDSVQVVSVSGMGGIGKTTLARQV 203

Query: 294 YNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI---DESLLKV-EATLSAEELMWR 349
           ++   V+RHF   +WV +        +DV   IL+ +   DE ++++ E TL  E     
Sbjct: 204 FHHDIVRRHFDGFSWVCVS--QQFTRKDVWQRILQDLRPYDEGIIQMDEYTLQGE----- 256

Query: 350 ITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDF---VEPLGA 406
           + + L+   +L+V+++    K + WD    K     + G  ++ TS  E      +P   
Sbjct: 257 LFELLESGRYLLVLDDV--WKEEDWDRI--KAVFPHKRGWKMLLTSRNEGLGLHADPTCF 312

Query: 407 AFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAG 466
           AF       L   +SW+LF +      D  + +  E   + K+++  C GLPL V +L G
Sbjct: 313 AFRP---RILTPEQSWKLFERIVSSRRDKTEFKVDE--AMGKEMVTYCGGLPLAVKVLGG 367

Query: 467 LLSTKQPSYEEWSKV-------IERANG---DN------LVALCYQDLPAQVKPCILYMG 510
           LL+ K  +  EW +V       I   +G   DN      +++L Y+DLP Q+K C  Y+ 
Sbjct: 368 LLAKKH-TVLEWKRVHSNIVTHIVGKSGLSDDNSNSVYRVLSLSYEDLPMQLKHCFFYLA 426

Query: 511 LFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGS 570
            FP +Y+I V+ L + W AEG   P  D  ++ +D  E YLEELV R+M+ V    L   
Sbjct: 427 HFPEDYKIDVKILFNYWVAEGIITPFHD-GSTIQDTGESYLEELVRRNMVVVEESYLTSR 485

Query: 571 PKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYS 630
            + C M  ++ ++   KA++  F+     P   +++  +      RRL  + G+      
Sbjct: 486 IEYCQMHDMMREVCLSKAKEENFIRVVKVPTTTSTTINAQSPCRSRRLVLHSGNALHMLG 545

Query: 631 SLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNAL 690
              + +  S L+F     G   K       +C     L +L+VLDL  V        +++
Sbjct: 546 HKDNKKARSVLIF-----GVEEKFWKPRGFQC-----LPLLRVLDLSYVQFEGGKLPSSI 595

Query: 691 GRLPFLEYLGLRSTFIDSLPDSTPILFCLATLD--VSHTKVQRLPYAFWPSRHLYLNWIF 748
           G L  L +L L    +  LP S   L  L  L+  V+   +  +P      + L   ++ 
Sbjct: 596 GDLIHLRFLSLYEAGVSHLPSSLGNLKLLLCLNLGVADRLLVHVPNVLKEMQEL--RYLR 653

Query: 749 LATNVFRHPQFVKWE----TSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTST 804
           L  ++   P   K E     +L++L     K   V  L    R+T L  L +  S   + 
Sbjct: 654 LPRSM---PAKTKLELGDLVNLESLTNFSTKHGSVTDL---LRMTKLSVLNVIFSGECTF 707

Query: 805 SLKKEIIGAVLQLSELHSLKLI-------CETPSYLPLLEMAEHYKLQKLYLSGHLP--P 855
                    +L L EL +L+ +           ++   L + +   L+ L LS HLP  P
Sbjct: 708 ET------LLLSLRELRNLETLSFHDFQKVSVANHGGELLVLDFIHLKDLTLSMHLPRFP 761

Query: 856 NSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFP 915
           +       FPP++  + L   R+E DPMPIL +L  LK + L  G++ G  M CS G FP
Sbjct: 762 DQY----RFPPHLAHIWLIGCRMEEDPMPILEKLLHLKSVYLSSGAFLGRRMVCSKGGFP 817

Query: 916 NLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVP-PTGLKHVTSSLREFLLTNM 973
            LL LK+     L +WR++EG+MPCLR L I +C  L   P GLK+VT  L+E  +  M
Sbjct: 818 QLLALKMSYKKELVEWRVEEGSMPCLRTLTIDNCKKLKQLPDGLKYVT-CLKELKIERM 875

Potential disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJB5|RP8L3_ARATH Disease resistance RPP8-like protein 3 OS=Arabidopsis thaliana GN=RPP8L3 PE=2 SV=1

 Score =  197 bits (502), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 208/755 (27%), Positives = 336/755 (44%), Gaps = 88/755 (11%)

Query: 272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI- 330
             QV+++ G  G GKTTLAR +++   V+RHF   AWV +        + V   IL+++ 
Sbjct: 182 NIQVVSISGMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVS--QQFTQKHVWQRILQELR 239

Query: 331 --DESLLKV-EATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQC 387
             D  +L++ E T+       ++ Q L+   +L+V+++    K + WD    K     + 
Sbjct: 240 PHDGEILQMDEYTIQG-----KLFQLLETGRYLVVLDDV--WKEEDWDRI--KEVFPRKR 290

Query: 388 GKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLK 447
           G  ++ TS  E           +     L   ESW+LF    RI     ++   E+  + 
Sbjct: 291 GWKMLLTSRNEGVGLHADPTCLSFRARILNPKESWKLF---ERIVPRRNETEYEEMEAIG 347

Query: 448 KQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANG---------DN-------LV 491
           K+++  C GLPL V +L GLL+ K  +  EW +V E             DN       ++
Sbjct: 348 KEMVTYCGGLPLAVKVLGGLLANKHTA-SEWKRVSENIGAQIVGKSCLDDNSLNSVYRIL 406

Query: 492 ALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYL 551
           +L Y+DLP  +K C LY+  FP +Y+I  R L   W AEG     L ++ S ED    YL
Sbjct: 407 SLSYEDLPTDLKHCFLYLAHFPEDYKIKTRTLYSYWAAEGIY-DGLTILDSGED----YL 461

Query: 552 EELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLP 611
           EELV R+++   +  L    K C M  ++ ++   KA+   FL     P   ++     P
Sbjct: 462 EELVRRNLVIAEKSNLSWRLKLCQMHDMMREVCISKAKVENFLQIIKVPTSTSTIIAQSP 521

Query: 612 KFAVRRLAANLG------SNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISK 665
             + RRL  + G       +     SLL   L   L   S  R                 
Sbjct: 522 SRS-RRLTVHSGKAFHILGHKKKVRSLLVLGLKEDLWIQSASRF---------------- 564

Query: 666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVS 725
           + L +L+VLDL  V        +++G L  L +L L    +  LP +   L  +  L++ 
Sbjct: 565 QSLPLLRVLDLSSVKFEGGKLPSSIGGLIHLRFLSLHQAVVSHLPSTIRNLKLMLYLNL- 623

Query: 726 HTKVQ---RLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWE-TSLQTLWGLCIKADEVQS 781
           H  +     +P        L L ++ L  ++    +    +  +L+ LW    +   V  
Sbjct: 624 HVAIGVPVHVPNVL--KEMLELRYLSLPLDMHDKTKLELGDLVNLEYLWCFSTQHSSVTD 681

Query: 782 LDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLE---M 838
           L    R+T LR  G+  S   +    + +  ++ Q  +L +L  I    +Y+       +
Sbjct: 682 L---LRMTKLRFFGVSFSERCTF---ENLSSSLRQFRKLETLSFIYSRKTYMVDYVGEFV 735

Query: 839 AEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLF 898
            +   L+KL L  HL  + +      PP++  + L    +E DPMPIL +L  LK + L 
Sbjct: 736 LDFIHLKKLSLGVHL--SKIPDQHQLPPHIAHIYLLFCHMEEDPMPILEKLLHLKSVELR 793

Query: 899 GGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVP-PTG 957
             ++ G  M CS G FP L  L++ + + L +W ++EG+MPCLR L I SC  L   P G
Sbjct: 794 RKAFIGRRMVCSKGGFPQLRALQISEQSELEEWIVEEGSMPCLRDLIIHSCEKLEELPDG 853

Query: 958 LKHVTSSLREFLLTNMPSTFGSVADIERVLGINVY 992
           LK+VT SL+E  +  M   +      E+++G + Y
Sbjct: 854 LKYVT-SLKELKIEGMKREWK-----EKLVGEDYY 882

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XIF0|DRL13_ARATH Putative disease resistance protein At1g59780 OS=Arabidopsis thaliana GN=At1g59780 PE=2 SV=1

 Score =  196 bits (499), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 201/735 (27%), Positives = 328/735 (44%), Gaps = 78/735 (10%)

Query: 272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQID 331
           ++  +++ G  G GKTTLAR +++   VK HF   AWV +        +DV   IL  + 
Sbjct: 179 SSHGVSITGLGGLGKTTLARQIFDHDKVKSHFDGLAWVCVS--QEFTRKDVWKTILGNLS 236

Query: 332 ESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKII 391
                 ++ L  +++  ++ Q L+    LIV ++    K + W              K++
Sbjct: 237 PKY--KDSDLPEDDIQKKLFQLLETKKALIVFDDL--WKREDWYRIAPMFPERKAGWKVL 292

Query: 392 ITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR--SSELIKLKKQ 449
           +T  S  D + P    F       L  +E W+L  + A   +  +       E++K+ K+
Sbjct: 293 LT--SRNDAIHPHCVTFKP---ELLTHDECWKLLQRIAFSKQKTITGYIIDKEMVKMAKE 347

Query: 450 ILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIER-----------------ANGDNLVA 492
           +   C  LPL V LL GLL  K  +  +W  + E                  ++ +++++
Sbjct: 348 MTKHCKRLPLAVKLLGGLLDAKH-TLRQWKLISENIISHIVVGGTSSNENDSSSVNHVLS 406

Query: 493 LCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLE 552
           L ++ LP  +K C+LY+  +P ++EI + RL ++W AEG   P     A+  D+A++Y+E
Sbjct: 407 LSFEGLPGYLKHCLLYLASYPEDHEIEIERLSYVWAAEGITYPGNYEGATIRDVADLYIE 466

Query: 553 ELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPK 612
           ELV R+M+   R  L    + C +  ++ +I   KA++  FL     P   +S       
Sbjct: 467 ELVKRNMVISERDALTSRFEKCQLHDLMREICLLKAKEENFLQIVTDPTSSSSVHSLASS 526

Query: 613 FAVRRLAANL----GSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRL 668
            + R +  N     G N    S L S      L+F       P       +G    +  L
Sbjct: 527 RSRRLVVYNTSIFSGENDMKNSKLRS------LLF------IPVGYSRFSMGSNFIE--L 572

Query: 669 GMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLD--VSH 726
            +L+VLDL+G         +++G+L  L+YL L    +  LP S   L  L  L+  ++ 
Sbjct: 573 PLLRVLDLDGAKFKGGKLPSSIGKLIHLKYLSLYQASVTYLPSSLRNLKSLLYLNLRINS 632

Query: 727 TKVQRLPYAF---WPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLD 783
            ++  +P  F      R+L L W   +         +K    L+TL     K   V  L 
Sbjct: 633 GQLINVPNVFKEMLELRYLSLPWERSSLTKLELGNLLK----LETLINFSTKDSSVTDL- 687

Query: 784 YFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYK 843
              R+T LR L +  S      L  E + + L +  L  L+ +  TPS     E +  +K
Sbjct: 688 --HRMTKLRTLQILISGE---GLHMETLSSALSM--LGHLEDLTVTPS-----ENSVQFK 735

Query: 844 LQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYT 903
             KL     LP       + FP ++ T++L    LE DPMP L +L QLK++ L+  +Y 
Sbjct: 736 HPKLIYRPMLPDV-----QHFPSHLTTISLVYCFLEEDPMPTLEKLLQLKVVSLWYNAYV 790

Query: 904 GEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVP-PTGLKHVT 962
           G  M C+ G FP L  L++W L+ L +W ++EG+MP L  L I  C  L   P GL+ + 
Sbjct: 791 GRRMVCTGGGFPPLHRLEIWGLDALEEWIVEEGSMPLLHTLHIVDCKKLKEIPDGLRFI- 849

Query: 963 SSLREFLLTNMPSTF 977
           SSL+E  +      F
Sbjct: 850 SSLKELAIRTNEKVF 864

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W474|DRL7_ARATH Probable disease resistance protein At1g58390 OS=Arabidopsis thaliana GN=At1g58390 PE=2 SV=4

 Score =  196 bits (497), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 212/742 (28%), Positives = 327/742 (44%), Gaps = 104/742 (14%)

Query: 272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQID 331
             QV+++ G  G GKTTLAR V+N   VK  F + AWV +        ++V   IL+ + 
Sbjct: 182 NVQVVSITGMGGLGKTTLARQVFNHEDVKHQFDRLAWVCVS--QEFTRKNVWQMILQNLT 239

Query: 332 ESLLKVEA-TLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKI 390
               K E   +   EL  ++ Q L+ S  LIV ++    K + WD  L K       G  
Sbjct: 240 SREKKDEILQMEEAELHDKLFQLLETSKSLIVFDDI--WKDEDWD--LIKPIFPPNKGWK 295

Query: 391 IITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLKKQ 449
           ++ TS  E         +       L   +SW LF + A   +D  +S+   E+  + KQ
Sbjct: 296 VLLTSQNESVAVRGDIKYLNFKPECLAIEDSWTLFQRIAFPKKDASESKVDEEMEDMGKQ 355

Query: 450 ILNICDGLPLRVVLLAGLLSTKQPSYEEW--------SKVIERANGDN-----LVALCYQ 496
           +L  C GLPL + +L GLL+ K  +  +W        S ++ R + +N     ++++ ++
Sbjct: 356 MLKHCGGLPLAIKVLGGLLAAKY-TMHDWERLSVNIGSDIVGRTSSNNSSIYHVLSMSFE 414

Query: 497 DLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASE--EDLAEMYLEEL 554
           +LP+ +K C LY+  FP +++I V +L + W AEG +  + D    E  +D+ + YLEEL
Sbjct: 415 ELPSYLKHCFLYLAHFPEDHKINVEKLSYCWAAEGISTAE-DYHNGETIQDVGQSYLEEL 473

Query: 555 VTRHMIQVIRWRLDGSPK---TCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSA--KS 609
           V R+MI    W  D +     TC +  ++ ++   KA++  FL        + SS+   S
Sbjct: 474 VRRNMII---WERDATASRFGTCHLHDMMREVCLFKAKEENFLQIAVKSVGVTSSSTGNS 530

Query: 610 LPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLG 669
                 RRL     +       + + +L S +V    +     K +G       S  RL 
Sbjct: 531 QSPCRSRRLVYQCPTTLHVERDINNPKLRSLVVLWHDLWVENWKLLGT------SFTRLK 584

Query: 670 MLKVLDL-----EGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDV 724
           +L+VLDL     EG+  P       +G L  L YL L+   +  LP S   L  L  L++
Sbjct: 585 LLRVLDLFYVDFEGMKLPF-----GIGNLIHLRYLSLQDAKVSHLPSSLGNLMLLIYLNL 639

Query: 725 S-HTKVQRLPYAFWPSRHL-YL---------------NWIFLATNVFRHPQFVKWETSLQ 767
              T+   +P  F     L YL               N + L T V+    F  W +S +
Sbjct: 640 DVDTEFIFVPDVFMRMHELRYLKLPLHMHKKTRLSLRNLVKLETLVY----FSTWHSSSK 695

Query: 768 TLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSEL-----HS 822
            L G+                T L  L ++ +  TST      I  +  L  L     HS
Sbjct: 696 DLCGM----------------TRLMTLAIRLTRVTSTETLSASISGLRNLEYLYIVGTHS 739

Query: 823 LKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDP 882
            K+  E         + +   L+ L L  ++P       + FP  +  + LS+  LE DP
Sbjct: 740 KKMREEGI-------VLDFIHLKHLLLDLYMPRQ-----QHFPSRLTFVKLSECGLEEDP 787

Query: 883 MPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLR 942
           MPIL +L  LK + L  GSY G  M CS G FP L  L++  LN+  +W ++EG+MP L 
Sbjct: 788 MPILEKLLHLKGVILLKGSYCGRRMVCSGGGFPQLKKLEIVGLNKWEEWLVEEGSMPLLE 847

Query: 943 QLEIRSCGYLVP-PTGLKHVTS 963
            L I  C  L   P GL+ + S
Sbjct: 848 TLSILDCEELKEIPDGLRFIYS 869

Possible disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39214|RPM1_ARATH Disease resistance protein RPM1 OS=Arabidopsis thaliana GN=RPM1 PE=1 SV=1

 Score =  191 bits (486), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 198/751 (26%), Positives = 347/751 (46%), Gaps = 88/751 (11%)

Query: 275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVED--RDVLADILKQIDE 332
           V+A++G  GSGKTTL+  ++    V+RHF   AWV I    ++ED  R ++ +  K+ D 
Sbjct: 195 VVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFYKEADT 254

Query: 333 SLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIII 392
            +     +L   EL+ ++ + L    +++V+++     + +W      L       ++++
Sbjct: 255 QIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDV--WTTGLWREISIALPDGIYGSRVMM 312

Query: 393 TTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILN 452
           TT        P G   +   +  L ++E+W LF  KA  A  + Q R+  L  + ++++ 
Sbjct: 313 TTRDMNVASFPYGIGSTKHEIELLKEDEAWVLFSNKAFPA-SLEQCRTQNLEPIARKLVE 371

Query: 453 ICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGD-----------NLVALCYQDLPAQ 501
            C GLPL +  L  ++STK+    EW KV    N +           +++ L + DLP  
Sbjct: 372 RCQGLPLAIASLGSMMSTKKFE-SEWKKVYSTLNWELNNNHELKIVRSIMFLSFNDLPYP 430

Query: 502 VKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQ 561
           +K C LY  LFP  Y +  +RLI +W A+ F  P   + A  E++A+ YL ELV R+M+Q
Sbjct: 431 LKRCFLYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKA--EEVADSYLNELVYRNMLQ 488

Query: 562 VIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAAN 621
           VI W   G PK   M  V+++I    ++   F   ++     + +A+++  +  R L   
Sbjct: 489 VILWNPFGRPKAFKMHDVIWEIALSVSKLERFCDVYNDDSDGDDAAETMENYGSRHLCI- 547

Query: 622 LGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYK 681
                    S+ +  LHS LV  S      AK    +L        L +L+ LDLE    
Sbjct: 548 --QKEMTPDSIRATNLHSLLVCSS------AKHKMELLPS------LNLLRALDLE---- 589

Query: 682 PMLTNNNALGRLP-------FLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPY 734
                ++++ +LP        L+YL L  T +  LP +   L  L TL+  H+K++ LP 
Sbjct: 590 -----DSSISKLPDCLVTMFNLKYLNLSKTQVKELPKNFHKLVNLETLNTKHSKIEELPL 644

Query: 735 AFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQT-----LWGLCIKADEVQSLDYFRRLT 789
             W  + L     +L T          W   L T     +W L     ++Q +D F    
Sbjct: 645 GMWKLKKLR----YLITFRRNEGHDSNWNYVLGTRVVPKIWQL----KDLQVMDCFNAED 696

Query: 790 SLRKLGLKC-SSTTSTSL-------KKEIIGAVLQLSELHSLKLIC---ETPSYLPLLEM 838
            L K  L C +  T  SL        +++  ++ ++  +  L L     E P  L + ++
Sbjct: 697 ELIK-NLGCMTQLTRISLVMVRREHGRDLCDSLNKIKRIRFLSLTSIDEEEP--LEIDDL 753

Query: 839 AEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLF 898
                ++KL+L+G L    V    +   N+  L L   +L+ + +  +  L +L  L  F
Sbjct: 754 IATASIEKLFLAGKL--ERVPSWFNTLQNLTYLGLRGSQLQENAILSIQTLPRLVWLS-F 810

Query: 899 GGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSC-GYLVPPTG 957
             +Y G  +  + G F NL +L++ ++  L +  I++GAM  L++L +R+C G    P G
Sbjct: 811 YNAYMGPRLRFAQG-FQNLKILEIVQMKHLTEVVIEDGAMFELQKLYVRACRGLEYVPRG 869

Query: 958 LKHVTSSLREFLLTNMPSTFGSVADIERVLG 988
           ++++  +L+E  L ++ +       +ER+ G
Sbjct: 870 IENLI-NLQELHLIHVSNQL-----VERIRG 894

Disease resistance (R) protein that specifically recognizes the AvrRpm1 type III effector avirulence protein from Pseudomonas syringae. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is phosphorylated by AvrRpm1. It is then degraded at the onset of the hypersensitive response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W4J9|RPP8_ARATH Disease resistance protein RPP8 OS=Arabidopsis thaliana GN=RPP8 PE=1 SV=2

 Score =  186 bits (472), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 202/732 (27%), Positives = 326/732 (44%), Gaps = 72/732 (9%)

Query: 274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI--- 330
           QV+++ G  G GKTTLAR V++   V+RHF   AWV +        + V   IL+++   
Sbjct: 186 QVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVS--QQFTQKHVWQRILQELQPH 243

Query: 331 DESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKI 390
           D  +L+++       L  ++ Q L+   +L+V+++    K + WD    K     + G  
Sbjct: 244 DGDILQMDEY----ALQRKLFQLLEAGRYLVVLDDV--WKKEDWDVI--KAVFPRKRGWK 295

Query: 391 IITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLKKQ 449
           ++ TS  E           T     L   ESW+L  +      D  + R   E+  + K+
Sbjct: 296 MLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPRRDETEVRLDEEMEAMGKE 355

Query: 450 ILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANG---------DN-------LVAL 493
           ++  C GLPL V  L GLL+ K  +  EW +V +             DN       +++L
Sbjct: 356 MVTHCGGLPLAVKALGGLLANKH-TVPEWKRVFDNIGSQIVGGSWLDDNSLNSVYRILSL 414

Query: 494 CYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEE 553
            Y+DLP  +K C L +  FP + EI    L + W AEG         ++ ED  E YLEE
Sbjct: 415 SYEDLPTHLKHCFLNLAHFPEDSEISTYSLFYYWAAEGIYDG-----STIEDSGEYYLEE 469

Query: 554 LVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKF 613
           LV R+++      L    K C M  ++ ++   KA++  FL     P   ++     P  
Sbjct: 470 LVRRNLVIADDNYLSWQSKYCQMHDMMREVCLSKAKEENFLQIIIDPTCTSTINAQSPSR 529

Query: 614 AVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKV 673
           + RRL+ + G            ++ S +V        P  +    +        L +L+V
Sbjct: 530 S-RRLSIHSGKAFHILGHKNKTKVRSLIV--------PRFEEDYWIRSASVFHNLTLLRV 580

Query: 674 LDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLP 733
           LDL  V         ++G L  L YL L    +  LP +   L  L  L++     + + 
Sbjct: 581 LDLSWVKFEGGKLPCSIGGLIHLRYLSLYEAKVSHLPSTMRNLKLLLYLNLRVDTEEPIH 640

Query: 734 YAFWPSRHLYLNWIFLATNVFRHPQFVKWE-TSLQTLWGLCIKADEVQSLDYFRRLTSLR 792
                   + L ++ L   +    +    +  +L+ L+G   +   V  L    R+T LR
Sbjct: 641 VPNVLKEMIQLRYLSLPLKMDDKTKLELGDLVNLEYLYGFSTQHSSVTDL---LRMTKLR 697

Query: 793 KLGLKCSS-----TTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAE----HY- 842
            L +  S      T S+SL+        +L  L +L  +    +Y+ +  M E    H+ 
Sbjct: 698 YLAVSLSERCNFETLSSSLR--------ELRNLETLNFLFSLETYM-VDYMGEFVLDHFI 748

Query: 843 KLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSY 902
            L++L L+  +  + +     FPP++V L L    +E DPMPIL +L  LK +RL   ++
Sbjct: 749 HLKQLGLAVRM--SKIPDQHQFPPHLVHLFLIYCGMEEDPMPILEKLLHLKSVRLARKAF 806

Query: 903 TGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVP-PTGLKHV 961
            G  M CS G FP L V+++ K + L +W ++EG+MPCLR L I  C  L   P GLK++
Sbjct: 807 LGSRMVCSKGGFPQLCVIEISKESELEEWIVEEGSMPCLRTLTIDDCKKLKELPDGLKYI 866

Query: 962 TSSLREFLLTNM 973
           T SL+E  +  M
Sbjct: 867 T-SLKELKIEGM 877

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. The interaction with TIP (TCV-interacting protein) may be essential for the recognition of the avirulence proteins, and the triggering of the defense response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9STE5|R13L2_ARATH Putative disease resistance RPP13-like protein 2 OS=Arabidopsis thaliana GN=RPP13L2 PE=3 SV=1

 Score =  184 bits (468), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 203/697 (29%), Positives = 338/697 (48%), Gaps = 79/697 (11%)

Query: 275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESL 334
           +I++ G  G GKT+LAR ++N   VK  F  R W ++        RD+L  I+  ++E+ 
Sbjct: 186 MISIFGMEGLGKTSLARKLFNSSDVKESFEYRVWTNVS--GECNTRDILMRIISSLEETS 243

Query: 335 LKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKL-CSFTQCGKIIIT 393
                 ++ +EL   +   L +  +L+V+++    +S+  +S    L CS+ Q  ++IIT
Sbjct: 244 EGELEKMAQQELEVYLHDILQEKRYLVVVDDI--WESEALESLKRALPCSY-QGSRVIIT 300

Query: 394 TSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKA-RIAEDVLQSRSSELIKLKKQILN 452
           TS      E       T ++  L   ESW LF KKA R    V Q    EL K+ K+++ 
Sbjct: 301 TS-IRVVAEGRDKRVYTHNIRFLTFKESWNLFEKKAFRYILKVDQ----ELQKIGKEMVQ 355

Query: 453 ICDGLPLRVVLLAGLLSTKQPSYEEWSKVIE--RANGDN-----LVALCYQDLPAQVKPC 505
            C GLP   V+LAGL+S K+P+  EW+ V    R   DN     L  L ++D+  ++K C
Sbjct: 356 KCGGLPRTTVVLAGLMSRKKPN--EWNDVWSSLRVKDDNIHVSSLFDLSFKDMGHELKLC 413

Query: 506 ILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRW 565
            LY+ +FP +YE+ V +LI L  AEGF   D ++  + ED+A  Y+E+LV   +++V++ 
Sbjct: 414 FLYLSVFPEDYEVDVEKLIQLLVAEGFIQEDEEM--TMEDVARYYIEDLVYISLVEVVKR 471

Query: 566 RLDGSPKTCCMPGVLYDILR----PKAEDIGFL--YHHHHPQRLNSSAKSLPKFAVRRLA 619
           +     K   M   ++D++R     K++++ F+  Y   H     SS  S      R + 
Sbjct: 472 K-----KGKLMSFRIHDLVREFTIKKSKELNFVNVYDEQH-----SSTTSR-----REVV 516

Query: 620 ANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGV 679
            +L  +++     ++ ++ S+L F  R R        I L       +L +L+VL+L G+
Sbjct: 517 HHLMDDNYLCDRRVNTQMRSFLFFGKR-RNDITYVETITL-------KLKLLRVLNLGGL 568

Query: 680 ------YKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLP 733
                 Y P  +  + +G L  L YLG+  T +++LPD    L  L TLD S    +R+ 
Sbjct: 569 HFICQGYSPW-SLPDVIGGLVHLRYLGIADTVVNNLPDFISNLRFLQTLDASGNSFERMT 627

Query: 734 --YAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSL 791
                   RHL        T  F     +    +LQTL    I +     L +   L +L
Sbjct: 628 DLSNLTSLRHL--------TGRFIGELLIGDAVNLQTLRS--ISSYSWSKLKH-ELLINL 676

Query: 792 RKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLI-CETPSYLPLLEMAEHYKLQKLYLS 850
           R L +      +  +K  +   ++ LS+L +L+++  E  S+    E    ++L  + L+
Sbjct: 677 RDLEIYEFHILNDQIKVPL--DLVSLSKLKNLRVLKIEVVSFSLFSEETVRFELL-VKLT 733

Query: 851 GHLPPNSVIGDRSFP-PNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSC 909
            H     +  D     P++ +LTL    L+ DPMP L +L++L+ L L+   Y G +M  
Sbjct: 734 LHCDVRRLPRDMDLIFPSLESLTLVT-NLQEDPMPTLQKLQRLENLVLYSCVYPGAKMFI 792

Query: 910 SSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEI 946
           ++  F  L  LK+  + RL +  I+E AMPCL +L +
Sbjct: 793 NAQGFGRLRKLKVI-IKRLDELEIEEEAMPCLMKLNL 828

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P0DI18|DRL45_ARATH Probable disease resistance protein RDL6 OS=Arabidopsis thaliana GN=RDL6 PE=2 SV=1

 Score =  183 bits (464), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 205/747 (27%), Positives = 332/747 (44%), Gaps = 104/747 (13%)

Query: 271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP--IMSMVEDRDVLADILK 328
              QV+++ G  G GKTTLA+ V+N   VK  F   +WV +      M   + +L D+  
Sbjct: 181 ANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDLKP 240

Query: 329 QIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCG 388
           + +E   K    ++ + L   + + L+ S  LIV+++   ++   W+  +  +   T+  
Sbjct: 241 KEEE---KKIMEMTQDTLQGELIRLLETSKSLIVLDDIWEKED--WE-LIKPIFPPTKGW 294

Query: 389 KIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLK 447
           K+++T S  E        ++       L   +SW LF + A   +D  + +   E  +L 
Sbjct: 295 KVLLT-SRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELG 353

Query: 448 KQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLV---------------- 491
           K ++  C GLPL + +L G+L+ K  S++ W ++ E   G +LV                
Sbjct: 354 KLMIKHCGGLPLAIRVLGGMLAEKYTSHD-WRRLSENI-GSHLVGGRTNFNDDNNNTCNY 411

Query: 492 --ALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPP---DLDLIASEEDL 546
             +L +++LP+ +K C LY+  FP +YEI V+ L + W AEG   P   D ++I    D+
Sbjct: 412 VLSLSFEELPSYLKHCFLYLAHFPDDYEINVKNLSYYWAAEGIFQPRHYDGEII---RDV 468

Query: 547 AEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSS 606
            ++Y+EELV R+M+   R       +TC +  ++ ++   KA++  FL          S+
Sbjct: 469 GDVYIEELVRRNMVISERDVKTSRFETCHLHDMMREVCLLKAKEENFL---QITSSRTST 525

Query: 607 AKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIG---IILGKCI 663
             SL     RRL             +   +L S +V    +  T     G   ++LG   
Sbjct: 526 GNSLSIVTSRRLVYQYPITLDVEKDINDPKLRSLVV----VANTYMFWGGWSWMLLGS-- 579

Query: 664 SKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLD 723
           S  RL +L+VLD+           +++G+L  L YL L+                     
Sbjct: 580 SFIRLELLRVLDIHRAKLKGGKLASSIGQLIHLRYLNLK--------------------- 618

Query: 724 VSHTKVQRLPYAFWPSRHL-YLNWIFLAT------NVFRHPQFVKW-------------- 762
             H +V  +PY+    + L YLN + L +      NV +  Q +++              
Sbjct: 619 --HAEVTHIPYSLGNLKLLIYLNLVILVSGSTLVPNVLKEMQQLRYLALPKDMGRKTKLE 676

Query: 763 ---ETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSE 819
                 L+TL     K     SL+  R +  LR L ++    TS       IG +  L  
Sbjct: 677 LSNLVKLETLKNFSTKN---CSLEDLRGMVRLRTLTIELRKETSLETLAASIGGLKYLES 733

Query: 820 LHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLE 879
           L    L  E  +    +     Y L+ L L  ++P  S   ++ FP ++ TL L   RLE
Sbjct: 734 LTITDLGSEMRTKEAGIVFDFVY-LKTLTLKLYMPRLS--KEQHFPSHLTTLYLQHCRLE 790

Query: 880 YDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMP 939
            DPMPIL +L QLK L L   S++G+EM CSSG FP L  L +  L     W+++E +MP
Sbjct: 791 EDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQLQKLSIKGLEEWEDWKVEESSMP 850

Query: 940 CLRQLEIRSCGYL--VPPTGL-KHVTS 963
            L  L+IR C  L  +P   L  H+TS
Sbjct: 851 VLHTLDIRDCRKLKQLPDEHLPSHLTS 877

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|P0DI17|DRL11_ARATH Probable disease resistance protein RF9 OS=Arabidopsis thaliana GN=RF9 PE=2 SV=1

 Score =  183 bits (464), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 205/747 (27%), Positives = 332/747 (44%), Gaps = 104/747 (13%)

Query: 271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP--IMSMVEDRDVLADILK 328
              QV+++ G  G GKTTLA+ V+N   VK  F   +WV +      M   + +L D+  
Sbjct: 181 ANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDLKP 240

Query: 329 QIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCG 388
           + +E   K    ++ + L   + + L+ S  LIV+++   ++   W+  +  +   T+  
Sbjct: 241 KEEE---KKIMEMTQDTLQGELIRLLETSKSLIVLDDIWEKED--WE-LIKPIFPPTKGW 294

Query: 389 KIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLK 447
           K+++T S  E        ++       L   +SW LF + A   +D  + +   E  +L 
Sbjct: 295 KVLLT-SRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELG 353

Query: 448 KQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLV---------------- 491
           K ++  C GLPL + +L G+L+ K  S++ W ++ E   G +LV                
Sbjct: 354 KLMIKHCGGLPLAIRVLGGMLAEKYTSHD-WRRLSENI-GSHLVGGRTNFNDDNNNTCNY 411

Query: 492 --ALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPP---DLDLIASEEDL 546
             +L +++LP+ +K C LY+  FP +YEI V+ L + W AEG   P   D ++I    D+
Sbjct: 412 VLSLSFEELPSYLKHCFLYLAHFPDDYEINVKNLSYYWAAEGIFQPRHYDGEII---RDV 468

Query: 547 AEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSS 606
            ++Y+EELV R+M+   R       +TC +  ++ ++   KA++  FL          S+
Sbjct: 469 GDVYIEELVRRNMVISERDVKTSRFETCHLHDMMREVCLLKAKEENFL---QITSSRTST 525

Query: 607 AKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIG---IILGKCI 663
             SL     RRL             +   +L S +V    +  T     G   ++LG   
Sbjct: 526 GNSLSIVTSRRLVYQYPITLDVEKDINDPKLRSLVV----VANTYMFWGGWSWMLLGS-- 579

Query: 664 SKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLD 723
           S  RL +L+VLD+           +++G+L  L YL L+                     
Sbjct: 580 SFIRLELLRVLDIHRAKLKGGKLASSIGQLIHLRYLNLK--------------------- 618

Query: 724 VSHTKVQRLPYAFWPSRHL-YLNWIFLAT------NVFRHPQFVKW-------------- 762
             H +V  +PY+    + L YLN + L +      NV +  Q +++              
Sbjct: 619 --HAEVTHIPYSLGNLKLLIYLNLVILVSGSTLVPNVLKEMQQLRYLALPKDMGRKTKLE 676

Query: 763 ---ETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSE 819
                 L+TL     K     SL+  R +  LR L ++    TS       IG +  L  
Sbjct: 677 LSNLVKLETLKNFSTKN---CSLEDLRGMVRLRTLTIELRKETSLETLAASIGGLKYLES 733

Query: 820 LHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLE 879
           L    L  E  +    +     Y L+ L L  ++P  S   ++ FP ++ TL L   RLE
Sbjct: 734 LTITDLGSEMRTKEAGIVFDFVY-LKTLTLKLYMPRLS--KEQHFPSHLTTLYLQHCRLE 790

Query: 880 YDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMP 939
            DPMPIL +L QLK L L   S++G+EM CSSG FP L  L +  L     W+++E +MP
Sbjct: 791 EDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQLQKLSIKGLEEWEDWKVEESSMP 850

Query: 940 CLRQLEIRSCGYL--VPPTGL-KHVTS 963
            L  L+IR C  L  +P   L  H+TS
Sbjct: 851 VLHTLDIRDCRKLKQLPDEHLPSHLTS 877

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W3K3|DRL8_ARATH Putative disease resistance protein At1g58400 OS=Arabidopsis thaliana GN=At1g58400 PE=3 SV=1

 Score =  182 bits (462), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 200/734 (27%), Positives = 336/734 (45%), Gaps = 89/734 (12%)

Query: 274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI--- 330
           Q++++ G  G GKTTLAR V+N   VK  F + AWV +        ++V   IL+ +   
Sbjct: 185 QIVSVTGMGGLGKTTLARQVFNHEDVKHQFDRLAWVCVS--QEFTRKNVWQMILQNLTSR 242

Query: 331 ---DESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQC 387
              DE L   EA L  E     + Q L+ S  LIV ++    K + W   +  +    + 
Sbjct: 243 ETKDEILQMEEAELHDE-----LFQLLETSKSLIVFDDI--WKEEDW-GLINPIFPPKKG 294

Query: 388 GKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKA--RIAEDVLQSRSSELIK 445
            K++IT S TE         +       L   ESW LF + A  R+ E   +    E+  
Sbjct: 295 WKVLIT-SRTETIAMHGNRRYVNFKPECLTILESWILFQRIAMPRVDESEFKV-DKEMEM 352

Query: 446 LKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIER-----------ANGDN----- 489
           + KQ++  C GLPL V +L GLL+ K  ++ +W ++ E            ++G+N     
Sbjct: 353 MGKQMIKYCGGLPLAVKVLGGLLAAKY-TFHDWKRLSENIGCHIVGRTDFSDGNNSSVYH 411

Query: 490 LVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEM 549
           +++L +++LP+ +K C LY+  FP ++ I V +L + W AEG   P      +  D+ E 
Sbjct: 412 VLSLSFEELPSYLKHCFLYLAHFPEDHNIKVEKLSYCWAAEGILEPRHYHGQTIRDVGES 471

Query: 550 YLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKS 609
           Y+EELV R+M+   R       + C +  ++ ++   KA++  F+        L  +A S
Sbjct: 472 YIEELVRRNMVIAERDVTTLRFEACHLHDMMREVCLLKAKEENFV---QIASILPPTANS 528

Query: 610 LPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLG 669
                 RR  +   +       + + +L S L+     R +       +LG   S  RL 
Sbjct: 529 QYPGTSRRFVSQNPTTLHVSRDINNPKLQSLLIVWENRRKSWK-----LLGS--SFIRLE 581

Query: 670 MLKVLDLEGVYKPMLTNNN---ALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSH 726
           +L+VLDL   YK      N    +G+L  L YL L    +  LP S   L  L  LD++ 
Sbjct: 582 LLRVLDL---YKAKFEGRNLPSGIGKLIHLRYLNLDLARVSRLPSSLGNLRLLIYLDINV 638

Query: 727 TKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKAD--------- 777
                       ++ L++    +  +  R+ + + + TS +   GLC   +         
Sbjct: 639 C-----------TKSLFVPNCLMGMHELRYLR-LPFNTSKEIKLGLCNLVNLETLENFST 686

Query: 778 EVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPS----YL 833
           E  SL+  R + SLR L +      S   K+ +  ++L +  L +L +   TP     + 
Sbjct: 687 ENSSLEDLRGMVSLRTLTIGLFKHIS---KETLFASILGMRHLENLSI--RTPDGSSKFK 741

Query: 834 PLLE---MAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLR 890
            ++E   + +   L++L L  ++P   +  ++ FP ++ +++L    L  DP+PIL +L 
Sbjct: 742 RIMEDGIVLDAIHLKQLNLRLYMP--KLPDEQHFPSHLTSISLDGCCLVEDPLPILEKLL 799

Query: 891 QLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCG 950
           +LK +RL   ++ G+ M  S G FP L  L +W L    +W ++EG+MP L  L I +C 
Sbjct: 800 ELKEVRLDFRAFCGKRMVSSDGGFPQLHRLYIWGLAEWEEWIVEEGSMPRLHTLTIWNCQ 859

Query: 951 YLVP-PTGLKHVTS 963
            L   P GL+ + S
Sbjct: 860 KLKQLPDGLRFIYS 873

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	1007
255544065	936	Disease resistance protein RPM1, putativ	0.685	0.737	0.436	1e-129
255544075	884	Disease resistance protein RPM1, putativ	0.681	0.776	0.403	1e-120
255538332	974	Disease resistance protein RPP13, putati	0.669	0.691	0.334	2e-93
147856113	2540	hypothetical protein VITISV_006121 [Viti	0.646	0.256	0.357	2e-90
359495927	1245	PREDICTED: putative disease resistance p	0.647	0.523	0.352	3e-90
147781606	1183	hypothetical protein VITISV_025760 [Viti	0.852	0.725	0.319	3e-90
225433944	1086	PREDICTED: disease resistance RPP8-like	0.852	0.790	0.318	5e-90
296081340	1282	unnamed protein product [Vitis vinifera]	0.647	0.508	0.352	8e-90
297743835	1020	unnamed protein product [Vitis vinifera]	0.684	0.675	0.336	1e-89
225433948	1045	PREDICTED: putative disease resistance p	0.660	0.636	0.358	3e-89

>gi|255544065|ref|XP_002513095.1| Disease resistance protein RPM1, putative [Ricinus communis] gi|223548106|gb|EEF49598.1| Disease resistance protein RPM1, putative [Ricinus communis]

 Score =  471 bits (1211), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 322/737 (43%), Positives = 429/737 (58%), Gaps = 47/737 (6%)

Query: 275 VIALIGKAGSGKTTLARIVYNRVY-VKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES 333
           VIA++G AGSGKTTL + +YNRV  VK+HF   AWV++      ++RDVL  IL+QI E 
Sbjct: 194 VIAVVGAAGSGKTTLVKFIYNRVQEVKQHFECCAWVNVS--EEFQERDVLISILRQISE- 250

Query: 334 LLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIIT 393
            +  E TLS E L  R+   L   T+LIV+++   + +  W+       +     ++I+T
Sbjct: 251 -VTEEETLSLEALRIRVKYFLSRRTYLIVLDDIHSRDA--WEILKFGFSTSVMGSRVILT 307

Query: 394 TSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNI 453
             S E     L    S   +  L   ESW+LFL+K R   +      SEL  L++ I+  
Sbjct: 308 MRSIE-VARSLTPWISLFQIRPLNPQESWQLFLQKLRRPAN-----GSELKSLQELIVRK 361

Query: 454 CDGLPLRVVLLAGLLSTKQPSYEEWSKVIE----RANGDNLVALCYQDLPAQVKPCILYM 509
           C GLPL VV L GLLSTK   Y EWS VIE    +++  N++A+ YQDLP+ VK C+LY 
Sbjct: 362 CAGLPLAVVTLGGLLSTK--PYAEWSMVIESDTFKSSSLNILAMSYQDLPSPVKSCLLYS 419

Query: 510 GLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDG 569
           GLFP+ +EIP+RRL+ LW AEG A          EDL E + EELV R+MI V +WRLDG
Sbjct: 420 GLFPKSHEIPIRRLLLLWLAEGLAISSHGGSIVPEDLVETHFEELVIRNMIVVEKWRLDG 479

Query: 570 SPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPY 629
           SPKTC +   LYD + P A D+GF + H      N   K  P F VRR+A  L  N +P 
Sbjct: 480 SPKTCKVQAALYDTILPTATDMGFFHVHR-----NYDYKDKPPFNVRRIAEYLDINCYPS 534

Query: 630 SSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNA 689
            +     L SY+ F++R   TPA Q+  +L K ISKR  G+L VLDLE VYKP+L+   A
Sbjct: 535 DTSHIGYLRSYISFNTRKGDTPADQVDNLLKK-ISKRGFGLLTVLDLEYVYKPVLSE--A 591

Query: 690 LGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPS---RHLYLNW 746
           LG+L  L YLGLR TF+D +P+S   L CL TLDV HT +  LP + W +   RHLY+N 
Sbjct: 592 LGKLLHLRYLGLRWTFLDWIPESIGKLPCLETLDVKHTNIPALPISIWKAKKLRHLYMND 651

Query: 747 IFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSL 806
           I    + F+        T+LQTLWGL +       +++ ++LT+LRKLGL C  ++    
Sbjct: 652 IHFGMS-FQKQGIKVSLTNLQTLWGLLV-GKSCSVINWLQQLTNLRKLGLTCLDSSV--- 706

Query: 807 KKEIIGAVLQLSE-LHSLKL--ICE--TPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGD 861
            ++II  + +L E L SL+L  I E   PS L L  M +H KL +L+L G L        
Sbjct: 707 -QKIINWIPELKENLESLRLRSINEFNEPSDLDLGTMKQHKKLSELHLFGRL---VTFDM 762

Query: 862 RSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLK 921
              PPN+  LTLS  +LE DPMPILG+L +L ILRLF  SY G++MS     FP L VLK
Sbjct: 763 HELPPNLTMLTLSVSQLEQDPMPILGKLPRLSILRLFANSYLGKQMSSPRNGFPELRVLK 822

Query: 922 LWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPSTFGSVA 981
           LW L  L +W ++EG+M  L++LEIR C  L  P GL ++ ++L E  LTNMP  F  VA
Sbjct: 823 LWMLEELEEWTVEEGSMRELQKLEIRCCTNLKLPGGLYNL-AALDELTLTNMPGKF--VA 879

Query: 982 DIERVLGINVYVRMNQW 998
           DI      +V +  + W
Sbjct: 880 DIRTNTKRSVKISTHYW 896

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255544075|ref|XP_002513100.1| Disease resistance protein RPM1, putative [Ricinus communis] gi|223548111|gb|EEF49603.1| Disease resistance protein RPM1, putative [Ricinus communis]

 Score =  440 bits (1132), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 298/738 (40%), Positives = 421/738 (57%), Gaps = 52/738 (7%)

Query: 275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESL 334
           +I+++G+ GSGKTTL + +Y+ V VK+HF   AWV++      E RDVL  IL+Q+  ++
Sbjct: 178 LISVVGEGGSGKTTLVKSMYDSVEVKQHFVCCAWVYVS--EKFEVRDVLTGILRQV--TV 233

Query: 335 LKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITT 394
           +K E  L  E L+ R+        +LIV+++       VW +      +  +  + +I T
Sbjct: 234 VKDEEKLPLESLLKRVRDFFLWKKYLIVLDDIPS--PDVWSTIKYAFPNSARAARRVILT 291

Query: 395 SSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNIC 454
               +    +    S   +  +   ESW LFLKK R AED      + +  LK+ IL+ C
Sbjct: 292 LPKIEVARAIDPRISLFQIRRMNHEESWALFLKKVRTAED------NSIRSLKENILSKC 345

Query: 455 DGLPLRVVLLAGLLSTKQPSYEEWSKVIERA--------NGDNLVALCYQDLPAQVKPCI 506
           DGLPL +V LAGLLST+ P+  +WS++I++A        +  N++A  ++DL   +K C+
Sbjct: 346 DGLPLAIVALAGLLSTRPPN--QWSRLIDQATVGADQSSSSSNILAAGFRDLLPSLKSCL 403

Query: 507 LYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIAS---EEDLAEMYLEELVTRHMIQVI 563
           LYM LFP+  EI +RRL  LW AEG   P +   +    +EDLA+ Y E+LV+R+MI+V+
Sbjct: 404 LYMSLFPKSREIKLRRLFGLWLAEGLTTPIVGESSKSIKKEDLAKSYFEKLVSRNMIEVV 463

Query: 564 RWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLG 623
           +WRLDGSPKTC +   L++ L   A  +GF   H HP     ++K   +F VRR+A  L 
Sbjct: 464 KWRLDGSPKTCYLSPTLHEALFHIAGKMGFF--HVHPL----TSKDTQQFNVRRIAEYLD 517

Query: 624 SNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPM 683
            N++  S      L SY+ F+SR   TPA  +  +L K I+KR  G+L VLDLE V++P 
Sbjct: 518 INTYLSSDPTIQDLRSYISFNSRKGDTPAGGVDKLLRKIIAKRGFGLLTVLDLENVHRPS 577

Query: 684 LTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPS---R 740
           L+    LG+L  L+YLGLR TF+DS+P     L CL TLD+ HT +  LP + W     R
Sbjct: 578 LS--ETLGKLLQLKYLGLRCTFLDSVPKCIGKLPCLETLDMKHTNITTLPISIWKVKKLR 635

Query: 741 HLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSS 800
           HLY+N I    ++ ++P        LQTL GL I  +    +     LT LRKLGL C  
Sbjct: 636 HLYMNEIHFDMSM-QNPSAGGCLPDLQTLSGLLI-GNNSSVIKLLEGLTGLRKLGLTC-- 691

Query: 801 TTSTSLKKEIIGAVLQLSELHSLKL--ICE--TPSYLPLLEMAEHYKLQKLYLSGHLPPN 856
               SL+K II  +  L  L SLKL  I E   PS L L+ + E+ KLQ+LYL G LP N
Sbjct: 692 -YKASLEK-IIQWLPTLKNLESLKLRSINELHQPSDLNLITLKENAKLQELYLLGKLPKN 749

Query: 857 SVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPN 916
             +     P N+   TLS  +L  DPMPILG+L  L ILR F  SY G+EM C  G FP 
Sbjct: 750 FAV--HQLPQNLRNFTLSVSKLHEDPMPILGKLNNLHILRFFAHSYLGKEMDCRKG-FPE 806

Query: 917 LLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTNMPST 976
           L VLKLW L  L +W ++EG+MP LR++EIR C  L    GL+ + +SL++  LT MP  
Sbjct: 807 LRVLKLWMLEELEEWTVEEGSMPKLRKVEIRCCIQLKQHRGLQ-LLASLKKLTLTAMPED 865

Query: 977 FGSVADIERVLGINVYVR 994
           F  VA+++  L  N+ ++
Sbjct: 866 F--VAEVKANLSQNIKIK 881

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538332|ref|XP_002510231.1| Disease resistance protein RPP13, putative [Ricinus communis] gi|223550932|gb|EEF52418.1| Disease resistance protein RPP13, putative [Ricinus communis]

 Score =  350 bits (899), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 274/819 (33%), Positives = 412/819 (50%), Gaps = 145/819 (17%)

Query: 216 DADVSTKKIVDGYEYARSS-----GEEITELPIPEQEGGGD-----ALSNEEEESGRCQS 265
           +A +S +K  D  +Y + +     G EI E  I E++          L ++ +  GR   
Sbjct: 258 EATISDEK--DNVQYVKPNIPSEPGAEINETTISEEKRPQQLPLIPGLDDDSDFIGRKVQ 315

Query: 266 SSTTTTTTQ-------VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI----PIM 314
           +   T   +       +I+++G AGSGKTT  R +YN+  + ++F  RAWV++    P  
Sbjct: 316 ADELTEVIRNHHKLRFLISVVGAAGSGKTTFLRNIYNKADIVQNFQLRAWVNVSEEFPET 375

Query: 315 SMVED-----RDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQ 369
            + +D     +++L DIL+Q+  + +K E  L  ++L  ++        FLIV+++   +
Sbjct: 376 VIPDDVEHKKKNLLIDILRQV--AAIKEEEKLPLDKLEEKVRDFFIRKRFLIVLDDV--K 431

Query: 370 KSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKA 429
            S +W+S      +     ++I+ T   +   E     F  + +  L  +ESW LFLKK 
Sbjct: 432 TSVMWESVKRTFPNSLNGSRMILITRDDKIAAEMNDQGFPPVKLLNLDIDESWALFLKKV 491

Query: 430 RIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERAN-GD 488
              E+ +   S     LK+ I + C GLPL +V+L GLLSTK P    WSK+++R + GD
Sbjct: 492 GQKEEGITDES-----LKQLIFDKCKGLPLAIVVLGGLLSTKDPG--SWSKMVDRLSFGD 544

Query: 489 N----LVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEE 544
           +    ++AL YQDL +++KPC+LY+GLFP+++EI VRRL  LW AEGFA P  +   + E
Sbjct: 545 DPSKAILALAYQDLASELKPCLLYLGLFPKDHEISVRRLFRLWAAEGFATPTKE-GETPE 603

Query: 545 DLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLN 604
            L E YL++L+ R+MI V +WR D SPK C +PG+LYD + P A +IGF    H  + LN
Sbjct: 604 FLVEKYLQDLIQRNMIDVSKWRSDESPKRCRVPGILYDNVFPSAAEIGFF---HVLRSLN 660

Query: 605 SSAKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCIS 664
              +      +RR+AA L   S P      + L SY+ F++R   TPA +I   + K I 
Sbjct: 661 YDQQC----NIRRVAAYLDI-SNPVLDRWVYNLRSYISFNTRKGDTPADEIDRFINKIIV 715

Query: 665 KRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPI-LFCLATLD 723
           KR  G+L VLDLE VYKP+LT    +G+L  L    L   + + L   T + L C     
Sbjct: 716 KRGFGLLTVLDLENVYKPVLT--ETIGKLIHLRKKSLGEDWFNRLKRLTKLGLTC----- 768

Query: 724 VSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLD 783
                        + S     NWI  +T                      ++A +++S+D
Sbjct: 769 ------------HFESLGQVTNWISKSTQ---------------------LRALKLRSID 795

Query: 784 YFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYK 843
            F R                         A L+L  ++  KL+ E               
Sbjct: 796 EFSR------------------------PADLELGTMNQHKLLSE--------------- 816

Query: 844 LQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYT 903
              LYL G L  +  I D   P ++  LTLS  +L+ DPM  LG+L  LK+LRLF  SY 
Sbjct: 817 ---LYLLGKL--SQAIDDYLLPQSLRMLTLSVSQLKNDPMQYLGQLPHLKVLRLFARSYL 871

Query: 904 GEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTS 963
           G EM+C +  FP L VLKLW L +L +W ++EG+MP L++LEIR C  L   +GL+++T+
Sbjct: 872 GSEMTCHAKGFPELRVLKLWMLEKLEKWTVEEGSMPLLKELEIRRCEALKETSGLQNLTT 931

Query: 964 SLREFLLTNMPSTFGSVADIERVL----GINVYVRMNQW 998
                 LTNMP+ F  VA IE  +    G  V V +N++
Sbjct: 932 LKEL-TLTNMPNDF--VAKIESSMEGISGRKVAVTVNKF 967

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147856113|emb|CAN82439.1| hypothetical protein VITISV_006121 [Vitis vinifera]

 Score =  340 bits (872), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 257/719 (35%), Positives = 360/719 (50%), Gaps = 68/719 (9%)

Query: 271  TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI 330
            T+  VI+++G  G GKTTLA+ +YN   V  HF  RAW         E  + L  I++Q 
Sbjct: 530  TSFSVISIVGMPGIGKTTLAKSIYNNKAVVDHFPFRAWTS-------ETWEFLEHIMRQ- 581

Query: 331  DESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKI 390
             E  L     ++ EE+  +    L     LIV ++A +  +  ++  +      +   ++
Sbjct: 582  -EICL-----MTLEEMRQKFISLLAGKRCLIVFDDAYN--ACFFNLLVTTFSDASNGSRL 633

Query: 391  IITTSSTEDFVEPLGAAFSTLHVPGL-GKNESWELFLKKARIAEDVLQSRSSELIKLKKQ 449
            I+TT S      P     S  H   L G +ESW LF    ++      +   +L+ L+++
Sbjct: 634  ILTTRSMS---LPSQLQKSVHHAVRLRGNDESWALFTHALKV------NIPQQLLTLRRE 684

Query: 450  ILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCY------QDLPAQVK 503
            I   C GLPL ++ LA LLS K  + EEW   I++ N D      Y      +DLP  ++
Sbjct: 685  IERTCGGLPLAIIKLANLLSQKGLTIEEWCTAIQQLNHDQEQLWSYHLSRINKDLPLYMR 744

Query: 504  PCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVI 563
             C+ Y GLFPR++EIP RRLI LW AEG      +  A E D+AE  L +L+   M+QV 
Sbjct: 745  QCLFYFGLFPRDFEIPARRLIALWVAEGLVQAKGEDEAPE-DVAERCLIKLIAEGMVQVT 803

Query: 564  RWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLG 623
            + + +G+ KTCC+P  L      KA++  FL  H       +S  S     + RLA +L 
Sbjct: 804  KKKRNGNIKTCCLPSALRQYWLSKAQETTFLQIHME----TTSHLSPSTGMISRLADHLD 859

Query: 624  SNSFPYSSLLSWRLH--------------SYLVFDSRIRGTPAKQIGIILGKCISKRRLG 669
                 +  +     H              S+L FD+R    P + +G  L +CIS R L 
Sbjct: 860  KEDVTFGHIHGCHDHMASSHLQPLYQQVISFLSFDTREGSKPGEDMGNFLHRCISGRCLL 919

Query: 670  MLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKV 729
             L+VLDLE V+KP L    ALG+L  L YLGLRSTF+D LP     L  L  LDV HT +
Sbjct: 920  QLRVLDLENVFKPKLPE--ALGKLNRLRYLGLRSTFLDMLPSFIKKLHSLQVLDVKHTNI 977

Query: 730  QRLPYAFW---PSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFR 786
              LP   W     R LYLN     + +   PQ   + T LQ L GL +  +E    D   
Sbjct: 978  TTLPSPVWNLQQLRILYLNE-RCHSKLMPQPQAGSFST-LQVLVGLLVD-EETPVKDGLD 1034

Query: 787  RLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL--ICETPSY--LPLLEMAEHY 842
            R  +LRKLGL C   +S   ++ ++  VL+++ L SL+L  I E      L L  +  H 
Sbjct: 1035 RFVNLRKLGLTCRLLSSQ--QEAMVEWVLKMNRLRSLRLESIDEQNQVGDLDLKPLTGHV 1092

Query: 843  KLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSY 902
             L  LYL G L   S++   + P +++ +TLS   L+ DPM  L +L  LKIL L   SY
Sbjct: 1093 NLSCLYLLGRLVNPSIVP--ALPHSLIDITLSGSELKDDPMQTLDKLPNLKILSLLANSY 1150

Query: 903  TGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYL-VPPTGLKH 960
            TG+ M CS G F  L VLKLWKL +L +W ++EGA+  LR LEIR C  L + P  L H
Sbjct: 1151 TGKNMHCSFGGFSQLRVLKLWKLEQLEEWNVEEGALQALRDLEIRGCMKLEMLPEALHH 1209

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495927|ref|XP_002272120.2| PREDICTED: putative disease resistance protein At1g59780-like [Vitis vinifera]

 Score =  340 bits (871), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 253/718 (35%), Positives = 361/718 (50%), Gaps = 66/718 (9%)

Query: 271  TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI 330
            T+  VI+++G  G GKTTLA+ +YN   V  HF  RAW         E  + L  I++Q 
Sbjct: 530  TSFSVISIVGMPGIGKTTLAKSIYNNKAVVDHFPFRAWTS-------ETWEFLEHIMRQ- 581

Query: 331  DESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKI 390
             E  L     ++ EE+  +    L     LIV ++A +  +  ++  +      +   ++
Sbjct: 582  -EICL-----MTLEEMRQKFISLLAGKRCLIVFDDAYN--ACFFNLLVTTFSDASNGSRL 633

Query: 391  IITTSSTEDFVEPLGAAFSTLHVPGL-GKNESWELFLKKARIAEDVLQSRSSELIKLKKQ 449
            I+TT S      P     S  H   L G +ESW LF    ++      +   +L+ L+++
Sbjct: 634  ILTTRSMS---LPSQLQKSVHHAVRLRGNDESWALFTHALKV------NIPQQLLTLRRE 684

Query: 450  ILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCY------QDLPAQVK 503
            I   C GLPL ++ LA LLS K  + EEW   I++ N D      Y      +DLP  ++
Sbjct: 685  IERTCGGLPLAIIKLANLLSQKGLTIEEWCTAIQQLNHDQEQLWSYHLSRINKDLPLYMR 744

Query: 504  PCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVI 563
             C+ Y GLFPR++EIP RRLI LW AEG      +  A E D+AE  L +L+   M+QV 
Sbjct: 745  QCLFYFGLFPRDFEIPARRLIALWVAEGLVQAKGEDEAPE-DVAERCLIKLIAEGMVQVT 803

Query: 564  RWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLG 623
            + + +G+ KTCC+P  L      KA++  FL  H       +S  S     + RLA +L 
Sbjct: 804  KKKRNGNIKTCCLPSALRQYWLSKAQETTFLQIHME----TTSHLSPSTGMISRLADHLD 859

Query: 624  SNSFPYSSLLSWRLH--------------SYLVFDSRIRGTPAKQIGIILGKCISKRRLG 669
                 +  +     H              S+L FD+R    P + +G  L +CIS R L 
Sbjct: 860  KEDVTFGHIHGCHDHMASSHLQPLYQQVISFLSFDTREGSKPGEDMGNFLHRCISGRCLL 919

Query: 670  MLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKV 729
             L+VLDLE V+KP L    ALG+L  L YLGLRSTF+D LP     L  L  LDV HT +
Sbjct: 920  QLRVLDLENVFKPKLPE--ALGKLNRLRYLGLRSTFLDMLPSFIKKLHSLQVLDVKHTNI 977

Query: 730  QRLPYAFWPSRHLYLNWIF--LATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRR 787
              LP   W  + L ++++     + +   PQ   + T LQ L GL +  +E    D   R
Sbjct: 978  TTLPSPVWNLQQLRISYLNERCHSKLMPQPQAGSFST-LQVLVGLLVD-EETPVKDGLDR 1035

Query: 788  LTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL--ICETPSY--LPLLEMAEHYK 843
              +LRKLGL C   +S   ++ ++  VL+++ L SL+L  I E      L L  +  H  
Sbjct: 1036 FVNLRKLGLTCRLLSSQ--QEAMVEWVLKMNRLRSLRLESIDEQNQVGDLDLKPLTGHVN 1093

Query: 844  LQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYT 903
            L  LYL G L   S++   + P +++ +TLS   L+ DPM  L +L  LKIL L   SYT
Sbjct: 1094 LSCLYLLGRLVNPSIVP--ALPHSLIDITLSGSELKDDPMQTLDKLPNLKILSLLANSYT 1151

Query: 904  GEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYL-VPPTGLKH 960
            G+ M CS G F  L VLKLWKL +L +W ++EGA+  LR LEIR C  L + P  L H
Sbjct: 1152 GKNMHCSFGGFSQLRVLKLWKLEQLEEWNVEEGALQALRDLEIRGCMKLEMLPEALHH 1209

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147781606|emb|CAN64832.1| hypothetical protein VITISV_025760 [Vitis vinifera]

 Score =  340 bits (871), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 307/960 (31%), Positives = 459/960 (47%), Gaps = 102/960 (10%)

Query: 64   DEARFMQAFY----SAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLR--L 117
            D+ RFM  F     S + A  G+   EE+C + R      + + V     +  E LR   
Sbjct: 282  DKFRFMNGFLKELESVELADGGMVWMEELCDISR------SAVDVLGLFINRREQLRRSW 335

Query: 118  RSLFSFGMNKFKRELEIRGSSSSSSSSYEHQQ---QLVEVNDTGPSFSPYQGGYSTHRSQ 174
            RS F       K  L +    S    S E +Q   ++++++   P   P  G + TH   
Sbjct: 336  RSPFR------KVALAVDYLKSRHKFSMEMEQIHCKILDISSRRPEKVPGHG-HKTHN-- 386

Query: 175  QQRWARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSS 234
                          +     G+ +Q     +++  +    + A +S  + V G+  +R  
Sbjct: 387  -------------REPASTFGILQQPAPEPNIISFDDDDDSQAVMSRPEEVPGHSQSREQ 433

Query: 235  GEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTTTTTQVIALIGKAGSGKTTLARIVY 294
            G     L  P QE   D +S  ++            +   VI+++G  G+GKTTLA+++Y
Sbjct: 434  GCTFQILQQPTQEH--DIISFYDDVYAVMARLLADDSCFSVISIVGMEGAGKTTLAKLIY 491

Query: 295  NRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQ-ID-ESLLKVEATLSAEELMWRITQ 352
                V  HF  RAW     M       +L DI+KQ ID +   +       EE+  ++  
Sbjct: 492  ENDVVVDHFPYRAWASATNMF-----KILDDIVKQFIDYKKSTRTSWRKEQEEMKQKLKA 546

Query: 353  ALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLH 412
             L D  +LIV+++A      + +  L  L       ++I+TTS   +   P      ++H
Sbjct: 547  FLMDKRYLIVLDHARSSSVCILNELLSALPETLNGSRMIVTTS---EMSLPSHLETRSIH 603

Query: 413  --VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLST 470
              +     +ESW LF  K ++      +   EL  +K++I+  C GLPL +V L  +LS 
Sbjct: 604  HALRLRSDDESWALFTHKLKM------NIPQELQTMKREIVKRCGGLPLAIVKLGAVLSQ 657

Query: 471  KQPSYEEWSKVIERANGD-----NLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIH 525
            K  + EEWS  +E+ + D     N +++  +  P  +K C+ Y GLFP++ ++P RRLI 
Sbjct: 658  KDANIEEWSIALEQLHRDKKLWSNTLSMIDRKCPLHMKRCLFYFGLFPQDIDVPARRLIA 717

Query: 526  LWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILR 585
            LW AEG   P+ +   SE D+AE+ L +L+ + M+QV + +L+G  KTC +P  L     
Sbjct: 718  LWVAEGLMQPEGENETSE-DVAEICLIKLIAQGMVQVTKKKLNGDVKTCRLPDALQRHWL 776

Query: 586  PKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPY-----------SSLLS 634
             KA    FL  H + +    S  SL    VRRL  +L    F Y           +SL  
Sbjct: 777  SKARQTTFLQFHTNTR----SELSLSTGLVRRLVDHLDKEDFSYGHIHGEYNRTLTSLKP 832

Query: 635  WRLH--SYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGR 692
               H  S+L FD++    P + IG  L +CIS     +L+VLDLE V++P L     +G+
Sbjct: 833  RYQHALSFLSFDTQEGSKPGEDIGNFLHRCISSSCFLLLRVLDLEHVFRPKLPE--TIGK 890

Query: 693  LPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPS---RHLYLNWIFL 749
            L  L YLGLR TF++ LP S   L  L TLD+ HT +  LP + W     RHLYL+  + 
Sbjct: 891  LSRLRYLGLRWTFLEMLPSSISKLQNLQTLDLKHTYINILPNSIWKIQQLRHLYLSESY- 949

Query: 750  ATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLK-- 807
             +     P+ V   T+LQTLWGL +  +E    D   RL +L+KLGL C    S      
Sbjct: 950  RSKFMPQPR-VGSLTNLQTLWGLFVD-EETPVKDGLDRLVNLKKLGLTCRLMPSQQQAML 1007

Query: 808  ---KEIIGAVLQLSELHSLKLICE----TPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIG 860
               + +   VL+L  LH+L+L  +     P  L L  ++   KL  +YL G L    V+ 
Sbjct: 1008 AQLEAVANWVLKLDHLHTLRLKSDDGENQPGDLDLKPLSGLEKLSSIYLLGRLKNPLVVF 1067

Query: 861  DRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVL 920
            +   P ++  LTLS   L  DP+  L +L  LKILRL   SY G+ M CSSG FP L VL
Sbjct: 1068 ES--PESLSDLTLSGSGLTEDPLQKLDKLPNLKILRLLAKSYMGKNMLCSSGGFPQLRVL 1125

Query: 921  KLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYL-VPPTGLKHVTSSLREFLLTNMPSTFGS 979
            KLWKL  L +W ++EGA+  LR LEIRSC  L + P  L+H   +L    L++M + F +
Sbjct: 1126 KLWKLEELEEWNVEEGALRALRDLEIRSCPRLKMLPKELQH--RNLMNLKLSDMRNEFTT 1183

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225433944|ref|XP_002267359.1| PREDICTED: disease resistance RPP8-like protein 3-like [Vitis vinifera]

 Score =  339 bits (870), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 306/960 (31%), Positives = 459/960 (47%), Gaps = 102/960 (10%)

Query: 64   DEARFMQAFY----SAQDAINGLAIREEVCQMWRIDPVWVTILTVTTFPFSSFENLR--L 117
            D+ RFM  F     S + A  G+   EE+C + R      + + V     +  E LR   
Sbjct: 185  DKFRFMNGFLKELESVELADGGMVWMEELCDISR------SAVDVLGLFINRREQLRRSW 238

Query: 118  RSLFSFGMNKFKRELEIRGSSSSSSSSYEHQQ---QLVEVNDTGPSFSPYQGGYSTHRSQ 174
            RS F       K  L +    S    S E +Q   ++++++   P   P  G  + +R  
Sbjct: 239  RSPFR------KVALAVDYLKSRHKFSMEMEQIHCKILDISSRRPEKVPGHGHKTHNR-- 290

Query: 175  QQRWARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSS 234
                          +     G+ +Q     +++  +    + A +S  + V G+  +R  
Sbjct: 291  --------------EPASTFGILQQPAPEPNIISFDDDDDSQAVMSRPEEVPGHSQSREQ 336

Query: 235  GEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTTTTTQVIALIGKAGSGKTTLARIVY 294
            G     L  P QE   D +S  ++            +   VI+++G  G+GKTTLA+++Y
Sbjct: 337  GCTFQILQQPTQEH--DIISFYDDVYAVMARLLADDSCFSVISIVGMEGAGKTTLAKLIY 394

Query: 295  NRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQ-ID-ESLLKVEATLSAEELMWRITQ 352
                V  HF  RAW     M       +L DI+KQ ID +   +       EE+  ++  
Sbjct: 395  ENDVVVDHFPYRAWASATNMF-----KILDDIVKQFIDYKKSTRTSWRKEQEEMKQKLKA 449

Query: 353  ALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLH 412
             L D  +LIV+++A      + +  L  L       ++I+TTS   +   P      ++H
Sbjct: 450  FLMDKRYLIVLDHARSSSVCILNELLSALPETLNGSRMIVTTS---EMSLPSHLETRSIH 506

Query: 413  --VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLST 470
              +     +ESW LF  K ++      +   EL  +K++I+  C GLPL +V L  +LS 
Sbjct: 507  HALRLRSDDESWALFTHKLKM------NIPQELQTMKREIVKRCGGLPLAIVKLGAVLSQ 560

Query: 471  KQPSYEEWSKVIERANGD-----NLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIH 525
            K  + EEWS  +E+ + D     N +++  +  P  +K C+ Y GLFP++ ++P RRLI 
Sbjct: 561  KDANIEEWSIALEQLHRDKKLWSNTLSMIDRKCPLHMKRCLFYFGLFPQDIDVPARRLIA 620

Query: 526  LWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILR 585
            LW AEG   P+ +   SE D+AE+ L +L+ + M+QV + +L+G  KTC +P  L     
Sbjct: 621  LWVAEGLMQPEGENETSE-DVAEICLIKLIAQGMVQVTKKKLNGDVKTCRLPDALQRHWL 679

Query: 586  PKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPY-----------SSLLS 634
             KA    FL  H + +    S  SL    VRRL  +L    F Y           +SL  
Sbjct: 680  SKARQTTFLQFHTNTR----SELSLSTGLVRRLVDHLDKEDFSYGHIHGEYNRTLTSLKP 735

Query: 635  WRLH--SYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGR 692
               H  S+L FD++    P + IG  L +CIS     +L+VLDLE V++P L     +G+
Sbjct: 736  RYQHALSFLSFDTQEGSKPGEDIGNFLHRCISSSCFLLLRVLDLEHVFRPKLPE--TIGK 793

Query: 693  LPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPS---RHLYLNWIFL 749
            L  L YLGLR TF++ LP S   L  L TLD+ HT +  LP + W     RHLYL+  + 
Sbjct: 794  LSRLRYLGLRWTFLEMLPSSISKLQNLQTLDLKHTYINILPNSIWKIQQLRHLYLSESY- 852

Query: 750  ATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLK-- 807
             +     P+ V   T+LQTLWGL +  +E    D   RL +L+KLGL C    S      
Sbjct: 853  RSKFMPQPR-VGSLTNLQTLWGLFVD-EETPVKDGLDRLVNLKKLGLTCRLMPSQQQAML 910

Query: 808  ---KEIIGAVLQLSELHSLKLICE----TPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIG 860
               + +   VL+L  LH+L+L  +     P  L L  ++   KL  +YL G L    V+ 
Sbjct: 911  AQLEAVANWVLKLDHLHTLRLKSDDGENQPGDLDLKPLSGLEKLSSIYLLGRLKNPLVVF 970

Query: 861  DRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVL 920
            +   P ++  LTLS   L  DP+  L +L  LKILRL   SY G+ M CSSG FP L VL
Sbjct: 971  ES--PESLSDLTLSGSGLTEDPLQKLDKLPNLKILRLLAKSYMGKNMLCSSGGFPQLRVL 1028

Query: 921  KLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYL-VPPTGLKHVTSSLREFLLTNMPSTFGS 979
            KLWKL  L +W ++EGA+  LR LEIRSC  L + P  L+H   +L    L++M + F +
Sbjct: 1029 KLWKLEELEEWNVEEGALRALRDLEIRSCPRLKMLPKELQH--RNLMNLKLSDMRNEFTT 1086

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296081340|emb|CBI17686.3| unnamed protein product [Vitis vinifera]

 Score =  338 bits (867), Expect = 8e-90,   Method: Compositional matrix adjust.
 Identities = 253/718 (35%), Positives = 360/718 (50%), Gaps = 66/718 (9%)

Query: 271  TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI 330
            T+  VI+++G  G GKTTLA+ +YN   V  HF  RAW         E  + L  I++Q 
Sbjct: 492  TSFSVISIVGMPGIGKTTLAKSIYNNKAVVDHFPFRAWTS-------ETWEFLEHIMRQ- 543

Query: 331  DESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKI 390
             E  L     ++ EE+  +    L     LIV ++A    +  ++  +      +   ++
Sbjct: 544  -EICL-----MTLEEMRQKFISLLAGKRCLIVFDDA--YNACFFNLLVTTFSDASNGSRL 595

Query: 391  IITTSSTEDFVEPLGAAFSTLHVPGL-GKNESWELFLKKARIAEDVLQSRSSELIKLKKQ 449
            I+TT S      P     S  H   L G +ESW LF    ++      +   +L+ L+++
Sbjct: 596  ILTTRSMS---LPSQLQKSVHHAVRLRGNDESWALFTHALKV------NIPQQLLTLRRE 646

Query: 450  ILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVALCY------QDLPAQVK 503
            I   C GLPL ++ LA LLS K  + EEW   I++ N D      Y      +DLP  ++
Sbjct: 647  IERTCGGLPLAIIKLANLLSQKGLTIEEWCTAIQQLNHDQEQLWSYHLSRINKDLPLYMR 706

Query: 504  PCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVI 563
             C+ Y GLFPR++EIP RRLI LW AEG      +  A E D+AE  L +L+   M+QV 
Sbjct: 707  QCLFYFGLFPRDFEIPARRLIALWVAEGLVQAKGEDEAPE-DVAERCLIKLIAEGMVQVT 765

Query: 564  RWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLG 623
            + + +G+ KTCC+P  L      KA++  FL  H       +S  S     + RLA +L 
Sbjct: 766  KKKRNGNIKTCCLPSALRQYWLSKAQETTFLQIHME----TTSHLSPSTGMISRLADHLD 821

Query: 624  SNSFPYSSLLSWRLH--------------SYLVFDSRIRGTPAKQIGIILGKCISKRRLG 669
                 +  +     H              S+L FD+R    P + +G  L +CIS R L 
Sbjct: 822  KEDVTFGHIHGCHDHMASSHLQPLYQQVISFLSFDTREGSKPGEDMGNFLHRCISGRCLL 881

Query: 670  MLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKV 729
             L+VLDLE V+KP L    ALG+L  L YLGLRSTF+D LP     L  L  LDV HT +
Sbjct: 882  QLRVLDLENVFKPKLPE--ALGKLNRLRYLGLRSTFLDMLPSFIKKLHSLQVLDVKHTNI 939

Query: 730  QRLPYAFWPSRHLYLNWIF--LATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRR 787
              LP   W  + L ++++     + +   PQ   + T LQ L GL +  +E    D   R
Sbjct: 940  TTLPSPVWNLQQLRISYLNERCHSKLMPQPQAGSFST-LQVLVGLLVD-EETPVKDGLDR 997

Query: 788  LTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL--ICETPSY--LPLLEMAEHYK 843
              +LRKLGL C   +S   ++ ++  VL+++ L SL+L  I E      L L  +  H  
Sbjct: 998  FVNLRKLGLTCRLLSSQ--QEAMVEWVLKMNRLRSLRLESIDEQNQVGDLDLKPLTGHVN 1055

Query: 844  LQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYT 903
            L  LYL G L   S++   + P +++ +TLS   L+ DPM  L +L  LKIL L   SYT
Sbjct: 1056 LSCLYLLGRLVNPSIVP--ALPHSLIDITLSGSELKDDPMQTLDKLPNLKILSLLANSYT 1113

Query: 904  GEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYL-VPPTGLKH 960
            G+ M CS G F  L VLKLWKL +L +W ++EGA+  LR LEIR C  L + P  L H
Sbjct: 1114 GKNMHCSFGGFSQLRVLKLWKLEQLEEWNVEEGALQALRDLEIRGCMKLEMLPEALHH 1171

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743835|emb|CBI36718.3| unnamed protein product [Vitis vinifera]

 Score =  338 bits (866), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 263/781 (33%), Positives = 387/781 (49%), Gaps = 92/781 (11%)

Query: 244  PEQEGGGDALSNEEEESGRCQSSSTTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHF 303
            P QE   D +S +++         +       I+++G  G GKTTLA++VY+   +  HF
Sbjct: 287  PSQEA--DIISFDDDVHAMMTRLLSDDKDFCAISIVGIEGIGKTTLAKLVYDHDAIVNHF 344

Query: 304  TKRAWVHIPIMSMVED--RDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLI 361
              R W          D   +++ D ++Q+ ++ L                    D  FLI
Sbjct: 345  PYRVWTSASDGPFSSDPLTNIMTDEMRQVLKAFLA-------------------DKRFLI 385

Query: 362  VMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGL----- 416
            V+++    +  + + F+    +  +  +II+TT  T        +  S L    +     
Sbjct: 386  VVDD--FIQDHILEEFVTAFLNTLRGSRIILTTRGTTPSYTKARSPPSYLKTMSVHHGLR 443

Query: 417  --GKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPS 474
              G +ESW LF    ++      +   EL++L+++I+  C GLPL +V LA +LS K  +
Sbjct: 444  LRGDDESWALFTHVMKV------NIPPELLELRREIVIRCGGLPLAIVRLADVLSQKDAN 497

Query: 475  YEEWSKVIERANG------DNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWC 528
             +EWS V+++ +          ++   +DLP   + C+ Y GLFP++YEIPVRRLI LW 
Sbjct: 498  IDEWSSVLQQLDQDQEQVWSKALSKISEDLPLYKQRCLFYFGLFPKDYEIPVRRLIMLWV 557

Query: 529  AEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKA 588
            AEG   P+++     ED+A   L EL+   ++QV + +LDG+ KTC +P  L      KA
Sbjct: 558  AEGLVQPEVE-NEDPEDVAGRCLIELIAEDVVQVTKKKLDGNVKTCRLPYALRQHWLSKA 616

Query: 589  EDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYSSL--------LSWRLH-- 638
            +   F+  +   +    S  S+    VRRL  +L    F +  +         S R H  
Sbjct: 617  QQATFVQVYAKTR----SELSISTGLVRRLVDHLDKEDFSFDHIHGDYSRISTSLRPHYQ 672

Query: 639  ---SYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPF 695
               S++ FDS+    P + IG  L +CIS     +L+VLDLE V++P L    ALG+L  
Sbjct: 673  GVVSFISFDSQEGNKPGEDIGKFLHQCISSSCFLLLRVLDLEHVFRPKLPE--ALGKLTR 730

Query: 696  LEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFR 755
            L YLGLR TF++ LP S   L  L TLD+ HT +  LP + W  +HL      L +  +R
Sbjct: 731  LRYLGLRWTFLEMLPSSIRKLQNLQTLDLKHTYISTLPSSIWKMQHLRH---LLLSESYR 787

Query: 756  -----HPQFVKWETSLQTLWGLCIKADEV--QSLDYFRRLTSLRKLGLKC-----SSTTS 803
                  P+      +LQTLWGL +    +    LD   RL ++RKLGL C        T 
Sbjct: 788  SRFTLQPRVCSL-IALQTLWGLFVDEKTLVKGGLD---RLVNVRKLGLACRLMPSQQQTM 843

Query: 804  TSLKKEIIGAVLQLSELHSLKLICE----TPSYLPLLEMAEHYKLQKLYLSGHLPPNSVI 859
             S  + +   VL+L  LH+L+L  +     P  L L  +  H  L  +YL G L   S++
Sbjct: 844  LSQLEAVANWVLKLKHLHTLRLKSDDEENQPWDLDLKPLLAHVNLSSIYLLGRLKNPSIV 903

Query: 860  GDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLV 919
             +  FP ++  LTLS      DPM  L +L  LKILRL   SYTG+ M C SG FP L V
Sbjct: 904  SE--FPRSLSDLTLSGSGQMEDPMLKLDKLPNLKILRLLAKSYTGKLMLCPSGSFPQLRV 961

Query: 920  LKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYL-VPPTGLKHVTSSLREFLLTNMPSTFG 978
            LKLWKL +L +W ++EGA+  LR LEIRSC  L + P  L H   SL E  LT+MPS F 
Sbjct: 962  LKLWKLEQLEEWNVEEGALQALRDLEIRSCIRLKMLPKELLH--RSLLELKLTDMPSQFT 1019

Query: 979  S 979
            +
Sbjct: 1020 A 1020

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225433948|ref|XP_002267553.1| PREDICTED: putative disease resistance protein At1g59780-like [Vitis vinifera]

 Score =  336 bits (862), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 265/739 (35%), Positives = 391/739 (52%), Gaps = 74/739 (10%)

Query: 275  VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESL 334
            V++++G  G+GKTTLA+++Y+   V  HF  RA+            ++L D+ K   E  
Sbjct: 347  VVSVVGMEGTGKTTLAKLIYHNDAVVNHFHYRAFGF----------ELLKDVRKPFGEP- 395

Query: 335  LKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITT 394
                +++S E+        L D   LIV+++A  +  +  +  +  L   +   ++I+T+
Sbjct: 396  ---GSSMSPEKRAQPFKAFLADKRCLIVLDDAHDESFK--NEMITALRDTSNGCRMILTS 450

Query: 395  SSTEDFVEPLGAAFSTLHVPGLG---KNESWELFLKKARIAEDVLQSRSSELIKLKKQIL 451
              TE    P      +L+  GL     +ESW LF    +I      S   EL+K +++I+
Sbjct: 451  WVTE---LPSNLQIGSLYY-GLRLRRDDESWTLFTHAMKI------SIPQELLKFRREIV 500

Query: 452  NICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGD-----NLVALCYQDLPAQVKPCI 506
              C GLP  +V LA  LS K+ + EEWS V+++ +GD     N ++   +DLP  +K C+
Sbjct: 501  RRCGGLPRVIVKLANALSQKEATIEEWSSVLQQLDGDQDLWSNALSRINKDLPLYMKRCL 560

Query: 507  LYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWR 566
             Y GLFP++ +IP RRLI LW AEG   P+    A E D+AE YL +L+ + M+QV + +
Sbjct: 561  FYFGLFPKDLDIPARRLIMLWVAEGLVQPEGGNEAPE-DVAERYLIKLIAQGMVQVTQKK 619

Query: 567  LDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNS 626
            LDG+ KTC +P VL      K ++  FL +H   +   S +  L    +RRL  +L +  
Sbjct: 620  LDGTVKTCRLPYVLQQEWLAKTQEATFLQYHAKTRSELSPSTGL----IRRLVDHLDNED 675

Query: 627  FPYSSL--------LSWRLH-----SYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKV 673
              +  +         S + H     S+L FD+R    P + +G  L +CIS     +L+V
Sbjct: 676  VSFGHIHGDENTTSTSLKPHYQDVLSFLSFDAREGSKPGEDVGNFLHECISSSCFLLLRV 735

Query: 674  LDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLP 733
            LDLE V++P L     LG+L  L Y+GLR TF+  LP S   L  L TLD+ HT +  LP
Sbjct: 736  LDLEHVFRPKLPKQ--LGKLTRLRYIGLRWTFLQMLPSSISKLQNLQTLDLKHTYIDTLP 793

Query: 734  YAFWPS---RHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTS 790
             + W     RHLYL+  + +  + R P+ V   TSLQTLWGL +  +E    +   RL +
Sbjct: 794  SSIWKVQQLRHLYLSESYRSKFMLR-PR-VGSLTSLQTLWGLFVD-EETPVKNGLDRLVN 850

Query: 791  LRKLGLKCSSTTSTSLK-----KEIIGAVLQLSELHSLKLICE----TPSYLPLLEMAEH 841
            +RKL L C  T S         + +   VL+L+ L SL+L  +     P  L L  ++ H
Sbjct: 851  IRKLSLTCRLTPSQDEAMLQQLEAVSNWVLKLNHLQSLRLKSDDADNQPWDLDLKPLSGH 910

Query: 842  YKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGS 901
              L ++YL G L   S++ +  FP ++  LTLS  RL  DPM  L +L  LKILRL   S
Sbjct: 911  ANLSRVYLLGRLKNPSIVSE--FPESLTDLTLSGSRLTEDPMQTLDKLPNLKILRLLSKS 968

Query: 902  YTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYL-VPPTGLKH 960
            Y G+EM CS G FP L +LKLWKL  L +W ++EGA+  L  LEIRSC  L + P GL+ 
Sbjct: 969  YVGKEMLCSLGGFPKLRILKLWKLELLEEWNVEEGALQALHDLEIRSCLKLKMLPQGLRQ 1028

Query: 961  VTSSLREFLLTNMPSTFGS 979
             T  L    LT+MP+ F +
Sbjct: 1029 RT--LWNLKLTDMPNDFTT 1045

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	1007
TAIR|locus:504956184	1017	AT1G58807 "AT1G58807" [Arabido	0.679	0.672	0.260	2.7e-41
TAIR|locus:2827038	1017	AT1G59124 "AT1G59124" [Arabido	0.679	0.672	0.260	2.7e-41
TAIR|locus:504956182	1049	AT1G58848 [Arabidopsis thalian	0.708	0.679	0.258	1.8e-40
TAIR|locus:2826978	1049	AT1G59218 [Arabidopsis thalian	0.708	0.679	0.258	1.8e-40
TAIR|locus:2037639	907	AT1G58390 "AT1G58390" [Arabido	0.654	0.726	0.266	2.2e-38
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.483	0.537	0.247	5e-38
TAIR|locus:2037623	899	AT1G58410 [Arabidopsis thalian	0.659	0.738	0.267	6.9e-38
TAIR|locus:2077572	926	RPM1 "RESISTANCE TO P. SYRINGA	0.357	0.388	0.282	8.8e-37
TAIR|locus:504956186	1138	AT1G58602 [Arabidopsis thalian	0.287	0.254	0.275	2.5e-24
TAIR|locus:2075170	835	RPP13 "RECOGNITION OF PERONOSP	0.317	0.383	0.291	2.7e-31

TAIR|locus:504956184 AT1G58807 "AT1G58807" [Arabidopsis thaliana (taxid:3702)]

 Score = 449 (163.1 bits), Expect = 2.7e-41, Sum P(2) = 2.7e-41
 Identities = 196/753 (26%), Positives = 334/753 (44%)

Query:   274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP--IMSMVEDRDVLADILKQID 331
             QV+++ G  G GKTTLA+ V+N   VK  F   +WV +      M   + +L D LK  +
Sbjct:   184 QVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRD-LKPKE 242

Query:   332 ESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKII 391
             E    +E T   + L   + + L+ S  LIV+++   ++   W+  +  +   T+  K++
Sbjct:   243 EEKKIMEMT--QDTLQGELIRLLETSKSLIVLDDIWEKED--WE-LIKPIFPPTKGWKVL 297

Query:   392 ITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLKKQI 450
             +T S  E        ++       L   +SW LF + A   +D  + +   E  +L K +
Sbjct:   298 LT-SRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKLM 356

Query:   451 LNICDXXXXXXXXXXXXXSTKQPSYEEWSKVIERA-----------NGDN------LVAL 493
             +  C              + K  S++ W ++ E             N DN      +++L
Sbjct:   357 IKHCGGLPLAIRVLGGMLAEKYTSHD-WRRLSENIGSHLVGGRTNFNDDNNNTCNNVLSL 415

Query:   494 CYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEG-FAPPDLDLIASEEDLAEMYLE 552
              +++LP+ +K C LY+  FP +YEI V  L + W AEG F P   D   +  D+ ++Y+E
Sbjct:   416 SFEELPSYLKHCFLYLAHFPEDYEIKVENLSYYWAAEGIFQPRHYDG-ETIRDVGDVYIE 474

Query:   553 ELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPK 612
             ELV R+M+   R       +TC +  ++ ++   KA++  FL       ++ SS  S   
Sbjct:   475 ELVRRNMVISERDVKTSRFETCHLHDMMREVCLLKAKEENFL-------QITSSRPS--- 524

Query:   613 FAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGI--ILGKCISKRRLGM 670
                  L + + S  F Y    +  +    + + ++R      +G   + G   +  RL +
Sbjct:   525 --TANLQSTVTSRRFVYQYPTTLHVEKD-INNPKLRALVVVTLGSWNLAGSSFT--RLEL 579

Query:   671 LKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDV-SHTKV 729
             L+VLDL  V        + +G+L  L YL L    +  +P S   L  L  L++ S  + 
Sbjct:   580 LRVLDLIEVKIKGGKLASCIGKLIHLRYLSLEYAEVTHIPYSLGNLKLLIYLNLASFGRS 639

Query:   730 QRLPYAFWPSRHLYLNWIFLATNVFRHPQF-VKWETSLQTLWGLCIKADEVQSLDYFRRL 788
               +P      + L   ++ L +++ R  +  +     L+TL     +   ++ L    RL
Sbjct:   640 TFVPNVLMGMQEL--RYLALPSDMGRKTKLELSNLVKLETLENFSTENSSLEDLCGMVRL 697

Query:   789 TSLRXXXXXXXXXXXXXXXXEIIGAVLQLSELHSLKLICETPSYLPLLEMA---EHYKLQ 845
             ++L                   IG +  L +L     I +  S +   E     +   L+
Sbjct:   698 STLNIKLIEETSLETLAAS---IGGLKYLEKLE----IYDHGSEMRTKEAGIVFDFVHLK 750

Query:   846 KLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGE 905
             +L+L  ++P  S   ++ FP ++ TL L   RLE DPMPIL +L QLK L L   S++G+
Sbjct:   751 RLWLKLYMPRLST--EQHFPSHLTTLYLESCRLEEDPMPILEKLLQLKELELGFESFSGK 808

Query:   906 EMSCSSGEFPXXXXXXXXXXXXXXQWRIKEGAMPCLRQLEIRSCGYL--VPPTGL-KHVT 962
             +M CSSG FP               W+++E +MP LR L+I+ C  L  +P   L  H+T
Sbjct:   809 KMVCSSGGFPQLQRLSLLKLEEWEDWKVEESSMPLLRTLDIQVCRKLKQLPDEHLPSHLT 868

Query:   963 S-SLREFLLTNMP-STFGSVADIERV-LGINVY 992
             S SL    L   P  T G +  ++ + LG   +
Sbjct:   869 SISLFFCCLEKDPLPTLGRLVYLKELQLGFRTF 901

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2827038 AT1G59124 "AT1G59124" [Arabidopsis thaliana (taxid:3702)]

 Score = 449 (163.1 bits), Expect = 2.7e-41, Sum P(2) = 2.7e-41
 Identities = 196/753 (26%), Positives = 334/753 (44%)

Query:   274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP--IMSMVEDRDVLADILKQID 331
             QV+++ G  G GKTTLA+ V+N   VK  F   +WV +      M   + +L D LK  +
Sbjct:   184 QVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRD-LKPKE 242

Query:   332 ESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKII 391
             E    +E T   + L   + + L+ S  LIV+++   ++   W+  +  +   T+  K++
Sbjct:   243 EEKKIMEMT--QDTLQGELIRLLETSKSLIVLDDIWEKED--WE-LIKPIFPPTKGWKVL 297

Query:   392 ITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLKKQI 450
             +T S  E        ++       L   +SW LF + A   +D  + +   E  +L K +
Sbjct:   298 LT-SRNESVAMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKLM 356

Query:   451 LNICDXXXXXXXXXXXXXSTKQPSYEEWSKVIERA-----------NGDN------LVAL 493
             +  C              + K  S++ W ++ E             N DN      +++L
Sbjct:   357 IKHCGGLPLAIRVLGGMLAEKYTSHD-WRRLSENIGSHLVGGRTNFNDDNNNTCNNVLSL 415

Query:   494 CYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEG-FAPPDLDLIASEEDLAEMYLE 552
              +++LP+ +K C LY+  FP +YEI V  L + W AEG F P   D   +  D+ ++Y+E
Sbjct:   416 SFEELPSYLKHCFLYLAHFPEDYEIKVENLSYYWAAEGIFQPRHYDG-ETIRDVGDVYIE 474

Query:   553 ELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPK 612
             ELV R+M+   R       +TC +  ++ ++   KA++  FL       ++ SS  S   
Sbjct:   475 ELVRRNMVISERDVKTSRFETCHLHDMMREVCLLKAKEENFL-------QITSSRPS--- 524

Query:   613 FAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGI--ILGKCISKRRLGM 670
                  L + + S  F Y    +  +    + + ++R      +G   + G   +  RL +
Sbjct:   525 --TANLQSTVTSRRFVYQYPTTLHVEKD-INNPKLRALVVVTLGSWNLAGSSFT--RLEL 579

Query:   671 LKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDV-SHTKV 729
             L+VLDL  V        + +G+L  L YL L    +  +P S   L  L  L++ S  + 
Sbjct:   580 LRVLDLIEVKIKGGKLASCIGKLIHLRYLSLEYAEVTHIPYSLGNLKLLIYLNLASFGRS 639

Query:   730 QRLPYAFWPSRHLYLNWIFLATNVFRHPQF-VKWETSLQTLWGLCIKADEVQSLDYFRRL 788
               +P      + L   ++ L +++ R  +  +     L+TL     +   ++ L    RL
Sbjct:   640 TFVPNVLMGMQEL--RYLALPSDMGRKTKLELSNLVKLETLENFSTENSSLEDLCGMVRL 697

Query:   789 TSLRXXXXXXXXXXXXXXXXEIIGAVLQLSELHSLKLICETPSYLPLLEMA---EHYKLQ 845
             ++L                   IG +  L +L     I +  S +   E     +   L+
Sbjct:   698 STLNIKLIEETSLETLAAS---IGGLKYLEKLE----IYDHGSEMRTKEAGIVFDFVHLK 750

Query:   846 KLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGE 905
             +L+L  ++P  S   ++ FP ++ TL L   RLE DPMPIL +L QLK L L   S++G+
Sbjct:   751 RLWLKLYMPRLST--EQHFPSHLTTLYLESCRLEEDPMPILEKLLQLKELELGFESFSGK 808

Query:   906 EMSCSSGEFPXXXXXXXXXXXXXXQWRIKEGAMPCLRQLEIRSCGYL--VPPTGL-KHVT 962
             +M CSSG FP               W+++E +MP LR L+I+ C  L  +P   L  H+T
Sbjct:   809 KMVCSSGGFPQLQRLSLLKLEEWEDWKVEESSMPLLRTLDIQVCRKLKQLPDEHLPSHLT 868

Query:   963 S-SLREFLLTNMP-STFGSVADIERV-LGINVY 992
             S SL    L   P  T G +  ++ + LG   +
Sbjct:   869 SISLFFCCLEKDPLPTLGRLVYLKELQLGFRTF 901

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:504956182 AT1G58848 [Arabidopsis thaliana (taxid:3702)]

 Score = 443 (161.0 bits), Expect = 1.8e-40, Sum P(2) = 1.8e-40
 Identities = 199/770 (25%), Positives = 330/770 (42%)

Query:   224 IVDGYEYARSSGEEITEL-PIPEQEGGGDALSNEEEESGRCQXXXXXXXXXQVIALIGKA 282
             IVDG  Y +  G++  E+ P   ++   D +  E     +           QV+++ G  
Sbjct:   135 IVDG-GYKQPQGDKQREMRPRFSKDDDSDFVGLEANVK-KLVGYLVDEANVQVVSITGMG 192

Query:   283 GSGKTTLARIVYNRVYVKRHFTKRAWVHIP--IMSMVEDRDVLADILKQIDESLLKVEAT 340
             G GKTTLA+ V+N   VK  F   +WV +      M   + +L D LK  +E    +E T
Sbjct:   193 GLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRD-LKPKEEEKKIMEMT 251

Query:   341 LSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDF 400
                + L   + + L+ S  LIV+++   ++   W+  +  +   T+  K+++T S  E  
Sbjct:   252 --QDTLQGELIRLLETSKSLIVLDDIWEKED--WE-LIKPIFPPTKGWKVLLT-SRNESV 305

Query:   401 VEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLKKQILNICDXXXX 459
                   ++       L   +SW LF + A   +D  + +   E  +L K ++  C     
Sbjct:   306 AMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKLMIKHCGGLPL 365

Query:   460 XXXXXXXXXSTKQPSYEEWSKVIERA-----------NGDN------LVALCYQDLPAQV 502
                      + K  S++ W ++ E             N DN      +++L +++LP+ +
Sbjct:   366 AIRVLGGMLAEKYTSHD-WRRLSENIGSHLVGGRTNFNDDNNNTCNYVLSLSFEELPSYL 424

Query:   503 KPCILYMGLFPREYEIPVRRLIHLWCAEGFAPP---DLDLIASEEDLAEMYLEELVTRHM 559
             K C LY+  FP +YEI V+ L + W AEG   P   D ++I    D+ ++Y+EELV R+M
Sbjct:   425 KHCFLYLAHFPDDYEINVKNLSYYWAAEGIFQPRHYDGEII---RDVGDVYIEELVRRNM 481

Query:   560 IQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLA 619
             +   R       +TC +  ++ ++   KA++  FL          S+  SL     RRL 
Sbjct:   482 VISERDVKTSRFETCHLHDMMREVCLLKAKEENFL---QITSSRTSTGNSLSIVTSRRLV 538

Query:   620 ANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGV 679
                         +   +L S +V  +           ++LG   S  RL +L+VLD+   
Sbjct:   539 YQYPITLDVEKDINDPKLRSLVVVANTYMFWGGWS-WMLLGS--SFIRLELLRVLDIHRA 595

Query:   680 YKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLD--VSHTKVQRLPYAFW 737
                     +++G+L  L YL L+   +  +P S   L  L  L+  +  +    +P    
Sbjct:   596 KLKGGKLASSIGQLIHLRYLNLKHAEVTHIPYSLGNLKLLIYLNLVILVSGSTLVPNVLK 655

Query:   738 PSRHLYLNWIFLATNVFRHPQF-VKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRXXXX 796
               + L   ++ L  ++ R  +  +     L+TL     K   ++ L   R +  LR    
Sbjct:   656 EMQQL--RYLALPKDMGRKTKLELSNLVKLETLKNFSTKNCSLEDL---RGMVRLRTLTI 710

Query:   797 XXXXXXXXXXXXEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPN 856
                           IG +  L  L    L  E  +    +     Y L+ L L  ++P  
Sbjct:   711 ELRKETSLETLAASIGGLKYLESLTITDLGSEMRTKEAGIVFDFVY-LKTLTLKLYMPRL 769

Query:   857 SVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPX 916
             S   ++ FP ++ TL L   RLE DPMPIL +L QLK L L   S++G+EM CSSG FP 
Sbjct:   770 SK--EQHFPSHLTTLYLQHCRLEEDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQ 827

Query:   917 XXXXXXXXXXXXXQWRIKEGAMPCLRQLEIRSCGYL--VPPTGL-KHVTS 963
                           W+++E +MP L  L+IR C  L  +P   L  H+TS
Sbjct:   828 LQKLSIKGLEEWEDWKVEESSMPVLHTLDIRDCRKLKQLPDEHLPSHLTS 877

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2826978 AT1G59218 [Arabidopsis thaliana (taxid:3702)]

 Score = 443 (161.0 bits), Expect = 1.8e-40, Sum P(2) = 1.8e-40
 Identities = 199/770 (25%), Positives = 330/770 (42%)

Query:   224 IVDGYEYARSSGEEITEL-PIPEQEGGGDALSNEEEESGRCQXXXXXXXXXQVIALIGKA 282
             IVDG  Y +  G++  E+ P   ++   D +  E     +           QV+++ G  
Sbjct:   135 IVDG-GYKQPQGDKQREMRPRFSKDDDSDFVGLEANVK-KLVGYLVDEANVQVVSITGMG 192

Query:   283 GSGKTTLARIVYNRVYVKRHFTKRAWVHIP--IMSMVEDRDVLADILKQIDESLLKVEAT 340
             G GKTTLA+ V+N   VK  F   +WV +      M   + +L D LK  +E    +E T
Sbjct:   193 GLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRD-LKPKEEEKKIMEMT 251

Query:   341 LSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDF 400
                + L   + + L+ S  LIV+++   ++   W+  +  +   T+  K+++T S  E  
Sbjct:   252 --QDTLQGELIRLLETSKSLIVLDDIWEKED--WE-LIKPIFPPTKGWKVLLT-SRNESV 305

Query:   401 VEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLKKQILNICDXXXX 459
                   ++       L   +SW LF + A   +D  + +   E  +L K ++  C     
Sbjct:   306 AMRRNTSYINFKPECLTTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKLMIKHCGGLPL 365

Query:   460 XXXXXXXXXSTKQPSYEEWSKVIERA-----------NGDN------LVALCYQDLPAQV 502
                      + K  S++ W ++ E             N DN      +++L +++LP+ +
Sbjct:   366 AIRVLGGMLAEKYTSHD-WRRLSENIGSHLVGGRTNFNDDNNNTCNYVLSLSFEELPSYL 424

Query:   503 KPCILYMGLFPREYEIPVRRLIHLWCAEGFAPP---DLDLIASEEDLAEMYLEELVTRHM 559
             K C LY+  FP +YEI V+ L + W AEG   P   D ++I    D+ ++Y+EELV R+M
Sbjct:   425 KHCFLYLAHFPDDYEINVKNLSYYWAAEGIFQPRHYDGEII---RDVGDVYIEELVRRNM 481

Query:   560 IQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLA 619
             +   R       +TC +  ++ ++   KA++  FL          S+  SL     RRL 
Sbjct:   482 VISERDVKTSRFETCHLHDMMREVCLLKAKEENFL---QITSSRTSTGNSLSIVTSRRLV 538

Query:   620 ANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGV 679
                         +   +L S +V  +           ++LG   S  RL +L+VLD+   
Sbjct:   539 YQYPITLDVEKDINDPKLRSLVVVANTYMFWGGWS-WMLLGS--SFIRLELLRVLDIHRA 595

Query:   680 YKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLD--VSHTKVQRLPYAFW 737
                     +++G+L  L YL L+   +  +P S   L  L  L+  +  +    +P    
Sbjct:   596 KLKGGKLASSIGQLIHLRYLNLKHAEVTHIPYSLGNLKLLIYLNLVILVSGSTLVPNVLK 655

Query:   738 PSRHLYLNWIFLATNVFRHPQF-VKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRXXXX 796
               + L   ++ L  ++ R  +  +     L+TL     K   ++ L   R +  LR    
Sbjct:   656 EMQQL--RYLALPKDMGRKTKLELSNLVKLETLKNFSTKNCSLEDL---RGMVRLRTLTI 710

Query:   797 XXXXXXXXXXXXEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPN 856
                           IG +  L  L    L  E  +    +     Y L+ L L  ++P  
Sbjct:   711 ELRKETSLETLAASIGGLKYLESLTITDLGSEMRTKEAGIVFDFVY-LKTLTLKLYMPRL 769

Query:   857 SVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPX 916
             S   ++ FP ++ TL L   RLE DPMPIL +L QLK L L   S++G+EM CSSG FP 
Sbjct:   770 SK--EQHFPSHLTTLYLQHCRLEEDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQ 827

Query:   917 XXXXXXXXXXXXXQWRIKEGAMPCLRQLEIRSCGYL--VPPTGL-KHVTS 963
                           W+++E +MP L  L+IR C  L  +P   L  H+TS
Sbjct:   828 LQKLSIKGLEEWEDWKVEESSMPVLHTLDIRDCRKLKQLPDEHLPSHLTS 877

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2037639 AT1G58390 "AT1G58390" [Arabidopsis thaliana (taxid:3702)]

 Score = 428 (155.7 bits), Expect = 2.2e-38, Sum P(2) = 2.2e-38
 Identities = 191/717 (26%), Positives = 304/717 (42%)

Query:   274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES 333
             QV+++ G  G GKTTLAR V+N   VK  F + AWV +        ++V   IL+ +   
Sbjct:   184 QVVSITGMGGLGKTTLARQVFNHEDVKHQFDRLAWVCVS--QEFTRKNVWQMILQNLTSR 241

Query:   334 LLKVEATLSAE-ELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIII 392
               K E     E EL  ++ Q L+ S  LIV ++    K + WD  L K       G  ++
Sbjct:   242 EKKDEILQMEEAELHDKLFQLLETSKSLIVFDDI--WKDEDWD--LIKPIFPPNKGWKVL 297

Query:   393 TTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLKKQIL 451
              TS  E         +       L   +SW LF + A   +D  +S+   E+  + KQ+L
Sbjct:   298 LTSQNESVAVRGDIKYLNFKPECLAIEDSWTLFQRIAFPKKDASESKVDEEMEDMGKQML 357

Query:   452 NICDXXXXXXXXXXXXXSTKQPSYEEW--------SKVIERANGDN-----LVALCYQDL 498
               C              + K   ++ W        S ++ R + +N     ++++ +++L
Sbjct:   358 KHCGGLPLAIKVLGGLLAAKYTMHD-WERLSVNIGSDIVGRTSSNNSSIYHVLSMSFEEL 416

Query:   499 PAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASE--EDLAEMYLEELVT 556
             P+ +K C LY+  FP +++I V +L + W AEG +  + D    E  +D+ + YLEELV 
Sbjct:   417 PSYLKHCFLYLAHFPEDHKINVEKLSYCWAAEGISTAE-DYHNGETIQDVGQSYLEELVR 475

Query:   557 RHMIQVIRWRLDGSPK---TCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSA--KSLP 611
             R+MI    W  D +     TC +  ++ ++   KA++  FL        + SS+   S  
Sbjct:   476 RNMII---WERDATASRFGTCHLHDMMREVCLFKAKEENFLQIAVKSVGVTSSSTGNSQS 532

Query:   612 KFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGML 671
                 RRL     +       + + +L S +V    +     K +G       S  RL +L
Sbjct:   533 PCRSRRLVYQCPTTLHVERDINNPKLRSLVVLWHDLWVENWKLLGT------SFTRLKLL 586

Query:   672 KVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVS-HTKVQ 730
             +VLDL  V    +     +G L  L YL L+   +  LP S   L  L  L++   T+  
Sbjct:   587 RVLDLFYVDFEGMKLPFGIGNLIHLRYLSLQDAKVSHLPSSLGNLMLLIYLNLDVDTEFI 646

Query:   731 RLPYAFWPSRHLYLNWIFLATNVFRHPQF-VKWETSLQTLWGLCIKADEVQSLDYFRRLT 789
              +P  F   R   L ++ L  ++ +  +  ++    L+TL          + L    RL 
Sbjct:   647 FVPDVFM--RMHELRYLKLPLHMHKKTRLSLRNLVKLETLVYFSTWHSSSKDLCGMTRLM 704

Query:   790 SLRXXXXXXXXXXXXXXXXEIIGAV--LQLSELHSLKLICETPSYLPLLEMAEHYKLQKL 847
             +L                   +  +  L +   HS K+  E    L  + + +H  L  L
Sbjct:   705 TLAIRLTRVTSTETLSASISGLRNLEYLYIVGTHSKKMR-EEGIVLDFIHL-KHLLLD-L 761

Query:   848 YLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEM 907
             Y+     P      + FP  +  + LS+  LE DPMPIL +L  LK + L  GSY G  M
Sbjct:   762 YM-----PRQ----QHFPSRLTFVKLSECGLEEDPMPILEKLLHLKGVILLKGSYCGRRM 812

Query:   908 SCSSGEFPXXXXXXXXXXXXXXQWRIKEGAMPCLRQLEIRSCGYLVP-PTGLKHVTS 963
              CS G FP              +W ++EG+MP L  L I  C  L   P GL+ + S
Sbjct:   813 VCSGGGFPQLKKLEIVGLNKWEEWLVEEGSMPLLETLSILDCEELKEIPDGLRFIYS 869

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2025916 AT1G59780 "AT1G59780" [Arabidopsis thaliana (taxid:3702)]

 Score = 292 (107.8 bits), Expect = 5.0e-38, Sum P(3) = 5.0e-38
 Identities = 134/542 (24%), Positives = 233/542 (42%)

Query:   276 IALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLL 335
             +++ G  G GKTTLAR +++   VK HF   AWV +        +DV   IL  +     
Sbjct:   183 VSITGLGGLGKTTLARQIFDHDKVKSHFDGLAWVCVS--QEFTRKDVWKTILGNLSPKYK 240

Query:   336 KVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCG-KIIITT 394
               ++ L  +++  ++ Q L+    LIV ++    K + W   +  +    + G K+++T 
Sbjct:   241 --DSDLPEDDIQKKLFQLLETKKALIVFDDL--WKREDWYR-IAPMFPERKAGWKVLLT- 294

Query:   395 SSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR--SSELIKLKKQILN 452
              S  D + P    F       L  +E W+L  + A   +  +       E++K+ K++  
Sbjct:   295 -SRNDAIHPHCVTFKP---ELLTHDECWKLLQRIAFSKQKTITGYIIDKEMVKMAKEMTK 350

Query:   453 ICDXXXXXXXXXXXXXSTKQPSYEEWSKVIER----------ANGDN-------LVALCY 495
              C                K  +  +W  + E           ++ +N       +++L +
Sbjct:   351 HCKRLPLAVKLLGGLLDAKH-TLRQWKLISENIISHIVVGGTSSNENDSSSVNHVLSLSF 409

Query:   496 QDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELV 555
             + LP  +K C+LY+  +P ++EI + RL ++W AEG   P     A+  D+A++Y+EELV
Sbjct:   410 EGLPGYLKHCLLYLASYPEDHEIEIERLSYVWAAEGITYPGNYEGATIRDVADLYIEELV 469

Query:   556 TRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAV 615
              R+M+   R  L    + C +  ++ +I   KA++  FL     P   +SS  SL     
Sbjct:   470 KRNMVISERDALTSRFEKCQLHDLMREICLLKAKEENFLQIVTDPTS-SSSVHSLASSRS 528

Query:   616 RRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLD 675
             RRL     S     + + + +L S L+F       P       +G    +  L +L+VLD
Sbjct:   529 RRLVVYNTSIFSGENDMKNSKLRS-LLF------IPVGYSRFSMGSNFIE--LPLLRVLD 579

Query:   676 LEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLD--VSHTKVQRLP 733
             L+G         +++G+L  L+YL L    +  LP S   L  L  L+  ++  ++  +P
Sbjct:   580 LDGAKFKGGKLPSSIGKLIHLKYLSLYQASVTYLPSSLRNLKSLLYLNLRINSGQLINVP 639

Query:   734 YAFWPS---RHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTS 790
               F      R+L L W   +         +K    L+TL     K   V  L    R+T 
Sbjct:   640 NVFKEMLELRYLSLPWERSSLTKLELGNLLK----LETLINFSTKDSSVTDL---HRMTK 692

Query:   791 LR 792
             LR
Sbjct:   693 LR 694

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2037623 AT1G58410 [Arabidopsis thaliana (taxid:3702)]

 Score = 430 (156.4 bits), Expect = 6.9e-38, Sum P(2) = 6.9e-38
 Identities = 193/722 (26%), Positives = 319/722 (44%)

Query:   274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDR-DVLADILKQIDE 332
             Q+++L G  G GKTTLAR V+N   VK  F   AWV +   S    R  V   IL+ +  
Sbjct:   183 QIVSLTGMGGLGKTTLARQVFNHDVVKDRFDGFAWVSV---SQEFTRISVWQTILQNLTS 239

Query:   333 SLLKVEA-TLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKII 391
                K E   +   +L   + + L+ S  LIV+++    K + WD  L K     + G  +
Sbjct:   240 KERKDEIQNMKEADLHDDLFRLLESSKTLIVLDDI--WKEEDWD--LIKPIFPPKKGWKV 295

Query:   392 ITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSR-SSELIKLKKQI 450
             + TS TE         + +     L   +SW LF   A   +D  + +   E+  + K++
Sbjct:   296 LLTSRTESIAMRGDTTYISFKPKCLSIPDSWTLFQSIAMPRKDTSEFKVDEEMENMGKKM 355

Query:   451 LNICDXXXXXXXXXXXXXSTKQPSYEEW--------SKVIERANGDN-----LVALCYQD 497
             +  C              + K  +  +W        S ++ER +G+N     ++++ +++
Sbjct:   356 IKHCGGLSLAVKVLGGLLAAKY-TLHDWKRLSENIGSHIVERTSGNNSSIDHVLSVSFEE 414

Query:   498 LPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTR 557
             LP  +K C LY+  FP ++EI V +L + W AEG +        +  D  + Y+EELV R
Sbjct:   415 LPNYLKHCFLYLAHFPEDHEIDVEKLHYYWAAEGISERRRYDGETIRDTGDSYIEELVRR 474

Query:   558 HMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLY--HHHHPQRLNSSAKSLPKFAV 615
             +M+   R  +    +TC +  ++ +I   KA++  FL    +H P    S+ ++L   A 
Sbjct:   475 NMVISERDVMTSRFETCRLHDMMREICLFKAKEENFLQIVSNHSP---TSNPQTLG--AS 529

Query:   616 RRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLD 675
             RR   +  +         + +L S +V    I      +  ++ G   +  R+ +L+VLD
Sbjct:   530 RRFVLHNPTTLHVERYKNNPKLRSLVVVYDDI----GNRRWMLSGSIFT--RVKLLRVLD 583

Query:   676 L-EGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDV--SHTKVQRL 732
             L +  +K     ++ +G+L  L YL L+   +  LP S   L  L  LD+    T +  +
Sbjct:   584 LVQAKFKGGKLPSD-IGKLIHLRYLSLKDAKVSHLPSSLRNLVLLIYLDIRTDFTDIF-V 641

Query:   733 PYAFWPSRHLYLNWIFLATNVFRHPQFVKWETS-LQTLWGLCIKADEVQSLDYFRRLTSL 791
             P  F   R L     +L    F H +  K E S L+ L  L   + +  SL+  R +  L
Sbjct:   642 PNVFMGMRELR----YLELPRFMHEK-TKLELSNLEKLEALENFSTKSSSLEDLRGMVRL 696

Query:   792 RXXXXXXXXXXXXXXXXEIIGAVLQLSELHSLKLICETPSYLPLLE---MAEHYKLQKLY 848
             R                 +  +V  L  L + K++ E      + E   + +   L+KL 
Sbjct:   697 RTLVIILSEGTSLQT---LSASVCGLRHLENFKIM-ENAGVNRMGEERMVLDFTYLKKLT 752

Query:   849 LSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMS 908
             LS  +P    I  +  P ++  L LS   LE DPMPIL +L +LK L L   S++G +M 
Sbjct:   753 LSIEMPRLPKI--QHLPSHLTVLDLSYCCLEEDPMPILEKLLELKDLSLDYLSFSGRKMV 810

Query:   909 CSSGEFPXXXXXXXXXXXXXXQWRIKEGAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREF 968
             CS+G FP              +W ++EG+M  L  L I S      P GL+ + S L+  
Sbjct:   811 CSAGGFPQLRKLALDEQEEWEEWIVEEGSMSRLHTLSIWSSTLKELPDGLRFIYS-LKNL 869

Query:   969 LL 970
             ++
Sbjct:   870 IM 871

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2077572 RPM1 "RESISTANCE TO P. SYRINGAE PV MACULICOLA 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 361 (132.1 bits), Expect = 8.8e-37, Sum P(2) = 8.8e-37
 Identities = 109/386 (28%), Positives = 185/386 (47%)

Query:   275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVED--RDVLADILKQIDE 332
             V+A++G  GSGKTTL+  ++    V+RHF   AWV I    ++ED  R ++ +  K+ D 
Sbjct:   195 VVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFYKEADT 254

Query:   333 SLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIII 392
              +     +L   EL+ ++ + L    +++V+++     + +W      L       ++++
Sbjct:   255 QIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDV--WTTGLWREISIALPDGIYGSRVMM 312

Query:   393 TTSSTEDFVEPLGAAFSTLH-VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQIL 451
             TT        P G   ST H +  L ++E+W LF  KA  A  + Q R+  L  + ++++
Sbjct:   313 TTRDMNVASFPYGIG-STKHEIELLKEDEAWVLFSNKAFPAS-LEQCRTQNLEPIARKLV 370

Query:   452 NICDXXXXXXXXXXXXXSTKQPSYE-EWSKVIERANGD-----------NLVALCYQDLP 499
               C              STK+  +E EW KV    N +           +++ L + DLP
Sbjct:   371 ERCQGLPLAIASLGSMMSTKK--FESEWKKVYSTLNWELNNNHELKIVRSIMFLSFNDLP 428

Query:   500 AQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHM 559
               +K C LY  LFP  Y +  +RLI +W A+ F  P   + A  E++A+ YL ELV R+M
Sbjct:   429 YPLKRCFLYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKA--EEVADSYLNELVYRNM 486

Query:   560 IQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLA 619
             +QVI W   G PK   M  V+++I    ++   F   ++     + +A+++  +  R L 
Sbjct:   487 LQVILWNPFGRPKAFKMHDVIWEIALSVSKLERFCDVYNDDSDGDDAAETMENYGSRHLC 546

Query:   620 ANLGSNSFPYSSLLSWRLHSYLVFDS 645
               +     P  S+ +  LHS LV  S
Sbjct:   547 --IQKEMTP-DSIRATNLHSLLVCSS 569

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009626 "plant-type hypersensitive response" evidence=IDA

TAIR|locus:504956186 AT1G58602 [Arabidopsis thaliana (taxid:3702)]

 Score = 195 (73.7 bits), Expect = 2.5e-24, Sum P(2) = 2.5e-24
 Identities = 86/312 (27%), Positives = 135/312 (43%)

Query:   667 RLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSH 726
             RL +L+VLDL           + +G+L  L YL L    +  +P S   L  L  L++  
Sbjct:   580 RLELLRVLDLVQAKLKGGKLASCIGKLIHLRYLSLEYAEVTHIPYSLGNLKLLIYLNLHI 639

Query:   727 TKVQR---LPYAFWPSRHLYLNWIFLATNVFRHPQF-VKWETSLQTLWGLCIKADEVQSL 782
             +   R   +P      + L   ++ L + + R  +  +     L+TL     K   ++ L
Sbjct:   640 SLSSRSNFVPNVLMGMQEL--RYLALPSLIERKTKLELSNLVKLETLENFSTKNSSLEDL 697

Query:   783 DYFRRLTSLRXXXXXXXXXXXXXXXXEIIGAVLQLSELHSLKLICETPSYLPLLEMA--- 839
                R +  LR                  IG +  L +L     I +  S +   E     
Sbjct:   698 ---RGMVRLRTLTIELIEETSLETLAASIGGLKYLEKLE----IDDLGSKMRTKEAGIVF 750

Query:   840 EHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFG 899
             +   L++L L  ++P  S   ++ FP ++ TL L   RLE DPMPIL +L QLK L L  
Sbjct:   751 DFVHLKRLRLELYMPRLSK--EQHFPSHLTTLYLQHCRLEEDPMPILEKLLQLKELELGH 808

Query:   900 GSYTGEEMSCSSGEFPXXXXXXXXXXXXXXQWRIKEGAMPCLRQLEIRSCGYL--VPPTG 957
              S++G++M CSS  FP               W+++E +MP L  L I  C  L  +P   
Sbjct:   809 KSFSGKKMVCSSCGFPQLQKLSISGLKEWEDWKVEESSMPLLLTLNIFDCRKLKQLPDEH 868

Query:   958 L-KHVTS-SLRE 967
             L  H+T+ SL++
Sbjct:   869 LPSHLTAISLKK 880

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2075170 RPP13 "RECOGNITION OF PERONOSPORA PARASITICA 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 340 (124.7 bits), Expect = 2.7e-31, Sum P(4) = 2.7e-31
 Identities = 102/350 (29%), Positives = 177/350 (50%)

Query:   275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQID--- 331
             +I++ G  G GKT LAR +YN   VK  F  RAW ++      +  D+L  I++ +    
Sbjct:   187 IISIFGMGGLGKTALARKLYNSRDVKERFEYRAWTYVS--QEYKTGDILMRIIRSLGMTS 244

Query:   332 -ESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKI 390
              E L K+    + EEL   +   L+   +L+V+++   +++  WDS    L    +  ++
Sbjct:   245 GEELEKIRK-FAEEELEVYLYGLLEGKKYLVVVDDIWEREA--WDSLKRALPCNHEGSRV 301

Query:   391 IITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQI 450
             IITT   +   E +   F    +  L   ESWELF ++A    ++ Q +  +L+K  K++
Sbjct:   302 IITTR-IKAVAEGVDGRFYAHKLRFLTFEESWELFEQRA--FRNI-QRKDEDLLKTGKEM 357

Query:   451 LNICDXXXXXXXXXXXXXSTKQPSYEEWSKVIE----RANGDNL-VA-----LCYQDLPA 500
             +  C              S K PS  EW+ V      R   D++ VA     L +++L  
Sbjct:   358 VQKCRGLPLCIVVLAGLLSRKTPS--EWNDVCNSLWRRLKDDSIHVAPIVFDLSFKELRH 415

Query:   501 QVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMI 560
             + K C LY+ +FP +YEI + +LIHL  AEGF   D +++   ED+A  Y+EEL+ R ++
Sbjct:   416 ESKLCFLYLSIFPEDYEIDLEKLIHLLVAEGFIQGDEEMMM--EDVARYYIEELIDRSLL 473

Query:   561 QVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFL--YHHHHPQRLNSSAK 608
             + +R R  G   +C +  +L D+   K++++ F+  Y+ H  Q  +++ +
Sbjct:   474 EAVR-RERGKVMSCRIHDLLRDVAIKKSKELNFVNVYNDHVAQHSSTTCR 522

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=TAS

GO:0009814 "defense response, incompatible interaction" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00010286001 SubName- Full=Chromosome chr5 scaffold_253, whole genome shotgun sequence; (736 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	1007
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-40
pfam13401	124	pfam13401, AAA_22, AAA domain	2e-05
pfam13207	114	pfam13207, AAA_17, AAA domain	4e-04
PRK08118	167	PRK08118, PRK08118, topology modulation protein; R	0.004

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score =  150 bits (382), Expect = 2e-40
 Identities = 90/276 (32%), Positives = 129/276 (46%), Gaps = 25/276 (9%)

Query: 274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVED--RDVLADILKQID 331
            V+ ++G  G GKTTLA+ +YN   V  HF   AWV +          +D+L ++     
Sbjct: 20  GVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQELGLDDS 79

Query: 332 ESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKII 391
           + + K E      EL  +I +AL    FL+V+++    +   WD             ++I
Sbjct: 80  DWVEKNE-----SELAVKIKEALLRKRFLLVLDDV--WEKNDWDKIGVPFPDGENGSRVI 132

Query: 392 ITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQIL 451
           +TT S E     +G       V  L   ESWELF  K    E        EL ++ K+I+
Sbjct: 133 VTTRS-ESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKEL---PPCPELEEVAKEIV 188

Query: 452 NICDGLPLRVVLLAGLLSTKQPSYEEWSKVI-----ERANGDNLV------ALCYQDLPA 500
             C GLPL + +L GLL+ K  + +EW  V+     E A  D L       +L Y +LP 
Sbjct: 189 EKCKGLPLALKVLGGLLAFKS-TVQEWEHVLEQLNNELAGRDGLNEVLSILSLSYDNLPM 247

Query: 501 QVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPD 536
            +K C LY+ LFP +Y I   +LI LW AEGF  P 
Sbjct: 248 HLKRCFLYLALFPEDYNIRKEQLIKLWIAEGFVIPS 283

Length = 285

>gnl|CDD|222104 pfam13401, AAA_22, AAA domain

 Score = 44.6 bits (106), Expect = 2e-05
 Identities = 27/96 (28%), Positives = 45/96 (46%), Gaps = 11/96 (11%)

Query: 274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES 333
            +  L G++GSGKTTL R       + R    R  V++   S+   +D+L  IL+ +   
Sbjct: 5   GIGVLTGESGSGKTTLLR------RLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLP 58

Query: 334 LLKVEATLSAEELMWRITQALDDS-TFLIVMENAEH 368
           L       +  EL+  I  AL      L++++ A+H
Sbjct: 59  LSG----GTTAELLEAILDALKRRGRPLLIIDEAQH 90

Length = 124

>gnl|CDD|221983 pfam13207, AAA_17, AAA domain

 Score = 40.7 bits (95), Expect = 4e-04
 Identities = 13/76 (17%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 275 VIALIGKAGSGKTTLARIV-----YNRVYVKRHFTKRAWVHIP---IMSMVEDRDVLADI 326
           +I + G  GSGK+TLA+ +        + +     +     +    +  +  D ++L +I
Sbjct: 1   IILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGLAELDDGELDDIDIDLELLEEI 60

Query: 327 LKQIDESLLKVEATLS 342
           L ++ +    ++    
Sbjct: 61  LDELAKQEWVIDGVRE 76

Length = 114

>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed

 Score = 38.8 bits (91), Expect = 0.004
 Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 8/59 (13%)

Query: 276 IALIGKAGSGKTTLARIVYNRVYVK-----RHFTKRAWVHIPIMSMVEDRDVLADILKQ 329
           I LIG  GSGK+TLAR +  ++ +        F K  W  +P     E   V  +++K+
Sbjct: 4   IILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVP---KEEQITVQNELVKE 59

Length = 167

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	1007
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.91
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.9
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.9
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.86
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.84
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.83
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.77
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.69
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.64
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.58
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.54
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.42
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.41
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.38
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.37
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	99.34
PRK04841	903	transcriptional regulator MalT; Provisional	99.34
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.31
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.3
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.23
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	99.09
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.05
KOG4237	498	consensus Extracellular matrix protein slit, conta	99.03
KOG4237	498	consensus Extracellular matrix protein slit, conta	98.99
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.98
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.93
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.88
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.87
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.87
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.79
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.78
PF05729	166	NACHT: NACHT domain	98.77
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.74
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.63
PRK13342	413	recombination factor protein RarA; Reviewed	98.59
COG3903	414	Predicted ATPase [General function prediction only	98.57
PRK06893	229	DNA replication initiation factor; Validated	98.57
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.56
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.55
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.52
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.52
KOG2028	554	consensus ATPase related to the helicase subunit o	98.48
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.47
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.46
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.46
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.41
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.4
PF13173	128	AAA_14: AAA domain	98.38
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.37
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.33
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.32
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.31
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.31
PRK12402	337	replication factor C small subunit 2; Reviewed	98.3
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.28
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.27
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.26
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.23
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.21
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.21
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.21
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.2
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.19
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.19
COG3899	849	Predicted ATPase [General function prediction only	98.18
PRK04195	482	replication factor C large subunit; Provisional	98.18
PLN03025	319	replication factor C subunit; Provisional	98.17
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.17
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.16
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.15
PRK13341	725	recombination factor protein RarA/unknown domain f	98.15
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.15
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.15
cd01128	249	rho_factor Transcription termination factor rho is	98.14
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.13
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.11
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.08
PRK09376	416	rho transcription termination factor Rho; Provisio	98.07
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.07
PLN03150	623	hypothetical protein; Provisional	98.06
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.03
PRK08727	233	hypothetical protein; Validated	98.01
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.01
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.98
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.98
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.98
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.97
KOG4341	483	consensus F-box protein containing LRR [General fu	97.97
PRK09087	226	hypothetical protein; Validated	97.97
PRK08084	235	DNA replication initiation factor; Provisional	97.97
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.96
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.94
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.93
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.91
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.9
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.88
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.87
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.86
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.86
PF14516	331	AAA_35: AAA-like domain	97.85
PHA02544	316	44 clamp loader, small subunit; Provisional	97.85
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.85
PTZ00202	550	tuzin; Provisional	97.85
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.84
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.82
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.79
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	97.77
KOG2982	418	consensus Uncharacterized conserved protein [Funct	97.77
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.76
PRK05642	234	DNA replication initiation factor; Validated	97.76
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.74
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.74
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.73
TIGR00767	415	rho transcription termination factor Rho. Members	97.73
PLN03150	623	hypothetical protein; Provisional	97.72
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	97.71
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.71
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.71
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.69
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.69
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.69
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.68
KOG4341	483	consensus F-box protein containing LRR [General fu	97.68
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.66
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.64
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.63
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.63
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.62
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.59
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.59
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.58
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.55
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.54
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.53
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.5
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.49
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.49
KOG2982	418	consensus Uncharacterized conserved protein [Funct	97.48
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.46
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.43
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.43
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.42
PRK12422	445	chromosomal replication initiation protein; Provis	97.41
PRK08116	268	hypothetical protein; Validated	97.4
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.37
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.35
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.35
PRK15386	426	type III secretion protein GogB; Provisional	97.34
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.32
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	97.32
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.29
CHL00181	287	cbbX CbbX; Provisional	97.28
PF00004	132	AAA: ATPase family associated with various cellula	97.27
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.24
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.23
CHL00095	821	clpC Clp protease ATP binding subunit	97.22
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.22
PRK06620	214	hypothetical protein; Validated	97.21
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.21
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.2
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.19
PRK15386	426	type III secretion protein GogB; Provisional	97.14
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.11
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.11
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.11
smart00382	148	AAA ATPases associated with a variety of cellular	97.09
PRK10865	857	protein disaggregation chaperone; Provisional	97.05
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.04
CHL00176	638	ftsH cell division protein; Validated	97.03
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.03
PRK08181	269	transposase; Validated	97.02
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	96.99
PRK12377	248	putative replication protein; Provisional	96.96
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.95
PRK07952	244	DNA replication protein DnaC; Validated	96.95
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.94
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	96.92
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	96.9
PRK10536	262	hypothetical protein; Provisional	96.88
PRK08118	167	topology modulation protein; Reviewed	96.84
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	96.81
PRK06871	325	DNA polymerase III subunit delta'; Validated	96.8
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.8
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.78
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.77
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.76
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.71
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.69
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	96.67
PRK08939	306	primosomal protein DnaI; Reviewed	96.67
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	96.67
PRK06835	329	DNA replication protein DnaC; Validated	96.64
PRK10865	857	protein disaggregation chaperone; Provisional	96.63
PRK07993	334	DNA polymerase III subunit delta'; Validated	96.61
PRK06921	266	hypothetical protein; Provisional	96.6
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.6
PRK06526	254	transposase; Provisional	96.6
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.56
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	96.52
PRK09183	259	transposase/IS protein; Provisional	96.51
PRK06090	319	DNA polymerase III subunit delta'; Validated	96.51
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.49
PRK06964	342	DNA polymerase III subunit delta'; Validated	96.49
PRK04132	846	replication factor C small subunit; Provisional	96.48
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	96.46
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.43
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	96.4
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.4
PRK12608	380	transcription termination factor Rho; Provisional	96.4
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.35
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.35
PRK13531	498	regulatory ATPase RavA; Provisional	96.31
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.31
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.31
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.26
PRK07261	171	topology modulation protein; Provisional	96.26
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.24
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.23
KOG1514	767	consensus Origin recognition complex, subunit 1, a	96.22
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.17
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.17
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.12
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.09
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.07
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.05
CHL00095	821	clpC Clp protease ATP binding subunit	96.04
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	96.02
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.02
PRK09354	349	recA recombinase A; Provisional	96.01
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.99
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	95.97
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	95.96
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.95
PRK04296	190	thymidine kinase; Provisional	95.94
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	95.93
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	95.9
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.87
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	95.82
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.79
PHA00729	226	NTP-binding motif containing protein	95.78
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	95.75
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	95.75
CHL00195	489	ycf46 Ycf46; Provisional	95.75
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.74
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	95.73
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.72
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.64
cd01394	218	radB RadB. The archaeal protein radB shares simila	95.63
PRK14974	336	cell division protein FtsY; Provisional	95.61
PRK10867	433	signal recognition particle protein; Provisional	95.61
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.56
PRK05541	176	adenylylsulfate kinase; Provisional	95.54
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.46
KOG1947	482	consensus Leucine rich repeat proteins, some prote	95.38
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.33
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	95.33
TIGR00959	428	ffh signal recognition particle protein. This mode	95.31
PRK06067	234	flagellar accessory protein FlaH; Validated	95.27
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.21
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	95.18
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	95.18
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	95.16
PRK07132	299	DNA polymerase III subunit delta'; Validated	95.15
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	95.14
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.13
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.13
PRK08233	182	hypothetical protein; Provisional	95.11
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	95.11
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.1
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.09
PRK05022	509	anaerobic nitric oxide reductase transcription reg	95.05
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.04
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.04
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	95.02
KOG1969	877	consensus DNA replication checkpoint protein CHL12	95.01
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.0
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	94.93
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	94.91
PRK06696	223	uridine kinase; Validated	94.9
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	94.89
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	94.87
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	94.84
PF00154	322	RecA: recA bacterial DNA recombination protein; In	94.79
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	94.78
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	94.74
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	94.73
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	94.71
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.7
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	94.69
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	94.68
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.67
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	94.64
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	94.57
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	94.57
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	94.56
cd03216	163	ABC_Carb_Monos_I This family represents the domain	94.55
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	94.53
PRK04301	317	radA DNA repair and recombination protein RadA; Va	94.52
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	94.51
PRK11608	326	pspF phage shock protein operon transcriptional ac	94.51
PRK05480	209	uridine/cytidine kinase; Provisional	94.48
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	94.47
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.45
PRK15455	644	PrkA family serine protein kinase; Provisional	94.44
PRK07667	193	uridine kinase; Provisional	94.41
PTZ00035	337	Rad51 protein; Provisional	94.4
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	94.33
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	94.32
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.31
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	94.28
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	94.25
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	94.25
KOG2123	388	consensus Uncharacterized conserved protein [Funct	94.23
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	94.19
PTZ00301	210	uridine kinase; Provisional	94.17
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	94.08
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	94.05
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	94.03
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	94.0
PRK04328	249	hypothetical protein; Provisional	93.95
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	93.93
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	93.92
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.91
TIGR00235	207	udk uridine kinase. Model contains a number of lon	93.9
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	93.89
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	93.87
PRK15453	290	phosphoribulokinase; Provisional	93.87
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	93.86
PRK06762	166	hypothetical protein; Provisional	93.85
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	93.83
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	93.83
PRK09519	790	recA DNA recombination protein RecA; Reviewed	93.82
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	93.74
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	93.72
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	93.7
PF07726	131	AAA_3: ATPase family associated with various cellu	93.68
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	93.67
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	93.62
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	93.62
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	93.6
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	93.57
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	93.57
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	93.56
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	93.55
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	93.51
PRK06547	172	hypothetical protein; Provisional	93.49
KOG2123	388	consensus Uncharacterized conserved protein [Funct	93.49
PRK10416	318	signal recognition particle-docking protein FtsY;	93.47
cd03246	173	ABCC_Protease_Secretion This family represents the	93.46
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	93.46
PRK03839	180	putative kinase; Provisional	93.46
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	93.43
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	93.34
cd03215	182	ABC_Carb_Monos_II This family represents domain II	93.33
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	93.33
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	93.31
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	93.3
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	93.3
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	93.27
PRK00625	173	shikimate kinase; Provisional	93.26
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	93.21
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	93.19
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	93.15
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	93.14
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	93.14
PRK04040	188	adenylate kinase; Provisional	93.12
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	93.08
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.0
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	92.99
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	92.96
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	92.93
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	92.88
PRK00131	175	aroK shikimate kinase; Reviewed	92.87
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	92.86
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	92.8
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	92.78
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	92.76
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	92.76
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	92.75
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	92.72
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	92.7
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.7
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	92.64
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	92.63
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	92.63
PRK11823	446	DNA repair protein RadA; Provisional	92.62
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	92.6
PRK07276	290	DNA polymerase III subunit delta'; Validated	92.54
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	92.52
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	92.5
PRK13947	171	shikimate kinase; Provisional	92.46
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	92.45
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	92.42
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	92.4
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	92.37
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	92.37
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	92.34
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	92.34
PRK13948	182	shikimate kinase; Provisional	92.33
PRK00889	175	adenylylsulfate kinase; Provisional	92.33
KOG3864	221	consensus Uncharacterized conserved protein [Funct	92.27
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	92.27
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	92.26
PRK03846	198	adenylylsulfate kinase; Provisional	92.25
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	92.23
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	92.17
PRK00409	782	recombination and DNA strand exchange inhibitor pr	92.14
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	92.13
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	92.12
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	92.11
PRK12678	672	transcription termination factor Rho; Provisional	92.09
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	92.09
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	92.09
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	92.08
COG2884	223	FtsE Predicted ATPase involved in cell division [C	91.98
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	91.98
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	91.94
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	91.93
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	91.91
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	91.91
PRK13949	169	shikimate kinase; Provisional	91.9
cd02034	116	CooC The accessory protein CooC, which contains a	91.9
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	91.9
PRK05917	290	DNA polymerase III subunit delta'; Validated	91.89
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	91.87
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	91.78
PRK06217	183	hypothetical protein; Validated	91.75
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	91.73
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	91.73
PRK15424	538	propionate catabolism operon regulatory protein Pr	91.71
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	91.7
PTZ00185	574	ATPase alpha subunit; Provisional	91.7
TIGR01287	275	nifH nitrogenase iron protein. This model describe	91.68
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	91.66
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	91.59
KOG0927	614	consensus Predicted transporter (ABC superfamily)	91.59
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	91.58
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	91.55
PRK05439	311	pantothenate kinase; Provisional	91.54
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	91.53
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	91.51
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	91.5
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	91.5
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	91.48
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	91.46
PTZ00088	229	adenylate kinase 1; Provisional	91.44
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	91.42
KOG1947	482	consensus Leucine rich repeat proteins, some prote	91.4
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	91.38
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	91.32
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	91.29
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	91.27
KOG0736	953	consensus Peroxisome assembly factor 2 containing	91.27
PRK13236	296	nitrogenase reductase; Reviewed	91.26
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	91.23
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	91.21
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	91.2
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	91.15
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	91.14
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	91.11
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	91.09
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	91.06
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	91.06
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	91.05
PRK08149	428	ATP synthase SpaL; Validated	91.05
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	91.0
PRK13946	184	shikimate kinase; Provisional	90.94
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	90.94
PRK05057	172	aroK shikimate kinase I; Reviewed	90.92
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	90.87
PRK12339	197	2-phosphoglycerate kinase; Provisional	90.85
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	90.85
PLN02200	234	adenylate kinase family protein	90.81
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	90.79
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	90.77
cd02040	270	NifH NifH gene encodes component II (iron protein)	90.75
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	90.74
PRK00300	205	gmk guanylate kinase; Provisional	90.73
PRK13765	637	ATP-dependent protease Lon; Provisional	90.71
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	90.65
PRK13768	253	GTPase; Provisional	90.65
PLN02165	334	adenylate isopentenyltransferase	90.63
PRK14530	215	adenylate kinase; Provisional	90.55
PRK14527	191	adenylate kinase; Provisional	90.54
PRK13230	279	nitrogenase reductase-like protein; Reviewed	90.52
PF00142	273	Fer4_NifH: 4Fe-4S iron sulfur cluster binding prot	90.41
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	90.41
PRK14737	186	gmk guanylate kinase; Provisional	90.38
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	90.38
PRK13975	196	thymidylate kinase; Provisional	90.34
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	90.3
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	90.28
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	90.26
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	90.25
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	90.24
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	90.22
PRK06936	439	type III secretion system ATPase; Provisional	90.13

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=6.1e-86  Score=801.14  Aligned_cols=806  Identities=25%  Similarity=0.310  Sum_probs=613.7

Q ss_pred             chhhHHHHHHHhhhhhhhhcccchhhhhhHHHHHH---HHHHHHHHhhccCCCCCcccCCcccCH-----HHHHHHhhcc
Q 001843            3 AESSVSLLIVKLKTLFPAADEGATISSWTQKRVLK---AIESLQLLIKNKKPCLDSSAGGEAADD-----EARFMQAFYS   74 (1007)
Q Consensus         3 a~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~---~l~~~~~~l~~~~~~~~~a~~~~~~~~-----~~~~r~~~yd   74 (1007)
                      |++.++..++|+.+++.+++   ..+.|+++.+..   +|..++++++|       |++++....     +..+++++|+
T Consensus         1 ~~~~~s~~~~~~~~~l~~~~---~~~~~~~~~i~~Lk~~L~~l~~~l~d-------~~a~~~~~~~~~~~~e~~~~~~~~   70 (889)
T KOG4658|consen    1 MGACVSFGVEKLDQLLNRES---ECLDGKDNYILELKENLKALQSALED-------LDAKRDDLERRVNWEEDVGDLVYL   70 (889)
T ss_pred             CCeEEEEehhhHHHHHHHHH---HHHhchHHHHHHHHHHHHHHHHHHHH-------HHhhcchHHHHHHHHHHHHHHHHH
Confidence            45677888999999999999   888899888877   99999999999       998876554     8899999999


Q ss_pred             hHHHHhHhHHhhhhccccccCCce--eeeeeeeccccch-hhhHHhHHH------HhcccchhhhhhhhhcCCCCCCCch
Q 001843           75 AQDAINGLAIREEVCQMWRIDPVW--VTILTVTTFPFSS-FENLRLRSL------FSFGMNKFKRELEIRGSSSSSSSSY  145 (1007)
Q Consensus        75 ~eD~lD~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~-~~~~~i~~l------i~~~~~~~~~~~~~~~~~~~~~~~~  145 (1007)
                      +||.++.|.......+..+.....  ..+  .++....+ ..+..+..+      +-+.++.|...              
T Consensus        71 ~e~~~~~~~v~~~~~~~~~~l~~~~~~~~--~~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~--------------  134 (889)
T KOG4658|consen   71 AEDIIWLFLVEEIERKANDLLSTRSVERQ--RLCLCGFCSKNVSDSYKYGKRVSKVLREVESLGSK--------------  134 (889)
T ss_pred             HHHHHHHHHHHHHHHHHhHHhhhhHHHHH--HHhhhhhHhHhhhhhHhHHHHHHHHHHHHHHhccc--------------
Confidence            999999999877665321111100  000  11111111 333333333      34444555111              


Q ss_pred             hhhhhhhcccCCCCCCCCCCCCCccchhhhhhhhhccccccccCCccEEecchhHHHHHHhhcCCCCCCCcccccccccc
Q 001843          146 EHQQQLVEVNDTGPSFSPYQGGYSTHRSQQQRWARISDYFCAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIV  225 (1007)
Q Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~~~~~~  225 (1007)
                      +...               .++   ..   ......+...+.....+ ||.+..++++.+.|.+++.             
T Consensus       135 ~~~~---------------~~~---~~---~~~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~~-------------  179 (889)
T KOG4658|consen  135 GVFE---------------VVG---ES---LDPREKVETRPIQSESD-VGLETMLEKLWNRLMEDDV-------------  179 (889)
T ss_pred             ccee---------------ccc---cc---ccchhhcccCCCCcccc-ccHHHHHHHHHHHhccCCC-------------
Confidence            1110               000   00   00222355566666666 9999999999999997664             


Q ss_pred             ccccccccCCcccccCCCCCcCCCCCCCCchhhccccccccCCCCCCcEEEEEEcCCCChHHHHHHHHHhhhh-cccCCC
Q 001843          226 DGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTTTTTQVIALIGKAGSGKTTLARIVYNRVY-VKRHFT  304 (1007)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~-~~~~F~  304 (1007)
                                                                      .+++|+||||+||||||++++|+.. ++.+|+
T Consensus       180 ------------------------------------------------~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd  211 (889)
T KOG4658|consen  180 ------------------------------------------------GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFD  211 (889)
T ss_pred             ------------------------------------------------CEEEEECCCcccHHHHHHHHhcccchhcccCc
Confidence                                                            8999999999999999999999987 999999


Q ss_pred             ceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHHcCCCcEEEEEeCcCccCchhhhhhc-cccCC
Q 001843          305 KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCS  383 (1007)
Q Consensus       305 ~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~  383 (1007)
                      .++||+||  +.++...++.+|++.++.. ...........++..+.+.|++|||||||||||  +..+|+.+. ++|..
T Consensus       212 ~~iWV~VS--k~f~~~~iq~~Il~~l~~~-~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW--~~~dw~~I~~~~p~~  286 (889)
T KOG4658|consen  212 GVIWVVVS--KEFTTRKIQQTILERLGLL-DEEWEDKEEDELASKLLNLLEGKRFLLVLDDIW--EEVDWDKIGVPFPSR  286 (889)
T ss_pred             eEEEEEEc--ccccHHhHHHHHHHHhccC-CcccchhhHHHHHHHHHHHhccCceEEEEeccc--ccccHHhcCCCCCCc
Confidence            99999999  9999999999999999874 122233344788999999999999999999999  888899999 99998


Q ss_pred             CCCCcEEEEEcCCCcccccc-cCCcceeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHH
Q 001843          384 FTQCGKIIITTSSTEDFVEP-LGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVV  462 (1007)
Q Consensus       384 ~~~gs~IliTTR~~~~va~~-~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~  462 (1007)
                       ..||||++|||+.. |+.. ++.. ..++++.|+++|||+||++.+|....   ...+.++++|++|+++|+|+|||++
T Consensus       287 -~~g~KvvlTTRs~~-V~~~~m~~~-~~~~v~~L~~~eaW~LF~~~v~~~~~---~~~~~i~~lak~v~~kC~GLPLAl~  360 (889)
T KOG4658|consen  287 -ENGSKVVLTTRSEE-VCGRAMGVD-YPIEVECLTPEEAWDLFQKKVGPNTL---GSHPDIEELAKEVAEKCGGLPLALN  360 (889)
T ss_pred             -cCCeEEEEEeccHh-hhhccccCC-ccccccccCccccHHHHHHhhccccc---cccccHHHHHHHHHHHhCChHHHHH
Confidence             89999999999999 9998 5554 99999999999999999999998754   2345589999999999999999999


Q ss_pred             HHHHHhcCCCCChHHHHHHHHHcc-------------cchhhhhhhcCCccCchhhhhhhccCCCCcccchhHHHHHHHh
Q 001843          463 LLAGLLSTKQPSYEEWSKVIERAN-------------GDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCA  529 (1007)
Q Consensus       463 ~~g~~L~~~~~~~~~w~~~l~~l~-------------i~~~l~~sy~~L~~~~k~cfl~la~fp~~~~i~~~~Li~~Wia  529 (1007)
                      ++|+.|+.+.. .++|+++.+.+.             +..+|.+||++||+++|.||+|||+||+||.|+++.||.+|+|
T Consensus       361 viG~~ma~K~t-~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWia  439 (889)
T KOG4658|consen  361 VLGGLLACKKT-VQEWRRALNVLKSSLAADFSGMEESILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIA  439 (889)
T ss_pred             HHHHHhcCCCc-HHHHHHHHccccccccCCCCchhhhhHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHh
Confidence            99999999986 889999999874             7799999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCccCCHHHHHHHHHHHHHhccceEEEeecCCCCcceEEcCHHHHHHHHhhhh-----hcCeEEEecCCCCcc
Q 001843          530 EGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAE-----DIGFLYHHHHPQRLN  604 (1007)
Q Consensus       530 eg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~~~~~g~~~~~~mHdlv~d~~~~~~~-----~e~f~~~~~~~~~~~  604 (1007)
                      |||+. +...+.+.++.|+.|+.+|++++|++.....  ++..+|+|||+||++|.++++     +|+++  +.++.+..
T Consensus       440 EGfi~-~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~--~~~~~~kmHDvvRe~al~ias~~~~~~e~~i--v~~~~~~~  514 (889)
T KOG4658|consen  440 EGFID-PLDGGETAEDVGYDYIEELVRASLLIEERDE--GRKETVKMHDVVREMALWIASDFGKQEENQI--VSDGVGLS  514 (889)
T ss_pred             ccCcC-ccccccchhcchHHHHHHHHHHHHHhhcccc--cceeEEEeeHHHHHHHHHHhccccccccceE--EECCcCcc
Confidence            99994 3466889999999999999999999987643  677899999999999999999     77765  33333333


Q ss_pred             cccCCCCCCCeEEEEEecCCCCCCCCCcCCCcceEEEEecccc--CCCCchhhhhhhccccccCCCCcccEEEecCCC-C
Q 001843          605 SSAKSLPKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRI--RGTPAKQIGIILGKCISKRRLGMLKVLDLEGVY-K  681 (1007)
Q Consensus       605 ~~~~~~~~~~~r~Lsl~~~~~~~~~~~~~~~~LRsL~l~~~~~--~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~-l  681 (1007)
                      ..+....+..+||++++++..........+++|+||.+.++..  ..        +...+|  ..++.||||||++|. +
T Consensus       515 ~~~~~~~~~~~rr~s~~~~~~~~~~~~~~~~~L~tLll~~n~~~l~~--------is~~ff--~~m~~LrVLDLs~~~~l  584 (889)
T KOG4658|consen  515 EIPQVKSWNSVRRMSLMNNKIEHIAGSSENPKLRTLLLQRNSDWLLE--------ISGEFF--RSLPLLRVLDLSGNSSL  584 (889)
T ss_pred             ccccccchhheeEEEEeccchhhccCCCCCCccceEEEeecchhhhh--------cCHHHH--hhCcceEEEECCCCCcc
Confidence            3445557788999999999988777777888999999999862  21        445678  999999999999876 4


Q ss_pred             CCcCCCccccCCCcCcEEecccCCCcccCcccccCCCCCEEeecCC-cccccccc---ccccceeccccccccccccccc
Q 001843          682 PMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHT-KVQRLPYA---FWPSRHLYLNWIFLATNVFRHP  757 (1007)
Q Consensus       682 ~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~-~l~~lP~~---i~~Lr~L~l~~~~~~~~~~~~p  757 (1007)
                      .  ++|..|++|.|||||+|+++.|+.||.++++|+.|++||+..+ .+..+|..   +.+||+|.+.   ... .....
T Consensus       585 ~--~LP~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~---~s~-~~~~~  658 (889)
T KOG4658|consen  585 S--KLPSSIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGRLESIPGILLELQSLRVLRLP---RSA-LSNDK  658 (889)
T ss_pred             C--cCChHHhhhhhhhcccccCCCccccchHHHHHHhhheeccccccccccccchhhhcccccEEEee---ccc-cccch
Confidence            4  8999999999999999999999999999999999999999998 55555553   4555888887   322 12222


Q ss_pred             ccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeec-C-CCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCc
Q 001843          758 QFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCS-S-TTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPL  835 (1007)
Q Consensus       758 ~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~-~-~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~  835 (1007)
                      ..++.+.+|++|..+.+...+......+..+++|+++...-. . .......    .++..+.+|+.|.+..+.......
T Consensus       659 ~~l~el~~Le~L~~ls~~~~s~~~~e~l~~~~~L~~~~~~l~~~~~~~~~~~----~~~~~l~~L~~L~i~~~~~~e~~~  734 (889)
T KOG4658|consen  659 LLLKELENLEHLENLSITISSVLLLEDLLGMTRLRSLLQSLSIEGCSKRTLI----SSLGSLGNLEELSILDCGISEIVI  734 (889)
T ss_pred             hhHHhhhcccchhhheeecchhHhHhhhhhhHHHHHHhHhhhhcccccceee----cccccccCcceEEEEcCCCchhhc
Confidence            334555666666555555443333445555555553322221 0 1123344    778889999999999855432111


Q ss_pred             cccc------CCCCCcEEEecccC-CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCcee
Q 001843          836 LEMA------EHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMS  908 (1007)
Q Consensus       836 ~~l~------~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~  908 (1007)
                      ....      .+++|.++.+.++. ...+. |..- .++|+.|.+..|...+.+++....+..+..+.+..+.+.+....
T Consensus       735 ~~~~~~~~~~~f~~l~~~~~~~~~~~r~l~-~~~f-~~~L~~l~l~~~~~~e~~i~~~k~~~~l~~~i~~f~~~~~l~~~  812 (889)
T KOG4658|consen  735 EWEESLIVLLCFPNLSKVSILNCHMLRDLT-WLLF-APHLTSLSLVSCRLLEDIIPKLKALLELKELILPFNKLEGLRML  812 (889)
T ss_pred             ccccccchhhhHHHHHHHHhhccccccccc-hhhc-cCcccEEEEecccccccCCCHHHHhhhcccEEecccccccceee
Confidence            1111      13355555555544 55555 6654 89999999999998888999888888888877765666554445


Q ss_pred             ecCCCCCCCcEEEeccCCCCcceEEcC----CCCccccEeEeecc-CCCC-CCcC
Q 001843          909 CSSGEFPNLLVLKLWKLNRLRQWRIKE----GAMPCLRQLEIRSC-GYLV-PPTG  957 (1007)
Q Consensus       909 ~~~~~fp~L~~L~L~~~~~L~~l~~~~----~~~p~L~~L~l~~c-~~L~-lp~~  957 (1007)
                      ...++||++..+.+... .+..|.++.    +.||.+.++.+.+| .++. +|.+
T Consensus       813 ~~l~~l~~i~~~~l~~~-~l~~~~ve~~p~l~~~P~~~~~~i~~~~~~~~~~~~~  866 (889)
T KOG4658|consen  813 CSLGGLPQLYWLPLSFL-KLEELIVEECPKLGKLPLLSTLTIVGCEEKLKEYPDG  866 (889)
T ss_pred             ecCCCCceeEecccCcc-chhheehhcCcccccCccccccceeccccceeecCCc
Confidence            56677777777777763 366666655    56777777777775 4444 5554

>PLN03210 Resistant to P

Probab=100.00  E-value=2.2e-60  Score=610.42  Aligned_cols=665  Identities=17%  Similarity=0.193  Sum_probs=444.1

Q ss_pred             cccCCccEEecchhHHHHHHhhcCCCCCCCccccccccccccccccccCCcccccCCCCCcCCCCCCCCchhhccccccc
Q 001843          186 CAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQS  265 (1007)
Q Consensus       186 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (1007)
                      +..+..++|||+..++++..+|..+..                                                 +.  
T Consensus       179 ~~~~~~~~vG~~~~l~~l~~lL~l~~~-------------------------------------------------~~--  207 (1153)
T PLN03210        179 PSNDFEDFVGIEDHIAKMSSLLHLESE-------------------------------------------------EV--  207 (1153)
T ss_pred             cCcccccccchHHHHHHHHHHHccccC-------------------------------------------------ce--
Confidence            334567899999999999998853322                                                 33  


Q ss_pred             cCCCCCCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEe---cCCC-C--------CC-HHHHHHHHHHHHhh
Q 001843          266 SSTTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI---PIMS-M--------VE-DRDVLADILKQIDE  332 (1007)
Q Consensus       266 ~~~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~---s~~~-~--------~~-~~~~l~~il~~l~~  332 (1007)
                              ++|+||||||+||||||+++|+  ++..+|+..+|+..   +... .        +. ...++.+++.++..
T Consensus       208 --------~vvgI~G~gGiGKTTLA~~l~~--~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~  277 (1153)
T PLN03210        208 --------RMVGIWGSSGIGKTTIARALFS--RLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILD  277 (1153)
T ss_pred             --------EEEEEEcCCCCchHHHHHHHHH--HHhhcCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhC
Confidence                    9999999999999999999999  78889999888742   1000 0        00 12344444444433


Q ss_pred             hhhhhccccCHHHHHHHHHHHcCCCcEEEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcCCCcccccccCCcceeee
Q 001843          333 SLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLH  412 (1007)
Q Consensus       333 ~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~  412 (1007)
                      .     ....... ...+++.|+++|+||||||||  +..+|+.+......++.||+||||||++. ++..++.. ++|+
T Consensus       278 ~-----~~~~~~~-~~~~~~~L~~krvLLVLDdv~--~~~~l~~L~~~~~~~~~GsrIIiTTrd~~-vl~~~~~~-~~~~  347 (1153)
T PLN03210        278 K-----KDIKIYH-LGAMEERLKHRKVLIFIDDLD--DQDVLDALAGQTQWFGSGSRIIVITKDKH-FLRAHGID-HIYE  347 (1153)
T ss_pred             C-----CCcccCC-HHHHHHHHhCCeEEEEEeCCC--CHHHHHHHHhhCccCCCCcEEEEEeCcHH-HHHhcCCC-eEEE
Confidence            2     0011111 245778899999999999999  88899998854555588999999999999 88877666 8999


Q ss_pred             cCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCChHHHHHHHHHcc------
Q 001843          413 VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERAN------  486 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~~~~w~~~l~~l~------  486 (1007)
                      ++.|++++||+||+++||+...    .++++++++++|+++|+|+||||+++|++|+.++  ..+|+.++.++.      
T Consensus       348 v~~l~~~ea~~LF~~~Af~~~~----~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~--~~~W~~~l~~L~~~~~~~  421 (1153)
T PLN03210        348 VCLPSNELALEMFCRSAFKKNS----PPDGFMELASEVALRAGNLPLGLNVLGSYLRGRD--KEDWMDMLPRLRNGLDGK  421 (1153)
T ss_pred             ecCCCHHHHHHHHHHHhcCCCC----CcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCC--HHHHHHHHHHHHhCccHH
Confidence            9999999999999999997643    3567899999999999999999999999999875  899999999887      


Q ss_pred             cchhhhhhhcCCcc-CchhhhhhhccCCCCcccchhHHHHHHHhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEee
Q 001843          487 GDNLVALCYQDLPA-QVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRW  565 (1007)
Q Consensus       487 i~~~l~~sy~~L~~-~~k~cfl~la~fp~~~~i~~~~Li~~Wiaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~~  565 (1007)
                      +..+|++||++|++ ..|.||+++|+||.+..++   .+..|++.+...            ++..++.|+++||++... 
T Consensus       422 I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l~~~~~~------------~~~~l~~L~~ksLi~~~~-  485 (1153)
T PLN03210        422 IEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVN---DIKLLLANSDLD------------VNIGLKNLVDKSLIHVRE-  485 (1153)
T ss_pred             HHHHHHHhhhccCccchhhhhheehhhcCCCCHH---HHHHHHHhcCCC------------chhChHHHHhcCCEEEcC-
Confidence            88999999999987 5999999999999987554   377788876551            233489999999998643 


Q ss_pred             cCCCCcceEEcCHHHHHHHHhhhhhcC-------eEEEecCCCCccc-ccCCCCCCCeEEEEEecCCCCCCC----CCcC
Q 001843          566 RLDGSPKTCCMPGVLYDILRPKAEDIG-------FLYHHHHPQRLNS-SAKSLPKFAVRRLAANLGSNSFPY----SSLL  633 (1007)
Q Consensus       566 ~~~g~~~~~~mHdlv~d~~~~~~~~e~-------f~~~~~~~~~~~~-~~~~~~~~~~r~Lsl~~~~~~~~~----~~~~  633 (1007)
                            ..+.|||++|++++.++.++.       |+   ++...... ........+++.+++..+......    ....
T Consensus       486 ------~~~~MHdLl~~~~r~i~~~~~~~~~~r~~l---~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~aF~~  556 (1153)
T PLN03210        486 ------DIVEMHSLLQEMGKEIVRAQSNEPGEREFL---VDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAFKG  556 (1153)
T ss_pred             ------CeEEhhhHHHHHHHHHHHhhcCCCCcceeE---eCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHHHhc
Confidence                  259999999999999987653       22   11111000 000114456788877655433211    1256


Q ss_pred             CCcceEEEEeccccCCCCchhhhhhhccccccCCC-CcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcc
Q 001843          634 SWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRL-GMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDS  712 (1007)
Q Consensus       634 ~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l-~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~  712 (1007)
                      +.+|+.|.+..+......  .+.-.++.-|  ..+ ..||.|.+.++.+.  .+|..+ .+.+|++|+|+++.+..+|..
T Consensus       557 m~~L~~L~~~~~~~~~~~--~~~~~lp~~~--~~lp~~Lr~L~~~~~~l~--~lP~~f-~~~~L~~L~L~~s~l~~L~~~  629 (1153)
T PLN03210        557 MRNLLFLKFYTKKWDQKK--EVRWHLPEGF--DYLPPKLRLLRWDKYPLR--CMPSNF-RPENLVKLQMQGSKLEKLWDG  629 (1153)
T ss_pred             CccccEEEEecccccccc--cceeecCcch--hhcCcccEEEEecCCCCC--CCCCcC-CccCCcEEECcCccccccccc
Confidence            788888887665321000  0000122223  333 34677777766666  666555 456666666666666666666


Q ss_pred             cccCCCCCEEeecCC-ccccccc--cccccceecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCC
Q 001843          713 TPILFCLATLDVSHT-KVQRLPY--AFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLT  789 (1007)
Q Consensus       713 i~~L~~L~~L~L~~~-~l~~lP~--~i~~Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~  789 (1007)
                      +..+++|++|+|++| .+..+|.  .+.+|++|++.   +|.....+|..+++|++|+.|....+... ...+..+ .++
T Consensus       630 ~~~l~~Lk~L~Ls~~~~l~~ip~ls~l~~Le~L~L~---~c~~L~~lp~si~~L~~L~~L~L~~c~~L-~~Lp~~i-~l~  704 (1153)
T PLN03210        630 VHSLTGLRNIDLRGSKNLKEIPDLSMATNLETLKLS---DCSSLVELPSSIQYLNKLEDLDMSRCENL-EILPTGI-NLK  704 (1153)
T ss_pred             cccCCCCCEEECCCCCCcCcCCccccCCcccEEEec---CCCCccccchhhhccCCCCEEeCCCCCCc-CccCCcC-CCC
Confidence            666666666666665 4555553  12334666666   66555666666666666666654443332 1122222 455


Q ss_pred             CCCeEEeeecCCCchhhHH----------------HHHHHhhcCCCCCeEEEeecCCCC------C-CcccccCCCCCcE
Q 001843          790 SLRKLGLKCSSTTSTSLKK----------------EIIGAVLQLSELHSLKLICETPSY------L-PLLEMAEHYKLQK  846 (1007)
Q Consensus       790 ~L~~L~l~~~~~~~~~l~~----------------~~~~~l~~l~~L~~L~L~~~~~~~------~-~~~~l~~~~~L~~  846 (1007)
                      +|+.|.+++|. ....+++                .+|..+ .+++|++|.+.......      . .......+++|+.
T Consensus       705 sL~~L~Lsgc~-~L~~~p~~~~nL~~L~L~~n~i~~lP~~~-~l~~L~~L~l~~~~~~~l~~~~~~l~~~~~~~~~sL~~  782 (1153)
T PLN03210        705 SLYRLNLSGCS-RLKSFPDISTNISWLDLDETAIEEFPSNL-RLENLDELILCEMKSEKLWERVQPLTPLMTMLSPSLTR  782 (1153)
T ss_pred             CCCEEeCCCCC-CccccccccCCcCeeecCCCccccccccc-cccccccccccccchhhccccccccchhhhhccccchh
Confidence            66666666553 1111110                011111 23444444443311000      0 0001112457888


Q ss_pred             EEecccC--CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEecc
Q 001843          847 LYLSGHL--PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWK  924 (1007)
Q Consensus       847 L~L~g~~--~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~  924 (1007)
                      |+|+++.  ..+|. ++.. +++|+.|+|++|..... +|....+++|+.|+|++|... ..++   ...++|+.|+|++
T Consensus       783 L~Ls~n~~l~~lP~-si~~-L~~L~~L~Ls~C~~L~~-LP~~~~L~sL~~L~Ls~c~~L-~~~p---~~~~nL~~L~Ls~  855 (1153)
T PLN03210        783 LFLSDIPSLVELPS-SIQN-LHKLEHLEIENCINLET-LPTGINLESLESLDLSGCSRL-RTFP---DISTNISDLNLSR  855 (1153)
T ss_pred             eeCCCCCCccccCh-hhhC-CCCCCEEECCCCCCcCe-eCCCCCccccCEEECCCCCcc-cccc---ccccccCEeECCC
Confidence            8888764  66787 7777 88888888888753322 333336788888888854332 2222   2245788888886


Q ss_pred             CCCCcceEEcCCCCccccEeEeeccCCCC-CCcCccccccCccEEEeccCCc
Q 001843          925 LNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLTNMPS  975 (1007)
Q Consensus       925 ~~~L~~l~~~~~~~p~L~~L~l~~c~~L~-lp~~l~~L~~~L~~L~l~~c~~  975 (1007)
                       +.++.+|...+.+++|+.|++.+|++|+ +|..+..+ ++|+.|++++|+.
T Consensus       856 -n~i~~iP~si~~l~~L~~L~L~~C~~L~~l~~~~~~L-~~L~~L~l~~C~~  905 (1153)
T PLN03210        856 -TGIEEVPWWIEKFSNLSFLDMNGCNNLQRVSLNISKL-KHLETVDFSDCGA  905 (1153)
T ss_pred             -CCCccChHHHhcCCCCCEEECCCCCCcCccCcccccc-cCCCeeecCCCcc
Confidence             4677777777789999999999999999 88888889 9999999999964

syringae 6; Provisional

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=100.00  E-value=8e-42  Score=377.18  Aligned_cols=250  Identities=31%  Similarity=0.545  Sum_probs=207.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ++|+|+||||+||||||+++|++..++.+|+.++|+.++  ...+..+++..|+.+++..........+.......+++.
T Consensus        20 ~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~--~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~   97 (287)
T PF00931_consen   20 RVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLS--KNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLREL   97 (287)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEE--S-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCcCCcceeeeecccccccccccccccccccc--cccccccccccccccccccccccccccccccccccchhh
Confidence            999999999999999999999987799999999999999  888889999999999987621122456788899999999


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIA  432 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~  432 (1007)
                      |+++++||||||||  +...|+.+. .++.. ..|++||||||+.. ++..+......+++++|+++||++||.+.++..
T Consensus        98 L~~~~~LlVlDdv~--~~~~~~~l~~~~~~~-~~~~kilvTTR~~~-v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~  173 (287)
T PF00931_consen   98 LKDKRCLLVLDDVW--DEEDLEELREPLPSF-SSGSKILVTTRDRS-VAGSLGGTDKVIELEPLSEEEALELFKKRAGRK  173 (287)
T ss_dssp             HCCTSEEEEEEEE---SHHHH-------HCH-HSS-EEEEEESCGG-GGTTHHSCEEEEECSS--HHHHHHHHHHHHTSH
T ss_pred             hccccceeeeeeec--ccccccccccccccc-cccccccccccccc-ccccccccccccccccccccccccccccccccc
Confidence            99999999999999  888999998 77666 78999999999998 888776533899999999999999999999876


Q ss_pred             cccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCChHHHHHHHHHcc------------cchhhhhhhcCCcc
Q 001843          433 EDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERAN------------GDNLVALCYQDLPA  500 (1007)
Q Consensus       433 ~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~~~~w~~~l~~l~------------i~~~l~~sy~~L~~  500 (1007)
                      ..   ...+..++.+++|+++|+|+||||+++|++|+.+. +..+|+.+++.+.            +..++.+||+.||+
T Consensus       174 ~~---~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~-~~~~w~~~~~~l~~~~~~~~~~~~~~~~~l~~s~~~L~~  249 (287)
T PF00931_consen  174 ES---ESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKS-TVDEWEEALEELENSLRESRDYDRSVFSALELSYDSLPD  249 (287)
T ss_dssp             S-------TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHH-SSSSHHHHHHHHHHCHTCSSGSCHHHHHHHHHHHHSSHT
T ss_pred             cc---ccccccccccccccccccccccccccccccccccc-cccccccccccccccccccccccccccccceechhcCCc
Confidence            51   22345567899999999999999999999997665 3788999887654            78899999999999


Q ss_pred             CchhhhhhhccCCCCcccchhHHHHHHHhcccC
Q 001843          501 QVKPCILYMGLFPREYEIPVRRLIHLWCAEGFA  533 (1007)
Q Consensus       501 ~~k~cfl~la~fp~~~~i~~~~Li~~Wiaeg~i  533 (1007)
                      ++|+||+|||+||+++.|+++.|+++|+++|||
T Consensus       250 ~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i  282 (287)
T PF00931_consen  250 ELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFI  282 (287)
T ss_dssp             CCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHT
T ss_pred             cHHHHHhhCcCCCCCceECHHHHHHHHHHCCCC
Confidence            999999999999999999999999999999999

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional

Probab=99.91  E-value=4e-24  Score=275.63  Aligned_cols=337  Identities=21%  Similarity=0.158  Sum_probs=163.8

Q ss_pred             CCeEEEEEecCCCCCCCCCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccC
Q 001843          613 FAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGR  692 (1007)
Q Consensus       613 ~~~r~Lsl~~~~~~~~~~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~  692 (1007)
                      .++|+|.+.++..........+++|++|.+.+|.+..        .++..+  .++++|++|+|++|.+.+ .+|..+++
T Consensus       118 ~~L~~L~Ls~n~l~~~~p~~~l~~L~~L~Ls~n~~~~--------~~p~~~--~~l~~L~~L~L~~n~l~~-~~p~~~~~  186 (968)
T PLN00113        118 SSLRYLNLSNNNFTGSIPRGSIPNLETLDLSNNMLSG--------EIPNDI--GSFSSLKVLDLGGNVLVG-KIPNSLTN  186 (968)
T ss_pred             CCCCEEECcCCccccccCccccCCCCEEECcCCcccc--------cCChHH--hcCCCCCEEECccCcccc-cCChhhhh
Confidence            3455555555543322222345556666666555421        233334  566666666666666543 45556666


Q ss_pred             CCcCcEEecccCCCc-ccCcccccCCCCCEEeecCCccc-ccccccccc---ceecccccccccccccccccccCcCCCc
Q 001843          693 LPFLEYLGLRSTFID-SLPDSTPILFCLATLDVSHTKVQ-RLPYAFWPS---RHLYLNWIFLATNVFRHPQFVKWETSLQ  767 (1007)
Q Consensus       693 L~~Lr~L~L~~n~i~-~LP~~i~~L~~L~~L~L~~~~l~-~lP~~i~~L---r~L~l~~~~~~~~~~~~p~~i~~L~~L~  767 (1007)
                      +++|++|+|++|.+. .+|..++++++|++|+|++|.+. .+|..+.++   ++|+++   +|.....+|..++++++|+
T Consensus       187 l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~---~n~l~~~~p~~l~~l~~L~  263 (968)
T PLN00113        187 LTSLEFLTLASNQLVGQIPRELGQMKSLKWIYLGYNNLSGEIPYEIGGLTSLNHLDLV---YNNLTGPIPSSLGNLKNLQ  263 (968)
T ss_pred             CcCCCeeeccCCCCcCcCChHHcCcCCccEEECcCCccCCcCChhHhcCCCCCEEECc---CceeccccChhHhCCCCCC
Confidence            666666666666554 45666666666666666666544 455444433   566665   5544445555566666666


Q ss_pred             cccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEE
Q 001843          768 TLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKL  847 (1007)
Q Consensus       768 ~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L  847 (1007)
                      +|....+. ..+..+..++.+++|+.|+++++. ....+    |..+.++++|+.|+++++......+..+..+++|+.|
T Consensus       264 ~L~L~~n~-l~~~~p~~l~~l~~L~~L~Ls~n~-l~~~~----p~~~~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L  337 (968)
T PLN00113        264 YLFLYQNK-LSGPIPPSIFSLQKLISLDLSDNS-LSGEI----PELVIQLQNLEILHLFSNNFTGKIPVALTSLPRLQVL  337 (968)
T ss_pred             EEECcCCe-eeccCchhHhhccCcCEEECcCCe-eccCC----ChhHcCCCCCcEEECCCCccCCcCChhHhcCCCCCEE
Confidence            55332221 112344455555666666665543 11112    2444555555555555544333334444455555555


Q ss_pred             EecccC--CCCCcCccCCCCCCceEEEEEeeecCCCCcCccc------------------------cCCCCcEEEeecCC
Q 001843          848 YLSGHL--PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILG------------------------RLRQLKILRLFGGS  901 (1007)
Q Consensus       848 ~L~g~~--~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~------------------------~Lp~L~~L~L~~~~  901 (1007)
                      +++++.  ..+|. ++.. +++|+.|+|++|.+....+..+.                        .+++|+.|+|++|.
T Consensus       338 ~L~~n~l~~~~p~-~l~~-~~~L~~L~Ls~n~l~~~~p~~~~~~~~L~~L~l~~n~l~~~~p~~~~~~~~L~~L~L~~n~  415 (968)
T PLN00113        338 QLWSNKFSGEIPK-NLGK-HNNLTVLDLSTNNLTGEIPEGLCSSGNLFKLILFSNSLEGEIPKSLGACRSLRRVRLQDNS  415 (968)
T ss_pred             ECcCCCCcCcCCh-HHhC-CCCCcEEECCCCeeEeeCChhHhCcCCCCEEECcCCEecccCCHHHhCCCCCCEEECcCCE
Confidence            555544  33444 4444 45555555555544333333333                        34444444444333


Q ss_pred             cCCCceeecCCCCCCCcEEEeccCCCCcceEEcCCCCccccEeEeeccCCCC-CCcCccccccCccEEEeccCC
Q 001843          902 YTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLTNMP  974 (1007)
Q Consensus       902 ~~~~~l~~~~~~fp~L~~L~L~~~~~L~~l~~~~~~~p~L~~L~l~~c~~L~-lp~~l~~L~~~L~~L~l~~c~  974 (1007)
                      +.+ .++.....+++|+.|+++++.-...++.....+++|+.|++++|.... +|..+ .. ++|+.|++++|.
T Consensus       416 l~~-~~p~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~n~~~~~~p~~~-~~-~~L~~L~ls~n~  486 (968)
T PLN00113        416 FSG-ELPSEFTKLPLVYFLDISNNNLQGRINSRKWDMPSLQMLSLARNKFFGGLPDSF-GS-KRLENLDLSRNQ  486 (968)
T ss_pred             eee-ECChhHhcCCCCCEEECcCCcccCccChhhccCCCCcEEECcCceeeeecCccc-cc-ccceEEECcCCc
Confidence            221 122222334444444444432222222222345556666666554333 44432 34 556666666553

>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional

Probab=99.90  E-value=1.7e-23  Score=269.82  Aligned_cols=339  Identities=18%  Similarity=0.121  Sum_probs=166.5

Q ss_pred             CeEEEEEecCCCCCCC--CCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCC--------
Q 001843          614 AVRRLAANLGSNSFPY--SSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPM--------  683 (1007)
Q Consensus       614 ~~r~Lsl~~~~~~~~~--~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~--------  683 (1007)
                      .++.|.+..+......  ....+++|++|.+.+|.+.+   .    ++..+|  .++++|++|+|++|.+.+        
T Consensus        70 ~v~~L~L~~~~i~~~~~~~~~~l~~L~~L~Ls~n~~~~---~----ip~~~~--~~l~~L~~L~Ls~n~l~~~~p~~~l~  140 (968)
T PLN00113         70 RVVSIDLSGKNISGKISSAIFRLPYIQTINLSNNQLSG---P----IPDDIF--TTSSSLRYLNLSNNNFTGSIPRGSIP  140 (968)
T ss_pred             cEEEEEecCCCccccCChHHhCCCCCCEEECCCCccCC---c----CChHHh--ccCCCCCEEECcCCccccccCccccC
Confidence            4556666554432211  12445666666666655421   0    222333  455555555555555442        


Q ss_pred             -------------cCCCccccCCCcCcEEecccCCCc-ccCcccccCCCCCEEeecCCccc-ccccccccc---ceeccc
Q 001843          684 -------------LTNNNALGRLPFLEYLGLRSTFID-SLPDSTPILFCLATLDVSHTKVQ-RLPYAFWPS---RHLYLN  745 (1007)
Q Consensus       684 -------------~~lp~~i~~L~~Lr~L~L~~n~i~-~LP~~i~~L~~L~~L~L~~~~l~-~lP~~i~~L---r~L~l~  745 (1007)
                                   ..+|..++++.+|++|+|++|.+. .+|..++++++|++|+|++|.+. .+|..++++   ++|++.
T Consensus       141 ~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~  220 (968)
T PLN00113        141 NLETLDLSNNMLSGEIPNDIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLTLASNQLVGQIPRELGQMKSLKWIYLG  220 (968)
T ss_pred             CCCEEECcCCcccccCChHHhcCCCCCEEECccCcccccCChhhhhCcCCCeeeccCCCCcCcCChHHcCcCCccEEECc
Confidence                         034444445555555555554443 44444555555555555544333 334333332   444444


Q ss_pred             ccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEE
Q 001843          746 WIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL  825 (1007)
Q Consensus       746 ~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L  825 (1007)
                         +|.....+|..++++++|++|+...+. ..+..+..++.+++|+.|++.++. -...+    |..+..+++|+.|++
T Consensus       221 ---~n~l~~~~p~~l~~l~~L~~L~L~~n~-l~~~~p~~l~~l~~L~~L~L~~n~-l~~~~----p~~l~~l~~L~~L~L  291 (968)
T PLN00113        221 ---YNNLSGEIPYEIGGLTSLNHLDLVYNN-LTGPIPSSLGNLKNLQYLFLYQNK-LSGPI----PPSIFSLQKLISLDL  291 (968)
T ss_pred             ---CCccCCcCChhHhcCCCCCEEECcCce-eccccChhHhCCCCCCEEECcCCe-eeccC----chhHhhccCcCEEEC
Confidence               343333444444555555544322221 112234444555555555554443 11111    244445555555555


Q ss_pred             eecCCCCCCcccccCCCCCcEEEecccC--CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcC
Q 001843          826 ICETPSYLPLLEMAEHYKLQKLYLSGHL--PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYT  903 (1007)
Q Consensus       826 ~~~~~~~~~~~~l~~~~~L~~L~L~g~~--~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~  903 (1007)
                      +++......+..+..+++|+.|+++++.  ..+|. ++.. +++|+.|+|++|.+....+..++.+++|+.|+|++|...
T Consensus       292 s~n~l~~~~p~~~~~l~~L~~L~l~~n~~~~~~~~-~~~~-l~~L~~L~L~~n~l~~~~p~~l~~~~~L~~L~Ls~n~l~  369 (968)
T PLN00113        292 SDNSLSGEIPELVIQLQNLEILHLFSNNFTGKIPV-ALTS-LPRLQVLQLWSNKFSGEIPKNLGKHNNLTVLDLSTNNLT  369 (968)
T ss_pred             cCCeeccCCChhHcCCCCCcEEECCCCccCCcCCh-hHhc-CCCCCEEECcCCCCcCcCChHHhCCCCCcEEECCCCeeE
Confidence            5444333233444455555555555544  33444 4444 555555555555554444444555555555555544332


Q ss_pred             CCceeecCCCCCCCcEEEeccCCCCcceEEcCCCCccccEeEeeccCCCC-CCcCccccccCccEEEeccCC
Q 001843          904 GEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLTNMP  974 (1007)
Q Consensus       904 ~~~l~~~~~~fp~L~~L~L~~~~~L~~l~~~~~~~p~L~~L~l~~c~~L~-lp~~l~~L~~~L~~L~l~~c~  974 (1007)
                      + .++.....+++|+.|.+.+++-...++...+.+++|+.|++.+|.... +|..+..+ ++|+.|++++|.
T Consensus       370 ~-~~p~~~~~~~~L~~L~l~~n~l~~~~p~~~~~~~~L~~L~L~~n~l~~~~p~~~~~l-~~L~~L~Ls~N~  439 (968)
T PLN00113        370 G-EIPEGLCSSGNLFKLILFSNSLEGEIPKSLGACRSLRRVRLQDNSFSGELPSEFTKL-PLVYFLDISNNN  439 (968)
T ss_pred             e-eCChhHhCcCCCCEEECcCCEecccCCHHHhCCCCCCEEECcCCEeeeECChhHhcC-CCCCEEECcCCc
Confidence            2 222223345556666666543333334444567888888888865444 77778888 888888888774

>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]

Probab=99.90  E-value=2.9e-26  Score=251.32  Aligned_cols=340  Identities=17%  Similarity=0.100  Sum_probs=272.1

Q ss_pred             CCCCeEEEEEecCCCCCCCC-CcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCcc
Q 001843          611 PKFAVRRLAANLGSNSFPYS-SLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNA  689 (1007)
Q Consensus       611 ~~~~~r~Lsl~~~~~~~~~~-~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~  689 (1007)
                      ....++.|.+........++ ...+.+|..|.+..|...         .+.+-+  +.++.||.+++..|++....+|..
T Consensus        30 qMt~~~WLkLnrt~L~~vPeEL~~lqkLEHLs~~HN~L~---------~vhGEL--s~Lp~LRsv~~R~N~LKnsGiP~d   98 (1255)
T KOG0444|consen   30 QMTQMTWLKLNRTKLEQVPEELSRLQKLEHLSMAHNQLI---------SVHGEL--SDLPRLRSVIVRDNNLKNSGIPTD   98 (1255)
T ss_pred             HhhheeEEEechhhhhhChHHHHHHhhhhhhhhhhhhhH---------hhhhhh--ccchhhHHHhhhccccccCCCCch
Confidence            34557777777766555543 366788888888887764         233445  888999999999999887678999


Q ss_pred             ccCCCcCcEEecccCCCcccCcccccCCCCCEEeecCCccccccccc-ccc---ceecccccccccccccccccccCcCC
Q 001843          690 LGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAF-WPS---RHLYLNWIFLATNVFRHPQFVKWETS  765 (1007)
Q Consensus       690 i~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i-~~L---r~L~l~~~~~~~~~~~~p~~i~~L~~  765 (1007)
                      |.+|..|..|+|++|++++.|..+.+-+++-+|+|++|+|..+|..+ .+|   -.|+++   .+. ...+|+.+..|..
T Consensus        99 iF~l~dLt~lDLShNqL~EvP~~LE~AKn~iVLNLS~N~IetIPn~lfinLtDLLfLDLS---~Nr-Le~LPPQ~RRL~~  174 (1255)
T KOG0444|consen   99 IFRLKDLTILDLSHNQLREVPTNLEYAKNSIVLNLSYNNIETIPNSLFINLTDLLFLDLS---NNR-LEMLPPQIRRLSM  174 (1255)
T ss_pred             hcccccceeeecchhhhhhcchhhhhhcCcEEEEcccCccccCCchHHHhhHhHhhhccc---cch-hhhcCHHHHHHhh
Confidence            99999999999999999999999989999999999999999998753 334   777888   554 6688888999999


Q ss_pred             CccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCc
Q 001843          766 LQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQ  845 (1007)
Q Consensus       766 L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~  845 (1007)
                      |++|...... .....+..+..++.|..|.+++.....    ..+|.++..+.+|..++++.|.... .++.+..+++|+
T Consensus       175 LqtL~Ls~NP-L~hfQLrQLPsmtsL~vLhms~TqRTl----~N~Ptsld~l~NL~dvDlS~N~Lp~-vPecly~l~~Lr  248 (1255)
T KOG0444|consen  175 LQTLKLSNNP-LNHFQLRQLPSMTSLSVLHMSNTQRTL----DNIPTSLDDLHNLRDVDLSENNLPI-VPECLYKLRNLR  248 (1255)
T ss_pred             hhhhhcCCCh-hhHHHHhcCccchhhhhhhcccccchh----hcCCCchhhhhhhhhccccccCCCc-chHHHhhhhhhh
Confidence            9998443222 212344455566667777777654222    3344889999999999999987776 788899999999


Q ss_pred             EEEecccC-CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEecc
Q 001843          846 KLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWK  924 (1007)
Q Consensus       846 ~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~  924 (1007)
                      .|+|++|. +++.. .... ..+|++|+|+.|+++ ..+..+.+|+.|+.|.+.+|...-+.++...+.+.+|+.+...+
T Consensus       249 rLNLS~N~iteL~~-~~~~-W~~lEtLNlSrNQLt-~LP~avcKL~kL~kLy~n~NkL~FeGiPSGIGKL~~Levf~aan  325 (1255)
T KOG0444|consen  249 RLNLSGNKITELNM-TEGE-WENLETLNLSRNQLT-VLPDAVCKLTKLTKLYANNNKLTFEGIPSGIGKLIQLEVFHAAN  325 (1255)
T ss_pred             eeccCcCceeeeec-cHHH-Hhhhhhhccccchhc-cchHHHhhhHHHHHHHhccCcccccCCccchhhhhhhHHHHhhc
Confidence            99999988 77765 5566 789999999999985 56778899999999999988888888999999999999999997


Q ss_pred             CCCCcceEEcCCCCccccEeEeeccCCCC-CCcCccccccCccEEEeccCCccc
Q 001843          925 LNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLTNMPSTF  977 (1007)
Q Consensus       925 ~~~L~~l~~~~~~~p~L~~L~l~~c~~L~-lp~~l~~L~~~L~~L~l~~c~~~~  977 (1007)
                       +.|+-+|.....|+.|+.|.++. +.|- +|++|.-| +.|+.|++..+|+.+
T Consensus       326 -N~LElVPEglcRC~kL~kL~L~~-NrLiTLPeaIHlL-~~l~vLDlreNpnLV  376 (1255)
T KOG0444|consen  326 -NKLELVPEGLCRCVKLQKLKLDH-NRLITLPEAIHLL-PDLKVLDLRENPNLV  376 (1255)
T ss_pred             -cccccCchhhhhhHHHHHhcccc-cceeechhhhhhc-CCcceeeccCCcCcc
Confidence             67888888778899999999985 6666 99999999 999999999999775

>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]

Probab=99.86  E-value=3.1e-24  Score=235.54  Aligned_cols=318  Identities=21%  Similarity=0.145  Sum_probs=256.3

Q ss_pred             CCeEEEEEecCCCC-CCCCCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCcccc
Q 001843          613 FAVRRLAANLGSNS-FPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALG  691 (1007)
Q Consensus       613 ~~~r~Lsl~~~~~~-~~~~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~  691 (1007)
                      .++.||++..|... ...+...++.||++++..|.....-      +++++|   ++..|.+||||+|++.  +.|..+.
T Consensus        55 qkLEHLs~~HN~L~~vhGELs~Lp~LRsv~~R~N~LKnsG------iP~diF---~l~dLt~lDLShNqL~--EvP~~LE  123 (1255)
T KOG0444|consen   55 QKLEHLSMAHNQLISVHGELSDLPRLRSVIVRDNNLKNSG------IPTDIF---RLKDLTILDLSHNQLR--EVPTNLE  123 (1255)
T ss_pred             hhhhhhhhhhhhhHhhhhhhccchhhHHHhhhccccccCC------CCchhc---ccccceeeecchhhhh--hcchhhh
Confidence            56788888877643 4445688999999999999884211      556665   8999999999999999  9999999


Q ss_pred             CCCcCcEEecccCCCcccCcc-cccCCCCCEEeecCCcccccccccccc---ceecccccccccccccccccccCcCCCc
Q 001843          692 RLPFLEYLGLRSTFIDSLPDS-TPILFCLATLDVSHTKVQRLPYAFWPS---RHLYLNWIFLATNVFRHPQFVKWETSLQ  767 (1007)
Q Consensus       692 ~L~~Lr~L~L~~n~i~~LP~~-i~~L~~L~~L~L~~~~l~~lP~~i~~L---r~L~l~~~~~~~~~~~~p~~i~~L~~L~  767 (1007)
                      +-+++-+|+|++|+|.+||.+ +-+|..|-+|||++|.+..+|+.+.+|   +.|.++   ++.....-...+..|++|+
T Consensus       124 ~AKn~iVLNLS~N~IetIPn~lfinLtDLLfLDLS~NrLe~LPPQ~RRL~~LqtL~Ls---~NPL~hfQLrQLPsmtsL~  200 (1255)
T KOG0444|consen  124 YAKNSIVLNLSYNNIETIPNSLFINLTDLLFLDLSNNRLEMLPPQIRRLSMLQTLKLS---NNPLNHFQLRQLPSMTSLS  200 (1255)
T ss_pred             hhcCcEEEEcccCccccCCchHHHhhHhHhhhccccchhhhcCHHHHHHhhhhhhhcC---CChhhHHHHhcCccchhhh
Confidence            999999999999999999987 468999999999999999999987777   889998   6543222223355678888


Q ss_pred             cccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEE
Q 001843          768 TLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKL  847 (1007)
Q Consensus       768 ~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L  847 (1007)
                      +|......+.-...+.++..|.||+.++++.+.  ...++    ..+-++.+|+.|+|++|.... .-.....-.+|+.|
T Consensus       201 vLhms~TqRTl~N~Ptsld~l~NL~dvDlS~N~--Lp~vP----ecly~l~~LrrLNLS~N~ite-L~~~~~~W~~lEtL  273 (1255)
T KOG0444|consen  201 VLHMSNTQRTLDNIPTSLDDLHNLRDVDLSENN--LPIVP----ECLYKLRNLRRLNLSGNKITE-LNMTEGEWENLETL  273 (1255)
T ss_pred             hhhcccccchhhcCCCchhhhhhhhhccccccC--CCcch----HHHhhhhhhheeccCcCceee-eeccHHHHhhhhhh
Confidence            886666655545578889999999999999876  55566    888999999999999976543 11222334589999


Q ss_pred             EecccC-CCCCcCccCCCCCCceEEEEEeeecCCCCc-CccccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEeccC
Q 001843          848 YLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPM-PILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKL  925 (1007)
Q Consensus       848 ~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~-~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~  925 (1007)
                      +|+.|. ..+|. .+.. ++.|++|.+.+|++.-..+ +.+|+|.+|+.+...+|..  +..+.+...+++|+.|.|++ 
T Consensus       274 NlSrNQLt~LP~-avcK-L~kL~kLy~n~NkL~FeGiPSGIGKL~~Levf~aanN~L--ElVPEglcRC~kL~kL~L~~-  348 (1255)
T KOG0444|consen  274 NLSRNQLTVLPD-AVCK-LTKLTKLYANNNKLTFEGIPSGIGKLIQLEVFHAANNKL--ELVPEGLCRCVKLQKLKLDH-  348 (1255)
T ss_pred             ccccchhccchH-HHhh-hHHHHHHHhccCcccccCCccchhhhhhhHHHHhhcccc--ccCchhhhhhHHHHHhcccc-
Confidence            999988 89998 8888 9999999999998865544 4589999999999985544  34566677899999999995 


Q ss_pred             CCCcceEEcCCCCccccEeEeeccCCCCCCc
Q 001843          926 NRLRQWRIKEGAMPCLRQLEIRSCGYLVPPT  956 (1007)
Q Consensus       926 ~~L~~l~~~~~~~p~L~~L~l~~c~~L~lp~  956 (1007)
                      +.|-.+|....-+|.|+.|++..+++|..|.
T Consensus       349 NrLiTLPeaIHlL~~l~vLDlreNpnLVMPP  379 (1255)
T KOG0444|consen  349 NRLITLPEAIHLLPDLKVLDLRENPNLVMPP  379 (1255)
T ss_pred             cceeechhhhhhcCCcceeeccCCcCccCCC
Confidence            6777788777779999999999999999443

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=99.84  E-value=2e-22  Score=220.73  Aligned_cols=347  Identities=18%  Similarity=0.140  Sum_probs=246.0

Q ss_pred             CCCeEEEEEecCCCCCCCCC-cCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCC-cc
Q 001843          612 KFAVRRLAANLGSNSFPYSS-LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNN-NA  689 (1007)
Q Consensus       612 ~~~~r~Lsl~~~~~~~~~~~-~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp-~~  689 (1007)
                      ..+...+.+..|....++.. ....+|..|.+.+|.+....        ...+  +-++.||+||||.|.+.  .+| .+
T Consensus       101 l~nLq~v~l~~N~Lt~IP~f~~~sghl~~L~L~~N~I~sv~--------se~L--~~l~alrslDLSrN~is--~i~~~s  168 (873)
T KOG4194|consen  101 LPNLQEVNLNKNELTRIPRFGHESGHLEKLDLRHNLISSVT--------SEEL--SALPALRSLDLSRNLIS--EIPKPS  168 (873)
T ss_pred             CCcceeeeeccchhhhcccccccccceeEEeeecccccccc--------HHHH--HhHhhhhhhhhhhchhh--cccCCC
Confidence            34566666666665544443 44567888888888775322        2334  77888999999999988  666 34


Q ss_pred             ccCCCcCcEEecccCCCcccC-cccccCCCCCEEeecCCccccccccccc-c---ceecccccccccccccccccccCcC
Q 001843          690 LGRLPFLEYLGLRSTFIDSLP-DSTPILFCLATLDVSHTKVQRLPYAFWP-S---RHLYLNWIFLATNVFRHPQFVKWET  764 (1007)
Q Consensus       690 i~~L~~Lr~L~L~~n~i~~LP-~~i~~L~~L~~L~L~~~~l~~lP~~i~~-L---r~L~l~~~~~~~~~~~~p~~i~~L~  764 (1007)
                      +..-.++++|+|++|.|+.+- ..|.+|.+|-+|.|++|.++.+|.-..+ |   +.|++.   .+.....--..|..|.
T Consensus       169 fp~~~ni~~L~La~N~It~l~~~~F~~lnsL~tlkLsrNrittLp~r~Fk~L~~L~~LdLn---rN~irive~ltFqgL~  245 (873)
T KOG4194|consen  169 FPAKVNIKKLNLASNRITTLETGHFDSLNSLLTLKLSRNRITTLPQRSFKRLPKLESLDLN---RNRIRIVEGLTFQGLP  245 (873)
T ss_pred             CCCCCCceEEeeccccccccccccccccchheeeecccCcccccCHHHhhhcchhhhhhcc---ccceeeehhhhhcCch
Confidence            666788999999999998875 4688888999999999999999875433 5   777877   5543222223467777


Q ss_pred             CCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCC
Q 001843          765 SLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKL  844 (1007)
Q Consensus       765 ~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L  844 (1007)
                      +|+.|..-. ++.+...-..+..+.+++.|++..+.  ...+.+   .++-+++.|+.|++++|.......++++-+++|
T Consensus       246 Sl~nlklqr-N~I~kL~DG~Fy~l~kme~l~L~~N~--l~~vn~---g~lfgLt~L~~L~lS~NaI~rih~d~WsftqkL  319 (873)
T KOG4194|consen  246 SLQNLKLQR-NDISKLDDGAFYGLEKMEHLNLETNR--LQAVNE---GWLFGLTSLEQLDLSYNAIQRIHIDSWSFTQKL  319 (873)
T ss_pred             hhhhhhhhh-cCcccccCcceeeecccceeecccch--hhhhhc---ccccccchhhhhccchhhhheeecchhhhcccc
Confidence            777774322 22212233346678888999998776  333332   667788999999999987766677888888999


Q ss_pred             cEEEecccC-CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCC--CceeecCCCCCCCcEEE
Q 001843          845 QKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTG--EEMSCSSGEFPNLLVLK  921 (1007)
Q Consensus       845 ~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~--~~l~~~~~~fp~L~~L~  921 (1007)
                      +.|+|+.|. .++++..+.. ++.|+.|.|+.|.+....-..|..+.+|+.|+|+.|....  ++-...+.++|+|+.|.
T Consensus       320 ~~LdLs~N~i~~l~~~sf~~-L~~Le~LnLs~Nsi~~l~e~af~~lssL~~LdLr~N~ls~~IEDaa~~f~gl~~LrkL~  398 (873)
T KOG4194|consen  320 KELDLSSNRITRLDEGSFRV-LSQLEELNLSHNSIDHLAEGAFVGLSSLHKLDLRSNELSWCIEDAAVAFNGLPSLRKLR  398 (873)
T ss_pred             eeEeccccccccCChhHHHH-HHHhhhhcccccchHHHHhhHHHHhhhhhhhcCcCCeEEEEEecchhhhccchhhhhee
Confidence            999999877 8887745666 8899999999998866666678889999999998775432  12223345689999999


Q ss_pred             eccCCCCcceEEcC-CCCccccEeEeeccCCCC-CCcCccccccCccEEEec------cCCccccccccccc
Q 001843          922 LWKLNRLRQWRIKE-GAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLT------NMPSTFGSVADIER  985 (1007)
Q Consensus       922 L~~~~~L~~l~~~~-~~~p~L~~L~l~~c~~L~-lp~~l~~L~~~L~~L~l~------~c~~~~~~~~~~~~  985 (1007)
                      |.+ ++++.++-.. ..+++|+.|++.+++-.. -|..+..+  .|++|.+.      +|.-.|  ...|-.
T Consensus       399 l~g-Nqlk~I~krAfsgl~~LE~LdL~~NaiaSIq~nAFe~m--~Lk~Lv~nSssflCDCql~W--l~qWl~  465 (873)
T KOG4194|consen  399 LTG-NQLKSIPKRAFSGLEALEHLDLGDNAIASIQPNAFEPM--ELKELVMNSSSFLCDCQLKW--LAQWLY  465 (873)
T ss_pred             ecC-ceeeecchhhhccCcccceecCCCCcceeecccccccc--hhhhhhhcccceEEeccHHH--HHHHHH
Confidence            998 6788887543 358899999999876555 66666664  67777654      565555  454443

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=99.83  E-value=1.8e-21  Score=213.38  Aligned_cols=323  Identities=21%  Similarity=0.162  Sum_probs=185.6

Q ss_pred             CCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccC-cc
Q 001843          634 SWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLP-DS  712 (1007)
Q Consensus       634 ~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP-~~  712 (1007)
                      .+..++|.+++|.++.+        -..+|  .++++|+.+.|.+|.++  .+|.......||+.|+|.+|.|+++. ++
T Consensus        77 p~~t~~LdlsnNkl~~i--------d~~~f--~nl~nLq~v~l~~N~Lt--~IP~f~~~sghl~~L~L~~N~I~sv~se~  144 (873)
T KOG4194|consen   77 PSQTQTLDLSNNKLSHI--------DFEFF--YNLPNLQEVNLNKNELT--RIPRFGHESGHLEKLDLRHNLISSVTSEE  144 (873)
T ss_pred             ccceeeeeccccccccC--------cHHHH--hcCCcceeeeeccchhh--hcccccccccceeEEeeeccccccccHHH
Confidence            34566777777766532        22345  67777777777777777  77766666677777777777777664 34


Q ss_pred             cccCCCCCEEeecCCcccccccc-cc---ccceecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcC
Q 001843          713 TPILFCLATLDVSHTKVQRLPYA-FW---PSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRL  788 (1007)
Q Consensus       713 i~~L~~L~~L~L~~~~l~~lP~~-i~---~Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L  788 (1007)
                      +.-++.|++|||+.|.|.++|.. +.   ++++|++.   ++.....-...|..|.+|-+|. +.-+..+...+..+.+|
T Consensus       145 L~~l~alrslDLSrN~is~i~~~sfp~~~ni~~L~La---~N~It~l~~~~F~~lnsL~tlk-LsrNrittLp~r~Fk~L  220 (873)
T KOG4194|consen  145 LSALPALRSLDLSRNLISEIPKPSFPAKVNIKKLNLA---SNRITTLETGHFDSLNSLLTLK-LSRNRITTLPQRSFKRL  220 (873)
T ss_pred             HHhHhhhhhhhhhhchhhcccCCCCCCCCCceEEeec---cccccccccccccccchheeee-cccCcccccCHHHhhhc
Confidence            66677777777777777776653 22   23777777   5544333334455666665552 22223323344556666


Q ss_pred             CCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEEEecccC-CCCCcCccCC----
Q 001843          789 TSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRS----  863 (1007)
Q Consensus       789 ~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~----  863 (1007)
                      ++|+.|++..+.  .....+   ..|.++++|+.|.|..|+.....-..|..+.+++.|+|..|. ..+...|+..    
T Consensus       221 ~~L~~LdLnrN~--irive~---ltFqgL~Sl~nlklqrN~I~kL~DG~Fy~l~kme~l~L~~N~l~~vn~g~lfgLt~L  295 (873)
T KOG4194|consen  221 PKLESLDLNRNR--IRIVEG---LTFQGLPSLQNLKLQRNDISKLDDGAFYGLEKMEHLNLETNRLQAVNEGWLFGLTSL  295 (873)
T ss_pred             chhhhhhccccc--eeeehh---hhhcCchhhhhhhhhhcCcccccCcceeeecccceeecccchhhhhhcccccccchh
Confidence            666666666554  111110   344455555555555444333223333444444444444433 3333334444    


Q ss_pred             -------------------CCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEecc
Q 001843          864 -------------------FPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWK  924 (1007)
Q Consensus       864 -------------------~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~  924 (1007)
                                         |.++|+.|+|++|+++..+...|..|..|+.|+|+.|...- .-...+.++.+|+.|+|.+
T Consensus       296 ~~L~lS~NaI~rih~d~WsftqkL~~LdLs~N~i~~l~~~sf~~L~~Le~LnLs~Nsi~~-l~e~af~~lssL~~LdLr~  374 (873)
T KOG4194|consen  296 EQLDLSYNAIQRIHIDSWSFTQKLKELDLSSNRITRLDEGSFRVLSQLEELNLSHNSIDH-LAEGAFVGLSSLHKLDLRS  374 (873)
T ss_pred             hhhccchhhhheeecchhhhcccceeEeccccccccCChhHHHHHHHhhhhcccccchHH-HHhhHHHHhhhhhhhcCcC
Confidence                               24555555555555544444455555555555555443210 0011233567888888886


Q ss_pred             CCCCcceEEcC-----CCCccccEeEeeccCCCC-CCc-CccccccCccEEEeccCCccccccccccccc
Q 001843          925 LNRLRQWRIKE-----GAMPCLRQLEIRSCGYLV-PPT-GLKHVTSSLREFLLTNMPSTFGSVADIERVL  987 (1007)
Q Consensus       925 ~~~L~~l~~~~-----~~~p~L~~L~l~~c~~L~-lp~-~l~~L~~~L~~L~l~~c~~~~~~~~~~~~~~  987 (1007)
                      . .+ +|.++.     ..||+|++|.+.+ ++++ +|. .+..| ++|++|++.+++     ++.++++.
T Consensus       375 N-~l-s~~IEDaa~~f~gl~~LrkL~l~g-Nqlk~I~krAfsgl-~~LE~LdL~~Na-----iaSIq~nA  435 (873)
T KOG4194|consen  375 N-EL-SWCIEDAAVAFNGLPSLRKLRLTG-NQLKSIPKRAFSGL-EALEHLDLGDNA-----IASIQPNA  435 (873)
T ss_pred             C-eE-EEEEecchhhhccchhhhheeecC-ceeeecchhhhccC-cccceecCCCCc-----ceeecccc
Confidence            3 23 343332     2489999999998 6798 776 67888 999999999987     44555543

>PLN03210 Resistant to P

Probab=99.77  E-value=6.1e-18  Score=218.57  Aligned_cols=266  Identities=21%  Similarity=0.149  Sum_probs=157.7

Q ss_pred             CCCCcccEEEecCCC-CCCcCCCccccCCCcCcEEecccC-CCcccCcccccCCCCCEEeecCC-ccccccccc--cccc
Q 001843          666 RRLGMLKVLDLEGVY-KPMLTNNNALGRLPFLEYLGLRST-FIDSLPDSTPILFCLATLDVSHT-KVQRLPYAF--WPSR  740 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~-l~~~~lp~~i~~L~~Lr~L~L~~n-~i~~LP~~i~~L~~L~~L~L~~~-~l~~lP~~i--~~Lr  740 (1007)
                      ..+++|+.|+|++|. +.  .+| .++.+++|++|+|++| .+..+|.+|++|++|++|++++| .+..+|..+  .+|+
T Consensus       631 ~~l~~Lk~L~Ls~~~~l~--~ip-~ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~~Lp~~i~l~sL~  707 (1153)
T PLN03210        631 HSLTGLRNIDLRGSKNLK--EIP-DLSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLEILPTGINLKSLY  707 (1153)
T ss_pred             ccCCCCCEEECCCCCCcC--cCC-ccccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcCccCCcCCCCCCC
Confidence            444555555555443 22  333 2444555555555442 24445555555555555555554 444444432  2334


Q ss_pred             eecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHH----HHHHhhc
Q 001843          741 HLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKE----IIGAVLQ  816 (1007)
Q Consensus       741 ~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~----~~~~l~~  816 (1007)
                      +|+++   +|.....+|..   .++|+.|...... .  ..+.....+++|+.|.+..+.  ...+.+.    .+.....
T Consensus       708 ~L~Ls---gc~~L~~~p~~---~~nL~~L~L~~n~-i--~~lP~~~~l~~L~~L~l~~~~--~~~l~~~~~~l~~~~~~~  776 (1153)
T PLN03210        708 RLNLS---GCSRLKSFPDI---STNISWLDLDETA-I--EEFPSNLRLENLDELILCEMK--SEKLWERVQPLTPLMTML  776 (1153)
T ss_pred             EEeCC---CCCCccccccc---cCCcCeeecCCCc-c--ccccccccccccccccccccc--hhhccccccccchhhhhc
Confidence            44444   44433333322   1233333211111 0  011111245566666665432  1111100    0011223


Q ss_pred             CCCCCeEEEeecCCCCCCcccccCCCCCcEEEecccC--CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcE
Q 001843          817 LSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL--PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKI  894 (1007)
Q Consensus       817 l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~--~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~  894 (1007)
                      .++|+.|+|+++......+..+..+++|+.|+|++|.  ..+|. .+ . +++|+.|+|++|...... +  ...++|+.
T Consensus       777 ~~sL~~L~Ls~n~~l~~lP~si~~L~~L~~L~Ls~C~~L~~LP~-~~-~-L~sL~~L~Ls~c~~L~~~-p--~~~~nL~~  850 (1153)
T PLN03210        777 SPSLTRLFLSDIPSLVELPSSIQNLHKLEHLEIENCINLETLPT-GI-N-LESLESLDLSGCSRLRTF-P--DISTNISD  850 (1153)
T ss_pred             cccchheeCCCCCCccccChhhhCCCCCCEEECCCCCCcCeeCC-CC-C-ccccCEEECCCCCccccc-c--ccccccCE
Confidence            4689999999876555567778889999999999865  77887 54 5 899999999998643222 2  22468999


Q ss_pred             EEeecCCcCCCceeecCCCCCCCcEEEeccCCCCcceEEcCCCCccccEeEeeccCCCC
Q 001843          895 LRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLV  953 (1007)
Q Consensus       895 L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~~~L~~l~~~~~~~p~L~~L~l~~c~~L~  953 (1007)
                      |+|++|.+.  .++.....+++|+.|+|.+|++++.++.....+++|+.|++++|.+|+
T Consensus       851 L~Ls~n~i~--~iP~si~~l~~L~~L~L~~C~~L~~l~~~~~~L~~L~~L~l~~C~~L~  907 (1153)
T PLN03210        851 LNLSRTGIE--EVPWWIEKFSNLSFLDMNGCNNLQRVSLNISKLKHLETVDFSDCGALT  907 (1153)
T ss_pred             eECCCCCCc--cChHHHhcCCCCCEEECCCCCCcCccCcccccccCCCeeecCCCcccc
Confidence            999976553  456666789999999999999999998888889999999999999887

syringae 6; Provisional

>KOG0472 consensus Leucine-rich repeat protein [Function unknown]

Probab=99.69  E-value=3.4e-19  Score=187.93  Aligned_cols=289  Identities=20%  Similarity=0.155  Sum_probs=164.4

Q ss_pred             CCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcccccCCCCCEEeecCCccccccccccccceecccc
Q 001843          667 RLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNW  746 (1007)
Q Consensus       667 ~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~~Lr~L~l~~  746 (1007)
                      .+..|..|+..+|++.  .+|..++++..|..|++.+|.++.+|+..-+++.|++||...|-++.+|+.++.|+.|.+-|
T Consensus       135 ~~~~l~dl~~~~N~i~--slp~~~~~~~~l~~l~~~~n~l~~l~~~~i~m~~L~~ld~~~N~L~tlP~~lg~l~~L~~Ly  212 (565)
T KOG0472|consen  135 RLLDLEDLDATNNQIS--SLPEDMVNLSKLSKLDLEGNKLKALPENHIAMKRLKHLDCNSNLLETLPPELGGLESLELLY  212 (565)
T ss_pred             HHhhhhhhhccccccc--cCchHHHHHHHHHHhhccccchhhCCHHHHHHHHHHhcccchhhhhcCChhhcchhhhHHHH
Confidence            3333444444444444  34444444444444444444444444333334444444444444444444444442222222


Q ss_pred             cccccccccccccccCcCCCccccceeeCCCcccChHh-hhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEE
Q 001843          747 IFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDY-FRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL  825 (1007)
Q Consensus       747 ~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~-l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L  825 (1007)
                      .+.+. ...+| .|+.+..|.+|+ ...+.. ...+.+ +..|++|..|++..+.  ..+++    ..+..+++|..|++
T Consensus       213 L~~Nk-i~~lP-ef~gcs~L~Elh-~g~N~i-~~lpae~~~~L~~l~vLDLRdNk--lke~P----de~clLrsL~rLDl  282 (565)
T KOG0472|consen  213 LRRNK-IRFLP-EFPGCSLLKELH-VGENQI-EMLPAEHLKHLNSLLVLDLRDNK--LKEVP----DEICLLRSLERLDL  282 (565)
T ss_pred             hhhcc-cccCC-CCCccHHHHHHH-hcccHH-HhhHHHHhcccccceeeeccccc--cccCc----hHHHHhhhhhhhcc
Confidence            11332 22333 344444444441 111111 112333 3478888899998876  66666    77888999999999


Q ss_pred             eecCCCCCCcccccCCCCCcEEEecccC-CC--------------------------------------CCcCccCC---
Q 001843          826 ICETPSYLPLLEMAEHYKLQKLYLSGHL-PP--------------------------------------NSVIGDRS---  863 (1007)
Q Consensus       826 ~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~--------------------------------------lp~~~i~~---  863 (1007)
                      ++|..+. .+.+++++ +|+.|-+.|+. ..                                      .|. |...   
T Consensus       283 SNN~is~-Lp~sLgnl-hL~~L~leGNPlrTiRr~ii~~gT~~vLKyLrs~~~~dglS~se~~~e~~~t~~~-~~~~~~~  359 (565)
T KOG0472|consen  283 SNNDISS-LPYSLGNL-HLKFLALEGNPLRTIRREIISKGTQEVLKYLRSKIKDDGLSQSEGGTETAMTLPS-ESFPDIY  359 (565)
T ss_pred             cCCcccc-CCcccccc-eeeehhhcCCchHHHHHHHHcccHHHHHHHHHHhhccCCCCCCcccccccCCCCC-Ccccchh
Confidence            9988776 66777777 88888777653 10                                      011 1100   


Q ss_pred             CCCC--------------------------ceEEEEEeeecCC-----------------------CCcCccccCCCCcE
Q 001843          864 FPPN--------------------------VVTLTLSQLRLEY-----------------------DPMPILGRLRQLKI  894 (1007)
Q Consensus       864 ~l~~--------------------------L~~L~L~~~~l~~-----------------------~~~~~l~~Lp~L~~  894 (1007)
                      ...+                          .+..+++.|++.+                       ..+..++.+++|..
T Consensus       360 ~~i~tkiL~~s~~qlt~VPdEVfea~~~~~Vt~VnfskNqL~elPk~L~~lkelvT~l~lsnn~isfv~~~l~~l~kLt~  439 (565)
T KOG0472|consen  360 AIITTKILDVSDKQLTLVPDEVFEAAKSEIVTSVNFSKNQLCELPKRLVELKELVTDLVLSNNKISFVPLELSQLQKLTF  439 (565)
T ss_pred             hhhhhhhhcccccccccCCHHHHHHhhhcceEEEecccchHhhhhhhhHHHHHHHHHHHhhcCccccchHHHHhhhccee
Confidence            0111                          4455555555432                       11223457889999


Q ss_pred             EEeecCCcCCCceeecCCCCCCCcEEEeccCCCCcceE-----------------------Ec-CCCCccccEeEeeccC
Q 001843          895 LRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWR-----------------------IK-EGAMPCLRQLEIRSCG  950 (1007)
Q Consensus       895 L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~~~L~~l~-----------------------~~-~~~~p~L~~L~l~~c~  950 (1007)
                      |+|++| +. ..++...+++..|+.|+++.. ....+|                       .+ .+.|.+|..|++.+ +
T Consensus       440 L~L~NN-~L-n~LP~e~~~lv~Lq~LnlS~N-rFr~lP~~~y~lq~lEtllas~nqi~~vd~~~l~nm~nL~tLDL~n-N  515 (565)
T KOG0472|consen  440 LDLSNN-LL-NDLPEEMGSLVRLQTLNLSFN-RFRMLPECLYELQTLETLLASNNQIGSVDPSGLKNMRNLTTLDLQN-N  515 (565)
T ss_pred             eecccc-hh-hhcchhhhhhhhhheeccccc-ccccchHHHhhHHHHHHHHhccccccccChHHhhhhhhcceeccCC-C
Confidence            999844 33 255666677777888888763 333332                       22 23588999999998 4


Q ss_pred             CCC-CCcCccccccCccEEEeccCCc
Q 001843          951 YLV-PPTGLKHVTSSLREFLLTNMPS  975 (1007)
Q Consensus       951 ~L~-lp~~l~~L~~~L~~L~l~~c~~  975 (1007)
                      .+. +|.+++++ ++|++|.+.|+|-
T Consensus       516 dlq~IPp~Lgnm-tnL~hLeL~gNpf  540 (565)
T KOG0472|consen  516 DLQQIPPILGNM-TNLRHLELDGNPF  540 (565)
T ss_pred             chhhCChhhccc-cceeEEEecCCcc
Confidence            577 99999999 9999999999983

>KOG0472 consensus Leucine-rich repeat protein [Function unknown]

Probab=99.64  E-value=6.7e-19  Score=185.73  Aligned_cols=217  Identities=23%  Similarity=0.147  Sum_probs=118.8

Q ss_pred             cCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCc
Q 001843          632 LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPD  711 (1007)
Q Consensus       632 ~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~  711 (1007)
                      ..+..+.+|.+.+|...         .+|..+  .++..+..|+.++|++.  .+|..++.+..|+.|+.++|.+.++|+
T Consensus        65 ~nL~~l~vl~~~~n~l~---------~lp~ai--g~l~~l~~l~vs~n~ls--~lp~~i~s~~~l~~l~~s~n~~~el~~  131 (565)
T KOG0472|consen   65 KNLACLTVLNVHDNKLS---------QLPAAI--GELEALKSLNVSHNKLS--ELPEQIGSLISLVKLDCSSNELKELPD  131 (565)
T ss_pred             hcccceeEEEeccchhh---------hCCHHH--HHHHHHHHhhcccchHh--hccHHHhhhhhhhhhhccccceeecCc
Confidence            44455555555555543         222223  44555555555555555  555555555555555555555555555


Q ss_pred             ccccCCCCCEEeecCCcccccccccccc--------------------------ceecccccccccccccccccccCcCC
Q 001843          712 STPILFCLATLDVSHTKVQRLPYAFWPS--------------------------RHLYLNWIFLATNVFRHPQFVKWETS  765 (1007)
Q Consensus       712 ~i~~L~~L~~L~L~~~~l~~lP~~i~~L--------------------------r~L~l~~~~~~~~~~~~p~~i~~L~~  765 (1007)
                      +|+.+..|+.|+..+|++..+|.+++++                          +||+..   .+. ...+|+.++.|.+
T Consensus       132 ~i~~~~~l~dl~~~~N~i~slp~~~~~~~~l~~l~~~~n~l~~l~~~~i~m~~L~~ld~~---~N~-L~tlP~~lg~l~~  207 (565)
T KOG0472|consen  132 SIGRLLDLEDLDATNNQISSLPEDMVNLSKLSKLDLEGNKLKALPENHIAMKRLKHLDCN---SNL-LETLPPELGGLES  207 (565)
T ss_pred             hHHHHhhhhhhhccccccccCchHHHHHHHHHHhhccccchhhCCHHHHHHHHHHhcccc---hhh-hhcCChhhcchhh
Confidence            5555555555555555555555554444                          444333   221 3344555555544


Q ss_pred             CccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHh-hcCCCCCeEEEeecCCCCCCcccccCCCCC
Q 001843          766 LQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAV-LQLSELHSLKLICETPSYLPLLEMAEHYKL  844 (1007)
Q Consensus       766 L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l-~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L  844 (1007)
                      |..|..-...   ...+.+|+.+..|+.|.+..+.  .+.++    +.. ..+++|..|+++.|.... .++.++-+.+|
T Consensus       208 L~~LyL~~Nk---i~~lPef~gcs~L~Elh~g~N~--i~~lp----ae~~~~L~~l~vLDLRdNklke-~Pde~clLrsL  277 (565)
T KOG0472|consen  208 LELLYLRRNK---IRFLPEFPGCSLLKELHVGENQ--IEMLP----AEHLKHLNSLLVLDLRDNKLKE-VPDEICLLRSL  277 (565)
T ss_pred             hHHHHhhhcc---cccCCCCCccHHHHHHHhcccH--HHhhH----HHHhcccccceeeecccccccc-CchHHHHhhhh
Confidence            4444211111   1123345555555555554443  33333    443 367788888888766554 66777777788


Q ss_pred             cEEEecccC-CCCCcCccCCCCCCceEEEEEeeec
Q 001843          845 QKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRL  878 (1007)
Q Consensus       845 ~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l  878 (1007)
                      .+|+++++. ..+|. .+++ + .|+.|-+.+|.+
T Consensus       278 ~rLDlSNN~is~Lp~-sLgn-l-hL~~L~leGNPl  309 (565)
T KOG0472|consen  278 ERLDLSNNDISSLPY-SLGN-L-HLKFLALEGNPL  309 (565)
T ss_pred             hhhcccCCccccCCc-cccc-c-eeeehhhcCCch
Confidence            888888777 77777 7777 6 788888887764

>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]

Probab=99.58  E-value=3.2e-17  Score=189.91  Aligned_cols=105  Identities=22%  Similarity=0.310  Sum_probs=69.6

Q ss_pred             CCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceee-cCCCCCCCcEEEeccCCCCcceEE-----------
Q 001843          866 PNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSC-SSGEFPNLLVLKLWKLNRLRQWRI-----------  933 (1007)
Q Consensus       866 ~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~-~~~~fp~L~~L~L~~~~~L~~l~~-----------  933 (1007)
                      +.|+.|.+.+|.+++...+.+-.+++|+.|+|++|...  .++. ....|+.|+.|+|++ +.|+.+|.           
T Consensus       359 ~~Lq~LylanN~Ltd~c~p~l~~~~hLKVLhLsyNrL~--~fpas~~~kle~LeeL~LSG-NkL~~Lp~tva~~~~L~tL  435 (1081)
T KOG0618|consen  359 AALQELYLANNHLTDSCFPVLVNFKHLKVLHLSYNRLN--SFPASKLRKLEELEELNLSG-NKLTTLPDTVANLGRLHTL  435 (1081)
T ss_pred             HHHHHHHHhcCcccccchhhhccccceeeeeecccccc--cCCHHHHhchHHhHHHhccc-chhhhhhHHHHhhhhhHHH
Confidence            45677777777777777777778888888888765432  2222 224566777777776 34555542           


Q ss_pred             -----------cCCCCccccEeEeeccCCCC---CCcCccccccCccEEEeccCCcc
Q 001843          934 -----------KEGAMPCLRQLEIRSCGYLV---PPTGLKHVTSSLREFLLTNMPST  976 (1007)
Q Consensus       934 -----------~~~~~p~L~~L~l~~c~~L~---lp~~l~~L~~~L~~L~l~~c~~~  976 (1007)
                                 +...+|.|+.+|++ |++|+   +|.....  ++|++|+++|++..
T Consensus       436 ~ahsN~l~~fPe~~~l~qL~~lDlS-~N~L~~~~l~~~~p~--p~LkyLdlSGN~~l  489 (1081)
T KOG0618|consen  436 RAHSNQLLSFPELAQLPQLKVLDLS-CNNLSEVTLPEALPS--PNLKYLDLSGNTRL  489 (1081)
T ss_pred             hhcCCceeechhhhhcCcceEEecc-cchhhhhhhhhhCCC--cccceeeccCCccc
Confidence                       23347888899998 57777   5543321  78999999999843

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.54  E-value=3.8e-14  Score=170.48  Aligned_cols=252  Identities=22%  Similarity=0.160  Sum_probs=153.1

Q ss_pred             cccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcccccCCCCCEEeecCCccccccccccccceeccccccc
Q 001843          670 MLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFL  749 (1007)
Q Consensus       670 ~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~~Lr~L~l~~~~~  749 (1007)
                      .-.+|+|+++.++  .+|..+.  .+|+.|++.+|+++.||..   +++|++|+|++|+|+.+|....+|++|++.   +
T Consensus       202 ~~~~LdLs~~~Lt--sLP~~l~--~~L~~L~L~~N~Lt~LP~l---p~~Lk~LdLs~N~LtsLP~lp~sL~~L~Ls---~  271 (788)
T PRK15387        202 GNAVLNVGESGLT--TLPDCLP--AHITTLVIPDNNLTSLPAL---PPELRTLEVSGNQLTSLPVLPPGLLELSIF---S  271 (788)
T ss_pred             CCcEEEcCCCCCC--cCCcchh--cCCCEEEccCCcCCCCCCC---CCCCcEEEecCCccCcccCcccccceeecc---C
Confidence            3456777777776  6776664  3677777777777777642   466777777777777777666666777766   4


Q ss_pred             ccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecC
Q 001843          750 ATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICET  829 (1007)
Q Consensus       750 ~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~  829 (1007)
                      |. ...+|...   ++|+.|.... +.. ...+.   .+++|+.|++++|.  ...++    .   -..+|+.|.+++|.
T Consensus       272 N~-L~~Lp~lp---~~L~~L~Ls~-N~L-t~LP~---~p~~L~~LdLS~N~--L~~Lp----~---lp~~L~~L~Ls~N~  333 (788)
T PRK15387        272 NP-LTHLPALP---SGLCKLWIFG-NQL-TSLPV---LPPGLQELSVSDNQ--LASLP----A---LPSELCKLWAYNNQ  333 (788)
T ss_pred             Cc-hhhhhhch---hhcCEEECcC-Ccc-ccccc---cccccceeECCCCc--cccCC----C---CcccccccccccCc
Confidence            43 33444322   2333332211 111 01111   23567888887765  22222    1   11356667777654


Q ss_pred             CCCCCcccccCC-CCCcEEEecccC-CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCce
Q 001843          830 PSYLPLLEMAEH-YKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEM  907 (1007)
Q Consensus       830 ~~~~~~~~l~~~-~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l  907 (1007)
                      ...     +..+ ++|+.|+|++|. ..+|.     ++++|+.|++++|.+..  ++.  ..++|+.|+|++|.+..  +
T Consensus       334 L~~-----LP~lp~~Lq~LdLS~N~Ls~LP~-----lp~~L~~L~Ls~N~L~~--LP~--l~~~L~~LdLs~N~Lt~--L  397 (788)
T PRK15387        334 LTS-----LPTLPSGLQELSVSDNQLASLPT-----LPSELYKLWAYNNRLTS--LPA--LPSGLKELIVSGNRLTS--L  397 (788)
T ss_pred             ccc-----ccccccccceEecCCCccCCCCC-----CCcccceehhhcccccc--Ccc--cccccceEEecCCcccC--C
Confidence            332     1122 478888888876 66775     14677888888887753  222  23578888888665542  2


Q ss_pred             eecCCCCCCCcEEEeccCCCCcceEEcCCCCccccEeEeeccCCCC-CCcCccccccCccEEEeccCC
Q 001843          908 SCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLTNMP  974 (1007)
Q Consensus       908 ~~~~~~fp~L~~L~L~~~~~L~~l~~~~~~~p~L~~L~l~~c~~L~-lp~~l~~L~~~L~~L~l~~c~  974 (1007)
                      +.   ..++|+.|+++++ .+..+|.   .+.+|+.|++++ ++++ +|..+..+ ++|+.|++++|+
T Consensus       398 P~---l~s~L~~LdLS~N-~LssIP~---l~~~L~~L~Ls~-NqLt~LP~sl~~L-~~L~~LdLs~N~  456 (788)
T PRK15387        398 PV---LPSELKELMVSGN-RLTSLPM---LPSGLLSLSVYR-NQLTRLPESLIHL-SSETTVNLEGNP  456 (788)
T ss_pred             CC---cccCCCEEEccCC-cCCCCCc---chhhhhhhhhcc-CcccccChHHhhc-cCCCeEECCCCC
Confidence            21   2467888888874 4666653   245678888887 4577 88888888 888888888886

>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]

Probab=99.42  E-value=8.6e-15  Score=170.07  Aligned_cols=260  Identities=19%  Similarity=0.155  Sum_probs=132.4

Q ss_pred             CCeEEEEEecCCCCCCCCCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccC
Q 001843          613 FAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGR  692 (1007)
Q Consensus       613 ~~~r~Lsl~~~~~~~~~~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~  692 (1007)
                      .+.++|....+..........-.+|.++.+..+...         .+|.+.  ..|.+|..|+..+|.+.  .+|..+..
T Consensus       219 ~~l~~L~a~~n~l~~~~~~p~p~nl~~~dis~n~l~---------~lp~wi--~~~~nle~l~~n~N~l~--~lp~ri~~  285 (1081)
T KOG0618|consen  219 PSLTALYADHNPLTTLDVHPVPLNLQYLDISHNNLS---------NLPEWI--GACANLEALNANHNRLV--ALPLRISR  285 (1081)
T ss_pred             cchheeeeccCcceeeccccccccceeeecchhhhh---------cchHHH--HhcccceEecccchhHH--hhHHHHhh
Confidence            345555555554332222233456666776666664         233555  67777777777777776  67777777


Q ss_pred             CCcCcEEecccCCCcccCcccccCCCCCEEeecCCcccccccccccc-----ceecccccccccccccccc-cccCcCCC
Q 001843          693 LPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPS-----RHLYLNWIFLATNVFRHPQ-FVKWETSL  766 (1007)
Q Consensus       693 L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~~L-----r~L~l~~~~~~~~~~~~p~-~i~~L~~L  766 (1007)
                      +..|++|++..|.++.+|...+.+++|++|+|..|+|..+|..+..-     +.|+.+   .+. ....|. +=..+.. 
T Consensus       286 ~~~L~~l~~~~nel~yip~~le~~~sL~tLdL~~N~L~~lp~~~l~v~~~~l~~ln~s---~n~-l~~lp~~~e~~~~~-  360 (1081)
T KOG0618|consen  286 ITSLVSLSAAYNELEYIPPFLEGLKSLRTLDLQSNNLPSLPDNFLAVLNASLNTLNVS---SNK-LSTLPSYEENNHAA-  360 (1081)
T ss_pred             hhhHHHHHhhhhhhhhCCCcccccceeeeeeehhccccccchHHHhhhhHHHHHHhhh---hcc-ccccccccchhhHH-
Confidence            77777777777777777777777777777777777777777633221     222222   111 111221 0112223 


Q ss_pred             ccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcE
Q 001843          767 QTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQK  846 (1007)
Q Consensus       767 ~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~  846 (1007)
                                              |+.|.+.++. -.+...    ..+.++++|+.|+|++|....-.-..+.+++.|++
T Consensus       361 ------------------------Lq~LylanN~-Ltd~c~----p~l~~~~hLKVLhLsyNrL~~fpas~~~kle~Lee  411 (1081)
T KOG0618|consen  361 ------------------------LQELYLANNH-LTDSCF----PVLVNFKHLKVLHLSYNRLNSFPASKLRKLEELEE  411 (1081)
T ss_pred             ------------------------HHHHHHhcCc-ccccch----hhhccccceeeeeecccccccCCHHHHhchHHhHH
Confidence                                    3333444333 111111    34445555555555554333212233444555555


Q ss_pred             EEecccC-CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEecc
Q 001843          847 LYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWK  924 (1007)
Q Consensus       847 L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~  924 (1007)
                      |+|+||. ..+|. .+.. ++.|+.|...+|++.  ..|.+..+|.|+.++|+.|....-.++.... -|+|++|+|+|
T Consensus       412 L~LSGNkL~~Lp~-tva~-~~~L~tL~ahsN~l~--~fPe~~~l~qL~~lDlS~N~L~~~~l~~~~p-~p~LkyLdlSG  485 (1081)
T KOG0618|consen  412 LNLSGNKLTTLPD-TVAN-LGRLHTLRAHSNQLL--SFPELAQLPQLKVLDLSCNNLSEVTLPEALP-SPNLKYLDLSG  485 (1081)
T ss_pred             HhcccchhhhhhH-HHHh-hhhhHHHhhcCCcee--echhhhhcCcceEEecccchhhhhhhhhhCC-CcccceeeccC
Confidence            5555555 55554 4444 555555555555542  2335555555555555544433222221111 15555555555

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.41  E-value=8.2e-13  Score=159.08  Aligned_cols=253  Identities=19%  Similarity=0.124  Sum_probs=137.2

Q ss_pred             EEEEecCCCCCCCCCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcC
Q 001843          617 RLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFL  696 (1007)
Q Consensus       617 ~Lsl~~~~~~~~~~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~L  696 (1007)
                      .|.+..+....++... .++|+.|.+.+|.+...|              ..+++|++|+|++|.++  .+|..   ..+|
T Consensus       205 ~LdLs~~~LtsLP~~l-~~~L~~L~L~~N~Lt~LP--------------~lp~~Lk~LdLs~N~Lt--sLP~l---p~sL  264 (788)
T PRK15387        205 VLNVGESGLTTLPDCL-PAHITTLVIPDNNLTSLP--------------ALPPELRTLEVSGNQLT--SLPVL---PPGL  264 (788)
T ss_pred             EEEcCCCCCCcCCcch-hcCCCEEEccCCcCCCCC--------------CCCCCCcEEEecCCccC--cccCc---cccc
Confidence            4455554444332221 236677777766654211              22356777777777776  56642   3466


Q ss_pred             cEEecccCCCcccCcccccCCCCCEEeecCCccccccccccccceecccccccccccccccccccCcCCCccccceeeCC
Q 001843          697 EYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKA  776 (1007)
Q Consensus       697 r~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~~Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~  776 (1007)
                      +.|+|++|.++.+|..   +.+|+.|++++|+++.+|....+|++|+++   +|. ...+|...                
T Consensus       265 ~~L~Ls~N~L~~Lp~l---p~~L~~L~Ls~N~Lt~LP~~p~~L~~LdLS---~N~-L~~Lp~lp----------------  321 (788)
T PRK15387        265 LELSIFSNPLTHLPAL---PSGLCKLWIFGNQLTSLPVLPPGLQELSVS---DNQ-LASLPALP----------------  321 (788)
T ss_pred             ceeeccCCchhhhhhc---hhhcCEEECcCCccccccccccccceeECC---CCc-cccCCCCc----------------
Confidence            7777777777766643   245667777777777776666666777776   443 22333221                


Q ss_pred             CcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEEEecccC-CC
Q 001843          777 DEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PP  855 (1007)
Q Consensus       777 ~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~  855 (1007)
                                  .+|+.|.+.+|.  ...++    .   -..+|+.|+|++|.... .+ .  .+++|+.|++++|. ..
T Consensus       322 ------------~~L~~L~Ls~N~--L~~LP----~---lp~~Lq~LdLS~N~Ls~-LP-~--lp~~L~~L~Ls~N~L~~  376 (788)
T PRK15387        322 ------------SELCKLWAYNNQ--LTSLP----T---LPSGLQELSVSDNQLAS-LP-T--LPSELYKLWAYNNRLTS  376 (788)
T ss_pred             ------------ccccccccccCc--ccccc----c---cccccceEecCCCccCC-CC-C--CCcccceehhhcccccc
Confidence                        123334444333  11121    1   01356666666544332 11 1  12366667776655 55


Q ss_pred             CCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEeccCCCCcceEEcC
Q 001843          856 NSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKE  935 (1007)
Q Consensus       856 lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~~~L~~l~~~~  935 (1007)
                      +|. .    +.+|+.|+|++|.+...  +.  ..++|+.|+|++|.+.  .++.   .+.+|+.|++++ ++++.+|...
T Consensus       377 LP~-l----~~~L~~LdLs~N~Lt~L--P~--l~s~L~~LdLS~N~Ls--sIP~---l~~~L~~L~Ls~-NqLt~LP~sl  441 (788)
T PRK15387        377 LPA-L----PSGLKELIVSGNRLTSL--PV--LPSELKELMVSGNRLT--SLPM---LPSGLLSLSVYR-NQLTRLPESL  441 (788)
T ss_pred             Ccc-c----ccccceEEecCCcccCC--CC--cccCCCEEEccCCcCC--CCCc---chhhhhhhhhcc-CcccccChHH
Confidence            654 1    35677777777776532  21  1356777777755543  2221   234667777776 4566666655


Q ss_pred             CCCccccEeEeeccCCCC
Q 001843          936 GAMPCLRQLEIRSCGYLV  953 (1007)
Q Consensus       936 ~~~p~L~~L~l~~c~~L~  953 (1007)
                      +.+++|+.|++++|+ +.
T Consensus       442 ~~L~~L~~LdLs~N~-Ls  458 (788)
T PRK15387        442 IHLSSETTVNLEGNP-LS  458 (788)
T ss_pred             hhccCCCeEECCCCC-CC
Confidence            667777777777754 44

>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]

Probab=99.38  E-value=1.5e-14  Score=136.12  Aligned_cols=150  Identities=21%  Similarity=0.180  Sum_probs=120.5

Q ss_pred             cCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCc
Q 001843          632 LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPD  711 (1007)
Q Consensus       632 ~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~  711 (1007)
                      .+++++..|.++.|....        .+|.+   ..+++|++|++++|++.  ++|.+|+.|+.||.|+++-|.+..+|.
T Consensus        30 f~~s~ITrLtLSHNKl~~--------vppni---a~l~nlevln~~nnqie--~lp~~issl~klr~lnvgmnrl~~lpr   96 (264)
T KOG0617|consen   30 FNMSNITRLTLSHNKLTV--------VPPNI---AELKNLEVLNLSNNQIE--ELPTSISSLPKLRILNVGMNRLNILPR   96 (264)
T ss_pred             cchhhhhhhhcccCceee--------cCCcH---HHhhhhhhhhcccchhh--hcChhhhhchhhhheecchhhhhcCcc
Confidence            456777888888887752        33444   78999999999999999  899999999999999999999999999


Q ss_pred             ccccCCCCCEEeecCCccc--ccccccccc---ceecccccccccccccccccccCcCCCccccceeeCCCcccChHhhh
Q 001843          712 STPILFCLATLDVSHTKVQ--RLPYAFWPS---RHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFR  786 (1007)
Q Consensus       712 ~i~~L~~L~~L~L~~~~l~--~lP~~i~~L---r~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~  786 (1007)
                      .||.++-|++|||.+|++.  .+|..+..+   +-|+++   .+. -..+|..+++|++||.|..-+.+ . ...+.+++
T Consensus        97 gfgs~p~levldltynnl~e~~lpgnff~m~tlralyl~---dnd-fe~lp~dvg~lt~lqil~lrdnd-l-l~lpkeig  170 (264)
T KOG0617|consen   97 GFGSFPALEVLDLTYNNLNENSLPGNFFYMTTLRALYLG---DND-FEILPPDVGKLTNLQILSLRDND-L-LSLPKEIG  170 (264)
T ss_pred             ccCCCchhhhhhccccccccccCCcchhHHHHHHHHHhc---CCC-cccCChhhhhhcceeEEeeccCc-h-hhCcHHHH
Confidence            9999999999999999665  788887777   667777   544 45678889999999988433332 2 45778888


Q ss_pred             cCCCCCeEEeeecC
Q 001843          787 RLTSLRKLGLKCSS  800 (1007)
Q Consensus       787 ~L~~L~~L~l~~~~  800 (1007)
                      .|++|+.|.|.++.
T Consensus       171 ~lt~lrelhiqgnr  184 (264)
T KOG0617|consen  171 DLTRLRELHIQGNR  184 (264)
T ss_pred             HHHHHHHHhcccce
Confidence            88888888888876

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.37  E-value=9.8e-13  Score=159.50  Aligned_cols=243  Identities=16%  Similarity=0.119  Sum_probs=130.8

Q ss_pred             eEEEEEecCCCCCCCCCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCC
Q 001843          615 VRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLP  694 (1007)
Q Consensus       615 ~r~Lsl~~~~~~~~~~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~  694 (1007)
                      ...|.+.......++.. -.++|+.|.+.+|.+...|        ..+     +++|++|+|++|.+.  .+|..+.  .
T Consensus       180 ~~~L~L~~~~LtsLP~~-Ip~~L~~L~Ls~N~LtsLP--------~~l-----~~nL~~L~Ls~N~Lt--sLP~~l~--~  241 (754)
T PRK15370        180 KTELRLKILGLTTIPAC-IPEQITTLILDNNELKSLP--------ENL-----QGNIKTLYANSNQLT--SIPATLP--D  241 (754)
T ss_pred             ceEEEeCCCCcCcCCcc-cccCCcEEEecCCCCCcCC--------hhh-----ccCCCEEECCCCccc--cCChhhh--c
Confidence            34455554443333221 1346778888777765322        122     246788888888877  6776553  3


Q ss_pred             cCcEEecccCCCcccCcccccCCCCCEEeecCCcccccccccc-ccceecccccccccccccccccccCcCCCcccccee
Q 001843          695 FLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFW-PSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLC  773 (1007)
Q Consensus       695 ~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~-~Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~  773 (1007)
                      +|+.|+|++|.+..+|..+.  .+|++|++++|++..+|..+. +|++|+++   +|. ...+|..+.  ++|+.|+...
T Consensus       242 ~L~~L~Ls~N~L~~LP~~l~--s~L~~L~Ls~N~L~~LP~~l~~sL~~L~Ls---~N~-Lt~LP~~lp--~sL~~L~Ls~  313 (754)
T PRK15370        242 TIQEMELSINRITELPERLP--SALQSLDLFHNKISCLPENLPEELRYLSVY---DNS-IRTLPAHLP--SGITHLNVQS  313 (754)
T ss_pred             cccEEECcCCccCcCChhHh--CCCCEEECcCCccCccccccCCCCcEEECC---CCc-cccCcccch--hhHHHHHhcC
Confidence            67888888888888877654  478888888887777776554 56777777   554 334454332  2344443222


Q ss_pred             eCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEEEecccC
Q 001843          774 IKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL  853 (1007)
Q Consensus       774 ~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~  853 (1007)
                      . .. ...+..+  .++|+.|.+.+|.  ...++    ..+.  ++|+.|++++|.... .+..+  +++|+.|+|++|.
T Consensus       314 N-~L-t~LP~~l--~~sL~~L~Ls~N~--Lt~LP----~~l~--~sL~~L~Ls~N~L~~-LP~~l--p~~L~~LdLs~N~  378 (754)
T PRK15370        314 N-SL-TALPETL--PPGLKTLEAGENA--LTSLP----ASLP--PELQVLDVSKNQITV-LPETL--PPTITTLDVSRNA  378 (754)
T ss_pred             C-cc-ccCCccc--cccceeccccCCc--cccCC----hhhc--CcccEEECCCCCCCc-CChhh--cCCcCEEECCCCc
Confidence            1 11 0111111  2456666666654  22233    2221  466666666654332 22222  2466666666655


Q ss_pred             -CCCCcCccCCCCCCceEEEEEeeecCCCC---cCccccCCCCcEEEeecCCc
Q 001843          854 -PPNSVIGDRSFPPNVVTLTLSQLRLEYDP---MPILGRLRQLKILRLFGGSY  902 (1007)
Q Consensus       854 -~~lp~~~i~~~l~~L~~L~L~~~~l~~~~---~~~l~~Lp~L~~L~L~~~~~  902 (1007)
                       ..+|. .+   ..+|+.|++++|++...+   +..++.+|++..|+|.+|.+
T Consensus       379 Lt~LP~-~l---~~sL~~LdLs~N~L~~LP~sl~~~~~~~~~l~~L~L~~Npl  427 (754)
T PRK15370        379 LTNLPE-NL---PAALQIMQASRNNLVRLPESLPHFRGEGPQPTRIIVEYNPF  427 (754)
T ss_pred             CCCCCH-hH---HHHHHHHhhccCCcccCchhHHHHhhcCCCccEEEeeCCCc
Confidence             55554 32   235666666666654221   11123345666666665544

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=99.34  E-value=1.2e-12  Score=160.98  Aligned_cols=310  Identities=19%  Similarity=0.147  Sum_probs=208.3

Q ss_pred             CCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCC--CCCcCCCcc-ccCCCcCcEEecccC-C
Q 001843          630 SSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVY--KPMLTNNNA-LGRLPFLEYLGLRST-F  705 (1007)
Q Consensus       630 ~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~--l~~~~lp~~-i~~L~~Lr~L~L~~n-~  705 (1007)
                      ........|...+.++.....+         ..   .+++.|++|-+.+|.  +.  .++.. |..|++|++|||++| .
T Consensus       518 ~~~~~~~~rr~s~~~~~~~~~~---------~~---~~~~~L~tLll~~n~~~l~--~is~~ff~~m~~LrVLDLs~~~~  583 (889)
T KOG4658|consen  518 QVKSWNSVRRMSLMNNKIEHIA---------GS---SENPKLRTLLLQRNSDWLL--EISGEFFRSLPLLRVLDLSGNSS  583 (889)
T ss_pred             cccchhheeEEEEeccchhhcc---------CC---CCCCccceEEEeecchhhh--hcCHHHHhhCcceEEEECCCCCc
Confidence            4456678899999988774322         22   577789999999996  45  55543 778999999999975 5


Q ss_pred             CcccCcccccCCCCCEEeecCCcccccccccccc---ceecccccccccccccccccccCcCCCccccceeeC-CCcccC
Q 001843          706 IDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPS---RHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIK-ADEVQS  781 (1007)
Q Consensus       706 i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~~L---r~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~-~~~~~~  781 (1007)
                      +..||++|++|-+|++|+++++.+..+|.++.+|   .||++.   .+......|..+..|++|++|...... ......
T Consensus       584 l~~LP~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~---~~~~l~~~~~i~~~L~~Lr~L~l~~s~~~~~~~~  660 (889)
T KOG4658|consen  584 LSKLPSSIGELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLE---VTGRLESIPGILLELQSLRVLRLPRSALSNDKLL  660 (889)
T ss_pred             cCcCChHHhhhhhhhcccccCCCccccchHHHHHHhhheeccc---cccccccccchhhhcccccEEEeeccccccchhh
Confidence            7899999999999999999999999999999888   888888   555444556666679999999766554 333456


Q ss_pred             hHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCC----eEEEeecCCCCCCcccccCCCCCcEEEecccC-CCC
Q 001843          782 LDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELH----SLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPN  856 (1007)
Q Consensus       782 ~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~----~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~l  856 (1007)
                      ..++..|.+|+.|.+....  . .+.    ..+..+..|.    .+.+.++.. ......+..+.+|+.|.+.++. .+.
T Consensus       661 l~el~~Le~L~~ls~~~~s--~-~~~----e~l~~~~~L~~~~~~l~~~~~~~-~~~~~~~~~l~~L~~L~i~~~~~~e~  732 (889)
T KOG4658|consen  661 LKELENLEHLENLSITISS--V-LLL----EDLLGMTRLRSLLQSLSIEGCSK-RTLISSLGSLGNLEELSILDCGISEI  732 (889)
T ss_pred             HHhhhcccchhhheeecch--h-HhH----hhhhhhHHHHHHhHhhhhccccc-ceeecccccccCcceEEEEcCCCchh
Confidence            6777788888888876543  2 222    2233333333    333332221 2245667778899999998866 322


Q ss_pred             CcCccCC----C-CCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeec---------CCCCCCCcEE-E
Q 001843          857 SVIGDRS----F-PPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCS---------SGEFPNLLVL-K  921 (1007)
Q Consensus       857 p~~~i~~----~-l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~---------~~~fp~L~~L-~  921 (1007)
                      ...|...    . +++|..+.+.+|... ..+.+..-.|+|+.|.+..+......++..         .-.|+++..+ .
T Consensus       733 ~~~~~~~~~~~~~f~~l~~~~~~~~~~~-r~l~~~~f~~~L~~l~l~~~~~~e~~i~~~k~~~~l~~~i~~f~~~~~l~~  811 (889)
T KOG4658|consen  733 VIEWEESLIVLLCFPNLSKVSILNCHML-RDLTWLLFAPHLTSLSLVSCRLLEDIIPKLKALLELKELILPFNKLEGLRM  811 (889)
T ss_pred             hcccccccchhhhHHHHHHHHhhccccc-cccchhhccCcccEEEEecccccccCCCHHHHhhhcccEEeccccccccee
Confidence            1112221    1 345666666666532 334444567999999998655433222210         1235666666 4


Q ss_pred             eccCCCCcceEEcCCCCccccEeEeeccCCCC-CCcCccccccCccEEEeccC
Q 001843          922 LWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLTNM  973 (1007)
Q Consensus       922 L~~~~~L~~l~~~~~~~p~L~~L~l~~c~~L~-lp~~l~~L~~~L~~L~l~~c  973 (1007)
                      +.+.+.+..+-...-.+++|+.+.+..|+++. +|        .+.++.+.+|
T Consensus       812 ~~~l~~l~~i~~~~l~~~~l~~~~ve~~p~l~~~P--------~~~~~~i~~~  856 (889)
T KOG4658|consen  812 LCSLGGLPQLYWLPLSFLKLEELIVEECPKLGKLP--------LLSTLTIVGC  856 (889)
T ss_pred             eecCCCCceeEecccCccchhheehhcCcccccCc--------cccccceecc
Confidence            66667777776666678889999999998777 54        4455666665

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.34  E-value=1.1e-10  Score=150.28  Aligned_cols=281  Identities=11%  Similarity=0.109  Sum_probs=174.5

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh----------cccc
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV----------EATL  341 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~----------~~~~  341 (1007)
                      ..+++.|.|++|.||||++.++...      ++.++|+++.. .+.+...++..++..+.......          ....
T Consensus        31 ~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~-~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~  103 (903)
T PRK04841         31 NYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDE-SDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYA  103 (903)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCc-ccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcC
Confidence            3489999999999999999998862      23689999851 33466677788888875321110          0012


Q ss_pred             CHHHHHHHHHHHcC--CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccc-cccCCcceeeecC---
Q 001843          342 SAEELMWRITQALD--DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFV-EPLGAAFSTLHVP---  414 (1007)
Q Consensus       342 ~~~~l~~~l~~~L~--~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va-~~~~~~~~~~~l~---  414 (1007)
                      +...+...+...+.  +++++|||||+...+......+. .+......+.++|||||...... ..........++.   
T Consensus       104 ~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~~~~~~l~~~~~~~~l~~~~  183 (903)
T PRK04841        104 SLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPPLGIANLRVRDQLLEIGSQQ  183 (903)
T ss_pred             CHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCCCchHhHHhcCcceecCHHh
Confidence            22333433433333  68999999999754433433333 44443255678889999853121 1111111445566   


Q ss_pred             -CCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCChHHHHHHHHH---cccchh
Q 001843          415 -GLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIER---ANGDNL  490 (1007)
Q Consensus       415 -~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~~~~w~~~l~~---l~i~~~  490 (1007)
                       +|+.+|+.++|.........         ...+.+|.+.|+|.|+++..++..+.....+.......+..   ..+...
T Consensus       184 l~f~~~e~~~ll~~~~~~~~~---------~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  254 (903)
T PRK04841        184 LAFDHQEAQQFFDQRLSSPIE---------AAESSRLCDDVEGWATALQLIALSARQNNSSLHDSARRLAGINASHLSDY  254 (903)
T ss_pred             CCCCHHHHHHHHHhccCCCCC---------HHHHHHHHHHhCChHHHHHHHHHHHhhCCCchhhhhHhhcCCCchhHHHH
Confidence             99999999999876554222         35678899999999999999998776543211111111100   012333


Q ss_pred             hh-hhhcCCccCchhhhhhhccCCCCcccchhHHHHHHHhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEeecCCC
Q 001843          491 VA-LCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDG  569 (1007)
Q Consensus       491 l~-~sy~~L~~~~k~cfl~la~fp~~~~i~~~~Li~~Wiaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~~~~~g  569 (1007)
                      +. -.++.||++.+..++..|+++.   +....      +..+.  .       .+.+...+++|.+++++.....   +
T Consensus       255 l~~~v~~~l~~~~~~~l~~~a~~~~---~~~~l------~~~l~--~-------~~~~~~~L~~l~~~~l~~~~~~---~  313 (903)
T PRK04841        255 LVEEVLDNVDLETRHFLLRCSVLRS---MNDAL------IVRVT--G-------EENGQMRLEELERQGLFIQRMD---D  313 (903)
T ss_pred             HHHHHHhcCCHHHHHHHHHhccccc---CCHHH------HHHHc--C-------CCcHHHHHHHHHHCCCeeEeec---C
Confidence            22 2378999999999999999873   33221      21112  1       1124678999999999754321   1


Q ss_pred             CcceEEcCHHHHHHHHhhhh
Q 001843          570 SPKTCCMPGVLYDILRPKAE  589 (1007)
Q Consensus       570 ~~~~~~mHdlv~d~~~~~~~  589 (1007)
                      ....|++|++++++++....
T Consensus       314 ~~~~yr~H~L~r~~l~~~l~  333 (903)
T PRK04841        314 SGEWFRYHPLFASFLRHRCQ  333 (903)
T ss_pred             CCCEEehhHHHHHHHHHHHH
Confidence            22358899999999987753

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.31  E-value=2.7e-12  Score=155.73  Aligned_cols=260  Identities=15%  Similarity=0.120  Sum_probs=182.2

Q ss_pred             CCCCeEEEEEecCCCCCCCCCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccc
Q 001843          611 PKFAVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNAL  690 (1007)
Q Consensus       611 ~~~~~r~Lsl~~~~~~~~~~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i  690 (1007)
                      .+..++.|.+.+|....++.. ..++|++|.+.+|.+...|         ..+    ...|+.|+|++|.+.  .+|..+
T Consensus       197 Ip~~L~~L~Ls~N~LtsLP~~-l~~nL~~L~Ls~N~LtsLP---------~~l----~~~L~~L~Ls~N~L~--~LP~~l  260 (754)
T PRK15370        197 IPEQITTLILDNNELKSLPEN-LQGNIKTLYANSNQLTSIP---------ATL----PDTIQEMELSINRIT--ELPERL  260 (754)
T ss_pred             cccCCcEEEecCCCCCcCChh-hccCCCEEECCCCccccCC---------hhh----hccccEEECcCCccC--cCChhH
Confidence            345789999998887665443 2468999999999875322         222    247999999999999  899877


Q ss_pred             cCCCcCcEEecccCCCcccCcccccCCCCCEEeecCCcccccccccc-ccceecccccccccccccccccccCcCCCccc
Q 001843          691 GRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFW-PSRHLYLNWIFLATNVFRHPQFVKWETSLQTL  769 (1007)
Q Consensus       691 ~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~-~Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L  769 (1007)
                      .  .+|++|+|++|.++.+|..+.  .+|++|+|++|+++.+|..+. .|++|+++   +|. ...+|..+.  ++|+.|
T Consensus       261 ~--s~L~~L~Ls~N~L~~LP~~l~--~sL~~L~Ls~N~Lt~LP~~lp~sL~~L~Ls---~N~-Lt~LP~~l~--~sL~~L  330 (754)
T PRK15370        261 P--SALQSLDLFHNKISCLPENLP--EELRYLSVYDNSIRTLPAHLPSGITHLNVQ---SNS-LTALPETLP--PGLKTL  330 (754)
T ss_pred             h--CCCCEEECcCCccCccccccC--CCCcEEECCCCccccCcccchhhHHHHHhc---CCc-cccCCcccc--ccceec
Confidence            5  589999999999999998775  589999999999999998665 45899998   665 335665443  567777


Q ss_pred             cceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEEEe
Q 001843          770 WGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYL  849 (1007)
Q Consensus       770 ~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L  849 (1007)
                      ....+. . ...+..+  .++|+.|++++|.  ...++    ..+  .++|+.|+|++|.... .+..+.  ..|+.|++
T Consensus       331 ~Ls~N~-L-t~LP~~l--~~sL~~L~Ls~N~--L~~LP----~~l--p~~L~~LdLs~N~Lt~-LP~~l~--~sL~~LdL  395 (754)
T PRK15370        331 EAGENA-L-TSLPASL--PPELQVLDVSKNQ--ITVLP----ETL--PPTITTLDVSRNALTN-LPENLP--AALQIMQA  395 (754)
T ss_pred             cccCCc-c-ccCChhh--cCcccEEECCCCC--CCcCC----hhh--cCCcCEEECCCCcCCC-CCHhHH--HHHHHHhh
Confidence            433332 2 1123333  2689999999886  44454    333  2689999999976543 333332  37999999


Q ss_pred             cccC-CCCCcCccCCC---CCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeecCCCCCCCcE
Q 001843          850 SGHL-PPNSVIGDRSF---PPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLV  919 (1007)
Q Consensus       850 ~g~~-~~lp~~~i~~~---l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~  919 (1007)
                      ++|. ..+|. .+..+   ++++..|+|.+|.+..      ..+++|+.| ++.+.+.+..+.+..+.|++++.
T Consensus       396 s~N~L~~LP~-sl~~~~~~~~~l~~L~L~~Npls~------~tl~~L~~L-l~s~~~~gp~i~~~~~~~~~l~~  461 (754)
T PRK15370        396 SRNNLVRLPE-SLPHFRGEGPQPTRIIVEYNPFSE------RTIQNMQRL-MSSVGYQGPRVLFAMGDFSIVRV  461 (754)
T ss_pred             ccCCcccCch-hHHHHhhcCCCccEEEeeCCCccH------HHHHHHHHh-hhcccccCCcccccccccccccc
Confidence            9987 77775 44321   5889999999998752      455666666 33466666555555555665554

>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]

Probab=99.30  E-value=1.1e-13  Score=130.43  Aligned_cols=160  Identities=23%  Similarity=0.182  Sum_probs=129.5

Q ss_pred             hhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcccccCCCCCEEeecCCcccccccccc
Q 001843          658 ILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFW  737 (1007)
Q Consensus       658 ~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~  737 (1007)
                      .++..|   ++.++..|.||+|.++  .+|..|..|.+|+.|++.+|+|+++|.+|+.|++|++|+++-|.+..+|.+++
T Consensus        25 ~~~gLf---~~s~ITrLtLSHNKl~--~vppnia~l~nlevln~~nnqie~lp~~issl~klr~lnvgmnrl~~lprgfg   99 (264)
T KOG0617|consen   25 ELPGLF---NMSNITRLTLSHNKLT--VVPPNIAELKNLEVLNLSNNQIEELPTSISSLPKLRILNVGMNRLNILPRGFG   99 (264)
T ss_pred             hccccc---chhhhhhhhcccCcee--ecCCcHHHhhhhhhhhcccchhhhcChhhhhchhhhheecchhhhhcCccccC
Confidence            344554   7888999999999999  89999999999999999999999999999999999999999999999999998


Q ss_pred             cc---ceecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHh
Q 001843          738 PS---RHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAV  814 (1007)
Q Consensus       738 ~L---r~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l  814 (1007)
                      .+   +.|++.|  ++-....+|..|-.|+.|+.|.. ..+.. ...+.++++|++|+.|.+..+.  .-+++    ..+
T Consensus       100 s~p~levldlty--nnl~e~~lpgnff~m~tlralyl-~dndf-e~lp~dvg~lt~lqil~lrdnd--ll~lp----kei  169 (264)
T KOG0617|consen  100 SFPALEVLDLTY--NNLNENSLPGNFFYMTTLRALYL-GDNDF-EILPPDVGKLTNLQILSLRDND--LLSLP----KEI  169 (264)
T ss_pred             CCchhhhhhccc--cccccccCCcchhHHHHHHHHHh-cCCCc-ccCChhhhhhcceeEEeeccCc--hhhCc----HHH
Confidence            87   8888884  23335578888888887777733 22222 3467789999999999998775  45555    777


Q ss_pred             hcCCCCCeEEEeecCCCC
Q 001843          815 LQLSELHSLKLICETPSY  832 (1007)
Q Consensus       815 ~~l~~L~~L~L~~~~~~~  832 (1007)
                      +.+..|++|+|.++....
T Consensus       170 g~lt~lrelhiqgnrl~v  187 (264)
T KOG0617|consen  170 GDLTRLRELHIQGNRLTV  187 (264)
T ss_pred             HHHHHHHHHhcccceeee
Confidence            888888888888765443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.23  E-value=1.6e-09  Score=125.19  Aligned_cols=293  Identities=15%  Similarity=0.124  Sum_probs=166.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.|+|++|+|||++++.++++  .........|+.+.+....+...++..++.++.... ......+...+...+.+.
T Consensus        56 ~~~lI~G~~GtGKT~l~~~v~~~--l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~-~~~~~~~~~~~~~~~~~~  132 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVKKVFEE--LEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHP-PPSSGLSFDELFDKIAEY  132 (394)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCC-CCCCCCCHHHHHHHHHHH
Confidence            55789999999999999999995  333333334444433377788899999999987520 111233566777777777


Q ss_pred             cC--CCcEEEEEeCcCccC----chhhhhhccccCCCCCCcE--EEEEcCCCcccccccCC------cceeeecCCCCHH
Q 001843          354 LD--DSTFLIVMENAEHQK----SQVWDSFLGKLCSFTQCGK--IIITTSSTEDFVEPLGA------AFSTLHVPGLGKN  419 (1007)
Q Consensus       354 L~--~kr~LlVlDdv~~~~----~~~~~~l~~l~~~~~~gs~--IliTTR~~~~va~~~~~------~~~~~~l~~L~~~  419 (1007)
                      +.  ++..+||||+++.-.    .+.+..+...... ..+++  +|.++.... +......      ....+.+++++.+
T Consensus       133 l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~-~~~~~v~vI~i~~~~~-~~~~l~~~~~s~~~~~~i~f~py~~~  210 (394)
T PRK00411        133 LDERDRVLIVALDDINYLFEKEGNDVLYSLLRAHEE-YPGARIGVIGISSDLT-FLYILDPRVKSVFRPEEIYFPPYTAD  210 (394)
T ss_pred             HHhcCCEEEEEECCHhHhhccCCchHHHHHHHhhhc-cCCCeEEEEEEECCcc-hhhhcCHHHHhcCCcceeecCCCCHH
Confidence            75  456899999998321    1223333222222 22333  555555543 3222110      0156799999999


Q ss_pred             HHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHh--c---CCC-CChHHHHHHHHHcccchhhhh
Q 001843          420 ESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL--S---TKQ-PSYEEWSKVIERANGDNLVAL  493 (1007)
Q Consensus       420 ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L--~---~~~-~~~~~w~~~l~~l~i~~~l~~  493 (1007)
                      +..+++..++........-.+..++.+++......|..+.|+.++-...  +   +.. -+......+.+... .....-
T Consensus       211 e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~-~~~~~~  289 (394)
T PRK00411        211 EIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSE-IVHLSE  289 (394)
T ss_pred             HHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHH-HHHHHH
Confidence            9999998776322110001123334444444444677888887765322  1   111 14566666666542 233455


Q ss_pred             hhcCCccCchhhhhhhccCCC--CcccchhHHHHH--HHhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEee--cC
Q 001843          494 CYQDLPAQVKPCILYMGLFPR--EYEIPVRRLIHL--WCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRW--RL  567 (1007)
Q Consensus       494 sy~~L~~~~k~cfl~la~fp~--~~~i~~~~Li~~--Wiaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~~--~~  567 (1007)
                      .+..||.+.|..+..++..-+  ...+....+...  .+++.+-  .  . ..-......|+++|.+.++|.....  ..
T Consensus       290 ~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~--~--~-~~~~~~~~~~l~~L~~~glI~~~~~~~g~  364 (394)
T PRK00411        290 VLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELG--Y--E-PRTHTRFYEYINKLDMLGIINTRYSGKGG  364 (394)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcC--C--C-cCcHHHHHHHHHHHHhcCCeEEEEecCCC
Confidence            688999988877666553221  123444444432  2332211  0  0 0012335669999999999987643  33


Q ss_pred             CCCcceEEcC
Q 001843          568 DGSPKTCCMP  577 (1007)
Q Consensus       568 ~g~~~~~~mH  577 (1007)
                      .|+.+.++++
T Consensus       365 ~g~~~~~~~~  374 (394)
T PRK00411        365 RGRTRLISLS  374 (394)
T ss_pred             CCCeEEEEec
Confidence            4566666554

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=99.09  E-value=1e-11  Score=139.40  Aligned_cols=64  Identities=28%  Similarity=0.178  Sum_probs=32.9

Q ss_pred             CCCCcccEEEecCCCCCCc---CCCccccCCCcCcEEecccCCCcc-------cCcccccCCCCCEEeecCCcc
Q 001843          666 RRLGMLKVLDLEGVYKPML---TNNNALGRLPFLEYLGLRSTFIDS-------LPDSTPILFCLATLDVSHTKV  729 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~---~lp~~i~~L~~Lr~L~L~~n~i~~-------LP~~i~~L~~L~~L~L~~~~l  729 (1007)
                      ..+..|++|++++|.+...   .++..+...+.|++|+++++.+..       ++..+.++++|+.|++++|.+
T Consensus        20 ~~l~~L~~l~l~~~~l~~~~~~~i~~~l~~~~~l~~l~l~~~~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~   93 (319)
T cd00116          20 PKLLCLQVLRLEGNTLGEEAAKALASALRPQPSLKELCLSLNETGRIPRGLQSLLQGLTKGCGLQELDLSDNAL   93 (319)
T ss_pred             HHHhhccEEeecCCCCcHHHHHHHHHHHhhCCCceEEeccccccCCcchHHHHHHHHHHhcCceeEEEccCCCC
Confidence            4455566666666665321   233444455556666666554442       223344555666666655544

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=99.05  E-value=1.1e-08  Score=111.89  Aligned_cols=182  Identities=18%  Similarity=0.225  Sum_probs=114.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH--
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT--  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~--  351 (1007)
                      .++.|+|++|+||||+++.+++.... ..+ ..+|+ +.  ...+..+++..|+..++..  .  ...+.......+.  
T Consensus        44 ~~~~l~G~~G~GKTtl~~~l~~~l~~-~~~-~~~~~-~~--~~~~~~~~l~~i~~~lG~~--~--~~~~~~~~~~~l~~~  114 (269)
T TIGR03015        44 GFILITGEVGAGKTTLIRNLLKRLDQ-ERV-VAAKL-VN--TRVDAEDLLRMVAADFGLE--T--EGRDKAALLRELEDF  114 (269)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHhcCC-CCe-EEeee-eC--CCCCHHHHHHHHHHHcCCC--C--CCCCHHHHHHHHHHH
Confidence            58999999999999999999984321 111 12333 23  4457778888888887654  1  1122223333333  


Q ss_pred             --HH-cCCCcEEEEEeCcCccCchhhhhhccccCC-C--CCCcEEEEEcCCCccccccc--------CCc-ceeeecCCC
Q 001843          352 --QA-LDDSTFLIVMENAEHQKSQVWDSFLGKLCS-F--TQCGKIIITTSSTEDFVEPL--------GAA-FSTLHVPGL  416 (1007)
Q Consensus       352 --~~-L~~kr~LlVlDdv~~~~~~~~~~l~~l~~~-~--~~gs~IliTTR~~~~va~~~--------~~~-~~~~~l~~L  416 (1007)
                        .. ..+++.+||+||++..+...++.++.+.+. .  .....|++|....  +....        ... ...+.++++
T Consensus       115 l~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~--~~~~l~~~~~~~l~~r~~~~~~l~~l  192 (269)
T TIGR03015       115 LIEQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE--FRETLQSPQLQQLRQRIIASCHLGPL  192 (269)
T ss_pred             HHHHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH--HHHHHcCchhHHHHhheeeeeeCCCC
Confidence              22 267889999999996666667766633221 0  2223445554422  21111        110 156889999


Q ss_pred             CHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHh
Q 001843          417 GKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL  468 (1007)
Q Consensus       417 ~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L  468 (1007)
                      +.+|..+++...+......  ....-..+..+.|++.++|.|..|..++..+
T Consensus       193 ~~~e~~~~l~~~l~~~g~~--~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       193 DREETREYIEHRLERAGNR--DAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             CHHHHHHHHHHHHHHcCCC--CCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            9999999988766432210  1112235788999999999999999998877

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]

Probab=99.03  E-value=9.3e-12  Score=132.36  Aligned_cols=248  Identities=16%  Similarity=0.043  Sum_probs=152.7

Q ss_pred             cceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEeccc-CCCcccCcc-c
Q 001843          636 RLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRS-TFIDSLPDS-T  713 (1007)
Q Consensus       636 ~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~-n~i~~LP~~-i  713 (1007)
                      ....+.+..|.+..        +++..|  +.+++||.||||+|.|.. --|+.|..+..|-.|-+-+ |+|+.+|+. |
T Consensus        68 ~tveirLdqN~I~~--------iP~~aF--~~l~~LRrLdLS~N~Is~-I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F  136 (498)
T KOG4237|consen   68 ETVEIRLDQNQISS--------IPPGAF--KTLHRLRRLDLSKNNISF-IAPDAFKGLASLLSLVLYGNNKITDLPKGAF  136 (498)
T ss_pred             cceEEEeccCCccc--------CChhhc--cchhhhceecccccchhh-cChHhhhhhHhhhHHHhhcCCchhhhhhhHh
Confidence            44566677777653        556788  888889999999888872 2367788888877776666 888888864 7


Q ss_pred             ccCCCCCEEeecCCcccccccc-cccc---ceecccccccccccccccc-cccCcCCCccccceeeCCCcc---------
Q 001843          714 PILFCLATLDVSHTKVQRLPYA-FWPS---RHLYLNWIFLATNVFRHPQ-FVKWETSLQTLWGLCIKADEV---------  779 (1007)
Q Consensus       714 ~~L~~L~~L~L~~~~l~~lP~~-i~~L---r~L~l~~~~~~~~~~~~p~-~i~~L~~L~~L~~~~~~~~~~---------  779 (1007)
                      ++|..||-|.+.-|.+..++.. +..|   +.|.+.   .+. ...++. .+..+.+++++..-.......         
T Consensus       137 ~gL~slqrLllNan~i~Cir~~al~dL~~l~lLsly---Dn~-~q~i~~~tf~~l~~i~tlhlA~np~icdCnL~wla~~  212 (498)
T KOG4237|consen  137 GGLSSLQRLLLNANHINCIRQDALRDLPSLSLLSLY---DNK-IQSICKGTFQGLAAIKTLHLAQNPFICDCNLPWLADD  212 (498)
T ss_pred             hhHHHHHHHhcChhhhcchhHHHHHHhhhcchhccc---chh-hhhhccccccchhccchHhhhcCccccccccchhhhH
Confidence            7888888888887777766542 4444   333333   332 223333 455666666653221110000         


Q ss_pred             --cChHhhhcCCCCCeEEeeecC------------------------CCchhhHHHHHHHhhcCCCCCeEEEeecCCCCC
Q 001843          780 --QSLDYFRRLTSLRKLGLKCSS------------------------TTSTSLKKEIIGAVLQLSELHSLKLICETPSYL  833 (1007)
Q Consensus       780 --~~~~~l~~L~~L~~L~l~~~~------------------------~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~  833 (1007)
                        ..+.+++..+......+...+                        ......+.   ..+.++++|+.|+|++|.....
T Consensus       213 ~a~~~ietsgarc~~p~rl~~~Ri~q~~a~kf~c~~esl~s~~~~~d~~d~~cP~---~cf~~L~~L~~lnlsnN~i~~i  289 (498)
T KOG4237|consen  213 LAMNPIETSGARCVSPYRLYYKRINQEDARKFLCSLESLPSRLSSEDFPDSICPA---KCFKKLPNLRKLNLSNNKITRI  289 (498)
T ss_pred             HhhchhhcccceecchHHHHHHHhcccchhhhhhhHHhHHHhhccccCcCCcChH---HHHhhcccceEeccCCCccchh
Confidence              011111111111111111000                        00011111   3467788888888888777665


Q ss_pred             CcccccCCCCCcEEEecccC-CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCc
Q 001843          834 PLLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSY  902 (1007)
Q Consensus       834 ~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~  902 (1007)
                      ...+|.....|++|.|..|. ..+....+.. +.+|+.|+|.+|+++...+..|..+.+|..|+|-.|.+
T Consensus       290 ~~~aFe~~a~l~eL~L~~N~l~~v~~~~f~~-ls~L~tL~L~~N~it~~~~~aF~~~~~l~~l~l~~Np~  358 (498)
T KOG4237|consen  290 EDGAFEGAAELQELYLTRNKLEFVSSGMFQG-LSGLKTLSLYDNQITTVAPGAFQTLFSLSTLNLLSNPF  358 (498)
T ss_pred             hhhhhcchhhhhhhhcCcchHHHHHHHhhhc-cccceeeeecCCeeEEEecccccccceeeeeehccCcc
Confidence            66777778888888888766 4444324445 78888888888888887778888888888888876654

>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]

Probab=98.99  E-value=2.8e-11  Score=128.73  Aligned_cols=253  Identities=19%  Similarity=0.120  Sum_probs=169.5

Q ss_pred             CCCCeEEEEEecCCCCCCCCC--cCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecC-CCCCCcCCC
Q 001843          611 PKFAVRRLAANLGSNSFPYSS--LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEG-VYKPMLTNN  687 (1007)
Q Consensus       611 ~~~~~r~Lsl~~~~~~~~~~~--~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~-~~l~~~~lp  687 (1007)
                      .|...-.+-+..|.++.++..  ..+++||.|.++.|.+..        +-++.|  .+++.|-.|-+-+ |+|+  .+|
T Consensus        65 LP~~tveirLdqN~I~~iP~~aF~~l~~LRrLdLS~N~Is~--------I~p~AF--~GL~~l~~Lvlyg~NkI~--~l~  132 (498)
T KOG4237|consen   65 LPPETVEIRLDQNQISSIPPGAFKTLHRLRRLDLSKNNISF--------IAPDAF--KGLASLLSLVLYGNNKIT--DLP  132 (498)
T ss_pred             CCCcceEEEeccCCcccCChhhccchhhhceecccccchhh--------cChHhh--hhhHhhhHHHhhcCCchh--hhh
Confidence            556677788888887776554  778999999999998753        667788  8998887766665 8888  788


Q ss_pred             cc-ccCCCcCcEEecccCCCcccC-cccccCCCCCEEeecCCccccccc-ccccc---ceecccccc---ccc------c
Q 001843          688 NA-LGRLPFLEYLGLRSTFIDSLP-DSTPILFCLATLDVSHTKVQRLPY-AFWPS---RHLYLNWIF---LAT------N  752 (1007)
Q Consensus       688 ~~-i~~L~~Lr~L~L~~n~i~~LP-~~i~~L~~L~~L~L~~~~l~~lP~-~i~~L---r~L~l~~~~---~~~------~  752 (1007)
                      +. |+.|..|+-|.+.-|.+.-++ ..+..|++|..|.+..|.++.++. .+..+   +++.+.-.-   .|.      .
T Consensus       133 k~~F~gL~slqrLllNan~i~Cir~~al~dL~~l~lLslyDn~~q~i~~~tf~~l~~i~tlhlA~np~icdCnL~wla~~  212 (498)
T KOG4237|consen  133 KGAFGGLSSLQRLLLNANHINCIRQDALRDLPSLSLLSLYDNKIQSICKGTFQGLAAIKTLHLAQNPFICDCNLPWLADD  212 (498)
T ss_pred             hhHhhhHHHHHHHhcChhhhcchhHHHHHHhhhcchhcccchhhhhhccccccchhccchHhhhcCccccccccchhhhH
Confidence            54 788888888888888888665 457788888888888888888877 34444   555544100   011      0


Q ss_pred             cccccccccCcCC----------------------Ccccc---ceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhH
Q 001843          753 VFRHPQFVKWETS----------------------LQTLW---GLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLK  807 (1007)
Q Consensus       753 ~~~~p~~i~~L~~----------------------L~~L~---~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~  807 (1007)
                      ....|..++...-                      ++.+.   ...+.........-+.+|++|++|+++++.  ...+.
T Consensus       213 ~a~~~ietsgarc~~p~rl~~~Ri~q~~a~kf~c~~esl~s~~~~~d~~d~~cP~~cf~~L~~L~~lnlsnN~--i~~i~  290 (498)
T KOG4237|consen  213 LAMNPIETSGARCVSPYRLYYKRINQEDARKFLCSLESLPSRLSSEDFPDSICPAKCFKKLPNLRKLNLSNNK--ITRIE  290 (498)
T ss_pred             HhhchhhcccceecchHHHHHHHhcccchhhhhhhHHhHHHhhccccCcCCcChHHHHhhcccceEeccCCCc--cchhh
Confidence            1111111111111                      11110   000001111123348899999999999987  44443


Q ss_pred             HHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEEEecccC-CCCCcCccCCCCCCceEEEEEeeecCCC
Q 001843          808 KEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYD  881 (1007)
Q Consensus       808 ~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~  881 (1007)
                      +   .+|.+...+++|.|..|......-..|..+..|+.|+|.+|. +.+....+.. +.+|.+|.|-.|.+.++
T Consensus       291 ~---~aFe~~a~l~eL~L~~N~l~~v~~~~f~~ls~L~tL~L~~N~it~~~~~aF~~-~~~l~~l~l~~Np~~Cn  361 (498)
T KOG4237|consen  291 D---GAFEGAAELQELYLTRNKLEFVSSGMFQGLSGLKTLSLYDNQITTVAPGAFQT-LFSLSTLNLLSNPFNCN  361 (498)
T ss_pred             h---hhhcchhhhhhhhcCcchHHHHHHHhhhccccceeeeecCCeeEEEecccccc-cceeeeeehccCcccCc
Confidence            3   788999999999999876554344567778899999999987 4443325666 88999999998876543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.98  E-value=1.3e-07  Score=108.15  Aligned_cols=279  Identities=15%  Similarity=0.158  Sum_probs=156.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCC------ceEEEEecCCCCCCHHHHHHHHHHHHhh-hhhhhccccCHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFT------KRAWVHIPIMSMVEDRDVLADILKQIDE-SLLKVEATLSAEEL  346 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~------~~~wv~~s~~~~~~~~~~l~~il~~l~~-~~~~~~~~~~~~~l  346 (1007)
                      ..+.|+|++|+|||++++.++++  .....+      ..+|+.+.  ...+...++..|+.++.. .........+..+.
T Consensus        41 ~~i~I~G~~GtGKT~l~~~~~~~--l~~~~~~~~~~~~~v~in~~--~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~  116 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTKYVMKE--LEEAAEDRDVRVVTVYVNCQ--ILDTLYQVLVELANQLRGSGEEVPTTGLSTSEV  116 (365)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH--HHHHhhccCCceEEEEEECC--CCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHH
Confidence            57899999999999999999984  222111      24566665  777788999999999842 00001122344555


Q ss_pred             HHHHHHHcC--CCcEEEEEeCcCccC---chhhhhhccc--cCC-CCCCcEEEEEcCCCccccccc----CCc--ceeee
Q 001843          347 MWRITQALD--DSTFLIVMENAEHQK---SQVWDSFLGK--LCS-FTQCGKIIITTSSTEDFVEPL----GAA--FSTLH  412 (1007)
Q Consensus       347 ~~~l~~~L~--~kr~LlVlDdv~~~~---~~~~~~l~~l--~~~-~~~gs~IliTTR~~~~va~~~----~~~--~~~~~  412 (1007)
                      ...+.+.+.  +++++||||+++.-.   .+....+..+  ... -+....+|.+|.... .....    ...  ...+.
T Consensus       117 ~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~-~~~~l~~~~~s~~~~~~i~  195 (365)
T TIGR02928       117 FRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGISNDLK-FRENLDPRVKSSLCEEEII  195 (365)
T ss_pred             HHHHHHHHHhcCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEECCcc-hHhhcCHHHhccCCcceee
Confidence            566666663  567899999998431   1112222222  111 012234455554443 21111    111  15689


Q ss_pred             cCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCc-hHHHHHHHHh--c---CC-CCChHHHHHHHHHc
Q 001843          413 VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLP-LRVVLLAGLL--S---TK-QPSYEEWSKVIERA  485 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g~~L--~---~~-~~~~~~w~~~l~~l  485 (1007)
                      +++++.++-.+++..++...... ....++..+.+.+++....|.| .|+.++-...  .   .. .-+.+....+.+..
T Consensus       196 f~p~~~~e~~~il~~r~~~~~~~-~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~  274 (365)
T TIGR02928       196 FPPYDAEELRDILENRAEKAFYD-GVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI  274 (365)
T ss_pred             eCCCCHHHHHHHHHHHHHhhccC-CCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            99999999999998876421110 0123444455566777777887 4444332211  1   11 12455555555543


Q ss_pred             ccchhhhhhhcCCccCchhhhhhhccCC--CCcccchhHHHHHH--HhcccCCCCCCccCCHHHHHHHHHHHHHhccceE
Q 001843          486 NGDNLVALCYQDLPAQVKPCILYMGLFP--REYEIPVRRLIHLW--CAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQ  561 (1007)
Q Consensus       486 ~i~~~l~~sy~~L~~~~k~cfl~la~fp--~~~~i~~~~Li~~W--iaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~  561 (1007)
                      . .....-.+..||.+.|..+..++..-  .+..+....+...+  +++. +  .  ...........++..|...|+|.
T Consensus       275 ~-~~~~~~~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~-~--~--~~~~~~~~~~~~l~~l~~~gli~  348 (365)
T TIGR02928       275 E-KDRLLELIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYKEVCED-I--G--VDPLTQRRISDLLNELDMLGLVE  348 (365)
T ss_pred             H-HHHHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHh-c--C--CCCCcHHHHHHHHHHHHhcCCeE
Confidence            2 23334566789888876666554211  33345566665533  1221 1  0  11123456778999999999999


Q ss_pred             EEe
Q 001843          562 VIR  564 (1007)
Q Consensus       562 ~~~  564 (1007)
                      ...
T Consensus       349 ~~~  351 (365)
T TIGR02928       349 AEE  351 (365)
T ss_pred             EEE
Confidence            764

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=98.93  E-value=1.5e-10  Score=129.81  Aligned_cols=261  Identities=17%  Similarity=0.043  Sum_probs=146.6

Q ss_pred             cCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCC-----cCCCccccCCCcCcEEecccCCC
Q 001843          632 LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPM-----LTNNNALGRLPFLEYLGLRSTFI  706 (1007)
Q Consensus       632 ~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~-----~~lp~~i~~L~~Lr~L~L~~n~i  706 (1007)
                      ..+.+|+.|.+.++.+......    .+...+  ...+.|+.|+++++.+..     ..++..+..+.+|++|+|++|.+
T Consensus        20 ~~l~~L~~l~l~~~~l~~~~~~----~i~~~l--~~~~~l~~l~l~~~~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~   93 (319)
T cd00116          20 PKLLCLQVLRLEGNTLGEEAAK----ALASAL--RPQPSLKELCLSLNETGRIPRGLQSLLQGLTKGCGLQELDLSDNAL   93 (319)
T ss_pred             HHHhhccEEeecCCCCcHHHHH----HHHHHH--hhCCCceEEeccccccCCcchHHHHHHHHHHhcCceeEEEccCCCC
Confidence            3455688888888876321111    344445  677888899998887651     12335567788999999998887


Q ss_pred             c-ccCcccccCCC---CCEEeecCCcccc-----ccc---cc-cccceecccccccccccccccccccCcCCCcccccee
Q 001843          707 D-SLPDSTPILFC---LATLDVSHTKVQR-----LPY---AF-WPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLC  773 (1007)
Q Consensus       707 ~-~LP~~i~~L~~---L~~L~L~~~~l~~-----lP~---~i-~~Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~  773 (1007)
                      . ..+..+..+.+   |++|++++|.+..     +..   .. .+|+.|++.   +|......+                
T Consensus        94 ~~~~~~~~~~l~~~~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~---~n~l~~~~~----------------  154 (319)
T cd00116          94 GPDGCGVLESLLRSSSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLG---RNRLEGASC----------------  154 (319)
T ss_pred             ChhHHHHHHHHhccCcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcC---CCcCCchHH----------------
Confidence            6 34444555554   9999998886652     111   11 233444444   322110000                


Q ss_pred             eCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCC----CcccccCCCCCcEEEe
Q 001843          774 IKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYL----PLLEMAEHYKLQKLYL  849 (1007)
Q Consensus       774 ~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~----~~~~l~~~~~L~~L~L  849 (1007)
                           ......+..+++|+.|++.++. -.......++..+..+++|+.|+++++.....    ....+..+++|+.|++
T Consensus       155 -----~~~~~~~~~~~~L~~L~l~~n~-l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~~~~~~L~~L~l  228 (319)
T cd00116         155 -----EALAKALRANRDLKELNLANNG-IGDAGIRALAEGLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNL  228 (319)
T ss_pred             -----HHHHHHHHhCCCcCEEECcCCC-CchHHHHHHHHHHHhCCCCCEEeccCCccChHHHHHHHHHhcccCCCCEEec
Confidence                 1123345556677777777665 11111122335555666777777776543321    1233445677888888


Q ss_pred             cccC-CC--CCcCccCC---CCCCceEEEEEeeecCCCCc----CccccCCCCcEEEeecCCcCCCc---eeecCCCC-C
Q 001843          850 SGHL-PP--NSVIGDRS---FPPNVVTLTLSQLRLEYDPM----PILGRLRQLKILRLFGGSYTGEE---MSCSSGEF-P  915 (1007)
Q Consensus       850 ~g~~-~~--lp~~~i~~---~l~~L~~L~L~~~~l~~~~~----~~l~~Lp~L~~L~L~~~~~~~~~---l~~~~~~f-p  915 (1007)
                      +++. ..  +.. ....   ..+.|+.|++++|.++....    ..+..+++|++|++++|.+..+.   +......+ +
T Consensus       229 s~n~l~~~~~~~-l~~~~~~~~~~L~~L~l~~n~i~~~~~~~l~~~~~~~~~L~~l~l~~N~l~~~~~~~~~~~~~~~~~  307 (319)
T cd00116         229 GDNNLTDAGAAA-LASALLSPNISLLTLSLSCNDITDDGAKDLAEVLAEKESLLELDLRGNKFGEEGAQLLAESLLEPGN  307 (319)
T ss_pred             CCCcCchHHHHH-HHHHHhccCCCceEEEccCCCCCcHHHHHHHHHHhcCCCccEEECCCCCCcHHHHHHHHHHHhhcCC
Confidence            7765 21  110 1111   03688889998887753222    33456688899999877665432   11122334 6


Q ss_pred             CCcEEEecc
Q 001843          916 NLLVLKLWK  924 (1007)
Q Consensus       916 ~L~~L~L~~  924 (1007)
                      .|+.|.+.+
T Consensus       308 ~~~~~~~~~  316 (319)
T cd00116         308 ELESLWVKD  316 (319)
T ss_pred             chhhcccCC
Confidence            777777665

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.88  E-value=1.2e-07  Score=111.39  Aligned_cols=283  Identities=16%  Similarity=0.164  Sum_probs=184.3

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh----------cccc
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV----------EATL  341 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~----------~~~~  341 (1007)
                      +.|++.|..+.|.|||||+-+.+.  .. ..=..+.|++++ ..+.++..+++.++..++.-....          ....
T Consensus        36 ~~RL~li~APAGfGKttl~aq~~~--~~-~~~~~v~Wlsld-e~dndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~  111 (894)
T COG2909          36 DYRLILISAPAGFGKTTLLAQWRE--LA-ADGAAVAWLSLD-ESDNDPARFLSYLIAALQQATPTLGDEAQTLLQKHQYV  111 (894)
T ss_pred             CceEEEEeCCCCCcHHHHHHHHHH--hc-CcccceeEeecC-CccCCHHHHHHHHHHHHHHhCccccHHHHHHHHhcccc
Confidence            449999999999999999999986  22 223458999976 145678888888888887431111          1234


Q ss_pred             CHHHHHHHHHHHcC--CCcEEEEEeCcCccCchhhhh-hccccCCCCCCcEEEEEcCCCc--ccccccCCcceeeecC--
Q 001843          342 SAEELMWRITQALD--DSTFLIVMENAEHQKSQVWDS-FLGKLCSFTQCGKIIITTSSTE--DFVEPLGAAFSTLHVP--  414 (1007)
Q Consensus       342 ~~~~l~~~l~~~L~--~kr~LlVlDdv~~~~~~~~~~-l~~l~~~~~~gs~IliTTR~~~--~va~~~~~~~~~~~l~--  414 (1007)
                      +...+...+..-+.  .++.++||||-.-........ +..|.+....+-..|||||...  .+++.--.. ..+++.  
T Consensus       112 ~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l~la~lRlr~-~llEi~~~  190 (894)
T COG2909         112 SLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQLGLARLRLRD-ELLEIGSE  190 (894)
T ss_pred             cHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCCcccceeehh-hHHhcChH
Confidence            45555555555443  578999999976433333333 3344444366789999999876  122211111 334443  


Q ss_pred             --CCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCChHHHHHHHHHcc--cc-h
Q 001843          415 --GLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERAN--GD-N  489 (1007)
Q Consensus       415 --~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~~~~w~~~l~~l~--i~-~  489 (1007)
                        .++.+|+-++|.......         -.+..++.+.+...|-+-|+..++-.++.+.. .+.-...+.-..  +. -
T Consensus       191 ~Lrf~~eE~~~fl~~~~~l~---------Ld~~~~~~L~~~teGW~~al~L~aLa~~~~~~-~~q~~~~LsG~~~~l~dY  260 (894)
T COG2909         191 ELRFDTEEAAAFLNDRGSLP---------LDAADLKALYDRTEGWAAALQLIALALRNNTS-AEQSLRGLSGAASHLSDY  260 (894)
T ss_pred             hhcCChHHHHHHHHHcCCCC---------CChHHHHHHHhhcccHHHHHHHHHHHccCCCc-HHHHhhhccchHHHHHHH
Confidence              578999999998875432         23567789999999999999999988884332 222222111000  11 1


Q ss_pred             hhhhhhcCCccCchhhhhhhccCCCCcccchhHHHHHHHhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEeecCCC
Q 001843          490 LVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDG  569 (1007)
Q Consensus       490 ~l~~sy~~L~~~~k~cfl~la~fp~~~~i~~~~Li~~Wiaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~~~~~g  569 (1007)
                      ...--++.||+++|..++-+|+++.-.    +.|+..-              +-++.+...+++|.+++++-..-.+   
T Consensus       261 L~eeVld~Lp~~l~~FLl~~svl~~f~----~eL~~~L--------------tg~~ng~amLe~L~~~gLFl~~Ldd---  319 (894)
T COG2909         261 LVEEVLDRLPPELRDFLLQTSVLSRFN----DELCNAL--------------TGEENGQAMLEELERRGLFLQRLDD---  319 (894)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHhHHHhh----HHHHHHH--------------hcCCcHHHHHHHHHhCCCceeeecC---
Confidence            122346889999999999999987532    2333222              1123467789999999998654432   


Q ss_pred             CcceEEcCHHHHHHHHhhhhh
Q 001843          570 SPKTCCMPGVLYDILRPKAED  590 (1007)
Q Consensus       570 ~~~~~~mHdlv~d~~~~~~~~  590 (1007)
                      .-.-|+.|.++.+|.+.....
T Consensus       320 ~~~WfryH~LFaeFL~~r~~~  340 (894)
T COG2909         320 EGQWFRYHHLFAEFLRQRLQR  340 (894)
T ss_pred             CCceeehhHHHHHHHHhhhcc
Confidence            223699999999999877665

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.87  E-value=4.3e-08  Score=109.13  Aligned_cols=245  Identities=20%  Similarity=0.173  Sum_probs=133.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh---c--cccCHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV---E--ATLSAEELMW  348 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~---~--~~~~~~~l~~  348 (1007)
                      ..+.++|++|+|||+||+.+++  .....|   ..+...  .... ...+...+..+...  ..   +  .... ....+
T Consensus        31 ~~~ll~Gp~G~GKT~la~~ia~--~~~~~~---~~~~~~--~~~~-~~~l~~~l~~~~~~--~vl~iDEi~~l~-~~~~e   99 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLAHIIAN--EMGVNL---KITSGP--ALEK-PGDLAAILTNLEEG--DVLFIDEIHRLS-PAVEE   99 (305)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH--HhCCCE---EEeccc--hhcC-chhHHHHHHhcccC--CEEEEehHhhhC-HHHHH
Confidence            5678999999999999999999  343322   122221  1111 12222223332211  00   0  0011 11233


Q ss_pred             HHHHHcCCCcEEEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcCCCcccccccCCcc-eeeecCCCCHHHHHHHHHh
Q 001843          349 RITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAF-STLHVPGLGKNESWELFLK  427 (1007)
Q Consensus       349 ~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~~~-~~~~l~~L~~~ea~~Lf~~  427 (1007)
                      .+...+.+.+..+|+++..  +...|..  .+    .+.+-|..||+... +........ ..+++++++.++..+++.+
T Consensus       100 ~l~~~~~~~~~~~v~~~~~--~~~~~~~--~~----~~~~li~~t~~~~~-l~~~l~sR~~~~~~l~~l~~~e~~~il~~  170 (305)
T TIGR00635       100 LLYPAMEDFRLDIVIGKGP--SARSVRL--DL----PPFTLVGATTRAGM-LTSPLRDRFGIILRLEFYTVEELAEIVSR  170 (305)
T ss_pred             HhhHHHhhhheeeeeccCc--cccceee--cC----CCeEEEEecCCccc-cCHHHHhhcceEEEeCCCCHHHHHHHHHH
Confidence            4555566666667777655  3332221  11    22455666777655 444322221 5789999999999999998


Q ss_pred             hhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhc------C-CCCChHHHHHHHHHcccchhhhhhhcCCcc
Q 001843          428 KARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLS------T-KQPSYEEWSKVIERANGDNLVALCYQDLPA  500 (1007)
Q Consensus       428 ~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~------~-~~~~~~~w~~~l~~l~i~~~l~~sy~~L~~  500 (1007)
                      .+.....      .-..+....|++.|+|.|-.+..++..+.      . ...+.+.....+..      +..+|..|++
T Consensus       171 ~~~~~~~------~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~------l~~~~~~l~~  238 (305)
T TIGR00635       171 SAGLLNV------EIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEM------LMIDELGLDE  238 (305)
T ss_pred             HHHHhCC------CcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHH------hCCCCCCCCH
Confidence            8764322      12245678899999999976554444321      1 11123333333332      5667888888


Q ss_pred             Cchhhhh-hhccCCCCcccchhHHHHHHHhcccCCCCCCccCCHHHHHHHHHH-HHHhccceEEEe
Q 001843          501 QVKPCIL-YMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLE-ELVTRHMIQVIR  564 (1007)
Q Consensus       501 ~~k~cfl-~la~fp~~~~i~~~~Li~~Wiaeg~i~~~~~~~~~~e~~~~~~l~-~Lv~rsll~~~~  564 (1007)
                      +.+..+. .++.++.+ .+..+.+....   |          .....+...++ .|++++||....
T Consensus       239 ~~~~~L~al~~~~~~~-~~~~~~ia~~l---g----------~~~~~~~~~~e~~Li~~~li~~~~  290 (305)
T TIGR00635       239 IDRKLLSVLIEQFQGG-PVGLKTLAAAL---G----------EDADTIEDVYEPYLLQIGFLQRTP  290 (305)
T ss_pred             HHHHHHHHHHHHhCCC-cccHHHHHHHh---C----------CCcchHHHhhhHHHHHcCCcccCC
Confidence            7776665 44555543 23333322211   1          11234666677 699999997433

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.87  E-value=7.6e-09  Score=110.24  Aligned_cols=177  Identities=19%  Similarity=0.181  Sum_probs=86.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHH----------HHHHhhhhhhhc-----
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADI----------LKQIDESLLKVE-----  338 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~i----------l~~l~~~~~~~~-----  338 (1007)
                      +.+.|+|+.|+|||+|++++.+  ..+..-..++|+...  ... .......+          ...+........     
T Consensus        21 ~~~~l~G~rg~GKTsLl~~~~~--~~~~~~~~~~y~~~~--~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~   95 (234)
T PF01637_consen   21 QHILLYGPRGSGKTSLLKEFIN--ELKEKGYKVVYIDFL--EES-NESSLRSFIEETSLADELSEALGISIPSITLEKIS   95 (234)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH--HCT--EECCCHHCCT--TBS-HHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEE
T ss_pred             cEEEEEcCCcCCHHHHHHHHHH--HhhhcCCcEEEEecc--cch-hhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhh
Confidence            7899999999999999999999  443222234444433  332 22223333          111221100000     


Q ss_pred             --cccCHHHHHHHHHHHc--CCCcEEEEEeCcCccC------chhhhhhc-cccC--CCCCCcEEEEEcCCCcccccc--
Q 001843          339 --ATLSAEELMWRITQAL--DDSTFLIVMENAEHQK------SQVWDSFL-GKLC--SFTQCGKIIITTSSTEDFVEP--  403 (1007)
Q Consensus       339 --~~~~~~~l~~~l~~~L--~~kr~LlVlDdv~~~~------~~~~~~l~-~l~~--~~~~gs~IliTTR~~~~va~~--  403 (1007)
                        ...........+.+.+  .+++++||+||+....      ......+. .+..  ...+.+.|+++|. .. +...  
T Consensus        96 ~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~-~~-~~~~~~  173 (234)
T PF01637_consen   96 KDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS-DS-LMEEFL  173 (234)
T ss_dssp             CTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS-HH-HHHHTT
T ss_pred             hcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc-hH-HHHHhh
Confidence              0111222223333333  2355999999997332      11122233 2222  1033444444444 22 2211  


Q ss_pred             ------cCCcceeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHH
Q 001843          404 ------LGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVL  463 (1007)
Q Consensus       404 ------~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~  463 (1007)
                            .+.. ..+.+++|+.+++++++....... .   .. +......++|...+||.|..|..
T Consensus       174 ~~~~~~~~~~-~~~~l~~l~~~e~~~~~~~~~~~~-~---~~-~~~~~~~~~i~~~~gG~P~~l~~  233 (234)
T PF01637_consen  174 DDKSPLFGRF-SHIELKPLSKEEAREFLKELFKEL-I---KL-PFSDEDIEEIYSLTGGNPRYLQE  233 (234)
T ss_dssp             -TTSTTTT----EEEE----HHHHHHHHHHHHHCC-----------HHHHHHHHHHHTT-HHHHHH
T ss_pred             cccCcccccc-ceEEEeeCCHHHHHHHHHHHHHHh-h---cc-cCCHHHHHHHHHHhCCCHHHHhc
Confidence                  1222 559999999999999998865432 1   11 22356679999999999998864

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.79  E-value=4.6e-08  Score=109.74  Aligned_cols=246  Identities=19%  Similarity=0.123  Sum_probs=129.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCH----HHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSA----EELMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~----~~l~~~  349 (1007)
                      ..+.|+|++|+||||+|+.+++  .....+   .++...   .......+..++..+...  ..--.++.    ....+.
T Consensus        52 ~~~ll~GppG~GKT~la~~ia~--~l~~~~---~~~~~~---~~~~~~~l~~~l~~l~~~--~vl~IDEi~~l~~~~~e~  121 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLANIIAN--EMGVNI---RITSGP---ALEKPGDLAAILTNLEEG--DVLFIDEIHRLSPVVEEI  121 (328)
T ss_pred             CcEEEECCCCccHHHHHHHHHH--HhCCCe---EEEecc---cccChHHHHHHHHhcccC--CEEEEecHhhcchHHHHH
Confidence            6778999999999999999999  443322   122221   111122223333322211  00000000    111223


Q ss_pred             HHHHcCCCcEEEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcCCCcccccccCCcc-eeeecCCCCHHHHHHHHHhh
Q 001843          350 ITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAF-STLHVPGLGKNESWELFLKK  428 (1007)
Q Consensus       350 l~~~L~~kr~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~~~-~~~~l~~L~~~ea~~Lf~~~  428 (1007)
                      +...+.+.+..+|+|+..  +...+..  .+    .+.+-|..||+... +........ ..+++++++.++..+++.+.
T Consensus       122 l~~~~e~~~~~~~l~~~~--~~~~~~~--~l----~~~~li~at~~~~~-l~~~L~sRf~~~~~l~~~~~~e~~~il~~~  192 (328)
T PRK00080        122 LYPAMEDFRLDIMIGKGP--AARSIRL--DL----PPFTLIGATTRAGL-LTSPLRDRFGIVQRLEFYTVEELEKIVKRS  192 (328)
T ss_pred             HHHHHHhcceeeeeccCc--cccceee--cC----CCceEEeecCCccc-CCHHHHHhcCeeeecCCCCHHHHHHHHHHH
Confidence            344444455555555543  1111100  11    12345666777555 443322221 57899999999999999988


Q ss_pred             hccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcC-------CCCChHHHHHHHHHcccchhhhhhhcCCccC
Q 001843          429 ARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLST-------KQPSYEEWSKVIERANGDNLVALCYQDLPAQ  501 (1007)
Q Consensus       429 a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~-------~~~~~~~w~~~l~~l~i~~~l~~sy~~L~~~  501 (1007)
                      +.....      .-..+.+..|++.|+|.|-.+..+...+..       ...+...-..      ....+...|..|++.
T Consensus       193 ~~~~~~------~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~------~l~~~~~~~~~l~~~  260 (328)
T PRK00080        193 ARILGV------EIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADK------ALDMLGVDELGLDEM  260 (328)
T ss_pred             HHHcCC------CcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHH------HHHHhCCCcCCCCHH
Confidence            765432      122457889999999999654444443211       0111111112      223456777888887


Q ss_pred             chhhhh-hhccCCCCcccchhHHHHHHHhcccCCCCCCccCCHHHHHHHHHH-HHHhccceEEEe
Q 001843          502 VKPCIL-YMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLE-ELVTRHMIQVIR  564 (1007)
Q Consensus       502 ~k~cfl-~la~fp~~~~i~~~~Li~~Wiaeg~i~~~~~~~~~~e~~~~~~l~-~Lv~rsll~~~~  564 (1007)
                      .+..+. ....|+.+ .+..+.+....     -    ..    .+.++..++ .|++.+|++...
T Consensus       261 ~~~~l~~~~~~~~~~-~~~~~~~a~~l-----g----~~----~~~~~~~~e~~Li~~~li~~~~  311 (328)
T PRK00080        261 DRKYLRTIIEKFGGG-PVGLDTLAAAL-----G----EE----RDTIEDVYEPYLIQQGFIQRTP  311 (328)
T ss_pred             HHHHHHHHHHHcCCC-ceeHHHHHHHH-----C----CC----cchHHHHhhHHHHHcCCcccCC
Confidence            777665 55566655 34444433222     1    11    223455566 899999997443

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=98.78  E-value=5.2e-08  Score=105.44  Aligned_cols=154  Identities=17%  Similarity=0.225  Sum_probs=98.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-.-.||++|+||||||+.++.  .....|     ..++  ...+-..-+++++++...                   ..
T Consensus        49 ~SmIl~GPPG~GKTTlA~liA~--~~~~~f-----~~~s--Av~~gvkdlr~i~e~a~~-------------------~~  100 (436)
T COG2256          49 HSMILWGPPGTGKTTLARLIAG--TTNAAF-----EALS--AVTSGVKDLREIIEEARK-------------------NR  100 (436)
T ss_pred             ceeEEECCCCCCHHHHHHHHHH--hhCCce-----EEec--cccccHHHHHHHHHHHHH-------------------HH
Confidence            5667899999999999999999  555555     3444  333333444444433322                   22


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhccccCCCCCCcEEEE--EcCCCc-ccccccCCcceeeecCCCCHHHHHHHHHhhhc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIII--TTSSTE-DFVEPLGAAFSTLHVPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~Ili--TTR~~~-~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~  430 (1007)
                      ..+++.+|++|.|..-+..+-+.+.+..   -.|.-|+|  ||.++. .+-....+.+.++.+++|+.++-.+++.+-+-
T Consensus       101 ~~gr~tiLflDEIHRfnK~QQD~lLp~v---E~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~  177 (436)
T COG2256         101 LLGRRTILFLDEIHRFNKAQQDALLPHV---ENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALL  177 (436)
T ss_pred             hcCCceEEEEehhhhcChhhhhhhhhhh---cCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHHHHHHHHh
Confidence            3489999999999866666666665444   44777777  888876 23334444448999999999999999988332


Q ss_pred             cccccccCCCh-HHHHHHHHHHHHcCCCc
Q 001843          431 IAEDVLQSRSS-ELIKLKKQILNICDGLP  458 (1007)
Q Consensus       431 ~~~~~~~~~~~-~~~~~~~~I~~~c~GlP  458 (1007)
                      ........... -.++...-|+..++|--
T Consensus       178 ~~~rgl~~~~~~i~~~a~~~l~~~s~GD~  206 (436)
T COG2256         178 DEERGLGGQIIVLDEEALDYLVRLSNGDA  206 (436)
T ss_pred             hhhcCCCcccccCCHHHHHHHHHhcCchH
Confidence            22211011111 12345566777777754

>PF05729 NACHT: NACHT domain

Probab=98.77  E-value=5e-08  Score=97.87  Aligned_cols=144  Identities=19%  Similarity=0.264  Sum_probs=86.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC----CCceEEEEecCCCCCCHH---HHHHHHHHHHhhhhhhhccccCHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH----FTKRAWVHIPIMSMVEDR---DVLADILKQIDESLLKVEATLSAEEL  346 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~s~~~~~~~~---~~l~~il~~l~~~~~~~~~~~~~~~l  346 (1007)
                      |++.|+|.+|+||||+++.++.+-.....    +...+|++..  ......   .+...|..+....      .......
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~l~~~~~~~------~~~~~~~   72 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLR--DISDSNNSRSLADLLFDQLPES------IAPIEEL   72 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeeh--hhhhccccchHHHHHHHhhccc------hhhhHHH
Confidence            58999999999999999999985333322    3456777765  332222   2222222222211      1111111


Q ss_pred             HHHHHHHcCCCcEEEEEeCcCccCc--h-----hhhhhc--cccCCCCCCcEEEEEcCCCccc---ccccCCcceeeecC
Q 001843          347 MWRITQALDDSTFLIVMENAEHQKS--Q-----VWDSFL--GKLCSFTQCGKIIITTSSTEDF---VEPLGAAFSTLHVP  414 (1007)
Q Consensus       347 ~~~l~~~L~~kr~LlVlDdv~~~~~--~-----~~~~l~--~l~~~~~~gs~IliTTR~~~~v---a~~~~~~~~~~~l~  414 (1007)
                      ...  -.-..++++||+|+++....  .     .+..+.  -+......+.+++||+|... .   ....... ..+++.
T Consensus        73 ~~~--~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~-~~~~~~~~~~~-~~~~l~  148 (166)
T PF05729_consen   73 LQE--LLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRA-FPDLRRRLKQA-QILELE  148 (166)
T ss_pred             HHH--HHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCCh-HHHHHHhcCCC-cEEEEC
Confidence            111  12257899999999973221  1     122222  22221256789999999877 4   3333343 689999


Q ss_pred             CCCHHHHHHHHHhhh
Q 001843          415 GLGKNESWELFLKKA  429 (1007)
Q Consensus       415 ~L~~~ea~~Lf~~~a  429 (1007)
                      +|++++..+++.++.
T Consensus       149 ~~~~~~~~~~~~~~f  163 (166)
T PF05729_consen  149 PFSEEDIKQYLRKYF  163 (166)
T ss_pred             CCCHHHHHHHHHHHh
Confidence            999999999987753

>KOG1259 consensus Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms; Cytoskeleton]

Probab=98.74  E-value=1.6e-09  Score=111.26  Aligned_cols=130  Identities=25%  Similarity=0.199  Sum_probs=102.3

Q ss_pred             hhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEEEecccC-CCCCcCccCC
Q 001843          785 FRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRS  863 (1007)
Q Consensus       785 l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~  863 (1007)
                      +.....|..|+++++.  ...+.    .+..-++.++.|+++.|...  ...++..+++|+.|+|++|. .++.. |-..
T Consensus       280 ~dTWq~LtelDLS~N~--I~~iD----ESvKL~Pkir~L~lS~N~i~--~v~nLa~L~~L~~LDLS~N~Ls~~~G-wh~K  350 (490)
T KOG1259|consen  280 ADTWQELTELDLSGNL--ITQID----ESVKLAPKLRRLILSQNRIR--TVQNLAELPQLQLLDLSGNLLAECVG-WHLK  350 (490)
T ss_pred             cchHhhhhhccccccc--hhhhh----hhhhhccceeEEecccccee--eehhhhhcccceEeecccchhHhhhh-hHhh
Confidence            3344567888999876  44444    66777899999999987655  45668889999999999988 77776 8888


Q ss_pred             CCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEeccCC
Q 001843          864 FPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLN  926 (1007)
Q Consensus       864 ~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~~  926 (1007)
                       +.|++.|.|++|.+  ..++.+++|-+|..|++++|.+..-+-.-..+.+|+|+.|.|.+.|
T Consensus       351 -LGNIKtL~La~N~i--E~LSGL~KLYSLvnLDl~~N~Ie~ldeV~~IG~LPCLE~l~L~~NP  410 (490)
T KOG1259|consen  351 -LGNIKTLKLAQNKI--ETLSGLRKLYSLVNLDLSSNQIEELDEVNHIGNLPCLETLRLTGNP  410 (490)
T ss_pred             -hcCEeeeehhhhhH--hhhhhhHhhhhheeccccccchhhHHHhcccccccHHHHHhhcCCC
Confidence             99999999999987  5677889999999999998876543334456778888888888754

>KOG0532 consensus Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton]

Probab=98.63  E-value=2.7e-09  Score=118.80  Aligned_cols=171  Identities=22%  Similarity=0.140  Sum_probs=115.3

Q ss_pred             CCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCccc
Q 001843          634 SWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDST  713 (1007)
Q Consensus       634 ~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i  713 (1007)
                      +..-....+..|.+..         +|.-+  ..|-.|..|.|..|.+-  .+|..++++..|.||+|+.|++..+|..+
T Consensus        74 ltdt~~aDlsrNR~~e---------lp~~~--~~f~~Le~liLy~n~~r--~ip~~i~~L~~lt~l~ls~NqlS~lp~~l  140 (722)
T KOG0532|consen   74 LTDTVFADLSRNRFSE---------LPEEA--CAFVSLESLILYHNCIR--TIPEAICNLEALTFLDLSSNQLSHLPDGL  140 (722)
T ss_pred             ccchhhhhcccccccc---------CchHH--HHHHHHHHHHHHhccce--ecchhhhhhhHHHHhhhccchhhcCChhh
Confidence            3344445566666542         22334  56667777788888777  77888888888888888888888888777


Q ss_pred             ccCCCCCEEeecCCcccccccccccc---ceecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCC
Q 001843          714 PILFCLATLDVSHTKVQRLPYAFWPS---RHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTS  790 (1007)
Q Consensus       714 ~~L~~L~~L~L~~~~l~~lP~~i~~L---r~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~  790 (1007)
                      +.|+ |+.|.+++|+++.+|.+++-+   .+|+.+   .|. ...+|..++.|.+|+.|......-  ...+.+++.|+ 
T Consensus       141 C~lp-Lkvli~sNNkl~~lp~~ig~~~tl~~ld~s---~ne-i~slpsql~~l~slr~l~vrRn~l--~~lp~El~~Lp-  212 (722)
T KOG0532|consen  141 CDLP-LKVLIVSNNKLTSLPEEIGLLPTLAHLDVS---KNE-IQSLPSQLGYLTSLRDLNVRRNHL--EDLPEELCSLP-  212 (722)
T ss_pred             hcCc-ceeEEEecCccccCCcccccchhHHHhhhh---hhh-hhhchHHhhhHHHHHHHHHhhhhh--hhCCHHHhCCc-
Confidence            7765 788888888888888877733   666666   443 556777777777777774322221  34566666554 


Q ss_pred             CCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCC
Q 001843          791 LRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPS  831 (1007)
Q Consensus       791 L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~  831 (1007)
                      |.+|++++|.  ...++    -.|.+|++|+.|.|.+|...
T Consensus       213 Li~lDfScNk--is~iP----v~fr~m~~Lq~l~LenNPLq  247 (722)
T KOG0532|consen  213 LIRLDFSCNK--ISYLP----VDFRKMRHLQVLQLENNPLQ  247 (722)
T ss_pred             eeeeecccCc--eeecc----hhhhhhhhheeeeeccCCCC
Confidence            7777877765  55555    77777888888888775544

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.59  E-value=4.3e-07  Score=105.01  Aligned_cols=158  Identities=15%  Similarity=0.188  Sum_probs=93.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.++|++|+||||+|+.+++.  ....     |+.++  ........++.++..+...                   .
T Consensus        37 ~~ilL~GppGtGKTtLA~~ia~~--~~~~-----~~~l~--a~~~~~~~ir~ii~~~~~~-------------------~   88 (413)
T PRK13342         37 SSMILWGPPGTGKTTLARIIAGA--TDAP-----FEALS--AVTSGVKDLREVIEEARQR-------------------R   88 (413)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--hCCC-----EEEEe--cccccHHHHHHHHHHHHHh-------------------h
Confidence            56788999999999999999993  3333     33333  2221122222222222110                   1


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhccccCCCCCCcEEEE--EcCCCc-ccccccCCcceeeecCCCCHHHHHHHHHhhhc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIII--TTSSTE-DFVEPLGAAFSTLHVPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~Ili--TTR~~~-~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~  430 (1007)
                      ..+++.+|++|+++.-.....+.+......   |..++|  ||.+.. .+.....+.+..+.+.+++.++.+.++.+.+.
T Consensus        89 ~~g~~~vL~IDEi~~l~~~~q~~LL~~le~---~~iilI~att~n~~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~  165 (413)
T PRK13342         89 SAGRRTILFIDEIHRFNKAQQDALLPHVED---GTITLIGATTENPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALE  165 (413)
T ss_pred             hcCCceEEEEechhhhCHHHHHHHHHHhhc---CcEEEEEeCCCChhhhccHHHhccceeeEeCCCCHHHHHHHHHHHHH
Confidence            145788999999986555566666533332   445555  344432 12223333337899999999999999988653


Q ss_pred             cccccccCCChHHHHHHHHHHHHcCCCchHHHHHH
Q 001843          431 IAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLA  465 (1007)
Q Consensus       431 ~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g  465 (1007)
                      .....  . ..-..+....|++.|+|.+..+.-+.
T Consensus       166 ~~~~~--~-i~i~~~al~~l~~~s~Gd~R~aln~L  197 (413)
T PRK13342        166 DKERG--L-VELDDEALDALARLANGDARRALNLL  197 (413)
T ss_pred             HhhcC--C-CCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            31110  0 01224567788999999987654443

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.57  E-value=1e-07  Score=104.08  Aligned_cols=282  Identities=17%  Similarity=0.200  Sum_probs=183.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCc-eEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTK-RAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      |.+.++|.|||||||++-++..   +...|.. +.++...  .-.+...+.-.+...++..      ..+.+.....+..
T Consensus        15 RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~--pitD~~~v~~~~ag~~gl~------~~~g~~~~~~~~~   83 (414)
T COG3903          15 RLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLA--PITDPALVFPTLAGALGLH------VQPGDSAVDTLVR   83 (414)
T ss_pred             heeeeeccCccceehhhhhhHh---Hhhhcccceeeeecc--ccCchhHhHHHHHhhcccc------cccchHHHHHHHH
Confidence            8999999999999999999988   5667865 5555555  4555566666666666664      1223334455667


Q ss_pred             HcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHH-HHHHHHHhhhc
Q 001843          353 ALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKN-ESWELFLKKAR  430 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~-ea~~Lf~~~a~  430 (1007)
                      +..++|.++|+||..+.-. .-..+. ++..+ +..-.|+.|+|..-    ...+. ..+.+++|+.- ++.++|...+.
T Consensus        84 ~~~~rr~llvldncehl~~-~~a~~i~all~~-~~~~~~~atsre~~----l~~ge-~~~~~~~L~~~d~a~~lf~~ra~  156 (414)
T COG3903          84 RIGDRRALLVLDNCEHLLD-ACAALIVALLGA-CPRLAILATSREAI----LVAGE-VHRRVPSLSLFDEAIELFVCRAV  156 (414)
T ss_pred             HHhhhhHHHHhcCcHHHHH-HHHHHHHHHHcc-chhhhhHHHhHhhh----ccccc-ccccCCccccCCchhHHHHHHHH
Confidence            7788999999999752111 111122 55555 55667999999765    22222 67778888765 78999987765


Q ss_pred             cccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCChHHHHHHHHH----cc------------cchhhhhh
Q 001843          431 IAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIER----AN------------GDNLVALC  494 (1007)
Q Consensus       431 ~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~~~~w~~~l~~----l~------------i~~~l~~s  494 (1007)
                      ..... ..........+.+|.++..|.|++|...++..+.-.  ..+-...++.    +.            ....+.+|
T Consensus       157 ~~~~~-f~l~~~~~a~v~~icr~ldg~~laielaaarv~sl~--~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws  233 (414)
T COG3903         157 LVALS-FWLTDDNAAAVAEICRRLDGIPLAIELAAARVRSLS--PDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWS  233 (414)
T ss_pred             Hhccc-eeecCCchHHHHHHHHHhhcchHHHHHHHHHHHhcC--HHHHHHHHhhHHHHHhcccccchhHHHhccchhhhh
Confidence            44332 122334467888999999999999999999998765  3322222221    11            88999999


Q ss_pred             hcCCccCchhhhhhhccCCCCcccchhHHHHHHHhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEeecCCCCcceE
Q 001843          495 YQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTC  574 (1007)
Q Consensus       495 y~~L~~~~k~cfl~la~fp~~~~i~~~~Li~~Wiaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~~~~~g~~~~~  574 (1007)
                      |.-|....+--|..++.|...+...    ...|.+.|-.      ..-..-.....+..+++.+++.....   .....|
T Consensus       234 ~~lLtgwe~~~~~rLa~~~g~f~~~----l~~~~a~g~~------~~~~~y~~~~a~~ll~~kslv~a~~~---~~~a~~  300 (414)
T COG3903         234 YALLTGWERALFGRLAVFVGGFDLG----LALAVAAGAD------VDVPRYLVLLALTLLVDKSLVVALDL---LGRARY  300 (414)
T ss_pred             hHhhhhHHHHHhcchhhhhhhhccc----HHHHHhcCCc------cccchHHHHHHHHHHhhccchhhhhh---hhHHHH
Confidence            9999999999999999998876544    2345443322      11122234445667888888764431   111235


Q ss_pred             EcCHHHHHHHHhhhh
Q 001843          575 CMPGVLYDILRPKAE  589 (1007)
Q Consensus       575 ~mHdlv~d~~~~~~~  589 (1007)
                      +.-+-++.|+..+..
T Consensus       301 Rl~eT~r~YalaeL~  315 (414)
T COG3903         301 RLLETGRRYALAELH  315 (414)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            555556666655544

>PRK06893 DNA replication initiation factor; Validated

Probab=98.57  E-value=2.9e-07  Score=97.47  Aligned_cols=151  Identities=11%  Similarity=0.107  Sum_probs=92.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +.+.|+|.+|+|||+||+++++.  .......+.|+++.  ...   ..                        ...+.+.
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~y~~~~--~~~---~~------------------------~~~~~~~   88 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNH--YLLNQRTAIYIPLS--KSQ---YF------------------------SPAVLEN   88 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEeeHH--Hhh---hh------------------------hHHHHhh
Confidence            67899999999999999999994  43344456777654  100   00                        0011112


Q ss_pred             cCCCcEEEEEeCcCccC-chhhhhhc-cccC-CCCCCcEEEEEcCCC----------cccccccCCcceeeecCCCCHHH
Q 001843          354 LDDSTFLIVMENAEHQK-SQVWDSFL-GKLC-SFTQCGKIIITTSST----------EDFVEPLGAAFSTLHVPGLGKNE  420 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~-~~~~~~l~-~l~~-~~~~gs~IliTTR~~----------~~va~~~~~~~~~~~l~~L~~~e  420 (1007)
                      +. +.-+|||||+|... ...|+... .+.+ ....|..+||+|.+.          . +...+... ..+++++++.++
T Consensus        89 ~~-~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~-L~sRl~~g-~~~~l~~pd~e~  165 (229)
T PRK06893         89 LE-QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPD-LASRLTWG-EIYQLNDLTDEQ  165 (229)
T ss_pred             cc-cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchh-HHHHHhcC-CeeeCCCCCHHH
Confidence            22 23499999998432 34565332 2222 113355665544432          3 44444444 789999999999


Q ss_pred             HHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          421 SWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       421 a~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                      .++++.+.+....-   .   -.++...-|++++.|-.-.+..+
T Consensus       166 ~~~iL~~~a~~~~l---~---l~~~v~~~L~~~~~~d~r~l~~~  203 (229)
T PRK06893        166 KIIVLQRNAYQRGI---E---LSDEVANFLLKRLDRDMHTLFDA  203 (229)
T ss_pred             HHHHHHHHHHHcCC---C---CCHHHHHHHHHhccCCHHHHHHH
Confidence            99999998875432   1   12456677888887665554433

>KOG0532 consensus Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton]

Probab=98.56  E-value=3.6e-09  Score=117.89  Aligned_cols=194  Identities=20%  Similarity=0.126  Sum_probs=150.6

Q ss_pred             CCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcccccCCCCCEEeecCCcccccccccccc--ceecc
Q 001843          667 RLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPS--RHLYL  744 (1007)
Q Consensus       667 ~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~~L--r~L~l  744 (1007)
                      .+..-...||+.|++.  .+|..++.+..|..|.|..|.|..+|..+++|..|.+|||+.|.+..+|..++.|  +.|.+
T Consensus        73 ~ltdt~~aDlsrNR~~--elp~~~~~f~~Le~liLy~n~~r~ip~~i~~L~~lt~l~ls~NqlS~lp~~lC~lpLkvli~  150 (722)
T KOG0532|consen   73 DLTDTVFADLSRNRFS--ELPEEACAFVSLESLILYHNCIRTIPEAICNLEALTFLDLSSNQLSHLPDGLCDLPLKVLIV  150 (722)
T ss_pred             cccchhhhhccccccc--cCchHHHHHHHHHHHHHHhccceecchhhhhhhHHHHhhhccchhhcCChhhhcCcceeEEE
Confidence            4455567899999999  9999999999999999999999999999999999999999999999999999988  88888


Q ss_pred             cccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEE
Q 001843          745 NWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLK  824 (1007)
Q Consensus       745 ~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~  824 (1007)
                      +   ++. ...+|..++.+..|..|+...++.  ...+..++.|..|+.|.+..+.  ...++    ..+..|+ |..|+
T Consensus       151 s---NNk-l~~lp~~ig~~~tl~~ld~s~nei--~slpsql~~l~slr~l~vrRn~--l~~lp----~El~~Lp-Li~lD  217 (722)
T KOG0532|consen  151 S---NNK-LTSLPEEIGLLPTLAHLDVSKNEI--QSLPSQLGYLTSLRDLNVRRNH--LEDLP----EELCSLP-LIRLD  217 (722)
T ss_pred             e---cCc-cccCCcccccchhHHHhhhhhhhh--hhchHHhhhHHHHHHHHHhhhh--hhhCC----HHHhCCc-eeeee
Confidence            8   544 779999999777888775444432  3567788999999999988775  44455    6666443 78888


Q ss_pred             EeecCCCCCCcccccCCCCCcEEEecccCCCCCcCccCC--CCCCceEEEEEee
Q 001843          825 LICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRS--FPPNVVTLTLSQL  876 (1007)
Q Consensus       825 L~~~~~~~~~~~~l~~~~~L~~L~L~g~~~~lp~~~i~~--~l~~L~~L~L~~~  876 (1007)
                      +++|.... .+-.|..+..|+.|-|.+|.-.-|+.-+..  ...=.++|+..-|
T Consensus       218 fScNkis~-iPv~fr~m~~Lq~l~LenNPLqSPPAqIC~kGkVHIFKyL~~qA~  270 (722)
T KOG0532|consen  218 FSCNKISY-LPVDFRKMRHLQVLQLENNPLQSPPAQICEKGKVHIFKYLSTQAC  270 (722)
T ss_pred             cccCceee-cchhhhhhhhheeeeeccCCCCCChHHHHhccceeeeeeecchhc
Confidence            88887766 677788888888888888773333312211  0223456666666

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.55  E-value=3.4e-06  Score=100.15  Aligned_cols=282  Identities=12%  Similarity=0.164  Sum_probs=145.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhc---ccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYV---KRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~---~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      .++-|+|.+|.|||+.++.|.+...-   ....+...++.+.++.-.+...++..|++++...  ..............+
T Consensus       782 nvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g~--~P~~GlsS~evLerL  859 (1164)
T PTZ00112        782 QILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNK--KPPNALNSFKILDRL  859 (1164)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcCC--CCCccccHHHHHHHH
Confidence            68889999999999999999874211   1223323334443337778889999999988543  112223334455555


Q ss_pred             HHHcC---CCcEEEEEeCcCccCchhhhhhccccCC-CCCCcEEEE--EcCCCc-------ccccccCCcceeeecCCCC
Q 001843          351 TQALD---DSTFLIVMENAEHQKSQVWDSFLGKLCS-FTQCGKIII--TTSSTE-------DFVEPLGAAFSTLHVPGLG  417 (1007)
Q Consensus       351 ~~~L~---~kr~LlVlDdv~~~~~~~~~~l~~l~~~-~~~gs~Ili--TTR~~~-------~va~~~~~~~~~~~l~~L~  417 (1007)
                      ...+.   ....+||||+|+.-....-+.|..+.++ ...+++|+|  +|....       ++...++.  ..+..+|++
T Consensus       860 F~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISNdlDLperLdPRLRSRLg~--eeIvF~PYT  937 (1164)
T PTZ00112        860 FNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISNTMDLPERLIPRCRSRLAF--GRLVFSPYK  937 (1164)
T ss_pred             HhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecCchhcchhhhhhhhhcccc--ccccCCCCC
Confidence            55442   2245899999973221111112222211 023455554  332211       02222221  347789999


Q ss_pred             HHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCC---ChHHHHHHHHHcccchhhhhh
Q 001843          418 KNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQP---SYEEWSKVIERANGDNLVALC  494 (1007)
Q Consensus       418 ~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~---~~~~w~~~l~~l~i~~~l~~s  494 (1007)
                      .++-.+++..++......  -.+..++-+|+.++..-|-.=.||.++-........   +...-..+...+ ....+.-.
T Consensus       938 aEQL~dILk~RAe~A~gV--LdDdAIELIArkVAq~SGDARKALDILRrAgEikegskVT~eHVrkAleei-E~srI~e~ 1014 (1164)
T PTZ00112        938 GDEIEKIIKERLENCKEI--IDHTAIQLCARKVANVSGDIRKALQICRKAFENKRGQKIVPRDITEATNQL-FDSPLTNA 1014 (1164)
T ss_pred             HHHHHHHHHHHHHhCCCC--CCHHHHHHHHHhhhhcCCHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHHH-HhhhHHHH
Confidence            999999999887642211  123344455555554455556666666554432211   233333333332 12223344


Q ss_pred             hcCCccCchhhhhhhccC-C--CCcccchhHHHHHH--HhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEe
Q 001843          495 YQDLPAQVKPCILYMGLF-P--REYEIPVRRLIHLW--CAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIR  564 (1007)
Q Consensus       495 y~~L~~~~k~cfl~la~f-p--~~~~i~~~~Li~~W--iaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~  564 (1007)
                      ...||.+.|-.++-+... -  ....++...+....  +++-.-  ..-+....-+....++.+|...++|-...
T Consensus      1015 IktLPlHqKLVLlALIlLlk~tg~~~i~TGEVYerYk~Lce~~G--k~iGv~plTqRV~d~L~eL~~LGIIl~ep 1087 (1164)
T PTZ00112       1015 INYLPWPFKMFLTCLIVELRMLNDFIIPYKKVLNRYKVLVETSG--KYIGMCSNNELFKIMLDKLVKMGILLIRP 1087 (1164)
T ss_pred             HHcCCHHHHHHHHHHHHHHhhcCCCceeHHHHHHHHHHHHHhhh--hhcCCCCcHHHHHHHHHHHHhcCeEEecC
Confidence            567888866554433321 1  12134444443322  333000  00011122225677888888888886543

>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A

Probab=98.52  E-value=5.4e-08  Score=96.98  Aligned_cols=87  Identities=25%  Similarity=0.233  Sum_probs=26.9

Q ss_pred             cCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCc
Q 001843          632 LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPD  711 (1007)
Q Consensus       632 ~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~  711 (1007)
                      .+..++|.|.+.++.+.         .+...-  ..+.+|++|+|++|.+.  .++ .+..+++|+.|++++|.|+.+++
T Consensus        16 ~n~~~~~~L~L~~n~I~---------~Ie~L~--~~l~~L~~L~Ls~N~I~--~l~-~l~~L~~L~~L~L~~N~I~~i~~   81 (175)
T PF14580_consen   16 NNPVKLRELNLRGNQIS---------TIENLG--ATLDKLEVLDLSNNQIT--KLE-GLPGLPRLKTLDLSNNRISSISE   81 (175)
T ss_dssp             -----------------------------S----TT-TT--EEE-TTS--S----T-T----TT--EEE--SS---S-CH
T ss_pred             ccccccccccccccccc---------cccchh--hhhcCCCEEECCCCCCc--ccc-CccChhhhhhcccCCCCCCcccc
Confidence            44556777888877764         222321  35677888888888877  554 56778888888888888888765


Q ss_pred             cc-ccCCCCCEEeecCCccccc
Q 001843          712 ST-PILFCLATLDVSHTKVQRL  732 (1007)
Q Consensus       712 ~i-~~L~~L~~L~L~~~~l~~l  732 (1007)
                      .+ ..+++|++|++++|+|..+
T Consensus        82 ~l~~~lp~L~~L~L~~N~I~~l  103 (175)
T PF14580_consen   82 GLDKNLPNLQELYLSNNKISDL  103 (175)
T ss_dssp             HHHHH-TT--EEE-TTS---SC
T ss_pred             chHHhCCcCCEEECcCCcCCCh
Confidence            55 3578888888888866654

>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]

Probab=98.52  E-value=2.5e-08  Score=108.24  Aligned_cols=205  Identities=17%  Similarity=0.123  Sum_probs=113.9

Q ss_pred             CCCCcccEEEecCCCCCCcCCC--ccccCCCcCcEEecccCCCccc---CcccccCCCCCEEeecCCccccccccccccc
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNN--NALGRLPFLEYLGLRSTFIDSL---PDSTPILFCLATLDVSHTKVQRLPYAFWPSR  740 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~~lp--~~i~~L~~Lr~L~L~~n~i~~L---P~~i~~L~~L~~L~L~~~~l~~lP~~i~~Lr  740 (1007)
                      +++++||...|.++.+.  ..+  .....|++++.|+|+.|-+...   -.-+..|++|+.|+|+.|.+...-.+     
T Consensus       118 sn~kkL~~IsLdn~~V~--~~~~~~~~k~~~~v~~LdLS~NL~~nw~~v~~i~eqLp~Le~LNls~Nrl~~~~~s-----  190 (505)
T KOG3207|consen  118 SNLKKLREISLDNYRVE--DAGIEEYSKILPNVRDLDLSRNLFHNWFPVLKIAEQLPSLENLNLSSNRLSNFISS-----  190 (505)
T ss_pred             hhHHhhhheeecCcccc--ccchhhhhhhCCcceeecchhhhHHhHHHHHHHHHhcccchhcccccccccCCccc-----
Confidence            56777777777777765  333  2556677777777777655432   22345667777777766644321100     


Q ss_pred             eecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCC
Q 001843          741 HLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSEL  820 (1007)
Q Consensus       741 ~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L  820 (1007)
                                                              ..  -..+++|+.|.++.|.-....+.    ..+..+++|
T Consensus       191 ----------------------------------------~~--~~~l~~lK~L~l~~CGls~k~V~----~~~~~fPsl  224 (505)
T KOG3207|consen  191 ----------------------------------------NT--TLLLSHLKQLVLNSCGLSWKDVQ----WILLTFPSL  224 (505)
T ss_pred             ----------------------------------------cc--hhhhhhhheEEeccCCCCHHHHH----HHHHhCCcH
Confidence                                                    00  01345666666666651122222    556667777


Q ss_pred             CeEEEeecCCCCCCcccccCCCCCcEEEecccC-CCCCc-CccCCCCCCceEEEEEeeecCCCCcCcc------ccCCCC
Q 001843          821 HSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSV-IGDRSFPPNVVTLTLSQLRLEYDPMPIL------GRLRQL  892 (1007)
Q Consensus       821 ~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~-~~i~~~l~~L~~L~L~~~~l~~~~~~~l------~~Lp~L  892 (1007)
                      +.|.|..|......-....-+..|+.|+|+++. ..++. ...+. ++.|..|+++.|.+.....+..      ..+|+|
T Consensus       225 ~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~N~li~~~~~~~~~~-l~~L~~Lnls~tgi~si~~~d~~s~~kt~~f~kL  303 (505)
T KOG3207|consen  225 EVLYLEANEIILIKATSTKILQTLQELDLSNNNLIDFDQGYKVGT-LPGLNQLNLSSTGIASIAEPDVESLDKTHTFPKL  303 (505)
T ss_pred             HHhhhhcccccceecchhhhhhHHhhccccCCccccccccccccc-ccchhhhhccccCcchhcCCCccchhhhcccccc
Confidence            777777753211111222234567777777765 33331 03445 7777778887777655444333      456777


Q ss_pred             cEEEeecCCcCCCceeecCCCCCCCcEEEecc
Q 001843          893 KILRLFGGSYTGEEMSCSSGEFPNLLVLKLWK  924 (1007)
Q Consensus       893 ~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~  924 (1007)
                      ++|++..|.............+++|+.|.+.+
T Consensus       304 ~~L~i~~N~I~~w~sl~~l~~l~nlk~l~~~~  335 (505)
T KOG3207|consen  304 EYLNISENNIRDWRSLNHLRTLENLKHLRITL  335 (505)
T ss_pred             eeeecccCccccccccchhhccchhhhhhccc
Confidence            77777766654333333334456666666543

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=98.48  E-value=2e-06  Score=91.19  Aligned_cols=158  Identities=18%  Similarity=0.266  Sum_probs=102.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.+||++|+||||||+.+.+.  -+.+  ...||..|  .......-+++|.++....                  ..
T Consensus       163 pSmIlWGppG~GKTtlArlia~t--sk~~--SyrfvelS--At~a~t~dvR~ife~aq~~------------------~~  218 (554)
T KOG2028|consen  163 PSMILWGPPGTGKTTLARLIAST--SKKH--SYRFVELS--ATNAKTNDVRDIFEQAQNE------------------KS  218 (554)
T ss_pred             CceEEecCCCCchHHHHHHHHhh--cCCC--ceEEEEEe--ccccchHHHHHHHHHHHHH------------------Hh
Confidence            67789999999999999999993  3333  25678887  6666666666666665443                  23


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhccccCCCCCCcEEEE--EcCCCc-ccccccCCcceeeecCCCCHHHHHHHHHhhhc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIII--TTSSTE-DFVEPLGAAFSTLHVPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~Ili--TTR~~~-~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~  430 (1007)
                      +..+|.+|++|.|..-+..+-+.+.+..   .+|+-++|  ||.++. ++-...-+.+.++.|++|+.++-..++.+-.-
T Consensus       219 l~krkTilFiDEiHRFNksQQD~fLP~V---E~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~v~~iL~raia  295 (554)
T KOG2028|consen  219 LTKRKTILFIDEIHRFNKSQQDTFLPHV---ENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIA  295 (554)
T ss_pred             hhcceeEEEeHHhhhhhhhhhhccccee---ccCceEEEecccCCCccchhHHHHhccceeEeccCCHHHHHHHHHHHHH
Confidence            4678999999999744444444443332   55777777  888876 22233334448999999999999988877322


Q ss_pred             ---cccccccCCC----hHHHHHHHHHHHHcCCCc
Q 001843          431 ---IAEDVLQSRS----SELIKLKKQILNICDGLP  458 (1007)
Q Consensus       431 ---~~~~~~~~~~----~~~~~~~~~I~~~c~GlP  458 (1007)
                         .........+    .-...+..-++..|.|-.
T Consensus       296 ~l~dser~~~~l~n~s~~ve~siidyla~lsdGDa  330 (554)
T KOG2028|consen  296 SLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDA  330 (554)
T ss_pred             hhccccccCCCCCCcchhhhHHHHHHHHHhcCchH
Confidence               1111100111    123345556666777754

>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A

Probab=98.47  E-value=1.6e-07  Score=93.55  Aligned_cols=128  Identities=26%  Similarity=0.284  Sum_probs=45.0

Q ss_pred             CCCCcccEEEecCCCCCCcCCCcccc-CCCcCcEEecccCCCcccCcccccCCCCCEEeecCCcccccccc----ccccc
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALG-RLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYA----FWPSR  740 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~~lp~~i~-~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~----i~~Lr  740 (1007)
                      .+...+|.|+|++|.+.  .+ ..++ .+.+|+.|+|++|.|+.++ .+..|++|++|++++|.|+.++..    +.+|+
T Consensus        16 ~n~~~~~~L~L~~n~I~--~I-e~L~~~l~~L~~L~Ls~N~I~~l~-~l~~L~~L~~L~L~~N~I~~i~~~l~~~lp~L~   91 (175)
T PF14580_consen   16 NNPVKLRELNLRGNQIS--TI-ENLGATLDKLEVLDLSNNQITKLE-GLPGLPRLKTLDLSNNRISSISEGLDKNLPNLQ   91 (175)
T ss_dssp             -----------------------S--TT-TT--EEE-TTS--S--T-T----TT--EEE--SS---S-CHHHHHH-TT--
T ss_pred             ccccccccccccccccc--cc-cchhhhhcCCCEEECCCCCCcccc-CccChhhhhhcccCCCCCCccccchHHhCCcCC
Confidence            56778999999999998  55 3566 5889999999999999997 688999999999999999887543    45668


Q ss_pred             eecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecC-CCchhhHHHHHHHhhcCCC
Q 001843          741 HLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSS-TTSTSLKKEIIGAVLQLSE  819 (1007)
Q Consensus       741 ~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~-~~~~~l~~~~~~~l~~l~~  819 (1007)
                      +|+++   ++.        |..+.                .+..+..+++|+.|++.++. .......   ...+..+++
T Consensus        92 ~L~L~---~N~--------I~~l~----------------~l~~L~~l~~L~~L~L~~NPv~~~~~YR---~~vi~~lP~  141 (175)
T PF14580_consen   92 ELYLS---NNK--------ISDLN----------------ELEPLSSLPKLRVLSLEGNPVCEKKNYR---LFVIYKLPS  141 (175)
T ss_dssp             EEE-T---TS-----------SCC----------------CCGGGGG-TT--EEE-TT-GGGGSTTHH---HHHHHH-TT
T ss_pred             EEECc---CCc--------CCChH----------------HhHHHHcCCCcceeeccCCcccchhhHH---HHHHHHcCh
Confidence            88877   443        11121                12334566778888887776 2222222   144566677


Q ss_pred             CCeEEEee
Q 001843          820 LHSLKLIC  827 (1007)
Q Consensus       820 L~~L~L~~  827 (1007)
                      |+.|+-..
T Consensus       142 Lk~LD~~~  149 (175)
T PF14580_consen  142 LKVLDGQD  149 (175)
T ss_dssp             -SEETTEE
T ss_pred             hheeCCEE
Confidence            77665443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.46  E-value=4.4e-06  Score=98.98  Aligned_cols=103  Identities=6%  Similarity=-0.006  Sum_probs=73.0

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      ++.-++|||+++.-+...|+.+. .+-.. ....++|+||.+..++...+.+.+..+.+++++.++..+.+.+.+.....
T Consensus       118 gr~KVIIIDEah~LT~~A~NALLKtLEEP-P~~v~FILaTtd~~KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI  196 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHAFNAMLKTLEEP-PPHVKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERI  196 (830)
T ss_pred             CCceEEEEeChhhCCHHHHHHHHHHHHhc-CCCeEEEEEECChhhccchhhhheEEEecCCcCHHHHHHHHHHHHHHcCC
Confidence            44558999999976667788777 44333 45678888777766576666666689999999999999999887654321


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCc-hHHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLP-LRVVLLA  465 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g  465 (1007)
                            .-..+....|++.++|.. -|+.++-
T Consensus       197 ------~id~eAL~lIA~~A~GsmRdALsLLd  222 (830)
T PRK07003        197 ------AFEPQALRLLARAAQGSMRDALSLTD  222 (830)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence                  122466778999998854 5655543

>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]

Probab=98.46  E-value=3.4e-08  Score=107.22  Aligned_cols=180  Identities=18%  Similarity=0.111  Sum_probs=79.1

Q ss_pred             hhcCCCCCeEEeeecC-CCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCccc-ccCCCCCcEEEecccC---CCCCcC
Q 001843          785 FRRLTSLRKLGLKCSS-TTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLE-MAEHYKLQKLYLSGHL---PPNSVI  859 (1007)
Q Consensus       785 l~~L~~L~~L~l~~~~-~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~-l~~~~~L~~L~L~g~~---~~lp~~  859 (1007)
                      ...+++++.|+++.+- .+...+.    .....+++|+.|+|+.|....+.-.. -..+++|+.|.|++|.   ..+-. 
T Consensus       142 ~k~~~~v~~LdLS~NL~~nw~~v~----~i~eqLp~Le~LNls~Nrl~~~~~s~~~~~l~~lK~L~l~~CGls~k~V~~-  216 (505)
T KOG3207|consen  142 SKILPNVRDLDLSRNLFHNWFPVL----KIAEQLPSLENLNLSSNRLSNFISSNTTLLLSHLKQLVLNSCGLSWKDVQW-  216 (505)
T ss_pred             hhhCCcceeecchhhhHHhHHHHH----HHHHhcccchhcccccccccCCccccchhhhhhhheEEeccCCCCHHHHHH-
Confidence            4455666666666543 2233333    55556666666666654332211100 0124456666665544   11111 


Q ss_pred             ccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEeccCCCCcceEEcC----
Q 001843          860 GDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKE----  935 (1007)
Q Consensus       860 ~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~~~L~~l~~~~----  935 (1007)
                      .... +|+|..|.|..|...........-+..|+.|+|++|.+.........+.||.|..|.++.+ .+.++.+..    
T Consensus       217 ~~~~-fPsl~~L~L~~N~~~~~~~~~~~i~~~L~~LdLs~N~li~~~~~~~~~~l~~L~~Lnls~t-gi~si~~~d~~s~  294 (505)
T KOG3207|consen  217 ILLT-FPSLEVLYLEANEIILIKATSTKILQTLQELDLSNNNLIDFDQGYKVGTLPGLNQLNLSST-GIASIAEPDVESL  294 (505)
T ss_pred             HHHh-CCcHHHhhhhcccccceecchhhhhhHHhhccccCCcccccccccccccccchhhhhcccc-CcchhcCCCccch
Confidence            1112 5556666665553111111122234455555565555443332233345555555555553 233332211    


Q ss_pred             ---CCCccccEeEeeccCCCC-CC--cCccccccCccEEEeccC
Q 001843          936 ---GAMPCLRQLEIRSCGYLV-PP--TGLKHVTSSLREFLLTNM  973 (1007)
Q Consensus       936 ---~~~p~L~~L~l~~c~~L~-lp--~~l~~L~~~L~~L~l~~c  973 (1007)
                         ..||+|+.|++..++ +. ++  ..+..+ ++|+.|.+..+
T Consensus       295 ~kt~~f~kL~~L~i~~N~-I~~w~sl~~l~~l-~nlk~l~~~~n  336 (505)
T KOG3207|consen  295 DKTHTFPKLEYLNISENN-IRDWRSLNHLRTL-ENLKHLRITLN  336 (505)
T ss_pred             hhhcccccceeeecccCc-cccccccchhhcc-chhhhhhcccc
Confidence               135566666665533 22 22  123444 44555544443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.41  E-value=2.2e-06  Score=91.00  Aligned_cols=153  Identities=14%  Similarity=0.196  Sum_probs=88.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..|.|+|..|+|||+||+.+++.  ........++++++  .-.+      .                 .    ..+...
T Consensus        39 ~~lll~G~~G~GKT~la~~~~~~--~~~~~~~~~~i~~~--~~~~------~-----------------~----~~~~~~   87 (226)
T TIGR03420        39 RFLYLWGESGSGKSHLLQAACAA--AEERGKSAIYLPLA--ELAQ------A-----------------D----PEVLEG   87 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHhcCCcEEEEeHH--HHHH------h-----------------H----HHHHhh
Confidence            78899999999999999999984  33334455666654  1110      0                 0    011112


Q ss_pred             cCCCcEEEEEeCcCccCch-hh-hhhc-cccCCCCCCcEEEEEcCCCc-c-------cccccCCcceeeecCCCCHHHHH
Q 001843          354 LDDSTFLIVMENAEHQKSQ-VW-DSFL-GKLCSFTQCGKIIITTSSTE-D-------FVEPLGAAFSTLHVPGLGKNESW  422 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~-~~-~~l~-~l~~~~~~gs~IliTTR~~~-~-------va~~~~~~~~~~~l~~L~~~ea~  422 (1007)
                      +.. .-+|||||++..... .| +.+. .+......+.++|+||+... .       +...+... ..++++++++++-.
T Consensus        88 ~~~-~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~-~~i~l~~l~~~e~~  165 (226)
T TIGR03420        88 LEQ-ADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWG-LVFQLPPLSDEEKI  165 (226)
T ss_pred             ccc-CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcC-eeEecCCCCHHHHH
Confidence            222 238999999843222 23 3333 22211123457889888542 0       11122112 67899999999989


Q ss_pred             HHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHH
Q 001843          423 ELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLA  465 (1007)
Q Consensus       423 ~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g  465 (1007)
                      .++...+.....   .   -..+....|++.+.|.|..+.-+-
T Consensus       166 ~~l~~~~~~~~~---~---~~~~~l~~L~~~~~gn~r~L~~~l  202 (226)
T TIGR03420       166 AALQSRAARRGL---Q---LPDEVADYLLRHGSRDMGSLMALL  202 (226)
T ss_pred             HHHHHHHHHcCC---C---CCHHHHHHHHHhccCCHHHHHHHH
Confidence            988765432111   1   123555777777888887666553

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.40  E-value=4.9e-06  Score=92.72  Aligned_cols=159  Identities=18%  Similarity=0.253  Sum_probs=102.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhh----hcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRV----YVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~----~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      ..+.++|+.|+||||+|+.+++.-    ....|.|...|.... .......+ ++++...+...                
T Consensus        27 ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~-~~~i~v~~-ir~~~~~~~~~----------------   88 (313)
T PRK05564         27 HAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPIN-KKSIGVDD-IRNIIEEVNKK----------------   88 (313)
T ss_pred             ceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecccc-CCCCCHHH-HHHHHHHHhcC----------------
Confidence            678899999999999999999831    123345554554422 02222222 33333333221                


Q ss_pred             HHHHcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhh
Q 001843          350 ITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKK  428 (1007)
Q Consensus       350 l~~~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~  428 (1007)
                         -..+++-++|+|+++.-+...|+.+. .+.+. ..++.+|++|.+...+.....+.+..+.+.++++++....+.+.
T Consensus        89 ---p~~~~~kv~iI~~ad~m~~~a~naLLK~LEep-p~~t~~il~~~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~l~~~  164 (313)
T PRK05564         89 ---PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEP-PKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEKFISYK  164 (313)
T ss_pred             ---cccCCceEEEEechhhcCHHHHHHHHHHhcCC-CCCeEEEEEeCChHhCcHHHHhhceeeeCCCcCHHHHHHHHHHH
Confidence               11245567777877755778888888 66555 67888888887766455555555589999999999998877654


Q ss_pred             hccccccccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          429 ARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       429 a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                      ..+ .      +   ...+..++..++|.|.-+...
T Consensus       165 ~~~-~------~---~~~~~~l~~~~~g~~~~a~~~  190 (313)
T PRK05564        165 YND-I------K---EEEKKSAIAFSDGIPGKVEKF  190 (313)
T ss_pred             hcC-C------C---HHHHHHHHHHcCCCHHHHHHH
Confidence            321 1      1   234678889999988765433

>PF13173 AAA_14: AAA domain

Probab=98.38  E-value=1.2e-06  Score=83.70  Aligned_cols=119  Identities=20%  Similarity=0.247  Sum_probs=79.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +++.|.|+.|+|||||+++++.+..   ....++++++.  .......                   .+.+ ..+.+.+.
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~--~~~~~~~-------------------~~~~-~~~~~~~~   57 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFD--DPRDRRL-------------------ADPD-LLEYFLEL   57 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccC--CHHHHHH-------------------hhhh-hHHHHHHh
Confidence            7999999999999999999998422   33456777665  2111000                   0000 23334444


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccc-----cccCCcceeeecCCCCHHHH
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFV-----EPLGAAFSTLHVPGLGKNES  421 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va-----~~~~~~~~~~~l~~L~~~ea  421 (1007)
                      ...++.+|+||++.  ....|.... .+.+. ....+|++|+.... ..     ....+....+++.||+-.|.
T Consensus        58 ~~~~~~~i~iDEiq--~~~~~~~~lk~l~d~-~~~~~ii~tgS~~~-~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   58 IKPGKKYIFIDEIQ--YLPDWEDALKFLVDN-GPNIKIILTGSSSS-LLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             hccCCcEEEEehhh--hhccHHHHHHHHHHh-ccCceEEEEccchH-HHhhcccccCCCeEEEEEECCCCHHHh
Confidence            44578899999998  666777766 77666 56689999998766 33     22233336789999998774

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=98.37  E-value=3.4e-07  Score=105.97  Aligned_cols=172  Identities=25%  Similarity=0.234  Sum_probs=108.7

Q ss_pred             CCCCcccEEEecCCCCCCcCCCccccCCC-cCcEEecccCCCcccCcccccCCCCCEEeecCCccccccccc---cccce
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGRLP-FLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAF---WPSRH  741 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~-~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i---~~Lr~  741 (1007)
                      ..++.+..|++.++.+.  .+|..++.+. +|++|++++|.+..+|..++.+++|+.|++++|.+..+|...   ..|+.
T Consensus       113 ~~~~~l~~L~l~~n~i~--~i~~~~~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N~l~~l~~~~~~~~~L~~  190 (394)
T COG4886         113 LELTNLTSLDLDNNNIT--DIPPLIGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFNDLSDLPKLLSNLSNLNN  190 (394)
T ss_pred             hcccceeEEecCCcccc--cCccccccchhhcccccccccchhhhhhhhhccccccccccCCchhhhhhhhhhhhhhhhh
Confidence            45677888888888888  7888888775 888888888888888888888888888888888888888843   44477


Q ss_pred             ecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCC
Q 001843          742 LYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELH  821 (1007)
Q Consensus       742 L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~  821 (1007)
                      |+++   ++. ...+|..++.+..|++|......  ....+..+..+.++..|.+..+.  ...+.    ..+..+++|+
T Consensus       191 L~ls---~N~-i~~l~~~~~~~~~L~~l~~~~N~--~~~~~~~~~~~~~l~~l~l~~n~--~~~~~----~~~~~l~~l~  258 (394)
T COG4886         191 LDLS---GNK-ISDLPPEIELLSALEELDLSNNS--IIELLSSLSNLKNLSGLELSNNK--LEDLP----ESIGNLSNLE  258 (394)
T ss_pred             eecc---CCc-cccCchhhhhhhhhhhhhhcCCc--ceecchhhhhcccccccccCCce--eeecc----chhccccccc
Confidence            8887   554 45666655555566666322211  12344455566666666555443  21112    4445555555


Q ss_pred             eEEEeecCCCCCCcccccCCCCCcEEEecccC
Q 001843          822 SLKLICETPSYLPLLEMAEHYKLQKLYLSGHL  853 (1007)
Q Consensus       822 ~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~  853 (1007)
                      .|+++++....  ...+.+..+|+.|+++++.
T Consensus       259 ~L~~s~n~i~~--i~~~~~~~~l~~L~~s~n~  288 (394)
T COG4886         259 TLDLSNNQISS--ISSLGSLTNLRELDLSGNS  288 (394)
T ss_pred             eeccccccccc--cccccccCccCEEeccCcc
Confidence            55555543332  1224444555555555443

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=98.33  E-value=1.3e-08  Score=104.93  Aligned_cols=132  Identities=23%  Similarity=0.098  Sum_probs=68.5

Q ss_pred             cCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecC-CCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccc-
Q 001843          761 KWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSS-TTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEM-  838 (1007)
Q Consensus       761 ~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~-~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l-  838 (1007)
                      ..+++|+.|+.-. ...+......+.+-.+|+.|+|+.+. -....+.    -.+.+++.|.+|+|+|+....+....+ 
T Consensus       207 s~C~kLk~lSlEg-~~LdD~I~~~iAkN~~L~~lnlsm~sG~t~n~~~----ll~~scs~L~~LNlsWc~l~~~~Vtv~V  281 (419)
T KOG2120|consen  207 SQCSKLKNLSLEG-LRLDDPIVNTIAKNSNLVRLNLSMCSGFTENALQ----LLLSSCSRLDELNLSWCFLFTEKVTVAV  281 (419)
T ss_pred             HHHHhhhhccccc-cccCcHHHHHHhccccceeeccccccccchhHHH----HHHHhhhhHhhcCchHhhccchhhhHHH
Confidence            3444555543222 22224466778888888888888876 2222333    556778888888888865443221111 


Q ss_pred             cC-CCCCcEEEecccCCCCCcC----ccCCCCCCceEEEEEeee-cCCCCcCccccCCCCcEEEee
Q 001843          839 AE-HYKLQKLYLSGHLPPNSVI----GDRSFPPNVVTLTLSQLR-LEYDPMPILGRLRQLKILRLF  898 (1007)
Q Consensus       839 ~~-~~~L~~L~L~g~~~~lp~~----~i~~~l~~L~~L~L~~~~-l~~~~~~~l~~Lp~L~~L~L~  898 (1007)
                      .. -++|..|+|+|+...+-..    .... +|+|..|+|++|. ++......+.+++.|++|.|+
T Consensus       282 ~hise~l~~LNlsG~rrnl~~sh~~tL~~r-cp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~lSls  346 (419)
T KOG2120|consen  282 AHISETLTQLNLSGYRRNLQKSHLSTLVRR-CPNLVHLDLSDSVMLKNDCFQEFFKFNYLQHLSLS  346 (419)
T ss_pred             hhhchhhhhhhhhhhHhhhhhhHHHHHHHh-CCceeeeccccccccCchHHHHHHhcchheeeehh
Confidence            11 2467777777654222110    1123 5666666666653 222222334444555555554

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.32  E-value=1.2e-06  Score=84.17  Aligned_cols=116  Identities=23%  Similarity=0.399  Sum_probs=79.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc---cCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK---RHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~---~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      +++.|+|.+|+|||+++++++++....   ..-..++|+.+.  ...+...+...|+.+++...   ....+...+.+.+
T Consensus         5 ~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~~~l~~~~---~~~~~~~~l~~~~   79 (131)
T PF13401_consen    5 RILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCP--SSRTPRDFAQEILEALGLPL---KSRQTSDELRSLL   79 (131)
T ss_dssp             --EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHH--HHSSHHHHHHHHHHHHT-SS---SSTS-HHHHHHHH
T ss_pred             cccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeC--CCCCHHHHHHHHHHHhCccc---cccCCHHHHHHHH
Confidence            899999999999999999999842110   013456799988  77789999999999998761   1235677777888


Q ss_pred             HHHcCCCcE-EEEEeCcCcc-CchhhhhhccccCCCCCCcEEEEEcCC
Q 001843          351 TQALDDSTF-LIVMENAEHQ-KSQVWDSFLGKLCSFTQCGKIIITTSS  396 (1007)
Q Consensus       351 ~~~L~~kr~-LlVlDdv~~~-~~~~~~~l~~l~~~~~~gs~IliTTR~  396 (1007)
                      .+.+...+. +||+|+++.- +...++.++.+.+  ..+.+||+..+.
T Consensus        80 ~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   80 IDALDRRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            888876554 9999999855 5455555554433  445667666554

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.31  E-value=7.4e-06  Score=98.77  Aligned_cols=186  Identities=18%  Similarity=0.138  Sum_probs=106.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC---CceEEEEecCCC-CCCHHHHHHHHHH---------------HHhhhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF---TKRAWVHIPIMS-MVEDRDVLADILK---------------QIDESL  334 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F---~~~~wv~~s~~~-~~~~~~~l~~il~---------------~l~~~~  334 (1007)
                      ..+.|+|++|+||||+|+.+++.......+   ...-|+.+.+.. ..+...+...++.               ..+...
T Consensus       176 ~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~  255 (615)
T TIGR02903       176 QHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVPE  255 (615)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCc
Confidence            679999999999999999999854333333   123455553111 1122222111111               111000


Q ss_pred             h---------------hhccccCHHHHHHHHHHHcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEE--EcCC
Q 001843          335 L---------------KVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIII--TTSS  396 (1007)
Q Consensus       335 ~---------------~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~Ili--TTR~  396 (1007)
                      .               .+-...+ ...+..+.+.+++++++++-|+.|..+...|+.++ .+... .+...|+|  ||++
T Consensus       256 ~~~g~v~~asgGvL~LDEi~~Ld-~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~-~~~~~VLI~aTt~~  333 (615)
T TIGR02903       256 PKTGLVTDAHGGVLFIDEIGELD-PLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEG-APADFVLIGATTRD  333 (615)
T ss_pred             hhcCchhhcCCCeEEEeccccCC-HHHHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccC-ccceEEEEEecccc
Confidence            0               0001111 23467788888899999998888866677788888 55444 45555555  6775


Q ss_pred             CcccccccCCcceeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHH
Q 001843          397 TEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGL  467 (1007)
Q Consensus       397 ~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~  467 (1007)
                      ...+..........+.+.+++.+|.+.++.+.+.....   ..+   .+....|.+.+..-+-|+..++..
T Consensus       334 ~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v---~ls---~eal~~L~~ys~~gRraln~L~~~  398 (615)
T TIGR02903       334 PEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINV---HLA---AGVEELIARYTIEGRKAVNILADV  398 (615)
T ss_pred             ccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCC---CCC---HHHHHHHHHCCCcHHHHHHHHHHH
Confidence            54233333333367889999999999999987653211   111   234445555554445555555443

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=98.31  E-value=6e-07  Score=103.94  Aligned_cols=190  Identities=26%  Similarity=0.271  Sum_probs=127.8

Q ss_pred             cEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcccccCC-CCCEEeecCCcccccccccccc---ceeccccc
Q 001843          672 KVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILF-CLATLDVSHTKVQRLPYAFWPS---RHLYLNWI  747 (1007)
Q Consensus       672 r~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i~~L~-~L~~L~L~~~~l~~lP~~i~~L---r~L~l~~~  747 (1007)
                      ..|+++.+.+.  ..+..+..+..+..|++.+|.++.+|..++.+. +|+.|++++|.+..+|..+..+   +.|++.  
T Consensus        96 ~~l~~~~~~~~--~~~~~~~~~~~l~~L~l~~n~i~~i~~~~~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~--  171 (394)
T COG4886          96 PSLDLNLNRLR--SNISELLELTNLTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLS--  171 (394)
T ss_pred             ceeeccccccc--cCchhhhcccceeEEecCCcccccCccccccchhhcccccccccchhhhhhhhhccccccccccC--
Confidence            36788888875  445566777889999999999999998888885 9999999999888876433322   444444  


Q ss_pred             ccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEee
Q 001843          748 FLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLIC  827 (1007)
Q Consensus       748 ~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~  827 (1007)
                       .|. ...+|.                         ..+.+++|+.|.++++.  ...++    ..+..+..|++|.+.+
T Consensus       172 -~N~-l~~l~~-------------------------~~~~~~~L~~L~ls~N~--i~~l~----~~~~~~~~L~~l~~~~  218 (394)
T COG4886         172 -FND-LSDLPK-------------------------LLSNLSNLNNLDLSGNK--ISDLP----PEIELLSALEELDLSN  218 (394)
T ss_pred             -Cch-hhhhhh-------------------------hhhhhhhhhheeccCCc--cccCc----hhhhhhhhhhhhhhcC
Confidence             322 112222                         22256677777777665  44444    4444455677777777


Q ss_pred             cCCCCCCcccccCCCCCcEEEecccC-CCCCcCccCCCCCCceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcC
Q 001843          828 ETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYT  903 (1007)
Q Consensus       828 ~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~  903 (1007)
                      +.... .+..+..+.++..|.+.++. ..++. .+.. +++|+.|++++|.+...  +.++.+.+|+.|+++++...
T Consensus       219 N~~~~-~~~~~~~~~~l~~l~l~~n~~~~~~~-~~~~-l~~l~~L~~s~n~i~~i--~~~~~~~~l~~L~~s~n~~~  290 (394)
T COG4886         219 NSIIE-LLSSLSNLKNLSGLELSNNKLEDLPE-SIGN-LSNLETLDLSNNQISSI--SSLGSLTNLRELDLSGNSLS  290 (394)
T ss_pred             Cccee-cchhhhhcccccccccCCceeeeccc-hhcc-ccccceecccccccccc--ccccccCccCEEeccCcccc
Confidence            63221 45556666677777766665 44466 7777 88899999999987533  33888889999999866554

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.30  E-value=9.8e-06  Score=91.66  Aligned_cols=100  Identities=13%  Similarity=0.072  Sum_probs=62.4

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      ..+-+||+||+..-.......+. .+-.. ...+++|+||.....+..........+++.+++.++....+.+.+.....
T Consensus       124 ~~~~vlilDe~~~l~~~~~~~L~~~le~~-~~~~~~Il~~~~~~~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~  202 (337)
T PRK12402        124 ADYKTILLDNAEALREDAQQALRRIMEQY-SRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGV  202 (337)
T ss_pred             CCCcEEEEeCcccCCHHHHHHHHHHHHhc-cCCCeEEEEeCChhhCchhhcCCceEEEecCCCHHHHHHHHHHHHHHcCC
Confidence            34458999999744444445555 33222 44567888775543244433444478899999999998888886543322


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVV  462 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~  462 (1007)
                         .   -..+....+++.++|.+-.+.
T Consensus       203 ---~---~~~~al~~l~~~~~gdlr~l~  224 (337)
T PRK12402        203 ---D---YDDDGLELIAYYAGGDLRKAI  224 (337)
T ss_pred             ---C---CCHHHHHHHHHHcCCCHHHHH
Confidence               1   124567788888888654443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.28  E-value=1.6e-05  Score=90.34  Aligned_cols=98  Identities=9%  Similarity=0.023  Sum_probs=65.6

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+...++.+. .+-.. ....++|++|.+...+.....+.+..+++.+++.++..+.+...+.....
T Consensus       118 ~~~kviIIDEa~~l~~~a~naLLk~lEe~-~~~~~fIl~t~~~~~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~  196 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSFNALLKTLEEP-PQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESI  196 (363)
T ss_pred             CCceEEEEEChhhcCHHHHHHHHHHHhcC-CCCeEEEEEcCChHhhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHHcCC
Confidence            45569999999865666677776 44433 45667777665544355444444489999999999999888776543221


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLa  460 (1007)
                            .-.++.+..|++.++|.|-.
T Consensus       197 ------~i~~~al~~ia~~s~G~~R~  216 (363)
T PRK14961        197 ------DTDEYALKLIAYHAHGSMRD  216 (363)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHH
Confidence                  11235677889999997753

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.27  E-value=1.3e-05  Score=96.99  Aligned_cols=103  Identities=7%  Similarity=0.027  Sum_probs=69.9

Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      .+++-++|||+++.-+...++.++ .+-.. ....++|++|.+...+.....+.+..|++++|+.++..+.+.+.+....
T Consensus       117 ~gk~KViIIDEAh~LT~eAqNALLKtLEEP-P~~vrFILaTTe~~kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~Eg  195 (944)
T PRK14949        117 RGRFKVYLIDEVHMLSRSSFNALLKTLEEP-PEHVKFLLATTDPQKLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQEQ  195 (944)
T ss_pred             cCCcEEEEEechHhcCHHHHHHHHHHHhcc-CCCeEEEEECCCchhchHHHHHhheEEeCCCCCHHHHHHHHHHHHHHcC
Confidence            356779999999877777778777 33332 4456666665554436555455558999999999999998887654321


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCch-HHHHH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPL-RVVLL  464 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPL-ai~~~  464 (1007)
                      .      ....+.+..|++.++|.|- |+.++
T Consensus       196 I------~~edeAL~lIA~~S~Gd~R~ALnLL  221 (944)
T PRK14949        196 L------PFEAEALTLLAKAANGSMRDALSLT  221 (944)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            1      1224567889999999884 44443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.26  E-value=3e-06  Score=99.30  Aligned_cols=178  Identities=15%  Similarity=0.136  Sum_probs=101.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCC-----CCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIM-----SMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~-----~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      ..+.++|++|+||||+|+.+++...-.+.+...+|.|.++.     ...+..        .+...  ......+..++..
T Consensus        37 ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~--------el~~~--~~~~vd~iR~l~~  106 (504)
T PRK14963         37 HAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVL--------EIDAA--SNNSVEDVRDLRE  106 (504)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceE--------Eeccc--ccCCHHHHHHHHH
Confidence            56799999999999999999984322223333344432210     000000        00000  0000111112222


Q ss_pred             HHHH-HcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHH
Q 001843          349 RITQ-ALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFL  426 (1007)
Q Consensus       349 ~l~~-~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~  426 (1007)
                      .+.. -..+++-++|+|+++..+...++.+. .+-.. ...+.+|++|.....+.......+..+++.+++.++..+.+.
T Consensus       107 ~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep-~~~t~~Il~t~~~~kl~~~I~SRc~~~~f~~ls~~el~~~L~  185 (504)
T PRK14963        107 KVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEP-PEHVIFILATTEPEKMPPTILSRTQHFRFRRLTEEEIAGKLR  185 (504)
T ss_pred             HHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhC-CCCEEEEEEcCChhhCChHHhcceEEEEecCCCHHHHHHHHH
Confidence            2211 12356669999999866666777777 55443 445555555544332655555555899999999999999998


Q ss_pred             hhhccccccccCCChHHHHHHHHHHHHcCCCch-HHHHHHHHh
Q 001843          427 KKARIAEDVLQSRSSELIKLKKQILNICDGLPL-RVVLLAGLL  468 (1007)
Q Consensus       427 ~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPL-ai~~~g~~L  468 (1007)
                      +.+...+.      ....+.+..|++.++|.+- |+..+-.++
T Consensus       186 ~i~~~egi------~i~~~Al~~ia~~s~GdlR~aln~Lekl~  222 (504)
T PRK14963        186 RLLEAEGR------EAEPEALQLVARLADGAMRDAESLLERLL  222 (504)
T ss_pred             HHHHHcCC------CCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            87654332      1124567889999999885 444443433

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.23  E-value=1.5e-05  Score=93.57  Aligned_cols=99  Identities=8%  Similarity=0.005  Sum_probs=66.3

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+...++.+. .+-.. ..+.++|++|.+...+.....+.+..+++++++.++..+.+.+.+.....
T Consensus       117 gk~KV~IIDEVh~LS~~A~NALLKtLEEP-P~~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI  195 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTHSFNALLKTLEEP-PEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQI  195 (702)
T ss_pred             CCcEEEEEechHhcCHHHHHHHHHHHhcC-CCCcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCC
Confidence            55669999999866666777777 44333 44567777776544244333344489999999999999888876654322


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai  461 (1007)
                            .-..+....|++.++|-+-.+
T Consensus       196 ------~id~eAL~~IA~~S~GdLRdA  216 (702)
T PRK14960        196 ------AADQDAIWQIAESAQGSLRDA  216 (702)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHHH
Confidence                  122456678889999877433

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.21  E-value=1.2e-06  Score=71.68  Aligned_cols=59  Identities=29%  Similarity=0.330  Sum_probs=48.5

Q ss_pred             CcccEEEecCCCCCCcCCC-ccccCCCcCcEEecccCCCcccCc-ccccCCCCCEEeecCCcc
Q 001843          669 GMLKVLDLEGVYKPMLTNN-NALGRLPFLEYLGLRSTFIDSLPD-STPILFCLATLDVSHTKV  729 (1007)
Q Consensus       669 ~~Lr~L~Ls~~~l~~~~lp-~~i~~L~~Lr~L~L~~n~i~~LP~-~i~~L~~L~~L~L~~~~l  729 (1007)
                      ++|++|++++|.+.  .+| ..|.++++|++|++++|.++.+|. .+.++++|++|++++|.|
T Consensus         1 p~L~~L~l~~n~l~--~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~l   61 (61)
T PF13855_consen    1 PNLESLDLSNNKLT--EIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLPNLRYLDLSNNNL   61 (61)
T ss_dssp             TTESEEEETSSTES--EECTTTTTTGTTESEEEETSSSESEEETTTTTTSTTESEEEETSSSB
T ss_pred             CcCcEEECCCCCCC--ccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCCCCCEEeCcCCcC
Confidence            46888899988888  776 467888999999999988888874 678899999999988864

...

>KOG1259 consensus Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms; Cytoskeleton]

Probab=98.21  E-value=3.4e-07  Score=94.46  Aligned_cols=111  Identities=23%  Similarity=0.215  Sum_probs=82.3

Q ss_pred             hHhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEEEecccC-CCCCcCc
Q 001843          782 LDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIG  860 (1007)
Q Consensus       782 ~~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~  860 (1007)
                      -+++.-++.++.|+++.+.  ...+     .++..+++|+.|+|++|.... .-.+-..+-+++.|.|.+|. ..+.  .
T Consensus       300 DESvKL~Pkir~L~lS~N~--i~~v-----~nLa~L~~L~~LDLS~N~Ls~-~~Gwh~KLGNIKtL~La~N~iE~LS--G  369 (490)
T KOG1259|consen  300 DESVKLAPKLRRLILSQNR--IRTV-----QNLAELPQLQLLDLSGNLLAE-CVGWHLKLGNIKTLKLAQNKIETLS--G  369 (490)
T ss_pred             hhhhhhccceeEEeccccc--eeee-----hhhhhcccceEeecccchhHh-hhhhHhhhcCEeeeehhhhhHhhhh--h
Confidence            3445566889999999876  3333     457788999999999875543 22233346789999999987 6555  4


Q ss_pred             cCCCCCCceEEEEEeeecCC-CCcCccccCCCCcEEEeecCCcC
Q 001843          861 DRSFPPNVVTLTLSQLRLEY-DPMPILGRLRQLKILRLFGGSYT  903 (1007)
Q Consensus       861 i~~~l~~L~~L~L~~~~l~~-~~~~~l~~Lp~L~~L~L~~~~~~  903 (1007)
                      +.. +-+|..|++++|++.. +....+|+||+|+.|.|.+|...
T Consensus       370 L~K-LYSLvnLDl~~N~Ie~ldeV~~IG~LPCLE~l~L~~NPl~  412 (490)
T KOG1259|consen  370 LRK-LYSLVNLDLSSNQIEELDEVNHIGNLPCLETLRLTGNPLA  412 (490)
T ss_pred             hHh-hhhheeccccccchhhHHHhcccccccHHHHHhhcCCCcc
Confidence            666 8899999999998754 34567899999999999977653

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.21  E-value=1.3e-05  Score=93.80  Aligned_cols=103  Identities=6%  Similarity=0.022  Sum_probs=69.4

Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      .++.-++|||+++.-+...++.+. .+-.- ....++|++|.+..++.....+.+..+.++.++.++..+.+.+.+....
T Consensus       122 ~gr~KViIIDEah~Ls~~AaNALLKTLEEP-P~~v~FILaTtep~kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Eg  200 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNHAFNAMLKTLEEP-PEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEG  200 (700)
T ss_pred             cCCceEEEEEChHhcCHHHHHHHHHhhccC-CCCceEEEEeCChHhhhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcC
Confidence            355669999999877777777777 44332 3455655554444437766666668999999999999998887664322


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                      .      ....+....|++.++|.|.-...+
T Consensus       201 i------~~d~eAL~~IA~~A~Gs~RdALsL  225 (700)
T PRK12323        201 I------AHEVNALRLLAQAAQGSMRDALSL  225 (700)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            1      112345678899999988644433

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=98.20  E-value=2.1e-05  Score=80.19  Aligned_cols=156  Identities=21%  Similarity=0.205  Sum_probs=85.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+-+||++|+||||||.-+++  .....|.   +++..  . .                       ....++...+.+ 
T Consensus        51 ~h~lf~GPPG~GKTTLA~IIA~--e~~~~~~---~~sg~--~-i-----------------------~k~~dl~~il~~-   98 (233)
T PF05496_consen   51 DHMLFYGPPGLGKTTLARIIAN--ELGVNFK---ITSGP--A-I-----------------------EKAGDLAAILTN-   98 (233)
T ss_dssp             -EEEEESSTTSSHHHHHHHHHH--HCT--EE---EEECC--C--------------------------SCHHHHHHHHT-
T ss_pred             ceEEEECCCccchhHHHHHHHh--ccCCCeE---eccch--h-h-----------------------hhHHHHHHHHHh-
Confidence            6788999999999999999999  5555552   33322  0 0                       011112222211 


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc-cc-------cCCCCC-----------CcEEEEEcCCCcccccccCCcc-eeeec
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GK-------LCSFTQ-----------CGKIIITTSSTEDFVEPLGAAF-STLHV  413 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~-~l-------~~~~~~-----------gs~IliTTR~~~~va~~~~~~~-~~~~l  413 (1007)
                      + .++-+|++|.+..-+..+-+.+. ++       .-+.+.           -+-|=.|||... +..-..... -..++
T Consensus        99 l-~~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~-ls~pLrdRFgi~~~l  176 (233)
T PF05496_consen   99 L-KEGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGL-LSSPLRDRFGIVLRL  176 (233)
T ss_dssp             ---TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCC-TSHCCCTTSSEEEE-
T ss_pred             c-CCCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccc-cchhHHhhcceecch
Confidence            2 24557777888643333322222 11       111011           233455888876 665555553 44589


Q ss_pred             CCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhc
Q 001843          414 PGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLS  469 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~  469 (1007)
                      +..+.+|-.++..+.+..-..      +-.++.+.+|+++|.|-|=-..-+-...+
T Consensus       177 ~~Y~~~el~~Iv~r~a~~l~i------~i~~~~~~~Ia~rsrGtPRiAnrll~rvr  226 (233)
T PF05496_consen  177 EFYSEEELAKIVKRSARILNI------EIDEDAAEEIARRSRGTPRIANRLLRRVR  226 (233)
T ss_dssp             ---THHHHHHHHHHCCHCTT-------EE-HHHHHHHHHCTTTSHHHHHHHHHHHC
T ss_pred             hcCCHHHHHHHHHHHHHHhCC------CcCHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            999999999999887754332      34468899999999999965554444433

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.19  E-value=3e-05  Score=79.63  Aligned_cols=91  Identities=16%  Similarity=0.238  Sum_probs=64.8

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +.+-++|+|+++.-+.+.++.+. .+-.. ...+.+|++|++...+..........+++.+++.++..+.+.+.  +  .
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~-~~~~~~il~~~~~~~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~--g--i  169 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEP-PPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIRQ--G--I  169 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCC-CCCeEEEEEECChHhChHHHHhhcEEeeCCCCCHHHHHHHHHHc--C--C
Confidence            55668999999866666677777 44433 45566777776544355544444589999999999998888776  1  1


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCch
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPL  459 (1007)
                           +   .+.+..|++.++|.|.
T Consensus       170 -----~---~~~~~~i~~~~~g~~r  186 (188)
T TIGR00678       170 -----S---EEAAELLLALAGGSPG  186 (188)
T ss_pred             -----C---HHHHHHHHHHcCCCcc
Confidence                 1   3568899999999885

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.19  E-value=2.1e-05  Score=92.34  Aligned_cols=162  Identities=15%  Similarity=0.113  Sum_probs=94.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhc-------------------ccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYV-------------------KRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESL  334 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~-------------------~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~  334 (1007)
                      ..+.++|+.|+||||+|+.+++.-.-                   ...|...+++...  ...... -.+++        
T Consensus        39 ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaa--s~~gvd-~ir~i--------  107 (546)
T PRK14957         39 HAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAA--SRTGVE-ETKEI--------  107 (546)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeecc--cccCHH-HHHHH--------
Confidence            56789999999999999999873110                   0112233333322  111111 11222        


Q ss_pred             hhhccccCHHHHHHHHHH-HcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEE-EcCCCcccccccCCcceee
Q 001843          335 LKVEATLSAEELMWRITQ-ALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIII-TTSSTEDFVEPLGAAFSTL  411 (1007)
Q Consensus       335 ~~~~~~~~~~~l~~~l~~-~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~Ili-TTR~~~~va~~~~~~~~~~  411 (1007)
                                  .+.+.. -..+++-++|+|+++.-+...++.+. .+-+. ...+.+|+ ||.... +.....+.+..+
T Consensus       108 ------------i~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEep-p~~v~fIL~Ttd~~k-il~tI~SRc~~~  173 (546)
T PRK14957        108 ------------LDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEP-PEYVKFILATTDYHK-IPVTILSRCIQL  173 (546)
T ss_pred             ------------HHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcC-CCCceEEEEECChhh-hhhhHHHheeeE
Confidence                        222221 12356679999999866667777777 44333 44555554 554333 554445445899


Q ss_pred             ecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCc-hHHHHHHH
Q 001843          412 HVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLP-LRVVLLAG  466 (1007)
Q Consensus       412 ~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g~  466 (1007)
                      ++++++.++-.+.+.+.+...+.      ...+.....|++.++|-+ -|+..+-.
T Consensus       174 ~f~~Ls~~eI~~~L~~il~~egi------~~e~~Al~~Ia~~s~GdlR~alnlLek  223 (546)
T PRK14957        174 HLKHISQADIKDQLKIILAKENI------NSDEQSLEYIAYHAKGSLRDALSLLDQ  223 (546)
T ss_pred             EeCCCCHHHHHHHHHHHHHHcCC------CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            99999999988777765433211      122455677888998855 45555543

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.18  E-value=3.2e-05  Score=96.56  Aligned_cols=289  Identities=13%  Similarity=0.091  Sum_probs=163.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCC-CC---CCHHHHHHHHHHHHhhhhhhh------------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIM-SM---VEDRDVLADILKQIDESLLKV------------  337 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~-~~---~~~~~~l~~il~~l~~~~~~~------------  337 (1007)
                      .++.+.|..|||||+|+++|..  .+.+.+...+--.+... .+   ....+.+++++.++.......            
T Consensus        25 ~~~lv~G~sGIGKsalv~ev~~--~i~~~~~~~i~~~f~q~~~~ipl~~lvq~~r~l~~~ll~~~~~~~~~~~~~il~~~  102 (849)
T COG3899          25 EVVLVAGESGIGKSALVNEVHK--PITQQRGYFIKGKFDQFERNIPLSPLVQAFRDLMGQLLSESDTRILSWRARLLAAL  102 (849)
T ss_pred             EEEEEeecCCCcHHHHHHHHHH--HHhccceeeeHhhcccccCCCchHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHh
Confidence            7999999999999999999998  45444222111111100 11   133556677777663220000            


Q ss_pred             ------------------c--------cccCHHH-----HHHHHHHHc-CCCcEEEEEeCcCccCchhhhhhccccCC--
Q 001843          338 ------------------E--------ATLSAEE-----LMWRITQAL-DDSTFLIVMENAEHQKSQVWDSFLGKLCS--  383 (1007)
Q Consensus       338 ------------------~--------~~~~~~~-----l~~~l~~~L-~~kr~LlVlDdv~~~~~~~~~~l~~l~~~--  383 (1007)
                                        +        .....+.     ....+.... +.++.++|+||+.-.|....+-+.-+-..  
T Consensus       103 g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi~leDlhWaD~~SL~lL~~lm~~~~  182 (849)
T COG3899         103 GENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVIVLEDLHWADSASLKLLQLLMDRIA  182 (849)
T ss_pred             cccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEEEEecccccChhHHHHHHHHHHhcc
Confidence                              0        0111111     122233333 35699999999953333333333311111  


Q ss_pred             --CCCCcEEEEEcCCCc--ccccccCCcceeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCch
Q 001843          384 --FTQCGKIIITTSSTE--DFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       384 --~~~gs~IliTTR~~~--~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPL  459 (1007)
                        .-.-..|..+.....  ............+.|.||+..+...+..........       ...+....|+++.+|+|+
T Consensus       183 ~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~~~~-------~~~p~~~~i~~kt~GnPf  255 (849)
T COG3899         183 IGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLGCTKL-------LPAPLLELIFEKTKGNPF  255 (849)
T ss_pred             hhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhCCccc-------ccchHHHHHHHHhcCCCc
Confidence              001112333222222  012222233389999999999999999887754222       235678899999999999


Q ss_pred             HHHHHHHHhcCCCC-----ChHHHHHHHHHcc-------cchhhhhhhcCCccCchhhhhhhccCCCCcccchhHHHHHH
Q 001843          460 RVVLLAGLLSTKQP-----SYEEWSKVIERAN-------GDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLW  527 (1007)
Q Consensus       460 ai~~~g~~L~~~~~-----~~~~w~~~l~~l~-------i~~~l~~sy~~L~~~~k~cfl~la~fp~~~~i~~~~Li~~W  527 (1007)
                      -+.-+-..+.....     ....|..=...+.       +...+..-.+.||...++.+...|++-..  |+.+.|...|
T Consensus       256 Fi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~~~~~~vv~~l~~rl~kL~~~t~~Vl~~AA~iG~~--F~l~~La~l~  333 (849)
T COG3899         256 FIEEFLKALYEEGLLVFNFDTGAWQCSIASLGILATTDAVVEFLAARLQKLPGTTREVLKAAACIGNR--FDLDTLAALA  333 (849)
T ss_pred             cHHHHHHHHHhCCeeEecCCCcceeccHHhcCCchhhHHHHHHHHHHHhcCCHHHHHHHHHHHHhCcc--CCHHHHHHHH
Confidence            99998888876421     2444544334443       22347777899999999999999988655  4555555555


Q ss_pred             HhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEeecCCCCcc-e--E-EcCHHHHHHHH
Q 001843          528 CAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRWRLDGSPK-T--C-CMPGVLYDILR  585 (1007)
Q Consensus       528 iaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~~~~~g~~~-~--~-~mHdlv~d~~~  585 (1007)
                      -.            .....+...++.|....++-..+....+... .  | ..|+.+++.+-
T Consensus       334 ~~------------~~~~~a~~l~~al~e~lI~~~~~~yr~~~~~~~~~Y~F~H~~vqqaaY  383 (849)
T COG3899         334 ED------------SPALEAAALLDALQEGLILPLSETYRFGSNVDIATYKFLHDRVQQAAY  383 (849)
T ss_pred             hh------------chHHHHHHHHHHhHhhceeccccccccccccchhhHHhhHHHHHHHHh
Confidence            21            3445566666666666555432222222111 1  1 46777777764

>PRK04195 replication factor C large subunit; Provisional

Probab=98.18  E-value=7.3e-05  Score=88.38  Aligned_cols=157  Identities=17%  Similarity=0.143  Sum_probs=90.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +.+.|+|++|+||||+|+.++++  +  .|+. +-++++  .. .....+..++......                 ...
T Consensus        40 ~~lLL~GppG~GKTtla~ala~e--l--~~~~-ielnas--d~-r~~~~i~~~i~~~~~~-----------------~sl   94 (482)
T PRK04195         40 KALLLYGPPGVGKTSLAHALAND--Y--GWEV-IELNAS--DQ-RTADVIERVAGEAATS-----------------GSL   94 (482)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--c--CCCE-EEEccc--cc-ccHHHHHHHHHHhhcc-----------------Ccc
Confidence            78999999999999999999994  3  2332 333444  22 2222333333322211                 001


Q ss_pred             cCCCcEEEEEeCcCccCc----hhhhhhccccCCCCCCcEEEEEcCCCccccc-ccCCcceeeecCCCCHHHHHHHHHhh
Q 001843          354 LDDSTFLIVMENAEHQKS----QVWDSFLGKLCSFTQCGKIIITTSSTEDFVE-PLGAAFSTLHVPGLGKNESWELFLKK  428 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~----~~~~~l~~l~~~~~~gs~IliTTR~~~~va~-~~~~~~~~~~l~~L~~~ea~~Lf~~~  428 (1007)
                      ...++-+||+|+++.-..    ..+..+..+... . +..||+|+.+...... .....+..+++.+++.++....+.+.
T Consensus        95 ~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~-~-~~~iIli~n~~~~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i  172 (482)
T PRK04195         95 FGARRKLILLDEVDGIHGNEDRGGARAILELIKK-A-KQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRI  172 (482)
T ss_pred             cCCCCeEEEEecCcccccccchhHHHHHHHHHHc-C-CCCEEEeccCccccchhhHhccceEEEecCCCHHHHHHHHHHH
Confidence            113677999999984322    334555522222 2 3346666644331322 23333378999999999999888877


Q ss_pred             hccccccccCCChHHHHHHHHHHHHcCCCchHHHH
Q 001843          429 ARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVL  463 (1007)
Q Consensus       429 a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~  463 (1007)
                      +.....   ..+   .+....|++.++|-.-.+..
T Consensus       173 ~~~egi---~i~---~eaL~~Ia~~s~GDlR~ain  201 (482)
T PRK04195        173 CRKEGI---ECD---DEALKEIAERSGGDLRSAIN  201 (482)
T ss_pred             HHHcCC---CCC---HHHHHHHHHHcCCCHHHHHH
Confidence            654332   122   35678888999886655443

>PLN03025 replication factor C subunit; Provisional

Probab=98.17  E-value=1.7e-05  Score=88.64  Aligned_cols=159  Identities=14%  Similarity=0.207  Sum_probs=90.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCc-eEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTK-RAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      .-+-++|++|+||||+|+.+++.- ....|.. ++-+..+  .... .+.+++++..+...  ..              .
T Consensus        35 ~~lll~Gp~G~GKTtla~~la~~l-~~~~~~~~~~eln~s--d~~~-~~~vr~~i~~~~~~--~~--------------~   94 (319)
T PLN03025         35 PNLILSGPPGTGKTTSILALAHEL-LGPNYKEAVLELNAS--DDRG-IDVVRNKIKMFAQK--KV--------------T   94 (319)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHH-hcccCccceeeeccc--cccc-HHHHHHHHHHHHhc--cc--------------c
Confidence            446799999999999999999831 1222321 1212222  1111 12233333222111  00              0


Q ss_pred             HcCCCcEEEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccc
Q 001843          353 ALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIA  432 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~  432 (1007)
                      .-.++.-++|+|+++.-.....+.+..........+++++++.....+.....+.+..++++++++++....+...+...
T Consensus        95 ~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~~e  174 (319)
T PLN03025         95 LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAE  174 (319)
T ss_pred             CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhhcccCCCCCHHHHHHHHHHHHHHc
Confidence            00234669999999855555555555222222455677776655432444444444789999999999998888776543


Q ss_pred             cccccCCChHHHHHHHHHHHHcCCCc
Q 001843          433 EDVLQSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       433 ~~~~~~~~~~~~~~~~~I~~~c~GlP  458 (1007)
                      ..   ..+   .+....|++.++|-.
T Consensus       175 gi---~i~---~~~l~~i~~~~~gDl  194 (319)
T PLN03025        175 KV---PYV---PEGLEAIIFTADGDM  194 (319)
T ss_pred             CC---CCC---HHHHHHHHHHcCCCH
Confidence            32   111   346778888888765

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.17  E-value=2.6e-05  Score=87.51  Aligned_cols=160  Identities=14%  Similarity=0.178  Sum_probs=89.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.++|.+|+||||+|+.+++.. ....+.. .++.+....... .....+.+.++...     .            ..
T Consensus        39 ~~~ll~G~~G~GKt~~~~~l~~~l-~~~~~~~-~~i~~~~~~~~~-~~~~~~~i~~~~~~-----~------------~~   98 (319)
T PRK00440         39 PHLLFAGPPGTGKTTAALALAREL-YGEDWRE-NFLELNASDERG-IDVIRNKIKEFART-----A------------PV   98 (319)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH-cCCcccc-ceEEeccccccc-hHHHHHHHHHHHhc-----C------------CC
Confidence            457999999999999999999842 1122221 233332001111 11122222221111     0            00


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIA  432 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~  432 (1007)
                      ....+-+||+|+++.-....+..+. .+... ...+++|+++.....+..........++++++++++....+.+.+...
T Consensus        99 ~~~~~~vviiDe~~~l~~~~~~~L~~~le~~-~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~  177 (319)
T PRK00440         99 GGAPFKIIFLDEADNLTSDAQQALRRTMEMY-SQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENE  177 (319)
T ss_pred             CCCCceEEEEeCcccCCHHHHHHHHHHHhcC-CCCCeEEEEeCCccccchhHHHHhheeeeCCCCHHHHHHHHHHHHHHc
Confidence            0133568999998754444555555 33332 445677776654332433333333678999999999988888776543


Q ss_pred             cccccCCChHHHHHHHHHHHHcCCCchH
Q 001843          433 EDVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       433 ~~~~~~~~~~~~~~~~~I~~~c~GlPLa  460 (1007)
                      ..   .   -..+....+++.++|.+--
T Consensus       178 ~~---~---i~~~al~~l~~~~~gd~r~  199 (319)
T PRK00440        178 GI---E---ITDDALEAIYYVSEGDMRK  199 (319)
T ss_pred             CC---C---CCHHHHHHHHHHcCCCHHH
Confidence            22   1   1245677888899887754

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=98.16  E-value=1.5e-05  Score=77.70  Aligned_cols=106  Identities=17%  Similarity=0.123  Sum_probs=57.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +.+.|+|.+|+||||+|+++++.  ....-..++++...  ...........+...               .........
T Consensus        20 ~~v~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~~--~~~~~~~~~~~~~~~---------------~~~~~~~~~   80 (151)
T cd00009          20 KNLLLYGPPGTGKTTLARAIANE--LFRPGAPFLYLNAS--DLLEGLVVAELFGHF---------------LVRLLFELA   80 (151)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--hhcCCCCeEEEehh--hhhhhhHHHHHhhhh---------------hHhHHHHhh
Confidence            78899999999999999999994  32223446677655  322211111100000               001111222


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc-cccCCC-----CCCcEEEEEcCCCc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GKLCSF-----TQCGKIIITTSSTE  398 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~-----~~gs~IliTTR~~~  398 (1007)
                      ...++.+||+||++.........+. .+....     ..+..||+||....
T Consensus        81 ~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          81 EKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             ccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence            3456789999999832122222222 111110     25678888888654

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.15  E-value=4e-06  Score=85.74  Aligned_cols=23  Identities=43%  Similarity=0.742  Sum_probs=18.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +++.|+|.+|+|||+|.++++..
T Consensus        25 ~~~ll~G~~G~GKT~ll~~~~~~   47 (185)
T PF13191_consen   25 RNLLLTGESGSGKTSLLRALLDR   47 (185)
T ss_dssp             --EEE-B-TTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            89999999999999999999984

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=98.15  E-value=9.8e-06  Score=98.61  Aligned_cols=153  Identities=18%  Similarity=0.256  Sum_probs=83.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.++|++|+||||+|+.+++  ....+|     +.++  .......-.+++                    .....+.
T Consensus        53 ~slLL~GPpGtGKTTLA~aIA~--~~~~~f-----~~ln--a~~~~i~dir~~--------------------i~~a~~~  103 (725)
T PRK13341         53 GSLILYGPPGVGKTTLARIIAN--HTRAHF-----SSLN--AVLAGVKDLRAE--------------------VDRAKER  103 (725)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HhcCcc-----eeeh--hhhhhhHHHHHH--------------------HHHHHHH
Confidence            5678999999999999999998  454444     2222  100000001111                    1111111


Q ss_pred             c--CCCcEEEEEeCcCccCchhhhhhccccCCCCCCcEEEE--EcCCCc-ccccccCCcceeeecCCCCHHHHHHHHHhh
Q 001843          354 L--DDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIII--TTSSTE-DFVEPLGAAFSTLHVPGLGKNESWELFLKK  428 (1007)
Q Consensus       354 L--~~kr~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~Ili--TTR~~~-~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~  428 (1007)
                      +  .+++.+|||||++.-+...++.+....   ..|+.++|  ||.+.. .+.....+....+.+++|+.++...++.+.
T Consensus       104 l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~l---E~g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~  180 (725)
T PRK13341        104 LERHGKRTILFIDEVHRFNKAQQDALLPWV---ENGTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRA  180 (725)
T ss_pred             hhhcCCceEEEEeChhhCCHHHHHHHHHHh---cCceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHHHHHHHHH
Confidence            1  246779999999854555566555322   33555665  344432 122222222378999999999999998876


Q ss_pred             hccccccc-cCCChHHHHHHHHHHHHcCCCc
Q 001843          429 ARIAEDVL-QSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       429 a~~~~~~~-~~~~~~~~~~~~~I~~~c~GlP  458 (1007)
                      +....... .....-.++....|++.+.|..
T Consensus       181 l~~~~~~~g~~~v~I~deaL~~La~~s~GD~  211 (725)
T PRK13341        181 LQDKERGYGDRKVDLEPEAEKHLVDVANGDA  211 (725)
T ss_pred             HHHHHhhcCCcccCCCHHHHHHHHHhCCCCH
Confidence            54110000 0001112345677777777753

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.15  E-value=2.7e-05  Score=90.95  Aligned_cols=98  Identities=10%  Similarity=0.076  Sum_probs=67.8

Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEE-EcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccc
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIII-TTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIA  432 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~Ili-TTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~  432 (1007)
                      .+++-++|+|+++.-+...|+.+. .+... ...+.+|+ ||+... +.......+..+++++++.++..+.+.+.+...
T Consensus       126 ~~~~KVvIIDEa~~Ls~~a~naLLk~LEep-p~~~vfI~aTte~~k-I~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~e  203 (507)
T PRK06645        126 QGKHKIFIIDEVHMLSKGAFNALLKTLEEP-PPHIIFIFATTEVQK-IPATIISRCQRYDLRRLSFEEIFKLLEYITKQE  203 (507)
T ss_pred             cCCcEEEEEEChhhcCHHHHHHHHHHHhhc-CCCEEEEEEeCChHH-hhHHHHhcceEEEccCCCHHHHHHHHHHHHHHc
Confidence            456779999999966677788887 55444 45556554 555444 665555555789999999999999998887543


Q ss_pred             cccccCCChHHHHHHHHHHHHcCCCchH
Q 001843          433 EDVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       433 ~~~~~~~~~~~~~~~~~I~~~c~GlPLa  460 (1007)
                      ..      .-..+....|++.++|.+--
T Consensus       204 gi------~ie~eAL~~Ia~~s~GslR~  225 (507)
T PRK06645        204 NL------KTDIEALRIIAYKSEGSARD  225 (507)
T ss_pred             CC------CCCHHHHHHHHHHcCCCHHH
Confidence            32      11234567788899887633

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.15  E-value=3.3e-05  Score=89.88  Aligned_cols=120  Identities=8%  Similarity=0.051  Sum_probs=72.1

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-.....+.+. .+-+. .....+|++|.+...+.......+..+++.+++.++....+.+.+.....
T Consensus       116 ~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p-~~~vv~Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi  194 (472)
T PRK14962        116 GKYKVYIIDEVHMLTKEAFNALLKTLEEP-PSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGI  194 (472)
T ss_pred             CCeEEEEEEChHHhHHHHHHHHHHHHHhC-CCcEEEEEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCC
Confidence            46679999999854455556666 44332 33344444444433265555555589999999999988888877643221


Q ss_pred             cccCCChHHHHHHHHHHHHcC-CCchHHHHHHHHhcCC--CCChHHHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICD-GLPLRVVLLAGLLSTK--QPSYEEWSKVI  482 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~-GlPLai~~~g~~L~~~--~~~~~~w~~~l  482 (1007)
                            .-..+....|++.++ +++.|+..+-.+....  .-+.+....++
T Consensus       195 ------~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~~~~It~e~V~~~l  239 (472)
T PRK14962        195 ------EIDREALSFIAKRASGGLRDALTMLEQVWKFSEGKITLETVHEAL  239 (472)
T ss_pred             ------CCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence                  112355677888775 5577777776544321  12345554444

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.14  E-value=3.7e-06  Score=89.21  Aligned_cols=93  Identities=16%  Similarity=0.113  Sum_probs=61.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhh---hhccccCHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLL---KVEATLSAEELMWRI  350 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~---~~~~~~~~~~l~~~l  350 (1007)
                      ..++|+|.+|+|||||++.+|++.... +|+.++|+++...+..+..++++.+...+-....   ......-........
T Consensus        17 qr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a   95 (249)
T cd01128          17 QRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKA   95 (249)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHH
Confidence            789999999999999999999964443 8999999997733338999999998333222100   000000111112222


Q ss_pred             HHH-cCCCcEEEEEeCcC
Q 001843          351 TQA-LDDSTFLIVMENAE  367 (1007)
Q Consensus       351 ~~~-L~~kr~LlVlDdv~  367 (1007)
                      ..+ -.+++.++++|++.
T Consensus        96 ~~~~~~G~~vll~iDei~  113 (249)
T cd01128          96 KRLVEHGKDVVILLDSIT  113 (249)
T ss_pred             HHHHHCCCCEEEEEECHH
Confidence            222 25899999999996

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.13  E-value=4.1e-05  Score=86.94  Aligned_cols=97  Identities=11%  Similarity=0.141  Sum_probs=66.8

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+....+.+. .+-.. ..+..+|++|.+...+.....+.+..+.+++++.++..+.+.+....   
T Consensus       116 ~~~kViiIDead~m~~~aanaLLk~LEep-~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~~---  191 (394)
T PRK07940        116 GRWRIVVIEDADRLTERAANALLKAVEEP-PPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDGV---  191 (394)
T ss_pred             CCcEEEEEechhhcCHHHHHHHHHHhhcC-CCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcCC---
Confidence            45568888999866666666666 43333 45666777666655466665555689999999999999888753211   


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                           +   .+.+..+++.++|.|.....+
T Consensus       192 -----~---~~~a~~la~~s~G~~~~A~~l  213 (394)
T PRK07940        192 -----D---PETARRAARASQGHIGRARRL  213 (394)
T ss_pred             -----C---HHHHHHHHHHcCCCHHHHHHH
Confidence                 1   245778899999999755444

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.11  E-value=2.8e-05  Score=89.02  Aligned_cols=174  Identities=14%  Similarity=0.063  Sum_probs=94.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhh-hhhhhccccCHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDE-SLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~-~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      ..+.++|+.|+||||+|+.+++.  +...-... ...+.  ....-..+...+...+.. +........+..++.+.+..
T Consensus        41 ha~Lf~GP~GtGKTTlAriLAk~--Lnce~~~~-~~pCg--~C~sC~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~  115 (484)
T PRK14956         41 HAYIFFGPRGVGKTTIARILAKR--LNCENPIG-NEPCN--ECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKF  115 (484)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh--cCcccccC-ccccC--CCcHHHHHHccCCccceeechhhcccHHHHHHHHHHHHh
Confidence            46789999999999999999983  32210000 00000  111111111100000000 00000001122222222222


Q ss_pred             H-cCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhc
Q 001843          353 A-LDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       353 ~-L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~  430 (1007)
                      . ..++.-++|+|+++.-+.+.++.+. .+-.. .....+|.+|.....+.....+.+..|.+.+++.++..+.+.+.+.
T Consensus       116 ~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEP-p~~viFILaTte~~kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~  194 (484)
T PRK14956        116 APMGGKYKVYIIDEVHMLTDQSFNALLKTLEEP-PAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVLQDYSEKLCK  194 (484)
T ss_pred             hhhcCCCEEEEEechhhcCHHHHHHHHHHhhcC-CCceEEEeecCChhhccHHHHhhhheeeecCCCHHHHHHHHHHHHH
Confidence            1 2355669999999877777888887 44332 3344444444443337666666658899999999998888887764


Q ss_pred             cccccccCCChHHHHHHHHHHHHcCCCch
Q 001843          431 IAEDVLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       431 ~~~~~~~~~~~~~~~~~~~I~~~c~GlPL  459 (1007)
                      ..+.      .-..+....|++.++|.+-
T Consensus       195 ~Egi------~~e~eAL~~Ia~~S~Gd~R  217 (484)
T PRK14956        195 IENV------QYDQEGLFWIAKKGDGSVR  217 (484)
T ss_pred             HcCC------CCCHHHHHHHHHHcCChHH
Confidence            3221      1124567889999999883

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.08  E-value=3.5e-05  Score=91.43  Aligned_cols=99  Identities=5%  Similarity=-0.015  Sum_probs=64.6

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|||+++..+....+.+. .+-.. ...+++|++|.+...+.....+.+..+.+++++.++....+.+.+.....
T Consensus       118 gk~KVIIIDEad~Ls~~A~NALLKtLEEP-p~~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi  196 (709)
T PRK08691        118 GKYKVYIIDEVHMLSKSAFNAMLKTLEEP-PEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKI  196 (709)
T ss_pred             CCcEEEEEECccccCHHHHHHHHHHHHhC-CCCcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCC
Confidence            56669999999855555566666 44322 34556666665544355444444478889999999998888876654322


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai  461 (1007)
                            .-.......|++.++|.+--+
T Consensus       197 ------~id~eAL~~Ia~~A~GslRdA  217 (709)
T PRK08691        197 ------AYEPPALQLLGRAAAGSMRDA  217 (709)
T ss_pred             ------CcCHHHHHHHHHHhCCCHHHH
Confidence                  122456788999999888443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.07  E-value=9.7e-06  Score=89.54  Aligned_cols=87  Identities=16%  Similarity=0.157  Sum_probs=59.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCC--CHHHHHHHHHHHHhhhhhhhcccc--------CH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMV--EDRDVLADILKQIDESLLKVEATL--------SA  343 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~--~~~~~l~~il~~l~~~~~~~~~~~--------~~  343 (1007)
                      +-..|+|++|+||||||++||++.... +|+.++||.+.  ...  +..++++.+...+-..  ..+...        ..
T Consensus       170 QR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLI--gER~~EVtdiqrsIlg~vv~s--t~d~~~~~~~~~a~~~  244 (416)
T PRK09376        170 QRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLI--DERPEEVTDMQRSVKGEVVAS--TFDEPAERHVQVAEMV  244 (416)
T ss_pred             ceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEe--CCchhHHHHHHHHhcCcEEEE--CCCCCHHHHHHHHHHH
Confidence            678999999999999999999965444 89999999988  665  7778888876433221  111111        11


Q ss_pred             HHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          344 EELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       344 ~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                      -...+.++  -.+++++|++|++.
T Consensus       245 ie~Ae~~~--e~G~dVlL~iDsIt  266 (416)
T PRK09376        245 IEKAKRLV--EHGKDVVILLDSIT  266 (416)
T ss_pred             HHHHHHHH--HcCCCEEEEEEChH
Confidence            11112222  36899999999996

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.07  E-value=3.9e-05  Score=91.50  Aligned_cols=102  Identities=7%  Similarity=0.056  Sum_probs=68.2

Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      .+++-++|||+++.-+....+.+. .+-.. ....++|++|.+...+.....+.+..|.+++|+.++..+.+.+.+....
T Consensus       117 ~g~~KV~IIDEah~Ls~~a~NALLKtLEEP-p~~v~FIL~Tt~~~kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~  195 (647)
T PRK07994        117 RGRFKVYLIDEVHMLSRHSFNALLKTLEEP-PEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRQQLEHILQAEQ  195 (647)
T ss_pred             cCCCEEEEEechHhCCHHHHHHHHHHHHcC-CCCeEEEEecCCccccchHHHhhheEeeCCCCCHHHHHHHHHHHHHHcC
Confidence            456679999999876777777776 33332 3455565555554436655555568999999999999988887653221


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCchHHHH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPLRVVL  463 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPLai~~  463 (1007)
                      .      .........|++.++|.+--+..
T Consensus       196 i------~~e~~aL~~Ia~~s~Gs~R~Al~  219 (647)
T PRK07994        196 I------PFEPRALQLLARAADGSMRDALS  219 (647)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHHHH
Confidence            1      11245567899999997754333

>PLN03150 hypothetical protein; Provisional

Probab=98.06  E-value=5.3e-06  Score=100.92  Aligned_cols=92  Identities=24%  Similarity=0.311  Sum_probs=67.8

Q ss_pred             cceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCc-ccCcccc
Q 001843          636 RLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFID-SLPDSTP  714 (1007)
Q Consensus       636 ~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~-~LP~~i~  714 (1007)
                      .++.|.+.++.+.+        .++..+  .++++|+.|+|++|.+.+ .+|..++.+.+|++|+|++|.+. .+|..++
T Consensus       419 ~v~~L~L~~n~L~g--------~ip~~i--~~L~~L~~L~Ls~N~l~g-~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~  487 (623)
T PLN03150        419 FIDGLGLDNQGLRG--------FIPNDI--SKLRHLQSINLSGNSIRG-NIPPSLGSITSLEVLDLSYNSFNGSIPESLG  487 (623)
T ss_pred             EEEEEECCCCCccc--------cCCHHH--hCCCCCCEEECCCCcccC-cCChHHhCCCCCCEEECCCCCCCCCCchHHh
Confidence            46677777776642        334455  778888888888888765 67777888888888888888877 6787888


Q ss_pred             cCCCCCEEeecCCccc-cccccccc
Q 001843          715 ILFCLATLDVSHTKVQ-RLPYAFWP  738 (1007)
Q Consensus       715 ~L~~L~~L~L~~~~l~-~lP~~i~~  738 (1007)
                      +|++|++|+|++|.+. .+|..+..
T Consensus       488 ~L~~L~~L~Ls~N~l~g~iP~~l~~  512 (623)
T PLN03150        488 QLTSLRILNLNGNSLSGRVPAALGG  512 (623)
T ss_pred             cCCCCCEEECcCCcccccCChHHhh
Confidence            8888888888888665 66766554

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.03  E-value=6e-05  Score=87.30  Aligned_cols=158  Identities=16%  Similarity=0.139  Sum_probs=95.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhh------------------cc-cCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVY------------------VK-RHFTKRAWVHIPIMSMVEDRDVLADILKQIDESL  334 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~------------------~~-~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~  334 (1007)
                      ..+-++|+.|+||||+|+.++.--.                  +. ..+..++.+..+  ...... -.++++..+... 
T Consensus        36 ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaa--s~~~vd-dIR~Iie~~~~~-  111 (491)
T PRK14964         36 QSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAA--SNTSVD-DIKVILENSCYL-  111 (491)
T ss_pred             ceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecc--cCCCHH-HHHHHHHHHHhc-
Confidence            5788999999999999999986210                  00 112233444433  222221 122232222110 


Q ss_pred             hhhccccCHHHHHHHHHHHcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeec
Q 001843          335 LKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHV  413 (1007)
Q Consensus       335 ~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l  413 (1007)
                                        -+.+++-++|+|+++.-+....+.+. .+-+. ...+++|++|.....+.......+..+++
T Consensus       112 ------------------P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEeP-p~~v~fIlatte~~Kl~~tI~SRc~~~~f  172 (491)
T PRK14964        112 ------------------PISSKFKVYIIDEVHMLSNSAFNALLKTLEEP-APHVKFILATTEVKKIPVTIISRCQRFDL  172 (491)
T ss_pred             ------------------cccCCceEEEEeChHhCCHHHHHHHHHHHhCC-CCCeEEEEEeCChHHHHHHHHHhheeeec
Confidence                              01245668999999865666677776 44333 45566666554433366555555589999


Q ss_pred             CCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchH
Q 001843          414 PGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLa  460 (1007)
                      ++++.++..+.+.+.+.....      .-..+....|++.++|.+-.
T Consensus       173 ~~l~~~el~~~L~~ia~~Egi------~i~~eAL~lIa~~s~GslR~  213 (491)
T PRK14964        173 QKIPTDKLVEHLVDIAKKENI------EHDEESLKLIAENSSGSMRN  213 (491)
T ss_pred             ccccHHHHHHHHHHHHHHcCC------CCCHHHHHHHHHHcCCCHHH
Confidence            999999999988887654332      12245667889999887753

>PRK08727 hypothetical protein; Validated

Probab=98.01  E-value=5.4e-05  Score=80.34  Aligned_cols=149  Identities=15%  Similarity=0.107  Sum_probs=88.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.|+|..|+|||+|++++++.  ..+....++|+++.  +      ....+.                    +.+ +.
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~--~~~~~~~~~y~~~~--~------~~~~~~--------------------~~~-~~   90 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAA--AEQAGRSSAYLPLQ--A------AAGRLR--------------------DAL-EA   90 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEeHH--H------hhhhHH--------------------HHH-HH
Confidence            56999999999999999999984  44444456677654  1      000000                    011 11


Q ss_pred             cCCCcEEEEEeCcCccC-chhhhhhc-cccCC-CCCCcEEEEEcCCCcc--------cccccCCcceeeecCCCCHHHHH
Q 001843          354 LDDSTFLIVMENAEHQK-SQVWDSFL-GKLCS-FTQCGKIIITTSSTED--------FVEPLGAAFSTLHVPGLGKNESW  422 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~-~~~~~~l~-~l~~~-~~~gs~IliTTR~~~~--------va~~~~~~~~~~~l~~L~~~ea~  422 (1007)
                      + .+.-+||+||+.... ...|.... .+.+. ...|..||+|++....        +...+... ..+++++++.++-.
T Consensus        91 l-~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~-~~~~l~~~~~e~~~  168 (233)
T PRK08727         91 L-EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRSRLAQC-IRIGLPVLDDVARA  168 (233)
T ss_pred             H-hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHHHHhcC-ceEEecCCCHHHHH
Confidence            1 233489999997321 22343332 22221 1346679999986431        11122222 68999999999999


Q ss_pred             HHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHH
Q 001843          423 ELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       423 ~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai  461 (1007)
                      +++.+++....-      .-.++...-|++.+.|-.-.+
T Consensus       169 ~iL~~~a~~~~l------~l~~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        169 AVLRERAQRRGL------ALDEAAIDWLLTHGERELAGL  201 (233)
T ss_pred             HHHHHHHHHcCC------CCCHHHHHHHHHhCCCCHHHH
Confidence            999987754321      122456677888887655443

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=98.01  E-value=2.4e-07  Score=95.72  Aligned_cols=161  Identities=19%  Similarity=0.166  Sum_probs=97.4

Q ss_pred             hhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCC--CcccccCCCCCcEEEecccC---CCCCc
Q 001843          784 YFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYL--PLLEMAEHYKLQKLYLSGHL---PPNSV  858 (1007)
Q Consensus       784 ~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~--~~~~l~~~~~L~~L~L~g~~---~~lp~  858 (1007)
                      -+..+.+|+.|.|.+++ -.+.+.    ..+.+-.+|+.|+|+.+.....  .---+.+|..|.+|+|+-|.   ..+..
T Consensus       205 iLs~C~kLk~lSlEg~~-LdD~I~----~~iAkN~~L~~lnlsm~sG~t~n~~~ll~~scs~L~~LNlsWc~l~~~~Vtv  279 (419)
T KOG2120|consen  205 ILSQCSKLKNLSLEGLR-LDDPIV----NTIAKNSNLVRLNLSMCSGFTENALQLLLSSCSRLDELNLSWCFLFTEKVTV  279 (419)
T ss_pred             HHHHHHhhhhccccccc-cCcHHH----HHHhccccceeeccccccccchhHHHHHHHhhhhHhhcCchHhhccchhhhH
Confidence            35667778888888776 333333    7777788888888887432211  11234567788888887654   22222


Q ss_pred             CccCCCCCCceEEEEEeee--cCCCCcCcc-ccCCCCcEEEeecCCcCCCceeecCCCCCCCcEEEeccCCCCcc-eEEc
Q 001843          859 IGDRSFPPNVVTLTLSQLR--LEYDPMPIL-GRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQ-WRIK  934 (1007)
Q Consensus       859 ~~i~~~l~~L~~L~L~~~~--l~~~~~~~l-~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~~~L~~-l~~~  934 (1007)
                       .+.+.-++|+.|+|++|.  +....+..+ ..+|+|..|+|+++.............|+.|++|.++.|..+.- --+.
T Consensus       280 -~V~hise~l~~LNlsG~rrnl~~sh~~tL~~rcp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~lSlsRCY~i~p~~~~~  358 (419)
T KOG2120|consen  280 -AVAHISETLTQLNLSGYRRNLQKSHLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFKFNYLQHLSLSRCYDIIPETLLE  358 (419)
T ss_pred             -HHhhhchhhhhhhhhhhHhhhhhhHHHHHHHhCCceeeeccccccccCchHHHHHHhcchheeeehhhhcCCChHHeee
Confidence             233334678888888873  222333333 35788888888765544333333445677888888887765432 2234


Q ss_pred             CCCCccccEeEeeccC
Q 001843          935 EGAMPCLRQLEIRSCG  950 (1007)
Q Consensus       935 ~~~~p~L~~L~l~~c~  950 (1007)
                      .+.+|+|.+|++.+|-
T Consensus       359 l~s~psl~yLdv~g~v  374 (419)
T KOG2120|consen  359 LNSKPSLVYLDVFGCV  374 (419)
T ss_pred             eccCcceEEEEecccc
Confidence            4567777777777764

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.98  E-value=9e-05  Score=88.30  Aligned_cols=100  Identities=5%  Similarity=0.044  Sum_probs=65.9

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      ++.-++|||+|+.-+...++.+. .+-.. ....++|++|.+...+.....+.+..+++++++.++..+.+.+.+...+.
T Consensus       123 g~~KV~IIDEvh~Ls~~a~NaLLKtLEEP-P~~~~fIL~Ttd~~kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi  201 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTAFNAMLKTLEEP-PEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENV  201 (618)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHHhcccC-CCCeEEEEEECCchhhhHHHHHhceeeecCCCCHHHHHHHHHHHHHHcCC
Confidence            34458999999977777787777 44333 34556665554433255444444589999999999998888876644322


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVV  462 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~  462 (1007)
                            .-..+....|++.++|.+--+.
T Consensus       202 ------~ie~~AL~~La~~s~GslR~al  223 (618)
T PRK14951        202 ------PAEPQALRLLARAARGSMRDAL  223 (618)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHHHH
Confidence                  1124567788889988774443

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.98  E-value=6.7e-06  Score=61.75  Aligned_cols=39  Identities=31%  Similarity=0.367  Sum_probs=22.7

Q ss_pred             cCcEEecccCCCcccCcccccCCCCCEEeecCCcccccc
Q 001843          695 FLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLP  733 (1007)
Q Consensus       695 ~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP  733 (1007)
                      +|++|+|++|.|+.+|..+++|++|++|++++|.++.+|
T Consensus         2 ~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i~~i~   40 (44)
T PF12799_consen    2 NLEELDLSNNQITDLPPELSNLPNLETLNLSNNPISDIS   40 (44)
T ss_dssp             T-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCCSBEG
T ss_pred             cceEEEccCCCCcccCchHhCCCCCCEEEecCCCCCCCc
Confidence            456666666666666655666666666666666555544

...

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.98  E-value=0.00017  Score=81.25  Aligned_cols=99  Identities=8%  Similarity=0.124  Sum_probs=69.8

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++..+....+.+. .+-.. ..++.+|++|.+...+.....+.+..+.+.+++.++..+++.......  
T Consensus       140 ~~~kVviIDead~m~~~aanaLLK~LEep-p~~~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~~--  216 (365)
T PRK07471        140 GGWRVVIVDTADEMNANAANALLKVLEEP-PARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPDL--  216 (365)
T ss_pred             CCCEEEEEechHhcCHHHHHHHHHHHhcC-CCCeEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhcccC--
Confidence            45679999999877777777777 43333 446677777777653655555555899999999999999998764221  


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLLA  465 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g  465 (1007)
                           .   ......+++.++|.|+....+.
T Consensus       217 -----~---~~~~~~l~~~s~Gsp~~Al~ll  239 (365)
T PRK07471        217 -----P---DDPRAALAALAEGSVGRALRLA  239 (365)
T ss_pred             -----C---HHHHHHHHHHcCCCHHHHHHHh
Confidence                 1   1122678999999998665543

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.97  E-value=0.00011  Score=82.43  Aligned_cols=175  Identities=15%  Similarity=0.211  Sum_probs=98.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC----CCceEEEEecCCCCCCHHHHHHHHHHHHhhhh--------hhh---c
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH----FTKRAWVHIPIMSMVEDRDVLADILKQIDESL--------LKV---E  338 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~--------~~~---~  338 (1007)
                      ..+.|+|..|+||||+|..+++.  +-.+    +...   ...  ..+..-...+.+...-..+.        .+.   .
T Consensus        46 ha~L~~G~~G~GKttlA~~lA~~--Llc~~~~~~~~~---~~~--~~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~  118 (351)
T PRK09112         46 HALLFEGPEGIGKATLAFHLANH--ILSHPDPAEAPE---TLA--DPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFK  118 (351)
T ss_pred             eeEeeECCCCCCHHHHHHHHHHH--HcCCCccccCcc---ccC--CCCCCCHHHHHHHcCCCCCEEEeeccccccccccc
Confidence            46889999999999999999883  3221    1111   000  11111112222222211000        000   0


Q ss_pred             cccCHHHHHHHHHHHc-----CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeee
Q 001843          339 ATLSAEELMWRITQAL-----DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLH  412 (1007)
Q Consensus       339 ~~~~~~~l~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~  412 (1007)
                      ..-..++ ++.+.+++     .+++-++|+|+++.-+....+.+. .+-.. .....+|++|.....+.....+.+..++
T Consensus       119 ~~I~vd~-iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEp-p~~~~fiLit~~~~~llptIrSRc~~i~  196 (351)
T PRK09112        119 TAITVDE-IRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEP-PARALFILISHSSGRLLPTIRSRCQPIS  196 (351)
T ss_pred             ccCCHHH-HHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcC-CCCceEEEEECChhhccHHHHhhccEEE
Confidence            1111232 22344443     346669999999876777777776 44333 3344544444444336555555568999


Q ss_pred             cCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHH
Q 001843          413 VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLA  465 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g  465 (1007)
                      +.+++.++..+++.......       . -..+.+..|++.++|.|.....+.
T Consensus       197 l~pl~~~~~~~~L~~~~~~~-------~-~~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        197 LKPLDDDELKKALSHLGSSQ-------G-SDGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             ecCCCHHHHHHHHHHhhccc-------C-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999999999998743211       1 113456789999999998655443

>KOG4341 consensus F-box protein containing LRR [General function prediction only]

Probab=97.97  E-value=2.7e-07  Score=99.80  Aligned_cols=80  Identities=21%  Similarity=0.157  Sum_probs=51.5

Q ss_pred             CcccEEEecCCCCCCc-CCCccccCCCcCcEEecccCC-Ccc--cCcccccCCCCCEEeecCC-ccc-----cccccccc
Q 001843          669 GMLKVLDLEGVYKPML-TNNNALGRLPFLEYLGLRSTF-IDS--LPDSTPILFCLATLDVSHT-KVQ-----RLPYAFWP  738 (1007)
Q Consensus       669 ~~Lr~L~Ls~~~l~~~-~lp~~i~~L~~Lr~L~L~~n~-i~~--LP~~i~~L~~L~~L~L~~~-~l~-----~lP~~i~~  738 (1007)
                      ..||.|.|.|+.-.+. .+-..-.+++++..|.+.++. |++  +-.--..+++|++|++..| .++     .+..+..+
T Consensus       138 g~lk~LSlrG~r~v~~sslrt~~~~CpnIehL~l~gc~~iTd~s~~sla~~C~~l~~l~L~~c~~iT~~~Lk~la~gC~k  217 (483)
T KOG4341|consen  138 GFLKELSLRGCRAVGDSSLRTFASNCPNIEHLALYGCKKITDSSLLSLARYCRKLRHLNLHSCSSITDVSLKYLAEGCRK  217 (483)
T ss_pred             cccccccccccccCCcchhhHHhhhCCchhhhhhhcceeccHHHHHHHHHhcchhhhhhhcccchhHHHHHHHHHHhhhh
Confidence            3588899999874321 222334577888888887743 331  1111245788999999886 433     45667778


Q ss_pred             cceeccccccccc
Q 001843          739 SRHLYLNWIFLAT  751 (1007)
Q Consensus       739 Lr~L~l~~~~~~~  751 (1007)
                      |.+|+++   .|.
T Consensus       218 L~~lNlS---wc~  227 (483)
T KOG4341|consen  218 LKYLNLS---WCP  227 (483)
T ss_pred             HHHhhhc---cCc
Confidence            8888888   554

>PRK09087 hypothetical protein; Validated

Probab=97.97  E-value=0.00018  Score=75.79  Aligned_cols=160  Identities=14%  Similarity=0.117  Sum_probs=92.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +.+.|||..|+|||+|++.+++..       ...+++..        .+..+++                        ..
T Consensus        45 ~~l~l~G~~GsGKThLl~~~~~~~-------~~~~i~~~--------~~~~~~~------------------------~~   85 (226)
T PRK09087         45 PVVVLAGPVGSGKTHLASIWREKS-------DALLIHPN--------EIGSDAA------------------------NA   85 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhc-------CCEEecHH--------HcchHHH------------------------Hh
Confidence            678999999999999999998742       11234321        0000000                        01


Q ss_pred             cCCCcEEEEEeCcCcc--Cchhhhhhc-cccCCCCCCcEEEEEcCCCc--------ccccccCCcceeeecCCCCHHHHH
Q 001843          354 LDDSTFLIVMENAEHQ--KSQVWDSFL-GKLCSFTQCGKIIITTSSTE--------DFVEPLGAAFSTLHVPGLGKNESW  422 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~--~~~~~~~l~-~l~~~~~~gs~IliTTR~~~--------~va~~~~~~~~~~~l~~L~~~ea~  422 (1007)
                      +..  -+|++||+...  +.+.+-.+. .+.   ..|..||+|++...        .+...+... .++++++++.++-.
T Consensus        86 ~~~--~~l~iDDi~~~~~~~~~lf~l~n~~~---~~g~~ilits~~~p~~~~~~~~dL~SRl~~g-l~~~l~~pd~e~~~  159 (226)
T PRK09087         86 AAE--GPVLIEDIDAGGFDETGLFHLINSVR---QAGTSLLMTSRLWPSSWNVKLPDLKSRLKAA-TVVEIGEPDDALLS  159 (226)
T ss_pred             hhc--CeEEEECCCCCCCCHHHHHHHHHHHH---hCCCeEEEECCCChHHhccccccHHHHHhCC-ceeecCCCCHHHHH
Confidence            111  27888999632  222222222 333   33667999987422        133333444 89999999999999


Q ss_pred             HHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHh------cCCCCChHHHHHHHHH
Q 001843          423 ELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL------STKQPSYEEWSKVIER  484 (1007)
Q Consensus       423 ~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L------~~~~~~~~~w~~~l~~  484 (1007)
                      +++.+.+....-   ..   .+++..-|++++.|..-++..+-..|      ..+.-+....+.+++.
T Consensus       160 ~iL~~~~~~~~~---~l---~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~~~~~it~~~~~~~l~~  221 (226)
T PRK09087        160 QVIFKLFADRQL---YV---DPHVVYYLVSRMERSLFAAQTIVDRLDRLALERKSRITRALAAEVLNE  221 (226)
T ss_pred             HHHHHHHHHcCC---CC---CHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Confidence            999988754321   11   24566777777777766655432222      2333355666665543

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.97  E-value=7.8e-05  Score=79.24  Aligned_cols=152  Identities=14%  Similarity=0.191  Sum_probs=89.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +.+.|+|+.|+|||+|++.+++.  ....-..+.++.+.  ....                       ......+.+.  
T Consensus        46 ~~l~l~Gp~G~GKThLl~a~~~~--~~~~~~~v~y~~~~--~~~~-----------------------~~~~~~~~~~--   96 (235)
T PRK08084         46 GYIYLWSREGAGRSHLLHAACAE--LSQRGRAVGYVPLD--KRAW-----------------------FVPEVLEGME--   96 (235)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEEHH--HHhh-----------------------hhHHHHHHhh--
Confidence            57899999999999999999984  43333456677665  1000                       0001111111  


Q ss_pred             cCCCcEEEEEeCcCccC-chhhhhhc-cccCC-CCCC-cEEEEEcCCCc--------ccccccCCcceeeecCCCCHHHH
Q 001843          354 LDDSTFLIVMENAEHQK-SQVWDSFL-GKLCS-FTQC-GKIIITTSSTE--------DFVEPLGAAFSTLHVPGLGKNES  421 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~-~~~~~~l~-~l~~~-~~~g-s~IliTTR~~~--------~va~~~~~~~~~~~l~~L~~~ea  421 (1007)
                        . --+|++||+.... ...|+... .+.+. ...| .++|+||+...        .+...+.+. .++++++++.++-
T Consensus        97 --~-~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g-~~~~l~~~~~~~~  172 (235)
T PRK08084         97 --Q-LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLPDLASRLDWG-QIYKLQPLSDEEK  172 (235)
T ss_pred             --h-CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccHHHHHHHhCC-ceeeecCCCHHHH
Confidence              1 2388999997322 23454322 11111 0123 47999998653        022233333 7899999999999


Q ss_pred             HHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          422 WELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       422 ~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                      .+++.+++....-   .   -.++...-|++.+.|-.-++..+
T Consensus       173 ~~~l~~~a~~~~~---~---l~~~v~~~L~~~~~~d~r~l~~~  209 (235)
T PRK08084        173 LQALQLRARLRGF---E---LPEDVGRFLLKRLDREMRTLFMT  209 (235)
T ss_pred             HHHHHHHHHHcCC---C---CCHHHHHHHHHhhcCCHHHHHHH
Confidence            9998876654221   1   22466777888887665544433

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.96  E-value=0.0001  Score=86.81  Aligned_cols=103  Identities=14%  Similarity=0.141  Sum_probs=65.4

Q ss_pred             CcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccccc
Q 001843          357 STFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDV  435 (1007)
Q Consensus       357 kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~  435 (1007)
                      ++-++|+|+++.-+...++.+. .+-.. ...+.+|++|.....+.......+..+++.++++++....+...+..... 
T Consensus       119 ~~KVIIIDEad~Lt~~A~NaLLKtLEEP-p~~tvfIL~Tt~~~KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi-  196 (605)
T PRK05896        119 KYKVYIIDEAHMLSTSAWNALLKTLEEP-PKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKI-  196 (605)
T ss_pred             CcEEEEEechHhCCHHHHHHHHHHHHhC-CCcEEEEEECCChHhhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHHcCC-
Confidence            3447999999865666777777 44333 34455555554443355444444488999999999998888876543221 


Q ss_pred             ccCCChHHHHHHHHHHHHcCCCc-hHHHHHHH
Q 001843          436 LQSRSSELIKLKKQILNICDGLP-LRVVLLAG  466 (1007)
Q Consensus       436 ~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g~  466 (1007)
                        ..+   .+.+..|++.++|-+ .|+..+-.
T Consensus       197 --~Is---~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        197 --KIE---DNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             --CCC---HHHHHHHHHHcCCcHHHHHHHHHH
Confidence              111   355778899999855 55555554

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.94  E-value=0.00011  Score=83.86  Aligned_cols=103  Identities=9%  Similarity=0.021  Sum_probs=66.0

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+...++.+. .+... ...+.+|++|.+...+..........+++.++++++..+.+...+.....
T Consensus       116 ~~~~vviidea~~l~~~~~~~Ll~~le~~-~~~~~lIl~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~  194 (355)
T TIGR02397       116 GKYKVYIIDEVHMLSKSAFNALLKTLEEP-PEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGI  194 (355)
T ss_pred             CCceEEEEeChhhcCHHHHHHHHHHHhCC-ccceeEEEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCC
Confidence            45558999998744555566666 54333 44566666665444244333333378899999999998888876643321


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLLA  465 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g  465 (1007)
                         .   -..+.+..|++.++|.|-.+....
T Consensus       195 ---~---i~~~a~~~l~~~~~g~~~~a~~~l  219 (355)
T TIGR02397       195 ---K---IEDEALELIARAADGSLRDALSLL  219 (355)
T ss_pred             ---C---CCHHHHHHHHHHcCCChHHHHHHH
Confidence               1   114677888999999886655443

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.93  E-value=9.4e-05  Score=87.08  Aligned_cols=159  Identities=13%  Similarity=0.112  Sum_probs=90.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc-------------------cCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK-------------------RHFTKRAWVHIPIMSMVEDRDVLADILKQIDESL  334 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~-------------------~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~  334 (1007)
                      ..+.++|+.|+||||+|+.+++.-.-.                   +.|..++.+...  ......+ .++++..+... 
T Consensus        39 ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaa--s~~~v~~-iR~l~~~~~~~-  114 (509)
T PRK14958         39 HAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAA--SRTKVED-TRELLDNIPYA-  114 (509)
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEccc--ccCCHHH-HHHHHHHHhhc-
Confidence            567899999999999999998832111                   112223333322  1111111 12222221110 


Q ss_pred             hhhccccCHHHHHHHHHHHcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeec
Q 001843          335 LKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHV  413 (1007)
Q Consensus       335 ~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l  413 (1007)
                                        -..++.-++|+|+++.-+....+.+. .+-.. ...+++|++|.+...+.....+.+..+++
T Consensus       115 ------------------p~~~~~kV~iIDE~~~ls~~a~naLLk~LEep-p~~~~fIlattd~~kl~~tI~SRc~~~~f  175 (509)
T PRK14958        115 ------------------PTKGRFKVYLIDEVHMLSGHSFNALLKTLEEP-PSHVKFILATTDHHKLPVTVLSRCLQFHL  175 (509)
T ss_pred             ------------------cccCCcEEEEEEChHhcCHHHHHHHHHHHhcc-CCCeEEEEEECChHhchHHHHHHhhhhhc
Confidence                              11345568999999866667777666 44333 44566666554443255444444478999


Q ss_pred             CCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHH
Q 001843          414 PGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai  461 (1007)
                      ++++.++-.+.+.+.+...+.      .-.......|++.++|-+--+
T Consensus       176 ~~l~~~~i~~~l~~il~~egi------~~~~~al~~ia~~s~GslR~a  217 (509)
T PRK14958        176 AQLPPLQIAAHCQHLLKEENV------EFENAALDLLARAANGSVRDA  217 (509)
T ss_pred             CCCCHHHHHHHHHHHHHHcCC------CCCHHHHHHHHHHcCCcHHHH
Confidence            999999877766655543221      112345677888898877443

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.91  E-value=3.8e-05  Score=87.54  Aligned_cols=153  Identities=16%  Similarity=0.161  Sum_probs=83.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-+.++|++|+|||++|+++++  .....|     +.+.  .    ..+.....   +.         ....+...+...
T Consensus       157 ~gvLL~GppGtGKT~lakaia~--~l~~~~-----~~v~--~----~~l~~~~~---g~---------~~~~i~~~f~~a  211 (364)
T TIGR01242       157 KGVLLYGPPGTGKTLLAKAVAH--ETNATF-----IRVV--G----SELVRKYI---GE---------GARLVREIFELA  211 (364)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--hCCCCE-----Eecc--h----HHHHHHhh---hH---------HHHHHHHHHHHH
Confidence            6689999999999999999999  444443     2222  1    11111110   00         011111122222


Q ss_pred             cCCCcEEEEEeCcCcc-----------Cch---hhhhhc-ccc--CCCCCCcEEEEEcCCCcccccccC---Ccceeeec
Q 001843          354 LDDSTFLIVMENAEHQ-----------KSQ---VWDSFL-GKL--CSFTQCGKIIITTSSTEDFVEPLG---AAFSTLHV  413 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~-----------~~~---~~~~l~-~l~--~~~~~gs~IliTTR~~~~va~~~~---~~~~~~~l  413 (1007)
                      -...+.+|+||+++..           +..   .+..+. .+.  .. ..+.+||.||.....+.....   .....+.+
T Consensus       212 ~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~-~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v  290 (364)
T TIGR01242       212 KEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDP-RGNVKVIAATNRPDILDPALLRPGRFDRIIEV  290 (364)
T ss_pred             HhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCC-CCCEEEEEecCChhhCChhhcCcccCceEEEe
Confidence            2346789999999731           111   122222 111  11 235678888876541222211   11167899


Q ss_pred             CCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCch
Q 001843          414 PGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPL  459 (1007)
                      +..+.++..++|..++......     +.  .....+++.+.|..-
T Consensus       291 ~~P~~~~r~~Il~~~~~~~~l~-----~~--~~~~~la~~t~g~sg  329 (364)
T TIGR01242       291 PLPDFEGRLEILKIHTRKMKLA-----ED--VDLEAIAKMTEGASG  329 (364)
T ss_pred             CCcCHHHHHHHHHHHHhcCCCC-----cc--CCHHHHHHHcCCCCH
Confidence            9999999999999887553321     10  124567777777653

Many proteins may score above the trusted cutoff because an internal

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=97.90  E-value=1.7e-06  Score=91.94  Aligned_cols=194  Identities=19%  Similarity=0.046  Sum_probs=107.9

Q ss_pred             CCCCcccEEEecCCCCCCc---CCCccccCCCcCcEEecccC--C--CcccCcc-------cccCCCCCEEeecCCccc-
Q 001843          666 RRLGMLKVLDLEGVYKPML---TNNNALGRLPFLEYLGLRST--F--IDSLPDS-------TPILFCLATLDVSHTKVQ-  730 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~---~lp~~i~~L~~Lr~L~L~~n--~--i~~LP~~-------i~~L~~L~~L~L~~~~l~-  730 (1007)
                      ..+..+..|+||+|.+..+   .+-..+.+.++|+.-++++-  .  ..++|+.       +-..++|++||||.|-+. 
T Consensus        27 ~~~~s~~~l~lsgnt~G~EAa~~i~~~L~~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~L~~ldLSDNA~G~  106 (382)
T KOG1909|consen   27 EPMDSLTKLDLSGNTFGTEAARAIAKVLASKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPKLQKLDLSDNAFGP  106 (382)
T ss_pred             cccCceEEEeccCCchhHHHHHHHHHHHhhcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCceeEeeccccccCc
Confidence            6888999999999987621   13345667789999999872  2  2356654       345678999999999433 


Q ss_pred             cccc-------cccccceecccccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecC-CC
Q 001843          731 RLPY-------AFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSS-TT  802 (1007)
Q Consensus       731 ~lP~-------~i~~Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~-~~  802 (1007)
                      .-+.       +...|+||+|.   +|..+..--..++  ..|..|.          ...-.+.-++|+.+....|. .+
T Consensus       107 ~g~~~l~~ll~s~~~L~eL~L~---N~Glg~~ag~~l~--~al~~l~----------~~kk~~~~~~Lrv~i~~rNrlen  171 (382)
T KOG1909|consen  107 KGIRGLEELLSSCTDLEELYLN---NCGLGPEAGGRLG--RALFELA----------VNKKAASKPKLRVFICGRNRLEN  171 (382)
T ss_pred             cchHHHHHHHHhccCHHHHhhh---cCCCChhHHHHHH--HHHHHHH----------HHhccCCCcceEEEEeecccccc
Confidence            2222       23333777776   5543221111111  1122221          11113445677888777776 11


Q ss_pred             --chhhHHHHHHHhhcCCCCCeEEEeecCCCCC----CcccccCCCCCcEEEecccC-CC-----CCcCccCCCCCCceE
Q 001843          803 --STSLKKEIIGAVLQLSELHSLKLICETPSYL----PLLEMAEHYKLQKLYLSGHL-PP-----NSVIGDRSFPPNVVT  870 (1007)
Q Consensus       803 --~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~----~~~~l~~~~~L~~L~L~g~~-~~-----lp~~~i~~~l~~L~~  870 (1007)
                        ...+.    ..+...+.|+.+.+..|.....    ....+..+++|+.|+|..|. +.     +.. .+.. +++|+.
T Consensus       172 ~ga~~~A----~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNtft~egs~~Lak-aL~s-~~~L~E  245 (382)
T KOG1909|consen  172 GGATALA----EAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNTFTLEGSVALAK-ALSS-WPHLRE  245 (382)
T ss_pred             ccHHHHH----HHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeecccchhhhHHHHHHHH-Hhcc-cchhee
Confidence              12222    5566667888888877544322    12345556666666666544 11     111 1222 556666


Q ss_pred             EEEEeeecCC
Q 001843          871 LTLSQLRLEY  880 (1007)
Q Consensus       871 L~L~~~~l~~  880 (1007)
                      |++++|.+..
T Consensus       246 l~l~dcll~~  255 (382)
T KOG1909|consen  246 LNLGDCLLEN  255 (382)
T ss_pred             eccccccccc
Confidence            6666665543

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.88  E-value=0.00012  Score=84.18  Aligned_cols=102  Identities=9%  Similarity=0.032  Sum_probs=65.5

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+...++.+. .+-+. ...+.+|++|.....+..........++++++++++..+.+...+.....
T Consensus       126 ~~~kvvIIdea~~l~~~~~~~LLk~LEep-~~~t~~Il~t~~~~kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~  204 (397)
T PRK14955        126 GRYRVYIIDEVHMLSIAAFNAFLKTLEEP-PPHAIFIFATTELHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGI  204 (397)
T ss_pred             CCeEEEEEeChhhCCHHHHHHHHHHHhcC-CCCeEEEEEeCChHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCC
Confidence            45568899999865666777777 54433 45566665553332255444433478999999999988887776533211


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCch-HHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPL-RVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPL-ai~~~  464 (1007)
                            .-..+.+..|++.++|.+- |+..+
T Consensus       205 ------~i~~~al~~l~~~s~g~lr~a~~~L  229 (397)
T PRK14955        205 ------SVDADALQLIGRKAQGSMRDAQSIL  229 (397)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                  1224677889999999774 44433

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.87  E-value=0.00018  Score=76.30  Aligned_cols=151  Identities=11%  Similarity=0.057  Sum_probs=85.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +.+.|+|..|+|||+||+.+++... ... ...++++..  ...      .    .+                     ..
T Consensus        43 ~~~~l~G~~G~GKT~La~ai~~~~~-~~~-~~~~~i~~~--~~~------~----~~---------------------~~   87 (227)
T PRK08903         43 RFFYLWGEAGSGRSHLLQALVADAS-YGG-RNARYLDAA--SPL------L----AF---------------------DF   87 (227)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH-hCC-CcEEEEehH--HhH------H----HH---------------------hh
Confidence            6788999999999999999999421 222 234555543  110      0    00                     11


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCc-EEEEEcCCCccccc--------ccCCcceeeecCCCCHHHHHH
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCG-KIIITTSSTEDFVE--------PLGAAFSTLHVPGLGKNESWE  423 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs-~IliTTR~~~~va~--------~~~~~~~~~~l~~L~~~ea~~  423 (1007)
                      . ...-+||+||+...+...-..+. .+......+. .||+|++... ...        .+... ..++++++++++-..
T Consensus        88 ~-~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~-~~~~l~~~L~sr~~~~-~~i~l~pl~~~~~~~  164 (227)
T PRK08903         88 D-PEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAP-LALPLREDLRTRLGWG-LVYELKPLSDADKIA  164 (227)
T ss_pred             c-ccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCH-HhCCCCHHHHHHHhcC-eEEEecCCCHHHHHH
Confidence            1 23347899999743332323333 2221102233 4666766433 222        21112 688999999988777


Q ss_pred             HHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHh
Q 001843          424 LFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL  468 (1007)
Q Consensus       424 Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L  468 (1007)
                      ++.+.+-....      .-.++....+++.+.|.+..+..+-..+
T Consensus       165 ~l~~~~~~~~v------~l~~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        165 ALKAAAAERGL------QLADEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             HHHHHHHHcCC------CCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            76654322111      1124577778888999888877666554

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.86  E-value=0.00021  Score=88.23  Aligned_cols=98  Identities=7%  Similarity=0.015  Sum_probs=64.9

Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      .++.-++|||+++..+...++.|+ .+-+- ...+.+|++|.+.+.+...+.+.+..|++..++.++-.+.+.+.+....
T Consensus       118 ~~~~KV~IIDEad~lt~~a~NaLLK~LEEp-P~~~~fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EG  196 (824)
T PRK07764        118 ESRYKIFIIDEAHMVTPQGFNALLKIVEEP-PEHLKFIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEG  196 (824)
T ss_pred             cCCceEEEEechhhcCHHHHHHHHHHHhCC-CCCeEEEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcC
Confidence            355568999999877777788777 44333 4455655555443326665565558999999999998888877553322


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCch
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPL  459 (1007)
                      .      .........|++.++|.+.
T Consensus       197 v------~id~eal~lLa~~sgGdlR  216 (824)
T PRK07764        197 V------PVEPGVLPLVIRAGGGSVR  216 (824)
T ss_pred             C------CCCHHHHHHHHHHcCCCHH
Confidence            1      1123456778889999774

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.86  E-value=0.00019  Score=85.18  Aligned_cols=103  Identities=7%  Similarity=0.002  Sum_probs=65.2

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+....+.+. .+-.. ...+.+|++|.+...+.....+.+..+++++++.++..+.+.+.+...+.
T Consensus       118 ~~~kVvIIDEad~ls~~a~naLLK~LEep-p~~~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi  196 (527)
T PRK14969        118 GRFKVYIIDEVHMLSKSAFNAMLKTLEEP-PEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENI  196 (527)
T ss_pred             CCceEEEEcCcccCCHHHHHHHHHHHhCC-CCCEEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCC
Confidence            56679999999866666666666 44333 34555665554443254444444489999999999998887776543221


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCch-HHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPL-RVVLLA  465 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPL-ai~~~g  465 (1007)
                            ...+.....|++.++|.+- |+..+-
T Consensus       197 ------~~~~~al~~la~~s~Gslr~al~lld  222 (527)
T PRK14969        197 ------PFDATALQLLARAAAGSMRDALSLLD  222 (527)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence                  1123556788899999764 444443

>PF14516 AAA_35: AAA-like domain

Probab=97.85  E-value=0.002  Score=72.19  Aligned_cols=188  Identities=14%  Similarity=0.134  Sum_probs=110.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCC---CCHHHHHHHHHHHHhhhhhhhc--------cccC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSM---VEDRDVLADILKQIDESLLKVE--------ATLS  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~---~~~~~~l~~il~~l~~~~~~~~--------~~~~  342 (1007)
                      +.+.|.|+-.+|||+|..++.+.  .++.=-.++++++.....   .+....++.++..+...+.-..        ....
T Consensus        32 ~~~~I~apRq~GKTSll~~l~~~--l~~~~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~  109 (331)
T PF14516_consen   32 SYIRIKAPRQMGKTSLLLRLLER--LQQQGYRCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGS  109 (331)
T ss_pred             CEEEEECcccCCHHHHHHHHHHH--HHHCCCEEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCC
Confidence            78999999999999999999884  433222356787652111   3566667777666655421110        1112


Q ss_pred             HHHHHHHHHHHc---CCCcEEEEEeCcCccC------chhhhhhccccCC------CCCCcEEEEEcCCCcccccc----
Q 001843          343 AEELMWRITQAL---DDSTFLIVMENAEHQK------SQVWDSFLGKLCS------FTQCGKIIITTSSTEDFVEP----  403 (1007)
Q Consensus       343 ~~~l~~~l~~~L---~~kr~LlVlDdv~~~~------~~~~~~l~~l~~~------~~~gs~IliTTR~~~~va~~----  403 (1007)
                      .......+.+.+   .+++.+|+||+|+..-      .+.+..++.+...      ..+=+-|++.+.........    
T Consensus       110 ~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SP  189 (331)
T PF14516_consen  110 KISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSP  189 (331)
T ss_pred             hhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCC
Confidence            233344444433   2689999999997321      1233333311111      01111122222111101111    


Q ss_pred             cCCcceeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCC
Q 001843          404 LGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPS  474 (1007)
Q Consensus       404 ~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~  474 (1007)
                      +.-. ..++|++++.+|...|..++...-       .   ....++|...+||+|.-+..++..+..+..+
T Consensus       190 FNIg-~~i~L~~Ft~~ev~~L~~~~~~~~-------~---~~~~~~l~~~tgGhP~Lv~~~~~~l~~~~~~  249 (331)
T PF14516_consen  190 FNIG-QPIELPDFTPEEVQELAQRYGLEF-------S---QEQLEQLMDWTGGHPYLVQKACYLLVEEQIT  249 (331)
T ss_pred             cccc-cceeCCCCCHHHHHHHHHhhhccC-------C---HHHHHHHHHHHCCCHHHHHHHHHHHHHccCc
Confidence            1111 689999999999999998874331       1   1228899999999999999999999876443

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.85  E-value=0.00038  Score=77.86  Aligned_cols=127  Identities=17%  Similarity=0.275  Sum_probs=71.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.++|.+|+||||+|+.+++.  ...   ....+..+  . .. .+.+++.+..+...                  ..
T Consensus        44 ~~lll~G~~G~GKT~la~~l~~~--~~~---~~~~i~~~--~-~~-~~~i~~~l~~~~~~------------------~~   96 (316)
T PHA02544         44 NMLLHSPSPGTGKTTVAKALCNE--VGA---EVLFVNGS--D-CR-IDFVRNRLTRFAST------------------VS   96 (316)
T ss_pred             eEEEeeCcCCCCHHHHHHHHHHH--hCc---cceEeccC--c-cc-HHHHHHHHHHHHHh------------------hc
Confidence            68888999999999999999983  322   22344444  3 11 22222222111111                  00


Q ss_pred             cCCCcEEEEEeCcCcc-CchhhhhhccccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHh
Q 001843          354 LDDSTFLIVMENAEHQ-KSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLK  427 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~-~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~  427 (1007)
                      +.+.+-+||+|+++.. ..+....+..+......++++|+||.....+..........+.++..+.++..+++..
T Consensus        97 ~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~sR~~~i~~~~p~~~~~~~il~~  171 (316)
T PHA02544         97 LTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQ  171 (316)
T ss_pred             ccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHHhhceEEEeCCCCHHHHHHHHHH
Confidence            1234568999999844 2223333333233225677888888755424333333336677777788877766543

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.85  E-value=0.00032  Score=80.22  Aligned_cols=156  Identities=15%  Similarity=0.167  Sum_probs=87.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhccc--------CCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR--------HFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEE  345 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~--------~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~  345 (1007)
                      ..+.++|+.|+||||+|+.+++.  +..        .|+..+ +.+....... .+..++++.++...            
T Consensus        40 ~~~L~~G~~G~GKt~~a~~la~~--l~~~~~~~~~~~~~~~~-~~l~~~~~~~-~~~i~~l~~~~~~~------------  103 (367)
T PRK14970         40 QALLFCGPRGVGKTTCARILARK--INQPGYDDPNEDFSFNI-FELDAASNNS-VDDIRNLIDQVRIP------------  103 (367)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--hcCCCCCCCCCCCCcce-EEeccccCCC-HHHHHHHHHHHhhc------------
Confidence            68889999999999999999883  321        122211 1111001111 11222222222110            


Q ss_pred             HHHHHHHHcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHH
Q 001843          346 LMWRITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWEL  424 (1007)
Q Consensus       346 l~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~L  424 (1007)
                             -..+++-++|+|+++......++.+. .+-.. ...+.+|++|.....+..........++++++++++....
T Consensus       104 -------p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~-~~~~~~Il~~~~~~kl~~~l~sr~~~v~~~~~~~~~l~~~  175 (367)
T PRK14970        104 -------PQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEP-PAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEH  175 (367)
T ss_pred             -------cccCCcEEEEEeChhhcCHHHHHHHHHHHhCC-CCceEEEEEeCCcccCCHHHHhcceeEecCCccHHHHHHH
Confidence                   11245558999999754555566666 34332 3345555555333225544443347899999999999888


Q ss_pred             HHhhhccccccccCCChHHHHHHHHHHHHcCCCch
Q 001843          425 FLKKARIAEDVLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       425 f~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPL  459 (1007)
                      +.+.+...+.   .   -..+.+..|++.++|.+-
T Consensus       176 l~~~~~~~g~---~---i~~~al~~l~~~~~gdlr  204 (367)
T PRK14970        176 LAGIAVKEGI---K---FEDDALHIIAQKADGALR  204 (367)
T ss_pred             HHHHHHHcCC---C---CCHHHHHHHHHhCCCCHH
Confidence            8876654322   1   124567788888888554

>PTZ00202 tuzin; Provisional

Probab=97.85  E-value=0.00012  Score=81.38  Aligned_cols=166  Identities=16%  Similarity=0.226  Sum_probs=100.4

Q ss_pred             cCCccEEecchhHHHHHHhhcCCCCCCCccccccccccccccccccCCcccccCCCCCcCCCCCCCCchhhccccccccC
Q 001843          188 EDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSS  267 (1007)
Q Consensus       188 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (1007)
                      .+..+|+||+.++..|...|...+.+                                                ..    
T Consensus       259 a~~~~FVGReaEla~Lr~VL~~~d~~------------------------------------------------~p----  286 (550)
T PTZ00202        259 AVIRQFVSREAEESWVRQVLRRLDTA------------------------------------------------HP----  286 (550)
T ss_pred             CCccCCCCcHHHHHHHHHHHhccCCC------------------------------------------------Cc----
Confidence            44568999999999999988643320                                                11    


Q ss_pred             CCCCCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHH
Q 001843          268 TTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELM  347 (1007)
Q Consensus       268 ~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~  347 (1007)
                            +++.|.|++|.|||||++.+...  ..  +  ..++.    ......++++.++.+++.+     ......++.
T Consensus       287 ------rivvLtG~~G~GKTTLlR~~~~~--l~--~--~qL~v----Nprg~eElLr~LL~ALGV~-----p~~~k~dLL  345 (550)
T PTZ00202        287 ------RIVVFTGFRGCGKSSLCRSAVRK--EG--M--PAVFV----DVRGTEDTLRSVVKALGVP-----NVEACGDLL  345 (550)
T ss_pred             ------eEEEEECCCCCCHHHHHHHHHhc--CC--c--eEEEE----CCCCHHHHHHHHHHHcCCC-----CcccHHHHH
Confidence                  79999999999999999999973  22  2  12222    3337799999999999974     122223444


Q ss_pred             HHHHHHc-----C-CCcEEEEEeCcCc-cCchhhhhhccccCCCCCCcEEEEEcCCCc-ccccccCCcceeeecCCCCHH
Q 001843          348 WRITQAL-----D-DSTFLIVMENAEH-QKSQVWDSFLGKLCSFTQCGKIIITTSSTE-DFVEPLGAAFSTLHVPGLGKN  419 (1007)
Q Consensus       348 ~~l~~~L-----~-~kr~LlVlDdv~~-~~~~~~~~l~~l~~~~~~gs~IliTTR~~~-~va~~~~~~~~~~~l~~L~~~  419 (1007)
                      +.|.+.+     . +++.+||+-=-.- .-...+++...+-.. ..-|.|++----+. -.++..-+.-..|-+++++.+
T Consensus       346 rqIqeaLl~~~~e~GrtPVLII~lreg~~l~rvyne~v~la~d-rr~ch~v~evpleslt~~~~~lprldf~~vp~fsr~  424 (550)
T PTZ00202        346 DFISEACRRAKKMNGETPLLVLKLREGSSLQRVYNEVVALACD-RRLCHVVIEVPLESLTIANTLLPRLDFYLVPNFSRS  424 (550)
T ss_pred             HHHHHHHHHHHHhCCCCEEEEEEecCCCcHHHHHHHHHHHHcc-chhheeeeeehHhhcchhcccCccceeEecCCCCHH
Confidence            4444443     2 6677777653220 011223333344444 45567776332222 011111111167888999999


Q ss_pred             HHHHHHHh
Q 001843          420 ESWELFLK  427 (1007)
Q Consensus       420 ea~~Lf~~  427 (1007)
                      +|.+.-..
T Consensus       425 qaf~y~~h  432 (550)
T PTZ00202        425 QAFAYTQH  432 (550)
T ss_pred             HHHHHHhh
Confidence            98876544

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.84  E-value=0.00022  Score=84.70  Aligned_cols=106  Identities=11%  Similarity=0.066  Sum_probs=67.8

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+....+.+. .+-.. .....+|++|.+...+.....+.+..+++.+++.++..+.+.+.+.....
T Consensus       117 ~~~KVvIIDEah~Lt~~A~NALLK~LEEp-p~~~~fIL~tte~~kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi  195 (584)
T PRK14952        117 SRYRIFIVDEAHMVTTAGFNALLKIVEEP-PEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPRTMRALIARICEQEGV  195 (584)
T ss_pred             CCceEEEEECCCcCCHHHHHHHHHHHhcC-CCCeEEEEEeCChHhhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCC
Confidence            45568999999866777777777 44443 44555555444333266554544589999999999988888776543221


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCc-hHHHHHHHHh
Q 001843          435 VLQSRSSELIKLKKQILNICDGLP-LRVVLLAGLL  468 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g~~L  468 (1007)
                            .-..+....|++.++|-+ -|+..+-.++
T Consensus       196 ------~i~~~al~~Ia~~s~GdlR~aln~Ldql~  224 (584)
T PRK14952        196 ------VVDDAVYPLVIRAGGGSPRDTLSVLDQLL  224 (584)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence                  112345677888888876 4555554443

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.82  E-value=0.00027  Score=83.74  Aligned_cols=108  Identities=10%  Similarity=0.062  Sum_probs=70.7

Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      .+++-+||+|+++.-+...++.|. .+-.. .....+|++|.+...+...+...+..+++++++.++..+.+...+....
T Consensus       117 ~g~~kVIIIDEad~Lt~~a~naLLk~LEEP-~~~~ifILaTt~~~kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~~eg  195 (624)
T PRK14959        117 EGRYKVFIIDEAHMLTREAFNALLKTLEEP-PARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLGREG  195 (624)
T ss_pred             cCCceEEEEEChHhCCHHHHHHHHHHhhcc-CCCEEEEEecCChhhhhHHHHhhhhccccCCCCHHHHHHHHHHHHHHcC
Confidence            356679999999866666777777 44332 3345566655543325544444447899999999999988887665432


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCc-hHHHHHHHHhc
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLP-LRVVLLAGLLS  469 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g~~L~  469 (1007)
                      .      .-..+.+..|++.++|.+ -|+..+...+.
T Consensus       196 i------~id~eal~lIA~~s~GdlR~Al~lLeqll~  226 (624)
T PRK14959        196 V------DYDPAAVRLIARRAAGSVRDSMSLLGQVLA  226 (624)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            1      112456778889999854 77777765543

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.79  E-value=0.00038  Score=83.26  Aligned_cols=101  Identities=8%  Similarity=-0.013  Sum_probs=66.5

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEc-CCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITT-SSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTT-R~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      +++-++|+|+++.-+....+.+. .+-+- ...+++|++| .... +.....+.+..+++.+++.++....+.+.+....
T Consensus       131 a~~KVvIIDEad~Ls~~a~naLLKtLEeP-p~~~~fIl~tte~~k-ll~tI~SRcq~~~f~~l~~~el~~~L~~i~~keg  208 (598)
T PRK09111        131 ARYKVYIIDEVHMLSTAAFNALLKTLEEP-PPHVKFIFATTEIRK-VPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEG  208 (598)
T ss_pred             CCcEEEEEEChHhCCHHHHHHHHHHHHhC-CCCeEEEEEeCChhh-hhHHHHhheeEEEecCCCHHHHHHHHHHHHHHcC
Confidence            45568999999865666666666 44333 4456665544 4444 5544555558999999999999988888764332


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                      .      .-..+....|++.++|.+.-+...
T Consensus       209 i------~i~~eAl~lIa~~a~Gdlr~al~~  233 (598)
T PRK09111        209 V------EVEDEALALIARAAEGSVRDGLSL  233 (598)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            2      112356788899999988655433

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=97.77  E-value=2e-05  Score=64.30  Aligned_cols=60  Identities=25%  Similarity=0.303  Sum_probs=51.6

Q ss_pred             CcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCC-ccccCCCcCcEEecccCCC
Q 001843          635 WRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNN-NALGRLPFLEYLGLRSTFI  706 (1007)
Q Consensus       635 ~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp-~~i~~L~~Lr~L~L~~n~i  706 (1007)
                      ++|++|.+.+|.+..        +.+..|  .++++|++|++++|.+.  .+| ..|..+++|++|++++|.|
T Consensus         1 p~L~~L~l~~n~l~~--------i~~~~f--~~l~~L~~L~l~~N~l~--~i~~~~f~~l~~L~~L~l~~N~l   61 (61)
T PF13855_consen    1 PNLESLDLSNNKLTE--------IPPDSF--SNLPNLETLDLSNNNLT--SIPPDAFSNLPNLRYLDLSNNNL   61 (61)
T ss_dssp             TTESEEEETSSTESE--------ECTTTT--TTGTTESEEEETSSSES--EEETTTTTTSTTESEEEETSSSB
T ss_pred             CcCcEEECCCCCCCc--------cCHHHH--cCCCCCCEeEccCCccC--ccCHHHHcCCCCCCEEeCcCCcC
Confidence            478999999998753        555788  99999999999999998  665 5789999999999999975

...

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.77  E-value=8.8e-06  Score=84.43  Aligned_cols=177  Identities=18%  Similarity=0.174  Sum_probs=101.0

Q ss_pred             CCCCCeEEeeecC-CCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccc-cCCCCCcEEEecccC---CCCCcCccC
Q 001843          788 LTSLRKLGLKCSS-TTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEM-AEHYKLQKLYLSGHL---PPNSVIGDR  862 (1007)
Q Consensus       788 L~~L~~L~l~~~~-~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l-~~~~~L~~L~L~g~~---~~lp~~~i~  862 (1007)
                      .+.++.|++.++. +...++.    ..+.+|+.|+.|+|++|.... ....+ .+..+|+.|.|.|..   ..... .+.
T Consensus        70 ~~~v~elDL~~N~iSdWseI~----~ile~lP~l~~LNls~N~L~s-~I~~lp~p~~nl~~lVLNgT~L~w~~~~s-~l~  143 (418)
T KOG2982|consen   70 VTDVKELDLTGNLISDWSEIG----AILEQLPALTTLNLSCNSLSS-DIKSLPLPLKNLRVLVLNGTGLSWTQSTS-SLD  143 (418)
T ss_pred             hhhhhhhhcccchhccHHHHH----HHHhcCccceEeeccCCcCCC-ccccCcccccceEEEEEcCCCCChhhhhh-hhh
Confidence            4778899999887 4444554    888999999999999987665 45555 356699999998854   33333 444


Q ss_pred             CCCCCceEEEEEeeecCCC--CcCcccc-CCCCcEEEeecCCcCCCceee-cCCCCCCCcEEEeccCCCCcceEEcC--C
Q 001843          863 SFPPNVVTLTLSQLRLEYD--PMPILGR-LRQLKILRLFGGSYTGEEMSC-SSGEFPNLLVLKLWKLNRLRQWRIKE--G  936 (1007)
Q Consensus       863 ~~l~~L~~L~L~~~~l~~~--~~~~l~~-Lp~L~~L~L~~~~~~~~~l~~-~~~~fp~L~~L~L~~~~~L~~l~~~~--~  936 (1007)
                      . +|.++.|.++.|.+...  .-..... -|.++.|.+..|......-.. -..-||++..+.+..|| ++....+.  .
T Consensus       144 ~-lP~vtelHmS~N~~rq~n~Dd~c~e~~s~~v~tlh~~~c~~~~w~~~~~l~r~Fpnv~sv~v~e~P-lK~~s~ek~se  221 (418)
T KOG2982|consen  144 D-LPKVTELHMSDNSLRQLNLDDNCIEDWSTEVLTLHQLPCLEQLWLNKNKLSRIFPNVNSVFVCEGP-LKTESSEKGSE  221 (418)
T ss_pred             c-chhhhhhhhccchhhhhccccccccccchhhhhhhcCCcHHHHHHHHHhHHhhcccchheeeecCc-ccchhhcccCC
Confidence            5 77888888888732111  0011111 123333333322110000000 01237777777777665 44443332  2


Q ss_pred             CCccccEeEeeccCCCC---CCcCccccccCccEEEeccCC
Q 001843          937 AMPCLRQLEIRSCGYLV---PPTGLKHVTSSLREFLLTNMP  974 (1007)
Q Consensus       937 ~~p~L~~L~l~~c~~L~---lp~~l~~L~~~L~~L~l~~c~  974 (1007)
                      .+|.+-.|++.. +++.   --..+..+ +.|..|.+.+.|
T Consensus       222 ~~p~~~~LnL~~-~~idswasvD~Ln~f-~~l~dlRv~~~P  260 (418)
T KOG2982|consen  222 PFPSLSCLNLGA-NNIDSWASVDALNGF-PQLVDLRVSENP  260 (418)
T ss_pred             CCCcchhhhhcc-cccccHHHHHHHcCC-chhheeeccCCc
Confidence            466666666665 3344   22245566 777777777766

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.76  E-value=2.7e-05  Score=58.47  Aligned_cols=40  Identities=30%  Similarity=0.297  Sum_probs=35.3

Q ss_pred             CcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccC
Q 001843          669 GMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLP  710 (1007)
Q Consensus       669 ~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP  710 (1007)
                      ++|++|++++|++.  .+|..+++|++|++|++++|.|+++|
T Consensus         1 ~~L~~L~l~~N~i~--~l~~~l~~l~~L~~L~l~~N~i~~i~   40 (44)
T PF12799_consen    1 KNLEELDLSNNQIT--DLPPELSNLPNLETLNLSNNPISDIS   40 (44)
T ss_dssp             TT-SEEEETSSS-S--SHGGHGTTCTTSSEEEETSSCCSBEG
T ss_pred             CcceEEEccCCCCc--ccCchHhCCCCCCEEEecCCCCCCCc
Confidence            47999999999999  89988999999999999999999876

...

>PRK05642 DNA replication initiation factor; Validated

Probab=97.76  E-value=0.0002  Score=75.97  Aligned_cols=152  Identities=13%  Similarity=0.187  Sum_probs=88.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.|+|..|+|||.|++++++  .....-..++|++..  .      +...                 .    ..+.+.
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~--~~~~~~~~v~y~~~~--~------~~~~-----------------~----~~~~~~   94 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACL--RFEQRGEPAVYLPLA--E------LLDR-----------------G----PELLDN   94 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH--HHHhCCCcEEEeeHH--H------HHhh-----------------h----HHHHHh
Confidence            6789999999999999999998  333333456777654  1      1100                 0    112222


Q ss_pred             cCCCcEEEEEeCcCcc-Cchhhhh-hccccCC-CCCCcEEEEEcCCCcccc--------cccCCcceeeecCCCCHHHHH
Q 001843          354 LDDSTFLIVMENAEHQ-KSQVWDS-FLGKLCS-FTQCGKIIITTSSTEDFV--------EPLGAAFSTLHVPGLGKNESW  422 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~-~~~~~~~-l~~l~~~-~~~gs~IliTTR~~~~va--------~~~~~~~~~~~l~~L~~~ea~  422 (1007)
                      +.+-. +||+||+... ....|.. +..+.+. ...|..||+|++....-.        ..+... .++++++++.++-.
T Consensus        95 ~~~~d-~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~g-l~~~l~~~~~e~~~  172 (234)
T PRK05642         95 LEQYE-LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLA-LVFQMRGLSDEDKL  172 (234)
T ss_pred             hhhCC-EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcC-eeeecCCCCHHHHH
Confidence            32222 6889999632 2234544 2222221 134678999888643111        112222 67899999999999


Q ss_pred             HHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          423 ELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       423 ~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                      +++.+++....-   ..+   ++...-|++++.|-.-.+..+
T Consensus       173 ~il~~ka~~~~~---~l~---~ev~~~L~~~~~~d~r~l~~~  208 (234)
T PRK05642        173 RALQLRASRRGL---HLT---DEVGHFILTRGTRSMSALFDL  208 (234)
T ss_pred             HHHHHHHHHcCC---CCC---HHHHHHHHHhcCCCHHHHHHH
Confidence            999866644321   112   466777777777765444433

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.74  E-value=0.00048  Score=83.17  Aligned_cols=102  Identities=8%  Similarity=-0.011  Sum_probs=65.7

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+.+..+.+. .+-.. ...+.+|++|.+...+.......+..+.+++++.++....+.+.+.....
T Consensus       119 ~~~kVvIIDEa~~L~~~a~naLLk~LEep-p~~tv~Il~t~~~~kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl  197 (585)
T PRK14950        119 ARYKVYIIDEVHMLSTAAFNALLKTLEEP-PPHAIFILATTEVHKVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGI  197 (585)
T ss_pred             CCeEEEEEeChHhCCHHHHHHHHHHHhcC-CCCeEEEEEeCChhhhhHHHHhccceeeCCCCCHHHHHHHHHHHHHHcCC
Confidence            45668999999755556666666 44333 44556666554433254444444478899999999988888877654322


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                         .   -..+.+..|++.++|.+-.+...
T Consensus       198 ---~---i~~eal~~La~~s~Gdlr~al~~  221 (585)
T PRK14950        198 ---N---LEPGALEAIARAATGSMRDAENL  221 (585)
T ss_pred             ---C---CCHHHHHHHHHHcCCCHHHHHHH
Confidence               1   12356788999999988644433

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=97.74  E-value=0.00083  Score=75.66  Aligned_cols=267  Identities=15%  Similarity=0.210  Sum_probs=145.1

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCc--eEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTK--RAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~--~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      -+.|+|.+|+|||+.++.|..  ++......  +++|.+-  ...+..+++.+|+.+++..   ........+..+.+.+
T Consensus        44 n~~iyG~~GTGKT~~~~~v~~--~l~~~~~~~~~~yINc~--~~~t~~~i~~~i~~~~~~~---p~~g~~~~~~~~~l~~  116 (366)
T COG1474          44 NIIIYGPTGTGKTATVKFVME--ELEESSANVEVVYINCL--ELRTPYQVLSKILNKLGKV---PLTGDSSLEILKRLYD  116 (366)
T ss_pred             cEEEECCCCCCHhHHHHHHHH--HHHhhhccCceEEEeee--eCCCHHHHHHHHHHHcCCC---CCCCCchHHHHHHHHH
Confidence            388999999999999999999  55544322  5677666  8999999999999999732   2245566777777777


Q ss_pred             HcC--CCcEEEEEeCcCccCch---hhhhhccccCCCCCCcEEEE--EcCCCc-------ccccccCCcceeeecCCCCH
Q 001843          353 ALD--DSTFLIVMENAEHQKSQ---VWDSFLGKLCSFTQCGKIII--TTSSTE-------DFVEPLGAAFSTLHVPGLGK  418 (1007)
Q Consensus       353 ~L~--~kr~LlVlDdv~~~~~~---~~~~l~~l~~~~~~gs~Ili--TTR~~~-------~va~~~~~~~~~~~l~~L~~  418 (1007)
                      .+.  ++.++||||+++.-...   ..-.+...+.. . .++|+|  .+-+..       +|-...+.  ..+..+|-+.
T Consensus       117 ~~~~~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~-~-~~~v~vi~i~n~~~~~~~ld~rv~s~l~~--~~I~F~pY~a  192 (366)
T COG1474         117 NLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGE-N-KVKVSIIAVSNDDKFLDYLDPRVKSSLGP--SEIVFPPYTA  192 (366)
T ss_pred             HHHhcCCeEEEEEcchhhhccccchHHHHHHhhccc-c-ceeEEEEEEeccHHHHHHhhhhhhhccCc--ceeeeCCCCH
Confidence            775  57889999999732111   11122222222 1 344443  232221       02222223  4478889999


Q ss_pred             HHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcC-CCchHHHHHHH--HhcCCCC----ChHHHHHHHHHcccchhh
Q 001843          419 NESWELFLKKARIAEDVLQSRSSELIKLKKQILNICD-GLPLRVVLLAG--LLSTKQP----SYEEWSKVIERANGDNLV  491 (1007)
Q Consensus       419 ~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~-GlPLai~~~g~--~L~~~~~----~~~~w~~~l~~l~i~~~l  491 (1007)
                      +|-.+.+...+-..-.+ ....+..-+++..++..-+ -.=.||.++-.  .++.+..    +...-..+.... -....
T Consensus       193 ~el~~Il~~R~~~~~~~-~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~-~~~~~  270 (366)
T COG1474         193 EELYDILRERVEEGFSA-GVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEI-ERDVL  270 (366)
T ss_pred             HHHHHHHHHHHHhhccC-CCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHh-hHHHH
Confidence            99999888776533221 1223333344444444444 44455555433  3332111    222222222211 12223


Q ss_pred             hhhhcCCccCchhhhhhhccCCCCcccchhHH--HHHHHhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEe
Q 001843          492 ALCYQDLPAQVKPCILYMGLFPREYEIPVRRL--IHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIR  564 (1007)
Q Consensus       492 ~~sy~~L~~~~k~cfl~la~fp~~~~i~~~~L--i~~Wiaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~  564 (1007)
                      .-....||.+.|-.+.-....-  ..+....+  ...++++.+-       . .+..-..++++|...+++....
T Consensus       271 ~~~~~~L~~~~ki~L~~i~~~~--~~~~~~~~y~~y~~~~~~~~-------~-~~~~~~~ii~~L~~lgiv~~~~  335 (366)
T COG1474         271 EEVLKTLPLHQKIVLLAIVELT--VEISTGELYDVYESLCERLR-------T-SQRRFSDIISELEGLGIVSASL  335 (366)
T ss_pred             HHHHHcCCHhHHHHHHHHHHhc--CCCChHHHHHHHHHHHhhhC-------c-hHHHHHHHHHHHHhcCeEEeee
Confidence            3336778877665544333221  12222222  2233333222       1 2333446777788888876543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.73  E-value=0.00034  Score=81.35  Aligned_cols=168  Identities=9%  Similarity=0.166  Sum_probs=99.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCC--ceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFT--KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .-+.|+|..|+|||+|++++++  .+.....  .+++++.        .++...+...+...          ......++
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~--~l~~~~~~~~v~yv~~--------~~f~~~~~~~l~~~----------~~~~~~~~  201 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKN--YIESNFSDLKVSYMSG--------DEFARKAVDILQKT----------HKEIEQFK  201 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHH--HHHHhCCCCeEEEEEH--------HHHHHHHHHHHHHh----------hhHHHHHH
Confidence            4588999999999999999999  4433222  2344433        35556665555432          01123344


Q ss_pred             HHcCCCcEEEEEeCcCccCc-hhh-hhhccccC-CCCCCcEEEEEcCCCc--------ccccccCCcceeeecCCCCHHH
Q 001843          352 QALDDSTFLIVMENAEHQKS-QVW-DSFLGKLC-SFTQCGKIIITTSSTE--------DFVEPLGAAFSTLHVPGLGKNE  420 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~~~-~~~-~~l~~l~~-~~~~gs~IliTTR~~~--------~va~~~~~~~~~~~l~~L~~~e  420 (1007)
                      +.++ +.-+||+||+..... ..| +.+..+.+ ....|..||+|+....        ++...+... -++.+++++.++
T Consensus       202 ~~~~-~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~G-l~~~L~~pd~e~  279 (450)
T PRK14087        202 NEIC-QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMG-LSIAIQKLDNKT  279 (450)
T ss_pred             HHhc-cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCC-ceeccCCcCHHH
Confidence            4444 334888999974322 222 33331111 1133557888876532        122233333 678899999999


Q ss_pred             HHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHH
Q 001843          421 SWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGL  467 (1007)
Q Consensus       421 a~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~  467 (1007)
                      -.+++.+++-....   . ..-.++...-|++.++|.|=.+.-+...
T Consensus       280 r~~iL~~~~~~~gl---~-~~l~~evl~~Ia~~~~gd~R~L~gaL~~  322 (450)
T PRK14087        280 ATAIIKKEIKNQNI---K-QEVTEEAINFISNYYSDDVRKIKGSVSR  322 (450)
T ss_pred             HHHHHHHHHHhcCC---C-CCCCHHHHHHHHHccCCCHHHHHHHHHH
Confidence            99999988754221   0 0122567788999999988766555433

>TIGR00767 rho transcription termination factor Rho

Probab=97.73  E-value=8.7e-05  Score=82.61  Aligned_cols=91  Identities=13%  Similarity=0.114  Sum_probs=61.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhcccc-CH----HHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATL-SA----EELMW  348 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~-~~----~~l~~  348 (1007)
                      +.++|+|.+|.|||||++.+++.... .+|+..+||.+...+..+..++++.++..+-..  ..+... ..    ....+
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~~-nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvas--t~d~p~~~~~~va~~v~e  245 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAITR-NHPEVELIVLLIDERPEEVTDMQRSVKGEVVAS--TFDEPASRHVQVAEMVIE  245 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhcc-cCCceEEEEEEcCCCCccHHHHHHHhhceEEEe--cCCCChHHHHHHHHHHHH
Confidence            78999999999999999999995332 369999999988334489999999986544332  111111 10    11111


Q ss_pred             HHHHH-cCCCcEEEEEeCcC
Q 001843          349 RITQA-LDDSTFLIVMENAE  367 (1007)
Q Consensus       349 ~l~~~-L~~kr~LlVlDdv~  367 (1007)
                      ..... -.+++.+|++|.+.
T Consensus       246 ~Ae~~~~~GkdVVLlIDEit  265 (415)
T TIGR00767       246 KAKRLVEHKKDVVILLDSIT  265 (415)
T ss_pred             HHHHHHHcCCCeEEEEEChh
Confidence            11121 35899999999996

Members of this family differ in the specificity of RNA binding.

>PLN03150 hypothetical protein; Provisional

Probab=97.72  E-value=3.2e-05  Score=94.16  Aligned_cols=89  Identities=22%  Similarity=0.204  Sum_probs=75.7

Q ss_pred             cccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCc-ccCcccccCCCCCEEeecCCccc-ccccccccc---ceecc
Q 001843          670 MLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFID-SLPDSTPILFCLATLDVSHTKVQ-RLPYAFWPS---RHLYL  744 (1007)
Q Consensus       670 ~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~-~LP~~i~~L~~L~~L~L~~~~l~-~lP~~i~~L---r~L~l  744 (1007)
                      .++.|+|++|.+.+ .+|..|++|.+|++|+|++|.+. .+|..+++|++|++|+|++|.+. .+|..+++|   ++|++
T Consensus       419 ~v~~L~L~~n~L~g-~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~L~L  497 (623)
T PLN03150        419 FIDGLGLDNQGLRG-FIPNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNL  497 (623)
T ss_pred             EEEEEECCCCCccc-cCCHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEEC
Confidence            48899999999886 78999999999999999999997 89999999999999999999887 677766655   88888


Q ss_pred             cccccccccccccccccC
Q 001843          745 NWIFLATNVFRHPQFVKW  762 (1007)
Q Consensus       745 ~~~~~~~~~~~~p~~i~~  762 (1007)
                      +   +|.....+|..++.
T Consensus       498 s---~N~l~g~iP~~l~~  512 (623)
T PLN03150        498 N---GNSLSGRVPAALGG  512 (623)
T ss_pred             c---CCcccccCChHHhh
Confidence            8   66666677776654

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=97.71  E-value=0.00067  Score=81.67  Aligned_cols=103  Identities=8%  Similarity=0.025  Sum_probs=65.0

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-....++.+. .+-.. ...+.+|++|.....+.......+..+++.+++.++..+.+...+...+.
T Consensus       117 g~~KV~IIDEa~~LT~~A~NALLKtLEEP-P~~tifILaTte~~KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI  195 (725)
T PRK07133        117 SKYKIYIIDEVHMLSKSAFNALLKTLEEP-PKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENI  195 (725)
T ss_pred             CCCEEEEEEChhhCCHHHHHHHHHHhhcC-CCceEEEEEcCChhhhhHHHHhhceeEEccCCCHHHHHHHHHHHHHHcCC
Confidence            56669999999866666777777 43332 33445444443333265554544589999999999998888775433221


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCc-hHHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLP-LRVVLLA  465 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g  465 (1007)
                            ....+.+..|++.++|-+ .|+..+-
T Consensus       196 ------~id~eAl~~LA~lS~GslR~AlslLe  221 (725)
T PRK07133        196 ------SYEKNALKLIAKLSSGSLRDALSIAE  221 (725)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence                  111345778899998866 4444443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.71  E-value=0.00059  Score=79.43  Aligned_cols=103  Identities=10%  Similarity=0.058  Sum_probs=64.8

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.......+.+. .+-+. .....+|++|.+...+.......+..++++++++++....+.+.+.....
T Consensus       120 ~~~kvvIIdead~lt~~~~n~LLk~lEep-~~~~~~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~  198 (451)
T PRK06305        120 SRYKIYIIDEVHMLTKEAFNSLLKTLEEP-PQHVKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGI  198 (451)
T ss_pred             CCCEEEEEecHHhhCHHHHHHHHHHhhcC-CCCceEEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCC
Confidence            56678999999755555556665 44333 34556666554333255544444488999999999988888776543221


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCc-hHHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLP-LRVVLLA  465 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g  465 (1007)
                            .-..+.+..|++.++|.+ .|+..+-
T Consensus       199 ------~i~~~al~~L~~~s~gdlr~a~~~Le  224 (451)
T PRK06305        199 ------ETSREALLPIARAAQGSLRDAESLYD  224 (451)
T ss_pred             ------CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence                  112457788999999865 4444443

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=97.71  E-value=4.7e-06  Score=96.79  Aligned_cols=77  Identities=25%  Similarity=0.200  Sum_probs=57.5

Q ss_pred             CCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcccccCCCCCEEeecCCcccccccc--ccccceec
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYA--FWPSRHLY  743 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~--i~~Lr~L~  743 (1007)
                      ..++.|..|++.+|.+.  .+...+..+.+|++|+|++|.|+.+. .+..|..|+.|++.+|.|..++..  +..|+.|+
T Consensus        92 ~~~~~l~~l~l~~n~i~--~i~~~l~~~~~L~~L~ls~N~I~~i~-~l~~l~~L~~L~l~~N~i~~~~~~~~l~~L~~l~  168 (414)
T KOG0531|consen   92 SKLKSLEALDLYDNKIE--KIENLLSSLVNLQVLDLSFNKITKLE-GLSTLTLLKELNLSGNLISDISGLESLKSLKLLD  168 (414)
T ss_pred             ccccceeeeeccccchh--hcccchhhhhcchheecccccccccc-chhhccchhhheeccCcchhccCCccchhhhccc
Confidence            77888888888888887  66554778888888888888888886 677788888888888877766542  34445555


Q ss_pred             cc
Q 001843          744 LN  745 (1007)
Q Consensus       744 l~  745 (1007)
                      ++
T Consensus       169 l~  170 (414)
T KOG0531|consen  169 LS  170 (414)
T ss_pred             CC
Confidence            54

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.69  E-value=1.3e-05  Score=97.06  Aligned_cols=157  Identities=22%  Similarity=0.186  Sum_probs=80.3

Q ss_pred             CcccEEEecCCCCCCcCCCcccc-CCCcCcEEecccCCCc--ccCcccccCCCCCEEeecCCccccccccccccceeccc
Q 001843          669 GMLKVLDLEGVYKPMLTNNNALG-RLPFLEYLGLRSTFID--SLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLN  745 (1007)
Q Consensus       669 ~~Lr~L~Ls~~~l~~~~lp~~i~-~L~~Lr~L~L~~n~i~--~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~~Lr~L~l~  745 (1007)
                      .+|+.||++|.......-|..++ -|+.|+.|.+.+-.+.  ++-.-..+++||..||+++++++.+             
T Consensus       122 ~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~TnI~nl-------------  188 (699)
T KOG3665|consen  122 QNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISGTNISNL-------------  188 (699)
T ss_pred             HhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCCCCccCc-------------
Confidence            35666666665433222333443 3556666666553332  2222234555666666666554432             


Q ss_pred             ccccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecC-CCchhhHHHHHHHhhcCCCCCeEE
Q 001843          746 WIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSS-TTSTSLKKEIIGAVLQLSELHSLK  824 (1007)
Q Consensus       746 ~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~-~~~~~l~~~~~~~l~~l~~L~~L~  824 (1007)
                                  .++++|++|++|...+....+...+.++-.|++|+.|+|+... .....+.....+.-..+++|+.|+
T Consensus       189 ------------~GIS~LknLq~L~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~~~~~~~ii~qYlec~~~LpeLrfLD  256 (699)
T KOG3665|consen  189 ------------SGISRLKNLQVLSMRNLEFESYQDLIDLFNLKKLRVLDISRDKNNDDTKIIEQYLECGMVLPELRFLD  256 (699)
T ss_pred             ------------HHHhccccHHHHhccCCCCCchhhHHHHhcccCCCeeeccccccccchHHHHHHHHhcccCccccEEe
Confidence                        3456666666665444444433456667777778888877655 222223333334445567777777


Q ss_pred             EeecCCCCCCccc-ccCCCCCcEEEec
Q 001843          825 LICETPSYLPLLE-MAEHYKLQKLYLS  850 (1007)
Q Consensus       825 L~~~~~~~~~~~~-l~~~~~L~~L~L~  850 (1007)
                      .++.......++. +..+|+|+.+.+-
T Consensus       257 cSgTdi~~~~le~ll~sH~~L~~i~~~  283 (699)
T KOG3665|consen  257 CSGTDINEEILEELLNSHPNLQQIAAL  283 (699)
T ss_pred             cCCcchhHHHHHHHHHhCccHhhhhhh
Confidence            7764433222222 2335555555443

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.69  E-value=0.00082  Score=74.74  Aligned_cols=98  Identities=13%  Similarity=0.210  Sum_probs=68.8

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+....+.+. .+-.. ..++.+|+||.+...+.....+.+..+.+.+++.+++.+.+...... . 
T Consensus       105 ~~~kv~iI~~a~~m~~~aaNaLLK~LEEP-p~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~~~-~-  181 (328)
T PRK05707        105 GGRKVVLIEPAEAMNRNAANALLKSLEEP-SGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQALPE-S-  181 (328)
T ss_pred             CCCeEEEECChhhCCHHHHHHHHHHHhCC-CCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhccc-C-
Confidence            34445577999877777788777 44333 45677778887776466666666689999999999999888765311 1 


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                           .   .+.+..++..++|.|+....+
T Consensus       182 -----~---~~~~~~~l~la~Gsp~~A~~l  203 (328)
T PRK05707        182 -----D---ERERIELLTLAGGSPLRALQL  203 (328)
T ss_pred             -----C---hHHHHHHHHHcCCCHHHHHHH
Confidence                 1   234567788999999765544

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=97.69  E-value=0.00032  Score=73.53  Aligned_cols=155  Identities=12%  Similarity=0.153  Sum_probs=85.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCC--ceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFT--KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      ..+.|+|..|+|||.|.+++++  ...+..+  .+++++..        +....+...+...        ..    ..++
T Consensus        35 ~~l~l~G~~G~GKTHLL~Ai~~--~~~~~~~~~~v~y~~~~--------~f~~~~~~~~~~~--------~~----~~~~   92 (219)
T PF00308_consen   35 NPLFLYGPSGLGKTHLLQAIAN--EAQKQHPGKRVVYLSAE--------EFIREFADALRDG--------EI----EEFK   92 (219)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH--HHHHHCTTS-EEEEEHH--------HHHHHHHHHHHTT--------SH----HHHH
T ss_pred             CceEEECCCCCCHHHHHHHHHH--HHHhccccccceeecHH--------HHHHHHHHHHHcc--------cc----hhhh
Confidence            5678999999999999999999  4444332  35565543        4444444444322        12    2233


Q ss_pred             HHcCCCcEEEEEeCcCccCc-hhhhhhc-cccCC-CCCCcEEEEEcCCCcccc--------cccCCcceeeecCCCCHHH
Q 001843          352 QALDDSTFLIVMENAEHQKS-QVWDSFL-GKLCS-FTQCGKIIITTSSTEDFV--------EPLGAAFSTLHVPGLGKNE  420 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~~~-~~~~~l~-~l~~~-~~~gs~IliTTR~~~~va--------~~~~~~~~~~~l~~L~~~e  420 (1007)
                      +.++ .-=+|++||++.-.. ..|.... .+.+. ...|-+||+|++....-.        ..+... -++++++++.++
T Consensus        93 ~~~~-~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~G-l~~~l~~pd~~~  170 (219)
T PF00308_consen   93 DRLR-SADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRSRLSWG-LVVELQPPDDED  170 (219)
T ss_dssp             HHHC-TSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHHHHHCS-EEEEE----HHH
T ss_pred             hhhh-cCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhhhHhhc-chhhcCCCCHHH
Confidence            4444 233889999974322 2333322 22211 134668999996543111        112222 789999999999


Q ss_pred             HHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCc
Q 001843          421 SWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       421 a~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlP  458 (1007)
                      -.+++.+.+....-      .--++++.-|++.+.+..
T Consensus       171 r~~il~~~a~~~~~------~l~~~v~~~l~~~~~~~~  202 (219)
T PF00308_consen  171 RRRILQKKAKERGI------ELPEEVIEYLARRFRRDV  202 (219)
T ss_dssp             HHHHHHHHHHHTT--------S-HHHHHHHHHHTTSSH
T ss_pred             HHHHHHHHHHHhCC------CCcHHHHHHHHHhhcCCH
Confidence            99999988765332      122455566666655443

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.68  E-value=0.00053  Score=82.62  Aligned_cols=98  Identities=9%  Similarity=0.046  Sum_probs=65.5

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEE-EcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIII-TTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~Ili-TTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      +++=++|+|+++.-+...++.+. .+-.- ...+.+|+ ||+... +.......+.++++.++++++....+.+.+...+
T Consensus       120 ~~~KVvIIdea~~Ls~~a~naLLK~LEep-p~~tifIL~tt~~~k-Il~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~eg  197 (614)
T PRK14971        120 GKYKIYIIDEVHMLSQAAFNAFLKTLEEP-PSYAIFILATTEKHK-ILPTILSRCQIFDFNRIQVADIVNHLQYVASKEG  197 (614)
T ss_pred             CCcEEEEEECcccCCHHHHHHHHHHHhCC-CCCeEEEEEeCCchh-chHHHHhhhheeecCCCCHHHHHHHHHHHHHHcC
Confidence            44558899999866667777777 44333 44555555 544444 7666565568999999999999888877654432


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCchHH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPLai  461 (1007)
                      .      ....+.+..|++.++|-.--+
T Consensus       198 i------~i~~~al~~La~~s~gdlr~a  219 (614)
T PRK14971        198 I------TAEPEALNVIAQKADGGMRDA  219 (614)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHH
Confidence            2      112356788889998866433

>KOG4341 consensus F-box protein containing LRR [General function prediction only]

Probab=97.68  E-value=1.5e-06  Score=94.24  Aligned_cols=302  Identities=20%  Similarity=0.133  Sum_probs=150.1

Q ss_pred             CcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccc-cCCCcCcEEeccc-CCCccc--C
Q 001843          635 WRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNAL-GRLPFLEYLGLRS-TFIDSL--P  710 (1007)
Q Consensus       635 ~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i-~~L~~Lr~L~L~~-n~i~~L--P  710 (1007)
                      ..||.|.+.|+......      .+..+-  .+++++..|.+.+|....+..-.++ ..+..|++|+|.. ..|+..  -
T Consensus       138 g~lk~LSlrG~r~v~~s------slrt~~--~~CpnIehL~l~gc~~iTd~s~~sla~~C~~l~~l~L~~c~~iT~~~Lk  209 (483)
T KOG4341|consen  138 GFLKELSLRGCRAVGDS------SLRTFA--SNCPNIEHLALYGCKKITDSSLLSLARYCRKLRHLNLHSCSSITDVSLK  209 (483)
T ss_pred             cccccccccccccCCcc------hhhHHh--hhCCchhhhhhhcceeccHHHHHHHHHhcchhhhhhhcccchhHHHHHH
Confidence            35666666666542211      334444  7888888888888763211222222 4677888888877 445422  1


Q ss_pred             cccccCCCCCEEeecCC-cccc-----ccccccccceecccccccccccccccccccCcCCCccccceeeCCCcccChHh
Q 001843          711 DSTPILFCLATLDVSHT-KVQR-----LPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDY  784 (1007)
Q Consensus       711 ~~i~~L~~L~~L~L~~~-~l~~-----lP~~i~~Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~  784 (1007)
                      .-...+++|.+|++++| .++.     +-.+..+++.+.+.   +|...           .|+.|....           
T Consensus       210 ~la~gC~kL~~lNlSwc~qi~~~gv~~~~rG~~~l~~~~~k---GC~e~-----------~le~l~~~~-----------  264 (483)
T KOG4341|consen  210 YLAEGCRKLKYLNLSWCPQISGNGVQALQRGCKELEKLSLK---GCLEL-----------ELEALLKAA-----------  264 (483)
T ss_pred             HHHHhhhhHHHhhhccCchhhcCcchHHhccchhhhhhhhc---ccccc-----------cHHHHHHHh-----------
Confidence            12345778888888888 5543     11111111122112   22100           001110000           


Q ss_pred             hhcCCCCCeEEeeecC-CCchhhHHHHHHHhhcCCCCCeEEEeecCC-CCCCcccc-cCCCCCcEEEecccC--CC--CC
Q 001843          785 FRRLTSLRKLGLKCSS-TTSTSLKKEIIGAVLQLSELHSLKLICETP-SYLPLLEM-AEHYKLQKLYLSGHL--PP--NS  857 (1007)
Q Consensus       785 l~~L~~L~~L~l~~~~-~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~-~~~~~~~l-~~~~~L~~L~L~g~~--~~--lp  857 (1007)
                       +....+.++++..+. -....+.    ..-..+..|+.|..++... ....+..+ ..+++|+.|.++++.  ..  +.
T Consensus       265 -~~~~~i~~lnl~~c~~lTD~~~~----~i~~~c~~lq~l~~s~~t~~~d~~l~aLg~~~~~L~~l~l~~c~~fsd~~ft  339 (483)
T KOG4341|consen  265 -AYCLEILKLNLQHCNQLTDEDLW----LIACGCHALQVLCYSSCTDITDEVLWALGQHCHNLQVLELSGCQQFSDRGFT  339 (483)
T ss_pred             -ccChHhhccchhhhccccchHHH----HHhhhhhHhhhhcccCCCCCchHHHHHHhcCCCceEEEeccccchhhhhhhh
Confidence             011112222222222 1111222    2223344555555554221 11122222 234566666666644  11  11


Q ss_pred             cCccCCCCCCceEEEEEeeecCCCC-cCc-cccCCCCcEEEeecCCcCCCc----eeecCCCCCCCcEEEeccCCCCcce
Q 001843          858 VIGDRSFPPNVVTLTLSQLRLEYDP-MPI-LGRLRQLKILRLFGGSYTGEE----MSCSSGEFPNLLVLKLWKLNRLRQW  931 (1007)
Q Consensus       858 ~~~i~~~l~~L~~L~L~~~~l~~~~-~~~-l~~Lp~L~~L~L~~~~~~~~~----l~~~~~~fp~L~~L~L~~~~~L~~l  931 (1007)
                      . .-.+ .+.|+.|++..|.+..+. +.. -.++|.|+.|.|+.+.....+    +.....+...|+.|.|++|+.+++-
T Consensus       340 ~-l~rn-~~~Le~l~~e~~~~~~d~tL~sls~~C~~lr~lslshce~itD~gi~~l~~~~c~~~~l~~lEL~n~p~i~d~  417 (483)
T KOG4341|consen  340 M-LGRN-CPHLERLDLEECGLITDGTLASLSRNCPRLRVLSLSHCELITDEGIRHLSSSSCSLEGLEVLELDNCPLITDA  417 (483)
T ss_pred             h-hhcC-ChhhhhhcccccceehhhhHhhhccCCchhccCChhhhhhhhhhhhhhhhhccccccccceeeecCCCCchHH
Confidence            1 1123 667777777777532222 222 235778888888744332222    1122345778999999999887765


Q ss_pred             EEc-CCCCccccEeEeeccCCCC---CCcCccccccCccEEEecc--CCccc
Q 001843          932 RIK-EGAMPCLRQLEIRSCGYLV---PPTGLKHVTSSLREFLLTN--MPSTF  977 (1007)
Q Consensus       932 ~~~-~~~~p~L~~L~l~~c~~L~---lp~~l~~L~~~L~~L~l~~--c~~~~  977 (1007)
                      ..+ ...+++|+.+++.+|....   +-..-.++ |+++...+..  .|..|
T Consensus       418 ~Le~l~~c~~Leri~l~~~q~vtk~~i~~~~~~l-p~i~v~a~~a~~t~p~~  468 (483)
T KOG4341|consen  418 TLEHLSICRNLERIELIDCQDVTKEAISRFATHL-PNIKVHAYFAPVTPPGF  468 (483)
T ss_pred             HHHHHhhCcccceeeeechhhhhhhhhHHHHhhC-ccceehhhccCCCCccc
Confidence            433 2458899999999999887   33334667 7777665543  34444

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=97.66  E-value=6.7e-06  Score=87.49  Aligned_cols=247  Identities=17%  Similarity=0.097  Sum_probs=135.3

Q ss_pred             cCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCC--CcCCCc-------cccCCCcCcEEecc
Q 001843          632 LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKP--MLTNNN-------ALGRLPFLEYLGLR  702 (1007)
Q Consensus       632 ~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~--~~~lp~-------~i~~L~~Lr~L~L~  702 (1007)
                      .....+..|.+++|.+......    .+...+  .+-+.||..++|+---.  ..++|.       .+-.+++|++|+||
T Consensus        27 ~~~~s~~~l~lsgnt~G~EAa~----~i~~~L--~~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~L~~ldLS  100 (382)
T KOG1909|consen   27 EPMDSLTKLDLSGNTFGTEAAR----AIAKVL--ASKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPKLQKLDLS  100 (382)
T ss_pred             cccCceEEEeccCCchhHHHHH----HHHHHH--hhcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCceeEeecc
Confidence            4455666677777666321211    334444  56667777777754211  113342       23345577888887


Q ss_pred             cCCCc-----ccCcccccCCCCCEEeecCCcccccccc-ccc-cceecccccccccccccccccccCcCCCccccceeeC
Q 001843          703 STFID-----SLPDSTPILFCLATLDVSHTKVQRLPYA-FWP-SRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIK  775 (1007)
Q Consensus       703 ~n~i~-----~LP~~i~~L~~L~~L~L~~~~l~~lP~~-i~~-Lr~L~l~~~~~~~~~~~~p~~i~~L~~L~~L~~~~~~  775 (1007)
                      .|-+.     .+-.-|..+..|++|.|.+|.+...... +++ |.+|...            ..++.-+.|+++. +..+
T Consensus       101 DNA~G~~g~~~l~~ll~s~~~L~eL~L~N~Glg~~ag~~l~~al~~l~~~------------kk~~~~~~Lrv~i-~~rN  167 (382)
T KOG1909|consen  101 DNAFGPKGIRGLEELLSSCTDLEELYLNNCGLGPEAGGRLGRALFELAVN------------KKAASKPKLRVFI-CGRN  167 (382)
T ss_pred             ccccCccchHHHHHHHHhccCHHHHhhhcCCCChhHHHHHHHHHHHHHHH------------hccCCCcceEEEE-eecc
Confidence            77654     2223356677888888888866543221 111 1233211            1122334455542 1222


Q ss_pred             CCcc----cChHhhhcCCCCCeEEeeecC---CCchhhHHHHHHHhhcCCCCCeEEEeecCCCCC----CcccccCCCCC
Q 001843          776 ADEV----QSLDYFRRLTSLRKLGLKCSS---TTSTSLKKEIIGAVLQLSELHSLKLICETPSYL----PLLEMAEHYKL  844 (1007)
Q Consensus       776 ~~~~----~~~~~l~~L~~L~~L~l~~~~---~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~----~~~~l~~~~~L  844 (1007)
                      +...    .....+...+.|+.+.+..+.   .....+.    ..+..+++|+.|+|..|.....    .-..++..++|
T Consensus       168 rlen~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~----eal~~~~~LevLdl~DNtft~egs~~LakaL~s~~~L  243 (382)
T KOG1909|consen  168 RLENGGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALA----EALEHCPHLEVLDLRDNTFTLEGSVALAKALSSWPHL  243 (382)
T ss_pred             ccccccHHHHHHHHHhccccceEEEecccccCchhHHHH----HHHHhCCcceeeecccchhhhHHHHHHHHHhcccchh
Confidence            1111    122335666778888877766   1122233    6777788888888877544321    12345566788


Q ss_pred             cEEEecccC-C-C----CCcCccCCCCCCceEEEEEeeecCCCCc----CccccCCCCcEEEeecCCc
Q 001843          845 QKLYLSGHL-P-P----NSVIGDRSFPPNVVTLTLSQLRLEYDPM----PILGRLRQLKILRLFGGSY  902 (1007)
Q Consensus       845 ~~L~L~g~~-~-~----lp~~~i~~~l~~L~~L~L~~~~l~~~~~----~~l~~Lp~L~~L~L~~~~~  902 (1007)
                      +.|+++.|. . .    +-...-.. .|+|..|.|.+|.++....    ..+...|.|+.|+|++|.+
T Consensus       244 ~El~l~dcll~~~Ga~a~~~al~~~-~p~L~vl~l~gNeIt~da~~~la~~~~ek~dL~kLnLngN~l  310 (382)
T KOG1909|consen  244 RELNLGDCLLENEGAIAFVDALKES-APSLEVLELAGNEITRDAALALAACMAEKPDLEKLNLNGNRL  310 (382)
T ss_pred             eeecccccccccccHHHHHHHHhcc-CCCCceeccCcchhHHHHHHHHHHHHhcchhhHHhcCCcccc
Confidence            888887765 1 1    11101123 6788888888887765432    2244588899999987776

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=97.64  E-value=0.00063  Score=73.75  Aligned_cols=145  Identities=17%  Similarity=0.289  Sum_probs=89.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHh-hhhhhhcc---ccCHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQID-ESLLKVEA---TLSAEELMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~-~~~~~~~~---~~~~~~l~~~  349 (1007)
                      ..|-|+|..|.|||.+.+++++..  .   -..+|+++-  ..+....++..|+.+.+ .+......   ..+....+..
T Consensus        31 S~~~iyG~sgTGKT~~~r~~l~~~--n---~~~vw~n~~--ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~  103 (438)
T KOG2543|consen   31 SIVHIYGHSGTGKTYLVRQLLRKL--N---LENVWLNCV--ECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYL  103 (438)
T ss_pred             eeEEEeccCCCchhHHHHHHHhhc--C---CcceeeehH--HhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHH
Confidence            778999999999999999999943  2   235899988  99999999999999995 22001111   1223333444


Q ss_pred             HHH--HcC--CCcEEEEEeCcCccCchhhhhhc-----cccCCCCCCcEEEEEcCCCcccccc---cCCcc-eeeecCCC
Q 001843          350 ITQ--ALD--DSTFLIVMENAEHQKSQVWDSFL-----GKLCSFTQCGKIIITTSSTEDFVEP---LGAAF-STLHVPGL  416 (1007)
Q Consensus       350 l~~--~L~--~kr~LlVlDdv~~~~~~~~~~l~-----~l~~~~~~gs~IliTTR~~~~va~~---~~~~~-~~~~l~~L  416 (1007)
                      +.+  ...  ++.++||||+++  ...+.+.+.     .+..-.....-+|+++-..- -...   .+..+ .++..+.-
T Consensus       104 l~q~~~~t~~d~~~~liLDnad--~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~-e~~y~~n~g~~~i~~l~fP~Y  180 (438)
T KOG2543|consen  104 LVQWPAATNRDQKVFLILDNAD--ALRDMDAILLQCLFRLYELLNEPTIVIILSAPSC-EKQYLINTGTLEIVVLHFPQY  180 (438)
T ss_pred             HHhhHHhhccCceEEEEEcCHH--hhhccchHHHHHHHHHHHHhCCCceEEEEecccc-HHHhhcccCCCCceEEecCCC
Confidence            444  222  468999999998  433333222     22211122233445444332 2222   23222 67778888


Q ss_pred             CHHHHHHHHHhh
Q 001843          417 GKNESWELFLKK  428 (1007)
Q Consensus       417 ~~~ea~~Lf~~~  428 (1007)
                      +.+|-.+++.+.
T Consensus       181 s~~e~~~Il~~~  192 (438)
T KOG2543|consen  181 SVEETQVILSRD  192 (438)
T ss_pred             CHHHHHHHHhcC
Confidence            999999888664

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.63  E-value=0.00059  Score=81.76  Aligned_cols=102  Identities=9%  Similarity=0.050  Sum_probs=63.2

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+....+.+. .+-.. ...+.+|++|.+...+.......+..+++.+++.++....+.+.+.....
T Consensus       126 ~~~KVvIIdEad~Lt~~a~naLLK~LEeP-p~~tv~IL~t~~~~kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi  204 (620)
T PRK14954        126 GRYRVYIIDEVHMLSTAAFNAFLKTLEEP-PPHAIFIFATTELHKIPATIASRCQRFNFKRIPLDEIQSQLQMICRAEGI  204 (620)
T ss_pred             CCCEEEEEeChhhcCHHHHHHHHHHHhCC-CCCeEEEEEeCChhhhhHHHHhhceEEecCCCCHHHHHHHHHHHHHHcCC
Confidence            45568899999855556677776 44333 33455554443333265544444489999999999988777765543221


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCc-hHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLP-LRVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~  464 (1007)
                            .-..+.+..|++.++|.. .|+..+
T Consensus       205 ------~I~~eal~~La~~s~Gdlr~al~eL  229 (620)
T PRK14954        205 ------QIDADALQLIARKAQGSMRDAQSIL  229 (620)
T ss_pred             ------CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence                  112456788999999954 444443

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.63  E-value=0.0011  Score=77.62  Aligned_cols=102  Identities=8%  Similarity=0.028  Sum_probs=68.1

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+.+..+.+. .+-.. ...+++|++|.+...+.....+.+..+++.+++.++....+...+...+.
T Consensus       116 ~~~KVvIIDEad~Lt~~A~NALLK~LEEp-p~~t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi  194 (535)
T PRK08451        116 ARFKIFIIDEVHMLTKEAFNALLKTLEEP-PSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGV  194 (535)
T ss_pred             CCeEEEEEECcccCCHHHHHHHHHHHhhc-CCceEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCC
Confidence            45568999999876677777776 44333 44566666665544355544555589999999999988888766543322


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                            .-..+.+..|++.++|.+--+..+
T Consensus       195 ------~i~~~Al~~Ia~~s~GdlR~alnl  218 (535)
T PRK08451        195 ------SYEPEALEILARSGNGSLRDTLTL  218 (535)
T ss_pred             ------CCCHHHHHHHHHHcCCcHHHHHHH
Confidence                  112457788999999988444333

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.62  E-value=0.00023  Score=74.93  Aligned_cols=162  Identities=15%  Similarity=0.148  Sum_probs=97.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceE-EEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRA-WVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~-wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      .....+|++|.|||+-|..++..---.+-|.+++ =.++|.....+   +.+.=             ..+...+......
T Consensus        58 p~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGis---vvr~K-------------ik~fakl~~~~~~  121 (346)
T KOG0989|consen   58 PHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGIS---VVREK-------------IKNFAKLTVLLKR  121 (346)
T ss_pred             ceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhccccccccc---chhhh-------------hcCHHHHhhcccc
Confidence            7889999999999999999887422234566643 23444111111   11000             0011111111100


Q ss_pred             Hc--CCCc-EEEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhh
Q 001843          353 AL--DDST-FLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKA  429 (1007)
Q Consensus       353 ~L--~~kr-~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a  429 (1007)
                      ..  ..++ -.||||+++....+.|..++...+.+...++.+..+-...++.....+.+.-|..++|..++..+-+...+
T Consensus       122 ~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia  201 (346)
T KOG0989|consen  122 SDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIA  201 (346)
T ss_pred             ccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhcCCCcchHHHHHHHHHHH
Confidence            00  1234 37899999987889999998333333666676555544432555444555788999999999999888887


Q ss_pred             ccccccccCCChHHHHHHHHHHHHcCCC
Q 001843          430 RIAEDVLQSRSSELIKLKKQILNICDGL  457 (1007)
Q Consensus       430 ~~~~~~~~~~~~~~~~~~~~I~~~c~Gl  457 (1007)
                      -..+.      +-..+..+.|++.++|-
T Consensus       202 ~~E~v------~~d~~al~~I~~~S~Gd  223 (346)
T KOG0989|consen  202 SKEGV------DIDDDALKLIAKISDGD  223 (346)
T ss_pred             HHhCC------CCCHHHHHHHHHHcCCc
Confidence            65443      23346677888888774

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=97.59  E-value=1e-05  Score=93.93  Aligned_cols=88  Identities=23%  Similarity=0.263  Sum_probs=52.9

Q ss_pred             cCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCc
Q 001843          632 LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPD  711 (1007)
Q Consensus       632 ~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~  711 (1007)
                      ..+++|..|.+.+|.+..         +...+  ..+.+|++|+|++|.|.  .+. .+..+..|+.|++++|.|+.++ 
T Consensus        92 ~~~~~l~~l~l~~n~i~~---------i~~~l--~~~~~L~~L~ls~N~I~--~i~-~l~~l~~L~~L~l~~N~i~~~~-  156 (414)
T KOG0531|consen   92 SKLKSLEALDLYDNKIEK---------IENLL--SSLVNLQVLDLSFNKIT--KLE-GLSTLTLLKELNLSGNLISDIS-  156 (414)
T ss_pred             ccccceeeeeccccchhh---------cccch--hhhhcchheeccccccc--ccc-chhhccchhhheeccCcchhcc-
Confidence            445666666666666531         12213  56667777777777666  342 4555666777777777766665 


Q ss_pred             ccccCCCCCEEeecCCccccccc
Q 001843          712 STPILFCLATLDVSHTKVQRLPY  734 (1007)
Q Consensus       712 ~i~~L~~L~~L~L~~~~l~~lP~  734 (1007)
                      .+..+.+|+.|++++|.+..++.
T Consensus       157 ~~~~l~~L~~l~l~~n~i~~ie~  179 (414)
T KOG0531|consen  157 GLESLKSLKLLDLSYNRIVDIEN  179 (414)
T ss_pred             CCccchhhhcccCCcchhhhhhh
Confidence            34456677777777776655543

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.59  E-value=0.00095  Score=78.24  Aligned_cols=101  Identities=10%  Similarity=0.021  Sum_probs=61.3

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEE-EcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIII-TTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~Ili-TTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      +++-++|+|+++.-+....+.+. .+-.. .....+|+ ||+... +.......+..+.+.+++.++-...+.+.+-...
T Consensus       118 ~~~KVvIIDEad~Lt~~a~naLLk~LEep-p~~~v~Il~tt~~~k-l~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~eg  195 (486)
T PRK14953        118 GKYKVYIIDEAHMLTKEAFNALLKTLEEP-PPRTIFILCTTEYDK-IPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEK  195 (486)
T ss_pred             CCeeEEEEEChhhcCHHHHHHHHHHHhcC-CCCeEEEEEECCHHH-HHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcC
Confidence            56669999999855555666666 44333 33444554 444333 4433333337899999999998888777654322


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                      .      ....+.+..|++.++|.+-.+..+
T Consensus       196 i------~id~~al~~La~~s~G~lr~al~~  220 (486)
T PRK14953        196 I------EYEEKALDLLAQASEGGMRDAASL  220 (486)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            1      112355677888888866544333

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.58  E-value=0.0013  Score=79.19  Aligned_cols=102  Identities=6%  Similarity=-0.022  Sum_probs=64.7

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+.+.++.+. .+-.. ...+.+|++|.+...+.......+..+++..++.++....+.+.+.....
T Consensus       120 ~~~KViIIDEad~Lt~~a~naLLK~LEeP-p~~tvfIL~t~~~~~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi  198 (620)
T PRK14948        120 ARWKVYVIDECHMLSTAAFNALLKTLEEP-PPRVVFVLATTDPQRVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEKESI  198 (620)
T ss_pred             CCceEEEEECccccCHHHHHHHHHHHhcC-CcCeEEEEEeCChhhhhHHHHhheeEEEecCCCHHHHHHHHHHHHHHhCC
Confidence            45568999999866666777777 44332 33445554454443355554554588999999999988877766543221


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                         .   -..+.+..|++.++|.+..+..+
T Consensus       199 ---~---is~~al~~La~~s~G~lr~A~~l  222 (620)
T PRK14948        199 ---E---IEPEALTLVAQRSQGGLRDAESL  222 (620)
T ss_pred             ---C---CCHHHHHHHHHHcCCCHHHHHHH
Confidence               1   11345778899999977544433

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.55  E-value=0.00058  Score=85.55  Aligned_cols=23  Identities=35%  Similarity=0.382  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-+.++|.+|+||||+|..+++.
T Consensus       209 ~n~lLvG~pGvGKTal~~~La~~  231 (852)
T TIGR03345       209 NNPILTGEAGVGKTAVVEGLALR  231 (852)
T ss_pred             CceeEECCCCCCHHHHHHHHHHH
Confidence            34469999999999999999983

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.54  E-value=0.0011  Score=76.85  Aligned_cols=156  Identities=13%  Similarity=0.135  Sum_probs=87.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCC--ceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFT--KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      ..+.|+|..|+|||+|++++++  .+.+...  .+++++..        ++...+...+...        .....    .
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~--~l~~~~~~~~v~yi~~~--------~~~~~~~~~~~~~--------~~~~~----~  194 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGN--EILENNPNAKVVYVSSE--------KFTNDFVNALRNN--------KMEEF----K  194 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHH--HHHHhCCCCcEEEEEHH--------HHHHHHHHHHHcC--------CHHHH----H
Confidence            5689999999999999999999  4444432  35555433        3334444443321        22222    2


Q ss_pred             HHcCCCcEEEEEeCcCccCch-hh-hhhc-cccCCCCCCcEEEEEcCCCc-c-------cccccCCcceeeecCCCCHHH
Q 001843          352 QALDDSTFLIVMENAEHQKSQ-VW-DSFL-GKLCSFTQCGKIIITTSSTE-D-------FVEPLGAAFSTLHVPGLGKNE  420 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~~~~-~~-~~l~-~l~~~~~~gs~IliTTR~~~-~-------va~~~~~~~~~~~l~~L~~~e  420 (1007)
                      +.++. .-+|||||++..... .+ +.+. .+-.-...+..+|||+.... .       +...+... ..+.+++.+.++
T Consensus       195 ~~~~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g-~~v~i~~pd~~~  272 (405)
T TIGR00362       195 EKYRS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWG-LVVDIEPPDLET  272 (405)
T ss_pred             HHHHh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCC-eEEEeCCCCHHH
Confidence            33322 338899999732222 11 2222 11110023456888876422 0       22222222 578999999999


Q ss_pred             HHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCch
Q 001843          421 SWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       421 a~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPL  459 (1007)
                      -..++.+.+.....   ..   .++....|++.+.|..-
T Consensus       273 r~~il~~~~~~~~~---~l---~~e~l~~ia~~~~~~~r  305 (405)
T TIGR00362       273 RLAILQKKAEEEGL---EL---PDEVLEFIAKNIRSNVR  305 (405)
T ss_pred             HHHHHHHHHHHcCC---CC---CHHHHHHHHHhcCCCHH
Confidence            99999888765322   11   24566677777766544

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.53  E-value=0.00027  Score=80.99  Aligned_cols=134  Identities=17%  Similarity=0.214  Sum_probs=72.7

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      ++-|.++|++|+|||++|+++++  .....     |+.++  .    .+    +.....+        .....+...+..
T Consensus       165 p~gvLL~GppGtGKT~lAkaia~--~~~~~-----~i~v~--~----~~----l~~~~~g--------~~~~~i~~~f~~  219 (389)
T PRK03992        165 PKGVLLYGPPGTGKTLLAKAVAH--ETNAT-----FIRVV--G----SE----LVQKFIG--------EGARLVRELFEL  219 (389)
T ss_pred             CCceEEECCCCCChHHHHHHHHH--HhCCC-----EEEee--h----HH----HhHhhcc--------chHHHHHHHHHH
Confidence            36789999999999999999999  34332     33333  1    11    1111100        011111112222


Q ss_pred             HcCCCcEEEEEeCcCcc-----------Cchhhhhhcccc---CCC--CCCcEEEEEcCCCccccccc-C--Ccceeeec
Q 001843          353 ALDDSTFLIVMENAEHQ-----------KSQVWDSFLGKL---CSF--TQCGKIIITTSSTEDFVEPL-G--AAFSTLHV  413 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~-----------~~~~~~~l~~l~---~~~--~~gs~IliTTR~~~~va~~~-~--~~~~~~~l  413 (1007)
                      .-...+.+|+||+++.-           +.+.+..+..+.   +++  ..+..||.||.....+-... .  .....+.+
T Consensus       220 a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v  299 (389)
T PRK03992        220 AREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEV  299 (389)
T ss_pred             HHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEE
Confidence            22356789999999731           011111222221   111  23556777777654122221 1  11167999


Q ss_pred             CCCCHHHHHHHHHhhhcc
Q 001843          414 PGLGKNESWELFLKKARI  431 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a~~  431 (1007)
                      ++.+.++-.++|+.+...
T Consensus       300 ~~P~~~~R~~Il~~~~~~  317 (389)
T PRK03992        300 PLPDEEGRLEILKIHTRK  317 (389)
T ss_pred             CCCCHHHHHHHHHHHhcc
Confidence            999999999999987654

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.50  E-value=0.0017  Score=76.24  Aligned_cols=178  Identities=14%  Similarity=0.161  Sum_probs=100.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCC--ceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFT--KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~--~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .-+.|+|..|+|||+|++++++  .+...+.  .+++++..        ++..++...+...        ...    .+.
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~--~~~~~~~~~~v~yi~~~--------~~~~~~~~~~~~~--------~~~----~~~  206 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGN--YILEKNPNAKVVYVTSE--------KFTNDFVNALRNN--------TME----EFK  206 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEEEHH--------HHHHHHHHHHHcC--------cHH----HHH
Confidence            5689999999999999999999  4555543  24555443        3333444443221        122    223


Q ss_pred             HHcCCCcEEEEEeCcCccCchh-h-hhhc----cccCCCCCCcEEEEEcCCCc-c-------cccccCCcceeeecCCCC
Q 001843          352 QALDDSTFLIVMENAEHQKSQV-W-DSFL----GKLCSFTQCGKIIITTSSTE-D-------FVEPLGAAFSTLHVPGLG  417 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~~~~~-~-~~l~----~l~~~~~~gs~IliTTR~~~-~-------va~~~~~~~~~~~l~~L~  417 (1007)
                      +.++ +.-+|||||+....... + +.+.    .+..   .|..|||||.... .       +...+... ..+++++++
T Consensus       207 ~~~~-~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~---~~~~iiits~~~p~~l~~l~~~l~SRl~~g-l~v~i~~pd  281 (450)
T PRK00149        207 EKYR-SVDVLLIDDIQFLAGKERTQEEFFHTFNALHE---AGKQIVLTSDRPPKELPGLEERLRSRFEWG-LTVDIEPPD  281 (450)
T ss_pred             HHHh-cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHH---CCCcEEEECCCCHHHHHHHHHHHHhHhcCC-eeEEecCCC
Confidence            3333 24489999997322111 1 2222    2222   3456888887542 1       12233332 689999999


Q ss_pred             HHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchH----HHHHHHH--hcCCCCChHHHHHHHHH
Q 001843          418 KNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLR----VVLLAGL--LSTKQPSYEEWSKVIER  484 (1007)
Q Consensus       418 ~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLa----i~~~g~~--L~~~~~~~~~w~~~l~~  484 (1007)
                      .++-.+++.+.+.....   ..+   +++..-|++.+.|..=.    +..+..+  +.++.-+....+.++..
T Consensus       282 ~~~r~~il~~~~~~~~~---~l~---~e~l~~ia~~~~~~~R~l~~~l~~l~~~~~~~~~~it~~~~~~~l~~  348 (450)
T PRK00149        282 LETRIAILKKKAEEEGI---DLP---DEVLEFIAKNITSNVRELEGALNRLIAYASLTGKPITLELAKEALKD  348 (450)
T ss_pred             HHHHHHHHHHHHHHcCC---CCC---HHHHHHHHcCcCCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHH
Confidence            99999999988764221   112   35677777777776543    2222222  22233345666666654

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.49  E-value=0.0018  Score=77.26  Aligned_cols=100  Identities=8%  Similarity=0.028  Sum_probs=64.9

Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      .+++-++|+|++..-+...++.+. .+-.. ...+.+|.+|.....+.......+..+++.+++.++-.+.+.+.+....
T Consensus       117 ~~~~KVvIIDEa~~Ls~~a~naLLK~LEep-p~~~vfI~~tte~~kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~~eg  195 (563)
T PRK06647        117 SSRYRVYIIDEVHMLSNSAFNALLKTIEEP-PPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQ  195 (563)
T ss_pred             cCCCEEEEEEChhhcCHHHHHHHHHhhccC-CCCEEEEEecCChHHhHHHHHHhceEEEecCCCHHHHHHHHHHHHHHcC
Confidence            356668999999866666677777 44433 4455666555443325544444447899999999998888877664322


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCchHH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPLai  461 (1007)
                      .      +-..+.+..|++.++|.+-.+
T Consensus       196 i------~id~eAl~lLa~~s~GdlR~a  217 (563)
T PRK06647        196 I------KYEDEALKWIAYKSTGSVRDA  217 (563)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHH
Confidence            1      122456777888999977433

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.49  E-value=0.0015  Score=70.05  Aligned_cols=175  Identities=13%  Similarity=0.164  Sum_probs=104.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC------CceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF------TKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELM  347 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F------~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~  347 (1007)
                      .-+.|||..|.|||+++++++...  -..+      -.++.|.+.  ..++...+...|+.+++.+   .....+...+.
T Consensus        62 p~lLivG~snnGKT~Ii~rF~~~h--p~~~d~~~~~~PVv~vq~P--~~p~~~~~Y~~IL~~lgaP---~~~~~~~~~~~  134 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMIIERFRRLH--PPQSDEDAERIPVVYVQMP--PEPDERRFYSAILEALGAP---YRPRDRVAKLE  134 (302)
T ss_pred             CceEEecCCCCcHHHHHHHHHHHC--CCCCCCCCccccEEEEecC--CCCChHHHHHHHHHHhCcc---cCCCCCHHHHH
Confidence            678999999999999999998742  1112      135666677  8899999999999999986   22334444555


Q ss_pred             HHHHHHcCC-CcEEEEEeCcCcc-------CchhhhhhccccCCCCCCcEEEEEcCCCcc-------cccccCCcceeee
Q 001843          348 WRITQALDD-STFLIVMENAEHQ-------KSQVWDSFLGKLCSFTQCGKIIITTSSTED-------FVEPLGAAFSTLH  412 (1007)
Q Consensus       348 ~~l~~~L~~-kr~LlVlDdv~~~-------~~~~~~~l~~l~~~~~~gs~IliTTR~~~~-------va~~~~~~~~~~~  412 (1007)
                      ..+...++. +-=+||+|.+.+.       ..+..+.++.+.+. -.-+-|.|-|+....       .++.+    .++.
T Consensus       135 ~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~Ne-L~ipiV~vGt~~A~~al~~D~QLa~RF----~~~~  209 (302)
T PF05621_consen  135 QQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNE-LQIPIVGVGTREAYRALRTDPQLASRF----EPFE  209 (302)
T ss_pred             HHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhc-cCCCeEEeccHHHHHHhccCHHHHhcc----CCcc
Confidence            555555544 3448999999741       12223333344333 344556666654220       22222    5666


Q ss_pred             cCCCCHH-HHHHHHHhhhccccccc-cCCChHHHHHHHHHHHHcCCCchHHH
Q 001843          413 VPGLGKN-ESWELFLKKARIAEDVL-QSRSSELIKLKKQILNICDGLPLRVV  462 (1007)
Q Consensus       413 l~~L~~~-ea~~Lf~~~a~~~~~~~-~~~~~~~~~~~~~I~~~c~GlPLai~  462 (1007)
                      ++.-..+ +...|+.....  .-+. ....-...+++..|...++|+.--+.
T Consensus       210 Lp~W~~d~ef~~LL~s~e~--~LPLr~~S~l~~~~la~~i~~~s~G~iG~l~  259 (302)
T PF05621_consen  210 LPRWELDEEFRRLLASFER--ALPLRKPSNLASPELARRIHERSEGLIGELS  259 (302)
T ss_pred             CCCCCCCcHHHHHHHHHHH--hCCCCCCCCCCCHHHHHHHHHHcCCchHHHH
Confidence            6665543 44445433211  1110 01122346789999999999875443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.48  E-value=1.9e-05  Score=82.05  Aligned_cols=59  Identities=22%  Similarity=0.216  Sum_probs=27.7

Q ss_pred             cccEEEecCCCCCCcCCCcccc-CCCcCcEEecccCCCcccC---cccccCCCCCEEeecCCc
Q 001843          670 MLKVLDLEGVYKPMLTNNNALG-RLPFLEYLGLRSTFIDSLP---DSTPILFCLATLDVSHTK  728 (1007)
Q Consensus       670 ~Lr~L~Ls~~~l~~~~lp~~i~-~L~~Lr~L~L~~n~i~~LP---~~i~~L~~L~~L~L~~~~  728 (1007)
                      .+..|.+.++.+........|+ ...+++.|+|.+|.|+...   .-+.+|+.|++|+|+.|.
T Consensus        46 a~ellvln~~~id~~gd~~~~~~~~~~v~elDL~~N~iSdWseI~~ile~lP~l~~LNls~N~  108 (418)
T KOG2982|consen   46 ALELLVLNGSIIDNEGDVMLFGSSVTDVKELDLTGNLISDWSEIGAILEQLPALTTLNLSCNS  108 (418)
T ss_pred             chhhheecCCCCCcchhHHHHHHHhhhhhhhhcccchhccHHHHHHHHhcCccceEeeccCCc
Confidence            3334555555544211112222 3455666666666555322   223456666666666553

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.46  E-value=0.0011  Score=79.68  Aligned_cols=102  Identities=10%  Similarity=-0.004  Sum_probs=64.2

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEE-EcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIII-TTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~Ili-TTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      +++-++|+|+++.-+....+.+. .+-.. ...+.+|+ ||.... +.....+.+..+++++++.++....+...+....
T Consensus       118 ~~~KVvIIdev~~Lt~~a~naLLk~LEep-p~~~~fIl~t~~~~k-l~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~eg  195 (576)
T PRK14965        118 SRYKIFIIDEVHMLSTNAFNALLKTLEEP-PPHVKFIFATTEPHK-VPITILSRCQRFDFRRIPLQKIVDRLRYIADQEG  195 (576)
T ss_pred             CCceEEEEEChhhCCHHHHHHHHHHHHcC-CCCeEEEEEeCChhh-hhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHHhC
Confidence            45558999999865666677676 44333 34455555 444444 6655555558899999999998877766543322


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCc-hHHHHHH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLP-LRVVLLA  465 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlP-Lai~~~g  465 (1007)
                      .      .-..+....|++.++|.. .|+..+-
T Consensus       196 i------~i~~~al~~la~~a~G~lr~al~~Ld  222 (576)
T PRK14965        196 I------SISDAALALVARKGDGSMRDSLSTLD  222 (576)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            1      112456677888888855 4555543

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=97.43  E-value=3e-06  Score=97.37  Aligned_cols=109  Identities=26%  Similarity=0.262  Sum_probs=62.9

Q ss_pred             HhhhcCCCCCeEEeeecCCCchhhHHHHHHHhhcCCCCCeEEEeecCCCCCCcccccCCCCCcEEEecccC-CCCCcCcc
Q 001843          783 DYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGD  861 (1007)
Q Consensus       783 ~~l~~L~~L~~L~l~~~~~~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i  861 (1007)
                      ..+.-++.|+.|+++.|.  ....     ..+..+++|++|+|++|......--+...+ .|+.|.|++|. ..+-  .+
T Consensus       181 ~SLqll~ale~LnLshNk--~~~v-----~~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc-~L~~L~lrnN~l~tL~--gi  250 (1096)
T KOG1859|consen  181 ESLQLLPALESLNLSHNK--FTKV-----DNLRRLPKLKHLDLSYNCLRHVPQLSMVGC-KLQLLNLRNNALTTLR--GI  250 (1096)
T ss_pred             HHHHHHHHhhhhccchhh--hhhh-----HHHHhcccccccccccchhccccccchhhh-hheeeeecccHHHhhh--hH
Confidence            345556677777777665  2211     455667777777777754433111111122 37777777765 4444  34


Q ss_pred             CCCCCCceEEEEEeeecCC-CCcCccccCCCCcEEEeecCCc
Q 001843          862 RSFPPNVVTLTLSQLRLEY-DPMPILGRLRQLKILRLFGGSY  902 (1007)
Q Consensus       862 ~~~l~~L~~L~L~~~~l~~-~~~~~l~~Lp~L~~L~L~~~~~  902 (1007)
                      .+ +.+|..|+|++|-+.+ ..+..++.|..|+.|+|.+|..
T Consensus       251 e~-LksL~~LDlsyNll~~hseL~pLwsLs~L~~L~LeGNPl  291 (1096)
T KOG1859|consen  251 EN-LKSLYGLDLSYNLLSEHSELEPLWSLSSLIVLWLEGNPL  291 (1096)
T ss_pred             Hh-hhhhhccchhHhhhhcchhhhHHHHHHHHHHHhhcCCcc
Confidence            55 7777777777775533 2345566677777777776643

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.43  E-value=0.0029  Score=75.79  Aligned_cols=99  Identities=6%  Similarity=-0.006  Sum_probs=62.1

Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhcccc
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      .+++-++|+|+++.-....++.+. .+-.. .....+|++|.....+.......+..+++.+++.++....+...+...+
T Consensus       117 ~~~~kViIIDE~~~Lt~~a~naLLKtLEep-p~~~ifIlatt~~~ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~~eg  195 (559)
T PRK05563        117 EAKYKVYIIDEVHMLSTGAFNALLKTLEEP-PAHVIFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKYILDKEG  195 (559)
T ss_pred             cCCeEEEEEECcccCCHHHHHHHHHHhcCC-CCCeEEEEEeCChhhCcHHHHhHheEEecCCCCHHHHHHHHHHHHHHcC
Confidence            355668899999865666677776 44332 3344444444333325554444447899999999998888877664322


Q ss_pred             ccccCCChHHHHHHHHHHHHcCCCchH
Q 001843          434 DVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       434 ~~~~~~~~~~~~~~~~I~~~c~GlPLa  460 (1007)
                      .      .-..+.+..|++.++|-+--
T Consensus       196 i------~i~~~al~~ia~~s~G~~R~  216 (559)
T PRK05563        196 I------EYEDEALRLIARAAEGGMRD  216 (559)
T ss_pred             C------CCCHHHHHHHHHHcCCCHHH
Confidence            1      11235567788888887643

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=97.42  E-value=0.00094  Score=83.04  Aligned_cols=132  Identities=16%  Similarity=0.187  Sum_probs=66.4

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhh---cccCC-CceEEE-EecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHH
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVY---VKRHF-TKRAWV-HIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~---~~~~F-~~~~wv-~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      -+.++|.+|+|||++|+.+++.-.   +...+ +..+|. +++                .+...   .....+.+.....
T Consensus       205 n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~----------------~l~a~---~~~~g~~e~~l~~  265 (731)
T TIGR02639       205 NPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMG----------------SLLAG---TKYRGDFEERLKA  265 (731)
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHH----------------HHhhh---ccccchHHHHHHH
Confidence            456999999999999999998421   11111 333442 211                11000   0011122223333


Q ss_pred             HHHHc-CCCcEEEEEeCcCccC---------chhhhhhccccCCCCCCcEEEE-EcCCCcccc------cccCCcceeee
Q 001843          350 ITQAL-DDSTFLIVMENAEHQK---------SQVWDSFLGKLCSFTQCGKIII-TTSSTEDFV------EPLGAAFSTLH  412 (1007)
Q Consensus       350 l~~~L-~~kr~LlVlDdv~~~~---------~~~~~~l~~l~~~~~~gs~Ili-TTR~~~~va------~~~~~~~~~~~  412 (1007)
                      +.+.+ +.++.+|++|+++.-.         .+.-+.+++.... + .-++|- ||+ .+ ..      .........++
T Consensus       266 i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~-g-~i~~IgaTt~-~e-~~~~~~~d~al~rRf~~i~  341 (731)
T TIGR02639       266 VVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSS-G-KLRCIGSTTY-EE-YKNHFEKDRALSRRFQKID  341 (731)
T ss_pred             HHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhC-C-CeEEEEecCH-HH-HHHHhhhhHHHHHhCceEE
Confidence            33333 3468899999987210         1112223332222 1 223333 454 11 11      11111126789


Q ss_pred             cCCCCHHHHHHHHHhhh
Q 001843          413 VPGLGKNESWELFLKKA  429 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a  429 (1007)
                      +++++.++..+++....
T Consensus       342 v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       342 VGEPSIEETVKILKGLK  358 (731)
T ss_pred             eCCCCHHHHHHHHHHHH
Confidence            99999999999998654

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.41  E-value=0.0011  Score=77.01  Aligned_cols=131  Identities=18%  Similarity=0.213  Sum_probs=76.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+.|+|..|+|||+|++++++  .+....-.+++++..        .+...+...+...        .    ...+++.
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~--~l~~~~~~v~yi~~~--------~f~~~~~~~l~~~--------~----~~~f~~~  199 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVH--ALRESGGKILYVRSE--------LFTEHLVSAIRSG--------E----MQRFRQF  199 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHH--HHHHcCCCEEEeeHH--------HHHHHHHHHHhcc--------h----HHHHHHH
Confidence            5678999999999999999999  443333344555432        2333333333221        1    1223444


Q ss_pred             cCCCcEEEEEeCcCccCchhh--hhhc----cccCCCCCCcEEEEEcCCCc--------ccccccCCcceeeecCCCCHH
Q 001843          354 LDDSTFLIVMENAEHQKSQVW--DSFL----GKLCSFTQCGKIIITTSSTE--------DFVEPLGAAFSTLHVPGLGKN  419 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~--~~l~----~l~~~~~~gs~IliTTR~~~--------~va~~~~~~~~~~~l~~L~~~  419 (1007)
                      ++ ..-+|++||+.......|  +.+.    .+..   .|..||+||....        ++...+... ..+.+++++.+
T Consensus       200 ~~-~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~---~~k~IIlts~~~p~~l~~l~~rL~SR~~~G-l~~~l~~pd~e  274 (445)
T PRK12422        200 YR-NVDALFIEDIEVFSGKGATQEEFFHTFNSLHT---EGKLIVISSTCAPQDLKAMEERLISRFEWG-IAIPLHPLTKE  274 (445)
T ss_pred             cc-cCCEEEEcchhhhcCChhhHHHHHHHHHHHHH---CCCcEEEecCCCHHHHhhhHHHHHhhhcCC-eEEecCCCCHH
Confidence            43 344888899873322222  2222    2222   3457888886531        122333333 68899999999


Q ss_pred             HHHHHHHhhhcc
Q 001843          420 ESWELFLKKARI  431 (1007)
Q Consensus       420 ea~~Lf~~~a~~  431 (1007)
                      +-..++.+++-.
T Consensus       275 ~r~~iL~~k~~~  286 (445)
T PRK12422        275 GLRSFLERKAEA  286 (445)
T ss_pred             HHHHHHHHHHHH
Confidence            999999887754

>PRK08116 hypothetical protein; Validated

Probab=97.40  E-value=0.00032  Score=75.89  Aligned_cols=104  Identities=22%  Similarity=0.342  Sum_probs=60.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.++|..|+|||.||.++++  .+..+...+++++++        +++..+.......     ...+...    +.+.
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~--~l~~~~~~v~~~~~~--------~ll~~i~~~~~~~-----~~~~~~~----~~~~  175 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIAN--ELIEKGVPVIFVNFP--------QLLNRIKSTYKSS-----GKEDENE----IIRS  175 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HHHHcCCeEEEEEHH--------HHHHHHHHHHhcc-----ccccHHH----HHHH
Confidence            4688999999999999999999  444444456666654        3343333332211     1112222    2333


Q ss_pred             cCCCcEEEEEeCcCccCchhhhh--hccccCC-CCCCcEEEEEcCCC
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDS--FLGKLCS-FTQCGKIIITTSST  397 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~--l~~l~~~-~~~gs~IliTTR~~  397 (1007)
                      +..-. ||||||+..+....|..  +..+.+. ...+..+||||...
T Consensus       176 l~~~d-lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        176 LVNAD-LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             hcCCC-EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            44334 89999995445555644  2222221 13456799998754

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.37  E-value=0.0023  Score=69.95  Aligned_cols=136  Identities=13%  Similarity=0.078  Sum_probs=70.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+.++|.+|+||||+|+.++.-..-.......-|+.++  .    .    +++..+.+.        ........+.+.
T Consensus        59 ~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~--~----~----~l~~~~~g~--------~~~~~~~~~~~a  120 (284)
T TIGR02880        59 LHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVT--R----D----DLVGQYIGH--------TAPKTKEILKRA  120 (284)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEec--H----H----HHhHhhccc--------chHHHHHHHHHc
Confidence            368899999999999998887732111112222355554  1    1    122222111        111122222222


Q ss_pred             cCCCcEEEEEeCcCcc---------CchhhhhhccccCCCCCCcEEEEEcCCCcccccccCC------c-ceeeecCCCC
Q 001843          354 LDDSTFLIVMENAEHQ---------KSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGA------A-FSTLHVPGLG  417 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~---------~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~------~-~~~~~l~~L~  417 (1007)
                         ..-+|+||++..-         ..+.++.+..+.+....+.+||+++.... .-.....      . ...+++++++
T Consensus       121 ---~~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~-~~~~~~~np~L~sR~~~~i~fp~l~  196 (284)
T TIGR02880       121 ---MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDR-MDSFFESNPGFSSRVAHHVDFPDYS  196 (284)
T ss_pred             ---cCcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHH-HHHHHhhCHHHHhhCCcEEEeCCcC
Confidence               2358899998621         12223444422233144556666654322 2111110      0 1578999999


Q ss_pred             HHHHHHHHHhhhcc
Q 001843          418 KNESWELFLKKARI  431 (1007)
Q Consensus       418 ~~ea~~Lf~~~a~~  431 (1007)
                      .+|-.+++...+-.
T Consensus       197 ~edl~~I~~~~l~~  210 (284)
T TIGR02880       197 EAELLVIAGLMLKE  210 (284)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999998877643

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.35  E-value=0.0038  Score=69.06  Aligned_cols=175  Identities=14%  Similarity=0.168  Sum_probs=98.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhc-------------ccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccc
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYV-------------KRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEAT  340 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~-------------~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~  340 (1007)
                      ..+-++|..|+||+++|..+++.---             ....+...|+.-.  ...+-..+-.+.+...+.. ......
T Consensus        27 ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~--~~~~g~~~~~~~~~~~~~~-~~~~~~  103 (314)
T PRK07399         27 PAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPT--YQHQGKLITASEAEEAGLK-RKAPPQ  103 (314)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEecc--ccccccccchhhhhhcccc-cccccc
Confidence            68899999999999999988773111             1123445565311  0000000000111111100 000001


Q ss_pred             cCHHHHHHHHHHHc-----CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecC
Q 001843          341 LSAEELMWRITQAL-----DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVP  414 (1007)
Q Consensus       341 ~~~~~l~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~  414 (1007)
                      -..++ ++.+.+.+     .+++-++|+|+++..+....+.+. .+-.. . .+.+|++|.+...+.....+.+..+++.
T Consensus       104 I~id~-ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEP-p-~~~fILi~~~~~~Ll~TI~SRcq~i~f~  180 (314)
T PRK07399        104 IRLEQ-IREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEP-G-NGTLILIAPSPESLLPTIVSRCQIIPFY  180 (314)
T ss_pred             CcHHH-HHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCC-C-CCeEEEEECChHhCcHHHHhhceEEecC
Confidence            11122 22333333     356669999999866677777777 33333 3 3455555555544777777777999999


Q ss_pred             CCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHH
Q 001843          415 GLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVL  463 (1007)
Q Consensus       415 ~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~  463 (1007)
                      ++++++..+.+.+.......         ......++..++|.|..+..
T Consensus       181 ~l~~~~~~~~L~~~~~~~~~---------~~~~~~l~~~a~Gs~~~al~  220 (314)
T PRK07399        181 RLSDEQLEQVLKRLGDEEIL---------NINFPELLALAQGSPGAAIA  220 (314)
T ss_pred             CCCHHHHHHHHHHhhccccc---------hhHHHHHHHHcCCCHHHHHH
Confidence            99999999999886432111         11135788899999976544

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.35  E-value=0.0013  Score=76.56  Aligned_cols=152  Identities=12%  Similarity=0.170  Sum_probs=88.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC-C-ceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF-T-KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~-~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .-+.|+|..|+|||+|++++++  .+.... . .++|++..        +++.++...+...        ...    .++
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~--~l~~~~~~~~v~yi~~~--------~f~~~~~~~~~~~--------~~~----~f~  188 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYITSE--------KFLNDLVDSMKEG--------KLN----EFR  188 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHH--HHHHhCCCCeEEEEEHH--------HHHHHHHHHHhcc--------cHH----HHH
Confidence            4589999999999999999999  444433 2 35566543        3444554444321        112    233


Q ss_pred             HHcCCCcEEEEEeCcCccC-chhh-hhhc----cccCCCCCCcEEEEEcCCC-ccc-------ccccCCcceeeecCCCC
Q 001843          352 QALDDSTFLIVMENAEHQK-SQVW-DSFL----GKLCSFTQCGKIIITTSST-EDF-------VEPLGAAFSTLHVPGLG  417 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~~-~~~~-~~l~----~l~~~~~~gs~IliTTR~~-~~v-------a~~~~~~~~~~~l~~L~  417 (1007)
                      +.+..+.-+||+||+.... ...+ +.+.    .+.+   .|..||+||... ..+       ...+... ..+++++.+
T Consensus       189 ~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~---~~k~iIitsd~~p~~l~~l~~rL~SR~~~g-l~v~i~~pd  264 (440)
T PRK14088        189 EKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHD---SGKQIVICSDREPQKLSEFQDRLVSRFQMG-LVAKLEPPD  264 (440)
T ss_pred             HHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHH---cCCeEEEECCCCHHHHHHHHHHHhhHHhcC-ceEeeCCCC
Confidence            3333345589999997321 1111 1222    2332   245788888532 211       1122222 588999999


Q ss_pred             HHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCC
Q 001843          418 KNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGL  457 (1007)
Q Consensus       418 ~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~Gl  457 (1007)
                      .++-.+++.+.+.....   ..+   +++..-|++.+.|.
T Consensus       265 ~e~r~~IL~~~~~~~~~---~l~---~ev~~~Ia~~~~~~  298 (440)
T PRK14088        265 EETRKKIARKMLEIEHG---ELP---EEVLNFVAENVDDN  298 (440)
T ss_pred             HHHHHHHHHHHHHhcCC---CCC---HHHHHHHHhccccC
Confidence            99999999888754222   112   35566677776654

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.34  E-value=0.00052  Score=76.93  Aligned_cols=64  Identities=19%  Similarity=0.167  Sum_probs=45.5

Q ss_pred             CCCCcccEEEecCCCCCCcCCCccccCCCcCcEEeccc-CCCcccCcccccCCCCCEEeecCC-ccccccccc
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRS-TFIDSLPDSTPILFCLATLDVSHT-KVQRLPYAF  736 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~-n~i~~LP~~i~~L~~L~~L~L~~~-~l~~lP~~i  736 (1007)
                      ..+++++.|++++|.+.  .+| .+  ..+|+.|.+++ +.++.+|..+  ..+|++|++++| .+..+|..+
T Consensus        49 ~~~~~l~~L~Is~c~L~--sLP-~L--P~sLtsL~Lsnc~nLtsLP~~L--P~nLe~L~Ls~Cs~L~sLP~sL  114 (426)
T PRK15386         49 EEARASGRLYIKDCDIE--SLP-VL--PNELTEITIENCNNLTTLPGSI--PEGLEKLTVCHCPEISGLPESV  114 (426)
T ss_pred             HHhcCCCEEEeCCCCCc--ccC-CC--CCCCcEEEccCCCCcccCCchh--hhhhhheEccCccccccccccc
Confidence            56788888888888877  777 22  23588888877 5567777655  357888888877 777777654

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.32  E-value=0.0007  Score=76.81  Aligned_cols=97  Identities=14%  Similarity=0.162  Sum_probs=58.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +.|.++|++|+|||++|+++++.......|+.+.||+++  +.++..+.+..+.-    .  ...-........+.+...
T Consensus       195 ~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFH--psySYeDFI~G~rP----~--~vgy~~~~G~f~~~~~~A  266 (459)
T PRK11331        195 KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFH--QSYSYEDFIQGYRP----N--GVGFRRKDGIFYNFCQQA  266 (459)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeec--ccccHHHHhcccCC----C--CCCeEecCchHHHHHHHH
Confidence            456789999999999999999954444567888999998  87776665532210    0  000000011112222222


Q ss_pred             cC--CCcEEEEEeCcCccCchh-hhhhc
Q 001843          354 LD--DSTFLIVMENAEHQKSQV-WDSFL  378 (1007)
Q Consensus       354 L~--~kr~LlVlDdv~~~~~~~-~~~l~  378 (1007)
                      -.  +++++||+|++...+.+. +..+.
T Consensus       267 ~~~p~~~~vliIDEINRani~kiFGel~  294 (459)
T PRK11331        267 KEQPEKKYVFIIDEINRANLSKVFGEVM  294 (459)
T ss_pred             HhcccCCcEEEEehhhccCHHHhhhhhh
Confidence            22  478999999997544333 34443

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=97.32  E-value=0.0059  Score=68.19  Aligned_cols=187  Identities=12%  Similarity=0.148  Sum_probs=107.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+-|.|-+|.|||.+...|+.+..-...=..++++.+.  .-....+++..|...+...  . .......+....+.++
T Consensus       176 gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~--sl~~~~aiF~kI~~~~~q~--~-~s~~~~~~~~~~~~~h  250 (529)
T KOG2227|consen  176 GSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCT--SLTEASAIFKKIFSSLLQD--L-VSPGTGMQHLEKFEKH  250 (529)
T ss_pred             cceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeec--cccchHHHHHHHHHHHHHH--h-cCCchhHHHHHHHHHH
Confidence            678899999999999999999953221111234555544  5567888999998888443  1 1222225556666666


Q ss_pred             cCCC--cEEEEEeCcCcc---CchhhhhhccccCCCCCCcEEEEE---------cCCCcccccccCCcceeeecCCCCHH
Q 001843          354 LDDS--TFLIVMENAEHQ---KSQVWDSFLGKLCSFTQCGKIIIT---------TSSTEDFVEPLGAAFSTLHVPGLGKN  419 (1007)
Q Consensus       354 L~~k--r~LlVlDdv~~~---~~~~~~~l~~l~~~~~~gs~IliT---------TR~~~~va~~~~~~~~~~~l~~L~~~  419 (1007)
                      ....  -+|+|+|..+.-   +...+-.+..+|.  -.++|+|+.         -|.-.++-.........+..+|.+.+
T Consensus       251 ~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~--lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~  328 (529)
T KOG2227|consen  251 TKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPK--LPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKD  328 (529)
T ss_pred             HhcccceEEEEechhhHHhhcccceeeeehhccc--CCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHH
Confidence            6543  589999998732   1111111112222  234454442         22111011111222278889999999


Q ss_pred             HHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHh
Q 001843          420 ESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL  468 (1007)
Q Consensus       420 ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L  468 (1007)
                      +-.++|..+....... ...+...+-.|++++...|-+=-|+.+.-+.+
T Consensus       329 qI~~Il~~rl~~~~t~-~~~~~Aie~~ArKvaa~SGDlRkaLdv~R~ai  376 (529)
T KOG2227|consen  329 QIVEILQQRLSEESTS-IFLNAAIELCARKVAAPSGDLRKALDVCRRAI  376 (529)
T ss_pred             HHHHHHHHHHhccccc-ccchHHHHHHHHHhccCchhHHHHHHHHHHHH
Confidence            9999999886543332 12233445555555555555556665555444

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=97.29  E-value=0.0014  Score=74.77  Aligned_cols=133  Identities=17%  Similarity=0.210  Sum_probs=72.7

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      ++-+.++|++|.|||+||+++++  .....|   +.+..+        .+    .....+        .....+.+.+..
T Consensus       179 pkgvLL~GppGTGKT~LAkalA~--~l~~~f---i~i~~s--------~l----~~k~~g--------e~~~~lr~lf~~  233 (398)
T PTZ00454        179 PRGVLLYGPPGTGKTMLAKAVAH--HTTATF---IRVVGS--------EF----VQKYLG--------EGPRMVRDVFRL  233 (398)
T ss_pred             CceEEEECCCCCCHHHHHHHHHH--hcCCCE---EEEehH--------HH----HHHhcc--------hhHHHHHHHHHH
Confidence            37788999999999999999999  333332   222111        11    111101        111222223333


Q ss_pred             HcCCCcEEEEEeCcCcc-------C---chh----hhhhccccCCC--CCCcEEEEEcCCCcccccc-cC--Ccceeeec
Q 001843          353 ALDDSTFLIVMENAEHQ-------K---SQV----WDSFLGKLCSF--TQCGKIIITTSSTEDFVEP-LG--AAFSTLHV  413 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~-------~---~~~----~~~l~~l~~~~--~~gs~IliTTR~~~~va~~-~~--~~~~~~~l  413 (1007)
                      .....+.+|+||+++.-       .   ...    +..+....+++  ..+..||+||.....+-.. ..  -....+.+
T Consensus       234 A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~  313 (398)
T PTZ00454        234 ARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEF  313 (398)
T ss_pred             HHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEe
Confidence            34567899999998621       0   011    11222111111  2456788888766623222 11  11167899


Q ss_pred             CCCCHHHHHHHHHhhhc
Q 001843          414 PGLGKNESWELFLKKAR  430 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a~  430 (1007)
                      +..+.++-.++|..+..
T Consensus       314 ~~P~~~~R~~Il~~~~~  330 (398)
T PTZ00454        314 PLPDRRQKRLIFQTITS  330 (398)
T ss_pred             CCcCHHHHHHHHHHHHh
Confidence            99999998888886654

>CHL00181 cbbX CbbX; Provisional

Probab=97.28  E-value=0.0041  Score=67.97  Aligned_cols=135  Identities=14%  Similarity=0.103  Sum_probs=70.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.++|.+|+||||+|+.+++...-.+.-...-|+.++  .    .+    +.....+.        ........+.+.
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~--~----~~----l~~~~~g~--------~~~~~~~~l~~a  121 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVT--R----DD----LVGQYIGH--------TAPKTKEVLKKA  121 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEec--H----HH----HHHHHhcc--------chHHHHHHHHHc
Confidence            458899999999999999998842111111122255544  1    11    22222111        111112222222


Q ss_pred             cCCCcEEEEEeCcCcc---------Cchhhhhhc-cccCCCCCCcEEEEEcCCCccccccc------CCc-ceeeecCCC
Q 001843          354 LDDSTFLIVMENAEHQ---------KSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPL------GAA-FSTLHVPGL  416 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~---------~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~------~~~-~~~~~l~~L  416 (1007)
                         ..-+|+||++..-         ..+..+.+. .+.+. ....+||+++.... .....      ... ...+.++++
T Consensus       122 ---~ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~-~~~~~vI~ag~~~~-~~~~~~~np~L~sR~~~~i~F~~~  196 (287)
T CHL00181        122 ---MGGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQ-RDDLVVIFAGYKDR-MDKFYESNPGLSSRIANHVDFPDY  196 (287)
T ss_pred             ---cCCEEEEEccchhccCCCccchHHHHHHHHHHHHhcC-CCCEEEEEeCCcHH-HHHHHhcCHHHHHhCCceEEcCCc
Confidence               2349999999621         122223333 23233 44556666664322 22111      011 157899999


Q ss_pred             CHHHHHHHHHhhhcc
Q 001843          417 GKNESWELFLKKARI  431 (1007)
Q Consensus       417 ~~~ea~~Lf~~~a~~  431 (1007)
                      +.+|-.+++...+..
T Consensus       197 t~~el~~I~~~~l~~  211 (287)
T CHL00181        197 TPEELLQIAKIMLEE  211 (287)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999999988877654

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.27  E-value=0.0012  Score=63.08  Aligned_cols=21  Identities=52%  Similarity=0.676  Sum_probs=19.5

Q ss_pred             EEEEcCCCChHHHHHHHHHhh
Q 001843          276 IALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      |.|+|.+|+||||+|+.+++.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            579999999999999999994

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=97.24  E-value=0.0034  Score=70.59  Aligned_cols=135  Identities=16%  Similarity=0.197  Sum_probs=84.7

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      ...+.|||..|.|||.|++++.+  ......+....++++      ......+++..+...            -.+.+++
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign--~~~~~~~~a~v~y~~------se~f~~~~v~a~~~~------------~~~~Fk~  172 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGN--EALANGPNARVVYLT------SEDFTNDFVKALRDN------------EMEKFKE  172 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHH--HHHhhCCCceEEecc------HHHHHHHHHHHHHhh------------hHHHHHH
Confidence            47899999999999999999999  666666644444443      233444444444332            2334555


Q ss_pred             HcCCCcEEEEEeCcCccCc-hhhhh-hc----cccCCCCCCcEEEEEcCCCcc--------cccccCCcceeeecCCCCH
Q 001843          353 ALDDSTFLIVMENAEHQKS-QVWDS-FL----GKLCSFTQCGKIIITTSSTED--------FVEPLGAAFSTLHVPGLGK  418 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~~~-~~~~~-l~----~l~~~~~~gs~IliTTR~~~~--------va~~~~~~~~~~~l~~L~~  418 (1007)
                      ..  .-=++++||++.-.. +.|+. +.    .+...   |-.||+|++....        +...+... -++++.+++.
T Consensus       173 ~y--~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~---~kqIvltsdr~P~~l~~~~~rL~SR~~~G-l~~~I~~Pd~  246 (408)
T COG0593         173 KY--SLDLLLIDDIQFLAGKERTQEEFFHTFNALLEN---GKQIVLTSDRPPKELNGLEDRLRSRLEWG-LVVEIEPPDD  246 (408)
T ss_pred             hh--ccCeeeechHhHhcCChhHHHHHHHHHHHHHhc---CCEEEEEcCCCchhhccccHHHHHHHhce-eEEeeCCCCH
Confidence            55  334889999973211 12221 21    44433   4489999975431        22333344 7899999999


Q ss_pred             HHHHHHHHhhhcccc
Q 001843          419 NESWELFLKKARIAE  433 (1007)
Q Consensus       419 ~ea~~Lf~~~a~~~~  433 (1007)
                      +....++.+.+....
T Consensus       247 e~r~aiL~kka~~~~  261 (408)
T COG0593         247 ETRLAILRKKAEDRG  261 (408)
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999988765443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.23  E-value=0.003  Score=74.69  Aligned_cols=154  Identities=12%  Similarity=0.194  Sum_probs=86.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC--CceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF--TKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      ..+.|+|..|+|||.|++++++  .....+  -.+++++..        +++.++...+...        ..    ..++
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~--~a~~~~~g~~V~Yitae--------ef~~el~~al~~~--------~~----~~f~  372 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGH--YARRLYPGTRVRYVSSE--------EFTNEFINSIRDG--------KG----DSFR  372 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEeeHH--------HHHHHHHHHHHhc--------cH----HHHH
Confidence            4589999999999999999999  444333  234555443        3333443333221        11    2233


Q ss_pred             HHcCCCcEEEEEeCcCccCc-hhhhh-hccccCC-CCCCcEEEEEcCCCc--------ccccccCCcceeeecCCCCHHH
Q 001843          352 QALDDSTFLIVMENAEHQKS-QVWDS-FLGKLCS-FTQCGKIIITTSSTE--------DFVEPLGAAFSTLHVPGLGKNE  420 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~~~-~~~~~-l~~l~~~-~~~gs~IliTTR~~~--------~va~~~~~~~~~~~l~~L~~~e  420 (1007)
                      +.+.. -=+|||||+..... +.|.. +..+.+. ...|..|||||....        ++...+... -++++++.+.+.
T Consensus       373 ~~y~~-~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~G-Lvv~I~~PD~Et  450 (617)
T PRK14086        373 RRYRE-MDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWG-LITDVQPPELET  450 (617)
T ss_pred             HHhhc-CCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcC-ceEEcCCCCHHH
Confidence            33332 34788999974322 22322 2211111 133557888888631        122333333 788999999999


Q ss_pred             HHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCC
Q 001843          421 SWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGL  457 (1007)
Q Consensus       421 a~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~Gl  457 (1007)
                      -.+++.+++....-   ..+   ++++.-|++.+.+.
T Consensus       451 R~aIL~kka~~r~l---~l~---~eVi~yLa~r~~rn  481 (617)
T PRK14086        451 RIAILRKKAVQEQL---NAP---PEVLEFIASRISRN  481 (617)
T ss_pred             HHHHHHHHHHhcCC---CCC---HHHHHHHHHhccCC
Confidence            99999988765332   112   34455555555433

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.22  E-value=0.0014  Score=82.45  Aligned_cols=133  Identities=20%  Similarity=0.200  Sum_probs=65.4

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhh---cccCC-CceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHH
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVY---VKRHF-TKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~---~~~~F-~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      -+.++|.+|+|||++|..++..-.   +.... +..+|. ++      .       ...+.+.    ....+.+.....+
T Consensus       202 n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~-l~------~-------~~l~ag~----~~~ge~e~rl~~i  263 (821)
T CHL00095        202 NPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVIT-LD------I-------GLLLAGT----KYRGEFEERLKRI  263 (821)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE-ee------H-------HHHhccC----CCccHHHHHHHHH
Confidence            446999999999999999988421   11111 234443 22      0       0001010    0111122222222


Q ss_pred             HHHc-CCCcEEEEEeCcCcc-------Cchhhhhhc-cccCCCCCCcEEEEEcCCCccccc------ccCCcceeeecCC
Q 001843          351 TQAL-DDSTFLIVMENAEHQ-------KSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVE------PLGAAFSTLHVPG  415 (1007)
Q Consensus       351 ~~~L-~~kr~LlVlDdv~~~-------~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~------~~~~~~~~~~l~~  415 (1007)
                      .+.+ ..++.+|++|++..-       .......+. +.... + .-++|.+|.... ...      .+......+.+..
T Consensus       264 ~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~r-g-~l~~IgaTt~~e-y~~~ie~D~aL~rRf~~I~v~e  340 (821)
T CHL00095        264 FDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALAR-G-ELQCIGATTLDE-YRKHIEKDPALERRFQPVYVGE  340 (821)
T ss_pred             HHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhC-C-CcEEEEeCCHHH-HHHHHhcCHHHHhcceEEecCC
Confidence            2222 356899999999521       011112222 22222 2 234444444332 211      1222226788999


Q ss_pred             CCHHHHHHHHHhh
Q 001843          416 LGKNESWELFLKK  428 (1007)
Q Consensus       416 L~~~ea~~Lf~~~  428 (1007)
                      .+.++...++...
T Consensus       341 p~~~e~~aILr~l  353 (821)
T CHL00095        341 PSVEETIEILFGL  353 (821)
T ss_pred             CCHHHHHHHHHHH
Confidence            9999988887653

>TIGR00763 lon ATP-dependent protease La

Probab=97.22  E-value=0.01  Score=74.42  Aligned_cols=28  Identities=32%  Similarity=0.700  Sum_probs=23.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  303 (1007)
                      .++.++|++|+|||++|+.+++  .....|
T Consensus       348 ~~lll~GppG~GKT~lAk~iA~--~l~~~~  375 (775)
T TIGR00763       348 PILCLVGPPGVGKTSLGKSIAK--ALNRKF  375 (775)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HhcCCe
Confidence            5899999999999999999999  454444

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK06620 hypothetical protein; Validated

Probab=97.21  E-value=0.002  Score=67.23  Aligned_cols=132  Identities=14%  Similarity=0.055  Sum_probs=74.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +.+.|+|++|+|||+|++.+++..  ..     .++...    +.                       . +       +.
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~--~~-----~~~~~~----~~-----------------------~-~-------~~   82 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLS--NA-----YIIKDI----FF-----------------------N-E-------EI   82 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhcc--CC-----EEcchh----hh-----------------------c-h-------hH
Confidence            678999999999999999988832  11     122110    00                       0 0       01


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCccc------ccccCCcceeeecCCCCHHHHHHHHH
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDF------VEPLGAAFSTLHVPGLGKNESWELFL  426 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~v------a~~~~~~~~~~~l~~L~~~ea~~Lf~  426 (1007)
                      + ...-++++||+..-.....-.+. .+..   .|..||+|++....-      ...+... .++++++++.++-..++.
T Consensus        83 ~-~~~d~lliDdi~~~~~~~lf~l~N~~~e---~g~~ilits~~~p~~l~l~~L~SRl~~g-l~~~l~~pd~~~~~~~l~  157 (214)
T PRK06620         83 L-EKYNAFIIEDIENWQEPALLHIFNIINE---KQKYLLLTSSDKSRNFTLPDLSSRIKSV-LSILLNSPDDELIKILIF  157 (214)
T ss_pred             H-hcCCEEEEeccccchHHHHHHHHHHHHh---cCCEEEEEcCCCccccchHHHHHHHhCC-ceEeeCCCCHHHHHHHHH
Confidence            1 12347889999721211111222 2223   356899999866511      1111222 589999999999888887


Q ss_pred             hhhccccccccCCChHHHHHHHHHHHHcCCCc
Q 001843          427 KKARIAEDVLQSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       427 ~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlP  458 (1007)
                      +.+....-   .   -.+++..-|++++.|--
T Consensus       158 k~~~~~~l---~---l~~ev~~~L~~~~~~d~  183 (214)
T PRK06620        158 KHFSISSV---T---ISRQIIDFLLVNLPREY  183 (214)
T ss_pred             HHHHHcCC---C---CCHHHHHHHHHHccCCH
Confidence            76643211   1   12456666777666544

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.21  E-value=0.0061  Score=66.04  Aligned_cols=135  Identities=19%  Similarity=0.195  Sum_probs=67.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+.++|++|+||||+|+.+++...-...-....++.++  .    .++    ....-+        .......+.+.+.
T Consensus        43 ~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~--~----~~l----~~~~~g--------~~~~~~~~~~~~a  104 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVE--R----ADL----VGEYIG--------HTAQKTREVIKKA  104 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEec--H----HHh----hhhhcc--------chHHHHHHHHHhc
Confidence            678899999999999999998832111111122234333  1    111    111100        0111222222222


Q ss_pred             cCCCcEEEEEeCcCccC--------chhhhhhc-cccCCCCCCcEEEEEcCCCccccc------ccCCcc-eeeecCCCC
Q 001843          354 LDDSTFLIVMENAEHQK--------SQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVE------PLGAAF-STLHVPGLG  417 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~--------~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~------~~~~~~-~~~~l~~L~  417 (1007)
                         ..-+|++|+++.-.        .+..+.+. .+.+. .....+++++.... ...      ...... ..+.+++++
T Consensus       105 ---~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~-~~~~~vila~~~~~-~~~~~~~~p~L~sRf~~~i~f~~~~  179 (261)
T TIGR02881       105 ---LGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDN-RNEFVLILAGYSDE-MDYFLSLNPGLRSRFPISIDFPDYT  179 (261)
T ss_pred             ---cCCEEEEechhhhccCCccchHHHHHHHHHHHHhcc-CCCEEEEecCCcch-hHHHHhcChHHHhccceEEEECCCC
Confidence               23488999997311        12333343 33222 23334455543322 211      111111 568899999


Q ss_pred             HHHHHHHHHhhhcc
Q 001843          418 KNESWELFLKKARI  431 (1007)
Q Consensus       418 ~~ea~~Lf~~~a~~  431 (1007)
                      .++-.+++.+.+..
T Consensus       180 ~~el~~Il~~~~~~  193 (261)
T TIGR02881       180 VEELMEIAERMVKE  193 (261)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999877654

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.20  E-value=0.0081  Score=66.28  Aligned_cols=97  Identities=9%  Similarity=0.107  Sum_probs=68.7

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++-++|+|+++.-+...-+.+. .+-.- ..++.+|++|.+...+.....+.+..+.+.+++.+++.+.+.....    
T Consensus       112 g~~kV~iI~~ae~m~~~AaNaLLKtLEEP-p~~~~fiL~~~~~~~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~~~----  186 (319)
T PRK08769        112 GIAQVVIVDPADAINRAACNALLKTLEEP-SPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEALAWLLAQGV----  186 (319)
T ss_pred             CCcEEEEeccHhhhCHHHHHHHHHHhhCC-CCCCeEEEEECChhhCchHHHhhheEeeCCCcCHHHHHHHHHHcCC----
Confidence            45669999999866666666666 33333 4567777777766547777777778999999999999888865411    


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLLA  465 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g  465 (1007)
                           +   +..+..++..++|.|+....+.
T Consensus       187 -----~---~~~a~~~~~l~~G~p~~A~~~~  209 (319)
T PRK08769        187 -----S---ERAAQEALDAARGHPGLAAQWL  209 (319)
T ss_pred             -----C---hHHHHHHHHHcCCCHHHHHHHh
Confidence                 1   2236678999999998765443

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=97.19  E-value=0.0013  Score=75.56  Aligned_cols=133  Identities=18%  Similarity=0.231  Sum_probs=72.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-+.++|.+|+|||++|+++++  .....|   +.+..+  .          +.....+.        ....+...+...
T Consensus       218 ~gVLL~GPPGTGKT~LAraIA~--el~~~f---i~V~~s--e----------L~~k~~Ge--------~~~~vr~lF~~A  272 (438)
T PTZ00361        218 KGVILYGPPGTGKTLLAKAVAN--ETSATF---LRVVGS--E----------LIQKYLGD--------GPKLVRELFRVA  272 (438)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH--hhCCCE---EEEecc--h----------hhhhhcch--------HHHHHHHHHHHH
Confidence            6678999999999999999999  444444   222222  1          11111110        111122223333


Q ss_pred             cCCCcEEEEEeCcCcc--------Cc--hh----hhhhccccCCC--CCCcEEEEEcCCCccccccc---CCcceeeecC
Q 001843          354 LDDSTFLIVMENAEHQ--------KS--QV----WDSFLGKLCSF--TQCGKIIITTSSTEDFVEPL---GAAFSTLHVP  414 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~--------~~--~~----~~~l~~l~~~~--~~gs~IliTTR~~~~va~~~---~~~~~~~~l~  414 (1007)
                      ....+.+|+||+++..        +.  ..    ...+....+++  ..+.+||+||.....+-..+   +-....+.++
T Consensus       273 ~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~  352 (438)
T PTZ00361        273 EENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFP  352 (438)
T ss_pred             HhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeC
Confidence            3467889999998521        00  00    11111111111  23567888887655222221   1111788999


Q ss_pred             CCCHHHHHHHHHhhhcc
Q 001843          415 GLGKNESWELFLKKARI  431 (1007)
Q Consensus       415 ~L~~~ea~~Lf~~~a~~  431 (1007)
                      ..+.++..++|..++..
T Consensus       353 ~Pd~~~R~~Il~~~~~k  369 (438)
T PTZ00361        353 NPDEKTKRRIFEIHTSK  369 (438)
T ss_pred             CCCHHHHHHHHHHHHhc
Confidence            99999999999877643

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.14  E-value=0.0021  Score=72.17  Aligned_cols=31  Identities=19%  Similarity=0.226  Sum_probs=14.3

Q ss_pred             CCCcEEEeccCCCCcceEEcCCCCccccEeEeec
Q 001843          915 PNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRS  948 (1007)
Q Consensus       915 p~L~~L~L~~~~~L~~l~~~~~~~p~L~~L~l~~  948 (1007)
                      ++|+.|.+.+|..+. +|  .+--++|+.|.++.
T Consensus       156 sSLk~L~Is~c~~i~-LP--~~LP~SLk~L~ls~  186 (426)
T PRK15386        156 PSLKTLSLTGCSNII-LP--EKLPESLQSITLHI  186 (426)
T ss_pred             CcccEEEecCCCccc-Cc--ccccccCcEEEecc
Confidence            356666666554321 11  11123566666554

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.11  E-value=0.0033  Score=79.44  Aligned_cols=23  Identities=35%  Similarity=0.499  Sum_probs=19.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-+.++|.+|+|||++|..++..
T Consensus       195 ~n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             CceEEEcCCCCCHHHHHHHHHHH
Confidence            34458999999999999999884

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.11  E-value=0.0029  Score=73.92  Aligned_cols=140  Identities=14%  Similarity=0.176  Sum_probs=74.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC-----CCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH-----FTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-----F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      +-+.++|++|.|||++|+++++  .+...     +....|+.+.  ..    +++.    ...+.     .......+..
T Consensus       217 ~GILLyGPPGTGKT~LAKAlA~--eL~~~i~~~~~~~~~fl~v~--~~----eLl~----kyvGe-----te~~ir~iF~  279 (512)
T TIGR03689       217 KGVLLYGPPGCGKTLIAKAVAN--SLAQRIGAETGDKSYFLNIK--GP----ELLN----KYVGE-----TERQIRLIFQ  279 (512)
T ss_pred             cceEEECCCCCcHHHHHHHHHH--hhccccccccCCceeEEecc--ch----hhcc----cccch-----HHHHHHHHHH
Confidence            6689999999999999999999  44333     2234555554  21    1111    11000     0001122222


Q ss_pred             HHHHHc-CCCcEEEEEeCcCcc----C---chh-----hhhhccccCCCC--CCcEEEEEcCCCccccccc-C--Cccee
Q 001843          349 RITQAL-DDSTFLIVMENAEHQ----K---SQV-----WDSFLGKLCSFT--QCGKIIITTSSTEDFVEPL-G--AAFST  410 (1007)
Q Consensus       349 ~l~~~L-~~kr~LlVlDdv~~~----~---~~~-----~~~l~~l~~~~~--~gs~IliTTR~~~~va~~~-~--~~~~~  410 (1007)
                      ..++.. .+++++|+||+++..    .   ...     ...+....+++.  .+..||.||-....+-..+ .  -....
T Consensus       280 ~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~LDgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~  359 (512)
T TIGR03689       280 RAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILRPGRLDVK  359 (512)
T ss_pred             HHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhcccccCCceEEEeccCChhhCCHhhcCccccceE
Confidence            233222 357899999999721    0   111     123332222211  2344555665444121111 1  11167


Q ss_pred             eecCCCCHHHHHHHHHhhhc
Q 001843          411 LHVPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       411 ~~l~~L~~~ea~~Lf~~~a~  430 (1007)
                      ++++..+.++..++|.++..
T Consensus       360 I~~~~Pd~e~r~~Il~~~l~  379 (512)
T TIGR03689       360 IRIERPDAEAAADIFSKYLT  379 (512)
T ss_pred             EEeCCCCHHHHHHHHHHHhh
Confidence            89999999999999998864

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.11  E-value=0.00017  Score=87.67  Aligned_cols=106  Identities=18%  Similarity=0.129  Sum_probs=67.8

Q ss_pred             CCCCeEEEEEecCCCC--CCCC--CcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCC
Q 001843          611 PKFAVRRLAANLGSNS--FPYS--SLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTN  686 (1007)
Q Consensus       611 ~~~~~r~Lsl~~~~~~--~~~~--~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~l  686 (1007)
                      ...+.|+|.+.+...-  ..+.  ...+|.||+|.+.+-....   .    .+...+  .++++|+.||+|+++++  .+
T Consensus       120 sr~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~---~----dF~~lc--~sFpNL~sLDIS~TnI~--nl  188 (699)
T KOG3665|consen  120 SRQNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDN---D----DFSQLC--ASFPNLRSLDISGTNIS--NL  188 (699)
T ss_pred             HHHhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecc---h----hHHHHh--hccCccceeecCCCCcc--Cc
Confidence            3456777777653211  1101  1457888888888765521   0    334556  77888888888888877  45


Q ss_pred             CccccCCCcCcEEecccCCCcccC--cccccCCCCCEEeecCCc
Q 001843          687 NNALGRLPFLEYLGLRSTFIDSLP--DSTPILFCLATLDVSHTK  728 (1007)
Q Consensus       687 p~~i~~L~~Lr~L~L~~n~i~~LP--~~i~~L~~L~~L~L~~~~  728 (1007)
                       ..|++|++|+.|.+++-.+..-+  ..+.+|++|++||+|...
T Consensus       189 -~GIS~LknLq~L~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~  231 (699)
T KOG3665|consen  189 -SGISRLKNLQVLSMRNLEFESYQDLIDLFNLKKLRVLDISRDK  231 (699)
T ss_pred             -HHHhccccHHHHhccCCCCCchhhHHHHhcccCCCeeeccccc
Confidence             67788888888888775555322  246678888888887663

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.09  E-value=0.0023  Score=61.42  Aligned_cols=86  Identities=20%  Similarity=0.135  Sum_probs=47.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.|+|.+|+||||+|+.++.  ........++++..+  ...........  .....   ..............+...
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~~~~--~~~~~~~~~~~--~~~~~---~~~~~~~~~~~~~~~~~~   73 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALAR--ELGPPGGGVIYIDGE--DILEEVLDQLL--LIIVG---GKKASGSGELRLRLALAL   73 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHh--ccCCCCCCEEEECCE--EccccCHHHHH--hhhhh---ccCCCCCHHHHHHHHHHH
Confidence            6889999999999999999999  444433345666554  22221111111  00000   011122222233344444


Q ss_pred             cCCC-cEEEEEeCcCc
Q 001843          354 LDDS-TFLIVMENAEH  368 (1007)
Q Consensus       354 L~~k-r~LlVlDdv~~  368 (1007)
                      .+.. ..+|++|+++.
T Consensus        74 ~~~~~~~viiiDei~~   89 (148)
T smart00382       74 ARKLKPDVLILDEITS   89 (148)
T ss_pred             HHhcCCCEEEEECCcc
Confidence            4433 48999999983

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.05  E-value=0.0032  Score=79.32  Aligned_cols=23  Identities=35%  Similarity=0.499  Sum_probs=20.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-+.++|.+|+|||+||..++..
T Consensus       200 ~n~lL~G~pGvGKT~l~~~la~~  222 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIVEGLAQR  222 (857)
T ss_pred             CceEEECCCCCCHHHHHHHHHHH
Confidence            34569999999999999999984

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.04  E-value=0.0087  Score=67.01  Aligned_cols=72  Identities=10%  Similarity=0.090  Sum_probs=53.1

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhh
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKK  428 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~  428 (1007)
                      +++=++|+|+++.-+....+.+. .+-+. ..++.+|++|.+...+.....+.+..+++.++++++..+.+.+.
T Consensus       109 ~~~kvviI~~a~~~~~~a~NaLLK~LEEP-p~~~~~Il~t~~~~~ll~TIrSRc~~i~~~~~~~~~~~~~L~~~  181 (329)
T PRK08058        109 SNKKVYIIEHADKMTASAANSLLKFLEEP-SGGTTAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQEE  181 (329)
T ss_pred             cCceEEEeehHhhhCHHHHHHHHHHhcCC-CCCceEEEEeCChHhCcHHHHhhceeeeCCCCCHHHHHHHHHHc
Confidence            45567999999866666677777 44443 55677777777665577766666699999999999998888654

>CHL00176 ftsH cell division protein; Validated

Probab=97.03  E-value=0.0076  Score=72.85  Aligned_cols=152  Identities=16%  Similarity=0.194  Sum_probs=82.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-|.++|++|+|||+||+++++.  ....     |+.++  .    .++    ......        .....+...+...
T Consensus       217 ~gVLL~GPpGTGKT~LAralA~e--~~~p-----~i~is--~----s~f----~~~~~g--------~~~~~vr~lF~~A  271 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLAKAIAGE--AEVP-----FFSIS--G----SEF----VEMFVG--------VGAARVRDLFKKA  271 (638)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--hCCC-----eeecc--H----HHH----HHHhhh--------hhHHHHHHHHHHH
Confidence            66899999999999999999984  3222     34333  1    011    011000        1122233344555


Q ss_pred             cCCCcEEEEEeCcCcc----------Cchhhhhhc-ccc---CCC--CCCcEEEEEcCCCccccccc---CCcceeeecC
Q 001843          354 LDDSTFLIVMENAEHQ----------KSQVWDSFL-GKL---CSF--TQCGKIIITTSSTEDFVEPL---GAAFSTLHVP  414 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~----------~~~~~~~l~-~l~---~~~--~~gs~IliTTR~~~~va~~~---~~~~~~~~l~  414 (1007)
                      ....+++|+||+++.-          ....+.+.. .+.   +++  ..+-.||.||.....+...+   +-....+.+.
T Consensus       272 ~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~  351 (638)
T CHL00176        272 KENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVS  351 (638)
T ss_pred             hcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhhhhhhhccccCceEEEEC
Confidence            5678899999999621          011222222 221   211  23455666666544122111   1111678888


Q ss_pred             CCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCC
Q 001843          415 GLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGL  457 (1007)
Q Consensus       415 ~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~Gl  457 (1007)
                      ..+.++-.++|+.++.....     .  .......+++.+.|.
T Consensus       352 lPd~~~R~~IL~~~l~~~~~-----~--~d~~l~~lA~~t~G~  387 (638)
T CHL00176        352 LPDREGRLDILKVHARNKKL-----S--PDVSLELIARRTPGF  387 (638)
T ss_pred             CCCHHHHHHHHHHHHhhccc-----c--hhHHHHHHHhcCCCC
Confidence            89999988999887754221     1  122345667776663

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=97.03  E-value=0.0026  Score=78.28  Aligned_cols=133  Identities=17%  Similarity=0.179  Sum_probs=66.2

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccC-----CCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHH
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRH-----FTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~-----F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      -+.++|.+|+|||++|+.+++.- +...     .++.+|.. .      ...    ++   .+.    ....+.+...+.
T Consensus       209 n~LLvGppGvGKT~lae~la~~i-~~~~vP~~l~~~~~~~l-~------~~~----ll---aG~----~~~Ge~e~rl~~  269 (758)
T PRK11034        209 NPLLVGESGVGKTAIAEGLAWRI-VQGDVPEVMADCTIYSL-D------IGS----LL---AGT----KYRGDFEKRFKA  269 (758)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHH-HhcCCCchhcCCeEEec-c------HHH----Hh---ccc----chhhhHHHHHHH
Confidence            34589999999999999999842 1111     13444421 1      111    11   000    001122222222


Q ss_pred             HHHHc-CCCcEEEEEeCcCcc--------Cchhhhhhc-cccCCCCCCcEEEEEcCCCcccccc------cCCcceeeec
Q 001843          350 ITQAL-DDSTFLIVMENAEHQ--------KSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEP------LGAAFSTLHV  413 (1007)
Q Consensus       350 l~~~L-~~kr~LlVlDdv~~~--------~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~------~~~~~~~~~l  413 (1007)
                      +.+.+ +.++.+|++|++..-        ...+...+. ++... + .-+||-+|.... ....      +......+.+
T Consensus       270 l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~-g-~i~vIgATt~~E-~~~~~~~D~AL~rRFq~I~v  346 (758)
T PRK11034        270 LLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS-G-KIRVIGSTTYQE-FSNIFEKDRALARRFQKIDI  346 (758)
T ss_pred             HHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhC-C-CeEEEecCChHH-HHHHhhccHHHHhhCcEEEe
Confidence            22222 346789999999721        112222223 43332 1 233444443222 2111      1112268999


Q ss_pred             CCCCHHHHHHHHHhhh
Q 001843          414 PGLGKNESWELFLKKA  429 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a  429 (1007)
                      ++++.++..+++....
T Consensus       347 ~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        347 TEPSIEETVQIINGLK  362 (758)
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            9999999999987653

>PRK08181 transposase; Validated

Probab=97.02  E-value=0.0013  Score=70.80  Aligned_cols=102  Identities=16%  Similarity=0.195  Sum_probs=55.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+.++|.+|+|||.||.++++.  .....-.++|+++.        +++..+....        ...+.......    
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~--a~~~g~~v~f~~~~--------~L~~~l~~a~--------~~~~~~~~l~~----  164 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFTRTT--------DLVQKLQVAR--------RELQLESAIAK----  164 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHH--HHHcCCceeeeeHH--------HHHHHHHHHH--------hCCcHHHHHHH----
Confidence            45899999999999999999983  33333445666543        3333332211        11122222222    


Q ss_pred             cCCCcEEEEEeCcCccCchhhh--hhccccCCCCCCcEEEEEcCCCc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWD--SFLGKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~--~l~~l~~~~~~gs~IliTTR~~~  398 (1007)
                      + .+.=||||||+.......|.  .+..+.+.--.+..+||||....
T Consensus       165 l-~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~~  210 (269)
T PRK08181        165 L-DKFDLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQPF  210 (269)
T ss_pred             H-hcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCCH
Confidence            2 23349999999643333332  22222221011236888888653

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=96.99  E-value=0.025  Score=58.91  Aligned_cols=79  Identities=15%  Similarity=0.243  Sum_probs=48.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+-+||..|.|||++++++.+.  ....=  .--|.|.                        .....+...+.+.++. 
T Consensus        53 nnvLL~G~rGtGKSSlVkall~~--y~~~G--LRlIev~------------------------k~~L~~l~~l~~~l~~-  103 (249)
T PF05673_consen   53 NNVLLWGARGTGKSSLVKALLNE--YADQG--LRLIEVS------------------------KEDLGDLPELLDLLRD-  103 (249)
T ss_pred             cceEEecCCCCCHHHHHHHHHHH--HhhcC--ceEEEEC------------------------HHHhccHHHHHHHHhc-
Confidence            45678999999999999999983  32211  1122333                        1122334444444442 


Q ss_pred             cCCCcEEEEEeCcCc-cCchhhhhhccccC
Q 001843          354 LDDSTFLIVMENAEH-QKSQVWDSFLGKLC  382 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~-~~~~~~~~l~~l~~  382 (1007)
                       +..||+|++||+.. ++...+..++.+.+
T Consensus       104 -~~~kFIlf~DDLsFe~~d~~yk~LKs~Le  132 (249)
T PF05673_consen  104 -RPYKFILFCDDLSFEEGDTEYKALKSVLE  132 (249)
T ss_pred             -CCCCEEEEecCCCCCCCcHHHHHHHHHhc
Confidence             35799999999963 34555666664443

>PRK12377 putative replication protein; Provisional

Probab=96.96  E-value=0.0022  Score=68.18  Aligned_cols=101  Identities=21%  Similarity=0.222  Sum_probs=56.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.++|.+|+|||+||.++++  .+....-.++++++.        +++..+-....       .......    +.+.
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~--~l~~~g~~v~~i~~~--------~l~~~l~~~~~-------~~~~~~~----~l~~  160 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGN--RLLAKGRSVIVVTVP--------DVMSRLHESYD-------NGQSGEK----FLQE  160 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH--HHHHcCCCeEEEEHH--------HHHHHHHHHHh-------ccchHHH----HHHH
Confidence            5789999999999999999999  444444456777654        23332222211       1111112    2222


Q ss_pred             cCCCcEEEEEeCcCccCchhhhh--hccccCC-CCCCcEEEEEcCC
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDS--FLGKLCS-FTQCGKIIITTSS  396 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~--l~~l~~~-~~~gs~IliTTR~  396 (1007)
                      + .+-=||||||+..+....|..  +..+.+. ..+.-.+||||-.
T Consensus       161 l-~~~dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl  205 (248)
T PRK12377        161 L-CKVDLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNL  205 (248)
T ss_pred             h-cCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCC
Confidence            2 345599999995434445543  2233222 1223346777753

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=96.95  E-value=0.021  Score=59.34  Aligned_cols=180  Identities=16%  Similarity=0.203  Sum_probs=105.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +++.++|.-|.|||++.++...  ...+  +.++-+.+. -+..+...+...+...+..+     ...........+.+.
T Consensus        52 g~~~vtGevGsGKTv~~Ral~~--s~~~--d~~~~v~i~-~~~~s~~~~~~ai~~~l~~~-----p~~~~~~~~e~~~~~  121 (269)
T COG3267          52 GILAVTGEVGSGKTVLRRALLA--SLNE--DQVAVVVID-KPTLSDATLLEAIVADLESQ-----PKVNVNAVLEQIDRE  121 (269)
T ss_pred             ceEEEEecCCCchhHHHHHHHH--hcCC--CceEEEEec-CcchhHHHHHHHHHHHhccC-----ccchhHHHHHHHHHH
Confidence            6999999999999999995444  2211  222223333 14556677777888777664     223333333333333


Q ss_pred             ----c-CCCc-EEEEEeCcCccCchhhhhhccccC---CCCCCcEEEEEcCCCc------ccccccCCccee-eecCCCC
Q 001843          354 ----L-DDST-FLIVMENAEHQKSQVWDSFLGKLC---SFTQCGKIIITTSSTE------DFVEPLGAAFST-LHVPGLG  417 (1007)
Q Consensus       354 ----L-~~kr-~LlVlDdv~~~~~~~~~~l~~l~~---~~~~gs~IliTTR~~~------~va~~~~~~~~~-~~l~~L~  417 (1007)
                          . +++| ..+++|+..+...+..+.++-|-+   .+..--+|+..-.-+-      .+.....-...+ |+++|++
T Consensus       122 L~al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~~  201 (269)
T COG3267         122 LAALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPLT  201 (269)
T ss_pred             HHHHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCcC
Confidence                3 4667 899999998666667776662222   1011112333211110      011111111134 9999999


Q ss_pred             HHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHH
Q 001843          418 KNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAG  466 (1007)
Q Consensus       418 ~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~  466 (1007)
                      .++...++..+..+...+   .+--..+....|.....|.|.+|..++.
T Consensus       202 ~~~t~~yl~~~Le~a~~~---~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         202 EAETGLYLRHRLEGAGLP---EPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             hHHHHHHHHHHHhccCCC---cccCChhHHHHHHHHhccchHHHHHHHH
Confidence            998888777766554332   1222345677889999999999987764

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.95  E-value=0.0018  Score=68.61  Aligned_cols=102  Identities=17%  Similarity=0.226  Sum_probs=57.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.++|.+|+|||+||.++++.  ....-..++++++.        +++..+-.... .     ...+...    +.+.
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~--l~~~g~~v~~it~~--------~l~~~l~~~~~-~-----~~~~~~~----~l~~  159 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNE--LLLRGKSVLIITVA--------DIMSAMKDTFS-N-----SETSEEQ----LLND  159 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEHH--------HHHHHHHHHHh-h-----ccccHHH----HHHH
Confidence            57899999999999999999994  44434456666554        23332222221 0     1112222    2233


Q ss_pred             cCCCcEEEEEeCcCccCchhhhh--hccccCC-CCCCcEEEEEcCC
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDS--FLGKLCS-FTQCGKIIITTSS  396 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~--l~~l~~~-~~~gs~IliTTR~  396 (1007)
                      +. +.=+|||||+.......|..  +..+.+. ....-.+||||-.
T Consensus       160 l~-~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl  204 (244)
T PRK07952        160 LS-NVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNS  204 (244)
T ss_pred             hc-cCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCC
Confidence            44 34488899997655566664  2233221 0223457777764

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=96.94  E-value=0.0077  Score=74.77  Aligned_cols=138  Identities=13%  Similarity=0.268  Sum_probs=69.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.++|++|+||||+|+.++.  .....|-.   +.++  ...+..++        .+.. ..........+...+...
T Consensus       350 ~~i~l~GppG~GKTtl~~~ia~--~l~~~~~~---i~~~--~~~d~~~i--------~g~~-~~~~g~~~G~~~~~l~~~  413 (784)
T PRK10787        350 PILCLVGPPGVGKTSLGQSIAK--ATGRKYVR---MALG--GVRDEAEI--------RGHR-RTYIGSMPGKLIQKMAKV  413 (784)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HhCCCEEE---EEcC--CCCCHHHh--------ccch-hccCCCCCcHHHHHHHhc
Confidence            6899999999999999999998  44444422   2233  22222111        1100 000000111222333322


Q ss_pred             cCCCcEEEEEeCcCccCchh----hhhhc-cccC-------------CCC-CCcEEEEEcCCCcccccccCCcceeeecC
Q 001843          354 LDDSTFLIVMENAEHQKSQV----WDSFL-GKLC-------------SFT-QCGKIIITTSSTEDFVEPLGAAFSTLHVP  414 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~----~~~l~-~l~~-------------~~~-~gs~IliTTR~~~~va~~~~~~~~~~~l~  414 (1007)
                       ....-+|+||.++......    .+.+. .+-.             .+. ...-+|.|+.... +...+-....++++.
T Consensus       414 -~~~~~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~~~-i~~aLl~R~~ii~~~  491 (784)
T PRK10787        414 -GVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMN-IPAPLLDRMEVIRLS  491 (784)
T ss_pred             -CCCCCEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCCCC-CCHHHhcceeeeecC
Confidence             2233478899997432221    11222 1110             001 2233333554333 444444444788999


Q ss_pred             CCCHHHHHHHHHhhh
Q 001843          415 GLGKNESWELFLKKA  429 (1007)
Q Consensus       415 ~L~~~ea~~Lf~~~a  429 (1007)
                      +++.+|-.++.+++.
T Consensus       492 ~~t~eek~~Ia~~~L  506 (784)
T PRK10787        492 GYTEDEKLNIAKRHL  506 (784)
T ss_pred             CCCHHHHHHHHHHhh
Confidence            999998888877765

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=96.92  E-value=7.8e-05  Score=69.02  Aligned_cols=72  Identities=15%  Similarity=0.150  Sum_probs=37.2

Q ss_pred             CCCCcccEEEecCCCCCCcCCCccccC-CCcCcEEecccCCCcccCcccccCCCCCEEeecCCcccccccccccc
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGR-LPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPS  739 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~~lp~~i~~-L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~~i~~L  739 (1007)
                      .+..+|...+|++|.+.  .+|..|.. .+.+..|+|++|.|+++|..+..++.|+.|+++.|.+...|.-+..|
T Consensus        50 ~~~~el~~i~ls~N~fk--~fp~kft~kf~t~t~lNl~~neisdvPeE~Aam~aLr~lNl~~N~l~~~p~vi~~L  122 (177)
T KOG4579|consen   50 SKGYELTKISLSDNGFK--KFPKKFTIKFPTATTLNLANNEISDVPEELAAMPALRSLNLRFNPLNAEPRVIAPL  122 (177)
T ss_pred             hCCceEEEEecccchhh--hCCHHHhhccchhhhhhcchhhhhhchHHHhhhHHhhhcccccCccccchHHHHHH
Confidence            34444555555555555  45544432 23555555555555555555555555555555555555555444444

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=96.90  E-value=0.00012  Score=67.78  Aligned_cols=91  Identities=18%  Similarity=0.189  Sum_probs=77.2

Q ss_pred             CCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcc
Q 001843          633 LSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDS  712 (1007)
Q Consensus       633 ~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~  712 (1007)
                      ...+|....+.+|.+..        +++.+-  .+++.++.|+|++|.+.  .+|..+..++.||.|++++|.+...|.-
T Consensus        51 ~~~el~~i~ls~N~fk~--------fp~kft--~kf~t~t~lNl~~neis--dvPeE~Aam~aLr~lNl~~N~l~~~p~v  118 (177)
T KOG4579|consen   51 KGYELTKISLSDNGFKK--------FPKKFT--IKFPTATTLNLANNEIS--DVPEELAAMPALRSLNLRFNPLNAEPRV  118 (177)
T ss_pred             CCceEEEEecccchhhh--------CCHHHh--hccchhhhhhcchhhhh--hchHHHhhhHHhhhcccccCccccchHH
Confidence            34567777788887753        333444  77889999999999999  8999999999999999999999999999


Q ss_pred             cccCCCCCEEeecCCcccccccc
Q 001843          713 TPILFCLATLDVSHTKVQRLPYA  735 (1007)
Q Consensus       713 i~~L~~L~~L~L~~~~l~~lP~~  735 (1007)
                      |..|.+|-+|+..+|.+.++|-.
T Consensus       119 i~~L~~l~~Lds~~na~~eid~d  141 (177)
T KOG4579|consen  119 IAPLIKLDMLDSPENARAEIDVD  141 (177)
T ss_pred             HHHHHhHHHhcCCCCccccCcHH
Confidence            99999999999999988887764

>PRK10536 hypothetical protein; Provisional

Probab=96.88  E-value=0.013  Score=61.89  Aligned_cols=119  Identities=16%  Similarity=0.248  Sum_probs=64.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEE--ecCCC-----CCCHHHHHHHHHHHHhhhhhhhccccCHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH--IPIMS-----MVEDRDVLADILKQIDESLLKVEATLSAEEL  346 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~--~s~~~-----~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l  346 (1007)
                      .++.+.|..|.|||+||.+++.+....+.|+.++-+.  +...+     +-+..+-+.-.+.-+...+...   ......
T Consensus        75 ~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI~RP~v~~ge~LGfLPG~~~eK~~p~~~pi~D~L~~~---~~~~~~  151 (262)
T PRK10536         75 QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGDIAEKFAPYFRPVYDVLVRR---LGASFM  151 (262)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEEeCCCCCchhhhCcCCCCHHHHHHHHHHHHHHHHHHH---hChHHH
Confidence            6899999999999999999988533345555443331  11000     1123333333333322221110   011111


Q ss_pred             HHHH-----------HHHcCCCcE---EEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcCCCc
Q 001843          347 MWRI-----------TQALDDSTF---LIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       347 ~~~l-----------~~~L~~kr~---LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~  398 (1007)
                      ...+           -.+++++.+   +||+|.+.+.+..+...+.  ..- +.+|++|+|--..+
T Consensus       152 ~~~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~~~~k~~l--tR~-g~~sk~v~~GD~~Q  214 (262)
T PRK10536        152 QYCLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTAAQMKMFL--TRL-GENVTVIVNGDITQ  214 (262)
T ss_pred             HHHHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCHHHHHHHH--hhc-CCCCEEEEeCChhh
Confidence            1111           134566655   9999999866665555544  222 77899998765443

>PRK08118 topology modulation protein; Reviewed

Probab=96.84  E-value=0.00063  Score=68.11  Aligned_cols=36  Identities=39%  Similarity=0.653  Sum_probs=28.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc-cCCCceEEE
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK-RHFTKRAWV  309 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv  309 (1007)
                      +-|.|+|++|+||||||+.+++...+. -+||..+|-
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~   38 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWK   38 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhcc
Confidence            468999999999999999999954443 457777753

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=96.81  E-value=0.0028  Score=66.39  Aligned_cols=35  Identities=34%  Similarity=0.594  Sum_probs=30.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEE
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  310 (1007)
                      -.++|+|..|.|||||++.+..  .....|+.+++++
T Consensus        14 fr~viIG~sGSGKT~li~~lL~--~~~~~f~~I~l~t   48 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLY--YLRHKFDHIFLIT   48 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--hhcccCCEEEEEe
Confidence            4678999999999999999998  5788898877775

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=96.80  E-value=0.031  Score=61.87  Aligned_cols=94  Identities=11%  Similarity=0.111  Sum_probs=67.4

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++=++|+|+++.-+....+.+. .+-.. ..++.+|++|.+...+.....+.+..+.+.++++++..+.+......   
T Consensus       106 g~~KV~iI~~a~~m~~~AaNaLLKtLEEP-p~~~~fiL~t~~~~~llpTI~SRC~~~~~~~~~~~~~~~~L~~~~~~---  181 (325)
T PRK06871        106 GGNKVVYIQGAERLTEAAANALLKTLEEP-RPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQQALDWLQAQSSA---  181 (325)
T ss_pred             CCceEEEEechhhhCHHHHHHHHHHhcCC-CCCeEEEEEECChHhCchHHHhhceEEeCCCCCHHHHHHHHHHHhcc---
Confidence            55568889999877777777777 44333 55677777777765477666666689999999999999888775421   


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai  461 (1007)
                           .   ...+...+..++|.|+..
T Consensus       182 -----~---~~~~~~~~~l~~g~p~~A  200 (325)
T PRK06871        182 -----E---ISEILTALRINYGRPLLA  200 (325)
T ss_pred             -----C---hHHHHHHHHHcCCCHHHH
Confidence                 1   113556788899999643

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=96.80  E-value=0.01  Score=59.13  Aligned_cols=119  Identities=13%  Similarity=0.219  Sum_probs=71.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc------------------cCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK------------------RHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLL  335 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~------------------~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~  335 (1007)
                      ..+-++|..|+||+|+|..+++.-.-.                  .......|+.-.  ...                  
T Consensus        20 ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~--~~~------------------   79 (162)
T PF13177_consen   20 HALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPD--KKK------------------   79 (162)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETT--TSS------------------
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecc--ccc------------------
Confidence            567899999999999999988732111                  123334444322  110                  


Q ss_pred             hhccccCHHHHHHHHHHHc-----CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcce
Q 001843          336 KVEATLSAEELMWRITQAL-----DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFS  409 (1007)
Q Consensus       336 ~~~~~~~~~~l~~~l~~~L-----~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~  409 (1007)
                         .....++.. .+.+.+     .+++=++|+||++..+.+.++.++ .+-+. ..++++|++|++...+.....+.+.
T Consensus        80 ---~~i~i~~ir-~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEep-p~~~~fiL~t~~~~~il~TI~SRc~  154 (162)
T PF13177_consen   80 ---KSIKIDQIR-EIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEP-PENTYFILITNNPSKILPTIRSRCQ  154 (162)
T ss_dssp             ---SSBSHHHHH-HHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHST-TTTEEEEEEES-GGGS-HHHHTTSE
T ss_pred             ---chhhHHHHH-HHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCC-CCCEEEEEEECChHHChHHHHhhce
Confidence               011222222 333333     235569999999988888888888 44444 6688999999988767777666667


Q ss_pred             eeecCCCC
Q 001843          410 TLHVPGLG  417 (1007)
Q Consensus       410 ~~~l~~L~  417 (1007)
                      .+.+++|+
T Consensus       155 ~i~~~~ls  162 (162)
T PF13177_consen  155 VIRFRPLS  162 (162)
T ss_dssp             EEEE----
T ss_pred             EEecCCCC
Confidence            88877764

...

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=96.78  E-value=0.0076  Score=61.01  Aligned_cols=22  Identities=27%  Similarity=0.357  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .-+.|.||+|+||||-+..+++
T Consensus        49 P~liisGpPG~GKTTsi~~LAr   70 (333)
T KOG0991|consen   49 PNLIISGPPGTGKTTSILCLAR   70 (333)
T ss_pred             CceEeeCCCCCchhhHHHHHHH
Confidence            6678999999999999999888

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.77  E-value=0.0043  Score=63.74  Aligned_cols=91  Identities=20%  Similarity=0.237  Sum_probs=51.5

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      ++||.++|+.|+||||.+-+++..  ...+-..+..++... ......+-++..++.++.+........+.........+
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~--~~~~~~~v~lis~D~-~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~   77 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAAR--LKLKGKKVALISADT-YRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALE   77 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHH--HHHTT--EEEEEEST-SSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHH--HhhccccceeecCCC-CCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHH
Confidence            489999999999999888888774  333344577777641 22345666777777777542111122233333333222


Q ss_pred             HcCCCc-EEEEEeCc
Q 001843          353 ALDDST-FLIVMENA  366 (1007)
Q Consensus       353 ~L~~kr-~LlVlDdv  366 (1007)
                      .++.++ =+|++|=.
T Consensus        78 ~~~~~~~D~vlIDT~   92 (196)
T PF00448_consen   78 KFRKKGYDLVLIDTA   92 (196)
T ss_dssp             HHHHTTSSEEEEEE-
T ss_pred             HHhhcCCCEEEEecC
Confidence            233333 36777754

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.76  E-value=0.0057  Score=72.73  Aligned_cols=152  Identities=17%  Similarity=0.158  Sum_probs=80.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-+.++|++|+|||++|+.+++.  ....     ++.++      ..++    .....        ......+...+...
T Consensus        89 ~giLL~GppGtGKT~la~alA~~--~~~~-----~~~i~------~~~~----~~~~~--------g~~~~~l~~~f~~a  143 (495)
T TIGR01241        89 KGVLLVGPPGTGKTLLAKAVAGE--AGVP-----FFSIS------GSDF----VEMFV--------GVGASRVRDLFEQA  143 (495)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHH--cCCC-----eeecc------HHHH----HHHHh--------cccHHHHHHHHHHH
Confidence            55889999999999999999984  3222     23333      1111    11110        11222333344444


Q ss_pred             cCCCcEEEEEeCcCccC----------chhhhhhc-ccc---CCC--CCCcEEEEEcCCCccccccc----CCcceeeec
Q 001843          354 LDDSTFLIVMENAEHQK----------SQVWDSFL-GKL---CSF--TQCGKIIITTSSTEDFVEPL----GAAFSTLHV  413 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~----------~~~~~~l~-~l~---~~~--~~gs~IliTTR~~~~va~~~----~~~~~~~~l  413 (1007)
                      ....+.+|+||+++.-.          ...+.... .+.   +++  ..+-.||.||.....+-..+    .-+ ..+.+
T Consensus       144 ~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~ld~al~r~gRfd-~~i~i  222 (495)
T TIGR01241       144 KKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFD-RQVVV  222 (495)
T ss_pred             HhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhhcCHHHhcCCcce-EEEEc
Confidence            45678899999996210          11122221 111   111  23445555665543122211    122 77889


Q ss_pred             CCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCc
Q 001843          414 PGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlP  458 (1007)
                      +..+.++-.++|..+......     .+  ......+++.+.|.-
T Consensus       223 ~~Pd~~~R~~il~~~l~~~~~-----~~--~~~l~~la~~t~G~s  260 (495)
T TIGR01241       223 DLPDIKGREEILKVHAKNKKL-----AP--DVDLKAVARRTPGFS  260 (495)
T ss_pred             CCCCHHHHHHHHHHHHhcCCC-----Cc--chhHHHHHHhCCCCC
Confidence            999998888888877643221     11  112346777777644

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.71  E-value=0.0017  Score=65.62  Aligned_cols=100  Identities=24%  Similarity=0.389  Sum_probs=52.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+.++|..|+|||.||.++.+.  .-.+=..+.|+++.            +++..+...    ..........+.    
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~--~~~~g~~v~f~~~~------------~L~~~l~~~----~~~~~~~~~~~~----  105 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANE--AIRKGYSVLFITAS------------DLLDELKQS----RSDGSYEELLKR----  105 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHH--HHHTT--EEEEEHH------------HHHHHHHCC----HCCTTHCHHHHH----
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHH--hccCCcceeEeecC------------ceecccccc----ccccchhhhcCc----
Confidence            56899999999999999999984  33333346777655            344444332    111122222222    


Q ss_pred             cCCCcEEEEEeCcCccCchhhhh--hccccCC-CCCCcEEEEEcCCC
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDS--FLGKLCS-FTQCGKIIITTSST  397 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~--l~~l~~~-~~~gs~IliTTR~~  397 (1007)
                      +. +-=||||||+-.+....|..  +..+.+. ..++ .+||||...
T Consensus       106 l~-~~dlLilDDlG~~~~~~~~~~~l~~ii~~R~~~~-~tIiTSN~~  150 (178)
T PF01695_consen  106 LK-RVDLLILDDLGYEPLSEWEAELLFEIIDERYERK-PTIITSNLS  150 (178)
T ss_dssp             HH-TSSCEEEETCTSS---HHHHHCTHHHHHHHHHT--EEEEEESS-
T ss_pred             cc-cccEecccccceeeecccccccchhhhhHhhccc-CeEeeCCCc
Confidence            22 23488899997544444432  1122211 0223 588888754

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.69  E-value=0.029  Score=64.39  Aligned_cols=118  Identities=20%  Similarity=0.268  Sum_probs=75.3

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHHc
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQAL  354 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~L  354 (1007)
                      ++.|.|+-++||||+++.+..  ...+.   .+++...  .......-+.+....                    +...-
T Consensus        39 i~~i~GpR~~GKTtll~~l~~--~~~~~---~iy~~~~--d~~~~~~~l~d~~~~--------------------~~~~~   91 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIK--GLLEE---IIYINFD--DLRLDRIELLDLLRA--------------------YIELK   91 (398)
T ss_pred             EEEEECCccccHHHHHHHHHh--hCCcc---eEEEEec--chhcchhhHHHHHHH--------------------HHHhh
Confidence            999999999999999966665  22222   5555543  111111111111111                    11111


Q ss_pred             CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcc----cccccCCcceeeecCCCCHHHHHH
Q 001843          355 DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTED----FVEPLGAAFSTLHVPGLGKNESWE  423 (1007)
Q Consensus       355 ~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~----va~~~~~~~~~~~l~~L~~~ea~~  423 (1007)
                      ..++.+|+||.|.  ....|.... .+.+. +.. +|+||+-+..-    .+....+....+++-||+..|...
T Consensus        92 ~~~~~yifLDEIq--~v~~W~~~lk~l~d~-~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~Efl~  161 (398)
T COG1373          92 EREKSYIFLDEIQ--NVPDWERALKYLYDR-GNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFREFLK  161 (398)
T ss_pred             ccCCceEEEeccc--CchhHHHHHHHHHcc-ccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHHHHh
Confidence            1278899999999  888898877 88777 555 89998887651    223333334889999999999865

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=96.67  E-value=4.6e-05  Score=87.92  Aligned_cols=123  Identities=21%  Similarity=0.079  Sum_probs=70.0

Q ss_pred             cccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCcccccCCCCCEEeecCCccccccc---cccccceecccc
Q 001843          670 MLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPY---AFWPSRHLYLNW  746 (1007)
Q Consensus       670 ~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~~i~~L~~L~~L~L~~~~l~~lP~---~i~~Lr~L~l~~  746 (1007)
                      .|.+.+.++|.+.  .+-.++.-+++|+.|+|++|++...- .+..|++|++|||++|.+..+|.   .-.+|..|.+. 
T Consensus       165 ~L~~a~fsyN~L~--~mD~SLqll~ale~LnLshNk~~~v~-~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc~L~~L~lr-  240 (1096)
T KOG1859|consen  165 KLATASFSYNRLV--LMDESLQLLPALESLNLSHNKFTKVD-NLRRLPKLKHLDLSYNCLRHVPQLSMVGCKLQLLNLR-  240 (1096)
T ss_pred             hHhhhhcchhhHH--hHHHHHHHHHHhhhhccchhhhhhhH-HHHhcccccccccccchhccccccchhhhhheeeeec-
Confidence            4555666666655  44455666667777777777766655 56666777777777776666554   22234556655 


Q ss_pred             cccccccccccccccCcCCCccccceeeCCCcccChHhhhcCCCCCeEEeeecC
Q 001843          747 IFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSS  800 (1007)
Q Consensus       747 ~~~~~~~~~~p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~l~~~~  800 (1007)
                        +|. . .-..++.+|.+|+.|+..+.--.....+..++.|..|+.|.+.+|.
T Consensus       241 --nN~-l-~tL~gie~LksL~~LDlsyNll~~hseL~pLwsLs~L~~L~LeGNP  290 (1096)
T KOG1859|consen  241 --NNA-L-TTLRGIENLKSLYGLDLSYNLLSEHSELEPLWSLSSLIVLWLEGNP  290 (1096)
T ss_pred             --ccH-H-HhhhhHHhhhhhhccchhHhhhhcchhhhHHHHHHHHHHHhhcCCc
Confidence              332 1 2223456666666664332211112244456666677777777665

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.67  E-value=0.006  Score=67.24  Aligned_cols=101  Identities=18%  Similarity=0.294  Sum_probs=60.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-+.++|..|+|||.||.++++.  ....-..+.++++.        +++.++......        .+....   + +.
T Consensus       157 ~gl~L~G~~G~GKThLa~Aia~~--l~~~g~~v~~~~~~--------~l~~~lk~~~~~--------~~~~~~---l-~~  214 (306)
T PRK08939        157 KGLYLYGDFGVGKSYLLAAIANE--LAKKGVSSTLLHFP--------EFIRELKNSISD--------GSVKEK---I-DA  214 (306)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEEEHH--------HHHHHHHHHHhc--------CcHHHH---H-HH
Confidence            67899999999999999999995  43333345677654        333443333221        122222   2 22


Q ss_pred             cCCCcEEEEEeCcCccCchhhhh--hc-cccCC-CCCCcEEEEEcCCC
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDS--FL-GKLCS-FTQCGKIIITTSST  397 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~--l~-~l~~~-~~~gs~IliTTR~~  397 (1007)
                      + .+-=||||||+..+....|..  +. .+.+. ...+-.+|+||--.
T Consensus       215 l-~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl~  261 (306)
T PRK08939        215 V-KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNFD  261 (306)
T ss_pred             h-cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCCC
Confidence            2 234599999997666777753  44 34321 12345678887643

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=96.67  E-value=0.012  Score=70.34  Aligned_cols=22  Identities=41%  Similarity=0.650  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .-|.|+|.+|+|||++|+.+++
T Consensus        87 ~~vLi~Ge~GtGKt~lAr~i~~  108 (531)
T TIGR02902        87 QHVIIYGPPGVGKTAAARLVLE  108 (531)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999987

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.64  E-value=0.0039  Score=69.23  Aligned_cols=37  Identities=16%  Similarity=0.249  Sum_probs=28.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      .-+.++|..|+|||.||.++++.  +...-..++++++.
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~--l~~~g~~V~y~t~~  220 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKE--LLDRGKSVIYRTAD  220 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHH--HHHCCCeEEEEEHH
Confidence            56899999999999999999994  43333356677654

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.63  E-value=0.0099  Score=74.94  Aligned_cols=92  Identities=14%  Similarity=0.272  Sum_probs=50.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.++|+.|+|||++|+.+++  ..-..-...+.+.++  . +........+   ++.+  +.....+.   ...+.+.
T Consensus       599 ~~~Lf~Gp~G~GKT~lA~aLa~--~l~~~~~~~i~id~s--e-~~~~~~~~~L---iG~~--pgy~g~~~---~g~l~~~  665 (857)
T PRK10865        599 GSFLFLGPTGVGKTELCKALAN--FMFDSDDAMVRIDMS--E-FMEKHSVSRL---VGAP--PGYVGYEE---GGYLTEA  665 (857)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HhhcCCCcEEEEEhH--H-hhhhhhHHHH---hCCC--Ccccccch---hHHHHHH
Confidence            5788999999999999999998  332222333444444  2 1111111111   1211  00011111   1123333


Q ss_pred             cCCCc-EEEEEeCcCccCchhhhhhc
Q 001843          354 LDDST-FLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       354 L~~kr-~LlVlDdv~~~~~~~~~~l~  378 (1007)
                      ++.++ -+|+||++...+++.++.+.
T Consensus       666 v~~~p~~vLllDEieka~~~v~~~Ll  691 (857)
T PRK10865        666 VRRRPYSVILLDEVEKAHPDVFNILL  691 (857)
T ss_pred             HHhCCCCeEEEeehhhCCHHHHHHHH
Confidence            33333 59999999877788887776

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=96.61  E-value=0.032  Score=62.30  Aligned_cols=95  Identities=7%  Similarity=0.055  Sum_probs=67.5

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++=++|+|+++.-+....+.+. .+-+- ..++.+|++|.+...+.....+.+..+.+.+++.+++.+.+......   
T Consensus       107 g~~kV~iI~~ae~m~~~AaNaLLKtLEEP-p~~t~fiL~t~~~~~lLpTIrSRCq~~~~~~~~~~~~~~~L~~~~~~---  182 (334)
T PRK07993        107 GGAKVVWLPDAALLTDAAANALLKTLEEP-PENTWFFLACREPARLLATLRSRCRLHYLAPPPEQYALTWLSREVTM---  182 (334)
T ss_pred             CCceEEEEcchHhhCHHHHHHHHHHhcCC-CCCeEEEEEECChhhChHHHHhccccccCCCCCHHHHHHHHHHccCC---
Confidence            56669999999876777777777 44333 55677777777665477666666688999999999998877654211   


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVV  462 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~  462 (1007)
                           +   .+.+..++..++|.|....
T Consensus       183 -----~---~~~a~~~~~la~G~~~~Al  202 (334)
T PRK07993        183 -----S---QDALLAALRLSAGAPGAAL  202 (334)
T ss_pred             -----C---HHHHHHHHHHcCCCHHHHH
Confidence                 1   2336788999999996443

>PRK06921 hypothetical protein; Provisional

Probab=96.60  E-value=0.0073  Score=65.27  Aligned_cols=36  Identities=33%  Similarity=0.406  Sum_probs=28.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC-CCceEEEEe
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH-FTKRAWVHI  311 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~  311 (1007)
                      .-+.++|..|+|||+||.++++  .+... -..+++++.
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~--~l~~~~g~~v~y~~~  154 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAAN--ELMRKKGVPVLYFPF  154 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHH--HHhhhcCceEEEEEH
Confidence            6789999999999999999999  44443 344566654

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=96.60  E-value=0.006  Score=62.49  Aligned_cols=122  Identities=20%  Similarity=0.238  Sum_probs=57.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecC--CCC--C---CHHHHHHHHHHHHhhhhhhhccccCHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPI--MSM--V---EDRDVLADILKQIDESLLKVEATLSAEEL  346 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~--~~~--~---~~~~~l~~il~~l~~~~~~~~~~~~~~~l  346 (1007)
                      .++.+.|++|.|||.||.+.+-+.-..+.|+.++++.-..  .+.  |   +..+-+.-.+.-+...+...-.....+.+
T Consensus        20 ~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~l~~~~~~~~~~~~   99 (205)
T PF02562_consen   20 DLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDALEELFGKEKLEEL   99 (205)
T ss_dssp             SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS-TTCHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHHHHHHhChHhHHHH
Confidence            6899999999999999999988755568888888875210  010  1   11111111111111110000011122222


Q ss_pred             HHH------HHHHcCCC---cEEEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcCCCc
Q 001843          347 MWR------ITQALDDS---TFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       347 ~~~------l~~~L~~k---r~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~  398 (1007)
                      .+.      --.+++++   ..+||+|++.+.+..++..+.  ... +.|||||++--..+
T Consensus       100 ~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~il--TR~-g~~skii~~GD~~Q  157 (205)
T PF02562_consen  100 IQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMIL--TRI-GEGSKIIITGDPSQ  157 (205)
T ss_dssp             HHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHH--TTB--TT-EEEEEE----
T ss_pred             hhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHH--ccc-CCCcEEEEecCcee
Confidence            210      01234554   459999999877777777775  222 77899999765443

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK06526 transposase; Provisional

Probab=96.60  E-value=0.003  Score=67.69  Aligned_cols=23  Identities=35%  Similarity=0.481  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-+.|+|.+|+|||+||..+.+.
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHH
Confidence            56899999999999999999884

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.56  E-value=0.0053  Score=77.09  Aligned_cols=92  Identities=14%  Similarity=0.192  Sum_probs=48.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.++|+.|+|||.+|+.++.  .+-+.....+-++++   .+....-..   .-++.+  +.....+.   ...+.+.
T Consensus       597 ~~~lf~Gp~GvGKT~lA~~La~--~l~~~~~~~~~~dms---e~~~~~~~~---~l~g~~--~gyvg~~~---~g~L~~~  663 (852)
T TIGR03345       597 GVFLLVGPSGVGKTETALALAE--LLYGGEQNLITINMS---EFQEAHTVS---RLKGSP--PGYVGYGE---GGVLTEA  663 (852)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH--HHhCCCcceEEEeHH---Hhhhhhhhc---cccCCC--CCcccccc---cchHHHH
Confidence            6899999999999999999988  332222222333333   111111111   111111  00011111   1122333


Q ss_pred             cC-CCcEEEEEeCcCccCchhhhhhc
Q 001843          354 LD-DSTFLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       354 L~-~kr~LlVlDdv~~~~~~~~~~l~  378 (1007)
                      ++ ....+|+||++...+++.++.+.
T Consensus       664 v~~~p~svvllDEieka~~~v~~~Ll  689 (852)
T TIGR03345       664 VRRKPYSVVLLDEVEKAHPDVLELFY  689 (852)
T ss_pred             HHhCCCcEEEEechhhcCHHHHHHHH
Confidence            33 34459999999987888877776

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.52  E-value=0.065  Score=58.27  Aligned_cols=182  Identities=17%  Similarity=0.311  Sum_probs=97.3

Q ss_pred             CCCCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHH
Q 001843          269 TTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       269 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      +-..++=|.++|++|.|||-||++|+|  +....|     +.+.  .        .++.+..-+         +...+++
T Consensus       181 GI~PPKGVLLYGPPGTGKTLLAkAVA~--~T~AtF-----Irvv--g--------SElVqKYiG---------EGaRlVR  234 (406)
T COG1222         181 GIDPPKGVLLYGPPGTGKTLLAKAVAN--QTDATF-----IRVV--G--------SELVQKYIG---------EGARLVR  234 (406)
T ss_pred             CCCCCCceEeeCCCCCcHHHHHHHHHh--ccCceE-----EEec--c--------HHHHHHHhc---------cchHHHH
Confidence            334557889999999999999999999  444433     4433  0        122222211         1223333


Q ss_pred             HHHHHcC-CCcEEEEEeCcCcc-----------Cchhh---hhhccccCCC--CCCcEEEEEcCCCccccccc--C--Cc
Q 001843          349 RITQALD-DSTFLIVMENAEHQ-----------KSQVW---DSFLGKLCSF--TQCGKIIITTSSTEDFVEPL--G--AA  407 (1007)
Q Consensus       349 ~l~~~L~-~kr~LlVlDdv~~~-----------~~~~~---~~l~~l~~~~--~~gs~IliTTR~~~~va~~~--~--~~  407 (1007)
                      .+-+.-+ ..++.|++|.++..           +.+.-   -++..-.++|  ...-|||..|-..+ +..-.  .  --
T Consensus       235 elF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~ATNR~D-~LDPALLRPGR~  313 (406)
T COG1222         235 ELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNRPD-ILDPALLRPGRF  313 (406)
T ss_pred             HHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEecCCcc-ccChhhcCCCcc
Confidence            3333333 56899999998621           11111   1121111222  23568888776665 44321  1  11


Q ss_pred             ceeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCc----hHHHHHHHHhcCCCC----ChHHHH
Q 001843          408 FSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLP----LRVVLLAGLLSTKQP----SYEEWS  479 (1007)
Q Consensus       408 ~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlP----Lai~~~g~~L~~~~~----~~~~w~  479 (1007)
                      ...++++.-+.+.=.++|+-|+..-.-   ...-++    +.|++.|.|.-    -||.+=|++++-+..    +.+.+.
T Consensus       314 DRkIEfplPd~~gR~~Il~IHtrkM~l---~~dvd~----e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~  386 (406)
T COG1222         314 DRKIEFPLPDEEGRAEILKIHTRKMNL---ADDVDL----ELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFL  386 (406)
T ss_pred             cceeecCCCCHHHHHHHHHHHhhhccC---ccCcCH----HHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHH
Confidence            167888866666667788777654332   112223    45666666665    345566666653322    344555


Q ss_pred             HHHHH
Q 001843          480 KVIER  484 (1007)
Q Consensus       480 ~~l~~  484 (1007)
                      +..++
T Consensus       387 ~Av~K  391 (406)
T COG1222         387 KAVEK  391 (406)
T ss_pred             HHHHH
Confidence            44443

>PRK09183 transposase/IS protein; Provisional

Probab=96.51  E-value=0.0043  Score=66.84  Aligned_cols=23  Identities=39%  Similarity=0.509  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ..+.|+|.+|+|||+||..+++.
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~  125 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYE  125 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHH
Confidence            56779999999999999999874

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=96.51  E-value=0.065  Score=59.17  Aligned_cols=94  Identities=12%  Similarity=0.159  Sum_probs=68.1

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++=++|+|+++.-+....+.+. .+-.- ..++.+|++|.+...+.....+.+..+.+.+++.+++.+.+.....    
T Consensus       107 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEP-p~~t~fiL~t~~~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~~----  181 (319)
T PRK06090        107 NGYRLFVIEPADAMNESASNALLKTLEEP-APNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQGI----  181 (319)
T ss_pred             CCceEEEecchhhhCHHHHHHHHHHhcCC-CCCeEEEEEECChhhChHHHHhcceeEeCCCCCHHHHHHHHHHcCC----
Confidence            44558899999877777888777 44333 5566777776665547777777779999999999999988865311    


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                           .     .+..+++.++|.|+....+
T Consensus       182 -----~-----~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        182 -----T-----VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             -----c-----hHHHHHHHcCCCHHHHHHH
Confidence                 1     1346788999999976544

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=96.49  E-value=0.045  Score=64.64  Aligned_cols=140  Identities=14%  Similarity=0.293  Sum_probs=72.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++++||++|+|||.|++.++.  ...+.|-.   +.++  .--|-.        ++.++ ...-...-+..+++.+++.
T Consensus       351 pILcLVGPPGVGKTSLgkSIA~--al~RkfvR---~sLG--GvrDEA--------EIRGH-RRTYIGamPGrIiQ~mkka  414 (782)
T COG0466         351 PILCLVGPPGVGKTSLGKSIAK--ALGRKFVR---ISLG--GVRDEA--------EIRGH-RRTYIGAMPGKIIQGMKKA  414 (782)
T ss_pred             cEEEEECCCCCCchhHHHHHHH--HhCCCEEE---EecC--ccccHH--------Hhccc-cccccccCChHHHHHHHHh
Confidence            7999999999999999999999  67776622   2333  111111        11111 0000111112222222222


Q ss_pred             cCCCcEEEEEeCcCcc----------------Cchhhhhhc--cccCCCCCCcEEEEEcCCCcc-cccccCCcceeeecC
Q 001843          354 LDDSTFLIVMENAEHQ----------------KSQVWDSFL--GKLCSFTQCGKIIITTSSTED-FVEPLGAAFSTLHVP  414 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~----------------~~~~~~~l~--~l~~~~~~gs~IliTTR~~~~-va~~~~~~~~~~~l~  414 (1007)
                       +.+.=+++||.++..                |+++=..|.  ++--.+.-.-.+.|||-+.-. +....-....++++.
T Consensus       415 -~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~PLlDRMEiI~ls  493 (782)
T COG0466         415 -GVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIPAPLLDRMEVIRLS  493 (782)
T ss_pred             -CCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhheEEEeecCccccCChHHhcceeeeeec
Confidence             345568899988631                122222222  111111222234456655421 111111122899999


Q ss_pred             CCCHHHHHHHHHhhhc
Q 001843          415 GLGKNESWELFLKKAR  430 (1007)
Q Consensus       415 ~L~~~ea~~Lf~~~a~  430 (1007)
                      +-+++|=.++-+++..
T Consensus       494 gYt~~EKl~IAk~~Li  509 (782)
T COG0466         494 GYTEDEKLEIAKRHLI  509 (782)
T ss_pred             CCChHHHHHHHHHhcc
Confidence            9999998888777654

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=96.49  E-value=0.044  Score=61.09  Aligned_cols=94  Identities=10%  Similarity=0.126  Sum_probs=65.8

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      +++=++|+|+++.-+...++.+. .+-.- ..++.+|++|.+...+.....+.+..+.+.+++.++..+.+.....    
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEP-p~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~~----  205 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEP-PPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQGV----  205 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCC-CcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcCC----
Confidence            44558899999987888888888 44333 5566666666665547766666668999999999999988876521    


Q ss_pred             cccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                           ++     ...++..++|.|+....+
T Consensus       206 -----~~-----~~~~l~~~~Gsp~~Al~~  225 (342)
T PRK06964        206 -----AD-----ADALLAEAGGAPLAALAL  225 (342)
T ss_pred             -----Ch-----HHHHHHHcCCCHHHHHHH
Confidence                 11     123577889999755443

>PRK04132 replication factor C small subunit; Provisional

Probab=96.48  E-value=0.031  Score=69.06  Aligned_cols=152  Identities=13%  Similarity=0.134  Sum_probs=96.0

Q ss_pred             CCCChHHHHHHHHHhhhhcccCCC-ceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHHcC-CCc
Q 001843          281 KAGSGKTTLARIVYNRVYVKRHFT-KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALD-DST  358 (1007)
Q Consensus       281 ~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~L~-~kr  358 (1007)
                      +.++||||+|..++++- ..+.++ .++-++++  .... .+.+++++..+...  .                -+. .+.
T Consensus       574 Ph~lGKTT~A~ala~~l-~g~~~~~~~lElNAS--d~rg-id~IR~iIk~~a~~--~----------------~~~~~~~  631 (846)
T PRK04132        574 PTVLHNTTAALALAREL-FGENWRHNFLELNAS--DERG-INVIREKVKEFART--K----------------PIGGASF  631 (846)
T ss_pred             CCcccHHHHHHHHHHhh-hcccccCeEEEEeCC--Cccc-HHHHHHHHHHHHhc--C----------------CcCCCCC
Confidence            67899999999999941 122232 25556665  3322 33444554443321  0                011 245


Q ss_pred             EEEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccccccC
Q 001843          359 FLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQS  438 (1007)
Q Consensus       359 ~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~  438 (1007)
                      -++|+|+++.-+.+..+.++.+.......+++|++|.+...+.....+.+..+++++++.++-.+.+...+.....   .
T Consensus       632 KVvIIDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi---~  708 (846)
T PRK04132        632 KIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGL---E  708 (846)
T ss_pred             EEEEEECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCC---C
Confidence            7999999997777777777733332144567776666655476666666699999999999988887766543221   1


Q ss_pred             CChHHHHHHHHHHHHcCCCchH
Q 001843          439 RSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       439 ~~~~~~~~~~~I~~~c~GlPLa  460 (1007)
                      .+   .+....|++.++|-+-.
T Consensus       709 i~---~e~L~~Ia~~s~GDlR~  727 (846)
T PRK04132        709 LT---EEGLQAILYIAEGDMRR  727 (846)
T ss_pred             CC---HHHHHHHHHHcCCCHHH
Confidence            11   45778999999998743

>TIGR00602 rad24 checkpoint protein rad24

Probab=96.46  E-value=0.013  Score=70.45  Aligned_cols=23  Identities=26%  Similarity=0.605  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +++.|+|++|.||||+++.++..
T Consensus       111 ~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602       111 RILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            78999999999999999999983

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.43  E-value=0.024  Score=63.63  Aligned_cols=124  Identities=12%  Similarity=0.196  Sum_probs=76.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhccc---------------------CCCceEEEEecCCCCCC---HHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR---------------------HFTKRAWVHIPIMSMVE---DRDVLADILKQ  329 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~---------------------~F~~~~wv~~s~~~~~~---~~~~l~~il~~  329 (1007)
                      ..+-++|++|+||||+|..+++.  +..                     ..+.+..+..+  ....   ..+..+++...
T Consensus        25 halL~~Gp~G~Gktt~a~~lA~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s--~~~~~~i~~~~vr~~~~~  100 (325)
T COG0470          25 HALLFYGPPGVGKTTAALALAKE--LLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPS--DLRKIDIIVEQVRELAEF  100 (325)
T ss_pred             ceeeeeCCCCCCHHHHHHHHHHH--HhCCCcccCCcccchhhhhHHhhcCCCceEEeccc--ccCCCcchHHHHHHHHHH
Confidence            35889999999999999999984  321                     12345555544  2222   22333333332


Q ss_pred             HhhhhhhhccccCHHHHHHHHHHHcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcc
Q 001843          330 IDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAF  408 (1007)
Q Consensus       330 l~~~~~~~~~~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~  408 (1007)
                      ....                   ...++.-++|+|+++..+.+.-+.+. .+-.. ...+.+|++|.....+.....+.+
T Consensus       101 ~~~~-------------------~~~~~~kviiidead~mt~~A~nallk~lEep-~~~~~~il~~n~~~~il~tI~SRc  160 (325)
T COG0470         101 LSES-------------------PLEGGYKVVIIDEADKLTEDAANALLKTLEEP-PKNTRFILITNDPSKILPTIRSRC  160 (325)
T ss_pred             hccC-------------------CCCCCceEEEeCcHHHHhHHHHHHHHHHhccC-CCCeEEEEEcCChhhccchhhhcc
Confidence            2221                   00356779999999866666666666 33333 567788888886655666666666


Q ss_pred             eeeecCCCCHHHH
Q 001843          409 STLHVPGLGKNES  421 (1007)
Q Consensus       409 ~~~~l~~L~~~ea  421 (1007)
                      ..+++.+.+..+.
T Consensus       161 ~~i~f~~~~~~~~  173 (325)
T COG0470         161 QRIRFKPPSRLEA  173 (325)
T ss_pred             eeeecCCchHHHH
Confidence            7888887444433

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=96.40  E-value=0.039  Score=59.72  Aligned_cols=43  Identities=30%  Similarity=0.318  Sum_probs=29.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVL  323 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l  323 (1007)
                      +-|.+.|.+|+|||++|+.+++  ....   ..+++++.  ...+..+++
T Consensus        22 ~~vLL~G~~GtGKT~lA~~la~--~lg~---~~~~i~~~--~~~~~~dll   64 (262)
T TIGR02640        22 YPVHLRGPAGTGKTTLAMHVAR--KRDR---PVMLINGD--AELTTSDLV   64 (262)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHH--HhCC---CEEEEeCC--ccCCHHHHh
Confidence            4556899999999999999997  3332   23455555  555444443

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=96.40  E-value=0.032  Score=58.70  Aligned_cols=66  Identities=20%  Similarity=0.085  Sum_probs=46.7

Q ss_pred             EEEEcCCCcccccccCCcc-eeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHH
Q 001843          390 IIITTSSTEDFVEPLGAAF-STLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVV  462 (1007)
Q Consensus       390 IliTTR~~~~va~~~~~~~-~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~  462 (1007)
                      |=-|||--. +.+-..... .+.+++..+++|-.+...+.+..-..      +-.++.+.+|+++..|-|--..
T Consensus       155 IGATTr~G~-lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i------~i~~~~a~eIA~rSRGTPRIAn  221 (332)
T COG2255         155 IGATTRAGM-LTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGI------EIDEEAALEIARRSRGTPRIAN  221 (332)
T ss_pred             eeecccccc-ccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCC------CCChHHHHHHHHhccCCcHHHH
Confidence            335898766 555444332 67889999999999999888754322      2335778999999999996433

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.40  E-value=0.016  Score=64.55  Aligned_cols=91  Identities=15%  Similarity=0.159  Sum_probs=56.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC-Cc-eEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhc--cccCHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF-TK-RAWVHIPIMSMVEDRDVLADILKQIDESLLKVE--ATLSAEELMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F-~~-~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~--~~~~~~~l~~~  349 (1007)
                      +-+.|+|..|+|||||++.+++  .+.... +. ++|+.+. .+..+..++++.+...+........  .....-.....
T Consensus       134 QR~LIvG~pGtGKTTLl~~la~--~i~~~~~dv~~vv~lIg-ER~~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~  210 (380)
T PRK12608        134 QRGLIVAPPRAGKTVLLQQIAA--AVAANHPEVHLMVLLID-ERPEEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLE  210 (380)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HHHhcCCCceEEEEEec-CCCCCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHH
Confidence            5669999999999999999998  443332 33 4677766 1445778888888776655310011  00011111112


Q ss_pred             HHHHc--CCCcEEEEEeCcC
Q 001843          350 ITQAL--DDSTFLIVMENAE  367 (1007)
Q Consensus       350 l~~~L--~~kr~LlVlDdv~  367 (1007)
                      +.+++  ++++.+||+|++.
T Consensus       211 ~Ae~f~~~GkdVVLvlDslt  230 (380)
T PRK12608        211 RAKRLVEQGKDVVILLDSLT  230 (380)
T ss_pred             HHHHHHHcCCCEEEEEeCcH
Confidence            22222  5899999999985

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.35  E-value=0.013  Score=74.30  Aligned_cols=92  Identities=16%  Similarity=0.304  Sum_probs=50.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.++|+.|+|||++|+.++.  .....-...+.++++  .-.. ......+   ++.+  +.....+.   ...+.+.
T Consensus       596 ~~~Lf~Gp~GvGKt~lA~~La~--~l~~~~~~~i~~d~s--~~~~-~~~~~~l---~g~~--~g~~g~~~---~g~l~~~  662 (852)
T TIGR03346       596 GSFLFLGPTGVGKTELAKALAE--FLFDDEDAMVRIDMS--EYME-KHSVARL---IGAP--PGYVGYEE---GGQLTEA  662 (852)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHH--HhcCCCCcEEEEech--hhcc-cchHHHh---cCCC--CCccCccc---ccHHHHH
Confidence            6788999999999999999998  333322334445554  2111 1111111   1211  00001100   1123333


Q ss_pred             cCCCc-EEEEEeCcCccCchhhhhhc
Q 001843          354 LDDST-FLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       354 L~~kr-~LlVlDdv~~~~~~~~~~l~  378 (1007)
                      ++.++ .+|+||++...+++.++.+.
T Consensus       663 v~~~p~~vlllDeieka~~~v~~~Ll  688 (852)
T TIGR03346       663 VRRKPYSVVLFDEVEKAHPDVFNVLL  688 (852)
T ss_pred             HHcCCCcEEEEeccccCCHHHHHHHH
Confidence            33333 49999999988888888777

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.35  E-value=0.013  Score=73.03  Aligned_cols=89  Identities=15%  Similarity=0.246  Sum_probs=51.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.++|+.|+|||+||+.++.  ..   +...+.++++  .-.+. .   .+...++..  ......+.   ...+.+.
T Consensus       485 ~~~lf~Gp~GvGKT~lA~~la~--~l---~~~~~~~d~s--e~~~~-~---~~~~lig~~--~gyvg~~~---~~~l~~~  548 (731)
T TIGR02639       485 GSFLFTGPTGVGKTELAKQLAE--AL---GVHLERFDMS--EYMEK-H---TVSRLIGAP--PGYVGFEQ---GGLLTEA  548 (731)
T ss_pred             eeEEEECCCCccHHHHHHHHHH--Hh---cCCeEEEeCc--hhhhc-c---cHHHHhcCC--CCCcccch---hhHHHHH
Confidence            5789999999999999999998  34   2334566655  21111 0   111112221  00011111   1223344


Q ss_pred             cCCCc-EEEEEeCcCccCchhhhhhc
Q 001843          354 LDDST-FLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       354 L~~kr-~LlVlDdv~~~~~~~~~~l~  378 (1007)
                      ++.++ -+|+||+++..+++.++.+.
T Consensus       549 ~~~~p~~VvllDEieka~~~~~~~Ll  574 (731)
T TIGR02639       549 VRKHPHCVLLLDEIEKAHPDIYNILL  574 (731)
T ss_pred             HHhCCCeEEEEechhhcCHHHHHHHH
Confidence            44444 49999999988888777776

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.31  E-value=0.015  Score=66.95  Aligned_cols=22  Identities=27%  Similarity=0.416  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .-|.|.|.+|+|||++|+.++.
T Consensus        40 ~hVLL~GpPGTGKT~LAraLa~   61 (498)
T PRK13531         40 ESVFLLGPPGIAKSLIARRLKF   61 (498)
T ss_pred             CCEEEECCCChhHHHHHHHHHH
Confidence            3467999999999999999998

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.31  E-value=0.019  Score=71.67  Aligned_cols=155  Identities=17%  Similarity=0.170  Sum_probs=77.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-|.++|.+|+|||+||+.+++  .....|   +.+..+        ++    .....        ......+...+...
T Consensus       213 ~giLL~GppGtGKT~laraia~--~~~~~~---i~i~~~--------~i----~~~~~--------g~~~~~l~~lf~~a  267 (733)
T TIGR01243       213 KGVLLYGPPGTGKTLLAKAVAN--EAGAYF---ISINGP--------EI----MSKYY--------GESEERLREIFKEA  267 (733)
T ss_pred             ceEEEECCCCCChHHHHHHHHH--HhCCeE---EEEecH--------HH----hcccc--------cHHHHHHHHHHHHH
Confidence            6788999999999999999999  333322   222221        00    00000        01112222333333


Q ss_pred             cCCCcEEEEEeCcCccC-----------chhhhhhccccCCC-CCCcEEEE-EcCCCcccccccCC---cceeeecCCCC
Q 001843          354 LDDSTFLIVMENAEHQK-----------SQVWDSFLGKLCSF-TQCGKIII-TTSSTEDFVEPLGA---AFSTLHVPGLG  417 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~-----------~~~~~~l~~l~~~~-~~gs~Ili-TTR~~~~va~~~~~---~~~~~~l~~L~  417 (1007)
                      ....+.+|+||+++...           ......+..+.+.. ..+..++| ||.....+......   ....+.+...+
T Consensus       268 ~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~  347 (733)
T TIGR01243       268 EENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPD  347 (733)
T ss_pred             HhcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcC
Confidence            44567899999986210           01122233222221 22334444 44433312221111   11567788888


Q ss_pred             HHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchH
Q 001843          418 KNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       418 ~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLa  460 (1007)
                      .++-.+++..+......     .  .......+++.+.|.--+
T Consensus       348 ~~~R~~Il~~~~~~~~l-----~--~d~~l~~la~~t~G~~ga  383 (733)
T TIGR01243       348 KRARKEILKVHTRNMPL-----A--EDVDLDKLAEVTHGFVGA  383 (733)
T ss_pred             HHHHHHHHHHHhcCCCC-----c--cccCHHHHHHhCCCCCHH
Confidence            88888888755432111     0  012245677777776543

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=96.31  E-value=0.049  Score=62.77  Aligned_cols=75  Identities=19%  Similarity=0.305  Sum_probs=52.8

Q ss_pred             CCCCCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHH
Q 001843          268 TTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELM  347 (1007)
Q Consensus       268 ~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~  347 (1007)
                      .+..+++=|.++|++|.|||.||+++++  ...-.|     +.++  .+        +|+..+        ...+.+.+.
T Consensus       218 lGv~PprGvLlHGPPGCGKT~lA~AiAg--el~vPf-----~~is--Ap--------eivSGv--------SGESEkkiR  272 (802)
T KOG0733|consen  218 LGVRPPRGVLLHGPPGCGKTSLANAIAG--ELGVPF-----LSIS--AP--------EIVSGV--------SGESEKKIR  272 (802)
T ss_pred             cCCCCCCceeeeCCCCccHHHHHHHHhh--hcCCce-----Eeec--ch--------hhhccc--------CcccHHHHH
Confidence            4556668899999999999999999999  444333     4443  11        222222        233556666


Q ss_pred             HHHHHHcCCCcEEEEEeCcC
Q 001843          348 WRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       348 ~~l~~~L~~kr~LlVlDdv~  367 (1007)
                      +.+.+.-..-++++++|+++
T Consensus       273 elF~~A~~~aPcivFiDeID  292 (802)
T KOG0733|consen  273 ELFDQAKSNAPCIVFIDEID  292 (802)
T ss_pred             HHHHHHhccCCeEEEeeccc
Confidence            66777777899999999997

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=96.26  E-value=0.011  Score=63.17  Aligned_cols=89  Identities=18%  Similarity=0.209  Sum_probs=52.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCc-eEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh-----ccccCH----
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTK-RAWVHIPIMSMVEDRDVLADILKQIDESLLKV-----EATLSA----  343 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~-~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~-----~~~~~~----  343 (1007)
                      +-++|+|-.|.|||||++.+++  .++.+|+. ++++.++ .+.....++.+++...=..+  ..     ..+...    
T Consensus        70 Qr~~If~~~G~GKTtLa~~i~~--~i~~~~~~~~V~~~iG-er~~Ev~e~~~~~~~~~~~~--~tvvv~~t~d~~~~~r~  144 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIMELIN--NIAKAHGGYSVFAGVG-ERTREGNDLYHEMKESGVLS--KTALVYGQMNEPPGARA  144 (274)
T ss_pred             CEEEEecCCCCChhHHHHHHHH--HHHhcCCCEEEEEEec-cCcHHHHHHHHHHHhcCCcc--eeEEEEECCCCCHHHHH
Confidence            7789999999999999999999  56656654 4555555 13334455555554321110  00     011111    


Q ss_pred             --HHHHHHHHHHc---CCCcEEEEEeCcC
Q 001843          344 --EELMWRITQAL---DDSTFLIVMENAE  367 (1007)
Q Consensus       344 --~~l~~~l~~~L---~~kr~LlVlDdv~  367 (1007)
                        -...-.+.+++   +++.+|+++||+-
T Consensus       145 ~~~~~a~~~AEyfr~~~g~~Vl~~~Dslt  173 (274)
T cd01133         145 RVALTGLTMAEYFRDEEGQDVLLFIDNIF  173 (274)
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEeChh
Confidence              11112233444   3899999999985

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>PRK07261 topology modulation protein; Provisional

Probab=96.26  E-value=0.011  Score=59.49  Aligned_cols=35  Identities=37%  Similarity=0.494  Sum_probs=24.9

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcc-cCCCceEEE
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVK-RHFTKRAWV  309 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv  309 (1007)
                      .|.|+|++|+||||||+++.....+. -+.|...|-
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~   37 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQ   37 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEec
Confidence            47899999999999999998742221 234555553

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=96.24  E-value=0.0052  Score=61.16  Aligned_cols=98  Identities=24%  Similarity=0.117  Sum_probs=63.9

Q ss_pred             EEEecCCCCCCCCCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCC--CccccCCCc
Q 001843          618 LAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTN--NNALGRLPF  695 (1007)
Q Consensus       618 Lsl~~~~~~~~~~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~l--p~~i~~L~~  695 (1007)
                      +.+..|........+.+++|.+|.+.+|.+..        +-+.+-  ..+++|.+|.|.+|++.  .+  ...+..++.
T Consensus        47 iDLtdNdl~~l~~lp~l~rL~tLll~nNrIt~--------I~p~L~--~~~p~l~~L~LtnNsi~--~l~dl~pLa~~p~  114 (233)
T KOG1644|consen   47 IDLTDNDLRKLDNLPHLPRLHTLLLNNNRITR--------IDPDLD--TFLPNLKTLILTNNSIQ--ELGDLDPLASCPK  114 (233)
T ss_pred             ecccccchhhcccCCCccccceEEecCCccee--------eccchh--hhccccceEEecCcchh--hhhhcchhccCCc
Confidence            34444444444444677788888888887743        223333  45577888888888766  33  234556778


Q ss_pred             CcEEecccCCCcccCc----ccccCCCCCEEeecCC
Q 001843          696 LEYLGLRSTFIDSLPD----STPILFCLATLDVSHT  727 (1007)
Q Consensus       696 Lr~L~L~~n~i~~LP~----~i~~L~~L~~L~L~~~  727 (1007)
                      |+||.+-+|.++.-+.    -+.++++|++||..+-
T Consensus       115 L~~Ltll~Npv~~k~~YR~yvl~klp~l~~LDF~kV  150 (233)
T KOG1644|consen  115 LEYLTLLGNPVEHKKNYRLYVLYKLPSLRTLDFQKV  150 (233)
T ss_pred             cceeeecCCchhcccCceeEEEEecCcceEeehhhh
Confidence            8888888887776654    3677888888887654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.23  E-value=0.032  Score=69.82  Aligned_cols=152  Identities=17%  Similarity=0.240  Sum_probs=79.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-|.++|++|.|||++|+++++  .....|     +.+.  .    .    +++...        .......+...+...
T Consensus       488 ~giLL~GppGtGKT~lakalA~--e~~~~f-----i~v~--~----~----~l~~~~--------vGese~~i~~~f~~A  542 (733)
T TIGR01243       488 KGVLLFGPPGTGKTLLAKAVAT--ESGANF-----IAVR--G----P----EILSKW--------VGESEKAIREIFRKA  542 (733)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--hcCCCE-----EEEe--h----H----HHhhcc--------cCcHHHHHHHHHHHH
Confidence            5688999999999999999999  343333     3332  1    0    111111        111222233333333


Q ss_pred             cCCCcEEEEEeCcCcc--------Cc----hhhhhhc-cccCC-CCCCcEEEEEcCCCcccccc-c-C--CcceeeecCC
Q 001843          354 LDDSTFLIVMENAEHQ--------KS----QVWDSFL-GKLCS-FTQCGKIIITTSSTEDFVEP-L-G--AAFSTLHVPG  415 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~--------~~----~~~~~l~-~l~~~-~~~gs~IliTTR~~~~va~~-~-~--~~~~~~~l~~  415 (1007)
                      -...+.+|++|+++.-        +.    ....++. .+..- ...+--||.||.... .... . .  -....+.++.
T Consensus       543 ~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~-~ld~allRpgRfd~~i~v~~  621 (733)
T TIGR01243       543 RQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPD-ILDPALLRPGRFDRLILVPP  621 (733)
T ss_pred             HhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChh-hCCHhhcCCCccceEEEeCC
Confidence            3467899999998621        00    1112232 22110 023344555776554 3321 1 1  1117888999


Q ss_pred             CCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCc
Q 001843          416 LGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       416 L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlP  458 (1007)
                      .+.++-.++|+.+......   ....+    ...+++.+.|.-
T Consensus       622 Pd~~~R~~i~~~~~~~~~~---~~~~~----l~~la~~t~g~s  657 (733)
T TIGR01243       622 PDEEARKEIFKIHTRSMPL---AEDVD----LEELAEMTEGYT  657 (733)
T ss_pred             cCHHHHHHHHHHHhcCCCC---CccCC----HHHHHHHcCCCC
Confidence            9999999999766543221   11111    345667776654

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=96.22  E-value=0.15  Score=60.11  Aligned_cols=182  Identities=10%  Similarity=0.189  Sum_probs=107.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhh---cccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVY---VKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~---~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      +.+-|.|-+|.|||..+..|-+.-.   -++.-+...+|.+..+.-....++...|+..+.+.      ..........+
T Consensus       423 ~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~~~lsg~------~~~~~~al~~L  496 (767)
T KOG1514|consen  423 SCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIWEALSGE------RVTWDAALEAL  496 (767)
T ss_pred             eeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHHHhcccC------cccHHHHHHHH
Confidence            6999999999999999999988432   12223333445555447778999999999999875      22333334444


Q ss_pred             HHHcC-----CCcEEEEEeCcC---ccCchhhhhhccccCCCCCCcEEEEEcCC--Cc--------ccccccCCcceeee
Q 001843          351 TQALD-----DSTFLIVMENAE---HQKSQVWDSFLGKLCSFTQCGKIIITTSS--TE--------DFVEPLGAAFSTLH  412 (1007)
Q Consensus       351 ~~~L~-----~kr~LlVlDdv~---~~~~~~~~~l~~l~~~~~~gs~IliTTR~--~~--------~va~~~~~~~~~~~  412 (1007)
                      ..++.     .+.+++++|+++   +.+.+..-.|..+|.  .++||++|.+=.  .+        +++..++.  ..+.
T Consensus       497 ~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt--~~~sKLvvi~IaNTmdlPEr~l~nrvsSRlg~--tRi~  572 (767)
T KOG1514|consen  497 NFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPT--LKNSKLVVIAIANTMDLPERLLMNRVSSRLGL--TRIC  572 (767)
T ss_pred             HHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCc--CCCCceEEEEecccccCHHHHhccchhhhccc--eeee
Confidence            44443     457899999875   222333333333332  456777765411  00        01112222  6777


Q ss_pred             cCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHh
Q 001843          413 VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL  468 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L  468 (1007)
                      ++|.++++-.+.......+...   -.....+-++++|+...|-.=.|+.+.-+..
T Consensus       573 F~pYth~qLq~Ii~~RL~~~~~---f~~~aielvarkVAavSGDaRraldic~RA~  625 (767)
T KOG1514|consen  573 FQPYTHEQLQEIISARLKGLDA---FENKAIELVARKVAAVSGDARRALDICRRAA  625 (767)
T ss_pred             cCCCCHHHHHHHHHHhhcchhh---cchhHHHHHHHHHHhccccHHHHHHHHHHHH
Confidence            7888888777777666554422   1234445556666666666666665554444

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.17  E-value=0.013  Score=62.35  Aligned_cols=91  Identities=16%  Similarity=0.252  Sum_probs=52.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC----CCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh------ccccCH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH----FTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV------EATLSA  343 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~------~~~~~~  343 (1007)
                      .++.|+|.+|.|||+||.+++-.......    -..++|++..  ..++.. -+.++++..+......      ....+.
T Consensus        20 ~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e--~~~~~~-rl~~~~~~~~~~~~~~~~~i~~~~~~~~   96 (235)
T cd01123          20 SITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTE--GTFRPE-RLVQIAERFGLDPEEVLDNIYVARAYNS   96 (235)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCC--CCcCHH-HHHHHHHHhccChHhHhcCEEEEecCCH
Confidence            89999999999999999999753222221    3578999877  666543 3344444433221000      011122


Q ss_pred             H---HHHHHHHHHcC-C-CcEEEEEeCcC
Q 001843          344 E---ELMWRITQALD-D-STFLIVMENAE  367 (1007)
Q Consensus       344 ~---~l~~~l~~~L~-~-kr~LlVlDdv~  367 (1007)
                      .   .....+.+.+. . +.-|||+|.+.
T Consensus        97 ~~l~~~l~~l~~~l~~~~~~~liVIDSis  125 (235)
T cd01123          97 DHQLQLLEELEAILIESSRIKLVIVDSVT  125 (235)
T ss_pred             HHHHHHHHHHHHHHhhcCCeeEEEEeCcH
Confidence            2   23334444443 2 45588888875

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.17  E-value=0.02  Score=59.73  Aligned_cols=45  Identities=20%  Similarity=0.325  Sum_probs=35.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVL  323 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l  323 (1007)
                      +++.|+|.+|+|||++|.+++..  .......++|++..  . ++...+.
T Consensus        13 ~i~~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e--~-~~~~rl~   57 (209)
T TIGR02237        13 TITQIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTE--G-LSPERFK   57 (209)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECC--C-CCHHHHH
Confidence            89999999999999999998873  43445678999876  4 5544433

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.12  E-value=0.051  Score=60.48  Aligned_cols=72  Identities=11%  Similarity=0.159  Sum_probs=47.6

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhh
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKK  428 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~  428 (1007)
                      +++-++|+|++..-+...-+.+. .+-.. ..++.+|++|.+...+.....+.+..+.+.+++.+++.+.+...
T Consensus       112 ~~~kV~iiEp~~~Ld~~a~naLLk~LEep-~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~  184 (325)
T PRK08699        112 GGLRVILIHPAESMNLQAANSLLKVLEEP-PPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRER  184 (325)
T ss_pred             CCceEEEEechhhCCHHHHHHHHHHHHhC-cCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhc
Confidence            33445566888755666666665 33322 34566777777665466665655689999999999998887654

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.09  E-value=0.015  Score=63.92  Aligned_cols=85  Identities=19%  Similarity=0.224  Sum_probs=55.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh--ccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV--EATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~--~~~~~~~~l~~~l~  351 (1007)
                      +++-|+|++|+||||||.+++-.  ....-..++||+..  ..++.     ..+++++.+....  ....+.++....+.
T Consensus        56 ~iteI~Gp~GsGKTtLal~~~~~--~~~~g~~~vyId~E--~~~~~-----~~a~~lGvd~~~l~v~~p~~~eq~l~i~~  126 (325)
T cd00983          56 RIIEIYGPESSGKTTLALHAIAE--AQKLGGTVAFIDAE--HALDP-----VYAKKLGVDLDNLLISQPDTGEQALEIAD  126 (325)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEECcc--ccHHH-----HHHHHcCCCHHHheecCCCCHHHHHHHHH
Confidence            89999999999999999998773  33445568899876  55554     2445554431111  12334555556665


Q ss_pred             HHcCC-CcEEEEEeCcC
Q 001843          352 QALDD-STFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~~-kr~LlVlDdv~  367 (1007)
                      ..++. ..-+||+|.|-
T Consensus       127 ~li~s~~~~lIVIDSva  143 (325)
T cd00983         127 SLVRSGAVDLIVVDSVA  143 (325)
T ss_pred             HHHhccCCCEEEEcchH
Confidence            55543 45589999874

RecA couples ATP hydrolysis to DNA strand exchange.

>TIGR02012 tigrfam_recA protein RecA

Probab=96.07  E-value=0.016  Score=63.77  Aligned_cols=85  Identities=15%  Similarity=0.223  Sum_probs=55.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh--ccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV--EATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~--~~~~~~~~l~~~l~  351 (1007)
                      +++-|+|.+|+||||||.+++..  ....-..++||+..  ..++..     .+++++.+....  ......++....+.
T Consensus        56 ~iteI~G~~GsGKTtLaL~~~~~--~~~~g~~v~yId~E--~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~  126 (321)
T TIGR02012        56 RIIEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAE--HALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAE  126 (321)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEccc--chhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            89999999999999999998773  33444567899776  555542     355554431111  12334555555555


Q ss_pred             HHcC-CCcEEEEEeCcC
Q 001843          352 QALD-DSTFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~-~kr~LlVlDdv~  367 (1007)
                      ..++ +..-+||+|.|-
T Consensus       127 ~li~~~~~~lIVIDSv~  143 (321)
T TIGR02012       127 TLVRSGAVDIIVVDSVA  143 (321)
T ss_pred             HHhhccCCcEEEEcchh
Confidence            5554 355699999875

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.05  E-value=0.017  Score=62.02  Aligned_cols=37  Identities=27%  Similarity=0.411  Sum_probs=29.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      .-+.++|.+|+|||.||.++.+.  +.+.--.+.++++.
T Consensus       106 ~nl~l~G~~G~GKThLa~Ai~~~--l~~~g~sv~f~~~~  142 (254)
T COG1484         106 ENLVLLGPPGVGKTHLAIAIGNE--LLKAGISVLFITAP  142 (254)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHH--HHHcCCeEEEEEHH
Confidence            56789999999999999999995  44433456777765

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.04  E-value=0.018  Score=72.67  Aligned_cols=92  Identities=15%  Similarity=0.260  Sum_probs=50.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.++|+.|+|||+||+.+++  .+-..-...+-++.+  .-.+...+ ..   -++.+  +.....+.   ...+.+.
T Consensus       540 ~~~lf~Gp~GvGKt~lA~~LA~--~l~~~~~~~~~~d~s--~~~~~~~~-~~---l~g~~--~gyvg~~~---~~~l~~~  606 (821)
T CHL00095        540 ASFLFSGPTGVGKTELTKALAS--YFFGSEDAMIRLDMS--EYMEKHTV-SK---LIGSP--PGYVGYNE---GGQLTEA  606 (821)
T ss_pred             eEEEEECCCCCcHHHHHHHHHH--HhcCCccceEEEEch--hccccccH-HH---hcCCC--CcccCcCc---cchHHHH
Confidence            5677999999999999999998  332222233444444  21111111 11   11211  00011111   1123444


Q ss_pred             cCCCc-EEEEEeCcCccCchhhhhhc
Q 001843          354 LDDST-FLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       354 L~~kr-~LlVlDdv~~~~~~~~~~l~  378 (1007)
                      ++.++ .+++||+++..+++.++.+.
T Consensus       607 ~~~~p~~VvllDeieka~~~v~~~Ll  632 (821)
T CHL00095        607 VRKKPYTVVLFDEIEKAHPDIFNLLL  632 (821)
T ss_pred             HHhCCCeEEEECChhhCCHHHHHHHH
Confidence            54555 48999999988888888777

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.02  E-value=0.083  Score=63.67  Aligned_cols=158  Identities=15%  Similarity=0.248  Sum_probs=90.3

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      -++=+-++|++|.|||-||++++-...|       =|+.++  .        .++.+.+.+.        ......+...
T Consensus       343 iPkGvLL~GPPGTGKTLLAKAiAGEAgV-------PF~svS--G--------SEFvE~~~g~--------~asrvr~lf~  397 (774)
T KOG0731|consen  343 IPKGVLLVGPPGTGKTLLAKAIAGEAGV-------PFFSVS--G--------SEFVEMFVGV--------GASRVRDLFP  397 (774)
T ss_pred             CcCceEEECCCCCcHHHHHHHHhcccCC-------ceeeec--h--------HHHHHHhccc--------chHHHHHHHH
Confidence            3477889999999999999999994332       245554  1        1222222221        0111111122


Q ss_pred             HHcCCCcEEEEEeCcCcc---------------CchhhhhhccccCCCCCCcEEEE--EcCCCccccccc----CCccee
Q 001843          352 QALDDSTFLIVMENAEHQ---------------KSQVWDSFLGKLCSFTQCGKIII--TTSSTEDFVEPL----GAAFST  410 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~---------------~~~~~~~l~~l~~~~~~gs~Ili--TTR~~~~va~~~----~~~~~~  410 (1007)
                      ..=...+++|.+|+++..               ....++++..-.++|..++.||+  +|...+ +....    +-....
T Consensus       398 ~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d-~ld~allrpGRfdr~  476 (774)
T KOG0731|consen  398 LARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPD-ILDPALLRPGRFDRQ  476 (774)
T ss_pred             HhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCcc-ccCHHhcCCCccccc
Confidence            222356889999988631               12233444422234343443333  555555 44321    111277


Q ss_pred             eecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHH
Q 001843          411 LHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       411 ~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai  461 (1007)
                      +.++.-+...-.++|.-++.....     ..+...+++ |+...-|.+=|.
T Consensus       477 i~i~~p~~~~r~~i~~~h~~~~~~-----~~e~~dl~~-~a~~t~gf~gad  521 (774)
T KOG0731|consen  477 IQIDLPDVKGRASILKVHLRKKKL-----DDEDVDLSK-LASLTPGFSGAD  521 (774)
T ss_pred             eeccCCchhhhHHHHHHHhhccCC-----CcchhhHHH-HHhcCCCCcHHH
Confidence            888888899999999998876443     234455666 888888887654

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.02  E-value=0.025  Score=60.84  Aligned_cols=91  Identities=19%  Similarity=0.268  Sum_probs=53.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC----CCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh------ccccCH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH----FTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV------EATLSA  343 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~------~~~~~~  343 (1007)
                      .|.-|+|.+|+|||.|+.+++-...+...    =..++|++-.  ..|+...+. +|++....+....      ....+.
T Consensus        39 ~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe--~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~  115 (256)
T PF08423_consen   39 SITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTE--GTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDL  115 (256)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESS--SSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSH
T ss_pred             cEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCC--CCCCHHHHH-HHhhccccccchhhhceeeeecCCH
Confidence            79999999999999999988764443322    2348999977  778776654 5666544321000      012233


Q ss_pred             HHHHHHH---HHHcC-CCcEEEEEeCcC
Q 001843          344 EELMWRI---TQALD-DSTFLIVMENAE  367 (1007)
Q Consensus       344 ~~l~~~l---~~~L~-~kr~LlVlDdv~  367 (1007)
                      +++...+   ...+. .+--|||+|.+-
T Consensus       116 ~~l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  116 EELLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHHHhhccccceEEEEecchH
Confidence            3333333   33332 333488888874

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PRK09354 recA recombinase A; Provisional

Probab=96.01  E-value=0.019  Score=63.65  Aligned_cols=85  Identities=16%  Similarity=0.225  Sum_probs=56.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh--ccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV--EATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~--~~~~~~~~l~~~l~  351 (1007)
                      +++-|+|.+|+||||||.+++..  ....-..++||+..  ..++.     ..+++++.+....  ......++....+.
T Consensus        61 ~IteI~G~~GsGKTtLal~~~~~--~~~~G~~~~yId~E--~s~~~-----~~a~~lGvdld~lli~qp~~~Eq~l~i~~  131 (349)
T PRK09354         61 RIVEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAE--HALDP-----VYAKKLGVDIDNLLVSQPDTGEQALEIAD  131 (349)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCc--cchHH-----HHHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            89999999999999999998873  33445678899876  66654     3455555432111  12334555556665


Q ss_pred             HHcCC-CcEEEEEeCcC
Q 001843          352 QALDD-STFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~~-kr~LlVlDdv~  367 (1007)
                      ..++. ..-+||+|.|-
T Consensus       132 ~li~s~~~~lIVIDSva  148 (349)
T PRK09354        132 TLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             HHhhcCCCCEEEEeChh
Confidence            55543 45599999875

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=95.99  E-value=0.013  Score=70.79  Aligned_cols=95  Identities=15%  Similarity=0.241  Sum_probs=57.7

Q ss_pred             CCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHH
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      .+..+...+|+.|+|||-||++++.  .+-+.=+..+-+++|   .|.-......   -++.+  +.....+.   ...|
T Consensus       519 rPigsFlF~GPTGVGKTELAkaLA~--~Lfg~e~aliR~DMS---Ey~EkHsVSr---LIGaP--PGYVGyee---GG~L  585 (786)
T COG0542         519 RPIGSFLFLGPTGVGKTELAKALAE--ALFGDEQALIRIDMS---EYMEKHSVSR---LIGAP--PGYVGYEE---GGQL  585 (786)
T ss_pred             CCceEEEeeCCCcccHHHHHHHHHH--HhcCCCccceeechH---HHHHHHHHHH---HhCCC--CCCceecc---ccch
Confidence            3447899999999999999999998  232111334444444   2222222222   22322  11111111   3456


Q ss_pred             HHHcCCCcE-EEEEeCcCccCchhhhhhc
Q 001843          351 TQALDDSTF-LIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       351 ~~~L~~kr~-LlVlDdv~~~~~~~~~~l~  378 (1007)
                      -+..+.++| +|.||.|...+++..+-+.
T Consensus       586 TEaVRr~PySViLlDEIEKAHpdV~nilL  614 (786)
T COG0542         586 TEAVRRKPYSVILLDEIEKAHPDVFNLLL  614 (786)
T ss_pred             hHhhhcCCCeEEEechhhhcCHHHHHHHH
Confidence            667778888 8889999988888888776

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=95.97  E-value=0.018  Score=67.00  Aligned_cols=95  Identities=9%  Similarity=0.044  Sum_probs=63.6

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHhhhccccc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      ++-=..|+|.|.-.+...|+.+. .+-.. ...-+.|..|.+.+.+....-+.++.|.++.++.++-...+...+.....
T Consensus       118 ~ryKVyiIDEvHMLS~~afNALLKTLEEP-P~hV~FIlATTe~~Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I  196 (515)
T COG2812         118 GRYKVYIIDEVHMLSKQAFNALLKTLEEP-PSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGI  196 (515)
T ss_pred             ccceEEEEecHHhhhHHHHHHHhcccccC-ccCeEEEEecCCcCcCchhhhhccccccccCCCHHHHHHHHHHHHHhcCC
Confidence            34448999999877888888887 44333 33445555555544487777777799999999999888888776654332


Q ss_pred             cccCCChHHHHHHHHHHHHcCCC
Q 001843          435 VLQSRSSELIKLKKQILNICDGL  457 (1007)
Q Consensus       435 ~~~~~~~~~~~~~~~I~~~c~Gl  457 (1007)
                            ....+...-|++..+|.
T Consensus       197 ------~~e~~aL~~ia~~a~Gs  213 (515)
T COG2812         197 ------NIEEDALSLIARAAEGS  213 (515)
T ss_pred             ------ccCHHHHHHHHHHcCCC
Confidence                  22344555666666663

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=95.96  E-value=0.0096  Score=59.35  Aligned_cols=103  Identities=19%  Similarity=0.241  Sum_probs=56.0

Q ss_pred             CCCeEEEeecCCCCCCcccccCCCCCcEEEecccC-CCCCcCccCCCCCCceEEEEEeeecCC-CCcCccccCCCCcEEE
Q 001843          819 ELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEY-DPMPILGRLRQLKILR  896 (1007)
Q Consensus       819 ~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~-~~~~~l~~Lp~L~~L~  896 (1007)
                      +...++|+++...  .+..|..++.|..|.|..|. ..+.. .+..++++|..|.|.+|.+.. ..+..+..+|+|++|.
T Consensus        43 ~~d~iDLtdNdl~--~l~~lp~l~rL~tLll~nNrIt~I~p-~L~~~~p~l~~L~LtnNsi~~l~dl~pLa~~p~L~~Lt  119 (233)
T KOG1644|consen   43 QFDAIDLTDNDLR--KLDNLPHLPRLHTLLLNNNRITRIDP-DLDTFLPNLKTLILTNNSIQELGDLDPLASCPKLEYLT  119 (233)
T ss_pred             ccceecccccchh--hcccCCCccccceEEecCCcceeecc-chhhhccccceEEecCcchhhhhhcchhccCCccceee
Confidence            3444455443322  24445556666677666655 55554 555556777777777776533 2345566677777777


Q ss_pred             eecCCcCCCcee--ecCCCCCCCcEEEecc
Q 001843          897 LFGGSYTGEEMS--CSSGEFPNLLVLKLWK  924 (1007)
Q Consensus       897 L~~~~~~~~~l~--~~~~~fp~L~~L~L~~  924 (1007)
                      +-+|......-+  .....+|+|+.|++..
T Consensus       120 ll~Npv~~k~~YR~yvl~klp~l~~LDF~k  149 (233)
T KOG1644|consen  120 LLGNPVEHKKNYRLYVLYKLPSLRTLDFQK  149 (233)
T ss_pred             ecCCchhcccCceeEEEEecCcceEeehhh
Confidence            765543221110  1122466666666654

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=95.95  E-value=0.019  Score=70.81  Aligned_cols=89  Identities=13%  Similarity=0.201  Sum_probs=49.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.++|+.|+|||++|+.++.  ....   ..+.++++  .-.... ....+   ++.+  ......+   ....+.+.
T Consensus       489 ~~~Lf~GP~GvGKT~lAk~LA~--~l~~---~~i~id~s--e~~~~~-~~~~L---iG~~--~gyvg~~---~~g~L~~~  552 (758)
T PRK11034        489 GSFLFAGPTGVGKTEVTVQLSK--ALGI---ELLRFDMS--EYMERH-TVSRL---IGAP--PGYVGFD---QGGLLTDA  552 (758)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HhCC---CcEEeech--hhcccc-cHHHH---cCCC--CCccccc---ccchHHHH
Confidence            6789999999999999999988  3432   23445544  221111 11111   1211  0000111   11123333


Q ss_pred             cCC-CcEEEEEeCcCccCchhhhhhc
Q 001843          354 LDD-STFLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       354 L~~-kr~LlVlDdv~~~~~~~~~~l~  378 (1007)
                      ++. ...+|+||+++..+++.++.+.
T Consensus       553 v~~~p~sVlllDEieka~~~v~~~LL  578 (758)
T PRK11034        553 VIKHPHAVLLLDEIEKAHPDVFNLLL  578 (758)
T ss_pred             HHhCCCcEEEeccHhhhhHHHHHHHH
Confidence            333 3459999999987787777776

>PRK04296 thymidine kinase; Provisional

Probab=95.94  E-value=0.015  Score=59.63  Aligned_cols=114  Identities=13%  Similarity=0.024  Sum_probs=64.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.|+|..|.||||+|...+.  +...+...++.+.    ..++.......++.+++..... .......++...+.+ 
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~--~~~~~g~~v~i~k----~~~d~~~~~~~i~~~lg~~~~~-~~~~~~~~~~~~~~~-   74 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAY--NYEERGMKVLVFK----PAIDDRYGEGKVVSRIGLSREA-IPVSSDTDIFELIEE-   74 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHH--HHHHcCCeEEEEe----ccccccccCCcEecCCCCcccc-eEeCChHHHHHHHHh-
Confidence            6889999999999999999988  4434433444442    2222222233445555432111 012334555555555 


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~  398 (1007)
                      ..++.-+||+|.+..-+.++..++. .+.   ..|..|++|.++..
T Consensus        75 ~~~~~dvviIDEaq~l~~~~v~~l~~~l~---~~g~~vi~tgl~~~  117 (190)
T PRK04296         75 EGEKIDCVLIDEAQFLDKEQVVQLAEVLD---DLGIPVICYGLDTD  117 (190)
T ss_pred             hCCCCCEEEEEccccCCHHHHHHHHHHHH---HcCCeEEEEecCcc
Confidence            2334459999999643333333333 322   45778999999865

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=95.93  E-value=0.006  Score=57.40  Aligned_cols=22  Identities=50%  Similarity=0.729  Sum_probs=20.6

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ||.|.|++|+||||+|+.+++.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999983

...

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=95.90  E-value=0.015  Score=64.01  Aligned_cols=27  Identities=19%  Similarity=0.501  Sum_probs=24.4

Q ss_pred             CCCcEEEEEEcCCCChHHHHHHHHHhh
Q 001843          270 TTTTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       270 ~~~~~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      -..++.++|||++|.|||.+|+++++.
T Consensus       145 ik~PlgllL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        145 IKVPLILGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             CCCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            456699999999999999999999993

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.87  E-value=0.047  Score=57.68  Aligned_cols=89  Identities=13%  Similarity=0.179  Sum_probs=53.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC------CceEEEEecCCCCCCHHHHHHHHHHHHhhhhhh------hcccc
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF------TKRAWVHIPIMSMVEDRDVLADILKQIDESLLK------VEATL  341 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F------~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~------~~~~~  341 (1007)
                      .++.|+|.+|.|||+||.+++..  ....-      ..++|++..  ..++...+ .++.+........      .....
T Consensus        20 ~v~~I~G~~GsGKT~l~~~ia~~--~~~~~~~~g~~~~v~yi~~e--~~~~~~rl-~~~~~~~~~~~~~~~~~i~~~~~~   94 (226)
T cd01393          20 RITEIFGEFGSGKTQLCLQLAVE--AQLPGELGGLEGKVVYIDTE--GAFRPERL-VQLAVRFGLDPEEVLDNIYVARPY   94 (226)
T ss_pred             cEEEEeCCCCCChhHHHHHHHHH--hhcccccCCCcceEEEEecC--CCCCHHHH-HHHHHHhccchhhhhccEEEEeCC
Confidence            89999999999999999999873  22233      457898876  66665433 3444433221000      01223


Q ss_pred             CHHHHHHHHHHHcC---C-CcEEEEEeCcC
Q 001843          342 SAEELMWRITQALD---D-STFLIVMENAE  367 (1007)
Q Consensus       342 ~~~~l~~~l~~~L~---~-kr~LlVlDdv~  367 (1007)
                      +.+++...+.+...   . +.-|||+|.+.
T Consensus        95 ~~~~~~~~l~~~~~~~~~~~~~lvVIDsis  124 (226)
T cd01393          95 NGEQQLEIVEELERIMSSGRVDLVVVDSVA  124 (226)
T ss_pred             CHHHHHHHHHHHHHHhhcCCeeEEEEcCcc
Confidence            45555555555442   3 44488888874

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=95.82  E-value=0.017  Score=61.14  Aligned_cols=37  Identities=19%  Similarity=0.314  Sum_probs=30.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      .++.|+|.+|+|||++|.+++..  ....-..++|++..
T Consensus        24 ~i~~i~G~~GsGKT~l~~~la~~--~~~~~~~v~yi~~e   60 (225)
T PRK09361         24 TITQIYGPPGSGKTNICLQLAVE--AAKNGKKVIYIDTE   60 (225)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEECC
Confidence            89999999999999999999884  33445678898764

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.79  E-value=0.072  Score=60.38  Aligned_cols=159  Identities=21%  Similarity=0.192  Sum_probs=91.0

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      +...+.+.|.+|+|||+||.+++.+    ..|+.+=-++-.     +.          ++.     .+...-..+.+...
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKiiSpe-----~m----------iG~-----sEsaKc~~i~k~F~  592 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKIISPE-----DM----------IGL-----SESAKCAHIKKIFE  592 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEeChH-----Hc----------cCc-----cHHHHHHHHHHHHH
Confidence            3478889999999999999999983    567754333211     00          000     01111222233344


Q ss_pred             HHcCCCcEEEEEeCcCccCchhhhhhc----------------cccCCCCCCcEEEEEcCCCcccccccCCcc---eeee
Q 001843          352 QALDDSTFLIVMENAEHQKSQVWDSFL----------------GKLCSFTQCGKIIITTSSTEDFVEPLGAAF---STLH  412 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~~~~~~~~l~----------------~l~~~~~~gs~IliTTR~~~~va~~~~~~~---~~~~  412 (1007)
                      ...+..--.||+||+.  ..-+|..+.                ..|.. ++.--|+-||.... |...|+-..   ..+.
T Consensus       593 DAYkS~lsiivvDdiE--rLiD~vpIGPRfSN~vlQaL~VllK~~ppk-g~kLli~~TTS~~~-vL~~m~i~~~F~~~i~  668 (744)
T KOG0741|consen  593 DAYKSPLSIIVVDDIE--RLLDYVPIGPRFSNLVLQALLVLLKKQPPK-GRKLLIFGTTSRRE-VLQEMGILDCFSSTIH  668 (744)
T ss_pred             HhhcCcceEEEEcchh--hhhcccccCchhhHHHHHHHHHHhccCCCC-CceEEEEecccHHH-HHHHcCHHHhhhheee
Confidence            4455666799999997  444443322                22333 23333444776666 777765322   6888


Q ss_pred             cCCCCH-HHHHHHHHhhh-ccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHh
Q 001843          413 VPGLGK-NESWELFLKKA-RIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL  468 (1007)
Q Consensus       413 l~~L~~-~ea~~Lf~~~a-~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L  468 (1007)
                      ++.++. ++..+.+...- |.        +.+.+.++.+.+.+|  +-.+|+-+-.++
T Consensus       669 Vpnl~~~~~~~~vl~~~n~fs--------d~~~~~~~~~~~~~~--~~vgIKklL~li  716 (744)
T KOG0741|consen  669 VPNLTTGEQLLEVLEELNIFS--------DDEVRAIAEQLLSKK--VNVGIKKLLMLI  716 (744)
T ss_pred             cCccCchHHHHHHHHHccCCC--------cchhHHHHHHHhccc--cchhHHHHHHHH
Confidence            888876 77777776653 33        234456666776666  334444444444

>PHA00729 NTP-binding motif containing protein

Probab=95.78  E-value=0.028  Score=58.35  Aligned_cols=24  Identities=42%  Similarity=0.430  Sum_probs=21.7

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhh
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ..-|.|.|.+|+||||||..+++.
T Consensus        17 f~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         17 FVSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHH
Confidence            367899999999999999999983

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=95.75  E-value=0.0094  Score=57.63  Aligned_cols=88  Identities=17%  Similarity=0.155  Sum_probs=49.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhc-ccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYV-KRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~-~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      .-|.|.|..|+||+++|+.++..... ...|..   +.+.  .                         ..    .+.+.+
T Consensus        22 ~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~---~~~~--~-------------------------~~----~~~l~~   67 (138)
T PF14532_consen   22 SPVLITGEPGTGKSLLARALHRYSGRANGPFIV---IDCA--S-------------------------LP----AELLEQ   67 (138)
T ss_dssp             S-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCC---CCHH--C-------------------------TC----HHHHHH
T ss_pred             CcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEE---echh--h-------------------------Cc----HHHHHH
Confidence            56789999999999999999984221 111211   1111  0                         01    111111


Q ss_pred             HcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCc
Q 001843          353 ALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~  398 (1007)
                         .+.--|+|+|++.-+.+....+. .+...-....|+|.||+..-
T Consensus        68 ---a~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l  111 (138)
T PF14532_consen   68 ---AKGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQDL  111 (138)
T ss_dssp             ---CTTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-C
T ss_pred             ---cCCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCCH
Confidence               14446789999865666666666 44322146779999988653

>COG5238 RNA1 Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

Probab=95.75  E-value=0.0027  Score=65.69  Aligned_cols=79  Identities=22%  Similarity=0.193  Sum_probs=45.1

Q ss_pred             CCCcccEEEecCCCCCCc---CCCccccCCCcCcEEecccCCC----cccCc-------ccccCCCCCEEeecCCccc-c
Q 001843          667 RLGMLKVLDLEGVYKPML---TNNNALGRLPFLEYLGLRSTFI----DSLPD-------STPILFCLATLDVSHTKVQ-R  731 (1007)
Q Consensus       667 ~l~~Lr~L~Ls~~~l~~~---~lp~~i~~L~~Lr~L~L~~n~i----~~LP~-------~i~~L~~L~~L~L~~~~l~-~  731 (1007)
                      .+..+..++||+|.+..+   .+...|.+-.+|+..+++.-..    .++|+       .+-++++|++.+|+.|-+. .
T Consensus        28 ~~d~~~evdLSGNtigtEA~e~l~~~ia~~~~L~vvnfsd~ftgr~kde~~~~L~~Ll~aLlkcp~l~~v~LSDNAfg~~  107 (388)
T COG5238          28 MMDELVEVDLSGNTIGTEAMEELCNVIANVRNLRVVNFSDAFTGRDKDELYSNLVMLLKALLKCPRLQKVDLSDNAFGSE  107 (388)
T ss_pred             hhcceeEEeccCCcccHHHHHHHHHHHhhhcceeEeehhhhhhcccHHHHHHHHHHHHHHHhcCCcceeeeccccccCcc
Confidence            466777777777776521   1234455566777777765221    13332       3456778888888877333 4


Q ss_pred             ccccccc-------cceeccc
Q 001843          732 LPYAFWP-------SRHLYLN  745 (1007)
Q Consensus       732 lP~~i~~-------Lr~L~l~  745 (1007)
                      .|..++.       |.||.++
T Consensus       108 ~~e~L~d~is~~t~l~HL~l~  128 (388)
T COG5238         108 FPEELGDLISSSTDLVHLKLN  128 (388)
T ss_pred             cchHHHHHHhcCCCceeEEee
Confidence            4443332       2667666

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.75  E-value=0.045  Score=64.18  Aligned_cols=134  Identities=13%  Similarity=0.105  Sum_probs=71.4

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .++-|.++|++|.|||.+|+++++  ...-.|   +-+..+  .      ++    ...        ...+...+.+.+.
T Consensus       258 ~pkGILL~GPpGTGKTllAkaiA~--e~~~~~---~~l~~~--~------l~----~~~--------vGese~~l~~~f~  312 (489)
T CHL00195        258 TPRGLLLVGIQGTGKSLTAKAIAN--DWQLPL---LRLDVG--K------LF----GGI--------VGESESRMRQMIR  312 (489)
T ss_pred             CCceEEEECCCCCcHHHHHHHHHH--HhCCCE---EEEEhH--H------hc----ccc--------cChHHHHHHHHHH
Confidence            347789999999999999999999  333222   112221  1      00    000        0111122222222


Q ss_pred             HHcCCCcEEEEEeCcCcc--------Cchhhhhhc-ccc---CCCCCCcEEEEEcCCCccccccc----CCcceeeecCC
Q 001843          352 QALDDSTFLIVMENAEHQ--------KSQVWDSFL-GKL---CSFTQCGKIIITTSSTEDFVEPL----GAAFSTLHVPG  415 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~--------~~~~~~~l~-~l~---~~~~~gs~IliTTR~~~~va~~~----~~~~~~~~l~~  415 (1007)
                      ..-...+++|++|+++..        +...-..+. .+.   +....+--||.||.+...+-..+    .-+ ..+.++.
T Consensus       313 ~A~~~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~~Ld~allR~GRFD-~~i~v~l  391 (489)
T CHL00195        313 IAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVFVVATANNIDLLPLEILRKGRFD-EIFFLDL  391 (489)
T ss_pred             HHHhcCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceEEEEecCChhhCCHHHhCCCcCC-eEEEeCC
Confidence            222357899999999721        000111111 111   11133334555776554222221    122 6788998


Q ss_pred             CCHHHHHHHHHhhhcc
Q 001843          416 LGKNESWELFLKKARI  431 (1007)
Q Consensus       416 L~~~ea~~Lf~~~a~~  431 (1007)
                      .+.++-.++|..+...
T Consensus       392 P~~~eR~~Il~~~l~~  407 (489)
T CHL00195        392 PSLEEREKIFKIHLQK  407 (489)
T ss_pred             cCHHHHHHHHHHHHhh
Confidence            9999999999887654

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.74  E-value=0.11  Score=61.18  Aligned_cols=73  Identities=22%  Similarity=0.234  Sum_probs=46.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-|-|.|..|+|||+||+++++... +.+.-.+.+|+++.........++                    ..+...+.+.
T Consensus       432 ~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQ--------------------k~l~~vfse~  490 (952)
T KOG0735|consen  432 GNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQ--------------------KFLNNVFSEA  490 (952)
T ss_pred             ccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHH--------------------HHHHHHHHHH
Confidence            5788999999999999999999433 333444566666511111111111                    1122334556


Q ss_pred             cCCCcEEEEEeCcC
Q 001843          354 LDDSTFLIVMENAE  367 (1007)
Q Consensus       354 L~~kr~LlVlDdv~  367 (1007)
                      +...+-+|||||++
T Consensus       491 ~~~~PSiIvLDdld  504 (952)
T KOG0735|consen  491 LWYAPSIIVLDDLD  504 (952)
T ss_pred             HhhCCcEEEEcchh
Confidence            67789999999996

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=95.73  E-value=0.34  Score=54.73  Aligned_cols=199  Identities=15%  Similarity=0.223  Sum_probs=108.3

Q ss_pred             cEEEEEeCcCcc---Cchhhhhhc---cccCCCCCCcEEEEEcCCCcccccc----cCCc-ceeeecCCCCHHHHHHHHH
Q 001843          358 TFLIVMENAEHQ---KSQVWDSFL---GKLCSFTQCGKIIITTSSTEDFVEP----LGAA-FSTLHVPGLGKNESWELFL  426 (1007)
Q Consensus       358 r~LlVlDdv~~~---~~~~~~~l~---~l~~~~~~gs~IliTTR~~~~va~~----~~~~-~~~~~l~~L~~~ea~~Lf~  426 (1007)
                      |=+||+||.-+.   +...|+.+.   +..-. .+--+||++|-+.. ....    +... .+.+.|.-.+++.|..+..
T Consensus       149 ~PVVVIdnF~~k~~~~~~iy~~laeWAa~Lv~-~nIAHVIFlT~dv~-~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~  226 (431)
T PF10443_consen  149 RPVVVIDNFLHKAEENDFIYDKLAEWAASLVQ-NNIAHVIFLTDDVS-YSKPLSKALPNRVFKTISLSDASPESAKQYVL  226 (431)
T ss_pred             CCEEEEcchhccCcccchHHHHHHHHHHHHHh-cCccEEEEECCCCc-hhhhHHHhCCCCceeEEeecCCCHHHHHHHHH
Confidence            558999998531   233344443   11222 34457888887765 4432    2221 1788999999999999998


Q ss_pred             hhhcccccc--------cc-CC-----ChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCChHHHHHHHHHcccchhhh
Q 001843          427 KKARIAEDV--------LQ-SR-----SSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNLVA  492 (1007)
Q Consensus       427 ~~a~~~~~~--------~~-~~-----~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~~~~w~~~l~~l~i~~~l~  492 (1007)
                      .+.......        .. ..     ...........++.+||=-.-+..+++.++.......-.+.+..+- ...+.+
T Consensus       227 ~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe~p~~Av~~iI~qs-a~eI~k  305 (431)
T PF10443_consen  227 SQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGESPEEAVEEIISQS-ASEIRK  305 (431)
T ss_pred             HHhcccccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHH-HHHHHH
Confidence            887653210        00 00     0234455667888999999999999999998765333344444332 122222


Q ss_pred             hhhc-------CCccCchhhhhhhccCCCCcccchhHHHHHHHhcccCCCCCCccCCHHHHHHHHHHHHHhccceEEEee
Q 001843          493 LCYQ-------DLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVIRW  565 (1007)
Q Consensus       493 ~sy~-------~L~~~~k~cfl~la~fp~~~~i~~~~Li~~Wiaeg~i~~~~~~~~~~e~~~~~~l~~Lv~rsll~~~~~  565 (1007)
                      ..+.       .++-.-.|...-+-.+-+...++...++.-    ..+    ..      .++..+..|.+..||.....
T Consensus       306 ~fl~~~~~~~~~~~Wt~~QaW~LIk~Ls~~~~v~Y~~ll~~----~lF----k~------~~E~~L~aLe~aeLItv~~~  371 (431)
T PF10443_consen  306 MFLLDDSDDAKSLKWTREQAWYLIKLLSKNDEVPYNELLLS----PLF----KG------NDETALRALEQAELITVTTD  371 (431)
T ss_pred             HHhcCCCCcccCCCCCHHHHHHHHHHhccCCcCcHHHHHcc----ccc----CC------CChHHHHHHHHCCcEEEEec
Confidence            2221       111112222222333334444444443321    011    01      13447889999999988764


Q ss_pred             cCCCCcceEE
Q 001843          566 RLDGSPKTCC  575 (1007)
Q Consensus       566 ~~~g~~~~~~  575 (1007)
                        +|+...++
T Consensus       372 --~G~p~~I~  379 (431)
T PF10443_consen  372 --NGRPSTIR  379 (431)
T ss_pred             --CCcCCeeE
Confidence              56555544

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.72  E-value=0.039  Score=61.68  Aligned_cols=87  Identities=23%  Similarity=0.232  Sum_probs=48.6

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCC--HHHHHHHHHHHHhhhhhhhccccCHHHHHHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVE--DRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~--~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      +++|+++|.+|+||||++..++..  ....-..+..++..   .+.  ..+-++.....++.+   .....+...+.+.+
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~--L~~~GkkVglI~aD---t~RiaAvEQLk~yae~lgip---v~v~~d~~~L~~aL  312 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQ--FHGKKKTVGFITTD---HSRIGTVQQLQDYVKTIGFE---VIAVRDEAAMTRAL  312 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHH--HHHcCCcEEEEecC---CcchHHHHHHHHHhhhcCCc---EEecCCHHHHHHHH
Confidence            389999999999999999999873  33332345556553   232  222333333333322   11234555565555


Q ss_pred             HHHcCC-CcEEEEEeCcC
Q 001843          351 TQALDD-STFLIVMENAE  367 (1007)
Q Consensus       351 ~~~L~~-kr~LlVlDdv~  367 (1007)
                      ...-.. +.=+|++|-.-
T Consensus       313 ~~lk~~~~~DvVLIDTaG  330 (436)
T PRK11889        313 TYFKEEARVDYILIDTAG  330 (436)
T ss_pred             HHHHhccCCCEEEEeCcc
Confidence            443322 23377778764

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.64  E-value=0.041  Score=63.42  Aligned_cols=91  Identities=24%  Similarity=0.251  Sum_probs=49.5

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .+.+|.++|.+|+||||.|..++.  .....-..+.-|++... .....+.++.++.+++.+........+.........
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~--~L~~~g~kV~lV~~D~~-R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al  170 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLAR--YFKKKGLKVGLVAADTY-RPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGL  170 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH--HHHHcCCeEEEecCCCC-CHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHH
Confidence            348999999999999999999998  34333224455554311 122344455556655443111111223333333333


Q ss_pred             HHcCCCcEEEEEeCc
Q 001843          352 QALDDSTFLIVMENA  366 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv  366 (1007)
                      +.+.+. =+||+|..
T Consensus       171 ~~~~~~-DvVIIDTA  184 (437)
T PRK00771        171 EKFKKA-DVIIVDTA  184 (437)
T ss_pred             HHhhcC-CEEEEECC
Confidence            333333 46777776

>cd01394 radB RadB

Probab=95.63  E-value=0.057  Score=56.72  Aligned_cols=37  Identities=24%  Similarity=0.311  Sum_probs=29.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +++.|.|.+|+||||+|.+++..  ....-..++|++..
T Consensus        20 ~i~~i~G~~GsGKT~l~~~~a~~--~~~~g~~v~yi~~e   56 (218)
T cd01394          20 TVTQVYGPPGTGKTNIAIQLAVE--TAGQGKKVAYIDTE   56 (218)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEECC
Confidence            89999999999999999999873  33333467888765

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK14974 cell division protein FtsY; Provisional

Probab=95.61  E-value=0.058  Score=60.04  Aligned_cols=100  Identities=17%  Similarity=0.247  Sum_probs=52.6

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccC-CCceEEEEecCCCCCC--HHHHHHHHHHHHhhhhhhhccccCHHHH-HH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRH-FTKRAWVHIPIMSMVE--DRDVLADILKQIDESLLKVEATLSAEEL-MW  348 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~s~~~~~~--~~~~l~~il~~l~~~~~~~~~~~~~~~l-~~  348 (1007)
                      +.+|.++|++|+||||++.+++.  ..... + .++.++.   ..+.  ..+-++..+..++.+........+.... ..
T Consensus       140 ~~vi~~~G~~GvGKTTtiakLA~--~l~~~g~-~V~li~~---Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~  213 (336)
T PRK14974        140 PVVIVFVGVNGTGKTTTIAKLAY--YLKKNGF-SVVIAAG---DTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYD  213 (336)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH--HHHHcCC-eEEEecC---CcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHH
Confidence            48999999999999999888887  33332 3 3444543   2332  2334455555555431111122233332 22


Q ss_pred             HHHHHcCCCcEEEEEeCcCcc--Cchhhhhhc
Q 001843          349 RITQALDDSTFLIVMENAEHQ--KSQVWDSFL  378 (1007)
Q Consensus       349 ~l~~~L~~kr~LlVlDdv~~~--~~~~~~~l~  378 (1007)
                      .+...-....=+|++|-.-..  +...++++.
T Consensus       214 ai~~~~~~~~DvVLIDTaGr~~~~~~lm~eL~  245 (336)
T PRK14974        214 AIEHAKARGIDVVLIDTAGRMHTDANLMDELK  245 (336)
T ss_pred             HHHHHHhCCCCEEEEECCCccCCcHHHHHHHH
Confidence            233222222238999987532  334445554

>PRK10867 signal recognition particle protein; Provisional

Probab=95.61  E-value=0.04  Score=63.42  Aligned_cols=38  Identities=34%  Similarity=0.457  Sum_probs=27.4

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccC-CCceEEEEe
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRH-FTKRAWVHI  311 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~~~wv~~  311 (1007)
                      .+.+|.++|.+|+||||.|.+++.  ..... -..++.|++
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~--~l~~~~G~kV~lV~~  137 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAK--YLKKKKKKKVLLVAA  137 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH--HHHHhcCCcEEEEEc
Confidence            348999999999999998888887  33333 233455554

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.56  E-value=0.038  Score=63.19  Aligned_cols=37  Identities=35%  Similarity=0.407  Sum_probs=27.6

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEe
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI  311 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~  311 (1007)
                      +.+|.++|.+|+||||+|.+++.  ..+.+-..++.|++
T Consensus       100 ~~vi~lvG~~GvGKTTtaaKLA~--~l~~~G~kV~lV~~  136 (429)
T TIGR01425       100 QNVIMFVGLQGSGKTTTCTKLAY--YYQRKGFKPCLVCA  136 (429)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEcC
Confidence            48999999999999999999887  33333224555554

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK05541 adenylylsulfate kinase; Provisional

Probab=95.54  E-value=0.034  Score=56.25  Aligned_cols=35  Identities=37%  Similarity=0.618  Sum_probs=29.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEE
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  310 (1007)
                      .+|.+.|+.|.||||+|+.+++  .....+...+++.
T Consensus         8 ~~I~i~G~~GsGKst~a~~l~~--~l~~~~~~~~~~~   42 (176)
T PRK05541          8 YVIWITGLAGSGKTTIAKALYE--RLKLKYSNVIYLD   42 (176)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH--HHHHcCCcEEEEe
Confidence            7999999999999999999999  5666666666653

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=95.46  E-value=0.038  Score=55.67  Aligned_cols=90  Identities=21%  Similarity=0.220  Sum_probs=44.9

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHH-HHHHHH
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELM-WRITQA  353 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~-~~l~~~  353 (1007)
                      ++.++|++|.||||++..++.  .....-..++.++... ......+.+...+...+.+........+...+. +.+...
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~--~~~~~g~~v~~i~~D~-~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLAL--YLKKKGKKVLLVAADT-YRPAAIEQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIEHA   78 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH--HHHHCCCcEEEEEcCC-CChHHHHHHHHhcccCCeEEEecCCCCCHHHHHHHHHHHH
Confidence            678999999999999999988  3433322344444330 111223333333443332211111223444333 333443


Q ss_pred             cCCCcEEEEEeCcC
Q 001843          354 LDDSTFLIVMENAE  367 (1007)
Q Consensus       354 L~~kr~LlVlDdv~  367 (1007)
                      .....-++|+|..-
T Consensus        79 ~~~~~d~viiDt~g   92 (173)
T cd03115          79 REENFDVVIVDTAG   92 (173)
T ss_pred             HhCCCCEEEEECcc
Confidence            44444366677654

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>KOG1947 consensus Leucine rich repeat proteins, some proteins contain F-box [General function prediction only]

Probab=95.38  E-value=0.0016  Score=77.41  Aligned_cols=38  Identities=26%  Similarity=0.190  Sum_probs=23.8

Q ss_pred             CCCCcccEEEecCCC-CCCcCCCccccCCCcCcEEeccc
Q 001843          666 RRLGMLKVLDLEGVY-KPMLTNNNALGRLPFLEYLGLRS  703 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~-l~~~~lp~~i~~L~~Lr~L~L~~  703 (1007)
                      ..++.|+.|.+.++. +....+-.....+++|+.|++++
T Consensus       185 ~~~~~L~~l~l~~~~~~~~~~~~~~~~~~~~L~~L~l~~  223 (482)
T KOG1947|consen  185 SSCPLLKRLSLSGCSKITDDSLDALALKCPNLEELDLSG  223 (482)
T ss_pred             hhCchhhHhhhcccccCChhhHHHHHhhCchhheecccC
Confidence            557788888888775 33111223455677777777765

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=95.33  E-value=0.0094  Score=57.69  Aligned_cols=85  Identities=21%  Similarity=0.342  Sum_probs=46.3

Q ss_pred             EEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHHcC
Q 001843          276 IALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALD  355 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~L~  355 (1007)
                      |.++|.+|+|||+||+.++.  .....   ..-+.++  ...+..+++...--. ...     .......+...+     
T Consensus         2 vlL~G~~G~GKt~l~~~la~--~~~~~---~~~i~~~--~~~~~~dl~g~~~~~-~~~-----~~~~~~~l~~a~-----   63 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAA--LLGRP---VIRINCS--SDTTEEDLIGSYDPS-NGQ-----FEFKDGPLVRAM-----   63 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHH--HHTCE---EEEEE-T--TTSTHHHHHCEEET--TTT-----TCEEE-CCCTTH-----
T ss_pred             EEEECCCCCCHHHHHHHHHH--Hhhcc---eEEEEec--cccccccceeeeeec-ccc-----cccccccccccc-----
Confidence            57999999999999999999  34221   2234555  666655544322211 000     000000000001     


Q ss_pred             CCcEEEEEeCcCccCchhhhhhc
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~  378 (1007)
                      .+..++|||++...+.+.+..+.
T Consensus        64 ~~~~il~lDEin~a~~~v~~~L~   86 (139)
T PF07728_consen   64 RKGGILVLDEINRAPPEVLESLL   86 (139)
T ss_dssp             HEEEEEEESSCGG--HHHHHTTH
T ss_pred             cceeEEEECCcccCCHHHHHHHH
Confidence            17899999999866666666665

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=95.33  E-value=0.016  Score=64.23  Aligned_cols=23  Identities=30%  Similarity=0.602  Sum_probs=21.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +++.++|++|.||||||+.+++.
T Consensus        79 ~il~L~GPPGsGKStla~~La~~  101 (361)
T smart00763       79 QILYLLGPVGGGKSSLVECLKRG  101 (361)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            89999999999999999999984

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>TIGR00959 ffh signal recognition particle protein

Probab=95.31  E-value=0.055  Score=62.21  Aligned_cols=91  Identities=21%  Similarity=0.271  Sum_probs=47.2

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcc-cCCCceEEEEecCCCCCC--HHHHHHHHHHHHhhhhhhhccccCHHHHHH
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVK-RHFTKRAWVHIPIMSMVE--DRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~~s~~~~~~--~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      ++.++.++|.+|+||||.|..++..  .. +.-..++-|++.   .+.  ..+-+.....+++.+........++..+..
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~--l~~~~g~kV~lV~~D---~~R~~a~~QL~~~a~~~gvp~~~~~~~~~P~~i~~  172 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYY--LKKKQGKKVLLVACD---LYRPAAIEQLKVLGQQVGVPVFALGKGQSPVEIAR  172 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH--HHHhCCCeEEEEecc---ccchHHHHHHHHHHHhcCCceEecCCCCCHHHHHH
Confidence            3489999999999999999998873  32 121234445543   222  233333444444332111112233444433


Q ss_pred             HHHHHcCCCcE-EEEEeCcC
Q 001843          349 RITQALDDSTF-LIVMENAE  367 (1007)
Q Consensus       349 ~l~~~L~~kr~-LlVlDdv~  367 (1007)
                      ...+....+.| +||+|-.-
T Consensus       173 ~al~~~~~~~~DvVIIDTaG  192 (428)
T TIGR00959       173 RALEYAKENGFDVVIVDTAG  192 (428)
T ss_pred             HHHHHHHhcCCCEEEEeCCC
Confidence            33333333444 67777653

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.27  E-value=0.1  Score=55.45  Aligned_cols=87  Identities=15%  Similarity=0.219  Sum_probs=54.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh----------------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV----------------  337 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~----------------  337 (1007)
                      +++.|+|.+|+|||++|.++... .++ +=..++|++..  +.  ..++.+.+ .+++-...+.                
T Consensus        26 ~~~~i~G~~GsGKt~l~~~~~~~-~~~-~g~~~~y~~~e--~~--~~~~~~~~-~~~g~~~~~~~~~g~l~i~~~~~~~~   98 (234)
T PRK06067         26 SLILIEGDHGTGKSVLSQQFVYG-ALK-QGKKVYVITTE--NT--SKSYLKQM-ESVKIDISDFFLWGYLRIFPLNTEGF   98 (234)
T ss_pred             cEEEEECCCCCChHHHHHHHHHH-HHh-CCCEEEEEEcC--CC--HHHHHHHH-HHCCCChhHHHhCCCceEEecccccc
Confidence            89999999999999999998653 222 34568888865  43  34444443 3333221110                


Q ss_pred             -ccccCHHHHHHHHHHHcCC-CcEEEEEeCcC
Q 001843          338 -EATLSAEELMWRITQALDD-STFLIVMENAE  367 (1007)
Q Consensus       338 -~~~~~~~~l~~~l~~~L~~-kr~LlVlDdv~  367 (1007)
                       ....+.+.+...+.+.+.. +.-++|+|.+.
T Consensus        99 ~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         99 EWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             ccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence             0112345666777777754 55689999875

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=95.21  E-value=0.038  Score=56.90  Aligned_cols=106  Identities=16%  Similarity=0.195  Sum_probs=53.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +++.|.|.+|.||||+++.+..  .....=..++++.-+       ......+.+..+..      ..+.+.........
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~--~~~~~g~~v~~~apT-------~~Aa~~L~~~~~~~------a~Ti~~~l~~~~~~   83 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAE--ALEAAGKRVIGLAPT-------NKAAKELREKTGIE------AQTIHSFLYRIPNG   83 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHH--HHHHTT--EEEEESS-------HHHHHHHHHHHTS-------EEEHHHHTTEECCE
T ss_pred             eEEEEEECCCCCHHHHHHHHHH--HHHhCCCeEEEECCc-------HHHHHHHHHhhCcc------hhhHHHHHhcCCcc
Confidence            7889999999999999999887  343332334444332       12222233332211      11111111110000


Q ss_pred             c------CCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCC
Q 001843          354 L------DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSST  397 (1007)
Q Consensus       354 L------~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~  397 (1007)
                      -      ..++-+||+|++.-.+...+..+. ....   .|+|+|+.=-..
T Consensus        84 ~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~---~~~klilvGD~~  131 (196)
T PF13604_consen   84 DDEGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK---SGAKLILVGDPN  131 (196)
T ss_dssp             ECCSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T----T-EEEEEE-TT
T ss_pred             cccccccCCcccEEEEecccccCHHHHHHHHHHHHh---cCCEEEEECCcc
Confidence            0      133459999999866666777776 4433   367777654433

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.18  E-value=0.047  Score=58.25  Aligned_cols=79  Identities=16%  Similarity=0.419  Sum_probs=51.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc--cCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK--RHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      |+|.++|++|.|||+|.++.++.-.++  ..|....-+.+.      ...++.+...+         ...-...+.+++.
T Consensus       178 RliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEin------shsLFSKWFsE---------SgKlV~kmF~kI~  242 (423)
T KOG0744|consen  178 RLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEIN------SHSLFSKWFSE---------SGKLVAKMFQKIQ  242 (423)
T ss_pred             eEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEe------hhHHHHHHHhh---------hhhHHHHHHHHHH
Confidence            899999999999999999999965443  345444445443      22233332222         2223566677777


Q ss_pred             HHcCCCcE--EEEEeCcC
Q 001843          352 QALDDSTF--LIVMENAE  367 (1007)
Q Consensus       352 ~~L~~kr~--LlVlDdv~  367 (1007)
                      +.+.++..  ++.+|.|.
T Consensus       243 ELv~d~~~lVfvLIDEVE  260 (423)
T KOG0744|consen  243 ELVEDRGNLVFVLIDEVE  260 (423)
T ss_pred             HHHhCCCcEEEEEeHHHH
Confidence            77777654  45578885

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=95.18  E-value=0.32  Score=54.56  Aligned_cols=27  Identities=33%  Similarity=0.516  Sum_probs=23.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH  302 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~  302 (1007)
                      .+|+|.|.=|+||||+.+.+.+  ..+..
T Consensus        21 ~~IgL~G~WGsGKSs~l~~l~~--~L~~~   47 (325)
T PF07693_consen   21 FVIGLYGEWGSGKSSFLNMLKE--ELKED   47 (325)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH--HHhcc
Confidence            8999999999999999999988  44444

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=95.16  E-value=0.067  Score=59.69  Aligned_cols=57  Identities=18%  Similarity=0.220  Sum_probs=41.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhccc----CCCceEEEEecCCCCCCHHHHHHHHHHHHhhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR----HFTKRAWVHIPIMSMVEDRDVLADILKQIDES  333 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~  333 (1007)
                      ++.-|+|.+|+|||+|+.+++-......    .-..++||+..  ..|+..++.+ +++.++.+
T Consensus       127 ~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE--~tF~peRl~~-ia~~~g~d  187 (344)
T PLN03187        127 CITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTE--GTFRPDRIVP-IAERFGMD  187 (344)
T ss_pred             eEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcC--CCCCHHHHHH-HHHHcCCC
Confidence            8999999999999999999875333321    12468999987  8888777544 55655443

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=95.15  E-value=0.5  Score=51.84  Aligned_cols=157  Identities=8%  Similarity=0.087  Sum_probs=89.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhh---h---cccC-CC-ceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRV---Y---VKRH-FT-KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEE  345 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~---~---~~~~-F~-~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~  345 (1007)
                      .+.-++|..|.||+++|+.+.+.-   .   +... .+ ...++... .......+ .+++.+.+...            
T Consensus        19 haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~-g~~i~vd~-Ir~l~~~~~~~------------   84 (299)
T PRK07132         19 HSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIF-DKDLSKSE-FLSAINKLYFS------------   84 (299)
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccC-CCcCCHHH-HHHHHHHhccC------------
Confidence            678899999999999999998731   0   0111 11 23333221 01111111 11222222111            


Q ss_pred             HHHHHHHHcC-CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHH
Q 001843          346 LMWRITQALD-DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWE  423 (1007)
Q Consensus       346 l~~~l~~~L~-~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~  423 (1007)
                             -.. +++=++|+|+++..+....+.+. .+-.. ...+.+|++|.+...+.....+.+..+++.++++++..+
T Consensus        85 -------~~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEP-p~~t~~il~~~~~~kll~TI~SRc~~~~f~~l~~~~l~~  156 (299)
T PRK07132         85 -------SFVQSQKKILIIKNIEKTSNSLLNALLKTIEEP-PKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQKILA  156 (299)
T ss_pred             -------CcccCCceEEEEecccccCHHHHHHHHHHhhCC-CCCeEEEEEeCChHhChHHHHhCeEEEECCCCCHHHHHH
Confidence                   011 46778899998865666666676 44443 556677765555443666555555999999999999987


Q ss_pred             HHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHH
Q 001843          424 LFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLL  464 (1007)
Q Consensus       424 Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~  464 (1007)
                      .+....    .     +   ++.+..++...+|.=-|+..+
T Consensus       157 ~l~~~~----~-----~---~~~a~~~a~~~~~~~~a~~~~  185 (299)
T PRK07132        157 KLLSKN----K-----E---KEYNWFYAYIFSNFEQAEKYI  185 (299)
T ss_pred             HHHHcC----C-----C---hhHHHHHHHHcCCHHHHHHHH
Confidence            776541    1     1   234556666677633455543

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=95.14  E-value=0.075  Score=58.79  Aligned_cols=56  Identities=14%  Similarity=0.203  Sum_probs=40.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc----cCCCceEEEEecCCCCCCHHHHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK----RHFTKRAWVHIPIMSMVEDRDVLADILKQIDE  332 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~  332 (1007)
                      +++-|+|.+|+|||+|+.+++-.....    ..=..++||+..  ..++..++. +++++++.
T Consensus        97 ~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE--~~f~~eRi~-~~a~~~g~  156 (313)
T TIGR02238        97 SITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTE--GTFRPDRIR-AIAERFGV  156 (313)
T ss_pred             eEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcC--CCCCHHHHH-HHHHHcCC
Confidence            899999999999999999877533332    112468999987  777777654 45666554

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.13  E-value=0.098  Score=56.73  Aligned_cols=90  Identities=18%  Similarity=0.193  Sum_probs=49.8

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCH--HHHHHHHHHHHhhhhhhhccccCHHH-HHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVED--RDVLADILKQIDESLLKVEATLSAEE-LMWR  349 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~--~~~l~~il~~l~~~~~~~~~~~~~~~-l~~~  349 (1007)
                      ++++.++|.+|+||||++..++.  .....-..+.++++.   .+..  .+-++..+...+..........+... ....
T Consensus        72 ~~vi~l~G~~G~GKTTt~akLA~--~l~~~g~~V~li~~D---~~r~~a~~ql~~~~~~~~i~~~~~~~~~dp~~~~~~~  146 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIAKLAN--KLKKQGKSVLLAAGD---TFRAAAIEQLEEWAKRLGVDVIKQKEGADPAAVAFDA  146 (272)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHH--HHHhcCCEEEEEeCC---CCCHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHH
Confidence            48999999999999999999987  344433456667654   2332  23334444444432111111122222 2333


Q ss_pred             HHHHcCCCcEEEEEeCcC
Q 001843          350 ITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       350 l~~~L~~kr~LlVlDdv~  367 (1007)
                      +........=++|+|-.-
T Consensus       147 l~~~~~~~~D~ViIDT~G  164 (272)
T TIGR00064       147 IQKAKARNIDVVLIDTAG  164 (272)
T ss_pred             HHHHHHCCCCEEEEeCCC
Confidence            444333444588888764

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.13  E-value=0.032  Score=57.65  Aligned_cols=107  Identities=16%  Similarity=0.189  Sum_probs=59.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHH-HHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDR-DVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~-~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      .+|.|+|..|.||||++..+..  .+.......+++--.   +.... .-...+..+-       +...+.....+.++.
T Consensus         2 GlilI~GptGSGKTTll~~ll~--~~~~~~~~~i~t~e~---~~E~~~~~~~~~i~q~-------~vg~~~~~~~~~i~~   69 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMID--YINKNKTHHILTIED---PIEFVHESKRSLINQR-------EVGLDTLSFENALKA   69 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH--HhhhcCCcEEEEEcC---CccccccCccceeeec-------ccCCCccCHHHHHHH
Confidence            5799999999999999998887  444444444444221   11100 0000011000       011123345566778


Q ss_pred             HcCCCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCc
Q 001843          353 ALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~  398 (1007)
                      .+...+=.|++|.+.  +.+.+..+. ..    ..|-.|+.|+-...
T Consensus        70 aLr~~pd~ii~gEir--d~e~~~~~l~~a----~~G~~v~~t~Ha~~  110 (198)
T cd01131          70 ALRQDPDVILVGEMR--DLETIRLALTAA----ETGHLVMSTLHTNS  110 (198)
T ss_pred             HhcCCcCEEEEcCCC--CHHHHHHHHHHH----HcCCEEEEEecCCc
Confidence            887778899999997  665555443 22    23445666665444

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK08233 hypothetical protein; Provisional

Probab=95.11  E-value=0.055  Score=54.94  Aligned_cols=22  Identities=32%  Similarity=0.555  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+|+|.|.+|+||||+|+.++.
T Consensus         4 ~iI~I~G~~GsGKtTla~~L~~   25 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTH   25 (182)
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            8999999999999999999987

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=95.11  E-value=0.0087  Score=37.46  Aligned_cols=17  Identities=47%  Similarity=0.769  Sum_probs=7.1

Q ss_pred             CcEEecccCCCcccCcc
Q 001843          696 LEYLGLRSTFIDSLPDS  712 (1007)
Q Consensus       696 Lr~L~L~~n~i~~LP~~  712 (1007)
                      |++|+|++|.++.+|.+
T Consensus         2 L~~Ldls~n~l~~ip~~   18 (22)
T PF00560_consen    2 LEYLDLSGNNLTSIPSS   18 (22)
T ss_dssp             ESEEEETSSEESEEGTT
T ss_pred             ccEEECCCCcCEeCChh
Confidence            34444444444444433

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.10  E-value=0.13  Score=50.58  Aligned_cols=122  Identities=16%  Similarity=0.088  Sum_probs=60.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCC-CCCCHHHHHHHHHHHHhhhh----------hhhccccC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIM-SMVEDRDVLADILKQIDESL----------LKVEATLS  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~-~~~~~~~~l~~il~~l~~~~----------~~~~~~~~  342 (1007)
                      ..|-|++-.|.||||+|...+-.  .-.+=-.+.++-+-.. ....-...++.+ ..+....          ........
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~r--a~~~g~~v~~vQFlKg~~~~gE~~~l~~l-~~v~~~~~g~~~~~~~~~~~~~~~~   79 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALR--ALGHGYRVGVVQFLKGGWKYGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEEeCCCCccCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHH
Confidence            47788888899999999888773  3333223444332211 122333333332 0000000          00001111


Q ss_pred             HHHHHHHHHHHcCCCcE-EEEEeCcCcc---CchhhhhhccccCCCCCCcEEEEEcCCCc
Q 001843          343 AEELMWRITQALDDSTF-LIVMENAEHQ---KSQVWDSFLGKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       343 ~~~l~~~l~~~L~~kr~-LlVlDdv~~~---~~~~~~~l~~l~~~~~~gs~IliTTR~~~  398 (1007)
                      .....+..++.+....| |||||++-..   ..-..+.+..+..+-..+..||+|.|+..
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            22334445555555555 9999998521   22223334422222144568999999865

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.09  E-value=0.092  Score=57.42  Aligned_cols=85  Identities=27%  Similarity=0.313  Sum_probs=46.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCC--HHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVE--DRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~--~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      ++++|+|.+|+||||++..++.....+..-..+..|+..   .+.  ..+.+......++.+   .....+...+...+.
T Consensus       195 ~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D---~~r~~a~eql~~~~~~~~~p---~~~~~~~~~l~~~l~  268 (282)
T TIGR03499       195 GVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTD---TYRIGAVEQLKTYAKILGVP---VKVARDPKELRKALD  268 (282)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECC---ccchhHHHHHHHHHHHhCCc---eeccCCHHHHHHHHH
Confidence            899999999999999999998742222111345666654   222  222333333333322   112234455554444


Q ss_pred             HHcCCCcEEEEEeCc
Q 001843          352 QALDDSTFLIVMENA  366 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv  366 (1007)
                      . +.+ .=+|++|..
T Consensus       269 ~-~~~-~d~vliDt~  281 (282)
T TIGR03499       269 R-LRD-KDLILIDTA  281 (282)
T ss_pred             H-ccC-CCEEEEeCC
Confidence            3 333 347777753

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=95.05  E-value=0.26  Score=58.92  Aligned_cols=23  Identities=26%  Similarity=0.497  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-|.|+|..|+|||++|+.+++.
T Consensus       211 ~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        211 LNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             CcEEEECCCCccHHHHHHHHHHh
Confidence            57889999999999999999983

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.04  E-value=0.13  Score=57.13  Aligned_cols=56  Identities=14%  Similarity=0.177  Sum_probs=38.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhccc----CCCceEEEEecCCCCCCHHHHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR----HFTKRAWVHIPIMSMVEDRDVLADILKQIDE  332 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~  332 (1007)
                      .++.|+|.+|+|||||+.+++.......    .-..++|++..  ..++... +.++++.++.
T Consensus        97 ~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE--~~f~~~R-l~~ia~~~~~  156 (316)
T TIGR02239        97 SITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTE--GTFRPER-LLAIAERYGL  156 (316)
T ss_pred             eEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECC--CCCCHHH-HHHHHHHcCC
Confidence            8999999999999999999876322211    12357999877  6666665 4445555443

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.04  E-value=0.093  Score=51.82  Aligned_cols=36  Identities=36%  Similarity=0.430  Sum_probs=27.9

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      ++.|+|.+|+||||+++.++..  ....-..++|+...
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~e   36 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALN--IATKGGKVVYVDIE   36 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHH--HHhcCCEEEEEECC
Confidence            4689999999999999999883  33344567777765

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=95.02  E-value=0.15  Score=63.27  Aligned_cols=23  Identities=30%  Similarity=0.641  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-|.|+|..|+|||++|+.+++.
T Consensus       400 ~pVLI~GE~GTGK~~lA~~ih~~  422 (686)
T PRK15429        400 STVLILGETGTGKELIARAIHNL  422 (686)
T ss_pred             CCEEEECCCCcCHHHHHHHHHHh
Confidence            57889999999999999999983

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=95.01  E-value=0.073  Score=62.80  Aligned_cols=73  Identities=19%  Similarity=0.329  Sum_probs=48.8

Q ss_pred             CCCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHH
Q 001843          270 TTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       270 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      -+..+++.++|++|+||||||.-|+.+    ..| .++=|.+|  ..-+...+-..|...+...                
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAkq----aGY-sVvEINAS--DeRt~~~v~~kI~~avq~~----------------  379 (877)
T KOG1969|consen  323 RPPKKILLLCGPPGLGKTTLAHVIAKQ----AGY-SVVEINAS--DERTAPMVKEKIENAVQNH----------------  379 (877)
T ss_pred             CCccceEEeecCCCCChhHHHHHHHHh----cCc-eEEEeccc--ccccHHHHHHHHHHHHhhc----------------
Confidence            344589999999999999999999983    223 35667777  5555444444444444332                


Q ss_pred             HHHHcC--CCcEEEEEeCcC
Q 001843          350 ITQALD--DSTFLIVMENAE  367 (1007)
Q Consensus       350 l~~~L~--~kr~LlVlDdv~  367 (1007)
                        ..+.  .++.-||+|.++
T Consensus       380 --s~l~adsrP~CLViDEID  397 (877)
T KOG1969|consen  380 --SVLDADSRPVCLVIDEID  397 (877)
T ss_pred             --cccccCCCcceEEEeccc
Confidence              1222  577789999997

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.00  E-value=0.26  Score=57.17  Aligned_cols=134  Identities=17%  Similarity=0.213  Sum_probs=77.9

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .+.=|.+||++|.|||-||++|+|  .-.-.|     ++|.   .+   +    ++...        ...+...+...++
T Consensus       544 ~PsGvLL~GPPGCGKTLlAKAVAN--Eag~NF-----isVK---GP---E----LlNkY--------VGESErAVR~vFq  598 (802)
T KOG0733|consen  544 APSGVLLCGPPGCGKTLLAKAVAN--EAGANF-----ISVK---GP---E----LLNKY--------VGESERAVRQVFQ  598 (802)
T ss_pred             CCCceEEeCCCCccHHHHHHHHhh--hccCce-----Eeec---CH---H----HHHHH--------hhhHHHHHHHHHH
Confidence            346788999999999999999999  455555     4443   11   1    11111        1122333334444


Q ss_pred             HHcCCCcEEEEEeCcCc-----cCchh------hhhhccccCCC--CCCcEEEEEcCCCccccccc--CC--cceeeecC
Q 001843          352 QALDDSTFLIVMENAEH-----QKSQV------WDSFLGKLCSF--TQCGKIIITTSSTEDFVEPL--GA--AFSTLHVP  414 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~-----~~~~~------~~~l~~l~~~~--~~gs~IliTTR~~~~va~~~--~~--~~~~~~l~  414 (1007)
                      +.-..-++.|+||.++.     .+...      .+++..-.++.  ..|--||-.|-.++ +....  ..  -...+-+.
T Consensus       599 RAR~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPD-iIDpAiLRPGRlDk~LyV~  677 (802)
T KOG0733|consen  599 RARASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPD-IIDPAILRPGRLDKLLYVG  677 (802)
T ss_pred             HhhcCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCc-ccchhhcCCCccCceeeec
Confidence            44456899999999862     11222      23333111221  34555666666555 43321  11  11677788


Q ss_pred             CCCHHHHHHHHHhhhcc
Q 001843          415 GLGKNESWELFLKKARI  431 (1007)
Q Consensus       415 ~L~~~ea~~Lf~~~a~~  431 (1007)
                      .-+.+|-.++++..+..
T Consensus       678 lPn~~eR~~ILK~~tkn  694 (802)
T KOG0733|consen  678 LPNAEERVAILKTITKN  694 (802)
T ss_pred             CCCHHHHHHHHHHHhcc
Confidence            88889999999888763

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=94.93  E-value=0.11  Score=52.68  Aligned_cols=122  Identities=11%  Similarity=0.165  Sum_probs=63.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHH------HHHHHHhhhhh--hhccccC-HH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLA------DILKQIDESLL--KVEATLS-AE  344 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~------~il~~l~~~~~--~~~~~~~-~~  344 (1007)
                      .+++|+|..|.|||||.+.++..  . ......+++.-......+......      ++++.++....  ......+ .+
T Consensus        26 ~~~~l~G~nGsGKStLl~~i~G~--~-~~~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G~  102 (180)
T cd03214          26 EIVGILGPNGAGKSTLLKTLAGL--L-KPSSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSGGE  102 (180)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC--C-CCCCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHHH
Confidence            79999999999999999999982  2 334444544311001112222111      13444333200  0011122 22


Q ss_pred             HHHHHHHHHcCCCcEEEEEeCcCc-cCchhhhhhc-cccCCCCC-CcEEEEEcCCCc
Q 001843          345 ELMWRITQALDDSTFLIVMENAEH-QKSQVWDSFL-GKLCSFTQ-CGKIIITTSSTE  398 (1007)
Q Consensus       345 ~l~~~l~~~L~~kr~LlVlDdv~~-~~~~~~~~l~-~l~~~~~~-gs~IliTTR~~~  398 (1007)
                      ...-.+.+.+-..+-++++|+.-. -|....+.+. .+...... +..||++|.+..
T Consensus       103 ~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~  159 (180)
T cd03214         103 RQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLN  159 (180)
T ss_pred             HHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            222335556667788999998752 1333344444 22221022 567888888766

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=94.91  E-value=0.84  Score=47.04  Aligned_cols=164  Identities=18%  Similarity=0.299  Sum_probs=83.8

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH-
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT-  351 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~-  351 (1007)
                      ++-+.++|++|.|||-||++||++       .++.|+.||  .    .++.+..+..             ....++.+. 
T Consensus       181 PKGvlLygppgtGktLlaraVahh-------t~c~firvs--g----selvqk~ige-------------gsrmvrelfv  234 (404)
T KOG0728|consen  181 PKGVLLYGPPGTGKTLLARAVAHH-------TDCTFIRVS--G----SELVQKYIGE-------------GSRMVRELFV  234 (404)
T ss_pred             CcceEEecCCCCchhHHHHHHHhh-------cceEEEEec--h----HHHHHHHhhh-------------hHHHHHHHHH
Confidence            367889999999999999999983       345667777  1    1222221111             011111111 


Q ss_pred             HHcCCCcEEEEEeCcCcc-----------Cchh-------hhhhccccCCCCCCcEEEEEcCCCccccccc--C--Ccce
Q 001843          352 QALDDSTFLIVMENAEHQ-----------KSQV-------WDSFLGKLCSFTQCGKIIITTSSTEDFVEPL--G--AAFS  409 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~~~-----------~~~~-------~~~l~~l~~~~~~gs~IliTTR~~~~va~~~--~--~~~~  409 (1007)
                      -.-..-+..|++|.++..           +.+.       ++++..|- . .+.-+||..|-.-+ +....  .  --..
T Consensus       235 marehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfe-a-tknikvimatnrid-ild~allrpgridr  311 (404)
T KOG0728|consen  235 MAREHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFE-A-TKNIKVIMATNRID-ILDPALLRPGRIDR  311 (404)
T ss_pred             HHHhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccc-c-ccceEEEEeccccc-cccHhhcCCCcccc
Confidence            111345778899988621           1111       11111221 1 45667887665544 43321  1  1116


Q ss_pred             eeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHh
Q 001843          410 TLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL  468 (1007)
Q Consensus       410 ~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L  468 (1007)
                      -++.++-+++.-.++++-+...-.-   ...-+++.+|.++....|.---++.+=|+..
T Consensus       312 kiefp~p~e~ar~~ilkihsrkmnl---~rgi~l~kiaekm~gasgaevk~vcteagm~  367 (404)
T KOG0728|consen  312 KIEFPPPNEEARLDILKIHSRKMNL---TRGINLRKIAEKMPGASGAEVKGVCTEAGMY  367 (404)
T ss_pred             cccCCCCCHHHHHHHHHHhhhhhch---hcccCHHHHHHhCCCCccchhhhhhhhhhHH
Confidence            7788888887777777665432211   1223445555544433333333444444443

>PRK06696 uridine kinase; Validated

Probab=94.90  E-value=0.04  Score=58.13  Aligned_cols=22  Identities=36%  Similarity=0.386  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+|+|.|.+|+||||||++++.
T Consensus        23 ~iI~I~G~sgsGKSTlA~~L~~   44 (223)
T PRK06696         23 LRVAIDGITASGKTTFADELAE   44 (223)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            8999999999999999999998

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=94.89  E-value=0.1  Score=53.63  Aligned_cols=82  Identities=18%  Similarity=0.222  Sum_probs=45.2

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccC-CC---ceEEEEecCCCCCCHHHHHHHHHHHHhhhh-hhhccccCHHHHHHH
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRH-FT---KRAWVHIPIMSMVEDRDVLADILKQIDESL-LKVEATLSAEELMWR  349 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~---~~~wv~~s~~~~~~~~~~l~~il~~l~~~~-~~~~~~~~~~~l~~~  349 (1007)
                      ||+|.|.+|+||||+|+++..  .+... +.   ....+...   .+.........-....... -......+.+.+.+.
T Consensus         1 IIgI~G~sgSGKTTla~~L~~--~L~~~~~~~~~~~~~~~~d---~~~~~~~~~~~~~~~~~~~~~~~p~a~d~~~l~~~   75 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQ--ILNKRGIPAMEMDIILSLD---DFYDDYHLRDRKGRGENRYNFDHPDAFDFDLLKED   75 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH--HHTTCTTTCCCSEEEEEGG---GGBHHHHHHHHHHHCTTTSSTTSGGGBSHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH--HhCccCcCccceeEEEeec---ccccccchhhHhhccccccCCCCccccCHHHHHHH
Confidence            799999999999999999998  44432 33   13333332   2222221111111110000 011245677778888


Q ss_pred             HHHHcCCCcEEE
Q 001843          350 ITQALDDSTFLI  361 (1007)
Q Consensus       350 l~~~L~~kr~Ll  361 (1007)
                      +....+++..-+
T Consensus        76 l~~L~~g~~i~~   87 (194)
T PF00485_consen   76 LKALKNGGSIEI   87 (194)
T ss_dssp             HHHHHTTSCEEE
T ss_pred             HHHHhCCCcccc
Confidence            877666666443

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=94.87  E-value=0.053  Score=52.26  Aligned_cols=44  Identities=30%  Similarity=0.450  Sum_probs=34.1

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES  333 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~  333 (1007)
                      +|.|-|.+|.||||+|+.++++  ..-             .-.+...++++|++..+.+
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~--~gl-------------~~vsaG~iFR~~A~e~gms   45 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEH--LGL-------------KLVSAGTIFREMARERGMS   45 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHH--hCC-------------ceeeccHHHHHHHHHcCCC
Confidence            6899999999999999999994  221             2223447889999888765

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.84  E-value=0.092  Score=59.60  Aligned_cols=87  Identities=20%  Similarity=0.166  Sum_probs=52.1

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcc--cCCCceEEEEecCCCCCCH--HHHHHHHHHHHhhhhhhhccccCHHHHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVK--RHFTKRAWVHIPIMSMVED--RDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~~F~~~~wv~~s~~~~~~~--~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      +++|.++|..|+||||.+.+++......  .+-..+..+++.   .+..  ..-++..+..++.+   .....+...+..
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~D---t~R~aa~eQL~~~a~~lgvp---v~~~~~~~~l~~  247 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITID---NYRIGAKKQIQTYGDIMGIP---VKAIESFKDLKE  247 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEecc---CccHHHHHHHHHHhhcCCcc---eEeeCcHHHHHH
Confidence            3899999999999999999998743222  122346666664   3332  22355555555443   223334455555


Q ss_pred             HHHHHcCCCcEEEEEeCcC
Q 001843          349 RITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       349 ~l~~~L~~kr~LlVlDdv~  367 (1007)
                      .+.+.  .+.-+|++|-+.
T Consensus       248 ~L~~~--~~~DlVLIDTaG  264 (388)
T PRK12723        248 EITQS--KDFDLVLVDTIG  264 (388)
T ss_pred             HHHHh--CCCCEEEEcCCC
Confidence            55443  345588899875

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=94.79  E-value=0.087  Score=57.91  Aligned_cols=85  Identities=18%  Similarity=0.295  Sum_probs=52.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhc--cccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVE--ATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~--~~~~~~~l~~~l~  351 (1007)
                      +++-|+|..|+||||||.++..  ...+.-..++||+..  ..++.     ..+..++.+....-  .....++..+.+.
T Consensus        54 ~ivEi~G~~ssGKttLaL~~ia--~~q~~g~~~a~ID~e--~~ld~-----~~a~~lGvdl~rllv~~P~~~E~al~~~e  124 (322)
T PF00154_consen   54 RIVEIYGPESSGKTTLALHAIA--EAQKQGGICAFIDAE--HALDP-----EYAESLGVDLDRLLVVQPDTGEQALWIAE  124 (322)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH--HHHHTT-EEEEEESS--S---H-----HHHHHTT--GGGEEEEE-SSHHHHHHHHH
T ss_pred             ceEEEeCCCCCchhhhHHHHHH--hhhcccceeEEecCc--ccchh-----hHHHhcCccccceEEecCCcHHHHHHHHH
Confidence            8999999999999999999887  344444568999876  55543     45556665522211  2334555556666


Q ss_pred             HHcCCC-cEEEEEeCcC
Q 001843          352 QALDDS-TFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~~k-r~LlVlDdv~  367 (1007)
                      +.++.. .-++|+|-|-
T Consensus       125 ~lirsg~~~lVVvDSv~  141 (322)
T PF00154_consen  125 QLIRSGAVDLVVVDSVA  141 (322)
T ss_dssp             HHHHTTSESEEEEE-CT
T ss_pred             HHhhcccccEEEEecCc
Confidence            666543 4488999875

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=94.78  E-value=0.016  Score=36.21  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=18.7

Q ss_pred             CCCEEeecCCcccccccccccc
Q 001843          718 CLATLDVSHTKVQRLPYAFWPS  739 (1007)
Q Consensus       718 ~L~~L~L~~~~l~~lP~~i~~L  739 (1007)
                      +|++|||++|+++.+|.++.+|
T Consensus         1 ~L~~Ldls~n~l~~ip~~~~~l   22 (22)
T PF00560_consen    1 NLEYLDLSGNNLTSIPSSFSNL   22 (22)
T ss_dssp             TESEEEETSSEESEEGTTTTT-
T ss_pred             CccEEECCCCcCEeCChhhcCC
Confidence            5899999999999999987654

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=94.74  E-value=0.2  Score=59.77  Aligned_cols=133  Identities=20%  Similarity=0.219  Sum_probs=76.9

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      ++.+-++|++|.|||.||+++++  ....+|-     .+.  ..    .    ++..        ........+...+..
T Consensus       276 ~~giLl~GpPGtGKT~lAkava~--~~~~~fi-----~v~--~~----~----l~sk--------~vGesek~ir~~F~~  330 (494)
T COG0464         276 PKGVLLYGPPGTGKTLLAKAVAL--ESRSRFI-----SVK--GS----E----LLSK--------WVGESEKNIRELFEK  330 (494)
T ss_pred             CCeeEEECCCCCCHHHHHHHHHh--hCCCeEE-----Eee--CH----H----Hhcc--------ccchHHHHHHHHHHH
Confidence            37899999999999999999999  4545543     222  00    1    1111        112233344444555


Q ss_pred             HcCCCcEEEEEeCcCc------cC-----chhhhhhccccCCCC--CCcEEEEEcCCCccccccc--C--CcceeeecCC
Q 001843          353 ALDDSTFLIVMENAEH------QK-----SQVWDSFLGKLCSFT--QCGKIIITTSSTEDFVEPL--G--AAFSTLHVPG  415 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~------~~-----~~~~~~l~~l~~~~~--~gs~IliTTR~~~~va~~~--~--~~~~~~~l~~  415 (1007)
                      ..+..++.|.+|.++.      .+     .....++....++..  .+..||-||-.+. .....  .  -....+.+.+
T Consensus       331 A~~~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~-~ld~a~lR~gRfd~~i~v~~  409 (494)
T COG0464         331 ARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPD-DLDPALLRPGRFDRLIYVPL  409 (494)
T ss_pred             HHcCCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCcc-ccCHhhcccCccceEeecCC
Confidence            5568899999999962      01     123334442222112  2323344444444 32211  1  1117888999


Q ss_pred             CCHHHHHHHHHhhhcc
Q 001843          416 LGKNESWELFLKKARI  431 (1007)
Q Consensus       416 L~~~ea~~Lf~~~a~~  431 (1007)
                      -+.++..+.|+.+...
T Consensus       410 pd~~~r~~i~~~~~~~  425 (494)
T COG0464         410 PDLEERLEIFKIHLRD  425 (494)
T ss_pred             CCHHHHHHHHHHHhcc
Confidence            9999999999998764

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=94.73  E-value=0.068  Score=54.89  Aligned_cols=78  Identities=13%  Similarity=0.122  Sum_probs=44.9

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      +.+|+|.|.+|.||||+|+.+++  .+...+  ++-++-.   .+-...-.....+....+ -..+...+.+-+.+.|..
T Consensus         8 ~iiIgIaG~SgSGKTTva~~l~~--~~~~~~--~~~I~~D---~YYk~~~~~~~~~~~~~n-~d~p~A~D~dLl~~~L~~   79 (218)
T COG0572           8 VIIIGIAGGSGSGKTTVAKELSE--QLGVEK--VVVISLD---DYYKDQSHLPFEERNKIN-YDHPEAFDLDLLIEHLKD   79 (218)
T ss_pred             eEEEEEeCCCCCCHHHHHHHHHH--HhCcCc--ceEeecc---ccccchhhcCHhhcCCcC-ccChhhhcHHHHHHHHHH
Confidence            48999999999999999999999  555442  2222211   111111111111111111 011245677778888888


Q ss_pred             HcCCCc
Q 001843          353 ALDDST  358 (1007)
Q Consensus       353 ~L~~kr  358 (1007)
                      .+++++
T Consensus        80 L~~g~~   85 (218)
T COG0572          80 LKQGKP   85 (218)
T ss_pred             HHcCCc
Confidence            888887

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=94.71  E-value=0.031  Score=56.00  Aligned_cols=84  Identities=13%  Similarity=0.124  Sum_probs=44.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.|.|.+|+||||+|..++..  ...   .++++.-.  ..+ ..+..+.|...................+.+.+...
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~--~~~---~~~~iat~--~~~-~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~   73 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQ--SGL---QVLYIATA--QPF-DDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRAD   73 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHH--cCC---CcEeCcCC--CCC-hHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhh
Confidence            46899999999999999999873  211   23333322  333 33444555443222100111112222344445443


Q ss_pred             cCCCcEEEEEeCc
Q 001843          354 LDDSTFLIVMENA  366 (1007)
Q Consensus       354 L~~kr~LlVlDdv  366 (1007)
                      ..+ .-++++|.+
T Consensus        74 ~~~-~~~VlID~L   85 (170)
T PRK05800         74 AAP-GRCVLVDCL   85 (170)
T ss_pred             cCC-CCEEEehhH
Confidence            433 337889986

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.70  E-value=0.13  Score=55.49  Aligned_cols=87  Identities=17%  Similarity=0.248  Sum_probs=53.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHH-HhhhhhhhccccCHHH---HHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQ-IDESLLKVEATLSAEE---LMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~-l~~~~~~~~~~~~~~~---l~~~  349 (1007)
                      +++-|+|+.|.||||+|.+++-  .....-..++|++.-  ..+++..+. ++... +..-  -.....+.++   ++..
T Consensus        61 ~ItEiyG~~gsGKT~lal~~~~--~aq~~g~~a~fIDtE--~~l~p~r~~-~l~~~~~d~l--~v~~~~~~e~q~~i~~~  133 (279)
T COG0468          61 RITEIYGPESSGKTTLALQLVA--NAQKPGGKAAFIDTE--HALDPERAK-QLGVDLLDNL--LVSQPDTGEQQLEIAEK  133 (279)
T ss_pred             eEEEEecCCCcchhhHHHHHHH--HhhcCCCeEEEEeCC--CCCCHHHHH-HHHHhhhcce--eEecCCCHHHHHHHHHH
Confidence            8999999999999999999887  344555588999987  777765433 33333 2111  0112223333   2333


Q ss_pred             HHHHcCCCcEEEEEeCcC
Q 001843          350 ITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       350 l~~~L~~kr~LlVlDdv~  367 (1007)
                      +......+--|+|+|.+-
T Consensus       134 ~~~~~~~~i~LvVVDSva  151 (279)
T COG0468         134 LARSGAEKIDLLVVDSVA  151 (279)
T ss_pred             HHHhccCCCCEEEEecCc
Confidence            333333334588888875

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=94.69  E-value=0.11  Score=55.05  Aligned_cols=128  Identities=18%  Similarity=0.207  Sum_probs=72.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec---CCCCCCHHHHHHHHHHHHhhhhh---hhccccCHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP---IMSMVEDRDVLADILKQIDESLL---KVEATLSAEELM  347 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s---~~~~~~~~~~l~~il~~l~~~~~---~~~~~~~~~~l~  347 (1007)
                      .+++|||..|.||||+++.+..  -. +.-...+++.-.   ........+...+++..++....   ..+...+..+++
T Consensus        40 e~~glVGESG~GKSTlgr~i~~--L~-~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQ  116 (268)
T COG4608          40 ETLGLVGESGCGKSTLGRLILG--LE-EPTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQ  116 (268)
T ss_pred             CEEEEEecCCCCHHHHHHHHHc--Cc-CCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhh
Confidence            7999999999999999999998  33 333444444321   00122344556666666664310   111222333333


Q ss_pred             -HHHHHHcCCCcEEEEEeCcCc-cCchhhhhhc----cccCCCCCCcEEEEEcCCCcccccccCCc
Q 001843          348 -WRITQALDDSTFLIVMENAEH-QKSQVWDSFL----GKLCSFTQCGKIIITTSSTEDFVEPLGAA  407 (1007)
Q Consensus       348 -~~l~~~L~~kr~LlVlDdv~~-~~~~~~~~l~----~l~~~~~~gs~IliTTR~~~~va~~~~~~  407 (1007)
                       -.+.+.|.-++-|+|.|..-. -|...-.++.    .+..  ..|-..+..|-+-. ++..+...
T Consensus       117 Ri~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~--~~~lt~lFIsHDL~-vv~~isdr  179 (268)
T COG4608         117 RIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQE--ELGLTYLFISHDLS-VVRYISDR  179 (268)
T ss_pred             hHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHH--HhCCeEEEEEEEHH-hhhhhccc
Confidence             346677888999999998541 0111112222    2222  34556777777777 77666543

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=94.68  E-value=0.059  Score=53.89  Aligned_cols=81  Identities=14%  Similarity=0.197  Sum_probs=43.1

Q ss_pred             EEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHHcC
Q 001843          276 IALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALD  355 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~L~  355 (1007)
                      +.|.|..|+|||++|.++...     ....++++.-.  +.++. ++.+.|...................+.+.+.+. .
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~-----~~~~~~y~at~--~~~d~-em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~-~   72 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE-----LGGPVTYIATA--EAFDD-EMAERIARHRKRRPAHWRTIETPRDLVSALKEL-D   72 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh-----cCCCeEEEEcc--CcCCH-HHHHHHHHHHHhCCCCceEeecHHHHHHHHHhc-C
Confidence            578999999999999999863     22456666555  55543 344443332111100011122223333333221 2


Q ss_pred             CCcEEEEEeCc
Q 001843          356 DSTFLIVMENA  366 (1007)
Q Consensus       356 ~kr~LlVlDdv  366 (1007)
                       +.-.+++|.+
T Consensus        73 -~~~~VLIDcl   82 (169)
T cd00544          73 -PGDVVLIDCL   82 (169)
T ss_pred             -CCCEEEEEcH
Confidence             2337999987

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.67  E-value=0.18  Score=53.74  Aligned_cols=46  Identities=17%  Similarity=0.242  Sum_probs=33.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLAD  325 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~  325 (1007)
                      +++.|.|.+|.|||++|.++... .. +.-+.++||+..  .  +..++.+.
T Consensus        22 s~~lI~G~pGsGKT~la~~~l~~-~~-~~ge~~lyvs~e--e--~~~~i~~~   67 (237)
T TIGR03877        22 NVVLLSGGPGTGKSIFSQQFLWN-GL-QMGEPGIYVALE--E--HPVQVRRN   67 (237)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH-HH-HcCCcEEEEEee--C--CHHHHHHH
Confidence            89999999999999999987663 22 345678888865  3  44455444

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.64  E-value=0.034  Score=53.50  Aligned_cols=30  Identities=27%  Similarity=0.442  Sum_probs=24.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC-CCc
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH-FTK  305 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F~~  305 (1007)
                      --|.|.||+|+||||+++.+++  ..+.. |..
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e--~L~~~g~kv   36 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAE--KLREKGYKV   36 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHH--HHHhcCcee
Confidence            5789999999999999999998  44433 544

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=94.57  E-value=0.24  Score=60.69  Aligned_cols=131  Identities=15%  Similarity=0.167  Sum_probs=70.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-|.++|++|.|||++|+.+++  .....|   +.+..+  .          +.....        ......+...+...
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~--~~~~~f---~~is~~--~----------~~~~~~--------g~~~~~~~~~f~~a  240 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAG--EAKVPF---FTISGS--D----------FVEMFV--------GVGASRVRDMFEQA  240 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHH--HcCCCE---EEEehH--H----------hHHhhh--------cccHHHHHHHHHHH
Confidence            4489999999999999999998  343333   222222  1          000000        01112222333333


Q ss_pred             cCCCcEEEEEeCcCcc----------Cchhhhhhc-cc---cCCC--CCCcEEEEEcCCCccccc-cc----CCcceeee
Q 001843          354 LDDSTFLIVMENAEHQ----------KSQVWDSFL-GK---LCSF--TQCGKIIITTSSTEDFVE-PL----GAAFSTLH  412 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~----------~~~~~~~l~-~l---~~~~--~~gs~IliTTR~~~~va~-~~----~~~~~~~~  412 (1007)
                      -...+++|++|+++.-          ....++... .+   .+++  ..+.-||.||...+ ... ..    .-+ ..+.
T Consensus       241 ~~~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~-~lD~Al~RpgRfd-r~i~  318 (644)
T PRK10733        241 KKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPD-VLDPALLRPGRFD-RQVV  318 (644)
T ss_pred             HhcCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChh-hcCHHHhCCcccc-eEEE
Confidence            3457899999999731          011222222 21   1221  22334455776655 322 11    112 6788


Q ss_pred             cCCCCHHHHHHHHHhhhcc
Q 001843          413 VPGLGKNESWELFLKKARI  431 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~  431 (1007)
                      +...+.++-.++++.+...
T Consensus       319 v~~Pd~~~R~~Il~~~~~~  337 (644)
T PRK10733        319 VGLPDVRGREQILKVHMRR  337 (644)
T ss_pred             cCCCCHHHHHHHHHHHhhc
Confidence            8888888888888877644

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=94.57  E-value=0.33  Score=52.47  Aligned_cols=150  Identities=17%  Similarity=0.184  Sum_probs=84.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCC-ceEEEEecCCCCC-CHHHHHHHHHHHHhhhhhhh-ccccCHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFT-KRAWVHIPIMSMV-EDRDVLADILKQIDESLLKV-EATLSAEELMWRI  350 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~-~~~wv~~s~~~~~-~~~~~l~~il~~l~~~~~~~-~~~~~~~~l~~~l  350 (1007)
                      --|.|+|+.|.|||+|.-.+..+   .+.|. ..+-|...  ... ..+-.++.|..|+....... ....+..+...++
T Consensus        50 nsviiigprgsgkT~li~~~Ls~---~q~~~E~~l~v~Ln--g~~~~dk~al~~I~rql~~e~~~~~k~~gsfte~l~~l  124 (408)
T KOG2228|consen   50 NSVIIIGPRGSGKTILIDTRLSD---IQENGENFLLVRLN--GELQTDKIALKGITRQLALELNRIVKSFGSFTENLSKL  124 (408)
T ss_pred             CceEEEccCCCCceEeeHHHHhh---HHhcCCeEEEEEEC--ccchhhHHHHHHHHHHHHHHHhhhheeecccchhHHHH
Confidence            46789999999999998888775   22232 22333333  222 23446777777776542222 1334444555555


Q ss_pred             HHHcC------CCcEEEEEeCcCccCchh----hhhhccccC--CCCCCcEEEEEcCCCc------ccccccCCcceeee
Q 001843          351 TQALD------DSTFLIVMENAEHQKSQV----WDSFLGKLC--SFTQCGKIIITTSSTE------DFVEPLGAAFSTLH  412 (1007)
Q Consensus       351 ~~~L~------~kr~LlVlDdv~~~~~~~----~~~l~~l~~--~~~~gs~IliTTR~~~------~va~~~~~~~~~~~  412 (1007)
                      -..|+      ..++.+|+|.++-.-...    .-.+....+  . .+-+-|-+|||-.-      +|-..+.-. .++-
T Consensus       125 L~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r-~Piciig~Ttrld~lE~LEKRVKSRFshr-~I~m  202 (408)
T KOG2228|consen  125 LEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSAR-APICIIGVTTRLDILELLEKRVKSRFSHR-VIFM  202 (408)
T ss_pred             HHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcC-CCeEEEEeeccccHHHHHHHHHHhhcccc-eeec
Confidence            55553      235788888775211111    011111111  2 45567788999532      122333332 5777


Q ss_pred             cCCCCHHHHHHHHHhhhc
Q 001843          413 VPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~  430 (1007)
                      +++++-++...++++...
T Consensus       203 ~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  203 LPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             cCCCChHHHHHHHHHHhc
Confidence            788889999999988763

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=94.56  E-value=0.091  Score=52.55  Aligned_cols=22  Identities=36%  Similarity=0.616  Sum_probs=19.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .-|.|+|..|+||+.+|+.+++
T Consensus        23 ~pVlI~GE~GtGK~~lA~~IH~   44 (168)
T PF00158_consen   23 LPVLITGETGTGKELLARAIHN   44 (168)
T ss_dssp             S-EEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEcCCCCcHHHHHHHHHH
Confidence            4556999999999999999999

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=94.55  E-value=0.063  Score=53.52  Aligned_cols=115  Identities=20%  Similarity=0.200  Sum_probs=59.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .+++|+|..|.|||||.+.++.-  . ......+++.-......+..+..+   ..++.-    ..-...+...-.+.+.
T Consensus        27 e~~~l~G~nGsGKSTLl~~i~G~--~-~~~~G~v~~~g~~~~~~~~~~~~~---~~i~~~----~qLS~G~~qrl~lara   96 (163)
T cd03216          27 EVHALLGENGAGKSTLMKILSGL--Y-KPDSGEILVDGKEVSFASPRDARR---AGIAMV----YQLSVGERQMVEIARA   96 (163)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC--C-CCCCeEEEECCEECCcCCHHHHHh---cCeEEE----EecCHHHHHHHHHHHH
Confidence            79999999999999999999982  2 334455555321001111111111   011100    0111122222234455


Q ss_pred             cCCCcEEEEEeCcCc-cCchhhhhhc-cccCCCCCCcEEEEEcCCCc
Q 001843          354 LDDSTFLIVMENAEH-QKSQVWDSFL-GKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~-~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~  398 (1007)
                      +-.++-++++|+.-. -|......+. .+......|..||++|.+..
T Consensus        97 l~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~  143 (163)
T cd03216          97 LARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLD  143 (163)
T ss_pred             HhcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH
Confidence            666778889998752 2333344444 22221123667888888765

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>TIGR01069 mutS2 MutS2 family protein

Probab=94.53  E-value=0.021  Score=70.89  Aligned_cols=116  Identities=16%  Similarity=0.097  Sum_probs=58.5

Q ss_pred             CCcEEEEEeCcCcc-Cchhhhhhc-cccCC-CCCCcEEEEEcCCCcccccccCCccee--eecCCCCHHHHHHHHHhhhc
Q 001843          356 DSTFLIVMENAEHQ-KSQVWDSFL-GKLCS-FTQCGKIIITTSSTEDFVEPLGAAFST--LHVPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~-~~~~~~~l~-~l~~~-~~~gs~IliTTR~~~~va~~~~~~~~~--~~l~~L~~~ea~~Lf~~~a~  430 (1007)
                      ..+-|+++|..-.. ++.....+. .+... ...|+.+|+||-... +.........+  ..+. ++. +......+..-
T Consensus       401 ~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l~~~g~~viitTH~~e-L~~~~~~~~~v~~~~~~-~d~-~~l~p~Ykl~~  477 (771)
T TIGR01069       401 TENSLVLFDELGAGTDPDEGSALAISILEYLLKQNAQVLITTHYKE-LKALMYNNEGVENASVL-FDE-ETLSPTYKLLK  477 (771)
T ss_pred             CCCcEEEecCCCCCCCHHHHHHHHHHHHHHHHhcCCEEEEECChHH-HHHHhcCCCCeEEeEEE-EcC-CCCceEEEECC
Confidence            57899999998632 333333332 22111 134788999999877 54332221111  1110 010 11111111111


Q ss_pred             cccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCChHHHHHHHHHcc
Q 001843          431 IAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERAN  486 (1007)
Q Consensus       431 ~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~~~~w~~~l~~l~  486 (1007)
                      +  .     +  -...|-+|++++ |+|-.|.--|..+....  ..++..++..+.
T Consensus       478 G--~-----~--g~S~a~~iA~~~-Glp~~ii~~A~~~~~~~--~~~~~~li~~L~  521 (771)
T TIGR01069       478 G--I-----P--GESYAFEIAQRY-GIPHFIIEQAKTFYGEF--KEEINVLIEKLS  521 (771)
T ss_pred             C--C-----C--CCcHHHHHHHHh-CcCHHHHHHHHHHHHhh--HHHHHHHHHHHH
Confidence            1  0     1  134577788877 88888888777776544  445666665543

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=94.52  E-value=0.093  Score=58.57  Aligned_cols=55  Identities=15%  Similarity=0.270  Sum_probs=39.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC----CCceEEEEecCCCCCCHHHHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH----FTKRAWVHIPIMSMVEDRDVLADILKQID  331 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~----F~~~~wv~~s~~~~~~~~~~l~~il~~l~  331 (1007)
                      .++-|+|.+|+|||++|.+++-.......    =..++||+..  ..++...+. ++++.++
T Consensus       103 ~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te--~~f~~~rl~-~~~~~~g  161 (317)
T PRK04301        103 SITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTE--GTFRPERIE-QMAEALG  161 (317)
T ss_pred             cEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCC--CCcCHHHHH-HHHHHcC
Confidence            89999999999999999999874322211    1368999987  777766554 4444443

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=94.51  E-value=0.068  Score=57.72  Aligned_cols=23  Identities=39%  Similarity=0.384  Sum_probs=18.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ..|.|.|.+|+||||+|+++...
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~   24 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKY   24 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHH
Confidence            57899999999999999999883

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=94.51  E-value=0.1  Score=58.33  Aligned_cols=22  Identities=27%  Similarity=0.499  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .-|.|+|..|+||+++|+.++.
T Consensus        30 ~pVlI~GE~GtGK~~lA~~iH~   51 (326)
T PRK11608         30 KPVLIIGERGTGKELIASRLHY   51 (326)
T ss_pred             CCEEEECCCCCcHHHHHHHHHH
Confidence            5678999999999999999987

>PRK05480 uridine/cytidine kinase; Provisional

Probab=94.48  E-value=0.036  Score=57.80  Aligned_cols=25  Identities=40%  Similarity=0.716  Sum_probs=22.7

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhh
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ...+|+|.|.+|+||||||+.++..
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3489999999999999999999983

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=94.47  E-value=0.12  Score=63.56  Aligned_cols=91  Identities=20%  Similarity=0.299  Sum_probs=60.1

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      +...+.+.|+.|+|||-||++++.  .+-+..+..+-|+.+  .      ... +.+-++.+     ...-..+-...|.
T Consensus       590 ~~awflflGpdgvGKt~lAkaLA~--~~Fgse~~~IriDms--e------~~e-vskligsp-----~gyvG~e~gg~Lt  653 (898)
T KOG1051|consen  590 PDAWFLFLGPDGVGKTELAKALAE--YVFGSEENFIRLDMS--E------FQE-VSKLIGSP-----PGYVGKEEGGQLT  653 (898)
T ss_pred             CCeEEEEECCCchhHHHHHHHHHH--HHcCCccceEEechh--h------hhh-hhhccCCC-----cccccchhHHHHH
Confidence            337899999999999999999999  564555555555554  1      111 22222332     2223344455778


Q ss_pred             HHcCCCcE-EEEEeCcCccCchhhhhhc
Q 001843          352 QALDDSTF-LIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       352 ~~L~~kr~-LlVlDdv~~~~~~~~~~l~  378 (1007)
                      +.++.++| +|.||||+..+.+....+.
T Consensus       654 eavrrrP~sVVLfdeIEkAh~~v~n~ll  681 (898)
T KOG1051|consen  654 EAVKRRPYSVVLFEEIEKAHPDVLNILL  681 (898)
T ss_pred             HHHhcCCceEEEEechhhcCHHHHHHHH
Confidence            88888887 7779999977777776444

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.45  E-value=0.13  Score=57.84  Aligned_cols=88  Identities=20%  Similarity=0.260  Sum_probs=50.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .+++++|+.|+||||++.+++.....+.....+..++... ......+-++...+.++.+   .....+...+...+. .
T Consensus       138 ~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~-~R~ga~EqL~~~a~~~gv~---~~~~~~~~~l~~~l~-~  212 (374)
T PRK14722        138 GVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDS-YRIGGHEQLRIFGKILGVP---VHAVKDGGDLQLALA-E  212 (374)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEeccc-ccccHHHHHHHHHHHcCCc---eEecCCcccHHHHHH-H
Confidence            7999999999999999999998422222223566666431 1223445555555555543   112222233333333 3


Q ss_pred             cCCCcEEEEEeCcC
Q 001843          354 LDDSTFLIVMENAE  367 (1007)
Q Consensus       354 L~~kr~LlVlDdv~  367 (1007)
                      +.++ -+|++|..-
T Consensus       213 l~~~-DlVLIDTaG  225 (374)
T PRK14722        213 LRNK-HMVLIDTIG  225 (374)
T ss_pred             hcCC-CEEEEcCCC
Confidence            4444 456689875

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=94.44  E-value=0.038  Score=64.48  Aligned_cols=22  Identities=36%  Similarity=0.668  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +++.++|++|+||||||+.+++
T Consensus       104 ~IL~LvGPpG~GKSsLa~~la~  125 (644)
T PRK15455        104 QILYLLGPVGGGKSSLAERLKS  125 (644)
T ss_pred             ceEEEecCCCCCchHHHHHHHH
Confidence            8999999999999999999998

>PRK07667 uridine kinase; Provisional

Probab=94.41  E-value=0.08  Score=54.44  Aligned_cols=22  Identities=27%  Similarity=0.360  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+|+|.|.+|.||||+|+.+..
T Consensus        18 ~iIgI~G~~gsGKStla~~L~~   39 (193)
T PRK07667         18 FILGIDGLSRSGKTTFVANLKE   39 (193)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            7999999999999999999998

>PTZ00035 Rad51 protein; Provisional

Probab=94.40  E-value=0.26  Score=55.23  Aligned_cols=56  Identities=14%  Similarity=0.212  Sum_probs=38.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc----cCCCceEEEEecCCCCCCHHHHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK----RHFTKRAWVHIPIMSMVEDRDVLADILKQIDE  332 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~----~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~  332 (1007)
                      .++.|+|.+|.|||||+.+++-.....    ..=..++||+..  ..++... +.++++.++.
T Consensus       119 ~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE--~~f~~er-i~~ia~~~g~  178 (337)
T PTZ00035        119 SITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTE--GTFRPER-IVQIAERFGL  178 (337)
T ss_pred             eEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEcc--CCCCHHH-HHHHHHHhCC
Confidence            899999999999999999987643321    112356799876  6666655 4445555443

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=94.33  E-value=0.71  Score=48.61  Aligned_cols=190  Identities=17%  Similarity=0.246  Sum_probs=105.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhh----cccCCCceEEEEecCC--------CC-----------CCHHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVY----VKRHFTKRAWVHIPIM--------SM-----------VEDRDVLADILKQI  330 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~----~~~~F~~~~wv~~s~~--------~~-----------~~~~~~l~~il~~l  330 (1007)
                      .-+.++|+.|.||-|.+..+.+.-.    .+-+-+...|.+-++.        .+           ...+-+.+++++++
T Consensus        35 PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKev  114 (351)
T KOG2035|consen   35 PHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKEV  114 (351)
T ss_pred             CeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHHH
Confidence            6678999999999998888776411    1112334455543310        11           12244566666665


Q ss_pred             hhhhhhhccccCHHHHHHHHHHHcCCCcE-EEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcc
Q 001843          331 DESLLKVEATLSAEELMWRITQALDDSTF-LIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAF  408 (1007)
Q Consensus       331 ~~~~~~~~~~~~~~~l~~~l~~~L~~kr~-LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~  408 (1007)
                      ...  ..-+             .-..+.| ++|+-.++.-..+.-..++ ..-.- ...+|+|+..-.-.++.....+.+
T Consensus       115 AQt--~qie-------------~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkY-s~~~RlIl~cns~SriIepIrSRC  178 (351)
T KOG2035|consen  115 AQT--QQIE-------------TQGQRPFKVVVINEADELTRDAQHALRRTMEKY-SSNCRLILVCNSTSRIIEPIRSRC  178 (351)
T ss_pred             Hhh--cchh-------------hccccceEEEEEechHhhhHHHHHHHHHHHHHH-hcCceEEEEecCcccchhHHhhhe
Confidence            443  0000             0012345 5566555533344444454 22222 556787774333222555555555


Q ss_pred             eeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCC---------CCChHHHH
Q 001843          409 STLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTK---------QPSYEEWS  479 (1007)
Q Consensus       409 ~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~---------~~~~~~w~  479 (1007)
                      -.++++..+++|-...+.+.+-...-   ..+   .+++.+|+++++|.---...+-...+-+         .....+|+
T Consensus       179 l~iRvpaps~eeI~~vl~~v~~kE~l---~lp---~~~l~rIa~kS~~nLRrAllmlE~~~~~n~~~~a~~~~i~~~dWe  252 (351)
T KOG2035|consen  179 LFIRVPAPSDEEITSVLSKVLKKEGL---QLP---KELLKRIAEKSNRNLRRALLMLEAVRVNNEPFTANSQVIPKPDWE  252 (351)
T ss_pred             eEEeCCCCCHHHHHHHHHHHHHHhcc---cCc---HHHHHHHHHHhcccHHHHHHHHHHHHhccccccccCCCCCCccHH
Confidence            88999999999999999887765433   122   6889999999887643322222222211         11345787


Q ss_pred             HHHHHc
Q 001843          480 KVIERA  485 (1007)
Q Consensus       480 ~~l~~l  485 (1007)
                      -...+.
T Consensus       253 ~~i~e~  258 (351)
T KOG2035|consen  253 IYIQEI  258 (351)
T ss_pred             HHHHHH
Confidence            766654

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=94.32  E-value=0.17  Score=54.68  Aligned_cols=37  Identities=16%  Similarity=0.212  Sum_probs=29.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +++.|.|.+|+|||++|.+++..  -...-..+++++..
T Consensus        37 s~~lI~G~pGtGKT~l~~qf~~~--~a~~Ge~vlyis~E   73 (259)
T TIGR03878        37 SVINITGVSDTGKSLMVEQFAVT--QASRGNPVLFVTVE   73 (259)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHH--HHhCCCcEEEEEec
Confidence            89999999999999999998663  22233567888865

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.31  E-value=0.27  Score=51.97  Aligned_cols=47  Identities=13%  Similarity=0.330  Sum_probs=32.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADI  326 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~i  326 (1007)
                      .++.|.|.+|.||||+|.+++.. -.+.. ..+++++.    ..+..++++.+
T Consensus        25 ~~~~i~G~~G~GKTtl~~~~~~~-~~~~g-~~~~yi~~----e~~~~~~~~~~   71 (230)
T PRK08533         25 SLILIEGDESTGKSILSQRLAYG-FLQNG-YSVSYVST----QLTTTEFIKQM   71 (230)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH-HHhCC-CcEEEEeC----CCCHHHHHHHH
Confidence            79999999999999998776653 22232 44566663    33455666665

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=94.28  E-value=0.2  Score=50.76  Aligned_cols=23  Identities=43%  Similarity=0.772  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+++|+|..|.|||||++.++.-
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          29 EKIALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcc
Confidence            78999999999999999999883

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=94.25  E-value=0.061  Score=53.95  Aligned_cols=37  Identities=22%  Similarity=0.264  Sum_probs=30.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc-cCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK-RHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~~s  312 (1007)
                      .++.++|+.|+|||.||+.++.  .+. +.....+-++++
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~--~l~~~~~~~~~~~d~s   41 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAE--LLFVGSERPLIRIDMS   41 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH--HHT-SSCCEEEEEEGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HhccCCccchHHHhhh
Confidence            7899999999999999999999  555 555566666665

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=94.25  E-value=0.098  Score=56.20  Aligned_cols=22  Identities=32%  Similarity=0.588  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +|.++|++|+||||+|++++..
T Consensus         1 LIvl~G~pGSGKST~a~~La~~   22 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKK   22 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            3789999999999999999983

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.23  E-value=0.0013  Score=68.06  Aligned_cols=77  Identities=17%  Similarity=0.027  Sum_probs=32.7

Q ss_pred             CCCeEEEeecCCCCCCcccccCCCCCcEEEecccC-CCCCcCccCCCCCCceEEEEEeeecCCC-CcCccccCCCCcEEE
Q 001843          819 ELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYD-PMPILGRLRQLKILR  896 (1007)
Q Consensus       819 ~L~~L~L~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~-~~~~l~~Lp~L~~L~  896 (1007)
                      +.+.|+.+++...  +..-...++.|+.|.|+-|. ..+..  +.. +.+|++|.|..|.|... .+..+.++|+|+.|.
T Consensus        20 ~vkKLNcwg~~L~--DIsic~kMp~lEVLsLSvNkIssL~p--l~r-CtrLkElYLRkN~I~sldEL~YLknlpsLr~LW   94 (388)
T KOG2123|consen   20 NVKKLNCWGCGLD--DISICEKMPLLEVLSLSVNKISSLAP--LQR-CTRLKELYLRKNCIESLDELEYLKNLPSLRTLW   94 (388)
T ss_pred             HhhhhcccCCCcc--HHHHHHhcccceeEEeeccccccchh--HHH-HHHHHHHHHHhcccccHHHHHHHhcCchhhhHh
Confidence            3444444443322  22223344555555555443 33321  223 45555555555544211 122344455555555


Q ss_pred             eecC
Q 001843          897 LFGG  900 (1007)
Q Consensus       897 L~~~  900 (1007)
                      |..|
T Consensus        95 L~EN   98 (388)
T KOG2123|consen   95 LDEN   98 (388)
T ss_pred             hccC
Confidence            5444

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=94.19  E-value=0.12  Score=58.67  Aligned_cols=26  Identities=38%  Similarity=0.562  Sum_probs=22.8

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhh
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRV  297 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~  297 (1007)
                      =++=|.++|++|.|||-||++|+-..
T Consensus       336 LPKGVLLvGPPGTGKTlLARAvAGEA  361 (752)
T KOG0734|consen  336 LPKGVLLVGPPGTGKTLLARAVAGEA  361 (752)
T ss_pred             CCCceEEeCCCCCchhHHHHHhhccc
Confidence            34778999999999999999999843

>PTZ00301 uridine kinase; Provisional

Probab=94.17  E-value=0.065  Score=55.61  Aligned_cols=28  Identities=32%  Similarity=0.538  Sum_probs=23.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  303 (1007)
                      .+|+|.|.+|+||||||+.+.+  ++...+
T Consensus         4 ~iIgIaG~SgSGKTTla~~l~~--~l~~~~   31 (210)
T PTZ00301          4 TVIGISGASGSGKSSLSTNIVS--ELMAHC   31 (210)
T ss_pred             EEEEEECCCcCCHHHHHHHHHH--HHHhhc
Confidence            7999999999999999999987  443433

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=94.08  E-value=0.039  Score=52.22  Aligned_cols=21  Identities=48%  Similarity=0.703  Sum_probs=19.5

Q ss_pred             EEEEcCCCChHHHHHHHHHhh
Q 001843          276 IALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      |.|.|..|+||||+|+.+...
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            689999999999999999884

...

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.05  E-value=0.4  Score=56.41  Aligned_cols=136  Identities=15%  Similarity=0.223  Sum_probs=75.7

Q ss_pred             CCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHH
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      ..++-|-.+|++|.|||++|+++++  .-.-.|     +.++  -+        ++....        ...++..+.+.+
T Consensus       466 ~ppkGVLlyGPPGC~KT~lAkalAn--e~~~nF-----lsvk--gp--------EL~sk~--------vGeSEr~ir~iF  520 (693)
T KOG0730|consen  466 SPPKGVLLYGPPGCGKTLLAKALAN--EAGMNF-----LSVK--GP--------ELFSKY--------VGESERAIREVF  520 (693)
T ss_pred             CCCceEEEECCCCcchHHHHHHHhh--hhcCCe-----eecc--CH--------HHHHHh--------cCchHHHHHHHH
Confidence            4558899999999999999999999  444444     4443  00        111111        122334444444


Q ss_pred             HHHcCCCcEEEEEeCcCcc-----------CchhhhhhccccCCCCCCcEEEE---EcCCCcccccc-cC---Ccceeee
Q 001843          351 TQALDDSTFLIVMENAEHQ-----------KSQVWDSFLGKLCSFTQCGKIII---TTSSTEDFVEP-LG---AAFSTLH  412 (1007)
Q Consensus       351 ~~~L~~kr~LlVlDdv~~~-----------~~~~~~~l~~l~~~~~~gs~Ili---TTR~~~~va~~-~~---~~~~~~~  412 (1007)
                      ++.=+--+++|.||.++..           ....+.++..-.+++.....|+|   |-|-.. +-.. +.   -+ ..+.
T Consensus       521 ~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~V~ViAATNRpd~-ID~ALlRPGRlD-~iiy  598 (693)
T KOG0730|consen  521 RKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKNVLVIAATNRPDM-IDPALLRPGRLD-RIIY  598 (693)
T ss_pred             HHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCcEEEEeccCChhh-cCHHHcCCcccc-eeEe
Confidence            4444556789999988621           11122233311223222323443   333332 2222 11   22 7788


Q ss_pred             cCCCCHHHHHHHHHhhhcccc
Q 001843          413 VPGLGKNESWELFLKKARIAE  433 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~~~  433 (1007)
                      ++.-+.+.-.++|+.++..-.
T Consensus       599 VplPD~~aR~~Ilk~~~kkmp  619 (693)
T KOG0730|consen  599 VPLPDLEARLEILKQCAKKMP  619 (693)
T ss_pred             ecCccHHHHHHHHHHHHhcCC
Confidence            888888888899998876543

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=94.03  E-value=0.24  Score=55.42  Aligned_cols=56  Identities=13%  Similarity=0.194  Sum_probs=40.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhccc----CCCceEEEEecCCCCCCHHHHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR----HFTKRAWVHIPIMSMVEDRDVLADILKQIDE  332 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~  332 (1007)
                      .++-|+|.+|+|||+||..++-......    .-..++||+..  ..|+..++ .+|++.++.
T Consensus       124 ~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE--~~f~~eRl-~qia~~~~~  183 (342)
T PLN03186        124 SITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTE--GTFRPQRL-IQIAERFGL  183 (342)
T ss_pred             eEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECC--CCccHHHH-HHHHHHcCC
Confidence            8999999999999999998886433211    11268999987  77777664 455666544

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=94.00  E-value=0.25  Score=49.89  Aligned_cols=22  Identities=41%  Similarity=0.753  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++|+|..|.|||||.+.++.
T Consensus        26 e~~~l~G~nGsGKSTLl~~l~G   47 (177)
T cd03222          26 EVIGIVGPNGTGKTTAVKILAG   47 (177)
T ss_pred             CEEEEECCCCChHHHHHHHHHc
Confidence            7999999999999999999987

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>PRK04328 hypothetical protein; Provisional

Probab=93.95  E-value=0.16  Score=54.45  Aligned_cols=37  Identities=19%  Similarity=0.294  Sum_probs=29.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +++.|.|.+|.|||+||.++... .. ..-+.++|++..
T Consensus        24 s~ili~G~pGsGKT~l~~~fl~~-~~-~~ge~~lyis~e   60 (249)
T PRK04328         24 NVVLLSGGPGTGKSIFSQQFLWN-GL-QMGEPGVYVALE   60 (249)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHH-HH-hcCCcEEEEEee
Confidence            89999999999999999997763 23 334677888865

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=93.93  E-value=0.31  Score=50.20  Aligned_cols=95  Identities=15%  Similarity=0.243  Sum_probs=55.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      --|.+||--|+||+.|++++.+  .+....-..  |.|.  +  +                    +..+...+.+.++. 
T Consensus        86 NnVLLwGaRGtGKSSLVKA~~~--e~~~~glrL--VEV~--k--~--------------------dl~~Lp~l~~~Lr~-  136 (287)
T COG2607          86 NNVLLWGARGTGKSSLVKALLN--EYADEGLRL--VEVD--K--E--------------------DLATLPDLVELLRA-  136 (287)
T ss_pred             cceEEecCCCCChHHHHHHHHH--HHHhcCCeE--EEEc--H--H--------------------HHhhHHHHHHHHhc-
Confidence            4568999999999999999999  555554432  3333  0  0                    11122222333322 


Q ss_pred             cCCCcEEEEEeCcCc-cCchhhhhhccccCCC---CCCcEEEEEcCCCc
Q 001843          354 LDDSTFLIVMENAEH-QKSQVWDSFLGKLCSF---TQCGKIIITTSSTE  398 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~-~~~~~~~~l~~l~~~~---~~gs~IliTTR~~~  398 (1007)
                       ..+||.|..||... ++.+.+..++...++.   .+.-.++..|.++.
T Consensus       137 -~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRR  184 (287)
T COG2607         137 -RPEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSNRR  184 (287)
T ss_pred             -CCceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecCCc
Confidence             36899999999964 3555666666333320   22334444555544

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=93.92  E-value=0.24  Score=48.18  Aligned_cols=96  Identities=15%  Similarity=0.242  Sum_probs=54.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEE----ecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH----IPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~----~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      .+++|+|..|.|||||++.++.-.   ......+|+.    +.  -.+.           +..          .+...-.
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~~~~~i~--~~~~-----------lS~----------G~~~rv~   80 (144)
T cd03221          27 DRIGLVGRNGAGKSTLLKLIAGEL---EPDEGIVTWGSTVKIG--YFEQ-----------LSG----------GEKMRLA   80 (144)
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCC---CCCceEEEECCeEEEE--EEcc-----------CCH----------HHHHHHH
Confidence            799999999999999999998832   2233444432    11  0000           111          1112223


Q ss_pred             HHHHcCCCcEEEEEeCcCc-cCchhhhhhc-cccCCCCCCcEEEEEcCCCc
Q 001843          350 ITQALDDSTFLIVMENAEH-QKSQVWDSFL-GKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       350 l~~~L~~kr~LlVlDdv~~-~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~  398 (1007)
                      +.+.+-.++-++++|+... -|......+. .+...   +..||++|.+..
T Consensus        81 laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~---~~til~~th~~~  128 (144)
T cd03221          81 LAKLLLENPNLLLLDEPTNHLDLESIEALEEALKEY---PGTVILVSHDRY  128 (144)
T ss_pred             HHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHc---CCEEEEEECCHH
Confidence            4455556777899998642 2444444554 33322   246788887765

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.91  E-value=0.17  Score=56.42  Aligned_cols=55  Identities=15%  Similarity=0.260  Sum_probs=39.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhccc----CCCceEEEEecCCCCCCHHHHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR----HFTKRAWVHIPIMSMVEDRDVLADILKQID  331 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~----~F~~~~wv~~s~~~~~~~~~~l~~il~~l~  331 (1007)
                      +++-|+|.+|+||||++.+++-......    .=..++||+..  ..++...+. ++++.++
T Consensus        96 ~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te--~~f~~~rl~-~~~~~~g  154 (310)
T TIGR02236        96 AITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTE--NTFRPERIM-QMAEARG  154 (310)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECC--CCCCHHHHH-HHHHHcC
Confidence            8999999999999999999987433211    11268999987  777766543 4455443

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>TIGR00235 udk uridine kinase

Probab=93.90  E-value=0.05  Score=56.64  Aligned_cols=22  Identities=50%  Similarity=0.800  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+|+|+|.+|+||||||+.++.
T Consensus         7 ~vi~I~G~sGsGKSTl~~~l~~   28 (207)
T TIGR00235         7 IIIGIGGGSGSGKTTVARKIYE   28 (207)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            8999999999999999999998

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=93.89  E-value=0.031  Score=58.22  Aligned_cols=65  Identities=25%  Similarity=0.198  Sum_probs=42.8

Q ss_pred             CCCCcccEEEecCC--CCCCcCCCccccCCCcCcEEecccCCCcccC--cccccCCCCCEEeecCCcccc
Q 001843          666 RRLGMLKVLDLEGV--YKPMLTNNNALGRLPFLEYLGLRSTFIDSLP--DSTPILFCLATLDVSHTKVQR  731 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~--~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP--~~i~~L~~L~~L~L~~~~l~~  731 (1007)
                      ..+++|+.|++|.|  ++.. .++.....+++|++|+|++|+|..+.  ..+.+|.||..|++.+|....
T Consensus        62 P~Lp~LkkL~lsdn~~~~~~-~l~vl~e~~P~l~~l~ls~Nki~~lstl~pl~~l~nL~~Ldl~n~~~~~  130 (260)
T KOG2739|consen   62 PKLPKLKKLELSDNYRRVSG-GLEVLAEKAPNLKVLNLSGNKIKDLSTLRPLKELENLKSLDLFNCSVTN  130 (260)
T ss_pred             CCcchhhhhcccCCcccccc-cceehhhhCCceeEEeecCCccccccccchhhhhcchhhhhcccCCccc
Confidence            67778888888888  4443 34444455688888888888776421  135667777788887775443

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.87  E-value=1.5  Score=49.70  Aligned_cols=155  Identities=18%  Similarity=0.194  Sum_probs=82.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      |-..++|++|.|||+++.+++|.  .  .|+. .=+..+  ...+..+ ++.++..                        
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~--L--~ydI-ydLeLt--~v~~n~d-Lr~LL~~------------------------  283 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANY--L--NYDI-YDLELT--EVKLDSD-LRHLLLA------------------------  283 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhh--c--CCce-EEeeec--cccCcHH-HHHHHHh------------------------
Confidence            67789999999999999999992  2  2332 112222  1111111 2221111                        


Q ss_pred             cCCCcEEEEEeCcCcc------Cc------------hhhhhhc----cccCCCCCCcEEEE-EcCCCcccccc-cC--Cc
Q 001843          354 LDDSTFLIVMENAEHQ------KS------------QVWDSFL----GKLCSFTQCGKIII-TTSSTEDFVEP-LG--AA  407 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~------~~------------~~~~~l~----~l~~~~~~gs~Ili-TTR~~~~va~~-~~--~~  407 (1007)
                       ...+-+||+.|++..      ..            -.+.-+.    ++... +.+=|||| ||-..+++-.. ++  -.
T Consensus       284 -t~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSs-cg~ERIivFTTNh~EkLDPALlRpGRm  361 (457)
T KOG0743|consen  284 -TPNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSS-CGDERIIVFTTNHKEKLDPALLRPGRM  361 (457)
T ss_pred             -CCCCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhcccccc-CCCceEEEEecCChhhcCHhhcCCCcc
Confidence             235667777777621      00            0111122    22222 22346666 77665522211 11  11


Q ss_pred             ceeeecCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCC
Q 001843          408 FSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTK  471 (1007)
Q Consensus       408 ~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~  471 (1007)
                      ...+.+.-=+.+.-..||.+......+         ..++.+|.+...|.-+.-..++..|-.+
T Consensus       362 DmhI~mgyCtf~~fK~La~nYL~~~~~---------h~L~~eie~l~~~~~~tPA~V~e~lm~~  416 (457)
T KOG0743|consen  362 DMHIYMGYCTFEAFKTLASNYLGIEED---------HRLFDEIERLIEETEVTPAQVAEELMKN  416 (457)
T ss_pred             eeEEEcCCCCHHHHHHHHHHhcCCCCC---------cchhHHHHHHhhcCccCHHHHHHHHhhc
Confidence            156777778889999999998876432         2455666666666655555555544433

>PRK15453 phosphoribulokinase; Provisional

Probab=93.87  E-value=0.83  Score=49.10  Aligned_cols=81  Identities=20%  Similarity=0.168  Sum_probs=45.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHH--Hhhhhhh-hccccCHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQ--IDESLLK-VEATLSAEELMWRI  350 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~--l~~~~~~-~~~~~~~~~l~~~l  350 (1007)
                      .+|+|.|-+|.||||+|+.+++  .....=...+.++......++..+.-..+...  -+.+... ..+..+.+.+.+.+
T Consensus         6 piI~ItG~SGsGKTTva~~l~~--if~~~~~~~~vi~~D~yh~ydr~~~~~~~~~~~r~g~nfdhf~PdAnd~dlL~~~l   83 (290)
T PRK15453          6 PIIAVTGSSGAGTTTVKRAFEK--IFRRENINAAVVEGDSFHRYTRPEMKAAIAKARAAGRHFSHFGPEANLFDELEQLF   83 (290)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH--HHhhcCCCeEEEecccccccChhhHhhhhHHHHhcCCCCCCCCCCcccHHHHHHHH
Confidence            7999999999999999999987  33322123455554422333433332222111  1111001 02455667777777


Q ss_pred             HHHcCC
Q 001843          351 TQALDD  356 (1007)
Q Consensus       351 ~~~L~~  356 (1007)
                      +...++
T Consensus        84 ~~l~~~   89 (290)
T PRK15453         84 REYGET   89 (290)
T ss_pred             HHHhcC
Confidence            776553

>TIGR01817 nifA Nif-specific regulatory protein

Probab=93.86  E-value=0.24  Score=59.73  Aligned_cols=23  Identities=26%  Similarity=0.486  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-|.|+|..|+|||++|+.+++.
T Consensus       220 ~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       220 STVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             CCEEEECCCCccHHHHHHHHHHh
Confidence            46789999999999999999983

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>PRK06762 hypothetical protein; Provisional

Probab=93.85  E-value=0.052  Score=54.28  Aligned_cols=22  Identities=41%  Similarity=0.674  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+|.|.|++|+||||+|+.+++
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~   24 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQE   24 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            7899999999999999999998

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=93.83  E-value=0.2  Score=52.51  Aligned_cols=36  Identities=22%  Similarity=0.366  Sum_probs=26.1

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccC-C-CceEEEEec
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRH-F-TKRAWVHIP  312 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~-F-~~~~wv~~s  312 (1007)
                      +|+|.|.+|+||||+|+.+..  .+... . ..+..++..
T Consensus         1 IigI~G~sGSGKTTla~~L~~--~l~~~~~~~~v~vi~~D   38 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQA--LLSRWPDHPNVELITTD   38 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHH--HHhhcCCCCcEEEEecC
Confidence            589999999999999999998  44321 1 235556554

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=93.83  E-value=0.31  Score=51.59  Aligned_cols=37  Identities=22%  Similarity=0.276  Sum_probs=28.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      .++.|.|.+|.||||+|.+++... . ..-..++|++..
T Consensus        21 ~~~~i~G~~G~GKT~l~~~~~~~~-~-~~g~~~~~is~e   57 (229)
T TIGR03881        21 FFVAVTGEPGTGKTIFCLHFAYKG-L-RDGDPVIYVTTE   57 (229)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHH-H-hcCCeEEEEEcc
Confidence            899999999999999999877632 2 234567888754

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=93.82  E-value=0.16  Score=62.29  Aligned_cols=85  Identities=16%  Similarity=0.200  Sum_probs=57.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh--ccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV--EATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~--~~~~~~~~l~~~l~  351 (1007)
                      +++-|+|.+|+||||||.+++..  ....-..++|+...  ..++.     ..+++++.+....  ......+.....+.
T Consensus        61 siteI~G~~GsGKTtLal~~~~~--a~~~G~~v~yId~E--~t~~~-----~~A~~lGvDl~~llv~~~~~~E~~l~~i~  131 (790)
T PRK09519         61 RVIEIYGPESSGKTTVALHAVAN--AQAAGGVAAFIDAE--HALDP-----DYAKKLGVDTDSLLVSQPDTGEQALEIAD  131 (790)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCc--cchhH-----HHHHHcCCChhHeEEecCCCHHHHHHHHH
Confidence            89999999999999999887663  22334568899876  66663     3667776642211  12334455666666


Q ss_pred             HHcCC-CcEEEEEeCcC
Q 001843          352 QALDD-STFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~~-kr~LlVlDdv~  367 (1007)
                      ..++. +--|||+|.+-
T Consensus       132 ~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        132 MLIRSGALDIVVIDSVA  148 (790)
T ss_pred             HHhhcCCCeEEEEcchh
Confidence            66654 55699999975

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=93.74  E-value=0.3  Score=49.06  Aligned_cols=22  Identities=36%  Similarity=0.780  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++|+|..|.|||||.+.++.
T Consensus        29 ~~~~l~G~nGsGKstLl~~i~G   50 (171)
T cd03228          29 EKVAIVGPSGSGKSTLLKLLLR   50 (171)
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            7999999999999999999998

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=93.72  E-value=0.51  Score=55.93  Aligned_cols=23  Identities=22%  Similarity=0.420  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ..|.|.|.+|+|||++|+.+++.
T Consensus       162 ~~vli~Ge~GtGK~~lA~~ih~~  184 (469)
T PRK10923        162 ISVLINGESGTGKELVAHALHRH  184 (469)
T ss_pred             CeEEEEeCCCCcHHHHHHHHHhc
Confidence            56889999999999999999983

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=93.70  E-value=0.054  Score=52.48  Aligned_cols=21  Identities=48%  Similarity=0.697  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHHh
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ||.++|++|+||||+|+.+..
T Consensus         1 lii~~G~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAK   21 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            688999999999999999986

...

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=93.68  E-value=0.038  Score=51.65  Aligned_cols=28  Identities=36%  Similarity=0.515  Sum_probs=19.7

Q ss_pred             EEEEcCCCChHHHHHHHHHhhhhcccCCCc
Q 001843          276 IALIGKAGSGKTTLARIVYNRVYVKRHFTK  305 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~  305 (1007)
                      |-|+|.+|+||||+|+.++.  .+...|..
T Consensus         2 vLleg~PG~GKT~la~~lA~--~~~~~f~R   29 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALAR--SLGLSFKR   29 (131)
T ss_dssp             EEEES---HHHHHHHHHHHH--HTT--EEE
T ss_pred             EeeECCCccHHHHHHHHHHH--HcCCceeE
Confidence            57999999999999999999  67777753

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.67  E-value=0.22  Score=56.54  Aligned_cols=23  Identities=35%  Similarity=0.543  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .++.++|.+|+||||++.+++..
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            79999999999999999999874

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=93.62  E-value=0.26  Score=52.04  Aligned_cols=128  Identities=16%  Similarity=0.234  Sum_probs=69.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhh-----hcc------cCC---CceEEEEec--CCCCC--CH----------------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRV-----YVK------RHF---TKRAWVHIP--IMSMV--ED----------------  319 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~-----~~~------~~F---~~~~wv~~s--~~~~~--~~----------------  319 (1007)
                      .+++|+|+.|.|||||.+.+..-.     ++.      ..+   ..+.||.=.  --..+  +.                
T Consensus        31 ~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~~~  110 (254)
T COG1121          31 EITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGWFR  110 (254)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCcccccccc
Confidence            799999999999999999998711     010      001   124444210  00000  11                


Q ss_pred             ------HHHHHHHHHHHhhhhhhhc--cccC-HHHHHHHHHHHcCCCcEEEEEeCcC----ccCchhhhhhc-cccCCCC
Q 001843          320 ------RDVLADILKQIDESLLKVE--ATLS-AEELMWRITQALDDSTFLIVMENAE----HQKSQVWDSFL-GKLCSFT  385 (1007)
Q Consensus       320 ------~~~l~~il~~l~~~~~~~~--~~~~-~~~l~~~l~~~L~~kr~LlVlDdv~----~~~~~~~~~l~-~l~~~~~  385 (1007)
                            .+...+.+++++...-...  ...+ .+.-.-.+.+.|..++=|++||.--    .......-++. .+.   .
T Consensus       111 ~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~---~  187 (254)
T COG1121         111 RLNKKDKEKVDEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELR---Q  187 (254)
T ss_pred             cccHHHHHHHHHHHHHcCchhhhCCcccccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHH---H
Confidence                  2444555555544311111  2223 3333345678888999999999643    11222333333 332   2


Q ss_pred             CCcEEEEEcCCCccccccc
Q 001843          386 QCGKIIITTSSTEDFVEPL  404 (1007)
Q Consensus       386 ~gs~IliTTR~~~~va~~~  404 (1007)
                      .|.-||++|-+-..|...+
T Consensus       188 eg~tIl~vtHDL~~v~~~~  206 (254)
T COG1121         188 EGKTVLMVTHDLGLVMAYF  206 (254)
T ss_pred             CCCEEEEEeCCcHHhHhhC
Confidence            3788999999877444443

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=93.62  E-value=0.056  Score=45.13  Aligned_cols=22  Identities=41%  Similarity=0.723  Sum_probs=20.0

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +|+|.|..|+||||+|+.+.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999984

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=93.60  E-value=0.17  Score=57.67  Aligned_cols=22  Identities=45%  Similarity=0.857  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++|+|+.|.||||||+.+.-
T Consensus       363 ~~lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         363 EALGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             ceEEEECCCCccHHHHHHHHHc
Confidence            6899999999999999999765

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.57  E-value=0.35  Score=54.12  Aligned_cols=88  Identities=16%  Similarity=0.171  Sum_probs=52.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ++++|+|+.|+||||++..++..  ....-..+.+|++.. ......+-++.....++.+   .....+...+...+...
T Consensus       207 ~ii~lvGptGvGKTTt~akLA~~--l~~~g~~V~lItaDt-yR~gAveQLk~yae~lgvp---v~~~~dp~dL~~al~~l  280 (407)
T PRK12726        207 RIISLIGQTGVGKTTTLVKLGWQ--LLKQNRTVGFITTDT-FRSGAVEQFQGYADKLDVE---LIVATSPAELEEAVQYM  280 (407)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEeCCc-cCccHHHHHHHHhhcCCCC---EEecCCHHHHHHHHHHH
Confidence            89999999999999999999874  322223566777641 1112244455555544432   11234566665555443


Q ss_pred             cC-CCcEEEEEeCcC
Q 001843          354 LD-DSTFLIVMENAE  367 (1007)
Q Consensus       354 L~-~kr~LlVlDdv~  367 (1007)
                      -. +..=+|++|-.-
T Consensus       281 ~~~~~~D~VLIDTAG  295 (407)
T PRK12726        281 TYVNCVDHILIDTVG  295 (407)
T ss_pred             HhcCCCCEEEEECCC
Confidence            21 334578888774

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=93.57  E-value=0.53  Score=51.21  Aligned_cols=52  Identities=21%  Similarity=0.215  Sum_probs=36.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI  330 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l  330 (1007)
                      .++.|.|.+|+||||++.+++.... ..+=..++|++..  .  +..++...+...+
T Consensus        31 ~~~~i~g~~G~GKT~l~~~~~~~~~-~~~g~~vl~iS~E--~--~~~~~~~r~~~~~   82 (271)
T cd01122          31 ELIILTAGTGVGKTTFLREYALDLI-TQHGVRVGTISLE--E--PVVRTARRLLGQY   82 (271)
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHH-HhcCceEEEEEcc--c--CHHHHHHHHHHHH
Confidence            7899999999999999999887421 2223467888764  3  4556666665544

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=93.56  E-value=0.14  Score=62.16  Aligned_cols=128  Identities=12%  Similarity=0.113  Sum_probs=68.2

Q ss_pred             EEEcCCCChHHHHHHHHHhhhhcc-cCCC-----c-eEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHH
Q 001843          277 ALIGKAGSGKTTLARIVYNRVYVK-RHFT-----K-RAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       277 ~I~G~gGiGKTtLa~~v~~~~~~~-~~F~-----~-~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      .++|.+|+|||++|.-++.  ++- +.-+     . ++=++++               .-+.+    ..-..+.++..+.
T Consensus       195 vLiGEpGVGKTAIvEGLA~--rIv~g~VP~~L~~~~i~sLD~g---------------~LvAG----akyRGeFEeRlk~  253 (786)
T COG0542         195 VLVGEPGVGKTAIVEGLAQ--RIVNGDVPESLKDKRIYSLDLG---------------SLVAG----AKYRGEFEERLKA  253 (786)
T ss_pred             eEecCCCCCHHHHHHHHHH--HHhcCCCCHHHcCCEEEEecHH---------------HHhcc----ccccCcHHHHHHH
Confidence            4689999999999888777  332 2211     1 1111111               11111    1234556666666


Q ss_pred             HHHHcC-CCcEEEEEeCcCcc-------C--chhhhhhccccCCCCCCcEEEEEcCCCcccccccC------Ccceeeec
Q 001843          350 ITQALD-DSTFLIVMENAEHQ-------K--SQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLG------AAFSTLHV  413 (1007)
Q Consensus       350 l~~~L~-~kr~LlVlDdv~~~-------~--~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~------~~~~~~~l  413 (1007)
                      +.+.++ .++..|++|.+...       .  .+.-+-+++.... +.--.|-.||-++.  -+++.      -..+.+.+
T Consensus       254 vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLAR-GeL~~IGATT~~EY--Rk~iEKD~AL~RRFQ~V~V  330 (786)
T COG0542         254 VLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALAR-GELRCIGATTLDEY--RKYIEKDAALERRFQKVLV  330 (786)
T ss_pred             HHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHhc-CCeEEEEeccHHHH--HHHhhhchHHHhcCceeeC
Confidence            666664 45899999998631       1  2233333322222 22223444664432  11111      11178889


Q ss_pred             CCCCHHHHHHHHHhh
Q 001843          414 PGLGKNESWELFLKK  428 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~  428 (1007)
                      ...+.+++...++-.
T Consensus       331 ~EPs~e~ti~ILrGl  345 (786)
T COG0542         331 DEPSVEDTIAILRGL  345 (786)
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999999888643

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=93.55  E-value=0.091  Score=52.94  Aligned_cols=120  Identities=18%  Similarity=0.202  Sum_probs=59.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhh--hccc--------cC-
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLK--VEAT--------LS-  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~--~~~~--------~~-  342 (1007)
                      .+++|+|..|.|||||.+.++...   ......+++.-.  ......   ..+...+.--...  ....        .+ 
T Consensus        27 e~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~g~--~~~~~~---~~~~~~i~~~~q~~~~~~~~tv~~~~~LS~   98 (173)
T cd03230          27 EIYGLLGPNGAGKTTLIKIILGLL---KPDSGEIKVLGK--DIKKEP---EEVKRRIGYLPEEPSLYENLTVRENLKLSG   98 (173)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCCC---CCCCeEEEECCE--Ecccch---HhhhccEEEEecCCccccCCcHHHHhhcCH
Confidence            799999999999999999998831   223344444211  000000   0010111000000  0000        11 


Q ss_pred             HHHHHHHHHHHcCCCcEEEEEeCcCc-cCchhhhhhc-cccCCCCCCcEEEEEcCCCccccc
Q 001843          343 AEELMWRITQALDDSTFLIVMENAEH-QKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVE  402 (1007)
Q Consensus       343 ~~~l~~~l~~~L~~kr~LlVlDdv~~-~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~  402 (1007)
                      .+...-.+...+..++=++++|+... -|......+. .+......|..||++|.+.. .+.
T Consensus        99 G~~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~~~-~~~  159 (173)
T cd03230          99 GMKQRLALAQALLHDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHILE-EAE  159 (173)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHH-HHH
Confidence            11222245566677888999998752 1333333333 22221123667888888876 444

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=93.51  E-value=0.13  Score=50.85  Aligned_cols=118  Identities=17%  Similarity=0.200  Sum_probs=60.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .+++|+|..|.|||||.+.++..  . ......+++.-..........    ....+.-.    ..-...+...-.+...
T Consensus        26 ~~~~i~G~nGsGKStll~~l~g~--~-~~~~G~i~~~~~~~~~~~~~~----~~~~i~~~----~qlS~G~~~r~~l~~~   94 (157)
T cd00267          26 EIVALVGPNGSGKSTLLRAIAGL--L-KPTSGEILIDGKDIAKLPLEE----LRRRIGYV----PQLSGGQRQRVALARA   94 (157)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC--C-CCCccEEEECCEEcccCCHHH----HHhceEEE----eeCCHHHHHHHHHHHH
Confidence            79999999999999999999983  3 234455555321001111111    11111100    0011112222234455


Q ss_pred             cCCCcEEEEEeCcCc-cCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccc
Q 001843          354 LDDSTFLIVMENAEH-QKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEP  403 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~-~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~  403 (1007)
                      +...+-++++|+... -|......+. .+......+..++++|.+.. ....
T Consensus        95 l~~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~-~~~~  145 (157)
T cd00267          95 LLLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPE-LAEL  145 (157)
T ss_pred             HhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHH-HHHH
Confidence            556678999998752 1333334443 22221022456888887766 4443

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK06547 hypothetical protein; Provisional

Probab=93.49  E-value=0.074  Score=53.40  Aligned_cols=25  Identities=40%  Similarity=0.533  Sum_probs=22.5

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhh
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+.+|+|.|..|+||||+|+.++..
T Consensus        14 ~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         14 GMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3489999999999999999999883

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.49  E-value=0.0043  Score=64.43  Aligned_cols=80  Identities=21%  Similarity=0.155  Sum_probs=64.2

Q ss_pred             CCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCCCcCcEEecccCCCcccCc-
Q 001843          633 LSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPD-  711 (1007)
Q Consensus       633 ~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L~~Lr~L~L~~n~i~~LP~-  711 (1007)
                      ++.+++.|.+.||.+.+++          ++  .+|+.|+||.||-|.|+  .+ ..+..|+.|+.|.|+.|.|..|-+ 
T Consensus        17 dl~~vkKLNcwg~~L~DIs----------ic--~kMp~lEVLsLSvNkIs--sL-~pl~rCtrLkElYLRkN~I~sldEL   81 (388)
T KOG2123|consen   17 DLENVKKLNCWGCGLDDIS----------IC--EKMPLLEVLSLSVNKIS--SL-APLQRCTRLKELYLRKNCIESLDEL   81 (388)
T ss_pred             HHHHhhhhcccCCCccHHH----------HH--HhcccceeEEeeccccc--cc-hhHHHHHHHHHHHHHhcccccHHHH
Confidence            4567888889998886422          45  89999999999999988  55 467889999999999999887753 


Q ss_pred             -ccccCCCCCEEeecCC
Q 001843          712 -STPILFCLATLDVSHT  727 (1007)
Q Consensus       712 -~i~~L~~L~~L~L~~~  727 (1007)
                       .+.+|++|++|.|..|
T Consensus        82 ~YLknlpsLr~LWL~EN   98 (388)
T KOG2123|consen   82 EYLKNLPSLRTLWLDEN   98 (388)
T ss_pred             HHHhcCchhhhHhhccC
Confidence             4678888888888776

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=93.47  E-value=0.27  Score=54.51  Aligned_cols=37  Identities=27%  Similarity=0.214  Sum_probs=27.4

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEe
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI  311 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~  311 (1007)
                      ..+++++|++|+||||++..++..  ....-..+..++.
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~--l~~~g~~V~Li~~  150 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHK--YKAQGKKVLLAAG  150 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH--HHhcCCeEEEEec
Confidence            389999999999999999999883  4333224454544

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=93.46  E-value=0.15  Score=51.28  Aligned_cols=22  Identities=50%  Similarity=0.906  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++|+|..|.|||||.+.++.
T Consensus        29 e~~~i~G~nGsGKStLl~~l~G   50 (173)
T cd03246          29 ESLAIIGPSGSGKSTLARLILG   50 (173)
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            7999999999999999999998

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.46  E-value=0.26  Score=57.49  Aligned_cols=88  Identities=30%  Similarity=0.328  Sum_probs=45.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .+|+|+|.+|+||||++.+++.....+.....+..++... ......+.++.....++..   .....+...+...+.+ 
T Consensus       351 ~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDt-yRigA~EQLk~ya~iLgv~---v~~a~d~~~L~~aL~~-  425 (559)
T PRK12727        351 GVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDT-QRVGGREQLHSYGRQLGIA---VHEADSAESLLDLLER-  425 (559)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEeccc-ccccHHHHHHHhhcccCce---eEecCcHHHHHHHHHH-
Confidence            8999999999999999999887322222223455555431 1111222222222222221   1122334444444443 


Q ss_pred             cCCCcEEEEEeCcC
Q 001843          354 LDDSTFLIVMENAE  367 (1007)
Q Consensus       354 L~~kr~LlVlDdv~  367 (1007)
                      +.+ .=+||+|..-
T Consensus       426 l~~-~DLVLIDTaG  438 (559)
T PRK12727        426 LRD-YKLVLIDTAG  438 (559)
T ss_pred             hcc-CCEEEecCCC
Confidence            333 4478888764

>PRK03839 putative kinase; Provisional

Probab=93.46  E-value=0.059  Score=54.73  Aligned_cols=22  Identities=36%  Similarity=0.768  Sum_probs=20.2

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .|.|+|++|+||||+|+.+++.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999999993

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=93.43  E-value=0.26  Score=52.36  Aligned_cols=22  Identities=32%  Similarity=0.652  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++|+|+.|.|||||.+.++.
T Consensus        29 ~i~~iiGpNG~GKSTLLk~l~g   50 (258)
T COG1120          29 EITGILGPNGSGKSTLLKCLAG   50 (258)
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            8999999999999999999887

>COG5238 RNA1 Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

Probab=93.34  E-value=0.063  Score=55.87  Aligned_cols=69  Identities=10%  Similarity=-0.019  Sum_probs=42.9

Q ss_pred             CCCCcccEEEecCCCCCCcCCC----ccccCCCcCcEEecccCCCcccC--------------cccccCCCCCEEeecCC
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNN----NALGRLPFLEYLGLRSTFIDSLP--------------DSTPILFCLATLDVSHT  727 (1007)
Q Consensus       666 ~~l~~Lr~L~Ls~~~l~~~~lp----~~i~~L~~Lr~L~L~~n~i~~LP--------------~~i~~L~~L~~L~L~~~  727 (1007)
                      .+|++|+..+||.|-+.. ..|    +.|++-..|.+|.|++|.+.-+.              +...+-+.|++.+...|
T Consensus        89 lkcp~l~~v~LSDNAfg~-~~~e~L~d~is~~t~l~HL~l~NnGlGp~aG~rigkal~~la~nKKaa~kp~Le~vicgrN  167 (388)
T COG5238          89 LKCPRLQKVDLSDNAFGS-EFPEELGDLISSSTDLVHLKLNNNGLGPIAGGRIGKALFHLAYNKKAADKPKLEVVICGRN  167 (388)
T ss_pred             hcCCcceeeeccccccCc-ccchHHHHHHhcCCCceeEEeecCCCCccchhHHHHHHHHHHHHhhhccCCCceEEEeccc
Confidence            577777777777776654 333    33456666777777777665332              12334567888888777


Q ss_pred             cccccccc
Q 001843          728 KVQRLPYA  735 (1007)
Q Consensus       728 ~l~~lP~~  735 (1007)
                      ++...|..
T Consensus       168 Rlengs~~  175 (388)
T COG5238         168 RLENGSKE  175 (388)
T ss_pred             hhccCcHH
Confidence            77665543

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=93.33  E-value=0.16  Score=51.55  Aligned_cols=22  Identities=27%  Similarity=0.702  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++|+|..|.|||||.+.++.
T Consensus        27 ~~~~i~G~nGsGKSTLl~~l~G   48 (182)
T cd03215          27 EIVGIAGLVGNGQTELAEALFG   48 (182)
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            7899999999999999999997

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=93.33  E-value=0.23  Score=57.06  Aligned_cols=87  Identities=21%  Similarity=0.190  Sum_probs=48.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhh-----hhhhc-------ccc
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES-----LLKVE-------ATL  341 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~-----~~~~~-------~~~  341 (1007)
                      ..++|+|..|.|||||++.++..   ......++|+.-.  +..+..++....+......     ....+       ...
T Consensus       166 qri~I~G~SGsGKTTLL~~Ia~l---~~pd~gvv~liGe--rgrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~  240 (450)
T PRK06002        166 QRIGIFAGSGVGKSTLLAMLARA---DAFDTVVIALVGE--RGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPL  240 (450)
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC---CCCCeeeeeeccc--CCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHH
Confidence            78999999999999999988872   1222344554322  3445555444444433111     00000       111


Q ss_pred             CHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          342 SAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       342 ~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                      ..-...+.++.  +++.+|+++||+-
T Consensus       241 ~a~~iAEyfrd--~G~~Vll~~DslT  264 (450)
T PRK06002        241 TATAIAEYFRD--RGENVLLIVDSVT  264 (450)
T ss_pred             HHHHHHHHHHH--cCCCEEEeccchH
Confidence            12223334443  4899999999985

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=93.31  E-value=0.11  Score=50.80  Aligned_cols=35  Identities=40%  Similarity=0.334  Sum_probs=29.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEE
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  310 (1007)
                      .||-|.|.+|.||||||+++..  +....-..++++.
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~--~L~~~g~~~~~LD   37 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALER--RLFARGIKVYLLD   37 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH--HHHHTTS-EEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHHHcCCcEEEec
Confidence            7899999999999999999999  6666656677775

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=93.30  E-value=0.54  Score=47.95  Aligned_cols=129  Identities=18%  Similarity=0.200  Sum_probs=70.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecC-----------------CCCC-------------------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPI-----------------MSMV-------------------  317 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~-----------------~~~~-------------------  317 (1007)
                      .|++|+|+.|.|||||.+.+..   ....=...+||.-..                 .+.|                   
T Consensus        29 evv~iiGpSGSGKSTlLRclN~---LE~~~~G~I~i~g~~~~~~~~~~~~R~~vGmVFQ~fnLFPHlTvleNv~lap~~v  105 (240)
T COG1126          29 EVVVIIGPSGSGKSTLLRCLNG---LEEPDSGSITVDGEDVGDKKDILKLRRKVGMVFQQFNLFPHLTVLENVTLAPVKV  105 (240)
T ss_pred             CEEEEECCCCCCHHHHHHHHHC---CcCCCCceEEECCEeccchhhHHHHHHhcCeecccccccccchHHHHHHhhhHHH
Confidence            8999999999999999999876   222223345553100                 0111                   


Q ss_pred             ------CHHHHHHHHHHHHhhhhhh--hcc-ccCHHHHHHHHHHHcCCCcEEEEEeCcCcc-Cchhhhhhc-cccCCCCC
Q 001843          318 ------EDRDVLADILKQIDESLLK--VEA-TLSAEELMWRITQALDDSTFLIVMENAEHQ-KSQVWDSFL-GKLCSFTQ  386 (1007)
Q Consensus       318 ------~~~~~l~~il~~l~~~~~~--~~~-~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~-~l~~~~~~  386 (1007)
                            ...+...+++..++.....  .+. -...++-.-.|.+.|.-++=++.+|..-.. |++...++. -+.+-...
T Consensus       106 ~~~~k~eA~~~A~~lL~~VGL~~ka~~yP~qLSGGQqQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA~e  185 (240)
T COG1126         106 KKLSKAEAREKALELLEKVGLADKADAYPAQLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLAEE  185 (240)
T ss_pred             cCCCHHHHHHHHHHHHHHcCchhhhhhCccccCcHHHHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHHHc
Confidence                  1123333444444332110  011 122333344577778888889999997522 454444444 22222244


Q ss_pred             CcEEEEEcCCCcccccccCC
Q 001843          387 CGKIIITTSSTEDFVEPLGA  406 (1007)
Q Consensus       387 gs~IliTTR~~~~va~~~~~  406 (1007)
                      |--.||.|-... .|..+..
T Consensus       186 GmTMivVTHEM~-FAr~Vad  204 (240)
T COG1126         186 GMTMIIVTHEMG-FAREVAD  204 (240)
T ss_pred             CCeEEEEechhH-HHHHhhh
Confidence            666666676666 7766544

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=93.30  E-value=0.23  Score=49.89  Aligned_cols=27  Identities=37%  Similarity=0.557  Sum_probs=22.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH  302 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~  302 (1007)
                      +.|-+.|.+|+||||+|++++.  ..++.
T Consensus         2 pLiIlTGyPgsGKTtfakeLak--~L~~~   28 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAK--ELRQE   28 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHH--HHHHh
Confidence            5688999999999999999998  44443

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=93.27  E-value=0.14  Score=54.07  Aligned_cols=88  Identities=23%  Similarity=0.297  Sum_probs=50.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh------------cc--
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV------------EA--  339 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~------------~~--  339 (1007)
                      +++.|.|.+|+|||++|.++... ..+..=+.++||+..  .+  ..++.+.+- .++-+....            ..  
T Consensus        20 s~~li~G~~GsGKT~l~~q~l~~-~~~~~ge~vlyvs~e--e~--~~~l~~~~~-s~g~d~~~~~~~g~l~~~d~~~~~~   93 (226)
T PF06745_consen   20 SVVLISGPPGSGKTTLALQFLYN-GLKNFGEKVLYVSFE--EP--PEELIENMK-SFGWDLEEYEDSGKLKIIDAFPERI   93 (226)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH-HHHHHT--EEEEESS--S---HHHHHHHHH-TTTS-HHHHHHTTSEEEEESSGGGS
T ss_pred             cEEEEEeCCCCCcHHHHHHHHHH-hhhhcCCcEEEEEec--CC--HHHHHHHHH-HcCCcHHHHhhcCCEEEEecccccc
Confidence            89999999999999999997653 222213467888765  33  344443332 333221110            01  


Q ss_pred             ---ccCHHHHHHHHHHHcCC-CcEEEEEeCcC
Q 001843          340 ---TLSAEELMWRITQALDD-STFLIVMENAE  367 (1007)
Q Consensus       340 ---~~~~~~l~~~l~~~L~~-kr~LlVlDdv~  367 (1007)
                         ..+...+...+.+.++. +...+|+|.+.
T Consensus        94 ~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls  125 (226)
T PF06745_consen   94 GWSPNDLEELLSKIREAIEELKPDRVVIDSLS  125 (226)
T ss_dssp             T-TSCCHHHHHHHHHHHHHHHTSSEEEEETHH
T ss_pred             cccccCHHHHHHHHHHHHHhcCCCEEEEECHH
Confidence               24566666666666553 34678888764

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PRK00625 shikimate kinase; Provisional

Probab=93.26  E-value=0.066  Score=53.80  Aligned_cols=21  Identities=29%  Similarity=0.389  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHHh
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .|.++||+|+||||+++.+++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~   22 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAK   22 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            378999999999999999988

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=93.21  E-value=0.14  Score=51.58  Aligned_cols=22  Identities=36%  Similarity=0.671  Sum_probs=20.1

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .|.|.|.+|.||||+|+.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999994

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=93.19  E-value=0.25  Score=50.85  Aligned_cols=26  Identities=38%  Similarity=0.560  Sum_probs=23.2

Q ss_pred             CCcEEEEEEcCCCChHHHHHHHHHhh
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+++-|.++|++|.|||.||++|+|+
T Consensus       187 dpprgvllygppg~gktml~kava~~  212 (408)
T KOG0727|consen  187 DPPRGVLLYGPPGTGKTMLAKAVANH  212 (408)
T ss_pred             CCCcceEEeCCCCCcHHHHHHHHhhc
Confidence            44588899999999999999999994

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=93.15  E-value=0.33  Score=50.50  Aligned_cols=84  Identities=17%  Similarity=0.210  Sum_probs=50.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCC-CHHHHHHHHHHHHhhhhhhh-----cccc------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMV-EDRDVLADILKQIDESLLKV-----EATL------  341 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~-~~~~~l~~il~~l~~~~~~~-----~~~~------  341 (1007)
                      +-++|+|..|+|||+|+..+.++.    .-+.++++.++  +.. ...++.+++...-..+  ..     ..++      
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~~----~~d~~V~~~iG--er~~Ev~~~~~~~~~~~~~~--~t~vv~~t~~~~~~~r~   87 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANNQ----DADVVVYALIG--ERGREVTEFIEELKGEGALE--RTVVVAATSDEPPAARY   87 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHC----TTTEEEEEEES--ECHHHHHHHHHHHHHTTGGG--GEEEEEEETTS-HHHHH
T ss_pred             CEEEEEcCcccccchhhHHHHhcc----cccceeeeecc--ccchhHHHHHHHHhhccccc--ccccccccchhhHHHHh
Confidence            678999999999999999999853    23345777776  443 3444444442221111  00     0111      


Q ss_pred             ----CHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          342 ----SAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       342 ----~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                          ..-...+.++.  +++.+|+++||+.
T Consensus        88 ~~~~~a~t~AEyfrd--~G~dVlli~Dslt  115 (215)
T PF00006_consen   88 RAPYTALTIAEYFRD--QGKDVLLIIDSLT  115 (215)
T ss_dssp             HHHHHHHHHHHHHHH--TTSEEEEEEETHH
T ss_pred             hhhccchhhhHHHhh--cCCceeehhhhhH
Confidence                11223444444  7999999999984

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=93.14  E-value=0.29  Score=54.78  Aligned_cols=22  Identities=27%  Similarity=0.493  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .-|.|+|..|+||+++|+.+++
T Consensus        23 ~pVLI~GE~GtGK~~lAr~iH~   44 (329)
T TIGR02974        23 RPVLIIGERGTGKELIAARLHY   44 (329)
T ss_pred             CCEEEECCCCChHHHHHHHHHH
Confidence            5678999999999999999987

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.14  E-value=0.33  Score=56.19  Aligned_cols=86  Identities=24%  Similarity=0.243  Sum_probs=47.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCH--HHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVED--RDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~--~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      ++++++|++|+||||++.+++........-..+..|+..   .+..  .+-++.....++.+   .....+...+...+.
T Consensus       222 ~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D---~~r~~a~eqL~~~a~~~~vp---~~~~~~~~~l~~~l~  295 (424)
T PRK05703        222 GVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLD---TYRIGAVEQLKTYAKIMGIP---VEVVYDPKELAKALE  295 (424)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECC---ccHHHHHHHHHHHHHHhCCc---eEccCCHHhHHHHHH
Confidence            799999999999999999887732212333456667654   2221  12233333333322   112334455555554


Q ss_pred             HHcCCCcEEEEEeCcC
Q 001843          352 QALDDSTFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~  367 (1007)
                      +. . ..=+||+|..-
T Consensus       296 ~~-~-~~DlVlIDt~G  309 (424)
T PRK05703        296 QL-R-DCDVILIDTAG  309 (424)
T ss_pred             Hh-C-CCCEEEEeCCC
Confidence            42 3 34588889763

>PRK04040 adenylate kinase; Provisional

Probab=93.12  E-value=0.078  Score=54.12  Aligned_cols=22  Identities=32%  Similarity=0.527  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+|+|+|++|+||||+++.+.+
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~   24 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALE   24 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHH
Confidence            7899999999999999999988

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.08  E-value=0.54  Score=48.35  Aligned_cols=58  Identities=14%  Similarity=0.102  Sum_probs=35.5

Q ss_pred             HHHHHHHcCCCcEEEEEeCcCccCchhhhhhc----cccCCCCCCcEEEEEcCCCcccccccCCc
Q 001843          347 MWRITQALDDSTFLIVMENAEHQKSQVWDSFL----GKLCSFTQCGKIIITTSSTEDFVEPLGAA  407 (1007)
Q Consensus       347 ~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~----~l~~~~~~gs~IliTTR~~~~va~~~~~~  407 (1007)
                      ...+.+.+--++-|.|||..+  +.-+.+.++    .+-.--..|+-+||.|-.+. ++.+..++
T Consensus       152 R~EilQ~~~lePkl~ILDE~D--SGLDIdalk~V~~~i~~lr~~~~~~liITHy~r-ll~~i~pD  213 (251)
T COG0396         152 RNEILQLLLLEPKLAILDEPD--SGLDIDALKIVAEGINALREEGRGVLIITHYQR-LLDYIKPD  213 (251)
T ss_pred             HHHHHHHHhcCCCEEEecCCC--cCccHHHHHHHHHHHHHHhcCCCeEEEEecHHH-HHhhcCCC
Confidence            334555555677899999987  444444333    11111134667777777777 88887765

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.00  E-value=0.4  Score=49.15  Aligned_cols=39  Identities=28%  Similarity=0.440  Sum_probs=27.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC--------CceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF--------TKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--------~~~~wv~~s  312 (1007)
                      .++.|+|.+|+||||++.+++........|        ..++|+...
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E   79 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLE   79 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESS
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEecc
Confidence            689999999999999999998854333333        247787754

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=92.99  E-value=0.23  Score=56.28  Aligned_cols=37  Identities=32%  Similarity=0.323  Sum_probs=29.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      .++.|.|.+|+|||||+.+++..  ....-..++|++..
T Consensus        83 slvLI~G~pG~GKStLllq~a~~--~a~~g~~VlYvs~E  119 (372)
T cd01121          83 SVILIGGDPGIGKSTLLLQVAAR--LAKRGGKVLYVSGE  119 (372)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEECC
Confidence            89999999999999999999873  33333567787654

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=92.96  E-value=0.23  Score=50.04  Aligned_cols=116  Identities=17%  Similarity=0.190  Sum_probs=60.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhh-hc--ccC---CC--ceEEEEecCCCCCCHHHHHHHHHHHHhhhh---hhhccccC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRV-YV--KRH---FT--KRAWVHIPIMSMVEDRDVLADILKQIDESL---LKVEATLS  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~-~~--~~~---F~--~~~wv~~s~~~~~~~~~~l~~il~~l~~~~---~~~~~~~~  342 (1007)
                      .+++|+|..|.|||||.+.+..+. .+  ...   |.  .+.|  +.  +        .+.+..++...   .......+
T Consensus        22 ~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~--~~--q--------~~~l~~~~L~~~~~~~~~~~LS   89 (176)
T cd03238          22 VLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIF--ID--Q--------LQFLIDVGLGYLTLGQKLSTLS   89 (176)
T ss_pred             CEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEE--Eh--H--------HHHHHHcCCCccccCCCcCcCC
Confidence            799999999999999999986421 11  111   10  1222  22  2        34555555320   01111111


Q ss_pred             H-HHHHHHHHHHcCCC--cEEEEEeCcCc-cCchhhhhhc-cccCCCCCCcEEEEEcCCCccccc
Q 001843          343 A-EELMWRITQALDDS--TFLIVMENAEH-QKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVE  402 (1007)
Q Consensus       343 ~-~~l~~~l~~~L~~k--r~LlVlDdv~~-~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~  402 (1007)
                      . +...-.+...+-.+  +=++++|..-. -+....+.+. .+......|..||++|.+.. ...
T Consensus        90 gGq~qrl~laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~-~~~  153 (176)
T cd03238          90 GGELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLD-VLS  153 (176)
T ss_pred             HHHHHHHHHHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHH-HHH
Confidence            1 22222344455555  67888898642 1333344444 22221124667888888877 544

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=92.93  E-value=0.088  Score=53.71  Aligned_cols=22  Identities=32%  Similarity=0.578  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+|.|+|.+|+||||+|+.++.
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            8999999999999999999987

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=92.88  E-value=0.2  Score=54.17  Aligned_cols=37  Identities=24%  Similarity=0.259  Sum_probs=33.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +++.|+|.+|+|||++|.++..  ...++...++||+..
T Consensus        24 ~~~lI~G~pGsGKT~f~~qfl~--~~~~~ge~vlyvs~~   60 (260)
T COG0467          24 SVVLITGPPGTGKTIFALQFLY--EGAREGEPVLYVSTE   60 (260)
T ss_pred             cEEEEEcCCCCcHHHHHHHHHH--HHHhcCCcEEEEEec
Confidence            8999999999999999999988  566668889999876

>PRK00131 aroK shikimate kinase; Reviewed

Probab=92.87  E-value=0.088  Score=52.93  Aligned_cols=22  Identities=41%  Similarity=0.682  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ..|.|+|++|+||||+|+.++.
T Consensus         5 ~~i~l~G~~GsGKstla~~La~   26 (175)
T PRK00131          5 PNIVLIGFMGAGKSTIGRLLAK   26 (175)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHH
Confidence            6899999999999999999999

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=92.86  E-value=0.054  Score=56.44  Aligned_cols=112  Identities=21%  Similarity=0.085  Sum_probs=71.4

Q ss_pred             CeEEEEEecCCCCCCCCCcCCCcceEEEEeccccCCCCchhhhhhhccccccCCCCcccEEEecCCCCCCcCCCccccCC
Q 001843          614 AVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRL  693 (1007)
Q Consensus       614 ~~r~Lsl~~~~~~~~~~~~~~~~LRsL~l~~~~~~~~~~~~i~~~l~~~~~~~~l~~Lr~L~Ls~~~l~~~~lp~~i~~L  693 (1007)
                      ...++++.+.........+.+++|+.|.++.|......      -+.-..  .++++|++|+|++|++....-...+..+
T Consensus        44 ~le~ls~~n~gltt~~~~P~Lp~LkkL~lsdn~~~~~~------~l~vl~--e~~P~l~~l~ls~Nki~~lstl~pl~~l  115 (260)
T KOG2739|consen   44 ELELLSVINVGLTTLTNFPKLPKLKKLELSDNYRRVSG------GLEVLA--EKAPNLKVLNLSGNKIKDLSTLRPLKEL  115 (260)
T ss_pred             chhhhhhhccceeecccCCCcchhhhhcccCCcccccc------cceehh--hhCCceeEEeecCCccccccccchhhhh
Confidence            34555555544444445578899999999999442111      233334  6789999999999998721111234567


Q ss_pred             CcCcEEecccCCCcccCc----ccccCCCCCEEeecCCcccccc
Q 001843          694 PFLEYLGLRSTFIDSLPD----STPILFCLATLDVSHTKVQRLP  733 (1007)
Q Consensus       694 ~~Lr~L~L~~n~i~~LP~----~i~~L~~L~~L~L~~~~l~~lP  733 (1007)
                      .+|..|++.+|..+.+-.    -+.-+++|.+||-....=.+.|
T Consensus       116 ~nL~~Ldl~n~~~~~l~dyre~vf~ll~~L~~LD~~dv~~~Ea~  159 (260)
T KOG2739|consen  116 ENLKSLDLFNCSVTNLDDYREKVFLLLPSLKYLDGCDVDGEEAP  159 (260)
T ss_pred             cchhhhhcccCCccccccHHHHHHHHhhhhccccccccCCcccc
Confidence            788899999887766532    2455777888776554333333

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=92.80  E-value=0.75  Score=50.41  Aligned_cols=118  Identities=17%  Similarity=0.243  Sum_probs=61.3

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhh-hcccCCCceEEEE----ecCCCCC-----CHHHHHHHHHHHHhhhhhhh--ccc
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRV-YVKRHFTKRAWVH----IPIMSMV-----EDRDVLADILKQIDESLLKV--EAT  340 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~-~~~~~F~~~~wv~----~s~~~~~-----~~~~~l~~il~~l~~~~~~~--~~~  340 (1007)
                      +..|.+.|.+|.|||-||.+..=.. ..++.|..++-..    ++  ++.     ...+-+.-.++.+..++...  ...
T Consensus       245 I~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG--~dIGfLPG~eEeKm~PWmq~i~DnLE~L~~~~~  322 (436)
T COG1875         245 IDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVG--EDIGFLPGTEEEKMGPWMQAIFDNLEVLFSPNE  322 (436)
T ss_pred             CCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcc--cccCcCCCchhhhccchHHHHHhHHHHHhcccc
Confidence            3899999999999999998765432 3355566544321    22  111     11222222222222211000  011


Q ss_pred             cCHHHHHHHHH---------HHcCCC---cEEEEEeCcCccCchhhhhhccccCCCCCCcEEEEEcC
Q 001843          341 LSAEELMWRIT---------QALDDS---TFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTS  395 (1007)
Q Consensus       341 ~~~~~l~~~l~---------~~L~~k---r~LlVlDdv~~~~~~~~~~l~~l~~~~~~gs~IliTTR  395 (1007)
                      .....+...+.         .+.+++   +-+||+|.+.+-.+.+...+.  ... +.||||+.|--
T Consensus       323 ~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLTpheikTil--tR~-G~GsKIVl~gd  386 (436)
T COG1875         323 PGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLTPHELKTIL--TRA-GEGSKIVLTGD  386 (436)
T ss_pred             cchHHHHHHHhccceeeeeeeeecccccccceEEEehhhccCHHHHHHHH--Hhc-cCCCEEEEcCC
Confidence            12222222211         123454   459999999865555544443  334 89999998865

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=92.78  E-value=0.66  Score=49.44  Aligned_cols=23  Identities=30%  Similarity=0.442  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+-.|+|+||+|||+||.+++-.
T Consensus         2 ~~~ll~g~~G~GKS~lal~la~~   24 (239)
T cd01125           2 YVSALVAPGGTGKSSLLLVLALA   24 (239)
T ss_pred             ceeEEEcCCCCCHHHHHHHHHHH
Confidence            46789999999999999999873

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.76  E-value=0.58  Score=53.68  Aligned_cols=38  Identities=34%  Similarity=0.398  Sum_probs=26.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEe
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI  311 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~  311 (1007)
                      .+++++|..|+||||++..++........-+.+.+++.
T Consensus       192 ~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~  229 (420)
T PRK14721        192 GVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTT  229 (420)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEec
Confidence            79999999999999999988873222222344555554

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=92.76  E-value=0.39  Score=53.98  Aligned_cols=61  Identities=26%  Similarity=0.299  Sum_probs=42.4

Q ss_pred             CCCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhh
Q 001843          270 TTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES  333 (1007)
Q Consensus       270 ~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~  333 (1007)
                      ...+.||-.+|.=|.||||-|-++++  .++++=..+.-|++. ...+...+-++.+.++++.+
T Consensus        97 ~~~P~vImmvGLQGsGKTTt~~KLA~--~lkk~~~kvllVaaD-~~RpAA~eQL~~La~q~~v~  157 (451)
T COG0541          97 KKPPTVILMVGLQGSGKTTTAGKLAK--YLKKKGKKVLLVAAD-TYRPAAIEQLKQLAEQVGVP  157 (451)
T ss_pred             CCCCeEEEEEeccCCChHhHHHHHHH--HHHHcCCceEEEecc-cCChHHHHHHHHHHHHcCCc
Confidence            34559999999999999999999998  565532334444432 13445566677777777665

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=92.75  E-value=0.025  Score=57.80  Aligned_cols=22  Identities=32%  Similarity=0.303  Sum_probs=19.3

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ++.|.|..|.||||+.+.+.-.
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~~   22 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGLI   22 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHHH
Confidence            4689999999999999999843

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=92.72  E-value=0.84  Score=47.55  Aligned_cols=129  Identities=15%  Similarity=0.246  Sum_probs=68.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH-H
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT-Q  352 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~-~  352 (1007)
                      +-|..+|++|.|||.+|++++|.  .+-.|   +-|...            +++..--+         +....+..+- +
T Consensus       152 knVLFyGppGTGKTm~Akalane--~kvp~---l~vkat------------~liGehVG---------dgar~Ihely~r  205 (368)
T COG1223         152 KNVLFYGPPGTGKTMMAKALANE--AKVPL---LLVKAT------------ELIGEHVG---------DGARRIHELYER  205 (368)
T ss_pred             ceeEEECCCCccHHHHHHHHhcc--cCCce---EEechH------------HHHHHHhh---------hHHHHHHHHHHH
Confidence            78899999999999999999994  33222   222211            12211111         1111222222 2


Q ss_pred             HcCCCcEEEEEeCcCcc-----------C-chhhhhhc-ccc--CCCCCCcEEEEEcCCCccccc-ccCCcc-eeeecCC
Q 001843          353 ALDDSTFLIVMENAEHQ-----------K-SQVWDSFL-GKL--CSFTQCGKIIITTSSTEDFVE-PLGAAF-STLHVPG  415 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~-----------~-~~~~~~l~-~l~--~~~~~gs~IliTTR~~~~va~-~~~~~~-~~~~l~~  415 (1007)
                      .-+.-+|.+.+|.++..           + .+..+.+. .+-  .. +-|-..|-.|-+.. ... ...+.. .-++..-
T Consensus       206 A~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~e-neGVvtIaaTN~p~-~LD~aiRsRFEeEIEF~L  283 (368)
T COG1223         206 ARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKE-NEGVVTIAATNRPE-LLDPAIRSRFEEEIEFKL  283 (368)
T ss_pred             HHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCccc-CCceEEEeecCChh-hcCHHHHhhhhheeeeeC
Confidence            22356899999987621           0 11112222 111  12 34555555555554 332 223322 5566667


Q ss_pred             CCHHHHHHHHHhhhc
Q 001843          416 LGKNESWELFLKKAR  430 (1007)
Q Consensus       416 L~~~ea~~Lf~~~a~  430 (1007)
                      -+++|-.+++..++.
T Consensus       284 P~~eEr~~ile~y~k  298 (368)
T COG1223         284 PNDEERLEILEYYAK  298 (368)
T ss_pred             CChHHHHHHHHHHHH
Confidence            788888888877764

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=92.70  E-value=0.45  Score=51.43  Aligned_cols=113  Identities=17%  Similarity=0.087  Sum_probs=59.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhh-hhhhhc---cccCHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDE-SLLKVE---ATLSAEELMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~-~~~~~~---~~~~~~~l~~~  349 (1007)
                      .-++|+|..|.|||||.+.++.  .+. .....+|+.-.   .-...+...++...... +.....   +..+...-...
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~--~~~-~~~G~i~~~g~---~v~~~d~~~ei~~~~~~~~q~~~~~r~~v~~~~~k~~~  185 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLAR--ILS-TGISQLGLRGK---KVGIVDERSEIAGCVNGVPQHDVGIRTDVLDGCPKAEG  185 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhC--ccC-CCCceEEECCE---EeecchhHHHHHHHhcccccccccccccccccchHHHH
Confidence            6889999999999999999998  333 33344454211   11000111233322211 100000   01111111112


Q ss_pred             HHHHcC-CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCc
Q 001843          350 ITQALD-DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       350 l~~~L~-~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~  398 (1007)
                      +...+. ..+=++++|.+-  ..+.+..+. .+    ..|..||+||-+..
T Consensus       186 ~~~~i~~~~P~villDE~~--~~e~~~~l~~~~----~~G~~vI~ttH~~~  230 (270)
T TIGR02858       186 MMMLIRSMSPDVIVVDEIG--REEDVEALLEAL----HAGVSIIATAHGRD  230 (270)
T ss_pred             HHHHHHhCCCCEEEEeCCC--cHHHHHHHHHHH----hCCCEEEEEechhH
Confidence            233332 478899999987  666566555 43    34678999998655

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.70  E-value=0.49  Score=56.10  Aligned_cols=51  Identities=16%  Similarity=0.184  Sum_probs=35.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQID  331 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~  331 (1007)
                      .++.|.|.+|+|||||+.+++..  ..++-+.+++++..    .+..++.+.+ +.++
T Consensus       264 s~~li~G~~G~GKt~l~~~f~~~--~~~~ge~~~y~s~e----Es~~~i~~~~-~~lg  314 (484)
T TIGR02655       264 SIILATGATGTGKTLLVSKFLEN--ACANKERAILFAYE----ESRAQLLRNA-YSWG  314 (484)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEee----CCHHHHHHHH-HHcC
Confidence            89999999999999999999884  33344566777643    4444555443 4443

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=92.64  E-value=0.34  Score=52.80  Aligned_cols=78  Identities=17%  Similarity=0.219  Sum_probs=44.1

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHhhhhcccCC--CceEEEEecCCCCCCHHHHHHHHHHHHhh-hhhhhccccCHHHHHH
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHF--TKRAWVHIPIMSMVEDRDVLADILKQIDE-SLLKVEATLSAEELMW  348 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F--~~~~wv~~s~~~~~~~~~~l~~il~~l~~-~~~~~~~~~~~~~l~~  348 (1007)
                      .+.+|+|.|..|+||||+|+.+..  .+....  ..+..++..  .-....+.+..    .+. +........+...+..
T Consensus        61 ~p~IIGIaG~~GSGKSTlar~L~~--ll~~~~~~g~V~vi~~D--~f~~~~~~l~~----~g~~~~~g~P~s~D~~~l~~  132 (290)
T TIGR00554        61 IPYIISIAGSVAVGKSTTARILQA--LLSRWPEHRKVELITTD--GFLHPNQVLKE----RNLMKKKGFPESYDMHRLVK  132 (290)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--HHhhcCCCCceEEEecc--cccccHHHHHH----cCCccccCCChhccHHHHHH
Confidence            348999999999999999988766  333222  135555544  22222222221    111 1012235667777777


Q ss_pred             HHHHHcCCC
Q 001843          349 RITQALDDS  357 (1007)
Q Consensus       349 ~l~~~L~~k  357 (1007)
                      .+.....++
T Consensus       133 ~L~~Lk~g~  141 (290)
T TIGR00554       133 FLSDLKSGK  141 (290)
T ss_pred             HHHHHHCCC
Confidence            776665554

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=92.63  E-value=0.041  Score=57.87  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +++.|.|..|.||||+.+.+...
T Consensus        31 ~~~~l~G~n~~GKstll~~i~~~   53 (222)
T cd03285          31 RFLIITGPNMGGKSTYIRQIGVI   53 (222)
T ss_pred             eEEEEECCCCCChHHHHHHHHHH
Confidence            89999999999999999987753

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=92.63  E-value=0.16  Score=59.86  Aligned_cols=28  Identities=29%  Similarity=0.699  Sum_probs=25.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  303 (1007)
                      ++++.+|++|+|||.+|+.++.  ...+.|
T Consensus       439 kIlCf~GPPGVGKTSI~kSIA~--ALnRkF  466 (906)
T KOG2004|consen  439 KILCFVGPPGVGKTSIAKSIAR--ALNRKF  466 (906)
T ss_pred             cEEEEeCCCCCCcccHHHHHHH--HhCCce
Confidence            8999999999999999999999  676666

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.62  E-value=0.67  Score=54.16  Aligned_cols=37  Identities=30%  Similarity=0.273  Sum_probs=28.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      .++.|.|.+|+|||||+.+++.+  ....-..++|++..
T Consensus        81 s~~lI~G~pG~GKTtL~lq~a~~--~a~~g~~vlYvs~E  117 (446)
T PRK11823         81 SVVLIGGDPGIGKSTLLLQVAAR--LAAAGGKVLYVSGE  117 (446)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEcc
Confidence            79999999999999999999884  32333457787754

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=92.60  E-value=0.2  Score=55.33  Aligned_cols=47  Identities=26%  Similarity=0.251  Sum_probs=33.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLA  324 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~  324 (1007)
                      +++.+.|.||+||||+|-+.+-  ........++-|+..  ...+..+++.
T Consensus         3 riv~f~GKGGVGKTT~aaA~A~--~lA~~g~kvLlvStD--PAhsL~d~f~   49 (322)
T COG0003           3 RIVFFTGKGGVGKTTIAAATAV--KLAESGKKVLLVSTD--PAHSLGDVFD   49 (322)
T ss_pred             EEEEEecCCcccHHHHHHHHHH--HHHHcCCcEEEEEeC--CCCchHhhhc
Confidence            8999999999999999999666  344444556666665  4445444443

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=92.54  E-value=2.6  Score=45.98  Aligned_cols=70  Identities=11%  Similarity=0.143  Sum_probs=50.5

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCCCHHHHHHHHHh
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLK  427 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~  427 (1007)
                      +++-++|+|+++.-....++.+. .+-.. ..++.+|++|.+...+.....+.+..+.+.+ +.++..+.+..
T Consensus       103 ~~~kV~II~~ad~m~~~AaNaLLKtLEEP-p~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~~  173 (290)
T PRK07276        103 GKQQVFIIKDADKMHVNAANSLLKVIEEP-QSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLEQ  173 (290)
T ss_pred             CCcEEEEeehhhhcCHHHHHHHHHHhcCC-CCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHHH
Confidence            55668999999977788888887 44333 5556777777666658887777778888877 66666666643

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.52  E-value=0.65  Score=54.71  Aligned_cols=159  Identities=16%  Similarity=0.144  Sum_probs=84.7

Q ss_pred             CCCCCcEEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHH
Q 001843          268 TTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELM  347 (1007)
Q Consensus       268 ~~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~  347 (1007)
                      .+...++-+-.+|++|.|||-++++|+++  ..-+     .+.+.      ..+    ++....        ......+.
T Consensus       213 ~g~~~prg~Ll~gppg~Gkt~l~~aVa~e--~~a~-----~~~i~------~pe----li~k~~--------gEte~~LR  267 (693)
T KOG0730|consen  213 IGIKPPRGLLLYGPPGTGKTFLVRAVANE--YGAF-----LFLIN------GPE----LISKFP--------GETESNLR  267 (693)
T ss_pred             cCCCCCCCccccCCCCCChHHHHHHHHHH--hCce-----eEecc------cHH----HHHhcc--------cchHHHHH
Confidence            45556688999999999999999999994  3211     11121      111    222222        22455566


Q ss_pred             HHHHHHcCCC-cEEEEEeCcCccC----------chhhhhhccccCCCCCCcEEE--EEcCCCcccccccC--Ccceeee
Q 001843          348 WRITQALDDS-TFLIVMENAEHQK----------SQVWDSFLGKLCSFTQCGKII--ITTSSTEDFVEPLG--AAFSTLH  412 (1007)
Q Consensus       348 ~~l~~~L~~k-r~LlVlDdv~~~~----------~~~~~~l~~l~~~~~~gs~Il--iTTR~~~~va~~~~--~~~~~~~  412 (1007)
                      ..+.+..+.+ +..|.+|+++..-          ...-.++..+.++.++.+++|  -||+.++.+-....  -...-+.
T Consensus       268 ~~f~~a~k~~~psii~IdEld~l~p~r~~~~~~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~sld~alRRgRfd~ev~  347 (693)
T KOG0730|consen  268 KAFAEALKFQVPSIIFIDELDALCPKREGADDVESRVVSQLLTLLDGLKPDAKVIVLAATNRPDSLDPALRRGRFDREVE  347 (693)
T ss_pred             HHHHHHhccCCCeeEeHHhHhhhCCcccccchHHHHHHHHHHHHHhhCcCcCcEEEEEecCCccccChhhhcCCCcceee
Confidence            7777777788 9999999986311          111223333444434334443  37776652322222  1114555


Q ss_pred             cCCCCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCc
Q 001843          413 VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlP  458 (1007)
                      +.-.+..+-.+++..+......     .  .......|+..+.|.-
T Consensus       348 IgiP~~~~RldIl~~l~k~~~~-----~--~~~~l~~iA~~thGyv  386 (693)
T KOG0730|consen  348 IGIPGSDGRLDILRVLTKKMNL-----L--SDVDLEDIAVSTHGYV  386 (693)
T ss_pred             ecCCCchhHHHHHHHHHHhcCC-----c--chhhHHHHHHHccchh
Confidence            5555655555555544332211     1  1233445666666654

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=92.50  E-value=0.55  Score=50.09  Aligned_cols=52  Identities=15%  Similarity=0.274  Sum_probs=37.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQI  330 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l  330 (1007)
                      .++.|.|.+|+|||++|.+++.+.. ..+=..++|++..    .+..++...++...
T Consensus        14 ~l~lI~G~~G~GKT~~~~~~~~~~~-~~~g~~vly~s~E----~~~~~~~~r~~~~~   65 (242)
T cd00984          14 DLIIIAARPSMGKTAFALNIAENIA-KKQGKPVLFFSLE----MSKEQLLQRLLASE   65 (242)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHH-HhCCCceEEEeCC----CCHHHHHHHHHHHh
Confidence            7999999999999999999877432 2213456777643    45667777766543

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK13947 shikimate kinase; Provisional

Probab=92.46  E-value=0.096  Score=52.60  Aligned_cols=21  Identities=48%  Similarity=0.631  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHHh
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      -|.|+|++|+||||+|+.+++
T Consensus         3 ~I~l~G~~GsGKst~a~~La~   23 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVAT   23 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHH
Confidence            489999999999999999998

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=92.45  E-value=0.13  Score=52.12  Aligned_cols=36  Identities=28%  Similarity=0.419  Sum_probs=26.0

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +|+|.|.+|+||||||+.+..  ........+..++..
T Consensus         1 ii~i~G~sgsGKttla~~l~~--~l~~~~~~~~~i~~D   36 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSN--QLRVNGIGPVVISLD   36 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH--HHHHcCCCEEEEehh
Confidence            589999999999999999998  443332334445443

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=92.42  E-value=0.68  Score=48.34  Aligned_cols=23  Identities=22%  Similarity=0.372  Sum_probs=21.1

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHh
Q 001843          273 TQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++.|+|..|.||||+.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            38999999999999999999885

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=92.40  E-value=1.5  Score=46.89  Aligned_cols=82  Identities=20%  Similarity=0.135  Sum_probs=45.8

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhh--hhhh-hccccCHHHHHHHHH
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDE--SLLK-VEATLSAEELMWRIT  351 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~--~~~~-~~~~~~~~~l~~~l~  351 (1007)
                      +|+|.|-.|.||||+|+++..  ..+..-..++.++......++....-..+......  +... .++..+.+.+.+.++
T Consensus         1 IIgItG~SGSGKTTv~~~l~~--~l~~~g~~v~vI~~D~yyr~~r~~~~~~~~~a~~~~~nfdHf~PeAnd~dlL~~~l~   78 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEH--IFAREGIHPAVVEGDSFHRYERMEMKMAIAEALDAGRNFSHFGPEANLFDLLEELFR   78 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHH--HHHhcCCceEEEeccccccCCchhHHHHHHHHhhcCCCCCCCCcccccHHHHHHHHH
Confidence            589999999999999999887  34332223555654422233333332222222211  1001 024556677777777


Q ss_pred             HHcCCCc
Q 001843          352 QALDDST  358 (1007)
Q Consensus       352 ~~L~~kr  358 (1007)
                      .+.+++.
T Consensus        79 ~L~~g~~   85 (277)
T cd02029          79 TYGETGR   85 (277)
T ss_pred             HHHcCCC
Confidence            7766553

PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.37  E-value=0.55  Score=57.55  Aligned_cols=86  Identities=23%  Similarity=0.310  Sum_probs=49.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCC--HHHHHHHHHHHHhhhhhhhccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVE--DRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~--~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      +|++++|..|+||||.+.+++...........+..++..   .+.  ..+-++...+.++.+   .....+..++.+.+.
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~D---t~RigA~eQL~~~a~~~gvp---v~~~~~~~~l~~al~  259 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTD---SFRIGALEQLRIYGRILGVP---VHAVKDAADLRFALA  259 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCc---ccchHHHHHHHHHHHhCCCC---ccccCCHHHHHHHHH
Confidence            799999999999999999988742222222345566543   233  344455555555433   112335555555554


Q ss_pred             HHcCCCcEEEEEeCcC
Q 001843          352 QALDDSTFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~  367 (1007)
                       .++++. +|++|-.-
T Consensus       260 -~~~~~D-~VLIDTAG  273 (767)
T PRK14723        260 -ALGDKH-LVLIDTVG  273 (767)
T ss_pred             -HhcCCC-EEEEeCCC
Confidence             344443 66677653

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=92.37  E-value=0.53  Score=50.51  Aligned_cols=90  Identities=13%  Similarity=0.137  Sum_probs=52.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhc--ccCCCceEEEEecCCCCC-CHHHHHHHHHHHHhhhhhhh-----ccccC---
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYV--KRHFTKRAWVHIPIMSMV-EDRDVLADILKQIDESLLKV-----EATLS---  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~--~~~F~~~~wv~~s~~~~~-~~~~~l~~il~~l~~~~~~~-----~~~~~---  342 (1007)
                      +-++|.|-.|+|||+|+..+.++..+  +.+-+.++++-++  +.. +..+++.++.+.=...  ..     .....   
T Consensus        70 QR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IG--eR~rev~e~~~~~~~~~~l~--~tv~v~~t~~~~~~~  145 (276)
T cd01135          70 QKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMG--ITMEDARFFKDDFEETGALE--RVVLFLNLANDPTIE  145 (276)
T ss_pred             CEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEec--cccHHHHHHHHHhhhcCCcc--eEEEEEecCCCCHHH
Confidence            67899999999999999999885331  2234677888877  544 4444554444421111  00     00111   


Q ss_pred             ---HHHHHHHHHHHc---CCCcEEEEEeCcC
Q 001843          343 ---AEELMWRITQAL---DDSTFLIVMENAE  367 (1007)
Q Consensus       343 ---~~~l~~~l~~~L---~~kr~LlVlDdv~  367 (1007)
                         .-...-.+.+++   +++++|+++||+.
T Consensus       146 r~~a~~~a~aiAEyfrd~~g~~VLl~~D~lt  176 (276)
T cd01135         146 RIITPRMALTTAEYLAYEKGKHVLVILTDMT  176 (276)
T ss_pred             HHHHHHHHHHHHHHHHhccCCeEEEEEcChh
Confidence               111112233444   3789999999985

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=92.34  E-value=0.17  Score=48.01  Aligned_cols=32  Identities=28%  Similarity=0.479  Sum_probs=25.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      .=|.|.|.+|+||||+|.+++.  ..  .|   -|+++|
T Consensus         8 PNILvtGTPG~GKstl~~~lae--~~--~~---~~i~is   39 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLAE--KT--GL---EYIEIS   39 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHHH--Hh--CC---ceEehh
Confidence            5678999999999999999997  22  22   477777

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=92.34  E-value=0.11  Score=52.70  Aligned_cols=23  Identities=35%  Similarity=0.603  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ++++|+|+.|+|||||++.++..
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999999883

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK13948 shikimate kinase; Provisional

Probab=92.33  E-value=0.12  Score=52.29  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=22.0

Q ss_pred             CcEEEEEEcCCCChHHHHHHHHHh
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ..+.|.++||.|+||||+++.+++
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~   32 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSR   32 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            348899999999999999999998

>PRK00889 adenylylsulfate kinase; Provisional

Probab=92.33  E-value=0.17  Score=51.00  Aligned_cols=23  Identities=35%  Similarity=0.577  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+|.|+|++|+||||+|+.++..
T Consensus         5 ~~i~~~G~~GsGKST~a~~la~~   27 (175)
T PRK00889          5 VTVWFTGLSGAGKTTIARALAEK   27 (175)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            79999999999999999999983

>KOG3864 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.27  E-value=0.018  Score=57.58  Aligned_cols=82  Identities=22%  Similarity=0.261  Sum_probs=41.4

Q ss_pred             CceEEEEEeeecCCCCcCccccCCCCcEEEeecCCcCCC-ceeecCCCCCCCcEEEeccCCCCcceEEc-CCCCccccEe
Q 001843          867 NVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGE-EMSCSSGEFPNLLVLKLWKLNRLRQWRIK-EGAMPCLRQL  944 (1007)
Q Consensus       867 ~L~~L~L~~~~l~~~~~~~l~~Lp~L~~L~L~~~~~~~~-~l~~~~~~fp~L~~L~L~~~~~L~~l~~~-~~~~p~L~~L  944 (1007)
                      .++.++-+++.+....+..+..+++++.|.+.++.+.+. .+..-.+.+|+|+.|+|++|+.+++--.. ...+++|+.|
T Consensus       102 ~IeaVDAsds~I~~eGle~L~~l~~i~~l~l~~ck~~dD~~L~~l~~~~~~L~~L~lsgC~rIT~~GL~~L~~lknLr~L  181 (221)
T KOG3864|consen  102 KIEAVDASDSSIMYEGLEHLRDLRSIKSLSLANCKYFDDWCLERLGGLAPSLQDLDLSGCPRITDGGLACLLKLKNLRRL  181 (221)
T ss_pred             eEEEEecCCchHHHHHHHHHhccchhhhheeccccchhhHHHHHhcccccchheeeccCCCeechhHHHHHHHhhhhHHH
Confidence            466677777776666666666777777777764333221 11111224555555555555544432111 1234555555


Q ss_pred             Eeec
Q 001843          945 EIRS  948 (1007)
Q Consensus       945 ~l~~  948 (1007)
                      .|.+
T Consensus       182 ~l~~  185 (221)
T KOG3864|consen  182 HLYD  185 (221)
T ss_pred             HhcC
Confidence            5544

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=92.27  E-value=0.54  Score=52.39  Aligned_cols=83  Identities=19%  Similarity=0.199  Sum_probs=50.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh--ccccCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV--EATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~--~~~~~~~~l~~~l~  351 (1007)
                      .+|.|-|-+|+|||||..+++.  +...+- .+++|+-    ..+..++ +--+.+++......  -...+.+...+.+.
T Consensus        94 s~iLIgGdPGIGKSTLLLQva~--~lA~~~-~vLYVsG----EES~~Qi-klRA~RL~~~~~~l~l~aEt~~e~I~~~l~  165 (456)
T COG1066          94 SVILIGGDPGIGKSTLLLQVAA--RLAKRG-KVLYVSG----EESLQQI-KLRADRLGLPTNNLYLLAETNLEDIIAELE  165 (456)
T ss_pred             cEEEEccCCCCCHHHHHHHHHH--HHHhcC-cEEEEeC----CcCHHHH-HHHHHHhCCCccceEEehhcCHHHHHHHHH
Confidence            8999999999999999999999  455444 6777753    3333222 22334444320000  02334444444443


Q ss_pred             HHcCCCcEEEEEeCcC
Q 001843          352 QALDDSTFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~~kr~LlVlDdv~  367 (1007)
                      +   .++-|+|+|-+.
T Consensus       166 ~---~~p~lvVIDSIQ  178 (456)
T COG1066         166 Q---EKPDLVVIDSIQ  178 (456)
T ss_pred             h---cCCCEEEEeccc
Confidence            3   678899999986

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=92.26  E-value=0.35  Score=55.39  Aligned_cols=84  Identities=15%  Similarity=0.192  Sum_probs=49.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCC-CHHHHHHHHHHHHhhhhhhh-----ccc-------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMV-EDRDVLADILKQIDESLLKV-----EAT-------  340 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~-~~~~~l~~il~~l~~~~~~~-----~~~-------  340 (1007)
                      ..++|+|..|+|||||++.+++.  .  ..+.++.+-++  +.. ...++..+++..-...  ..     ..+       
T Consensus       163 qrigI~G~sG~GKSTLL~~I~~~--~--~~dv~Vi~lIG--ER~rEv~efi~~~l~~~~l~--rtvvv~atsd~p~~~R~  234 (444)
T PRK08972        163 QRMGLFAGSGVGKSVLLGMMTRG--T--TADVIVVGLVG--ERGREVKEFIEEILGEEGRA--RSVVVAAPADTSPLMRL  234 (444)
T ss_pred             CEEEEECCCCCChhHHHHHhccC--C--CCCEEEEEEEc--CChHHHHHHHHHhhccCCcc--cEEEEEECCCCCHHHHH
Confidence            78999999999999999999872  2  22455556565  433 3344555544331111  00     011       


Q ss_pred             ---cCHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          341 ---LSAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       341 ---~~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                         ...-...+.++.  +++.+|+++||+-
T Consensus       235 ~a~~~A~tiAEyfrd--~G~~VLl~~DslT  262 (444)
T PRK08972        235 KGCETATTIAEYFRD--QGLNVLLLMDSLT  262 (444)
T ss_pred             HHHHHHHHHHHHHHH--cCCCEEEEEcChH
Confidence               111223344443  5899999999985

>PRK03846 adenylylsulfate kinase; Provisional

Probab=92.25  E-value=0.2  Score=51.73  Aligned_cols=23  Identities=35%  Similarity=0.465  Sum_probs=21.8

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHh
Q 001843          273 TQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ..+|+|+|++|.||||||+.+..
T Consensus        24 ~~~i~i~G~~GsGKSTla~~l~~   46 (198)
T PRK03846         24 GVVLWFTGLSGSGKSTVAGALEE   46 (198)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            38999999999999999999998

>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D

Probab=92.23  E-value=0.098  Score=30.40  Aligned_cols=16  Identities=44%  Similarity=0.717  Sum_probs=6.4

Q ss_pred             CCCEEeecCCcccccc
Q 001843          718 CLATLDVSHTKVQRLP  733 (1007)
Q Consensus       718 ~L~~L~L~~~~l~~lP  733 (1007)
                      +|++|+|++|+++++|
T Consensus         2 ~L~~L~l~~n~L~~lP   17 (17)
T PF13504_consen    2 NLRTLDLSNNRLTSLP   17 (17)
T ss_dssp             T-SEEEETSS--SSE-
T ss_pred             ccCEEECCCCCCCCCc
Confidence            4555555555555444

...

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=92.17  E-value=0.24  Score=50.96  Aligned_cols=41  Identities=29%  Similarity=0.351  Sum_probs=27.5

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCC
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVE  318 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~  318 (1007)
                      .|+|.|-||+||||+|...+.. ...++=..++-|+..  .+++
T Consensus         2 kIaI~GKGG~GKTtiaalll~~-l~~~~~~~VLvVDaD--pd~n   42 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKR-LLSKGGYNVLVVDAD--PDSN   42 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHH-HHhcCCceEEEEeCC--CCCC
Confidence            5899999999999999985552 333331234556655  5554

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=92.14  E-value=0.44  Score=59.54  Aligned_cols=183  Identities=14%  Similarity=0.081  Sum_probs=89.1

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcc--c------------CCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhc
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVK--R------------HFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVE  338 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~--~------------~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~  338 (1007)
                      .+++.|.|+.+.||||+.+.+.-..-..  +            .|+ .++..++  ...++..-+..+...         
T Consensus       327 ~~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~-~i~~~ig--~~~si~~~lStfS~~---------  394 (782)
T PRK00409        327 KTVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFK-EIFADIG--DEQSIEQSLSTFSGH---------  394 (782)
T ss_pred             ceEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccc-eEEEecC--CccchhhchhHHHHH---------
Confidence            3899999999999999999986531110  1            111 2333333  222222211111111         


Q ss_pred             cccCHHHHHHHHHHHcCCCcEEEEEeCcCcc-Cchhhhhhc-cccCC-CCCCcEEEEEcCCCcccccccCCcceeeecCC
Q 001843          339 ATLSAEELMWRITQALDDSTFLIVMENAEHQ-KSQVWDSFL-GKLCS-FTQCGKIIITTSSTEDFVEPLGAAFSTLHVPG  415 (1007)
Q Consensus       339 ~~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~-~l~~~-~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~  415 (1007)
                          .......+ ..+ ..+-|+++|..-.. ++..-..+. .+... ...|+.+|+||-... ++........+.....
T Consensus       395 ----m~~~~~Il-~~~-~~~sLvLlDE~~~GtDp~eg~ala~aile~l~~~~~~vIitTH~~e-l~~~~~~~~~v~~~~~  467 (782)
T PRK00409        395 ----MTNIVRIL-EKA-DKNSLVLFDELGAGTDPDEGAALAISILEYLRKRGAKIIATTHYKE-LKALMYNREGVENASV  467 (782)
T ss_pred             ----HHHHHHHH-HhC-CcCcEEEecCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECChHH-HHHHHhcCCCeEEEEE
Confidence                11112222 222 47789999998621 222222332 21111 034789999999877 6655433211111000


Q ss_pred             CCHHHHHHHHHhhhccccccccCCChHHHHHHHHHHHHcCCCchHHHHHHHHhcCCCCChHHHHHHHHHcc
Q 001843          416 LGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERAN  486 (1007)
Q Consensus       416 L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~~~~~~I~~~c~GlPLai~~~g~~L~~~~~~~~~w~~~l~~l~  486 (1007)
                      .-+.+......+...+..         -..-|-+|++++ |+|-.|.--|..+....  ...+..++..+.
T Consensus       468 ~~d~~~l~~~Ykl~~G~~---------g~S~a~~iA~~~-Glp~~ii~~A~~~~~~~--~~~~~~li~~l~  526 (782)
T PRK00409        468 EFDEETLRPTYRLLIGIP---------GKSNAFEIAKRL-GLPENIIEEAKKLIGED--KEKLNELIASLE  526 (782)
T ss_pred             EEecCcCcEEEEEeeCCC---------CCcHHHHHHHHh-CcCHHHHHHHHHHHhhh--hhHHHHHHHHHH
Confidence            001111111111111110         134577788877 78888887777776554  445555555543

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=92.13  E-value=0.12  Score=52.47  Aligned_cols=23  Identities=39%  Similarity=0.590  Sum_probs=21.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+|+|-||=|+||||||+.+++.
T Consensus         5 ~~IvI~G~IG~GKSTLa~~La~~   27 (216)
T COG1428           5 MVIVIEGMIGAGKSTLAQALAEH   27 (216)
T ss_pred             cEEEEecccccCHHHHHHHHHHH
Confidence            89999999999999999999993

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=92.12  E-value=0.1  Score=53.13  Aligned_cols=21  Identities=33%  Similarity=0.536  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHHh
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ||.|+|++|+||||+|+.++.
T Consensus         1 ~i~i~G~pGsGKst~a~~la~   21 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVE   21 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999999988

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=92.11  E-value=1.5  Score=52.19  Aligned_cols=23  Identities=22%  Similarity=0.537  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-|.|.|..|+||+++|+.+++.
T Consensus       236 ~pVLI~GE~GTGKe~lA~~IH~~  258 (526)
T TIGR02329       236 ATVLILGESGTGKELVAQAIHQL  258 (526)
T ss_pred             CcEEEECCCCcCHHHHHHHHHHh
Confidence            57889999999999999999983

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK12678 transcription termination factor Rho; Provisional

Probab=92.09  E-value=0.7  Score=54.10  Aligned_cols=89  Identities=15%  Similarity=0.150  Sum_probs=46.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhccc-CCCceEEE-EecCCCCCCHHHHHHHHHHHHhhhhhhhcc----ccCHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR-HFTKRAWV-HIPIMSMVEDRDVLADILKQIDESLLKVEA----TLSAEELM  347 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~-~F~~~~wv-~~s~~~~~~~~~~l~~il~~l~~~~~~~~~----~~~~~~l~  347 (1007)
                      +-..|+|.+|+|||||++.+++  .+.. +-++.++| -|. .....+.++.+.+-.++-..  ....    ......+.
T Consensus       417 QR~LIvgpp~aGKTtLL~~IAn--~i~~n~~~~~~ivvLIg-ERpeEVtdm~rsVkgeVVas--T~D~p~~~~~~~a~~a  491 (672)
T PRK12678        417 QRGLIVSPPKAGKTTILQNIAN--AITTNNPECHLMVVLVD-ERPEEVTDMQRSVKGEVIAS--TFDRPPSDHTTVAELA  491 (672)
T ss_pred             CEeEEeCCCCCCHHHHHHHHHH--HHhhcCCCeEEEEEEEe-CchhhHHHHHHhccceEEEE--CCCCCHHHHHHHHHHH
Confidence            6779999999999999999999  4433 22444333 344 12223333332221111110  0000    01111122


Q ss_pred             HHHHHHc--CCCcEEEEEeCcC
Q 001843          348 WRITQAL--DDSTFLIVMENAE  367 (1007)
Q Consensus       348 ~~l~~~L--~~kr~LlVlDdv~  367 (1007)
                      -.+-+++  .++.+||++|++-
T Consensus       492 i~~Ae~fre~G~dVlillDSlT  513 (672)
T PRK12678        492 IERAKRLVELGKDVVVLLDSIT  513 (672)
T ss_pred             HHHHHHHHHcCCCEEEEEeCch
Confidence            2233344  6899999999985

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=92.09  E-value=0.1  Score=53.91  Aligned_cols=21  Identities=43%  Similarity=0.714  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHHh
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +|+|.|..|+||||||+.+..
T Consensus         1 iigi~G~~GsGKSTl~~~l~~   21 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIE   21 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999988

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=92.09  E-value=0.28  Score=53.25  Aligned_cols=22  Identities=32%  Similarity=0.616  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +-+.++|..|+|||++++....
T Consensus        34 ~pvLl~G~~GtGKT~li~~~l~   55 (272)
T PF12775_consen   34 RPVLLVGPSGTGKTSLIQNFLS   55 (272)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             CcEEEECCCCCchhHHHHhhhc
Confidence            6779999999999999999886

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=92.08  E-value=0.46  Score=51.43  Aligned_cols=29  Identities=34%  Similarity=0.418  Sum_probs=24.6

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhhcccCC
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  303 (1007)
                      ..+|.|+|.+|.|||||...+.+  ......
T Consensus       104 ~~~v~l~G~pGsGKTTLl~~l~~--~l~~~~  132 (290)
T PRK10463        104 QLVLNLVSSPGSGKTTLLTETLM--RLKDSV  132 (290)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH--HhccCC
Confidence            38999999999999999999998  444444

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=91.98  E-value=0.76  Score=45.85  Aligned_cols=57  Identities=11%  Similarity=0.140  Sum_probs=36.8

Q ss_pred             HHHHHHHcCCCcEEEEEeC----cCccCchhhhhhccccCCCCCCcEEEEEcCCCcccccccCC
Q 001843          347 MWRITQALDDSTFLIVMEN----AEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGA  406 (1007)
Q Consensus       347 ~~~l~~~L~~kr~LlVlDd----v~~~~~~~~~~l~~l~~~~~~gs~IliTTR~~~~va~~~~~  406 (1007)
                      .-.|.+.+-+++-+|+=|.    ++  ..-.|+-+.-|-.-...|+.||++|-+.. +.+.+..
T Consensus       145 RvaIARAiV~~P~vLlADEPTGNLD--p~~s~~im~lfeeinr~GtTVl~ATHd~~-lv~~~~~  205 (223)
T COG2884         145 RVAIARAIVNQPAVLLADEPTGNLD--PDLSWEIMRLFEEINRLGTTVLMATHDLE-LVNRMRH  205 (223)
T ss_pred             HHHHHHHHccCCCeEeecCCCCCCC--hHHHHHHHHHHHHHhhcCcEEEEEeccHH-HHHhccC
Confidence            3345666678888899884    44  44456554433221156999999999988 6655543

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=91.98  E-value=0.85  Score=46.17  Aligned_cols=122  Identities=17%  Similarity=0.111  Sum_probs=62.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCC-CCCHHHHHHHHHHHH-----hhh--h---hhhccccC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMS-MVEDRDVLADILKQI-----DES--L---LKVEATLS  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~-~~~~~~~l~~il~~l-----~~~--~---~~~~~~~~  342 (1007)
                      ..|-|+|-.|-||||.|..++-.  .-.+=-.+..+-+-... ...-...+..+- .+     +..  .   ........
T Consensus        23 g~v~v~~g~GkGKtt~a~g~a~r--a~g~G~~V~ivQFlKg~~~~GE~~~l~~l~-~v~~~~~g~~~~~~~~~~~e~~~~   99 (191)
T PRK05986         23 GLLIVHTGNGKGKSTAAFGMALR--AVGHGKKVGVVQFIKGAWSTGERNLLEFGG-GVEFHVMGTGFTWETQDRERDIAA   99 (191)
T ss_pred             CeEEEECCCCCChHHHHHHHHHH--HHHCCCeEEEEEEecCCCccCHHHHHhcCC-CcEEEECCCCCcccCCCcHHHHHH
Confidence            68899999999999999988773  32222223333322111 223333333210 00     000  0   00001122


Q ss_pred             HHHHHHHHHHHcCCCcE-EEEEeCcCcc---CchhhhhhccccCCCCCCcEEEEEcCCCc
Q 001843          343 AEELMWRITQALDDSTF-LIVMENAEHQ---KSQVWDSFLGKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       343 ~~~l~~~l~~~L~~kr~-LlVlDdv~~~---~~~~~~~l~~l~~~~~~gs~IliTTR~~~  398 (1007)
                      .....+..++.+...+| |||||.+-..   ..-..+++..+...-..+..||+|-|+..
T Consensus       100 ~~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p  159 (191)
T PRK05986        100 AREGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAP  159 (191)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            33344555666666666 9999998411   12223344422222145578999999875

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=91.94  E-value=0.11  Score=52.78  Aligned_cols=22  Identities=36%  Similarity=0.614  Sum_probs=20.3

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +|+|.|.+|+||||+|+.++..
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999983

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=91.93  E-value=0.69  Score=46.18  Aligned_cols=114  Identities=11%  Similarity=0.066  Sum_probs=58.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEE-------EecCCCCCCH--HHHHHHHHHHHhhhhhhhccccCHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWV-------HIPIMSMVED--RDVLADILKQIDESLLKVEATLSAE  344 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv-------~~s~~~~~~~--~~~l~~il~~l~~~~~~~~~~~~~~  344 (1007)
                      .+++|+|..|.|||||++.++.-..   .....+++       .+.  +....  ..+...+...   .   ...-...+
T Consensus        28 e~~~i~G~nGsGKSTLl~~l~G~~~---~~~G~i~~~~~~~i~~~~--q~~~~~~~tv~~nl~~~---~---~~~LS~G~   96 (166)
T cd03223          28 DRLLITGPSGTGKSSLFRALAGLWP---WGSGRIGMPEGEDLLFLP--QRPYLPLGTLREQLIYP---W---DDVLSGGE   96 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCC---CCCceEEECCCceEEEEC--CCCccccccHHHHhhcc---C---CCCCCHHH
Confidence            7999999999999999999988321   11222222       122  22211  1222222110   0   01111122


Q ss_pred             HHHHHHHHHcCCCcEEEEEeCcCc-cCchhhhhhc-cccCCCCCCcEEEEEcCCCccccc
Q 001843          345 ELMWRITQALDDSTFLIVMENAEH-QKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVE  402 (1007)
Q Consensus       345 ~l~~~l~~~L~~kr~LlVlDdv~~-~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~  402 (1007)
                      ...-.+.+.+-.++=++++|+--. -|......+. .+...   +..||++|.+.. ...
T Consensus        97 ~~rv~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~---~~tiiivsh~~~-~~~  152 (166)
T cd03223          97 QQRLAFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL---GITVISVGHRPS-LWK  152 (166)
T ss_pred             HHHHHHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh---CCEEEEEeCChh-HHh
Confidence            222334455556777889998642 1333334444 22222   356788887766 554

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=91.91  E-value=0.17  Score=50.47  Aligned_cols=23  Identities=30%  Similarity=0.476  Sum_probs=21.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+++|+|..|+|||||++.+...
T Consensus         7 ~ii~ivG~sgsGKTTLi~~li~~   29 (173)
T PRK10751          7 PLLAIAAWSGTGKTTLLKKLIPA   29 (173)
T ss_pred             eEEEEECCCCChHHHHHHHHHHH
Confidence            79999999999999999999983

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=91.91  E-value=0.22  Score=48.09  Aligned_cols=37  Identities=35%  Similarity=0.517  Sum_probs=27.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc-cCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK-RHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~~s  312 (1007)
                      .+|.|+|..|+|||||++.+.+.  .. +.+...+..+..
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~~--l~~~g~~v~~ik~~~   38 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLINE--LKRRGYRVAVIKHTD   38 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHH--HHHTT--EEEEEE-S
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HhHcCCceEEEEEcc
Confidence            47999999999999999999994  44 556666666655

>PRK13949 shikimate kinase; Provisional

Probab=91.90  E-value=0.13  Score=51.59  Aligned_cols=22  Identities=41%  Similarity=0.594  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +-|.|+|++|.||||+++.++.
T Consensus         2 ~~I~liG~~GsGKstl~~~La~   23 (169)
T PRK13949          2 ARIFLVGYMGAGKTTLGKALAR   23 (169)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4589999999999999999998

>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH)

Probab=91.90  E-value=0.68  Score=43.10  Aligned_cols=34  Identities=32%  Similarity=0.462  Sum_probs=24.9

Q ss_pred             EEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEe
Q 001843          276 IALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI  311 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~  311 (1007)
                      |.+.|.||+||||++..++.  ...+.-..++-++.
T Consensus         2 i~~~GkgG~GKTt~a~~la~--~l~~~g~~V~~id~   35 (116)
T cd02034           2 IAITGKGGVGKTTIAALLAR--YLAEKGKPVLAIDA   35 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHHHCCCcEEEEEC
Confidence            68999999999999999988  44443333444443

CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=91.90  E-value=0.16  Score=53.82  Aligned_cols=25  Identities=28%  Similarity=0.570  Sum_probs=22.7

Q ss_pred             CCcEEEEEEcCCCChHHHHHHHHHh
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ..+.+|+|.|..|.|||||++.+..
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~   55 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEA   55 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3448999999999999999999998

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=91.89  E-value=2.2  Score=46.36  Aligned_cols=60  Identities=17%  Similarity=0.246  Sum_probs=41.5

Q ss_pred             CCcEEEEEeCcCccCchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCCcceeeecCCC
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGL  416 (1007)
Q Consensus       356 ~kr~LlVlDdv~~~~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~~~~~~~l~~L  416 (1007)
                      ++.=++|+|+++.-+.+.++.+. .+-.. ..++.+|++|.+...+.....+.+..+.+.++
T Consensus        94 ~~~kv~ii~~ad~mt~~AaNaLLK~LEEP-p~~~~fiL~~~~~~~ll~TI~SRcq~~~~~~~  154 (290)
T PRK05917         94 SPYKIYIIHEADRMTLDAISAFLKVLEDP-PQHGVIILTSAKPQRLPPTIRSRSLSIHIPME  154 (290)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhhcC-CCCeEEEEEeCChhhCcHHHHhcceEEEccch
Confidence            45558899999877888888888 43333 55667777766655476665655577777765

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=91.87  E-value=0.11  Score=50.38  Aligned_cols=21  Identities=48%  Similarity=0.787  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHHh
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +|.|+|.+|+||||+|+.+..
T Consensus         1 ~I~i~G~~GsGKst~a~~la~   21 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAK   21 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999998

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=91.78  E-value=0.62  Score=54.01  Aligned_cols=89  Identities=18%  Similarity=0.193  Sum_probs=52.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCC-CCHHHHHHHHHHHHhhhhhhh-----ccccC-----
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSM-VEDRDVLADILKQIDESLLKV-----EATLS-----  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~-~~~~~~l~~il~~l~~~~~~~-----~~~~~-----  342 (1007)
                      +-++|+|..|+|||||+..+++... +.+-+.++++-++  +. -...+++.++...-...  +.     ..+..     
T Consensus       144 QR~gIfa~~G~GKt~Ll~~~~~~~~-~~~~dv~V~~liG--ER~rEv~ef~~~~~~~~~l~--rsvvv~atsd~~~~~R~  218 (461)
T PRK12597        144 GKTGLFGGAGVGKTVLMMELIFNIS-KQHSGSSVFAGVG--ERSREGHELYHEMKESGVLD--KTVMVYGQMNEPPGARM  218 (461)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHH-hhCCCEEEEEcCC--cchHHHHHHHHHHHhcCCcc--eeEEEecCCCCCHHHHH
Confidence            6789999999999999999888422 2345677777665  33 34445555554321111  00     01111     


Q ss_pred             -HHHHHHHHHHHc---CCCcEEEEEeCcC
Q 001843          343 -AEELMWRITQAL---DDSTFLIVMENAE  367 (1007)
Q Consensus       343 -~~~l~~~l~~~L---~~kr~LlVlDdv~  367 (1007)
                       .....-.+.+++   +++.+|+++||+-
T Consensus       219 ~a~~~a~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        219 RVVLTGLTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEeccch
Confidence             111222334444   3799999999994

>PRK06217 hypothetical protein; Validated

Probab=91.75  E-value=0.13  Score=52.41  Aligned_cols=23  Identities=39%  Similarity=0.559  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ..|.|.|.+|.||||+|+++...
T Consensus         2 ~~I~i~G~~GsGKSTla~~L~~~   24 (183)
T PRK06217          2 MRIHITGASGSGTTTLGAALAER   24 (183)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            45899999999999999999984

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=91.73  E-value=0.16  Score=49.32  Aligned_cols=23  Identities=35%  Similarity=0.637  Sum_probs=21.3

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHh
Q 001843          273 TQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .++++|+|.+|+||||+.+.+-.
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~   26 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALK   26 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHH
Confidence            48999999999999999998877

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=91.73  E-value=0.38  Score=53.59  Aligned_cols=36  Identities=28%  Similarity=0.332  Sum_probs=24.7

Q ss_pred             EEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          276 IALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +.+.|++|.||||+++.+.+.-.....+ .+.+++..
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l~~~~g~-~v~~~~~D   37 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATLRRERGW-AVAVITYD   37 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhccCC-eEEEEccc
Confidence            5789999999999999999832212222 34555543

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=91.71  E-value=1.1  Score=53.20  Aligned_cols=23  Identities=22%  Similarity=0.452  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .-|.|.|..|+||+++|+.+++.
T Consensus       243 ~pVLI~GE~GTGKe~~A~~IH~~  265 (538)
T PRK15424        243 AAVLIQGETGTGKELAAQAIHRE  265 (538)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHh
Confidence            57889999999999999999984

>TIGR00416 sms DNA repair protein RadA

Probab=91.70  E-value=0.94  Score=52.97  Aligned_cols=37  Identities=27%  Similarity=0.300  Sum_probs=28.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      .++.|.|.+|+|||||+.+++..  ....-..++|++..
T Consensus        95 svilI~G~pGsGKTTL~lq~a~~--~a~~g~kvlYvs~E  131 (454)
T TIGR00416        95 SLILIGGDPGIGKSTLLLQVACQ--LAKNQMKVLYVSGE  131 (454)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH--HHhcCCcEEEEECc
Confidence            89999999999999999999774  32222357788654

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PTZ00185 ATPase alpha subunit; Provisional

Probab=91.70  E-value=0.71  Score=53.43  Aligned_cols=89  Identities=17%  Similarity=0.210  Sum_probs=52.9

Q ss_pred             EEEEEEcCCCChHHHHH-HHHHhhhhc-----ccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh-------c--
Q 001843          274 QVIALIGKAGSGKTTLA-RIVYNRVYV-----KRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV-------E--  338 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa-~~v~~~~~~-----~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~-------~--  338 (1007)
                      +-++|.|-.|+|||+|| -.+.|...+     .++-+.++++.++  +..+...-+.+.+++-+.- ...       .  
T Consensus       190 QR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIG--eR~rEV~ei~~~L~e~GaL-~~TvVV~AtAdep  266 (574)
T PTZ00185        190 QRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIG--QRCSNVARIHRLLRSYGAL-RYTTVMAATAAEP  266 (574)
T ss_pred             CEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEec--cchHHHHHHHHHHHhcCCc-cceEEEEECCCCC
Confidence            67899999999999997 556774322     1234567888887  6654444344444443311 000       0  


Q ss_pred             ------cccCHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          339 ------ATLSAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       339 ------~~~~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                            .....-...+.++.  +++.+|||+||+.
T Consensus       267 ~~~r~~Apy~a~tiAEYFrd--~GkdVLiv~DDLT  299 (574)
T PTZ00185        267 AGLQYLAPYSGVTMGEYFMN--RGRHCLCVYDDLS  299 (574)
T ss_pred             HHHHHHHHHHHHHHHHHHHH--cCCCEEEEEcCch
Confidence                  11122333444443  5899999999995

>TIGR01287 nifH nitrogenase iron protein

Probab=91.68  E-value=0.17  Score=55.28  Aligned_cols=37  Identities=27%  Similarity=0.269  Sum_probs=25.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +.|+|+|-||+||||+|..++.-  ....=..++-|+..
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~~--La~~G~~VlliD~D   37 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAAA--LAEMGKKVMIVGCD   37 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHHH--HHHCCCeEEEEeCC
Confidence            47899999999999999998873  32221234445544

This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=91.66  E-value=0.19  Score=51.17  Aligned_cols=36  Identities=31%  Similarity=0.433  Sum_probs=29.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEe
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI  311 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~  311 (1007)
                      ++|.|+|+.|+|||||++++..  ....+|..+++.+-
T Consensus         3 r~ivl~Gpsg~GK~~l~~~L~~--~~~~~~~~~v~~TT   38 (183)
T PF00625_consen    3 RPIVLVGPSGSGKSTLAKRLIQ--EFPDKFGRVVSHTT   38 (183)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHH--HSTTTEEEEEEEES
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--hcccccccceeecc
Confidence            7999999999999999999999  56667765555543

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=91.59  E-value=1.5  Score=52.17  Aligned_cols=26  Identities=35%  Similarity=0.502  Sum_probs=22.9

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHhhhh
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVY  298 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~~~~  298 (1007)
                      ++-+..+|++|.|||.||++++....
T Consensus       183 PkGvlLvGpPGTGKTLLAkAvAgEA~  208 (596)
T COG0465         183 PKGVLLVGPPGTGKTLLAKAVAGEAG  208 (596)
T ss_pred             ccceeEecCCCCCcHHHHHHHhcccC
Confidence            47889999999999999999999533

>KOG0927 consensus Predicted transporter (ABC superfamily) [General function prediction only]

Probab=91.59  E-value=0.4  Score=55.04  Aligned_cols=57  Identities=11%  Similarity=0.104  Sum_probs=34.5

Q ss_pred             HHHHHHHcCCCcEEEEEeCcCcc-Cchhhhhhc-cccCCCCCCcEEEEEcCCCcccccccCC
Q 001843          347 MWRITQALDDSTFLIVMENAEHQ-KSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGA  406 (1007)
Q Consensus       347 ~~~l~~~L~~kr~LlVlDdv~~~-~~~~~~~l~-~l~~~~~~gs~IliTTR~~~~va~~~~~  406 (1007)
                      ...|.+.|-.++.|+.||+-.+. |.+...-+. .+-.. ..+ .++|++|.++ ..+.+++
T Consensus       229 R~aLAr~Lf~kP~LLLLDEPtnhLDleA~~wLee~L~k~-d~~-~lVi~sh~QD-fln~vCT  287 (614)
T KOG0927|consen  229 RAALARALFQKPDLLLLDEPTNHLDLEAIVWLEEYLAKY-DRI-ILVIVSHSQD-FLNGVCT  287 (614)
T ss_pred             HHHHHHHHhcCCCEEEecCCccCCCHHHHHHHHHHHHhc-cCc-eEEEEecchh-hhhhHhh
Confidence            34455556678999999987521 222222222 22222 223 6889999998 7777666

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=91.58  E-value=0.13  Score=50.42  Aligned_cols=22  Identities=36%  Similarity=0.750  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ++.|.|++|+||||+|+.+...
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            4789999999999999999883

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=91.55  E-value=0.62  Score=51.56  Aligned_cols=87  Identities=16%  Similarity=0.179  Sum_probs=48.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhh-----hhhc--------cc
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESL-----LKVE--------AT  340 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~-----~~~~--------~~  340 (1007)
                      ..++|+|..|.|||||.+.+++.  ..  -+..+...+. .+..+..++....+..-...-     ...+        ..
T Consensus        70 qri~I~G~sG~GKTtLl~~Ia~~--~~--~~~~vi~~iG-er~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~~~  144 (326)
T cd01136          70 QRLGIFAGSGVGKSTLLGMIARG--TT--ADVNVIALIG-ERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVKAA  144 (326)
T ss_pred             cEEEEECCCCCChHHHHHHHhCC--CC--CCEEEEEEEe-cCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHHHH
Confidence            78899999999999999999883  22  1233333333 133445555554444322110     0000        01


Q ss_pred             cCHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          341 LSAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       341 ~~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                      ...-...+.+++  +++.+|+++||+-
T Consensus       145 ~~a~~~AEyfr~--~g~~Vll~~Dslt  169 (326)
T cd01136         145 YTATAIAEYFRD--QGKDVLLLMDSLT  169 (326)
T ss_pred             HHHHHHHHHHHH--cCCCeEEEeccch
Confidence            112223334443  5899999999985

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>PRK05439 pantothenate kinase; Provisional

Probab=91.54  E-value=0.6  Score=51.31  Aligned_cols=81  Identities=16%  Similarity=0.252  Sum_probs=45.6

Q ss_pred             CCcEEEEEEcCCCChHHHHHHHHHhhhhcccC--CCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHH
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRH--FTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~--F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      +.+-+|+|.|.+|+||||+|+.+..  .....  -..+.-++..  .-+...+.+..  ..+... ...+...+.+.+..
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~--~l~~~~~~~~v~vi~~D--dFy~~~~~l~~--~~l~~~-kg~Pes~D~~~l~~  156 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQA--LLSRWPEHPKVELVTTD--GFLYPNAVLEE--RGLMKR-KGFPESYDMRALLR  156 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH--HHHhhCCCCceEEEecc--ccccCHHHHhh--hhcccc-CCCcccccHHHHHH
Confidence            3448999999999999999999887  44332  1234455544  22222222211  011000 01234556777777


Q ss_pred             HHHHHcCCCc
Q 001843          349 RITQALDDST  358 (1007)
Q Consensus       349 ~l~~~L~~kr  358 (1007)
                      .+.....++.
T Consensus       157 ~L~~Lk~G~~  166 (311)
T PRK05439        157 FLSDVKSGKP  166 (311)
T ss_pred             HHHHHHcCCC
Confidence            7776666665

>TIGR03263 guanyl_kin guanylate kinase

Probab=91.53  E-value=0.14  Score=51.93  Aligned_cols=22  Identities=32%  Similarity=0.614  Sum_probs=21.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ++|+|+|+.|+||||||+.+++
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~   23 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLE   23 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHc
Confidence            6899999999999999999998

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=91.51  E-value=0.86  Score=53.19  Aligned_cols=39  Identities=31%  Similarity=0.382  Sum_probs=28.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +|++++|..|+||||++.+++.....+..-..+..++..
T Consensus       257 ~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~~D  295 (484)
T PRK06995        257 GVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTD  295 (484)
T ss_pred             cEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEeCC
Confidence            799999999999999999999843222222245556543

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=91.50  E-value=0.36  Score=49.08  Aligned_cols=36  Identities=25%  Similarity=0.210  Sum_probs=26.8

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      ++.|.|.+|+|||+||.+++..  ..+.=..++|++..
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~--~~~~g~~v~~~s~e   36 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYA--GLARGEPGLYVTLE   36 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH--HHHCCCcEEEEECC
Confidence            3679999999999999998774  22333567788754

A related protein is found in archaea.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=91.50  E-value=0.13  Score=47.11  Aligned_cols=21  Identities=38%  Similarity=0.539  Sum_probs=18.8

Q ss_pred             EEEEcCCCChHHHHHHHHHhh
Q 001843          276 IALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      |-|+|.+|+|||++|+.++.+
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~   21 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKD   21 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999884

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=91.48  E-value=0.16  Score=51.23  Aligned_cols=23  Identities=30%  Similarity=0.551  Sum_probs=21.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ++|.+.|++|+||||+|+.+...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            78999999999999999999883

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=91.46  E-value=0.21  Score=51.80  Aligned_cols=22  Identities=41%  Similarity=0.853  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++|+|..|.|||||++.++-
T Consensus        34 e~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          34 ETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CEEEEEcCCCCCHHHHHHHHhc
Confidence            7999999999999999999986

>PTZ00088 adenylate kinase 1; Provisional

Probab=91.44  E-value=0.22  Score=52.45  Aligned_cols=21  Identities=43%  Similarity=0.638  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHHh
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      -|.|+|++|+||||+|+.++.
T Consensus         8 rIvl~G~PGsGK~T~a~~La~   28 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSK   28 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            488999999999999999988

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=91.42  E-value=0.24  Score=47.14  Aligned_cols=23  Identities=39%  Similarity=0.554  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+|.+.|.-|.||||+++.++..
T Consensus        23 ~~i~l~G~lGaGKTtl~~~l~~~   45 (133)
T TIGR00150        23 TVVLLKGDLGAGKTTLVQGLLQG   45 (133)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHH
Confidence            69999999999999999999984

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>KOG1947 consensus Leucine rich repeat proteins, some proteins contain F-box [General function prediction only]

Probab=91.40  E-value=0.02  Score=68.10  Aligned_cols=164  Identities=24%  Similarity=0.175  Sum_probs=98.2

Q ss_pred             HhhcCCCCCeEEEeecCCCCC--CcccccCCCCCcEEEeccc-C--CCCCc--CccCCCCCCceEEEEEeee-cCCCCcC
Q 001843          813 AVLQLSELHSLKLICETPSYL--PLLEMAEHYKLQKLYLSGH-L--PPNSV--IGDRSFPPNVVTLTLSQLR-LEYDPMP  884 (1007)
Q Consensus       813 ~l~~l~~L~~L~L~~~~~~~~--~~~~l~~~~~L~~L~L~g~-~--~~lp~--~~i~~~l~~L~~L~L~~~~-l~~~~~~  884 (1007)
                      .....++|+.|.+........  .......+++|+.|+++++ .  ...+.  ..+...+++|+.|++++|. ++...+.
T Consensus       183 l~~~~~~L~~l~l~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~L~~l~l~~~~~isd~~l~  262 (482)
T KOG1947|consen  183 LLSSCPLLKRLSLSGCSKITDDSLDALALKCPNLEELDLSGCCLLITLSPLLLLLLLSICRKLKSLDLSGCGLVTDIGLS  262 (482)
T ss_pred             HHhhCchhhHhhhcccccCChhhHHHHHhhCchhheecccCcccccccchhHhhhhhhhcCCcCccchhhhhccCchhHH
Confidence            334478899998887433221  2244556889999999873 2  11111  0122237899999999997 6555555


Q ss_pred             cccc-CCCCcEEEeecCC-cCCCceeecCCCCCCCcEEEeccCCCCcce--EEcCCCCccccEeEeeccC---CCC--CC
Q 001843          885 ILGR-LRQLKILRLFGGS-YTGEEMSCSSGEFPNLLVLKLWKLNRLRQW--RIKEGAMPCLRQLEIRSCG---YLV--PP  955 (1007)
Q Consensus       885 ~l~~-Lp~L~~L~L~~~~-~~~~~l~~~~~~fp~L~~L~L~~~~~L~~l--~~~~~~~p~L~~L~l~~c~---~L~--lp  955 (1007)
                      .+.. +|+|+.|.+..+. ...+.+......+|.|++|+|++|..++.-  ......+|+|+.|.+..+.   .++  .-
T Consensus       263 ~l~~~c~~L~~L~l~~c~~lt~~gl~~i~~~~~~L~~L~l~~c~~~~d~~l~~~~~~c~~l~~l~~~~~~~c~~l~~~~l  342 (482)
T KOG1947|consen  263 ALASRCPNLETLSLSNCSNLTDEGLVSIAERCPSLRELDLSGCHGLTDSGLEALLKNCPNLRELKLLSLNGCPSLTDLSL  342 (482)
T ss_pred             HHHhhCCCcceEccCCCCccchhHHHHHHHhcCcccEEeeecCccchHHHHHHHHHhCcchhhhhhhhcCCCccHHHHHH
Confidence            5554 8999999976444 244455445567899999999998876432  1112346766666655443   344  11


Q ss_pred             cCcccccc-CccEEEeccCCcc
Q 001843          956 TGLKHVTS-SLREFLLTNMPST  976 (1007)
Q Consensus       956 ~~l~~L~~-~L~~L~l~~c~~~  976 (1007)
                      .++...+. .+..+.+.+|+..
T Consensus       343 ~~~~~~~~d~~~~~~~~~~~~l  364 (482)
T KOG1947|consen  343 SGLLTLTSDDLAELILRSCPKL  364 (482)
T ss_pred             HHhhccCchhHhHHHHhcCCCc
Confidence            12222211 5667777777643

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=91.38  E-value=1.1  Score=44.68  Aligned_cols=121  Identities=15%  Similarity=0.086  Sum_probs=61.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCC-CCCCHHHHHHHHHHHHhhhhhhh----------ccccC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIM-SMVEDRDVLADILKQIDESLLKV----------EATLS  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~-~~~~~~~~l~~il~~l~~~~~~~----------~~~~~  342 (1007)
                      ..|-|++-.|.||||.|..++-. .....+. ++.+-+-+. ....-...++.+  .+.......          .....
T Consensus         6 Gli~v~~g~GkGKtt~a~g~a~r-a~~~g~~-v~ivQFlKg~~~~GE~~~l~~~--~~~~~~~g~g~~~~~~~~~~~~~~   81 (173)
T TIGR00708         6 GIIIVHTGNGKGKTTAAFGMALR-ALGHGKK-VGVIQFIKGAWPNGERAAFEPH--GVEFQVMGTGFTWETQNREADTAI   81 (173)
T ss_pred             cEEEEECCCCCChHHHHHHHHHH-HHHCCCe-EEEEEEecCCcccChHHHHHhc--CcEEEECCCCCeecCCCcHHHHHH
Confidence            57778888999999999888773 2223333 222222100 223333344332  111000000          01111


Q ss_pred             HHHHHHHHHHHcCCCcE-EEEEeCcCcc---CchhhhhhccccCCCCCCcEEEEEcCCCc
Q 001843          343 AEELMWRITQALDDSTF-LIVMENAEHQ---KSQVWDSFLGKLCSFTQCGKIIITTSSTE  398 (1007)
Q Consensus       343 ~~~l~~~l~~~L~~kr~-LlVlDdv~~~---~~~~~~~l~~l~~~~~~gs~IliTTR~~~  398 (1007)
                      .....+..++.+...+| |||||.+-..   ..-..+++..+...-..+..||+|-|+..
T Consensus        82 ~~~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p  141 (173)
T TIGR00708        82 AKAAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCP  141 (173)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCC
Confidence            33344555666666666 9999998410   11122233322222144578999999875

Alternate name: corrinoid adenosyltransferase.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=91.32  E-value=0.15  Score=49.08  Aligned_cols=21  Identities=38%  Similarity=0.642  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHHh
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +|+|+|+.|+|||||++.+..
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~   21 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLE   21 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHh
Confidence            378999999999999999998

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=91.29  E-value=0.93  Score=46.58  Aligned_cols=22  Identities=32%  Similarity=0.629  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+++|.|..|.|||||.+.++.
T Consensus        36 e~~~l~G~nGsGKStLl~~i~G   57 (194)
T cd03213          36 ELTAIMGPSGAGKSTLLNALAG   57 (194)
T ss_pred             cEEEEECCCCCCHHHHHHHHhC
Confidence            7999999999999999999988

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=91.27  E-value=0.69  Score=54.14  Aligned_cols=122  Identities=22%  Similarity=0.324  Sum_probs=65.5

Q ss_pred             EEEEEEcCCCChHHH-HHHHHHhhhhcccCCCceEEEEecCCCCC--CHHHHHHHHHHHHhhhhhhh-c------c----
Q 001843          274 QVIALIGKAGSGKTT-LARIVYNRVYVKRHFTKRAWVHIPIMSMV--EDRDVLADILKQIDESLLKV-E------A----  339 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTt-La~~v~~~~~~~~~F~~~~wv~~s~~~~~--~~~~~l~~il~~l~~~~~~~-~------~----  339 (1007)
                      +||.|||..|.|||| ||+.+|.+     .|...=-|.+.  ++-  ....+.+.+.++++..+... +      +    
T Consensus       372 ~vvvivgETGSGKTTQl~QyL~ed-----GY~~~GmIGcT--QPRRvAAiSVAkrVa~EM~~~lG~~VGYsIRFEdvT~~  444 (1042)
T KOG0924|consen  372 QVVVIVGETGSGKTTQLAQYLYED-----GYADNGMIGCT--QPRRVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVTSE  444 (1042)
T ss_pred             cEEEEEecCCCCchhhhHHHHHhc-----ccccCCeeeec--CchHHHHHHHHHHHHHHhCCccccccceEEEeeecCCC
Confidence            899999999999985 77777774     23211123333  443  33456677777775542111 0      0    


Q ss_pred             ------ccCHHHHHHHHHHHcCCCcEEEEEeCcCccCchhhhhhc-ccc----CCCCCCcEEEEEcCCCc--ccccccC
Q 001843          340 ------TLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFL-GKL----CSFTQCGKIIITTSSTE--DFVEPLG  405 (1007)
Q Consensus       340 ------~~~~~~l~~~l~~~L~~kr~LlVlDdv~~~~~~~~~~l~-~l~----~~~~~gs~IliTTR~~~--~va~~~~  405 (1007)
                            -.+.--+.+.|.+..-+|=-.||+|.+..  ...=.++. ++.    .. ...-|+||||-..+  .++++++
T Consensus       445 ~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHE--RslNtDilfGllk~~lar-RrdlKliVtSATm~a~kf~nfFg  520 (1042)
T KOG0924|consen  445 DTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHE--RSLNTDILFGLLKKVLAR-RRDLKLIVTSATMDAQKFSNFFG  520 (1042)
T ss_pred             ceeEEEeccchHHHHHhhhhhhhheeEEEechhhh--cccchHHHHHHHHHHHHh-hccceEEEeeccccHHHHHHHhC
Confidence                  11222333334443334455899999862  21111222 221    11 34569999987654  3455555

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=91.27  E-value=0.76  Score=54.92  Aligned_cols=69  Identities=22%  Similarity=0.297  Sum_probs=46.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +=|-++|++|.|||-+||+|+..  ..     .-|++|.   .+       +++..-        ...+++.+.+...+.
T Consensus       706 SGILLYGPPGTGKTLlAKAVATE--cs-----L~FlSVK---GP-------ELLNMY--------VGqSE~NVR~VFerA  760 (953)
T KOG0736|consen  706 SGILLYGPPGTGKTLLAKAVATE--CS-----LNFLSVK---GP-------ELLNMY--------VGQSEENVREVFERA  760 (953)
T ss_pred             ceeEEECCCCCchHHHHHHHHhh--ce-----eeEEeec---CH-------HHHHHH--------hcchHHHHHHHHHHh
Confidence            57889999999999999999983  22     2356664   21       122222        122445555555566


Q ss_pred             cCCCcEEEEEeCcC
Q 001843          354 LDDSTFLIVMENAE  367 (1007)
Q Consensus       354 L~~kr~LlVlDdv~  367 (1007)
                      =..++|.|.||.++
T Consensus       761 R~A~PCVIFFDELD  774 (953)
T KOG0736|consen  761 RSAAPCVIFFDELD  774 (953)
T ss_pred             hccCCeEEEecccc
Confidence            66799999999987

>PRK13236 nitrogenase reductase; Reviewed

Probab=91.26  E-value=0.28  Score=54.11  Aligned_cols=23  Identities=35%  Similarity=0.497  Sum_probs=20.9

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHh
Q 001843          273 TQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .+||++.|-||+||||+|..++.
T Consensus         6 ~~~~~~~GKGGVGKTt~a~NLA~   28 (296)
T PRK13236          6 IRQIAFYGKGGIGKSTTSQNTLA   28 (296)
T ss_pred             ceEEEEECCCcCCHHHHHHHHHH
Confidence            39999999999999999888776

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=91.23  E-value=0.55  Score=53.98  Aligned_cols=84  Identities=14%  Similarity=0.131  Sum_probs=48.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCC-CHHHHHHHHHHHHhhhhhhh-----cccc------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMV-EDRDVLADILKQIDESLLKV-----EATL------  341 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~-~~~~~l~~il~~l~~~~~~~-----~~~~------  341 (1007)
                      +.++|+|..|+|||||++.+++.  ..  -+.++++-++  +.. ...++..+.+..-+..  ..     ..+.      
T Consensus       159 qri~I~G~sG~GKTtLL~~I~~~--~~--~d~~v~~~iG--ER~rEv~ef~~~~l~~~~l~--rsvvv~atsd~~~~~r~  230 (442)
T PRK08927        159 QRMGIFAGSGVGKSVLLSMLARN--AD--ADVSVIGLIG--ERGREVQEFLQDDLGPEGLA--RSVVVVATSDEPALMRR  230 (442)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhc--cC--CCEEEEEEEe--cCcHHHHHHHHHHhhccCce--eEEEEEECCCCCHHHHH
Confidence            78899999999999999999983  21  2345555555  333 3344444444332111  00     0111      


Q ss_pred             ----CHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          342 ----SAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       342 ----~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                          ..-...+.+++  +++.+|+++||+-
T Consensus       231 ~a~~~a~tiAEyfrd--~G~~Vll~~DslT  258 (442)
T PRK08927        231 QAAYLTLAIAEYFRD--QGKDVLCLMDSVT  258 (442)
T ss_pred             HHHHHHHHHHHHHHH--CCCcEEEEEeCcH
Confidence                11223333432  5899999999985

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=91.21  E-value=0.42  Score=49.07  Aligned_cols=22  Identities=41%  Similarity=0.634  Sum_probs=20.6

Q ss_pred             EEEEEcCCCChHHHHHHHHHhh
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +|+|.|+.|+||||+++.+++.
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~~   23 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAER   23 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999983

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=91.20  E-value=0.25  Score=51.65  Aligned_cols=87  Identities=17%  Similarity=0.306  Sum_probs=47.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEe----c---CCCCCCHHH--HHHHHHHHHhhhhhhhcc-----
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI----P---IMSMVEDRD--VLADILKQIDESLLKVEA-----  339 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~----s---~~~~~~~~~--~l~~il~~l~~~~~~~~~-----  339 (1007)
                      .+|.++||+|.||||..++++.+  ....+....-|..    .   -..+.++++  -.++..++.+..  +.+.     
T Consensus        20 ~~ilVvGMAGSGKTTF~QrL~~h--l~~~~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LG--PNGgI~TsL   95 (366)
T KOG1532|consen   20 VIILVVGMAGSGKTTFMQRLNSH--LHAKKTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLG--PNGGIVTSL   95 (366)
T ss_pred             cEEEEEecCCCCchhHHHHHHHH--HhhccCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCC--CCcchhhhH
Confidence            78999999999999999999984  4344433222221    1   002334444  345666665543  2221     


Q ss_pred             ---ccCHHHHHHHHHHHcCCCcEEEEEeC
Q 001843          340 ---TLSAEELMWRITQALDDSTFLIVMEN  365 (1007)
Q Consensus       340 ---~~~~~~l~~~l~~~L~~kr~LlVlDd  365 (1007)
                         ....++.+..+.+.-..-+|.| +|-
T Consensus        96 NLF~tk~dqv~~~iek~~~~~~~~l-iDT  123 (366)
T KOG1532|consen   96 NLFATKFDQVIELIEKRAEEFDYVL-IDT  123 (366)
T ss_pred             HHHHHHHHHHHHHHHHhhcccCEEE-EcC
Confidence               1234555555555544444443 443

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=91.15  E-value=0.26  Score=55.62  Aligned_cols=92  Identities=16%  Similarity=0.212  Sum_probs=55.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..|.|.|..|.||||+.+.+.+  .+..+....+|.- .  .+....  ... ...+-.+   .+...+.......++..
T Consensus       123 g~ili~G~tGSGKTT~l~al~~--~i~~~~~~~i~ti-E--dp~E~~--~~~-~~~~i~q---~evg~~~~~~~~~l~~~  191 (343)
T TIGR01420       123 GLILVTGPTGSGKSTTLASMID--YINKNAAGHIITI-E--DPIEYV--HRN-KRSLINQ---REVGLDTLSFANALRAA  191 (343)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH--hhCcCCCCEEEEE-c--CChhhh--ccC-ccceEEc---cccCCCCcCHHHHHHHh
Confidence            7899999999999999999887  4555555555543 2  221110  000 0000000   01111223456667888


Q ss_pred             cCCCcEEEEEeCcCccCchhhhhhc
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~l~  378 (1007)
                      |+..+=.|++|.+.  +.+.+....
T Consensus       192 lr~~pd~i~vgEir--d~~~~~~~l  214 (343)
T TIGR01420       192 LREDPDVILIGEMR--DLETVELAL  214 (343)
T ss_pred             hccCCCEEEEeCCC--CHHHHHHHH
Confidence            88899999999998  666665533

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=91.14  E-value=0.33  Score=51.80  Aligned_cols=33  Identities=33%  Similarity=0.436  Sum_probs=27.8

Q ss_pred             CCCCcEEEEEEcCCCChHHHHHHHHHhhhhcccCC
Q 001843          269 TTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       269 ~~~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  303 (1007)
                      +-..+..+.|||.+|.|||-+|+.|+.  .+.-.|
T Consensus       162 gIk~Pkg~ll~GppGtGKTlla~~Vaa--~mg~nf  194 (388)
T KOG0651|consen  162 GIKPPKGLLLYGPPGTGKTLLARAVAA--TMGVNF  194 (388)
T ss_pred             CCCCCceeEEeCCCCCchhHHHHHHHH--hcCCce
Confidence            445668999999999999999999999  565555

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=91.11  E-value=0.71  Score=55.23  Aligned_cols=22  Identities=27%  Similarity=0.375  Sum_probs=19.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .-|.|+|..|+||+++|+.+++
T Consensus       228 ~pvlI~GE~GtGK~~lA~aiH~  249 (520)
T PRK10820        228 APLLITGDTGTGKDLLAYACHL  249 (520)
T ss_pred             CCEEEECCCCccHHHHHHHHHH
Confidence            4578999999999999999876

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=91.09  E-value=0.79  Score=49.09  Aligned_cols=95  Identities=17%  Similarity=0.141  Sum_probs=67.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEE-EecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWV-HIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv-~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      +.+.++|+.|+|||+-++.+++.  .     ..+|+ ..+  ..+....++..+.......     ...........+..
T Consensus        95 ~l~~vyg~~g~gKt~a~~~y~~s--~-----p~~~l~~~~--p~~~a~~~i~~i~~~~~~~-----~~~~~~d~~~~~~~  160 (297)
T COG2842          95 SLVVVYGYAGLGKTQAAKNYAPS--N-----PNALLIEAD--PSYTALVLILIICAAAFGA-----TDGTINDLTERLMI  160 (297)
T ss_pred             ceEEEeccccchhHHHHHhhccc--C-----ccceeecCC--hhhHHHHHHHHHHHHHhcc-----cchhHHHHHHHHHH
Confidence            68899999999999999999982  1     23344 355  5556666666665555443     34455666667777


Q ss_pred             HcCCCcEEEEEeCcCccCchhhhhhccccC
Q 001843          353 ALDDSTFLIVMENAEHQKSQVWDSFLGKLC  382 (1007)
Q Consensus       353 ~L~~kr~LlVlDdv~~~~~~~~~~l~~l~~  382 (1007)
                      .+++..-+|+.|+.+.-....++.++...+
T Consensus       161 ~l~~~~~~iivDEA~~L~~~ale~lr~i~d  190 (297)
T COG2842         161 RLRDTVRLIIVDEADRLPYRALEELRRIHD  190 (297)
T ss_pred             HHccCcceeeeehhhccChHHHHHHHHHHH
Confidence            778888899999998767777777774443

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=91.06  E-value=0.18  Score=49.80  Aligned_cols=28  Identities=36%  Similarity=0.533  Sum_probs=23.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCC
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  303 (1007)
                      +-|.++||.|.||||+.+++++  ...-+|
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk--~L~~~F   30 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAK--ALNLPF   30 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHH--HcCCCc
Confidence            5678999999999999999998  555454

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=91.06  E-value=0.22  Score=51.53  Aligned_cols=31  Identities=35%  Similarity=0.459  Sum_probs=25.0

Q ss_pred             CCcEEEEEEcCCCChHHHHHHHHHhhhhcccCC
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F  303 (1007)
                      ..++-|..+|++|.|||-+|++|+|  +....|
T Consensus       209 dppkgvllygppgtgktl~aravan--rtdacf  239 (435)
T KOG0729|consen  209 DPPKGVLLYGPPGTGKTLCARAVAN--RTDACF  239 (435)
T ss_pred             CCCCceEEeCCCCCchhHHHHHHhc--ccCceE
Confidence            3447788999999999999999999  554443

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=91.05  E-value=0.27  Score=54.29  Aligned_cols=22  Identities=36%  Similarity=0.496  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      |++.+.|-||+||||+|-+.+-
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~   23 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALAL   23 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCcHHHHHHHHH
Confidence            7899999999999999988776

...

>PRK08149 ATP synthase SpaL; Validated

Probab=91.05  E-value=0.41  Score=54.91  Aligned_cols=85  Identities=14%  Similarity=0.164  Sum_probs=49.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhh-----ccc--------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV-----EAT--------  340 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~-----~~~--------  340 (1007)
                      ..++|+|..|.|||||...+++..    .-+.++...+. ....+..++..+.+......  ..     ..+        
T Consensus       152 q~i~I~G~sG~GKTTLl~~i~~~~----~~dv~v~g~Ig-~rg~ev~e~~~~~l~~~~~~--~~~vV~~~sd~p~~~r~~  224 (428)
T PRK08149        152 QRMGIFASAGCGKTSLMNMLIEHS----EADVFVIGLIG-ERGREVTEFVESLRASSRRE--KCVLVYATSDFSSVDRCN  224 (428)
T ss_pred             CEEEEECCCCCChhHHHHHHhcCC----CCCeEEEEEEe-eCCccHHHHHHHHhhccccc--ceEEEEECCCCCHHHHHh
Confidence            788999999999999999998832    12333333333 13445555655555532211  00     011        


Q ss_pred             --cCHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          341 --LSAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       341 --~~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                        .......+.++.  +++.+||++||+-
T Consensus       225 a~~~a~tiAE~fr~--~G~~Vll~~DslT  251 (428)
T PRK08149        225 AALVATTVAEYFRD--QGKRVVLFIDSMT  251 (428)
T ss_pred             HHHHHHHHHHHHHH--cCCCEEEEccchH
Confidence              111222333332  5899999999985

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=91.00  E-value=0.17  Score=49.61  Aligned_cols=20  Identities=50%  Similarity=0.821  Sum_probs=19.0

Q ss_pred             EEEEcCCCChHHHHHHHHHh
Q 001843          276 IALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       276 i~I~G~gGiGKTtLa~~v~~  295 (1007)
                      |.|+|++|.||||+|+.++.
T Consensus         2 i~l~G~~GsGKstla~~la~   21 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAK   21 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            68999999999999999988

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PRK13946 shikimate kinase; Provisional

Probab=90.94  E-value=0.19  Score=51.14  Aligned_cols=22  Identities=32%  Similarity=0.634  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +.|.++|++|+||||+|+.+++
T Consensus        11 ~~I~l~G~~GsGKsti~~~LA~   32 (184)
T PRK13946         11 RTVVLVGLMGAGKSTVGRRLAT   32 (184)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999999

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=90.94  E-value=0.67  Score=57.22  Aligned_cols=22  Identities=36%  Similarity=0.527  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .-|.|+|..|+||+++|+.+++
T Consensus       349 ~pvli~Ge~GtGK~~~A~~ih~  370 (638)
T PRK11388        349 FPVLLCGEEGVGKALLAQAIHN  370 (638)
T ss_pred             CCEEEECCCCcCHHHHHHHHHH
Confidence            4478999999999999999998

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=90.92  E-value=0.19  Score=50.53  Aligned_cols=23  Identities=35%  Similarity=0.621  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      +.|.|+|+.|.||||+|+.+++.
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~   27 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQ   27 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHH
Confidence            57999999999999999999983

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=90.87  E-value=0.21  Score=51.95  Aligned_cols=27  Identities=30%  Similarity=0.443  Sum_probs=24.0

Q ss_pred             CCCcEEEEEEcCCCChHHHHHHHHHhh
Q 001843          270 TTTTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       270 ~~~~~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+++++|+++|..|+|||||..++.+.
T Consensus        19 ~~~~~~i~~~G~~gsGKTTli~~l~~~   45 (207)
T TIGR00073        19 KHGLVVLNFMSSPGSGKTTLIEKLIDN   45 (207)
T ss_pred             hcCcEEEEEECCCCCCHHHHHHHHHHH
Confidence            446699999999999999999999883

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=90.85  E-value=0.22  Score=51.21  Aligned_cols=23  Identities=22%  Similarity=0.365  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+|.|.|.+|+||||+|+.++..
T Consensus         4 ~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          4 TIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            79999999999999999999983

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=90.85  E-value=0.18  Score=49.44  Aligned_cols=20  Identities=40%  Similarity=0.760  Sum_probs=18.6

Q ss_pred             EEEEEcCCCChHHHHHHHHH
Q 001843          275 VIALIGKAGSGKTTLARIVY  294 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~  294 (1007)
                      .|+|.|.+|+||||+++.+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999887

>PLN02200 adenylate kinase family protein

Probab=90.81  E-value=0.26  Score=52.24  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=21.4

Q ss_pred             cEEEEEEcCCCChHHHHHHHHHh
Q 001843          273 TQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +.+|.|.|++|+||||+|+.++.
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~   65 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVE   65 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            37899999999999999999987

>PF13504 LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OOK_G 1QYY_G 1SQ0_B 1P9A_G 1GWB_A 1P8V_A 1M0Z_A 1U0N_D

Probab=90.79  E-value=0.15  Score=29.61  Aligned_cols=16  Identities=38%  Similarity=0.461  Sum_probs=6.0

Q ss_pred             cCcEEecccCCCcccC
Q 001843          695 FLEYLGLRSTFIDSLP  710 (1007)
Q Consensus       695 ~Lr~L~L~~n~i~~LP  710 (1007)
                      +|+.|+|++|.++++|
T Consensus         2 ~L~~L~l~~n~L~~lP   17 (17)
T PF13504_consen    2 NLRTLDLSNNRLTSLP   17 (17)
T ss_dssp             T-SEEEETSS--SSE-
T ss_pred             ccCEEECCCCCCCCCc
Confidence            4455555555554444

...

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=90.77  E-value=1.1  Score=48.28  Aligned_cols=54  Identities=13%  Similarity=0.239  Sum_probs=39.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDE  332 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~  332 (1007)
                      .++.|-|.+|+|||++|.+++.+...... ..++|++    -..+..++...++.....
T Consensus        20 ~L~vi~a~pg~GKT~~~l~ia~~~a~~~~-~~vly~S----lEm~~~~l~~R~la~~s~   73 (259)
T PF03796_consen   20 ELTVIAARPGVGKTAFALQIALNAALNGG-YPVLYFS----LEMSEEELAARLLARLSG   73 (259)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTTS-SEEEEEE----SSS-HHHHHHHHHHHHHT
T ss_pred             cEEEEEecccCCchHHHHHHHHHHHHhcC-CeEEEEc----CCCCHHHHHHHHHHHhhc
Confidence            68999999999999999999996443322 5667776    456677788888777654

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase

Probab=90.75  E-value=0.32  Score=52.88  Aligned_cols=37  Identities=27%  Similarity=0.246  Sum_probs=27.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      ++|+|.|-||+||||+|..++.  .....=..++-|+..
T Consensus         2 ~~iav~~KGGvGKTT~~~nLA~--~La~~G~kVlliD~D   38 (270)
T cd02040           2 RQIAIYGKGGIGKSTTTQNLSA--ALAEMGKKVMIVGCD   38 (270)
T ss_pred             cEEEEEeCCcCCHHHHHHHHHH--HHHhCCCeEEEEEcC
Confidence            6788889999999999999888  343322245666665

Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=90.74  E-value=0.41  Score=54.80  Aligned_cols=22  Identities=50%  Similarity=0.643  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ..|.++|++|+|||++|+.++.
T Consensus       117 ~~iLL~GP~GsGKT~lAraLA~  138 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQTLAR  138 (413)
T ss_pred             ceEEEECCCCcCHHHHHHHHHH
Confidence            5789999999999999999997

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PRK00300 gmk guanylate kinase; Provisional

Probab=90.73  E-value=0.22  Score=51.61  Aligned_cols=23  Identities=39%  Similarity=0.703  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+|+|+|+.|+||||||+.++..
T Consensus         6 ~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          6 LLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhh
Confidence            79999999999999999999983

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=90.71  E-value=0.28  Score=59.40  Aligned_cols=55  Identities=13%  Similarity=0.199  Sum_probs=41.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcc-cCCCceEEEEecCCCCCCHHHHHHHHHHHHhhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK-RHFTKRAWVHIPIMSMVEDRDVLADILKQIDES  333 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~-~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~  333 (1007)
                      +.+.++|.+|+||||+|+.+++  .+- .+|+..+|+.-   ...+...+++.++.+++..
T Consensus        51 ~~~l~~G~~G~GKttla~~l~~--~l~~~~~~~~~~~~n---p~~~~~~~~~~v~~~~G~~  106 (637)
T PRK13765         51 RHVMMIGSPGTGKSMLAKAMAE--LLPKEELQDILVYPN---PEDPNNPKIRTVPAGKGKQ  106 (637)
T ss_pred             CeEEEECCCCCcHHHHHHHHHH--HcChHhHHHheEeeC---CCcchHHHHHHHHHhcCHH
Confidence            4678999999999999999998  343 34577788653   4557778888888777665

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=90.65  E-value=0.55  Score=53.85  Aligned_cols=22  Identities=27%  Similarity=0.496  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ..++|+|..|+|||||++.++.
T Consensus       141 q~i~I~G~sG~GKTtLl~~I~~  162 (418)
T TIGR03498       141 QRLGIFAGSGVGKSTLLSMLAR  162 (418)
T ss_pred             cEEEEECCCCCChHHHHHHHhC
Confidence            7899999999999999999887

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK13768 GTPase; Provisional

Probab=90.65  E-value=0.35  Score=51.99  Aligned_cols=36  Identities=31%  Similarity=0.523  Sum_probs=26.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEe
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI  311 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~  311 (1007)
                      .++.|+|.||+||||++..+..  .....-..++.|+.
T Consensus         3 ~~i~v~G~~G~GKTt~~~~~~~--~l~~~g~~v~~i~~   38 (253)
T PRK13768          3 YIVFFLGTAGSGKTTLTKALSD--WLEEQGYDVAIVNL   38 (253)
T ss_pred             EEEEEECCCCccHHHHHHHHHH--HHHhcCCceEEEEC
Confidence            7899999999999999998887  33333334555554

>PLN02165 adenylate isopentenyltransferase

Probab=90.63  E-value=0.26  Score=54.33  Aligned_cols=23  Identities=35%  Similarity=0.641  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+|+|+|+.|+||||||..++..
T Consensus        44 ~iivIiGPTGSGKStLA~~LA~~   66 (334)
T PLN02165         44 KVVVIMGATGSGKSRLSVDLATR   66 (334)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHH
Confidence            69999999999999999999883

>PRK14530 adenylate kinase; Provisional

Probab=90.55  E-value=0.2  Score=52.50  Aligned_cols=22  Identities=32%  Similarity=0.453  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      +.|.|+|++|+||||+|+.++.
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~   25 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAE   25 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999988

>PRK14527 adenylate kinase; Provisional

Probab=90.54  E-value=0.24  Score=50.73  Aligned_cols=23  Identities=30%  Similarity=0.533  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+|.|+|.+|.||||+|+.+++.
T Consensus         7 ~~i~i~G~pGsGKsT~a~~La~~   29 (191)
T PRK14527          7 KVVIFLGPPGAGKGTQAERLAQE   29 (191)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            79999999999999999999873

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=90.52  E-value=0.27  Score=53.81  Aligned_cols=37  Identities=22%  Similarity=0.162  Sum_probs=26.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      ++|+|+|-||+||||+|..++.  .....=..++-|+..
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~--~La~~G~rVLliD~D   38 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAA--ALAESGKKVLVVGCD   38 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHH--HHHhCCCEEEEEeeC
Confidence            6899999999999999999887  333332345555544

>PF00142 Fer4_NifH: 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family; InterPro: IPR000392 This entry represents members of the NifH/BchL/ChlL family

Probab=90.41  E-value=0.32  Score=51.34  Aligned_cols=37  Identities=27%  Similarity=0.230  Sum_probs=28.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +.|+|+|-|||||+|.+..+.-  .....-..++-|-++
T Consensus         1 r~IAiYGKGGIGKST~~~Nlsa--ala~~G~kVl~iGCD   37 (273)
T PF00142_consen    1 RKIAIYGKGGIGKSTTASNLSA--ALAEMGKKVLQIGCD   37 (273)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH--HHHHTT--EEEEEES
T ss_pred             CeEEEEcCCCcccChhhhHHHH--HHHhccceeeEeccc
Confidence            4689999999999999999877  455555667777665

Nitrogen fixing bacteria possess a nitrogenase enzyme complex that catalyses the reduction of molecular nitrogen to ammonia [, , ]. The nitrogenase enzyme complex consists of two components: Component I is nitrogenase MoFe protein or dinitrogenase, which contains 2 molecules each of 2 non-identical subunits. Component II is nitrogenase Fe protein or dinitrogenase reductase, which is a homodimer. The monomer is encoded by the nifH gene []. Component II has 2 ATP-binding domains and one 4Fe-4S cluster per homodimer: it supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component I for the reduction of molecular nitrogen to ammonia []. There are a number of conserved regions in the sequence of these proteins: in the N-terminal section there is an ATP-binding site motif 'A' (P-loop) IPR001687 from INTERPRO and in the central section there are two conserved cysteines which have been shown, in nifH, to be the ligands of the 4Fe-4S cluster. Protochlorophyllide reductase is involved in light-independent chlorophyll biosynthesis. The light-independent reaction uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This enzyme complex is composed of three subunits: ChlL, ChlN and ChlB. ChlL is present as a homodimer, and binds one 4Fe-4S cluster per dimer. The conserved domains, including the ATP-binding motif and the Fe-S binding motif found in the three subunits, are similar to those in nitrogenases []. ; GO: 0005524 ATP binding, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1CP2_A 2AFI_F 1N2C_F 1FP6_C 2AFK_G 1M34_M 1XD8_A 1NIP_A 1M1Y_N 1G21_H ....

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=90.41  E-value=1.1  Score=53.99  Aligned_cols=22  Identities=36%  Similarity=0.678  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ..++|+|..|.|||||++.+..
T Consensus       362 ~~vaIvG~SGsGKSTLl~lL~g  383 (529)
T TIGR02868       362 ERVAILGPSGSGKSTLLMLLTG  383 (529)
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            7899999999999999999876

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK14737 gmk guanylate kinase; Provisional

Probab=90.38  E-value=0.25  Score=50.41  Aligned_cols=22  Identities=23%  Similarity=0.483  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      ++|.|+|+.|+|||||++++..
T Consensus         5 ~~ivl~GpsG~GK~tl~~~l~~   26 (186)
T PRK14737          5 KLFIISSVAGGGKSTIIQALLE   26 (186)
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            8999999999999999999988

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=90.38  E-value=0.21  Score=51.00  Aligned_cols=22  Identities=36%  Similarity=0.599  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHh
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~  295 (1007)
                      .++.|+|+.|.|||||++.++.
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~   24 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQ   24 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            5899999999999999999987

>PRK13975 thymidylate kinase; Provisional

Probab=90.34  E-value=0.23  Score=51.03  Aligned_cols=23  Identities=39%  Similarity=0.614  Sum_probs=21.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      .+|+|.|+.|+||||+|+.++..
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~   25 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEK   25 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999993

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=90.30  E-value=0.99  Score=42.70  Aligned_cols=36  Identities=19%  Similarity=0.067  Sum_probs=26.5

Q ss_pred             EEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEE
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH  310 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~  310 (1007)
                      .+.|.|..|.|||+.+..+............++|++
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~   37 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLA   37 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEc
Confidence            467999999999999988877533333455677775

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=90.28  E-value=0.43  Score=51.60  Aligned_cols=86  Identities=14%  Similarity=0.153  Sum_probs=48.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCCCHHHHHHHHHHHHhhhhhhhccccCHHHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .+|.|.|..|.||||+++.+.+  .+.. ....+ +++.....+....     ..|+...      ..........++..
T Consensus        81 GlilisG~tGSGKTT~l~all~--~i~~-~~~~i-itiEdp~E~~~~~-----~~q~~v~------~~~~~~~~~~l~~~  145 (264)
T cd01129          81 GIILVTGPTGSGKTTTLYSALS--ELNT-PEKNI-ITVEDPVEYQIPG-----INQVQVN------EKAGLTFARGLRAI  145 (264)
T ss_pred             CEEEEECCCCCcHHHHHHHHHh--hhCC-CCCeE-EEECCCceecCCC-----ceEEEeC------CcCCcCHHHHHHHH
Confidence            6899999999999999998876  3322 12222 2232001111100     0011100      01112355667778


Q ss_pred             cCCCcEEEEEeCcCccCchhhhh
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDS  376 (1007)
Q Consensus       354 L~~kr~LlVlDdv~~~~~~~~~~  376 (1007)
                      |+..+=.|+++++.  +.+....
T Consensus       146 lR~~PD~i~vgEiR--~~e~a~~  166 (264)
T cd01129         146 LRQDPDIIMVGEIR--DAETAEI  166 (264)
T ss_pred             hccCCCEEEeccCC--CHHHHHH
Confidence            88888899999998  6654443

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=90.26  E-value=1.5  Score=48.68  Aligned_cols=48  Identities=21%  Similarity=0.207  Sum_probs=34.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCC-CCHHHHHHHHH
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSM-VEDRDVLADIL  327 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~-~~~~~~l~~il  327 (1007)
                      +.++|.|..|+|||+|++++++.    .+-+.++++-++  +. ....+++.++-
T Consensus       158 qr~~I~G~~G~GKT~L~~~Iak~----~~~dvvVyv~iG--ERg~Ev~e~l~ef~  206 (369)
T cd01134         158 GTAAIPGPFGCGKTVIQQSLSKY----SNSDIVIYVGCG--ERGNEMTEVLEEFP  206 (369)
T ss_pred             CEEEEECCCCCChHHHHHHHHhC----CCCCEEEEEEeC--CChHHHHHHHHHHH
Confidence            68899999999999999999994    233567777776  43 34455555543

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=90.25  E-value=0.67  Score=49.74  Aligned_cols=84  Identities=17%  Similarity=0.143  Sum_probs=47.6

Q ss_pred             EEEEEEcCCCChHHHHH-HHHHhhhhcccCCCce-EEEEecCCCC-CCHHHHHHHHHHHHhhhhhhh-----cccc----
Q 001843          274 QVIALIGKAGSGKTTLA-RIVYNRVYVKRHFTKR-AWVHIPIMSM-VEDRDVLADILKQIDESLLKV-----EATL----  341 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa-~~v~~~~~~~~~F~~~-~wv~~s~~~~-~~~~~~l~~il~~l~~~~~~~-----~~~~----  341 (1007)
                      +-++|+|..|+|||+|| ..+.+.  .  +-+.+ +++-+.  +. ....++.+++...-...  ..     ..++    
T Consensus        70 Qr~~Ifg~~g~GKt~L~l~~i~~~--~--~~~v~~V~~~iG--er~~ev~e~~~~~~~~~~~~--~tvvv~~t~d~~~~~  141 (274)
T cd01132          70 QRELIIGDRQTGKTAIAIDTIINQ--K--GKKVYCIYVAIG--QKASTVAQVVKTLEEHGAME--YTIVVAATASDPAPL  141 (274)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHHh--c--CCCeEEEEEecc--cchHHHHHHHHHHHhcCccc--eeEEEEeCCCCchhH
Confidence            77899999999999996 556662  2  23444 555555  44 34445555544321111  00     0111    


Q ss_pred             ------CHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          342 ------SAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       342 ------~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                            ..-...+.++.  +++.+|||+||+.
T Consensus       142 r~~a~~~a~aiAE~fr~--~G~~Vlvl~DslT  171 (274)
T cd01132         142 QYLAPYTGCAMGEYFMD--NGKHALIIYDDLS  171 (274)
T ss_pred             HHHHHHHHHHHHHHHHH--CCCCEEEEEcChH
Confidence                  11223344443  5899999999986

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=90.24  E-value=0.62  Score=47.83  Aligned_cols=23  Identities=35%  Similarity=0.468  Sum_probs=21.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhh
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~  296 (1007)
                      ..|+|.|..|+||||+|+.+++.
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~   26 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKL   26 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            78999999999999999999984

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=90.22  E-value=0.92  Score=47.77  Aligned_cols=37  Identities=30%  Similarity=0.454  Sum_probs=28.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEec
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s  312 (1007)
                      +++.|.|.+|+|||++|.+++.. ..+ .=..++|++..
T Consensus        17 ~~~li~G~~G~GKt~~~~~~~~~-~~~-~g~~~~y~s~e   53 (224)
T TIGR03880        17 HVIVVIGEYGTGKTTFSLQFLYQ-GLK-NGEKAMYISLE   53 (224)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH-HHh-CCCeEEEEECC
Confidence            89999999999999999998773 222 23467788765

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>PRK06936 type III secretion system ATPase; Provisional

Probab=90.13  E-value=0.84  Score=52.45  Aligned_cols=84  Identities=18%  Similarity=0.227  Sum_probs=50.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHHhhhhcccCCCceEEEEecCCCCC-CHHHHHHHHHHHHhhhhhhh-----ccc-------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMV-EDRDVLADILKQIDESLLKV-----EAT-------  340 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLa~~v~~~~~~~~~F~~~~wv~~s~~~~~-~~~~~l~~il~~l~~~~~~~-----~~~-------  340 (1007)
                      ..++|+|..|.|||||.+.+++.  ..  -+.++++-++  +.. ...++....+..-+..  ..     ..+       
T Consensus       163 q~~~I~G~sG~GKStLl~~Ia~~--~~--~dv~V~~liG--ERgrEv~ef~~~~l~~~~l~--rtvvv~atsd~p~~~R~  234 (439)
T PRK06936        163 QRMGIFAAAGGGKSTLLASLIRS--AE--VDVTVLALIG--ERGREVREFIESDLGEEGLR--KAVLVVATSDRPSMERA  234 (439)
T ss_pred             CEEEEECCCCCChHHHHHHHhcC--CC--CCEEEEEEEc--cCcHHHHHHHHHHhcccccc--eeEEEEECCCCCHHHHH
Confidence            78999999999999999999983  22  2456666666  433 3344443333221110  00     011       


Q ss_pred             ---cCHHHHHHHHHHHcCCCcEEEEEeCcC
Q 001843          341 ---LSAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       341 ---~~~~~l~~~l~~~L~~kr~LlVlDdv~  367 (1007)
                         ...-...+.++.  +++++|+++||+-
T Consensus       235 ~a~~~a~tiAEyfrd--~G~~Vll~~DslT  262 (439)
T PRK06936        235 KAGFVATSIAEYFRD--QGKRVLLLMDSVT  262 (439)
T ss_pred             HHHHHHHHHHHHHHH--cCCCEEEeccchh
Confidence               112223444443  5899999999985

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	1007
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	9e-50
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	7e-48
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-38
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-12
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	5e-10
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	6e-09
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	1e-08
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	3e-06
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	6e-04
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	4e-08
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	4e-08
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	3e-05
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	2e-07
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	4e-07
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	9e-07
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	7e-07
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	5e-05
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-04
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	9e-07
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	2e-06
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	7e-06
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	9e-07
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	1e-06
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	1e-04
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	2e-04
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	2e-06
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-06
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	3e-06
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	5e-06
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	4e-06
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	5e-06
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-05
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	1e-04
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-04
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	6e-05
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	7e-05
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	7e-05
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	9e-05
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	1e-04
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	2e-04
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	3e-04
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	3e-04
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	4e-04
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	4e-04
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	8e-04

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  185 bits (471), Expect = 9e-50
 Identities = 74/464 (15%), Positives = 152/464 (32%), Gaps = 69/464 (14%)

Query: 274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF--TKRAWVHIPIMSMVEDRDVLADILKQID 331
             + + G AG GK+ LA        +          WV +           L ++  ++D
Sbjct: 148 GWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLD 207

Query: 332 -ESLLKVEATLSAEELMWRITQALDDST--FLIVMENAEHQKSQVWDSFLGKLCSFTQCG 388
            +        L+ EE   R+   +       L+++++       VWDS++  L +F    
Sbjct: 208 QDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDD-------VWDSWV--LKAFDSQC 258

Query: 389 KIIITTSSTEDFVEPLGAAFSTLHVP-GLGKNESWELFLKKARIAEDVLQSRSSELIKLK 447
           +I++TT   +   + +      + V   LGK +  E+      + +       ++L +  
Sbjct: 259 QILLTTRD-KSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK-------ADLPEQA 310

Query: 448 KQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNL--------------VAL 493
             I+  C G PL V L+  LL      +E + K ++      +              +++
Sbjct: 311 HSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSI 370

Query: 494 CYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEE 553
             + L   +K     + +  ++ ++P + L  LW               E +  E  L+E
Sbjct: 371 SVEMLREDIKDYYTDLSILQKDVKVPTKVLCILW------------DM-ETEEVEDILQE 417

Query: 554 LVTRHMIQVIRWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKF 613
            V + ++   R   +G      +  +  D L  K              +L    K +   
Sbjct: 418 FVNKSLLFCDR---NGKSFRYYLHDLQVDFLTEKNCS-----------QLQDLHKKIITQ 463

Query: 614 AVRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPA--KQIGIILGKCISKRRLGML 671
             R    +  S            L  ++      +   A    +  I  K      +G  
Sbjct: 464 FQRYHQPHTLSPDQEDCMYWYNFLAYHMASAKMHKELCALMFSLDWIKAKT---ELVGPA 520

Query: 672 KVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPI 715
            ++     Y+ +L   +      F E+L L    +   P    +
Sbjct: 521 HLIHEFVEYRHILDEKDCAVSENFQEFLSLNGHLLGRQPFPNIV 564

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score =  179 bits (454), Expect = 7e-48
 Identities = 42/333 (12%), Positives = 101/333 (30%), Gaps = 43/333 (12%)

Query: 275 VIALIGKAGSGKTTLARIVYN--RVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDE 332
            + L G+AGSGK+ +A    +     +  ++    W+     +     D+  DIL  +  
Sbjct: 154 FLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKS 213

Query: 333 -----SLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQC 387
                +   VE   S           +D    L V ++       V      +     + 
Sbjct: 214 EDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDD-------VVQEETIRWAQELRL 266

Query: 388 GKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLK 447
            + ++TT    +           + V  L  +E ++                  +   + 
Sbjct: 267 -RCLVTTRD-VEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV-----GEKEEDVL 319

Query: 448 KQILNICDGLPLRVVLLAGLLSTKQPSYEEW-SKVIERANGDNL--------------VA 492
            + + +  G P  +++       K        +  +E      +              + 
Sbjct: 320 NKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVGVECITPYSYKSLAMALQ 379

Query: 493 LCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLE 552
            C + L  + +  + +  + P   +IPV+    +   +  +  +  L    +D     L+
Sbjct: 380 RCVEVLSDEDRSALAFAVVMPPGVDIPVKLWSCVIPVDICSNEEEQL----DDEVADRLK 435

Query: 553 ELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILR 585
            L  R  +   +        T  +  +++  L+
Sbjct: 436 RLSKRGALLSGK---RMPVLTFKIDHIIHMFLK 465

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score =  155 bits (391), Expect = 2e-38
 Identities = 113/680 (16%), Positives = 211/680 (31%), Gaps = 175/680 (25%)

Query: 118 RSLFSFGMNKFKRELEIRGSSSS-----SSSSYEHQQQLVEVNDTGPSFSPYQGGYSTHR 172
           + + S   + F    + +          S    +H   ++                S   
Sbjct: 19  KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDH---IIM---------------SKDA 60

Query: 173 SQQQRWARISDYFCAEDETDVLGLERQVKELLHV----LIPEHHGINDADVSTKKIVDGY 228
                  R+     ++ E  V   ++ V+E+L +    L+     I         +   Y
Sbjct: 61  VSGTL--RLFWTLLSKQEEMV---QKFVEEVLRINYKFLMSP---IKTEQRQPSMMTRMY 112

Query: 229 EYARS----SGEEITELPIPEQEGGG---DALSNEEEESGRCQSSSTTTTTTQVIALIGK 281
              R       +   +  +   +       AL                      + + G 
Sbjct: 113 IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKN--------------VLIDGV 158

Query: 282 AGSGKTTLARIVYNRVYVKRHFTKRA-WVHIPIMSMVEDR-DVLADILKQIDESLLK--- 336
            GSGKT +A  V     V+     +  W+++   +  E   ++L  +L QID +      
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218

Query: 337 --VEATLSAEELMWRITQALDDSTF---LIVMENAEHQKSQVWDSFLGKLCSFTQCGKII 391
                 L    +   + + L    +   L+V+ N ++  ++ W++F         C KI+
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQN--AKAWNAFNL------SC-KIL 269

Query: 392 ITT--SSTEDFVEPLGAAFSTL--HVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLK 447
           +TT      DF+        +L  H   L  +E   L LK                  L 
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ----------DLP 319

Query: 448 KQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNL---VALCYQDL-PAQVK 503
           ++   +    P R+ ++A  +     +++ W  V    N D L   +      L PA+ +
Sbjct: 320 RE---VLTTNPRRLSIIAESIRDGLATWDNWKHV----NCDKLTTIIESSLNVLEPAEYR 372

Query: 504 PCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEELVTRHMIQVI 563
                + +FP    IP   L  +W                +    + + +L    +++  
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWF------------DVIKSDVMVVVNKLHKYSLVE-- 418

Query: 564 RWRLDGSPKTCCMPGVLYDILRPKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLG 623
           +   +    T  +P  +Y  L+ K E+    Y  H  + +         F    L     
Sbjct: 419 KQPKES---TISIPS-IYLELKVKLEN---EYALH--RSIVDHYNIPKTFDSDDLIPPYL 469

Query: 624 SNSFPYSSL---LSWRLHS---------YLVF---DSRIR--GTPAKQIGIILGKCISKR 666
              F YS +   L    H          +L F   + +IR   T     G IL       
Sbjct: 470 DQYF-YSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN------ 522

Query: 667 RLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDV-- 724
                 +  L+  YKP + +N+        +Y  L +  +D LP     L C    D+  
Sbjct: 523 -----TLQQLK-FYKPYICDNDP-------KYERLVNAILDFLPKIEENLICSKYTDLLR 569

Query: 725 -------------SHTKVQR 731
                        +H +VQR
Sbjct: 570 IALMAEDEAIFEEAHKQVQR 589

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 70.7 bits (172), Expect = 2e-12
 Identities = 112/683 (16%), Positives = 202/683 (29%), Gaps = 226/683 (33%)

Query: 302 HFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLI 361
            +  +  + +   + V++ D      K + +    +   LS EE+   I      S  L 
Sbjct: 15  QYQYKDILSVFEDAFVDNFDC-----KDVQDMPKSI---LSKEEIDHIIMSKDAVSGTLR 66

Query: 362 VMENAEHQKSQVWDSFLGKLC----SF------TQCGKIIITTSSTEDFVEPL---GAAF 408
           +      ++ ++   F+ ++      F      T+  +  + T    +  + L      F
Sbjct: 67  LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF 126

Query: 409 STLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLL 468
           +  +V                         R    +KL++ +L +    P + VL+ G+L
Sbjct: 127 AKYNVS------------------------RLQPYLKLRQALLEL---RPAKNVLIDGVL 159

Query: 469 -STKQPSYEEWSKVIERANGDNLVALCYQDLPAQVKPCILYMGLFPREYEIPVRRLIHLW 527
            S K      W           +          Q K           +        I  W
Sbjct: 160 GSGKT-----W-----------VALDVCLSYKVQCK--------MDFK--------IF-W 186

Query: 528 CAEGFAPPDLDL--IASEEDLAEMYLEELVTRHMIQVIRWRLDGSPKTCCMPGVLYDILR 585
                    L+L    S E + EM L++L+ + +      R D S               
Sbjct: 187 ---------LNLKNCNSPETVLEM-LQKLLYQ-IDPNWTSRSDHSSNI------------ 223

Query: 586 PKAEDIGFLYHHHHPQRLNSSAKSLPKFAVRRLAANLGSNSFPYSSLLS----WRLHSYL 641
                           R++S    L     RRL   L S  +  + LL         ++ 
Sbjct: 224 --------------KLRIHSIQAEL-----RRL---LKSKPYE-NCLLVLLNVQNAKAWN 260

Query: 642 VFDSRIR---GTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEY 698
            F+   +    T  KQ+   L    +         + L+      LT +     L  L+Y
Sbjct: 261 AFNLSCKILLTTRFKQVTDFLSAATTTH-------ISLDHHSMT-LTPDEVKS-L-LLKY 310

Query: 699 LGLRSTFIDSLP----DSTPILFCL---------ATLD----VSHTKVQRL--------- 732
           L  R      LP     + P    +         AT D    V+  K+  +         
Sbjct: 311 LDCR---PQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE 367

Query: 733 PYAFWPSRHLYLNWIFLATNVFRHPQFVKWETS-LQTLWGLCIKADEVQSLDYFRRLTSL 791
           P  +   R ++     L+  VF  P      T  L  +W   IK+D +  ++   +  SL
Sbjct: 368 PAEY---RKMFDR---LS--VF--PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY-SL 416

Query: 792 RKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSG 851
            +   K S+ +  S+  E+   +     LH   ++             +HY + K + S 
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHR-SIV-------------DHYNIPKTFDSD 462

Query: 852 HLPPNSV-------IGDRSFPPNVVTLTLSQLRLEYDPMP-ILGRLR--QLKILRLFGGS 901
            L P  +       IG          L   +          +    R  + KI       
Sbjct: 463 DLIPPYLDQYFYSHIGHH--------LKNIEHPERMTLFRMVFLDFRFLEQKI------R 508

Query: 902 YTGEEMSCSSGEFPNLLVLKLWK 924
           +     + S      L  LK +K
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYK 531

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A* Length = 330

 Score = 61.2 bits (149), Expect = 5e-10
 Identities = 52/279 (18%), Positives = 98/279 (35%), Gaps = 43/279 (15%)

Query: 686 NNNALGRLPFLEYLGLRSTFIDSLPDST-PILFCLATLDVSHTKVQRLPYAFWPS-RHLY 743
            +     L  L  L L +  I  +       L  L  L +S  +++ LP     + + L 
Sbjct: 68  KDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELR 127

Query: 744 L--NWIF-LATNVFRHPQFVKWETSLQTLW--GLCIKADEVQSLDYFRRLTSLRKLGLKC 798
           +  N I  +  +VF           +  +      +K+  +++   F+ +  L  + +  
Sbjct: 128 VHENEITKVRKSVFNGL------NQMIVVELGTNPLKSSGIEN-GAFQGMKKLSYIRI-- 178

Query: 799 SSTTSTSLKKEIIGAVLQLSELH----SLKLICETPSYLPLLEMAEHYKLQKLYLSGHLP 854
           + T  T++ +   G    L+ELH     +  +    + L  L       L KL LS    
Sbjct: 179 ADTNITTIPQ---GLPPSLTELHLDGNKITKV--DAASLKGL-----NNLAKLGLSF--- 225

Query: 855 PN--SVIGDRSFP--PNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGG--SYTGEEMS 908
            N  S + + S    P++  L L+  +L   P   L   + ++++ L     S  G    
Sbjct: 226 -NSISAVDNGSLANTPHLRELHLNNNKLVKVP-GGLADHKYIQVVYLHNNNISAIGSNDF 283

Query: 909 CSSGEFPNLLVLKLWKL--NRLRQWRIKEGAMPCLRQLE 945
           C  G            L  N ++ W I+     C+    
Sbjct: 284 CPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRA 322

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score = 59.1 bits (143), Expect = 6e-09
 Identities = 58/303 (19%), Positives = 109/303 (35%), Gaps = 48/303 (15%)

Query: 274 QVIALIGKAGSGKTTLAR-IVYNRVYVKRHFTKRA-WVHIPIMSMVEDRDVLADILKQID 331
             + + G AG GK+ LA   V +   ++  F+    WV I           L ++  ++D
Sbjct: 148 GWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLD 207

Query: 332 -ESLLKVEATLSAEELMWRITQALDD--STFLIVMENAEHQKSQVWDSFLGKLCSFTQCG 388
            E        L+ EE   R+   +       L+++++       VWD ++ K     QC 
Sbjct: 208 QEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDD-------VWDPWVLKAFDN-QC- 258

Query: 389 KIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKK 448
           +I++TT         +G         GLG+ +  E+      +       +  +L     
Sbjct: 259 QILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNM-------KKEDLPAEAH 311

Query: 449 QILNICDGLPLRVVLLAGL--------------LSTKQPSYEEWSKVIERANGDNLVALC 494
            I+  C G PL V L+  L              L  KQ      S   +    D  +++ 
Sbjct: 312 SIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSIS 371

Query: 495 YQDLPAQVKPCILYMGLFPREYEIPVRRLIHLWCAEGFAPPDLDLIASEEDLAEMYLEEL 554
            + L   +K     + +  ++ ++P + L  LW        +++ I          L+E 
Sbjct: 372 VEMLREDIKDYYTDLSILQKDVKVPTKVLCVLW---DLETEEVEDI----------LQEF 418

Query: 555 VTR 557
           V +
Sbjct: 419 VNK 421

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 57.4 bits (139), Expect = 1e-08
 Identities = 63/329 (19%), Positives = 105/329 (31%), Gaps = 45/329 (13%)

Query: 666 RRLGMLKVLDLEGVYKPMLTN-----NNALGRLPFLEYLGLRSTFIDSLPDSTPILFC-- 718
           + L  L+V  L         N      +AL  L  L     R  ++D   D    LF   
Sbjct: 222 QGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCL 281

Query: 719 --LATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKA 776
             +++  +    ++R+    +     +L  +      F   +      SL+ L     K 
Sbjct: 282 TNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKL----KSLKRLTFTSNKG 337

Query: 777 DEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELH-SLKLICETPSYLPL 835
               S      L SL  L L  +  +      +       L  L  S   +    S    
Sbjct: 338 GNAFS---EVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLG 394

Query: 836 LEMAEHYKLQKLYLSG----HLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQ 891
           LE     +L+ L         +   SV        N++ L +S          I   L  
Sbjct: 395 LE-----QLEHLDFQHSNLKQMSEFSVF---LSLRNLIYLDISHTHTRVAFNGIFNGLSS 446

Query: 892 LKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLE------ 945
           L++L++ G S+    +     E  NL  L L +  +L Q  +   A   L  L+      
Sbjct: 447 LEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQ-CQLEQ--LSPTAFNSLSSLQVLNMAS 503

Query: 946 --IRSCGYLVPPTGLKHVTSSLREFLLTN 972
             ++S    VP      +T SL++  L  
Sbjct: 504 NQLKS----VPDGIFDRLT-SLQKIWLHT 527

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 50.1 bits (120), Expect = 3e-06
 Identities = 64/337 (18%), Positives = 114/337 (33%), Gaps = 50/337 (14%)

Query: 671 LKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFIDSLPDSTPILFC----LA 720
            K LDL         N        +    P L+ L L    I ++ D     +     L+
Sbjct: 30  TKNLDLSF-------NPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGA---YQSLSHLS 79

Query: 721 TLDVSHTKVQRLP-YAFWPSRHLYLNWIFLATNVFR--HPQFVKWETSLQTLWGL---CI 774
           TL ++   +Q L   AF       L  +              +    +L+ L  +    I
Sbjct: 80  TLILTGNPIQSLALGAFSGLSS--LQKLVAVETNLASLENFPIGHLKTLKELN-VAHNLI 136

Query: 775 KADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELH-SLKLICETPSYL 833
           +    +  +YF  LT+L  L L  SS    S+    +  + Q+  L+ SL L     +++
Sbjct: 137 Q--SFKLPEYFSNLTNLEHLDL--SSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFI 192

Query: 834 PLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQL---------RLEYDPMP 884
                 +  +L KL L  +   +S+   ++    +  L + +L          LE     
Sbjct: 193 Q-PGAFKEIRLHKLTLRNNF--DSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKS 249

Query: 885 ILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGA-MPCLRQ 943
            L  L  L I      +Y    +      F  L  +  + L  +   R+K+ +     + 
Sbjct: 250 ALEGLCNLTIEEF-RLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQH 308

Query: 944 LEIRSCGY-LVPPTGLKHVTS-SLREFLLTNMPSTFG 978
           LE+ +C +   P   LK +   +       N  S   
Sbjct: 309 LELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVD 345

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens} Length = 570

 Score = 42.4 bits (100), Expect = 6e-04
 Identities = 44/249 (17%), Positives = 79/249 (31%), Gaps = 70/249 (28%)

Query: 659 LGKCISKRRLGMLKVLDLEG--VYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPIL 716
            G   S+  L  L+ LDL    +      +  +      L+YL L    + ++  +   L
Sbjct: 337 GGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQ-SDFGTTSLKYLDLSFNGVITMSSNFLGL 395

Query: 717 FCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKA 776
             L  LD  H+ ++++                   +VF          +L  L    I  
Sbjct: 396 EQLEHLDFQHSNLKQMSEF----------------SVFLSL------RNLIYLD---ISH 430

Query: 777 DEVQSL--DYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLP 834
              +      F  L+SL  L +        S ++  +  +   +EL +            
Sbjct: 431 THTRVAFNGIFNGLSSLEVLKM-----AGNSFQENFLPDI--FTELRN------------ 471

Query: 835 LLEMAEHYKLQKLYLSG----HLPPNSVIGDRSFP--PNVVTLTLSQLRLEYDPMPILGR 888
                    L  L LS      L P       +F    ++  L ++  +L+  P  I  R
Sbjct: 472 ---------LTFLDLSQCQLEQLSPT------AFNSLSSLQVLNMASNQLKSVPDGIFDR 516

Query: 889 LRQLKILRL 897
           L  L+ + L
Sbjct: 517 LTSLQKIWL 525

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 56.3 bits (136), Expect = 4e-08
 Identities = 52/303 (17%), Positives = 104/303 (34%), Gaps = 28/303 (9%)

Query: 666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTF-IDSLPDSTPI-LFCLATLD 723
             L  LK L+L G     L   +    L  L+ L + +      +       L  L  L+
Sbjct: 95  GPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELE 154

Query: 724 VSHTKVQRL-PYAFWPSRHLYLNWIFLATNVFRH--PQFVKWETSLQTLW--GLCIKADE 778
           +    ++     +    R +  + + L  +        F    +S++ L      +   +
Sbjct: 155 IKALSLRNYQSQSLKSIRDI--HHLTLHLSESAFLLEIFADILSSVRYLELRDTNLARFQ 212

Query: 779 VQSLDYFRRLTSLRKLGLKCSSTTSTSLKK--EIIGAVLQLSELHSLKLICETPSYLPLL 836
              L      + ++KL  + S  T  S  +  +++  +L+LSE+                
Sbjct: 213 FSPLPVDEVSSPMKKLAFRGSVLTDESFNELLKLLRYILELSEVEFDDCTLNGLGDFNPS 272

Query: 837 E---MAEHYKLQKLYLSG-HLPPN--SVIGDRSFP--PNVVTLTLSQLRLEYDPMPILGR 888
           E   ++E  K++ + +   H+P           +     V  +T+   ++   P      
Sbjct: 273 ESDVVSELGKVETVTIRRLHIPQFYLFYDLSTVYSLLEKVKRITVENSKVFLVPCSFSQH 332

Query: 889 LRQLKILRLFGGSY-----TGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQ 943
           L+ L+ L L   S         + S   G +P+L  L L + N LR  +     +  L+ 
Sbjct: 333 LKSLEFLDL---SENLMVEEYLKNSACKGAWPSLQTLVLSQ-NHLRSMQKTGEILLTLKN 388

Query: 944 LEI 946
           L  
Sbjct: 389 LTS 391

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 55.9 bits (135), Expect = 4e-08
 Identities = 48/257 (18%), Positives = 92/257 (35%), Gaps = 48/257 (18%)

Query: 662 CISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPI-LFCLA 720
            + K     ++ L +   Y      +     L  ++ + + ++ +  +P S    L  L 
Sbjct: 279 ELGKVETVTIRRLHIPQFYLFYD-LSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLE 337

Query: 721 TLDVSHTKVQRLP------YAFWPS-RHLYL--NWIFLATNVFRHPQFVKWETSLQTLWG 771
            LD+S   +             WPS + L L  N +    ++ +  + +    +L +L  
Sbjct: 338 FLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQNHL---RSMQKTGEILLTLKNLTSLD- 393

Query: 772 LCIKADEVQSLDY-FRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL----I 826
             I  +    +    +    +R L    SST    +K  I         L  L +    +
Sbjct: 394 --ISRNTFHPMPDSCQWPEKMRFL--NLSSTGIRVVKTCI------PQTLEVLDVSNNNL 443

Query: 827 CETPSYLPLLEMAEHYKLQKLYLSG----HLPPNSVIGDRSFPPNVVTLTLSQLRLEYDP 882
                +LP        +LQ+LY+S      LP  S        P ++ + +S+ +L+  P
Sbjct: 444 DSFSLFLP--------RLQELYISRNKLKTLPDAS------LFPVLLVMKISRNQLKSVP 489

Query: 883 MPILGRLRQLKILRLFG 899
             I  RL  L+ + L  
Sbjct: 490 DGIFDRLTSLQKIWLHT 506

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A* Length = 549

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 50/283 (17%), Positives = 81/283 (28%), Gaps = 73/283 (25%)

Query: 671 LKVLDLEGVYKPMLTN--NNALGRLPFLEYLGLRSTFIDSLPDST-PILFCLATLDVSHT 727
           +K LDL       +T   +  L     L+ L L+S+ I+++       L  L  LD+S  
Sbjct: 28  MKSLDLSFNK---ITYIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDN 84

Query: 728 KVQRLP-YAFWPSRHL-YLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYF 785
            +  L    F P   L YLN   L  N +                        +     F
Sbjct: 85  HLSSLSSSWFGPLSSLKYLN---LMGNPY----------------------QTLGVTSLF 119

Query: 786 RRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQ 845
             LT+L+ L +               G V   SE+          + L          L 
Sbjct: 120 PNLTNLQTLRI---------------GNVETFSEIRR-----IDFAGLT--------SLN 151

Query: 846 KLYLSGHLPPN--SVIGDRSFP--PNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGS 901
           +L +              +S     ++  LTL      +        L  ++ L L   +
Sbjct: 152 ELEIKA----LSLRNYQSQSLKSIRDIHHLTLHLSESAFLLEIFADILSSVRYLELRDTN 207

Query: 902 YTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQL 944
                        P   V    K    R   + + +   L +L
Sbjct: 208 LA----RFQFSPLPVDEVSSPMKKLAFRGSVLTDESFNELLKL 246

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus} Length = 562

 Score = 54.1 bits (130), Expect = 2e-07
 Identities = 39/302 (12%), Positives = 81/302 (26%), Gaps = 30/302 (9%)

Query: 667 RLGMLKVLDLEGVYKPMLTNNNALGRLPF-----LEYLGLRSTFIDSLPDSTPI--LFCL 719
               L+ LD+         ++N L  +       L +L L     D LP       L  L
Sbjct: 98  FNQDLEYLDV---------SHNRLQNISCCPMASLRHLDLSFNDFDVLPVCKEFGNLTKL 148

Query: 720 ATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWE---TSLQTLWGLCIKA 776
             L +S  K ++L        HL    + L +   +  +    +   T++  L       
Sbjct: 149 TFLGLSAAKFRQLDLLPVAHLHLSCILLDLVSYHIKGGETESLQIPNTTVLHLVFHPNSL 208

Query: 777 DEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAV--LQLSELHSLKLICETPSYLP 834
             VQ       L  L+   +K +      L   +        L  +    +       + 
Sbjct: 209 FSVQVNMSVNALGHLQLSNIKLNDENCQRLMTFLSELTRGPTLLNVTLQHIETTWKCSVK 268

Query: 835 LLEMAEHYKLQKLYLS-----GHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRL 889
           L +      ++ L +        +         +   +++   +      +    +    
Sbjct: 269 LFQFFWPRPVEYLNIYNLTITERIDREEFTYSETALKSLMIEHVKNQVFLFSKEALYSVF 328

Query: 890 RQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSC 949
            ++ I  L         M C      +   L   + N              L++L+    
Sbjct: 329 AEMNIKMLSISDTPFIHMVCPPS-PSSFTFLNFTQ-NVFTD--SVFQGCSTLKRLQTLIL 384

Query: 950 GY 951
             
Sbjct: 385 QR 386

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens} Length = 844

 Score = 53.3 bits (128), Expect = 4e-07
 Identities = 45/239 (18%), Positives = 79/239 (33%), Gaps = 25/239 (10%)

Query: 668 LGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDST-PILFCLATLDVSH 726
           L  LKVL+L       +  + A   L  L+ L L    +  L  S    L  +A +D+  
Sbjct: 289 LKDLKVLNLAYNKINKI-ADEAFYGLDNLQVLNLSYNLLGELYSSNFYGLPKVAYIDLQK 347

Query: 727 TKVQRLP-YAFWPSRHL-YLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDY 784
             +  +    F     L  L+   L  N      F+    S+  ++    K   +  ++ 
Sbjct: 348 NHIAIIQDQTFKFLEKLQTLD---LRDNALTTIHFI---PSIPDIFLSGNKLVTLPKINL 401

Query: 785 FRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEH-YK 843
              L  L +  L+                +L++  L  L L     S     +       
Sbjct: 402 TANLIHLSENRLENLDILYF---------LLRVPHLQILILNQNRFSSCSGDQTPSENPS 452

Query: 844 LQKLYLSG---HLPPNSVIGDRSFP--PNVVTLTLSQLRLEYDPMPILGRLRQLKILRL 897
           L++L+L      L   + +    F    ++  L L+   L   P  +   L  L+ L L
Sbjct: 453 LEQLFLGENMLQLAWETELCWDVFEGLSHLQVLYLNHNYLNSLPPGVFSHLTALRGLSL 511

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens} Length = 844

 Score = 52.1 bits (125), Expect = 9e-07
 Identities = 52/334 (15%), Positives = 102/334 (30%), Gaps = 34/334 (10%)

Query: 666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPI-LFCLATLDV 724
             L  L++L+L   Y P+  +  A   LP L  L L S+ I  L       LF L  L +
Sbjct: 45  PFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHLFELRL 104

Query: 725 SHTKVQRLPYAFWPSRHLY-LNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSL- 782
               +          R+L  L  + L+ N  R          L +L  +   ++++  + 
Sbjct: 105 YFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSNQIFLVC 164

Query: 783 -DYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLI--------------- 826
                 L          ++ +  S      G  +       L+++               
Sbjct: 165 EHELEPLQGKTLSFFSLAANSLYSRVSVDWGKCMNPFRNMVLEILDVSGNGWTVDITGNF 224

Query: 827 CETPSYLPLLEMAEHYKLQKLYLSGH----LPPNSVIGDRSFPPNVVTLTLSQLRLEYDP 882
               S      +   + +       H       N+  G      +V  L LS   +    
Sbjct: 225 SNAISKSQAFSLILAHHIMGAGFGFHNIKDPDQNTFAGLAR--SSVRHLDLSHGFVFSLN 282

Query: 883 MPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGA---MP 939
             +   L+ LK+L L            +   F  L  L++  L+      +       +P
Sbjct: 283 SRVFETLKDLKVLNLAYNKIN----KIADEAFYGLDNLQVLNLSYNLLGELYSSNFYGLP 338

Query: 940 CLRQLEIRSCG-YLVPPTGLKHVTSSLREFLLTN 972
            +  ++++     ++     K +   L+   L +
Sbjct: 339 KVAYIDLQKNHIAIIQDQTFKFL-EKLQTLDLRD 371

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 52.3 bits (126), Expect = 7e-07
 Identities = 57/301 (18%), Positives = 91/301 (30%), Gaps = 48/301 (15%)

Query: 668 LGMLKVLDL-----EGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFC---- 718
           L  L+V  L              + +AL  L  L     R  ++D   D    LF     
Sbjct: 224 LAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTN 283

Query: 719 LATLDVSHTKVQRLPYA--FWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKA 776
           +++  +    ++R+      +  +HL L                    SL+ L     K 
Sbjct: 284 VSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKL------KSLKRLTFTSNKG 337

Query: 777 DEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL-------ICET 829
               S      L SL  L L   S    S K     +    + L  L L       +   
Sbjct: 338 GNAFS---EVDLPSLEFLDL---SRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSN 391

Query: 830 PSYLPLLEMAEHYKLQKLYLSG----HLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPI 885
              L         +L+ L         +   SV        N++ L +S          I
Sbjct: 392 FLGLE--------QLEHLDFQHSNLKQMSEFSVFLS---LRNLIYLDISHTHTRVAFNGI 440

Query: 886 LGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLE 945
              L  L++L++ G S+    +     E  NL  L L    +L Q  +   A   L  L+
Sbjct: 441 FNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDL-SQCQLEQ--LSPTAFNSLSSLQ 497

Query: 946 I 946
           +
Sbjct: 498 V 498

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 46.2 bits (110), Expect = 5e-05
 Identities = 59/342 (17%), Positives = 104/342 (30%), Gaps = 59/342 (17%)

Query: 671 LKVLDLEGVYKPMLTN--NNALGRLPFLEYLGLRSTFIDSLPDSTPILFC----LATLDV 724
            K LDL       L +  + +    P L+ L L    I ++ D     +     L+TL +
Sbjct: 30  TKNLDLSFNP---LRHLGSYSFFSFPELQVLDLSRCEIQTIEDGA---YQSLSHLSTLIL 83

Query: 725 SHTKVQRL-PYAFWPSRHLYLNWIFLATNVFRH--PQFVKWETSLQTLW----GLCIKAD 777
           +   +Q L   AF       L  +              +    +L+ L      +     
Sbjct: 84  TGNPIQSLALGAFSGLSS--LQKLVAVETNLASLENFPIGHLKTLKELNVAHNLI----Q 137

Query: 778 EVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSL---------KLICE 828
             +  +YF  LT+L  L L      S  ++      +  L ++  L          +   
Sbjct: 138 SFKLPEYFSNLTNLEHLDLS-----SNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFI 192

Query: 829 TPSYLPLLEMAEHYKLQKLYLS-----GHLPPNSVIGDRSFPPNVVTLTLSQLR----LE 879
            P     +      +L KL L       ++    + G       V  L L + R    LE
Sbjct: 193 QPGAFKEI------RLHKLTLRNNFDSLNVMKTCIQGLAGL--EVHRLVLGEFRNEGNLE 244

Query: 880 YDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGA-M 938
                 L  L  L I      +Y    +      F  L  +  + L  +   R+K+ +  
Sbjct: 245 KFDKSALEGLCNLTIEEF-RLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYN 303

Query: 939 PCLRQLEIRSCGY-LVPPTGLKHVTSSLREFLLTNMPSTFGS 979
              + LE+ +C +   P   LK +              +   
Sbjct: 304 FGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVD 345

>3fxi_A TLR4, htoll, TOLL-like receptor 4; leucine rich repeat, glycoprotein, immune response, inflamma response, innate immunity, membrane, receptor; HET: PA1 KDO GMH FTT DAO MYR NAG GCS; 3.10A {Homo sapiens} Length = 605

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 49/273 (17%), Positives = 73/273 (26%), Gaps = 54/273 (19%)

Query: 663 ISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRS---TFIDSLPDSTPILFCL 719
               +L  LK L           N  +   LP LE+L L     +F      S      L
Sbjct: 319 FPTLKLKSLKRLTFTSNK---GGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSL 375

Query: 720 ATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEV 779
             LD+S   V  +   F     L    +    +            +L+ +          
Sbjct: 376 KYLDLSFNGVITMSSNFLGLEQL--EHLDFQHS------------NLKQMS--------- 412

Query: 780 QSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL----ICET--PSYL 833
                F  L +L  L +       T  +    G    LS L  LK+      E   P   
Sbjct: 413 -EFSVFLSLRNLIYLDIS-----HTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIF 466

Query: 834 PLLEMAEHYKLQKLYLSG----HLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRL 889
             L       L  L LS      L P +     +   ++  L +S              L
Sbjct: 467 TELR-----NLTFLDLSQCQLEQLSPTAF----NSLSSLQVLNMSHNNFFSLDTFPYKCL 517

Query: 890 RQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKL 922
             L++L          +         +L  L L
Sbjct: 518 NSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNL 550

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 51.9 bits (125), Expect = 9e-07
 Identities = 56/295 (18%), Positives = 95/295 (32%), Gaps = 63/295 (21%)

Query: 666 RRLGMLKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFIDSLPDSTPILFC- 718
           ++L MLKVL+L+        N               L  L L S  I  + ++    F  
Sbjct: 70  QKLPMLKVLNLQH-------NELSQLSDKTFAFCTNLTELHLMSNSIQKIKNNP---FVK 119

Query: 719 ---LATLDVSHTKVQRLPY-AFWPSRHL-YLNWIFLATNVFRHPQFVKWE----TSLQTL 769
              L TLD+SH  +            +L  L    L+ N  +  +  + +    +SL+ L
Sbjct: 120 QKNLITLDLSHNGLSSTKLGTQVQLENLQELL---LSNNKIQALKSEELDIFANSSLKKL 176

Query: 770 W-------GLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHS 822
                                 F  +  L  L L  ++        E +   L  + + +
Sbjct: 177 ELSSNQIKEFSPGC--------FHAIGRLFGLFL--NNVQLGPSLTEKLCLELANTSIRN 226

Query: 823 LKL----ICETPSYLPLLEMAEHYKLQKLYLSGHLPPN--SVIGDRSFP--PNVVTLTLS 874
           L L    +  T +        +   L  L LS     N  +V+G+ SF   P +    L 
Sbjct: 227 LSLSNSQLSTTSN--TTFLGLKWTNLTMLDLSY----NNLNVVGNDSFAWLPQLEYFFLE 280

Query: 875 QLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLR 929
              +++     L  L  ++ L L     +  + S S    P +       L  L 
Sbjct: 281 YNNIQHLFSHSLHGLFNVRYLNL---KRSFTKQSISLASLPKIDDFSFQWLKCLE 332

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 50.4 bits (121), Expect = 2e-06
 Identities = 52/324 (16%), Positives = 97/324 (29%), Gaps = 52/324 (16%)

Query: 654 QIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFID 707
           +I  +  + +       LK L+L         N            +  L  L L +  + 
Sbjct: 156 KIQALKSEELDIFANSSLKKLELSS-------NQIKEFSPGCFHAIGRLFGLFLNNVQLG 208

Query: 708 SLPDSTPILFC----LATLDVSHTKVQRL-PYAFWPSRHLYLNWIFLATNVFRH--PQFV 760
                   L      +  L +S++++       F   +   L  + L+ N          
Sbjct: 209 PSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYNNLNVVGNDSF 268

Query: 761 KWETSLQTLW--GLCIKADEVQSLDYFRRLTSLRKLGL----KCSSTTSTSLKKEIIGAV 814
            W   L+  +     I+     S      L ++R L L       S +  SL K    + 
Sbjct: 269 AWLPQLEYFFLEYNNIQHLFSHS---LHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSF 325

Query: 815 LQLSELHSLKL----ICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFP----P 866
             L  L  L +    I      +          L+ L LS        + + +F      
Sbjct: 326 QWLKCLEHLNMEDNDI----PGIKSNMFTGLINLKYLSLSNSFTSLRTLTNETFVSLAHS 381

Query: 867 NVVTLTLSQLRLEYDPMPILGRLRQLKILRL----FGGSYTGEEMSCSSGEFPNLLVLKL 922
            +  L L++ ++          L  L++L L     G   TG+E         N+  + L
Sbjct: 382 PLHILNLTKNKISKIESDAFSWLGHLEVLDLGLNEIGQELTGQEWRG----LENIFEIYL 437

Query: 923 WKLNRLRQWRIKEGAMPCLRQLEI 946
              N+  Q  +   +   +  L+ 
Sbjct: 438 SY-NKYLQ--LTRNSFALVPSLQR 458

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 48.8 bits (117), Expect = 7e-06
 Identities = 57/294 (19%), Positives = 93/294 (31%), Gaps = 62/294 (21%)

Query: 671 LKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFC----LATLDVSH 726
           + VL+L       L       R   L  L +    I  L             L  L++ H
Sbjct: 27  ITVLNLTHNQLRRL-PAANFTRYSQLTSLDVGFNTISKLEPEL---CQKLPMLKVLNLQH 82

Query: 727 TKVQRLP-YAFWPSRHL-YLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDY 784
            ++ +L    F    +L  L+   L +N            S+Q +             + 
Sbjct: 83  NELSQLSDKTFAFCTNLTELH---LMSN------------SIQKI-----------KNNP 116

Query: 785 FRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL----ICETPSYLPLLEMAE 840
           F +  +L  L L     +   L    +G  +QL  L  L L    I    S    L++  
Sbjct: 117 FVKQKNLITLDL-----SHNGLSSTKLGTQVQLENLQELLLSNNKIQALKS--EELDIFA 169

Query: 841 HYKLQKLYLSG----HLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILG---RLRQLK 893
           +  L+KL LS        P            +  L L+ ++L       L        ++
Sbjct: 170 NSSLKKLELSSNQIKEFSPGCFHA----IGRLFGLFLNNVQLGPSLTEKLCLELANTSIR 225

Query: 894 ILRLFGGSYTGEEMSCSSG-EFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEI 946
            L L     +    +   G ++ NL +L L   N L    +   +   L QLE 
Sbjct: 226 NLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSY-NNLN--VVGNDSFAWLPQLEY 276

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A* Length = 680

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 39/261 (14%), Positives = 72/261 (27%), Gaps = 53/261 (20%)

Query: 668 LGMLKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFIDSLPDSTPILFCLA- 720
           L  +  + L         N       N+   +P L+ L LR   + ++  S      L  
Sbjct: 429 LENIFEIYLSY-------NKYLQLTRNSFALVPSLQRLMLRRVALKNVDSSPSPFQPLRN 481

Query: 721 --TLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADE 778
              LD+S+  +  +           L  + L  N            +L  LW     A+ 
Sbjct: 482 LTILDLSNNNIANINDDMLEG-LEKLEILDLQHN------------NLARLWK---HANP 525

Query: 779 VQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL----ICETPSYLP 834
              + + + L+ L  L L      S    +  +     L EL  + L    +    + LP
Sbjct: 526 GGPIYFLKGLSHLHILNL-----ESNGFDEIPVEVFKDLFELKIIDLGLNNL----NTLP 576

Query: 835 LLEMAEHYKLQKLYLSG----HLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLR 890
                    L+ L L       +             N+  L +     +     I   + 
Sbjct: 577 ASVFNNQVSLKSLNLQKNLITSVEKKVF---GPAFRNLTELDMRFNPFDCTCESIAWFVN 633

Query: 891 QLKILRLFGGSYTGEEMSCSS 911
            +                C++
Sbjct: 634 WINETHTN-IPELSSHYLCNT 653

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 52.0 bits (125), Expect = 9e-07
 Identities = 42/248 (16%), Positives = 69/248 (27%), Gaps = 49/248 (19%)

Query: 671 LKVLDLEGVYKPMLTNNNALGRLPF-----LEYLGLRSTFIDSLPDSTPILFCLATLDVS 725
            + L +             L + P      L+ L L              L  L+ LD+S
Sbjct: 309 WQSLSI---------IRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVA-LPSLSYLDLS 358

Query: 726 HTKVQRLP-YAFWPSRHLYLNWIFLATNVFR-HPQFVKWETSLQTLW--GLCIKADEVQS 781
              +      ++       L  + L+ N              LQ L      +K   V  
Sbjct: 359 RNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLK--RVTE 416

Query: 782 LDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEH 841
              F  L  L  L +     + T+ K +  G  L L+ L++LK+     +     +    
Sbjct: 417 FSAFLSLEKLLYLDI-----SYTNTKIDFDGIFLGLTSLNTLKM-----AGNSFKDNTLS 466

Query: 842 Y------KLQKLYLSG----HLPPNSVIGDRSFP--PNVVTLTLSQLRLEYDPMPILGRL 889
                   L  L LS      +          F     +  L +S   L +       +L
Sbjct: 467 NVFANTTNLTFLDLSKCQLEQISWGV------FDTLHRLQLLNMSHNNLLFLDSSHYNQL 520

Query: 890 RQLKILRL 897
             L  L  
Sbjct: 521 YSLSTLDC 528

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 51.6 bits (124), Expect = 1e-06
 Identities = 53/312 (16%), Positives = 96/312 (30%), Gaps = 43/312 (13%)

Query: 653 KQIGIILGKCISKRRLGMLKVLDL-----EGVYKPMLTNNNALGRLPFLEYLGLRSTFID 707
                I+  C+    L  L V  L     +      +   + +  L  +     R T+ +
Sbjct: 215 FNSSNIMKTCLQN--LAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTN 272

Query: 708 SLPDSTPILFCLA---TLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWET 764
              D      CLA    + ++   ++ L       +   L+   +     +    +    
Sbjct: 273 DFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLS---IIRCQLKQFPTLDL-P 328

Query: 765 SLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAV--LQLSELHS 822
            L++L    +  ++         L SL  L L     +  +L      +   L  + L  
Sbjct: 329 FLKSLT---LTMNKGSISFKKVALPSLSYLDL-----SRNALSFSGCCSYSDLGTNSLRH 380

Query: 823 LKL----ICETPSYLPLLEMAEHYKLQKLYLSG----HLPPNSVIGDRSFPPNVVTLTLS 874
           L L         +    LE     +LQ L         +   S          ++ L +S
Sbjct: 381 LDLSFNGAIIMSANFMGLE-----ELQHLDFQHSTLKRVTEFSAF---LSLEKLLYLDIS 432

Query: 875 QLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIK 934
               + D   I   L  L  L++ G S+    +S       NL  L L    +L Q  I 
Sbjct: 433 YTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDL-SKCQLEQ--IS 489

Query: 935 EGAMPCLRQLEI 946
            G    L +L++
Sbjct: 490 WGVFDTLHRLQL 501

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 53/307 (17%), Positives = 94/307 (30%), Gaps = 56/307 (18%)

Query: 666 RRLGMLKVLDLEGVYKPMLTNNN-------ALGRLPFLEYLGLRSTFIDSLPDSTPILFC 718
             L  L  L L        T N        +   L  LE L    T + SL         
Sbjct: 77  HGLHHLSNLIL--------TGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFP---IG 125

Query: 719 ----LATLDVSHTKVQR--LPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGL 772
               L  L+V+H  +    LP  F    +  L  + L+ N  +         ++  L  L
Sbjct: 126 QLITLKKLNVAHNFIHSCKLPAYFSNLTN--LVHVDLSYNYIQTI-------TVNDLQFL 176

Query: 773 CIKADEVQSLDYFR-RLTSLRKLGLKCSSTTSTSL------KKEIIGAVLQLSELHSLKL 825
                   SLD     +  ++    +       +L         +   +  L+ LH  +L
Sbjct: 177 RENPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRL 236

Query: 826 ICETPSYLPLLEMAEH------YKLQKLYLSGHLPPNSVIGDRSFP--PNVVTLTLSQLR 877
           I         LE+ E         +           +       F    NV  ++L+ + 
Sbjct: 237 ILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVS 296

Query: 878 LEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGA 937
           ++Y  +  + +  + + L +             + + P L  L L  +N+      K+ A
Sbjct: 297 IKY--LEDVPKHFKWQSLSIIRCQLK----QFPTLDLPFLKSLTL-TMNKGSI-SFKKVA 348

Query: 938 MPCLRQL 944
           +P L  L
Sbjct: 349 LPSLSYL 355

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A* Length = 606

 Score = 44.6 bits (106), Expect = 2e-04
 Identities = 48/304 (15%), Positives = 88/304 (28%), Gaps = 78/304 (25%)

Query: 671 LKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFIDSLPDSTPILFC----LA 720
            K +DL         N        +      L++L L    I+++ D     +     L+
Sbjct: 34  TKNIDLSF-------NPLKILKSYSFSNFSELQWLDLSRCEIETIEDKA---WHGLHHLS 83

Query: 721 TLDVSHTKVQRL-PYAFWPS---RHLYLNWIFLAT---NVFRHPQFVKWETSLQTLWGL- 772
            L ++   +Q   P +F       +L      LA+                +L+ L  + 
Sbjct: 84  NLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFPIGQL------ITLKKLN-VA 136

Query: 773 --CIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETP 830
              I     +   YF  LT+L  + L         ++   +  +  L E   +       
Sbjct: 137 HNFIH--SCKLPAYFSNLTNLVHVDLS-----YNYIQTITVNDLQFLRENPQV------- 182

Query: 831 SYLPLLEMAEHYKLQKLYLSGHLPPN--SVIGDRSF-PPNVVTLTLSQLRLEYDPMP-IL 886
                           L +S     N    I D++F    +  LTL       + M   L
Sbjct: 183 -------------NLSLDMSL----NPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCL 225

Query: 887 GRLRQLKILRLFGGSYTGEE-----MSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCL 941
             L  L + RL  G +  E               ++ + +  +L     +        CL
Sbjct: 226 QNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEF-RLTYTNDFSDDIVKFHCL 284

Query: 942 RQLE 945
             + 
Sbjct: 285 ANVS 288

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 487

 Score = 50.2 bits (120), Expect = 2e-06
 Identities = 32/238 (13%), Positives = 71/238 (29%), Gaps = 21/238 (8%)

Query: 668 LGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHT 727
              ++ LDL+      +           LE+L L+  FI  +         L TLD+S  
Sbjct: 143 RSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQVV-FAKLKTLDLSSN 201

Query: 728 KVQRLPYAFWPSRHLYLNWIFLATNVFRH-PQFVKWETSLQTLW-------GLCIKADEV 779
           K+  +   F  +    + WI L  N      + +++  +L+             ++    
Sbjct: 202 KLAFMGPEFQSAAG--VTWISLRNNKLVLIEKALRFSQNLEHFDLRGNGFHCGTLR---- 255

Query: 780 QSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMA 839
              D+F +   ++ +     +    + + E    V  L    +         +   L   
Sbjct: 256 ---DFFSKNQRVQTVAK--QTVKKLTGQNEEECTVPTLGHYGAYCCEDLPAPFADRLIAL 310

Query: 840 EHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRL 897
           +  +   L   G      +  +R        +   + +       +  R +    L  
Sbjct: 311 KRKEHALLSGQG-SETERLECERENQARQREIDALKEQYRTVIDQVTLRKQAKITLEQ 367

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 50.4 bits (121), Expect = 2e-06
 Identities = 39/295 (13%), Positives = 72/295 (24%), Gaps = 59/295 (20%)

Query: 666 RRLGMLKVLDLEGVYKPMLTNN-------NALGRLPFLEYLGLRSTFIDSLPDST-PILF 717
           +    L  L L        T N        AL     L++L    T I S+         
Sbjct: 78  QSQHRLDTLVL--------TANPLIFMAETALSGPKALKHLFFIQTGISSIDFIPLHNQK 129

Query: 718 CLATLDVSHTKVQRLPY-AFWPSRHL-YLNWIFLATNVFRHPQFVKWETSLQTLWGLCIK 775
            L +L +    +  +     +P+  L  L+      N   +                 + 
Sbjct: 130 TLESLYLGSNHISSIKLPKGFPTEKLKVLD---FQNNAIHY-----------------LS 169

Query: 776 ADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEII-GAVLQLSELHSLKLICETPSYLP 834
            ++         L     L L  +      ++      AV Q       + +      L 
Sbjct: 170 KED------MSSLQQATNLSLNLNGNDIAGIEPGAFDSAVFQSLNFGGTQNLLVIFKGLK 223

Query: 835 LLEMAEHYKLQKLYLSG----HLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLR 890
              +     L            + P    G      +V ++ L +               
Sbjct: 224 NSTI---QSLWLGTFEDMDDEDISPAVFEGLC--EMSVESINLQKHYFFNISSNTFHCFS 278

Query: 891 QLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLE 945
            L+ L L     +  E+         L  L L   N+     + + +      L 
Sbjct: 279 GLQELDLTATHLS--ELPSGLVGLSTLKKLVLSA-NKFEN--LCQISASNFPSLT 328

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 50.0 bits (120), Expect = 3e-06
 Identities = 53/244 (21%), Positives = 88/244 (36%), Gaps = 33/244 (13%)

Query: 671 LKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQ 730
           ++ ++L+  Y   + ++N       L+ L L +T +  LP     L  L  L +S  K +
Sbjct: 256 VESINLQKHYFFNI-SSNTFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSANKFE 314

Query: 731 RLP-YAFWPSRHLYLNWIFLATNVFR---HPQFVKWETSLQTLWGL---CIKADEVQSLD 783
            L   +        L  + +  N  R       ++   +L+ L  L    I+  +  +  
Sbjct: 315 NLCQISASNFPS--LTHLSIKGNTKRLELGTGCLENLENLRELD-LSHDDIETSDCCN-L 370

Query: 784 YFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELH----SLKLICETPSYLPLLEMA 839
             R L+ L+ L L  S     SLK E      QL  L      LK+      +  L    
Sbjct: 371 QLRNLSHLQSLNL--SYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNL---- 424

Query: 840 EHYKLQKLYLSG-HLPPNSVIGDRSFP--PNVVTLTLSQLRLE---YDPMPILGRLRQLK 893
             + L+ L LS   L    +  ++ F   P +  L L               L  L +L+
Sbjct: 425 --HLLKVLNLSHSLL---DISSEQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQTLGRLE 479

Query: 894 ILRL 897
           IL L
Sbjct: 480 ILVL 483

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A* Length = 606

 Score = 49.2 bits (118), Expect = 5e-06
 Identities = 46/287 (16%), Positives = 86/287 (29%), Gaps = 50/287 (17%)

Query: 668 LGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLA---TLDV 724
              L  L ++G  K +      L  L  L  L L    I++       L  L+   +L++
Sbjct: 324 FPSLTHLSIKGNTKRLELGTGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNL 383

Query: 725 SHTKVQRLPYAFWPS----RHLYL--NWI--FLATNVFRHPQFVKWETSLQTLW----GL 772
           S+ +   L    +        L L    +    A + F++         L+ L      L
Sbjct: 384 SYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPFQNL------HLLKVLNLSHSLL 437

Query: 773 CIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL----ICE 828
            I ++++     F  L +L+ L L            +   ++  L  L  L L    +  
Sbjct: 438 DISSEQL-----FDGLPALQHLNL--QGNHFPKGNIQKTNSLQTLGRLEILVLSFCDL-- 488

Query: 829 TPSYLPLLEMAEHYKLQKLYLSG----HLPPNSVIGDRSFPP-NVVTLTLSQLRLEYDPM 883
             S +          +  + LS                +      + L L+   +     
Sbjct: 489 --SSIDQHAFTSLKMMNHVDLSHNRLTSSSIE------ALSHLKGIYLNLASNHISIILP 540

Query: 884 PILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQ 930
            +L  L Q + + L          +CS+  F       + KL     
Sbjct: 541 SLLPILSQQRTINLRQNPLDC---TCSNIYFLEWYKENMQKLEDTED 584

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 48.9 bits (117), Expect = 4e-06
 Identities = 55/289 (19%), Positives = 93/289 (32%), Gaps = 51/289 (17%)

Query: 684 LTNNN-------ALGRLPFLEYLGLRSTFIDSLPDSTPI-LFCLATLDVSHTKVQRLPYA 735
           L NN+           L  L  L L +  I  + +     L  L  L +S   +  +P  
Sbjct: 61  LQNNDISELRKDDFKGLQHLYALVLVNNKISKIHEKAFSPLRKLQKLYISKNHLVEIPPN 120

Query: 736 FWPS-RHLYL--NWIF-LATNVFRHPQFVKWETSLQTLW--GLCIKADEVQSLDYFRRLT 789
              S   L +  N I  +   VF          ++  +   G  ++    +    F  L 
Sbjct: 121 LPSSLVELRIHDNRIRKVPKGVFSGL------RNMNCIEMGGNPLENSGFEP-GAFDGL- 172

Query: 790 SLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKL----ICETPSYLPLLEMAEHYKLQ 845
            L  L +  S    T + K++         L+ L L    I      + L ++  + KL 
Sbjct: 173 KLNYLRI--SEAKLTGIPKDL------PETLNELHLDHNKI----QAIELEDLLRYSKLY 220

Query: 846 KLYLSGHLPPN--SVIGDRSFP--PNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGG- 900
           +L L      N   +I + S    P +  L L   +L   P   L  L+ L+++ L    
Sbjct: 221 RLGLGH----NQIRMIENGSLSFLPTLRELHLDNNKLSRVP-AGLPDLKLLQVVYLHTNN 275

Query: 901 -SYTGEEMSCSSGEFPNLLVLKLWKL--NRLRQWRIKEGAMPCLRQLEI 946
            +  G    C  G            L  N +  W ++     C+     
Sbjct: 276 ITKVGVNDFCPVGFGVKRAYYNGISLFNNPVPYWEVQPATFRCVTDRLA 324

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 49.9 bits (119), Expect = 5e-06
 Identities = 45/345 (13%), Positives = 97/345 (28%), Gaps = 66/345 (19%)

Query: 662 CISKRRLGMLKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFIDSLPDSTPI 715
            +     G +  L L G               +A+G+L  L+ L   +            
Sbjct: 316 GVDLDNNGRVTGLSLAG-------FGAKGRVPDAIGQLTELKVLSFGTHSETVSGR--LF 366

Query: 716 LFCLATLDVSHTKVQRLPYAFWP---SRHLYLNWIFLATNVF-RHPQFVKWETSLQTLWG 771
                T D+S  +  R+   +          LN   L  +   R+P+       ++    
Sbjct: 367 GDEELTPDMSEERKHRIRMHYKKMFLDYDQRLNLSDLLQDAINRNPEM----KPIKKDSR 422

Query: 772 LCIKADEVQSL--------DYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSL 823
           + +K  ++ +L           +RLT L+ +    +++  T     +             
Sbjct: 423 ISLKDTQIGNLTNRITFISKAIQRLTKLQIIYF--ANSPFTYDNIAVDWEDANSDYAKQY 480

Query: 824 KLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDRSFP------PNVVTLTLSQLR 877
           +    + S L          L  + L         +     P      P + +L ++  R
Sbjct: 481 ENEELSWSNLK--------DLTDVELYN----CPNMT--QLPDFLYDLPELQSLNIACNR 526

Query: 878 LEYDPM---------PILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRL 928
                                 +++I  +   +      S S  +   L +L     N++
Sbjct: 527 GISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLLDCVH-NKV 585

Query: 929 RQWRIKE-GAMPCLRQLEIRSCGYLVPPTGLKHVTSSLREFLLTN 972
           R   ++  G    L  L++        P      T  +     ++
Sbjct: 586 RH--LEAFGTNVKLTDLKLDYNQIEEIPEDFCAFTDQVEGLGFSH 628

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 47.2 bits (112), Expect = 3e-05
 Identities = 36/307 (11%), Positives = 74/307 (24%), Gaps = 86/307 (28%)

Query: 621 NLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVY 680
              ++ F Y ++      +   +  +                 S   L  L  ++L    
Sbjct: 454 YFANSPFTYDNIAVDWEDANSDYAKQYENEEL-----------SWSNLKDLTDVEL---- 498

Query: 681 KPMLTNNN-------ALGRLPFLEYLGLRS----------TFIDSLPDSTPILFCLATLD 723
                N          L  LP L+ L +                 L D       +    
Sbjct: 499 ----YNCPNMTQLPDFLYDLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIFY 554

Query: 724 VSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLD 783
           + +  ++  P +    + + L  +    N  RH                         L+
Sbjct: 555 MGYNNLEEFPASASLQKMVKLGLLDCVHNKVRH-------------------------LE 589

Query: 784 YFRRLTSLRKLGLKCSSTTS----TSLKKEIIGAVLQLSELHSLKL----ICETPSYLPL 835
            F     L  L L             + ++         ++  L      +   P+    
Sbjct: 590 AFGTNVKLTDLKL------DYNQIEEIPEDFCA---FTDQVEGLGFSHNKLKYIPNIFNA 640

Query: 836 LEMAEHYKLQKLYLSG----HLPPNSVIGDRSF-PPNVVTLTLSQLRLEYDPMPILGRLR 890
             +   Y +  +  S         N       +   N  T+TLS   ++  P  +     
Sbjct: 641 KSV---YVMGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFATGS 697

Query: 891 QLKILRL 897
            +  + L
Sbjct: 698 PISTIIL 704

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 45.3 bits (107), Expect = 1e-04
 Identities = 32/245 (13%), Positives = 70/245 (28%), Gaps = 58/245 (23%)

Query: 659 LGKCISKRRLGMLKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFIDSLPDS 712
           +   +   +      + L         N               +  + L +  + S+P++
Sbjct: 663 ISCSMDDYKGINASTVTLSY-------NEIQKFPTELFATGSPISTIILSNNLMTSIPEN 715

Query: 713 T----PILFC----LATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWET 764
           +       +     L T+D+   K+  L   F  +   YL+ + ++ N F         +
Sbjct: 716 SLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDFRATTLPYLSNMDVSYNCF---------S 766

Query: 765 SLQTLWGLCIKADEVQSLDYFRRLTSLRKLGL-KCSSTTSTSLKKEIIGAVLQLSELHSL 823
           S  T                    + L+  G+          + ++    +     L  L
Sbjct: 767 SFPTQ---------------PLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQL 811

Query: 824 KLICETPSYLP--LLEMAEHYKLQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYD 881
           ++       +   L       +L  L ++ +  PN  I   S  P    +      L YD
Sbjct: 812 QIGSNDIRKVDEKLTP-----QLYILDIADN--PNISIDVTSVCPY---IEAGMYVLLYD 861

Query: 882 PMPIL 886
               +
Sbjct: 862 KTQDI 866

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 44.5 bits (105), Expect = 2e-04
 Identities = 35/271 (12%), Positives = 68/271 (25%), Gaps = 68/271 (25%)

Query: 667 RLGMLKVLDLEGVYKPMLTNNN-----ALGRLPFLEYLGLRSTFIDSLPDST-PILFCLA 720
           ++  L +LD          +N      A G    L  L L    I+ +P+        + 
Sbjct: 571 KMVKLGLLDCV--------HNKVRHLEAFGTNVKLTDLKLDYNQIEEIPEDFCAFTDQVE 622

Query: 721 TLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQ 780
            L  SH K++ +P  F       +  +  + N             + +          + 
Sbjct: 623 GLGFSHNKLKYIPNIFNAKSVYVMGSVDFSYN------------KIGSEG------RNIS 664

Query: 781 SLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELH----SLKLICETPSYLPLL 836
                 +  +   + L  S         E+      +S +      +  I E        
Sbjct: 665 CSMDDYKGINASTVTL--SYNEIQKFPTELFATGSPISTIILSNNLMTSIPENSLKPKDG 722

Query: 837 EMAEHYKLQKLYLSG----HLPPNSVIGD--------------RSFPPNVVTLT-LSQLR 877
                Y L  + L       L  +                    SFP   +  + L    
Sbjct: 723 NYKNTYLLTTIDLRFNKLTSLSDDFRATTLPYLSNMDVSYNCFSSFPTQPLNSSQLKAFG 782

Query: 878 LEY----------DPMP-ILGRLRQLKILRL 897
           + +             P  +     L  L++
Sbjct: 783 IRHQRDAEGNRILRQWPTGITTCPSLIQLQI 813

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 45.5 bits (108), Expect = 6e-05
 Identities = 55/256 (21%), Positives = 94/256 (36%), Gaps = 60/256 (23%)

Query: 671 LKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFIDSLPDST-PILFCLATLD 723
            ++L+L         N       N+   L  LE L L    I ++       L  L TL+
Sbjct: 66  TRLLNLHE-------NQIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLE 118

Query: 724 VSHTKVQRLPY-AFWPS---RHLYL--NWI-FLATNVFRHPQFVKWETSLQTLWGLCIKA 776
           +   ++  +P  AF      + L+L  N I  + +  F           + +L  L +  
Sbjct: 119 LFDNRLTTIPNGAFVYLSKLKELWLRNNPIESIPSYAFNR---------IPSLRRLDL-- 167

Query: 777 DEVQSLDY-----FRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPS 831
            E++ L Y     F  L++LR L L        +L++  I  +  L +L  L L     S
Sbjct: 168 GELKRLSYISEGAFEGLSNLRYLNL-----AMCNLRE--IPNLTPLIKLDELDL-----S 215

Query: 832 YLPLLEMAEH-----YKLQKLYLSG-HLPPNSVIGDRSFP--PNVVTLTLSQLRLEYDPM 883
              L  +          LQKL++    +    VI   +F    ++V + L+   L   P 
Sbjct: 216 GNHLSAIRPGSFQGLMHLQKLWMIQSQI---QVIERNAFDNLQSLVEINLAHNNLTLLPH 272

Query: 884 PILGRLRQLKILRLFG 899
            +   L  L+ + L  
Sbjct: 273 DLFTPLHHLERIHLHH 288

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 45.3 bits (108), Expect = 7e-05
 Identities = 57/330 (17%), Positives = 93/330 (28%), Gaps = 74/330 (22%)

Query: 668 LGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHT 727
               ++    G       +       P    L LRS  +   PD    L  L  + +   
Sbjct: 55  SNNPQIETRTGRALKATADLLEDATQPGRVALELRSVPLPQFPDQAFRLSHLQHMTIDAA 114

Query: 728 KVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSL-DYFR 786
            +  LP                                L+TL    +  + +++L     
Sbjct: 115 GLMELPDTMQ---QF---------------------AGLETLT---LARNPLRALPASIA 147

Query: 787 RLTSLRKLGL-KCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQ 845
            L  LR+L +  C     T L +  + +     E   L                    LQ
Sbjct: 148 SLNRLRELSIRACPE--LTELPEP-LASTDASGEHQGLV------------------NLQ 186

Query: 846 KLYLSG----HLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGS 901
            L L       LP +  I +     N+ +L +    L     P +  L +L+ L L G +
Sbjct: 187 SLRLEWTGIRSLPAS--IANLQ---NLKSLKIRNSPLSALG-PAIHHLPKLEELDLRGCT 240

Query: 902 YTGEEMSCSSGEFPNLLVLKLWKLNRLRQ--WRIKEGAMPCLRQLEIRSCGYL--VPP-- 955
                     G    L  L L   + L      I    +  L +L++R C  L  +P   
Sbjct: 241 AL-RNYPPIFGGRAPLKRLILKDCSNLLTLPLDI--HRLTQLEKLDLRGCVNLSRLPSLI 297

Query: 956 ---TGLKH--VTSSLREFLLTNMPSTFGSV 980
                     V   L+  L  + P    + 
Sbjct: 298 AQLPANCIILVPPHLQAQLDQHRPVARPAE 327

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Length = 386

 Score = 45.1 bits (106), Expect = 7e-05
 Identities = 23/131 (17%), Positives = 49/131 (37%), Gaps = 5/131 (3%)

Query: 278 LIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV 337
           + G  G+GKT + + V +++  K+   K   V+I    +     VLAD+L+ +D  +   
Sbjct: 50  IYGLTGTGKTAVVKFVLSKL-HKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFT 108

Query: 338 EATLSAEELMWRITQALDDSTFLIVMEN----AEHQKSQVWDSFLGKLCSFTQCGKIIIT 393
             +++              S  +IV++      +     +            +     I 
Sbjct: 109 GLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIG 168

Query: 394 TSSTEDFVEPL 404
            ++   FV+ L
Sbjct: 169 ITNDVKFVDLL 179

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae} Length = 597

 Score = 45.3 bits (107), Expect = 9e-05
 Identities = 43/250 (17%), Positives = 76/250 (30%), Gaps = 56/250 (22%)

Query: 667 RLGMLKVLDLEGVYKPMLTNNN-------ALGRLPFLEYLGLRSTFIDSLPDST-PILFC 718
            L   K++           N+         L     +E L L    I+ +          
Sbjct: 49  TLNNQKIVTF--------KNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHT 100

Query: 719 LATLDVSHTKVQRLP-YAFWPS---RHLYL--NWI-FLATNVFRHPQFVKWETSLQTLWG 771
           +  L +    ++ LP + F        L L  N +  L   +F +            L  
Sbjct: 101 IQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHN---------TPKLTT 151

Query: 772 LCIKADEVQSLDY--FRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICET 829
           L +  + ++ ++   F+  TSL+ L L  SS   T +          +  L    +    
Sbjct: 152 LSMSNNNLERIEDDTFQATTSLQNLQL--SSNRLTHVDLS------LIPSLFHANV---- 199

Query: 830 PSYLPLLEMAEHYKLQKLYLSGHLPPN--SVIGDRSFPPNVVTLTLSQLRLEYDPMPILG 887
            SY  L  +A    +++L  S     N  +V+        +  L L    L       L 
Sbjct: 200 -SYNLLSTLAIPIAVEELDASH----NSINVVRGPVN-VELTILKLQHNNLT--DTAWLL 251

Query: 888 RLRQLKILRL 897
               L  + L
Sbjct: 252 NYPGLVEVDL 261

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 44.6 bits (106), Expect = 1e-04
 Identities = 42/249 (16%), Positives = 76/249 (30%), Gaps = 54/249 (21%)

Query: 667 RLGMLKVLDLEGVYKPMLTNN------NALGRLPFLEYLGLRSTFIDSLPDST-PILFCL 719
            L   K++  +        +         L     +E L L    I+ +          +
Sbjct: 43  TLNNQKIVTFKN-------STMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTI 95

Query: 720 ATLDVSHTKVQRLP-YAFWPS---RHLYL--NWI-FLATNVFRHPQFVKWETSLQTLWGL 772
             L +    ++ LP + F        L L  N +  L   +F +            L  L
Sbjct: 96  QKLYMGFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHN---------TPKLTTL 146

Query: 773 CIKADEVQSLDY--FRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETP 830
            +  + ++ ++   F+  TSL+ L L  SS   T +          +  L    +     
Sbjct: 147 SMSNNNLERIEDDTFQATTSLQNLQL--SSNRLTHVDLS------LIPSLFHANV----- 193

Query: 831 SYLPLLEMAEHYKLQKLYLSGHLPPN--SVIGDRSFPPNVVTLTLSQLRLEYDPMPILGR 888
           SY  L  +A    +++L  S     N  +V+        +  L L    L       L  
Sbjct: 194 SYNLLSTLAIPIAVEELDASH----NSINVVRGPVN-VELTILKLQHNNLT--DTAWLLN 246

Query: 889 LRQLKILRL 897
              L  + L
Sbjct: 247 YPGLVEVDL 255

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae} Length = 318

 Score = 43.7 bits (102), Expect = 2e-04
 Identities = 20/130 (15%), Positives = 39/130 (30%), Gaps = 3/130 (2%)

Query: 276 IALIGKAGSGKTTLARIVYNRVYVK---RHFTKRAWVHIPIMSMVEDRDVLADILKQIDE 332
             +     S K  L   V + +      +      ++HI  + +     +   I   I +
Sbjct: 48  FYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISK 107

Query: 333 SLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIII 392
             L  + +L A                LI+++N E+  S+    +  K  S       II
Sbjct: 108 ENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSII 167

Query: 393 TTSSTEDFVE 402
                   + 
Sbjct: 168 CVGGHNVTIR 177

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens} Length = 353

 Score = 43.2 bits (102), Expect = 3e-04
 Identities = 45/261 (17%), Positives = 85/261 (32%), Gaps = 50/261 (19%)

Query: 666 RRLGMLKVLDLEGVYKPMLTNN-------NALGRLPFLEYLGLRSTFIDSLPDSTPILFC 718
           +R   L+ L L        T+N       ++   L  LE+L L   ++ +L  S    F 
Sbjct: 73  QRCVNLQALVL--------TSNGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSW---FK 121

Query: 719 ----LATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATN---------VFRHPQFVKWETS 765
               L  L++     + L      S    L  + +             F         T 
Sbjct: 122 PLSSLTFLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGL------TF 175

Query: 766 LQTLW--GLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAV--LQLSELH 821
           L+ L      +++ E +S    + + ++  L L         L +  +     ++  EL 
Sbjct: 176 LEELEIDASDLQSYEPKS---LKSIQNVSHLIL--HMKQHILLLEIFVDVTSSVECLELR 230

Query: 822 SLKLICETPSYLPLLEMAEHYK---LQKLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRL 878
              L     S L   E     K    + + ++       V+   +    ++ L  S+ +L
Sbjct: 231 DTDLDTFHFSELSTGETNSLIKKFTFRNVKIT-DESLFQVMKLLNQISGLLELEFSRNQL 289

Query: 879 EYDPMPILGRLRQLKILRLFG 899
           +  P  I  RL  L+ + L  
Sbjct: 290 KSVPDGIFDRLTSLQKIWLHT 310

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A* Length = 276

 Score = 42.7 bits (101), Expect = 3e-04
 Identities = 44/227 (19%), Positives = 71/227 (31%), Gaps = 52/227 (22%)

Query: 687 NNALGRLPFLEYLGLRSTFIDSLPDSTPI-LFCLATLDVSHTKVQRLPY-AFWP---SRH 741
           + +    P L+ L L    I ++ D     L  L+TL ++   +Q L   AF      + 
Sbjct: 45  SYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQK 104

Query: 742 LYL--NWIF-LATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKC 798
           L      +  L      H        +L+ L          +  +YF  LT+L  L    
Sbjct: 105 LVAVETNLASLENFPIGHL------KTLKELNVAHNLIQSFKLPEYFSNLTNLEHLD--- 155

Query: 799 SSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSV 858
                           L  +++ S+   C     L         ++  L LS  L  N +
Sbjct: 156 ----------------LSSNKIQSIY--CTDLRVLH--------QMPLLNLSLDLSLNPM 189

Query: 859 IGDRSFPPNV------VTLTLSQLRLEYDPMPILGRLRQLKILRLFG 899
                  P          L L   +L+  P  I  RL  L+ + L  
Sbjct: 190 ---NFIQPGAFKEIRLKELALDTNQLKSVPDGIFDRLTSLQKIWLHT 233

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri} Length = 306

 Score = 42.7 bits (101), Expect = 4e-04
 Identities = 40/234 (17%), Positives = 62/234 (26%), Gaps = 58/234 (24%)

Query: 684 LTNNN-------ALGRLPFLEYLGLRS---TFIDSLPDSTPILFCLATLDVSHTKVQRLP 733
           L +N           +L  L  L L S   +F      S      L  LD+S   V  + 
Sbjct: 35  LESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMS 94

Query: 734 YAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRK 793
             F       L  +    +            +L+ +               F  L +L  
Sbjct: 95  SNFLGLEQ--LEHLDFQHS------------NLKQMS----------EFSVFLSLRNLIY 130

Query: 794 LGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHY------KLQKL 847
           L +  S T +        G    LS L  LK+     +     E            L  L
Sbjct: 131 LDI--SHTHTRVAFN---GIFNGLSSLEVLKM-----AGNSFQENFLPDIFTELRNLTFL 180

Query: 848 YLSGHLPPN--SVIGDRSFP--PNVVTLTLSQLRLEYDPMPILGRLRQLKILRL 897
            LS          +   +F    ++  L +S              L  L++L  
Sbjct: 181 DLSQ----CQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDY 230

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A* Length = 455

 Score = 43.2 bits (102), Expect = 4e-04
 Identities = 39/261 (14%), Positives = 71/261 (27%), Gaps = 34/261 (13%)

Query: 666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDST-PILFCLATLDV 724
            RL  L+ L +E     ++  NN    L  L  L L       L       L  L  L +
Sbjct: 51  SRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTL 110

Query: 725 SHTKVQRL---PYAFWPSRHLYLNWIFLATN----VFRHPQFVKWETSLQTLWGL----- 772
           +   +         F P     L  + L  N    +     F+        L  L     
Sbjct: 111 TQCNLDGAVLSGNFFKPLTS--LEMLVLRDNNIKKIQPASFFLNM-RRFHVLD-LTFNKV 166

Query: 773 -CIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSL-----KLI 826
             I  +++ +    +  T LR   +         L  E  G   + + + +L        
Sbjct: 167 KSICEEDLLNFQG-KHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFK 225

Query: 827 CETPSY----LPLLEMAEHYKLQKLYLSGHLPPNSV--IGDRSF----PPNVVTLTLSQL 876
                     +   ++          +       +     + +F       V T  LS+ 
Sbjct: 226 ESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTNFKDPDNFTFKGLEASGVKTCDLSKS 285

Query: 877 RLEYDPMPILGRLRQLKILRL 897
           ++      +      L+ L L
Sbjct: 286 KIFALLKSVFSHFTDLEQLTL 306

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens} Length = 520

 Score = 42.2 bits (99), Expect = 8e-04
 Identities = 36/283 (12%), Positives = 71/283 (25%), Gaps = 70/283 (24%)

Query: 667 RLGMLKVLDLEGVYKPMLTNNNALGRLPF-----LEYLGLRSTFIDSLPDSTPI--LFCL 719
               L+ LDL         ++N L ++       L++L L     D+LP       +  L
Sbjct: 67  FNQELEYLDL---------SHNKLVKISCHPTVNLKHLDLSFNAFDALPICKEFGNMSQL 117

Query: 720 ATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGL------- 772
             L +S T +++         ++    + L                LQ            
Sbjct: 118 KFLGLSTTHLEKSSVLPIAHLNISKVLLVLGETYGEKEDP----EGLQDFNTESLHIVFP 173

Query: 773 ------------------------------CIKADEVQSLDYFRRLTSLRKLGLKCSSTT 802
                                            +  +  L   +    L  L L    TT
Sbjct: 174 TNKEFHFILDVSVKTVANLELSNIKCVLEDNKCSYFLSILAKLQTNPKLSNLTLNNIETT 233

Query: 803 STSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHLPPNSVIGDR 862
             S  +  I  ++  + +    +              ++       LS H   + V    
Sbjct: 234 WNSFIR--ILQLVWHTTVWYFSISNVKLQGQLDFRDFDYSGTSLKALSIHQVVSDVF--- 288

Query: 863 SFPPNVVTLTLSQLRLEY--------DPMPILGRLRQLKILRL 897
            FP + +    S + ++           M    ++     L  
Sbjct: 289 GFPQSYIYEIFSNMNIKNFTVSGTRMVHMLCPSKISPFLHLDF 331

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	1007
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	4e-26
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	1e-05
d1np6a_	170	c.37.1.10 (A:) Molybdopterin-guanine dinucleotide	0.001
d1ye8a1	178	c.37.1.11 (A:1-178) Hypothetical kinase-like prote	0.004

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score =  107 bits (267), Expect = 4e-26
 Identities = 33/250 (13%), Positives = 81/250 (32%), Gaps = 29/250 (11%)

Query: 273 TQVIALIGKAGSGKTTLARIVYN--RVYVKRHFTKRAWVHIPIMSMVEDRDVLADIL--- 327
           +  + L G+AGSGK+ +A    +     +  ++    W+     +     D+  DIL   
Sbjct: 44  SFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLML 103

Query: 328 --KQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFT 385
             +    +   VE   S           +D    L V ++   +++  W   L       
Sbjct: 104 KSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLR---- 159

Query: 386 QCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIK 445
                 + T+   +           + V  L  +E ++           +      +   
Sbjct: 160 -----CLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYG-----MPMPVGEKEED 209

Query: 446 LKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERANGDNL------VALCYQDLP 499
           +  + + +  G P  +++       K  ++E+ +++  +     L          Y+ L 
Sbjct: 210 VLNKTIELSSGNPATLMMFFKSCEPK--TFEKMAQLNNKLESRGLVGVECITPYSYKSLA 267

Query: 500 AQVKPCILYM 509
             ++ C+  +
Sbjct: 268 MALQRCVEVL 277

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]} Length = 305

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 46.2 bits (108), Expect = 1e-05
 Identities = 44/283 (15%), Positives = 80/283 (28%), Gaps = 38/283 (13%)

Query: 666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVS 725
           + L  L  L L       + +  A   L  LE L L    +  LP+              
Sbjct: 52  KNLKNLHTLILINNKISKI-SPGAFAPLVKLERLYLSKNQLKELPEK------------- 97

Query: 726 HTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYF 785
                       P     L          R   F      +    G             F
Sbjct: 98  -----------MPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAF 146

Query: 786 RRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQ 845
           + +  L  + +  + T  T++ + +         L  L L     + +    +     L 
Sbjct: 147 QGMKKLSYIRI--ADTNITTIPQGL------PPSLTELHLDGNKITKVDAASLKGLNNLA 198

Query: 846 KLYLSGHLPPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYT-- 903
           KL LS +       G  +  P++  L L+  +L   P  +    + ++++ L   + +  
Sbjct: 199 KLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGL-ADHKYIQVVYLHNNNISAI 257

Query: 904 GEEMSCSSGEFPNLLVLKLWKL--NRLRQWRIKEGAMPCLRQL 944
           G    C  G            L  N ++ W I+     C+   
Sbjct: 258 GSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVR 300

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]} Length = 170

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

 Score = 38.4 bits (88), Expect = 0.001
 Identities = 22/143 (15%), Positives = 48/143 (33%), Gaps = 13/143 (9%)

Query: 275 VIALIGKAGSGKTTLARIVYN-------RVYVKRHFTKRAWVHIP------IMSMVEDRD 321
           ++A    +G+GKTTL + +         R  + +H      V  P      +      + 
Sbjct: 4   LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIKHTHHDMDVDKPGKDSYELRKAGAAQT 63

Query: 322 VLADILKQIDESLLKVEATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKL 381
           ++A   +    +    E  L  + L  R+  +  D   +   ++ E  K  ++    G  
Sbjct: 64  IVASQQRWALMTETPDEEELDLQFLASRMDTSKLDLILVEGFKHEEIAKIVLFRDGAGHR 123

Query: 382 CSFTQCGKIIITTSSTEDFVEPL 404
                  + +I  +S       +
Sbjct: 124 PEELVIDRHVIAVASDVPLNLDV 146

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]} Length = 178

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

 Score = 37.3 bits (85), Expect = 0.004
 Identities = 15/135 (11%), Positives = 37/135 (27%), Gaps = 15/135 (11%)

Query: 276 IALIGKAGSGKTTLARIVYN---------RVYVKRHFTKRAWVHIPIMSMVEDRDVLADI 326
           I + G+ G GKTTL + +                R    +      I++    + + +  
Sbjct: 3   IIITGEPGVGKTTLVKKIVERLGKRAIGFWTEEVRDPETKKRTGFRIITTEGKKKIFSSK 62

Query: 327 LKQIDESLLKVEATLSAEELMW------RITQALDDSTFLIVMENAEHQKSQVWDSFLGK 380
                + +      +   E +          +A  D   +I+++     +          
Sbjct: 63  FFTSKKLVGSYGVNVQYFEELAIPILERAYREAKKDRRKVIIIDEIGKMELFSKKFRDLV 122

Query: 381 LCSFTQCGKIIITTS 395
                     ++ T 
Sbjct: 123 RQIMHDPNVNVVATI 137

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	1007
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.92
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.89
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.85
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.85
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.83
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.82
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.75
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.74
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.72
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.7
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.65
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.65
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.64
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.61
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.55
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.53
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.53
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.53
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.49
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.46
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.46
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.44
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.27
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.22
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	99.19
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.18
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.16
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.16
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.04
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.03
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	98.98
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.98
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.97
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	98.95
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.94
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.92
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.88
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.88
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	98.87
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.82
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.81
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.81
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	98.79
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.72
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.69
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.63
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.61
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.59
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.57
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.51
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.49
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.48
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.48
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.45
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.44
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.41
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.1
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.97
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.88
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.59
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.48
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.45
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.39
d1okkd2	207	GTPase domain of the signal recognition particle r	97.33
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.31
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.29
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.25
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.19
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.19
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.18
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.16
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.01
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.0
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.98
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	96.96
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.95
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.85
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	96.82
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	96.79
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.77
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.76
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.72
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.71
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.69
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.67
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	96.67
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.62
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.61
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.61
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.59
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.54
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.5
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.46
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	96.46
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	96.44
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.44
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.37
d1xpua3	289	Transcription termination factor Rho, ATPase domai	96.36
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.34
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.32
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.32
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.29
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.24
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.21
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.19
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.19
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.17
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.14
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.13
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	96.02
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.01
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.98
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.89
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.88
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	95.87
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.84
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.73
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	95.7
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	95.7
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	95.69
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.64
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.59
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.55
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.49
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.47
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	95.46
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.46
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.43
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.4
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.4
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	95.32
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.23
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.21
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	95.2
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.11
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	95.11
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.1
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.08
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	95.03
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.03
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	94.92
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	94.88
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.85
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.74
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.72
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.67
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.48
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	94.25
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.21
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	94.07
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.05
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.03
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	94.03
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	94.0
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	94.0
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	93.93
d1g2912	240	Maltose transport protein MalK, N-terminal domain	93.79
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	93.79
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	93.78
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	93.77
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	93.74
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.72
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	93.68
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	93.68
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.62
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	93.57
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	93.53
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	93.47
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	93.37
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	93.32
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	93.18
d2awna2	232	Maltose transport protein MalK, N-terminal domain	93.09
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	93.06
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	93.03
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	92.9
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.81
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	92.68
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	92.64
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	92.62
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	92.61
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	92.6
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	92.59
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	92.56
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	92.5
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	92.49
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	92.49
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.48
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	92.47
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	92.45
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	92.45
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	92.44
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	92.37
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	92.33
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	92.31
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	92.3
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	92.3
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.27
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	92.27
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	92.25
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.24
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	92.24
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.23
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	92.22
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	92.09
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.08
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.07
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	92.02
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	91.89
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	91.87
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	91.86
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	91.84
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	91.75
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	91.71
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	91.68
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	91.65
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	91.61
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	91.52
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.52
d2fh5b1	207	Signal recognition particle receptor beta-subunit	91.51
d1nrjb_	209	Signal recognition particle receptor beta-subunit	91.51
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.5
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.39
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	91.35
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	91.3
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	91.29
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	91.22
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	91.2
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	91.19
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	91.13
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	91.09
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	91.05
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.04
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	90.96
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	90.95
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	90.73
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	90.57
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	90.56
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	90.55
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	90.5
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	90.49
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	90.49
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	90.43
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	90.41
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.22
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	89.9
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	89.83
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	89.8
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	89.77
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	89.66
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	89.3
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	89.16
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	88.75
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	88.7
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	88.7
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	88.27
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	88.05
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	88.03
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	87.73
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	87.39
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	87.32
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	87.25
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.17
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	87.13
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	86.03
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	85.57
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	85.36
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	85.31
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	84.48
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	83.99
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	82.96
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	82.3
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	81.8
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	80.93
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	80.77
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	80.36
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	80.21
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	80.1

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=0  Score=306.86  Aligned_cols=248  Identities=12%  Similarity=0.141  Sum_probs=201.2

Q ss_pred             CCCCCCCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC
Q ss_conf             55677517725021999998412788888865554321013321013677642347898768999888801110263224
Q 001843          186 CAEDETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQS  265 (1007)
Q Consensus       186 ~~~~~~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (1007)
                      .......+|||+.++++|+++|....+                                                ...  
T Consensus        15 ~~p~~~~~~gR~~~~~~i~~~L~~~~~------------------------------------------------~~~--   44 (277)
T d2a5yb3          15 NVPKQMTCYIREYHVDRVIKKLDEMCD------------------------------------------------LDS--   44 (277)
T ss_dssp             TCBCCCCSCCCHHHHHHHHHHHHHHTT------------------------------------------------SSS--
T ss_pred             CCCCCCCEECCHHHHHHHHHHHHHCCC------------------------------------------------CCC--
T ss_conf             899988623739999999999873468------------------------------------------------784--


Q ss_pred             CCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH--CCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHH------
Q ss_conf             678999968999993899808899999985320--003788269999268988898999999999975533211------
Q 001843          266 SSTTTTTTQVIALIGKAGSGKTTLARIVYNRVY--VKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV------  337 (1007)
Q Consensus       266 ~~~~~~~~~vi~I~G~gGiGKTtLA~~v~~~~~--v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~------  337 (1007)
                              ++|+|+||||+||||||+++|++..  ...+|++++|++++  +.++...+...+...+.......      
T Consensus        45 --------~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs--~~~~~~~l~~~~~~~~~~~~~~~~~~~~~  114 (277)
T d2a5yb3          45 --------FFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDS--GTAPKSTFDLFTDILLMLKSEDDLLNFPS  114 (277)
T ss_dssp             --------EEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECC--CCSTTHHHHHHHHHHHHHTTTSCCTTCCC
T ss_pred             --------EEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEC--CCCCHHHHHHHHHHHHHHHCCHHHCCCCC
T ss_conf             --------08999779978889999999985565540127648999936--87777789999999998722022027863


Q ss_pred             -CCCCCHHHHHHHHHHHCCCCCEEEEEECCCCCCCHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCC
Q ss_conf             -0233899999999988199837999929675570001121022377799948999848873112233785203664999
Q 001843          338 -EATLSAEELMWRITQALDDSTFLIVMENAEHQKSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGL  416 (1007)
Q Consensus       338 -~~~~~~~~l~~~l~~~L~~kr~LiVlDdv~~~~~~~w~~l~~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L  416 (1007)
                       ....+.......+...+.++|+|+|+||+|  +...|..+.      ..||+||||||+.. ++..+....+.|+|++|
T Consensus       115 ~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~--~~~~~~~~~------~~~srilvTTR~~~-v~~~~~~~~~~~~l~~L  185 (277)
T d2a5yb3         115 VEHVTSVVLKRMICNALIDRPNTLFVFDDVV--QEETIRWAQ------ELRLRCLVTTRDVE-ISNAASQTCEFIEVTSL  185 (277)
T ss_dssp             CTTCCHHHHHHHHHHHHTTSTTEEEEEEEEC--CHHHHHHHH------HTTCEEEEEESBGG-GGGGCCSCEEEEECCCC
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCEEEECCHHH--HHHHHHHHC------CCCCEEEEEEEHHH-HHHHCCCCCCEEECCCC
T ss_conf             2123369999999999844688167525066--776655520------45755999964489-99863788716877889


Q ss_pred             CHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHCC------CCHH
Q ss_conf             9799999999630124432357994899999999998199726999999775179999689999998703------3023
Q 001843          417 GKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLSTKQPSYEEWSKVIERAN------GDNL  490 (1007)
Q Consensus       417 ~~~ea~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~lg~~L~~~~~~~~~w~~~l~~l~------~~~~  490 (1007)
                      +.++||+||.+++|....     ++..++++++|+++|+|+|||++++|+.|+.++  .+.|.+..+.+.      +..+
T Consensus       186 ~~~ea~~Lf~~~~~~~~~-----~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~--~~~~~~~~~~L~~~~~~~v~~i  258 (277)
T d2a5yb3         186 EIDECYDFLEAYGMPMPV-----GEKEEDVLNKTIELSSGNPATLMMFFKSCEPKT--FEKMAQLNNKLESRGLVGVECI  258 (277)
T ss_dssp             CHHHHHHHHHHTSCCCC-------CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSS--HHHHHHHHHHHHHHCSSTTCCC
T ss_pred             CHHHHHHHHHHHHCCCCC-----CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC--HHHHHHHHHHHHCCCHHHHHHH
T ss_conf             979999999998477667-----425679999999995899899999999865598--9999999999734867889999


Q ss_pred             HHHHHCCCCCCCHHHHHHH
Q ss_conf             6642038954763366641
Q 001843          491 VALCYQDLPAQVKPCILYM  509 (1007)
Q Consensus       491 l~~sy~~L~~~~k~cfl~l  509 (1007)
                      +.+||++||+++|+||-++
T Consensus       259 l~~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         259 TPYSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             SSSSSSSHHHHHHHHHHTS
T ss_pred             HHHHHHCCCHHHHHHHHHC
T ss_conf             9998851269999999739

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.92  E-value=3.1e-23  Score=149.43  Aligned_cols=299  Identities=16%  Similarity=0.160  Sum_probs=144.7

Q ss_pred             CCCCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCC
Q ss_conf             77750099995255679980123433102334489883019992688789867870006987685885136777534832
Q 001843          633 LSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDS  712 (1007)
Q Consensus       633 ~~~~LRsL~l~~~~~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~  712 (1007)
                      ++.+|++|.+.++.+.         .+.. +  ..++.|++|++++|.+.  .++ .++++.+|++|++++|.+..++ .
T Consensus        42 ~l~~l~~L~l~~~~I~---------~l~g-l--~~L~nL~~L~Ls~N~l~--~l~-~l~~L~~L~~L~L~~n~i~~i~-~  105 (384)
T d2omza2          42 DLDQVTTLQADRLGIK---------SIDG-V--EYLNNLTQINFSNNQLT--DIT-PLKNLTKLVDILMNNNQIADIT-P  105 (384)
T ss_dssp             HHTTCCEEECCSSCCC---------CCTT-G--GGCTTCCEEECCSSCCC--CCG-GGTTCTTCCEEECCSSCCCCCG-G
T ss_pred             HHCCCCEEECCCCCCC---------CCCC-C--CCCCCCCEEECCCCCCC--CCC-CCCCCCCCCCCCCCCCCCCCCC-C
T ss_conf             9578789989998987---------7624-2--45899998968188179--886-3347711010301343332222-1


Q ss_pred             CCCCCCCCEEEECCCCCCCCCCCCCCC--CEECCCC-----CCCC---------------------------------CC
Q ss_conf             326879989861587432134422333--5020332-----1233---------------------------------43
Q 001843          713 TPILFCLATLDVSHTKVQRLPYAFWPS--RHLYLNW-----IFLA---------------------------------TN  752 (1007)
Q Consensus       713 i~~L~~L~~Ldl~~~~l~~lP~~i~~L--r~L~l~~-----~~~~---------------------------------~~  752 (1007)
                      ++.+++|+.|++.++.+..++......  ..+....     ....                                 ..
T Consensus       106 l~~l~~L~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  185 (384)
T d2omza2         106 LANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSN  185 (384)
T ss_dssp             GTTCTTCCEEECCSSCCCCCGGGTTCTTCSEEEEEEEEECCCGGGTTCTTCSEEEEEESCCCCGGGTTCTTCCEEECCSS
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCC
T ss_conf             11233433344332222222222222222112134663131002322221122222123220111124542110112224


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCC
Q ss_conf             43466435676877542303637875437376513899994985306888403689889975158997758985259997
Q 001843          753 VFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSY  832 (1007)
Q Consensus       753 ~~~lp~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~i~~~~~~~~~l~~~~~~~l~~l~~L~~L~l~~~~~~~  832 (1007)
                      ....+.....++++..+..   ...........+..++|+.|.+.++.  ...+     ..+..+++|+.|.+..+... 
T Consensus       186 ~~~~~~~~~~l~~~~~l~l---~~n~i~~~~~~~~~~~L~~L~l~~n~--l~~~-----~~l~~l~~L~~L~l~~n~l~-  254 (384)
T d2omza2         186 KVSDISVLAKLTNLESLIA---TNNQISDITPLGILTNLDELSLNGNQ--LKDI-----GTLASLTNLTDLDLANNQIS-  254 (384)
T ss_dssp             CCCCCGGGGGCTTCSEEEC---CSSCCCCCGGGGGCTTCCEEECCSSC--CCCC-----GGGGGCTTCSEEECCSSCCC-
T ss_pred             CCCCCCCCCCCCCCCEEEC---CCCCCCCCCCCCCCCCCCEEECCCCC--CCCC-----CHHHCCCCCCHHCCCCCCCC-
T ss_conf             3332110022353233303---57744787864445778788887777--7896-----13432565341004467447-


Q ss_pred             CCCCCCCCCCCCCEEEECCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCCCEEECC
Q ss_conf             792223379998578824558-9999576578999915999972204779967112587774999526875897024428
Q 001843          833 LPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSS  911 (1007)
Q Consensus       833 ~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~l~~l~~Lp~L~~L~L~~~~~~~~~l~~~~  911 (1007)
                       ....+..+++|+.|.++++. ..++.  +.. ++.+..+.+..+.+.  .++.+..+++++.|+++++...+  +. ..
T Consensus       255 -~~~~~~~~~~L~~L~l~~~~l~~~~~--~~~-~~~l~~l~~~~n~l~--~~~~~~~~~~l~~L~ls~n~l~~--l~-~l  325 (384)
T d2omza2         255 -NLAPLSGLTKLTELKLGANQISNISP--LAG-LTALTNLELNENQLE--DISPISNLKNLTYLTLYFNNISD--IS-PV  325 (384)
T ss_dssp             -CCGGGTTCTTCSEEECCSSCCCCCGG--GTT-CTTCSEEECCSSCCS--CCGGGGGCTTCSEEECCSSCCSC--CG-GG
T ss_pred             -CCCCCCCCCCCCEEECCCCCCCCCCC--CCC-CCCCCCCCCCCCCCC--CCCCCCHHCCCCEEECCCCCCCC--CC-CC
T ss_conf             -87753554668775456744578773--235-652222332323333--32210000246767777887789--84-53


Q ss_pred             CCCCCCCEEEECCCCCCCCEEECCCCCCCCCEEEEECCCCCC-CCCCCCCCCCCCCEEEECC
Q ss_conf             999988689962479986458768977653475750367878-8867300003766899236
Q 001843          912 GEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLTN  972 (1007)
Q Consensus       912 ~~fp~L~~L~L~~~~~l~~l~~~~~~~p~L~~L~i~~C~~L~-lp~~l~~L~~~Lk~L~i~~  972 (1007)
                      ..+|+|+.|.+.++ .++.++ ....+|+|+.|++++| +++ ++. +.++ ++|+.|++++
T Consensus       326 ~~l~~L~~L~L~~n-~l~~l~-~l~~l~~L~~L~l~~N-~l~~l~~-l~~l-~~L~~L~L~~  382 (384)
T d2omza2         326 SSLTKLQRLFFANN-KVSDVS-SLANLTNINWLSAGHN-QISDLTP-LANL-TRITQLGLND  382 (384)
T ss_dssp             GGCTTCCEEECCSS-CCCCCG-GGGGCTTCCEEECCSS-CCCBCGG-GTTC-TTCSEEECCC
T ss_pred             CCCCCCCEEECCCC-CCCCCH-HHCCCCCCCEEECCCC-CCCCCHH-HCCC-CCCCEEECCC
T ss_conf             66898898989899-899974-6708999998989799-5899800-0039-9999963978

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.89  E-value=6.8e-21  Score=135.75  Aligned_cols=278  Identities=15%  Similarity=0.129  Sum_probs=174.9

Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC--CCCCCCEEC
Q ss_conf             898830199926887898678700069876858851367775348323268799898615874321344--223335020
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPY--AFWPSRHLY  743 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP~--~i~~Lr~L~  743 (1007)
                      ..+..|++|+++++.+.  .+ ..+..+.+|++|++++|.++.+|. +++|++|++|++++|.+..++.  .+.+|+.|+
T Consensus        41 ~~l~~l~~L~l~~~~I~--~l-~gl~~L~nL~~L~Ls~N~l~~l~~-l~~L~~L~~L~L~~n~i~~i~~l~~l~~L~~L~  116 (384)
T d2omza2          41 TDLDQVTTLQADRLGIK--SI-DGVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQIADITPLANLTNLTGLT  116 (384)
T ss_dssp             HHHTTCCEEECCSSCCC--CC-TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCCGGGTTCTTCCEEE
T ss_pred             HHHCCCCEEECCCCCCC--CC-CCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             89578789989998987--76-242458999989681881798863-347711010301343332222111233433344


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCC----------------------------------------EEECCCCCCCHH
Q ss_conf             3321233434346643567687754230----------------------------------------363787543737
Q 001843          744 LNWIFLATNVFRHPQFVKWETSLQTLWG----------------------------------------LCIKADEVQSLD  783 (1007)
Q Consensus       744 l~~~~~~~~~~~lp~~i~~L~~L~~L~~----------------------------------------~~~~~~~~~~~~  783 (1007)
                      +.   ++. ...++. ......+..+..                                        ............
T Consensus       117 ~~---~~~-~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  191 (384)
T d2omza2         117 LF---NNQ-ITDIDP-LKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDIS  191 (384)
T ss_dssp             CC---SSC-CCCCGG-GTTCTTCSEEEEEEEEECCCGGGTTCTTCSEEEEEESCCCCGGGTTCTTCCEEECCSSCCCCCG
T ss_pred             CC---CCC-CCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf             33---222-222222-2222222112134663131002322221122222123220111124542110112224333211


Q ss_pred             HHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEECCCC-CCCCCCCCC
Q ss_conf             6513899994985306888403689889975158997758985259997792223379998578824558-999957657
Q 001843          784 YFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDR  862 (1007)
Q Consensus       784 ~l~~L~~L~~L~i~~~~~~~~~l~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~  862 (1007)
                      ....++++..+.+..+.  ...+     .....+++|+.|.++++...  .+..+..+++|+.|.+.++. ..++.  +.
T Consensus       192 ~~~~l~~~~~l~l~~n~--i~~~-----~~~~~~~~L~~L~l~~n~l~--~~~~l~~l~~L~~L~l~~n~l~~~~~--~~  260 (384)
T d2omza2         192 VLAKLTNLESLIATNNQ--ISDI-----TPLGILTNLDELSLNGNQLK--DIGTLASLTNLTDLDLANNQISNLAP--LS  260 (384)
T ss_dssp             GGGGCTTCSEEECCSSC--CCCC-----GGGGGCTTCCEEECCSSCCC--CCGGGGGCTTCSEEECCSSCCCCCGG--GT
T ss_pred             CCCCCCCCCEEECCCCC--CCCC-----CCCCCCCCCCEEECCCCCCC--CCCHHHCCCCCCHHCCCCCCCCCCCC--CC
T ss_conf             00223532333035774--4787-----86444577878888777778--96134325653410044674478775--35


Q ss_pred             CCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCCCEEECCCCCCCCCEEEECCCCCCCCEEECCCCCCCCC
Q ss_conf             89999159999722047799671125877749995268758970244289999886899624799864587689776534
Q 001843          863 SFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLR  942 (1007)
Q Consensus       863 ~~l~~L~~L~L~~~~l~~~~l~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~~~l~~l~~~~~~~p~L~  942 (1007)
                      . +++|+.|.++++.+.  .++.+..++.++.+.+..+...+  + .....++.++.|.++++ .+..+. ....+|+|+
T Consensus       261 ~-~~~L~~L~l~~~~l~--~~~~~~~~~~l~~l~~~~n~l~~--~-~~~~~~~~l~~L~ls~n-~l~~l~-~l~~l~~L~  332 (384)
T d2omza2         261 G-LTKLTELKLGANQIS--NISPLAGLTALTNLELNENQLED--I-SPISNLKNLTYLTLYFN-NISDIS-PVSSLTKLQ  332 (384)
T ss_dssp             T-CTTCSEEECCSSCCC--CCGGGTTCTTCSEEECCSSCCSC--C-GGGGGCTTCSEEECCSS-CCSCCG-GGGGCTTCC
T ss_pred             C-CCCCCEEECCCCCCC--CCCCCCCCCCCCCCCCCCCCCCC--C-CCCCHHCCCCEEECCCC-CCCCCC-CCCCCCCCC
T ss_conf             5-466877545674457--87732356522223323233333--2-21000024676777788-778984-536689889


Q ss_pred             EEEEECCCCCC-CCCCCCCCCCCCCEEEECCCC
Q ss_conf             75750367878-886730000376689923698
Q 001843          943 QLEIRSCGYLV-PPTGLKHVTSSLREFLLTNMP  974 (1007)
Q Consensus       943 ~L~i~~C~~L~-lp~~l~~L~~~Lk~L~i~~~~  974 (1007)
                      +|++++| +++ ++ .+..+ ++|+.|+++++.
T Consensus       333 ~L~L~~n-~l~~l~-~l~~l-~~L~~L~l~~N~  362 (384)
T d2omza2         333 RLFFANN-KVSDVS-SLANL-TNINWLSAGHNQ  362 (384)
T ss_dssp             EEECCSS-CCCCCG-GGGGC-TTCCEEECCSSC
T ss_pred             EEECCCC-CCCCCH-HHCCC-CCCCEEECCCCC
T ss_conf             8989899-899974-67089-999989897995

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.85  E-value=4.4e-20  Score=131.02  Aligned_cols=75  Identities=21%  Similarity=0.204  Sum_probs=54.3

Q ss_pred             CCCCEEEECCCCCCCCCCCC-CCCCCCCCCEEECCCCCCCCC-CCCCCCCCCCCEEEECCCCCCCCCCCCC-CCCEECCC
Q ss_conf             83019992688789867870-006987685885136777534-8323268799898615874321344223-33502033
Q 001843          669 GMLKVLDLEGVYKPMLTNNN-ALGRLPFLEYLGLRSTFIDSL-PDSTPILFCLATLDVSHTKVQRLPYAFW-PSRHLYLN  745 (1007)
Q Consensus       669 ~~LrvLdL~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~L-P~~i~~L~~L~~Ldl~~~~l~~lP~~i~-~Lr~L~l~  745 (1007)
                      +.+++|++++|.+.  .+|. .|.++.+|++|+++++.+..+ |..+.++++|++|++++|.++.+|..+. .++.|...
T Consensus        31 ~~l~~L~Ls~N~i~--~l~~~~f~~l~~L~~L~l~~n~~~~i~~~~f~~l~~L~~L~l~~n~l~~l~~~~~~~l~~L~~~  108 (305)
T d1xkua_          31 PDTALLDLQNNKIT--EIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVH  108 (305)
T ss_dssp             TTCCEEECCSSCCC--CBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCSSCCTTCCEEECC
T ss_pred             CCCCEEECCCCCCC--CCCHHHHHCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCEECCCCCCCCCCCCCHHHHHHHHHCC
T ss_conf             99798978499189--8696576046565231123443445235665279855783156875676764001113232102

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=99.85  E-value=1e-21  Score=140.50  Aligned_cols=220  Identities=16%  Similarity=0.069  Sum_probs=96.8

Q ss_pred             CCCCEEEECCCCCCCC-CCCCCCCCCCCCCEEECCC-CCCC-CCCCCCCCCCCCCEEEECCCCCCCCCC-CCCC---CCE
Q ss_conf             8301999268878986-7870006987685885136-7775-348323268799898615874321344-2233---350
Q 001843          669 GMLKVLDLEGVYKPML-TNNNALGRLPFLEYLGLRS-TFID-SLPDSTPILFCLATLDVSHTKVQRLPY-AFWP---SRH  741 (1007)
Q Consensus       669 ~~LrvLdL~~~~~~~~-~lp~~i~~L~~Lr~L~L~~-~~i~-~LP~~i~~L~~L~~Ldl~~~~l~~lP~-~i~~---Lr~  741 (1007)
                      .+++.|+|+++.+.+. .+|..++++.+|++|+|++ +.+. .+|.+|++|++|++|++++|.+..++. .+..   |++
T Consensus        50 ~~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~L~~  129 (313)
T d1ogqa_          50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVT  129 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCE
T ss_pred             EEEEEEECCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCHHHHCC
T ss_conf             79889989899888888798478467533520202654333002431145420011020356434433222220111001


Q ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHHHCCCCC-CEEEEEECCCCCH-HHHHHHHHHHHCCCC
Q ss_conf             20332123343434664356768775423036378754373765138999-9498530688840-368988997515899
Q 001843          742 LYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSL-RKLGLKCSSTTST-SLKKEIIGAVLQLSE  819 (1007)
Q Consensus       742 L~l~~~~~~~~~~~lp~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L-~~L~i~~~~~~~~-~l~~~~~~~l~~l~~  819 (1007)
                      +++.   .+.....+|..+++++.|+.+.... +......+..+..+..+ +.+.+..+.  .. ..+    ..+..+..
T Consensus       130 l~l~---~N~~~~~~p~~l~~l~~L~~l~l~~-n~l~~~ip~~~~~l~~l~~~l~~~~n~--l~~~~~----~~~~~l~~  199 (313)
T d1ogqa_         130 LDFS---YNALSGTLPPSISSLPNLVGITFDG-NRISGAIPDSYGSFSKLFTSMTISRNR--LTGKIP----PTFANLNL  199 (313)
T ss_dssp             EECC---SSEEESCCCGGGGGCTTCCEEECCS-SCCEEECCGGGGCCCTTCCEEECCSSE--EEEECC----GGGGGCCC
T ss_pred             CCCC---CCCCCCCCCHHHCCCCCCCEEECCC-CCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCC----CCCCCCCC
T ss_conf             1112---2455556851220674000000235-533562031214431123231022464--353324----33222222


Q ss_pred             CCEEEEEECCCCCCCCCCCCCCCCCCEEEECCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEE
Q ss_conf             7758985259997792223379998578824558-999957657899991599997220477996711258777499952
Q 001843          820 LHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLF  898 (1007)
Q Consensus       820 L~~L~l~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~l~~l~~Lp~L~~L~L~  898 (1007)
                      + .+.+..+.........+...+.|+.+.+.++. ...+. .+.. +++|+.|+|++|.+....+..++.+++|+.|+|+
T Consensus       200 ~-~l~l~~~~~~~~~~~~~~~~~~l~~l~~~~~~l~~~~~-~~~~-~~~L~~L~Ls~N~l~g~iP~~l~~L~~L~~L~Ls  276 (313)
T d1ogqa_         200 A-FVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFDLG-KVGL-SKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVS  276 (313)
T ss_dssp             S-EEECCSSEEEECCGGGCCTTSCCSEEECCSSEECCBGG-GCCC-CTTCCEEECCSSCCEECCCGGGGGCTTCCEEECC
T ss_pred             C-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCC-CCCCCCCCCCCCEECCCCCHHHHCCCCCCEEECC
T ss_conf             2-33333343322222222222221112222222222222-2224-5544444476570666087688479999989795


Q ss_pred             CCC
Q ss_conf             687
Q 001843          899 GGS  901 (1007)
Q Consensus       899 ~~~  901 (1007)
                      +|.
T Consensus       277 ~N~  279 (313)
T d1ogqa_         277 FNN  279 (313)
T ss_dssp             SSE
T ss_pred             CCC
T ss_conf             883

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=99.83  E-value=6.2e-21  Score=136.00  Aligned_cols=247  Identities=15%  Similarity=0.054  Sum_probs=172.6

Q ss_pred             CCCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECC-CCCCCCCCCCCCCCCCCCCEEECCCCCCCCCC-C
Q ss_conf             775009999525567998012343310233448988301999268-87898678700069876858851367775348-3
Q 001843          634 SWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEG-VYKPMLTNNNALGRLPFLEYLGLRSTFIDSLP-D  711 (1007)
Q Consensus       634 ~~~LRsL~l~~~~~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~-~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP-~  711 (1007)
                      ..+++.|.+.++...+..      .++..+  ..++.|++|+|++ +.+.+ .+|..|+++.+|++|+|++|.+..++ .
T Consensus        49 ~~~v~~L~L~~~~l~g~~------~lp~~l--~~L~~L~~L~Ls~~N~l~g-~iP~~i~~L~~L~~L~Ls~N~l~~~~~~  119 (313)
T d1ogqa_          49 TYRVNNLDLSGLNLPKPY------PIPSSL--ANLPYLNFLYIGGINNLVG-PIPPAIAKLTQLHYLYITHTNVSGAIPD  119 (313)
T ss_dssp             CCCEEEEEEECCCCSSCE------ECCGGG--GGCTTCSEEEEEEETTEES-CCCGGGGGCTTCSEEEEEEECCEEECCG
T ss_pred             CEEEEEEECCCCCCCCCC------CCCHHH--HCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCHHHHCCCCCCCCCCC
T ss_conf             479889989899888888------798478--4675335202026543330-0243114542001102035643443322


Q ss_pred             CCCCCCCCCEEEECCC-CCCCCCCCCCCC---CEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHHHC
Q ss_conf             2326879989861587-432134422333---502033212334343466435676877542303637875437376513
Q 001843          712 STPILFCLATLDVSHT-KVQRLPYAFWPS---RHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRR  787 (1007)
Q Consensus       712 ~i~~L~~L~~Ldl~~~-~l~~lP~~i~~L---r~L~l~~~~~~~~~~~lp~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~  787 (1007)
                      .+..+.+|+++++..+ ....+|..+..+   +++++.   ++.....+|..+..+..+...-....+......+..+..
T Consensus       120 ~~~~~~~L~~l~l~~N~~~~~~p~~l~~l~~L~~l~l~---~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~~~  196 (313)
T d1ogqa_         120 FLSQIKTLVTLDFSYNALSGTLPPSISSLPNLVGITFD---GNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFAN  196 (313)
T ss_dssp             GGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECC---SSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGGG
T ss_pred             CCCCHHHHCCCCCCCCCCCCCCCHHHCCCCCCCEEECC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             22201110011112245555685122067400000023---553356203121443112323102246435332433222


Q ss_pred             CCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEECCCC--CCCCCCCCCCCC
Q ss_conf             899994985306888403689889975158997758985259997792223379998578824558--999957657899
Q 001843          788 LTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL--PPNSVIGDRSFP  865 (1007)
Q Consensus       788 L~~L~~L~i~~~~~~~~~l~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~l~~~~~L~~L~L~g~~--~~lp~~~i~~~l  865 (1007)
                      +..+ .+.+..+. .....+    ..+..+++++.+.+..+.... .+..+..+++|+.|+++++.  ..+|. ++.. +
T Consensus       197 l~~~-~l~l~~~~-~~~~~~----~~~~~~~~l~~l~~~~~~l~~-~~~~~~~~~~L~~L~Ls~N~l~g~iP~-~l~~-L  267 (313)
T d1ogqa_         197 LNLA-FVDLSRNM-LEGDAS----VLFGSDKNTQKIHLAKNSLAF-DLGKVGLSKNLNGLDLRNNRIYGTLPQ-GLTQ-L  267 (313)
T ss_dssp             CCCS-EEECCSSE-EEECCG----GGCCTTSCCSEEECCSSEECC-BGGGCCCCTTCCEEECCSSCCEECCCG-GGGG-C
T ss_pred             CCCC-CCCCCCCC-CCCCCC----CCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCEECCCCCH-HHHC-C
T ss_conf             2222-33333343-322222----222222221112222222222-222222455444444765706660876-8847-9


Q ss_pred             CCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf             9915999972204779967112587774999526875
Q 001843          866 PNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSY  902 (1007)
Q Consensus       866 ~~L~~L~L~~~~l~~~~l~~l~~Lp~L~~L~L~~~~~  902 (1007)
                      ++|+.|+|++|.+.. .+|.++.+.+|+.+.+.+|..
T Consensus       268 ~~L~~L~Ls~N~l~g-~iP~~~~L~~L~~l~l~~N~~  303 (313)
T d1ogqa_         268 KFLHSLNVSFNNLCG-EIPQGGNLQRFDVSAYANNKC  303 (313)
T ss_dssp             TTCCEEECCSSEEEE-ECCCSTTGGGSCGGGTCSSSE
T ss_pred             CCCCEEECCCCCCCC-CCCCCCCCCCCCHHHHCCCCC
T ss_conf             999989795883516-689866679989788688950

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.82  E-value=4e-18  Score=119.62  Aligned_cols=64  Identities=23%  Similarity=0.221  Sum_probs=28.1

Q ss_pred             CCCCCCCEEEECCCCCCCCCC-CCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCC
Q ss_conf             898830199926887898678-70006987685885136777534832326879989861587432134
Q 001843          666 RRLGMLKVLDLEGVYKPMLTN-NNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLP  733 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~~~~~l-p~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP  733 (1007)
                      ..++.|++|+++++.+.  .+ |..|.++.+|++|++++|.++.+|..+  ...|..|++..+.+..++
T Consensus        52 ~~l~~L~~L~l~~n~~~--~i~~~~f~~l~~L~~L~l~~n~l~~l~~~~--~~~l~~L~~~~n~l~~l~  116 (305)
T d1xkua_          52 KNLKNLHTLILINNKIS--KISPGAFAPLVKLERLYLSKNQLKELPEKM--PKTLQELRVHENEITKVR  116 (305)
T ss_dssp             TTCTTCCEEECCSSCCC--CBCTTTTTTCTTCCEEECCSSCCSBCCSSC--CTTCCEEECCSSCCCBBC
T ss_pred             HCCCCCCCCCCCCCCCC--CCCHHHHHCCCCCCEECCCCCCCCCCCCCH--HHHHHHHHCCCCCHHHHH
T ss_conf             04656523112344344--523566527985578315687567676400--111323210246102344

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=99.75  E-value=1.5e-15  Score=104.53  Aligned_cols=295  Identities=16%  Similarity=0.074  Sum_probs=146.2

Q ss_pred             EEEEEEECCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCC
Q ss_conf             48999955999888777677750099995255679980123433102334489883019992688789867870006987
Q 001843          615 VRRLAANLGSNSFPYSSLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLP  694 (1007)
Q Consensus       615 ~rrlsi~~~~~~~~~~~~~~~~LRsL~l~~~~~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~~~~~~~~lp~~i~~L~  694 (1007)
                      .++|.+..+....++..  .++|++|.+..+....         ++     ..+..|+.|+++++.+.  .++..   ..
T Consensus        40 l~~LdLs~~~L~~lp~~--~~~L~~L~Ls~N~l~~---------lp-----~~~~~L~~L~l~~n~l~--~l~~l---p~   98 (353)
T d1jl5a_          40 AHELELNNLGLSSLPEL--PPHLESLVASCNSLTE---------LP-----ELPQSLKSLLVDNNNLK--ALSDL---PP   98 (353)
T ss_dssp             CSEEECTTSCCSCCCSC--CTTCSEEECCSSCCSS---------CC-----CCCTTCCEEECCSSCCS--CCCSC---CT
T ss_pred             CCEEEECCCCCCCCCCC--CCCCCEEECCCCCCCC---------CC-----CCHHHHHHHHHHHCCCC--HHHHH---CC
T ss_conf             98999379998878898--7898889899997963---------36-----20332033266551432--03210---22


Q ss_pred             CCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE
Q ss_conf             68588513677753483232687998986158743213442233350203321233434346643567687754230363
Q 001843          695 FLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAFWPSRHLYLNWIFLATNVFRHPQFVKWETSLQTLWGLCI  774 (1007)
Q Consensus       695 ~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP~~i~~Lr~L~l~~~~~~~~~~~lp~~i~~L~~L~~L~~~~~  774 (1007)
                      .|++|+++++.+..+|. ++.+.+|++|+++++.+...|.....+..+.+.   .+.  ...+..++.++.++.|.....
T Consensus        99 ~L~~L~L~~n~l~~lp~-~~~l~~L~~L~l~~~~~~~~~~~~~~l~~l~~~---~~~--~~~~~~l~~l~~l~~L~l~~n  172 (353)
T d1jl5a_          99 LLEYLGVSNNQLEKLPE-LQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAG---NNQ--LEELPELQNLPFLTAIYADNN  172 (353)
T ss_dssp             TCCEEECCSSCCSSCCC-CTTCTTCCEEECCSSCCSCCCCCCTTCCEEECC---SSC--CSSCCCCTTCTTCCEEECCSS
T ss_pred             CCCCCCCCCCCCCCCCC-HHHHCCCEEECCCCCCCCCCCCCCCCCCCHHHC---CCC--CCCCCCCCCCCCCEECCCCCC
T ss_conf             11111334554322210-011013123113565100132233332100001---222--223332000122200111233


Q ss_pred             CCCCCCCHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCCCCCCCCCCCEEEECCCC-
Q ss_conf             7875437376513899994985306888403689889975158997758985259997792223379998578824558-
Q 001843          775 KADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYLPLLEMAEHYKLQKLYLSGHL-  853 (1007)
Q Consensus       775 ~~~~~~~~~~l~~L~~L~~L~i~~~~~~~~~l~~~~~~~l~~l~~L~~L~l~~~~~~~~~~~~l~~~~~L~~L~L~g~~-  853 (1007)
                      ...   ...  ........+......  ...+     .....++.|+.+.++.+.... .   .....++..+.+.... 
T Consensus       173 ~~~---~~~--~~~~~~~~l~~~~~~--~~~~-----~~~~~l~~L~~l~l~~n~~~~-~---~~~~~~l~~~~~~~~~~  236 (353)
T d1jl5a_         173 SLK---KLP--DLPLSLESIVAGNNI--LEEL-----PELQNLPFLTTIYADNNLLKT-L---PDLPPSLEALNVRDNYL  236 (353)
T ss_dssp             CCS---SCC--CCCTTCCEEECCSSC--CSSC-----CCCTTCTTCCEEECCSSCCSS-C---CSCCTTCCEEECCSSCC
T ss_pred             CCC---CCC--CCCCCCCCCCCCCCC--CCCC-----CCCCCCCCCCCCCCCCCCCCC-C---CCCCCCCCCCCCCCCCC
T ss_conf             443---222--212222223344432--2221-----223455533312225422234-5---53233433322233333


Q ss_pred             CCCCCCCCCCCCCCCEEEEEEEEECC---------------CCCC-CCCCCCCCCCEEEEECCCCCCCCEEECCCCCCCC
Q ss_conf             99995765789999159999722047---------------7996-7112587774999526875897024428999988
Q 001843          854 PPNSVIGDRSFPPNVVTLTLSQLRLE---------------YDPM-PILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNL  917 (1007)
Q Consensus       854 ~~lp~~~i~~~l~~L~~L~L~~~~l~---------------~~~l-~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L  917 (1007)
                      ...+. .    ++++..+.+..+...               ...+ .....+|+|+.|+|++|...  .++   ..+++|
T Consensus       237 ~~~~~-~----~~~l~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~L~~L~Ls~N~l~--~lp---~~~~~L  306 (353)
T d1jl5a_         237 TDLPE-L----PQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLCDLPPSLEELNVSNNKLI--ELP---ALPPRL  306 (353)
T ss_dssp             SCCCC-C----CTTCCEEECCSSCCSEESCCCTTCCEEECCSSCCSEECCCCTTCCEEECCSSCCS--CCC---CCCTTC
T ss_pred             CCCCC-C----CCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCEEECCCCCCC--CCC---CCCCCC
T ss_conf             44433-3----4432222222233322234530001233335753234566898898979799168--356---654879


Q ss_pred             CEEEECCCCCCCCEEECCCCCCCCCEEEEECCCCCC-CCCCCCCCCCCCCEEEEC
Q ss_conf             689962479986458768977653475750367878-886730000376689923
Q 001843          918 LVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLT  971 (1007)
Q Consensus       918 ~~L~L~~~~~l~~l~~~~~~~p~L~~L~i~~C~~L~-lp~~l~~L~~~Lk~L~i~  971 (1007)
                      +.|.+.++ .++.++   ..+++|+.|++++|+ ++ +|...    .+|+.|.+.
T Consensus       307 ~~L~L~~N-~L~~l~---~~~~~L~~L~L~~N~-L~~lp~~~----~~L~~L~~~  352 (353)
T d1jl5a_         307 ERLIASFN-HLAEVP---ELPQNLKQLHVEYNP-LREFPDIP----ESVEDLRMN  352 (353)
T ss_dssp             CEEECCSS-CCSCCC---CCCTTCCEEECCSSC-CSSCCCCC----TTCCEEECC
T ss_pred             CEEECCCC-CCCCCC---CCCCCCCEEECCCCC-CCCCCCCC----CCCCEEECC
T ss_conf             98989999-687545---322888989876991-89777652----656712896

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=99.74  E-value=2.6e-15  Score=103.15  Aligned_cols=122  Identities=20%  Similarity=0.223  Sum_probs=71.7

Q ss_pred             CCCCCCCCCCCEEEECCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCCCC----------
Q ss_conf             2223379998578824558-99995765789999159999722047799671125877749995268758----------
Q 001843          835 LLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYT----------  903 (1007)
Q Consensus       835 ~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~l~~l~~Lp~L~~L~L~~~~~~----------  903 (1007)
                      ......++.|+.+.++++. ..++.     ...++..+.+..+.+....    ...+++..+.+..+...          
T Consensus       197 ~~~~~~l~~L~~l~l~~n~~~~~~~-----~~~~l~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~l~~l~~~~~  267 (353)
T d1jl5a_         197 LPELQNLPFLTTIYADNNLLKTLPD-----LPPSLEALNVRDNYLTDLP----ELPQSLTFLDVSENIFSGLSELPPNLY  267 (353)
T ss_dssp             CCCCTTCTTCCEEECCSSCCSSCCS-----CCTTCCEEECCSSCCSCCC----CCCTTCCEEECCSSCCSEESCCCTTCC
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCCCCHHC
T ss_conf             1223455533312225422234553-----2334333222333334443----334432222222233322234530001


Q ss_pred             -----CCCEEECCCCCCCCCEEEECCCCCCCCEEECCCCCCCCCEEEEECCCCCC-CCCCCCCCCCCCCEEEECCCC
Q ss_conf             -----97024428999988689962479986458768977653475750367878-886730000376689923698
Q 001843          904 -----GEEMSCSSGEFPNLLVLKLWKLNRLRQWRIKEGAMPCLRQLEIRSCGYLV-PPTGLKHVTSSLREFLLTNMP  974 (1007)
Q Consensus       904 -----~~~l~~~~~~fp~L~~L~L~~~~~l~~l~~~~~~~p~L~~L~i~~C~~L~-lp~~l~~L~~~Lk~L~i~~~~  974 (1007)
                           ...+......+|+|++|.|+++ .+..++   ..+++|+.|++++| +++ +|..   + ++|++|++++|+
T Consensus       268 ~~~~~~~~~~~~~~~~~~L~~L~Ls~N-~l~~lp---~~~~~L~~L~L~~N-~L~~l~~~---~-~~L~~L~L~~N~  335 (353)
T d1jl5a_         268 YLNASSNEIRSLCDLPPSLEELNVSNN-KLIELP---ALPPRLERLIASFN-HLAEVPEL---P-QNLKQLHVEYNP  335 (353)
T ss_dssp             EEECCSSCCSEECCCCTTCCEEECCSS-CCSCCC---CCCTTCCEEECCSS-CCSCCCCC---C-TTCCEEECCSSC
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCC-CCCCCC---CCCCCCCEEECCCC-CCCCCCCC---C-CCCCEEECCCCC
T ss_conf             233335753234566898898979799-168356---65487998989999-68754532---2-888989876991

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1.5e-16  Score=110.44  Aligned_cols=213  Identities=19%  Similarity=0.099  Sum_probs=98.0

Q ss_pred             EEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCEEEECCCCCCCCCCCCCC----CCEECCCCC
Q ss_conf             999268878986787000698768588513677753483-232687998986158743213442233----350203321
Q 001843          673 VLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPD-STPILFCLATLDVSHTKVQRLPYAFWP----SRHLYLNWI  747 (1007)
Q Consensus       673 vLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~Ldl~~~~l~~lP~~i~~----Lr~L~l~~~  747 (1007)
                      +++.+++.+.  .+|..+.  ..+++|+|++|.++.+|. .+.++.+|++|+++++.+..++.....    ++++...  
T Consensus        15 ~v~c~~~~L~--~iP~~ip--~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~--   88 (284)
T d1ozna_          15 TTSCPQQGLQ--AVPVGIP--AASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLS--   88 (284)
T ss_dssp             EEECCSSCCS--SCCTTCC--TTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECC--
T ss_pred             EEECCCCCCC--CCCCCCC--CCCCEEECCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--
T ss_conf             9984799989--4497889--998889774881798797786414213000013445433211121222222222222--


Q ss_pred             CCCCCCCCC-CCCCCCCCCCCCCCCEEECCCCCCCHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEEE
Q ss_conf             233434346-6435676877542303637875437376513899994985306888403689889975158997758985
Q 001843          748 FLATNVFRH-PQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHSLKLI  826 (1007)
Q Consensus       748 ~~~~~~~~l-p~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~i~~~~~~~~~l~~~~~~~l~~l~~L~~L~l~  826 (1007)
                       .......+ +..+.++++|++|                         .+..+.  ...+.   ...+....+|+.+.+.
T Consensus        89 -~~~~~~~l~~~~~~~l~~L~~L-------------------------~l~~n~--~~~~~---~~~~~~~~~L~~l~l~  137 (284)
T d1ozna_          89 -DNAQLRSVDPATFHGLGRLHTL-------------------------HLDRCG--LQELG---PGLFRGLAALQYLYLQ  137 (284)
T ss_dssp             -SCTTCCCCCTTTTTTCTTCCEE-------------------------ECTTSC--CCCCC---TTTTTTCTTCCEEECC
T ss_pred             -CCCCCCCCCCHHHCCCCCCCEE-------------------------ECCCCC--CCCCC---CCCCCHHCCCCHHHHC
T ss_conf             -1022354462010101027787-------------------------568854--43201---3533200012110200


Q ss_pred             ECCCCCCCCCCCCCCCCCCEEEECCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCC
Q ss_conf             259997792223379998578824558-9999576578999915999972204779967112587774999526875897
Q 001843          827 CETPSYLPLLEMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGGSYTGE  905 (1007)
Q Consensus       827 ~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~l~~l~~Lp~L~~L~L~~~~~~~~  905 (1007)
                      .+.........+...++|+.|++.++. ..++..++.. +++|+.+.+.++.+.......++.+++|+.|+++.+.... 
T Consensus       138 ~N~l~~i~~~~f~~~~~L~~L~l~~N~l~~l~~~~f~~-l~~L~~l~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~i~~-  215 (284)
T d1ozna_         138 DNALQALPDDTFRDLGNLTHLFLHGNRISSVPERAFRG-LHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSA-  215 (284)
T ss_dssp             SSCCCCCCTTTTTTCTTCCEEECCSSCCCEECTTTTTT-CTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSC-
T ss_pred             CCCCCCCCHHHHCCCCCHHHCCCCCCCCCCCCHHHHCC-CCCCCHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCC-
T ss_conf             14314458057404340502231417656625666546-5634131421143466281676653200023333352210-


Q ss_pred             CEEECCCCCCCCCEEEECC
Q ss_conf             0244289999886899624
Q 001843          906 EMSCSSGEFPNLLVLKLWK  924 (1007)
Q Consensus       906 ~l~~~~~~fp~L~~L~L~~  924 (1007)
                      ......+.+++|+.|.+.+
T Consensus       216 ~~~~~~~~~~~L~~L~l~~  234 (284)
T d1ozna_         216 LPTEALAPLRALQYLRLND  234 (284)
T ss_dssp             CCHHHHTTCTTCCEEECCS
T ss_pred             CCCCCCCCCCCCCEEEECC
T ss_conf             0000235546568898119

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.8e-16  Score=108.86  Aligned_cols=61  Identities=10%  Similarity=0.036  Sum_probs=30.5

Q ss_pred             CCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCEEEECCCCCCCCC
Q ss_conf             8301999268878986787000698768588513677753483-2326879989861587432134
Q 001843          669 GMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPD-STPILFCLATLDVSHTKVQRLP  733 (1007)
Q Consensus       669 ~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~Ldl~~~~l~~lP  733 (1007)
                      ..+..++.+++.+.  .+|..+.  .+|++|+|++|.++.+|. .+.++++|++|++++|.+..+|
T Consensus        10 ~~~~~v~C~~~~L~--~iP~~lp--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N~l~~l~   71 (266)
T d1p9ag_          10 ASHLEVNCDKRNLT--ALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQ   71 (266)
T ss_dssp             TTCCEEECTTSCCS--SCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCCEEE
T ss_pred             CCCEEEECCCCCCC--EECCCCC--CCCCEEECCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf             89869980699988--6196757--68898988499289859778634565522135665444431

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2e-15  Score=103.90  Aligned_cols=65  Identities=28%  Similarity=0.212  Sum_probs=49.7

Q ss_pred             CCCCEEEECCCCCCCCCCC-CCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCC
Q ss_conf             8301999268878986787-0006987685885136777534832326879989861587432134422
Q 001843          669 GMLKVLDLEGVYKPMLTNN-NALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAF  736 (1007)
Q Consensus       669 ~~LrvLdL~~~~~~~~~lp-~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP~~i  736 (1007)
                      +.|++|+|++|.+.  .+| ..|.++.+|++|+|++|.++.+|. ++.+++|++|++++|.+...|..+
T Consensus        31 ~~l~~L~Ls~N~i~--~l~~~~f~~l~~L~~L~L~~N~l~~l~~-~~~l~~L~~L~Ls~N~l~~~~~~~   96 (266)
T d1p9ag_          31 KDTTILHLSENLLY--TFSLATLMPYTRLTQLNLDRAELTKLQV-DGTLPVLGTLDLSHNQLQSLPLLG   96 (266)
T ss_dssp             TTCCEEECTTSCCS--EEEGGGGTTCTTCCEEECTTSCCCEEEC-CSCCTTCCEEECCSSCCSSCCCCT
T ss_pred             CCCCEEECCCCCCC--CCCHHHHHCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             68898988499289--8597786345655221356654444311-111223211111222221111121

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.8e-15  Score=103.01  Aligned_cols=197  Identities=21%  Similarity=0.166  Sum_probs=102.4

Q ss_pred             CCCEEEECCCCCCCCCCC-CCCCCCCCCCEEECCCCCCCCCCCC-CCCCCCCCEEEECCC-CCCCCCC-CCC---CCCEE
Q ss_conf             301999268878986787-0006987685885136777534832-326879989861587-4321344-223---33502
Q 001843          670 MLKVLDLEGVYKPMLTNN-NALGRLPFLEYLGLRSTFIDSLPDS-TPILFCLATLDVSHT-KVQRLPY-AFW---PSRHL  742 (1007)
Q Consensus       670 ~LrvLdL~~~~~~~~~lp-~~i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~Ldl~~~-~l~~lP~-~i~---~Lr~L  742 (1007)
                      .+++|+|++|.+.  .+| ..+.++.+|++|+++++.+..++.. +..+..+..+++... .+..++. .+.   +|+.|
T Consensus        33 ~~~~L~Ls~N~i~--~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~l~~L~~L  110 (284)
T d1ozna_          33 ASQRIFLHGNRIS--HVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTL  110 (284)
T ss_dssp             TCSEEECTTSCCC--EECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEE
T ss_pred             CCCEEECCCCCCC--CCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCEE
T ss_conf             9888977488179--87977864142130000134454332111212222222222221022354462010101027787


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCCE
Q ss_conf             03321233434346643567687754230363787543737651389999498530688840368988997515899775
Q 001843          743 YLNWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCSSTTSTSLKKEIIGAVLQLSELHS  822 (1007)
Q Consensus       743 ~l~~~~~~~~~~~lp~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~i~~~~~~~~~l~~~~~~~l~~l~~L~~  822 (1007)
                      ++.   .+......+..+..+.+|+.+                         .+..+.  ...+..   ..+..+++|+.
T Consensus       111 ~l~---~n~~~~~~~~~~~~~~~L~~l-------------------------~l~~N~--l~~i~~---~~f~~~~~L~~  157 (284)
T d1ozna_         111 HLD---RCGLQELGPGLFRGLAALQYL-------------------------YLQDNA--LQALPD---DTFRDLGNLTH  157 (284)
T ss_dssp             ECT---TSCCCCCCTTTTTTCTTCCEE-------------------------ECCSSC--CCCCCT---TTTTTCTTCCE
T ss_pred             ECC---CCCCCCCCCCCCCHHCCCCHH-------------------------HHCCCC--CCCCCH---HHHCCCCCHHH
T ss_conf             568---854432013533200012110-------------------------200143--144580---57404340502


Q ss_pred             EEEEECCCCCCCCCCCCCCCCCCEEEECCCC-CC-CCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECC
Q ss_conf             8985259997792223379998578824558-99-995765789999159999722047799671125877749995268
Q 001843          823 LKLICETPSYLPLLEMAEHYKLQKLYLSGHL-PP-NSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKILRLFGG  900 (1007)
Q Consensus       823 L~l~~~~~~~~~~~~l~~~~~L~~L~L~g~~-~~-lp~~~i~~~l~~L~~L~L~~~~l~~~~l~~l~~Lp~L~~L~L~~~  900 (1007)
                      |+++++.........+..+++|+.+.+.++. .. .|. ++.. +++|+.|+++++.+.......++.+++|+.|+|++|
T Consensus       158 L~l~~N~l~~l~~~~f~~l~~L~~l~l~~N~l~~i~~~-~f~~-l~~L~~L~l~~N~i~~~~~~~~~~~~~L~~L~l~~N  235 (284)
T d1ozna_         158 LFLHGNRISSVPERAFRGLHSLDRLLLHQNRVAHVHPH-AFRD-LGRLMTLYLFANNLSALPTEALAPLRALQYLRLNDN  235 (284)
T ss_dssp             EECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTT-TTTT-CTTCCEEECCSSCCSCCCHHHHTTCTTCCEEECCSS
T ss_pred             CCCCCCCCCCCCHHHHCCCCCCCHHHHHHCCCCCCCHH-HHHH-HHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCC
T ss_conf             23141765662566654656341314211434662816-7665-320002333335221000002355465688981199


Q ss_pred             CCC
Q ss_conf             758
Q 001843          901 SYT  903 (1007)
Q Consensus       901 ~~~  903 (1007)
                      ...
T Consensus       236 ~l~  238 (284)
T d1ozna_         236 PWV  238 (284)
T ss_dssp             CEE
T ss_pred             CCC
T ss_conf             887

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.64  E-value=1.9e-15  Score=103.95  Aligned_cols=55  Identities=13%  Similarity=0.093  Sum_probs=29.6

Q ss_pred             EEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCC
Q ss_conf             99268878986787000698768588513677753483232687998986158743213
Q 001843          674 LDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRL  732 (1007)
Q Consensus       674 LdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~l  732 (1007)
                      ++++.+.+.  .. ..+..+..|++|++.+++++.++ .+..+++|++|++++|.+..+
T Consensus        24 ~~l~~~~~~--d~-~~~~~l~~L~~L~l~~~~i~~l~-~l~~l~~L~~L~ls~n~i~~~   78 (227)
T d1h6ua2          24 IAAGKSNVT--DT-VTQADLDGITTLSAFGTGVTTIE-GVQYLNNLIGLELKDNQITDL   78 (227)
T ss_dssp             HHTTCSSTT--SE-ECHHHHHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCC
T ss_pred             HHHCCCCCC--CC-CCHHHCCCCCEEECCCCCCCCCH-HHHCCCCCCEEECCCCEEECC
T ss_conf             984888767--75-79878488689977799997664-574488883763578532025

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.61  E-value=1.6e-15  Score=104.41  Aligned_cols=63  Identities=21%  Similarity=0.161  Sum_probs=42.9

Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCC
Q ss_conf             8988301999268878986787000698768588513677753483232687998986158743213
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRL  732 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~l  732 (1007)
                      ..+..|+.|++.+|.+.  .++ .+.++.+|++|++++|.+..++ .+.++.+|++|++++|.++.+
T Consensus        38 ~~l~~L~~L~l~~~~i~--~l~-~l~~l~~L~~L~ls~n~i~~~~-~l~~l~~l~~l~~~~n~~~~i  100 (227)
T d1h6ua2          38 ADLDGITTLSAFGTGVT--TIE-GVQYLNNLIGLELKDNQITDLA-PLKNLTKITELELSGNPLKNV  100 (227)
T ss_dssp             HHHHTCCEEECTTSCCC--CCT-TGGGCTTCCEEECCSSCCCCCG-GGTTCCSCCEEECCSCCCSCC
T ss_pred             HHCCCCCEEECCCCCCC--CCH-HHHCCCCCCEEECCCCEEECCC-CCCCCCCCCCCCCCCCCCCCC
T ss_conf             78488689977799997--664-5744888837635785320254-311233432012111222222

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.1e-15  Score=105.27  Aligned_cols=61  Identities=30%  Similarity=0.283  Sum_probs=24.4

Q ss_pred             CCCCEEEEEEEEE-CCCCCCCCCCCCCCCCEEEEECCCCCCCCEEECCCCCCCCCEEEECCC
Q ss_conf             9991599997220-477996711258777499952687589702442899998868996247
Q 001843          865 PPNVVTLTLSQLR-LEYDPMPILGRLRQLKILRLFGGSYTGEEMSCSSGEFPNLLVLKLWKL  925 (1007)
Q Consensus       865 l~~L~~L~L~~~~-l~~~~l~~l~~Lp~L~~L~L~~~~~~~~~l~~~~~~fp~L~~L~L~~~  925 (1007)
                      +++|+.|++++|. +++..+..+..+|+|++|+|+++.............+|+|+.|.+.+|
T Consensus       174 ~~~L~~L~L~~~~~itd~~~~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~L~l~~~  235 (284)
T d2astb2         174 CPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGI  235 (284)
T ss_dssp             CTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTS
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHCCCCCCCEEECCCCCCCCHHHHHHHHCCCCCCEEEEECC
T ss_conf             22212355322347783033332135768779899999787378999726999898964488

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.53  E-value=1e-13  Score=93.85  Aligned_cols=54  Identities=19%  Similarity=0.242  Sum_probs=25.7

Q ss_pred             CCCCCCCCCEEEECCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCEE
Q ss_conf             23379998578824558-999957657899991599997220477996711258777499
Q 001843          837 EMAEHYKLQKLYLSGHL-PPNSVIGDRSFPPNVVTLTLSQLRLEYDPMPILGRLRQLKIL  895 (1007)
Q Consensus       837 ~l~~~~~L~~L~L~g~~-~~lp~~~i~~~l~~L~~L~L~~~~l~~~~l~~l~~Lp~L~~L  895 (1007)
                      .+..+++|+.|.+.++. ..++  .+.. +++|+.|++++|.+.  .++.++.+++|+.|
T Consensus       145 ~l~~~~~L~~L~l~~n~l~~l~--~l~~-l~~L~~L~ls~N~i~--~i~~l~~L~~L~~L  199 (199)
T d2omxa2         145 ALSGLTSLQQLNFSSNQVTDLK--PLAN-LTTLERLDISSNKVS--DISVLAKLTNLESL  199 (199)
T ss_dssp             GGTTCTTCSEEECCSSCCCCCG--GGTT-CTTCCEEECCSSCCC--CCGGGGGCTTCSEE
T ss_pred             CCCCCCCCCCCCCCCCCCCCCC--CCCC-CCCCCEEECCCCCCC--CCCCCCCCCCCCCC
T ss_conf             3332111111223455556770--1167-998999978799799--88101278998949

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.53  E-value=1.4e-13  Score=92.99  Aligned_cols=184  Identities=15%  Similarity=0.228  Sum_probs=102.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECC---CCCCCHHHHHHHHHHHHHHHHHH--------------
Q ss_conf             8999993899808899999985320003788269999268---98889899999999997553321--------------
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPI---MSMVEDRDVLADILKQIDESLLK--------------  336 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~---~~~~~~~~~l~~il~~l~~~~~~--------------  336 (1007)
                      +++.|+|++|+|||+|++++.+  .....   ..|+.+..   ........+...+..........              
T Consensus        30 ~~i~i~G~~G~GKTsLl~~~~~--~~~~~---~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  104 (283)
T d2fnaa2          30 PITLVLGLRRTGKSSIIKIGIN--ELNLP---YIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGI  104 (283)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH--HHTCC---EEEEEGGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTE
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HCCCC---EEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             8799986999829999999999--77998---699972145333324399999999997544555557777777753033


Q ss_pred             ------------HCCCCCHHHHHHHHHHHCCCCCEEEEEECCCCC----CCHHHHHHCCCCCCCCCCCEEEEECCCCCCC
Q ss_conf             ------------102338999999999881998379999296755----7000112102237779994899984887311
Q 001843          337 ------------VEATLSAEELMWRITQALDDSTFLIVMENAEHQ----KSQVWDSFLGKLCSFTQCGKIIITTSSTEDF  400 (1007)
Q Consensus       337 ------------~~~~~~~~~l~~~l~~~L~~kr~LiVlDdv~~~----~~~~w~~l~~l~~~~~~gskIiiTTR~~~~v  400 (1007)
                                  .....+...+.+.+. ...+++.++++|++..-    ....+..+...... ......+++.+... .
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~l~~l~-~~~~~~~~i~id~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~i~~~~~~~-~  181 (283)
T d2fnaa2         105 VIMGNEIKFNWNRKDRLSFANLLESFE-QASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDN-LKRIKFIMSGSEMG-L  181 (283)
T ss_dssp             EECSSSEEEC-----CCCHHHHHHHHH-HTCSSCEEEEEETGGGGGGCTTCCCHHHHHHHHHH-CTTEEEEEEESSHH-H
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHH-HHCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHH-HHHHHHHHCCCCCH-H
T ss_conf             434432223410013458999999987-63155554566405541333269999999999875-31134420356506-7


Q ss_pred             CCCC-----------CCCCEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf             2233-----------78520366499997999999996301244323579948999999999981997269999997751
Q 001843          401 VEPL-----------GAAFSTLHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRVVLLAGLLS  469 (1007)
Q Consensus       401 a~~~-----------~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai~~lg~~L~  469 (1007)
                      ....           +.....+.|.+++.+++.+++.+.......   . .+    ...+|++.++|.|..+..++..+.
T Consensus       182 ~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~---~-~~----~~~~i~~~~~G~P~~L~~~~~~~~  253 (283)
T d2fnaa2         182 LYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADI---D-FK----DYEVVYEKIGGIPGWLTYFGFIYL  253 (283)
T ss_dssp             HHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTC---C-CC----CHHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCHHCCCCEEEEEECCCCHHHHHHHHHHHHHHCCC---C-HH----HHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             899997542100010341058862887889999999966545699---9-99----999999996997999999999998


Q ss_pred             CCCC
Q ss_conf             7999
Q 001843          470 TKQP  473 (1007)
Q Consensus       470 ~~~~  473 (1007)
                      ....
T Consensus       254 ~~~~  257 (283)
T d2fnaa2         254 DNKN  257 (283)
T ss_dssp             HHCC
T ss_pred             HCCC
T ss_conf             0565

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.53  E-value=1.5e-13  Score=92.94  Aligned_cols=60  Identities=17%  Similarity=0.109  Sum_probs=29.1

Q ss_pred             CCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCC
Q ss_conf             8830199926887898678700069876858851367775348323268799898615874321
Q 001843          668 LGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQR  731 (1007)
Q Consensus       668 l~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~  731 (1007)
                      +..|+.|+++++.+.  .++ .+..+.+|++|++++|.++.++ .++.+++|++|++++|.++.
T Consensus        45 L~~L~~L~l~~~~i~--~l~-~l~~l~~L~~L~L~~n~i~~l~-~~~~l~~L~~L~l~~n~i~~  104 (210)
T d1h6ta2          45 LNSIDQIIANNSDIK--SVQ-GIQYLPNVTKLFLNGNKLTDIK-PLANLKNLGWLFLDENKVKD  104 (210)
T ss_dssp             HHTCCEEECTTSCCC--CCT-TGGGCTTCCEEECCSSCCCCCG-GGTTCTTCCEEECCSSCCCC
T ss_pred             HCCCCEEECCCCCCC--CCH-HHHHCCCCCEEECCCCCCCCCC-CCCCCCCCCCCCCCCCCCCC
T ss_conf             548458978279888--744-4764899898769896025860-11358621201433333212

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=6e-13  Score=89.39  Aligned_cols=55  Identities=13%  Similarity=-0.005  Sum_probs=33.8

Q ss_pred             CEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCC-CCCCCCCCEEEECCCCCC
Q ss_conf             19992688789867870006987685885136777534832-326879989861587432
Q 001843          672 KVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDS-TPILFCLATLDVSHTKVQ  730 (1007)
Q Consensus       672 rvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~Ldl~~~~l~  730 (1007)
                      ++++.++..+.  .+|..+.  .++++|++++|.++.+|.. +.++++|++|++++|.+.
T Consensus        11 ~~i~c~~~~l~--~iP~~l~--~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~   66 (242)
T d1xwdc1          11 RVFLCQESKVT--EIPSDLP--RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVL   66 (242)
T ss_dssp             SEEEEESCSCS--SCCSCSC--SCCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTC
T ss_pred             CEEEEECCCCC--CCCCCCC--CCCCEEECCCCCCCCCCHHHHHCCCHHHHHHHCCCCCC
T ss_conf             99998189988--7688889--98899987699189649668614643232110221124

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.46  E-value=6.3e-13  Score=89.28  Aligned_cols=40  Identities=15%  Similarity=0.141  Sum_probs=20.2

Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCC
Q ss_conf             98768588513677753483232687998986158743213
Q 001843          692 RLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRL  732 (1007)
Q Consensus       692 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~l  732 (1007)
                      .+..|++|+++++.++.++ .+..+++|++|++++|.+..+
T Consensus        44 ~L~~L~~L~l~~~~i~~l~-~l~~l~~L~~L~L~~n~i~~l   83 (210)
T d1h6ta2          44 ELNSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLNGNKLTDI   83 (210)
T ss_dssp             HHHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCC
T ss_pred             HHCCCCEEECCCCCCCCCH-HHHHCCCCCEEECCCCCCCCC
T ss_conf             9548458978279888744-476489989876989602586

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=1.5e-14  Score=98.79  Aligned_cols=59  Identities=17%  Similarity=0.126  Sum_probs=27.2

Q ss_pred             CCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCC-CCCCCCCCCCCCCEEEECCC
Q ss_conf             830199926887898678700069876858851367775-34832326879989861587
Q 001843          669 GMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFID-SLPDSTPILFCLATLDVSHT  727 (1007)
Q Consensus       669 ~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~-~LP~~i~~L~~L~~Ldl~~~  727 (1007)
                      ..|+.||+++|.+....+...+.++.+|++|+++++.+. ..+..++.+++|++|++++|
T Consensus        46 ~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~Ls~c  105 (284)
T d2astb2          46 FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC  105 (284)
T ss_dssp             BCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTC
T ss_pred             CCCCEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCC
T ss_conf             878878898984577799999974877651452346798678999851899757151001

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.44  E-value=8.9e-13  Score=88.37  Aligned_cols=37  Identities=19%  Similarity=0.173  Sum_probs=17.2

Q ss_pred             CCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCC
Q ss_conf             98768588513677753483232687998986158743
Q 001843          692 RLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKV  729 (1007)
Q Consensus       692 ~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l  729 (1007)
                      .+.+|++|+++++.++.++ .+..+++|++|++++|.+
T Consensus        38 ~l~~l~~L~l~~~~i~~l~-~l~~l~nL~~L~Ls~N~l   74 (199)
T d2omxa2          38 DLDQVTTLQADRLGIKSID-GVEYLNNLTQINFSNNQL   74 (199)
T ss_dssp             HHTTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCC
T ss_pred             HHCCCCEEECCCCCCCCCC-CCCCCCCCCCCCCCCCCC
T ss_conf             9468789989999997752-021378867575456556

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=1.2e-10  Score=75.92  Aligned_cols=57  Identities=12%  Similarity=-0.004  Sum_probs=33.3

Q ss_pred             CCCCEEEECCCCCCCCCCCC-CCCCCCCCCEEECCCCCCCC-CC-CCCCCCCCCCEEEECCC
Q ss_conf             83019992688789867870-00698768588513677753-48-32326879989861587
Q 001843          669 GMLKVLDLEGVYKPMLTNNN-ALGRLPFLEYLGLRSTFIDS-LP-DSTPILFCLATLDVSHT  727 (1007)
Q Consensus       669 ~~LrvLdL~~~~~~~~~lp~-~i~~L~~Lr~L~L~~~~i~~-LP-~~i~~L~~L~~Ldl~~~  727 (1007)
                      +.++.|+++++.+.  .+|. .|.++.+|++|+++++.+.. +| ..+..+.+++.|.+..+
T Consensus        29 ~~l~~L~Ls~n~i~--~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~   88 (242)
T d1xwdc1          29 RNAIELRFVLTKLR--VIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKA   88 (242)
T ss_dssp             SCCSEEEEESCCCC--EECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECC
T ss_pred             CCCCEEECCCCCCC--CCCHHHHHCCCHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCCC
T ss_conf             98899987699189--6496686146432321102211242010011222222222111112

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=2.3e-11  Score=80.09  Aligned_cols=77  Identities=23%  Similarity=0.218  Sum_probs=57.2

Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCC----CCCCCE
Q ss_conf             8988301999268878986787000698768588513677753483232687998986158743213442----233350
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYA----FWPSRH  741 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP~~----i~~Lr~  741 (1007)
                      ..+..||.|+|++|.+.  .++..+..+.+|++|+|++|.++.++ .+..+++|++|++++|.+..+|..    +..|++
T Consensus        15 ~n~~~lr~L~L~~n~I~--~i~~~~~~l~~L~~L~Ls~N~i~~l~-~~~~l~~L~~L~ls~N~i~~l~~~~~~~l~~L~~   91 (162)
T d1a9na_          15 TNAVRDRELDLRGYKIP--VIENLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLVNNNRICRIGEGLDQALPDLTE   91 (162)
T ss_dssp             ECTTSCEEEECTTSCCC--SCCCGGGGTTCCSEEECCSSCCCEEC-CCCCCSSCCEEECCSSCCCEECSCHHHHCTTCCE
T ss_pred             CCCCCCCEEECCCCCCC--CCCCCCCCCCCCCEEECCCCCCCCCC-CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             68574848978899788--65762004145998989799787647-7445761306431021345777632233453443


Q ss_pred             ECCC
Q ss_conf             2033
Q 001843          742 LYLN  745 (1007)
Q Consensus       742 L~l~  745 (1007)
                      |++.
T Consensus        92 L~L~   95 (162)
T d1a9na_          92 LILT   95 (162)
T ss_dssp             EECC
T ss_pred             CEEC
T ss_conf             4203

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=6.8e-14  Score=94.91  Aligned_cols=348  Identities=14%  Similarity=0.027  Sum_probs=170.7

Q ss_pred             CEEEEEEECCCCCCC--CC-CCCCCCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCC---CC
Q ss_conf             748999955999888--77-7677750099995255679980123433102334489883019992688789867---87
Q 001843          614 AVRRLAANLGSNSFP--YS-SLLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLT---NN  687 (1007)
Q Consensus       614 ~~rrlsi~~~~~~~~--~~-~~~~~~LRsL~l~~~~~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~~~~~~~~---lp  687 (1007)
                      +++.+.++++.....  .. ...++++++|.+.++........    .+...+  ..++.|+.|||++|.+.+..   +.
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~----~l~~~L--~~~~~L~~LdLs~N~i~~~~~~~l~   76 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCK----DISSAL--RVNPALAELNLRSNELGDVGVHCVL   76 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHH----HHHHHH--HTCTTCCEEECTTCCCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCCEEEECCCCCCHHHHH----HHHHHH--HCCCCCCEEECCCCCCCHHHHHHHH
T ss_conf             8777982089588689999997677999998289999889999----999998--5399988897959859728999999


Q ss_pred             CCCC-CCCCCCEEECCCCCCCC-----CCCCCCCCCCCCEEEECCCCCCCCC-----CCCCCC----CEECCCCCCCCCC
Q ss_conf             0006-98768588513677753-----4832326879989861587432134-----422333----5020332123343
Q 001843          688 NALG-RLPFLEYLGLRSTFIDS-----LPDSTPILFCLATLDVSHTKVQRLP-----YAFWPS----RHLYLNWIFLATN  752 (1007)
Q Consensus       688 ~~i~-~L~~Lr~L~L~~~~i~~-----LP~~i~~L~~L~~Ldl~~~~l~~lP-----~~i~~L----r~L~l~~~~~~~~  752 (1007)
                      ..+. ....|++|+|++|.++.     ++..+..+++|++|++++|.+...+     ..+...    ..+...   ....
T Consensus        77 ~~l~~~~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~~N~i~~~~~~~l~~~l~~~~~~~~~~~~~---~~~~  153 (460)
T d1z7xw1          77 QGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQLE---YCSL  153 (460)
T ss_dssp             HTTCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECT---TSCC
T ss_pred             HHHHCCCCCCCEEECCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCC---CCCC
T ss_conf             9984378877887788877543221012110000343200244433202345555443013554333222222---3222


Q ss_pred             -C---CCCCCCCCCCCCCCCC-----------------------------CCEEECCCC---CCCHHHHHCCCCCCEEEE
Q ss_conf             -4---3466435676877542-----------------------------303637875---437376513899994985
Q 001843          753 -V---FRHPQFVKWETSLQTL-----------------------------WGLCIKADE---VQSLDYFRRLTSLRKLGL  796 (1007)
Q Consensus       753 -~---~~lp~~i~~L~~L~~L-----------------------------~~~~~~~~~---~~~~~~l~~L~~L~~L~i  796 (1007)
                       .   ...-..+.....++.+                             ....+....   ......+.....++.+.+
T Consensus       154 ~~~~~~~~~~~l~~~~~~~~~~ls~~~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~  233 (460)
T d1z7xw1         154 SAASCEPLASVLRAKPDFKELTVSNNDINEAGVRVLCQGLKDSPCQLEALKLESCGVTSDNCRDLCGIVASKASLRELAL  233 (460)
T ss_dssp             BGGGHHHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHHHSCCCCCEEECTTSCCBTTHHHHHHHHHHHCTTCCEEEC
T ss_pred             CHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCH
T ss_conf             00110011222333322222332222124555543234332112210012411245421011012233222222100100


Q ss_pred             EECCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCCCC----CCCCCCCCCCCCEEEECCCC-CC-----CCCCCCCCCCC
Q ss_conf             3068884036898899751589977589852599977----92223379998578824558-99-----99576578999
Q 001843          797 KCSSTTSTSLKKEIIGAVLQLSELHSLKLICETPSYL----PLLEMAEHYKLQKLYLSGHL-PP-----NSVIGDRSFPP  866 (1007)
Q Consensus       797 ~~~~~~~~~l~~~~~~~l~~l~~L~~L~l~~~~~~~~----~~~~l~~~~~L~~L~L~g~~-~~-----lp~~~i~~~l~  866 (1007)
                      ..+..........+.........++.|+++.+.....    ....+...+.++.+.++++. ..     +.. .+.....
T Consensus       234 ~~n~~~~~~~~~~~~~~~~~~~~l~~l~l~~n~i~~~~~~~~~~~l~~~~~l~~l~l~~n~i~~~~~~~l~~-~l~~~~~  312 (460)
T d1z7xw1         234 GSNKLGDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGARLLCE-TLLEPGC  312 (460)
T ss_dssp             CSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHHHHHHHHH-HHTSTTC
T ss_pred             HHCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHC-CCCCCCC
T ss_conf             211223344201100011111110000134543321233433221112343334444433322456421110-1233344


Q ss_pred             CCEEEEEEEEECCCCCCCCC----CCCCCCCEEEEECCCCCCCCE---EECC-CCCCCCCEEEECCCCCCCCEEE-----
Q ss_conf             91599997220477996711----258777499952687589702---4428-9999886899624799864587-----
Q 001843          867 NVVTLTLSQLRLEYDPMPIL----GRLRQLKILRLFGGSYTGEEM---SCSS-GEFPNLLVLKLWKLNRLRQWRI-----  933 (1007)
Q Consensus       867 ~L~~L~L~~~~l~~~~l~~l----~~Lp~L~~L~L~~~~~~~~~l---~~~~-~~fp~L~~L~L~~~~~l~~l~~-----  933 (1007)
                      .|+.+.+++|.+....+..+    ...++|+.|+|+++....+.+   .... ...+.|+.|.|++| .++.-..     
T Consensus       313 ~L~~l~l~~~~l~~~~~~~l~~~~~~~~~L~~L~Ls~N~i~~~g~~~l~~~l~~~~~~L~~L~Ls~n-~i~~~~~~~l~~  391 (460)
T d1z7xw1         313 QLESLWVKSCSFTAACCSHFSSVLAQNRFLLELQISNNRLEDAGVRELCQGLGQPGSVLRVLWLADC-DVSDSSCSSLAA  391 (460)
T ss_dssp             CCCEEECTTSCCBGGGHHHHHHHHHHCSSCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTS-CCCHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHEEEECCCCCCCCHHHHHHHCCCCCCCEEECCCC-CCCHHHHHHHHH
T ss_conf             4333323334102334432133221101111320121013576640011122045677788989799-797599999999


Q ss_pred             CCCCCCCCCEEEEECCCCCC------CCCCCC-CCCCCCCEEEECCCC
Q ss_conf             68977653475750367878------886730-000376689923698
Q 001843          934 KEGAMPCLRQLEIRSCGYLV------PPTGLK-HVTSSLREFLLTNMP  974 (1007)
Q Consensus       934 ~~~~~p~L~~L~i~~C~~L~------lp~~l~-~L~~~Lk~L~i~~~~  974 (1007)
                      ....+++|++|+++++ ++.      +...+. .. +.|+.|.+.++.
T Consensus       392 ~l~~~~~L~~L~Ls~N-~i~~~g~~~l~~~l~~~~-~~L~~l~l~~~~  437 (460)
T d1z7xw1         392 TLLANHSLRELDLSNN-CLGDAGILQLVESVRQPG-CLLEQLVLYDIY  437 (460)
T ss_dssp             HHHHCCCCCEEECCSS-SCCHHHHHHHHHHHTSTT-CCCCEEECTTCC
T ss_pred             HHHCCCCCCEEECCCC-CCCHHHHHHHHHHHHHCC-CCCCEEECCCCC
T ss_conf             9962998898989999-698799999999997478-866789898987

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.18  E-value=3.9e-11  Score=78.77  Aligned_cols=71  Identities=23%  Similarity=0.257  Sum_probs=45.4

Q ss_pred             CEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC--CCCCCCEECCC
Q ss_conf             199926887898678700069876858851367775348323268799898615874321344--22333502033
Q 001843          672 KVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPY--AFWPSRHLYLN  745 (1007)
Q Consensus       672 rvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP~--~i~~Lr~L~l~  745 (1007)
                      |+|+|+++.+.  .++ .+..+.+|++|++++|.++.+|..++.+++|++|++++|.+..+|.  .+.+|++|++.
T Consensus         1 R~L~Ls~n~l~--~l~-~l~~l~~L~~L~ls~N~l~~lp~~~~~l~~L~~L~l~~N~i~~l~~~~~l~~L~~L~l~   73 (124)
T d1dcea3           1 RVLHLAHKDLT--VLC-HLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDGVANLPRLQELLLC   73 (124)
T ss_dssp             SEEECTTSCCS--SCC-CGGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCGGGTTCSSCCEEECC
T ss_pred             CEEECCCCCCC--CCC-CCCCCCCCCEEECCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEECC
T ss_conf             98986899898--871-01058988989797871686521565543135453243211235741233555768888

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.16  E-value=2.9e-09  Score=67.87  Aligned_cols=177  Identities=15%  Similarity=0.210  Sum_probs=107.8

Q ss_pred             CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             51772502199999841278888886555432101332101367764234789876899988880111026322467899
Q 001843          191 TDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTT  270 (1007)
Q Consensus       191 ~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (1007)
                      ..++||+.+++.+.++|...-.                                                       ..+
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~-------------------------------------------------------~~~   40 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLR-------------------------------------------------------NPG   40 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHH-------------------------------------------------------STT
T ss_pred             CCCCCHHHHHHHHHHHHHHHHH-------------------------------------------------------CCC
T ss_conf             8788779999999999999985-------------------------------------------------------789


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCC-EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             99689999938998088999999853200037882-69999268988898999999999975533211023389999999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTK-RAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~-~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      ..+..+.|+|++|+|||++|+.+++  ........ .+|+...  ........+..+....+..  ..........+...
T Consensus        41 ~~~~~lll~GppGtGKT~l~~~l~~--~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~  114 (276)
T d1fnna2          41 HHYPRATLLGRPGTGKTVTLRKLWE--LYKDKTTARFVYINGF--IYRNFTAIIGEIARSLNIP--FPRRGLSRDEFLAL  114 (276)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHHH--HHTTSCCCEEEEEETT--TCCSHHHHHHHHHHHTTCC--CCSSCCCHHHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHH--HHHCCCCCCEEEECCH--HHHHHHHHHHHHHHHHHHH--HHHHCCCHHHHHHH
T ss_conf             8888168889899989999999999--9754468857873230--0112466654567764334--55532543578999


Q ss_pred             HHHHCC--CCCEEEEEECCCCCCCHHHHHHC----CCCCCCCCCCEEEEECCCCCCCCCCCC-------CCCEEEECCCC
Q ss_conf             998819--98379999296755700011210----223777999489998488731122337-------85203664999
Q 001843          350 ITQALD--DSTFLIVMENAEHQKSQVWDSFL----GKLCSFTQCGKIIITTSSTEDFVEPLG-------AAFSTLHVPGL  416 (1007)
Q Consensus       350 l~~~L~--~kr~LiVlDdv~~~~~~~w~~l~----~l~~~~~~gskIiiTTR~~~~va~~~~-------~~~~~~~l~~L  416 (1007)
                      +...+.  .....+++|++++..........    ...........++.++.... ......       .. ..+.+.++
T Consensus       115 ~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~-~~~~~~~~~~~r~~~-~~i~~~~~  192 (276)
T d1fnna2         115 LVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDA-VLNNLDPSTRGIMGK-YVIRFSPY  192 (276)
T ss_dssp             HHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTH-HHHTSCHHHHHHHTT-CEEECCCC
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCHH-HHHHCCHHHHHHHCC-HHCCCCCH
T ss_conf             9998752065433203688875354310688887404433565248862587645-443113036655110-11034412


Q ss_pred             CHHHHHHHHHHHHC
Q ss_conf             97999999996301
Q 001843          417 GKNESWELFLKKAR  430 (1007)
Q Consensus       417 ~~~ea~~Lf~~~a~  430 (1007)
                      +.++.++++.+.+-
T Consensus       193 ~~~e~~~il~~r~~  206 (276)
T d1fnna2         193 TKDQIFDILLDRAK  206 (276)
T ss_dssp             BHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             38889999999999

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.16  E-value=5.5e-11  Score=77.95  Aligned_cols=100  Identities=13%  Similarity=0.035  Sum_probs=71.5

Q ss_pred             CCCCCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCC
Q ss_conf             67775009999525567998012343310233448988301999268878986787000698768588513677753483
Q 001843          632 LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPD  711 (1007)
Q Consensus       632 ~~~~~LRsL~l~~~~~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~  711 (1007)
                      ....++|.|.+.++.+.         .++..+  ..++.|++|++++|.+.  .++ .+..+.+|++|++++|.++.+|.
T Consensus        15 ~n~~~lr~L~L~~n~I~---------~i~~~~--~~l~~L~~L~Ls~N~i~--~l~-~~~~l~~L~~L~ls~N~i~~l~~   80 (162)
T d1a9na_          15 TNAVRDRELDLRGYKIP---------VIENLG--ATLDQFDAIDFSDNEIR--KLD-GFPLLRRLKTLLVNNNRICRIGE   80 (162)
T ss_dssp             ECTTSCEEEECTTSCCC---------SCCCGG--GGTTCCSEEECCSSCCC--EEC-CCCCCSSCCEEECCSSCCCEECS
T ss_pred             CCCCCCCEEECCCCCCC---------CCCCCC--CCCCCCCEEECCCCCCC--CCC-CCCCCCCHHHHHCCCCCCCCCCC
T ss_conf             68574848978899788---------657620--04145998989799787--647-74457613064310213457776


Q ss_pred             CC-CCCCCCCEEEECCCCCCCCCC--CC---CCCCEECCC
Q ss_conf             23-268799898615874321344--22---333502033
Q 001843          712 ST-PILFCLATLDVSHTKVQRLPY--AF---WPSRHLYLN  745 (1007)
Q Consensus       712 ~i-~~L~~L~~Ldl~~~~l~~lP~--~i---~~Lr~L~l~  745 (1007)
                      .+ ..+++|++|++++|.+..++.  .+   .+|++|++.
T Consensus        81 ~~~~~l~~L~~L~L~~N~i~~~~~l~~l~~l~~L~~L~l~  120 (162)
T d1a9na_          81 GLDQALPDLTELILTNNSLVELGDLDPLASLKSLTYLCIL  120 (162)
T ss_dssp             CHHHHCTTCCEEECCSCCCCCGGGGGGGGGCTTCCEEECC
T ss_pred             CCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCHHHCC
T ss_conf             3223345344342030001665421100136532066407

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.04  E-value=1.5e-09  Score=69.56  Aligned_cols=178  Identities=11%  Similarity=0.131  Sum_probs=108.2

Q ss_pred             CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             51772502199999841278888886555432101332101367764234789876899988880111026322467899
Q 001843          191 TDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTT  270 (1007)
Q Consensus       191 ~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (1007)
                      .+++|.++.++.+..|+..+..                                                          
T Consensus        14 ~divg~~~~~~~L~~~i~~~~~----------------------------------------------------------   35 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEGKL----------------------------------------------------------   35 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTCC----------------------------------------------------------
T ss_pred             HHCCCCHHHHHHHHHHHHCCCC----------------------------------------------------------
T ss_conf             9835969999999999976999----------------------------------------------------------


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHCCCC-CCC-EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             99689999938998088999999853200037-882-6999926898889899999999997553321102338999999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRH-FTK-RAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~-F~~-~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                         ..+-++|++|+||||+|+.+++.  +... +.. ..-...+  .... ..............               
T Consensus        36 ---~~lLl~Gp~G~GKttl~~~la~~--l~~~~~~~~~~e~~~~--~~~~-~~~~~~~~~~~~~~---------------   92 (227)
T d1sxjc2          36 ---PHLLFYGPPGTGKTSTIVALARE--IYGKNYSNMVLELNAS--DDRG-IDVVRNQIKDFAST---------------   92 (227)
T ss_dssp             ---CCEEEECSSSSSHHHHHHHHHHH--HHTTSHHHHEEEECTT--SCCS-HHHHHTHHHHHHHB---------------
T ss_pred             ---CEEEEECCCCCCHHHHHHHHHHH--HHCCCCCCEEEEECCC--CCCC-EEEEECCHHHCCCC---------------
T ss_conf             ---85999889987755899999998--5167776415773155--5687-54321000101110---------------


Q ss_pred             HHHHHCCCCCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHH
Q ss_conf             999881998379999296755700011210-2237779994899984887311223378520366499997999999996
Q 001843          349 RITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLK  427 (1007)
Q Consensus       349 ~l~~~L~~kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~  427 (1007)
                        ......++-.+|+|++.......-..++ .+... ...++++++|....++.......+..+++.+++.++-...+.+
T Consensus        93 --~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~-~~~~~~~~~~~~~~~i~~~i~sr~~~i~~~~~~~~~i~~~l~~  169 (227)
T d1sxjc2          93 --RQIFSKGFKLIILDEADAMTNAAQNALRRVIERY-TKNTRFCVLANYAHKLTPALLSQCTRFRFQPLPQEAIERRIAN  169 (227)
T ss_dssp             --CCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHT-TTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHH
T ss_pred             --CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHC-CCCEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             --0025777189999663200023789999886311-2002320126708775999998875401235652000110212


Q ss_pred             HHCCCCCCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             3012443235799489999999999819972
Q 001843          428 KARIAEDVLQSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       428 ~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlP  458 (1007)
                      .+.....   ..+   .+....|++.++|-.
T Consensus       170 I~~~e~i---~i~---~~~l~~i~~~s~Gd~  194 (227)
T d1sxjc2         170 VLVHEKL---KLS---PNAEKALIELSNGDM  194 (227)
T ss_dssp             HHHTTTC---CBC---HHHHHHHHHHHTTCH
T ss_pred             CCCCCCC---CCC---HHHHHHHHHHCCCCH
T ss_conf             2111124---589---899999999849969

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.03  E-value=2.3e-09  Score=68.48  Aligned_cols=180  Identities=11%  Similarity=0.159  Sum_probs=111.1

Q ss_pred             CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             51772502199999841278888886555432101332101367764234789876899988880111026322467899
Q 001843          191 TDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTT  270 (1007)
Q Consensus       191 ~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (1007)
                      ++++|-++.++.+..|+.....                                                          
T Consensus        15 ~d~ig~~~~~~~L~~~~~~~~~----------------------------------------------------------   36 (224)
T d1sxjb2          15 SDIVGNKETIDRLQQIAKDGNM----------------------------------------------------------   36 (224)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCCC----------------------------------------------------------
T ss_pred             HHHCCCHHHHHHHHHHHHCCCC----------------------------------------------------------
T ss_conf             9902979999999999986998----------------------------------------------------------


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCC-C-CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             996899999389980889999998532000378-8-26999926898889899999999997553321102338999999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHF-T-KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F-~-~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                         .-+-++|++|+||||+|+.+++.  +...+ . ...-+..+  ....... .......+...  .  .         
T Consensus        37 ---~~~ll~Gp~G~GKTt~a~~la~~--l~~~~~~~~~~~~n~~--~~~~~~~-i~~~~~~~~~~--~--~---------   95 (224)
T d1sxjb2          37 ---PHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNAS--DDRGIDV-VRNQIKHFAQK--K--L---------   95 (224)
T ss_dssp             ---CCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTT--SCCSHHH-HHTHHHHHHHB--C--C---------
T ss_pred             ---CEEEEECCCCCCCHHHHHHHHHH--HHCCCCCCCCCCCCCC--CCCCCEE-HHHHHHHHHHH--H--C---------
T ss_conf             ---74999889998705469999999--7256643221111134--5578521-16678878876--2--2---------


Q ss_pred             HHHHHCCCCCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHH
Q ss_conf             999881998379999296755700011210-2237779994899984887311223378520366499997999999996
Q 001843          349 RITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLK  427 (1007)
Q Consensus       349 ~l~~~L~~kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~  427 (1007)
                         .....+.-++|+|++..........++ .+... ...+++++++.....+.......+..+++++++.++-...+.+
T Consensus        96 ---~~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~-~~~~~~i~~~~~~~~i~~~l~sr~~~i~~~~~~~~~i~~~l~~  171 (224)
T d1sxjb2          96 ---HLPPGKHKIVILDEADSMTAGAQQALRRTMELY-SNSTRFAFACNQSNKIIEPLQSQCAILRYSKLSDEDVLKRLLQ  171 (224)
T ss_dssp             ---CCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHT-TTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHH
T ss_pred             ---CCCCCCEEEEEEECCCCCCHHHHHHHHHHCCCC-CCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             ---477763599998244323215778775201123-3333665314743021067887777765313322456788877


Q ss_pred             HHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCH
Q ss_conf             30124432357994899999999998199726
Q 001843          428 KARIAEDVLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       428 ~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPL  459 (1007)
                      .+.....   ..+   .+....|++.|+|.+-
T Consensus       172 i~~~e~~---~i~---~~~l~~I~~~s~Gd~R  197 (224)
T d1sxjb2         172 IIKLEDV---KYT---NDGLEAIIFTAEGDMR  197 (224)
T ss_dssp             HHHHHTC---CBC---HHHHHHHHHHHTTCHH
T ss_pred             HHHHCCC---CCC---HHHHHHHHHHCCCCHH
T ss_conf             7774046---789---9999999998699699

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.98  E-value=1.2e-09  Score=70.10  Aligned_cols=77  Identities=21%  Similarity=0.161  Sum_probs=54.4

Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC--CCCC---CC
Q ss_conf             898830199926887898678700069876858851367775348323268799898615874321344--2233---35
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPY--AFWP---SR  740 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP~--~i~~---Lr  740 (1007)
                      ..+..|++|++++|.+.  .+|..++.+.+|++|++++|.++.+| .++.+++|++|++++|.+..+|.  .+..   |+
T Consensus        17 ~~l~~L~~L~ls~N~l~--~lp~~~~~l~~L~~L~l~~N~i~~l~-~~~~l~~L~~L~l~~N~i~~~~~~~~l~~~~~L~   93 (124)
T d1dcea3          17 EQLLLVTHLDLSHNRLR--ALPPALAALRCLEVLQASDNALENVD-GVANLPRLQELLLCNNRLQQSAAIQPLVSCPRLV   93 (124)
T ss_dssp             GGGTTCCEEECCSSCCC--CCCGGGGGCTTCCEEECCSSCCCCCG-GGTTCSSCCEEECCSSCCCSSSTTGGGGGCTTCC
T ss_pred             CCCCCCCEEECCCCCCC--CCHHHHHHHHCCCCCCCCCCCCCCCC-CCCCCCCCCEEECCCCCCCCCCCCHHHCCCCCCC
T ss_conf             05898898979787168--65215655431354532432112357-4123355576888898658888825653799999


Q ss_pred             EECCC
Q ss_conf             02033
Q 001843          741 HLYLN  745 (1007)
Q Consensus       741 ~L~l~  745 (1007)
                      +|++.
T Consensus        94 ~L~l~   98 (124)
T d1dcea3          94 LLNLQ   98 (124)
T ss_dssp             EEECT
T ss_pred             EEECC
T ss_conf             99897

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.98  E-value=1.3e-09  Score=69.89  Aligned_cols=196  Identities=13%  Similarity=0.122  Sum_probs=112.7

Q ss_pred             CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             51772502199999841278888886555432101332101367764234789876899988880111026322467899
Q 001843          191 TDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTT  270 (1007)
Q Consensus       191 ~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (1007)
                      ++++|.++.++.+..|+.....                                                          
T Consensus        12 ~diig~~~~~~~l~~~i~~~~~----------------------------------------------------------   33 (237)
T d1sxjd2          12 DEVTAQDHAVTVLKKTLKSANL----------------------------------------------------------   33 (237)
T ss_dssp             TTCCSCCTTHHHHHHHTTCTTC----------------------------------------------------------
T ss_pred             HHCCCCHHHHHHHHHHHHCCCC----------------------------------------------------------
T ss_conf             8726939999999999986998----------------------------------------------------------


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHCCC-CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             9968999993899808899999985320003-788269999268988898999999999975533211023389999999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKR-HFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~-~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                         ..+-++|++|+||||+|+.+++.-.... .......+..+  .......... ........  . .....    ...
T Consensus        34 ---~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~--~~~~~~~~~~-~~~~~~~~--~-~~~~~----~~~  100 (237)
T d1sxjd2          34 ---PHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNAS--DERGISIVRE-KVKNFARL--T-VSKPS----KHD  100 (237)
T ss_dssp             ---CCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSS--SCCCHHHHTT-HHHHHHHS--C-CCCCC----TTH
T ss_pred             ---CEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCHHHEECC--CCCCCHHHHH-HHHHHHHH--H-HHHHH----HHH
T ss_conf             ---8599989999984999999999970976334321220021--1356067899-99887654--4-43246----787


Q ss_pred             HHHHCCCCCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHH
Q ss_conf             99881998379999296755700011210-22377799948999848873112233785203664999979999999963
Q 001843          350 ITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKK  428 (1007)
Q Consensus       350 l~~~L~~kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~  428 (1007)
                      +......+.-.+|+|++.......+..+. .+... ....++++|+....++..........+++++++.++...++.+.
T Consensus       101 ~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~-~~~~~~i~~~~~~~~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i  179 (237)
T d1sxjd2         101 LENYPCPPYKIIILDEADSMTADAQSALRRTMETY-SGVTRFCLICNYVTRIIDPLASQCSKFRFKALDASNAIDRLRFI  179 (237)
T ss_dssp             HHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHT-TTTEEEEEEESCGGGSCHHHHHHSEEEECCCCCHHHHHHHHHHH
T ss_pred             HHHCCCCCCEEEEEECCCCCCHHHHHHHHHCCCCC-CCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHH
T ss_conf             76135667369999551336777788876301222-23333212246642223311100011023333332110010114


Q ss_pred             HCCCCCCCCCCCHHHHHHHHHHHHHCCCCC-HHHHHH
Q ss_conf             012443235799489999999999819972-699999
Q 001843          429 ARIAEDVLQSRSSELIKLKKQILNICDGLP-LRVVLL  464 (1007)
Q Consensus       429 a~~~~~~~~~~~~~l~~~~~~I~~~c~GlP-Lai~~l  464 (1007)
                      +.....   ..+   .+....|++.++|-. -|+..+
T Consensus       180 ~~~e~i---~i~---~~~l~~ia~~s~gd~R~ai~~L  210 (237)
T d1sxjd2         180 SEQENV---KCD---DGVLERILDISAGDLRRGITLL  210 (237)
T ss_dssp             HHTTTC---CCC---HHHHHHHHHHTSSCHHHHHHHH
T ss_pred             HHHHCC---CCC---HHHHHHHHHHCCCCHHHHHHHH
T ss_conf             555267---578---9999999998599899999999

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.97  E-value=8.4e-11  Score=76.87  Aligned_cols=122  Identities=16%  Similarity=0.149  Sum_probs=56.3

Q ss_pred             CCCEEEECCCC--CCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCC---CCCCEECC
Q ss_conf             30199926887--89867870006987685885136777534832326879989861587432134422---33350203
Q 001843          670 MLKVLDLEGVY--KPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPYAF---WPSRHLYL  744 (1007)
Q Consensus       670 ~LrvLdL~~~~--~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP~~i---~~Lr~L~l  744 (1007)
                      .++.+++++..  +.  .++..+..+.+|++|+|++|.|+.++ .+..|++|++|++++|.+..+|...   ..|++|++
T Consensus        24 ~~~~~~l~~~~~~i~--~l~~sl~~L~~L~~L~Ls~n~I~~i~-~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l  100 (198)
T d1m9la_          24 EAEKVELHGMIPPIE--KMDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWI  100 (198)
T ss_dssp             TCSCEECCBCCTTCC--CCHHHHHHTTTCCEEECSEEEESCCC-CHHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEEC
T ss_pred             CCCEEEEECCCCCHH--HHHHHHHCCCCCCEEECCCCCCCCCC-CCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             331002555568520--02467762604615199446899864-424782535734135343210000332212333333


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCHHHHHCCCCCCEEEEEEC
Q ss_conf             3212334343466435676877542303637875437376513899994985306
Q 001843          745 NWIFLATNVFRHPQFVKWETSLQTLWGLCIKADEVQSLDYFRRLTSLRKLGLKCS  799 (1007)
Q Consensus       745 ~~~~~~~~~~~lp~~i~~L~~L~~L~~~~~~~~~~~~~~~l~~L~~L~~L~i~~~  799 (1007)
                      .   ++. ...+ ..+..+++|+.|......-.....+..+..+++|+.|.+.++
T Consensus       101 ~---~N~-i~~l-~~~~~l~~L~~L~L~~N~i~~~~~~~~l~~l~~L~~L~L~~N  150 (198)
T d1m9la_         101 S---YNQ-IASL-SGIEKLVNLRVLYMSNNKITNWGEIDKLAALDKLEDLLLAGN  150 (198)
T ss_dssp             S---EEE-CCCH-HHHHHHHHSSEEEESEEECCCHHHHHHHTTTTTCSEEEECSS
T ss_pred             C---CCC-CCCC-CCCCCCCCCCCCCCCCCHHCCCCCCCCCCCCCCCCEEECCCC
T ss_conf             3---322-2222-222222234111234102125542212367776302342798

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.95  E-value=6e-09  Score=66.05  Aligned_cols=89  Identities=18%  Similarity=0.126  Sum_probs=46.4

Q ss_pred             CCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCC-CCCCCCCCCCCEEECCCCCCCCCCCC-
Q ss_conf             7500999952556799801234331023344898830199926887898678-70006987685885136777534832-
Q 001843          635 WRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTN-NNALGRLPFLEYLGLRSTFIDSLPDS-  712 (1007)
Q Consensus       635 ~~LRsL~l~~~~~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~~~~~~~~l-p~~i~~L~~Lr~L~L~~~~i~~LP~~-  712 (1007)
                      ..++.|.+..+.+...       .....|  ..++.|+.|+++++.+.  .+ +..+..+..|++|+|++|.++.+|.. 
T Consensus        29 ~~l~~L~Ls~N~i~~~-------~~~~~f--~~l~~L~~L~L~~N~i~--~~~~~~~~~~~~L~~L~Ls~N~l~~l~~~~   97 (192)
T d1w8aa_          29 LHTTELLLNDNELGRI-------SSDGLF--GRLPHLVKLELKRNQLT--GIEPNAFEGASHIQELQLGENKIKEISNKM   97 (192)
T ss_dssp             TTCSEEECCSCCCCSB-------CCSCSG--GGCTTCCEEECCSSCCC--CBCTTTTTTCTTCCEEECCSCCCCEECSSS
T ss_pred             CCCCEEEECCCCCCCC-------CCCCCC--CCCCEEEEEECCCCCCC--CCCCCCCCCCCCCCEEEECCCCCCCCCHHH
T ss_conf             7878898489877553-------020025--78762721301363221--212122211222210100355344349799


Q ss_pred             CCCCCCCCEEEECCCCCCCCCC
Q ss_conf             3268799898615874321344
Q 001843          713 TPILFCLATLDVSHTKVQRLPY  734 (1007)
Q Consensus       713 i~~L~~L~~Ldl~~~~l~~lP~  734 (1007)
                      +.+|++|++|+++++.+..+|.
T Consensus        98 F~~l~~L~~L~L~~N~l~~i~~  119 (192)
T d1w8aa_          98 FLGLHQLKTLNLYDNQISCVMP  119 (192)
T ss_dssp             STTCTTCCEEECCSSCCCEECT
T ss_pred             HHCCCCCCCCCCCCCCCCCCCH
T ss_conf             8079746552457745353597

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.94  E-value=5.1e-08  Score=60.59  Aligned_cols=197  Identities=13%  Similarity=0.132  Sum_probs=113.5

Q ss_pred             CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             51772502199999841278888886555432101332101367764234789876899988880111026322467899
Q 001843          191 TDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTT  270 (1007)
Q Consensus       191 ~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (1007)
                      .+++|.++.++.+..++....-                                                          
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~~----------------------------------------------------------   33 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGRI----------------------------------------------------------   33 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTCC----------------------------------------------------------
T ss_pred             HHCCCHHHHHHHHHHHHHCCCC----------------------------------------------------------
T ss_conf             8815959999999999985998----------------------------------------------------------


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH--HCCCCCHHHHHH
Q ss_conf             996899999389980889999998532000378826999926898889899999999997553321--102338999999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLK--VEATLSAEELMW  348 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~--~~~~~~~~~l~~  348 (1007)
                        +..+-++|..|+||||+|+.+++.-......+.         ...........+...-......  .......+...+
T Consensus        34 --~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~---------~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~ir~  102 (239)
T d1njfa_          34 --HHAYLFSGTRGVGKTSIARLLAKGLNCETGITA---------TPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRD  102 (239)
T ss_dssp             --CSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCS---------SCCSCSHHHHHHHHTCCTTEEEEETTCSSSHHHHHH
T ss_pred             --CEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCC---------CCCCCCHHHHHHHCCCCCEEEEECCHHCCCHHHHHH
T ss_conf             --705988889987589999999998468556666---------755542479999747987079961120078999999


Q ss_pred             HHHHHC-----CCCCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHH
Q ss_conf             999881-----998379999296755700011210-22377799948999848873112233785203664999979999
Q 001843          349 RITQAL-----DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESW  422 (1007)
Q Consensus       349 ~l~~~L-----~~kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L~~~ea~  422 (1007)
                       +.+..     .++..++|+|+++.-+......++ .+-.. ..++++|++|.+..++-......+..+.+.+++.++-.
T Consensus       103 -~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~-~~~~~~il~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~  180 (239)
T d1njfa_         103 -LLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEP-PEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIR  180 (239)
T ss_dssp             -HHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSC-CTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHHH
T ss_pred             -HHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCC-CCCEEEEEECCCCCCCCHHHHHHHCCCCCCCCCHHHHH
T ss_conf             -9999974652599879999781108999999999998568-98869999738856367657612102222467678766


Q ss_pred             HHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCC-HHHHHH
Q ss_conf             999963012443235799489999999999819972-699999
Q 001843          423 ELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLP-LRVVLL  464 (1007)
Q Consensus       423 ~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlP-Lai~~l  464 (1007)
                      ..+...+.....   ..+   ++....|++.++|.+ -|+..+
T Consensus       181 ~~l~~i~~~e~~---~~~---~~~l~~i~~~s~Gd~R~ain~l  217 (239)
T d1njfa_         181 HQLEHILNEEHI---AHE---PRALQLLARAAEGSLRDALSLT  217 (239)
T ss_dssp             HHHHHHHHHHTC---CBC---HHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHHCC---CCC---HHHHHHHHHHCCCCHHHHHHHH
T ss_conf             688787764314---789---9999999997699799999999

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.92  E-value=4e-09  Score=67.06  Aligned_cols=179  Identities=16%  Similarity=0.151  Sum_probs=106.3

Q ss_pred             CCCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCC
Q ss_conf             75177250219999984127888888655543210133210136776423478987689998888011102632246789
Q 001843          190 ETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTT  269 (1007)
Q Consensus       190 ~~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (1007)
                      -++++|-++.++.+..|+.....                                                         
T Consensus        23 ~~diig~~~~~~~l~~~i~~~~~---------------------------------------------------------   45 (231)
T d1iqpa2          23 LDDIVGQEHIVKRLKHYVKTGSM---------------------------------------------------------   45 (231)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTCC---------------------------------------------------------
T ss_pred             HHHCCCCHHHHHHHHHHHHCCCC---------------------------------------------------------
T ss_conf             99913939999999999985999---------------------------------------------------------


Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHCCC-CCCC-EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             99968999993899808899999985320003-7882-699992689888989999999999755332110233899999
Q 001843          270 TTTTQVIALIGKAGSGKTTLARIVYNRVYVKR-HFTK-RAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELM  347 (1007)
Q Consensus       270 ~~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~-~F~~-~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~  347 (1007)
                          .-+-++|++|+||||+|+.+++.  +.. .+.. .+-+..+  ... .....+.........              
T Consensus        46 ----~~lll~Gp~G~GKTtla~~iak~--l~~~~~~~~~~e~n~s--~~~-~~~~~~~~~~~~~~~--------------  102 (231)
T d1iqpa2          46 ----PHLLFAGPPGVGKTTAALALARE--LFGENWRHNFLELNAS--DER-GINVIREKVKEFART--------------  102 (231)
T ss_dssp             ----CEEEEESCTTSSHHHHHHHHHHH--HHGGGHHHHEEEEETT--CHH-HHHTTHHHHHHHHHS--------------
T ss_pred             ----CEEEEECCCCCCHHHHHHHHHHH--HHHCCCCCCEEEEECC--CCC-CHHHHHHHHHHHHHH--------------
T ss_conf             ----76999789997487999999999--8731467771587567--666-634888888888751--------------


Q ss_pred             HHHHHHCCCCCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHH
Q ss_conf             9999881998379999296755700011210-223777999489998488731122337852036649999799999999
Q 001843          348 WRITQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFL  426 (1007)
Q Consensus       348 ~~l~~~L~~kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~  426 (1007)
                         ......++..+++|++.......+..+. .+... .....++.||.....+..........+.+.+.+.++....+.
T Consensus       103 ---~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~-~~~~~~i~~~n~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~  178 (231)
T d1iqpa2         103 ---KPIGGASFKIIFLDEADALTQDAQQALRRTMEMF-SSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLR  178 (231)
T ss_dssp             ---CCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHT-TTTEEEEEEESCGGGSCHHHHHTEEEEECCCCCHHHHHHHHH
T ss_pred             ---HHCCCCCCEEEEEHHHHHCCHHHHHHHHHHCCCC-CCCEEEEECCCCHHHCHHHHHCCCCCCCCCCCCHHHHHHHHH
T ss_conf             ---0015787228861434431214789876411247-764478861487665657684731210123343046778998


Q ss_pred             HHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCC
Q ss_conf             63012443235799489999999999819972
Q 001843          427 KKARIAEDVLQSRSSELIKLKKQILNICDGLP  458 (1007)
Q Consensus       427 ~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlP  458 (1007)
                      +.+.....      .-..+....|++.|+|-.
T Consensus       179 ~~~~~e~i------~i~~~~l~~I~~~~~gdi  204 (231)
T d1iqpa2         179 YIAENEGL------ELTEEGLQAILYIAEGDM  204 (231)
T ss_dssp             HHHHTTTC------EECHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCC------CCCHHHHHHHHHHCCCCH
T ss_conf             88998399------989999999999839979

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.88  E-value=7.5e-09  Score=65.48  Aligned_cols=98  Identities=10%  Similarity=0.095  Sum_probs=60.9

Q ss_pred             CCCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             98379999296755700011210-22377799948999848873112233785203664999979999999963012443
Q 001843          356 DSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNESWELFLKKARIAED  434 (1007)
Q Consensus       356 ~kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~  434 (1007)
                      .+.-++|+|+++......+..++ .+-.. ...+++|+||.+...+..........+++.+++.++..+.+...+-...-
T Consensus       130 ~~~~iiiide~d~l~~~~~~~l~~~~e~~-~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~  208 (252)
T d1sxje2         130 HRYKCVIINEANSLTKDAQAALRRTMEKY-SKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERI  208 (252)
T ss_dssp             -CCEEEEEECTTSSCHHHHHHHHHHHHHS-TTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCCCCCCHHHHCCCCCC-CCCCCCEEEECCCCCHHHHHHCCHHEEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf             87249994243334543111221002213-56643000102111002544210002430353304689999999998399


Q ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCH
Q ss_conf             2357994899999999998199726
Q 001843          435 VLQSRSSELIKLKKQILNICDGLPL  459 (1007)
Q Consensus       435 ~~~~~~~~l~~~~~~I~~~c~GlPL  459 (1007)
                           ....++....|++.+.|.+-
T Consensus       209 -----~~~~~~~l~~i~~~s~Gd~R  228 (252)
T d1sxje2         209 -----QLETKDILKRIAQASNGNLR  228 (252)
T ss_dssp             -----EECCSHHHHHHHHHHTTCHH
T ss_pred             -----CCCCHHHHHHHHHHCCCCHH
T ss_conf             -----98969999999998699499

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.88  E-value=2.4e-08  Score=62.53  Aligned_cols=155  Identities=15%  Similarity=0.171  Sum_probs=96.9

Q ss_pred             CEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCC
Q ss_conf             17725021999998412788888865554321013321013677642347898768999888801110263224678999
Q 001843          192 DVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTTT  271 (1007)
Q Consensus       192 ~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  271 (1007)
                      .++||++++++++..|.....                                                           
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~k-----------------------------------------------------------   39 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRRK-----------------------------------------------------------   39 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSS-----------------------------------------------------------
T ss_pred             CCCCHHHHHHHHHHHHHCCCC-----------------------------------------------------------
T ss_conf             663809999999999954766-----------------------------------------------------------


Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHH---HCCCC-CCCEEEE-EECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             96899999389980889999998532---00037-8826999-9268988898999999999975533211023389999
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRV---YVKRH-FTKRAWV-HIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEEL  346 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~~---~v~~~-F~~~~wv-~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l  346 (1007)
                        .-+.++|.+|+|||+++..+++.-   .+... .+..+|. +.+                .+..   ......+.++.
T Consensus        40 --~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~----------------~lia---g~~~~g~~e~r   98 (268)
T d1r6bx2          40 --NNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIG----------------SLLA---GTKYRGDFEKR   98 (268)
T ss_dssp             --CEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC-------------------C---CCCCSSCHHHH
T ss_pred             --CCCEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEC----------------HHHC---CCCCCHHHHHH
T ss_conf             --89679888988677999999999981784500035412786405----------------6750---67630058999


Q ss_pred             HHHHHHHC-CCCCEEEEEECCCCC------C--CHHHHHH-CCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------EE
Q ss_conf             99999881-998379999296755------7--0001121-0223777999489998488731122337852------03
Q 001843          347 MWRITQAL-DDSTFLIVMENAEHQ------K--SQVWDSF-LGKLCSFTQCGKIIITTSSTEDFVEPLGAAF------ST  410 (1007)
Q Consensus       347 ~~~l~~~L-~~kr~LiVlDdv~~~------~--~~~w~~l-~~l~~~~~~gskIiiTTR~~~~va~~~~~~~------~~  410 (1007)
                      ...+...+ ..+..++++|++..-      +  ..+...+ +++...  ..-++|.||...+ .........      ..
T Consensus        99 ~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~r--g~i~vIgatT~ee-y~~~~e~d~al~rrF~~  175 (268)
T d1r6bx2          99 FKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSS--GKIRVIGSTTYQE-FSNIFEKDRALARRFQK  175 (268)
T ss_dssp             HHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSS--CCCEEEEEECHHH-HHCCCCCTTSSGGGEEE
T ss_pred             HHHHHHHHHCCCCCEEEECCHHHHHCCCCCCCCCCCHHHHHHHHHHC--CCCEEEEECCHHH-HHHHHHHCHHHHHHHCC
T ss_conf             99999986126784688433698862777788641179876488747--9875999579999-99998616788865210


Q ss_pred             EECCCCCHHHHHHHHHHHH
Q ss_conf             6649999799999999630
Q 001843          411 LHVPGLGKNESWELFLKKA  429 (1007)
Q Consensus       411 ~~l~~L~~~ea~~Lf~~~a  429 (1007)
                      +.+.+++.+++..++....
T Consensus       176 I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         176 IDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             EECCCCCHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH
T ss_conf             0368989999999999866

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.87  E-value=9.8e-12  Score=82.30  Aligned_cols=320  Identities=17%  Similarity=0.075  Sum_probs=163.7

Q ss_pred             CCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCC---CCCCCCCCCCCCCEEECCCCCCCC---
Q ss_conf             75009999525567998012343310233448988301999268878986---787000698768588513677753---
Q 001843          635 WRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPML---TNNNALGRLPFLEYLGLRSTFIDS---  708 (1007)
Q Consensus       635 ~~LRsL~l~~~~~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~~~~~~~---~lp~~i~~L~~Lr~L~L~~~~i~~---  708 (1007)
                      .+|++|.+..+....   .    .+..++  +.++++++|+|++|.+.+.   .+...+..+++|++|+|++|.++.   
T Consensus         2 ~~l~~ld~~~~~i~~---~----~~~~l~--~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~   72 (460)
T d1z7xw1           2 LDIQSLDIQCEELSD---A----RWAELL--PLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGV   72 (460)
T ss_dssp             EEEEEEEEESCCCCH---H----HHHHHH--HHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHH
T ss_pred             CCCCEEEEECCCCCH---H----HHHHHH--HHCCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHH
T ss_conf             987779820895886---8----999999--7677999998289999889999999998539998889795985972899


Q ss_pred             --CCCCCC-CCCCCCEEEECCCCCCC-----CCCCC---CCCCEECCCCCCCCCCCC----CCCCCCCCCCCCCCCCCEE
Q ss_conf             --483232-68799898615874321-----34422---333502033212334343----4664356768775423036
Q 001843          709 --LPDSTP-ILFCLATLDVSHTKVQR-----LPYAF---WPSRHLYLNWIFLATNVF----RHPQFVKWETSLQTLWGLC  773 (1007)
Q Consensus       709 --LP~~i~-~L~~L~~Ldl~~~~l~~-----lP~~i---~~Lr~L~l~~~~~~~~~~----~lp~~i~~L~~L~~L~~~~  773 (1007)
                        +...+. ...+|++|++++|.+..     ++..+   ..|++|++.   ++....    .+...+........  ...
T Consensus        73 ~~l~~~l~~~~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~---~N~i~~~~~~~l~~~l~~~~~~~~--~~~  147 (460)
T d1z7xw1          73 HCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLS---DNLLGDAGLQLLCEGLLDPQCRLE--KLQ  147 (460)
T ss_dssp             HHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECC---SSBCHHHHHHHHHHHHTSTTCCCC--EEE
T ss_pred             HHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCHHHCCCCCCCCCCC---CCCCHHHHHHHHHHCCCCCCCCCC--CCC
T ss_conf             999999843788778877888775432210121100003432002444---332023455554430135543332--222


Q ss_pred             ECCC--C----CCCHHHHHCCCCCCEEEEEECCCCCH----HHH-------------------------HHHHHHHHCCC
Q ss_conf             3787--5----43737651389999498530688840----368-------------------------98899751589
Q 001843          774 IKAD--E----VQSLDYFRRLTSLRKLGLKCSSTTST----SLK-------------------------KEIIGAVLQLS  818 (1007)
Q Consensus       774 ~~~~--~----~~~~~~l~~L~~L~~L~i~~~~~~~~----~l~-------------------------~~~~~~l~~l~  818 (1007)
                      ....  .    ......+.....++.+.+..+. ...    ...                         ......+...+
T Consensus       148 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~ls~~~-~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~  226 (460)
T d1z7xw1         148 LEYCSLSAASCEPLASVLRAKPDFKELTVSNND-INEAGVRVLCQGLKDSPCQLEALKLESCGVTSDNCRDLCGIVASKA  226 (460)
T ss_dssp             CTTSCCBGGGHHHHHHHHHHCTTCCEEECCSSB-CHHHHHHHHHHHHHHSCCCCCEEECTTSCCBTTHHHHHHHHHHHCT
T ss_pred             CCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC
T ss_conf             223222001100112223333222223322221-2455554323433211221001241124542101101223322222


Q ss_pred             CCCEEEEEECCCCCC-----CCCCCCCCCCCCEEEECCCC-CC-----CCCCCCCCCCCCCEEEEEEEEECCCCCCCCC-
Q ss_conf             977589852599977-----92223379998578824558-99-----9957657899991599997220477996711-
Q 001843          819 ELHSLKLICETPSYL-----PLLEMAEHYKLQKLYLSGHL-PP-----NSVIGDRSFPPNVVTLTLSQLRLEYDPMPIL-  886 (1007)
Q Consensus       819 ~L~~L~l~~~~~~~~-----~~~~l~~~~~L~~L~L~g~~-~~-----lp~~~i~~~l~~L~~L~L~~~~l~~~~l~~l-  886 (1007)
                      .++.+.+..+.....     ..........++.+.++++. ..     +.. ++.. .+.+..+.++++.+....+..+ 
T Consensus       227 ~~~~l~~~~n~~~~~~~~~~~~~~~~~~~~l~~l~l~~n~i~~~~~~~~~~-~l~~-~~~l~~l~l~~n~i~~~~~~~l~  304 (460)
T d1z7xw1         227 SLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCR-VLRA-KESLKELSLAGNELGDEGARLLC  304 (460)
T ss_dssp             TCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHH-HHHH-CTTCCEEECTTCCCHHHHHHHHH
T ss_pred             CCCCCCHHHCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCC-CCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             210010021122334420110001111111000013454332123343322-1112-34333444443332245642111


Q ss_pred             ----CCCCCCCEEEEECCCCCCCCEE---ECCCCCCCCCEEEECCCCCCCCEE---E--C-CCCCCCCCEEEEECCCCCC
Q ss_conf             ----2587774999526875897024---428999988689962479986458---7--6-8977653475750367878
Q 001843          887 ----GRLRQLKILRLFGGSYTGEEMS---CSSGEFPNLLVLKLWKLNRLRQWR---I--K-EGAMPCLRQLEIRSCGYLV  953 (1007)
Q Consensus       887 ----~~Lp~L~~L~L~~~~~~~~~l~---~~~~~fp~L~~L~L~~~~~l~~l~---~--~-~~~~p~L~~L~i~~C~~L~  953 (1007)
                          ...+.|+.+.+..+........   ......++|++|.|+++ .+..-.   +  . ....+.|+.|++++|. +.
T Consensus       305 ~~l~~~~~~L~~l~l~~~~l~~~~~~~l~~~~~~~~~L~~L~Ls~N-~i~~~g~~~l~~~l~~~~~~L~~L~Ls~n~-i~  382 (460)
T d1z7xw1         305 ETLLEPGCQLESLWVKSCSFTAACCSHFSSVLAQNRFLLELQISNN-RLEDAGVRELCQGLGQPGSVLRVLWLADCD-VS  382 (460)
T ss_dssp             HHHTSTTCCCCEEECTTSCCBGGGHHHHHHHHHHCSSCCEEECCSS-BCHHHHHHHHHHHHTSTTCCCCEEECTTSC-CC
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCHHHHHEEEE-CCCCCCCCHHHHHHHCCCCCCCEEECCCCC-CC
T ss_conf             0123334443333233341023344321332211011113201210-135766400111220456777889897997-97


Q ss_pred             ------CCCCCCCCCCCCCEEEECCCC
Q ss_conf             ------886730000376689923698
Q 001843          954 ------PPTGLKHVTSSLREFLLTNMP  974 (1007)
Q Consensus       954 ------lp~~l~~L~~~Lk~L~i~~~~  974 (1007)
                            ++..+..+ ++|++|++++++
T Consensus       383 ~~~~~~l~~~l~~~-~~L~~L~Ls~N~  408 (460)
T d1z7xw1         383 DSSCSSLAATLLAN-HSLRELDLSNNC  408 (460)
T ss_dssp             HHHHHHHHHHHHHC-CCCCEEECCSSS
T ss_pred             HHHHHHHHHHHHCC-CCCCEEECCCCC
T ss_conf             59999999999629-988989899996

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=98.82  E-value=1.5e-10  Score=75.38  Aligned_cols=16  Identities=19%  Similarity=0.013  Sum_probs=7.0

Q ss_pred             CCCCCCCEEEECCCCC
Q ss_conf             8988301999268878
Q 001843          666 RRLGMLKVLDLEGVYK  681 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~  681 (1007)
                      .....|+.|+|++|.+
T Consensus        28 ~~~~~l~~L~Ls~n~i   43 (344)
T d2ca6a1          28 LEDDSVKEIVLSGNTI   43 (344)
T ss_dssp             HHCSCCCEEECTTSEE
T ss_pred             HHCCCCCEEECCCCCC
T ss_conf             6389978897849837

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=98.81  E-value=6.5e-10  Score=71.68  Aligned_cols=63  Identities=16%  Similarity=0.116  Sum_probs=25.0

Q ss_pred             CCCCCCCEEEECCCCCCCC--C-------CCCCCCCCCCCCEEECCCCCCCC-----CCCCCCCCCCCCEEEECCCC
Q ss_conf             8988301999268878986--7-------87000698768588513677753-----48323268799898615874
Q 001843          666 RRLGMLKVLDLEGVYKPML--T-------NNNALGRLPFLEYLGLRSTFIDS-----LPDSTPILFCLATLDVSHTK  728 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~~~~--~-------lp~~i~~L~~Lr~L~L~~~~i~~-----LP~~i~~L~~L~~Ldl~~~~  728 (1007)
                      ...+.|+.|+++++.....  .       +...+..+.+|+.|+|+++.+..     +...+...++|+.|++++|.
T Consensus        56 ~~~~~L~~l~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~l~~n~  132 (344)
T d2ca6a1          56 ASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNG  132 (344)
T ss_dssp             TTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSC
T ss_pred             HHCCCCCEEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHEECCCCC
T ss_conf             85899888888777543345421067879998875477756330000134554333101110023432100000246

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.81  E-value=1.2e-07  Score=58.39  Aligned_cols=165  Identities=10%  Similarity=0.052  Sum_probs=94.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCC-CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH-----HHCCCCCHHHHH
Q ss_conf             89999938998088999999853200037-882699992689888989999999999755332-----110233899999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH-FTKRAWVHIPIMSMVEDRDVLADILKQIDESLL-----KVEATLSAEELM  347 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~-F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~-----~~~~~~~~~~l~  347 (1007)
                      ..+-++|+.|+||||+|+.+++.  +-.. -..  +      .......-.+.+.........     .....-..++. 
T Consensus        25 h~lLl~Gp~G~GKtt~a~~~a~~--l~~~~~~~--~------~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~i-   93 (207)
T d1a5ta2          25 HALLIQALPGMGDDALIYALSRY--LLCQQPQG--H------KSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAV-   93 (207)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHH--HTCSSCBT--T------BCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHH-
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH--CCCCCCCC--C------CCCCCCCHHHHHHHCCCCCCCHHHHHHCCCCCCCCHH-
T ss_conf             37988899987599999999982--10101232--1------2233420155654303431101234313453332114-


Q ss_pred             HHHHHHC-----CCCCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCCCHHHH
Q ss_conf             9999881-----998379999296755700011210-2237779994899984887311223378520366499997999
Q 001843          348 WRITQAL-----DDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGKNES  421 (1007)
Q Consensus       348 ~~l~~~L-----~~kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L~~~ea  421 (1007)
                      +.+.+.+     .+++-++|+|+++.-+......++ .+-.. ..+..+|.||++..++.....+.+..+.+.+++.++.
T Consensus        94 r~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep-~~~~~fIl~t~~~~~ll~tI~SRc~~i~~~~~~~~~~  172 (207)
T d1a5ta2          94 REVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEP-PAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYA  172 (207)
T ss_dssp             HHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSC-CTTEEEEEEESCGGGSCHHHHTTSEEEECCCCCHHHH
T ss_pred             HHHHHHHHHCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHH-CCCCEEEEEECCHHHHHHHHCCEEEEEECCCCCHHHH
T ss_conf             677653211003576404773134420000149999999850-1111045530686551032002157882689999999


Q ss_pred             HHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             9999963012443235799489999999999819972699
Q 001843          422 WELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       422 ~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  461 (1007)
                      ...+.+....        +   ++....|++.++|.|-.+
T Consensus       173 ~~~L~~~~~~--------~---~~~~~~i~~~s~Gs~r~a  201 (207)
T d1a5ta2         173 VTWLSREVTM--------S---QDALLAALRLSAGSPGAA  201 (207)
T ss_dssp             HHHHHHHCCC--------C---HHHHHHHHHHTTTCHHHH
T ss_pred             HHHHHHCCCC--------C---HHHHHHHHHHCCCCHHHH
T ss_conf             9999974899--------9---999999999769999999

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.79  E-value=2.4e-08  Score=62.50  Aligned_cols=106  Identities=14%  Similarity=0.045  Sum_probs=49.2

Q ss_pred             CCEEEEEEECCCCCC-CCCC--CCCCCCEEEEEECCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCCC-C
Q ss_conf             974899995599988-8777--67775009999525567998012343310233448988301999268878986787-0
Q 001843          613 FAVRRLAANLGSNSF-PYSS--LLSWRLHSYLVFDSRIRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTNN-N  688 (1007)
Q Consensus       613 ~~~rrlsi~~~~~~~-~~~~--~~~~~LRsL~l~~~~~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~~~~~~~~lp-~  688 (1007)
                      ..+++|.++.+.... ....  ..+++|+.|.+.++....        ..+..|  ..++.|+.|+|++|.+.  .+| .
T Consensus        29 ~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~--------~~~~~~--~~~~~L~~L~Ls~N~l~--~l~~~   96 (192)
T d1w8aa_          29 LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTG--------IEPNAF--EGASHIQELQLGENKIK--EISNK   96 (192)
T ss_dssp             TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCC--------BCTTTT--TTCTTCCEEECCSCCCC--EECSS
T ss_pred             CCCCEEEECCCCCCCCCCCCCCCCCCEEEEEECCCCCCCC--------CCCCCC--CCCCCCCEEEECCCCCC--CCCHH
T ss_conf             7878898489877553020025787627213013632212--------121222--11222210100355344--34979


Q ss_pred             CCCCCCCCCEEECCCCCCCCCCCC-CCCCCCCCEEEECCCCCC
Q ss_conf             006987685885136777534832-326879989861587432
Q 001843          689 ALGRLPFLEYLGLRSTFIDSLPDS-TPILFCLATLDVSHTKVQ  730 (1007)
Q Consensus       689 ~i~~L~~Lr~L~L~~~~i~~LP~~-i~~L~~L~~Ldl~~~~l~  730 (1007)
                      .|.++.+|++|+|++|.++.+|.. +..+++|++|++.++.+.
T Consensus        97 ~F~~l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~~N~~~  139 (192)
T d1w8aa_          97 MFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             SSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             HHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCC
T ss_conf             9807974655245774535359778568753342000364434

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.72  E-value=3.3e-07  Score=55.91  Aligned_cols=152  Identities=18%  Similarity=0.239  Sum_probs=84.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHH---CCCCC-CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             8999993899808899999985320---00378-8269999268988898999999999975533211023389999999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVY---VKRHF-TKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~---v~~~F-~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      .++.++|++|+|||++++.+++.-.   ..... ....++...  ........+..+...+...  ..............
T Consensus        47 ~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~  122 (287)
T d1w5sa2          47 MIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAF--NAPNLYTILSLIVRQTGYP--IQVRGAPALDILKA  122 (287)
T ss_dssp             EEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGG--GCCSHHHHHHHHHHHHTCC--CCCTTCCHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEECCC--CCCCHHHHHHHHHHHCCCC--CCCCCCHHHHHHHH
T ss_conf             4899678999899999999999987541555678416630333--3465046788876530432--33345127889999


Q ss_pred             HHHHCC--CCCEEEEEECCCCC------CCHHH---HHHC-CCCCCC--CCCCEEEEECCCCCCCC-------CCCCCCC
Q ss_conf             998819--98379999296755------70001---1210-223777--99948999848873112-------2337852
Q 001843          350 ITQALD--DSTFLIVMENAEHQ------KSQVW---DSFL-GKLCSF--TQCGKIIITTSSTEDFV-------EPLGAAF  408 (1007)
Q Consensus       350 l~~~L~--~kr~LiVlDdv~~~------~~~~w---~~l~-~l~~~~--~~gskIiiTTR~~~~va-------~~~~~~~  408 (1007)
                      +.....  +...++++|.+...      ..+..   ..+. .+....  ..-..|++++.... ..       ....-..
T Consensus       123 l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~i~~~~~~-~~~~~~~~~~~~~r~~  201 (287)
T d1w5sa2         123 LVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRA-LSYMREKIPQVESQIG  201 (287)
T ss_dssp             HHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHH-HHHHHHHCHHHHTTCS
T ss_pred             HHHHHHHCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHCCHHHCCCCEEEEEECCCHHH-HHHHHHHCCCHHCCCC
T ss_conf             999998546766541257888515665542678988999874320104565147762430899-9999862520112322


Q ss_pred             EEEECCCCCHHHHHHHHHHHHC
Q ss_conf             0366499997999999996301
Q 001843          409 STLHVPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       409 ~~~~l~~L~~~ea~~Lf~~~a~  430 (1007)
                      ..+.+.+++.++..+++...+-
T Consensus       202 ~~i~f~~y~~~el~~Il~~r~~  223 (287)
T d1w5sa2         202 FKLHLPAYKSRELYTILEQRAE  223 (287)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHH
T ss_pred             EEEECCCCCHHHHHHHHHHHHH
T ss_conf             0652257759999998766677

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.69  E-value=3.2e-06  Score=50.15  Aligned_cols=149  Identities=15%  Similarity=0.086  Sum_probs=78.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755332110233899999999988
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .-+-++|++|+||||+|+.+++.  ....   ..++..+  ...                        ........+...
T Consensus        36 ~~~Ll~GPpG~GKTtla~~la~~--~~~~---~~~~~~~--~~~------------------------~~~~~~~~~~~~   84 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLAHVIAHE--LGVN---LRVTSGP--AIE------------------------KPGDLAAILANS   84 (239)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH--HTCC---EEEEETT--TCC------------------------SHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HCCC---EEECCCC--CCC------------------------CCHHHHHHHHHH
T ss_conf             73898897998788899999998--4987---4754687--534------------------------321468998851


Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHC-CC------------------CCCCCCCCEEE-EECCCCCCCCCCCCCCCEEEEC
Q ss_conf             1998379999296755700011210-22------------------37779994899-9848873112233785203664
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFL-GK------------------LCSFTQCGKII-ITTSSTEDFVEPLGAAFSTLHV  413 (1007)
Q Consensus       354 L~~kr~LiVlDdv~~~~~~~w~~l~-~l------------------~~~~~~gskIi-iTTR~~~~va~~~~~~~~~~~l  413 (1007)
                      +. .+..+++|.+.......-+.+. ..                  ... .+...++ .|++...............+.+
T Consensus        85 ~~-~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~-~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~  162 (239)
T d1ixsb2          85 LE-EGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLE-LPRFTLIGATTRPGLITAPLLSRFGIVEHL  162 (239)
T ss_dssp             CC-TTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEE-CCCCEEEEEESCCSSCSCGGGGGCSEEEEC
T ss_pred             CC-CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCC-CCCEEEEEECCCCCCCCCHHHCCCCEEEEE
T ss_conf             03-8873443110011044787500124333212110465565433468-997799963068333441010122145675


Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             999979999999963012443235799489999999999819972699
Q 001843          414 PGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       414 ~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  461 (1007)
                      ...+.++...+..+.+.....      ....+....|++.++|.+=.+
T Consensus       163 ~~~~~~~~~~i~~~~~~~~~i------~~~~~~l~~ia~~s~gd~R~a  204 (239)
T d1ixsb2         163 EYYTPEELAQGVMRDARLLGV------RITEEAALEIGRRSRGTMRVA  204 (239)
T ss_dssp             CCCCHHHHHHHHHHHHGGGCC------CBCHHHHHHHHHHTTSSHHHH
T ss_pred             ECCCHHHHHHHHHHHHHHHCC------CCCHHHHHHHHHHCCCCHHHH
T ss_conf             205745555788999998487------652678999999769999999

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.63  E-value=3.8e-07  Score=55.56  Aligned_cols=210  Identities=15%  Similarity=0.128  Sum_probs=105.3

Q ss_pred             CCCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCC
Q ss_conf             75177250219999984127888888655543210133210136776423478987689998888011102632246789
Q 001843          190 ETDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTT  269 (1007)
Q Consensus       190 ~~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (1007)
                      -.+++|.++.++.+.+|+..-..       ..          +.      .+                     .-....+
T Consensus        13 ~~dlig~~~~~~~L~~~l~~~~~-------~~----------~~------~~---------------------~~~~~~~   48 (253)
T d1sxja2          13 LQQVCGNKGSVMKLKNWLANWEN-------SK----------KN------SF---------------------KHAGKDG   48 (253)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHH-------HH----------HT------TT---------------------CCCCTTS
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHH-------CC----------HH------HH---------------------HHHCCCC
T ss_conf             99966989999999999996253-------00----------23------43---------------------2320257


Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             99968999993899808899999985320003788269999268988898999999999975533211023389999999
Q 001843          270 TTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       270 ~~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      .+..+.+.++|++|+||||+|+.+++.  ..  + ...++..+  ...+. ..+...................     ..
T Consensus        49 ~~~~~~lll~GPpG~GKTt~a~~la~~--~~--~-~~~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~~~~~~-----~~  115 (253)
T d1sxja2          49 SGVFRAAMLYGPPGIGKTTAAHLVAQE--LG--Y-DILEQNAS--DVRSK-TLLNAGVKNALDNMSVVGYFKH-----NE  115 (253)
T ss_dssp             TTSCSEEEEECSTTSSHHHHHHHHHHH--TT--C-EEEEECTT--SCCCH-HHHHHTGGGGTTBCCSTTTTTC-------
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHH--HH--H-HHHCCCCC--CCHHH-HHHHHHHHHHHHCCHHHHHHHH-----HH
T ss_conf             888744999879999888999999999--87--5-12013443--22116-8899999887631212101334-----32


Q ss_pred             HHHHCCCCCEEEEEECCCCCC---CHHHHHHCCCCCCCCCCCEEEEEC-CCCCCCCCCCCCCCEEEECCCCCHHHHHHHH
Q ss_conf             998819983799992967557---000112102237779994899984-8873112233785203664999979999999
Q 001843          350 ITQALDDSTFLIVMENAEHQK---SQVWDSFLGKLCSFTQCGKIIITT-SSTEDFVEPLGAAFSTLHVPGLGKNESWELF  425 (1007)
Q Consensus       350 l~~~L~~kr~LiVlDdv~~~~---~~~w~~l~~l~~~~~~gskIiiTT-R~~~~va~~~~~~~~~~~l~~L~~~ea~~Lf  425 (1007)
                      .......+..++++|++....   ...+..+..+... .....+++++ .... ...........+++.+++.++-...+
T Consensus       116 ~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~-~~~~ii~i~~~~~~~-~~~~l~~~~~~i~f~~~~~~~i~~~l  193 (253)
T d1sxja2         116 EAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK-TSTPLILICNERNLP-KMRPFDRVCLDIQFRRPDANSIKSRL  193 (253)
T ss_dssp             --CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHH-CSSCEEEEESCTTSS-TTGGGTTTSEEEECCCCCHHHHHHHH
T ss_pred             HCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCC-CCCCCCCCCCCCCCC-CCCCCCCEEEEEECCCCCHHHHHHHH
T ss_conf             0145566513777630111110001346777654012-342221113555521-13532440365311453146788999


Q ss_pred             HHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCC-HHHHHH
Q ss_conf             963012443235799489999999999819972-699999
Q 001843          426 LKKARIAEDVLQSRSSELIKLKKQILNICDGLP-LRVVLL  464 (1007)
Q Consensus       426 ~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlP-Lai~~l  464 (1007)
                      ...+....-   ..++   +....|++.++|-. -||..+
T Consensus       194 ~~i~~~e~i---~i~~---~~l~~i~~~s~GDiR~ai~~L  227 (253)
T d1sxja2         194 MTIAIREKF---KLDP---NVIDRLIQTTRGDIRQVINLL  227 (253)
T ss_dssp             HHHHHHHTC---CCCT---THHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHCC---CCCH---HHHHHHHHHCCCCHHHHHHHH
T ss_conf             999998099---9999---999999996797099999999

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.61  E-value=1.5e-10  Score=75.33  Aligned_cols=98  Identities=18%  Similarity=0.152  Sum_probs=54.3

Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCC--CCCCCCEEC
Q ss_conf             898830199926887898678700069876858851367775348323268799898615874321344--223335020
Q 001843          666 RRLGMLKVLDLEGVYKPMLTNNNALGRLPFLEYLGLRSTFIDSLPDSTPILFCLATLDVSHTKVQRLPY--AFWPSRHLY  743 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~~~~~lp~~i~~L~~Lr~L~L~~~~i~~LP~~i~~L~~L~~Ldl~~~~l~~lP~--~i~~Lr~L~  743 (1007)
                      ..++.|+.|+|++|.+.  .++ .+..+.+|++|+|++|.++.+|..+..+.+|++|++++|.+..++.  .+.+|++|+
T Consensus        45 ~~L~~L~~L~Ls~n~I~--~i~-~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l~~N~i~~l~~~~~l~~L~~L~  121 (198)
T d1m9la_          45 STLKACKHLALSTNNIE--KIS-SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLSGIEKLVNLRVLY  121 (198)
T ss_dssp             HHTTTCCEEECSEEEES--CCC-CHHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEECSEEECCCHHHHHHHHHSSEEE
T ss_pred             HCCCCCCEEECCCCCCC--CCC-CCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             62604615199446899--864-424782535734135343210000332212333333332222222222222341112


Q ss_pred             CCCCCCCCCCCCCC--CCCCCCCCCCCCC
Q ss_conf             33212334343466--4356768775423
Q 001843          744 LNWIFLATNVFRHP--QFVKWETSLQTLW  770 (1007)
Q Consensus       744 l~~~~~~~~~~~lp--~~i~~L~~L~~L~  770 (1007)
                      ++   ++. ...++  ..+..+++|+.|.
T Consensus       122 L~---~N~-i~~~~~~~~l~~l~~L~~L~  146 (198)
T d1m9la_         122 MS---NNK-ITNWGEIDKLAALDKLEDLL  146 (198)
T ss_dssp             ES---EEE-CCCHHHHHHHTTTTTCSEEE
T ss_pred             CC---CCH-HCCCCCCCCCCCCCCCCEEE
T ss_conf             34---102-12554221236777630234

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.59  E-value=2.2e-07  Score=56.90  Aligned_cols=151  Identities=14%  Similarity=0.197  Sum_probs=85.9

Q ss_pred             CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             51772502199999841278888886555432101332101367764234789876899988880111026322467899
Q 001843          191 TDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTT  270 (1007)
Q Consensus       191 ~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (1007)
                      ..++||++++++++..|.....                                                          
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~k----------------------------------------------------------   43 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRTK----------------------------------------------------------   43 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSS----------------------------------------------------------
T ss_pred             CCCCCCHHHHHHHHHHHHCCCC----------------------------------------------------------
T ss_conf             9872809999999999953588----------------------------------------------------------


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHH---HCCCC-CCCEEEE-EECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             996899999389980889999998532---00037-8826999-926898889899999999997553321102338999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRV---YVKRH-FTKRAWV-HIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEE  345 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~---~v~~~-F~~~~wv-~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~  345 (1007)
                         .-+.++|.+|+|||+++..++..-   .+-.. -+..+|. +.+               .-+.+.    ....+.++
T Consensus        44 ---~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~---------------~LiAg~----~~rG~~E~  101 (195)
T d1jbka_          44 ---NNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMG---------------ALVAGA----KYRGEFEE  101 (195)
T ss_dssp             ---CEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHH---------------HHHTTT----CSHHHHHH
T ss_pred             ---CCEEEEECCCCCCHHHHHHHHHHHHHCCCCHHHCCCEEEEEEHH---------------HHHCCC----CCCHHHHH
T ss_conf             ---87399835875447999999999980899978818569996699---------------986458----74077999


Q ss_pred             HHHHHHHHC--CCCCEEEEEECCCCC--------CCHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------E
Q ss_conf             999999881--998379999296755--------700011210223777999489998488731122337852------0
Q 001843          346 LMWRITQAL--DDSTFLIVMENAEHQ--------KSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAF------S  409 (1007)
Q Consensus       346 l~~~l~~~L--~~kr~LiVlDdv~~~--------~~~~w~~l~~l~~~~~~gskIiiTTR~~~~va~~~~~~~------~  409 (1007)
                      ....+...+  ...+.++++|++..-        ..+.-+-+++....  ..-++|.||.... .........      .
T Consensus       102 rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~r--g~l~~IgatT~ee-y~~~~e~d~aL~rrF~  178 (195)
T d1jbka_         102 RLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLDE-YRQYIEKDAALERRFQ  178 (195)
T ss_dssp             HHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHT--TSCCEEEEECHHH-HHHHTTTCHHHHTTEE
T ss_pred             HHHHHHHHHHCCCCCEEEECCHHHHHHCCCCCCCCCCHHHHHHHHHHC--CCCEEEECCCHHH-HHHHHHCCHHHHHCCC
T ss_conf             999999987317980899726089984378777752389999999857--9954985189999-9999873889996398


Q ss_pred             EEECCCCCHHHHHHH
Q ss_conf             366499997999999
Q 001843          410 TLHVPGLGKNESWEL  424 (1007)
Q Consensus       410 ~~~l~~L~~~ea~~L  424 (1007)
                      .+.+...+.+++..+
T Consensus       179 ~I~V~Ep~~e~t~~I  193 (195)
T d1jbka_         179 KVFVAEPSVEDTIAI  193 (195)
T ss_dssp             EEECCCCCHHHHHTT
T ss_pred             EEECCCCCHHHHHHH
T ss_conf             754589898999998

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.57  E-value=4.9e-07  Score=54.87  Aligned_cols=156  Identities=15%  Similarity=0.185  Sum_probs=90.6

Q ss_pred             CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             51772502199999841278888886555432101332101367764234789876899988880111026322467899
Q 001843          191 TDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTT  270 (1007)
Q Consensus       191 ~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (1007)
                      ..++||++++.+++..|.....                                                          
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k----------------------------------------------------------   43 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTK----------------------------------------------------------   43 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSC----------------------------------------------------------
T ss_pred             CCCCCCHHHHHHHHHHHHCCCC----------------------------------------------------------
T ss_conf             9874808999999999824889----------------------------------------------------------


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHH---HCCCC-CCCEEEEE-ECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             996899999389980889999998532---00037-88269999-26898889899999999997553321102338999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRV---YVKRH-FTKRAWVH-IPIMSMVEDRDVLADILKQIDESLLKVEATLSAEE  345 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~---~v~~~-F~~~~wv~-vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~  345 (1007)
                         .-+.++|.+|+|||+++..+++.-   .+-.. .+.++|.- ++                .+...   .......++
T Consensus        44 ---~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~----------------~l~ag---~~~~g~~e~  101 (387)
T d1qvra2          44 ---NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMG----------------SLLAG---AKYRGEFEE  101 (387)
T ss_dssp             ---CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC------------------------------CHHH
T ss_pred             ---CCCEEECCCCCCHHHHHHHHHHHHHHCCCCHHHCCCEEEEEEHH----------------HHHCC---CCCCHHHHH
T ss_conf             ---99768799998899999999999980899978869668995576----------------66526---674136899


Q ss_pred             HHHHHHHHC-C-CCCEEEEEECCCCC--------CCHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------E
Q ss_conf             999999881-9-98379999296755--------700011210223777999489998488731122337852------0
Q 001843          346 LMWRITQAL-D-DSTFLIVMENAEHQ--------KSQVWDSFLGKLCSFTQCGKIIITTSSTEDFVEPLGAAF------S  409 (1007)
Q Consensus       346 l~~~l~~~L-~-~kr~LiVlDdv~~~--------~~~~w~~l~~l~~~~~~gskIiiTTR~~~~va~~~~~~~------~  409 (1007)
                      ....+...+ . ..+.++++|++..-        +...-+-+++....  ..-++|.+|.... .... ....      .
T Consensus       102 r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~r--g~~~~I~~tT~~e-y~~~-e~d~al~rrF~  177 (387)
T d1qvra2         102 RLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR--GELRLIGATTLDE-YREI-EKDPALERRFQ  177 (387)
T ss_dssp             HHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHT--TCCCEEEEECHHH-HHHH-TTCTTTCSCCC
T ss_pred             HHHHHHHHHCCCCCCEEEEECCHHHHHCCCCCCCCCCHHHHHHHHHHC--CCCCEEEECCHHH-HHHH-CCCHHHHHHCC
T ss_conf             999999985058996698724088884277787741389999999737--8851666368999-9876-33679998246


Q ss_pred             EEECCCCCHHHHHHHHHHHHC
Q ss_conf             366499997999999996301
Q 001843          410 TLHVPGLGKNESWELFLKKAR  430 (1007)
Q Consensus       410 ~~~l~~L~~~ea~~Lf~~~a~  430 (1007)
                      .+.+.+.+.+++..++.....
T Consensus       178 ~v~v~ep~~~~~~~il~~~~~  198 (387)
T d1qvra2         178 PVYVDEPTVEETISILRGLKE  198 (387)
T ss_dssp             CEEECCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHH
T ss_conf             112799867889999999999

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.51  E-value=1.7e-06  Score=51.78  Aligned_cols=157  Identities=13%  Similarity=0.077  Sum_probs=82.8

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             96899999389980889999998532000378826999926898889899999999997553321102338999999999
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .++-+-++|++|.|||++|+.+++  ....+   .+.+..+                .+...    ........+...+.
T Consensus        41 ~~~giLl~GppGtGKT~la~aia~--~~~~~---~~~i~~~----------------~l~~~----~~g~~~~~l~~~f~   95 (247)
T d1ixza_          41 IPKGVLLVGPPGVGKTHLARAVAG--EARVP---FITASGS----------------DFVEM----FVGVGAARVRDLFE   95 (247)
T ss_dssp             CCSEEEEECCTTSSHHHHHHHHHH--HTTCC---EEEEEHH----------------HHHHS----CTTHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH--HCCCC---EEEEEHH----------------HHHHC----CCCHHHHHHHHHHH
T ss_conf             886488766898883599999998--73997---7997869----------------96462----45389999999999


Q ss_pred             HHCCCCCEEEEEECCCCC------C----CH----HHHHHCCCCCCCCCCC-EEEE-ECCCCCCCCCCCC---CCCEEEE
Q ss_conf             881998379999296755------7----00----0112102237779994-8999-8488731122337---8520366
Q 001843          352 QALDDSTFLIVMENAEHQ------K----SQ----VWDSFLGKLCSFTQCG-KIII-TTSSTEDFVEPLG---AAFSTLH  412 (1007)
Q Consensus       352 ~~L~~kr~LiVlDdv~~~------~----~~----~w~~l~~l~~~~~~gs-kIii-TTR~~~~va~~~~---~~~~~~~  412 (1007)
                      ..-...++.|++||++..      .    ..    ....+....++..... -++| ||.....+-....   -..+.+.
T Consensus        96 ~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~  175 (247)
T d1ixza_          96 TAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA  175 (247)
T ss_dssp             HHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGSCGGGGSTTSSCEEEE
T ss_pred             HHHHCCCEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCHHHCCCCCCCEEEE
T ss_conf             99976997999977366474678998887589999999999996387778998999807994006996758987857999


Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             499997999999996301244323579948999999999981997269
Q 001843          413 VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  460 (1007)
                      +.+.+.++-.++|..........   ...    ....+++.|.|..-+
T Consensus       176 ~~~P~~~eR~~il~~~l~~~~~~---~~~----~~~~la~~t~g~s~~  216 (247)
T d1ixza_         176 IDAPDVKGREQILRIHARGKPLA---EDV----DLALLAKRTPGFVGA  216 (247)
T ss_dssp             CCSCCHHHHHHHHHHHHTTSCBC---TTC----CHHHHHHTCTTCCHH
T ss_pred             ECCCCHHHHHHHHHHHHCCCCCC---CCC----CHHHHHHHCCCCCHH
T ss_conf             79969999999999875065776---546----899999778898899

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.49  E-value=4.7e-07  Score=54.99  Aligned_cols=158  Identities=17%  Similarity=0.116  Sum_probs=86.7

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             99689999938998088999999853200037882699992689888989999999999755332110233899999999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      +.++-+-++|++|.|||++|+.+++  ....+|   +.+..+                .+...    ........+...+
T Consensus        36 ~~~~giLL~GppGtGKT~l~~ala~--~~~~~~---~~i~~~----------------~l~~~----~~g~~~~~l~~~f   90 (258)
T d1e32a2          36 KPPRGILLYGPPGTGKTLIARAVAN--ETGAFF---FLINGP----------------EIMSK----LAGESESNLRKAF   90 (258)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHH--HTTCEE---EEECHH----------------HHTTS----CTTHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHH--HHCCEE---EEEECH----------------HHCCC----CCCCHHHHHHHHH
T ss_conf             9886468766998883089999998--748837---999730----------------43025----4561788889999


Q ss_pred             HHHCCCCCEEEEEECCCCC-------CCHHH----HHHC-CCCC-CCCCCCEEEEECCCCCCCCCCCCC---CCEEEECC
Q ss_conf             9881998379999296755-------70001----1210-2237-779994899984887311223378---52036649
Q 001843          351 TQALDDSTFLIVMENAEHQ-------KSQVW----DSFL-GKLC-SFTQCGKIIITTSSTEDFVEPLGA---AFSTLHVP  414 (1007)
Q Consensus       351 ~~~L~~kr~LiVlDdv~~~-------~~~~w----~~l~-~l~~-~~~~gskIiiTTR~~~~va~~~~~---~~~~~~l~  414 (1007)
                      ...-..++++|++||++..       +.+..    ..+. .+.. ....+.-||.||.....+-.....   ..+.+.++
T Consensus        91 ~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~  170 (258)
T d1e32a2          91 EEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIG  170 (258)
T ss_dssp             HHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGGTSTTSSCEEEECC
T ss_pred             HHHHHCCCEEEEEHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCHHHHHCCCCCCEEECC
T ss_conf             99986499499852111322578877770689998775001101234688117975799310252454246302323789


Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             9997999999996301244323579948999999999981997269
Q 001843          415 GLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       415 ~L~~~ea~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  460 (1007)
                      ..+.++-..+|.........   ....    ....|++.+.|.-.|
T Consensus       171 ~P~~~~R~~il~~~l~~~~~---~~~~----~~~~la~~t~G~s~a  209 (258)
T d1e32a2         171 IPDATGRLEILQIHTKNMKL---ADDV----DLEQVANETHGHVGA  209 (258)
T ss_dssp             CCCHHHHHHHHHHTTTTSCB---CTTC----CHHHHHHHCTTCCHH
T ss_pred             CCCHHHHHHHHHHHCCCCCC---CCCC----CHHHHHHCCCCCCHH
T ss_conf             99988999873220457633---4553----034444206677899

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.48  E-value=4.1e-07  Score=55.35  Aligned_cols=86  Identities=20%  Similarity=0.115  Sum_probs=43.5

Q ss_pred             CCCCCCEEEEEECCC-CCCCCCHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCCCC-CCCCCCCCCCCEEECCCCCCCCC
Q ss_conf             677750099995255-6799801234331023344898830199926887898678-70006987685885136777534
Q 001843          632 LLSWRLHSYLVFDSR-IRGTPAKQIGIILGKCISKRRLGMLKVLDLEGVYKPMLTN-NNALGRLPFLEYLGLRSTFIDSL  709 (1007)
Q Consensus       632 ~~~~~LRsL~l~~~~-~~~~~~~~~~~~l~~~f~~~~l~~LrvLdL~~~~~~~~~l-p~~i~~L~~Lr~L~L~~~~i~~L  709 (1007)
                      ...++++.|.+.++. ...        +.+..|  ..++.|+.|++++|.+.  .+ +..|..+.+|++|+|++|.++.+
T Consensus        28 ~~l~~l~~L~l~~n~~l~~--------i~~~~f--~~l~~L~~L~Ls~N~l~--~i~~~~f~~l~~L~~L~Ls~N~l~~l   95 (156)
T d2ifga3          28 PGAENLTELYIENQQHLQH--------LELRDL--RGLGELRNLTIVKSGLR--FVAPDAFHFTPRLSRLNLSFNALESL   95 (156)
T ss_dssp             CSCSCCSEEECCSCSSCCE--------ECGGGS--CSCCCCSEEECCSSCCC--EECTTGGGSCSCCCEEECCSSCCSCC
T ss_pred             CCCCCCCEEECCCCCCCCC--------CCCHHH--CCCCCCCCCEEECCCCC--CCCCCCCCCCCCCCCEECCCCCCCCC
T ss_conf             5765657431689866443--------692122--56666672162021247--74201112455433332267878515


Q ss_pred             CCCCCCCCCCCEEEECCCCC
Q ss_conf             83232687998986158743
Q 001843          710 PDSTPILFCLATLDVSHTKV  729 (1007)
Q Consensus       710 P~~i~~L~~L~~Ldl~~~~l  729 (1007)
                      |..+....+|+.|+++++.+
T Consensus        96 ~~~~~~~~~l~~L~L~~Np~  115 (156)
T d2ifga3          96 SWKTVQGLSLQELVLSGNPL  115 (156)
T ss_dssp             CSTTTCSCCCCEEECCSSCC
T ss_pred             CHHHHCCCCCCCCCCCCCCC
T ss_conf             74563353212433579863

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.48  E-value=5e-07  Score=54.83  Aligned_cols=78  Identities=17%  Similarity=0.094  Sum_probs=62.4

Q ss_pred             CCCCCCCEEEECCCC-CCCCCCC-CCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCEEEECCCCCCCCCCCCCC---C
Q ss_conf             898830199926887-8986787-000698768588513677753483-232687998986158743213442233---3
Q 001843          666 RRLGMLKVLDLEGVY-KPMLTNN-NALGRLPFLEYLGLRSTFIDSLPD-STPILFCLATLDVSHTKVQRLPYAFWP---S  739 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~-~~~~~lp-~~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~Ldl~~~~l~~lP~~i~~---L  739 (1007)
                      ..++.|+.|++.+++ +.  .++ ..|..+.+|+.|+|++|.++.++. .+..+++|++|++++|.++.+|.++..   |
T Consensus        28 ~~l~~l~~L~l~~n~~l~--~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~N~l~~l~~~~~~~~~l  105 (156)
T d2ifga3          28 PGAENLTELYIENQQHLQ--HLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSL  105 (156)
T ss_dssp             CSCSCCSEEECCSCSSCC--EECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCCSTTTCSCCC
T ss_pred             CCCCCCCEEECCCCCCCC--CCCCHHHCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCHHHHCCCCC
T ss_conf             576565743168986644--369212256666672162021247742011124554333322678785157456335321


Q ss_pred             CEECCC
Q ss_conf             502033
Q 001843          740 RHLYLN  745 (1007)
Q Consensus       740 r~L~l~  745 (1007)
                      ++|++.
T Consensus       106 ~~L~L~  111 (156)
T d2ifga3         106 QELVLS  111 (156)
T ss_dssp             CEEECC
T ss_pred             CCCCCC
T ss_conf             243357

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.45  E-value=9e-07  Score=53.33  Aligned_cols=133  Identities=14%  Similarity=0.212  Sum_probs=76.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755332110233899999999988
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      ..+.|+|..|.|||.|++.+++.  .......+++++..        +....+...+...        ......+.+   
T Consensus        37 n~l~l~G~~G~GKTHLl~A~~~~--~~~~~~~~~~~~~~--------~~~~~~~~~~~~~--------~~~~~~~~~---   95 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYSSAD--------DFAQAMVEHLKKG--------TINEFRNMY---   95 (213)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEEEHH--------HHHHHHHHHHHHT--------CHHHHHHHH---
T ss_pred             CCEEEECCCCCCHHHHHHHHHHH--HCCCCCCEEEECHH--------HHHHHHHHHHHCC--------CHHHHHHHH---
T ss_conf             85799888998399999999987--44676504884437--------8799999998716--------626678987---


Q ss_pred             CCCCCEEEEEECCCCCC-CHHHHHHC-CCC-CCCCCCCEEEEECCCCCCC--------CCCCCCCCEEEECCCCCHHHHH
Q ss_conf             19983799992967557-00011210-223-7779994899984887311--------2233785203664999979999
Q 001843          354 LDDSTFLIVMENAEHQK-SQVWDSFL-GKL-CSFTQCGKIIITTSSTEDF--------VEPLGAAFSTLHVPGLGKNESW  422 (1007)
Q Consensus       354 L~~kr~LiVlDdv~~~~-~~~w~~l~-~l~-~~~~~gskIiiTTR~~~~v--------a~~~~~~~~~~~l~~L~~~ea~  422 (1007)
                        ..--+|++||+.... ...|+... .+. .....|.+||+|++....-        ....... .+++++ +++++-.
T Consensus        96 --~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g-~~~~i~-p~d~~~~  171 (213)
T d1l8qa2          96 --KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGG-ILVEIE-LDNKTRF  171 (213)
T ss_dssp             --HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHHHHHTS-EEEECC-CCHHHHH
T ss_pred             --HHCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHCCCCCHHHHHHHHCC-EEEEEC-CCCHHHH
T ss_conf             --621301011265505865778899999998763166389954875100134326788886185-689978-8827999


Q ss_pred             HHHHHHHCC
Q ss_conf             999963012
Q 001843          423 ELFLKKARI  431 (1007)
Q Consensus       423 ~Lf~~~a~~  431 (1007)
                      +++.+.+-.
T Consensus       172 ~iL~~~a~~  180 (213)
T d1l8qa2         172 KIIKEKLKE  180 (213)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
T ss_conf             999999998

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.44  E-value=1.7e-06  Score=51.79  Aligned_cols=156  Identities=15%  Similarity=0.069  Sum_probs=85.8

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             96899999389980889999998532000378826999926898889899999999997553321102338999999999
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .++-+.++|++|.|||++|+.+++  ....+|   +-+..+  .-.+                  .........+...+.
T Consensus        44 ~~~~iLL~GppGtGKT~la~~iA~--~~~~~~---~~i~~~--~l~~------------------~~~g~~~~~l~~~f~   98 (256)
T d1lv7a_          44 IPKGVLMVGPPGTGKTLLAKAIAG--EAKVPF---FTISGS--DFVE------------------MFVGVGASRVRDMFE   98 (256)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH--HHTCCE---EEECSC--SSTT------------------SCCCCCHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHH--HCCCCE---EEEEHH--HHHH------------------CCHHHHHHHHHHHHH
T ss_conf             888678668998882289999999--829987---998869--9426------------------001078999999999


Q ss_pred             HHCCCCCEEEEEECCCCC----------CCHHH----HHHC-CCC--CCCCCCCEEEEECCCCCCCCCCCC---CCCEEE
Q ss_conf             881998379999296755----------70001----1210-223--777999489998488731122337---852036
Q 001843          352 QALDDSTFLIVMENAEHQ----------KSQVW----DSFL-GKL--CSFTQCGKIIITTSSTEDFVEPLG---AAFSTL  411 (1007)
Q Consensus       352 ~~L~~kr~LiVlDdv~~~----------~~~~w----~~l~-~l~--~~~~~gskIiiTTR~~~~va~~~~---~~~~~~  411 (1007)
                      ..-+..+++|++||++..          .....    ..+. .+.  .. ..+.-||.||...+.+-....   -..+.+
T Consensus        99 ~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~-~~~v~vIatTn~~~~ld~al~R~gRfd~~i  177 (256)
T d1lv7a_          99 QAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG-NEGIIVIAATNRPDVLDPALLRPGRFDRQV  177 (256)
T ss_dssp             HHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCS-SSCEEEEEEESCTTTSCGGGGSTTSSCEEE
T ss_pred             HHHHCCCEEEEEECHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCC-CCCEEEEEECCCCCCCCHHHCCCCCCCEEE
T ss_conf             9997599899997756657567898888748999999999999538777-799899980799310798576898787798


Q ss_pred             ECCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             6499997999999996301244323579948999999999981997269
Q 001843          412 HVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       412 ~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  460 (1007)
                      .+.+.+.++-.++|.........   ...    .....+++.+.|..-|
T Consensus       178 ~i~~P~~~~R~~il~~~l~~~~~---~~~----~~~~~la~~t~G~s~a  219 (256)
T d1lv7a_         178 VVGLPDVRGREQILKVHMRRVPL---APD----IDAAIIARGTPGFSGA  219 (256)
T ss_dssp             ECCCCCHHHHHHHHHHHHTTSCB---CTT----CCHHHHHHTCTTCCHH
T ss_pred             ECCCCCHHHHHHHHHHHCCCCCC---CCC----CCHHHHHHHCCCCCHH
T ss_conf             77995999999999984259986---865----6999999868998999

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.41  E-value=4.8e-06  Score=49.12  Aligned_cols=175  Identities=17%  Similarity=0.143  Sum_probs=92.7

Q ss_pred             CCEEECCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             51772502199999841278888886555432101332101367764234789876899988880111026322467899
Q 001843          191 TDVLGLERQVKELLHVLIPEHHGINDADVSTKKIVDGYEYARSSGEEITELPIPEQEGGGDALSNEEEESGRCQSSSTTT  270 (1007)
Q Consensus       191 ~~~vGr~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  270 (1007)
                      ++++|-++.++.+..|+.....                                                        .+
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~--------------------------------------------------------~~   32 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKM--------------------------------------------------------RG   32 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHH--------------------------------------------------------HT
T ss_pred             HHCCCHHHHHHHHHHHHHHHHH--------------------------------------------------------CC
T ss_conf             9908959999999999997885--------------------------------------------------------38


Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             99689999938998088999999853200037882699992689888989999999999755332110233899999999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      ....-+-++|++|+||||+|+.+++  .....   .+.++.+  .....                        ..+...+
T Consensus        33 ~~~~~~L~~GPpGtGKT~lA~~la~--~~~~~---~~~~~~~--~~~~~------------------------~~~~~~~   81 (238)
T d1in4a2          33 EVLDHVLLAGPPGLGKTTLAHIIAS--ELQTN---IHVTSGP--VLVKQ------------------------GDMAAIL   81 (238)
T ss_dssp             CCCCCEEEESSTTSSHHHHHHHHHH--HHTCC---EEEEETT--TCCSH------------------------HHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHH--CCCCC---CCCCCCC--CCCCH------------------------HHHHHHH
T ss_conf             8777489879999738899999985--03888---5332574--42248------------------------8899998


Q ss_pred             HHHCCCCCEEEEEECCCCCCCHHHHHHC-C------------------CCCCCCCCCEEEEECCCCCCCCCCCCCC-CEE
Q ss_conf             9881998379999296755700011210-2------------------2377799948999848873112233785-203
Q 001843          351 TQALDDSTFLIVMENAEHQKSQVWDSFL-G------------------KLCSFTQCGKIIITTSSTEDFVEPLGAA-FST  410 (1007)
Q Consensus       351 ~~~L~~kr~LiVlDdv~~~~~~~w~~l~-~------------------l~~~~~~gskIiiTTR~~~~va~~~~~~-~~~  410 (1007)
                      ..  ..++..+++|.+...+...-+.+. .                  .... .....+|.+|.....+....... ...
T Consensus        82 ~~--~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~I~at~~~~~~~~~~~~r~~~~  158 (238)
T d1in4a2          82 TS--LERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRID-IQPFTLVGATTRSGLLSSPLRSRFGII  158 (238)
T ss_dssp             HH--CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC----------------CCCEEEEEESCGGGSCHHHHTTCSEE
T ss_pred             HH--HCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCCCC-CCCEEEEEECCCCCCCCCCCEEEEEEE
T ss_conf             75--435882477789884067776421402441454454376002444457-887699995478755554311330079


Q ss_pred             EECCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             664999979999999963012443235799489999999999819972699
Q 001843          411 LHVPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLRV  461 (1007)
Q Consensus       411 ~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLai  461 (1007)
                      +.+++.+.++...++...+.....      ...++....|++.++|.+=.+
T Consensus       159 ~~~~~~~~~~~~~~l~~~~~~~~~------~~~~~~l~~i~~~s~gd~R~a  203 (238)
T d1in4a2         159 LELDFYTVKELKEIIKRAASLMDV------EIEDAAAEMIAKRSRGTPRIA  203 (238)
T ss_dssp             EECCCCCHHHHHHHHHHHHHHTTC------CBCHHHHHHHHHTSTTCHHHH
T ss_pred             EEECCCCHHHHHHHHHHHHHHCCC------HHHHHHHHHHHHHCCCCHHHH
T ss_conf             984478778777777776530110------025799999999679989999

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.10  E-value=4.1e-06  Score=49.49  Aligned_cols=157  Identities=13%  Similarity=0.096  Sum_probs=84.0

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             96899999389980889999998532000378826999926898889899999999997553321102338999999999
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      .++-|-++|++|.|||++|+.+++  ....+|     +.++      ..        .+...    ........+...+.
T Consensus        40 ~~~giLL~Gp~GtGKT~l~~ala~--~~~~~~-----~~~~------~~--------~l~~~----~~~~~~~~l~~~f~   94 (265)
T d1r7ra3          40 PSKGVLFYGPPGCGKTLLAKAIAN--ECQANF-----ISIK------GP--------ELLTM----WFGESEANVREIFD   94 (265)
T ss_dssp             CCCEEEEBCCTTSSHHHHHHHHHH--HTTCEE-----EEEC------HH--------HHHTS----CTTTHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHH--HHCCCE-----EEEE------HH--------HHHHC----CCCCHHHHHHHHHH
T ss_conf             887578878998763047788787--718947-----9988------79--------95253----16515899999999


Q ss_pred             HHCCCCCEEEEEECCCCCC-------CH-------HHHHHC-CCCCC-CCCCCEEEEECCCCCCCCCCCC---CCCEEEE
Q ss_conf             8819983799992967557-------00-------011210-22377-7999489998488731122337---8520366
Q 001843          352 QALDDSTFLIVMENAEHQK-------SQ-------VWDSFL-GKLCS-FTQCGKIIITTSSTEDFVEPLG---AAFSTLH  412 (1007)
Q Consensus       352 ~~L~~kr~LiVlDdv~~~~-------~~-------~w~~l~-~l~~~-~~~gskIiiTTR~~~~va~~~~---~~~~~~~  412 (1007)
                      ..-...+++|++||++.--       ..       ....+. .+... ...+--||.||...+.+-....   -....++
T Consensus        95 ~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~  174 (265)
T d1r7ra3          95 KARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIY  174 (265)
T ss_dssp             HHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTSCGGGSSTTSEEEEE
T ss_pred             HHHHCCCCCEEHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHCCHHHHCCCCCCEEEE
T ss_conf             99863984356875463245578767887379999999999996286777998999917992227997807877647999


Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHH
Q ss_conf             499997999999996301244323579948999999999981997269
Q 001843          413 VPGLGKNESWELFLKKARIAEDVLQSRSSELIKLKKQILNICDGLPLR  460 (1007)
Q Consensus       413 l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~l~~~~~~I~~~c~GlPLa  460 (1007)
                      ++..+.++-.++|.........   ..    .....++++++.|...+
T Consensus       175 ~~~p~~~~R~~il~~~l~~~~~---~~----~~~l~~la~~t~g~s~~  215 (265)
T d1r7ra3         175 IPLPDEKSRVAILKANLRKSPV---AK----DVDLEFLAKMTNGFSGA  215 (265)
T ss_dssp             CCCCCCHHHHHHHHHHTTCC-----------CCCCHHHHHHHCSSCCH
T ss_pred             ECCHHHHHHHHHHHHHHCCCCC---HH----HHHHHHHHHCCCCCCHH
T ss_conf             5660788899999999605771---02----43689998258999999

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=97.97  E-value=0.00019  Score=39.71  Aligned_cols=131  Identities=22%  Similarity=0.218  Sum_probs=61.8

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             68999993899808899999985320003788269999268988898999999999975533211023389999999998
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQ  352 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~  352 (1007)
                      ++-|-++|++|.|||++|+.+++  ....+|   +.+..+  ....             +    .........+...+..
T Consensus        40 ~~~vLL~GppGtGKT~la~alA~--~~~~~~---~~i~~~--~~~~-------------g----~~~~~~~~~i~~if~~   95 (246)
T d1d2na_          40 LVSVLLEGPPHSGKTALAAKIAE--ESNFPF---IKICSP--DKMI-------------G----FSETAKCQAMKKIFDD   95 (246)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH--HHTCSE---EEEECG--GGCT-------------T----CCHHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--CCCCCC---CCCCCC--CCCC-------------C----CCCCCHHHHHHHHHHH
T ss_conf             80799889699988999999862--010023---334565--2235-------------6----5421122444445655


Q ss_pred             HCCCCCEEEEEECCCCC----------CCHHHHHHCCCCC-CCCCCCEE--EEECCCCCCCCCCC---CCCCEEEECCCC
Q ss_conf             81998379999296755----------7000112102237-77999489--99848873112233---785203664999
Q 001843          353 ALDDSTFLIVMENAEHQ----------KSQVWDSFLGKLC-SFTQCGKI--IITTSSTEDFVEPL---GAAFSTLHVPGL  416 (1007)
Q Consensus       353 ~L~~kr~LiVlDdv~~~----------~~~~w~~l~~l~~-~~~~gskI--iiTTR~~~~va~~~---~~~~~~~~l~~L  416 (1007)
                      ..+..+++|++|+++.-          .......+..+.+ ....+.+|  |.||.... ....+   +-....+.++.+
T Consensus        96 A~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~-~ld~~~~~~rF~~~i~~P~~  174 (246)
T d1d2na_          96 AYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKD-VLQEMEMLNAFSTTIHVPNI  174 (246)
T ss_dssp             HHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHH-HHHHTTCTTTSSEEEECCCE
T ss_pred             HHHCCCCEEEHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCHH-HCCCHHHCCCCCEEEECCCC
T ss_conf             55324222331025667651345441247899999998607776545014553248832-25610201866338855991


Q ss_pred             C-HHHHHHHHHHH
Q ss_conf             9-79999999963
Q 001843          417 G-KNESWELFLKK  428 (1007)
Q Consensus       417 ~-~~ea~~Lf~~~  428 (1007)
                      . .++-++.+...
T Consensus       175 ~~r~~il~~l~~~  187 (246)
T d1d2na_         175 ATGEQLLEALELL  187 (246)
T ss_dssp             EEHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHC
T ss_conf             0599999999742

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.88  E-value=0.00018  Score=39.94  Aligned_cols=121  Identities=12%  Similarity=0.029  Sum_probs=72.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCC---CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             899999389980889999998532000378---82699992689888989999999999755332110233899999999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF---TKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRI  350 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F---~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l  350 (1007)
                      ..+-++|.+|.|||++|..+.+.  +...+   ....++.-.  ...--.+..+++...+...                 
T Consensus        16 ~~~l~~G~~g~gk~~~a~~l~~~--i~~~~~~h~D~~~i~~~--~~~I~Id~IR~i~~~~~~~-----------------   74 (198)
T d2gnoa2          16 ISILINGEDLSYPREVSLELPEY--VEKFPPKASDVLEIDPE--GENIGIDDIRTIKDFLNYS-----------------   74 (198)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHH--HHTSCCCTTTEEEECCS--SSCBCHHHHHHHHHHHTSC-----------------
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HHCCCCCCCCEEEEECC--CCCCCHHHHHHHHHHHHHC-----------------
T ss_conf             55998898998889999999999--84345679988998077--6789989999999999617-----------------


Q ss_pred             HHHCCCCCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCCCCCCCEEEECCCCCH
Q ss_conf             9881998379999296755700011210-2237779994899984887311223378520366499997
Q 001843          351 TQALDDSTFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEPLGAAFSTLHVPGLGK  418 (1007)
Q Consensus       351 ~~~L~~kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~~~~~~~~~~l~~L~~  418 (1007)
                        -..+++-++|+|+++.-+...++.+. .+-.. ..++..+++|.+...+.....+.+..+.+.+..+
T Consensus        75 --~~~~~~KviIId~ad~l~~~aqNaLLK~LEEP-p~~t~fiLit~~~~~ll~TI~SRC~~i~~~~p~~  140 (198)
T d2gnoa2          75 --PELYTRKYVIVHDCERMTQQAANAFLKALEEP-PEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKE  140 (198)
T ss_dssp             --CSSSSSEEEEETTGGGBCHHHHHHTHHHHHSC-CTTEEEEEEESCGGGSCHHHHTTSEEEECCCCHH
T ss_pred             --CCCCCCEEEEEECCCCCCHHHHHHHHHHHHCC-CCCCEEEECCCCHHHCHHHHHCCEEEEECCCCHH
T ss_conf             --54589879999473103666664788877378-9885222206995668788735227776799368

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.59  E-value=0.00026  Score=39.02  Aligned_cols=92  Identities=13%  Similarity=0.135  Sum_probs=52.0

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCH--HHHHHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             99968999993899808899999985320003788269999268988898--9999999999755332110233899999
Q 001843          270 TTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVED--RDVLADILKQIDESLLKVEATLSAEELM  347 (1007)
Q Consensus       270 ~~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~--~~~l~~il~~l~~~~~~~~~~~~~~~l~  347 (1007)
                      ++.+.||.++|+.|+||||-+-+++..  .+..=..+..++.   ..+..  .+-++...+.++.+........+.....
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~--~~~~g~kV~lit~---Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l   80 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQ--FEQQGKSVMLAAG---DTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVI   80 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHH--HHTTTCCEEEECC---CTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEEC---CCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHH
T ss_conf             999979999899999989999999999--9977994799823---21366612045554343388621135687799999


Q ss_pred             HHHHHHCCCCC-EEEEEECC
Q ss_conf             99998819983-79999296
Q 001843          348 WRITQALDDST-FLIVMENA  366 (1007)
Q Consensus       348 ~~l~~~L~~kr-~LiVlDdv  366 (1007)
                      ....+..+.+. =+|++|=.
T Consensus        81 ~~~~~~a~~~~~d~ilIDTa  100 (211)
T d2qy9a2          81 FDAIQAAKARNIDVLIADTA  100 (211)
T ss_dssp             HHHHHHHHHTTCSEEEECCC
T ss_pred             HHHHHHHHHCCCCEEEECCC
T ss_conf             99999998769988996568

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.48  E-value=0.00061  Score=36.80  Aligned_cols=85  Identities=15%  Similarity=0.179  Sum_probs=57.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHH--CCCCCHHHHHHHHH
Q ss_conf             8999993899808899999985320003788269999268988898999999999975533211--02338999999999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKV--EATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~--~~~~~~~~l~~~l~  351 (1007)
                      +++-|+|..|.|||++|.+++...  ...-..++|++..  ..++..     .+++++.+..+.  -.....++..+.+.
T Consensus        61 ~i~e~~G~~~~GKT~l~l~~~~~~--q~~g~~~vyIDtE--~~~~~e-----~a~~~GvD~d~il~~~~~~~E~~~~~~~  131 (269)
T d1mo6a1          61 RVIEIYGPESSGKTTVALHAVANA--QAAGGVAAFIDAE--HALDPD-----YAKKLGVDTDSLLVSQPDTGEQALEIAD  131 (269)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHHH--HHTTCEEEEEESS--CCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHH--HCCCCEEEEEECC--CCCCHH-----HHHHHCCCHHHEEEECCCCHHHHHHHHH
T ss_conf             369996488748899999999987--5489889999897--667999-----9998099889958966998999999999


Q ss_pred             HHCC-CCCEEEEEECCC
Q ss_conf             8819-983799992967
Q 001843          352 QALD-DSTFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~-~kr~LiVlDdv~  367 (1007)
                      .... ++.-|||+|-+-
T Consensus       132 ~l~~~~~~~liIiDSi~  148 (269)
T d1mo6a1         132 MLIRSGALDIVVIDSVA  148 (269)
T ss_dssp             HHHHTTCEEEEEEECST
T ss_pred             HHHHCCCCCEEEEECCC
T ss_conf             99855998789993302

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.45  E-value=0.00059  Score=36.90  Aligned_cols=85  Identities=12%  Similarity=0.164  Sum_probs=58.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC--CCCCHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755332110--2338999999999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVE--ATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~--~~~~~~~l~~~l~  351 (1007)
                      ++.-|+|.+|.|||++|.+++....  ..=..++|++..  ..++..     ++++++.+..+.-  ...+.++..+.+.
T Consensus        58 ~itei~G~~~sGKT~l~l~~~~~aq--k~g~~v~yiDtE--~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~  128 (268)
T d1xp8a1          58 RITEIYGPESGGKTTLALAIVAQAQ--KAGGTCAFIDAE--HALDPV-----YARALGVNTDELLVSQPDNGEQALEIME  128 (268)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESS--CCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH--HCCCEEEEEECC--CCCCHH-----HHHHHCCCCHHEEEECCCCHHHHHHHHH
T ss_conf             4789805876522799999999997--079989999887--658999-----9998289812379974899999999999


Q ss_pred             HHCCC-CCEEEEEECCC
Q ss_conf             88199-83799992967
Q 001843          352 QALDD-STFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~~-kr~LiVlDdv~  367 (1007)
                      ..++. ..-|||+|-+-
T Consensus       129 ~l~~~~~~~liIiDSi~  145 (268)
T d1xp8a1         129 LLVRSGAIDVVVVDSVA  145 (268)
T ss_dssp             HHHTTTCCSEEEEECTT
T ss_pred             HHHHCCCCCEEEEECCC
T ss_conf             99865897199994545

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.39  E-value=0.0012  Score=35.13  Aligned_cols=91  Identities=23%  Similarity=0.224  Sum_probs=49.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755332110233899999999988
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +|+.++|+.|+||||.+.+++..  ...+-..+..+++. .......+.++...+.++.+........+...........
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~--~~~~g~kV~lit~D-t~R~gA~eQL~~~a~~l~v~~~~~~~~~~~~~~~~~~~~~   87 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALY--YKGKGRRPLLVAAD-TQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEK   87 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHH--HHHTTCCEEEEECC-SSCHHHHHHHHHHHHHHTCCEEECCTTCCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             68999899999889999999999--99779927999544-3464088889999986288631112442036788889888


Q ss_pred             CC-CCCEEEEEECCC
Q ss_conf             19-983799992967
Q 001843          354 LD-DSTFLIVMENAE  367 (1007)
Q Consensus       354 L~-~kr~LiVlDdv~  367 (1007)
                      .+ ...=++++|=..
T Consensus        88 ~~~~~~d~vlIDTaG  102 (207)
T d1ls1a2          88 ARLEARDLILVDTAG  102 (207)
T ss_dssp             HHHHTCCEEEEECCC
T ss_pred             HHHCCCCCEEECCCC
T ss_conf             763367640334544

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.33  E-value=0.00052  Score=37.23  Aligned_cols=57  Identities=18%  Similarity=0.119  Sum_probs=40.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             899999389980889999998532000378826999926898889899999999997553
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES  333 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~  333 (1007)
                      +++.++|+.|+||||.+-+++..  ...+=..+..++.. .......+.++...+.++.+
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~--~~~~g~kV~lit~D-t~R~gA~eQL~~~a~~l~i~   63 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRY--YQNLGKKVMFCAGD-TFRAAGGTQLSEWGKRLSIP   63 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHH--HHTTTCCEEEECCC-CSSTTHHHHHHHHHHHHTCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEEEC-CCCCCCHHHHHHCCCCCCCE
T ss_conf             79999899999889999999999--99779907999813-66654026676405456823

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.31  E-value=0.0007  Score=36.48  Aligned_cols=90  Identities=12%  Similarity=0.146  Sum_probs=51.0

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCC--HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             96899999389980889999998532000378826999926898889--8999999999975533211023389999999
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVE--DRDVLADILKQIDESLLKVEATLSAEELMWR  349 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~--~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~  349 (1007)
                      .+.|+.++|+.|+||||-+-+++..  ...+-..+..+++.   .+.  ..+.++...+.++..........+.......
T Consensus        10 ~p~vi~lvGptGvGKTTTiAKLAa~--~~~~~~kV~lit~D---t~R~gA~eQL~~~a~~l~i~~~~~~~~~d~~~~~~~   84 (213)
T d1vmaa2          10 PPFVIMVVGVNGTGKTTSCGKLAKM--FVDEGKSVVLAAAD---TFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFD   84 (213)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH--HHHTTCCEEEEEEC---TTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEEEC---CCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHH
T ss_conf             9989999899999889999999999--99779906999601---334204678887764327641036777768998788


Q ss_pred             HHHH-CCCCCEEEEEECC
Q ss_conf             9988-1998379999296
Q 001843          350 ITQA-LDDSTFLIVMENA  366 (1007)
Q Consensus       350 l~~~-L~~kr~LiVlDdv  366 (1007)
                      .... ..+..=+|++|=.
T Consensus        85 ~~~~~~~~~~d~ilIDTa  102 (213)
T d1vmaa2          85 AVAHALARNKDVVIIDTA  102 (213)
T ss_dssp             HHHHHHHTTCSEEEEEEC
T ss_pred             HHHHHHHCCCCEEEEECC
T ss_conf             789998769998998245

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.29  E-value=0.0003  Score=38.58  Aligned_cols=65  Identities=18%  Similarity=0.205  Sum_probs=39.8

Q ss_pred             CCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             99996899999389980889999998532000378826999926898889899999999997553321102338999999
Q 001843          269 TTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       269 ~~~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      ..+.+.+|.++|++|.||||+|++.+..  .     ...+++..                          .......+..
T Consensus        10 ~~~~p~liil~G~pGsGKST~a~~l~~~--~-----~~~~i~~D--------------------------~~~~~~~~~~   56 (172)
T d1yj5a2          10 LSPNPEVVVAVGFPGAGKSTFIQEHLVS--A-----GYVHVNRD--------------------------TLGSWQRCVS   56 (172)
T ss_dssp             SCSSCCEEEEECCTTSSHHHHHHHHTGG--G-----TCEEEEHH--------------------------HHCSHHHHHH
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHH--C-----CCEEECHH--------------------------HHHHHHHHHH
T ss_conf             7999989999899999899999999976--5-----97897607--------------------------7778889999


Q ss_pred             HHHHHCCCCCEEEEEECCC
Q ss_conf             9998819983799992967
Q 001843          349 RITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       349 ~l~~~L~~kr~LiVlDdv~  367 (1007)
                      .++..|..+ ..+|+|+..
T Consensus        57 ~~~~~l~~g-~~vIiD~t~   74 (172)
T d1yj5a2          57 SCQAALRQG-KRVVIDNTN   74 (172)
T ss_dssp             HHHHHHHTT-CCEEEESCC
T ss_pred             HHHHHHHCC-CCCEEECCC
T ss_conf             999999779-995551767

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.25  E-value=1e-05  Score=47.18  Aligned_cols=70  Identities=16%  Similarity=0.070  Sum_probs=43.5

Q ss_pred             HHCCCCCCCCCCCCCEEEECCCCCCCCCC---CCCCCCCCCCCEEECCCCCCCCCCC-CCCCCCCCCEEEECCCCCCC
Q ss_conf             31023344898830199926887898678---7000698768588513677753483-23268799898615874321
Q 001843          658 ILGKCISKRRLGMLKVLDLEGVYKPMLTN---NNALGRLPFLEYLGLRSTFIDSLPD-STPILFCLATLDVSHTKVQR  731 (1007)
Q Consensus       658 ~l~~~f~~~~l~~LrvLdL~~~~~~~~~l---p~~i~~L~~Lr~L~L~~~~i~~LP~-~i~~L~~L~~Ldl~~~~l~~  731 (1007)
                      .++.++  ..++.|++|+|++|.+.  .+   +..+..+.+|++|+|++|.++.++. ......+|+.|++.++.+..
T Consensus        56 ~l~~~~--~~~~~L~~L~Ls~N~i~--~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~Npl~~  129 (162)
T d1koha1          56 TLRIIE--ENIPELLSLNLSNNRLY--RLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLSD  129 (162)
T ss_dssp             HHHHHH--HHCTTCCCCCCCSSCCC--CCSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTSTTSS
T ss_pred             HHHHHH--HHCCCCCEEECCCCCCC--CCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEEECCCCCCCC
T ss_conf             607889--74878788637776666--773158898658856100043572134234422203310426648997676

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.19  E-value=0.0023  Score=33.45  Aligned_cols=91  Identities=12%  Similarity=0.169  Sum_probs=48.4

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             96899999389980889999998532000378826999926898889899999999997553321102338999999999
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRIT  351 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~  351 (1007)
                      +..++..+|+.|+|||.||+.++.  .+.   ...+-++++.......      +.+-++..     ...-.......+.
T Consensus        51 p~~~~lf~Gp~GvGKT~lak~la~--~l~---~~~i~~d~s~~~~~~~------~~~l~g~~-----~gy~g~~~~~~l~  114 (315)
T d1r6bx3          51 PVGSFLFAGPTGVGKTEVTVQLSK--ALG---IELLRFDMSEYMERHT------VSRLIGAP-----PGYVGFDQGGLLT  114 (315)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHH--HHT---CEEEEEEGGGCSSSSC------CSSSCCCC-----SCSHHHHHTTHHH
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHH--HCC---CCEEEECCCCCCCHHH------HHHHCCCC-----CCCCCCCCCCHHH
T ss_conf             765899977875006999999986--336---7706741544455446------66521467-----8750114687033


Q ss_pred             HHC-CCCCEEEEEECCCCCCCHHHHHHC
Q ss_conf             881-998379999296755700011210
Q 001843          352 QAL-DDSTFLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       352 ~~L-~~kr~LiVlDdv~~~~~~~w~~l~  378 (1007)
                      ..+ +.....+.+|+++..+.+.|+.+.
T Consensus       115 ~~~~~~~~~vvl~DeieKa~~~V~~~lL  142 (315)
T d1r6bx3         115 DAVIKHPHAVLLLDEIEKAHPDVFNILL  142 (315)
T ss_dssp             HHHHHCSSEEEEEETGGGSCHHHHHHHH
T ss_pred             HHHHHCCCCHHHHCCCCCCCCHHHHHHH
T ss_conf             7777385430221222301633766567

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=97.19  E-value=0.0014  Score=34.81  Aligned_cols=85  Identities=15%  Similarity=0.203  Sum_probs=53.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHC--CCCCHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755332110--2338999999999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVE--ATLSAEELMWRIT  351 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~--~~~~~~~l~~~l~  351 (1007)
                      +++-|+|.+|.||||+|.+++...  ...=..++|++..  ..++..     .++.++.+..+.-  .....++..+.+.
T Consensus        55 ~itei~G~~gsGKTtl~l~~~~~~--q~~g~~~vyidtE--~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~  125 (263)
T d1u94a1          55 RIVEIYGPESSGKTTLTLQVIAAA--QREGKTCAFIDAE--HALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  125 (263)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHH--HHTTCCEEEEESS--CCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHH--HCCCCEEEEECCC--CCCCHH-----HHHHHCCCHHHEEEECCCCHHHHHHHHH
T ss_conf             589980577747899999999998--7089879998654--454899-----9998399879979962898999999999


Q ss_pred             HHCC-CCCEEEEEECCC
Q ss_conf             8819-983799992967
Q 001843          352 QALD-DSTFLIVMENAE  367 (1007)
Q Consensus       352 ~~L~-~kr~LiVlDdv~  367 (1007)
                      ...+ +..-|||+|-+-
T Consensus       126 ~l~~~~~~~liViDSi~  142 (263)
T d1u94a1         126 ALARSGAVDVIVVDSVA  142 (263)
T ss_dssp             HHHHHTCCSEEEEECGG
T ss_pred             HHHHCCCCCEEEEECCC
T ss_conf             99854999899998865

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=97.18  E-value=0.0012  Score=35.02  Aligned_cols=95  Identities=20%  Similarity=0.194  Sum_probs=49.8

Q ss_pred             CCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             99996899999389980889999998532000378826999926898889899999999997553321102338999999
Q 001843          269 TTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       269 ~~~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      ++..+.|+.++|+.|+||||.+-+++..  .+..=..+..+++. .......+-++...+.++.+........+......
T Consensus         8 ~~k~p~vi~lvGptGvGKTTTiAKLA~~--~~~~g~kV~lit~D-t~R~ga~eQL~~~a~~l~v~~~~~~~~~~~~~~~~   84 (211)
T d1j8yf2           8 PDKIPYVIMLVGVQGTGKATTAGKLAYF--YKKKGFKVGLVGAD-VYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAK   84 (211)
T ss_dssp             CSSSSEEEEEECSCCC----HHHHHHHH--HHHTTCCEEEEECC-CSSHHHHHHHHHHHHHHTCCEECCTTCCCHHHHHH
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEEEE-CCCCCHHHHHHHHCCCCCCCEEECCCCHHHHHHHH
T ss_conf             9999989999899999989999999999--99779936999720-23551567898740146842230244102447899


Q ss_pred             H-HHHHCCCCCEEEEEECC
Q ss_conf             9-99881998379999296
Q 001843          349 R-ITQALDDSTFLIVMENA  366 (1007)
Q Consensus       349 ~-l~~~L~~kr~LiVlDdv  366 (1007)
                      . +........=+|++|=.
T Consensus        85 ~a~~~~~~~~~d~IlIDTa  103 (211)
T d1j8yf2          85 RGVEKFLSEKMEIIIVDTA  103 (211)
T ss_dssp             HHHHHHHHTTCSEEEEECC
T ss_pred             HHHHHHHCCCCCEEEEECC
T ss_conf             9998740267736998537

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.16  E-value=0.00055  Score=37.10  Aligned_cols=93  Identities=13%  Similarity=0.220  Sum_probs=49.1

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHH
Q ss_conf             689999938998088999999853200037882699992689888989999999999755332110233-8999999999
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATL-SAEELMWRIT  351 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~-~~~~l~~~l~  351 (1007)
                      ..++..+|+.|+|||.+|+.++.  .+-..-...+-+..+   .+........+.   +.+  ...... ....+.+.++
T Consensus        53 ~~~~lf~Gp~G~GKt~lak~la~--~l~~~~~~~~~~~~~---~~~~~~~~~~L~---g~~--~gyvG~~~~~~l~~~~~  122 (315)
T d1qvra3          53 IGSFLFLGPTGVGKTELAKTLAA--TLFDTEEAMIRIDMT---EYMEKHAVSRLI---GAP--PGYVGYEEGGQLTEAVR  122 (315)
T ss_dssp             SEEEEEBSCSSSSHHHHHHHHHH--HHHSSGGGEEEECTT---TCCSSGGGGGC-------------------CHHHHHH
T ss_pred             CEEEEEECCCCCHHHHHHHHHHH--HHCCCCCCEEEEECC---CCCCCHHHHHHC---CCC--CCCCCCCCCCHHHHHHH
T ss_conf             66999978886248999999999--835887534887315---545421566514---899--98767466784899998


Q ss_pred             HHCCCCCEEEEEECCCCCCCHHHHHHC
Q ss_conf             881998379999296755700011210
Q 001843          352 QALDDSTFLIVMENAEHQKSQVWDSFL  378 (1007)
Q Consensus       352 ~~L~~kr~LiVlDdv~~~~~~~w~~l~  378 (1007)
                      +   .....|++|+++..+...++.+.
T Consensus       123 ~---~p~~Vvl~DEieK~~~~v~~~ll  146 (315)
T d1qvra3         123 R---RPYSVILFDEIEKAHPDVFNILL  146 (315)
T ss_dssp             H---CSSEEEEESSGGGSCHHHHHHHH
T ss_pred             H---CCCCEEEEEHHHHCCHHHHHHHH
T ss_conf             4---99837997147540789998999

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.01  E-value=0.00062  Score=36.79  Aligned_cols=38  Identities=26%  Similarity=0.289  Sum_probs=28.6

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             9689999938998088999999853200037882699992
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHI  311 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~v  311 (1007)
                      ++-+|+|.|..|.||||||+.+..  ...........++.
T Consensus        21 ~~~iIgI~G~~GSGKSTla~~L~~--~l~~~~~~~~~~~~   58 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKTTLANQLSQ--TLREQGISVCVFHM   58 (198)
T ss_dssp             SSEEEEEEECTTSSHHHHHHHHHH--HHHHTTCCEEEEEG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--HHCCCCCCCEECCC
T ss_conf             988999789887899999999999--83634665200122

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.00  E-value=0.00053  Score=37.17  Aligned_cols=35  Identities=23%  Similarity=0.193  Sum_probs=27.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCC-CCCCEEEEE
Q ss_conf             8999993899808899999985320003-788269999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR-HFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~-~F~~~~wv~  310 (1007)
                      .+|.++|++|.||||+|+.++.  +... .++...++.
T Consensus         7 ~~I~l~G~~GsGKTTia~~La~--~L~~~~~~~~~~~~   42 (183)
T d1m8pa3           7 FTIFLTGYMNSGKDAIARALQV--TLNQQGGRSVSLLL   42 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH--HHHHHCSSCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHHHCCCCCHHHHH
T ss_conf             6999889999999999999999--98650798403211

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.98  E-value=0.00025  Score=39.06  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=21.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +.|.|.|+.|+||||||+.++..
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             28999899999899999999998

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.96  E-value=0.0028  Score=32.99  Aligned_cols=23  Identities=26%  Similarity=0.512  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .-|.|.|..|+|||++|+.+++.
T Consensus        24 ~pvlI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2          24 CPVLITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             SCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHH
T ss_conf             97899899981799999999996

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=96.95  E-value=0.0018  Score=34.02  Aligned_cols=37  Identities=19%  Similarity=0.213  Sum_probs=31.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEC
Q ss_conf             899999389980889999998532000378826999926
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs  312 (1007)
                      +++.|+|.+|.|||++|.+++.  ....+...++|++..
T Consensus        27 sl~li~G~pGsGKT~l~~qia~--~~~~~~~~~~~is~e   63 (242)
T d1tf7a2          27 SIILATGATGTGKTLLVSRFVE--NACANKERAILFAYE   63 (242)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH--HHHTTTCCEEEEESS
T ss_pred             EEEEEEECCCCCHHHHHHHHHH--HHHHHCCCCCEEECC
T ss_conf             4999991899999999999999--998723244112126

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=96.85  E-value=0.00062  Score=36.78  Aligned_cols=29  Identities=28%  Similarity=0.473  Sum_probs=23.8

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             6899999389980889999998532000378
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F  303 (1007)
                      ++.|.++|++|.||||||+.+++  .....|
T Consensus        32 P~~ilL~GpPGtGKT~la~~la~--~~~~~~   60 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTSLRSAIFE--ETQGNV   60 (273)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHH--HTTTCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--HHHCCE
T ss_conf             97999889799889999999999--865154

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.82  E-value=0.00011  Score=41.10  Aligned_cols=44  Identities=18%  Similarity=0.113  Sum_probs=27.4

Q ss_pred             CCCCCCCEEECCCCCCCCCC---CCCCCCCCCCEEEECCCCCCCCCC
Q ss_conf             69876858851367775348---323268799898615874321344
Q 001843          691 GRLPFLEYLGLRSTFIDSLP---DSTPILFCLATLDVSHTKVQRLPY  734 (1007)
Q Consensus       691 ~~L~~Lr~L~L~~~~i~~LP---~~i~~L~~L~~Ldl~~~~l~~lP~  734 (1007)
                      ..+.+|++|+|++|.++.++   ..+..+++|++|++++|.+..++.
T Consensus        62 ~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~  108 (162)
T d1koha1          62 ENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERE  108 (162)
T ss_dssp             HHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGG
T ss_pred             HHCCCCCEEECCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCHH
T ss_conf             74878788637776666773158898658856100043572134234

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=96.79  E-value=0.0011  Score=35.26  Aligned_cols=37  Identities=22%  Similarity=0.221  Sum_probs=27.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEC
Q ss_conf             899999389980889999998532000378826999926
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs  312 (1007)
                      +.|+|+|-||+||||+|..++..  ....-..++-++..
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~--LA~~G~rVllID~D   38 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSG--LHAMGKTIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEEEC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEECC
T ss_conf             79999899857799999999999--99689958999637

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.77  E-value=0.00054  Score=37.12  Aligned_cols=23  Identities=35%  Similarity=0.424  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +.|.|.|.+|+|||||+++++..
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             69999889997199999999999

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.76  E-value=0.00069  Score=36.49  Aligned_cols=35  Identities=26%  Similarity=0.274  Sum_probs=27.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             8999993899808899999985320003788269999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~  310 (1007)
                      .+|.++|++|.||||+|+.++.  +....+....++.
T Consensus        20 ~vI~L~G~pGSGKTTiAk~La~--~l~~~~~~~~~~~   54 (195)
T d1x6va3          20 CTVWLTGLSGAGKTTVSMALEE--YLVCHGIPCYTLD   54 (195)
T ss_dssp             EEEEEESSCHHHHHHHHHHHHH--HHHHTTCCEEEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHHHCCCCCCCHH
T ss_conf             6999889999999999999999--9974479731000

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.72  E-value=0.0033  Score=32.54  Aligned_cols=81  Identities=14%  Similarity=0.234  Sum_probs=49.4

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHCCCCCC--CEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             9968999993899808899999985320003788--26999926898889899999999997553321102338999999
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYNRVYVKRHFT--KRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMW  348 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~--~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~  348 (1007)
                      +.+-+|+|.|..|.||||+|+.+..  .....+.  .+.-++..  .-+-..+.+..  ..+... .......+.+.+.+
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~--lL~~~~~~~~v~~Is~D--~F~~~~~~l~~--~~~~~~-~g~Pes~D~~~L~~  150 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQA--LLSRWPEHRRVELITTD--GFLHPNQVLKE--RGLMKK-KGFPESYDMHRLVK  150 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHH--HHTTSTTCCCEEEEEGG--GGBCCHHHHHH--HTCTTC-TTSGGGBCHHHHHH
T ss_pred             CCCEEEEEECCCCCCCCHHHHHHHH--HHHHHCCCCCEEEEEEE--EEECCCHHHHH--HCCCCC-CCCHHHHHHHHHHH
T ss_conf             9988999968999987689999999--97304689965999521--56898458888--368766-88167631999999


Q ss_pred             HHHHHCCCCC
Q ss_conf             9998819983
Q 001843          349 RITQALDDST  358 (1007)
Q Consensus       349 ~l~~~L~~kr  358 (1007)
                      .+.....++.
T Consensus       151 ~L~~lk~g~~  160 (308)
T d1sq5a_         151 FVSDLKSGVP  160 (308)
T ss_dssp             HHHHHTTTCS
T ss_pred             HHHHHHCCCC
T ss_conf             9999975998

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=96.71  E-value=0.00037  Score=38.07  Aligned_cols=23  Identities=35%  Similarity=0.621  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +.|.+.|++|+||||+|+.++..
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~   25 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQ   25 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             74999899999999999999999

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.69  E-value=0.00066  Score=36.61  Aligned_cols=24  Identities=21%  Similarity=0.422  Sum_probs=21.8

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             689999938998088999999853
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      |.+|.++|.+|.||||+|++++..
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~   25 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRY   25 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             989999899999999999999999

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.67  E-value=0.00093  Score=35.75  Aligned_cols=25  Identities=32%  Similarity=0.558  Sum_probs=22.3

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9689999938998088999999853
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..+++.|.|++|.||||+|+.+...
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~La~~   29 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASEVAHQ   29 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             8718999899998989999999998

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.67  E-value=0.0017  Score=34.24  Aligned_cols=23  Identities=26%  Similarity=0.382  Sum_probs=20.9

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             68999993899808899999985
Q 001843          273 TQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ++++.+.|-||+||||+|..++.
T Consensus         8 p~~i~~sGKGGVGKTTvaa~lA~   30 (296)
T d1ihua1           8 PPYLFFTGKGGVGKTSISCATAI   30 (296)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCHHHHHHHHHHH
T ss_conf             85999979986749999999999

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.62  E-value=0.00076  Score=36.27  Aligned_cols=22  Identities=27%  Similarity=0.465  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ++|.|.|++|.||||+|+.+..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             0899989999998999999999

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=96.61  E-value=0.001  Score=35.46  Aligned_cols=27  Identities=26%  Similarity=0.364  Sum_probs=23.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             89999938998088999999853200037
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH  302 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~  302 (1007)
                      .|+.|+|..|.|||||+.++.+  ....+
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~--~l~~~   29 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIP--ALCAR   29 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH--HHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHHHC
T ss_conf             8899991899989999999999--99977

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=96.61  E-value=0.0019  Score=33.90  Aligned_cols=38  Identities=29%  Similarity=0.307  Sum_probs=25.9

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEC
Q ss_conf             6899999389980889999998532000378826999926
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs  312 (1007)
                      .++|.+.|-||+||||+|..++..  ....-..++-|+..
T Consensus        20 ~~iii~sGKGGVGKTT~a~nLA~~--lA~~G~rVllvD~D   57 (279)
T d1ihua2          20 HGLIMLMGKGGVGKTTMAAAIAVR--LADMGFDVHLTTSD   57 (279)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEECC
T ss_conf             789999799988789999999999--99789938999379

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.59  E-value=0.0068  Score=30.72  Aligned_cols=91  Identities=20%  Similarity=0.239  Sum_probs=51.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCC-HHHHHHHHHHHHHHH----HHHH-----CCCCCH
Q ss_conf             899999389980889999998532000378826999926898889-899999999997553----3211-----023389
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVE-DRDVLADILKQIDES----LLKV-----EATLSA  343 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~-~~~~l~~il~~l~~~----~~~~-----~~~~~~  343 (1007)
                      .-++|.|..|+|||+|+.++.++. .+.+=+..+++.++  +... ..++.+++.+.--..    ..+.     ...+..
T Consensus        69 Qr~~If~~~g~GKt~l~~~i~~~~-~~~~~~v~V~~~iG--er~~ev~~~~~~~~~~~~~~~~~~~~~tvvv~~~s~~~~  145 (276)
T d2jdid3          69 GKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVG--ERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPP  145 (276)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH-TTTCSSEEEEEEES--CCHHHHHHHHHHHHHHTSSCSSSSCCCEEEEEECTTSCH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH-HHHCCCEEEEEEEC--CCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEECCCCCH
T ss_conf             877766799989899999999988-76179969999955--575999999999886176545666423899997899999


Q ss_pred             H--H----HHHHHHHHC---CCCCEEEEEECCC
Q ss_conf             9--9----999999881---9983799992967
Q 001843          344 E--E----LMWRITQAL---DDSTFLIVMENAE  367 (1007)
Q Consensus       344 ~--~----l~~~l~~~L---~~kr~LiVlDdv~  367 (1007)
                      .  .    ..-.+.+++   +++..|+++||+.
T Consensus       146 ~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dslt  178 (276)
T d2jdid3         146 GARARVALTGLTVAEYFRDQEGQDVLLFIDNIF  178 (276)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHH
T ss_conf             999999999999999988637984899970606

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.54  E-value=0.00096  Score=35.66  Aligned_cols=22  Identities=45%  Similarity=0.601  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ++|.|+|++|.||||+|+++..
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             7999989999999999999999

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.50  E-value=0.0007  Score=36.47  Aligned_cols=26  Identities=31%  Similarity=0.517  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             89999938998088999999853200037
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH  302 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~  302 (1007)
                      ++| +.|++|+||||+|+.++.  +..-.
T Consensus         3 ~Iv-liG~~G~GKSTig~~La~--~l~~~   28 (165)
T d2iyva1           3 KAV-LVGLPGSGKSTIGRRLAK--ALGVG   28 (165)
T ss_dssp             SEE-EECSTTSSHHHHHHHHHH--HHTCC
T ss_pred             CEE-EECCCCCCHHHHHHHHHH--HHCCC
T ss_conf             489-988999988999999999--84998

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=96.46  E-value=0.0011  Score=35.31  Aligned_cols=24  Identities=29%  Similarity=0.458  Sum_probs=21.9

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             689999938998088999999853
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +.+|.|+|++|.||||+|+.++..
T Consensus         6 p~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           6 PNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             948999899999889999999999

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=96.46  E-value=0.0024  Score=33.40  Aligned_cols=37  Identities=24%  Similarity=0.222  Sum_probs=27.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEC
Q ss_conf             899999389980889999998532000378826999926
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs  312 (1007)
                      +.|+|.|-||+||||+|..++..  ....-..++-|+..
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~--LA~~G~rVLlID~D   39 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAA--LAEMGKKVMIVGCD   39 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEEEEEC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEECC
T ss_conf             28999899987799999999999--99789978999518

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=96.44  E-value=0.0072  Score=30.56  Aligned_cols=69  Identities=19%  Similarity=0.178  Sum_probs=38.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755332110233899999999988
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      .++.++|++|+|||.||+.++.  .+..++.. +-+..+  +-.+                   ....+.+..++.+.+.
T Consensus       124 g~~l~~G~pG~GKT~la~ala~--~~~~~~~~-~~~~~~--~~~~-------------------~~~G~~e~~~~~~f~~  179 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGE--ALGGKDKY-ATVRFG--EPLS-------------------GYNTDFNVFVDDIARA  179 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHH--HHHTTSCC-EEEEBS--CSST-------------------TCBCCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHCCCCCE-EEEEHH--HHHH-------------------CCCCHHHHHHHHHHHH
T ss_conf             6388877998508899999999--86379980-897826--8544-------------------2444578999999999


Q ss_pred             CCCCCEEEEEECCC
Q ss_conf             19983799992967
Q 001843          354 LDDSTFLIVMENAE  367 (1007)
Q Consensus       354 L~~kr~LiVlDdv~  367 (1007)
                      .+ +..+|++|.++
T Consensus       180 a~-~~~ilf~DEid  192 (321)
T d1w44a_         180 ML-QHRVIVIDSLK  192 (321)
T ss_dssp             HH-HCSEEEEECCT
T ss_pred             HH-HCCEEEEEHHH
T ss_conf             86-26589741012

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=96.44  E-value=0.003  Score=32.78  Aligned_cols=71  Identities=15%  Similarity=0.070  Sum_probs=39.6

Q ss_pred             HHCCCCCCCCCCCCCEEEECCCC-CCCCC---CCCCCCCCCCCCEEECCCCCCC-----CCCCCCCCCCCCCEEEECCCC
Q ss_conf             31023344898830199926887-89867---8700069876858851367775-----348323268799898615874
Q 001843          658 ILGKCISKRRLGMLKVLDLEGVY-KPMLT---NNNALGRLPFLEYLGLRSTFID-----SLPDSTPILFCLATLDVSHTK  728 (1007)
Q Consensus       658 ~l~~~f~~~~l~~LrvLdL~~~~-~~~~~---lp~~i~~L~~Lr~L~L~~~~i~-----~LP~~i~~L~~L~~Ldl~~~~  728 (1007)
                      .+..+.  ...+.|+.|+|+++. +....   +-..+....+|++|+|+++.+.     .+...+...+.|++|++++|.
T Consensus         6 ~l~~l~--~n~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~   83 (167)
T d1pgva_           6 CINRLR--EDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNF   83 (167)
T ss_dssp             HHHHHH--TTCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSB
T ss_pred             HHHHHH--HCCCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEEHHH
T ss_conf             999998--289998197827999989899999999976377645401201562156798875310002343300330102


Q ss_pred             CC
Q ss_conf             32
Q 001843          729 VQ  730 (1007)
Q Consensus       729 l~  730 (1007)
                      +.
T Consensus        84 i~   85 (167)
T d1pgva_          84 LT   85 (167)
T ss_dssp             CC
T ss_pred             CC
T ss_conf             14

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.37  E-value=0.0012  Score=35.07  Aligned_cols=22  Identities=27%  Similarity=0.505  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ++|.|.|.+|.||||+|+.++.
T Consensus         4 kiI~l~G~~GsGKsTva~~L~~   25 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             5999989999998999999999

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=96.36  E-value=0.0045  Score=31.73  Aligned_cols=86  Identities=14%  Similarity=0.167  Sum_probs=45.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEE-ECCCCCCCHHHHHHHHHHHHHHHHHHHCCC----------CC
Q ss_conf             8999993899808899999985320003788269999-268988898999999999975533211023----------38
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH-IPIMSMVEDRDVLADILKQIDESLLKVEAT----------LS  342 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~-vs~~~~~~~~~~l~~il~~l~~~~~~~~~~----------~~  342 (1007)
                      .-++|.|..|+|||+|+.++.+... ..+-++++.+. +.  +....   ..++........-.....          ..
T Consensus        44 Qr~~I~g~~g~GKT~l~~~i~~~~~-~~~~~~v~~~~~ig--er~~e---v~~~~~~~~~~vv~~t~d~~~~~r~~~~~~  117 (289)
T d1xpua3          44 QRGLIVAPPKAGKTMLLQNIAQSIA-YNHPDCVLMVLLID--ERPEE---VTEMQRLVKGEVVASTFDEPASRHVQVAEM  117 (289)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHH-HHCTTSEEEEEEEE--ECHHH---HHHHHHHCSSEEEEEETTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH-HCCCCEEEEEEEEC--EEHHH---HHHHHHHCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             7556867999887899999999775-15897699987611--00878---876775405079960588835678999999


Q ss_pred             HHHHHHHHHHHCCCCCEEEEEECCC
Q ss_conf             9999999998819983799992967
Q 001843          343 AEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       343 ~~~l~~~l~~~L~~kr~LiVlDdv~  367 (1007)
                      .-...+.++.  +++.+|+++||+-
T Consensus       118 a~~iAEyfrd--~G~dVLli~Dslt  140 (289)
T d1xpua3         118 VIEKAKRLVE--HKKDVIILLDSIT  140 (289)
T ss_dssp             HHHHHHHHHT--TTCEEEEEESCHH
T ss_pred             HHHHHHHHHH--HCCCCEEECCCHH
T ss_conf             9999999998--2657515517689

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.34  E-value=0.002  Score=33.82  Aligned_cols=28  Identities=21%  Similarity=0.456  Sum_probs=23.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             899999389980889999998532000378
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F  303 (1007)
                      ++|.|.|+.|.||||+++.+..  +.....
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~--~l~~~~   29 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMD--NLRKEG   29 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH--HHHTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHHHCC
T ss_conf             8899989999898999999999--998769

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.32  E-value=0.0016  Score=34.33  Aligned_cols=22  Identities=41%  Similarity=0.696  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ++|.|.|++|.||||+|+.+..
T Consensus         5 ~iI~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           5 NILLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             5999988999988999999999

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.32  E-value=0.001  Score=35.53  Aligned_cols=23  Identities=39%  Similarity=0.564  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..|.|.|++|.||||+|+.++..
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~   27 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASK   27 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             97989899999989999999999

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.29  E-value=0.0021  Score=33.69  Aligned_cols=24  Identities=29%  Similarity=0.459  Sum_probs=22.0

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             689999938998088999999853
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..+|.|.|++|.||||+|+.++..
T Consensus         8 ~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           8 VSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             728999899999989999999998

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.24  E-value=0.016  Score=28.49  Aligned_cols=86  Identities=16%  Similarity=0.183  Sum_probs=50.5

Q ss_pred             CCCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCC--C-CCEEEEEECCCCCCCHHHHHHHHHHHHHHH-H---HHHCCC
Q ss_conf             89999689999938998088999999853200037--8-826999926898889899999999997553-3---211023
Q 001843          268 TTTTTTQVIALIGKAGSGKTTLARIVYNRVYVKRH--F-TKRAWVHIPIMSMVEDRDVLADILKQIDES-L---LKVEAT  340 (1007)
Q Consensus       268 ~~~~~~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~--F-~~~~wv~vs~~~~~~~~~~l~~il~~l~~~-~---~~~~~~  340 (1007)
                      .+++.+-+|+|.|..|.||||||..+..  .....  + ..++.++..  .-+-..+-...+....... .   ......
T Consensus        22 ~~~~~P~iIGi~G~qGSGKSTl~~~l~~--~L~~~~~~~~~v~~iS~D--dfY~t~~~r~~L~~~~~~~pl~~~RG~PgT   97 (286)
T d1odfa_          22 TGNKCPLFIFFSGPQGSGKSFTSIQIYN--HLMEKYGGEKSIGYASID--DFYLTHEDQLKLNEQFKNNKLLQGRGLPGT   97 (286)
T ss_dssp             TTCCSCEEEEEECCTTSSHHHHHHHHHH--HHHHHHGGGSCEEEEEGG--GGBCCHHHHHHHHHHTTTCGGGSSSCSTTS
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHH--HHHHHHCCCCCEEEECCC--CCCCCHHHHHHHHHHCCCCCCCEECCCCCC
T ss_conf             4899988998379987889999999999--999872778606763567--777888999998521355531100478740


Q ss_pred             CCHHHHHHHHHHHCCCC
Q ss_conf             38999999999881998
Q 001843          341 LSAEELMWRITQALDDS  357 (1007)
Q Consensus       341 ~~~~~l~~~l~~~L~~k  357 (1007)
                      -+...+.+.+....++.
T Consensus        98 hD~~ll~~~l~~l~~~~  114 (286)
T d1odfa_          98 HDMKLLQEVLNTIFNNN  114 (286)
T ss_dssp             BCHHHHHHHHHHHTC--
T ss_pred             HHHHHHHHHHHHHHHHC
T ss_conf             34889999999997402

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.21  E-value=0.0024  Score=33.33  Aligned_cols=28  Identities=32%  Similarity=0.245  Sum_probs=23.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             899999389980889999998532000378
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F  303 (1007)
                      ++++|+|..|.|||||+.++..  ..+.+-
T Consensus         2 kii~I~G~~gSGKTTli~~l~~--~L~~~g   29 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVA--AAVREG   29 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH--HHHHTT
T ss_pred             CEEEEEECCCCCHHHHHHHHHH--HHHHCC
T ss_conf             0999980999989999999999--998679

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.19  E-value=0.0013  Score=34.94  Aligned_cols=21  Identities=52%  Similarity=0.725  Sum_probs=19.0

Q ss_pred             EEEECCCCCHHHHHHHHHHHH
Q ss_conf             999938998088999999853
Q 001843          276 IALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       276 i~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      |.+.||+|.||||+|+.++..
T Consensus         3 I~liG~~GsGKsTi~k~La~~   23 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKD   23 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
T ss_conf             999899999889999999998

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=96.19  E-value=0.0046  Score=31.71  Aligned_cols=22  Identities=41%  Similarity=0.913  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..++|+|..|.|||||++.+..
T Consensus        30 e~vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9999999999989999999973

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.17  E-value=0.0037  Score=32.27  Aligned_cols=35  Identities=17%  Similarity=0.243  Sum_probs=25.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             8999993899808899999985320003788269999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~  310 (1007)
                      ++|.|.|+.|.||||+++.+..  ......-....+.
T Consensus         2 kiivi~G~~GsGKTT~~~~La~--~L~~~~~~~~~~~   36 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKE--ILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH--HHHTTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEE
T ss_conf             1999989899898999999999--9987699889997

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=96.14  E-value=0.002  Score=33.77  Aligned_cols=23  Identities=30%  Similarity=0.564  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..|.|.|++|.||||+|+.++..
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCHHHHHHHHHHH
T ss_conf             88999828999889999999998

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.13  E-value=0.0012  Score=35.10  Aligned_cols=23  Identities=39%  Similarity=0.566  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +-+.++|++|+|||.||+.+++.
T Consensus        50 ~~iLl~GPpG~GKT~lAkalA~~   72 (309)
T d1ofha_          50 KNILMIGPTGVGKTEIARRLAKL   72 (309)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHC
T ss_conf             66999899998888999998621

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=96.02  E-value=0.0014  Score=34.65  Aligned_cols=23  Identities=30%  Similarity=0.488  Sum_probs=19.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +.|.+.|++|.||||+|+.+++.
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~   25 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARA   25 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHH
T ss_conf             98899889999889999999999

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.01  E-value=0.0027  Score=33.02  Aligned_cols=24  Identities=25%  Similarity=0.466  Sum_probs=21.7

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             689999938998088999999853
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      |.+|.|.|++|.||||+|+.+++.
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             939999799999989999999998

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=95.98  E-value=0.0029  Score=32.83  Aligned_cols=23  Identities=30%  Similarity=0.491  Sum_probs=20.1

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             968999993899808899999985
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ++++| |.|++|.||||+|+.++.
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHH
T ss_pred             CCEEE-EECCCCCCHHHHHHHHHH
T ss_conf             63899-989999988999999999

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.89  E-value=0.0036  Score=32.31  Aligned_cols=83  Identities=8%  Similarity=0.148  Sum_probs=41.2

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHCCCC-C----CCEEEEEECCC-CCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             689999938998088999999853200037-8----82699992689-88898999999999975533211023389999
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNRVYVKRH-F----TKRAWVHIPIM-SMVEDRDVLADILKQIDESLLKVEATLSAEEL  346 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~~~v~~~-F----~~~~wv~vs~~-~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l  346 (1007)
                      |=+|+|.|..|.||||+|+.+...  .... +    ..+.-++..+. ............  .-... .......+.+.+
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~--l~~~~~~~~~~~~~vi~~D~yy~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~l   76 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQL--LGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKAL--KGQFN-FDHPDAFDNELI   76 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH--TTGGGSCGGGCSEEEEEGGGGBCCCCHHHHHHHH--TTCSC-TTSGGGBCHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHH--HCHHCCCCCCCCEEEEECCCCCCCCCHHHHHHHH--HCCCC-CCCCHHHHHHHH
T ss_conf             989999899978799999999999--6410134578843999346532244022203555--14555-578278887777


Q ss_pred             HHHHHHHCCCCCEE
Q ss_conf             99999881998379
Q 001843          347 MWRITQALDDSTFL  360 (1007)
Q Consensus       347 ~~~l~~~L~~kr~L  360 (1007)
                      .+.+.....++...
T Consensus        77 ~~~~~~~~~~~~~~   90 (213)
T d1uj2a_          77 LKTLKEITEGKTVQ   90 (213)
T ss_dssp             HHHHHHHHTTCCEE
T ss_pred             HHHHHHHHCCCCCC
T ss_conf             76666653288631

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=95.88  E-value=0.0029  Score=32.89  Aligned_cols=44  Identities=18%  Similarity=0.306  Sum_probs=31.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDE  332 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~  332 (1007)
                      .||+|.|++|.||+|+|+.+++.  ..  |   .+++        .-+++|.++.....
T Consensus         4 piI~I~GppGSGKgT~ak~La~~--~g--l---~~iS--------tGdLlR~~a~~~~~   47 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAEA--LQ--W---HLLD--------SGAIYRVLALAALH   47 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH--HT--C---EEEE--------HHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH--HC--C---CEEC--------HHHHHHHHHHHHHH
T ss_conf             88997799988989999999999--69--9---0898--------88999999999987

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.87  E-value=0.0064  Score=30.85  Aligned_cols=37  Identities=24%  Similarity=0.261  Sum_probs=29.2

Q ss_pred             EEEEEE-CCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEC
Q ss_conf             899999-389980889999998532000378826999926
Q 001843          274 QVIALI-GKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~-G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs  312 (1007)
                      ++|+|+ |-||+||||+|..++.  .....-..++.++..
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~--~la~~g~~VlliD~D   39 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGV--ALAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHH--HHHHTTCCEEEEECC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH--HHHHCCCCEEEEECC
T ss_conf             79999799999809999999999--999689989999598

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=95.84  E-value=0.0093  Score=29.91  Aligned_cols=54  Identities=22%  Similarity=0.217  Sum_probs=34.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQ  329 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~  329 (1007)
                      .+|+|.|.+|.|||||...+...  .......++-+.+....+++-..++.+-.+.
T Consensus        55 ~~IgitG~pGaGKSTLi~~l~~~--~~~~g~~vavlavDpss~~~ggailgdr~rm  108 (327)
T d2p67a1          55 LRLGVTGTPGAGKSTFLEAFGML--LIREGLKVAVIAVDPSSPVTGGSILGDKTRM  108 (327)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH--HHHTTCCEEEEEECCC---------------
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEECCCCCEEEECCCCCCCHHHH
T ss_conf             28974389999899999999999--9756983322037776100065155413678

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.73  E-value=0.012  Score=29.27  Aligned_cols=83  Identities=13%  Similarity=0.166  Sum_probs=44.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH---HHH-HCCCCCHHHHHHH
Q ss_conf             899999389980889999998532000378826999926898889899999999997553---321-1023389999999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES---LLK-VEATLSAEELMWR  349 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~---~~~-~~~~~~~~~l~~~  349 (1007)
                      .+|+|.|..|.||||+|+.+.+  ..+..--..+.++..+...++..+.-..+...-...   ... ....-+.+.+.+.
T Consensus         5 pIIgIaG~SGSGKTTva~~l~~--i~~~~~v~~~iI~~Dsfyr~~R~~~~~~~~~~~~~~~~~~~~~~P~A~d~dlL~~~   82 (288)
T d1a7ja_           5 PIISVTGSSGAGTSTVKHTFDQ--IFRREGVKAVSIEGDAFHRFNRADMKAELDRRYAAGDATFSHFSYEANELKELERV   82 (288)
T ss_dssp             CEEEEESCC---CCTHHHHHHH--HHHHHTCCEEEEEGGGGBSCCHHHHHHHHHHHHHHTCTTCSTTSGGGBCHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHH
T ss_conf             8999989997809999999999--97156997699947778756502201113333354046779898442659999999


Q ss_pred             HHHHCCCCC
Q ss_conf             998819983
Q 001843          350 ITQALDDST  358 (1007)
Q Consensus       350 l~~~L~~kr  358 (1007)
                      ++...+++.
T Consensus        83 l~~L~~g~~   91 (288)
T d1a7ja_          83 FREYGETGQ   91 (288)
T ss_dssp             HHHHHHHSC
T ss_pred             HHHHHCCCC
T ss_conf             999987996

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.70  E-value=0.0034  Score=32.46  Aligned_cols=22  Identities=41%  Similarity=0.675  Sum_probs=19.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|+|..|.|||||++.+...
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~   23 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCHHHHHHHHHHHC
T ss_conf             8999989993899999999814

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=95.70  E-value=0.014  Score=28.89  Aligned_cols=85  Identities=16%  Similarity=0.172  Sum_probs=46.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH-HH--------CC-----
Q ss_conf             89999938998088999999853200037882699992689888989999999999755332-11--------02-----
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLL-KV--------EA-----  339 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~-~~--------~~-----  339 (1007)
                      .-++|.|..|+|||+|+.....  ....+.+.++++.+.  +.....   .++.+.+..... +.        ++     
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~--~~~~~~~v~V~~~iG--er~~Ev---~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r  140 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTIL--NQQGQNVICVYVAIG--QKASSV---AQVVTNFQERGAMEYTIVVAETADSPATLQ  140 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHH--TCCTTTCEEEEEEES--CCHHHH---HHHHHHTGGGTGGGSEEEEEECTTSCGGGT
T ss_pred             CEEEECCCCCCCHHHHHHHHHH--HHCCCCCEEEEEEEC--CHHHHH---HHHHHHHCCCCCCEEEEECCCCCCCCHHHH
T ss_conf             6676006778885799999776--540467535555522--126778---899985115775033100123467659999


Q ss_pred             ---CCCHHHHHHHHHHHCCCCCEEEEEECCC
Q ss_conf             ---3389999999998819983799992967
Q 001843          340 ---TLSAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       340 ---~~~~~~l~~~l~~~L~~kr~LiVlDdv~  367 (1007)
                         ....-...+.++.  ++++.|+++||+-
T Consensus       141 ~~a~~~a~tiAEyfrd--~G~~Vlll~Dslt  169 (276)
T d1fx0a3         141 YLAPYTGAALAEYFMY--RERHTLIIYDDLS  169 (276)
T ss_dssp             THHHHHHHHHHHHHHH--TTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHH--CCCCEEEEEECCH
T ss_conf             9999999988889997--5996457750538

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=95.69  E-value=0.0082  Score=30.24  Aligned_cols=70  Identities=17%  Similarity=0.208  Sum_probs=38.8

Q ss_pred             HHCCCCCCCCCCCCCEEEECCCC-CCCCC---CCCCCCCCCCCCEEECCCCCCC-----CCCCCCCCCCCCCEEEECCCC
Q ss_conf             31023344898830199926887-89867---8700069876858851367775-----348323268799898615874
Q 001843          658 ILGKCISKRRLGMLKVLDLEGVY-KPMLT---NNNALGRLPFLEYLGLRSTFID-----SLPDSTPILFCLATLDVSHTK  728 (1007)
Q Consensus       658 ~l~~~f~~~~l~~LrvLdL~~~~-~~~~~---lp~~i~~L~~Lr~L~L~~~~i~-----~LP~~i~~L~~L~~Ldl~~~~  728 (1007)
                      .+..+.  ...+.|+.|+++++. +....   +-..+....+|+.|+|+++.+.     .+-..+...+.|+.|++++|.
T Consensus         8 ~l~~~~--~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~   85 (166)
T d1io0a_           8 TLKRIQ--NNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNF   85 (166)
T ss_dssp             HHHHHH--TTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSC
T ss_pred             HHHHHH--HCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCHHHHHCCCC
T ss_conf             999999--559998688768999989899999998884198257430158961177899999877521221012102543


Q ss_pred             C
Q ss_conf             3
Q 001843          729 V  729 (1007)
Q Consensus       729 l  729 (1007)
                      +
T Consensus        86 ~   86 (166)
T d1io0a_          86 I   86 (166)
T ss_dssp             C
T ss_pred             C
T ss_conf             2

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.64  E-value=0.029  Score=27.07  Aligned_cols=35  Identities=20%  Similarity=0.220  Sum_probs=25.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             8999993899808899999985320003788269999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~  310 (1007)
                      ..|+|-|+.|.||||+++.+.+  ....+--.+.++.
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~--~L~~~g~~v~~~~   38 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVE--ALCAAGHRAELLR   38 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEE
T ss_conf             5999989988899999999999--9987799689996

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=95.59  E-value=0.0044  Score=31.78  Aligned_cols=45  Identities=22%  Similarity=0.248  Sum_probs=31.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             899999389980889999998532000378826999926898889899999999997553
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDES  333 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~  333 (1007)
                      -+|+|-|++|.||||+|+.++..  .    .. .+++        .-++++.++......
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~--l----g~-~~is--------tGdl~R~~a~~~~~~   48 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKD--F----GF-TYLD--------TGAMYRAATYMALKN   48 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHH--H----CC-EEEE--------HHHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH--H----CC-CEEC--------HHHHHHHHHHHHHHC
T ss_conf             59997899987989999999999--6----99-4787--------799999999999870

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=95.55  E-value=0.013  Score=29.01  Aligned_cols=23  Identities=22%  Similarity=0.289  Sum_probs=21.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .+|+|.|.+|.|||||..++...
T Consensus        52 ~~igitG~pGaGKSTli~~l~~~   74 (323)
T d2qm8a1          52 IRVGITGVPGVGKSTTIDALGSL   74 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             59861179988899999999998

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.49  E-value=0.006  Score=31.02  Aligned_cols=25  Identities=16%  Similarity=0.408  Sum_probs=22.7

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9689999938998088999999853
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ||+.|+|-|.-|+||||+++.+...
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~~   25 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             9819999899888599999999998

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.47  E-value=0.033  Score=26.73  Aligned_cols=45  Identities=22%  Similarity=0.327  Sum_probs=31.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCC----CCCCCEEEEEECCCCCCCHH
Q ss_conf             899999389980889999998532000----37882699992689888989
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK----RHFTKRAWVHIPIMSMVEDR  320 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~----~~F~~~~wv~vs~~~~~~~~  320 (1007)
                      +++.|+|.+|.|||++|.+++.+....    ......+|+...  ...+..
T Consensus        37 ~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~   85 (254)
T d1pzna2          37 AITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTE--NTFRPE   85 (254)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESS--SCCCHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHCHHHHCCCCCEEEEEECC--CHHHHH
T ss_conf             7999985898988999999999863448763889628998310--125899

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=95.46  E-value=0.0054  Score=31.28  Aligned_cols=25  Identities=32%  Similarity=0.365  Sum_probs=21.6

Q ss_pred             CCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             9968999993899808899999985
Q 001843          271 TTTQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       271 ~~~~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..+-+|+|-|.-|+||||+++.+..
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
T ss_conf             9861999889999888999999998

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=95.46  E-value=0.0035  Score=32.41  Aligned_cols=123  Identities=12%  Similarity=0.139  Sum_probs=56.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHH-HCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH-HH------CCCCCHH-
Q ss_conf             899999389980889999998532-00037882699992689888989999999999755332-11------0233899-
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRV-YVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLL-KV------EATLSAE-  344 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~-~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~-~~------~~~~~~~-  344 (1007)
                      ++..|.|.+|.||||++..+...- +....-...+.++..  .......+...+......-.. ..      ......+ 
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~Ap--TgkAA~~L~e~~~~~~~~~~~~~~~~~~~~~~~~t~~~  241 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAP--TGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTLHR  241 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBS--SHHHHHHHHHHHTHHHHHSSCCSCCCCSCSCCCBTTTS
T ss_pred             CEEEEECCCCCCCEEHHHHHHHHHHHHHHCCCCEEEEECC--CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             8599976898875216999999999987526982898437--59999999988877776458104455420134557899


Q ss_pred             -----HHHHHHHHH-CCC-CCEEEEEECCCCCCCHHHHHHC-CCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             -----999999988-199-8379999296755700011210-2237779994899984887311223
Q 001843          345 -----ELMWRITQA-LDD-STFLIVMENAEHQKSQVWDSFL-GKLCSFTQCGKIIITTSSTEDFVEP  403 (1007)
Q Consensus       345 -----~l~~~l~~~-L~~-kr~LiVlDdv~~~~~~~w~~l~-~l~~~~~~gskIiiTTR~~~~va~~  403 (1007)
                           .....+... -.. .--++|+|.+...+......+. .+    ..++++|+.--..+ +...
T Consensus       242 ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~~~l~~~ll~~~----~~~~~lILvGD~~Q-LppV  303 (359)
T d1w36d1         242 LLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDAL----PDHARVIFLGDRDQ-LASV  303 (359)
T ss_dssp             CC-----------CTTSCCSCSEEEECSGGGCBHHHHHHHHHTC----CTTCEEEEEECTTS-GGGT
T ss_pred             HHHHHHCCHHHHHHHHCCCCCCEEEEHHHHCCCHHHHHHHHHHH----CCCCEEEEECCHHH-CCCC
T ss_conf             87631000677775436665413465332144899999999872----59998999777221-6687

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=95.43  E-value=0.0061  Score=30.98  Aligned_cols=24  Identities=33%  Similarity=0.614  Sum_probs=20.5

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             968999993899808899999985
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+-+|+|.|..|.||||+|..+-.
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
T ss_conf             998999989887789999999998

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=95.40  E-value=0.0059  Score=31.08  Aligned_cols=27  Identities=30%  Similarity=0.320  Sum_probs=23.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             89999938998088999999853200037
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH  302 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~  302 (1007)
                      +.+.++|++|+|||++|+.+++  .....
T Consensus       155 ~~~~~~g~~~~gk~~~~~~~~~--~~~~~  181 (362)
T d1svma_         155 RYWLFKGPIDSGKTTLAAALLE--LCGGK  181 (362)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH--HHCCE
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HCCCC
T ss_conf             7699989999888999999999--85997

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.40  E-value=0.0041  Score=32.02  Aligned_cols=30  Identities=27%  Similarity=0.462  Sum_probs=23.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             89999938998088999999853200037882
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTK  305 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~  305 (1007)
                      +.|.|+|+.|+|||||++.+++  .....|..
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~--~~~~~~~~   31 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFA--EYPDSFGF   31 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH--HCTTTEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HCCCCEEE
T ss_conf             7699989999998999999997--48866247

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=95.32  E-value=0.0084  Score=30.17  Aligned_cols=35  Identities=29%  Similarity=0.242  Sum_probs=25.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCC-CCCCEEEEE
Q ss_conf             8999993899808899999985320003-788269999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR-HFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~-~F~~~~wv~  310 (1007)
                      .+|-+.|++|.||||||+.+..  +... ..-..+++.
T Consensus        25 ~vIwltGlsGsGKTTia~~L~~--~l~~~~~~~~~~ld   60 (208)
T d1m7ga_          25 LTIWLTGLSASGKSTLAVELEH--QLVRDRRVHAYRLD   60 (208)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH--HHHHHHCCCEEEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHHHHCCCEEEEEC
T ss_conf             6999989999998999999998--87774275089975

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=95.23  E-value=0.0057  Score=31.16  Aligned_cols=23  Identities=22%  Similarity=0.390  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..|.|.|++|.||||+|+.+++.
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             29999889999989999999998

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.21  E-value=0.0047  Score=31.63  Aligned_cols=22  Identities=32%  Similarity=0.661  Sum_probs=19.5

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .|.|+|+.|+|||||++++...
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~   23 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQE   23 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             1999999999999999999974

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=95.20  E-value=0.0044  Score=31.80  Aligned_cols=21  Identities=29%  Similarity=0.507  Sum_probs=18.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHH
Q ss_conf             999993899808899999985
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      -|-+.|.+|+||||||+.+..
T Consensus        30 ~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_          30 GVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             CEEEECCGGGCTTHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
T ss_conf             089988998529999999987

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=95.11  E-value=0.007  Score=30.62  Aligned_cols=23  Identities=30%  Similarity=0.475  Sum_probs=19.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.|.|++|.||||+|+.++..
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             16999889999879999999999

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.11  E-value=0.016  Score=28.47  Aligned_cols=37  Identities=27%  Similarity=0.307  Sum_probs=28.2

Q ss_pred             EEEEEE-CCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEC
Q ss_conf             899999-389980889999998532000378826999926
Q 001843          274 QVIALI-GKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~-G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs  312 (1007)
                      ++|+|+ +-||+||||+|..++.  .....-..++-++..
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~--~la~~g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSV--ALGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHH--HHHHTTCCEEEEECC
T ss_pred             EEEEEECCCCCCCHHHHHHHHHH--HHHHCCCCEEEEECC
T ss_conf             29999899998819999999999--999689989999498

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.10  E-value=0.018  Score=28.25  Aligned_cols=43  Identities=14%  Similarity=0.213  Sum_probs=30.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCC----CCCEEEEEECCCCCCC
Q ss_conf             89999938998088999999853200037----8826999926898889
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH----FTKRAWVHIPIMSMVE  318 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~----F~~~~wv~vs~~~~~~  318 (1007)
                      +++.|.|.+|.|||++|.++.........    -...+|++..  ..++
T Consensus        35 ~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~--~~~~   81 (251)
T d1szpa2          35 SITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE--GTFR   81 (251)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS--SCCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEC--CHHH
T ss_conf             6999983899988999999999863124312689639999402--3078

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=95.08  E-value=0.0075  Score=30.45  Aligned_cols=22  Identities=32%  Similarity=0.560  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+|.|.|++|.||||+|+.++.
T Consensus         9 ~iI~l~G~pGSGKsT~a~~La~   30 (194)
T d3adka_           9 KIIFVVGGPGSGKGTQCEKIVQ   30 (194)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             2899989999987999999999

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.03  E-value=0.0053  Score=31.32  Aligned_cols=22  Identities=32%  Similarity=0.697  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..++|+|..|.|||||++.+..
T Consensus        45 e~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          45 ETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             CEEEEECSTTSSHHHHHTTTTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             8999988999809999999971

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.03  E-value=0.0078  Score=30.37  Aligned_cols=21  Identities=33%  Similarity=0.529  Sum_probs=19.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHH
Q ss_conf             999938998088999999853
Q 001843          276 IALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       276 i~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      |.|.|++|.||||+|+.++..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
T ss_conf             999889999989999999998

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=94.92  E-value=0.062  Score=25.11  Aligned_cols=88  Identities=15%  Similarity=0.058  Sum_probs=45.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCC-----CCC-CEEEEEECCCCCCCHH-HHHHHHHHHHHHHHHHH-----CCCC
Q ss_conf             8999993899808899999985320003-----788-2699992689888989-99999999975533211-----0233
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKR-----HFT-KRAWVHIPIMSMVEDR-DVLADILKQIDESLLKV-----EATL  341 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~-----~F~-~~~wv~vs~~~~~~~~-~~l~~il~~l~~~~~~~-----~~~~  341 (1007)
                      .-++|.|..|+|||+|+..+........     .-. .++++-++  +..... ++...+...-...  +.     ...+
T Consensus        69 Qr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IG--er~~E~~e~~~~~~~~~~~~--~tvvv~~ts~~  144 (285)
T d2jdia3          69 QRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIG--QKRSTVAQLVKRLTDADAMK--YTIVVSATASD  144 (285)
T ss_dssp             CBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEES--CCHHHHHHHHHHHHHTTCGG--GEEEEEECTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEC--CCHHHHHHHHHHHCCCCCCC--CEEEEEECCCC
T ss_conf             778765688888589999999757764156544563289996307--63878999999861456120--04999978999


Q ss_pred             ----------CHHHHHHHHHHHCCCCCEEEEEECCC
Q ss_conf             ----------89999999998819983799992967
Q 001843          342 ----------SAEELMWRITQALDDSTFLIVMENAE  367 (1007)
Q Consensus       342 ----------~~~~l~~~l~~~L~~kr~LiVlDdv~  367 (1007)
                                ..-...+.++.  +++..|+++||+-
T Consensus       145 ~~~~r~~~~~~a~tiAEyfrd--~G~~VLll~Dslt  178 (285)
T d2jdia3         145 AAPLQYLAPYSGCSMGEYFRD--NGKHALIIYDDLS  178 (285)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHH--TTCEEEEEEETHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHH--CCCCEEEEECCHH
T ss_conf             999999999999999999997--6996799971728

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=94.88  E-value=0.0046  Score=31.70  Aligned_cols=63  Identities=14%  Similarity=0.144  Sum_probs=28.2

Q ss_pred             CCCCCCCEEEECCCCCCCC---CCCCCCCCCCCCCEEECCCCCCCC-----CCCCCCCCCCCCEEEECCCC
Q ss_conf             8988301999268878986---787000698768588513677753-----48323268799898615874
Q 001843          666 RRLGMLKVLDLEGVYKPML---TNNNALGRLPFLEYLGLRSTFIDS-----LPDSTPILFCLATLDVSHTK  728 (1007)
Q Consensus       666 ~~l~~LrvLdL~~~~~~~~---~lp~~i~~L~~Lr~L~L~~~~i~~-----LP~~i~~L~~L~~Ldl~~~~  728 (1007)
                      ...+.|+.|++++|.+.+.   .+...+.....|+.|+|++|.+..     +-..+..-+.|++|++.++.
T Consensus        41 ~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~l~~aL~~n~sL~~L~l~~n~  111 (167)
T d1pgva_          41 CNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTLVTQSIVEFKADNQR  111 (167)
T ss_dssp             TTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHHHHTTTTCCCSEEECCCCS
T ss_pred             HHCCCCCEEECCCCCCCHHHHHHHHHHHHHCCCCCCEEEEHHHCCHHHHHHHHHHHHHCCCCCEEECCCCC
T ss_conf             63776454012015621567988753100023433003301021459999999999848938987788776

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.85  E-value=0.0092  Score=29.94  Aligned_cols=22  Identities=32%  Similarity=0.483  Sum_probs=19.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|.|++|.||||+|+.++..
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             8999889999979999999999

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=94.74  E-value=0.01  Score=29.66  Aligned_cols=22  Identities=36%  Similarity=0.543  Sum_probs=19.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .|.|.|++|.||||+|+.++..
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             8999889999879999999998

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.72  E-value=0.01  Score=29.61  Aligned_cols=29  Identities=17%  Similarity=0.437  Sum_probs=23.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf             8999993899808899999985320003788
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFT  304 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~  304 (1007)
                      +.|.|+|+.|+|||||++++..  +....|.
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~--~~~~~~~   32 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLIT--KHPDRFA   32 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH--HCTTTEE
T ss_pred             CCEEEECCCCCCHHHHHHHHHH--HCCCCEE
T ss_conf             7199999899999999999997--0976765

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.67  E-value=0.011  Score=29.44  Aligned_cols=23  Identities=35%  Similarity=0.606  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ++|.|+|+.|+|||||++.+...
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             49999899999999999999845

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=94.48  E-value=0.014  Score=28.80  Aligned_cols=22  Identities=41%  Similarity=0.600  Sum_probs=20.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ||.|.|+.|.|||||..++.++
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~   23 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRY   23 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             8999918998399999999998

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.25  E-value=0.015  Score=28.64  Aligned_cols=22  Identities=41%  Similarity=0.594  Sum_probs=18.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ++ .|.|++|.||||+|+.++..
T Consensus         4 rI-vl~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           4 RM-VLIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             EE-EEECCTTSSHHHHHHHHHHH
T ss_pred             EE-EEECCCCCCHHHHHHHHHHH
T ss_conf             99-99899999989999999999

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.21  E-value=0.092  Score=24.10  Aligned_cols=44  Identities=14%  Similarity=0.157  Sum_probs=31.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHC----CCCCCCEEEEEECCCCCCCH
Q ss_conf             89999938998088999999853200----03788269999268988898
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYV----KRHFTKRAWVHIPIMSMVED  319 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v----~~~F~~~~wv~vs~~~~~~~  319 (1007)
                      +++.|+|.+|.|||++|.+++.....    ...+..+.|+...  ..+..
T Consensus        38 ~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~   85 (258)
T d1v5wa_          38 AITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTE--NTFRP   85 (258)
T ss_dssp             EEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESS--SCCCH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECHH--HHHHH
T ss_conf             7999988998878899999999997444316666248874017--77789

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=94.07  E-value=0.098  Score=23.93  Aligned_cols=23  Identities=35%  Similarity=0.439  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .+..|+|.+|+||||+|.+++-.
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~~   52 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAAQ   52 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCHHHHHHHHHHH
T ss_conf             58999928999899999999999

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=94.05  E-value=0.026  Score=27.29  Aligned_cols=33  Identities=21%  Similarity=0.530  Sum_probs=24.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf             899999389980889999998532000378826999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWV  309 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv  309 (1007)
                      .+++|+|..|.|||||.+.++.   ....-.+.+++
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~g---l~~p~sG~I~~   64 (230)
T d1l2ta_          32 EFVSIMGPSGSGKSTMLNIIGC---LDKPTEGEVYI   64 (230)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT---SSCCSEEEEEE
T ss_pred             CEEEEECCCCCCCCHHHHHCCC---CCCCCCCEEEE
T ss_conf             7999988999982165575068---87777662699

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.03  E-value=0.018  Score=28.30  Aligned_cols=22  Identities=32%  Similarity=0.505  Sum_probs=19.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|.|++|.||||+|+.++..
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             8999879999989999999998

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.03  E-value=0.026  Score=27.28  Aligned_cols=33  Identities=33%  Similarity=0.510  Sum_probs=24.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf             899999389980889999998532000378826999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWV  309 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv  309 (1007)
                      .+++|+|..|.|||||++.+..   +...-.+.+++
T Consensus        29 Ei~~iiG~sGsGKSTLl~~i~G---l~~p~~G~I~~   61 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRCINF---LEKPSEGAIIV   61 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT---SSCCSEEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHC---CCCCCCCCEEE
T ss_conf             7999998999829999999974---76678997799

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=94.00  E-value=0.1  Score=23.85  Aligned_cols=24  Identities=29%  Similarity=0.378  Sum_probs=22.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             899999389980889999998532
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRV  297 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~  297 (1007)
                      +++.|.|.+|.|||++|.+++.+.
T Consensus        35 ~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          35 SVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
T ss_conf             599999179999899999999999

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.00  E-value=0.061  Score=25.16  Aligned_cols=27  Identities=30%  Similarity=0.505  Sum_probs=23.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             89999938998088999999853200037
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH  302 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~  302 (1007)
                      +.|+|-|+-|.||||+++.+..  ..+.+
T Consensus         4 k~I~iEG~DGsGKST~~~~L~~--~L~~~   30 (214)
T d1tmka_           4 KLILIEGLDRTGKTTQCNILYK--KLQPN   30 (214)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH--HTTTS
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHHHC
T ss_conf             8999989988869999999999--99719

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.93  E-value=0.033  Score=26.74  Aligned_cols=33  Identities=15%  Similarity=0.349  Sum_probs=24.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf             899999389980889999998532000378826999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWV  309 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv  309 (1007)
                      .+++|.|+.|.|||||.+.++.   ....-.+.+|+
T Consensus        25 e~~~liGpnGaGKSTll~~i~G---l~~p~~G~I~~   57 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAG---IVKPDRGEVRL   57 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHT---SSCCSEEEEEE
T ss_pred             EEEEEECCCCCHHHHHHHHHHC---CCCCCCEEEEE
T ss_conf             7999997999809999999973---99989628999

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=93.79  E-value=0.036  Score=26.47  Aligned_cols=22  Identities=36%  Similarity=0.681  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|..|.|||||++.++.
T Consensus        30 e~~~liG~sGaGKSTll~~i~g   51 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAG   51 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             8999999999809999999964

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.79  E-value=0.022  Score=27.75  Aligned_cols=22  Identities=36%  Similarity=0.585  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|+.|.|||||.+.++.
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~g   49 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTIST   49 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             8999999999719999999966

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=93.78  E-value=0.028  Score=27.12  Aligned_cols=27  Identities=30%  Similarity=0.443  Sum_probs=22.4

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             999689999938998088999999853
Q 001843          270 TTTTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       270 ~~~~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..+...|+|+|.+|+|||||...+.+.
T Consensus        20 ~~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          20 EGGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CSCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHCCC
T ss_conf             889989999899998799999985298

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=93.77  E-value=0.021  Score=27.81  Aligned_cols=22  Identities=41%  Similarity=0.854  Sum_probs=20.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..++|+|..|.|||||++.+..
T Consensus        42 e~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             9999999999859999999862

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.74  E-value=0.021  Score=27.86  Aligned_cols=22  Identities=50%  Similarity=0.797  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..++|+|..|.|||||++.+..
T Consensus        41 e~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          41 EVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             8999999999849999999861

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.72  E-value=0.09  Score=24.17  Aligned_cols=35  Identities=23%  Similarity=0.392  Sum_probs=26.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCC-CCCEEEEE
Q ss_conf             89999938998088999999853200037-88269999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRH-FTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~-F~~~~wv~  310 (1007)
                      +.|+|-|..|.||||+++.+..  ..... +..+.+..
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~--~L~~~g~~~~~~~~   38 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVE--TLEQLGIRDMVFTR   38 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHH--HHHHTTCCCEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEEC
T ss_conf             7899989988879999999999--99967997399832

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.68  E-value=0.023  Score=27.60  Aligned_cols=23  Identities=17%  Similarity=0.408  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .++.|+|+.|+|||||.+.+...
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~   25 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKT   25 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
T ss_conf             09999999999999999999863

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.68  E-value=0.02  Score=27.95  Aligned_cols=25  Identities=16%  Similarity=0.316  Sum_probs=22.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf             8999993899808899999985320
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVY  298 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~  298 (1007)
                      +++.|.|.+|.|||++|.+++.+..
T Consensus        24 ~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          24 SITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHH
T ss_conf             7999995899999999999999998

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=93.62  E-value=0.048  Score=25.77  Aligned_cols=29  Identities=28%  Similarity=0.360  Sum_probs=22.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHCCCC-CCC
Q ss_conf             9999938998088999999853200037-882
Q 001843          275 VIALIGKAGSGKTTLARIVYNRVYVKRH-FTK  305 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~~~v~~~-F~~  305 (1007)
                      .|+|-|.-|.||||+++.+..  ....+ ++.
T Consensus         2 lI~ieG~dGsGKST~~~~L~~--~l~~~g~~v   31 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSG--AFRAAGRSV   31 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH--HHHHTTCCE
T ss_pred             EEEEECCCCCCHHHHHHHHHH--HHHHCCCCE
T ss_conf             899989987899999999999--998789978

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.57  E-value=0.025  Score=27.38  Aligned_cols=22  Identities=36%  Similarity=0.727  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|..|.|||||++.+..
T Consensus        63 e~vaivG~nGsGKSTLl~~i~G   84 (281)
T d1r0wa_          63 EMLAITGSTGSGKTSLLMLILG   84 (281)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             9999998999829999999957

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=93.53  E-value=0.12  Score=23.35  Aligned_cols=54  Identities=17%  Similarity=0.103  Sum_probs=35.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDE  332 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~  332 (1007)
                      .++.|.|.+|.|||+++.+++.+......+ .+++++    -..+...+...++.....
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~~~a~~~g~-~v~~~s----~E~~~~~~~~r~~~~~~~   89 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAM----LEESVEETAEDLIGLHNR   89 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEE----SSSCHHHHHHHHHHHHTT
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHHHCCC-CEEEEE----ECCCHHHHHHHHHHHHHC
T ss_conf             089999479997999999999726553366-345764----011113577699998645

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.47  E-value=0.015  Score=28.66  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=21.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +.|+|-|+-|.||||+|+.+...
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
T ss_conf             88999878887799999999999

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=93.37  E-value=0.028  Score=27.10  Aligned_cols=22  Identities=32%  Similarity=0.626  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..++|+|..|.|||||++.+..
T Consensus        29 e~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          29 SIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
T ss_conf             9999999999979999999999

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=93.32  E-value=0.026  Score=27.36  Aligned_cols=22  Identities=45%  Similarity=0.697  Sum_probs=21.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|..|.|||||++.++-
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHCC
T ss_conf             7999989998988899998758

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.18  E-value=0.033  Score=26.71  Aligned_cols=22  Identities=36%  Similarity=0.699  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|+.|.|||||.+.+..
T Consensus        33 e~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             8999999999829999999975

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.09  E-value=0.035  Score=26.58  Aligned_cols=22  Identities=32%  Similarity=0.742  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|+.|.|||||.+.++-
T Consensus        27 ei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCHHHHHHHHHHC
T ss_conf             8999998999829999999965

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.06  E-value=0.04  Score=26.19  Aligned_cols=22  Identities=27%  Similarity=0.451  Sum_probs=19.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|+|.+|+|||+|+.++.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999994989999999729

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.03  E-value=0.041  Score=26.16  Aligned_cols=22  Identities=32%  Similarity=0.386  Sum_probs=19.5

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||..++.+.
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999992989999999739

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.90  E-value=0.043  Score=26.04  Aligned_cols=22  Identities=27%  Similarity=0.403  Sum_probs=19.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|+.++.+.
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999993989999999829

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=92.81  E-value=0.039  Score=26.27  Aligned_cols=22  Identities=27%  Similarity=0.317  Sum_probs=19.3

Q ss_pred             EEEECCCCCHHHHHHHHHHHHH
Q ss_conf             9999389980889999998532
Q 001843          276 IALIGKAGSGKTTLARIVYNRV  297 (1007)
Q Consensus       276 i~I~G~gGiGKTtLA~~v~~~~  297 (1007)
                      |.|+|.+|+|||||..++..+.
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHCCC
T ss_conf             9999999989899999996598

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=92.68  E-value=0.039  Score=26.25  Aligned_cols=22  Identities=41%  Similarity=0.628  Sum_probs=18.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      -+|+|+|+.|.||||.|+.+-.
T Consensus         4 ~iIgitG~igSGKStv~~~l~~   25 (208)
T d1vhta_           4 YIVALTGGIGSGKSTVANAFAD   25 (208)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             7999789886889999999998

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.64  E-value=0.049  Score=25.73  Aligned_cols=22  Identities=32%  Similarity=0.563  Sum_probs=19.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||+.++..+
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999990999999999709

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.62  E-value=0.05  Score=25.65  Aligned_cols=22  Identities=23%  Similarity=0.493  Sum_probs=19.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||..++.++
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             8999998994999999999739

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.61  E-value=0.049  Score=25.73  Aligned_cols=23  Identities=22%  Similarity=0.450  Sum_probs=19.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.|+|.+|+|||+|...+.+.
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHC
T ss_conf             79999997996989999999739

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.60  E-value=0.05  Score=25.63  Aligned_cols=22  Identities=32%  Similarity=0.599  Sum_probs=19.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|..++.++
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999998997899999999739

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.59  E-value=0.05  Score=25.67  Aligned_cols=22  Identities=50%  Similarity=0.635  Sum_probs=19.5

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|..++.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999991989999999729

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.56  E-value=0.043  Score=26.02  Aligned_cols=22  Identities=27%  Similarity=0.448  Sum_probs=19.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|+.++.++
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999993999999999629

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=92.50  E-value=0.07  Score=24.81  Aligned_cols=38  Identities=16%  Similarity=0.166  Sum_probs=26.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEC
Q ss_conf             899999389980889999998532000378826999926
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIP  312 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs  312 (1007)
                      +++.|.|.+|.|||++|.+++.... ...-..++|++..
T Consensus        27 ~~~~I~G~~G~GKT~la~~~~~~~~-~~~~~~~~~~s~e   64 (242)
T d1tf7a1          27 RSTLVSGTSGTGKTLFSIQFLYNGI-IEFDEPGVFVTFE   64 (242)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHH-HHHCCCEEEEESS
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHH-HHCCCCCCCCCCC
T ss_conf             3999994799999999999999999-8568874201266

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.49  E-value=0.044  Score=25.95  Aligned_cols=22  Identities=14%  Similarity=0.385  Sum_probs=19.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||+.++.+.
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999998995989999999829

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=92.49  E-value=0.044  Score=25.95  Aligned_cols=57  Identities=21%  Similarity=0.299  Sum_probs=35.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCC---CCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             899999389980889999998532000378---826999926898889899999999997553
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF---TKRAWVHIPIMSMVEDRDVLADILKQIDES  333 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F---~~~~wv~vs~~~~~~~~~~l~~il~~l~~~  333 (1007)
                      +=|-++|+.|+|||.||+.++.  ...-.|   |+.-+.-+ ..-..++..+++++++.....
T Consensus        50 sNILliGPTGvGKTlLAr~LAk--~l~VPFv~~daT~fTea-GYvG~DVesii~~L~~~a~~~  109 (443)
T d1g41a_          50 KNILMIGPTGVGKTEIARRLAK--LANAPFIKVEATKFTEV-GYVGKEVDSIIRDLTDSAMKL  109 (443)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH--HTTCCEEEEEGGGGC-----CCCCTHHHHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHH--HHCCCEEEEECCEEEEC-CEEECCHHHHHHHHHHHHHHH
T ss_conf             6479989999889999999998--73898898625511411-111044457899999987550

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=92.48  E-value=0.045  Score=25.93  Aligned_cols=23  Identities=30%  Similarity=0.371  Sum_probs=20.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             99999389980889999998532
Q 001843          275 VIALIGKAGSGKTTLARIVYNRV  297 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~~  297 (1007)
                      -|+|+|.+|+|||||...+..+.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
T ss_conf             99999999989999999996798

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.47  E-value=0.054  Score=25.45  Aligned_cols=22  Identities=23%  Similarity=0.454  Sum_probs=19.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|..++...
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999998998999999999709

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.45  E-value=0.055  Score=25.42  Aligned_cols=22  Identities=27%  Similarity=0.356  Sum_probs=19.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||...+.++
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999991989999999739

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.45  E-value=0.055  Score=25.42  Aligned_cols=22  Identities=23%  Similarity=0.418  Sum_probs=19.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|+.++.+.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999994989999999859

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=92.44  E-value=0.037  Score=26.39  Aligned_cols=22  Identities=23%  Similarity=0.575  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|+.|.|||||.+.+..
T Consensus        27 e~~~liGpsGaGKSTll~~l~G   48 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAG   48 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             8999998999829999999964

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.37  E-value=0.056  Score=25.35  Aligned_cols=22  Identities=23%  Similarity=0.456  Sum_probs=19.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|-+|+|||+|..++.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999998993999999999719

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.33  E-value=0.056  Score=25.38  Aligned_cols=21  Identities=24%  Similarity=0.434  Sum_probs=18.9

Q ss_pred             EEEECCCCCHHHHHHHHHHHH
Q ss_conf             999938998088999999853
Q 001843          276 IALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       276 i~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      |.++|.+|+|||+|+.++.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHC
T ss_conf             999998990989999999849

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=92.31  E-value=0.045  Score=25.94  Aligned_cols=22  Identities=41%  Similarity=0.662  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|.|+.|.|||||.+.+..
T Consensus        33 ei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             7999999999859999999967

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.30  E-value=0.045  Score=25.94  Aligned_cols=22  Identities=41%  Similarity=0.694  Sum_probs=20.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|+.|.|||||++.++-
T Consensus        31 ei~~liG~nGaGKSTLl~~i~G   52 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITG   52 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             7999999999849999999977

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=92.30  E-value=0.1  Score=23.86  Aligned_cols=28  Identities=29%  Similarity=0.239  Sum_probs=22.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             899999389980889999998532000378
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF  303 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F  303 (1007)
                      -.|.|-|.-|+||||+++.+.+  ....+.
T Consensus         7 ~rI~iEG~iGsGKSTl~~~L~~--~l~~~~   34 (333)
T d1p6xa_           7 VRIYLDGVYGIGKSTTGRVMAS--AASGGS   34 (333)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHS--GGGCSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHCCCC
T ss_conf             8999988866789999999999--865699

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=92.27  E-value=0.042  Score=26.10  Aligned_cols=25  Identities=40%  Similarity=0.586  Sum_probs=21.1

Q ss_pred             CCEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9689999938998088999999853
Q 001843          272 TTQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       272 ~~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .+.-+-.+|+-|+|||.||+.++..
T Consensus        67 p~~niLfiGPTGvGKTElAk~LA~~   91 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMAQTLAKH   91 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHH
T ss_conf             8753244189986378999999864

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.27  E-value=0.043  Score=26.01  Aligned_cols=22  Identities=27%  Similarity=0.398  Sum_probs=19.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999991989999999619

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=92.25  E-value=0.045  Score=25.90  Aligned_cols=22  Identities=45%  Similarity=0.764  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|+.|.|||||.+.+..
T Consensus        29 ei~glvG~nGaGKSTLl~~l~G   50 (238)
T d1vpla_          29 EIFGLIGPNGAGKTTTLRIIST   50 (238)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             7999999999999999999966

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=92.24  E-value=0.097  Score=23.98  Aligned_cols=35  Identities=17%  Similarity=0.069  Sum_probs=24.8

Q ss_pred             EEEEEECCC-CCHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             899999389-9808899999985320003788269999
Q 001843          274 QVIALIGKA-GSGKTTLARIVYNRVYVKRHFTKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~g-GiGKTtLA~~v~~~~~v~~~F~~~~wv~  310 (1007)
                      +.+-|.|.| |+||||++..++.  .....=..++.+.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~--aLa~~G~rVl~id   37 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQ--AAKAAGYRTAGYK   37 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHH--HHHHTTCCEEEEC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--HHHHCCCEEEEEC
T ss_conf             51999989999429999999999--9997799399988

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.24  E-value=0.058  Score=25.29  Aligned_cols=22  Identities=36%  Similarity=0.481  Sum_probs=19.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||..++.+.
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999996789999999868

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.23  E-value=0.047  Score=25.79  Aligned_cols=21  Identities=29%  Similarity=0.504  Sum_probs=18.8

Q ss_pred             EEEECCCCCHHHHHHHHHHHH
Q ss_conf             999938998088999999853
Q 001843          276 IALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       276 i~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      |.++|.+|+|||||..++.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHHC
T ss_conf             999998997989999999709

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.22  E-value=0.054  Score=25.44  Aligned_cols=22  Identities=27%  Similarity=0.314  Sum_probs=19.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|+|.+|+|||+|..++.++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999998999999999649

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=92.09  E-value=0.052  Score=25.53  Aligned_cols=22  Identities=41%  Similarity=0.688  Sum_probs=19.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      -+|+|.|..|.||||+|+.+-.
T Consensus         3 ~iIgITG~igSGKStv~~~l~~   24 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFTD   24 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             8999888887889999999998

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.08  E-value=0.061  Score=25.13  Aligned_cols=22  Identities=23%  Similarity=0.448  Sum_probs=19.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|..++.++
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             8999999997999999999739

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.07  E-value=0.062  Score=25.10  Aligned_cols=23  Identities=22%  Similarity=0.414  Sum_probs=19.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .-|.|+|.+|+|||+|..++.+.
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHC
T ss_conf             79999998993889999999719

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.02  E-value=0.052  Score=25.56  Aligned_cols=22  Identities=41%  Similarity=0.616  Sum_probs=18.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|+..+.+.
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999898993999999998188

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.89  E-value=0.056  Score=25.37  Aligned_cols=22  Identities=32%  Similarity=0.472  Sum_probs=19.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|+|.+|+|||||..++.+.
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999990989999999619

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=91.87  E-value=0.056  Score=25.38  Aligned_cols=22  Identities=36%  Similarity=0.723  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|.|..|.|||||.+.+..
T Consensus        32 e~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             8999998999809999999975

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.86  E-value=0.071  Score=24.76  Aligned_cols=22  Identities=23%  Similarity=0.440  Sum_probs=19.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|..|+|||+|..++.+.
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999991989999999729

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.84  E-value=0.069  Score=24.85  Aligned_cols=23  Identities=26%  Similarity=0.394  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .-|.|+|..|+|||+|..++.+.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHC
T ss_conf             38999998992989999999719

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.75  E-value=0.061  Score=25.16  Aligned_cols=22  Identities=32%  Similarity=0.555  Sum_probs=19.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||..++.++
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999996989999999709

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.71  E-value=0.075  Score=24.64  Aligned_cols=22  Identities=32%  Similarity=0.604  Sum_probs=19.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||+..+.+.
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999991989999999719

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.68  E-value=0.073  Score=24.69  Aligned_cols=22  Identities=23%  Similarity=0.496  Sum_probs=19.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|..++.++
T Consensus         5 Ki~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999997998999999999809

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.65  E-value=0.095  Score=24.03  Aligned_cols=23  Identities=22%  Similarity=0.228  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.|+|.+|+|||+|..++..+
T Consensus         6 iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHC
T ss_conf             99999999997999999999749

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.61  E-value=0.058  Score=25.28  Aligned_cols=22  Identities=27%  Similarity=0.404  Sum_probs=18.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|-+|+|||+|..++..+
T Consensus         4 KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999998889999988408

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.52  E-value=0.078  Score=24.53  Aligned_cols=22  Identities=27%  Similarity=0.492  Sum_probs=19.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|..|+|||+|+..+.+.
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999995989999999729

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=91.52  E-value=0.056  Score=25.39  Aligned_cols=22  Identities=23%  Similarity=0.416  Sum_probs=19.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|+|.+|+|||||...+.+.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHCCC
T ss_conf             9999999998999999998089

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.51  E-value=0.069  Score=24.84  Aligned_cols=23  Identities=26%  Similarity=0.371  Sum_probs=20.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +-|.|+|.+|+|||||..++...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             98999999998989999999809

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.51  E-value=0.075  Score=24.61  Aligned_cols=23  Identities=30%  Similarity=0.460  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..|+|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             89999999998899999999679

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.50  E-value=0.078  Score=24.51  Aligned_cols=22  Identities=23%  Similarity=0.267  Sum_probs=19.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|..|+|||+|..++.+.
T Consensus         5 KvvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999996999999999719

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.39  E-value=0.063  Score=25.07  Aligned_cols=20  Identities=35%  Similarity=0.521  Sum_probs=17.6

Q ss_pred             EEEEECCCCCHHHHHHHHHH
Q ss_conf             99999389980889999998
Q 001843          275 VIALIGKAGSGKTTLARIVY  294 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~  294 (1007)
                      -|.++|.+|+|||||..++.
T Consensus         4 KivllG~~~vGKTsll~r~~   23 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQMR   23 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             99999899999899999884

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.35  E-value=0.071  Score=24.76  Aligned_cols=24  Identities=46%  Similarity=0.576  Sum_probs=21.2

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             689999938998088999999853
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +.|..|.|+-|.|||||.+++...
T Consensus         3 iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           3 IAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             EEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHC
T ss_conf             788998648889999999999856

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=91.30  E-value=0.071  Score=24.75  Aligned_cols=22  Identities=23%  Similarity=0.526  Sum_probs=19.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .|+|+|..|+|||||..++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             8999999999899999999677

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.29  E-value=0.074  Score=24.67  Aligned_cols=22  Identities=32%  Similarity=0.517  Sum_probs=19.5

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|..|+|||||+.++.++
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999990989999999829

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=91.22  E-value=0.084  Score=24.34  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=21.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..|+|+|..|+|||||...+...
T Consensus         6 ~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           6 GFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             69999999999999999999688

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.20  E-value=0.091  Score=24.12  Aligned_cols=22  Identities=32%  Similarity=0.508  Sum_probs=19.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|..++.+.
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             8999998990889999999719

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=91.19  E-value=0.24  Score=21.69  Aligned_cols=93  Identities=12%  Similarity=0.120  Sum_probs=49.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             89999938998088999999853200037882699992689888989999999999755332110233899999999988
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEATLSAEELMWRITQA  353 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~~~~~~l~~~l~~~  353 (1007)
                      +-+.|.|..|.||||+.+.+..  .+.... .++-+--.  ........ .   .....   ......   ...+.++..
T Consensus       167 ~nili~G~tgSGKTT~l~al~~--~i~~~~-rivtiEd~--~El~l~~~-~---~~~~~---~~~~~~---~~~~ll~~~  231 (323)
T d1g6oa_         167 KNVIVCGGTGSGKTTYIKSIME--FIPKEE-RIISIEDT--EEIVFKHH-K---NYTQL---FFGGNI---TSADCLKSC  231 (323)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGG--GSCTTC-CEEEEESS--CCCCCSSC-S---SEEEE---ECBTTB---CHHHHHHHH
T ss_pred             CCEEEEEECCCCCHHHHHHHHH--HCCCCC-CEEECCCH--HHHHCCCC-C---CCCEE---CCCCCH---HHHHHHHHH
T ss_conf             8889994035662578999865--301456-23311322--65511112-4---54100---146542---499999997


Q ss_pred             CCCCCEEEEEECCCCCCCHHHHHHCCCCCC
Q ss_conf             199837999929675570001121022377
Q 001843          354 LDDSTFLIVMENAEHQKSQVWDSFLGKLCS  383 (1007)
Q Consensus       354 L~~kr~LiVlDdv~~~~~~~w~~l~~l~~~  383 (1007)
                      |+...=-||+..+.  +.+.|..+.+...+
T Consensus       232 lR~~pd~iivgEiR--~~ea~~~l~a~~tG  259 (323)
T d1g6oa_         232 LRMRPDRIILGELR--SSEAYDFYNVLCSG  259 (323)
T ss_dssp             TTSCCSEEEESCCC--STHHHHHHHHHHTT
T ss_pred             HCCCCCCCCCCCCC--CHHHHHHHHHHHHC
T ss_conf             43499854578667--46599999999816

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.13  E-value=0.095  Score=24.03  Aligned_cols=23  Identities=26%  Similarity=0.419  Sum_probs=20.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.++|.+|+|||+|..++.+.
T Consensus         6 ~ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           6 LRLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHC
T ss_conf             79999998997899999999719

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=91.09  E-value=0.095  Score=24.02  Aligned_cols=23  Identities=22%  Similarity=0.452  Sum_probs=19.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.++|.+|+|||+|..++.++
T Consensus         5 ~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHHC
T ss_conf             69999998995889999999729

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.05  E-value=0.08  Score=24.46  Aligned_cols=22  Identities=32%  Similarity=0.471  Sum_probs=19.5

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.|+|.+|+|||+|+.++.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999992999999999719

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.04  E-value=0.085  Score=24.30  Aligned_cols=22  Identities=27%  Similarity=0.391  Sum_probs=19.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|..++..+
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999999889999999679

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=90.96  E-value=0.059  Score=25.24  Aligned_cols=23  Identities=26%  Similarity=0.479  Sum_probs=19.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .-|.++|.+|+|||||..++...
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             78999999998989999999678

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=90.95  E-value=0.071  Score=24.77  Aligned_cols=23  Identities=35%  Similarity=0.452  Sum_probs=19.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.++|.+|+|||||..++...
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHHCC
T ss_conf             79999999998999999999648

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=90.73  E-value=0.11  Score=23.67  Aligned_cols=22  Identities=36%  Similarity=0.468  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+|+|.|..|.||+|+|+.+.+
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             8999979999889999999998

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.57  E-value=0.083  Score=24.38  Aligned_cols=21  Identities=48%  Similarity=0.718  Sum_probs=18.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHH
Q ss_conf             999993899808899999985
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      -|.++|.+|+|||+|+..+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHH
T ss_conf             999999899299999999972

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=90.56  E-value=0.15  Score=22.81  Aligned_cols=24  Identities=38%  Similarity=0.548  Sum_probs=22.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             899999389980889999998532
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRV  297 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~  297 (1007)
                      .+|.+.|.=|.||||+++.+++.-
T Consensus        34 ~ii~L~G~LGaGKTtfvr~~~~~l   57 (158)
T d1htwa_          34 IMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             299996687765889999987642

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=90.55  E-value=0.091  Score=24.15  Aligned_cols=23  Identities=26%  Similarity=0.407  Sum_probs=19.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.++|.+|+|||||.+++...
T Consensus         7 ~KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             77999989999889999989509

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.50  E-value=0.12  Score=23.52  Aligned_cols=22  Identities=23%  Similarity=0.608  Sum_probs=19.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|..|+|||+|..++.++
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999998995989999999709

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=90.49  E-value=0.063  Score=25.07  Aligned_cols=22  Identities=32%  Similarity=0.617  Sum_probs=20.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .+++|+|..|.|||||.+.++.
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             8999998999809999999948

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.49  E-value=0.12  Score=23.53  Aligned_cols=22  Identities=27%  Similarity=0.504  Sum_probs=19.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||..++.+.
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999997999999999849

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=90.43  E-value=0.047  Score=25.79  Aligned_cols=20  Identities=25%  Similarity=0.521  Sum_probs=18.5

Q ss_pred             EEEECCCCCHHHHHHHHHHH
Q ss_conf             99993899808899999985
Q 001843          276 IALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       276 i~I~G~gGiGKTtLA~~v~~  295 (1007)
                      |+|+|.+++|||||...+.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHHC
T ss_conf             99989999989999999968

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.41  E-value=0.11  Score=23.56  Aligned_cols=23  Identities=30%  Similarity=0.564  Sum_probs=20.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      ..|+|+|..++|||||..++.+.
T Consensus         6 ~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           6 GFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             19999979999899999999589

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=90.22  E-value=0.096  Score=24.00  Aligned_cols=23  Identities=22%  Similarity=0.326  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.++|.+|+|||||..++...
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHCC
T ss_conf             79999999998989999999668

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=89.90  E-value=0.15  Score=22.79  Aligned_cols=34  Identities=26%  Similarity=0.151  Sum_probs=24.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf             899999389980889999998532000378826999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHFTKRAWV  309 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F~~~~wv  309 (1007)
                      -.|.|-|.-|+||||+++.+.+  ....+-..+.++
T Consensus         6 lrI~IEG~iGsGKSTl~~~L~~--~l~~~g~~v~~~   39 (331)
T d1osna_           6 LRIYLDGAYGIGKTTAAEEFLH--HFAITPNRILLI   39 (331)
T ss_dssp             EEEEEEESSSSCTTHHHHHHHH--TTTTSGGGEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEE
T ss_conf             6999988877889999999999--873468856997

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.83  E-value=0.12  Score=23.47  Aligned_cols=22  Identities=32%  Similarity=0.520  Sum_probs=19.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||...+...
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             8999999999999999999589

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=89.80  E-value=0.15  Score=22.82  Aligned_cols=23  Identities=22%  Similarity=0.281  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      |-|+|+|.+|.|||||+.++...
T Consensus         7 Rni~i~gh~~~GKTtL~e~ll~~   29 (276)
T d2bv3a2           7 RNIGIAAHIDAGKTTTTERILYY   29 (276)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             EEEEEEECCCCCHHHHHHHHHHH
T ss_conf             29999958989989999999996

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=89.77  E-value=0.12  Score=23.42  Aligned_cols=22  Identities=32%  Similarity=0.489  Sum_probs=19.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||..++...
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999998989999999719

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=89.66  E-value=0.1  Score=23.83  Aligned_cols=22  Identities=27%  Similarity=0.456  Sum_probs=19.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             8999999998899999999689

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=89.30  E-value=0.089  Score=24.19  Aligned_cols=22  Identities=32%  Similarity=0.493  Sum_probs=19.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .-|+|+|.+++|||||...+.+
T Consensus         2 ~~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           2 ADVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CCEEEESSTTSSHHHHHHHSEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             8699989999879999999968

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=89.16  E-value=0.14  Score=23.12  Aligned_cols=23  Identities=30%  Similarity=0.600  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|+|+|..|+|||||...+.+.
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             88999999999999999999778

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.75  E-value=0.071  Score=24.77  Aligned_cols=22  Identities=32%  Similarity=0.587  Sum_probs=18.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||+|..++.+.
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC--
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999990889999999849

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=88.70  E-value=0.16  Score=22.71  Aligned_cols=22  Identities=50%  Similarity=0.786  Sum_probs=19.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      |-|+|+|..|.|||||+.++..
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~   24 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLY   24 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             0999994889809999999999

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=88.70  E-value=0.1  Score=23.91  Aligned_cols=22  Identities=27%  Similarity=0.388  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..|.|-|.-|+||||+++.+.+
T Consensus         5 lrI~IEG~iGsGKTTl~~~La~   26 (329)
T d1e2ka_           5 LRVYIDGPHGMGKTTTTQLLVA   26 (329)
T ss_dssp             EEEEECSCTTSSHHHHHHHHTC
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             2999989867789999999999

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=88.27  E-value=0.1  Score=23.89  Aligned_cols=23  Identities=30%  Similarity=0.366  Sum_probs=19.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.++|.+|+|||||..++...
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHHCC
T ss_conf             89999999999889999887338

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=88.05  E-value=0.17  Score=22.54  Aligned_cols=22  Identities=23%  Similarity=0.522  Sum_probs=18.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|+++|.+++|||||..++...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999899999899999999688

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=88.03  E-value=0.091  Score=24.13  Aligned_cols=22  Identities=27%  Similarity=0.311  Sum_probs=19.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||..++.+.
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999998789999998448

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=87.73  E-value=0.15  Score=22.83  Aligned_cols=23  Identities=22%  Similarity=0.400  Sum_probs=20.0

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             68999993899808899999985
Q 001843          273 TQVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..-|+|+|.+++|||||..++..
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHC
T ss_conf             97899988999989999999858

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=87.39  E-value=0.076  Score=24.59  Aligned_cols=40  Identities=15%  Similarity=0.142  Sum_probs=21.9

Q ss_pred             CCCCCCCEEECCC-CCCC-----CCCCCCCCCCCCCEEEECCCCCC
Q ss_conf             6987685885136-7775-----34832326879989861587432
Q 001843          691 GRLPFLEYLGLRS-TFID-----SLPDSTPILFCLATLDVSHTKVQ  730 (1007)
Q Consensus       691 ~~L~~Lr~L~L~~-~~i~-----~LP~~i~~L~~L~~Ldl~~~~l~  730 (1007)
                      .+.+.|++|+|++ +.+.     .+-..+...++|++|++++|.+.
T Consensus        14 ~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~   59 (166)
T d1io0a_          14 NNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSN   59 (166)
T ss_dssp             TTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCC
T ss_pred             HCCCCCCEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEECCCCCCC
T ss_conf             5599986887689999898999999988841982574301589611

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=87.32  E-value=0.33  Score=20.84  Aligned_cols=108  Identities=12%  Similarity=0.113  Sum_probs=55.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCC-------------CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             899999389980889999998532000-------------3788269999268988898999999999975533211023
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVK-------------RHFTKRAWVHIPIMSMVEDRDVLADILKQIDESLLKVEAT  340 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~-------------~~F~~~~wv~vs~~~~~~~~~~l~~il~~l~~~~~~~~~~  340 (1007)
                      +++.|.|+-.-||||+.+.+.-..-..             ..|+. ++..+.  ...+...-.-..             .
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~-I~~~~~--~~d~~~~~~StF-------------~   99 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDG-IYTRIG--ASDDLAGGKSTF-------------M   99 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSE-EEEECC--C------CCSHH-------------H
T ss_pred             CEEEEECCCCCCCCHHHHHHHHHHHHHHCCCEEECCCEEEEECCE-EEEEEC--CCCCCCCCCCHH-------------H
T ss_conf             679997887345323455658999998525046137519940116-999987--776023783078-------------9


Q ss_pred             CCHHHHHHHHHHHCCCCCEEEEEECCCCCCCH------HHHHHCCCCCCCCCCCEEEEECCCCCCCCCC
Q ss_conf             38999999999881998379999296755700------0112102237779994899984887311223
Q 001843          341 LSAEELMWRITQALDDSTFLIVMENAEHQKSQ------VWDSFLGKLCSFTQCGKIIITTSSTEDFVEP  403 (1007)
Q Consensus       341 ~~~~~l~~~l~~~L~~kr~LiVlDdv~~~~~~------~w~~l~~l~~~~~~gskIiiTTR~~~~va~~  403 (1007)
                      .+..++...+. . .+++.|+++|.+-.....      .|.-+..|.   ..++.+++||-..+ +...
T Consensus       100 ~el~~~~~il~-~-~~~~sLvliDE~~~gT~~~eg~ala~aile~L~---~~~~~~i~tTH~~e-L~~l  162 (224)
T d1ewqa2         100 VEMEEVALILK-E-ATENSLVLLDEVGRGTSSLDGVAIATAVAEALH---ERRAYTLFATHYFE-LTAL  162 (224)
T ss_dssp             HHHHHHHHHHH-H-CCTTEEEEEESTTTTSCHHHHHHHHHHHHHHHH---HHTCEEEEECCCHH-HHTC
T ss_pred             HHHHHHHHHHC-C-CCCCCEEEECCCCCCCCHHHHCCHHHHHHHHHH---HCCCCEEEEEECHH-HHHH
T ss_conf             86788987750-2-897727855454568623320025888888886---23761378652023-3322

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.25  E-value=0.11  Score=23.69  Aligned_cols=22  Identities=32%  Similarity=0.415  Sum_probs=18.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|.++|.+|+|||||..++.++
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEEECCCCC------------
T ss_pred             EEEEECCCCCCHHHHHHHHHHC
T ss_conf             9999999994999999999709

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=87.13  E-value=0.28  Score=21.32  Aligned_cols=34  Identities=24%  Similarity=0.295  Sum_probs=24.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCC--CCEEEEE
Q ss_conf             899999389980889999998532000378--8269999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF--TKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F--~~~~wv~  310 (1007)
                      +-|.|.|.+|.||||+|..+...   ...|  |.++++.
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~---g~~lv~DD~~~i~   50 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR---GHRLIADDRVDVY   50 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT---TCEEEEEEEEEEE
T ss_pred             EEEEEEECCCCCHHHHHHHHHHC---CCEEEECCEEEEE
T ss_conf             99999808999989999999985---9919816868999

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=86.03  E-value=0.31  Score=21.01  Aligned_cols=22  Identities=32%  Similarity=0.406  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      .-|.|.|..|.||||+|..+..
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             9999981899998999999998

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.57  E-value=0.29  Score=21.20  Aligned_cols=24  Identities=25%  Similarity=0.405  Sum_probs=22.0

Q ss_pred             CEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             689999938998088999999853
Q 001843          273 TQVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       273 ~~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +.||+|+|.-+.||++|...++..
T Consensus        32 v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          32 MVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             EEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             EEEEEEECCCCCCHHHHHHHHCCC
T ss_conf             799998899999799999998099

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=85.36  E-value=0.31  Score=21.06  Aligned_cols=34  Identities=18%  Similarity=0.283  Sum_probs=25.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHCCCCC--CCEEEEE
Q ss_conf             899999389980889999998532000378--8269999
Q 001843          274 QVIALIGKAGSGKTTLARIVYNRVYVKRHF--TKRAWVH  310 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~~~v~~~F--~~~~wv~  310 (1007)
                      .-|.|.|..|.||||+|......   ...|  |.++++.
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~---g~~li~DD~~~~~   51 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR---GHRLVADDNVEIR   51 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT---TCEEEESSEEEEE
T ss_pred             EEEEEEECCCCCHHHHHHHHHHC---CCEEEECCEEEEE
T ss_conf             99999808999999999999984---9938817868999

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.31  E-value=0.23  Score=21.73  Aligned_cols=23  Identities=22%  Similarity=0.458  Sum_probs=19.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      +...++|..|+|||||...+..+
T Consensus        96 kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          96 KISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             CEEEEECCCCCCHHHHHHHHCCH
T ss_conf             80899788987788887730535

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=84.48  E-value=0.41  Score=20.30  Aligned_cols=23  Identities=26%  Similarity=0.515  Sum_probs=20.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      .+|+|+|-...|||||+..+...
T Consensus         6 p~IaIiGh~d~GKSTL~~~L~~~   28 (227)
T d1g7sa4           6 PIVSVLGHVDHGKTTLLDHIRGS   28 (227)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCHHHHHHHHHHH
T ss_conf             87999969985499999999823

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=83.99  E-value=0.37  Score=20.61  Aligned_cols=23  Identities=26%  Similarity=0.504  Sum_probs=20.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|.++|..|+|||||...++..
T Consensus        33 l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          33 LTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             48999899998699999998589

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=82.96  E-value=0.13  Score=23.25  Aligned_cols=22  Identities=32%  Similarity=0.554  Sum_probs=19.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999938998088999999853
Q 001843          275 VIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      -|+++|.+++|||||...+...
T Consensus         2 kI~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             8999999999999999999589

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=81.80  E-value=0.58  Score=19.45  Aligned_cols=23  Identities=22%  Similarity=0.296  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             89999938998088999999853
Q 001843          274 QVIALIGKAGSGKTTLARIVYNR  296 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~~  296 (1007)
                      --|+|+|++.+|||||-..+-+.
T Consensus         3 ~~~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           3 FKCGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             34888899999889999999779

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=80.93  E-value=0.9  Score=18.31  Aligned_cols=22  Identities=36%  Similarity=0.525  Sum_probs=20.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      ..+.++|.|+.|||+++..+..
T Consensus       105 n~~~l~G~~~tGKS~f~~~i~~  126 (267)
T d1u0ja_         105 NTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
T ss_conf             7999985898877899999999

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=80.77  E-value=0.39  Score=20.46  Aligned_cols=36  Identities=22%  Similarity=0.294  Sum_probs=21.1

Q ss_pred             EEEEECCCCCHHHHHHHH-HHHHHHCC-CCC--CCEEEEEEC
Q ss_conf             999993899808899999-98532000-378--826999926
Q 001843          275 VIALIGKAGSGKTTLARI-VYNRVYVK-RHF--TKRAWVHIP  312 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~-v~~~~~v~-~~F--~~~~wv~vs  312 (1007)
                      .+.|.|.+|.||||.+.+ +..  .+. ..+  ..++.++.+
T Consensus        16 ~~lI~g~aGTGKTt~l~~rv~~--ll~~~~~~~~~ILvlt~t   55 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVITNKIAH--LIRGCGYQARHIAAVTFT   55 (306)
T ss_dssp             EEEECCCTTSCHHHHHHHHHHH--HHHHHCCCGGGEEEEESS
T ss_pred             CEEEEEECCCCHHHHHHHHHHH--HHHHCCCCHHHEEEEECC
T ss_conf             9899962884389999999999--999569995578999686

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.36  E-value=0.6  Score=19.37  Aligned_cols=22  Identities=27%  Similarity=0.519  Sum_probs=18.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      --|+|+|..|+|||||...+..
T Consensus        57 l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          57 LNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
T ss_conf             1799989999978999999958

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=80.21  E-value=0.61  Score=19.33  Aligned_cols=22  Identities=27%  Similarity=0.543  Sum_probs=19.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             8999993899808899999985
Q 001843          274 QVIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       274 ~vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      --|+|+|....|||||..++..
T Consensus         6 inIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           6 INLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEEECCCCCHHHHHHHHHH
T ss_conf             7999990778709999999997

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=80.10  E-value=0.6  Score=19.34  Aligned_cols=21  Identities=33%  Similarity=0.442  Sum_probs=18.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHH
Q ss_conf             999993899808899999985
Q 001843          275 VIALIGKAGSGKTTLARIVYN  295 (1007)
Q Consensus       275 vi~I~G~gGiGKTtLA~~v~~  295 (1007)
                      -|+|+|..+.|||||+.++..
T Consensus         5 ni~iiGhvd~GKSTL~~~Ll~   25 (204)
T d2c78a3           5 NVGTIGHVDHGKTTLTAALTY   25 (204)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCHHHHHHHHHH
T ss_conf             999994789849999999999