Citrus Sinensis ID: 003387

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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----
Protein Sequence
MHINFRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPDLATVMDEINWFTYESEKVIDTFINSITQQKTQSSCSKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKTSKAEAGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFEDKEQCGIQLYPYGI
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEcHHcHHHHHHHHHccccccEEEEEEccccccHHHHHHHHcccccccccccEEEEEEccccccccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHcccccEEEEEEEccccHHHHHHHHHHccccccccEEEEEcccHHHHHHccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHccccHHHHHHcccccccccccccccccHHHHHHcccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHHcccEEEEEcccccEEcEEEccHHHHHHHHHHccccccEEEEccccccccccccEEEEEEcccccccccccccccEEEEEEccccccccccHHHHHHcccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccHHHcccccccEEEEccccccccccccccccccccEEccccccccHHHHHcccccccEEEEEccccccHHHHHHHccccccccEEEEEcccccccccEEEEccccccccccEEEEEcccccccccccccccccccEEEEEEcEEcccEEEEEcccccccccEEcccccccccEEEcccccccccEEEEEEccccccccccccccccccEEEEccccHHHHHHHHHHccccccccEEEEccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHEccccccHHHHHHHHHcccccEEEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEEEEcccccHHHHHHHHHHHHccccccccHHHccHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHHHccccccccEEEEEEccHHHHHHccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHccccHHHHHHHHHHHHccHHHcccHccHHEEEEEEccccccEcHHHHHHHHHHHccccccHHHHHHHHHHHHHHccEEEEEEEcccccEEEEEHHHHHHHHHHHHHHHccEEEEEcccccccccccEEEEEEEEccccccccccccccEEEEEEEccccccccHHHHHHHHHHccEEEEEEccccccHcccHHccccHHHHEEcccccccccccHHHHHHHHHccEEEccccccccccHHHHHHHHccEEEEccccccccccccccccHHHHEEEEEEcccccHHHHcHHHHHcEEEEEcccccccHHHHHHHHHcccccEEEEccccccccccHHcccccccccccEEEEEEccccccccHHHHHcccccEEEEEEcccccccEEEcccccccccEEEEEcccHcccEEEccccccccccEEEEcccHHHccccccccccccccEEEEccccHHHHHHHccccccccEEEEEEcccc
Coil and Loop (DISEMBL)
MHINFRLFSERLRRVLAgeevtlpdaakqpiQNLHAEVEIVTSWLSEFEDDISLLLFEKMaeeeshdpdlatVMDEINWFTYESEKVIDTFINSITqqktqsscSKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKtskaeagissssksrdtvglDDRMEELLDLLIEGPPQLSVVAILDSigldktafageAYNSSYVKHyfdchawitepysneydadQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEilpdnqngsrVLITLTDIRIIISfqfedgenmrldlvptggplratykgrpfliLYHGSISLEENIREAVEtplglryikclmlpfclkpcfiylsvfpahqeisTRQLYQLWIAegfipdnseaTAESYLEQLIKEGFVEAKkrkaggtintcsipgrwrpvlhtvpYMVEFicspfmdpkgkspkkakRLNAveregdfaclddydsqlhsllccspetrhldpidweKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKlnipslnslpssLLSNLLnlytldmpfsyidHTADEFWKMnklrhlnfgsitlpahpgkfcgslenlnfisalhpccctedilgrlpnlrnlrirgdlsynqSLLSKSLCRLSCLESLKlaneskmprlsKIVLAEylfphslthlsfsntdlmddpmptleklplLQVLKLKqnsysgrkltcgsygfpnlkvLHLKSMLWLEEWtmgnaampklecliinpcaylkkMPEQLWYIKSLnkfdcwwpqpelrQKLREFEdkeqcgiqlypygi
Flexible Loop (DISEMBL)
mhinfrlfSERLRRVLAGEEVtlpdaakqpiqNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPDLATVMDEINWFTYESEKVIDTFINSITQQKTQSSCSKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRiktskaeagissssksrdtvglDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEIlpdnqngsrVLITLTDIRIIISFqfedgenmrlDLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVeakkrkaggtintcsipgrwrpVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKlaneskmprlSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLRefedkeqcgiqlypygi
Low Complexity Region (SEG)
MHINFRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPDLATVMDEINWFTYESEKVIDTFINSITQQKTQSSCSKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKTSKAEAGISSSSKSRDTVGlddrmeelldllieGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKllrvldlgslvlIQYPSGIENLFLLRYlklnipslnslpssllsnllnlYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQsllskslcrlscleslklANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTleklpllqvlklkQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFEDKEQCGIQLYPYGI
Disordered region (IsUnstruct)
****FRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMA*******DLATVMDEINWFTYESEKVIDTFINSITQQ*****CSKDIFDALQGLQSRI***********************************************ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFM*****************REGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFEDKEQCGIQLYP***
Disordered Region (DISOPRED)
*HINFRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAE*ESHDPDLATVMDEINWFTYESEKVIDTFINSIT**********DIFDALQGLQSRITDIKQRMQQ****************************DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFL***************MKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPF**********AKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSIT***********L*NLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPE*************CGIQLYPYGI
Disordered Region (DISEMBL)
MHINFRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPDLATVMDEINWFTYESEKVIDTFINSIT********SKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKTS***************VGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDP**********LNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFEDKEQCGIQLYPYGI
Disordered Region (DISPRO)
*HINFRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPDLATVMDEINWFTYESEKVIDTFINSITQQKTQSSCSKDIFDALQGLQSRITDIKQRMQQLK******************ISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFEDKEQCGIQLYPYGI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHINFRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPDLATVMDEINWFTYESEKVIDTFINSITQQKTQSSCSKDIFDAxxxxxxxxxxxxxxxxxxxxxDSKIIDRIKTSKAEAGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFEDKEQCGIQLYPYGI
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	824	2.2.26 [Sep-21-2011]
Q8W474	907	Probable disease resistan	yes	no	0.900	0.818	0.272	5e-50
Q9FJB5	901	Disease resistance RPP8-l	no	no	0.881	0.805	0.253	3e-47
Q9XIF0	906	Putative disease resistan	no	no	0.881	0.801	0.274	4e-46
Q9FJK8	908	Probable disease resistan	no	no	0.883	0.801	0.240	2e-44
Q8W4J9	908	Disease resistance protei	no	no	0.883	0.801	0.237	7e-44
P59584	910	Disease resistance protei	no	no	0.884	0.801	0.238	8e-44
Q9M667	835	Disease resistance protei	no	no	0.859	0.847	0.267	2e-43
P0C8S1	906	Probable disease resistan	no	no	0.850	0.773	0.254	5e-43
Q8W3K3	910	Putative disease resistan	no	no	0.899	0.814	0.257	7e-42
P0DI18	1049	Probable disease resistan	no	no	0.887	0.696	0.256	2e-39

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

 Score =  200 bits (508), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 246/903 (27%), Positives = 389/903 (43%), Gaps = 161/903 (17%)

Query: 16  LAGEEVT-----LPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLL-FEKMAEEESHDPD 69
           +AGE V+     L D   Q  +      + VT      + D++LL  F K A+ + H   
Sbjct: 1   MAGELVSFGIKKLWDLLSQECEQFQGVEDQVTG----LKRDLNLLSSFLKDADAKKHTTA 56

Query: 70  LA-TVMDEINWFTYESEKVIDTFI--------NSITQQKTQSSC-----SKDIFDALQGL 115
           +   V++EI    Y++E +I+T++        + I  +  + +C      ++  D + G+
Sbjct: 57  VVRNVVEEIKEIVYDAEDIIETYLLKEKLWKTSGIKMRIRRHACIISDRRRNALD-VGGI 115

Query: 116 QSRITDIKQRMQQLKHMDSKIID------RIKTSKAEAGISSSSKSRDTVGLDDRMEELL 169
           ++RI+D+ + MQ    +   I+D      +    +      S     D VGL+  +++L+
Sbjct: 116 RTRISDVIRDMQSFG-VQQAIVDGGYMQPQGDRQREMRQTFSKDYESDFVGLEVNVKKLV 174

Query: 170 DLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQIL 229
             L++    + VV+I    GL KT  A + +N   VKH FD  AW+    S E+    + 
Sbjct: 175 GYLVD-EENVQVVSITGMGGLGKTTLARQVFNHEDVKHQFDRLAWVC--VSQEFTRKNVW 231

Query: 230 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM----TKRYLIVIDDVWSIDMWDVIQEI 285
            ++++ L    +  EI+    +M++  LH+ L     T + LIV DD+W  + WD+I+ I
Sbjct: 232 QMILQNLTSREKKDEIL----QMEEAELHDKLFQLLETSKSLIVFDDIWKDEDWDLIKPI 287

Query: 286 LPDNQNGSRVLIT--------LTDIRII------------------ISFQFEDGENMRLD 319
            P N+ G +VL+T          DI+ +                  I+F  +D    ++D
Sbjct: 288 FPPNK-GWKVLLTSQNESVAVRGDIKYLNFKPECLAIEDSWTLFQRIAFPKKDASESKVD 346

Query: 320 --LVPTGGPLRATYKGRPFLILYHG---------------SISLEENIREAVETPLGLRY 362
             +   G  +     G P  I   G               S+++  +I     +     Y
Sbjct: 347 EEMEDMGKQMLKHCGGLPLAIKVLGGLLAAKYTMHDWERLSVNIGSDIVGRTSSNNSSIY 406

Query: 363 IKCLM----LPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIP----DNSEA---TA 411
               M    LP  LK CF+YL+ FP   +I+  +L   W AEG        N E      
Sbjct: 407 HVLSMSFEELPSYLKHCFLYLAHFPEDHKINVEKLSYCWAAEGISTAEDYHNGETIQDVG 466

Query: 412 ESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFI--------CSPFM 463
           +SYLE+L++   +  ++        TC +    R V         F+         +   
Sbjct: 467 QSYLEELVRRNMIIWERDATASRFGTCHLHDMMREVCLFKAKEENFLQIAVKSVGVTSSS 526

Query: 464 DPKGKSPKKAKRLN-------AVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKF 516
               +SP +++RL         VER       D  + +L SL+    +   L   +W+  
Sbjct: 527 TGNSQSPCRSRRLVYQCPTTLHVER-------DINNPKLRSLVVLWHD---LWVENWKLL 576

Query: 517 CGMF---KLLRVLDLGSLVL--IQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY 571
              F   KLLRVLDL  +    ++ P GI NL  LRYL L    ++ LPSSL + +L +Y
Sbjct: 577 GTSFTRLKLLRVLDLFYVDFEGMKLPFGIGNLIHLRYLSLQDAKVSHLPSSLGNLMLLIY 636

Query: 572 -TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCG-------SLENLNFISAL 623
             LD+   +I    D F +M++LR+L      LP H  K           LE L + S  
Sbjct: 637 LNLDVDTEFI-FVPDVFMRMHELRYLK-----LPLHMHKKTRLSLRNLVKLETLVYFSTW 690

Query: 624 HPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKL-ANESKMPRLSKI 682
           H    ++D+ G +  L  L IR     +   LS S+  L  LE L +    SK  R   I
Sbjct: 691 HSS--SKDLCG-MTRLMTLAIRLTRVTSTETLSASISGLRNLEYLYIVGTHSKKMREEGI 747

Query: 683 VL---------------AEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSY 727
           VL                +  FP  LT +  S   L +DPMP LEKL  L+ + L + SY
Sbjct: 748 VLDFIHLKHLLLDLYMPRQQHFPSRLTFVKLSECGLEEDPMPILEKLLHLKGVILLKGSY 807

Query: 728 SGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYI 787
            GR++ C   GFP LK L +  +   EEW +   +MP LE L I  C  LK++P+ L +I
Sbjct: 808 CGRRMVCSGGGFPQLKKLEIVGLNKWEEWLVEEGSMPLLETLSILDCEELKEIPDGLRFI 867

Query: 788 KSL 790
            SL
Sbjct: 868 YSL 870

Possible 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 =  191 bits (484), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 216/853 (25%), Positives = 363/853 (42%), Gaps = 127/853 (14%)

Query: 59  KMAEEESHDPD-LATVMDEINWFTYESEKVIDTFI--------NSITQQKTQSSC----S 105
           K A+ + H  D +   ++++    +++E +I++++          +     + +C     
Sbjct: 46  KDADAKKHGSDRVRNFLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKNHVRRLACFLTDR 105

Query: 106 KDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKT-------SKAEAGISSSSKSRDT 158
             +   ++G+  RI+ +   MQ L  +  +IID  ++        +      +SS+S D 
Sbjct: 106 HKVASDIEGITKRISKVIGEMQSLG-IQQQIIDGGRSLSLQDIQREIRQTFPNSSES-DL 163

Query: 159 VGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEP 218
           VG++  +EEL+  ++E    + VV+I    G+ KT  A + ++   V+ +FD  AW+   
Sbjct: 164 VGVEQSVEELVGPMVE-IDNIQVVSISGMGGIGKTTLARQIFHHDLVRRHFDGFAWVC-- 220

Query: 219 YSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDM 278
            S ++    +   +++ L P     EI+  +    +  L + L T RYL+V+DDVW  + 
Sbjct: 221 VSQQFTQKHVWQRILQELRPHD--GEILQMDEYTIQGKLFQLLETGRYLVVLDDVWKEED 278

Query: 279 WDVIQEILPDNQNGSRVL------ITLTDIRIIISF------------------------ 308
           WD I+E+ P  +    +L      + L      +SF                        
Sbjct: 279 WDRIKEVFPRKRGWKMLLTSRNEGVGLHADPTCLSFRARILNPKESWKLFERIVPRRNET 338

Query: 309 QFEDGENMRLDLVPTGGPLRATYKGRPFLILYH------------------GSISLEENI 350
           ++E+ E +  ++V   G L    K    L+                     G   L++N 
Sbjct: 339 EYEEMEAIGKEMVTYCGGLPLAVKVLGGLLANKHTASEWKRVSENIGAQIVGKSCLDDNS 398

Query: 351 REAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEA- 409
             +V   L L Y     LP  LK CF+YL+ FP   +I TR LY  W AEG I D     
Sbjct: 399 LNSVYRILSLSYED---LPTDLKHCFLYLAHFPEDYKIKTRTLYSYWAAEG-IYDGLTIL 454

Query: 410 -TAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHT---VPYMVEFICSPFMDP 465
            + E YLE+L++   V A+K      +  C +    R V  +   V   ++ I  P    
Sbjct: 455 DSGEDYLEELVRRNLVIAEKSNLSWRLKLCQMHDMMREVCISKAKVENFLQIIKVPTSTS 514

Query: 466 K--GKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFK-- 521
               +SP +++RL      G    +  +  ++ SLL        L    W +    F+  
Sbjct: 515 TIIAQSPSRSRRLTV--HSGKAFHILGHKKKVRSLLVLG-----LKEDLWIQSASRFQSL 567

Query: 522 -LLRVLDLGSLVL--IQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY-TLDMPF 577
            LLRVLDL S+     + PS I  L  LR+L L+   ++ LPS++ +  L LY  L +  
Sbjct: 568 PLLRVLDLSSVKFEGGKLPSSIGGLIHLRFLSLHQAVVSHLPSTIRNLKLMLYLNLHVAI 627

Query: 578 SYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFC--GSLENLNFISALHPCCCTEDILGR 635
               H  +   +M +LR+L   S+ L  H       G L NL ++        +   L R
Sbjct: 628 GVPVHVPNVLKEMLELRYL---SLPLDMHDKTKLELGDLVNLEYLWCFSTQHSSVTDLLR 684

Query: 636 LPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKM------------------- 676
           +  LR   +          LS SL +   LE+L      K                    
Sbjct: 685 MTKLRFFGVSFSERCTFENLSSSLRQFRKLETLSFIYSRKTYMVDYVGEFVLDFIHLKKL 744

Query: 677 ---PRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLT 733
                LSKI     L PH + H+      + +DPMP LEKL  L+ ++L++ ++ GR++ 
Sbjct: 745 SLGVHLSKIPDQHQLPPH-IAHIYLLFCHMEEDPMPILEKLLHLKSVELRRKAFIGRRMV 803

Query: 734 CGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKF 793
           C   GFP L+ L +     LEEW +   +MP L  LII+ C  L+++P+ L Y+ SL + 
Sbjct: 804 CSKGGFPQLRALQISEQSELEEWIVEEGSMPCLRDLIIHSCEKLEELPDGLKYVTSLKEL 863

Query: 794 DCWWPQPELRQKL 806
                + E ++KL
Sbjct: 864 KIEGMKREWKEKL 876

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 =  187 bits (474), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 234/851 (27%), Positives = 374/851 (43%), Gaps = 125/851 (14%)

Query: 41  VTSWLSEFEDDISLLL-FEKMAEEESHDPDLA-TVMDEINWFTYESEKVIDTFINSITQQ 98
           V   ++E  DD+ +L+ F   A+ +     LA   ++EI   TY++E +I+ F+   +  
Sbjct: 32  VEEQITELRDDLKMLMAFLSDADAKKQTRALARNCLEEIKEITYDAEDIIEIFLLKGSVN 91

Query: 99  KTQSSC----SKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKT-----SKAEAGI 149
               +C     ++I   +  +  RI+ + Q MQ L  + S I+D + +      K E   
Sbjct: 92  MRSLACFPGGRREIALQITSISKRISKVIQVMQNLG-IKSDIMDGVDSHAQLERKRELRH 150

Query: 150 SSSSKSR-DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY 208
           + SS+S  + VGL+  +E+L++ L+ G      V+I    GL KT  A + ++   VK +
Sbjct: 151 TFSSESESNLVGLEKNVEKLVEELV-GNDSSHGVSITGLGGLGKTTLARQIFDHDKVKSH 209

Query: 209 FDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLI 268
           FD  AW+    S E+    +   ++  L P  + S++ + + + K   L + L TK+ LI
Sbjct: 210 FDGLAWVC--VSQEFTRKDVWKTILGNLSPKYKDSDLPEDDIQKK---LFQLLETKKALI 264

Query: 269 VIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRI---IISFQFE-------------- 311
           V DD+W  + W  I  + P+ + G +VL+T  +  I    ++F+ E              
Sbjct: 265 VFDDLWKREDWYRIAPMFPERKAGWKVLLTSRNDAIHPHCVTFKPELLTHDECWKLLQRI 324

Query: 312 -------------DGENMRLDLVPT-------------GGPLRATYKGRPFL-----ILY 340
                        D E +++    T             GG L A +  R +      I+ 
Sbjct: 325 AFSKQKTITGYIIDKEMVKMAKEMTKHCKRLPLAVKLLGGLLDAKHTLRQWKLISENIIS 384

Query: 341 H---GSISLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLW 397
           H   G  S  EN   +V   L L +     LP  LK C +YL+ +P   EI   +L  +W
Sbjct: 385 HIVVGGTSSNENDSSSVNHVLSLSFEG---LPGYLKHCLLYLASYPEDHEIEIERLSYVW 441

Query: 398 IAEGFI-PDNSEAT-----AESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTV 451
            AEG   P N E       A+ Y+E+L+K   V +++         C +    R +   +
Sbjct: 442 AAEGITYPGNYEGATIRDVADLYIEELVKRNMVISERDALTSRFEKCQLHDLMREIC-LL 500

Query: 452 PYMVEFICSPFMDPKGKSPK------KAKRLNAVEREGDFACLDDY-DSQLHSLLCCSPE 504
               E       DP   S        +++RL  V     F+  +D  +S+L SLL     
Sbjct: 501 KAKEENFLQIVTDPTSSSSVHSLASSRSRRL-VVYNTSIFSGENDMKNSKLRSLLFI--- 556

Query: 505 TRHLDPIDWEKFCGM-----FKLLRVLDLGSLVLI--QYPSGIENLFLLRYLKLNIPSLN 557
                P+ + +F          LLRVLDL        + PS I  L  L+YL L   S+ 
Sbjct: 557 -----PVGYSRFSMGSNFIELPLLRVLDLDGAKFKGGKLPSSIGKLIHLKYLSLYQASVT 611

Query: 558 SLPSSLLSNLLNLYTLDMPFS--YIDHTADEFWKMNKLRHLNFGSITLPAHPGKFC---- 611
            LPSSL  NL +L  L++  +   + +  + F +M +LR+L     +LP           
Sbjct: 612 YLPSSL-RNLKSLLYLNLRINSGQLINVPNVFKEMLELRYL-----SLPWERSSLTKLEL 665

Query: 612 GSLENLNFISALHPCCCTEDILGRLPNLRNLRI--RGDLSYNQSLLSKSLCRLSCLESLK 669
           G+L  L  +        +   L R+  LR L+I   G+   +   LS +L  L  LE L 
Sbjct: 666 GNLLKLETLINFSTKDSSVTDLHRMTKLRTLQILISGE-GLHMETLSSALSMLGHLEDLT 724

Query: 670 L--ANESKMPRLSKIVLAEYL-----FPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKL 722
           +  +  S   +  K++    L     FP  LT +S     L +DPMPTLEKL  L+V+ L
Sbjct: 725 VTPSENSVQFKHPKLIYRPMLPDVQHFPSHLTTISLVYCFLEEDPMPTLEKLLQLKVVSL 784

Query: 723 KQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPE 782
             N+Y GR++ C   GFP L  L +  +  LEEW +   +MP L  L I  C  LK++P+
Sbjct: 785 WYNAYVGRRMVCTGGGFPPLHRLEIWGLDALEEWIVEEGSMPLLHTLHIVDCKKLKEIPD 844

Query: 783 QLWYIKSLNKF 793
            L +I SL + 
Sbjct: 845 GLRFISSLKEL 855

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJK8|RP8L4_ARATH Probable disease resistance RPP8-like protein 4 OS=Arabidopsis thaliana GN=RPP8L4 PE=2 SV=1

 Score =  181 bits (459), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 207/860 (24%), Positives = 354/860 (41%), Gaps = 132/860 (15%)

Query: 59  KMAEEESHDPD-LATVMDEINWFTYESEKVIDTFINSITQQKTQS------------SCS 105
           K A+ + H  D +   ++++    +++E +I++++ +  + + +             +  
Sbjct: 46  KDADAKKHGSDRVRNFLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKKHVRRLARFLTDR 105

Query: 106 KDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKT------SKAEAGISSS---SKSR 156
             +   ++G+  RI+D+   MQ       +IID +++       + +  I  +   S   
Sbjct: 106 HKVASDIEGITKRISDVIGEMQSFG--IQQIIDGVRSLSLQERQRVQREIRQTYPDSSES 163

Query: 157 DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT 216
           D VG++  +EEL+  L+E      VV+I    G+ KT  A + ++   V+ +FD  AW+ 
Sbjct: 164 DLVGVEQSVEELVGHLVENDI-YQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVC 222

Query: 217 EPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI 276
              S ++    +   +++ L P       MD++    K  L + L T RYL+V+DDVW  
Sbjct: 223 --VSQQFTLKHVWQRILQELQPHDGNILQMDESALQPK--LFQLLETGRYLLVLDDVWKK 278

Query: 277 DMWDVIQEILPDNQNGSRVLITLTDIRIIIS--------------------------FQF 310
           + WD I+ + P  + G ++L+T  +  + I                           F  
Sbjct: 279 EDWDRIKAVFP-RKRGWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPR 337

Query: 311 EDGENMRLD--LVPTGGPLRATYKGRPFLILYHGSI------------------------ 344
            D   +RLD  +   G  +     G P  +   G +                        
Sbjct: 338 RDETEVRLDEEMEAMGKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVSDNIGSQIVGG 397

Query: 345 -SLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFI 403
             L++N   +V   L L Y     LP  LK  F+YL+ FP   +I T+ L+  W AEG  
Sbjct: 398 SCLDDNSLNSVNRILSLSYED---LPTHLKHRFLYLAHFPEDSKIYTQDLFNYWAAEGIY 454

Query: 404 PDNS-EATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPF 462
             ++ + + E YLE+L++   V A  R      N C +    R V  +      F+    
Sbjct: 455 DGSTIQDSGEYYLEELVRRNLVIADNRYLSLEFNFCQMHDMMREVCLSKAKEENFL-QII 513

Query: 463 MDP------KGKSPKKAKRLNAVEREGDFACLDDYDS-QLHSLLCCSPETRHLDPIDWEK 515
            DP        +SP +++R  ++     F  L   ++ ++ SL+    E        W +
Sbjct: 514 KDPTSTSTINAQSPSRSRRF-SIHSGKAFHILGHRNNPKVRSLIVSRFEEDF-----WIR 567

Query: 516 FCGMFK---LLRVLDLGSLVL--IQYPSGIENLFLLRYLKLNIPSLNSLPSSL------- 563
              +F    LLRVLDL  +     + PS I  L  LRYL L    ++ LPS++       
Sbjct: 568 SASVFHNLTLLRVLDLSRVKFEGGKLPSSIGGLIHLRYLSLYGAVVSHLPSTMRNLKLLL 627

Query: 564 -----------------LSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAH 606
                            L  +L L  L +P    D T  E   +  L +L + S T  + 
Sbjct: 628 FLNLRVDNKEPIHVPNVLKEMLELRYLSLPQEMDDKTKLELGDLVNLEYLWYFS-TQHSS 686

Query: 607 PGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLE 666
                   +  N   +L   C  E +   L  LRNL +   L   + ++   +       
Sbjct: 687 VTDLLRMTKLRNLGVSLSERCNFETLSSSLRELRNLEMLNVLFSPEIVMVDHMGEFVLDH 746

Query: 667 SLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNS 726
            + L       R+SKI   ++ FP  L H+   +  + +DPMP LEKL  L+ + L   +
Sbjct: 747 FIHLKQLGLAVRMSKIP-DQHQFPPHLAHIHLVHCVMKEDPMPILEKLLHLKSVALSYGA 805

Query: 727 YSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWY 786
           + GR++ C   GFP L  L +     LEEW +   +MP L  L I+ C  LK++P+ L Y
Sbjct: 806 FIGRRVVCSKGGFPQLCALGISGESELEEWIVEEGSMPCLRTLTIHDCEKLKELPDGLKY 865

Query: 787 IKSLNKFDCWWPQPELRQKL 806
           I SL +      + E ++KL
Sbjct: 866 ITSLKELKIREMKREWKEKL 885

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  179 bits (455), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 204/860 (23%), Positives = 350/860 (40%), Gaps = 132/860 (15%)

Query: 59  KMAEEESHDPD-LATVMDEINWFTYESEKVIDTFI--------NSITQQKTQSSC----S 105
           K A+ + H  D +   ++++    +++E +I++++          + +   + +C     
Sbjct: 46  KDADAKKHGSDRVRNFLEDVKDLVFDAEDIIESYVLNKLSGKGKGVKKHVRRLACFLTDR 105

Query: 106 KDIFDALQGLQSRITDIKQRMQQLKHMDSKIID---------RIKTSKAEAGISSSSKSR 156
             +   ++G+  RI+++   MQ       +IID         R +  +        S   
Sbjct: 106 HKVASDIEGITKRISEVIGEMQSFG--IQQIIDGGRSLSLQERQRVQREIRQTYPDSSES 163

Query: 157 DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT 216
           D VG++  ++EL+  L+E      VV+I    G+ KT  A + ++   V+ +FD  AW+ 
Sbjct: 164 DLVGVEQSVKELVGHLVENDVH-QVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVC 222

Query: 217 EPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI 276
              S ++    +   +++ L P       MD+    +K  L + L   RYL+V+DDVW  
Sbjct: 223 --VSQQFTQKHVWQRILQELQPHDGDILQMDEYALQRK--LFQLLEAGRYLVVLDDVWKK 278

Query: 277 DMWDVIQEILPDNQNGSRVLITLTDIRIIIS--------------------------FQF 310
           + WDVI+ + P  + G ++L+T  +  + I                           F  
Sbjct: 279 EDWDVIKAVFP-RKRGWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPR 337

Query: 311 EDGENMRLD--LVPTGGPLRATYKGRPFLILYHGSIS----------------------- 345
            D   +RLD  +   G  +     G P  +   G +                        
Sbjct: 338 RDETEVRLDEEMEAMGKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVFDNIGSQIVGG 397

Query: 346 --LEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFI 403
             L++N   +V   L L Y     LP  LK CF+ L+ FP   EIST  L+  W AEG  
Sbjct: 398 SWLDDNSLNSVYRILSLSYED---LPTHLKHCFLNLAHFPEDSEISTYSLFYYWAAEGIY 454

Query: 404 PDNS-EATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPF 462
             ++ E + E YLE+L++   V A           C +    R V  +      F+    
Sbjct: 455 DGSTIEDSGEYYLEELVRRNLVIADDNYLSWQSKYCQMHDMMREVCLSKAKEENFL-QII 513

Query: 463 MDP------KGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKF 516
           +DP        +SP +++RL+    +          +++ SL+    E  +     W + 
Sbjct: 514 IDPTCTSTINAQSPSRSRRLSIHSGKAFHILGHKNKTKVRSLIVPRFEEDY-----WIRS 568

Query: 517 CGMFK---LLRVLDLGSLVL--IQYPSGIENLFLLRYLKLNIPSLNSLPSSL-------- 563
             +F    LLRVLDL  +     + P  I  L  LRYL L    ++ LPS++        
Sbjct: 569 ASVFHNLTLLRVLDLSWVKFEGGKLPCSIGGLIHLRYLSLYEAKVSHLPSTMRNLKLLLY 628

Query: 564 ----------------LSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHP 607
                           L  ++ L  L +P    D T  E   +  L +L +G  T  +  
Sbjct: 629 LNLRVDTEEPIHVPNVLKEMIQLRYLSLPLKMDDKTKLELGDLVNLEYL-YGFSTQHSSV 687

Query: 608 GKFCGSLENLNFIS-ALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLE 666
                 +  L +++ +L   C  E +   L  LRNL     L   ++ +   +       
Sbjct: 688 TDLL-RMTKLRYLAVSLSERCNFETLSSSLRELRNLETLNFLFSLETYMVDYMGEFVLDH 746

Query: 667 SLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNS 726
            + L       R+SKI   ++ FP  L HL      + +DPMP LEKL  L+ ++L + +
Sbjct: 747 FIHLKQLGLAVRMSKIP-DQHQFPPHLVHLFLIYCGMEEDPMPILEKLLHLKSVRLARKA 805

Query: 727 YSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWY 786
           + G ++ C   GFP L V+ +     LEEW +   +MP L  L I+ C  LK++P+ L Y
Sbjct: 806 FLGSRMVCSKGGFPQLCVIEISKESELEEWIVEEGSMPCLRTLTIDDCKKLKELPDGLKY 865

Query: 787 IKSLNKFDCWWPQPELRQKL 806
           I SL +      + E ++KL
Sbjct: 866 ITSLKELKIEGMKREWKEKL 885

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|P59584|RP8HA_ARATH Disease resistance protein RPH8A OS=Arabidopsis thaliana GN=RPH8A PE=3 SV=1

 Score =  179 bits (454), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 205/861 (23%), Positives = 358/861 (41%), Gaps = 132/861 (15%)

Query: 59  KMAEEESHDPD-LATVMDEINWFTYESEKVIDTFINSITQQKTQS------------SCS 105
           K A+ + H  D +   ++++    +++E +I++++ +  + + +             +  
Sbjct: 46  KDADAKKHGSDRVRNFLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKKHVRRLARFLTDR 105

Query: 106 KDIFDALQGLQSRITDIKQRMQQLKHMDSKIID---------RIKTSKAEAGISSSSKSR 156
             +   ++G+  RI+++   MQ       +IID         R +  +        S   
Sbjct: 106 HKVASDIEGITKRISEVIGEMQSFG--IQQIIDGGRSLSLQERQRVQREIRQTYPDSSES 163

Query: 157 DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT 216
           D VG++  + EL+  L+E      VV+I    G+ KT  A + ++   V+ +FD  AW+ 
Sbjct: 164 DLVGVEQSVTELVCHLVENDVH-QVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVC 222

Query: 217 EPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI 276
              S ++    +   +++ L P     EI+  +    +  L + L T RYL+V+DDVW  
Sbjct: 223 --VSQQFTQKHVWQRILQELQPHD--GEILQMDEYTIQGKLFQLLETGRYLVVLDDVWKK 278

Query: 277 DMWDVIQEILPDNQNGSRVLITLTDIRIIIS--------------------------FQF 310
           + WD I+ + P  + G ++L+T  +  + I                           F  
Sbjct: 279 EDWDRIKAVFP-RKRGWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPR 337

Query: 311 EDGENMRLD--LVPTGGPLRATYKGRPFLILYHGSI------------------------ 344
            D   +RLD  +   G  +     G P  +   G +                        
Sbjct: 338 RDETEVRLDEEMEAMGKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVSDNIGSQIVGG 397

Query: 345 -SLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFI 403
             L++N   +V   L L Y     LP  LK CF++L+ +P   +I T+ L+  W AEG  
Sbjct: 398 SCLDDNSLNSVYRILSLSYED---LPTHLKHCFLHLAHYPEDSKIYTQDLFNYWAAEGIY 454

Query: 404 PDNS-EATAESYLEQLIKEGFVEAKKRK--AGGTINTCSIPGRWRPVLHTVPYMVEFICS 460
             ++ + + E YLE+L++   V A  R   +   I  C +    R V  +      F+  
Sbjct: 455 DGSTIQDSGEYYLEELVRRNLVIADNRYLISEFKIKNCQMHDMMREVCLSKAKEENFL-Q 513

Query: 461 PFMDP------KGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWE 514
              DP        +SP +++RL+    +         ++++ SL+    E        W 
Sbjct: 514 IIKDPTCTSTINAQSPSRSRRLSIHSGKAFHILGHKRNAKVRSLIVSRFEEDF-----WI 568

Query: 515 KFCGMFK---LLRVLDLGSLVL--IQYPSGIENLFLLRYLKLNIPSLNSLPSSL-LSNLL 568
           +   +F    LLRVLDL  +     + P  I  L  LRYL+L    ++ LPS++    LL
Sbjct: 569 RSASVFHNLTLLRVLDLSWVKFEGGKLPCSIGGLIHLRYLRLYGAVVSHLPSTMRNLKLL 628

Query: 569 NLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCC 628
               L +    + H  +   +M +LR+L+   + +        G L NL ++        
Sbjct: 629 LYLNLSVHNEDLIHVPNVLKEMIELRYLSI-PVKMDDKTKLELGDLVNLEYLYGFSTQHT 687

Query: 629 TEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESK------------- 675
           +   L R+  LRNL +     YN   LS SL  L  LE+L +    K             
Sbjct: 688 SVTDLLRMTKLRNLTVSLSERYNFKTLSSSLRELRNLETLYVLFSRKTYMVDHMGEFVLD 747

Query: 676 ----------MPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQN 725
                     + R+SKI   ++ FP  L H+      + +DPMP LEKL  L+ ++L+  
Sbjct: 748 HFIHLKELGLVVRMSKIP-DQHQFPPHLVHIFLFYCGMEEDPMPILEKLHHLKSVQLRYK 806

Query: 726 SYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLW 785
           ++ GR++ C   GF  L  L +     LE+W +   +MP L  L I+ C  LK++P+ L 
Sbjct: 807 AFVGRRMVCSKDGFTQLCALDISKQSELEDWIVEEGSMPCLRTLTIHDCEKLKELPDGLK 866

Query: 786 YIKSLNKFDCWWPQPELRQKL 806
           YI SL +      + E ++KL
Sbjct: 867 YITSLKELKIEGMKREWKEKL 887

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. In contrast to RPP8, it does not specifically recognize the Emco5 avirulence protein from Hyaloperonospora parasitica.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M667|RPP13_ARATH Disease resistance protein RPP13 OS=Arabidopsis thaliana GN=RPP13 PE=2 SV=2

 Score =  177 bits (450), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 222/829 (26%), Positives = 368/829 (44%), Gaps = 121/829 (14%)

Query: 19  EEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPDLATVMDEIN 78
           EE ++  A K+ ++ L  E+  +  +L + E         +  E+E        V+D   
Sbjct: 19  EEASMFMAVKEDLEELKTELTCIHGYLKDVE--------AREREDEVSKEWSKLVLD--- 67

Query: 79  WFTYESEKVIDTF------------INSITQQKTQSSCSKDIFDALQGLQSRITDIKQRM 126
            F Y+ E V+DT+            +  +T +  +   +  I D ++ L+ RI DI ++ 
Sbjct: 68  -FAYDVEDVLDTYHLKLEERSQRRGLRRLTNKIGRKMDAYSIVDDIRILKRRILDITRKR 126

Query: 127 QQLKHMDSKIIDRIKTSKAEAGISS-------SSKSRD----TVGLDDRMEELLDLLIEG 175
           +         I  +K  +     SS        ++S D     VGL+D  + LL+ L++ 
Sbjct: 127 ETYG------IGGLKEPQGGGNTSSLRVRQLRRARSVDQEEVVVGLEDDAKILLEKLLDY 180

Query: 176 PPQLS-VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK 234
             +   +++I    GL KTA A + YNS  VK  F+  AW     S EY    IL  +I+
Sbjct: 181 EEKNRFIISIFGMGGLGKTALARKLYNSRDVKERFEYRAWTY--VSQEYKTGDILMRIIR 238

Query: 235 FLMPSS--RLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNG 292
            L  +S   L +I     E  ++ L+  L  K+YL+V+DD+W  + WD ++  LP N  G
Sbjct: 239 SLGMTSGEELEKIRKFAEEELEVYLYGLLEGKKYLVVVDDIWEREAWDSLKRALPCNHEG 298

Query: 293 SRVLITLTDIRII---------------ISFQ----------FEDGENMRLDLVPTGGPL 327
           SRV+IT T I+ +               ++F+          F + +    DL+ TG  +
Sbjct: 299 SRVIIT-TRIKAVAEGVDGRFYAHKLRFLTFEESWELFEQRAFRNIQRKDEDLLKTGKEM 357

Query: 328 RATYKGRPF-LILYHGSISLE-----ENIREAVETPLGLRYIKCLMLPFCL--------- 372
               +G P  +++  G +S +      ++  ++   L    I    + F L         
Sbjct: 358 VQKCRGLPLCIVVLAGLLSRKTPSEWNDVCNSLWRRLKDDSIHVAPIVFDLSFKELRHES 417

Query: 373 KPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEA----TAESYLEQLIKEGFVEAKK 428
           K CF+YLS+FP   EI   +L  L +AEGFI  + E      A  Y+E+LI    +EA +
Sbjct: 418 KLCFLYLSIFPEDYEIDLEKLIHLLVAEGFIQGDEEMMMEDVARYYIEELIDRSLLEAVR 477

Query: 429 RKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVERE-GDFAC 487
           R+  G + +C I    R V       + F+ + + D   +      R   V  +   ++ 
Sbjct: 478 RER-GKVMSCRIHDLLRDVAIKKSKELNFV-NVYNDHVAQHSSTTCRREVVHHQFKRYSS 535

Query: 488 LDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLR 547
               + ++ S L    E  HL  +D+E      KLLRVLD GSL L    +G  +L  LR
Sbjct: 536 EKRKNKRMRSFLYFG-EFDHLVGLDFE----TLKLLRVLDFGSLWLPFKING--DLIHLR 588

Query: 548 YLKLNIPSLNSLP-SSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL--NFGSITLP 604
           YL ++  S+N    ++++S L  L TL +  +Y      +  K+  LRH+  NF      
Sbjct: 589 YLGIDGNSINDFDIAAIISKLRFLQTLFVSDNYFIEETIDLRKLTSLRHVIGNF------ 642

Query: 605 AHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQS----LLSKSLC 660
              G   G + NL  ++++      +     L NLR+L I  ++S ++     +   SL 
Sbjct: 643 -FGGLLIGDVANLQTLTSISFDSWNKLKPELLINLRDLGI-SEMSRSKERRVHVSWASLT 700

Query: 661 RLSCLESLKLANESKMP---RLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLL 717
           +L  L  LKLA  +++       + V +  +   SL  ++       +DPMP L+K+P L
Sbjct: 701 KLESLRVLKLATPTEVHLSLESEEAVRSMDVISRSLESVTLVGITFEEDPMPFLQKMPRL 760

Query: 718 QVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKL 766
           + L L   +YSG K++    GF  L+ L L  M  L+E  +   AMP L
Sbjct: 761 EDLILLSCNYSG-KMSVSEQGFGRLRKLDL-LMRSLDELQIEEEAMPNL 807

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. In contrast to other resistance proteins, it works independently of ESD1 and NSD1 proteins and does not require the accumulation of salicylic acid, suggesting the existence of an independent signaling pathway. The specificity to avirulence proteins differs in the different cultivars.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  176 bits (447), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 211/828 (25%), Positives = 352/828 (42%), Gaps = 127/828 (15%)

Query: 74  MDEINWFTYESEKVIDTFI--------NSITQQKTQSSC----SKDIFDALQGLQSRITD 121
           ++++    Y+++ +I++F+          I +Q    +C     +     ++G+  RI++
Sbjct: 62  LEDVKDIVYDADDIIESFLLNELRGKEKGIKKQVRTLACFLVDRRKFASDIEGITKRISE 121

Query: 122 IKQRMQQL--KHMDSKIIDRIKTSKAEAGIS---SSSKSRDTVGLDDRMEELLDLLIEGP 176
           +   MQ L  +H+       +   + +  I    S +   D VGLD  +EEL+D L+E  
Sbjct: 122 VIVGMQSLGIQHIADGGGRSLSLQERQREIRQTFSRNSESDLVGLDQSVEELVDHLVEND 181

Query: 177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFL 236
             + VV++    G+ KT  A + ++   V+ +FD  +W+    S ++    +   +++ L
Sbjct: 182 S-VQVVSVSGMGGIGKTTLARQVFHHDIVRRHFDGFSWVC--VSQQFTRKDVWQRILQDL 238

Query: 237 MPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVL 296
            P       MD+ Y ++   L E L + RYL+V+DDVW  + WD I+ + P ++ G ++L
Sbjct: 239 RPYDEGIIQMDE-YTLQGE-LFELLESGRYLLVLDDVWKEEDWDRIKAVFP-HKRGWKML 295

Query: 297 ITLTDI----------------------------RIIIS----FQFEDGENMRLDLVPTG 324
           +T  +                             RI+ S     +F+  E M  ++V   
Sbjct: 296 LTSRNEGLGLHADPTCFAFRPRILTPEQSWKLFERIVSSRRDKTEFKVDEAMGKEMVTYC 355

Query: 325 GPLRATYKGRPFL----------------ILYH--GSISLEENIREAVETPLGLRYIKCL 366
           G L    K    L                I+ H  G   L ++   +V   L L Y    
Sbjct: 356 GGLPLAVKVLGGLLAKKHTVLEWKRVHSNIVTHIVGKSGLSDDNSNSVYRVLSLSYED-- 413

Query: 367 MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIP---DNS--EATAESYLEQLIKE 421
            LP  LK CF YL+ FP   +I  + L+  W+AEG I    D S  + T ESYLE+L++ 
Sbjct: 414 -LPMQLKHCFFYLAHFPEDYKIDVKILFNYWVAEGIITPFHDGSTIQDTGESYLEELVRR 472

Query: 422 GFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFI------CSPFMDPKGKSPKKAKR 475
             V  ++      I  C +    R V  +      FI       +       +SP +++R
Sbjct: 473 NMVVVEESYLTSRIEYCQMHDMMREVCLSKAKEENFIRVVKVPTTTSTTINAQSPCRSRR 532

Query: 476 LNAVEREGDFACLDDYDSQ-LHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVL- 533
           L  +        L   D++   S+L    E +   P  ++  C    LLRVLDL  +   
Sbjct: 533 L-VLHSGNALHMLGHKDNKKARSVLIFGVEEKFWKPRGFQ--C--LPLLRVLDLSYVQFE 587

Query: 534 -IQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLD-MPFSYIDHTADEFWKMN 591
             + PS I +L  LR+L L    ++ LPSSL +  L L     +    + H  +   +M 
Sbjct: 588 GGKLPSSIGDLIHLRFLSLYEAGVSHLPSSLGNLKLLLCLNLGVADRLLVHVPNVLKEMQ 647

Query: 592 KLRHLNFGSITLPAHPGKFCGSLENL----NF---------------ISALHPC----CC 628
           +LR+L     ++PA      G L NL    NF               +S L+      C 
Sbjct: 648 ELRYLRLPR-SMPAKTKLELGDLVNLESLTNFSTKHGSVTDLLRMTKLSVLNVIFSGECT 706

Query: 629 TEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES---KMPRLSKIVLA 685
            E +L  L  LRNL       + +  ++     L  L+ + L + +    +PR       
Sbjct: 707 FETLLLSLRELRNLETLSFHDFQKVSVANHGGELLVLDFIHLKDLTLSMHLPRFPD---- 762

Query: 686 EYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVL 745
           +Y FP  L H+      + +DPMP LEKL  L+ + L   ++ GR++ C   GFP L  L
Sbjct: 763 QYRFPPHLAHIWLIGCRMEEDPMPILEKLLHLKSVYLSSGAFLGRRMVCSKGGFPQLLAL 822

Query: 746 HLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKF 793
            +     L EW +   +MP L  L I+ C  LK++P+ L Y+  L + 
Sbjct: 823 KMSYKKELVEWRVEEGSMPCLRTLTIDNCKKLKQLPDGLKYVTCLKEL 870

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 =  172 bits (437), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 226/877 (25%), Positives = 371/877 (42%), Gaps = 136/877 (15%)

Query: 35  HAEVEIVTSWLSEFEDDISLLL-FEKMAEEESHDPDLAT-VMDEINWFTYESEKVIDTFI 92
           + + + V   ++E + +++LL  F K AE + +   +    ++EI    Y++E +I+TFI
Sbjct: 21  YEQFQGVEDRIAELKSNLNLLKSFLKDAEAKKNTSQMVRHCVEEIKEIVYDTENMIETFI 80

Query: 93  --------NSITQQKTQSSCSK----DIFDALQGLQSRITDIKQRM-----QQLKHMDSK 135
                   + I ++ T+ +C K    +    + G+  RI+ + Q M     QQ+    S+
Sbjct: 81  LKEAARKRSGIIRRITKLTCIKVHRWEFASDIGGISKRISKVIQDMHSFGVQQMISDGSQ 140

Query: 136 IIDRIKTSKAEAGIS-SSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTA 194
               ++  + E   + S     D VGL+  +++L+  L+E    + +V++    GL KT 
Sbjct: 141 SSHLLQEREREMRQTFSRGYESDFVGLEVNVKKLVGYLVE-EDDIQIVSVTGMGGLGKTT 199

Query: 195 FAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKK 254
            A + +N   VKH FD  AW+    S E+    +  ++++ L  +SR  E  D+  +M++
Sbjct: 200 LARQVFNHEDVKHQFDRLAWVC--VSQEFTRKNVWQMILQNL--TSR--ETKDEILQMEE 253

Query: 255 IILHEYLM----TKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVL-------ITLTDIR 303
             LH+ L     T + LIV DD+W  + W +I  I P  + G +VL       I +   R
Sbjct: 254 AELHDELFQLLETSKSLIVFDDIWKEEDWGLINPIFPPKK-GWKVLITSRTETIAMHGNR 312

Query: 304 IIISFQFE-------------------DGENMRLD--LVPTGGPLRATYKGRPFLI---- 338
             ++F+ E                   D    ++D  +   G  +     G P  +    
Sbjct: 313 RYVNFKPECLTILESWILFQRIAMPRVDESEFKVDKEMEMMGKQMIKYCGGLPLAVKVLG 372

Query: 339 -------LYHGSISLEENI--------------REAVETPLGLRYIKCLMLPFCLKPCFI 377
                   +H    L ENI                +V   L L + +   LP  LK CF+
Sbjct: 373 GLLAAKYTFHDWKRLSENIGCHIVGRTDFSDGNNSSVYHVLSLSFEE---LPSYLKHCFL 429

Query: 378 YLSVFPAHQEISTRQLYQLWIAEGFI-PDNSEA-----TAESYLEQLIKEGFVEAKKRKA 431
           YL+ FP    I   +L   W AEG + P +          ESY+E+L++   V A++   
Sbjct: 430 YLAHFPEDHNIKVEKLSYCWAAEGILEPRHYHGQTIRDVGESYIEELVRRNMVIAERDVT 489

Query: 432 GGTINTCSIPGRWRPVLHTVPYMVEFI-CSPFMDPKGKS--PKKAKRLNAVEREGDFACL 488
                 C +    R V         F+  +  + P   S  P  ++R  +          
Sbjct: 490 TLRFEACHLHDMMREVCLLKAKEENFVQIASILPPTANSQYPGTSRRFVSQNPTTLHVSR 549

Query: 489 DDYDSQLHSLLCCSPETRHLDPIDWEKFCGMF---KLLRVLDL--GSLVLIQYPSGIENL 543
           D  + +L SLL      R      W+     F   +LLRVLDL          PSGI  L
Sbjct: 550 DINNPKLQSLLIVWENRRK----SWKLLGSSFIRLELLRVLDLYKAKFEGRNLPSGIGKL 605

Query: 544 FLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYID-HTADEFWKMNKLRHLNFGSIT 602
             LRYL L++  ++ LPSSL  NL  L  LD+          +    M++LR+L     T
Sbjct: 606 IHLRYLNLDLARVSRLPSSL-GNLRLLIYLDINVCTKSLFVPNCLMGMHELRYLRLPFNT 664

Query: 603 LPAHPGKFCG--SLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLC 660
                   C   +LE L   S  +     ED+ G + +LR L I      ++  L  S+ 
Sbjct: 665 SKEIKLGLCNLVNLETLENFSTENSSL--EDLRG-MVSLRTLTIGLFKHISKETLFASIL 721

Query: 661 RLSCLESLKLA---NESKMPRLSK--IVLA------------------EYLFPHSLTHLS 697
            +  LE+L +      SK  R+ +  IVL                   E  FP  LT +S
Sbjct: 722 GMRHLENLSIRTPDGSSKFKRIMEDGIVLDAIHLKQLNLRLYMPKLPDEQHFPSHLTSIS 781

Query: 698 FSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWT 757
                L++DP+P LEKL  L+ ++L   ++ G+++     GFP L  L++  +   EEW 
Sbjct: 782 LDGCCLVEDPLPILEKLLELKEVRLDFRAFCGKRMVSSDGGFPQLHRLYIWGLAEWEEWI 841

Query: 758 MGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFD 794
           +   +MP+L  L I  C  LK++P+ L +I S+   D
Sbjct: 842 VEEGSMPRLHTLTIWNCQKLKQLPDGLRFIYSIKDLD 878

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 =  164 bits (416), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 226/881 (25%), Positives = 357/881 (40%), Gaps = 150/881 (17%)

Query: 41  VTSWLSEFEDDISLLL-FEKMAEEESHDPDLA-TVMDEINWFTYESEKVIDTFINSITQQ 98
           V   ++E + D++LL  F K A+ + H   +    ++EI    Y+ E  I+TF+      
Sbjct: 27  VEDQVTELKRDLNLLSSFLKDADAKKHTSAVVKNCVEEIKEIIYDGEDTIETFVLEQNLG 86

Query: 99  KTQSSCSKDIFD-------------ALQGLQSRITDIKQRMQQLKHMDSKIIDRIKTSKA 145
           KT S   K I                + GL +RI+ + + MQ      + +    K  + 
Sbjct: 87  KT-SGIKKSIRRLACIIPDRRRYALGIGGLSNRISKVIRDMQSFGVQQAIVDGGYKQPQG 145

Query: 146 EAGIS-----SSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAY 200
           +         S     D VGL+  +++L+  L++    + VV+I    GL KT  A + +
Sbjct: 146 DKQREMRPRFSKDDDSDFVGLEANVKKLVGYLVD-EANVQVVSITGMGGLGKTTLAKQVF 204

Query: 201 NSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY 260
           N   VKH FD  +W+    S ++    +   +++ L P     +IM+   +  +  L   
Sbjct: 205 NHEDVKHQFDGLSWVC--VSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIRL 262

Query: 261 LMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRII--------------- 305
           L T + LIV+DD+W  + W++I+ I P  + G +VL+T  +  +                
Sbjct: 263 LETSKSLIVLDDIWEKEDWELIKPIFPPTK-GWKVLLTSRNESVAMRRNTSYINFKPECL 321

Query: 306 -----------ISFQFEDGENMRLD----------LVPTGG-PLRATYKGRPFLILY--H 341
                      I+   +D    ++D          +   GG PL     G      Y  H
Sbjct: 322 TTEDSWTLFQRIALPMKDAAEFKIDEEKEELGKLMIKHCGGLPLAIRVLGGMLAEKYTSH 381

Query: 342 GSISLEENI-------REAVETPLGLRYIKCLMLPFCLKPCF-----IYLSVFPAHQEIS 389
               L ENI       R              L L F   P +     +YL+ FP   EI+
Sbjct: 382 DWRRLSENIGSHLVGGRTNFNDDNNNTCNYVLSLSFEELPSYLKHCFLYLAHFPDDYEIN 441

Query: 390 TRQLYQLWIAEG-FIPDNSEA-----TAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGR 443
            + L   W AEG F P + +        + Y+E+L++   V +++        TC +   
Sbjct: 442 VKNLSYYWAAEGIFQPRHYDGEIIRDVGDVYIEELVRRNMVISERDVKTSRFETCHLHDM 501

Query: 444 WRPVL---HTVPYMVEFICSPFMDPKGKSPKKAKRLN-----AVEREGDFACLDDYDSQL 495
            R V          ++   S        S   ++RL       ++ E D       D +L
Sbjct: 502 MREVCLLKAKEENFLQITSSRTSTGNSLSIVTSRRLVYQYPITLDVEKDIN-----DPKL 556

Query: 496 HSLLCCSPETRHLDPIDWEKFCGMF---KLLRVLDL--GSLVLIQYPSGIENLFLLRYLK 550
            SL+  +          W      F   +LLRVLD+    L   +  S I  L  LRYL 
Sbjct: 557 RSLVVVANTYMFWGGWSWMLLGSSFIRLELLRVLDIHRAKLKGGKLASSIGQLIHLRYLN 616

Query: 551 LNIPSLNSLPSSLLSNL-----LNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPA 605
           L    +  +P S L NL     LNL  L    + + +   E   M +LR+L      LP 
Sbjct: 617 LKHAEVTHIPYS-LGNLKLLIYLNLVILVSGSTLVPNVLKE---MQQLRYL-----ALPK 667

Query: 606 HPGKFCG-SLENLNFISALH----PCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLC 660
             G+     L NL  +  L       C  ED+ G +  LR L I      +   L+ S+ 
Sbjct: 668 DMGRKTKLELSNLVKLETLKNFSTKNCSLEDLRG-MVRLRTLTIELRKETSLETLAASIG 726

Query: 661 RLSCLESLK---LANESK---------------------MPRLSKIVLAEYLFPHSLTHL 696
            L  LESL    L +E +                     MPRLSK    E  FP  LT L
Sbjct: 727 GLKYLESLTITDLGSEMRTKEAGIVFDFVYLKTLTLKLYMPRLSK----EQHFPSHLTTL 782

Query: 697 SFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEW 756
              +  L +DPMP LEKL  L+ L+L++ S+SG+++ C S GFP L+ L +K +   E+W
Sbjct: 783 YLQHCRLEEDPMPILEKLHQLKELELRRKSFSGKEMVCSSGGFPQLQKLSIKGLEEWEDW 842

Query: 757 TMGNAAMPKLECLIINPCAYLKKMPEQLW--YIKSLNKFDC 795
            +  ++MP L  L I  C  LK++P++    ++ S++ F C
Sbjct: 843 KVEESSMPVLHTLDIRDCRKLKQLPDEHLPSHLTSISLFFC 883

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	824
147766035	902	hypothetical protein VITISV_038742 [Viti	0.756	0.690	0.297	4e-64
297745275	1136	unnamed protein product [Vitis vinifera]	0.912	0.661	0.286	3e-62
359491404	922	PREDICTED: probable disease resistance R	0.888	0.793	0.288	1e-61
297745279	920	unnamed protein product [Vitis vinifera]	0.917	0.821	0.269	1e-61
224096480	910	nbs-lrr resistance protein [Populus tric	0.866	0.784	0.277	3e-61
359489148	897	PREDICTED: probable disease resistance R	0.939	0.862	0.272	5e-61
359489792	916	PREDICTED: probable disease resistance p	0.889	0.800	0.276	2e-60
359489156	899	PREDICTED: probable disease resistance p	0.956	0.876	0.269	2e-59
224075299	896	nbs-lrr resistance protein [Populus tric	0.896	0.824	0.266	1e-58
225454212	936	PREDICTED: putative disease resistance p	0.890	0.784	0.271	4e-58

>gi|147766035|emb|CAN70214.1| hypothetical protein VITISV_038742 [Vitis vinifera]

 Score =  253 bits (645), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 213/716 (29%), Positives = 326/716 (45%), Gaps = 93/716 (12%)

Query: 157 DTVGLDDRMEELL-DLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWI 215
           D +G D+ +  L+  LL +  P+ S ++I+   GL KT  A + YN   VK  FD  AW+
Sbjct: 171 DVIGFDEDINMLVARLLDQETPRRSTISIVGMGGLGKTTLAKKVYNCRSVKRRFDFCAWV 230

Query: 216 TEPYSNEYDADQIL-DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVW 274
               S +Y A ++L +I  K L        +M++ +  +++     L  KRYLIV+DD+W
Sbjct: 231 Y--VSQDYRAGELLHEIGEKILRIEKGRLAMMNRQHLEERV--STVLRKKRYLIVLDDIW 286

Query: 275 SIDMWDVIQEILPDNQNGSRVLITLTDIRIII---------------------------S 307
             ++WD ++ + PD  N SRVL T T IR +                            +
Sbjct: 287 ETEVWDDLKTLFPDVMNASRVLFT-TRIRDVAIHADPRSATHELHFLNQAQSWELFLKKA 345

Query: 308 FQFE-DGENMRLDLVPTGGPLRATYKGRPFLILYHGSI--------------------SL 346
           F  E D      +L   G  + A   G P  I+  G +                     L
Sbjct: 346 FPMEGDSVTCPPELERLGTQIVAKCGGLPLAIVIIGGLLSRKEKXPSVWLRVLQSISWQL 405

Query: 347 EENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDN 406
             + R+ +E  L L Y     LP+ LKPCF+Y  +FP   EI   +L  LWIAEGF+   
Sbjct: 406 NNDSRQLMEI-LALSYND---LPYYLKPCFLYFGLFPEDLEIPVGKLVLLWIAEGFVQQR 461

Query: 407 SEAT----AESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPY---MVEFIC 459
            E +    AE +LE+L+    ++  +++  G I  C I    R +  +       +E + 
Sbjct: 462 GEESMEDVAEDFLEELVDRSMIQVAEKRYNGKIKMCRIHDLLRDLAMSEAKECKFLEILD 521

Query: 460 SPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGM 519
           S  +D    +  +A+R++      ++  L   +    S+L  S     L    W+     
Sbjct: 522 STNIDTSVTT--RARRISVHSSLEEYMKLRHPNPHFRSMLHFSRCEESLRREQWKSLFES 579

Query: 520 FKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY 579
            KLLRVLDL  +     P  I  L  LRYL L    L  LPSS+  N  NL TLD+  + 
Sbjct: 580 LKLLRVLDLERVQTHALPKEIRELVHLRYLGLRRTGLQRLPSSV-QNFCNLQTLDIRATK 638

Query: 580 IDHTADEFWKMNKLRHLNFGSITLPAHPGKFCG--SLENLNFISALHPCCCTEDILGRLP 637
           +     + W M  LRHL     ++  HP        L+ L+ +S ++      D+LG+L 
Sbjct: 639 VSRLPIQLWNMPGLRHLYLEKTSIAGHPPVHVSVMHLQTLSTVS-IYGNQWIPDLLGKLT 697

Query: 638 NLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES-----------KMPRLSKIVLA- 685
           NLR L I G  +     LS+ L +LS L++L+L                 P + K+ L+ 
Sbjct: 698 NLRKLGIHGYFASQTEALSRCLVKLSNLQNLQLRGTELILEPTIKLLLNQPNIHKLHLSG 757

Query: 686 --------EYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSY 737
                   + + P +LT +    + L+ D    L KLP LQ+LKL  NS+ G+++TC + 
Sbjct: 758 PIEKLPDPQEIQP-NLTKIILEKSLLVQDIFVILGKLPNLQMLKLLINSFFGKEITCSAS 816

Query: 738 GFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKF 793
           GFP L  L L  ++ LEEW + + AMP L  L+I+ C  LKK+PE   Y+ +L + 
Sbjct: 817 GFPKLHGLELSELVNLEEWRVDDGAMPSLRHLVIDHCDQLKKIPEGFQYLTALREL 872

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745275|emb|CBI40355.3| unnamed protein product [Vitis vinifera]

 Score =  246 bits (629), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 247/862 (28%), Positives = 392/862 (45%), Gaps = 110/862 (12%)

Query: 7   LFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESH 66
            F+E+L  ++  E         Q I+ L  E+E    W+  F  D           +  +
Sbjct: 8   FFAEKLSNLILQEASVFGQVEGQ-IKLLRNELE----WMRLFLKDAD--------SKRIY 54

Query: 67  DPDLATVMDEINWFTYESEKVIDTFI----------NSITQQKTQSSCS--KDIFDALQG 114
           D  +   +++I   T+++E VID FI          N++   K   +C    D    +  
Sbjct: 55  DERIKLWVNQIRNATHDAEDVIDEFILNMDHRQRRLNTLKFLKCLPACVGFADKLPFIHE 114

Query: 115 LQSRITDIKQRMQQLKHMDSK--IIDRIKTSKAEAGISSSSKSR--------DTVGLDDR 164
           L SR+ DI   +  +    SK  + D + +S +     ++ K +        D VG++D 
Sbjct: 115 LDSRVKDINVMIGAIMANRSKYGLGDLVASSSSTTDQVAAHKEKRPPVVEESDVVGIEDG 174

Query: 165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD 224
           +EE+  +L++   + SVV+I+   GL KT FA + YN   V+ +FDC AW+    S E+ 
Sbjct: 175 IEEVKQMLMKEETRRSVVSIVGMGGLGKTTFAKKVYNQRDVQQHFDCKAWVY--VSQEFR 232

Query: 225 ADQIL-DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQ 283
           A +IL DI   F+  S +  E+ +     K   L EYL  K+YLIV+DDVWS ++W  ++
Sbjct: 233 AREILLDIANHFMSLSEKEKEMRESELGEK---LCEYLKEKKYLIVMDDVWSSEVWSRLR 289

Query: 284 EILPDNQNGSRVLITLTDIRIII-----SFQFE-----DGENMRLDLVPT---------- 323
             LP+ ++GS+VLIT  +  I +     +F +E     D E+ +L L  T          
Sbjct: 290 SHLPEAKDGSKVLITTRNKEIALQATSQAFIYELRLMNDDESWQLFLKKTFQGTSTPHTL 349

Query: 324 -------GGPLRATYKGRPFLILYHGSI----------------SLEENIREAVETPLGL 360
                  G  + A  KG P  ++  G +                S+E  + +  E+ +G+
Sbjct: 350 SRELEEPGKKIVAKCKGLPLAVVVLGGLLSTKEKTKPSWEKVLASIEWYLDQGPESCMGI 409

Query: 361 RYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEAT----AESYLE 416
             +    LP+ LK CF+Y  +FP   EI   +L +LW+AEGFI    + T    AE Y+ 
Sbjct: 410 LALSYNDLPYYLKSCFLYCGIFPEDSEIKASKLIRLWLAEGFIQRRGKETLEDIAEDYMH 469

Query: 417 QLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRL 476
           +LI    ++  KR+  G + +C +    R +         F      +     P   +RL
Sbjct: 470 ELIHRSLIQVAKRRVDGEVESCRMHDLLRDLAVLEAKDANFF-EVHENIDFTFPISVRRL 528

Query: 477 ---NAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVL 533
                + ++    CL  ++SQL SL+  S ET+      W       KLL VL+LG+  +
Sbjct: 529 VIHQNLMKKNISQCL--HNSQLRSLVSFS-ETK--GKKSWRYLQEHIKLLTVLELGNTNM 583

Query: 534 IQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKL 593
           +  P  I     L+ L +N     +LPSS +  L+NL +LD+   Y        WK+ +L
Sbjct: 584 L--PRDIGEFIHLKCLCINGYGRVTLPSS-ICRLVNLQSLDLGDQY-GSIPYSIWKLQQL 639

Query: 594 RHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILG--RLPNLRNLRIRGDLSYN 651
           RHLN G  T     G F    E++  ++AL     + +     RL N   L  + ++   
Sbjct: 640 RHLNCGLFTPYLKKGFF----ESITKLTALQTLALSIEKYSKKRLLNHLGLEWQKNVIEE 695

Query: 652 QSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTL 711
           ++L    L   SC     L     + +L K+      +P +L  L     +L DDPM  L
Sbjct: 696 KTLFP-GLEPFSC--HAYLYELCLVGKLEKLPEQFEFYPPNLLQLDLWKCELRDDPMMIL 752

Query: 712 EKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLII 771
           EKLP L++L L  ++Y G K+ C S GF  L+ L L  +  LEE T+G  AM  L+ L I
Sbjct: 753 EKLPSLRMLGLYFDAYVGIKMICSSGGFLQLERLSLVELKKLEELTVGEGAMSSLKTLQI 812

Query: 772 NPCAYLKKMPEQLWYIKSLNKF 793
             C  +KK+P  L  + +L K 
Sbjct: 813 LNCNEMKKLPHGLLQLTNLEKL 834

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359491404|ref|XP_002274414.2| PREDICTED: probable disease resistance RPP8-like protein 2-like [Vitis vinifera]

 Score =  244 bits (624), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 256/887 (28%), Positives = 383/887 (43%), Gaps = 155/887 (17%)

Query: 57  FEKMAE-EESHDPDLATVMDEINWFTYESEKVIDTFINSITQQKTQSSCSKDIFDALQGL 115
           F K AE ++  D  +   + +I    Y+ + VIDTF+    QQ+      K+ F  L G 
Sbjct: 60  FLKDAEAKQDGDQRVKNWVADIRDVAYDIDDVIDTFLCKTAQQR------KEGFFRLSGR 113

Query: 116 QSRITDIKQRMQQLKHMDSKIIDRIKT---SKAEAGI----------------------S 150
            + +        ++    ++I+++I     S++  GI                      S
Sbjct: 114 YAFVLSDPVAHWKISKKINRIMEKIHEITDSRSTYGIENIGRGGGRSFATDRLQEKRRSS 173

Query: 151 SSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD 210
           S +   D VG    +  L   LI G  +L +++I+   GL KT  A + Y+S+ VK  FD
Sbjct: 174 SHACEEDVVGPLQDIRTLESWLIHGETRLCILSIVGMAGLGKTTLAKKLYHSNDVKKNFD 233

Query: 211 CHAWITEPYSNEYDADQILDIVIKFL--MPSSRLSEIMDKNYEMKKIILHEYLMTKRYLI 268
              W+    S EY     L  ++K +  +P + L E MDK  E  +  L ++L  K+Y I
Sbjct: 234 FCGWVY--VSQEYRPKDTLQNLVKRVTGLPRAEL-EKMDK--EDLEEALSKFLEEKKYFI 288

Query: 269 VIDDVWSIDMWDVIQEILPDNQNGSRVLIT--LTDIRIIIS----------FQFEDGE-- 314
           V+DD+W  ++WD ++   PD +NGSR++ T    D+ +                EDG   
Sbjct: 289 VLDDIWKKEVWDDLKAAFPDRKNGSRIIFTTRFKDVALHADPRSPLHEPCLLSDEDGWEL 348

Query: 315 ---------NMRLDLVP----TGGPLRATYKGRPFLILYHGSISLEEN--------IREA 353
                    N +  L P     G  +     G P  I+  G +   ++        + ++
Sbjct: 349 LSRKVCLEWNAKTSLPPWSKELGIQIVKRCGGLPLAIVVMGGLLSRKDATFNEWLKVLQS 408

Query: 354 VETPLGLRYIKCLM--------LPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPD 405
           V   L     +C          LP+ LK CF+Y  +FP   EIS R+L  LW+AEGF+  
Sbjct: 409 VHWQLAQDPTQCAEILALSYSDLPYYLKSCFLYFGLFPEDYEISARRLILLWVAEGFVQP 468

Query: 406 NS----EATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPY-------M 454
                 E  AE YLE+L+    ++   RK+ G I TC +      +LH +          
Sbjct: 469 RGQEPLEDVAEDYLEELVGRSMIQVATRKSNGRIKTCCV----HDLLHELSVSKGKEDQF 524

Query: 455 VEFICSPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLLC---CSPETRHLDPI 511
           ++ I   F      +     R+  +             S++ SLLC   C P  + L   
Sbjct: 525 LDIIHGEF------TVSSLTRVRRLAIHLGVPPTTKNTSKVRSLLCFDICEPSFQELRK- 577

Query: 512 DWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY 571
                   FKLLR+LDL  + + +  S I NL  LRYL L    L  LP S+   LLNL 
Sbjct: 578 --------FKLLRILDLEGVYISRLHSSIGNLIHLRYLGLRGTWLKKLPPSI-QFLLNLQ 628

Query: 572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCC--- 628
           TLD+  + ++      WKM KLRHL F  +   A       SL NL     LH  C    
Sbjct: 629 TLDLRSTLLNPIPIVIWKMQKLRHLYFNELEEMAVNPPTDASLANLQ---TLHGICINQT 685

Query: 629 --TEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLA--------------- 671
              E+ L +L NLR L + GDL  ++  + K +     LE LKL                
Sbjct: 686 SYVENGLSKLTNLRELGLHGDLLLHEEAIGKWIFSSERLECLKLHTRDVMGDFAKNAIPK 745

Query: 672 -NESKMPRLSKIVL---------AEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLK 721
            N S  P L K+ L         AEY FP +LT LS   + LM+DPM  LE L  L+VLK
Sbjct: 746 LNFSSHPHLIKLHLKGFMAKLFDAEY-FPQNLTELSLKGSFLMEDPMVKLEMLQSLRVLK 804

Query: 722 LKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMP 781
           LK ++Y G+++ C   GFP L  L L  +  +E W + + AM +L  L I  C  LK +P
Sbjct: 805 LKHSAYLGKEMICSCGGFPQLHFLKLSFLNTVERWRIEDGAMGRLRQLEIIECKRLKIVP 864

Query: 782 EQLWYIKSLNKFDCWWPQPELRQKLREFEDK-----EQCGIQLYPYG 823
             L  + +++K    +   E   K++E + +     E   + L P G
Sbjct: 865 RGLQPVTTIHKLKLGYMPREFEMKVQERQGENWYKIEHAVVALNPGG 911

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745279|emb|CBI40359.3| unnamed protein product [Vitis vinifera]

 Score =  244 bits (624), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 246/914 (26%), Positives = 403/914 (44%), Gaps = 158/914 (17%)

Query: 7   LFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESH 66
            F+E+L  ++  +E ++    +  I+ L  E+E    W+  F  D           +  H
Sbjct: 8   FFAEKLSNLIL-QEASVFGQVEGQIKLLRNELE----WMRLFLKDAD--------SKRIH 54

Query: 67  DPDLATVMDEINWFTYESEKVIDTFI----------NSITQQKTQSSCS--KDIFDALQG 114
           D  +   +++I   T+++E VID FI          N++   K   +C    D    +  
Sbjct: 55  DERIKLWVNQIRNATHDAEDVIDEFIVNMDHRQRRLNTLKLLKCLPTCVGFADKLPFIHE 114

Query: 115 LQSRITDIKQRMQQLKHMDSK--IIDRIKTSKAEAGISSSSKSR--------DTVGLDDR 164
           L SR+ DI   +  +    SK  + D + +S +     ++ K +        D VG++D 
Sbjct: 115 LDSRVKDINVMIGAIMANRSKYGLGDLVASSSSTTDQVAAHKEKRPPVVEESDVVGIEDG 174

Query: 165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD 224
            EE+  +L++   + SVV+I+   GL KT  A + YN   V+ +FDC AW+    S E+ 
Sbjct: 175 TEEVKQMLMKEETRRSVVSIVGMGGLGKTTLAKKVYNQRDVQQHFDCKAWVY--VSQEFR 232

Query: 225 ADQIL-DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQ 283
           A +IL DI  +F+  S +  E+ +     K   L EYL  K+YL+V+DDVWS ++W  ++
Sbjct: 233 AREILLDIANRFMSLSEKEKEMRESELGEK---LCEYLKEKKYLVVMDDVWSSEVWSRLR 289

Query: 284 EILPDNQNGSRVLITLTDIRIII-----SFQFE-----DGENMRLDLVPT---------- 323
             LP+ ++GS+VLIT  +  I +     +F +E     D E+ +L L  T          
Sbjct: 290 SHLPEAKDGSKVLITTRNKEIALHATSQAFIYELRLMNDDESWQLFLKKTFQGTSTPHTL 349

Query: 324 -------GGPLRATYKGRPFLILYHGSI----------------SLEENIREAVETPLGL 360
                  G  + A  KG P  ++  G +                S+E  + +  E+ +G+
Sbjct: 350 IRELEEPGKKIVAKCKGLPLAVVVLGGLLSTKEKTKPSWEKVLASIEWYLDQGPESCMGI 409

Query: 361 RYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEAT----AESYLE 416
             +    LP+ LK CF+Y  +FP   EI   +L +LW+AEGFI    + T    AE Y+ 
Sbjct: 410 LALSYNDLPYYLKSCFLYCGIFPEDSEIKASKLIRLWLAEGFIQRRGKETLEDIAEDYMH 469

Query: 417 QLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRL 476
           +LI    ++  +R+  G + +C +    R +        +F      +     P   +RL
Sbjct: 470 ELIHRSLIQVAERRVDGGVESCRMHDLLRDLAVLEAKDAKFF-EVHENIDFTFPISVRRL 528

Query: 477 ---NAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVL 533
                + ++    CL  ++SQL SL+  S  T       W       KLL VL+LG   +
Sbjct: 529 VIHQNLMKKNISKCL--HNSQLRSLVSFSETT---GKKSWRYLQEHIKLLTVLELGKTNM 583

Query: 534 IQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD---EFWKM 590
           +  P  I     L++L +N     +LPSS +  L+NL +L++     DH        WK+
Sbjct: 584 L--PRDIGEFIHLKFLCINGHGRVTLPSS-ICRLVNLQSLNLG----DHYGSIPYSIWKL 636

Query: 591 NKLRHLNFGSITLPAHP------GKFCG--SLENLNFISALHPCCCTEDILGRLPNLRNL 642
            +LRHL   +  +            + G   L NL  ++         D LG+L  LR L
Sbjct: 637 QQLRHLICWNCKISGQSKTSKCVNGYLGVEQLTNLQTLALQGGSWLEGDGLGKLTQLRKL 696

Query: 643 RIRGDLS-YNQSLLSKSLCRLSCLESLKLANES-----------KMPRLSKIVLAEYLFP 690
            + G L+ Y +    +S+ +L+ L++L L  E             + R   ++  + LFP
Sbjct: 697 VLGGLLTPYLKKGFFESITKLTALQTLALGIEKYSKKRLLNHLVGLERQKNVIEEKTLFP 756

Query: 691 H-------------------------------SLTHLSFSNTDLMDDPMPTLEKLPLLQV 719
                                           +L  L   + +L DDPM  LEKLP L+ 
Sbjct: 757 GLVPFSCHAYLDVVNLIGKFEKLPEQFEFYPPNLLKLGLWDCELRDDPMMILEKLPSLRK 816

Query: 720 LKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKK 779
           L+L  ++Y G+K+ C S GF  L+ L L  +  LEE T+   AM  L+ L I  C  +KK
Sbjct: 817 LELGSDAYVGKKMICSSGGFLQLESLILIGLNKLEELTVEEGAMSSLKTLEIWSCGKMKK 876

Query: 780 MPEQLWYIKSLNKF 793
           +P  L  + +L K 
Sbjct: 877 LPHGLLQLTNLEKL 890

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224096480|ref|XP_002334697.1| nbs-lrr resistance protein [Populus trichocarpa] gi|222874531|gb|EEF11662.1| nbs-lrr resistance protein [Populus trichocarpa]

 Score =  243 bits (620), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 228/822 (27%), Positives = 364/822 (44%), Gaps = 108/822 (13%)

Query: 67  DPDLATVMDE--INWFT------YESEKVIDTFINSITQQKTQSSCSK------------ 106
           D D    +DE   NW +      Y++E +IDTF   I+  K +    K            
Sbjct: 72  DADAKQDVDERVCNWVSDIRNVAYDAEDLIDTFTLKISPLKKKHFIRKYTSLVKEWKQRS 131

Query: 107 DIFDALQGLQSRITDIKQRMQQ--LKHMDSKIIDRIKTSKAEAGISSSSKSRDTVGLDDR 164
            I + L  L+SR+ DI        ++++        +T +     S  S+ RD +GL++ 
Sbjct: 132 KIAEGLAALRSRLQDISASRDTYGIQNIGEGTTTASETMRKLRRSSPRSEERDIIGLEND 191

Query: 165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD 224
             +L++ LI+   + S V+I+   G+ KT    + YN   ++  F   AWI    S E+ 
Sbjct: 192 TAKLVEQLIQMGDRWSAVSIVGMGGIGKTTLGIKIYNHGAIRARFPSRAWIY--VSQEFS 249

Query: 225 ADQILDIVIKFLM-PSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQ 283
           A  IL  VI+ +  P  RL  + D+  E    +++E L  KRYL+V+DD+WS   WD ++
Sbjct: 250 ARDILQRVIRQIASPRERLEALTDEELED---LVYENLRRKRYLVVLDDIWSTKAWDCLK 306

Query: 284 EILP-DNQNGSRVLITLTDIRIII---------SFQFEDGEN--------MRLDLVPTGG 325
           +  P D  NGSR+L+T  +    +           +F   +N          +D    G 
Sbjct: 307 KAFPADRSNGSRLLLTTRNKNAALHVDPQTTPYDLEFLSKQNSWELFCKKAFIDGKEIGK 366

Query: 326 PLRATYKGRPFLILYHGSI-------SLEENIREAVET-----PLGLRYIKCLM---LPF 370
            +     G P  I+  G +       S  E I   ++      P G+  I  L    LPF
Sbjct: 367 EIVERCAGLPLAIIVIGGLLSRKRRPSEWERILNNLDAHFARDPNGVSAILALSYNDLPF 426

Query: 371 CLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEA---TAESYLEQLIKEGFVEAK 427
            LK CF YL  FP    I   +L++LWIAEG IP   E     AE YL +LI+   V+A+
Sbjct: 427 YLKSCFFYLGHFPEDYSIHAHKLFRLWIAEGLIPHQGERMEDVAEDYLNELIQRNMVQAE 486

Query: 428 KRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFAC 487
           +    G +  C +    R +  +      F+  P  D    S  + +R + +  +   + 
Sbjct: 487 RMSVNGRVKQCRLHDLLRDLSTSKAKAQNFLQIP-GDENFTSLARCRR-HPIYSDSHLSS 544

Query: 488 LDDYDSQLHSLLCCSPETR---------------HLDPIDWEKFCGMFKLLRVLDLGSLV 532
           L  +   L SLL     TR                L   +++     F+LLR+L+L  + 
Sbjct: 545 LGFFSPHLRSLLFFRVVTRVRYRYFIGRHVYGFYELSNANFDYISRNFRLLRILELEGIS 604

Query: 533 LIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFS-YIDHTADEFWKMN 591
             + PS I +L  L YL L   ++  LPS+L  +L NL TLD+  + ++    +  W M 
Sbjct: 605 CGRIPSTIGDLIHLSYLGLKETNIQVLPSTL-GSLCNLQTLDIARNLHLRIVPNVIWNMR 663

Query: 592 KLRHLNFGSITLPAHPGKF--CGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLS 649
            LRHL      +    G F    +L++L  +S +      ++    L +LR L++RG+LS
Sbjct: 664 NLRHL-----YMCGQSGGFLRIDNLKHLQTLSGIDVSRWKQNNSAHLTSLRKLKMRGNLS 718

Query: 650 YNQSLLSKSLCRLSCLESLKLANE-SKMPRLSKIVLAEYL-----------------FPH 691
            +   +  S+  L  L SL L  E ++ P LS++     L                 FP 
Sbjct: 719 LDTIAIFDSISALLQLRSLYLRAEGAEFPTLSQLGSLHSLVKLHLKGGITRLPSLQEFPP 778

Query: 692 SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSML 751
           +L+ L+   T L    +  LEKLP L + +LK  SYS  +L   + GFP L+ L   S+ 
Sbjct: 779 NLSQLTLEYTHLEQVSIEVLEKLPKLSIFRLKAKSYSKEELGISANGFPQLEFLEFNSLE 838

Query: 752 WLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKF 793
            L E  +  +A+P+LE   I  C  L+ +P ++  + SL++ 
Sbjct: 839 SLTELKIEASALPRLEIFQIVNCKELRMLPAEMKLMTSLHEL 880

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489148|ref|XP_003633887.1| PREDICTED: probable disease resistance RPP8-like protein 4-like [Vitis vinifera]

 Score =  242 bits (618), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 245/900 (27%), Positives = 392/900 (43%), Gaps = 126/900 (14%)

Query: 7   LFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESH 66
           +F E+L  +L+ E   L    +Q ++ L +E+E    W+  F  D           +  +
Sbjct: 8   VFLEKLTDLLSKEAFLLSRVEEQ-VKLLSSELE----WMRLFLKDAD--------AKRRY 54

Query: 67  DPDLATVMDEINWFTYESEKVIDTFINSITQQKTQS-SCSKDI-FDALQGLQSRITDIKQ 124
           DP +   + +I   TY++E VID F+  +  Q+  S  C + +    +  L+SRI +I  
Sbjct: 55  DPRIKLWVSQIRDVTYDAEDVIDRFMFEMNHQQQGSLKCLQFLKLRFVHKLESRIREINI 114

Query: 125 RMQQLKHMDSKI-IDRIKTSKAEAGISSSSKSR------DTVGLDDRMEELLDLLIEGPP 177
           +++++    S+  ++ +  + +        + R      + VG+ +  + +   L+ G  
Sbjct: 115 KIEKIMANKSRYGVETLPAASSSNEAVPHKEKRAPIVEVNVVGIQEDAKSVKQNLLNGEM 174

Query: 178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQIL---DIVIK 234
           + +VV+I+   GL KT  A + YN + V+  FDCHAWI    S EY   ++L    + ++
Sbjct: 175 RRAVVSIVGMGGLGKTTLAKKVYNDNDVRQCFDCHAWIY--VSQEYTIRELLLGVAVCVR 232

Query: 235 FLMPSSRL----SEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQ 290
            L    R     SE+ D+        L +YL TK+YLIV+DD+W  + WD +    PD+ 
Sbjct: 233 ILSEEERSKMDESELGDR--------LRDYLTTKKYLIVLDDMWRNEAWDRLGLYFPDSV 284

Query: 291 NGSRVLITLTDIRII-----------ISFQFEDGENMRL-----------------DLVP 322
           NGSRVLIT  +  I            +SF  E+ E+  L                 +L  
Sbjct: 285 NGSRVLITSRNKEIGFYADPQAIPHELSFLTEE-ESWELFLKKIFLAGSANAVCPRELEE 343

Query: 323 TGGPLRATYKGRPFLILYHGSI----------------SLEENIREAVETPLGLRYIKCL 366
            G  + A   G P  I+  G +                SL  ++ +  ++ LG+  +   
Sbjct: 344 LGKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQKVLDSLTWHLNQGPDSCLGVLALSYN 403

Query: 367 MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDN----SEATAESYLEQLIKEG 422
            +P+ LK CF+Y  +FP   EI T +L +LW+AEGFI       +E  AE +L++L+   
Sbjct: 404 DMPYYLKSCFLYCGLFPEDSEIWTDKLIRLWVAEGFIQRRGVEIAEDVAEDHLQELVHRS 463

Query: 423 FVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVERE 482
            ++   R   G + +C +    R +  +     +F    +      SP   +RL   + +
Sbjct: 464 MIQVAARSFDGRVMSCRMHDLLRDLAISEAKDTKFF-EGYESIDSTSPVSVRRLTIHQGK 522

Query: 483 GDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIEN 542
              +        L S +C S                  KLL VLDL  + +   P GI  
Sbjct: 523 KTNSKHLHTSRSLRSFICFSV---CFQKNSLRSLHRRVKLLTVLDLEGMTINTIPEGIGE 579

Query: 543 LFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNF-GSI 601
           L  L+YL L    +  LPSS+   L NL TLD   + I+      WK++ LRHL   G +
Sbjct: 580 LIHLKYLCLRRTRIKRLPSSI-GRLTNLQTLDFRSTLIEIIPSTIWKLHHLRHLYCRGVV 638

Query: 602 TLPAHPGKF------CGSLENLNFISALHPCCCTEDILGRLPNLRNLRI---RGDLSYNQ 652
           +  +   KF       G L NL  +       C  + LG+L  LR L I       + NQ
Sbjct: 639 SSQSVIDKFRNGPLSVGHLTNLQSLCLRAGSWCCGEGLGKLIELRELTIVWTEIAQTKNQ 698

Query: 653 SLLSKSLCRLSCLESLKLANESK----MPRLSKIVLAEYLF------------------P 690
              S+S+ +L+ L+SL+L    +    MP L       YL+                  P
Sbjct: 699 GF-SESVKKLTALQSLRLYTLGEEMLTMPHLMPFSDHTYLYHLSLNGRLERFPDEIEFYP 757

Query: 691 HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSM 750
            +L  L     +   +PM TLEKLP L+ L+L   S   +K+ C S GF  L+ L L  +
Sbjct: 758 PNLISLELRYRNAEQNPMVTLEKLPNLRFLRLSLCSSMLKKMVCTSGGFQQLETLRLWGL 817

Query: 751 LWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFE 810
             LEE      AMP L+ L+I+ C  +K++   L   K+L     +   PEL  +L   E
Sbjct: 818 KELEELIAEEGAMPDLKDLVIDACPKMKRLSHGLLQRKNLQHLKLYDLSPELMDELSRIE 877

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489792|ref|XP_002274076.2| PREDICTED: probable disease resistance protein RDL6/RF9-like [Vitis vinifera]

 Score =  240 bits (613), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 247/893 (27%), Positives = 397/893 (44%), Gaps = 160/893 (17%)

Query: 56  LFEKMAEEES-HDPDLATVMDEINWFTYESEKVIDTFI----------NSITQQKTQSSC 104
           LF K A+ +S ++  +   +++I   T+++E VID FI          N++   K   +C
Sbjct: 42  LFLKDADSQSLYNEKIKLWVEQIRNVTHDAEDVIDEFILDMDHRQLRLNTLKFLKCLPTC 101

Query: 105 S--KDIFDALQGLQSRITDIKQRMQQLKHMDSK-----IIDRIKTSKAEAGISSSSK--- 154
               D    +  L  R+ +I  R++++    SK     ++    +S  +  ++   K   
Sbjct: 102 VGFADKLPFIHELDGRVKEINIRIERIMANRSKYGLEALMASSSSSTTDQVVAHKEKWAQ 161

Query: 155 ---SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDC 211
                D VG++D  E +  +L++G  + +VV+I+   GL KT  A + YN S VK +FDC
Sbjct: 162 VVEGSDVVGIEDGTEVVTQMLMKGEMRRAVVSIVGMGGLGKTTLAKKVYNHSDVKQHFDC 221

Query: 212 HAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKII-------LHEYLMTK 264
           HAW+    S E+ A +IL  V   +M  S      +K  E+K++        + EYL  K
Sbjct: 222 HAWVY--VSQEFKAREILLGVAYCVMSLSD-----EKKKEVKEMGEAELGRNVREYLKEK 274

Query: 265 RYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQ----------FEDGE 314
           +YL+ +DDVWS ++W  ++  LP+ ++GS+VLIT  +  I +               D E
Sbjct: 275 KYLVAMDDVWSREVWSSLRSYLPEAKDGSKVLITTRNEEIALHANSQALIYRLRIMNDDE 334

Query: 315 NMRLDLVPT-----------------GGPLRATYKGRPFLILYHGSI------------- 344
           + +L L  T                 G  + A  KG P  I+  G +             
Sbjct: 335 SWQLLLKKTFGSRSTSGILTPELEVLGKNIVAKCKGLPLAIVVVGGLLSTKEKTKSSWEK 394

Query: 345 ---SLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEG 401
              S++ ++ +  E+ +G+  +    LP+ LK CF+Y  +FP   EI T +L QLW+ EG
Sbjct: 395 VLASIDWHLIQGPESCMGILALSYNDLPYYLKSCFLYCGIFPEDSEIKTSKLIQLWLVEG 454

Query: 402 FIPDNS----EATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVE- 456
           FI        E  AE YL +LI    ++   RK  G + +C I    R +  +       
Sbjct: 455 FIQRRGKEPLEDIAEDYLYELIHRSMIQVAARKIDGRVTSCRIHDLLRDLAISEARDARL 514

Query: 457 FICSPFMDPKGKSPKKAKRLNAVERE-GDFACLDDYDSQLHSLLCCSPETRHLDPIDWEK 515
           F     +D     P   +RL+  +    +      ++S+L SL+     T   +   W+ 
Sbjct: 515 FEVHENIDV--AFPIGVRRLSIHQHLINNNISQHLHNSRLRSLIFF---TEPFERKSWKS 569

Query: 516 FCGMFKLLRVLDLGS-----LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNL 570
                KLL VLDLGS     +V    P  I  L  L++L +      +LPSS +  L+NL
Sbjct: 570 LKEHIKLLTVLDLGSTDDNYIV----PEEIGELVHLKFLHIRGFQRVTLPSS-IDRLVNL 624

Query: 571 YTLDMPFS--YIDHTADEFWKMNKLRHLN--FGSIT----LPAHPGKFCG--SLENLNFI 620
            + D+  +  YI HT    WK+ +LR+LN   G I+    L      + G   L NL  +
Sbjct: 625 RSFDLGNNDCYIPHT---IWKLQQLRYLNCCLGEISSQFKLSKCVNGYLGVEKLTNLQTL 681

Query: 621 SALHPCCCTEDILGRLPNLRNLRIRGDLSYN------------QSLLSKSLCRLSCLESL 668
             L       D LG+L  L+ L + G L+ +             +L + +L  L   E  
Sbjct: 682 DLLPGSWLEGDGLGKLTQLKELDLGGLLNPHLKKGFFECIANLTALRTLNLSHLRGFEKK 741

Query: 669 KLANESKMPRLSKIVLAEYL------------------------------FPHSLTHLSF 698
            L +  ++ R  K++  + L                              +P +L  L  
Sbjct: 742 TLLSHIRLKRWKKVIEEKTLIPGLMPFSHHTYLYKVILGGKLELSEEIGFYPPNLLELCL 801

Query: 699 SNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM 758
              +L +DPM  LEKLP L+VL+L   SY G+KL C S GF  L+ L L ++  LEE  +
Sbjct: 802 CFCELKNDPMFILEKLPKLKVLRLSDGSYVGKKLVCSSGGFLQLQSLELYALFPLEELIV 861

Query: 759 GNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFED 811
              A+P L+ L I  C  +KK+P  L  +K+L K +   P+    + + EFE+
Sbjct: 862 EEGALPHLKTLQIEHCYGMKKLPRGLLQLKNLEKVE---PKFMFDRLIEEFEE 911

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489156|ref|XP_003633889.1| PREDICTED: probable disease resistance protein RDL6/RF9-like [Vitis vinifera]

 Score =  237 bits (605), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 247/915 (26%), Positives = 397/915 (43%), Gaps = 127/915 (13%)

Query: 7   LFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESH 66
           +F E+L  +L+ E   L    +Q   NL   + I   W+ +F  D           +  +
Sbjct: 8   VFLEKLTDLLSQEAFLLSRVEEQV--NL---LSIDLEWMRQFLKDAD--------AKRRY 54

Query: 67  DPDLATVMDEINWFTYESEKVIDTFINSITQQKTQS-SCSKDI-FDALQGLQSRITDIKQ 124
           DP +   + +I   TY++E VID F+  +  Q+  S  C K +    +  L+SRI +I  
Sbjct: 55  DPRIKLWVSQIRDVTYDAEDVIDRFMFEMNHQQQGSLKCLKFLKLRLVHKLESRIREINT 114

Query: 125 RMQQLKHMDSK-IIDRIKTSKAEAGISSSSKSR-------DTVGLDDRMEELLDLLIEGP 176
           +++++K   S  I++ +  +     +    + R       + VG+ +  + +   L+ G 
Sbjct: 115 KIEKIKAAKSTFIVETLPAASWPNEVVPHRERRAPIVEEVNVVGIQEDAKSVKQKLLNGE 174

Query: 177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQIL-DIVIKF 235
            + +VV+I+   GL KT  A + YN + V+  FDCHAWI    S EY   ++L  + ++ 
Sbjct: 175 MRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIY--VSQEYTIRELLLGVAVRV 232

Query: 236 LMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRV 295
            + S      M+++       L +YL TK+YLIV+DD+W  + WD +    PD+ NGSRV
Sbjct: 233 GILSEEERSKMNESDLGNS--LRDYLTTKKYLIVMDDMWRNEAWDRLGLYFPDSVNGSRV 290

Query: 296 LITLTDIRIII-----------SFQFEDGENMRL-----------------DLVPTGGPL 327
           LIT  + +I +           SF  E+ E+  L                 +L   G  +
Sbjct: 291 LITSRNKQIGLYADPQTIPHELSFLTEE-ESWELFLKKIFLAGSANAVCPRELEELGKKI 349

Query: 328 RATYKGRPFLILYHGSI----------------SLEENIREAVETPLGLRYIKCLMLPFC 371
            A   G P  I+  G +                SL  ++ +  ++ LG+  +    +P+ 
Sbjct: 350 VANCGGLPLAIVVLGGLLSRKEKTPLSWQKVLDSLTWHLNQGPDSCLGVLALSYNDMPYY 409

Query: 372 LKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDN----SEATAESYLEQLIKEGFVEAK 427
           LK CF+Y  +FP   EI T +L +LW+AEGFI       +E  AE +L++L+    ++  
Sbjct: 410 LKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIAEDVAEDHLQELVHRSMIQVA 469

Query: 428 KRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFAC 487
            R   G + +C +    R +  +     +F    +      SP   +RL   + +   + 
Sbjct: 470 ARSFDGRVMSCRMHDLLRDLAISEAKDTKFF-EGYESIDSTSPVSVRRLTIHQGKKTNSK 528

Query: 488 LDDYDSQLHSLLC---CSPET--RHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIEN 542
                  L S +C   C  E   R L            KLL VLDL  + +   P GI  
Sbjct: 529 HLHTSRSLRSFICFSVCFQENILRSLHR--------RVKLLTVLDLERMPINTIPEGIGE 580

Query: 543 LFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSIT 602
           L  L+YL L    +  LPSS +  L NL TLD   ++I+      WK++ LRHL    + 
Sbjct: 581 LIHLKYLCLRRTRIKRLPSS-IGRLTNLQTLDFQSTFIEIIPSTIWKLHHLRHLYGRGVV 639

Query: 603 LPAHPGKFCGS-------LENLNFISALHPCCCTEDILGRLPNLRNLRI---RGDLSYNQ 652
                   C +       L NL  +       C  + LG+L  LR L I   +   + N 
Sbjct: 640 SSQSVIDKCRNGPLSVDHLTNLQSLGLRAGSWCCGEGLGKLTELRELIIEWTKMAQTKNH 699

Query: 653 SLLSKSLCRLSCLESLKL----ANESKMPRLSKIVLAEYL------------------FP 690
              S+S+ +L+ L+SL+L    A    +P L       YL                  +P
Sbjct: 700 G-FSESVKKLTALQSLRLYTLGAEMFTLPHLMPFSDHTYLYHLSLRGRLERFPDEIEFYP 758

Query: 691 HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSM 750
            +L  L     ++  DPM TLEKLP L+ L L       +K+ C S GF  L+ L L  +
Sbjct: 759 PNLISLELECWNIEQDPMVTLEKLPNLRFLILSLCYSMVKKMVCTSGGFQQLETLTLWGL 818

Query: 751 LWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLR--E 808
             LEE  +   AMP  + L+I  C  +K++   L   K+L     +   PEL  +L   E
Sbjct: 819 KELEELIVEEGAMPDPKDLVIETCPKMKRLSHGLLQRKNLQHLKLYDLSPELMDELSLIE 878

Query: 809 FEDKEQCGIQLYPYG 823
            ED+E+  +    +G
Sbjct: 879 GEDREKICLATSIHG 893

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224075299|ref|XP_002304589.1| nbs-lrr resistance protein [Populus trichocarpa] gi|222842021|gb|EEE79568.1| nbs-lrr resistance protein [Populus trichocarpa]

 Score =  234 bits (598), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 230/864 (26%), Positives = 379/864 (43%), Gaps = 125/864 (14%)

Query: 33  NLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPDLATVMDEINWFTYESEKVIDTFI 92
           ++H EVE +   L      I   L +  A+++  D  +   + +I    Y++E +ID FI
Sbjct: 25  DVHKEVERLQDELRR----IRCFLRDADAKQDE-DERVRNWVSDIRDVAYDAEDLIDRFI 79

Query: 93  -------------------NSITQQKTQSSCSKDIFDALQGLQSRITDIKQRMQQ--LKH 131
                              + +   K +S  ++D    L  ++SR+ DI    +   +++
Sbjct: 80  MNNDPLKKKKKNHFIKKCTSYVKGWKQRSKIAED----LMAIRSRLQDISASRETYGIQN 135

Query: 132 MDSKIIDRIKTSKAEAGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLD 191
           +        +T +     S   + RD VGL+D   +L+D L++     S V+I+   G+ 
Sbjct: 136 VGEGTTAAGETLRKLRRSSPRDEERDIVGLEDDTAKLVDHLLQMGDHWSAVSIVGMGGIG 195

Query: 192 KTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLM-PSSRLSEIMDKNY 250
           KT    + YN S V+  F   AWI    S E+ A  IL  VI+ +  P  RL  + D+  
Sbjct: 196 KTTLGIKIYNHSAVRARFPSRAWIC--VSQEFSARDILQRVIRQIASPRERLEALTDEEL 253

Query: 251 EMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILP-DNQNGSRVLITLTDIRIIISFQ 309
           E    +++E L  KRYL+V+DD+WS + WD +++  P D  NGSR+L+T  +  + +   
Sbjct: 254 ED---LVYENLRRKRYLVVLDDIWSTNAWDCLKKAFPVDRSNGSRLLLTTRNKNVALHVD 310

Query: 310 ------------------------FEDGENMRLD--LVPTGGPLRATYKGRPF-LILYHG 342
                                   F DG +      L   G  +     G P  +I+  G
Sbjct: 311 PQTTPYDLGFLSKQNSWELFCKKTFIDGRDTSCSPILEEIGREIVERCAGLPLAIIVIGG 370

Query: 343 SISLEENIRE-----------AVETPLGLRYIKCLM---LPFCLKPCFIYLSVFPAHQEI 388
            +S ++ + E               P G+  I  L    LP+ LK CF+YL +FP    I
Sbjct: 371 LLSRKKRLNEWERILNNMDSHFARHPNGVAAILALSYNDLPYYLKSCFLYLGLFPEDCTI 430

Query: 389 STRQLYQLWIAEGFIPDN---SEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWR 445
              +L++LW+AEG IP      E  AE YL +LI+   V+ +     G +  C +    R
Sbjct: 431 QAHKLFRLWVAEGLIPHQELRGEDVAEDYLNELIERNMVQMEGMSVNGRVKQCRLHDLLR 490

Query: 446 PVLHTVPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDSQLHSLL----CC 501
            +  +      F+  P  +    S  + +R + +  +   +C++     L SLL      
Sbjct: 491 DLSISKAKTENFLQIP-GNENIPSLTRCRR-HPIYSDSHLSCVERLSPHLRSLLFFRVVS 548

Query: 502 SPETRHLDPIDWEKFCGM-----------FKLLRVLDLGSLVLIQYPSGIENLFLLRYLK 550
               R+    +   FC +           F LLR+L+L  +     PS I  L  L YL 
Sbjct: 549 RVRYRYFIGRNVYGFCELSGAKFDYITRNFNLLRILELEGISCSSIPSTIGELIHLSYLG 608

Query: 551 LNIPSLNSLPSSLLSNLLNLYTLDMPFS-YIDHTADEFWKMNKLRHLNFGSITLPAHPGK 609
           L   ++  LPS+L  +L NL TLD+  + ++    D    M  LRHL      +  H G 
Sbjct: 609 LKETNIRVLPSTL-GSLCNLQTLDIAGNLHLRIIPDVICNMKNLRHL-----YMCGHSGG 662

Query: 610 F--CGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLES 667
                +L++L  ++ +      ++    L +LR L IRG+L  +   +  S+  L  L S
Sbjct: 663 HLRIDTLKHLQTLTEIDVSRWKQNNTADLVSLRKLGIRGNLCSDTIKIFDSISALLQLRS 722

Query: 668 LKLANE-SKMPRLSKIVLAEYL-----------------FPHSLTHLSFSNTDLMDDPMP 709
           L L  E ++ P L ++     L                 FP +L+ L+  +T L  + + 
Sbjct: 723 LYLRAEGAEFPSLVQLGSLRSLIKLHLRGGISQLPSQQDFPPNLSQLTLEHTQLEQESIE 782

Query: 710 TLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECL 769
            LEKLP L +L+ K  SYS  KLT  + GFP L+ L   S+  L E+ +   A+P+LE  
Sbjct: 783 ILEKLPKLSILRFKAESYSKEKLTISADGFPQLEFLEFNSLESLHEFNIEENAVPRLESF 842

Query: 770 IINPCAYLKKMPEQLWYIKSLNKF 793
           +I  C  L+ +PE++ ++ +L+K 
Sbjct: 843 LIVNCKGLRMLPEEMRFVATLHKL 866

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454212|ref|XP_002274233.1| PREDICTED: putative disease resistance protein At1g50180-like [Vitis vinifera]

 Score =  233 bits (594), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 251/925 (27%), Positives = 394/925 (42%), Gaps = 191/925 (20%)

Query: 56  LFEKMAEEESH-DPDLATVMDEINWFTYESEKVIDTFI----------NSITQQKTQSSC 104
           LF K A+ +S  +  +   +++I   T+++E VID FI          N++   K   +C
Sbjct: 42  LFLKDADSQSLCNEKIKLWVEQIRNVTHDAEDVIDEFILDMDRRQLRLNTLKFLKCLPTC 101

Query: 105 S--KDIFDALQGLQSRITDIKQRMQQLKHMDSK-----IIDRIKTSKAEAGISSSSK--- 154
               D    +  L  R+ +I  R++++    SK     ++    +S  +  ++   K   
Sbjct: 102 VGFADKLPFIHELDGRVKEINIRIERIMANRSKYGLEALMASNSSSTTDQVVAYKEKWAQ 161

Query: 155 ---SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDC 211
                D VG++D  E +  +L +G  + +VV+I+   GL KT  A + YN S VK +FDC
Sbjct: 162 VVEGSDVVGIEDGTEVVTQMLTKGEMRRAVVSIVGMGGLGKTTLAKKVYNHSGVKRHFDC 221

Query: 212 HAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKI----ILHEYLMTKRYL 267
            AW+    S E+   ++L  +I  +M  S      ++  EM+++     L E L  K+YL
Sbjct: 222 IAWVC--VSQEFKPRELLLSIISSVMSLSN-----EEKKEMREVELGGKLRECLNDKKYL 274

Query: 268 IVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIISFQ------------------ 309
           +V+DDVWSI+ W  +   LP+++NGS+VL+T  +  I                       
Sbjct: 275 VVMDDVWSIEAWSSLCSYLPESRNGSKVLMTTRNKEIAAQANGHEVVGHTDSQALVYELP 334

Query: 310 -FEDGENMRLDLVPTGGPLRATY------------------KGRPFLILYHGSI------ 344
             +D E+  L L  T G    T+                   G P  I+  G +      
Sbjct: 335 IMDDDESWELFLKKTFGARDNTHVPSSKTLEELGRKIVAKCNGLPLAIVVLGGLLSTKER 394

Query: 345 ----------SLEENIREAVETPLGLRYIKCLMLPFCLKPCFIYLSVFPAHQEISTRQLY 394
                     S++ ++    E+  G+  +    LP+ LK CF+Y  +FP   EI   +L 
Sbjct: 395 TEPSWERVLESIDWHLNRGPESCFGILALSYNDLPYYLKSCFLYCGIFPEDSEIKASKLI 454

Query: 395 QLWIAEGFIPDNS----EATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHT 450
            LWIAEGF+        E  AE YL +LI    V+  ++KA G + +C I    R +   
Sbjct: 455 HLWIAEGFVQRRGIEKLEDIAEDYLYELIHRSMVQVARKKANGRVMSCRIHDLLRDL--- 511

Query: 451 VPYMVEFICSPFMDPKGKSPKKAKRLNAVEREGDFACLDDYDS-QLHSLLCCSPETRHL- 508
                             S  +  +L  V    DF   +      +H  L  +  ++HL 
Sbjct: 512 ----------------AISEARDAKLFEVHENIDFTFPNSIRRLSIHQHLIKNNISQHLH 555

Query: 509 ----------DPI---DWEKFCGMFKLLRVLDLGSL----VLIQYPSGIENLFLLRYLKL 551
                     DPI   DW       KLL VLDLG +    +L   P  I  L  L++L +
Sbjct: 556 NSLRSLIFFTDPIERKDWRSIQKHVKLLGVLDLGRIEEDYIL---PKEIGELIHLKFLCI 612

Query: 552 -NIPSLNSLPSSLLSNLLNLYTLDMPF--SYIDHTADEFWKMNKLRHLN--FGSITLPAH 606
               +  +LPSS +  L+NL  L++ +  SYI  T    WK+ +LRHLN  +G ++    
Sbjct: 613 KGYFNRVTLPSS-IKRLVNLQNLNLGYNDSYIPCT---IWKLQELRHLNCCYGEMSSQFK 668

Query: 607 PGK----FCG--SLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLS-YNQSLLSKSL 659
             K    + G   L NL  ++         D LG+L  LR LR+ G L+ Y +     S+
Sbjct: 669 LNKCMNGYLGVEQLTNLQTLALPVGSWLEGDGLGKLTQLRKLRLVGPLAPYLKKGFFDSI 728

Query: 660 CRLSCLESLKLAN------------------------ESKMPRLSKIVLAEYL------- 688
             L+ L +L L N                        ++ +P L       YL       
Sbjct: 729 AELTTLRTLFLGNWQVDKKKTLLNRVGLKWQENVVEEKTLLPGLMSFSRHTYLYKVHLYG 788

Query: 689 -----------FPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSY 737
                      +P +L  L+ S  +L DDPM  LEKLP L++L L + SY G+K+ C   
Sbjct: 789 KVDKLPEQTEFYPPNLLKLTLSKCELEDDPMLILEKLPTLRILGLLRGSYVGKKMVCSCG 848

Query: 738 GFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWW 797
           GF  L+ L L  +  LEE T+   AM  L  L I  C  +KK P  L  +K L K     
Sbjct: 849 GFLQLESLELNGLNELEELTVEEGAMCNLRTLQILSCDKMKKFPHGLLQMKKLEKLGLIR 908

Query: 798 PQPELRQKLREFEDKEQCGIQLYPY 822
              +L +++++ E +E   I+L  +
Sbjct: 909 TSGKLIEEVQQTEGEEWDRIRLITF 933

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	824
TAIR|locus:2037639	907	AT1G58390 "AT1G58390" [Arabido	0.294	0.267	0.268	8.8e-32
TAIR|locus:2169523	901	AT5G35450 [Arabidopsis thalian	0.154	0.140	0.312	1.9e-31
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.305	0.278	0.256	4.2e-31
TAIR|locus:2176486	908	RPP8 "RECOGNITION OF PERONOSPO	0.280	0.254	0.255	1.3e-29
TAIR|locus:504956182	1049	AT1G58848 [Arabidopsis thalian	0.305	0.240	0.261	2.3e-29
TAIR|locus:2826978	1049	AT1G59218 [Arabidopsis thalian	0.305	0.240	0.261	2.3e-29
TAIR|locus:2152536	908	AT5G48620 [Arabidopsis thalian	0.155	0.140	0.317	4.6e-29
TAIR|locus:504956184	1017	AT1G58807 "AT1G58807" [Arabido	0.305	0.247	0.258	1.5e-27
TAIR|locus:2827038	1017	AT1G59124 "AT1G59124" [Arabido	0.305	0.247	0.258	1.5e-27
TAIR|locus:2037623	899	AT1G58410 [Arabidopsis thalian	0.283	0.260	0.260	1.5e-26

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

 Score = 195 (73.7 bits), Expect = 8.8e-32, Sum P(3) = 8.8e-32
 Identities = 72/268 (26%), Positives = 124/268 (46%)

Query:    51 DISLLL-FEKMAEEESHDPDLA-TVMDEINWFTYESEKVIDTFI--------NSITQQKT 100
             D++LL  F K A+ + H   +   V++EI    Y++E +I+T++        + I  +  
Sbjct:    37 DLNLLSSFLKDADAKKHTTAVVRNVVEEIKEIVYDAEDIIETYLLKEKLWKTSGIKMRIR 96

Query:   101 QSSC--SKDIFDALQ--GLQSRITDIKQRMQQLKHMDSKIID----RIKTSKAEAGISSS 152
             + +C  S    +AL   G+++RI+D+ + MQ    +   I+D    + +  +      + 
Sbjct:    97 RHACIISDRRRNALDVGGIRTRISDVIRDMQSFG-VQQAIVDGGYMQPQGDRQREMRQTF 155

Query:   153 SKS--RDTVGXXXXXXXXXXXXXXGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD 210
             SK    D VG                  + VV+I    GL KT  A + +N   VKH FD
Sbjct:   156 SKDYESDFVGLEVNVKKLVGYLVD-EENVQVVSITGMGGLGKTTLARQVFNHEDVKHQFD 214

Query:   211 CHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVI 270
               AW+    S E+    +  ++++ L    +  EI+          L + L T + LIV 
Sbjct:   215 RLAWVC--VSQEFTRKNVWQMILQNLTSREKKDEILQMEEAELHDKLFQLLETSKSLIVF 272

Query:   271 DDVWSIDMWDVIQEILPDNQNGSRVLIT 298
             DD+W  + WD+I+ I P N+ G +VL+T
Sbjct:   273 DDIWKDEDWDLIKPIFPPNK-GWKVLLT 299

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2169523 AT5G35450 [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 1.9e-31, Sum P(3) = 1.9e-31
 Identities = 40/128 (31%), Positives = 63/128 (49%)

Query:   679 LSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTXXXXXXXXXXXXXQNSYSGRKLTCGSYG 738
             LSKI     L PH + H+      + +DPMP              + ++ GR++ C   G
Sbjct:   750 LSKIPDQHQLPPH-IAHIYLLFCHMEEDPMPILEKLLHLKSVELRRKAFIGRRMVCSKGG 808

Query:   739 FPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWP 798
             FP L+ L +     LEEW +   +MP L  LII+ C  L+++P+ L Y+ SL +      
Sbjct:   809 FPQLRALQISEQSELEEWIVEEGSMPCLRDLIIHSCEKLEELPDGLKYVTSLKELKIEGM 868

Query:   799 QPELRQKL 806
             + E ++KL
Sbjct:   869 KREWKEKL 876

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

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

 Score = 202 (76.2 bits), Expect = 4.2e-31, Sum P(3) = 4.2e-31
 Identities = 69/269 (25%), Positives = 123/269 (45%)

Query:    41 VTSWLSEFEDDISLLL-FEKMAEEESHDPDLA-TVMDEINWFTYESEKVIDTFINSITQQ 98
             V   ++E  DD+ +L+ F   A+ +     LA   ++EI   TY++E +I+ F+   +  
Sbjct:    32 VEEQITELRDDLKMLMAFLSDADAKKQTRALARNCLEEIKEITYDAEDIIEIFLLKGSVN 91

Query:    99 KTQSSC----SKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKTS-----KAEAGI 149
                 +C     ++I   +  +  RI+ + Q MQ L  + S I+D + +      K E   
Sbjct:    92 MRSLACFPGGRREIALQITSISKRISKVIQVMQNLG-IKSDIMDGVDSHAQLERKRELRH 150

Query:   150 SSSSKSRDTVGXXXXXXXXXXXXXXGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF 209
             + SS+S   +               G      V+I    GL KT  A + ++   VK +F
Sbjct:   151 TFSSESESNLVGLEKNVEKLVEELVGNDSSHGVSITGLGGLGKTTLARQIFDHDKVKSHF 210

Query:   210 DCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIV 269
             D  AW+    S E+    +   ++  L P  + S++ + + + K   L + L TK+ LIV
Sbjct:   211 DGLAWVC--VSQEFTRKDVWKTILGNLSPKYKDSDLPEDDIQKK---LFQLLETKKALIV 265

Query:   270 IDDVWSIDMWDVIQEILPDNQNGSRVLIT 298
              DD+W  + W  I  + P+ + G +VL+T
Sbjct:   266 FDDLWKREDWYRIAPMFPERKAGWKVLLT 294

GO:0005575 "cellular_component" evidence=ND

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2176486 RPP8 "RECOGNITION OF PERONOSPORA PARASITICA 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.3e-29, Sum P(3) = 1.3e-29
 Identities = 60/235 (25%), Positives = 94/235 (40%)

Query:   573 LDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFIS-ALHPCCCTED 631
             L +P    D T  E   +  L +L +G  T  +        +  L +++ +L   C  E 
Sbjct:   654 LSLPLKMDDKTKLELGDLVNLEYL-YGFSTQHSSVTDLL-RMTKLRYLAVSLSERCNFET 711

Query:   632 ILGRLPNLRNLRIRGDLSYNQXXXXXXXXXXXXXXXXXXANESKMPRLSKIVLAEYLFPH 691
             +   L  LRNL     L   +                         R+SKI   ++ FP 
Sbjct:   712 LSSSLRELRNLETLNFLFSLETYMVDYMGEFVLDHFIHLKQLGLAVRMSKIP-DQHQFPP 770

Query:   692 SLTHLSFSNTDLMDDPMPTXXXXXXXXXXXXXQNSYSGRKLTCGSYGFPNLKVLHLKSML 751
              L HL      + +DPMP              + ++ G ++ C   GFP L V+ +    
Sbjct:   771 HLVHLFLIYCGMEEDPMPILEKLLHLKSVRLARKAFLGSRMVCSKGGFPQLCVIEISKES 830

Query:   752 WLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKL 806
              LEEW +   +MP L  L I+ C  LK++P+ L YI SL +      + E ++KL
Sbjct:   831 ELEEWIVEEGSMPCLRTLTIDDCKKLKELPDGLKYITSLKELKIEGMKREWKEKL 885

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

GO:0043531 "ADP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009416 "response to light stimulus" evidence=IMP

GO:0051607 "defense response to virus" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

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

GO:0051707 "response to other organism" evidence=IMP

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

 Score = 179 (68.1 bits), Expect = 2.3e-29, Sum P(3) = 2.3e-29
 Identities = 73/279 (26%), Positives = 122/279 (43%)

Query:    41 VTSWLSEFEDDISLLL-FEKMAEEESHDPDLA-TVMDEINWFTYESEKVIDTFINSITQQ 98
             V   ++E + D++LL  F K A+ + H   +    ++EI    Y+ E  I+TF+      
Sbjct:    27 VEDQVTELKRDLNLLSSFLKDADAKKHTSAVVKNCVEEIKEIIYDGEDTIETFVLEQNLG 86

Query:    99 KTQSSCSKDIF-------D------ALQGLQSRITDIKQRMQQLKHMDSKIID----RIK 141
             KT S   K I        D       + GL +RI+ + + MQ    +   I+D    + +
Sbjct:    87 KT-SGIKKSIRRLACIIPDRRRYALGIGGLSNRISKVIRDMQSFG-VQQAIVDGGYKQPQ 144

Query:   142 TSKAEAGISSSSKSRDT--VGXXXXXXXXXXXXXXGPPQLSVVAILDSIGLDKTAFAGEA 199
               K        SK  D+  VG                  + VV+I    GL KT  A + 
Sbjct:   145 GDKQREMRPRFSKDDDSDFVGLEANVKKLVGYLVD-EANVQVVSITGMGGLGKTTLAKQV 203

Query:   200 YNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE 259
             +N   VKH FD  +W+    S ++    +   +++ L P     +IM+   +  +  L  
Sbjct:   204 FNHEDVKHQFDGLSWVC--VSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIR 261

Query:   260 YLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLIT 298
              L T + LIV+DD+W  + W++I+ I P  + G +VL+T
Sbjct:   262 LLETSKSLIVLDDIWEKEDWELIKPIFPPTK-GWKVLLT 299

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

GO:0043531 "ADP binding" evidence=IEA

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

 Score = 179 (68.1 bits), Expect = 2.3e-29, Sum P(3) = 2.3e-29
 Identities = 73/279 (26%), Positives = 122/279 (43%)

Query:    41 VTSWLSEFEDDISLLL-FEKMAEEESHDPDLA-TVMDEINWFTYESEKVIDTFINSITQQ 98
             V   ++E + D++LL  F K A+ + H   +    ++EI    Y+ E  I+TF+      
Sbjct:    27 VEDQVTELKRDLNLLSSFLKDADAKKHTSAVVKNCVEEIKEIIYDGEDTIETFVLEQNLG 86

Query:    99 KTQSSCSKDIF-------D------ALQGLQSRITDIKQRMQQLKHMDSKIID----RIK 141
             KT S   K I        D       + GL +RI+ + + MQ    +   I+D    + +
Sbjct:    87 KT-SGIKKSIRRLACIIPDRRRYALGIGGLSNRISKVIRDMQSFG-VQQAIVDGGYKQPQ 144

Query:   142 TSKAEAGISSSSKSRDT--VGXXXXXXXXXXXXXXGPPQLSVVAILDSIGLDKTAFAGEA 199
               K        SK  D+  VG                  + VV+I    GL KT  A + 
Sbjct:   145 GDKQREMRPRFSKDDDSDFVGLEANVKKLVGYLVD-EANVQVVSITGMGGLGKTTLAKQV 203

Query:   200 YNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE 259
             +N   VKH FD  +W+    S ++    +   +++ L P     +IM+   +  +  L  
Sbjct:   204 FNHEDVKHQFDGLSWVC--VSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIR 261

Query:   260 YLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLIT 298
              L T + LIV+DD+W  + W++I+ I P  + G +VL+T
Sbjct:   262 LLETSKSLIVLDDIWEKEDWELIKPIFPPTK-GWKVLLT 299

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2152536 AT5G48620 [Arabidopsis thaliana (taxid:3702)]

 Score = 175 (66.7 bits), Expect = 4.6e-29, Sum P(3) = 4.6e-29
 Identities = 41/129 (31%), Positives = 63/129 (48%)

Query:   678 RLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTXXXXXXXXXXXXXQNSYSGRKLTCGSY 737
             R+SKI   ++ FP  L H+   +  + +DPMP                ++ GR++ C   
Sbjct:   758 RMSKIP-DQHQFPPHLAHIHLVHCVMKEDPMPILEKLLHLKSVALSYGAFIGRRVVCSKG 816

Query:   738 GFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWW 797
             GFP L  L +     LEEW +   +MP L  L I+ C  LK++P+ L YI SL +     
Sbjct:   817 GFPQLCALGISGESELEEWIVEEGSMPCLRTLTIHDCEKLKELPDGLKYITSLKELKIRE 876

Query:   798 PQPELRQKL 806
              + E ++KL
Sbjct:   877 MKREWKEKL 885

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

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

 Score = 177 (67.4 bits), Expect = 1.5e-27, Sum P(3) = 1.5e-27
 Identities = 72/279 (25%), Positives = 121/279 (43%)

Query:    41 VTSWLSEFEDDISLLL-FEKMAEEESHDPDLA-TVMDEINWFTYESEKVIDTFINSITQQ 98
             V   ++E + D+++L  F K A  + H   +    ++EI    Y+ E  I+TF+      
Sbjct:    27 VEDQVTELKRDLNMLSSFLKDANAKKHTSAVVKNCVEEIKEIIYDGEDTIETFVLEQNLG 86

Query:    99 KTQSSCSKDIF-------D------ALQGLQSRITDIKQRMQQLKHMDSKIID----RIK 141
             KT S   K I        D       + GL +RI+ + + MQ    +   I+D    + +
Sbjct:    87 KT-SGIKKSIRRLACIIPDRRRYALGIGGLSNRISKVIRDMQSFG-VQQAIVDGGYKQPQ 144

Query:   142 TSKAEAGISSSSKSRDT--VGXXXXXXXXXXXXXXGPPQLSVVAILDSIGLDKTAFAGEA 199
               K        SK  D+  VG                  + VV+I    GL KT  A + 
Sbjct:   145 GDKQREMRQKFSKDDDSDFVGLEANVKKLVGYLVD-EANVQVVSITGMGGLGKTTLAKQV 203

Query:   200 YNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE 259
             +N   VKH FD  +W+    S ++    +   +++ L P     +IM+   +  +  L  
Sbjct:   204 FNHEDVKHQFDGLSWVC--VSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIR 261

Query:   260 YLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLIT 298
              L T + LIV+DD+W  + W++I+ I P  + G +VL+T
Sbjct:   262 LLETSKSLIVLDDIWEKEDWELIKPIFPPTK-GWKVLLT 299

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 = 177 (67.4 bits), Expect = 1.5e-27, Sum P(3) = 1.5e-27
 Identities = 72/279 (25%), Positives = 121/279 (43%)

Query:    41 VTSWLSEFEDDISLLL-FEKMAEEESHDPDLA-TVMDEINWFTYESEKVIDTFINSITQQ 98
             V   ++E + D+++L  F K A  + H   +    ++EI    Y+ E  I+TF+      
Sbjct:    27 VEDQVTELKRDLNMLSSFLKDANAKKHTSAVVKNCVEEIKEIIYDGEDTIETFVLEQNLG 86

Query:    99 KTQSSCSKDIF-------D------ALQGLQSRITDIKQRMQQLKHMDSKIID----RIK 141
             KT S   K I        D       + GL +RI+ + + MQ    +   I+D    + +
Sbjct:    87 KT-SGIKKSIRRLACIIPDRRRYALGIGGLSNRISKVIRDMQSFG-VQQAIVDGGYKQPQ 144

Query:   142 TSKAEAGISSSSKSRDT--VGXXXXXXXXXXXXXXGPPQLSVVAILDSIGLDKTAFAGEA 199
               K        SK  D+  VG                  + VV+I    GL KT  A + 
Sbjct:   145 GDKQREMRQKFSKDDDSDFVGLEANVKKLVGYLVD-EANVQVVSITGMGGLGKTTLAKQV 203

Query:   200 YNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE 259
             +N   VKH FD  +W+    S ++    +   +++ L P     +IM+   +  +  L  
Sbjct:   204 FNHEDVKHQFDGLSWVC--VSQDFTRMNVWQKILRDLKPKEEEKKIMEMTQDTLQGELIR 261

Query:   260 YLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLIT 298
              L T + LIV+DD+W  + W++I+ I P  + G +VL+T
Sbjct:   262 LLETSKSLIVLDDIWEKEDWELIKPIFPPTK-GWKVLLT 299

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 = 167 (63.8 bits), Expect = 1.5e-26, Sum P(3) = 1.5e-26
 Identities = 69/265 (26%), Positives = 118/265 (44%)

Query:    57 FEKMAEEESHDPDLAT-VMDEINWFTYESEKVIDTFI--------NSITQQ-KTQSSCSK 106
             F K A+ + H  ++    ++EI    Y++E +I+TFI          I ++ K  +S   
Sbjct:    42 FLKDADAKKHISEMVRHCVEEIKDIVYDTEDIIETFILKEKVEMKRGIMKRIKRFASTIM 101

Query:   107 D---IFDALQGLQSRITDIKQRMQ-----QLKHMDSKIIDRIKTSKAEAGISSSSKSR-D 157
             D   +   + G+  RI+ + Q MQ     Q+    S+    ++  + E   + S  S  D
Sbjct:   102 DRRELASDIGGISKRISKVIQDMQSFGVQQIITDGSRSSHPLQERQREMRHTFSRDSEND 161

Query:   158 TVGXXXXXXXXXXXXXXGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE 217
              VG                    +V++    GL KT  A + +N   VK  FD  AW++ 
Sbjct:   162 FVGMEANVKKLVGYLVE-KDDYQIVSLTGMGGLGKTTLARQVFNHDVVKDRFDGFAWVS- 219

Query:   218 PYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM----TKRYLIVIDDV 273
               S E+    +   +++ L    R  EI +    MK+  LH+ L     + + LIV+DD+
Sbjct:   220 -VSQEFTRISVWQTILQNLTSKERKDEIQN----MKEADLHDDLFRLLESSKTLIVLDDI 274

Query:   274 WSIDMWDVIQEILPDNQNGSRVLIT 298
             W  + WD+I+ I P  + G +VL+T
Sbjct:   275 WKEEDWDLIKPIFPPKK-GWKVLLT 298

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

---

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

Fail to connect to STRING server

---

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	824
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	9e-33

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

 Score =  127 bits (322), Expect = 9e-33
 Identities = 79/285 (27%), Positives = 122/285 (42%), Gaps = 47/285 (16%)

Query: 162 DDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN 221
           +D +E L++ L+E    L VV I+   G+ KT  A + YN   V  +FD  AW+    S 
Sbjct: 2   EDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVV--SK 59

Query: 222 EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDV 281
            Y   ++   +++ L      S+ ++KN     + + E L+ KR+L+V+DDVW  + WD 
Sbjct: 60  TYTEFRLQKDILQELGLDD--SDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKNDWDK 117

Query: 282 IQEILPDNQNGSRVLITLTDIRIIIS---------------------FQFEDGENMRL-- 318
           I    PD +NGSRV++T     +                        F  +  E      
Sbjct: 118 IGVPFPDGENGSRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPC 177

Query: 319 -DLVPTGGPLRATYKGRPFLILYHGSI------------SLEENIREAVETPLGLRYIKC 365
            +L      +    KG P  +   G +             LE+   E      GL  +  
Sbjct: 178 PELEEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRD-GLNEVLS 236

Query: 366 LM------LPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIP 404
           ++      LP  LK CF+YL++FP    I   QL +LWIAEGF+ 
Sbjct: 237 ILSLSYDNLPMHLKRCFLYLALFPEDYNIRKEQLIKLWIAEGFVI 281

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	824
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
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.91
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.91
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.91
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.86
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	99.8
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.79
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.79
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.78
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.7
KOG0472	565	consensus Leucine-rich repeat protein [Function un	99.67
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	99.61
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.53
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.51
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	99.49
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.44
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	99.43
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	99.36
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	99.35
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.35
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	99.26
KOG4237	498	consensus Extracellular matrix protein slit, conta	99.24
KOG4237	498	consensus Extracellular matrix protein slit, conta	99.14
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	99.05
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.94
KOG4341	483	consensus F-box protein containing LRR [General fu	98.93
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.91
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.89
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.82
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	98.81
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	98.8
PRK04841	903	transcriptional regulator MalT; Provisional	98.79
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.79
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.78
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.75
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.68
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.67
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	98.57
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	98.51
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.51
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	98.5
cd01128	249	rho_factor Transcription termination factor rho is	98.49
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.47
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.43
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.43
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.42
KOG4341	483	consensus F-box protein containing LRR [General fu	98.42
PF05729	166	NACHT: NACHT domain	98.42
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.39
KOG2982	418	consensus Uncharacterized conserved protein [Funct	98.35
PRK09376	416	rho transcription termination factor Rho; Provisio	98.33
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.33
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	98.25
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	98.25
PF13173	128	AAA_14: AAA domain	98.24
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.24
PLN03150	623	hypothetical protein; Provisional	98.22
KOG2982	418	consensus Uncharacterized conserved protein [Funct	98.21
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	98.17
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.14
TIGR00767	415	rho transcription termination factor Rho. Members	98.09
PTZ00202	550	tuzin; Provisional	98.03
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	98.02
PTZ00112	1164	origin recognition complex 1 protein; Provisional	98.01
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	97.96
PLN03150	623	hypothetical protein; Provisional	97.96
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.93
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.92
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.89
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.88
PRK15386	426	type III secretion protein GogB; Provisional	97.87
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.86
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.84
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.82
PRK13342	413	recombination factor protein RarA; Reviewed	97.8
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.74
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.7
PRK06893	229	DNA replication initiation factor; Validated	97.67
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.66
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.66
PRK12402	337	replication factor C small subunit 2; Reviewed	97.65
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.61
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.6
KOG1947	482	consensus Leucine rich repeat proteins, some prote	97.58
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.55
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.52
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.49
PRK13341	725	recombination factor protein RarA/unknown domain f	97.48
smart00382	148	AAA ATPases associated with a variety of cellular	97.46
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.45
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.44
PHA02544	316	44 clamp loader, small subunit; Provisional	97.43
PRK04195	482	replication factor C large subunit; Provisional	97.4
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.39
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.38
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	97.38
PRK08116	268	hypothetical protein; Validated	97.37
PLN03025	319	replication factor C subunit; Provisional	97.37
PRK15386	426	type III secretion protein GogB; Provisional	97.35
KOG1947	482	consensus Leucine rich repeat proteins, some prote	97.33
PRK08727	233	hypothetical protein; Validated	97.33
PRK08118	167	topology modulation protein; Reviewed	97.31
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.3
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.3
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.29
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.24
COG3899	849	Predicted ATPase [General function prediction only	97.19
COG3903	414	Predicted ATPase [General function prediction only	97.19
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.16
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.16
PRK05642	234	DNA replication initiation factor; Validated	97.15
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.14
PRK10536	262	hypothetical protein; Provisional	97.12
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.11
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.11
PF00004	132	AAA: ATPase family associated with various cellula	97.11
KOG2028	554	consensus ATPase related to the helicase subunit o	97.1
PRK12377	248	putative replication protein; Provisional	97.08
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.06
CHL00095	821	clpC Clp protease ATP binding subunit	97.04
PRK08181	269	transposase; Validated	97.04
PRK08084	235	DNA replication initiation factor; Provisional	97.02
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.01
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.0
PRK08939	306	primosomal protein DnaI; Reviewed	96.98
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	96.95
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	96.92
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	96.91
CHL00181	287	cbbX CbbX; Provisional	96.91
PRK10865	857	protein disaggregation chaperone; Provisional	96.89
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.88
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	96.88
PRK07940	394	DNA polymerase III subunit delta'; Validated	96.87
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.87
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.87
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.86
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.86
COG5238	388	RNA1 Ran GTPase-activating protein (RanGAP) involv	96.86
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	96.85
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.84
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.83
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	96.81
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	96.81
PRK09087	226	hypothetical protein; Validated	96.81
PRK12608	380	transcription termination factor Rho; Provisional	96.8
PRK07471	365	DNA polymerase III subunit delta'; Validated	96.79
PHA00729	226	NTP-binding motif containing protein	96.78
PRK06526	254	transposase; Provisional	96.77
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.76
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.75
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	96.75
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.74
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.73
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	96.72
PRK07261	171	topology modulation protein; Provisional	96.72
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.71
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	96.69
PRK07952	244	DNA replication protein DnaC; Validated	96.68
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.66
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.66
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.63
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.63
PRK09183	259	transposase/IS protein; Provisional	96.62
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.6
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.6
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	96.6
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	96.59
PRK06620	214	hypothetical protein; Validated	96.57
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.57
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.56
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.54
PRK06921	266	hypothetical protein; Provisional	96.53
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.53
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	96.53
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.51
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.51
KOG2123	388	consensus Uncharacterized conserved protein [Funct	96.5
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	96.48
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.47
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.46
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.46
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	96.46
PRK10865	857	protein disaggregation chaperone; Provisional	96.46
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.45
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.45
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.44
CHL00095	821	clpC Clp protease ATP binding subunit	96.42
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	96.42
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.42
PRK06835	329	DNA replication protein DnaC; Validated	96.41
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	96.41
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.4
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.4
PRK13695	174	putative NTPase; Provisional	96.4
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.39
PRK05541	176	adenylylsulfate kinase; Provisional	96.38
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.37
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.37
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.37
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.36
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.36
KOG2123	388	consensus Uncharacterized conserved protein [Funct	96.33
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.32
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.26
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.24
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.2
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.2
PRK07667	193	uridine kinase; Provisional	96.17
PRK06696	223	uridine kinase; Validated	96.15
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.14
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.11
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.11
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.1
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.1
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.09
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.08
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.08
PRK12422	445	chromosomal replication initiation protein; Provis	96.06
CHL00176	638	ftsH cell division protein; Validated	96.06
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.04
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.02
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.01
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.0
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.0
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.99
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.95
PRK09354	349	recA recombinase A; Provisional	95.95
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.94
PRK15455	644	PrkA family serine protein kinase; Provisional	95.94
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.93
PRK08233	182	hypothetical protein; Provisional	95.93
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	95.89
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.88
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.88
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	95.87
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	95.87
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	95.84
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.84
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	95.84
PRK06762	166	hypothetical protein; Provisional	95.83
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	95.83
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	95.82
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.81
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	95.81
PRK04301	317	radA DNA repair and recombination protein RadA; Va	95.81
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.79
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	95.76
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.73
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.73
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	95.73
CHL00195	489	ycf46 Ycf46; Provisional	95.73
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	95.72
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	95.7
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	95.66
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	95.66
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	95.65
PRK04296	190	thymidine kinase; Provisional	95.64
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	95.61
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	95.57
TIGR02236	310	recomb_radA DNA repair and recombination protein R	95.57
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	95.53
KOG4252	246	consensus GTP-binding protein [Signal transduction	95.51
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.5
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.46
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	95.46
cd03246	173	ABCC_Protease_Secretion This family represents the	95.44
PRK08149	428	ATP synthase SpaL; Validated	95.44
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.43
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	95.42
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	95.42
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	95.41
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.4
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.32
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	95.32
PTZ00301	210	uridine kinase; Provisional	95.32
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	95.32
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	95.3
PRK07399	314	DNA polymerase III subunit delta'; Validated	95.28
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.26
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	95.26
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	95.24
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.23
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	95.21
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.21
PRK11608	326	pspF phage shock protein operon transcriptional ac	95.19
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	95.19
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.16
PRK04040	188	adenylate kinase; Provisional	95.15
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.15
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	95.14
PTZ00035	337	Rad51 protein; Provisional	95.14
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	95.13
PRK06547	172	hypothetical protein; Provisional	95.12
PRK05480	209	uridine/cytidine kinase; Provisional	95.11
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.11
COG2884	223	FtsE Predicted ATPase involved in cell division [C	95.11
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	95.11
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	95.1
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	95.09
PRK05022	509	anaerobic nitric oxide reductase transcription reg	95.09
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.08
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	95.08
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	95.08
PF14516	331	AAA_35: AAA-like domain	95.06
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.05
TIGR00235	207	udk uridine kinase. Model contains a number of lon	95.03
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	94.99
COG0593	408	DnaA ATPase involved in DNA replication initiation	94.99
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	94.98
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	94.97
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	94.96
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	94.96
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	94.92
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	94.9
cd03215	182	ABC_Carb_Monos_II This family represents domain II	94.9
PRK10867	433	signal recognition particle protein; Provisional	94.87
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	94.85
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	94.82
PRK06067	234	flagellar accessory protein FlaH; Validated	94.81
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	94.78
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	94.78
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	94.77
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	94.74
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.73
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	94.67
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	94.67
PRK07594	433	type III secretion system ATPase SsaN; Validated	94.66
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	94.66
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	94.64
PRK08058	329	DNA polymerase III subunit delta'; Validated	94.62
PRK14974	336	cell division protein FtsY; Provisional	94.6
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	94.59
PRK09099	441	type III secretion system ATPase; Provisional	94.58
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	94.58
PRK05922	434	type III secretion system ATPase; Validated	94.58
PF12061	402	DUF3542: Protein of unknown function (DUF3542); In	94.58
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	94.57
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	94.56
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	94.55
TIGR00959	428	ffh signal recognition particle protein. This mode	94.52
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	94.51
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	94.49
KOG1514	767	consensus Origin recognition complex, subunit 1, a	94.49
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	94.46
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	94.45
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	94.43
PRK03839	180	putative kinase; Provisional	94.41
PRK12678	672	transcription termination factor Rho; Provisional	94.41
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	94.38
cd03278	197	ABC_SMC_barmotin Barmotin is a tight junction-asso	94.37
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	94.34
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	94.33
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.33
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.32
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	94.31
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	94.28
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	94.23
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	94.23
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	94.23
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	94.21
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	94.2
PF07726	131	AAA_3: ATPase family associated with various cellu	94.2
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	94.19
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	94.18
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	94.18
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	94.18
PRK00625	173	shikimate kinase; Provisional	94.18
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	94.16
PRK13531	498	regulatory ATPase RavA; Provisional	94.16
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	94.16
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	94.14
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	94.14
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	94.13
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	94.13
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	94.11
PLN02318	656	phosphoribulokinase/uridine kinase	94.1
PTZ00185	574	ATPase alpha subunit; Provisional	94.09
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.07
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	94.07
PRK05439	311	pantothenate kinase; Provisional	94.04
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.02
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	94.02
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	94.02
PRK06217	183	hypothetical protein; Validated	94.01
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	94.0
PRK06936	439	type III secretion system ATPase; Provisional	94.0
cd03236	255	ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 o	93.96
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	93.95
PF00154	322	RecA: recA bacterial DNA recombination protein; In	93.94
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	93.93
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.92
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	93.91
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	93.9
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	93.86
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	93.85
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	93.83
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	93.82
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	93.81
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	93.76
KOG1969	877	consensus DNA replication checkpoint protein CHL12	93.71
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	93.7
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	93.69
PRK14738	206	gmk guanylate kinase; Provisional	93.68
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	93.68
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	93.68
PRK09519	790	recA DNA recombination protein RecA; Reviewed	93.68
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	93.65
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	93.64
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	93.63
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	93.63
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	93.62
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	93.61
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	93.61
PRK00131	175	aroK shikimate kinase; Reviewed	93.6
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	93.6
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.57
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	93.56
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	93.56
PTZ00088	229	adenylate kinase 1; Provisional	93.56
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	93.54
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	93.52
PRK00409	782	recombination and DNA strand exchange inhibitor pr	93.5
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	93.48
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	93.48
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	93.47
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	93.44
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	93.44
COG0488	530	Uup ATPase components of ABC transporters with dup	93.43
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	93.42
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	93.4
PRK13947	171	shikimate kinase; Provisional	93.37
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	93.36
PRK04328	249	hypothetical protein; Provisional	93.32
PRK11823	446	DNA repair protein RadA; Provisional	93.32
PRK00889	175	adenylylsulfate kinase; Provisional	93.29
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	93.27
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.25
PRK13949	169	shikimate kinase; Provisional	93.24
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	93.24
KOG0473	326	consensus Leucine-rich repeat protein [Function un	93.24
cd02029	277	PRK_like Phosphoribulokinase-like (PRK-like) is a	93.23
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	93.22
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	93.21
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	93.21
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	93.16
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	93.15
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	93.15
PRK06820	440	type III secretion system ATPase; Validated	93.14
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	93.12
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	93.11
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	93.1
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	93.07
TIGR01287	275	nifH nitrogenase iron protein. This model describe	93.05
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	93.03
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	93.02
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	93.01
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	92.98
PRK03846	198	adenylylsulfate kinase; Provisional	92.97
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	92.95
KOG3864	221	consensus Uncharacterized conserved protein [Funct	92.95
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	92.94
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	92.93
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	92.93
cd02117	212	NifH_like This family contains the NifH (iron prot	92.91
PF13306	129	LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_	92.91
PRK00300	205	gmk guanylate kinase; Provisional	92.89
PRK15064	530	ABC transporter ATP-binding protein; Provisional	92.88
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	92.86
KOG3864	221	consensus Uncharacterized conserved protein [Funct	92.82
PRK15453	290	phosphoribulokinase; Provisional	92.8
PRK13230	279	nitrogenase reductase-like protein; Reviewed	92.78
CHL00059	485	atpA ATP synthase CF1 alpha subunit	92.77
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	92.67
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	92.66
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	92.66
PRK13975	196	thymidylate kinase; Provisional	92.65
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	92.64
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	92.62
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	92.62
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	92.59
PF13504	17	LRR_7: Leucine rich repeat; PDB: 3OJA_B 3G06_A 1OO	92.59
PRK13232	273	nifH nitrogenase reductase; Reviewed	92.59
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	92.58
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	92.49
PRK10416	318	signal recognition particle-docking protein FtsY;	92.46
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	92.45
PRK05057	172	aroK shikimate kinase I; Reviewed	92.45
PF00005	137	ABC_tran: ABC transporter This structure is on hol	92.45
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	92.45
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	92.44
PRK09435	332	membrane ATPase/protein kinase; Provisional	92.41
COG0125	208	Tmk Thymidylate kinase [Nucleotide transport and m	92.4
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	92.39
COG1100	219	GTPase SAR1 and related small G proteins [General	92.37
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	92.37
PRK13765	637	ATP-dependent protease Lon; Provisional	92.36
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	92.35
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	92.34

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=4.5e-86  Score=770.75  Aligned_cols=751  Identities=25%  Similarity=0.335  Sum_probs=558.6

Q ss_pred             CcchHHHHHHHHHHhhcccccccchhchHHHHHHHHHHHHHHHHHccccchhhHHHhhhcccc-ccCChhHHHHHHHHHH
Q 003387            1 MHINFRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEE-ESHDPDLATVMDEINW   79 (824)
Q Consensus         1 ~~~~~~~~~~kl~~~~~~~~~~~~~~~~~~~~~l~~~l~~i~~~l~~~~~~~~~~~~~~~a~~-~~~~~~~~~wl~~l~~   79 (824)
                      |+.-++..++|+.+++. +++..+.+.++.+..|+++|..++.+++|             |+. +.....+..|...+++
T Consensus         1 ~~~~~s~~~~~~~~~l~-~~~~~~~~~~~~i~~Lk~~L~~l~~~l~d-------------~~a~~~~~~~~~~~~e~~~~   66 (889)
T KOG4658|consen    1 MGACVSFGVEKLDQLLN-RESECLDGKDNYILELKENLKALQSALED-------------LDAKRDDLERRVNWEEDVGD   66 (889)
T ss_pred             CCeEEEEehhhHHHHHH-HHHHHHhchHHHHHHHHHHHHHHHHHHHH-------------HHhhcchHHHHHHHHHHHHH
Confidence            56667778899999999 99999999999999999999999999999             999 7778899999999999


Q ss_pred             HhhhhHHHHHHhHHhhcccccc---------------CcchHHHHHHHHHHHHHHHHHHHHHHhhccccccccccCc-cc
Q 003387           80 FTYESEKVIDTFINSITQQKTQ---------------SSCSKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIK-TS  143 (824)
Q Consensus        80 ~~~~~ed~ld~~~~~~~~~~~~---------------~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  143 (824)
                      ++|++||.++.|..+....+..               ..++.+.+..+..+.+++.++.+..+.|+ ........+. ..
T Consensus        67 ~~~~~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~-~~~~~~~~~~~~~  145 (889)
T KOG4658|consen   67 LVYLAEDIIWLFLVEEIERKANDLLSTRSVERQRLCLCGFCSKNVSDSYKYGKRVSKVLREVESLG-SKGVFEVVGESLD  145 (889)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHHHhhhhhHhHhhhhhHhHHHHHHHHHHHHHHhc-cccceeccccccc
Confidence            9999999999999877654221               13344777888888999999988888887 4331111111 11


Q ss_pred             ccc-cCCCCCCCCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcc-ccCCCceeEEEECCCCC
Q 003387          144 KAE-AGISSSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSY-VKHYFDCHAWITEPYSN  221 (824)
Q Consensus       144 ~~~-~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~-~~~~F~~~~wv~~~vs~  221 (824)
                      .+. +++.+...... ||.+..++++++.|.+++.  .++||+||||+||||||+.++|+.. ++.+||.++||+  ||+
T Consensus       146 ~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~~--~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~--VSk  220 (889)
T KOG4658|consen  146 PREKVETRPIQSESD-VGLETMLEKLWNRLMEDDV--GIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVV--VSK  220 (889)
T ss_pred             chhhcccCCCCcccc-ccHHHHHHHHHHHhccCCC--CEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEE--Ecc
Confidence            111 45555555555 9999999999999998874  9999999999999999999999987 999999999999  999


Q ss_pred             CCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEech
Q 003387          222 EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTD  301 (824)
Q Consensus       222 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~  301 (824)
                      .|+..+++++|++.++.....  ......++++..|.+.|++|||+|||||||+..+|+.++.|+|...+||||++|||+
T Consensus       221 ~f~~~~iq~~Il~~l~~~~~~--~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs  298 (889)
T KOG4658|consen  221 EFTTRKIQQTILERLGLLDEE--WEDKEEDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRS  298 (889)
T ss_pred             cccHHhHHHHHHHHhccCCcc--cchhhHHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEecc
Confidence            999999999999999884432  233345899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHh---------------------hcccccCC---cCcCccccchhhHHHhcCCCchhHHHHHhHHH-------hhhh
Q 003387          302 IRIII---------------------SFQFEDGE---NMRLDLVPTGGPLRATYKGRPFLILYHGSISL-------EENI  350 (824)
Q Consensus       302 ~~v~~---------------------~f~~~~~~---~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~-------~~~~  350 (824)
                      +.||.                     +|....+.   ...+.+.++|++|+++|+|+|||++++|+.|.       |+..
T Consensus       299 ~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~  378 (889)
T KOG4658|consen  299 EEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRA  378 (889)
T ss_pred             HhhhhccccCCccccccccCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHH
Confidence            99998                     55554431   22344899999999999999999999999992       3322


Q ss_pred             hhhc--------cCCC-cccccccc---cCCCCchHHHhHhccCCCCceechhHHHHHHHHcCCCCC-----ChHHHHHH
Q 003387          351 REAV--------ETPL-GLRYIKCL---MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPD-----NSEATAES  413 (824)
Q Consensus       351 ~~~~--------~~~~-~~~~~l~~---~L~~~lk~cfl~~s~fp~~~~i~~~~Li~~W~a~g~i~~-----~~e~~~~~  413 (824)
                      ...+        .... .++++|++   +||+++|.||+|||+||+||.|+++.||.+|+||||+.+     ++++.|++
T Consensus       379 ~~~l~s~~~~~~~~~~~~i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~  458 (889)
T KOG4658|consen  379 LNVLKSSLAADFSGMEESILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYD  458 (889)
T ss_pred             HccccccccCCCCchhhhhHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHH
Confidence            2222        1123 78899988   999999999999999999999999999999999999977     77899999


Q ss_pred             HHHHHHhccccceeecCCCCcEEEEEcCccHHHHHHhhcc-cE-----EEccCC---CCCCCCCCCCCeeEEEEEecCCC
Q 003387          414 YLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPY-MV-----EFICSP---FMDPKGKSPKKAKRLNAVEREGD  484 (824)
Q Consensus       414 ~~~~Lv~rsllq~~~~~~~g~~~~~~mHdlv~dla~~~~~-~~-----~~~~~~---~~~~~~~~~~~~r~lsl~~~~~~  484 (824)
                      |+++|+++||++.....  ++..+|+|||++||+|.++|. +.     .++...   ........+..+||++++ ++..
T Consensus       459 ~i~~LV~~~Ll~~~~~~--~~~~~~kmHDvvRe~al~ias~~~~~~e~~iv~~~~~~~~~~~~~~~~~~rr~s~~-~~~~  535 (889)
T KOG4658|consen  459 YIEELVRASLLIEERDE--GRKETVKMHDVVREMALWIASDFGKQEENQIVSDGVGLSEIPQVKSWNSVRRMSLM-NNKI  535 (889)
T ss_pred             HHHHHHHHHHHhhcccc--cceeEEEeeHHHHHHHHHHhccccccccceEEECCcCccccccccchhheeEEEEe-ccch
Confidence            99999999999988744  567899999999999999991 11     222221   111122355678999999 7777


Q ss_pred             ccccccc-CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc-CccCCccCCCCCcceEEeecCCCCCccChh
Q 003387          485 FACLDDY-DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV-LIQYPSGIENLFLLRYLKLNIPSLNSLPSS  562 (824)
Q Consensus       485 ~~~~~~~-~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~-i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~  562 (824)
                      ..++... +++++||.+.++...  .......+|..++.||||||++|. +.++|.+|++|.|||||+++++.+..+|..
T Consensus       536 ~~~~~~~~~~~L~tLll~~n~~~--l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~LryL~L~~t~I~~LP~~  613 (889)
T KOG4658|consen  536 EHIAGSSENPKLRTLLLQRNSDW--LLEISGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHLRYLDLSDTGISHLPSG  613 (889)
T ss_pred             hhccCCCCCCccceEEEeecchh--hhhcCHHHHhhCcceEEEECCCCCccCcCChHHhhhhhhhcccccCCCccccchH
Confidence            6677777 999999999998631  133567899999999999999876 779999999999999999999999999999


Q ss_pred             hhhcCCCccEeecCCc-cccccchhhhccccCceecCCCccCCCC--CCCCCCCCCCCCeeeccCCCc-chhhhcCCCCc
Q 003387          563 LLSNLLNLYTLDMPFS-YIDHTADEFWKMNKLRHLNFGSITLPAH--PGKFCGSLENLNFISALHPCC-CTEDILGRLPN  638 (824)
Q Consensus       563 i~~~L~~L~~L~L~~~-~l~~lp~~i~~L~~L~~L~L~~~~~~~~--~~p~i~~L~~L~~l~~~~~~~-~~~~~l~~l~~  638 (824)
                      + ++|.+|.+||+..+ .+..+|..+..|++||+|.+........  .+..+.+|++|+.+....... .... +..+.+
T Consensus       614 l-~~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~~s~~~~~~~~l~el~~Le~L~~ls~~~~s~~~~e~-l~~~~~  691 (889)
T KOG4658|consen  614 L-GNLKKLIYLNLEVTGRLESIPGILLELQSLRVLRLPRSALSNDKLLLKELENLEHLENLSITISSVLLLED-LLGMTR  691 (889)
T ss_pred             H-HHHHhhheeccccccccccccchhhhcccccEEEeeccccccchhhHHhhhcccchhhheeecchhHhHhh-hhhhHH
Confidence            9 99999999999998 6666677677799999998866543222  222455566666666552222 1222 444444


Q ss_pred             cceEEEecc-cccchhhHHHHhccCCCCCeEEEeccC---------------C-CCCccEEEeCcc---------CcCCC
Q 003387          639 LRNLRIRGD-LSYNQSLLSKSLCRLSCLESLKLANES---------------K-MPRLSKIVLAEY---------LFPHS  692 (824)
Q Consensus       639 L~~L~l~~~-~~~~~~~l~~~l~~l~~L~~L~l~~~~---------------~-~~~L~~l~l~~~---------~~~~~  692 (824)
                      |.++...-. ........+.++..+.+|+.|.+....               . ++++..+.+..+         ...++
T Consensus       692 L~~~~~~l~~~~~~~~~~~~~~~~l~~L~~L~i~~~~~~e~~~~~~~~~~~~~~f~~l~~~~~~~~~~~r~l~~~~f~~~  771 (889)
T KOG4658|consen  692 LRSLLQSLSIEGCSKRTLISSLGSLGNLEELSILDCGISEIVIEWEESLIVLLCFPNLSKVSILNCHMLRDLTWLLFAPH  771 (889)
T ss_pred             HHHHhHhhhhcccccceeecccccccCcceEEEEcCCCchhhcccccccchhhhHHHHHHHHhhccccccccchhhccCc
Confidence            443222211 011334455566777778888777521               0 112222222222         34566


Q ss_pred             ceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceecc----CcccCccE
Q 003387          693 LTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGN----AAMPKLEC  768 (824)
Q Consensus       693 L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~----~~lp~L~~  768 (824)
                      |+.|.+..|....++++....+..+..+.+..+.+.+.......++|+++..+.+.... +..|..+.    +.+|.+..
T Consensus       772 L~~l~l~~~~~~e~~i~~~k~~~~l~~~i~~f~~~~~l~~~~~l~~l~~i~~~~l~~~~-l~~~~ve~~p~l~~~P~~~~  850 (889)
T KOG4658|consen  772 LTSLSLVSCRLLEDIIPKLKALLELKELILPFNKLEGLRMLCSLGGLPQLYWLPLSFLK-LEELIVEECPKLGKLPLLST  850 (889)
T ss_pred             ccEEEEecccccccCCCHHHHhhhcccEEecccccccceeeecCCCCceeEecccCccc-hhheehhcCcccccCccccc
Confidence            77777776666556665555555555555554444443334444555555555544422 33333322    44444445


Q ss_pred             EEEecC-CCCCCCc
Q 003387          769 LIINPC-AYLKKMP  781 (824)
Q Consensus       769 L~l~~c-~~l~~lp  781 (824)
                      +.+.+| +++..+|
T Consensus       851 ~~i~~~~~~~~~~~  864 (889)
T KOG4658|consen  851 LTIVGCEEKLKEYP  864 (889)
T ss_pred             cceeccccceeecC
Confidence            555544 3333334

>PLN03210 Resistant to P

Probab=100.00  E-value=1.5e-58  Score=570.28  Aligned_cols=608  Identities=17%  Similarity=0.145  Sum_probs=366.4

Q ss_pred             CCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-CCCCC----------
Q 003387          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-PYSNE----------  222 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~vs~~----------  222 (824)
                      +.+++|||+++++++..+|..+.++++||+||||||+||||||+++|+  ++..+|+..+|+.. -++..          
T Consensus       182 ~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~--~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~  259 (1153)
T PLN03210        182 DFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFS--RLSRQFQSSVFIDRAFISKSMEIYSSANPD  259 (1153)
T ss_pred             ccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHH--HHhhcCCeEEEeeccccccchhhccccccc
Confidence            456799999999999999977777899999999999999999999999  78899999888751 01111          


Q ss_pred             -CC-HHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEec
Q 003387          223 -YD-ADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLT  300 (824)
Q Consensus       223 -~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR  300 (824)
                       ++ ...++++++.++....+   .....    ...+++.|++||+||||||||+..+|+.+.....+.++||+||||||
T Consensus       260 ~~~~~~~l~~~~l~~il~~~~---~~~~~----~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTr  332 (1153)
T PLN03210        260 DYNMKLHLQRAFLSEILDKKD---IKIYH----LGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITK  332 (1153)
T ss_pred             ccchhHHHHHHHHHHHhCCCC---cccCC----HHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeC
Confidence             11 23466677776654332   11111    24577889999999999999999999999988788889999999999


Q ss_pred             hHHHHh-------------------------hcccccCCcCcCccccchhhHHHhcCCCchhHHHHHhHH------Hhhh
Q 003387          301 DIRIII-------------------------SFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSIS------LEEN  349 (824)
Q Consensus       301 ~~~v~~-------------------------~f~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l------~~~~  349 (824)
                      +++++.                         ||+..   ..+.++.+++++|+++|+|+|||++++|+.|      .|+.
T Consensus       333 d~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~---~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~~  409 (1153)
T PLN03210        333 DKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKN---SPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWMD  409 (1153)
T ss_pred             cHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCC---CCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHHHHHH
Confidence            999875                         34332   3345678899999999999999999999999      3444


Q ss_pred             hhhhccCC-C-cccccccc---cCCC-CchHHHhHhccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHHHHHhccc
Q 003387          350 IREAVETP-L-GLRYIKCL---MLPF-CLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGF  423 (824)
Q Consensus       350 ~~~~~~~~-~-~~~~~l~~---~L~~-~lk~cfl~~s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~~Lv~rsl  423 (824)
                      ....+... . .+..+|++   +|++ ..|.||++||+||.+..++   .+..|++.+.+.      ++..++.|+++||
T Consensus       410 ~l~~L~~~~~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l~~~~~~------~~~~l~~L~~ksL  480 (1153)
T PLN03210        410 MLPRLRNGLDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVN---DIKLLLANSDLD------VNIGLKNLVDKSL  480 (1153)
T ss_pred             HHHHHHhCccHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHH---HHHHHHHhcCCC------chhChHHHHhcCC
Confidence            43344322 2 78888888   9987 5999999999999987553   477788876652      3445999999999


Q ss_pred             cceeecCCCCcEEEEEcCccHHHHHHhhc-ccE--------EEccCC-C-CCCCCCCCCCeeEEEEEecCCCc-cccc-c
Q 003387          424 VEAKKRKAGGTINTCSIPGRWRPVLHTVP-YMV--------EFICSP-F-MDPKGKSPKKAKRLNAVEREGDF-ACLD-D  490 (824)
Q Consensus       424 lq~~~~~~~g~~~~~~mHdlv~dla~~~~-~~~--------~~~~~~-~-~~~~~~~~~~~r~lsl~~~~~~~-~~~~-~  490 (824)
                      ++...       ..+.|||++|+||+.++ ...        .+.... . .........+++.+++....... .+.. .
T Consensus       481 i~~~~-------~~~~MHdLl~~~~r~i~~~~~~~~~~r~~l~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~a  553 (1153)
T PLN03210        481 IHVRE-------DIVEMHSLLQEMGKEIVRAQSNEPGEREFLVDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENA  553 (1153)
T ss_pred             EEEcC-------CeEEhhhHHHHHHHHHHHhhcCCCCcceeEeCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHH
Confidence            98753       24899999999999987 211        000000 0 00011233456666665222111 0111 1


Q ss_pred             c--CCceeEeeccCCCCCC--CCcchhHhhhc-----------------------ccCcccEEEeeCccCccCCccCCCC
Q 003387          491 Y--DSQLHSLLCCSPETRH--LDPIDWEKFCG-----------------------MFKLLRVLDLGSLVLIQYPSGIENL  543 (824)
Q Consensus       491 ~--~~~Lr~L~l~~~~~~~--~~~~~~~~~~~-----------------------~~~~Lr~L~L~~~~i~~lp~~i~~l  543 (824)
                      +  +++|+.|.+.......  .....++..|.                       .+.+|+.|+++++.+..+|..+..+
T Consensus       554 F~~m~~L~~L~~~~~~~~~~~~~~~~lp~~~~~lp~~Lr~L~~~~~~l~~lP~~f~~~~L~~L~L~~s~l~~L~~~~~~l  633 (1153)
T PLN03210        554 FKGMRNLLFLKFYTKKWDQKKEVRWHLPEGFDYLPPKLRLLRWDKYPLRCMPSNFRPENLVKLQMQGSKLEKLWDGVHSL  633 (1153)
T ss_pred             HhcCccccEEEEecccccccccceeecCcchhhcCcccEEEEecCCCCCCCCCcCCccCCcEEECcCccccccccccccC
Confidence            1  5566666554332100  00001111122                       2344555555555555555555555


Q ss_pred             CcceEEeecCCC-CCccChhhhhcCCCccEeecCCc-cccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeee
Q 003387          544 FLLRYLKLNIPS-LNSLPSSLLSNLLNLYTLDMPFS-YIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFIS  621 (824)
Q Consensus       544 ~~Lr~L~L~~~~-i~~lp~~i~~~L~~L~~L~L~~~-~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~  621 (824)
                      ++|++|+|+++. +..+|. + +.+++|++|+|++| .+..+|..++++++|++|++++|.... .+|...++++|+.|+
T Consensus       634 ~~Lk~L~Ls~~~~l~~ip~-l-s~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~~L~-~Lp~~i~l~sL~~L~  710 (1153)
T PLN03210        634 TGLRNIDLRGSKNLKEIPD-L-SMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCENLE-ILPTGINLKSLYRLN  710 (1153)
T ss_pred             CCCCEEECCCCCCcCcCCc-c-ccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCCCcC-ccCCcCCCCCCCEEe
Confidence            555555555432 334442 3 45555555555555 445555555555555555555443221 333111445555555


Q ss_pred             ccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC---CCCCccEEEeCccCcCCCceEEEE
Q 003387          622 ALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES---KMPRLSKIVLAEYLFPHSLTHLSF  698 (824)
Q Consensus       622 ~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~---~~~~L~~l~l~~~~~~~~L~~L~L  698 (824)
                      ++.... +.......++|+.|+++++.   ...+|..+ .+++|++|.+....   -...+..+.......+++|+.|+|
T Consensus       711 Lsgc~~-L~~~p~~~~nL~~L~L~~n~---i~~lP~~~-~l~~L~~L~l~~~~~~~l~~~~~~l~~~~~~~~~sL~~L~L  785 (1153)
T PLN03210        711 LSGCSR-LKSFPDISTNISWLDLDETA---IEEFPSNL-RLENLDELILCEMKSEKLWERVQPLTPLMTMLSPSLTRLFL  785 (1153)
T ss_pred             CCCCCC-ccccccccCCcCeeecCCCc---cccccccc-cccccccccccccchhhccccccccchhhhhccccchheeC
Confidence            442110 11101112345555554442   22233322 33444444443210   000000000000012345666666


Q ss_pred             EcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCC--------------------Ccccee
Q 003387          699 SNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLW--------------------LEEWTM  758 (824)
Q Consensus       699 ~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~--------------------l~~l~~  758 (824)
                      ++|.....+|..++++++|+.|+|++|.... .++.. ..+++|+.|+|++|..                    ++.+|.
T Consensus       786 s~n~~l~~lP~si~~L~~L~~L~Ls~C~~L~-~LP~~-~~L~sL~~L~Ls~c~~L~~~p~~~~nL~~L~Ls~n~i~~iP~  863 (1153)
T PLN03210        786 SDIPSLVELPSSIQNLHKLEHLEIENCINLE-TLPTG-INLESLESLDLSGCSRLRTFPDISTNISDLNLSRTGIEEVPW  863 (1153)
T ss_pred             CCCCCccccChhhhCCCCCCEEECCCCCCcC-eeCCC-CCccccCEEECCCCCccccccccccccCEeECCCCCCccChH
Confidence            6665445555566666666666666543221 12211 1344455555544433                    445565


Q ss_pred             ccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          759 GNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       759 ~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      .+..+++|+.|++++|+.+..+|..+..+++|+.+++++|+
T Consensus       864 si~~l~~L~~L~L~~C~~L~~l~~~~~~L~~L~~L~l~~C~  904 (1153)
T PLN03210        864 WIEKFSNLSFLDMNGCNNLQRVSLNISKLKHLETVDFSDCG  904 (1153)
T ss_pred             HHhcCCCCCEEECCCCCCcCccCcccccccCCCeeecCCCc
Confidence            66778999999999999999999988999999999999998

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=2.5e-38  Score=335.66  Aligned_cols=242  Identities=29%  Similarity=0.430  Sum_probs=190.1

Q ss_pred             chhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCC
Q 003387          161 LDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSS  240 (824)
Q Consensus       161 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~  240 (824)
                      ||.++++|.+.|....++.++|+|+||||+||||||+.++++.+++.+|+.++||.  +++.++..+++.+|+.+++...
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~--~~~~~~~~~~~~~i~~~l~~~~   78 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVS--LSKNPSLEQLLEQILRQLGEPD   78 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEE--EES-SCCHHHHHHHHHHHTCC-
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccc--cccccccccccccccccccccc
Confidence            78999999999999667899999999999999999999999766999999999999  9999999999999999999863


Q ss_pred             CcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh--------------
Q 003387          241 RLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII--------------  306 (824)
Q Consensus       241 ~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~--------------  306 (824)
                      ... ....+.++....+.+.|+++++||||||||+...|+.+...++....||+||||||+..++.              
T Consensus        79 ~~~-~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L  157 (287)
T PF00931_consen   79 SSI-SDPKDIEELQDQLRELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPL  157 (287)
T ss_dssp             STS-SCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS-
T ss_pred             ccc-ccccccccccccchhhhccccceeeeeeeccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            211 14567788999999999999999999999999999999988888888999999999998875              


Q ss_pred             -------hcccccCC---cCcCccccchhhHHHhcCCCchhHHHHHhHH-------Hhhhhhhhc----c---CCC-ccc
Q 003387          307 -------SFQFEDGE---NMRLDLVPTGGPLRATYKGRPFLILYHGSIS-------LEENIREAV----E---TPL-GLR  361 (824)
Q Consensus       307 -------~f~~~~~~---~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l-------~~~~~~~~~----~---~~~-~~~  361 (824)
                             +|....+.   ..++.+.+.+++|+++|+|+|||++++|++|       .|+.....+    .   +.. .+.
T Consensus       158 ~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~~  237 (287)
T PF00931_consen  158 SEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSVF  237 (287)
T ss_dssp             -HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence                   33333221   2245678899999999999999999999999       122222122    1   112 677


Q ss_pred             ccccc---cCCCCchHHHhHhccCCCCceechhHHHHHHHHcCCCCC
Q 003387          362 YIKCL---MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPD  405 (824)
Q Consensus       362 ~~l~~---~L~~~lk~cfl~~s~fp~~~~i~~~~Li~~W~a~g~i~~  405 (824)
                      .++.+   .||+++|.||+|||+||+++.|+++.|+++|+++|||.+
T Consensus       238 ~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~~  284 (287)
T PF00931_consen  238 SALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFISS  284 (287)
T ss_dssp             HHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC-
T ss_pred             ccceechhcCCccHHHHHhhCcCCCCCceECHHHHHHHHHHCCCCcc
Confidence            77766   999999999999999999999999999999999999853

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.

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

Probab=99.91  E-value=4.9e-27  Score=247.98  Aligned_cols=315  Identities=20%  Similarity=0.224  Sum_probs=268.6

Q ss_pred             CCCeeEEEEEecCCCccccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcce
Q 003387          470 PKKAKRLNAVEREGDFACLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLR  547 (824)
Q Consensus       470 ~~~~r~lsl~~~~~~~~~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr  547 (824)
                      .+++.||++. .+....+...+  .|.||++.+..+....  ..++++ +-++..|.+||||.|.+...|..+..-+++-
T Consensus        54 lqkLEHLs~~-HN~L~~vhGELs~Lp~LRsv~~R~N~LKn--sGiP~d-iF~l~dLt~lDLShNqL~EvP~~LE~AKn~i  129 (1255)
T KOG0444|consen   54 LQKLEHLSMA-HNQLISVHGELSDLPRLRSVIVRDNNLKN--SGIPTD-IFRLKDLTILDLSHNQLREVPTNLEYAKNSI  129 (1255)
T ss_pred             Hhhhhhhhhh-hhhhHhhhhhhccchhhHHHhhhcccccc--CCCCch-hcccccceeeecchhhhhhcchhhhhhcCcE
Confidence            4567888888 44444355555  9999999999887753  334544 4568999999999999999999999999999


Q ss_pred             EEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC-
Q 003387          548 YLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC-  626 (824)
Q Consensus       548 ~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~-  626 (824)
                      +|+|++|+|..+|.++|-+|+.|-+||||+|.+..+|+.+..|.+|+.|+|++|.+....+..+..|++|+.|.+++.. 
T Consensus       130 VLNLS~N~IetIPn~lfinLtDLLfLDLS~NrLe~LPPQ~RRL~~LqtL~Ls~NPL~hfQLrQLPsmtsL~vLhms~TqR  209 (1255)
T KOG0444|consen  130 VLNLSYNNIETIPNSLFINLTDLLFLDLSNNRLEMLPPQIRRLSMLQTLKLSNNPLNHFQLRQLPSMTSLSVLHMSNTQR  209 (1255)
T ss_pred             EEEcccCccccCCchHHHhhHhHhhhccccchhhhcCHHHHHHhhhhhhhcCCChhhHHHHhcCccchhhhhhhcccccc
Confidence            9999999999999999899999999999999999999999999999999999998864444466778888888887432 


Q ss_pred             --cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCC
Q 003387          627 --CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLM  704 (824)
Q Consensus       627 --~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~  704 (824)
                        ..++..+..+.||+.++++.+   +...+|..+.++.+|+.|+|++|    .++.|.+.. ..-.+|++|++|.|+++
T Consensus       210 Tl~N~Ptsld~l~NL~dvDlS~N---~Lp~vPecly~l~~LrrLNLS~N----~iteL~~~~-~~W~~lEtLNlSrNQLt  281 (1255)
T KOG0444|consen  210 TLDNIPTSLDDLHNLRDVDLSEN---NLPIVPECLYKLRNLRRLNLSGN----KITELNMTE-GEWENLETLNLSRNQLT  281 (1255)
T ss_pred             hhhcCCCchhhhhhhhhcccccc---CCCcchHHHhhhhhhheeccCcC----ceeeeeccH-HHHhhhhhhccccchhc
Confidence              233334888999999999988   67788999999999999999987    577776543 44578999999999975


Q ss_pred             CCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCcccc
Q 003387          705 DDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQL  784 (824)
Q Consensus       705 ~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l  784 (824)
                       ..|..+++++.|+.|.+.+|+++-+.++..++.+.+|+++...++. ++-.|.+++.++.|++|.++.|. +-.+|.++
T Consensus       282 -~LP~avcKL~kL~kLy~n~NkL~FeGiPSGIGKL~~Levf~aanN~-LElVPEglcRC~kL~kL~L~~Nr-LiTLPeaI  358 (1255)
T KOG0444|consen  282 -VLPDAVCKLTKLTKLYANNNKLTFEGIPSGIGKLIQLEVFHAANNK-LELVPEGLCRCVKLQKLKLDHNR-LITLPEAI  358 (1255)
T ss_pred             -cchHHHhhhHHHHHHHhccCcccccCCccchhhhhhhHHHHhhccc-cccCchhhhhhHHHHHhcccccc-eeechhhh
Confidence             6788999999999999999998888899999999999999999865 88889999999999999999666 55799999


Q ss_pred             ccCccCcEEEecCCc
Q 003387          785 WYIKSLNKFDCWWPQ  799 (824)
Q Consensus       785 ~~l~~L~~L~l~~c~  799 (824)
                      .-++.|+.|++..+|
T Consensus       359 HlL~~l~vLDlreNp  373 (1255)
T KOG0444|consen  359 HLLPDLKVLDLRENP  373 (1255)
T ss_pred             hhcCCcceeeccCCc
Confidence            999999999999998

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

Probab=99.91  E-value=9.9e-24  Score=261.50  Aligned_cols=275  Identities=23%  Similarity=0.222  Sum_probs=145.4

Q ss_pred             cCcccEEEeeCccCc-cCCccCCCCCcceEEeecCCCCC-ccChhhhhcCCCccEeecCCcccc-ccchhhhccccCcee
Q 003387          520 FKLLRVLDLGSLVLI-QYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLLNLYTLDMPFSYID-HTADEFWKMNKLRHL  596 (824)
Q Consensus       520 ~~~Lr~L~L~~~~i~-~lp~~i~~l~~Lr~L~L~~~~i~-~lp~~i~~~L~~L~~L~L~~~~l~-~lp~~i~~L~~L~~L  596 (824)
                      +++|++|+|++|.+. .+|..++.+++|++|+|++|.+. .+|..+ +++++|++|++++|.+. .+|..++++++|++|
T Consensus       139 l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~~-~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L  217 (968)
T PLN00113        139 IPNLETLDLSNNMLSGEIPNDIGSFSSLKVLDLGGNVLVGKIPNSL-TNLTSLEFLTLASNQLVGQIPRELGQMKSLKWI  217 (968)
T ss_pred             cCCCCEEECcCCcccccCChHHhcCCCCCEEECccCcccccCChhh-hhCcCCCeeeccCCCCcCcCChHHcCcCCccEE
Confidence            344444444444443 44444555555555555555543 444444 55555555555555333 345555555555555


Q ss_pred             cCCCccCCCCCCC-CCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEecc
Q 003387          597 NFGSITLPAHPGK-FCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANE  673 (824)
Q Consensus       597 ~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~  673 (824)
                      ++++|.+.. .+| .++++++|+.|+++.+.  ..++..++++++|+.|+++++.  ....+|..+.++++|++|++++|
T Consensus       218 ~L~~n~l~~-~~p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~--l~~~~p~~l~~l~~L~~L~Ls~n  294 (968)
T PLN00113        218 YLGYNNLSG-EIPYEIGGLTSLNHLDLVYNNLTGPIPSSLGNLKNLQYLFLYQNK--LSGPIPPSIFSLQKLISLDLSDN  294 (968)
T ss_pred             ECcCCccCC-cCChhHhcCCCCCEEECcCceeccccChhHhCCCCCCEEECcCCe--eeccCchhHhhccCcCEEECcCC
Confidence            555555443 333 55555555555554221  1122225555555555555543  22334455555556666665543


Q ss_pred             C----------CCCCccEEEeCcc----------CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeee
Q 003387          674 S----------KMPRLSKIVLAEY----------LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLT  733 (824)
Q Consensus       674 ~----------~~~~L~~l~l~~~----------~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~  733 (824)
                      .          ..++|+.|.+.++          ..+++|+.|++++|.+.+..|..++.+++|+.|++++|.+.+ .++
T Consensus       295 ~l~~~~p~~~~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~p~~l~~~~~L~~L~Ls~n~l~~-~~p  373 (968)
T PLN00113        295 SLSGEIPELVIQLQNLEILHLFSNNFTGKIPVALTSLPRLQVLQLWSNKFSGEIPKNLGKHNNLTVLDLSTNNLTG-EIP  373 (968)
T ss_pred             eeccCCChhHcCCCCCcEEECCCCccCCcCChhHhcCCCCCEEECcCCCCcCcCChHHhCCCCCcEEECCCCeeEe-eCC
Confidence            2          2234445544433          234555555555555555555555555555555555554443 122


Q ss_pred             ecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          734 CGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       734 ~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      .....+++|+.|++++|.....+|..++.+++|+.|++++|.....+|..+..+++|+.|++++|.
T Consensus       374 ~~~~~~~~L~~L~l~~n~l~~~~p~~~~~~~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~Ls~N~  439 (968)
T PLN00113        374 EGLCSSGNLFKLILFSNSLEGEIPKSLGACRSLRRVRLQDNSFSGELPSEFTKLPLVYFLDISNNN  439 (968)
T ss_pred             hhHhCcCCCCEEECcCCEecccCCHHHhCCCCCCEEECcCCEeeeECChhHhcCCCCCEEECcCCc
Confidence            333445566666666655444555556667777888877777666677777777888888887765

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

Probab=99.91  E-value=5.7e-24  Score=263.59  Aligned_cols=300  Identities=22%  Similarity=0.258  Sum_probs=155.7

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc-cCCccCCCCCcceEEeecCCCCC-ccChhhhhcCCC
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-QYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLLN  569 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-~lp~~i~~l~~Lr~L~L~~~~i~-~lp~~i~~~L~~  569 (824)
                      .++|++|.+.++...    ...+..+..+++|++|+|++|.+. .+|..++++++|++|+|++|.+. .+|..+ +++++
T Consensus       139 l~~L~~L~Ls~n~~~----~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l-~~l~~  213 (968)
T PLN00113        139 IPNLETLDLSNNMLS----GEIPNDIGSFSSLKVLDLGGNVLVGKIPNSLTNLTSLEFLTLASNQLVGQIPREL-GQMKS  213 (968)
T ss_pred             cCCCCEEECcCCccc----ccCChHHhcCCCCCEEECccCcccccCChhhhhCcCCCeeeccCCCCcCcCChHH-cCcCC
Confidence            455555555544432    122344555556666666665544 55555555666666666555544 344444 55555


Q ss_pred             ccEeecCCcccc-ccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEe
Q 003387          570 LYTLDMPFSYID-HTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIR  645 (824)
Q Consensus       570 L~~L~L~~~~l~-~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~  645 (824)
                      |++|+|++|.+. .+|..++++++|++|++++|.+.+ .+| .++++++|+.|++..+.  ...+..+..+++|+.|+++
T Consensus       214 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~~L~Ls  292 (968)
T PLN00113        214 LKWIYLGYNNLSGEIPYEIGGLTSLNHLDLVYNNLTG-PIPSSLGNLKNLQYLFLYQNKLSGPIPPSIFSLQKLISLDLS  292 (968)
T ss_pred             ccEEECcCCccCCcCChhHhcCCCCCEEECcCceecc-ccChhHhCCCCCCEEECcCCeeeccCchhHhhccCcCEEECc
Confidence            666665555443 445555555555555555555443 333 55555555555554211  1111124444455555554


Q ss_pred             cccc----------------------cchhhHHHHhccCCCCCeEEEeccC----------CCCCccEEEeCcc------
Q 003387          646 GDLS----------------------YNQSLLSKSLCRLSCLESLKLANES----------KMPRLSKIVLAEY------  687 (824)
Q Consensus       646 ~~~~----------------------~~~~~l~~~l~~l~~L~~L~l~~~~----------~~~~L~~l~l~~~------  687 (824)
                      +|.-                      ......|..+..+++|+.|++++|.          ..++|+.+++.++      
T Consensus       293 ~n~l~~~~p~~~~~l~~L~~L~l~~n~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~p~~l~~~~~L~~L~Ls~n~l~~~~  372 (968)
T PLN00113        293 DNSLSGEIPELVIQLQNLEILHLFSNNFTGKIPVALTSLPRLQVLQLWSNKFSGEIPKNLGKHNNLTVLDLSTNNLTGEI  372 (968)
T ss_pred             CCeeccCCChhHcCCCCCcEEECCCCccCCcCChhHhcCCCCCEEECcCCCCcCcCChHHhCCCCCcEEECCCCeeEeeC
Confidence            4420                      0222334444445555555554431          2234444444433      


Q ss_pred             ----CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcc
Q 003387          688 ----LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAM  763 (824)
Q Consensus       688 ----~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~l  763 (824)
                          ..+++|+.|++++|.+.+..|..++.+++|+.|++++|.+.+ .++..+..+++|+.|++++|.....++.....+
T Consensus       373 p~~~~~~~~L~~L~l~~n~l~~~~p~~~~~~~~L~~L~L~~n~l~~-~~p~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l  451 (968)
T PLN00113        373 PEGLCSSGNLFKLILFSNSLEGEIPKSLGACRSLRRVRLQDNSFSG-ELPSEFTKLPLVYFLDISNNNLQGRINSRKWDM  451 (968)
T ss_pred             ChhHhCcCCCCEEECcCCEecccCCHHHhCCCCCCEEECcCCEeee-ECChhHhcCCCCCEEECcCCcccCccChhhccC
Confidence                123445555555555555555555666666666666655544 233344556666666666665444444445566


Q ss_pred             cCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          764 PKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       764 p~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ++|+.|++++|.....+|..+ ..++|+.|++++|.
T Consensus       452 ~~L~~L~L~~n~~~~~~p~~~-~~~~L~~L~ls~n~  486 (968)
T PLN00113        452 PSLQMLSLARNKFFGGLPDSF-GSKRLENLDLSRNQ  486 (968)
T ss_pred             CCCcEEECcCceeeeecCccc-ccccceEEECcCCc
Confidence            777777777777666666543 34677777777765

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

Probab=99.86  E-value=1.7e-22  Score=212.92  Aligned_cols=317  Identities=18%  Similarity=0.184  Sum_probs=214.9

Q ss_pred             CCCeeEEEEEecCCCccccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcc
Q 003387          470 PKKAKRLNAVEREGDFACLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLL  546 (824)
Q Consensus       470 ~~~~r~lsl~~~~~~~~~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~L  546 (824)
                      ..+++.+.+. ++....+|...  ..++..|.+..+....    +-...+.-++.||+||||.|.|+.+|. ++..-.++
T Consensus       101 l~nLq~v~l~-~N~Lt~IP~f~~~sghl~~L~L~~N~I~s----v~se~L~~l~alrslDLSrN~is~i~~~sfp~~~ni  175 (873)
T KOG4194|consen  101 LPNLQEVNLN-KNELTRIPRFGHESGHLEKLDLRHNLISS----VTSEELSALPALRSLDLSRNLISEIPKPSFPAKVNI  175 (873)
T ss_pred             CCcceeeeec-cchhhhcccccccccceeEEeeecccccc----ccHHHHHhHhhhhhhhhhhchhhcccCCCCCCCCCc
Confidence            4566667777 55555577666  7779999988887643    445667778999999999999987774 46667899


Q ss_pred             eEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCC
Q 003387          547 RYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHP  625 (824)
Q Consensus       547 r~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~  625 (824)
                      ++|+|++|.|+.+-..-|.+|.+|-+|.|+.|.++.+|.. |.+|++|+.|+|..|.+.-...-.+..|.+|+.+.+..+
T Consensus       176 ~~L~La~N~It~l~~~~F~~lnsL~tlkLsrNrittLp~r~Fk~L~~L~~LdLnrN~irive~ltFqgL~Sl~nlklqrN  255 (873)
T KOG4194|consen  176 KKLNLASNRITTLETGHFDSLNSLLTLKLSRNRITTLPQRSFKRLPKLESLDLNRNRIRIVEGLTFQGLPSLQNLKLQRN  255 (873)
T ss_pred             eEEeeccccccccccccccccchheeeecccCcccccCHHHhhhcchhhhhhccccceeeehhhhhcCchhhhhhhhhhc
Confidence            9999999999988776678999999999999999999865 666999999999999886322225666777766666521


Q ss_pred             -Ccc-hhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccC
Q 003387          626 -CCC-TEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDL  703 (824)
Q Consensus       626 -~~~-~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l  703 (824)
                       ... -...+-.|.+++.|++..+.  ....-..++.+++.|+.|+++.|    .++..++.+..++++|+.|+|++|.+
T Consensus       256 ~I~kL~DG~Fy~l~kme~l~L~~N~--l~~vn~g~lfgLt~L~~L~lS~N----aI~rih~d~WsftqkL~~LdLs~N~i  329 (873)
T KOG4194|consen  256 DISKLDDGAFYGLEKMEHLNLETNR--LQAVNEGWLFGLTSLEQLDLSYN----AIQRIHIDSWSFTQKLKELDLSSNRI  329 (873)
T ss_pred             CcccccCcceeeecccceeecccch--hhhhhcccccccchhhhhccchh----hhheeecchhhhcccceeEecccccc
Confidence             111 12236668889999998875  33333457888999999999887    47888888888888888888888888


Q ss_pred             CCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccce---eccCcccCccEEEEecCCCCCCC
Q 003387          704 MDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWT---MGNAAMPKLECLIINPCAYLKKM  780 (824)
Q Consensus       704 ~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~---~~~~~lp~L~~L~l~~c~~l~~l  780 (824)
                      +...+..|..|..|++|+|+.|.+.-- -...+.++.+|++|+|.++..--.+.   ..+..+|+|++|.+.+|. ++++
T Consensus       330 ~~l~~~sf~~L~~Le~LnLs~Nsi~~l-~e~af~~lssL~~LdLr~N~ls~~IEDaa~~f~gl~~LrkL~l~gNq-lk~I  407 (873)
T KOG4194|consen  330 TRLDEGSFRVLSQLEELNLSHNSIDHL-AEGAFVGLSSLHKLDLRSNELSWCIEDAAVAFNGLPSLRKLRLTGNQ-LKSI  407 (873)
T ss_pred             ccCChhHHHHHHHhhhhcccccchHHH-HhhHHHHhhhhhhhcCcCCeEEEEEecchhhhccchhhhheeecCce-eeec
Confidence            777777777777777777777664320 01112344555555555543111110   112235555555555543 3444


Q ss_pred             cc-ccccCccCcEEEecCCc
Q 003387          781 PE-QLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       781 p~-~l~~l~~L~~L~l~~c~  799 (824)
                      |. .+..+++|++|++.+++
T Consensus       408 ~krAfsgl~~LE~LdL~~Na  427 (873)
T KOG4194|consen  408 PKRAFSGLEALEHLDLGDNA  427 (873)
T ss_pred             chhhhccCcccceecCCCCc
Confidence            43 34444555555544443

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

Probab=99.80  E-value=8.1e-21  Score=200.41  Aligned_cols=323  Identities=18%  Similarity=0.139  Sum_probs=250.7

Q ss_pred             CCCCeeEEEEEecCCCccc-cccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCC
Q 003387          469 SPKKAKRLNAVEREGDFAC-LDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLF  544 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~-~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~  544 (824)
                      ....+.+|.+. .+.+..+ .+.+  .+.||+|.++.+....    +....|..-.+++.|+|++|.|+.+- ..|..+.
T Consensus       123 ~sghl~~L~L~-~N~I~sv~se~L~~l~alrslDLSrN~is~----i~~~sfp~~~ni~~L~La~N~It~l~~~~F~~ln  197 (873)
T KOG4194|consen  123 ESGHLEKLDLR-HNLISSVTSEELSALPALRSLDLSRNLISE----IPKPSFPAKVNIKKLNLASNRITTLETGHFDSLN  197 (873)
T ss_pred             cccceeEEeee-ccccccccHHHHHhHhhhhhhhhhhchhhc----ccCCCCCCCCCceEEeeccccccccccccccccc
Confidence            34568899998 5554433 3344  8999999999887743    45567777788999999999999664 4678899


Q ss_pred             cceEEeecCCCCCccChhhhhcCCCccEeecCCcccccc-chhhhccccCceecCCCccCCCCCCC--CCCCCCCCCeee
Q 003387          545 LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGSITLPAHPGK--FCGSLENLNFIS  621 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~~~~~~~~~p--~i~~L~~L~~l~  621 (824)
                      +|-.|.|+.|.++.+|.-.|.+|++|+.|+|..|.+... --.|..|++|+.|.|..|.+.  .+.  .+-.|.++++++
T Consensus       198 sL~tlkLsrNrittLp~r~Fk~L~~L~~LdLnrN~irive~ltFqgL~Sl~nlklqrN~I~--kL~DG~Fy~l~kme~l~  275 (873)
T KOG4194|consen  198 SLLTLKLSRNRITTLPQRSFKRLPKLESLDLNRNRIRIVEGLTFQGLPSLQNLKLQRNDIS--KLDDGAFYGLEKMEHLN  275 (873)
T ss_pred             hheeeecccCcccccCHHHhhhcchhhhhhccccceeeehhhhhcCchhhhhhhhhhcCcc--cccCcceeeecccceee
Confidence            999999999999999999888899999999999987766 345889999999999999887  444  566777888888


Q ss_pred             ccCC--CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEE
Q 003387          622 ALHP--CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFS  699 (824)
Q Consensus       622 ~~~~--~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~  699 (824)
                      +..+  ...-...+-.|+.|+.|+++.+.  ....-++....+++|+.|+|+.|    ++++|.-..+..++.|+.|.|+
T Consensus       276 L~~N~l~~vn~g~lfgLt~L~~L~lS~Na--I~rih~d~WsftqkL~~LdLs~N----~i~~l~~~sf~~L~~Le~LnLs  349 (873)
T KOG4194|consen  276 LETNRLQAVNEGWLFGLTSLEQLDLSYNA--IQRIHIDSWSFTQKLKELDLSSN----RITRLDEGSFRVLSQLEELNLS  349 (873)
T ss_pred             cccchhhhhhcccccccchhhhhccchhh--hheeecchhhhcccceeEecccc----ccccCChhHHHHHHHhhhhccc
Confidence            8732  12223337789999999999985  33334566777899999999987    5888877777888999999999


Q ss_pred             cccCCCCCcccccCCCCCCeEEeeccccCCC--eeeecCCCCCCccEEeeccCCCCcccee-ccCcccCccEEEEecCCC
Q 003387          700 NTDLMDDPMPTLEKLPLLQVLKLKQNSYSGR--KLTCGSYGFPNLKVLHLKSMLWLEEWTM-GNAAMPKLECLIINPCAY  776 (824)
Q Consensus       700 ~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~--~~~~~~~~~~~L~~L~L~~~~~l~~l~~-~~~~lp~L~~L~l~~c~~  776 (824)
                      .|.+....-..|..+.+|+.|+|+.|.+...  .-...+.++++|+.|.+.++. ++.++. .+..+++|+.|++.+|+.
T Consensus       350 ~Nsi~~l~e~af~~lssL~~LdLr~N~ls~~IEDaa~~f~gl~~LrkL~l~gNq-lk~I~krAfsgl~~LE~LdL~~Nai  428 (873)
T KOG4194|consen  350 HNSIDHLAEGAFVGLSSLHKLDLRSNELSWCIEDAAVAFNGLPSLRKLRLTGNQ-LKSIPKRAFSGLEALEHLDLGDNAI  428 (873)
T ss_pred             ccchHHHHhhHHHHhhhhhhhcCcCCeEEEEEecchhhhccchhhhheeecCce-eeecchhhhccCcccceecCCCCcc
Confidence            9987655555678899999999998876531  112234679999999999976 788864 466799999999999996


Q ss_pred             CCCCccccccCccCcEEEe------cCCcHHHHHHH
Q 003387          777 LKKMPEQLWYIKSLNKFDC------WWPQPELRQKL  806 (824)
Q Consensus       777 l~~lp~~l~~l~~L~~L~l------~~c~~~l~~~~  806 (824)
                      ..--|..+..+ .|++|.+      -+|.-.|..++
T Consensus       429 aSIq~nAFe~m-~Lk~Lv~nSssflCDCql~Wl~qW  463 (873)
T KOG4194|consen  429 ASIQPNAFEPM-ELKELVMNSSSFLCDCQLKWLAQW  463 (873)
T ss_pred             eeecccccccc-hhhhhhhcccceEEeccHHHHHHH
Confidence            55457777777 7887754      46775555443

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

Probab=99.79  E-value=7.6e-22  Score=199.61  Aligned_cols=175  Identities=21%  Similarity=0.197  Sum_probs=107.7

Q ss_pred             ccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhh
Q 003387          487 CLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLL  564 (824)
Q Consensus       487 ~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~  564 (824)
                      +|+.+  ...++.+.+..+...     ..++.+..+..|..|+..+|++.++|..++.+..|..|++.+|.++++|+.. 
T Consensus       106 lp~~i~s~~~l~~l~~s~n~~~-----el~~~i~~~~~l~dl~~~~N~i~slp~~~~~~~~l~~l~~~~n~l~~l~~~~-  179 (565)
T KOG0472|consen  106 LPEQIGSLISLVKLDCSSNELK-----ELPDSIGRLLDLEDLDATNNQISSLPEDMVNLSKLSKLDLEGNKLKALPENH-  179 (565)
T ss_pred             ccHHHhhhhhhhhhhcccccee-----ecCchHHHHhhhhhhhccccccccCchHHHHHHHHHHhhccccchhhCCHHH-
Confidence            55554  555666655555443     2345556666777777777777777777777777777777777777777776 


Q ss_pred             hcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC--cchhhhcCCCCccceE
Q 003387          565 SNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC--CCTEDILGRLPNLRNL  642 (824)
Q Consensus       565 ~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L  642 (824)
                      -+++.|+.||...|.++.+|++++.|.+|..|++..|.+.  .+|.|+.+..|.+|.++.+.  ..+.+.+.++++|..|
T Consensus       180 i~m~~L~~ld~~~N~L~tlP~~lg~l~~L~~LyL~~Nki~--~lPef~gcs~L~Elh~g~N~i~~lpae~~~~L~~l~vL  257 (565)
T KOG0472|consen  180 IAMKRLKHLDCNSNLLETLPPELGGLESLELLYLRRNKIR--FLPEFPGCSLLKELHVGENQIEMLPAEHLKHLNSLLVL  257 (565)
T ss_pred             HHHHHHHhcccchhhhhcCChhhcchhhhHHHHhhhcccc--cCCCCCccHHHHHHHhcccHHHhhHHHHhcccccceee
Confidence            4577777777777777777777777777777777777765  55666666666666655321  2223333345555555


Q ss_pred             EEecccccchhhHHHHhccCCCCCeEEEec
Q 003387          643 RIRGDLSYNQSLLSKSLCRLSCLESLKLAN  672 (824)
Q Consensus       643 ~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~  672 (824)
                      ++..+   ...+.|..+..+.+|+.|++++
T Consensus       258 DLRdN---klke~Pde~clLrsL~rLDlSN  284 (565)
T KOG0472|consen  258 DLRDN---KLKEVPDEICLLRSLERLDLSN  284 (565)
T ss_pred             ecccc---ccccCchHHHHhhhhhhhcccC
Confidence            55444   3344444444444444444444

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

Probab=99.79  E-value=1e-21  Score=207.98  Aligned_cols=307  Identities=18%  Similarity=0.157  Sum_probs=236.2

Q ss_pred             CCCeeEEEEEecCCC-ccccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcc
Q 003387          470 PKKAKRLNAVEREGD-FACLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLL  546 (824)
Q Consensus       470 ~~~~r~lsl~~~~~~-~~~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~L  546 (824)
                      .+-+|-+.+..++.. ..+|..+  +..++-|.+......     -.++-++.+.+|..|.++.|.+.++-..+..|+.|
T Consensus         6 LpFVrGvDfsgNDFsg~~FP~~v~qMt~~~WLkLnrt~L~-----~vPeEL~~lqkLEHLs~~HN~L~~vhGELs~Lp~L   80 (1255)
T KOG0444|consen    6 LPFVRGVDFSGNDFSGDRFPHDVEQMTQMTWLKLNRTKLE-----QVPEELSRLQKLEHLSMAHNQLISVHGELSDLPRL   80 (1255)
T ss_pred             cceeecccccCCcCCCCcCchhHHHhhheeEEEechhhhh-----hChHHHHHHhhhhhhhhhhhhhHhhhhhhccchhh
Confidence            344666666633333 3467777  889999988776654     35677888999999999999988888888999999


Q ss_pred             eEEeecCCCCC--ccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCC--CCCCCCCCCeeec
Q 003387          547 RYLKLNIPSLN--SLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK--FCGSLENLNFISA  622 (824)
Q Consensus       547 r~L~L~~~~i~--~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p--~i~~L~~L~~l~~  622 (824)
                      |.+.++.|+++  .+|..+ -+|..|.+||||+|.+.+.|.++..-+++-+|+|++|.+.  .+|  -+-+|+.|-.|++
T Consensus        81 Rsv~~R~N~LKnsGiP~di-F~l~dLt~lDLShNqL~EvP~~LE~AKn~iVLNLS~N~Ie--tIPn~lfinLtDLLfLDL  157 (1255)
T KOG0444|consen   81 RSVIVRDNNLKNSGIPTDI-FRLKDLTILDLSHNQLREVPTNLEYAKNSIVLNLSYNNIE--TIPNSLFINLTDLLFLDL  157 (1255)
T ss_pred             HHHhhhccccccCCCCchh-cccccceeeecchhhhhhcchhhhhhcCcEEEEcccCccc--cCCchHHHhhHhHhhhcc
Confidence            99999999876  899999 8999999999999999999999999999999999999987  566  6778888888888


Q ss_pred             cCC--CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC-----CCCCccEEEeCccCcCCCceE
Q 003387          623 LHP--CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES-----KMPRLSKIVLAEYLFPHSLTH  695 (824)
Q Consensus       623 ~~~--~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~-----~~~~L~~l~l~~~~~~~~L~~  695 (824)
                      +.+  ...++. +..|.+|++|.++++.  ....-...+..+++|+.|.+++..     -++++        ..+.||..
T Consensus       158 S~NrLe~LPPQ-~RRL~~LqtL~Ls~NP--L~hfQLrQLPsmtsL~vLhms~TqRTl~N~Ptsl--------d~l~NL~d  226 (1255)
T KOG0444|consen  158 SNNRLEMLPPQ-IRRLSMLQTLKLSNNP--LNHFQLRQLPSMTSLSVLHMSNTQRTLDNIPTSL--------DDLHNLRD  226 (1255)
T ss_pred             ccchhhhcCHH-HHHHhhhhhhhcCCCh--hhHHHHhcCccchhhhhhhcccccchhhcCCCch--------hhhhhhhh
Confidence            842  334555 8888899999998874  221122334455667777777521     12222        44678999


Q ss_pred             EEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCC
Q 003387          696 LSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCA  775 (824)
Q Consensus       696 L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~  775 (824)
                      +++|.|.+. ..|..+.++++|+.|+|++|.++.  +....+.-.+|++|+++.+. +..+|.....++.|++|++.+|.
T Consensus       227 vDlS~N~Lp-~vPecly~l~~LrrLNLS~N~ite--L~~~~~~W~~lEtLNlSrNQ-Lt~LP~avcKL~kL~kLy~n~Nk  302 (1255)
T KOG0444|consen  227 VDLSENNLP-IVPECLYKLRNLRRLNLSGNKITE--LNMTEGEWENLETLNLSRNQ-LTVLPDAVCKLTKLTKLYANNNK  302 (1255)
T ss_pred             ccccccCCC-cchHHHhhhhhhheeccCcCceee--eeccHHHHhhhhhhccccch-hccchHHHhhhHHHHHHHhccCc
Confidence            999988863 667888899999999999998865  33444566789999999875 88888888889999999988776


Q ss_pred             C-CCCCccccccCccCcEEEecCCc
Q 003387          776 Y-LKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       776 ~-l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      . ...+|++++.+.+|+.+...++.
T Consensus       303 L~FeGiPSGIGKL~~Levf~aanN~  327 (1255)
T KOG0444|consen  303 LTFEGIPSGIGKLIQLEVFHAANNK  327 (1255)
T ss_pred             ccccCCccchhhhhhhHHHHhhccc
Confidence            4 35689899888888877665543

>PLN03210 Resistant to P

Probab=99.78  E-value=3.8e-18  Score=211.97  Aligned_cols=289  Identities=19%  Similarity=0.151  Sum_probs=208.4

Q ss_pred             CCCCeeEEEEEecCCCccccccc-CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc-CccCCccCCCCCcc
Q 003387          469 SPKKAKRLNAVEREGDFACLDDY-DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV-LIQYPSGIENLFLL  546 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~~~~-~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~-i~~lp~~i~~l~~L  546 (824)
                      .+.++|.+.+. +.....+|..+ ..+|+.|.+.++...     .++..+..+++|++|+|+++. +..+|. ++.+++|
T Consensus       587 lp~~Lr~L~~~-~~~l~~lP~~f~~~~L~~L~L~~s~l~-----~L~~~~~~l~~Lk~L~Ls~~~~l~~ip~-ls~l~~L  659 (1153)
T PLN03210        587 LPPKLRLLRWD-KYPLRCMPSNFRPENLVKLQMQGSKLE-----KLWDGVHSLTGLRNIDLRGSKNLKEIPD-LSMATNL  659 (1153)
T ss_pred             cCcccEEEEec-CCCCCCCCCcCCccCCcEEECcCcccc-----ccccccccCCCCCEEECCCCCCcCcCCc-cccCCcc
Confidence            34567888777 55555567666 788888888876653     233456789999999999876 667774 8889999


Q ss_pred             eEEeecCCC-CCccChhhhhcCCCccEeecCCc-cccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccC
Q 003387          547 RYLKLNIPS-LNSLPSSLLSNLLNLYTLDMPFS-YIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALH  624 (824)
Q Consensus       547 r~L~L~~~~-i~~lp~~i~~~L~~L~~L~L~~~-~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~  624 (824)
                      ++|+|++|. +..+|.++ +++++|+.|++++| .++.+|..+ ++++|++|++++|.... .+|.+  .++|+.|++..
T Consensus       660 e~L~L~~c~~L~~lp~si-~~L~~L~~L~L~~c~~L~~Lp~~i-~l~sL~~L~Lsgc~~L~-~~p~~--~~nL~~L~L~~  734 (1153)
T PLN03210        660 ETLKLSDCSSLVELPSSI-QYLNKLEDLDMSRCENLEILPTGI-NLKSLYRLNLSGCSRLK-SFPDI--STNISWLDLDE  734 (1153)
T ss_pred             cEEEecCCCCccccchhh-hccCCCCEEeCCCCCCcCccCCcC-CCCCCCEEeCCCCCCcc-ccccc--cCCcCeeecCC
Confidence            999999865 77899998 99999999999998 888999866 78999999998885432 33321  23344444442


Q ss_pred             CC-cchhh------------------------------hcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEecc
Q 003387          625 PC-CCTED------------------------------ILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANE  673 (824)
Q Consensus       625 ~~-~~~~~------------------------------~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~  673 (824)
                      +. ..++.                              ....+++|+.|+++++.  ....+|.+++++++|+.|++++ 
T Consensus       735 n~i~~lP~~~~l~~L~~L~l~~~~~~~l~~~~~~l~~~~~~~~~sL~~L~Ls~n~--~l~~lP~si~~L~~L~~L~Ls~-  811 (1153)
T PLN03210        735 TAIEEFPSNLRLENLDELILCEMKSEKLWERVQPLTPLMTMLSPSLTRLFLSDIP--SLVELPSSIQNLHKLEHLEIEN-  811 (1153)
T ss_pred             CccccccccccccccccccccccchhhccccccccchhhhhccccchheeCCCCC--CccccChhhhCCCCCCEEECCC-
Confidence            11 11111                              01123456666666654  4455677777888888888874 


Q ss_pred             CCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCC
Q 003387          674 SKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWL  753 (824)
Q Consensus       674 ~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l  753 (824)
                        +++++.+...  ..+++|+.|++++|......|.   ..++|+.|+|++|.+..  ++.....+++|+.|++.+|+.+
T Consensus       812 --C~~L~~LP~~--~~L~sL~~L~Ls~c~~L~~~p~---~~~nL~~L~Ls~n~i~~--iP~si~~l~~L~~L~L~~C~~L  882 (1153)
T PLN03210        812 --CINLETLPTG--INLESLESLDLSGCSRLRTFPD---ISTNISDLNLSRTGIEE--VPWWIEKFSNLSFLDMNGCNNL  882 (1153)
T ss_pred             --CCCcCeeCCC--CCccccCEEECCCCCccccccc---cccccCEeECCCCCCcc--ChHHHhcCCCCCEEECCCCCCc
Confidence              3345544221  2578899999999865444333   24689999999887764  5667788999999999999999


Q ss_pred             ccceeccCcccCccEEEEecCCCCCCCc
Q 003387          754 EEWTMGNAAMPKLECLIINPCAYLKKMP  781 (824)
Q Consensus       754 ~~l~~~~~~lp~L~~L~l~~c~~l~~lp  781 (824)
                      ..++.....+++|+.|++++|+.+..++
T Consensus       883 ~~l~~~~~~L~~L~~L~l~~C~~L~~~~  910 (1153)
T PLN03210        883 QRVSLNISKLKHLETVDFSDCGALTEAS  910 (1153)
T ss_pred             CccCcccccccCCCeeecCCCccccccc
Confidence            9999888899999999999999887543

syringae 6; Provisional

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

Probab=99.70  E-value=1.1e-18  Score=194.37  Aligned_cols=78  Identities=24%  Similarity=0.268  Sum_probs=46.8

Q ss_pred             CCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEE
Q 003387          690 PHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECL  769 (824)
Q Consensus       690 ~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L  769 (824)
                      ++.|+.|.+.+|.++....+.+.++++|+.|+|++|.+.. ........++.|+.|+|++|+ ++.+|.....++.|+.|
T Consensus       358 ~~~Lq~LylanN~Ltd~c~p~l~~~~hLKVLhLsyNrL~~-fpas~~~kle~LeeL~LSGNk-L~~Lp~tva~~~~L~tL  435 (1081)
T KOG0618|consen  358 HAALQELYLANNHLTDSCFPVLVNFKHLKVLHLSYNRLNS-FPASKLRKLEELEELNLSGNK-LTTLPDTVANLGRLHTL  435 (1081)
T ss_pred             hHHHHHHHHhcCcccccchhhhccccceeeeeeccccccc-CCHHHHhchHHhHHHhcccch-hhhhhHHHHhhhhhHHH
Confidence            3456667777777777777777777788888887775542 111223556677777777764 55555443333333333

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

Probab=99.67  E-value=2.5e-19  Score=181.53  Aligned_cols=260  Identities=20%  Similarity=0.195  Sum_probs=174.5

Q ss_pred             cccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCc
Q 003387          522 LLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSI  601 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~  601 (824)
                      -|..|++++|.++.+-+.+.++..|.+|++.++++.++|+++ +.+.+++.|+.+++++.++|+.++.+.+|++|+.++|
T Consensus        46 ~l~~lils~N~l~~l~~dl~nL~~l~vl~~~~n~l~~lp~ai-g~l~~l~~l~vs~n~ls~lp~~i~s~~~l~~l~~s~n  124 (565)
T KOG0472|consen   46 DLQKLILSHNDLEVLREDLKNLACLTVLNVHDNKLSQLPAAI-GELEALKSLNVSHNKLSELPEQIGSLISLVKLDCSSN  124 (565)
T ss_pred             chhhhhhccCchhhccHhhhcccceeEEEeccchhhhCCHHH-HHHHHHHHhhcccchHhhccHHHhhhhhhhhhhcccc
Confidence            455666666666666666666667777777777777777776 7777777777777777777777777777777766666


Q ss_pred             cCCCCCCC-CCCCCCCCCeeeccC-CCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCc
Q 003387          602 TLPAHPGK-FCGSLENLNFISALH-PCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRL  679 (824)
Q Consensus       602 ~~~~~~~p-~i~~L~~L~~l~~~~-~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L  679 (824)
                      .+.  .+| +++.+..|+.++..+ .....++.+..+..|..|.+.++   ...++|+..-+++.|++|+...|.    |
T Consensus       125 ~~~--el~~~i~~~~~l~dl~~~~N~i~slp~~~~~~~~l~~l~~~~n---~l~~l~~~~i~m~~L~~ld~~~N~----L  195 (565)
T KOG0472|consen  125 ELK--ELPDSIGRLLDLEDLDATNNQISSLPEDMVNLSKLSKLDLEGN---KLKALPENHIAMKRLKHLDCNSNL----L  195 (565)
T ss_pred             cee--ecCchHHHHhhhhhhhccccccccCchHHHHHHHHHHhhcccc---chhhCCHHHHHHHHHHhcccchhh----h
Confidence            665  334 666666666666552 22333333666667777766666   455555555557777777766542    2


Q ss_pred             cEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeec-CCCCCCccEEeeccCCCCcccee
Q 003387          680 SKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCG-SYGFPNLKVLHLKSMLWLEEWTM  758 (824)
Q Consensus       680 ~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~-~~~~~~L~~L~L~~~~~l~~l~~  758 (824)
                      +.+ ....+.+.+|..|+|..|.+.  ..+.|++|..|++|++..|.+..  ++.. ...+++|.+|++.+++ +++.|.
T Consensus       196 ~tl-P~~lg~l~~L~~LyL~~Nki~--~lPef~gcs~L~Elh~g~N~i~~--lpae~~~~L~~l~vLDLRdNk-lke~Pd  269 (565)
T KOG0472|consen  196 ETL-PPELGGLESLELLYLRRNKIR--FLPEFPGCSLLKELHVGENQIEM--LPAEHLKHLNSLLVLDLRDNK-LKEVPD  269 (565)
T ss_pred             hcC-ChhhcchhhhHHHHhhhcccc--cCCCCCccHHHHHHHhcccHHHh--hHHHHhcccccceeeeccccc-cccCch
Confidence            222 122345567777777777753  23478888888888888776543  2222 3467888888888876 788888


Q ss_pred             ccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          759 GNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       759 ~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ++.-+.+|+.|++++|. +..+|..++++ .|+.|-+.|+|
T Consensus       270 e~clLrsL~rLDlSNN~-is~Lp~sLgnl-hL~~L~leGNP  308 (565)
T KOG0472|consen  270 EICLLRSLERLDLSNND-ISSLPYSLGNL-HLKFLALEGNP  308 (565)
T ss_pred             HHHHhhhhhhhcccCCc-cccCCcccccc-eeeehhhcCCc
Confidence            88888888888888776 56788888888 88888888888

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

Probab=99.61  E-value=1.9e-17  Score=184.62  Aligned_cols=106  Identities=25%  Similarity=0.234  Sum_probs=85.6

Q ss_pred             CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCcc
Q 003387          688 LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLE  767 (824)
Q Consensus       688 ~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~  767 (824)
                      ..+.+|+.|+|++|.+...+-..+.+++.|++|+|++|++..  ++.....++.|++|...+|. +..+| ++..+|.|+
T Consensus       380 ~~~~hLKVLhLsyNrL~~fpas~~~kle~LeeL~LSGNkL~~--Lp~tva~~~~L~tL~ahsN~-l~~fP-e~~~l~qL~  455 (1081)
T KOG0618|consen  380 VNFKHLKVLHLSYNRLNSFPASKLRKLEELEELNLSGNKLTT--LPDTVANLGRLHTLRAHSNQ-LLSFP-ELAQLPQLK  455 (1081)
T ss_pred             ccccceeeeeecccccccCCHHHHhchHHhHHHhcccchhhh--hhHHHHhhhhhHHHhhcCCc-eeech-hhhhcCcce
Confidence            577899999999999865555668899999999999999876  55667889999999988765 77778 788899999


Q ss_pred             EEEEecCCCCCC--CccccccCccCcEEEecCCc
Q 003387          768 CLIINPCAYLKK--MPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       768 ~L~l~~c~~l~~--lp~~l~~l~~L~~L~l~~c~  799 (824)
                      .++++.|. ++.  +|..... ++|++|+++|++
T Consensus       456 ~lDlS~N~-L~~~~l~~~~p~-p~LkyLdlSGN~  487 (1081)
T KOG0618|consen  456 VLDLSCNN-LSEVTLPEALPS-PNLKYLDLSGNT  487 (1081)
T ss_pred             EEecccch-hhhhhhhhhCCC-cccceeeccCCc
Confidence            99999655 432  3443333 799999999998

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.53  E-value=2.9e-14  Score=164.72  Aligned_cols=234  Identities=20%  Similarity=0.101  Sum_probs=149.6

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCC
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGS  600 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~  600 (824)
                      ++|+.|++++|.++.+|..   +++|++|++++|.++.+|..    .++|+.|++++|.+..+|..   ..+|+.|++++
T Consensus       222 ~~L~~L~L~~N~Lt~LP~l---p~~Lk~LdLs~N~LtsLP~l----p~sL~~L~Ls~N~L~~Lp~l---p~~L~~L~Ls~  291 (788)
T PRK15387        222 AHITTLVIPDNNLTSLPAL---PPELRTLEVSGNQLTSLPVL----PPGLLELSIFSNPLTHLPAL---PSGLCKLWIFG  291 (788)
T ss_pred             cCCCEEEccCCcCCCCCCC---CCCCcEEEecCCccCcccCc----ccccceeeccCCchhhhhhc---hhhcCEEECcC
Confidence            3678888888888877753   46788888888888887753    35778888888877777753   35677888888


Q ss_pred             ccCCCCCCCCCCCCCCCCeeeccCCC-cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCc
Q 003387          601 ITLPAHPGKFCGSLENLNFISALHPC-CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRL  679 (824)
Q Consensus       601 ~~~~~~~~p~i~~L~~L~~l~~~~~~-~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L  679 (824)
                      |.+.  .+|.  .+++|+.|+++.+. ..++.   -..+|+.|++++|.   ...+|..   ..+|+.|++++|.    +
T Consensus       292 N~Lt--~LP~--~p~~L~~LdLS~N~L~~Lp~---lp~~L~~L~Ls~N~---L~~LP~l---p~~Lq~LdLS~N~----L  354 (788)
T PRK15387        292 NQLT--SLPV--LPPGLQELSVSDNQLASLPA---LPSELCKLWAYNNQ---LTSLPTL---PSGLQELSVSDNQ----L  354 (788)
T ss_pred             Cccc--cccc--cccccceeECCCCccccCCC---CcccccccccccCc---ccccccc---ccccceEecCCCc----c
Confidence            8776  4442  13567777777431 11111   12356677777663   2233321   1467888887762    3


Q ss_pred             cEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceec
Q 003387          680 SKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMG  759 (824)
Q Consensus       680 ~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~  759 (824)
                      +.+.    ..+++|+.|++++|.+.. +|..   .++|+.|++++|.+..  ++.   ..++|+.|++++|. +..+|..
T Consensus       355 s~LP----~lp~~L~~L~Ls~N~L~~-LP~l---~~~L~~LdLs~N~Lt~--LP~---l~s~L~~LdLS~N~-LssIP~l  420 (788)
T PRK15387        355 ASLP----TLPSELYKLWAYNNRLTS-LPAL---PSGLKELIVSGNRLTS--LPV---LPSELKELMVSGNR-LTSLPML  420 (788)
T ss_pred             CCCC----CCCcccceehhhcccccc-Cccc---ccccceEEecCCcccC--CCC---cccCCCEEEccCCc-CCCCCcc
Confidence            3321    123567777777777653 3322   3467788888777654  221   23578888888765 5666532


Q ss_pred             cCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          760 NAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       760 ~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                         +.+|+.|++++|. ++.+|..+.++++|+.|+++++|
T Consensus       421 ---~~~L~~L~Ls~Nq-Lt~LP~sl~~L~~L~~LdLs~N~  456 (788)
T PRK15387        421 ---PSGLLSLSVYRNQ-LTRLPESLIHLSSETTVNLEGNP  456 (788)
T ss_pred             ---hhhhhhhhhccCc-ccccChHHhhccCCCeEECCCCC
Confidence               3467778887766 45678777778888888888876

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.51  E-value=3.1e-14  Score=165.68  Aligned_cols=241  Identities=20%  Similarity=0.191  Sum_probs=130.2

Q ss_pred             ccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCcc
Q 003387          523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~  602 (824)
                      ..+|+++++.++.+|..+.  .+|+.|+|++|+++.+|..+ .  .+|++|++++|.++.+|..+.  .+|+.|++++|.
T Consensus       180 ~~~L~L~~~~LtsLP~~Ip--~~L~~L~Ls~N~LtsLP~~l-~--~nL~~L~Ls~N~LtsLP~~l~--~~L~~L~Ls~N~  252 (754)
T PRK15370        180 KTELRLKILGLTTIPACIP--EQITTLILDNNELKSLPENL-Q--GNIKTLYANSNQLTSIPATLP--DTIQEMELSINR  252 (754)
T ss_pred             ceEEEeCCCCcCcCCcccc--cCCcEEEecCCCCCcCChhh-c--cCCCEEECCCCccccCChhhh--ccccEEECcCCc
Confidence            4455555555555555443  24555555555555555544 2  355555555555555554332  245555555555


Q ss_pred             CCCCCCC-CCCCCCCCCeeeccCCC-cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCcc
Q 003387          603 LPAHPGK-FCGSLENLNFISALHPC-CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLS  680 (824)
Q Consensus       603 ~~~~~~p-~i~~L~~L~~l~~~~~~-~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~  680 (824)
                      +.  .+| .+.  ++|+.|+++.+. ..++..+  .++|+.|++++|.   ...+|..+.  ++|+.|++++|    +++
T Consensus       253 L~--~LP~~l~--s~L~~L~Ls~N~L~~LP~~l--~~sL~~L~Ls~N~---Lt~LP~~lp--~sL~~L~Ls~N----~Lt  317 (754)
T PRK15370        253 IT--ELPERLP--SALQSLDLFHNKISCLPENL--PEELRYLSVYDNS---IRTLPAHLP--SGITHLNVQSN----SLT  317 (754)
T ss_pred             cC--cCChhHh--CCCCEEECcCCccCcccccc--CCCCcEEECCCCc---cccCcccch--hhHHHHHhcCC----ccc
Confidence            44  333 222  234555554211 1111112  2367777776663   222332221  35666666655    233


Q ss_pred             EEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceecc
Q 003387          681 KIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGN  760 (824)
Q Consensus       681 ~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~  760 (824)
                      .+..   ..+++|+.|++++|.+.. +|..+  .++|+.|++++|.+..  ++..  -.++|++|+|++|. +..+|..+
T Consensus       318 ~LP~---~l~~sL~~L~Ls~N~Lt~-LP~~l--~~sL~~L~Ls~N~L~~--LP~~--lp~~L~~LdLs~N~-Lt~LP~~l  386 (754)
T PRK15370        318 ALPE---TLPPGLKTLEAGENALTS-LPASL--PPELQVLDVSKNQITV--LPET--LPPTITTLDVSRNA-LTNLPENL  386 (754)
T ss_pred             cCCc---cccccceeccccCCcccc-CChhh--cCcccEEECCCCCCCc--CChh--hcCCcCEEECCCCc-CCCCCHhH
Confidence            2211   123678888888887654 44443  3688888888777653  2221  23678888888875 56666433


Q ss_pred             CcccCccEEEEecCCCCCCCccccc----cCccCcEEEecCCc
Q 003387          761 AAMPKLECLIINPCAYLKKMPEQLW----YIKSLNKFDCWWPQ  799 (824)
Q Consensus       761 ~~lp~L~~L~l~~c~~l~~lp~~l~----~l~~L~~L~l~~c~  799 (824)
                        .++|+.|++++|. +..+|..+.    .++++..|++.++|
T Consensus       387 --~~sL~~LdLs~N~-L~~LP~sl~~~~~~~~~l~~L~L~~Np  426 (754)
T PRK15370        387 --PAALQIMQASRNN-LVRLPESLPHFRGEGPQPTRIIVEYNP  426 (754)
T ss_pred             --HHHHHHHhhccCC-cccCchhHHHHhhcCCCccEEEeeCCC
Confidence              2468888888776 446665443    34777888888877

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=99.49  E-value=1e-13  Score=160.18  Aligned_cols=260  Identities=18%  Similarity=0.084  Sum_probs=179.6

Q ss_pred             EEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCC
Q 003387          475 RLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIP  554 (824)
Q Consensus       475 ~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~  554 (824)
                      .|.+. +.....+|..+.++++.|.+.++....     ++   ...++|++|+|++|.++.+|..   .++|++|++++|
T Consensus       205 ~LdLs-~~~LtsLP~~l~~~L~~L~L~~N~Lt~-----LP---~lp~~Lk~LdLs~N~LtsLP~l---p~sL~~L~Ls~N  272 (788)
T PRK15387        205 VLNVG-ESGLTTLPDCLPAHITTLVIPDNNLTS-----LP---ALPPELRTLEVSGNQLTSLPVL---PPGLLELSIFSN  272 (788)
T ss_pred             EEEcC-CCCCCcCCcchhcCCCEEEccCCcCCC-----CC---CCCCCCcEEEecCCccCcccCc---ccccceeeccCC
Confidence            34444 333334666556678888888776542     11   2357899999999999988864   358899999999


Q ss_pred             CCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcC
Q 003387          555 SLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILG  634 (824)
Q Consensus       555 ~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~  634 (824)
                      .+..+|...    .+|+.|++++|.++.+|.   .+++|+.|++++|.+.  .+|.+  ..+|..|.+..+.  +.. +.
T Consensus       273 ~L~~Lp~lp----~~L~~L~Ls~N~Lt~LP~---~p~~L~~LdLS~N~L~--~Lp~l--p~~L~~L~Ls~N~--L~~-LP  338 (788)
T PRK15387        273 PLTHLPALP----SGLCKLWIFGNQLTSLPV---LPPGLQELSVSDNQLA--SLPAL--PSELCKLWAYNNQ--LTS-LP  338 (788)
T ss_pred             chhhhhhch----hhcCEEECcCCccccccc---cccccceeECCCCccc--cCCCC--cccccccccccCc--ccc-cc
Confidence            999888633    568889999999999986   3578999999999887  34421  1235555555321  111 22


Q ss_pred             CC-CccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccC
Q 003387          635 RL-PNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEK  713 (824)
Q Consensus       635 ~l-~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~  713 (824)
                      .+ .+|+.|+++++.   ...+|..   .++|+.|++++|    .+..+.    ..+++|+.|++++|.+.. +|..   
T Consensus       339 ~lp~~Lq~LdLS~N~---Ls~LP~l---p~~L~~L~Ls~N----~L~~LP----~l~~~L~~LdLs~N~Lt~-LP~l---  400 (788)
T PRK15387        339 TLPSGLQELSVSDNQ---LASLPTL---PSELYKLWAYNN----RLTSLP----ALPSGLKELIVSGNRLTS-LPVL---  400 (788)
T ss_pred             ccccccceEecCCCc---cCCCCCC---Ccccceehhhcc----ccccCc----ccccccceEEecCCcccC-CCCc---
Confidence            22 479999999874   3334432   246777887765    233221    123579999999998764 3332   


Q ss_pred             CCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCcccc
Q 003387          714 LPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQL  784 (824)
Q Consensus       714 l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l  784 (824)
                      .++|+.|++++|.+..  ++.   .+.+|+.|++++|. ++.+|..+..+++|+.|++++|+.....|..+
T Consensus       401 ~s~L~~LdLS~N~Lss--IP~---l~~~L~~L~Ls~Nq-Lt~LP~sl~~L~~L~~LdLs~N~Ls~~~~~~L  465 (788)
T PRK15387        401 PSELKELMVSGNRLTS--LPM---LPSGLLSLSVYRNQ-LTRLPESLIHLSSETTVNLEGNPLSERTLQAL  465 (788)
T ss_pred             ccCCCEEEccCCcCCC--CCc---chhhhhhhhhccCc-ccccChHHhhccCCCeEECCCCCCCchHHHHH
Confidence            3689999999998764  222   24578999999876 78899888899999999999999765555443

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

Probab=99.44  E-value=2.3e-15  Score=135.78  Aligned_cols=150  Identities=22%  Similarity=0.248  Sum_probs=113.8

Q ss_pred             ccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecC
Q 003387          519 MFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNF  598 (824)
Q Consensus       519 ~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L  598 (824)
                      .+.+...|-||.|.++.+|+.|..|.+|+.|++++|+++++|.++ +.+++|+.|++.-|.+..+|.+|+.++.|++||+
T Consensus        31 ~~s~ITrLtLSHNKl~~vppnia~l~nlevln~~nnqie~lp~~i-ssl~klr~lnvgmnrl~~lprgfgs~p~levldl  109 (264)
T KOG0617|consen   31 NMSNITRLTLSHNKLTVVPPNIAELKNLEVLNLSNNQIEELPTSI-SSLPKLRILNVGMNRLNILPRGFGSFPALEVLDL  109 (264)
T ss_pred             chhhhhhhhcccCceeecCCcHHHhhhhhhhhcccchhhhcChhh-hhchhhhheecchhhhhcCccccCCCchhhhhhc
Confidence            456677778888888888888888888888888888888888888 8888888888887888888888888888888888


Q ss_pred             CCccCCCCCCC-CCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEecc
Q 003387          599 GSITLPAHPGK-FCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANE  673 (824)
Q Consensus       599 ~~~~~~~~~~p-~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~  673 (824)
                      .+|.+....+| .+-.|+.|+-|+++.+.  ..+++ .+++++|+.|.+..+   ..-++|..++.++.|++|.+.+|
T Consensus       110 tynnl~e~~lpgnff~m~tlralyl~dndfe~lp~d-vg~lt~lqil~lrdn---dll~lpkeig~lt~lrelhiqgn  183 (264)
T KOG0617|consen  110 TYNNLNENSLPGNFFYMTTLRALYLGDNDFEILPPD-VGKLTNLQILSLRDN---DLLSLPKEIGDLTRLRELHIQGN  183 (264)
T ss_pred             cccccccccCCcchhHHHHHHHHHhcCCCcccCChh-hhhhcceeEEeeccC---chhhCcHHHHHHHHHHHHhcccc
Confidence            88887766777 66666777777766332  23444 777777777777665   55667777777777777777765

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=99.43  E-value=1.5e-13  Score=159.85  Aligned_cols=117  Identities=19%  Similarity=0.169  Sum_probs=76.3

Q ss_pred             eeEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeec
Q 003387          473 AKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLN  552 (824)
Q Consensus       473 ~r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~  552 (824)
                      ...+.+. +.....+|..+.++++.|.+.++....    ++...+   ++|++|++++|.++.+|..+.  .+|+.|+|+
T Consensus       180 ~~~L~L~-~~~LtsLP~~Ip~~L~~L~Ls~N~Lts----LP~~l~---~nL~~L~Ls~N~LtsLP~~l~--~~L~~L~Ls  249 (754)
T PRK15370        180 KTELRLK-ILGLTTIPACIPEQITTLILDNNELKS----LPENLQ---GNIKTLYANSNQLTSIPATLP--DTIQEMELS  249 (754)
T ss_pred             ceEEEeC-CCCcCcCCcccccCCcEEEecCCCCCc----CChhhc---cCCCEEECCCCccccCChhhh--ccccEEECc
Confidence            3445555 333333554445667777777765532    222222   467888888887777776554  367888888


Q ss_pred             CCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCC
Q 003387          553 IPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       553 ~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~  604 (824)
                      +|.+..+|..+ .  .+|++|++++|.+..+|..+.  ++|++|++++|.+.
T Consensus       250 ~N~L~~LP~~l-~--s~L~~L~Ls~N~L~~LP~~l~--~sL~~L~Ls~N~Lt  296 (754)
T PRK15370        250 INRITELPERL-P--SALQSLDLFHNKISCLPENLP--EELRYLSVYDNSIR  296 (754)
T ss_pred             CCccCcCChhH-h--CCCCEEECcCCccCccccccC--CCCcEEECCCCccc
Confidence            88887777766 3  467888888777777776553  47888888777765

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=99.36  E-value=7.7e-13  Score=156.41  Aligned_cols=281  Identities=24%  Similarity=0.213  Sum_probs=169.7

Q ss_pred             ccccc-CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc--CccCCcc-CCCCCcceEEeecCCC-CCccCh
Q 003387          487 CLDDY-DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV--LIQYPSG-IENLFLLRYLKLNIPS-LNSLPS  561 (824)
Q Consensus       487 ~~~~~-~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~--i~~lp~~-i~~l~~Lr~L~L~~~~-i~~lp~  561 (824)
                      .+... ....|...+.++....     . ..-..++.|++|-+.++.  +..++.. |..+++||+|+|++|. +.++|.
T Consensus       516 ~~~~~~~~~~rr~s~~~~~~~~-----~-~~~~~~~~L~tLll~~n~~~l~~is~~ff~~m~~LrVLDLs~~~~l~~LP~  589 (889)
T KOG4658|consen  516 IPQVKSWNSVRRMSLMNNKIEH-----I-AGSSENPKLRTLLLQRNSDWLLEISGEFFRSLPLLRVLDLSGNSSLSKLPS  589 (889)
T ss_pred             cccccchhheeEEEEeccchhh-----c-cCCCCCCccceEEEeecchhhhhcCHHHHhhCcceEEEECCCCCccCcCCh
Confidence            34444 6677888877766542     1 112334579999999986  5566654 6679999999999765 789999


Q ss_pred             hhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccC-----CCcchhhhcCC
Q 003387          562 SLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALH-----PCCCTEDILGR  635 (824)
Q Consensus       562 ~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~-----~~~~~~~~l~~  635 (824)
                      +| ++|-+|++|+++++.+..+|.++++|.+|.+||+..+.... .+| ....|++|++|.+..     ....+.+ +.+
T Consensus       590 ~I-~~Li~LryL~L~~t~I~~LP~~l~~Lk~L~~Lnl~~~~~l~-~~~~i~~~L~~Lr~L~l~~s~~~~~~~~l~e-l~~  666 (889)
T KOG4658|consen  590 SI-GELVHLRYLDLSDTGISHLPSGLGNLKKLIYLNLEVTGRLE-SIPGILLELQSLRVLRLPRSALSNDKLLLKE-LEN  666 (889)
T ss_pred             HH-hhhhhhhcccccCCCccccchHHHHHHhhheeccccccccc-cccchhhhcccccEEEeeccccccchhhHHh-hhc
Confidence            99 99999999999999999999999999999999998776543 346 445599999998763     2334555 677


Q ss_pred             CCccceEEEecccccchhhHHHHhccCCCCC----eEEEeccC---------CCCCccEEEeCccCc-------------
Q 003387          636 LPNLRNLRIRGDLSYNQSLLSKSLCRLSCLE----SLKLANES---------KMPRLSKIVLAEYLF-------------  689 (824)
Q Consensus       636 l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~----~L~l~~~~---------~~~~L~~l~l~~~~~-------------  689 (824)
                      +.+|+.|.+.....    .+...+..+..|.    .+.+....         ...+++.|.+..+..             
T Consensus       667 Le~L~~ls~~~~s~----~~~e~l~~~~~L~~~~~~l~~~~~~~~~~~~~~~~l~~L~~L~i~~~~~~e~~~~~~~~~~~  742 (889)
T KOG4658|consen  667 LEHLENLSITISSV----LLLEDLLGMTRLRSLLQSLSIEGCSKRTLISSLGSLGNLEELSILDCGISEIVIEWEESLIV  742 (889)
T ss_pred             ccchhhheeecchh----HhHhhhhhhHHHHHHhHhhhhcccccceeecccccccCcceEEEEcCCCchhhcccccccch
Confidence            77888777765531    1112222222222    12211100         233444444444311             


Q ss_pred             ---CCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeee---------cCCCCCCccEE-eeccCCCCccc
Q 003387          690 ---PHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTC---------GSYGFPNLKVL-HLKSMLWLEEW  756 (824)
Q Consensus       690 ---~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~---------~~~~~~~L~~L-~L~~~~~l~~l  756 (824)
                         ++++..+.+.+|... ..+.+.--.|+|+.|.+..|....+.++.         ..-.|+++..+ .+.+...+..+
T Consensus       743 ~~~f~~l~~~~~~~~~~~-r~l~~~~f~~~L~~l~l~~~~~~e~~i~~~k~~~~l~~~i~~f~~~~~l~~~~~l~~l~~i  821 (889)
T KOG4658|consen  743 LLCFPNLSKVSILNCHML-RDLTWLLFAPHLTSLSLVSCRLLEDIIPKLKALLELKELILPFNKLEGLRMLCSLGGLPQL  821 (889)
T ss_pred             hhhHHHHHHHHhhccccc-cccchhhccCcccEEEEecccccccCCCHHHHhhhcccEEecccccccceeeecCCCCcee
Confidence               223333333333211 11222234567777777766543322211         01234455555 35555555555


Q ss_pred             eeccCcccCccEEEEecCCCCCCCc
Q 003387          757 TMGNAAMPKLECLIINPCAYLKKMP  781 (824)
Q Consensus       757 ~~~~~~lp~L~~L~l~~c~~l~~lp  781 (824)
                      ....-.+++|+.+.+..||+++.+|
T Consensus       822 ~~~~l~~~~l~~~~ve~~p~l~~~P  846 (889)
T KOG4658|consen  822 YWLPLSFLKLEELIVEECPKLGKLP  846 (889)
T ss_pred             EecccCccchhheehhcCcccccCc
Confidence            4444456667777777777776665

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

Probab=99.35  E-value=2e-13  Score=147.31  Aligned_cols=265  Identities=20%  Similarity=0.128  Sum_probs=148.7

Q ss_pred             hhHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCCc-------cChhhhhcCCCccEeecCCcc
Q 003387          512 DWEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLNS-------LPSSLLSNLLNLYTLDMPFSY  579 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~~-------lp~~i~~~L~~L~~L~L~~~~  579 (824)
                      .....+..+..|++|+++++.++     .++..+...++|++|+++++.+..       ++..+ .++++|+.|++++|.
T Consensus        14 ~~~~~~~~l~~L~~l~l~~~~l~~~~~~~i~~~l~~~~~l~~l~l~~~~~~~~~~~~~~~~~~l-~~~~~L~~L~l~~~~   92 (319)
T cd00116          14 RATELLPKLLCLQVLRLEGNTLGEEAAKALASALRPQPSLKELCLSLNETGRIPRGLQSLLQGL-TKGCGLQELDLSDNA   92 (319)
T ss_pred             chHHHHHHHhhccEEeecCCCCcHHHHHHHHHHHhhCCCceEEeccccccCCcchHHHHHHHHH-HhcCceeEEEccCCC
Confidence            34567777788999999998874     466667777888899888877653       22334 678888888888886


Q ss_pred             cc-ccchhhhcccc---CceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCC-CccceEEEeccccc--ch
Q 003387          580 ID-HTADEFWKMNK---LRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRL-PNLRNLRIRGDLSY--NQ  652 (824)
Q Consensus       580 l~-~lp~~i~~L~~---L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l-~~L~~L~l~~~~~~--~~  652 (824)
                      +. ..+..+..+.+   |++|++++|.+....                  ...+...+..+ ++|+.|+++++.-.  ..
T Consensus        93 ~~~~~~~~~~~l~~~~~L~~L~ls~~~~~~~~------------------~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~  154 (319)
T cd00116          93 LGPDGCGVLESLLRSSSLQELKLNNNGLGDRG------------------LRLLAKGLKDLPPALEKLVLGRNRLEGASC  154 (319)
T ss_pred             CChhHHHHHHHHhccCcccEEEeeCCccchHH------------------HHHHHHHHHhCCCCceEEEcCCCcCCchHH
Confidence            65 34455555555   888888887664210                  01111124555 77788888777521  12


Q ss_pred             hhHHHHhccCCCCCeEEEeccCCCCCccEEEe----CccCcCCCceEEEEEcccCCCCC----cccccCCCCCCeEEeec
Q 003387          653 SLLSKSLCRLSCLESLKLANESKMPRLSKIVL----AEYLFPHSLTHLSFSNTDLMDDP----MPTLEKLPLLQVLKLKQ  724 (824)
Q Consensus       653 ~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l----~~~~~~~~L~~L~L~~~~l~~~~----~~~l~~l~~L~~L~L~~  724 (824)
                      ..++..+..+++|++|+++++.    ++.-.+    ..+..+++|+.|++++|.+.+..    ...+..+++|++|++++
T Consensus       155 ~~~~~~~~~~~~L~~L~l~~n~----l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~~~~~~L~~L~ls~  230 (319)
T cd00116         155 EALAKALRANRDLKELNLANNG----IGDAGIRALAEGLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNLGD  230 (319)
T ss_pred             HHHHHHHHhCCCcCEEECcCCC----CchHHHHHHHHHHHhCCCCCEEeccCCccChHHHHHHHHHhcccCCCCEEecCC
Confidence            3345556666677777776541    221000    01123356777777776654322    22344566777777776


Q ss_pred             cccCCCeeeecCC----CCCCccEEeeccCCCC----ccceeccCcccCccEEEEecCCCCCC----CccccccC-ccCc
Q 003387          725 NSYSGRKLTCGSY----GFPNLKVLHLKSMLWL----EEWTMGNAAMPKLECLIINPCAYLKK----MPEQLWYI-KSLN  791 (824)
Q Consensus       725 ~~~~~~~~~~~~~----~~~~L~~L~L~~~~~l----~~l~~~~~~lp~L~~L~l~~c~~l~~----lp~~l~~l-~~L~  791 (824)
                      |.+.+..+.....    ..+.|++|++++|...    ..+......+++|+.+++++|..-..    +...+... +.|+
T Consensus       231 n~l~~~~~~~l~~~~~~~~~~L~~L~l~~n~i~~~~~~~l~~~~~~~~~L~~l~l~~N~l~~~~~~~~~~~~~~~~~~~~  310 (319)
T cd00116         231 NNLTDAGAAALASALLSPNISLLTLSLSCNDITDDGAKDLAEVLAEKESLLELDLRGNKFGEEGAQLLAESLLEPGNELE  310 (319)
T ss_pred             CcCchHHHHHHHHHHhccCCCceEEEccCCCCCcHHHHHHHHHHhcCCCccEEECCCCCCcHHHHHHHHHHHhhcCCchh
Confidence            6654321111111    2356666666666421    11122233446666666666664422    22222333 4566


Q ss_pred             EEEecCCc
Q 003387          792 KFDCWWPQ  799 (824)
Q Consensus       792 ~L~l~~c~  799 (824)
                      .+++.+.|
T Consensus       311 ~~~~~~~~  318 (319)
T cd00116         311 SLWVKDDS  318 (319)
T ss_pred             hcccCCCC
Confidence            66655543

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).

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

Probab=99.35  E-value=1.6e-14  Score=130.37  Aligned_cols=159  Identities=26%  Similarity=0.372  Sum_probs=134.5

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      .+++..|.++.+...     ..+.-+..+.+|++|++++|.++.+|.+|+.++.||.|++.-|.+..+|..+ +.++-|+
T Consensus        32 ~s~ITrLtLSHNKl~-----~vppnia~l~nlevln~~nnqie~lp~~issl~klr~lnvgmnrl~~lprgf-gs~p~le  105 (264)
T KOG0617|consen   32 MSNITRLTLSHNKLT-----VVPPNIAELKNLEVLNLSNNQIEELPTSISSLPKLRILNVGMNRLNILPRGF-GSFPALE  105 (264)
T ss_pred             hhhhhhhhcccCcee-----ecCCcHHHhhhhhhhhcccchhhhcChhhhhchhhhheecchhhhhcCcccc-CCCchhh
Confidence            677777777776654     3445678899999999999999999999999999999999999999999998 9999999


Q ss_pred             EeecCCcccc--ccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEec
Q 003387          572 TLDMPFSYID--HTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRG  646 (824)
Q Consensus       572 ~L~L~~~~l~--~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~  646 (824)
                      +|||.+|++.  .+|..|..|+.|+-|+++.|.+.  .+| .+++|++|+.|.+..+  -..+.+ ++.++.|+.|.|.+
T Consensus       106 vldltynnl~e~~lpgnff~m~tlralyl~dndfe--~lp~dvg~lt~lqil~lrdndll~lpke-ig~lt~lrelhiqg  182 (264)
T KOG0617|consen  106 VLDLTYNNLNENSLPGNFFYMTTLRALYLGDNDFE--ILPPDVGKLTNLQILSLRDNDLLSLPKE-IGDLTRLRELHIQG  182 (264)
T ss_pred             hhhccccccccccCCcchhHHHHHHHHHhcCCCcc--cCChhhhhhcceeEEeeccCchhhCcHH-HHHHHHHHHHhccc
Confidence            9999999665  68999999999999999999887  667 9999999999998843  345566 99999999999999


Q ss_pred             ccccchhhHHHHhccC
Q 003387          647 DLSYNQSLLSKSLCRL  662 (824)
Q Consensus       647 ~~~~~~~~l~~~l~~l  662 (824)
                      +.   ...+|..++++
T Consensus       183 nr---l~vlppel~~l  195 (264)
T KOG0617|consen  183 NR---LTVLPPELANL  195 (264)
T ss_pred             ce---eeecChhhhhh
Confidence            84   44455555443

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

Probab=99.26  E-value=1.2e-12  Score=141.28  Aligned_cols=250  Identities=22%  Similarity=0.218  Sum_probs=168.9

Q ss_pred             EEEeeCccCc--cCCccCCCCCcceEEeecCCCCC-----ccChhhhhcCCCccEeecCCccccc-------cchhhhcc
Q 003387          525 VLDLGSLVLI--QYPSGIENLFLLRYLKLNIPSLN-----SLPSSLLSNLLNLYTLDMPFSYIDH-------TADEFWKM  590 (824)
Q Consensus       525 ~L~L~~~~i~--~lp~~i~~l~~Lr~L~L~~~~i~-----~lp~~i~~~L~~L~~L~L~~~~l~~-------lp~~i~~L  590 (824)
                      .|+|.++.++  ..+..+..+.+|++|+++++.++     .++..+ ...++|++|+++++.+..       ++..+..+
T Consensus         2 ~l~L~~~~l~~~~~~~~~~~l~~L~~l~l~~~~l~~~~~~~i~~~l-~~~~~l~~l~l~~~~~~~~~~~~~~~~~~l~~~   80 (319)
T cd00116           2 QLSLKGELLKTERATELLPKLLCLQVLRLEGNTLGEEAAKALASAL-RPQPSLKELCLSLNETGRIPRGLQSLLQGLTKG   80 (319)
T ss_pred             ccccccCcccccchHHHHHHHhhccEEeecCCCCcHHHHHHHHHHH-hhCCCceEEeccccccCCcchHHHHHHHHHHhc
Confidence            3566666654  45555666778999999999884     456665 788889999999886553       34557778


Q ss_pred             ccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccccc--chhhHHHHhccC-CCCCe
Q 003387          591 NKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSY--NQSLLSKSLCRL-SCLES  667 (824)
Q Consensus       591 ~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~--~~~~l~~~l~~l-~~L~~  667 (824)
                      ++|++|++++|.+... .                 ...+...... ++|+.|+++++.-.  ....+...+..+ ++|+.
T Consensus        81 ~~L~~L~l~~~~~~~~-~-----------------~~~~~~l~~~-~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~  141 (319)
T cd00116          81 CGLQELDLSDNALGPD-G-----------------CGVLESLLRS-SSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEK  141 (319)
T ss_pred             CceeEEEccCCCCChh-H-----------------HHHHHHHhcc-CcccEEEeeCCccchHHHHHHHHHHHhCCCCceE
Confidence            8999999988876420 0                 1111111223 56999999988521  123444566677 89999


Q ss_pred             EEEeccCCCCCccEEE----eCccCcCCCceEEEEEcccCCCCC----cccccCCCCCCeEEeeccccCCCe---eeecC
Q 003387          668 LKLANESKMPRLSKIV----LAEYLFPHSLTHLSFSNTDLMDDP----MPTLEKLPLLQVLKLKQNSYSGRK---LTCGS  736 (824)
Q Consensus       668 L~l~~~~~~~~L~~l~----l~~~~~~~~L~~L~L~~~~l~~~~----~~~l~~l~~L~~L~L~~~~~~~~~---~~~~~  736 (824)
                      |+++++.    ++.-.    ...+..+++|++|++++|.+.+..    +..+..+++|++|++++|.+.+..   +....
T Consensus       142 L~L~~n~----l~~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~  217 (319)
T cd00116         142 LVLGRNR----LEGASCEALAKALRANRDLKELNLANNGIGDAGIRALAEGLKANCNLEVLDLNNNGLTDEGASALAETL  217 (319)
T ss_pred             EEcCCCc----CCchHHHHHHHHHHhCCCcCEEECcCCCCchHHHHHHHHHHHhCCCCCEEeccCCccChHHHHHHHHHh
Confidence            9998762    22110    111245578999999999886533    233456789999999998876432   22345


Q ss_pred             CCCCCccEEeeccCCCCccce-ecc-C----cccCccEEEEecCCCCC----CCccccccCccCcEEEecCCc
Q 003387          737 YGFPNLKVLHLKSMLWLEEWT-MGN-A----AMPKLECLIINPCAYLK----KMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       737 ~~~~~L~~L~L~~~~~l~~l~-~~~-~----~lp~L~~L~l~~c~~l~----~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ..+++|++|++++|. +.... ..+ .    ..+.|+.|++.+|....    .++..+..+++|+.+++++++
T Consensus       218 ~~~~~L~~L~ls~n~-l~~~~~~~l~~~~~~~~~~L~~L~l~~n~i~~~~~~~l~~~~~~~~~L~~l~l~~N~  289 (319)
T cd00116         218 ASLKSLEVLNLGDNN-LTDAGAAALASALLSPNISLLTLSLSCNDITDDGAKDLAEVLAEKESLLELDLRGNK  289 (319)
T ss_pred             cccCCCCEEecCCCc-CchHHHHHHHHHHhccCCCceEEEccCCCCCcHHHHHHHHHHhcCCCccEEECCCCC
Confidence            678999999999986 44321 111 1    24899999999997542    334456677899999999988

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).

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

Probab=99.24  E-value=4.8e-13  Score=136.34  Aligned_cols=273  Identities=17%  Similarity=0.088  Sum_probs=178.3

Q ss_pred             ccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCcc-CCccCCCCCcceEEeecC-CCCCccChhh
Q 003387          486 ACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQ-YPSGIENLFLLRYLKLNI-PSLNSLPSSL  563 (824)
Q Consensus       486 ~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~-lp~~i~~l~~Lr~L~L~~-~~i~~lp~~i  563 (824)
                      ++|..+.+....+.+..+...    .+++..|+.++.||.|||+.|.|+. -|..|..|..|-.|-+.+ |+|+.+|...
T Consensus        60 eVP~~LP~~tveirLdqN~I~----~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~  135 (498)
T KOG4237|consen   60 EVPANLPPETVEIRLDQNQIS----SIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDLPKGA  135 (498)
T ss_pred             cCcccCCCcceEEEeccCCcc----cCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhhhhhH
Confidence            466666677777777777763    4788999999999999999999984 477888899998888777 8899999999


Q ss_pred             hhcCCCccEeecCCccccccch-hhhccccCceecCCCccCCCCCCC--CCCCCCCCCeeeccCCCcchhhhcCCCCccc
Q 003387          564 LSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITLPAHPGK--FCGSLENLNFISALHPCCCTEDILGRLPNLR  640 (824)
Q Consensus       564 ~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~~~~~~p--~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~  640 (824)
                      |++|..|+-|.+.-|.+..++. .+..|++|..|.+..|.+.  .++  .+..+.+++.+.+..+..  .. ..+++.+.
T Consensus       136 F~gL~slqrLllNan~i~Cir~~al~dL~~l~lLslyDn~~q--~i~~~tf~~l~~i~tlhlA~np~--ic-dCnL~wla  210 (498)
T KOG4237|consen  136 FGGLSSLQRLLLNANHINCIRQDALRDLPSLSLLSLYDNKIQ--SICKGTFQGLAAIKTLHLAQNPF--IC-DCNLPWLA  210 (498)
T ss_pred             hhhHHHHHHHhcChhhhcchhHHHHHHhhhcchhcccchhhh--hhccccccchhccchHhhhcCcc--cc-ccccchhh
Confidence            9999999999999998887764 4899999999988888775  444  566677777766552110  00 12222221


Q ss_pred             eE------EEecccc--------cchhhHHHHhccCCCCCeE--EEec--cC--CCCCccEEEeCccCcCCCceEEEEEc
Q 003387          641 NL------RIRGDLS--------YNQSLLSKSLCRLSCLESL--KLAN--ES--KMPRLSKIVLAEYLFPHSLTHLSFSN  700 (824)
Q Consensus       641 ~L------~l~~~~~--------~~~~~l~~~l~~l~~L~~L--~l~~--~~--~~~~L~~l~l~~~~~~~~L~~L~L~~  700 (824)
                      .-      ..++..-        .....+.+.=. ...++.+  .+..  +.  .+|      ...+..+++|++|+|++
T Consensus       211 ~~~a~~~ietsgarc~~p~rl~~~Ri~q~~a~kf-~c~~esl~s~~~~~d~~d~~cP------~~cf~~L~~L~~lnlsn  283 (498)
T KOG4237|consen  211 DDLAMNPIETSGARCVSPYRLYYKRINQEDARKF-LCSLESLPSRLSSEDFPDSICP------AKCFKKLPNLRKLNLSN  283 (498)
T ss_pred             hHHhhchhhcccceecchHHHHHHHhcccchhhh-hhhHHhHHHhhccccCcCCcCh------HHHHhhcccceEeccCC
Confidence            10      0000000        00000000000 0001111  0000  00  000      00125678889999999


Q ss_pred             ccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccc-eeccCcccCccEEEEecCCC
Q 003387          701 TDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEW-TMGNAAMPKLECLIINPCAY  776 (824)
Q Consensus       701 ~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l-~~~~~~lp~L~~L~l~~c~~  776 (824)
                      |+++..-..+|..+..+++|.|..|++.... ...+.++..|+.|+|.++. ++.+ |..+..+.+|..|.+-.||.
T Consensus       284 N~i~~i~~~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  284 NKITRIEDGAFEGAAELQELYLTRNKLEFVS-SGMFQGLSGLKTLSLYDNQ-ITTVAPGAFQTLFSLSTLNLLSNPF  358 (498)
T ss_pred             CccchhhhhhhcchhhhhhhhcCcchHHHHH-HHhhhccccceeeeecCCe-eEEEecccccccceeeeeehccCcc
Confidence            9887777788888888999999888764311 1234677888888888876 4433 44566677888888887775

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

Probab=99.14  E-value=2.6e-12  Score=131.03  Aligned_cols=270  Identities=16%  Similarity=0.134  Sum_probs=162.4

Q ss_pred             ccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCC-ccccccchh-hhccccCceecCC
Q 003387          523 LRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPF-SYIDHTADE-FWKMNKLRHLNFG  599 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~-~~l~~lp~~-i~~L~~L~~L~L~  599 (824)
                      -..+.|..|.|+.+|+ .|+.+++||.|+|+.|.|+.+.+..|..|.+|-+|-+.+ |+|+.+|.+ |+.|..|+.|.+.
T Consensus        69 tveirLdqN~I~~iP~~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~gL~slqrLllN  148 (498)
T KOG4237|consen   69 TVEIRLDQNQISSIPPGAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDLPKGAFGGLSSLQRLLLN  148 (498)
T ss_pred             ceEEEeccCCcccCChhhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhhhhhHhhhHHHHHHHhcC
Confidence            3567788888888875 467788888888888888887776668888877776666 688888866 7888888888887


Q ss_pred             CccCCCCCCC-CCCCCCCCCeeeccCCC-cch-hhhcCCCCccceEEEeccccc----------chhhHHHHhccCCCCC
Q 003387          600 SITLPAHPGK-FCGSLENLNFISALHPC-CCT-EDILGRLPNLRNLRIRGDLSY----------NQSLLSKSLCRLSCLE  666 (824)
Q Consensus       600 ~~~~~~~~~p-~i~~L~~L~~l~~~~~~-~~~-~~~l~~l~~L~~L~l~~~~~~----------~~~~l~~~l~~l~~L~  666 (824)
                      -|++.. ... .+..|++|..|.+.++. ..+ ...+..+.+++.+.+..+...          .....+..++......
T Consensus       149 an~i~C-ir~~al~dL~~l~lLslyDn~~q~i~~~tf~~l~~i~tlhlA~np~icdCnL~wla~~~a~~~ietsgarc~~  227 (498)
T KOG4237|consen  149 ANHINC-IRQDALRDLPSLSLLSLYDNKIQSICKGTFQGLAAIKTLHLAQNPFICDCNLPWLADDLAMNPIETSGARCVS  227 (498)
T ss_pred             hhhhcc-hhHHHHHHhhhcchhcccchhhhhhccccccchhccchHhhhcCccccccccchhhhHHhhchhhcccceecc
Confidence            777652 122 55556666555554211 111 112444555555554433200          0000011111111111


Q ss_pred             eEEEeccCCCCCccEEEeCcc-CcCCCceEEEEEcccCCCCC-cccccCCCCCCeEEeeccccCCCeeeecCCCCCCccE
Q 003387          667 SLKLANESKMPRLSKIVLAEY-LFPHSLTHLSFSNTDLMDDP-MPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKV  744 (824)
Q Consensus       667 ~L~l~~~~~~~~L~~l~l~~~-~~~~~L~~L~L~~~~l~~~~-~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~  744 (824)
                      ...+...    .+..++-..+ .....+.+=-.+.|...... ...|..||+|+.|+|++|+++.. -...+.+...++.
T Consensus       228 p~rl~~~----Ri~q~~a~kf~c~~esl~s~~~~~d~~d~~cP~~cf~~L~~L~~lnlsnN~i~~i-~~~aFe~~a~l~e  302 (498)
T KOG4237|consen  228 PYRLYYK----RINQEDARKFLCSLESLPSRLSSEDFPDSICPAKCFKKLPNLRKLNLSNNKITRI-EDGAFEGAAELQE  302 (498)
T ss_pred             hHHHHHH----HhcccchhhhhhhHHhHHHhhccccCcCCcChHHHHhhcccceEeccCCCccchh-hhhhhcchhhhhh
Confidence            1111100    0000000000 00111111112233322222 23478999999999999988763 2344667889999


Q ss_pred             EeeccCCCCcccee-ccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          745 LHLKSMLWLEEWTM-GNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       745 L~L~~~~~l~~l~~-~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      |.|..++ ++.+.. .+..+..|+.|++.+|....-.|..+..+.+|.+|++-.+|
T Consensus       303 L~L~~N~-l~~v~~~~f~~ls~L~tL~L~~N~it~~~~~aF~~~~~l~~l~l~~Np  357 (498)
T KOG4237|consen  303 LYLTRNK-LEFVSSGMFQGLSGLKTLSLYDNQITTVAPGAFQTLFSLSTLNLLSNP  357 (498)
T ss_pred             hhcCcch-HHHHHHHhhhccccceeeeecCCeeEEEecccccccceeeeeehccCc
Confidence            9999876 555532 35678899999999999877778889999999999998766

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

Probab=99.05  E-value=1e-10  Score=121.21  Aligned_cols=235  Identities=21%  Similarity=0.163  Sum_probs=152.0

Q ss_pred             CCCCcceEEeecCCCCCccCh--hhhhcCCCccEeecCCccc---cccchhhhccccCceecCCCccCCCCCCCCCCCCC
Q 003387          541 ENLFLLRYLKLNIPSLNSLPS--SLLSNLLNLYTLDMPFSYI---DHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLE  615 (824)
Q Consensus       541 ~~l~~Lr~L~L~~~~i~~lp~--~i~~~L~~L~~L~L~~~~l---~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~  615 (824)
                      .++..||...|.++.+...+.  .. ..|++++.|||+.|-+   ..+-.-..+|++|+.|+++.|.+..   | .    
T Consensus       118 sn~kkL~~IsLdn~~V~~~~~~~~~-k~~~~v~~LdLS~NL~~nw~~v~~i~eqLp~Le~LNls~Nrl~~---~-~----  188 (505)
T KOG3207|consen  118 SNLKKLREISLDNYRVEDAGIEEYS-KILPNVRDLDLSRNLFHNWFPVLKIAEQLPSLENLNLSSNRLSN---F-I----  188 (505)
T ss_pred             hhHHhhhheeecCccccccchhhhh-hhCCcceeecchhhhHHhHHHHHHHHHhcccchhcccccccccC---C-c----
Confidence            456677777777777665553  34 6788888888888733   3334446688888888888887742   1 0    


Q ss_pred             CCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceE
Q 003387          616 NLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTH  695 (824)
Q Consensus       616 ~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~  695 (824)
                                +...   -..+++|+.|.++.|.- +...+-..+..+++|+.|++..|.   .+ ...-....-+..|+.
T Consensus       189 ----------~s~~---~~~l~~lK~L~l~~CGl-s~k~V~~~~~~fPsl~~L~L~~N~---~~-~~~~~~~~i~~~L~~  250 (505)
T KOG3207|consen  189 ----------SSNT---TLLLSHLKQLVLNSCGL-SWKDVQWILLTFPSLEVLYLEANE---II-LIKATSTKILQTLQE  250 (505)
T ss_pred             ----------cccc---hhhhhhhheEEeccCCC-CHHHHHHHHHhCCcHHHhhhhccc---cc-ceecchhhhhhHHhh
Confidence                      0000   12467788888888852 355555666778888888888762   00 000111144677899


Q ss_pred             EEEEcccCCC-CCcccccCCCCCCeEEeeccccCCCeeeec-----CCCCCCccEEeeccCCCCcccee--ccCcccCcc
Q 003387          696 LSFSNTDLMD-DPMPTLEKLPLLQVLKLKQNSYSGRKLTCG-----SYGFPNLKVLHLKSMLWLEEWTM--GNAAMPKLE  767 (824)
Q Consensus       696 L~L~~~~l~~-~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~-----~~~~~~L~~L~L~~~~~l~~l~~--~~~~lp~L~  767 (824)
                      |+|++|.+.. ...+..+.||.|..|+++.|.+..-..+..     ...||+|++|++..|+ +.+|+.  .+..+++|+
T Consensus       251 LdLs~N~li~~~~~~~~~~l~~L~~Lnls~tgi~si~~~d~~s~~kt~~f~kL~~L~i~~N~-I~~w~sl~~l~~l~nlk  329 (505)
T KOG3207|consen  251 LDLSNNNLIDFDQGYKVGTLPGLNQLNLSSTGIASIAEPDVESLDKTHTFPKLEYLNISENN-IRDWRSLNHLRTLENLK  329 (505)
T ss_pred             ccccCCcccccccccccccccchhhhhccccCcchhcCCCccchhhhcccccceeeecccCc-cccccccchhhccchhh
Confidence            9999987644 334677899999999999887765433332     4579999999999987 555653  345678999


Q ss_pred             EEEEecCCCCCCC----ccccccCccCcEEEecCCcHHHH
Q 003387          768 CLIINPCAYLKKM----PEQLWYIKSLNKFDCWWPQPELR  803 (824)
Q Consensus       768 ~L~l~~c~~l~~l----p~~l~~l~~L~~L~l~~c~~~l~  803 (824)
                      .|.+..++..+.-    -..+..+++|..|+=.+|.+..+
T Consensus       330 ~l~~~~n~ln~e~~~a~~~VIAr~~~l~~LN~~di~p~eR  369 (505)
T KOG3207|consen  330 HLRITLNYLNKETDTAKLLVIARISQLVKLNDVDISPNER  369 (505)
T ss_pred             hhhcccccccccccceeEEeeeehhhhhhhcccccChHHh
Confidence            9998877754321    11344556666666555654443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.94  E-value=6.8e-08  Score=107.33  Aligned_cols=117  Identities=15%  Similarity=0.161  Sum_probs=85.5

Q ss_pred             CCCCceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC--ceeEEEECCCCCCCCHHHHH
Q 003387          154 KSRDTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF--DCHAWITEPYSNEYDADQIL  229 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~~~vs~~~~~~~~~  229 (824)
                      .++.++||++++++|...+...  ......+.|+|++|+||||+++.++++  .....  -.++++.  .....+...++
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~--l~~~~~~~~~v~in--~~~~~~~~~~~  103 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEE--LEEIAVKVVYVYIN--CQIDRTRYAIF  103 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHH--HHHhcCCcEEEEEE--CCcCCCHHHHH
Confidence            4568999999999999998553  223455789999999999999999984  33322  3455665  66667788999


Q ss_pred             HHHHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCCh
Q 003387          230 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSI  276 (824)
Q Consensus       230 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~  276 (824)
                      .+|+.++..... + ....+.++....+.+.++  ++..+||+|+++..
T Consensus       104 ~~i~~~l~~~~~-~-~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l  150 (394)
T PRK00411        104 SEIARQLFGHPP-P-SSGLSFDELFDKIAEYLDERDRVLIVALDDINYL  150 (394)
T ss_pred             HHHHHHhcCCCC-C-CCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHh
Confidence            999999976221 1 122345667777777775  45789999999864

>KOG4341 consensus F-box protein containing LRR [General function prediction only]

Probab=98.93  E-value=6.3e-11  Score=122.17  Aligned_cols=121  Identities=21%  Similarity=0.302  Sum_probs=84.4

Q ss_pred             cCCCceEEEEEccc-CCCCCccccc-CCCCCCeEEeeccccCCCe-eeecCCCCCCccEEeeccCCCCccc-----eecc
Q 003387          689 FPHSLTHLSFSNTD-LMDDPMPTLE-KLPLLQVLKLKQNSYSGRK-LTCGSYGFPNLKVLHLKSMLWLEEW-----TMGN  760 (824)
Q Consensus       689 ~~~~L~~L~L~~~~-l~~~~~~~l~-~l~~L~~L~L~~~~~~~~~-~~~~~~~~~~L~~L~L~~~~~l~~l-----~~~~  760 (824)
                      .+++|+.|.++.|+ ++......++ +++.|+.+++..+....+. +.....++|.|+.|.+++|..++.-     ...-
T Consensus       318 ~~~~L~~l~l~~c~~fsd~~ft~l~rn~~~Le~l~~e~~~~~~d~tL~sls~~C~~lr~lslshce~itD~gi~~l~~~~  397 (483)
T KOG4341|consen  318 HCHNLQVLELSGCQQFSDRGFTMLGRNCPHLERLDLEECGLITDGTLASLSRNCPRLRVLSLSHCELITDEGIRHLSSSS  397 (483)
T ss_pred             CCCceEEEeccccchhhhhhhhhhhcCChhhhhhcccccceehhhhHhhhccCCchhccCChhhhhhhhhhhhhhhhhcc
Confidence            44666666666664 3333344443 6788888888876544322 4444567899999999988766544     3334


Q ss_pred             CcccCccEEEEecCCCCCC-CccccccCccCcEEEecCCcHHHHHHHhhc
Q 003387          761 AAMPKLECLIINPCAYLKK-MPEQLWYIKSLNKFDCWWPQPELRQKLREF  809 (824)
Q Consensus       761 ~~lp~L~~L~l~~c~~l~~-lp~~l~~l~~L~~L~l~~c~~~l~~~~~~~  809 (824)
                      ..+..|+.+.+++||.+.. .-..+..+++|+.+++.+|..-.++.+++.
T Consensus       398 c~~~~l~~lEL~n~p~i~d~~Le~l~~c~~Leri~l~~~q~vtk~~i~~~  447 (483)
T KOG4341|consen  398 CSLEGLEVLELDNCPLITDATLEHLSICRNLERIELIDCQDVTKEAISRF  447 (483)
T ss_pred             ccccccceeeecCCCCchHHHHHHHhhCcccceeeeechhhhhhhhhHHH
Confidence            5678899999999998753 334577889999999999997777777763

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

Probab=98.91  E-value=1.8e-09  Score=102.89  Aligned_cols=130  Identities=22%  Similarity=0.252  Sum_probs=47.5

Q ss_pred             cccCcccEEEeeCccCccCCccCC-CCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhh-hccccCce
Q 003387          518 GMFKLLRVLDLGSLVLIQYPSGIE-NLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEF-WKMNKLRH  595 (824)
Q Consensus       518 ~~~~~Lr~L~L~~~~i~~lp~~i~-~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i-~~L~~L~~  595 (824)
                      .+...+|.|+|+|+.|+.+. .++ .+.+|+.|+|++|.|+.++. + ..|++|++|++++|.++.+++.+ ..+++|++
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~~~l~~~lp~L~~   92 (175)
T PF14580_consen   16 NNPVKLRELNLRGNQISTIE-NLGATLDKLEVLDLSNNQITKLEG-L-PGLPRLKTLDLSNNRISSISEGLDKNLPNLQE   92 (175)
T ss_dssp             ---------------------S--TT-TT--EEE-TTS--S--TT------TT--EEE--SS---S-CHHHHHH-TT--E
T ss_pred             cccccccccccccccccccc-chhhhhcCCCEEECCCCCCccccC-c-cChhhhhhcccCCCCCCccccchHHhCCcCCE
Confidence            34456788999999888664 465 57889999999999888864 4 78899999999999888887665 36889999


Q ss_pred             ecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccc-hhhHHHHhccCCCCCeEEEe
Q 003387          596 LNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYN-QSLLSKSLCRLSCLESLKLA  671 (824)
Q Consensus       596 L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~-~~~l~~~l~~l~~L~~L~l~  671 (824)
                      |++++|.+..                    ...+.. +..+++|+.|++.++.-.. ...-...+..+++|+.|+-.
T Consensus        93 L~L~~N~I~~--------------------l~~l~~-L~~l~~L~~L~L~~NPv~~~~~YR~~vi~~lP~Lk~LD~~  148 (175)
T PF14580_consen   93 LYLSNNKISD--------------------LNELEP-LSSLPKLRVLSLEGNPVCEKKNYRLFVIYKLPSLKVLDGQ  148 (175)
T ss_dssp             EE-TTS---S--------------------CCCCGG-GGG-TT--EEE-TT-GGGGSTTHHHHHHHH-TT-SEETTE
T ss_pred             EECcCCcCCC--------------------hHHhHH-HHcCCCcceeeccCCcccchhhHHHHHHHHcChhheeCCE
Confidence            9998887752                    111222 6677788888887765221 12223455566777766543

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

Probab=98.89  E-value=1.8e-10  Score=113.59  Aligned_cols=182  Identities=20%  Similarity=0.221  Sum_probs=107.7

Q ss_pred             CccEeecCCcccc--ccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEec
Q 003387          569 NLYTLDMPFSYID--HTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRG  646 (824)
Q Consensus       569 ~L~~L~L~~~~l~--~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~  646 (824)
                      .||+|||+...++  .+..-+..+.+|+.|.+.++.+..                     ..... +.+-.+|+.|+++.
T Consensus       186 Rlq~lDLS~s~it~stl~~iLs~C~kLk~lSlEg~~LdD---------------------~I~~~-iAkN~~L~~lnlsm  243 (419)
T KOG2120|consen  186 RLQHLDLSNSVITVSTLHGILSQCSKLKNLSLEGLRLDD---------------------PIVNT-IAKNSNLVRLNLSM  243 (419)
T ss_pred             hhHHhhcchhheeHHHHHHHHHHHHhhhhccccccccCc---------------------HHHHH-Hhccccceeecccc
Confidence            3777777776544  444446677777777666666542                     22222 56667788888887


Q ss_pred             ccccchhhHHHHhccCCCCCeEEEeccCCC-CCccEEEeCccCcCCCceEEEEEccc--CCCCCccc-ccCCCCCCeEEe
Q 003387          647 DLSYNQSLLSKSLCRLSCLESLKLANESKM-PRLSKIVLAEYLFPHSLTHLSFSNTD--LMDDPMPT-LEKLPLLQVLKL  722 (824)
Q Consensus       647 ~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~-~~L~~l~l~~~~~~~~L~~L~L~~~~--l~~~~~~~-l~~l~~L~~L~L  722 (824)
                      +......+..-.+.+|+.|.+|+|+|++.. +..+.+ +.  .--++|+.|+|++|.  +....... ...+|+|.+|+|
T Consensus       244 ~sG~t~n~~~ll~~scs~L~~LNlsWc~l~~~~Vtv~-V~--hise~l~~LNlsG~rrnl~~sh~~tL~~rcp~l~~LDL  320 (419)
T KOG2120|consen  244 CSGFTENALQLLLSSCSRLDELNLSWCFLFTEKVTVA-VA--HISETLTQLNLSGYRRNLQKSHLSTLVRRCPNLVHLDL  320 (419)
T ss_pred             ccccchhHHHHHHHhhhhHhhcCchHhhccchhhhHH-Hh--hhchhhhhhhhhhhHhhhhhhHHHHHHHhCCceeeecc
Confidence            776666666666777788888888875411 011100 00  112456666666663  11122222 236778888888


Q ss_pred             eccccCCCeeeecCCCCCCccEEeeccCCCCcc-ceeccCcccCccEEEEecCC
Q 003387          723 KQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEE-WTMGNAAMPKLECLIINPCA  775 (824)
Q Consensus       723 ~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~-l~~~~~~lp~L~~L~l~~c~  775 (824)
                      ++|.-........+..|+.|++|.++.|..+.. --..+..+|+|..|++.+|-
T Consensus       321 SD~v~l~~~~~~~~~kf~~L~~lSlsRCY~i~p~~~~~l~s~psl~yLdv~g~v  374 (419)
T KOG2120|consen  321 SDSVMLKNDCFQEFFKFNYLQHLSLSRCYDIIPETLLELNSKPSLVYLDVFGCV  374 (419)
T ss_pred             ccccccCchHHHHHHhcchheeeehhhhcCCChHHeeeeccCcceEEEEecccc
Confidence            766433323334456778888888888764431 22346677888888888775

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

Probab=98.82  E-value=1.5e-10  Score=123.58  Aligned_cols=153  Identities=24%  Similarity=0.257  Sum_probs=122.7

Q ss_pred             hHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhcccc
Q 003387          513 WEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNK  592 (824)
Q Consensus       513 ~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~  592 (824)
                      ++.-+..|..|..|.|+.|.+..+|..++++..|.||+|+.|++..+|..+ +.|+ |+.|-+++|+++.+|+.++.++.
T Consensus        90 lp~~~~~f~~Le~liLy~n~~r~ip~~i~~L~~lt~l~ls~NqlS~lp~~l-C~lp-Lkvli~sNNkl~~lp~~ig~~~t  167 (722)
T KOG0532|consen   90 LPEEACAFVSLESLILYHNCIRTIPEAICNLEALTFLDLSSNQLSHLPDGL-CDLP-LKVLIVSNNKLTSLPEEIGLLPT  167 (722)
T ss_pred             CchHHHHHHHHHHHHHHhccceecchhhhhhhHHHHhhhccchhhcCChhh-hcCc-ceeEEEecCccccCCcccccchh
Confidence            345556667778888888888888888888888888888888888888887 6665 88888888888888888888888


Q ss_pred             CceecCCCccCCCCCCC-CCCCCCCCCeeeccC--CCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEE
Q 003387          593 LRHLNFGSITLPAHPGK-FCGSLENLNFISALH--PCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLK  669 (824)
Q Consensus       593 L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~--~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~  669 (824)
                      |.+||.+.|.+.  .+| .++.|.+|+.+.+..  ....+++ +..|+ |.+|+++++   ....+|..+.++++|++|.
T Consensus       168 l~~ld~s~nei~--slpsql~~l~slr~l~vrRn~l~~lp~E-l~~Lp-Li~lDfScN---kis~iPv~fr~m~~Lq~l~  240 (722)
T KOG0532|consen  168 LAHLDVSKNEIQ--SLPSQLGYLTSLRDLNVRRNHLEDLPEE-LCSLP-LIRLDFSCN---KISYLPVDFRKMRHLQVLQ  240 (722)
T ss_pred             HHHhhhhhhhhh--hchHHhhhHHHHHHHHHhhhhhhhCCHH-HhCCc-eeeeecccC---ceeecchhhhhhhhheeee
Confidence            888888888776  556 888888888877762  3445566 77665 889999988   6788899999999999999


Q ss_pred             EeccC
Q 003387          670 LANES  674 (824)
Q Consensus       670 l~~~~  674 (824)
                      |.+|.
T Consensus       241 LenNP  245 (722)
T KOG0532|consen  241 LENNP  245 (722)
T ss_pred             eccCC
Confidence            99874

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=98.81  E-value=4.2e-10  Score=113.83  Aligned_cols=254  Identities=18%  Similarity=0.145  Sum_probs=159.4

Q ss_pred             hhHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCC----CCccChhh------hhcCCCccEeecC
Q 003387          512 DWEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPS----LNSLPSSL------LSNLLNLYTLDMP  576 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~----i~~lp~~i------~~~L~~L~~L~L~  576 (824)
                      ........+..+..|+|+||.+.     .+-+.+.+.++|+.-+++.--    ..++|+.+      +-.+++|++||||
T Consensus        21 ~v~~~~~~~~s~~~l~lsgnt~G~EAa~~i~~~L~~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~L~~ldLS  100 (382)
T KOG1909|consen   21 DVEEELEPMDSLTKLDLSGNTFGTEAARAIAKVLASKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPKLQKLDLS  100 (382)
T ss_pred             hHHHHhcccCceEEEeccCCchhHHHHHHHHHHHhhcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCceeEeecc
Confidence            34456677888899999998875     445566677788888888632    22455433      2467799999999


Q ss_pred             Ccccc--ccc---hhhhccccCceecCCCccCCCCCCCCCCCCCC-CCeeeccCCCcchhhhcCCCCccceEEEecccc-
Q 003387          577 FSYID--HTA---DEFWKMNKLRHLNFGSITLPAHPGKFCGSLEN-LNFISALHPCCCTEDILGRLPNLRNLRIRGDLS-  649 (824)
Q Consensus       577 ~~~l~--~lp---~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~-L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~-  649 (824)
                      .|-+.  .++   +-+.++..|++|+|.+|-+...   +=+.+.. |.++...       ...+.-++|+.+....+.- 
T Consensus       101 DNA~G~~g~~~l~~ll~s~~~L~eL~L~N~Glg~~---ag~~l~~al~~l~~~-------kk~~~~~~Lrv~i~~rNrle  170 (382)
T KOG1909|consen  101 DNAFGPKGIRGLEELLSSCTDLEELYLNNCGLGPE---AGGRLGRALFELAVN-------KKAASKPKLRVFICGRNRLE  170 (382)
T ss_pred             ccccCccchHHHHHHHHhccCHHHHhhhcCCCChh---HHHHHHHHHHHHHHH-------hccCCCcceEEEEeeccccc
Confidence            98432  332   3367889999999988876421   0001100 2222111       1145556788888777762 


Q ss_pred             -cchhhHHHHhccCCCCCeEEEeccC-CCCCccEEEeCccCcCCCceEEEEEcccCCCCC----cccccCCCCCCeEEee
Q 003387          650 -YNQSLLSKSLCRLSCLESLKLANES-KMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDP----MPTLEKLPLLQVLKLK  723 (824)
Q Consensus       650 -~~~~~l~~~l~~l~~L~~L~l~~~~-~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~----~~~l~~l~~L~~L~L~  723 (824)
                       .....+...+...+.|+.+.+..|. .++.. .+-..++..+++|+.|+|..|.++...    ...+..+|+|++|+++
T Consensus       171 n~ga~~~A~~~~~~~~leevr~~qN~I~~eG~-~al~eal~~~~~LevLdl~DNtft~egs~~LakaL~s~~~L~El~l~  249 (382)
T KOG1909|consen  171 NGGATALAEAFQSHPTLEEVRLSQNGIRPEGV-TALAEALEHCPHLEVLDLRDNTFTLEGSVALAKALSSWPHLRELNLG  249 (382)
T ss_pred             cccHHHHHHHHHhccccceEEEecccccCchh-HHHHHHHHhCCcceeeecccchhhhHHHHHHHHHhcccchheeeccc
Confidence             2234455666777888888888764 12222 122223366788888888888775433    2345678889999999


Q ss_pred             ccccCCCeee----ecCCCCCCccEEeeccCCCCcc----ceeccCcccCccEEEEecCCC
Q 003387          724 QNSYSGRKLT----CGSYGFPNLKVLHLKSMLWLEE----WTMGNAAMPKLECLIINPCAY  776 (824)
Q Consensus       724 ~~~~~~~~~~----~~~~~~~~L~~L~L~~~~~l~~----l~~~~~~lp~L~~L~l~~c~~  776 (824)
                      +|.+....-.    ....++|+|++|.+.+|..-..    +.......|.|++|+|++|..
T Consensus       250 dcll~~~Ga~a~~~al~~~~p~L~vl~l~gNeIt~da~~~la~~~~ek~dL~kLnLngN~l  310 (382)
T KOG1909|consen  250 DCLLENEGAIAFVDALKESAPSLEVLELAGNEITRDAALALAACMAEKPDLEKLNLNGNRL  310 (382)
T ss_pred             ccccccccHHHHHHHHhccCCCCceeccCcchhHHHHHHHHHHHHhcchhhHHhcCCcccc
Confidence            8877653211    1124589999999988763221    122344589999999999985

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

Probab=98.80  E-value=7.8e-10  Score=114.86  Aligned_cols=42  Identities=24%  Similarity=0.227  Sum_probs=17.8

Q ss_pred             hhcccCcccEEEeeCccCc---cCCccCCCCCcceEEeecCCCCC
Q 003387          516 FCGMFKLLRVLDLGSLVLI---QYPSGIENLFLLRYLKLNIPSLN  557 (824)
Q Consensus       516 ~~~~~~~Lr~L~L~~~~i~---~lp~~i~~l~~Lr~L~L~~~~i~  557 (824)
                      ....|+++|.|||+.|-+.   .+-+-+..|++|+.|+|+.|.+.
T Consensus       141 ~~k~~~~v~~LdLS~NL~~nw~~v~~i~eqLp~Le~LNls~Nrl~  185 (505)
T KOG3207|consen  141 YSKILPNVRDLDLSRNLFHNWFPVLKIAEQLPSLENLNLSSNRLS  185 (505)
T ss_pred             hhhhCCcceeecchhhhHHhHHHHHHHHHhcccchhccccccccc
Confidence            3344455555555544433   11122233444444454444433

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.79  E-value=1.6e-07  Score=116.40  Aligned_cols=268  Identities=15%  Similarity=0.160  Sum_probs=156.3

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC-CCCHHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN-EYDADQILDIVIK  234 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~-~~~~~~~~~~i~~  234 (824)
                      ..++-|+    +|.+.|... ...+++.|.|++|.||||++......      ++.++|++  +.. +-+...+...++.
T Consensus        14 ~~~~~R~----rl~~~l~~~-~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~--l~~~d~~~~~f~~~l~~   80 (903)
T PRK04841         14 HNTVVRE----RLLAKLSGA-NNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYS--LDESDNQPERFASYLIA   80 (903)
T ss_pred             cccCcch----HHHHHHhcc-cCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEe--cCcccCCHHHHHHHHHH
Confidence            3444454    455555443 35789999999999999999998752      23689999  864 3466667777777


Q ss_pred             HhCCCCCc--cc-------ccccCHHHHHHHHHHhcC--CCeEEEEEecCCChh--h-HHHHHhhCCCCCCCcEEEEEec
Q 003387          235 FLMPSSRL--SE-------IMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSID--M-WDVIQEILPDNQNGSRVLITLT  300 (824)
Q Consensus       235 ~l~~~~~~--~~-------~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~~--~-~~~l~~~~~~~~~gs~ilvTtR  300 (824)
                      .+......  +.       ....+.......+...+.  +.+++|||||+...+  . .+.+...++....+-++|||||
T Consensus        81 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR  160 (903)
T PRK04841         81 ALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSR  160 (903)
T ss_pred             HHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeC
Confidence            77421110  00       011223333444444443  689999999997542  2 2233333334445678889999


Q ss_pred             hHH---HHh---------------hcccccC-----CcCc-CccccchhhHHHhcCCCchhHHHHHhHHHhhh-----hh
Q 003387          301 DIR---III---------------SFQFEDG-----ENMR-LDLVPTGGPLRATYKGRPFLILYHGSISLEEN-----IR  351 (824)
Q Consensus       301 ~~~---v~~---------------~f~~~~~-----~~~~-~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~-----~~  351 (824)
                      ...   ...               .|...+.     .... +--.+...+|.+.|+|.|+++..++..+....     ..
T Consensus       161 ~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~~~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~~~~~~  240 (903)
T PRK04841        161 NLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSPIEAAESSRLCDDVEGWATALQLIALSARQNNSSLHDSA  240 (903)
T ss_pred             CCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCCCCHHHHHHHHHHhCChHHHHHHHHHHHhhCCCchhhhh
Confidence            831   111               1221110     0001 11234567899999999999998876652111     11


Q ss_pred             hhccC-CC-ccccccc---c-cCCCCchHHHhHhccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHHHHHhccccc
Q 003387          352 EAVET-PL-GLRYIKC---L-MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVE  425 (824)
Q Consensus       352 ~~~~~-~~-~~~~~l~---~-~L~~~lk~cfl~~s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~~Lv~rsllq  425 (824)
                      +.+.. .. .+...+.   + .||+..+..++..|+++.   ++. .+...-.  |      .+.+...+++|.+.+++.
T Consensus       241 ~~~~~~~~~~~~~~l~~~v~~~l~~~~~~~l~~~a~~~~---~~~-~l~~~l~--~------~~~~~~~L~~l~~~~l~~  308 (903)
T PRK04841        241 RRLAGINASHLSDYLVEEVLDNVDLETRHFLLRCSVLRS---MND-ALIVRVT--G------EENGQMRLEELERQGLFI  308 (903)
T ss_pred             HhhcCCCchhHHHHHHHHHHhcCCHHHHHHHHHhccccc---CCH-HHHHHHc--C------CCcHHHHHHHHHHCCCee
Confidence            12211 11 2333221   2 899999999999999873   342 2222111  1      123578899999999875


Q ss_pred             eeecCCCCcEEEEEcCccHHHHHHhh
Q 003387          426 AKKRKAGGTINTCSIPGRWRPVLHTV  451 (824)
Q Consensus       426 ~~~~~~~g~~~~~~mHdlv~dla~~~  451 (824)
                      ..... .+  ..|+.|++++++.+.-
T Consensus       309 ~~~~~-~~--~~yr~H~L~r~~l~~~  331 (903)
T PRK04841        309 QRMDD-SG--EWFRYHPLFASFLRHR  331 (903)
T ss_pred             EeecC-CC--CEEehhHHHHHHHHHH
Confidence            43211 11  3477899999998764

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.79  E-value=9.4e-07  Score=97.13  Aligned_cols=117  Identities=18%  Similarity=0.097  Sum_probs=83.0

Q ss_pred             CCCceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC------ceeEEEECCCCCCCCHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF------DCHAWITEPYSNEYDAD  226 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F------~~~~wv~~~vs~~~~~~  226 (824)
                      ++.++||++++++|...|...  ......+.|+|++|+|||++++.++++  .....      -..+|+.  .....+..
T Consensus        14 p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~--l~~~~~~~~~~~~~v~in--~~~~~~~~   89 (365)
T TIGR02928        14 PDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKE--LEEAAEDRDVRVVTVYVN--CQILDTLY   89 (365)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHH--HHHHhhccCCceEEEEEE--CCCCCCHH
Confidence            458999999999999998752  223457899999999999999999983  32211      1356776  77666788


Q ss_pred             HHHHHHHHHhCC-CCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCCh
Q 003387          227 QILDIVIKFLMP-SSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSI  276 (824)
Q Consensus       227 ~~~~~i~~~l~~-~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~  276 (824)
                      .++..|+.++.. ....+ ....+..+....+.+.+.  +++++||||+++..
T Consensus        90 ~~~~~i~~~l~~~~~~~~-~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L  141 (365)
T TIGR02928        90 QVLVELANQLRGSGEEVP-TTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYL  141 (365)
T ss_pred             HHHHHHHHHHhhcCCCCC-CCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhh
Confidence            899999999942 11111 122344556666666663  56899999999866

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.

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

Probab=98.78  E-value=1.7e-09  Score=106.69  Aligned_cols=128  Identities=25%  Similarity=0.357  Sum_probs=70.1

Q ss_pred             hcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEE
Q 003387          565 SNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRI  644 (824)
Q Consensus       565 ~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l  644 (824)
                      ...+.|++|||++|.++.+-+++.-+|+++.|++++|.+..                       +.. +..+++|..|++
T Consensus       281 dTWq~LtelDLS~N~I~~iDESvKL~Pkir~L~lS~N~i~~-----------------------v~n-La~L~~L~~LDL  336 (490)
T KOG1259|consen  281 DTWQELTELDLSGNLITQIDESVKLAPKLRRLILSQNRIRT-----------------------VQN-LAELPQLQLLDL  336 (490)
T ss_pred             chHhhhhhccccccchhhhhhhhhhccceeEEeccccceee-----------------------ehh-hhhcccceEeec
Confidence            45677888888888888888888888888888888887641                       112 566777788888


Q ss_pred             ecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCC-CCcccccCCCCCCeEEee
Q 003387          645 RGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMD-DPMPTLEKLPLLQVLKLK  723 (824)
Q Consensus       645 ~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~-~~~~~l~~l~~L~~L~L~  723 (824)
                      +++.   ...+..+-.++-+++.|.+..|.    ++.  ++|...+-+|..|++++|++.. +....+|++|+|+.|.|.
T Consensus       337 S~N~---Ls~~~Gwh~KLGNIKtL~La~N~----iE~--LSGL~KLYSLvnLDl~~N~Ie~ldeV~~IG~LPCLE~l~L~  407 (490)
T KOG1259|consen  337 SGNL---LAECVGWHLKLGNIKTLKLAQNK----IET--LSGLRKLYSLVNLDLSSNQIEELDEVNHIGNLPCLETLRLT  407 (490)
T ss_pred             ccch---hHhhhhhHhhhcCEeeeehhhhh----Hhh--hhhhHhhhhheeccccccchhhHHHhcccccccHHHHHhhc
Confidence            7763   22222232333444444444431    221  1233344444445554444322 112234444444444444


Q ss_pred             cc
Q 003387          724 QN  725 (824)
Q Consensus       724 ~~  725 (824)
                      +|
T Consensus       408 ~N  409 (490)
T KOG1259|consen  408 GN  409 (490)
T ss_pred             CC
Confidence            33

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

Probab=98.75  E-value=3.4e-07  Score=95.95  Aligned_cols=170  Identities=15%  Similarity=0.142  Sum_probs=98.3

Q ss_pred             HHHHHHHHHcC-CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcc
Q 003387          165 MEELLDLLIEG-PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLS  243 (824)
Q Consensus       165 ~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~  243 (824)
                      .+++++.+... ..+..++.|+|++|+||||+++.+++.... ..+ ..+|+.   ....+..+++..|+..++....  
T Consensus        28 ~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~-~~~-~~~~~~---~~~~~~~~~l~~i~~~lG~~~~--  100 (269)
T TIGR03015        28 HKRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQ-ERV-VAAKLV---NTRVDAEDLLRMVAADFGLETE--  100 (269)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcCC-CCe-EEeeee---CCCCCHHHHHHHHHHHcCCCCC--
Confidence            34455554432 223568899999999999999999984321 111 233443   3456788999999998876422  


Q ss_pred             cccccCHHHHHHHHH----Hhc-CCCeEEEEEecCCCh--hhHHHHHhhCC---CCCCCcEEEEEechHHHHh-------
Q 003387          244 EIMDKNYEMKKIILH----EYL-MTKRYLIVIDDVWSI--DMWDVIQEILP---DNQNGSRVLITLTDIRIII-------  306 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~----~~L-~~kr~LlVlDdv~~~--~~~~~l~~~~~---~~~~gs~ilvTtR~~~v~~-------  306 (824)
                         ..+.......+.    ... .+++++||+||+|..  ..++.+.....   +......|++|.... ...       
T Consensus       101 ---~~~~~~~~~~l~~~l~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~  176 (269)
T TIGR03015       101 ---GRDKAALLRELEDFLIEQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQL  176 (269)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchh
Confidence               122222333333    322 678899999999875  35665553222   112223445554322 111       


Q ss_pred             -----------------------hccc---ccCCcCcCcc-ccchhhHHHhcCCCchhHHHHHhHH
Q 003387          307 -----------------------SFQF---EDGENMRLDL-VPTGGPLRATYKGRPFLILYHGSIS  345 (824)
Q Consensus       307 -----------------------~f~~---~~~~~~~~~~-~~~~~~i~~~c~GlPlai~~~~~~l  345 (824)
                                             .+..   ..+......+ .+..+.|++.++|.|..|..++..+
T Consensus       177 ~~l~~r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       177 QQLRQRIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHHHhheeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence                                   0000   0000111122 4567888999999999999988877

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.

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

Probab=98.68  E-value=1.4e-08  Score=112.81  Aligned_cols=177  Identities=25%  Similarity=0.232  Sum_probs=117.9

Q ss_pred             hhcccCcccEEEeeCccCccCCccCCCCC-cceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCc
Q 003387          516 FCGMFKLLRVLDLGSLVLIQYPSGIENLF-LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLR  594 (824)
Q Consensus       516 ~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~-~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~  594 (824)
                      ....++.+..|++.++.+..+|..++.+. +|++|+++++.+..+|..+ +.+++|+.|++++|.+..+|...+.+++|+
T Consensus       111 ~~~~~~~l~~L~l~~n~i~~i~~~~~~~~~nL~~L~l~~N~i~~l~~~~-~~l~~L~~L~l~~N~l~~l~~~~~~~~~L~  189 (394)
T COG4886         111 ELLELTNLTSLDLDNNNITDIPPLIGLLKSNLKELDLSDNKIESLPSPL-RNLPNLKNLDLSFNDLSDLPKLLSNLSNLN  189 (394)
T ss_pred             hhhcccceeEEecCCcccccCccccccchhhcccccccccchhhhhhhh-hccccccccccCCchhhhhhhhhhhhhhhh
Confidence            34455789999999999999998888885 9999999999999998777 999999999999999999998877999999


Q ss_pred             eecCCCccCCCCCCC-CCCCCCCCCeeeccCC-CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEec
Q 003387          595 HLNFGSITLPAHPGK-FCGSLENLNFISALHP-CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLAN  672 (824)
Q Consensus       595 ~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~-~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~  672 (824)
                      .|++++|.+.  .+| .++.+..|+.+.+..+ .......+.++.++..|.+.++.   ...++..+             
T Consensus       190 ~L~ls~N~i~--~l~~~~~~~~~L~~l~~~~N~~~~~~~~~~~~~~l~~l~l~~n~---~~~~~~~~-------------  251 (394)
T COG4886         190 NLDLSGNKIS--DLPPEIELLSALEELDLSNNSIIELLSSLSNLKNLSGLELSNNK---LEDLPESI-------------  251 (394)
T ss_pred             heeccCCccc--cCchhhhhhhhhhhhhhcCCcceecchhhhhcccccccccCCce---eeeccchh-------------
Confidence            9999999887  455 3344444666665533 12222224444444444433321   11112233             


Q ss_pred             cCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccC
Q 003387          673 ESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYS  728 (824)
Q Consensus       673 ~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~  728 (824)
                                     ..+++|+.|++++|.+... .. ++.+.+|+.|+++++.+.
T Consensus       252 ---------------~~l~~l~~L~~s~n~i~~i-~~-~~~~~~l~~L~~s~n~~~  290 (394)
T COG4886         252 ---------------GNLSNLETLDLSNNQISSI-SS-LGSLTNLRELDLSGNSLS  290 (394)
T ss_pred             ---------------ccccccceecccccccccc-cc-ccccCccCEEeccCcccc
Confidence                           3444556666666654322 11 556666666666655443

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

Probab=98.67  E-value=1.3e-08  Score=96.95  Aligned_cols=107  Identities=23%  Similarity=0.260  Sum_probs=44.9

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      +.++|.|.+.++....     +...-..+..|++|+|++|.|+.++ .+..+++|++|++++|.|+.+++.+...+++|+
T Consensus        18 ~~~~~~L~L~~n~I~~-----Ie~L~~~l~~L~~L~Ls~N~I~~l~-~l~~L~~L~~L~L~~N~I~~i~~~l~~~lp~L~   91 (175)
T PF14580_consen   18 PVKLRELNLRGNQIST-----IENLGATLDKLEVLDLSNNQITKLE-GLPGLPRLKTLDLSNNRISSISEGLDKNLPNLQ   91 (175)
T ss_dssp             -----------------------S--TT-TT--EEE-TTS--S--T-T----TT--EEE--SS---S-CHHHHHH-TT--
T ss_pred             cccccccccccccccc-----ccchhhhhcCCCEEECCCCCCcccc-CccChhhhhhcccCCCCCCccccchHHhCCcCC
Confidence            5567888888877652     2222236789999999999999886 478899999999999999999876634799999


Q ss_pred             EeecCCccccccc--hhhhccccCceecCCCccCC
Q 003387          572 TLDMPFSYIDHTA--DEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       572 ~L~L~~~~l~~lp--~~i~~L~~L~~L~L~~~~~~  604 (824)
                      +|++++|.+..+-  ..+..+++|++|++.+|.+.
T Consensus        92 ~L~L~~N~I~~l~~l~~L~~l~~L~~L~L~~NPv~  126 (175)
T PF14580_consen   92 ELYLSNNKISDLNELEPLSSLPKLRVLSLEGNPVC  126 (175)
T ss_dssp             EEE-TTS---SCCCCGGGGG-TT--EEE-TT-GGG
T ss_pred             EEECcCCcCCChHHhHHHHcCCCcceeeccCCccc
Confidence            9999999877653  34788999999999999876

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

Probab=98.57  E-value=5.7e-08  Score=108.04  Aligned_cols=194  Identities=27%  Similarity=0.293  Sum_probs=139.4

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCC-CccEeecCCccccccchhhhccccCceecCCCcc
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLL-NLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~-~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~  602 (824)
                      ..|++.++.+...+..+..+..+..|++.++.+..+|... +.+. +|+.|+++++.+..+|..++.+++|+.|++++|.
T Consensus        96 ~~l~~~~~~~~~~~~~~~~~~~l~~L~l~~n~i~~i~~~~-~~~~~nL~~L~l~~N~i~~l~~~~~~l~~L~~L~l~~N~  174 (394)
T COG4886          96 PSLDLNLNRLRSNISELLELTNLTSLDLDNNNITDIPPLI-GLLKSNLKELDLSDNKIESLPSPLRNLPNLKNLDLSFND  174 (394)
T ss_pred             ceeeccccccccCchhhhcccceeEEecCCcccccCcccc-ccchhhcccccccccchhhhhhhhhccccccccccCCch
Confidence            3578888877555556677789999999999999999988 7785 9999999999999998889999999999999998


Q ss_pred             CCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEE
Q 003387          603 LPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKI  682 (824)
Q Consensus       603 ~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l  682 (824)
                      +.  .+|..                     .+.+++|+.|.++++   ....+|........|++|.+..|.    . .-
T Consensus       175 l~--~l~~~---------------------~~~~~~L~~L~ls~N---~i~~l~~~~~~~~~L~~l~~~~N~----~-~~  223 (394)
T COG4886         175 LS--DLPKL---------------------LSNLSNLNNLDLSGN---KISDLPPEIELLSALEELDLSNNS----I-IE  223 (394)
T ss_pred             hh--hhhhh---------------------hhhhhhhhheeccCC---ccccCchhhhhhhhhhhhhhcCCc----c-ee
Confidence            76  23210                     225566666666666   444455444445556666666541    0 01


Q ss_pred             EeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCC
Q 003387          683 VLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWL  753 (824)
Q Consensus       683 ~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l  753 (824)
                      .+.....+.++..|.+.++.+. ..+..++.+++|+.|++++|.+...  .. .+.+.+|+.|+++++...
T Consensus       224 ~~~~~~~~~~l~~l~l~~n~~~-~~~~~~~~l~~l~~L~~s~n~i~~i--~~-~~~~~~l~~L~~s~n~~~  290 (394)
T COG4886         224 LLSSLSNLKNLSGLELSNNKLE-DLPESIGNLSNLETLDLSNNQISSI--SS-LGSLTNLRELDLSGNSLS  290 (394)
T ss_pred             cchhhhhcccccccccCCceee-eccchhccccccceecccccccccc--cc-ccccCccCEEeccCcccc
Confidence            1122244566666777776643 3367788999999999998887652  22 778899999999987644

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=98.51  E-value=1.4e-08  Score=103.08  Aligned_cols=241  Identities=20%  Similarity=0.164  Sum_probs=157.6

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc----CccCCc-------cCCCCCcceEEeecCCCCC---
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV----LIQYPS-------GIENLFLLRYLKLNIPSLN---  557 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~----i~~lp~-------~i~~l~~Lr~L~L~~~~i~---  557 (824)
                      ...+..+.++++....--...+...+.+-+.||..++++.-    ...+|+       .+-.+++|++|+||.|-+.   
T Consensus        29 ~~s~~~l~lsgnt~G~EAa~~i~~~L~~~~~L~~v~~sd~ftGR~~~Ei~e~L~~l~~aL~~~~~L~~ldLSDNA~G~~g  108 (382)
T KOG1909|consen   29 MDSLTKLDLSGNTFGTEAARAIAKVLASKKELREVNLSDMFTGRLKDEIPEALKMLSKALLGCPKLQKLDLSDNAFGPKG  108 (382)
T ss_pred             cCceEEEeccCCchhHHHHHHHHHHHhhcccceeeehHhhhcCCcHHHHHHHHHHHHHHHhcCCceeEeeccccccCccc
Confidence            66777778887776421123566788888899999998753    124453       3445679999999998766   


Q ss_pred             --ccChhhhhcCCCccEeecCCccccccchh--------------hhccccCceecCCCccCCCCCCCCCCCCCCCCeee
Q 003387          558 --SLPSSLLSNLLNLYTLDMPFSYIDHTADE--------------FWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFIS  621 (824)
Q Consensus       558 --~lp~~i~~~L~~L~~L~L~~~~l~~lp~~--------------i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~  621 (824)
                        .+-.- +.+++.|+.|.|.+|.+......              +.+-++||++..++|++.+.               
T Consensus       109 ~~~l~~l-l~s~~~L~eL~L~N~Glg~~ag~~l~~al~~l~~~kk~~~~~~Lrv~i~~rNrlen~---------------  172 (382)
T KOG1909|consen  109 IRGLEEL-LSSCTDLEELYLNNCGLGPEAGGRLGRALFELAVNKKAASKPKLRVFICGRNRLENG---------------  172 (382)
T ss_pred             hHHHHHH-HHhccCHHHHhhhcCCCChhHHHHHHHHHHHHHHHhccCCCcceEEEEeeccccccc---------------
Confidence              23333 48899999999999987643221              23345677777777665421               


Q ss_pred             ccCCCcchhhhcCCCCccceEEEecccccc--hhhHHHHhccCCCCCeEEEeccCCCCCccEEEeC-ccCcCCCceEEEE
Q 003387          622 ALHPCCCTEDILGRLPNLRNLRIRGDLSYN--QSLLSKSLCRLSCLESLKLANESKMPRLSKIVLA-EYLFPHSLTHLSF  698 (824)
Q Consensus       622 ~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~--~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~-~~~~~~~L~~L~L  698 (824)
                         +...+...+...+.|+.+.+..+....  ...+...+..+++|+.|+|..|. +..--...+. -++.+++|+.|++
T Consensus       173 ---ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNt-ft~egs~~LakaL~s~~~L~El~l  248 (382)
T KOG1909|consen  173 ---GATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNT-FTLEGSVALAKALSSWPHLRELNL  248 (382)
T ss_pred             ---cHHHHHHHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeecccch-hhhHHHHHHHHHhcccchheeecc
Confidence               123344446777888888887775222  23566778888888888888763 0000000000 0145678999999


Q ss_pred             EcccCCCCCcccc-----cCCCCCCeEEeeccccCCCe---eeecCCCCCCccEEeeccCCC
Q 003387          699 SNTDLMDDPMPTL-----EKLPLLQVLKLKQNSYSGRK---LTCGSYGFPNLKVLHLKSMLW  752 (824)
Q Consensus       699 ~~~~l~~~~~~~l-----~~l~~L~~L~L~~~~~~~~~---~~~~~~~~~~L~~L~L~~~~~  752 (824)
                      +.|.+.......+     ...|+|+.|.+.+|.++.+.   +.......|.|+.|+|++|..
T Consensus       249 ~dcll~~~Ga~a~~~al~~~~p~L~vl~l~gNeIt~da~~~la~~~~ek~dL~kLnLngN~l  310 (382)
T KOG1909|consen  249 GDCLLENEGAIAFVDALKESAPSLEVLELAGNEITRDAALALAACMAEKPDLEKLNLNGNRL  310 (382)
T ss_pred             cccccccccHHHHHHHHhccCCCCceeccCcchhHHHHHHHHHHHHhcchhhHHhcCCcccc
Confidence            9998765544333     24899999999998875432   222345589999999999873

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

Probab=98.51  E-value=1.5e-08  Score=100.06  Aligned_cols=127  Identities=20%  Similarity=0.237  Sum_probs=91.6

Q ss_pred             hcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCcee
Q 003387          517 CGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL  596 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L  596 (824)
                      ......|..||||+|.|+.+-+++.-++.+|.|+++.|++..+.. + ..|++|+.|||++|.+.++-..-.+|-|.+.|
T Consensus       280 ~dTWq~LtelDLS~N~I~~iDESvKL~Pkir~L~lS~N~i~~v~n-L-a~L~~L~~LDLS~N~Ls~~~Gwh~KLGNIKtL  357 (490)
T KOG1259|consen  280 ADTWQELTELDLSGNLITQIDESVKLAPKLRRLILSQNRIRTVQN-L-AELPQLQLLDLSGNLLAECVGWHLKLGNIKTL  357 (490)
T ss_pred             cchHhhhhhccccccchhhhhhhhhhccceeEEeccccceeeehh-h-hhcccceEeecccchhHhhhhhHhhhcCEeee
Confidence            344567888899999888888888888889999999988887766 5 78888999999988877776555577788888


Q ss_pred             cCCCccCCCCCCCCCCCCCCCCeeeccCCC----cchhhhcCCCCccceEEEeccc
Q 003387          597 NFGSITLPAHPGKFCGSLENLNFISALHPC----CCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       597 ~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~----~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      .|+.|.+.  .+.++++|-+|..|++..+.    ..... +++++.|+.|.+.++.
T Consensus       358 ~La~N~iE--~LSGL~KLYSLvnLDl~~N~Ie~ldeV~~-IG~LPCLE~l~L~~NP  410 (490)
T KOG1259|consen  358 KLAQNKIE--TLSGLRKLYSLVNLDLSSNQIEELDEVNH-IGNLPCLETLRLTGNP  410 (490)
T ss_pred             ehhhhhHh--hhhhhHhhhhheeccccccchhhHHHhcc-cccccHHHHHhhcCCC
Confidence            88888765  44466666666666665221    12223 6666777666666654

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

Probab=98.50  E-value=5.3e-09  Score=103.37  Aligned_cols=169  Identities=21%  Similarity=0.167  Sum_probs=122.1

Q ss_pred             CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCc-cCcCCCceEEEEEcccCC
Q 003387          626 CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAE-YLFPHSLTHLSFSNTDLM  704 (824)
Q Consensus       626 ~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~-~~~~~~L~~L~L~~~~l~  704 (824)
                      ...+..++..|.+|+.|++.+..  ..+.+...+.+..+|+.|+|+...   .++...+.- +.+|+.|..|+|+.|.+.
T Consensus       199 ~stl~~iLs~C~kLk~lSlEg~~--LdD~I~~~iAkN~~L~~lnlsm~s---G~t~n~~~ll~~scs~L~~LNlsWc~l~  273 (419)
T KOG2120|consen  199 VSTLHGILSQCSKLKNLSLEGLR--LDDPIVNTIAKNSNLVRLNLSMCS---GFTENALQLLLSSCSRLDELNLSWCFLF  273 (419)
T ss_pred             HHHHHHHHHHHHhhhhccccccc--cCcHHHHHHhccccceeecccccc---ccchhHHHHHHHhhhhHhhcCchHhhcc
Confidence            34445558889999999999987  677788889999999999998632   222222111 156889999999999876


Q ss_pred             CCCccccc--CCCCCCeEEeecccc--CCCeeeecCCCCCCccEEeeccCCCCccce-eccCcccCccEEEEecCCCCCC
Q 003387          705 DDPMPTLE--KLPLLQVLKLKQNSY--SGRKLTCGSYGFPNLKVLHLKSMLWLEEWT-MGNAAMPKLECLIINPCAYLKK  779 (824)
Q Consensus       705 ~~~~~~l~--~l~~L~~L~L~~~~~--~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~-~~~~~lp~L~~L~l~~c~~l~~  779 (824)
                      .+....+-  --++|..|+|+++.-  ....+..-...+|+|..|+|++|..++.-. ..+..|+-|++|.++.|..+. 
T Consensus       274 ~~~Vtv~V~hise~l~~LNlsG~rrnl~~sh~~tL~~rcp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~lSlsRCY~i~-  352 (419)
T KOG2120|consen  274 TEKVTVAVAHISETLTQLNLSGYRRNLQKSHLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFKFNYLQHLSLSRCYDII-  352 (419)
T ss_pred             chhhhHHHhhhchhhhhhhhhhhHhhhhhhHHHHHHHhCCceeeeccccccccCchHHHHHHhcchheeeehhhhcCCC-
Confidence            54433221  246899999998642  222233334579999999999998777532 346679999999999999653 


Q ss_pred             Ccc---ccccCccCcEEEecCCcHH
Q 003387          780 MPE---QLWYIKSLNKFDCWWPQPE  801 (824)
Q Consensus       780 lp~---~l~~l~~L~~L~l~~c~~~  801 (824)
                       |.   .+...|+|..|++.||-..
T Consensus       353 -p~~~~~l~s~psl~yLdv~g~vsd  376 (419)
T KOG2120|consen  353 -PETLLELNSKPSLVYLDVFGCVSD  376 (419)
T ss_pred             -hHHeeeeccCcceEEEEeccccCc
Confidence             43   4567799999999998755

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.49  E-value=2e-07  Score=94.74  Aligned_cols=95  Identities=13%  Similarity=-0.012  Sum_probs=63.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC--CCHHHHHHHHHHHhCCCC-Cccccccc-CHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE--YDADQILDIVIKFLMPSS-RLSEIMDK-NYEMKK  254 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~--~~~~~~~~~i~~~l~~~~-~~~~~~~~-~~~~~~  254 (824)
                      -..++|+|++|+|||||++.+|++.... +|+.++|++  ++++  +++.++++++...+-... +.+..... -.....
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~--vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~   92 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVL--LIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVL   92 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEE--EccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHH
Confidence            4588999999999999999999964444 899999999  8887  899999999933322111 00101111 111222


Q ss_pred             HHHHHh-cCCCeEEEEEecCCCh
Q 003387          255 IILHEY-LMTKRYLIVIDDVWSI  276 (824)
Q Consensus       255 ~~l~~~-L~~kr~LlVlDdv~~~  276 (824)
                      .....+ -+++++++++|++..-
T Consensus        93 ~~a~~~~~~G~~vll~iDei~r~  115 (249)
T cd01128          93 EKAKRLVEHGKDVVILLDSITRL  115 (249)
T ss_pred             HHHHHHHHCCCCEEEEEECHHHh
Confidence            222222 2589999999999654

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.

>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=98.47  E-value=8.9e-08  Score=74.83  Aligned_cols=58  Identities=29%  Similarity=0.388  Sum_probs=30.0

Q ss_pred             cceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch-hhhccccCceecCCCcc
Q 003387          545 LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~  602 (824)
                      +|++|++++|++..+|...|.++++|++|++++|.+..+|. .|..+++|++|++++|.
T Consensus         2 ~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    2 NLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TESEEEETSSTESEECTTTTTTGTTESEEEETSSSESEEETTTTTTSTTESEEEETSSS
T ss_pred             cCcEEECCCCCCCccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCCCCCEEeCcCCc
Confidence            44555555555555554444555555555555555555543 24555555555555543

...

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

Probab=98.43  E-value=2.2e-08  Score=107.44  Aligned_cols=162  Identities=22%  Similarity=0.205  Sum_probs=123.4

Q ss_pred             cccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhh
Q 003387          486 ACLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSL  563 (824)
Q Consensus       486 ~~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i  563 (824)
                      +++..+  +-.|.++.+..+...     ..+..+..+..|.+|+|+.|.++.+|..++.|+ |+.|-+++|+++.+|..+
T Consensus        89 elp~~~~~f~~Le~liLy~n~~r-----~ip~~i~~L~~lt~l~ls~NqlS~lp~~lC~lp-Lkvli~sNNkl~~lp~~i  162 (722)
T KOG0532|consen   89 ELPEEACAFVSLESLILYHNCIR-----TIPEAICNLEALTFLDLSSNQLSHLPDGLCDLP-LKVLIVSNNKLTSLPEEI  162 (722)
T ss_pred             cCchHHHHHHHHHHHHHHhccce-----ecchhhhhhhHHHHhhhccchhhcCChhhhcCc-ceeEEEecCccccCCccc
Confidence            355555  677777777776654     356778888889999999999998998888764 888999999999999998


Q ss_pred             hhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeecc-CCCcchhhhcCCCCccce
Q 003387          564 LSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISAL-HPCCCTEDILGRLPNLRN  641 (824)
Q Consensus       564 ~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~-~~~~~~~~~l~~l~~L~~  641 (824)
                       +.+..|..||.+.|.+..+|..++.+.+|+.|++..|++.  .+| .+..| .|..|+++ +....++--+.+|+.|+.
T Consensus       163 -g~~~tl~~ld~s~nei~slpsql~~l~slr~l~vrRn~l~--~lp~El~~L-pLi~lDfScNkis~iPv~fr~m~~Lq~  238 (722)
T KOG0532|consen  163 -GLLPTLAHLDVSKNEIQSLPSQLGYLTSLRDLNVRRNHLE--DLPEELCSL-PLIRLDFSCNKISYLPVDFRKMRHLQV  238 (722)
T ss_pred             -ccchhHHHhhhhhhhhhhchHHhhhHHHHHHHHHhhhhhh--hCCHHHhCC-ceeeeecccCceeecchhhhhhhhhee
Confidence             8888899999999999999998999999999988888876  566 66533 36677777 233333333888999999


Q ss_pred             EEEecccccchhhHHHHhc
Q 003387          642 LRIRGDLSYNQSLLSKSLC  660 (824)
Q Consensus       642 L~l~~~~~~~~~~l~~~l~  660 (824)
                      |.+.++   -..+-|+.+.
T Consensus       239 l~LenN---PLqSPPAqIC  254 (722)
T KOG0532|consen  239 LQLENN---PLQSPPAQIC  254 (722)
T ss_pred             eeeccC---CCCCChHHHH
Confidence            998887   3444455444

>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=98.43  E-value=1.7e-07  Score=73.19  Aligned_cols=60  Identities=35%  Similarity=0.417  Sum_probs=53.7

Q ss_pred             CcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccc
Q 003387          521 KLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI  580 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l  580 (824)
                      ++|++|++++|.++.+|. .+..+++|++|++++|.+..+|+..|.++++|++|++++|.+
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 PNLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNNNLTSIPPDAFSNLPNLRYLDLSNNNL   61 (61)
T ss_dssp             TTESEEEETSSTESEECTTTTTTGTTESEEEETSSSESEEETTTTTTSTTESEEEETSSSB
T ss_pred             CcCcEEECCCCCCCccCHHHHcCCCCCCEeEccCCccCccCHHHHcCCCCCCEEeCcCCcC
Confidence            578999999999998885 678899999999999999999987779999999999999864

...

>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=98.42  E-value=1.2e-06  Score=89.67  Aligned_cols=55  Identities=25%  Similarity=0.294  Sum_probs=40.6

Q ss_pred             ceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          158 TVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ++||++++++|.+++..+.  ...+.|+|+.|+|||+|++.+.+  ..+..-..++|+.
T Consensus         1 F~gR~~el~~l~~~l~~~~--~~~~~l~G~rg~GKTsLl~~~~~--~~~~~~~~~~y~~   55 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGP--SQHILLYGPRGSGKTSLLKEFIN--ELKEKGYKVVYID   55 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----SSEEEEEESTTSSHHHHHHHHHH--HCT--EECCCHHC
T ss_pred             CCCHHHHHHHHHHHHHhhc--CcEEEEEcCCcCCHHHHHHHHHH--HhhhcCCcEEEEe
Confidence            6899999999999998764  66899999999999999999999  4433222455555

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

>KOG4341 consensus F-box protein containing LRR [General function prediction only]

Probab=98.42  E-value=1.7e-08  Score=104.51  Aligned_cols=278  Identities=15%  Similarity=0.084  Sum_probs=158.2

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc-Cc-cCCccC-CCCCcceEEeecCCC-CC--ccChhhhh
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV-LI-QYPSGI-ENLFLLRYLKLNIPS-LN--SLPSSLLS  565 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~-i~-~lp~~i-~~l~~Lr~L~L~~~~-i~--~lp~~i~~  565 (824)
                      |+++..|.+.++...  .......+-..|++|++|+|.+|. ++ ...+.+ ..+++|.||++++|. |.  .+-.-. .
T Consensus       163 CpnIehL~l~gc~~i--Td~s~~sla~~C~~l~~l~L~~c~~iT~~~Lk~la~gC~kL~~lNlSwc~qi~~~gv~~~~-r  239 (483)
T KOG4341|consen  163 CPNIEHLALYGCKKI--TDSSLLSLARYCRKLRHLNLHSCSSITDVSLKYLAEGCRKLKYLNLSWCPQISGNGVQALQ-R  239 (483)
T ss_pred             CCchhhhhhhcceec--cHHHHHHHHHhcchhhhhhhcccchhHHHHHHHHHHhhhhHHHhhhccCchhhcCcchHHh-c
Confidence            666666666655532  233445555667777777777754 44 222222 236667777777654 33  122222 5


Q ss_pred             cCCCccEeecCCcc-cc--ccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceE
Q 003387          566 NLLNLYTLDMPFSY-ID--HTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNL  642 (824)
Q Consensus       566 ~L~~L~~L~L~~~~-l~--~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L  642 (824)
                      ++.+|+.+.+++|. +.  .+-..=..+.-+..+++..|..                  ++  ...+..+-..+..|+.|
T Consensus       240 G~~~l~~~~~kGC~e~~le~l~~~~~~~~~i~~lnl~~c~~------------------lT--D~~~~~i~~~c~~lq~l  299 (483)
T KOG4341|consen  240 GCKELEKLSLKGCLELELEALLKAAAYCLEILKLNLQHCNQ------------------LT--DEDLWLIACGCHALQVL  299 (483)
T ss_pred             cchhhhhhhhcccccccHHHHHHHhccChHhhccchhhhcc------------------cc--chHHHHHhhhhhHhhhh
Confidence            56666666666652 11  1111111223333343333321                  11  11222223456778888


Q ss_pred             EEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCcc-CcCCCceEEEEEcccCCCCC--cccccCCCCCCe
Q 003387          643 RIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEY-LFPHSLTHLSFSNTDLMDDP--MPTLEKLPLLQV  719 (824)
Q Consensus       643 ~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~-~~~~~L~~L~L~~~~l~~~~--~~~l~~l~~L~~  719 (824)
                      ..+++.......+-+--.++.+|+.|.++.   +.++..-.+..+ .+++.|+.+++..|....+.  ...-.++|.|+.
T Consensus       300 ~~s~~t~~~d~~l~aLg~~~~~L~~l~l~~---c~~fsd~~ft~l~rn~~~Le~l~~e~~~~~~d~tL~sls~~C~~lr~  376 (483)
T KOG4341|consen  300 CYSSCTDITDEVLWALGQHCHNLQVLELSG---CQQFSDRGFTMLGRNCPHLERLDLEECGLITDGTLASLSRNCPRLRV  376 (483)
T ss_pred             cccCCCCCchHHHHHHhcCCCceEEEeccc---cchhhhhhhhhhhcCChhhhhhcccccceehhhhHhhhccCCchhcc
Confidence            888876544444545555667888888873   344443333322 56788999999988643222  222347999999


Q ss_pred             EEeeccccCCCe----eeecCCCCCCccEEeeccCCCCccce-eccCcccCccEEEEecCCCCCCCc--cccccCccCcE
Q 003387          720 LKLKQNSYSGRK----LTCGSYGFPNLKVLHLKSMLWLEEWT-MGNAAMPKLECLIINPCAYLKKMP--EQLWYIKSLNK  792 (824)
Q Consensus       720 L~L~~~~~~~~~----~~~~~~~~~~L~~L~L~~~~~l~~l~-~~~~~lp~L~~L~l~~c~~l~~lp--~~l~~l~~L~~  792 (824)
                      |.++.|....+.    +.....+...|+.|.+.+|+.+.+-. .....+++|+.+++-+|.....-|  ....++|+++.
T Consensus       377 lslshce~itD~gi~~l~~~~c~~~~l~~lEL~n~p~i~d~~Le~l~~c~~Leri~l~~~q~vtk~~i~~~~~~lp~i~v  456 (483)
T KOG4341|consen  377 LSLSHCELITDEGIRHLSSSSCSLEGLEVLELDNCPLITDATLEHLSICRNLERIELIDCQDVTKEAISRFATHLPNIKV  456 (483)
T ss_pred             CChhhhhhhhhhhhhhhhhccccccccceeeecCCCCchHHHHHHHhhCcccceeeeechhhhhhhhhHHHHhhCcccee
Confidence            999987654332    11223457789999999998766432 235578999999999998765433  23456777665


Q ss_pred             EEe
Q 003387          793 FDC  795 (824)
Q Consensus       793 L~l  795 (824)
                      ...
T Consensus       457 ~a~  459 (483)
T KOG4341|consen  457 HAY  459 (483)
T ss_pred             hhh
Confidence            543

>PF05729 NACHT: NACHT domain

Probab=98.42  E-value=7.9e-07  Score=85.59  Aligned_cols=114  Identities=19%  Similarity=0.248  Sum_probs=67.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCC----CceeEEEECCCCCCCCHH---HHHHHHHHHhCCCCCcccccccCHHH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHY----FDCHAWITEPYSNEYDAD---QILDIVIKFLMPSSRLSEIMDKNYEM  252 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv~~~vs~~~~~~---~~~~~i~~~l~~~~~~~~~~~~~~~~  252 (824)
                      +++.|+|.+|+||||+++.++.+-.....    +...+|+.  .+...+..   .+...|..+......       ....
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~l~~~~~~~~~-------~~~~   71 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFS--LRDISDSNNSRSLADLLFDQLPESIA-------PIEE   71 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEe--ehhhhhccccchHHHHHHHhhccchh-------hhHH
Confidence            57899999999999999999884222222    45566776  44332222   344444444432211       1111


Q ss_pred             HHHHHHHhc-CCCeEEEEEecCCChhh---------HHHHH-hhCCC-CCCCcEEEEEechHHHH
Q 003387          253 KKIILHEYL-MTKRYLIVIDDVWSIDM---------WDVIQ-EILPD-NQNGSRVLITLTDIRII  305 (824)
Q Consensus       253 ~~~~l~~~L-~~kr~LlVlDdv~~~~~---------~~~l~-~~~~~-~~~gs~ilvTtR~~~v~  305 (824)
                         .+...+ +.++++||+|++++...         +..+. ..++. ..++++++||+|.....
T Consensus        72 ---~~~~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~  133 (166)
T PF05729_consen   72 ---LLQELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFP  133 (166)
T ss_pred             ---HHHHHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHH
Confidence               222222 57899999999976432         22222 22332 35689999999987663

>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=98.39  E-value=2.7e-06  Score=79.83  Aligned_cols=122  Identities=18%  Similarity=0.188  Sum_probs=72.2

Q ss_pred             eechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          159 VGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       159 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      +|++..++.+...+....  .+.+.|+|.+|+||||+|+.+++  .....-..++++.  .++..........+...   
T Consensus         1 ~~~~~~~~~i~~~~~~~~--~~~v~i~G~~G~GKT~l~~~i~~--~~~~~~~~v~~~~--~~~~~~~~~~~~~~~~~---   71 (151)
T cd00009           1 VGQEEAIEALREALELPP--PKNLLLYGPPGTGKTTLARAIAN--ELFRPGAPFLYLN--ASDLLEGLVVAELFGHF---   71 (151)
T ss_pred             CchHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHH--HhhcCCCCeEEEe--hhhhhhhhHHHHHhhhh---
Confidence            377888888888887643  56888999999999999999999  3322223456666  44432222211111000   


Q ss_pred             CCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh-----hhHHHHHhhCCCC---CCCcEEEEEechH
Q 003387          239 SSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI-----DMWDVIQEILPDN---QNGSRVLITLTDI  302 (824)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~-----~~~~~l~~~~~~~---~~gs~ilvTtR~~  302 (824)
                                   ............+..+||+||++..     ..+..+.......   ..+..||+||...
T Consensus        72 -------------~~~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~  130 (151)
T cd00009          72 -------------LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRP  130 (151)
T ss_pred             -------------hHhHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCcc
Confidence                         0111112233457789999999853     2233333333221   3578888888765

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.

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.35  E-value=1e-07  Score=94.39  Aligned_cols=92  Identities=24%  Similarity=0.177  Sum_probs=54.5

Q ss_pred             hhHhhhcccCcccEEEeeCccCc---cCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCcc--ccccchh
Q 003387          512 DWEKFCGMFKLLRVLDLGSLVLI---QYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY--IDHTADE  586 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~~i~---~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~--l~~lp~~  586 (824)
                      ....+-..+..++.|||.+|.|+   .+..-+.+|++|++|+|+.|++..--.+.-..+.+|++|-|.++.  .+..-..
T Consensus        62 d~~~~~~~~~~v~elDL~~N~iSdWseI~~ile~lP~l~~LNls~N~L~s~I~~lp~p~~nl~~lVLNgT~L~w~~~~s~  141 (418)
T KOG2982|consen   62 DVMLFGSSVTDVKELDLTGNLISDWSEIGAILEQLPALTTLNLSCNSLSSDIKSLPLPLKNLRVLVLNGTGLSWTQSTSS  141 (418)
T ss_pred             hHHHHHHHhhhhhhhhcccchhccHHHHHHHHhcCccceEeeccCCcCCCccccCcccccceEEEEEcCCCCChhhhhhh
Confidence            34445566777777777777765   333344567777777777776542111110234577777777763  3344455


Q ss_pred             hhccccCceecCCCccC
Q 003387          587 FWKMNKLRHLNFGSITL  603 (824)
Q Consensus       587 i~~L~~L~~L~L~~~~~  603 (824)
                      +..+|+++.|+++.|.+
T Consensus       142 l~~lP~vtelHmS~N~~  158 (418)
T KOG2982|consen  142 LDDLPKVTELHMSDNSL  158 (418)
T ss_pred             hhcchhhhhhhhccchh
Confidence            66677777776665543

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.33  E-value=5.7e-07  Score=95.02  Aligned_cols=106  Identities=14%  Similarity=0.055  Sum_probs=66.7

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC--CHHHHHHHHHHHhCCCC-Ccc
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY--DADQILDIVIKFLMPSS-RLS  243 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~--~~~~~~~~i~~~l~~~~-~~~  243 (824)
                      ++++++..=. .-...+|+|++|+||||||+.||++.... +|+.++||.  +++.+  ++.+++++|...+-.+. +.+
T Consensus       158 rvID~l~PIG-kGQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~Vv--LIgER~~EVtdiqrsIlg~vv~st~d~~  233 (416)
T PRK09376        158 RIIDLIAPIG-KGQRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVL--LIDERPEEVTDMQRSVKGEVVASTFDEP  233 (416)
T ss_pred             eeeeeecccc-cCceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEE--EeCCchhHHHHHHHHhcCcEEEECCCCC
Confidence            4555554311 23567899999999999999999964433 899999999  99888  77888888863221111 100


Q ss_pred             cccccCHHHHHHHHHHh--cCCCeEEEEEecCCCh
Q 003387          244 EIMDKNYEMKKIILHEY--LMTKRYLIVIDDVWSI  276 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~~~--L~~kr~LlVlDdv~~~  276 (824)
                      .....-....+....++  -.+++++|++|++..-
T Consensus       234 ~~~~~~~a~~~ie~Ae~~~e~G~dVlL~iDsItR~  268 (416)
T PRK09376        234 AERHVQVAEMVIEKAKRLVEHGKDVVILLDSITRL  268 (416)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCEEEEEEChHHH
Confidence            00000111112222222  2679999999999654

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

Probab=98.33  E-value=1.1e-06  Score=81.04  Aligned_cols=113  Identities=12%  Similarity=0.185  Sum_probs=78.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCC-----CceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHY-----FDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMK  253 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~-----F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~  253 (824)
                      -+++.|+|.+|+|||++++.+.++  ....     -..++|+.  ++...+...+...|+.+++....    ...+..++
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~--~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~i~~~l~~~~~----~~~~~~~l   75 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQ--LNAEAEIKNHPDVIYVN--CPSSRTPRDFAQEILEALGLPLK----SRQTSDEL   75 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHH--HHHHHHHCCCEEEEEEE--HHHHSSHHHHHHHHHHHHT-SSS----STS-HHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHH--hHHhhhccCCCcEEEEE--eCCCCCHHHHHHHHHHHhCcccc----ccCCHHHH
Confidence            578999999999999999999984  2221     34567998  87777899999999999998653    23456777


Q ss_pred             HHHHHHhcCCC-eEEEEEecCCCh---hhHHHHHhhCCCCCCCcEEEEEech
Q 003387          254 KIILHEYLMTK-RYLIVIDDVWSI---DMWDVIQEILPDNQNGSRVLITLTD  301 (824)
Q Consensus       254 ~~~l~~~L~~k-r~LlVlDdv~~~---~~~~~l~~~~~~~~~gs~ilvTtR~  301 (824)
                      ...+.+.+... ..+||+||+...   ..++.+.....  ..+.++|+.-+.
T Consensus        76 ~~~~~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   76 RSLLIDALDRRRVVLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HHHHHHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            78888888654 469999999754   34555544333  556677766543

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=98.25  E-value=1e-05  Score=91.98  Aligned_cols=265  Identities=15%  Similarity=0.153  Sum_probs=160.6

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC-CCHHHHHHHHHHHhCCCCCcc
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE-YDADQILDIVIKFLMPSSRLS  243 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~-~~~~~~~~~i~~~l~~~~~~~  243 (824)
                      ..++.+.|..+. +.+.+-|.-++|.|||||+.....  +. ..=..+.|..  ..++ -|+.+....++..++.-.+..
T Consensus        24 R~rL~~~L~~~~-~~RL~li~APAGfGKttl~aq~~~--~~-~~~~~v~Wls--lde~dndp~rF~~yLi~al~~~~p~~   97 (894)
T COG2909          24 RPRLLDRLRRAN-DYRLILISAPAGFGKTTLLAQWRE--LA-ADGAAVAWLS--LDESDNDPARFLSYLIAALQQATPTL   97 (894)
T ss_pred             cHHHHHHHhcCC-CceEEEEeCCCCCcHHHHHHHHHH--hc-CcccceeEee--cCCccCCHHHHHHHHHHHHHHhCccc
Confidence            456777776653 589999999999999999988865  11 1223688998  6544 477788888888887422100


Q ss_pred             --------c-ccccCHHHHHHHHHHhcCC--CeEEEEEecCCCh---hhHHHHHhhCCCCCCCcEEEEEechHH---HHh
Q 003387          244 --------E-IMDKNYEMKKIILHEYLMT--KRYLIVIDDVWSI---DMWDVIQEILPDNQNGSRVLITLTDIR---III  306 (824)
Q Consensus       244 --------~-~~~~~~~~~~~~l~~~L~~--kr~LlVlDdv~~~---~~~~~l~~~~~~~~~gs~ilvTtR~~~---v~~  306 (824)
                              + ....+...+...+...|..  ++..+||||---.   .--+.+...+....++=..+||||+.-   +++
T Consensus        98 ~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l~la~  177 (894)
T COG2909          98 GDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQLGLAR  177 (894)
T ss_pred             cHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCCcccc
Confidence                    0 2233455566666666654  6899999997543   223334444445556778999999863   222


Q ss_pred             ---------------hcccccCC------cCcCccccchhhHHHhcCCCchhHHHHHhHHH-hhhhhhhc---cCCC-cc
Q 003387          307 ---------------SFQFEDGE------NMRLDLVPTGGPLRATYKGRPFLILYHGSISL-EENIREAV---ETPL-GL  360 (824)
Q Consensus       307 ---------------~f~~~~~~------~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~-~~~~~~~~---~~~~-~~  360 (824)
                                     +|..+...      ...+--+...+.+.+...|.+-|+..++-.+- ..+....+   ++.. .+
T Consensus       178 lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld~~~~~~L~~~teGW~~al~L~aLa~~~~~~~~q~~~~LsG~~~~l  257 (894)
T COG2909         178 LRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPLDAADLKALYDRTEGWAAALQLIALALRNNTSAEQSLRGLSGAASHL  257 (894)
T ss_pred             eeehhhHHhcChHhhcCChHHHHHHHHHcCCCCCChHHHHHHHhhcccHHHHHHHHHHHccCCCcHHHHhhhccchHHHH
Confidence                           33333210      11122233456666777777766666555442 01111111   1111 11


Q ss_pred             cccccc----cCCCCchHHHhHhccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHHHHHhccccceeecCCCCcEE
Q 003387          361 RYIKCL----MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTIN  436 (824)
Q Consensus       361 ~~~l~~----~L~~~lk~cfl~~s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~~Lv~rsllq~~~~~~~g~~~  436 (824)
                      .+-|.-    .||+++|.-.+-||+++.=    -++|+..-.        .++-|...+++|..++|+-..-.+..   .
T Consensus       258 ~dYL~eeVld~Lp~~l~~FLl~~svl~~f----~~eL~~~Lt--------g~~ng~amLe~L~~~gLFl~~Ldd~~---~  322 (894)
T COG2909         258 SDYLVEEVLDRLPPELRDFLLQTSVLSRF----NDELCNALT--------GEENGQAMLEELERRGLFLQRLDDEG---Q  322 (894)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhHHHh----hHHHHHHHh--------cCCcHHHHHHHHHhCCCceeeecCCC---c
Confidence            111111    7899999999999988652    134444333        23458899999999998875443222   4


Q ss_pred             EEEcCccHHHHHHh
Q 003387          437 TCSIPGRWRPVLHT  450 (824)
Q Consensus       437 ~~~mHdlv~dla~~  450 (824)
                      -|+.|.+..||-+.
T Consensus       323 WfryH~LFaeFL~~  336 (894)
T COG2909         323 WFRYHHLFAEFLRQ  336 (894)
T ss_pred             eeehhHHHHHHHHh
Confidence            58999999998776

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=98.25  E-value=1.6e-07  Score=104.63  Aligned_cols=241  Identities=24%  Similarity=0.222  Sum_probs=112.9

Q ss_pred             cCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCC
Q 003387          520 FKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFG  599 (824)
Q Consensus       520 ~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~  599 (824)
                      +..+..+++..+.+...-..++.+.+|.+|++.+|.|..+...+ ..+++|++|++++|.|+.+.. +..++.|+.|+++
T Consensus        71 l~~l~~l~l~~n~i~~~~~~l~~~~~l~~l~l~~n~i~~i~~~l-~~~~~L~~L~ls~N~I~~i~~-l~~l~~L~~L~l~  148 (414)
T KOG0531|consen   71 LTSLKELNLRQNLIAKILNHLSKLKSLEALDLYDNKIEKIENLL-SSLVNLQVLDLSFNKITKLEG-LSTLTLLKELNLS  148 (414)
T ss_pred             hHhHHhhccchhhhhhhhcccccccceeeeeccccchhhcccch-hhhhcchheeccccccccccc-hhhccchhhheec
Confidence            34444444555555443333555555555555555555554433 555555555555555555543 4455555555555


Q ss_pred             CccCCCCCCCCCCCCCCCCeeeccCCCcchhhh--cCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCC
Q 003387          600 SITLPAHPGKFCGSLENLNFISALHPCCCTEDI--LGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMP  677 (824)
Q Consensus       600 ~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~--l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~  677 (824)
                      +|.+.  .++++..+.+|+.++++.+.....+.  +..+.+|+.+.+.++......    .+..+..+..+++..|    
T Consensus       149 ~N~i~--~~~~~~~l~~L~~l~l~~n~i~~ie~~~~~~~~~l~~l~l~~n~i~~i~----~~~~~~~l~~~~l~~n----  218 (414)
T KOG0531|consen  149 GNLIS--DISGLESLKSLKLLDLSYNRIVDIENDELSELISLEELDLGGNSIREIE----GLDLLKKLVLLSLLDN----  218 (414)
T ss_pred             cCcch--hccCCccchhhhcccCCcchhhhhhhhhhhhccchHHHhccCCchhccc----chHHHHHHHHhhcccc----
Confidence            55554  33344444444444444322222221  245556666666655311111    1111111222222222    


Q ss_pred             CccEEEeCccCcCCC--ceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcc
Q 003387          678 RLSKIVLAEYLFPHS--LTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEE  755 (824)
Q Consensus       678 ~L~~l~l~~~~~~~~--L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~  755 (824)
                      .+..  +.+...+..  |+.++++++.+.. .+..+..++++..|++.++.+...   .....++.+..+....++....
T Consensus       219 ~i~~--~~~l~~~~~~~L~~l~l~~n~i~~-~~~~~~~~~~l~~l~~~~n~~~~~---~~~~~~~~~~~~~~~~~~~~~~  292 (414)
T KOG0531|consen  219 KISK--LEGLNELVMLHLRELYLSGNRISR-SPEGLENLKNLPVLDLSSNRISNL---EGLERLPKLSELWLNDNKLALS  292 (414)
T ss_pred             ccee--ccCcccchhHHHHHHhcccCcccc-ccccccccccccccchhhcccccc---ccccccchHHHhccCcchhcch
Confidence            1111  112122222  6777777776532 224556677777777776655431   1223445555555555442211


Q ss_pred             c---ee-ccCcccCccEEEEecCCCCC
Q 003387          756 W---TM-GNAAMPKLECLIINPCAYLK  778 (824)
Q Consensus       756 l---~~-~~~~lp~L~~L~l~~c~~l~  778 (824)
                      +   .. .....+.++.+.+.+++.-.
T Consensus       293 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  319 (414)
T KOG0531|consen  293 EAISQEYITSAAPTLVTLTLELNPIRK  319 (414)
T ss_pred             hhhhccccccccccccccccccCcccc
Confidence            1   11 14456677777777766433

>PF13173 AAA_14: AAA domain

Probab=98.24  E-value=2.5e-06  Score=78.03  Aligned_cols=101  Identities=14%  Similarity=0.230  Sum_probs=68.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      -+++.|.|+-|+||||++++++++..   ....+++++  ..........                    +.+ ....+.
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~--~~~~~~~~~~--------------------~~~-~~~~~~   55 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYIN--FDDPRDRRLA--------------------DPD-LLEYFL   55 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeec--cCCHHHHHHh--------------------hhh-hHHHHH
Confidence            46899999999999999999998422   334566666  3332110000                    000 223333


Q ss_pred             HhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHH
Q 003387          259 EYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRII  305 (824)
Q Consensus       259 ~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~  305 (824)
                      +....++.+|++|++....+|......+.+..+..+|++|+.+....
T Consensus        56 ~~~~~~~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l  102 (128)
T PF13173_consen   56 ELIKPGKKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLL  102 (128)
T ss_pred             HhhccCCcEEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHH
Confidence            33444788899999999989988888777766778999999887655

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.24  E-value=1.2e-06  Score=86.07  Aligned_cols=46  Identities=22%  Similarity=0.258  Sum_probs=32.1

Q ss_pred             CceechhhHHHHHHHHHc-CCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          157 DTVGLDDRMEELLDLLIE-GPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~-~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ++|||+++.+++...|.. .....+.+.|+|.+|+|||||++.++..
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~   47 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDR   47 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999952 2345799999999999999999999884

>PLN03150 hypothetical protein; Provisional

Probab=98.22  E-value=2.4e-06  Score=99.79  Aligned_cols=86  Identities=23%  Similarity=0.356  Sum_probs=72.1

Q ss_pred             cccEEEeeCccCc-cCCccCCCCCcceEEeecCCCCC-ccChhhhhcCCCccEeecCCcccc-ccchhhhccccCceecC
Q 003387          522 LLRVLDLGSLVLI-QYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLLNLYTLDMPFSYID-HTADEFWKMNKLRHLNF  598 (824)
Q Consensus       522 ~Lr~L~L~~~~i~-~lp~~i~~l~~Lr~L~L~~~~i~-~lp~~i~~~L~~L~~L~L~~~~l~-~lp~~i~~L~~L~~L~L  598 (824)
                      .++.|+|+++.+. .+|..++++++|++|+|++|.+. .+|..+ +.+++|++|+|++|.+. .+|..+++|++|++|+|
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 FIDGLGLDNQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSL-GSITSLEVLDLSYNSFNGSIPESLGQLTSLRILNL  497 (623)
T ss_pred             EEEEEECCCCCccccCCHHHhCCCCCCEEECCCCcccCcCChHH-hCCCCCCEEECCCCCCCCCCchHHhcCCCCCEEEC
Confidence            3778889988887 78888899999999999998887 777777 89999999999999776 67888899999999999


Q ss_pred             CCccCCCCCCC
Q 003387          599 GSITLPAHPGK  609 (824)
Q Consensus       599 ~~~~~~~~~~p  609 (824)
                      ++|.+.+ .+|
T Consensus       498 s~N~l~g-~iP  507 (623)
T PLN03150        498 NGNSLSG-RVP  507 (623)
T ss_pred             cCCcccc-cCC
Confidence            9888764 444

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.21  E-value=6e-07  Score=89.12  Aligned_cols=83  Identities=17%  Similarity=0.204  Sum_probs=46.7

Q ss_pred             cccEEEeeCccCccCC--ccCC-CCCcceEEeecCCCCCccC--hhhhhcCCCccEeecCCccccccchhh-hccccCce
Q 003387          522 LLRVLDLGSLVLIQYP--SGIE-NLFLLRYLKLNIPSLNSLP--SSLLSNLLNLYTLDMPFSYIDHTADEF-WKMNKLRH  595 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp--~~i~-~l~~Lr~L~L~~~~i~~lp--~~i~~~L~~L~~L~L~~~~l~~lp~~i-~~L~~L~~  595 (824)
                      .+..|.+.++.|...-  ..|+ ...+++.|+|.+|.|+.-.  ..|+.+|+.|++|+|+.|.+..-...+ -.+.+|+.
T Consensus        46 a~ellvln~~~id~~gd~~~~~~~~~~v~elDL~~N~iSdWseI~~ile~lP~l~~LNls~N~L~s~I~~lp~p~~nl~~  125 (418)
T KOG2982|consen   46 ALELLVLNGSIIDNEGDVMLFGSSVTDVKELDLTGNLISDWSEIGAILEQLPALTTLNLSCNSLSSDIKSLPLPLKNLRV  125 (418)
T ss_pred             chhhheecCCCCCcchhHHHHHHHhhhhhhhhcccchhccHHHHHHHHhcCccceEeeccCCcCCCccccCcccccceEE
Confidence            3445666666665222  2233 3567777777777776322  123357777777777777544322211 24557777


Q ss_pred             ecCCCccCC
Q 003387          596 LNFGSITLP  604 (824)
Q Consensus       596 L~L~~~~~~  604 (824)
                      |-|.++.++
T Consensus       126 lVLNgT~L~  134 (418)
T KOG2982|consen  126 LVLNGTGLS  134 (418)
T ss_pred             EEEcCCCCC
Confidence            766666654

>COG5238 RNA1 Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

Probab=98.17  E-value=1.1e-07  Score=93.02  Aligned_cols=249  Identities=18%  Similarity=0.144  Sum_probs=161.2

Q ss_pred             cccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCC----ccChhh------hhcCCCccEeecCCcccc-
Q 003387          518 GMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLN----SLPSSL------LSNLLNLYTLDMPFSYID-  581 (824)
Q Consensus       518 ~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~----~lp~~i------~~~L~~L~~L~L~~~~l~-  581 (824)
                      ..+..+..++||||.|.     .+-..|.+-.+|+..+++.-...    ++|+++      +-+|++|++.+||.|.+. 
T Consensus        27 ~~~d~~~evdLSGNtigtEA~e~l~~~ia~~~~L~vvnfsd~ftgr~kde~~~~L~~Ll~aLlkcp~l~~v~LSDNAfg~  106 (388)
T COG5238          27 EMMDELVEVDLSGNTIGTEAMEELCNVIANVRNLRVVNFSDAFTGRDKDELYSNLVMLLKALLKCPRLQKVDLSDNAFGS  106 (388)
T ss_pred             HhhcceeEEeccCCcccHHHHHHHHHHHhhhcceeEeehhhhhhcccHHHHHHHHHHHHHHHhcCCcceeeeccccccCc
Confidence            34788889999999875     45566777788998888863222    344332      368999999999999433 


Q ss_pred             ccc----hhhhccccCceecCCCccCCCCCCCCCCCCC-CCCeeeccCCCcchhhhcCCCCccceEEEeccc--ccchhh
Q 003387          582 HTA----DEFWKMNKLRHLNFGSITLPAHPGKFCGSLE-NLNFISALHPCCCTEDILGRLPNLRNLRIRGDL--SYNQSL  654 (824)
Q Consensus       582 ~lp----~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~-~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~--~~~~~~  654 (824)
                      +.|    +.|++-+.|.||.+++|.+..  +. =+++- .|.+|...      .. ...-|.|+...+..++  +.....
T Consensus       107 ~~~e~L~d~is~~t~l~HL~l~NnGlGp--~a-G~rigkal~~la~n------KK-aa~kp~Le~vicgrNRlengs~~~  176 (388)
T COG5238         107 EFPEELGDLISSSTDLVHLKLNNNGLGP--IA-GGRIGKALFHLAYN------KK-AADKPKLEVVICGRNRLENGSKEL  176 (388)
T ss_pred             ccchHHHHHHhcCCCceeEEeecCCCCc--cc-hhHHHHHHHHHHHH------hh-hccCCCceEEEeccchhccCcHHH
Confidence            334    346778899999998886641  11 11111 02222111      11 3445677777776664  112233


Q ss_pred             HHHHhccCCCCCeEEEeccC-CCCCccEEEeCccCcCCCceEEEEEcccCCCCCc----ccccCCCCCCeEEeeccccCC
Q 003387          655 LSKSLCRLSCLESLKLANES-KMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPM----PTLEKLPLLQVLKLKQNSYSG  729 (824)
Q Consensus       655 l~~~l~~l~~L~~L~l~~~~-~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~----~~l~~l~~L~~L~L~~~~~~~  729 (824)
                      ....+....+|+.+.+..|. .+..+..|.+.|...+.+|+.|+|..|.++....    ..+..++.|++|.+.+|-+..
T Consensus       177 ~a~~l~sh~~lk~vki~qNgIrpegv~~L~~~gl~y~~~LevLDlqDNtft~~gS~~La~al~~W~~lrEL~lnDClls~  256 (388)
T COG5238         177 SAALLESHENLKEVKIQQNGIRPEGVTMLAFLGLFYSHSLEVLDLQDNTFTLEGSRYLADALCEWNLLRELRLNDCLLSN  256 (388)
T ss_pred             HHHHHHhhcCceeEEeeecCcCcchhHHHHHHHHHHhCcceeeeccccchhhhhHHHHHHHhcccchhhhccccchhhcc
Confidence            33445555789999998875 4445666666677888999999999998764432    235567889999999887664


Q ss_pred             Ceee-----ecCCCCCCccEEeeccCCCCccc-------eeccCcccCccEEEEecCCC
Q 003387          730 RKLT-----CGSYGFPNLKVLHLKSMLWLEEW-------TMGNAAMPKLECLIINPCAY  776 (824)
Q Consensus       730 ~~~~-----~~~~~~~~L~~L~L~~~~~l~~l-------~~~~~~lp~L~~L~l~~c~~  776 (824)
                      ....     +.-..+|+|..|.+.++..-..+       .+..+++|-|..|.+.+|..
T Consensus       257 ~G~~~v~~~f~e~~~p~l~~L~~~Yne~~~~~i~~~~l~~~e~~~~p~L~~le~ngNr~  315 (388)
T COG5238         257 EGVKSVLRRFNEKFVPNLMPLPGDYNERRGGIILDISLNEFEQDAVPLLVDLERNGNRI  315 (388)
T ss_pred             ccHHHHHHHhhhhcCCCccccccchhhhcCceeeeechhhhhhcccHHHHHHHHccCcc
Confidence            3211     12235899999988876532221       12456789999999998874

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.14  E-value=2.5e-05  Score=84.13  Aligned_cols=250  Identities=15%  Similarity=0.061  Sum_probs=124.0

Q ss_pred             CCCceechhhHHHHHHHHHc---CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIE---GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      -.+++|++..++.+..++..   .......+.|+|++|+||||+|+.+.+  +....|.   ++.  .+ ......-+..
T Consensus        24 ~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~--~l~~~~~---~~~--~~-~~~~~~~l~~   95 (328)
T PRK00080         24 LDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIAN--EMGVNIR---ITS--GP-ALEKPGDLAA   95 (328)
T ss_pred             HHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHH--HhCCCeE---EEe--cc-cccChHHHHH
Confidence            46799999999999888764   233466788999999999999999999  4443321   222  11 1111222333


Q ss_pred             HHHHhCCCCC--cccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh---
Q 003387          232 VIKFLMPSSR--LSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII---  306 (824)
Q Consensus       232 i~~~l~~~~~--~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~---  306 (824)
                      ++..+....-  .++.+..+ ....+.+...+.+.+..+|+|+..+...+.   ..++   +.+-|..|||...+..   
T Consensus        96 ~l~~l~~~~vl~IDEi~~l~-~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~---~~l~---~~~li~at~~~~~l~~~L~  168 (328)
T PRK00080         96 ILTNLEEGDVLFIDEIHRLS-PVVEEILYPAMEDFRLDIMIGKGPAARSIR---LDLP---PFTLIGATTRAGLLTSPLR  168 (328)
T ss_pred             HHHhcccCCEEEEecHhhcc-hHHHHHHHHHHHhcceeeeeccCcccccee---ecCC---CceEEeecCCcccCCHHHH
Confidence            3443322110  00011111 112334555566666667777655443221   1111   2455666766433222   


Q ss_pred             -hccccc--C---------------CcCc-CccccchhhHHHhcCCCchhHHHHHhHHHhhhhh--h-hccCCC--cccc
Q 003387          307 -SFQFED--G---------------ENMR-LDLVPTGGPLRATYKGRPFLILYHGSISLEENIR--E-AVETPL--GLRY  362 (824)
Q Consensus       307 -~f~~~~--~---------------~~~~-~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~~~--~-~~~~~~--~~~~  362 (824)
                       -|+...  .               .... .--.+....|++.|+|.|-.+..+...+..-...  . .+....  ....
T Consensus       169 sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~  248 (328)
T PRK00080        169 DRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALD  248 (328)
T ss_pred             HhcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence             121110  0               0001 1112456789999999996544444433100000  0 010000  1111


Q ss_pred             cccc---cCCCCchHHHh-HhccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHH-HHHhcccccee
Q 003387          363 IKCL---MLPFCLKPCFI-YLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLE-QLIKEGFVEAK  427 (824)
Q Consensus       363 ~l~~---~L~~~lk~cfl-~~s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~-~Lv~rsllq~~  427 (824)
                      .+..   .|++..+.-+. ....|+.+ .+..+.+....   |    ...+.+++.++ .|++.+|++..
T Consensus       249 ~~~~~~~~l~~~~~~~l~~~~~~~~~~-~~~~~~~a~~l---g----~~~~~~~~~~e~~Li~~~li~~~  310 (328)
T PRK00080        249 MLGVDELGLDEMDRKYLRTIIEKFGGG-PVGLDTLAAAL---G----EERDTIEDVYEPYLIQQGFIQRT  310 (328)
T ss_pred             HhCCCcCCCCHHHHHHHHHHHHHcCCC-ceeHHHHHHHH---C----CCcchHHHHhhHHHHHcCCcccC
Confidence            2222   56655555553 55566655 35555543221   1    22334666677 89999999744

>TIGR00767 rho transcription termination factor Rho

Probab=98.09  E-value=5.8e-06  Score=88.03  Aligned_cols=95  Identities=12%  Similarity=0.009  Sum_probs=63.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC--CCHHHHHHHHHHHhCCCC-CcccccccCH-HHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE--YDADQILDIVIKFLMPSS-RLSEIMDKNY-EMKK  254 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~--~~~~~~~~~i~~~l~~~~-~~~~~~~~~~-~~~~  254 (824)
                      -..++|+|.+|.|||||++.+++.... ++|+..+||.  +++.  .++.++++.|...+-... +.+....... ....
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~-nhfdv~v~Vl--LIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~  244 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITR-NHPEVELIVL--LIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVI  244 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhcc-cCCceEEEEE--EcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHH
Confidence            457899999999999999999995332 3799999999  8866  799999999854432211 1010011111 1122


Q ss_pred             HHHHHh-cCCCeEEEEEecCCCh
Q 003387          255 IILHEY-LMTKRYLIVIDDVWSI  276 (824)
Q Consensus       255 ~~l~~~-L~~kr~LlVlDdv~~~  276 (824)
                      +....+ -++++++|++|++..-
T Consensus       245 e~Ae~~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       245 EKAKRLVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHHHHHHcCCCeEEEEEChhHH
Confidence            222222 2589999999999654

Members of this family differ in the specificity of RNA binding.

>PTZ00202 tuzin; Provisional

Probab=98.03  E-value=5.6e-05  Score=80.49  Aligned_cols=80  Identities=15%  Similarity=0.126  Sum_probs=61.5

Q ss_pred             CCCCCCCCceechhhHHHHHHHHHcCC-CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHH
Q 003387          150 SSSSKSRDTVGLDDRMEELLDLLIEGP-PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQI  228 (824)
Q Consensus       150 ~~~~~~~~~vGr~~~~~~l~~~L~~~~-~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~  228 (824)
                      ..+.+...++||+.+...+...|...+ ...+++.|.|++|+|||||++.+...  ..  + ...+++   +.  +..++
T Consensus       256 ~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~--l~--~-~qL~vN---pr--g~eEl  325 (550)
T PTZ00202        256 SAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRK--EG--M-PAVFVD---VR--GTEDT  325 (550)
T ss_pred             CCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhc--CC--c-eEEEEC---CC--CHHHH
Confidence            344567899999999999999997543 34569999999999999999999973  32  1 133333   22  67999


Q ss_pred             HHHHHHHhCCC
Q 003387          229 LDIVIKFLMPS  239 (824)
Q Consensus       229 ~~~i~~~l~~~  239 (824)
                      +..|+.+|+..
T Consensus       326 Lr~LL~ALGV~  336 (550)
T PTZ00202        326 LRSVVKALGVP  336 (550)
T ss_pred             HHHHHHHcCCC
Confidence            99999999973

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=98.02  E-value=6.4e-07  Score=99.83  Aligned_cols=220  Identities=20%  Similarity=0.172  Sum_probs=110.7

Q ss_pred             hhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCce
Q 003387          516 FCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRH  595 (824)
Q Consensus       516 ~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~  595 (824)
                      .+..++.|..|++.+|.|..+...+..+++|++|++++|.|..+.. + ..+..|+.|++++|.+..++. +..+++|+.
T Consensus        90 ~l~~~~~l~~l~l~~n~i~~i~~~l~~~~~L~~L~ls~N~I~~i~~-l-~~l~~L~~L~l~~N~i~~~~~-~~~l~~L~~  166 (414)
T KOG0531|consen   90 HLSKLKSLEALDLYDNKIEKIENLLSSLVNLQVLDLSFNKITKLEG-L-STLTLLKELNLSGNLISDISG-LESLKSLKL  166 (414)
T ss_pred             ccccccceeeeeccccchhhcccchhhhhcchheeccccccccccc-h-hhccchhhheeccCcchhccC-Cccchhhhc
Confidence            3556667777777777776665556667777777777777776654 2 566667777777776666554 445677777


Q ss_pred             ecCCCccCCCCCCCC--CCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCC--CCCeEEEe
Q 003387          596 LNFGSITLPAHPGKF--CGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLS--CLESLKLA  671 (824)
Q Consensus       596 L~L~~~~~~~~~~p~--i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~--~L~~L~l~  671 (824)
                      +++++|.+.  .++.  ...+.+|+.+.+..+.....+.+..+..+..+++..+.-.....+    ..+.  +|+.+++.
T Consensus       167 l~l~~n~i~--~ie~~~~~~~~~l~~l~l~~n~i~~i~~~~~~~~l~~~~l~~n~i~~~~~l----~~~~~~~L~~l~l~  240 (414)
T KOG0531|consen  167 LDLSYNRIV--DIENDELSELISLEELDLGGNSIREIEGLDLLKKLVLLSLLDNKISKLEGL----NELVMLHLRELYLS  240 (414)
T ss_pred             ccCCcchhh--hhhhhhhhhccchHHHhccCCchhcccchHHHHHHHHhhcccccceeccCc----ccchhHHHHHHhcc
Confidence            777776665  3333  355566666655532222111133333333333333221111111    1111  25566665


Q ss_pred             ccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCC-eee-e-cCCCCCCccEEeec
Q 003387          672 NESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGR-KLT-C-GSYGFPNLKVLHLK  748 (824)
Q Consensus       672 ~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~-~~~-~-~~~~~~~L~~L~L~  748 (824)
                      .|.    +.... .+...+.++..|++.++.+..  ...+...+.+..+....+.+... ... . .....+.+....+.
T Consensus       241 ~n~----i~~~~-~~~~~~~~l~~l~~~~n~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  313 (414)
T KOG0531|consen  241 GNR----ISRSP-EGLENLKNLPVLDLSSNRISN--LEGLERLPKLSELWLNDNKLALSEAISQEYITSAAPTLVTLTLE  313 (414)
T ss_pred             cCc----ccccc-ccccccccccccchhhccccc--cccccccchHHHhccCcchhcchhhhhccccccccccccccccc
Confidence            541    11110 233455666667776665432  22233444445555544443311 111 1 13345566666665


Q ss_pred             cCC
Q 003387          749 SML  751 (824)
Q Consensus       749 ~~~  751 (824)
                      .++
T Consensus       314 ~~~  316 (414)
T KOG0531|consen  314 LNP  316 (414)
T ss_pred             cCc
Confidence            544

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=98.01  E-value=4.5e-05  Score=87.51  Aligned_cols=117  Identities=13%  Similarity=0.012  Sum_probs=79.9

Q ss_pred             CCCceechhhHHHHHHHHHc---CCCCeEEEEEEcCCCChHHHHHHHHhCCcc--c-cCCCc--eeEEEECCCCCCCCHH
Q 003387          155 SRDTVGLDDRMEELLDLLIE---GPPQLSVVAILDSIGLDKTAFAGEAYNSSY--V-KHYFD--CHAWITEPYSNEYDAD  226 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~--~-~~~F~--~~~wv~~~vs~~~~~~  226 (824)
                      ++.+.|||+++++|...|..   +.....++-|+|++|.|||+.++.|.+.-+  . +....  .+++|.  ...-.+..
T Consensus       754 PD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYIN--Cm~Lstp~  831 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEIN--GMNVVHPN  831 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEe--CCccCCHH
Confidence            35689999999999998875   233346788999999999999999987311  0 11222  245555  66666788


Q ss_pred             HHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCC---CeEEEEEecCCCh
Q 003387          227 QILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT---KRYLIVIDDVWSI  276 (824)
Q Consensus       227 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~---kr~LlVlDdv~~~  276 (824)
                      .+...|+.++....+   ............+...+..   ...+||||+|+..
T Consensus       832 sIYqvI~qqL~g~~P---~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L  881 (1164)
T PTZ00112        832 AAYQVLYKQLFNKKP---PNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYL  881 (1164)
T ss_pred             HHHHHHHHHHcCCCC---CccccHHHHHHHHHhhhhcccccceEEEeehHhhh
Confidence            899999999965432   1233344555666665522   3458999999754

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=97.96  E-value=2e-05  Score=84.18  Aligned_cols=249  Identities=15%  Similarity=0.087  Sum_probs=125.7

Q ss_pred             CCceechhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      .+++|++..++++..++...   ......+.++|++|+|||+||+.+.+  +....|   ..+.  .+....... +...
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~--~~~~~~---~~~~--~~~~~~~~~-l~~~   75 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIAN--EMGVNL---KITS--GPALEKPGD-LAAI   75 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHH--HhCCCE---EEec--cchhcCchh-HHHH
Confidence            46899999999999888642   23356688999999999999999998  444332   1222  111111222 2223


Q ss_pred             HHHhCCCCC--cccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHhh---
Q 003387          233 IKFLMPSSR--LSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIIIS---  307 (824)
Q Consensus       233 ~~~l~~~~~--~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~~---  307 (824)
                      +..+....-  .++.+..+ ....+.+...+.+.+..+|+|+......|..   +++   +.+-|..||+...+..+   
T Consensus        76 l~~~~~~~vl~iDEi~~l~-~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~---~~~---~~~li~~t~~~~~l~~~l~s  148 (305)
T TIGR00635        76 LTNLEEGDVLFIDEIHRLS-PAVEELLYPAMEDFRLDIVIGKGPSARSVRL---DLP---PFTLVGATTRAGMLTSPLRD  148 (305)
T ss_pred             HHhcccCCEEEEehHhhhC-HHHHHHhhHHHhhhheeeeeccCccccceee---cCC---CeEEEEecCCccccCHHHHh
Confidence            333332110  00011111 1234556777777777788888766654431   122   24556666765332221   


Q ss_pred             -ccccc--C---------------CcCcCcc-ccchhhHHHhcCCCchhHHHHHhHHHhhh--hh-hhccCCC--ccccc
Q 003387          308 -FQFED--G---------------ENMRLDL-VPTGGPLRATYKGRPFLILYHGSISLEEN--IR-EAVETPL--GLRYI  363 (824)
Q Consensus       308 -f~~~~--~---------------~~~~~~~-~~~~~~i~~~c~GlPlai~~~~~~l~~~~--~~-~~~~~~~--~~~~~  363 (824)
                       |....  .               ......+ .+....|++.|+|.|-.+..+...+..-.  .. .......  .....
T Consensus       149 R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~  228 (305)
T TIGR00635       149 RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEM  228 (305)
T ss_pred             hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHH
Confidence             11100  0               0001111 24567899999999976655554431000  00 0010000  11111


Q ss_pred             ccc---cCCCCchHHHh-HhccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHH-HHHhcccccee
Q 003387          364 KCL---MLPFCLKPCFI-YLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLE-QLIKEGFVEAK  427 (824)
Q Consensus       364 l~~---~L~~~lk~cfl-~~s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~-~Lv~rsllq~~  427 (824)
                      +..   .++++.+.-+. ..+.++.+ .+..+++....   |    .....++..++ .|++++|++..
T Consensus       229 l~~~~~~l~~~~~~~L~al~~~~~~~-~~~~~~ia~~l---g----~~~~~~~~~~e~~Li~~~li~~~  289 (305)
T TIGR00635       229 LMIDELGLDEIDRKLLSVLIEQFQGG-PVGLKTLAAAL---G----EDADTIEDVYEPYLLQIGFLQRT  289 (305)
T ss_pred             hCCCCCCCCHHHHHHHHHHHHHhCCC-cccHHHHHHHh---C----CCcchHHHhhhHHHHHcCCcccC
Confidence            222   55655554444 44555433 34443322211   1    22344677778 69999999743

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.

>PLN03150 hypothetical protein; Provisional

Probab=97.96  E-value=9e-06  Score=94.96  Aligned_cols=91  Identities=18%  Similarity=0.191  Sum_probs=47.7

Q ss_pred             CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCc-ccCc
Q 003387          688 LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAA-MPKL  766 (824)
Q Consensus       688 ~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~-lp~L  766 (824)
                      ..+++|+.|+|++|.+.+.+|..++.+++|+.|+|++|.+.+. ++..++.+++|+.|+|++|.....+|..++. +.++
T Consensus       439 ~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~-iP~~l~~L~~L~~L~Ls~N~l~g~iP~~l~~~~~~~  517 (623)
T PLN03150        439 SKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGS-IPESLGQLTSLRILNLNGNSLSGRVPAALGGRLLHR  517 (623)
T ss_pred             hCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCC-CchHHhcCCCCCEEECcCCcccccCChHHhhccccC
Confidence            3445556666666555555555555566666666665555542 3334455556666666555543444444333 2344


Q ss_pred             cEEEEecCCCCCC
Q 003387          767 ECLIINPCAYLKK  779 (824)
Q Consensus       767 ~~L~l~~c~~l~~  779 (824)
                      ..+.+.+|+.+..
T Consensus       518 ~~l~~~~N~~lc~  530 (623)
T PLN03150        518 ASFNFTDNAGLCG  530 (623)
T ss_pred             ceEEecCCccccC
Confidence            5555555554443

>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=97.93  E-value=1e-05  Score=57.83  Aligned_cols=39  Identities=36%  Similarity=0.423  Sum_probs=21.7

Q ss_pred             cceEEeecCCCCCccChhhhhcCCCccEeecCCccccccc
Q 003387          545 LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA  584 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp  584 (824)
                      +|++|++++|+|+.+|+.+ ++|++|++|++++|.++.+|
T Consensus         2 ~L~~L~l~~N~i~~l~~~l-~~l~~L~~L~l~~N~i~~i~   40 (44)
T PF12799_consen    2 NLEELDLSNNQITDLPPEL-SNLPNLETLNLSNNPISDIS   40 (44)
T ss_dssp             T-SEEEETSSS-SSHGGHG-TTCTTSSEEEETSSCCSBEG
T ss_pred             cceEEEccCCCCcccCchH-hCCCCCCEEEecCCCCCCCc
Confidence            4556666666666665555 56666666666666555543

...

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.92  E-value=6.1e-06  Score=96.04  Aligned_cols=108  Identities=21%  Similarity=0.176  Sum_probs=53.3

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc--cCCccCCCCCcceEEeecCCCCCccChhhhhcCCC
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI--QYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLN  569 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~--~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~  569 (824)
                      ..+|+.|.+.+....  ...++...-..+|.||.|.++|-.+.  .+..-..++++|+.||+|+|+++.+ ..+ ++|+|
T Consensus       121 r~nL~~LdI~G~~~~--s~~W~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~TnI~nl-~GI-S~Lkn  196 (699)
T KOG3665|consen  121 RQNLQHLDISGSELF--SNGWPKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISGTNISNL-SGI-SRLKN  196 (699)
T ss_pred             HHhhhhcCccccchh--hccHHHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCCCCccCc-HHH-hcccc
Confidence            334444444443222  23344455555555555555555432  2222234455566666666655555 444 56666


Q ss_pred             ccEeecCCccccccc--hhhhccccCceecCCCccC
Q 003387          570 LYTLDMPFSYIDHTA--DEFWKMNKLRHLNFGSITL  603 (824)
Q Consensus       570 L~~L~L~~~~l~~lp--~~i~~L~~L~~L~L~~~~~  603 (824)
                      ||+|.+++-.+..-.  ..+.+|++|++||+|....
T Consensus       197 Lq~L~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~~  232 (699)
T KOG3665|consen  197 LQVLSMRNLEFESYQDLIDLFNLKKLRVLDISRDKN  232 (699)
T ss_pred             HHHHhccCCCCCchhhHHHHhcccCCCeeecccccc
Confidence            666665544333221  2355566666666555433

>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=97.89  E-value=1.1e-05  Score=57.73  Aligned_cols=41  Identities=27%  Similarity=0.353  Sum_probs=36.0

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccCh
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPS  561 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~  561 (824)
                      ++|++|++++|.|+.+|..+++|++|++|++++|.++.++.
T Consensus         1 ~~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i~~i~~   41 (44)
T PF12799_consen    1 KNLEELDLSNNQITDLPPELSNLPNLETLNLSNNPISDISP   41 (44)
T ss_dssp             TT-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCCSBEGG
T ss_pred             CcceEEEccCCCCcccCchHhCCCCCCEEEecCCCCCCCcC
Confidence            47999999999999999989999999999999999997764

...

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.88  E-value=0.0002  Score=76.67  Aligned_cols=125  Identities=13%  Similarity=0.226  Sum_probs=82.1

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC----ccccCCCceeEEEECCC-CCCCCHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS----SYVKHYFDCHAWITEPY-SNEYDADQILD  230 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~----~~~~~~F~~~~wv~~~v-s~~~~~~~~~~  230 (824)
                      .+++|-+..++.+.+.+..+. -....-++|+.|+||||+|+.+++.    .....|+|...|..  . +....+.+ .+
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~-~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~--~~~~~i~v~~-ir   79 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNR-FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKP--INKKSIGVDD-IR   79 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecc--ccCCCCCHHH-HH
Confidence            468899999999999987654 3457789999999999999888762    12245667666654  2 22233333 22


Q ss_pred             HHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEe-cCCChhhHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          231 IVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVID-DVWSIDMWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlD-dv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                      ++.+.+....                   ...++|++||=| |.++...++.+...+.....++.+|++|.+.+
T Consensus        80 ~~~~~~~~~p-------------------~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~  134 (313)
T PRK05564         80 NIIEEVNKKP-------------------YEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLE  134 (313)
T ss_pred             HHHHHHhcCc-------------------ccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChH
Confidence            3333332211                   112455555555 55566789999998888778899999887664

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.87  E-value=3.9e-05  Score=82.28  Aligned_cols=134  Identities=17%  Similarity=0.156  Sum_probs=81.9

Q ss_pred             hcccCcccEEEeeCccCccCCccCCCCCcceEEeecCC-CCCccChhhhhcCCCccEeecCCc-cccccchhhhccccCc
Q 003387          517 CGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIP-SLNSLPSSLLSNLLNLYTLDMPFS-YIDHTADEFWKMNKLR  594 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~-~i~~lp~~i~~~L~~L~~L~L~~~-~l~~lp~~i~~L~~L~  594 (824)
                      +..++.++.|++++|.++.+|. +  -.+|+.|.+++| .++.+|..+   ..+|+.|++++| .+..+|..      |+
T Consensus        48 ~~~~~~l~~L~Is~c~L~sLP~-L--P~sLtsL~Lsnc~nLtsLP~~L---P~nLe~L~Ls~Cs~L~sLP~s------Le  115 (426)
T PRK15386         48 IEEARASGRLYIKDCDIESLPV-L--PNELTEITIENCNNLTTLPGSI---PEGLEKLTVCHCPEISGLPES------VR  115 (426)
T ss_pred             HHHhcCCCEEEeCCCCCcccCC-C--CCCCcEEEccCCCCcccCCchh---hhhhhheEccCcccccccccc------cc
Confidence            4557889999999999988883 2  236999999884 477888765   368999999999 88888864      56


Q ss_pred             eecCCCccCCCCCCCCCCCCC-CCCeeeccCCCcchhhhcC-CC-CccceEEEecccccchhhHHHHhccCCCCCeEEEe
Q 003387          595 HLNFGSITLPAHPGKFCGSLE-NLNFISALHPCCCTEDILG-RL-PNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLA  671 (824)
Q Consensus       595 ~L~L~~~~~~~~~~p~i~~L~-~L~~l~~~~~~~~~~~~l~-~l-~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~  671 (824)
                      .|+++.+...     .++.|+ +|+.|.+..........+. .+ ++|+.|.+++|..   ..+|..+.  .+|+.|.++
T Consensus       116 ~L~L~~n~~~-----~L~~LPssLk~L~I~~~n~~~~~~lp~~LPsSLk~L~Is~c~~---i~LP~~LP--~SLk~L~ls  185 (426)
T PRK15386        116 SLEIKGSATD-----SIKNVPNGLTSLSINSYNPENQARIDNLISPSLKTLSLTGCSN---IILPEKLP--ESLQSITLH  185 (426)
T ss_pred             eEEeCCCCCc-----ccccCcchHhheeccccccccccccccccCCcccEEEecCCCc---ccCccccc--ccCcEEEec
Confidence            6666544332     223332 2555554311100000011 12 4788888887741   12232222  467777776


Q ss_pred             c
Q 003387          672 N  672 (824)
Q Consensus       672 ~  672 (824)
                      .
T Consensus       186 ~  186 (426)
T PRK15386        186 I  186 (426)
T ss_pred             c
Confidence            4

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=97.86  E-value=8.6e-05  Score=80.10  Aligned_cols=113  Identities=15%  Similarity=0.135  Sum_probs=86.5

Q ss_pred             CCceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCce--eEEEECCCCCCCCHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDC--HAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~--~~wv~~~vs~~~~~~~~~~~  231 (824)
                      +.+.+|+++++++...|..-  .....-+.|+|..|.|||+.++.|.+  ++......  ++.|.  +-......+++..
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~--~l~~~~~~~~~~yIN--c~~~~t~~~i~~~   92 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVME--ELEESSANVEVVYIN--CLELRTPYQVLSK   92 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHH--HHHhhhccCceEEEe--eeeCCCHHHHHHH
Confidence            34889999999999988752  22233389999999999999999999  55554322  56776  7788899999999


Q ss_pred             HHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCCh
Q 003387          232 VIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSI  276 (824)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~  276 (824)
                      |+++++...    .......+....+.+.+.  ++.+++|||++...
T Consensus        93 i~~~~~~~p----~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L  135 (366)
T COG1474          93 ILNKLGKVP----LTGDSSLEILKRLYDNLSKKGKTVIVILDEVDAL  135 (366)
T ss_pred             HHHHcCCCC----CCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhh
Confidence            999997322    234556677777877774  58999999999754

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.84  E-value=8.5e-06  Score=94.82  Aligned_cols=109  Identities=24%  Similarity=0.288  Sum_probs=87.7

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccC--hhhhhcCCC
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLP--SSLLSNLLN  569 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp--~~i~~~L~~  569 (824)
                      +|.||+|.+.+....   ...+...+.+|++|+.||+|+++++.+ ..+++|++|+.|.+++-.+..-.  ..+ .+|++
T Consensus       147 LPsL~sL~i~~~~~~---~~dF~~lc~sFpNL~sLDIS~TnI~nl-~GIS~LknLq~L~mrnLe~e~~~~l~~L-F~L~~  221 (699)
T KOG3665|consen  147 LPSLRSLVISGRQFD---NDDFSQLCASFPNLRSLDISGTNISNL-SGISRLKNLQVLSMRNLEFESYQDLIDL-FNLKK  221 (699)
T ss_pred             CcccceEEecCceec---chhHHHHhhccCccceeecCCCCccCc-HHHhccccHHHHhccCCCCCchhhHHHH-hcccC
Confidence            999999999987764   334678889999999999999999988 77999999999999987776433  345 78999


Q ss_pred             ccEeecCCccccccch-------hhhccccCceecCCCccCCC
Q 003387          570 LYTLDMPFSYIDHTAD-------EFWKMNKLRHLNFGSITLPA  605 (824)
Q Consensus       570 L~~L~L~~~~l~~lp~-------~i~~L~~L~~L~L~~~~~~~  605 (824)
                      |++||+|......-+.       .-..||+||.||.+++.+..
T Consensus       222 L~vLDIS~~~~~~~~~ii~qYlec~~~LpeLrfLDcSgTdi~~  264 (699)
T KOG3665|consen  222 LRVLDISRDKNNDDTKIIEQYLECGMVLPELRFLDCSGTDINE  264 (699)
T ss_pred             CCeeeccccccccchHHHHHHHHhcccCccccEEecCCcchhH
Confidence            9999999874333322       12348999999999887754

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=97.82  E-value=0.00011  Score=76.20  Aligned_cols=118  Identities=11%  Similarity=0.153  Sum_probs=84.4

Q ss_pred             CCCceechhhHHHHHHHHHcCCC-CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPP-QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~-~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      ++.+.+|+..+..+..++...+. -...|-|+|-.|.|||.+++.+++..  ..   ..+|++  +-..|..+-++..|+
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~--n~---~~vw~n--~~ecft~~~lle~IL   77 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKL--NL---ENVWLN--CVECFTYAILLEKIL   77 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhc--CC---cceeee--hHHhccHHHHHHHHH
Confidence            46777999999999999987764 35666899999999999999999943  22   358999  999999999999999


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHhcC-------CCeEEEEEecCCChhhH
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEYLM-------TKRYLIVIDDVWSIDMW  279 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~-------~kr~LlVlDdv~~~~~~  279 (824)
                      .+.+..+..+.....+.+.....+..+-+       ++.++||||++....+.
T Consensus        78 ~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~  130 (438)
T KOG2543|consen   78 NKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDM  130 (438)
T ss_pred             HHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhcc
Confidence            99963222111111122333333332222       46899999999876443

>PRK13342 recombination factor protein RarA; Reviewed

Probab=97.80  E-value=4.7e-05  Score=84.59  Aligned_cols=44  Identities=23%  Similarity=0.298  Sum_probs=34.7

Q ss_pred             CCceechhhHHH---HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEE---LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~---l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +++||.+..+..   +.+++..+.  ...+.++|++|+||||+|+.+.+
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~~~--~~~ilL~GppGtGKTtLA~~ia~   58 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEAGR--LSSMILWGPPGTGKTTLARIIAG   58 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHcCC--CceEEEECCCCCCHHHHHHHHHH
Confidence            467787776555   666665544  55788899999999999999998

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=97.74  E-value=1.3e-06  Score=96.59  Aligned_cols=94  Identities=16%  Similarity=0.190  Sum_probs=45.5

Q ss_pred             EEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCC--CCCCCCCCCeeeccCC
Q 003387          548 YLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK--FCGSLENLNFISALHP  625 (824)
Q Consensus       548 ~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p--~i~~L~~L~~l~~~~~  625 (824)
                      ..+.++|.+..+..++ .-++.|+.|||++|++...- .+..|++|+||||++|.+.  .+|  +...+. |..|.+.++
T Consensus       168 ~a~fsyN~L~~mD~SL-qll~ale~LnLshNk~~~v~-~Lr~l~~LkhLDlsyN~L~--~vp~l~~~gc~-L~~L~lrnN  242 (1096)
T KOG1859|consen  168 TASFSYNRLVLMDESL-QLLPALESLNLSHNKFTKVD-NLRRLPKLKHLDLSYNCLR--HVPQLSMVGCK-LQLLNLRNN  242 (1096)
T ss_pred             hhhcchhhHHhHHHHH-HHHHHhhhhccchhhhhhhH-HHHhcccccccccccchhc--cccccchhhhh-heeeeeccc
Confidence            3334444444444554 55555666666666555544 4555666666666665554  333  111112 444444422


Q ss_pred             C-cchhhhcCCCCccceEEEecc
Q 003387          626 C-CCTEDILGRLPNLRNLRIRGD  647 (824)
Q Consensus       626 ~-~~~~~~l~~l~~L~~L~l~~~  647 (824)
                      . ..+.. +.+|++|+.|+++.|
T Consensus       243 ~l~tL~g-ie~LksL~~LDlsyN  264 (1096)
T KOG1859|consen  243 ALTTLRG-IENLKSLYGLDLSYN  264 (1096)
T ss_pred             HHHhhhh-HHhhhhhhccchhHh
Confidence            1 22333 455555555555554

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.70  E-value=0.00055  Score=79.50  Aligned_cols=142  Identities=15%  Similarity=0.138  Sum_probs=87.8

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC---ceeEEEECCCCC---CCCHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF---DCHAWITEPYSN---EYDADQIL  229 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~~~vs~---~~~~~~~~  229 (824)
                      ++++|.+..+..+.+.+....  ...+.|+|++|+||||+|+.+++.......+   ...-|+.  +..   ..+...+.
T Consensus       154 ~~iiGqs~~~~~l~~~ia~~~--~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~--i~~~~l~~d~~~i~  229 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVASPF--PQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVE--VDGTTLRWDPREVT  229 (615)
T ss_pred             HhceeCcHHHHHHHHHHhcCC--CCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEE--EechhccCCHHHHh
Confidence            578999999999888875443  5679999999999999999998854333332   1234554  321   12333322


Q ss_pred             HHH---------------HHHhCCCC-----------C---cccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hh
Q 003387          230 DIV---------------IKFLMPSS-----------R---LSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DM  278 (824)
Q Consensus       230 ~~i---------------~~~l~~~~-----------~---~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~  278 (824)
                      ..+               +...+...           +   ..+....+ ...+..+.+.+++++++++-|+.|..  ..
T Consensus       230 ~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld-~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~  308 (615)
T TIGR02903       230 NPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELD-PLLQNKLLKVLEDKRVEFSSSYYDPDDPNV  308 (615)
T ss_pred             HHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCC-HHHHHHHHHHHhhCeEEeecceeccCCccc
Confidence            211               11111100           0   00111122 33578899999999999998877765  46


Q ss_pred             HHHHHhhCCCCCCCcEEEE--EechH
Q 003387          279 WDVIQEILPDNQNGSRVLI--TLTDI  302 (824)
Q Consensus       279 ~~~l~~~~~~~~~gs~ilv--TtR~~  302 (824)
                      |+.+...+....+...|++  ||++.
T Consensus       309 ~~~ik~~~~~~~~~~~VLI~aTt~~~  334 (615)
T TIGR02903       309 PKYIKKLFEEGAPADFVLIGATTRDP  334 (615)
T ss_pred             chhhhhhcccCccceEEEEEeccccc
Confidence            8888777776666666666  56644

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=97.67  E-value=9.5e-05  Score=75.06  Aligned_cols=36  Identities=11%  Similarity=-0.025  Sum_probs=28.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ...+.++|..|+|||+||+++++  +.......+.|++
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~--~~~~~~~~~~y~~   74 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSN--HYLLNQRTAIYIP   74 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH--HHHHcCCCeEEee
Confidence            35789999999999999999999  4444444567777

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=97.66  E-value=4.6e-06  Score=73.57  Aligned_cols=84  Identities=24%  Similarity=0.268  Sum_probs=58.6

Q ss_pred             CcccEEEeeCccCccCC---ccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceec
Q 003387          521 KLLRVLDLGSLVLIQYP---SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLN  597 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp---~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~  597 (824)
                      +.+-.++|++|.+..++   ..+....+|...+|++|.++.+|+.+-.+.+.+.+|++++|.+..+|.++..++.|+.|+
T Consensus        27 kE~h~ldLssc~lm~i~davy~l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~neisdvPeE~Aam~aLr~lN  106 (177)
T KOG4579|consen   27 KELHFLDLSSCQLMYIADAVYMLSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANNEISDVPEELAAMPALRSLN  106 (177)
T ss_pred             HHhhhcccccchhhHHHHHHHHHhCCceEEEEecccchhhhCCHHHhhccchhhhhhcchhhhhhchHHHhhhHHhhhcc
Confidence            34556777777655333   344556677777777777777777764455577777777777777777777777778777


Q ss_pred             CCCccCC
Q 003387          598 FGSITLP  604 (824)
Q Consensus       598 L~~~~~~  604 (824)
                      ++.|.+.
T Consensus       107 l~~N~l~  113 (177)
T KOG4579|consen  107 LRFNPLN  113 (177)
T ss_pred             cccCccc
Confidence            7777765

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.66  E-value=9.2e-05  Score=75.31  Aligned_cols=52  Identities=10%  Similarity=0.043  Sum_probs=37.0

Q ss_pred             chhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          161 LDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       161 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .+..++.+.+++...  ....+.|+|..|+||||||+.+++  +........++++
T Consensus        22 ~~~~~~~l~~~~~~~--~~~~lll~G~~G~GKT~la~~~~~--~~~~~~~~~~~i~   73 (226)
T TIGR03420        22 NAELLAALRQLAAGK--GDRFLYLWGESGSGKSHLLQAACA--AAEERGKSAIYLP   73 (226)
T ss_pred             cHHHHHHHHHHHhcC--CCCeEEEECCCCCCHHHHHHHHHH--HHHhcCCcEEEEe
Confidence            455667777775533  367889999999999999999998  3333344455665

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.65  E-value=0.0002  Score=77.77  Aligned_cols=44  Identities=23%  Similarity=0.208  Sum_probs=37.8

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|++..++.+.+++..+.  ...+-++|+.|+||||+|+.+.+
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~GtGKT~la~~~~~   58 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSPN--LPHLLVQGPPGSGKTAAVRALAR   58 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCCC--CceEEEECCCCCCHHHHHHHHHH
Confidence            568899999999999887654  44678999999999999999887

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=97.61  E-value=1.3e-06  Score=96.63  Aligned_cols=121  Identities=20%  Similarity=0.189  Sum_probs=71.5

Q ss_pred             cccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCC
Q 003387          522 LLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGS  600 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~  600 (824)
                      .|.+.++++|.+..+-.++.-+++|+.|+|++|++.+.. .+ ..|++|++|||++|.+..+|.- ...+. |+.|++++
T Consensus       165 ~L~~a~fsyN~L~~mD~SLqll~ale~LnLshNk~~~v~-~L-r~l~~LkhLDlsyN~L~~vp~l~~~gc~-L~~L~lrn  241 (1096)
T KOG1859|consen  165 KLATASFSYNRLVLMDESLQLLPALESLNLSHNKFTKVD-NL-RRLPKLKHLDLSYNCLRHVPQLSMVGCK-LQLLNLRN  241 (1096)
T ss_pred             hHhhhhcchhhHHhHHHHHHHHHHhhhhccchhhhhhhH-HH-Hhcccccccccccchhccccccchhhhh-heeeeecc
Confidence            355556666666555555666666666666666666554 33 6666666666666666666542 22233 66666666


Q ss_pred             ccCCCCCCCCCCCCCCCCeeeccC----CCcchhhhcCCCCccceEEEeccc
Q 003387          601 ITLPAHPGKFCGSLENLNFISALH----PCCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       601 ~~~~~~~~p~i~~L~~L~~l~~~~----~~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      |.+.  .+-++.+|.+|+.|+++.    ....+.. +..|..|+.|++.+|.
T Consensus       242 N~l~--tL~gie~LksL~~LDlsyNll~~hseL~p-LwsLs~L~~L~LeGNP  290 (1096)
T KOG1859|consen  242 NALT--TLRGIENLKSLYGLDLSYNLLSEHSELEP-LWSLSSLIVLWLEGNP  290 (1096)
T ss_pred             cHHH--hhhhHHhhhhhhccchhHhhhhcchhhhH-HHHHHHHHHHhhcCCc
Confidence            6554  344666666666666652    1222333 5566677777777764

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.60  E-value=0.00027  Score=76.89  Aligned_cols=108  Identities=13%  Similarity=0.090  Sum_probs=72.4

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKF  235 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~  235 (824)
                      .++++.+...+.++..|..+    +.|.++|++|+||||+|+.+++.......|+.+.||+  +++.++..+......-.
T Consensus       175 ~d~~i~e~~le~l~~~L~~~----~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~Vt--FHpsySYeDFI~G~rP~  248 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK----KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQ--FHQSYSYEDFIQGYRPN  248 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEe--ecccccHHHHhcccCCC
Confidence            46888999999999998864    3678899999999999999988543345778889999  99988877765432110


Q ss_pred             hCCCCCcccccccCHHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          236 LMPSSRLSEIMDKNYEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       236 l~~~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                         ..+   .... ..-....+.+.-  .+++++||+|++...
T Consensus       249 ---~vg---y~~~-~G~f~~~~~~A~~~p~~~~vliIDEINRa  284 (459)
T PRK11331        249 ---GVG---FRRK-DGIFYNFCQQAKEQPEKKYVFIIDEINRA  284 (459)
T ss_pred             ---CCC---eEec-CchHHHHHHHHHhcccCCcEEEEehhhcc
Confidence               000   0000 011112222222  247899999999765

>KOG1947 consensus Leucine rich repeat proteins, some proteins contain F-box [General function prediction only]

Probab=97.58  E-value=1.8e-05  Score=90.60  Aligned_cols=245  Identities=22%  Similarity=0.129  Sum_probs=135.0

Q ss_pred             hhHhhhcccCcccEEEeeCcc-Ccc--CCccCCCCCcceEEeecCC-C-CCccC---hhhhhcCCCccEeecCCcc-ccc
Q 003387          512 DWEKFCGMFKLLRVLDLGSLV-LIQ--YPSGIENLFLLRYLKLNIP-S-LNSLP---SSLLSNLLNLYTLDMPFSY-IDH  582 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~~-i~~--lp~~i~~l~~Lr~L~L~~~-~-i~~lp---~~i~~~L~~L~~L~L~~~~-l~~  582 (824)
                      ........+++|+.|.+.++. +..  +-.....+++|+.|+++++ . +...+   ..+...+.+|+.|++++|. ++.
T Consensus       179 ~~~~l~~~~~~L~~l~l~~~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~L~~l~l~~~~~isd  258 (482)
T KOG1947|consen  179 ILLRLLSSCPLLKRLSLSGCSKITDDSLDALALKCPNLEELDLSGCCLLITLSPLLLLLLLSICRKLKSLDLSGCGLVTD  258 (482)
T ss_pred             HHHHHHhhCchhhHhhhcccccCChhhHHHHHhhCchhheecccCcccccccchhHhhhhhhhcCCcCccchhhhhccCc
Confidence            344455557778888887775 443  3334456777788877762 1 11111   1122556777777777774 443


Q ss_pred             cc-hhhh-ccccCceecCCCcc-CCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHh
Q 003387          583 TA-DEFW-KMNKLRHLNFGSIT-LPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSL  659 (824)
Q Consensus       583 lp-~~i~-~L~~L~~L~L~~~~-~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l  659 (824)
                      .- ..+. .+++|++|.+.+|. ++                     ...+..+...+++|++|+++++.......+....
T Consensus       259 ~~l~~l~~~c~~L~~L~l~~c~~lt---------------------~~gl~~i~~~~~~L~~L~l~~c~~~~d~~l~~~~  317 (482)
T KOG1947|consen  259 IGLSALASRCPNLETLSLSNCSNLT---------------------DEGLVSIAERCPSLRELDLSGCHGLTDSGLEALL  317 (482)
T ss_pred             hhHHHHHhhCCCcceEccCCCCccc---------------------hhHHHHHHHhcCcccEEeeecCccchHHHHHHHH
Confidence            21 1122 36677777655554 22                     3344444677888999999888755455555555


Q ss_pred             ccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCC---CCcccccCCCCCCeEEeeccccCCCeeeecC
Q 003387          660 CRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMD---DPMPTLEKLPLLQVLKLKQNSYSGRKLTCGS  736 (824)
Q Consensus       660 ~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~---~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~  736 (824)
                      .++++|+.|.+..              +..++.++.+.+..+....   .....+..+++|+.+.+..+.......    
T Consensus       318 ~~c~~l~~l~~~~--------------~~~c~~l~~~~l~~~~~~~~d~~~~~~~~~~~~l~~~~l~~~~~~~~~~----  379 (482)
T KOG1947|consen  318 KNCPNLRELKLLS--------------LNGCPSLTDLSLSGLLTLTSDDLAELILRSCPKLTDLSLSYCGISDLGL----  379 (482)
T ss_pred             HhCcchhhhhhhh--------------cCCCccHHHHHHHHhhccCchhHhHHHHhcCCCcchhhhhhhhccCcch----
Confidence            6666666655442              2224556666665553211   122345678888888888766333221    


Q ss_pred             CCCCCccEEeeccCCCC-ccceeccCcccCccEEEEecCCCCCCCcc-cccc-CccCcEEEecCCcHHH
Q 003387          737 YGFPNLKVLHLKSMLWL-EEWTMGNAAMPKLECLIINPCAYLKKMPE-QLWY-IKSLNKFDCWWPQPEL  802 (824)
Q Consensus       737 ~~~~~L~~L~L~~~~~l-~~l~~~~~~lp~L~~L~l~~c~~l~~lp~-~l~~-l~~L~~L~l~~c~~~l  802 (824)
                             .+.+.+|+.+ ..+.......++|+.|.+..|...+.--. .... +.++..+.+.+|+...
T Consensus       380 -------~~~l~gc~~l~~~l~~~~~~~~~l~~L~l~~~~~~t~~~l~~~~~~~~~~~~l~~~~~~~~~  441 (482)
T KOG1947|consen  380 -------ELSLRGCPNLTESLELRLCRSDSLRVLNLSDCRLVTDKGLRCLADSCSNLKDLDLSGCRVIT  441 (482)
T ss_pred             -------HHHhcCCcccchHHHHHhccCCccceEecccCccccccchHHHhhhhhccccCCccCccccc
Confidence                   2333444444 22222223334488888888876542111 1111 6677888888887333

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.55  E-value=0.00011  Score=80.42  Aligned_cols=55  Identities=18%  Similarity=0.172  Sum_probs=42.2

Q ss_pred             CCCCCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +...++.|+++.+++|.+.+...           -...+-+.++|++|+|||++|+++++  +....|
T Consensus       119 ~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~--~l~~~~  184 (364)
T TIGR01242       119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH--ETNATF  184 (364)
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHH--hCCCCE
Confidence            34567899999999999887532           12245688999999999999999999  444443

Many proteins may score above the trusted cutoff because an internal

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

Probab=97.52  E-value=0.00027  Score=74.17  Aligned_cols=111  Identities=20%  Similarity=0.271  Sum_probs=65.0

Q ss_pred             CCCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHH
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      +...+++|-+..+.+++   ..+.  +.-.-.||++|+||||||+.+..  .....|...       |-..+-.+=++++
T Consensus        27 vGQ~HLlg~~~~lrr~v---~~~~--l~SmIl~GPPG~GKTTlA~liA~--~~~~~f~~~-------sAv~~gvkdlr~i   92 (436)
T COG2256          27 VGQEHLLGEGKPLRRAV---EAGH--LHSMILWGPPGTGKTTLARLIAG--TTNAAFEAL-------SAVTSGVKDLREI   92 (436)
T ss_pred             cChHhhhCCCchHHHHH---hcCC--CceeEEECCCCCCHHHHHHHHHH--hhCCceEEe-------ccccccHHHHHHH
Confidence            34455666655555444   3333  66667899999999999999999  566666432       2222222222222


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEec
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLT  300 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR  300 (824)
                      ++...                    .....++|.+|++|.|..-  .+-+.+   +|.-.+|.-|+|-+.
T Consensus        93 ~e~a~--------------------~~~~~gr~tiLflDEIHRfnK~QQD~l---Lp~vE~G~iilIGAT  139 (436)
T COG2256          93 IEEAR--------------------KNRLLGRRTILFLDEIHRFNKAQQDAL---LPHVENGTIILIGAT  139 (436)
T ss_pred             HHHHH--------------------HHHhcCCceEEEEehhhhcChhhhhhh---hhhhcCCeEEEEecc
Confidence            22110                    1223489999999999643  344433   344556887877443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.49  E-value=0.00062  Score=78.10  Aligned_cols=137  Identities=12%  Similarity=0.119  Sum_probs=74.4

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~  234 (824)
                      -++++|.+..++.|.+++..+. -...+-++|..|+||||+|+.+.+.-.....+         -+..+...+.-+.|..
T Consensus        15 FdEVIGQe~Vv~~L~~aL~~gR-L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~---------~~~PCG~C~sCr~I~~   84 (830)
T PRK07003         15 FASLVGQEHVVRALTHALDGGR-LHHAYLFTGTRGVGKTTLSRIFAKALNCETGV---------TSQPCGVCRACREIDE   84 (830)
T ss_pred             HHHHcCcHHHHHHHHHHHhcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCccCC---------CCCCCcccHHHHHHhc
Confidence            3689999999999999987654 23455699999999999998776621111100         0111111111111111


Q ss_pred             HhCCCCCcccc---cccCHHHHHHHHHHh----cCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          235 FLMPSSRLSEI---MDKNYEMKKIILHEY----LMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       235 ~l~~~~~~~~~---~~~~~~~~~~~l~~~----L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                      .-.  .+..++   .....++....+...    ..++.-++|+|++...  ..|+.+...+.......++|+||++..
T Consensus        85 G~h--~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~  160 (830)
T PRK07003         85 GRF--VDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQ  160 (830)
T ss_pred             CCC--ceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChh
Confidence            000  000000   001122222222211    1245558889999865  357877776665555778888777654

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=97.48  E-value=0.00031  Score=82.32  Aligned_cols=50  Identities=20%  Similarity=0.236  Sum_probs=36.9

Q ss_pred             CCceechhhHH---HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          156 RDTVGLDDRME---ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       156 ~~~vGr~~~~~---~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      ++++|.+..+.   .+.+.+..+.  ...+.++|++|+||||+|+.+++  .....|
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~~--~~slLL~GPpGtGKTTLA~aIA~--~~~~~f   80 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKADR--VGSLILYGPPGVGKTTLARIIAN--HTRAHF   80 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHH--HhcCcc
Confidence            46889887764   4555555443  55678999999999999999998  444444

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.46  E-value=0.00054  Score=63.45  Aligned_cols=89  Identities=11%  Similarity=0.013  Sum_probs=49.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  259 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  259 (824)
                      ..+.|+|.+|+||||+|+.+.+  ........++.+.  .+........... .......     ............+.+
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~~--~~~~~~~~~~~~~-~~~~~~~-----~~~~~~~~~~~~~~~   72 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALAR--ELGPPGGGVIYID--GEDILEEVLDQLL-LIIVGGK-----KASGSGELRLRLALA   72 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHh--ccCCCCCCEEEEC--CEEccccCHHHHH-hhhhhcc-----CCCCCHHHHHHHHHH
Confidence            5789999999999999999999  4443333455555  3333222221111 0111111     111122333344444


Q ss_pred             hcCCC-eEEEEEecCCChhh
Q 003387          260 YLMTK-RYLIVIDDVWSIDM  278 (824)
Q Consensus       260 ~L~~k-r~LlVlDdv~~~~~  278 (824)
                      ..+.. ..+|++|+++....
T Consensus        73 ~~~~~~~~viiiDei~~~~~   92 (148)
T smart00382       73 LARKLKPDVLILDEITSLLD   92 (148)
T ss_pred             HHHhcCCCEEEEECCcccCC
Confidence            45444 49999999987643

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.45  E-value=0.0012  Score=72.15  Aligned_cols=46  Identities=20%  Similarity=0.159  Sum_probs=38.9

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+..++.+.+.+..+. -...+-++|+.|+||||+|+.+.+
T Consensus        15 ~~~iiGq~~~~~~l~~~~~~~~-~~h~~L~~Gp~G~GKTtla~~la~   60 (363)
T PRK14961         15 FRDIIGQKHIVTAISNGLSLGR-IHHAWLLSGTRGVGKTTIARLLAK   60 (363)
T ss_pred             hhhccChHHHHHHHHHHHHcCC-CCeEEEEecCCCCCHHHHHHHHHH
Confidence            3578999999999999887653 345678999999999999999887

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.44  E-value=0.0014  Score=74.33  Aligned_cols=46  Identities=15%  Similarity=0.109  Sum_probs=38.4

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+++||-+..++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 FddVIGQe~vv~~L~~al~~gR-LpHA~LFtGP~GvGKTTLAriLAk   60 (700)
T PRK12323         15 FTTLVGQEHVVRALTHALEQQR-LHHAYLFTGTRGVGKTTLSRILAK   60 (700)
T ss_pred             HHHHcCcHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHH
Confidence            3579999999999999997664 235668899999999999988866

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.43  E-value=0.00066  Score=72.90  Aligned_cols=119  Identities=15%  Similarity=0.137  Sum_probs=71.6

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~  234 (824)
                      -++++|.+...+.+..++..+. -..++-++|..|+||||+|+.+++  +....   ...+.  .+. .....+...+ .
T Consensus        20 ~~~~~~~~~~~~~l~~~~~~~~-~~~~lll~G~~G~GKT~la~~l~~--~~~~~---~~~i~--~~~-~~~~~i~~~l-~   89 (316)
T PHA02544         20 IDECILPAADKETFKSIVKKGR-IPNMLLHSPSPGTGKTTVAKALCN--EVGAE---VLFVN--GSD-CRIDFVRNRL-T   89 (316)
T ss_pred             HHHhcCcHHHHHHHHHHHhcCC-CCeEEEeeCcCCCCHHHHHHHHHH--HhCcc---ceEec--cCc-ccHHHHHHHH-H
Confidence            3678999999999999988643 356777899999999999999988  33222   23344  333 2222221111 1


Q ss_pred             HhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh---hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          235 FLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI---DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      ......                   .+.+.+-+||+||+...   ...+.+...+.....++++|+||...
T Consensus        90 ~~~~~~-------------------~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~  141 (316)
T PHA02544         90 RFASTV-------------------SLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNK  141 (316)
T ss_pred             HHHHhh-------------------cccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCCh
Confidence            110000                   01134557889999754   22333433344445577888888654

>PRK04195 replication factor C large subunit; Provisional

Probab=97.40  E-value=0.00065  Score=77.15  Aligned_cols=117  Identities=20%  Similarity=0.242  Sum_probs=70.7

Q ss_pred             CCceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      ++++|.+..++++.+|+..-  ....+.+-|+|++|+||||+|+.+.+.  ..  |+ .+-+.  .|...+. .....++
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~e--l~--~~-~ieln--asd~r~~-~~i~~~i   85 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALAND--YG--WE-VIELN--ASDQRTA-DVIERVA   85 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH--cC--CC-EEEEc--ccccccH-HHHHHHH
Confidence            57999999999999998752  223678999999999999999999993  32  32 22233  4433222 2333333


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChh------hHHHHHhhCCCCCCCcEEEEEec
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSID------MWDVIQEILPDNQNGSRVLITLT  300 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~------~~~~l~~~~~~~~~gs~ilvTtR  300 (824)
                      ........                  ....++-+||+|+++...      .+..+...+..  .+..||+|+.
T Consensus        86 ~~~~~~~s------------------l~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~~~~iIli~n  138 (482)
T PRK04195         86 GEAATSGS------------------LFGARRKLILLDEVDGIHGNEDRGGARAILELIKK--AKQPIILTAN  138 (482)
T ss_pred             HHhhccCc------------------ccCCCCeEEEEecCcccccccchhHHHHHHHHHHc--CCCCEEEecc
Confidence            33221110                  001367799999997642      24555544442  2344666653

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.39  E-value=0.001  Score=75.23  Aligned_cols=46  Identities=13%  Similarity=0.130  Sum_probs=38.3

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|-+..++.+.+.+..+. -...+-++|+.|+||||+|+.+.+
T Consensus        15 f~diiGq~~~v~~L~~~i~~~r-l~ha~Lf~Gp~GvGKTTlAr~lAk   60 (546)
T PRK14957         15 FAEVAGQQHALNSLVHALETQK-VHHAYLFTGTRGVGKTTLGRLLAK   60 (546)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999887653 235577899999999999999876

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.38  E-value=0.00018  Score=81.12  Aligned_cols=139  Identities=13%  Similarity=0.017  Sum_probs=74.5

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKF  235 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~  235 (824)
                      ++++|-+..++.|.+++..+. -...+-++|+.|+||||+|+.+.+.-.....+...+|.|  .+.. .+..-....+..
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C--~sc~-~i~~~~h~dv~e   89 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGEC--ESCL-AVRRGAHPDVLE   89 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcC--hhhH-HHhcCCCCceEE
Confidence            578999999998988887754 235678999999999999999887322122233345554  2110 000000000000


Q ss_pred             hCCCCCcccccccCHHHHHHHHHH-hcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEech
Q 003387          236 LMPSSRLSEIMDKNYEMKKIILHE-YLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTD  301 (824)
Q Consensus       236 l~~~~~~~~~~~~~~~~~~~~l~~-~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~  301 (824)
                      +.....   ....+..++...+.. -..+++-++|+|+++..  ..++.+...+........+|++|..
T Consensus        90 l~~~~~---~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~  155 (504)
T PRK14963         90 IDAASN---NSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTE  155 (504)
T ss_pred             eccccc---CCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCC
Confidence            000000   011111122222211 12346668999999855  4577777777655455555555543

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=97.38  E-value=0.0038  Score=64.22  Aligned_cols=115  Identities=12%  Similarity=0.121  Sum_probs=78.4

Q ss_pred             CCCceechh---hHHHHHHHHHcC-CCCeEEEEEEcCCCChHHHHHHHHhCCccc-----cCCCceeEEEECCCCCCCCH
Q 003387          155 SRDTVGLDD---RMEELLDLLIEG-PPQLSVVAILDSIGLDKTAFAGEAYNSSYV-----KHYFDCHAWITEPYSNEYDA  225 (824)
Q Consensus       155 ~~~~vGr~~---~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~-----~~~F~~~~wv~~~vs~~~~~  225 (824)
                      .+..+|...   ..+++.++|... .....-+.|||..|.|||++++++.+..-.     ...+ .++.|.  ....++.
T Consensus        33 ~~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~-PVv~vq--~P~~p~~  109 (302)
T PF05621_consen   33 ADRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERI-PVVYVQ--MPPEPDE  109 (302)
T ss_pred             cCCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccc-cEEEEe--cCCCCCh
Confidence            456666443   345555555544 234566899999999999999998864211     1111 466777  8899999


Q ss_pred             HHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCC-CeEEEEEecCCCh
Q 003387          226 DQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT-KRYLIVIDDVWSI  276 (824)
Q Consensus       226 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~~  276 (824)
                      .++...|+.+++....    ...+...+.......|+. +-=+||+|++.+.
T Consensus       110 ~~~Y~~IL~~lgaP~~----~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~l  157 (302)
T PF05621_consen  110 RRFYSAILEALGAPYR----PRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNL  157 (302)
T ss_pred             HHHHHHHHHHhCcccC----CCCCHHHHHHHHHHHHHHcCCcEEEeechHHH
Confidence            9999999999998543    233445555555566654 4558899999753

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK08116 hypothetical protein; Validated

Probab=97.37  E-value=0.00086  Score=69.54  Aligned_cols=102  Identities=17%  Similarity=0.188  Sum_probs=58.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  259 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  259 (824)
                      .-+.++|..|+|||.||.+|++  ++...-..+++++        ..+++..|........      ..+    ...+.+
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~--~l~~~~~~v~~~~--------~~~ll~~i~~~~~~~~------~~~----~~~~~~  174 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIAN--ELIEKGVPVIFVN--------FPQLLNRIKSTYKSSG------KED----ENEIIR  174 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HHHHcCCeEEEEE--------HHHHHHHHHHHHhccc------ccc----HHHHHH
Confidence            4588999999999999999999  5544434455665        3445555555443211      111    222334


Q ss_pred             hcCCCeEEEEEecCCC--hhhHHH--HHhhCCC-CCCCcEEEEEechH
Q 003387          260 YLMTKRYLIVIDDVWS--IDMWDV--IQEILPD-NQNGSRVLITLTDI  302 (824)
Q Consensus       260 ~L~~kr~LlVlDdv~~--~~~~~~--l~~~~~~-~~~gs~ilvTtR~~  302 (824)
                      .+.+-. ||||||+..  ..+|..  +...+.. -.+|..+||||...
T Consensus       175 ~l~~~d-lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        175 SLVNAD-LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             HhcCCC-EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            444434 899999943  344432  2222221 12456688888643

>PLN03025 replication factor C subunit; Provisional

Probab=97.37  E-value=0.00084  Score=71.98  Aligned_cols=122  Identities=14%  Similarity=0.169  Sum_probs=69.0

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccc-cCCCce-eEEEECCCCCCCCHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYV-KHYFDC-HAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~-~~~F~~-~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      .+++|.++.++.|.+++..+.  ...+-++|++|+||||+|+.+.+  .. ...|.. ++-+.  .|...... ..++++
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~G~GKTtla~~la~--~l~~~~~~~~~~eln--~sd~~~~~-~vr~~i   85 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDGN--MPNLILSGPPGTGKTTSILALAH--ELLGPNYKEAVLELN--ASDDRGID-VVRNKI   85 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHH--HHhcccCccceeeec--ccccccHH-HHHHHH
Confidence            568898888888887776554  44567999999999999999887  33 222321 22222  33332222 222222


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEech
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTD  301 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~  301 (824)
                      +.......    .             .-.++.-++++|++...  ...+.+...+......+++++++..
T Consensus        86 ~~~~~~~~----~-------------~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~  138 (319)
T PLN03025         86 KMFAQKKV----T-------------LPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNT  138 (319)
T ss_pred             HHHHhccc----c-------------CCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCC
Confidence            22111000    0             00245678999999865  3344454444443445777776643

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.35  E-value=0.00038  Score=74.84  Aligned_cols=55  Identities=16%  Similarity=0.112  Sum_probs=44.9

Q ss_pred             CCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCc-cccccchhhhccccCceecCCCc
Q 003387          541 ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFS-YIDHTADEFWKMNKLRHLNFGSI  601 (824)
Q Consensus       541 ~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~-~l~~lp~~i~~L~~L~~L~L~~~  601 (824)
                      ..+.++++|++++|.++.+|. +   ..+|++|.+++| .++.+|..+  .++|++|++++|
T Consensus        49 ~~~~~l~~L~Is~c~L~sLP~-L---P~sLtsL~Lsnc~nLtsLP~~L--P~nLe~L~Ls~C  104 (426)
T PRK15386         49 EEARASGRLYIKDCDIESLPV-L---PNELTEITIENCNNLTTLPGSI--PEGLEKLTVCHC  104 (426)
T ss_pred             HHhcCCCEEEeCCCCCcccCC-C---CCCCcEEEccCCCCcccCCchh--hhhhhheEccCc
Confidence            346889999999999999983 3   356999999998 888888755  358999998887

>KOG1947 consensus Leucine rich repeat proteins, some proteins contain F-box [General function prediction only]

Probab=97.33  E-value=6.7e-05  Score=85.85  Aligned_cols=239  Identities=20%  Similarity=0.130  Sum_probs=138.3

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCc-c-CccC----CccCCCCCcceEEeecCCC-CCccC-hhh
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSL-V-LIQY----PSGIENLFLLRYLKLNIPS-LNSLP-SSL  563 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~-~-i~~l----p~~i~~l~~Lr~L~L~~~~-i~~lp-~~i  563 (824)
                      ++.++.|.+.++....  ..........++.|+.|+++++ . +...    +.....+.+|+.|+++++. ++..- ..+
T Consensus       187 ~~~L~~l~l~~~~~~~--~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~~~~~~~~~L~~l~l~~~~~isd~~l~~l  264 (482)
T KOG1947|consen  187 CPLLKRLSLSGCSKIT--DDSLDALALKCPNLEELDLSGCCLLITLSPLLLLLLLSICRKLKSLDLSGCGLVTDIGLSAL  264 (482)
T ss_pred             CchhhHhhhcccccCC--hhhHHHHHhhCchhheecccCcccccccchhHhhhhhhhcCCcCccchhhhhccCchhHHHH
Confidence            7889999888876642  2225678889999999999984 2 2211    2233447899999999987 55322 333


Q ss_pred             hhcCCCccEeecCCcc-cc--ccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccc
Q 003387          564 LSNLLNLYTLDMPFSY-ID--HTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLR  640 (824)
Q Consensus       564 ~~~L~~L~~L~L~~~~-l~--~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~  640 (824)
                      ...+++|++|.+.+|. ++  .+-.....+++|++|++++|....                    ...+.....++++|+
T Consensus       265 ~~~c~~L~~L~l~~c~~lt~~gl~~i~~~~~~L~~L~l~~c~~~~--------------------d~~l~~~~~~c~~l~  324 (482)
T KOG1947|consen  265 ASRCPNLETLSLSNCSNLTDEGLVSIAERCPSLRELDLSGCHGLT--------------------DSGLEALLKNCPNLR  324 (482)
T ss_pred             HhhCCCcceEccCCCCccchhHHHHHHHhcCcccEEeeecCccch--------------------HHHHHHHHHhCcchh
Confidence            2458999999988884 54  334445678999999998776531                    222222255577777


Q ss_pred             eEEEecccccchhhHHHHhccCCCCCeEEEeccC-CC-CCccEEEeCccCcCCCceEEEEEcccCCCCC-cccccCCCCC
Q 003387          641 NLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES-KM-PRLSKIVLAEYLFPHSLTHLSFSNTDLMDDP-MPTLEKLPLL  717 (824)
Q Consensus       641 ~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~-~~-~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~-~~~l~~l~~L  717 (824)
                      .|.+.....            +..++.+.+.... .. ..+..+   ....+++|+.+.|..|...... ...+.++|+|
T Consensus       325 ~l~~~~~~~------------c~~l~~~~l~~~~~~~~d~~~~~---~~~~~~~l~~~~l~~~~~~~~~~~~~l~gc~~l  389 (482)
T KOG1947|consen  325 ELKLLSLNG------------CPSLTDLSLSGLLTLTSDDLAEL---ILRSCPKLTDLSLSYCGISDLGLELSLRGCPNL  389 (482)
T ss_pred             hhhhhhcCC------------CccHHHHHHHHhhccCchhHhHH---HHhcCCCcchhhhhhhhccCcchHHHhcCCccc
Confidence            766554431            2223322222100 00 011111   1145667777777777633222 2445566766


Q ss_pred             CeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceec-cCc-ccCccEEEEecCCCCC
Q 003387          718 QVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMG-NAA-MPKLECLIINPCAYLK  778 (824)
Q Consensus       718 ~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~-~~~-lp~L~~L~l~~c~~l~  778 (824)
                      . ..+..+          ...+..|+.|.+..|.....-... ... +.+++.+.+.+|+...
T Consensus       390 ~-~~l~~~----------~~~~~~l~~L~l~~~~~~t~~~l~~~~~~~~~~~~l~~~~~~~~~  441 (482)
T KOG1947|consen  390 T-ESLELR----------LCRSDSLRVLNLSDCRLVTDKGLRCLADSCSNLKDLDLSGCRVIT  441 (482)
T ss_pred             c-hHHHHH----------hccCCccceEecccCccccccchHHHhhhhhccccCCccCccccc
Confidence            3 322211          122333788888887654432211 111 6677888888887654

>PRK08727 hypothetical protein; Validated

Probab=97.33  E-value=0.00045  Score=70.26  Aligned_cols=36  Identities=14%  Similarity=0.058  Sum_probs=28.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ...+.|+|..|+|||+|++++++  +..+....+++++
T Consensus        41 ~~~l~l~G~~G~GKThL~~a~~~--~~~~~~~~~~y~~   76 (233)
T PRK08727         41 SDWLYLSGPAGTGKTHLALALCA--AAEQAGRSSAYLP   76 (233)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH--HHHHcCCcEEEEe
Confidence            35699999999999999999988  4444444566776

>PRK08118 topology modulation protein; Reviewed

Probab=97.31  E-value=9.9e-05  Score=70.75  Aligned_cols=36  Identities=19%  Similarity=0.305  Sum_probs=27.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccc-CCCceeEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVK-HYFDCHAWI  215 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv  215 (824)
                      +.|.|+|++|+||||||+.+++...+. -+||..+|-
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~   38 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWK   38 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhcc
Confidence            358999999999999999999954333 456777753

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=97.30  E-value=5.7e-05  Score=66.86  Aligned_cols=87  Identities=15%  Similarity=0.157  Sum_probs=62.2

Q ss_pred             hhcccCcccEEEeeCccCccCCccCCC-CCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCc
Q 003387          516 FCGMFKLLRVLDLGSLVLIQYPSGIEN-LFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLR  594 (824)
Q Consensus       516 ~~~~~~~Lr~L~L~~~~i~~lp~~i~~-l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~  594 (824)
                      .+.....|...+|++|.++++|+.+.. .+.+..|+|++|.+.++|.++ ..++.|+.|+++.|.+...|.-|..|.+|-
T Consensus        48 ~l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~neisdvPeE~-Aam~aLr~lNl~~N~l~~~p~vi~~L~~l~  126 (177)
T KOG4579|consen   48 MLSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANNEISDVPEEL-AAMPALRSLNLRFNPLNAEPRVIAPLIKLD  126 (177)
T ss_pred             HHhCCceEEEEecccchhhhCCHHHhhccchhhhhhcchhhhhhchHHH-hhhHHhhhcccccCccccchHHHHHHHhHH
Confidence            344555667777777777777776644 447777777777777777776 777777777777777777777777777777


Q ss_pred             eecCCCccC
Q 003387          595 HLNFGSITL  603 (824)
Q Consensus       595 ~L~L~~~~~  603 (824)
                      .|+..+|..
T Consensus       127 ~Lds~~na~  135 (177)
T KOG4579|consen  127 MLDSPENAR  135 (177)
T ss_pred             HhcCCCCcc
Confidence            776665544

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.30  E-value=0.0015  Score=70.30  Aligned_cols=44  Identities=20%  Similarity=0.201  Sum_probs=38.2

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|+++.++.+.+++..+.  ...+.++|..|+||||+|+.+.+
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~~--~~~~ll~G~~G~GKt~~~~~l~~   60 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEKN--MPHLLFAGPPGTGKTTAALALAR   60 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHH
Confidence            568899999999999987654  44579999999999999999988

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.29  E-value=0.0012  Score=77.45  Aligned_cols=46  Identities=17%  Similarity=0.151  Sum_probs=38.4

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|-+.-++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 FddIIGQe~Iv~~LknaI~~~r-l~HAyLFtGPpGtGKTTLARiLAk   60 (944)
T PRK14949         15 FEQMVGQSHVLHALTNALTQQR-LHHAYLFTGTRGVGKTSLARLFAK   60 (944)
T ss_pred             HHHhcCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3579999999999999987653 234557999999999999999987

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.24  E-value=0.002  Score=73.17  Aligned_cols=46  Identities=20%  Similarity=0.150  Sum_probs=39.2

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+...+.|.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        14 FddVIGQe~vv~~L~~aI~~gr-l~HAyLF~GPpGvGKTTlAriLAK   59 (702)
T PRK14960         14 FNELVGQNHVSRALSSALERGR-LHHAYLFTGTRGVGKTTIARILAK   59 (702)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3689999999999999998664 246778999999999999998876

>COG3899 Predicted ATPase [General function prediction only]

Probab=97.19  E-value=0.0046  Score=74.52  Aligned_cols=259  Identities=15%  Similarity=0.111  Sum_probs=136.6

Q ss_pred             CceechhhHHHHHHHHHcC-CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE-CCCCCCC---CHHHHHHH
Q 003387          157 DTVGLDDRMEELLDLLIEG-PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT-EPYSNEY---DADQILDI  231 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-~~vs~~~---~~~~~~~~  231 (824)
                      +++||+.+.+.|...+... .+...|+.|.|..|||||+|++.|..  .+.+.+...+--. ++...+.   ...+.+++
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~--~i~~~~~~~i~~~f~q~~~~ipl~~lvq~~r~   78 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHK--PITQQRGYFIKGKFDQFERNIPLSPLVQAFRD   78 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHH--HHhccceeeeHhhcccccCCCchHHHHHHHHH
Confidence            4689999999999998763 34577999999999999999999998  5554432222111 0011111   12234445


Q ss_pred             HHHHhCCCC-------------------C------------------cccccccCHHHH-----HHHHHHhcC-CCeEEE
Q 003387          232 VIKFLMPSS-------------------R------------------LSEIMDKNYEMK-----KIILHEYLM-TKRYLI  268 (824)
Q Consensus       232 i~~~l~~~~-------------------~------------------~~~~~~~~~~~~-----~~~l~~~L~-~kr~Ll  268 (824)
                      ++.++....                   .                  ..++.......+     ...|..+.. .|+.++
T Consensus        79 l~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi  158 (849)
T COG3899          79 LMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVI  158 (849)
T ss_pred             HHHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEE
Confidence            554442111                   0                  000111112222     233444443 469999


Q ss_pred             EEecC-CChh-hHHHHHhhCCCCC----CCcEEEEEechHHHHh------------------------hcccccCCcCcC
Q 003387          269 VIDDV-WSID-MWDVIQEILPDNQ----NGSRVLITLTDIRIII------------------------SFQFEDGENMRL  318 (824)
Q Consensus       269 VlDdv-~~~~-~~~~l~~~~~~~~----~gs~ilvTtR~~~v~~------------------------~f~~~~~~~~~~  318 (824)
                      |+||+ |-+. .++-+........    .-..|..+........                        +..... .....
T Consensus       159 ~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l-~~~~~  237 (849)
T COG3899         159 VLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATL-GCTKL  237 (849)
T ss_pred             EEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHh-CCccc
Confidence            99999 4332 2222221111110    0112222222111111                        111100 01134


Q ss_pred             ccccchhhHHHhcCCCchhHHHHHhHHHhh--------hhhhhcc----CCC-ccccc---c--cc-cCCCCchHHHhHh
Q 003387          319 DLVPTGGPLRATYKGRPFLILYHGSISLEE--------NIREAVE----TPL-GLRYI---K--CL-MLPFCLKPCFIYL  379 (824)
Q Consensus       319 ~~~~~~~~i~~~c~GlPlai~~~~~~l~~~--------~~~~~~~----~~~-~~~~~---l--~~-~L~~~lk~cfl~~  379 (824)
                      ...+....|++|..|.|+-+.-+-..+..+        ...|..+    ... ....+   +  ++ .||...++..-..
T Consensus       238 ~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~~~~~~~vv~~l~~rl~kL~~~t~~Vl~~A  317 (849)
T COG3899         238 LPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGILATTDAVVEFLAARLQKLPGTTREVLKAA  317 (849)
T ss_pred             ccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCCchhhHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            456778999999999999998888877332        2223221    111 12221   2  22 9999999988888


Q ss_pred             ccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHHHHHhccccce
Q 003387          380 SVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEA  426 (824)
Q Consensus       380 s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~~Lv~rsllq~  426 (824)
                      |++-..  |+.+-|-..|-.      .....+....+.|....++..
T Consensus       318 A~iG~~--F~l~~La~l~~~------~~~~~a~~l~~al~e~lI~~~  356 (849)
T COG3899         318 ACIGNR--FDLDTLAALAED------SPALEAAALLDALQEGLILPL  356 (849)
T ss_pred             HHhCcc--CCHHHHHHHHhh------chHHHHHHHHHHhHhhceecc
Confidence            887654  445555554432      234556666776666655543

>COG3903 Predicted ATPase [General function prediction only]

Probab=97.19  E-value=0.00021  Score=75.38  Aligned_cols=156  Identities=15%  Similarity=0.102  Sum_probs=100.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCc-eeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD-CHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKII  256 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  256 (824)
                      ..+-+.++|.|||||||++-.+..   +..-|. .+.+|.  ...--|...+.-.+...++...       .+.+.....
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vd--l~pitD~~~v~~~~ag~~gl~~-------~~g~~~~~~   80 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVD--LAPITDPALVFPTLAGALGLHV-------QPGDSAVDT   80 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh---Hhhhcccceeeee--ccccCchhHhHHHHHhhccccc-------ccchHHHHH
Confidence            478899999999999999988876   566675 566666  4444455555555555565432       222445567


Q ss_pred             HHHhcCCCeEEEEEecCCChh-hHHHHHhhCCCCCCCcEEEEEechHHHHh-----------hccc-------ccC----
Q 003387          257 LHEYLMTKRYLIVIDDVWSID-MWDVIQEILPDNQNGSRVLITLTDIRIII-----------SFQF-------EDG----  313 (824)
Q Consensus       257 l~~~L~~kr~LlVlDdv~~~~-~~~~l~~~~~~~~~gs~ilvTtR~~~v~~-----------~f~~-------~~~----  313 (824)
                      +..++.++|.++|+||.-... +-..+.-.+..+...-.|+.|+|..-...           .|..       ...    
T Consensus        81 ~~~~~~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~  160 (414)
T COG3903          81 LVRRIGDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAILVAGEVHRRVPSLSLFDEAIELFVCRAVLVAL  160 (414)
T ss_pred             HHHHHhhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhcccccccccCCccccCCchhHHHHHHHHHhcc
Confidence            778888999999999997652 22223333344444566888888765444           1210       000    


Q ss_pred             C-cCcCccccchhhHHHhcCCCchhHHHHHhHH
Q 003387          314 E-NMRLDLVPTGGPLRATYKGRPFLILYHGSIS  345 (824)
Q Consensus       314 ~-~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  345 (824)
                      . .....-.....+|.++..|.|++|...++..
T Consensus       161 ~f~l~~~~~a~v~~icr~ldg~~laielaaarv  193 (414)
T COG3903         161 SFWLTDDNAAAVAEICRRLDGIPLAIELAAARV  193 (414)
T ss_pred             ceeecCCchHHHHHHHHHhhcchHHHHHHHHHH
Confidence            0 0111224467889999999999999988776

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.16  E-value=0.003  Score=71.60  Aligned_cols=46  Identities=13%  Similarity=0.095  Sum_probs=38.5

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+++||-+.-++.|.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        15 f~divGq~~v~~~L~~~~~~~~-l~ha~Lf~Gp~G~GKTt~A~~lAk   60 (509)
T PRK14958         15 FQEVIGQAPVVRALSNALDQQY-LHHAYLFTGTRGVGKTTISRILAK   60 (509)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCC-CCeeEEEECCCCCCHHHHHHHHHH
Confidence            3579999999999999997664 234578999999999999988876

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.16  E-value=0.00097  Score=73.33  Aligned_cols=49  Identities=18%  Similarity=0.169  Sum_probs=39.4

Q ss_pred             CCCCCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +..+++.|+++.++++.+.+...           -...+-|-++|++|.|||++|+++++
T Consensus       128 ~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~  187 (389)
T PRK03992        128 VTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH  187 (389)
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHH
Confidence            34457899999999998876431           12356788999999999999999998

>PRK05642 DNA replication initiation factor; Validated

Probab=97.15  E-value=0.0012  Score=67.07  Aligned_cols=36  Identities=8%  Similarity=0.102  Sum_probs=27.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ...+.|+|..|+|||.|++++++  +....-..++|++
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~--~~~~~~~~v~y~~   80 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACL--RFEQRGEPAVYLP   80 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH--HHHhCCCcEEEee
Confidence            36789999999999999999987  4333324566776

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.14  E-value=0.0031  Score=70.69  Aligned_cols=45  Identities=18%  Similarity=0.160  Sum_probs=36.8

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|.+...+.+...+..+. -...+-++|++|+||||+|+.+.+
T Consensus        14 ~divGq~~i~~~L~~~i~~~~-l~~~~Lf~GPpGtGKTTlA~~lA~   58 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKNS-ISHAYIFAGPRGTGKTTVARILAK   58 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            579999888888887776554 235678999999999999999977

>PRK10536 hypothetical protein; Provisional

Probab=97.12  E-value=0.0032  Score=63.52  Aligned_cols=57  Identities=9%  Similarity=0.083  Sum_probs=42.0

Q ss_pred             CCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEE
Q 003387          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAW  214 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~w  214 (824)
                      +...+.++......++.+|...    .+|.+.|..|.|||+||.++.-+.-..+.|+..+-
T Consensus        53 ~~~~i~p~n~~Q~~~l~al~~~----~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~kIiI  109 (262)
T PRK10536         53 DTSPILARNEAQAHYLKAIESK----QLIFATGEAGCGKTWISAAKAAEALIHKDVDRIIV  109 (262)
T ss_pred             CCccccCCCHHHHHHHHHHhcC----CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeEEEE
Confidence            3456778999999999988663    39999999999999999987774222344544443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.11  E-value=0.0029  Score=72.62  Aligned_cols=46  Identities=24%  Similarity=0.233  Sum_probs=39.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+..++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 FddIIGQe~vv~~L~~ai~~~r-l~Ha~Lf~GP~GvGKTTlAriLAk   60 (709)
T PRK08691         15 FADLVGQEHVVKALQNALDEGR-LHHAYLLTGTRGVGKTTIARILAK   60 (709)
T ss_pred             HHHHcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHH
Confidence            3689999999999999988654 235678999999999999998876

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.11  E-value=0.0041  Score=70.01  Aligned_cols=46  Identities=13%  Similarity=0.013  Sum_probs=37.9

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|-+..+..+...+..+. -...+-++|+.|+||||+|+.+++
T Consensus        20 f~dliGq~~vv~~L~~ai~~~r-i~~a~Lf~Gp~G~GKTT~ArilAk   65 (507)
T PRK06645         20 FAELQGQEVLVKVLSYTILNDR-LAGGYLLTGIRGVGKTTSARIIAK   65 (507)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            3578999999998888776653 245778999999999999999977

>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=97.11  E-value=0.00077  Score=61.80  Aligned_cols=21  Identities=19%  Similarity=0.180  Sum_probs=19.3

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |-|+|+.|+||||+|+.+.++
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            568999999999999999993

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 ....

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

Probab=97.10  E-value=0.0015  Score=67.20  Aligned_cols=117  Identities=18%  Similarity=0.254  Sum_probs=66.8

Q ss_pred             CCCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHH
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      +...+++|-+.-+..   ++..+  .+.-+..||++|+||||||+.+.+..+...    ..||.  .|-.-.-..=.++|
T Consensus       141 vGQ~hlv~q~gllrs---~ieq~--~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfve--lSAt~a~t~dvR~i  209 (554)
T KOG2028|consen  141 VGQSHLVGQDGLLRS---LIEQN--RIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVE--LSATNAKTNDVRDI  209 (554)
T ss_pred             cchhhhcCcchHHHH---HHHcC--CCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEE--EeccccchHHHHHH
Confidence            334455555443333   33333  477788999999999999999999543333    44565  44432222223333


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEE--EechH
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLI--TLTDI  302 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilv--TtR~~  302 (824)
                      +++-..                   ...+-++|..|.+|.|..-  .+-+.   .+|.-.+|+-++|  ||.++
T Consensus       210 fe~aq~-------------------~~~l~krkTilFiDEiHRFNksQQD~---fLP~VE~G~I~lIGATTENP  261 (554)
T KOG2028|consen  210 FEQAQN-------------------EKSLTKRKTILFIDEIHRFNKSQQDT---FLPHVENGDITLIGATTENP  261 (554)
T ss_pred             HHHHHH-------------------HHhhhcceeEEEeHHhhhhhhhhhhc---ccceeccCceEEEecccCCC
Confidence            333211                   1123468899999999643  22222   3466667887776  44444

>PRK12377 putative replication protein; Provisional

Probab=97.08  E-value=0.0025  Score=64.92  Aligned_cols=74  Identities=15%  Similarity=0.060  Sum_probs=46.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      ...+.++|..|+|||+||.++.+  .+......+++++  +      .+++..|-......        ....    .+.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~--~l~~~g~~v~~i~--~------~~l~~~l~~~~~~~--------~~~~----~~l  158 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGN--RLLAKGRSVIVVT--V------PDVMSRLHESYDNG--------QSGE----KFL  158 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH--HHHHcCCCeEEEE--H------HHHHHHHHHHHhcc--------chHH----HHH
Confidence            46789999999999999999999  5555555567776  3      24444444332111        0111    222


Q ss_pred             HhcCCCeEEEEEecCCC
Q 003387          259 EYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       259 ~~L~~kr~LlVlDdv~~  275 (824)
                      +.+ .+-=||||||+..
T Consensus       159 ~~l-~~~dLLiIDDlg~  174 (248)
T PRK12377        159 QEL-CKVDLLVLDEIGI  174 (248)
T ss_pred             HHh-cCCCEEEEcCCCC
Confidence            223 3556999999943

>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=97.06  E-value=0.001  Score=66.72  Aligned_cols=35  Identities=29%  Similarity=0.369  Sum_probs=30.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      -.++|+|..|.|||||+..+..  .....|+.+++++
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            3578999999999999999998  5778898877776

This is thought to be an ATPase involved in viral DNA packaging [].

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.04  E-value=0.0018  Score=78.34  Aligned_cols=44  Identities=18%  Similarity=0.281  Sum_probs=37.6

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++||+++++++++.|....  ..-+.++|.+|+|||++|+.+..
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~--~~n~lL~G~pGvGKTal~~~la~  222 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRT--KNNPILIGEPGVGKTAIAEGLAQ  222 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccc--cCCeEEECCCCCCHHHHHHHHHH
Confidence            468999999999999998654  22446999999999999998877

>PRK08181 transposase; Validated

Probab=97.04  E-value=0.0032  Score=64.94  Aligned_cols=35  Identities=9%  Similarity=-0.102  Sum_probs=26.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .-+.++|..|+|||.||.++.+  +.......++|++
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~--~a~~~g~~v~f~~  141 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGL--ALIENGWRVLFTR  141 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHH--HHHHcCCceeeee
Confidence            3489999999999999999988  4444444556665

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.02  E-value=0.0018  Score=66.06  Aligned_cols=58  Identities=10%  Similarity=0.111  Sum_probs=36.2

Q ss_pred             CCCceechhh-HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          155 SRDTVGLDDR-MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       155 ~~~~vGr~~~-~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ++-++|-... ...+.++....  ....+.|+|+.|+|||+|++.+++  .....-..+.++.
T Consensus        22 d~f~~~~n~~a~~~l~~~~~~~--~~~~l~l~Gp~G~GKThLl~a~~~--~~~~~~~~v~y~~   80 (235)
T PRK08084         22 ASFYPGDNDSLLAALQNALRQE--HSGYIYLWSREGAGRSHLLHAACA--ELSQRGRAVGYVP   80 (235)
T ss_pred             cccccCccHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHH--HHHhCCCeEEEEE
Confidence            3445573333 33333333322  245789999999999999999998  4433334556776

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.01  E-value=0.0065  Score=69.35  Aligned_cols=46  Identities=17%  Similarity=0.151  Sum_probs=37.8

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|-+.-++.+.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 f~divGq~~v~~~L~~~i~~~~-~~ha~Lf~Gp~G~GKTt~A~~lAk   60 (527)
T PRK14969         15 FSELVGQEHVVRALTNALEQQR-LHHAYLFTGTRGVGKTTLARILAK   60 (527)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCEEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999988654 234567899999999999998866

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.00  E-value=0.0046  Score=68.31  Aligned_cols=46  Identities=15%  Similarity=-0.011  Sum_probs=37.7

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+..++.|.+++..+. -...+-++|+.|+||||+|..+.+
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~-~~ha~lf~Gp~G~GKtt~A~~~a~   60 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGR-VGHGYIFSGLRGVGKTTAARVFAK   60 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCC-cceeEEEECCCCCCHHHHHHHHHH
Confidence            3578899999998888887654 234578899999999999988776

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.98  E-value=0.0066  Score=64.14  Aligned_cols=118  Identities=11%  Similarity=0.156  Sum_probs=67.5

Q ss_pred             echhhHHHHHHHHHcCC--CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhC
Q 003387          160 GLDDRMEELLDLLIEGP--PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLM  237 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~~~--~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~  237 (824)
                      ++....+...+++..-.  ...+-+.++|..|+|||.||.++.+  +....=..+.+++  ++      +++.++.....
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~--~l~~~g~~v~~~~--~~------~l~~~lk~~~~  204 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIAN--ELAKKGVSSTLLH--FP------EFIRELKNSIS  204 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHH--HHHHcCCCEEEEE--HH------HHHHHHHHHHh
Confidence            44455555566665321  1346789999999999999999999  4443334466776  32      45555544432


Q ss_pred             CCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHH--HHHhhC-CCC-CCCcEEEEEech
Q 003387          238 PSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWD--VIQEIL-PDN-QNGSRVLITLTD  301 (824)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~--~l~~~~-~~~-~~gs~ilvTtR~  301 (824)
                      ..         +..   ..+ +.+ .+-=||||||+..+  .+|.  ++...+ ... ..+-.+|+||--
T Consensus       205 ~~---------~~~---~~l-~~l-~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        205 DG---------SVK---EKI-DAV-KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             cC---------cHH---HHH-HHh-cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence            11         111   222 223 24558999999654  4564  343333 221 234457777764

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=96.95  E-value=0.0091  Score=65.28  Aligned_cols=46  Identities=17%  Similarity=0.177  Sum_probs=38.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|.+..++.+.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        13 ~~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~   58 (355)
T TIGR02397        13 FEDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAK   58 (355)
T ss_pred             HhhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999987654 245678899999999999988765

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.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.92  E-value=0.0069  Score=67.67  Aligned_cols=128  Identities=15%  Similarity=0.178  Sum_probs=74.2

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC------cc------------cc-CCCceeEEE
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS------SY------------VK-HYFDCHAWI  215 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~------~~------------~~-~~F~~~~wv  215 (824)
                      -.++||-+..++.+.+.+..+. -...+-++|+.|+||||+|+.+.+-      +.            +. ..+..++.+
T Consensus        12 f~dliGQe~vv~~L~~a~~~~r-i~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~ei   90 (491)
T PRK14964         12 FKDLVGQDVLVRILRNAFTLNK-IPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEI   90 (491)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEE
Confidence            3688999998888888887654 2347889999999999999888651      00            00 111223334


Q ss_pred             ECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCc
Q 003387          216 TEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGS  293 (824)
Q Consensus       216 ~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs  293 (824)
                      +  .+....+.+ .++|++.....                    -..+++-++|+|++...  ...+.+...+..-.+.+
T Consensus        91 d--aas~~~vdd-IR~Iie~~~~~--------------------P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v  147 (491)
T PRK14964         91 D--AASNTSVDD-IKVILENSCYL--------------------PISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHV  147 (491)
T ss_pred             e--cccCCCHHH-HHHHHHHHHhc--------------------cccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCe
Confidence            3  332222222 11222221100                    01245668999999754  45677777666655667


Q ss_pred             EEEEEech-HHHHh
Q 003387          294 RVLITLTD-IRIII  306 (824)
Q Consensus       294 ~ilvTtR~-~~v~~  306 (824)
                      ++|++|.. ..+..
T Consensus       148 ~fIlatte~~Kl~~  161 (491)
T PRK14964        148 KFILATTEVKKIPV  161 (491)
T ss_pred             EEEEEeCChHHHHH
Confidence            67666543 34433

>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=96.91  E-value=0.00099  Score=65.32  Aligned_cols=54  Identities=20%  Similarity=0.178  Sum_probs=37.0

Q ss_pred             CCCceechhhHHHHHHHHH---cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCc
Q 003387          155 SRDTVGLDDRMEELLDLLI---EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD  210 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~---~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~  210 (824)
                      -+++||-+.-++.+.-++.   ...+.+.-+-.||++|+||||||..|.+  +....|.
T Consensus        23 L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~--e~~~~~~   79 (233)
T PF05496_consen   23 LDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIAN--ELGVNFK   79 (233)
T ss_dssp             CCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHH--HCT--EE
T ss_pred             HHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHh--ccCCCeE
Confidence            3689999888887655544   2344578889999999999999999999  6666663

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.

>CHL00181 cbbX CbbX; Provisional

Probab=96.91  E-value=0.0079  Score=63.07  Aligned_cols=46  Identities=20%  Similarity=0.168  Sum_probs=31.8

Q ss_pred             CCceechhhHHHHHHHHH---c-------C---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLI---E-------G---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~---~-------~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.+..+++|.++..   -       +   ......+.++|.+|+||||+|+.+++
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~   81 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMAD   81 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            357787777776554432   1       1   11234578899999999999999977

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.89  E-value=0.0032  Score=76.21  Aligned_cols=44  Identities=16%  Similarity=0.267  Sum_probs=37.8

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++||+.+++++++.|....  -.-+.++|.+|+||||+|+.+..
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~--~~n~lL~G~pGvGKT~l~~~la~  221 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQ  221 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCC--cCceEEECCCCCCHHHHHHHHHH
Confidence            579999999999999998765  33455899999999999999887

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.88  E-value=0.0029  Score=75.58  Aligned_cols=44  Identities=20%  Similarity=0.256  Sum_probs=37.6

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++||+.+++++++.|....  ..-+.++|.+|+|||++|+.+.+
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~--~~n~lL~G~pG~GKT~l~~~la~  225 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRK--KNNPLLVGEPGVGKTAIAEGLAL  225 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHH
Confidence            479999999999999887664  23456899999999999999987

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=96.88  E-value=0.006  Score=60.78  Aligned_cols=122  Identities=14%  Similarity=0.187  Sum_probs=71.2

Q ss_pred             CCCCCceechhhHHHHHHHHH---cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHH
Q 003387          153 SKSRDTVGLDDRMEELLDLLI---EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQIL  229 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~---~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~  229 (824)
                      +.-+.++|.|..++.|++=..   .+. ...-+-+||..|.|||++++++.+.  ....= .+ -|.  |++.       
T Consensus        24 ~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~-pannvLL~G~rGtGKSSlVkall~~--y~~~G-LR-lIe--v~k~-------   89 (249)
T PF05673_consen   24 IRLDDLIGIERQKEALIENTEQFLQGL-PANNVLLWGARGTGKSSLVKALLNE--YADQG-LR-LIE--VSKE-------   89 (249)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHcCC-CCcceEEecCCCCCHHHHHHHHHHH--HhhcC-ce-EEE--ECHH-------
Confidence            456789999999998876432   232 3556678999999999999999883  32211 11 122  3221       


Q ss_pred             HHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCC---hhhHHHHHhhCCCC---CCCcEEEE-EechH
Q 003387          230 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWS---IDMWDVIQEILPDN---QNGSRVLI-TLTDI  302 (824)
Q Consensus       230 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~---~~~~~~l~~~~~~~---~~gs~ilv-TtR~~  302 (824)
                                      +-.+...+.+.|+.  +..||+|.+||+.=   +.....++..+..+   .+...+|. ||-..
T Consensus        90 ----------------~L~~l~~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~LeGgle~~P~NvliyATSNRR  151 (249)
T PF05673_consen   90 ----------------DLGDLPELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLEGGLEARPDNVLIYATSNRR  151 (249)
T ss_pred             ----------------HhccHHHHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhcCccccCCCcEEEEEecchh
Confidence                            11122333333331  35799999999963   34566676666532   23344444 44334


Q ss_pred             HHHh
Q 003387          303 RIII  306 (824)
Q Consensus       303 ~v~~  306 (824)
                      +...
T Consensus       152 HLv~  155 (249)
T PF05673_consen  152 HLVP  155 (249)
T ss_pred             hccc
Confidence            4433

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=96.87  E-value=0.0083  Score=65.62  Aligned_cols=46  Identities=15%  Similarity=0.063  Sum_probs=37.6

Q ss_pred             CCceechhhHHHHHHHHHcCCC--------CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPP--------QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~--------~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|-+..++.+.+++..+..        -..-+-++|+.|+||||+|+.+.+
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~   58 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAA   58 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHH
Confidence            4688999999999999976531        246688999999999999988755

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.87  E-value=0.0031  Score=63.95  Aligned_cols=101  Identities=14%  Similarity=0.036  Sum_probs=58.0

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHH-hCC-CCCcccc
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKF-LMP-SSRLSEI  245 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~-l~~-~~~~~~~  245 (824)
                      |-++|..+=..-.++-|+|.+|+|||++|.++..  .....-..++|++  .. .++..++.+ ++.. +.. .....-.
T Consensus        12 lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~--~~~~~~~~v~yi~--~e-~~~~~r~~~-~~~~~~~~~~~~~~~~   85 (225)
T PRK09361         12 LDELLGGGFERGTITQIYGPPGSGKTNICLQLAV--EAAKNGKKVIYID--TE-GLSPERFKQ-IAGEDFEELLSNIIIF   85 (225)
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHH--HHHHCCCeEEEEE--CC-CCCHHHHHH-HHhhChHhHhhCeEEE
Confidence            4445545544578999999999999999999887  3434456789998  55 566655432 3322 100 0000001


Q ss_pred             cccCH---HHHHHHHHHhcCCCeEEEEEecCC
Q 003387          246 MDKNY---EMKKIILHEYLMTKRYLIVIDDVW  274 (824)
Q Consensus       246 ~~~~~---~~~~~~l~~~L~~kr~LlVlDdv~  274 (824)
                      ...+.   .+..+.+.+.++.+--++|+|.+.
T Consensus        86 ~~~~~~~~~~~i~~~~~~~~~~~~lvVIDsi~  117 (225)
T PRK09361         86 EPSSFEEQSEAIRKAEKLAKENVGLIVLDSAT  117 (225)
T ss_pred             eCCCHHHHHHHHHHHHHHHHhcccEEEEeCcH
Confidence            11222   223344444444566688888874

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.87  E-value=0.0045  Score=71.36  Aligned_cols=46  Identities=20%  Similarity=0.164  Sum_probs=38.4

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.++||-+..++.|.+.+..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 f~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk   60 (647)
T PRK07994         15 FAEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAK   60 (647)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999998887654 234567899999999999999877

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=96.86  E-value=0.00096  Score=63.39  Aligned_cols=107  Identities=23%  Similarity=0.203  Sum_probs=76.5

Q ss_pred             cccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch--hhhccccCceecCC
Q 003387          522 LLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD--EFWKMNKLRHLNFG  599 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~--~i~~L~~L~~L~L~  599 (824)
                      ..-.+||++|.+..++. +..+..|.+|.|+.|.|+.+.+.+-..+++|.+|.|.+|++.++-+  -+..+++|++|.+-
T Consensus        43 ~~d~iDLtdNdl~~l~~-lp~l~rL~tLll~nNrIt~I~p~L~~~~p~l~~L~LtnNsi~~l~dl~pLa~~p~L~~Ltll  121 (233)
T KOG1644|consen   43 QFDAIDLTDNDLRKLDN-LPHLPRLHTLLLNNNRITRIDPDLDTFLPNLKTLILTNNSIQELGDLDPLASCPKLEYLTLL  121 (233)
T ss_pred             ccceecccccchhhccc-CCCccccceEEecCCcceeeccchhhhccccceEEecCcchhhhhhcchhccCCccceeeec
Confidence            45678888888765543 6678889999999999998888774567789999999988877643  26678888888777


Q ss_pred             CccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccc
Q 003387          600 SITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       600 ~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      +|.+...        .          ..... .+..+++|+.|+.....
T Consensus       122 ~Npv~~k--------~----------~YR~y-vl~klp~l~~LDF~kVt  151 (233)
T KOG1644|consen  122 GNPVEHK--------K----------NYRLY-VLYKLPSLRTLDFQKVT  151 (233)
T ss_pred             CCchhcc--------c----------CceeE-EEEecCcceEeehhhhh
Confidence            7665421        0          11111 26678888888887764

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=96.86  E-value=0.0029  Score=64.81  Aligned_cols=101  Identities=11%  Similarity=0.158  Sum_probs=59.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCc-eeEEEECCCCCCCC-HHHHHHHHHHHhCCC--------CCccccccc
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD-CHAWITEPYSNEYD-ADQILDIVIKFLMPS--------SRLSEIMDK  248 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~~~vs~~~~-~~~~~~~i~~~l~~~--------~~~~~~~~~  248 (824)
                      -.-++|+|..|+|||||++.+++  .++.+|+ .++++-  +.+..+ +.++.+++...=...        .+.+.....
T Consensus        69 GQr~~If~~~G~GKTtLa~~i~~--~i~~~~~~~~V~~~--iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~  144 (274)
T cd01133          69 GGKIGLFGGAGVGKTVLIMELIN--NIAKAHGGYSVFAG--VGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARA  144 (274)
T ss_pred             CCEEEEecCCCCChhHHHHHHHH--HHHhcCCCEEEEEE--eccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHH
Confidence            45789999999999999999999  6666664 445555  655543 345555554421110        110101111


Q ss_pred             CHHHHHHHHHHhc--C-CCeEEEEEecCCCh-hhHHHHH
Q 003387          249 NYEMKKIILHEYL--M-TKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       249 ~~~~~~~~l~~~L--~-~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      -....+..+.+++  + ++.+|+++||+-.. ..+.++.
T Consensus       145 ~~~~~a~~~AEyfr~~~g~~Vl~~~Dsltr~a~A~reis  183 (274)
T cd01133         145 RVALTGLTMAEYFRDEEGQDVLLFIDNIFRFTQAGSEVS  183 (274)
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEeChhHHHHHHHHHH
Confidence            1122334455555  3 89999999999654 3344444

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.

>COG5238 RNA1 Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]

Probab=96.86  E-value=0.00024  Score=70.14  Aligned_cols=241  Identities=16%  Similarity=0.101  Sum_probs=141.7

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc----cCC-------ccCCCCCcceEEeecCCCCC-cc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI----QYP-------SGIENLFLLRYLKLNIPSLN-SL  559 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~----~lp-------~~i~~l~~Lr~L~L~~~~i~-~l  559 (824)
                      ...+..+.++++....--...+...+.+-++|++.+++.-...    .+|       +.+-+|++|+..+||.|-+. +.
T Consensus        29 ~d~~~evdLSGNtigtEA~e~l~~~ia~~~~L~vvnfsd~ftgr~kde~~~~L~~Ll~aLlkcp~l~~v~LSDNAfg~~~  108 (388)
T COG5238          29 MDELVEVDLSGNTIGTEAMEELCNVIANVRNLRVVNFSDAFTGRDKDELYSNLVMLLKALLKCPRLQKVDLSDNAFGSEF  108 (388)
T ss_pred             hcceeEEeccCCcccHHHHHHHHHHHhhhcceeEeehhhhhhcccHHHHHHHHHHHHHHHhcCCcceeeeccccccCccc
Confidence            5666777777777642112356677788888999988865321    333       44568899999999998876 44


Q ss_pred             Chhh---hhcCCCccEeecCCccccccchh-hh-------------ccccCceecCCCccCCCCCCCCCCCCCCCCeeec
Q 003387          560 PSSL---LSNLLNLYTLDMPFSYIDHTADE-FW-------------KMNKLRHLNFGSITLPAHPGKFCGSLENLNFISA  622 (824)
Q Consensus       560 p~~i---~~~L~~L~~L~L~~~~l~~lp~~-i~-------------~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~  622 (824)
                      |+.+   +++-++|.+|.+++|.+..+... |+             +-|.|+......|++.++.               
T Consensus       109 ~e~L~d~is~~t~l~HL~l~NnGlGp~aG~rigkal~~la~nKKaa~kp~Le~vicgrNRlengs---------------  173 (388)
T COG5238         109 PEELGDLISSSTDLVHLKLNNNGLGPIAGGRIGKALFHLAYNKKAADKPKLEVVICGRNRLENGS---------------  173 (388)
T ss_pred             chHHHHHHhcCCCceeEEeecCCCCccchhHHHHHHHHHHHHhhhccCCCceEEEeccchhccCc---------------
Confidence            4432   37889999999999977655322 22             3456777777666664321               


Q ss_pred             cCCCcchhhhcCCCCccceEEEecccccc---hhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCc-cCcCCCceEEEE
Q 003387          623 LHPCCCTEDILGRLPNLRNLRIRGDLSYN---QSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAE-YLFPHSLTHLSF  698 (824)
Q Consensus       623 ~~~~~~~~~~l~~l~~L~~L~l~~~~~~~---~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~-~~~~~~L~~L~L  698 (824)
                         .......+..-.+|+.+.+..+....   ..-+...+.-+.+|+.|+|..|. +...-+..+.. +..-+.|+.|.+
T Consensus       174 ---~~~~a~~l~sh~~lk~vki~qNgIrpegv~~L~~~gl~y~~~LevLDlqDNt-ft~~gS~~La~al~~W~~lrEL~l  249 (388)
T COG5238         174 ---KELSAALLESHENLKEVKIQQNGIRPEGVTMLAFLGLFYSHSLEVLDLQDNT-FTLEGSRYLADALCEWNLLRELRL  249 (388)
T ss_pred             ---HHHHHHHHHhhcCceeEEeeecCcCcchhHHHHHHHHHHhCcceeeeccccc-hhhhhHHHHHHHhcccchhhhccc
Confidence               01111113333567766666554111   11122334455677777777652 11111110000 123355788888


Q ss_pred             EcccCCCCCccc----cc--CCCCCCeEEeeccccCCCeeee------cCCCCCCccEEeeccCC
Q 003387          699 SNTDLMDDPMPT----LE--KLPLLQVLKLKQNSYSGRKLTC------GSYGFPNLKVLHLKSML  751 (824)
Q Consensus       699 ~~~~l~~~~~~~----l~--~l~~L~~L~L~~~~~~~~~~~~------~~~~~~~L~~L~L~~~~  751 (824)
                      ..|-++......    +.  ..|+|..|...+|...+..+..      .....|-|..|.+.+|.
T Consensus       250 nDClls~~G~~~v~~~f~e~~~p~l~~L~~~Yne~~~~~i~~~~l~~~e~~~~p~L~~le~ngNr  314 (388)
T COG5238         250 NDCLLSNEGVKSVLRRFNEKFVPNLMPLPGDYNERRGGIILDISLNEFEQDAVPLLVDLERNGNR  314 (388)
T ss_pred             cchhhccccHHHHHHHhhhhcCCCccccccchhhhcCceeeeechhhhhhcccHHHHHHHHccCc
Confidence            888765543322    21  3688888888888766544333      23467888888888765

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.85  E-value=0.0083  Score=69.01  Aligned_cols=46  Identities=15%  Similarity=0.158  Sum_probs=37.6

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+++||-+..++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 f~dviGQe~vv~~L~~~l~~~r-l~ha~Lf~Gp~GvGKTtlAr~lAk   60 (618)
T PRK14951         15 FSEMVGQEHVVQALTNALTQQR-LHHAYLFTGTRGVGKTTVSRILAK   60 (618)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3578998888888888887764 235678999999999999998844

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.84  E-value=0.0061  Score=68.37  Aligned_cols=49  Identities=24%  Similarity=0.201  Sum_probs=38.7

Q ss_pred             CCCCCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.-.++.|.+..+++|.+.+...           -...+-+-++|++|.|||++|+++++
T Consensus       179 v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~  238 (512)
T TIGR03689       179 VTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVAN  238 (512)
T ss_pred             CCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHH
Confidence            33456889999999998876431           12345688999999999999999999

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.

>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=96.83  E-value=0.0025  Score=64.07  Aligned_cols=122  Identities=14%  Similarity=0.143  Sum_probs=66.8

Q ss_pred             Cceechh-hHHHHHHHHHcC-CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC-c-eeEEEECCCCCCCCHHHHHHHH
Q 003387          157 DTVGLDD-RMEELLDLLIEG-PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF-D-CHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       157 ~~vGr~~-~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F-~-~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      -++|-.. ..-...+.+... +.....+.|+|..|+|||.|.+++++  ++.+.. . .+++++        ..+....+
T Consensus        10 fv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~--~~~~~~~~~~v~y~~--------~~~f~~~~   79 (219)
T PF00308_consen   10 FVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIAN--EAQKQHPGKRVVYLS--------AEEFIREF   79 (219)
T ss_dssp             S--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHH--HHHHHCTTS-EEEEE--------HHHHHHHH
T ss_pred             CCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHH--HHHhccccccceeec--------HHHHHHHH
Confidence            3456433 233444444443 33455688999999999999999999  554332 2 344554        44555555


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh---hhHHHHHh-hCCC-CCCCcEEEEEechH
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI---DMWDVIQE-ILPD-NQNGSRVLITLTDI  302 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~-~~~~-~~~gs~ilvTtR~~  302 (824)
                      +..+...         .    ...+++.+++ -=+|++||+...   ..|..... .+.. ...|-+||+|++..
T Consensus        80 ~~~~~~~---------~----~~~~~~~~~~-~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~  140 (219)
T PF00308_consen   80 ADALRDG---------E----IEEFKDRLRS-ADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRP  140 (219)
T ss_dssp             HHHHHTT---------S----HHHHHHHHCT-SSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-
T ss_pred             HHHHHcc---------c----chhhhhhhhc-CCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCC
Confidence            5554321         1    1334444443 337889999754   22332222 1211 13466899998543

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=96.81  E-value=0.0039  Score=64.73  Aligned_cols=45  Identities=22%  Similarity=0.198  Sum_probs=33.0

Q ss_pred             CceechhhHHHHHHHHHc----------C---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          157 DTVGLDDRMEELLDLLIE----------G---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~----------~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.+..+++|.+....          +   .+...-+.++|++|.||||+|+.+++
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHH
Confidence            578888877766543221          1   23456778999999999999999976

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.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=96.81  E-value=0.0036  Score=68.59  Aligned_cols=49  Identities=20%  Similarity=0.124  Sum_probs=38.7

Q ss_pred             CCCCCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.-.++.|.+..+++|.+.+...           -...+-+.++|++|.|||++|+++.+
T Consensus       142 v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~  201 (398)
T PTZ00454        142 VTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAH  201 (398)
T ss_pred             CCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            33457889999998888776421           12457788999999999999999998

>PRK09087 hypothetical protein; Validated

Probab=96.81  E-value=0.0068  Score=61.18  Aligned_cols=24  Identities=25%  Similarity=0.246  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ...+.|+|..|+|||+|++.+++.
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh
Confidence            456899999999999999999874

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.80  E-value=0.0033  Score=66.96  Aligned_cols=108  Identities=11%  Similarity=-0.021  Sum_probs=65.2

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC-ce-eEEEECCCCCC-CCHHHHHHHHHHHhCCCC
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF-DC-HAWITEPYSNE-YDADQILDIVIKFLMPSS  240 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F-~~-~~wv~~~vs~~-~~~~~~~~~i~~~l~~~~  240 (824)
                      -..++++.+..-.. -.-+.|+|..|+|||||++.+.+  .+.... +. ++|+.  +.+. -++.++.+.+...+....
T Consensus       119 ~~~RvID~l~PiGk-GQR~LIvG~pGtGKTTLl~~la~--~i~~~~~dv~~vv~l--IgER~~EV~df~~~i~~~Vvast  193 (380)
T PRK12608        119 LSMRVVDLVAPIGK-GQRGLIVAPPRAGKTVLLQQIAA--AVAANHPEVHLMVLL--IDERPEEVTDMRRSVKGEVYAST  193 (380)
T ss_pred             hhHhhhhheeecCC-CceEEEECCCCCCHHHHHHHHHH--HHHhcCCCceEEEEE--ecCCCCCHHHHHHHHhhhEEeec
Confidence            34557777764221 24569999999999999999888  443322 33 35666  5544 367788888877665532


Q ss_pred             C-cccccccCHHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          241 R-LSEIMDKNYEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       241 ~-~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      . .+.............+.+++  ++++++||+|++-..
T Consensus       194 ~de~~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsltr~  232 (380)
T PRK12608        194 FDRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTRL  232 (380)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcHHH
Confidence            1 11111111222222333333  579999999999644

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=96.79  E-value=0.021  Score=61.93  Aligned_cols=47  Identities=19%  Similarity=0.147  Sum_probs=38.3

Q ss_pred             CCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+++|.+..++.+.+.+..+. -...+-++|+.|+||||+|..+.+
T Consensus        17 ~~~~iiGq~~~~~~L~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~~A~   63 (365)
T PRK07471         17 ETTALFGHAAAEAALLDAYRSGR-LHHAWLIGGPQGIGKATLAYRMAR   63 (365)
T ss_pred             chhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            34689999999999999888764 234688999999999999976554

>PHA00729 NTP-binding motif containing protein

Probab=96.78  E-value=0.0038  Score=61.90  Aligned_cols=33  Identities=15%  Similarity=0.203  Sum_probs=25.9

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++.+...+  ...|.|.|.+|+||||||..+.+
T Consensus         7 ~~~~~l~~~~--f~nIlItG~pGvGKT~LA~aLa~   39 (226)
T PHA00729          7 KIVSAYNNNG--FVSAVIFGKQGSGKTTYALKVAR   39 (226)
T ss_pred             HHHHHHhcCC--eEEEEEECCCCCCHHHHHHHHHH
Confidence            3445554443  56789999999999999999988

>PRK06526 transposase; Provisional

Probab=96.77  E-value=0.0012  Score=67.83  Aligned_cols=23  Identities=26%  Similarity=0.056  Sum_probs=20.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.-+.|+|++|+|||+||..+.+
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~  120 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGI  120 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHH
Confidence            34589999999999999999987

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.76  E-value=0.0095  Score=60.46  Aligned_cols=103  Identities=17%  Similarity=0.143  Sum_probs=61.6

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC------ceeEEEECCCCCCCCHHHHHHHHHHHhCCCC-
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF------DCHAWITEPYSNEYDADQILDIVIKFLMPSS-  240 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F------~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~-  240 (824)
                      +-++|..+-..-.++.|+|.+|.|||+||..+.-.  ....-      ..++|++  ....++..++. +++....... 
T Consensus         8 lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~--~~~~~~~~g~~~~v~yi~--~e~~~~~~rl~-~~~~~~~~~~~   82 (226)
T cd01393           8 LDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVE--AQLPGELGGLEGKVVYID--TEGAFRPERLV-QLAVRFGLDPE   82 (226)
T ss_pred             HHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHH--hhcccccCCCcceEEEEe--cCCCCCHHHHH-HHHHHhccchh
Confidence            44444445445789999999999999999988662  22223      5678998  77777766554 3333332211 


Q ss_pred             ----CcccccccCHHHHHHHHHHhcC---C-CeEEEEEecCCC
Q 003387          241 ----RLSEIMDKNYEMKKIILHEYLM---T-KRYLIVIDDVWS  275 (824)
Q Consensus       241 ----~~~~~~~~~~~~~~~~l~~~L~---~-kr~LlVlDdv~~  275 (824)
                          ...-....+.++....+.+.++   . +--|||+|.+..
T Consensus        83 ~~~~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~lvVIDsis~  125 (226)
T cd01393          83 EVLDNIYVARPYNGEQQLEIVEELERIMSSGRVDLVVVDSVAA  125 (226)
T ss_pred             hhhccEEEEeCCCHHHHHHHHHHHHHHhhcCCeeEEEEcCcch
Confidence                0000122345555555555443   3 455899999853

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.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.75  E-value=0.018  Score=56.45  Aligned_cols=40  Identities=10%  Similarity=0.219  Sum_probs=27.8

Q ss_pred             CCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          263 TKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       263 ~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      +.+-++|+||+...  ..++.+...+....+.+.+|++|++.
T Consensus        95 ~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~  136 (188)
T TIGR00678        95 SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSP  136 (188)
T ss_pred             CCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECCh
Confidence            45668999999754  45777777776655566777777654

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.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.75  E-value=0.011  Score=64.99  Aligned_cols=45  Identities=20%  Similarity=0.195  Sum_probs=38.6

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|.+...+.+.+.+..+. -...+-++|+.|+||||+|+.+.+
T Consensus        17 ~~iig~~~~~~~l~~~i~~~~-~~~~~L~~G~~G~GKt~~a~~la~   61 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENNH-LAQALLFCGPRGVGKTTCARILAR   61 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            578899999999999998754 245788999999999999999877

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.74  E-value=0.009  Score=62.66  Aligned_cols=45  Identities=16%  Similarity=0.183  Sum_probs=30.3

Q ss_pred             CceechhhHHHHHHHHH---c-------C---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          157 DTVGLDDRMEELLDLLI---E-------G---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~---~-------~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.++.+++|.++..   .       +   .....-+.++|.+|.||||+|+.+.+
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~   80 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQ   80 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHH
Confidence            46787777776655422   1       1   01123578999999999999977766

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.73  E-value=0.0045  Score=75.21  Aligned_cols=44  Identities=16%  Similarity=0.268  Sum_probs=37.4

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++||+.+++++++.|....  -.-+.++|.+|+|||++|..+..
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~--~~n~lL~G~pGvGKT~l~~~la~  216 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRT--KNNPVLIGEPGVGKTAIVEGLAQ  216 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHH
Confidence            569999999999999997764  23445899999999999999887

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.72  E-value=0.0052  Score=67.89  Aligned_cols=46  Identities=22%  Similarity=0.181  Sum_probs=38.7

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|-+..+..|..++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        17 f~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriLAk   62 (484)
T PRK14956         17 FRDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARILAK   62 (484)
T ss_pred             HHHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999888765 224578999999999999999987

>PRK07261 topology modulation protein; Provisional

Probab=96.72  E-value=0.0036  Score=60.34  Aligned_cols=67  Identities=15%  Similarity=0.177  Sum_probs=41.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccc-CCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHH
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVK-HYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  259 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  259 (824)
                      .|.|+|++|+||||||+.+.....+. -+.|...|-.  ..                         ...+.++....+.+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~--~~-------------------------~~~~~~~~~~~~~~   54 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQP--NW-------------------------QERDDDDMIADISN   54 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEecc--cc-------------------------ccCCHHHHHHHHHH
Confidence            48999999999999999987632111 1234444432  11                         12233455566666


Q ss_pred             hcCCCeEEEEEecCCCh
Q 003387          260 YLMTKRYLIVIDDVWSI  276 (824)
Q Consensus       260 ~L~~kr~LlVlDdv~~~  276 (824)
                      .+.+.+  .|+|+....
T Consensus        55 ~~~~~~--wIidg~~~~   69 (171)
T PRK07261         55 FLLKHD--WIIDGNYSW   69 (171)
T ss_pred             HHhCCC--EEEcCcchh
Confidence            666655  677888654

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.71  E-value=0.0031  Score=75.39  Aligned_cols=115  Identities=11%  Similarity=0.210  Sum_probs=67.0

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQI  228 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~  228 (824)
                      ..++|.+..++.|.+.+...       .....++.++|+.|+|||+||+.+..  ..   +...+.++  .|+..+..  
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~--~l---~~~~~~~d--~se~~~~~--  524 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAE--AL---GVHLERFD--MSEYMEKH--  524 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHH--Hh---cCCeEEEe--Cchhhhcc--
Confidence            45889999999998887642       12355788999999999999999988  33   23345555  44422211  


Q ss_pred             HHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCC-CeEEEEEecCCCh--hhHHHHHhhCC
Q 003387          229 LDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT-KRYLIVIDDVWSI--DMWDVIQEILP  287 (824)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~~--~~~~~l~~~~~  287 (824)
                        .+...++...+.  .......    .+.+.++. ..-+++||++...  +.++.+...+.
T Consensus       525 --~~~~lig~~~gy--vg~~~~~----~l~~~~~~~p~~VvllDEieka~~~~~~~Ll~~ld  578 (731)
T TIGR02639       525 --TVSRLIGAPPGY--VGFEQGG----LLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMD  578 (731)
T ss_pred             --cHHHHhcCCCCC--cccchhh----HHHHHHHhCCCeEEEEechhhcCHHHHHHHHHhhc
Confidence              112222221110  1111112    23334433 3459999999865  45666665554

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=96.69  E-value=0.011  Score=67.29  Aligned_cols=46  Identities=13%  Similarity=0.140  Sum_probs=38.7

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|.+..++.+.+.+..+. -...+-++|+.|+||||+|+.+.+
T Consensus        15 F~dIIGQe~iv~~L~~aI~~~r-l~hA~Lf~GP~GvGKTTlA~~lAk   60 (605)
T PRK05896         15 FKQIIGQELIKKILVNAILNNK-LTHAYIFSGPRGIGKTSIAKIFAK   60 (605)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999887653 235788999999999999999876

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.68  E-value=0.0066  Score=61.66  Aligned_cols=95  Identities=16%  Similarity=0.107  Sum_probs=53.6

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcc
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLS  243 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~  243 (824)
                      .+..+.++...-..+...+.++|.+|+|||+||.++.+  .....-..+++++        ..++...+-.....     
T Consensus        84 al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~--~l~~~g~~v~~it--------~~~l~~~l~~~~~~-----  148 (244)
T PRK07952         84 ALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICN--ELLLRGKSVLIIT--------VADIMSAMKDTFSN-----  148 (244)
T ss_pred             HHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHH--HHHhcCCeEEEEE--------HHHHHHHHHHHHhh-----
Confidence            34444444433233345789999999999999999999  4443334555665        34444444433211     


Q ss_pred             cccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHH
Q 003387          244 EIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWD  280 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~  280 (824)
                        ...+..    .+.+.+. +-=+||+||+...  .+|+
T Consensus       149 --~~~~~~----~~l~~l~-~~dlLvIDDig~~~~s~~~  180 (244)
T PRK07952        149 --SETSEE----QLLNDLS-NVDLLVIDEIGVQTESRYE  180 (244)
T ss_pred             --ccccHH----HHHHHhc-cCCEEEEeCCCCCCCCHHH
Confidence              011111    2333344 3448888999654  3454

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.66  E-value=0.018  Score=62.00  Aligned_cols=48  Identities=19%  Similarity=0.160  Sum_probs=40.1

Q ss_pred             CCCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .....++|-+...+.+...+..+. -...+-|+|..|+||||+|..+.+
T Consensus        20 ~~~~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~lA~   67 (351)
T PRK09112         20 SENTRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFHLAN   67 (351)
T ss_pred             CchhhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHHHHH
Confidence            345789999999999999997764 345688999999999999988766

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.66  E-value=0.0082  Score=67.07  Aligned_cols=120  Identities=19%  Similarity=0.261  Sum_probs=64.9

Q ss_pred             CceechhhH--HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC-c-eeEEEECCCCCCCCHHHHHHHH
Q 003387          157 DTVGLDDRM--EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF-D-CHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       157 ~~vGr~~~~--~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F-~-~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      -++|-....  ....++..... ...-+.|+|..|+|||+|++++.+  ++.... . .++|++        ..++..++
T Consensus       107 Fv~g~~n~~a~~~~~~~~~~~~-~~n~l~lyG~~G~GKTHLl~ai~~--~l~~~~~~~~v~yi~--------~~~f~~~~  175 (440)
T PRK14088        107 FVVGPGNSFAYHAALEVAKNPG-RYNPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYIT--------SEKFLNDL  175 (440)
T ss_pred             cccCCchHHHHHHHHHHHhCcC-CCCeEEEEcCCCCcHHHHHHHHHH--HHHHhCCCCeEEEEE--------HHHHHHHH
Confidence            355744432  23333333222 245599999999999999999999  554433 3 355665        23456666


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh---hhH-HHHHhhCCC-CCCCcEEEEEec
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI---DMW-DVIQEILPD-NQNGSRVLITLT  300 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~-~~l~~~~~~-~~~gs~ilvTtR  300 (824)
                      ...+...         +.+    .+.+..+.+.-+|++||+...   ..+ +.+...+.. ...|..||+||.
T Consensus       176 ~~~~~~~---------~~~----~f~~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd  235 (440)
T PRK14088        176 VDSMKEG---------KLN----EFREKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSD  235 (440)
T ss_pred             HHHHhcc---------cHH----HHHHHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECC
Confidence            6555321         112    223333334558999999743   111 222222211 112456888874

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.63  E-value=0.0092  Score=60.61  Aligned_cols=44  Identities=14%  Similarity=0.171  Sum_probs=29.6

Q ss_pred             eechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          159 VGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       159 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .|.+.........+..+......+.|+|..|+|||+||+.+++.
T Consensus        22 ~~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         22 AGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             cCCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            45544443333333232233567889999999999999999983

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.63  E-value=0.0064  Score=62.13  Aligned_cols=104  Identities=14%  Similarity=0.129  Sum_probs=59.4

Q ss_pred             HHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCC----CceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC---
Q 003387          169 LDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY----FDCHAWITEPYSNEYDADQILDIVIKFLMPSSR---  241 (824)
Q Consensus       169 ~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~---  241 (824)
                      -++|..+-..-.++.|+|.+|+||||||.++.-.......    -..++|++  ....++..++.+ +++..+....   
T Consensus         9 D~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~--~e~~~~~~rl~~-~~~~~~~~~~~~~   85 (235)
T cd01123           9 DELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID--TEGTFRPERLVQ-IAERFGLDPEEVL   85 (235)
T ss_pred             HhhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEe--CCCCcCHHHHHH-HHHHhccChHhHh
Confidence            3444444445689999999999999999998643222221    36789999  777777655443 3444332110   


Q ss_pred             --cccccccCH---HHHHHHHHHhcC-C-CeEEEEEecCCC
Q 003387          242 --LSEIMDKNY---EMKKIILHEYLM-T-KRYLIVIDDVWS  275 (824)
Q Consensus       242 --~~~~~~~~~---~~~~~~l~~~L~-~-kr~LlVlDdv~~  275 (824)
                        ..-....+.   ......+.+.+. . +--+||+|-+..
T Consensus        86 ~~i~~~~~~~~~~l~~~l~~l~~~l~~~~~~~liVIDSis~  126 (235)
T cd01123          86 DNIYVARAYNSDHQLQLLEELEAILIESSRIKLVIVDSVTA  126 (235)
T ss_pred             cCEEEEecCCHHHHHHHHHHHHHHHhhcCCeeEEEEeCcHH
Confidence              000111122   223344444443 3 566888888853

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 .

>PRK09183 transposase/IS protein; Provisional

Probab=96.62  E-value=0.0025  Score=65.74  Aligned_cols=22  Identities=23%  Similarity=0.205  Sum_probs=19.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+.|+|..|+|||+||..+.+
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~  124 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGY  124 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHH
Confidence            4677999999999999999977

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.60  E-value=0.0031  Score=64.80  Aligned_cols=76  Identities=22%  Similarity=0.095  Sum_probs=47.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  257 (824)
                      +..-+.++|.+|+|||.||.++.+  ++...=-.+.+++        ..++..++......            ......|
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~--~l~~~g~sv~f~~--------~~el~~~Lk~~~~~------------~~~~~~l  161 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGN--ELLKAGISVLFIT--------APDLLSKLKAAFDE------------GRLEEKL  161 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHH--HHHHcCCeEEEEE--------HHHHHHHHHHHHhc------------CchHHHH
Confidence            466789999999999999999999  5553323566666        34455555544332            1112223


Q ss_pred             HHhcCCCeEEEEEecCCCh
Q 003387          258 HEYLMTKRYLIVIDDVWSI  276 (824)
Q Consensus       258 ~~~L~~kr~LlVlDdv~~~  276 (824)
                      .+.++ +-=||||||+-..
T Consensus       162 ~~~l~-~~dlLIiDDlG~~  179 (254)
T COG1484         162 LRELK-KVDLLIIDDIGYE  179 (254)
T ss_pred             HHHhh-cCCEEEEecccCc
Confidence            33221 2338999999653

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.60  E-value=0.0058  Score=61.20  Aligned_cols=97  Identities=12%  Similarity=0.036  Sum_probs=56.2

Q ss_pred             HHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHh-CCC-CCcccccc--
Q 003387          172 LIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFL-MPS-SRLSEIMD--  247 (824)
Q Consensus       172 L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l-~~~-~~~~~~~~--  247 (824)
                      |..+=..-+++-|+|.+|+|||++|.++..  .....-..++|++  ... ++..++.+. ++.. ... ....-...  
T Consensus         5 l~GGi~~g~i~~i~G~~GsGKT~l~~~~~~--~~~~~g~~v~yi~--~e~-~~~~rl~~~-~~~~~~~~~~~i~~~~~~~   78 (209)
T TIGR02237         5 LGGGVERGTITQIYGPPGSGKTNICMILAV--NAARQGKKVVYID--TEG-LSPERFKQI-AEDRPERALSNFIVFEVFD   78 (209)
T ss_pred             hcCCCCCCeEEEEECCCCCCHHHHHHHHHH--HHHhCCCeEEEEE--CCC-CCHHHHHHH-HHhChHHHhcCEEEEECCC
Confidence            444434568999999999999999998876  3434457899998  654 666665543 2221 000 00000111  


Q ss_pred             -cCHHHHHHHHHHhcCC-CeEEEEEecCC
Q 003387          248 -KNYEMKKIILHEYLMT-KRYLIVIDDVW  274 (824)
Q Consensus       248 -~~~~~~~~~l~~~L~~-kr~LlVlDdv~  274 (824)
                       .+.......+.+.+.. +.-+||+|-+.
T Consensus        79 ~~~~~~~~~~l~~~~~~~~~~lvVIDSis  107 (209)
T TIGR02237        79 FDEQGVAIQKTSKFIDRDSASLVVVDSFT  107 (209)
T ss_pred             HHHHHHHHHHHHHHHhhcCccEEEEeCcH
Confidence             1122334555555543 44578888874

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>smart00763 AAA_PrkA PrkA AAA domain

Probab=96.60  E-value=0.0018  Score=68.64  Aligned_cols=58  Identities=12%  Similarity=0.254  Sum_probs=45.8

Q ss_pred             CceechhhHHHHHHHHHcC----CCCeEEEEEEcCCCChHHHHHHHHhCCccc-----cCCCceeEE
Q 003387          157 DTVGLDDRMEELLDLLIEG----PPQLSVVAILDSIGLDKTAFAGEAYNSSYV-----KHYFDCHAW  214 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~-----~~~F~~~~w  214 (824)
                      +++|.++.++++++++...    ....+++.++|++|.||||||+.+.+.-+.     .+.|...-|
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~  118 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKW  118 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEe
Confidence            7999999999999999763    235689999999999999999999883211     225555666

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.59  E-value=0.013  Score=67.57  Aligned_cols=46  Identities=13%  Similarity=-0.058  Sum_probs=37.4

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|-+..++.+.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        15 f~eivGQe~i~~~L~~~i~~~r-i~ha~Lf~Gp~GvGKttlA~~lAk   60 (620)
T PRK14954         15 FADITAQEHITHTIQNSLRMDR-VGHGYIFSGLRGVGKTTAARVFAK   60 (620)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHH
Confidence            3678999999999888887653 234588999999999999988766

>PRK06620 hypothetical protein; Validated

Probab=96.57  E-value=0.0071  Score=60.46  Aligned_cols=49  Identities=12%  Similarity=-0.098  Sum_probs=31.4

Q ss_pred             CCCCceec-hh-hHHHHHHHHHcCCCCe--EEEEEEcCCCChHHHHHHHHhCC
Q 003387          154 KSRDTVGL-DD-RMEELLDLLIEGPPQL--SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       154 ~~~~~vGr-~~-~~~~l~~~L~~~~~~~--~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .++-+||- .. ....+.++-.....+.  +.+.|+|+.|+|||+|++.+.+.
T Consensus        15 fd~Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         15 PDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             chhhEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhc
Confidence            34566775 22 2344444432111112  67899999999999999998884

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.57  E-value=0.0095  Score=65.55  Aligned_cols=96  Identities=18%  Similarity=0.242  Sum_probs=62.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC-CCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHH
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN-EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  259 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~-~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  259 (824)
                      ++.|+|+-++||||+++.+..  ...+.   .+++.  .-. ..+..++ .+...                     .+.+
T Consensus        39 i~~i~GpR~~GKTtll~~l~~--~~~~~---~iy~~--~~d~~~~~~~l-~d~~~---------------------~~~~   89 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIK--GLLEE---IIYIN--FDDLRLDRIEL-LDLLR---------------------AYIE   89 (398)
T ss_pred             EEEEECCccccHHHHHHHHHh--hCCcc---eEEEE--ecchhcchhhH-HHHHH---------------------HHHH
Confidence            999999999999999977766  23222   44443  111 1111111 11111                     1111


Q ss_pred             hcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          260 YLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       260 ~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      .-..++.+|+||.|....+|+.....+.+.++. +|++|+-+.....
T Consensus        90 ~~~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~  135 (398)
T COG1373          90 LKEREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLS  135 (398)
T ss_pred             hhccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhc
Confidence            111178899999999999999999988888777 8999988876554

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=96.56  E-value=0.0056  Score=67.58  Aligned_cols=52  Identities=21%  Similarity=0.204  Sum_probs=39.7

Q ss_pred             CCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          156 RDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      .++.|.+..+++|.+.+...           -...+-+.++|++|.|||++|+++.+  +....|
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~--el~~~f  245 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVAN--ETSATF  245 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHH--hhCCCE
Confidence            45788999999888877421           12345678999999999999999999  555444

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.54  E-value=0.0014  Score=63.43  Aligned_cols=36  Identities=19%  Similarity=0.005  Sum_probs=25.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ..-+.++|..|+|||.||.++.+  +....=..+.|++
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~--~~~~~g~~v~f~~   82 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIAN--EAIRKGYSVLFIT   82 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHH--HHHHTT--EEEEE
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHH--HhccCCcceeEee
Confidence            45699999999999999999988  3333223466776

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.

>PRK06921 hypothetical protein; Provisional

Probab=96.53  E-value=0.008  Score=62.24  Aligned_cols=36  Identities=19%  Similarity=0.076  Sum_probs=28.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCC-CceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHY-FDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~~~~wv~  216 (824)
                      ..-+.++|..|+|||+||.++.+  ++... -..+++++
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~--~l~~~~g~~v~y~~  153 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAAN--ELMRKKGVPVLYFP  153 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHH--HHhhhcCceEEEEE
Confidence            56789999999999999999999  55444 34567776

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.53  E-value=0.025  Score=64.92  Aligned_cols=46  Identities=22%  Similarity=0.096  Sum_probs=38.5

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+..++.|.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        12 f~eivGq~~i~~~L~~~i~~~r-~~ha~Lf~Gp~G~GKTt~A~~lAk   57 (584)
T PRK14952         12 FAEVVGQEHVTEPLSSALDAGR-INHAYLFSGPRGCGKTSSARILAR   57 (584)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999988654 234578999999999999998877

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.53  E-value=0.02  Score=66.51  Aligned_cols=135  Identities=13%  Similarity=0.139  Sum_probs=73.2

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~  234 (824)
                      -++++|-+..++.|.+++..+. -...+-++|..|+||||+|+.+.+  .+.-..    +-.  ....++.....+.|..
T Consensus        15 ~~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~--~l~c~~----~~~--~~~~c~~c~~c~~i~~   85 (585)
T PRK14950         15 FAELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAK--AVNCTT----NDP--KGRPCGTCEMCRAIAE   85 (585)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHH--HhcCCC----CCC--CCCCCccCHHHHHHhc
Confidence            3589999999999988887654 235667999999999999999876  221000    000  1112222233333322


Q ss_pred             HhCCCCCcccc---cccCHHHHHHHHHHhc-----CCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEech
Q 003387          235 FLMPSSRLSEI---MDKNYEMKKIILHEYL-----MTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTD  301 (824)
Q Consensus       235 ~l~~~~~~~~~---~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~  301 (824)
                      .....  ..++   .....++..+ +.+.+     .+++-++|+|++...  ...+.+...+......+.+|++|..
T Consensus        86 ~~~~d--~~~i~~~~~~~vd~ir~-ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~  159 (585)
T PRK14950         86 GSAVD--VIEMDAASHTSVDDARE-IIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTE  159 (585)
T ss_pred             CCCCe--EEEEeccccCCHHHHHH-HHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCC
Confidence            21110  0000   0111222221 11211     245678999998644  4567776666554456666666543

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.51  E-value=0.01  Score=66.09  Aligned_cols=121  Identities=17%  Similarity=0.213  Sum_probs=63.0

Q ss_pred             CceechhhH--HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCc--eeEEEECCCCCCCCHHHHHHHH
Q 003387          157 DTVGLDDRM--EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD--CHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       157 ~~vGr~~~~--~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      -++|.+...  ..+.++..........+.|+|..|+|||+|++++++  ++.....  .+++++        ..++..++
T Consensus       112 fi~g~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~--~l~~~~~~~~v~yi~--------~~~~~~~~  181 (405)
T TIGR00362       112 FVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGN--EILENNPNAKVVYVS--------SEKFTNDF  181 (405)
T ss_pred             cccCCcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHH--HHHHhCCCCcEEEEE--------HHHHHHHH
Confidence            356755542  223333332222345688999999999999999999  5544332  344554        23444455


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChh---hH-HHHHhhCCC-CCCCcEEEEEech
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSID---MW-DVIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~---~~-~~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                      ...+...         ..+.    +.+.+++ .-+||+||+....   .+ +.+...+.. ...|..+|+|+..
T Consensus       182 ~~~~~~~---------~~~~----~~~~~~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~  241 (405)
T TIGR00362       182 VNALRNN---------KMEE----FKEKYRS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDR  241 (405)
T ss_pred             HHHHHcC---------CHHH----HHHHHHh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCC
Confidence            5554321         1122    2333322 2388899997431   11 222222221 1234567777753

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).

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.51  E-value=0.0062  Score=72.06  Aligned_cols=44  Identities=18%  Similarity=0.225  Sum_probs=37.1

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++||+.+++++++.|....  ..-+-++|.+|+|||++|+.+.+
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~--~~n~LLvGppGvGKT~lae~la~  229 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccC--CCCeEEECCCCCCHHHHHHHHHH
Confidence            469999999999999988753  22345799999999999999887

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.50  E-value=0.00043  Score=68.69  Aligned_cols=83  Identities=19%  Similarity=0.169  Sum_probs=62.0

Q ss_pred             cccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch--hhhccccCce
Q 003387          518 GMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD--EFWKMNKLRH  595 (824)
Q Consensus       518 ~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~--~i~~L~~L~~  595 (824)
                      +.+.+.+.|++.||.+..+. -+.+++.|++|.|+-|+|+.|.+  +..|++|+.|.|+.|.|..+-+  -+.++++|+.
T Consensus        16 sdl~~vkKLNcwg~~L~DIs-ic~kMp~lEVLsLSvNkIssL~p--l~rCtrLkElYLRkN~I~sldEL~YLknlpsLr~   92 (388)
T KOG2123|consen   16 SDLENVKKLNCWGCGLDDIS-ICEKMPLLEVLSLSVNKISSLAP--LQRCTRLKELYLRKNCIESLDELEYLKNLPSLRT   92 (388)
T ss_pred             hHHHHhhhhcccCCCccHHH-HHHhcccceeEEeeccccccchh--HHHHHHHHHHHHHhcccccHHHHHHHhcCchhhh
Confidence            34567788888888887552 23568889999999888888865  3788899999998887777643  3667888888


Q ss_pred             ecCCCccC
Q 003387          596 LNFGSITL  603 (824)
Q Consensus       596 L~L~~~~~  603 (824)
                      |-|..|.-
T Consensus        93 LWL~ENPC  100 (388)
T KOG2123|consen   93 LWLDENPC  100 (388)
T ss_pred             HhhccCCc
Confidence            87765543

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=96.48  E-value=0.014  Score=62.67  Aligned_cols=117  Identities=12%  Similarity=0.063  Sum_probs=76.7

Q ss_pred             CCCCceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHH
Q 003387          154 KSRDTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      .+..++||+.++..+.+++...  .+..+-+-|.|.+|.|||.+...++.+......=-.++.+.  ...--....++..
T Consensus       148 ~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~in--c~sl~~~~aiF~k  225 (529)
T KOG2227|consen  148 PPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYIN--CTSLTEASAIFKK  225 (529)
T ss_pred             CCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEe--eccccchHHHHHH
Confidence            4567999999999999998763  34577899999999999999999999632211111234443  2222355677888


Q ss_pred             HHHHhCCCCCcccccccCHHHHHHHHHHhcCC--CeEEEEEecCCCh
Q 003387          232 VIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT--KRYLIVIDDVWSI  276 (824)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~LlVlDdv~~~  276 (824)
                      |...+.....    ......+....+.+..+.  +-+|+|||.++.-
T Consensus       226 I~~~~~q~~~----s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L  268 (529)
T KOG2227|consen  226 IFSSLLQDLV----SPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHL  268 (529)
T ss_pred             HHHHHHHHhc----CCchhHHHHHHHHHHHhcccceEEEEechhhHH
Confidence            8777732111    111124555666666644  3689999999753

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.47  E-value=0.0062  Score=73.50  Aligned_cols=46  Identities=20%  Similarity=0.276  Sum_probs=38.0

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.+..++.+.+.+...       .....++.++|+.|+|||.+|+.+..
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~  618 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAE  618 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999988531       23456889999999999999988866

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.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.46  E-value=0.0022  Score=58.77  Aligned_cols=40  Identities=15%  Similarity=0.179  Sum_probs=29.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCC-CceeEEEECCCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHY-FDCHAWITEPYS  220 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~~~~wv~~~vs  220 (824)
                      ..-|+|.||+|+||||+++.+.+  ..+.. |...-+++.+|.
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e--~L~~~g~kvgGf~t~EVR   45 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAE--KLREKGYKVGGFITPEVR   45 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHH--HHHhcCceeeeEEeeeee
Confidence            45689999999999999999998  55444 765555553343

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.46  E-value=0.006  Score=73.59  Aligned_cols=44  Identities=20%  Similarity=0.322  Sum_probs=37.9

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++||+.++.++++.|....  ..-+.++|.+|+||||+|+.+.+
T Consensus       187 d~~iGr~~ei~~~i~~l~r~~--~~n~lLvG~pGvGKTal~~~La~  230 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRRR--QNNPILTGEAGVGKTAVVEGLAL  230 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcCC--cCceeEECCCCCCHHHHHHHHHH
Confidence            579999999999999987764  33456999999999999999887

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.

>TIGR00763 lon ATP-dependent protease La

Probab=96.46  E-value=0.0086  Score=72.09  Aligned_cols=52  Identities=21%  Similarity=0.362  Sum_probs=40.8

Q ss_pred             CCceechhhHHHHHHHHHc----CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          156 RDTVGLDDRMEELLDLLIE----GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      .+++|.+..+++|.+++..    +.....++.++|++|+||||+|+.+.+  .....|
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~--~l~~~~  375 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAK--ALNRKF  375 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHH--HhcCCe
Confidence            4588999999999987753    222345899999999999999999998  555444

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.46  E-value=0.015  Score=70.57  Aligned_cols=46  Identities=15%  Similarity=0.290  Sum_probs=37.7

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.+..++.+.+.+...       .....++.++|+.|+|||++|+.+.+
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~  620 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALAN  620 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            46889999999998888642       22246888999999999999999987

>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=96.45  E-value=0.011  Score=54.94  Aligned_cols=21  Identities=14%  Similarity=0.229  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ||.++|++|+||||+|+.+..
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

...

>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=96.45  E-value=0.0018  Score=58.47  Aligned_cols=21  Identities=29%  Similarity=0.316  Sum_probs=20.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ||+|+|++|+||||+|+.+.+
T Consensus         1 vI~I~G~~gsGKST~a~~La~   21 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAE   21 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999988

...

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.44  E-value=0.01  Score=56.47  Aligned_cols=39  Identities=13%  Similarity=0.126  Sum_probs=29.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY  223 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~  223 (824)
                      ++.|+|.+|+||||+++.+..  .....-..++|+.  .....
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~--~~~~~~~~v~~~~--~e~~~   39 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLAL--NIATKGGKVVYVD--IEEEI   39 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHH--HHHhcCCEEEEEE--CCcch
Confidence            468999999999999999988  4444445677887  55443

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.42  E-value=0.013  Score=71.08  Aligned_cols=132  Identities=14%  Similarity=0.211  Sum_probs=73.7

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQI  228 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~  228 (824)
                      ..++|-+..++.|.+.+...       .....++-++|+.|+|||+||+.+.+  .+-..-...+-++  .+...+...+
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~--~l~~~~~~~~~~d--~s~~~~~~~~  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALAS--YFFGSEDAMIRLD--MSEYMEKHTV  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHH--HhcCCccceEEEE--chhccccccH
Confidence            56899999999998888632       22345677899999999999998876  3211112333444  4432221111


Q ss_pred             HHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCe-EEEEEecCCCh--hhHHHHHhhCCCC-----------CCCcE
Q 003387          229 LDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKR-YLIVIDDVWSI--DMWDVIQEILPDN-----------QNGSR  294 (824)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr-~LlVlDdv~~~--~~~~~l~~~~~~~-----------~~gs~  294 (824)
                          ..-++...+.  .......    .+.+.++.++ -+++||++...  +.++.+...+..+           ...+-
T Consensus       585 ----~~l~g~~~gy--vg~~~~~----~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i  654 (821)
T CHL00095        585 ----SKLIGSPPGY--VGYNEGG----QLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTL  654 (821)
T ss_pred             ----HHhcCCCCcc--cCcCccc----hHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHhccCceecCCCcEEecCceE
Confidence                1112211110  1111112    3344454444 58889999865  4566666665542           13455


Q ss_pred             EEEEech
Q 003387          295 VLITLTD  301 (824)
Q Consensus       295 ilvTtR~  301 (824)
                      +|+||..
T Consensus       655 ~I~Tsn~  661 (821)
T CHL00095        655 IIMTSNL  661 (821)
T ss_pred             EEEeCCc
Confidence            6667654

>TIGR00602 rad24 checkpoint protein rad24

Probab=96.42  E-value=0.0073  Score=69.62  Aligned_cols=47  Identities=13%  Similarity=0.089  Sum_probs=39.9

Q ss_pred             CCCceechhhHHHHHHHHHcCC---CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGP---PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~---~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|-+..++++..++....   ...+++.|+|+.|.||||+++.+.+
T Consensus        83 ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~  132 (637)
T TIGR00602        83 QHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSK  132 (637)
T ss_pred             HHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3579999999999999987642   2346899999999999999999998

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.42  E-value=0.021  Score=65.81  Aligned_cols=46  Identities=17%  Similarity=0.166  Sum_probs=39.0

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|.+..++.|.+.+..+. -...+-++|+.|+||||+|+.+.+
T Consensus        23 f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk   68 (598)
T PRK09111         23 FDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILAR   68 (598)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999987654 244678899999999999999877

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.41  E-value=0.0057  Score=65.14  Aligned_cols=35  Identities=11%  Similarity=-0.002  Sum_probs=27.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .-+.++|..|+|||+||.++.+  ++...-..+++++
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~--~l~~~g~~V~y~t  218 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAK--ELLDRGKSVIYRT  218 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHH--HHHHCCCeEEEEE
Confidence            6799999999999999999999  4433334566776

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.41  E-value=0.032  Score=62.93  Aligned_cols=45  Identities=13%  Similarity=0.067  Sum_probs=37.4

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|-+..++.+.+++..+. -...+-++|+.|+||||+|+.+..
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk   60 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAK   60 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            578899999999999997754 234567899999999999988766

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=96.40  E-value=0.0044  Score=69.95  Aligned_cols=53  Identities=19%  Similarity=0.328  Sum_probs=44.3

Q ss_pred             CCCceechhhHHHHHHHHHcC----CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          155 SRDTVGLDDRMEELLDLLIEG----PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +.+-+|.++-+++|++.|.-.    .-.-.+++.||++|||||.|++.|.+  .....|
T Consensus       322 d~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~--al~Rkf  378 (782)
T COG0466         322 DKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAK--ALGRKF  378 (782)
T ss_pred             cccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHH--HhCCCE
Confidence            456789999999999999642    33457999999999999999999999  677766

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.40  E-value=0.013  Score=66.05  Aligned_cols=121  Identities=16%  Similarity=0.199  Sum_probs=63.9

Q ss_pred             Cceechhh--HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCc--eeEEEECCCCCCCCHHHHHHHH
Q 003387          157 DTVGLDDR--MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD--CHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       157 ~~vGr~~~--~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      -++|....  ......+.........-+.|+|..|+|||+|++++.+  ++...+.  .+++++        ..++..++
T Consensus       124 fv~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~--~~~~~~~~~~v~yi~--------~~~~~~~~  193 (450)
T PRK00149        124 FVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGN--YILEKNPNAKVVYVT--------SEKFTNDF  193 (450)
T ss_pred             cccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEEE--------HHHHHHHH
Confidence            35565443  3333333333222345689999999999999999999  5555442  344555        23344445


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh---hhH-HHHHhhCCC-CCCCcEEEEEech
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI---DMW-DVIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~-~~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                      ...+...         ..    ..+.+.++ +--+||+||+...   ..+ +.+...+.. ...|..|++||..
T Consensus       194 ~~~~~~~---------~~----~~~~~~~~-~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~  253 (450)
T PRK00149        194 VNALRNN---------TM----EEFKEKYR-SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDR  253 (450)
T ss_pred             HHHHHcC---------cH----HHHHHHHh-cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCC
Confidence            4444221         11    22333333 2348999999643   111 223222211 1124557777754

>PRK13695 putative NTPase; Provisional

Probab=96.40  E-value=0.0031  Score=61.12  Aligned_cols=34  Identities=18%  Similarity=0.232  Sum_probs=24.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCcccc-CCCceeEEEE
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVK-HYFDCHAWIT  216 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~  216 (824)
                      .|+|+|.+|+|||||++.+++.  .. ..|....|++
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~--l~~~G~~~~g~~~   36 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAEL--LKEEGYKVGGFYT   36 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEc
Confidence            4789999999999999999873  32 2344444554

>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=96.39  E-value=0.065  Score=57.73  Aligned_cols=166  Identities=16%  Similarity=0.153  Sum_probs=95.2

Q ss_pred             hhhHHHHHHHHHcCC-CCeEEEEEEcCCCChHHHHHHHHhCCccccCC----C---ceeEEEECCCCCCCCHHHHHHHHH
Q 003387          162 DDRMEELLDLLIEGP-PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY----F---DCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       162 ~~~~~~l~~~L~~~~-~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~----F---~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      +.-.+.|.+.+...+ ....+|||.|.=|+||||+.+.+.+  +.+..    +   ..-+|-.  -...--...++.+|.
T Consensus         2 ~~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~--~L~~~~~~~~~~i~fn~w~~--~~~~~~~~~~~~~l~   77 (325)
T PF07693_consen    2 KPYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKE--ELKEDNKEKYIFIYFNAWEY--DGEDDLWASFLEELF   77 (325)
T ss_pred             hHHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHH--HHhcccccceeeEEEccccC--CCcchHHHHHHHHHH
Confidence            455677888887754 6789999999999999999999988  44443    1   1223333  221212334555555


Q ss_pred             HHhCCCCCc----------------------------cc----------------------------------ccccCHH
Q 003387          234 KFLMPSSRL----------------------------SE----------------------------------IMDKNYE  251 (824)
Q Consensus       234 ~~l~~~~~~----------------------------~~----------------------------------~~~~~~~  251 (824)
                      .++......                            +.                                  ....+.+
T Consensus        78 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (325)
T PF07693_consen   78 DQLEKHFGSKKIKLYAKKKLKSLKIKFKIKINLSKAIPLALIGLPALILAVAIAKLKAELKNAFKSLEEKFLKKLKKEVE  157 (325)
T ss_pred             HHHHHhcCccchhHHHhhhhhhhhceeeeeeecceeehHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHhhhhhHHHH
Confidence            555431100                            00                                  0001122


Q ss_pred             HHHHHHHHhcC--CCeEEEEEecCCCh------hhHHHHHhhCCCCCCCcEEEEEechHHHHhhcccccCCcCcCccccc
Q 003387          252 MKKIILHEYLM--TKRYLIVIDDVWSI------DMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPT  323 (824)
Q Consensus       252 ~~~~~l~~~L~--~kr~LlVlDdv~~~------~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~~f~~~~~~~~~~~~~~~  323 (824)
                      +....+.+.|.  ++|.++|+||++..      +.|+.+...+..  ++..+|+..-.+.++.+.....+...   ....
T Consensus       158 ~~~~~~~~~l~~~~~~iViiIDdLDR~~~~~i~~~l~~ik~~~~~--~~i~~Il~~D~~~l~~ai~~~~~~~~---~~~~  232 (325)
T PF07693_consen  158 ELISKIKKKLKESKKRIVIIIDDLDRCSPEEIVELLEAIKLLLDF--PNIIFILAFDPEILEKAIEKNYGEGF---DEID  232 (325)
T ss_pred             HHHHHHHHhhhcCCceEEEEEcchhcCCcHHHHHHHHHHHHhcCC--CCeEEEEEecHHHHHHHHHhhcCccc---cccc
Confidence            23455666664  48999999999873      245555544433  67778888777777776655432100   2344


Q ss_pred             hhhHHHhcCCCch
Q 003387          324 GGPLRATYKGRPF  336 (824)
Q Consensus       324 ~~~i~~~c~GlPl  336 (824)
                      +.+-.+|.=..|+
T Consensus       233 ~~~yLeKiiq~~~  245 (325)
T PF07693_consen  233 GREYLEKIIQVPF  245 (325)
T ss_pred             HHHHHHhhcCeEE
Confidence            5555555544444

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 [].

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.38  E-value=0.023  Score=55.10  Aligned_cols=37  Identities=22%  Similarity=0.227  Sum_probs=30.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ...+|.++|+.|+||||+|+.+++  +....+...+++.
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~--~l~~~~~~~~~~~   42 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYE--RLKLKYSNVIYLD   42 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHH--HHHHcCCcEEEEe
Confidence            356999999999999999999998  6666676666665

>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=96.37  E-value=0.018  Score=56.06  Aligned_cols=123  Identities=14%  Similarity=0.180  Sum_probs=67.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-CCCCCCCHHHHH------HHHHHHhCCCCCccc-ccccCH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-PYSNEYDADQIL------DIVIKFLMPSSRLSE-IMDKNY  250 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~vs~~~~~~~~~------~~i~~~l~~~~~~~~-~~~~~~  250 (824)
                      -.+++|+|..|.|||||++.+..-  . ......+++.. ++.. .+..+..      -++++.++....... ....+.
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~--~-~~~~G~v~~~g~~~~~-~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~  100 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGL--L-KPSSGEILLDGKDLAS-LSPKELARKIAYVPQALELLGLAHLADRPFNELSG  100 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC--C-CCCCcEEEECCEECCc-CCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCH
Confidence            469999999999999999999983  2 33445555531 1322 2222221      124555544211000 112222


Q ss_pred             -HHHHHHHHHhcCCCeEEEEEecCCCh---hhHHHHHhhCCCC-CC-CcEEEEEechHHHH
Q 003387          251 -EMKKIILHEYLMTKRYLIVIDDVWSI---DMWDVIQEILPDN-QN-GSRVLITLTDIRII  305 (824)
Q Consensus       251 -~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~~-~~-gs~ilvTtR~~~v~  305 (824)
                       +...-.|.+.+....-+++||+.-..   ...+.+...+... .. |..||++|.+....
T Consensus       101 G~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~  161 (180)
T cd03214         101 GERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLA  161 (180)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHH
Confidence             33334566667778889999998643   2233333333221 12 56788888776544

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.37  E-value=0.019  Score=69.82  Aligned_cols=133  Identities=15%  Similarity=0.230  Sum_probs=74.4

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQI  228 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~  228 (824)
                      ..++|.+..++.+.+.+...       .....++.++|+.|+|||++|+.+..  .....-...+.++  .+...+...+
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~--~l~~~~~~~i~~d--~s~~~~~~~~  640 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAE--FLFDDEDAMVRID--MSEYMEKHSV  640 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHH--HhcCCCCcEEEEe--chhhcccchH
Confidence            46899999999999998752       12256788999999999999999987  3322222334444  4432221111


Q ss_pred             HHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCC----C-------CCcEE
Q 003387          229 LDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDN----Q-------NGSRV  295 (824)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~----~-------~gs~i  295 (824)
                          ..-++...+.  ........+...+++   ....+|+||++...  +.++.+...+..+    +       ..+-|
T Consensus       641 ----~~l~g~~~g~--~g~~~~g~l~~~v~~---~p~~vlllDeieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~ii  711 (852)
T TIGR03346       641 ----ARLIGAPPGY--VGYEEGGQLTEAVRR---KPYSVVLFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVI  711 (852)
T ss_pred             ----HHhcCCCCCc--cCcccccHHHHHHHc---CCCcEEEEeccccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEE
Confidence                1112211110  111111222233222   23348999999865  4667666665432    1       23447


Q ss_pred             EEEech
Q 003387          296 LITLTD  301 (824)
Q Consensus       296 lvTtR~  301 (824)
                      |+||..
T Consensus       712 I~TSn~  717 (852)
T TIGR03346       712 IMTSNL  717 (852)
T ss_pred             EEeCCc
Confidence            777654

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.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.37  E-value=0.026  Score=67.44  Aligned_cols=45  Identities=20%  Similarity=0.114  Sum_probs=37.9

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.+..++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r-i~Ha~Lf~Gp~G~GKTt~A~~lAr   59 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR-INHAYLFSGPRGCGKTSSARILAR   59 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999988654 234578999999999999998866

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=96.36  E-value=0.011  Score=66.43  Aligned_cols=68  Identities=21%  Similarity=0.313  Sum_probs=52.1

Q ss_pred             CCCCceechhhHHHHHHHHHcC----CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHH
Q 003387          154 KSRDTVGLDDRMEELLDLLIEG----PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQI  228 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~  228 (824)
                      -+++-+|+++-+++|++++.-+    .-+-++++.+|++|||||.+|+.|..  .....|-.   +.  |..-.|+.+|
T Consensus       409 LdeDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~--ALnRkFfR---fS--vGG~tDvAeI  480 (906)
T KOG2004|consen  409 LDEDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIAR--ALNRKFFR---FS--VGGMTDVAEI  480 (906)
T ss_pred             hcccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHH--HhCCceEE---Ee--ccccccHHhh
Confidence            3456789999999999999753    44578999999999999999999998  66666632   23  5555555553

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=96.36  E-value=0.007  Score=72.19  Aligned_cols=53  Identities=15%  Similarity=0.283  Sum_probs=42.4

Q ss_pred             CCCceechhhHHHHHHHHHc----CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          155 SRDTVGLDDRMEELLDLLIE----GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +.+.+|.+.-+++|+++|..    +.....++.++|++|+||||+|+.+..  .....|
T Consensus       321 ~~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~--~l~~~~  377 (784)
T PRK10787        321 DTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAK--ATGRKY  377 (784)
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHH--HhCCCE
Confidence            35689999999999998874    223456899999999999999999998  454444

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.33  E-value=0.0006  Score=67.69  Aligned_cols=99  Identities=21%  Similarity=0.229  Sum_probs=77.1

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhh-hhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSL-LSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i-~~~L~~L  570 (824)
                      ..+++-|.++++...+      -.++.+|+.|.||.|+-|.|+++- .+..|++|+.|.|+.|.|..+.+-. +.+|++|
T Consensus        18 l~~vkKLNcwg~~L~D------Isic~kMp~lEVLsLSvNkIssL~-pl~rCtrLkElYLRkN~I~sldEL~YLknlpsL   90 (388)
T KOG2123|consen   18 LENVKKLNCWGCGLDD------ISICEKMPLLEVLSLSVNKISSLA-PLQRCTRLKELYLRKNCIESLDELEYLKNLPSL   90 (388)
T ss_pred             HHHhhhhcccCCCccH------HHHHHhcccceeEEeeccccccch-hHHHHHHHHHHHHHhcccccHHHHHHHhcCchh
Confidence            3466777888887652      367899999999999999998774 4788999999999999998776522 3799999


Q ss_pred             cEeecCCc-cccccch-----hhhccccCceec
Q 003387          571 YTLDMPFS-YIDHTAD-----EFWKMNKLRHLN  597 (824)
Q Consensus       571 ~~L~L~~~-~l~~lp~-----~i~~L~~L~~L~  597 (824)
                      ++|.|..| .-..-+.     .+.-||||+.||
T Consensus        91 r~LWL~ENPCc~~ag~nYR~~VLR~LPnLkKLD  123 (388)
T KOG2123|consen   91 RTLWLDENPCCGEAGQNYRRKVLRVLPNLKKLD  123 (388)
T ss_pred             hhHhhccCCcccccchhHHHHHHHHcccchhcc
Confidence            99999887 3333322     266788999885

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.32  E-value=0.05  Score=56.24  Aligned_cols=132  Identities=11%  Similarity=0.012  Sum_probs=73.8

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-CCCCCCCHHHHHHHHHHHhCCC--C
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-PYSNEYDADQILDIVIKFLMPS--S  240 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~vs~~~~~~~~~~~i~~~l~~~--~  240 (824)
                      ..+.++..|... .+..-++|+|..|.|||||.+.+..  .+. .....+++.. .|...-+.    .+++.....-  .
T Consensus        97 ~~~~~l~~l~~~-~~~~~~~i~g~~g~GKttl~~~l~~--~~~-~~~G~i~~~g~~v~~~d~~----~ei~~~~~~~~q~  168 (270)
T TIGR02858        97 AADKLLPYLVRN-NRVLNTLIISPPQCGKTTLLRDLAR--ILS-TGISQLGLRGKKVGIVDER----SEIAGCVNGVPQH  168 (270)
T ss_pred             cHHHHHHHHHhC-CCeeEEEEEcCCCCCHHHHHHHHhC--ccC-CCCceEEECCEEeecchhH----HHHHHHhcccccc
Confidence            445555555533 2367899999999999999999998  333 2234444430 12211111    2333332221  0


Q ss_pred             Cc-ccccccCHHHHHHHHHHhcC-CCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          241 RL-SEIMDKNYEMKKIILHEYLM-TKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       241 ~~-~~~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      .. ...+..+......-+...+. ...=+|++|.+-..+.+..+...+.   .|..||+||-+..+..
T Consensus       169 ~~~~r~~v~~~~~k~~~~~~~i~~~~P~villDE~~~~e~~~~l~~~~~---~G~~vI~ttH~~~~~~  233 (270)
T TIGR02858       169 DVGIRTDVLDGCPKAEGMMMLIRSMSPDVIVVDEIGREEDVEALLEALH---AGVSIIATAHGRDVED  233 (270)
T ss_pred             cccccccccccchHHHHHHHHHHhCCCCEEEEeCCCcHHHHHHHHHHHh---CCCEEEEEechhHHHH
Confidence            00 00111111111222333333 4788999999988777777766553   4778999999877654

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.26  E-value=0.012  Score=65.79  Aligned_cols=123  Identities=14%  Similarity=0.228  Sum_probs=66.1

Q ss_pred             Cceechhh--HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC--ceeEEEECCCCCCCCHHHHHHHH
Q 003387          157 DTVGLDDR--MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF--DCHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       157 ~~vGr~~~--~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      -++|-...  ......+.........-+.|+|..|+|||+|++++.+  .+....  ..+++++        ..++...+
T Consensus       117 Fv~g~~n~~A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~--~l~~~~~~~~v~yv~--------~~~f~~~~  186 (450)
T PRK14087        117 FVIGSSNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKN--YIESNFSDLKVSYMS--------GDEFARKA  186 (450)
T ss_pred             ccCCCcHHHHHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHH--HHHHhCCCCeEEEEE--------HHHHHHHH
Confidence            35565443  2223333322222345688999999999999999998  443322  2344554        34566666


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh---hhH-HHHHhhCCC-CCCCcEEEEEech
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI---DMW-DVIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~-~~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                      ...+...           ......+++.++ +.-+||+||+...   ..+ +.+...+.. ...|..||+|+..
T Consensus       187 ~~~l~~~-----------~~~~~~~~~~~~-~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~  248 (450)
T PRK14087        187 VDILQKT-----------HKEIEQFKNEIC-QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDK  248 (450)
T ss_pred             HHHHHHh-----------hhHHHHHHHHhc-cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCC
Confidence            6665421           011233444444 3347889999643   222 233332221 1234578888653

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.24  E-value=0.032  Score=63.92  Aligned_cols=45  Identities=16%  Similarity=0.066  Sum_probs=36.8

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|-+..++.|.+.+..+. -...+-++|+.|+||||+|+.+.+
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~r-i~ha~Lf~GPpG~GKTtiArilAk   60 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENR-VAPAYLFSGTRGVGKTTIARIFAK   60 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            578898888888888887643 245777899999999999998887

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=96.20  E-value=0.0024  Score=63.49  Aligned_cols=87  Identities=17%  Similarity=0.190  Sum_probs=56.0

Q ss_pred             hhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCC--CCC-ccChhhhhcCCCccEeecCCccccc---cchhhh
Q 003387          515 KFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIP--SLN-SLPSSLLSNLLNLYTLDMPFSYIDH---TADEFW  588 (824)
Q Consensus       515 ~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~--~i~-~lp~~i~~~L~~L~~L~L~~~~l~~---lp~~i~  588 (824)
                      .....+..|..|++.++.++++- .+..|++|++|.++.|  .+. .++..+ .++++|++|++++|+++.   ++. +.
T Consensus        37 gl~d~~~~le~ls~~n~gltt~~-~~P~Lp~LkkL~lsdn~~~~~~~l~vl~-e~~P~l~~l~ls~Nki~~lstl~p-l~  113 (260)
T KOG2739|consen   37 GLTDEFVELELLSVINVGLTTLT-NFPKLPKLKKLELSDNYRRVSGGLEVLA-EKAPNLKVLNLSGNKIKDLSTLRP-LK  113 (260)
T ss_pred             cccccccchhhhhhhccceeecc-cCCCcchhhhhcccCCcccccccceehh-hhCCceeEEeecCCccccccccch-hh
Confidence            34445556666666666554332 2445778888888887  433 566655 667888888888886553   222 56


Q ss_pred             ccccCceecCCCccCC
Q 003387          589 KMNKLRHLNFGSITLP  604 (824)
Q Consensus       589 ~L~~L~~L~L~~~~~~  604 (824)
                      .+.+|..|++..|..+
T Consensus       114 ~l~nL~~Ldl~n~~~~  129 (260)
T KOG2739|consen  114 ELENLKSLDLFNCSVT  129 (260)
T ss_pred             hhcchhhhhcccCCcc
Confidence            6777778877777655

>cd01394 radB RadB

Probab=96.20  E-value=0.023  Score=57.23  Aligned_cols=54  Identities=20%  Similarity=0.044  Sum_probs=38.0

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD  224 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~  224 (824)
                      .+-++|..+=..-.++.|.|.+|+||||+|.++..  .....=..++|++  ....++
T Consensus         7 ~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~--~~~~~g~~v~yi~--~e~~~~   60 (218)
T cd01394           7 GLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAV--ETAGQGKKVAYID--TEGLSS   60 (218)
T ss_pred             HHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHH--HHHhcCCeEEEEE--CCCCCH
Confidence            34455544444578999999999999999999876  3333334678888  655554

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK07667 uridine kinase; Provisional

Probab=96.17  E-value=0.0061  Score=60.07  Aligned_cols=37  Identities=16%  Similarity=0.198  Sum_probs=31.5

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+.|.+.+....+...+|+|.|.+|.||||+|+.+..
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~   39 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKE   39 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4667777776666679999999999999999999987

>PRK06696 uridine kinase; Validated

Probab=96.15  E-value=0.0059  Score=61.73  Aligned_cols=42  Identities=24%  Similarity=0.208  Sum_probs=34.6

Q ss_pred             echhhHHHHHHHHHc-CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          160 GLDDRMEELLDLLIE-GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~-~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|++-+++|.+.+.. ......+|+|.|.+|+||||+|+.+.+
T Consensus         2 ~~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~   44 (223)
T PRK06696          2 SRKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAE   44 (223)
T ss_pred             cHHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            356677788888765 344689999999999999999999988

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.14  E-value=0.019  Score=60.86  Aligned_cols=106  Identities=13%  Similarity=0.105  Sum_probs=62.7

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcccc----CCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVK----HYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR  241 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~  241 (824)
                      ..+-++|..+=..-+++-|+|.+|+|||+|+..++-.....    ..=..++||+  ....|+.+++.+ ++++++....
T Consensus        83 ~~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYId--tE~~f~~eRi~~-~a~~~g~d~~  159 (313)
T TIGR02238        83 QALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYID--TEGTFRPDRIRA-IAERFGVDPD  159 (313)
T ss_pred             HHHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEE--cCCCCCHHHHHH-HHHHcCCChH
Confidence            33445565554456899999999999999998765322221    1124789999  888889888764 5666654321


Q ss_pred             c-----ccccccCHHHHH---HHHHHhcC-CCeEEEEEecCC
Q 003387          242 L-----SEIMDKNYEMKK---IILHEYLM-TKRYLIVIDDVW  274 (824)
Q Consensus       242 ~-----~~~~~~~~~~~~---~~l~~~L~-~kr~LlVlDdv~  274 (824)
                      .     .-....+.++..   ..+...+. ++--|||+|-+-
T Consensus       160 ~~l~~i~~~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSis  201 (313)
T TIGR02238       160 AVLDNILYARAYTSEHQMELLDYLAAKFSEEPFRLLIVDSIM  201 (313)
T ss_pred             HhcCcEEEecCCCHHHHHHHHHHHHHHhhccCCCEEEEEcch
Confidence            0     001112233333   33333343 344478888874

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.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.11  E-value=0.04  Score=53.51  Aligned_cols=120  Identities=8%  Similarity=-0.013  Sum_probs=60.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCccc----------cccc
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSE----------IMDK  248 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~----------~~~~  248 (824)
                      -.+++|+|..|.|||||++.+..-.   ..-...+++.  -.   ++......+-+.++--...+.          ....
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~--g~---~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~i~~~L   99 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGDL---KPQQGEITLD--GV---PVSDLEKALSSLISVLNQRPYLFDTTLRNNLGRRF   99 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccC---CCCCCEEEEC--CE---EHHHHHHHHHhhEEEEccCCeeecccHHHhhcccC
Confidence            4589999999999999999998842   1122334433  10   111111111111110000000          0111


Q ss_pred             C-HHHHHHHHHHhcCCCeEEEEEecCCChh---hHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          249 N-YEMKKIILHEYLMTKRYLIVIDDVWSID---MWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       249 ~-~~~~~~~l~~~L~~kr~LlVlDdv~~~~---~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      + -+...-.|.+.+..++=+++||+....-   ..+.+...+....+|..||++|.+.....
T Consensus       100 S~G~~qrv~laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~  161 (178)
T cd03247         100 SGGERQRLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHLTGIE  161 (178)
T ss_pred             CHHHHHHHHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCHHHHH
Confidence            1 1233345666666777889999987542   22222222221123667888888776554

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.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.11  E-value=0.051  Score=63.17  Aligned_cols=46  Identities=15%  Similarity=0.089  Sum_probs=38.0

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|-+..++.+.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        16 f~~viGq~~~~~~L~~~i~~~~-l~hayLf~Gp~G~GKtt~A~~lAk   61 (614)
T PRK14971         16 FESVVGQEALTTTLKNAIATNK-LAHAYLFCGPRGVGKTTCARIFAK   61 (614)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHH
Confidence            3588999999999999998764 235578999999999999987655

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.10  E-value=0.012  Score=69.69  Aligned_cols=115  Identities=10%  Similarity=0.179  Sum_probs=65.6

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQI  228 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~  228 (824)
                      ..++|-++.++.|.+.+...       ......+-++|+.|+|||++|+.+..  ....   ..+.++  .+...+..  
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~--~l~~---~~i~id--~se~~~~~--  528 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSK--ALGI---ELLRFD--MSEYMERH--  528 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHH--HhCC---CcEEee--chhhcccc--
Confidence            35899999999999988731       22356789999999999999999977  3322   233444  44322111  


Q ss_pred             HHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCC-CeEEEEEecCCCh--hhHHHHHhhCC
Q 003387          229 LDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT-KRYLIVIDDVWSI--DMWDVIQEILP  287 (824)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~~--~~~~~l~~~~~  287 (824)
                        .+.+-++...+   ....+   ....+.+.++. ..-+|+||++...  +.++.+...+.
T Consensus       529 --~~~~LiG~~~g---yvg~~---~~g~L~~~v~~~p~sVlllDEieka~~~v~~~LLq~ld  582 (758)
T PRK11034        529 --TVSRLIGAPPG---YVGFD---QGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMD  582 (758)
T ss_pred             --cHHHHcCCCCC---ccccc---ccchHHHHHHhCCCcEEEeccHhhhhHHHHHHHHHHHh
Confidence              11112222111   00001   01123333333 4469999999875  45666665554

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.10  E-value=0.059  Score=60.96  Aligned_cols=45  Identities=16%  Similarity=0.001  Sum_probs=37.3

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|-+..++.+...+..+. -..+.-++|..|+||||+|+.+.+
T Consensus        14 deiiGqe~v~~~L~~~I~~gr-l~hayLf~Gp~G~GKTt~Ar~LAk   58 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNR-LAHAYLFSGLRGSGKTSSARIFAR   58 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHH
Confidence            579999999999999987664 345668999999999999997665

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=96.09  E-value=0.0063  Score=58.01  Aligned_cols=11  Identities=27%  Similarity=0.365  Sum_probs=4.1

Q ss_pred             CceEEEEEccc
Q 003387          692 SLTHLSFSNTD  702 (824)
Q Consensus       692 ~L~~L~L~~~~  702 (824)
                      .|.+|.|.+|.
T Consensus        65 rL~tLll~nNr   75 (233)
T KOG1644|consen   65 RLHTLLLNNNR   75 (233)
T ss_pred             ccceEEecCCc
Confidence            33333333333

>TIGR02012 tigrfam_recA protein RecA

Probab=96.08  E-value=0.017  Score=60.99  Aligned_cols=100  Identities=20%  Similarity=0.059  Sum_probs=62.9

Q ss_pred             HHHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC-cc
Q 003387          166 EELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR-LS  243 (824)
Q Consensus       166 ~~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~-~~  243 (824)
                      ..|-.+|. .+=..-+++-|+|.+|+||||||.++..  .....-..++||+  ..+.++..     .+++++...+ ..
T Consensus        41 ~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~--~~~~~g~~v~yId--~E~~~~~~-----~a~~lGvd~~~l~  111 (321)
T TIGR02012        41 LSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIA--EAQKAGGTAAFID--AEHALDPV-----YARKLGVDIDNLL  111 (321)
T ss_pred             HHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHH--HHHHcCCcEEEEc--ccchhHHH-----HHHHcCCCHHHeE
Confidence            33445554 4444568999999999999999988776  3334445678998  66666653     3455544211 00


Q ss_pred             cccccCHHHHHHHHHHhcC-CCeEEEEEecCC
Q 003387          244 EIMDKNYEMKKIILHEYLM-TKRYLIVIDDVW  274 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~  274 (824)
                      ..+..+.++....+...++ +.--+||+|-|-
T Consensus       112 v~~p~~~eq~l~~~~~li~~~~~~lIVIDSv~  143 (321)
T TIGR02012       112 VSQPDTGEQALEIAETLVRSGAVDIIVVDSVA  143 (321)
T ss_pred             EecCCCHHHHHHHHHHHhhccCCcEEEEcchh
Confidence            0223345566666666554 456689999985

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.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.08  E-value=0.048  Score=63.16  Aligned_cols=46  Identities=17%  Similarity=0.127  Sum_probs=38.2

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+.-++.|.+.+..+. -...+-++|..|+||||+|+.+.+
T Consensus        15 f~~iiGq~~v~~~L~~~i~~~~-~~hayLf~Gp~G~GKtt~A~~lak   60 (576)
T PRK14965         15 FSDLTGQEHVSRTLQNAIDTGR-VAHAFLFTGARGVGKTSTARILAK   60 (576)
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999987754 235567899999999999988876

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.06  E-value=0.011  Score=65.76  Aligned_cols=99  Identities=9%  Similarity=0.138  Sum_probs=54.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      ..-+.|+|..|+|||+|++++.+  ++...-..+++++        ..++...+...+...             ....++
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~--~l~~~~~~v~yi~--------~~~f~~~~~~~l~~~-------------~~~~f~  197 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVH--ALRESGGKILYVR--------SELFTEHLVSAIRSG-------------EMQRFR  197 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHH--HHHHcCCCEEEee--------HHHHHHHHHHHHhcc-------------hHHHHH
Confidence            45688999999999999999999  4443333345554        234444555554321             012334


Q ss_pred             HhcCCCeEEEEEecCCChhh----HHHHHhhCCC-CCCCcEEEEEech
Q 003387          259 EYLMTKRYLIVIDDVWSIDM----WDVIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       259 ~~L~~kr~LlVlDdv~~~~~----~~~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                      +.++. .-+|++||+.....    .+.+...+.. ...|..||+||..
T Consensus       198 ~~~~~-~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~  244 (445)
T PRK12422        198 QFYRN-VDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTC  244 (445)
T ss_pred             HHccc-CCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCC
Confidence            44433 34788899865321    1222222211 1135578888754

>CHL00176 ftsH cell division protein; Validated

Probab=96.06  E-value=0.013  Score=68.15  Aligned_cols=48  Identities=21%  Similarity=0.252  Sum_probs=35.3

Q ss_pred             CCCCceechhhHHHHHHHH---HcCC-------CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLL---IEGP-------PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L---~~~~-------~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.++.|.++.++++.+.+   ....       ...+-|.++|++|.|||++|+++.+
T Consensus       181 ~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~  238 (638)
T CHL00176        181 TFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAG  238 (638)
T ss_pred             CHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            3467889887776665554   3221       1245688999999999999999988

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.04  E-value=0.029  Score=59.96  Aligned_cols=68  Identities=16%  Similarity=0.125  Sum_probs=47.5

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcccc----CCCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVK----HYFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      |-++|..+=..-.++=|+|.+|+|||+|+..++-.....    ..-..++||+  ....|+..++.+ +++.++.
T Consensus       115 LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyId--TE~tF~peRl~~-ia~~~g~  186 (344)
T PLN03187        115 LDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYID--TEGTFRPDRIVP-IAERFGM  186 (344)
T ss_pred             HHhhcCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEE--cCCCCCHHHHHH-HHHHcCC
Confidence            444555554456888999999999999998775322221    1224789999  888899888755 5666654

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.02  E-value=0.018  Score=55.01  Aligned_cols=115  Identities=10%  Similarity=0.018  Sum_probs=62.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-CCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-PYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  257 (824)
                      -.+++|+|..|.|||||.+.+..-  . ......+++.. ++.. .+..+..   .+.++.-     .+-..-+...-.+
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~--~-~~~~G~v~~~g~~~~~-~~~~~~~---~~~i~~~-----~qLS~G~~qrl~l   93 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGL--Y-KPDSGEILVDGKEVSF-ASPRDAR---RAGIAMV-----YQLSVGERQMVEI   93 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC--C-CCCCeEEEECCEECCc-CCHHHHH---hcCeEEE-----EecCHHHHHHHHH
Confidence            458999999999999999999983  2 33455666641 1221 1111111   1111110     0111123334456


Q ss_pred             HHhcCCCeEEEEEecCCCh---hhHHHHHhhCCC-CCCCcEEEEEechHHHH
Q 003387          258 HEYLMTKRYLIVIDDVWSI---DMWDVIQEILPD-NQNGSRVLITLTDIRII  305 (824)
Q Consensus       258 ~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~-~~~gs~ilvTtR~~~v~  305 (824)
                      .+.+-.+.-++++|+.-..   ...+.+...+.. ...|..||++|.+...+
T Consensus        94 aral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~  145 (163)
T cd03216          94 ARALARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDEV  145 (163)
T ss_pred             HHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHH
Confidence            6666677788899998654   223333333321 12366788888876543

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.01  E-value=0.044  Score=61.43  Aligned_cols=46  Identities=17%  Similarity=0.059  Sum_probs=38.0

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+..++.+.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk   61 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAK   61 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHH
Confidence            3588999999999999987654 235677899999999999988765

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.00  E-value=0.021  Score=65.01  Aligned_cols=120  Identities=9%  Similarity=0.187  Sum_probs=63.4

Q ss_pred             ceechhh--HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC--ceeEEEECCCCCCCCHHHHHHHHH
Q 003387          158 TVGLDDR--MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF--DCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       158 ~vGr~~~--~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      ++|-...  ......+..........+.|+|..|+|||.|++++.+  .....+  ..+++++        ..++..++.
T Consensus       291 vvG~sN~~A~aaa~avae~~~~~~NpL~LyG~sGsGKTHLL~AIa~--~a~~~~~g~~V~Yit--------aeef~~el~  360 (617)
T PRK14086        291 VIGASNRFAHAAAVAVAEAPAKAYNPLFIYGESGLGKTHLLHAIGH--YARRLYPGTRVRYVS--------SEEFTNEFI  360 (617)
T ss_pred             cCCCccHHHHHHHHHHHhCccccCCcEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEee--------HHHHHHHHH
Confidence            4465443  2233333333222234589999999999999999999  554433  2344554        344444554


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh---hhHH-HHHhhCCC-CCCCcEEEEEech
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI---DMWD-VIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~-~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                      ..+...         .    ...+++.++. -=+|||||+...   ..|+ .+...+.. ...|..|||||+.
T Consensus       361 ~al~~~---------~----~~~f~~~y~~-~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~  419 (617)
T PRK14086        361 NSIRDG---------K----GDSFRRRYRE-MDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDR  419 (617)
T ss_pred             HHHHhc---------c----HHHHHHHhhc-CCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCC
Confidence            443221         1    1223333332 247889999754   2232 22222221 1235568888875

>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=96.00  E-value=0.092  Score=49.99  Aligned_cols=120  Identities=18%  Similarity=0.190  Sum_probs=68.7

Q ss_pred             echhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC----Ccccc--------------CCCceeEEEECCCCC
Q 003387          160 GLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN----SSYVK--------------HYFDCHAWITEPYSN  221 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~----~~~~~--------------~~F~~~~wv~~~vs~  221 (824)
                      |-++..+.+.+.+..+. -...+-++|..|+||+|+|..+.+    .....              .......|+.  -..
T Consensus         1 gq~~~~~~L~~~~~~~~-l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~--~~~   77 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGR-LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIK--PDK   77 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC---SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEE--TTT
T ss_pred             CcHHHHHHHHHHHHcCC-cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEe--ccc
Confidence            44556666666665553 345678999999999999977654    21110              1222334444  221


Q ss_pred             ---CCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEE
Q 003387          222 ---EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVL  296 (824)
Q Consensus       222 ---~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~il  296 (824)
                         ...++++- ++...+.....                    .+++=.+|+||+...  +.++.+...+..-..++++|
T Consensus        78 ~~~~i~i~~ir-~i~~~~~~~~~--------------------~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fi  136 (162)
T PF13177_consen   78 KKKSIKIDQIR-EIIEFLSLSPS--------------------EGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFI  136 (162)
T ss_dssp             SSSSBSHHHHH-HHHHHCTSS-T--------------------TSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEE
T ss_pred             ccchhhHHHHH-HHHHHHHHHHh--------------------cCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEE
Confidence               23333322 33333322111                    135668899999864  56777777776666789999


Q ss_pred             EEechHH
Q 003387          297 ITLTDIR  303 (824)
Q Consensus       297 vTtR~~~  303 (824)
                      ++|++.+
T Consensus       137 L~t~~~~  143 (162)
T PF13177_consen  137 LITNNPS  143 (162)
T ss_dssp             EEES-GG
T ss_pred             EEECChH
Confidence            9988764

...

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=95.99  E-value=0.062  Score=57.85  Aligned_cols=121  Identities=14%  Similarity=0.123  Sum_probs=75.5

Q ss_pred             CceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC---------------------CCceeEEE
Q 003387          157 DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH---------------------YFDCHAWI  215 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~---------------------~F~~~~wv  215 (824)
                      .++|-+....++..+..........+-++|+.|+||||+|..+.+.  +..                     ....+..+
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel   79 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKE--LLCENPTGLLPCGHCRSCKLIPAGNHPDFLEL   79 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHH--HhCCCcccCCcccchhhhhHHhhcCCCceEEe
Confidence            4677788888888888754433445899999999999999888773  211                     11234444


Q ss_pred             ECCCCCCCC---HHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChh--hHHHHHhhCCCCC
Q 003387          216 TEPYSNEYD---ADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSID--MWDVIQEILPDNQ  290 (824)
Q Consensus       216 ~~~vs~~~~---~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~--~~~~l~~~~~~~~  290 (824)
                      .  .|....   ..+..+++.+.......                    .++.-++++|+++...  .-+.+...+....
T Consensus        80 ~--~s~~~~~~i~~~~vr~~~~~~~~~~~--------------------~~~~kviiidead~mt~~A~nallk~lEep~  137 (325)
T COG0470          80 N--PSDLRKIDIIVEQVRELAEFLSESPL--------------------EGGYKVVIIDEADKLTEDAANALLKTLEEPP  137 (325)
T ss_pred             c--ccccCCCcchHHHHHHHHHHhccCCC--------------------CCCceEEEeCcHHHHhHHHHHHHHHHhccCC
Confidence            4  343333   23444444444433210                    3567789999998753  4555555555555


Q ss_pred             CCcEEEEEech
Q 003387          291 NGSRVLITLTD  301 (824)
Q Consensus       291 ~gs~ilvTtR~  301 (824)
                      ..+++|++|..
T Consensus       138 ~~~~~il~~n~  148 (325)
T COG0470         138 KNTRFILITND  148 (325)
T ss_pred             CCeEEEEEcCC
Confidence            67778877763

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.95  E-value=0.019  Score=60.68  Aligned_cols=99  Identities=22%  Similarity=0.082  Sum_probs=62.3

Q ss_pred             HHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC-ccc
Q 003387          167 ELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR-LSE  244 (824)
Q Consensus       167 ~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~-~~~  244 (824)
                      .|-.+|. .+=+.-+++-|+|++|+||||||.+++-  .....-..++||+  ..+.++..     .+++++...+ ..-
T Consensus        42 ~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~--~~~~~g~~~vyId--~E~~~~~~-----~a~~lGvd~~~l~v  112 (325)
T cd00983          42 SLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIA--EAQKLGGTVAFID--AEHALDPV-----YAKKLGVDLDNLLI  112 (325)
T ss_pred             HHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHH--HHHHcCCCEEEEC--ccccHHHH-----HHHHcCCCHHHhee
Confidence            3445554 4434567899999999999999998776  3334445788998  77766653     3444443211 000


Q ss_pred             ccccCHHHHHHHHHHhcCC-CeEEEEEecCC
Q 003387          245 IMDKNYEMKKIILHEYLMT-KRYLIVIDDVW  274 (824)
Q Consensus       245 ~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~  274 (824)
                      .+..+.++....+...++. .--+||+|-|-
T Consensus       113 ~~p~~~eq~l~i~~~li~s~~~~lIVIDSva  143 (325)
T cd00983         113 SQPDTGEQALEIADSLVRSGAVDLIVVDSVA  143 (325)
T ss_pred             cCCCCHHHHHHHHHHHHhccCCCEEEEcchH
Confidence            2233456666666665543 56689999975

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK09354 recA recombinase A; Provisional

Probab=95.95  E-value=0.023  Score=60.45  Aligned_cols=100  Identities=23%  Similarity=0.066  Sum_probs=64.5

Q ss_pred             HHHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC-cc
Q 003387          166 EELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR-LS  243 (824)
Q Consensus       166 ~~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~-~~  243 (824)
                      ..|-.+|. .+=..-+++-|+|+.|+||||||.++..  .....=..++||+  .-..++..     .+++++...+ ..
T Consensus        46 ~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~--~~~~~G~~~~yId--~E~s~~~~-----~a~~lGvdld~ll  116 (349)
T PRK09354         46 LALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIA--EAQKAGGTAAFID--AEHALDPV-----YAKKLGVDIDNLL  116 (349)
T ss_pred             HHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHH--HHHHcCCcEEEEC--CccchHHH-----HHHHcCCCHHHeE
Confidence            34555565 4444568999999999999999998876  3334446788999  77777753     4555544211 00


Q ss_pred             cccccCHHHHHHHHHHhcC-CCeEEEEEecCC
Q 003387          244 EIMDKNYEMKKIILHEYLM-TKRYLIVIDDVW  274 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~  274 (824)
                      ..+..+.++....+...++ ++--+||+|-|-
T Consensus       117 i~qp~~~Eq~l~i~~~li~s~~~~lIVIDSva  148 (349)
T PRK09354        117 VSQPDTGEQALEIADTLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             EecCCCHHHHHHHHHHHhhcCCCCEEEEeChh
Confidence            0223345566666666654 356699999985

>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=95.94  E-value=0.017  Score=56.66  Aligned_cols=128  Identities=17%  Similarity=0.149  Sum_probs=64.1

Q ss_pred             echhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCH----HH-------H
Q 003387          160 GLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDA----DQ-------I  228 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~----~~-------~  228 (824)
                      .+..+....++.|..    ..++.+.|++|.|||.||.+..-+.-..+.|+..+++.-.|.-.-++    .+       .
T Consensus         4 p~~~~Q~~~~~al~~----~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~   79 (205)
T PF02562_consen    4 PKNEEQKFALDALLN----NDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPY   79 (205)
T ss_dssp             --SHHHHHHHHHHHH-----SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TT
T ss_pred             CCCHHHHHHHHHHHh----CCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHH
Confidence            456677778888873    56999999999999999988766533457888888875222211111    01       1


Q ss_pred             HHHHHHHhCCCCCcccccccCHHHHHH------HHHHhcCCC---eEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEE
Q 003387          229 LDIVIKFLMPSSRLSEIMDKNYEMKKI------ILHEYLMTK---RYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLI  297 (824)
Q Consensus       229 ~~~i~~~l~~~~~~~~~~~~~~~~~~~------~l~~~L~~k---r~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilv  297 (824)
                      +.-+...+..-     ......+.+.+      .--.+++|+   ..+||+|++.+.  .++..+..   -.+.||||++
T Consensus        80 ~~p~~d~l~~~-----~~~~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilT---R~g~~skii~  151 (205)
T PF02562_consen   80 LRPIYDALEEL-----FGKEKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILT---RIGEGSKIII  151 (205)
T ss_dssp             THHHHHHHTTT-----S-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHT---TB-TT-EEEE
T ss_pred             HHHHHHHHHHH-----hChHhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHHc---ccCCCcEEEE
Confidence            11122222110     01111111111      012355664   469999999765  46666654   3467999997


Q ss_pred             Ee
Q 003387          298 TL  299 (824)
Q Consensus       298 Tt  299 (824)
                      +=
T Consensus       152 ~G  153 (205)
T PF02562_consen  152 TG  153 (205)
T ss_dssp             EE
T ss_pred             ec
Confidence            74

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=95.94  E-value=0.0068  Score=67.68  Aligned_cols=46  Identities=13%  Similarity=0.320  Sum_probs=39.9

Q ss_pred             CCceechhhHHHHHHHHHc----CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIE----GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.++.+++|++.|..    -...-+++.++|++|+||||||+.+.+
T Consensus        76 ~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~  125 (644)
T PRK15455         76 EEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKS  125 (644)
T ss_pred             hcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHH
Confidence            3689999999999999943    234568999999999999999999988

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.93  E-value=0.02  Score=60.81  Aligned_cols=71  Identities=14%  Similarity=0.058  Sum_probs=48.0

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC----CCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH----YFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      .+.+-++|..+=..-.++.|+|.+|+|||||+..++.......    .-..++|++  ....|+..++ .++++.++.
T Consensus        82 ~~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyId--tE~~f~~~Rl-~~ia~~~~~  156 (316)
T TIGR02239        82 SKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYID--TEGTFRPERL-LAIAERYGL  156 (316)
T ss_pred             CHHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEE--CCCCCCHHHH-HHHHHHcCC
Confidence            3445566666645678999999999999999988865322211    123679999  7777777764 445555543

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).

>PRK08233 hypothetical protein; Provisional

Probab=95.93  E-value=0.023  Score=55.34  Aligned_cols=23  Identities=17%  Similarity=0.208  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|.+|+||||+|+.+..
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~   25 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTH   25 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            57999999999999999999987

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=95.89  E-value=0.016  Score=56.76  Aligned_cols=80  Identities=15%  Similarity=0.008  Sum_probs=44.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHH
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKII  256 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  256 (824)
                      ..+.+|||-|.+|.||||+|+.+++  .++..+  ++-++  -..-+. ..=.....+.....-+.  ....+.+-+...
T Consensus         6 ~~~iiIgIaG~SgSGKTTva~~l~~--~~~~~~--~~~I~--~D~YYk-~~~~~~~~~~~~~n~d~--p~A~D~dLl~~~   76 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSE--QLGVEK--VVVIS--LDDYYK-DQSHLPFEERNKINYDH--PEAFDLDLLIEH   76 (218)
T ss_pred             CceEEEEEeCCCCCCHHHHHHHHHH--HhCcCc--ceEee--cccccc-chhhcCHhhcCCcCccC--hhhhcHHHHHHH
Confidence            3578999999999999999999999  555442  11222  011111 00011111111111111  244566777777


Q ss_pred             HHHhcCCCe
Q 003387          257 LHEYLMTKR  265 (824)
Q Consensus       257 l~~~L~~kr  265 (824)
                      |...++++.
T Consensus        77 L~~L~~g~~   85 (218)
T COG0572          77 LKDLKQGKP   85 (218)
T ss_pred             HHHHHcCCc
Confidence            777777776

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.88  E-value=0.12  Score=57.26  Aligned_cols=38  Identities=24%  Similarity=0.080  Sum_probs=26.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      -+++.++|++|+||||++..+.........-..+..|+
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~  258 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALIT  258 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEE
Confidence            46999999999999999888766211012234566676

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.88  E-value=0.1  Score=56.15  Aligned_cols=24  Identities=17%  Similarity=0.297  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.++|+++|.+|+||||++..+..
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~  263 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAW  263 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHH
Confidence            458999999999999999999976

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=95.87  E-value=0.04  Score=58.95  Aligned_cols=71  Identities=13%  Similarity=0.087  Sum_probs=49.5

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC----CCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH----YFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      ...+-++|..+=..-.++-|+|.+|+|||+||..++-......    .=..++||+  ....|+.+++. +|++.++.
T Consensus       109 ~~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyId--tE~~f~~eRl~-qia~~~~~  183 (342)
T PLN03186        109 SRELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYID--TEGTFRPQRLI-QIAERFGL  183 (342)
T ss_pred             CHHHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEE--CCCCccHHHHH-HHHHHcCC
Confidence            3445556666545578999999999999999987764322211    113689999  88888888764 55666654

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=95.87  E-value=0.014  Score=66.54  Aligned_cols=50  Identities=24%  Similarity=0.350  Sum_probs=36.1

Q ss_pred             CCCCCceechhhHHHHHHHHH---c-------CCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLI---E-------GPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~---~-------~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +.-++++|.+..++++.+++.   .       +....+-+-++|++|.|||++|+.+.+.
T Consensus        52 ~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~  111 (495)
T TIGR01241        52 VTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE  111 (495)
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            344678898887776665443   2       1122445789999999999999999983

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.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=95.84  E-value=0.011  Score=60.91  Aligned_cols=105  Identities=20%  Similarity=0.149  Sum_probs=59.8

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC----CCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC-
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH----YFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR-  241 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~-  241 (824)
                      .|-++|..+=..-.|.=|+|.+|+|||.||-.++-+..+..    .=..++|++  -...|...++. +|++....... 
T Consensus        26 ~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyid--Te~~f~~~Rl~-~i~~~~~~~~~~  102 (256)
T PF08423_consen   26 SLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYID--TEGTFSPERLQ-QIAERFGLDPEE  102 (256)
T ss_dssp             HHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEE--SSSSS-HHHHH-HHHHHTTS-HHH
T ss_pred             HHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEe--CCCCCCHHHHH-HHhhccccccch
Confidence            34455544423457999999999999999977654323322    124689999  88889988875 46665543210 


Q ss_pred             ----cccccccCHHHHHH---HHHHhc-CCCeEEEEEecCC
Q 003387          242 ----LSEIMDKNYEMKKI---ILHEYL-MTKRYLIVIDDVW  274 (824)
Q Consensus       242 ----~~~~~~~~~~~~~~---~l~~~L-~~kr~LlVlDdv~  274 (824)
                          ..-....+.+++..   .+...+ ..+=-|||+|.+-
T Consensus       103 ~l~~I~v~~~~~~~~l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  103 ILDNIFVIRVFDLEELLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHTEEEEE-SSHHHHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             hhhceeeeecCCHHHHHHHHHHHHhhccccceEEEEecchH
Confidence                00011123333333   333333 2344588888884

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 ....

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.84  E-value=0.033  Score=61.24  Aligned_cols=93  Identities=13%  Similarity=0.172  Sum_probs=52.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC-------CCCcccccccCHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP-------SSRLSEIMDKNYE  251 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~-------~~~~~~~~~~~~~  251 (824)
                      -..++|+|..|+|||||++.+....   .....+++..  --+.-++.++....+.....       ..+.+.....-..
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~---~pd~gvv~li--Gergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~  239 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARAD---AFDTVVIALV--GERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAP  239 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC---CCCeeeeeec--ccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHH
Confidence            4589999999999999999998732   2233455553  22333555554444443311       1111111111122


Q ss_pred             HHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          252 MKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       252 ~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      ..+..+.+++  +++.+|+++||+-..
T Consensus       240 ~~a~~iAEyfrd~G~~Vll~~DslTr~  266 (450)
T PRK06002        240 LTATAIAEYFRDRGENVLLIVDSVTRF  266 (450)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchHHH
Confidence            2233444444  579999999999654

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=95.84  E-value=0.058  Score=62.85  Aligned_cols=46  Identities=22%  Similarity=0.174  Sum_probs=37.9

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|-+..++.+.+.+..+. -...+-++|+.|+||||+|+.+.+
T Consensus        17 f~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriLAk   62 (725)
T PRK07133         17 FDDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIFAN   62 (725)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHH
Confidence            3578999999999999987654 245567899999999999988866

>PRK06762 hypothetical protein; Provisional

Probab=95.83  E-value=0.031  Score=53.55  Aligned_cols=23  Identities=22%  Similarity=0.265  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|+.|+||||+|+.+.+
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~   24 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQE   24 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999987

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=95.83  E-value=0.043  Score=56.57  Aligned_cols=101  Identities=19%  Similarity=0.094  Sum_probs=63.5

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC---CCCccc
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP---SSRLSE  244 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~---~~~~~~  244 (824)
                      +-+.|..+=..-+++=|+|+.|.||||+|-+++-  ..+..-..++|++  .-+.+++..+.+--...+..   ..+   
T Consensus        49 LD~~LGGGl~~g~ItEiyG~~gsGKT~lal~~~~--~aq~~g~~a~fID--tE~~l~p~r~~~l~~~~~d~l~v~~~---  121 (279)
T COG0468          49 LDEALGGGLPRGRITEIYGPESSGKTTLALQLVA--NAQKPGGKAAFID--TEHALDPERAKQLGVDLLDNLLVSQP---  121 (279)
T ss_pred             HHHHhcCCcccceEEEEecCCCcchhhHHHHHHH--HhhcCCCeEEEEe--CCCCCCHHHHHHHHHhhhcceeEecC---
Confidence            3444445445678999999999999999988877  3444555899999  88888888754432221221   111   


Q ss_pred             ccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          245 IMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       245 ~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      .......+.++.+.+....+=-|+|+|-|-.
T Consensus       122 ~~~e~q~~i~~~~~~~~~~~i~LvVVDSvaa  152 (279)
T COG0468         122 DTGEQQLEIAEKLARSGAEKIDLLVVDSVAA  152 (279)
T ss_pred             CCHHHHHHHHHHHHHhccCCCCEEEEecCcc
Confidence            1112223334444444444467999999854

>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=95.82  E-value=0.046  Score=52.71  Aligned_cols=116  Identities=13%  Similarity=0.174  Sum_probs=62.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC---ccccC---CCc--eeEEEECCCCCCCCHHHHHHHHHHHhCCCCC-ccc-cccc
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS---SYVKH---YFD--CHAWITEPYSNEYDADQILDIVIKFLMPSSR-LSE-IMDK  248 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~---~~~~~---~F~--~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~-~~~-~~~~  248 (824)
                      -.+++|+|..|.|||||.+.+..+   ..+..   .|.  ...|+.    +        .+.++.++.... ... ....
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~~----q--------~~~l~~~~L~~~~~~~~~~~L   88 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFID----Q--------LQFLIDVGLGYLTLGQKLSTL   88 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEEh----H--------HHHHHHcCCCccccCCCcCcC
Confidence            468999999999999999998642   11111   111  122322    2        345566654321 000 1122


Q ss_pred             CH-HHHHHHHHHhcCCC--eEEEEEecCCCh---hhHHHHHhhCCC-CCCCcEEEEEechHHHHh
Q 003387          249 NY-EMKKIILHEYLMTK--RYLIVIDDVWSI---DMWDVIQEILPD-NQNGSRVLITLTDIRIII  306 (824)
Q Consensus       249 ~~-~~~~~~l~~~L~~k--r~LlVlDdv~~~---~~~~~l~~~~~~-~~~gs~ilvTtR~~~v~~  306 (824)
                      +. +...-.+.+.+..+  .=+++||+.-..   ...+.+...+.. ...|..||++|.+.+...
T Consensus        89 SgGq~qrl~laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~~  153 (176)
T cd03238          89 SGGELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLS  153 (176)
T ss_pred             CHHHHHHHHHHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHH
Confidence            22 22334455556556  678888998653   223333333222 124667888888876654

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.81  E-value=0.019  Score=56.84  Aligned_cols=112  Identities=13%  Similarity=0.130  Sum_probs=63.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  259 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  259 (824)
                      .+|.|+|..|.||||++..+.+  .+......++++-+ -...+.... ...++.+-.       . ..+.......++.
T Consensus         2 GlilI~GptGSGKTTll~~ll~--~~~~~~~~~i~t~e-~~~E~~~~~-~~~~i~q~~-------v-g~~~~~~~~~i~~   69 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMID--YINKNKTHHILTIE-DPIEFVHES-KRSLINQRE-------V-GLDTLSFENALKA   69 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH--HhhhcCCcEEEEEc-CCccccccC-ccceeeecc-------c-CCCccCHHHHHHH
Confidence            4789999999999999998877  44444445555431 110111000 000111100       0 1112334566777


Q ss_pred             hcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          260 YLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       260 ~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      .|+...=.|++|++.+.+.+..+....   ..|..++.|+-..++..
T Consensus        70 aLr~~pd~ii~gEird~e~~~~~l~~a---~~G~~v~~t~Ha~~~~~  113 (198)
T cd01131          70 ALRQDPDVILVGEMRDLETIRLALTAA---ETGHLVMSTLHTNSAAK  113 (198)
T ss_pred             HhcCCcCEEEEcCCCCHHHHHHHHHHH---HcCCEEEEEecCCcHHH
Confidence            777667799999998876655544332   23556777776665554

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=95.81  E-value=0.067  Score=55.48  Aligned_cols=56  Identities=18%  Similarity=0.125  Sum_probs=34.9

Q ss_pred             hhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHH
Q 003387          163 DRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQIL  229 (824)
Q Consensus       163 ~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~  229 (824)
                      .-++++..++..+    .-|-+.|.+|+|||++|+.+.+  ....   ..++++  .+...+..+++
T Consensus         9 ~l~~~~l~~l~~g----~~vLL~G~~GtGKT~lA~~la~--~lg~---~~~~i~--~~~~~~~~dll   64 (262)
T TIGR02640         9 RVTSRALRYLKSG----YPVHLRGPAGTGKTTLAMHVAR--KRDR---PVMLIN--GDAELTTSDLV   64 (262)
T ss_pred             HHHHHHHHHHhcC----CeEEEEcCCCCCHHHHHHHHHH--HhCC---CEEEEe--CCccCCHHHHh
Confidence            3344555555443    2456899999999999999987  3332   234555  55555555443

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).

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=95.81  E-value=0.029  Score=60.01  Aligned_cols=69  Identities=17%  Similarity=0.170  Sum_probs=46.8

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC----ceeEEEECCCCCCCCHHHHHHHHHHHhC
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF----DCHAWITEPYSNEYDADQILDIVIKFLM  237 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F----~~~~wv~~~vs~~~~~~~~~~~i~~~l~  237 (824)
                      ..+-++|..+=..-.++-|+|.+|+|||++|.++.-.......+    ..++||+  ....|+..++.+ +++.++
T Consensus        89 ~~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~--te~~f~~~rl~~-~~~~~g  161 (317)
T PRK04301         89 KELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYID--TEGTFRPERIEQ-MAEALG  161 (317)
T ss_pred             HHHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEe--CCCCcCHHHHHH-HHHHcC
Confidence            33445555554457899999999999999998886532221111    4789999  888888877654 445544

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.79  E-value=0.17  Score=56.71  Aligned_cols=23  Identities=22%  Similarity=0.251  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|.+|+||||++.++..
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa  372 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQ  372 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999988876

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=95.76  E-value=0.042  Score=54.23  Aligned_cols=82  Identities=12%  Similarity=0.062  Sum_probs=44.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCC-Cc---eeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHH
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHY-FD---CHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKII  256 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~---~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  256 (824)
                      ||||.|.+|+||||+|+.+..  ..... +.   ....+.  ....++....... -...............+.+.+...
T Consensus         1 IIgI~G~sgSGKTTla~~L~~--~L~~~~~~~~~~~~~~~--~d~~~~~~~~~~~-~~~~~~~~~~~~p~a~d~~~l~~~   75 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQ--ILNKRGIPAMEMDIILS--LDDFYDDYHLRDR-KGRGENRYNFDHPDAFDFDLLKED   75 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH--HHTTCTTTCCCSEEEEE--GGGGBHHHHHHHH-HHHCTTTSSTTSGGGBSHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH--HhCccCcCccceeEEEe--ecccccccchhhH-hhccccccCCCCccccCHHHHHHH
Confidence            799999999999999999987  44322 22   233333  2222222222222 111111111001245567777777


Q ss_pred             HHHhcCCCeEE
Q 003387          257 LHEYLMTKRYL  267 (824)
Q Consensus       257 l~~~L~~kr~L  267 (824)
                      |....+++.+-
T Consensus        76 l~~L~~g~~i~   86 (194)
T PF00485_consen   76 LKALKNGGSIE   86 (194)
T ss_dssp             HHHHHTTSCEE
T ss_pred             HHHHhCCCccc
Confidence            77766666543

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 ....

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=95.73  E-value=0.031  Score=65.04  Aligned_cols=117  Identities=20%  Similarity=0.304  Sum_probs=72.0

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC---ceeEEEECCCCCCCCH
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF---DCHAWITEPYSNEYDA  225 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~~~vs~~~~~  225 (824)
                      ..++|-+..++.+.+.+...       ...+.++-.+|+.|||||.||+++..     ..|   +.-+-++  .|+. ..
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~-----~Lfg~e~aliR~D--MSEy-~E  562 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAE-----ALFGDEQALIRID--MSEY-ME  562 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHH-----HhcCCCccceeec--hHHH-HH
Confidence            46899999999999988642       23567888899999999999998877     234   2333333  3322 11


Q ss_pred             HHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeE-EEEEecCCCh--hhHHHHHhhCCCC
Q 003387          226 DQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRY-LIVIDDVWSI--DMWDVIQEILPDN  289 (824)
Q Consensus       226 ~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-LlVlDdv~~~--~~~~~l~~~~~~~  289 (824)
                      +.   .+.+-++...+.  ..-   ++ ...|-+.++.+.| +|.||+|...  +..+-+..-+.++
T Consensus       563 kH---sVSrLIGaPPGY--VGy---ee-GG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdG  620 (786)
T COG0542         563 KH---SVSRLIGAPPGY--VGY---EE-GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDG  620 (786)
T ss_pred             HH---HHHHHhCCCCCC--cee---cc-ccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCC
Confidence            11   222333332211  111   11 2344555667877 7888999865  5667777666643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.73  E-value=0.023  Score=68.30  Aligned_cols=49  Identities=20%  Similarity=0.171  Sum_probs=38.5

Q ss_pred             CCCCCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.-+++.|.+..+++|.+++...           -...+-|.++|.+|.||||||+.+.+
T Consensus       175 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~  234 (733)
T TIGR01243       175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVAN  234 (733)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHH
Confidence            34456889999999998877431           12346688999999999999999998

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.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=95.73  E-value=0.12  Score=59.51  Aligned_cols=46  Identities=20%  Similarity=0.137  Sum_probs=38.4

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+..++.+.+.+..+. -...+-++|..|.||||+|+.+.+
T Consensus        15 f~~viGq~~v~~~L~~~i~~~~-~~hayLf~Gp~GtGKTt~Ak~lAk   60 (559)
T PRK05563         15 FEDVVGQEHITKTLKNAIKQGK-ISHAYLFSGPRGTGKTSAAKIFAK   60 (559)
T ss_pred             HHhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999998754 245667899999999999988865

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.73  E-value=0.23  Score=55.98  Aligned_cols=47  Identities=23%  Similarity=0.181  Sum_probs=34.3

Q ss_pred             CCCceechhhHHHHHHHHHc--------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIE--------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~--------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+++.|.+.-++.+.+....        +-...+-|-++|++|.|||.+|+++.+
T Consensus       227 ~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~  281 (489)
T CHL00195        227 ISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAN  281 (489)
T ss_pred             HHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHH
Confidence            45788887777666543211        112356788999999999999999998

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=95.72  E-value=0.042  Score=55.81  Aligned_cols=26  Identities=23%  Similarity=0.286  Sum_probs=23.7

Q ss_pred             CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          176 PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       176 ~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .....+|+|.|..|.|||||++.+.+
T Consensus        30 ~~~~~iigi~G~~GsGKTTl~~~L~~   55 (229)
T PRK09270         30 PQRRTIVGIAGPPGAGKSTLAEFLEA   55 (229)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            35689999999999999999999987

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=95.70  E-value=0.11  Score=59.87  Aligned_cols=46  Identities=17%  Similarity=0.047  Sum_probs=39.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|-+..++.+.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        15 f~diiGqe~iv~~L~~~i~~~~-i~hayLf~Gp~G~GKTt~Ar~lAk   60 (563)
T PRK06647         15 FNSLEGQDFVVETLKHSIESNK-IANAYIFSGPRGVGKTSSARAFAR   60 (563)
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3588999999999999998754 345688999999999999999877

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=95.66  E-value=0.0092  Score=59.96  Aligned_cols=52  Identities=21%  Similarity=0.226  Sum_probs=42.8

Q ss_pred             CCceechhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          156 RDTVGLDDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      .+++|-++-++++.=++...   ...+..+-++|++|.||||||..|.+  ++...+
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~--Emgvn~   80 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIAN--ELGVNL   80 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHH--HhcCCe
Confidence            57999999888887666543   45688999999999999999999999  666544

>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=95.66  E-value=0.042  Score=52.13  Aligned_cols=115  Identities=14%  Similarity=0.150  Sum_probs=61.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-CCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-PYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  257 (824)
                      -.+++|+|..|.|||||++.+...  . ......+++.. ++.. ....+.    ...+.-..     +-..-+...-.+
T Consensus        25 g~~~~i~G~nGsGKStll~~l~g~--~-~~~~G~i~~~~~~~~~-~~~~~~----~~~i~~~~-----qlS~G~~~r~~l   91 (157)
T cd00267          25 GEIVALVGPNGSGKSTLLRAIAGL--L-KPTSGEILIDGKDIAK-LPLEEL----RRRIGYVP-----QLSGGQRQRVAL   91 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC--C-CCCccEEEECCEEccc-CCHHHH----HhceEEEe-----eCCHHHHHHHHH
Confidence            369999999999999999999983  3 23456666651 0111 111111    11111100     001113333446


Q ss_pred             HHhcCCCeEEEEEecCCCh---hhHHHHHhhCCC-CCCCcEEEEEechHHHHh
Q 003387          258 HEYLMTKRYLIVIDDVWSI---DMWDVIQEILPD-NQNGSRVLITLTDIRIII  306 (824)
Q Consensus       258 ~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~-~~~gs~ilvTtR~~~v~~  306 (824)
                      ...+....-++++|+.-..   .....+...+.. ...+..++++|.+.+...
T Consensus        92 ~~~l~~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~  144 (157)
T cd00267          92 ARALLLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELAE  144 (157)
T ss_pred             HHHHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            6666667788999998643   222223222221 112567888887765543

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.65  E-value=0.1  Score=60.64  Aligned_cols=45  Identities=20%  Similarity=0.133  Sum_probs=37.9

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.+..++.|.+++..+. -...+-++|..|+||||+|+.+.+
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r-l~~a~Lf~Gp~G~GKttlA~~lAk   60 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR-IAPAYLFTGPRGTGKTSSARILAK   60 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCChHHHHHHHHH
Confidence            578899999999999988653 234677899999999999999877

>PRK04296 thymidine kinase; Provisional

Probab=95.64  E-value=0.017  Score=56.61  Aligned_cols=113  Identities=13%  Similarity=-0.040  Sum_probs=63.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  259 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  259 (824)
                      .++.|+|..|.||||+|..+..  +...+-..++.+.    ..++.+.-...++.+++....  ........+....+.+
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~--~~~~~g~~v~i~k----~~~d~~~~~~~i~~~lg~~~~--~~~~~~~~~~~~~~~~   74 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAY--NYEERGMKVLVFK----PAIDDRYGEGKVVSRIGLSRE--AIPVSSDTDIFELIEE   74 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHH--HHHHcCCeEEEEe----ccccccccCCcEecCCCCccc--ceEeCChHHHHHHHHh
Confidence            4778899999999999988877  4433333334332    112222223345555543211  0112234455555555


Q ss_pred             hcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          260 YLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       260 ~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                       ..++.-+||+|.+.--  ++..++...+  ...|-.|++|.++.+
T Consensus        75 -~~~~~dvviIDEaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~~  117 (190)
T PRK04296         75 -EGEKIDCVLIDEAQFLDKEQVVQLAEVL--DDLGIPVICYGLDTD  117 (190)
T ss_pred             -hCCCCCEEEEEccccCCHHHHHHHHHHH--HHcCCeEEEEecCcc
Confidence             3334458999999542  2233333222  235788999998864

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=95.61  E-value=0.01  Score=54.99  Aligned_cols=44  Identities=25%  Similarity=0.135  Sum_probs=32.9

Q ss_pred             eechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          159 VGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       159 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ||....++++.+.+..-.....-|-|+|..|.||+++|+.++..
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~   44 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRY   44 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHT
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhh
Confidence            57777788888877653333456789999999999999999884

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=95.57  E-value=0.14  Score=51.84  Aligned_cols=126  Identities=13%  Similarity=0.172  Sum_probs=75.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCc-----ccc------CCC---ceeEEEEC--CCCCCC--CH---------------
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSS-----YVK------HYF---DCHAWITE--PYSNEY--DA---------------  225 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~-----~~~------~~F---~~~~wv~~--~vs~~~--~~---------------  225 (824)
                      -.+++|+|+.|.|||||.+.+..--     ++.      ..+   ..+.||..  ++...|  .+               
T Consensus        30 G~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~~  109 (254)
T COG1121          30 GEITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGWF  109 (254)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCccccccc
Confidence            3699999999999999999998821     010      011   23455541  011111  11               


Q ss_pred             -------HHHHHHHHHHhCCCCC-cccccccCHHHHH-HHHHHhcCCCeEEEEEecCCCh------hhHHHHHhhCCCCC
Q 003387          226 -------DQILDIVIKFLMPSSR-LSEIMDKNYEMKK-IILHEYLMTKRYLIVIDDVWSI------DMWDVIQEILPDNQ  290 (824)
Q Consensus       226 -------~~~~~~i~~~l~~~~~-~~~~~~~~~~~~~-~~l~~~L~~kr~LlVlDdv~~~------~~~~~l~~~~~~~~  290 (824)
                             ++...+.+++.+...- ..++...+-.+.+ -.|.+.|..+.=|+|||.--..      ...-++...+... 
T Consensus       110 ~~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~e-  188 (254)
T COG1121         110 RRLNKKDKEKVDEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQE-  188 (254)
T ss_pred             ccccHHHHHHHHHHHHHcCchhhhCCcccccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHC-
Confidence                   2445556666655211 0113444445554 4667888999999999986543      3444555555444 


Q ss_pred             CCcEEEEEechHHHHh
Q 003387          291 NGSRVLITLTDIRIII  306 (824)
Q Consensus       291 ~gs~ilvTtR~~~v~~  306 (824)
                       |.-|+++|-+-+...
T Consensus       189 -g~tIl~vtHDL~~v~  203 (254)
T COG1121         189 -GKTVLMVTHDLGLVM  203 (254)
T ss_pred             -CCEEEEEeCCcHHhH
Confidence             888999999876665

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=95.57  E-value=0.045  Score=58.50  Aligned_cols=67  Identities=15%  Similarity=0.170  Sum_probs=45.7

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC----CCceeEEEECCCCCCCCHHHHHHHHHHHhC
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH----YFDCHAWITEPYSNEYDADQILDIVIKFLM  237 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~  237 (824)
                      +-++|..+=..-.++-|+|.+|+||||++.+++-+.....    .=..++||+  ....|+..++. ++++.++
T Consensus        84 lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~--te~~f~~~rl~-~~~~~~g  154 (310)
T TIGR02236        84 LDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYID--TENTFRPERIM-QMAEARG  154 (310)
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEE--CCCCCCHHHHH-HHHHHcC
Confidence            4455555534578999999999999999988865322211    113789999  88888887755 4455544

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.

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.53  E-value=0.058  Score=54.52  Aligned_cols=127  Identities=11%  Similarity=0.056  Sum_probs=72.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE-CCCCC--CCCHHHHHHHHHHHhCCCCCccc--ccccCHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT-EPYSN--EYDADQILDIVIKFLMPSSRLSE--IMDKNYEMK  253 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-~~vs~--~~~~~~~~~~i~~~l~~~~~~~~--~~~~~~~~~  253 (824)
                      -.++||||..|.||||+++.+..  -..... ..+++. .++..  .....+-..++++..+.....-.  ...-+-.++
T Consensus        39 ge~~glVGESG~GKSTlgr~i~~--L~~pt~-G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQr  115 (268)
T COG4608          39 GETLGLVGESGCGKSTLGRLILG--LEEPTS-GEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQR  115 (268)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHc--CcCCCC-ceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhh
Confidence            56999999999999999999998  333333 334333 11111  12233456667777665332100  011222333


Q ss_pred             -HHHHHHhcCCCeEEEEEecCCChhh---HHHHHhhCC--CCCCCcEEEEEechHHHHhhc
Q 003387          254 -KIILHEYLMTKRYLIVIDDVWSIDM---WDVIQEILP--DNQNGSRVLITLTDIRIIISF  308 (824)
Q Consensus       254 -~~~l~~~L~~kr~LlVlDdv~~~~~---~~~l~~~~~--~~~~gs~ilvTtR~~~v~~~f  308 (824)
                       .-.|.+.|.-+.=+||.|..-+..+   -.++...+.  ....|-..+..|-+-.|+..+
T Consensus       116 QRi~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~i  176 (268)
T COG4608         116 QRIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRYI  176 (268)
T ss_pred             hhHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhhh
Confidence             3467788888999999999865421   122222222  122355577777777777633

>KOG4252 consensus GTP-binding protein [Signal transduction mechanisms]

Probab=95.51  E-value=0.018  Score=53.15  Aligned_cols=107  Identities=12%  Similarity=0.140  Sum_probs=64.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  259 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  259 (824)
                      --+.|+|-|||||+++.|..|.- -..+.+...+||+  .-..    ++.                  -+.+.....+  
T Consensus        21 iK~vivGng~VGKssmiqryCkg-ifTkdykktIgvd--fler----qi~------------------v~~Edvr~ml--   73 (246)
T KOG4252|consen   21 IKFVIVGNGSVGKSSMIQRYCKG-IFTKDYKKTIGVD--FLER----QIK------------------VLIEDVRSML--   73 (246)
T ss_pred             EEEEEECCCccchHHHHHHHhcc-ccccccccccchh--hhhH----HHH------------------hhHHHHHHHH--
Confidence            34579999999999999999972 2234567788987  2211    100                  0011111111  


Q ss_pred             hcCCCeEEEEEecCCCh---hhHHHHHhhCCCCCCCcEEEEEechHHHHhhcccccCCcCcCccccchhhHHHhcCCCch
Q 003387          260 YLMTKRYLIVIDDVWSI---DMWDVIQEILPDNQNGSRVLITLTDIRIIISFQFEDGENMRLDLVPTGGPLRATYKGRPF  336 (824)
Q Consensus       260 ~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~~f~~~~~~~~~~~~~~~~~~i~~~c~GlPl  336 (824)
                                    |+.   ++.+.|..+...+...|..+..|.+..-.            ....+.-++|.+.|+..|.
T Consensus        74 --------------WdtagqeEfDaItkAyyrgaqa~vLVFSTTDr~SF------------ea~~~w~~kv~~e~~~IPt  127 (246)
T KOG4252|consen   74 --------------WDTAGQEEFDAITKAYYRGAQASVLVFSTTDRYSF------------EATLEWYNKVQKETERIPT  127 (246)
T ss_pred             --------------HHhccchhHHHHHHHHhccccceEEEEecccHHHH------------HHHHHHHHHHHHHhccCCe
Confidence                          322   45667766666667778777766665322            2233456788899999998


Q ss_pred             hHH
Q 003387          337 LIL  339 (824)
Q Consensus       337 ai~  339 (824)
                      .++
T Consensus       128 V~v  130 (246)
T KOG4252|consen  128 VFV  130 (246)
T ss_pred             EEe
Confidence            754

>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=95.50  E-value=0.066  Score=49.91  Aligned_cols=103  Identities=11%  Similarity=0.050  Sum_probs=57.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      -.+++|+|..|.|||||++.+..-.   ......+|+.  -.             ..+.--   +  +-...+...-.|.
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~--~~-------------~~i~~~---~--~lS~G~~~rv~la   82 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGEL---EPDEGIVTWG--ST-------------VKIGYF---E--QLSGGEKMRLALA   82 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCC---CCCceEEEEC--Ce-------------EEEEEE---c--cCCHHHHHHHHHH
Confidence            4689999999999999999998842   2234445543  10             000000   0  0001122334456


Q ss_pred             HhcCCCeEEEEEecCCCh---hhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          259 EYLMTKRYLIVIDDVWSI---DMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       259 ~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      +.+..+.-++++|+.-..   .....+...+...  +..|+++|.+.+.+.
T Consensus        83 ral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~~  131 (144)
T cd03221          83 KLLLENPNLLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFLD  131 (144)
T ss_pred             HHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHHH
Confidence            666667778899998643   2233333333222  245777777765543

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.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=95.46  E-value=0.034  Score=54.09  Aligned_cols=44  Identities=27%  Similarity=0.249  Sum_probs=36.6

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++||-++.++++.-.-.+++  ..-+.|.||+|+||||-+..+.+
T Consensus        27 ~dIVGNe~tv~rl~via~~gn--mP~liisGpPG~GKTTsi~~LAr   70 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAKEGN--MPNLIISGPPGTGKTTSILCLAR   70 (333)
T ss_pred             HHhhCCHHHHHHHHHHHHcCC--CCceEeeCCCCCchhhHHHHHHH
Confidence            579999999998876666665  77888999999999998777666

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=95.46  E-value=0.052  Score=52.30  Aligned_cols=120  Identities=17%  Similarity=0.161  Sum_probs=60.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-CCCCCCCHHHHHHHHHHHhCC--CC-Cccc--c-cc-cCH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-PYSNEYDADQILDIVIKFLMP--SS-RLSE--I-MD-KNY  250 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~vs~~~~~~~~~~~i~~~l~~--~~-~~~~--~-~~-~~~  250 (824)
                      -.+++|+|..|.|||||.+.+..-  . ......+++.. ++.+ ......    ...++-  .. ....  . +. .+.
T Consensus        28 G~~~~l~G~nGsGKstLl~~i~G~--~-~~~~G~i~~~g~~~~~-~~~~~~----~~~i~~~~~~~~~~~~t~~e~lLS~   99 (171)
T cd03228          28 GEKVAIVGPSGSGKSTLLKLLLRL--Y-DPTSGEILIDGVDLRD-LDLESL----RKNIAYVPQDPFLFSGTIRENILSG   99 (171)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcC--C-CCCCCEEEECCEEhhh-cCHHHH----HhhEEEEcCCchhccchHHHHhhCH
Confidence            468999999999999999999983  2 22344444430 0111 111111    111110  00 0000  0 00 111


Q ss_pred             -HHHHHHHHHhcCCCeEEEEEecCCCh---hhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          251 -EMKKIILHEYLMTKRYLIVIDDVWSI---DMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       251 -~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                       +...-.|...+..+.=+++||+....   ...+.+...+.....+..||++|.+.+...
T Consensus       100 G~~~rl~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~~~~~  159 (171)
T cd03228         100 GQRQRIAIARALLRDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLSTIR  159 (171)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCHHHHH
Confidence             22233456666677789999998754   122222222222122467888888765543

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.

>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=95.44  E-value=0.046  Score=52.78  Aligned_cols=120  Identities=12%  Similarity=0.116  Sum_probs=59.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-CCCCCCCHHHHHHHHHHHhCCCCCccc-ccc------cC-
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-PYSNEYDADQILDIVIKFLMPSSRLSE-IMD------KN-  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~vs~~~~~~~~~~~i~~~l~~~~~~~~-~~~------~~-  249 (824)
                      -.+++|+|..|.|||||++.+..-  . ......+++.. ++.. .+.....    ..+.--...+. ...      .+ 
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~--~-~~~~G~i~~~g~~~~~-~~~~~~~----~~i~~~~q~~~~~~~tv~~~lLS~   99 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGL--L-RPTSGRVRLDGADISQ-WDPNELG----DHVGYLPQDDELFSGSIAENILSG   99 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc--c-CCCCCeEEECCEEccc-CCHHHHH----hheEEECCCCccccCcHHHHCcCH
Confidence            458999999999999999999883  2 22334444430 0111 1111111    11111000000 000      11 


Q ss_pred             HHHHHHHHHHhcCCCeEEEEEecCCCh---hhHHHHHhhCCC-CCCCcEEEEEechHHHHh
Q 003387          250 YEMKKIILHEYLMTKRYLIVIDDVWSI---DMWDVIQEILPD-NQNGSRVLITLTDIRIII  306 (824)
Q Consensus       250 ~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~-~~~gs~ilvTtR~~~v~~  306 (824)
                      -+...-.|.+.+..+.=+++||+....   .....+...+.. ...|..||++|.+.....
T Consensus       100 G~~qrv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~~  160 (173)
T cd03246         100 GQRQRLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPETLA  160 (173)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHH
Confidence            122334455666666678899998754   222222222221 123667888887775443

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

>PRK08149 ATP synthase SpaL; Validated

Probab=95.44  E-value=0.057  Score=59.20  Aligned_cols=92  Identities=17%  Similarity=0.157  Sum_probs=53.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC-CCCHHHHHHHHHHHhCCC--------CCcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN-EYDADQILDIVIKFLMPS--------SRLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~-~~~~~~~~~~i~~~l~~~--------~~~~~~~~~~  249 (824)
                      -..++|+|..|+|||||++.+.+....    +.++...  +.. .-++.++..+........        .+.+......
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~i~~~~~~----dv~v~g~--Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~  224 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNMLIEHSEA----DVFVIGL--IGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCN  224 (428)
T ss_pred             CCEEEEECCCCCChhHHHHHHhcCCCC----CeEEEEE--EeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHh
Confidence            468899999999999999999984322    2333332  222 235556666666543221        1111111111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      ....+..+.+++  ++|++||++||+-..
T Consensus       225 a~~~a~tiAE~fr~~G~~Vll~~DslTr~  253 (428)
T PRK08149        225 AALVATTVAEYFRDQGKRVVLFIDSMTRY  253 (428)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEccchHHH
Confidence            222334444444  589999999999654

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.43  E-value=0.066  Score=55.62  Aligned_cols=93  Identities=13%  Similarity=0.027  Sum_probs=49.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHH--HHHHHHHHHhCCCCCcccccccCH-HHH
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDAD--QILDIVIKFLMPSSRLSEIMDKNY-EMK  253 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~--~~~~~i~~~l~~~~~~~~~~~~~~-~~~  253 (824)
                      ...++|.++|++|+||||.+..+..  .....-..+.+++  .. .|...  +-++..++..+...- ......+. ...
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~--~l~~~g~~V~li~--~D-~~r~~a~~ql~~~~~~~~i~~~-~~~~~~dp~~~~  143 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLAN--KLKKQGKSVLLAA--GD-TFRAAAIEQLEEWAKRLGVDVI-KQKEGADPAAVA  143 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHH--HHHhcCCEEEEEe--CC-CCCHHHHHHHHHHHHhCCeEEE-eCCCCCCHHHHH
Confidence            3478999999999999999988876  3333333566666  33 23332  223334444442100 00011122 222


Q ss_pred             HHHHHHhcCCCeEEEEEecCCC
Q 003387          254 KIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       254 ~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      ...+.....+..=++++|-.-.
T Consensus       144 ~~~l~~~~~~~~D~ViIDT~G~  165 (272)
T TIGR00064       144 FDAIQKAKARNIDVVLIDTAGR  165 (272)
T ss_pred             HHHHHHHHHCCCCEEEEeCCCC
Confidence            3344444444455778887743

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.

>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=95.42  E-value=0.097  Score=50.13  Aligned_cols=114  Identities=11%  Similarity=0.051  Sum_probs=59.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccc-cCC--Cc---eeEEEECCCCCCCCH--HHHHHHHHHHhCCCCCcccccccCH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYV-KHY--FD---CHAWITEPYSNEYDA--DQILDIVIKFLMPSSRLSEIMDKNY  250 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~-~~~--F~---~~~wv~~~vs~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~  250 (824)
                      -.+++|+|..|.|||||++.+..-... ...  |+   ...++    .+.+..  ..+.+.+.-.  ...     .-..-
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~~----~q~~~~~~~tv~~nl~~~--~~~-----~LS~G   95 (166)
T cd03223          27 GDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFL----PQRPYLPLGTLREQLIYP--WDD-----VLSGG   95 (166)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEEE----CCCCccccccHHHHhhcc--CCC-----CCCHH
Confidence            458999999999999999999884211 111  11   12232    232211  1233333210  110     11112


Q ss_pred             HHHHHHHHHhcCCCeEEEEEecCCCh---hhHHHHHhhCCCCCCCcEEEEEechHHHH
Q 003387          251 EMKKIILHEYLMTKRYLIVIDDVWSI---DMWDVIQEILPDNQNGSRVLITLTDIRII  305 (824)
Q Consensus       251 ~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~~~~gs~ilvTtR~~~v~  305 (824)
                      +...-.+.+.+..+.=+++||+--..   .....+...+...  +..||++|.+....
T Consensus        96 ~~~rv~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~~~~  151 (166)
T cd03223          96 EQQRLAFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRPSLW  151 (166)
T ss_pred             HHHHHHHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCChhHH
Confidence            33344556666667778899987643   2222222222222  35677777776544

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

>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=95.42  E-value=0.11  Score=50.26  Aligned_cols=103  Identities=12%  Similarity=0.087  Sum_probs=56.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-C---CCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-P---YSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKK  254 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~---vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~  254 (824)
                      -.+++|+|..|.|||||++.+..-  . ......+++.. .   +.+...           +.           .-+...
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl--~-~p~~G~i~~~g~~i~~~~q~~~-----------LS-----------gGq~qr   79 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQ--L-IPNGDNDEWDGITPVYKPQYID-----------LS-----------GGELQR   79 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcC--C-CCCCcEEEECCEEEEEEcccCC-----------CC-----------HHHHHH
Confidence            459999999999999999999883  2 22233333320 0   122111           11           112333


Q ss_pred             HHHHHhcCCCeEEEEEecCCCh---hhHHHHHhhCCC--CCCCcEEEEEechHHHHh
Q 003387          255 IILHEYLMTKRYLIVIDDVWSI---DMWDVIQEILPD--NQNGSRVLITLTDIRIII  306 (824)
Q Consensus       255 ~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~--~~~gs~ilvTtR~~~v~~  306 (824)
                      -.+.+.+..+.-+++||+.-..   ...+.+...+..  ...+..||++|.+.....
T Consensus        80 v~laral~~~p~lllLDEPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~~~~~  136 (177)
T cd03222          80 VAIAAALLRNATFYLFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDLAVLD  136 (177)
T ss_pred             HHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCHHHHH
Confidence            4556666677788999998643   222222222221  111245677776665443

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.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=95.41  E-value=0.13  Score=51.07  Aligned_cols=128  Identities=13%  Similarity=0.147  Sum_probs=70.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccc-------------------cCCC--ceeEEEE------------CCC------
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYV-------------------KHYF--DCHAWIT------------EPY------  219 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~-------------------~~~F--~~~~wv~------------~~v------  219 (824)
                      -.+++|+|+.|+|||||...+..-.+-                   ...|  +.+-||.            +||      
T Consensus        31 Ge~vaI~GpSGSGKSTLLniig~ld~pt~G~v~i~g~d~~~l~~~~~~~~R~~~iGfvFQ~~nLl~~ltv~ENv~lpl~~  110 (226)
T COG1136          31 GEFVAIVGPSGSGKSTLLNLLGGLDKPTSGEVLINGKDLTKLSEKELAKLRRKKIGFVFQNFNLLPDLTVLENVELPLLI  110 (226)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcccCCCCceEEECCEEcCcCCHHHHHHHHHHhEEEECccCCCCCCCCHHHHHHhHHHH
Confidence            458999999999999999988752110                   0111  1122222            000      


Q ss_pred             CCCC--CHHHHHHHHHHHhCCCCCcc-c-cccc-CHHHHHHHHHHhcCCCeEEEEEecCCCh---hhHHHHHhhCCC--C
Q 003387          220 SNEY--DADQILDIVIKFLMPSSRLS-E-IMDK-NYEMKKIILHEYLMTKRYLIVIDDVWSI---DMWDVIQEILPD--N  289 (824)
Q Consensus       220 s~~~--~~~~~~~~i~~~l~~~~~~~-~-~~~~-~~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~~~~~--~  289 (824)
                      ....  ...+....+++.++...... . .... .-++..-.|.+.|....-+|+-|+--..   ..=+.+...+..  .
T Consensus       111 ~~~~~~~~~~~~~~l~~~lgl~~~~~~~~p~eLSGGqqQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~  190 (226)
T COG1136         111 AGKSAGRRKRAAEELLEVLGLEDRLLKKKPSELSGGQQQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNK  190 (226)
T ss_pred             cCCChhHHHHHHHHHHHhcCChhhhccCCchhcCHHHHHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHH
Confidence            0000  12334556666655532110 0 1122 2344445778888888889999986432   111222222221  2


Q ss_pred             CCCcEEEEEechHHHHh
Q 003387          290 QNGSRVLITLTDIRIII  306 (824)
Q Consensus       290 ~~gs~ilvTtR~~~v~~  306 (824)
                      ..|..||+.|-++.+|.
T Consensus       191 ~~g~tii~VTHd~~lA~  207 (226)
T COG1136         191 ERGKTIIMVTHDPELAK  207 (226)
T ss_pred             hcCCEEEEEcCCHHHHH
Confidence            34778999999999997

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.40  E-value=0.057  Score=50.71  Aligned_cols=120  Identities=10%  Similarity=-0.035  Sum_probs=62.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECC-CCCCCCHHHHHHHHHHHhCC---CCC------cccccccC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEP-YSNEYDADQILDIVIKFLMP---SSR------LSEIMDKN  249 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~-vs~~~~~~~~~~~i~~~l~~---~~~------~~~~~~~~  249 (824)
                      .+|-|++-.|.||||+|-.+.-  +...+=..+.+|.-- -........+++.+ ..+..   ..+      .+......
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~--ra~~~g~~v~~vQFlKg~~~~gE~~~l~~l-~~v~~~~~g~~~~~~~~~~~~~~~~   79 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLAL--RALGHGYRVGVVQFLKGGWKYGELKALERL-PNIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHHHCCCeEEEEEEeCCCCccCHHHHHHhC-CCcEEEECCCCCccCCCChHHHHHH
Confidence            4678889999999999977655  332222233333200 22234444544444 10100   000      00000011


Q ss_pred             HHHHHHHHHHhcCC-CeEEEEEecCCCh-----hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          250 YEMKKIILHEYLMT-KRYLIVIDDVWSI-----DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       250 ~~~~~~~l~~~L~~-kr~LlVlDdv~~~-----~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      ..+.....++.+.. +-=|||||++-..     .+.+.+...+.....+.-||+|.|+.
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence            12233444555544 4459999999644     24455555555555677899999974

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.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=95.32  E-value=0.029  Score=55.35  Aligned_cols=114  Identities=7%  Similarity=0.055  Sum_probs=57.1

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcc
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLS  243 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~  243 (824)
                      +..+.+..+..+.  -+++.|.|.+|.||||+++.+.+  .....=..++++.  .+     .+....+.+..+...   
T Consensus         5 ~Q~~a~~~~l~~~--~~~~~l~G~aGtGKT~~l~~~~~--~~~~~g~~v~~~a--pT-----~~Aa~~L~~~~~~~a---   70 (196)
T PF13604_consen    5 EQREAVRAILTSG--DRVSVLQGPAGTGKTTLLKALAE--ALEAAGKRVIGLA--PT-----NKAAKELREKTGIEA---   70 (196)
T ss_dssp             HHHHHHHHHHHCT--CSEEEEEESTTSTHHHHHHHHHH--HHHHTT--EEEEE--SS-----HHHHHHHHHHHTS-E---
T ss_pred             HHHHHHHHHHhcC--CeEEEEEECCCCCHHHHHHHHHH--HHHhCCCeEEEEC--Cc-----HHHHHHHHHhhCcch---
Confidence            3444555554443  45788899999999999999877  3333212344444  22     223333444433211   


Q ss_pred             cccccCHHHHHHHHHHhc------CCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEE
Q 003387          244 EIMDKNYEMKKIILHEYL------MTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLI  297 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~~~L------~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilv  297 (824)
                          .+...........-      ..++-+||+|+.+..  ..+..+....+.  .|+|+|+
T Consensus        71 ----~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~~~~~~~ll~~~~~--~~~klil  126 (196)
T PF13604_consen   71 ----QTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVDSRQLARLLRLAKK--SGAKLIL  126 (196)
T ss_dssp             ----EEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-BHHHHHHHHHHS-T---T-EEEE
T ss_pred             ----hhHHHHHhcCCcccccccccCCcccEEEEecccccCHHHHHHHHHHHHh--cCCEEEE
Confidence                11111100000000      123349999999865  467777766654  4678873

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=95.32  E-value=0.054  Score=59.26  Aligned_cols=99  Identities=11%  Similarity=0.080  Sum_probs=56.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCH-HHHHHHHHHHhCCCC--------CcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDA-DQILDIVIKFLMPSS--------RLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~-~~~~~~i~~~l~~~~--------~~~~~~~~~  249 (824)
                      -..++|+|..|+|||||++.+.+.  ..  .+.++.+-  +.+..+. .++.++++..-....        +.+.....-
T Consensus       162 GqrigI~G~sG~GKSTLL~~I~~~--~~--~dv~Vi~l--IGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (444)
T PRK08972        162 GQRMGLFAGSGVGKSVLLGMMTRG--TT--ADVIVVGL--VGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLK  235 (444)
T ss_pred             CCEEEEECCCCCChhHHHHHhccC--CC--CCEEEEEE--EcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHH
Confidence            467999999999999999999873  22  24556665  6555433 345555433311110        101011111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ....+..+.+++  +++++|+++||+-.. ..+.++.
T Consensus       236 a~~~A~tiAEyfrd~G~~VLl~~DslTR~A~A~REIs  272 (444)
T PRK08972        236 GCETATTIAEYFRDQGLNVLLLMDSLTRYAQAQREIA  272 (444)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEEcChHHHHHHHHHHH
Confidence            122233344444  689999999999654 3444444

>PTZ00301 uridine kinase; Provisional

Probab=95.32  E-value=0.015  Score=57.77  Aligned_cols=23  Identities=17%  Similarity=0.300  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|||.|.+|.||||||+.+.+
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~   25 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVS   25 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHH
Confidence            57999999999999999998876

>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=95.32  E-value=0.097  Score=50.52  Aligned_cols=119  Identities=13%  Similarity=0.080  Sum_probs=62.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-CCCCCCCHHHHHHHHHHHhCC--CC-Cc-cc---ccc--c
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-PYSNEYDADQILDIVIKFLMP--SS-RL-SE---IMD--K  248 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-~vs~~~~~~~~~~~i~~~l~~--~~-~~-~~---~~~--~  248 (824)
                      -.+++|+|..|.|||||++.+....   ......+++.. +++.. .     ..+...++.  .. .. +.   .+.  .
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~g~~~~~~-~-----~~~~~~i~~~~q~~~~~~~~tv~~~~~L   96 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGLL---KPDSGEIKVLGKDIKKE-P-----EEVKRRIGYLPEEPSLYENLTVRENLKL   96 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC---CCCCeEEEECCEEcccc-h-----HhhhccEEEEecCCccccCCcHHHHhhc
Confidence            4689999999999999999998832   22344555431 01110 0     011111110  00 00 00   000  1


Q ss_pred             CH-HHHHHHHHHhcCCCeEEEEEecCCChh---hHHHHHhhCCC-CCCCcEEEEEechHHHHh
Q 003387          249 NY-EMKKIILHEYLMTKRYLIVIDDVWSID---MWDVIQEILPD-NQNGSRVLITLTDIRIII  306 (824)
Q Consensus       249 ~~-~~~~~~l~~~L~~kr~LlVlDdv~~~~---~~~~l~~~~~~-~~~gs~ilvTtR~~~v~~  306 (824)
                      +. +...-.|...|..+.=++++|+.-..-   ..+.+...+.. ...|..||++|.+...+.
T Consensus        97 S~G~~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~~~~~~  159 (173)
T cd03230          97 SGGMKQRLALAQALLHDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHILEEAE  159 (173)
T ss_pred             CHHHHHHHHHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHH
Confidence            22 223345677777788899999986542   22223222221 122667888888776544

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.

>TIGR01069 mutS2 MutS2 family protein

Probab=95.30  E-value=0.07  Score=63.71  Aligned_cols=157  Identities=15%  Similarity=0.102  Sum_probs=75.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      .+++.|+|+.|.||||+.+.+.... +  ....-++|.  +..... -.++.++...++......+ ...+...-...+.
T Consensus       322 ~~~liItGpNg~GKSTlLK~i~~~~-l--~aq~G~~Vp--a~~~~~-~~~~d~i~~~i~~~~si~~-~LStfS~~m~~~~  394 (771)
T TIGR01069       322 KRVLAITGPNTGGKTVTLKTLGLLA-L--MFQSGIPIP--ANEHSE-IPYFEEIFADIGDEQSIEQ-NLSTFSGHMKNIS  394 (771)
T ss_pred             ceEEEEECCCCCCchHHHHHHHHHH-H--HHHhCCCcc--CCcccc-ccchhheeeecChHhHHhh-hhhHHHHHHHHHH
Confidence            5799999999999999999986631 0  011111222  111000 0011111111111100000 0000011111223


Q ss_pred             HhcC--CCeEEEEEecCCChhh---HHHH----HhhCCCCCCCcEEEEEechHHHHhhcccccC----------CcCcCc
Q 003387          259 EYLM--TKRYLIVIDDVWSIDM---WDVI----QEILPDNQNGSRVLITLTDIRIIISFQFEDG----------ENMRLD  319 (824)
Q Consensus       259 ~~L~--~kr~LlVlDdv~~~~~---~~~l----~~~~~~~~~gs~ilvTtR~~~v~~~f~~~~~----------~~~~~~  319 (824)
                      ..+.  ..+-|+++|..-...+   -..+    ...+.  ..|+.+|+||....+........+          +...+.
T Consensus       395 ~il~~~~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l~--~~g~~viitTH~~eL~~~~~~~~~v~~~~~~~d~~~l~p~  472 (771)
T TIGR01069       395 AILSKTTENSLVLFDELGAGTDPDEGSALAISILEYLL--KQNAQVLITTHYKELKALMYNNEGVENASVLFDEETLSPT  472 (771)
T ss_pred             HHHHhcCCCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHHHhcCCCCeEEeEEEEcCCCCceE
Confidence            3332  4789999999976422   2222    22222  357899999999887651111000          000010


Q ss_pred             c--------ccchhhHHHhcCCCchhHHHHHhHH
Q 003387          320 L--------VPTGGPLRATYKGRPFLILYHGSIS  345 (824)
Q Consensus       320 ~--------~~~~~~i~~~c~GlPlai~~~~~~l  345 (824)
                      +        ...|-+|++++ |+|-.+.--|..+
T Consensus       473 Ykl~~G~~g~S~a~~iA~~~-Glp~~ii~~A~~~  505 (771)
T TIGR01069       473 YKLLKGIPGESYAFEIAQRY-GIPHFIIEQAKTF  505 (771)
T ss_pred             EEECCCCCCCcHHHHHHHHh-CcCHHHHHHHHHH
Confidence            0        23466677666 7898888877776

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=95.28  E-value=0.082  Score=56.16  Aligned_cols=45  Identities=11%  Similarity=0.024  Sum_probs=37.0

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.+..++.+.+.+..+. -....-++|..|+||+|+|..+.+
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r-l~ha~Lf~G~~G~Gk~~~A~~~a~   48 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR-IAPAYLFAGPEGVGRKLAALCFIE   48 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            468899999999999987764 236888999999999998866544

>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=95.26  E-value=0.097  Score=50.51  Aligned_cols=21  Identities=24%  Similarity=0.260  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++.++|++|+||||++..+..
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~   22 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLAL   22 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            688999999999999999887

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.

>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=95.26  E-value=0.012  Score=53.44  Aligned_cols=20  Identities=30%  Similarity=0.260  Sum_probs=19.0

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      |+|.|+.|+||||+|+.+.+
T Consensus         1 I~i~G~~GsGKtTia~~L~~   20 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAE   20 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            78999999999999999988

...

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=95.24  E-value=0.26  Score=58.86  Aligned_cols=48  Identities=23%  Similarity=0.179  Sum_probs=39.3

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ...++|....+.++.+.+..-...-.-|-|+|..|+|||++|+.+++.
T Consensus       375 ~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~  422 (686)
T PRK15429        375 FGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNL  422 (686)
T ss_pred             ccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            357999999999998877653333457889999999999999999984

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.23  E-value=0.1  Score=57.73  Aligned_cols=91  Identities=13%  Similarity=0.002  Sum_probs=51.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCH--HHHHHHHHHHhCCCCCcccccccCHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDA--DQILDIVIKFLMPSSRLSEIMDKNYEMKKI  255 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~  255 (824)
                      ...+|.++|..|+||||.|..+..  .....-..++-|+  . ..+..  .+.++.++.+++...... ....+......
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~--~L~~~g~kV~lV~--~-D~~R~aa~eQL~~la~~~gvp~~~~-~~~~d~~~i~~  167 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLAR--YFKKKGLKVGLVA--A-DTYRPAAYDQLKQLAEKIGVPFYGD-PDNKDAVEIAK  167 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH--HHHHcCCeEEEec--C-CCCCHHHHHHHHHHHHHcCCcEEec-CCccCHHHHHH
Confidence            478999999999999999999987  3433322444554  2 22333  445666677665421100 01123333333


Q ss_pred             HHHHhcCCCeEEEEEecCCC
Q 003387          256 ILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       256 ~l~~~L~~kr~LlVlDdv~~  275 (824)
                      ...+.+++. =+||+|..-.
T Consensus       168 ~al~~~~~~-DvVIIDTAGr  186 (437)
T PRK00771        168 EGLEKFKKA-DVIIVDTAGR  186 (437)
T ss_pred             HHHHHhhcC-CEEEEECCCc
Confidence            333334444 5788998853

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=95.21  E-value=0.069  Score=55.13  Aligned_cols=143  Identities=13%  Similarity=0.102  Sum_probs=82.7

Q ss_pred             CCCceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCC-ccccCCCceeEEEECCCCCCCCH-HHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNS-SYVKHYFDCHAWITEPYSNEYDA-DQILD  230 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~-~~~~~~F~~~~wv~~~vs~~~~~-~~~~~  230 (824)
                      ...++|..++..++-+++...  .+...-+.|+|+.|.|||+|...+..| .+..++|   +-|.  ....... +-.++
T Consensus        23 ~~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~---l~v~--Lng~~~~dk~al~   97 (408)
T KOG2228|consen   23 HINLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENF---LLVR--LNGELQTDKIALK   97 (408)
T ss_pred             CcceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeE---EEEE--ECccchhhHHHHH
Confidence            457889888888888888652  223567789999999999999888875 2233333   3333  3333322 23556


Q ss_pred             HHHHHhCCCCCcccccccCHHHHHHHHHHhcCC------CeEEEEEecCCChh-------hHHHHHhhCCCCCCCcEEEE
Q 003387          231 IVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT------KRYLIVIDDVWSID-------MWDVIQEILPDNQNGSRVLI  297 (824)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~------kr~LlVlDdv~~~~-------~~~~l~~~~~~~~~gs~ilv  297 (824)
                      .|.+|+............+..+....|-..|+.      -++..|+|..+--.       -++-+...-....+=|-|-+
T Consensus        98 ~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~  177 (408)
T KOG2228|consen   98 GITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGV  177 (408)
T ss_pred             HHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEe
Confidence            666666442111012233334444455555532      25788888776321       12222222223556788999


Q ss_pred             EechH
Q 003387          298 TLTDI  302 (824)
Q Consensus       298 TtR~~  302 (824)
                      |||-.
T Consensus       178 Ttrld  182 (408)
T KOG2228|consen  178 TTRLD  182 (408)
T ss_pred             ecccc
Confidence            99964

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.21  E-value=0.063  Score=59.56  Aligned_cols=98  Identities=17%  Similarity=0.185  Sum_probs=66.1

Q ss_pred             CCCCCCceechhhHHHHHHHHHcC----------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC
Q 003387          152 SSKSRDTVGLDDRMEELLDLLIEG----------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN  221 (824)
Q Consensus       152 ~~~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~  221 (824)
                      .+.-.++-|.+..+.++.+++..-          -...+=|-+.|++|.|||.||+++.+  +..-.|     +.  ++.
T Consensus       186 nv~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAg--el~vPf-----~~--isA  256 (802)
T KOG0733|consen  186 NVSFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAG--ELGVPF-----LS--ISA  256 (802)
T ss_pred             CcchhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhh--hcCCce-----Ee--ecc
Confidence            344567889999999988887641          12456788999999999999999999  555444     33  332


Q ss_pred             CCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          222 EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       222 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      .        +|+....+         .+++.+.+...+.-..-.+++++|+++-
T Consensus       257 p--------eivSGvSG---------ESEkkiRelF~~A~~~aPcivFiDeIDA  293 (802)
T KOG0733|consen  257 P--------EIVSGVSG---------ESEKKIRELFDQAKSNAPCIVFIDEIDA  293 (802)
T ss_pred             h--------hhhcccCc---------ccHHHHHHHHHHHhccCCeEEEeecccc
Confidence            2        23333322         2334444445555566899999999974

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=95.19  E-value=0.078  Score=56.87  Aligned_cols=46  Identities=20%  Similarity=0.200  Sum_probs=38.5

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|....+.++.+.+..-...-.-|-|+|-.|+||+++|+.++.
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~   51 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHY   51 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHH
Confidence            4689999999999998876433345678999999999999999987

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=95.19  E-value=0.06  Score=52.52  Aligned_cols=21  Identities=24%  Similarity=0.246  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ||.|+|++|+||||+|+.+..
T Consensus         1 ~i~i~G~pGsGKst~a~~la~   21 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVE   21 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999987

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.16  E-value=0.073  Score=55.76  Aligned_cols=39  Identities=26%  Similarity=0.200  Sum_probs=27.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ..++|+|+|.+|+||||++..+......+..-..+..|+
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~  231 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALIT  231 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEE
Confidence            357999999999999999998877322121112455665

>PRK04040 adenylate kinase; Provisional

Probab=95.15  E-value=0.052  Score=53.05  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|+|++|+||||+++.+.+
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~   24 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALE   24 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHH
Confidence            36899999999999999999988

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.15  E-value=0.32  Score=52.00  Aligned_cols=40  Identities=10%  Similarity=0.199  Sum_probs=26.2

Q ss_pred             CeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          264 KRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       264 kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                      ++-++|+|++...  ...+.+...+..-..++.+|+||.+.+
T Consensus       106 ~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~  147 (328)
T PRK05707        106 GRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPS  147 (328)
T ss_pred             CCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChh
Confidence            3444567999864  456777766665545677777777653

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=95.14  E-value=0.054  Score=59.48  Aligned_cols=100  Identities=14%  Similarity=0.093  Sum_probs=55.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCH-HHHHHHHHHHhCCC--------CCccccccc
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDA-DQILDIVIKFLMPS--------SRLSEIMDK  248 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~-~~~~~~i~~~l~~~--------~~~~~~~~~  248 (824)
                      .-..++|+|..|+|||||++.+.+..  .  -+..+++-  +.+..+. .+...+.+..-+..        .+.+.....
T Consensus       157 ~Gqri~I~G~sG~GKTtLL~~I~~~~--~--~d~~v~~~--iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~  230 (442)
T PRK08927        157 RGQRMGIFAGSGVGKSVLLSMLARNA--D--ADVSVIGL--IGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRR  230 (442)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc--C--CCEEEEEE--EecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHH
Confidence            35688999999999999999999842  2  23445555  5554333 34444443332111        110101111


Q ss_pred             CHHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          249 NYEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       249 ~~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      -....+..+.+++  +++.+|+++||+-.. ..+.++.
T Consensus       231 ~a~~~a~tiAEyfrd~G~~Vll~~DslTr~A~A~REis  268 (442)
T PRK08927        231 QAAYLTLAIAEYFRDQGKDVLCLMDSVTRFAMAQREIG  268 (442)
T ss_pred             HHHHHHHHHHHHHHHCCCcEEEEEeCcHHHHhhhhHHH
Confidence            1122233455555  589999999999654 3344443

>PTZ00035 Rad51 protein; Provisional

Probab=95.14  E-value=0.16  Score=54.50  Aligned_cols=70  Identities=13%  Similarity=0.066  Sum_probs=47.0

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcccc----CCCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVK----HYFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      ..+-++|..+=..-.++.|+|..|.|||||+..++-..+..    ..=..++|++  ....|+.+++ .+++++++.
T Consensus       105 ~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyId--tE~~f~~eri-~~ia~~~g~  178 (337)
T PTZ00035        105 TQLDKLLGGGIETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYID--TEGTFRPERI-VQIAERFGL  178 (337)
T ss_pred             HHHHHHhCCCCCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEE--ccCCCCHHHH-HHHHHHhCC
Confidence            34555665554567899999999999999998886432221    1123567998  7777787774 445665544

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=95.13  E-value=0.011  Score=58.96  Aligned_cols=91  Identities=22%  Similarity=0.124  Sum_probs=48.5

Q ss_pred             eCccCcCCCceEEEEEcc--cCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcccee---
Q 003387          684 LAEYLFPHSLTHLSFSNT--DLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM---  758 (824)
Q Consensus       684 l~~~~~~~~L~~L~L~~~--~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~---  758 (824)
                      +.++..+++|++|.++.|  +...........+|+|++|++++|.+....-......+++|..|++.+|.-.. +..   
T Consensus        58 ~~~~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~lstl~pl~~l~nL~~Ldl~n~~~~~-l~dyre  136 (260)
T KOG2739|consen   58 LTNFPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKDLSTLRPLKELENLKSLDLFNCSVTN-LDDYRE  136 (260)
T ss_pred             cccCCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCCccccccccchhhhhcchhhhhcccCCccc-cccHHH
Confidence            344456667777777776  44333333444567777777777766542222334456666666666665322 110   


Q ss_pred             -ccCcccCccEEEEecCC
Q 003387          759 -GNAAMPKLECLIINPCA  775 (824)
Q Consensus       759 -~~~~lp~L~~L~l~~c~  775 (824)
                       .+.-+|+|+.|+-..+.
T Consensus       137 ~vf~ll~~L~~LD~~dv~  154 (260)
T KOG2739|consen  137 KVFLLLPSLKYLDGCDVD  154 (260)
T ss_pred             HHHHHhhhhccccccccC
Confidence             12235666666544443

>PRK06547 hypothetical protein; Provisional

Probab=95.12  E-value=0.025  Score=54.31  Aligned_cols=26  Identities=27%  Similarity=0.216  Sum_probs=23.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ....+|+|.|+.|+||||+|+.+.+.
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            34889999999999999999999873

>PRK05480 uridine/cytidine kinase; Provisional

Probab=95.11  E-value=0.015  Score=58.10  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=22.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +..+|+|+|.+|+||||||+.+..
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~   28 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYE   28 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999999988

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.11  E-value=0.098  Score=55.40  Aligned_cols=92  Identities=13%  Similarity=0.157  Sum_probs=51.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCC-CCCCHHHHHHHHHHHhCCC--------CCcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYS-NEYDADQILDIVIKFLMPS--------SRLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs-~~~~~~~~~~~i~~~l~~~--------~~~~~~~~~~  249 (824)
                      -..++|+|..|.|||||.+.+.+.  ...  +..+..-  +. +.-++.++.......-...        .+.+.....-
T Consensus        69 Gqri~I~G~sG~GKTtLl~~Ia~~--~~~--~~~vi~~--iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~  142 (326)
T cd01136          69 GQRLGIFAGSGVGKSTLLGMIARG--TTA--DVNVIAL--IGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVK  142 (326)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCC--CCC--CEEEEEE--EecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHH
Confidence            457899999999999999999984  222  2223232  22 2235555555554432211        1111111111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      .......+.+++  ++|.+|+++||+-..
T Consensus       143 ~~~~a~~~AEyfr~~g~~Vll~~Dsltr~  171 (326)
T cd01136         143 AAYTATAIAEYFRDQGKDVLLLMDSLTRF  171 (326)
T ss_pred             HHHHHHHHHHHHHHcCCCeEEEeccchHH
Confidence            222233444444  589999999998654

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.

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=95.11  E-value=0.12  Score=49.07  Aligned_cols=124  Identities=13%  Similarity=0.176  Sum_probs=72.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE-----------------------------------CCCC---
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT-----------------------------------EPYS---  220 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-----------------------------------~~vs---  220 (824)
                      -.++.|+|..|.||||+.+.+|...+-.   ...+|+.                                   +||.   
T Consensus        28 Gef~fl~GpSGAGKSTllkLi~~~e~pt---~G~i~~~~~dl~~l~~~~iP~LRR~IGvVFQD~rLL~~~tvyeNVA~pL  104 (223)
T COG2884          28 GEFVFLTGPSGAGKSTLLKLIYGEERPT---RGKILVNGHDLSRLKGREIPFLRRQIGVVFQDFRLLPDRTVYENVALPL  104 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhhcCC---CceEEECCeecccccccccchhhheeeeEeeeccccccchHhhhhhhhh
Confidence            4689999999999999999999853221   1233332                                   1111   


Q ss_pred             --CCCCHHHHHH---HHHHHhCCCCC---cccccccCHHHHHHHHHHhcCCCeEEEEEecC----CChhhHHHHHhhCCC
Q 003387          221 --NEYDADQILD---IVIKFLMPSSR---LSEIMDKNYEMKKIILHEYLMTKRYLIVIDDV----WSIDMWDVIQEILPD  288 (824)
Q Consensus       221 --~~~~~~~~~~---~i~~~l~~~~~---~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv----~~~~~~~~l~~~~~~  288 (824)
                        ......++.+   +.++..+....   .|. +-..-++-.-.|.+.+-++.-+|+=|.-    +....|+-+...-.-
T Consensus       105 ~v~G~~~~~i~~rV~~~L~~VgL~~k~~~lP~-~LSGGEQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeei  183 (223)
T COG2884         105 RVIGKPPREIRRRVSEVLDLVGLKHKARALPS-QLSGGEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEI  183 (223)
T ss_pred             hccCCCHHHHHHHHHHHHHHhccchhhhcCcc-ccCchHHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHH
Confidence              0112223333   33333333221   111 1122344445677777888888888865    334456655433333


Q ss_pred             CCCCcEEEEEechHHHHh
Q 003387          289 NQNGSRVLITLTDIRIII  306 (824)
Q Consensus       289 ~~~gs~ilvTtR~~~v~~  306 (824)
                      +..|..|+++|-+.++.+
T Consensus       184 nr~GtTVl~ATHd~~lv~  201 (223)
T COG2884         184 NRLGTTVLMATHDLELVN  201 (223)
T ss_pred             hhcCcEEEEEeccHHHHH
Confidence            456899999999998876

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.11  E-value=0.17  Score=49.31  Aligned_cols=124  Identities=8%  Similarity=0.040  Sum_probs=68.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC-----------------CCCCCCCH----------------
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE-----------------PYSNEYDA----------------  225 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~-----------------~vs~~~~~----------------  225 (824)
                      -.|++|+|+.|.|||||.+.+..=+..   =+..+||..                 .|-|.|+.                
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~LE~~---~~G~I~i~g~~~~~~~~~~~~R~~vGmVFQ~fnLFPHlTvleNv~lap~~  104 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNGLEEP---DSGSITVDGEDVGDKKDILKLRRKVGMVFQQFNLFPHLTVLENVTLAPVK  104 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCcCC---CCceEEECCEeccchhhHHHHHHhcCeecccccccccchHHHHHHhhhHH
Confidence            469999999999999999999873322   234555541                 11222321                


Q ss_pred             ---------HHHHHHHHHHhCCCCC---cccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhh---HHHHHhhCC-CC
Q 003387          226 ---------DQILDIVIKFLMPSSR---LSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDM---WDVIQEILP-DN  289 (824)
Q Consensus       226 ---------~~~~~~i~~~l~~~~~---~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~---~~~l~~~~~-~~  289 (824)
                               ++...++++.++..+.   .| .+-..-++-.-.|.+.|.-+.=++.+|..-+.-+   -.++..-.. -.
T Consensus       105 v~~~~k~eA~~~A~~lL~~VGL~~ka~~yP-~qLSGGQqQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA  183 (240)
T COG1126         105 VKKLSKAEAREKALELLEKVGLADKADAYP-AQLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLA  183 (240)
T ss_pred             HcCCCHHHHHHHHHHHHHHcCchhhhhhCc-cccCcHHHHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHH
Confidence                     2334445555554221   11 1112234445578888888888999999976522   222222111 12


Q ss_pred             CCCcEEEEEechHHHHh
Q 003387          290 QNGSRVLITLTDIRIII  306 (824)
Q Consensus       290 ~~gs~ilvTtR~~~v~~  306 (824)
                      ..|-..++.|....-|.
T Consensus       184 ~eGmTMivVTHEM~FAr  200 (240)
T COG1126         184 EEGMTMIIVTHEMGFAR  200 (240)
T ss_pred             HcCCeEEEEechhHHHH
Confidence            34555666666654444

>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=95.10  E-value=0.028  Score=55.32  Aligned_cols=55  Identities=22%  Similarity=0.171  Sum_probs=34.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC--CHHHHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY--DADQILDIVIKFLMP  238 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~--~~~~~~~~i~~~l~~  238 (824)
                      .+||.+||+.|+||||.+-++..  +.+..=..+..++  . ..+  ...+-++..++.++.
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa--~~~~~~~~v~lis--~-D~~R~ga~eQL~~~a~~l~v   57 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAA--RLKLKGKKVALIS--A-DTYRIGAVEQLKTYAEILGV   57 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHH--HHHHTT--EEEEE--E-STSSTHHHHHHHHHHHHHTE
T ss_pred             CEEEEEECCCCCchHhHHHHHHH--HHhhccccceeec--C-CCCCccHHHHHHHHHHHhcc
Confidence            37999999999999999888776  3333333455665  2 222  233445566666653

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 ....

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=95.09  E-value=0.23  Score=54.35  Aligned_cols=23  Identities=17%  Similarity=0.180  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.||||||+.+..
T Consensus       362 G~~lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         362 GEALGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             CceEEEECCCCccHHHHHHHHHc
Confidence            35899999999999999999876

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=95.09  E-value=0.25  Score=56.58  Aligned_cols=49  Identities=20%  Similarity=0.180  Sum_probs=41.3

Q ss_pred             CCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ....++|....+.++.+.+..-...-.-|-|+|..|+|||++|+.+++.
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            3567999999999999988765444567889999999999999999984

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.08  E-value=0.085  Score=59.61  Aligned_cols=96  Identities=15%  Similarity=0.137  Sum_probs=57.5

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC--CCHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE--YDADQILDIVI  233 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~--~~~~~~~~~i~  233 (824)
                      .+++-....+++..+.....--...-|-|.|..|+|||+||+++++-.. +.+.-.+.+|+  .|.-  -..+++|+.+ 
T Consensus       408 ~d~i~~~s~kke~~n~~~spv~~~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~--Cs~l~~~~~e~iQk~l-  483 (952)
T KOG0735|consen  408 HDFIQVPSYKKENANQELSPVFRHGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVS--CSTLDGSSLEKIQKFL-  483 (952)
T ss_pred             CceeecchhhhhhhhhhcccccccccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEe--chhccchhHHHHHHHH-
Confidence            3444444444444443333322356788999999999999999999433 44444556666  4432  1223333332 


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                                          ...+...+....-+|||||+.-
T Consensus       484 --------------------~~vfse~~~~~PSiIvLDdld~  505 (952)
T KOG0735|consen  484 --------------------NNVFSEALWYAPSIIVLDDLDC  505 (952)
T ss_pred             --------------------HHHHHHHHhhCCcEEEEcchhh
Confidence                                2333445556788999999963

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=95.08  E-value=0.022  Score=56.97  Aligned_cols=120  Identities=13%  Similarity=0.101  Sum_probs=59.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      .+++.|+|..|.||||+.+.+...... .+-...+|..     ...+ ....++...+.......+ .......-..++.
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~~~~l-a~~G~~v~a~-----~~~~-~~~d~i~~~l~~~~si~~-~~S~f~~el~~l~  100 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVALIVFL-AHIGSFVPAD-----SATI-GLVDKIFTRMSSRESVSS-GQSAFMIDLYQVS  100 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHHHHHH-HhCCCeeEcC-----CcEE-eeeeeeeeeeCCccChhh-ccchHHHHHHHHH
Confidence            488999999999999999998742111 1111122211     0000 012222222322221110 0001111112222


Q ss_pred             H--hcCCCeEEEEEecCCChhh---H----HHHHhhCCCC-CCCcEEEEEechHHHHh
Q 003387          259 E--YLMTKRYLIVIDDVWSIDM---W----DVIQEILPDN-QNGSRVLITLTDIRIII  306 (824)
Q Consensus       259 ~--~L~~kr~LlVlDdv~~~~~---~----~~l~~~~~~~-~~gs~ilvTtR~~~v~~  306 (824)
                      .  .+..++-|++||..-...+   .    ..+...+... ..+..+|+||-..+++.
T Consensus       101 ~~l~~~~~~slvllDE~~~gtd~~~~~~~~~ail~~l~~~~~~~~~vli~TH~~~l~~  158 (213)
T cd03281         101 KALRLATRRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFN  158 (213)
T ss_pred             HHHHhCCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEcChHHHHH
Confidence            2  2246789999999976432   1    1222223222 23468999999998877

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

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=95.08  E-value=0.06  Score=56.20  Aligned_cols=38  Identities=26%  Similarity=0.318  Sum_probs=31.3

Q ss_pred             echhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHH
Q 003387          160 GLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEA  199 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v  199 (824)
                      +|..+..--+++|.+++  +..|.+.|.+|.|||-||-+.
T Consensus       228 prn~eQ~~ALdlLld~d--I~lV~L~G~AGtGKTlLALaA  265 (436)
T COG1875         228 PRNAEQRVALDLLLDDD--IDLVSLGGKAGTGKTLLALAA  265 (436)
T ss_pred             cccHHHHHHHHHhcCCC--CCeEEeeccCCccHhHHHHHH
Confidence            36666666778888877  999999999999999998553

>PF14516 AAA_35: AAA-like domain

Probab=95.06  E-value=0.41  Score=51.49  Aligned_cols=116  Identities=16%  Similarity=0.111  Sum_probs=69.6

Q ss_pred             CCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC-----CCCHHHH
Q 003387          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN-----EYDADQI  228 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~-----~~~~~~~  228 (824)
                      +.+-.|.|...-+++.+.|...   -..+.|.|+-.+|||||...+.+..+- ..+ .+++++  ...     ..+..+.
T Consensus         9 ~~~~Yi~R~~~e~~~~~~i~~~---G~~~~I~apRq~GKTSll~~l~~~l~~-~~~-~~v~id--~~~~~~~~~~~~~~f   81 (331)
T PF14516_consen    9 DSPFYIERPPAEQECYQEIVQP---GSYIRIKAPRQMGKTSLLLRLLERLQQ-QGY-RCVYID--LQQLGSAIFSDLEQF   81 (331)
T ss_pred             CCCcccCchHHHHHHHHHHhcC---CCEEEEECcccCCHHHHHHHHHHHHHH-CCC-EEEEEE--eecCCCcccCCHHHH
Confidence            4455668886777777777663   248899999999999999999883222 233 345666  332     1245555


Q ss_pred             HHHHH----HHhCCCCCccc-c--cccCHHHHHHHHHHhc-C--CCeEEEEEecCCCh
Q 003387          229 LDIVI----KFLMPSSRLSE-I--MDKNYEMKKIILHEYL-M--TKRYLIVIDDVWSI  276 (824)
Q Consensus       229 ~~~i~----~~l~~~~~~~~-~--~~~~~~~~~~~l~~~L-~--~kr~LlVlDdv~~~  276 (824)
                      ++.++    +++........ +  ...........+.+.+ +  +++.+|++|+|+..
T Consensus        82 ~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l  139 (331)
T PF14516_consen   82 LRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRL  139 (331)
T ss_pred             HHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhh
Confidence            55444    44444322111 0  1112234444455543 2  58999999999754

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=95.05  E-value=0.075  Score=53.10  Aligned_cols=61  Identities=15%  Similarity=0.175  Sum_probs=40.0

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCc--eeEEEE-----CCCCCCCCHHHH--HHHHHHHhCCC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD--CHAWIT-----EPYSNEYDADQI--LDIVIKFLMPS  239 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~-----~~vs~~~~~~~~--~~~i~~~l~~~  239 (824)
                      ++...|.|+||+|.||||..|.++.+  +...+.  .++=.+     .+..-+.|+++.  .++..++.+..
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~h--l~~~~~ppYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LG   86 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSH--LHAKKTPPYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLG   86 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHH--HhhccCCCeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCC
Confidence            45778889999999999999999984  333332  222221     124455677765  45788877653

>TIGR00235 udk uridine kinase

Probab=95.03  E-value=0.017  Score=57.60  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|+|+.|+||||||+.+..
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~~l~~   28 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVARKIYE   28 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999987

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=94.99  E-value=0.097  Score=56.89  Aligned_cols=100  Identities=20%  Similarity=0.127  Sum_probs=56.4

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc-c
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL-S  243 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~-~  243 (824)
                      ...+-+.|..+-..-.++.|.|.+|+|||||+.++..  .....-..++|++  ..+.  ..++. .-++.++...+. .
T Consensus        68 i~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~--~~a~~g~~VlYvs--~EEs--~~qi~-~Ra~rlg~~~~~l~  140 (372)
T cd01121          68 IEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAA--RLAKRGGKVLYVS--GEES--PEQIK-LRADRLGISTENLY  140 (372)
T ss_pred             CHHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHH--HHHhcCCeEEEEE--CCcC--HHHHH-HHHHHcCCCcccEE
Confidence            4455566655544467999999999999999998876  3333335677887  4332  33332 223445432110 0


Q ss_pred             cccccCHHHHHHHHHHhcCCCeEEEEEecCC
Q 003387          244 EIMDKNYEMKKIILHEYLMTKRYLIVIDDVW  274 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~  274 (824)
                      .....+.+.+...+.   +.+.-+||+|.+.
T Consensus       141 l~~e~~le~I~~~i~---~~~~~lVVIDSIq  168 (372)
T cd01121         141 LLAETNLEDILASIE---ELKPDLVIIDSIQ  168 (372)
T ss_pred             EEccCcHHHHHHHHH---hcCCcEEEEcchH
Confidence            012223344333332   2355678888874

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.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=94.99  E-value=0.076  Score=57.58  Aligned_cols=124  Identities=16%  Similarity=0.132  Sum_probs=67.1

Q ss_pred             CCCceechhhHHH-HHHHHHc-CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHH
Q 003387          155 SRDTVGLDDRMEE-LLDLLIE-GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       155 ~~~~vGr~~~~~~-l~~~L~~-~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      ++-++|-...... +...... .......+-|||..|.|||.|++++.|  ...........++  ++    ......++
T Consensus        87 dnFv~g~~N~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign--~~~~~~~~a~v~y--~~----se~f~~~~  158 (408)
T COG0593          87 DNFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGN--EALANGPNARVVY--LT----SEDFTNDF  158 (408)
T ss_pred             hheeeCCchHHHHHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHH--HHHhhCCCceEEe--cc----HHHHHHHH
Confidence            3446665444332 3333333 233478999999999999999999999  6666665333333  22    22333344


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChh---hH-HHHHhhCCC-CCCCcEEEEEech
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSID---MW-DVIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~---~~-~~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                      +..+..             .-.+..++..  .-=++++||++-..   .| +.+...|.. ...|-.||+|++.
T Consensus       159 v~a~~~-------------~~~~~Fk~~y--~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr  217 (408)
T COG0593         159 VKALRD-------------NEMEKFKEKY--SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDR  217 (408)
T ss_pred             HHHHHh-------------hhHHHHHHhh--ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCC
Confidence            333321             1223444444  23388899997531   22 222222221 1223389999864

>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=94.98  E-value=0.01  Score=35.25  Aligned_cols=18  Identities=22%  Similarity=0.290  Sum_probs=8.6

Q ss_pred             ccEeecCCccccccchhh
Q 003387          570 LYTLDMPFSYIDHTADEF  587 (824)
Q Consensus       570 L~~L~L~~~~l~~lp~~i  587 (824)
                      |++|||++|.++.+|.+|
T Consensus         2 L~~Ldls~n~l~~ip~~~   19 (22)
T PF00560_consen    2 LEYLDLSGNNLTSIPSSF   19 (22)
T ss_dssp             ESEEEETSSEESEEGTTT
T ss_pred             ccEEECCCCcCEeCChhh
Confidence            444555555444444443

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 ....

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=94.97  E-value=0.06  Score=59.66  Aligned_cols=95  Identities=12%  Similarity=0.138  Sum_probs=58.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCCC--------CcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPSS--------RLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~~--------~~~~~~~~~  249 (824)
                      -.-++|.|..|+|||||+..+.+... +.+-+.++++-  +.+.. .+.++..++...=....        +.+.....-
T Consensus       143 GQR~gIfa~~G~GKt~Ll~~~~~~~~-~~~~dv~V~~l--iGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~  219 (461)
T PRK12597        143 GGKTGLFGGAGVGKTVLMMELIFNIS-KQHSGSSVFAG--VGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMR  219 (461)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHH-hhCCCEEEEEc--CCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHH
Confidence            45789999999999999988877422 22457777777  76654 33455555554321111        111111112


Q ss_pred             HHHHHHHHHHhc---CCCeEEEEEecCCCh
Q 003387          250 YEMKKIILHEYL---MTKRYLIVIDDVWSI  276 (824)
Q Consensus       250 ~~~~~~~l~~~L---~~kr~LlVlDdv~~~  276 (824)
                      ....+..+.+++   +++++|+++||+-..
T Consensus       220 a~~~a~tiAEyfrd~~G~~VLl~~DslTR~  249 (461)
T PRK12597        220 VVLTGLTIAEYLRDEEKEDVLLFIDNIFRF  249 (461)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEeccchHH
Confidence            233345566666   389999999999543

>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=94.96  E-value=0.074  Score=53.46  Aligned_cols=21  Identities=19%  Similarity=0.267  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +|||.|..|+||||+|+.+.+
T Consensus         1 IigI~G~sGSGKTTla~~L~~   21 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQA   21 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHH
Confidence            589999999999999999987

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>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=94.96  E-value=0.018  Score=45.96  Aligned_cols=21  Identities=24%  Similarity=0.319  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +|+|.|..|+||||+|+.+.+
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~   21 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAE   21 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999999887

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.

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=94.92  E-value=0.12  Score=56.41  Aligned_cols=52  Identities=21%  Similarity=0.310  Sum_probs=39.1

Q ss_pred             CCCCCCceechhh---HHHHHHHHHcCC-------CCeEEEEEEcCCCChHHHHHHHHhCCc
Q 003387          152 SSKSRDTVGLDDR---MEELLDLLIEGP-------PQLSVVAILDSIGLDKTAFAGEAYNSS  203 (824)
Q Consensus       152 ~~~~~~~vGr~~~---~~~l~~~L~~~~-------~~~~vi~I~G~gGvGKTtLa~~v~~~~  203 (824)
                      .+.-+++-|.|+.   +++|+++|.+..       .=.+=|-.+|++|-|||-||++|....
T Consensus       300 nv~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA  361 (752)
T KOG0734|consen  300 NVTFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA  361 (752)
T ss_pred             ccccccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc
Confidence            3445677787664   567788887752       235678899999999999999999943

>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=94.90  E-value=0.012  Score=34.89  Aligned_cols=19  Identities=37%  Similarity=0.455  Sum_probs=9.6

Q ss_pred             ccEEEeeCccCccCCccCC
Q 003387          523 LRVLDLGSLVLIQYPSGIE  541 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~~i~  541 (824)
                      |++|+|++|.++.+|++|+
T Consensus         2 L~~Ldls~n~l~~ip~~~~   20 (22)
T PF00560_consen    2 LEYLDLSGNNLTSIPSSFS   20 (22)
T ss_dssp             ESEEEETSSEESEEGTTTT
T ss_pred             ccEEECCCCcCEeCChhhc
Confidence            4555555555555554443

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 ....

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=94.90  E-value=0.11  Score=50.58  Aligned_cols=24  Identities=21%  Similarity=0.282  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||++.+..-
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (182)
T cd03215          26 GEIVGIAGLVGNGQTELAEALFGL   49 (182)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999983

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.

>PRK10867 signal recognition particle protein; Provisional

Probab=94.87  E-value=0.096  Score=57.84  Aligned_cols=91  Identities=15%  Similarity=0.103  Sum_probs=47.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCC-CceeEEEECCCCCCCCHH--HHHHHHHHHhCCCCCcccccccCHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHY-FDCHAWITEPYSNEYDAD--QILDIVIKFLMPSSRLSEIMDKNYEMKK  254 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~~~~wv~~~vs~~~~~~--~~~~~i~~~l~~~~~~~~~~~~~~~~~~  254 (824)
                      ...+|.++|.+|+||||.|..+..  ..... -..++.|+   ...+...  +-++..+++.+..--.. ....+...+.
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~--~l~~~~G~kV~lV~---~D~~R~aa~eQL~~~a~~~gv~v~~~-~~~~dp~~i~  172 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAK--YLKKKKKKKVLLVA---ADVYRPAAIEQLKTLGEQIGVPVFPS-GDGQDPVDIA  172 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH--HHHHhcCCcEEEEE---ccccchHHHHHHHHHHhhcCCeEEec-CCCCCHHHHH
Confidence            478999999999999998877766  33333 12344454   2223332  23334445444211000 0122344444


Q ss_pred             HHHHHhcCCCeE-EEEEecCC
Q 003387          255 IILHEYLMTKRY-LIVIDDVW  274 (824)
Q Consensus       255 ~~l~~~L~~kr~-LlVlDdv~  274 (824)
                      ....+..+.+.| ++|+|-.-
T Consensus       173 ~~a~~~a~~~~~DvVIIDTaG  193 (433)
T PRK10867        173 KAALEEAKENGYDVVIVDTAG  193 (433)
T ss_pred             HHHHHHHHhcCCCEEEEeCCC
Confidence            434444444445 67777665

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=94.85  E-value=0.061  Score=52.19  Aligned_cols=34  Identities=18%  Similarity=0.041  Sum_probs=25.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWI  215 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv  215 (824)
                      -.+++|+|..|.|||||++.+...  . ......+.+
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~--~-~~~~G~i~~   59 (178)
T cd03229          26 GEIVALLGPSGSGKSTLLRCIAGL--E-EPDSGSILI   59 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC--C-CCCceEEEE
Confidence            469999999999999999999873  2 223445554

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. 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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=94.82  E-value=0.11  Score=55.78  Aligned_cols=45  Identities=20%  Similarity=0.186  Sum_probs=35.8

Q ss_pred             ceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          158 TVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ++|....+.++.+.+..-...-.-|-|+|..|.||+++|+.+++.
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHh
Confidence            468888888888887764333456789999999999999999873

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

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=94.81  E-value=0.099  Score=53.31  Aligned_cols=102  Identities=19%  Similarity=0.104  Sum_probs=61.7

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc---
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL---  242 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~---  242 (824)
                      ..+-++|..+=..-.++.|+|.+|+||||+|.++... ..+ .=..++|++  ..+.  ..++.+++ ++++-....   
T Consensus        12 ~~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~-~~~-~g~~~~y~~--~e~~--~~~~~~~~-~~~g~~~~~~~~   84 (234)
T PRK06067         12 EELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYG-ALK-QGKKVYVIT--TENT--SKSYLKQM-ESVKIDISDFFL   84 (234)
T ss_pred             HHHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHH-HHh-CCCEEEEEE--cCCC--HHHHHHHH-HHCCCChhHHHh
Confidence            3444555555455789999999999999999998542 222 234678888  6554  44555543 333321100   


Q ss_pred             ----c-------c--ccccCHHHHHHHHHHhcCC-CeEEEEEecCC
Q 003387          243 ----S-------E--IMDKNYEMKKIILHEYLMT-KRYLIVIDDVW  274 (824)
Q Consensus       243 ----~-------~--~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~  274 (824)
                          .       .  ....+.+.+...+.+.++. +.-++|+|.+-
T Consensus        85 ~g~l~i~~~~~~~~~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t  130 (234)
T PRK06067         85 WGYLRIFPLNTEGFEWNSTLANKLLELIIEFIKSKREDVIIIDSLT  130 (234)
T ss_pred             CCCceEEeccccccccCcchHHHHHHHHHHHHHhcCCCEEEEecHH
Confidence                0       0  0122345677777777754 55589999976

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=94.78  E-value=0.17  Score=47.36  Aligned_cols=21  Identities=19%  Similarity=0.159  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ||.|+|.+|.||||+|+.+..
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~   21 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEE   21 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHH
Confidence            578999999999999999887

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=94.78  E-value=0.12  Score=53.10  Aligned_cols=102  Identities=15%  Similarity=0.114  Sum_probs=55.9

Q ss_pred             eEEEEEEcCCCChHHHHH-HHHhCCccccCCCcee-EEEECCCCCCC-CHHHHHHHHHHHhCCCCCcc--cccccCHHH-
Q 003387          179 LSVVAILDSIGLDKTAFA-GEAYNSSYVKHYFDCH-AWITEPYSNEY-DADQILDIVIKFLMPSSRLS--EIMDKNYEM-  252 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa-~~v~~~~~~~~~F~~~-~wv~~~vs~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~~~-  252 (824)
                      -.-++|.|..|+|||+|| +.+.+.  .  .-+.+ +++-  +.+.. .+.++.+++.+.=......-  ...++.... 
T Consensus        69 GQr~~Ifg~~g~GKt~L~l~~i~~~--~--~~~v~~V~~~--iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r  142 (274)
T cd01132          69 GQRELIIGDRQTGKTAIAIDTIINQ--K--GKKVYCIYVA--IGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQ  142 (274)
T ss_pred             CCEEEeeCCCCCCccHHHHHHHHHh--c--CCCeEEEEEe--cccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHH
Confidence            457899999999999995 667662  2  23444 5555  55554 34455555554321110000  001111111 


Q ss_pred             -----HHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHHhhC
Q 003387          253 -----KKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQEIL  286 (824)
Q Consensus       253 -----~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~~~~  286 (824)
                           .+..+.+++  ++|.+|+|+||+-.. ..|.++...+
T Consensus       143 ~~a~~~a~aiAE~fr~~G~~Vlvl~DslTr~A~A~rEisl~~  184 (274)
T cd01132         143 YLAPYTGCAMGEYFMDNGKHALIIYDDLSKQAVAYRQMSLLL  184 (274)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEcChHHHHHHHHHHHHhc
Confidence                 123333333  589999999999765 4566665443

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=94.77  E-value=0.14  Score=59.27  Aligned_cols=49  Identities=18%  Similarity=0.117  Sum_probs=40.5

Q ss_pred             CCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ....++|....+.++.+.+..-...-.-|-|+|..|+|||++|+.|++.
T Consensus       194 ~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       194 KEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             ccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHh
Confidence            4568999999999999988764333445679999999999999999984

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.

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=94.74  E-value=0.13  Score=52.82  Aligned_cols=104  Identities=15%  Similarity=0.080  Sum_probs=60.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccc--cCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCCC--------Ccccccc
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYV--KHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPSS--------RLSEIMD  247 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~--~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~~--------~~~~~~~  247 (824)
                      -.-++|.|-.|+|||||+..+.++..+  +..-+.++++-  +.+.. ++.++..++...=....        +.+....
T Consensus        69 GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~--IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r  146 (276)
T cd01135          69 GQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAA--MGITMEDARFFKDDFEETGALERVVLFLNLANDPTIER  146 (276)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEE--eccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHH
Confidence            357899999999999999998885331  12346777877  76654 44556666555321111        0000111


Q ss_pred             cCHHHHHHHHHHhc---CCCeEEEEEecCCCh-hhHHHHHh
Q 003387          248 KNYEMKKIILHEYL---MTKRYLIVIDDVWSI-DMWDVIQE  284 (824)
Q Consensus       248 ~~~~~~~~~l~~~L---~~kr~LlVlDdv~~~-~~~~~l~~  284 (824)
                      .-..-....+.+++   ++|++|+++||+-.. ..+.++..
T Consensus       147 ~~a~~~a~aiAEyfrd~~g~~VLl~~D~ltr~A~A~rEisl  187 (276)
T cd01135         147 IITPRMALTTAEYLAYEKGKHVLVILTDMTNYAEALREISA  187 (276)
T ss_pred             HHHHHHHHHHHHHHHhccCCeEEEEEcChhHHHHHHHHHHh
Confidence            11122233455555   378999999999754 34555543

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.73  E-value=0.19  Score=54.27  Aligned_cols=88  Identities=20%  Similarity=0.153  Sum_probs=49.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCC--ceeEEEECCCCC-CCCHHHHHHHHHHHhCCCCCcccccccCHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYF--DCHAWITEPYSN-EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKI  255 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~~~vs~-~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~  255 (824)
                      -.++.++|+.|+||||++.++..  +....+  ..+..++  ... .....+-++...+.++....    ...+..++..
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~--~~~~~~G~~~V~lit--~D~~R~ga~EqL~~~a~~~gv~~~----~~~~~~~l~~  208 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAA--RCVMRFGASKVALLT--TDSYRIGGHEQLRIFGKILGVPVH----AVKDGGDLQL  208 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH--HHHHhcCCCeEEEEe--cccccccHHHHHHHHHHHcCCceE----ecCCcccHHH
Confidence            46999999999999999999987  332223  3455665  221 22334455555555554221    1122223333


Q ss_pred             HHHHhcCCCeEEEEEecCCCh
Q 003387          256 ILHEYLMTKRYLIVIDDVWSI  276 (824)
Q Consensus       256 ~l~~~L~~kr~LlVlDdv~~~  276 (824)
                      .+. .+.++ =+|++|..-..
T Consensus       209 ~l~-~l~~~-DlVLIDTaG~~  227 (374)
T PRK14722        209 ALA-ELRNK-HMVLIDTIGMS  227 (374)
T ss_pred             HHH-HhcCC-CEEEEcCCCCC
Confidence            333 34455 45558988543

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=94.67  E-value=0.07  Score=56.53  Aligned_cols=31  Identities=10%  Similarity=-0.018  Sum_probs=26.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      ...+.++|+|++|.|||.+|+++++  +..-.|
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~--elg~~~  176 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFK--KMGIEP  176 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHH--HcCCCe
Confidence            4579999999999999999999999  554443

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.67  E-value=0.2  Score=58.81  Aligned_cols=87  Identities=23%  Similarity=0.194  Sum_probs=46.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCC--HHHHHHHHHHHhCCCCCcccccccCHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD--ADQILDIVIKFLMPSSRLSEIMDKNYEMKKII  256 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~--~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  256 (824)
                      -+||+++|+.|+||||.+.++.........-..+..++  . ..+.  ..+-++...+.++....    ...+..++...
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit--~-Dt~RigA~eQL~~~a~~~gvpv~----~~~~~~~l~~a  257 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLT--T-DSFRIGALEQLRIYGRILGVPVH----AVKDAADLRFA  257 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEec--C-cccchHHHHHHHHHHHhCCCCcc----ccCCHHHHHHH
Confidence            47999999999999999998887321111123455555  2 2333  23444444554443221    12234444444


Q ss_pred             HHHhcCCCeEEEEEecCC
Q 003387          257 LHEYLMTKRYLIVIDDVW  274 (824)
Q Consensus       257 l~~~L~~kr~LlVlDdv~  274 (824)
                      +. .++++. +|++|=.-
T Consensus       258 l~-~~~~~D-~VLIDTAG  273 (767)
T PRK14723        258 LA-ALGDKH-LVLIDTVG  273 (767)
T ss_pred             HH-HhcCCC-EEEEeCCC
Confidence            43 233333 55566654

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=94.66  E-value=0.11  Score=57.17  Aligned_cols=99  Identities=13%  Similarity=0.147  Sum_probs=54.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC-CCHHHHHHHHHHHhCCC--------CCcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE-YDADQILDIVIKFLMPS--------SRLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~-~~~~~~~~~i~~~l~~~--------~~~~~~~~~~  249 (824)
                      -..++|+|..|+|||||++.+.+..    ..+..+++.  +.+. ..+.+.+.+....=...        .+.+.....-
T Consensus       155 GqrigI~G~sG~GKSTLL~~I~~~~----~~d~~vi~~--iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~  228 (433)
T PRK07594        155 GQRVGIFSAPGVGKSTLLAMLCNAP----DADSNVLVL--IGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVR  228 (433)
T ss_pred             CCEEEEECCCCCCccHHHHHhcCCC----CCCEEEEEE--ECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHH
Confidence            5689999999999999999999832    234445544  4433 33445555543211000        0001011111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ....+..+.+++  +++++||++||+-.- ....++.
T Consensus       229 a~~~a~tiAEyfrd~G~~VLl~~Dsltr~A~A~REis  265 (433)
T PRK07594        229 ALFVATTIAEFFRDNGKRVVLLADSLTRYARAAREIA  265 (433)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeCHHHHHHHHHHHH
Confidence            122233445555  579999999999654 2334443

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.66  E-value=0.45  Score=51.90  Aligned_cols=89  Identities=11%  Similarity=0.053  Sum_probs=50.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCcccc--CCCceeEEEECCCCCCCCHHHH--HHHHHHHhCCCCCcccccccCHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVK--HYFDCHAWITEPYSNEYDADQI--LDIVIKFLMPSSRLSEIMDKNYEMK  253 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~--~~F~~~~wv~~~vs~~~~~~~~--~~~i~~~l~~~~~~~~~~~~~~~~~  253 (824)
                      ..++|.++|..|+||||.+..+.......  ..=..+..++  . ..|.....  ++..++.++..-    ....+...+
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit--~-Dt~R~aa~eQL~~~a~~lgvpv----~~~~~~~~l  245 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIIT--I-DNYRIGAKKQIQTYGDIMGIPV----KAIESFKDL  245 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEe--c-cCccHHHHHHHHHHhhcCCcce----EeeCcHHHH
Confidence            36799999999999999998887632211  1123455565  3 34444332  444444444321    122234445


Q ss_pred             HHHHHHhcCCCeEEEEEecCCC
Q 003387          254 KIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       254 ~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      ...+.+.  .+.=+|++|..-.
T Consensus       246 ~~~L~~~--~~~DlVLIDTaGr  265 (388)
T PRK12723        246 KEEITQS--KDFDLVLVDTIGK  265 (388)
T ss_pred             HHHHHHh--CCCCEEEEcCCCC
Confidence            4444443  3455888888854

>PF13306 LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_A 3V47_B 3V44_A 3ZYN_A 3ZYO_A 3SB4_A

Probab=94.64  E-value=0.055  Score=49.17  Aligned_cols=82  Identities=15%  Similarity=0.206  Sum_probs=35.3

Q ss_pred             hhhcccCcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhcccc
Q 003387          515 KFCGMFKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNK  592 (824)
Q Consensus       515 ~~~~~~~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~  592 (824)
                      ..|..++.|+.+.+.. .+..++.. +..+.+|+.+.+..+ +..++...|..+.+|+.+.+.. .+..++.. +..+++
T Consensus         6 ~~F~~~~~l~~i~~~~-~~~~I~~~~F~~~~~l~~i~~~~~-~~~i~~~~F~~~~~l~~i~~~~-~~~~i~~~~F~~~~~   82 (129)
T PF13306_consen    6 NAFYNCSNLESITFPN-TIKKIGENAFSNCTSLKSINFPNN-LTSIGDNAFSNCKSLESITFPN-NLKSIGDNAFSNCTN   82 (129)
T ss_dssp             TTTTT-TT--EEEETS-T--EE-TTTTTT-TT-SEEEESST-TSCE-TTTTTT-TT-EEEEETS-TT-EE-TTTTTT-TT
T ss_pred             HHHhCCCCCCEEEECC-CeeEeChhhccccccccccccccc-ccccceeeeecccccccccccc-ccccccccccccccc
Confidence            4555566666666653 34444332 444556666666553 5555555555565666666643 34444332 344556


Q ss_pred             CceecCC
Q 003387          593 LRHLNFG  599 (824)
Q Consensus       593 L~~L~L~  599 (824)
                      |+.+++.
T Consensus        83 l~~i~~~   89 (129)
T PF13306_consen   83 LKNIDIP   89 (129)
T ss_dssp             ECEEEET
T ss_pred             ccccccC
Confidence            6666543

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=94.62  E-value=0.28  Score=52.76  Aligned_cols=44  Identities=11%  Similarity=-0.072  Sum_probs=32.4

Q ss_pred             Ccee-chhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          157 DTVG-LDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       157 ~~vG-r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++| -+.-++.+.+.+..+. -....-++|+.|+||||+|+.+.+
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~~-l~ha~Lf~G~~G~gk~~~a~~la~   50 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKNR-LSHAYLFEGAKGTGKKATALWLAK   50 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            4566 5666777777776543 345678999999999999988755

>PRK14974 cell division protein FtsY; Provisional

Probab=94.60  E-value=0.2  Score=53.44  Aligned_cols=91  Identities=13%  Similarity=0.073  Sum_probs=47.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccC-CCceeEEEECCCCCCCCHH--HHHHHHHHHhCCCCCcccccccCHHHH-
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFDCHAWITEPYSNEYDAD--QILDIVIKFLMPSSRLSEIMDKNYEMK-  253 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~~~vs~~~~~~--~~~~~i~~~l~~~~~~~~~~~~~~~~~-  253 (824)
                      +..+|.++|+.|+||||++..+..  .... .+ .++.+.   ...+...  +-++..+..++...... ....+.... 
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~--~l~~~g~-~V~li~---~Dt~R~~a~eqL~~~a~~lgv~v~~~-~~g~dp~~v~  211 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAY--YLKKNGF-SVVIAA---GDTFRAGAIEQLEEHAERLGVKVIKH-KYGADPAAVA  211 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHH--HHHHcCC-eEEEec---CCcCcHHHHHHHHHHHHHcCCceecc-cCCCCHHHHH
Confidence            478999999999999998877776  3332 23 344454   3333332  33455566655321100 111222222 


Q ss_pred             HHHHHHhc-CCCeEEEEEecCCCh
Q 003387          254 KIILHEYL-MTKRYLIVIDDVWSI  276 (824)
Q Consensus       254 ~~~l~~~L-~~kr~LlVlDdv~~~  276 (824)
                      .+.+...- .+.. +|++|-.-..
T Consensus       212 ~~ai~~~~~~~~D-vVLIDTaGr~  234 (336)
T PRK14974        212 YDAIEHAKARGID-VVLIDTAGRM  234 (336)
T ss_pred             HHHHHHHHhCCCC-EEEEECCCcc
Confidence            23333222 2333 8888988543

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=94.59  E-value=0.081  Score=57.31  Aligned_cols=77  Identities=12%  Similarity=0.156  Sum_probs=49.8

Q ss_pred             CCceechhhHHHHHHHHHcC------------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC---ceeEEEECCCC
Q 003387          156 RDTVGLDDRMEELLDLLIEG------------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF---DCHAWITEPYS  220 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~~~vs  220 (824)
                      ..++|.++.++.+.-.+...            +...+-|-++|++|+||||+|+.+..  .....|   +..-++.  ..
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~--~l~~~fi~vdat~~~e--~g   87 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAK--LANAPFIKVEATKFTE--VG   87 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHH--HhCCeEEEeecceeec--CC
Confidence            56888888888876655531            11246788999999999999999988  555444   2222222  11


Q ss_pred             -CCCCHHHHHHHHHHHh
Q 003387          221 -NEYDADQILDIVIKFL  236 (824)
Q Consensus       221 -~~~~~~~~~~~i~~~l  236 (824)
                       ...+..++++.+....
T Consensus        88 ~vG~dvE~i~r~l~e~A  104 (441)
T TIGR00390        88 YVGRDVESMVRDLTDAA  104 (441)
T ss_pred             cccCCHHHHHHHHHHHH
Confidence             1235667666665554

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK09099 type III secretion system ATPase; Provisional

Probab=94.58  E-value=0.095  Score=57.81  Aligned_cols=94  Identities=12%  Similarity=0.126  Sum_probs=51.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCC--------CcccccccC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSS--------RLSEIMDKN  249 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~--------~~~~~~~~~  249 (824)
                      .-..++|.|..|+|||||++.+.......   ..+++..  -.+.-.+.++.+.+...-....        +.+.....-
T Consensus       162 ~Gq~~~I~G~sG~GKTtLl~~ia~~~~~d---~~vi~~i--Ger~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~  236 (441)
T PRK09099        162 EGQRMGIFAPAGVGKSTLMGMFARGTQCD---VNVIALI--GERGREVREFIELILGEDGMARSVVVCATSDRSSIERAK  236 (441)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCCC---eEEEEEE--ccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHH
Confidence            35689999999999999999998743221   2344443  2222334444444443321110        101011111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      ....+..+.+++  ++|.+|+++||+-..
T Consensus       237 a~~~a~tiAEyfrd~G~~VLl~~DslTr~  265 (441)
T PRK09099        237 AAYVATAIAEYFRDRGLRVLLMMDSLTRF  265 (441)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhHH
Confidence            122233445555  579999999999654

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=94.58  E-value=0.043  Score=49.81  Aligned_cols=40  Identities=15%  Similarity=0.160  Sum_probs=29.8

Q ss_pred             hhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          163 DRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       163 ~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ++.+++-+.|...-..-.+|.+.|.-|.||||+++.+.+.
T Consensus         6 ~~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~   45 (133)
T TIGR00150         6 KAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQG   45 (133)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            4455555655543223458999999999999999999984

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.

>PRK05922 type III secretion system ATPase; Validated

Probab=94.58  E-value=0.16  Score=55.86  Aligned_cols=99  Identities=10%  Similarity=0.118  Sum_probs=53.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC-CCHHHHHHHHHHHhCCCCCc--------ccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE-YDADQILDIVIKFLMPSSRL--------SEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~-~~~~~~~~~i~~~l~~~~~~--------~~~~~~~  249 (824)
                      -..++|+|..|+|||||.+.+.+..  .  -+..+.+-  +.+. -.+.+.+.+...........        +.....-
T Consensus       157 GqrigI~G~nG~GKSTLL~~Ia~~~--~--~d~gvi~l--iGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~  230 (434)
T PRK05922        157 GQRIGVFSEPGSGKSSLLSTIAKGS--K--STINVIAL--IGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVI  230 (434)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccC--C--CCceEEEE--eCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHH
Confidence            4568999999999999999999832  2  23333332  2222 23344555544333221110        0011111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ....+..+.+++  +++++|+++||+-.. ....++.
T Consensus       231 a~~~a~tiAEyfrd~G~~VLl~~DslTR~A~A~REis  267 (434)
T PRK05922        231 AGRAAMTIAEYFRDQGHRVLFIMDSLSRWIAALQEVA  267 (434)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhHHHHHHHHHH
Confidence            222334455555  589999999999654 2344443

>PF12061 DUF3542: Protein of unknown function (DUF3542); InterPro: IPR021929 R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide

Probab=94.58  E-value=0.065  Score=54.36  Aligned_cols=76  Identities=21%  Similarity=0.261  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHhhcccccccchhchHHHHHHHHHHHHHHHHHccccchhhHHHhhhcccc-ccCChhHHHHHHHHHHHhhh
Q 003387            5 FRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEE-ESHDPDLATVMDEINWFTYE   83 (824)
Q Consensus         5 ~~~~~~kl~~~~~~~~~~~~~~~~~~~~~l~~~l~~i~~~l~~~~~~~~~~~~~~~a~~-~~~~~~~~~wl~~l~~~~~~   83 (824)
                      +..++..|-.... +....+.-++.+++-++.+++.+|.||+++            ++. ...-...+....++...||+
T Consensus       298 VdFlL~NLkdfq~-rysdSlaflKnQiqvIQ~elesLqpFLk~V------------~ee~~nkh~~~ed~a~~ii~kAye  364 (402)
T PF12061_consen  298 VDFLLKNLKDFQG-RYSDSLAFLKNQIQVIQTELESLQPFLKHV------------VEEPHNKHDTNEDCATQIIRKAYE  364 (402)
T ss_pred             HHHHHhhHHHHhc-cccchHHHHHHHHHHHHHHHHHhhHHHHHH------------HhccchhhhhhhhHHHHHHHHHhh
Confidence            5677888888877 788888889999999999999999999993            555 33233489999999999999


Q ss_pred             hHHHHHHhHH
Q 003387           84 SEKVIDTFIN   93 (824)
Q Consensus        84 ~ed~ld~~~~   93 (824)
                      +|.++|-+-.
T Consensus       365 vEYVVDaCi~  374 (402)
T PF12061_consen  365 VEYVVDACIS  374 (402)
T ss_pred             eeeeeehhhc
Confidence            9999998743

The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain []. Most proteins matching this entry are found associated with PF00931 from PFAM.

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=94.57  E-value=0.078  Score=58.20  Aligned_cols=93  Identities=13%  Similarity=0.091  Sum_probs=49.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCC--------CcccccccCH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSS--------RLSEIMDKNY  250 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~--------~~~~~~~~~~  250 (824)
                      -..++|+|..|+|||||++.+.+.  .+. ...++...  --+.-.+.++.++.+..-+...        +.+.....-.
T Consensus       140 Gq~i~I~G~sG~GKTtLl~~I~~~--~~~-~~gvi~~i--Ger~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a  214 (418)
T TIGR03498       140 GQRLGIFAGSGVGKSTLLSMLARN--TDA-DVVVIALV--GERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQA  214 (418)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCC--CCC-CEEEEEEE--eeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHH
Confidence            468999999999999999999983  222 22233222  1222234444444433221111        1000111111


Q ss_pred             HHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          251 EMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       251 ~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      ...+..+.+++  +++.+||++||+-..
T Consensus       215 ~~~a~~iAEyfrd~G~~Vll~~DslTr~  242 (418)
T TIGR03498       215 AYTATAIAEYFRDQGKDVLLLMDSVTRF  242 (418)
T ss_pred             HHHHHHHHHHHHHcCCCEEEeccchhHH
Confidence            22233455555  579999999999654

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.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=94.56  E-value=0.083  Score=58.35  Aligned_cols=102  Identities=10%  Similarity=0.129  Sum_probs=58.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCC--------CCcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPS--------SRLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~--------~~~~~~~~~~  249 (824)
                      -.-++|.|..|+|||||+..+..+.... +=+.++++-  +.+.. .+.++.+++...=...        .+.+......
T Consensus       144 GQR~gIfa~~GvGKt~Ll~~i~~~~~~~-~~~v~V~~l--iGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~  220 (463)
T PRK09280        144 GGKIGLFGGAGVGKTVLIQELINNIAKE-HGGYSVFAG--VGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLR  220 (463)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHhc-CCCEEEEEE--eccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            4578999999999999999876532111 113566666  65543 3445666655432111        1111111111


Q ss_pred             HHHHHHHHHHhc---CCCeEEEEEecCCCh-hhHHHHH
Q 003387          250 YEMKKIILHEYL---MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       250 ~~~~~~~l~~~L---~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ....+..+.+++   ++|.+||++||+-.- ..+.++.
T Consensus       221 a~~~a~tiAEyfrd~~G~~VLll~DslTR~A~A~REis  258 (463)
T PRK09280        221 VALTGLTMAEYFRDVEGQDVLLFIDNIFRFTQAGSEVS  258 (463)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEecchHHHHHHHHHHH
Confidence            223344566666   679999999999653 3344444

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=94.55  E-value=0.2  Score=49.45  Aligned_cols=114  Identities=18%  Similarity=0.196  Sum_probs=71.4

Q ss_pred             CCCCceechhhHHHHHHHHH---cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHH
Q 003387          154 KSRDTVGLDDRMEELLDLLI---EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILD  230 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~---~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~  230 (824)
                      +-..++|.|..++.+++=-.   .+. ...-|-.||.-|.||+.|++++.+  ++....-.-+  .  |++.        
T Consensus        58 ~L~~l~Gvd~qk~~L~~NT~~F~~G~-pANnVLLwGaRGtGKSSLVKA~~~--e~~~~glrLV--E--V~k~--------  122 (287)
T COG2607          58 DLADLVGVDRQKEALVRNTEQFAEGL-PANNVLLWGARGTGKSSLVKALLN--EYADEGLRLV--E--VDKE--------  122 (287)
T ss_pred             CHHHHhCchHHHHHHHHHHHHHHcCC-cccceEEecCCCCChHHHHHHHHH--HHHhcCCeEE--E--EcHH--------
Confidence            34578999999988876332   232 345678999999999999999999  5555544433  2  3221        


Q ss_pred             HHHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCCh---hhHHHHHhhCCCC---CCCcEEEEEech
Q 003387          231 IVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSI---DMWDVIQEILPDN---QNGSRVLITLTD  301 (824)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~---~~~~~l~~~~~~~---~~gs~ilvTtR~  301 (824)
                                        +... ...|.+.|+  .+||.|..||..-+   +.+..+...+..+   .+...++..|.+
T Consensus       123 ------------------dl~~-Lp~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSN  182 (287)
T COG2607         123 ------------------DLAT-LPDLVELLRARPEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSN  182 (287)
T ss_pred             ------------------HHhh-HHHHHHHHhcCCceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecC
Confidence                              1111 123333443  48999999999633   4677777777643   233444444443

>TIGR00959 ffh signal recognition particle protein

Probab=94.52  E-value=0.29  Score=54.09  Aligned_cols=91  Identities=13%  Similarity=0.072  Sum_probs=47.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccC-CCceeEEEECCCCCCCCH--HHHHHHHHHHhCCCCCcccccccCHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFDCHAWITEPYSNEYDA--DQILDIVIKFLMPSSRLSEIMDKNYEMKK  254 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~~~vs~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~~~  254 (824)
                      ...++.++|..|+||||.|..+..  .... .-..++-|+  .. .+..  .+-++...++++..... .....+.....
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~--~l~~~~g~kV~lV~--~D-~~R~~a~~QL~~~a~~~gvp~~~-~~~~~~P~~i~  171 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAY--YLKKKQGKKVLLVA--CD-LYRPAAIEQLKVLGQQVGVPVFA-LGKGQSPVEIA  171 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH--HHHHhCCCeEEEEe--cc-ccchHHHHHHHHHHHhcCCceEe-cCCCCCHHHHH
Confidence            368999999999999999888776  3221 112344444  21 2222  23344444544432110 01122344444


Q ss_pred             HHHHHhcCCCeE-EEEEecCC
Q 003387          255 IILHEYLMTKRY-LIVIDDVW  274 (824)
Q Consensus       255 ~~l~~~L~~kr~-LlVlDdv~  274 (824)
                      ....+....+.| +||+|-.-
T Consensus       172 ~~al~~~~~~~~DvVIIDTaG  192 (428)
T TIGR00959       172 RRALEYAKENGFDVVIVDTAG  192 (428)
T ss_pred             HHHHHHHHhcCCCEEEEeCCC
Confidence            444444444445 77777765

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.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=94.51  E-value=0.16  Score=51.88  Aligned_cols=125  Identities=17%  Similarity=0.238  Sum_probs=73.4

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEE-EECCCCCCCCHHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAW-ITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~w-v~~~vs~~~~~~~~~~~i~~  234 (824)
                      ++++|-+..+.-+.+.+...  ...+.-.+|++|-|||+-|.++...---.+.|.+++. .+  +|..-.+. +    .+
T Consensus        36 de~~gQe~vV~~L~~a~~~~--~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~ln--aSderGis-v----vr  106 (346)
T KOG0989|consen   36 DELAGQEHVVQVLKNALLRR--ILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELN--ASDERGIS-V----VR  106 (346)
T ss_pred             HhhcchHHHHHHHHHHHhhc--CCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhc--cccccccc-c----hh
Confidence            57889999999999888873  4778889999999999999887763212355655442 22  44332211 0    00


Q ss_pred             HhCCCCCcccccccCHHHHHHHHHHhc--CCCe-EEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEe
Q 003387          235 FLMPSSRLSEIMDKNYEMKKIILHEYL--MTKR-YLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITL  299 (824)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~~~~~l~~~L--~~kr-~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTt  299 (824)
                      .          ...+.+.+.....+..  ..++ =.+|||+++..  +.|..+..-..+....+|.+..+
T Consensus       107 ~----------Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIc  166 (346)
T KOG0989|consen  107 E----------KIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILIC  166 (346)
T ss_pred             h----------hhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEc
Confidence            0          0111111111111111  0134 36788999875  67999988777655555544433

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=94.49  E-value=0.047  Score=53.62  Aligned_cols=43  Identities=14%  Similarity=0.018  Sum_probs=27.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHH
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDAD  226 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~  226 (824)
                      .|+|+|-||+||||+|..+... -..++=..+.=|+  ...+++..
T Consensus         2 kIaI~GKGG~GKTtiaalll~~-l~~~~~~~VLvVD--aDpd~nL~   44 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKR-LLSKGGYNVLVVD--ADPDSNLP   44 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHHH-HHhcCCceEEEEe--CCCCCChH
Confidence            6899999999999999884441 2222212344455  55555543

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=94.49  E-value=0.37  Score=54.83  Aligned_cols=134  Identities=15%  Similarity=0.074  Sum_probs=85.1

Q ss_pred             CCceechhhHHHHHHHHHc---CCCCeEEEEEEcCCCChHHHHHHHHhCCc------cccCCCceeEEEECCCCCCCCHH
Q 003387          156 RDTVGLDDRMEELLDLLIE---GPPQLSVVAILDSIGLDKTAFAGEAYNSS------YVKHYFDCHAWITEPYSNEYDAD  226 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~---~~~~~~vi~I~G~gGvGKTtLa~~v~~~~------~~~~~F~~~~wv~~~vs~~~~~~  226 (824)
                      ..+-+|+.+..+|-..+..   .+..-..+-|.|.+|.|||..+..|.+.-      .--..|+ .+.|.  .-.-....
T Consensus       396 ~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~-yveIN--gm~l~~~~  472 (767)
T KOG1514|consen  396 ESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFD-YVEIN--GLRLASPR  472 (767)
T ss_pred             ccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCcc-EEEEc--ceeecCHH
Confidence            4567899999999998865   22345599999999999999999998831      1123343 33343  44445688


Q ss_pred             HHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcC-----CCeEEEEEecCCChhh-HHHHH-hhCCC-CCCCcEEEEE
Q 003387          227 QILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM-----TKRYLIVIDDVWSIDM-WDVIQ-EILPD-NQNGSRVLIT  298 (824)
Q Consensus       227 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~-----~kr~LlVlDdv~~~~~-~~~l~-~~~~~-~~~gs~ilvT  298 (824)
                      ++...|...+.+...       ......+.|..+..     .+..++++|+++..-. =+++. ..|.| ..++||++|-
T Consensus       473 ~~Y~~I~~~lsg~~~-------~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi  545 (767)
T KOG1514|consen  473 EIYEKIWEALSGERV-------TWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVI  545 (767)
T ss_pred             HHHHHHHHhcccCcc-------cHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEE
Confidence            999999999988543       11223333333332     3578888898864311 11222 22333 4568888766


Q ss_pred             e
Q 003387          299 L  299 (824)
Q Consensus       299 t  299 (824)
                      +
T Consensus       546 ~  546 (767)
T KOG1514|consen  546 A  546 (767)
T ss_pred             E
Confidence            4

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=94.46  E-value=0.046  Score=53.40  Aligned_cols=117  Identities=12%  Similarity=0.041  Sum_probs=56.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHh
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  260 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  260 (824)
                      |+.|.|..|.||||+.+.+.-... -.+-.+.+|..  ...-    ....+++..++...... ........-...+...
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~~~~-la~~G~~v~a~--~~~~----~~~d~il~~~~~~d~~~-~~~s~fs~~~~~l~~~   72 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGLIVI-MAQIGSFVPAE--SAEL----PVFDRIFTRIGASDSLA-QGLSTFMVEMKETANI   72 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHH-HHHhCCCeeeh--heEe----cccceEEEEeCCCCchh-ccccHHHHHHHHHHHH
Confidence            467999999999999999884211 11111111111  0000    00011111111111000 0011112222345555


Q ss_pred             cCC--CeEEEEEecCCChhh-------HHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          261 LMT--KRYLIVIDDVWSIDM-------WDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       261 L~~--kr~LlVlDdv~~~~~-------~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      +..  ++-|+++|..-...+       ...+...+.. ..|+.+|++|...++..
T Consensus        73 l~~~~~~~llllDEp~~g~d~~~~~~~~~~~l~~l~~-~~~~~iii~TH~~~l~~  126 (185)
T smart00534       73 LKNATENSLVLLDELGRGTSTYDGVAIAAAVLEYLLE-KIGALTLFATHYHELTK  126 (185)
T ss_pred             HHhCCCCeEEEEecCCCCCCHHHHHHHHHHHHHHHHh-cCCCeEEEEecHHHHHH
Confidence            544  889999999965421       1122222222 23678999999988776

>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=94.45  E-value=0.062  Score=53.45  Aligned_cols=88  Identities=14%  Similarity=0.113  Sum_probs=50.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCC--------CCcccccc---
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPS--------SRLSEIMD---  247 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~--------~~~~~~~~---  247 (824)
                      .-++|.|..|+|||+|++.+.++.  .  =+..+++-  +.+.. .+.++.+++...=...        .+.+....   
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~~--~--~d~~V~~~--iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~   89 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANNQ--D--ADVVVYAL--IGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRA   89 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHC--T--TTEEEEEE--ESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHH
T ss_pred             CEEEEEcCcccccchhhHHHHhcc--c--ccceeeee--ccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhh
Confidence            468999999999999999998842  2  23346666  66543 4445555553321000        00000000   


Q ss_pred             -cCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          248 -KNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       248 -~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                       ...-..++.+++  ++|.+|+++||+-.
T Consensus        90 ~~~a~t~AEyfrd--~G~dVlli~Dsltr  116 (215)
T PF00006_consen   90 PYTALTIAEYFRD--QGKDVLLIIDSLTR  116 (215)
T ss_dssp             HHHHHHHHHHHHH--TTSEEEEEEETHHH
T ss_pred             hccchhhhHHHhh--cCCceeehhhhhHH
Confidence             001122334444  78999999999954

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 ....

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=94.43  E-value=0.16  Score=56.02  Aligned_cols=99  Identities=12%  Similarity=0.102  Sum_probs=54.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC-CCHHHHHHHHHHHhCCCC--------CcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE-YDADQILDIVIKFLMPSS--------RLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~-~~~~~~~~~i~~~l~~~~--------~~~~~~~~~  249 (824)
                      -..++|+|..|+|||||++.+.+..    ..+.++...  +... .++.++...+...-....        +.+.....-
T Consensus       168 GqrigI~G~sG~GKSTLl~~I~g~~----~~dv~V~g~--Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~  241 (451)
T PRK05688        168 GQRLGLFAGTGVGKSVLLGMMTRFT----EADIIVVGL--IGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLR  241 (451)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC----CCCEEEEEE--eCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHH
Confidence            4579999999999999999998732    123434433  3332 244455555544322211        100011111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ....+..+.+++  +++++||++||+-.. ....++.
T Consensus       242 a~~~a~aiAEyfrd~G~~VLl~~DslTR~A~A~REis  278 (451)
T PRK05688        242 AAMYCTRIAEYFRDKGKNVLLLMDSLTRFAQAQREIA  278 (451)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEecchhHHHHHHHHHH
Confidence            122233444444  589999999999654 3344444

>PRK03839 putative kinase; Provisional

Probab=94.41  E-value=0.025  Score=55.02  Aligned_cols=21  Identities=24%  Similarity=0.317  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.|+|++|+||||+|+.+.+
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~   22 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAE   22 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999998

>PRK12678 transcription termination factor Rho; Provisional

Probab=94.41  E-value=0.063  Score=59.95  Aligned_cols=103  Identities=12%  Similarity=0.090  Sum_probs=55.7

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC-CCceeEEEECCCCCCCCHHHHHHHHHHHhCC-----CC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFDCHAWITEPYSNEYDADQILDIVIKFLMP-----SS  240 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~-----~~  240 (824)
                      +++++|..-. .-.-.+|+|..|+|||||++.|.|  .+.. +=++.++|. .|.+.+..-   .+|-+.+..     ..
T Consensus       405 RvIDll~PIG-kGQR~LIvgpp~aGKTtLL~~IAn--~i~~n~~~~~~ivv-LIgERpeEV---tdm~rsVkgeVVasT~  477 (672)
T PRK12678        405 RVIDLIMPIG-KGQRGLIVSPPKAGKTTILQNIAN--AITTNNPECHLMVV-LVDERPEEV---TDMQRSVKGEVIASTF  477 (672)
T ss_pred             eeeeeecccc-cCCEeEEeCCCCCCHHHHHHHHHH--HHhhcCCCeEEEEE-EEeCchhhH---HHHHHhccceEEEECC
Confidence            3455444311 234679999999999999999998  4422 223333332 034333222   223333321     11


Q ss_pred             CcccccccCHHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          241 RLSEIMDKNYEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       241 ~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      +.+.....-...+...+.+++  +++.+||++|++-..
T Consensus       478 D~p~~~~~~~a~~ai~~Ae~fre~G~dVlillDSlTR~  515 (672)
T PRK12678        478 DRPPSDHTTVAELAIERAKRLVELGKDVVVLLDSITRL  515 (672)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCchHH
Confidence            111111222344455566666  679999999999644

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=94.38  E-value=0.18  Score=51.39  Aligned_cols=61  Identities=15%  Similarity=0.183  Sum_probs=40.4

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHH
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      +.+-++|..+=..-.++-|.|.+|.|||++|.++... .. ..-+.++||+  ...  +..++.+.+
T Consensus         8 ~~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~-~~-~~ge~~lyvs--~ee--~~~~i~~~~   68 (237)
T TIGR03877         8 PGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWN-GL-QMGEPGIYVA--LEE--HPVQVRRNM   68 (237)
T ss_pred             HhHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHH-HH-HcCCcEEEEE--eeC--CHHHHHHHH
Confidence            3344556556456789999999999999999876441 12 2345678887  544  455555543

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.

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function

Probab=94.37  E-value=0.32  Score=47.99  Aligned_cols=20  Identities=20%  Similarity=0.242  Sum_probs=18.9

Q ss_pred             EEEEEcCCCChHHHHHHHHh
Q 003387          181 VVAILDSIGLDKTAFAGEAY  200 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~  200 (824)
                      +++|+|..|.|||||+++++
T Consensus        24 ~~~i~G~nGsGKStll~al~   43 (197)
T cd03278          24 LTAIVGPNGSGKSNIIDAIR   43 (197)
T ss_pred             cEEEECCCCCCHHHHHHHHH
Confidence            88999999999999999986

Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=94.34  E-value=0.14  Score=52.74  Aligned_cols=21  Identities=19%  Similarity=0.363  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.++|++|+||||+|+.+..
T Consensus         1 LIvl~G~pGSGKST~a~~La~   21 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAK   21 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHH
Confidence            378999999999999999987

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.

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=94.33  E-value=0.026  Score=54.58  Aligned_cols=24  Identities=25%  Similarity=0.271  Sum_probs=22.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..+|+|-||=|+||||||+.+.++
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~   27 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEH   27 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHH
Confidence            578999999999999999999993

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.33  E-value=0.32  Score=45.52  Aligned_cols=22  Identities=9%  Similarity=0.247  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +|.|+|++|+||||+|+.+.+.
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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.32  E-value=0.17  Score=60.96  Aligned_cols=48  Identities=23%  Similarity=0.210  Sum_probs=36.8

Q ss_pred             CCCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.++.|.+..++.|.+.+..           +-...+-|-++|++|.|||++|+++.+
T Consensus       451 ~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~  509 (733)
T TIGR01243       451 RWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVAT  509 (733)
T ss_pred             chhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            345688988888888776642           112345578899999999999999999

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.

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=94.31  E-value=0.068  Score=53.81  Aligned_cols=119  Identities=13%  Similarity=0.093  Sum_probs=58.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  257 (824)
                      +.+++.|.|..|.||||+.+.+.-..-   .+..-++|.  ... . .-.+...++..++..+... ........-...+
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~~~~~---la~~g~~vp--a~~-~-~~~~~~~il~~~~l~d~~~-~~lS~~~~e~~~~  100 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIGVIVL---MAQIGCFVP--CDS-A-DIPIVDCILARVGASDSQL-KGVSTFMAEMLET  100 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHH---HHHhCCCcC--ccc-E-EEeccceeEeeeccccchh-cCcChHHHHHHHH
Confidence            367999999999999999888664210   111112222  111 0 0111222333332221100 0011112222333


Q ss_pred             HHhc--CCCeEEEEEecCC---Chh-----hHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          258 HEYL--MTKRYLIVIDDVW---SID-----MWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       258 ~~~L--~~kr~LlVlDdv~---~~~-----~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      ...+  ...+-|++||..-   +..     .|..+ ..+.. ..|+.+|+||-..++..
T Consensus       101 a~il~~~~~~sLvLLDEp~~gT~~lD~~~~~~~il-~~l~~-~~~~~vlisTH~~el~~  157 (222)
T cd03285         101 AAILKSATENSLIIIDELGRGTSTYDGFGLAWAIA-EYIAT-QIKCFCLFATHFHELTA  157 (222)
T ss_pred             HHHHHhCCCCeEEEEecCcCCCChHHHHHHHHHHH-HHHHh-cCCCeEEEEechHHHHH
Confidence            3334  3578899999993   322     22222 22222 34788999998877665

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

>cd03243 ABC_MutS_homologs 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

Probab=94.28  E-value=0.029  Score=55.77  Aligned_cols=22  Identities=9%  Similarity=-0.067  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|+|..|.||||+.+.+..
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            7999999999999999999984

Members of the MutS family also possess 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 clamps, and recognition of specific DNA stru

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=94.23  E-value=0.45  Score=52.40  Aligned_cols=121  Identities=13%  Similarity=0.111  Sum_probs=66.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCC--------CcccccccCH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSS--------RLSEIMDKNY  250 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~--------~~~~~~~~~~  250 (824)
                      -..++|+|..|+|||||++.+....+  . ...++...  -.+...+.+...+.+..-+...        +.+.....-.
T Consensus       156 Gqri~I~G~sG~GKTtLl~~Ia~~~~--~-~~gvI~~i--Gerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra  230 (432)
T PRK06793        156 GQKIGIFAGSGVGKSTLLGMIAKNAK--A-DINVISLV--GERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRA  230 (432)
T ss_pred             CcEEEEECCCCCChHHHHHHHhccCC--C-CeEEEEeC--CCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHH
Confidence            45889999999999999999988432  1 22333332  2233566666665554422211        1000111112


Q ss_pred             HHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHHhh---CCCCCCCcEEEEEechHHHHh
Q 003387          251 EMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQEI---LPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       251 ~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~~~---~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      ...+..+.+++  ++|.+||++||+-.. +...++...   .|.  .|--..+.|....++.
T Consensus       231 ~~~a~~iAEyfr~~G~~VLlilDslTr~a~A~reisl~~~e~p~--~G~~~~~~s~l~~L~E  290 (432)
T PRK06793        231 AKLATSIAEYFRDQGNNVLLMMDSVTRFADARRSVDIAVKELPI--GGKTLLMESYMKKLLE  290 (432)
T ss_pred             HHHHHHHHHHHHHcCCcEEEEecchHHHHHHHHHHHHHhcCCCC--CCeeeeeeccchhHHH
Confidence            22333444444  479999999999765 334444433   232  2555566555555554

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=94.23  E-value=0.049  Score=57.52  Aligned_cols=49  Identities=12%  Similarity=0.087  Sum_probs=33.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      .+++.+.|.|||||||+|.+..-  ........++-|+  +....+..+++..
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~--~lA~~g~kvLlvS--tDPAhsL~d~f~~   50 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAV--KLAESGKKVLLVS--TDPAHSLGDVFDL   50 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHH--HHHHcCCcEEEEE--eCCCCchHhhhcc
Confidence            57899999999999999988554  3444445566665  5555555554443

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=94.23  E-value=0.035  Score=54.43  Aligned_cols=24  Identities=13%  Similarity=0.173  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +..+|.|+|++|+||||+|+.+..
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999986

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.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=94.21  E-value=0.055  Score=53.61  Aligned_cols=120  Identities=12%  Similarity=0.018  Sum_probs=59.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      .+++.|.|..|.||||+.+.+....-..   ..-++|.  ... ... .+.+.|...++..+.... .......-..++.
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~~~la---~~G~~vp--a~~-~~l-~~~d~I~~~~~~~d~~~~-~~S~fs~e~~~~~  100 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALLAIMA---QIGCFVP--AEY-ATL-PIFNRLLSRLSNDDSMER-NLSTFASEMSETA  100 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHH---HcCCCcc--hhh-cCc-cChhheeEecCCccccch-hhhHHHHHHHHHH
Confidence            4789999999999999999886531111   1112222  110 111 223333333333211000 0000001111122


Q ss_pred             Hhc--CCCeEEEEEecCCCh---hh----HHHHHhhCCCCCCCcEEEEEechHHHHhhc
Q 003387          259 EYL--MTKRYLIVIDDVWSI---DM----WDVIQEILPDNQNGSRVLITLTDIRIIISF  308 (824)
Q Consensus       259 ~~L--~~kr~LlVlDdv~~~---~~----~~~l~~~~~~~~~gs~ilvTtR~~~v~~~f  308 (824)
                      ..+  ..++-|+++|.....   .+    ...+...+..  .|+.+|+||-..+++..+
T Consensus       101 ~il~~~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~~--~~~~~i~~TH~~~l~~~~  157 (204)
T cd03282         101 YILDYADGDSLVLIDELGRGTSSADGFAISLAILECLIK--KESTVFFATHFRDIAAIL  157 (204)
T ss_pred             HHHHhcCCCcEEEeccccCCCCHHHHHHHHHHHHHHHHh--cCCEEEEECChHHHHHHh
Confidence            222  356789999998543   22    1122222322  278999999999888744

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

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=94.20  E-value=0.12  Score=56.83  Aligned_cols=100  Identities=16%  Similarity=0.155  Sum_probs=53.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCC--------CCccccccc
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPS--------SRLSEIMDK  248 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~--------~~~~~~~~~  248 (824)
                      .-..++|+|..|+|||||++.+.+.  ...  +..+..-  +.+.. .+.++..+.+.+-+..        .+.+.....
T Consensus       136 ~Gqri~I~G~sG~GKTtLl~~i~~~--~~~--~~gvi~~--~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~  209 (413)
T TIGR03497       136 KGQRVGIFAGSGVGKSTLLGMIARN--AKA--DINVIAL--IGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRL  209 (413)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC--CCC--CeEEEEE--EccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHH
Confidence            3568999999999999999999883  222  2222222  33322 3344444433321111        111111111


Q ss_pred             CHHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          249 NYEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       249 ~~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      -....+..+.+++  +++.+|+++||+-.. ..+.++.
T Consensus       210 ~~~~~a~tiAEyfr~~G~~Vll~~Dsltr~A~A~rEis  247 (413)
T TIGR03497       210 KAAFTATAIAEYFRDQGKDVLLMMDSVTRFAMAQREIG  247 (413)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEcCcHHHHHHHHHHH
Confidence            1222334455555  579999999999654 2344443

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.

>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=94.20  E-value=0.025  Score=50.41  Aligned_cols=28  Identities=21%  Similarity=0.169  Sum_probs=19.9

Q ss_pred             EEEEcCCCChHHHHHHHHhCCccccCCCce
Q 003387          182 VAILDSIGLDKTAFAGEAYNSSYVKHYFDC  211 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~~~~~~~F~~  211 (824)
                      |-|+|.+|+||||+|+.+..  .+...|..
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            56899999999999999999  67777754

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=94.19  E-value=0.21  Score=54.43  Aligned_cols=23  Identities=22%  Similarity=0.153  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++.|+|.+|+||||++.++..
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~  245 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAA  245 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999876

>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=94.18  E-value=0.027  Score=54.01  Aligned_cols=36  Identities=17%  Similarity=-0.000  Sum_probs=28.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcccc-CCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVK-HYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~  216 (824)
                      ..++-++|+.|+|||.||+.+.+  .+. +.....+-++
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~--~l~~~~~~~~~~~d   39 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAE--LLFVGSERPLIRID   39 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHH--HHT-SSCCEEEEEE
T ss_pred             EEEEEEECCCCCCHHHHHHHHHH--HhccCCccchHHHh
Confidence            56788999999999999999988  454 4455555565

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 ....

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=94.18  E-value=0.49  Score=47.15  Aligned_cols=23  Identities=13%  Similarity=0.213  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        34 G~~~~i~G~nGsGKSTLl~~l~G   56 (207)
T cd03369          34 GEKIGIVGRTGAGKSTLILALFR   56 (207)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999976

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>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=94.18  E-value=0.097  Score=54.40  Aligned_cols=90  Identities=21%  Similarity=0.190  Sum_probs=49.3

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCccc
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSE  244 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~  244 (824)
                      ...+++.+....   +-+-++|+.|+|||++++...+.- -...| ...-+.  .|..-....+++.|-..+...... .
T Consensus        22 ~~~ll~~l~~~~---~pvLl~G~~GtGKT~li~~~l~~l-~~~~~-~~~~~~--~s~~Tts~~~q~~ie~~l~k~~~~-~   93 (272)
T PF12775_consen   22 YSYLLDLLLSNG---RPVLLVGPSGTGKTSLIQNFLSSL-DSDKY-LVITIN--FSAQTTSNQLQKIIESKLEKRRGR-V   93 (272)
T ss_dssp             HHHHHHHHHHCT---EEEEEESSTTSSHHHHHHHHHHCS-TTCCE-EEEEEE--S-TTHHHHHHHHCCCTTECECTTE-E
T ss_pred             HHHHHHHHHHcC---CcEEEECCCCCchhHHHHhhhccC-Ccccc-ceeEee--ccCCCCHHHHHHHHhhcEEcCCCC-C
Confidence            455667666653   456899999999999999988631 11122 233455  555544444443222222111110 0


Q ss_pred             ccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          245 IMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       245 ~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      ..             --.+|+.++.+||+--
T Consensus        94 ~g-------------P~~~k~lv~fiDDlN~  111 (272)
T PF12775_consen   94 YG-------------PPGGKKLVLFIDDLNM  111 (272)
T ss_dssp             EE-------------EESSSEEEEEEETTT-
T ss_pred             CC-------------CCCCcEEEEEecccCC
Confidence            00             0136899999999963

>PRK00625 shikimate kinase; Provisional

Probab=94.18  E-value=0.03  Score=53.82  Aligned_cols=21  Identities=14%  Similarity=0.120  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.++||.|+||||+++.+.+
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~   22 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAK   22 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999987

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=94.16  E-value=0.027  Score=55.84  Aligned_cols=21  Identities=29%  Similarity=0.379  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +|+|.|..|+||||+|+.+.+
T Consensus         1 iigi~G~~GsGKSTl~~~l~~   21 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIE   21 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999877

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=94.16  E-value=0.049  Score=60.20  Aligned_cols=42  Identities=17%  Similarity=0.135  Sum_probs=36.9

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|+++.++.+...+..+.    -|-|.|.+|+|||++|+.+..
T Consensus        20 ~~i~gre~vI~lll~aalag~----hVLL~GpPGTGKT~LAraLa~   61 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKF   61 (498)
T ss_pred             hhccCcHHHHHHHHHHHccCC----CEEEECCCChhHHHHHHHHHH
Confidence            568899999999988887654    578999999999999999988

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=94.16  E-value=0.13  Score=56.43  Aligned_cols=104  Identities=13%  Similarity=0.119  Sum_probs=61.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccC--CCc---------eeEEEECCCCCCCCHHHHHHHHHHHhC-CCC------
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKH--YFD---------CHAWITEPYSNEYDADQILDIVIKFLM-PSS------  240 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~--~F~---------~~~wv~~~vs~~~~~~~~~~~i~~~l~-~~~------  240 (824)
                      -.-++|.|-.|+|||||+..+.+..+...  ..|         .++++-  +.+.....+.+.+.+..-+ ...      
T Consensus       141 GQRigIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~--IGerre~~efi~~~l~~~g~l~rtvvv~a  218 (466)
T TIGR01040       141 GQKIPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAA--MGVNMETARFFKQDFEENGSMERVCLFLN  218 (466)
T ss_pred             CCeeeeecCCCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEE--eeeehHHHHHHHHHHHhcCCcceEEEEEE
Confidence            45789999999999999999987543100  022         556666  7777565565555555544 111      


Q ss_pred             --CcccccccCHHHHHHHHHHhcC---CCeEEEEEecCCCh-hhHHHHHh
Q 003387          241 --RLSEIMDKNYEMKKIILHEYLM---TKRYLIVIDDVWSI-DMWDVIQE  284 (824)
Q Consensus       241 --~~~~~~~~~~~~~~~~l~~~L~---~kr~LlVlDdv~~~-~~~~~l~~  284 (824)
                        +.+.....-....+..+.++++   ++.+|+++||+-.. ..+.++..
T Consensus       219 tsd~p~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslTr~A~A~REisl  268 (466)
T TIGR01040       219 LANDPTIERIITPRLALTTAEYLAYQCEKHVLVILTDMSSYADALREVSA  268 (466)
T ss_pred             CCCCCHHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChHHHHHHHHHHHH
Confidence              1111111112223344566655   59999999999654 34444443

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=94.14  E-value=0.095  Score=56.84  Aligned_cols=78  Identities=14%  Similarity=0.206  Sum_probs=51.0

Q ss_pred             CCCceechhhHHHHHHHHHcC------------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC---ceeEEEECCC
Q 003387          155 SRDTVGLDDRMEELLDLLIEG------------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF---DCHAWITEPY  219 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~~~v  219 (824)
                      ...++|.+..++.+..++...            +...+.|-++|+.|+||||+|+.+..  .....|   +..-|..  .
T Consensus        14 d~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk--~l~~~fi~vD~t~f~e--~   89 (443)
T PRK05201         14 DKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAK--LANAPFIKVEATKFTE--V   89 (443)
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHH--HhCChheeecchhhcc--C
Confidence            356889999999988777541            11246789999999999999999988  444444   2222222  1


Q ss_pred             C-CCCCHHHHHHHHHHHh
Q 003387          220 S-NEYDADQILDIVIKFL  236 (824)
Q Consensus       220 s-~~~~~~~~~~~i~~~l  236 (824)
                      . ...+...+.+++....
T Consensus        90 GyvG~d~e~~ir~L~~~A  107 (443)
T PRK05201         90 GYVGRDVESIIRDLVEIA  107 (443)
T ss_pred             CcccCCHHHHHHHHHHHH
Confidence            1 1235666666666555

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=94.14  E-value=0.22  Score=49.04  Aligned_cols=24  Identities=17%  Similarity=0.201  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        35 Ge~~~l~G~nGsGKStLl~~i~Gl   58 (194)
T cd03213          35 GELTAIMGPSGAGKSTLLNALAGR   58 (194)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999873

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.

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=94.13  E-value=0.41  Score=47.69  Aligned_cols=95  Identities=19%  Similarity=0.137  Sum_probs=59.3

Q ss_pred             CCCCCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN  221 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~  221 (824)
                      +..+++-|-.+.++++-+.....           -+..+=|-.+|++|.|||-+|++|.|  +....|     +.  |-.
T Consensus       174 vty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravan--rtdacf-----ir--vig  244 (435)
T KOG0729|consen  174 VTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVAN--RTDACF-----IR--VIG  244 (435)
T ss_pred             cccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhc--ccCceE-----Ee--ehh
Confidence            44456777777777776655432           13466788999999999999999999  666554     33  211


Q ss_pred             CCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCC-CeEEEEEecCC
Q 003387          222 EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMT-KRYLIVIDDVW  274 (824)
Q Consensus       222 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~  274 (824)
                              .++....-+          ....+..+|.+.-+. |-++|.+|.++
T Consensus       245 --------selvqkyvg----------egarmvrelf~martkkaciiffdeid  280 (435)
T KOG0729|consen  245 --------SELVQKYVG----------EGARMVRELFEMARTKKACIIFFDEID  280 (435)
T ss_pred             --------HHHHHHHhh----------hhHHHHHHHHHHhcccceEEEEeeccc
Confidence                    112211111          113445566666665 56788888885

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=94.13  E-value=0.19  Score=55.69  Aligned_cols=93  Identities=12%  Similarity=0.080  Sum_probs=49.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC--------CCCcccccccC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP--------SSRLSEIMDKN  249 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~--------~~~~~~~~~~~  249 (824)
                      .-.+++|+|..|+|||||++.+.+.  ... -..++++.  --+.-++.++..+.+..-..        ..+.+.....-
T Consensus       157 ~Gq~i~I~G~sG~GKStLl~~I~~~--~~~-~~gvI~~~--Gerg~ev~e~~~~~l~~~~l~r~v~vv~~~~~~~~~r~~  231 (438)
T PRK07721        157 KGQRVGIFAGSGVGKSTLMGMIARN--TSA-DLNVIALI--GERGREVREFIERDLGPEGLKRSIVVVATSDQPALMRIK  231 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcc--cCC-CeEEEEEE--ecCCccHHHHHHhhcChhhhcCeEEEEECCCCCHHHHHH
Confidence            3578999999999999999999883  222 12344443  11222344443332211100        11111111111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCC
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWS  275 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~  275 (824)
                      ....+..+.+++  +++.+||++||+-.
T Consensus       232 ~~~~a~~iAEyfr~~g~~Vll~~Dsltr  259 (438)
T PRK07721        232 GAYTATAIAEYFRDQGLNVMLMMDSVTR  259 (438)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeChHH
Confidence            223334455555  57999999999964

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=94.11  E-value=0.21  Score=49.52  Aligned_cols=24  Identities=21%  Similarity=0.213  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||.+.+...
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          26 GEVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999884

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>PLN02318 phosphoribulokinase/uridine kinase

Probab=94.10  E-value=0.061  Score=60.59  Aligned_cols=34  Identities=24%  Similarity=0.334  Sum_probs=28.0

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+.+....+++.+|+|.|..|.||||||+.+..
T Consensus        54 a~qlL~~~~~~riIIGIaGpSGSGKTTLAk~Lag   87 (656)
T PLN02318         54 ACQLLAQKNDGIILVGVAGPSGAGKTVFTEKVLN   87 (656)
T ss_pred             HHHHHHhcCCCeEEEEEECCCCCcHHHHHHHHHh
Confidence            3444554555789999999999999999999987

>PTZ00185 ATPase alpha subunit; Provisional

Probab=94.09  E-value=0.28  Score=54.44  Aligned_cols=96  Identities=11%  Similarity=0.084  Sum_probs=52.5

Q ss_pred             eEEEEEEcCCCChHHHHH-HHHhCCcccc-----CCCceeEEEECCCCCCCCHHHHHHHHHHHhCC-CCCcc--cccccC
Q 003387          179 LSVVAILDSIGLDKTAFA-GEAYNSSYVK-----HYFDCHAWITEPYSNEYDADQILDIVIKFLMP-SSRLS--EIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa-~~v~~~~~~~-----~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~-~~~~~--~~~~~~  249 (824)
                      -.-++|.|-.|+|||||| -.|.|...+.     +.-+.++++-  +.+..+.-.-+.+.++.-+. ....-  ...+..
T Consensus       189 GQR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~Vyva--IGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep  266 (574)
T PTZ00185        189 GQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVS--IGQRCSNVARIHRLLRSYGALRYTTVMAATAAEP  266 (574)
T ss_pred             CCEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEE--eccchHHHHHHHHHHHhcCCccceEEEEECCCCC
Confidence            357899999999999997 6666643221     2335677777  77765433323333333331 10000  000111


Q ss_pred             H------HHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          250 Y------EMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       250 ~------~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      .      .-....+.+++  +++.+|||+||+-..
T Consensus       267 ~~~r~~Apy~a~tiAEYFrd~GkdVLiv~DDLTr~  301 (574)
T PTZ00185        267 AGLQYLAPYSGVTMGEYFMNRGRHCLCVYDDLSKQ  301 (574)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCEEEEEcCchHH
Confidence            1      11122333444  579999999999754

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.07  E-value=0.3  Score=49.54  Aligned_cols=48  Identities=27%  Similarity=0.135  Sum_probs=33.5

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .+-++|..+=..-.++.|.|.+|.||||+|..+...  ....-+.++|++
T Consensus         8 ~LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~--~~~~g~~~~~is   55 (229)
T TIGR03881         8 GLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYK--GLRDGDPVIYVT   55 (229)
T ss_pred             hHHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHH--HHhcCCeEEEEE
Confidence            444455455445689999999999999999886542  222335678887

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.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.07  E-value=0.47  Score=52.14  Aligned_cols=23  Identities=22%  Similarity=0.254  Sum_probs=20.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+++|..|+||||++..+..
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~  213 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAA  213 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999987765

>PRK05439 pantothenate kinase; Provisional

Probab=94.04  E-value=0.22  Score=52.47  Aligned_cols=82  Identities=12%  Similarity=0.061  Sum_probs=44.7

Q ss_pred             CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC--ceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHH
Q 003387          176 PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF--DCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMK  253 (824)
Q Consensus       176 ~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~  253 (824)
                      ....-+|||.|.+|+||||+|+.+..  ......  ..+.-++  ...-+...+.+..  ..+....+.|  +.-|.+.+
T Consensus        83 ~~~~~iIgIaG~~gsGKSTla~~L~~--~l~~~~~~~~v~vi~--~DdFy~~~~~l~~--~~l~~~kg~P--es~D~~~l  154 (311)
T PRK05439         83 QKVPFIIGIAGSVAVGKSTTARLLQA--LLSRWPEHPKVELVT--TDGFLYPNAVLEE--RGLMKRKGFP--ESYDMRAL  154 (311)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHH--HHHhhCCCCceEEEe--ccccccCHHHHhh--hhccccCCCc--ccccHHHH
Confidence            34578999999999999999998877  443321  2233444  3333333332221  1111111111  33455666


Q ss_pred             HHHHHHhcCCCe
Q 003387          254 KIILHEYLMTKR  265 (824)
Q Consensus       254 ~~~l~~~L~~kr  265 (824)
                      ...|.....++.
T Consensus       155 ~~~L~~Lk~G~~  166 (311)
T PRK05439        155 LRFLSDVKSGKP  166 (311)
T ss_pred             HHHHHHHHcCCC
Confidence            666666655554

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=94.02  E-value=0.055  Score=63.10  Aligned_cols=103  Identities=12%  Similarity=0.181  Sum_probs=60.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHH-HHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQI-LDIVI  233 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~-~~~i~  233 (824)
                      -++++||+++++++++.|.....+-.  ..+|-+|||||++|.-+..  ++...         +|+......++ --+|.
T Consensus       169 lDPvIGRd~EI~r~iqIL~RR~KNNP--vLiGEpGVGKTAIvEGLA~--rIv~g---------~VP~~L~~~~i~sLD~g  235 (786)
T COG0542         169 LDPVIGRDEEIRRTIQILSRRTKNNP--VLVGEPGVGKTAIVEGLAQ--RIVNG---------DVPESLKDKRIYSLDLG  235 (786)
T ss_pred             CCCCcChHHHHHHHHHHHhccCCCCC--eEecCCCCCHHHHHHHHHH--HHhcC---------CCCHHHcCCEEEEecHH
Confidence            36789999999999999987542222  3589999999998755554  22110         02221111111 11222


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHhcC-CCeEEEEEecCCC
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEYLM-TKRYLIVIDDVWS  275 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~~  275 (824)
                      .-+.+..     -..+.+++...+.+.++ .++..|++|.+..
T Consensus       236 ~LvAGak-----yRGeFEeRlk~vl~ev~~~~~vILFIDEiHt  273 (786)
T COG0542         236 SLVAGAK-----YRGEFEERLKAVLKEVEKSKNVILFIDEIHT  273 (786)
T ss_pred             HHhcccc-----ccCcHHHHHHHHHHHHhcCCCeEEEEechhh
Confidence            3333322     12345566666666664 4689999999863

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=94.02  E-value=0.12  Score=53.81  Aligned_cols=25  Identities=16%  Similarity=0.133  Sum_probs=21.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ....+|||.|..|+||||+|+.+..
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~   84 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQA   84 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999987755

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.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=94.02  E-value=0.39  Score=50.16  Aligned_cols=53  Identities=11%  Similarity=0.002  Sum_probs=36.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCC-CceeEEEECCCCCCCCHHHHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHY-FDCHAWITEPYSNEYDADQILDIVIKFLM  237 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~~~~wv~~~vs~~~~~~~~~~~i~~~l~  237 (824)
                      -.++.|.|.+|+||||++.++..+  .... =..++|++  ...  ...++...+...+.
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~--~~~~~g~~vl~iS--~E~--~~~~~~~r~~~~~~   83 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALD--LITQHGVRVGTIS--LEE--PVVRTARRLLGQYA   83 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH--HHHhcCceEEEEE--ccc--CHHHHHHHHHHHHh
Confidence            468889999999999999988763  3222 24677887  544  45666666665543

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK06217 hypothetical protein; Validated

Probab=94.01  E-value=0.096  Score=51.10  Aligned_cols=23  Identities=13%  Similarity=0.134  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..|.|.|++|.||||+|+++.+.
T Consensus         2 ~~I~i~G~~GsGKSTla~~L~~~   24 (183)
T PRK06217          2 MRIHITGASGSGTTTLGAALAER   24 (183)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35899999999999999999883

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=94.00  E-value=0.18  Score=55.44  Aligned_cols=99  Identities=13%  Similarity=0.121  Sum_probs=52.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCC--------CCcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPS--------SRLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~--------~~~~~~~~~~  249 (824)
                      -..++|+|..|+|||||++.+.+..  +.  +..+.+.  +.+.. .+.++..++...=...        .+.+.....-
T Consensus       137 Gq~~~I~G~sG~GKTtLl~~I~~~~--~~--~~~vi~~--iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~  210 (411)
T TIGR03496       137 GQRMGIFAGSGVGKSTLLGMMARYT--EA--DVVVVGL--IGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLR  210 (411)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCC--CC--CEEEEEE--EecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHH
Confidence            4579999999999999999998832  21  2333343  33332 2334444433321110        1101011111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ....+..+.+++  +++++|+++||+-.. ..+.++.
T Consensus       211 a~~~a~tiAEyfr~~G~~Vll~~Dsltr~A~A~REis  247 (411)
T TIGR03496       211 AAFYATAIAEYFRDQGKDVLLLMDSLTRFAMAQREIA  247 (411)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEeChHHHHHHHHHHH
Confidence            122233444444  589999999999654 2334443

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.

>PRK06936 type III secretion system ATPase; Provisional

Probab=94.00  E-value=0.19  Score=55.32  Aligned_cols=99  Identities=14%  Similarity=0.126  Sum_probs=54.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCC--------CCcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPS--------SRLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~--------~~~~~~~~~~  249 (824)
                      -..++|.|..|+|||||.+.+++..  .  -+.++++-  +.+.. .+.++..+.+..-+..        .+.+.....-
T Consensus       162 Gq~~~I~G~sG~GKStLl~~Ia~~~--~--~dv~V~~l--iGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (439)
T PRK06936        162 GQRMGIFAAAGGGKSTLLASLIRSA--E--VDVTVLAL--IGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAK  235 (439)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcCC--C--CCEEEEEE--EccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHH
Confidence            5689999999999999999999942  2  24566665  55543 2333333322221110        0000000001


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ....+..+.+++  ++|++|+++||+-.. ....++.
T Consensus       236 a~~~a~tiAEyfrd~G~~Vll~~DslTR~A~A~REis  272 (439)
T PRK06936        236 AGFVATSIAEYFRDQGKRVLLLMDSVTRFARAQREIG  272 (439)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEeccchhHHHHHHHHHH
Confidence            111123344444  589999999999654 3344444

>cd03236 ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 of RNase L inhibitor

Probab=93.96  E-value=0.33  Score=50.07  Aligned_cols=24  Identities=13%  Similarity=0.119  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        26 Ge~~~IvG~nGsGKSTLlk~l~Gl   49 (255)
T cd03236          26 GQVLGLVGPNGIGKSTALKILAGK   49 (255)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            459999999999999999999874

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. 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, RLIs 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.

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=93.95  E-value=0.041  Score=55.25  Aligned_cols=66  Identities=15%  Similarity=0.106  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHH
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      ...++++.+.....+..+|||.|.+|+||+||.-.+....+-+.+==.++-|+  -|.+++--.++-+
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVD--PSSp~tGGAlLGD   79 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVD--PSSPFTGGALLGD   79 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE---GGGGCC---SS--
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEEC--CCCCCCCCccccc
Confidence            55667777776555688999999999999999988877322222222455666  6777776665554

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>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=93.94  E-value=0.15  Score=53.77  Aligned_cols=114  Identities=18%  Similarity=0.084  Sum_probs=64.1

Q ss_pred             HHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcc-c
Q 003387          167 ELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLS-E  244 (824)
Q Consensus       167 ~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~-~  244 (824)
                      .|-..|. .+=+.-+++-|+|..|+||||||-.+..  +.+..-..++||+  ....++..     .+++++...+.- -
T Consensus        40 ~LD~aLg~GG~p~G~ivEi~G~~ssGKttLaL~~ia--~~q~~g~~~a~ID--~e~~ld~~-----~a~~lGvdl~rllv  110 (322)
T PF00154_consen   40 ALDYALGIGGLPRGRIVEIYGPESSGKTTLALHAIA--EAQKQGGICAFID--AEHALDPE-----YAESLGVDLDRLLV  110 (322)
T ss_dssp             HHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHH--HHHHTT-EEEEEE--SSS---HH-----HHHHTT--GGGEEE
T ss_pred             ccchhhccCccccCceEEEeCCCCCchhhhHHHHHH--hhhcccceeEEec--Ccccchhh-----HHHhcCccccceEE
Confidence            3444443 2223457999999999999999999887  5555556789999  77766654     344554422110 0


Q ss_pred             ccccCHHHHHHHHHHhcC-CCeEEEEEecCCChhhHHHHHhhCCCC
Q 003387          245 IMDKNYEMKKIILHEYLM-TKRYLIVIDDVWSIDMWDVIQEILPDN  289 (824)
Q Consensus       245 ~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~~~~~~~~l~~~~~~~  289 (824)
                      ..+...++....+...++ +.--++|+|-|-....-.++...+.+.
T Consensus       111 ~~P~~~E~al~~~e~lirsg~~~lVVvDSv~al~p~~E~e~~~~~~  156 (322)
T PF00154_consen  111 VQPDTGEQALWIAEQLIRSGAVDLVVVDSVAALVPKAELEGEIGDQ  156 (322)
T ss_dssp             EE-SSHHHHHHHHHHHHHTTSESEEEEE-CTT-B-HHHHTTSTSST
T ss_pred             ecCCcHHHHHHHHHHHhhcccccEEEEecCcccCCHHHHhhccccc
Confidence            233345555566666664 455689999997653333444444333

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 ....

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=93.93  E-value=0.36  Score=48.26  Aligned_cols=23  Identities=26%  Similarity=0.195  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|+.|+|||||.+.|..
T Consensus        29 GEfvsilGpSGcGKSTLLriiAG   51 (248)
T COG1116          29 GEFVAILGPSGCGKSTLLRLIAG   51 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999876

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=93.92  E-value=0.29  Score=50.71  Aligned_cols=127  Identities=17%  Similarity=0.135  Sum_probs=67.8

Q ss_pred             eechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          159 VGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       159 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      .|...+..+.+..+....  -.+|.|.|..|.||||+++.+.+  .+...-..++.+.  -+.++....+     .++. 
T Consensus        62 lg~~~~~~~~l~~~~~~~--~GlilisG~tGSGKTT~l~all~--~i~~~~~~iitiE--dp~E~~~~~~-----~q~~-  129 (264)
T cd01129          62 LGLKPENLEIFRKLLEKP--HGIILVTGPTGSGKTTTLYSALS--ELNTPEKNIITVE--DPVEYQIPGI-----NQVQ-  129 (264)
T ss_pred             cCCCHHHHHHHHHHHhcC--CCEEEEECCCCCcHHHHHHHHHh--hhCCCCCeEEEEC--CCceecCCCc-----eEEE-
Confidence            355555444444444333  45899999999999999998876  3432212233343  1111111110     0111 


Q ss_pred             CCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          239 SSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                            ............++..|+...=.|+++++.+.+....+.....   .|-.++-|....++..
T Consensus       130 ------v~~~~~~~~~~~l~~~lR~~PD~i~vgEiR~~e~a~~~~~aa~---tGh~v~tTlHa~~~~~  188 (264)
T cd01129         130 ------VNEKAGLTFARGLRAILRQDPDIIMVGEIRDAETAEIAVQAAL---TGHLVLSTLHTNDAPG  188 (264)
T ss_pred             ------eCCcCCcCHHHHHHHHhccCCCEEEeccCCCHHHHHHHHHHHH---cCCcEEEEeccCCHHH
Confidence                  1111112356677788887888999999998875443332222   2434555544444433

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.

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=93.91  E-value=0.055  Score=55.14  Aligned_cols=69  Identities=17%  Similarity=0.109  Sum_probs=50.4

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHH
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKF  235 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~  235 (824)
                      -.+++..+.....+..||||.|.+|+||+||.-.+-....-+.+==.++=|+  -|.+|.--.|+-+=++.
T Consensus        37 a~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVD--PSSp~TGGsiLGDRiRM  105 (323)
T COG1703          37 ARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVD--PSSPFTGGSILGDRIRM  105 (323)
T ss_pred             HHHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEEC--CCCCCCCccccccHhhH
Confidence            4567777777667789999999999999999988777433334434566777  88888777776654443

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=93.90  E-value=0.13  Score=60.55  Aligned_cols=52  Identities=25%  Similarity=0.219  Sum_probs=34.9

Q ss_pred             CCceechhhHHHHHHHHHc---CC-------CCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          156 RDTVGLDDRMEELLDLLIE---GP-------PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~---~~-------~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      .++.|.+..++++.+.+..   ..       .-.+-|.++|++|.||||+|+.+.+  +....|
T Consensus       152 ~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~--~~~~~f  213 (644)
T PRK10733        152 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG--EAKVPF  213 (644)
T ss_pred             HHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHH--HcCCCE
Confidence            4567877776666554432   10       1123488999999999999999988  444333

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=93.86  E-value=0.033  Score=54.09  Aligned_cols=22  Identities=23%  Similarity=0.126  Sum_probs=20.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +|+|.|.+|+||||+|+.+...
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999883

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.

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=93.85  E-value=0.12  Score=56.88  Aligned_cols=103  Identities=9%  Similarity=0.112  Sum_probs=61.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCC-HHHHHHHHHHHhCCC--------CCcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD-ADQILDIVIKFLMPS--------SRLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~-~~~~~~~i~~~l~~~--------~~~~~~~~~~  249 (824)
                      -.-++|.|..|+|||+|+..+.++.. +.+-+.++++-  +.+..+ +.++.+++...=...        .+.+.....-
T Consensus       138 GQr~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v~V~~~--iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~  214 (449)
T TIGR03305       138 GGKAGLFGGAGVGKTVLLTEMIHNMV-GQHQGVSIFCG--IGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFR  214 (449)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHH-hcCCCEEEEEE--eccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHH
Confidence            45789999999999999999877422 23346788887  766553 345555554431111        1111111111


Q ss_pred             HHHHHHHHHHhcC---CCeEEEEEecCCCh-hhHHHHHh
Q 003387          250 YEMKKIILHEYLM---TKRYLIVIDDVWSI-DMWDVIQE  284 (824)
Q Consensus       250 ~~~~~~~l~~~L~---~kr~LlVlDdv~~~-~~~~~l~~  284 (824)
                      ....+..+.++++   ++++|+++||+-.. ..+.++..
T Consensus       215 ~~~~a~tiAEyfrd~~G~~VLl~~DslTR~A~A~REisl  253 (449)
T TIGR03305       215 VGHTALTMAEYFRDDEKQDVLLLIDNIFRFIQAGSEVSG  253 (449)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEecChHHHHHHHHHHHH
Confidence            2233445666654   69999999999654 33444443

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.83  E-value=0.23  Score=53.27  Aligned_cols=89  Identities=12%  Similarity=0.038  Sum_probs=51.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCH--HHHHHHHHHHhCCCCCcccccccCHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDA--DQILDIVIKFLMPSSRLSEIMDKNYEMKKI  255 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~  255 (824)
                      +.+++.|+|+.|+||||++..+...  ....-..+.+|+  .. .+..  .+-++..++.++...    ....+..++..
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~--l~~~g~~V~lIt--aD-tyR~gAveQLk~yae~lgvpv----~~~~dp~dL~~  275 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQ--LLKQNRTVGFIT--TD-TFRSGAVEQFQGYADKLDVEL----IVATSPAELEE  275 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEe--CC-ccCccHHHHHHHHhhcCCCCE----EecCCHHHHHH
Confidence            4689999999999999999988763  322223566776  33 3322  333444444443211    12234555555


Q ss_pred             HHHHhc-CCCeEEEEEecCCC
Q 003387          256 ILHEYL-MTKRYLIVIDDVWS  275 (824)
Q Consensus       256 ~l~~~L-~~kr~LlVlDdv~~  275 (824)
                      .+...- .+..=+|++|-.-.
T Consensus       276 al~~l~~~~~~D~VLIDTAGr  296 (407)
T PRK12726        276 AVQYMTYVNCVDHILIDTVGR  296 (407)
T ss_pred             HHHHHHhcCCCCEEEEECCCC
Confidence            554332 13446788888754

>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=93.82  E-value=0.18  Score=48.30  Aligned_cols=45  Identities=20%  Similarity=0.159  Sum_probs=33.7

Q ss_pred             ceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          158 TVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ++|.+..+.++++.+..-.....-|-|+|..|.||+.+|+.|++.
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~   45 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNN   45 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHC
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            578888999999888763222345569999999999999999993

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 ....

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=93.81  E-value=0.043  Score=53.35  Aligned_cols=23  Identities=13%  Similarity=0.200  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .++.|+|+.|+||||+++.+...
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999998773

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.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=93.76  E-value=0.21  Score=54.98  Aligned_cols=100  Identities=11%  Similarity=0.068  Sum_probs=52.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC-CCCHHHHHHHHHHHhCCCC--------Cccccccc
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN-EYDADQILDIVIKFLMPSS--------RLSEIMDK  248 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~-~~~~~~~~~~i~~~l~~~~--------~~~~~~~~  248 (824)
                      .-..++|+|..|+|||||++.+.+...    .+..+...  +.. .-++.++..+.+..-+...        +.+.....
T Consensus       154 ~GQ~igI~G~sGaGKSTLl~~I~g~~~----~dv~vig~--IGerg~ev~ef~~~~l~~~gl~rsvvv~~~~d~s~~~rl  227 (434)
T PRK07196        154 KGQRVGLMAGSGVGKSVLLGMITRYTQ----ADVVVVGL--IGERGREVKEFIEHSLQAAGMAKSVVVAAPADESPLMRI  227 (434)
T ss_pred             cceEEEEECCCCCCccHHHHHHhcccC----CCeEEEEE--EeeecHHHHHHHHHHhhhcccceEEEEEecCCCChhhhH
Confidence            357899999999999999999988321    12332232  222 2233333333333222110        00001122


Q ss_pred             CHHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          249 NYEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       249 ~~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ...+....+.++.  +++.+|+++||+-.. ..+.++.
T Consensus       228 ~a~e~a~~iAEyfr~~g~~Vll~~Dsltr~a~A~REis  265 (434)
T PRK07196        228 KATELCHAIATYYRDKGHDVLLLVDSLTRYAMAQREIA  265 (434)
T ss_pred             HHHHHHHHHHHHhhhccCCEEEeecchhHHHhhhhHHH
Confidence            2233344445444  579999999999654 2344443

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=93.71  E-value=0.16  Score=57.71  Aligned_cols=73  Identities=19%  Similarity=0.185  Sum_probs=48.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  257 (824)
                      .-+|.-.+|++|+||||||..|.++.    -| .++=|.  .|..-....+-..|...+....                 
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqa----GY-sVvEIN--ASDeRt~~~v~~kI~~avq~~s-----------------  380 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQA----GY-SVVEIN--ASDERTAPMVKEKIENAVQNHS-----------------  380 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhc----Cc-eEEEec--ccccccHHHHHHHHHHHHhhcc-----------------
Confidence            46899999999999999999998842    12 234444  7766555555555544443321                 


Q ss_pred             HHhcC--CCeEEEEEecCCCh
Q 003387          258 HEYLM--TKRYLIVIDDVWSI  276 (824)
Q Consensus       258 ~~~L~--~kr~LlVlDdv~~~  276 (824)
                        .|.  ++..-||+|.++..
T Consensus       381 --~l~adsrP~CLViDEIDGa  399 (877)
T KOG1969|consen  381 --VLDADSRPVCLVIDEIDGA  399 (877)
T ss_pred             --ccccCCCcceEEEecccCC
Confidence              121  46777999999875

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=93.70  E-value=0.47  Score=46.27  Aligned_cols=24  Identities=17%  Similarity=0.104  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|.|.|.+|.||||+|+.+..
T Consensus        17 ~~~~i~i~G~~GsGKstla~~l~~   40 (184)
T TIGR00455        17 RGVVIWLTGLSGSGKSTIANALEK   40 (184)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999987

Important residue (active site in E.coli) is residue 100 of the seed alignment.

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=93.69  E-value=0.28  Score=52.12  Aligned_cols=24  Identities=17%  Similarity=0.072  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||.+.+...
T Consensus        28 Gei~~l~G~NGaGKTTLl~~l~Gl   51 (301)
T TIGR03522        28 GRIVGFLGPNGAGKSTTMKIITGY   51 (301)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999874

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>PRK14738 gmk guanylate kinase; Provisional

Probab=93.68  E-value=0.053  Score=54.01  Aligned_cols=31  Identities=23%  Similarity=0.295  Sum_probs=25.6

Q ss_pred             HHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          171 LLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       171 ~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      |+..+....+.|.|+|+.|+|||||++.+.+
T Consensus         5 ~~~~~~~~~~~ivi~GpsG~GK~tl~~~L~~   35 (206)
T PRK14738          5 WLFNKPAKPLLVVISGPSGVGKDAVLARMRE   35 (206)
T ss_pred             cccCCCCCCeEEEEECcCCCCHHHHHHHHHh
Confidence            3444455678999999999999999999976

>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=93.68  E-value=0.063  Score=50.20  Aligned_cols=36  Identities=14%  Similarity=-0.142  Sum_probs=29.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ..||-|.|..|.||||||+++..  +....-..+.+++
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~--~L~~~g~~~~~LD   37 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALER--RLFARGIKVYLLD   37 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHH--HHHHTTS-EEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--HHHHcCCcEEEec
Confidence            35889999999999999999999  6666656677776

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 ....

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=93.68  E-value=0.068  Score=51.02  Aligned_cols=24  Identities=21%  Similarity=0.216  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+++|+|..|+|||||++.+..
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~   28 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIP   28 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHH
Confidence            467999999999999999999987

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=93.68  E-value=0.23  Score=58.50  Aligned_cols=100  Identities=21%  Similarity=0.059  Sum_probs=64.6

Q ss_pred             HHHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc-c
Q 003387          166 EELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL-S  243 (824)
Q Consensus       166 ~~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~-~  243 (824)
                      ..+-.+|. .+=..-+++-|+|..|+||||||.++.-.  ....=..++|++  ..+.++.     ..+++++...+. .
T Consensus        46 ~~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~--a~~~G~~v~yId--~E~t~~~-----~~A~~lGvDl~~ll  116 (790)
T PRK09519         46 IALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVAN--AQAAGGVAAFID--AEHALDP-----DYAKKLGVDTDSLL  116 (790)
T ss_pred             HHHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEC--CccchhH-----HHHHHcCCChhHeE
Confidence            44555665 44345688889999999999999775552  223335678998  7777774     367777664221 1


Q ss_pred             cccccCHHHHHHHHHHhcCC-CeEEEEEecCC
Q 003387          244 EIMDKNYEMKKIILHEYLMT-KRYLIVIDDVW  274 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~  274 (824)
                      -......++....+...++. +--|||+|-+-
T Consensus       117 v~~~~~~E~~l~~i~~lv~~~~~~LVVIDSI~  148 (790)
T PRK09519        117 VSQPDTGEQALEIADMLIRSGALDIVVIDSVA  148 (790)
T ss_pred             EecCCCHHHHHHHHHHHhhcCCCeEEEEcchh
Confidence            12333445566666666644 56689999985

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=93.65  E-value=0.17  Score=56.10  Aligned_cols=24  Identities=17%  Similarity=0.267  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -..++|+|..|+|||||++.+.+.
T Consensus       163 Gq~~~I~G~sG~GKStLl~~I~~~  186 (440)
T TIGR01026       163 GQRIGIFAGSGVGKSTLLGMIARN  186 (440)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999999884

This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.

>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=93.64  E-value=0.05  Score=52.76  Aligned_cols=21  Identities=43%  Similarity=0.476  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +|+|.|..|+||||||+.+..
T Consensus         1 ii~i~G~sgsGKttla~~l~~   21 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSN   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999987

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=93.63  E-value=0.056  Score=50.02  Aligned_cols=23  Identities=30%  Similarity=0.250  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++.|+|.+|+||||+.+.+-.
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~   26 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALK   26 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHH
Confidence            68999999999999999988877

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=93.63  E-value=0.2  Score=55.20  Aligned_cols=97  Identities=15%  Similarity=0.099  Sum_probs=51.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCH-HHHHHHHHHHhCCC----------CCcccccc
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDA-DQILDIVIKFLMPS----------SRLSEIMD  247 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~-~~~~~~i~~~l~~~----------~~~~~~~~  247 (824)
                      -..++|+|..|+|||||++.+...  ..  -+..+..-  +.+.... .+..+.   .++..          .+.+....
T Consensus       157 Gq~~~i~G~sG~GKStLl~~i~~~--~~--~~v~vi~~--iGergrev~e~~~~---~l~~~l~~tvvV~atsddsp~~R  227 (434)
T PRK08472        157 GQKLGIFAGSGVGKSTLMGMIVKG--CL--APIKVVAL--IGERGREIPEFIEK---NLGGDLENTVIVVATSDDSPLMR  227 (434)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhc--cC--CCEEEEEe--eCccchhHHHHHHH---HhcCcccceEEEEECCCCCHHHh
Confidence            468899999999999999999973  22  23333343  4444333 232222   22221          00000000


Q ss_pred             cCHHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHHh
Q 003387          248 KNYEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQE  284 (824)
Q Consensus       248 ~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~~  284 (824)
                      .-.-.....+.+++  +++++|+++||+-.. ..+.++..
T Consensus       228 ~~~~~~a~~iAEyFrd~G~~Vll~~DslTr~A~A~REi~l  267 (434)
T PRK08472        228 KYGAFCAMSVAEYFKNQGLDVLFIMDSVTRFAMAQREIGL  267 (434)
T ss_pred             hHHHHHHHHHHHHHHHcCCCEEEecccchHHHHHHHHHHH
Confidence            00011133344444  589999999999654 34455543

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=93.62  E-value=0.082  Score=52.38  Aligned_cols=23  Identities=17%  Similarity=0.146  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.++||+|..|.|||||++.+..
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhc
Confidence            46899999999999999999865

>TIGR03263 guanyl_kin guanylate kinase

Probab=93.61  E-value=0.052  Score=52.79  Aligned_cols=22  Identities=14%  Similarity=0.274  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|+|+|+.|+||||||+.+.+
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~   23 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLE   23 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHc
Confidence            5799999999999999999998

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.

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=93.61  E-value=0.19  Score=55.77  Aligned_cols=104  Identities=13%  Similarity=0.113  Sum_probs=58.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCc--eeEEEECCCCCCC-CHHHHHHHHHHHhCCCC--------Ccccccc
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD--CHAWITEPYSNEY-DADQILDIVIKFLMPSS--------RLSEIMD  247 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~~--------~~~~~~~  247 (824)
                      -.-++|.|-.|+|||||+..+.+.....+.+.  .++++-  +.+.. .+.++.+++...=....        +.+....
T Consensus       141 GQR~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~--iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R  218 (458)
T TIGR01041       141 GQKLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAA--MGITYEEANFFMKDFEETGALERAVVFLNLADDPAVER  218 (458)
T ss_pred             CCEEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEE--ccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHH
Confidence            35789999999999999999998544332222  455555  65543 34455555543221111        1111111


Q ss_pred             cCHHHHHHHHHHhcC---CCeEEEEEecCCCh-hhHHHHHh
Q 003387          248 KNYEMKKIILHEYLM---TKRYLIVIDDVWSI-DMWDVIQE  284 (824)
Q Consensus       248 ~~~~~~~~~l~~~L~---~kr~LlVlDdv~~~-~~~~~l~~  284 (824)
                      .-..-.+..+.++++   ++++||++||+-.. ..+.++..
T Consensus       219 ~~a~~~a~tiAEyfr~d~G~~VLli~DslTR~A~A~REIsl  259 (458)
T TIGR01041       219 IVTPRMALTAAEYLAFEKDMHVLVILTDMTNYCEALREISA  259 (458)
T ss_pred             HHHHHHHHHHHHHHHHccCCcEEEEEcChhHHHHHHHHHHH
Confidence            112222344555554   68999999999654 34445443

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=93.60  E-value=0.047  Score=52.68  Aligned_cols=23  Identities=9%  Similarity=0.122  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...|.|+|++|+||||+|+.+..
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~   26 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAK   26 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHH
Confidence            45899999999999999999988

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=93.60  E-value=0.93  Score=45.41  Aligned_cols=22  Identities=9%  Similarity=0.070  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +++.|.|+.|.||||+.+.+..
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            7899999999999999999853

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 clam

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.57  E-value=0.25  Score=50.10  Aligned_cols=59  Identities=12%  Similarity=0.141  Sum_probs=34.7

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHH
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      +-+.+..+=..-.++.|.|..|.||||+|.++... -.+.. ..+++++  ...  +..++.+.+
T Consensus        13 ld~~l~ggi~~g~~~~i~G~~G~GKTtl~~~~~~~-~~~~g-~~~~yi~--~e~--~~~~~~~~~   71 (230)
T PRK08533         13 LHKRLGGGIPAGSLILIEGDESTGKSILSQRLAYG-FLQNG-YSVSYVS--TQL--TTTEFIKQM   71 (230)
T ss_pred             eehhhCCCCCCCcEEEEECCCCCCHHHHHHHHHHH-HHhCC-CcEEEEe--CCC--CHHHHHHHH
Confidence            33344333334569999999999999998554432 22222 3456665  333  445666665

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=93.56  E-value=0.28  Score=53.97  Aligned_cols=37  Identities=14%  Similarity=0.052  Sum_probs=26.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ...+|.++|..|+||||+|.++..  ..+..=..++.|+
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~--~l~~~G~kV~lV~  135 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAY--YYQRKGFKPCLVC  135 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEc
Confidence            468999999999999999988876  3333222445554

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.

>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=93.56  E-value=0.1  Score=53.95  Aligned_cols=21  Identities=19%  Similarity=0.039  Sum_probs=17.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.|+|.+|+||||+|+.+..
T Consensus         3 Liil~G~P~SGKTt~a~~L~~   23 (270)
T PF08433_consen    3 LIILCGLPCSGKTTRAKELKK   23 (270)
T ss_dssp             EEEEE--TTSSHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHH
Confidence            588999999999999999988

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PTZ00088 adenylate kinase 1; Provisional

Probab=93.56  E-value=0.079  Score=53.44  Aligned_cols=21  Identities=19%  Similarity=0.314  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -|.|+|++|+||||+|+.+.+
T Consensus         8 rIvl~G~PGsGK~T~a~~La~   28 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSK   28 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            388999999999999999977

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=93.54  E-value=0.056  Score=49.86  Aligned_cols=21  Identities=10%  Similarity=0.287  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.|+|+.|+|||||++.+.+
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.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=93.52  E-value=0.069  Score=52.10  Aligned_cols=36  Identities=14%  Similarity=0.093  Sum_probs=31.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .++|.|+|+.|+|||||++.+..  .....|...++.+
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~--~~~~~~~~~v~~T   37 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQ--EFPDKFGRVVSHT   37 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHH--HSTTTEEEEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH--hcccccccceeec
Confidence            46899999999999999999999  6677887777776

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 ....

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=93.50  E-value=0.92  Score=54.53  Aligned_cols=158  Identities=12%  Similarity=0.049  Sum_probs=76.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  257 (824)
                      +.+++.|.|+.+.||||+.+.+.-..-   ..++-++|.  +.... .-.++..|...++....... ...+...-...+
T Consensus       326 ~~~~~iITGpN~gGKTt~lktigl~~~---maq~G~~vp--a~~~~-~i~~~~~i~~~ig~~~si~~-~lStfS~~m~~~  398 (782)
T PRK00409        326 DKTVLVITGPNTGGKTVTLKTLGLAAL---MAKSGLPIP--ANEPS-EIPVFKEIFADIGDEQSIEQ-SLSTFSGHMTNI  398 (782)
T ss_pred             CceEEEEECCCCCCcHHHHHHHHHHHH---HHHhCCCcc--cCCCc-cccccceEEEecCCccchhh-chhHHHHHHHHH
Confidence            357899999999999999988854210   011112222  21100 00111111111211111000 000111111222


Q ss_pred             HHhcC--CCeEEEEEecCCChhh---HHHH----HhhCCCCCCCcEEEEEechHHHHhhcccccC----------CcCcC
Q 003387          258 HEYLM--TKRYLIVIDDVWSIDM---WDVI----QEILPDNQNGSRVLITLTDIRIIISFQFEDG----------ENMRL  318 (824)
Q Consensus       258 ~~~L~--~kr~LlVlDdv~~~~~---~~~l----~~~~~~~~~gs~ilvTtR~~~v~~~f~~~~~----------~~~~~  318 (824)
                      ...+.  ..+-|+++|..-...+   -..+    ...+.  ..|+.+|+||...+++........          +...+
T Consensus       399 ~~Il~~~~~~sLvLlDE~~~GtDp~eg~ala~aile~l~--~~~~~vIitTH~~el~~~~~~~~~v~~~~~~~d~~~l~~  476 (782)
T PRK00409        399 VRILEKADKNSLVLFDELGAGTDPDEGAALAISILEYLR--KRGAKIIATTHYKELKALMYNREGVENASVEFDEETLRP  476 (782)
T ss_pred             HHHHHhCCcCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--HCCCEEEEECChHHHHHHHhcCCCeEEEEEEEecCcCcE
Confidence            22222  4778999999976432   1222    22222  247899999999888761111100          00001


Q ss_pred             c--------cccchhhHHHhcCCCchhHHHHHhHH
Q 003387          319 D--------LVPTGGPLRATYKGRPFLILYHGSIS  345 (824)
Q Consensus       319 ~--------~~~~~~~i~~~c~GlPlai~~~~~~l  345 (824)
                      .        -...|-+|++++ |+|-.+.--|..+
T Consensus       477 ~Ykl~~G~~g~S~a~~iA~~~-Glp~~ii~~A~~~  510 (782)
T PRK00409        477 TYRLLIGIPGKSNAFEIAKRL-GLPENIIEEAKKL  510 (782)
T ss_pred             EEEEeeCCCCCcHHHHHHHHh-CcCHHHHHHHHHH
Confidence            1        123466777766 7998888888777

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=93.48  E-value=0.59  Score=47.90  Aligned_cols=120  Identities=17%  Similarity=0.113  Sum_probs=80.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~  234 (824)
                      .++++|.... .+++.++......-+.+.|+|+.|+|||+-++..++..       ..+|.- ..+..+....++..+..
T Consensus        71 ~~~~l~tkt~-r~~~~~~~~A~k~g~l~~vyg~~g~gKt~a~~~y~~s~-------p~~~l~-~~~p~~~a~~~i~~i~~  141 (297)
T COG2842          71 APDFLETKTV-RRIFFRTRPASKTGSLVVVYGYAGLGKTQAAKNYAPSN-------PNALLI-EADPSYTALVLILIICA  141 (297)
T ss_pred             cccccccchh-HhHhhhhhhhhhcCceEEEeccccchhHHHHHhhcccC-------ccceee-cCChhhHHHHHHHHHHH
Confidence            4566665543 34556665544344588999999999999999999832       233432 16777777777777777


Q ss_pred             HhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCC
Q 003387          235 FLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDN  289 (824)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~  289 (824)
                      .+....      ..........+...+++..-+|+.|+....  ..++.+.......
T Consensus       142 ~~~~~~------~~~~~d~~~~~~~~l~~~~~~iivDEA~~L~~~ale~lr~i~d~~  192 (297)
T COG2842         142 AAFGAT------DGTINDLTERLMIRLRDTVRLIIVDEADRLPYRALEELRRIHDKT  192 (297)
T ss_pred             HHhccc------chhHHHHHHHHHHHHccCcceeeeehhhccChHHHHHHHHHHHhh
Confidence            776643      234455666777777888889999988764  4566666544433

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=93.48  E-value=0.34  Score=57.53  Aligned_cols=114  Identities=14%  Similarity=0.196  Sum_probs=71.6

Q ss_pred             CceechhhHHHHHHHHHcCC------CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHH
Q 003387          157 DTVGLDDRMEELLDLLIEGP------PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILD  230 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~------~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~  230 (824)
                      .++|-++.+..|.+.+....      ...-.+-+.|+.|+|||-||+++..  .+-+..+..+-++  .|+      .+.
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~--~~Fgse~~~IriD--mse------~~e  632 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAE--YVFGSEENFIRLD--MSE------FQE  632 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHH--HHcCCccceEEec--hhh------hhh
Confidence            47888888888888876531      2467888999999999999999887  4544444455554  443      222


Q ss_pred             HHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeE-EEEEecCCChh--hHHHHHhhCC
Q 003387          231 IVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRY-LIVIDDVWSID--MWDVIQEILP  287 (824)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~-LlVlDdv~~~~--~~~~l~~~~~  287 (824)
                       +.+.++...+   +   -..+....|-+.++.+.| +|+||||...+  ....+...+.
T Consensus       633 -vskligsp~g---y---vG~e~gg~LteavrrrP~sVVLfdeIEkAh~~v~n~llq~lD  685 (898)
T KOG1051|consen  633 -VSKLIGSPPG---Y---VGKEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQLLD  685 (898)
T ss_pred             -hhhccCCCcc---c---ccchhHHHHHHHHhcCCceEEEEechhhcCHHHHHHHHHHHh
Confidence             3343343222   1   112334477778888776 55669998753  4444444443

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=93.47  E-value=0.43  Score=45.40  Aligned_cols=20  Identities=15%  Similarity=0.262  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      |.|+|+.|+||||+|+.+.+
T Consensus         1 i~l~G~~GsGKSTla~~l~~   20 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAH   20 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999988

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=93.44  E-value=0.21  Score=55.08  Aligned_cols=102  Identities=11%  Similarity=0.147  Sum_probs=58.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCC--------CCcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPS--------SRLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~--------~~~~~~~~~~  249 (824)
                      -.-++|.|..|+|||||+..+..+.. ..+=+.++++-  +.+.. .+.++.+++...=...        .+.+.....-
T Consensus       143 GQr~~If~~~G~GKt~L~~~~~~~~~-~~~~~v~V~al--IGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~  219 (461)
T TIGR01039       143 GGKIGLFGGAGVGKTVLIQELINNIA-KEHGGYSVFAG--VGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMR  219 (461)
T ss_pred             CCEEEeecCCCCChHHHHHHHHHHHH-hcCCCeEEEEE--ecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            45789999999999999999876311 11113566666  65543 3456666664321111        0111011111


Q ss_pred             HHHHHHHHHHhc---CCCeEEEEEecCCCh-hhHHHHH
Q 003387          250 YEMKKIILHEYL---MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       250 ~~~~~~~l~~~L---~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      ....+..+.+++   +++.+|+++||+-.. ..+.++.
T Consensus       220 a~~~a~tiAEyfrd~~G~~VLll~DslTR~A~A~REis  257 (461)
T TIGR01039       220 VALTGLTMAEYFRDEQGQDVLLFIDNIFRFTQAGSEVS  257 (461)
T ss_pred             HHHHHHHHHHHHHHhcCCeeEEEecchhHHHHHHHHHH
Confidence            222344566666   468999999999654 3344444

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=93.44  E-value=0.1  Score=53.05  Aligned_cols=35  Identities=11%  Similarity=0.038  Sum_probs=27.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      -.+++|+|+.|+|||||.+.++.   +-..=...++++
T Consensus        28 G~i~~iiGpNG~GKSTLLk~l~g---~l~p~~G~V~l~   62 (258)
T COG1120          28 GEITGILGPNGSGKSTLLKCLAG---LLKPKSGEVLLD   62 (258)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc---cCCCCCCEEEEC
Confidence            57999999999999999999998   223334566665

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=93.43  E-value=1  Score=51.36  Aligned_cols=126  Identities=14%  Similarity=0.122  Sum_probs=63.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCc-cccC-----CCceeEEEECCCCC-------------CC-CH-HHHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSS-YVKH-----YFDCHAWITEPYSN-------------EY-DA-DQILDIVIKFLM  237 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~-~~~~-----~F~~~~wv~~~vs~-------------~~-~~-~~~~~~i~~~l~  237 (824)
                      -..|+|+|+.|+|||||.+.+...- ....     .--.+.+++...+.             .+ +. ..-.+..+.+++
T Consensus       348 g~riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~  427 (530)
T COG0488         348 GDRIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFG  427 (530)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHcC
Confidence            4579999999999999999995521 1111     11112233210111             01 10 222333333333


Q ss_pred             CCCCcc--cccccCHHHH-HHHHHHhcCCCeEEEEEecCCChh---hHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          238 PSSRLS--EIMDKNYEMK-KIILHEYLMTKRYLIVIDDVWSID---MWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       238 ~~~~~~--~~~~~~~~~~-~~~l~~~L~~kr~LlVlDdv~~~~---~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      -..+..  .....+-.+. .-.+...+-.+.=+||||.--+.-   ..+.+..++.+.. |+ ||+.|-++....
T Consensus       428 F~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPTNhLDi~s~~aLe~aL~~f~-Gt-vl~VSHDr~Fl~  500 (530)
T COG0488         428 FTGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLDFE-GT-VLLVSHDRYFLD  500 (530)
T ss_pred             CChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCCccCCHHHHHHHHHHHHhCC-Ce-EEEEeCCHHHHH
Confidence            221100  0222333333 345566667788899999887653   2333344444332 65 677777775544

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=93.42  E-value=0.054  Score=50.67  Aligned_cols=20  Identities=25%  Similarity=0.293  Sum_probs=18.5

Q ss_pred             EEEEEcCCCChHHHHHHHHh
Q 003387          181 VVAILDSIGLDKTAFAGEAY  200 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~  200 (824)
                      .|+|.|.+|+||||+++.+-
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999886

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=93.40  E-value=0.48  Score=50.56  Aligned_cols=20  Identities=10%  Similarity=0.031  Sum_probs=18.4

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.++|+.|.||||+++.+.+
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~   21 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSA   21 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999987

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.

>PRK13947 shikimate kinase; Provisional

Probab=93.37  E-value=0.05  Score=52.40  Aligned_cols=21  Identities=14%  Similarity=0.262  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -|.|+||+|+||||+|+.+.+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~   23 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVAT   23 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHH
Confidence            488999999999999999988

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.36  E-value=0.51  Score=46.44  Aligned_cols=56  Identities=21%  Similarity=0.159  Sum_probs=35.3

Q ss_pred             HHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHh---hCC-CCCCCcEEEEEechHHHHh
Q 003387          251 EMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQE---ILP-DNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       251 ~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~---~~~-~~~~gs~ilvTtR~~~v~~  306 (824)
                      +....+|.+.+-=+.=|.|||..++--+.+.+..   ... -..+|+-++|.|..+.++.
T Consensus       149 EkKR~EilQ~~~lePkl~ILDE~DSGLDIdalk~V~~~i~~lr~~~~~~liITHy~rll~  208 (251)
T COG0396         149 EKKRNEILQLLLLEPKLAILDEPDSGLDIDALKIVAEGINALREEGRGVLIITHYQRLLD  208 (251)
T ss_pred             hHHHHHHHHHHhcCCCEEEecCCCcCccHHHHHHHHHHHHHHhcCCCeEEEEecHHHHHh
Confidence            3345566666666777999999987644333322   211 1233667888888888887

>PRK04328 hypothetical protein; Provisional

Probab=93.32  E-value=0.26  Score=50.67  Aligned_cols=52  Identities=15%  Similarity=0.236  Sum_probs=35.4

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE  222 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~  222 (824)
                      .+-++|..+=..-.++-|.|.+|.|||+||.++... .. ..-+.++||+  ..+.
T Consensus        11 ~LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~-~~-~~ge~~lyis--~ee~   62 (249)
T PRK04328         11 GMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWN-GL-QMGEPGVYVA--LEEH   62 (249)
T ss_pred             hHHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHH-HH-hcCCcEEEEE--eeCC
Confidence            344555555445689999999999999999886552 22 2345678887  5553

>PRK11823 DNA repair protein RadA; Provisional

Probab=93.32  E-value=0.32  Score=54.45  Aligned_cols=101  Identities=24%  Similarity=0.140  Sum_probs=55.6

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC-c
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR-L  242 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~-~  242 (824)
                      -...+-+.|..+=..-.++.|.|.+|+|||||+.++..+  ....=..++|++  ..+.  ..++... ++.++...+ .
T Consensus        65 Gi~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~--~a~~g~~vlYvs--~Ees--~~qi~~r-a~rlg~~~~~l  137 (446)
T PRK11823         65 GIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAAR--LAAAGGKVLYVS--GEES--ASQIKLR-AERLGLPSDNL  137 (446)
T ss_pred             CcHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEE--cccc--HHHHHHH-HHHcCCChhcE
Confidence            345555666655444679999999999999999998773  322234677887  4433  3333222 445543211 0


Q ss_pred             ccccccCHHHHHHHHHHhcCCCeEEEEEecCC
Q 003387          243 SEIMDKNYEMKKIILHEYLMTKRYLIVIDDVW  274 (824)
Q Consensus       243 ~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~  274 (824)
                      .-....+.+++...+.+   .+.-+||+|.+.
T Consensus       138 ~~~~e~~l~~i~~~i~~---~~~~lVVIDSIq  166 (446)
T PRK11823        138 YLLAETNLEAILATIEE---EKPDLVVIDSIQ  166 (446)
T ss_pred             EEeCCCCHHHHHHHHHh---hCCCEEEEechh
Confidence            00112233333333322   244578888774

>PRK00889 adenylylsulfate kinase; Provisional

Probab=93.29  E-value=0.073  Score=51.49  Aligned_cols=23  Identities=22%  Similarity=0.032  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|.|+|++|+||||+|+.+..
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~   26 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAE   26 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999988

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=93.27  E-value=0.18  Score=54.58  Aligned_cols=113  Identities=12%  Similarity=0.111  Sum_probs=66.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      -..|.|+|..|.||||+.+.+.+  .+......+++.-   ..+...  ..... ..+-....   .. .+.......++
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~--~i~~~~~~~i~ti---Edp~E~--~~~~~-~~~i~q~e---vg-~~~~~~~~~l~  189 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMID--YINKNAAGHIITI---EDPIEY--VHRNK-RSLINQRE---VG-LDTLSFANALR  189 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH--hhCcCCCCEEEEE---cCChhh--hccCc-cceEEccc---cC-CCCcCHHHHHH
Confidence            46899999999999999999887  5555555666653   111110  00000 00000000   01 11223566678


Q ss_pred             HhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          259 EYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       259 ~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      ..|+...=.|++|.+.+.+.+......   ...|-.|+.|+-..++..
T Consensus       190 ~~lr~~pd~i~vgEird~~~~~~~l~a---a~tGh~v~~T~Ha~~~~~  234 (343)
T TIGR01420       190 AALREDPDVILIGEMRDLETVELALTA---AETGHLVFGTLHTNSAAQ  234 (343)
T ss_pred             HhhccCCCEEEEeCCCCHHHHHHHHHH---HHcCCcEEEEEcCCCHHH
Confidence            888888889999999988766653332   233555776666555444

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=93.25  E-value=0.081  Score=51.77  Aligned_cols=110  Identities=15%  Similarity=0.101  Sum_probs=57.1

Q ss_pred             hhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc
Q 003387          163 DRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL  242 (824)
Q Consensus       163 ~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~  242 (824)
                      .+..++++.....   -..+.|+|..|.||||+++.+..  .+... ...+-+.  -.......  ..... ++......
T Consensus        12 ~~~~~~l~~~v~~---g~~i~I~G~tGSGKTTll~aL~~--~i~~~-~~~i~ie--d~~E~~~~--~~~~~-~~~~~~~~   80 (186)
T cd01130          12 PLQAAYLWLAVEA---RKNILISGGTGSGKTTLLNALLA--FIPPD-ERIITIE--DTAELQLP--HPNWV-RLVTRPGN   80 (186)
T ss_pred             HHHHHHHHHHHhC---CCEEEEECCCCCCHHHHHHHHHh--hcCCC-CCEEEEC--CccccCCC--CCCEE-EEEEecCC
Confidence            3444444444433   35899999999999999999887  33322 1222222  11000000  00000 00000000


Q ss_pred             ccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHhh
Q 003387          243 SEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEI  285 (824)
Q Consensus       243 ~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~  285 (824)
                        ..........+.++..++...=.++++.+.+.+.|..+...
T Consensus        81 --~~~~~~~~~~~~l~~~lR~~pd~i~igEir~~ea~~~~~a~  121 (186)
T cd01130          81 --VEGSGEVTMADLLRSALRMRPDRIIVGEVRGGEALDLLQAM  121 (186)
T ss_pred             --CCCCCccCHHHHHHHHhccCCCEEEEEccCcHHHHHHHHHH
Confidence              00111233455666677777778899999998877755543

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK13949 shikimate kinase; Provisional

Probab=93.24  E-value=0.057  Score=51.83  Aligned_cols=21  Identities=14%  Similarity=0.227  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -|.|+|+.|.||||+++.+.+
T Consensus         3 ~I~liG~~GsGKstl~~~La~   23 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAR   23 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999988

>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=93.24  E-value=0.13  Score=47.54  Aligned_cols=76  Identities=16%  Similarity=0.120  Sum_probs=43.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhc
Q 003387          182 VAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL  261 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L  261 (824)
                      |-++|..|+|||+||+.+..  ....   ...-+.  ++...+..++....--. .....   +...   .+...+    
T Consensus         2 vlL~G~~G~GKt~l~~~la~--~~~~---~~~~i~--~~~~~~~~dl~g~~~~~-~~~~~---~~~~---~l~~a~----   63 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAA--LLGR---PVIRIN--CSSDTTEEDLIGSYDPS-NGQFE---FKDG---PLVRAM----   63 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHH--HHTC---EEEEEE---TTTSTHHHHHCEEET--TTTTC---EEE----CCCTTH----
T ss_pred             EEEECCCCCCHHHHHHHHHH--Hhhc---ceEEEE--eccccccccceeeeeec-ccccc---cccc---cccccc----
Confidence            56899999999999999988  4422   222345  77777887766533222 11110   1110   000000    


Q ss_pred             CCCeEEEEEecCCCh
Q 003387          262 MTKRYLIVIDDVWSI  276 (824)
Q Consensus       262 ~~kr~LlVlDdv~~~  276 (824)
                       .+..++|||++...
T Consensus        64 -~~~~il~lDEin~a   77 (139)
T PF07728_consen   64 -RKGGILVLDEINRA   77 (139)
T ss_dssp             -HEEEEEEESSCGG-
T ss_pred             -cceeEEEECCcccC
Confidence             18899999999843

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.

>KOG0473 consensus Leucine-rich repeat protein [Function unknown]

Probab=93.24  E-value=0.004  Score=60.40  Aligned_cols=90  Identities=17%  Similarity=0.068  Sum_probs=74.3

Q ss_pred             HhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccC
Q 003387          514 EKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKL  593 (824)
Q Consensus       514 ~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L  593 (824)
                      ..-+..++...+||++.+.+-.+-..+..+..|..|+++.+.+..+|.+. +.+..+..+++..|+.+.+|.++++++.+
T Consensus        35 v~ei~~~kr~tvld~~s~r~vn~~~n~s~~t~~~rl~~sknq~~~~~~d~-~q~~e~~~~~~~~n~~~~~p~s~~k~~~~  113 (326)
T KOG0473|consen   35 VREIASFKRVTVLDLSSNRLVNLGKNFSILTRLVRLDLSKNQIKFLPKDA-KQQRETVNAASHKNNHSQQPKSQKKEPHP  113 (326)
T ss_pred             hhhhhccceeeeehhhhhHHHhhccchHHHHHHHHHhccHhhHhhChhhH-HHHHHHHHHHhhccchhhCCccccccCCc
Confidence            34456677788899988887777777778888888889888888888888 88888888888888888889888889999


Q ss_pred             ceecCCCccCC
Q 003387          594 RHLNFGSITLP  604 (824)
Q Consensus       594 ~~L~L~~~~~~  604 (824)
                      +++++.++.+.
T Consensus       114 k~~e~k~~~~~  124 (326)
T KOG0473|consen  114 KKNEQKKTEFF  124 (326)
T ss_pred             chhhhccCcch
Confidence            98888777654

>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=93.23  E-value=0.28  Score=50.02  Aligned_cols=81  Identities=12%  Similarity=0.083  Sum_probs=43.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE-CCCCCCCCHHHHHHHHHHHhCC--CCCcccccccCHHHHHHHH
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT-EPYSNEYDADQILDIVIKFLMP--SSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-~~vs~~~~~~~~~~~i~~~l~~--~~~~~~~~~~~~~~~~~~l  257 (824)
                      +|+|.|-.|.||||+|+.+..  ..+..=..++.++ ++.-. ++....-+.+......  +-+....+..+.+.+.+.+
T Consensus         1 IIgItG~SGSGKTTv~~~l~~--~l~~~g~~v~vI~~D~yyr-~~r~~~~~~~~~a~~~~~nfdHf~PeAnd~dlL~~~l   77 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEH--IFAREGIHPAVVEGDSFHR-YERMEMKMAIAEALDAGRNFSHFGPEANLFDLLEELF   77 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHH--HHHhcCCceEEEecccccc-CCchhHHHHHHHHhhcCCCCCCCCcccccHHHHHHHH
Confidence            589999999999999998876  3322111244454 11111 3333333333333221  1111002445667777777


Q ss_pred             HHhcCCC
Q 003387          258 HEYLMTK  264 (824)
Q Consensus       258 ~~~L~~k  264 (824)
                      +...+++
T Consensus        78 ~~L~~g~   84 (277)
T cd02029          78 RTYGETG   84 (277)
T ss_pred             HHHHcCC
Confidence            7776654

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.

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=93.22  E-value=0.39  Score=53.15  Aligned_cols=92  Identities=12%  Similarity=0.164  Sum_probs=50.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC-CCCHHHHHHHHHHHhCCCCC--------cccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN-EYDADQILDIVIKFLMPSSR--------LSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~-~~~~~~~~~~i~~~l~~~~~--------~~~~~~~~  249 (824)
                      -..++|+|..|+|||||.+.+.+.  ...  +..+.+.  +.. ..++.+...+....-.....        .+......
T Consensus       145 Gq~~~I~G~sG~GKStLl~~I~~~--~~~--~~~vi~~--iG~~~~ev~~~~~~~~~~~~~~~tvvv~~~s~~p~~~r~~  218 (422)
T TIGR02546       145 GQRIGIFAGAGVGKSTLLGMIARG--ASA--DVNVIAL--IGERGREVREFIEHHLGEEGRKRSVLVVSTSDRPSLERLK  218 (422)
T ss_pred             CCEEEEECCCCCChHHHHHHHhCC--CCC--CEEEEEE--EccCCcCHHHHHHHHhccccccceEEEeccccCCHHHHHH
Confidence            457899999999999999999983  322  2233332  222 33444554444332211110        00000111


Q ss_pred             HHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          250 YEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       250 ~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      ....+..+.+++  +++++|+++||+-..
T Consensus       219 ~~~~a~~~AE~f~~~g~~Vl~~~Dsltr~  247 (422)
T TIGR02546       219 AAYTATAIAEYFRDQGKRVLLMMDSLTRF  247 (422)
T ss_pred             HHHHHHHHHHHHHHCCCcEEEEEeCchHH
Confidence            112333445555  578999999999643

>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=93.21  E-value=0.056  Score=50.44  Aligned_cols=21  Identities=24%  Similarity=0.227  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ||.|+|..|+||||+|+.+..
T Consensus         1 ~I~i~G~~GsGKst~a~~la~   21 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAK   21 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999987

>cd04159 Arl10_like Arl10-like subfamily

Probab=93.21  E-value=0.3  Score=45.69  Aligned_cols=21  Identities=10%  Similarity=0.121  Sum_probs=19.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |+|+|..|+|||||.+.+.+.
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            689999999999999999885

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=93.16  E-value=0.16  Score=53.99  Aligned_cols=114  Identities=14%  Similarity=0.091  Sum_probs=59.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      -..+.|+|..|.||||+++.+..  .+.... ..+.+.  -..+.....  .....-......    .....-...+.+.
T Consensus       144 ~~~ili~G~tGsGKTTll~al~~--~~~~~~-~iv~ie--d~~El~~~~--~~~~~l~~~~~~----~~~~~~~~~~~l~  212 (308)
T TIGR02788       144 RKNIIISGGTGSGKTTFLKSLVD--EIPKDE-RIITIE--DTREIFLPH--PNYVHLFYSKGG----QGLAKVTPKDLLQ  212 (308)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHc--cCCccc-cEEEEc--CccccCCCC--CCEEEEEecCCC----CCcCccCHHHHHH
Confidence            46899999999999999999987  333222 222222  111111100  000000000000    0111123455666


Q ss_pred             HhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          259 EYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       259 ~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      ..|+...=.||+|.+.+.+.|+.+... ..+..|  ++.|+...+++.
T Consensus       213 ~~Lr~~pd~ii~gE~r~~e~~~~l~a~-~~g~~~--~i~T~Ha~~~~~  257 (308)
T TIGR02788       213 SCLRMRPDRIILGELRGDEAFDFIRAV-NTGHPG--SITTLHAGSPEE  257 (308)
T ss_pred             HHhcCCCCeEEEeccCCHHHHHHHHHH-hcCCCe--EEEEEeCCCHHH
Confidence            777777778999999998777654433 333322  466665554443

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>TIGR00416 sms DNA repair protein RadA

Probab=93.15  E-value=0.37  Score=54.08  Aligned_cols=54  Identities=15%  Similarity=0.092  Sum_probs=38.3

Q ss_pred             chhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          161 LDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       161 r~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ...-...+-++|..+=..-.++.|.|.+|+|||||+.++...  ....=..++||+
T Consensus        76 i~TGi~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~--~a~~g~kvlYvs  129 (454)
T TIGR00416        76 FSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQ--LAKNQMKVLYVS  129 (454)
T ss_pred             cccCcHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHH--HHhcCCcEEEEE
Confidence            444556666777666445689999999999999999988663  222223577887

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)).

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=93.15  E-value=0.061  Score=49.70  Aligned_cols=35  Identities=17%  Similarity=0.165  Sum_probs=26.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccc-CCCceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVK-HYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~  216 (824)
                      .+|.|+|..|+|||||++.+.+  +.. ..+...+..+
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~--~l~~~g~~v~~ik~   36 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLIN--ELKRRGYRVAVIKH   36 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHH--HHHHTT--EEEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHhHcCCceEEEEE
Confidence            4899999999999999999999  454 4555555555

>PRK06820 type III secretion system ATPase; Validated

Probab=93.14  E-value=0.19  Score=55.42  Aligned_cols=24  Identities=17%  Similarity=0.295  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -..++|+|..|+|||||++.+.+.
T Consensus       163 Gqri~I~G~sG~GKStLl~~I~~~  186 (440)
T PRK06820        163 GQRIGIFAAAGVGKSTLLGMLCAD  186 (440)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcc
Confidence            457899999999999999999883

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=93.12  E-value=0.21  Score=54.89  Aligned_cols=24  Identities=13%  Similarity=0.185  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -..++|+|..|+|||||++.+.+.
T Consensus       175 Gqri~I~G~sG~GKTTLL~~Ia~~  198 (455)
T PRK07960        175 GQRMGLFAGSGVGKSVLLGMMARY  198 (455)
T ss_pred             CcEEEEECCCCCCccHHHHHHhCC
Confidence            468999999999999999999983

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=93.11  E-value=0.059  Score=47.31  Aligned_cols=20  Identities=25%  Similarity=0.343  Sum_probs=18.1

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      |-|+|.+|+|||++|+.+..
T Consensus         1 I~i~G~~G~GKS~l~~~l~~   20 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAK   20 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999887

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

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=93.10  E-value=0.064  Score=47.93  Aligned_cols=22  Identities=18%  Similarity=0.370  Sum_probs=19.8

Q ss_pred             EEEEcCCCChHHHHHHHHhCCc
Q 003387          182 VAILDSIGLDKTAFAGEAYNSS  203 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~~  203 (824)
                      |.|+|..|+|||||.+.+.+.+
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            7899999999999999998753

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>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=93.07  E-value=0.14  Score=50.49  Aligned_cols=22  Identities=14%  Similarity=0.025  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|.|+.|+||||+++.+.+
T Consensus         1 ~~I~ieG~~GsGKtT~~~~L~~   22 (200)
T cd01672           1 MFIVFEGIDGAGKTTLIELLAE   22 (200)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            3689999999999999999988

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>TIGR01287 nifH nitrogenase iron protein

Probab=93.05  E-value=0.061  Score=56.39  Aligned_cols=22  Identities=18%  Similarity=0.203  Sum_probs=19.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.|+|+|-|||||||+|..+..
T Consensus         1 ~~ia~~gKGGVGKTT~a~nLA~   22 (275)
T TIGR01287         1 RQIAIYGKGGIGKSTTTQNIAA   22 (275)
T ss_pred             CeeEEeCCCcCcHHHHHHHHHH
Confidence            4789999999999998877665

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.

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=93.03  E-value=0.71  Score=52.05  Aligned_cols=24  Identities=17%  Similarity=0.166  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||++.+..-
T Consensus        50 GEivgIiGpNGSGKSTLLkiLaGL   73 (549)
T PRK13545         50 GEIVGIIGLNGSGKSTLSNLIAGV   73 (549)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCC
Confidence            469999999999999999999884

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=93.02  E-value=0.072  Score=52.11  Aligned_cols=23  Identities=9%  Similarity=0.196  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .++.|+|+.|+|||||++.+...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcc
Confidence            47899999999999999999873

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=93.01  E-value=0.8  Score=52.68  Aligned_cols=24  Identities=21%  Similarity=0.113  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        37 Ge~~~liG~NGsGKSTLl~~l~Gl   60 (510)
T PRK15439         37 GEVHALLGGNGAGKSTLMKIIAGI   60 (510)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999873

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=92.98  E-value=1.2  Score=46.99  Aligned_cols=24  Identities=17%  Similarity=0.109  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.++++.|+.|.|||||.+.+..-
T Consensus        31 Gei~gllG~NGAGKTTllk~l~gl   54 (293)
T COG1131          31 GEIFGLLGPNGAGKTTLLKILAGL   54 (293)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999883

>PRK03846 adenylylsulfate kinase; Provisional

Probab=92.97  E-value=0.085  Score=52.21  Aligned_cols=24  Identities=21%  Similarity=0.135  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|+|+.|+||||||+.+..
T Consensus        23 ~~~~i~i~G~~GsGKSTla~~l~~   46 (198)
T PRK03846         23 KGVVLWFTGLSGSGKSTVAGALEE   46 (198)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999988

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=92.95  E-value=0.07  Score=51.62  Aligned_cols=22  Identities=9%  Similarity=0.141  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.+.|++|+||||+|+.+..
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~   24 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQS   24 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999987

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>KOG3864 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.95  E-value=0.018  Score=55.07  Aligned_cols=62  Identities=18%  Similarity=0.371  Sum_probs=35.9

Q ss_pred             CCCCccEEeeccCCCCccceec--cCcccCccEEEEecCCCCCCC-ccccccCccCcEEEecCCc
Q 003387          738 GFPNLKVLHLKSMLWLEEWTMG--NAAMPKLECLIINPCAYLKKM-PEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       738 ~~~~L~~L~L~~~~~l~~l~~~--~~~lp~L~~L~l~~c~~l~~l-p~~l~~l~~L~~L~l~~c~  799 (824)
                      .+++++.|.+.+|..+..|..+  -+-.|+|+.|+|++|+.+++- -.++..+++|+.|.+.+.|
T Consensus       123 ~l~~i~~l~l~~ck~~dD~~L~~l~~~~~~L~~L~lsgC~rIT~~GL~~L~~lknLr~L~l~~l~  187 (221)
T KOG3864|consen  123 DLRSIKSLSLANCKYFDDWCLERLGGLAPSLQDLDLSGCPRITDGGLACLLKLKNLRRLHLYDLP  187 (221)
T ss_pred             ccchhhhheeccccchhhHHHHHhcccccchheeeccCCCeechhHHHHHHHhhhhHHHHhcCch
Confidence            4455555555666555555322  224567777777777766532 2245566677777777666

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=92.94  E-value=0.11  Score=53.91  Aligned_cols=54  Identities=22%  Similarity=0.186  Sum_probs=40.7

Q ss_pred             cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHH
Q 003387          174 EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       174 ~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      .+=+.-+++.|+|.+|.|||++|.++..  +.......++||+  ..+.  ..++.+.+.
T Consensus        18 GG~p~g~~~lI~G~pGsGKT~f~~qfl~--~~~~~ge~vlyvs--~~e~--~~~l~~~~~   71 (260)
T COG0467          18 GGLPRGSVVLITGPPGTGKTIFALQFLY--EGAREGEPVLYVS--TEES--PEELLENAR   71 (260)
T ss_pred             CCCcCCcEEEEEcCCCCcHHHHHHHHHH--HHHhcCCcEEEEE--ecCC--HHHHHHHHH
Confidence            4445678999999999999999988877  5666688999998  6553  444444443

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=92.93  E-value=0.09  Score=49.56  Aligned_cols=32  Identities=16%  Similarity=0.171  Sum_probs=24.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCC-CceeEE
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHY-FDCHAW  214 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~~~~w  214 (824)
                      |++|+|+.|+|||||+.++..  +.+.. +...+.
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~--~l~~~G~~V~vi   33 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVK--ALKARGYRVATI   33 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHH--HHHhcCCeEEEE
Confidence            689999999999999999998  44433 444333

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=92.93  E-value=0.2  Score=58.35  Aligned_cols=75  Identities=11%  Similarity=0.007  Sum_probs=53.2

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC-CCceeEEEECCCCCCCCHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFDCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      -++++|.++.++.+...+..+.    .+-++|+.|+||||+|+.+.+  .+.. .|...+++.   ...-+...+++.++
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~----~~ll~G~pG~GKT~la~~la~--~l~~~~~~~~~~~~---n~~~~~~~~~~~v~   87 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKR----NVLLIGEPGVGKSMLAKAMAE--LLPDEELEDILVYP---NPEDPNMPRIVEVP   87 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCC----CEEEECCCCCCHHHHHHHHHH--HcCchhheeEEEEe---CCCCCchHHHHHHH
Confidence            3678899988887777776543    455999999999999999998  5544 344444443   23335566788888


Q ss_pred             HHhCC
Q 003387          234 KFLMP  238 (824)
Q Consensus       234 ~~l~~  238 (824)
                      .+++.
T Consensus        88 ~~~g~   92 (608)
T TIGR00764        88 AGEGR   92 (608)
T ss_pred             Hhhch
Confidence            77765

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase

Probab=92.91  E-value=0.071  Score=53.43  Aligned_cols=22  Identities=18%  Similarity=0.209  Sum_probs=18.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|+|.|-||+||||++..+..
T Consensus         1 ~~iav~gKGGvGKTt~~~nLA~   22 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSA   22 (212)
T ss_pred             CEEEEECCCcCcHHHHHHHHHH
Confidence            4799999999999998876655

Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.

>PF13306 LRR_5: Leucine rich repeats (6 copies); PDB: 3ZYJ_A 3V47_B 3V44_A 3ZYN_A 3ZYO_A 3SB4_A

Probab=92.91  E-value=0.2  Score=45.39  Aligned_cols=100  Identities=21%  Similarity=0.210  Sum_probs=57.0

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L  570 (824)
                      +.+|+.+.+....     ..+....|..++.|+.+.+.++ +..++. .+.++..|+++.+.. .+..++...|..+++|
T Consensus        11 ~~~l~~i~~~~~~-----~~I~~~~F~~~~~l~~i~~~~~-~~~i~~~~F~~~~~l~~i~~~~-~~~~i~~~~F~~~~~l   83 (129)
T PF13306_consen   11 CSNLESITFPNTI-----KKIGENAFSNCTSLKSINFPNN-LTSIGDNAFSNCKSLESITFPN-NLKSIGDNAFSNCTNL   83 (129)
T ss_dssp             -TT--EEEETST-------EE-TTTTTT-TT-SEEEESST-TSCE-TTTTTT-TT-EEEEETS-TT-EE-TTTTTT-TTE
T ss_pred             CCCCCEEEECCCe-----eEeChhhccccccccccccccc-ccccceeeeecccccccccccc-cccccccccccccccc
Confidence            5577777765421     2355677888888999998875 665554 356677899999965 6667777666778999


Q ss_pred             cEeecCCccccccchh-hhccccCceecCCC
Q 003387          571 YTLDMPFSYIDHTADE-FWKMNKLRHLNFGS  600 (824)
Q Consensus       571 ~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~  600 (824)
                      +.+++..+ +..++.. +.++ +|+.+.+..
T Consensus        84 ~~i~~~~~-~~~i~~~~f~~~-~l~~i~~~~  112 (129)
T PF13306_consen   84 KNIDIPSN-ITEIGSSSFSNC-NLKEINIPS  112 (129)
T ss_dssp             CEEEETTT--BEEHTTTTTT--T--EEE-TT
T ss_pred             cccccCcc-ccEEchhhhcCC-CceEEEECC
Confidence            99998654 6666544 5565 777775543

>PRK00300 gmk guanylate kinase; Provisional

Probab=92.89  E-value=0.07  Score=53.11  Aligned_cols=24  Identities=8%  Similarity=0.130  Sum_probs=21.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+|+|+|+.|+||||||+.+...
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999999983

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=92.88  E-value=0.88  Score=52.64  Aligned_cols=24  Identities=13%  Similarity=0.094  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||++.+...
T Consensus        27 Ge~~~liG~NGsGKSTLl~~l~Gl   50 (530)
T PRK15064         27 GNRYGLIGANGCGKSTFMKILGGD   50 (530)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999874

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=92.86  E-value=0.38  Score=55.20  Aligned_cols=47  Identities=13%  Similarity=0.058  Sum_probs=37.0

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+.++|....+.++++.+..-...-.-|-|+|..|.||+++|+.+++
T Consensus       203 f~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~  249 (520)
T PRK10820        203 FSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHL  249 (520)
T ss_pred             ccceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHH
Confidence            45799999998888888764221233477999999999999999976

>KOG3864 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.82  E-value=0.0075  Score=57.58  Aligned_cols=87  Identities=17%  Similarity=0.170  Sum_probs=66.0

Q ss_pred             CceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCe-eeecCCCCCCccEEeeccCCCCccce-eccCcccCccEE
Q 003387          692 SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRK-LTCGSYGFPNLKVLHLKSMLWLEEWT-MGNAAMPKLECL  769 (824)
Q Consensus       692 ~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~-~~~~~~~~~~L~~L~L~~~~~l~~l~-~~~~~lp~L~~L  769 (824)
                      .++.++-+++.+......-+.+++.++.|.+.+|...++. +....+.+|+|+.|+|++|+.+++-- ..+..+++|+.|
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            4677888888887777888889999999999988765432 22233468999999999999887542 235678999999


Q ss_pred             EEecCCCCC
Q 003387          770 IINPCAYLK  778 (824)
Q Consensus       770 ~l~~c~~l~  778 (824)
                      .|.+-+...
T Consensus       182 ~l~~l~~v~  190 (221)
T KOG3864|consen  182 HLYDLPYVA  190 (221)
T ss_pred             HhcCchhhh
Confidence            998766543

>PRK15453 phosphoribulokinase; Provisional

Probab=92.80  E-value=0.44  Score=48.99  Aligned_cols=84  Identities=12%  Similarity=0.034  Sum_probs=43.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHH--HhCCCCCcccccccCHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK--FLMPSSRLSEIMDKNYEMKKI  255 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~--~l~~~~~~~~~~~~~~~~~~~  255 (824)
                      ...+|+|.|-.|.||||+|+.+.+  ..+..=...+.++..-=..++..++-..+..  .-+.+-+....+..+.+.+.+
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~--if~~~~~~~~vi~~D~yh~ydr~~~~~~~~~~~r~g~nfdhf~PdAnd~dlL~~   81 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEK--IFRRENINAAVVEGDSFHRYTRPEMKAAIAKARAAGRHFSHFGPEANLFDELEQ   81 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH--HHhhcCCCeEEEecccccccChhhHhhhhHHHHhcCCCCCCCCCCcccHHHHHH
Confidence            356999999999999999998875  2221101234444111122344343333321  112111110024455667777


Q ss_pred             HHHHhcCC
Q 003387          256 ILHEYLMT  263 (824)
Q Consensus       256 ~l~~~L~~  263 (824)
                      .++...++
T Consensus        82 ~l~~l~~~   89 (290)
T PRK15453         82 LFREYGET   89 (290)
T ss_pred             HHHHHhcC
Confidence            77766553

>PRK13230 nitrogenase reductase-like protein; Reviewed

Probab=92.78  E-value=0.076  Score=55.79  Aligned_cols=22  Identities=9%  Similarity=0.058  Sum_probs=19.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|+|+|-|||||||+|..+..
T Consensus         2 ~~i~~~gKGGVGKTT~a~nLA~   23 (279)
T PRK13230          2 RKFCFYGKGGIGKSTTVCNIAA   23 (279)
T ss_pred             cEEEEECCCCCcHHHHHHHHHH
Confidence            5789999999999998877655

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=92.77  E-value=0.44  Score=52.87  Aligned_cols=99  Identities=16%  Similarity=0.142  Sum_probs=53.1

Q ss_pred             eEEEEEEcCCCChHHHHH-HHHhCCccccCCCcee-EEEECCCCCCC-CHHHHHHHHHHHhCCCCCcc--cccccCH---
Q 003387          179 LSVVAILDSIGLDKTAFA-GEAYNSSYVKHYFDCH-AWITEPYSNEY-DADQILDIVIKFLMPSSRLS--EIMDKNY---  250 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa-~~v~~~~~~~~~F~~~-~wv~~~vs~~~-~~~~~~~~i~~~l~~~~~~~--~~~~~~~---  250 (824)
                      -.-++|.|-.|+|||||| ..+.|.  .  .-+.+ +++-  +.+.. .+.++.+++...=......-  ...+.+.   
T Consensus       141 GQR~~I~g~~g~GKt~Lal~~I~~q--~--~~dv~cV~~~--IGer~rev~e~~~~l~~~~~l~~tvvV~atad~~~~~r  214 (485)
T CHL00059        141 GQRELIIGDRQTGKTAVATDTILNQ--K--GQNVICVYVA--IGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQ  214 (485)
T ss_pred             CCEEEeecCCCCCHHHHHHHHHHhc--c--cCCeEEEEEE--ecCCchHHHHHHHHhhcccchhceEEEEeCCCCCHHHH
Confidence            457899999999999995 566663  2  23433 5666  66543 44455555544321110000  0001111   


Q ss_pred             ---HHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          251 ---EMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       251 ---~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                         .-.+..+.+++  +++.+|+|+||+-.. ..+.++.
T Consensus       215 ~~ap~~a~aiAEyfr~~G~~VLlv~DdlTr~A~A~REis  253 (485)
T CHL00059        215 YLAPYTGAALAEYFMYRGRHTLIIYDDLSKQAQAYRQMS  253 (485)
T ss_pred             HHHHHHHhhHHHHHHHcCCCEEEEEcChhHHHHHHHHHH
Confidence               11122233333  579999999999764 3455554

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=92.67  E-value=0.14  Score=48.72  Aligned_cols=25  Identities=8%  Similarity=0.181  Sum_probs=22.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCc
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSS  203 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~  203 (824)
                      -.++.|.|+.|+|||||+++++.+.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            4688999999999999999999954

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=92.66  E-value=0.2  Score=51.92  Aligned_cols=91  Identities=16%  Similarity=0.094  Sum_probs=48.8

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCC---CcccccccCHHHH
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSS---RLSEIMDKNYEMK  253 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~---~~~~~~~~~~~~~  253 (824)
                      .+..+|.|+|..|.|||||+..+.+  ....... .+.+..+.....|.     +.++..+...   .....--.+...+
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~--~l~~~~~-~~VI~gD~~t~~Da-----~rI~~~g~pvvqi~tG~~Chl~a~mv  173 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLM--RLKDSVP-CAVIEGDQQTVNDA-----ARIRATGTPAIQVNTGKGCHLDAQMI  173 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHH--HhccCCC-EEEECCCcCcHHHH-----HHHHhcCCcEEEecCCCCCcCcHHHH
Confidence            4689999999999999999999988  4444443 33332112222122     2233332210   0000011233444


Q ss_pred             HHHHHHhcCCCeEEEEEecCCC
Q 003387          254 KIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       254 ~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      ...+...-...-=++|+++|-.
T Consensus       174 ~~Al~~L~~~~~d~liIEnvGn  195 (290)
T PRK10463        174 ADAAPRLPLDDNGILFIENVGN  195 (290)
T ss_pred             HHHHHHHhhcCCcEEEEECCCC
Confidence            5555554444456778899864

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=92.66  E-value=0.082  Score=48.76  Aligned_cols=43  Identities=23%  Similarity=0.115  Sum_probs=32.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      +|.|-|.+|.||||+|+.+.++  ..-.|         +|    ...++++|++.-+.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~--~gl~~---------vs----aG~iFR~~A~e~gm   44 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEH--LGLKL---------VS----AGTIFREMARERGM   44 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHH--hCCce---------ee----ccHHHHHHHHHcCC
Confidence            7899999999999999999984  22111         22    34678888887765

>PRK13975 thymidylate kinase; Provisional

Probab=92.65  E-value=0.081  Score=52.22  Aligned_cols=22  Identities=18%  Similarity=0.009  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|.|+.|+||||+|+.+.+
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~   24 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAE   24 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999998

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=92.64  E-value=0.1  Score=45.27  Aligned_cols=22  Identities=32%  Similarity=0.217  Sum_probs=20.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHh
Q 003387          179 LSVVAILDSIGLDKTAFAGEAY  200 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~  200 (824)
                      -..++|+|..|.|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4689999999999999999986

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.62  E-value=0.69  Score=50.80  Aligned_cols=76  Identities=22%  Similarity=0.196  Sum_probs=47.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  257 (824)
                      .+.-+-+-|++|+|||+||..+..+    ..|..+=-++    ..    +                 +-..++......+
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKiiS----pe----~-----------------miG~sEsaKc~~i  587 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKIIS----PE----D-----------------MIGLSESAKCAHI  587 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEeC----hH----H-----------------ccCccHHHHHHHH
Confidence            5677778999999999999999873    5565443332    11    0                 1122333334444


Q ss_pred             HHhc----CCCeEEEEEecCCChhhHHHH
Q 003387          258 HEYL----MTKRYLIVIDDVWSIDMWDVI  282 (824)
Q Consensus       258 ~~~L----~~kr~LlVlDdv~~~~~~~~l  282 (824)
                      ++..    +..=-.||+||+...-+|-.+
T Consensus       588 ~k~F~DAYkS~lsiivvDdiErLiD~vpI  616 (744)
T KOG0741|consen  588 KKIFEDAYKSPLSIIVVDDIERLLDYVPI  616 (744)
T ss_pred             HHHHHHhhcCcceEEEEcchhhhhccccc
Confidence            4433    445678999999776555433

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=92.62  E-value=0.28  Score=50.48  Aligned_cols=81  Identities=12%  Similarity=0.092  Sum_probs=47.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCc--cccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSS--YVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKII  256 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~--~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  256 (824)
                      -++|-+.|++|-|||+|++++++.-  |....|.....+.  ++.    ..++..-...          ...-+..+-+.
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liE--ins----hsLFSKWFsE----------SgKlV~kmF~k  240 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIE--INS----HSLFSKWFSE----------SGKLVAKMFQK  240 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEE--Eeh----hHHHHHHHhh----------hhhHHHHHHHH
Confidence            4889999999999999999999963  3344554444444  221    1222222111          11123445555


Q ss_pred             HHHhcCCCe--EEEEEecCCC
Q 003387          257 LHEYLMTKR--YLIVIDDVWS  275 (824)
Q Consensus       257 l~~~L~~kr--~LlVlDdv~~  275 (824)
                      |.+.++++.  +++.+|.|.+
T Consensus       241 I~ELv~d~~~lVfvLIDEVES  261 (423)
T KOG0744|consen  241 IQELVEDRGNLVFVLIDEVES  261 (423)
T ss_pred             HHHHHhCCCcEEEEEeHHHHH
Confidence            566665543  4556688854

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=92.59  E-value=0.14  Score=54.02  Aligned_cols=47  Identities=15%  Similarity=0.336  Sum_probs=41.4

Q ss_pred             CCCceechhhHHHHHHHHHcC----CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEG----PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +..++|+++.++++++.+...    +..-+|+-.+|+.|.||||||..+-+
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~  110 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKR  110 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHH
Confidence            358999999999999999864    34579999999999999999998877

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>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=92.59  E-value=0.068  Score=29.42  Aligned_cols=15  Identities=33%  Similarity=0.394  Sum_probs=5.3

Q ss_pred             CccEeecCCcccccc
Q 003387          569 NLYTLDMPFSYIDHT  583 (824)
Q Consensus       569 ~L~~L~L~~~~l~~l  583 (824)
                      +|++|+|++|.++++
T Consensus         2 ~L~~L~l~~n~L~~l   16 (17)
T PF13504_consen    2 NLRTLDLSNNRLTSL   16 (17)
T ss_dssp             T-SEEEETSS--SSE
T ss_pred             ccCEEECCCCCCCCC
Confidence            344444444444443

...

>PRK13232 nifH nitrogenase reductase; Reviewed

Probab=92.59  E-value=0.082  Score=55.35  Aligned_cols=22  Identities=18%  Similarity=0.202  Sum_probs=18.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|+|+|-|||||||+|..+..
T Consensus         2 ~~iav~gKGGVGKTT~a~nLA~   23 (273)
T PRK13232          2 RQIAIYGKGGIGKSTTTQNLTA   23 (273)
T ss_pred             CEEEEECCCCCcHHHHHHHHHH
Confidence            5789999999999998877655

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=92.58  E-value=0.11  Score=49.93  Aligned_cols=27  Identities=22%  Similarity=0.274  Sum_probs=21.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHY  208 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~  208 (824)
                      ..|-+.|.+|+||||+|+.+..  ..++.
T Consensus         2 pLiIlTGyPgsGKTtfakeLak--~L~~~   28 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAK--ELRQE   28 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHH--HHHHh
Confidence            3567899999999999999887  44433

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=92.49  E-value=0.097  Score=51.45  Aligned_cols=23  Identities=17%  Similarity=0.284  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|||+|+.|+||||.|+.+-+
T Consensus         2 ~~iIglTG~igsGKStva~~~~~   24 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAE   24 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHH
Confidence            46899999999999999988766

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=92.46  E-value=0.48  Score=50.45  Aligned_cols=24  Identities=21%  Similarity=0.284  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+++|++|+||||++..+..
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~  136 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAH  136 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            468999999999999999999887

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=92.45  E-value=0.25  Score=56.64  Aligned_cols=94  Identities=18%  Similarity=0.137  Sum_probs=57.5

Q ss_pred             CCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCC
Q 003387          156 RDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD  224 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~  224 (824)
                      .++.|.+..++.+.+.+..           +-...+.+-++|++|.|||.||+++.+  .....|-.+.+-.        
T Consensus       242 ~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~--~~~~~fi~v~~~~--------  311 (494)
T COG0464         242 DDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVAL--ESRSRFISVKGSE--------  311 (494)
T ss_pred             ehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHh--hCCCeEEEeeCHH--------
Confidence            4566766666665554432           113567889999999999999999999  5555553322211        


Q ss_pred             HHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          225 ADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       225 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                             ++..         .-..............-+.....|.+|+++.
T Consensus       312 -------l~sk---------~vGesek~ir~~F~~A~~~~p~iiFiDEiDs  346 (494)
T COG0464         312 -------LLSK---------WVGESEKNIRELFEKARKLAPSIIFIDEIDS  346 (494)
T ss_pred             -------Hhcc---------ccchHHHHHHHHHHHHHcCCCcEEEEEchhh
Confidence                   1110         1111233344444445567889999999964

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=92.45  E-value=0.09  Score=50.64  Aligned_cols=23  Identities=9%  Similarity=0.208  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+.|.|+|+.|.||||+|+.+.+
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~   26 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQ   26 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHH
Confidence            35699999999999999999988

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=92.45  E-value=0.1  Score=47.97  Aligned_cols=23  Identities=22%  Similarity=0.250  Sum_probs=21.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .+++|+|..|.|||||.+.+...
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~g~   34 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALAGL   34 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CEEEEEccCCCccccceeeeccc
Confidence            58999999999999999999884

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=92.45  E-value=0.45  Score=50.41  Aligned_cols=100  Identities=15%  Similarity=0.148  Sum_probs=56.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCCC--CC-ccc------cccc
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMPS--SR-LSE------IMDK  248 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~~--~~-~~~------~~~~  248 (824)
                      -..++|.|..|+|||+|++.+.+..    +-+.++++-  +.+.. .+.+++.++-+.....  .+ ...      ..++
T Consensus       157 Gqr~~I~G~~G~GKT~L~~~Iak~~----~~dvvVyv~--iGERg~Ev~e~l~ef~~l~~~~~~~~~m~rtvlV~nts~~  230 (369)
T cd01134         157 GGTAAIPGPFGCGKTVIQQSLSKYS----NSDIVIYVG--CGERGNEMTEVLEEFPELTDPVTGEPLMKRTVLIANTSNM  230 (369)
T ss_pred             CCEEEEECCCCCChHHHHHHHHhCC----CCCEEEEEE--eCCChHHHHHHHHHHHhhccccccCCccceEEEEEECCCC
Confidence            3488999999999999999999942    235677776  66553 3345555543321110  00 000      0111


Q ss_pred             CH------HHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHHh
Q 003387          249 NY------EMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQE  284 (824)
Q Consensus       249 ~~------~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~~  284 (824)
                      ..      --....+.+++  +++.+|+++|++..- +...++..
T Consensus       231 p~~~R~~s~yta~tiAEYfrd~G~dVll~~Ds~tR~A~A~REIs~  275 (369)
T cd01134         231 PVAAREASIYTGITIAEYFRDMGYNVALMADSTSRWAEALREISG  275 (369)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHcCCCEEEEEcChhHHHHHHHHHHH
Confidence            11      11122344444  579999999998433 34444443

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.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=92.44  E-value=0.43  Score=56.56  Aligned_cols=48  Identities=15%  Similarity=0.077  Sum_probs=38.3

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .+.++|....+.++.+.+..-...-.-|-|+|..|+||+++|+.+++.
T Consensus       324 ~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~  371 (638)
T PRK11388        324 FDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNE  371 (638)
T ss_pred             ccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHh
Confidence            456899999999888887753322334679999999999999999983

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=92.41  E-value=0.18  Score=53.67  Aligned_cols=37  Identities=24%  Similarity=0.267  Sum_probs=29.1

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+.+.+........+|+|.|.+|+|||||+..+..
T Consensus        42 ~~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~   78 (332)
T PRK09435         42 AQELLDALLPHTGNALRIGITGVPGVGKSTFIEALGM   78 (332)
T ss_pred             HHHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHH
Confidence            3456666654445688999999999999999998766

>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]

Probab=92.40  E-value=0.3  Score=48.27  Aligned_cols=36  Identities=14%  Similarity=-0.151  Sum_probs=29.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      -..|+|=|+.|+||||.++.++.  ..+.....++|..
T Consensus         3 g~fI~iEGiDGaGKTT~~~~L~~--~l~~~g~~v~~tr   38 (208)
T COG0125           3 GMFIVIEGIDGAGKTTQAELLKE--RLEERGIKVVLTR   38 (208)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH--HHHHcCCeEEEEe
Confidence            46799999999999999999999  6666655667665

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=92.39  E-value=0.51  Score=52.67  Aligned_cols=99  Identities=13%  Similarity=0.022  Sum_probs=55.8

Q ss_pred             eEEEEEEcCCCChHHHHH-HHHhCCccccCCCce-eEEEECCCCCCC-CHHHHHHHHHHHhCCCC--------Ccccccc
Q 003387          179 LSVVAILDSIGLDKTAFA-GEAYNSSYVKHYFDC-HAWITEPYSNEY-DADQILDIVIKFLMPSS--------RLSEIMD  247 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~~~vs~~~-~~~~~~~~i~~~l~~~~--------~~~~~~~  247 (824)
                      -.-++|.|-.|+|||||| ..+.|.  .  .-+. ++++-  +.+.. .+.++.+++...=....        +.+....
T Consensus       162 GQR~~Ifg~~g~GKT~Lal~~I~~q--~--~~dv~~V~~~--IGeR~rev~e~i~~l~~~~~l~~tvvV~atsd~p~~~r  235 (497)
T TIGR03324       162 GQRELILGDRQTGKTAIAIDTILNQ--K--GRNVLCIYCA--IGQRASAVAKVVANLREHGAMDYTIVVVTEGNDPPGLQ  235 (497)
T ss_pred             CCEEEeecCCCCCHHHHHHHHHHHh--c--CCCcEEEEEE--eccCcHHHHHHHHHhhhcCCcceeEEEEeCCCCCHHHH
Confidence            457899999999999996 577773  2  2343 56666  66653 34455555544321110        1010000


Q ss_pred             cCHHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHH
Q 003387          248 KNYEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQ  283 (824)
Q Consensus       248 ~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~  283 (824)
                      .-..-.+..+.+++  +++.+|||+||+-.. ..+.++.
T Consensus       236 ~~ap~~a~aiAEyfrd~G~~VLlv~DdlTr~A~A~REis  274 (497)
T TIGR03324       236 YIAPYAATSIGEHFMEQGRDVLIVYDDLTQHARAYRELS  274 (497)
T ss_pred             HHHHHHHHHHHHHHHhCCCCEEEEEcChhHHHHHHHHHH
Confidence            01111233344544  589999999999754 3444443

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=92.37  E-value=0.092  Score=52.82  Aligned_cols=23  Identities=17%  Similarity=0.247  Sum_probs=21.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .-|.|+|++|+|||||+..+.++
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~   28 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGD   28 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcC
Confidence            56899999999999999999986

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=92.37  E-value=0.35  Score=51.26  Aligned_cols=59  Identities=20%  Similarity=0.183  Sum_probs=41.6

Q ss_pred             CCCceechhhHHH---HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEE
Q 003387          155 SRDTVGLDDRMEE---LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWI  215 (824)
Q Consensus       155 ~~~~vGr~~~~~~---l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv  215 (824)
                      ...+||..+.++.   +++++..+.-.-+.|-+.|++|.|||+||..+.+  +.......+...
T Consensus        23 ~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~--eLG~~~PF~~is   84 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAK--ELGEDVPFVSIS   84 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHH--HCTTTS-EEEEE
T ss_pred             cccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHH--HhCCCCCeeEcc
Confidence            4689998777665   6788877765567888999999999999999999  676655544443

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=92.36  E-value=0.21  Score=58.04  Aligned_cols=75  Identities=12%  Similarity=0.032  Sum_probs=57.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcccc-CCCceeEEEECCCCCCCCHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVK-HYFDCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      -++++|.+..++.+...+..+    +.+-++|.+|.||||+|+.+.+  .+. ..|+..+|..  - ..-+...+++.++
T Consensus        30 ~~~vigq~~a~~~L~~~~~~~----~~~l~~G~~G~GKttla~~l~~--~l~~~~~~~~~~~~--n-p~~~~~~~~~~v~  100 (637)
T PRK13765         30 IDQVIGQEHAVEVIKKAAKQR----RHVMMIGSPGTGKSMLAKAMAE--LLPKEELQDILVYP--N-PEDPNNPKIRTVP  100 (637)
T ss_pred             HHHcCChHHHHHHHHHHHHhC----CeEEEECCCCCcHHHHHHHHHH--HcChHhHHHheEee--C-CCcchHHHHHHHH
Confidence            357889988888888777654    3688999999999999999987  343 3457888886  3 4447778888888


Q ss_pred             HHhCC
Q 003387          234 KFLMP  238 (824)
Q Consensus       234 ~~l~~  238 (824)
                      .+++.
T Consensus       101 ~~~G~  105 (637)
T PRK13765        101 AGKGK  105 (637)
T ss_pred             HhcCH
Confidence            76665

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.35  E-value=0.43  Score=53.39  Aligned_cols=38  Identities=21%  Similarity=0.213  Sum_probs=26.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      -+|++++|..|+||||++.++......+..-..+..|+
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~~kV~LI~  293 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLT  293 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCCCeEEEEe
Confidence            47999999999999999999987322222122455565

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=92.34  E-value=2  Score=48.10  Aligned_cols=75  Identities=16%  Similarity=0.111  Sum_probs=49.4

Q ss_pred             ceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhC
Q 003387          158 TVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLM  237 (824)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~  237 (824)
                      ..|...-...+-+++. +-..-.++.|-|.+|+||||+|..+..+.-.+.. ..++|++    -+.+..++...++....
T Consensus       174 ~~gi~tG~~~LD~~~~-G~~~g~liviag~pg~GKT~~al~ia~~~a~~~g-~~v~~fS----lEm~~~~l~~Rl~~~~~  247 (421)
T TIGR03600       174 LTGLSTGLPKLDRLTN-GLVKGDLIVIGARPSMGKTTLALNIAENVALREG-KPVLFFS----LEMSAEQLGERLLASKS  247 (421)
T ss_pred             CcceeCCChhHHHHhc-CCCCCceEEEEeCCCCCHHHHHHHHHHHHHHhCC-CcEEEEE----CCCCHHHHHHHHHHHHc
Confidence            4455555666666554 4334568899999999999999988753221222 2455554    44577888888877655


Q ss_pred             C
Q 003387          238 P  238 (824)
Q Consensus       238 ~  238 (824)
                      +
T Consensus       248 ~  248 (421)
T TIGR03600       248 G  248 (421)
T ss_pred             C
Confidence            4

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

---

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	824
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-32
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	8e-24
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	2e-09
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	2e-17
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	4e-09
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	1e-14
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	3e-10
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	3e-10
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	3e-08
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-14
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	6e-13
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	5e-12
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	2e-08
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	4e-07
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	6e-05
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	6e-04
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	5e-14
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-13
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	7e-11
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	4e-09
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	3e-08
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	1e-07
3fxi_A	605	TLR4, htoll, TOLL-like receptor 4; leucine rich re	3e-07
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	9e-14
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	2e-11
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	3e-13
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-12
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	7e-12
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	1e-11
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	3e-09
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	2e-12
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-12
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-11
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	2e-04
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	4e-12
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	6e-12
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	7e-11
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	2e-09
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	7e-08
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	9e-12
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	4e-10
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	2e-08
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	7e-08
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	1e-11
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	1e-09
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	2e-09
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	1e-08
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	4e-11
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	7e-09
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	2e-08
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	2e-05
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	4e-11
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	1e-07
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	5e-11
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	3e-09
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	8e-11
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	1e-07
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	4e-06
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	2e-10
3jqh_A	167	C-type lectin domain family 4 member M; DC-signr,	4e-06
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	4e-10
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	3e-07
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	1e-06
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	5e-10
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	5e-09
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	3e-08
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	5e-10
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	9e-10
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	7e-10
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	2e-09
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	3e-09
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	1e-07
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	6e-06
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-09
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	3e-09
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	2e-08
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	4e-06
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	3e-09
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	8e-05
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	5e-09
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	3e-08
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	9e-08
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	6e-06
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	5e-09
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	1e-08
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	3e-04
1o6v_A	466	Internalin A; bacterial infection, extracellular r	1e-08
1o6v_A	466	Internalin A; bacterial infection, extracellular r	8e-07
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	3e-08
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	8e-06
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	1e-05
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	3e-08
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	1e-07
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	3e-06
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	6e-04
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	1e-07
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	2e-07
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	2e-04
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	7e-07
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	2e-04
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	2e-06
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	4e-06
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	5e-06
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	7e-06
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	1e-05
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	2e-05
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	4e-05
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	2e-05
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	5e-04
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	2e-05
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	3e-05
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	3e-04
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	3e-04
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	3e-04
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	5e-04

>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 =  135 bits (341), Expect = 1e-32
 Identities = 113/611 (18%), Positives = 202/611 (33%), Gaps = 162/611 (26%)

Query: 45  LSEFEDDISLLLFEKMAEEESHDPDLATVMDEINWFTYESEKVIDTFINSITQQKTQSSC 104
           LS FED      F         + D   V D           +    I+ I   K   S 
Sbjct: 22  LSVFEDA-----FVD-------NFDCKDVQD------MPKSILSKEEIDHIIMSKDAVSG 63

Query: 105 SKDIFDALQGLQSRITDIKQRMQQLKHMDSK-IIDRIKT-SKAEAGISSS-SKSRDTVGL 161
           +  +F  L   Q  +  +++ ++++  ++ K ++  IKT  +  + ++    + RD +  
Sbjct: 64  TLRLFWTLLSKQEEM--VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN 121

Query: 162 DD---------RMEELLDL---LIEGPPQLSVVAILDS-IGLDKTAFAGEAYNSSYVKHY 208
           D+         R++  L L   L+E  P  +V+  +D  +G  KT  A +   S  V+  
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL--IDGVLGSGKTWVALDVCLSYKVQCK 179

Query: 209 FDCHA-WITEPYSNEYDADQILDIVIKFLM----PSSRLSEIMDK---NYEMKKIILHEY 260
            D    W+     N    + +L+++ K L       +  S+            +  L   
Sbjct: 180 MDFKIFWLN--LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237

Query: 261 LMTKRY---LIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRII------------ 305
           L +K Y   L+V+ +V +   W+             ++L+T    ++             
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVTDFLSAATTTHIS 290

Query: 306 ---ISFQFEDGENMRL-----DLVPTGGPLRATYKGRPFLILYHGSISLEENIREAVETP 357
               S      E   L     D  P   P        P  +     I+  E+IR+ + T 
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVL-TTNPRRL---SIIA--ESIRDGLATW 344

Query: 358 LGLRYIKCLML------------PFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPD 405
              +++ C  L            P   +  F  LSVFP    I T  L  +W       D
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIW------FD 398

Query: 406 NSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFICSPFMDP 465
             ++     + +L K   VE K+ K      T SIP      ++             ++ 
Sbjct: 399 VIKSDVMVVVNKLHKYSLVE-KQPKES----TISIPS-----IY-------------LEL 435

Query: 466 KGKSPKKA---KRLNAVER--------EGDFA--CLDDYDSQLHSLLCCSPETRHLDPID 512
           K K   +    + +  V+           D     LD Y    +S +       HL  I+
Sbjct: 436 KVKLENEYALHRSI--VDHYNIPKTFDSDDLIPPYLDQY---FYSHI-----GHHLKNIE 485

Query: 513 WEKFCGMFKLLRVLDLGSL--------VLIQYPSGIENLFL-----LRYLKLNIPSLNSL 559
             +   +F+++  LD   L                I N          Y+  N P    L
Sbjct: 486 HPERMTLFRMV-FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERL 544

Query: 560 PSSLLSNLLNL 570
            +++L  L  +
Sbjct: 545 VNAILDFLPKI 555

>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 = 51.4 bits (122), Expect = 1e-06
 Identities = 55/453 (12%), Positives = 130/453 (28%), Gaps = 137/453 (30%)

Query: 10  ERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEEESHDPD 69
           ++L   +     +  D +      +H             + ++  LL  K      ++  
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKLRIH-----------SIQAELRRLLKSKP-----YENC 246

Query: 70  LATVMDEINWFTYESEKVIDTF-INS---ITQQKTQSSCSKDIFDALQGLQSRITDIKQR 125
           L  V+  +      + K  + F ++    +T   T+    K + D L    +    +   
Sbjct: 247 L-LVLLNV-Q----NAKAWNAFNLSCKILLT---TR---FKQVTDFLSAATTTHISLDHH 294

Query: 126 MQQLKHMDS-----KIID-RIKTSKAEA------GISSSSKS-RDTVGLDDRMEELLDLL 172
              L   +      K +D R +    E        +S  ++S RD +      +    + 
Sbjct: 295 SMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL---ATWDNWKHVN 351

Query: 173 IEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF-DC-----HAWITEP-------Y 219
            +   +L+ + I  S+              +  +  F         A I           
Sbjct: 352 CD---KLTTI-IESSL---------NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFD 398

Query: 220 SNEYDADQILDIVIKFLM----PSSRLSEIMD----------KNYEMKKIILHEYLMTKR 265
             + D   +++ + K+ +    P      I              Y + + I+  Y + K 
Sbjct: 399 VIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT 458

Query: 266 YLIVIDDVWSIDMWDVIQEILPDN-------------QNGSRV-LITLTDIRIIISFQFE 311
           +          D  D+I   L D              ++  R+ L       + + F+F 
Sbjct: 459 F----------DSDDLIPPYL-DQYFYSHIGHHLKNIEHPERMTLFR----MVFLDFRF- 502

Query: 312 DGENMRLDLVPTGGPLRATYKGRPFLI---LYHGSISLEENIREAVETPLGLRYI----- 363
               +   +        A+      L     Y   I   +   E +   + L ++     
Sbjct: 503 ----LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAI-LDFLPKIEE 557

Query: 364 KCLMLPFCLKPCFIYLSVFPAHQEI---STRQL 393
             +   +      + +++    + I   + +Q+
Sbjct: 558 NLICSKYT---DLLRIALMAEDEAIFEEAHKQV 587

>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 =  105 bits (264), Expect = 8e-24
 Identities = 37/267 (13%), Positives = 83/267 (31%), Gaps = 35/267 (13%)

Query: 56  LFEKMAEEESHDPDLATVMDEI---NWFTYESEKVIDTFINSITQ--------QKTQSSC 104
              +  E    D   + +MD +    + T   E+ +        +         K  +  
Sbjct: 8   CLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDS 67

Query: 105 SKDIFDALQGLQSRITDIKQRMQQLKHMDSKIIDRIKTSKAEAGISSSS-------KSRD 157
               ++AL        D+   +     + S    +   S   + + +         +   
Sbjct: 68  YVSFYNALLH--EGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVV 125

Query: 158 TVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSY-VKHYFDCH-AWI 215
            V     +  +   L +   +   V I    G  K+  A EA      ++  F     W+
Sbjct: 126 FVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWV 185

Query: 216 TEPYSNEYDADQILDI--VIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVID 271
           +     +  +  ++ +  +   L      S+ +  N E  K  L   ++    R L+++D
Sbjct: 186 S--VGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILD 243

Query: 272 DVWSIDMWDVIQEILPDNQNGSRVLIT 298
           DVW   +            +  ++L+T
Sbjct: 244 DVWDSWVLKAF-------DSQCQILLT 263

>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 = 60.2 bits (146), Expect = 2e-09
 Identities = 12/73 (16%), Positives = 25/73 (34%), Gaps = 10/73 (13%)

Query: 368 LPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAK 427
           L   +K  +  LS+     ++ T+ L  LW  E           E  L++ + +  +   
Sbjct: 375 LREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEE-------VEDILQEFVNKSLLFCD 427

Query: 428 KRKAGGTINTCSI 440
           +    G      +
Sbjct: 428 RN---GKSFRYYL 437

>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 = 85.4 bits (211), Expect = 2e-17
 Identities = 33/259 (12%), Positives = 79/259 (30%), Gaps = 32/259 (12%)

Query: 66  HDPDLATVMDEINWFTYESEKVIDTFINSITQQK----------TQSSCSKDIFDA-LQG 114
           HD +    +  +      +E   +      T+ +           Q+S    + D     
Sbjct: 19  HDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELGPLIDFFNYN 78

Query: 115 LQSRITDIKQRMQQLKHMDSKIIDRIKTSKAEAGISSSSKSRDT--------VGLDDRME 166
            QS + D  +        +  ++  +  +   +      K               +  ++
Sbjct: 79  NQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTCYIREYHVD 138

Query: 167 ELLDLLIE-GPPQLSVVAILDSIGLDKTAFAGEAYNSS--YVKHYFDCHAWITEPYSNEY 223
            ++  L E        + +    G  K+  A +A + S   +   +D   W+ +  +   
Sbjct: 139 RVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPK 198

Query: 224 DADQILDIVIKFL----MPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMW 279
               +   ++  L       +  S     +  +K++I +  +     L V DDV      
Sbjct: 199 STFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQ---E 255

Query: 280 DVIQEILPDNQNGSRVLIT 298
           + I+      +   R L+T
Sbjct: 256 ETIR---WAQELRLRCLVT 271

>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 = 58.9 bits (142), Expect = 4e-09
 Identities = 12/75 (16%), Positives = 25/75 (33%), Gaps = 5/75 (6%)

Query: 368 LPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDN--SEATAESYLEQLIKEGFVE 425
           L    +    +  V P   +I  +    +   +    +    +      L++L K G + 
Sbjct: 385 LSDEDRSALAFAVVMPPGVDIPVKLWSCVIPVDICSNEEEQLDDEVADRLKRLSKRGALL 444

Query: 426 AKKRKAGGTINTCSI 440
           + KR     + T  I
Sbjct: 445 SGKR---MPVLTFKI 456

>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 = 77.0 bits (190), Expect = 1e-14
 Identities = 45/240 (18%), Positives = 80/240 (33%), Gaps = 38/240 (15%)

Query: 511 IDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNL 570
            D  KF  +  +   + L  + +          F  + L +    L   P+    +L  L
Sbjct: 276 DDIVKFHCLANV-SAMSLAGVSIKYLEDVP-KHFKWQSLSIIRCQLKQFPTL---DLPFL 330

Query: 571 YTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTE 630
            +L +  +     + +   +  L +L+                    N +S    C  ++
Sbjct: 331 KSLTLTMNKGS-ISFKKVALPSLSYLDLSR-----------------NALSFSGCCSYSD 372

Query: 631 DILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLF 689
                  +LR+L    DLS+N   ++S +   L  L+ L   +      L ++      F
Sbjct: 373 ---LGTNSLRHL----DLSFNGAIIMSANFMGLEELQHLDFQHS----TLKRV-TEFSAF 420

Query: 690 PH--SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
                L +L  S T+   D       L  L  LK+  NS+    L+       NL  L L
Sbjct: 421 LSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDL 480

>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 = 62.7 bits (153), Expect = 3e-10
 Identities = 38/278 (13%), Positives = 80/278 (28%), Gaps = 48/278 (17%)

Query: 506 RHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKL-------------- 551
           + +   D +      ++   LD+    +            L  L L              
Sbjct: 166 QTITVNDLQFLRENPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCL 225

Query: 552 -----------------NIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHT---ADEFWKMN 591
                            +  +L     S++  L ++   +   +Y +       +F  + 
Sbjct: 226 QNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLA 285

Query: 592 KLRHLNFG--SITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLS 649
            +  ++    SI             ++L+    +  C   +     LP L++L     L+
Sbjct: 286 NVSAMSLAGVSIKYL-EDVPKHFKWQSLS----IIRCQLKQFPTLDLPFLKSL----TLT 336

Query: 650 YNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMP 709
            N+  +S     L  L  L L+  + +        ++ L  +SL HL  S    +     
Sbjct: 337 MNKGSISFKKVALPSLSYLDLSR-NALSFSGCCSYSD-LGTNSLRHLDLSFNGAIIMS-A 393

Query: 710 TLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
               L  LQ L  + ++               L  L +
Sbjct: 394 NFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDI 431

>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 = 62.7 bits (153), Expect = 3e-10
 Identities = 40/244 (16%), Positives = 75/244 (30%), Gaps = 22/244 (9%)

Query: 520 FKLLRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPF 577
           F  L+ LDL    +  I+       L  L  L L    + S      S L +L  L    
Sbjct: 55  FSELQWLDLSRCEIETIE-DKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVE 113

Query: 578 SYIDH-TADEFWKMNKLRHLNFGS--ITLPAHPGKFCG--SLENL----NFISALHPCCC 628
           + +    +    ++  L+ LN     I     P  F    +L ++    N+I  +     
Sbjct: 114 TKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITV--- 170

Query: 629 TEDILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLAN---ESKMPRLSKIVL 684
             + L  L     + +  D+S N    +     +   L  L L      S + +     L
Sbjct: 171 --NDLQFLRENPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNL 228

Query: 685 AEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGS-YGFPNLK 743
           A       +        +L       +E L  + + + +    +         +   N+ 
Sbjct: 229 AGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVS 288

Query: 744 VLHL 747
            + L
Sbjct: 289 AMSL 292

>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 = 56.6 bits (137), Expect = 3e-08
 Identities = 42/292 (14%), Positives = 85/292 (29%), Gaps = 57/292 (19%)

Query: 525 VLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-T 583
                   L + P  I +    + + L+   L  L S   SN   L  LD+    I+   
Sbjct: 15  TYQCMDQKLSKVPDDIPSS--TKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCEIETIE 72

Query: 584 ADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NFISALHPCCCTEDILGRL 636
              +  ++ L +L        +          SLENL      +++L         +G+L
Sbjct: 73  DKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLES-----FPIGQL 127

Query: 637 PNLRNLRIRGDLSYNQ---SLLSKSLCRLSCLESLKLAN--------------ESKMPRL 679
             L+ L    ++++N      L      L+ L  + L+                      
Sbjct: 128 ITLKKL----NVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVN 183

Query: 680 SKIVLAEYLFPH---------SLTHLSFSNTDLMDDPMPT-LEKLPLLQVLKLKQNSYSG 729
             + ++                L  L+        + M T L+ L  L V +L    +  
Sbjct: 184 LSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKD 243

Query: 730 -RKLTCGS----YGFPNLKVLHLK----SMLWLEEWTMGNAAMPKLECLIIN 772
            R L         G  ++ +   +    +    +        +  +  + + 
Sbjct: 244 ERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHC--LANVSAMSLA 293

>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 = 75.8 bits (187), Expect = 2e-14
 Identities = 63/272 (23%), Positives = 101/272 (37%), Gaps = 30/272 (11%)

Query: 493 SQLHSLLCCSPETRHLDPIDWEKFCGMFKL-LRVLDLGSLVLIQYPSGI-ENLFLLRYLK 550
           S + SL   + E    + I    F G+ ++ +  ++L         S        L+ L 
Sbjct: 225 STIQSLWLGTFEDMDDEDISPAVFEGLCEMSVESINLQKHYFFNISSNTFHCFSGLQELD 284

Query: 551 LNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNFG--SITLPAHP 607
           L    L+ LPS L   L  L  L +  +  ++           L HL+    +  L    
Sbjct: 285 LTATHLSELPSGL-VGLSTLKKLVLSANKFENLCQISASNFPSLTHLSIKGNTKRLELGT 343

Query: 608 GKFCG--SLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSL 659
           G      +L  L    + I     C      L  L +L++L    +LSYN+  SL +++ 
Sbjct: 344 GCLENLENLRELDLSHDDIETSDCC---NLQLRNLSHLQSL----NLSYNEPLSLKTEAF 396

Query: 660 CRLSCLESLKLANESKMPRLSKIVLAEYLF--PHSLTHLSFSNTDLMDDPMPTLEKLPLL 717
                LE L LA      RL     A+  F   H L  L+ S++ L        + LP L
Sbjct: 397 KECPQLELLDLAFT----RLKVK-DAQSPFQNLHLLKVLNLSHSLLDISSEQLFDGLPAL 451

Query: 718 QVLKLKQNSYSGRKLTCGS--YGFPNLKVLHL 747
           Q L L+ N +    +   +       L++L L
Sbjct: 452 QHLNLQGNHFPKGNIQKTNSLQTLGRLEILVL 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 = 71.6 bits (176), Expect = 6e-13
 Identities = 49/252 (19%), Positives = 79/252 (31%), Gaps = 36/252 (14%)

Query: 514 EKFCGMFKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLN-SLPSSLLSNLLNLY 571
               G+  L + L L +            N   L +L +   +    L +  L NL NL 
Sbjct: 295 SGLVGLSTL-KKLVLSANKFENLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLENLR 353

Query: 572 TLDM---PFSYIDHTADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NFIS 621
            LD+        D    +   ++ L+ LN      ++L     K C  LE L      + 
Sbjct: 354 ELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLK 413

Query: 622 ALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRL 679
                   +     L  L+ L    +LS++       +    L  L+ L L         
Sbjct: 414 VKDA----QSPFQNLHLLKVL----NLSHSLLDISSEQLFDGLPALQHLNLQG----NHF 461

Query: 680 SKI-VLAEYLFPH--SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGS 736
            K  +           L  L  S  DL          L ++  + L  N     +LT  S
Sbjct: 462 PKGNIQKTNSLQTLGRLEILVLSFCDLSSIDQHAFTSLKMMNHVDLSHN-----RLTSSS 516

Query: 737 YG-FPNLKVLHL 747
                +LK ++L
Sbjct: 517 IEALSHLKGIYL 528

>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 = 68.5 bits (168), Expect = 5e-12
 Identities = 46/241 (19%), Positives = 78/241 (32%), Gaps = 30/241 (12%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNL--LNLYTLDMPFS 578
           L  L LGS  +  I+ P        L+ L     +++ L    +S+L      +L++  +
Sbjct: 131 LESLYLGSNHISSIKLPK-GFPTEKLKVLDFQNNAIHYLSKEDMSSLQQATNLSLNLNGN 189

Query: 579 YIDHTADEFWKMNKLRHLNFGS-----ITLPAHPGKFCGSLENLNF----ISALHPCCCT 629
            I       +     + LNFG      +           SL    F       + P    
Sbjct: 190 DIAGIEPGAFDSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTFEDMDDEDISP---- 245

Query: 630 EDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEY 687
             +   L  +    I  +L  +   ++ S +    S L+ L L        LS++     
Sbjct: 246 -AVFEGLCEMSVESI--NLQKHYFFNISSNTFHCFSGLQELDLTAT----HLSELPSG-- 296

Query: 688 LFP-HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLH 746
           L    +L  L  S     +    +    P L  L +K N+      T       NL+ L 
Sbjct: 297 LVGLSTLKKLVLSANKFENLCQISASNFPSLTHLSIKGNTKRLELGTGCLENLENLRELD 356

Query: 747 L 747
           L
Sbjct: 357 L 357

>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 = 56.9 bits (138), Expect = 2e-08
 Identities = 38/233 (16%), Positives = 63/233 (27%), Gaps = 39/233 (16%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI 580
           L+ L      +  I     + N   L  L L    ++S+          L  LD      
Sbjct: 107 LKHLFFIQTGISSID-FIPLHNQKTLESLYLGSNHISSIKLPKGFPTEKLKVLDF----- 160

Query: 581 DHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL------NFISALHPCCCTEDILG 634
                   + N + +L+   ++             NL      N I+ + P         
Sbjct: 161 --------QNNAIHYLSKEDMS-------SLQQATNLSLNLNGNDIAGIEPGA------F 199

Query: 635 RLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLT 694
                ++L   G  +            +  L      +      +S  V    L   S+ 
Sbjct: 200 DSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTFED-MDDEDISPAVFEG-LCEMSVE 257

Query: 695 HLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
            ++       +    T      LQ L L     S  +L  G  G   LK L L
Sbjct: 258 SINLQKHYFFNISSNTFHCFSGLQELDLTATHLS--ELPSGLVGLSTLKKLVL 308

>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 = 52.7 bits (127), Expect = 4e-07
 Identities = 31/200 (15%), Positives = 56/200 (28%), Gaps = 45/200 (22%)

Query: 555 SLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNFGSITLPAHPGKFCGS 613
            LN +P +L ++      L+  F+ +       F ++  L  L+                
Sbjct: 23  GLNEIPGTLPNST---ECLEFSFNVLPTIQNTTFSRLINLTFLDLTR------------- 66

Query: 614 LENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLA 671
                 I  +H      D       L  L     L+ N    +   +L     L+ L   
Sbjct: 67  ----CQIYWIHE-----DTFQSQHRLDTL----VLTANPLIFMAETALSGPKALKHLFFI 113

Query: 672 -NESKMPRLSKIVLAEYLFPH--SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYS 728
                   +S I        +  +L  L   +  +    +P       L+VL  + N+  
Sbjct: 114 QT-----GISSI--DFIPLHNQKTLESLYLGSNHISSIKLPKGFPTEKLKVLDFQNNAIH 166

Query: 729 GRKLTCGS-YGFPNLKVLHL 747
              L+            L L
Sbjct: 167 Y--LSKEDMSSLQQATNLSL 184

>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 = 45.4 bits (108), Expect = 6e-05
 Identities = 36/160 (22%), Positives = 52/160 (32%), Gaps = 35/160 (21%)

Query: 624 HPCCCTEDILGRLPNLRNLRIRG------------DLSYNQ--SLLSKSLCRLSCLESLK 669
               C E  + +  N  NL +              + S+N   ++ + +  RL  L  L 
Sbjct: 4   SDQKCIEKEVNKTYNCENLGLNEIPGTLPNSTECLEFSFNVLPTIQNTTFSRLINLTFLD 63

Query: 670 LA-NE---------SKMPRLSKIVLA--------EYLF--PHSLTHLSFSNTDLMDDPMP 709
           L   +             RL  +VL         E     P +L HL F  T +      
Sbjct: 64  LTRCQIYWIHEDTFQSQHRLDTLVLTANPLIFMAETALSGPKALKHLFFIQTGISSIDFI 123

Query: 710 TLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKS 749
            L     L+ L L  N  S  KL  G      LKVL  ++
Sbjct: 124 PLHNQKTLESLYLGSNHISSIKLPKGF-PTEKLKVLDFQN 162

>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 = 42.3 bits (100), Expect = 6e-04
 Identities = 38/210 (18%), Positives = 68/210 (32%), Gaps = 55/210 (26%)

Query: 507 HLDPIDWEKFCGMFKLLRVLDLG----SLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSS 562
            LD    + F G+  L + L+L         IQ  + ++ L  L  L L+   L+S+   
Sbjct: 436 LLDISSEQLFDGLPAL-QHLNLQGNHFPKGNIQKTNSLQTLGRLEILVLSFCDLSSIDQH 494

Query: 563 LLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL----- 617
             ++L  +  +D+  S+           N+L   +  ++            L+ +     
Sbjct: 495 AFTSLKMMNHVDL--SH-----------NRLTSSSIEAL----------SHLKGIYLNLA 531

Query: 618 -NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSC---LESLKLANE 673
            N IS + P      +L  L   R +    +L  N          L C           +
Sbjct: 532 SNHISIILP-----SLLPILSQQRTI----NLRQNP---------LDCTCSNIYFLEWYK 573

Query: 674 SKMPRLSKIVLAEYLFPHSLTHLSFSNTDL 703
             M +L          P  L  +  S+  L
Sbjct: 574 ENMQKLEDTEDTLCENPPLLRGVRLSDVTL 603

>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 = 74.7 bits (184), Expect = 5e-14
 Identities = 53/293 (18%), Positives = 94/293 (32%), Gaps = 68/293 (23%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLL-------------- 568
           +    L S+ + +        F  ++L+L        P+  L +L               
Sbjct: 284 VSSFSLVSVTIERVKD-FSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFS 342

Query: 569 -----NLYTLDM---PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCG--SLENLN 618
                +L  LD+     S+    +   +    L++L+     +      F G   LE+L+
Sbjct: 343 EVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLD 402

Query: 619 F----ISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLAN 672
           F    +  +        +   L NL  L    D+S+       +     LS LE LK+A 
Sbjct: 403 FQHSNLKQMSE----FSVFLSLRNLIYL----DISHTHTRVAFNGIFNGLSSLEVLKMAG 454

Query: 673 -----------ESKMPRLSKIVLA----EYLFP------HSLTHLSFSNTDLMDDPMPTL 711
                       +++  L+ + L+    E L P       SL  L+ S+ +         
Sbjct: 455 NSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPY 514

Query: 712 EKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLK--------SMLWLEEW 756
           + L  LQVL    N     K     +   +L  L+L               +W
Sbjct: 515 KCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQW 567

>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 = 73.9 bits (182), Expect = 1e-13
 Identities = 49/245 (20%), Positives = 75/245 (30%), Gaps = 31/245 (12%)

Query: 518 GMFKLLRVLDLGSLVL-------IQYPSGIENLFLLRYLKLNIPSLNSLPS-SLLSNLLN 569
              + L  L +    L                L  +    L   ++  +   S      +
Sbjct: 249 SALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQH 308

Query: 570 LYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLP-AHPGKFCGSLENL----NFISALH 624
           L  ++  F           K+  L+ L F S     A       SLE L    N +S   
Sbjct: 309 LELVNCKFGQFP-----TLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKG 363

Query: 625 PCCCTEDILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLANESKMPRLSKIV 683
              C         +L+ L    DLS+N    +S +   L  LE L   +      L ++ 
Sbjct: 364 ---CCSQSDFGTTSLKYL----DLSFNGVITMSSNFLGLEQLEHLDFQHS----NLKQMS 412

Query: 684 LAEYLFP-HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNL 742
                    +L +L  S+T            L  L+VLK+  NS+    L        NL
Sbjct: 413 EFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNL 472

Query: 743 KVLHL 747
             L L
Sbjct: 473 TFLDL 477

>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 = 64.7 bits (158), Expect = 7e-11
 Identities = 43/256 (16%), Positives = 81/256 (31%), Gaps = 40/256 (15%)

Query: 516 FCGMFKLLRVLDLG--SLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTL 573
           +  +   L  L L    +  +        L  L+ L     +L SL +  + +L  L  L
Sbjct: 72  YQSL-SHLSTLILTGNPIQSLA-LGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKEL 129

Query: 574 DMPFSYIDHT--ADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL-----------NFI 620
           ++  + I      + F  +  L HL+  S  + +        L  +           N +
Sbjct: 130 NVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPM 189

Query: 621 SALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ---SLLSKSLCRLSCLESLKLA-----N 672
           + + P         +   L  L     L  N    +++   +  L+ LE  +L      N
Sbjct: 190 NFIQPGA------FKEIRLHKL----TLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRN 239

Query: 673 ESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMP-TLEKLPLLQVLKLKQNSYSGRK 731
           E  + +  K  L E L   ++     +  D   D +      L  +    L   +     
Sbjct: 240 EGNLEKFDKSAL-EGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIER-- 296

Query: 732 LTCGSYGFPNLKVLHL 747
           +   SY     + L L
Sbjct: 297 VKDFSY-NFGWQHLEL 311

>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 = 59.3 bits (144), Expect = 4e-09
 Identities = 47/243 (19%), Positives = 86/243 (35%), Gaps = 27/243 (11%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI 580
            + LDL    L  +       +   L+ L L+   + ++      +L +L TL +  + I
Sbjct: 30  TKNLDLSFNPLRHLG-SYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPI 88

Query: 581 DH-TADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NFISALHPCCCTEDI 632
                  F  ++ L+ L        +L   P     +L+ L    N I +        + 
Sbjct: 89  QSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLP----EY 144

Query: 633 LGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFP 690
              L NL +L    DLS N+  S+    L  L  +  L L+ +  +  ++ I      F 
Sbjct: 145 FSNLTNLEHL----DLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPG--AFK 198

Query: 691 H-SLTHLSFS-NTDLMDDPMPTLEKLPLLQVLKLKQNSYSG-RKLTCGSYG-FPNLKVLH 746
              L  L+   N D ++     ++ L  L+V +L    +     L          L  L 
Sbjct: 199 EIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLT 258

Query: 747 LKS 749
           ++ 
Sbjct: 259 IEE 261

>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 = 56.2 bits (136), Expect = 3e-08
 Identities = 43/241 (17%), Positives = 81/241 (33%), Gaps = 28/241 (11%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNL----YTLDMP 576
           L+ L++    +   + P    NL  L +L L+   + S+  + L  L  +     +LD+ 
Sbjct: 126 LKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLS 185

Query: 577 FSYIDHTADEFWKMNKLRHL----NFGSITLPAHPGKFCGSLENLNFISALHPCC--CTE 630
            + ++      +K  +L  L    NF S+ +     +    LE    +           +
Sbjct: 186 LNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEK 245

Query: 631 DILGRLPNLRNLRIRG-DLSYN---QSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAE 686
                L  L NL I    L+Y       +      L+ + S  L +      + ++   +
Sbjct: 246 FDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVS----VTIERVK--D 299

Query: 687 YLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLH 746
           + +     HL   N      P   L+ L  L     K  +             P+L+ L 
Sbjct: 300 FSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAF------SEVDLPSLEFLD 353

Query: 747 L 747
           L
Sbjct: 354 L 354

>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 = 53.9 bits (130), Expect = 1e-07
 Identities = 40/207 (19%), Positives = 71/207 (34%), Gaps = 31/207 (14%)

Query: 555 SLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNFGSITLPAHPGKFCGS 613
           +   +P +L     +   LD+ F+ + H  +  F+   +L+ L+     +         S
Sbjct: 18  NFYKIPDNLPF---STKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQS 74

Query: 614 LENL-------NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSC 664
           L +L       N I +L            L +L+ L            SL +  +  L  
Sbjct: 75  LSHLSTLILTGNPIQSLAL-----GAFSGLSSLQKL----VAVETNLASLENFPIGHLKT 125

Query: 665 LESLKLA-NESKMPRLSKIVLAEYLFP-HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKL 722
           L+ L +A N      +    L EY     +L HL  S+  +       L  L  + +L L
Sbjct: 126 LKELNVAHN-----LIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNL 180

Query: 723 KQN--SYSGRKLTCGSYGFPNLKVLHL 747
             +        +  G++    L  L L
Sbjct: 181 SLDLSLNPMNFIQPGAFKEIRLHKLTL 207

>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 = 53.1 bits (128), Expect = 3e-07
 Identities = 39/164 (23%), Positives = 55/164 (33%), Gaps = 26/164 (15%)

Query: 593 LRHLNFGSITLPAHPGKFCGSLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDL 648
              LNF  I     P     S +NL    N +  L             P L+ L    DL
Sbjct: 14  CMELNFYKI-----PDNLPFSTKNLDLSFNPLRHLGS-----YSFFSFPELQVL----DL 59

Query: 649 SYNQ--SLLSKSLCRLSCLESLKLA-NESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMD 705
           S  +  ++   +   LS L +L L  N      +  + L  +    SL  L    T+L  
Sbjct: 60  SRCEIQTIEDGAYQSLSHLSTLILTGN-----PIQSLALGAFSGLSSLQKLVAVETNLAS 114

Query: 706 DPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKS 749
                +  L  L+ L +  N     KL        NL+ L L S
Sbjct: 115 LENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSS 158

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens} Length = 477

 Score = 73.6 bits (181), Expect = 9e-14
 Identities = 60/272 (22%), Positives = 103/272 (37%), Gaps = 43/272 (15%)

Query: 502 SPETRHLD-------PIDWEKFCGMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNI 553
             ETR LD        ++ ++F      L  L+L   ++     G   NLF LR L L  
Sbjct: 31  PTETRLLDLGKNRIKTLNQDEFASF-PHLEELELNENIVSAVEPGAFNNLFNLRTLGLRS 89

Query: 554 PSLNSLPSSLLSNLLNLYTLDM---PFSYIDHTADEFWKMNKLRHLNFGS--IT-LPAHP 607
             L  +P  + + L NL  LD+       +      F  +  L+ L  G   +  +    
Sbjct: 90  NRLKLIPLGVFTGLSNLTKLDISENKIVILLDYM--FQDLYNLKSLEVGDNDLVYIS--H 145

Query: 608 GKFCG--SLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSL 659
             F G  SLE L      ++++       + L  L  L  LR    L +    ++   S 
Sbjct: 146 RAFSGLNSLEQLTLEKCNLTSIPT-----EALSHLHGLIVLR----LRHLNINAIRDYSF 196

Query: 660 CRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQV 719
            RL  L+ L++++   +  ++       L+  +LT LS ++ +L   P   +  L  L+ 
Sbjct: 197 KRLYRLKVLEISHWPYLDTMT----PNCLYGLNLTSLSITHCNLTAVPYLAVRHLVYLRF 252

Query: 720 LKLKQNSYSGRKLTCGS-YGFPNLKVLHLKSM 750
           L L  N  S   +     +    L+ + L   
Sbjct: 253 LNLSYNPIS--TIEGSMLHELLRLQEIQLVGG 282

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens} Length = 477

 Score = 65.9 bits (161), Expect = 2e-11
 Identities = 57/301 (18%), Positives = 100/301 (33%), Gaps = 58/301 (19%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM---PF 577
           L+ L++G   LV I        L  L  L L   +L S+P+  LS+L  L  L +     
Sbjct: 130 LKSLEVGDNDLVYIS-HRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLNI 188

Query: 578 SYIDHTADEFWKMNKLRHLNFGS--ITLPAHPGKFCG-SLENLNF----ISALHPCCCTE 630
           + I   +  F ++ +L+ L            P    G +L +L+     ++A+       
Sbjct: 189 NAIRDYS--FKRLYRLKVLEISHWPYLDTMTPNCLYGLNLTSLSITHCNLTAVPY----- 241

Query: 631 DILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYL 688
             +  L  LR L    +LSYN   ++    L  L  L+ ++L       +L+ +    Y 
Sbjct: 242 LAVRHLVYLRFL----NLSYNPISTIEGSMLHELLRLQEIQLVGG----QLAVV--EPYA 291

Query: 689 FPH--SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLH 746
           F     L  L+ S   L          +  L+ L L  N      L C            
Sbjct: 292 FRGLNYLRVLNVSGNQLTTLEESVFHSVGNLETLILDSNP-----LACDC---------- 336

Query: 747 LKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQ-LWYIKSLNKF-DCWWPQPELRQ 804
              +LW+           +        CA  + +  +       +         +  +R 
Sbjct: 337 --RLLWVFRRRWRLNFNRQQP-----TCATPEFVQGKEFKDFPDVLLPNYFTCRRARIRD 389

Query: 805 K 805
           +
Sbjct: 390 R 390

>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 = 72.3 bits (178), Expect = 3e-13
 Identities = 52/251 (20%), Positives = 81/251 (32%), Gaps = 35/251 (13%)

Query: 523 LRVLDLGS---LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY 579
           L+ L L +     L      I     L+ L+L+   +          +  L+ L +    
Sbjct: 147 LQELLLSNNKIQALKSEELDIFANSSLKKLELSSNQIKEFSPGCFHAIGRLFGLFLNNVQ 206

Query: 580 IDHTADE----FWKMNKLRHLNFGSITLPA-HPGKFCG----SLENL----NFISALHPC 626
           +  +  E          +R+L+  +  L       F G    +L  L    N ++ +   
Sbjct: 207 LGPSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYNNLNVVGN- 265

Query: 627 CCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKM-----PRL 679
               D    LP L        L YN    L S SL  L  +  L L             L
Sbjct: 266 ----DSFAWLPQLEYF----FLEYNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASL 317

Query: 680 SKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKL---TCGS 736
            KI    + +   L HL+  + D+          L  L+ L L  +  S R L   T  S
Sbjct: 318 PKIDDFSFQWLKCLEHLNMEDNDIPGIKSNMFTGLINLKYLSLSNSFTSLRTLTNETFVS 377

Query: 737 YGFPNLKVLHL 747
                L +L+L
Sbjct: 378 LAHSPLHILNL 388

>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 = 70.8 bits (174), Expect = 1e-12
 Identities = 54/285 (18%), Positives = 93/285 (32%), Gaps = 53/285 (18%)

Query: 508 LDPIDWEKFCGM-FKLLRVLDLG--SLVLIQYPSGIENLFLLRYLKLNIPSLNSL----P 560
           L  +  E F  +    L +L+L    +  I+       L  L  L L    LN +     
Sbjct: 367 LRTLTNETFVSLAHSPLHILNLTKNKISKIE-SDAFSWLGHLEVLDL---GLNEIGQELT 422

Query: 561 SSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNFGS--IT-LPAHPGKFCG--SL 614
                 L N++ + + ++     T + F  +  L+ L      +  + + P  F    +L
Sbjct: 423 GQEWRGLENIFEIYLSYNKYLQLTRNSFALVPSLQRLMLRRVALKNVDSSPSPFQPLRNL 482

Query: 615 ENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ----------SLLSKSLC 660
             L    N I+ ++      D+L  L  L  L    DL +N                 L 
Sbjct: 483 TILDLSNNNIANIND-----DMLEGLEKLEIL----DLQHNNLARLWKHANPGGPIYFLK 533

Query: 661 RLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVL 720
            LS L  L L +        +I +  +     L  +     +L   P         L+ L
Sbjct: 534 GLSHLHILNLESN----GFDEIPVEVFKDLFELKIIDLGLNNLNTLPASVFNNQVSLKSL 589

Query: 721 KLKQNSYSGRKLTCGSYGFPNLKVLHL---------KSMLWLEEW 756
            L++N  +  +       F NL  L +         +S+ W   W
Sbjct: 590 NLQKNLITSVEKKVFGPAFRNLTELDMRFNPFDCTCESIAWFVNW 634

>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 = 68.1 bits (167), Expect = 7e-12
 Identities = 49/248 (19%), Positives = 83/248 (33%), Gaps = 33/248 (13%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI 580
           L +LDL    L ++        L  L Y  L   ++  L S  L  L N+  L++  S+ 
Sbjct: 250 LTMLDLSYNNLNVVG-NDSFAWLPQLEYFFLEYNNIQHLFSHSLHGLFNVRYLNLKRSFT 308

Query: 581 DHT----------ADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL-------NFISAL 623
             +             F  +  L HLN     +P         L NL       +F S  
Sbjct: 309 KQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSNMFTGLINLKYLSLSNSFTSLR 368

Query: 624 HPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSK 681
                T   L     L  L    +L+ N+   + S +   L  LE L L        + +
Sbjct: 369 TLTNETFVSLA-HSPLHIL----NLTKNKISKIESDAFSWLGHLEVLDLGLN----EIGQ 419

Query: 682 IVLAEYLFP-HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSY-GF 739
            +  +      ++  +  S    +     +   +P LQ L L++ +      +   +   
Sbjct: 420 ELTGQEWRGLENIFEIYLSYNKYLQLTRNSFALVPSLQRLMLRRVALKNVDSSPSPFQPL 479

Query: 740 PNLKVLHL 747
            NL +L L
Sbjct: 480 RNLTILDL 487

>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 = 67.3 bits (165), Expect = 1e-11
 Identities = 46/261 (17%), Positives = 80/261 (30%), Gaps = 38/261 (14%)

Query: 518 GMFKLLRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM 575
            +   + VL+L    L  +   +       L  L +   +++ L   L   L  L  L++
Sbjct: 22  DLPTNITVLNLTHNQLRRLP-AANFTRYSQLTSLDVGFNTISKLEPELCQKLPMLKVLNL 80

Query: 576 PFSYIDH-TADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILG 634
             + +   +   F     L  L+  S                 N I  +       +   
Sbjct: 81  QHNELSQLSDKTFAFCTNLTELHLMS-----------------NSIQKIKN-----NPFV 118

Query: 635 RLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHS 692
           +  NL  L    DLS+N   S    +  +L  L+ L L+N +K+  L    L       S
Sbjct: 119 KQKNLITL----DLSHNGLSSTKLGTQVQLENLQELLLSN-NKIQALKSEELD-IFANSS 172

Query: 693 LTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGR--KLTCGSYGFPNLKVLHLK-- 748
           L  L  S+  + +        +  L  L L          +  C      +++ L L   
Sbjct: 173 LKKLELSSNQIKEFSPGCFHAIGRLFGLFLNNVQLGPSLTEKLCLELANTSIRNLSLSNS 232

Query: 749 SMLWLEEWTMGNAAMPKLECL 769
            +      T        L  L
Sbjct: 233 QLSTTSNTTFLGLKWTNLTML 253

>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 = 59.2 bits (144), Expect = 3e-09
 Identities = 44/208 (21%), Positives = 76/208 (36%), Gaps = 37/208 (17%)

Query: 546 LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNFGSITLP 604
                 +   L  +P  L +N+     L++  + +    A  F + ++L  L+ G     
Sbjct: 6   HEVADCSHLKLTQVPDDLPTNIT---VLNLTHNQLRRLPAANFTRYSQLTSLDVGF---- 58

Query: 605 AHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRL 662
                        N IS L P     ++  +LP L+ L    +L +N+   L  K+    
Sbjct: 59  -------------NTISKLEP-----ELCQKLPMLKVL----NLQHNELSQLSDKTFAFC 96

Query: 663 SCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKL 722
           + L  L L +      + KI    ++   +L  L  S+  L    + T  +L  LQ L L
Sbjct: 97  TNLTELHLMSN----SIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELLL 152

Query: 723 KQNSYSG-RKLTCGSYGFPNLKVLHLKS 749
             N     +      +   +LK L L S
Sbjct: 153 SNNKIQALKSEELDIFANSSLKKLELSS 180

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens} Length = 440

 Score = 69.0 bits (169), Expect = 2e-12
 Identities = 71/326 (21%), Positives = 104/326 (31%), Gaps = 73/326 (22%)

Query: 502 SPETRHLD-------PIDWEKFCGMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNI 553
           S  TR L+        I    F  + + L +L L    +     G    L  L  L+L  
Sbjct: 63  STNTRLLNLHENQIQIIKVNSFKHL-RHLEILQLSRNHIRTIEIGAFNGLANLNTLELFD 121

Query: 554 PSLNSLPSSLLSNLLNLYTLDM---PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKF 610
             L ++P+     L  L  L +   P   I   A  F ++  LR L+             
Sbjct: 122 NRLTTIPNGAFVYLSKLKELWLRNNPIESIPSYA--FNRIPSLRRLD------------- 166

Query: 611 CGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSK--SLCRLSCLESL 668
              L  L  +S +            L NLR L    +L+     L +  +L  L  L+ L
Sbjct: 167 ---LGELKRLSYISE-----GAFEGLSNLRYL----NLAMCN--LREIPNLTPLIKLDEL 212

Query: 669 KLANESKMPRLSKIVLAEYLFP--HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNS 726
            L+       LS I      F     L  L    + +        + L  L  + L  N+
Sbjct: 213 DLSGN----HLSAI--RPGSFQGLMHLQKLWMIQSQIQVIERNAFDNLQSLVEINLAHNN 266

Query: 727 YSGRKLTCGSY-GFPNLKVLHLKS--------MLWLEEWTMGNAAMPKLECLIINPCAYL 777
            +   L    +    +L+ +HL          +LWL  W    A      C     C   
Sbjct: 267 LT--LLPHDLFTPLHHLERIHLHHNPWNCNCDILWLSWWIKDMAPSNTACCAR---CNT- 320

Query: 778 KKMPEQL--WYIKSL--NKFDCWWPQ 799
              P  L   YI  L  N F C+ P 
Sbjct: 321 ---PPNLKGRYIGELDQNYFTCYAPV 343

>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 = 68.0 bits (167), Expect = 3e-12
 Identities = 42/221 (19%), Positives = 78/221 (35%), Gaps = 32/221 (14%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
              L+L S+ L Q+P     L  L+++ ++   L  LP + +     L TL +  + +  
Sbjct: 83  RVALELRSVPLPQFPDQAFRLSHLQHMTIDAAGLMELPDT-MQQFAGLETLTLARNPLRA 141

Query: 583 TADEFWKMNKLRHLN-------------FGSITLPAHPGKFCGSLENLNFISALHPCCCT 629
                  +N+LR L+               S            +L++L     L      
Sbjct: 142 LPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQG-LVNLQSLR----LEWTGIR 196

Query: 630 E--DILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAE 686
                +  L NL++L     +  +  S L  ++  L  LE L L   + +     I    
Sbjct: 197 SLPASIANLQNLKSL----KIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIF--G 250

Query: 687 YLFPHSLTHLSFSN-TDLMDDPMPTLEKLPLLQVLKLKQNS 726
                 L  L   + ++L+  P   + +L  L+ L L+   
Sbjct: 251 GR--APLKRLILKDCSNLLTLP-LDIHRLTQLEKLDLRGCV 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 = 64.6 bits (158), Expect = 3e-11
 Identities = 38/289 (13%), Positives = 81/289 (28%), Gaps = 61/289 (21%)

Query: 513 WEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSL-LSNLLNLY 571
              +  +    +                 N    +       +L +    L  +      
Sbjct: 25  LRPYHDVLSQWQRHYNADRNRWHSAWRQANSNNPQIETRTGRALKATADLLEDATQPGRV 84

Query: 572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTED 631
            L++    +    D+ ++++ L+H+   +                   +  L        
Sbjct: 85  ALELRSVPLPQFPDQAFRLSHLQHMTIDA-----------------AGLMELPDT----- 122

Query: 632 ILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLANESKMPRL-----SKIVLA 685
            + +   L  L     L+ N    L  S+  L+ L  L +    ++  L     S     
Sbjct: 123 -MQQFAGLETL----TLARNPLRALPASIASLNRLRELSIRACPELTELPEPLASTDASG 177

Query: 686 EYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVL 745
           E+    +L  L    T +   P  ++  L  L+ LK++ +      L+            
Sbjct: 178 EHQGLVNLQSLRLEWTGIRSLP-ASIANLQNLKSLKIRNS-----PLS----ALGP---- 223

Query: 746 HLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFD 794
                       + +  +PKLE L +  C  L+  P        L +  
Sbjct: 224 -----------AIHH--LPKLEELDLRGCTALRNYPPIFGGRAPLKRLI 259

>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 = 43.0 bits (102), Expect = 2e-04
 Identities = 30/138 (21%), Positives = 53/138 (38%), Gaps = 14/138 (10%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMP-FSYID 581
           L+ L L    +   P+ I NL  L+ LK+    L++L  ++  +L  L  LD+   + + 
Sbjct: 185 LQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAI-HHLPKLEELDLRGCTALR 243

Query: 582 HTADEFWKMNKLRHLNFGS----ITLPAHPGKFCGSLENLNFISALHPCCCTEDI---LG 634
           +    F     L+ L        +TLP    +    LE L+    L  C     +   + 
Sbjct: 244 NYPPIFGGRAPLKRLILKDCSNLLTLPLDIHR-LTQLEKLD----LRGCVNLSRLPSLIA 298

Query: 635 RLPNLRNLRIRGDLSYNQ 652
           +LP    + +   L    
Sbjct: 299 QLPANCIILVPPHLQAQL 316

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A Length = 452

 Score = 68.2 bits (167), Expect = 4e-12
 Identities = 68/321 (21%), Positives = 99/321 (30%), Gaps = 71/321 (22%)

Query: 502 SPETRHLD-------PIDWEKFCGMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNI 553
              TR+L+        I  + F  +   L VL LG   + Q   G    L  L  L+L  
Sbjct: 74  PSNTRYLNLMENNIQMIQADTFRHL-HHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFD 132

Query: 554 PSLNSLPSSLLSNLLNLYTLDM---PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKF 610
             L  +PS     L  L  L +   P   I   A  F ++  L  L+             
Sbjct: 133 NWLTVIPSGAFEYLSKLRELWLRNNPIESIPSYA--FNRVPSLMRLD------------- 177

Query: 611 CGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKL 670
              L  L  +  +            L NL+ L    +L         +L  L  LE L++
Sbjct: 178 ---LGELKKLEYISE-----GAFEGLFNLKYL----NLGMCNIKDMPNLTPLVGLEELEM 225

Query: 671 A-NESKMPRLSKIVLAEYLFP--HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSY 727
           + N        +I      F    SL  L   N+ +        + L  L  L L  N+ 
Sbjct: 226 SGN-----HFPEI--RPGSFHGLSSLKKLWVMNSQVSLIERNAFDGLASLVELNLAHNNL 278

Query: 728 SGRKLTCGSY-GFPNLKVLHLKS--------MLWLEEWTMGNAAMPKLECLIINPCAYLK 778
           S   L    +     L  LHL          +LWL  W           C     C    
Sbjct: 279 S--SLPHDLFTPLRYLVELHLHHNPWNCDCDILWLAWWLREYIPTNSTCCGR---CHA-- 331

Query: 779 KMPEQLW--YIKSLNK--FDC 795
             P  +   Y+  +++  F C
Sbjct: 332 --PMHMRGRYLVEVDQASFQC 350

>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 = 67.8 bits (166), Expect = 6e-12
 Identities = 53/267 (19%), Positives = 83/267 (31%), Gaps = 29/267 (10%)

Query: 493 SQLHSLLCCSPETRHLDPIDWEKFCGMFKL-LRVLDLGSLVLI--QYPSGIENLFLLRYL 549
                +L       +L+  D     G+  L +    L  L             L  +   
Sbjct: 228 EVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSF 287

Query: 550 KLNIPSLNSLPS-SLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHP- 607
            L   ++  +   S      +L  ++  F           K+  L+ L F S        
Sbjct: 288 SLVSVTIERVKDFSYNFGWQHLELVNCKFGQFP-----TLKLKSLKRLTFTSNKGGNAFS 342

Query: 608 GKFCGSLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRL 662
                SLE L    N +S      C         +L+ L    DLS+N    +S +   L
Sbjct: 343 EVDLPSLEFLDLSRNGLSFKG---CCSQSDFGTTSLKYL----DLSFNGVITMSSNFLGL 395

Query: 663 SCLESLKLANESKMPRLSKIVLAEYLF--PHSLTHLSFSNTDLMDDPMPTLEKLPLLQVL 720
             LE L   +      L ++     +F    +L +L  S+T            L  L+VL
Sbjct: 396 EQLEHLDFQH----SNLKQM-SEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVL 450

Query: 721 KLKQNSYSGRKLTCGSYGFPNLKVLHL 747
           K+  NS+    L        NL  L L
Sbjct: 451 KMAGNSFQENFLPDIFTELRNLTFLDL 477

>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 = 64.7 bits (158), Expect = 7e-11
 Identities = 48/251 (19%), Positives = 82/251 (32%), Gaps = 40/251 (15%)

Query: 491 YDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLK 550
           Y+     L   + +      +         K L+ L   S       S + +L  L +L 
Sbjct: 302 YNFGWQHLELVNCKFGQFPTLK-------LKSLKRLTFTSNKGGNAFSEV-DLPSLEFLD 353

Query: 551 L--NIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGS--ITLPAH 606
           L  N  S     S       +L  LD+ F+ +   +  F  + +L HL+F    +   + 
Sbjct: 354 LSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSE 413

Query: 607 PGKFCG--SLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ---SLLSK 657
              F    +L  L                  I   L +L  L     ++ N    + L  
Sbjct: 414 FSVFLSLRNLIYLDISHTHTRVAFN-----GIFNGLSSLEVL----KMAGNSFQENFLPD 464

Query: 658 SLCRLSCLESLKLA-NESKMPRLSKIVLAEYLFP--HSLTHLSFSNTDLMDDPMPTLEKL 714
               L  L  L L+       +L ++  +   F    SL  L+ ++  L   P    ++L
Sbjct: 465 IFTELRNLTFLDLSQC-----QLEQL--SPTAFNSLSSLQVLNMASNQLKSVPDGIFDRL 517

Query: 715 PLLQVLKLKQN 725
             LQ + L  N
Sbjct: 518 TSLQKIWLHTN 528

>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 = 59.7 bits (145), Expect = 2e-09
 Identities = 54/247 (21%), Positives = 84/247 (34%), Gaps = 21/247 (8%)

Query: 520 FKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFS 578
           F  L+VLDL    +     G  ++L  L  L L    + SL     S L +L  L    +
Sbjct: 51  FPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVET 110

Query: 579 YIDHTADE-FWKMNKLRHLNFGS--ITLPAHPGKFCG--SLENL----NFISALHPCCCT 629
            +    +     +  L+ LN     I     P  F    +LE+L    N I +++     
Sbjct: 111 NLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYC---- 166

Query: 630 EDILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLANESKMPRLSKIVLA--E 686
              L  L  +  L +  DLS N  + +     +   L  L L N      + K  +    
Sbjct: 167 -TDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLA 225

Query: 687 YLFPHSLTHLSF-SNTDLMDDPMPTLEKLPLLQV--LKLKQNSYSGRKLTCGSYGFPNLK 743
            L  H L    F +  +L       LE L  L +   +L    Y    +        N+ 
Sbjct: 226 GLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVS 285

Query: 744 VLHLKSM 750
              L S+
Sbjct: 286 SFSLVSV 292

>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 = 55.1 bits (133), Expect = 7e-08
 Identities = 47/244 (19%), Positives = 87/244 (35%), Gaps = 27/244 (11%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI 580
            + LDL    L  +       +   L+ L L+   + ++      +L +L TL +  + I
Sbjct: 30  TKNLDLSFNPLRHLG-SYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPI 88

Query: 581 DH-TADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NFISALHPCCCTEDI 632
                  F  ++ L+ L        +L   P     +L+ L    N I +        + 
Sbjct: 89  QSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKL----PEY 144

Query: 633 LGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFP 690
              L NL +L    DLS N+  S+    L  L  +  L L+ +  +  ++ I      F 
Sbjct: 145 FSNLTNLEHL----DLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFI--QPGAFK 198

Query: 691 H-SLTHLSFS-NTDLMDDPMPTLEKLPLLQVLKLKQNSY-SGRKLTCGSYG-FPNLKVLH 746
              L  L+   N D ++     ++ L  L+V +L    + +   L          L  L 
Sbjct: 199 EIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLT 258

Query: 747 LKSM 750
           ++  
Sbjct: 259 IEEF 262

>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 = 67.4 bits (165), Expect = 9e-12
 Identities = 49/270 (18%), Positives = 93/270 (34%), Gaps = 40/270 (14%)

Query: 492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKL 551
           D   + LL        L  ++++        L   +     ++     +E + + R L +
Sbjct: 237 DESFNELLKLLRYILELSEVEFDDC--TLNGLGDFNPSESDVVSELGKVETVTI-RRLHI 293

Query: 552 NIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNFGS---ITLPAHP 607
               L    S++ S L  +  + +  S +          +  L  L+      +      
Sbjct: 294 PQFYLFYDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKN 353

Query: 608 GKFCGSLENL-------NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ-SLLSKSL 659
               G+  +L       N + ++       +IL  L NL +L    D+S N    +  S 
Sbjct: 354 SACKGAWPSLQTLVLSQNHLRSMQKTG---EILLTLKNLTSL----DISRNTFHPMPDSC 406

Query: 660 CRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQV 719
                +  L L++       + I + +   P +L  L  SN +L    +     LP LQ 
Sbjct: 407 QWPEKMRFLNLSS-------TGIRVVKTCIPQTLEVLDVSNNNLDSFSLF----LPRLQE 455

Query: 720 LKLKQNSYSGRKLTC--GSYGFPNLKVLHL 747
           L + +N     KL     +  FP L V+ +
Sbjct: 456 LYISRN-----KLKTLPDASLFPVLLVMKI 480

>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 = 62.4 bits (152), Expect = 4e-10
 Identities = 45/250 (18%), Positives = 83/250 (33%), Gaps = 32/250 (12%)

Query: 523 LRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYID 581
           L+VL L S  +         +L  L +L L+   L+SL SS    L +L  L++  +   
Sbjct: 52  LQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQ 111

Query: 582 --HTADEFWKMNKLRHLNFGSITLPAH--PGKFCG--SLENL----NFISALHPCCCTED 631
                  F  +  L+ L  G++   +      F G  SL  L      +           
Sbjct: 112 TLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQS-----Q 166

Query: 632 ILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLF 689
            L  + ++ +L     L  ++   LL      LS +  L+L + + + R     L     
Sbjct: 167 SLKSIRDIHHL----TLHLSESAFLLEIFADILSSVRYLELRD-TNLARFQFSPLPVDEV 221

Query: 690 PHSLTHLSFSNTDLMDDPMPTLEKLP---------LLQVLKLKQNSYSGRKLTCGSYGFP 740
              +  L+F  + L D+    L KL                L          +       
Sbjct: 222 SSPMKKLAFRGSVLTDESFNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELG 281

Query: 741 NLKVLHLKSM 750
            ++ + ++ +
Sbjct: 282 KVETVTIRRL 291

>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 = 2e-08
 Identities = 41/268 (15%), Positives = 88/268 (32%), Gaps = 23/268 (8%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI 580
           ++ LDL    +  I     +     L+ L L    +N++      +L +L  LD+  +++
Sbjct: 28  MKSLDLSFNKITYIG-HGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHL 86

Query: 581 DH-TADEFWKMNKLRHLNFG--SITLPAHPGKFCG--SLENLNFISALHPCCCTEDILGR 635
              ++  F  ++ L++LN              F    +L+ L   +              
Sbjct: 87  SSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAG 146

Query: 636 LPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSL 693
           L +L  L    ++      +  S+SL  +  +  L L         + ++        S+
Sbjct: 147 LTSLNEL----EIKALSLRNYQSQSLKSIRDIHHLTLHL----SESAFLLEIFADILSSV 198

Query: 694 THLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWL 753
            +L   +T+L       L    +   +K        R        F  L  L  + +L L
Sbjct: 199 RYLELRDTNLARFQFSPLPVDEVSSPMKKLAF----RGSVLTDESFNELLKLL-RYILEL 253

Query: 754 EEWTMGNAAMPKLECLIINPCAYLKKMP 781
            E    +  +  L     +    + ++ 
Sbjct: 254 SEVEFDDCTLNGLGDFNPSESDVVSELG 281

>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 = 55.1 bits (133), Expect = 7e-08
 Identities = 42/205 (20%), Positives = 79/205 (38%), Gaps = 27/205 (13%)

Query: 555 SLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNFGSITLPA-HPGKFCG 612
           S  S+PS L +    + +LD+ F+ I +    +      L+ L   S  +       F  
Sbjct: 16  SFTSIPSGLTA---AMKSLDLSFNKITYIGHGDLRACANLQVLILKSSRINTIEGDAFYS 72

Query: 613 --SLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SL-LSKSLCRLS 663
             SLE+L    N +S+L          G L +L+ L    +L  N   +L ++     L+
Sbjct: 73  LGSLEHLDLSDNHLSSLSS-----SWFGPLSSLKYL----NLMGNPYQTLGVTSLFPNLT 123

Query: 664 CLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLK 723
            L++L++ N      + +I  A      SL  L      L +    +L+ +  +  L L 
Sbjct: 124 NLQTLRIGNVETFSEIRRIDFAG---LTSLNELEIKALSLRNYQSQSLKSIRDIHHLTLH 180

Query: 724 QNSYSGRKLTCGSYGFPNLKVLHLK 748
            +  +            +++ L L+
Sbjct: 181 LSESAFLLEIFAD-ILSSVRYLELR 204

>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 = 67.5 bits (165), Expect = 1e-11
 Identities = 53/308 (17%), Positives = 102/308 (33%), Gaps = 52/308 (16%)

Query: 482 EGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKL--LRVLDLGSLVLIQYPSG 539
           E +   L        SL   S  +     +DW K    F+   L +LD+         +G
Sbjct: 165 EHELEPLQGKTLSFFSLAANSLYS--RVSVDWGKCMNPFRNMVLEILDVSGNGWTVDITG 222

Query: 540 IENLFL-------------LRYLKLNIPSLNSLPSSLLSNL--LNLYTLDMPFSYIDH-T 583
             +  +             +        ++     +  + L   ++  LD+   ++    
Sbjct: 223 NFSNAISKSQAFSLILAHHIMGAGFGFHNIKDPDQNTFAGLARSSVRHLDLSHGFVFSLN 282

Query: 584 ADEFWKMNKLRHLNFGSITLPA-HPGKFCG--SLENL----NFISALHPCCCTEDILGRL 636
           +  F  +  L+ LN     +       F G  +L+ L    N +  L+           L
Sbjct: 283 SRVFETLKDLKVLNLAYNKINKIADEAFYGLDNLQVLNLSYNLLGELYS-----SNFYGL 337

Query: 637 PNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLAN-----ESKMPRLSKIVLAEYLF 689
           P +  +    DL  N    +  ++   L  L++L L +        +P +  I L     
Sbjct: 338 PKVAYI----DLQKNHIAIIQDQTFKFLEKLQTLDLRDNALTTIHFIPSIPDIFL-SGNK 392

Query: 690 PHSLTHLSFSNTDLM--------DDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPN 741
             +L  ++ +   +          D +  L ++P LQ+L L QN +S           P+
Sbjct: 393 LVTLPKINLTANLIHLSENRLENLDILYFLLRVPHLQILILNQNRFSSCSGDQTPSENPS 452

Query: 742 LKVLHLKS 749
           L+ L L  
Sbjct: 453 LEQLFLGE 460

>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 = 61.0 bits (148), Expect = 1e-09
 Identities = 55/301 (18%), Positives = 93/301 (30%), Gaps = 59/301 (19%)

Query: 503 PETRHLD-------PIDWEKFCGMFKLLRVLDLGS--LVLIQYPSGIENLFLLRYLKLNI 553
             T  L         +    F  + + L++L+LGS    L        NL  LR L L  
Sbjct: 24  NTTERLLLSFNYIRTVTASSFPFL-EQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGS 82

Query: 554 PSLNSLPSSLLSNLLNLYTLDMPFSYIDHT---ADEFWKMNKLRHLNFG--SITLPAHPG 608
             +  L       L +L+ L + F  +         F  +  L  L+     I       
Sbjct: 83  SKIYFLHPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHP 142

Query: 609 KFCG--SLENL----NFISALHP----------------------CCCTEDILGRLPNLR 640
            F    SL+++    N I  +                           + D    +   R
Sbjct: 143 SFGKLNSLKSIDFSSNQIFLVCEHELEPLQGKTLSFFSLAANSLYSRVSVDWGKCMNPFR 202

Query: 641 NLRIRG-DLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLA------------EY 687
           N+ +   D+S N   +  +    + +   +  +      +                    
Sbjct: 203 NMVLEILDVSGNGWTVDITGNFSNAISKSQAFSLILAHHIMGAGFGFHNIKDPDQNTFAG 262

Query: 688 LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGS-YGFPNLKVLH 746
           L   S+ HL  S+  +        E L  L+VL L  N  +  K+   + YG  NL+VL+
Sbjct: 263 LARSSVRHLDLSHGFVFSLNSRVFETLKDLKVLNLAYNKIN--KIADEAFYGLDNLQVLN 320

Query: 747 L 747
           L
Sbjct: 321 L 321

>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 = 60.2 bits (146), Expect = 2e-09
 Identities = 49/252 (19%), Positives = 85/252 (33%), Gaps = 24/252 (9%)

Query: 524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHT 583
           R+       L Q P  +        L L+   + ++ +S    L  L  L++   Y   T
Sbjct: 7   RIAFYRFCNLTQVPQVLNTT---ERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTPLT 63

Query: 584 --ADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENLNFIS-ALHPCCCTEDILGRLP 637
              + F  +  LR L+ GS     L     +    L  L      L      +     L 
Sbjct: 64  IDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLK 123

Query: 638 NLRNLRIRGDLSYNQ--SL-LSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLT 694
            L  L    DLS NQ  SL L  S  +L+ L+S+  ++ +++  + +  L   L   +L+
Sbjct: 124 ALTRL----DLSKNQIRSLYLHPSFGKLNSLKSIDFSS-NQIFLVCEHELE-PLQGKTLS 177

Query: 695 HLSFSNTDLMDDPMPTLEKLP------LLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLK 748
             S +   L         K        +L++L +  N ++       S      +   L 
Sbjct: 178 FFSLAANSLYSRVSVDWGKCMNPFRNMVLEILDVSGNGWTVDITGNFSNAISKSQAFSLI 237

Query: 749 SMLWLEEWTMGN 760
               +     G 
Sbjct: 238 LAHHIMGAGFGF 249

>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 = 57.5 bits (139), Expect = 1e-08
 Identities = 48/233 (20%), Positives = 82/233 (35%), Gaps = 38/233 (16%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPS-SLLSNLLNLYTLDMPFSYID 581
           L+ LDL    L    + I  +  +  + L+   L +LP  +L +NL++L   +     +D
Sbjct: 364 LQTLDLRDNAL----TTIHFIPSIPDIFLSGNKLVTLPKINLTANLIHL--SENRLENLD 417

Query: 582 HTADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL-------NFISALHPCCCTED 631
                  ++  L+ L        +      +      +L       N +          D
Sbjct: 418 ILYF-LLRVPHLQILILNQNRFSSCSGD--QTPSENPSLEQLFLGENMLQLAWETELCWD 474

Query: 632 ILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLF 689
           +   L +L+ L     L++N   SL       L+ L  L L +     RL+  VL+    
Sbjct: 475 VFEGLSHLQVL----YLNHNYLNSLPPGVFSHLTALRGLSLNSN----RLT--VLSHNDL 524

Query: 690 PHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNL 742
           P +L  L  S   L+    P  +    L VL +  N +      C    F N 
Sbjct: 525 PANLEILDISRNQLL---APNPDVFVSLSVLDITHNKFIC---ECELSTFINW 571

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 64.7 bits (158), Expect = 4e-11
 Identities = 48/230 (20%), Positives = 85/230 (36%), Gaps = 37/230 (16%)

Query: 530 SLVLIQYPSGIENLFL--LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADE 586
            +       G E++ L   + +     ++  LP++LL +   +  L++    I+      
Sbjct: 29  DMQTQDVYFGFEDITLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYA 88

Query: 587 FWKMNKLRHLNFGS--IT-LPAHPGKFCGSLENL----NFISALHPCCCTEDILGRLPNL 639
           F   + ++ L  G   I  LP H  +    L  L    N +S+L        I    P L
Sbjct: 89  FAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPR-----GIFHNTPKL 143

Query: 640 RNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLS 697
             L     +S N    +   +    + L++L+L++     RL+ + L+  L P SL H +
Sbjct: 144 TTL----SMSNNNLERIEDDTFQATTSLQNLQLSSN----RLTHVDLS--LIP-SLFHAN 192

Query: 698 FSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
            S   L      TL     ++ L    NS +             L +L L
Sbjct: 193 VSYNLL-----STLAIPIAVEELDASHNSIN----VVRGPVNVELTILKL 233

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 57.7 bits (140), Expect = 7e-09
 Identities = 44/251 (17%), Positives = 83/251 (33%), Gaps = 45/251 (17%)

Query: 523 LRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM---PFS 578
           + +L+L  L + +  +        ++ L +   ++  LP  +  N+  L  L +     S
Sbjct: 71  VELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERNDLS 130

Query: 579 YIDHTADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NFISALHPCCCTED 631
            +      F    KL  L+  +     +     +   SL+NL    N ++ +        
Sbjct: 131 SLPRGI--FHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTHVDL------ 182

Query: 632 ILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLAN-------ESKMPRLSKIVL 684
               +P+L +     ++SYN      +L     +E L  ++             L+ + L
Sbjct: 183 --SLIPSLFHA----NVSYNLL---STLAIPIAVEELDASHNSINVVRGPVNVELTILKL 233

Query: 685 A--------EYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGS 736
                      L    L  +  S  +L         K+  L+ L +  N      L    
Sbjct: 234 QHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISNNRLV--ALNLYG 291

Query: 737 YGFPNLKVLHL 747
              P LKVL L
Sbjct: 292 QPIPTLKVLDL 302

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 56.6 bits (137), Expect = 2e-08
 Identities = 47/246 (19%), Positives = 84/246 (34%), Gaps = 51/246 (20%)

Query: 507 HLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLS 565
            ++ ID   F      ++ L +G   +   P  + +N+ LL  L L    L+SLP  +  
Sbjct: 80  QIEEIDTYAFAYA-HTIQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFH 138

Query: 566 NLLNLYTLDM---PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISA 622
           N   L TL M       I+     F     L++L   S                 N ++ 
Sbjct: 139 NTPKLTTLSMSNNNLERIEDDT--FQATTSLQNLQLSS-----------------NRLTH 179

Query: 623 LHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKI 682
           +            +P+L +     ++SYN      +L     +E L  ++      ++ +
Sbjct: 180 VDL--------SLIPSLFHA----NVSYNL---LSTLAIPIAVEELDASHN----SINVV 220

Query: 683 VLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGS-YGFPN 741
                +    LT L   + +L D     L   P L  + L  N     K+          
Sbjct: 221 --RGPVNV-ELTILKLQHNNLTD--TAWLLNYPGLVEVDLSYNELE--KIMYHPFVKMQR 273

Query: 742 LKVLHL 747
           L+ L++
Sbjct: 274 LERLYI 279

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae} Length = 390

 Score = 47.0 bits (112), Expect = 2e-05
 Identities = 26/142 (18%), Positives = 45/142 (31%), Gaps = 21/142 (14%)

Query: 518 GMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPF 577
            +   L +L L    L      + N   L  + L+   L  +       +  L  L +  
Sbjct: 223 PVNVELTILKLQHNNLTDTAW-LLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISN 281

Query: 578 SYIDHTADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NFISALHPCCCTE 630
           + +         +  L+ L+      + +  +  +F   LENL    N I  L       
Sbjct: 282 NRLVALNLYGQPIPTLKVLDLSHNHLLHVERNQPQF-DRLENLYLDHNSIVTLKL----- 335

Query: 631 DILGRLPNLRNLRIRGDLSYNQ 652
                   L+NL     LS+N 
Sbjct: 336 ---STHHTLKNL----TLSHND 350

>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 = 63.9 bits (156), Expect = 4e-11
 Identities = 53/263 (20%), Positives = 85/263 (32%), Gaps = 39/263 (14%)

Query: 518 GMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKL--NIPSLNSLPSSLLSNLLNLYTLD 574
           G+      L+L S  L   P G+ + L  L  L L  N  S     S       +L  LD
Sbjct: 25  GIPSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLD 84

Query: 575 MPFSYIDHTADEFWKMNKLRHLNFGS--ITLPAHPGKFCG--SLENL----NFISALHPC 626
           + F+ +   +  F  + +L HL+F    +   +    F    +L  L             
Sbjct: 85  LSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFN- 143

Query: 627 CCTEDILGRLPNLRNLRIRGDLSYNQ---SLLSKSLCRLSCLESLKLANESKMPRLSKIV 683
                I   L +L  L     ++ N    + L      L  L  L L+      +L ++ 
Sbjct: 144 ----GIFNGLSSLEVL----KMAGNSFQENFLPDIFTELRNLTFLDLSQC----QLEQL- 190

Query: 684 LAEYLFP--HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPN 741
            +   F    SL  L+ S+ +         + L  LQVL    N     K     +   +
Sbjct: 191 -SPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSS 249

Query: 742 LKVLHLK--------SMLWLEEW 756
           L  L+L               +W
Sbjct: 250 LAFLNLTQNDFACTCEHQSFLQW 272

>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 = 53.1 bits (128), Expect = 1e-07
 Identities = 43/196 (21%), Positives = 67/196 (34%), Gaps = 34/196 (17%)

Query: 555 SLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSL 614
            L S+P+ + S+   L         + H    F K+ +L  L+  S              
Sbjct: 18  GLTSVPTGIPSSATRLELESNKLQSLPHGV--FDKLTQLTKLSLSS-------------- 61

Query: 615 ENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLANE 673
              N +S      C         +L+ L    DLS+N    +S +   L  LE L   + 
Sbjct: 62  ---NGLSFKG---CCSQSDFGTTSLKYL----DLSFNGVITMSSNFLGLEQLEHLDFQHS 111

Query: 674 SKMPRLSKIVLAEYLFPH--SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRK 731
                L ++     +F    +L +L  S+T            L  L+VLK+  NS+    
Sbjct: 112 ----NLKQM-SEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENF 166

Query: 732 LTCGSYGFPNLKVLHL 747
           L        NL  L L
Sbjct: 167 LPDIFTELRNLTFLDL 182

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 65.1 bits (159), Expect = 5e-11
 Identities = 35/245 (14%), Positives = 72/245 (29%), Gaps = 37/245 (15%)

Query: 522 LLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSS-----LLSNLLNLYTLDMP 576
                    +      + ++      +  L    +NS P            L    +   
Sbjct: 134 SDEQKQKMRMHYQ--KTFVDYDPREDFSDLIKDCINSDPQQKSIKKSSRITLKDTQIGQL 191

Query: 577 FSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRL 636
            + I   +    ++ KLR    G+    A         EN  +          +     L
Sbjct: 192 SNNITFVSKAVMRLTKLRQFYMGNSPFVAENICEAWENENSEYAQQYKT---EDLKWDNL 248

Query: 637 PNLRNLRIRGDLSYNQSL--LSKSLCRLSCLESLKLAN----ESKMPRLSKIVLAEYLFP 690
            +L ++    ++    +L  L   L  L  ++ + +A       +  +     LA+    
Sbjct: 249 KDLTDV----EVYNCPNLTKLPTFLKALPEMQLINVACNRGISGEQLKDDWQALADAPVG 304

Query: 691 HSLTHLSFSNTDLMDDPMPT-LEKLPLLQVLKLKQNSYSGRKLTCGSYGFP-------NL 742
             +  +     +L   P+ T L+K+  L +L+   N     +L     G          L
Sbjct: 305 EKIQIIYIGYNNLKTFPVETSLQKMKKLGMLECLYN-----QLE----GKLPAFGSEIKL 355

Query: 743 KVLHL 747
             L+L
Sbjct: 356 ASLNL 360

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697} Length = 636

 Score = 59.7 bits (145), Expect = 3e-09
 Identities = 38/314 (12%), Positives = 92/314 (29%), Gaps = 54/314 (17%)

Query: 518 GMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKL---NIPSLNSLPSSL-----LSNLL 568
              K L  +++ +   +   P+ ++ L  ++ + +      S   L              
Sbjct: 246 DNLKDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGISGEQLKDDWQALADAPVGE 305

Query: 569 NLYTLDMPFSYIDH--TADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NF 619
            +  + + ++ +          KM KL  L              G     L +L    N 
Sbjct: 306 KIQIIYIGYNNLKTFPVETSLQKMKKLGMLECLYNQLEGKLPAFGS-EIKLASLNLAYNQ 364

Query: 620 ISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSK-----SLCRLSCLESLKLAN-- 672
           I+ +       +  G    + NL      ++N+  L           +S + ++  +   
Sbjct: 365 ITEIPA-----NFCGFTEQVENL----SFAHNK--LKYIPNIFDAKSVSVMSAIDFSYNE 413

Query: 673 -ESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRK 731
             S   +    +        +++ ++ SN  +   P         L  + L  N  +   
Sbjct: 414 IGSVDGKNFDPLDPTPFKGINVSSINLSNNQISKFPKELFSTGSPLSSINLMGNMLTE-- 471

Query: 732 LTCGSYGFPNLKVLHLKSMLWL-----------EEWTMGNAAMPKLECLIINPCAYLKKM 780
           +   S    N    +   +  +           +++      +P L  + ++  +   K 
Sbjct: 472 IPKNSLKDENENFKNTYLLTSIDLRFNKLTKLSDDFRATT--LPYLVGIDLSYNS-FSKF 528

Query: 781 PEQLWYIKSLNKFD 794
           P Q     +L  F 
Sbjct: 529 PTQPLNSSTLKGFG 542

>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 = 64.6 bits (157), Expect = 8e-11
 Identities = 48/230 (20%), Positives = 86/230 (37%), Gaps = 37/230 (16%)

Query: 530 SLVLIQYPSGIENLFL--LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADE 586
            +       G E++ L   + +     ++  LP++LL +   +  L++    I+      
Sbjct: 35  DMQTQDVYFGFEDITLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYA 94

Query: 587 FWKMNKLRHLNFGS--IT-LPAHPGKFCGSLENL----NFISALHPCCCTEDILGRLPNL 639
           F   + ++ L  G   I  LP H  +    L  L    N +S+L        I    P L
Sbjct: 95  FAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPR-----GIFHNTPKL 149

Query: 640 RNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLS 697
             L     +S N    +   +    + L++L+L++     RL+ + L+  L P SL H +
Sbjct: 150 TTL----SMSNNNLERIEDDTFQATTSLQNLQLSSN----RLTHVDLS--LIP-SLFHAN 198

Query: 698 FSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
            S   L      TL     ++ L    NS +   +         L +L L
Sbjct: 199 VSYNLL-----STLAIPIAVEELDASHNSIN--VVRGPV--NVELTILKL 239

>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 = 54.2 bits (130), Expect = 1e-07
 Identities = 44/230 (19%), Positives = 79/230 (34%), Gaps = 50/230 (21%)

Query: 523 LRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM---PFS 578
           ++ L +G   +   P  + +N+ LL  L L    L+SLP  +  N   L TL M      
Sbjct: 101 IQKLYMGFNAIRYLPPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLE 160

Query: 579 YIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPN 638
            I+     F     L++L   S                 N ++ +            +P+
Sbjct: 161 RIEDDT--FQATTSLQNLQLSS-----------------NRLTHVDL--------SLIPS 193

Query: 639 LRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSF 698
           L +     ++SYN      +L     +E L  ++      ++ +     +    LT L  
Sbjct: 194 LFHA----NVSYNL---LSTLAIPIAVEELDASHN----SINVV--RGPVNV-ELTILKL 239

Query: 699 SNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGS-YGFPNLKVLHL 747
            + +L D     L   P L  + L  N     K+          L+ L++
Sbjct: 240 QHNNLTD--TAWLLNYPGLVEVDLSYNELE--KIMYHPFVKMQRLERLYI 285

>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 = 49.5 bits (118), Expect = 4e-06
 Identities = 45/335 (13%), Positives = 91/335 (27%), Gaps = 47/335 (14%)

Query: 518 GMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPF 577
            +   L +L L    L    + + N   L  + L+   L  +       +  L  L +  
Sbjct: 229 PVNVELTILKLQHNNLTD-TAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLERLYISN 287

Query: 578 SYIDHTADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NFISALHPCCCTE 630
           + +         +  L+ L+      + +  +  +F   LENL    N I  L       
Sbjct: 288 NRLVALNLYGQPIPTLKVLDLSHNHLLHVERNQPQF-DRLENLYLDHNSIVTLKL----- 341

Query: 631 DILGRLPNLRNLRIRG---------------------DLSYNQSLLSKSLCRLSCLESLK 669
                   L+NL +                       D   +  +  +    L C ES K
Sbjct: 342 ---STHHTLKNLTLSHNDWDCNSLRALFRNVARPAVDDADQHCKIDYQLEHGLCCKESDK 398

Query: 670 LANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPL-----LQVLKLKQ 724
              +  +  ++   + E +        +    + +      + +         + L+ + 
Sbjct: 399 PYLDRLLQYIALTSVVEKVQRAQGRCSATDTINSVQSLSHYITQQGGVPLQGNEQLEAEV 458

Query: 725 NSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQL 784
           N          +      ++L                    L     N       + E+ 
Sbjct: 459 NELRAEVQQLTNEQIQQEQLLQGLHAEIDTNLRRYRLPKDGLARSSDNLNKVFTHLKERQ 518

Query: 785 WYIKSLNKFDCWWPQPELRQKLREFEDKEQCGIQL 819
            +     +      + E   K +E ED EQ  I L
Sbjct: 519 AFKLRETQAR----RTEADAKQKETEDLEQENIAL 549

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 61.2 bits (149), Expect = 4e-10
 Identities = 39/209 (18%), Positives = 67/209 (32%), Gaps = 39/209 (18%)

Query: 540 IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNF 598
            +N    +  K+   SL    +SL  +  N+  LD+  + +   +A +     KL  LN 
Sbjct: 6   KQNGNRYKIEKVTDSSLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNL 65

Query: 599 GSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKS 658
            S                 N +            L  L  LR L    DL+ N   +   
Sbjct: 66  SS-----------------NVLYETLD-------LESLSTLRTL----DLNNNY--VQ-E 94

Query: 659 LCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQ 718
           L     +E+L  AN      +S++  +         ++  +N  +             +Q
Sbjct: 95  LLVGPSIETLHAANN----NISRV--SCSRGQ-GKKNIYLANNKITMLRDLDEGCRSRVQ 147

Query: 719 VLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
            L LK N          +     L+ L+L
Sbjct: 148 YLDLKLNEIDTVNFAELAASSDTLEHLNL 176

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 52.3 bits (126), Expect = 3e-07
 Identities = 44/302 (14%), Positives = 86/302 (28%), Gaps = 58/302 (19%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
           L +L+L S VL +    +E+L  LR L LN   +  L         ++ TL         
Sbjct: 60  LELLNLSSNVLYETLD-LESLSTLRTLDLNNNYVQELL-----VGPSIETLHAAN----- 108

Query: 583 TADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL----NFISALHPCCCTEDILGRLPN 638
                   N +  ++                 +N+    N I+ L          G    
Sbjct: 109 --------NNISRVSCSRGQ----------GKKNIYLANNKITMLRD-----LDEGCRSR 145

Query: 639 LRNLRIRGDLSYNQ--SL-LSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTH 695
           ++ L    DL  N+  ++  ++       LE L L        +  +     +    L  
Sbjct: 146 VQYL----DLKLNEIDTVNFAELAASSDTLEHLNLQYN----FIYDV--KGQVVFAKLKT 195

Query: 696 LSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLK----SML 751
           L  S+  L     P  +    +  + L+ N      +        NL+   L+       
Sbjct: 196 LDLSSNKLAFMG-PEFQSAAGVTWISLRNNKLV--LIEKALRFSQNLEHFDLRGNGFHCG 252

Query: 752 WLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPELRQKLREFED 811
            L ++   N  +  +    +       +    +  +     + C         +L     
Sbjct: 253 TLRDFFSKNQRVQTVAKQTVKKLTGQNEEECTVPTLGHYGAYCCEDLPAPFADRLIALGH 312

Query: 812 KE 813
             
Sbjct: 313 HH 314

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae} Length = 317

 Score = 50.4 bits (121), Expect = 1e-06
 Identities = 30/216 (13%), Positives = 63/216 (29%), Gaps = 41/216 (18%)

Query: 507 HLDPIDWEKFCGMFKLLRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLL 564
            +  +         ++ + LDL    +  + +     +   L +L L    +  +   + 
Sbjct: 131 KITMLRDLDEGCRSRV-QYLDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQV- 188

Query: 565 SNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALH 624
                L TLD+  + +     EF     +  ++                L N N +  + 
Sbjct: 189 -VFAKLKTLDLSSNKLAFMGPEFQSAAGVTWIS----------------LRN-NKLVLI- 229

Query: 625 PCCCTEDILGRLPNLRNLRIRGDLSYNQ---SLLSKSLCRLSCLESLKLANESKMPRLSK 681
                E  L    NL +     DL  N      L     +   ++++      K+   ++
Sbjct: 230 -----EKALRFSQNLEHF----DLRGNGFHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNE 280

Query: 682 IVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLL 717
                       T   +      D P P  ++L  L
Sbjct: 281 EECT------VPTLGHYGAYCCEDLPAPFADRLIAL 310

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 61.0 bits (149), Expect = 5e-10
 Identities = 45/213 (21%), Positives = 81/213 (38%), Gaps = 31/213 (14%)

Query: 520 FKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY 579
              L  L +G+   I   S ++NL  LR L LN  +++ +    L+NL  +Y+L++  ++
Sbjct: 87  LVKLTNLYIGTN-KITDISALQNLTNLRELYLNEDNISDISP--LANLTKMYSLNLGANH 143

Query: 580 IDHTADEFWKMNKLRHLNFGS--IT-LPAHPGKFCGSLENL----NFISALHPCCCTEDI 632
                     M  L +L      +  +   P      L +L    N I  + P       
Sbjct: 144 NLSDLSPLSNMTGLNYLTVTESKVKDVT--PIANLTDLYSLSLNYNQIEDISP------- 194

Query: 633 LGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHS 692
           L  L +L           NQ      +  ++ L SLK+ N     +++ +     L    
Sbjct: 195 LASLTSLHYF----TAYVNQITDITPVANMTRLNSLKIGNN----KITDLSPLANL--SQ 244

Query: 693 LTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQN 725
           LT L      + D  +  ++ L  L++L +  N
Sbjct: 245 LTWLEIGTNQISD--INAVKDLTKLKMLNVGSN 275

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 57.9 bits (141), Expect = 5e-09
 Identities = 45/210 (21%), Positives = 82/210 (39%), Gaps = 29/210 (13%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
           +  L+LG+   +   S + N+  L YL +    +  +    ++NL +LY+L + ++ I  
Sbjct: 134 MYSLNLGANHNLSDLSPLSNMTGLNYLTVTESKVKDVTP--IANLTDLYSLSLNYNQI-E 190

Query: 583 TADEFWKMNKLRHLNFGSITLPAHPG-KFCGSLENL----NFISALHPCCCTEDILGRLP 637
                  +  L +       +           L +L    N I+ L P       L  L 
Sbjct: 191 DISPLASLTSLHYFTAYVNQITDITPVANMTRLNSLKIGNNKITDLSP-------LANLS 243

Query: 638 NLRNLRIRGDLSYNQSLLSK--SLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTH 695
            L  L    ++  NQ  +S   ++  L+ L+ L + +     ++S I +   L    L  
Sbjct: 244 QLTWL----EIGTNQ--ISDINAVKDLTKLKMLNVGSN----QISDISVLNNL--SQLNS 291

Query: 696 LSFSNTDLMDDPMPTLEKLPLLQVLKLKQN 725
           L  +N  L ++ M  +  L  L  L L QN
Sbjct: 292 LFLNNNQLGNEDMEVIGGLTNLTTLFLSQN 321

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B} Length = 347

 Score = 55.6 bits (135), Expect = 3e-08
 Identities = 51/254 (20%), Positives = 85/254 (33%), Gaps = 56/254 (22%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLN------IPSLNSLPS--------------S 562
           +  L +     +    GIE L  L YL LN      I  L++L                S
Sbjct: 46  ITKLVVAGE-KVASIQGIEYLTNLEYLNLNGNQITDISPLSNLVKLTNLYIGTNKITDIS 104

Query: 563 LLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENLNF 619
            L NL NL  L +    I         + K+  LN G+   ++  +        L  L  
Sbjct: 105 ALQNLTNLRELYLNEDNISD-ISPLANLTKMYSLNLGANHNLSDLSPLSN-MTGLNYLTV 162

Query: 620 ----ISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESK 675
               +  + P       +  L +L +L     L+YNQ      L  L+ L          
Sbjct: 163 TESKVKDVTP-------IANLTDLYSL----SLNYNQIEDISPLASLTSLHYFTAYVN-- 209

Query: 676 MPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCG 735
             +++ I     +    L  L   N  + D  +  L  L  L  L++  N     +++  
Sbjct: 210 --QITDITPVANM--TRLNSLKIGNNKITD--LSPLANLSQLTWLEIGTN-----QISDI 258

Query: 736 SY--GFPNLKVLHL 747
           +       LK+L++
Sbjct: 259 NAVKDLTKLKMLNV 272

>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 = 61.8 bits (150), Expect = 5e-10
 Identities = 34/249 (13%), Positives = 72/249 (28%), Gaps = 44/249 (17%)

Query: 507 HLDPIDWEKFCGMFKLLRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLL 564
            +  +         ++ + LDL    +  + +     +   L +L L    +  +   + 
Sbjct: 131 KITMLRDLDEGCRSRV-QYLDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQV- 188

Query: 565 SNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALH 624
                L TLD+  + +     EF     +  ++                L N N +  + 
Sbjct: 189 -VFAKLKTLDLSSNKLAFMGPEFQSAAGVTWIS----------------LRN-NKLVLI- 229

Query: 625 PCCCTEDILGRLPNLRNLRIRGDLSYNQ---SLLSKSLCRLSCLESLKLANESKMPRLSK 681
                E  L    NL +     DL  N      L     +   ++++      K+   ++
Sbjct: 230 -----EKALRFSQNLEHF----DLRGNGFHCGTLRDFFSKNQRVQTVAKQTVKKLTGQNE 280

Query: 682 IVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG---RKLTCGSYG 738
                       T   +      D P P  ++L  L+  +    S  G    +L C    
Sbjct: 281 EEC------TVPTLGHYGAYCCEDLPAPFADRLIALKRKEHALLSGQGSETERLECEREN 334

Query: 739 FPNLKVLHL 747
               + +  
Sbjct: 335 QARQREIDA 343

>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 = 61.0 bits (148), Expect = 9e-10
 Identities = 39/209 (18%), Positives = 67/209 (32%), Gaps = 39/209 (18%)

Query: 540 IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHLNF 598
            +N    +  K+   SL    +SL  +  N+  LD+  + +   +A +     KL  LN 
Sbjct: 6   KQNGNRYKIEKVTDSSLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNL 65

Query: 599 GSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKS 658
            S                 N +            L  L  LR L    DL+ N   +   
Sbjct: 66  SS-----------------NVLYETLD-------LESLSTLRTL----DLNNNY--VQ-E 94

Query: 659 LCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQ 718
           L     +E+L  AN      +S++  +         ++  +N  +             +Q
Sbjct: 95  LLVGPSIETLHAANN----NISRV--SCSRGQ-GKKNIYLANNKITMLRDLDEGCRSRVQ 147

Query: 719 VLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
            L LK N          +     L+ L+L
Sbjct: 148 YLDLKLNEIDTVNFAELAASSDTLEHLNL 176

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 61.8 bits (151), Expect = 7e-10
 Identities = 54/292 (18%), Positives = 97/292 (33%), Gaps = 75/292 (25%)

Query: 518 GMFKLLRVLDLGSLVL---IQYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLLNLYTL 573
                L  LDL    L   +   + + +   L++L ++  +L+     S    L +L  L
Sbjct: 97  KCSASLTSLDLSRNSLSGPVTTLTSLGSCSGLKFLNVSSNTLDFPGKVSGGLKLNSLEVL 156

Query: 574 DMPFSY----IDHTADEFWKMNKLRHLNF------GSITLPAHPGKFCGSLENLNFISAL 623
           D+  +                 +L+HL        G + +            NL F+  +
Sbjct: 157 DLSANSISGANVVGWVLSDGCGELKHLAISGNKISGDVDV--------SRCVNLEFLD-V 207

Query: 624 HPCCCTEDI--LGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLAN------- 672
                +  I  LG    L++L    D+S N+     S+++   + L+ L +++       
Sbjct: 208 SSNNFSTGIPFLGDCSALQHL----DISGNKLSGDFSRAISTCTELKLLNISSNQFVGPI 263

Query: 673 -ESKMPRLSKIVLA-------------------EYL----------FPHS------LTHL 696
               +  L  + LA                     L           P        L  L
Sbjct: 264 PPLPLKSLQYLSLAENKFTGEIPDFLSGACDTLTGLDLSGNHFYGAVPPFFGSCSLLESL 323

Query: 697 SFSNTDLMDD-PMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
           + S+ +   + PM TL K+  L+VL L  N +SG      +    +L  L L
Sbjct: 324 ALSSNNFSGELPMDTLLKMRGLKVLDLSFNEFSGELPESLTNLSASLLTLDL 375

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 59.9 bits (146), Expect = 2e-09
 Identities = 54/248 (21%), Positives = 87/248 (35%), Gaps = 38/248 (15%)

Query: 518 GMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLN-SLPSSL-LSNLLNLYTLDM 575
                L  L L +  +    SG +    L  L L+  SL+  + +   L +   L  L++
Sbjct: 74  LSLTGLESLFLSNSHINGSVSGFKCSASLTSLDLSRNSLSGPVTTLTSLGSCSGLKFLNV 133

Query: 576 PFSYIDHT--ADEFWKMNKLRHLNF------GSITLPAHPGKFCGSLENLNFISALHPCC 627
             + +D         K+N L  L+       G+  +       CG L++L     +    
Sbjct: 134 SSNTLDFPGKVSGGLKLNSLEVLDLSANSISGANVVGWVLSDGCGELKHLA----ISGNK 189

Query: 628 CTEDI-LGRLPNLRNLRIRGDLSYNQSLLSK---SLCRLSCLESLKLAN---ESKMPR-L 679
            + D+ + R  NL  L    D+S N    S     L   S L+ L ++         R +
Sbjct: 190 ISGDVDVSRCVNLEFL----DVSSNN--FSTGIPFLGDCSALQHLDISGNKLSGDFSRAI 243

Query: 680 SKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGF 739
           S            L  L+ S+      P+P    L  LQ L L +N ++G      S   
Sbjct: 244 STC--------TELKLLNISSNQF-VGPIPP-LPLKSLQYLSLAENKFTGEIPDFLSGAC 293

Query: 740 PNLKVLHL 747
             L  L L
Sbjct: 294 DTLTGLDL 301

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 59.5 bits (145), Expect = 3e-09
 Identities = 62/273 (22%), Positives = 92/273 (33%), Gaps = 57/273 (20%)

Query: 516 FCGMFKLLRVLDL------GSLVLIQYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLL 568
             G    L  LDL      G++     P    +  LL  L L+  + +  LP   L  + 
Sbjct: 289 LSGACDTLTGLDLSGNHFYGAV-----PPFFGSCSLLESLALSSNNFSGELPMDTLLKMR 343

Query: 569 NLYTLDMPF-SYIDHTADEFWKM-NKLRHLNFGS--IT--LPAHPGKFCGSLENLNFISA 622
            L  LD+ F  +     +    +   L  L+  S   +  +  +  +       L  +  
Sbjct: 344 GLKVLDLSFNEFSGELPESLTNLSASLLTLDLSSNNFSGPILPNLCQN--PKNTLQELY- 400

Query: 623 LHPCCCTEDI---LGRLPNLRNLRIRGDLSYNQSLLS----KSLCRLSCLESLKLAN--- 672
           L     T  I   L     L +L     LS+N   LS     SL  LS L  LKL     
Sbjct: 401 LQNNGFTGKIPPTLSNCSELVSL----HLSFNY--LSGTIPSSLGSLSKLRDLKLWLNML 454

Query: 673 -------ESKMPRLSKIVLAEYLF----PHS------LTHLSFSNTDLMDD-PMPTLEKL 714
                     +  L  ++L         P        L  +S SN  L  + P   + +L
Sbjct: 455 EGEIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIP-KWIGRL 513

Query: 715 PLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
             L +LKL  NS+SG  +        +L  L L
Sbjct: 514 ENLAILKLSNNSFSGN-IPAELGDCRSLIWLDL 545

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 54.1 bits (131), Expect = 1e-07
 Identities = 41/226 (18%), Positives = 72/226 (31%), Gaps = 52/226 (23%)

Query: 546 LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPA 605
           L    LN+   +++ SSL  +L  L +L +  S+I+ +   F     L  L+        
Sbjct: 57  LSSKPLNV-GFSAVSSSL-LSLTGLESLFLSNSHINGSVSGFKCSASLTSLD-------- 106

Query: 606 HPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ---SLLSKSLCRL 662
                   L   +    +         LG    L+ L    ++S N            +L
Sbjct: 107 --------LSRNSLSGPVTTLTS----LGSCSGLKFL----NVSSNTLDFPGKVSGGLKL 150

Query: 663 SCLESLKLAN-------------ESKMPRLSKIVLAEYLF----P----HSLTHLSFSNT 701
           + LE L L+                    L  + ++              +L  L  S+ 
Sbjct: 151 NSLEVLDLSANSISGANVVGWVLSDGCGELKHLAISGNKISGDVDVSRCVNLEFLDVSSN 210

Query: 702 DLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
           +     +P L     LQ L +  N  SG   +        LK+L++
Sbjct: 211 NF-STGIPFLGDCSALQHLDISGNKLSG-DFSRAISTCTELKLLNI 254

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A* Length = 768

 Score = 49.1 bits (118), Expect = 6e-06
 Identities = 37/233 (15%), Positives = 65/233 (27%), Gaps = 68/233 (29%)

Query: 518 GMFKLLRVLDL------GSLVLIQYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLLNL 570
           G    LR L L      G +     P  +  +  L  L L+   L   +PS L SN  NL
Sbjct: 439 GSLSKLRDLKLWLNMLEGEI-----PQELMYVKTLETLILDFNDLTGEIPSGL-SNCTNL 492

Query: 571 YTLDM---------PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFIS 621
             + +         P            ++  L  L   +         F G++       
Sbjct: 493 NWISLSNNRLTGEIPKW--------IGRLENLAILKLSN-------NSFSGNI------- 530

Query: 622 ALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLS----KSLCRLSCLESLKLANESKMP 677
              P       LG   +L  L    DL+ N    +     ++ + S   +       +  
Sbjct: 531 ---PAE-----LGDCRSLIWL----DLNTNL--FNGTIPAAMFKQSGKIAANFIAGKRYV 576

Query: 678 RLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGR 730
            +    + +        H + +  +        L +L       +    Y G 
Sbjct: 577 YIKNDGMKKEC------HGAGNLLEFQGIRSEQLNRLSTRNPCNITSRVYGGH 623

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 59.9 bits (145), Expect = 2e-09
 Identities = 25/227 (11%), Positives = 54/227 (23%), Gaps = 32/227 (14%)

Query: 537 PSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL 596
              I+ L  L+ +            ++     N           ++    +  +  L  +
Sbjct: 441 SKAIQRLTKLQIIYFANSPFTYDNIAVDWEDANSDYA----KQYENEELSWSNLKDLTDV 496

Query: 597 NFGSIT-LPAHPGKFCG--SLENL----NFISALHPCCCTE----DILGRLPNLRNLRIR 645
              +   +   P        L++L    N   +            D     P ++     
Sbjct: 497 ELYNCPNMTQLPDFLYDLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIF--- 553

Query: 646 GDLSYNQ--SL-LSKSLCRLSCLESLKLA-NE-SKMPRLSKIVLAEYLFPHSLTHLSFSN 700
             + YN       S SL ++  L  L    N+   +                LT L    
Sbjct: 554 -YMGYNNLEEFPASASLQKMVKLGLLDCVHNKVRHLEAFGT--------NVKLTDLKLDY 604

Query: 701 TDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
             + + P         ++ L    N          +     +  +  
Sbjct: 605 NQIEEIPEDFCAFTDQVEGLGFSHNKLKYIPNIFNAKSVYVMGSVDF 651

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 59.9 bits (145), Expect = 3e-09
 Identities = 41/258 (15%), Positives = 75/258 (29%), Gaps = 49/258 (18%)

Query: 522 LLRVLDLGSLVLIQ-YPSGIENLFLLRYLKL-NIPSLNSLPSSL--LSNL--LNLY---- 571
                +       +       NL  L  ++L N P++  LP  L  L  L  LN+     
Sbjct: 468 DWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQSLNIACNRG 527

Query: 572 -TLDMPFSYIDHTADEFWKMNKLRHLNFGS---ITLPAHPGKF-CGSLENL----NFISA 622
            +     +     AD+     K++    G       PA         L  L    N +  
Sbjct: 528 ISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLLDCVHNKVRH 587

Query: 623 LHPCCCTEDILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCR-LSCLESLKLANESKMPRLS 680
           L          G    L +L     L YNQ   + +  C     +E L  ++     +L 
Sbjct: 588 LEA-------FGTNVKLTDL----KLDYNQIEEIPEDFCAFTDQVEGLGFSHN----KLK 632

Query: 681 KIVLAEYLFP-HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGF 739
            I         + +  + FS   +  +       +   + +     + S  ++      F
Sbjct: 633 YIPNIFNAKSVYVMGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNEIQ----KF 688

Query: 740 P--------NLKVLHLKS 749
           P         +  + L +
Sbjct: 689 PTELFATGSPISTIILSN 706

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron} Length = 876

 Score = 57.2 bits (138), Expect = 2e-08
 Identities = 29/233 (12%), Positives = 63/233 (27%), Gaps = 45/233 (19%)

Query: 523 LRVLDLGSLVLIQYPSGIE------NLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM- 575
           +  +D     +      I              + L+   +   P+ L +    + T+ + 
Sbjct: 646 MGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFATGSPISTIILS 705

Query: 576 -------PFSYIDHTADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL-------N 618
                  P + +      +     L  ++       +L         +L  L       N
Sbjct: 706 NNLMTSIPENSLKPKDGNYKNTYLLTTIDLRFNKLTSLS--DDFRATTLPYLSNMDVSYN 763

Query: 619 FISALHPCCCTEDILGRLPNLRNLRIRG--DLSYNQSL--LSKSLCRLSCLESLKLA-NE 673
             S+                L+   IR   D   N+ L      +     L  L++  N 
Sbjct: 764 CFSSFPTQ------PLNSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQIGSN- 816

Query: 674 SKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNS 726
                + K+   E L P  L  L  ++   +   + ++       +  L  + 
Sbjct: 817 ----DIRKV--DEKLTP-QLYILDIADNPNISIDVTSVCPYIEAGMYVLLYDK 862

>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 = 4e-06
 Identities = 34/244 (13%), Positives = 69/244 (28%), Gaps = 48/244 (19%)

Query: 523 LRVLDLGSLVLIQYPSGI-----------------------------ENLFLLRYLKLNI 553
           L+VL  G+                                       + L L   L+  I
Sbjct: 349 LKVLSFGTHSETVSGRLFGDEELTPDMSEERKHRIRMHYKKMFLDYDQRLNLSDLLQDAI 408

Query: 554 PSLNSLPSSLLSNLLNLYTLDMPFSY--IDHTADEFWKMNKLRHLNFGSITLPAHPGKFC 611
                +      + ++L    +      I   +    ++ KL+ + F +           
Sbjct: 409 NRNPEMKPIKKDSRISLKDTQIGNLTNRITFISKAIQRLTKLQIIYFANSPFTYDNIAVD 468

Query: 612 GSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSL--LSKSLCRLSCLESLK 669
               N ++          E     L +L ++    +L    ++  L   L  L  L+SL 
Sbjct: 469 WEDANSDYAKQYEN---EELSWSNLKDLTDV----ELYNCPNMTQLPDFLYDLPELQSLN 521

Query: 670 LAN------ESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMP-TLEKLPLLQVLKL 722
           +A              +++   E   P  +        +L + P   +L+K+  L +L  
Sbjct: 522 IACNRGISAAQLKADWTRLADDEDTGP-KIQIFYMGYNNLEEFPASASLQKMVKLGLLDC 580

Query: 723 KQNS 726
             N 
Sbjct: 581 VHNK 584

>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 = 58.6 bits (142), Expect = 3e-09
 Identities = 43/251 (17%), Positives = 78/251 (31%), Gaps = 32/251 (12%)

Query: 518 GMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM- 575
           G+ + ++ LDL +  +    +   +    L+ L L    +N++     S+L +L  LD+ 
Sbjct: 49  GLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLS 108

Query: 576 --PFSYIDHTADEFWKMNKLRHLNFGS--ITLPAHPGKFCGSLENLNFISALHPCCCTE- 630
               S +  +   F  ++ L  LN              F   L  L  +   +    T+ 
Sbjct: 109 YNYLSNLSSSW--FKPLSSLTFLNLLGNPYKTLGETSLFSH-LTKLQILRVGNMDTFTKI 165

Query: 631 --DILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAE 686
                  L  L  L    ++  +   S   KSL  +  +  L L       +   +   E
Sbjct: 166 QRKDFAGLTFLEEL----EIDASDLQSYEPKSLKSIQNVSHLILHM----KQHILL--LE 215

Query: 687 YLFP--HSLTHLSFSNTDLMDDPM---PTLEKLPLLQVLKLKQNSYSGRKLTCGSYGF-- 739
                  S+  L   +TDL         T E   L++    +    +   L         
Sbjct: 216 IFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDESLFQVMKLLNQ 275

Query: 740 -PNLKVLHLKS 749
              L  L    
Sbjct: 276 ISGLLELEFSR 286

>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 = 44.7 bits (106), Expect = 8e-05
 Identities = 25/172 (14%), Positives = 46/172 (26%), Gaps = 21/172 (12%)

Query: 516 FCGMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLD 574
           F  + KL  +         +        L  L  L+++   L S     L ++ N+  L 
Sbjct: 145 FSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLI 204

Query: 575 M---PFSYIDHTADEFWKMNKLRHLNFGSITLPAHP---------GKFCGSLENLNFISA 622
           +       +          + +  L      L                       N    
Sbjct: 205 LHMKQHILLLEIF--VDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKIT 262

Query: 623 LHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLAN 672
                    +L ++  L  L    + S NQ  S+      RL+ L+ + L  
Sbjct: 263 DESLFQVMKLLNQISGLLEL----EFSRNQLKSVPDGIFDRLTSLQKIWLHT 310

>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 = 57.7 bits (140), Expect = 5e-09
 Identities = 44/248 (17%), Positives = 81/248 (32%), Gaps = 46/248 (18%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFL-LRYLKLNIPSLNSLPSSLLSNLLNLYTLDM---- 575
           L  L L    L  +      E +   L+ L+++   +  +  S+ + L  +  +++    
Sbjct: 102 LERLYLSKNQLKELP-----EKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNP 156

Query: 576 -PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL----NFISALHPCCCTE 630
              S I++ A  F  M KL ++      +   P     SL  L    N I+ +       
Sbjct: 157 LKSSGIENGA--FQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKVDA----- 209

Query: 631 DILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYL 688
             L  L NL  L     LS+N   ++ + SL     L  L L N     +L K+      
Sbjct: 210 ASLKGLNNLAKL----GLSFNSISAVDNGSLANTPHLRELHLNNN----KLVKV---PGG 258

Query: 689 FP--HSLTHLSFSNTDLMD------DPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSY-GF 739
                 +  +   N ++         P     K      + L  N     ++   ++   
Sbjct: 259 LADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCV 318

Query: 740 PNLKVLHL 747
                + L
Sbjct: 319 YVRAAVQL 326

>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 = 55.4 bits (134), Expect = 3e-08
 Identities = 46/245 (18%), Positives = 80/245 (32%), Gaps = 42/245 (17%)

Query: 523 LRVLDLGS--LVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI 580
           L  L L +  +  I  P     L  L  L L+   L  LP  +   L  L   +   + +
Sbjct: 78  LHTLILINNKISKIS-PGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKV 136

Query: 581 DHTADEFWKMNKLRHLNFGS--ITLPA-HPGKFCG--SLENL----NFISALHPCCCTED 631
             +   F  +N++  +  G+  +       G F G   L  +      I+ +        
Sbjct: 137 RKSV--FNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQ------ 188

Query: 632 ILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLF 689
             G  P+L  L     L  N+   + + SL  L+ L  L L+       +S +       
Sbjct: 189 --GLPPSLTEL----HLDGNKITKVDAASLKGLNNLAKLGLSF----NSISAV--DNGSL 236

Query: 690 PH--SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQN-----SYSGRKLTCGSYGFPNL 742
            +   L  L  +N  L+  P   L     +QV+ L  N       +       +    + 
Sbjct: 237 ANTPHLRELHLNNNKLVKVP-GGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASY 295

Query: 743 KVLHL 747
             + L
Sbjct: 296 SGVSL 300

>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 = 53.9 bits (130), Expect = 9e-08
 Identities = 35/211 (16%), Positives = 72/211 (34%), Gaps = 36/211 (17%)

Query: 523 LRVLDLGS--LVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY 579
           + V++LG+  L      +G  + +  L Y+++   ++ ++P  L  +L  L+      + 
Sbjct: 147 MIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITK 206

Query: 580 IDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNL 639
           +D  A     +N L  L                     N ISA+         L   P+L
Sbjct: 207 VD--AASLKGLNNLAKLGLSF-----------------NSISAVDN-----GSLANTPHL 242

Query: 640 RNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLA-NE-SKMPRLSKIVLAEYLFPHSLTHL 696
           R L     L+ N+   +   L     ++ + L  N  S +               S + +
Sbjct: 243 REL----HLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGV 298

Query: 697 SFSNTDLMDDPMP--TLEKLPLLQVLKLKQN 725
           S  +  +    +   T   + +   ++L   
Sbjct: 299 SLFSNPVQYWEIQPSTFRCVYVRAAVQLGNY 329

>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 = 48.1 bits (115), Expect = 6e-06
 Identities = 22/161 (13%), Positives = 52/161 (32%), Gaps = 27/161 (16%)

Query: 518 GMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMP 576
           G+   L  L L    + +  +   + L  L  L L+  S++++ +  L+N  +L  L + 
Sbjct: 189 GLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLN 248

Query: 577 FSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCC-CTEDILGR 635
            + +            ++ +   +                 N ISA+     C      +
Sbjct: 249 NNKLVKVPGGLADHKYIQVVYLHN-----------------NNISAIGSNDFCPPGYNTK 291

Query: 636 LPNLRNLRIRGDLSYNQ----SLLSKSLCRLSCLESLKLAN 672
             +   +     L  N      +   +   +    +++L N
Sbjct: 292 KASYSGV----SLFSNPVQYWEIQPSTFRCVYVRAAVQLGN 328

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A* Length = 285

 Score = 57.3 bits (139), Expect = 5e-09
 Identities = 47/257 (18%), Positives = 74/257 (28%), Gaps = 54/257 (21%)

Query: 518 GMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM- 575
           G+    + + L    +   P+        L  L L+   L  + ++  + L  L  LD+ 
Sbjct: 29  GIPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLS 88

Query: 576 ---PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDI 632
                  +D     F  + +L  L+                L+    +  L P      +
Sbjct: 89  DNAQLRSVDPAT--FHGLGRLHTLH----------------LDR-CGLQELGP-----GL 124

Query: 633 LGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFP 690
              L  L+ L     L  N   +L   +   L  L  L L       R+S   + E  F 
Sbjct: 125 FRGLAALQYL----YLQDNALQALPDDTFRDLGNLTHLFLHG----NRIS--SVPERAFR 174

Query: 691 H--SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSY-GFPNLKVLHL 747
              SL  L      +          L  L  L L  N+ S   L   +      L+ L L
Sbjct: 175 GLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLS--ALPTEALAPLRALQYLRL 232

Query: 748 KS--------MLWLEEW 756
                        L  W
Sbjct: 233 NDNPWVCDCRARPLWAW 249

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 56.6 bits (137), Expect = 1e-08
 Identities = 45/244 (18%), Positives = 85/244 (34%), Gaps = 37/244 (15%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFL-LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYID 581
           L+ L +    L++ P     L   L  L+++   +  +P  + S L N+  ++M  + ++
Sbjct: 104 LQKLYISKNHLVEIPPN---LPSSLVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLE 160

Query: 582 HTADE---FWKMNKLRHLNFGSITLPAHPGKFCGSLENL----NFISALHPCCCTEDILG 634
           ++  E   F  +  L +L      L   P     +L  L    N I A+       + L 
Sbjct: 161 NSGFEPGAFDGLK-LNYLRISEAKLTGIPKDLPETLNELHLDHNKIQAIEL-----EDLL 214

Query: 635 RLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFP-H 691
           R   L  L     L +NQ   + + SL  L  L  L L N     +LS++     L    
Sbjct: 215 RYSKLYRL----GLGHNQIRMIENGSLSFLPTLRELHLDNN----KLSRV--PAGLPDLK 264

Query: 692 SLTHLSFSNTDLMD------DPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSY-GFPNLKV 744
            L  +     ++         P+    K      + L  N     ++   ++    +   
Sbjct: 265 LLQVVYLHTNNITKVGVNDFCPVGFGVKRAYYNGISLFNNPVPYWEVQPATFRCVTDRLA 324

Query: 745 LHLK 748
           +   
Sbjct: 325 IQFG 328

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus} Length = 332

 Score = 43.1 bits (102), Expect = 3e-04
 Identities = 26/132 (19%), Positives = 43/132 (32%), Gaps = 18/132 (13%)

Query: 618 NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESK 675
           N IS L       D    L +L  L     L  N+   +  K+   L  L+ L ++    
Sbjct: 64  NDISELRK-----DDFKGLQHLYAL----VLVNNKISKIHEKAFSPLRKLQKLYISKN-- 112

Query: 676 MPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCG 735
              L +I     L   SL  L   +  +   P      L  +  +++  N         G
Sbjct: 113 --HLVEI--PPNLPS-SLVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPG 167

Query: 736 SYGFPNLKVLHL 747
           ++    L  L +
Sbjct: 168 AFDGLKLNYLRI 179

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 56.9 bits (138), Expect = 1e-08
 Identities = 47/227 (20%), Positives = 75/227 (33%), Gaps = 48/227 (21%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
           +  L    L  I+   G+E L  L  +  +   L  +    L NL  L  + M  + I  
Sbjct: 48  VTTLQADRL-GIKSIDGVEYLNNLTQINFSNNQLTDITP--LKNLTKLVDILMNNNQIAD 104

Query: 583 TADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNL 642
                  +  L  L   +                 N I+ + P       L  L NL  L
Sbjct: 105 I-TPLANLTNLTGLTLFN-----------------NQITDIDP-------LKNLTNLNRL 139

Query: 643 RIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTD 702
               +LS N      +L  L+ L+ L   N     +++ +     L   +L  L  S+  
Sbjct: 140 ----ELSSNTISDISALSGLTSLQQLSFGN-----QVTDLKPLANL--TTLERLDISSNK 188

Query: 703 LMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTC--GSYGFPNLKVLHL 747
           + D  +  L KL  L+ L    N     +++         NL  L L
Sbjct: 189 VSD--ISVLAKLTNLESLIATNN-----QISDITPLGILTNLDELSL 228

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A Length = 466

 Score = 51.5 bits (124), Expect = 8e-07
 Identities = 55/232 (23%), Positives = 83/232 (35%), Gaps = 36/232 (15%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
           L  L+L S   I   S +  L  L+ L       +  P   L+NL  L  LD+  + +  
Sbjct: 136 LNRLELSS-NTISDISALSGLTSLQQLSFGNQVTDLKP---LANLTTLERLDISSNKVSD 191

Query: 583 TADEFWKMNKLRHLNFGS--IT-LPAHPGKFCGSLENL----NFISALHPCCCTEDILGR 635
                 K+  L  L   +  I+ +   P     +L+ L    N +  +         L  
Sbjct: 192 I-SVLAKLTNLESLIATNNQISDIT--PLGILTNLDELSLNGNQLKDI-------GTLAS 241

Query: 636 LPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTH 695
           L NL +L    DL+ NQ      L  L+ L  LKL       ++S I     L   +LT+
Sbjct: 242 LTNLTDL----DLANNQISNLAPLSGLTKLTELKLGAN----QISNISPLAGL--TALTN 291

Query: 696 LSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
           L  +   L D  +  +  L  L  L L  N+ S             L+ L  
Sbjct: 292 LELNENQLED--ISPISNLKNLTYLTLYFNNISDIS---PVSSLTKLQRLFF 338

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 56.2 bits (136), Expect = 3e-08
 Identities = 48/229 (20%), Positives = 75/229 (32%), Gaps = 41/229 (17%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
           L  L      L + P   ++L  L     N+ +L+ LP  L    L +   +     +  
Sbjct: 93  LESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPLLEY--LGVS--NNQLEKL-- 146

Query: 583 TADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL----NFISALHPCCCTEDILGRLPN 638
              E    + L+ ++  + +L   P     SLE +    N +  L         L  LP 
Sbjct: 147 --PELQNSSFLKIIDVDNNSLKKLPDLP-PSLEFIAAGNNQLEELPE-------LQNLPF 196

Query: 639 LRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSF 698
           L  +        N   L K       LES+   N      L +  L E      LT +  
Sbjct: 197 LTAI----YADNNS--LKKLPDLPLSLESIVAGNN----ILEE--LPELQNLPFLTTIYA 244

Query: 699 SNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
            N  L   P    +  P L+ L ++ N      LT       +L  L +
Sbjct: 245 DNNLLKTLP----DLPPSLEALNVRDN-----YLTDLPELPQSLTFLDV 284

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 48.1 bits (115), Expect = 8e-06
 Identities = 41/219 (18%), Positives = 68/219 (31%), Gaps = 43/219 (19%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
           L  L++    L   P   ++L  L   +     L+ LP        NLY L+   + I  
Sbjct: 259 LEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELPP-------NLYYLNASSNEIRS 311

Query: 583 TADEFWKMNKLRHLNFGS---ITLPAHPGKFCGSLENL----NFISALHPCCCTEDILGR 635
             D       L  LN  +   I LPA P +    LE L    N ++ +            
Sbjct: 312 LCDL---PPSLEELNVSNNKLIELPALPPR----LERLIASFNHLAEVPEL--------- 355

Query: 636 LPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLANE--SKMPRLSKIVLAE----YL 688
             NL+ L     + YN           +  L       E       L ++ +        
Sbjct: 356 PQNLKQL----HVEYNPLREFPDIPESVEDLRMNSHLAEVPELPQNLKQLHVETNPLREF 411

Query: 689 --FPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQN 725
              P S+  L  ++  ++D      E    L+    + +
Sbjct: 412 PDIPESVEDLRMNSERVVDPYEFAHETTDKLEDDVFEHH 450

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A Length = 454

 Score = 47.7 bits (114), Expect = 1e-05
 Identities = 46/220 (20%), Positives = 71/220 (32%), Gaps = 46/220 (20%)

Query: 546 LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPA 605
              L+LN   L+SLP        +L +L    + +    +    +  L   N     L  
Sbjct: 73  AHELELNNLGLSSLPELPP----HLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSD 128

Query: 606 HPGKFCGSLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCR 661
            P      LE L    N +  L         L     L+ +    D+  N   L K    
Sbjct: 129 LP----PLLEYLGVSNNQLEKLPE-------LQNSSFLKII----DVDNNS--LKKLPDL 171

Query: 662 LSCLESLKLAN--------ESKMPRLSKIVLA----EYLF--PHSLTHLSFSNTDLMDDP 707
              LE +   N           +P L+ I       + L   P SL  +   N  L +  
Sbjct: 172 PPSLEFIAAGNNQLEELPELQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGNNILEE-- 229

Query: 708 MPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
           +P L+ LP L  +    N      L       P+L+ L++
Sbjct: 230 LPELQNLPFLTTIYADNN-----LLKTLPDLPPSLEALNV 264

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes} Length = 457

 Score = 55.8 bits (135), Expect = 3e-08
 Identities = 61/319 (19%), Positives = 99/319 (31%), Gaps = 46/319 (14%)

Query: 492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKL 551
           D    S +  + E +  D I  E+       L  LD  +   I   +GIE L  L  L  
Sbjct: 17  DDNFASEVAAAFEMQATDTISEEQL----ATLTSLDCHNS-SITDMTGIEKLTGLTKLIC 71

Query: 552 NIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFC 611
              ++ +L  S  +NL  L       + +D        + KL +LN  +  L        
Sbjct: 72  TSNNITTLDLSQNTNLTYLACDSNKLTNLD-----VTPLTKLTYLNCDTNKLTKLDVSQN 126

Query: 612 GSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLA 671
             L  LN          TE  +     L  L    D   N+ +    +   + L +L  +
Sbjct: 127 PLLTYLN----CARNTLTEIDVSHNTQLTEL----DCHLNKKITKLDVTPQTQLTTLDCS 178

Query: 672 N-------ESKMPRLSKIVLA-------EYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLL 717
                    S+   L+++          +      LT L  S+  L +     +  L  L
Sbjct: 179 FNKITELDVSQNKLLNRLNCDTNNITKLDLNQNIQLTFLDCSSNKLTEID---VTPLTQL 235

Query: 718 QVLKLKQNSYSGRKLTC-GSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAY 776
                  N      LT         L  LH      L E  + +    +L       C  
Sbjct: 236 TYFDCSVN-----PLTELDVSTLSKLTTLHCIQTD-LLEIDLTH--NTQLIYFQAEGCRK 287

Query: 777 LKKMPEQLWYIKSLNKFDC 795
           +K++   + +   L   DC
Sbjct: 288 IKELD--VTHNTQLYLLDC 304

>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 = 54.0 bits (130), Expect = 1e-07
 Identities = 41/256 (16%), Positives = 79/256 (30%), Gaps = 33/256 (12%)

Query: 523 LRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNS--LPSSLLSNLLNLYTLDMPFSY 579
           L +L L     +Q  +G    L  L  L L   +L+   L  +    L +L  L +  + 
Sbjct: 81  LIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNN 140

Query: 580 IDHTADE--FWKMNKLRHLNFGSITLPAHPGKFCGSLENL---------NFISALHPCCC 628
           I        F  M +   L+     + +   +   + +             +  ++    
Sbjct: 141 IKKIQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNFQGKHFTLLRLSSITLQDMNEYWL 200

Query: 629 TEDILGRLPNLRNLRIRGDLSYNQ--SLLSK---SLCRLSCLESLKLANESKMP------ 677
             +  G      ++    DLS N     ++K        + ++SL L+N   M       
Sbjct: 201 GWEKCGNPFKNTSITTL-DLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHT 259

Query: 678 ---RLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTC 734
                        L    +     S + +             L+ L L QN  +  K+  
Sbjct: 260 NFKDPDNFTFKG-LEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEIN--KIDD 316

Query: 735 GS-YGFPNLKVLHLKS 749
            + +G  +L  L+L  
Sbjct: 317 NAFWGLTHLLKLNLSQ 332

>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 = 49.4 bits (118), Expect = 3e-06
 Identities = 36/237 (15%), Positives = 59/237 (24%), Gaps = 52/237 (21%)

Query: 523 LRVLDLGSLVLIQY-PSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI 580
           L+ L +          +     L  L  LKL+      L +   + L NL  L +    +
Sbjct: 56  LQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLANLEVLTLTQCNL 115

Query: 581 DHT---ADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLP 637
           D      + F  +  L  L                     N I  + P          + 
Sbjct: 116 DGAVLSGNFFKPLTSLEMLVLRD-----------------NNIKKIQP----ASFFLNMR 154

Query: 638 NLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLS 697
               L    DL++N+         +  +    L N               L   S+T   
Sbjct: 155 RFHVL----DLTFNK---------VKSICEEDLLN------FQGKHF-TLLRLSSITLQD 194

Query: 698 FSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTC-GSYGFPNLKVLHLKSMLWL 753
            +   L  +      K   +  L L  N           +  F +         L L
Sbjct: 195 MNEYWLGWEKCGNPFKNTSITTLDLSGN-----GFKESMAKRFFDAIAGTKIQSLIL 246

>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 = 42.0 bits (99), Expect = 6e-04
 Identities = 31/154 (20%), Positives = 54/154 (35%), Gaps = 30/154 (19%)

Query: 523 LRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYID 581
           ++  DL    +      +  +   L  L L    +N +  +    L +L  L++  +++ 
Sbjct: 277 VKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLG 336

Query: 582 H-TADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLR 640
              +  F  ++KL  L+                L   N I AL            LPNL+
Sbjct: 337 SIDSRMFENLDKLEVLD----------------LSY-NHIRALGD-----QSFLGLPNLK 374

Query: 641 NLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLAN 672
            L     L  NQ  S+      RL+ L+ + L  
Sbjct: 375 EL----ALDTNQLKSVPDGIFDRLTSLQKIWLHT 404

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 Length = 308

 Score = 53.2 bits (128), Expect = 1e-07
 Identities = 42/230 (18%), Positives = 75/230 (32%), Gaps = 43/230 (18%)

Query: 520 FKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY 579
                 +  G   +        +L  +  L      + ++    +  L NL  L++  + 
Sbjct: 18  LANAIKIAAGKSNVTD-TVTQADLDGITTLSAFGTGVTTIEG--VQYLNNLIGLELKDNQ 74

Query: 580 IDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNL 639
           I         + K+  L                     N +  +         +  L ++
Sbjct: 75  ITDL-APLKNLTKITELELSG-----------------NPLKNVSA-------IAGLQSI 109

Query: 640 RNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFS 699
           + L    DL+  Q      L  LS L+ L L       +++ I     L   +L +LS  
Sbjct: 110 KTL----DLTSTQITDVTPLAGLSNLQVLYLDL----NQITNISPLAGL--TNLQYLSIG 159

Query: 700 NTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKS 749
           N  + D  +  L  L  L  LK   N  S   ++  +   PNL  +HLK+
Sbjct: 160 NAQVSD--LTPLANLSKLTTLKADDNKIS--DISPLA-SLPNLIEVHLKN 204

>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 = 53.7 bits (129), Expect = 2e-07
 Identities = 38/218 (17%), Positives = 73/218 (33%), Gaps = 24/218 (11%)

Query: 521 KLLRVLDLGSLVLIQYPSGIENLF-LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY 579
           K L +  + S V     S I  +F  +      +     +     S +     LD   + 
Sbjct: 276 KALSIHQVVSDVFGFPQSYIYEIFSNMNIKNFTVSGTRMVHMLCPSKISPFLHLDFSNNL 335

Query: 580 I-DHTADEFWKMNKLRHLNFGSI---TLPAHPGKFCG--SLENL----NFISALHPCCCT 629
           + D   +    + +L  L         L           SL+ L    N +S        
Sbjct: 336 LTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNSVSYDEK---- 391

Query: 630 EDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLF 689
           +       +L +L    ++S N    +   C    ++ L L + +K+  + K V+     
Sbjct: 392 KGDCSWTKSLLSL----NMSSNILTDTIFRCLPPRIKVLDLHS-NKIKSIPKQVVKL--- 443

Query: 690 PHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSY 727
             +L  L+ ++  L   P    ++L  LQ + L  N +
Sbjct: 444 -EALQELNVASNQLKSVPDGIFDRLTSLQKIWLHTNPW 480

>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 = 43.7 bits (103), Expect = 2e-04
 Identities = 44/264 (16%), Positives = 80/264 (30%), Gaps = 38/264 (14%)

Query: 537 PSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL 596
            S I +L  LR L ++   +  L  S+      L  LD+               NKL  +
Sbjct: 38  TSDILSLSKLRILIISHNRIQYLDISVFKFNQELEYLDLSH-------------NKLVKI 84

Query: 597 NFGSITLPAHPGKFCGSLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ 652
           +               +L++L    N   AL  C       G +  L+ L     LS   
Sbjct: 85  SCHPTV----------NLKHLDLSFNAFDALPIC----KEFGNMSQLKFL----GLSTTH 126

Query: 653 SLLSKSLCRLSCLESLKLANESKMPRLSKIVLA--EYLFPHSLTHLSFSNTDLMDDPMPT 710
            L   S+  ++ L   K+          K      +     SL  +  +N +       +
Sbjct: 127 -LEKSSVLPIAHLNISKVLLVLGETYGEKEDPEGLQDFNTESLHIVFPTNKEFHFILDVS 185

Query: 711 LEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLI 770
           ++ +  L++  +K      +     S          L ++      T  N+ +  L+ + 
Sbjct: 186 VKTVANLELSNIKCVLEDNKCSYFLSILAKLQTNPKLSNLTLNNIETTWNSFIRILQLVW 245

Query: 771 INPCAYLKKMPEQLWYIKSLNKFD 794
                Y      +L        FD
Sbjct: 246 HTTVWYFSISNVKLQGQLDFRDFD 269

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 51.8 bits (124), Expect = 7e-07
 Identities = 46/236 (19%), Positives = 74/236 (31%), Gaps = 57/236 (24%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSL----LSN---------LLN 569
           LR L++    L   P     L  L      +  L +LPS L    +              
Sbjct: 83  LRTLEVSGNQLTSLPVLPPGLLELSIFSNPLTHLPALPSGLCKLWIFGNQLTSLPVLPPG 142

Query: 570 LYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL----NFISALHP 625
           L  L +  + +        ++ KL   N    +LP  P      L+ L    N +++L P
Sbjct: 143 LQELSVSDNQLASLPALPSELCKLWAYNNQLTSLPMLP----SGLQELSVSDNQLASL-P 197

Query: 626 CCCTEDILGRLPNLR--NLRIRG-----------DLSYNQ-SLLSKSLCRLSCLESLKLA 671
                 +   L  L   N R+              +S N+ + L         L+ L ++
Sbjct: 198 -----TLPSELYKLWAYNNRLTSLPALPSGLKELIVSGNRLTSLPVLPSE---LKELMVS 249

Query: 672 NE--SKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQN 725
               + +P L          P  L  LS     L   P  +L  L     + L+ N
Sbjct: 250 GNRLTSLPML----------PSGLLSLSVYRNQLTRLP-ESLIHLSSETTVNLEGN 294

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium} Length = 622

 Score = 44.1 bits (104), Expect = 2e-04
 Identities = 44/223 (19%), Positives = 68/223 (30%), Gaps = 57/223 (25%)

Query: 546 LRYLKLNIPSLNSLPSSLLSNLLNLY-----------------TLDMPFSYIDHTADEFW 588
              L +    L +LP  L +++  L                  TL++  + +        
Sbjct: 42  NAVLNVGESGLTTLPDCLPAHITTLVIPDNNLTSLPALPPELRTLEVSGNQLTSLPVLPP 101

Query: 589 KMNKLRHLNFGSITLPAHPGKFCGSLENL----NFISALHPCCCTEDILGRLPNLRNLRI 644
            + +L   +     LPA P      L  L    N +++L             P L+ L  
Sbjct: 102 GLLELSIFSNPLTHLPALP----SGLCKLWIFGNQLTSLPVL---------PPGLQEL-- 146

Query: 645 RGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLM 704
              +S NQ  L+      S L  L   N +++  L          P  L  LS S+  L 
Sbjct: 147 --SVSDNQ--LASLPALPSELCKLWAYN-NQLTSLPM-------LPSGLQELSVSDNQLA 194

Query: 705 DDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL 747
             P         L  L    N     +LT        LK L +
Sbjct: 195 SLP----TLPSELYKLWAYNN-----RLTSLPALPSGLKELIV 228

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A} Length = 571

 Score = 50.4 bits (120), Expect = 2e-06
 Identities = 30/179 (16%), Positives = 58/179 (32%), Gaps = 40/179 (22%)

Query: 518 GMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPF 577
            +   + VL++    LI  P    +   L YL      L++LP  L ++L +L   +   
Sbjct: 77  NLPPQITVLEITQNALISLPELPAS---LEYLDACDNRLSTLP-ELPASLKHLDVDNNQL 132

Query: 578 SYIDHTADEFWKMNKLRHLNFGS---ITLPAHPGK----------------FCGSLENL- 617
           + +            L ++N  +     LP  P                     SLE L 
Sbjct: 133 TMLPEL------PALLEYINADNNQLTMLPELPTSLEVLSVRNNQLTFLPELPESLEALD 186

Query: 618 ---NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLAN 672
              N + +L           R  +     I      N+ + + +++  L    ++ L +
Sbjct: 187 VSTNLLESLPAV------PVRNHHSEETEIFFRCRENRITHIPENILSLDPTCTIILED 239

>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 = 49.8 bits (119), Expect = 4e-06
 Identities = 56/343 (16%), Positives = 107/343 (31%), Gaps = 77/343 (22%)

Query: 166 EELLDLLIEGPPQLS----VVAILDSIGLDKTAFAGE-AYNSSYVKHYF-DCHAWITEPY 219
           ++L+  + +   +L+     V I    G  K+  A E   + S ++  F     W++   
Sbjct: 130 KKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGK 189

Query: 220 SNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTK--RYLIVIDDVWSID 277
            ++      L  +   L      S+ +  N E  K  L   ++ K  R L+++DDVW   
Sbjct: 190 QDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWD-- 247

Query: 278 MWDVIQEILPDNQNGSRVLITLTDIRIIISF-----------QFEDGENMRL-------- 318
                  +L    N  ++L+T  D  +  S                 + + +        
Sbjct: 248 -----PWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMK 302

Query: 319 --DLVPTGGPLRATYKGRPFLI-LYHGSISLEENIREAVETPLGLRYIKCL--------- 366
             DL      +    KG P ++ L    +    N        L  +  K +         
Sbjct: 303 KEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKSSSYDYE 362

Query: 367 -----------MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYL 415
                      ML   +K  +  LS+     ++ T+ L  LW       D      E  L
Sbjct: 363 ALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLW-------DLETEEVEDIL 415

Query: 416 EQLIKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVPYMVEFI 458
           ++ + +  +   +                   LH     V+F+
Sbjct: 416 QEFVNKSLLFCNRNGKSF-----------CYYLH--DLQVDFL 445

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus} Length = 312

 Score = 48.4 bits (115), Expect = 5e-06
 Identities = 44/234 (18%), Positives = 74/234 (31%), Gaps = 43/234 (18%)

Query: 508 LDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLF-----LLRYLKLNIPSLNSLPSS 562
                          L +L+L ++      + +  L       L+ L +      +    
Sbjct: 108 TGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCE 167

Query: 563 LLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL----N 618
            +     L TLD+  S            N    L    +     P KF  +L+ L     
Sbjct: 168 QVRVFPALSTLDL--SD-----------NPE--LGERGLISALCPLKF-PTLQVLALRNA 211

Query: 619 FISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCR-LSCLESLKLANESK 675
            +      C    +      L+ L    DLS+N          C   S L SL L+  + 
Sbjct: 212 GMETPSGVCSA--LAAARVQLQGL----DLSHNSLRDAAGAPSCDWPSQLNSLNLSF-TG 264

Query: 676 MPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG 729
           + ++ K +      P  L+ L  S   L     P+ ++LP +  L LK N +  
Sbjct: 265 LKQVPKGL------PAKLSVLDLSYNRLDR--NPSPDELPQVGNLSLKGNPFLD 310

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus} Length = 312

 Score = 47.6 bits (113), Expect = 7e-06
 Identities = 36/201 (17%), Positives = 62/201 (30%), Gaps = 29/201 (14%)

Query: 556 LNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMN-----KLRHLNFGSITLPAHPGKF 610
            N L ++ +       +L+     +D  AD     +      L+ L   +  +P+     
Sbjct: 28  FNCLGAADVELYGGGRSLEYLLKRVDTEADLGQFTDIIKSLSLKRLTVRAARIPSR--IL 85

Query: 611 CGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQS-LLSKSLCRLSCLESLK 669
            G+L  L                  +  L+ L +  +L    +            L  L 
Sbjct: 86  FGALRVLG-----------------ISGLQELTLE-NLEVTGTAPPPLLEATGPDLNILN 127

Query: 670 LANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG 729
           L N S   R + +   +      L  LS +    ++     +   P L  L L  N   G
Sbjct: 128 LRNVSWATRDAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELG 187

Query: 730 RK---LTCGSYGFPNLKVLHL 747
            +          FP L+VL L
Sbjct: 188 ERGLISALCPLKFPTLQVLAL 208

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A Length = 290

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 45/248 (18%), Positives = 73/248 (29%), Gaps = 54/248 (21%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
              ++     L   P  +        L L+   L +   + L     L  L++  + +  
Sbjct: 12  HLEVNCDKRNLTALPPDL--PKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAEL-T 68

Query: 583 TADEFWKMNKLRHLNFGSITLPAHPGKFCG--SLENL----NFISALHPCCCTEDILGRL 636
                  +  L  L+     L + P       +L  L    N +++L         L  L
Sbjct: 69  KLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPL-----GALRGL 123

Query: 637 PNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHL 696
             L+ L     L  N+         L  L    L          K           L  L
Sbjct: 124 GELQEL----YLKGNE---------LKTLPPGLLT------PTPK-----------LEKL 153

Query: 697 SFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKS------- 749
           S +N +L + P   L  L  L  L L++NS     +  G +G   L    L         
Sbjct: 154 SLANNNLTELPAGLLNGLENLDTLLLQENSL--YTIPKGFFGSHLLPFAFLHGNPWLCNC 211

Query: 750 -MLWLEEW 756
            +L+   W
Sbjct: 212 EILYFRRW 219

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 47.1 bits (112), Expect = 2e-05
 Identities = 45/201 (22%), Positives = 72/201 (35%), Gaps = 36/201 (17%)

Query: 516 FCGMFKL--LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTL 573
           F  + KL  +R+    +L+ I  P   +NL  L+YL ++   +  LP     + L    L
Sbjct: 75  FSNLPKLHEIRIEKANNLLYIN-PEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLL 133

Query: 574 DMPF----SYIDHTADEFWKM-NKLRHLNFGSITLPA-HPGKFCG-SLENL-----NFIS 621
           D+        I+  +  F  +  +   L      +   H   F G  L+ L     N + 
Sbjct: 134 DIQDNINIHTIERNS--FVGLSFESVILWLNKNGIQEIHNSAFNGTQLDELNLSDNNNLE 191

Query: 622 ALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRL 679
            L       D+         L    D+S  +  SL S  L  L  L +    N  K+P L
Sbjct: 192 ELPN-----DVFHGASGPVIL----DISRTRIHSLPSYGLENLKKLRARSTYNLKKLPTL 242

Query: 680 SKIVLAEYLFPHSLTHLSFSN 700
            K+V        +L   S + 
Sbjct: 243 EKLV--------ALMEASLTY 255

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C* Length = 350

 Score = 45.6 bits (108), Expect = 4e-05
 Identities = 32/230 (13%), Positives = 66/230 (28%), Gaps = 38/230 (16%)

Query: 524 RVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
           RV       + + PS +  N   L    L    L  +     S   +L  +++  + +  
Sbjct: 12  RVFLCQESKVTEIPSDLPRNAIEL-RFVLT--KLRVIQKGAFSGFGDLEKIEISQNDVLE 68

Query: 583 T--ADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLR 640
              AD F  + KL  +                 +E  N +  ++P     +    LPNL+
Sbjct: 69  VIEADVFSNLPKLHEI----------------RIEKANNLLYINP-----EAFQNLPNLQ 107

Query: 641 NLRIRGDLSYNQ--SLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSF 698
            L     +S      L             L + +   +  + +              L  
Sbjct: 108 YL----LISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVG--LSFESVILWL 161

Query: 699 SNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGS-YGFPNLKVLHL 747
           +   + +          L ++     N+    +L     +G     +L +
Sbjct: 162 NKNGIQEIHNSAFNGTQLDELNLSDNNNLE--ELPNDVFHGASGPVILDI 209

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus} Length = 361

 Score = 46.8 bits (111), Expect = 2e-05
 Identities = 54/291 (18%), Positives = 86/291 (29%), Gaps = 79/291 (27%)

Query: 518 GMFKLLRVLDLG--SLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM 575
            +     +LDL   +L  ++       L  L  L L+   LN + S     + NL  LD+
Sbjct: 36  SLPSYTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDL 95

Query: 576 ---PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDI 632
                  +D     F  +  L  L                 L N N I  +       + 
Sbjct: 96  SSNHLHTLDEFL--FSDLQALEVLL----------------LYN-NHIVVVDR-----NA 131

Query: 633 LGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHS 692
              +  L+ L     LS NQ         +S      + + +K+P               
Sbjct: 132 FEDMAQLQKL----YLSQNQ---------ISRFPVELIKDGNKLP--------------K 164

Query: 693 LTHLSFSNTDLMDDPMPTLEKLPLLQV--LKLKQNSYSGRKLTCGSYGFPNLKVLHLKSM 750
           L  L  S+  L   P+  L+KLP      L L  N      L C               +
Sbjct: 165 LMLLDLSSNKLKKLPLTDLQKLPAWVKNGLYLHNNP-----LECDC------------KL 207

Query: 751 LWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQPE 801
             L            ++      C +     ++L  I SL+ F+C   +  
Sbjct: 208 YQLFSHWQYRQLSSVMDFQEDLYCMH----SKKLHNIFSLDFFNCSEYKES 254

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus} Length = 361

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 37/161 (22%), Positives = 53/161 (32%), Gaps = 32/161 (19%)

Query: 516 FCGMFKLLRVLDLGSLVLIQYPSGI-ENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLD 574
              +  L   L L    L    S     +  LRYL L+   L++L   L S+L  L  L 
Sbjct: 60  PTRLTNL-HSLLLSHNHLNFISSEAFVPVPNLRYLDLSSNHLHTLDEFLFSDLQALEVLL 118

Query: 575 M---PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTED 631
           +       +D  A  F  M +L+ L                 L   N IS         +
Sbjct: 119 LYNNHIVVVDRNA--FEDMAQLQKLY----------------LSQ-NQISRFPV-----E 154

Query: 632 ILGRLPNLRNLRIRGDLSYNQ--SLLSKSLCRLSCLESLKL 670
           ++     L  L +  DLS N+   L    L +L       L
Sbjct: 155 LIKDGNKLPKLMLL-DLSSNKLKKLPLTDLQKLPAWVKNGL 194

>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 = 46.1 bits (110), Expect = 2e-05
 Identities = 42/199 (21%), Positives = 72/199 (36%), Gaps = 29/199 (14%)

Query: 542 NLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM---PFSYIDHTADEFWKMNKLRHLNF 598
           +   L+ L L+   + ++      +L +L TL +   P   +   A  F  ++ L+ L  
Sbjct: 50  SFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGA--FSGLSSLQKLVA 107

Query: 599 GS---ITLPAHPGKFCGSLENL----NFISALHPCCCTEDILGRLPNLRNLRIRGDLSYN 651
                 +L   P     +L+ L    N I +        +    L NL +L    DLS N
Sbjct: 108 VETNLASLENFPIGHLKTLKELNVAHNLIQSFK----LPEYFSNLTNLEHL----DLSSN 159

Query: 652 Q--SLLSKSLCRLSCLESLKLA---NESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDD 706
           +  S+    L  L  +  L L+   + + M  +      E      L  L+     L   
Sbjct: 160 KIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEI----RLKELALDTNQLKSV 215

Query: 707 PMPTLEKLPLLQVLKLKQN 725
           P    ++L  LQ + L  N
Sbjct: 216 PDGIFDRLTSLQKIWLHTN 234

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A* Length = 567

 Score = 46.7 bits (110), Expect = 3e-05
 Identities = 42/248 (16%), Positives = 74/248 (29%), Gaps = 49/248 (19%)

Query: 507 HLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKL-NIPSLNSLPSSL-- 563
              P  W +     + L   +L         S +E+   L+ L+  N   L ++   +  
Sbjct: 335 KDRPECWCRDSATDEQLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRA 394

Query: 564 ---LSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFI 620
              L               +D     +    + + L   S+    +       L +   +
Sbjct: 395 LDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRSKFLLENSVLKMEYADVRVLHLAH-KDL 453

Query: 621 SALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ-SLLSKSLCRLSCLESLKLANESKMPRL 679
           + L         L +L  + +L    DLS+N+   L  +L  L CLE L+ ++      L
Sbjct: 454 TVLCH-------LEQLLLVTHL----DLSHNRLRALPPALAALRCLEVLQASDN----AL 498

Query: 680 SKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGF 739
             +                            +  LP LQ L L  N              
Sbjct: 499 ENV--------------------------DGVANLPRLQELLLCNNRLQQSAAIQPLVSC 532

Query: 740 PNLKVLHL 747
           P L +L+L
Sbjct: 533 PRLVLLNL 540

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8 Length = 313

 Score = 42.9 bits (102), Expect = 3e-04
 Identities = 44/243 (18%), Positives = 77/243 (31%), Gaps = 72/243 (29%)

Query: 523 LRVLDLGSLVL---IQYPSGIENLFLLRYLKL-NIPSLN-SLPSSLLSNLLNLYTLDM-- 575
           +  LDL  L L      PS + NL  L +L +  I +L   +P ++ + L  L+ L +  
Sbjct: 52  VNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAI-AKLTQLHYLYITH 110

Query: 576 -------PFSYIDHTADEFWKMNKLRHLNF------GSITLPAHPGKFCGSLENL----N 618
                  P        D   ++  L  L+F      G++  P        +L  +    N
Sbjct: 111 TNVSGAIP--------DFLSQIKTLVTLDFSYNALSGTL--PPSISS-LPNLVGITFDGN 159

Query: 619 FISALHPCCCTEDILGRLP----NLRNLRIRGDLSYNQSLLS----KSLCRLSCLESLKL 670
            IS            G +P    +   L     +S N+  L+     +   L+ L  + L
Sbjct: 160 RIS------------GAIPDSYGSFSKLFTSMTISRNR--LTGKIPPTFANLN-LAFVDL 204

Query: 671 AN---ESKMPR-LSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNS 726
           +    E                   +   +  +   L    +  +     L  L L+ N 
Sbjct: 205 SRNMLEGDASVLFGSDK--------NTQKIHLAKNSL-AFDLGKVGLSKNLNGLDLRNNR 255

Query: 727 YSG 729
             G
Sbjct: 256 IYG 258

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes} Length = 197

 Score = 41.9 bits (99), Expect = 3e-04
 Identities = 25/154 (16%), Positives = 53/154 (34%), Gaps = 29/154 (18%)

Query: 520 FKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY 579
              ++ L + ++      + I  L  L  L++    + S     LS L +L  LD+  S 
Sbjct: 65  AHNIKDLTINNI-HATNYNPISGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLLDISHSA 123

Query: 580 IDHTA-DEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPN 638
            D +   +   + K+  ++                L     I+ + P       L  LP 
Sbjct: 124 HDDSILTKINTLPKVNSID----------------LSYNGAITDIMP-------LKTLPE 160

Query: 639 LRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLAN 672
           L++L    ++ ++     + +     L  L   +
Sbjct: 161 LKSL----NIQFDGVHDYRGIEDFPKLNQLYAFS 190

>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 = 42.9 bits (101), Expect = 3e-04
 Identities = 36/214 (16%), Positives = 74/214 (34%), Gaps = 20/214 (9%)

Query: 521 KLLRVLDLGSLVLIQYPSGIENLFL-LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY 579
           K L +  + + V +     + ++F  +    L+I     +      +  +   L+   + 
Sbjct: 305 KSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSISDTPFIHMVCPPSPSSFTFLNFTQNV 364

Query: 580 I-DHTADEFWKMNKLRHLNFGS---ITLPAHPGKFCG--SLENLNFISALHPCCCTEDIL 633
             D        + +L+ L                     SLE L+           +   
Sbjct: 365 FTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALMTKNMSSLETLDVSLNSLNSHAYDRTC 424

Query: 634 GRLPNLRNLRIRGDLSYNQSLLSKSL--CRLSCLESLKLANESKMPRLSKIVLAEYLFPH 691
               ++  L    +LS N   L+ S+  C    ++ L L N +++  + K V   +L   
Sbjct: 425 AWAESILVL----NLSSNM--LTGSVFRCLPPKVKVLDLHN-NRIMSIPKDV--THL--Q 473

Query: 692 SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQN 725
           +L  L+ ++  L   P    ++L  LQ + L  N
Sbjct: 474 ALQELNVASNQLKSVPDGVFDRLTSLQYIWLHDN 507

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes} Length = 263

 Score = 41.9 bits (99), Expect = 5e-04
 Identities = 33/186 (17%), Positives = 62/186 (33%), Gaps = 45/186 (24%)

Query: 564 LSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISAL 623
              L N    ++    +        +++ +++ N  +                 + I +L
Sbjct: 15  DPGLANAVKQNLGKQSVTDL-VSQKELSGVQNFNGDN-----------------SNIQSL 56

Query: 624 HPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIV 683
                    +    NL+ L     LS+NQ      L  L+ LE L +         +++ 
Sbjct: 57  AG-------MQFFTNLKEL----HLSHNQISDLSPLKDLTKLEELSVNR-------NRLK 98

Query: 684 LAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLT--CGSYGFPN 741
               +    L+ L   N +L D    +L  L  L++L ++ N     KL           
Sbjct: 99  NLNGIPSACLSRLFLDNNELRD--TDSLIHLKNLEILSIRNN-----KLKSIVMLGFLSK 151

Query: 742 LKVLHL 747
           L+VL L
Sbjct: 152 LEVLDL 157

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	824
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.97
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.93
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.93
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.93
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.93
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.92
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.92
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.92
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.92
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.92
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.92
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.91
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.91
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.91
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.91
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.91
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.91
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.91
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.9
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.9
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.9
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.9
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.9
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.9
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.9
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.89
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.89
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.89
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.89
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.89
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.89
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.88
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.88
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.88
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.88
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.88
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.88
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.87
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.87
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.87
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.87
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.86
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.86
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.86
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.85
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.84
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.83
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.83
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.83
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.82
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.81
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.81
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.81
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.8
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.8
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	99.8
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.8
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.8
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	99.79
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.79
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.79
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.79
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	99.79
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.78
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.78
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.77
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	99.77
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.76
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	99.75
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.74
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.74
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	99.72
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.7
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.7
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.7
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.7
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.69
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.69
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.69
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.69
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	99.68
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.67
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.66
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.66
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	99.65
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.64
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.63
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.63
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.61
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.59
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.58
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.58
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.56
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.56
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	99.55
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.55
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.55
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.53
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.51
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.5
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.49
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.48
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.48
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.46
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	99.46
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.44
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.43
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.41
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.4
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.39
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	99.39
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.38
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.38
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.37
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.37
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.36
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.35
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.35
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.34
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.33
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.29
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.29
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.29
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.23
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.23
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.23
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.2
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.19
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.18
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.15
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	99.15
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.14
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.11
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.11
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.1
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.1
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.09
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.01
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.98
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.95
2fna_A	357	Conserved hypothetical protein; structural genomic	98.93
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.92
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.92
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.92
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	98.91
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.91
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	98.89
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	98.88
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	98.8
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.77
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.68
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.65
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	98.59
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.59
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.57
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.55
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.55
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.5
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	98.46
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.3
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	98.24
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	98.16
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.14
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	98.07
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	98.07
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.06
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	98.03
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	97.97
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.95
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.89
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.81
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.8
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.77
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	97.69
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.66
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.62
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.61
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.57
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.51
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.5
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.49
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.46
3co5_A	143	Putative two-component system transcriptional RES	97.41
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.38
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.35
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.33
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.32
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	97.25
3bos_A	242	Putative DNA replication factor; P-loop containing	97.24
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.22
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.22
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.21
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.19
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.17
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.04
3pvs_A	447	Replication-associated recombination protein A; ma	97.03
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.03
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.03
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.03
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.02
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.98
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	96.93
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	96.92
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	96.91
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.81
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.76
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.75
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	96.7
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	96.66
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.64
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	96.64
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.64
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	96.62
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	96.54
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.53
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	96.44
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.34
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.34
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	96.33
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.32
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.16
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.1
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.08
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.08
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.06
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.05
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	95.98
1u94_A	356	RECA protein, recombinase A; homologous recombinat	95.91
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	95.89
2qgz_A	308	Helicase loader, putative primosome component; str	95.81
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.8
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.74
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.73
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	95.71
1xp8_A	366	RECA protein, recombinase A; recombination, radior	95.71
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.67
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.66
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.65
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.63
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.62
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	95.6
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	95.6
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.59
2z43_A	324	DNA repair and recombination protein RADA; archaea	95.56
3io5_A	333	Recombination and repair protein; storage dimer, i	95.44
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	95.36
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.25
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.18
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	95.16
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	95.06
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	95.01
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	94.99
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	94.97
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	94.86
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	94.83
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	94.81
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	94.8
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	94.79
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	94.79
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	94.58
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	94.55
3fwy_A	314	Light-independent protochlorophyllide reductase I	94.53
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	94.43
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	94.34
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	94.29
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	94.29
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.22
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.21
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	94.19
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	94.17
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	94.17
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	94.09
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	94.04
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	94.03
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.99
3ice_A	422	Transcription termination factor RHO; transcriptio	93.96
2r44_A	331	Uncharacterized protein; putative ATPase, structur	93.92
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	93.92
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	93.9
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	93.9
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	93.84
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	93.76
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	93.74
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	93.72
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	93.69
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	93.64
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	93.62
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	93.62
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	93.6
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	93.59
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	93.59
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.56
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	93.56
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	93.55
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	93.52
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	93.49
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	93.43
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	93.39
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	93.36
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	93.34
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	93.33
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	93.25
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	93.23
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	93.23
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	93.21
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	93.21
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	93.2
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	93.2
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	93.2
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.15
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	93.14
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	93.11
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	93.11
4a74_A	231	DNA repair and recombination protein RADA; hydrola	93.08
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	93.06
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	93.04
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	93.03
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	92.99
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	92.99
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	92.98
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	92.97
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	92.96
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	92.96
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	92.95
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	92.95
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	92.93
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	92.91
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	92.91
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	92.9
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	92.89
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	92.88
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	92.88
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	92.85
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	92.84
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	92.82
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	92.8
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	92.79
1via_A	175	Shikimate kinase; structural genomics, transferase	92.77
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	92.66
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	92.65
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	92.61
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	92.61
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	92.57
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	92.55
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	92.52
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.51
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	92.46
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	92.46
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	92.45
3l0o_A	427	Transcription termination factor RHO; helicase, RH	92.45
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	92.43
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	92.39
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	92.38
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	92.37
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	92.34
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	92.33
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	92.33
2ewv_A	372	Twitching motility protein PILT; pilus retraction	92.27
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	92.27
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	92.25
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	92.22
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	92.2
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	92.18
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	92.18
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	92.16
2vli_A	183	Antibiotic resistance protein; transferase, tunica	92.14
1b0u_A	262	Histidine permease; ABC transporter, transport pro	92.12
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	92.12
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	92.11
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	92.11
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	92.1
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	92.03
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	91.97
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	91.96
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	91.92
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	91.91
2og2_A	359	Putative signal recognition particle receptor; nuc	91.86
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	91.84
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	91.84
1ji0_A	240	ABC transporter; ATP binding protein, structural g	91.82
1sgw_A	214	Putative ABC transporter; structural genomics, P p	91.81
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	91.79
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	91.78
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.78
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	91.72
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	91.71
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	91.71
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	91.69
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	91.68
1g6h_A	257	High-affinity branched-chain amino acid transport	91.67
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	91.67
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	91.66
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	91.62
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	91.62
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	91.61
2xxa_A	433	Signal recognition particle protein; protein trans	91.6
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	91.58
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	91.56
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.56
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	91.52
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	91.49
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	91.45
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	91.41
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	91.4
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	91.4
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.36
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	91.34
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	91.29
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	91.27
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	91.26
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	91.23
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	91.15
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	91.14
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	91.09
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	91.05
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	91.05
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	91.03
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	91.02
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	90.99
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	90.9
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	90.89
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	90.85
2wji_A	165	Ferrous iron transport protein B homolog; membrane	90.79
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	90.78
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	90.77
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	90.77
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	90.77
1tue_A	212	Replication protein E1; helicase, replication, E1E	90.75
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	90.67
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	90.65
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	90.64
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	90.64
2ghi_A	260	Transport protein; multidrug resistance protein, M	90.58
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	90.56
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	90.49
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	90.48
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	90.47
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	90.47
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	90.45
3end_A	307	Light-independent protochlorophyllide reductase ir	90.39
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	90.29
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	90.24
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	90.22
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	90.11
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	90.09
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	90.07
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	90.04
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	90.03
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	90.02
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	90.02
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	89.98
2r6a_A	454	DNAB helicase, replicative helicase; replication,	89.91
2eyu_A	261	Twitching motility protein PILT; pilus retraction	89.9
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	89.88
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	89.87
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	89.85
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	89.82
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	89.76
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	89.7
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	89.51
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	89.46
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	89.44
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	89.37
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	89.36
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	89.3
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	89.25
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	89.22
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	89.19
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	89.18
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	89.17
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.15
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	89.09
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	88.96
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	88.96
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	88.95
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	88.94
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	88.92
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	88.92
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	88.92
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	88.89
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	88.86
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	88.85
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	88.74
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	88.73
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	88.71
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	88.71
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	88.71
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	88.7
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	88.48
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	88.47
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	88.45
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	88.44
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	88.41
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	88.4
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	88.37
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	88.32
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	88.23

>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*

Probab=100.00  E-value=5.2e-43  Score=402.80  Aligned_cols=278  Identities=17%  Similarity=0.184  Sum_probs=222.6

Q ss_pred             eechhhHHHHHHHHHcC-CCCeEEEEEEcCCCChHHHHHHHHhC--CccccCCCceeEEEECCCCCCC--CHHHHHHHHH
Q 003387          159 VGLDDRMEELLDLLIEG-PPQLSVVAILDSIGLDKTAFAGEAYN--SSYVKHYFDCHAWITEPYSNEY--DADQILDIVI  233 (824)
Q Consensus       159 vGr~~~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLa~~v~~--~~~~~~~F~~~~wv~~~vs~~~--~~~~~~~~i~  233 (824)
                      |||+.++++|.++|..+ +.+.+||+|+|||||||||||+++|+  |.+++.+|+.++||+  +++.+  +..+++++|+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~--vs~~~~~~~~~~~~~il  208 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLK--DSGTAPKSTFDLFTDIL  208 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE--CCCCSTTHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEE--ECCCCCCCHHHHHHHHH
Confidence            69999999999999765 44689999999999999999999998  678999999999999  99985  8999999999


Q ss_pred             HHhCCCCC---cccccccCHHHHHHHHHHhcCCC-eEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh---
Q 003387          234 KFLMPSSR---LSEIMDKNYEMKKIILHEYLMTK-RYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII---  306 (824)
Q Consensus       234 ~~l~~~~~---~~~~~~~~~~~~~~~l~~~L~~k-r~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~---  306 (824)
                      .+++....   .+..+..+.+.+...+++.|++| ||||||||||+.+++ .+..     .+||+||||||++.++.   
T Consensus       209 ~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~~-----~~gs~ilvTTR~~~v~~~~~  282 (549)
T 2a5y_B          209 LMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWAQ-----ELRLRCLVTTRDVEISNAAS  282 (549)
T ss_dssp             HHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHHH-----HTTCEEEEEESBGGGGGGCC
T ss_pred             HHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cccc-----cCCCEEEEEcCCHHHHHHcC
Confidence            99987532   11123445678899999999996 999999999998765 2211     16999999999998876   


Q ss_pred             ------------------hcccccCC-cCcCccccchhhHHHhcCCCchhHHHHHhHHHhh------hhhhhc-c-CCCc
Q 003387          307 ------------------SFQFEDGE-NMRLDLVPTGGPLRATYKGRPFLILYHGSISLEE------NIREAV-E-TPLG  359 (824)
Q Consensus       307 ------------------~f~~~~~~-~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~------~~~~~~-~-~~~~  359 (824)
                                        +|...... ..++.+.+++++|+++|+|+||||+++|+.|..+      ...+.+ . ...+
T Consensus       283 ~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~w~~~~~l~~~l~~~~~~~  362 (549)
T 2a5y_B          283 QTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVG  362 (549)
T ss_dssp             SCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHHHHCSST
T ss_pred             CCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccchHHHHHHhHHHhhcccHHH
Confidence                              33333211 1135677899999999999999999999987211      111122 1 2227


Q ss_pred             ccccccc---cCCCCchHHHh-----------HhccCCCCceechhHHHHHHHHc--CCCCC-----ChHHHHHHHHHHH
Q 003387          360 LRYIKCL---MLPFCLKPCFI-----------YLSVFPAHQEISTRQLYQLWIAE--GFIPD-----NSEATAESYLEQL  418 (824)
Q Consensus       360 ~~~~l~~---~L~~~lk~cfl-----------~~s~fp~~~~i~~~~Li~~W~a~--g~i~~-----~~e~~~~~~~~~L  418 (824)
                      +..++.+   +||+++|.||+           |||+||+++.|+    +++|+|+  ||+.+     +.+++++ |+++|
T Consensus       363 i~~~l~~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~~~~~~~~~~~~~~-~l~~L  437 (549)
T 2a5y_B          363 VECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWSCVIPVDICSNEEEQLDDEVAD-RLKRL  437 (549)
T ss_dssp             TCCCSSSSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHHHHSCC-------CCCTHHHHH-HHHHT
T ss_pred             HHHHHhcccccccHHHHHHHhccchhhhhHhhheeeeCCCCeee----eeeeeeeccceeccCCCCCCHHHHHH-HHHHH
Confidence            8888877   99999999999           999999999999    8999999  99975     4677777 99999


Q ss_pred             HhccccceeecCCCCcEEEEEcCccHHHHHHhhc
Q 003387          419 IKEGFVEAKKRKAGGTINTCSIPGRWRPVLHTVP  452 (824)
Q Consensus       419 v~rsllq~~~~~~~g~~~~~~mHdlv~dla~~~~  452 (824)
                      +++||++....+   ...+|+|||++|++|++++
T Consensus       438 ~~rsLl~~~~~~---~~~~~~mHdlv~~~a~~~~  468 (549)
T 2a5y_B          438 SKRGALLSGKRM---PVLTFKIDHIIHMFLKHVV  468 (549)
T ss_dssp             TTBSSCSEEECS---SSCEEECCHHHHHHHHTTS
T ss_pred             HHcCCeeEecCC---CceEEEeChHHHHHHHHHH
Confidence            999999987643   3457999999999999988

>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*

Probab=100.00  E-value=1.1e-34  Score=369.11  Aligned_cols=282  Identities=18%  Similarity=0.215  Sum_probs=222.8

Q ss_pred             CCCCCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccc-cCCC-ceeEEEECCCCCCCC--HH
Q 003387          151 SSSKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYV-KHYF-DCHAWITEPYSNEYD--AD  226 (824)
Q Consensus       151 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~-~~~F-~~~~wv~~~vs~~~~--~~  226 (824)
                      .+.+...+|||++++++|.++|...+++.++|+|+||||+||||||+++|++.+. ..+| +.++||+  +++..+  ..
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~--~~~~~~~~~~  196 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVS--IGKQDKSGLL  196 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEE--CCSCCHHHHH
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEE--ECCcCchHHH
Confidence            3445678999999999999999877677999999999999999999999997543 5556 5677999  988644  34


Q ss_pred             HHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCC--eEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHH
Q 003387          227 QILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTK--RYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRI  304 (824)
Q Consensus       227 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~k--r~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v  304 (824)
                      ..++.++..+............+.+.+...++..|.+|  ||||||||||+..+|..+       ++||+||||||++.+
T Consensus       197 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~~~~~~-------~~~~~ilvTtR~~~~  269 (1249)
T 3sfz_A          197 MKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAF-------DNQCQILLTTRDKSV  269 (1249)
T ss_dssp             HHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHHHHTTT-------CSSCEEEEEESSTTT
T ss_pred             HHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHHHHHhh-------cCCCEEEEEcCCHHH
Confidence            55777888887644322223457788999999999887  999999999998777643       579999999999988


Q ss_pred             Hh----------------------hcccccCCcCcCccccchhhHHHhcCCCchhHHHHHhHHHhhh-----hhhhc-c-
Q 003387          305 II----------------------SFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEEN-----IREAV-E-  355 (824)
Q Consensus       305 ~~----------------------~f~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~-----~~~~~-~-  355 (824)
                      +.                      +|.... ....+.+.+++++|+++|+|+||||+++|+.|....     ....+ . 
T Consensus       270 ~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~-~~~~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~~~~~~~l~~l~~~  348 (1249)
T 3sfz_A          270 TDSVMGPKHVVPVESGLGREKGLEILSLFV-NMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNK  348 (1249)
T ss_dssp             TTTCCSCBCCEECCSSCCHHHHHHHHHHHH-TSCSTTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSSSCHHHHHHHHHSC
T ss_pred             HHhhcCCceEEEecCCCCHHHHHHHHHHhh-CCChhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcChhHHHHHHHHHhhh
Confidence            74                      222211 133456678899999999999999999999993221     11122 0 


Q ss_pred             ----------CCC-cccccccc---cCCCCchHHHhHhccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHHHHHhc
Q 003387          356 ----------TPL-GLRYIKCL---MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKE  421 (824)
Q Consensus       356 ----------~~~-~~~~~l~~---~L~~~lk~cfl~~s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~~Lv~r  421 (824)
                                ... .+..++.+   .||++.|.||+|||+||+++.|+++.++.+|.++       ++.++.++++|+++
T Consensus       349 ~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~-------~~~~~~~l~~L~~~  421 (1249)
T 3sfz_A          349 QFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-------TEEVEDILQEFVNK  421 (1249)
T ss_dssp             CCCCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHTCC-------HHHHHHHHHHHHHT
T ss_pred             hhhhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhCCC-------HHHHHHHHHHHHhc
Confidence                      011 35666666   9999999999999999999999999999999765       46689999999999


Q ss_pred             cccceeecCCCCcEEEEEcCccHHHHHHhhc
Q 003387          422 GFVEAKKRKAGGTINTCSIPGRWRPVLHTVP  452 (824)
Q Consensus       422 sllq~~~~~~~g~~~~~~mHdlv~dla~~~~  452 (824)
                      ||++...   ++...+|+|||++|++++..+
T Consensus       422 sl~~~~~---~~~~~~~~~h~l~~~~~~~~~  449 (1249)
T 3sfz_A          422 SLLFCNR---NGKSFCYYLHDLQVDFLTEKN  449 (1249)
T ss_dssp             TSCEEEE---SSSSEEEECCHHHHHHHHHHT
T ss_pred             cceEEec---CCCceEEEecHHHHHHHHhhh
Confidence            9999765   345568999999999999876

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=100.00  E-value=2e-34  Score=333.93  Aligned_cols=269  Identities=18%  Similarity=0.129  Sum_probs=204.4

Q ss_pred             CceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCce-eEEEECCCCCCCCHHHHHHHHHHH
Q 003387          157 DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDC-HAWITEPYSNEYDADQILDIVIKF  235 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~-~~wv~~~vs~~~~~~~~~~~i~~~  235 (824)
                      ..|||+.++++|.++|...+ +.++|+|+||||+||||||+++|++.+++.+|+. ++||+  +++.++...++..|+..
T Consensus       129 ~~VGRe~eLeeL~elL~~~d-~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVs--Vs~~~d~~~IL~~Ll~l  205 (1221)
T 1vt4_I          129 YNVSRLQPYLKLRQALLELR-PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN--LKNCNSPETVLEMLQKL  205 (1221)
T ss_dssp             SCCCCHHHHHHHHHHHHHCC-SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEE--CCCSSSHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhccC-CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEE--eCCCCCHHHHHHHHHHH
Confidence            35999999999999998643 3899999999999999999999998788999986 89999  99999998888888775


Q ss_pred             hCCCC-----Ccc--cccccCHHHHHHHHHHhc---CCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHH
Q 003387          236 LMPSS-----RLS--EIMDKNYEMKKIILHEYL---MTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRII  305 (824)
Q Consensus       236 l~~~~-----~~~--~~~~~~~~~~~~~l~~~L---~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~  305 (824)
                      ++...     ...  .....+.+.+...+++.|   ++||+||||||||+.+.|+.+.       +||+||||||++.++
T Consensus       206 L~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~eqLe~f~-------pGSRILVTTRd~~Va  278 (1221)
T 1vt4_I          206 LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-------LSCKILLTTRFKQVT  278 (1221)
T ss_dssp             HHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHHHHHHHH-------SSCCEEEECSCSHHH
T ss_pred             HhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHHHHHhhC-------CCeEEEEeccChHHH
Confidence            43210     000  001123456677777766   7899999999999999998763       599999999999988


Q ss_pred             hhcccccC---C-------------------cCcCccccchhhHHHhcCCCchhHHHHHhHHHhh---hhhhhccCCCcc
Q 003387          306 ISFQFEDG---E-------------------NMRLDLVPTGGPLRATYKGRPFLILYHGSISLEE---NIREAVETPLGL  360 (824)
Q Consensus       306 ~~f~~~~~---~-------------------~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~---~~~~~~~~~~~~  360 (824)
                      ........   +                   .......++..   +.|+|+||||+++|+.|...   ...|.......+
T Consensus       279 ~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~~eeL~~---eICgGLPLALkLaGs~Lr~k~~s~eeW~~~~~~~I  355 (1221)
T 1vt4_I          279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR---EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKL  355 (1221)
T ss_dssp             HHHHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCCTTTHHH---HHCCCCHHHHHHHHHHHHHSCSSHHHHHHCSCHHH
T ss_pred             HhcCCCeEEEecCccccCCcCHHHHHHHHHHHcCCCHHHHHH---HHhCCCHHHHHHHHHHHhCCCCCHHHHhcCChhHH
Confidence            51111000   0                   00001122222   34999999999999999433   122332222267


Q ss_pred             cccccc---cCCCCc-hHHHhHhccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHHHHHhccccceeecCCCCcEE
Q 003387          361 RYIKCL---MLPFCL-KPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTIN  436 (824)
Q Consensus       361 ~~~l~~---~L~~~l-k~cfl~~s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~~Lv~rsllq~~~~~~~g~~~  436 (824)
                      ..+|++   .||++. |.||+|||+||+++.|+++.++.+|+++|.      +.++.++++|+++||++...     ...
T Consensus       356 ~aaLelSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~aeGe------edAe~~L~eLvdRSLLq~d~-----~~~  424 (1221)
T 1vt4_I          356 TTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIK------SDVMVVVNKLHKYSLVEKQP-----KES  424 (1221)
T ss_dssp             HHHHHHHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSCS------HHHHHHHHHHHTSSSSSBCS-----SSS
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCCH------HHHHHHHHHHHhhCCEEEeC-----CCC
Confidence            777777   999999 999999999999999999999999999872      45889999999999999842     224


Q ss_pred             EEEcCccHHHHHH
Q 003387          437 TCSIPGRWRPVLH  449 (824)
Q Consensus       437 ~~~mHdlv~dla~  449 (824)
                      .|+|||++++++.
T Consensus       425 rYrMHDLllELr~  437 (1221)
T 1vt4_I          425 TISIPSIYLELKV  437 (1221)
T ss_dssp             EEBCCCHHHHHHH
T ss_pred             EEEehHHHHHHhc
Confidence            6999999999764

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.97  E-value=8e-31  Score=306.04  Aligned_cols=278  Identities=18%  Similarity=0.237  Sum_probs=209.0

Q ss_pred             CCCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccc-cCCC-ceeEEEECCCCCCCCHHHHHH
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYV-KHYF-DCHAWITEPYSNEYDADQILD  230 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~-~~~F-~~~~wv~~~vs~~~~~~~~~~  230 (824)
                      .....+|||+.++++|.++|....++.++|+|+||||+||||||+.+|++.++ ..+| +.++|++  +++. +...++.
T Consensus       121 ~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~--~~~~-~~~~~~~  197 (591)
T 1z6t_A          121 QRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVS--VGKQ-DKSGLLM  197 (591)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEE--EESC-CHHHHHH
T ss_pred             CCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEE--CCCC-chHHHHH
Confidence            34578999999999999999875556899999999999999999999997666 7889 5899999  8765 4444444


Q ss_pred             HH---HHHhCCCCCcccccccCHHHHHHHHHHhcCC--CeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHH
Q 003387          231 IV---IKFLMPSSRLSEIMDKNYEMKKIILHEYLMT--KRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRII  305 (824)
Q Consensus       231 ~i---~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~--kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~  305 (824)
                      .+   +..++...........+.+.....+...+.+  +++||||||||+...++.    +   ++||+||||||+..++
T Consensus       198 ~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~~l~~----l---~~~~~ilvTsR~~~~~  270 (591)
T 1z6t_A          198 KLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWVLKA----F---DSQCQILLTTRDKSVT  270 (591)
T ss_dssp             HHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHHHHHT----T---CSSCEEEEEESCGGGG
T ss_pred             HHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHHHHHH----h---cCCCeEEEECCCcHHH
Confidence            43   4455532111112345667788888888866  799999999998766543    2   5689999999999876


Q ss_pred             h----------------------hcccccCCcCcCccccchhhHHHhcCCCchhHHHHHhHHHhhh-----hhhhccC--
Q 003387          306 I----------------------SFQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSISLEEN-----IREAVET--  356 (824)
Q Consensus       306 ~----------------------~f~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l~~~~-----~~~~~~~--  356 (824)
                      .                      +|....+ .......+.+.+|+++|+|+|+|+..+|+.+....     ....+..  
T Consensus       271 ~~~~~~~~~v~~l~~L~~~ea~~L~~~~~~-~~~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~~~w~~~l~~l~~~~  349 (591)
T 1z6t_A          271 DSVMGPKYVVPVESSLGKEKGLEILSLFVN-MKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQ  349 (591)
T ss_dssp             TTCCSCEEEEECCSSCCHHHHHHHHHHHHT-SCGGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHSTTCHHHHHHHHHSCC
T ss_pred             HhcCCCceEeecCCCCCHHHHHHHHHHHhC-CCcccccHHHHHHHHHhCCCcHHHHHHHHHHhcCchhHHHHHHHHHHhH
Confidence            5                      2222111 11233467789999999999999999999993222     2222211  


Q ss_pred             ----------CC-cccccccc---cCCCCchHHHhHhccCCCCceechhHHHHHHHHcCCCCCChHHHHHHHHHHHHhcc
Q 003387          357 ----------PL-GLRYIKCL---MLPFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEGFIPDNSEATAESYLEQLIKEG  422 (824)
Q Consensus       357 ----------~~-~~~~~l~~---~L~~~lk~cfl~~s~fp~~~~i~~~~Li~~W~a~g~i~~~~e~~~~~~~~~Lv~rs  422 (824)
                                .. .+..++..   .||++.|.||++||+||+++.|+.+.++..|.++       .+.+..++++|+++|
T Consensus       350 ~~~~~~~~~~~~~~l~~~l~~s~~~L~~~~~~~l~~la~f~~~~~i~~~~l~~l~~~~-------~~~~~~~l~~L~~~~  422 (591)
T 1z6t_A          350 FKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME-------TEEVEDILQEFVNKS  422 (591)
T ss_dssp             CCCSSCCCSSCCHHHHHHHHHHHHTSCTTTHHHHHHGGGCCTTCCEEHHHHHHHHTCC-------HHHHHHHHHHHHHTT
T ss_pred             HHHhhhccccchHHHHHHHHHHHHhCCHHHHHHHHHccccCCCCccCHHHHHHHhccC-------HHHHHHHHHHHHhCc
Confidence                      11 34455555   9999999999999999999999999999999653       345789999999999


Q ss_pred             ccceeecCCCCcEEEEEcCccHHHHHHhh
Q 003387          423 FVEAKKRKAGGTINTCSIPGRWRPVLHTV  451 (824)
Q Consensus       423 llq~~~~~~~g~~~~~~mHdlv~dla~~~  451 (824)
                      |++...   ++....|+||+++|++++..
T Consensus       423 Ll~~~~---~~~~~~~~~H~lv~~~~~~~  448 (591)
T 1z6t_A          423 LLFCDR---NGKSFRYYLHDLQVDFLTEK  448 (591)
T ss_dssp             SSEEEE---ETTEEEEECCHHHHHHHHHH
T ss_pred             CeEEec---CCCccEEEEcHHHHHHHHhh
Confidence            998654   33456799999999999886

>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*

Probab=99.93  E-value=2.9e-25  Score=260.29  Aligned_cols=324  Identities=19%  Similarity=0.114  Sum_probs=202.2

Q ss_pred             CCCCeeEEEEEecCCCccccc-cc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCC
Q 003387          469 SPKKAKRLNAVEREGDFACLD-DY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLF  544 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~~-~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~  544 (824)
                      .+..++++.+. ++....++. .+  +++|++|.+.++...    ...+..|..+++|++|+|++|.++.+ |..+++++
T Consensus        30 ~~~~l~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~----~i~~~~~~~l~~L~~L~Ls~n~l~~~~p~~~~~l~  104 (606)
T 3vq2_A           30 IPSSTKNIDLS-FNPLKILKSYSFSNFSELQWLDLSRCEIE----TIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLT  104 (606)
T ss_dssp             SCTTCCEEECT-TSCCCEECTTTTTTCTTCCEEECTTCCCC----EECTTTTTTCTTCCEEECTTCCCCCCCTTSSTTCT
T ss_pred             CCCCcCEEECC-CCCcCEeChhhccCCccCcEEeCCCCccc----ccCHHHhhchhhcCEeECCCCcccccChhhcCCcc
Confidence            45678888888 554444443 33  788888888877653    24456778888888888888887755 67788888


Q ss_pred             cceEEeecCCCCCccChhhhhcCCCccEeecCCcccc--ccchhhhccccCceecCCCccCCCCCCCC------------
Q 003387          545 LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYID--HTADEFWKMNKLRHLNFGSITLPAHPGKF------------  610 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~--~lp~~i~~L~~L~~L~L~~~~~~~~~~p~------------  610 (824)
                      +|++|++++|.+..+|+..++++++|++|++++|.+.  .+|..++++++|++|++++|.+.......            
T Consensus       105 ~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~~l~  184 (606)
T 3vq2_A          105 SLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNL  184 (606)
T ss_dssp             TCCEEECTTSCCCCSSSSCCTTCTTCCEEECCSSCCCCCCCCGGGGTCTTCCEEECCSSCCCEECTTTTHHHHHCTTCCC
T ss_pred             cCCEEEccCCccccccccccCCCCCCCEEeCCCCcccceechHhHhhcCCCCEEEccCCcceecChhhhhhhhccccccc
Confidence            8888888888887776333378888888888888776  36777888888888888777554210001            


Q ss_pred             --------------------------------------------------------------------------------
Q 003387          611 --------------------------------------------------------------------------------  610 (824)
Q Consensus       611 --------------------------------------------------------------------------------  610 (824)
                                                                                                      
T Consensus       185 ~L~l~~n~l~~~~~~~~~~~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~l~l~~~~~~~~~~l~~~~~~~~~~l~~l~l~  264 (606)
T 3vq2_A          185 SLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTID  264 (606)
T ss_dssp             EEECTTCCCCEECTTTTTTCEEEEEEEESCCSCHHHHHHHHHTTTTCEEEEEEEECCTTSCCCSCCCGGGGTTGGGSEEE
T ss_pred             eeeccCCCcceeCcccccCceeeeeeccCCccchhHHHHHhccccccccccccccccccCCcccccChHHhhhhhhccHh
Confidence                                                                                            


Q ss_pred             --------------------------------------CCCCCCCCeeeccCC-CcchhhhcCCCCccceEEEecc----
Q 003387          611 --------------------------------------CGSLENLNFISALHP-CCCTEDILGRLPNLRNLRIRGD----  647 (824)
Q Consensus       611 --------------------------------------i~~L~~L~~l~~~~~-~~~~~~~l~~l~~L~~L~l~~~----  647 (824)
                                                            ++.+++|+.|++..+ ...++. + .+++|+.|+++++    
T Consensus       265 ~l~l~~~~~~~~~~~~~~~l~~L~~L~l~~~~~~~l~~l~~~~~L~~L~l~~n~l~~lp~-~-~l~~L~~L~l~~n~~~~  342 (606)
T 3vq2_A          265 EFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLSIIRCQLKQFPT-L-DLPFLKSLTLTMNKGSI  342 (606)
T ss_dssp             EEEECCCTTCCGGGGSCGGGTTCSEEEEESCCCCCCCCCCTTCCCSEEEEESCCCSSCCC-C-CCSSCCEEEEESCSSCE
T ss_pred             heeccccccccccccccccCCCCCEEEecCccchhhhhccccccCCEEEcccccCccccc-C-CCCccceeeccCCcCcc
Confidence                                                  111112222222210 011111 1 3444444444444    


Q ss_pred             ------------------cccchhhHHHHhccCCCCCeEEEeccC---------CCCCccEEEeCcc-----------Cc
Q 003387          648 ------------------LSYNQSLLSKSLCRLSCLESLKLANES---------KMPRLSKIVLAEY-----------LF  689 (824)
Q Consensus       648 ------------------~~~~~~~l~~~l~~l~~L~~L~l~~~~---------~~~~L~~l~l~~~-----------~~  689 (824)
                                        .-......+..+..+++|++|++++|.         ..++|+.|.+.++           ..
T Consensus       343 ~~~~~~l~~L~~L~ls~n~l~~~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~  422 (606)
T 3vq2_A          343 SFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLS  422 (606)
T ss_dssp             ECCCCCCTTCCEEECCSSCEEEEEECCHHHHCCSCCCEEECCSCSEEEECCCCTTCTTCCEEECTTSEEESTTTTTTTTT
T ss_pred             chhhccCCCCCEEECcCCccCCCcchhhhhccCCcccEeECCCCccccchhhccCCCCCCeeECCCCccCCccChhhhhc
Confidence                              211111125566777788888877653         3466777777654           34


Q ss_pred             CCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEE
Q 003387          690 PHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECL  769 (824)
Q Consensus       690 ~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L  769 (824)
                      +++|+.|++++|.+.+..+..++.+++|+.|++++|.+.+..++..++.+++|++|++++|......+..+..+++|+.|
T Consensus       423 l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L  502 (606)
T 3vq2_A          423 LEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRLQLL  502 (606)
T ss_dssp             CTTCCEEECTTSCCEECCTTTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEE
T ss_pred             cccCCEEECcCCCCCccchhhhcCCCCCCEEECCCCcCCCcchHHhhccCCCCCEEECCCCcCCccChhhhcccccCCEE
Confidence            67788888888877666677777778888888877776654445556667777777777765333333445566667777


Q ss_pred             EEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          770 IINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       770 ~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ++++|......|..+.++++|+.|++++|.
T Consensus       503 ~Ls~N~l~~~~~~~~~~l~~L~~L~l~~N~  532 (606)
T 3vq2_A          503 NMSHNNLLFLDSSHYNQLYSLSTLDCSFNR  532 (606)
T ss_dssp             ECCSSCCSCEEGGGTTTCTTCCEEECTTSC
T ss_pred             ECCCCcCCCcCHHHccCCCcCCEEECCCCc
Confidence            776665544445566666666666666664

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=99.93  E-value=1.8e-26  Score=277.20  Aligned_cols=343  Identities=19%  Similarity=0.104  Sum_probs=179.6

Q ss_pred             CCeeEEEEEecCCCccccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc-cCCccCCC-----
Q 003387          471 KKAKRLNAVEREGDFACLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-QYPSGIEN-----  542 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~~~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-~lp~~i~~-----  542 (824)
                      .+++++.+..+......+..+  +++|++|.+.++...   ..++...+..+++|++|++++|.+. .+|..+++     
T Consensus       294 ~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~L~~n~l~---~~ip~~~l~~l~~L~~L~Ls~n~l~~~~p~~l~~l~~~L  370 (768)
T 3rgz_A          294 DTLTGLDLSGNHFYGAVPPFFGSCSLLESLALSSNNFS---GELPMDTLLKMRGLKVLDLSFNEFSGELPESLTNLSASL  370 (768)
T ss_dssp             TTCSEEECCSSEEEECCCGGGGGCTTCCEEECCSSEEE---EECCHHHHTTCTTCCEEECCSSEEEECCCTTHHHHTTTC
T ss_pred             CcCCEEECcCCcCCCccchHHhcCCCccEEECCCCccc---CcCCHHHHhcCCCCCEEeCcCCccCccccHHHHhhhcCC
Confidence            456666665222222233334  666666666665442   1233344556666666666666554 45544443     


Q ss_pred             ----------------------CCcceEEeecCCCCC-ccChhhhhcCCCccEeecCCcccc-ccchhhhccccCceecC
Q 003387          543 ----------------------LFLLRYLKLNIPSLN-SLPSSLLSNLLNLYTLDMPFSYID-HTADEFWKMNKLRHLNF  598 (824)
Q Consensus       543 ----------------------l~~Lr~L~L~~~~i~-~lp~~i~~~L~~L~~L~L~~~~l~-~lp~~i~~L~~L~~L~L  598 (824)
                                            +++|++|++++|.+. .+|..+ +++++|++|++++|.+. .+|..++++++|++|++
T Consensus       371 ~~L~Ls~N~l~~~~~~~~~~~~~~~L~~L~L~~n~l~~~~p~~l-~~l~~L~~L~Ls~N~l~~~~p~~l~~l~~L~~L~L  449 (768)
T 3rgz_A          371 LTLDLSSNNFSGPILPNLCQNPKNTLQELYLQNNGFTGKIPPTL-SNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKL  449 (768)
T ss_dssp             SEEECCSSEEEEECCTTTTCSTTCCCCEEECCSSEEEEECCGGG-GGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEEC
T ss_pred             cEEEccCCCcCCCcChhhhhcccCCccEEECCCCccccccCHHH-hcCCCCCEEECcCCcccCcccHHHhcCCCCCEEEC
Confidence                                  344555555555544 445555 66666777777666554 45666666777777777


Q ss_pred             CCccCCCCCCC-CCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC-
Q 003387          599 GSITLPAHPGK-FCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES-  674 (824)
Q Consensus       599 ~~~~~~~~~~p-~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~-  674 (824)
                      ++|.+.+ .+| .++.+++|+.|+++.+.  ..++..+..+++|+.|+++++.  ..+.+|..++.+++|+.|++++|. 
T Consensus       450 ~~n~l~~-~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~L~~N~--l~~~~p~~~~~l~~L~~L~L~~N~l  526 (768)
T 3rgz_A          450 WLNMLEG-EIPQELMYVKTLETLILDFNDLTGEIPSGLSNCTNLNWISLSNNR--LTGEIPKWIGRLENLAILKLSNNSF  526 (768)
T ss_dssp             CSSCCCS-CCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSC--CCSCCCGGGGGCTTCCEEECCSSCC
T ss_pred             CCCcccC-cCCHHHcCCCCceEEEecCCcccCcCCHHHhcCCCCCEEEccCCc--cCCcCChHHhcCCCCCEEECCCCcc
Confidence            6666654 344 66667777777766321  1223336677777777777764  334555666666677777766642 


Q ss_pred             ---------CCCCccEEEeCcc----------------------------------------------------------
Q 003387          675 ---------KMPRLSKIVLAEY----------------------------------------------------------  687 (824)
Q Consensus       675 ---------~~~~L~~l~l~~~----------------------------------------------------------  687 (824)
                               .+++|+.|++.++                                                          
T Consensus       527 ~~~~p~~l~~l~~L~~L~Ls~N~l~g~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  606 (768)
T 3rgz_A          527 SGNIPAELGDCRSLIWLDLNTNLFNGTIPAAMFKQSGKIAANFIAGKRYVYIKNDGMKKECHGAGNLLEFQGIRSEQLNR  606 (768)
T ss_dssp             EEECCGGGGGCTTCCEEECCSSEEESBCCGGGGTTTTCBCCSTTCSCEEEEEECCSCCTTCCSSEEEEECTTCCGGGGGG
T ss_pred             cCcCCHHHcCCCCCCEEECCCCccCCcCChHHhcccchhhhhccccccccccccccccccccccccccccccccchhhhc
Confidence                     2334444444332                                                          


Q ss_pred             ----------------------CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEE
Q 003387          688 ----------------------LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVL  745 (824)
Q Consensus       688 ----------------------~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L  745 (824)
                                            ..+++|+.|+|++|.+.+.+|..++++++|+.|+|++|.+.+ .++..++.+++|+.|
T Consensus       607 l~~~~~~~l~~~~~~g~~~~~~~~l~~L~~LdLs~N~l~g~ip~~l~~l~~L~~L~Ls~N~l~g-~ip~~l~~L~~L~~L  685 (768)
T 3rgz_A          607 LSTRNPCNITSRVYGGHTSPTFDNNGSMMFLDMSYNMLSGYIPKEIGSMPYLFILNLGHNDISG-SIPDEVGDLRGLNIL  685 (768)
T ss_dssp             GGGTCCSCTTSCEEEEECCCSCSSSBCCCEEECCSSCCBSCCCGGGGGCTTCCEEECCSSCCCS-CCCGGGGGCTTCCEE
T ss_pred             cccccccccccceecccCchhhhccccccEEECcCCcccccCCHHHhccccCCEEeCcCCccCC-CCChHHhCCCCCCEE
Confidence                                  012345556666666655566666666666666666555554 234445556666666


Q ss_pred             eeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc----HHHHHHHhhccCcceeeeeecc
Q 003387          746 HLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ----PELRQKLREFEDKEQCGIQLYP  821 (824)
Q Consensus       746 ~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~----~~l~~~~~~~~~~~~~~i~hip  821 (824)
                      +|++|.....+|..++.+++|+.|++++|+....+|.. ..+.++....+.++|    ..+. .+...++++|.+|+|+|
T Consensus       686 dLs~N~l~g~ip~~l~~l~~L~~L~ls~N~l~g~iP~~-~~~~~~~~~~~~gN~~Lcg~~l~-~C~~~~~~~~~~~~~~~  763 (768)
T 3rgz_A          686 DLSSNKLDGRIPQAMSALTMLTEIDLSNNNLSGPIPEM-GQFETFPPAKFLNNPGLCGYPLP-RCDPSNADGYAHHQRSH  763 (768)
T ss_dssp             ECCSSCCEECCCGGGGGCCCCSEEECCSSEEEEECCSS-SSGGGSCGGGGCSCTEEESTTSC-CCCSCC-----------
T ss_pred             ECCCCcccCcCChHHhCCCCCCEEECcCCcccccCCCc-hhhccCCHHHhcCCchhcCCCCc-CCCCCccCCCCCCCCcc
Confidence            66665544455555556666666666666555555532 223333333333332    1121 46667788999999998


Q ss_pred             CC
Q 003387          822 YG  823 (824)
Q Consensus       822 ~~  823 (824)
                      .+
T Consensus       764 ~~  765 (768)
T 3rgz_A          764 HH  765 (768)
T ss_dssp             --
T ss_pred             cc
Confidence            75

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.93  E-value=2.1e-25  Score=246.39  Aligned_cols=289  Identities=17%  Similarity=0.161  Sum_probs=185.1

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L  570 (824)
                      .++++.|.+.++...    .++...|..+++|++|+|++|.++.+|. .++.+++|++|++++|.+..+|+..++++++|
T Consensus        44 l~~l~~l~l~~~~l~----~l~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L  119 (390)
T 3o6n_A           44 LNNQKIVTFKNSTMR----KLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLL  119 (390)
T ss_dssp             GCCCSEEEEESCEES----EECTHHHHHCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTC
T ss_pred             cCCceEEEecCCchh----hCChhHhcccccCcEEECCCCcccccChhhccCCCCcCEEECCCCCCCcCCHHHhcCCCCC
Confidence            455555555554432    2334455556666666666666554432 55556666666666666665554433566666


Q ss_pred             cEeecCCccccccchh-hhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccc
Q 003387          571 YTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       571 ~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      ++|++++|.+..+|.. +.++++|++|++++|.+.. ..| .++.+++|+.|+++.+...... +..+++|+.|+++++.
T Consensus       120 ~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~-~~~~~~~~l~~L~~L~l~~n~l~~~~-~~~l~~L~~L~l~~n~  197 (390)
T 3o6n_A          120 TVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLER-IEDDTFQATTSLQNLQLSSNRLTHVD-LSLIPSLFHANVSYNL  197 (390)
T ss_dssp             CEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCB-CCTTTTSSCTTCCEEECCSSCCSBCC-GGGCTTCSEEECCSSC
T ss_pred             CEEECCCCccCcCCHHHhcCCCCCcEEECCCCccCc-cChhhccCCCCCCEEECCCCcCCccc-cccccccceeeccccc
Confidence            6666666666666554 3556666666666665542 222 4555666666665532222122 4455555555555542


Q ss_pred             ccchhhHHHHhccCCCCCeEEEeccC-------CCCCccEEEeCcc--------CcCCCceEEEEEcccCCCCCcccccC
Q 003387          649 SYNQSLLSKSLCRLSCLESLKLANES-------KMPRLSKIVLAEY--------LFPHSLTHLSFSNTDLMDDPMPTLEK  713 (824)
Q Consensus       649 ~~~~~~l~~~l~~l~~L~~L~l~~~~-------~~~~L~~l~l~~~--------~~~~~L~~L~L~~~~l~~~~~~~l~~  713 (824)
                      -.       .+...++|+.|++++|.       .+++|+.|.+.++        ..+++|++|++++|.+.+..+..++.
T Consensus       198 l~-------~~~~~~~L~~L~l~~n~l~~~~~~~~~~L~~L~l~~n~l~~~~~l~~l~~L~~L~Ls~n~l~~~~~~~~~~  270 (390)
T 3o6n_A          198 LS-------TLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVK  270 (390)
T ss_dssp             CS-------EEECCSSCSEEECCSSCCCEEECCCCSSCCEEECCSSCCCCCGGGGGCTTCSEEECCSSCCCEEESGGGTT
T ss_pred             cc-------ccCCCCcceEEECCCCeeeeccccccccccEEECCCCCCcccHHHcCCCCccEEECCCCcCCCcChhHccc
Confidence            10       11222345555555432       2234555554443        56789999999999988777888999


Q ss_pred             CCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEE
Q 003387          714 LPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKF  793 (824)
Q Consensus       714 l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L  793 (824)
                      +++|+.|++++|.+.+  ++.....+++|++|++++|. +..++.....+++|+.|++++|+. ..+|  +..+++|+.|
T Consensus       271 l~~L~~L~L~~n~l~~--~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~l~~L~~L~L~~N~i-~~~~--~~~~~~L~~L  344 (390)
T 3o6n_A          271 MQRLERLYISNNRLVA--LNLYGQPIPTLKVLDLSHNH-LLHVERNQPQFDRLENLYLDHNSI-VTLK--LSTHHTLKNL  344 (390)
T ss_dssp             CSSCCEEECCSSCCCE--EECSSSCCTTCCEEECCSSC-CCCCGGGHHHHTTCSEEECCSSCC-CCCC--CCTTCCCSEE
T ss_pred             cccCCEEECCCCcCcc--cCcccCCCCCCCEEECCCCc-ceecCccccccCcCCEEECCCCcc-ceeC--chhhccCCEE
Confidence            9999999999988765  45556789999999999985 777887788899999999999984 4555  6788999999


Q ss_pred             EecCCc
Q 003387          794 DCWWPQ  799 (824)
Q Consensus       794 ~l~~c~  799 (824)
                      +++++|
T Consensus       345 ~l~~N~  350 (390)
T 3o6n_A          345 TLSHND  350 (390)
T ss_dssp             ECCSSC
T ss_pred             EcCCCC
Confidence            999988

>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}

Probab=99.93  E-value=2.1e-25  Score=260.08  Aligned_cols=289  Identities=17%  Similarity=0.157  Sum_probs=221.2

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccChhhhhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L  570 (824)
                      .++++.|.+.++...    .+++.+|..+++|++|+|++|.+..+| ..++.+++|++|+|++|.+..+|+..|+++++|
T Consensus        50 l~~l~~l~l~~~~l~----~lp~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L  125 (597)
T 3oja_B           50 LNNQKIVTFKNSTMR----KLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLL  125 (597)
T ss_dssp             GCCCSEEEESSCEES----EECTHHHHHCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTC
T ss_pred             CCCceEEEeeCCCCC----CcCHHHHccCCCCcEEECCCCCCCCCChHHhcCCCCCCEEECCCCcCCCCCHHHHcCCCCC
Confidence            677777777776553    355667788888888888888887554 477888888888888888888777665888888


Q ss_pred             cEeecCCccccccchh-hhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccc
Q 003387          571 YTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       571 ~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      ++|+|++|.+..+|.. ++++++|++|++++|.+.. ..| .++.+++|+.|+++.+...... ++.+++|+.|+++++.
T Consensus       126 ~~L~L~~n~l~~l~~~~~~~l~~L~~L~Ls~N~l~~-~~~~~~~~l~~L~~L~L~~N~l~~~~-~~~l~~L~~L~l~~n~  203 (597)
T 3oja_B          126 TVLVLERNDLSSLPRGIFHNTPKLTTLSMSNNNLER-IEDDTFQATTSLQNLQLSSNRLTHVD-LSLIPSLFHANVSYNL  203 (597)
T ss_dssp             CEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCB-CCTTTTTTCTTCCEEECTTSCCSBCC-GGGCTTCSEEECCSSC
T ss_pred             CEEEeeCCCCCCCCHHHhccCCCCCEEEeeCCcCCC-CChhhhhcCCcCcEEECcCCCCCCcC-hhhhhhhhhhhcccCc
Confidence            8888888888888766 4788888888888887764 344 6788888888888743332223 5667788888887764


Q ss_pred             ccchhhHHHHhccCCCCCeEEEeccC-------CCCCccEEEeCcc--------CcCCCceEEEEEcccCCCCCcccccC
Q 003387          649 SYNQSLLSKSLCRLSCLESLKLANES-------KMPRLSKIVLAEY--------LFPHSLTHLSFSNTDLMDDPMPTLEK  713 (824)
Q Consensus       649 ~~~~~~l~~~l~~l~~L~~L~l~~~~-------~~~~L~~l~l~~~--------~~~~~L~~L~L~~~~l~~~~~~~l~~  713 (824)
                      -.       .+...++|+.|++++|.       .+++|+.|.+.++        ..+++|+.|+|++|.+.+..|..++.
T Consensus       204 l~-------~l~~~~~L~~L~ls~n~l~~~~~~~~~~L~~L~L~~n~l~~~~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~  276 (597)
T 3oja_B          204 LS-------TLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVK  276 (597)
T ss_dssp             CS-------EEECCTTCSEEECCSSCCCEEECSCCSCCCEEECCSSCCCCCGGGGGCTTCSEEECCSSCCCEEESGGGTT
T ss_pred             cc-------cccCCchhheeeccCCcccccccccCCCCCEEECCCCCCCCChhhccCCCCCEEECCCCccCCCCHHHhcC
Confidence            11       12344567777777643       2346677766654        56789999999999988877889999


Q ss_pred             CCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEE
Q 003387          714 LPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKF  793 (824)
Q Consensus       714 l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L  793 (824)
                      +++|+.|+|++|.+.+  ++.....+|+|++|+|++|. +..+|..+..+++|+.|++++|+. ..+|  +..+++|+.|
T Consensus       277 l~~L~~L~Ls~N~l~~--l~~~~~~l~~L~~L~Ls~N~-l~~i~~~~~~l~~L~~L~L~~N~l-~~~~--~~~~~~L~~L  350 (597)
T 3oja_B          277 MQRLERLYISNNRLVA--LNLYGQPIPTLKVLDLSHNH-LLHVERNQPQFDRLENLYLDHNSI-VTLK--LSTHHTLKNL  350 (597)
T ss_dssp             CSSCCEEECTTSCCCE--EECSSSCCTTCCEEECCSSC-CCCCGGGHHHHTTCSEEECCSSCC-CCCC--CCTTCCCSEE
T ss_pred             ccCCCEEECCCCCCCC--CCcccccCCCCcEEECCCCC-CCccCcccccCCCCCEEECCCCCC-CCcC--hhhcCCCCEE
Confidence            9999999999988875  55666789999999999986 667887788899999999999985 4455  6788999999


Q ss_pred             EecCCc
Q 003387          794 DCWWPQ  799 (824)
Q Consensus       794 ~l~~c~  799 (824)
                      ++++||
T Consensus       351 ~l~~N~  356 (597)
T 3oja_B          351 TLSHND  356 (597)
T ss_dssp             ECCSSC
T ss_pred             EeeCCC
Confidence            999988

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.92  E-value=5e-25  Score=262.97  Aligned_cols=292  Identities=17%  Similarity=0.168  Sum_probs=141.7

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc-Cc--cCCccCCCCC-------cceEEeecCCCCCccCh
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV-LI--QYPSGIENLF-------LLRYLKLNIPSLNSLPS  561 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~-i~--~lp~~i~~l~-------~Lr~L~L~~~~i~~lp~  561 (824)
                      +++|+.|.+.++...    ..++..|..+++|++|+|++|. ++  .+|..++++.       +|++|+|++|.+..+|.
T Consensus       490 L~~L~~L~Ls~N~l~----~~iP~~l~~L~~L~~L~Ls~N~~lsg~~iP~~i~~L~~~~~~l~~L~~L~Ls~N~L~~ip~  565 (876)
T 4ecn_A          490 LKDLTDVELYNCPNM----TQLPDFLYDLPELQSLNIACNRGISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPA  565 (876)
T ss_dssp             CTTCCEEEEESCTTC----CSCCGGGGGCSSCCEEECTTCTTSCHHHHHHHHHHHHHCTTTTTTCCEEECCSSCCCBCCC
T ss_pred             CCCCCEEECcCCCCC----ccChHHHhCCCCCCEEECcCCCCcccccchHHHHhhhhcccccCCccEEEeeCCcCCccCC
Confidence            344555555444321    1222444455555555555554 43  2444333332       55555555555555554


Q ss_pred             --hhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCC-CCeeeccCC-CcchhhhcCCC
Q 003387          562 --SLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLEN-LNFISALHP-CCCTEDILGRL  636 (824)
Q Consensus       562 --~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~-L~~l~~~~~-~~~~~~~l~~l  636 (824)
                        .+ +++++|++|+|++|.+..+| .++++++|++|++++|.+.  .+| .++++++ |+.|+++.+ ...++..+..+
T Consensus       566 ~~~l-~~L~~L~~L~Ls~N~l~~lp-~~~~L~~L~~L~Ls~N~l~--~lp~~l~~l~~~L~~L~Ls~N~L~~lp~~~~~~  641 (876)
T 4ecn_A          566 SASL-QKMVKLGLLDCVHNKVRHLE-AFGTNVKLTDLKLDYNQIE--EIPEDFCAFTDQVEGLGFSHNKLKYIPNIFNAK  641 (876)
T ss_dssp             HHHH-TTCTTCCEEECTTSCCCBCC-CCCTTSEESEEECCSSCCS--CCCTTSCEECTTCCEEECCSSCCCSCCSCCCTT
T ss_pred             hhhh-hcCCCCCEEECCCCCcccch-hhcCCCcceEEECcCCccc--cchHHHhhccccCCEEECcCCCCCcCchhhhcc
Confidence              44 55555555555555444555 4455555555555555544  333 4555554 555555421 11122212222


Q ss_pred             C--ccceEEEecccccchhh---HHHHhc--cCCCCCeEEEeccC----------CCCCccEEEeCcc----------C-
Q 003387          637 P--NLRNLRIRGDLSYNQSL---LSKSLC--RLSCLESLKLANES----------KMPRLSKIVLAEY----------L-  688 (824)
Q Consensus       637 ~--~L~~L~l~~~~~~~~~~---l~~~l~--~l~~L~~L~l~~~~----------~~~~L~~l~l~~~----------~-  688 (824)
                      +  +|+.|+++++.  ....   ++..+.  .+++|+.|++++|.          .+++|+.|.++++          . 
T Consensus       642 ~~~~L~~L~Ls~N~--l~g~ip~l~~~l~~~~~~~L~~L~Ls~N~L~~lp~~~~~~l~~L~~L~Ls~N~L~~ip~~~~~~  719 (876)
T 4ecn_A          642 SVYVMGSVDFSYNK--IGSEGRNISCSMDDYKGINASTVTLSYNEIQKFPTELFATGSPISTIILSNNLMTSIPENSLKP  719 (876)
T ss_dssp             CSSCEEEEECCSSC--TTTTSSSCSSCTTTCCCCCEEEEECCSSCCCSCCHHHHHTTCCCSEEECCSCCCSCCCTTSSSC
T ss_pred             ccCCCCEEECcCCc--CCCccccchhhhccccCCCcCEEEccCCcCCccCHHHHccCCCCCEEECCCCcCCccChHHhcc
Confidence            2  24555554442  1111   111111  12245555555432          2344555555443          0 


Q ss_pred             ------cCCCceEEEEEcccCCCCCccccc--CCCCCCeEEeeccccCCCeeeecCCCCCCccEEeecc------CCCCc
Q 003387          689 ------FPHSLTHLSFSNTDLMDDPMPTLE--KLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKS------MLWLE  754 (824)
Q Consensus       689 ------~~~~L~~L~L~~~~l~~~~~~~l~--~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~------~~~l~  754 (824)
                            .+++|+.|+|++|.+. .+|..+.  .+++|+.|+|++|.+.+  ++.....+++|+.|+|++      |....
T Consensus       720 ~~~~l~nl~~L~~L~Ls~N~L~-~lp~~l~~~~l~~L~~L~Ls~N~L~~--lp~~l~~L~~L~~L~Ls~N~~ls~N~l~~  796 (876)
T 4ecn_A          720 KDGNYKNTYLLTTIDLRFNKLT-SLSDDFRATTLPYLSNMDVSYNCFSS--FPTQPLNSSQLKAFGIRHQRDAEGNRILR  796 (876)
T ss_dssp             TTSCCTTGGGCCEEECCSSCCC-CCCGGGSTTTCTTCCEEECCSSCCSS--CCCGGGGCTTCCEEECCCCBCTTCCBCCC
T ss_pred             ccccccccCCccEEECCCCCCc-cchHHhhhccCCCcCEEEeCCCCCCc--cchhhhcCCCCCEEECCCCCCcccccccc
Confidence                  1125666666666655 4455554  66666666666666654  444455666666666654      33334


Q ss_pred             cceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          755 EWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       755 ~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      .+|..+..+++|+.|++++|.. ..+|..+.  ++|+.|++++||
T Consensus       797 ~ip~~l~~L~~L~~L~Ls~N~L-~~Ip~~l~--~~L~~LdLs~N~  838 (876)
T 4ecn_A          797 QWPTGITTCPSLIQLQIGSNDI-RKVDEKLT--PQLYILDIADNP  838 (876)
T ss_dssp             CCCTTGGGCSSCCEEECCSSCC-CBCCSCCC--SSSCEEECCSCT
T ss_pred             cChHHHhcCCCCCEEECCCCCC-CccCHhhc--CCCCEEECCCCC
Confidence            4555556666666666666654 56665543  466666666665

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=99.92  E-value=2.3e-24  Score=244.75  Aligned_cols=303  Identities=20%  Similarity=0.170  Sum_probs=236.2

Q ss_pred             CcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEeecCCCCCccChh
Q 003387          484 DFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSLPSS  562 (824)
Q Consensus       484 ~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~i~~lp~~  562 (824)
                      ...+|..+.++++.|.+.++...    ...+..|..+++|++|+|++|.++.+ |..++++++|++|+|++|.+..+|..
T Consensus        23 l~~ip~~~~~~l~~L~L~~n~l~----~~~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~   98 (477)
T 2id5_A           23 FVAVPEGIPTETRLLDLGKNRIK----TLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPLG   98 (477)
T ss_dssp             CSSCCSCCCTTCSEEECCSSCCC----EECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCSCCTT
T ss_pred             cCcCCCCCCCCCcEEECCCCccc----eECHhHccCCCCCCEEECCCCccCEeChhhhhCCccCCEEECCCCcCCccCcc
Confidence            34466656788999999888764    24567889999999999999998855 77899999999999999999999987


Q ss_pred             hhhcCCCccEeecCCcccccc-chhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCC--CcchhhhcCCCCc
Q 003387          563 LLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHP--CCCTEDILGRLPN  638 (824)
Q Consensus       563 i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~  638 (824)
                      .|.++++|++|+|++|.+..+ |..+..+++|++|++++|.+.. ..| .++.+++|+.|++..+  .......+..+++
T Consensus        99 ~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~-~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~l~~  177 (477)
T 2id5_A           99 VFTGLSNLTKLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVY-ISHRAFSGLNSLEQLTLEKCNLTSIPTEALSHLHG  177 (477)
T ss_dssp             SSTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEEECCTTCCE-ECTTSSTTCTTCCEEEEESCCCSSCCHHHHTTCTT
T ss_pred             cccCCCCCCEEECCCCccccCChhHccccccCCEEECCCCccce-eChhhccCCCCCCEEECCCCcCcccChhHhcccCC
Confidence            668999999999999988877 4568899999999999998864 333 8889999999998842  2233334788999


Q ss_pred             cceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCC
Q 003387          639 LRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQ  718 (824)
Q Consensus       639 L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~  718 (824)
                      |+.|+++++.  .....+..+..+++|+.|+++++.   .+..+.. ......+|++|+|++|.+.......+..+++|+
T Consensus       178 L~~L~l~~n~--i~~~~~~~~~~l~~L~~L~l~~~~---~~~~~~~-~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~  251 (477)
T 2id5_A          178 LIVLRLRHLN--INAIRDYSFKRLYRLKVLEISHWP---YLDTMTP-NCLYGLNLTSLSITHCNLTAVPYLAVRHLVYLR  251 (477)
T ss_dssp             CCEEEEESCC--CCEECTTCSCSCTTCCEEEEECCT---TCCEECT-TTTTTCCCSEEEEESSCCCSCCHHHHTTCTTCC
T ss_pred             CcEEeCCCCc--CcEeChhhcccCcccceeeCCCCc---cccccCc-ccccCccccEEECcCCcccccCHHHhcCccccC
Confidence            9999999875  222333467788899999998642   2333322 223345899999999998765556789999999


Q ss_pred             eEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCcc-ccccCccCcEEEecC
Q 003387          719 VLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPE-QLWYIKSLNKFDCWW  797 (824)
Q Consensus       719 ~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~-~l~~l~~L~~L~l~~  797 (824)
                      .|+|++|.+.. .....+..+++|+.|+|++|......+..+..+++|+.|++++|.. +.+|. .+..+++|+.|++++
T Consensus       252 ~L~Ls~n~l~~-~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l-~~~~~~~~~~l~~L~~L~l~~  329 (477)
T 2id5_A          252 FLNLSYNPIST-IEGSMLHELLRLQEIQLVGGQLAVVEPYAFRGLNYLRVLNVSGNQL-TTLEESVFHSVGNLETLILDS  329 (477)
T ss_dssp             EEECCSSCCCE-ECTTSCTTCTTCCEEECCSSCCSEECTTTBTTCTTCCEEECCSSCC-SCCCGGGBSCGGGCCEEECCS
T ss_pred             eeECCCCcCCc-cChhhccccccCCEEECCCCccceECHHHhcCcccCCEEECCCCcC-ceeCHhHcCCCcccCEEEccC
Confidence            99999988764 2233467899999999999874333356678899999999999974 45554 578899999999998


Q ss_pred             Cc
Q 003387          798 PQ  799 (824)
Q Consensus       798 c~  799 (824)
                      +|
T Consensus       330 N~  331 (477)
T 2id5_A          330 NP  331 (477)
T ss_dssp             SC
T ss_pred             CC
Confidence            76

>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*

Probab=99.92  E-value=2.4e-24  Score=243.08  Aligned_cols=321  Identities=15%  Similarity=0.106  Sum_probs=242.3

Q ss_pred             CCCCeeEEEEEecCCCccc-cccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCC
Q 003387          469 SPKKAKRLNAVEREGDFAC-LDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLF  544 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~-~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~  544 (824)
                      .+..+++|.+. ++....+ +..+  +++|++|.+.++...   ..+.+..|..+++|++|+|++|.+..+ |..+++++
T Consensus        28 l~~~l~~L~Ls-~n~i~~~~~~~~~~l~~L~~L~L~~n~~~---~~i~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~  103 (455)
T 3v47_A           28 LPAHVNYVDLS-LNSIAELNETSFSRLQDLQFLKVEQQTPG---LVIRNNTFRGLSSLIILKLDYNQFLQLETGAFNGLA  103 (455)
T ss_dssp             CCTTCCEEECC-SSCCCEECTTTTSSCTTCCEEECCCCSTT---CEECTTTTTTCTTCCEEECTTCTTCEECTTTTTTCT
T ss_pred             CCCccCEEEec-CCccCcCChhHhccCccccEEECcCCccc---ceECcccccccccCCEEeCCCCccCccChhhccCcc
Confidence            55788999998 5554444 4445  899999999988653   234567789999999999999998854 77899999


Q ss_pred             cceEEeecCCCCCc-cChh-hhhcCCCccEeecCCcccccc-chh-hhccccCceecCCCccCCCCCCC-CCCCC--CCC
Q 003387          545 LLRYLKLNIPSLNS-LPSS-LLSNLLNLYTLDMPFSYIDHT-ADE-FWKMNKLRHLNFGSITLPAHPGK-FCGSL--ENL  617 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~-lp~~-i~~~L~~L~~L~L~~~~l~~l-p~~-i~~L~~L~~L~L~~~~~~~~~~p-~i~~L--~~L  617 (824)
                      +|++|++++|.+.. .|.. .++++++|++|++++|.+..+ |.. +.++++|++|++++|.+.. ..| .++.+  .+|
T Consensus       104 ~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~l~~l~~~~L  182 (455)
T 3v47_A          104 NLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFLNMRRFHVLDLTFNKVKS-ICEEDLLNFQGKHF  182 (455)
T ss_dssp             TCCEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSBCCSCCCCGGGGGCTTCCEEECTTCCBSC-CCTTTSGGGTTCEE
T ss_pred             cCCEEeCCCCCCCccccCcccccCcccCCEEECCCCccCccCcccccCCCCcccEEeCCCCcccc-cChhhhhccccccc
Confidence            99999999999885 3333 238999999999999988887 554 8899999999999998875 333 66655  457


Q ss_pred             CeeeccCCCc-chh---------hhcCCCCccceEEEecccccchhhHHHHhccC---CCCCeEEEeccC----------
Q 003387          618 NFISALHPCC-CTE---------DILGRLPNLRNLRIRGDLSYNQSLLSKSLCRL---SCLESLKLANES----------  674 (824)
Q Consensus       618 ~~l~~~~~~~-~~~---------~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l---~~L~~L~l~~~~----------  674 (824)
                      +.+++..+.. .+.         ..+..+++|+.|+++++.  .....+..+...   ++|+.|+++.+.          
T Consensus       183 ~~L~l~~n~l~~~~~~~~~~~~~~~~~~~~~L~~L~Ls~n~--l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~~~  260 (455)
T 3v47_A          183 TLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNG--FKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFGHTN  260 (455)
T ss_dssp             EEEECTTCBCTTCSTTCTTHHHHCCTTTTCEEEEEECTTSC--CCHHHHHHHHHHTTTCCEEEEECTTCTTTSCCTTCCS
T ss_pred             cccccccCcccccchhhccccccccccccceeeeEecCCCc--ccccchhhhhccccccceeeEeeccccccccccchhh
Confidence            7777663211 000         113456789999999885  444555554443   677777776531          


Q ss_pred             ------------CCCCccEEEeCcc----------CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCee
Q 003387          675 ------------KMPRLSKIVLAEY----------LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKL  732 (824)
Q Consensus       675 ------------~~~~L~~l~l~~~----------~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~  732 (824)
                                  ..++++.+.+.++          ..+++|+.|+|++|.+.+..+..++.+++|+.|++++|.+.+ ..
T Consensus       261 ~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~-~~  339 (455)
T 3v47_A          261 FKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKIDDNAFWGLTHLLKLNLSQNFLGS-ID  339 (455)
T ss_dssp             SCCCCTTTTGGGTTSCCCEEECCSSCCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCE-EC
T ss_pred             hccCcccccccccccCceEEEecCccccccchhhcccCCCCCEEECCCCcccccChhHhcCcccCCEEECCCCccCC-cC
Confidence                        1246777776654          567899999999999987778899999999999999988754 33


Q ss_pred             eecCCCCCCccEEeeccCCCCccc-eeccCcccCccEEEEecCCCCCCCcc-ccccCccCcEEEecCCc
Q 003387          733 TCGSYGFPNLKVLHLKSMLWLEEW-TMGNAAMPKLECLIINPCAYLKKMPE-QLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       733 ~~~~~~~~~L~~L~L~~~~~l~~l-~~~~~~lp~L~~L~l~~c~~l~~lp~-~l~~l~~L~~L~l~~c~  799 (824)
                      +..+..+++|++|+|++|. +..+ +..+..+++|+.|++++|... .+|. .+..+++|+.|+++++|
T Consensus       340 ~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~-~~~~~~~~~l~~L~~L~l~~N~  406 (455)
T 3v47_A          340 SRMFENLDKLEVLDLSYNH-IRALGDQSFLGLPNLKELALDTNQLK-SVPDGIFDRLTSLQKIWLHTNP  406 (455)
T ss_dssp             GGGGTTCTTCCEEECCSSC-CCEECTTTTTTCTTCCEEECCSSCCS-CCCTTTTTTCTTCCEEECCSSC
T ss_pred             hhHhcCcccCCEEECCCCc-ccccChhhccccccccEEECCCCccc-cCCHhHhccCCcccEEEccCCC
Confidence            4556889999999999987 4544 667888999999999999754 5665 46899999999999865

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=99.92  E-value=7.3e-24  Score=230.09  Aligned_cols=299  Identities=17%  Similarity=0.149  Sum_probs=225.1

Q ss_pred             CCCeeEEEEEecCCCccccccc-CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceE
Q 003387          470 PKKAKRLNAVEREGDFACLDDY-DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRY  548 (824)
Q Consensus       470 ~~~~r~lsl~~~~~~~~~~~~~-~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~  548 (824)
                      ..+++++.+. +.....++... +++|++|.+.++....    .. . +..+++|++|++++|.++.+| .+..+++|++
T Consensus        43 l~~L~~L~l~-~~~i~~~~~~~~~~~L~~L~l~~n~i~~----~~-~-~~~l~~L~~L~L~~n~i~~~~-~~~~l~~L~~  114 (347)
T 4fmz_A           43 LESITKLVVA-GEKVASIQGIEYLTNLEYLNLNGNQITD----IS-P-LSNLVKLTNLYIGTNKITDIS-ALQNLTNLRE  114 (347)
T ss_dssp             HTTCSEEECC-SSCCCCCTTGGGCTTCCEEECCSSCCCC----CG-G-GTTCTTCCEEECCSSCCCCCG-GGTTCTTCSE
T ss_pred             cccccEEEEe-CCccccchhhhhcCCccEEEccCCcccc----ch-h-hhcCCcCCEEEccCCcccCch-HHcCCCcCCE
Confidence            3567788887 55444444423 8889999988876542    22 2 788889999999998888775 5888889999


Q ss_pred             EeecCCCCCccChhhhhcCCCccEeecCCc-cccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCC-C
Q 003387          549 LKLNIPSLNSLPSSLLSNLLNLYTLDMPFS-YIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHP-C  626 (824)
Q Consensus       549 L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~-~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~-~  626 (824)
                      |++++|.+..+|. + .++++|++|++++| .+..++ .+..+++|++|++++|.+.  .++.++.+++|+.|+++.+ .
T Consensus       115 L~l~~n~i~~~~~-~-~~l~~L~~L~l~~n~~~~~~~-~~~~l~~L~~L~l~~~~~~--~~~~~~~l~~L~~L~l~~n~l  189 (347)
T 4fmz_A          115 LYLNEDNISDISP-L-ANLTKMYSLNLGANHNLSDLS-PLSNMTGLNYLTVTESKVK--DVTPIANLTDLYSLSLNYNQI  189 (347)
T ss_dssp             EECTTSCCCCCGG-G-TTCTTCCEEECTTCTTCCCCG-GGTTCTTCCEEECCSSCCC--CCGGGGGCTTCSEEECTTSCC
T ss_pred             EECcCCcccCchh-h-ccCCceeEEECCCCCCccccc-chhhCCCCcEEEecCCCcC--CchhhccCCCCCEEEccCCcc
Confidence            9999988888877 5 88899999999888 444444 4888899999988888776  4445778888888888743 2


Q ss_pred             cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCC
Q 003387          627 CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDD  706 (824)
Q Consensus       627 ~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~  706 (824)
                      ..+.. +..+++|+.|+++++.-..   .+. +..+++|++|++++|.    ++.+.  ....+++|+.|++++|.+.. 
T Consensus       190 ~~~~~-~~~l~~L~~L~l~~n~l~~---~~~-~~~~~~L~~L~l~~n~----l~~~~--~~~~l~~L~~L~l~~n~l~~-  257 (347)
T 4fmz_A          190 EDISP-LASLTSLHYFTAYVNQITD---ITP-VANMTRLNSLKIGNNK----ITDLS--PLANLSQLTWLEIGTNQISD-  257 (347)
T ss_dssp             CCCGG-GGGCTTCCEEECCSSCCCC---CGG-GGGCTTCCEEECCSSC----CCCCG--GGTTCTTCCEEECCSSCCCC-
T ss_pred             ccccc-ccCCCccceeecccCCCCC---Cch-hhcCCcCCEEEccCCc----cCCCc--chhcCCCCCEEECCCCccCC-
Confidence            23334 7778888888888875221   111 6778888999888762    33322  14678999999999998764 


Q ss_pred             CcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCcccccc
Q 003387          707 PMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWY  786 (824)
Q Consensus       707 ~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~  786 (824)
                       .+.+..+++|+.|++++|.+...   .....+++|++|++++|......+..++.+++|+.|++++|+.. .++. +..
T Consensus       258 -~~~~~~l~~L~~L~l~~n~l~~~---~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~L~~L~L~~n~l~-~~~~-~~~  331 (347)
T 4fmz_A          258 -INAVKDLTKLKMLNVGSNQISDI---SVLNNLSQLNSLFLNNNQLGNEDMEVIGGLTNLTTLFLSQNHIT-DIRP-LAS  331 (347)
T ss_dssp             -CGGGTTCTTCCEEECCSSCCCCC---GGGGGCTTCSEEECCSSCCCGGGHHHHHTCTTCSEEECCSSSCC-CCGG-GGG
T ss_pred             -ChhHhcCCCcCEEEccCCccCCC---hhhcCCCCCCEEECcCCcCCCcChhHhhccccCCEEEccCCccc-cccC-hhh
Confidence             35788999999999999987763   34678899999999999754444555778999999999999854 4554 788


Q ss_pred             CccCcEEEecCCc
Q 003387          787 IKSLNKFDCWWPQ  799 (824)
Q Consensus       787 l~~L~~L~l~~c~  799 (824)
                      +++|+.|++++|+
T Consensus       332 l~~L~~L~l~~N~  344 (347)
T 4fmz_A          332 LSKMDSADFANQV  344 (347)
T ss_dssp             CTTCSEESSSCC-
T ss_pred             hhccceeehhhhc
Confidence            9999999999997

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.92  E-value=2.3e-24  Score=250.60  Aligned_cols=325  Identities=18%  Similarity=0.097  Sum_probs=207.6

Q ss_pred             CCCCeeEEEEEecCCCccccc-cc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCC
Q 003387          469 SPKKAKRLNAVEREGDFACLD-DY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLF  544 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~~-~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~  544 (824)
                      .+..++++.+. ++....++. .+  +++|++|.+.++...    ...+..|..+++|++|+|++|.++.+| ..++.++
T Consensus        26 l~~~l~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~----~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~  100 (570)
T 2z63_A           26 LPFSTKNLDLS-FNPLRHLGSYSFFSFPELQVLDLSRCEIQ----TIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLS  100 (570)
T ss_dssp             SCSSCCEEECC-SCCCCEECTTTTTTCSSCCEEECTTCCCC----EECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCT
T ss_pred             ccccccEEEcc-CCccCccChhHhhCCCCceEEECCCCcCC----ccCcccccCchhCCEEeCcCCcCCccCHhhhcCcc
Confidence            45567777777 444433332 33  777777777776542    244556677777777777777776544 5667777


Q ss_pred             cceEEeecCCCCCccChhhhhcCCCccEeecCCccccc--cchhhhccccCceecCCCccCCCCCCC-CC----------
Q 003387          545 LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH--TADEFWKMNKLRHLNFGSITLPAHPGK-FC----------  611 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~--lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i----------  611 (824)
                      +|++|++++|.+..+|...++++++|++|++++|.+..  +|..++++++|++|++++|.+... .| .+          
T Consensus       101 ~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~l~~n~l~~~-~~~~~~~l~~L~~~~  179 (570)
T 2z63_A          101 SLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSI-YCTDLRVLHQMPLLN  179 (570)
T ss_dssp             TCCEEECTTSCCCCSTTCSCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECTTSCCCEE-CGGGGHHHHTCTTCC
T ss_pred             ccccccccccccccCCCccccccccccEEecCCCccceecChhhhcccCCCCEEeCcCCcccee-cHHHccchhccchhh
Confidence            77777777777776665223777777777777776654  566677777777777776654320 00 11          


Q ss_pred             --------------------------------------------------------------------------------
Q 003387          612 --------------------------------------------------------------------------------  611 (824)
Q Consensus       612 --------------------------------------------------------------------------------  611 (824)
                                                                                                      
T Consensus       180 ~~L~l~~n~l~~~~~~~~~~~~L~~L~l~~n~~~~~~~~~~~~~l~~l~~~~l~~~~~~~~~~l~~~~~~~~~~l~~l~l  259 (570)
T 2z63_A          180 LSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTI  259 (570)
T ss_dssp             CEEECTTCCCCEECTTTTTTCEEEEEEEESCCSCTTHHHHHHHTTTTCEEEEEEEEECCCCSSCEECCTTTTGGGGGSEE
T ss_pred             hhcccCCCCceecCHHHhccCcceeEecccccccccchhhhhcCccccceeeeccccccCchhhhhcchhhhccccccch
Confidence                                                                                            


Q ss_pred             -------------------CCCCCCCeeeccCCC-cchhhhc--------------------------------------
Q 003387          612 -------------------GSLENLNFISALHPC-CCTEDIL--------------------------------------  633 (824)
Q Consensus       612 -------------------~~L~~L~~l~~~~~~-~~~~~~l--------------------------------------  633 (824)
                                         +.+++|+.+++..+. ..++..+                                      
T Consensus       260 ~~l~l~~~~~~~~~~~~~~~~l~~L~~L~l~~~~l~~l~~~~~~~~L~~L~l~~n~~~~l~~~~l~~L~~L~l~~n~~~~  339 (570)
T 2z63_A          260 EEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGN  339 (570)
T ss_dssp             EEEEEEETTEEESCSTTTTGGGTTCSEEEEESCEECSCCBCCSCCCCSEEEEESCBCSSCCBCBCSSCCEEEEESCBSCC
T ss_pred             hhhhhhcchhhhhhchhhhcCcCcccEEEecCccchhhhhhhccCCccEEeeccCcccccCcccccccCEEeCcCCcccc
Confidence                               112222222222100 0000001                                      


Q ss_pred             ----CCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC---------CCCCccEEEeCcc-----------Cc
Q 003387          634 ----GRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES---------KMPRLSKIVLAEY-----------LF  689 (824)
Q Consensus       634 ----~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~---------~~~~L~~l~l~~~-----------~~  689 (824)
                          ..+++|+.|+++++.-......+..+..+++|++|++++|.         .+++|+.|.+.++           ..
T Consensus       340 ~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~  419 (570)
T 2z63_A          340 AFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLS  419 (570)
T ss_dssp             BCCCCBCTTCCEEECCSSCCBEEEEEEHHHHTCSCCCEEECCSCSEEEEEEEEETCTTCCEEECTTSEEESCTTSCTTTT
T ss_pred             ccccccCCCCCEEeCcCCccCccccccccccccCccCEEECCCCccccccccccccCCCCEEEccCCccccccchhhhhc
Confidence                12233333333333211111124455666777777777643         4567777777654           45


Q ss_pred             CCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEE
Q 003387          690 PHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECL  769 (824)
Q Consensus       690 ~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L  769 (824)
                      +++|++|++++|.+.+..+..++.+++|+.|++++|.+.+..++..+..+++|++|++++|......+..+..+++|+.|
T Consensus       420 l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~p~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L  499 (570)
T 2z63_A          420 LRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVL  499 (570)
T ss_dssp             CTTCCEEECTTSCCEECCTTTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEE
T ss_pred             CCCCCEEeCcCCcccccchhhhhcCCcCcEEECcCCcCccccchhhhhcccCCCEEECCCCccccCChhhhhcccCCCEE
Confidence            67888999988888777778888999999999998887754566777889999999999987443336678889999999


Q ss_pred             EEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          770 IINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       770 ~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ++++|......|..+.++++|+.|+++++|
T Consensus       500 ~l~~n~l~~~~~~~~~~l~~L~~L~l~~N~  529 (570)
T 2z63_A          500 NMASNQLKSVPDGIFDRLTSLQKIWLHTNP  529 (570)
T ss_dssp             ECCSSCCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             eCCCCcCCCCCHHHhhcccCCcEEEecCCc
Confidence            999997555445568899999999999965

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.92  E-value=3.5e-24  Score=255.67  Aligned_cols=294  Identities=14%  Similarity=0.094  Sum_probs=233.2

Q ss_pred             CCCeeEEEEEecCCCccccccc--CCceeEeeccCCC-CCCCCcchhHhhhc-------ccCcccEEEeeCccCccCCc-
Q 003387          470 PKKAKRLNAVEREGDFACLDDY--DSQLHSLLCCSPE-TRHLDPIDWEKFCG-------MFKLLRVLDLGSLVLIQYPS-  538 (824)
Q Consensus       470 ~~~~r~lsl~~~~~~~~~~~~~--~~~Lr~L~l~~~~-~~~~~~~~~~~~~~-------~~~~Lr~L~L~~~~i~~lp~-  538 (824)
                      ..+++.|.+..+.....+|..+  +++|+.|.+.++. ..   ...++..+.       .+++|++|+|++|.+..+|. 
T Consensus       490 L~~L~~L~Ls~N~l~~~iP~~l~~L~~L~~L~Ls~N~~ls---g~~iP~~i~~L~~~~~~l~~L~~L~Ls~N~L~~ip~~  566 (876)
T 4ecn_A          490 LKDLTDVELYNCPNMTQLPDFLYDLPELQSLNIACNRGIS---AAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPAS  566 (876)
T ss_dssp             CTTCCEEEEESCTTCCSCCGGGGGCSSCCEEECTTCTTSC---HHHHHHHHHHHHHCTTTTTTCCEEECCSSCCCBCCCH
T ss_pred             CCCCCEEECcCCCCCccChHHHhCCCCCCEEECcCCCCcc---cccchHHHHhhhhcccccCCccEEEeeCCcCCccCCh
Confidence            4678999999555455577666  9999999999987 42   202344344       44599999999999999999 


Q ss_pred             -cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhcccc-CceecCCCccCCCCCCC-CCCCCC
Q 003387          539 -GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNK-LRHLNFGSITLPAHPGK-FCGSLE  615 (824)
Q Consensus       539 -~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~-L~~L~L~~~~~~~~~~p-~i~~L~  615 (824)
                       .++++++|++|+|++|.+..+| .+ +++++|++|+|++|.+..+|..+.++++ |++|++++|.+.  .+| .++.+.
T Consensus       567 ~~l~~L~~L~~L~Ls~N~l~~lp-~~-~~L~~L~~L~Ls~N~l~~lp~~l~~l~~~L~~L~Ls~N~L~--~lp~~~~~~~  642 (876)
T 4ecn_A          567 ASLQKMVKLGLLDCVHNKVRHLE-AF-GTNVKLTDLKLDYNQIEEIPEDFCAFTDQVEGLGFSHNKLK--YIPNIFNAKS  642 (876)
T ss_dssp             HHHTTCTTCCEEECTTSCCCBCC-CC-CTTSEESEEECCSSCCSCCCTTSCEECTTCCEEECCSSCCC--SCCSCCCTTC
T ss_pred             hhhhcCCCCCEEECCCCCcccch-hh-cCCCcceEEECcCCccccchHHHhhccccCCEEECcCCCCC--cCchhhhccc
Confidence             9999999999999999999999 66 9999999999999999999999999999 999999999987  566 666665


Q ss_pred             C--CCeeeccCCCc--chhh---hcC--CCCccceEEEecccccchhhHHHHh-ccCCCCCeEEEeccC---------C-
Q 003387          616 N--LNFISALHPCC--CTED---ILG--RLPNLRNLRIRGDLSYNQSLLSKSL-CRLSCLESLKLANES---------K-  675 (824)
Q Consensus       616 ~--L~~l~~~~~~~--~~~~---~l~--~l~~L~~L~l~~~~~~~~~~l~~~l-~~l~~L~~L~l~~~~---------~-  675 (824)
                      .  |+.|+++.+..  .++.   .+.  .+++|+.|+++++.   ...+|..+ ..+++|+.|+|++|.         . 
T Consensus       643 ~~~L~~L~Ls~N~l~g~ip~l~~~l~~~~~~~L~~L~Ls~N~---L~~lp~~~~~~l~~L~~L~Ls~N~L~~ip~~~~~~  719 (876)
T 4ecn_A          643 VYVMGSVDFSYNKIGSEGRNISCSMDDYKGINASTVTLSYNE---IQKFPTELFATGSPISTIILSNNLMTSIPENSLKP  719 (876)
T ss_dssp             SSCEEEEECCSSCTTTTSSSCSSCTTTCCCCCEEEEECCSSC---CCSCCHHHHHTTCCCSEEECCSCCCSCCCTTSSSC
T ss_pred             cCCCCEEECcCCcCCCccccchhhhccccCCCcCEEEccCCc---CCccCHHHHccCCCCCEEECCCCcCCccChHHhcc
Confidence            4  99999884321  1111   022  34589999999885   23555554 478999999999853         1 


Q ss_pred             C-------CCccEEEeCcc---------C--cCCCceEEEEEcccCCCCCcccccCCCCCCeEEeec------cccCCCe
Q 003387          676 M-------PRLSKIVLAEY---------L--FPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQ------NSYSGRK  731 (824)
Q Consensus       676 ~-------~~L~~l~l~~~---------~--~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~------~~~~~~~  731 (824)
                      .       ++|+.|.++++         .  .+++|+.|+|++|.+.+ +|..++++++|+.|+|++      |.+.+ .
T Consensus       720 ~~~~l~nl~~L~~L~Ls~N~L~~lp~~l~~~~l~~L~~L~Ls~N~L~~-lp~~l~~L~~L~~L~Ls~N~~ls~N~l~~-~  797 (876)
T 4ecn_A          720 KDGNYKNTYLLTTIDLRFNKLTSLSDDFRATTLPYLSNMDVSYNCFSS-FPTQPLNSSQLKAFGIRHQRDAEGNRILR-Q  797 (876)
T ss_dssp             TTSCCTTGGGCCEEECCSSCCCCCCGGGSTTTCTTCCEEECCSSCCSS-CCCGGGGCTTCCEEECCCCBCTTCCBCCC-C
T ss_pred             ccccccccCCccEEECCCCCCccchHHhhhccCCCcCEEEeCCCCCCc-cchhhhcCCCCCEEECCCCCCcccccccc-c
Confidence            1       17899998876         3  67999999999999876 788899999999999987      44443 3


Q ss_pred             eeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCC
Q 003387          732 LTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLK  778 (824)
Q Consensus       732 ~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~  778 (824)
                      ++..+..+++|+.|+|++|. +..+|..+.  ++|+.|+|++|+...
T Consensus       798 ip~~l~~L~~L~~L~Ls~N~-L~~Ip~~l~--~~L~~LdLs~N~l~~  841 (876)
T 4ecn_A          798 WPTGITTCPSLIQLQIGSND-IRKVDEKLT--PQLYILDIADNPNIS  841 (876)
T ss_dssp             CCTTGGGCSSCCEEECCSSC-CCBCCSCCC--SSSCEEECCSCTTCE
T ss_pred             ChHHHhcCCCCCEEECCCCC-CCccCHhhc--CCCCEEECCCCCCCc
Confidence            55567789999999999997 488886643  799999999999653

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.91  E-value=7.1e-25  Score=257.22  Aligned_cols=292  Identities=17%  Similarity=0.176  Sum_probs=193.0

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc-Cc--cCCccCCCC------CcceEEeecCCCCCccCh-
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV-LI--QYPSGIENL------FLLRYLKLNIPSLNSLPS-  561 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~-i~--~lp~~i~~l------~~Lr~L~L~~~~i~~lp~-  561 (824)
                      +++|++|.+.++...    ...+..+..+++|++|++++|. ++  .+|..++++      ++|++|++++|.+..+|. 
T Consensus       248 l~~L~~L~L~~n~l~----~~~p~~l~~l~~L~~L~Ls~n~~l~~~~lp~~~~~L~~~~~l~~L~~L~L~~n~l~~ip~~  323 (636)
T 4eco_A          248 LKDLTDVEVYNCPNL----TKLPTFLKALPEMQLINVACNRGISGEQLKDDWQALADAPVGEKIQIIYIGYNNLKTFPVE  323 (636)
T ss_dssp             CTTCCEEEEECCTTC----SSCCTTTTTCSSCCEEECTTCTTSCHHHHHHHHHHHHHSGGGGTCCEEECCSSCCSSCCCH
T ss_pred             cCCCCEEEecCCcCC----ccChHHHhcCCCCCEEECcCCCCCccccchHHHHhhhccccCCCCCEEECCCCcCCccCch
Confidence            466666666666542    1234556666677777777766 55  366666555      667777777776666666 


Q ss_pred             -hhhhcCCCccEeecCCcccc-ccchhhhccccCceecCCCccCCCCCCC-CCCCCCC-CCeeeccCCC-cchhhhcCCC
Q 003387          562 -SLLSNLLNLYTLDMPFSYID-HTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLEN-LNFISALHPC-CCTEDILGRL  636 (824)
Q Consensus       562 -~i~~~L~~L~~L~L~~~~l~-~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~-L~~l~~~~~~-~~~~~~l~~l  636 (824)
                       .+ +++++|++|++++|.+. .+| .++.+++|++|++++|.+.  .+| .++++++ |+.|+++.+. ..++..+..+
T Consensus       324 ~~l-~~l~~L~~L~L~~N~l~g~ip-~~~~l~~L~~L~L~~N~l~--~lp~~l~~l~~~L~~L~Ls~N~l~~lp~~~~~~  399 (636)
T 4eco_A          324 TSL-QKMKKLGMLECLYNQLEGKLP-AFGSEIKLASLNLAYNQIT--EIPANFCGFTEQVENLSFAHNKLKYIPNIFDAK  399 (636)
T ss_dssp             HHH-TTCTTCCEEECCSCCCEEECC-CCEEEEEESEEECCSSEEE--ECCTTSEEECTTCCEEECCSSCCSSCCSCCCTT
T ss_pred             hhh-ccCCCCCEEeCcCCcCccchh-hhCCCCCCCEEECCCCccc--cccHhhhhhcccCcEEEccCCcCcccchhhhhc
Confidence             55 67777777777777666 666 6666777777777776665  455 6777777 7777776321 1223324443


Q ss_pred             C--ccceEEEecccccchhhHHHHhc-------cCCCCCeEEEeccC----------CCCCccEEEeCcc-------Cc-
Q 003387          637 P--NLRNLRIRGDLSYNQSLLSKSLC-------RLSCLESLKLANES----------KMPRLSKIVLAEY-------LF-  689 (824)
Q Consensus       637 ~--~L~~L~l~~~~~~~~~~l~~~l~-------~l~~L~~L~l~~~~----------~~~~L~~l~l~~~-------~~-  689 (824)
                      +  +|+.|+++++.  .....|..+.       .+++|+.|++++|.          ..++|+.|.+.++       .. 
T Consensus       400 ~l~~L~~L~Ls~N~--l~~~~p~~l~~~~~~~~~~~~L~~L~Ls~N~l~~lp~~~~~~l~~L~~L~Ls~N~l~~i~~~~~  477 (636)
T 4eco_A          400 SVSVMSAIDFSYNE--IGSVDGKNFDPLDPTPFKGINVSSINLSNNQISKFPKELFSTGSPLSSINLMGNMLTEIPKNSL  477 (636)
T ss_dssp             CSSCEEEEECCSSC--TTTTTTCSSCTTCSSCCCCCCEEEEECCSSCCCSCCTHHHHTTCCCSEEECCSSCCSBCCSSSS
T ss_pred             ccCccCEEECcCCc--CCCcchhhhcccccccccCCCCCEEECcCCccCcCCHHHHccCCCCCEEECCCCCCCCcCHHHh
Confidence            3  67777777764  3344444454       56677788877753          2466777777665       11 


Q ss_pred             ---------CCCceEEEEEcccCCCCCccccc--CCCCCCeEEeeccccCCCeeeecCCCCCCccEEeecc------CCC
Q 003387          690 ---------PHSLTHLSFSNTDLMDDPMPTLE--KLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKS------MLW  752 (824)
Q Consensus       690 ---------~~~L~~L~L~~~~l~~~~~~~l~--~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~------~~~  752 (824)
                               +++|+.|+|++|.+. .+|..+.  .+++|+.|+|++|.+.+  ++.....+++|++|+|++      |..
T Consensus       478 ~~~~~~~~~l~~L~~L~Ls~N~l~-~lp~~~~~~~l~~L~~L~Ls~N~l~~--ip~~~~~l~~L~~L~Ls~N~~ls~N~l  554 (636)
T 4eco_A          478 KDENENFKNTYLLTSIDLRFNKLT-KLSDDFRATTLPYLVGIDLSYNSFSK--FPTQPLNSSTLKGFGIRNQRDAQGNRT  554 (636)
T ss_dssp             EETTEECTTGGGCCEEECCSSCCC-BCCGGGSTTTCTTCCEEECCSSCCSS--CCCGGGGCSSCCEEECCSCBCTTCCBC
T ss_pred             ccccccccccCCccEEECcCCcCC-ccChhhhhccCCCcCEEECCCCCCCC--cChhhhcCCCCCEEECCCCcccccCcc
Confidence                     127888888888776 5666665  78888888888887775  556666788888888843      444


Q ss_pred             CccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          753 LEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       753 l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ...+|..++.+++|+.|++++|.. +.+|..+.  ++|+.|++++||
T Consensus       555 ~~~~p~~l~~l~~L~~L~Ls~N~l-~~ip~~~~--~~L~~L~Ls~N~  598 (636)
T 4eco_A          555 LREWPEGITLCPSLTQLQIGSNDI-RKVNEKIT--PNISVLDIKDNP  598 (636)
T ss_dssp             CCCCCTTGGGCSSCCEEECCSSCC-CBCCSCCC--TTCCEEECCSCT
T ss_pred             cccChHHHhcCCCCCEEECCCCcC-CccCHhHh--CcCCEEECcCCC
Confidence            556676777788888888888875 77787654  788888888886

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.91  E-value=4e-24  Score=250.85  Aligned_cols=315  Identities=13%  Similarity=0.099  Sum_probs=245.7

Q ss_pred             CCCeeEEEEEecCCCccccccc--CCceeEeeccCCC-CCCCCcchhHhhhccc------CcccEEEeeCccCccCCc--
Q 003387          470 PKKAKRLNAVEREGDFACLDDY--DSQLHSLLCCSPE-TRHLDPIDWEKFCGMF------KLLRVLDLGSLVLIQYPS--  538 (824)
Q Consensus       470 ~~~~r~lsl~~~~~~~~~~~~~--~~~Lr~L~l~~~~-~~~~~~~~~~~~~~~~------~~Lr~L~L~~~~i~~lp~--  538 (824)
                      ..++++|.+..+.....+|..+  +++|++|.+.++. ..   ...++..+..+      ++|++|++++|.++.+|.  
T Consensus       248 l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~n~~l~---~~~lp~~~~~L~~~~~l~~L~~L~L~~n~l~~ip~~~  324 (636)
T 4eco_A          248 LKDLTDVEVYNCPNLTKLPTFLKALPEMQLINVACNRGIS---GEQLKDDWQALADAPVGEKIQIIYIGYNNLKTFPVET  324 (636)
T ss_dssp             CTTCCEEEEECCTTCSSCCTTTTTCSSCCEEECTTCTTSC---HHHHHHHHHHHHHSGGGGTCCEEECCSSCCSSCCCHH
T ss_pred             cCCCCEEEecCCcCCccChHHHhcCCCCCEEECcCCCCCc---cccchHHHHhhhccccCCCCCEEECCCCcCCccCchh
Confidence            4678999999555455577777  9999999999987 42   21344555554      999999999999999999  


Q ss_pred             cCCCCCcceEEeecCCCCC-ccChhhhhcCCCccEeecCCccccccchhhhcccc-CceecCCCccCCCCCCC-CCCCCC
Q 003387          539 GIENLFLLRYLKLNIPSLN-SLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNK-LRHLNFGSITLPAHPGK-FCGSLE  615 (824)
Q Consensus       539 ~i~~l~~Lr~L~L~~~~i~-~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~-L~~L~L~~~~~~~~~~p-~i~~L~  615 (824)
                      .++++++|++|++++|.+. .+| .+ +++++|++|++++|.+..+|..++.+++ |++|++++|.+.  .+| .++.++
T Consensus       325 ~l~~l~~L~~L~L~~N~l~g~ip-~~-~~l~~L~~L~L~~N~l~~lp~~l~~l~~~L~~L~Ls~N~l~--~lp~~~~~~~  400 (636)
T 4eco_A          325 SLQKMKKLGMLECLYNQLEGKLP-AF-GSEIKLASLNLAYNQITEIPANFCGFTEQVENLSFAHNKLK--YIPNIFDAKS  400 (636)
T ss_dssp             HHTTCTTCCEEECCSCCCEEECC-CC-EEEEEESEEECCSSEEEECCTTSEEECTTCCEEECCSSCCS--SCCSCCCTTC
T ss_pred             hhccCCCCCEEeCcCCcCccchh-hh-CCCCCCCEEECCCCccccccHhhhhhcccCcEEEccCCcCc--ccchhhhhcc
Confidence            9999999999999999999 999 76 9999999999999999999999999999 999999999988  566 666655


Q ss_pred             --CCCeeeccCCCc--chhhhcC-------CCCccceEEEecccccchhhHHHH-hccCCCCCeEEEeccC----C---C
Q 003387          616 --NLNFISALHPCC--CTEDILG-------RLPNLRNLRIRGDLSYNQSLLSKS-LCRLSCLESLKLANES----K---M  676 (824)
Q Consensus       616 --~L~~l~~~~~~~--~~~~~l~-------~l~~L~~L~l~~~~~~~~~~l~~~-l~~l~~L~~L~l~~~~----~---~  676 (824)
                        +|+.|+++.+..  ..+..+.       .+++|+.|+++++.   ...+|.. +..+++|+.|++++|.    +   +
T Consensus       401 l~~L~~L~Ls~N~l~~~~p~~l~~~~~~~~~~~~L~~L~Ls~N~---l~~lp~~~~~~l~~L~~L~Ls~N~l~~i~~~~~  477 (636)
T 4eco_A          401 VSVMSAIDFSYNEIGSVDGKNFDPLDPTPFKGINVSSINLSNNQ---ISKFPKELFSTGSPLSSINLMGNMLTEIPKNSL  477 (636)
T ss_dssp             SSCEEEEECCSSCTTTTTTCSSCTTCSSCCCCCCEEEEECCSSC---CCSCCTHHHHTTCCCSEEECCSSCCSBCCSSSS
T ss_pred             cCccCEEECcCCcCCCcchhhhcccccccccCCCCCEEECcCCc---cCcCCHHHHccCCCCCEEECCCCCCCCcCHHHh
Confidence              899999984321  1222255       67799999999985   2244443 4458999999999864    1   1


Q ss_pred             ----------CCccEEEeCcc---------C--cCCCceEEEEEcccCCCCCcccccCCCCCCeEEeec------cccCC
Q 003387          677 ----------PRLSKIVLAEY---------L--FPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQ------NSYSG  729 (824)
Q Consensus       677 ----------~~L~~l~l~~~---------~--~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~------~~~~~  729 (824)
                                ++|+.|.++++         .  .+++|+.|+|++|.+.+ +|..++++++|+.|+|++      |.+.+
T Consensus       478 ~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~~~l~~L~~L~Ls~N~l~~-ip~~~~~l~~L~~L~Ls~N~~ls~N~l~~  556 (636)
T 4eco_A          478 KDENENFKNTYLLTSIDLRFNKLTKLSDDFRATTLPYLVGIDLSYNSFSK-FPTQPLNSSTLKGFGIRNQRDAQGNRTLR  556 (636)
T ss_dssp             EETTEECTTGGGCCEEECCSSCCCBCCGGGSTTTCTTCCEEECCSSCCSS-CCCGGGGCSSCCEEECCSCBCTTCCBCCC
T ss_pred             ccccccccccCCccEEECcCCcCCccChhhhhccCCCcCEEECCCCCCCC-cChhhhcCCCCCEEECCCCcccccCcccc
Confidence                      17889988876         3  67899999999999886 788899999999999965      43443


Q ss_pred             CeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCC-----Ccc---ccccCccCcEEEecCCc
Q 003387          730 RKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKK-----MPE---QLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       730 ~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~-----lp~---~l~~l~~L~~L~l~~c~  799 (824)
                       .++..+..+++|++|+|++|. +..+|..+.  ++|+.|++++|+...-     .|.   ....+...+..++.+||
T Consensus       557 -~~p~~l~~l~~L~~L~Ls~N~-l~~ip~~~~--~~L~~L~Ls~N~l~~~~~~~~~~~~~~~~~~l~~~~~~~i~~C~  630 (636)
T 4eco_A          557 -EWPEGITLCPSLTQLQIGSND-IRKVNEKIT--PNISVLDIKDNPNISIDLSYVCPYIEAGMYMLFYDKTQDIRGCD  630 (636)
T ss_dssp             -CCCTTGGGCSSCCEEECCSSC-CCBCCSCCC--TTCCEEECCSCTTCEEECTTTHHHHHTTCCEEECCTTSEEESCG
T ss_pred             -cChHHHhcCCCCCEEECCCCc-CCccCHhHh--CcCCEEECcCCCCccccHHhcchhhhcccceeecCCccccCCCc
Confidence             355567789999999999988 488886644  8999999999985431     121   12233344566888998

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=99.91  E-value=7e-24  Score=239.84  Aligned_cols=301  Identities=19%  Similarity=0.172  Sum_probs=228.7

Q ss_pred             CCeeEEEEEecCCCccccccc-CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEE
Q 003387          471 KKAKRLNAVEREGDFACLDDY-DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYL  549 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~~~~~~~-~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L  549 (824)
                      ..++.+.+. +.....++... +++|++|.+.++....    .++  +..+++|++|++++|.+..+|. ++++++|++|
T Consensus        46 ~~l~~L~l~-~~~i~~l~~~~~l~~L~~L~Ls~n~l~~----~~~--~~~l~~L~~L~l~~n~l~~~~~-~~~l~~L~~L  117 (466)
T 1o6v_A           46 DQVTTLQAD-RLGIKSIDGVEYLNNLTQINFSNNQLTD----ITP--LKNLTKLVDILMNNNQIADITP-LANLTNLTGL  117 (466)
T ss_dssp             HTCCEEECC-SSCCCCCTTGGGCTTCCEEECCSSCCCC----CGG--GTTCTTCCEEECCSSCCCCCGG-GTTCTTCCEE
T ss_pred             ccccEEecC-CCCCccCcchhhhcCCCEEECCCCccCC----chh--hhccccCCEEECCCCccccChh-hcCCCCCCEE
Confidence            467888887 55554455433 8899999998887642    222  7889999999999999887776 8889999999


Q ss_pred             eecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC-cc
Q 003387          550 KLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC-CC  628 (824)
Q Consensus       550 ~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~-~~  628 (824)
                      ++++|.+..+|. + .++++|++|++++|.+..+|. ++.+++|++|++++ .+.  .++.++++++|+.|+++.+. ..
T Consensus       118 ~L~~n~l~~~~~-~-~~l~~L~~L~l~~n~l~~~~~-~~~l~~L~~L~l~~-~~~--~~~~~~~l~~L~~L~l~~n~l~~  191 (466)
T 1o6v_A          118 TLFNNQITDIDP-L-KNLTNLNRLELSSNTISDISA-LSGLTSLQQLSFGN-QVT--DLKPLANLTTLERLDISSNKVSD  191 (466)
T ss_dssp             ECCSSCCCCCGG-G-TTCTTCSEEEEEEEEECCCGG-GTTCTTCSEEEEEE-SCC--CCGGGTTCTTCCEEECCSSCCCC
T ss_pred             ECCCCCCCCChH-H-cCCCCCCEEECCCCccCCChh-hccCCcccEeecCC-ccc--CchhhccCCCCCEEECcCCcCCC
Confidence            999999988876 5 899999999999998888875 88899999998863 332  34468888999999988432 23


Q ss_pred             hhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC--------CCCCccEEEeCcc--------CcCCC
Q 003387          629 TEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES--------KMPRLSKIVLAEY--------LFPHS  692 (824)
Q Consensus       629 ~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~--------~~~~L~~l~l~~~--------~~~~~  692 (824)
                      +.. +..+++|+.|+++++.-  ....+  +..+++|+.|++++|.        .+++|+.|.+.++        ..+++
T Consensus       192 ~~~-l~~l~~L~~L~l~~n~l--~~~~~--~~~l~~L~~L~l~~n~l~~~~~l~~l~~L~~L~l~~n~l~~~~~~~~l~~  266 (466)
T 1o6v_A          192 ISV-LAKLTNLESLIATNNQI--SDITP--LGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTK  266 (466)
T ss_dssp             CGG-GGGCTTCSEEECCSSCC--CCCGG--GGGCTTCCEEECCSSCCCCCGGGGGCTTCSEEECCSSCCCCCGGGTTCTT
T ss_pred             Chh-hccCCCCCEEEecCCcc--ccccc--ccccCCCCEEECCCCCcccchhhhcCCCCCEEECCCCccccchhhhcCCC
Confidence            344 78889999999998852  22222  6678899999998753        4567777777765        45678


Q ss_pred             ceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEe
Q 003387          693 LTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIIN  772 (824)
Q Consensus       693 L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~  772 (824)
                      |+.|++++|.+.+..+  ++.+++|+.|++++|.+.+..   ....+++|+.|++++|. +..++. ...+++|+.|+++
T Consensus       267 L~~L~l~~n~l~~~~~--~~~l~~L~~L~L~~n~l~~~~---~~~~l~~L~~L~L~~n~-l~~~~~-~~~l~~L~~L~l~  339 (466)
T 1o6v_A          267 LTELKLGANQISNISP--LAGLTALTNLELNENQLEDIS---PISNLKNLTYLTLYFNN-ISDISP-VSSLTKLQRLFFY  339 (466)
T ss_dssp             CSEEECCSSCCCCCGG--GTTCTTCSEEECCSSCCSCCG---GGGGCTTCSEEECCSSC-CSCCGG-GGGCTTCCEEECC
T ss_pred             CCEEECCCCccCcccc--ccCCCccCeEEcCCCcccCch---hhcCCCCCCEEECcCCc-CCCchh-hccCccCCEeECC
Confidence            8888888888764332  778888888888888776522   25678899999998886 444433 6688999999999


Q ss_pred             cCCCCCCCccccccCccCcEEEecCCc
Q 003387          773 PCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       773 ~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      +|+ +..++ .+.++++|+.|++++|+
T Consensus       340 ~n~-l~~~~-~l~~l~~L~~L~l~~n~  364 (466)
T 1o6v_A          340 NNK-VSDVS-SLANLTNINWLSAGHNQ  364 (466)
T ss_dssp             SSC-CCCCG-GGTTCTTCCEEECCSSC
T ss_pred             CCc-cCCch-hhccCCCCCEEeCCCCc
Confidence            886 44454 67889999999999887

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=99.91  E-value=2.5e-23  Score=235.27  Aligned_cols=303  Identities=18%  Similarity=0.177  Sum_probs=217.9

Q ss_pred             CCCCeeEEEEEecCCCccccccc-CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcce
Q 003387          469 SPKKAKRLNAVEREGDFACLDDY-DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLR  547 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~~~~-~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr  547 (824)
                      ....+++|.+. ++....++... +++|+.|.+.++....    ..+  +..+++|++|++++|.++.+|. +.++++|+
T Consensus        66 ~l~~L~~L~Ls-~n~l~~~~~~~~l~~L~~L~l~~n~l~~----~~~--~~~l~~L~~L~L~~n~l~~~~~-~~~l~~L~  137 (466)
T 1o6v_A           66 YLNNLTQINFS-NNQLTDITPLKNLTKLVDILMNNNQIAD----ITP--LANLTNLTGLTLFNNQITDIDP-LKNLTNLN  137 (466)
T ss_dssp             GCTTCCEEECC-SSCCCCCGGGTTCTTCCEEECCSSCCCC----CGG--GTTCTTCCEEECCSSCCCCCGG-GTTCTTCS
T ss_pred             hhcCCCEEECC-CCccCCchhhhccccCCEEECCCCcccc----Chh--hcCCCCCCEEECCCCCCCCChH-HcCCCCCC
Confidence            45678999999 55555455533 9999999999887652    222  8999999999999999998876 89999999


Q ss_pred             EEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC-
Q 003387          548 YLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC-  626 (824)
Q Consensus       548 ~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~-  626 (824)
                      +|++++|.+..+|. + +++++|++|+++ +.+..++. +.++++|++|++++|.+.  .++.+..+++|+.|+++.+. 
T Consensus       138 ~L~l~~n~l~~~~~-~-~~l~~L~~L~l~-~~~~~~~~-~~~l~~L~~L~l~~n~l~--~~~~l~~l~~L~~L~l~~n~l  211 (466)
T 1o6v_A          138 RLELSSNTISDISA-L-SGLTSLQQLSFG-NQVTDLKP-LANLTTLERLDISSNKVS--DISVLAKLTNLESLIATNNQI  211 (466)
T ss_dssp             EEEEEEEEECCCGG-G-TTCTTCSEEEEE-ESCCCCGG-GTTCTTCCEEECCSSCCC--CCGGGGGCTTCSEEECCSSCC
T ss_pred             EEECCCCccCCChh-h-ccCCcccEeecC-CcccCchh-hccCCCCCEEECcCCcCC--CChhhccCCCCCEEEecCCcc
Confidence            99999999888764 4 677777777764 33444443 666677777777666654  34455666666666666321 


Q ss_pred             cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC--------CCCCccEEEeCcc--------CcC
Q 003387          627 CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES--------KMPRLSKIVLAEY--------LFP  690 (824)
Q Consensus       627 ~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~--------~~~~L~~l~l~~~--------~~~  690 (824)
                      ..... ++.+++|+.|+++++.-..   + ..+..+++|+.|++++|.        .+++|+.|.+.++        ..+
T Consensus       212 ~~~~~-~~~l~~L~~L~l~~n~l~~---~-~~l~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~l  286 (466)
T 1o6v_A          212 SDITP-LGILTNLDELSLNGNQLKD---I-GTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGL  286 (466)
T ss_dssp             CCCGG-GGGCTTCCEEECCSSCCCC---C-GGGGGCTTCSEEECCSSCCCCCGGGTTCTTCSEEECCSSCCCCCGGGTTC
T ss_pred             ccccc-ccccCCCCEEECCCCCccc---c-hhhhcCCCCCEEECCCCccccchhhhcCCCCCEEECCCCccCccccccCC
Confidence            12222 5556666666666653111   1 234556666666666542        3445666666554        567


Q ss_pred             CCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEE
Q 003387          691 HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLI  770 (824)
Q Consensus       691 ~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~  770 (824)
                      ++|+.|++++|.+.+..  .++.+++|+.|++++|.+.+...   ...+++|+.|++++|. +..++ .+..+++|+.|+
T Consensus       287 ~~L~~L~L~~n~l~~~~--~~~~l~~L~~L~L~~n~l~~~~~---~~~l~~L~~L~l~~n~-l~~~~-~l~~l~~L~~L~  359 (466)
T 1o6v_A          287 TALTNLELNENQLEDIS--PISNLKNLTYLTLYFNNISDISP---VSSLTKLQRLFFYNNK-VSDVS-SLANLTNINWLS  359 (466)
T ss_dssp             TTCSEEECCSSCCSCCG--GGGGCTTCSEEECCSSCCSCCGG---GGGCTTCCEEECCSSC-CCCCG-GGTTCTTCCEEE
T ss_pred             CccCeEEcCCCcccCch--hhcCCCCCCEEECcCCcCCCchh---hccCccCCEeECCCCc-cCCch-hhccCCCCCEEe
Confidence            89999999999886533  38899999999999998876322   5689999999999986 55554 577899999999


Q ss_pred             EecCCCCCCCccccccCccCcEEEecCCc
Q 003387          771 INPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       771 l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      +++|+.....|  +..+++|+.|++++|+
T Consensus       360 l~~n~l~~~~~--~~~l~~L~~L~l~~n~  386 (466)
T 1o6v_A          360 AGHNQISDLTP--LANLTRITQLGLNDQA  386 (466)
T ss_dssp             CCSSCCCBCGG--GTTCTTCCEEECCCEE
T ss_pred             CCCCccCccch--hhcCCCCCEEeccCCc
Confidence            99998654444  7899999999999987

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=99.91  E-value=1.2e-23  Score=228.42  Aligned_cols=279  Identities=17%  Similarity=0.178  Sum_probs=229.5

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      ++++++|.+.++....     + ..+..+++|++|++++|.++.+|. +..+++|++|++++|.+..+|. + .++++|+
T Consensus        43 l~~L~~L~l~~~~i~~-----~-~~~~~~~~L~~L~l~~n~i~~~~~-~~~l~~L~~L~L~~n~i~~~~~-~-~~l~~L~  113 (347)
T 4fmz_A           43 LESITKLVVAGEKVAS-----I-QGIEYLTNLEYLNLNGNQITDISP-LSNLVKLTNLYIGTNKITDISA-L-QNLTNLR  113 (347)
T ss_dssp             HTTCSEEECCSSCCCC-----C-TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCCGG-G-TTCTTCS
T ss_pred             cccccEEEEeCCcccc-----c-hhhhhcCCccEEEccCCccccchh-hhcCCcCCEEEccCCcccCchH-H-cCCCcCC
Confidence            8899999999887653     2 237889999999999999998887 8999999999999999999864 5 9999999


Q ss_pred             EeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC-cchhhhcCCCCccceEEEeccccc
Q 003387          572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC-CCTEDILGRLPNLRNLRIRGDLSY  650 (824)
Q Consensus       572 ~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~-~~~~~~l~~l~~L~~L~l~~~~~~  650 (824)
                      +|++++|.+..+|. +..+++|++|++++|.... .++.++.+++|+.+++..+. ..... +..+++|+.|+++++.- 
T Consensus       114 ~L~l~~n~i~~~~~-~~~l~~L~~L~l~~n~~~~-~~~~~~~l~~L~~L~l~~~~~~~~~~-~~~l~~L~~L~l~~n~l-  189 (347)
T 4fmz_A          114 ELYLNEDNISDISP-LANLTKMYSLNLGANHNLS-DLSPLSNMTGLNYLTVTESKVKDVTP-IANLTDLYSLSLNYNQI-  189 (347)
T ss_dssp             EEECTTSCCCCCGG-GTTCTTCCEEECTTCTTCC-CCGGGTTCTTCCEEECCSSCCCCCGG-GGGCTTCSEEECTTSCC-
T ss_pred             EEECcCCcccCchh-hccCCceeEEECCCCCCcc-cccchhhCCCCcEEEecCCCcCCchh-hccCCCCCEEEccCCcc-
Confidence            99999999999987 8999999999999996543 45578999999999998432 23333 78899999999998852 


Q ss_pred             chhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCC
Q 003387          651 NQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGR  730 (824)
Q Consensus       651 ~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~  730 (824)
                        ..++. +..+++|+.|+++++.    +....  ....+++|++|++++|.+....+  +..+++|+.|++++|.+...
T Consensus       190 --~~~~~-~~~l~~L~~L~l~~n~----l~~~~--~~~~~~~L~~L~l~~n~l~~~~~--~~~l~~L~~L~l~~n~l~~~  258 (347)
T 4fmz_A          190 --EDISP-LASLTSLHYFTAYVNQ----ITDIT--PVANMTRLNSLKIGNNKITDLSP--LANLSQLTWLEIGTNQISDI  258 (347)
T ss_dssp             --CCCGG-GGGCTTCCEEECCSSC----CCCCG--GGGGCTTCCEEECCSSCCCCCGG--GTTCTTCCEEECCSSCCCCC
T ss_pred             --ccccc-ccCCCccceeecccCC----CCCCc--hhhcCCcCCEEEccCCccCCCcc--hhcCCCCCEEECCCCccCCC
Confidence              22222 7788999999998762    33221  14678999999999999865433  88999999999999988762


Q ss_pred             eeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          731 KLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       731 ~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                         .....+++|++|++++|. +..++ .+..+++|+.|++++|+.....|..+..+++|+.|++++|+
T Consensus       259 ---~~~~~l~~L~~L~l~~n~-l~~~~-~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~~L~~L~L~~n~  322 (347)
T 4fmz_A          259 ---NAVKDLTKLKMLNVGSNQ-ISDIS-VLNNLSQLNSLFLNNNQLGNEDMEVIGGLTNLTTLFLSQNH  322 (347)
T ss_dssp             ---GGGTTCTTCCEEECCSSC-CCCCG-GGGGCTTCSEEECCSSCCCGGGHHHHHTCTTCSEEECCSSS
T ss_pred             ---hhHhcCCCcCEEEccCCc-cCCCh-hhcCCCCCCEEECcCCcCCCcChhHhhccccCCEEEccCCc
Confidence               346789999999999985 66664 46789999999999998766667788999999999999998

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=99.91  E-value=3.2e-24  Score=257.61  Aligned_cols=315  Identities=18%  Similarity=0.113  Sum_probs=198.4

Q ss_pred             CCCCeeEEEEEecCCCccccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc-cCCccCCCCCc
Q 003387          469 SPKKAKRLNAVEREGDFACLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-QYPSGIENLFL  545 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-~lp~~i~~l~~  545 (824)
                      ...+++++.+..+......+. +  +++|+.|.+.++...    ...+..+..+++|++|++++|.+. .+|..  .+++
T Consensus       198 ~l~~L~~L~Ls~n~l~~~~~~-l~~l~~L~~L~Ls~n~l~----~~~~~~l~~l~~L~~L~Ls~n~l~~~~~~~--~l~~  270 (768)
T 3rgz_A          198 RCVNLEFLDVSSNNFSTGIPF-LGDCSALQHLDISGNKLS----GDFSRAISTCTELKLLNISSNQFVGPIPPL--PLKS  270 (768)
T ss_dssp             TCTTCCEEECCSSCCCSCCCB-CTTCCSCCEEECCSSCCC----SCHHHHTTTCSSCCEEECCSSCCEESCCCC--CCTT
T ss_pred             cCCcCCEEECcCCcCCCCCcc-cccCCCCCEEECcCCcCC----CcccHHHhcCCCCCEEECCCCcccCccCcc--ccCC
Confidence            345666777763322222333 4  677777777766543    234556666777777777766655 33332  5555


Q ss_pred             ceEEeecCCCCC-ccChhhhhc-CCCccEeecCCcccc-ccchhhhccccCceecCCCccCCCCCCC--CCCCCCCCCee
Q 003387          546 LRYLKLNIPSLN-SLPSSLLSN-LLNLYTLDMPFSYID-HTADEFWKMNKLRHLNFGSITLPAHPGK--FCGSLENLNFI  620 (824)
Q Consensus       546 Lr~L~L~~~~i~-~lp~~i~~~-L~~L~~L~L~~~~l~-~lp~~i~~L~~L~~L~L~~~~~~~~~~p--~i~~L~~L~~l  620 (824)
                      |++|++++|.+. .+|..+ .+ +++|++|++++|.+. .+|..++++++|++|++++|.+.+ .+|  .++++++|+.|
T Consensus       271 L~~L~L~~n~l~~~ip~~~-~~~~~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~-~ip~~~l~~l~~L~~L  348 (768)
T 3rgz_A          271 LQYLSLAENKFTGEIPDFL-SGACDTLTGLDLSGNHFYGAVPPFFGSCSLLESLALSSNNFSG-ELPMDTLLKMRGLKVL  348 (768)
T ss_dssp             CCEEECCSSEEEESCCCCS-CTTCTTCSEEECCSSEEEECCCGGGGGCTTCCEEECCSSEEEE-ECCHHHHTTCTTCCEE
T ss_pred             CCEEECcCCccCCccCHHH-HhhcCcCCEEECcCCcCCCccchHHhcCCCccEEECCCCcccC-cCCHHHHhcCCCCCEE
Confidence            555665555555 455544 33 355555555555444 345555555555555555555432 233  25555555555


Q ss_pred             eccCCCc--chhhhcCC---------------------------CCccceEEEecccccchhhHHHHhccCCCCCeEEEe
Q 003387          621 SALHPCC--CTEDILGR---------------------------LPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLA  671 (824)
Q Consensus       621 ~~~~~~~--~~~~~l~~---------------------------l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~  671 (824)
                      +++.+..  .++..+..                           +++|+.|+++++.  ....+|..+.++++|+.|+++
T Consensus       349 ~Ls~n~l~~~~p~~l~~l~~~L~~L~Ls~N~l~~~~~~~~~~~~~~~L~~L~L~~n~--l~~~~p~~l~~l~~L~~L~Ls  426 (768)
T 3rgz_A          349 DLSFNEFSGELPESLTNLSASLLTLDLSSNNFSGPILPNLCQNPKNTLQELYLQNNG--FTGKIPPTLSNCSELVSLHLS  426 (768)
T ss_dssp             ECCSSEEEECCCTTHHHHTTTCSEEECCSSEEEEECCTTTTCSTTCCCCEEECCSSE--EEEECCGGGGGCTTCCEEECC
T ss_pred             eCcCCccCccccHHHHhhhcCCcEEEccCCCcCCCcChhhhhcccCCccEEECCCCc--cccccCHHHhcCCCCCEEECc
Confidence            5542211  11111333                           3444455444442  222344445555555555555


Q ss_pred             ccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCC
Q 003387          672 NESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSML  751 (824)
Q Consensus       672 ~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~  751 (824)
                      +|    .+.......+..+++|+.|++++|.+.+..|..++.+++|+.|++++|.+.+. ++..+..+++|++|++++|.
T Consensus       427 ~N----~l~~~~p~~l~~l~~L~~L~L~~n~l~~~~p~~~~~l~~L~~L~L~~N~l~~~-~p~~l~~l~~L~~L~L~~N~  501 (768)
T 3rgz_A          427 FN----YLSGTIPSSLGSLSKLRDLKLWLNMLEGEIPQELMYVKTLETLILDFNDLTGE-IPSGLSNCTNLNWISLSNNR  501 (768)
T ss_dssp             SS----EEESCCCGGGGGCTTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCCSC-CCGGGGGCTTCCEEECCSSC
T ss_pred             CC----cccCcccHHHhcCCCCCEEECCCCcccCcCCHHHcCCCCceEEEecCCcccCc-CCHHHhcCCCCCEEEccCCc
Confidence            43    12222222235678999999999999888899999999999999998888763 45567789999999999998


Q ss_pred             CCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          752 WLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       752 ~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ....+|..++.+++|+.|++++|.....+|..+.++++|+.|++++|+
T Consensus       502 l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~Ls~N~  549 (768)
T 3rgz_A          502 LTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSLIWLDLNTNL  549 (768)
T ss_dssp             CCSCCCGGGGGCTTCCEEECCSSCCEEECCGGGGGCTTCCEEECCSSE
T ss_pred             cCCcCChHHhcCCCCCEEECCCCcccCcCCHHHcCCCCCCEEECCCCc
Confidence            666788888899999999999999888899999999999999999876

>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*

Probab=99.91  E-value=1.9e-23  Score=244.87  Aligned_cols=273  Identities=18%  Similarity=0.138  Sum_probs=182.6

Q ss_pred             cccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCcccccc-chhhhccccCceecCC
Q 003387          522 LLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFG  599 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~  599 (824)
                      .|++|++++|.+..+|.. ++.+++|++|++++|.+..+|..+ +++++|++|++++|.+..+ |..+..+++|++|+++
T Consensus       255 ~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~lp~~l-~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~  333 (606)
T 3t6q_A          255 SVESINLQKHYFFNISSNTFHCFSGLQELDLTATHLSELPSGL-VGLSTLKKLVLSANKFENLCQISASNFPSLTHLSIK  333 (606)
T ss_dssp             EEEEEECTTCCCSSCCTTTTTTCTTCSEEECTTSCCSCCCSSC-CSCTTCCEEECTTCCCSBGGGGCGGGCTTCSEEECC
T ss_pred             ceeEEEeecCccCccCHHHhccccCCCEEeccCCccCCCChhh-cccccCCEEECccCCcCcCchhhhhccCcCCEEECC
Confidence            566666666666655443 677788888888888888888777 7888888888888877766 4457788888888888


Q ss_pred             CccCCCCCCC-CCCCCCCCCeeeccCCCc-ch---hhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC
Q 003387          600 SITLPAHPGK-FCGSLENLNFISALHPCC-CT---EDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES  674 (824)
Q Consensus       600 ~~~~~~~~~p-~i~~L~~L~~l~~~~~~~-~~---~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~  674 (824)
                      +|.+.....+ .++.+++|+.|+++.+.. ..   ...+..+++|+.|+++++.  .....+..+..+++|++|++++|.
T Consensus       334 ~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~n~--l~~~~~~~~~~l~~L~~L~l~~n~  411 (606)
T 3t6q_A          334 GNTKRLELGTGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNE--PLSLKTEAFKECPQLELLDLAFTR  411 (606)
T ss_dssp             SCSSCCBCCSSTTTTCTTCCEEECCSSCCCEEEESTTTTTTCTTCCEEECCSCS--CEEECTTTTTTCTTCSEEECTTCC
T ss_pred             CCCcccccchhhhhccCcCCEEECCCCccccccCcchhcccCCCCCEEECCCCc--CCcCCHHHhcCCccCCeEECCCCc
Confidence            8776542333 577888888888773221 11   2237778888888888774  333345567777888888887642


Q ss_pred             -----------CCCCccEEEeCcc----------CcCCCceEEEEEcccCCCC---CcccccCCCCCCeEEeeccccCCC
Q 003387          675 -----------KMPRLSKIVLAEY----------LFPHSLTHLSFSNTDLMDD---PMPTLEKLPLLQVLKLKQNSYSGR  730 (824)
Q Consensus       675 -----------~~~~L~~l~l~~~----------~~~~~L~~L~L~~~~l~~~---~~~~l~~l~~L~~L~L~~~~~~~~  730 (824)
                                 ..++|+.|.+.++          ..+++|++|++++|.+.+.   .+..++.+++|+.|++++|.+.+ 
T Consensus       412 l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~l~~L~~L~Ls~n~l~~-  490 (606)
T 3t6q_A          412 LKVKDAQSPFQNLHLLKVLNLSHSLLDISSEQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQTLGRLEILVLSFCDLSS-  490 (606)
T ss_dssp             EECCTTCCTTTTCTTCCEEECTTCCCBTTCTTTTTTCTTCCEEECTTCBCGGGEECSSCGGGGCTTCCEEECTTSCCCE-
T ss_pred             CCCcccchhhhCcccCCEEECCCCccCCcCHHHHhCCCCCCEEECCCCCCCccccccchhhccCCCccEEECCCCccCc-
Confidence                       2345666666554          3356677777776665442   22346666777777777665543 


Q ss_pred             eeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          731 KLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       731 ~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ..+..+..+++|++|++++|......+..+..+++| .|++++|......|..+..+++|+.|++++||
T Consensus       491 ~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~l~~l~~L-~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~  558 (606)
T 3t6q_A          491 IDQHAFTSLKMMNHVDLSHNRLTSSSIEALSHLKGI-YLNLASNHISIILPSLLPILSQQRTINLRQNP  558 (606)
T ss_dssp             ECTTTTTTCTTCCEEECCSSCCCGGGGGGGTTCCSC-EEECCSSCCCCCCGGGHHHHHTSSEEECTTCC
T ss_pred             cChhhhccccCCCEEECCCCccCcCChhHhCccccc-EEECcCCcccccCHhhcccCCCCCEEeCCCCC
Confidence            223345667777777777776444445566677777 77777777655556567788889999998876

>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}

Probab=99.90  E-value=1.9e-23  Score=242.22  Aligned_cols=124  Identities=17%  Similarity=0.145  Sum_probs=88.8

Q ss_pred             eEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEeec
Q 003387          474 KRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLN  552 (824)
Q Consensus       474 r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~  552 (824)
                      +++.+. +.....+|..+.++++.|.+.++....    ..+..|..+++|++|+|++|.++.+ |..++++++|++|+|+
T Consensus        34 ~~l~ls-~~~L~~ip~~~~~~L~~L~Ls~N~i~~----~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls  108 (562)
T 3a79_B           34 SMVDYS-NRNLTHVPKDLPPRTKALSLSQNSISE----LRMPDISFLSELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVS  108 (562)
T ss_dssp             CEEECT-TSCCCSCCTTSCTTCCEEECCSSCCCC----CCGGGTTTCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECT
T ss_pred             cEEEcC-CCCCccCCCCCCCCcCEEECCCCCccc----cChhhhccCCCccEEECCCCCCCcCCHHHhCCCCCCCEEECC
Confidence            566666 444444665556778888887776542    4456777788888888888887755 5667778888888888


Q ss_pred             CCCCCccChhhhhcCCCccEeecCCccccccc--hhhhccccCceecCCCccCCC
Q 003387          553 IPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA--DEFWKMNKLRHLNFGSITLPA  605 (824)
Q Consensus       553 ~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp--~~i~~L~~L~~L~L~~~~~~~  605 (824)
                      +|.+..+|..   .+++|++|++++|.+..+|  ..++++++|++|++++|.+..
T Consensus       109 ~N~l~~lp~~---~l~~L~~L~Ls~N~l~~l~~p~~~~~l~~L~~L~L~~n~l~~  160 (562)
T 3a79_B          109 HNRLQNISCC---PMASLRHLDLSFNDFDVLPVCKEFGNLTKLTFLGLSAAKFRQ  160 (562)
T ss_dssp             TSCCCEECSC---CCTTCSEEECCSSCCSBCCCCGGGGGCTTCCEEEEECSBCCT
T ss_pred             CCcCCccCcc---ccccCCEEECCCCCccccCchHhhcccCcccEEecCCCcccc
Confidence            8888877764   6788888888888777654  667788888888887777653

>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*

Probab=99.90  E-value=2e-23  Score=244.65  Aligned_cols=137  Identities=19%  Similarity=0.101  Sum_probs=117.9

Q ss_pred             CCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEeecCCCCCcc-C
Q 003387          483 GDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSL-P  560 (824)
Q Consensus       483 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~i~~l-p  560 (824)
                      ....+|..+.+++++|.+.++...    ...+..|..+++|++|+|++|.++.+ |..++++++|++|+|++|.+..+ |
T Consensus        22 ~l~~ip~~~~~~l~~L~Ls~n~l~----~~~~~~~~~l~~L~~L~Ls~n~l~~i~~~~~~~l~~L~~L~Ls~n~l~~~~p   97 (606)
T 3vq2_A           22 KLSKVPDDIPSSTKNIDLSFNPLK----ILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSP   97 (606)
T ss_dssp             CCSSCCTTSCTTCCEEECTTSCCC----EECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCCCCT
T ss_pred             CcccCCCCCCCCcCEEECCCCCcC----EeChhhccCCccCcEEeCCCCcccccCHHHhhchhhcCEeECCCCcccccCh
Confidence            344466666889999999998764    35566899999999999999999866 66789999999999999999988 5


Q ss_pred             hhhhhcCCCccEeecCCccccccc-hhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccC
Q 003387          561 SSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALH  624 (824)
Q Consensus       561 ~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~  624 (824)
                      ..+ +++++|++|++++|.+..+| ..++++++|++|++++|.+....+| .++++++|++|+++.
T Consensus        98 ~~~-~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~Ls~  162 (606)
T 3vq2_A           98 GSF-SGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSY  162 (606)
T ss_dssp             TSS-TTCTTCCEEECTTSCCCCSSSSCCTTCTTCCEEECCSSCCCCCCCCGGGGTCTTCCEEECCS
T ss_pred             hhc-CCcccCCEEEccCCccccccccccCCCCCCCEEeCCCCcccceechHhHhhcCCCCEEEccC
Confidence            555 99999999999999999887 5699999999999999999765667 899999999998873

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.90  E-value=5.5e-23  Score=226.94  Aligned_cols=269  Identities=14%  Similarity=0.129  Sum_probs=226.4

Q ss_pred             ccCcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch-hhhccccCcee
Q 003387          519 MFKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHL  596 (824)
Q Consensus       519 ~~~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L  596 (824)
                      .+++|++|+++++.++.+|.. +..+++|++|++++|.+..+|...++++++|++|++++|.+..+|. .++++++|++|
T Consensus        43 ~l~~l~~l~l~~~~l~~l~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L  122 (390)
T 3o6n_A           43 TLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVL  122 (390)
T ss_dssp             GGCCCSEEEEESCEESEECTHHHHHCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEE
T ss_pred             ccCCceEEEecCCchhhCChhHhcccccCcEEECCCCcccccChhhccCCCCcCEEECCCCCCCcCCHHHhcCCCCCCEE
Confidence            468999999999999999886 5789999999999999999887545999999999999999998865 48999999999


Q ss_pred             cCCCccCCCCCCC--CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEec
Q 003387          597 NFGSITLPAHPGK--FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLAN  672 (824)
Q Consensus       597 ~L~~~~~~~~~~p--~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~  672 (824)
                      ++++|.+.  .+|  .++++++|+.|+++.+  ....+..+..+++|+.|+++++.-..   +  .+..+++|+.|++++
T Consensus       123 ~L~~n~l~--~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~---~--~~~~l~~L~~L~l~~  195 (390)
T 3o6n_A          123 VLERNDLS--SLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTH---V--DLSLIPSLFHANVSY  195 (390)
T ss_dssp             ECCSSCCC--CCCTTTTTTCTTCCEEECCSSCCCBCCTTTTSSCTTCCEEECCSSCCSB---C--CGGGCTTCSEEECCS
T ss_pred             ECCCCccC--cCCHHHhcCCCCCcEEECCCCccCccChhhccCCCCCCEEECCCCcCCc---c--ccccccccceeeccc
Confidence            99999987  555  4689999999999843  22333348899999999999885221   1  256789999999998


Q ss_pred             cC-----CCCCccEEEeCcc-------CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCC
Q 003387          673 ES-----KMPRLSKIVLAEY-------LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFP  740 (824)
Q Consensus       673 ~~-----~~~~L~~l~l~~~-------~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~  740 (824)
                      |.     .+++++.|.+.++       ..+++|+.|++++|.+.+  ++.++.+++|++|++++|.+.+ ..+..+..++
T Consensus       196 n~l~~~~~~~~L~~L~l~~n~l~~~~~~~~~~L~~L~l~~n~l~~--~~~l~~l~~L~~L~Ls~n~l~~-~~~~~~~~l~  272 (390)
T 3o6n_A          196 NLLSTLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHNNLTD--TAWLLNYPGLVEVDLSYNELEK-IMYHPFVKMQ  272 (390)
T ss_dssp             SCCSEEECCSSCSEEECCSSCCCEEECCCCSSCCEEECCSSCCCC--CGGGGGCTTCSEEECCSSCCCE-EESGGGTTCS
T ss_pred             ccccccCCCCcceEEECCCCeeeeccccccccccEEECCCCCCcc--cHHHcCCCCccEEECCCCcCCC-cChhHccccc
Confidence            64     4567888888876       346789999999999865  3688999999999999998765 3355678899


Q ss_pred             CccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          741 NLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       741 ~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      +|++|++++|. +..++.....+|+|+.|++++|. +..+|..+..+++|+.|++++|+
T Consensus       273 ~L~~L~L~~n~-l~~~~~~~~~l~~L~~L~L~~n~-l~~~~~~~~~l~~L~~L~L~~N~  329 (390)
T 3o6n_A          273 RLERLYISNNR-LVALNLYGQPIPTLKVLDLSHNH-LLHVERNQPQFDRLENLYLDHNS  329 (390)
T ss_dssp             SCCEEECCSSC-CCEEECSSSCCTTCCEEECCSSC-CCCCGGGHHHHTTCSEEECCSSC
T ss_pred             cCCEEECCCCc-CcccCcccCCCCCCCEEECCCCc-ceecCccccccCcCCEEECCCCc
Confidence            99999999986 77788778889999999999996 56789888999999999999997

>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*

Probab=99.90  E-value=2.5e-23  Score=243.76  Aligned_cols=322  Identities=18%  Similarity=0.069  Sum_probs=192.3

Q ss_pred             CCCCeeEEEEEecCCCccc-cccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCcc-CCccCCCCC
Q 003387          469 SPKKAKRLNAVEREGDFAC-LDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQ-YPSGIENLF  544 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~-~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~-lp~~i~~l~  544 (824)
                      .+..++++.+. ++....+ +..+  +++|++|.+.++...    ...+..|..+++|++|+|++|.+.. .|..+++++
T Consensus        31 l~~~l~~L~Ls-~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~----~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~  105 (606)
T 3t6q_A           31 LPNSTECLEFS-FNVLPTIQNTTFSRLINLTFLDLTRCQIY----WIHEDTFQSQHRLDTLVLTANPLIFMAETALSGPK  105 (606)
T ss_dssp             SCTTCCEEECT-TCCCSEECTTTSTTCTTCSEEECTTCCCC----EECTTTTTTCTTCCEEECTTCCCSEECTTTTSSCT
T ss_pred             CCCcCcEEEcc-CCccCcCChhHhccCccceEEECCCCccc----eeChhhccCccccCeeeCCCCcccccChhhhcccc
Confidence            45567777777 4444334 3333  677777777766542    2445666777777777777777663 355677777


Q ss_pred             cceEEeecCCCCCccChhhhhcCCCccEeecCCccccccc-hhhhccccCceecCCCccCCCCCCC-CCCCCCCCC--ee
Q 003387          545 LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLN--FI  620 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~--~l  620 (824)
                      +|++|++++|.+..+++..++++++|++|++++|.+..++ ..+..+++|++|++++|.+.. ..| .++.+++|+  .+
T Consensus       106 ~L~~L~L~~n~i~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~~~~l~~L~~l~L  184 (606)
T 3t6q_A          106 ALKHLFFIQTGISSIDFIPLHNQKTLESLYLGSNHISSIKLPKGFPTEKLKVLDFQNNAIHY-LSKEDMSSLQQATNLSL  184 (606)
T ss_dssp             TCCEEECTTSCCSCGGGSCCTTCTTCCEEECCSSCCCCCCCCTTCCCTTCCEEECCSSCCCE-ECHHHHHTTTTCCSEEE
T ss_pred             cccEeeccccCcccCCcchhccCCcccEEECCCCcccccCcccccCCcccCEEEcccCcccc-cChhhhhhhcccceeEE
Confidence            7777777777777663322377777777777777666652 223447777777777776652 223 556666666  45


Q ss_pred             eccCCC--cchhhhcCCCCccce----------------------------------------------------EEEec
Q 003387          621 SALHPC--CCTEDILGRLPNLRN----------------------------------------------------LRIRG  646 (824)
Q Consensus       621 ~~~~~~--~~~~~~l~~l~~L~~----------------------------------------------------L~l~~  646 (824)
                      +++.+.  ...+. .....+|+.                                                    |++++
T Consensus       185 ~l~~n~l~~~~~~-~~~~~~L~~L~l~~~~~~~~~~~~l~~~~l~~l~~~~~~~~~~~~i~~~~~~~l~~~~L~~L~l~~  263 (606)
T 3t6q_A          185 NLNGNDIAGIEPG-AFDSAVFQSLNFGGTQNLLVIFKGLKNSTIQSLWLGTFEDMDDEDISPAVFEGLCEMSVESINLQK  263 (606)
T ss_dssp             ECTTCCCCEECTT-TTTTCEEEEEECTTCSCHHHHHHHTTTCEEEEEECCCCTTSCCCCCCGGGGGGGGGSEEEEEECTT
T ss_pred             ecCCCccCccChh-HhhhccccccccCCchhHHHHhhhccccchhheechhhccccccccChhHhchhhcCceeEEEeec
Confidence            554211  11111 111222333                                                    33333


Q ss_pred             ccccchhhHHHHhccCCCCCeEEEeccC---------CCCCccEEEeCcc----------CcCCCceEEEEEcccCCCCC
Q 003387          647 DLSYNQSLLSKSLCRLSCLESLKLANES---------KMPRLSKIVLAEY----------LFPHSLTHLSFSNTDLMDDP  707 (824)
Q Consensus       647 ~~~~~~~~l~~~l~~l~~L~~L~l~~~~---------~~~~L~~l~l~~~----------~~~~~L~~L~L~~~~l~~~~  707 (824)
                      +.  .....+..+.++++|++|++++|.         ..++|+.|.+.++          ..+++|++|++++|.+.+..
T Consensus       264 n~--l~~~~~~~~~~l~~L~~L~l~~n~l~~lp~~l~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~~~~~~  341 (606)
T 3t6q_A          264 HY--FFNISSNTFHCFSGLQELDLTATHLSELPSGLVGLSTLKKLVLSANKFENLCQISASNFPSLTHLSIKGNTKRLEL  341 (606)
T ss_dssp             CC--CSSCCTTTTTTCTTCSEEECTTSCCSCCCSSCCSCTTCCEEECTTCCCSBGGGGCGGGCTTCSEEECCSCSSCCBC
T ss_pred             Cc--cCccCHHHhccccCCCEEeccCCccCCCChhhcccccCCEEECccCCcCcCchhhhhccCcCCEEECCCCCccccc
Confidence            21  111122335566777777777642         2356666666654          34567777777777665444


Q ss_pred             cc-cccCCCCCCeEEeeccccCCCee-eecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCcc-cc
Q 003387          708 MP-TLEKLPLLQVLKLKQNSYSGRKL-TCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPE-QL  784 (824)
Q Consensus       708 ~~-~l~~l~~L~~L~L~~~~~~~~~~-~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~-~l  784 (824)
                      +. .++.+++|++|++++|.+.+... +.....+++|++|++++|......+..+..+++|+.|++++|......|. .+
T Consensus       342 ~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~  421 (606)
T 3t6q_A          342 GTGCLENLENLRELDLSHDDIETSDCCNLQLRNLSHLQSLNLSYNEPLSLKTEAFKECPQLELLDLAFTRLKVKDAQSPF  421 (606)
T ss_dssp             CSSTTTTCTTCCEEECCSSCCCEEEESTTTTTTCTTCCEEECCSCSCEEECTTTTTTCTTCSEEECTTCCEECCTTCCTT
T ss_pred             chhhhhccCcCCEEECCCCccccccCcchhcccCCCCCEEECCCCcCCcCCHHHhcCCccCCeEECCCCcCCCcccchhh
Confidence            33 36777777777777776654211 23456777888888887763333344566778888888888876554443 37


Q ss_pred             ccCccCcEEEecCCc
Q 003387          785 WYIKSLNKFDCWWPQ  799 (824)
Q Consensus       785 ~~l~~L~~L~l~~c~  799 (824)
                      .++++|+.|++++|.
T Consensus       422 ~~l~~L~~L~l~~n~  436 (606)
T 3t6q_A          422 QNLHLLKVLNLSHSL  436 (606)
T ss_dssp             TTCTTCCEEECTTCC
T ss_pred             hCcccCCEEECCCCc
Confidence            788888888888875

>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}

Probab=99.90  E-value=1.9e-23  Score=240.01  Aligned_cols=125  Identities=15%  Similarity=0.110  Sum_probs=93.1

Q ss_pred             CCCCeeEEEEEecCCCcccc-ccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCc
Q 003387          469 SPKKAKRLNAVEREGDFACL-DDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFL  545 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~-~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~  545 (824)
                      .+.+++++.+. ++....++ ..+  +++|++|.+.++...    ...+..|..+++|++|+|++|.++.+|..  .+++
T Consensus        19 ~~~~L~~L~Ls-~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~----~~~~~~~~~l~~L~~L~Ls~N~l~~lp~~--~l~~   91 (520)
T 2z7x_B           19 LSQKTTILNIS-QNYISELWTSDILSLSKLRILIISHNRIQ----YLDISVFKFNQELEYLDLSHNKLVKISCH--PTVN   91 (520)
T ss_dssp             CCTTCSEEECC-SSCCCCCCHHHHTTCTTCCEEECCSSCCC----EEEGGGGTTCTTCCEEECCSSCCCEEECC--CCCC
T ss_pred             ccccccEEECC-CCcccccChhhccccccccEEecCCCccC----CcChHHhhcccCCCEEecCCCceeecCcc--ccCC
Confidence            34678888888 44444343 333  788888888887653    24566788888888888888888887776  7888


Q ss_pred             ceEEeecCCCCCc--cChhhhhcCCCccEeecCCccccccchhhhccccC--ceecCCCccC
Q 003387          546 LRYLKLNIPSLNS--LPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKL--RHLNFGSITL  603 (824)
Q Consensus       546 Lr~L~L~~~~i~~--lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L--~~L~L~~~~~  603 (824)
                      |++|++++|.+..  +|..+ +++++|++|++++|.+..  ..+..+++|  ++|++++|.+
T Consensus        92 L~~L~L~~N~l~~~~~p~~~-~~l~~L~~L~L~~n~l~~--~~~~~l~~L~L~~L~l~~n~l  150 (520)
T 2z7x_B           92 LKHLDLSFNAFDALPICKEF-GNMSQLKFLGLSTTHLEK--SSVLPIAHLNISKVLLVLGET  150 (520)
T ss_dssp             CSEEECCSSCCSSCCCCGGG-GGCTTCCEEEEEESSCCG--GGGGGGTTSCEEEEEEEECTT
T ss_pred             ccEEeccCCccccccchhhh-ccCCcceEEEecCcccch--hhccccccceeeEEEeecccc
Confidence            8888888888875  45666 888888888888887765  346777777  8888888776

>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*

Probab=99.90  E-value=5.9e-23  Score=231.75  Aligned_cols=304  Identities=13%  Similarity=0.089  Sum_probs=239.1

Q ss_pred             cccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc-cC-CccCCCCCcceEEeecCCCCCccC-hhh
Q 003387          487 CLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-QY-PSGIENLFLLRYLKLNIPSLNSLP-SSL  563 (824)
Q Consensus       487 ~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-~l-p~~i~~l~~Lr~L~L~~~~i~~lp-~~i  563 (824)
                      +|. +.+++++|.+.++...    ...+..|..+++|++|+|++|.+. .+ |..+.++++|++|+|++|.+..++ ..+
T Consensus        25 lp~-l~~~l~~L~Ls~n~i~----~~~~~~~~~l~~L~~L~L~~n~~~~~i~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~   99 (455)
T 3v47_A           25 VPE-LPAHVNYVDLSLNSIA----ELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQLETGAF   99 (455)
T ss_dssp             CCC-CCTTCCEEECCSSCCC----EECTTTTSSCTTCCEEECCCCSTTCEECTTTTTTCTTCCEEECTTCTTCEECTTTT
T ss_pred             CCC-CCCccCEEEecCCccC----cCChhHhccCccccEEECcCCcccceECcccccccccCCEEeCCCCccCccChhhc
Confidence            444 5689999999988764    345678899999999999999986 55 567899999999999999999774 455


Q ss_pred             hhcCCCccEeecCCccccc-cchh--hhccccCceecCCCccCCCCCCC-C-CCCCCCCCeeeccCCC--cchhhhcCCC
Q 003387          564 LSNLLNLYTLDMPFSYIDH-TADE--FWKMNKLRHLNFGSITLPAHPGK-F-CGSLENLNFISALHPC--CCTEDILGRL  636 (824)
Q Consensus       564 ~~~L~~L~~L~L~~~~l~~-lp~~--i~~L~~L~~L~L~~~~~~~~~~p-~-i~~L~~L~~l~~~~~~--~~~~~~l~~l  636 (824)
                       +++++|++|++++|.+.. .|..  +.++++|++|++++|.+.. ..| . ++++++|+.|+++.+.  ...+..+..+
T Consensus       100 -~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l  177 (455)
T 3v47_A          100 -NGLANLEVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKK-IQPASFFLNMRRFHVLDLTFNKVKSICEEDLLNF  177 (455)
T ss_dssp             -TTCTTCCEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSBCCS-CCCCGGGGGCTTCCEEECTTCCBSCCCTTTSGGG
T ss_pred             -cCcccCCEEeCCCCCCCccccCcccccCcccCCEEECCCCccCc-cCcccccCCCCcccEEeCCCCcccccChhhhhcc
Confidence             999999999999998886 4554  8899999999999999875 334 3 8999999999998432  1122224444


Q ss_pred             --CccceEEEecccccch------hhHHHHhccCCCCCeEEEeccC-------------CCCCccEEEeCccC-------
Q 003387          637 --PNLRNLRIRGDLSYNQ------SLLSKSLCRLSCLESLKLANES-------------KMPRLSKIVLAEYL-------  688 (824)
Q Consensus       637 --~~L~~L~l~~~~~~~~------~~l~~~l~~l~~L~~L~l~~~~-------------~~~~L~~l~l~~~~-------  688 (824)
                        .+|+.|+++++.-...      ......+..+++|++|++++|.             ..++++.+.+.++.       
T Consensus       178 ~~~~L~~L~l~~n~l~~~~~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~  257 (455)
T 3v47_A          178 QGKHFTLLRLSSITLQDMNEYWLGWEKCGNPFKNTSITTLDLSGNGFKESMAKRFFDAIAGTKIQSLILSNSYNMGSSFG  257 (455)
T ss_dssp             TTCEEEEEECTTCBCTTCSTTCTTHHHHCCTTTTCEEEEEECTTSCCCHHHHHHHHHHTTTCCEEEEECTTCTTTSCCTT
T ss_pred             ccccccccccccCcccccchhhccccccccccccceeeeEecCCCcccccchhhhhccccccceeeEeeccccccccccc
Confidence              6788999888752111      1112234466889999999863             23688888887651       


Q ss_pred             ---------------cCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCC
Q 003387          689 ---------------FPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWL  753 (824)
Q Consensus       689 ---------------~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l  753 (824)
                                     .+++|+.|++++|.+.+..+..++.+++|+.|++++|.+.+ ..+..+..+++|++|++++|. +
T Consensus       258 ~~~~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~-~~~~~~~~l~~L~~L~Ls~N~-l  335 (455)
T 3v47_A          258 HTNFKDPDNFTFKGLEASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINK-IDDNAFWGLTHLLKLNLSQNF-L  335 (455)
T ss_dssp             CCSSCCCCTTTTGGGTTSCCCEEECCSSCCCEECTTTTTTCTTCCEEECTTSCCCE-ECTTTTTTCTTCCEEECCSSC-C
T ss_pred             hhhhccCcccccccccccCceEEEecCccccccchhhcccCCCCCEEECCCCcccc-cChhHhcCcccCCEEECCCCc-c
Confidence                           23689999999999988888899999999999999998764 234456789999999999987 4


Q ss_pred             ccc-eeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          754 EEW-TMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       754 ~~l-~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ..+ +..++.+++|+.|++++|......|..+..+++|+.|++++|.
T Consensus       336 ~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~  382 (455)
T 3v47_A          336 GSIDSRMFENLDKLEVLDLSYNHIRALGDQSFLGLPNLKELALDTNQ  382 (455)
T ss_dssp             CEECGGGGTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC
T ss_pred             CCcChhHhcCcccCCEEECCCCcccccChhhccccccccEEECCCCc
Confidence            555 5567889999999999998655557789999999999999986

>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*

Probab=99.90  E-value=4.7e-23  Score=238.44  Aligned_cols=321  Identities=20%  Similarity=0.139  Sum_probs=211.4

Q ss_pred             CCCCeeEEEEEecCCCccc-cccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCcc-CCCCC
Q 003387          469 SPKKAKRLNAVEREGDFAC-LDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSG-IENLF  544 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~-~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~-i~~l~  544 (824)
                      .+..++++.+. ++....+ +..+  +++|++|.+.++...    ...+..|..+++|++|+|++|.+..+|.. +++++
T Consensus        24 ~~~~L~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~----~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~   98 (549)
T 2z81_A           24 LTAAMKSLDLS-FNKITYIGHGDLRACANLQVLILKSSRIN----TIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLS   98 (549)
T ss_dssp             CCTTCCEEECC-SSCCCEECSSTTSSCTTCCEEECTTSCCC----EECTTTTTTCTTCCEEECTTSCCCSCCHHHHTTCT
T ss_pred             CCCCccEEECc-CCccCccChhhhhcCCcccEEECCCCCcC----ccChhhccccccCCEEECCCCccCccCHHHhccCC
Confidence            34678888888 4444434 3444  888999998887653    34556788888999999999888876654 88888


Q ss_pred             cceEEeecCCCCCcc--ChhhhhcCCCccEeecCCcc-ccccc-hhhhccccCceecCCCccCCCCCCC-CCCCCCCCCe
Q 003387          545 LLRYLKLNIPSLNSL--PSSLLSNLLNLYTLDMPFSY-IDHTA-DEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNF  619 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~l--p~~i~~~L~~L~~L~L~~~~-l~~lp-~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~  619 (824)
                      +|++|++++|.+..+  |..+ +++++|++|++++|. +..+| ..+.++++|++|++++|.+.. ..| .++++++|+.
T Consensus        99 ~L~~L~Ls~n~l~~~~~~~~~-~~l~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~l~~l~~L~~  176 (549)
T 2z81_A           99 SLKYLNLMGNPYQTLGVTSLF-PNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRN-YQSQSLKSIRDIHH  176 (549)
T ss_dssp             TCCEEECTTCCCSSSCSSCSC-TTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCE-ECTTTTTTCSEEEE
T ss_pred             CCcEEECCCCcccccchhhhh-hccCCccEEECCCCccccccCHhhhhcccccCeeeccCCcccc-cChhhhhccccCce
Confidence            999999998888743  5556 888899999998885 77776 468888888888888887764 233 5655555444


Q ss_pred             eeccCCC--cchhhhcCCCCccceEEEeccccc-----------------------------------------------
Q 003387          620 ISALHPC--CCTEDILGRLPNLRNLRIRGDLSY-----------------------------------------------  650 (824)
Q Consensus       620 l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~-----------------------------------------------  650 (824)
                      |++..+.  ......+..+++|+.|+++++.-.                                               
T Consensus       177 L~l~~n~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~l~~~~~~~~~L~~l  256 (549)
T 2z81_A          177 LTLHLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDESFNELLKLLRYILELSEV  256 (549)
T ss_dssp             EEEECSBSTTHHHHHHHSTTTBSEEEEESCBCTTCCCCCCSSCCCCCCCCEEEEESCEEEHHHHHHHHGGGGGCTTCCEE
T ss_pred             EecccCcccccchhhHhhcccccEEEccCCccccccccccchhhhhhcccceeccccccchhHHHHHHHHhhhhcccccc
Confidence            4443110  000000111222222222221100                                               


Q ss_pred             ----------------------------------------------------------------chhhHHHHh-ccCCCC
Q 003387          651 ----------------------------------------------------------------NQSLLSKSL-CRLSCL  665 (824)
Q Consensus       651 ----------------------------------------------------------------~~~~l~~~l-~~l~~L  665 (824)
                                                                                      ....+|..+ ..+++|
T Consensus       257 ~l~~~~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~i~~~~~~~~l~~~~~~~~~L~~L~l~~n~l~~ip~~~~~~l~~L  336 (549)
T 2z81_A          257 EFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLFYDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSL  336 (549)
T ss_dssp             EEESCEEECCSCCCCCTTTCCCCCTTCCEEEEESCBCSCGGGSCCCCHHHHHSTTCCEEEEESSCCCCCCHHHHHHCTTC
T ss_pred             ccccccccccccccccchhhhhhhcccccccccccccchhhhcccchhhhhhcccceEEEeccCccccCCHHHHhcCccc
Confidence                                                                            001123333 356777


Q ss_pred             CeEEEeccC-------------CCCCccEEEeCcc------------CcCCCceEEEEEcccCCCCCcccccCCCCCCeE
Q 003387          666 ESLKLANES-------------KMPRLSKIVLAEY------------LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVL  720 (824)
Q Consensus       666 ~~L~l~~~~-------------~~~~L~~l~l~~~------------~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L  720 (824)
                      +.|++++|.             ..++|+.|.++++            ..+++|+.|++++|.+. .+|..++.+++|+.|
T Consensus       337 ~~L~Ls~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~l~~L~~L~Ls~N~l~-~lp~~~~~~~~L~~L  415 (549)
T 2z81_A          337 EFLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFH-PMPDSCQWPEKMRFL  415 (549)
T ss_dssp             CEEECCSSCCCHHHHHHHTCTTSSTTCCEEECTTSCCCCHHHHHHHGGGCTTCCEEECTTCCCC-CCCSCCCCCTTCCEE
T ss_pred             cEEEccCCccccccccchhhhhccccCcEEEccCCcccccccchhhhhcCCCCCEEECCCCCCc-cCChhhcccccccEE
Confidence            777777642             2356777777654            34677888888888775 556667777777777


Q ss_pred             EeeccccCCCe--e--------------eecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCcccc
Q 003387          721 KLKQNSYSGRK--L--------------TCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQL  784 (824)
Q Consensus       721 ~L~~~~~~~~~--~--------------~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l  784 (824)
                      ++++|.+..-.  +              ......+++|++|++++|. ++.+|. ...+++|+.|++++|......|..+
T Consensus       416 ~Ls~N~l~~l~~~~~~~L~~L~Ls~N~l~~~~~~l~~L~~L~Ls~N~-l~~ip~-~~~l~~L~~L~Ls~N~l~~~~~~~~  493 (549)
T 2z81_A          416 NLSSTGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNK-LKTLPD-ASLFPVLLVMKISRNQLKSVPDGIF  493 (549)
T ss_dssp             ECTTSCCSCCCTTSCTTCSEEECCSSCCSCCCCCCTTCCEEECCSSC-CSSCCC-GGGCTTCCEEECCSSCCCCCCTTGG
T ss_pred             ECCCCCcccccchhcCCceEEECCCCChhhhcccCChhcEEECCCCc-cCcCCC-cccCccCCEEecCCCccCCcCHHHH
Confidence            77777654210  0              0012367888888888875 667775 4578999999999997655455568


Q ss_pred             ccCccCcEEEecCCc
Q 003387          785 WYIKSLNKFDCWWPQ  799 (824)
Q Consensus       785 ~~l~~L~~L~l~~c~  799 (824)
                      ..+++|+.|++++||
T Consensus       494 ~~l~~L~~L~l~~N~  508 (549)
T 2z81_A          494 DRLTSLQKIWLHTNP  508 (549)
T ss_dssp             GGCTTCCEEECCSSC
T ss_pred             hcCcccCEEEecCCC
Confidence            999999999998887

>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*

Probab=99.89  E-value=7.9e-23  Score=236.53  Aligned_cols=306  Identities=17%  Similarity=0.128  Sum_probs=226.6

Q ss_pred             CcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccChh
Q 003387          484 DFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSS  562 (824)
Q Consensus       484 ~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~  562 (824)
                      ...+|..+.+++++|.+.++...    ...+..|..+++|++|+|++|.+..+| ..++++++|++|++++|.+..+|+.
T Consensus        17 l~~ip~~~~~~L~~L~Ls~n~l~----~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~   92 (549)
T 2z81_A           17 FTSIPSGLTAAMKSLDLSFNKIT----YIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSS   92 (549)
T ss_dssp             CSSCCSCCCTTCCEEECCSSCCC----EECSSTTSSCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCCSCCHH
T ss_pred             cccccccCCCCccEEECcCCccC----ccChhhhhcCCcccEEECCCCCcCccChhhccccccCCEEECCCCccCccCHH
Confidence            33466655789999999998764    244567899999999999999998555 6799999999999999999999988


Q ss_pred             hhhcCCCccEeecCCcccccc--chhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCC--cchhhhcCCCC
Q 003387          563 LLSNLLNLYTLDMPFSYIDHT--ADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPC--CCTEDILGRLP  637 (824)
Q Consensus       563 i~~~L~~L~~L~L~~~~l~~l--p~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~--~~~~~~l~~l~  637 (824)
                      .++++++|++|++++|.+..+  |..++++++|++|++++|.......+ .++++++|++|++..+.  ...+..++.++
T Consensus        93 ~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~l~~L~~L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~~l~  172 (549)
T 2z81_A           93 WFGPLSSLKYLNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIR  172 (549)
T ss_dssp             HHTTCTTCCEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTTTCS
T ss_pred             HhccCCCCcEEECCCCcccccchhhhhhccCCccEEECCCCccccccCHhhhhcccccCeeeccCCcccccChhhhhccc
Confidence            559999999999999988854  67799999999999999985432333 78999999999998322  22333488999


Q ss_pred             ccceEEEecccccchhhHHHH-hccCCCCCeEEEeccC-------------CCCCccEEEeCcc--------------Cc
Q 003387          638 NLRNLRIRGDLSYNQSLLSKS-LCRLSCLESLKLANES-------------KMPRLSKIVLAEY--------------LF  689 (824)
Q Consensus       638 ~L~~L~l~~~~~~~~~~l~~~-l~~l~~L~~L~l~~~~-------------~~~~L~~l~l~~~--------------~~  689 (824)
                      +|+.|+++.+.   ...++.. +..+++|+.|++++|.             ..++++.+.+.+.              ..
T Consensus       173 ~L~~L~l~~n~---~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~l~~~~~~  249 (549)
T 2z81_A          173 DIHHLTLHLSE---SAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDESFNELLKLLRY  249 (549)
T ss_dssp             EEEEEEEECSB---STTHHHHHHHSTTTBSEEEEESCBCTTCCCCCCSSCCCCCCCCEEEEESCEEEHHHHHHHHGGGGG
T ss_pred             cCceEecccCc---ccccchhhHhhcccccEEEccCCccccccccccchhhhhhcccceeccccccchhHHHHHHHHhhh
Confidence            99999999885   2334443 3567889999998753             1234444444322              01


Q ss_pred             -----------------------------------------------------------CCCceEEEEEcccCCCCCccc
Q 003387          690 -----------------------------------------------------------PHSLTHLSFSNTDLMDDPMPT  710 (824)
Q Consensus       690 -----------------------------------------------------------~~~L~~L~L~~~~l~~~~~~~  710 (824)
                                                                                 +++|+.|++++|.+. .+|..
T Consensus       250 ~~~L~~l~l~~~~~~~~~~~~~~~~~~~~~l~~L~~L~l~~~~i~~~~~~~~l~~~~~~~~~L~~L~l~~n~l~-~ip~~  328 (549)
T 2z81_A          250 ILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLFYDLSTVYSLLEKVKRITVENSKVF-LVPCS  328 (549)
T ss_dssp             CTTCCEEEEESCEEECCSCCCCCTTTCCCCCTTCCEEEEESCBCSCGGGSCCCCHHHHHSTTCCEEEEESSCCC-CCCHH
T ss_pred             hccccccccccccccccccccccchhhhhhhcccccccccccccchhhhcccchhhhhhcccceEEEeccCccc-cCCHH
Confidence                                                                       134566666666553 33444


Q ss_pred             c-cCCCCCCeEEeeccccCCCee--eecCCCCCCccEEeeccCCCCccce---eccCcccCccEEEEecCCCCCCCcccc
Q 003387          711 L-EKLPLLQVLKLKQNSYSGRKL--TCGSYGFPNLKVLHLKSMLWLEEWT---MGNAAMPKLECLIINPCAYLKKMPEQL  784 (824)
Q Consensus       711 l-~~l~~L~~L~L~~~~~~~~~~--~~~~~~~~~L~~L~L~~~~~l~~l~---~~~~~lp~L~~L~l~~c~~l~~lp~~l  784 (824)
                      + +.+++|+.|++++|.+.+...  ....+.+++|++|++++|. ++.++   ..+..+++|+.|++++|. ++.+|..+
T Consensus       329 ~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N~-l~~~~~~~~~~~~l~~L~~L~Ls~N~-l~~lp~~~  406 (549)
T 2z81_A          329 FSQHLKSLEFLDLSENLMVEEYLKNSACKGAWPSLQTLVLSQNH-LRSMQKTGEILLTLKNLTSLDISRNT-FHPMPDSC  406 (549)
T ss_dssp             HHHHCTTCCEEECCSSCCCHHHHHHHTCTTSSTTCCEEECTTSC-CCCHHHHHHHGGGCTTCCEEECTTCC-CCCCCSCC
T ss_pred             HHhcCccccEEEccCCccccccccchhhhhccccCcEEEccCCc-ccccccchhhhhcCCCCCEEECCCCC-CccCChhh
Confidence            3 468889999998887765221  1235678899999999876 55554   236778899999999885 55788888


Q ss_pred             ccCccCcEEEecCCc
Q 003387          785 WYIKSLNKFDCWWPQ  799 (824)
Q Consensus       785 ~~l~~L~~L~l~~c~  799 (824)
                      ..+++|+.|++++|.
T Consensus       407 ~~~~~L~~L~Ls~N~  421 (549)
T 2z81_A          407 QWPEKMRFLNLSSTG  421 (549)
T ss_dssp             CCCTTCCEEECTTSC
T ss_pred             cccccccEEECCCCC
Confidence            888888888888876

>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}

Probab=99.89  E-value=2.5e-22  Score=230.62  Aligned_cols=306  Identities=19%  Similarity=0.164  Sum_probs=198.7

Q ss_pred             eEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEeec
Q 003387          474 KRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLN  552 (824)
Q Consensus       474 r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~  552 (824)
                      +++.+. ++....+|..+.++++.|.+.++...    ...+..|..+++|++|+|++|.++.+ |..++++++|++|+|+
T Consensus         3 ~~l~ls-~n~l~~ip~~~~~~L~~L~Ls~n~i~----~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls   77 (520)
T 2z7x_B            3 FLVDRS-KNGLIHVPKDLSQKTTILNISQNYIS----ELWTSDILSLSKLRILIISHNRIQYLDISVFKFNQELEYLDLS   77 (520)
T ss_dssp             CEEECT-TSCCSSCCCSCCTTCSEEECCSSCCC----CCCHHHHTTCTTCCEEECCSSCCCEEEGGGGTTCTTCCEEECC
T ss_pred             ceEecC-CCCcccccccccccccEEECCCCccc----ccChhhccccccccEEecCCCccCCcChHHhhcccCCCEEecC
Confidence            345555 44444566655789999999998764    24567889999999999999999865 7789999999999999


Q ss_pred             CCCCCccChhhhhcCCCccEeecCCccccc--cchhhhccccCceecCCCccCCCCCCCCCCCCCCC--CeeeccCCCc-
Q 003387          553 IPSLNSLPSSLLSNLLNLYTLDMPFSYIDH--TADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL--NFISALHPCC-  627 (824)
Q Consensus       553 ~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~--lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L--~~l~~~~~~~-  627 (824)
                      +|.++.+|..   .+++|++|++++|.+..  +|..++++++|++|++++|.+...   .++.+++|  +.+++..+.. 
T Consensus        78 ~N~l~~lp~~---~l~~L~~L~L~~N~l~~~~~p~~~~~l~~L~~L~L~~n~l~~~---~~~~l~~L~L~~L~l~~n~l~  151 (520)
T 2z7x_B           78 HNKLVKISCH---PTVNLKHLDLSFNAFDALPICKEFGNMSQLKFLGLSTTHLEKS---SVLPIAHLNISKVLLVLGETY  151 (520)
T ss_dssp             SSCCCEEECC---CCCCCSEEECCSSCCSSCCCCGGGGGCTTCCEEEEEESSCCGG---GGGGGTTSCEEEEEEEECTTT
T ss_pred             CCceeecCcc---ccCCccEEeccCCccccccchhhhccCCcceEEEecCcccchh---hccccccceeeEEEeeccccc
Confidence            9999999875   79999999999998876  578899999999999999887532   22222222  3333321000 


Q ss_pred             ----c--------------------------------------------------------hhhhcCCCC----------
Q 003387          628 ----C--------------------------------------------------------TEDILGRLP----------  637 (824)
Q Consensus       628 ----~--------------------------------------------------------~~~~l~~l~----------  637 (824)
                          .                                                        ++. ++.++          
T Consensus       152 ~~~~~~~~l~~l~~~~l~l~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~~~-l~~l~~L~~L~l~~~  230 (520)
T 2z7x_B          152 GEKEDPEGLQDFNTESLHIVFPTNKEFHFILDVSVKTVANLELSNIKCVLEDNKCSYFLSILAK-LQTNPKLSNLTLNNI  230 (520)
T ss_dssp             TSSCCTTTTTTCCEEEEEEECCSSSCCCCCCCCCCTTCSEEEECCEEECCSTTTTHHHHHHHHG-GGGCTTCCEEEEEEE
T ss_pred             ccccccccccccccceEEEEeccCcchhhhhhhhhhcccceeeccccccccccccceeecchhh-hccccchhhcccccc
Confidence                0                                                        000 11112          


Q ss_pred             -----------------ccceEEEecccccchhhHHHHh-----------------------------------------
Q 003387          638 -----------------NLRNLRIRGDLSYNQSLLSKSL-----------------------------------------  659 (824)
Q Consensus       638 -----------------~L~~L~l~~~~~~~~~~l~~~l-----------------------------------------  659 (824)
                                       +|+.|+++++.  ..+.+|..+                                         
T Consensus       231 ~l~~~~~~~~~~~~~~~~L~~L~l~~n~--l~~~~p~~~~~~~~~~l~~L~~l~l~~n~~~~p~~~~~~~~~~~~L~~L~  308 (520)
T 2z7x_B          231 ETTWNSFIRILQLVWHTTVWYFSISNVK--LQGQLDFRDFDYSGTSLKALSIHQVVSDVFGFPQSYIYEIFSNMNIKNFT  308 (520)
T ss_dssp             EEEHHHHHHHHHHHHTSSCSEEEEEEEE--EESCCCCCCCCCCSCCCCEEEEEEEEECCCCSCTHHHHHHHHTCCCSEEE
T ss_pred             ccCHHHHHHHHHHhhhCcccEEEeeccc--ccCccccchhhcccccCceeEeccccccceecchhhhhcccccCceeEEE
Confidence                             33333333332  000111111                                         


Q ss_pred             ------------ccCCCCCeEEEeccC----------CCCCccEEEeCcc------------CcCCCceEEEEEcccCCC
Q 003387          660 ------------CRLSCLESLKLANES----------KMPRLSKIVLAEY------------LFPHSLTHLSFSNTDLMD  705 (824)
Q Consensus       660 ------------~~l~~L~~L~l~~~~----------~~~~L~~l~l~~~------------~~~~~L~~L~L~~~~l~~  705 (824)
                                  ..+++|++|++++|.          ..++|+.|.+.++            ..+++|++|++++|.+.+
T Consensus       309 l~~n~l~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~l~~L~~L~Ls~N~l~~  388 (520)
T 2z7x_B          309 VSGTRMVHMLCPSKISPFLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNSVSY  388 (520)
T ss_dssp             EESSCCCCCCCCSSCCCCCEEECCSSCCCTTTTTTCCCCSSCCEEECCSSCCCBHHHHHHHHTTCTTCCEEECCSSCCBC
T ss_pred             cCCCccccccchhhCCcccEEEeECCccChhhhhhhccCCCCCEEEccCCccCccccchHHHhhCCCCCEEECCCCcCCc
Confidence                        344555555555432          2334555554433            234556666666665544


Q ss_pred             CCcc-cccCCCCCCeEEeeccccCCCeeeecCCCC-CCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccc
Q 003387          706 DPMP-TLEKLPLLQVLKLKQNSYSGRKLTCGSYGF-PNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQ  783 (824)
Q Consensus       706 ~~~~-~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~-~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~  783 (824)
                      ..+. .+..+++|+.|++++|.+.+.. +   ..+ ++|++|++++|. +..+|.....+++|+.|++++|. ++.+|..
T Consensus       389 ~l~~~~~~~l~~L~~L~Ls~N~l~~~~-~---~~l~~~L~~L~Ls~N~-l~~ip~~~~~l~~L~~L~L~~N~-l~~l~~~  462 (520)
T 2z7x_B          389 DEKKGDCSWTKSLLSLNMSSNILTDTI-F---RCLPPRIKVLDLHSNK-IKSIPKQVVKLEALQELNVASNQ-LKSVPDG  462 (520)
T ss_dssp             CGGGCSCCCCTTCCEEECCSSCCCGGG-G---GSCCTTCCEEECCSSC-CCCCCGGGGGCTTCCEEECCSSC-CCCCCTT
T ss_pred             ccccchhccCccCCEEECcCCCCCcch-h---hhhcccCCEEECCCCc-ccccchhhhcCCCCCEEECCCCc-CCccCHH
Confidence            2332 2555566666666655554311 1   122 688888888875 66788777789999999999996 5578876


Q ss_pred             -cccCccCcEEEecCCc
Q 003387          784 -LWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       784 -l~~l~~L~~L~l~~c~  799 (824)
                       +..+++|+.|+++++|
T Consensus       463 ~~~~l~~L~~L~l~~N~  479 (520)
T 2z7x_B          463 IFDRLTSLQKIWLHTNP  479 (520)
T ss_dssp             TTTTCTTCCEEECCSSC
T ss_pred             HhccCCcccEEECcCCC
Confidence             8899999999999877

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.89  E-value=5.2e-23  Score=239.26  Aligned_cols=136  Identities=18%  Similarity=0.126  Sum_probs=116.5

Q ss_pred             cccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccChhh
Q 003387          485 FACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSSL  563 (824)
Q Consensus       485 ~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~i  563 (824)
                      ..+|..+.+.+++|.+.++...    ...+..|..+++|++|+|++|.++.+| ..++++++|++|+|++|.+..+|+..
T Consensus        20 ~~ip~~l~~~l~~L~Ls~n~l~----~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~   95 (570)
T 2z63_A           20 YKIPDNLPFSTKNLDLSFNPLR----HLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGA   95 (570)
T ss_dssp             SSCCSSSCSSCCEEECCSCCCC----EECTTTTTTCSSCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEECTTT
T ss_pred             cccCCCccccccEEEccCCccC----ccChhHhhCCCCceEEECCCCcCCccCcccccCchhCCEEeCcCCcCCccCHhh
Confidence            3456555778999999988764    244567899999999999999998664 56899999999999999999888655


Q ss_pred             hhcCCCccEeecCCccccccch-hhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccC
Q 003387          564 LSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALH  624 (824)
Q Consensus       564 ~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~  624 (824)
                      |+++++|++|++++|.+..+|. .++++++|++|++++|.+....+| .++++++|+.|+++.
T Consensus        96 ~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~l~~  158 (570)
T 2z63_A           96 FSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSS  158 (570)
T ss_dssp             TTTCTTCCEEECTTSCCCCSTTCSCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECTT
T ss_pred             hcCccccccccccccccccCCCccccccccccEEecCCCccceecChhhhcccCCCCEEeCcC
Confidence            5999999999999999999876 599999999999999998755567 899999999998873

>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}

Probab=99.89  E-value=6.6e-23  Score=220.14  Aligned_cols=232  Identities=21%  Similarity=0.174  Sum_probs=186.0

Q ss_pred             ccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecC
Q 003387          519 MFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNF  598 (824)
Q Consensus       519 ~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L  598 (824)
                      ....+++|+|+++.++.+|..++++++|++|+|++|.+..+|..+ +++++|++|+|++|.+..+|..++++++|++|++
T Consensus        79 ~~~~l~~L~L~~n~l~~lp~~l~~l~~L~~L~L~~n~l~~lp~~~-~~l~~L~~L~Ls~n~l~~lp~~l~~l~~L~~L~L  157 (328)
T 4fcg_A           79 TQPGRVALELRSVPLPQFPDQAFRLSHLQHMTIDAAGLMELPDTM-QQFAGLETLTLARNPLRALPASIASLNRLRELSI  157 (328)
T ss_dssp             TSTTCCEEEEESSCCSSCCSCGGGGTTCSEEEEESSCCCCCCSCG-GGGTTCSEEEEESCCCCCCCGGGGGCTTCCEEEE
T ss_pred             cccceeEEEccCCCchhcChhhhhCCCCCEEECCCCCccchhHHH-hccCCCCEEECCCCccccCcHHHhcCcCCCEEEC
Confidence            357899999999999999999999999999999999999999988 9999999999999999999999999999999999


Q ss_pred             CCccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCC
Q 003387          599 GSITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMP  677 (824)
Q Consensus       599 ~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~  677 (824)
                      ++|.... .+| .++..      .       ....+..+++|+.|+++++.   ...+|..+                  
T Consensus       158 ~~n~~~~-~~p~~~~~~------~-------~~~~~~~l~~L~~L~L~~n~---l~~lp~~l------------------  202 (328)
T 4fcg_A          158 RACPELT-ELPEPLAST------D-------ASGEHQGLVNLQSLRLEWTG---IRSLPASI------------------  202 (328)
T ss_dssp             EEETTCC-CCCSCSEEE------C--------CCCEEESTTCCEEEEEEEC---CCCCCGGG------------------
T ss_pred             CCCCCcc-ccChhHhhc------c-------chhhhccCCCCCEEECcCCC---cCcchHhh------------------
Confidence            9987653 333 22210      0       00114456666666666652   11222222                  


Q ss_pred             CccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccce
Q 003387          678 RLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWT  757 (824)
Q Consensus       678 ~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~  757 (824)
                                ..+++|++|+|++|.+. ..+..++.+++|+.|++++|.+.+ .++..++.+++|++|+|++|.....+|
T Consensus       203 ----------~~l~~L~~L~L~~N~l~-~l~~~l~~l~~L~~L~Ls~n~~~~-~~p~~~~~l~~L~~L~L~~n~~~~~~p  270 (328)
T 4fcg_A          203 ----------ANLQNLKSLKIRNSPLS-ALGPAIHHLPKLEELDLRGCTALR-NYPPIFGGRAPLKRLILKDCSNLLTLP  270 (328)
T ss_dssp             ----------GGCTTCCEEEEESSCCC-CCCGGGGGCTTCCEEECTTCTTCC-BCCCCTTCCCCCCEEECTTCTTCCBCC
T ss_pred             ----------cCCCCCCEEEccCCCCC-cCchhhccCCCCCEEECcCCcchh-hhHHHhcCCCCCCEEECCCCCchhhcc
Confidence                      34566777777777765 356678889999999999888766 355667889999999999998888888


Q ss_pred             eccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCC
Q 003387          758 MGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWP  798 (824)
Q Consensus       758 ~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c  798 (824)
                      ..++.+++|+.|++++|+.++.+|..+.++++|+.+.+...
T Consensus       271 ~~~~~l~~L~~L~L~~n~~~~~iP~~l~~L~~L~~l~l~~~  311 (328)
T 4fcg_A          271 LDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCIILVPPH  311 (328)
T ss_dssp             TTGGGCTTCCEEECTTCTTCCCCCGGGGGSCTTCEEECCGG
T ss_pred             hhhhcCCCCCEEeCCCCCchhhccHHHhhccCceEEeCCHH
Confidence            88899999999999999999999999999999999987653

>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}

Probab=99.89  E-value=1.1e-22  Score=237.32  Aligned_cols=269  Identities=14%  Similarity=0.123  Sum_probs=227.1

Q ss_pred             ccCcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCcee
Q 003387          519 MFKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHL  596 (824)
Q Consensus       519 ~~~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L  596 (824)
                      .++++++|+++++.+..+|.. +..+++|++|+|++|.+..+|+..|+.+++|++|+|++|.+..+|.. ++++++|++|
T Consensus        49 ~l~~l~~l~l~~~~l~~lp~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L  128 (597)
T 3oja_B           49 TLNNQKIVTFKNSTMRKLPAALLDSFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYLPPHVFQNVPLLTVL  128 (597)
T ss_dssp             GGCCCSEEEESSCEESEECTHHHHHCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEE
T ss_pred             cCCCceEEEeeCCCCCCcCHHHHccCCCCcEEECCCCCCCCCChHHhcCCCCCCEEECCCCcCCCCCHHHHcCCCCCCEE
Confidence            467899999999999988876 57799999999999999988874449999999999999999988765 7999999999


Q ss_pred             cCCCccCCCCCCC--CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEec
Q 003387          597 NFGSITLPAHPGK--FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLAN  672 (824)
Q Consensus       597 ~L~~~~~~~~~~p--~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~  672 (824)
                      ++++|.+.  .+|  .++++++|+.|+++.+  ....+..++.+++|+.|+++++.-.   .+  .+..+++|+.|++++
T Consensus       129 ~L~~n~l~--~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~---~~--~~~~l~~L~~L~l~~  201 (597)
T 3oja_B          129 VLERNDLS--SLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLT---HV--DLSLIPSLFHANVSY  201 (597)
T ss_dssp             ECCSSCCC--CCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECTTSCCS---BC--CGGGCTTCSEEECCS
T ss_pred             EeeCCCCC--CCCHHHhccCCCCCEEEeeCCcCCCCChhhhhcCCcCcEEECcCCCCC---Cc--Chhhhhhhhhhhccc
Confidence            99999987  455  4699999999999843  2233434889999999999988521   12  256788999999998


Q ss_pred             cC-----CCCCccEEEeCcc-------CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCC
Q 003387          673 ES-----KMPRLSKIVLAEY-------LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFP  740 (824)
Q Consensus       673 ~~-----~~~~L~~l~l~~~-------~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~  740 (824)
                      |.     .+++|+.|.+.++       ..+++|+.|+|++|.+.+  +..++.+++|+.|+|++|.+.+ ..+..++.++
T Consensus       202 n~l~~l~~~~~L~~L~ls~n~l~~~~~~~~~~L~~L~L~~n~l~~--~~~l~~l~~L~~L~Ls~N~l~~-~~~~~~~~l~  278 (597)
T 3oja_B          202 NLLSTLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHNNLTD--TAWLLNYPGLVEVDLSYNELEK-IMYHPFVKMQ  278 (597)
T ss_dssp             SCCSEEECCTTCSEEECCSSCCCEEECSCCSCCCEEECCSSCCCC--CGGGGGCTTCSEEECCSSCCCE-EESGGGTTCS
T ss_pred             CccccccCCchhheeeccCCcccccccccCCCCCEEECCCCCCCC--ChhhccCCCCCEEECCCCccCC-CCHHHhcCcc
Confidence            64     5668889988876       345789999999999865  5788999999999999998875 3455678899


Q ss_pred             CccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          741 NLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       741 ~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      +|++|+|++|. +..++.....+|+|+.|++++|+. ..+|..+..+++|+.|++++|+
T Consensus       279 ~L~~L~Ls~N~-l~~l~~~~~~l~~L~~L~Ls~N~l-~~i~~~~~~l~~L~~L~L~~N~  335 (597)
T 3oja_B          279 RLERLYISNNR-LVALNLYGQPIPTLKVLDLSHNHL-LHVERNQPQFDRLENLYLDHNS  335 (597)
T ss_dssp             SCCEEECTTSC-CCEEECSSSCCTTCCEEECCSSCC-CCCGGGHHHHTTCSEEECCSSC
T ss_pred             CCCEEECCCCC-CCCCCcccccCCCCcEEECCCCCC-CccCcccccCCCCCEEECCCCC
Confidence            99999999976 777888888899999999999975 5799889999999999999997

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.89  E-value=5.5e-22  Score=222.63  Aligned_cols=290  Identities=17%  Similarity=0.082  Sum_probs=172.9

Q ss_pred             CCeeEEEEEecCCCccccccc-CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEE
Q 003387          471 KKAKRLNAVEREGDFACLDDY-DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYL  549 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~~~~~~~-~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L  549 (824)
                      ..++++.+. ++....++... +++|+.|.+.++....    .   .+..+++|++|++++|.++.+|  ++++++|++|
T Consensus        42 ~~L~~L~Ls-~n~l~~~~~l~~l~~L~~L~Ls~n~l~~----~---~~~~l~~L~~L~Ls~N~l~~~~--~~~l~~L~~L  111 (457)
T 3bz5_A           42 ATLTSLDCH-NSSITDMTGIEKLTGLTKLICTSNNITT----L---DLSQNTNLTYLACDSNKLTNLD--VTPLTKLTYL  111 (457)
T ss_dssp             TTCCEEECC-SSCCCCCTTGGGCTTCSEEECCSSCCSC----C---CCTTCTTCSEEECCSSCCSCCC--CTTCTTCCEE
T ss_pred             CCCCEEEcc-CCCcccChhhcccCCCCEEEccCCcCCe----E---ccccCCCCCEEECcCCCCceee--cCCCCcCCEE
Confidence            455666666 33333343212 6666666666665432    1   1556666666666666666554  6666666666


Q ss_pred             eecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcch
Q 003387          550 KLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCT  629 (824)
Q Consensus       550 ~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~  629 (824)
                      ++++|.+..+|  + +++++|++|++++|.++.+|  ++.+++|++|++++|.... .+ .++.+++|+.|+++.+.-.-
T Consensus       112 ~L~~N~l~~l~--~-~~l~~L~~L~l~~N~l~~l~--l~~l~~L~~L~l~~n~~~~-~~-~~~~l~~L~~L~ls~n~l~~  184 (457)
T 3bz5_A          112 NCDTNKLTKLD--V-SQNPLLTYLNCARNTLTEID--VSHNTQLTELDCHLNKKIT-KL-DVTPQTQLTTLDCSFNKITE  184 (457)
T ss_dssp             ECCSSCCSCCC--C-TTCTTCCEEECTTSCCSCCC--CTTCTTCCEEECTTCSCCC-CC-CCTTCTTCCEEECCSSCCCC
T ss_pred             ECCCCcCCeec--C-CCCCcCCEEECCCCccceec--cccCCcCCEEECCCCCccc-cc-ccccCCcCCEEECCCCccce
Confidence            66666666664  4 66666666666666666654  5666666666666664322 11 45566666666666322111


Q ss_pred             hhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcc
Q 003387          630 EDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMP  709 (824)
Q Consensus       630 ~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~  709 (824)
                      .. +..+++|+.|+++++.-.   .+  .+..+++|+.|++++|    +++.+.   ...+++|+.|++++|.+.+..+ 
T Consensus       185 l~-l~~l~~L~~L~l~~N~l~---~~--~l~~l~~L~~L~Ls~N----~l~~ip---~~~l~~L~~L~l~~N~l~~~~~-  250 (457)
T 3bz5_A          185 LD-VSQNKLLNRLNCDTNNIT---KL--DLNQNIQLTFLDCSSN----KLTEID---VTPLTQLTYFDCSVNPLTELDV-  250 (457)
T ss_dssp             CC-CTTCTTCCEEECCSSCCS---CC--CCTTCTTCSEEECCSS----CCSCCC---CTTCTTCSEEECCSSCCSCCCC-
T ss_pred             ec-cccCCCCCEEECcCCcCC---ee--ccccCCCCCEEECcCC----cccccC---ccccCCCCEEEeeCCcCCCcCH-
Confidence            22 556666666666665311   11  2556666667766655    233322   3556788888888887766443 


Q ss_pred             cccCCCCCCeE----------EeeccccCCCeeeecCCCCCCccEEeeccCCCCccceec--------cCcccCccEEEE
Q 003387          710 TLEKLPLLQVL----------KLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMG--------NAAMPKLECLII  771 (824)
Q Consensus       710 ~l~~l~~L~~L----------~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~--------~~~lp~L~~L~l  771 (824)
                        +.+++|+.|          ++++|.+.+ .++  .+.+++|+.|++++|..+..+|..        +..+|+|+.|++
T Consensus       251 --~~l~~L~~L~l~~n~L~~L~l~~n~~~~-~~~--~~~l~~L~~L~Ls~n~~l~~l~~~~~~L~~L~l~~~~~L~~L~L  325 (457)
T 3bz5_A          251 --STLSKLTTLHCIQTDLLEIDLTHNTQLI-YFQ--AEGCRKIKELDVTHNTQLYLLDCQAAGITELDLSQNPKLVYLYL  325 (457)
T ss_dssp             --TTCTTCCEEECTTCCCSCCCCTTCTTCC-EEE--CTTCTTCCCCCCTTCTTCCEEECTTCCCSCCCCTTCTTCCEEEC
T ss_pred             --HHCCCCCEEeccCCCCCEEECCCCccCC-ccc--ccccccCCEEECCCCcccceeccCCCcceEechhhcccCCEEEC
Confidence              344444444          444443333 122  466788999999888777666532        445677888888


Q ss_pred             ecCCCCCCCccccccCccCcEEEecCCc
Q 003387          772 NPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       772 ~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ++|.. +.++  +.++++|+.|+++++.
T Consensus       326 ~~N~l-~~l~--l~~l~~L~~L~l~~N~  350 (457)
T 3bz5_A          326 NNTEL-TELD--VSHNTKLKSLSCVNAH  350 (457)
T ss_dssp             TTCCC-SCCC--CTTCTTCSEEECCSSC
T ss_pred             CCCcc-cccc--cccCCcCcEEECCCCC
Confidence            87764 3454  7788999999988775

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=99.88  E-value=3.6e-22  Score=237.21  Aligned_cols=317  Identities=18%  Similarity=0.104  Sum_probs=155.3

Q ss_pred             CCCeeEEEEEecCCCccccc-cc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCc
Q 003387          470 PKKAKRLNAVEREGDFACLD-DY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFL  545 (824)
Q Consensus       470 ~~~~r~lsl~~~~~~~~~~~-~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~  545 (824)
                      +.++++|.+. ++....++. .+  +++|++|.+.++...    ...+..|..+++|++|+|++|.++.+|. .++++++
T Consensus        24 ~~~l~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~----~~~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~   98 (680)
T 1ziw_A           24 PTNITVLNLT-HNQLRRLPAANFTRYSQLTSLDVGFNTIS----KLEPELCQKLPMLKVLNLQHNELSQLSDKTFAFCTN   98 (680)
T ss_dssp             CTTCSEEECC-SSCCCCCCGGGGGGGTTCSEEECCSSCCC----CCCTTHHHHCTTCCEEECCSSCCCCCCTTTTTTCTT
T ss_pred             CCCCcEEECC-CCCCCCcCHHHHhCCCcCcEEECCCCccC----ccCHHHHhcccCcCEEECCCCccCccChhhhccCCC
Confidence            3455555555 333322322 22  555555555554432    1233445555555555555555555554 3555555


Q ss_pred             ceEEeecCCCCCccChhhhhcCCCccEeecCCcccccc-chhhhccccCceecCCCccCCCCCCC-C--CCCCCCCCeee
Q 003387          546 LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGSITLPAHPGK-F--CGSLENLNFIS  621 (824)
Q Consensus       546 Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~~~~~~~~~p-~--i~~L~~L~~l~  621 (824)
                      |++|++++|.+..+|+..|+++++|++|++++|.+... |..++++++|++|++++|.+.. ..+ .  ...+++|+.|+
T Consensus        99 L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~~~~~~~~~L~~L~  177 (680)
T 1ziw_A           99 LTELHLMSNSIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQVQLENLQELLLSNNKIQA-LKSEELDIFANSSLKKLE  177 (680)
T ss_dssp             CSEEECCSSCCCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEECCSSCCCC-BCHHHHGGGTTCEESEEE
T ss_pred             CCEEECCCCccCccChhHccccCCCCEEECCCCcccccCchhhcccccCCEEEccCCcccc-cCHHHhhccccccccEEE
Confidence            55555555555555533225555555555555554443 2334555555555555555442 111 1  22334555555


Q ss_pred             ccCC--CcchhhhcCCCCccceEEEeccccc--chhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcC--CCceE
Q 003387          622 ALHP--CCCTEDILGRLPNLRNLRIRGDLSY--NQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFP--HSLTH  695 (824)
Q Consensus       622 ~~~~--~~~~~~~l~~l~~L~~L~l~~~~~~--~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~--~~L~~  695 (824)
                      ++.+  ....+..+..+++|+.|.+.++.-.  ....++..+ ..++|+.|+++++.    +.......+..+  ++|+.
T Consensus       178 L~~n~l~~~~~~~~~~l~~L~~L~l~~~~l~~~~~~~~~~~l-~~~~L~~L~L~~n~----l~~~~~~~~~~l~~~~L~~  252 (680)
T 1ziw_A          178 LSSNQIKEFSPGCFHAIGRLFGLFLNNVQLGPSLTEKLCLEL-ANTSIRNLSLSNSQ----LSTTSNTTFLGLKWTNLTM  252 (680)
T ss_dssp             CTTCCCCCBCTTGGGGSSEECEEECTTCCCHHHHHHHHHHHH-TTSCCCEEECTTSC----CCEECTTTTGGGGGSCCCE
T ss_pred             CCCCcccccChhhhhhhhhhhhhhccccccChhhHHHHHHHh-hhccccEEEccCCc----ccccChhHhhccCcCCCCE
Confidence            5421  1111222444555555555444210  011111111 23556666665541    222211112222  23777


Q ss_pred             EEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCc-----ccee----ccCcccCc
Q 003387          696 LSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLE-----EWTM----GNAAMPKL  766 (824)
Q Consensus       696 L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~-----~l~~----~~~~lp~L  766 (824)
                      |++++|.+.+..+..++.+++|+.|++++|.+.+ ..+..+.++++|++|+++++....     .+|.    .+..+++|
T Consensus       253 L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~lp~i~~~~~~~l~~L  331 (680)
T 1ziw_A          253 LDLSYNNLNVVGNDSFAWLPQLEYFFLEYNNIQH-LFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQWLKCL  331 (680)
T ss_dssp             EECTTSCCCEECTTTTTTCTTCCEEECCSCCBSE-ECTTTTTTCTTCCEEECTTCBCCC------CCEECTTTTTTCTTC
T ss_pred             EECCCCCcCccCcccccCcccccEeeCCCCccCc-cChhhhcCCCCccEEeccchhhhcccccccccccChhhcccCCCC
Confidence            7777776665555666677777777777665543 223344566667777666543111     1221    34456666


Q ss_pred             cEEEEecCCCCCCCccccccCccCcEEEecCC
Q 003387          767 ECLIINPCAYLKKMPEQLWYIKSLNKFDCWWP  798 (824)
Q Consensus       767 ~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c  798 (824)
                      +.|++++|......|..+..+++|+.|++++|
T Consensus       332 ~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n  363 (680)
T 1ziw_A          332 EHLNMEDNDIPGIKSNMFTGLINLKYLSLSNS  363 (680)
T ss_dssp             CEEECCSCCBCCCCTTTTTTCTTCCEEECTTC
T ss_pred             CEEECCCCccCCCChhHhccccCCcEEECCCC
Confidence            66666666644434445566666666666655

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=99.88  E-value=6.3e-22  Score=224.68  Aligned_cols=270  Identities=17%  Similarity=0.114  Sum_probs=222.4

Q ss_pred             CcccEEEeeCccCccC-CccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecC
Q 003387          521 KLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNF  598 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L  598 (824)
                      +.|++|+|++|.++.+ |..+.++++|++|+|++|.+..+++..|+++++|++|+|++|.+..+|.. +.++++|++|++
T Consensus        32 ~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L  111 (477)
T 2id5_A           32 TETRLLDLGKNRIKTLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKLIPLGVFTGLSNLTKLDI  111 (477)
T ss_dssp             TTCSEEECCSSCCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCSCCTTSSTTCTTCCEEEC
T ss_pred             CCCcEEECCCCccceECHhHccCCCCCCEEECCCCccCEeChhhhhCCccCCEEECCCCcCCccCcccccCCCCCCEEEC
Confidence            5799999999999966 56799999999999999999988544449999999999999999999875 789999999999


Q ss_pred             CCccCCCCCCC-CCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCC
Q 003387          599 GSITLPAHPGK-FCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESK  675 (824)
Q Consensus       599 ~~~~~~~~~~p-~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~  675 (824)
                      ++|.+.. ..| .++++++|+.|+++.+.  ......+..+++|+.|+++++.  .....+..+.++++|+.|++++|  
T Consensus       112 s~n~i~~-~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~--l~~~~~~~l~~l~~L~~L~l~~n--  186 (477)
T 2id5_A          112 SENKIVI-LLDYMFQDLYNLKSLEVGDNDLVYISHRAFSGLNSLEQLTLEKCN--LTSIPTEALSHLHGLIVLRLRHL--  186 (477)
T ss_dssp             TTSCCCE-ECTTTTTTCTTCCEEEECCTTCCEECTTSSTTCTTCCEEEEESCC--CSSCCHHHHTTCTTCCEEEEESC--
T ss_pred             CCCcccc-CChhHccccccCCEEECCCCccceeChhhccCCCCCCEEECCCCc--CcccChhHhcccCCCcEEeCCCC--
Confidence            9998874 344 88999999999998432  2223348889999999999985  33334567889999999999986  


Q ss_pred             CCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcc
Q 003387          676 MPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEE  755 (824)
Q Consensus       676 ~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~  755 (824)
                        .+..+....+..+++|+.|++++|...+..+......++|+.|++++|.+... ....+..+++|++|+|++|. +..
T Consensus       187 --~i~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~-~~~~~~~l~~L~~L~Ls~n~-l~~  262 (477)
T 2id5_A          187 --NINAIRDYSFKRLYRLKVLEISHWPYLDTMTPNCLYGLNLTSLSITHCNLTAV-PYLAVRHLVYLRFLNLSYNP-IST  262 (477)
T ss_dssp             --CCCEECTTCSCSCTTCCEEEEECCTTCCEECTTTTTTCCCSEEEEESSCCCSC-CHHHHTTCTTCCEEECCSSC-CCE
T ss_pred             --cCcEeChhhcccCcccceeeCCCCccccccCcccccCccccEEECcCCccccc-CHHHhcCccccCeeECCCCc-CCc
Confidence              46666555667889999999999987777777777777999999999987742 22346789999999999987 555


Q ss_pred             ce-eccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          756 WT-MGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       756 l~-~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ++ ..+..+++|+.|++++|......|..+..+++|+.|++++|.
T Consensus       263 ~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~  307 (477)
T 2id5_A          263 IEGSMLHELLRLQEIQLVGGQLAVVEPYAFRGLNYLRVLNVSGNQ  307 (477)
T ss_dssp             ECTTSCTTCTTCCEEECCSSCCSEECTTTBTTCTTCCEEECCSSC
T ss_pred             cChhhccccccCCEEECCCCccceECHHHhcCcccCCEEECCCCc
Confidence            54 346789999999999998666567789999999999999985

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=99.88  E-value=4.1e-22  Score=236.72  Aligned_cols=321  Identities=16%  Similarity=0.060  Sum_probs=209.3

Q ss_pred             CCCeeEEEEEecCCCccc-cccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCCc
Q 003387          470 PKKAKRLNAVEREGDFAC-LDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFL  545 (824)
Q Consensus       470 ~~~~r~lsl~~~~~~~~~-~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~  545 (824)
                      ..+++++.+. ++..... +..+  +++|++|.+.++...    ..++..|..+++|++|+|++|.+..+| ..++++++
T Consensus        48 l~~L~~L~Ls-~n~l~~~~~~~~~~l~~L~~L~L~~n~l~----~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~  122 (680)
T 1ziw_A           48 YSQLTSLDVG-FNTISKLEPELCQKLPMLKVLNLQHNELS----QLSDKTFAFCTNLTELHLMSNSIQKIKNNPFVKQKN  122 (680)
T ss_dssp             GTTCSEEECC-SSCCCCCCTTHHHHCTTCCEEECCSSCCC----CCCTTTTTTCTTCSEEECCSSCCCCCCSCTTTTCTT
T ss_pred             CCcCcEEECC-CCccCccCHHHHhcccCcCEEECCCCccC----ccChhhhccCCCCCEEECCCCccCccChhHccccCC
Confidence            3578999998 4444334 4444  999999999988764    245567899999999999999999776 57999999


Q ss_pred             ceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hh--ccccCceecCCCccCCCCCCC-CCCCCC------
Q 003387          546 LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FW--KMNKLRHLNFGSITLPAHPGK-FCGSLE------  615 (824)
Q Consensus       546 Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~--~L~~L~~L~L~~~~~~~~~~p-~i~~L~------  615 (824)
                      |++|++++|.+...+...++++++|++|++++|.+..++.. +.  .+++|++|++++|.+.. ..| .++.+.      
T Consensus       123 L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~~~L~~L~L~~n~l~~-~~~~~~~~l~~L~~L~  201 (680)
T 1ziw_A          123 LITLDLSHNGLSSTKLGTQVQLENLQELLLSNNKIQALKSEELDIFANSSLKKLELSSNQIKE-FSPGCFHAIGRLFGLF  201 (680)
T ss_dssp             CCEEECCSSCCSCCCCCSSSCCTTCCEEECCSSCCCCBCHHHHGGGTTCEESEEECTTCCCCC-BCTTGGGGSSEECEEE
T ss_pred             CCEEECCCCcccccCchhhcccccCCEEEccCCcccccCHHHhhccccccccEEECCCCcccc-cChhhhhhhhhhhhhh
Confidence            99999999999877655448999999999999999888654 43  56899999999998764 223 444443      


Q ss_pred             ---------------------CCCeeeccCCC--cchhhhcCCCCc--cceEEEecccccchhhHHHHhccCCCCCeEEE
Q 003387          616 ---------------------NLNFISALHPC--CCTEDILGRLPN--LRNLRIRGDLSYNQSLLSKSLCRLSCLESLKL  670 (824)
Q Consensus       616 ---------------------~L~~l~~~~~~--~~~~~~l~~l~~--L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l  670 (824)
                                           +|+.|+++.+.  ...+..+..++.  |+.|+++++.  .....+..+..+++|++|++
T Consensus       202 l~~~~l~~~~~~~~~~~l~~~~L~~L~L~~n~l~~~~~~~~~~l~~~~L~~L~Ls~n~--l~~~~~~~~~~l~~L~~L~L  279 (680)
T 1ziw_A          202 LNNVQLGPSLTEKLCLELANTSIRNLSLSNSQLSTTSNTTFLGLKWTNLTMLDLSYNN--LNVVGNDSFAWLPQLEYFFL  279 (680)
T ss_dssp             CTTCCCHHHHHHHHHHHHTTSCCCEEECTTSCCCEECTTTTGGGGGSCCCEEECTTSC--CCEECTTTTTTCTTCCEEEC
T ss_pred             ccccccChhhHHHHHHHhhhccccEEEccCCcccccChhHhhccCcCCCCEEECCCCC--cCccCcccccCcccccEeeC
Confidence                                 34455544211  111222444543  8888888774  22333456777888888888


Q ss_pred             eccC----------CCCCccEEEeCc-------------------cCcCCCceEEEEEcccCCCCCcccccCCCCCCeEE
Q 003387          671 ANES----------KMPRLSKIVLAE-------------------YLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLK  721 (824)
Q Consensus       671 ~~~~----------~~~~L~~l~l~~-------------------~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~  721 (824)
                      ++|.          .+++|+.+.+.+                   +..+++|++|++++|.+.+..+..+.++++|++|+
T Consensus       280 ~~n~l~~~~~~~~~~l~~L~~L~L~~~~~~~~~~~~~lp~i~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~  359 (680)
T 1ziw_A          280 EYNNIQHLFSHSLHGLFNVRYLNLKRSFTKQSISLASLPKIDDFSFQWLKCLEHLNMEDNDIPGIKSNMFTGLINLKYLS  359 (680)
T ss_dssp             CSCCBSEECTTTTTTCTTCCEEECTTCBCCC------CCEECTTTTTTCTTCCEEECCSCCBCCCCTTTTTTCTTCCEEE
T ss_pred             CCCccCccChhhhcCCCCccEEeccchhhhcccccccccccChhhcccCCCCCEEECCCCccCCCChhHhccccCCcEEE
Confidence            8753          345677777653                   24578899999999998887777889999999999


Q ss_pred             eeccccCCCeeeecC---CCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCc-cccccCccCcEEEecC
Q 003387          722 LKQNSYSGRKLTCGS---YGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMP-EQLWYIKSLNKFDCWW  797 (824)
Q Consensus       722 L~~~~~~~~~~~~~~---~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp-~~l~~l~~L~~L~l~~  797 (824)
                      +++|.+....+....   ...++|+.|++++|......+..+..+++|+.|++++|.....+| ..+..+++|+.|++++
T Consensus       360 Ls~n~~~~~~l~~~~f~~~~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~l~~L~~L~Ls~  439 (680)
T 1ziw_A          360 LSNSFTSLRTLTNETFVSLAHSPLHILNLTKNKISKIESDAFSWLGHLEVLDLGLNEIGQELTGQEWRGLENIFEIYLSY  439 (680)
T ss_dssp             CTTCBSCCCEECTTTTGGGTTSCCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCEEECCSGGGTTCTTCCEEECCS
T ss_pred             CCCCchhhhhcchhhhcccccCcCceEECCCCCCCeEChhhhhCCCCCCEEeCCCCcCccccCcccccCcccccEEecCC
Confidence            987764332221100   011344555554443222222233344444444444444332232 2333344444444444


Q ss_pred             C
Q 003387          798 P  798 (824)
Q Consensus       798 c  798 (824)
                      |
T Consensus       440 n  440 (680)
T 1ziw_A          440 N  440 (680)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.88  E-value=4.6e-23  Score=220.03  Aligned_cols=248  Identities=16%  Similarity=0.185  Sum_probs=144.0

Q ss_pred             CceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeC-ccCc-cCCccCCCCCcceEEeecCCCCC-ccChhhhhcCCC
Q 003387          493 SQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGS-LVLI-QYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLLN  569 (824)
Q Consensus       493 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~-~~i~-~lp~~i~~l~~Lr~L~L~~~~i~-~lp~~i~~~L~~  569 (824)
                      .+++.|.+.++....  ....+..+..+++|++|++++ +.+. .+|..++++++|++|++++|.+. .+|..+ +++++
T Consensus        50 ~~l~~L~L~~~~l~~--~~~~~~~l~~l~~L~~L~L~~~n~l~~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~-~~l~~  126 (313)
T 1ogq_A           50 YRVNNLDLSGLNLPK--PYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFL-SQIKT  126 (313)
T ss_dssp             CCEEEEEEECCCCSS--CEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGG-GGCTT
T ss_pred             ceEEEEECCCCCccC--CcccChhHhCCCCCCeeeCCCCCcccccCChhHhcCCCCCEEECcCCeeCCcCCHHH-hCCCC
Confidence            456666666554421  002234555666666666663 5544 55666666666666666666665 555555 66666


Q ss_pred             ccEeecCCcccc-ccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCC-ccceEEEecc
Q 003387          570 LYTLDMPFSYID-HTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLP-NLRNLRIRGD  647 (824)
Q Consensus       570 L~~L~L~~~~l~-~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~-~L~~L~l~~~  647 (824)
                      |++|++++|.+. .+|..+..+++|++|++++|.+.+                     ..+.. +..++ +|+.|+++++
T Consensus       127 L~~L~Ls~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~---------------------~~p~~-l~~l~~~L~~L~L~~N  184 (313)
T 1ogq_A          127 LVTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISG---------------------AIPDS-YGSFSKLFTSMTISRN  184 (313)
T ss_dssp             CCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEE---------------------ECCGG-GGCCCTTCCEEECCSS
T ss_pred             CCEEeCCCCccCCcCChHHhcCCCCCeEECcCCcccC---------------------cCCHH-HhhhhhcCcEEECcCC
Confidence            666666666555 455566666666666666665431                     11122 55555 6666666665


Q ss_pred             cccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeecccc
Q 003387          648 LSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSY  727 (824)
Q Consensus       648 ~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~  727 (824)
                      .  .....|..+..++                             |+.|++++|.+.+..+..++.+++|+.|++++|.+
T Consensus       185 ~--l~~~~~~~~~~l~-----------------------------L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l  233 (313)
T 1ogq_A          185 R--LTGKIPPTFANLN-----------------------------LAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSL  233 (313)
T ss_dssp             E--EEEECCGGGGGCC-----------------------------CSEEECCSSEEEECCGGGCCTTSCCSEEECCSSEE
T ss_pred             e--eeccCChHHhCCc-----------------------------ccEEECcCCcccCcCCHHHhcCCCCCEEECCCCce
Confidence            3  2222333333332                             55556666655555566666777777777776666


Q ss_pred             CCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          728 SGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       728 ~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      .+.  ......+++|++|++++|.....+|..+..+++|+.|++++|+....+|.. .++++|+.+++.++|
T Consensus       234 ~~~--~~~~~~l~~L~~L~Ls~N~l~~~~p~~l~~l~~L~~L~Ls~N~l~~~ip~~-~~l~~L~~l~l~~N~  302 (313)
T 1ogq_A          234 AFD--LGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQG-GNLQRFDVSAYANNK  302 (313)
T ss_dssp             CCB--GGGCCCCTTCCEEECCSSCCEECCCGGGGGCTTCCEEECCSSEEEEECCCS-TTGGGSCGGGTCSSS
T ss_pred             eee--cCcccccCCCCEEECcCCcccCcCChHHhcCcCCCEEECcCCcccccCCCC-ccccccChHHhcCCC
Confidence            542  222455677777777776643355666667777777777777665566654 667777777777665

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.88  E-value=4.5e-22  Score=241.44  Aligned_cols=316  Identities=22%  Similarity=0.186  Sum_probs=217.0

Q ss_pred             CCCCeeEEEEEecCCCccc-cccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCC
Q 003387          469 SPKKAKRLNAVEREGDFAC-LDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLF  544 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~-~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~  544 (824)
                      .+.++++|.+. ++....+ +..+  +++|++|.+.++...   ..+.+..|..+++|++|+|++|.+..+ |..+++++
T Consensus        22 lp~~l~~LdLs-~N~i~~i~~~~~~~l~~L~~LdLs~n~~~---~~i~~~~f~~L~~L~~L~Ls~N~l~~~~p~~~~~l~   97 (844)
T 3j0a_A           22 VLNTTERLLLS-FNYIRTVTASSFPFLEQLQLLELGSQYTP---LTIDKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLF   97 (844)
T ss_dssp             SCTTCCEEEEE-SCCCCEECSSSCSSCCSCSEEEECTTCCC---CEECTTTTSSCTTCCEEECTTCCCCEECTTSSCSCS
T ss_pred             CCCCcCEEECC-CCcCCccChhHCcccccCeEEeCCCCCCc---cccCHHHhcCCCCCCEEECCCCcCcccCHhHccCCc
Confidence            56788899888 5444433 4444  888999998887542   334467788899999999999988844 77888899


Q ss_pred             cceEEeecCCCCCc-cChh-hhhcCCCccEeecCCccccccc--hhhhccccCceecCCCccCCCCCCC-CCCCC--CCC
Q 003387          545 LLRYLKLNIPSLNS-LPSS-LLSNLLNLYTLDMPFSYIDHTA--DEFWKMNKLRHLNFGSITLPAHPGK-FCGSL--ENL  617 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~-lp~~-i~~~L~~L~~L~L~~~~l~~lp--~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L--~~L  617 (824)
                      +|++|+|++|.+.. +|.. .++++++|++|+|++|.+..++  ..++++++|++|++++|.+.. ..| .++.+  ++|
T Consensus        98 ~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~N~i~~-~~~~~l~~l~~~~L  176 (844)
T 3j0a_A           98 HLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSNQIFL-VCEHELEPLQGKTL  176 (844)
T ss_dssp             SCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEESSCCCC-CCSGGGHHHHHCSS
T ss_pred             ccCEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHhhCCCCCEEECCCCcCCe-eCHHHcccccCCcc
Confidence            99999999988875 4544 2388999999999998877663  568889999999998888764 333 66666  678


Q ss_pred             CeeeccCCC---cchhhhcCCCCc------cceEEEecccccchhhHHHHhc---cCCCCCeEEEeccC-----------
Q 003387          618 NFISALHPC---CCTEDILGRLPN------LRNLRIRGDLSYNQSLLSKSLC---RLSCLESLKLANES-----------  674 (824)
Q Consensus       618 ~~l~~~~~~---~~~~~~l~~l~~------L~~L~l~~~~~~~~~~l~~~l~---~l~~L~~L~l~~~~-----------  674 (824)
                      +.|+++.+.   ..... ++.+++      |+.|+++++.  .....+..+.   ...++..|.+..+.           
T Consensus       177 ~~L~L~~n~l~~~~~~~-~~~~~~~~~~~~L~~L~Ls~n~--l~~~~~~~~~~~l~~~~l~~L~l~~~~~~~~~~~~~l~  253 (844)
T 3j0a_A          177 SFFSLAANSLYSRVSVD-WGKCMNPFRNMVLEILDVSGNG--WTVDITGNFSNAISKSQAFSLILAHHIMGAGFGFHNIK  253 (844)
T ss_dssp             CCCEECCSBSCCCCCCC-CCSSSCTTTTCCBSEEBCSSCC--SSTTTTSGGGGTSCSCCBSEEECCSSCCBCSSSCSSST
T ss_pred             ceEECCCCccccccccc-hhhcCCccccCceeEEecCCCc--CchhHHHHHHhhcCcccccceecccccccccccccccC
Confidence            888777321   11122 344443      8889888774  1111121111   11344444443100           


Q ss_pred             ----------CCCCccEEEeCc----------cCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeee
Q 003387          675 ----------KMPRLSKIVLAE----------YLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTC  734 (824)
Q Consensus       675 ----------~~~~L~~l~l~~----------~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~  734 (824)
                                .+++++.|.+++          +..+++|+.|+|++|.+.+..+..++.+++|+.|++++|.+.. ..+.
T Consensus       254 ~~~~~~f~~l~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~N~l~~-~~~~  332 (844)
T 3j0a_A          254 DPDQNTFAGLARSSVRHLDLSHGFVFSLNSRVFETLKDLKVLNLAYNKINKIADEAFYGLDNLQVLNLSYNLLGE-LYSS  332 (844)
T ss_dssp             TGGGTTTTTTTTSCCCEEECTTCCCCEECSCCSSSCCCCCEEEEESCCCCEECTTTTTTCSSCCEEEEESCCCSC-CCSC
T ss_pred             CCChhhhhccccCCccEEECCCCcccccChhhhhcCCCCCEEECCCCcCCCCChHHhcCCCCCCEEECCCCCCCc-cCHH
Confidence                      123444444443          3567889999999998877777788889999999999887764 2344


Q ss_pred             cCCCCCCccEEeeccCCCCcccee-ccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          735 GSYGFPNLKVLHLKSMLWLEEWTM-GNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       735 ~~~~~~~L~~L~L~~~~~l~~l~~-~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      .+..+++|++|++++|. +..++. .+..+++|+.|++++|.. ..++    .+++|+.|.+++|.
T Consensus       333 ~~~~l~~L~~L~L~~N~-i~~~~~~~~~~l~~L~~L~Ls~N~l-~~i~----~~~~L~~L~l~~N~  392 (844)
T 3j0a_A          333 NFYGLPKVAYIDLQKNH-IAIIQDQTFKFLEKLQTLDLRDNAL-TTIH----FIPSIPDIFLSGNK  392 (844)
T ss_dssp             SCSSCTTCCEEECCSCC-CCCCCSSCSCSCCCCCEEEEETCCS-CCCS----SCCSCSEEEEESCC
T ss_pred             HhcCCCCCCEEECCCCC-CCccChhhhcCCCCCCEEECCCCCC-Cccc----CCCCcchhccCCCC
Confidence            56788899999999875 555543 466789999999998873 4444    36778888887775

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.88  E-value=1.2e-21  Score=237.55  Aligned_cols=108  Identities=20%  Similarity=0.081  Sum_probs=51.7

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc-cCCcc--CCCCCcceEEeecCCCCCccC--hhhhhc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-QYPSG--IENLFLLRYLKLNIPSLNSLP--SSLLSN  566 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-~lp~~--i~~l~~Lr~L~L~~~~i~~lp--~~i~~~  566 (824)
                      +++|++|.+.++...    ...+..|..+++|++|+|++|.+. .+|..  ++++++|++|+|++|.+..++  ..+ ++
T Consensus        72 L~~L~~L~Ls~N~l~----~~~p~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~-~~  146 (844)
T 3j0a_A           72 LPNLRILDLGSSKIY----FLHPDAFQGLFHLFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSF-GK  146 (844)
T ss_dssp             CTTCCEEECTTCCCC----EECTTSSCSCSSCCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGG-GT
T ss_pred             CCCCCEEECCCCcCc----ccCHhHccCCcccCEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhH-hh
Confidence            455555555554432    123344555555555555555544 23332  455555555555555554332  223 55


Q ss_pred             CCCccEeecCCcccccc-chhhhcc--ccCceecCCCccCC
Q 003387          567 LLNLYTLDMPFSYIDHT-ADEFWKM--NKLRHLNFGSITLP  604 (824)
Q Consensus       567 L~~L~~L~L~~~~l~~l-p~~i~~L--~~L~~L~L~~~~~~  604 (824)
                      +++|++|+|++|.+..+ |..+..+  ++|+.|++++|.+.
T Consensus       147 L~~L~~L~Ls~N~i~~~~~~~l~~l~~~~L~~L~L~~n~l~  187 (844)
T 3j0a_A          147 LNSLKSIDFSSNQIFLVCEHELEPLQGKTLSFFSLAANSLY  187 (844)
T ss_dssp             CSSCCEEEEESSCCCCCCSGGGHHHHHCSSCCCEECCSBSC
T ss_pred             CCCCCEEECCCCcCCeeCHHHcccccCCccceEECCCCccc
Confidence            55555555555544432 3334444  45555555555444

>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}

Probab=99.87  E-value=8.5e-22  Score=228.29  Aligned_cols=297  Identities=18%  Similarity=0.156  Sum_probs=193.1

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccChhhhhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L  570 (824)
                      +...+++.+.++....    ++...   .++|++|+|++|.+..+| ..++++++|++|+|++|.+..+++..|+++++|
T Consensus        30 ~~~~~~l~ls~~~L~~----ip~~~---~~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L  102 (562)
T 3a79_B           30 NELESMVDYSNRNLTH----VPKDL---PPRTKALSLSQNSISELRMPDISFLSELRVLRLSHNRIRSLDFHVFLFNQDL  102 (562)
T ss_dssp             ---CCEEECTTSCCCS----CCTTS---CTTCCEEECCSSCCCCCCGGGTTTCTTCCEEECCSCCCCEECTTTTTTCTTC
T ss_pred             cCCCcEEEcCCCCCcc----CCCCC---CCCcCEEECCCCCccccChhhhccCCCccEEECCCCCCCcCCHHHhCCCCCC
Confidence            5556888888876642    23222   278999999999999776 589999999999999999998865545999999


Q ss_pred             cEeecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCcc--ceEEEecc
Q 003387          571 YTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNL--RNLRIRGD  647 (824)
Q Consensus       571 ~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L--~~L~l~~~  647 (824)
                      ++|++++|.+..+|..  .+++|++|++++|.+....+| .++++++|+.|+++.+.-.... +..+++|  +.|+++++
T Consensus       103 ~~L~Ls~N~l~~lp~~--~l~~L~~L~Ls~N~l~~l~~p~~~~~l~~L~~L~L~~n~l~~~~-~~~l~~L~L~~L~L~~n  179 (562)
T 3a79_B          103 EYLDVSHNRLQNISCC--PMASLRHLDLSFNDFDVLPVCKEFGNLTKLTFLGLSAAKFRQLD-LLPVAHLHLSCILLDLV  179 (562)
T ss_dssp             CEEECTTSCCCEECSC--CCTTCSEEECCSSCCSBCCCCGGGGGCTTCCEEEEECSBCCTTT-TGGGTTSCEEEEEEEES
T ss_pred             CEEECCCCcCCccCcc--ccccCCEEECCCCCccccCchHhhcccCcccEEecCCCccccCc-hhhhhhceeeEEEeecc
Confidence            9999999999999987  899999999999999854555 8999999999998843322222 4444444  66666654


Q ss_pred             cc--c----------------------------------------------------chhhHHHHhccC-----------
Q 003387          648 LS--Y----------------------------------------------------NQSLLSKSLCRL-----------  662 (824)
Q Consensus       648 ~~--~----------------------------------------------------~~~~l~~~l~~l-----------  662 (824)
                      .-  .                                                    ........+..+           
T Consensus       180 ~l~~~~~~~~~l~~l~~~~l~l~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~~~~~~l~~~~~~l~~l~~L~~L~L~~~  259 (562)
T 3a79_B          180 SYHIKGGETESLQIPNTTVLHLVFHPNSLFSVQVNMSVNALGHLQLSNIKLNDENCQRLMTFLSELTRGPTLLNVTLQHI  259 (562)
T ss_dssp             SCCCCSSSCCEEEECCEEEEEEEECSSSCCCCCCEEEESSEEEEEEEEEECCSTTHHHHHHHHHHHHSCSSCEEEEEEEE
T ss_pred             cccccccCcccccccCcceEEEEecCccchhhhhhhcccccceEEEecccccccccchHHHHHHHHhccCcceEEEecCC
Confidence            21  0                                                    000011112222           


Q ss_pred             ----------------CCCCeEEEeccC-----CC-------CC-----------------------------ccEEEeC
Q 003387          663 ----------------SCLESLKLANES-----KM-------PR-----------------------------LSKIVLA  685 (824)
Q Consensus       663 ----------------~~L~~L~l~~~~-----~~-------~~-----------------------------L~~l~l~  685 (824)
                                      ++|++|+++++.     |.       ++                             ++.|.+.
T Consensus       260 ~l~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~ip~~~~~~~~~~L~~L~~~~~~~~~~~~p~~~~~~~~~~~~L~~L~l~  339 (562)
T 3a79_B          260 ETTWKCSVKLFQFFWPRPVEYLNIYNLTITERIDREEFTYSETALKSLMIEHVKNQVFLFSKEALYSVFAEMNIKMLSIS  339 (562)
T ss_dssp             EECHHHHHHHHHHHTTSSEEEEEEEEEEECSCCCCCCCCCCSCSCCEEEEEEEEECCCSSCHHHHHHHHHTCCCSEEEEE
T ss_pred             cCcHHHHHHHHHhhhcccccEEEEeccEeeccccchhhhcccccchheehhhcccceeecChhhhhhhhccCcceEEEcc
Confidence                            245555554421     00       11                             3333333


Q ss_pred             cc--------CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCC-eeeecCCCCCCccEEeeccCCCCccc
Q 003387          686 EY--------LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGR-KLTCGSYGFPNLKVLHLKSMLWLEEW  756 (824)
Q Consensus       686 ~~--------~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~-~~~~~~~~~~~L~~L~L~~~~~l~~l  756 (824)
                      ++        ..+++|++|++++|.+.+..+..++++++|+.|++++|.+.+. .++..+..+++|++|++++|.....+
T Consensus       340 ~n~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~l~~L~~L~l~~N~l~~~~  419 (562)
T 3a79_B          340 DTPFIHMVCPPSPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALMTKNMSSLETLDVSLNSLNSHA  419 (562)
T ss_dssp             SSCCCCCCCCSSCCCCCEEECCSSCCCTTTTTTCCSCSSCCEEECCSSCCCBTTHHHHTTTTCTTCCEEECTTSCCBSCC
T ss_pred             CCCcccccCccCCCCceEEECCCCccccchhhhhcccCCCCEEECCCCCcCCcccchhhhcCCCCCCEEECCCCcCCCcc
Confidence            32        3456777777877777766677777777788888777766542 22333556677777777766532223


Q ss_pred             eec-cCcc----------------------cCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          757 TMG-NAAM----------------------PKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       757 ~~~-~~~l----------------------p~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      +.. ...+                      ++|+.|++++|. ++.+|..+..+++|+.|++++|.
T Consensus       420 ~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~~L~~L~L~~N~-l~~ip~~~~~l~~L~~L~L~~N~  484 (562)
T 3a79_B          420 YDRTCAWAESILVLNLSSNMLTGSVFRCLPPKVKVLDLHNNR-IMSIPKDVTHLQALQELNVASNQ  484 (562)
T ss_dssp             SSCCCCCCTTCCEEECCSSCCCGGGGSSCCTTCSEEECCSSC-CCCCCTTTTSSCCCSEEECCSSC
T ss_pred             ChhhhcCcccCCEEECCCCCCCcchhhhhcCcCCEEECCCCc-CcccChhhcCCCCCCEEECCCCC
Confidence            321 2222                      466666666663 44666666677777777777765

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.87  E-value=9.5e-22  Score=220.72  Aligned_cols=270  Identities=17%  Similarity=0.060  Sum_probs=215.0

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      +++|++|.+.++....    . + .+..+++|++|++++|.++.+|  ++.+++|++|++++|.+..+|  + +++++|+
T Consensus        41 l~~L~~L~Ls~n~l~~----~-~-~l~~l~~L~~L~Ls~n~l~~~~--~~~l~~L~~L~Ls~N~l~~~~--~-~~l~~L~  109 (457)
T 3bz5_A           41 LATLTSLDCHNSSITD----M-T-GIEKLTGLTKLICTSNNITTLD--LSQNTNLTYLACDSNKLTNLD--V-TPLTKLT  109 (457)
T ss_dssp             HTTCCEEECCSSCCCC----C-T-TGGGCTTCSEEECCSSCCSCCC--CTTCTTCSEEECCSSCCSCCC--C-TTCTTCC
T ss_pred             cCCCCEEEccCCCccc----C-h-hhcccCCCCEEEccCCcCCeEc--cccCCCCCEEECcCCCCceee--c-CCCCcCC
Confidence            8899999999987652    2 2 5788999999999999999886  899999999999999999986  5 9999999


Q ss_pred             EeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCc-chhhhcCCCCccceEEEeccccc
Q 003387          572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCC-CTEDILGRLPNLRNLRIRGDLSY  650 (824)
Q Consensus       572 ~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~-~~~~~l~~l~~L~~L~l~~~~~~  650 (824)
                      +|++++|.+..+|  ++.+++|++|++++|.+..  + .++++++|+.|+++.+.. .... +..+++|+.|+++++.  
T Consensus       110 ~L~L~~N~l~~l~--~~~l~~L~~L~l~~N~l~~--l-~l~~l~~L~~L~l~~n~~~~~~~-~~~l~~L~~L~ls~n~--  181 (457)
T 3bz5_A          110 YLNCDTNKLTKLD--VSQNPLLTYLNCARNTLTE--I-DVSHNTQLTELDCHLNKKITKLD-VTPQTQLTTLDCSFNK--  181 (457)
T ss_dssp             EEECCSSCCSCCC--CTTCTTCCEEECTTSCCSC--C-CCTTCTTCCEEECTTCSCCCCCC-CTTCTTCCEEECCSSC--
T ss_pred             EEECCCCcCCeec--CCCCCcCCEEECCCCccce--e-ccccCCcCCEEECCCCCcccccc-cccCCcCCEEECCCCc--
Confidence            9999999999987  8999999999999998874  3 378899999999985421 1113 7889999999999885  


Q ss_pred             chhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCC
Q 003387          651 NQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGR  730 (824)
Q Consensus       651 ~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~  730 (824)
                       ...++  +..+++|+.|++++|    +++.+.   ...+++|+.|++++|.+.+ +|  ++.+++|+.|++++|.+.+.
T Consensus       182 -l~~l~--l~~l~~L~~L~l~~N----~l~~~~---l~~l~~L~~L~Ls~N~l~~-ip--~~~l~~L~~L~l~~N~l~~~  248 (457)
T 3bz5_A          182 -ITELD--VSQNKLLNRLNCDTN----NITKLD---LNQNIQLTFLDCSSNKLTE-ID--VTPLTQLTYFDCSVNPLTEL  248 (457)
T ss_dssp             -CCCCC--CTTCTTCCEEECCSS----CCSCCC---CTTCTTCSEEECCSSCCSC-CC--CTTCTTCSEEECCSSCCSCC
T ss_pred             -cceec--cccCCCCCEEECcCC----cCCeec---cccCCCCCEEECcCCcccc-cC--ccccCCCCEEEeeCCcCCCc
Confidence             22233  778899999999876    355442   4667999999999999876 33  88999999999999998763


Q ss_pred             eeeecCCCCCCccE----------EeeccCCCCccceeccCcccCccEEEEecCCCCCCCccc--------cccCccCcE
Q 003387          731 KLTCGSYGFPNLKV----------LHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQ--------LWYIKSLNK  792 (824)
Q Consensus       731 ~~~~~~~~~~~L~~----------L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~--------l~~l~~L~~  792 (824)
                      .    .+.|++|+.          |++++|..+..+|  .+.+++|+.|++++|+.++.+|..        +.++++|+.
T Consensus       249 ~----~~~l~~L~~L~l~~n~L~~L~l~~n~~~~~~~--~~~l~~L~~L~Ls~n~~l~~l~~~~~~L~~L~l~~~~~L~~  322 (457)
T 3bz5_A          249 D----VSTLSKLTTLHCIQTDLLEIDLTHNTQLIYFQ--AEGCRKIKELDVTHNTQLYLLDCQAAGITELDLSQNPKLVY  322 (457)
T ss_dssp             C----CTTCTTCCEEECTTCCCSCCCCTTCTTCCEEE--CTTCTTCCCCCCTTCTTCCEEECTTCCCSCCCCTTCTTCCE
T ss_pred             C----HHHCCCCCEEeccCCCCCEEECCCCccCCccc--ccccccCCEEECCCCcccceeccCCCcceEechhhcccCCE
Confidence            2    345666554          4555555555555  467899999999999987776642        445577777


Q ss_pred             EEecCCc
Q 003387          793 FDCWWPQ  799 (824)
Q Consensus       793 L~l~~c~  799 (824)
                      |+++++.
T Consensus       323 L~L~~N~  329 (457)
T 3bz5_A          323 LYLNNTE  329 (457)
T ss_dssp             EECTTCC
T ss_pred             EECCCCc
Confidence            7777665

>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*

Probab=99.87  E-value=2e-21  Score=209.21  Aligned_cols=282  Identities=15%  Similarity=0.127  Sum_probs=171.7

Q ss_pred             ceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCcc-ChhhhhcCCCcc
Q 003387          494 QLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSL-PSSLLSNLLNLY  571 (824)
Q Consensus       494 ~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~l-p~~i~~~L~~L~  571 (824)
                      +++.+.+.+.....    ++ ..+  .+.|++|+|++|.++.+|. .++++++|++|++++|.+..+ |..+ +++++|+
T Consensus        32 ~l~~l~~~~~~l~~----lp-~~~--~~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~-~~l~~L~  103 (330)
T 1xku_A           32 HLRVVQCSDLGLEK----VP-KDL--PPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAF-APLVKLE  103 (330)
T ss_dssp             ETTEEECTTSCCCS----CC-CSC--CTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTT-TTCTTCC
T ss_pred             CCeEEEecCCCccc----cC-ccC--CCCCeEEECCCCcCCEeChhhhccCCCCCEEECCCCcCCeeCHHHh-cCCCCCC
Confidence            56666666554432    11 111  2567777887777776654 577777788888877777766 4444 7777788


Q ss_pred             EeecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCCc----chhhhcCCCCccceEEEec
Q 003387          572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPCC----CTEDILGRLPNLRNLRIRG  646 (824)
Q Consensus       572 ~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~----~~~~~l~~l~~L~~L~l~~  646 (824)
                      +|++++|.++.+|..+.  ++|++|++++|.+.. ..+ .++++++|+.|+++.+..    .....+..+++|+.|++++
T Consensus       104 ~L~Ls~n~l~~l~~~~~--~~L~~L~l~~n~l~~-~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~  180 (330)
T 1xku_A          104 RLYLSKNQLKELPEKMP--KTLQELRVHENEITK-VRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIAD  180 (330)
T ss_dssp             EEECCSSCCSBCCSSCC--TTCCEEECCSSCCCB-BCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCS
T ss_pred             EEECCCCcCCccChhhc--ccccEEECCCCcccc-cCHhHhcCCccccEEECCCCcCCccCcChhhccCCCCcCEEECCC
Confidence            88887777777776554  677777777777652 222 466677777777663221    2222356667777777766


Q ss_pred             ccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccc
Q 003387          647 DLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNS  726 (824)
Q Consensus       647 ~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~  726 (824)
                      +.   ...+|..+.  ++|++|++++|    .++.+....+..+++|+.|++++|.+.+..+..++.+++|+.|++++|.
T Consensus       181 n~---l~~l~~~~~--~~L~~L~l~~n----~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~  251 (330)
T 1xku_A          181 TN---ITTIPQGLP--PSLTELHLDGN----KITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNK  251 (330)
T ss_dssp             SC---CCSCCSSCC--TTCSEEECTTS----CCCEECTGGGTTCTTCCEEECCSSCCCEECTTTGGGSTTCCEEECCSSC
T ss_pred             Cc---cccCCcccc--ccCCEEECCCC----cCCccCHHHhcCCCCCCEEECCCCcCceeChhhccCCCCCCEEECCCCc
Confidence            63   122222221  56677776654    3454444444566777777777777665555567777777777777776


Q ss_pred             cCCCeeeecCCCCCCccEEeeccCCCCccceecc-------CcccCccEEEEecCCCCC--CCccccccCccCcEEEecC
Q 003387          727 YSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGN-------AAMPKLECLIINPCAYLK--KMPEQLWYIKSLNKFDCWW  797 (824)
Q Consensus       727 ~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~-------~~lp~L~~L~l~~c~~l~--~lp~~l~~l~~L~~L~l~~  797 (824)
                      +..  ++.....+++|++|++++|. ++.++...       ...++|+.|++.+|+...  ..|..+..+++|+.+++++
T Consensus       252 l~~--lp~~l~~l~~L~~L~l~~N~-i~~~~~~~f~~~~~~~~~~~l~~l~l~~N~~~~~~i~~~~f~~~~~l~~l~L~~  328 (330)
T 1xku_A          252 LVK--VPGGLADHKYIQVVYLHNNN-ISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQLGN  328 (330)
T ss_dssp             CSS--CCTTTTTCSSCCEEECCSSC-CCCCCTTSSSCSSCCTTSCCCSEEECCSSSSCGGGSCGGGGTTCCCGGGEEC--
T ss_pred             Ccc--CChhhccCCCcCEEECCCCc-CCccChhhcCCcccccccccccceEeecCcccccccCccccccccceeEEEecc
Confidence            652  44455667777777777765 44443221       124667777777777432  2345666677777777765


Q ss_pred             C
Q 003387          798 P  798 (824)
Q Consensus       798 c  798 (824)
                      +
T Consensus       329 N  329 (330)
T 1xku_A          329 Y  329 (330)
T ss_dssp             -
T ss_pred             c
Confidence            4

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.87  E-value=1.1e-21  Score=211.52  Aligned_cols=283  Identities=17%  Similarity=0.140  Sum_probs=200.7

Q ss_pred             ceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccChhhhhcCCCccE
Q 003387          494 QLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYT  572 (824)
Q Consensus       494 ~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~  572 (824)
                      +++.+.+.++....    ++..+   .+.|++|++++|.+..+| ..+.++++|++|++++|.+..+++..++++++|++
T Consensus        34 ~l~~l~~~~~~l~~----ip~~~---~~~l~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  106 (332)
T 2ft3_A           34 HLRVVQCSDLGLKA----VPKEI---SPDTTLLDLQNNDISELRKDDFKGLQHLYALVLVNNKISKIHEKAFSPLRKLQK  106 (332)
T ss_dssp             ETTEEECCSSCCSS----CCSCC---CTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECGGGSTTCTTCCE
T ss_pred             cCCEEECCCCCccc----cCCCC---CCCCeEEECCCCcCCccCHhHhhCCCCCcEEECCCCccCccCHhHhhCcCCCCE
Confidence            67888777665532    22112   367888999998888664 57888899999999998888774443488899999


Q ss_pred             eecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCCc----chhhhcCCCCccceEEEecc
Q 003387          573 LDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPCC----CTEDILGRLPNLRNLRIRGD  647 (824)
Q Consensus       573 L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~----~~~~~l~~l~~L~~L~l~~~  647 (824)
                      |++++|.+..+|..+.  ++|++|++++|.+.. ..+ .++++++|+.|+++.+..    .....+..+ +|+.|+++++
T Consensus       107 L~L~~n~l~~l~~~~~--~~L~~L~l~~n~i~~-~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l-~L~~L~l~~n  182 (332)
T 2ft3_A          107 LYISKNHLVEIPPNLP--SSLVELRIHDNRIRK-VPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGL-KLNYLRISEA  182 (332)
T ss_dssp             EECCSSCCCSCCSSCC--TTCCEEECCSSCCCC-CCSGGGSSCSSCCEEECCSCCCBGGGSCTTSSCSC-CCSCCBCCSS
T ss_pred             EECCCCcCCccCcccc--ccCCEEECCCCccCc-cCHhHhCCCccCCEEECCCCccccCCCCcccccCC-ccCEEECcCC
Confidence            9999888888887665  789999998888863 222 578888888888874322    222325555 7888888877


Q ss_pred             cccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeecccc
Q 003387          648 LSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSY  727 (824)
Q Consensus       648 ~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~  727 (824)
                      .   ...+|..+.  ++|++|++++|    .++.+....+..+++|+.|++++|.+.+..+..++.+++|+.|++++|.+
T Consensus       183 ~---l~~l~~~~~--~~L~~L~l~~n----~i~~~~~~~l~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l  253 (332)
T 2ft3_A          183 K---LTGIPKDLP--ETLNELHLDHN----KIQAIELEDLLRYSKLYRLGLGHNQIRMIENGSLSFLPTLRELHLDNNKL  253 (332)
T ss_dssp             B---CSSCCSSSC--SSCSCCBCCSS----CCCCCCTTSSTTCTTCSCCBCCSSCCCCCCTTGGGGCTTCCEEECCSSCC
T ss_pred             C---CCccCcccc--CCCCEEECCCC----cCCccCHHHhcCCCCCCEEECCCCcCCcCChhHhhCCCCCCEEECCCCcC
Confidence            4   222333322  57888888776    34544444556778899999999988777677788899999999998877


Q ss_pred             CCCeeeecCCCCCCccEEeeccCCCCccceec-cC------cccCccEEEEecCCCC--CCCccccccCccCcEEEecCC
Q 003387          728 SGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMG-NA------AMPKLECLIINPCAYL--KKMPEQLWYIKSLNKFDCWWP  798 (824)
Q Consensus       728 ~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~-~~------~lp~L~~L~l~~c~~l--~~lp~~l~~l~~L~~L~l~~c  798 (824)
                      .  .++.....+++|++|++++|. +..++.. +.      .+++|+.|++.+|+..  ...|..+.++++|+.++++++
T Consensus       254 ~--~lp~~l~~l~~L~~L~l~~N~-l~~~~~~~~~~~~~~~~~~~l~~L~l~~N~~~~~~~~~~~~~~l~~L~~l~l~~n  330 (332)
T 2ft3_A          254 S--RVPAGLPDLKLLQVVYLHTNN-ITKVGVNDFCPVGFGVKRAYYNGISLFNNPVPYWEVQPATFRCVTDRLAIQFGNY  330 (332)
T ss_dssp             C--BCCTTGGGCTTCCEEECCSSC-CCBCCTTSSSCSSCCSSSCCBSEEECCSSSSCGGGSCGGGGTTBCCSTTEEC---
T ss_pred             e--ecChhhhcCccCCEEECCCCC-CCccChhHccccccccccccccceEeecCcccccccCcccccccchhhhhhcccc
Confidence            6  355556778899999999876 5555432 11      2577899999999865  344667888899999998887


Q ss_pred             c
Q 003387          799 Q  799 (824)
Q Consensus       799 ~  799 (824)
                      .
T Consensus       331 ~  331 (332)
T 2ft3_A          331 K  331 (332)
T ss_dssp             -
T ss_pred             c
Confidence            5

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.86  E-value=1.9e-22  Score=215.14  Aligned_cols=223  Identities=16%  Similarity=0.130  Sum_probs=161.6

Q ss_pred             CCeeEEEEEecCCCc--cccccc--CCceeEeeccC-CCCCCCCcchhHhhhcccCcccEEEeeCccCc-cCCccCCCCC
Q 003387          471 KKAKRLNAVEREGDF--ACLDDY--DSQLHSLLCCS-PETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-QYPSGIENLF  544 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~--~~~~~~--~~~Lr~L~l~~-~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-~lp~~i~~l~  544 (824)
                      ..++++.+..+....  .++..+  +++|++|.+.+ +...    ...+..|..+++|++|+|++|.+. .+|..+++++
T Consensus        50 ~~l~~L~L~~~~l~~~~~~~~~l~~l~~L~~L~L~~~n~l~----~~~p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~  125 (313)
T 1ogq_A           50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLV----GPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIK  125 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEE----SCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCT
T ss_pred             ceEEEEECCCCCccCCcccChhHhCCCCCCeeeCCCCCccc----ccCChhHhcCCCCCEEECcCCeeCCcCCHHHhCCC
Confidence            679999999443333  466666  99999999985 5442    234567899999999999999998 8999999999


Q ss_pred             cceEEeecCCCCC-ccChhhhhcCCCccEeecCCcccc-ccchhhhccc-cCceecCCCccCCCCCCCCCCCCCCCCeee
Q 003387          545 LLRYLKLNIPSLN-SLPSSLLSNLLNLYTLDMPFSYID-HTADEFWKMN-KLRHLNFGSITLPAHPGKFCGSLENLNFIS  621 (824)
Q Consensus       545 ~Lr~L~L~~~~i~-~lp~~i~~~L~~L~~L~L~~~~l~-~lp~~i~~L~-~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~  621 (824)
                      +|++|++++|.+. .+|..+ +++++|++|++++|.+. .+|..++.++ +|++|++++|.+.+                
T Consensus       126 ~L~~L~Ls~N~l~~~~p~~~-~~l~~L~~L~L~~N~l~~~~p~~l~~l~~~L~~L~L~~N~l~~----------------  188 (313)
T 1ogq_A          126 TLVTLDFSYNALSGTLPPSI-SSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTG----------------  188 (313)
T ss_dssp             TCCEEECCSSEEESCCCGGG-GGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEE----------------
T ss_pred             CCCEEeCCCCccCCcCChHH-hcCCCCCeEECcCCcccCcCCHHHhhhhhcCcEEECcCCeeec----------------
Confidence            9999999999998 788887 99999999999999888 7899999998 99999999998752                


Q ss_pred             ccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcc
Q 003387          622 ALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNT  701 (824)
Q Consensus       622 ~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~  701 (824)
                           ..+.. +..++ |+.|+++++.  .....+..+..+++|+.|++++|.    +... +.....+++|++|+|++|
T Consensus       189 -----~~~~~-~~~l~-L~~L~Ls~N~--l~~~~~~~~~~l~~L~~L~L~~N~----l~~~-~~~~~~l~~L~~L~Ls~N  254 (313)
T 1ogq_A          189 -----KIPPT-FANLN-LAFVDLSRNM--LEGDASVLFGSDKNTQKIHLAKNS----LAFD-LGKVGLSKNLNGLDLRNN  254 (313)
T ss_dssp             -----ECCGG-GGGCC-CSEEECCSSE--EEECCGGGCCTTSCCSEEECCSSE----ECCB-GGGCCCCTTCCEEECCSS
T ss_pred             -----cCChH-HhCCc-ccEEECcCCc--ccCcCCHHHhcCCCCCEEECCCCc----eeee-cCcccccCCCCEEECcCC
Confidence                 12222 66666 9999999885  333455566667777777776542    1111 111233455555555555


Q ss_pred             cCCCCCcccccCCCCCCeEEeeccccC
Q 003387          702 DLMDDPMPTLEKLPLLQVLKLKQNSYS  728 (824)
Q Consensus       702 ~l~~~~~~~l~~l~~L~~L~L~~~~~~  728 (824)
                      .+.+..|..++.+++|+.|++++|.+.
T Consensus       255 ~l~~~~p~~l~~l~~L~~L~Ls~N~l~  281 (313)
T 1ogq_A          255 RIYGTLPQGLTQLKFLHSLNVSFNNLC  281 (313)
T ss_dssp             CCEECCCGGGGGCTTCCEEECCSSEEE
T ss_pred             cccCcCChHHhcCcCCCEEECcCCccc
Confidence            555455555555555555555555544

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.86  E-value=1.7e-21  Score=209.98  Aligned_cols=285  Identities=16%  Similarity=0.095  Sum_probs=215.4

Q ss_pred             eeEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEee
Q 003387          473 AKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKL  551 (824)
Q Consensus       473 ~r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L  551 (824)
                      .+.+.+. +.....+|..+.++++.|.+.++...    ...+..|..+++|++|++++|.++.+ |..++++++|++|++
T Consensus        35 l~~l~~~-~~~l~~ip~~~~~~l~~L~l~~n~i~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L  109 (332)
T 2ft3_A           35 LRVVQCS-DLGLKAVPKEISPDTTLLDLQNNDIS----ELRKDDFKGLQHLYALVLVNNKISKIHEKAFSPLRKLQKLYI  109 (332)
T ss_dssp             TTEEECC-SSCCSSCCSCCCTTCCEEECCSSCCC----EECTTTTTTCTTCCEEECCSSCCCEECGGGSTTCTTCCEEEC
T ss_pred             CCEEECC-CCCccccCCCCCCCCeEEECCCCcCC----ccCHhHhhCCCCCcEEECCCCccCccCHhHhhCcCCCCEEEC
Confidence            5566666 44444566666889999999988763    34556789999999999999999865 778999999999999


Q ss_pred             cCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCccCCCC-CCC-CCCCCCCCCeeeccCCC-c
Q 003387          552 NIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAH-PGK-FCGSLENLNFISALHPC-C  627 (824)
Q Consensus       552 ~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~-~~p-~i~~L~~L~~l~~~~~~-~  627 (824)
                      ++|.+..+|..+ .  ++|++|++++|.+..+|.. +..+++|++|++++|.+... ..| .++.+ +|+.|+++.+. .
T Consensus       110 ~~n~l~~l~~~~-~--~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l-~L~~L~l~~n~l~  185 (332)
T 2ft3_A          110 SKNHLVEIPPNL-P--SSLVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGL-KLNYLRISEAKLT  185 (332)
T ss_dssp             CSSCCCSCCSSC-C--TTCCEEECCSSCCCCCCSGGGSSCSSCCEEECCSCCCBGGGSCTTSSCSC-CCSCCBCCSSBCS
T ss_pred             CCCcCCccCccc-c--ccCCEEECCCCccCccCHhHhCCCccCCEEECCCCccccCCCCcccccCC-ccCEEECcCCCCC
Confidence            999999999977 4  8999999999999999765 88999999999999988632 334 67777 88999887422 1


Q ss_pred             chhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCC
Q 003387          628 CTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDP  707 (824)
Q Consensus       628 ~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~  707 (824)
                      .++.  .-.++|+.|+++++.  .....+..+..+++|+.|++++|    .++.+....+..+++|+.|++++|.+. .+
T Consensus       186 ~l~~--~~~~~L~~L~l~~n~--i~~~~~~~l~~l~~L~~L~L~~N----~l~~~~~~~~~~l~~L~~L~L~~N~l~-~l  256 (332)
T 2ft3_A          186 GIPK--DLPETLNELHLDHNK--IQAIELEDLLRYSKLYRLGLGHN----QIRMIENGSLSFLPTLRELHLDNNKLS-RV  256 (332)
T ss_dssp             SCCS--SSCSSCSCCBCCSSC--CCCCCTTSSTTCTTCSCCBCCSS----CCCCCCTTGGGGCTTCCEEECCSSCCC-BC
T ss_pred             ccCc--cccCCCCEEECCCCc--CCccCHHHhcCCCCCCEEECCCC----cCCcCChhHhhCCCCCCEEECCCCcCe-ec
Confidence            1222  123689999999885  33333456788999999999986    355544444567899999999999986 67


Q ss_pred             cccccCCCCCCeEEeeccccCCCeeeec-----CCCCCCccEEeeccCCCC--ccceeccCcccCccEEEEecCC
Q 003387          708 MPTLEKLPLLQVLKLKQNSYSGRKLTCG-----SYGFPNLKVLHLKSMLWL--EEWTMGNAAMPKLECLIINPCA  775 (824)
Q Consensus       708 ~~~l~~l~~L~~L~L~~~~~~~~~~~~~-----~~~~~~L~~L~L~~~~~l--~~l~~~~~~lp~L~~L~l~~c~  775 (824)
                      |..++.+++|+.|++++|.+........     ...+++|+.|++.+|+..  ...+..+..+++|+.|++++|.
T Consensus       257 p~~l~~l~~L~~L~l~~N~l~~~~~~~~~~~~~~~~~~~l~~L~l~~N~~~~~~~~~~~~~~l~~L~~l~l~~n~  331 (332)
T 2ft3_A          257 PAGLPDLKLLQVVYLHTNNITKVGVNDFCPVGFGVKRAYYNGISLFNNPVPYWEVQPATFRCVTDRLAIQFGNYK  331 (332)
T ss_dssp             CTTGGGCTTCCEEECCSSCCCBCCTTSSSCSSCCSSSCCBSEEECCSSSSCGGGSCGGGGTTBCCSTTEEC----
T ss_pred             ChhhhcCccCCEEECCCCCCCccChhHccccccccccccccceEeecCcccccccCcccccccchhhhhhccccc
Confidence            7789999999999999998764221110     122688999999998843  2234456778999999999886

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=99.86  E-value=1.1e-20  Score=222.46  Aligned_cols=323  Identities=16%  Similarity=0.082  Sum_probs=213.5

Q ss_pred             CCCCeeEEEEEecCCCccccc-cc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCC
Q 003387          469 SPKKAKRLNAVEREGDFACLD-DY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLF  544 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~~-~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~  544 (824)
                      .|..+++|.+. .+....++. .+  +++|++|.+.++...    .+.+..|..+++|++|+|++|.++.+|. .|.+++
T Consensus        50 lp~~~~~LdLs-~N~i~~l~~~~f~~l~~L~~L~Ls~N~i~----~i~~~~f~~L~~L~~L~Ls~N~l~~l~~~~f~~L~  124 (635)
T 4g8a_A           50 LPFSTKNLDLS-FNPLRHLGSYSFFSFPELQVLDLSRCEIQ----TIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLS  124 (635)
T ss_dssp             SCTTCCEEECT-TSCCCEECTTTTTTCTTCCEEECTTCCCC----EECTTTTTTCTTCCEEECTTCCCCEECGGGGTTCT
T ss_pred             CCcCCCEEEee-CCCCCCCCHHHHhCCCCCCEEECCCCcCC----CcChhHhcCCCCCCEEEccCCcCCCCCHHHhcCCC
Confidence            56788999999 666655654 34  899999999988763    3556789999999999999999998875 578899


Q ss_pred             cceEEeecCCCCCccChhhhhcCCCccEeecCCccccc--cchhhhccccCceecCCCccCCCCCCCCCC----------
Q 003387          545 LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH--TADEFWKMNKLRHLNFGSITLPAHPGKFCG----------  612 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~--lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~----------  612 (824)
                      +|++|+|++|.++.+|...|++|++|++|++++|.+..  +|..++.+++|++|++++|.+.......+.          
T Consensus       125 ~L~~L~Ls~N~l~~l~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~l~~L~~l~~~~~  204 (635)
T 4g8a_A          125 SLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNL  204 (635)
T ss_dssp             TCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCSSCCCEECGGGGHHHHTCTTCCC
T ss_pred             CCCEEECCCCcCCCCChhhhhcCcccCeeccccCccccCCCchhhccchhhhhhcccCccccccccccccchhhhhhhhh
Confidence            99999999999999988655999999999999998765  477889999999999998866420000000          


Q ss_pred             ------------------------------------------CCCCCC--------------------------------
Q 003387          613 ------------------------------------------SLENLN--------------------------------  618 (824)
Q Consensus       613 ------------------------------------------~L~~L~--------------------------------  618 (824)
                                                                .+..++                                
T Consensus       205 ~~~ls~n~l~~i~~~~~~~~~~~~l~l~~n~~~~~~~~~~~~~l~~l~~~~l~~~~~~~~~~l~~~~~~~~~~~~~l~~~  284 (635)
T 4g8a_A          205 SLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIE  284 (635)
T ss_dssp             EEECTTCCCCEECTTTTTTCEEEEEEEESCCSSHHHHHHHHHTTTTCEEEEEEEECCTTSCCCSCCCTTTTGGGGGSEEE
T ss_pred             hhhcccCcccccCcccccchhhhhhhhhcccccccccchhhcCCcccccccccccccccccccccccccccccccchhhh
Confidence                                                      000000                                


Q ss_pred             -----------------------------------------------eeeccCCC----------------------cch
Q 003387          619 -----------------------------------------------FISALHPC----------------------CCT  629 (824)
Q Consensus       619 -----------------------------------------------~l~~~~~~----------------------~~~  629 (824)
                                                                     .+++....                      ...
T Consensus       285 ~l~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~L~~L~l~~~~~~~~~~~~l~~L~~l~l~~n~~~~~  364 (635)
T 4g8a_A          285 EFRLAYLDYYLDGIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNA  364 (635)
T ss_dssp             EEEEECCCSCEEECTTTTGGGTTCSEEEEESCEEEECGGGGSCCCCSEEEEESCEESSCCCCBCTTCCEEEEESCCSCCB
T ss_pred             hhhhhhhcccccchhhhhhhhcccccccccccccccccccccchhhhhhhcccccccCcCcccchhhhhcccccccCCCC
Confidence                                                           00000000                      000


Q ss_pred             hhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC---------CCCCccEE------------------
Q 003387          630 EDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES---------KMPRLSKI------------------  682 (824)
Q Consensus       630 ~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~---------~~~~L~~l------------------  682 (824)
                      .. ...+++|+.|+++.+.-......+.....+.+|+.|++..+.         ..++++.+                  
T Consensus       365 ~~-~~~l~~L~~L~ls~n~l~~~~~~~~~~~~~~~L~~L~~~~~~~~~~~~~~~~l~~L~~l~l~~~~~~~~~~~~~~~~  443 (635)
T 4g8a_A          365 FS-EVDLPSLEFLDLSRNGLSFKGCCSQSDFGTISLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLS  443 (635)
T ss_dssp             CC-CCBCTTCCEEECCSSCCBEEEECCHHHHSCSCCCEEECCSCSEEEECSCCTTCTTCCEEECTTSEEESTTSSCTTTT
T ss_pred             cc-cccccccccchhhccccccccccccchhhhhhhhhhhccccccccccccccccccccchhhhhcccccccccccccc
Confidence            00 012333444444433211112222333344445555444321         12233333                  


Q ss_pred             -------EeCcc----------CcCCCceEEEEEcccCC-CCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccE
Q 003387          683 -------VLAEY----------LFPHSLTHLSFSNTDLM-DDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKV  744 (824)
Q Consensus       683 -------~l~~~----------~~~~~L~~L~L~~~~l~-~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~  744 (824)
                             .+...          ..+++|+.|++++|... ...+..+..+++|+.|+|++|.+.+ ..+..+.++++|++
T Consensus       444 l~~l~~l~ls~n~l~~~~~~~~~~~~~L~~L~Ls~N~~~~~~~~~~~~~l~~L~~L~Ls~N~L~~-l~~~~f~~l~~L~~  522 (635)
T 4g8a_A          444 LRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQ-LSPTAFNSLSSLQV  522 (635)
T ss_dssp             CTTCCEEECTTSCCEECCTTTTTTCTTCCEEECTTCEEGGGEECSCCTTCTTCCEEECTTSCCCE-ECTTTTTTCTTCCE
T ss_pred             ccccccccccccccccccccccccchhhhhhhhhhcccccccCchhhhhccccCEEECCCCccCC-cChHHHcCCCCCCE
Confidence                   33222          34567888888877533 2345678889999999999887764 23445678899999


Q ss_pred             EeeccCCCCccce-eccCcccCccEEEEecCCCCCCCccccccC-ccCcEEEecCCc
Q 003387          745 LHLKSMLWLEEWT-MGNAAMPKLECLIINPCAYLKKMPEQLWYI-KSLNKFDCWWPQ  799 (824)
Q Consensus       745 L~L~~~~~l~~l~-~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l-~~L~~L~l~~c~  799 (824)
                      |+|++|. +..++ ..+..+++|+.|++++|......|..+.++ ++|+.|+++++|
T Consensus       523 L~Ls~N~-l~~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~l~~l~~~L~~L~L~~Np  578 (635)
T 4g8a_A          523 LNMSHNN-FFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQND  578 (635)
T ss_dssp             EECTTSC-CCBCCCGGGTTCTTCCEEECTTSCCCBCCSSCTTCCCTTCCEEECTTCC
T ss_pred             EECCCCc-CCCCChhHHhCCCCCCEEECCCCcCCCCCHHHHHhhhCcCCEEEeeCCC
Confidence            9999986 56554 457789999999999998766667778887 689999998765

>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*

Probab=99.85  E-value=1e-20  Score=203.69  Aligned_cols=285  Identities=17%  Similarity=0.138  Sum_probs=216.9

Q ss_pred             eeEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEee
Q 003387          473 AKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKL  551 (824)
Q Consensus       473 ~r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L  551 (824)
                      .+.+.+. +.....+|..+.++++.|.+.++....    ..+..|..+++|++|+|++|.++.+ |..++.+++|++|++
T Consensus        33 l~~l~~~-~~~l~~lp~~~~~~l~~L~L~~n~i~~----~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L  107 (330)
T 1xku_A           33 LRVVQCS-DLGLEKVPKDLPPDTALLDLQNNKITE----IKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYL  107 (330)
T ss_dssp             TTEEECT-TSCCCSCCCSCCTTCCEEECCSSCCCC----BCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEEC
T ss_pred             CeEEEec-CCCccccCccCCCCCeEEECCCCcCCE----eChhhhccCCCCCEEECCCCcCCeeCHHHhcCCCCCCEEEC
Confidence            4555554 444444665557899999999887642    4456789999999999999999866 788999999999999


Q ss_pred             cCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCccCCCC-CCC-CCCCCCCCCeeeccCCC-c
Q 003387          552 NIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAH-PGK-FCGSLENLNFISALHPC-C  627 (824)
Q Consensus       552 ~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~-~~p-~i~~L~~L~~l~~~~~~-~  627 (824)
                      ++|.++.+|..+ .  ++|++|++++|.+..++.. +.++++|++|++++|.+... ..+ .++++++|+.|+++.+. .
T Consensus       108 s~n~l~~l~~~~-~--~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~~L~~L~l~~n~l~  184 (330)
T 1xku_A          108 SKNQLKELPEKM-P--KTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNIT  184 (330)
T ss_dssp             CSSCCSBCCSSC-C--TTCCEEECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCC
T ss_pred             CCCcCCccChhh-c--ccccEEECCCCcccccCHhHhcCCccccEEECCCCcCCccCcChhhccCCCCcCEEECCCCccc
Confidence            999999999877 3  7999999999999888754 88999999999999988632 333 78889999999998422 1


Q ss_pred             chhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCC
Q 003387          628 CTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDP  707 (824)
Q Consensus       628 ~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~  707 (824)
                      .++.  ...++|+.|+++++.  .....+..+..+++|+.|++++|    .++.+....+..+++|+.|+|++|.+. .+
T Consensus       185 ~l~~--~~~~~L~~L~l~~n~--l~~~~~~~~~~l~~L~~L~Ls~n----~l~~~~~~~~~~l~~L~~L~L~~N~l~-~l  255 (330)
T 1xku_A          185 TIPQ--GLPPSLTELHLDGNK--ITKVDAASLKGLNNLAKLGLSFN----SISAVDNGSLANTPHLRELHLNNNKLV-KV  255 (330)
T ss_dssp             SCCS--SCCTTCSEEECTTSC--CCEECTGGGTTCTTCCEEECCSS----CCCEECTTTGGGSTTCCEEECCSSCCS-SC
T ss_pred             cCCc--cccccCCEEECCCCc--CCccCHHHhcCCCCCCEEECCCC----cCceeChhhccCCCCCCEEECCCCcCc-cC
Confidence            2222  223789999999885  33334567889999999999987    466665555677899999999999986 67


Q ss_pred             cccccCCCCCCeEEeeccccCCCeeee-----cCCCCCCccEEeeccCCCCccc---eeccCcccCccEEEEecCC
Q 003387          708 MPTLEKLPLLQVLKLKQNSYSGRKLTC-----GSYGFPNLKVLHLKSMLWLEEW---TMGNAAMPKLECLIINPCA  775 (824)
Q Consensus       708 ~~~l~~l~~L~~L~L~~~~~~~~~~~~-----~~~~~~~L~~L~L~~~~~l~~l---~~~~~~lp~L~~L~l~~c~  775 (824)
                      |..+..+++|++|++++|.+.......     ....+++|+.|++.+++ +..+   +..+..+++|+.+++++|.
T Consensus       256 p~~l~~l~~L~~L~l~~N~i~~~~~~~f~~~~~~~~~~~l~~l~l~~N~-~~~~~i~~~~f~~~~~l~~l~L~~N~  330 (330)
T 1xku_A          256 PGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFSNP-VQYWEIQPSTFRCVYVRAAVQLGNYK  330 (330)
T ss_dssp             CTTTTTCSSCCEEECCSSCCCCCCTTSSSCSSCCTTSCCCSEEECCSSS-SCGGGSCGGGGTTCCCGGGEEC----
T ss_pred             ChhhccCCCcCEEECCCCcCCccChhhcCCcccccccccccceEeecCc-ccccccCccccccccceeEEEecccC
Confidence            788999999999999999886522111     11235889999999987 3332   3456678899999998874

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=99.84  E-value=6e-20  Score=205.89  Aligned_cols=290  Identities=20%  Similarity=0.172  Sum_probs=207.3

Q ss_pred             CCCCeeEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceE
Q 003387          469 SPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRY  548 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~  548 (824)
                      .+.+++.+.+. ++....++. ..++|+.|.+.++.....     +   ...++|++|++++|.++.+| .++++++|++
T Consensus        89 ~~~~L~~L~l~-~n~l~~lp~-~~~~L~~L~l~~n~l~~l-----~---~~~~~L~~L~L~~n~l~~lp-~~~~l~~L~~  157 (454)
T 1jl5_A           89 LPPHLESLVAS-CNSLTELPE-LPQSLKSLLVDNNNLKAL-----S---DLPPLLEYLGVSNNQLEKLP-ELQNSSFLKI  157 (454)
T ss_dssp             CCTTCSEEECC-SSCCSSCCC-CCTTCCEEECCSSCCSCC-----C---SCCTTCCEEECCSSCCSSCC-CCTTCTTCCE
T ss_pred             CcCCCCEEEcc-CCcCCcccc-ccCCCcEEECCCCccCcc-----c---CCCCCCCEEECcCCCCCCCc-ccCCCCCCCE
Confidence            56788999998 555444442 268899999988766421     1   11268999999999999998 5999999999


Q ss_pred             EeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCC-Cc
Q 003387          549 LKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHP-CC  627 (824)
Q Consensus       549 L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~-~~  627 (824)
                      |++++|.+..+|..+    .+|++|++++|.+..+| .++++++|++|++++|.+.  .+|.+  ..+|+.|+++.+ -.
T Consensus       158 L~l~~N~l~~lp~~~----~~L~~L~L~~n~l~~l~-~~~~l~~L~~L~l~~N~l~--~l~~~--~~~L~~L~l~~n~l~  228 (454)
T 1jl5_A          158 IDVDNNSLKKLPDLP----PSLEFIAAGNNQLEELP-ELQNLPFLTAIYADNNSLK--KLPDL--PLSLESIVAGNNILE  228 (454)
T ss_dssp             EECCSSCCSCCCCCC----TTCCEEECCSSCCSSCC-CCTTCTTCCEEECCSSCCS--SCCCC--CTTCCEEECCSSCCS
T ss_pred             EECCCCcCcccCCCc----ccccEEECcCCcCCcCc-cccCCCCCCEEECCCCcCC--cCCCC--cCcccEEECcCCcCC
Confidence            999999999988644    58999999999999998 5999999999999999887  35522  247888888832 22


Q ss_pred             chhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC------CCCCccEEEeCcc------CcCCCceE
Q 003387          628 CTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES------KMPRLSKIVLAEY------LFPHSLTH  695 (824)
Q Consensus       628 ~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~------~~~~L~~l~l~~~------~~~~~L~~  695 (824)
                      .++. ++.+++|+.|+++++.   ...+|.   ..++|+.|++++|.      .+++++.|.++++      ..+++|+.
T Consensus       229 ~lp~-~~~l~~L~~L~l~~N~---l~~l~~---~~~~L~~L~l~~N~l~~l~~~~~~L~~L~ls~N~l~~l~~~~~~L~~  301 (454)
T 1jl5_A          229 ELPE-LQNLPFLTTIYADNNL---LKTLPD---LPPSLEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELPPNLYY  301 (454)
T ss_dssp             SCCC-CTTCTTCCEEECCSSC---CSSCCS---CCTTCCEEECCSSCCSCCCCCCTTCCEEECCSSCCSEESCCCTTCCE
T ss_pred             cccc-cCCCCCCCEEECCCCc---CCcccc---cccccCEEECCCCcccccCcccCcCCEEECcCCccCcccCcCCcCCE
Confidence            4455 8899999999999874   222322   24788999998763      2356777777765      23367888


Q ss_pred             EEEEcccCCCCCcccccCC-CCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecC
Q 003387          696 LSFSNTDLMDDPMPTLEKL-PLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPC  774 (824)
Q Consensus       696 L~L~~~~l~~~~~~~l~~l-~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c  774 (824)
                      |++++|.+.+     +..+ ++|+.|++++|.+.+  ++   ..+++|++|++++|. +..+|.   .+++|+.|++++|
T Consensus       302 L~l~~N~l~~-----i~~~~~~L~~L~Ls~N~l~~--lp---~~~~~L~~L~L~~N~-l~~lp~---~l~~L~~L~L~~N  367 (454)
T 1jl5_A          302 LNASSNEIRS-----LCDLPPSLEELNVSNNKLIE--LP---ALPPRLERLIASFNH-LAEVPE---LPQNLKQLHVEYN  367 (454)
T ss_dssp             EECCSSCCSE-----ECCCCTTCCEEECCSSCCSC--CC---CCCTTCCEEECCSSC-CSCCCC---CCTTCCEEECCSS
T ss_pred             EECcCCcCCc-----ccCCcCcCCEEECCCCcccc--cc---ccCCcCCEEECCCCc-cccccc---hhhhccEEECCCC
Confidence            8888887643     2234 488999998888765  22   236889999998875 666765   5789999999998


Q ss_pred             CCCC--CCccccccC-------------ccCcEEEecCCc
Q 003387          775 AYLK--KMPEQLWYI-------------KSLNKFDCWWPQ  799 (824)
Q Consensus       775 ~~l~--~lp~~l~~l-------------~~L~~L~l~~c~  799 (824)
                      +...  .+|..+.++             ++|+.|++++++
T Consensus       368 ~l~~l~~ip~~l~~L~~n~~~~~i~~~~~~L~~L~ls~N~  407 (454)
T 1jl5_A          368 PLREFPDIPESVEDLRMNSHLAEVPELPQNLKQLHVETNP  407 (454)
T ss_dssp             CCSSCCCCCTTCCEEECCC---------------------
T ss_pred             CCCcCCCChHHHHhhhhcccccccccccCcCCEEECCCCc
Confidence            8766  677777777             788999988876

>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}

Probab=99.83  E-value=1.2e-20  Score=202.53  Aligned_cols=223  Identities=18%  Similarity=0.201  Sum_probs=175.1

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      .++++.|.+.++....     ++..+..+++|++|+|++|.+..+|..++++++|++|+|++|.+..+|..+ +++++|+
T Consensus        80 ~~~l~~L~L~~n~l~~-----lp~~l~~l~~L~~L~L~~n~l~~lp~~~~~l~~L~~L~Ls~n~l~~lp~~l-~~l~~L~  153 (328)
T 4fcg_A           80 QPGRVALELRSVPLPQ-----FPDQAFRLSHLQHMTIDAAGLMELPDTMQQFAGLETLTLARNPLRALPASI-ASLNRLR  153 (328)
T ss_dssp             STTCCEEEEESSCCSS-----CCSCGGGGTTCSEEEEESSCCCCCCSCGGGGTTCSEEEEESCCCCCCCGGG-GGCTTCC
T ss_pred             ccceeEEEccCCCchh-----cChhhhhCCCCCEEECCCCCccchhHHHhccCCCCEEECCCCccccCcHHH-hcCcCCC
Confidence            4667777777666532     234466699999999999999999999999999999999999999999998 9999999


Q ss_pred             EeecCCc-cccccchhhhc---------cccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccce
Q 003387          572 TLDMPFS-YIDHTADEFWK---------MNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRN  641 (824)
Q Consensus       572 ~L~L~~~-~l~~lp~~i~~---------L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~  641 (824)
                      +|++++| .+..+|..++.         +++|++|++++|.+.  .+|                    .. ++.+++|+.
T Consensus       154 ~L~L~~n~~~~~~p~~~~~~~~~~~~~~l~~L~~L~L~~n~l~--~lp--------------------~~-l~~l~~L~~  210 (328)
T 4fcg_A          154 ELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIR--SLP--------------------AS-IANLQNLKS  210 (328)
T ss_dssp             EEEEEEETTCCCCCSCSEEEC-CCCEEESTTCCEEEEEEECCC--CCC--------------------GG-GGGCTTCCE
T ss_pred             EEECCCCCCccccChhHhhccchhhhccCCCCCEEECcCCCcC--cch--------------------Hh-hcCCCCCCE
Confidence            9999998 67788877665         999999999988764  222                    22 777888999


Q ss_pred             EEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEE
Q 003387          642 LRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLK  721 (824)
Q Consensus       642 L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~  721 (824)
                      |+++++.   ...+|..+.                            .+++|+.|+|++|.+.+..|..++.+++|+.|+
T Consensus       211 L~L~~N~---l~~l~~~l~----------------------------~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~  259 (328)
T 4fcg_A          211 LKIRNSP---LSALGPAIH----------------------------HLPKLEELDLRGCTALRNYPPIFGGRAPLKRLI  259 (328)
T ss_dssp             EEEESSC---CCCCCGGGG----------------------------GCTTCCEEECTTCTTCCBCCCCTTCCCCCCEEE
T ss_pred             EEccCCC---CCcCchhhc----------------------------cCCCCCEEECcCCcchhhhHHHhcCCCCCCEEE
Confidence            9888874   112222233                            345666666667777777788888899999999


Q ss_pred             eeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCC
Q 003387          722 LKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCA  775 (824)
Q Consensus       722 L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~  775 (824)
                      +++|.+.+ .++..+..+++|++|+|++|+.+..+|..++.+++|+.+.+..+.
T Consensus       260 L~~n~~~~-~~p~~~~~l~~L~~L~L~~n~~~~~iP~~l~~L~~L~~l~l~~~~  312 (328)
T 4fcg_A          260 LKDCSNLL-TLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQLPANCIILVPPHL  312 (328)
T ss_dssp             CTTCTTCC-BCCTTGGGCTTCCEEECTTCTTCCCCCGGGGGSCTTCEEECCGGG
T ss_pred             CCCCCchh-hcchhhhcCCCCCEEeCCCCCchhhccHHHhhccCceEEeCCHHH
Confidence            99877765 345556788999999999998888999888999999998887543

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=99.83  E-value=2.7e-20  Score=202.38  Aligned_cols=252  Identities=16%  Similarity=0.171  Sum_probs=159.5

Q ss_pred             CcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecC
Q 003387          521 KLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNF  598 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L  598 (824)
                      ++|++|++++|.++.+|. .+.++++|++|++++|.+..+++..|+++++|++|++++|.+..+|.. ++++++|++|++
T Consensus        52 ~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L  131 (353)
T 2z80_A           52 EAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNL  131 (353)
T ss_dssp             TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSSCCHHHHTTCTTCSEEEC
T ss_pred             ccCcEEECCCCcCcccCHHHhccCCCCCEEECCCCccCccCHhhcCCCCCCCEEECCCCcCCcCCHhHhCCCccCCEEEC
Confidence            467777777777776655 577777777777777777766554337777777777777777777665 677777777777


Q ss_pred             CCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCC
Q 003387          599 GSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPR  678 (824)
Q Consensus       599 ~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~  678 (824)
                      ++|.+..  +|.                   ...+..+++|+.|+++++.. .....+..+.++++|++|++++|    .
T Consensus       132 ~~n~l~~--l~~-------------------~~~~~~l~~L~~L~l~~n~~-~~~~~~~~~~~l~~L~~L~l~~n----~  185 (353)
T 2z80_A          132 LGNPYKT--LGE-------------------TSLFSHLTKLQILRVGNMDT-FTKIQRKDFAGLTFLEELEIDAS----D  185 (353)
T ss_dssp             TTCCCSS--SCS-------------------SCSCTTCTTCCEEEEEESSS-CCEECTTTTTTCCEEEEEEEEET----T
T ss_pred             CCCCCcc--cCc-------------------hhhhccCCCCcEEECCCCcc-ccccCHHHccCCCCCCEEECCCC----C
Confidence            7776652  221                   01255566666666666520 11112334556667777777665    3


Q ss_pred             ccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeee--ecCCCCCCccEEeeccCCCCc--
Q 003387          679 LSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLT--CGSYGFPNLKVLHLKSMLWLE--  754 (824)
Q Consensus       679 L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~--~~~~~~~~L~~L~L~~~~~l~--  754 (824)
                      +.......+..+++|++|++++|.+.......+..+++|+.|++++|.+.+....  ......+.++.+++.++..-.  
T Consensus       186 l~~~~~~~l~~l~~L~~L~l~~n~l~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~l~~~~~~~~l~~l~L~~~~l~~~~  265 (353)
T 2z80_A          186 LQSYEPKSLKSIQNVSHLILHMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDES  265 (353)
T ss_dssp             CCEECTTTTTTCSEEEEEEEECSCSTTHHHHHHHHTTTEEEEEEESCBCTTCCCC------CCCCCCEEEEESCBCCHHH
T ss_pred             cCccCHHHHhccccCCeecCCCCccccchhhhhhhcccccEEECCCCccccccccccccccccchhhccccccccccCcc
Confidence            4444444556667778888877776432222344577888888887776542211  112335667777777664221  


Q ss_pred             --cceeccCcccCccEEEEecCCCCCCCcccc-ccCccCcEEEecCCc
Q 003387          755 --EWTMGNAAMPKLECLIINPCAYLKKMPEQL-WYIKSLNKFDCWWPQ  799 (824)
Q Consensus       755 --~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l-~~l~~L~~L~l~~c~  799 (824)
                        .+|..+..+++|+.|++++|. ++.+|..+ .++++|+.|+++++|
T Consensus       266 l~~l~~~l~~l~~L~~L~Ls~N~-l~~i~~~~~~~l~~L~~L~L~~N~  312 (353)
T 2z80_A          266 LFQVMKLLNQISGLLELEFSRNQ-LKSVPDGIFDRLTSLQKIWLHTNP  312 (353)
T ss_dssp             HHHHHHHHHTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             hhhhHHHHhcccCCCEEECCCCC-CCccCHHHHhcCCCCCEEEeeCCC
Confidence              345456678888888888886 45777764 788888888888876

>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}

Probab=99.83  E-value=2.2e-20  Score=198.79  Aligned_cols=225  Identities=21%  Similarity=0.193  Sum_probs=112.2

Q ss_pred             CcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCcc---ChhhhhcCCCccEeecCCccccccchhhhccccCcee
Q 003387          521 KLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSL---PSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL  596 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~l---p~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L  596 (824)
                      ++|++|+|++|.++.+|.. +.++++|++|++++|.+..+   |..+ ..+++|++|++++|.+..+|..+..+++|++|
T Consensus        28 ~~l~~L~L~~n~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~-~~~~~L~~L~Ls~n~i~~l~~~~~~l~~L~~L  106 (306)
T 2z66_A           28 SSATRLELESNKLQSLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSD-FGTTSLKYLDLSFNGVITMSSNFLGLEQLEHL  106 (306)
T ss_dssp             TTCCEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCEEEEEEHHH-HSCSCCCEEECCSCSEEEEEEEEETCTTCCEE
T ss_pred             CCCCEEECCCCccCccCHhHhhccccCCEEECCCCccCcccCccccc-ccccccCEEECCCCccccChhhcCCCCCCCEE
Confidence            3556666666665555543 35556666666666555533   3444 45566666666666555555555556666666


Q ss_pred             cCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCC
Q 003387          597 NFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKM  676 (824)
Q Consensus       597 ~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~  676 (824)
                      ++++|.+..                     ......+..+++|+.|+++++.  .....+..+..+++|++|+++     
T Consensus       107 ~l~~n~l~~---------------------~~~~~~~~~l~~L~~L~l~~n~--l~~~~~~~~~~l~~L~~L~l~-----  158 (306)
T 2z66_A          107 DFQHSNLKQ---------------------MSEFSVFLSLRNLIYLDISHTH--TRVAFNGIFNGLSSLEVLKMA-----  158 (306)
T ss_dssp             ECTTSEEES---------------------STTTTTTTTCTTCCEEECTTSC--CEECSTTTTTTCTTCCEEECT-----
T ss_pred             ECCCCcccc---------------------cccchhhhhccCCCEEECCCCc--CCccchhhcccCcCCCEEECC-----
Confidence            555555431                     0000125566777777776664  222233334445555555554     


Q ss_pred             CCccEEEeCccCcCCCceEEEEEcccCCC-CCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcc
Q 003387          677 PRLSKIVLAEYLFPHSLTHLSFSNTDLMD-DPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEE  755 (824)
Q Consensus       677 ~~L~~l~l~~~~~~~~L~~L~L~~~~l~~-~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~  755 (824)
                                             +|.+.+ ..+..++.+++|+.|++++|.+.+ ..+..+..+++|++|++++|. +..
T Consensus       159 -----------------------~n~l~~~~~~~~~~~l~~L~~L~Ls~n~l~~-~~~~~~~~l~~L~~L~L~~N~-l~~  213 (306)
T 2z66_A          159 -----------------------GNSFQENFLPDIFTELRNLTFLDLSQCQLEQ-LSPTAFNSLSSLQVLNMSHNN-FFS  213 (306)
T ss_dssp             -----------------------TCEEGGGEECSCCTTCTTCCEEECTTSCCCE-ECTTTTTTCTTCCEEECTTSC-CSB
T ss_pred             -----------------------CCccccccchhHHhhCcCCCEEECCCCCcCC-cCHHHhcCCCCCCEEECCCCc-cCc
Confidence                                   443322 233344445555555555444432 112223444555555555543 222


Q ss_pred             ce-eccCcccCccEEEEecCCCCCCCccccccCc-cCcEEEecCCc
Q 003387          756 WT-MGNAAMPKLECLIINPCAYLKKMPEQLWYIK-SLNKFDCWWPQ  799 (824)
Q Consensus       756 l~-~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~-~L~~L~l~~c~  799 (824)
                      ++ ..+..+++|+.|++++|+.....|..+..++ +|+.|++++++
T Consensus       214 ~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~~L~~L~L~~N~  259 (306)
T 2z66_A          214 LDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQND  259 (306)
T ss_dssp             CCSGGGTTCTTCCEEECTTSCCCBCSSSSCCCCCTTCCEEECTTCC
T ss_pred             cChhhccCcccCCEeECCCCCCcccCHHHHHhhhccCCEEEccCCC
Confidence            22 2334455555555555554444444455553 55556555544

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=99.82  E-value=1.8e-20  Score=203.69  Aligned_cols=261  Identities=17%  Similarity=0.099  Sum_probs=168.0

Q ss_pred             cCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEeecCCCCCcc
Q 003387          481 REGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSL  559 (824)
Q Consensus       481 ~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~i~~l  559 (824)
                      +.....+|..+.+++++|.+.++...    ..+...|..+++|++|++++|.++.+ |..++++++|++|++++|.++.+
T Consensus        40 ~~~l~~iP~~~~~~L~~L~l~~n~i~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~  115 (353)
T 2z80_A           40 SGSLNSIPSGLTEAVKSLDLSNNRIT----YISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYNYLSNL  115 (353)
T ss_dssp             STTCSSCCTTCCTTCCEEECTTSCCC----EECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSSC
T ss_pred             CCCcccccccccccCcEEECCCCcCc----ccCHHHhccCCCCCEEECCCCccCccCHhhcCCCCCCCEEECCCCcCCcC
Confidence            33444466666789999999988764    34556789999999999999999866 56799999999999999999999


Q ss_pred             ChhhhhcCCCccEeecCCccccccch--hhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCC--CcchhhhcC
Q 003387          560 PSSLLSNLLNLYTLDMPFSYIDHTAD--EFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHP--CCCTEDILG  634 (824)
Q Consensus       560 p~~i~~~L~~L~~L~L~~~~l~~lp~--~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~--~~~~~~~l~  634 (824)
                      |...++++++|++|++++|.+..+|.  .+.++++|++|++++|.......| .++++++|+.|+++.+  ....+..+.
T Consensus       116 ~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~  195 (353)
T 2z80_A          116 SSSWFKPLSSLTFLNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLK  195 (353)
T ss_dssp             CHHHHTTCTTCSEEECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTT
T ss_pred             CHhHhCCCccCCEEECCCCCCcccCchhhhccCCCCcEEECCCCccccccCHHHccCCCCCCEEECCCCCcCccCHHHHh
Confidence            99855999999999999999999987  688999999999999853222223 5666666666666521  111122255


Q ss_pred             CCCccceEEEecccccchhhHHHH-hccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccc--
Q 003387          635 RLPNLRNLRIRGDLSYNQSLLSKS-LCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTL--  711 (824)
Q Consensus       635 ~l~~L~~L~l~~~~~~~~~~l~~~-l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l--  711 (824)
                      .+++|+.|+++++.   ...++.. +..+++|+.|+++                            +|.+.+..+..+  
T Consensus       196 ~l~~L~~L~l~~n~---l~~~~~~~~~~~~~L~~L~L~----------------------------~n~l~~~~~~~l~~  244 (353)
T 2z80_A          196 SIQNVSHLILHMKQ---HILLLEIFVDVTSSVECLELR----------------------------DTDLDTFHFSELST  244 (353)
T ss_dssp             TCSEEEEEEEECSC---STTHHHHHHHHTTTEEEEEEE----------------------------SCBCTTCCCC----
T ss_pred             ccccCCeecCCCCc---cccchhhhhhhcccccEEECC----------------------------CCcccccccccccc
Confidence            66666666666653   2223322 2234555555555                            444333222211  


Q ss_pred             -cCCCCCCeEEeeccccCCC---eeeecCCCCCCccEEeeccCCCCccceecc-CcccCccEEEEecCCCC
Q 003387          712 -EKLPLLQVLKLKQNSYSGR---KLTCGSYGFPNLKVLHLKSMLWLEEWTMGN-AAMPKLECLIINPCAYL  777 (824)
Q Consensus       712 -~~l~~L~~L~L~~~~~~~~---~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~-~~lp~L~~L~l~~c~~l  777 (824)
                       ..++.++.++++++.+.+.   .++..+..+++|++|++++|. +..+|... +.+++|+.|++++|+..
T Consensus       245 ~~~~~~l~~l~L~~~~l~~~~l~~l~~~l~~l~~L~~L~Ls~N~-l~~i~~~~~~~l~~L~~L~L~~N~~~  314 (353)
T 2z80_A          245 GETNSLIKKFTFRNVKITDESLFQVMKLLNQISGLLELEFSRNQ-LKSVPDGIFDRLTSLQKIWLHTNPWD  314 (353)
T ss_dssp             --CCCCCCEEEEESCBCCHHHHHHHHHHHHTCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCSSCBC
T ss_pred             ccccchhhccccccccccCcchhhhHHHHhcccCCCEEECCCCC-CCccCHHHHhcCCCCCEEEeeCCCcc
Confidence             2244455555554443321   122223455666666666654 44555443 55666666666666543

>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}

Probab=99.81  E-value=5.7e-20  Score=195.57  Aligned_cols=213  Identities=21%  Similarity=0.185  Sum_probs=149.8

Q ss_pred             CCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC---CccCCCCCcceEEeecCCCCCcc
Q 003387          483 GDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY---PSGIENLFLLRYLKLNIPSLNSL  559 (824)
Q Consensus       483 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l---p~~i~~l~~Lr~L~L~~~~i~~l  559 (824)
                      ....+|..+.++++.|.+.++...    .++...|..+++|++|+|++|.+..+   |..+..+++|++|++++|.+..+
T Consensus        18 ~l~~ip~~~~~~l~~L~L~~n~l~----~i~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~l   93 (306)
T 2z66_A           18 GLTSVPTGIPSSATRLELESNKLQ----SLPHGVFDKLTQLTKLSLSSNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITM   93 (306)
T ss_dssp             CCSSCCSCCCTTCCEEECCSSCCC----CCCTTTTTTCTTCSEEECCSSCCCEEEEEEHHHHSCSCCCEEECCSCSEEEE
T ss_pred             CcccCCCCCCCCCCEEECCCCccC----ccCHhHhhccccCCEEECCCCccCcccCcccccccccccCEEECCCCccccC
Confidence            334466655789999999988764    24556789999999999999998744   67777899999999999999999


Q ss_pred             ChhhhhcCCCccEeecCCccccccch--hhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCC
Q 003387          560 PSSLLSNLLNLYTLDMPFSYIDHTAD--EFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLP  637 (824)
Q Consensus       560 p~~i~~~L~~L~~L~L~~~~l~~lp~--~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~  637 (824)
                      |..+ .++++|++|++++|.+..+|.  .+..+++|++|++++|.+..                      .....+..++
T Consensus        94 ~~~~-~~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~----------------------~~~~~~~~l~  150 (306)
T 2z66_A           94 SSNF-LGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRV----------------------AFNGIFNGLS  150 (306)
T ss_dssp             EEEE-ETCTTCCEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCCEE----------------------CSTTTTTTCT
T ss_pred             hhhc-CCCCCCCEEECCCCcccccccchhhhhccCCCEEECCCCcCCc----------------------cchhhcccCc
Confidence            9987 999999999999999998875  68999999999999987642                      1112277889


Q ss_pred             ccceEEEecccccchh-hHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCC
Q 003387          638 NLRNLRIRGDLSYNQS-LLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPL  716 (824)
Q Consensus       638 ~L~~L~l~~~~~~~~~-~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~  716 (824)
                      +|+.|+++++.  ... ..|..+..+++|++|++++|    .++.+....+..+++|+.|++++|.+.+..+..+..+++
T Consensus       151 ~L~~L~l~~n~--l~~~~~~~~~~~l~~L~~L~Ls~n----~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~  224 (306)
T 2z66_A          151 SLEVLKMAGNS--FQENFLPDIFTELRNLTFLDLSQC----QLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNS  224 (306)
T ss_dssp             TCCEEECTTCE--EGGGEECSCCTTCTTCCEEECTTS----CCCEECTTTTTTCTTCCEEECTTSCCSBCCSGGGTTCTT
T ss_pred             CCCEEECCCCc--cccccchhHHhhCcCCCEEECCCC----CcCCcCHHHhcCCCCCCEEECCCCccCccChhhccCccc
Confidence            99999999874  222 24445555566666666544    233333333344455555555555544333334444555


Q ss_pred             CCeEEeeccccC
Q 003387          717 LQVLKLKQNSYS  728 (824)
Q Consensus       717 L~~L~L~~~~~~  728 (824)
                      |+.|++++|.+.
T Consensus       225 L~~L~L~~N~l~  236 (306)
T 2z66_A          225 LQVLDYSLNHIM  236 (306)
T ss_dssp             CCEEECTTSCCC
T ss_pred             CCEeECCCCCCc
Confidence            555555544443

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=99.81  E-value=2e-19  Score=202.38  Aligned_cols=240  Identities=18%  Similarity=0.138  Sum_probs=109.2

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccc-hhhhccccCceecCCCcc
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~  602 (824)
                      +.++.++..++.+|..+.  .+|++|+|++|.+..+++..|.++++|++|+|++|.+..++ ..+.++++|++|+|++|.
T Consensus        57 ~~v~c~~~~l~~iP~~~~--~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~  134 (452)
T 3zyi_A           57 SKVVCTRRGLSEVPQGIP--SNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNW  134 (452)
T ss_dssp             CEEECCSSCCSSCCSCCC--TTCSEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC
T ss_pred             cEEEECCCCcCccCCCCC--CCccEEECcCCcCceECHHHcCCCCCCCEEECCCCccCCcChhhccCcccCCEEECCCCc
Confidence            344444444444444333  34455555555444443322244555555555554444443 234444555555554444


Q ss_pred             CCCCCCC-CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCc
Q 003387          603 LPAHPGK-FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRL  679 (824)
Q Consensus       603 ~~~~~~p-~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L  679 (824)
                      +.. ..+ .++.+++|+.|+++.+  .......+..+++|+.|+++++.                             .+
T Consensus       135 l~~-~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~-----------------------------~l  184 (452)
T 3zyi_A          135 LTV-IPSGAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELK-----------------------------KL  184 (452)
T ss_dssp             CSB-CCTTTSSSCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCT-----------------------------TC
T ss_pred             CCc-cChhhhcccCCCCEEECCCCCcceeCHhHHhcCCcccEEeCCCCC-----------------------------Cc
Confidence            431 111 1222222222222210  01111125556666666666532                             22


Q ss_pred             cEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceec
Q 003387          680 SKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMG  759 (824)
Q Consensus       680 ~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~  759 (824)
                      ..+....+..+++|+.|+|++|.+..  .+.+..+++|+.|+|++|.+.+ ..+..+.++++|+.|++++|......+..
T Consensus       185 ~~i~~~~~~~l~~L~~L~L~~n~l~~--~~~~~~l~~L~~L~Ls~N~l~~-~~~~~~~~l~~L~~L~L~~n~l~~~~~~~  261 (452)
T 3zyi_A          185 EYISEGAFEGLFNLKYLNLGMCNIKD--MPNLTPLVGLEELEMSGNHFPE-IRPGSFHGLSSLKKLWVMNSQVSLIERNA  261 (452)
T ss_dssp             CEECTTTTTTCTTCCEEECTTSCCSS--CCCCTTCTTCCEEECTTSCCSE-ECGGGGTTCTTCCEEECTTSCCCEECTTT
T ss_pred             cccChhhccCCCCCCEEECCCCcccc--cccccccccccEEECcCCcCcc-cCcccccCccCCCEEEeCCCcCceECHHH
Confidence            22222223344555555555555432  1245555666666666555543 12333455566666666655422222333


Q ss_pred             cCcccCccEEEEecCCCCCCCcc-ccccCccCcEEEecCCc
Q 003387          760 NAAMPKLECLIINPCAYLKKMPE-QLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       760 ~~~lp~L~~L~l~~c~~l~~lp~-~l~~l~~L~~L~l~~c~  799 (824)
                      +..+++|+.|++++|.. ..+|. .+..+++|+.|+++++|
T Consensus       262 ~~~l~~L~~L~L~~N~l-~~~~~~~~~~l~~L~~L~L~~Np  301 (452)
T 3zyi_A          262 FDGLASLVELNLAHNNL-SSLPHDLFTPLRYLVELHLHHNP  301 (452)
T ss_dssp             TTTCTTCCEEECCSSCC-SCCCTTSSTTCTTCCEEECCSSC
T ss_pred             hcCCCCCCEEECCCCcC-CccChHHhccccCCCEEEccCCC
Confidence            45566666666666643 33332 34556666666666654

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=99.81  E-value=4.5e-19  Score=208.69  Aligned_cols=135  Identities=19%  Similarity=0.119  Sum_probs=118.8

Q ss_pred             cccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhh
Q 003387          485 FACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSL  563 (824)
Q Consensus       485 ~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i  563 (824)
                      ..+|..+.+.++.|.+.++...    .+++..|..+++|++|+|++|.|+.+|+ .|.+|++|++|+|++|+++.+|...
T Consensus        44 ~~vP~~lp~~~~~LdLs~N~i~----~l~~~~f~~l~~L~~L~Ls~N~i~~i~~~~f~~L~~L~~L~Ls~N~l~~l~~~~  119 (635)
T 4g8a_A           44 YKIPDNLPFSTKNLDLSFNPLR----HLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGA  119 (635)
T ss_dssp             SSCCSSSCTTCCEEECTTSCCC----EECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEECGGG
T ss_pred             CccCCCCCcCCCEEEeeCCCCC----CCCHHHHhCCCCCCEEECCCCcCCCcChhHhcCCCCCCEEEccCCcCCCCCHHH
Confidence            3467666779999999998764    3566789999999999999999998865 5899999999999999999999887


Q ss_pred             hhcCCCccEeecCCccccccchh-hhccccCceecCCCccCCCCCCC-CCCCCCCCCeeecc
Q 003387          564 LSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISAL  623 (824)
Q Consensus       564 ~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~  623 (824)
                      |++|++|++|++++|.+..+|.. |+++++|++|++++|.+.....| .++.+++|+.|+++
T Consensus       120 f~~L~~L~~L~Ls~N~l~~l~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~  181 (635)
T 4g8a_A          120 FSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLS  181 (635)
T ss_dssp             GTTCTTCCEEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECC
T ss_pred             hcCCCCCCEEECCCCcCCCCChhhhhcCcccCeeccccCccccCCCchhhccchhhhhhccc
Confidence            79999999999999999999865 89999999999999998765566 78889999988876

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=99.80  E-value=7.2e-19  Score=203.22  Aligned_cols=257  Identities=18%  Similarity=0.073  Sum_probs=191.0

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      ..++++|.+.++....    ++ ..+.  ++|++|+|++|.++.+|.   .+++|++|+|++|.++.+|.    .+++|+
T Consensus        39 ~~~l~~L~ls~n~L~~----lp-~~l~--~~L~~L~L~~N~l~~lp~---~l~~L~~L~Ls~N~l~~lp~----~l~~L~  104 (622)
T 3g06_A           39 NNGNAVLNVGESGLTT----LP-DCLP--AHITTLVIPDNNLTSLPA---LPPELRTLEVSGNQLTSLPV----LPPGLL  104 (622)
T ss_dssp             HHCCCEEECCSSCCSC----CC-SCCC--TTCSEEEECSCCCSCCCC---CCTTCCEEEECSCCCSCCCC----CCTTCC
T ss_pred             CCCCcEEEecCCCcCc----cC-hhhC--CCCcEEEecCCCCCCCCC---cCCCCCEEEcCCCcCCcCCC----CCCCCC
Confidence            3467888888777643    22 2222  688999999998888887   56889999999998888886    578889


Q ss_pred             EeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccc
Q 003387          572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYN  651 (824)
Q Consensus       572 ~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~  651 (824)
                      +|++++|.+..+|.   .+++|+.|++++|.+.  .+|.  .+++|+.|+++.+.  +...-..+++|+.|+++++.   
T Consensus       105 ~L~Ls~N~l~~l~~---~l~~L~~L~L~~N~l~--~lp~--~l~~L~~L~Ls~N~--l~~l~~~~~~L~~L~L~~N~---  172 (622)
T 3g06_A          105 ELSIFSNPLTHLPA---LPSGLCKLWIFGNQLT--SLPV--LPPGLQELSVSDNQ--LASLPALPSELCKLWAYNNQ---  172 (622)
T ss_dssp             EEEECSCCCCCCCC---CCTTCCEEECCSSCCS--CCCC--CCTTCCEEECCSSC--CSCCCCCCTTCCEEECCSSC---
T ss_pred             EEECcCCcCCCCCC---CCCCcCEEECCCCCCC--cCCC--CCCCCCEEECcCCc--CCCcCCccCCCCEEECCCCC---
Confidence            99999988888887   6788899999888876  4552  23678888887432  11111245678888888874   


Q ss_pred             hhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCe
Q 003387          652 QSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRK  731 (824)
Q Consensus       652 ~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~  731 (824)
                      ...+|   ..+++|+.|++++|.    ++.+.    ..+++|+.|++++|.+.. ++.   .+++|+.|++++|.+.+  
T Consensus       173 l~~l~---~~~~~L~~L~Ls~N~----l~~l~----~~~~~L~~L~L~~N~l~~-l~~---~~~~L~~L~Ls~N~L~~--  235 (622)
T 3g06_A          173 LTSLP---MLPSGLQELSVSDNQ----LASLP----TLPSELYKLWAYNNRLTS-LPA---LPSGLKELIVSGNRLTS--  235 (622)
T ss_dssp             CSCCC---CCCTTCCEEECCSSC----CSCCC----CCCTTCCEEECCSSCCSS-CCC---CCTTCCEEECCSSCCSC--
T ss_pred             CCCCc---ccCCCCcEEECCCCC----CCCCC----CccchhhEEECcCCcccc-cCC---CCCCCCEEEccCCccCc--
Confidence            22233   456788888888762    33321    235789999999998753 332   35899999999988775  


Q ss_pred             eeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          732 LTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       732 ~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ++   ..+++|++|++++|. +..+|.   .+++|+.|++++|. +..+|..+.++++|+.|++++|+
T Consensus       236 lp---~~l~~L~~L~Ls~N~-L~~lp~---~~~~L~~L~Ls~N~-L~~lp~~l~~l~~L~~L~L~~N~  295 (622)
T 3g06_A          236 LP---VLPSELKELMVSGNR-LTSLPM---LPSGLLSLSVYRNQ-LTRLPESLIHLSSETTVNLEGNP  295 (622)
T ss_dssp             CC---CCCTTCCEEECCSSC-CSCCCC---CCTTCCEEECCSSC-CCSCCGGGGGSCTTCEEECCSCC
T ss_pred             CC---CCCCcCcEEECCCCC-CCcCCc---ccccCcEEeCCCCC-CCcCCHHHhhccccCEEEecCCC
Confidence            22   567899999999985 677775   68899999999996 55889999999999999999998

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.80  E-value=3.7e-19  Score=199.42  Aligned_cols=238  Identities=19%  Similarity=0.122  Sum_probs=102.6

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccc-hhhhccccCceecCCCcc
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~  602 (824)
                      +.++.++..++.+|..+.  .++++|+|++|.+..++...|.++++|++|+|++|.+..++ ..+.++++|++|++++|.
T Consensus        46 ~~v~c~~~~l~~iP~~~~--~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n~  123 (440)
T 3zyj_A           46 SKVICVRKNLREVPDGIS--TNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNR  123 (440)
T ss_dssp             CEEECCSCCCSSCCSCCC--TTCSEEECCSCCCCEECTTTTSSCSSCCEEECCSSCCCEECGGGGTTCSSCCEEECCSSC
T ss_pred             CEEEeCCCCcCcCCCCCC--CCCcEEEccCCcCCeeCHHHhhCCCCCCEEECCCCcCCccChhhccCCccCCEEECCCCc
Confidence            344444444555554443  34555555555555444333355555555555555554443 234455555555555554


Q ss_pred             CCCCCCC--CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEecccccchhhHH-HHhccCCCCCeEEEeccCCCC
Q 003387          603 LPAHPGK--FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRGDLSYNQSLLS-KSLCRLSCLESLKLANESKMP  677 (824)
Q Consensus       603 ~~~~~~p--~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~-~~l~~l~~L~~L~l~~~~~~~  677 (824)
                      +.  .+|  .+..+++|+.|+++.+  .......+..+++|+.|+++++.  ....++ ..+.++++|++|++++|.   
T Consensus       124 l~--~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~--~l~~i~~~~~~~l~~L~~L~L~~n~---  196 (440)
T 3zyj_A          124 LT--TIPNGAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELK--RLSYISEGAFEGLSNLRYLNLAMCN---  196 (440)
T ss_dssp             CS--SCCTTTSCSCSSCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCT--TCCEECTTTTTTCSSCCEEECTTSC---
T ss_pred             CC--eeCHhHhhccccCceeeCCCCcccccCHHHhhhCcccCEeCCCCCC--CcceeCcchhhcccccCeecCCCCc---
Confidence            43  111  2333333333333311  11111225666777777776542  111111 234445555555555431   


Q ss_pred             CccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccce
Q 003387          678 RLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWT  757 (824)
Q Consensus       678 ~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~  757 (824)
                       ++.+  ..+..+++|+.|+|++|.+....+..+.++++|+.|++++|.+.. .....+..+++|++|+|++|. +..++
T Consensus       197 -l~~~--~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~~~~~l~~L~~L~L~~N~-l~~~~  271 (440)
T 3zyj_A          197 -LREI--PNLTPLIKLDELDLSGNHLSAIRPGSFQGLMHLQKLWMIQSQIQV-IERNAFDNLQSLVEINLAHNN-LTLLP  271 (440)
T ss_dssp             -CSSC--CCCTTCSSCCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCCCE-ECTTSSTTCTTCCEEECTTSC-CCCCC
T ss_pred             -Cccc--cccCCCcccCEEECCCCccCccChhhhccCccCCEEECCCCceeE-EChhhhcCCCCCCEEECCCCC-CCccC
Confidence             2211  122344445555555554444444444455555555555444332 111223344444444444443 33332


Q ss_pred             ec-cCcccCccEEEEecCC
Q 003387          758 MG-NAAMPKLECLIINPCA  775 (824)
Q Consensus       758 ~~-~~~lp~L~~L~l~~c~  775 (824)
                      .. +..+++|+.|++++||
T Consensus       272 ~~~~~~l~~L~~L~L~~Np  290 (440)
T 3zyj_A          272 HDLFTPLHHLERIHLHHNP  290 (440)
T ss_dssp             TTTTSSCTTCCEEECCSSC
T ss_pred             hhHhccccCCCEEEcCCCC
Confidence            21 2334444444444444

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=99.80  E-value=7.6e-19  Score=196.91  Aligned_cols=289  Identities=20%  Similarity=0.130  Sum_probs=192.5

Q ss_pred             CCCCeeEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceE
Q 003387          469 SPKKAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRY  548 (824)
Q Consensus       469 ~~~~~r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~  548 (824)
                      ...+++.+.+. ++....++. ..++|++|.+.++....    + + .|..+++|++|++++|.++.+|..+   .+|++
T Consensus       109 ~~~~L~~L~l~-~n~l~~l~~-~~~~L~~L~L~~n~l~~----l-p-~~~~l~~L~~L~l~~N~l~~lp~~~---~~L~~  177 (454)
T 1jl5_A          109 LPQSLKSLLVD-NNNLKALSD-LPPLLEYLGVSNNQLEK----L-P-ELQNSSFLKIIDVDNNSLKKLPDLP---PSLEF  177 (454)
T ss_dssp             CCTTCCEEECC-SSCCSCCCS-CCTTCCEEECCSSCCSS----C-C-CCTTCTTCCEEECCSSCCSCCCCCC---TTCCE
T ss_pred             ccCCCcEEECC-CCccCcccC-CCCCCCEEECcCCCCCC----C-c-ccCCCCCCCEEECCCCcCcccCCCc---ccccE
Confidence            34678888888 544432322 24789999998887642    2 2 4888999999999999998888654   48999


Q ss_pred             EeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC-c
Q 003387          549 LKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC-C  627 (824)
Q Consensus       549 L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~-~  627 (824)
                      |++++|.+..+| .+ +++++|++|++++|.+..+|...   ++|++|++++|.+.  .+|.++.+++|+.|+++.+. .
T Consensus       178 L~L~~n~l~~l~-~~-~~l~~L~~L~l~~N~l~~l~~~~---~~L~~L~l~~n~l~--~lp~~~~l~~L~~L~l~~N~l~  250 (454)
T 1jl5_A          178 IAAGNNQLEELP-EL-QNLPFLTAIYADNNSLKKLPDLP---LSLESIVAGNNILE--ELPELQNLPFLTTIYADNNLLK  250 (454)
T ss_dssp             EECCSSCCSSCC-CC-TTCTTCCEEECCSSCCSSCCCCC---TTCCEEECCSSCCS--SCCCCTTCTTCCEEECCSSCCS
T ss_pred             EECcCCcCCcCc-cc-cCCCCCCEEECCCCcCCcCCCCc---CcccEEECcCCcCC--cccccCCCCCCCEEECCCCcCC
Confidence            999999999988 46 99999999999999888887633   58999999999887  67778899999999988432 1


Q ss_pred             chhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC------CCCCccEEEeCcc-----CcC-CCceE
Q 003387          628 CTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES------KMPRLSKIVLAEY-----LFP-HSLTH  695 (824)
Q Consensus       628 ~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~------~~~~L~~l~l~~~-----~~~-~~L~~  695 (824)
                      .++   ..+++|+.|+++++.   ...+|.   ..++|+.|++++|.      .+++++.|.+.++     ..+ ++|+.
T Consensus       251 ~l~---~~~~~L~~L~l~~N~---l~~l~~---~~~~L~~L~ls~N~l~~l~~~~~~L~~L~l~~N~l~~i~~~~~~L~~  321 (454)
T 1jl5_A          251 TLP---DLPPSLEALNVRDNY---LTDLPE---LPQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLCDLPPSLEE  321 (454)
T ss_dssp             SCC---SCCTTCCEEECCSSC---CSCCCC---CCTTCCEEECCSSCCSEESCCCTTCCEEECCSSCCSEECCCCTTCCE
T ss_pred             ccc---ccccccCEEECCCCc---ccccCc---ccCcCCEEECcCCccCcccCcCCcCCEEECcCCcCCcccCCcCcCCE
Confidence            122   234789999998874   222332   23688899988763      2357888887765     223 68999


Q ss_pred             EEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCc--cceeccCcc----------
Q 003387          696 LSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLE--EWTMGNAAM----------  763 (824)
Q Consensus       696 L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~--~l~~~~~~l----------  763 (824)
                      |++++|.+.+ ++..   +++|+.|++++|.+..  ++.   .+++|++|++++|....  .+|..++.+          
T Consensus       322 L~Ls~N~l~~-lp~~---~~~L~~L~L~~N~l~~--lp~---~l~~L~~L~L~~N~l~~l~~ip~~l~~L~~n~~~~~i~  392 (454)
T 1jl5_A          322 LNVSNNKLIE-LPAL---PPRLERLIASFNHLAE--VPE---LPQNLKQLHVEYNPLREFPDIPESVEDLRMNSHLAEVP  392 (454)
T ss_dssp             EECCSSCCSC-CCCC---CTTCCEEECCSSCCSC--CCC---CCTTCCEEECCSSCCSSCCCCCTTCCEEECCC------
T ss_pred             EECCCCcccc-cccc---CCcCCEEECCCCcccc--ccc---hhhhccEEECCCCCCCcCCCChHHHHhhhhcccccccc
Confidence            9999999865 4433   6899999999998874  333   57899999999987444  456566655          


Q ss_pred             ---cCccEEEEecCCCCC--CCccccccCccCcEEEecCCc
Q 003387          764 ---PKLECLIINPCAYLK--KMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       764 ---p~L~~L~l~~c~~l~--~lp~~l~~l~~L~~L~l~~c~  799 (824)
                         ++|+.|++++|+...  .+|.      +|+.|.+.+|.
T Consensus       393 ~~~~~L~~L~ls~N~l~~~~~iP~------sl~~L~~~~~~  427 (454)
T 1jl5_A          393 ELPQNLKQLHVETNPLREFPDIPE------SVEDLRMNSER  427 (454)
T ss_dssp             -----------------------------------------
T ss_pred             cccCcCCEEECCCCcCCccccchh------hHhheeCcCcc
Confidence               899999999998654  5564      34555555544

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=99.80  E-value=1e-19  Score=191.50  Aligned_cols=248  Identities=19%  Similarity=0.164  Sum_probs=139.6

Q ss_pred             CcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCcc-cccc-chhhhccccCceec
Q 003387          521 KLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY-IDHT-ADEFWKMNKLRHLN  597 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~-l~~l-p~~i~~L~~L~~L~  597 (824)
                      +.|++|++++|.++.+| ..+..+++|++|++++|.+..+++..+.++++|++|++++|. +..+ |..+..+++|++|+
T Consensus        32 ~~l~~L~l~~n~i~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~~l~~~~~~~~~~l~~L~~L~  111 (285)
T 1ozn_A           32 AASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLH  111 (285)
T ss_dssp             TTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEEE
T ss_pred             CCceEEEeeCCcCCccCHHHcccCCCCCEEECCCCccceeCHhhcCCccCCCEEeCCCCCCccccCHHHhcCCcCCCEEE
Confidence            45666666666665444 345566666666666666665533222666666666666663 5555 34456666666666


Q ss_pred             CCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCC
Q 003387          598 FGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMP  677 (824)
Q Consensus       598 L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~  677 (824)
                      +++|.+.. .                     .+..+..+++|+.|+++++.  .....+..+..+++|++|++++|    
T Consensus       112 l~~n~l~~-~---------------------~~~~~~~l~~L~~L~l~~n~--l~~~~~~~~~~l~~L~~L~l~~n----  163 (285)
T 1ozn_A          112 LDRCGLQE-L---------------------GPGLFRGLAALQYLYLQDNA--LQALPDDTFRDLGNLTHLFLHGN----  163 (285)
T ss_dssp             CTTSCCCC-C---------------------CTTTTTTCTTCCEEECCSSC--CCCCCTTTTTTCTTCCEEECCSS----
T ss_pred             CCCCcCCE-E---------------------CHhHhhCCcCCCEEECCCCc--ccccCHhHhccCCCccEEECCCC----
Confidence            66665542 1                     11224556666666666553  11112233556667777777655    


Q ss_pred             CccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccce
Q 003387          678 RLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWT  757 (824)
Q Consensus       678 ~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~  757 (824)
                      +++.+....+..+++|+.|++++|.+.+..+..++.+++|+.|++++|.+.+. ....+..+++|++|++++|+.....+
T Consensus       164 ~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~-~~~~~~~l~~L~~L~l~~N~~~c~~~  242 (285)
T 1ozn_A          164 RISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSAL-PTEALAPLRALQYLRLNDNPWVCDCR  242 (285)
T ss_dssp             CCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSCC-CHHHHTTCTTCCEEECCSSCEECSGG
T ss_pred             cccccCHHHhcCccccCEEECCCCcccccCHhHccCcccccEeeCCCCcCCcC-CHHHcccCcccCEEeccCCCccCCCC
Confidence            35544433445667778888888777666677777788888888887776652 22235667788888887775222111


Q ss_pred             eccCcccCccEEEEecCCCCCCCccccc--cCccCcEEEecCC
Q 003387          758 MGNAAMPKLECLIINPCAYLKKMPEQLW--YIKSLNKFDCWWP  798 (824)
Q Consensus       758 ~~~~~lp~L~~L~l~~c~~l~~lp~~l~--~l~~L~~L~l~~c  798 (824)
                       ....+..|+.+....+......|..+.  .+..++..++.+|
T Consensus       243 -~~~~~~~l~~~~~~~~~~~c~~p~~l~g~~l~~l~~~~l~~C  284 (285)
T 1ozn_A          243 -ARPLWAWLQKFRGSSSEVPCSLPQRLAGRDLKRLAANDLQGC  284 (285)
T ss_dssp             -GHHHHHHHHHCCSEECCCBEEESGGGTTCBGGGSCGGGSCCC
T ss_pred             -cHHHHHHHHhcccccCccccCCchHhCCcChhhcCHHHhccC
Confidence             111123344444454444444555443  2455666666666

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.80  E-value=6.1e-21  Score=204.02  Aligned_cols=247  Identities=15%  Similarity=0.091  Sum_probs=160.9

Q ss_pred             hhHhhhcccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhcc
Q 003387          512 DWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKM  590 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L  590 (824)
                      .+...+..+++|++|+|++|.++.++ ..++++++|++|+|++|.+...++ + ..+++|++|++++|.+..+|    .+
T Consensus        25 ~~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~-~-~~l~~L~~L~Ls~n~l~~l~----~~   98 (317)
T 3o53_A           25 ALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD-L-ESLSTLRTLDLNNNYVQELL----VG   98 (317)
T ss_dssp             HHHHHHTTGGGCSEEECTTSCCCCCCHHHHTTCTTCCEEECTTSCCEEEEE-E-TTCTTCCEEECCSSEEEEEE----EC
T ss_pred             hHHHHhccCCCCCEEECcCCccCcCCHHHhhCCCcCCEEECCCCcCCcchh-h-hhcCCCCEEECcCCcccccc----CC
Confidence            45677788899999999999998665 578999999999999999987776 5 99999999999999998877    34


Q ss_pred             ccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEecccccchhhHHHHh-ccCCCCCe
Q 003387          591 NKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSL-CRLSCLES  667 (824)
Q Consensus       591 ~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l-~~l~~L~~  667 (824)
                      ++|++|++++|.+..  ++ ...+++|+.|+++.+.  ......+..+++|+.|+++++.  .....+..+ ..+++|++
T Consensus        99 ~~L~~L~l~~n~l~~--~~-~~~~~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~Ls~N~--l~~~~~~~~~~~l~~L~~  173 (317)
T 3o53_A           99 PSIETLHAANNNISR--VS-CSRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNE--IDTVNFAELAASSDTLEH  173 (317)
T ss_dssp             TTCCEEECCSSCCSE--EE-ECCCSSCEEEECCSSCCCSGGGBCTGGGSSEEEEECTTSC--CCEEEGGGGGGGTTTCCE
T ss_pred             CCcCEEECCCCccCC--cC-ccccCCCCEEECCCCCCCCccchhhhccCCCCEEECCCCC--CCcccHHHHhhccCcCCE
Confidence            899999999998763  22 1224556666666321  1122225556677777776664  122122222 34566677


Q ss_pred             EEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEee
Q 003387          668 LKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHL  747 (824)
Q Consensus       668 L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L  747 (824)
                      |++++|    .++.+  .+...+++|+.|+|++|.+.+ .++.+..+++|+.|++++|.+..  ++.....+++|+.|++
T Consensus       174 L~L~~N----~l~~~--~~~~~l~~L~~L~Ls~N~l~~-l~~~~~~l~~L~~L~L~~N~l~~--l~~~~~~l~~L~~L~l  244 (317)
T 3o53_A          174 LNLQYN----FIYDV--KGQVVFAKLKTLDLSSNKLAF-MGPEFQSAAGVTWISLRNNKLVL--IEKALRFSQNLEHFDL  244 (317)
T ss_dssp             EECTTS----CCCEE--ECCCCCTTCCEEECCSSCCCE-ECGGGGGGTTCSEEECTTSCCCE--ECTTCCCCTTCCEEEC
T ss_pred             EECCCC----cCccc--ccccccccCCEEECCCCcCCc-chhhhcccCcccEEECcCCcccc--hhhHhhcCCCCCEEEc
Confidence            776655    24443  222345666677776666543 33346666667777776666552  3444555666666666


Q ss_pred             ccCCCC-ccceeccCcccCccEEEEecCCCCC
Q 003387          748 KSMLWL-EEWTMGNAAMPKLECLIINPCAYLK  778 (824)
Q Consensus       748 ~~~~~l-~~l~~~~~~lp~L~~L~l~~c~~l~  778 (824)
                      ++|+.. ..++.....+++|+.|++.+|+.++
T Consensus       245 ~~N~~~~~~~~~~~~~~~~L~~l~l~~~~~l~  276 (317)
T 3o53_A          245 RGNGFHCGTLRDFFSKNQRVQTVAKQTVKKLT  276 (317)
T ss_dssp             TTCCCBHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             cCCCccCcCHHHHHhccccceEEECCCchhcc
Confidence            666533 2344445556666666666555443

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=99.79  E-value=5.6e-20  Score=214.64  Aligned_cols=324  Identities=12%  Similarity=0.030  Sum_probs=194.2

Q ss_pred             CCeeEEEEEecCCCccccccc---CCc-eeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCcc-----CCccCC
Q 003387          471 KKAKRLNAVEREGDFACLDDY---DSQ-LHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQ-----YPSGIE  541 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~~~~~~~---~~~-Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~-----lp~~i~  541 (824)
                      ..++.|.+..+......+..+   ++. |+.|.+.++...  ....+......+++|++|+|++|.+..     ++..+.
T Consensus       112 ~~L~~L~L~~~~i~~~~~~~l~~~~~~~L~~L~L~~~~~~--~~~~l~~~~~~~~~L~~L~L~~~~~~~~~~~~l~~~~~  189 (592)
T 3ogk_B          112 RQLKSVHFRRMIVSDLDLDRLAKARADDLETLKLDKCSGF--TTDGLLSIVTHCRKIKTLLMEESSFSEKDGKWLHELAQ  189 (592)
T ss_dssp             TTCCEEEEESCBCCHHHHHHHHHHHGGGCCEEEEESCEEE--EHHHHHHHHHHCTTCSEEECTTCEEECCCSHHHHHHHH
T ss_pred             CCCCeEEeeccEecHHHHHHHHHhccccCcEEECcCCCCc--CHHHHHHHHhhCCCCCEEECccccccCcchhHHHHHHh
Confidence            567888888332222222222   334 999999887632  122355666789999999999998652     333445


Q ss_pred             CCCcceEEeecCCCCC-----ccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCC--CCCC-CCCC
Q 003387          542 NLFLLRYLKLNIPSLN-----SLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPA--HPGK-FCGS  613 (824)
Q Consensus       542 ~l~~Lr~L~L~~~~i~-----~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~--~~~p-~i~~  613 (824)
                      .+++|++|++++|.+.     .++..+ .++++|++|++++|.+..+|..+..+++|++|+++.+....  ...+ .++.
T Consensus       190 ~~~~L~~L~L~~n~~~~~~~~~l~~~~-~~~~~L~~L~L~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~l~~  268 (592)
T 3ogk_B          190 HNTSLEVLNFYMTEFAKISPKDLETIA-RNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVF  268 (592)
T ss_dssp             HCCCCCEEECTTCCCSSCCHHHHHHHH-HHCTTCCEEECSSCBGGGGHHHHHHCTTCCEEEECBCCCCTTCTTSSSCCCC
T ss_pred             cCCCccEEEeeccCCCccCHHHHHHHH-hhCCCCcEEeccCccHHHHHHHHhhhhHHHhhcccccccccchHHHHHHhhc
Confidence            6889999999999886     344444 78999999999999999999889999999999987533221  1122 5666


Q ss_pred             CCCCCeeeccC-CCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC----------CCCCccEE
Q 003387          614 LENLNFISALH-PCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES----------KMPRLSKI  682 (824)
Q Consensus       614 L~~L~~l~~~~-~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~----------~~~~L~~l  682 (824)
                      +++|+.+.+.. ....++..+..+++|++|+++++. .....++..+..+++|++|++..+.          .+++|+.|
T Consensus       269 ~~~L~~L~l~~~~~~~l~~~~~~~~~L~~L~Ls~~~-l~~~~~~~~~~~~~~L~~L~L~~~~~~~~l~~~~~~~~~L~~L  347 (592)
T 3ogk_B          269 PRKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYAL-LETEDHCTLIQKCPNLEVLETRNVIGDRGLEVLAQYCKQLKRL  347 (592)
T ss_dssp             CTTCCEEEETTCCTTTGGGGGGGGGGCCEEEETTCC-CCHHHHHHHHTTCTTCCEEEEEGGGHHHHHHHHHHHCTTCCEE
T ss_pred             cccccccCccccchhHHHHHHhhcCCCcEEecCCCc-CCHHHHHHHHHhCcCCCEEeccCccCHHHHHHHHHhCCCCCEE
Confidence            66677766652 122333335566677777776664 2233333445566666666665321          34556666


Q ss_pred             EeCc----------c------------CcCCCceEEEEEcccCCCCCcccccC-CCCCCeEEeec----cccCC------
Q 003387          683 VLAE----------Y------------LFPHSLTHLSFSNTDLMDDPMPTLEK-LPLLQVLKLKQ----NSYSG------  729 (824)
Q Consensus       683 ~l~~----------~------------~~~~~L~~L~L~~~~l~~~~~~~l~~-l~~L~~L~L~~----~~~~~------  729 (824)
                      .+..          +            ..+++|++|+++.+.+++..+..++. +++|+.|++++    |.+++      
T Consensus       348 ~L~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~L~~L~l~~~~l~~~~~~~l~~~~~~L~~L~l~~~~~~n~l~~~p~~~~  427 (592)
T 3ogk_B          348 RIERGADEQGMEDEEGLVSQRGLIALAQGCQELEYMAVYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNG  427 (592)
T ss_dssp             EEECCCCSSTTSSTTCCCCHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHCCSCCEEEEEECSCCSCCSSCCCHHH
T ss_pred             EeecCccccccccccCccCHHHHHHHHhhCccCeEEEeecCCccHHHHHHHHhhCCCCcEEEEeecCCCccccCchHHHH
Confidence            6662          2            22455566665555444333333333 55555555541    22221      


Q ss_pred             -------------------------CeeeecCCCCCCccEEeeccCCCCcc--ceeccCcccCccEEEEecCCCCCC-Cc
Q 003387          730 -------------------------RKLTCGSYGFPNLKVLHLKSMLWLEE--WTMGNAAMPKLECLIINPCAYLKK-MP  781 (824)
Q Consensus       730 -------------------------~~~~~~~~~~~~L~~L~L~~~~~l~~--l~~~~~~lp~L~~L~l~~c~~l~~-lp  781 (824)
                                               ..+......+++|++|+|++|. +..  ++.....+++|++|+|++|+.... ++
T Consensus       428 ~~~~~~~~~~L~~L~L~~~~~~l~~~~~~~~~~~~~~L~~L~L~~n~-l~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~  506 (592)
T 3ogk_B          428 VRSLLIGCKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVG-ESDEGLMEFSRGCPNLQKLEMRGCCFSERAIA  506 (592)
T ss_dssp             HHHHHHHCTTCCEEEEECCGGGCCHHHHHHHHHSCTTCCEEEECSCC-SSHHHHHHHHTCCTTCCEEEEESCCCBHHHHH
T ss_pred             HHHHHHhCCCCCEEEEecCCCCccHHHHHHHHHhCccceEeeccCCC-CCHHHHHHHHhcCcccCeeeccCCCCcHHHHH
Confidence                                     1111111235666666666654 322  222345677888888888873211 34


Q ss_pred             cccccCccCcEEEecCCc
Q 003387          782 EQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       782 ~~l~~l~~L~~L~l~~c~  799 (824)
                      ..+..+++|+.|++++|+
T Consensus       507 ~~~~~l~~L~~L~ls~n~  524 (592)
T 3ogk_B          507 AAVTKLPSLRYLWVQGYR  524 (592)
T ss_dssp             HHHHHCSSCCEEEEESCB
T ss_pred             HHHHhcCccCeeECcCCc
Confidence            445567788888888887

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=99.79  E-value=7.5e-19  Score=197.68  Aligned_cols=235  Identities=21%  Similarity=0.194  Sum_probs=171.0

Q ss_pred             CCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccC
Q 003387          482 EGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLP  560 (824)
Q Consensus       482 ~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp  560 (824)
                      .....+|..+.++++.|.+.++...    ...+..|..+++|++|+|++|.+..++ ..+..+++|++|+|++|.+..+|
T Consensus        64 ~~l~~iP~~~~~~l~~L~L~~n~i~----~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~  139 (452)
T 3zyi_A           64 RGLSEVPQGIPSNTRYLNLMENNIQ----MIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNWLTVIP  139 (452)
T ss_dssp             SCCSSCCSCCCTTCSEEECCSSCCC----EECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSBCC
T ss_pred             CCcCccCCCCCCCccEEECcCCcCc----eECHHHcCCCCCCCEEECCCCccCCcChhhccCcccCCEEECCCCcCCccC
Confidence            3334466555778888888887663    245567888889999999998888554 66888889999999999888888


Q ss_pred             hhhhhcCCCccEeecCCccccccch-hhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCC-CcchhhhcCCCC
Q 003387          561 SSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHP-CCCTEDILGRLP  637 (824)
Q Consensus       561 ~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~-~~~~~~~l~~l~  637 (824)
                      ...|.++++|++|+|++|.+..+|. .+.++++|++|++++|.......+ .+..+++|+.|+++.+ -..++. +..++
T Consensus       140 ~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~~-~~~l~  218 (452)
T 3zyi_A          140 SGAFEYLSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFEGLFNLKYLNLGMCNIKDMPN-LTPLV  218 (452)
T ss_dssp             TTTSSSCTTCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCTTCCEEECTTSCCSSCCC-CTTCT
T ss_pred             hhhhcccCCCCEEECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhccCCCCCCEEECCCCccccccc-ccccc
Confidence            8765888899999999888888875 478888999998887544332222 5777888888887732 223344 67777


Q ss_pred             ccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCC
Q 003387          638 NLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLL  717 (824)
Q Consensus       638 ~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L  717 (824)
                      +|+.|+++++.  .....+..+.++++|+.|++++|    .++.+....+..+++|+.|+|++|.+....+..+..+++|
T Consensus       219 ~L~~L~Ls~N~--l~~~~~~~~~~l~~L~~L~L~~n----~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L  292 (452)
T 3zyi_A          219 GLEELEMSGNH--FPEIRPGSFHGLSSLKKLWVMNS----QVSLIERNAFDGLASLVELNLAHNNLSSLPHDLFTPLRYL  292 (452)
T ss_dssp             TCCEEECTTSC--CSEECGGGGTTCTTCCEEECTTS----CCCEECTTTTTTCTTCCEEECCSSCCSCCCTTSSTTCTTC
T ss_pred             cccEEECcCCc--CcccCcccccCccCCCEEEeCCC----cCceECHHHhcCCCCCCEEECCCCcCCccChHHhccccCC
Confidence            88888887774  33334566777778888888765    4566555555667788888888887776666667778888


Q ss_pred             CeEEeecccc
Q 003387          718 QVLKLKQNSY  727 (824)
Q Consensus       718 ~~L~L~~~~~  727 (824)
                      +.|+|++|.+
T Consensus       293 ~~L~L~~Np~  302 (452)
T 3zyi_A          293 VELHLHHNPW  302 (452)
T ss_dssp             CEEECCSSCE
T ss_pred             CEEEccCCCc
Confidence            8888877654

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.79  E-value=6.5e-19  Score=197.48  Aligned_cols=234  Identities=18%  Similarity=0.189  Sum_probs=158.1

Q ss_pred             CCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccCh
Q 003387          483 GDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPS  561 (824)
Q Consensus       483 ~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~  561 (824)
                      ....+|..+.++++.|.+.++...    ......|..+++|++|+|++|.+..++ ..+..+++|++|+|++|.++.+|.
T Consensus        54 ~l~~iP~~~~~~l~~L~L~~n~i~----~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~~~~  129 (440)
T 3zyj_A           54 NLREVPDGISTNTRLLNLHENQIQ----IIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNRLTTIPN  129 (440)
T ss_dssp             CCSSCCSCCCTTCSEEECCSCCCC----EECTTTTSSCSSCCEEECCSSCCCEECGGGGTTCSSCCEEECCSSCCSSCCT
T ss_pred             CcCcCCCCCCCCCcEEEccCCcCC----eeCHHHhhCCCCCCEEECCCCcCCccChhhccCCccCCEEECCCCcCCeeCH
Confidence            334456555777888888777653    244466778888888888888877554 567778888888888888888877


Q ss_pred             hhhhcCCCccEeecCCccccccch-hhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCC-CcchhhhcCCCCc
Q 003387          562 SLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHP-CCCTEDILGRLPN  638 (824)
Q Consensus       562 ~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~-~~~~~~~l~~l~~  638 (824)
                      ..|..+++|++|+|++|.+..+|. .+.++++|++|++++|.......+ .+.++++|+.|+++.+ -..++. +..+++
T Consensus       130 ~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~~l~~L~~L~L~~n~l~~~~~-~~~l~~  208 (440)
T 3zyj_A          130 GAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGLSNLRYLNLAMCNLREIPN-LTPLIK  208 (440)
T ss_dssp             TTSCSCSSCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTTTCSSCCEEECTTSCCSSCCC-CTTCSS
T ss_pred             hHhhccccCceeeCCCCcccccCHHHhhhCcccCEeCCCCCCCcceeCcchhhcccccCeecCCCCcCccccc-cCCCcc
Confidence            555788888888888888877765 477788888888877544332222 5677777777777632 223344 666777


Q ss_pred             cceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCC
Q 003387          639 LRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQ  718 (824)
Q Consensus       639 L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~  718 (824)
                      |+.|+++++.  .....+..+.++++|+.|++++|    .++.+....+..+++|+.|+|++|.+....+..+..+++|+
T Consensus       209 L~~L~Ls~N~--l~~~~~~~~~~l~~L~~L~L~~n----~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~  282 (440)
T 3zyj_A          209 LDELDLSGNH--LSAIRPGSFQGLMHLQKLWMIQS----QIQVIERNAFDNLQSLVEINLAHNNLTLLPHDLFTPLHHLE  282 (440)
T ss_dssp             CCEEECTTSC--CCEECTTTTTTCTTCCEEECTTC----CCCEECTTSSTTCTTCCEEECTTSCCCCCCTTTTSSCTTCC
T ss_pred             cCEEECCCCc--cCccChhhhccCccCCEEECCCC----ceeEEChhhhcCCCCCCEEECCCCCCCccChhHhccccCCC
Confidence            7777777764  22333455666777777777665    35555555556667777777777777665556667777777


Q ss_pred             eEEeecccc
Q 003387          719 VLKLKQNSY  727 (824)
Q Consensus       719 ~L~L~~~~~  727 (824)
                      .|+|++|.+
T Consensus       283 ~L~L~~Np~  291 (440)
T 3zyj_A          283 RIHLHHNPW  291 (440)
T ss_dssp             EEECCSSCE
T ss_pred             EEEcCCCCc
Confidence            777776654

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.79  E-value=3.5e-20  Score=209.88  Aligned_cols=235  Identities=15%  Similarity=0.093  Sum_probs=153.6

Q ss_pred             cccCcccEEEeeCccCccCC-ccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCcee
Q 003387          518 GMFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL  596 (824)
Q Consensus       518 ~~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L  596 (824)
                      ..+++|++|+|++|.+..+| ..++.+++|++|+|++|.+...++ + +.+++|++|+|++|.+..+|.    .++|++|
T Consensus        31 ~~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~-l-~~l~~L~~L~Ls~N~l~~l~~----~~~L~~L  104 (487)
T 3oja_A           31 QSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD-L-ESLSTLRTLDLNNNYVQELLV----GPSIETL  104 (487)
T ss_dssp             TTGGGCCEEECCSSCCCCCCGGGGTTCTTCCEEECTTSCCEEEEE-C-TTCTTCCEEECCSSEEEEEEE----CTTCCEE
T ss_pred             ccCCCccEEEeeCCcCCCCCHHHHhCCCCCCEEEeeCCCCCCCcc-c-ccCCCCCEEEecCCcCCCCCC----CCCcCEE
Confidence            44558999999999988664 678889999999999999887666 5 899999999999998888774    3889999


Q ss_pred             cCCCccCCCCCCCCCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEecccccchhhHHHHhc-cCCCCCeEEEecc
Q 003387          597 NFGSITLPAHPGKFCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLC-RLSCLESLKLANE  673 (824)
Q Consensus       597 ~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~-~l~~L~~L~l~~~  673 (824)
                      ++++|.+..  ++ ...+++|+.|+++.+.  ...+..++.+++|+.|+++++.  .....|..+. .+++|+.|++++|
T Consensus       105 ~L~~N~l~~--~~-~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~--l~~~~~~~l~~~l~~L~~L~Ls~N  179 (487)
T 3oja_A          105 HAANNNISR--VS-CSRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNE--IDTVNFAELAASSDTLEHLNLQYN  179 (487)
T ss_dssp             ECCSSCCCC--EE-ECCCSSCEEEECCSSCCCSGGGBCGGGGSSEEEEECTTSC--CCEEEGGGGGGGTTTCCEEECTTS
T ss_pred             ECcCCcCCC--CC-ccccCCCCEEECCCCCCCCCCchhhcCCCCCCEEECCCCC--CCCcChHHHhhhCCcccEEecCCC
Confidence            999988763  22 1234556666666321  1222225667777777777664  2222344443 5667777777665


Q ss_pred             CCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCC
Q 003387          674 SKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWL  753 (824)
Q Consensus       674 ~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l  753 (824)
                          .++.+  .+...+++|+.|+|++|.+.+ .++.++.+++|+.|++++|.+.+  ++.....+++|+.|++++|+..
T Consensus       180 ----~l~~~--~~~~~l~~L~~L~Ls~N~l~~-~~~~~~~l~~L~~L~Ls~N~l~~--lp~~l~~l~~L~~L~l~~N~l~  250 (487)
T 3oja_A          180 ----FIYDV--KGQVVFAKLKTLDLSSNKLAF-MGPEFQSAAGVTWISLRNNKLVL--IEKALRFSQNLEHFDLRGNGFH  250 (487)
T ss_dssp             ----CCCEE--ECCCCCTTCCEEECCSSCCCE-ECGGGGGGTTCSEEECTTSCCCE--ECTTCCCCTTCCEEECTTCCBC
T ss_pred             ----ccccc--cccccCCCCCEEECCCCCCCC-CCHhHcCCCCccEEEecCCcCcc--cchhhccCCCCCEEEcCCCCCc
Confidence                24443  222346677777777776654 33346667777777777666653  4444556677777777766533


Q ss_pred             -ccceeccCcccCccEEEEe
Q 003387          754 -EEWTMGNAAMPKLECLIIN  772 (824)
Q Consensus       754 -~~l~~~~~~lp~L~~L~l~  772 (824)
                       ..++.....+++|+.|.+.
T Consensus       251 c~~~~~~~~~l~~L~~l~~~  270 (487)
T 3oja_A          251 CGTLRDFFSKNQRVQTVAKQ  270 (487)
T ss_dssp             HHHHHHHHTTCHHHHHHHHH
T ss_pred             CcchHHHHHhCCCCcEEecc
Confidence             2344445566666666665

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=99.79  E-value=1.3e-18  Score=201.20  Aligned_cols=262  Identities=16%  Similarity=0.039  Sum_probs=202.1

Q ss_pred             CeeEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEee
Q 003387          472 KAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKL  551 (824)
Q Consensus       472 ~~r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L  551 (824)
                      .++.+.+. ++....+|..+.++|+.|.+.++....    ++ .   .+++|++|+|++|.++.+|.   .+++|++|++
T Consensus        41 ~l~~L~ls-~n~L~~lp~~l~~~L~~L~L~~N~l~~----lp-~---~l~~L~~L~Ls~N~l~~lp~---~l~~L~~L~L  108 (622)
T 3g06_A           41 GNAVLNVG-ESGLTTLPDCLPAHITTLVIPDNNLTS----LP-A---LPPELRTLEVSGNQLTSLPV---LPPGLLELSI  108 (622)
T ss_dssp             CCCEEECC-SSCCSCCCSCCCTTCSEEEECSCCCSC----CC-C---CCTTCCEEEECSCCCSCCCC---CCTTCCEEEE
T ss_pred             CCcEEEec-CCCcCccChhhCCCCcEEEecCCCCCC----CC-C---cCCCCCEEEcCCCcCCcCCC---CCCCCCEEEC
Confidence            46778887 555555776668899999999987653    12 1   57899999999999999987   6799999999


Q ss_pred             cCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhh
Q 003387          552 NIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTED  631 (824)
Q Consensus       552 ~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~  631 (824)
                      ++|.++.+|.    .+++|++|++++|.+..+|..   +++|++|++++|.+.  .+|.  .+.+|+.|++..+.  +..
T Consensus       109 s~N~l~~l~~----~l~~L~~L~L~~N~l~~lp~~---l~~L~~L~Ls~N~l~--~l~~--~~~~L~~L~L~~N~--l~~  175 (622)
T 3g06_A          109 FSNPLTHLPA----LPSGLCKLWIFGNQLTSLPVL---PPGLQELSVSDNQLA--SLPA--LPSELCKLWAYNNQ--LTS  175 (622)
T ss_dssp             CSCCCCCCCC----CCTTCCEEECCSSCCSCCCCC---CTTCCEEECCSSCCS--CCCC--CCTTCCEEECCSSC--CSC
T ss_pred             cCCcCCCCCC----CCCCcCEEECCCCCCCcCCCC---CCCCCEEECcCCcCC--CcCC--ccCCCCEEECCCCC--CCC
Confidence            9999999987    478999999999999999974   589999999999887  4452  23567778777322  111


Q ss_pred             hcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccc
Q 003387          632 ILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTL  711 (824)
Q Consensus       632 ~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l  711 (824)
                      +-..+++|+.|+++++.   ...+|.   ..++|+.|++++|.    ++.+.    ..+++|+.|+|++|.+.+ ++   
T Consensus       176 l~~~~~~L~~L~Ls~N~---l~~l~~---~~~~L~~L~L~~N~----l~~l~----~~~~~L~~L~Ls~N~L~~-lp---  237 (622)
T 3g06_A          176 LPMLPSGLQELSVSDNQ---LASLPT---LPSELYKLWAYNNR----LTSLP----ALPSGLKELIVSGNRLTS-LP---  237 (622)
T ss_dssp             CCCCCTTCCEEECCSSC---CSCCCC---CCTTCCEEECCSSC----CSSCC----CCCTTCCEEECCSSCCSC-CC---
T ss_pred             CcccCCCCcEEECCCCC---CCCCCC---ccchhhEEECcCCc----ccccC----CCCCCCCEEEccCCccCc-CC---
Confidence            12457899999999885   222332   34789999998762    33221    235889999999998865 33   


Q ss_pred             cCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCcc
Q 003387          712 EKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPE  782 (824)
Q Consensus       712 ~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~  782 (824)
                      ..+++|+.|++++|.+..  ++.   .+++|++|+|++|. +..+|..+..+++|+.|++++|+.....|.
T Consensus       238 ~~l~~L~~L~Ls~N~L~~--lp~---~~~~L~~L~Ls~N~-L~~lp~~l~~l~~L~~L~L~~N~l~~~~~~  302 (622)
T 3g06_A          238 VLPSELKELMVSGNRLTS--LPM---LPSGLLSLSVYRNQ-LTRLPESLIHLSSETTVNLEGNPLSERTLQ  302 (622)
T ss_dssp             CCCTTCCEEECCSSCCSC--CCC---CCTTCCEEECCSSC-CCSCCGGGGGSCTTCEEECCSCCCCHHHHH
T ss_pred             CCCCcCcEEECCCCCCCc--CCc---ccccCcEEeCCCCC-CCcCCHHHhhccccCEEEecCCCCCCcCHH
Confidence            567999999999998874  332   67899999999986 778888889999999999999986554444

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=99.78  E-value=2.4e-21  Score=218.84  Aligned_cols=306  Identities=18%  Similarity=0.085  Sum_probs=139.8

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCcc-CCccC-CCCC----cceEEeecCCCCC-----ccC
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQ-YPSGI-ENLF----LLRYLKLNIPSLN-----SLP  560 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~-lp~~i-~~l~----~Lr~L~L~~~~i~-----~lp  560 (824)
                      ++++++|.+.++.........++..+..+++|++|+|++|.+.. .+..+ ..+.    +|++|++++|.+.     .+|
T Consensus        27 ~~~L~~L~L~~~~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~L~~n~i~~~~~~~l~  106 (461)
T 1z7x_W           27 LQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLS  106 (461)
T ss_dssp             HTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHH
T ss_pred             cCCccEEEccCCCCCHHHHHHHHHHHHhCCCcCEEeCCCCcCChHHHHHHHHHHhhCCCceeEEEccCCCCCHHHHHHHH
Confidence            55666666665554210001233445555666666666665541 11111 1122    4666666666555     234


Q ss_pred             hhhhhcCCCccEeecCCcccccc-chhhh-----ccccCceecCCCccCCCC---CCC-CCCCCCCCCeeeccCCCcc--
Q 003387          561 SSLLSNLLNLYTLDMPFSYIDHT-ADEFW-----KMNKLRHLNFGSITLPAH---PGK-FCGSLENLNFISALHPCCC--  628 (824)
Q Consensus       561 ~~i~~~L~~L~~L~L~~~~l~~l-p~~i~-----~L~~L~~L~L~~~~~~~~---~~p-~i~~L~~L~~l~~~~~~~~--  628 (824)
                      ..+ .++++|++|++++|.+... +..+.     .+++|++|++++|.+...   .++ .+..+++|+.|+++.+...  
T Consensus       107 ~~l-~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~  185 (461)
T 1z7x_W          107 STL-RTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQLEYCSLSAASCEPLASVLRAKPDFKELTVSNNDINEA  185 (461)
T ss_dssp             HHT-TSCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCBGGGHHHHHHHHHHCTTCCEEECCSSBCHHH
T ss_pred             HHH-ccCCceeEEECCCCcCchHHHHHHHHHHhcCCCcceEEECCCCCCCHHHHHHHHHHHhhCCCCCEEECcCCCcchH
Confidence            444 5566666666666554422 11111     134566666655554421   112 3344455555555532110  


Q ss_pred             -hhh---hc-CCCCccceEEEecccccc--hhhHHHHhccCCCCCeEEEeccC---------------CCCCccEEEeCc
Q 003387          629 -TED---IL-GRLPNLRNLRIRGDLSYN--QSLLSKSLCRLSCLESLKLANES---------------KMPRLSKIVLAE  686 (824)
Q Consensus       629 -~~~---~l-~~l~~L~~L~l~~~~~~~--~~~l~~~l~~l~~L~~L~l~~~~---------------~~~~L~~l~l~~  686 (824)
                       ...   .+ ..+++|+.|+++++.-..  ...++..+..+++|++|++++|.               ..++|+.|.+.+
T Consensus       186 ~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~~~~~~~~L~~L~L~~  265 (461)
T 1z7x_W          186 GVRVLCQGLKDSPCQLEALKLESCGVTSDNCRDLCGIVASKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWE  265 (461)
T ss_dssp             HHHHHHHHHHHSCCCCCEEECTTSCCBTTHHHHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTT
T ss_pred             HHHHHHHHHhcCCCCceEEEccCCCCcHHHHHHHHHHHHhCCCccEEeccCCcCChHHHHHHHHHHhcCCCCceEEECcC
Confidence             011   01 123455555555553111  12344555555555555555532               134555555554


Q ss_pred             c--------------CcCCCceEEEEEcccCCCCCccccc-----CCCCCCeEEeeccccCCCe---eeecCCCCCCccE
Q 003387          687 Y--------------LFPHSLTHLSFSNTDLMDDPMPTLE-----KLPLLQVLKLKQNSYSGRK---LTCGSYGFPNLKV  744 (824)
Q Consensus       687 ~--------------~~~~~L~~L~L~~~~l~~~~~~~l~-----~l~~L~~L~L~~~~~~~~~---~~~~~~~~~~L~~  744 (824)
                      +              ..+++|++|++++|.+....+..+.     ..++|+.|++++|.+.+..   ++.....+++|++
T Consensus       266 n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~  345 (461)
T 1z7x_W          266 CGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGARLLCETLLEPGCQLESLWVKSCSFTAACCSHFSSVLAQNRFLLE  345 (461)
T ss_dssp             SCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHHHHHHHHHHHTSTTCCCCEEECTTSCCBGGGHHHHHHHHHHCSSCCE
T ss_pred             CCCCHHHHHHHHHHHhhCCCcceEECCCCCCchHHHHHHHHHhccCCccceeeEcCCCCCchHHHHHHHHHHhhCCCccE
Confidence            4              1245566666666554322222221     1245666666655544321   1222234456666


Q ss_pred             EeeccCCCCccc-eecc----C-cccCccEEEEecCCCCC----CCccccccCccCcEEEecCCc
Q 003387          745 LHLKSMLWLEEW-TMGN----A-AMPKLECLIINPCAYLK----KMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       745 L~L~~~~~l~~l-~~~~----~-~lp~L~~L~l~~c~~l~----~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      |++++|. +... +..+    . ..++|+.|++++|....    .+|..+..+++|++|++++|+
T Consensus       346 L~Ls~n~-i~~~~~~~l~~~l~~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~l~~N~  409 (461)
T 1z7x_W          346 LQISNNR-LEDAGVRELCQGLGQPGSVLRVLWLADCDVSDSSCSSLAATLLANHSLRELDLSNNC  409 (461)
T ss_dssp             EECCSSB-CHHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCCCCCEEECCSSS
T ss_pred             EEccCCc-cccccHHHHHHHHcCCCCceEEEECCCCCCChhhHHHHHHHHHhCCCccEEECCCCC
Confidence            6666553 2221 1111    1 14566666666665332    455555556666666666665

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.78  E-value=7.5e-20  Score=195.56  Aligned_cols=261  Identities=13%  Similarity=0.074  Sum_probs=196.6

Q ss_pred             CcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCC
Q 003387          521 KLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFG  599 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~  599 (824)
                      ..++.++++.+.+...+.. +..+++|++|+|++|.+..+++..++++++|++|++++|.+..++. +..+++|++|+++
T Consensus        10 ~~l~i~~ls~~~l~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~-~~~l~~L~~L~Ls   88 (317)
T 3o53_A           10 NRYKIEKVTDSSLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD-LESLSTLRTLDLN   88 (317)
T ss_dssp             TEEEEESCCTTTHHHHHHHHHTTGGGCSEEECTTSCCCCCCHHHHTTCTTCCEEECTTSCCEEEEE-ETTCTTCCEEECC
T ss_pred             CceeEeeccccchhhhHHHHhccCCCCCEEECcCCccCcCCHHHhhCCCcCCEEECCCCcCCcchh-hhhcCCCCEEECc
Confidence            3456667777776644433 3457799999999999998876545999999999999998887776 8899999999999


Q ss_pred             CccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCc
Q 003387          600 SITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRL  679 (824)
Q Consensus       600 ~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L  679 (824)
                      +|.+.     .+...++|+.|+++.+...-.. ...+++|+.|+++++.  .....+..+..+++|+.|++++|    .+
T Consensus        89 ~n~l~-----~l~~~~~L~~L~l~~n~l~~~~-~~~~~~L~~L~l~~N~--l~~~~~~~~~~l~~L~~L~Ls~N----~l  156 (317)
T 3o53_A           89 NNYVQ-----ELLVGPSIETLHAANNNISRVS-CSRGQGKKNIYLANNK--ITMLRDLDEGCRSRVQYLDLKLN----EI  156 (317)
T ss_dssp             SSEEE-----EEEECTTCCEEECCSSCCSEEE-ECCCSSCEEEECCSSC--CCSGGGBCTGGGSSEEEEECTTS----CC
T ss_pred             CCccc-----cccCCCCcCEEECCCCccCCcC-ccccCCCCEEECCCCC--CCCccchhhhccCCCCEEECCCC----CC
Confidence            98876     2233477888888743322222 4457889999999885  23333446677889999999876    46


Q ss_pred             cEEEeCcc-CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcccee
Q 003387          680 SKIVLAEY-LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM  758 (824)
Q Consensus       680 ~~l~l~~~-~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~  758 (824)
                      +.+....+ ..+++|+.|++++|.+...  +....+++|+.|++++|.+.+  ++..+..+++|++|++++|. +..+|.
T Consensus       157 ~~~~~~~~~~~l~~L~~L~L~~N~l~~~--~~~~~l~~L~~L~Ls~N~l~~--l~~~~~~l~~L~~L~L~~N~-l~~l~~  231 (317)
T 3o53_A          157 DTVNFAELAASSDTLEHLNLQYNFIYDV--KGQVVFAKLKTLDLSSNKLAF--MGPEFQSAAGVTWISLRNNK-LVLIEK  231 (317)
T ss_dssp             CEEEGGGGGGGTTTCCEEECTTSCCCEE--ECCCCCTTCCEEECCSSCCCE--ECGGGGGGTTCSEEECTTSC-CCEECT
T ss_pred             CcccHHHHhhccCcCCEEECCCCcCccc--ccccccccCCEEECCCCcCCc--chhhhcccCcccEEECcCCc-ccchhh
Confidence            66655554 3678999999999987543  344468999999999888764  44456778999999999985 677887


Q ss_pred             ccCcccCccEEEEecCCCC-CCCccccccCccCcEEEecCCc
Q 003387          759 GNAAMPKLECLIINPCAYL-KKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       759 ~~~~lp~L~~L~l~~c~~l-~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      .+..+++|+.|++++|+.. ..+|..+..+++|+.+++.+|+
T Consensus       232 ~~~~l~~L~~L~l~~N~~~~~~~~~~~~~~~~L~~l~l~~~~  273 (317)
T 3o53_A          232 ALRFSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTVAKQTVK  273 (317)
T ss_dssp             TCCCCTTCCEEECTTCCCBHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HhhcCCCCCEEEccCCCccCcCHHHHHhccccceEEECCCch
Confidence            7888999999999999876 5677778888888888887665

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.77  E-value=2.4e-19  Score=202.99  Aligned_cols=244  Identities=13%  Similarity=0.092  Sum_probs=155.6

Q ss_pred             cCCccCCC----CCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCC
Q 003387          535 QYPSGIEN----LFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKF  610 (824)
Q Consensus       535 ~lp~~i~~----l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~  610 (824)
                      .+|..+..    +++|++|+|++|.+..+++..|+++++|++|+|++|.+...++ ++.+++|++|++++|.+..  +| 
T Consensus        21 ~l~~~l~~l~~~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N~l~~--l~-   96 (487)
T 3oja_A           21 SLKQALASLRQSAWNVKELDLSGNPLSQISAADLAPFTKLELLNLSSNVLYETLD-LESLSTLRTLDLNNNYVQE--LL-   96 (487)
T ss_dssp             THHHHHHTTSTTGGGCCEEECCSSCCCCCCGGGGTTCTTCCEEECTTSCCEEEEE-CTTCTTCCEEECCSSEEEE--EE-
T ss_pred             hhHHHHHHhcccCCCccEEEeeCCcCCCCCHHHHhCCCCCCEEEeeCCCCCCCcc-cccCCCCCEEEecCCcCCC--CC-
Confidence            44554444    4489999999999998876545999999999999999987776 9999999999999998762  22 


Q ss_pred             CCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccC-c
Q 003387          611 CGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYL-F  689 (824)
Q Consensus       611 i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~-~  689 (824)
                        ..++|+.|+++.+...-.. ...+++|+.|+++++.  .....+..++++++|+.|++++|    .+.......+. .
T Consensus        97 --~~~~L~~L~L~~N~l~~~~-~~~l~~L~~L~L~~N~--l~~~~~~~~~~l~~L~~L~Ls~N----~l~~~~~~~l~~~  167 (487)
T 3oja_A           97 --VGPSIETLHAANNNISRVS-CSRGQGKKNIYLANNK--ITMLRDLDEGCRSRVQYLDLKLN----EIDTVNFAELAAS  167 (487)
T ss_dssp             --ECTTCCEEECCSSCCCCEE-ECCCSSCEEEECCSSC--CCSGGGBCGGGGSSEEEEECTTS----CCCEEEGGGGGGG
T ss_pred             --CCCCcCEEECcCCcCCCCC-ccccCCCCEEECCCCC--CCCCCchhhcCCCCCCEEECCCC----CCCCcChHHHhhh
Confidence              2356777776633222111 3345667777777664  22333445556666666666655    35544444432 4


Q ss_pred             CCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEE
Q 003387          690 PHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECL  769 (824)
Q Consensus       690 ~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L  769 (824)
                      +++|+.|+|++|.+.+.  +....+++|+.|+|++|.+.+  ++..+..+++|+.|+|++|. +..+|..+..+++|+.|
T Consensus       168 l~~L~~L~Ls~N~l~~~--~~~~~l~~L~~L~Ls~N~l~~--~~~~~~~l~~L~~L~Ls~N~-l~~lp~~l~~l~~L~~L  242 (487)
T 3oja_A          168 SDTLEHLNLQYNFIYDV--KGQVVFAKLKTLDLSSNKLAF--MGPEFQSAAGVTWISLRNNK-LVLIEKALRFSQNLEHF  242 (487)
T ss_dssp             TTTCCEEECTTSCCCEE--ECCCCCTTCCEEECCSSCCCE--ECGGGGGGTTCSEEECTTSC-CCEECTTCCCCTTCCEE
T ss_pred             CCcccEEecCCCccccc--cccccCCCCCEEECCCCCCCC--CCHhHcCCCCccEEEecCCc-CcccchhhccCCCCCEE
Confidence            56666666666665432  233356666666666666553  33335556666666666654 45566556666666666


Q ss_pred             EEecCCCC-CCCccccccCccCcEEEec
Q 003387          770 IINPCAYL-KKMPEQLWYIKSLNKFDCW  796 (824)
Q Consensus       770 ~l~~c~~l-~~lp~~l~~l~~L~~L~l~  796 (824)
                      ++++|+.. ..+|..+..+++|+.+.+.
T Consensus       243 ~l~~N~l~c~~~~~~~~~l~~L~~l~~~  270 (487)
T 3oja_A          243 DLRGNGFHCGTLRDFFSKNQRVQTVAKQ  270 (487)
T ss_dssp             ECTTCCBCHHHHHHHHTTCHHHHHHHHH
T ss_pred             EcCCCCCcCcchHHHHHhCCCCcEEecc
Confidence            66666654 3445555556665555543

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=99.77  E-value=3.4e-20  Score=209.43  Aligned_cols=304  Identities=16%  Similarity=0.061  Sum_probs=216.2

Q ss_pred             CceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCCc-cChhhhhc
Q 003387          493 SQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLNS-LPSSLLSN  566 (824)
Q Consensus       493 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~~-lp~~i~~~  566 (824)
                      +++++|.+.++...   .......+..+++|++|+|++|.+.     .+|..+..+++|++|+|++|.+.. .+..++..
T Consensus         3 ~~l~~L~Ls~~~l~---~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l~~~~~~~l~~~   79 (461)
T 1z7x_W            3 LDIQSLDIQCEELS---DARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQG   79 (461)
T ss_dssp             EEEEEEEEESCCCC---HHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHT
T ss_pred             ccceehhhhhcccC---chhHHHHHhhcCCccEEEccCCCCCHHHHHHHHHHHHhCCCcCEEeCCCCcCChHHHHHHHHH
Confidence            57888888777653   3345566899999999999999987     567888899999999999999875 34444355


Q ss_pred             CC----CccEeecCCcccc-----ccchhhhccccCceecCCCccCCCC---CCC-C-CCCCCCCCeeeccCCCc-----
Q 003387          567 LL----NLYTLDMPFSYID-----HTADEFWKMNKLRHLNFGSITLPAH---PGK-F-CGSLENLNFISALHPCC-----  627 (824)
Q Consensus       567 L~----~L~~L~L~~~~l~-----~lp~~i~~L~~L~~L~L~~~~~~~~---~~p-~-i~~L~~L~~l~~~~~~~-----  627 (824)
                      +.    +|++|++++|.+.     .+|..+..+++|++|++++|.+...   .+. . ...+++|+.|+++.+..     
T Consensus        80 l~~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~  159 (461)
T 1z7x_W           80 LQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQLEYCSLSAASC  159 (461)
T ss_dssp             TCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCBGGGH
T ss_pred             HhhCCCceeEEEccCCCCCHHHHHHHHHHHccCCceeEEECCCCcCchHHHHHHHHHHhcCCCcceEEECCCCCCCHHHH
Confidence            66    7999999999887     5688899999999999999987532   111 1 23356799999884322     


Q ss_pred             -chhhhcCCCCccceEEEecccccc--hhhHHHHhc-cCCCCCeEEEeccC--------------CCCCccEEEeCcc--
Q 003387          628 -CTEDILGRLPNLRNLRIRGDLSYN--QSLLSKSLC-RLSCLESLKLANES--------------KMPRLSKIVLAEY--  687 (824)
Q Consensus       628 -~~~~~l~~l~~L~~L~l~~~~~~~--~~~l~~~l~-~l~~L~~L~l~~~~--------------~~~~L~~l~l~~~--  687 (824)
                       .+...+..+++|+.|+++++.-..  ...+...+. ..++|++|++++|.              .+++|+.|.++++  
T Consensus       160 ~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~l  239 (461)
T 1z7x_W          160 EPLASVLRAKPDFKELTVSNNDINEAGVRVLCQGLKDSPCQLEALKLESCGVTSDNCRDLCGIVASKASLRELALGSNKL  239 (461)
T ss_dssp             HHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHHHSCCCCCEEECTTSCCBTTHHHHHHHHHHHCTTCCEEECCSSBC
T ss_pred             HHHHHHHhhCCCCCEEECcCCCcchHHHHHHHHHHhcCCCCceEEEccCCCCcHHHHHHHHHHHHhCCCccEEeccCCcC
Confidence             123346778999999999885111  122223332 35699999999853              3478889988876  


Q ss_pred             -------------CcCCCceEEEEEcccCCCC----CcccccCCCCCCeEEeeccccCCCee---eec-CCCCCCccEEe
Q 003387          688 -------------LFPHSLTHLSFSNTDLMDD----PMPTLEKLPLLQVLKLKQNSYSGRKL---TCG-SYGFPNLKVLH  746 (824)
Q Consensus       688 -------------~~~~~L~~L~L~~~~l~~~----~~~~l~~l~~L~~L~L~~~~~~~~~~---~~~-~~~~~~L~~L~  746 (824)
                                   ..+++|++|++++|.+...    .+..+..+++|++|++++|.+.+...   ... ....++|++|+
T Consensus       240 ~~~~~~~l~~~~~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~  319 (461)
T 1z7x_W          240 GDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGARLLCETLLEPGCQLESLW  319 (461)
T ss_dssp             HHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHHHHHHHHHHHTSTTCCCCEEE
T ss_pred             ChHHHHHHHHHHhcCCCCceEEECcCCCCCHHHHHHHHHHHhhCCCcceEECCCCCCchHHHHHHHHHhccCCccceeeE
Confidence                         1468899999999987643    35556678999999999887643211   111 12346899999


Q ss_pred             eccCCCCcc----ceeccCcccCccEEEEecCCCCCCCccc----ccc-CccCcEEEecCCc
Q 003387          747 LKSMLWLEE----WTMGNAAMPKLECLIINPCAYLKKMPEQ----LWY-IKSLNKFDCWWPQ  799 (824)
Q Consensus       747 L~~~~~l~~----l~~~~~~lp~L~~L~l~~c~~l~~lp~~----l~~-l~~L~~L~l~~c~  799 (824)
                      +++|..-..    ++..+..+++|+.|++++|......+..    +.. .++|+.|++++|.
T Consensus       320 L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~  381 (461)
T 1z7x_W          320 VKSCSFTAACCSHFSSVLAQNRFLLELQISNNRLEDAGVRELCQGLGQPGSVLRVLWLADCD  381 (461)
T ss_dssp             CTTSCCBGGGHHHHHHHHHHCSSCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSC
T ss_pred             cCCCCCchHHHHHHHHHHhhCCCccEEEccCCccccccHHHHHHHHcCCCCceEEEECCCCC
Confidence            999873222    3344556799999999999643322222    222 6799999999997

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=99.76  E-value=6.9e-19  Score=185.12  Aligned_cols=216  Identities=22%  Similarity=0.204  Sum_probs=164.3

Q ss_pred             CCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEeecCCC-CCcc
Q 003387          482 EGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPS-LNSL  559 (824)
Q Consensus       482 ~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~-i~~l  559 (824)
                      .....+|..+.++++.|.+.++...    ...+..|..+++|++|++++|.++.+ |..+..+++|++|++++|. +..+
T Consensus        21 ~~l~~ip~~~~~~l~~L~l~~n~i~----~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~~l~~~   96 (285)
T 1ozn_A           21 QGLQAVPVGIPAASQRIFLHGNRIS----HVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSV   96 (285)
T ss_dssp             SCCSSCCTTCCTTCSEEECTTSCCC----EECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCC
T ss_pred             CCcccCCcCCCCCceEEEeeCCcCC----ccCHHHcccCCCCCEEECCCCccceeCHhhcCCccCCCEEeCCCCCCcccc
Confidence            3344455555789999999988764    34556789999999999999999866 7789999999999999997 8888


Q ss_pred             ChhhhhcCCCccEeecCCcccccc-chhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCc
Q 003387          560 PSSLLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPN  638 (824)
Q Consensus       560 p~~i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~  638 (824)
                      ++..+.++++|++|++++|.+..+ |..+..+++|++|++++|.+..  ++                    ...++.+++
T Consensus        97 ~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~--~~--------------------~~~~~~l~~  154 (285)
T 1ozn_A           97 DPATFHGLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQA--LP--------------------DDTFRDLGN  154 (285)
T ss_dssp             CTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCC--CC--------------------TTTTTTCTT
T ss_pred             CHHHhcCCcCCCEEECCCCcCCEECHhHhhCCcCCCEEECCCCcccc--cC--------------------HhHhccCCC
Confidence            554449999999999999999888 4568899999999999998762  22                    111445556


Q ss_pred             cceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCC
Q 003387          639 LRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQ  718 (824)
Q Consensus       639 L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~  718 (824)
                      |+.|+++++.  .....+..+..+++|+.|++++|    .+..+....+..+++|+.|++++|.+.+..+..+..+++|+
T Consensus       155 L~~L~l~~n~--l~~~~~~~~~~l~~L~~L~l~~n----~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~  228 (285)
T 1ozn_A          155 LTHLFLHGNR--ISSVPERAFRGLHSLDRLLLHQN----RVAHVHPHAFRDLGRLMTLYLFANNLSALPTEALAPLRALQ  228 (285)
T ss_dssp             CCEEECCSSC--CCEECTTTTTTCTTCCEEECCSS----CCCEECTTTTTTCTTCCEEECCSSCCSCCCHHHHTTCTTCC
T ss_pred             ccEEECCCCc--ccccCHHHhcCccccCEEECCCC----cccccCHhHccCcccccEeeCCCCcCCcCCHHHcccCcccC
Confidence            6666666553  11111224566777777777765    35555555567788999999999998876667789999999


Q ss_pred             eEEeeccccCC
Q 003387          719 VLKLKQNSYSG  729 (824)
Q Consensus       719 ~L~L~~~~~~~  729 (824)
                      .|++++|.+..
T Consensus       229 ~L~l~~N~~~c  239 (285)
T 1ozn_A          229 YLRLNDNPWVC  239 (285)
T ss_dssp             EEECCSSCEEC
T ss_pred             EEeccCCCccC
Confidence            99999988754

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=99.75  E-value=6.4e-19  Score=205.68  Aligned_cols=305  Identities=16%  Similarity=0.058  Sum_probs=208.8

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCC----CccChhhhhcC
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSL----NSLPSSLLSNL  567 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i----~~lp~~i~~~L  567 (824)
                      +++|++|.+..+.........+...+..+++|++|++++|.+..+|..+..+++|++|+++.+..    ...+..+ ..+
T Consensus       191 ~~~L~~L~L~~n~~~~~~~~~l~~~~~~~~~L~~L~L~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~l-~~~  269 (592)
T 3ogk_B          191 NTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNL-VFP  269 (592)
T ss_dssp             CCCCCEEECTTCCCSSCCHHHHHHHHHHCTTCCEEECSSCBGGGGHHHHHHCTTCCEEEECBCCCCTTCTTSSSCC-CCC
T ss_pred             CCCccEEEeeccCCCccCHHHHHHHHhhCCCCcEEeccCccHHHHHHHHhhhhHHHhhcccccccccchHHHHHHh-hcc
Confidence            66777777766554321223455566667777777777777666666667777777777764321    2334444 677


Q ss_pred             CCccEeecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEE
Q 003387          568 LNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRI  644 (824)
Q Consensus       568 ~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l  644 (824)
                      ++|+.|+++++....+|..+..+++|++|++++|.+....++ .++.+++|+.|++...  ...+......+++|++|++
T Consensus       270 ~~L~~L~l~~~~~~~l~~~~~~~~~L~~L~Ls~~~l~~~~~~~~~~~~~~L~~L~L~~~~~~~~l~~~~~~~~~L~~L~L  349 (592)
T 3ogk_B          270 RKLCRLGLSYMGPNEMPILFPFAAQIRKLDLLYALLETEDHCTLIQKCPNLEVLETRNVIGDRGLEVLAQYCKQLKRLRI  349 (592)
T ss_dssp             TTCCEEEETTCCTTTGGGGGGGGGGCCEEEETTCCCCHHHHHHHHTTCTTCCEEEEEGGGHHHHHHHHHHHCTTCCEEEE
T ss_pred             ccccccCccccchhHHHHHHhhcCCCcEEecCCCcCCHHHHHHHHHhCcCCCEEeccCccCHHHHHHHHHhCCCCCEEEe
Confidence            777777777776677888888899999999999885432332 4678888999988621  1223343467889999999


Q ss_pred             ec----------ccccchhhHHHHhccCCCCCeEEEeccC-----------CCCCccEEEeCcc----------------
Q 003387          645 RG----------DLSYNQSLLSKSLCRLSCLESLKLANES-----------KMPRLSKIVLAEY----------------  687 (824)
Q Consensus       645 ~~----------~~~~~~~~l~~~l~~l~~L~~L~l~~~~-----------~~~~L~~l~l~~~----------------  687 (824)
                      ++          +.......+......+++|++|++..+.           .+++|+.|.+.++                
T Consensus       350 ~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~L~~L~l~~~~l~~~~~~~l~~~~~~L~~L~l~~~~~~n~l~~~p~~~~~~  429 (592)
T 3ogk_B          350 ERGADEQGMEDEEGLVSQRGLIALAQGCQELEYMAVYVSDITNESLESIGTYLKNLCDFRLVLLDREERITDLPLDNGVR  429 (592)
T ss_dssp             ECCCCSSTTSSTTCCCCHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHCCSCCEEEEEECSCCSCCSSCCCHHHHH
T ss_pred             ecCccccccccccCccCHHHHHHHHhhCccCeEEEeecCCccHHHHHHHHhhCCCCcEEEEeecCCCccccCchHHHHHH
Confidence            94          4333444556666678999999996532           3778999998631                


Q ss_pred             ---CcCCCceEEEEEccc--CCCCCccccc-CCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcc--ceec
Q 003387          688 ---LFPHSLTHLSFSNTD--LMDDPMPTLE-KLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEE--WTMG  759 (824)
Q Consensus       688 ---~~~~~L~~L~L~~~~--l~~~~~~~l~-~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~--l~~~  759 (824)
                         ..+++|++|+++.|.  +++..+..++ .+++|+.|++++|.+.+..+.....++++|++|+|++|. +..  ++..
T Consensus       430 ~~~~~~~~L~~L~L~~~~~~l~~~~~~~~~~~~~~L~~L~L~~n~l~~~~~~~~~~~~~~L~~L~l~~n~-l~~~~~~~~  508 (592)
T 3ogk_B          430 SLLIGCKKLRRFAFYLRQGGLTDLGLSYIGQYSPNVRWMLLGYVGESDEGLMEFSRGCPNLQKLEMRGCC-FSERAIAAA  508 (592)
T ss_dssp             HHHHHCTTCCEEEEECCGGGCCHHHHHHHHHSCTTCCEEEECSCCSSHHHHHHHHTCCTTCCEEEEESCC-CBHHHHHHH
T ss_pred             HHHHhCCCCCEEEEecCCCCccHHHHHHHHHhCccceEeeccCCCCCHHHHHHHHhcCcccCeeeccCCC-CcHHHHHHH
Confidence               237899999998764  4444444444 489999999998887765555556789999999999998 442  3333


Q ss_pred             cCcccCccEEEEecCCCCCC-CccccccCccCcEEEecCC
Q 003387          760 NAAMPKLECLIINPCAYLKK-MPEQLWYIKSLNKFDCWWP  798 (824)
Q Consensus       760 ~~~lp~L~~L~l~~c~~l~~-lp~~l~~l~~L~~L~l~~c  798 (824)
                      ...+|+|+.|++++|+.... +..-...+|.|....+...
T Consensus       509 ~~~l~~L~~L~ls~n~it~~~~~~l~~~~p~l~~~~~~~~  548 (592)
T 3ogk_B          509 VTKLPSLRYLWVQGYRASMTGQDLMQMARPYWNIELIPSR  548 (592)
T ss_dssp             HHHCSSCCEEEEESCBCCTTCTTGGGGCCTTEEEEEECCC
T ss_pred             HHhcCccCeeECcCCcCCHHHHHHHHHhCCCcEEEEecCc
Confidence            45789999999999994432 1222345677777766665

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.74  E-value=4e-19  Score=189.43  Aligned_cols=82  Identities=20%  Similarity=0.196  Sum_probs=55.7

Q ss_pred             ccEEEeeCccCc--cCCccCC-------CCCcceEEeecCCCCC-ccChhhh-hcCCCccEeecCCccccccchhhhcc-
Q 003387          523 LRVLDLGSLVLI--QYPSGIE-------NLFLLRYLKLNIPSLN-SLPSSLL-SNLLNLYTLDMPFSYIDHTADEFWKM-  590 (824)
Q Consensus       523 Lr~L~L~~~~i~--~lp~~i~-------~l~~Lr~L~L~~~~i~-~lp~~i~-~~L~~L~~L~L~~~~l~~lp~~i~~L-  590 (824)
                      |++|+|+++.+.  .+|..+.       ++++|++|+|++|.+. .+|..++ +.+++|++|++++|.+..+|..++.+ 
T Consensus        65 L~~L~L~~n~l~~~~~~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~l~  144 (312)
T 1wwl_A           65 IKSLSLKRLTVRAARIPSRILFGALRVLGISGLQELTLENLEVTGTAPPPLLEATGPDLNILNLRNVSWATRDAWLAELQ  144 (312)
T ss_dssp             HHHCCCCEEEEEEEECBHHHHHHHHHHHTTSCCCEEEEEEEBCBSCCCCCSSSCCSCCCSEEEEESCBCSSSSSHHHHHH
T ss_pred             HhhcccccccccCCCcCHHHHHHHHHhcCcCCccEEEccCCcccchhHHHHHHhcCCCccEEEccCCCCcchhHHHHHHH
Confidence            667777777664  4555554       5777777777777776 4555532 66777777777777777666666666 


Q ss_pred             ----ccCceecCCCccCC
Q 003387          591 ----NKLRHLNFGSITLP  604 (824)
Q Consensus       591 ----~~L~~L~L~~~~~~  604 (824)
                          ++|++|++++|.+.
T Consensus       145 ~~~~~~L~~L~L~~N~l~  162 (312)
T 1wwl_A          145 QWLKPGLKVLSIAQAHSL  162 (312)
T ss_dssp             TTCCTTCCEEEEESCSCC
T ss_pred             HhhcCCCcEEEeeCCCCc
Confidence                77777777777664

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.74  E-value=4.9e-20  Score=196.54  Aligned_cols=250  Identities=16%  Similarity=0.112  Sum_probs=144.4

Q ss_pred             hhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCC--ccChhhhh-------cCCCccEeecCCcccc-ccch
Q 003387          516 FCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLN--SLPSSLLS-------NLLNLYTLDMPFSYID-HTAD  585 (824)
Q Consensus       516 ~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~--~lp~~i~~-------~L~~L~~L~L~~~~l~-~lp~  585 (824)
                      ++...+.|+.|++++|.+ .+|..+...  |++|+|+++.+.  .+|..+ .       ++++|++|++++|.+. .+|.
T Consensus        38 ~~~~~~~L~~l~l~~n~l-~~p~~~~~~--L~~L~L~~n~l~~~~~~~~~-~~~~~~~~~l~~L~~L~L~~n~l~~~~~~  113 (312)
T 1wwl_A           38 LYGGGRSLEYLLKRVDTE-ADLGQFTDI--IKSLSLKRLTVRAARIPSRI-LFGALRVLGISGLQELTLENLEVTGTAPP  113 (312)
T ss_dssp             EEEEEEECTTHHHHCCTT-CCCHHHHHH--HHHCCCCEEEEEEEECBHHH-HHHHHHHHTTSCCCEEEEEEEBCBSCCCC
T ss_pred             EEccCCCceeEeeccccc-ccHHHHHHH--HhhcccccccccCCCcCHHH-HHHHHHhcCcCCccEEEccCCcccchhHH
Confidence            455666777777777777 677666543  777777777764  455554 4       6778888888877776 4666


Q ss_pred             hh--hccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccC
Q 003387          586 EF--WKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRL  662 (824)
Q Consensus       586 ~i--~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l  662 (824)
                      .+  ..+++|++|++++|.+...  | .++.+.                 ...+++|+.|+++++.  .....+..+.++
T Consensus       114 ~~~~~~l~~L~~L~Ls~N~l~~~--~~~~~~l~-----------------~~~~~~L~~L~L~~N~--l~~~~~~~~~~l  172 (312)
T 1wwl_A          114 PLLEATGPDLNILNLRNVSWATR--DAWLAELQ-----------------QWLKPGLKVLSIAQAH--SLNFSCEQVRVF  172 (312)
T ss_dssp             CSSSCCSCCCSEEEEESCBCSSS--SSHHHHHH-----------------TTCCTTCCEEEEESCS--CCCCCTTTCCCC
T ss_pred             HHHHhcCCCccEEEccCCCCcch--hHHHHHHH-----------------HhhcCCCcEEEeeCCC--CccchHHHhccC
Confidence            55  7777888888877777631  3 232220                 0001455555555443  122222344445


Q ss_pred             CCCCeEEEeccCCCCCccEE-E-eCcc--CcCCCceEEEEEcccCCCC--Cc-ccccCCCCCCeEEeeccccCCCeeeec
Q 003387          663 SCLESLKLANESKMPRLSKI-V-LAEY--LFPHSLTHLSFSNTDLMDD--PM-PTLEKLPLLQVLKLKQNSYSGRKLTCG  735 (824)
Q Consensus       663 ~~L~~L~l~~~~~~~~L~~l-~-l~~~--~~~~~L~~L~L~~~~l~~~--~~-~~l~~l~~L~~L~L~~~~~~~~~~~~~  735 (824)
                      ++|++|++++|.    +... . +...  ..+++|++|++++|.+...  .+ ..+.++++|+.|++++|.+.+......
T Consensus       173 ~~L~~L~Ls~N~----l~~~~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~  248 (312)
T 1wwl_A          173 PALSTLDLSDNP----ELGERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPS  248 (312)
T ss_dssp             SSCCEEECCSCT----TCHHHHHHHHSCTTSCTTCCEEECTTSCCCCHHHHHHHHHHTTCCCSEEECTTSCCCSSCCCSC
T ss_pred             CCCCEEECCCCC----cCcchHHHHHHHhccCCCCCEEECCCCcCcchHHHHHHHHhcCCCCCEEECCCCcCCcccchhh
Confidence            555555555431    1100 0 0001  3445666666666665421  11 223466777777777776665332223


Q ss_pred             CCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          736 SYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       736 ~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ...+++|++|++++|. ++.+|....  ++|+.|++++|. ++.+|. +..+++|+.|++++++
T Consensus       249 ~~~l~~L~~L~Ls~N~-l~~ip~~~~--~~L~~L~Ls~N~-l~~~p~-~~~l~~L~~L~L~~N~  307 (312)
T 1wwl_A          249 CDWPSQLNSLNLSFTG-LKQVPKGLP--AKLSVLDLSYNR-LDRNPS-PDELPQVGNLSLKGNP  307 (312)
T ss_dssp             CCCCTTCCEEECTTSC-CSSCCSSCC--SEEEEEECCSSC-CCSCCC-TTTSCEEEEEECTTCT
T ss_pred             hhhcCCCCEEECCCCc-cChhhhhcc--CCceEEECCCCC-CCCChh-HhhCCCCCEEeccCCC
Confidence            3456777777777765 456655443  777788887775 445565 6777778888777775

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=99.72  E-value=5.5e-19  Score=206.35  Aligned_cols=323  Identities=13%  Similarity=0.069  Sum_probs=205.1

Q ss_pred             CCeeEEEEEecCCCccccccc---CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCcc-----CCccCCC
Q 003387          471 KKAKRLNAVEREGDFACLDDY---DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQ-----YPSGIEN  542 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~~~~~~~---~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~-----lp~~i~~  542 (824)
                      .+++++.+..+......+..+   +++|++|.+.++....  ...+...+..+++|++|+|++|.++.     ++.....
T Consensus       105 ~~L~~L~L~~~~~~~~~~~~l~~~~~~L~~L~L~~~~~~~--~~~l~~~~~~~~~L~~L~L~~~~i~~~~~~~l~~~~~~  182 (594)
T 2p1m_B          105 TWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCEGFS--TDGLAAIAATCRNLKELDLRESDVDDVSGHWLSHFPDT  182 (594)
T ss_dssp             TTCCEEEEESCBCCHHHHHHHHHHCTTCCEEEEESCEEEE--HHHHHHHHHHCTTCCEEECTTCEEECCCGGGGGGSCTT
T ss_pred             CCCCeEEeeCcEEcHHHHHHHHHhCCCCcEEeCCCcCCCC--HHHHHHHHHhCCCCCEEeCcCCccCCcchHHHHHHhhc
Confidence            467888888433222222233   7899999998885321  22356677789999999999998652     3344457


Q ss_pred             CCcceEEeecCCC--CC--ccChhhhhcCCCccEeecCCc-cccccchhhhccccCceecCCCccCC-------------
Q 003387          543 LFLLRYLKLNIPS--LN--SLPSSLLSNLLNLYTLDMPFS-YIDHTADEFWKMNKLRHLNFGSITLP-------------  604 (824)
Q Consensus       543 l~~Lr~L~L~~~~--i~--~lp~~i~~~L~~L~~L~L~~~-~l~~lp~~i~~L~~L~~L~L~~~~~~-------------  604 (824)
                      +++|++|++++|.  +.  .++.-+ .++++|++|++++| .+..+|..+.++++|++|+++.+...             
T Consensus       183 ~~~L~~L~l~~~~~~~~~~~l~~l~-~~~~~L~~L~L~~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~l~~~l  261 (594)
T 2p1m_B          183 YTSLVSLNISCLASEVSFSALERLV-TRCPNLKSLKLNRAVPLEKLATLLQRAPQLEELGTGGYTAEVRPDVYSGLSVAL  261 (594)
T ss_dssp             CCCCCEEECTTCCSCCCHHHHHHHH-HHCTTCCEEECCTTSCHHHHHHHHHHCTTCSEEECSBCCCCCCHHHHHHHHHHH
T ss_pred             CCcCcEEEecccCCcCCHHHHHHHH-HhCCCCcEEecCCCCcHHHHHHHHhcCCcceEcccccccCccchhhHHHHHHHH
Confidence            8899999999986  22  233323 67899999999999 77788888889999999987655310             


Q ss_pred             -------------C---CCCC-CCCCCCCCCeeeccCCCc---chhhhcCCCCccceEEEecccccchhhHHHHhccCCC
Q 003387          605 -------------A---HPGK-FCGSLENLNFISALHPCC---CTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSC  664 (824)
Q Consensus       605 -------------~---~~~p-~i~~L~~L~~l~~~~~~~---~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~  664 (824)
                                   .   ..+| .+..+++|+.|+++.+..   .+...+..+++|++|++.++.  ....++.....+++
T Consensus       262 ~~~~~L~~Ls~~~~~~~~~l~~~~~~~~~L~~L~L~~~~l~~~~l~~~~~~~~~L~~L~l~~~~--~~~~l~~l~~~~~~  339 (594)
T 2p1m_B          262 SGCKELRCLSGFWDAVPAYLPAVYSVCSRLTTLNLSYATVQSYDLVKLLCQCPKLQRLWVLDYI--EDAGLEVLASTCKD  339 (594)
T ss_dssp             HTCTTCCEEECCBTCCGGGGGGGHHHHTTCCEEECTTCCCCHHHHHHHHTTCTTCCEEEEEGGG--HHHHHHHHHHHCTT
T ss_pred             hcCCCcccccCCcccchhhHHHHHHhhCCCCEEEccCCCCCHHHHHHHHhcCCCcCEEeCcCcc--CHHHHHHHHHhCCC
Confidence                         0   0111 112456677777763321   122335577888888887762  33444444556778


Q ss_pred             CCeEEEec---------cC-----------CCCCccEEEeCcc-----------CcCCCceEEEEE--c---c-cCCCCC
Q 003387          665 LESLKLAN---------ES-----------KMPRLSKIVLAEY-----------LFPHSLTHLSFS--N---T-DLMDDP  707 (824)
Q Consensus       665 L~~L~l~~---------~~-----------~~~~L~~l~l~~~-----------~~~~~L~~L~L~--~---~-~l~~~~  707 (824)
                      |++|++..         +.           .+++|+.|.+...           ..+++|+.|+++  +   | .++...
T Consensus       340 L~~L~L~~~~~~g~~~~~~l~~~~l~~l~~~~~~L~~L~~~~~~l~~~~~~~l~~~~~~L~~L~L~~~~~~~~~~l~~~~  419 (594)
T 2p1m_B          340 LRELRVFPSEPFVMEPNVALTEQGLVSVSMGCPKLESVLYFCRQMTNAALITIARNRPNMTRFRLCIIEPKAPDYLTLEP  419 (594)
T ss_dssp             CCEEEEECSCTTCSSCSSCCCHHHHHHHHHHCTTCCEEEEEESCCCHHHHHHHHHHCTTCCEEEEEESSTTCCCTTTCCC
T ss_pred             CCEEEEecCcccccccCCCCCHHHHHHHHHhchhHHHHHHhcCCcCHHHHHHHHhhCCCcceeEeecccCCCcccccCCc
Confidence            88887732         10           2567777755332           246788888887  2   2 332211


Q ss_pred             c-----ccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceecc-CcccCccEEEEecCCCCCCC-
Q 003387          708 M-----PTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGN-AAMPKLECLIINPCAYLKKM-  780 (824)
Q Consensus       708 ~-----~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~-~~lp~L~~L~l~~c~~l~~l-  780 (824)
                      .     ..+..+++|+.|++++ .+.+..+......+++|++|+|++|.........+ ..+|+|+.|++++|+..... 
T Consensus       420 ~~~~~~~l~~~~~~L~~L~L~~-~l~~~~~~~l~~~~~~L~~L~L~~~~i~~~~~~~l~~~~~~L~~L~L~~n~~~~~~~  498 (594)
T 2p1m_B          420 LDIGFGAIVEHCKDLRRLSLSG-LLTDKVFEYIGTYAKKMEMLSVAFAGDSDLGMHHVLSGCDSLRKLEIRDCPFGDKAL  498 (594)
T ss_dssp             THHHHHHHHHHCTTCCEEECCS-SCCHHHHHHHHHHCTTCCEEEEESCCSSHHHHHHHHHHCTTCCEEEEESCSCCHHHH
T ss_pred             hhhHHHHHHhhCCCccEEeecC-cccHHHHHHHHHhchhccEeeccCCCCcHHHHHHHHhcCCCcCEEECcCCCCcHHHH
Confidence            1     1245677888888864 33332222112237889999999887322222222 46899999999999973222 


Q ss_pred             ccccccCccCcEEEecCCc
Q 003387          781 PEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       781 p~~l~~l~~L~~L~l~~c~  799 (824)
                      +..+..+++|+.|++++|+
T Consensus       499 ~~~~~~l~~L~~L~l~~~~  517 (594)
T 2p1m_B          499 LANASKLETMRSLWMSSCS  517 (594)
T ss_dssp             HHTGGGGGGSSEEEEESSC
T ss_pred             HHHHHhCCCCCEEeeeCCC
Confidence            2345678999999999998

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.70  E-value=2.9e-17  Score=171.25  Aligned_cols=85  Identities=21%  Similarity=0.226  Sum_probs=60.3

Q ss_pred             hcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCce
Q 003387          517 CGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRH  595 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~  595 (824)
                      ...++.|+.|+++++.+..++ .+..+++|++|++++|.+..++ .+ +++++|++|++++|.+..+|.. +..+++|++
T Consensus        37 ~~~l~~L~~L~l~~~~i~~~~-~l~~l~~L~~L~l~~n~l~~~~-~l-~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  113 (272)
T 3rfs_A           37 QNELNSIDQIIANNSDIKSVQ-GIQYLPNVRYLALGGNKLHDIS-AL-KELTNLTYLILTGNQLQSLPNGVFDKLTNLKE  113 (272)
T ss_dssp             HHHHTTCCEEECTTSCCCCCT-TGGGCTTCCEEECTTSCCCCCG-GG-TTCTTCCEEECTTSCCCCCCTTTTTTCTTCCE
T ss_pred             cccccceeeeeeCCCCccccc-ccccCCCCcEEECCCCCCCCch-hh-cCCCCCCEEECCCCccCccChhHhcCCcCCCE
Confidence            345677777777777776655 3667777777777777777654 44 7777777777777777776654 567777777


Q ss_pred             ecCCCccCC
Q 003387          596 LNFGSITLP  604 (824)
Q Consensus       596 L~L~~~~~~  604 (824)
                      |++++|.+.
T Consensus       114 L~L~~n~l~  122 (272)
T 3rfs_A          114 LVLVENQLQ  122 (272)
T ss_dssp             EECTTSCCC
T ss_pred             EECCCCcCC
Confidence            777777664

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.70  E-value=5.2e-17  Score=172.53  Aligned_cols=193  Identities=20%  Similarity=0.209  Sum_probs=104.3

Q ss_pred             cccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceec
Q 003387          518 GMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLN  597 (824)
Q Consensus       518 ~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~  597 (824)
                      ..+++|++|++++|.+..+| .+..+++|++|++++|.+..++. + .++++|++|++++|.+..+| .+..+++|++|+
T Consensus        38 ~~l~~L~~L~l~~~~i~~l~-~~~~l~~L~~L~L~~n~i~~~~~-~-~~l~~L~~L~L~~n~l~~~~-~~~~l~~L~~L~  113 (308)
T 1h6u_A           38 ADLDGITTLSAFGTGVTTIE-GVQYLNNLIGLELKDNQITDLAP-L-KNLTKITELELSGNPLKNVS-AIAGLQSIKTLD  113 (308)
T ss_dssp             HHHHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-G-TTCCSCCEEECCSCCCSCCG-GGTTCTTCCEEE
T ss_pred             HHcCCcCEEEeeCCCccCch-hhhccCCCCEEEccCCcCCCChh-H-ccCCCCCEEEccCCcCCCch-hhcCCCCCCEEE
Confidence            34566666666666666655 46666666666666666666665 4 66666666666666666665 366666666666


Q ss_pred             CCCccCCCCCCCCCCCCCCCCeeeccCC-CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCC
Q 003387          598 FGSITLPAHPGKFCGSLENLNFISALHP-CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKM  676 (824)
Q Consensus       598 L~~~~~~~~~~p~i~~L~~L~~l~~~~~-~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~  676 (824)
                      +++|.+.  .++.++.+++|+.|+++.+ -..+.. +..+++|+.|+++++.   ...++. +..+++|+.|++++|.  
T Consensus       114 l~~n~l~--~~~~l~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L~l~~n~---l~~~~~-l~~l~~L~~L~l~~n~--  184 (308)
T 1h6u_A          114 LTSTQIT--DVTPLAGLSNLQVLYLDLNQITNISP-LAGLTNLQYLSIGNAQ---VSDLTP-LANLSKLTTLKADDNK--  184 (308)
T ss_dssp             CTTSCCC--CCGGGTTCTTCCEEECCSSCCCCCGG-GGGCTTCCEEECCSSC---CCCCGG-GTTCTTCCEEECCSSC--
T ss_pred             CCCCCCC--CchhhcCCCCCCEEECCCCccCcCcc-ccCCCCccEEEccCCc---CCCChh-hcCCCCCCEEECCCCc--
Confidence            6666654  2333444444444444421 111222 5555666666666553   111221 4555556666555441  


Q ss_pred             CCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCC
Q 003387          677 PRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG  729 (824)
Q Consensus       677 ~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~  729 (824)
                        ++.+.  ....+++|++|++++|.+.+..  .+..+++|+.|++++|.+..
T Consensus       185 --l~~~~--~l~~l~~L~~L~L~~N~l~~~~--~l~~l~~L~~L~l~~N~i~~  231 (308)
T 1h6u_A          185 --ISDIS--PLASLPNLIEVHLKNNQISDVS--PLANTSNLFIVTLTNQTITN  231 (308)
T ss_dssp             --CCCCG--GGGGCTTCCEEECTTSCCCBCG--GGTTCTTCCEEEEEEEEEEC
T ss_pred             --cCcCh--hhcCCCCCCEEEccCCccCccc--cccCCCCCCEEEccCCeeec
Confidence              22211  1234555666666666554322  25556666666666555543

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=99.70  E-value=1.2e-16  Score=168.13  Aligned_cols=200  Identities=20%  Similarity=0.154  Sum_probs=137.6

Q ss_pred             hcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCcee
Q 003387          517 CGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL  596 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L  596 (824)
                      +.++++|+.++++++.++.+|..+.  .+|++|+|++|.+..++...|.++++|++|++++|.+..+|.. +.+++|++|
T Consensus         6 ~~~l~~l~~l~~~~~~l~~ip~~~~--~~l~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~-~~l~~L~~L   82 (290)
T 1p9a_G            6 VSKVASHLEVNCDKRNLTALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQVD-GTLPVLGTL   82 (290)
T ss_dssp             EECSTTCCEEECTTSCCSSCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCCEEECC-SCCTTCCEE
T ss_pred             ccccCCccEEECCCCCCCcCCCCCC--CCCCEEEcCCCcCCccCHHHhhcCCCCCEEECCCCccCcccCC-CCCCcCCEE
Confidence            5677889999999999998888775  5899999999999887765558999999999999988888764 788999999


Q ss_pred             cCCCccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCC
Q 003387          597 NFGSITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESK  675 (824)
Q Consensus       597 ~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~  675 (824)
                      ++++|.+.  .+| .                      +..+++|+.|+++++.  .....+..+.++++|+.|++++|  
T Consensus        83 ~Ls~N~l~--~l~~~----------------------~~~l~~L~~L~l~~N~--l~~l~~~~~~~l~~L~~L~L~~N--  134 (290)
T 1p9a_G           83 DLSHNQLQ--SLPLL----------------------GQTLPALTVLDVSFNR--LTSLPLGALRGLGELQELYLKGN--  134 (290)
T ss_dssp             ECCSSCCS--SCCCC----------------------TTTCTTCCEEECCSSC--CCCCCSSTTTTCTTCCEEECTTS--
T ss_pred             ECCCCcCC--cCchh----------------------hccCCCCCEEECCCCc--CcccCHHHHcCCCCCCEEECCCC--
Confidence            99988775  333 2                      3445555555555542  11111233445556666666554  


Q ss_pred             CCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCC
Q 003387          676 MPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSML  751 (824)
Q Consensus       676 ~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~  751 (824)
                        .++.+....+..+++|+.|+|++|.+....+..+..+++|+.|++++|.+..  ++.....+++|+.|.|++|+
T Consensus       135 --~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L~~N~l~~--ip~~~~~~~~L~~l~L~~Np  206 (290)
T 1p9a_G          135 --ELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYT--IPKGFFGSHLLPFAFLHGNP  206 (290)
T ss_dssp             --CCCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCTTCCEEECCSSCCCC--CCTTTTTTCCCSEEECCSCC
T ss_pred             --CCCccChhhcccccCCCEEECCCCcCCccCHHHhcCcCCCCEEECCCCcCCc--cChhhcccccCCeEEeCCCC
Confidence              2333332333456777777887777765555556777788888887777653  44445556677777777765

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.70  E-value=8.7e-17  Score=167.48  Aligned_cols=82  Identities=24%  Similarity=0.220  Sum_probs=59.9

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCC
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFG  599 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~  599 (824)
                      ..++.++++++.++.+|..+.  .+|++|++++|.+..+|...|.++++|++|++++|.+..+|.. +..+++|++|+++
T Consensus        16 ~~~~~l~~~~~~l~~ip~~~~--~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~   93 (270)
T 2o6q_A           16 NNKNSVDCSSKKLTAIPSNIP--ADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVT   93 (270)
T ss_dssp             TTTTEEECTTSCCSSCCSCCC--TTCSEEECCSSCCSCCCTTSSSSCTTCCEEECCSSCCSCCCTTTTSSCTTCCEEECC
T ss_pred             CCCCEEEccCCCCCccCCCCC--CCCCEEECcCCCCCeeCHHHhcCCCCCCEEECCCCccCeeChhhhcCCCCCCEEECC
Confidence            346777888777777776654  4777888888877777764447778888888887777777765 4667788888777


Q ss_pred             CccCC
Q 003387          600 SITLP  604 (824)
Q Consensus       600 ~~~~~  604 (824)
                      +|.+.
T Consensus        94 ~n~l~   98 (270)
T 2o6q_A           94 DNKLQ   98 (270)
T ss_dssp             SSCCC
T ss_pred             CCcCC
Confidence            77664

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=99.69  E-value=3.9e-18  Score=183.93  Aligned_cols=257  Identities=16%  Similarity=0.130  Sum_probs=170.0

Q ss_pred             ceeEeeccCCCCCCCCcchhHhhhccc--CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCc--cChhhhhcCCC
Q 003387          494 QLHSLLCCSPETRHLDPIDWEKFCGMF--KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNS--LPSSLLSNLLN  569 (824)
Q Consensus       494 ~Lr~L~l~~~~~~~~~~~~~~~~~~~~--~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~--lp~~i~~~L~~  569 (824)
                      .++.+.+.++...       +..+..+  +.+++|+++++.+...+..+..+++|++|++++|.+..  +|..+ .++++
T Consensus        48 ~~~~l~l~~~~~~-------~~~~~~~~~~~l~~L~l~~n~l~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~~~-~~~~~  119 (336)
T 2ast_B           48 LWQTLDLTGKNLH-------PDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGIL-SQCSK  119 (336)
T ss_dssp             TSSEEECTTCBCC-------HHHHHHHHHTTCSEEECTTCEECSCCCSCCCCBCCCEEECTTCEECHHHHHHHH-TTBCC
T ss_pred             hheeeccccccCC-------HHHHHhhhhccceEEEcCCccccccchhhccCCCCCEEEccCCCcCHHHHHHHH-hhCCC
Confidence            3566666554432       3445555  77888888888877666667778888888888877663  55555 78888


Q ss_pred             ccEeecCCcccc-ccchhhhccccCceecCCCc-cCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecc
Q 003387          570 LYTLDMPFSYID-HTADEFWKMNKLRHLNFGSI-TLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGD  647 (824)
Q Consensus       570 L~~L~L~~~~l~-~lp~~i~~L~~L~~L~L~~~-~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~  647 (824)
                      |++|++++|.+. ..|..++++++|++|++++| .+.                     ...+...+..+++|+.|+++++
T Consensus       120 L~~L~L~~~~l~~~~~~~l~~~~~L~~L~L~~~~~l~---------------------~~~l~~~~~~~~~L~~L~l~~~  178 (336)
T 2ast_B          120 LQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFS---------------------EFALQTLLSSCSRLDELNLSWC  178 (336)
T ss_dssp             CSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCC---------------------HHHHHHHHHHCTTCCEEECCCC
T ss_pred             CCEEeCcCcccCHHHHHHHhcCCCCCEEECCCCCCCC---------------------HHHHHHHHhcCCCCCEEcCCCC
Confidence            888888888665 45666777888888888777 332                     2223344778899999999988


Q ss_pred             cccchhhHHHHhccCC-CCCeEEEeccCCCCCccEEEe-CccCcCCCceEEEEEccc-CCCCCcccccCCCCCCeEEeec
Q 003387          648 LSYNQSLLSKSLCRLS-CLESLKLANESKMPRLSKIVL-AEYLFPHSLTHLSFSNTD-LMDDPMPTLEKLPLLQVLKLKQ  724 (824)
Q Consensus       648 ~~~~~~~l~~~l~~l~-~L~~L~l~~~~~~~~L~~l~l-~~~~~~~~L~~L~L~~~~-l~~~~~~~l~~l~~L~~L~L~~  724 (824)
                      .......++..+..++ +|++|+++++.  ..+..-.+ .....+++|++|++++|. +++..+..++++++|+.|++++
T Consensus       179 ~~l~~~~~~~~~~~l~~~L~~L~l~~~~--~~~~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~l~~l~~L~~L~l~~  256 (336)
T 2ast_B          179 FDFTEKHVQVAVAHVSETITQLNLSGYR--KNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSR  256 (336)
T ss_dssp             TTCCHHHHHHHHHHSCTTCCEEECCSCG--GGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEECTT
T ss_pred             CCcChHHHHHHHHhcccCCCEEEeCCCc--ccCCHHHHHHHHhhCCCCCEEeCCCCCcCCHHHHHHHhCCCCCCEeeCCC
Confidence            4333445777788888 99999998651  01111000 112457889999999988 6666777888899999999988


Q ss_pred             cccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcc-cCccEEEEecCCCCCCCccccc
Q 003387          725 NSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAM-PKLECLIINPCAYLKKMPEQLW  785 (824)
Q Consensus       725 ~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~l-p~L~~L~l~~c~~l~~lp~~l~  785 (824)
                      |..........+..+++|++|++++|  +..-  ....+ .+|+.|++++|......|..+.
T Consensus       257 ~~~~~~~~~~~l~~~~~L~~L~l~~~--i~~~--~~~~l~~~l~~L~l~~n~l~~~~~~~~~  314 (336)
T 2ast_B          257 CYDIIPETLLELGEIPTLKTLQVFGI--VPDG--TLQLLKEALPHLQINCSHFTTIARPTIG  314 (336)
T ss_dssp             CTTCCGGGGGGGGGCTTCCEEECTTS--SCTT--CHHHHHHHSTTSEESCCCSCCTTCSSCS
T ss_pred             CCCCCHHHHHHHhcCCCCCEEeccCc--cCHH--HHHHHHhhCcceEEecccCccccCCccc
Confidence            75222221223566889999999987  2211  11223 3466666877776665665544

>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*

Probab=99.69  E-value=1.2e-16  Score=167.02  Aligned_cols=200  Identities=22%  Similarity=0.220  Sum_probs=109.8

Q ss_pred             cccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccc-hhhhccccCceecCC
Q 003387          522 LLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFG  599 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~  599 (824)
                      .|++|++++|.++.+|. .+.++++|++|++++|.+..++...+.++++|++|++++|.+..++ ..+.++++|++|+++
T Consensus        29 ~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~  108 (276)
T 2z62_A           29 STKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAV  108 (276)
T ss_dssp             TCCEEECTTCCCCEECTTTTTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECT
T ss_pred             CccEEECCCCcccccCHhHhccccCCcEEECCCCcCCccCHHHccCCcCCCEEECCCCccCccChhhhcCCccccEEECC
Confidence            45566666665554443 4555666666666666655555433355666666666666555554 335556666666665


Q ss_pred             CccCCCCCCC-CCCCCCCCCeeeccCCC---cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCC----eEEEe
Q 003387          600 SITLPAHPGK-FCGSLENLNFISALHPC---CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLE----SLKLA  671 (824)
Q Consensus       600 ~~~~~~~~~p-~i~~L~~L~~l~~~~~~---~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~----~L~l~  671 (824)
                      +|.+.. ..+ .++++++|+.|+++.+.   ..++..+..+++|+.|+++++.  .....+..+..+++|+    +|+++
T Consensus       109 ~n~l~~-~~~~~~~~l~~L~~L~l~~n~l~~~~l~~~~~~l~~L~~L~Ls~N~--l~~~~~~~~~~l~~L~~l~l~L~ls  185 (276)
T 2z62_A          109 ETNLAS-LENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK--IQSIYCTDLRVLHQMPLLNLSLDLS  185 (276)
T ss_dssp             TSCCCC-STTCCCTTCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCSSC--CCEECGGGGHHHHTCTTCCEEEECC
T ss_pred             CCCccc-cCchhcccCCCCCEEECcCCccceecCchhhccCCCCCEEECCCCC--CCcCCHHHhhhhhhccccceeeecC
Confidence            555542 111 34555555555554211   1122336777778888777764  1111112233333333    66666


Q ss_pred             ccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCC
Q 003387          672 NESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG  729 (824)
Q Consensus       672 ~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~  729 (824)
                      +|    .++.+....+ ...+|+.|++++|.+....+..++.+++|+.|++++|.+..
T Consensus       186 ~n----~l~~~~~~~~-~~~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~N~~~c  238 (276)
T 2z62_A          186 LN----PMNFIQPGAF-KEIRLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDC  238 (276)
T ss_dssp             SS----CCCEECTTSS-CSCCEEEEECCSSCCSCCCTTTTTTCCSCCEEECCSSCBCC
T ss_pred             CC----cccccCcccc-CCCcccEEECCCCceeecCHhHhcccccccEEEccCCcccc
Confidence            55    3444432222 23368888888887766555566778888888888776653

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=99.69  E-value=1.8e-17  Score=178.72  Aligned_cols=226  Identities=18%  Similarity=0.164  Sum_probs=119.7

Q ss_pred             CcccEEEeeCccCccCCccCCCC--CcceEEeecCCCCCccChhhhhcCCCccEeecCCccccc--cchhhhccccCcee
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENL--FLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH--TADEFWKMNKLRHL  596 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l--~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~--lp~~i~~L~~L~~L  596 (824)
                      ..++.|+++++.+.  |..+..+  .++++|+++++.+...+..+ .++++|++|++++|.+..  +|..+..+++|++|
T Consensus        47 ~~~~~l~l~~~~~~--~~~~~~~~~~~l~~L~l~~n~l~~~~~~~-~~~~~L~~L~L~~~~l~~~~~~~~~~~~~~L~~L  123 (336)
T 2ast_B           47 SLWQTLDLTGKNLH--PDVTGRLLSQGVIAFRCPRSFMDQPLAEH-FSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNL  123 (336)
T ss_dssp             TTSSEEECTTCBCC--HHHHHHHHHTTCSEEECTTCEECSCCCSC-CCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEE
T ss_pred             hhheeeccccccCC--HHHHHhhhhccceEEEcCCccccccchhh-ccCCCCCEEEccCCCcCHHHHHHHHhhCCCCCEE
Confidence            34566666666554  3334444  56666666666666555555 566666666666665542  55556666666666


Q ss_pred             cCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCC
Q 003387          597 NFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKM  676 (824)
Q Consensus       597 ~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~  676 (824)
                      ++++|.+.                     ...+.. +..+++|++|++++|.......++..+.++++|++|+++++.  
T Consensus       124 ~L~~~~l~---------------------~~~~~~-l~~~~~L~~L~L~~~~~l~~~~l~~~~~~~~~L~~L~l~~~~--  179 (336)
T 2ast_B          124 SLEGLRLS---------------------DPIVNT-LAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCF--  179 (336)
T ss_dssp             ECTTCBCC---------------------HHHHHH-HTTCTTCSEEECTTCBSCCHHHHHHHHHHCTTCCEEECCCCT--
T ss_pred             eCcCcccC---------------------HHHHHH-HhcCCCCCEEECCCCCCCCHHHHHHHHhcCCCCCEEcCCCCC--
Confidence            66666543                     122222 555666666666665322333455556666666666666431  


Q ss_pred             CCccEEEe-CccCcCC-CceEEEEEcc--cCC-CCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCC
Q 003387          677 PRLSKIVL-AEYLFPH-SLTHLSFSNT--DLM-DDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSML  751 (824)
Q Consensus       677 ~~L~~l~l-~~~~~~~-~L~~L~L~~~--~l~-~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~  751 (824)
                       .++...+ .....++ +|++|++++|  .+. ...+..+.++++|+.|++++|..........+..+++|++|++++|.
T Consensus       180 -~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~l~~l~~L~~L~l~~~~  258 (336)
T 2ast_B          180 -DFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCY  258 (336)
T ss_dssp             -TCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEECTTCT
T ss_pred             -CcChHHHHHHHHhcccCCCEEEeCCCcccCCHHHHHHHHhhCCCCCEEeCCCCCcCCHHHHHHHhCCCCCCEeeCCCCC
Confidence             1221100 1113445 6666666666  232 12234445566666666666652222223344556666666666664


Q ss_pred             CCccc-eeccCcccCccEEEEecC
Q 003387          752 WLEEW-TMGNAAMPKLECLIINPC  774 (824)
Q Consensus       752 ~l~~l-~~~~~~lp~L~~L~l~~c  774 (824)
                      .+... ...++.+|+|+.|++++|
T Consensus       259 ~~~~~~~~~l~~~~~L~~L~l~~~  282 (336)
T 2ast_B          259 DIIPETLLELGEIPTLKTLQVFGI  282 (336)
T ss_dssp             TCCGGGGGGGGGCTTCCEEECTTS
T ss_pred             CCCHHHHHHHhcCCCCCEEeccCc
Confidence            22211 113445666666666666

>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*

Probab=99.69  E-value=1.1e-16  Score=167.43  Aligned_cols=78  Identities=19%  Similarity=0.261  Sum_probs=66.1

Q ss_pred             EEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch-hhhccccCceecCCCccC
Q 003387          525 VLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITL  603 (824)
Q Consensus       525 ~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~  603 (824)
                      +.+..+..+..+|..+.  ++|++|++++|.+..++...+.++++|++|++++|.+..++. .+.++++|++|++++|.+
T Consensus        11 ~~~c~~~~l~~ip~~l~--~~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l   88 (276)
T 2z62_A           11 TYQCMELNFYKIPDNLP--FSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPI   88 (276)
T ss_dssp             EEECTTSCCSSCCSSSC--TTCCEEECTTCCCCEECTTTTTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTCCC
T ss_pred             eEEecCCCccccCCCCC--CCccEEECCCCcccccCHhHhccccCCcEEECCCCcCCccCHHHccCCcCCCEEECCCCcc
Confidence            45566666778888775  589999999999999887444999999999999999998875 588999999999999987


Q ss_pred             C
Q 003387          604 P  604 (824)
Q Consensus       604 ~  604 (824)
                      .
T Consensus        89 ~   89 (276)
T 2z62_A           89 Q   89 (276)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=99.68  E-value=6.5e-18  Score=197.19  Aligned_cols=304  Identities=16%  Similarity=0.110  Sum_probs=184.5

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc--Cc--cCCccCCCCCcceEEeecCC-CCCccChhhhhc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV--LI--QYPSGIENLFLLRYLKLNIP-SLNSLPSSLLSN  566 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~--i~--~lp~~i~~l~~Lr~L~L~~~-~i~~lp~~i~~~  566 (824)
                      +++|++|.+.++.........+..+...+++|++|++++|.  +.  .++..+..+++|++|++++| .+..+|..+ .+
T Consensus       155 ~~~L~~L~L~~~~i~~~~~~~l~~~~~~~~~L~~L~l~~~~~~~~~~~l~~l~~~~~~L~~L~L~~~~~~~~l~~~~-~~  233 (594)
T 2p1m_B          155 CRNLKELDLRESDVDDVSGHWLSHFPDTYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATLL-QR  233 (594)
T ss_dssp             CTTCCEEECTTCEEECCCGGGGGGSCTTCCCCCEEECTTCCSCCCHHHHHHHHHHCTTCCEEECCTTSCHHHHHHHH-HH
T ss_pred             CCCCCEEeCcCCccCCcchHHHHHHhhcCCcCcEEEecccCCcCCHHHHHHHHHhCCCCcEEecCCCCcHHHHHHHH-hc
Confidence            55666666655543211112233344455566666665554  21  12222233455566665554 233343333 45


Q ss_pred             CCCccEeec-------------------------------CCccccccchhhhccccCceecCCCccCCCCCCC-CCCCC
Q 003387          567 LLNLYTLDM-------------------------------PFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSL  614 (824)
Q Consensus       567 L~~L~~L~L-------------------------------~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L  614 (824)
                      +++|+.|++                               .+.....+|..+..+++|++|++++|.+....++ .+.++
T Consensus       234 ~~~L~~L~l~~~~~~~~~~~~~~l~~~l~~~~~L~~Ls~~~~~~~~~l~~~~~~~~~L~~L~L~~~~l~~~~l~~~~~~~  313 (594)
T 2p1m_B          234 APQLEELGTGGYTAEVRPDVYSGLSVALSGCKELRCLSGFWDAVPAYLPAVYSVCSRLTTLNLSYATVQSYDLVKLLCQC  313 (594)
T ss_dssp             CTTCSEEECSBCCCCCCHHHHHHHHHHHHTCTTCCEEECCBTCCGGGGGGGHHHHTTCCEEECTTCCCCHHHHHHHHTTC
T ss_pred             CCcceEcccccccCccchhhHHHHHHHHhcCCCcccccCCcccchhhHHHHHHhhCCCCEEEccCCCCCHHHHHHHHhcC
Confidence            555555543                               3333344565566789999999999986432233 46688


Q ss_pred             CCCCeeeccCCC--cchhhhcCCCCccceEEEecc--------cccchhhHHHHhccCCCCCeEEEeccC----------
Q 003387          615 ENLNFISALHPC--CCTEDILGRLPNLRNLRIRGD--------LSYNQSLLSKSLCRLSCLESLKLANES----------  674 (824)
Q Consensus       615 ~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~--------~~~~~~~l~~~l~~l~~L~~L~l~~~~----------  674 (824)
                      ++|+.|.+....  ..+......+++|++|++..+        .......+......+++|++|.+..+.          
T Consensus       314 ~~L~~L~l~~~~~~~~l~~l~~~~~~L~~L~L~~~~~~g~~~~~~l~~~~l~~l~~~~~~L~~L~~~~~~l~~~~~~~l~  393 (594)
T 2p1m_B          314 PKLQRLWVLDYIEDAGLEVLASTCKDLRELRVFPSEPFVMEPNVALTEQGLVSVSMGCPKLESVLYFCRQMTNAALITIA  393 (594)
T ss_dssp             TTCCEEEEEGGGHHHHHHHHHHHCTTCCEEEEECSCTTCSSCSSCCCHHHHHHHHHHCTTCCEEEEEESCCCHHHHHHHH
T ss_pred             CCcCEEeCcCccCHHHHHHHHHhCCCCCEEEEecCcccccccCCCCCHHHHHHHHHhchhHHHHHHhcCCcCHHHHHHHH
Confidence            899999987431  122332346899999999542        222333444444558899999776542          


Q ss_pred             -CCCCccEEEeC--c---c----------------CcCCCceEEEEEcccCCCCCcccccC-CCCCCeEEeeccccCCCe
Q 003387          675 -KMPRLSKIVLA--E---Y----------------LFPHSLTHLSFSNTDLMDDPMPTLEK-LPLLQVLKLKQNSYSGRK  731 (824)
Q Consensus       675 -~~~~L~~l~l~--~---~----------------~~~~~L~~L~L~~~~l~~~~~~~l~~-l~~L~~L~L~~~~~~~~~  731 (824)
                       .+++|+.|.+.  +   +                ..+++|+.|+|++ .+....+..++. +++|+.|+|++|.+++..
T Consensus       394 ~~~~~L~~L~L~~~~~~~~~~l~~~~~~~~~~~l~~~~~~L~~L~L~~-~l~~~~~~~l~~~~~~L~~L~L~~~~i~~~~  472 (594)
T 2p1m_B          394 RNRPNMTRFRLCIIEPKAPDYLTLEPLDIGFGAIVEHCKDLRRLSLSG-LLTDKVFEYIGTYAKKMEMLSVAFAGDSDLG  472 (594)
T ss_dssp             HHCTTCCEEEEEESSTTCCCTTTCCCTHHHHHHHHHHCTTCCEEECCS-SCCHHHHHHHHHHCTTCCEEEEESCCSSHHH
T ss_pred             hhCCCcceeEeecccCCCcccccCCchhhHHHHHHhhCCCccEEeecC-cccHHHHHHHHHhchhccEeeccCCCCcHHH
Confidence             36889999998  2   1                3467899999977 555444555555 899999999998876543


Q ss_pred             eeecCCCCCCccEEeeccCCCCccce--eccCcccCccEEEEecCCCCCCCcccc-ccCccCcEEEecCC
Q 003387          732 LTCGSYGFPNLKVLHLKSMLWLEEWT--MGNAAMPKLECLIINPCAYLKKMPEQL-WYIKSLNKFDCWWP  798 (824)
Q Consensus       732 ~~~~~~~~~~L~~L~L~~~~~l~~l~--~~~~~lp~L~~L~l~~c~~l~~lp~~l-~~l~~L~~L~l~~c  798 (824)
                      +.....++++|++|+|++|+. ....  .....+++|+.|++++|+........+ ..+|+|+...+.+.
T Consensus       473 ~~~l~~~~~~L~~L~L~~n~~-~~~~~~~~~~~l~~L~~L~l~~~~~~~~~~~~l~~~lp~l~i~~~~~~  541 (594)
T 2p1m_B          473 MHHVLSGCDSLRKLEIRDCPF-GDKALLANASKLETMRSLWMSSCSVSFGACKLLGQKMPKLNVEVIDER  541 (594)
T ss_dssp             HHHHHHHCTTCCEEEEESCSC-CHHHHHHTGGGGGGSSEEEEESSCCBHHHHHHHHHHCTTEEEEEECSS
T ss_pred             HHHHHhcCCCcCEEECcCCCC-cHHHHHHHHHhCCCCCEEeeeCCCCCHHHHHHHHHhCCCCEEEEecCC
Confidence            333335689999999999985 4322  234568999999999998732211122 35577765555443

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.67  E-value=4.5e-16  Score=162.10  Aligned_cols=199  Identities=25%  Similarity=0.273  Sum_probs=119.6

Q ss_pred             ceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccE
Q 003387          494 QLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYT  572 (824)
Q Consensus       494 ~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~  572 (824)
                      ..+++.+.+.....    ++ ..+  .+.|+.|+|++|.+..+|. .+.++++|++|++++|.+..+|..+|.++++|++
T Consensus        17 ~~~~l~~~~~~l~~----ip-~~~--~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~   89 (270)
T 2o6q_A           17 NKNSVDCSSKKLTA----IP-SNI--PADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLET   89 (270)
T ss_dssp             TTTEEECTTSCCSS----CC-SCC--CTTCSEEECCSSCCSCCCTTSSSSCTTCCEEECCSSCCSCCCTTTTSSCTTCCE
T ss_pred             CCCEEEccCCCCCc----cC-CCC--CCCCCEEECcCCCCCeeCHHHhcCCCCCCEEECCCCccCeeChhhhcCCCCCCE
Confidence            35566666555432    11 111  2578999999999887765 6888999999999999999998887788999999


Q ss_pred             eecCCccccccchh-hhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccc
Q 003387          573 LDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYN  651 (824)
Q Consensus       573 L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~  651 (824)
                      |++++|.+..+|.. +..+++|++|++++|.+..  ++                    ...+..+++|+.|+++++.  .
T Consensus        90 L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~--~~--------------------~~~~~~l~~L~~L~Ls~n~--l  145 (270)
T 2o6q_A           90 LWVTDNKLQALPIGVFDQLVNLAELRLDRNQLKS--LP--------------------PRVFDSLTKLTYLSLGYNE--L  145 (270)
T ss_dssp             EECCSSCCCCCCTTTTTTCSSCCEEECCSSCCCC--CC--------------------TTTTTTCTTCCEEECCSSC--C
T ss_pred             EECCCCcCCcCCHhHcccccCCCEEECCCCccCe--eC--------------------HHHhCcCcCCCEEECCCCc--C
Confidence            99999988888754 6789999999998887752  11                    1114455566666665552  1


Q ss_pred             hhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeecccc
Q 003387          652 QSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSY  727 (824)
Q Consensus       652 ~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~  727 (824)
                      ....+..+..+++|+.|++++|    .++.+....+..+++|+.|+|++|.+....+..+..+++|+.|++++|.+
T Consensus       146 ~~~~~~~~~~l~~L~~L~L~~n----~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~~  217 (270)
T 2o6q_A          146 QSLPKGVFDKLTSLKELRLYNN----QLKRVPEGAFDKLTELKTLKLDNNQLKRVPEGAFDSLEKLKMLQLQENPW  217 (270)
T ss_dssp             CCCCTTTTTTCTTCCEEECCSS----CCSCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSCB
T ss_pred             CccCHhHccCCcccceeEecCC----cCcEeChhHhccCCCcCEEECCCCcCCcCCHHHhccccCCCEEEecCCCe
Confidence            1111112333444444444432    12222212223344555555555544433333444555555555554443

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=99.66  E-value=1.3e-17  Score=183.64  Aligned_cols=263  Identities=15%  Similarity=0.087  Sum_probs=170.2

Q ss_pred             hHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCCc----cChhh------hhcCCCccEeecCC
Q 003387          513 WEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLNS----LPSSL------LSNLLNLYTLDMPF  577 (824)
Q Consensus       513 ~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~~----lp~~i------~~~L~~L~~L~L~~  577 (824)
                      +...+..+++|++|+|++|.+.     .++..+..+++|++|+|++|.+..    +|..+      +.++++|++|+|++
T Consensus        24 l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~~~~~~l~~~~~~~~~~l~~~l~~~~~L~~L~Ls~  103 (386)
T 2ca6_A           24 VFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSD  103 (386)
T ss_dssp             TSHHHHHCSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCS
T ss_pred             HHHHHhcCCCccEEECCCCCCCHHHHHHHHHHHHhCCCccEEeCcccccCccccchhHHHHHHHHHHhhCCcccEEECCC
Confidence            3456677788888888888876     244557778888888888876553    34333      25788888888888


Q ss_pred             ccccc-----cchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCC---------CccceEE
Q 003387          578 SYIDH-----TADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRL---------PNLRNLR  643 (824)
Q Consensus       578 ~~l~~-----lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l---------~~L~~L~  643 (824)
                      |.+..     +|..+.++++|++|++++|.+... .                 ...+...+..+         ++|+.|+
T Consensus       104 n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~-~-----------------~~~l~~~l~~l~~~~~~~~~~~L~~L~  165 (386)
T 2ca6_A          104 NAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQ-A-----------------GAKIARALQELAVNKKAKNAPPLRSII  165 (386)
T ss_dssp             CCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHH-H-----------------HHHHHHHHHHHHHHHHHHTCCCCCEEE
T ss_pred             CcCCHHHHHHHHHHHHhCCCCCEEECcCCCCCHH-H-----------------HHHHHHHHHHHhhhhhcccCCCCcEEE
Confidence            87765     677788888888888888876310 0                 00111113333         7788888


Q ss_pred             Eeccccc--chhhHHHHhccCCCCCeEEEeccCCCCCccE-----EEeCccCcCCCceEEEEEcccCC----CCCccccc
Q 003387          644 IRGDLSY--NQSLLSKSLCRLSCLESLKLANESKMPRLSK-----IVLAEYLFPHSLTHLSFSNTDLM----DDPMPTLE  712 (824)
Q Consensus       644 l~~~~~~--~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~-----l~l~~~~~~~~L~~L~L~~~~l~----~~~~~~l~  712 (824)
                      ++++.-.  ....+...+..+++|++|++++|.    +..     +....+..+++|+.|+|++|.+.    ..++..+.
T Consensus       166 L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~----l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~g~~~l~~~l~  241 (386)
T 2ca6_A          166 CGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNG----IRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALK  241 (386)
T ss_dssp             CCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSC----CCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHHHGG
T ss_pred             CCCCCCCcHHHHHHHHHHHhCCCcCEEECcCCC----CCHhHHHHHHHHHhhcCCCccEEECcCCCCCcHHHHHHHHHHc
Confidence            8777521  222333566777888888887652    221     11113356778888888888864    34566778


Q ss_pred             CCCCCCeEEeeccccCCCe---eeecC--CCCCCccEEeeccCCCCc----cceecc-CcccCccEEEEecCCCCCCCc-
Q 003387          713 KLPLLQVLKLKQNSYSGRK---LTCGS--YGFPNLKVLHLKSMLWLE----EWTMGN-AAMPKLECLIINPCAYLKKMP-  781 (824)
Q Consensus       713 ~l~~L~~L~L~~~~~~~~~---~~~~~--~~~~~L~~L~L~~~~~l~----~l~~~~-~~lp~L~~L~l~~c~~l~~lp-  781 (824)
                      .+++|+.|+|++|.+.+..   ++..+  +.+++|++|+|++|..-.    .++..+ ..+|+|+.|++++|+.....| 
T Consensus       242 ~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~i~~~g~~~l~~~l~~~l~~L~~L~l~~N~l~~~~~~  321 (386)
T 2ca6_A          242 SWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDV  321 (386)
T ss_dssp             GCTTCCEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHHHHHHHHHHHHHHCTTCCEEECTTSBSCTTSHH
T ss_pred             cCCCcCEEECCCCCCchhhHHHHHHHHhhccCCCeEEEECcCCcCCHHHHHHHHHHHHhcCCCceEEEccCCcCCcchhH
Confidence            8999999999988876421   12222  448899999999887333    266555 558999999999998665443 


Q ss_pred             -ccc-ccCccCcEEEecC
Q 003387          782 -EQL-WYIKSLNKFDCWW  797 (824)
Q Consensus       782 -~~l-~~l~~L~~L~l~~  797 (824)
                       ..+ ..+++++.+++..
T Consensus       322 ~~~l~~~l~~~~~~~l~~  339 (386)
T 2ca6_A          322 VDEIREVFSTRGRGELDE  339 (386)
T ss_dssp             HHHHHHHHHHHTCCEECC
T ss_pred             HHHHHHHhhhcCcchhhh
Confidence             111 2344555455443

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.66  E-value=2e-16  Score=164.96  Aligned_cols=229  Identities=18%  Similarity=0.145  Sum_probs=153.1

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCC
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGS  600 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~  600 (824)
                      ..+..+++.++.+... .....+.+|++|+++++.+..++. + ..+++|++|++++|.+..++ .+..+++|++|++++
T Consensus        19 ~~l~~l~l~~~~~~~~-~~~~~l~~L~~L~l~~~~i~~~~~-l-~~l~~L~~L~l~~n~l~~~~-~l~~l~~L~~L~L~~   94 (272)
T 3rfs_A           19 AETIKANLKKKSVTDA-VTQNELNSIDQIIANNSDIKSVQG-I-QYLPNVRYLALGGNKLHDIS-ALKELTNLTYLILTG   94 (272)
T ss_dssp             HHHHHHHHTCSCTTSE-ECHHHHTTCCEEECTTSCCCCCTT-G-GGCTTCCEEECTTSCCCCCG-GGTTCTTCCEEECTT
T ss_pred             HHHHHHHhcCcccccc-cccccccceeeeeeCCCCcccccc-c-ccCCCCcEEECCCCCCCCch-hhcCCCCCCEEECCC
Confidence            3444555666655533 235678899999999999998775 5 89999999999999998876 689999999999999


Q ss_pred             ccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCc
Q 003387          601 ITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRL  679 (824)
Q Consensus       601 ~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L  679 (824)
                      |.+.. ..+ .++++++|                      +.|+++++.  .....+..+..+++|++|++++|    ++
T Consensus        95 n~l~~-~~~~~~~~l~~L----------------------~~L~L~~n~--l~~~~~~~~~~l~~L~~L~L~~n----~l  145 (272)
T 3rfs_A           95 NQLQS-LPNGVFDKLTNL----------------------KELVLVENQ--LQSLPDGVFDKLTNLTYLNLAHN----QL  145 (272)
T ss_dssp             SCCCC-CCTTTTTTCTTC----------------------CEEECTTSC--CCCCCTTTTTTCTTCCEEECCSS----CC
T ss_pred             CccCc-cChhHhcCCcCC----------------------CEEECCCCc--CCccCHHHhccCCCCCEEECCCC----cc
Confidence            98863 222 34444444                      444444442  11111223445556666666554    23


Q ss_pred             cEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceec
Q 003387          680 SKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMG  759 (824)
Q Consensus       680 ~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~  759 (824)
                      +.+....+..+++|+.|++++|.+.+..+..++.+++|+.|++++|.+.+. ....+..+++|++|++++|+.       
T Consensus       146 ~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~-~~~~~~~l~~L~~L~l~~N~~-------  217 (272)
T 3rfs_A          146 QSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSV-PDGVFDRLTSLQYIWLHDNPW-------  217 (272)
T ss_dssp             CCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCC-CTTTTTTCTTCCEEECCSSCB-------
T ss_pred             CccCHHHhccCccCCEEECCCCCcCccCHHHhcCCccCCEEECCCCcCCcc-CHHHHhCCcCCCEEEccCCCc-------
Confidence            333323335567788888888877766666677888888888887777652 223356778888888887752       


Q ss_pred             cCcccCccEEEEecCCCCCCCccccccCccC
Q 003387          760 NAAMPKLECLIINPCAYLKKMPEQLWYIKSL  790 (824)
Q Consensus       760 ~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L  790 (824)
                      .+.+|+|+.|.+..|.....+|..+..++..
T Consensus       218 ~~~~~~l~~l~~~~n~~~g~ip~~~~~~~~~  248 (272)
T 3rfs_A          218 DCTCPGIRYLSEWINKHSGVVRNSAGSVAPD  248 (272)
T ss_dssp             CCCTTTTHHHHHHHHHTGGGBBCTTSCBCGG
T ss_pred             cccCcHHHHHHHHHHhCCCcccCcccccCCC
Confidence            2457778888888887777777776665543

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=99.65  E-value=4.7e-18  Score=187.06  Aligned_cols=254  Identities=13%  Similarity=0.102  Sum_probs=181.6

Q ss_pred             ccEEEeeCccCccCCccCCCCCcceEEeecCCCCCc-----cChhhhhcCCCccEeecCCcccc----ccchhh------
Q 003387          523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNS-----LPSSLLSNLLNLYTLDMPFSYID----HTADEF------  587 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~-----lp~~i~~~L~~L~~L~L~~~~l~----~lp~~i------  587 (824)
                      |++..++...+..++..+..+++|++|+|++|.+..     ++..+ .++++|++|+|++|.+.    .+|..+      
T Consensus        11 L~~~~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l-~~~~~L~~L~Ls~~~~~~l~~~~~~~~~~l~~~   89 (386)
T 2ca6_A           11 LKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENI-ASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQA   89 (386)
T ss_dssp             CEESSCCSHHHHTTSHHHHHCSCCCEEECTTSEECHHHHHHHHHTT-TTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHH
T ss_pred             cccCCCCHHHHHHHHHHHhcCCCccEEECCCCCCCHHHHHHHHHHH-HhCCCccEEeCcccccCccccchhHHHHHHHHH
Confidence            444444455566788888889999999999998874     33334 68999999999998554    335444      


Q ss_pred             -hccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccccc--chhhHHHHhccC--
Q 003387          588 -WKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSY--NQSLLSKSLCRL--  662 (824)
Q Consensus       588 -~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~--~~~~l~~~l~~l--  662 (824)
                       ..+++|++|++++|.+...                  ....++..+..+++|+.|++++|.-.  ....++..+..+  
T Consensus        90 l~~~~~L~~L~Ls~n~l~~~------------------~~~~l~~~l~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~l~~  151 (386)
T 2ca6_A           90 LLKCPKLHTVRLSDNAFGPT------------------AQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAV  151 (386)
T ss_dssp             HTTCTTCCEEECCSCCCCTT------------------THHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHH
T ss_pred             HhhCCcccEEECCCCcCCHH------------------HHHHHHHHHHhCCCCCEEECcCCCCCHHHHHHHHHHHHHHhh
Confidence             6889999999999887520                  01123334788999999999998621  123445555555  


Q ss_pred             -------CCCCeEEEeccCCCCCccEEEeC----ccCcCCCceEEEEEcccCCCC-----CcccccCCCCCCeEEeeccc
Q 003387          663 -------SCLESLKLANESKMPRLSKIVLA----EYLFPHSLTHLSFSNTDLMDD-----PMPTLEKLPLLQVLKLKQNS  726 (824)
Q Consensus       663 -------~~L~~L~l~~~~~~~~L~~l~l~----~~~~~~~L~~L~L~~~~l~~~-----~~~~l~~l~~L~~L~L~~~~  726 (824)
                             ++|++|++++|.    +..-.+.    .+..+++|++|++++|.+...     .+..+..+++|+.|+|++|.
T Consensus       152 ~~~~~~~~~L~~L~L~~n~----l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~  227 (386)
T 2ca6_A          152 NKKAKNAPPLRSIICGRNR----LENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNT  227 (386)
T ss_dssp             HHHHHTCCCCCEEECCSSC----CTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSC
T ss_pred             hhhcccCCCCcEEECCCCC----CCcHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECcCCC
Confidence                   899999999762    3211111    224678999999999987532     23378899999999999998


Q ss_pred             cCC---CeeeecCCCCCCccEEeeccCCCCcc----ceecc--CcccCccEEEEecCCCCC----CCcccc-ccCccCcE
Q 003387          727 YSG---RKLTCGSYGFPNLKVLHLKSMLWLEE----WTMGN--AAMPKLECLIINPCAYLK----KMPEQL-WYIKSLNK  792 (824)
Q Consensus       727 ~~~---~~~~~~~~~~~~L~~L~L~~~~~l~~----l~~~~--~~lp~L~~L~l~~c~~l~----~lp~~l-~~l~~L~~  792 (824)
                      +..   ..++..+..+++|++|+|++|..-..    ++..+  +.+++|+.|++++|....    .+|..+ .++++|+.
T Consensus       228 l~~~g~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~i~~~g~~~l~~~l~~~l~~L~~  307 (386)
T 2ca6_A          228 FTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLF  307 (386)
T ss_dssp             CHHHHHHHHHHHGGGCTTCCEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHHHHHHHHHHHHHHCTTCCE
T ss_pred             CCcHHHHHHHHHHccCCCcCEEECCCCCCchhhHHHHHHHHhhccCCCeEEEECcCCcCCHHHHHHHHHHHHhcCCCceE
Confidence            752   23444567889999999999873322    23333  458999999999998655    388777 67899999


Q ss_pred             EEecCCc
Q 003387          793 FDCWWPQ  799 (824)
Q Consensus       793 L~l~~c~  799 (824)
                      |++++|+
T Consensus       308 L~l~~N~  314 (386)
T 2ca6_A          308 LELNGNR  314 (386)
T ss_dssp             EECTTSB
T ss_pred             EEccCCc
Confidence            9999987

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.64  E-value=2.1e-16  Score=161.35  Aligned_cols=208  Identities=18%  Similarity=0.249  Sum_probs=120.3

Q ss_pred             CccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCcc-ccccch-hhhccccCceecCCC-ccCCCCCCC
Q 003387          533 LIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSY-IDHTAD-EFWKMNKLRHLNFGS-ITLPAHPGK  609 (824)
Q Consensus       533 i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~-l~~lp~-~i~~L~~L~~L~L~~-~~~~~~~~p  609 (824)
                      ++.+|. +..  +|++|++++|.++.+|...|.++++|++|++++|. ++.+|. .+.++++|++|++++ |.+..    
T Consensus        23 l~~ip~-~~~--~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~----   95 (239)
T 2xwt_C           23 IQRIPS-LPP--STQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNLTY----   95 (239)
T ss_dssp             CSSCCC-CCT--TCCEEEEESCCCSEECTTTTTTCTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEETTCCE----
T ss_pred             ccccCC-CCC--cccEEEEeCCcceEECHHHccCCCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCCCCeeE----
Confidence            555665 433  67777777777776666444667777777777774 666654 466667777776665 54431    


Q ss_pred             CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCc
Q 003387          610 FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLF  689 (824)
Q Consensus       610 ~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~  689 (824)
                                        .....+..+++|+.|+++++.   ...+|. +..++                         .
T Consensus        96 ------------------i~~~~f~~l~~L~~L~l~~n~---l~~lp~-~~~l~-------------------------~  128 (239)
T 2xwt_C           96 ------------------IDPDALKELPLLKFLGIFNTG---LKMFPD-LTKVY-------------------------S  128 (239)
T ss_dssp             ------------------ECTTSEECCTTCCEEEEEEEC---CCSCCC-CTTCC-------------------------B
T ss_pred             ------------------cCHHHhCCCCCCCEEeCCCCC---Cccccc-ccccc-------------------------c
Confidence                              011114555666666666552   110111 11111                         1


Q ss_pred             CCCceEEEEEcc-cCCCCCcccccCCCCCC-eEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcccee-ccCcc-cC
Q 003387          690 PHSLTHLSFSNT-DLMDDPMPTLEKLPLLQ-VLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM-GNAAM-PK  765 (824)
Q Consensus       690 ~~~L~~L~L~~~-~l~~~~~~~l~~l~~L~-~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~-~~~~l-p~  765 (824)
                      +..|+.|++++| .+....+..++.+++|+ .|++++|.+.  .++......++|++|++++|+.++.++. .+..+ ++
T Consensus       129 L~~L~~L~l~~N~~l~~i~~~~~~~l~~L~~~L~l~~n~l~--~i~~~~~~~~~L~~L~L~~n~~l~~i~~~~~~~l~~~  206 (239)
T 2xwt_C          129 TDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNNGFT--SVQGYAFNGTKLDAVYLNKNKYLTVIDKDAFGGVYSG  206 (239)
T ss_dssp             CCSEEEEEEESCTTCCEECTTTTTTTBSSEEEEECCSCCCC--EECTTTTTTCEEEEEECTTCTTCCEECTTTTTTCSBC
T ss_pred             cccccEEECCCCcchhhcCcccccchhcceeEEEcCCCCCc--ccCHhhcCCCCCCEEEcCCCCCcccCCHHHhhccccC
Confidence            122336666666 55444445567777777 7777766654  2332222236788888877755666643 35566 78


Q ss_pred             ccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          766 LECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       766 L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      |+.|++++|+ ++.+|..  .+++|+.|.+.+++
T Consensus       207 L~~L~l~~N~-l~~l~~~--~~~~L~~L~l~~~~  237 (239)
T 2xwt_C          207 PSLLDVSQTS-VTALPSK--GLEHLKELIARNTW  237 (239)
T ss_dssp             CSEEECTTCC-CCCCCCT--TCTTCSEEECTTC-
T ss_pred             CcEEECCCCc-cccCChh--HhccCceeeccCcc
Confidence            8888888776 4466654  57788888887775

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.63  E-value=9.1e-16  Score=162.90  Aligned_cols=192  Identities=21%  Similarity=0.203  Sum_probs=118.8

Q ss_pred             CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCe
Q 003387          540 IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNF  619 (824)
Q Consensus       540 i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~  619 (824)
                      ...+.+|++|+++++.+..+| .+ ..+++|++|++++|.+..+|. +..+++|++|++++|.+.  .++.++.+++|+.
T Consensus        37 ~~~l~~L~~L~l~~~~i~~l~-~~-~~l~~L~~L~L~~n~i~~~~~-~~~l~~L~~L~L~~n~l~--~~~~~~~l~~L~~  111 (308)
T 1h6u_A           37 QADLDGITTLSAFGTGVTTIE-GV-QYLNNLIGLELKDNQITDLAP-LKNLTKITELELSGNPLK--NVSAIAGLQSIKT  111 (308)
T ss_dssp             HHHHHTCCEEECTTSCCCCCT-TG-GGCTTCCEEECCSSCCCCCGG-GTTCCSCCEEECCSCCCS--CCGGGTTCTTCCE
T ss_pred             HHHcCCcCEEEeeCCCccCch-hh-hccCCCCEEEccCCcCCCChh-HccCCCCCEEEccCCcCC--CchhhcCCCCCCE
Confidence            456889999999999999988 46 999999999999999999988 999999999999999876  3344555555555


Q ss_pred             eeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEE
Q 003387          620 ISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFS  699 (824)
Q Consensus       620 l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~  699 (824)
                      |+++                      ++.-   ..++ .+..+++|++|++++|.    ++.+.  .+..+++|+.|+++
T Consensus       112 L~l~----------------------~n~l---~~~~-~l~~l~~L~~L~l~~n~----l~~~~--~l~~l~~L~~L~l~  159 (308)
T 1h6u_A          112 LDLT----------------------STQI---TDVT-PLAGLSNLQVLYLDLNQ----ITNIS--PLAGLTNLQYLSIG  159 (308)
T ss_dssp             EECT----------------------TSCC---CCCG-GGTTCTTCCEEECCSSC----CCCCG--GGGGCTTCCEEECC
T ss_pred             EECC----------------------CCCC---CCch-hhcCCCCCCEEECCCCc----cCcCc--cccCCCCccEEEcc
Confidence            5554                      4321   1111 13444445555444431    11111  12344555566666


Q ss_pred             cccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCC
Q 003387          700 NTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCA  775 (824)
Q Consensus       700 ~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~  775 (824)
                      +|.+.+. +. +..+++|+.|++++|.+.+..   ....+++|++|++++|. +..++ .+..+++|+.|++++|+
T Consensus       160 ~n~l~~~-~~-l~~l~~L~~L~l~~n~l~~~~---~l~~l~~L~~L~L~~N~-l~~~~-~l~~l~~L~~L~l~~N~  228 (308)
T 1h6u_A          160 NAQVSDL-TP-LANLSKLTTLKADDNKISDIS---PLASLPNLIEVHLKNNQ-ISDVS-PLANTSNLFIVTLTNQT  228 (308)
T ss_dssp             SSCCCCC-GG-GTTCTTCCEEECCSSCCCCCG---GGGGCTTCCEEECTTSC-CCBCG-GGTTCTTCCEEEEEEEE
T ss_pred             CCcCCCC-hh-hcCCCCCCEEECCCCccCcCh---hhcCCCCCCEEEccCCc-cCccc-cccCCCCCCEEEccCCe
Confidence            5555432 22 556666666666655554321   14455666666666654 34443 24556666666666665

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.63  E-value=4.7e-16  Score=158.75  Aligned_cols=84  Identities=19%  Similarity=0.173  Sum_probs=71.9

Q ss_pred             CcccEEEeeCccCccCCc-cCCCCCcceEEeecCCC-CCccChhhhhcCCCccEeecCC-ccccccch-hhhccccCcee
Q 003387          521 KLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPS-LNSLPSSLLSNLLNLYTLDMPF-SYIDHTAD-EFWKMNKLRHL  596 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~-i~~lp~~i~~~L~~L~~L~L~~-~~l~~lp~-~i~~L~~L~~L  596 (824)
                      +.|++|++++|.++.+|. .+..+++|++|++++|. +..+|...|.++++|++|++++ |.++.+|. .+..+++|++|
T Consensus        31 ~~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~~L~~L  110 (239)
T 2xwt_C           31 PSTQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELPLLKFL  110 (239)
T ss_dssp             TTCCEEEEESCCCSEECTTTTTTCTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEETTCCEECTTSEECCTTCCEE
T ss_pred             CcccEEEEeCCcceEECHHHccCCCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCCCCeeEcCHHHhCCCCCCCEE
Confidence            378999999999987776 68889999999999997 8888875558999999999998 78888874 47889999999


Q ss_pred             cCCCccCC
Q 003387          597 NFGSITLP  604 (824)
Q Consensus       597 ~L~~~~~~  604 (824)
                      ++++|.+.
T Consensus       111 ~l~~n~l~  118 (239)
T 2xwt_C          111 GIFNTGLK  118 (239)
T ss_dssp             EEEEECCC
T ss_pred             eCCCCCCc
Confidence            99988876

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=99.61  E-value=1.9e-15  Score=163.58  Aligned_cols=218  Identities=16%  Similarity=0.102  Sum_probs=107.6

Q ss_pred             cccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCC-ccChhhhhcCCCccE-eecCCccccccc-hhhhccccCceec
Q 003387          522 LLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLN-SLPSSLLSNLLNLYT-LDMPFSYIDHTA-DEFWKMNKLRHLN  597 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~-~lp~~i~~~L~~L~~-L~L~~~~l~~lp-~~i~~L~~L~~L~  597 (824)
                      +++.|+|++|.|+.+|. .|.++++|++|+|++|.+. .+|...|.++++|+. +.+++|.+..+| ..+..+++|++|+
T Consensus        31 ~l~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~N~l~~l~~~~f~~l~~L~~L~  110 (350)
T 4ay9_X           31 NAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLL  110 (350)
T ss_dssp             TCSEEEEESCCCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEETTCCEECTTSBCCCTTCCEEE
T ss_pred             CCCEEEccCCcCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccCCcccccCchhhhhcccccccc
Confidence            45555555555555543 3455555555555555542 344433345555443 233334555553 2244555555555


Q ss_pred             CCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHH-HHhccC-CCCCeEEEeccCC
Q 003387          598 FGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLS-KSLCRL-SCLESLKLANESK  675 (824)
Q Consensus       598 L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~-~~l~~l-~~L~~L~l~~~~~  675 (824)
                      +++|.+..  +|                    ...+....++..|++..+.  ....++ ..+..+ ..++.|++++|  
T Consensus       111 l~~n~l~~--~~--------------------~~~~~~~~~l~~l~l~~~~--~i~~l~~~~f~~~~~~l~~L~L~~N--  164 (350)
T 4ay9_X          111 ISNTGIKH--LP--------------------DVHKIHSLQKVLLDIQDNI--NIHTIERNSFVGLSFESVILWLNKN--  164 (350)
T ss_dssp             EEEECCSS--CC--------------------CCTTCCBSSCEEEEEESCT--TCCEECTTSSTTSBSSCEEEECCSS--
T ss_pred             cccccccc--CC--------------------chhhcccchhhhhhhcccc--ccccccccchhhcchhhhhhccccc--
Confidence            55554431  11                    0012233345566665432  111111 122222 34666666655  


Q ss_pred             CCCccEEEeCccCcCCCceEEEEEcc-cCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCc
Q 003387          676 MPRLSKIVLAEYLFPHSLTHLSFSNT-DLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLE  754 (824)
Q Consensus       676 ~~~L~~l~l~~~~~~~~L~~L~L~~~-~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~  754 (824)
                        .++.+.-.. ....+|+.|.++++ .+.......++.+++|+.|++++|.+..  ++  .+.|.+|+.|.+.++..++
T Consensus       165 --~i~~i~~~~-f~~~~L~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~N~l~~--lp--~~~~~~L~~L~~l~~~~l~  237 (350)
T 4ay9_X          165 --GIQEIHNSA-FNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHS--LP--SYGLENLKKLRARSTYNLK  237 (350)
T ss_dssp             --CCCEECTTS-STTEEEEEEECTTCTTCCCCCTTTTTTEECCSEEECTTSCCCC--CC--SSSCTTCCEEECTTCTTCC
T ss_pred             --cccCCChhh-ccccchhHHhhccCCcccCCCHHHhccCcccchhhcCCCCcCc--cC--hhhhccchHhhhccCCCcC
Confidence              344443222 22345667777643 3333333456677777777777666553  22  2446667777766666666


Q ss_pred             cceeccCcccCccEEEEec
Q 003387          755 EWTMGNAAMPKLECLIINP  773 (824)
Q Consensus       755 ~l~~~~~~lp~L~~L~l~~  773 (824)
                      .+| .+..+++|+.+++.+
T Consensus       238 ~lP-~l~~l~~L~~l~l~~  255 (350)
T 4ay9_X          238 KLP-TLEKLVALMEASLTY  255 (350)
T ss_dssp             CCC-CTTTCCSCCEEECSC
T ss_pred             cCC-CchhCcChhhCcCCC
Confidence            666 355677777776654

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=99.59  E-value=6.7e-15  Score=151.36  Aligned_cols=178  Identities=24%  Similarity=0.301  Sum_probs=110.8

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCC
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFG  599 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~  599 (824)
                      ...++++++++.++.+|..+.  .+|++|+|++|.+..++...+.++++|++|+|++|.+..++.. +..+++|++|+++
T Consensus        14 ~~~~~l~~~~~~l~~~p~~~~--~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~   91 (251)
T 3m19_A           14 EGKKEVDCQGKSLDSVPSGIP--ADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLA   91 (251)
T ss_dssp             GGGTEEECTTCCCSSCCSCCC--TTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECT
T ss_pred             CCCeEEecCCCCccccCCCCC--CCCCEEEccCCCcCccCHhHhcCcccCCEEECCCCcCCccCHhHhccCCcCCEEECC
Confidence            457889999998888888776  5889999999998888775558899999999999988887654 7889999999998


Q ss_pred             CccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCc
Q 003387          600 SITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRL  679 (824)
Q Consensus       600 ~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L  679 (824)
                      +|.+..  +|                    ...+..+++|+.|+++++.  .....+..+..+++|+.|++++|    ++
T Consensus        92 ~n~l~~--~~--------------------~~~~~~l~~L~~L~L~~N~--l~~~~~~~~~~l~~L~~L~Ls~N----~l  143 (251)
T 3m19_A           92 NNQLAS--LP--------------------LGVFDHLTQLDKLYLGGNQ--LKSLPSGVFDRLTKLKELRLNTN----QL  143 (251)
T ss_dssp             TSCCCC--CC--------------------TTTTTTCTTCCEEECCSSC--CCCCCTTTTTTCTTCCEEECCSS----CC
T ss_pred             CCcccc--cC--------------------hhHhcccCCCCEEEcCCCc--CCCcChhHhccCCcccEEECcCC----cC
Confidence            887752  11                    1114455566666665552  11111112334444444444433    12


Q ss_pred             cEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccC
Q 003387          680 SKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYS  728 (824)
Q Consensus       680 ~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~  728 (824)
                      +.+....+..+++|+.|+|++|.+....+..+..+++|+.|++++|.+.
T Consensus       144 ~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~  192 (251)
T 3m19_A          144 QSIPAGAFDKLTNLQTLSLSTNQLQSVPHGAFDRLGKLQTITLFGNQFD  192 (251)
T ss_dssp             CCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSCCBC
T ss_pred             CccCHHHcCcCcCCCEEECCCCcCCccCHHHHhCCCCCCEEEeeCCcee
Confidence            2222222334455555555555554444445555555555555555543

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.58  E-value=3.1e-15  Score=159.12  Aligned_cols=228  Identities=15%  Similarity=0.106  Sum_probs=135.2

Q ss_pred             CCceeEeeccCCCCCCCCcchhHh--hhcccCcccEEEeeCccCc-cCCccC--CCCCcceEEeecCCCCCcc-C----h
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEK--FCGMFKLLRVLDLGSLVLI-QYPSGI--ENLFLLRYLKLNIPSLNSL-P----S  561 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~--~~~~~~~Lr~L~L~~~~i~-~lp~~i--~~l~~Lr~L~L~~~~i~~l-p----~  561 (824)
                      ...++.+.+.+....   ......  .+..++.|++|++++|.+. ..|..+  +.+++|++|+|++|.+... |    .
T Consensus        63 ~~~l~~l~l~~~~~~---~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~~~~~~L~~L~Ls~n~i~~~~~~~~~~  139 (310)
T 4glp_A           63 ALRVRRLTVGAAQVP---AQLLVGALRVLAYSRLKELTLEDLKITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAEL  139 (310)
T ss_dssp             SCCCCEEEECSCCCB---HHHHHHHHHHHHHSCCCEEEEESCCCBSCCCCCSSSCCCBCCSSCEEESCCCSSTTSSHHHH
T ss_pred             hcceeEEEEeCCcCC---HHHHHHHHHhcccCceeEEEeeCCEeccchhhhhhhccCCCCCEEEeecccccchhhhhHHH
Confidence            445666666655442   111111  1223466999999999987 667777  8899999999999998852 2    2


Q ss_pred             hhhhcCCCccEeecCCccccccc-hhhhccccCceecCCCccCCCC-CCCCCCCCCCCCeeeccCCCcchhhhcCCCCcc
Q 003387          562 SLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSITLPAH-PGKFCGSLENLNFISALHPCCCTEDILGRLPNL  639 (824)
Q Consensus       562 ~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~~~~~-~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L  639 (824)
                      .+ ..+++|++|++++|.+..+| ..++.+++|++|++++|.+... .++                   ....++.+++|
T Consensus       140 ~~-~~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~-------------------~~~~~~~l~~L  199 (310)
T 4glp_A          140 QQ-WLKPGLKVLSIAQAHSPAFSCEQVRAFPALTSLDLSDNPGLGERGLM-------------------AALCPHKFPAI  199 (310)
T ss_dssp             HT-TBCSCCCEEEEECCSSCCCCTTSCCCCTTCCEEECCSCTTCHHHHHH-------------------TTSCTTSSCCC
T ss_pred             Hh-hhccCCCEEEeeCCCcchhhHHHhccCCCCCEEECCCCCCccchhhh-------------------HHHhhhcCCCC
Confidence            33 57889999999999888776 4588899999999998876410 000                   01113567778


Q ss_pred             ceEEEecccccchhhHHHH-hccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCC---C
Q 003387          640 RNLRIRGDLSYNQSLLSKS-LCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKL---P  715 (824)
Q Consensus       640 ~~L~l~~~~~~~~~~l~~~-l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l---~  715 (824)
                      +.|+++++.-......+.. +..+++|++|++++|                            .+.+..|..++.+   +
T Consensus       200 ~~L~Ls~N~l~~l~~~~~~l~~~l~~L~~L~Ls~N----------------------------~l~~~~p~~~~~~~~~~  251 (310)
T 4glp_A          200 QNLALRNTGMETPTGVCAALAAAGVQPHSLDLSHN----------------------------SLRATVNPSAPRCMWSS  251 (310)
T ss_dssp             CSCBCCSSCCCCHHHHHHHHHHHTCCCSSEECTTS----------------------------CCCCCCCSCCSSCCCCT
T ss_pred             CEEECCCCCCCchHHHHHHHHhcCCCCCEEECCCC----------------------------CCCccchhhHHhccCcC
Confidence            8888877742222222222 355566666666544                            3333333333333   4


Q ss_pred             CCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCCC
Q 003387          716 LLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAY  776 (824)
Q Consensus       716 ~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~  776 (824)
                      +|++|++++|.+..  ++..  -+++|++|+|++|. +..+|. ...+|+|+.|++++|+.
T Consensus       252 ~L~~L~Ls~N~l~~--lp~~--~~~~L~~L~Ls~N~-l~~~~~-~~~l~~L~~L~L~~N~l  306 (310)
T 4glp_A          252 ALNSLNLSFAGLEQ--VPKG--LPAKLRVLDLSSNR-LNRAPQ-PDELPEVDNLTLDGNPF  306 (310)
T ss_dssp             TCCCEECCSSCCCS--CCSC--CCSCCSCEECCSCC-CCSCCC-TTSCCCCSCEECSSTTT
T ss_pred             cCCEEECCCCCCCc--hhhh--hcCCCCEEECCCCc-CCCCch-hhhCCCccEEECcCCCC
Confidence            55555555555442  2211  12556666665554 444433 45566666666666654

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=99.58  E-value=8.1e-16  Score=167.46  Aligned_cols=93  Identities=20%  Similarity=0.204  Sum_probs=64.9

Q ss_pred             hhHhhhcccCcccEEEeeCccCccCC-----ccCCCCC-cceEEeecCCCCCccChhhhhcC-----CCccEeecCCccc
Q 003387          512 DWEKFCGMFKLLRVLDLGSLVLIQYP-----SGIENLF-LLRYLKLNIPSLNSLPSSLLSNL-----LNLYTLDMPFSYI  580 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~~i~~lp-----~~i~~l~-~Lr~L~L~~~~i~~lp~~i~~~L-----~~L~~L~L~~~~l  580 (824)
                      ..+.++...++|++|+|++|.+...+     ..+.+++ +|++|+|++|.+.......+..+     ++|++|+|++|.+
T Consensus        13 ~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l   92 (362)
T 3goz_A           13 PVEEFTSIPHGVTSLDLSLNNLYSISTVELIQAFANTPASVTSLNLSGNSLGFKNSDELVQILAAIPANVTSLNLSGNFL   92 (362)
T ss_dssp             HHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTCCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCG
T ss_pred             HHHHHHhCCCCceEEEccCCCCChHHHHHHHHHHHhCCCceeEEECcCCCCCHHHHHHHHHHHhccCCCccEEECcCCcC
Confidence            45566666677888888888877555     5566777 78888888888776543322554     7888888888877


Q ss_pred             cccc-hh----hhcc-ccCceecCCCccCC
Q 003387          581 DHTA-DE----FWKM-NKLRHLNFGSITLP  604 (824)
Q Consensus       581 ~~lp-~~----i~~L-~~L~~L~L~~~~~~  604 (824)
                      ...+ ..    +..+ ++|++|++++|.+.
T Consensus        93 ~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~  122 (362)
T 3goz_A           93 SYKSSDELVKTLAAIPFTITVLDLGWNDFS  122 (362)
T ss_dssp             GGSCHHHHHHHHHTSCTTCCEEECCSSCGG
T ss_pred             ChHHHHHHHHHHHhCCCCccEEECcCCcCC
Confidence            7554 32    3344 78888888888775

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=99.56  E-value=1.4e-14  Score=152.28  Aligned_cols=144  Identities=18%  Similarity=0.098  Sum_probs=83.8

Q ss_pred             CeeEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEee
Q 003387          472 KAKRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKL  551 (824)
Q Consensus       472 ~~r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L  551 (824)
                      +.+.+... +.....++..+.++++.|.+.++...    ...+..|..+++|++|+|++|.++.+|.. +.+++|++|++
T Consensus        11 ~l~~l~~~-~~~l~~ip~~~~~~l~~L~L~~N~l~----~~~~~~~~~l~~L~~L~L~~n~l~~~~~~-~~l~~L~~L~L   84 (290)
T 1p9a_G           11 SHLEVNCD-KRNLTALPPDLPKDTTILHLSENLLY----TFSLATLMPYTRLTQLNLDRAELTKLQVD-GTLPVLGTLDL   84 (290)
T ss_dssp             TCCEEECT-TSCCSSCCSCCCTTCCEEECTTSCCS----EEEGGGGTTCTTCCEEECTTSCCCEEECC-SCCTTCCEEEC
T ss_pred             CccEEECC-CCCCCcCCCCCCCCCCEEEcCCCcCC----ccCHHHhhcCCCCCEEECCCCccCcccCC-CCCCcCCEEEC
Confidence            34445444 33333344444566666666666542    23345566666677777777666655543 56666777777


Q ss_pred             cCCCCCccChhhhhcCCCccEeecCCccccccc-hhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeecc
Q 003387          552 NIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISAL  623 (824)
Q Consensus       552 ~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~  623 (824)
                      ++|.+..+|..+ ..+++|++|++++|.++.+| ..+..+++|++|++++|.+.. ..+ .+..+++|+.|+++
T Consensus        85 s~N~l~~l~~~~-~~l~~L~~L~l~~N~l~~l~~~~~~~l~~L~~L~L~~N~l~~-~~~~~~~~l~~L~~L~L~  156 (290)
T 1p9a_G           85 SHNQLQSLPLLG-QTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKT-LPPGLLTPTPKLEKLSLA  156 (290)
T ss_dssp             CSSCCSSCCCCT-TTCTTCCEEECCSSCCCCCCSSTTTTCTTCCEEECTTSCCCC-CCTTTTTTCTTCCEEECT
T ss_pred             CCCcCCcCchhh-ccCCCCCEEECCCCcCcccCHHHHcCCCCCCEEECCCCCCCc-cChhhcccccCCCEEECC
Confidence            776666666655 66667777777666666665 336666667777666666652 111 33444444444444

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.56  E-value=1.4e-15  Score=161.87  Aligned_cols=104  Identities=18%  Similarity=0.114  Sum_probs=78.2

Q ss_pred             cCCCceEEEEEcccCCCCCcc----cccCCCCCCeEEeeccccCCCeeeecCCC---CCCccEEeeccCCCCccceeccC
Q 003387          689 FPHSLTHLSFSNTDLMDDPMP----TLEKLPLLQVLKLKQNSYSGRKLTCGSYG---FPNLKVLHLKSMLWLEEWTMGNA  761 (824)
Q Consensus       689 ~~~~L~~L~L~~~~l~~~~~~----~l~~l~~L~~L~L~~~~~~~~~~~~~~~~---~~~L~~L~L~~~~~l~~l~~~~~  761 (824)
                      .+++|++|+|++|.+.. .+.    .++.+++|++|++++|.+.+.. +.....   +++|++|++++|. ++.+|... 
T Consensus       195 ~l~~L~~L~Ls~N~l~~-l~~~~~~l~~~l~~L~~L~Ls~N~l~~~~-p~~~~~~~~~~~L~~L~Ls~N~-l~~lp~~~-  270 (310)
T 4glp_A          195 KFPAIQNLALRNTGMET-PTGVCAALAAAGVQPHSLDLSHNSLRATV-NPSAPRCMWSSALNSLNLSFAG-LEQVPKGL-  270 (310)
T ss_dssp             SSCCCCSCBCCSSCCCC-HHHHHHHHHHHTCCCSSEECTTSCCCCCC-CSCCSSCCCCTTCCCEECCSSC-CCSCCSCC-
T ss_pred             cCCCCCEEECCCCCCCc-hHHHHHHHHhcCCCCCEEECCCCCCCccc-hhhHHhccCcCcCCEEECCCCC-CCchhhhh-
Confidence            45677777777777642 222    2568899999999999987632 222333   4899999999986 66777654 


Q ss_pred             cccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          762 AMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       762 ~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                       +++|+.|++++|. +..+|. +..+++|+.|++++++
T Consensus       271 -~~~L~~L~Ls~N~-l~~~~~-~~~l~~L~~L~L~~N~  305 (310)
T 4glp_A          271 -PAKLRVLDLSSNR-LNRAPQ-PDELPEVDNLTLDGNP  305 (310)
T ss_dssp             -CSCCSCEECCSCC-CCSCCC-TTSCCCCSCEECSSTT
T ss_pred             -cCCCCEEECCCCc-CCCCch-hhhCCCccEEECcCCC
Confidence             4899999999997 456665 6788999999999987

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=99.55  E-value=4.8e-16  Score=169.28  Aligned_cols=247  Identities=15%  Similarity=0.092  Sum_probs=134.7

Q ss_pred             EEEeeCccCc-cCCccCCCCCcceEEeecCCCCCccCh----hhhhcCC-CccEeecCCcccccc-chhhhcc-----cc
Q 003387          525 VLDLGSLVLI-QYPSGIENLFLLRYLKLNIPSLNSLPS----SLLSNLL-NLYTLDMPFSYIDHT-ADEFWKM-----NK  592 (824)
Q Consensus       525 ~L~L~~~~i~-~lp~~i~~l~~Lr~L~L~~~~i~~lp~----~i~~~L~-~L~~L~L~~~~l~~l-p~~i~~L-----~~  592 (824)
                      +++++.+.++ .+|..+....+|++|+|++|.+...+.    ..+.+++ +|++|+|++|.+... +..+..+     ++
T Consensus         2 ~~~ls~n~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~   81 (362)
T 3goz_A            2 NYKLTLHPGSNPVEEFTSIPHGVTSLDLSLNNLYSISTVELIQAFANTPASVTSLNLSGNSLGFKNSDELVQILAAIPAN   81 (362)
T ss_dssp             EEECCCCTTCCHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTCCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTT
T ss_pred             ccccccccchHHHHHHHhCCCCceEEEccCCCCChHHHHHHHHHHHhCCCceeEEECcCCCCCHHHHHHHHHHHhccCCC
Confidence            4678888887 455555666779999999999998875    4448888 899999999988876 5556665     99


Q ss_pred             CceecCCCccCCCCCCCC----CCCC-CCCCeeeccCCCc------chhhhcCC-CCccceEEEecccc--cchhhHHHH
Q 003387          593 LRHLNFGSITLPAHPGKF----CGSL-ENLNFISALHPCC------CTEDILGR-LPNLRNLRIRGDLS--YNQSLLSKS  658 (824)
Q Consensus       593 L~~L~L~~~~~~~~~~p~----i~~L-~~L~~l~~~~~~~------~~~~~l~~-l~~L~~L~l~~~~~--~~~~~l~~~  658 (824)
                      |++|++++|.+.......    +..+ ++|+.|+++.+.-      .+...+.. .++|+.|+++++.-  .....++..
T Consensus        82 L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~  161 (362)
T 3goz_A           82 VTSLNLSGNFLSYKSSDELVKTLAAIPFTITVLDLGWNDFSSKSSSEFKQAFSNLPASITSLNLRGNDLGIKSSDELIQI  161 (362)
T ss_dssp             CCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHHHTTSCTTCCEEECTTSCGGGSCHHHHHHH
T ss_pred             ccEEECcCCcCChHHHHHHHHHHHhCCCCccEEECcCCcCCcHHHHHHHHHHHhCCCceeEEEccCCcCCHHHHHHHHHH
Confidence            999999999886311111    2333 4566666552211      11111223 24566666665531  112344444


Q ss_pred             hccCC-CCCeEEEeccCCCCCccEEEeCc----cCcC-CCceEEEEEcccCCCCC----cccccC-CCCCCeEEeecccc
Q 003387          659 LCRLS-CLESLKLANESKMPRLSKIVLAE----YLFP-HSLTHLSFSNTDLMDDP----MPTLEK-LPLLQVLKLKQNSY  727 (824)
Q Consensus       659 l~~l~-~L~~L~l~~~~~~~~L~~l~l~~----~~~~-~~L~~L~L~~~~l~~~~----~~~l~~-l~~L~~L~L~~~~~  727 (824)
                      +..++ +|++|++++|.    +.......    ...+ ++|+.|+|++|.+....    +..+.. .++|+.|+|++|.+
T Consensus       162 l~~~~~~L~~L~Ls~n~----l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~i~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l  237 (362)
T 3goz_A          162 LAAIPANVNSLNLRGNN----LASKNCAELAKFLASIPASVTSLDLSANLLGLKSYAELAYIFSSIPNHVVSLNLCLNCL  237 (362)
T ss_dssp             HHTSCTTCCEEECTTSC----GGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHHSCTTCCEEECCSSCC
T ss_pred             HhcCCccccEeeecCCC----CchhhHHHHHHHHHhCCCCCCEEECCCCCCChhHHHHHHHHHhcCCCCceEEECcCCCC
Confidence            44443 55565555441    22111100    0122 35666666666554322    222222 23566666665555


Q ss_pred             CCCe---eeecCCCCCCccEEeeccCC---C----CccceeccCcccCccEEEEecCC
Q 003387          728 SGRK---LTCGSYGFPNLKVLHLKSML---W----LEEWTMGNAAMPKLECLIINPCA  775 (824)
Q Consensus       728 ~~~~---~~~~~~~~~~L~~L~L~~~~---~----l~~l~~~~~~lp~L~~L~l~~c~  775 (824)
                      ....   +......+++|++|++++|.   .    +..++.....+++|+.|++++|+
T Consensus       238 ~~~~~~~l~~~~~~l~~L~~L~L~~n~l~~i~~~~~~~l~~~~~~l~~L~~LdL~~N~  295 (362)
T 3goz_A          238 HGPSLENLKLLKDSLKHLQTVYLDYDIVKNMSKEQCKALGAAFPNIQKIILVDKNGKE  295 (362)
T ss_dssp             CCCCHHHHHHTTTTTTTCSEEEEEHHHHTTCCHHHHHHHHTTSTTCCEEEEECTTSCB
T ss_pred             CcHHHHHHHHHHhcCCCccEEEeccCCccccCHHHHHHHHHHhccCCceEEEecCCCc
Confidence            4421   12223445566666665553   0    11122233445555556665555

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=99.55  E-value=6.6e-15  Score=154.84  Aligned_cols=173  Identities=23%  Similarity=0.231  Sum_probs=115.4

Q ss_pred             hcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCcee
Q 003387          517 CGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL  596 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L  596 (824)
                      +..++.|++|++++|.+..+|. +..+++|++|++++|.+..++. + +++++|++|++++|.+..+|. +..+++|++|
T Consensus        42 ~~~l~~L~~L~l~~~~i~~~~~-~~~l~~L~~L~L~~n~l~~~~~-l-~~l~~L~~L~l~~n~l~~~~~-l~~l~~L~~L  117 (291)
T 1h6t_A           42 QNELNSIDQIIANNSDIKSVQG-IQYLPNVTKLFLNGNKLTDIKP-L-ANLKNLGWLFLDENKVKDLSS-LKDLKKLKSL  117 (291)
T ss_dssp             HHHHHTCCEEECTTSCCCCCTT-GGGCTTCCEEECCSSCCCCCGG-G-TTCTTCCEEECCSSCCCCGGG-GTTCTTCCEE
T ss_pred             hhhcCcccEEEccCCCcccChh-HhcCCCCCEEEccCCccCCCcc-c-ccCCCCCEEECCCCcCCCChh-hccCCCCCEE
Confidence            3456778888888888777754 7778888888888888887776 5 788888888888887777665 7788888888


Q ss_pred             cCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCC
Q 003387          597 NFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKM  676 (824)
Q Consensus       597 ~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~  676 (824)
                      ++++|.+..  ++.                      +..+++|+.|+++++.-   ..+ ..+..+++|+.|++++|   
T Consensus       118 ~L~~n~i~~--~~~----------------------l~~l~~L~~L~l~~n~l---~~~-~~l~~l~~L~~L~L~~N---  166 (291)
T 1h6t_A          118 SLEHNGISD--ING----------------------LVHLPQLESLYLGNNKI---TDI-TVLSRLTKLDTLSLEDN---  166 (291)
T ss_dssp             ECTTSCCCC--CGG----------------------GGGCTTCCEEECCSSCC---CCC-GGGGGCTTCSEEECCSS---
T ss_pred             ECCCCcCCC--Chh----------------------hcCCCCCCEEEccCCcC---Ccc-hhhccCCCCCEEEccCC---
Confidence            888877652  222                      44455555555555531   111 24555666666666654   


Q ss_pred             CCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCC
Q 003387          677 PRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG  729 (824)
Q Consensus       677 ~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~  729 (824)
                       .++.+.  .+..+++|+.|++++|.+..  .+.+..+++|+.|++++|.+..
T Consensus       167 -~l~~~~--~l~~l~~L~~L~L~~N~i~~--l~~l~~l~~L~~L~l~~n~i~~  214 (291)
T 1h6t_A          167 -QISDIV--PLAGLTKLQNLYLSKNHISD--LRALAGLKNLDVLELFSQECLN  214 (291)
T ss_dssp             -CCCCCG--GGTTCTTCCEEECCSSCCCB--CGGGTTCTTCSEEEEEEEEEEC
T ss_pred             -ccccch--hhcCCCccCEEECCCCcCCC--ChhhccCCCCCEEECcCCcccC
Confidence             122221  13556777777777777653  2347788888888888777654

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=99.55  E-value=6e-15  Score=170.26  Aligned_cols=83  Identities=20%  Similarity=0.173  Sum_probs=54.3

Q ss_pred             cccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceec
Q 003387          518 GMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLN  597 (824)
Q Consensus       518 ~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~  597 (824)
                      ..++.|+.|++++|.+..+| .+..|++|++|+|++|.+..+|+ + +.|++|+.|+|++|.+..+| .+..+++|++|+
T Consensus        40 ~~L~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~Ls~N~l~~~~~-l-~~l~~L~~L~Ls~N~l~~l~-~l~~l~~L~~L~  115 (605)
T 1m9s_A           40 NELNSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLNGNKLTDIKP-L-TNLKNLGWLFLDENKIKDLS-SLKDLKKLKSLS  115 (605)
T ss_dssp             HHHTTCCCCBCTTCCCCCCT-TGGGCTTCCEEECTTSCCCCCGG-G-GGCTTCCEEECCSSCCCCCT-TSTTCTTCCEEE
T ss_pred             hcCCCCCEEECcCCCCCCCh-HHccCCCCCEEEeeCCCCCCChh-h-ccCCCCCEEECcCCCCCCCh-hhccCCCCCEEE
Confidence            45566666666666666655 36666677777777666666665 4 66677777777666666655 366666677776


Q ss_pred             CCCccCC
Q 003387          598 FGSITLP  604 (824)
Q Consensus       598 L~~~~~~  604 (824)
                      |++|.+.
T Consensus       116 Ls~N~l~  122 (605)
T 1m9s_A          116 LEHNGIS  122 (605)
T ss_dssp             CTTSCCC
T ss_pred             ecCCCCC
Confidence            6666654

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.53  E-value=1.5e-14  Score=164.96  Aligned_cols=75  Identities=23%  Similarity=0.256  Sum_probs=65.9

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCC
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGS  600 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~  600 (824)
                      .+|++|+|++|.++.+|..+.  ++|++|+|++|.++.+| .   .+++|++|++++|.++.+|. +.+  +|++|++++
T Consensus        59 ~~L~~L~Ls~n~L~~lp~~l~--~~L~~L~Ls~N~l~~ip-~---~l~~L~~L~Ls~N~l~~ip~-l~~--~L~~L~Ls~  129 (571)
T 3cvr_A           59 NQFSELQLNRLNLSSLPDNLP--PQITVLEITQNALISLP-E---LPASLEYLDACDNRLSTLPE-LPA--SLKHLDVDN  129 (571)
T ss_dssp             TTCSEEECCSSCCSCCCSCCC--TTCSEEECCSSCCSCCC-C---CCTTCCEEECCSSCCSCCCC-CCT--TCCEEECCS
T ss_pred             CCccEEEeCCCCCCccCHhHc--CCCCEEECcCCCCcccc-c---ccCCCCEEEccCCCCCCcch-hhc--CCCEEECCC
Confidence            389999999999999998774  78999999999999998 3   47899999999999999988 665  999999999


Q ss_pred             ccCC
Q 003387          601 ITLP  604 (824)
Q Consensus       601 ~~~~  604 (824)
                      |.+.
T Consensus       130 N~l~  133 (571)
T 3cvr_A          130 NQLT  133 (571)
T ss_dssp             SCCS
T ss_pred             CcCC
Confidence            8876

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.51  E-value=6.3e-14  Score=139.59  Aligned_cols=180  Identities=20%  Similarity=0.247  Sum_probs=115.3

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCcc
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSIT  602 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~  602 (824)
                      +.++.+++.+..+|..+.  .+|++|++++|.+..+|...+.++++|++|++++|.+..+|.. +..+++|++|++++|.
T Consensus        10 ~~v~c~~~~l~~~p~~~~--~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~   87 (208)
T 2o6s_A           10 TTVECYSQGRTSVPTGIP--AQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQ   87 (208)
T ss_dssp             TEEECCSSCCSSCCSCCC--TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             CEEEecCCCccCCCCCCC--CCCcEEEcCCCccCcCChhhhcccccCcEEECCCCccCccChhhcCCCCCcCEEECCCCc
Confidence            567777777777776553  4888888888888888876657888888888888888887765 5778888888888877


Q ss_pred             CCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEE
Q 003387          603 LPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKI  682 (824)
Q Consensus       603 ~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l  682 (824)
                      +..  +|                    ...+..+++|+.|+++++.                              ++.+
T Consensus        88 l~~--~~--------------------~~~~~~l~~L~~L~L~~N~------------------------------l~~~  115 (208)
T 2o6s_A           88 LQS--LP--------------------NGVFDKLTQLKELALNTNQ------------------------------LQSL  115 (208)
T ss_dssp             CCC--CC--------------------TTTTTTCTTCCEEECCSSC------------------------------CCCC
T ss_pred             CCc--cC--------------------HhHhcCccCCCEEEcCCCc------------------------------Cccc
Confidence            642  11                    1114455566666655542                              1111


Q ss_pred             EeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCc
Q 003387          683 VLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAA  762 (824)
Q Consensus       683 ~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~  762 (824)
                      ....+..+++|+.|++++|.+.+..+..+..+++|+.|++++|.+.+        .+++|+.|.++.+.....+|..++.
T Consensus       116 ~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~~--------~~~~l~~L~~~~n~~~g~ip~~~~~  187 (208)
T 2o6s_A          116 PDGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDC--------TCPGIRYLSEWINKHSGVVRNSAGS  187 (208)
T ss_dssp             CTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSCCBCC--------CTTTTHHHHHHHHHCTTTBBCTTSS
T ss_pred             CHhHhccCCcCCEEECCCCccceeCHHHhccCCCccEEEecCCCeec--------CCCCHHHHHHHHHhCCceeeccCcc
Confidence            00111334556666666666655445556777777777777765432        4567777777666555566655555


Q ss_pred             ccC
Q 003387          763 MPK  765 (824)
Q Consensus       763 lp~  765 (824)
                      ++.
T Consensus       188 l~~  190 (208)
T 2o6s_A          188 VAP  190 (208)
T ss_dssp             BCT
T ss_pred             ccC
Confidence            544

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=99.50  E-value=2.4e-14  Score=165.24  Aligned_cols=189  Identities=20%  Similarity=0.183  Sum_probs=146.6

Q ss_pred             cccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCc
Q 003387          522 LLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSI  601 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~  601 (824)
                      .+..+.++.+.+..++. +..|.+|++|++++|.+..+|. + ..|++|+.|+|++|.+..+|. +..|++|++|+|++|
T Consensus        22 ~l~~l~l~~~~i~~~~~-~~~L~~L~~L~l~~n~i~~l~~-l-~~l~~L~~L~Ls~N~l~~~~~-l~~l~~L~~L~Ls~N   97 (605)
T 1m9s_A           22 ETIKDNLKKKSVTDAVT-QNELNSIDQIIANNSDIKSVQG-I-QYLPNVTKLFLNGNKLTDIKP-LTNLKNLGWLFLDEN   97 (605)
T ss_dssp             HHHHHHTTCSCTTSEEC-HHHHTTCCCCBCTTCCCCCCTT-G-GGCTTCCEEECTTSCCCCCGG-GGGCTTCCEEECCSS
T ss_pred             HHHHHhccCCCcccccc-hhcCCCCCEEECcCCCCCCChH-H-ccCCCCCEEEeeCCCCCCChh-hccCCCCCEEECcCC
Confidence            34455666666654433 5678999999999999999974 6 999999999999999999987 999999999999999


Q ss_pred             cCCCCCCCCCCCCCCCCeeeccCC-CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCcc
Q 003387          602 TLPAHPGKFCGSLENLNFISALHP-CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLS  680 (824)
Q Consensus       602 ~~~~~~~p~i~~L~~L~~l~~~~~-~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~  680 (824)
                      .+.  .+|.++.+++|+.|+++.+ ...++. +..|++|+.|++++|.-   ..+ ..+..+++|+.|+|++|.    +.
T Consensus        98 ~l~--~l~~l~~l~~L~~L~Ls~N~l~~l~~-l~~l~~L~~L~Ls~N~l---~~l-~~l~~l~~L~~L~Ls~N~----l~  166 (605)
T 1m9s_A           98 KIK--DLSSLKDLKKLKSLSLEHNGISDING-LVHLPQLESLYLGNNKI---TDI-TVLSRLTKLDTLSLEDNQ----IS  166 (605)
T ss_dssp             CCC--CCTTSTTCTTCCEEECTTSCCCCCGG-GGGCTTCSEEECCSSCC---CCC-GGGGSCTTCSEEECCSSC----CC
T ss_pred             CCC--CChhhccCCCCCEEEecCCCCCCCcc-ccCCCccCEEECCCCcc---CCc-hhhcccCCCCEEECcCCc----CC
Confidence            987  5678888999999998843 223444 88889999999988852   222 467788888888888762    33


Q ss_pred             EEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCC
Q 003387          681 KIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG  729 (824)
Q Consensus       681 ~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~  729 (824)
                      .+..  +..+++|+.|+|++|.+.+  ++.+..+++|+.|+|++|.+..
T Consensus       167 ~~~~--l~~l~~L~~L~Ls~N~i~~--l~~l~~l~~L~~L~L~~N~l~~  211 (605)
T 1m9s_A          167 DIVP--LAGLTKLQNLYLSKNHISD--LRALAGLKNLDVLELFSQECLN  211 (605)
T ss_dssp             CCGG--GTTCTTCCEEECCSSCCCB--CGGGTTCTTCSEEECCSEEEEC
T ss_pred             Cchh--hccCCCCCEEECcCCCCCC--ChHHccCCCCCEEEccCCcCcC
Confidence            3322  4667888888998888754  2568888889999988887765

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.49  E-value=3.3e-14  Score=125.04  Aligned_cols=81  Identities=26%  Similarity=0.349  Sum_probs=75.2

Q ss_pred             hHHHHHHHHHHhhcccccccchhchHHHHHHHHHHHHHHHHHccccchhhHHHhhhcccc---ccCChhHHHHHHHHHHH
Q 003387            4 NFRLFSERLRRVLAGEEVTLPDAAKQPIQNLHAEVEIVTSWLSEFEDDISLLLFEKMAEE---ESHDPDLATVMDEINWF   80 (824)
Q Consensus         4 ~~~~~~~kl~~~~~~~~~~~~~~~~~~~~~l~~~l~~i~~~l~~~~~~~~~~~~~~~a~~---~~~~~~~~~wl~~l~~~   80 (824)
                      +++++++||.+++. +|+.++.||+++++.|+++|+.|+++|.|             |+.   +..++.++.|+++||++
T Consensus         2 ~v~~ll~KL~~ll~-~E~~l~~gv~~~i~~Lk~eL~~m~a~L~d-------------a~~~~~~~~d~~vk~W~~~vrdl   67 (115)
T 3qfl_A            2 AISNLIPKLGELLT-EEFKLHKGVKKNIEDLGKELESMNAALIK-------------IGEVPREQLDSQDKLWADEVREL   67 (115)
T ss_dssp             TTCSHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HTTSCGGGCCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHH-HHHHHHhchHHHHHHHHHHHHHHHHHHHH-------------HHHhccccCCHHHHHHHHHHHHH
Confidence            57789999999999 99999999999999999999999999999             776   35789999999999999


Q ss_pred             hhhhHHHHHHhHHhhccc
Q 003387           81 TYESEKVIDTFINSITQQ   98 (824)
Q Consensus        81 ~~~~ed~ld~~~~~~~~~   98 (824)
                      +||+||++|+|.++....
T Consensus        68 aYD~ED~iD~f~~~~~~~   85 (115)
T 3qfl_A           68 SYVIEDVVDKFLVQVDGI   85 (115)
T ss_dssp             HHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhccc
Confidence            999999999999988643

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=99.48  E-value=8.9e-14  Score=146.15  Aligned_cols=184  Identities=22%  Similarity=0.196  Sum_probs=145.2

Q ss_pred             EEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCC
Q 003387          525 VLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       525 ~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~  604 (824)
                      .+.+....+..++ .+..+.+|++|++++|.+..+|. + ..+++|++|++++|.+..++. +.++++|++|++++|.+.
T Consensus        28 ~~~l~~~~~~~~~-~~~~l~~L~~L~l~~~~i~~~~~-~-~~l~~L~~L~L~~n~l~~~~~-l~~l~~L~~L~l~~n~l~  103 (291)
T 1h6t_A           28 KDNLKKKSVTDAV-TQNELNSIDQIIANNSDIKSVQG-I-QYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDENKVK  103 (291)
T ss_dssp             HHHTTCSCTTSEE-CHHHHHTCCEEECTTSCCCCCTT-G-GGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCC
T ss_pred             HHHhcCCCccccc-chhhcCcccEEEccCCCcccChh-H-hcCCCCCEEEccCCccCCCcc-cccCCCCCEEECCCCcCC
Confidence            3345555554332 24568899999999999999875 5 899999999999999999987 999999999999998875


Q ss_pred             CCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEe
Q 003387          605 AHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVL  684 (824)
Q Consensus       605 ~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l  684 (824)
                      .                       ++. +..+++|+.|+++++.-.   .+ ..+..+++|+.|++++|    .++.+  
T Consensus       104 ~-----------------------~~~-l~~l~~L~~L~L~~n~i~---~~-~~l~~l~~L~~L~l~~n----~l~~~--  149 (291)
T 1h6t_A          104 D-----------------------LSS-LKDLKKLKSLSLEHNGIS---DI-NGLVHLPQLESLYLGNN----KITDI--  149 (291)
T ss_dssp             C-----------------------GGG-GTTCTTCCEEECTTSCCC---CC-GGGGGCTTCCEEECCSS----CCCCC--
T ss_pred             C-----------------------Chh-hccCCCCCEEECCCCcCC---CC-hhhcCCCCCCEEEccCC----cCCcc--
Confidence            2                       123 677788888888877421   22 35778999999999987    34443  


Q ss_pred             CccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCC
Q 003387          685 AEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSML  751 (824)
Q Consensus       685 ~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~  751 (824)
                      ..+..+++|+.|++++|.+.+..+  ++.+++|+.|++++|.+...   .....+++|+.|++++|+
T Consensus       150 ~~l~~l~~L~~L~L~~N~l~~~~~--l~~l~~L~~L~L~~N~i~~l---~~l~~l~~L~~L~l~~n~  211 (291)
T 1h6t_A          150 TVLSRLTKLDTLSLEDNQISDIVP--LAGLTKLQNLYLSKNHISDL---RALAGLKNLDVLELFSQE  211 (291)
T ss_dssp             GGGGGCTTCSEEECCSSCCCCCGG--GTTCTTCCEEECCSSCCCBC---GGGTTCTTCSEEEEEEEE
T ss_pred             hhhccCCCCCEEEccCCccccchh--hcCCCccCEEECCCCcCCCC---hhhccCCCCCEEECcCCc
Confidence            455788999999999999865433  89999999999999988752   247889999999999986

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=99.48  E-value=2.5e-13  Score=139.49  Aligned_cols=169  Identities=18%  Similarity=0.148  Sum_probs=115.2

Q ss_pred             eEEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeec
Q 003387          474 KRLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLN  552 (824)
Q Consensus       474 r~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~  552 (824)
                      +++... +.....+|..+.+.++.|.+.++....    ..+..|..+++|++|+|++|.++.++. .+..+++|++|+|+
T Consensus        17 ~~l~~~-~~~l~~~p~~~~~~l~~L~L~~n~l~~----~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~   91 (251)
T 3m19_A           17 KEVDCQ-GKSLDSVPSGIPADTEKLDLQSTGLAT----LSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLA   91 (251)
T ss_dssp             TEEECT-TCCCSSCCSCCCTTCCEEECTTSCCCC----CCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECT
T ss_pred             eEEecC-CCCccccCCCCCCCCCEEEccCCCcCc----cCHhHhcCcccCCEEECCCCcCCccCHhHhccCCcCCEEECC
Confidence            344444 444444555556778888887776642    344567788888888888888875544 46778888888888


Q ss_pred             CCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCC--Ccc
Q 003387          553 IPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHP--CCC  628 (824)
Q Consensus       553 ~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~--~~~  628 (824)
                      +|.+..+|...|..+++|++|+|++|.+..+|.. +..+++|++|++++|.+.. ..+ .++.+++|+.|+++.+  ...
T Consensus        92 ~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~-~~~~~~~~l~~L~~L~L~~N~l~~~  170 (251)
T 3m19_A           92 NNQLASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQS-IPAGAFDKLTNLQTLSLSTNQLQSV  170 (251)
T ss_dssp             TSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCC-CCTTTTTTCTTCCEEECCSSCCSCC
T ss_pred             CCcccccChhHhcccCCCCEEEcCCCcCCCcChhHhccCCcccEEECcCCcCCc-cCHHHcCcCcCCCEEECCCCcCCcc
Confidence            8888888776667888888888888888888765 5778888888888887763 222 5666677777766632  112


Q ss_pred             hhhhcCCCCccceEEEeccc
Q 003387          629 TEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       629 ~~~~l~~l~~L~~L~l~~~~  648 (824)
                      ....+..+++|+.|+++++.
T Consensus       171 ~~~~~~~l~~L~~L~l~~N~  190 (251)
T 3m19_A          171 PHGAFDRLGKLQTITLFGNQ  190 (251)
T ss_dssp             CTTTTTTCTTCCEEECCSCC
T ss_pred             CHHHHhCCCCCCEEEeeCCc
Confidence            22235566666666666654

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=99.46  E-value=8.3e-14  Score=137.38  Aligned_cols=153  Identities=16%  Similarity=0.175  Sum_probs=92.3

Q ss_pred             cccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccc-cchhhhccccCcee
Q 003387          518 GMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHL  596 (824)
Q Consensus       518 ~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~-lp~~i~~L~~L~~L  596 (824)
                      ..+++|++|++++|.+..+| .+..+++|++|++++|.+..++ .+ ..+++|++|++++|.+.. .|..+..+++|++|
T Consensus        41 ~~l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~l~~n~~~~~~-~l-~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L  117 (197)
T 4ezg_A           41 AQMNSLTYITLANINVTDLT-GIEYAHNIKDLTINNIHATNYN-PI-SGLSNLERLRIMGKDVTSDKIPNLSGLTSLTLL  117 (197)
T ss_dssp             HHHHTCCEEEEESSCCSCCT-TGGGCTTCSEEEEESCCCSCCG-GG-TTCTTCCEEEEECTTCBGGGSCCCTTCTTCCEE
T ss_pred             hhcCCccEEeccCCCccChH-HHhcCCCCCEEEccCCCCCcch-hh-hcCCCCCEEEeECCccCcccChhhcCCCCCCEE
Confidence            45667777777777777666 5677777777777777666554 34 677777777777776664 45556677777777


Q ss_pred             cCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCC
Q 003387          597 NFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKM  676 (824)
Q Consensus       597 ~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~  676 (824)
                      ++++|.+.                     ...+.. +..+++|+.|++++|.  ....++ .+                 
T Consensus       118 ~Ls~n~i~---------------------~~~~~~-l~~l~~L~~L~L~~n~--~i~~~~-~l-----------------  155 (197)
T 4ezg_A          118 DISHSAHD---------------------DSILTK-INTLPKVNSIDLSYNG--AITDIM-PL-----------------  155 (197)
T ss_dssp             ECCSSBCB---------------------GGGHHH-HTTCSSCCEEECCSCT--BCCCCG-GG-----------------
T ss_pred             EecCCccC---------------------cHhHHH-HhhCCCCCEEEccCCC--CccccH-hh-----------------
Confidence            77766654                     112222 5556666666666552  011111 12                 


Q ss_pred             CCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccC
Q 003387          677 PRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYS  728 (824)
Q Consensus       677 ~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~  728 (824)
                                 ..+++|+.|++++|.+.+  .+.+..+++|+.|++++|.+.
T Consensus       156 -----------~~l~~L~~L~l~~n~i~~--~~~l~~l~~L~~L~l~~N~i~  194 (197)
T 4ezg_A          156 -----------KTLPELKSLNIQFDGVHD--YRGIEDFPKLNQLYAFSQTIG  194 (197)
T ss_dssp             -----------GGCSSCCEEECTTBCCCC--CTTGGGCSSCCEEEECBC---
T ss_pred             -----------cCCCCCCEEECCCCCCcC--hHHhccCCCCCEEEeeCcccC
Confidence                       344556666666666543  225667777777777776654

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=99.46  E-value=1.8e-13  Score=148.09  Aligned_cols=240  Identities=15%  Similarity=0.114  Sum_probs=174.0

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccc-cccchh-hhccccCcee-cCCC
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI-DHTADE-FWKMNKLRHL-NFGS  600 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l-~~lp~~-i~~L~~L~~L-~L~~  600 (824)
                      ++++.+++.++.+|..+.  .++++|+|++|+|+.+|...|.+|++|++|+|++|.+ +.+|.. |.++++|+.+ .+++
T Consensus        12 ~~v~C~~~~Lt~iP~~l~--~~l~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~   89 (350)
T 4ay9_X           12 RVFLCQESKVTEIPSDLP--RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKA   89 (350)
T ss_dssp             TEEEEESTTCCSCCTTCC--TTCSEEEEESCCCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEE
T ss_pred             CEEEecCCCCCccCcCcC--CCCCEEEccCCcCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccC
Confidence            678889999999998774  6899999999999999987669999999999999976 456644 7788888764 4444


Q ss_pred             ccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCcc
Q 003387          601 ITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLS  680 (824)
Q Consensus       601 ~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~  680 (824)
                      |.+.                      ...+..+..+++|+.|+++++.-  ....+..+....++..|++..+   .++.
T Consensus        90 N~l~----------------------~l~~~~f~~l~~L~~L~l~~n~l--~~~~~~~~~~~~~l~~l~l~~~---~~i~  142 (350)
T 4ay9_X           90 NNLL----------------------YINPEAFQNLPNLQYLLISNTGI--KHLPDVHKIHSLQKVLLDIQDN---INIH  142 (350)
T ss_dssp             TTCC----------------------EECTTSBCCCTTCCEEEEEEECC--SSCCCCTTCCBSSCEEEEEESC---TTCC
T ss_pred             Cccc----------------------ccCchhhhhcccccccccccccc--ccCCchhhcccchhhhhhhccc---cccc
Confidence            5543                      11122377788888888888741  1111122334456677777642   2455


Q ss_pred             EEEeCccCcC-CCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceec
Q 003387          681 KIVLAEYLFP-HSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMG  759 (824)
Q Consensus       681 ~l~l~~~~~~-~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~  759 (824)
                      .+....+..+ ..++.|++++|.+.. ++......++|+.|.+.+++.........+.++++|++|++++|. ++.+|. 
T Consensus       143 ~l~~~~f~~~~~~l~~L~L~~N~i~~-i~~~~f~~~~L~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~N~-l~~lp~-  219 (350)
T 4ay9_X          143 TIERNSFVGLSFESVILWLNKNGIQE-IHNSAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTR-IHSLPS-  219 (350)
T ss_dssp             EECTTSSTTSBSSCEEEECCSSCCCE-ECTTSSTTEEEEEEECTTCTTCCCCCTTTTTTEECCSEEECTTSC-CCCCCS-
T ss_pred             cccccchhhcchhhhhhccccccccC-CChhhccccchhHHhhccCCcccCCCHHHhccCcccchhhcCCCC-cCccCh-
Confidence            5544433333 468999999998863 444445667899999986544432222345788999999999985 788874 


Q ss_pred             cCcccCccEEEEecCCCCCCCccccccCccCcEEEecC
Q 003387          760 NAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWW  797 (824)
Q Consensus       760 ~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~  797 (824)
                       ..+.+|+.|.+.+|..++.+|. +..+++|+.+++.+
T Consensus       220 -~~~~~L~~L~~l~~~~l~~lP~-l~~l~~L~~l~l~~  255 (350)
T 4ay9_X          220 -YGLENLKKLRARSTYNLKKLPT-LEKLVALMEASLTY  255 (350)
T ss_dssp             -SSCTTCCEEECTTCTTCCCCCC-TTTCCSCCEEECSC
T ss_pred             -hhhccchHhhhccCCCcCcCCC-chhCcChhhCcCCC
Confidence             4588999999999999999994 88999999999864

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=99.44  E-value=1.8e-13  Score=134.88  Aligned_cols=153  Identities=19%  Similarity=0.221  Sum_probs=113.3

Q ss_pred             CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCe
Q 003387          540 IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNF  619 (824)
Q Consensus       540 i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~  619 (824)
                      ...+++|++|++++|.+..+| .+ ..+++|++|++++|.+..++ .+..+++|++|++++|.+..              
T Consensus        40 ~~~l~~L~~L~l~~n~i~~l~-~l-~~l~~L~~L~l~~n~~~~~~-~l~~l~~L~~L~l~~n~l~~--------------  102 (197)
T 4ezg_A           40 EAQMNSLTYITLANINVTDLT-GI-EYAHNIKDLTINNIHATNYN-PISGLSNLERLRIMGKDVTS--------------  102 (197)
T ss_dssp             HHHHHTCCEEEEESSCCSCCT-TG-GGCTTCSEEEEESCCCSCCG-GGTTCTTCCEEEEECTTCBG--------------
T ss_pred             hhhcCCccEEeccCCCccChH-HH-hcCCCCCEEEccCCCCCcch-hhhcCCCCCEEEeECCccCc--------------
Confidence            366888999999999999888 56 89999999999999777766 58889999999998887752              


Q ss_pred             eeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEE
Q 003387          620 ISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFS  699 (824)
Q Consensus       620 l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~  699 (824)
                             ..+.. +..+++|+.|+++++.  .....+..+..+++|++                            |+++
T Consensus       103 -------~~~~~-l~~l~~L~~L~Ls~n~--i~~~~~~~l~~l~~L~~----------------------------L~L~  144 (197)
T 4ezg_A          103 -------DKIPN-LSGLTSLTLLDISHSA--HDDSILTKINTLPKVNS----------------------------IDLS  144 (197)
T ss_dssp             -------GGSCC-CTTCTTCCEEECCSSB--CBGGGHHHHTTCSSCCE----------------------------EECC
T ss_pred             -------ccChh-hcCCCCCCEEEecCCc--cCcHhHHHHhhCCCCCE----------------------------EEcc
Confidence                   12222 6778888888888874  33334555555554444                            4445


Q ss_pred             cccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCC
Q 003387          700 NTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSML  751 (824)
Q Consensus       700 ~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~  751 (824)
                      +|......+ .++.+++|+.|++++|.+.+.  . ....+++|++|++++++
T Consensus       145 ~n~~i~~~~-~l~~l~~L~~L~l~~n~i~~~--~-~l~~l~~L~~L~l~~N~  192 (197)
T 4ezg_A          145 YNGAITDIM-PLKTLPELKSLNIQFDGVHDY--R-GIEDFPKLNQLYAFSQT  192 (197)
T ss_dssp             SCTBCCCCG-GGGGCSSCCEEECTTBCCCCC--T-TGGGCSSCCEEEECBC-
T ss_pred             CCCCccccH-hhcCCCCCCEEECCCCCCcCh--H-HhccCCCCCEEEeeCcc
Confidence            554223333 688999999999999988762  2 56789999999999876

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.43  E-value=8.8e-14  Score=143.84  Aligned_cols=40  Identities=15%  Similarity=0.232  Sum_probs=24.5

Q ss_pred             CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCC
Q 003387          688 LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG  729 (824)
Q Consensus       688 ~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~  729 (824)
                      ..+++|+.|++++|.+.+.  ..+..+++|+.|++++|.+..
T Consensus       147 ~~l~~L~~L~L~~N~i~~~--~~l~~l~~L~~L~l~~N~~~~  186 (263)
T 1xeu_A          147 GFLSKLEVLDLHGNEITNT--GGLTRLKKVNWIDLTGQKCVN  186 (263)
T ss_dssp             GGCTTCCEEECTTSCCCBC--TTSTTCCCCCEEEEEEEEEEC
T ss_pred             ccCCCCCEEECCCCcCcch--HHhccCCCCCEEeCCCCcccC
Confidence            3445566666666665433  556667777777777666554

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.41  E-value=3.5e-13  Score=134.15  Aligned_cols=132  Identities=23%  Similarity=0.252  Sum_probs=93.3

Q ss_pred             cccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhh
Q 003387          487 CLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLS  565 (824)
Q Consensus       487 ~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~  565 (824)
                      ++..+.++++.|.+.++...    ......|..+++|++|++++|.++.+|.. +..+++|++|++++|.+..+|...+.
T Consensus        22 ~p~~~~~~l~~L~l~~n~l~----~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~   97 (208)
T 2o6s_A           22 VPTGIPAQTTYLDLETNSLK----SLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQSLPNGVFD   97 (208)
T ss_dssp             CCSCCCTTCSEEECCSSCCC----CCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT
T ss_pred             CCCCCCCCCcEEEcCCCccC----cCChhhhcccccCcEEECCCCccCccChhhcCCCCCcCEEECCCCcCCccCHhHhc
Confidence            44444667788887777653    23445677788888888888887766654 46788888888888888877776557


Q ss_pred             cCCCccEeecCCccccccchh-hhccccCceecCCCccCCCCCCC-CCCCCCCCCeeecc
Q 003387          566 NLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISAL  623 (824)
Q Consensus       566 ~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~  623 (824)
                      ++++|++|++++|.+..+|.. +..+++|++|++++|.+.. ..+ .++.+++|+.|++.
T Consensus        98 ~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~-~~~~~~~~l~~L~~L~l~  156 (208)
T 2o6s_A           98 KLTQLKELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKS-VPDGVFDRLTSLQYIWLH  156 (208)
T ss_dssp             TCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSC-CCTTTTTTCTTCCEEECC
T ss_pred             CccCCCEEEcCCCcCcccCHhHhccCCcCCEEECCCCccce-eCHHHhccCCCccEEEec
Confidence            888888888888877777655 6778888888888877762 222 35556666666655

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=99.40  E-value=8.5e-13  Score=132.48  Aligned_cols=151  Identities=18%  Similarity=0.263  Sum_probs=106.0

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCcccccc-chhhhccccCceecCCCcc
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~~~  602 (824)
                      +.++++++.++.+|..+.  .+|++|++++|.+..+|...|..+++|++|+|++|.+..+ |..|..+++|++|+|++|.
T Consensus        14 ~~v~c~~~~l~~iP~~l~--~~l~~L~l~~n~i~~i~~~~~~~l~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~N~   91 (220)
T 2v9t_B           14 NIVDCRGKGLTEIPTNLP--ETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGNK   91 (220)
T ss_dssp             TEEECTTSCCSSCCSSCC--TTCCEEECCSSCCCEECTTSSTTCTTCCEEECCSSCCCEECTTTTTTCSSCCEEECCSSC
T ss_pred             CEEEcCCCCcCcCCCccC--cCCCEEECCCCcCCCcCHhHhhCCCCCCEEECCCCcCCCcCHHHhhCCcCCCEEECCCCc
Confidence            678888888888888765  6889999999999888875558899999999999988877 6678889999999888887


Q ss_pred             CCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEE
Q 003387          603 LPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKI  682 (824)
Q Consensus       603 ~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l  682 (824)
                      +..  +|                    ...+..+++|+.|+++++.                              ++.+
T Consensus        92 l~~--l~--------------------~~~f~~l~~L~~L~L~~N~------------------------------l~~~  119 (220)
T 2v9t_B           92 ITE--LP--------------------KSLFEGLFSLQLLLLNANK------------------------------INCL  119 (220)
T ss_dssp             CCC--CC--------------------TTTTTTCTTCCEEECCSSC------------------------------CCCC
T ss_pred             CCc--cC--------------------HhHccCCCCCCEEECCCCC------------------------------CCEe
Confidence            752  22                    1114555666666666552                              1111


Q ss_pred             EeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccC
Q 003387          683 VLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYS  728 (824)
Q Consensus       683 ~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~  728 (824)
                      ....+..+++|+.|+|++|.+....+..+..+++|+.|++++|.+.
T Consensus       120 ~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~~~  165 (220)
T 2v9t_B          120 RVDAFQDLHNLNLLSLYDNKLQTIAKGTFSPLRAIQTMHLAQNPFI  165 (220)
T ss_dssp             CTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSCEE
T ss_pred             CHHHcCCCCCCCEEECCCCcCCEECHHHHhCCCCCCEEEeCCCCcC
Confidence            1122234456666666677666555566777788888888777654

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=99.39  E-value=8e-15  Score=168.20  Aligned_cols=120  Identities=22%  Similarity=0.226  Sum_probs=94.5

Q ss_pred             CCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCcc
Q 003387          664 CLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLK  743 (824)
Q Consensus       664 ~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~  743 (824)
                      .|+.|++++|    .++.+  ..+..+++|+.|+|++|.+. .+|..++++++|+.|+|++|.+.+  ++ .++.+++|+
T Consensus       442 ~L~~L~Ls~n----~l~~l--p~~~~l~~L~~L~Ls~N~l~-~lp~~~~~l~~L~~L~Ls~N~l~~--lp-~l~~l~~L~  511 (567)
T 1dce_A          442 DVRVLHLAHK----DLTVL--CHLEQLLLVTHLDLSHNRLR-ALPPALAALRCLEVLQASDNALEN--VD-GVANLPRLQ  511 (567)
T ss_dssp             TCSEEECTTS----CCSSC--CCGGGGTTCCEEECCSSCCC-CCCGGGGGCTTCCEEECCSSCCCC--CG-GGTTCSSCC
T ss_pred             CceEEEecCC----CCCCC--cCccccccCcEeecCccccc-ccchhhhcCCCCCEEECCCCCCCC--Cc-ccCCCCCCc
Confidence            5888888876    34443  23567889999999999987 678889999999999999998886  44 678899999


Q ss_pred             EEeeccCCCCccc--eeccCcccCccEEEEecCCCCCCCcccc----ccCccCcEEEe
Q 003387          744 VLHLKSMLWLEEW--TMGNAAMPKLECLIINPCAYLKKMPEQL----WYIKSLNKFDC  795 (824)
Q Consensus       744 ~L~L~~~~~l~~l--~~~~~~lp~L~~L~l~~c~~l~~lp~~l----~~l~~L~~L~l  795 (824)
                      +|+|++|. +..+  |..++.+++|+.|++++|+.. .+|+.+    ..+|+|+.|++
T Consensus       512 ~L~Ls~N~-l~~~~~p~~l~~l~~L~~L~L~~N~l~-~~~~~~~~l~~~lp~L~~L~l  567 (567)
T 1dce_A          512 ELLLCNNR-LQQSAAIQPLVSCPRLVLLNLQGNSLC-QEEGIQERLAEMLPSVSSILT  567 (567)
T ss_dssp             EEECCSSC-CCSSSTTGGGGGCTTCCEEECTTSGGG-GSSSCTTHHHHHCTTCSEEEC
T ss_pred             EEECCCCC-CCCCCCcHHHhcCCCCCEEEecCCcCC-CCccHHHHHHHHCcccCccCC
Confidence            99999986 6666  778889999999999999854 444432    34788988863

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=99.39  E-value=1.6e-12  Score=148.30  Aligned_cols=189  Identities=19%  Similarity=0.162  Sum_probs=137.4

Q ss_pred             cceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccC
Q 003387          545 LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALH  624 (824)
Q Consensus       545 ~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~  624 (824)
                      +|++|+|++|.++.+|..+   +++|++|+|++|.++.+|   ..+++|++|++++|.+..  +|.+             
T Consensus        60 ~L~~L~Ls~n~L~~lp~~l---~~~L~~L~Ls~N~l~~ip---~~l~~L~~L~Ls~N~l~~--ip~l-------------  118 (571)
T 3cvr_A           60 QFSELQLNRLNLSSLPDNL---PPQITVLEITQNALISLP---ELPASLEYLDACDNRLST--LPEL-------------  118 (571)
T ss_dssp             TCSEEECCSSCCSCCCSCC---CTTCSEEECCSSCCSCCC---CCCTTCCEEECCSSCCSC--CCCC-------------
T ss_pred             CccEEEeCCCCCCccCHhH---cCCCCEEECcCCCCcccc---cccCCCCEEEccCCCCCC--cchh-------------
Confidence            8999999999999999877   378999999999999999   568999999999998863  3321             


Q ss_pred             CCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCC
Q 003387          625 PCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLM  704 (824)
Q Consensus       625 ~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~  704 (824)
                               ..  +|+.|++++|.   ...+|.   .+++|+.|++++|    .++.+.  .  .+++|+.|+|++|.+.
T Consensus       119 ---------~~--~L~~L~Ls~N~---l~~lp~---~l~~L~~L~Ls~N----~l~~lp--~--~l~~L~~L~Ls~N~L~  173 (571)
T 3cvr_A          119 ---------PA--SLKHLDVDNNQ---LTMLPE---LPALLEYINADNN----QLTMLP--E--LPTSLEVLSVRNNQLT  173 (571)
T ss_dssp             ---------CT--TCCEEECCSSC---CSCCCC---CCTTCCEEECCSS----CCSCCC--C--CCTTCCEEECCSSCCS
T ss_pred             ---------hc--CCCEEECCCCc---CCCCCC---cCccccEEeCCCC----ccCcCC--C--cCCCcCEEECCCCCCC
Confidence                     11  56666666653   111333   4567778887766    233321  1  4678999999999876


Q ss_pred             CCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCc-------cEEeeccCCCCccceeccCcccCccEEEEecCCCC
Q 003387          705 DDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNL-------KVLHLKSMLWLEEWTMGNAAMPKLECLIINPCAYL  777 (824)
Q Consensus       705 ~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L-------~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~~l  777 (824)
                      + +|. +.  ++|+.|+|++|.+..  ++. +..  +|       +.|+|++|. ++.+|..+..+++|+.|++++|+..
T Consensus       174 ~-lp~-l~--~~L~~L~Ls~N~L~~--lp~-~~~--~L~~~~~~L~~L~Ls~N~-l~~lp~~l~~l~~L~~L~L~~N~l~  243 (571)
T 3cvr_A          174 F-LPE-LP--ESLEALDVSTNLLES--LPA-VPV--RNHHSEETEIFFRCRENR-ITHIPENILSLDPTCTIILEDNPLS  243 (571)
T ss_dssp             C-CCC-CC--TTCCEEECCSSCCSS--CCC-CC----------CCEEEECCSSC-CCCCCGGGGGSCTTEEEECCSSSCC
T ss_pred             C-cch-hh--CCCCEEECcCCCCCc--hhh-HHH--hhhcccccceEEecCCCc-ceecCHHHhcCCCCCEEEeeCCcCC
Confidence            5 444 55  899999999888773  232 222  66       999999875 7778887778999999999999877


Q ss_pred             CCCccccccCcc
Q 003387          778 KKMPEQLWYIKS  789 (824)
Q Consensus       778 ~~lp~~l~~l~~  789 (824)
                      ..+|..+..+++
T Consensus       244 ~~~p~~l~~l~~  255 (571)
T 3cvr_A          244 SRIRESLSQQTA  255 (571)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             CcCHHHHHHhhc
Confidence            767766665443

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.38  E-value=1.5e-12  Score=130.75  Aligned_cols=153  Identities=17%  Similarity=0.226  Sum_probs=109.2

Q ss_pred             ccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccC-hhhhhcCCCccEeecCCccccccch-hhhccccCceecCCC
Q 003387          523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLP-SSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGS  600 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp-~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~  600 (824)
                      -++++++++.++.+|..+..  .+++|+|++|.+..++ ...|.++++|++|+|++|.+..++. .+..+++|++|++++
T Consensus        13 ~~~l~~s~n~l~~iP~~~~~--~~~~L~L~~N~l~~~~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~   90 (220)
T 2v70_A           13 GTTVDCSNQKLNKIPEHIPQ--YTAELRLNNNEFTVLEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILLTS   90 (220)
T ss_dssp             TTEEECCSSCCSSCCSCCCT--TCSEEECCSSCCCEECCCCCGGGCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCS
T ss_pred             CCEeEeCCCCcccCccCCCC--CCCEEEcCCCcCCccCchhhhccCCCCCEEECCCCcCCEECHHHhCCCCCCCEEECCC
Confidence            36899999999999987754  5689999999999884 3444899999999999999988875 588999999999998


Q ss_pred             ccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCcc
Q 003387          601 ITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLS  680 (824)
Q Consensus       601 ~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~  680 (824)
                      |.+..  +                    ....+..+++|+.|+++++.                              ++
T Consensus        91 N~l~~--~--------------------~~~~~~~l~~L~~L~Ls~N~------------------------------l~  118 (220)
T 2v70_A           91 NRLEN--V--------------------QHKMFKGLESLKTLMLRSNR------------------------------IT  118 (220)
T ss_dssp             SCCCC--C--------------------CGGGGTTCSSCCEEECTTSC------------------------------CC
T ss_pred             CccCc--c--------------------CHhHhcCCcCCCEEECCCCc------------------------------CC
Confidence            88752  1                    11125566667777666652                              11


Q ss_pred             EEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCC
Q 003387          681 KIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG  729 (824)
Q Consensus       681 ~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~  729 (824)
                      .+....+..+++|+.|+|++|.+.+..+..+..+++|+.|++++|.+..
T Consensus       119 ~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~c  167 (220)
T 2v70_A          119 CVGNDSFIGLSSVRLLSLYDNQITTVAPGAFDTLHSLSTLNLLANPFNC  167 (220)
T ss_dssp             CBCTTSSTTCTTCSEEECTTSCCCCBCTTTTTTCTTCCEEECCSCCEEC
T ss_pred             eECHhHcCCCccCCEEECCCCcCCEECHHHhcCCCCCCEEEecCcCCcC
Confidence            1111122345666777777777766667777788888888888776653

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.38  E-value=2.9e-13  Score=147.01  Aligned_cols=171  Identities=20%  Similarity=0.275  Sum_probs=91.0

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhh-cCCCccEeecCCccccccch-hhhccccCceecCCCc
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLS-NLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSI  601 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~-~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~  601 (824)
                      ++++++++.++.+|..+..  ++++|+|++|.+..++...+. ++++|++|+|++|.+..+|. .+..+++|++|+|++|
T Consensus        21 ~~l~c~~~~l~~iP~~~~~--~l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~N   98 (361)
T 2xot_A           21 NILSCSKQQLPNVPQSLPS--YTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDLSSN   98 (361)
T ss_dssp             TEEECCSSCCSSCCSSCCT--TCSEEECCSSCCCEECTTSSSSCCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSS
T ss_pred             CEEEeCCCCcCccCccCCC--CCCEEECCCCCCCccChhhhhhcccccCEEECCCCcCCccChhhccCCCCCCEEECCCC
Confidence            5667777777666665543  466777777777766665544 67777777777777766653 3667777777777776


Q ss_pred             cCCCCCCC-CCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCC
Q 003387          602 TLPAHPGK-FCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPR  678 (824)
Q Consensus       602 ~~~~~~~p-~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~  678 (824)
                      .+.. ..+ .+..+++|+.|+++.+.  ...+..+..+++|+.|+++++.                              
T Consensus        99 ~l~~-~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~------------------------------  147 (361)
T 2xot_A           99 HLHT-LDEFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQ------------------------------  147 (361)
T ss_dssp             CCCE-ECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC------------------------------
T ss_pred             cCCc-CCHHHhCCCcCCCEEECCCCcccEECHHHhCCcccCCEEECCCCc------------------------------
Confidence            6542 111 23333333333333110  0111114444555555554442                              


Q ss_pred             ccEEEeCcc---CcCCCceEEEEEcccCCCCCcccccCCCC--CCeEEeecccc
Q 003387          679 LSKIVLAEY---LFPHSLTHLSFSNTDLMDDPMPTLEKLPL--LQVLKLKQNSY  727 (824)
Q Consensus       679 L~~l~l~~~---~~~~~L~~L~L~~~~l~~~~~~~l~~l~~--L~~L~L~~~~~  727 (824)
                      ++.+....+   ..+++|+.|+|++|.+....+..+..++.  |+.|+|.+|.+
T Consensus       148 l~~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~~~l~~l~l~~N~~  201 (361)
T 2xot_A          148 ISRFPVELIKDGNKLPKLMLLDLSSNKLKKLPLTDLQKLPAWVKNGLYLHNNPL  201 (361)
T ss_dssp             CCSCCGGGTC----CTTCCEEECCSSCCCCCCHHHHHHSCHHHHTTEECCSSCE
T ss_pred             CCeeCHHHhcCcccCCcCCEEECCCCCCCccCHHHhhhccHhhcceEEecCCCc
Confidence            222111111   33566666666666665444445556665  36667766554

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.37  E-value=2.7e-12  Score=129.66  Aligned_cols=117  Identities=21%  Similarity=0.219  Sum_probs=92.4

Q ss_pred             CcccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChh
Q 003387          484 DFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSS  562 (824)
Q Consensus       484 ~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~  562 (824)
                      ...+|..+.++++.|.+.++....    ..+..|..+++|++|+|++|.+..+|.. +..+++|++|+|++|.+..+|..
T Consensus        31 l~~ip~~~~~~L~~L~Ls~n~i~~----~~~~~~~~l~~L~~L~L~~N~l~~i~~~~~~~l~~L~~L~Ls~N~l~~l~~~  106 (229)
T 3e6j_A           31 HASVPAGIPTNAQILYLHDNQITK----LEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQLTVLPSA  106 (229)
T ss_dssp             CSSCCSCCCTTCSEEECCSSCCCC----CCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTT
T ss_pred             cCccCCCCCCCCCEEEcCCCccCc----cCHHHhhCccCCcEEECCCCCCCCcChhhcccCCCcCEEECCCCcCCccChh
Confidence            334555557888888888877642    4456778888888888888888877754 57788888888888888888877


Q ss_pred             hhhcCCCccEeecCCccccccchhhhccccCceecCCCccCC
Q 003387          563 LLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       563 i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~  604 (824)
                      .|..+++|++|+|++|.+..+|..+..+++|++|++++|.+.
T Consensus       107 ~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N~l~  148 (229)
T 3e6j_A          107 VFDRLVHLKELFMCCNKLTELPRGIERLTHLTHLALDQNQLK  148 (229)
T ss_dssp             TTTTCTTCCEEECCSSCCCSCCTTGGGCTTCSEEECCSSCCC
T ss_pred             HhCcchhhCeEeccCCcccccCcccccCCCCCEEECCCCcCC
Confidence            668888888888888888888888888888888888888775

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.37  E-value=1.1e-12  Score=135.59  Aligned_cols=152  Identities=17%  Similarity=0.172  Sum_probs=100.3

Q ss_pred             hhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCce
Q 003387          516 FCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRH  595 (824)
Q Consensus       516 ~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~  595 (824)
                      .+..+++|++|++++|.++.+| .+..+++|++|++++|.+..+|. + .++++|++|++++|.+..+|... . ++|++
T Consensus        36 ~~~~l~~L~~L~l~~n~i~~l~-~l~~l~~L~~L~L~~N~i~~~~~-l-~~l~~L~~L~L~~N~l~~l~~~~-~-~~L~~  110 (263)
T 1xeu_A           36 SQKELSGVQNFNGDNSNIQSLA-GMQFFTNLKELHLSHNQISDLSP-L-KDLTKLEELSVNRNRLKNLNGIP-S-ACLSR  110 (263)
T ss_dssp             CHHHHTTCSEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-G-TTCSSCCEEECCSSCCSCCTTCC-C-SSCCE
T ss_pred             chhhcCcCcEEECcCCCcccch-HHhhCCCCCEEECCCCccCCChh-h-ccCCCCCEEECCCCccCCcCccc-c-CcccE
Confidence            3566777777777777777666 56777777777777777777766 4 77777777777777777766532 3 77777


Q ss_pred             ecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCC
Q 003387          596 LNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESK  675 (824)
Q Consensus       596 L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~  675 (824)
                      |++++|.+..  +                     +. +..+++|+.|+++++.   ...++ .+..+++|+.|++++|  
T Consensus       111 L~L~~N~l~~--~---------------------~~-l~~l~~L~~L~Ls~N~---i~~~~-~l~~l~~L~~L~L~~N--  160 (263)
T 1xeu_A          111 LFLDNNELRD--T---------------------DS-LIHLKNLEILSIRNNK---LKSIV-MLGFLSKLEVLDLHGN--  160 (263)
T ss_dssp             EECCSSCCSB--S---------------------GG-GTTCTTCCEEECTTSC---CCBCG-GGGGCTTCCEEECTTS--
T ss_pred             EEccCCccCC--C---------------------hh-hcCcccccEEECCCCc---CCCCh-HHccCCCCCEEECCCC--
Confidence            7777776642  2                     22 5566666777666663   11222 4666777777777765  


Q ss_pred             CCCccEEEeCccCcCCCceEEEEEcccCCCC
Q 003387          676 MPRLSKIVLAEYLFPHSLTHLSFSNTDLMDD  706 (824)
Q Consensus       676 ~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~  706 (824)
                        .++.+  ..+..+++|+.|++++|.+...
T Consensus       161 --~i~~~--~~l~~l~~L~~L~l~~N~~~~~  187 (263)
T 1xeu_A          161 --EITNT--GGLTRLKKVNWIDLTGQKCVNE  187 (263)
T ss_dssp             --CCCBC--TTSTTCCCCCEEEEEEEEEECC
T ss_pred             --cCcch--HHhccCCCCCEEeCCCCcccCC
Confidence              23333  4446677888888888876544

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.36  E-value=2.2e-13  Score=161.24  Aligned_cols=149  Identities=20%  Similarity=0.173  Sum_probs=91.0

Q ss_pred             CCeeEEEEEecCCCccccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceE
Q 003387          471 KKAKRLNAVEREGDFACLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRY  548 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~~~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~  548 (824)
                      ..++++++. .+.....+...  ..+|+.+.+............++..|..++.|++|+|++|.+..+|..++++++|++
T Consensus       173 ~~~~~l~L~-~n~~~~~~~~~l~~l~Ls~~~i~~~~~~~n~~~~~~~~~~~l~~L~~L~Ls~n~l~~l~~~~~~l~~L~~  251 (727)
T 4b8c_D          173 PLTPKIELF-ANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANIFKYDFLTR  251 (727)
T ss_dssp             --------------------------------------------------CCCCCCEEECTTSCCSCCCGGGGGCCSCSC
T ss_pred             CccceEEee-CCCCCcchhhHhhcCccCcccccCccccccceecChhhhccCCCCcEEECCCCCCCCCChhhcCCCCCCE
Confidence            446677775 33332233222  445555544433221101124577889999999999999999999999999999999


Q ss_pred             EeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeecc
Q 003387          549 LKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISAL  623 (824)
Q Consensus       549 L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~  623 (824)
                      |+|++|.++.+|..+ ++|++|++|+|++|.+..+|..|+.|++|++|+|++|.+.  .+| .+++|++|+.|+++
T Consensus       252 L~Ls~N~l~~lp~~~-~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~L~~N~l~--~lp~~~~~l~~L~~L~L~  324 (727)
T 4b8c_D          252 LYLNGNSLTELPAEI-KNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVT--TLPWEFGNLCNLQFLGVE  324 (727)
T ss_dssp             CBCTTSCCSCCCGGG-GGGTTCCEEECTTSCCSSCCSSGGGGTTCSEEECCSSCCC--CCCSSTTSCTTCCCEECT
T ss_pred             EEeeCCcCcccChhh-hCCCCCCEEeCcCCcCCccChhhcCCCCCCEEECCCCCCC--ccChhhhcCCCccEEeCC
Confidence            999999999999988 9999999999999999999999999999999999999886  555 56666666666555

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=99.35  E-value=3.3e-12  Score=128.15  Aligned_cols=114  Identities=20%  Similarity=0.226  Sum_probs=76.6

Q ss_pred             cccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEeecCCCCCccChhhhh
Q 003387          487 CLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSLPSSLLS  565 (824)
Q Consensus       487 ~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~i~~lp~~i~~  565 (824)
                      +|..+.++++.|.+.++...    .+.+..|..+++|++|+|++|.+..+ |..+..+++|++|+|++|.+..+|..+|.
T Consensus        26 iP~~l~~~l~~L~l~~n~i~----~i~~~~~~~l~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~  101 (220)
T 2v9t_B           26 IPTNLPETITEIRLEQNTIK----VIPPGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGNKITELPKSLFE  101 (220)
T ss_dssp             CCSSCCTTCCEEECCSSCCC----EECTTSSTTCTTCCEEECCSSCCCEECTTTTTTCSSCCEEECCSSCCCCCCTTTTT
T ss_pred             CCCccCcCCCEEECCCCcCC----CcCHhHhhCCCCCCEEECCCCcCCCcCHHHhhCCcCCCEEECCCCcCCccCHhHcc
Confidence            44444566777777666553    23445666777777777777777644 56677777777777777777777776556


Q ss_pred             cCCCccEeecCCccccccc-hhhhccccCceecCCCccCC
Q 003387          566 NLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       566 ~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~~~  604 (824)
                      ++++|++|+|++|.+..++ ..+..+++|++|++++|.+.
T Consensus       102 ~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~  141 (220)
T 2v9t_B          102 GLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNKLQ  141 (220)
T ss_dssp             TCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCS
T ss_pred             CCCCCCEEECCCCCCCEeCHHHcCCCCCCCEEECCCCcCC
Confidence            7777777777777777663 44667777777777777665

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=99.35  E-value=9e-15  Score=167.76  Aligned_cols=120  Identities=22%  Similarity=0.224  Sum_probs=61.8

Q ss_pred             cceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCC
Q 003387          639 LRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQ  718 (824)
Q Consensus       639 L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~  718 (824)
                      |+.|+++++.   ...+|. ++.+++|+.|++++|    +++.+ ...+..+++|+.|+|++|.+++ +| .++++++|+
T Consensus       443 L~~L~Ls~n~---l~~lp~-~~~l~~L~~L~Ls~N----~l~~l-p~~~~~l~~L~~L~Ls~N~l~~-lp-~l~~l~~L~  511 (567)
T 1dce_A          443 VRVLHLAHKD---LTVLCH-LEQLLLVTHLDLSHN----RLRAL-PPALAALRCLEVLQASDNALEN-VD-GVANLPRLQ  511 (567)
T ss_dssp             CSEEECTTSC---CSSCCC-GGGGTTCCEEECCSS----CCCCC-CGGGGGCTTCCEEECCSSCCCC-CG-GGTTCSSCC
T ss_pred             ceEEEecCCC---CCCCcC-ccccccCcEeecCcc----ccccc-chhhhcCCCCCEEECCCCCCCC-Cc-ccCCCCCCc
Confidence            4555555542   122332 455555555555544    23322 1233455566666666666543 33 566666666


Q ss_pred             eEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccC----cccCccEEE
Q 003387          719 VLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNA----AMPKLECLI  770 (824)
Q Consensus       719 ~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~----~lp~L~~L~  770 (824)
                      .|+|++|.+.+...+..++.+++|+.|+|++|+ +..++....    .+|+|+.|+
T Consensus       512 ~L~Ls~N~l~~~~~p~~l~~l~~L~~L~L~~N~-l~~~~~~~~~l~~~lp~L~~L~  566 (567)
T 1dce_A          512 ELLLCNNRLQQSAAIQPLVSCPRLVLLNLQGNS-LCQEEGIQERLAEMLPSVSSIL  566 (567)
T ss_dssp             EEECCSSCCCSSSTTGGGGGCTTCCEEECTTSG-GGGSSSCTTHHHHHCTTCSEEE
T ss_pred             EEECCCCCCCCCCCcHHHhcCCCCCEEEecCCc-CCCCccHHHHHHHHCcccCccC
Confidence            666666666542214445566666666666654 444433222    266776664

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.34  E-value=4e-12  Score=127.50  Aligned_cols=138  Identities=14%  Similarity=0.144  Sum_probs=81.5

Q ss_pred             ccccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhh
Q 003387          486 ACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLL  564 (824)
Q Consensus       486 ~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~  564 (824)
                      .+|..+.+.++.|.+.++....   ......|..+++|++|+|++|.++.++. .+..+++|++|+|++|.+..+|...|
T Consensus        25 ~iP~~~~~~~~~L~L~~N~l~~---~~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~  101 (220)
T 2v70_A           25 KIPEHIPQYTAELRLNNNEFTV---LEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILLTSNRLENVQHKMF  101 (220)
T ss_dssp             SCCSCCCTTCSEEECCSSCCCE---ECCCCCGGGCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCCCCGGGG
T ss_pred             cCccCCCCCCCEEEcCCCcCCc---cCchhhhccCCCCCEEECCCCcCCEECHHHhCCCCCCCEEECCCCccCccCHhHh
Confidence            3444445555666666655431   1122345666666666666666664443 56666666666666666666666544


Q ss_pred             hcCCCccEeecCCcccccc-chhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEE
Q 003387          565 SNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLR  643 (824)
Q Consensus       565 ~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~  643 (824)
                      .++++|++|+|++|.+..+ |..+..+++|++|++++|.+..                      ..+..+..+++|+.|+
T Consensus       102 ~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~----------------------~~~~~~~~l~~L~~L~  159 (220)
T 2v70_A          102 KGLESLKTLMLRSNRITCVGNDSFIGLSSVRLLSLYDNQITT----------------------VAPGAFDTLHSLSTLN  159 (220)
T ss_dssp             TTCSSCCEEECTTSCCCCBCTTSSTTCTTCSEEECTTSCCCC----------------------BCTTTTTTCTTCCEEE
T ss_pred             cCCcCCCEEECCCCcCCeECHhHcCCCccCCEEECCCCcCCE----------------------ECHHHhcCCCCCCEEE
Confidence            6666666666666666665 3446666666666666666542                      1122256666777777


Q ss_pred             Eeccc
Q 003387          644 IRGDL  648 (824)
Q Consensus       644 l~~~~  648 (824)
                      ++++.
T Consensus       160 L~~N~  164 (220)
T 2v70_A          160 LLANP  164 (220)
T ss_dssp             CCSCC
T ss_pred             ecCcC
Confidence            76664

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.33  E-value=2.5e-12  Score=129.98  Aligned_cols=152  Identities=22%  Similarity=0.266  Sum_probs=94.7

Q ss_pred             ccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCc
Q 003387          523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSI  601 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~  601 (824)
                      .+.++.+++.+..+|..+.  .+|++|+|++|.+..+++..|.++++|++|+|++|.+..+|.. +..+++|++|++++|
T Consensus        21 ~~~v~c~~~~l~~ip~~~~--~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~N~l~~i~~~~~~~l~~L~~L~Ls~N   98 (229)
T 3e6j_A           21 GTTVDCRSKRHASVPAGIP--TNAQILYLHDNQITKLEPGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTN   98 (229)
T ss_dssp             TTEEECTTSCCSSCCSCCC--TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             CCEeEccCCCcCccCCCCC--CCCCEEEcCCCccCccCHHHhhCccCCcEEECCCCCCCCcChhhcccCCCcCEEECCCC
Confidence            4567777777777777664  6788888888888877554447888888888888888777754 577888888888877


Q ss_pred             cCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccE
Q 003387          602 TLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSK  681 (824)
Q Consensus       602 ~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~  681 (824)
                      .+..  +|                    ...+..+++|+.|+++++.   ...+|..+..                    
T Consensus        99 ~l~~--l~--------------------~~~~~~l~~L~~L~Ls~N~---l~~lp~~~~~--------------------  133 (229)
T 3e6j_A           99 QLTV--LP--------------------SAVFDRLVHLKELFMCCNK---LTELPRGIER--------------------  133 (229)
T ss_dssp             CCCC--CC--------------------TTTTTTCTTCCEEECCSSC---CCSCCTTGGG--------------------
T ss_pred             cCCc--cC--------------------hhHhCcchhhCeEeccCCc---ccccCccccc--------------------
Confidence            7652  11                    1114455666666666552   1122222233                    


Q ss_pred             EEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCC
Q 003387          682 IVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSG  729 (824)
Q Consensus       682 l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~  729 (824)
                              +++|+.|+|++|.+....+..+..+++|+.|++.+|.+..
T Consensus       134 --------l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~~~c  173 (229)
T 3e6j_A          134 --------LTHLTHLALDQNQLKSIPHGAFDRLSSLTHAYLFGNPWDC  173 (229)
T ss_dssp             --------CTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECTTSCBCT
T ss_pred             --------CCCCCEEECCCCcCCccCHHHHhCCCCCCEEEeeCCCccC
Confidence                    3444455555555544444456666777777776665543

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.29  E-value=5.5e-12  Score=118.09  Aligned_cols=131  Identities=19%  Similarity=0.097  Sum_probs=95.1

Q ss_pred             cccCcccEEEeeCccCc--cCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccc-cchhhhccccCc
Q 003387          518 GMFKLLRVLDLGSLVLI--QYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLR  594 (824)
Q Consensus       518 ~~~~~Lr~L~L~~~~i~--~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~-lp~~i~~L~~L~  594 (824)
                      ...+.|+.|++++|.+.  .+|..++.+++|++|++++|.+..+ ..+ +++++|++|++++|.+.. +|..++.+++|+
T Consensus        14 ~~~~~l~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~-~~~-~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~   91 (149)
T 2je0_A           14 RTPSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSI-ANL-PKLNKLKKLELSDNRVSGGLEVLAEKCPNLT   91 (149)
T ss_dssp             CCGGGCSEEECTTCBCBTTBCCSCCTTCTTCCEEECTTSCCCCC-TTC-CCCTTCCEEECCSSCCCSCTHHHHHHCTTCC
T ss_pred             CCCccCeEEEccCCcCChhHHHHHHhhcCCCcEEECcCCCCCCc-hhh-hcCCCCCEEECCCCcccchHHHHhhhCCCCC
Confidence            44577889999998887  8888888889999999999888877 555 888999999999888887 777777889999


Q ss_pred             eecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhH-HHHhccCCCCCeEEEe
Q 003387          595 HLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLL-SKSLCRLSCLESLKLA  671 (824)
Q Consensus       595 ~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l-~~~l~~l~~L~~L~l~  671 (824)
                      +|++++|.+..  +                  ..+.. +..+++|+.|+++++.-...... ...+..+++|+.|+++
T Consensus        92 ~L~ls~N~i~~--~------------------~~~~~-~~~l~~L~~L~l~~N~l~~~~~~~~~~~~~l~~L~~L~l~  148 (149)
T 2je0_A           92 HLNLSGNKIKD--L------------------STIEP-LKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYLDGY  148 (149)
T ss_dssp             EEECTTSCCCS--H------------------HHHGG-GGGCTTCCEEECTTCGGGGSTTHHHHHHHHCTTCCEETTB
T ss_pred             EEECCCCcCCC--h------------------HHHHH-HhhCCCCCEEeCcCCcccchHHHHHHHHHHCCCcccccCC
Confidence            99888887752  0                  11122 66777788887777741111111 1356667777777654

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.29  E-value=2.8e-11  Score=134.07  Aligned_cols=266  Identities=15%  Similarity=0.124  Sum_probs=156.1

Q ss_pred             CCCceechhhHHHHHHHH-Hc---C-CCCeEEEEE--EcCCCChHHHHHHHHhCCccccC-----CCc-eeEEEECCCCC
Q 003387          155 SRDTVGLDDRMEELLDLL-IE---G-PPQLSVVAI--LDSIGLDKTAFAGEAYNSSYVKH-----YFD-CHAWITEPYSN  221 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L-~~---~-~~~~~vi~I--~G~gGvGKTtLa~~v~~~~~~~~-----~F~-~~~wv~~~vs~  221 (824)
                      +..++||+.+++++.+++ ..   + ......+.|  +|++|+||||||+.+++  +...     .|+ .++|+.  +..
T Consensus        21 p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~--~~~~~~~~~~~~~~~~~~~--~~~   96 (412)
T 1w5s_A           21 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVK--RVSEAAAKEGLTVKQAYVN--AFN   96 (412)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHH--HHHHHHHHTTCCEEEEEEE--GGG
T ss_pred             CCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHH--HHHHHHhccCCceeEEEEE--CCC
Confidence            468999999999999998 42   2 012345555  99999999999999998  3332     123 357777  767


Q ss_pred             CCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCCh--------hhHHHHHhhC---CC
Q 003387          222 EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSI--------DMWDVIQEIL---PD  288 (824)
Q Consensus       222 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~--------~~~~~l~~~~---~~  288 (824)
                      ..+...++..++.+++...+   ....+.......+.+.+.  +++++||+||+|..        +.+..+...+   +.
T Consensus        97 ~~~~~~~~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~  173 (412)
T 1w5s_A           97 APNLYTILSLIVRQTGYPIQ---VRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPS  173 (412)
T ss_dssp             CCSHHHHHHHHHHHHTCCCC---CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCC
T ss_pred             CCCHHHHHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhccc
Confidence            77899999999999976432   122344566677777775  68999999999864        2233332222   21


Q ss_pred             CC--CCcEEEEEechHHHHh-----------hccccc--C------------------CcCcCccccchhhHHHhcC---
Q 003387          289 NQ--NGSRVLITLTDIRIII-----------SFQFED--G------------------ENMRLDLVPTGGPLRATYK---  332 (824)
Q Consensus       289 ~~--~gs~ilvTtR~~~v~~-----------~f~~~~--~------------------~~~~~~~~~~~~~i~~~c~---  332 (824)
                      .+  ....+|+||+...+..           .|....  .                  .....--.+....|++.|+   
T Consensus       174 ~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~~~~~~~~  253 (412)
T 1w5s_A          174 RDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDK  253 (412)
T ss_dssp             TTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHHHHHCGGG
T ss_pred             CCCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhc
Confidence            12  3455888887554321           111000  0                  0000111345667888999   


Q ss_pred             ---CCchhHHHHHhHHH---hhhhhhhc-----cCCC-cc--ccccc--c-cCCCCchHHHhHhccCC--CCceechhHH
Q 003387          333 ---GRPFLILYHGSISL---EENIREAV-----ETPL-GL--RYIKC--L-MLPFCLKPCFIYLSVFP--AHQEISTRQL  393 (824)
Q Consensus       333 ---GlPlai~~~~~~l~---~~~~~~~~-----~~~~-~~--~~~l~--~-~L~~~lk~cfl~~s~fp--~~~~i~~~~L  393 (824)
                         |.|..+..+.....   .....+.+     .... ..  ...+.  + .||.+.+.++..++.+.  .+..++..++
T Consensus       254 ~~~G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~~~~~~~~~l~~l~~~~~~~l~aia~l~~~~~~~~~~~~~  333 (412)
T 1w5s_A          254 GGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLL  333 (412)
T ss_dssp             TSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC------CCSSSSSCHHHHHHHHHHHHHHHTTCSSBCHHHH
T ss_pred             cCCCcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccchHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHH
Confidence               99976655544321   11000000     0000 01  11121  1 78888888888888653  2335555555


Q ss_pred             HHHHH--H---cCCCCCChHHHHHHHHHHHHhccccceee
Q 003387          394 YQLWI--A---EGFIPDNSEATAESYLEQLIKEGFVEAKK  428 (824)
Q Consensus       394 i~~W~--a---~g~i~~~~e~~~~~~~~~Lv~rsllq~~~  428 (824)
                      ...+.  +   .|. .+........+++.|.+.+++....
T Consensus       334 ~~~~~~~~~~~~~~-~~~~~~~~~~~l~~L~~~gli~~~~  372 (412)
T 1w5s_A          334 RQRYEDASLTMYNV-KPRGYTQYHIYLKHLTSLGLVDAKP  372 (412)
T ss_dssp             HHHHHHHHHHHSCC-CCCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHhhcCC-CCCCHHHHHHHHHHHHhCCCEEeec
Confidence            54442  2   232 1123345678999999999998764

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=99.29  E-value=4.9e-12  Score=121.06  Aligned_cols=83  Identities=24%  Similarity=0.153  Sum_probs=56.2

Q ss_pred             cCcccEEEeeCccCc--cCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccc-cchhhhccccCcee
Q 003387          520 FKLLRVLDLGSLVLI--QYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TADEFWKMNKLRHL  596 (824)
Q Consensus       520 ~~~Lr~L~L~~~~i~--~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~-lp~~i~~L~~L~~L  596 (824)
                      .+.|++|++++|.+.  .+|..+..+++|++|++++|.+..+ ..+ +.+++|++|++++|.+.. +|..+..+++|++|
T Consensus        23 ~~~L~~L~l~~n~l~~~~i~~~~~~l~~L~~L~l~~n~l~~~-~~~-~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L  100 (168)
T 2ell_A           23 PAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISV-SNL-PKLPKLKKLELSENRIFGGLDMLAEKLPNLTHL  100 (168)
T ss_dssp             TTSCSEEECCSCBCBTTBCSSCCGGGGGCCEEEEESSCCCCC-SSC-CCCSSCCEEEEESCCCCSCCCHHHHHCTTCCEE
T ss_pred             cccCCEEECCCCCCChhhHHHHHHhCCCCCEEeCcCCCCCCh-hhh-ccCCCCCEEECcCCcCchHHHHHHhhCCCCCEE
Confidence            356777777777766  6666666677777777777776666 444 667777777777776666 55556667777777


Q ss_pred             cCCCccCC
Q 003387          597 NFGSITLP  604 (824)
Q Consensus       597 ~L~~~~~~  604 (824)
                      ++++|.+.
T Consensus       101 ~Ls~N~l~  108 (168)
T 2ell_A          101 NLSGNKLK  108 (168)
T ss_dssp             ECBSSSCC
T ss_pred             eccCCccC
Confidence            77776654

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=99.23  E-value=1.9e-11  Score=116.88  Aligned_cols=108  Identities=19%  Similarity=0.196  Sum_probs=89.1

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCc-cChhhhhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNS-LPSSLLSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~-lp~~i~~~L~~L  570 (824)
                      .++++.|.+.++...   ...++..+..+++|++|++++|.++.+ ..++.+++|++|++++|.+.. +|..+ .++++|
T Consensus        23 ~~~L~~L~l~~n~l~---~~~i~~~~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~N~l~~~~~~~~-~~l~~L   97 (168)
T 2ell_A           23 PAAVRELVLDNCKSN---DGKIEGLTAEFVNLEFLSLINVGLISV-SNLPKLPKLKKLELSENRIFGGLDMLA-EKLPNL   97 (168)
T ss_dssp             TTSCSEEECCSCBCB---TTBCSSCCGGGGGCCEEEEESSCCCCC-SSCCCCSSCCEEEEESCCCCSCCCHHH-HHCTTC
T ss_pred             cccCCEEECCCCCCC---hhhHHHHHHhCCCCCEEeCcCCCCCCh-hhhccCCCCCEEECcCCcCchHHHHHH-hhCCCC
Confidence            577888888877653   112345578889999999999998877 778899999999999999987 55555 789999


Q ss_pred             cEeecCCccccccc--hhhhccccCceecCCCccCC
Q 003387          571 YTLDMPFSYIDHTA--DEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       571 ~~L~L~~~~l~~lp--~~i~~L~~L~~L~L~~~~~~  604 (824)
                      ++|++++|.+..+|  ..+..+++|++|++++|.+.
T Consensus        98 ~~L~Ls~N~l~~~~~~~~l~~l~~L~~L~l~~N~l~  133 (168)
T 2ell_A           98 THLNLSGNKLKDISTLEPLKKLECLKSLDLFNCEVT  133 (168)
T ss_dssp             CEEECBSSSCCSSGGGGGGSSCSCCCEEECCSSGGG
T ss_pred             CEEeccCCccCcchhHHHHhcCCCCCEEEeeCCcCc
Confidence            99999999999886  67889999999999999876

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.23  E-value=9.2e-12  Score=116.53  Aligned_cols=108  Identities=18%  Similarity=0.196  Sum_probs=90.8

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCc-cChhhhhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNS-LPSSLLSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~-lp~~i~~~L~~L  570 (824)
                      .++++.|.+.++...   ....+..+..+++|++|++++|.++.+ ..++.+++|++|++++|.+.. +|..+ +++++|
T Consensus        16 ~~~l~~L~l~~n~l~---~~~~~~~~~~l~~L~~L~l~~n~l~~~-~~~~~l~~L~~L~Ls~n~i~~~~~~~~-~~l~~L   90 (149)
T 2je0_A           16 PSDVKELVLDNSRSN---EGKLEGLTDEFEELEFLSTINVGLTSI-ANLPKLNKLKKLELSDNRVSGGLEVLA-EKCPNL   90 (149)
T ss_dssp             GGGCSEEECTTCBCB---TTBCCSCCTTCTTCCEEECTTSCCCCC-TTCCCCTTCCEEECCSSCCCSCTHHHH-HHCTTC
T ss_pred             CccCeEEEccCCcCC---hhHHHHHHhhcCCCcEEECcCCCCCCc-hhhhcCCCCCEEECCCCcccchHHHHh-hhCCCC
Confidence            577888888887653   123345678899999999999999877 778999999999999999998 66655 889999


Q ss_pred             cEeecCCccccccc--hhhhccccCceecCCCccCC
Q 003387          571 YTLDMPFSYIDHTA--DEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       571 ~~L~L~~~~l~~lp--~~i~~L~~L~~L~L~~~~~~  604 (824)
                      ++|++++|.+..+|  ..++.+++|++|++++|.+.
T Consensus        91 ~~L~ls~N~i~~~~~~~~~~~l~~L~~L~l~~N~l~  126 (149)
T 2je0_A           91 THLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVT  126 (149)
T ss_dssp             CEEECTTSCCCSHHHHGGGGGCTTCCEEECTTCGGG
T ss_pred             CEEECCCCcCCChHHHHHHhhCCCCCEEeCcCCccc
Confidence            99999999999876  77999999999999999876

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.23  E-value=1.7e-11  Score=133.14  Aligned_cols=167  Identities=18%  Similarity=0.094  Sum_probs=117.7

Q ss_pred             EEEEEecCCCcccccccCCceeEeeccCCCCCCCCcchhHhhhc-ccCcccEEEeeCccCccCC-ccCCCCCcceEEeec
Q 003387          475 RLNAVEREGDFACLDDYDSQLHSLLCCSPETRHLDPIDWEKFCG-MFKLLRVLDLGSLVLIQYP-SGIENLFLLRYLKLN  552 (824)
Q Consensus       475 ~lsl~~~~~~~~~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~-~~~~Lr~L~L~~~~i~~lp-~~i~~l~~Lr~L~L~  552 (824)
                      .+... +.....+|..+.+.++.|.+.++...    ......|. .+++|++|+|++|.++.+| ..+..+++|++|+|+
T Consensus        22 ~l~c~-~~~l~~iP~~~~~~l~~L~Ls~N~l~----~l~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls   96 (361)
T 2xot_A           22 ILSCS-KQQLPNVPQSLPSYTALLDLSHNNLS----RLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDLS   96 (361)
T ss_dssp             EEECC-SSCCSSCCSSCCTTCSEEECCSSCCC----EECTTSSSSCCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECC
T ss_pred             EEEeC-CCCcCccCccCCCCCCEEECCCCCCC----ccChhhhhhcccccCEEECCCCcCCccChhhccCCCCCCEEECC
Confidence            44444 34444466656677888888887663    24445565 8888999999999888666 458888999999999


Q ss_pred             CCCCCccChhhhhcCCCccEeecCCcccccc-chhhhccccCceecCCCccCCCCCCC--CC---CCCCCCCeeeccCCC
Q 003387          553 IPSLNSLPSSLLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGSITLPAHPGK--FC---GSLENLNFISALHPC  626 (824)
Q Consensus       553 ~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~~~~~~~~~p--~i---~~L~~L~~l~~~~~~  626 (824)
                      +|.+..+|...|.++++|++|+|++|.+..+ |..+..+++|++|+|++|.+.  .+|  .+   +.+++|+.|+++.+.
T Consensus        97 ~N~l~~~~~~~~~~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~l~--~l~~~~~~~~~~l~~L~~L~L~~N~  174 (361)
T 2xot_A           97 SNHLHTLDEFLFSDLQALEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQIS--RFPVELIKDGNKLPKLMLLDLSSNK  174 (361)
T ss_dssp             SSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCC--SCCGGGTC----CTTCCEEECCSSC
T ss_pred             CCcCCcCCHHHhCCCcCCCEEECCCCcccEECHHHhCCcccCCEEECCCCcCC--eeCHHHhcCcccCCcCCEEECCCCC
Confidence            9998888876668899999999999988877 456888899999999988887  344  23   567778888777321


Q ss_pred             --cchhhhcCCCCc--cceEEEeccc
Q 003387          627 --CCTEDILGRLPN--LRNLRIRGDL  648 (824)
Q Consensus       627 --~~~~~~l~~l~~--L~~L~l~~~~  648 (824)
                        ......+..+++  |+.|++.++.
T Consensus       175 l~~l~~~~~~~l~~~~l~~l~l~~N~  200 (361)
T 2xot_A          175 LKKLPLTDLQKLPAWVKNGLYLHNNP  200 (361)
T ss_dssp             CCCCCHHHHHHSCHHHHTTEECCSSC
T ss_pred             CCccCHHHhhhccHhhcceEEecCCC
Confidence              112222455555  3677777764

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.20  E-value=6.3e-11  Score=127.93  Aligned_cols=268  Identities=11%  Similarity=0.064  Sum_probs=155.6

Q ss_pred             CCCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC------CHH
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY------DAD  226 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~------~~~  226 (824)
                      ..+..++||+.+.++|.+++..+    +++.|+|++|+|||||++.+.+.  .    . .+|+.  +....      +..
T Consensus         9 ~~~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~--~----~-~~~~~--~~~~~~~~~~~~~~   75 (350)
T 2qen_A            9 TRREDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNE--R----P-GILID--CRELYAERGHITRE   75 (350)
T ss_dssp             CSGGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHH--S----S-EEEEE--HHHHHHTTTCBCHH
T ss_pred             CChHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHH--c----C-cEEEE--eecccccccCCCHH
Confidence            34578999999999999998764    68999999999999999999983  3    1 66776  54332      566


Q ss_pred             HHHHHHHHHhCCC---------------CCcccccccCHHHHHHHHHHhcCC-CeEEEEEecCCChhh---------HHH
Q 003387          227 QILDIVIKFLMPS---------------SRLSEIMDKNYEMKKIILHEYLMT-KRYLIVIDDVWSIDM---------WDV  281 (824)
Q Consensus       227 ~~~~~i~~~l~~~---------------~~~~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~~~~---------~~~  281 (824)
                      .+...+...+...               ...+ ....+..++...+.+..+. ++++||+||++....         +..
T Consensus        76 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~~~~~~~~~~  154 (350)
T 2qen_A           76 ELIKELQSTISPFQKFQSKFKISLNLKFLTLE-PRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLAL  154 (350)
T ss_dssp             HHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSC-GGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTTTTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHhHhhhceeEEEecceeec-cccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCccchhhHHHH
Confidence            6777776665420               0000 1123456666667666643 499999999976432         233


Q ss_pred             HHhhCCCCCCCcEEEEEechHHH-Hh----------hccccc-----CC---------------cCc-CccccchhhHHH
Q 003387          282 IQEILPDNQNGSRVLITLTDIRI-II----------SFQFED-----GE---------------NMR-LDLVPTGGPLRA  329 (824)
Q Consensus       282 l~~~~~~~~~gs~ilvTtR~~~v-~~----------~f~~~~-----~~---------------~~~-~~~~~~~~~i~~  329 (824)
                      +..... ..++.++|+|++.... ..          .++...     ..               ... .--.+....|+.
T Consensus       155 L~~~~~-~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~~~~~~~~i~~  233 (350)
T 2qen_A          155 FAYAYD-SLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNLDVPENEIEEAVE  233 (350)
T ss_dssp             HHHHHH-HCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHH
T ss_pred             HHHHHH-hcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            332221 1247889999887543 11          111100     00               000 011235667899


Q ss_pred             hcCCCchhHHHHHhHHHhhhhhhhc-cCCC-cccccc--cc-cC---CCCchHHHhHhccCCCCceechhHHHHHHHHcC
Q 003387          330 TYKGRPFLILYHGSISLEENIREAV-ETPL-GLRYIK--CL-ML---PFCLKPCFIYLSVFPAHQEISTRQLYQLWIAEG  401 (824)
Q Consensus       330 ~c~GlPlai~~~~~~l~~~~~~~~~-~~~~-~~~~~l--~~-~L---~~~lk~cfl~~s~fp~~~~i~~~~Li~~W~a~g  401 (824)
                      .|+|.|+++..++..+......+.. .... .+...+  .+ .+   ++..+..+..+|.   + .++...+........
T Consensus       234 ~tgG~P~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~l~~la~---g-~~~~~~l~~~~~~~~  309 (350)
T 2qen_A          234 LLDGIPGWLVVFGVEYLRNGDFGRAMKRTLEVAKGLIMGELEELRRRSPRYVDILRAIAL---G-YNRWSLIRDYLAVKG  309 (350)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHT---T-CCSHHHHHHHHHHTT
T ss_pred             HhCCCHHHHHHHHHHHhccccHhHHHHHHHHHHHHHHHHHHHHHHhCChhHHHHHHHHHh---C-CCCHHHHHHHHHHHh
Confidence            9999999999888754211000110 0000 011111  01 33   5677888888887   2 235555555432211


Q ss_pred             CCCCChHHHHHHHHHHHHhccccceeecCCCCcEEEEEc-CccHHHHH
Q 003387          402 FIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCSI-PGRWRPVL  448 (824)
Q Consensus       402 ~i~~~~e~~~~~~~~~Lv~rsllq~~~~~~~g~~~~~~m-Hdlv~dla  448 (824)
                       - .........+++.|.+.+++....    +   .|.+ |.++++..
T Consensus       310 -~-~~~~~~~~~~l~~L~~~gli~~~~----~---~y~~~~p~~~~~~  348 (350)
T 2qen_A          310 -T-KIPEPRLYALLENLKKMNWIVEED----N---TYKIADPVVATVL  348 (350)
T ss_dssp             -C-CCCHHHHHHHHHHHHHTTSEEEET----T---EEEESSHHHHHHH
T ss_pred             -C-CCCHHHHHHHHHHHHhCCCEEecC----C---EEEEecHHHHHHH
Confidence             0 112345778999999999998652    2   2444 55666543

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=99.19  E-value=2.2e-11  Score=117.46  Aligned_cols=132  Identities=14%  Similarity=0.094  Sum_probs=96.2

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      +++++.|.+.++....     ++.+....++|++|++++|.++.+ ..++.+++|++|++++|.+..+|+.+++.+++|+
T Consensus        18 ~~~L~~L~l~~n~l~~-----i~~~~~~~~~L~~L~Ls~N~l~~~-~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~   91 (176)
T 1a9n_A           18 AVRDRELDLRGYKIPV-----IENLGATLDQFDAIDFSDNEIRKL-DGFPLLRRLKTLLVNNNRICRIGEGLDQALPDLT   91 (176)
T ss_dssp             TTSCEEEECTTSCCCS-----CCCGGGGTTCCSEEECCSSCCCEE-CCCCCCSSCCEEECCSSCCCEECSCHHHHCTTCC
T ss_pred             cCCceEEEeeCCCCch-----hHHhhhcCCCCCEEECCCCCCCcc-cccccCCCCCEEECCCCcccccCcchhhcCCCCC
Confidence            6778888888776542     123333344888888888888876 5688888888888888888888876668888888


Q ss_pred             EeecCCccccccch--hhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccc
Q 003387          572 TLDMPFSYIDHTAD--EFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       572 ~L~L~~~~l~~lp~--~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      +|++++|.+..+|.  .+..+++|++|++++|.+..  +|                ... ...+..+++|+.|+++.+.
T Consensus        92 ~L~L~~N~i~~~~~~~~l~~l~~L~~L~l~~N~i~~--~~----------------~~~-~~~~~~l~~L~~Ld~~~n~  151 (176)
T 1a9n_A           92 ELILTNNSLVELGDLDPLASLKSLTYLCILRNPVTN--KK----------------HYR-LYVIYKVPQVRVLDFQKVK  151 (176)
T ss_dssp             EEECCSCCCCCGGGGGGGGGCTTCCEEECCSSGGGG--ST----------------THH-HHHHHHCTTCSEETTEECC
T ss_pred             EEECCCCcCCcchhhHhhhcCCCCCEEEecCCCCCC--cH----------------hHH-HHHHHHCCccceeCCCcCC
Confidence            88888888888876  68888888888888887651  11                000 1126677888888887764

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=99.18  E-value=2.1e-11  Score=117.57  Aligned_cols=131  Identities=15%  Similarity=0.083  Sum_probs=103.8

Q ss_pred             hhcccCcccEEEeeCccCccCCccCCCCC-cceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhh-hccccC
Q 003387          516 FCGMFKLLRVLDLGSLVLIQYPSGIENLF-LLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEF-WKMNKL  593 (824)
Q Consensus       516 ~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~-~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i-~~L~~L  593 (824)
                      .+..++.|++|++++|.++.+|. +..+. +|++|++++|.+..+ ..+ +++++|++|++++|.+..+|..+ ..+++|
T Consensus        14 ~~~~~~~L~~L~l~~n~l~~i~~-~~~~~~~L~~L~Ls~N~l~~~-~~l-~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L   90 (176)
T 1a9n_A           14 QYTNAVRDRELDLRGYKIPVIEN-LGATLDQFDAIDFSDNEIRKL-DGF-PLLRRLKTLLVNNNRICRIGEGLDQALPDL   90 (176)
T ss_dssp             EEECTTSCEEEECTTSCCCSCCC-GGGGTTCCSEEECCSSCCCEE-CCC-CCCSSCCEEECCSSCCCEECSCHHHHCTTC
T ss_pred             hcCCcCCceEEEeeCCCCchhHH-hhhcCCCCCEEECCCCCCCcc-ccc-ccCCCCCEEECCCCcccccCcchhhcCCCC
Confidence            35678899999999999998865 55555 999999999999988 455 99999999999999999998665 899999


Q ss_pred             ceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHH----HhccCCCCCeEE
Q 003387          594 RHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSK----SLCRLSCLESLK  669 (824)
Q Consensus       594 ~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~----~l~~l~~L~~L~  669 (824)
                      ++|++++|.+..  +|                  .+.. +..+++|+.|+++++.   ...++.    .+..+++|+.|+
T Consensus        91 ~~L~L~~N~i~~--~~------------------~~~~-l~~l~~L~~L~l~~N~---i~~~~~~~~~~~~~l~~L~~Ld  146 (176)
T 1a9n_A           91 TELILTNNSLVE--LG------------------DLDP-LASLKSLTYLCILRNP---VTNKKHYRLYVIYKVPQVRVLD  146 (176)
T ss_dssp             CEEECCSCCCCC--GG------------------GGGG-GGGCTTCCEEECCSSG---GGGSTTHHHHHHHHCTTCSEET
T ss_pred             CEEECCCCcCCc--ch------------------hhHh-hhcCCCCCEEEecCCC---CCCcHhHHHHHHHHCCccceeC
Confidence            999999998752  11                  1112 7788899999999885   222333    467788888888


Q ss_pred             Eecc
Q 003387          670 LANE  673 (824)
Q Consensus       670 l~~~  673 (824)
                      ++.+
T Consensus       147 ~~~n  150 (176)
T 1a9n_A          147 FQKV  150 (176)
T ss_dssp             TEEC
T ss_pred             CCcC
Confidence            7764

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=99.15  E-value=3.8e-12  Score=125.51  Aligned_cols=131  Identities=18%  Similarity=0.156  Sum_probs=101.8

Q ss_pred             hHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhcccc
Q 003387          513 WEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNK  592 (824)
Q Consensus       513 ~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~  592 (824)
                      ++..+..+++|++|++++|.++.+| .+..+++|++|++++|.+..+|..+ ..+++|++|++++|.+..+| .+..+++
T Consensus        40 l~~~~~~l~~L~~L~ls~n~l~~l~-~~~~l~~L~~L~l~~n~l~~l~~~~-~~~~~L~~L~L~~N~l~~l~-~~~~l~~  116 (198)
T 1ds9_A           40 MDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIENLD-AVADTLEELWISYNQIASLS-GIEKLVN  116 (198)
T ss_dssp             CHHHHHHTTTCSEEECSEEEESCCC-CHHHHTTCCEEEEEEEEECSCSSHH-HHHHHCSEEEEEEEECCCHH-HHHHHHH
T ss_pred             hhHHHhcCCCCCEEECCCCCCcccc-ccccCCCCCEEECCCCCcccccchh-hcCCcCCEEECcCCcCCcCC-ccccCCC
Confidence            3457888999999999999998888 8888999999999999999999877 88899999999999998888 5889999


Q ss_pred             CceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhH----------HHHhccC
Q 003387          593 LRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLL----------SKSLCRL  662 (824)
Q Consensus       593 L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l----------~~~l~~l  662 (824)
                      |++|++++|.+..  +                  ..+.. +..+++|+.|+++++.  .....          ...+..+
T Consensus       117 L~~L~l~~N~i~~--~------------------~~~~~-l~~l~~L~~L~l~~N~--l~~~~~~~~~~~~~~~~~~~~l  173 (198)
T 1ds9_A          117 LRVLYMSNNKITN--W------------------GEIDK-LAALDKLEDLLLAGNP--LYNDYKENNATSEYRIEVVKRL  173 (198)
T ss_dssp             SSEEEESEEECCC--H------------------HHHHH-HTTTTTCSEEEECSCH--HHHHHHTTTTHHHHHHHHHHHC
T ss_pred             CCEEECCCCcCCc--h------------------hHHHH-HhcCCCCCEEEecCCc--cccccccccchHHHHHHHHHhC
Confidence            9999999988752  0                  11123 6778888888888774  21111          1235666


Q ss_pred             CCCCeEE
Q 003387          663 SCLESLK  669 (824)
Q Consensus       663 ~~L~~L~  669 (824)
                      ++|+.|+
T Consensus       174 ~~L~~Ld  180 (198)
T 1ds9_A          174 PNLKKLD  180 (198)
T ss_dssp             SSCSEEC
T ss_pred             CCcEEEC
Confidence            7777665

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=99.15  E-value=9.5e-11  Score=125.40  Aligned_cols=283  Identities=13%  Similarity=0.033  Sum_probs=172.8

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcc-cCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhc----
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGM-FKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSN----  566 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~-~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~----  566 (824)
                      ..+++.|.+.+.-..    ..+ ..+.. +++|++|||++|.+..+...-+.++.++++.+..+   .+|...|.+    
T Consensus        24 ~~~l~~L~l~g~i~~----~~~-~~l~~~l~~L~~LdLs~n~i~~~~~~~~~~~~~~~~~~~~~---~I~~~aF~~~~~~   95 (329)
T 3sb4_A           24 ANSITHLTLTGKLNA----EDF-RHLRDEFPSLKVLDISNAEIKMYSGKAGTYPNGKFYIYMAN---FVPAYAFSNVVNG   95 (329)
T ss_dssp             HHHCSEEEEEEEECH----HHH-HHHHHSCTTCCEEEEEEEEECCEEESSSSSGGGCCEEECTT---EECTTTTEEEETT
T ss_pred             hCceeEEEEeccccH----HHH-HHHHHhhccCeEEecCcceeEEecCcccccccccccccccc---ccCHHHhcccccc
Confidence            556777777654221    122 23333 88899999999998722211223334555555554   567666678    


Q ss_pred             ----CCCccEeecCCccccccchh-hhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCCC------cchhhhcC
Q 003387          567 ----LLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHPC------CCTEDILG  634 (824)
Q Consensus       567 ----L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~------~~~~~~l~  634 (824)
                          |++|+.|+|.+ .++.+++. |..|++|+.|++++|.+.. ..+ .+..+.++..+......      ......+.
T Consensus        96 ~~~g~~~L~~l~L~~-~i~~I~~~aF~~~~~L~~l~l~~n~i~~-i~~~aF~~~~~l~~l~~~~~~~~~~~~~i~~~~f~  173 (329)
T 3sb4_A           96 VTKGKQTLEKVILSE-KIKNIEDAAFKGCDNLKICQIRKKTAPN-LLPEALADSVTAIFIPLGSSDAYRFKNRWEHFAFI  173 (329)
T ss_dssp             EEEECTTCCC-CBCT-TCCEECTTTTTTCTTCCEEEBCCSSCCE-ECTTSSCTTTCEEEECTTCTHHHHTSTTTTTSCEE
T ss_pred             cccccCCCcEEECCc-cccchhHHHhhcCcccceEEcCCCCccc-cchhhhcCCCceEEecCcchhhhhccccccccccc
Confidence                99999999988 88888754 8889999999998887652 222 55555555555443210      01111144


Q ss_pred             CCCccc-eEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCcc-CcCCCceEEEEEcccCCCCCccccc
Q 003387          635 RLPNLR-NLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEY-LFPHSLTHLSFSNTDLMDDPMPTLE  712 (824)
Q Consensus       635 ~l~~L~-~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~-~~~~~L~~L~L~~~~l~~~~~~~l~  712 (824)
                      .+.+|+ .+.+..... ....+...-....++..+.+.+..     ........ ..+++|+.|+|++|.+.......|.
T Consensus       174 ~~~~L~~~i~~~~~~~-l~~~~~~~~~~~~~~~~l~~~~~l-----~~~~~~~l~~~~~~L~~l~L~~n~i~~I~~~aF~  247 (329)
T 3sb4_A          174 EGEPLETTIQVGAMGK-LEDEIMKAGLQPRDINFLTIEGKL-----DNADFKLIRDYMPNLVSLDISKTNATTIPDFTFA  247 (329)
T ss_dssp             ESCCCEEEEEECTTCC-HHHHHHHTTCCGGGCSEEEEEECC-----CHHHHHHHHHHCTTCCEEECTTBCCCEECTTTTT
T ss_pred             cccccceeEEecCCCc-HHHHHhhcccCccccceEEEeeee-----cHHHHHHHHHhcCCCeEEECCCCCcceecHhhhh
Confidence            556666 444443320 111111111123455555555321     00000000 2368899999998887666667799


Q ss_pred             CCCCCCeEEeeccccCCCeeeecCCCCCCcc-EEeeccCCCCccce-eccCcccCccEEEEecCCCCCCCcc-ccccCcc
Q 003387          713 KLPLLQVLKLKQNSYSGRKLTCGSYGFPNLK-VLHLKSMLWLEEWT-MGNAAMPKLECLIINPCAYLKKMPE-QLWYIKS  789 (824)
Q Consensus       713 ~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~-~L~L~~~~~l~~l~-~~~~~lp~L~~L~l~~c~~l~~lp~-~l~~l~~  789 (824)
                      +|++|+.|.+.+| +.. .-...+.++++|+ .+.+.+  .++.++ ..+..+++|+.|++.++. ++.++. .+.++++
T Consensus       248 ~~~~L~~l~l~~n-i~~-I~~~aF~~~~~L~~~l~l~~--~l~~I~~~aF~~c~~L~~l~l~~n~-i~~I~~~aF~~~~~  322 (329)
T 3sb4_A          248 QKKYLLKIKLPHN-LKT-IGQRVFSNCGRLAGTLELPA--SVTAIEFGAFMGCDNLRYVLATGDK-ITTLGDELFGNGVP  322 (329)
T ss_dssp             TCTTCCEEECCTT-CCE-ECTTTTTTCTTCCEEEEECT--TCCEECTTTTTTCTTEEEEEECSSC-CCEECTTTTCTTCC
T ss_pred             CCCCCCEEECCcc-cce-ehHHHhhCChhccEEEEEcc--cceEEchhhhhCCccCCEEEeCCCc-cCccchhhhcCCcc
Confidence            9999999999865 321 1223356788899 999987  467765 456778999999997765 555554 6888999


Q ss_pred             CcEEEe
Q 003387          790 LNKFDC  795 (824)
Q Consensus       790 L~~L~l  795 (824)
                      |+.|+.
T Consensus       323 L~~ly~  328 (329)
T 3sb4_A          323 SKLIYK  328 (329)
T ss_dssp             CCEEEC
T ss_pred             hhhhcc
Confidence            998863

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.14  E-value=4.2e-12  Score=150.27  Aligned_cols=160  Identities=15%  Similarity=0.042  Sum_probs=98.8

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccE-----EEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRV-----LDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSN  566 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~-----L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~  566 (824)
                      .+.++.|.+..+....     .+..+.....|+.     ++++.+.+...|..+..+.+|++|+|++|.+..+|..+ .+
T Consensus       172 ~~~~~~l~L~~n~~~~-----~~~~~l~~l~Ls~~~i~~~~~~~n~~~~~~~~~~~l~~L~~L~Ls~n~l~~l~~~~-~~  245 (727)
T 4b8c_D          172 TPLTPKIELFANGKDE-----ANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNISANI-FK  245 (727)
T ss_dssp             -------------------------------------------------------CCCCCCEEECTTSCCSCCCGGG-GG
T ss_pred             CCccceEEeeCCCCCc-----chhhHhhcCccCcccccCccccccceecChhhhccCCCCcEEECCCCCCCCCChhh-cC
Confidence            4566777776655431     1111222222333     23333444455778899999999999999999999999 79


Q ss_pred             CCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCCCeeeccCC-CcchhhhcCCCCccceEEE
Q 003387          567 LLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISALHP-CCCTEDILGRLPNLRNLRI  644 (824)
Q Consensus       567 L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~-~~~~~~~l~~l~~L~~L~l  644 (824)
                      +++|++|+|++|.+..+|..|++|++|++|+|++|.+.  .+| .+++|++|+.|+++.+ ...++..++.|++|+.|++
T Consensus       246 l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~--~lp~~~~~l~~L~~L~L~~N~l~~lp~~~~~l~~L~~L~L  323 (727)
T 4b8c_D          246 YDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLT--SLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGV  323 (727)
T ss_dssp             CCSCSCCBCTTSCCSCCCGGGGGGTTCCEEECTTSCCS--SCCSSGGGGTTCSEEECCSSCCCCCCSSTTSCTTCCCEEC
T ss_pred             CCCCCEEEeeCCcCcccChhhhCCCCCCEEeCcCCcCC--ccChhhcCCCCCCEEECCCCCCCccChhhhcCCCccEEeC
Confidence            99999999999999999999999999999999999998  667 8999999999999842 2233433889999999999


Q ss_pred             ecccccchhhHHHHhcc
Q 003387          645 RGDLSYNQSLLSKSLCR  661 (824)
Q Consensus       645 ~~~~~~~~~~l~~~l~~  661 (824)
                      ++|.  ....+|..+..
T Consensus       324 ~~N~--l~~~~p~~~~~  338 (727)
T 4b8c_D          324 EGNP--LEKQFLKILTE  338 (727)
T ss_dssp             TTSC--CCSHHHHHHHH
T ss_pred             CCCc--cCCCChHHHhh
Confidence            9886  44455555544

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=99.11  E-value=1e-10  Score=114.53  Aligned_cols=101  Identities=17%  Similarity=0.149  Sum_probs=50.5

Q ss_pred             cccEEEeeCccCccCCcc--CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecC
Q 003387          522 LLRVLDLGSLVLIQYPSG--IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNF  598 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~~--i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L  598 (824)
                      .|++|++++|.+..+|..  ++.+++|++|+|++|.++.+++..|.++++|++|+|++|.+..+|.. +..+++|++|++
T Consensus        30 ~l~~L~l~~n~i~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L  109 (192)
T 1w8a_A           30 HTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLKTLNL  109 (192)
T ss_dssp             TCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSCCCCEECSSSSTTCTTCCEEEC
T ss_pred             CCCEEECCCCcCCccCCccccccCCCCCEEECCCCCCCCcCHhHcCCcccCCEEECCCCcCCccCHHHhcCCCCCCEEEC
Confidence            455555555555544432  45555555555555555544322225555555555555555554432 445555555555


Q ss_pred             CCccCCCCCCC-CCCCCCCCCeeecc
Q 003387          599 GSITLPAHPGK-FCGSLENLNFISAL  623 (824)
Q Consensus       599 ~~~~~~~~~~p-~i~~L~~L~~l~~~  623 (824)
                      ++|.+.. ..| .++.+++|+.|++.
T Consensus       110 ~~N~l~~-~~~~~~~~l~~L~~L~L~  134 (192)
T 1w8a_A          110 YDNQISC-VMPGSFEHLNSLTSLNLA  134 (192)
T ss_dssp             CSSCCCE-ECTTSSTTCTTCCEEECT
T ss_pred             CCCcCCe-eCHHHhhcCCCCCEEEeC
Confidence            5555442 222 45555555555554

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.11  E-value=3.4e-10  Score=110.77  Aligned_cols=121  Identities=22%  Similarity=0.237  Sum_probs=57.4

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch-hhhccccCceecCCCcc
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~  602 (824)
                      ++++++++.++.+|..+.  .+|++|++++|.+..+|..+ .++++|++|+|++|.+..++. .|..+++|++|++++|.
T Consensus        13 ~~l~~~~~~l~~ip~~~~--~~l~~L~L~~n~i~~ip~~~-~~l~~L~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~   89 (193)
T 2wfh_A           13 TVVRCSNKGLKVLPKGIP--RDVTELYLDGNQFTLVPKEL-SNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYNR   89 (193)
T ss_dssp             TEEECTTSCCSSCCSCCC--TTCCEEECCSSCCCSCCGGG-GGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC
T ss_pred             CEEEcCCCCCCcCCCCCC--CCCCEEECCCCcCchhHHHh-hcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCCCc
Confidence            345555555555554433  34555555555555555444 555555555555555555442 24555555555555555


Q ss_pred             CCCCCCC-CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEeccc
Q 003387          603 LPAHPGK-FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       603 ~~~~~~p-~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      +.. ..| .++.+++|+.|+++.+  .......+..+++|+.|+++++.
T Consensus        90 l~~-i~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~  137 (193)
T 2wfh_A           90 LRC-IPPRTFDGLKSLRLLSLHGNDISVVPEGAFNDLSALSHLAIGANP  137 (193)
T ss_dssp             CCB-CCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECCSSC
T ss_pred             cCE-eCHHHhCCCCCCCEEECCCCCCCeeChhhhhcCccccEEEeCCCC
Confidence            442 111 3444444444444311  11112225556666666666553

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=99.10  E-value=2.2e-10  Score=112.16  Aligned_cols=122  Identities=18%  Similarity=0.243  Sum_probs=94.6

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChh-hhhcCCCccEeecCCcccccc-chhhhccccCceecCCCc
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSS-LLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGSI  601 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~-i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~~  601 (824)
                      ++++++++.++.+|..+..  +|++|++++|.+..++.. +++++++|++|+|++|.+..+ |..+..+++|++|++++|
T Consensus        11 ~~l~~s~~~l~~ip~~~~~--~l~~L~l~~n~i~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N   88 (192)
T 1w8a_A           11 TTVDCTGRGLKEIPRDIPL--HTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGEN   88 (192)
T ss_dssp             TEEECTTSCCSSCCSCCCT--TCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSC
T ss_pred             CEEEcCCCCcCcCccCCCC--CCCEEECCCCcCCccCCccccccCCCCCEEECCCCCCCCcCHhHcCCcccCCEEECCCC
Confidence            7999999999999988765  999999999999999874 339999999999999999988 677999999999999999


Q ss_pred             cCCCCCCC-CCCCCCCCCeeeccCCC--cchhhhcCCCCccceEEEeccc
Q 003387          602 TLPAHPGK-FCGSLENLNFISALHPC--CCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       602 ~~~~~~~p-~i~~L~~L~~l~~~~~~--~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      .+.. ..| .++.+++|+.|+++.+.  ...+..+..+++|+.|+++++.
T Consensus        89 ~l~~-~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~  137 (192)
T 1w8a_A           89 KIKE-ISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNP  137 (192)
T ss_dssp             CCCE-ECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCC
T ss_pred             cCCc-cCHHHhcCCCCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCCCC
Confidence            9874 223 46667777777666321  1222235566666666666553

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.10  E-value=2.6e-10  Score=109.99  Aligned_cols=101  Identities=24%  Similarity=0.286  Sum_probs=50.7

Q ss_pred             CcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecC
Q 003387          521 KLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNF  598 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L  598 (824)
                      +.|++|++++|.++.+|.. ++.+++|++|++++|.+..+|...++.+++|++|++++|.+..+|.. +..+++|++|++
T Consensus        28 ~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l  107 (177)
T 2o6r_A           28 SSATRLELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHENKLQSLPNGVFDKLTQLKELAL  107 (177)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEEC
T ss_pred             CCCcEEEeCCCcccEeCHHHhcCcccccEEECCCCcceEeChhHccCCCccCEEECCCCCccccCHHHhhCCcccCEEEC
Confidence            3455555555555544432 34455555555555555555544335555555555555555555433 345555555555


Q ss_pred             CCccCCCCCCC--CCCCCCCCCeeecc
Q 003387          599 GSITLPAHPGK--FCGSLENLNFISAL  623 (824)
Q Consensus       599 ~~~~~~~~~~p--~i~~L~~L~~l~~~  623 (824)
                      ++|.+.  .+|  .+..+++|+.|++.
T Consensus       108 ~~N~l~--~~~~~~~~~l~~L~~L~l~  132 (177)
T 2o6r_A          108 DTNQLK--SVPDGIFDRLTSLQKIWLH  132 (177)
T ss_dssp             CSSCCS--CCCTTTTTTCTTCCEEECC
T ss_pred             cCCcce--EeCHHHhcCCcccCEEEec
Confidence            555544  222  23445555555554

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.09  E-value=2.7e-10  Score=111.54  Aligned_cols=102  Identities=18%  Similarity=0.211  Sum_probs=68.1

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch-hhhccccCceecCC
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFG  599 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~  599 (824)
                      +.|++|+|++|.++.+|..+..+++|++|+|++|.+..++...|.++++|++|+|++|.+..+|. .+..+++|++|+++
T Consensus        31 ~~l~~L~L~~n~i~~ip~~~~~l~~L~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~L~  110 (193)
T 2wfh_A           31 RDVTELYLDGNQFTLVPKELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYNRLRCIPPRTFDGLKSLRLLSLH  110 (193)
T ss_dssp             TTCCEEECCSSCCCSCCGGGGGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECC
T ss_pred             CCCCEEECCCCcCchhHHHhhcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCCCccCEeCHHHhCCCCCCCEEECC
Confidence            45677777777777676666777777777777777776665544677777777777776666654 36667777777777


Q ss_pred             CccCCCCCCC--CCCCCCCCCeeeccC
Q 003387          600 SITLPAHPGK--FCGSLENLNFISALH  624 (824)
Q Consensus       600 ~~~~~~~~~p--~i~~L~~L~~l~~~~  624 (824)
                      +|.+.  .+|  .+..+++|+.|++..
T Consensus       111 ~N~l~--~~~~~~~~~l~~L~~L~L~~  135 (193)
T 2wfh_A          111 GNDIS--VVPEGAFNDLSALSHLAIGA  135 (193)
T ss_dssp             SSCCC--BCCTTTTTTCTTCCEEECCS
T ss_pred             CCCCC--eeChhhhhcCccccEEEeCC
Confidence            77665  233  466666777776663

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.01  E-value=1.8e-09  Score=104.07  Aligned_cols=124  Identities=23%  Similarity=0.259  Sum_probs=99.0

Q ss_pred             cccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCC
Q 003387          522 LLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGS  600 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~  600 (824)
                      ..+.++++++.+..+|..+.  .+|++|++++|.+..+|...++++++|++|++++|.+..+|.. +..+++|++|++++
T Consensus         8 ~~~~l~~~~~~l~~~p~~~~--~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~   85 (177)
T 2o6r_A            8 SGTEIRCNSKGLTSVPTGIP--SSATRLELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHE   85 (177)
T ss_dssp             ETTEEECCSSCCSSCCTTCC--TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCS
T ss_pred             CCCEEEecCCCCccCCCCCC--CCCcEEEeCCCcccEeCHHHhcCcccccEEECCCCcceEeChhHccCCCccCEEECCC
Confidence            35789999999999997664  6999999999999999987668999999999999999999865 68999999999999


Q ss_pred             ccCCCCCCC-CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEeccc
Q 003387          601 ITLPAHPGK-FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       601 ~~~~~~~~p-~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      |.+.. ..+ .++.+++|+.|+++.+  .......+..+++|+.|+++++.
T Consensus        86 N~l~~-~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~  135 (177)
T 2o6r_A           86 NKLQS-LPNGVFDKLTQLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNP  135 (177)
T ss_dssp             SCCCC-CCTTTTTTCTTCCEEECCSSCCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             CCccc-cCHHHhhCCcccCEEECcCCcceEeCHHHhcCCcccCEEEecCCC
Confidence            99873 223 5677888888887732  22233335667777778777764

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=98.98  E-value=3.3e-08  Score=108.18  Aligned_cols=266  Identities=14%  Similarity=0.052  Sum_probs=158.1

Q ss_pred             CCceechhhHHHHHHHHHc----CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC-ceeEEEECCCCCCCCHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIE----GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF-DCHAWITEPYSNEYDADQILD  230 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F-~~~~wv~~~vs~~~~~~~~~~  230 (824)
                      +.++||+.+++++.+++..    +....+.+.|+|+.|+||||||+.+.+  ...... ..++|+.  .+...+...+..
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~i~--~~~~~~~~~~~~   92 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWE--LYKDKTTARFVYIN--GFIYRNFTAIIG   92 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHH--HHTTSCCCEEEEEE--TTTCCSHHHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHH--HHhhhcCeeEEEEe--CccCCCHHHHHH
Confidence            6799999999999999876    222234899999999999999999998  444332 3467777  788888889999


Q ss_pred             HHHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCCh--hhHHHHHhhCCCCC----CCcEEEEEechH
Q 003387          231 IVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSI--DMWDVIQEILPDNQ----NGSRVLITLTDI  302 (824)
Q Consensus       231 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~--~~~~~l~~~~~~~~----~gs~ilvTtR~~  302 (824)
                      .++..++...+   ....+.......+.+.+.  +++.+|||||++..  ..+..+...+....    .+..||+||+..
T Consensus        93 ~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~  169 (389)
T 1fnn_A           93 EIARSLNIPFP---RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHND  169 (389)
T ss_dssp             HHHHHTTCCCC---SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESST
T ss_pred             HHHHHhCccCC---CCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCc
Confidence            99999865422   122345566666666663  57899999999764  44555555543321    367788888766


Q ss_pred             HHHh--------hccc-c--cC----------------C--cCcCccccchhhHHHhc---------CCCchhHHHHHhH
Q 003387          303 RIII--------SFQF-E--DG----------------E--NMRLDLVPTGGPLRATY---------KGRPFLILYHGSI  344 (824)
Q Consensus       303 ~v~~--------~f~~-~--~~----------------~--~~~~~~~~~~~~i~~~c---------~GlPlai~~~~~~  344 (824)
                      ....        .|.. .  ..                .  ....--.+....|++.+         +|.|-.+..+...
T Consensus       170 ~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~  249 (389)
T 1fnn_A          170 AVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYR  249 (389)
T ss_dssp             HHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHH
T ss_pred             hHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHH
Confidence            4333        1110 0  00                0  00011123456677788         6776544443332


Q ss_pred             HHh---hhhhhhccCC-----C-cc-cccc-c-c-cCCCCchHHHhHhccCC---CCceechhHHHHHHHH----cCCCC
Q 003387          345 SLE---ENIREAVETP-----L-GL-RYIK-C-L-MLPFCLKPCFIYLSVFP---AHQEISTRQLYQLWIA----EGFIP  404 (824)
Q Consensus       345 l~~---~~~~~~~~~~-----~-~~-~~~l-~-~-~L~~~lk~cfl~~s~fp---~~~~i~~~~Li~~W~a----~g~i~  404 (824)
                      ...   ....+.+...     . .+ ...+ . + .||.+.+.++..++.+.   .+..+....+...+..    .|. .
T Consensus       250 a~~~a~~~~~~~i~~~~v~~~~~~~~~~~~~~~l~~l~~~~~~~L~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~-~  328 (389)
T 1fnn_A          250 SAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGE-R  328 (389)
T ss_dssp             HHHHHHHTTCSSCCHHHHHHHHHHHSCCCCHHHHHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHHHTTC-C
T ss_pred             HHHHHHHhCCCCcCHHHHHHHHHHHhhhhHHHHHHcCCHHHHHHHHHHHHHHhhccCCCccHHHHHHHHHHHHHHcCC-C
Confidence            211   0000000000     0 00 0011 1 1 67777777766666543   2225666666665443    342 2


Q ss_pred             CChHHHHHHHHHHHHhccccceeec
Q 003387          405 DNSEATAESYLEQLIKEGFVEAKKR  429 (824)
Q Consensus       405 ~~~e~~~~~~~~~Lv~rsllq~~~~  429 (824)
                      +-.......++++|..++++.....
T Consensus       329 ~~~~~~~~~~l~~L~~~gli~~~~~  353 (389)
T 1fnn_A          329 PRVHSQLWSYLNDLREKGIVETRQN  353 (389)
T ss_dssp             CCCHHHHHHHHHHHHHTTSSEEEEC
T ss_pred             CCCHHHHHHHHHHHHhCCCeEEeee
Confidence            2233457789999999999998654

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.95  E-value=1.6e-09  Score=103.93  Aligned_cols=83  Identities=19%  Similarity=0.260  Sum_probs=38.1

Q ss_pred             CcccEEEeeCccCccC-CccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecC
Q 003387          521 KLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNF  598 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L  598 (824)
                      +.|++|+|++|.++.+ |..++++++|++|+|++|.+..+|..+|.++++|++|+|++|.+..+|.. +..+++|++|++
T Consensus        33 ~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~l~~L~~L~L  112 (174)
T 2r9u_A           33 TDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRGAFDNLKSLTHIYL  112 (174)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCSEEEC
T ss_pred             CCCcEEEeCCCCccccCHHHhcCCcCCCEEECCCCCCCccChhHhCCcchhhEEECCCCccceeCHHHhccccCCCEEEe
Confidence            3444444444444433 23344444444444444444444444334444444444444444444433 444444444444


Q ss_pred             CCccC
Q 003387          599 GSITL  603 (824)
Q Consensus       599 ~~~~~  603 (824)
                      ++|.+
T Consensus       113 ~~N~~  117 (174)
T 2r9u_A          113 YNNPW  117 (174)
T ss_dssp             CSSCB
T ss_pred             CCCCc
Confidence            44443

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=98.93  E-value=3.1e-09  Score=114.86  Aligned_cols=265  Identities=12%  Similarity=0.080  Sum_probs=148.1

Q ss_pred             CCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCC-----CCHHHH
Q 003387          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNE-----YDADQI  228 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~-----~~~~~~  228 (824)
                      ....++||+.+++.|.+ +..     +++.|+|++|+|||||++.+.+  +...   ..+|+.  ....     .+....
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~-----~~v~i~G~~G~GKT~L~~~~~~--~~~~---~~~~~~--~~~~~~~~~~~~~~~   77 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA-----PITLVLGLRRTGKSSIIKIGIN--ELNL---PYIYLD--LRKFEERNYISYKDF   77 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS-----SEEEEEESTTSSHHHHHHHHHH--HHTC---CEEEEE--GGGGTTCSCCCHHHH
T ss_pred             CHHHhcChHHHHHHHHH-hcC-----CcEEEECCCCCCHHHHHHHHHH--hcCC---CEEEEE--chhhccccCCCHHHH
Confidence            45789999999999999 643     5999999999999999999998  3332   257887  5532     344555


Q ss_pred             HHHHHHHhC--------------CCCCc--c----cc-----cccCHHHHHHHHHHhcCCCeEEEEEecCCChh-----h
Q 003387          229 LDIVIKFLM--------------PSSRL--S----EI-----MDKNYEMKKIILHEYLMTKRYLIVIDDVWSID-----M  278 (824)
Q Consensus       229 ~~~i~~~l~--------------~~~~~--~----~~-----~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~-----~  278 (824)
                      ...+.+.+.              .-.+.  +    ..     .......+...+.+.-+ ++++||+||++..+     +
T Consensus        78 ~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~~~vlvlDe~~~~~~~~~~~  156 (357)
T 2fna_A           78 LLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK-DNVIIVLDEAQELVKLRGVN  156 (357)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS-SCEEEEEETGGGGGGCTTCC
T ss_pred             HHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCC-CCeEEEEECHHHhhccCchh
Confidence            555444331              00000  0    00     12234555555555433 59999999997532     2


Q ss_pred             HHHHHhhCCCCCCCcEEEEEechHHHHh-----------hcccccC----Cc----------------CcCccccchhhH
Q 003387          279 WDVIQEILPDNQNGSRVLITLTDIRIII-----------SFQFEDG----EN----------------MRLDLVPTGGPL  327 (824)
Q Consensus       279 ~~~l~~~~~~~~~gs~ilvTtR~~~v~~-----------~f~~~~~----~~----------------~~~~~~~~~~~i  327 (824)
                      |..+...+.+...+.++|+|+|......           .++....    ..                ......+ ...|
T Consensus       157 ~~~~l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~-~~~i  235 (357)
T 2fna_A          157 LLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADIDFKD-YEVV  235 (357)
T ss_dssp             CHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCCCCC-HHHH
T ss_pred             HHHHHHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCCCCc-HHHH
Confidence            3222222222224678999999764311           1111000    00                0001111 2678


Q ss_pred             HHhcCCCchhHHHHHhHHHhhhhhhh----c-cCC---C--ccccccc--ccCCCCchHHHhHhccCCCCceechhHHHH
Q 003387          328 RATYKGRPFLILYHGSISLEENIREA----V-ETP---L--GLRYIKC--LMLPFCLKPCFIYLSVFPAHQEISTRQLYQ  395 (824)
Q Consensus       328 ~~~c~GlPlai~~~~~~l~~~~~~~~----~-~~~---~--~~~~~l~--~~L~~~lk~cfl~~s~fp~~~~i~~~~Li~  395 (824)
                      +..|+|.|+++..++..+......+.    + +..   .  .+...+.  ..+|+..+..+..+|.   +.  +...+..
T Consensus       236 ~~~t~G~P~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~l~~la~---g~--~~~~l~~  310 (357)
T 2fna_A          236 YEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENFLHGREIARKRYLNIMRTLSK---CG--KWSDVKR  310 (357)
T ss_dssp             HHHHCSCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHTT---CB--CHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHc---CC--CHHHHHH
Confidence            99999999999998876521110011    0 000   0  1111110  1467788888888887   22  4445443


Q ss_pred             HHH-HcCCCCCChHHHHHHHHHHHHhccccceeecCCCCcEEEEE-cCccHHHH
Q 003387          396 LWI-AEGFIPDNSEATAESYLEQLIKEGFVEAKKRKAGGTINTCS-IPGRWRPV  447 (824)
Q Consensus       396 ~W~-a~g~i~~~~e~~~~~~~~~Lv~rsllq~~~~~~~g~~~~~~-mHdlv~dl  447 (824)
                      ..- ..|.  +........+++.|++.+++....    +   .|+ .|.++++.
T Consensus       311 ~~~~~~g~--~~~~~~~~~~L~~L~~~gli~~~~----~---~y~f~~~~~~~~  355 (357)
T 2fna_A          311 ALELEEGI--EISDSEIYNYLTQLTKHSWIIKEG----E---KYCPSEPLISLA  355 (357)
T ss_dssp             HHHHHHCS--CCCHHHHHHHHHHHHHTTSEEESS----S---CEEESSHHHHHH
T ss_pred             HHHHhcCC--CCCHHHHHHHHHHHHhCCCEEecC----C---EEEecCHHHHHh
Confidence            221 1231  012345678999999999997653    2   244 46676654

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.92  E-value=2.9e-09  Score=102.19  Aligned_cols=97  Identities=21%  Similarity=0.253  Sum_probs=80.5

Q ss_pred             ccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCc
Q 003387          523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSI  601 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~  601 (824)
                      -++++++++.+..+|..+.  .+|++|+|++|.+..+++..|+++++|++|+|++|.+..+|.. +.++++|++|+|++|
T Consensus        14 ~~~l~~~~n~l~~iP~~~~--~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~L~~N   91 (174)
T 2r9u_A           14 QTLVNCQNIRLASVPAGIP--TDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDN   91 (174)
T ss_dssp             SSEEECCSSCCSSCCSCCC--TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             CcEEEeCCCCCCccCCCcC--CCCcEEEeCCCCccccCHHHhcCCcCCCEEECCCCCCCccChhHhCCcchhhEEECCCC
Confidence            3789999999999999876  7999999999999999765559999999999999999999876 589999999999999


Q ss_pred             cCCCCCCC--CCCCCCCCCeeecc
Q 003387          602 TLPAHPGK--FCGSLENLNFISAL  623 (824)
Q Consensus       602 ~~~~~~~p--~i~~L~~L~~l~~~  623 (824)
                      .+.  .+|  .++.+++|+.|++.
T Consensus        92 ~l~--~l~~~~~~~l~~L~~L~L~  113 (174)
T 2r9u_A           92 HLK--SIPRGAFDNLKSLTHIYLY  113 (174)
T ss_dssp             CCC--CCCTTTTTTCTTCSEEECC
T ss_pred             ccc--eeCHHHhccccCCCEEEeC
Confidence            887  333  24445555554444

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.92  E-value=3e-09  Score=101.72  Aligned_cols=80  Identities=21%  Similarity=0.258  Sum_probs=62.9

Q ss_pred             ccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCc
Q 003387          523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSI  601 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~  601 (824)
                      .++|+++++.++.+|..+.  .+|++|+|++|.+..+++..|.++++|++|+|++|.+..+|.. +..+++|++|+|++|
T Consensus        11 ~~~l~~s~n~l~~ip~~~~--~~l~~L~L~~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N   88 (170)
T 3g39_A           11 GTTVDCSGKSLASVPTGIP--TTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDN   88 (170)
T ss_dssp             TTEEECTTSCCSSCCSCCC--TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSS
T ss_pred             CCEEEeCCCCcCccCccCC--CCCcEEEcCCCcCCccChhhhcCcccCCEEECCCCCcCccChhhccCCCCCCEEECCCC
Confidence            5778888888888887664  6888888888888887555448888888888888888888765 578888888888888


Q ss_pred             cCC
Q 003387          602 TLP  604 (824)
Q Consensus       602 ~~~  604 (824)
                      .+.
T Consensus        89 ~l~   91 (170)
T 3g39_A           89 QLK   91 (170)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            775

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.92  E-value=2.6e-09  Score=102.14  Aligned_cols=84  Identities=20%  Similarity=0.244  Sum_probs=75.8

Q ss_pred             CcccEEEeeCccCccC-CccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecC
Q 003387          521 KLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNF  598 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L  598 (824)
                      +.|++|+|++|.++.+ |..+..+++|++|+|++|.+..+|...|.++++|++|+|++|.+..+|.. +..+++|++|++
T Consensus        30 ~~l~~L~L~~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L  109 (170)
T 3g39_A           30 TTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDNQLKSIPRGAFDNLKSLTHIWL  109 (170)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEEC
T ss_pred             CCCcEEEcCCCcCCccChhhhcCcccCCEEECCCCCcCccChhhccCCCCCCEEECCCCccCEeCHHHhcCCCCCCEEEe
Confidence            7899999999999977 56789999999999999999999988778999999999999999999875 889999999999


Q ss_pred             CCccCC
Q 003387          599 GSITLP  604 (824)
Q Consensus       599 ~~~~~~  604 (824)
                      ++|.+.
T Consensus       110 ~~N~~~  115 (170)
T 3g39_A          110 LNNPWD  115 (170)
T ss_dssp             CSSCBC
T ss_pred             CCCCCC
Confidence            999775

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=98.91  E-value=2.5e-08  Score=109.07  Aligned_cols=268  Identities=10%  Similarity=0.037  Sum_probs=165.1

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L  570 (824)
                      +..+.++.+...-.     .+....|..+ +|+.+.+..+ ++.++.. |.+ .+|+.+.+.. .+..++...|.+|.+|
T Consensus       112 ~~~l~~i~ip~~i~-----~I~~~aF~~~-~L~~i~l~~~-i~~I~~~aF~~-~~L~~i~lp~-~l~~I~~~aF~~c~~L  182 (401)
T 4fdw_A          112 LKGYNEIILPNSVK-----SIPKDAFRNS-QIAKVVLNEG-LKSIGDMAFFN-STVQEIVFPS-TLEQLKEDIFYYCYNL  182 (401)
T ss_dssp             CSSCSEEECCTTCC-----EECTTTTTTC-CCSEEECCTT-CCEECTTTTTT-CCCCEEECCT-TCCEECSSTTTTCTTC
T ss_pred             cCCccEEEECCccC-----EehHhhcccC-CccEEEeCCC-ccEECHHhcCC-CCceEEEeCC-CccEehHHHhhCcccC
Confidence            45555555544322     2344566665 6888888765 6655543 444 4688888875 6777777666888888


Q ss_pred             cEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccccc
Q 003387          571 YTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSY  650 (824)
Q Consensus       571 ~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~  650 (824)
                      +.+++.++.+..+|.....+.+|+.+.+..+ +.  .++                    ...+..|++|+.+.+..+-..
T Consensus       183 ~~l~l~~n~l~~I~~~aF~~~~L~~l~lp~~-l~--~I~--------------------~~aF~~~~~L~~l~l~~~l~~  239 (401)
T 4fdw_A          183 KKADLSKTKITKLPASTFVYAGIEEVLLPVT-LK--EIG--------------------SQAFLKTSQLKTIEIPENVST  239 (401)
T ss_dssp             CEEECTTSCCSEECTTTTTTCCCSEEECCTT-CC--EEC--------------------TTTTTTCTTCCCEECCTTCCE
T ss_pred             CeeecCCCcceEechhhEeecccCEEEeCCc-hh--eeh--------------------hhHhhCCCCCCEEecCCCccC
Confidence            8888888888888776545678888866533 21  111                    112445555555555432100


Q ss_pred             chhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCC-----CCCcccccCCCCCCeEEeecc
Q 003387          651 NQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLM-----DDPMPTLEKLPLLQVLKLKQN  725 (824)
Q Consensus       651 ~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~-----~~~~~~l~~l~~L~~L~L~~~  725 (824)
                      ..   ...+.+ .+|+.+.+..     +++.+.-..+..|++|+.+.+.++.+.     ......|.+|++|+.+.|. +
T Consensus       240 I~---~~aF~~-~~L~~i~lp~-----~i~~I~~~aF~~c~~L~~l~l~~~~~~~~~~~~I~~~aF~~c~~L~~l~l~-~  309 (401)
T 4fdw_A          240 IG---QEAFRE-SGITTVKLPN-----GVTNIASRAFYYCPELAEVTTYGSTFNDDPEAMIHPYCLEGCPKLARFEIP-E  309 (401)
T ss_dssp             EC---TTTTTT-CCCSEEEEET-----TCCEECTTTTTTCTTCCEEEEESSCCCCCTTCEECTTTTTTCTTCCEECCC-T
T ss_pred             cc---cccccc-CCccEEEeCC-----CccEEChhHhhCCCCCCEEEeCCccccCCcccEECHHHhhCCccCCeEEeC-C
Confidence            00   112223 5777777753     366665556677888888888877643     1334568889999999998 3


Q ss_pred             ccCCCeeeecCCCCCCccEEeeccCCCCcccee-ccCcccCccEEEEecCCCCCCCccccccCc-cCcEEEecCCcHHHH
Q 003387          726 SYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM-GNAAMPKLECLIINPCAYLKKMPEQLWYIK-SLNKFDCWWPQPELR  803 (824)
Q Consensus       726 ~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~-~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~-~L~~L~l~~c~~~l~  803 (824)
                      .+.. .-...+.++++|+.+.|.++  +..+.. .+..+ +|+.|.+.++....-.+..+..++ +++.|.+-..   ..
T Consensus       310 ~i~~-I~~~aF~~c~~L~~l~lp~~--l~~I~~~aF~~~-~L~~l~l~~n~~~~l~~~~F~~~~~~l~~l~vp~~---~~  382 (401)
T 4fdw_A          310 SIRI-LGQGLLGGNRKVTQLTIPAN--VTQINFSAFNNT-GIKEVKVEGTTPPQVFEKVWYGFPDDITVIRVPAE---SV  382 (401)
T ss_dssp             TCCE-ECTTTTTTCCSCCEEEECTT--CCEECTTSSSSS-CCCEEEECCSSCCBCCCSSCCCSCTTCCEEEECGG---GH
T ss_pred             ceEE-EhhhhhcCCCCccEEEECcc--ccEEcHHhCCCC-CCCEEEEcCCCCcccccccccCCCCCccEEEeCHH---HH
Confidence            3321 11223456789999999653  566643 35566 999999998854322233455664 7888886543   45


Q ss_pred             HHHhh
Q 003387          804 QKLRE  808 (824)
Q Consensus       804 ~~~~~  808 (824)
                      +.++.
T Consensus       383 ~~y~~  387 (401)
T 4fdw_A          383 EKYKN  387 (401)
T ss_dssp             HHHHH
T ss_pred             HHhhh
Confidence            55554

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.91  E-value=2.9e-08  Score=108.52  Aligned_cols=265  Identities=13%  Similarity=0.044  Sum_probs=150.7

Q ss_pred             CCCceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCCccccCC------CceeEEEECCCCCCCCHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY------FDCHAWITEPYSNEYDAD  226 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~------F~~~~wv~~~vs~~~~~~  226 (824)
                      ++.++||+.+++++.+++...  ......+.|+|++|+||||+|+.+++  .....      -...+|+.  .....+..
T Consensus        18 p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~--~~~~~~~~~~~~~~~~~i~--~~~~~~~~   93 (387)
T 2v1u_A           18 PDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLR--RLEARASSLGVLVKPIYVN--ARHRETPY   93 (387)
T ss_dssp             CSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHH--HHHHHHHHHTCCEEEEEEE--TTTSCSHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHH--HHHHHHhccCCCeEEEEEE--CCcCCCHH
Confidence            378999999999999998542  33467889999999999999999998  44221      12466787  88888899


Q ss_pred             HHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCChhh----HHHHH---hhCCCC--CCCcEE
Q 003387          227 QILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSIDM----WDVIQ---EILPDN--QNGSRV  295 (824)
Q Consensus       227 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~~~----~~~l~---~~~~~~--~~gs~i  295 (824)
                      .++..++.+++...+   ....+.......+.+.+.  +++.+|||||++....    .+.+.   ......  ..+..+
T Consensus        94 ~~~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~  170 (387)
T 2v1u_A           94 RVASAIAEAVGVRVP---FTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSL  170 (387)
T ss_dssp             HHHHHHHHHHSCCCC---SSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEE
T ss_pred             HHHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEE
Confidence            999999999976432   223345666677777773  4689999999986532    22222   211111  345677


Q ss_pred             EEEechHHH--------Hhhccc-cc--C----------------C--cCcCccccchhhHHHhcC---CCchhH-HHHH
Q 003387          296 LITLTDIRI--------IISFQF-ED--G----------------E--NMRLDLVPTGGPLRATYK---GRPFLI-LYHG  342 (824)
Q Consensus       296 lvTtR~~~v--------~~~f~~-~~--~----------------~--~~~~~~~~~~~~i~~~c~---GlPlai-~~~~  342 (824)
                      |.||+....        ...|.. ..  .                .  ....--.+....+++.++   |.|-.+ ..+.
T Consensus       171 I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~  250 (387)
T 2v1u_A          171 VGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLR  250 (387)
T ss_dssp             EEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCHHHHHHHHH
T ss_pred             EEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCHHHHHHHHH
Confidence            888876522        111111 00  0                0  000111234456677777   888433 3332


Q ss_pred             hHHHhhhh-h-hhccCCCcccccc---------c-c-cCCCCchHHHhHhc-cCCCCceechhHHHHH----HHHcCCCC
Q 003387          343 SISLEENI-R-EAVETPLGLRYIK---------C-L-MLPFCLKPCFIYLS-VFPAHQEISTRQLYQL----WIAEGFIP  404 (824)
Q Consensus       343 ~~l~~~~~-~-~~~~~~~~~~~~l---------~-~-~L~~~lk~cfl~~s-~fp~~~~i~~~~Li~~----W~a~g~i~  404 (824)
                      ........ . ..+... .+..++         . + .+|.+.+..++..+ ++-....+...++.+.    .-..| +.
T Consensus       251 ~a~~~a~~~~~~~i~~~-~v~~a~~~~~~~~~~~~~~~l~~~~~~~l~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  328 (387)
T 2v1u_A          251 VAGEIAERRREERVRRE-HVYSARAEIERDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKELTSTLG-LE  328 (387)
T ss_dssp             HHHHHHHHTTCSCBCHH-HHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHSSSSCCEEHHHHHHHHHHHHHHTT-CC
T ss_pred             HHHHHHHHcCCCCcCHH-HHHHHHHHHhhchHHHHHHcCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhcC-CC
Confidence            22210000 0 000000 111111         0 1 66666665555454 4432234555533332    22344 33


Q ss_pred             CChHHHHHHHHHHHHhccccceee
Q 003387          405 DNSEATAESYLEQLIKEGFVEAKK  428 (824)
Q Consensus       405 ~~~e~~~~~~~~~Lv~rsllq~~~  428 (824)
                      +........+++.|...++++...
T Consensus       329 ~~~~~~~~~~l~~L~~~gli~~~~  352 (387)
T 2v1u_A          329 HVTLRRVSGIISELDMLGIVKSRV  352 (387)
T ss_dssp             CCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHHHHHhCCCeEEEe
Confidence            344566889999999999999864

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=98.89  E-value=5.3e-09  Score=111.78  Aligned_cols=262  Identities=13%  Similarity=0.001  Sum_probs=160.4

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCC--------CCcceEEeecCCCCCccChhh
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIEN--------LFLLRYLKLNIPSLNSLPSSL  563 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~--------l~~Lr~L~L~~~~i~~lp~~i  563 (824)
                      .++|++|.+.++....  ....   ...++.++.+.+..+.+.  +..|..        +.+|+.|.|.. .++.++...
T Consensus        48 l~~L~~LdLs~n~i~~--~~~~---~~~~~~~~~~~~~~~~I~--~~aF~~~~~~~~~g~~~L~~l~L~~-~i~~I~~~a  119 (329)
T 3sb4_A           48 FPSLKVLDISNAEIKM--YSGK---AGTYPNGKFYIYMANFVP--AYAFSNVVNGVTKGKQTLEKVILSE-KIKNIEDAA  119 (329)
T ss_dssp             CTTCCEEEEEEEEECC--EEES---SSSSGGGCCEEECTTEEC--TTTTEEEETTEEEECTTCCC-CBCT-TCCEECTTT
T ss_pred             hccCeEEecCcceeEE--ecCc---cccccccccccccccccC--HHHhcccccccccccCCCcEEECCc-cccchhHHH
Confidence            5678888887766531  0001   112222455555555332  123445        78888888887 788887776


Q ss_pred             hhcCCCccEeecCCccccccchh-hhccccCceecCCCccCC--CCCCC--CCCCCCCCC-eeeccCCCcchhhh---cC
Q 003387          564 LSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLP--AHPGK--FCGSLENLN-FISALHPCCCTEDI---LG  634 (824)
Q Consensus       564 ~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~--~~~~p--~i~~L~~L~-~l~~~~~~~~~~~~---l~  634 (824)
                      |.+|++|+.|+++++.+..++.. |..+.++..+.+......  ...+.  .+.++..|+ .+.+..........   --
T Consensus       120 F~~~~~L~~l~l~~n~i~~i~~~aF~~~~~l~~l~~~~~~~~~~~~~i~~~~f~~~~~L~~~i~~~~~~~l~~~~~~~~~  199 (329)
T 3sb4_A          120 FKGCDNLKICQIRKKTAPNLLPEALADSVTAIFIPLGSSDAYRFKNRWEHFAFIEGEPLETTIQVGAMGKLEDEIMKAGL  199 (329)
T ss_dssp             TTTCTTCCEEEBCCSSCCEECTTSSCTTTCEEEECTTCTHHHHTSTTTTTSCEEESCCCEEEEEECTTCCHHHHHHHTTC
T ss_pred             hhcCcccceEEcCCCCccccchhhhcCCCceEEecCcchhhhhccccccccccccccccceeEEecCCCcHHHHHhhccc
Confidence            68888888888888877777544 666777777755442210  00111  233344444 23333212211111   12


Q ss_pred             CCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCC
Q 003387          635 RLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKL  714 (824)
Q Consensus       635 ~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l  714 (824)
                      ...++..+.+.+..  ...........+++|++|++..|    +++.+.-..+..+++|+.|+|.++ +.......|.+|
T Consensus       200 ~~~~~~~l~~~~~l--~~~~~~~l~~~~~~L~~l~L~~n----~i~~I~~~aF~~~~~L~~l~l~~n-i~~I~~~aF~~~  272 (329)
T 3sb4_A          200 QPRDINFLTIEGKL--DNADFKLIRDYMPNLVSLDISKT----NATTIPDFTFAQKKYLLKIKLPHN-LKTIGQRVFSNC  272 (329)
T ss_dssp             CGGGCSEEEEEECC--CHHHHHHHHHHCTTCCEEECTTB----CCCEECTTTTTTCTTCCEEECCTT-CCEECTTTTTTC
T ss_pred             CccccceEEEeeee--cHHHHHHHHHhcCCCeEEECCCC----CcceecHhhhhCCCCCCEEECCcc-cceehHHHhhCC
Confidence            35677888887763  22333333334889999999764    477776666788899999999887 555556678999


Q ss_pred             CCCC-eEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcccee-ccCcccCccEEEE
Q 003387          715 PLLQ-VLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM-GNAAMPKLECLII  771 (824)
Q Consensus       715 ~~L~-~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~-~~~~lp~L~~L~l  771 (824)
                      ++|+ .+.+.+ .+.. .-...+.++++|+.|.+.++. +..++. .+..+++|+.|+.
T Consensus       273 ~~L~~~l~l~~-~l~~-I~~~aF~~c~~L~~l~l~~n~-i~~I~~~aF~~~~~L~~ly~  328 (329)
T 3sb4_A          273 GRLAGTLELPA-SVTA-IEFGAFMGCDNLRYVLATGDK-ITTLGDELFGNGVPSKLIYK  328 (329)
T ss_dssp             TTCCEEEEECT-TCCE-ECTTTTTTCTTEEEEEECSSC-CCEECTTTTCTTCCCCEEEC
T ss_pred             hhccEEEEEcc-cceE-EchhhhhCCccCCEEEeCCCc-cCccchhhhcCCcchhhhcc
Confidence            9999 999985 3321 112345678999999997654 666654 4667888888763

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=98.88  E-value=8.9e-11  Score=115.58  Aligned_cols=112  Identities=21%  Similarity=0.235  Sum_probs=81.6

Q ss_pred             CccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCC
Q 003387          533 LIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCG  612 (824)
Q Consensus       533 i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~  612 (824)
                      ++.+|..++.+++|++|++++|.+..+| .+ .++++|++|++++|.+..+|..+..+++|++|++++|.+..       
T Consensus        37 l~~l~~~~~~l~~L~~L~ls~n~l~~l~-~~-~~l~~L~~L~l~~n~l~~l~~~~~~~~~L~~L~L~~N~l~~-------  107 (198)
T 1ds9_A           37 IEKMDATLSTLKACKHLALSTNNIEKIS-SL-SGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIAS-------  107 (198)
T ss_dssp             CCCCHHHHHHTTTCSEEECSEEEESCCC-CH-HHHTTCCEEEEEEEEECSCSSHHHHHHHCSEEEEEEEECCC-------
T ss_pred             HhhhhHHHhcCCCCCEEECCCCCCcccc-cc-ccCCCCCEEECCCCCcccccchhhcCCcCCEEECcCCcCCc-------
Confidence            3445557888888999999888888888 66 88888999999888888888878888888888888887641       


Q ss_pred             CCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHH--HHhccCCCCCeEEEecc
Q 003387          613 SLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLS--KSLCRLSCLESLKLANE  673 (824)
Q Consensus       613 ~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~--~~l~~l~~L~~L~l~~~  673 (824)
                                      ++. +..+++|+.|+++++.   ...++  ..+..+++|++|++++|
T Consensus       108 ----------------l~~-~~~l~~L~~L~l~~N~---i~~~~~~~~l~~l~~L~~L~l~~N  150 (198)
T 1ds9_A          108 ----------------LSG-IEKLVNLRVLYMSNNK---ITNWGEIDKLAALDKLEDLLLAGN  150 (198)
T ss_dssp             ----------------HHH-HHHHHHSSEEEESEEE---CCCHHHHHHHTTTTTCSEEEECSC
T ss_pred             ----------------CCc-cccCCCCCEEECCCCc---CCchhHHHHHhcCCCCCEEEecCC
Confidence                            223 6677888888888774   22222  35556666666666543

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=98.80  E-value=1e-07  Score=104.29  Aligned_cols=240  Identities=12%  Similarity=0.132  Sum_probs=156.6

Q ss_pred             hcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch-hhhccccCc
Q 003387          517 CGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLR  594 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~  594 (824)
                      +..+..++.+.+.+. ++.++. .+.++ +|+.+.+..+ ++.++...|.++ +|+.+.+.. .+..++. .|.+|++|+
T Consensus       109 ~~~~~~l~~i~ip~~-i~~I~~~aF~~~-~L~~i~l~~~-i~~I~~~aF~~~-~L~~i~lp~-~l~~I~~~aF~~c~~L~  183 (401)
T 4fdw_A          109 TEILKGYNEIILPNS-VKSIPKDAFRNS-QIAKVVLNEG-LKSIGDMAFFNS-TVQEIVFPS-TLEQLKEDIFYYCYNLK  183 (401)
T ss_dssp             EEECSSCSEEECCTT-CCEECTTTTTTC-CCSEEECCTT-CCEECTTTTTTC-CCCEEECCT-TCCEECSSTTTTCTTCC
T ss_pred             EEecCCccEEEECCc-cCEehHhhcccC-CccEEEeCCC-ccEECHHhcCCC-CceEEEeCC-CccEehHHHhhCcccCC
Confidence            334456666666543 444443 34443 6888887665 777777665664 688888875 5666653 477888888


Q ss_pred             eecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC
Q 003387          595 HLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES  674 (824)
Q Consensus       595 ~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~  674 (824)
                      .++++.|.+.  .++                    ...+. +.+|+.+.+...-   ...-...+.++++|+.+.+..  
T Consensus       184 ~l~l~~n~l~--~I~--------------------~~aF~-~~~L~~l~lp~~l---~~I~~~aF~~~~~L~~l~l~~--  235 (401)
T 4fdw_A          184 KADLSKTKIT--KLP--------------------ASTFV-YAGIEEVLLPVTL---KEIGSQAFLKTSQLKTIEIPE--  235 (401)
T ss_dssp             EEECTTSCCS--EEC--------------------TTTTT-TCCCSEEECCTTC---CEECTTTTTTCTTCCCEECCT--
T ss_pred             eeecCCCcce--Eec--------------------hhhEe-ecccCEEEeCCch---heehhhHhhCCCCCCEEecCC--
Confidence            8888776554  122                    11122 3566666665331   111123567889999999864  


Q ss_pred             CCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCC----eeeecCCCCCCccEEeeccC
Q 003387          675 KMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGR----KLTCGSYGFPNLKVLHLKSM  750 (824)
Q Consensus       675 ~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~----~~~~~~~~~~~L~~L~L~~~  750 (824)
                         +++.+.-..+.. .+|+.+.|.++ +.......|.+|++|+.+.+.++.....    .....+.++++|+.+.|.+ 
T Consensus       236 ---~l~~I~~~aF~~-~~L~~i~lp~~-i~~I~~~aF~~c~~L~~l~l~~~~~~~~~~~~I~~~aF~~c~~L~~l~l~~-  309 (401)
T 4fdw_A          236 ---NVSTIGQEAFRE-SGITTVKLPNG-VTNIASRAFYYCPELAEVTTYGSTFNDDPEAMIHPYCLEGCPKLARFEIPE-  309 (401)
T ss_dssp             ---TCCEECTTTTTT-CCCSEEEEETT-CCEECTTTTTTCTTCCEEEEESSCCCCCTTCEECTTTTTTCTTCCEECCCT-
T ss_pred             ---CccCcccccccc-CCccEEEeCCC-ccEEChhHhhCCCCCCEEEeCCccccCCcccEECHHHhhCCccCCeEEeCC-
Confidence               366665444445 68999999554 4444466789999999999987655311    1122356788999999984 


Q ss_pred             CCCcccee-ccCcccCccEEEEecCCCCCCCc-cccccCccCcEEEecCCc
Q 003387          751 LWLEEWTM-GNAAMPKLECLIINPCAYLKKMP-EQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       751 ~~l~~l~~-~~~~lp~L~~L~l~~c~~l~~lp-~~l~~l~~L~~L~l~~c~  799 (824)
                       .+..++. .+..+++|+.+.|..+  ++.++ ..+.++ +|+.|.+.++.
T Consensus       310 -~i~~I~~~aF~~c~~L~~l~lp~~--l~~I~~~aF~~~-~L~~l~l~~n~  356 (401)
T 4fdw_A          310 -SIRILGQGLLGGNRKVTQLTIPAN--VTQINFSAFNNT-GIKEVKVEGTT  356 (401)
T ss_dssp             -TCCEECTTTTTTCCSCCEEEECTT--CCEECTTSSSSS-CCCEEEECCSS
T ss_pred             -ceEEEhhhhhcCCCCccEEEECcc--ccEEcHHhCCCC-CCCEEEEcCCC
Confidence             3666653 4556899999999654  55654 357788 99999998764

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=98.77  E-value=1.2e-08  Score=111.57  Aligned_cols=140  Identities=14%  Similarity=0.064  Sum_probs=97.8

Q ss_pred             CCceechhhHHHHHHHHHc--CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCC--------CceeEEEECCCCCCC-C
Q 003387          156 RDTVGLDDRMEELLDLLIE--GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY--------FDCHAWITEPYSNEY-D  224 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~--~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~--------F~~~~wv~~~vs~~~-~  224 (824)
                      +.++||+.+++++.+++..  .....+.+.|+|++|+||||+|+.+++  +....        ....+|+.  .+... +
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~--~~~~~~~~~~~~~~~~~~~i~--~~~~~~~   95 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFN--EIEEVKKEDEEYKDVKQAYVN--CREVGGT   95 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHH--HHHHHHHHSSSSTTCEEEEEE--HHHHCSC
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHH--HHHHHhhhhcCCCCceEEEEE--CccCCCC
Confidence            6899999999999988865  233466899999999999999999998  33221        23466777  66666 7


Q ss_pred             HHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChhh---HHH-HHhhCCCCCCCcEEEEEec
Q 003387          225 ADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDM---WDV-IQEILPDNQNGSRVLITLT  300 (824)
Q Consensus       225 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~---~~~-l~~~~~~~~~gs~ilvTtR  300 (824)
                      ...++.+++.++.+... + ....+.......+.+.++.++.+|||||++....   .+. +...+... .+..+|+||+
T Consensus        96 ~~~~~~~l~~~l~~~~~-~-~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~  172 (384)
T 2qby_B           96 PQAVLSSLAGKLTGFSV-P-KHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISN  172 (384)
T ss_dssp             HHHHHHHHHHHHHCSCC-C-SSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECS
T ss_pred             HHHHHHHHHHHhcCCCC-C-CCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEEC
Confidence            88889999988843211 0 1223346667788888887766999999976532   222 22222222 6788999998


Q ss_pred             hH
Q 003387          301 DI  302 (824)
Q Consensus       301 ~~  302 (824)
                      ..
T Consensus       173 ~~  174 (384)
T 2qby_B          173 DI  174 (384)
T ss_dssp             ST
T ss_pred             CC
Confidence            65

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=98.68  E-value=7.5e-08  Score=97.60  Aligned_cols=180  Identities=14%  Similarity=0.029  Sum_probs=95.9

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~  234 (824)
                      ..+++|++..++.+.+++..+. ....+.|+|++|+||||+|+.+++  +....+....+.   ....   .. ...+..
T Consensus        22 ~~~~~g~~~~~~~l~~~l~~~~-~~~~~ll~G~~G~GKT~l~~~~~~--~~~~~~~~~~~~---~~~~---~~-~~~~~~   91 (250)
T 1njg_A           22 FADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAK--GLNCETGITATP---CGVC---DN-CREIEQ   91 (250)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHTC-CCSEEEEECSTTSCHHHHHHHHHH--HHHCTTCSCSSC---CSCS---HH-HHHHHT
T ss_pred             HHHHhCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH--HhcCCCCCCCCC---Cccc---HH-HHHHhc
Confidence            3569999999999999997654 234889999999999999999987  333222110000   0000   00 001110


Q ss_pred             HhCCCC-CcccccccCHHHHHHHHHHhc-----CCCeEEEEEecCCC--hhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          235 FLMPSS-RLSEIMDKNYEMKKIILHEYL-----MTKRYLIVIDDVWS--IDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       235 ~l~~~~-~~~~~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~--~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      ...... ..........+.. ..+.+.+     .+++.+||+||++.  ...++.+...+.....+.++|+||+......
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~  170 (250)
T 1njg_A           92 GRFVDLIEIDAASRTKVEDT-RDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLP  170 (250)
T ss_dssp             TCCSSEEEEETTCGGGHHHH-HHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSC
T ss_pred             cCCcceEEecCcccccHHHH-HHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCC
Confidence            000000 0000000111222 2222322     35689999999965  4567777666655556788999987643211


Q ss_pred             -h---------------------cccccCCcCcCccccchhhHHHhcCCCchhHHHHHhHH
Q 003387          307 -S---------------------FQFEDGENMRLDLVPTGGPLRATYKGRPFLILYHGSIS  345 (824)
Q Consensus       307 -~---------------------f~~~~~~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  345 (824)
                       .                     +..........--.+....|++.|+|.|..+..+...+
T Consensus       171 ~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~~~~~~~~~~~  231 (250)
T 1njg_A          171 VTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQA  231 (250)
T ss_dssp             HHHHTTSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHhhhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence             1                     00000000001112345678888889888877655433

>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}

Probab=98.65  E-value=1.4e-08  Score=111.09  Aligned_cols=142  Identities=14%  Similarity=0.137  Sum_probs=95.6

Q ss_pred             CCCceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC---ceeEEEECCCCCCCCHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF---DCHAWITEPYSNEYDADQIL  229 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~~~vs~~~~~~~~~  229 (824)
                      ++.++||+.+++.+.+++...  ......+.|+|++|+||||||+.+++  .....|   ...+|+.  .+...+...++
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~~~i~--~~~~~~~~~~~   94 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLS--KLHKKFLGKFKHVYIN--TRQIDTPYRVL   94 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHH--HHHHHTCSSCEEEEEE--HHHHCSHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHH--HHHHHhcCCceEEEEE--CCCCCCHHHHH
Confidence            478999999999999998752  33467899999999999999999998  444332   2466776  66666777888


Q ss_pred             HHHHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCCh------hhHHHHHhhCCC-CCCCcEEEEEec
Q 003387          230 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSI------DMWDVIQEILPD-NQNGSRVLITLT  300 (824)
Q Consensus       230 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~------~~~~~l~~~~~~-~~~gs~ilvTtR  300 (824)
                      ..++.+++...+   ....+..+....+.+.+.  +++.+||+|+++..      ..+..+...+.. ...+..+|+||+
T Consensus        95 ~~i~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~  171 (386)
T 2qby_A           95 ADLLESLDVKVP---FTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITN  171 (386)
T ss_dssp             HHHTTTTSCCCC---SSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEES
T ss_pred             HHHHHHhCCCCC---CCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEEC
Confidence            888887755322   122334555666666664  45899999999753      233344332211 233556788887


Q ss_pred             hHH
Q 003387          301 DIR  303 (824)
Q Consensus       301 ~~~  303 (824)
                      ...
T Consensus       172 ~~~  174 (386)
T 2qby_A          172 DVK  174 (386)
T ss_dssp             CGG
T ss_pred             CCC
Confidence            654

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=98.59  E-value=6.9e-07  Score=97.80  Aligned_cols=278  Identities=13%  Similarity=0.040  Sum_probs=133.4

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCC----------------
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIP----------------  554 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~----------------  554 (824)
                      |.+|+++.+...-     ..+....|..|++|+.++|..+ ++.++. .+..+..|+.+.+..+                
T Consensus        70 c~~L~~i~lp~~i-----~~I~~~aF~~c~~L~~i~lp~~-l~~I~~~aF~~c~~L~~i~~p~~l~~i~~~aF~~~~~~~  143 (394)
T 4fs7_A           70 CRKVTEIKIPSTV-----REIGEFAFENCSKLEIINIPDS-VKMIGRCTFSGCYALKSILLPLMLKSIGVEAFKGCDFKE  143 (394)
T ss_dssp             CTTEEEEECCTTC-----CEECTTTTTTCTTCCEECCCTT-CCEECTTTTTTCTTCCCCCCCTTCCEECTTTTTTCCCSE
T ss_pred             CCCceEEEeCCCc-----cCcchhHhhCCCCCcEEEeCCC-ceEccchhhcccccchhhcccCceeeecceeeecccccc
Confidence            6677777764321     2244566777777777777544 443332 2444555554443321                


Q ss_pred             -----CCCccChhhhhcCCCccEeecCCccccccch-hhhccccCceecCCCccCCCCCCC--CCCCCCCCCeeeccCCC
Q 003387          555 -----SLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITLPAHPGK--FCGSLENLNFISALHPC  626 (824)
Q Consensus       555 -----~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~~~~~~p--~i~~L~~L~~l~~~~~~  626 (824)
                           .+..+....|.++.+|+.+.+.++ +..++. .+..+.+|+.+++..+ +.  .++  .+.++..|+.+.+....
T Consensus       144 ~~~~~~~~~i~~~aF~~c~~L~~i~l~~~-~~~I~~~~F~~c~~L~~i~l~~~-~~--~I~~~~F~~~~~L~~i~~~~~~  219 (394)
T 4fs7_A          144 ITIPEGVTVIGDEAFATCESLEYVSLPDS-METLHNGLFSGCGKLKSIKLPRN-LK--IIRDYCFAECILLENMEFPNSL  219 (394)
T ss_dssp             EECCTTCCEECTTTTTTCTTCCEEECCTT-CCEECTTTTTTCTTCCBCCCCTT-CC--EECTTTTTTCTTCCBCCCCTTC
T ss_pred             cccCccccccchhhhcccCCCcEEecCCc-cceeccccccCCCCceEEEcCCC-ce--EeCchhhccccccceeecCCCc
Confidence                 112223333466677777776543 334433 3566677777765443 11  122  44555556555554333


Q ss_pred             cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCC
Q 003387          627 CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDD  706 (824)
Q Consensus       627 ~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~  706 (824)
                      ...........+|+.+.+.......   -...+..+..|+.+.+..+     +..+.-..+..++.++.+......+.  
T Consensus       220 ~~i~~~~~~~~~l~~i~ip~~~~~i---~~~~f~~~~~l~~~~~~~~-----~~~i~~~~F~~~~~l~~~~~~~~~i~--  289 (394)
T 4fs7_A          220 YYLGDFALSKTGVKNIIIPDSFTEL---GKSVFYGCTDLESISIQNN-----KLRIGGSLFYNCSGLKKVIYGSVIVP--  289 (394)
T ss_dssp             CEECTTTTTTCCCCEEEECTTCCEE---CSSTTTTCSSCCEEEECCT-----TCEECSCTTTTCTTCCEEEECSSEEC--
T ss_pred             eEeehhhcccCCCceEEECCCceec---ccccccccccceeEEcCCC-----cceeeccccccccccceeccCceeec--
Confidence            2222223344566666654332100   0123445666666666542     22232222344455555554433221  


Q ss_pred             CcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccce-eccCcccCccEEEEecCCCCCCCcc-cc
Q 003387          707 PMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWT-MGNAAMPKLECLIINPCAYLKKMPE-QL  784 (824)
Q Consensus       707 ~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~-~~~~~lp~L~~L~l~~c~~l~~lp~-~l  784 (824)
                       -..+..+.+|+.+.+..+ +.. .-...+.++.+|+.+.|.+  .++.+. ..+..+.+|+.+.+..+  ++.++. .+
T Consensus       290 -~~~F~~~~~L~~i~l~~~-i~~-I~~~aF~~c~~L~~i~lp~--~v~~I~~~aF~~c~~L~~i~lp~~--l~~I~~~aF  362 (394)
T 4fs7_A          290 -EKTFYGCSSLTEVKLLDS-VKF-IGEEAFESCTSLVSIDLPY--LVEEIGKRSFRGCTSLSNINFPLS--LRKIGANAF  362 (394)
T ss_dssp             -TTTTTTCTTCCEEEECTT-CCE-ECTTTTTTCTTCCEECCCT--TCCEECTTTTTTCTTCCEECCCTT--CCEECTTTB
T ss_pred             -cccccccccccccccccc-cce-echhhhcCCCCCCEEEeCC--cccEEhHHhccCCCCCCEEEECcc--ccEehHHHh
Confidence             123455666666666522 110 0011234456666666643  244443 22344566666666433  444432 45


Q ss_pred             ccCccCcEEEec
Q 003387          785 WYIKSLNKFDCW  796 (824)
Q Consensus       785 ~~l~~L~~L~l~  796 (824)
                      .+|++|+.+.+.
T Consensus       363 ~~C~~L~~i~lp  374 (394)
T 4fs7_A          363 QGCINLKKVELP  374 (394)
T ss_dssp             TTCTTCCEEEEE
T ss_pred             hCCCCCCEEEEC
Confidence            666666666664

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=98.59  E-value=6.5e-08  Score=96.59  Aligned_cols=124  Identities=14%  Similarity=0.123  Sum_probs=78.5

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCC-Cc-eeEEEECCCCCCCCHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY-FD-CHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~-~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      ..+++|++..++.+.+++....  ...+.|+|++|+||||+|+.+++  +.... +. ..+.+.  .+.......+...+
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~l~~--~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~   89 (226)
T 2chg_A           16 LDEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALAR--DLFGENWRDNFIEMN--ASDERGIDVVRHKI   89 (226)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTTC--CCCEEEECSTTSSHHHHHHHHHH--HHHGGGGGGGEEEEE--TTCTTCHHHHHHHH
T ss_pred             HHHHcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHH--HHhccccccceEEec--cccccChHHHHHHH
Confidence            3568999999999999998764  33489999999999999999988  43222 22 234444  44433333322222


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                      ........                   .-.+++.+||+||++..  ..++.+...+.....+.++|+||+...
T Consensus        90 ~~~~~~~~-------------------~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~  143 (226)
T 2chg_A           90 KEFARTAP-------------------IGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVS  143 (226)
T ss_dssp             HHHHTSCC-------------------STTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGG
T ss_pred             HHHhcccC-------------------CCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence            21111100                   01257899999999764  345555555444455788999987653

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.57  E-value=6e-08  Score=104.38  Aligned_cols=88  Identities=16%  Similarity=0.087  Sum_probs=58.2

Q ss_pred             hcccCcccEEEeeC-ccCccCC-ccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCc
Q 003387          517 CGMFKLLRVLDLGS-LVLIQYP-SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLR  594 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~-~~i~~lp-~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~  594 (824)
                      +..+++|++|+|++ |.+..+| ..|+.|.+|++|+|++|.+..+|+..|.+|++|+.|+|++|.+..+|..+....+|+
T Consensus        27 l~~~~~L~~L~l~~~n~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~~~L~  106 (347)
T 2ifg_A           27 LPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQ  106 (347)
T ss_dssp             SCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCCSTTTCSCCCC
T ss_pred             CCCCCCeeEEEccCCCCCCCcChhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCCccceeCHHHcccCCce
Confidence            66666777777775 6666555 456667777777777777776666555677777777777777777765544333377


Q ss_pred             eecCCCccCC
Q 003387          595 HLNFGSITLP  604 (824)
Q Consensus       595 ~L~L~~~~~~  604 (824)
                      .|+|.+|.+.
T Consensus       107 ~l~l~~N~~~  116 (347)
T 2ifg_A          107 ELVLSGNPLH  116 (347)
T ss_dssp             EEECCSSCCC
T ss_pred             EEEeeCCCcc
Confidence            7777766654

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.55  E-value=1.3e-08  Score=110.17  Aligned_cols=83  Identities=18%  Similarity=0.228  Sum_probs=40.5

Q ss_pred             CcccEEEeeCccCcc-----CCccCCC-CCcceEEeecCCCCCcc-ChhhhhcCCCccEeecCCccccccc-----hhh-
Q 003387          521 KLLRVLDLGSLVLIQ-----YPSGIEN-LFLLRYLKLNIPSLNSL-PSSLLSNLLNLYTLDMPFSYIDHTA-----DEF-  587 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~-----lp~~i~~-l~~Lr~L~L~~~~i~~l-p~~i~~~L~~L~~L~L~~~~l~~lp-----~~i-  587 (824)
                      +.|+.|+|++|.++.     +...+.. ..+|++|+|++|.+... ...++..+.+|++|+|++|.+....     ..+ 
T Consensus        72 ~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~L~~L~Ls~n~l~~~~~~~L~~~L~  151 (372)
T 3un9_A           72 SSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLL  151 (372)
T ss_dssp             TTCCEEECTTSCCCHHHHHHHHHHHSSCSSCEEEEECTTCCCCHHHHHHTHHHHHTEEEEECCSSCCCHHHHHHHHHHHH
T ss_pred             hhCCEEEecCCCCCHHHHHHHHHHHhhCCCCceEEEecCCCCCHHHHHHHHHHHHhccHhhcCCCCCCHHHHHHHHHHHH
Confidence            456666666666541     2222221 24666666666665421 1222234556666666666554322     111 


Q ss_pred             hccccCceecCCCccC
Q 003387          588 WKMNKLRHLNFGSITL  603 (824)
Q Consensus       588 ~~L~~L~~L~L~~~~~  603 (824)
                      ...++|++|+|++|.+
T Consensus       152 ~~~~~L~~L~Ls~n~l  167 (372)
T 3un9_A          152 HDQCQITTLRLSNNPL  167 (372)
T ss_dssp             STTCCCCEEECCSSCC
T ss_pred             hcCCccceeeCCCCCC
Confidence            1345566666666654

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.55  E-value=1.3e-07  Score=101.78  Aligned_cols=95  Identities=20%  Similarity=0.064  Sum_probs=80.8

Q ss_pred             EEEeeCc-cCccCCccCCCCCcceEEeecC-CCCCccChhhhhcCCCccEeecCCccccccch-hhhccccCceecCCCc
Q 003387          525 VLDLGSL-VLIQYPSGIENLFLLRYLKLNI-PSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSI  601 (824)
Q Consensus       525 ~L~L~~~-~i~~lp~~i~~l~~Lr~L~L~~-~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~  601 (824)
                      .++++++ .++.+|. |+.+.+|++|+|++ |.+..+|+..|++|++|++|+|++|.+..+|. .|.+|++|++|+|++|
T Consensus        12 ~v~~~~~n~l~~ip~-l~~~~~L~~L~l~~~n~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N   90 (347)
T 2ifg_A           12 GLRCTRDGALDSLHH-LPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFN   90 (347)
T ss_dssp             CEECCSSCCCTTTTT-SCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSS
T ss_pred             EEEcCCCCCCCccCC-CCCCCCeeEEEccCCCCCCCcChhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCC
Confidence            4688888 8999999 99999999999996 99999997655999999999999999999875 5899999999999999


Q ss_pred             cCCCCCCC--CCCCCCCCCeeecc
Q 003387          602 TLPAHPGK--FCGSLENLNFISAL  623 (824)
Q Consensus       602 ~~~~~~~p--~i~~L~~L~~l~~~  623 (824)
                      .+.  .+|  .+..+. |+.|++.
T Consensus        91 ~l~--~~~~~~~~~~~-L~~l~l~  111 (347)
T 2ifg_A           91 ALE--SLSWKTVQGLS-LQELVLS  111 (347)
T ss_dssp             CCS--CCCSTTTCSCC-CCEEECC
T ss_pred             ccc--eeCHHHcccCC-ceEEEee
Confidence            987  344  334443 7777766

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.50  E-value=1.6e-08  Score=109.47  Aligned_cols=164  Identities=19%  Similarity=0.200  Sum_probs=97.8

Q ss_pred             CCcceEEeecCCCCCccChhhhhc-----CCCccEeecCCcccccc--chhhhccccCceecCCCccCCCCCCCCCCCCC
Q 003387          543 LFLLRYLKLNIPSLNSLPSSLLSN-----LLNLYTLDMPFSYIDHT--ADEFWKMNKLRHLNFGSITLPAHPGKFCGSLE  615 (824)
Q Consensus       543 l~~Lr~L~L~~~~i~~lp~~i~~~-----L~~L~~L~L~~~~l~~l--p~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~  615 (824)
                      +.+|++|+|++|.+.......+..     ..+|++|+|++|.+...  ..-...+++|++|+|++|.+....        
T Consensus        71 ~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~L~~L~Ls~n~l~~~~--------  142 (372)
T 3un9_A           71 LSSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEA--------  142 (372)
T ss_dssp             HTTCCEEECTTSCCCHHHHHHHHHHHSSCSSCEEEEECTTCCCCHHHHHHTHHHHHTEEEEECCSSCCCHHH--------
T ss_pred             HhhCCEEEecCCCCCHHHHHHHHHHHhhCCCCceEEEecCCCCCHHHHHHHHHHHHhccHhhcCCCCCCHHH--------
Confidence            457999999999988543322233     37999999999987642  222345788999999999775200        


Q ss_pred             CCCeeeccCCCcchhhhc-CCCCccceEEEeccccc--chhhHHHHhccCCCCCeEEEeccCCCCCccEEEe----CccC
Q 003387          616 NLNFISALHPCCCTEDIL-GRLPNLRNLRIRGDLSY--NQSLLSKSLCRLSCLESLKLANESKMPRLSKIVL----AEYL  688 (824)
Q Consensus       616 ~L~~l~~~~~~~~~~~~l-~~l~~L~~L~l~~~~~~--~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l----~~~~  688 (824)
                                ...+...+ ...++|+.|++++|.-.  ....++..+..+++|++|+|++|.    +....+    ..+.
T Consensus       143 ----------~~~L~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~L~~L~Ls~N~----l~~~g~~~L~~~L~  208 (372)
T 3un9_A          143 ----------CKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTG----LGDEGLELLAAQLD  208 (372)
T ss_dssp             ----------HHHHHHHHHSTTCCCCEEECCSSCCHHHHHHHHHHHHHTCSSCCEEECTTSS----CHHHHHHHHHHHGG
T ss_pred             ----------HHHHHHHHHhcCCccceeeCCCCCCChHHHHHHHHHHhcCCCcCEEeCCCCC----CCcHHHHHHHHHHh
Confidence                      11111212 34678899999888521  224456666777778888887652    221110    0113


Q ss_pred             cCCCceEEEEEcccCCCCC----cccccCCCCCCeEEeeccccC
Q 003387          689 FPHSLTHLSFSNTDLMDDP----MPTLEKLPLLQVLKLKQNSYS  728 (824)
Q Consensus       689 ~~~~L~~L~L~~~~l~~~~----~~~l~~l~~L~~L~L~~~~~~  728 (824)
                      .+++|+.|+|++|.+....    ...+..+++|++|+|++|.+.
T Consensus       209 ~~~~L~~L~Ls~N~i~~~g~~~l~~~L~~~~~L~~L~Ls~N~i~  252 (372)
T 3un9_A          209 RNRQLQELNVAYNGAGDTAALALARAAREHPSLELLHLYFNELS  252 (372)
T ss_dssp             GCSCCCEEECCSSCCCHHHHHHHHHHHHHCSSCCEEECTTSSCC
T ss_pred             cCCCcCeEECCCCCCCHHHHHHHHHHHHhCCCCCEEeccCCCCC
Confidence            3456666666666654322    122334566666666666554

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=98.46  E-value=5.4e-08  Score=104.48  Aligned_cols=168  Identities=20%  Similarity=0.203  Sum_probs=106.0

Q ss_pred             cCCCCccceEEEeccccc-------chhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCC
Q 003387          633 LGRLPNLRNLRIRGDLSY-------NQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMD  705 (824)
Q Consensus       633 l~~l~~L~~L~l~~~~~~-------~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~  705 (824)
                      +.++++|+.|.+......       ....+...+..+++|++|.|+++.   .+   .+... ..++|++|+|..|.+..
T Consensus       135 ~~~l~~L~~L~l~~~~~e~~~is~~~~~~L~~ll~~~P~L~~L~L~g~~---~l---~l~~~-~~~~L~~L~L~~~~l~~  207 (362)
T 2ra8_A          135 KEKFAHFEGLFWGDIDFEEQEISWIEQVDLSPVLDAMPLLNNLKIKGTN---NL---SIGKK-PRPNLKSLEIISGGLPD  207 (362)
T ss_dssp             HHHHTTCSEEEECCCCTTTCCGGGCBCCBCHHHHHTCTTCCEEEEECCB---TC---BCCSC-BCTTCSEEEEECSBCCH
T ss_pred             hhhcchhhheeecCcchhhcccccccccCHHHHHhcCCCCcEEEEeCCC---Cc---eeccc-cCCCCcEEEEecCCCCh
Confidence            455677888877554210       122456677788899999998642   11   11221 26789999999887755


Q ss_pred             CCccccc--CCCCCCeEEeec--cccCCCe-e-----eecCCCCCCccEEeeccCCCCccce---eccCcccCccEEEEe
Q 003387          706 DPMPTLE--KLPLLQVLKLKQ--NSYSGRK-L-----TCGSYGFPNLKVLHLKSMLWLEEWT---MGNAAMPKLECLIIN  772 (824)
Q Consensus       706 ~~~~~l~--~l~~L~~L~L~~--~~~~~~~-~-----~~~~~~~~~L~~L~L~~~~~l~~l~---~~~~~lp~L~~L~l~  772 (824)
                      .....++  .+|+|+.|+|+.  +...+.. +     ......||+|++|.|.+|......+   .....+|+|+.|+++
T Consensus       208 ~~l~~l~~~~lp~L~~L~L~~~~~~~~~~~~~~~l~~~l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs  287 (362)
T 2ra8_A          208 SVVEDILGSDLPNLEKLVLYVGVEDYGFDGDMNVFRPLFSKDRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDIS  287 (362)
T ss_dssp             HHHHHHHHSBCTTCCEEEEECBCGGGTCCSCGGGTGGGSCTTTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECC
T ss_pred             HHHHHHHHccCCCCcEEEEeccccccccchhHHHHHHHHhcCCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECC
Confidence            4444444  789999999863  2222211 1     1122468999999998876433221   122468999999998


Q ss_pred             cCCCCC----CCccccccCccCcEEEecCCc--HHHHHHHh
Q 003387          773 PCAYLK----KMPEQLWYIKSLNKFDCWWPQ--PELRQKLR  807 (824)
Q Consensus       773 ~c~~l~----~lp~~l~~l~~L~~L~l~~c~--~~l~~~~~  807 (824)
                      .|....    .++.++.++++|+.|++++|+  .+..+.+.
T Consensus       288 ~n~L~d~G~~~L~~~L~~l~~L~~L~L~~n~i~d~~~~~l~  328 (362)
T 2ra8_A          288 AGVLTDEGARLLLDHVDKIKHLKFINMKYNYLSDEMKKELQ  328 (362)
T ss_dssp             SSCCBHHHHHHHHTTHHHHTTCSEEECCSBBCCHHHHHHHH
T ss_pred             CCCCChHHHHHHHhhcccCCcceEEECCCCcCCHHHHHHHH
Confidence            776332    245566788999999999887  33444443

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.30  E-value=5e-07  Score=95.92  Aligned_cols=123  Identities=15%  Similarity=0.175  Sum_probs=75.9

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC-CCc-eeEEEECCCCCCCCHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFD-CHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~-~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      ..+++|++..++.+.+++..+.  ...+.|+|++|+||||+|+.+++  .+.. .+. ..+++.  .+.......+ +++
T Consensus        20 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~--~l~~~~~~~~~~~~~--~~~~~~~~~i-~~~   92 (323)
T 1sxj_B           20 LSDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHCLAH--ELLGRSYADGVLELN--ASDDRGIDVV-RNQ   92 (323)
T ss_dssp             GGGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHHHHH--HHHGGGHHHHEEEEC--TTSCCSHHHH-HTH
T ss_pred             HHHHHCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHHHHH--HhcCCcccCCEEEec--CccccChHHH-HHH
Confidence            3568999999999999998765  33388999999999999999988  4322 222 244554  4443332222 222


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhc-CCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYL-MTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      +..+....                  ..+ .+++.+||+||++..  ..++.+...+.....++++|+||+..
T Consensus        93 ~~~~~~~~------------------~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~  147 (323)
T 1sxj_B           93 IKHFAQKK------------------LHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  147 (323)
T ss_dssp             HHHHHHBC------------------CCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             HHHHHhcc------------------ccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCCh
Confidence            22211000                  011 356899999999863  34444444433334567888888764

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=98.24  E-value=1.2e-05  Score=87.74  Aligned_cols=262  Identities=11%  Similarity=0.055  Sum_probs=147.8

Q ss_pred             hhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch-----
Q 003387          512 DWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-----  585 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-----  585 (824)
                      +-...|..|.+|+.+.|..+ ++.++. .+.++.+|+.+++..+ ++.++...|.++.+|+.+.+..+ +..+..     
T Consensus        62 Ig~~AF~~c~~L~~i~lp~~-i~~I~~~aF~~c~~L~~i~lp~~-l~~I~~~aF~~c~~L~~i~~p~~-l~~i~~~aF~~  138 (394)
T 4fs7_A           62 IGYAAFQGCRKVTEIKIPST-VREIGEFAFENCSKLEIINIPDS-VKMIGRCTFSGCYALKSILLPLM-LKSIGVEAFKG  138 (394)
T ss_dssp             ECTTTTTTCTTEEEEECCTT-CCEECTTTTTTCTTCCEECCCTT-CCEECTTTTTTCTTCCCCCCCTT-CCEECTTTTTT
T ss_pred             hHHHHhhCCCCceEEEeCCC-ccCcchhHhhCCCCCcEEEeCCC-ceEccchhhcccccchhhcccCc-eeeecceeeec
Confidence            34578899999999999754 666654 4778999999999754 77777777788899988777543 222221     


Q ss_pred             ------------------hhhccccCceecCCCccCCCCCCC--CCCCCCCCCeeeccCCCcc-hhhhcCCCCccceEEE
Q 003387          586 ------------------EFWKMNKLRHLNFGSITLPAHPGK--FCGSLENLNFISALHPCCC-TEDILGRLPNLRNLRI  644 (824)
Q Consensus       586 ------------------~i~~L~~L~~L~L~~~~~~~~~~p--~i~~L~~L~~l~~~~~~~~-~~~~l~~l~~L~~L~l  644 (824)
                                        .|.++++|+.+.+..+..   .++  .+..+.+|+.+.+..+... ....+..+..|+.+.+
T Consensus       139 ~~~~~~~~~~~~~~i~~~aF~~c~~L~~i~l~~~~~---~I~~~~F~~c~~L~~i~l~~~~~~I~~~~F~~~~~L~~i~~  215 (394)
T 4fs7_A          139 CDFKEITIPEGVTVIGDEAFATCESLEYVSLPDSME---TLHNGLFSGCGKLKSIKLPRNLKIIRDYCFAECILLENMEF  215 (394)
T ss_dssp             CCCSEEECCTTCCEECTTTTTTCTTCCEEECCTTCC---EECTTTTTTCTTCCBCCCCTTCCEECTTTTTTCTTCCBCCC
T ss_pred             ccccccccCccccccchhhhcccCCCcEEecCCccc---eeccccccCCCCceEEEcCCCceEeCchhhccccccceeec
Confidence                              133444444444332211   111  3333444444443321111 1111333444444333


Q ss_pred             ecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeec
Q 003387          645 RGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQ  724 (824)
Q Consensus       645 ~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~  724 (824)
                      ......    +.........|+.+.+..     .++.+.-..+..+.+|+.+.+..+.. ......+..++.|+.+.+..
T Consensus       216 ~~~~~~----i~~~~~~~~~l~~i~ip~-----~~~~i~~~~f~~~~~l~~~~~~~~~~-~i~~~~F~~~~~l~~~~~~~  285 (394)
T 4fs7_A          216 PNSLYY----LGDFALSKTGVKNIIIPD-----SFTELGKSVFYGCTDLESISIQNNKL-RIGGSLFYNCSGLKKVIYGS  285 (394)
T ss_dssp             CTTCCE----ECTTTTTTCCCCEEEECT-----TCCEECSSTTTTCSSCCEEEECCTTC-EECSCTTTTCTTCCEEEECS
T ss_pred             CCCceE----eehhhcccCCCceEEECC-----CceecccccccccccceeEEcCCCcc-eeeccccccccccceeccCc
Confidence            222100    001112234455554432     23333333335677888888876532 23345677788888887764


Q ss_pred             cccCCCeeeecCCCCCCccEEeeccCCCCcccee-ccCcccCccEEEEecCCCCCCCcc-ccccCccCcEEEecC
Q 003387          725 NSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM-GNAAMPKLECLIINPCAYLKKMPE-QLWYIKSLNKFDCWW  797 (824)
Q Consensus       725 ~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~-~~~~lp~L~~L~l~~c~~l~~lp~-~l~~l~~L~~L~l~~  797 (824)
                      ..+..    .....+++|+.+.+.+.  +..+.. .+..+++|+.+.|...  ++.++. .+.+|++|+.+.+..
T Consensus       286 ~~i~~----~~F~~~~~L~~i~l~~~--i~~I~~~aF~~c~~L~~i~lp~~--v~~I~~~aF~~c~~L~~i~lp~  352 (394)
T 4fs7_A          286 VIVPE----KTFYGCSSLTEVKLLDS--VKFIGEEAFESCTSLVSIDLPYL--VEEIGKRSFRGCTSLSNINFPL  352 (394)
T ss_dssp             SEECT----TTTTTCTTCCEEEECTT--CCEECTTTTTTCTTCCEECCCTT--CCEECTTTTTTCTTCCEECCCT
T ss_pred             eeecc----ccccccccccccccccc--cceechhhhcCCCCCCEEEeCCc--ccEEhHHhccCCCCCCEEEECc
Confidence            33221    12456789999998653  565543 3556889999998643  555643 577889999988743

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=98.16  E-value=8.6e-07  Score=83.53  Aligned_cols=87  Identities=10%  Similarity=0.090  Sum_probs=49.1

Q ss_pred             CceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCC----CCCccEEeeccCCCCccce-eccCcccCc
Q 003387          692 SLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYG----FPNLKVLHLKSMLWLEEWT-MGNAAMPKL  766 (824)
Q Consensus       692 ~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~----~~~L~~L~L~~~~~l~~l~-~~~~~lp~L  766 (824)
                      +|++|++++|.++......+.++++|+.|+|++|...++.-...+..    .++|++|+|++|..++.-. ..+..+|+|
T Consensus        62 ~L~~LDLs~~~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~~~L  141 (176)
T 3e4g_A           62 KIQAIDATDSCIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGIIALHHFRNL  141 (176)
T ss_dssp             CEEEEEEESCCCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGCTTC
T ss_pred             eEeEEeCcCCCccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHHHHhcCCCC
Confidence            57777777777666656666677777777777664322211111222    2356666666666555321 123456666


Q ss_pred             cEEEEecCCCCC
Q 003387          767 ECLIINPCAYLK  778 (824)
Q Consensus       767 ~~L~l~~c~~l~  778 (824)
                      +.|+|++|+.++
T Consensus       142 ~~L~L~~c~~It  153 (176)
T 3e4g_A          142 KYLFLSDLPGVK  153 (176)
T ss_dssp             CEEEEESCTTCC
T ss_pred             CEEECCCCCCCC
Confidence            666666666554

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.14  E-value=6.9e-06  Score=85.56  Aligned_cols=111  Identities=10%  Similarity=0.051  Sum_probs=76.8

Q ss_pred             CceechhhHHHHHHHHHcC--CCCeEEEEEEcCCCChHHHHHHHHhCCccccC--------CCceeEEEECCCCCCCCHH
Q 003387          157 DTVGLDDRMEELLDLLIEG--PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH--------YFDCHAWITEPYSNEYDAD  226 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~--~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~--------~F~~~~wv~~~vs~~~~~~  226 (824)
                      .+.|||+++++|...|...  ......+-|+|++|.|||++|+.|.+  +...        .| .++.|.  ...-.+..
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~--~L~~~~~~~~~~~~-~~v~IN--c~~~~t~~   95 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMD--ELITSSARKELPIF-DYIHID--ALELAGMD   95 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHH--HHHHTTTTTSSCCE-EEEEEE--TTCCC--H
T ss_pred             ccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHH--HHHHHhhhccCCce-EEEEEe--ccccCCHH
Confidence            4789999999999888752  34567889999999999999999998  4422        12 345565  66777888


Q ss_pred             HHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhc---CCCeEEEEEecCCCh
Q 003387          227 QILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYL---MTKRYLIVIDDVWSI  276 (824)
Q Consensus       227 ~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L---~~kr~LlVlDdv~~~  276 (824)
                      .+...|++++.+...   ......+.+. .+.+.+   ++++++++||+++..
T Consensus        96 ~~~~~I~~~L~g~~~---~~~~~~~~L~-~~f~~~~~~~~~~~ii~lDE~d~l  144 (318)
T 3te6_A           96 ALYEKIWFAISKENL---CGDISLEALN-FYITNVPKAKKRKTLILIQNPENL  144 (318)
T ss_dssp             HHHHHHHHHHSCCC-----CCCCHHHHH-HHHHHSCGGGSCEEEEEEECCSSS
T ss_pred             HHHHHHHHHhcCCCC---CchHHHHHHH-HHHHHhhhccCCceEEEEecHHHh
Confidence            999999999976421   1112223333 333333   457899999999864

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=98.07  E-value=0.00012  Score=79.77  Aligned_cols=283  Identities=12%  Similarity=0.028  Sum_probs=159.1

Q ss_pred             ceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCcc---CccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCC
Q 003387          494 QLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLV---LIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLN  569 (824)
Q Consensus       494 ~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~---i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~  569 (824)
                      .|+++.+...-     ..+-...|..|.+|+.+.+..+.   ++.++. .+..+.+|+.+.+.. .+..++...|..+.+
T Consensus        65 ~L~sI~iP~sv-----t~Ig~~AF~~C~~L~~i~~~~n~p~~l~~Ig~~aF~~c~~L~~i~~~~-~~~~I~~~aF~~c~~  138 (394)
T 4gt6_A           65 VLTSVQIPDTV-----TEIGSNAFYNCTSLKRVTIQDNKPSCVKKIGRQAFMFCSELTDIPILD-SVTEIDSEAFHHCEE  138 (394)
T ss_dssp             CCCEEEECTTC-----CEECTTTTTTCTTCCEEEEGGGCCCCCCEECTTTTTTCTTCCBCGGGT-TCSEECTTTTTTCTT
T ss_pred             cCEEEEECCCe-----eEEhHHHhhCCccCceEeecCCCCCeeeEechhhchhcccceeeccCC-ccceehhhhhhhhcc
Confidence            47777775432     22445778888888888887653   555543 356677777776654 366666666678888


Q ss_pred             ccEeecCCccccccch-hhhccccCceecCCCccCCCCCCC--CCCCCCCCCeeeccCCCc-chhhhcCCCCccceEEEe
Q 003387          570 LYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITLPAHPGK--FCGSLENLNFISALHPCC-CTEDILGRLPNLRNLRIR  645 (824)
Q Consensus       570 L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~~~~~~p--~i~~L~~L~~l~~~~~~~-~~~~~l~~l~~L~~L~l~  645 (824)
                      |+.+.+... +..++. .+..+.+|+.+.+..+-.   .+.  .+. ...|..+.+..... .-...+..+.+|......
T Consensus       139 L~~i~lp~~-~~~I~~~~F~~c~~L~~i~~~~~~~---~I~~~aF~-~~~l~~i~ip~~~~~i~~~af~~c~~l~~~~~~  213 (394)
T 4gt6_A          139 LDTVTIPEG-VTSVADGMFSYCYSLHTVTLPDSVT---AIEERAFT-GTALTQIHIPAKVTRIGTNAFSECFALSTITSD  213 (394)
T ss_dssp             CCEEECCTT-CCEECTTTTTTCTTCCEEECCTTCC---EECTTTTT-TCCCSEEEECTTCCEECTTTTTTCTTCCEEEEC
T ss_pred             cccccccce-eeeecccceecccccccccccceee---Eecccccc-ccceeEEEECCcccccccchhhhccccceeccc
Confidence            888888543 444443 366778888886654311   111  222 23466666552211 112225556666665554


Q ss_pred             cccccchhhH-H----------HHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCC
Q 003387          646 GDLSYNQSLL-S----------KSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKL  714 (824)
Q Consensus       646 ~~~~~~~~~l-~----------~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l  714 (824)
                      .......... .          ........+..+.+     +..++...-..+..+.+|+.+.+..... ......+.++
T Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i-----p~~v~~i~~~aF~~c~~L~~i~lp~~~~-~I~~~aF~~c  287 (394)
T 4gt6_A          214 SESYPAIDNVLYEKSANGDYALIRYPSQREDPAFKI-----PNGVARIETHAFDSCAYLASVKMPDSVV-SIGTGAFMNC  287 (394)
T ss_dssp             CSSSCBSSSCEEEECTTSCEEEEECCTTCCCSEEEC-----CTTEEEECTTTTTTCSSCCEEECCTTCC-EECTTTTTTC
T ss_pred             ccccccccceeecccccccccccccccccccceEEc-----CCcceEcccceeeecccccEEecccccc-eecCcccccc
Confidence            3321000000 0          00000111222221     1233333333345677888888765431 2234467788


Q ss_pred             CCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcccee-ccCcccCccEEEEecCCCCCCCcc-ccccCccCcE
Q 003387          715 PLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM-GNAAMPKLECLIINPCAYLKKMPE-QLWYIKSLNK  792 (824)
Q Consensus       715 ~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~-~~~~lp~L~~L~l~~c~~l~~lp~-~l~~l~~L~~  792 (824)
                      ++|+.+.+. +.+.. .-...+.++.+|+.+.|.+  .++.+.. .+..+.+|+.+.|-.+  ++.++. .+.+|++|+.
T Consensus       288 ~~L~~i~l~-~~i~~-I~~~aF~~c~~L~~i~lp~--~v~~I~~~aF~~C~~L~~i~ip~s--v~~I~~~aF~~C~~L~~  361 (394)
T 4gt6_A          288 PALQDIEFS-SRITE-LPESVFAGCISLKSIDIPE--GITQILDDAFAGCEQLERIAIPSS--VTKIPESAFSNCTALNN  361 (394)
T ss_dssp             TTCCEEECC-TTCCE-ECTTTTTTCTTCCEEECCT--TCCEECTTTTTTCTTCCEEEECTT--CCBCCGGGGTTCTTCCE
T ss_pred             cccccccCC-Ccccc-cCceeecCCCCcCEEEeCC--cccEehHhHhhCCCCCCEEEECcc--cCEEhHhHhhCCCCCCE
Confidence            889988886 32221 1112345678899988864  2555542 3556789999998643  556654 5788999999


Q ss_pred             EEecCCc
Q 003387          793 FDCWWPQ  799 (824)
Q Consensus       793 L~l~~c~  799 (824)
                      +.+.+..
T Consensus       362 i~~~~~~  368 (394)
T 4gt6_A          362 IEYSGSR  368 (394)
T ss_dssp             EEESSCH
T ss_pred             EEECCce
Confidence            9998876

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=98.07  E-value=4.4e-06  Score=89.56  Aligned_cols=84  Identities=21%  Similarity=0.250  Sum_probs=37.8

Q ss_pred             CCCccceEEEecccccchhhHHHHh---ccCCCCCeEEEeccCCCCCccEEE----eCccCcCCCceEEEEEcccCCCCC
Q 003387          635 RLPNLRNLRIRGDLSYNQSLLSKSL---CRLSCLESLKLANESKMPRLSKIV----LAEYLFPHSLTHLSFSNTDLMDDP  707 (824)
Q Consensus       635 ~l~~L~~L~l~~~~~~~~~~l~~~l---~~l~~L~~L~l~~~~~~~~L~~l~----l~~~~~~~~L~~L~L~~~~l~~~~  707 (824)
                      .+++|+.|++.+|.  .....+..+   ..+++|++|+|+.|.    +..-.    ..+...+++|+.|+|++|.++...
T Consensus       250 ~~p~Lr~L~L~~~~--i~~~~~~~la~a~~~~~L~~LdLs~n~----L~d~G~~~L~~~L~~l~~L~~L~L~~n~i~d~~  323 (362)
T 2ra8_A          250 RFPNLKWLGIVDAE--EQNVVVEMFLESDILPQLETMDISAGV----LTDEGARLLLDHVDKIKHLKFINMKYNYLSDEM  323 (362)
T ss_dssp             TCTTCCEEEEESCT--THHHHHHHHHHCSSGGGCSEEECCSSC----CBHHHHHHHHTTHHHHTTCSEEECCSBBCCHHH
T ss_pred             CCCCcCEEeCCCCC--CchHHHHHHHhCccCCCCCEEECCCCC----CChHHHHHHHhhcccCCcceEEECCCCcCCHHH
Confidence            35566666666553  111111111   234566666665431    22110    111134566777777777654433


Q ss_pred             cccccC-CCCCCeEEeeccc
Q 003387          708 MPTLEK-LPLLQVLKLKQNS  726 (824)
Q Consensus       708 ~~~l~~-l~~L~~L~L~~~~  726 (824)
                      ...+.. +  ...++++++.
T Consensus       324 ~~~l~~al--g~~~~~~~~~  341 (362)
T 2ra8_A          324 KKELQKSL--PMKIDVSDSQ  341 (362)
T ss_dssp             HHHHHHHC--CSEEECCSBC
T ss_pred             HHHHHHHc--CCEEEecCCc
Confidence            333332 2  2345555443

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.06  E-value=6e-06  Score=79.89  Aligned_cols=45  Identities=16%  Similarity=0.245  Sum_probs=39.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...++|+++.++++.+.+..+.  ...+.|+|++|+||||+|+.+++
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~~~~   65 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQ   65 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHH
T ss_pred             ccccccchHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999987744  45678999999999999999988

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=98.03  E-value=3.2e-06  Score=81.63  Aligned_cols=118  Identities=12%  Similarity=0.079  Sum_probs=83.7

Q ss_pred             hhHhhhcccCcccEEEeeCc-cCc-----cCCccCCCCCcceEEeecCCCCCc-----cChhhhhcCCCccEeecCCccc
Q 003387          512 DWEKFCGMFKLLRVLDLGSL-VLI-----QYPSGIENLFLLRYLKLNIPSLNS-----LPSSLLSNLLNLYTLDMPFSYI  580 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~-~i~-----~lp~~i~~l~~Lr~L~L~~~~i~~-----lp~~i~~~L~~L~~L~L~~~~l  580 (824)
                      .+...+...+.|++|+|++| .+.     .+...+...++|++|+|++|.+..     +...+ ...++|++|+|++|.+
T Consensus        27 ~l~~~l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L-~~n~~L~~L~L~~N~i  105 (185)
T 1io0_A           27 TLKRIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEML-KVNNTLKSLNVESNFI  105 (185)
T ss_dssp             HHHHHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHH-HHCSSCCEEECCSSCC
T ss_pred             HHHHHHhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHH-HhCCCcCEEECcCCcC
Confidence            45567788889999999998 775     455666777889999999988873     44444 6678899999998877


Q ss_pred             cc-----cchhhhccccCceecC--CCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccc
Q 003387          581 DH-----TADEFWKMNKLRHLNF--GSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       581 ~~-----lp~~i~~L~~L~~L~L--~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      ..     +...+...++|++|++  ++|.+...                  ....+.+.+...++|++|+++++.
T Consensus       106 ~~~g~~~l~~~L~~n~~L~~L~L~~~~N~i~~~------------------g~~~l~~~L~~n~~L~~L~L~~n~  162 (185)
T 1io0_A          106 SGSGILALVEALQSNTSLIELRIDNQSQPLGNN------------------VEMEIANMLEKNTTLLKFGYHFTQ  162 (185)
T ss_dssp             CHHHHHHHHHGGGGCSSCCEEECCCCSSCCCHH------------------HHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             CHHHHHHHHHHHHhCCCceEEEecCCCCCCCHH------------------HHHHHHHHHHhCCCcCEEeccCCC
Confidence            64     4566777788888888  66766410                  011223335666788888888775

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=97.97  E-value=4.5e-06  Score=88.67  Aligned_cols=119  Identities=14%  Similarity=0.140  Sum_probs=74.4

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCC-Cc-eeEEEECCCCCCCCHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY-FD-CHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~-~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      .+++|++..++.+.+++..+.  ...+.|+|++|+||||+|+.+++  .+... +. ..+.+.  .+.......+ .+.+
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~l~~--~l~~~~~~~~~~~~~--~~~~~~~~~~-~~~~   97 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALAR--ELFGENWRHNFLELN--ASDERGINVI-REKV   97 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHH--HHHGGGHHHHEEEEE--TTCHHHHHTT-HHHH
T ss_pred             HHhhCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHHHHH--HhcCCcccCceEEee--ccccCchHHH-HHHH
Confidence            569999999999999998764  33489999999999999999998  43222 11 233444  3321111111 1111


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHh--c-CCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEY--L-MTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~--L-~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      .                     .....  + .+++.+||+||++..  ..++.+...+.....++++|+||...
T Consensus        98 ~---------------------~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~  150 (327)
T 1iqp_A           98 K---------------------EFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYS  150 (327)
T ss_dssp             H---------------------HHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             H---------------------HHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCc
Confidence            1                     11110  1 257889999999764  45555655554445578888888764

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.95  E-value=2.9e-06  Score=81.94  Aligned_cols=112  Identities=10%  Similarity=0.007  Sum_probs=86.5

Q ss_pred             CCceeEeeccCC-CCCCCCcchhHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCCc-----cC
Q 003387          492 DSQLHSLLCCSP-ETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLNS-----LP  560 (824)
Q Consensus       492 ~~~Lr~L~l~~~-~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~~-----lp  560 (824)
                      .+.|++|.+.++ .........+...+...+.|++|+|++|.+.     .+...+...++|++|+|++|.|..     +.
T Consensus        35 ~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N~i~~~g~~~l~  114 (185)
T 1io0_A           35 DPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSGILALV  114 (185)
T ss_dssp             CTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHHHHHHH
T ss_pred             CCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcCEEECcCCcCCHHHHHHHH
Confidence            788999999887 5532111245567778899999999999986     345556667899999999999884     55


Q ss_pred             hhhhhcCCCccEeec--CCccccc-----cchhhhccccCceecCCCccCC
Q 003387          561 SSLLSNLLNLYTLDM--PFSYIDH-----TADEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       561 ~~i~~~L~~L~~L~L--~~~~l~~-----lp~~i~~L~~L~~L~L~~~~~~  604 (824)
                      ..+ ...++|++|+|  ++|.+..     +...+...++|++|++++|.+.
T Consensus       115 ~~L-~~n~~L~~L~L~~~~N~i~~~g~~~l~~~L~~n~~L~~L~L~~n~i~  164 (185)
T 1io0_A          115 EAL-QSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHFTQQG  164 (185)
T ss_dssp             HGG-GGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCCSSHH
T ss_pred             HHH-HhCCCceEEEecCCCCCCCHHHHHHHHHHHHhCCCcCEEeccCCCCC
Confidence            555 78889999999  7787764     4556777899999999988763

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=97.89  E-value=2.7e-06  Score=90.31  Aligned_cols=47  Identities=19%  Similarity=0.210  Sum_probs=38.4

Q ss_pred             CCCceechhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|++..++.+.+++...   ......+.|+|+.|+||||+|+.+++
T Consensus        11 ~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~   60 (324)
T 1hqc_A           11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAH   60 (324)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHH
T ss_pred             HHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHH
Confidence            467999999999988887631   22346788999999999999999988

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.81  E-value=9.8e-06  Score=77.97  Aligned_cols=45  Identities=18%  Similarity=0.213  Sum_probs=38.7

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -..++|++..++.+.+.+....  ...+.|+|..|+||||+|+.+.+
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~--~~~vll~G~~G~GKT~la~~~~~   65 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRRT--KNNPILLGDPGVGKTAIVEGLAI   65 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSS--SCEEEEESCGGGCHHHHHHHHHH
T ss_pred             cchhhcchHHHHHHHHHHhCCC--CCceEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999997643  45668999999999999999987

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=97.80  E-value=1e-05  Score=76.17  Aligned_cols=84  Identities=10%  Similarity=0.046  Sum_probs=65.2

Q ss_pred             CCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcccee-ccCc----ccCccEEEEecCCCCCCC-ccccccCc
Q 003387          715 PLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM-GNAA----MPKLECLIINPCAYLKKM-PEQLWYIK  788 (824)
Q Consensus       715 ~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~-~~~~----lp~L~~L~l~~c~~l~~l-p~~l~~l~  788 (824)
                      .+|+.|++++|.++...+. .+.++++|++|+|++|..++.... .+..    .++|+.|+|++|+.++.- -..+.+++
T Consensus        61 ~~L~~LDLs~~~Itd~GL~-~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~~  139 (176)
T 3e4g_A           61 YKIQAIDATDSCIMSIGFD-HMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKGIIALHHFR  139 (176)
T ss_dssp             CCEEEEEEESCCCCGGGGG-GGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGCT
T ss_pred             ceEeEEeCcCCCccHHHHH-HhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHHHHHHhcCC
Confidence            4799999999987664443 357899999999999998876532 1223    368999999999987641 12466789


Q ss_pred             cCcEEEecCCc
Q 003387          789 SLNKFDCWWPQ  799 (824)
Q Consensus       789 ~L~~L~l~~c~  799 (824)
                      +|+.|++++||
T Consensus       140 ~L~~L~L~~c~  150 (176)
T 3e4g_A          140 NLKYLFLSDLP  150 (176)
T ss_dssp             TCCEEEEESCT
T ss_pred             CCCEEECCCCC
Confidence            99999999998

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.77  E-value=1.8e-05  Score=82.12  Aligned_cols=49  Identities=18%  Similarity=0.213  Sum_probs=39.7

Q ss_pred             CCCCCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..-++++|.+..+++|.+.+...           -...+-+.|+|++|+||||+|+.+++
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~   73 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVAT   73 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            34568999999999998887531           12355689999999999999999988

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=97.69  E-value=0.00038  Score=75.82  Aligned_cols=303  Identities=10%  Similarity=0.049  Sum_probs=171.5

Q ss_pred             CeeEEEEEecCCCccccc-cc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCc-cCCCCCcce
Q 003387          472 KAKRLNAVEREGDFACLD-DY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPS-GIENLFLLR  547 (824)
Q Consensus       472 ~~r~lsl~~~~~~~~~~~-~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr  547 (824)
                      .++.+.+. +.... +.. ..  |.+|+++.+..+.... ...+....|..|..|+.+.+..+ ++.++. .+..+.+|+
T Consensus        65 ~L~sI~iP-~svt~-Ig~~AF~~C~~L~~i~~~~n~p~~-l~~Ig~~aF~~c~~L~~i~~~~~-~~~I~~~aF~~c~~L~  140 (394)
T 4gt6_A           65 VLTSVQIP-DTVTE-IGSNAFYNCTSLKRVTIQDNKPSC-VKKIGRQAFMFCSELTDIPILDS-VTEIDSEAFHHCEELD  140 (394)
T ss_dssp             CCCEEEEC-TTCCE-ECTTTTTTCTTCCEEEEGGGCCCC-CCEECTTTTTTCTTCCBCGGGTT-CSEECTTTTTTCTTCC
T ss_pred             cCEEEEEC-CCeeE-EhHHHhhCCccCceEeecCCCCCe-eeEechhhchhcccceeeccCCc-cceehhhhhhhhcccc
Confidence            36667666 43322 322 22  8999999887643211 12345678889999988777654 444443 467789999


Q ss_pred             EEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC-
Q 003387          548 YLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC-  626 (824)
Q Consensus       548 ~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~-  626 (824)
                      .+.+.. .+..++...|..+.+|+.+.+..+ +..+........+|+.+.+..+...- ....+..+.+|......... 
T Consensus       141 ~i~lp~-~~~~I~~~~F~~c~~L~~i~~~~~-~~~I~~~aF~~~~l~~i~ip~~~~~i-~~~af~~c~~l~~~~~~~~~~  217 (394)
T 4gt6_A          141 TVTIPE-GVTSVADGMFSYCYSLHTVTLPDS-VTAIEERAFTGTALTQIHIPAKVTRI-GTNAFSECFALSTITSDSESY  217 (394)
T ss_dssp             EEECCT-TCCEECTTTTTTCTTCCEEECCTT-CCEECTTTTTTCCCSEEEECTTCCEE-CTTTTTTCTTCCEEEECCSSS
T ss_pred             cccccc-eeeeecccceecccccccccccce-eeEeccccccccceeEEEECCccccc-ccchhhhccccceeccccccc
Confidence            999964 456677766789999999999654 55555443345678888665432210 11144555555555433110 


Q ss_pred             cchhhh--------------cCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCC
Q 003387          627 CCTEDI--------------LGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHS  692 (824)
Q Consensus       627 ~~~~~~--------------l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~  692 (824)
                      ......              ......+..+.+...   ....-...+.++..|+.+.+..     ++..+.-..+..+++
T Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ip~~---v~~i~~~aF~~c~~L~~i~lp~-----~~~~I~~~aF~~c~~  289 (394)
T 4gt6_A          218 PAIDNVLYEKSANGDYALIRYPSQREDPAFKIPNG---VARIETHAFDSCAYLASVKMPD-----SVVSIGTGAFMNCPA  289 (394)
T ss_dssp             CBSSSCEEEECTTSCEEEEECCTTCCCSEEECCTT---EEEECTTTTTTCSSCCEEECCT-----TCCEECTTTTTTCTT
T ss_pred             ccccceeecccccccccccccccccccceEEcCCc---ceEcccceeeecccccEEeccc-----ccceecCcccccccc
Confidence            000000              111122233322211   0011123456778888888753     344443344466788


Q ss_pred             ceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccce-eccCcccCccEEEE
Q 003387          693 LTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWT-MGNAAMPKLECLII  771 (824)
Q Consensus       693 L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~-~~~~~lp~L~~L~l  771 (824)
                      |+.+.+... +.......|.+|.+|+.+.|..+ +.. .-...+.++.+|+.+.|...  +..+. ..+..+++|+.+++
T Consensus       290 L~~i~l~~~-i~~I~~~aF~~c~~L~~i~lp~~-v~~-I~~~aF~~C~~L~~i~ip~s--v~~I~~~aF~~C~~L~~i~~  364 (394)
T 4gt6_A          290 LQDIEFSSR-ITELPESVFAGCISLKSIDIPEG-ITQ-ILDDAFAGCEQLERIAIPSS--VTKIPESAFSNCTALNNIEY  364 (394)
T ss_dssp             CCEEECCTT-CCEECTTTTTTCTTCCEEECCTT-CCE-ECTTTTTTCTTCCEEEECTT--CCBCCGGGGTTCTTCCEEEE
T ss_pred             cccccCCCc-ccccCceeecCCCCcCEEEeCCc-ccE-ehHhHhhCCCCCCEEEECcc--cCEEhHhHhhCCCCCCEEEE
Confidence            888888543 33333456888999999999743 211 11123467789999999642  55553 34667899999999


Q ss_pred             ecCCCCCCCccccccCccCcEEEecC
Q 003387          772 NPCAYLKKMPEQLWYIKSLNKFDCWW  797 (824)
Q Consensus       772 ~~c~~l~~lp~~l~~l~~L~~L~l~~  797 (824)
                      .++...   ...+..+.+|+.+.+..
T Consensus       365 ~~~~~~---~~~~~~~~~L~~i~i~~  387 (394)
T 4gt6_A          365 SGSRSQ---WNAISTDSGLQNLPVAP  387 (394)
T ss_dssp             SSCHHH---HHTCBCCCCC-------
T ss_pred             CCceee---hhhhhccCCCCEEEeCC
Confidence            876421   13455667788777643

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.66  E-value=3.4e-05  Score=78.34  Aligned_cols=81  Identities=20%  Similarity=0.075  Sum_probs=62.8

Q ss_pred             hhhcccCcccEEEeeCccCccC---CccCCCCCcceEEeecCCCCCccChhhhhcCC--CccEeecCCccccc-cc----
Q 003387          515 KFCGMFKLLRVLDLGSLVLIQY---PSGIENLFLLRYLKLNIPSLNSLPSSLLSNLL--NLYTLDMPFSYIDH-TA----  584 (824)
Q Consensus       515 ~~~~~~~~Lr~L~L~~~~i~~l---p~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~--~L~~L~L~~~~l~~-lp----  584 (824)
                      .....++.|++|+|++|.+..+   |..+..+++|++|+|++|.+..+ ..+ ..+.  +|++|+|++|.+.. +|    
T Consensus       164 i~~~~l~~L~~L~Ls~N~l~~l~~l~~~~~~l~~L~~L~Ls~N~i~~~-~~l-~~l~~l~L~~L~L~~Npl~~~~~~~~~  241 (267)
T 3rw6_A          164 IIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSE-REL-DKIKGLKLEELWLDGNSLCDTFRDQST  241 (267)
T ss_dssp             HHHHHCTTCCEEECTTSCCCCCGGGTTHHHHSTTCCEEECTTSCCCSG-GGG-GGGTTSCCSEEECTTSTTGGGCSSHHH
T ss_pred             HHHhhCCCCCEEECCCCCCCCCccchhHHhhCCCCCEEECCCCccCCc-hhh-hhcccCCcceEEccCCcCccccCcchh
Confidence            3446788999999999998754   45667899999999999999877 334 5565  89999999997763 33    


Q ss_pred             ---hhhhccccCceec
Q 003387          585 ---DEFWKMNKLRHLN  597 (824)
Q Consensus       585 ---~~i~~L~~L~~L~  597 (824)
                         ..+..+++|+.||
T Consensus       242 y~~~il~~~P~L~~LD  257 (267)
T 3rw6_A          242 YISAIRERFPKLLRLD  257 (267)
T ss_dssp             HHHHHHHHCTTCCEES
T ss_pred             HHHHHHHHCcccCeEC
Confidence               2367889999985

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.62  E-value=8e-05  Score=68.48  Aligned_cols=46  Identities=11%  Similarity=0.016  Sum_probs=35.7

Q ss_pred             CceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          157 DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +++|+...+.++.+.+..-.....-|-|+|..|+|||++|+.+++.
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~   47 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQF   47 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHS
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHh
Confidence            5789999999999988642222334679999999999999999984

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.61  E-value=3.1e-05  Score=74.20  Aligned_cols=116  Identities=13%  Similarity=0.120  Sum_probs=61.9

Q ss_pred             chhhHHHHHHHHHcCC-CCeEEEEEEcCCCChHHHHHHHHhCCcccc--CCCceeEEEECCCCCCCCHHHHHHHHHHHhC
Q 003387          161 LDDRMEELLDLLIEGP-PQLSVVAILDSIGLDKTAFAGEAYNSSYVK--HYFDCHAWITEPYSNEYDADQILDIVIKFLM  237 (824)
Q Consensus       161 r~~~~~~l~~~L~~~~-~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~--~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~  237 (824)
                      .+...+.+.+++..-. ..-..+.|+|+.|+||||||+.+++  ...  ..+ .+++++        ..++...+.....
T Consensus        19 ~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~--~~~~~~g~-~~~~~~--------~~~~~~~~~~~~~   87 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLK--AIYEKKGI-RGYFFD--------TKDLIFRLKHLMD   87 (180)
T ss_dssp             HHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHH--HHHHHSCC-CCCEEE--------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHH--HHHHHcCC-eEEEEE--------HHHHHHHHHHHhc
Confidence            3344444555554322 2357899999999999999999998  432  111 233443        3445555444432


Q ss_pred             CCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCC--hhhHH--HHHhhCCC-CCCCcEEEEEech
Q 003387          238 PSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWS--IDMWD--VIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~--~~~~~--~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                      ....         ......+.     +.-+|||||++.  .+.|.  .+...+.. ...|..+|+||..
T Consensus        88 ~~~~---------~~~~~~~~-----~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~  142 (180)
T 3ec2_A           88 EGKD---------TKFLKTVL-----NSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNY  142 (180)
T ss_dssp             HTCC---------SHHHHHHH-----TCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCC
T ss_pred             CchH---------HHHHHHhc-----CCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCC
Confidence            2111         11222221     456899999983  33332  22222211 1246778888854

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=97.57  E-value=0.00019  Score=77.47  Aligned_cols=45  Identities=22%  Similarity=0.196  Sum_probs=38.5

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|++..++.+.+.+..+. ....+.|+|+.|+||||+|+.+.+
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~-~~~~~ll~G~~G~GKT~la~~la~   60 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAK   60 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTC-CCSEEEEESCTTSSHHHHHHHHHH
T ss_pred             hhccCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            469999999999999997654 234778999999999999999877

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=97.51  E-value=0.00013  Score=74.51  Aligned_cols=48  Identities=17%  Similarity=0.148  Sum_probs=36.9

Q ss_pred             CCCCceechhhHHHHHHHHHc---CC-------CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE---GP-------PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~---~~-------~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-++++|.+..++.+.+++..   .+       ...+-+.|+|++|+||||+|+.+.+
T Consensus         4 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~   61 (262)
T 2qz4_A            4 SFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT   61 (262)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            346789999888888766532   11       2345678999999999999999998

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=97.50  E-value=4e-05  Score=80.90  Aligned_cols=120  Identities=14%  Similarity=0.133  Sum_probs=74.2

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccc-cCCCc-eeEEEECCCCCCCCHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYV-KHYFD-CHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~-~~~F~-~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      .+++|++..++.+.+++..+.  ...+.++|++|+||||+|+.+.+  .+ ...+. ..+.+.  .+.......      
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~--~l~~~~~~~~~~~~~--~~~~~~~~~------   84 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALAR--DLFGENWRDNFIEMN--ASDERGIDV------   84 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTTC--CCCEEEESSSSSSHHHHHHHHHH--HHHTTCHHHHCEEEE--TTSTTCTTT------
T ss_pred             HHHhCCHHHHHHHHHHHhCCC--CCeEEEECcCCcCHHHHHHHHHH--HhcCCcccCCeEEEe--CccccChHH------
Confidence            568999999999988887654  33489999999999999999987  33 12222 233444  333211000      


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHh--c-CCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEY--L-MTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~--L-~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                                      ...........  + .+++.++|+||+...  ...+.+...+.....+.++|+||....
T Consensus        85 ----------------~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~  143 (319)
T 2chq_A           85 ----------------VRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVS  143 (319)
T ss_dssp             ----------------SSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGG
T ss_pred             ----------------HHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence                            01111111111  1 256889999999754  345666666665556788888886543

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=97.49  E-value=0.00018  Score=76.06  Aligned_cols=120  Identities=14%  Similarity=0.117  Sum_probs=74.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~  234 (824)
                      -++++|.+..++.+.+++..+. ...++-+.|+.|+||||+|+.+.+  ...   ...+.+.  .+.. ....+ ++++.
T Consensus        25 ~~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~--~l~---~~~~~i~--~~~~-~~~~i-~~~~~   94 (324)
T 3u61_B           25 IDECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCH--DVN---ADMMFVN--GSDC-KIDFV-RGPLT   94 (324)
T ss_dssp             TTTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHH--HTT---EEEEEEE--TTTC-CHHHH-HTHHH
T ss_pred             HHHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHH--HhC---CCEEEEc--cccc-CHHHH-HHHHH
Confidence            3679999999999999998654 235778889999999999999988  432   2344555  4432 22222 22111


Q ss_pred             HhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChh---hHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          235 FLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSID---MWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       235 ~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~---~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                      ......                   ...+++-+|++||+....   ..+.+...+.....+.++|+||....
T Consensus        95 ~~~~~~-------------------~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~  147 (324)
T 3u61_B           95 NFASAA-------------------SFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNID  147 (324)
T ss_dssp             HHHHBC-------------------CCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGG
T ss_pred             HHHhhc-------------------ccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCcc
Confidence            110000                   012478899999998653   34444443333234567888876643

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.46  E-value=0.00014  Score=76.32  Aligned_cols=45  Identities=13%  Similarity=0.082  Sum_probs=35.7

Q ss_pred             CceechhhHHHHHHHHHcC-------------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          157 DTVGLDDRMEELLDLLIEG-------------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~-------------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.+..++.|.+++...             ......+.|+|.+|+|||++|+.+.+
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~   89 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAG   89 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            5889999988888766421             23456789999999999999998877

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.41  E-value=0.00011  Score=67.44  Aligned_cols=47  Identities=15%  Similarity=0.074  Sum_probs=34.0

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.++|.+..++++.+.+..-.....-|-|+|..|+|||++|+.+++.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            46789999999988887642111234679999999999999999983

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=97.38  E-value=0.00018  Score=75.94  Aligned_cols=48  Identities=23%  Similarity=0.245  Sum_probs=38.8

Q ss_pred             CCCCceechhhHHHHHHHHHc----------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE----------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-++++|.+..++.|.+.+..          .....+-|-++|++|+|||+||+++.+
T Consensus        16 ~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~   73 (322)
T 3eie_A           16 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVAT   73 (322)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHH
T ss_pred             CHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            346899999999999888731          122346789999999999999999998

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=97.35  E-value=0.00054  Score=70.37  Aligned_cols=47  Identities=19%  Similarity=0.140  Sum_probs=36.4

Q ss_pred             CCCceechhhHHHHHHH-------HHc-CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDL-------LIE-GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~-------L~~-~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...++|.+..+++++..       +.. .......+-|+|+.|+|||++|+.+.+
T Consensus        32 ~~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~   86 (272)
T 1d2n_A           32 MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAE   86 (272)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             hcCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHH
Confidence            35688888887777763       322 234577899999999999999999998

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.33  E-value=0.00088  Score=70.55  Aligned_cols=49  Identities=22%  Similarity=0.277  Sum_probs=38.9

Q ss_pred             CCCCCceechhhHHHHHHHHHc---------C-CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE---------G-PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~---------~-~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.-++++|.+..++.|.+.+..         + ....+-|-++|++|+|||+||+++.+
T Consensus         9 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~   67 (322)
T 1xwi_A            9 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVAT   67 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHH
Confidence            3446899999999998887742         1 12346788999999999999999998

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.32  E-value=0.00033  Score=68.35  Aligned_cols=51  Identities=14%  Similarity=0.067  Sum_probs=36.0

Q ss_pred             hHHHHHHHHHcCCCC--eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          164 RMEELLDLLIEGPPQ--LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~--~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .++.+.+++......  ...+.|+|.+|+||||||+.+++  ........++|++
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~--~~~~~~~~~~~~~   89 (202)
T 2w58_A           37 AIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIAN--ELAKRNVSSLIVY   89 (202)
T ss_dssp             HHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHH--HHHTTTCCEEEEE
T ss_pred             HHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHH--HHHHcCCeEEEEE
Confidence            445555666544221  26889999999999999999998  5544445667776

>4h09_A Hypothetical leucine rich repeat protein; two LRR_5 domains, PF13306 family, structural genomics, JOIN for structural genomics, JCSG; 2.50A {Eubacterium ventriosum}

Probab=97.25  E-value=0.0035  Score=67.64  Aligned_cols=77  Identities=9%  Similarity=0.029  Sum_probs=38.9

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCcc-CCCCCcceEEeecCCCCCccChhhhhcCCCc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSG-IENLFLLRYLKLNIPSLNSLPSSLLSNLLNL  570 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~-i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L  570 (824)
                      ..+++++.+...-     ..+....|..|.+|+.+.|..+ ++.++.. +.++ .|..+.+.. .+..++...|.. .+|
T Consensus        45 ~~~i~~v~ip~~v-----t~Ig~~aF~~C~~L~~I~lp~~-v~~Ig~~aF~~c-~l~~i~~~~-~l~~I~~~aF~~-~~L  115 (379)
T 4h09_A           45 RDRISEVRVNSGI-----TSIGEANFNSCYNMTKVTVAST-VTSIGDGAFADT-KLQSYTGME-RVKKFGDYVFQG-TDL  115 (379)
T ss_dssp             GGGCSEEEECTTE-----EEECTTTTTTCTTCCEEEECTT-CCEECTTTTTTC-CCCEEEECT-TCCEECTTTTTT-CCC
T ss_pred             ccCCEEEEeCCCc-----cChHHHHhhCCCCCCEEEeCCc-ceEechhhhcCC-CCceEECCc-eeeEeccceecc-CCc
Confidence            4455665554321     1234456677777777777543 4444433 3333 455555432 345555544333 356


Q ss_pred             cEeecCC
Q 003387          571 YTLDMPF  577 (824)
Q Consensus       571 ~~L~L~~  577 (824)
                      +.+.+..
T Consensus       116 ~~i~lp~  122 (379)
T 4h09_A          116 DDFEFPG  122 (379)
T ss_dssp             SEEECCT
T ss_pred             ccccCCC
Confidence            6666643

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=97.24  E-value=8.3e-05  Score=74.74  Aligned_cols=57  Identities=9%  Similarity=0.050  Sum_probs=38.7

Q ss_pred             CCceec---hhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          156 RDTVGL---DDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       156 ~~~vGr---~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      +.++|.   +...+.+..+...+  ....+.|+|++|+||||+|+.+.+  ........+.|+.
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~--~~~~~~~~~~~~~   87 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACA--RANELERRSFYIP   87 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHH--HHHHcCCeEEEEE
Confidence            456663   34455555555543  356788999999999999999988  4443334566776

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=97.22  E-value=0.00048  Score=75.90  Aligned_cols=121  Identities=18%  Similarity=0.233  Sum_probs=67.7

Q ss_pred             Cce-echhh--HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCc--eeEEEECCCCCCCCHHHHHHH
Q 003387          157 DTV-GLDDR--MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD--CHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       157 ~~v-Gr~~~--~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      .++ |....  ...+......... ...+.|+|.+|+||||||+.+++  .....|.  .+++++        ...+..+
T Consensus       106 ~fv~g~~n~~a~~~~~~~a~~~~~-~~~lll~Gp~G~GKTtLa~aia~--~l~~~~~~~~v~~v~--------~~~~~~~  174 (440)
T 2z4s_A          106 NFVVGPGNSFAYHAALEVAKHPGR-YNPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYIT--------SEKFLND  174 (440)
T ss_dssp             GCCCCTTTHHHHHHHHHHHHSTTS-SCCEEEECSSSSSHHHHHHHHHH--HHHHHCCSSCEEEEE--------HHHHHHH
T ss_pred             hcCCCCchHHHHHHHHHHHhCCCC-CCeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEee--------HHHHHHH
Confidence            444 64433  3334444433332 67889999999999999999998  5544432  234554        2234444


Q ss_pred             HHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCChh----hHHHHHhhCCC-CCCCcEEEEEech
Q 003387          232 VIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSID----MWDVIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~----~~~~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                      +...+...         .    ...+.+.+..+.-+|++||+....    ..+.+...+.. ...|..||+||..
T Consensus       175 ~~~~~~~~---------~----~~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          175 LVDSMKEG---------K----LNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             HHHHHHTT---------C----HHHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             HHHHHHcc---------c----HHHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            54444321         1    112333444466799999996432    22333333221 2346789998875

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.22  E-value=0.00024  Score=72.03  Aligned_cols=62  Identities=27%  Similarity=0.228  Sum_probs=47.5

Q ss_pred             CCCCcceEEeecCCCCCccC---hhhhhcCCCccEeecCCccccccchhhhccc--cCceecCCCccCC
Q 003387          541 ENLFLLRYLKLNIPSLNSLP---SSLLSNLLNLYTLDMPFSYIDHTADEFWKMN--KLRHLNFGSITLP  604 (824)
Q Consensus       541 ~~l~~Lr~L~L~~~~i~~lp---~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~--~L~~L~L~~~~~~  604 (824)
                      .++++|++|+|++|.+..++   ..+ .++++|++|+|++|.+..+. .+..+.  +|+.|+|++|.+.
T Consensus       167 ~~l~~L~~L~Ls~N~l~~l~~l~~~~-~~l~~L~~L~Ls~N~i~~~~-~l~~l~~l~L~~L~L~~Npl~  233 (267)
T 3rw6_A          167 ENIPELLSLNLSNNRLYRLDDMSSIV-QKAPNLKILNLSGNELKSER-ELDKIKGLKLEELWLDGNSLC  233 (267)
T ss_dssp             HHCTTCCEEECTTSCCCCCGGGTTHH-HHSTTCCEEECTTSCCCSGG-GGGGGTTSCCSEEECTTSTTG
T ss_pred             hhCCCCCEEECCCCCCCCCccchhHH-hhCCCCCEEECCCCccCCch-hhhhcccCCcceEEccCCcCc
Confidence            35778999999998887654   444 78899999999988888773 355555  8888888888765

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=97.21  E-value=0.0012  Score=68.78  Aligned_cols=48  Identities=29%  Similarity=0.256  Sum_probs=39.0

Q ss_pred             CCCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-++++|.+..+++|.+++..           +-...+.|.|+|++|.||||||+.+.+
T Consensus        13 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~   71 (301)
T 3cf0_A           13 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN   71 (301)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHH
Confidence            345799999999988887753           123356789999999999999999998

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=97.19  E-value=0.00031  Score=75.28  Aligned_cols=48  Identities=10%  Similarity=0.076  Sum_probs=38.9

Q ss_pred             CCCCceechhhHHHHHHHHHc----------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE----------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+++|.+..++.|.+.+..          .....+.|.|+|+.|+||||+|+.+.+
T Consensus        82 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~  139 (357)
T 3d8b_A           82 NWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIAS  139 (357)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHH
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHH
Confidence            345799999999999888753          112356788999999999999999988

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.17  E-value=0.0027  Score=68.22  Aligned_cols=47  Identities=28%  Similarity=0.232  Sum_probs=37.6

Q ss_pred             CCCceechhhHHH---HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEE---LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~---l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+.++|++..++.   +.+.+..+....+.+-|+|++|+|||++|+.+.+
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~   92 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQ   92 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            4579999988776   4555555543346889999999999999999998

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.04  E-value=0.0011  Score=70.78  Aligned_cols=44  Identities=9%  Similarity=-0.051  Sum_probs=35.6

Q ss_pred             CCceechhhHHHHHHHH-HcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLL-IEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L-~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.+..++.+.+++ ..+. ... +.|+|+.|+||||+|+.+.+
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~~-~~~-~ll~Gp~G~GKTtl~~~la~   58 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPRD-LPH-LLLYGPNGTGKKTRCMALLE   58 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTTC-CCC-EEEECSTTSSHHHHHHTHHH
T ss_pred             HHhcCCHHHHHHHHHHHhhCCC-CCe-EEEECCCCCCHHHHHHHHHH
Confidence            56889999998888887 4433 223 89999999999999998766

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.03  E-value=0.00037  Score=76.75  Aligned_cols=45  Identities=18%  Similarity=0.203  Sum_probs=38.3

Q ss_pred             CCCceechhhH---HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRM---EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~---~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+..+   ..+...+..+.  ...+.|+|.+|+||||+|+.+.+
T Consensus        25 l~~ivGq~~~~~~~~~L~~~i~~~~--~~~vLL~GppGtGKTtlAr~ia~   72 (447)
T 3pvs_A           25 LAQYIGQQHLLAAGKPLPRAIEAGH--LHSMILWGPPGTGKTTLAEVIAR   72 (447)
T ss_dssp             TTTCCSCHHHHSTTSHHHHHHHHTC--CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHhCCcHHHHhchHHHHHHHHcCC--CcEEEEECCCCCcHHHHHHHHHH
Confidence            35789988888   67777887765  57789999999999999999998

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=97.03  E-value=0.00066  Score=72.58  Aligned_cols=48  Identities=23%  Similarity=0.231  Sum_probs=37.9

Q ss_pred             CCCCceechhhHHHHHHHHHcC----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIEG----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+++|.+..++.|.+.+...          ....+-|-++|++|+|||+||+++++
T Consensus        49 ~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~  106 (355)
T 2qp9_X           49 KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVAT  106 (355)
T ss_dssp             CGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHH
Confidence            3467999999999998877421          12234578999999999999999998

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=97.03  E-value=0.00055  Score=73.23  Aligned_cols=45  Identities=16%  Similarity=0.079  Sum_probs=38.6

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|++..++.+..++..+.  ...+.|+|+.|+||||+|+.+.+
T Consensus        36 ~~~i~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~la~   80 (353)
T 1sxj_D           36 LDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILALTK   80 (353)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHhcCC--CCEEEEECCCCCCHHHHHHHHHH
Confidence            3579999999999999987764  22388999999999999999988

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=97.03  E-value=0.00089  Score=68.41  Aligned_cols=47  Identities=19%  Similarity=0.181  Sum_probs=34.5

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +.++|.+..+.++.+.+..-.....-|-|+|..|+|||++|+.+++.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHT
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            46889999999988877652222345779999999999999999983

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.02  E-value=0.00093  Score=72.51  Aligned_cols=48  Identities=21%  Similarity=0.185  Sum_probs=38.7

Q ss_pred             CCCCceechhhHHHHHHHHHcC----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIEG----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+++|.+..++.|.+++...          ....+-|-|+|..|+|||++|+.+.+
T Consensus       113 ~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~  170 (389)
T 3vfd_A          113 KFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAA  170 (389)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHH
T ss_pred             ChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            3468999999999999887321          11246789999999999999999987

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=96.98  E-value=0.0015  Score=68.83  Aligned_cols=113  Identities=15%  Similarity=0.092  Sum_probs=59.7

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCccc
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSE  244 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~  244 (824)
                      ...+..++.........+.|+|++|+||||||+.+++  .....-..+++++  .      .++..++...+...     
T Consensus        23 ~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~--~~~~~~~~~~~i~--~------~~~~~~~~~~~~~~-----   87 (324)
T 1l8q_A           23 YEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGN--EAKKRGYRVIYSS--A------DDFAQAMVEHLKKG-----   87 (324)
T ss_dssp             HHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHH--HHHHTTCCEEEEE--H------HHHHHHHHHHHHHT-----
T ss_pred             HHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHH--HHHHCCCEEEEEE--H------HHHHHHHHHHHHcC-----
Confidence            3445555544433456789999999999999999998  3322111234444  2      23334444333211     


Q ss_pred             ccccCHHHHHHHHHHhcCCCeEEEEEecCCChh---h-HHHHHhhCCC-CCCCcEEEEEech
Q 003387          245 IMDKNYEMKKIILHEYLMTKRYLIVIDDVWSID---M-WDVIQEILPD-NQNGSRVLITLTD  301 (824)
Q Consensus       245 ~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~---~-~~~l~~~~~~-~~~gs~ilvTtR~  301 (824)
                          .....    .+.+ .+.-+|++||+....   . .+.+...+.. ...|.+||+||..
T Consensus        88 ----~~~~~----~~~~-~~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~  140 (324)
T 1l8q_A           88 ----TINEF----RNMY-KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDR  140 (324)
T ss_dssp             ----CHHHH----HHHH-HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             ----cHHHH----HHHh-cCCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecC
Confidence                11111    1222 235699999996542   1 2233322221 1235678888763

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.93  E-value=0.0017  Score=73.22  Aligned_cols=47  Identities=15%  Similarity=0.125  Sum_probs=39.8

Q ss_pred             CCCceechhhHHHHHHHHHcCC---------------CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGP---------------PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~---------------~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|++..++++.+++....               +..+.+.|+|++|+||||+|+.+.+
T Consensus        38 ~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~   99 (516)
T 1sxj_A           38 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQ   99 (516)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3679999999999999997510               1347899999999999999999998

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=96.92  E-value=0.0014  Score=68.22  Aligned_cols=48  Identities=19%  Similarity=0.181  Sum_probs=38.8

Q ss_pred             CCCCceechhhHHHHHHHHHcC----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIEG----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-++++|.+..++.+.+++...          ....+.+.|+|++|+||||+|+.+.+
T Consensus        19 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~   76 (297)
T 3b9p_A           19 EWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVAT   76 (297)
T ss_dssp             CGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHH
T ss_pred             CHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHH
Confidence            3467999999999998887431          11246789999999999999999998

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=96.91  E-value=0.0012  Score=72.84  Aligned_cols=49  Identities=20%  Similarity=0.225  Sum_probs=39.1

Q ss_pred             CCCCCceechhhHHHHHHHHHc----------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE----------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.-++++|.+..++.|.+.+..          .....+-|-++|++|+|||+||+.+++
T Consensus       131 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~  189 (444)
T 2zan_A          131 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVAT  189 (444)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            3446799999999999887731          112346788999999999999999998

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.81  E-value=0.00071  Score=62.28  Aligned_cols=36  Identities=11%  Similarity=-0.009  Sum_probs=26.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      -..++|+|..|+|||||++.+++  .....=..++++.
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~--~~~~~g~~~~~~~   71 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVA--QALEAGKNAAYID   71 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHH--HHHTTTCCEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH--HHHhcCCcEEEEc
Confidence            46899999999999999999998  3322111256666

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.76  E-value=0.0016  Score=69.24  Aligned_cols=44  Identities=16%  Similarity=0.198  Sum_probs=37.0

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.+..++.+...+..+.  ...+.++|+.|+||||+|+.+.+
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g~--~~~~ll~Gp~G~GKTtla~~la~   68 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALAR   68 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHH
T ss_pred             HHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHH
Confidence            467898888888888887764  33389999999999999999988

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.75  E-value=0.00094  Score=69.99  Aligned_cols=46  Identities=20%  Similarity=0.317  Sum_probs=37.4

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.+..++.+...+...       ......+.++|..|+||||+|+.+.+
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~   69 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA   69 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHH
Confidence            35779999988888887653       11246899999999999999999988

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=96.70  E-value=0.00032  Score=71.90  Aligned_cols=48  Identities=21%  Similarity=0.275  Sum_probs=36.4

Q ss_pred             CCCCceechhhHHHHHHHHHc----------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE----------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-++++|.+..++.+.+.+..          +....+-+.|+|++|+|||++|+.+++
T Consensus         9 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   66 (268)
T 2r62_A            9 RFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAG   66 (268)
T ss_dssp             CSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHH
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHH
Confidence            346799999998888876652          111123367999999999999999998

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=96.66  E-value=0.0019  Score=71.79  Aligned_cols=44  Identities=16%  Similarity=0.283  Sum_probs=37.9

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|++..++++++.|....  ..-+-++|.+|+||||+|+.+.+
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~--~~~~LL~G~pG~GKT~la~~la~  223 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRT--KNNPVLIGEPGVGKTAIAEGLAQ  223 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSS--SCEEEEESCTTTTTHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhccC--CCCeEEECCCCCCHHHHHHHHHH
Confidence            579999999999999997644  33457999999999999999987

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=96.64  E-value=0.0019  Score=77.68  Aligned_cols=45  Identities=16%  Similarity=0.310  Sum_probs=38.6

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++||+.+++++++.|....  ..-+.++|.+|+||||+|+.+.+
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~--~~~vlL~G~pG~GKT~la~~la~  213 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRT--KNNPVLIGEPGVGKTAIVEGLAQ  213 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSS--CCCCEEEECTTSCHHHHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHH
Confidence            3578999999999999997754  33468999999999999999987

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=96.64  E-value=0.0031  Score=65.65  Aligned_cols=46  Identities=22%  Similarity=0.221  Sum_probs=37.2

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.++|....+.++.+.+..-.....-|-|+|..|+|||++|+.+++
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~   47 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHA   47 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHH
Confidence            4688999999999998876322234567999999999999999988

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=96.64  E-value=0.0048  Score=60.68  Aligned_cols=90  Identities=11%  Similarity=0.025  Sum_probs=53.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC-------ccc-ccccC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR-------LSE-IMDKN  249 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~-------~~~-~~~~~  249 (824)
                      .-.++.|+|.+|+||||||..+..  .   .-..++|++  ....++..++.+ +.+..+....       ... ....+
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~--~---~~~~v~~i~--~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL--L---SGKKVAYVD--TEGGFSPERLVQ-MAETRGLNPEEALSRFILFTPSDFKE   90 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH--H---HCSEEEEEE--SSCCCCHHHHHH-HHHTTTCCHHHHHHHEEEECCTTTSH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--H---cCCcEEEEE--CCCCCCHHHHHH-HHHhcCCChHHHhhcEEEEecCCHHH
Confidence            356899999999999999999877  1   124678888  666556655543 3333322100       000 01111


Q ss_pred             HHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          250 YEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       250 ~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      ..+....++..++.+.-+||+|.+-.
T Consensus        91 ~~~~~~~~~~l~~~~~~lliiD~~~~  116 (220)
T 2cvh_A           91 QRRVIGSLKKTVDSNFALVVVDSITA  116 (220)
T ss_dssp             HHHHHHHHHHHCCTTEEEEEEECCCC
T ss_pred             HHHHHHHHHHHhhcCCCEEEEcCcHH
Confidence            23344555556554577999999854

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=96.62  E-value=0.0026  Score=70.18  Aligned_cols=48  Identities=19%  Similarity=0.212  Sum_probs=35.8

Q ss_pred             CCCCceechhhHHHHHHHHHc---C-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE---G-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~---~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+++|.++.++++.+.+..   .       ..-.+-|.++|++|.||||||+.+.+
T Consensus        14 ~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~   71 (476)
T 2ce7_A           14 TFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAG   71 (476)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CHHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            346799999888777766532   1       11123477999999999999999998

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=96.54  E-value=0.0025  Score=64.67  Aligned_cols=48  Identities=25%  Similarity=0.231  Sum_probs=35.6

Q ss_pred             CCCCceechhhHHHHHHHHH---cC-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLI---EG-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~---~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-++++|.+..++++.+.+.   ..       ....+-+.|+|..|+||||+|+.+.+
T Consensus        10 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   67 (257)
T 1lv7_A           10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG   67 (257)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHH
Confidence            34679999988887766543   21       01133478999999999999999998

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=96.53  E-value=0.0057  Score=72.63  Aligned_cols=44  Identities=18%  Similarity=0.225  Sum_probs=38.1

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++||+.+++++++.|....  ..-+.++|.+|+||||+|+.+.+
T Consensus       186 d~~iGr~~~i~~l~~~l~~~~--~~~vlL~G~~GtGKT~la~~la~  229 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhccC--CCCeEEEcCCCCCHHHHHHHHHH
Confidence            578999999999999987654  34567999999999999999987

>4h09_A Hypothetical leucine rich repeat protein; two LRR_5 domains, PF13306 family, structural genomics, JOIN for structural genomics, JCSG; 2.50A {Eubacterium ventriosum}

Probab=96.44  E-value=0.031  Score=60.13  Aligned_cols=277  Identities=9%  Similarity=-0.002  Sum_probs=121.5

Q ss_pred             CCeeEEEEEecCCCcccccc-c--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcce
Q 003387          471 KKAKRLNAVEREGDFACLDD-Y--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLR  547 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~~~~~~-~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr  547 (824)
                      .+++.+.+. ..... +.+. .  |.+|+++.+...-     ..+....|..+ .|..+.+..+ ++.++.......+|+
T Consensus        46 ~~i~~v~ip-~~vt~-Ig~~aF~~C~~L~~I~lp~~v-----~~Ig~~aF~~c-~l~~i~~~~~-l~~I~~~aF~~~~L~  116 (379)
T 4h09_A           46 DRISEVRVN-SGITS-IGEANFNSCYNMTKVTVASTV-----TSIGDGAFADT-KLQSYTGMER-VKKFGDYVFQGTDLD  116 (379)
T ss_dssp             GGCSEEEEC-TTEEE-ECTTTTTTCTTCCEEEECTTC-----CEECTTTTTTC-CCCEEEECTT-CCEECTTTTTTCCCS
T ss_pred             cCCEEEEeC-CCccC-hHHHHhhCCCCCCEEEeCCcc-----eEechhhhcCC-CCceEECCce-eeEeccceeccCCcc
Confidence            345666665 32222 3322 2  7889998885432     22445677777 4666665433 555554443445788


Q ss_pred             EEeecCCCCCccChhhhhcCCCccEeecCCccccccc-hhhhccccCceecCCCccCCC----------C-CCC-CCCCC
Q 003387          548 YLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSITLPA----------H-PGK-FCGSL  614 (824)
Q Consensus       548 ~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~~~~----------~-~~p-~i~~L  614 (824)
                      .+.+..+ +..+....|.+. +|..+.+..+ +..+. ..+..+.+|....+..+....          . ... .+...
T Consensus       117 ~i~lp~~-~~~i~~~~F~~~-~l~~~~~~~~-v~~i~~~~f~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  193 (379)
T 4h09_A          117 DFEFPGA-TTEIGNYIFYNS-SVKRIVIPKS-VTTIKDGIGYKAENLEKIEVSSNNKNYVAENYVLYNKNKTILESYPAA  193 (379)
T ss_dssp             EEECCTT-CCEECTTTTTTC-CCCEEEECTT-CCEECSCTTTTCTTCCEEEECTTCSSEEEETTEEEETTSSEEEECCTT
T ss_pred             cccCCCc-cccccccccccc-eeeeeeccce-eeccccchhcccccccccccccccceeecccceecccccceecccccc
Confidence            8887653 444444443333 4444444322 22222 224455555555443321110          0 000 12222


Q ss_pred             CCCCeeeccCCC-cchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCc
Q 003387          615 ENLNFISALHPC-CCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSL  693 (824)
Q Consensus       615 ~~L~~l~~~~~~-~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L  693 (824)
                      ..+..+.+.... ......+..+.+|+.+.+....   ...-...+.++..|+.+.+..     +++.+.-..+..+.+|
T Consensus       194 ~~~~~~~~~~~~~~i~~~~f~~~~~l~~i~~~~~~---~~i~~~~f~~~~~L~~i~lp~-----~v~~I~~~aF~~~~~l  265 (379)
T 4h09_A          194 KTGTEFTIPSTVKTVTAYGFSYGKNLKKITITSGV---TTLGDGAFYGMKALDEIAIPK-----NVTSIGSFLLQNCTAL  265 (379)
T ss_dssp             CCCSEEECCTTCCEECTTTTTTCSSCSEEECCTTC---CEECTTTTTTCSSCCEEEECT-----TCCEECTTTTTTCTTC
T ss_pred             ccccccccccceeEEeecccccccccceeeeccce---eEEccccccCCccceEEEcCC-----CccEeCccccceeehh
Confidence            333333333111 1111114445556665554321   111112344556666666543     2343333333445555


Q ss_pred             eEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcccee-ccCcccCccEEEE
Q 003387          694 THLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM-GNAAMPKLECLII  771 (824)
Q Consensus       694 ~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~-~~~~lp~L~~L~l  771 (824)
                      +.+.+..+ +.......+.++++|+.+.+.++.+.. .-...+.++.+|+.+.|.+  .++.+.. .+..+++|+.+.+
T Consensus       266 ~~i~l~~~-i~~i~~~aF~~c~~L~~i~l~~~~i~~-I~~~aF~~c~~L~~i~lp~--~l~~I~~~aF~~C~~L~~i~i  340 (379)
T 4h09_A          266 KTLNFYAK-VKTVPYLLCSGCSNLTKVVMDNSAIET-LEPRVFMDCVKLSSVTLPT--ALKTIQVYAFKNCKALSTISY  340 (379)
T ss_dssp             CEEEECCC-CSEECTTTTTTCTTCCEEEECCTTCCE-ECTTTTTTCTTCCEEECCT--TCCEECTTTTTTCTTCCCCCC
T ss_pred             cccccccc-ceeccccccccccccccccccccccce-ehhhhhcCCCCCCEEEcCc--cccEEHHHHhhCCCCCCEEEE
Confidence            55555432 122223345556666666665333221 0011233455566665542  1333321 2334455555544

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=96.34  E-value=0.0026  Score=70.68  Aligned_cols=47  Identities=15%  Similarity=0.137  Sum_probs=38.3

Q ss_pred             CCCceechhhHHHHHHHHHcC-----------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEG-----------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|.+..+++|.+++...           ....+-|-|+|.+|.|||++|+++.+
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~  260 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN  260 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHH
Confidence            356899999999998877532           23345688999999999999999988

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=96.34  E-value=0.018  Score=60.87  Aligned_cols=39  Identities=15%  Similarity=0.123  Sum_probs=29.6

Q ss_pred             hhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          162 DDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       162 ~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++..+.+.+.+..+. -...+-++|+.|+||||+|+.+.+
T Consensus         8 ~~~~~~l~~~i~~~~-~~~a~L~~G~~G~GKt~~a~~la~   46 (334)
T 1a5t_A            8 RPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSR   46 (334)
T ss_dssp             HHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCC-cceeEEEECCCCchHHHHHHHHHH
Confidence            455666777766543 245788999999999999998866

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=96.33  E-value=0.015  Score=60.41  Aligned_cols=118  Identities=13%  Similarity=0.056  Sum_probs=69.9

Q ss_pred             echhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCc-cccCCCceeEEEECCCCC-CCCHHHHHHHHHHHhC
Q 003387          160 GLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSS-YVKHYFDCHAWITEPYSN-EYDADQILDIVIKFLM  237 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~-~~~~~F~~~~wv~~~vs~-~~~~~~~~~~i~~~l~  237 (824)
                      |-++.++.+.+.+..+.  ....-++|+.|+||||+|+.+.+.. .....+....++.  .+. ...+.++ +++.+.+.
T Consensus         1 g~~~~~~~L~~~i~~~~--~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~--~~~~~~~id~i-r~li~~~~   75 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEID--PEGENIGIDDI-RTIKDFLN   75 (305)
T ss_dssp             ---CHHHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEEC--CSSSCBCHHHH-HHHHHHHT
T ss_pred             ChHHHHHHHHHHHHCCC--CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEc--CCcCCCCHHHH-HHHHHHHh
Confidence            34556677777777665  6788899999999999999997621 0111122334554  432 3343333 33444443


Q ss_pred             CCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          238 PSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      ...                    ..+++-++|+|++...  ...+.+...+....+.+.+|++|.+.
T Consensus        76 ~~p--------------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~  122 (305)
T 2gno_A           76 YSP--------------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  122 (305)
T ss_dssp             SCC--------------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             hcc--------------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECCh
Confidence            211                    1246678899999754  45566665555445567777777554

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=96.32  E-value=0.018  Score=60.85  Aligned_cols=101  Identities=21%  Similarity=0.076  Sum_probs=63.0

Q ss_pred             HHHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc-c
Q 003387          166 EELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL-S  243 (824)
Q Consensus       166 ~~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~-~  243 (824)
                      ..+-..|. .+=..-+++.|+|.+|+||||||..+...  ....=..++|++  ....++..     .+++++..... .
T Consensus        47 ~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~--~~~~gg~VlyId--~E~s~~~~-----ra~rlgv~~~~l~  117 (356)
T 3hr8_A           47 LAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAE--AQKMGGVAAFID--AEHALDPV-----YAKNLGVDLKSLL  117 (356)
T ss_dssp             HHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEE--SSCCCCHH-----HHHHHTCCGGGCE
T ss_pred             HHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEe--cccccchH-----HHHHcCCchhhhh
Confidence            44555554 33234579999999999999999998873  322223578998  66666654     55666543211 0


Q ss_pred             cccccCHHHHHHHHHHhcC-CCeEEEEEecCCC
Q 003387          244 EIMDKNYEMKKIILHEYLM-TKRYLIVIDDVWS  275 (824)
Q Consensus       244 ~~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~~  275 (824)
                      -....+.++....+...++ .+.-++|+|.+-.
T Consensus       118 i~~~~~~e~~l~~~~~l~~~~~~dlvVIDSi~~  150 (356)
T 3hr8_A          118 ISQPDHGEQALEIVDELVRSGVVDLIVVDSVAA  150 (356)
T ss_dssp             EECCSSHHHHHHHHHHHHHTSCCSEEEEECTTT
T ss_pred             hhhccCHHHHHHHHHHHhhhcCCCeEEehHhhh
Confidence            1223455666666666554 4555899999854

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.16  E-value=0.0059  Score=66.25  Aligned_cols=53  Identities=21%  Similarity=0.218  Sum_probs=40.6

Q ss_pred             CCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          155 SRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      -+++.|.++.+++|.+.+..           +-...+=|-++|++|.|||+||+++.+  +..-.|
T Consensus       180 ~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~--e~~~~~  243 (437)
T 4b4t_L          180 FDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAA--TIGANF  243 (437)
T ss_dssp             SGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHH--HHTCEE
T ss_pred             hhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHH--HhCCCE
Confidence            35688999998888776643           123457788999999999999999999  554433

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.10  E-value=0.0059  Score=66.09  Aligned_cols=55  Identities=24%  Similarity=0.200  Sum_probs=41.8

Q ss_pred             CCCCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +.-+++.|.++.+++|.+.+..           +-...+=|-++|++|.|||+||+++.+  +..-.|
T Consensus       169 v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~--~~~~~~  234 (428)
T 4b4t_K          169 VTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVAN--STKAAF  234 (428)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHH--HHTCEE
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHH--HhCCCe
Confidence            3346789999999998876642           223456688999999999999999999  554433

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.08  E-value=0.0042  Score=66.33  Aligned_cols=55  Identities=22%  Similarity=0.216  Sum_probs=41.4

Q ss_pred             CCCCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +.-+++.|.++.+++|.+.+.-           +-...+=|-++|++|.|||.||+++.+  +....|
T Consensus       145 v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~--e~~~~f  210 (405)
T 4b4t_J          145 STYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAH--HTDCKF  210 (405)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHH--HHTCEE
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHH--hhCCCc
Confidence            3446789999999888776542           223356688999999999999999999  554444

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=96.08  E-value=0.0029  Score=65.16  Aligned_cols=70  Identities=13%  Similarity=0.119  Sum_probs=45.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCC--CCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPY--SNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKII  256 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~v--s~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~  256 (824)
                      -+++-|+|++|+||||||.++...     .-..++|++  .  .+..+             .      .. .+.+.....
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~-----~G~~VlyIs--~~~eE~v~-------------~------~~-~~le~~l~~  175 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA-----LGGKDKYAT--VRFGEPLS-------------G------YN-TDFNVFVDD  175 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH-----HHTTSCCEE--EEBSCSST-------------T------CB-CCHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh-----CCCCEEEEE--ecchhhhh-------------h------hh-cCHHHHHHH
Confidence            456789999999999999999873     122355676  4  22211             0      01 234556666


Q ss_pred             HHHhcCCCeEEEEEecCCCh
Q 003387          257 LHEYLMTKRYLIVIDDVWSI  276 (824)
Q Consensus       257 l~~~L~~kr~LlVlDdv~~~  276 (824)
                      +.+.+.+.+ +||+|++...
T Consensus       176 i~~~l~~~~-LLVIDsI~aL  194 (331)
T 2vhj_A          176 IARAMLQHR-VIVIDSLKNV  194 (331)
T ss_dssp             HHHHHHHCS-EEEEECCTTT
T ss_pred             HHHHHhhCC-EEEEeccccc
Confidence            666666556 9999999653

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.06  E-value=0.0061  Score=72.26  Aligned_cols=44  Identities=16%  Similarity=0.283  Sum_probs=38.1

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|++..++++++.|....  ..-+-++|.+|+||||+|+.+.+
T Consensus       180 d~iiG~~~~i~~l~~~l~~~~--~~~vLL~G~pGtGKT~la~~la~  223 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRRT--KNNPVLIGEPGVGKTAIAEGLAQ  223 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSS--SCEEEEESCTTTTTHHHHHHHHH
T ss_pred             CCccCchHHHHHHHHHHhCCC--CCCeEEECCCCCCHHHHHHHHHH
Confidence            579999999999999998754  33467999999999999999887

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.05  E-value=0.0048  Score=66.78  Aligned_cols=55  Identities=22%  Similarity=0.217  Sum_probs=41.4

Q ss_pred             CCCCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +.-+++.|.++.+++|.+.+..           +-...+=|-++|++|.|||+||+++.+  +....|
T Consensus       206 vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~--e~~~~f  271 (467)
T 4b4t_H          206 VTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVAN--RTDATF  271 (467)
T ss_dssp             CCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHH--HHTCEE
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHh--ccCCCe
Confidence            3345789999999888776432           223467788999999999999999999  555443

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=95.98  E-value=0.0098  Score=53.07  Aligned_cols=55  Identities=25%  Similarity=0.255  Sum_probs=46.0

Q ss_pred             cEEEeeCccCc--cCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccc
Q 003387          524 RVLDLGSLVLI--QYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYI  580 (824)
Q Consensus       524 r~L~L~~~~i~--~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l  580 (824)
                      .+++.++..++  .+|..+.  .+|++|+|++|.|+.+|..+|..+++|++|+|++|.+
T Consensus        11 ~~v~Cs~~~L~~~~vP~~lp--~~l~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~NP~   67 (130)
T 3rfe_A           11 TLVDCGRRGLTWASLPTAFP--VDTTELVLTGNNLTALPPGLLDALPALRTAHLGANPW   67 (130)
T ss_dssp             TEEECCSSCCCTTTSCSCCC--TTCSEEECTTSCCSSCCTTTGGGCTTCCEEECCSSCC
T ss_pred             CEEEeCCCCCccccCCCCCC--cCCCEEECCCCcCCccChhhhhhccccCEEEecCCCe
Confidence            47888888887  8887654  3789999999999999988878999999999988744

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=95.91  E-value=0.02  Score=60.63  Aligned_cols=105  Identities=17%  Similarity=0.013  Sum_probs=61.3

Q ss_pred             chhhHHHHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCC
Q 003387          161 LDDRMEELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPS  239 (824)
Q Consensus       161 r~~~~~~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~  239 (824)
                      ...-...|-.+|. .+=..-+++.|.|.+|+||||||..+...  ....=..++|++  ....++..     .+..++..
T Consensus        44 i~TG~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~--~~~~g~~vlyid--~E~s~~~~-----~a~~~g~~  114 (356)
T 1u94_A           44 ISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFID--AEHALDPI-----YARKLGVD  114 (356)
T ss_dssp             ECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEE--SSCCCCHH-----HHHHTTCC
T ss_pred             ccCCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEe--CCCCccHH-----HHHHcCCC
Confidence            3334444555554 33223568999999999999999888763  322223688999  77777643     24455432


Q ss_pred             CCc-ccccccCHHHHHHHHHHhcC-CCeEEEEEecCC
Q 003387          240 SRL-SEIMDKNYEMKKIILHEYLM-TKRYLIVIDDVW  274 (824)
Q Consensus       240 ~~~-~~~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~  274 (824)
                      .+. .-.+..+.++....+....+ .+--+||+|.+-
T Consensus       115 ~~~l~i~~~~~~e~~~~~~~~l~~~~~~~lVVIDsl~  151 (356)
T 1u94_A          115 IDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVA  151 (356)
T ss_dssp             GGGCEEECCSSHHHHHHHHHHHHHHTCCSEEEEECGG
T ss_pred             hhheeeeCCCCHHHHHHHHHHHHhccCCCEEEEcCHH
Confidence            110 00122344555555544432 344589999984

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=95.89  E-value=0.032  Score=59.01  Aligned_cols=104  Identities=21%  Similarity=0.071  Sum_probs=62.2

Q ss_pred             hhHHHHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC
Q 003387          163 DRMEELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR  241 (824)
Q Consensus       163 ~~~~~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~  241 (824)
                      .-...+-..|. .+=..-+++.|+|.+|+||||||.++...  ....=..++|++  ....++..     .++.++...+
T Consensus        44 TG~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~--~~~~g~~vlyi~--~E~~~~~~-----~a~~lG~~~~  114 (349)
T 2zr9_A           44 TGSISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVAN--AQAAGGIAAFID--AEHALDPE-----YAKKLGVDTD  114 (349)
T ss_dssp             CSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEE--SSCCCCHH-----HHHHTTCCGG
T ss_pred             cCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEE--CCCCcCHH-----HHHHcCCCHH
Confidence            33344445554 33233568999999999999999988762  322224678998  77666653     2455553211


Q ss_pred             c-ccccccCHHHHHHHHHHhcCC-CeEEEEEecCCC
Q 003387          242 L-SEIMDKNYEMKKIILHEYLMT-KRYLIVIDDVWS  275 (824)
Q Consensus       242 ~-~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~~  275 (824)
                      . .-....+.++....+....+. +.-+||+|.+-.
T Consensus       115 ~l~i~~~~~~e~~l~~~~~l~~~~~~~lIVIDsl~~  150 (349)
T 2zr9_A          115 SLLVSQPDTGEQALEIADMLVRSGALDIIVIDSVAA  150 (349)
T ss_dssp             GCEEECCSSHHHHHHHHHHHHTTTCCSEEEEECGGG
T ss_pred             HeEEecCCCHHHHHHHHHHHHhcCCCCEEEEcChHh
Confidence            0 001233455665555555543 456999999853

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.81  E-value=0.0097  Score=61.99  Aligned_cols=52  Identities=10%  Similarity=0.181  Sum_probs=35.0

Q ss_pred             hhHHHHHHHHHcCCC-CeEEEEEEcCCCChHHHHHHHHhCCcccc-CCCceeEEEE
Q 003387          163 DRMEELLDLLIEGPP-QLSVVAILDSIGLDKTAFAGEAYNSSYVK-HYFDCHAWIT  216 (824)
Q Consensus       163 ~~~~~l~~~L~~~~~-~~~vi~I~G~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~  216 (824)
                      ...+.+.+++..... ....+.|+|..|+|||+||+++++  ... ..-..+++++
T Consensus       135 ~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~--~~~~~~g~~v~~~~  188 (308)
T 2qgz_A          135 EAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAH--ELSEKKGVSTTLLH  188 (308)
T ss_dssp             HHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHH--HHHHHSCCCEEEEE
T ss_pred             HHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHH--HHHHhcCCcEEEEE
Confidence            344455566664322 246788999999999999999998  443 3333455666

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=95.80  E-value=0.0038  Score=66.21  Aligned_cols=47  Identities=17%  Similarity=0.154  Sum_probs=39.5

Q ss_pred             CCCceechhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|++..++.+..++...   ......|-|+|+.|+||||+|+.+.+
T Consensus        28 ~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~   77 (338)
T 3pfi_A           28 FDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISY   77 (338)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHH
Confidence            467999999999999988752   33455689999999999999999987

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.74  E-value=0.027  Score=55.68  Aligned_cols=117  Identities=17%  Similarity=-0.008  Sum_probs=62.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcc-----c---------
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLS-----E---------  244 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~-----~---------  244 (824)
                      -.+++|+|..|+|||||++.+...  ....=..++|+.  ...  ...++...+. .++......     .         
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~--~~~~~~~v~~~~--~~~--~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~   95 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAK--GLRDGDPCIYVT--TEE--SRDSIIRQAK-QFNWDFEEYIEKKLIIIDALMKEK   95 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHH--HHHHTCCEEEEE--SSS--CHHHHHHHHH-HTTCCCGGGBTTTEEEEECCC---
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH--HHHCCCeEEEEE--ccc--CHHHHHHHHH-HhcchHHHHhhCCEEEEecccccc
Confidence            368999999999999999998862  221112456666  332  3444444332 333211000     0         


Q ss_pred             -----ccccCHHHHHHHHHHhcC---CCeEEEEEecCC-----ChhhHHHHHhhCCC--CCCCcEEEEEechH
Q 003387          245 -----IMDKNYEMKKIILHEYLM---TKRYLIVIDDVW-----SIDMWDVIQEILPD--NQNGSRVLITLTDI  302 (824)
Q Consensus       245 -----~~~~~~~~~~~~l~~~L~---~kr~LlVlDdv~-----~~~~~~~l~~~~~~--~~~gs~ilvTtR~~  302 (824)
                           ....+..+....+.+.+.   -+..+||+|...     +......+...+..  ...|..||+||...
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d~~~~~~~~~~l~~~~~~~~~~vi~~~h~~  168 (235)
T 2w0m_A           96 EDQWSLVNLTPEELVNKVIEAKQKLGYGKARLVIDSVSALFLDKPAMARKISYYLKRVLNKWNFTIYATSQYA  168 (235)
T ss_dssp             -CTTBCSSCCHHHHHHHHHHHHHHHCSSCEEEEEETGGGGSSSCGGGHHHHHHHHHHHHHHTTEEEEEEEC--
T ss_pred             CceeeecCCCHHHHHHHHHHHHHhhCCCceEEEEECchHhhcCCHHHHHHHHHHHHHHHHhCCCeEEEEeccC
Confidence                 011144555555555543   234599999986     22222333222221  12467888888765

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=95.73  E-value=0.0095  Score=69.65  Aligned_cols=97  Identities=13%  Similarity=0.116  Sum_probs=61.1

Q ss_pred             CCCCCceechhhHHHHHHHHHc----C-------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE----G-------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN  221 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~----~-------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~  221 (824)
                      +.-+++.|.++.+++|.+++.-    .       -...+-|-++|++|.|||+||+++.+  +...+|   +.|.  .+ 
T Consensus       201 v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~--elg~~~---~~v~--~~-  272 (806)
T 3cf2_A          201 VGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETGAFF---FLIN--GP-  272 (806)
T ss_dssp             CCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHT--TTTCEE---EEEE--HH-
T ss_pred             CChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHH--HhCCeE---EEEE--hH-
Confidence            4446788999999888877542    1       13457789999999999999999999  444333   3343  11 


Q ss_pred             CCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          222 EYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       222 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                               ++.   ..      ........+...+....+....+|++|+++.
T Consensus       273 ---------~l~---sk------~~gese~~lr~lF~~A~~~~PsIIfIDEiDa  308 (806)
T 3cf2_A          273 ---------EIM---SK------LAGESESNLRKAFEEAEKNAPAIIFIDELDA  308 (806)
T ss_dssp             ---------HHH---SS------CTTHHHHHHHHHHHHHTTSCSEEEEEESGGG
T ss_pred             ---------Hhh---cc------cchHHHHHHHHHHHHHHHcCCeEEEEehhcc
Confidence                     111   11      0111223333344444456789999999964

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=95.71  E-value=0.022  Score=56.80  Aligned_cols=94  Identities=11%  Similarity=0.075  Sum_probs=54.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccC----CCceeEEEECCCCCCCCHHHHHHHHHHHhCCCC-----CcccccccC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKH----YFDCHAWITEPYSNEYDADQILDIVIKFLMPSS-----RLSEIMDKN  249 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~-----~~~~~~~~~  249 (824)
                      -.++.|+|.+|+|||||++.+........    .-..++|++  ....++..++. ++++.++...     ...-....+
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~--~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~~  100 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYID--TEGTFRPERLL-AVAERYGLSGSDVLDNVAYARAFN  100 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEE--SSSCCCHHHHH-HHHHHTTCCHHHHHHTEEEEECCS
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEE--CCCCcCHHHHH-HHHHHcCCCHHHHhhCeEEEecCC
Confidence            46999999999999999999876211111    135788998  66555555443 3445554321     000011122


Q ss_pred             HHH---HHHHHHHhcC-CCeEEEEEecCCC
Q 003387          250 YEM---KKIILHEYLM-TKRYLIVIDDVWS  275 (824)
Q Consensus       250 ~~~---~~~~l~~~L~-~kr~LlVlDdv~~  275 (824)
                      ..+   ....+.+.+. .+.-+||+|.+..
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~lliiD~~~~  130 (243)
T 1n0w_A          101 TDHQTQLLYQASAMMVESRYALLIVDSATA  130 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHSCEEEEEEETSSG
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEEeCchH
Confidence            222   2333555553 4677999999864

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=95.71  E-value=0.049  Score=57.88  Aligned_cols=105  Identities=18%  Similarity=0.064  Sum_probs=63.3

Q ss_pred             chhhHHHHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCC
Q 003387          161 LDDRMEELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPS  239 (824)
Q Consensus       161 r~~~~~~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~  239 (824)
                      ...-...|-.+|. .+=..-+++-|+|.+|+||||||..+...  ....=..++|++  ....++..     .++.++..
T Consensus        55 i~TG~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~--~~~~g~~vlyi~--~E~s~~~~-----~a~~~g~d  125 (366)
T 1xp8_A           55 VSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQ--AQKAGGTCAFID--AEHALDPV-----YARALGVN  125 (366)
T ss_dssp             ECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEE--SSCCCCHH-----HHHHTTCC
T ss_pred             ecCCCHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHH--HHHCCCeEEEEE--CCCChhHH-----HHHHcCCC
Confidence            3333444555554 23223458888999999999999888763  322224788999  77766654     24455442


Q ss_pred             CC-cccccccCHHHHHHHHHHhcCC-CeEEEEEecCC
Q 003387          240 SR-LSEIMDKNYEMKKIILHEYLMT-KRYLIVIDDVW  274 (824)
Q Consensus       240 ~~-~~~~~~~~~~~~~~~l~~~L~~-kr~LlVlDdv~  274 (824)
                      .. ..-....+.++....+.+.++. +--+||+|.+-
T Consensus       126 ~~~l~i~~~~~~e~~l~~l~~l~~~~~~~lVVIDsl~  162 (366)
T 1xp8_A          126 TDELLVSQPDNGEQALEIMELLVRSGAIDVVVVDSVA  162 (366)
T ss_dssp             GGGCEEECCSSHHHHHHHHHHHHTTTCCSEEEEECTT
T ss_pred             HHHceeecCCcHHHHHHHHHHHHhcCCCCEEEEeChH
Confidence            11 0001233556666667666654 44589999985

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=95.67  E-value=0.005  Score=63.73  Aligned_cols=29  Identities=10%  Similarity=0.040  Sum_probs=24.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHY  208 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~  208 (824)
                      ..+.+.++|++|+|||+||+.+++  .....
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~--~l~~~   63 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFR--KMGIN   63 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHH--HHTCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HhCCC
Confidence            456788999999999999999998  55433

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.66  E-value=0.0048  Score=73.17  Aligned_cols=46  Identities=15%  Similarity=0.247  Sum_probs=37.8

Q ss_pred             CCceechhhHHHHHHHHHcCC-------CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGP-------PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~-------~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.+..++.+.+.+....       .....+-++|+.|+|||++|+.+.+
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~  543 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAE  543 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHH
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999988886421       2234799999999999999999988

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=95.65  E-value=0.015  Score=64.28  Aligned_cols=47  Identities=21%  Similarity=0.105  Sum_probs=36.5

Q ss_pred             CCCceechhhHHHHHH---HHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLD---LLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~---~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++++|.+..++.+..   ++..+....+-+-++|++|+|||++|+.+.+
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~   85 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQ   85 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHH
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHH
Confidence            4689999998876544   4444443345688999999999999999998

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.63  E-value=0.011  Score=63.47  Aligned_cols=55  Identities=22%  Similarity=0.238  Sum_probs=41.3

Q ss_pred             CCCCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +.-+++.|.++.+++|.+.+..           +-...+=|-++|++|.|||.||+++.+  +....|
T Consensus       179 v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~--e~~~~f  244 (437)
T 4b4t_I          179 ESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVAN--QTSATF  244 (437)
T ss_dssp             CCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHH--HHTCEE
T ss_pred             CcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHH--HhCCCE
Confidence            3345688999999888876642           123457788999999999999999999  554443

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.62  E-value=0.0078  Score=65.24  Aligned_cols=55  Identities=24%  Similarity=0.295  Sum_probs=41.5

Q ss_pred             CCCCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +.-+++.|.++.+++|.+.+..           +-...+=|-++|++|.|||+||+++.+  +....|
T Consensus       178 ~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~--e~~~~f  243 (434)
T 4b4t_M          178 ETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAA--QTNATF  243 (434)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHH--HHTCEE
T ss_pred             CChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHH--HhCCCE
Confidence            3446789999999988876432           123467788999999999999999999  554433

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=95.60  E-value=0.029  Score=59.36  Aligned_cols=105  Identities=11%  Similarity=0.057  Sum_probs=60.1

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC----CCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC--
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH----YFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR--  241 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~--  241 (824)
                      +-.+|..+=..-.++.|+|.+|+||||||..+........    .=..++|++  ....++..++.+ ++..++....  
T Consensus       111 LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~--~E~~~~~~~l~~-~~~~~g~~~~~~  187 (343)
T 1v5w_A          111 FDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFID--TENTFRPDRLRD-IADRFNVDHDAV  187 (343)
T ss_dssp             HHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEE--SSSCCCHHHHHH-HHHHTTCCHHHH
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEE--CCCCCCHHHHHH-HHHHcCCCHHHH
Confidence            4444444434467999999999999999998876322211    224688999  777778776654 4455543210  


Q ss_pred             ---cccccccCH---HHHHHHHHHhcC---CCeEEEEEecCCC
Q 003387          242 ---LSEIMDKNY---EMKKIILHEYLM---TKRYLIVIDDVWS  275 (824)
Q Consensus       242 ---~~~~~~~~~---~~~~~~l~~~L~---~kr~LlVlDdv~~  275 (824)
                         ..-....+.   .++...+.+.++   .+--+||+|.+-.
T Consensus       188 l~~l~~~~~~~~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~  230 (343)
T 1v5w_A          188 LDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMA  230 (343)
T ss_dssp             HHTEEEEECCSTTHHHHHHHHHHHHHHHSCSSEEEEEEETSGG
T ss_pred             HhceeEeecCCHHHHHHHHHHHHHHHHhcCCCccEEEEechHH
Confidence               000011111   223333444443   4566888998853

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.59  E-value=0.019  Score=58.72  Aligned_cols=47  Identities=26%  Similarity=0.216  Sum_probs=33.1

Q ss_pred             CCCCceechhhHHHHHHHHHc---C---------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE---G---------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~---~---------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.++.|.++.+++|.+.+..   .         ..... +.++|+.|.||||||+.+.+
T Consensus         8 ~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~G-vlL~Gp~GtGKTtLakala~   66 (274)
T 2x8a_A            8 TWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAG-VLLAGPPGCGKTLLAKAVAN   66 (274)
T ss_dssp             ----CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSE-EEEESSTTSCHHHHHHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCe-EEEECCCCCcHHHHHHHHHH
Confidence            346788998888888765431   1         11123 99999999999999999998

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=95.56  E-value=0.019  Score=60.32  Aligned_cols=105  Identities=20%  Similarity=0.140  Sum_probs=60.5

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCC----CceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC--
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY----FDCHAWITEPYSNEYDADQILDIVIKFLMPSSR--  241 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~--  241 (824)
                      +-.+|..+=..-.++.|+|.+|+||||||..+.........    =..++|++  ....++..++.+ +++.++....  
T Consensus        96 LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~--~e~~~~~~~l~~-~~~~~g~~~~~~  172 (324)
T 2z43_A           96 LDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYID--TEGTFRWERIEN-MAKALGLDIDNV  172 (324)
T ss_dssp             HHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEE--SSSCCCHHHHHH-HHHHTTCCHHHH
T ss_pred             HHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEE--CCCCCCHHHHHH-HHHHhCCCHHHH
Confidence            33344333223468999999999999999988763211110    24688999  777777777654 4555544210  


Q ss_pred             ---cccccccCHH---HHHHHHHHhcC--CCeEEEEEecCCC
Q 003387          242 ---LSEIMDKNYE---MKKIILHEYLM--TKRYLIVIDDVWS  275 (824)
Q Consensus       242 ---~~~~~~~~~~---~~~~~l~~~L~--~kr~LlVlDdv~~  275 (824)
                         ..-....+.+   ++...+.+.++  .+--+||+|.+..
T Consensus       173 ~~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~  214 (324)
T 2z43_A          173 MNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTS  214 (324)
T ss_dssp             HHTEEEEECCSHHHHHHHHHHHHHHHHHCTTEEEEEETTTTH
T ss_pred             hccEEEEeCCCHHHHHHHHHHHHHHHHhccCCCEEEEeCcHH
Confidence               0001112222   23445555553  4566888888853

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=95.44  E-value=0.063  Score=55.08  Aligned_cols=87  Identities=6%  Similarity=-0.000  Sum_probs=55.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCC--CceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc-ccccccCHHHH-HHH
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHY--FDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL-SEIMDKNYEMK-KII  256 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~--F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~~~-~~~  256 (824)
                      ++-|+|.+|+||||||.++..  .....  =..++||+  ..+.++..     .+++++...+. .-....+.++. ...
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~--~~~~~g~g~~vlyId--~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~i  100 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVS--SYMRQYPDAVCLFYD--SEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRIDM  100 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHH--HHHHHCTTCEEEEEE--SSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH--HHHhcCCCceEEEEe--ccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHHH
Confidence            789999999999999988766  33322  24688999  77777754     36777764221 01233445555 333


Q ss_pred             HHHh--c-CCCeEEEEEecCCCh
Q 003387          257 LHEY--L-MTKRYLIVIDDVWSI  276 (824)
Q Consensus       257 l~~~--L-~~kr~LlVlDdv~~~  276 (824)
                      +...  + +++.-+||+|-|-..
T Consensus       101 ~~~l~~i~~~~~~lvVIDSI~aL  123 (333)
T 3io5_A          101 VNQLDAIERGEKVVVFIDSLGNL  123 (333)
T ss_dssp             HHHHHTCCTTCCEEEEEECSTTC
T ss_pred             HHHHHHhhccCceEEEEeccccc
Confidence            3332  3 457789999998643

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=95.36  E-value=0.023  Score=59.66  Aligned_cols=105  Identities=15%  Similarity=0.123  Sum_probs=61.7

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC---------CC-----ceeEEEECCCCCCCCHHHHHHHH
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH---------YF-----DCHAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~---------~F-----~~~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      .+-.+|..+=..-.++.|+|.+|+||||||..+..+.....         ..     ..++|++  ....++..++.+ +
T Consensus        86 ~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~--~e~~~~~~~l~~-~  162 (322)
T 2i1q_A           86 ELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYID--TEGTFRPERIMQ-M  162 (322)
T ss_dssp             HHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEE--SSSCCCHHHHHH-H
T ss_pred             hHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEE--CCCCCCHHHHHH-H
Confidence            34444433323457999999999999999988875321111         11     4788999  887788777664 4


Q ss_pred             HHHhCCCCC-----cccccccCHH---HHHHHHHHhcC--CCeEEEEEecCC
Q 003387          233 IKFLMPSSR-----LSEIMDKNYE---MKKIILHEYLM--TKRYLIVIDDVW  274 (824)
Q Consensus       233 ~~~l~~~~~-----~~~~~~~~~~---~~~~~l~~~L~--~kr~LlVlDdv~  274 (824)
                      ++.++....     ..-....+.+   ++...+.+.++  .+--+||+|.+-
T Consensus       163 ~~~~g~~~~~~~~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~  214 (322)
T 2i1q_A          163 AEHAGIDGQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  214 (322)
T ss_dssp             HHHHTCCHHHHHHTEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             HHHcCCCHHHHhcCEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcH
Confidence            555554210     0001112223   23445555554  345688999885

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.25  E-value=0.017  Score=56.04  Aligned_cols=41  Identities=22%  Similarity=0.178  Sum_probs=32.9

Q ss_pred             chhhHHHHHHHHHcC-CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          161 LDDRMEELLDLLIEG-PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       161 r~~~~~~l~~~L~~~-~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      |+..++.+.+.+... .....+|+|+|..|+||||+++.+..
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            455677788877753 23568999999999999999999876

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.18  E-value=0.011  Score=57.74  Aligned_cols=37  Identities=19%  Similarity=0.231  Sum_probs=28.0

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.+.+......-.+|+|+|..|.|||||++.+..
T Consensus         8 ~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~   44 (208)
T 3c8u_A            8 CQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAA   44 (208)
T ss_dssp             HHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3444454443334578999999999999999999887

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=95.16  E-value=0.0088  Score=63.22  Aligned_cols=46  Identities=22%  Similarity=0.194  Sum_probs=36.2

Q ss_pred             CCceechhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.++|.+..++.+...+..+   ......+.++|+.|+||||||+.+.+
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~   73 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS   73 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            46788887777776666543   22356799999999999999999998

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=95.06  E-value=0.027  Score=62.38  Aligned_cols=50  Identities=20%  Similarity=0.252  Sum_probs=36.5

Q ss_pred             CCCCCCceechhhHHHHHHHHH---cCC-------CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          152 SSKSRDTVGLDDRMEELLDLLI---EGP-------PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       152 ~~~~~~~vGr~~~~~~l~~~L~---~~~-------~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+.-++++|.++.++++.+...   ...       .-.+=+.|+|..|.||||||+.+.+
T Consensus        27 ~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~   86 (499)
T 2dhr_A           27 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAG   86 (499)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            3445689999988877766543   210       0122389999999999999999998

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=95.01  E-value=0.027  Score=63.56  Aligned_cols=46  Identities=20%  Similarity=0.306  Sum_probs=35.8

Q ss_pred             CCceechhhHHHHHHHHHc----CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIE----GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.++-++.+.+.+.-    ......++.++|++|+||||||+.+.+
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~  130 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAK  130 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            4578988888877665432    122456899999999999999999988

>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics secsg; 1.80A {Caenorhabditis elegans} SCOP: c.10.1.1

Probab=94.99  E-value=0.024  Score=54.20  Aligned_cols=88  Identities=7%  Similarity=0.040  Sum_probs=47.9

Q ss_pred             hhHhhhcccCcccEEEeeCc-cCc-----cCCccCCCCCcceEEeecCCCCC-----ccChhhhhcCCCccEeecCCccc
Q 003387          512 DWEKFCGMFKLLRVLDLGSL-VLI-----QYPSGIENLFLLRYLKLNIPSLN-----SLPSSLLSNLLNLYTLDMPFSYI  580 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~-~i~-----~lp~~i~~l~~Lr~L~L~~~~i~-----~lp~~i~~~L~~L~~L~L~~~~l  580 (824)
                      .+...+..-+.|+.|+|+++ .|.     .+-+.+..-.+|+.|+|++|.+.     .+-..+ ..-+.|++|+|++|.|
T Consensus        32 ~l~~ll~~n~~L~~L~L~~nn~igd~ga~~la~aL~~N~~L~~L~L~~n~igd~ga~alA~aL-~~N~tL~~L~L~~N~I  110 (197)
T 1pgv_A           32 CINRLREDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELI-ETSPSLRVLNVESNFL  110 (197)
T ss_dssp             HHHHHHTTCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHH-HHCSSCCEEECCSSBC
T ss_pred             HHHHHHhcCCCccEEECCCCCCCCHHHHHHHHHHHhhCCCcCEEEccCCCCChHHHHHHHHHH-hcCCccCeEecCCCcC
Confidence            34455566677777887764 553     33344455566777777777665     233333 4445566666666655


Q ss_pred             cc-----cchhhhccccCceecCCC
Q 003387          581 DH-----TADEFWKMNKLRHLNFGS  600 (824)
Q Consensus       581 ~~-----lp~~i~~L~~L~~L~L~~  600 (824)
                      ..     +-+.+..-+.|++|+|++
T Consensus       111 g~~Ga~ala~aL~~N~tL~~L~L~n  135 (197)
T 1pgv_A          111 TPELLARLLRSTLVTQSIVEFKADN  135 (197)
T ss_dssp             CHHHHHHHHHHTTTTCCCSEEECCC
T ss_pred             CHHHHHHHHHHHhhCCceeEEECCC
Confidence            42     222333334455555543

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=94.97  E-value=0.02  Score=54.48  Aligned_cols=119  Identities=10%  Similarity=0.001  Sum_probs=61.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC---CCCHHHHHHHHHHHhC--CCC---Cccc--ccccC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN---EYDADQILDIVIKFLM--PSS---RLSE--IMDKN  249 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~---~~~~~~~~~~i~~~l~--~~~---~~~~--~~~~~  249 (824)
                      ..|-|++-.|.||||.|-.+.-  +...+=..+.++.  ..+   .+...+++..+.-.+.  +..   ..+.  .+...
T Consensus        29 g~i~v~tG~GkGKTTaA~Glal--RA~g~G~rV~~vQ--F~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~  104 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAA--RAVGHGKNVGVVQ--FIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAA  104 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHH--HHHHTTCCEEEEE--SSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HHHHCCCeEEEEE--eeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHH
Confidence            4566677777999999976655  3333322445554  322   3344444444310000  000   0000  01112


Q ss_pred             HHHHHHHHHHhcCCCeE-EEEEecCCCh-----hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          250 YEMKKIILHEYLMTKRY-LIVIDDVWSI-----DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       250 ~~~~~~~l~~~L~~kr~-LlVlDdv~~~-----~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      ........++.+.+.+| |||||++-..     ...+++...+.......-||+|+|..
T Consensus       105 a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          105 CMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            24445566777766555 9999999432     23344444443444456799999975

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=94.86  E-value=0.024  Score=68.05  Aligned_cols=45  Identities=20%  Similarity=0.305  Sum_probs=36.9

Q ss_pred             CceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          157 DTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.+..++.+...+...       ......+.|+|..|+|||++|+.+.+
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~  610 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA  610 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            5789999999888887642       12246889999999999999999988

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=94.83  E-value=0.079  Score=55.36  Aligned_cols=24  Identities=21%  Similarity=0.146  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+++|+|..|+||||+++.+..
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag  151 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLAN  151 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999999887

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=94.81  E-value=0.026  Score=58.06  Aligned_cols=27  Identities=19%  Similarity=0.133  Sum_probs=23.6

Q ss_pred             CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          175 GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       175 ~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ......+|+|+|..|+||||||+.+..
T Consensus        27 ~~~~~~ii~I~G~sGsGKSTla~~L~~   53 (290)
T 1odf_A           27 GNKCPLFIFFSGPQGSGKSFTSIQIYN   53 (290)
T ss_dssp             TCCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            345678999999999999999998877

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=94.80  E-value=0.013  Score=55.03  Aligned_cols=108  Identities=15%  Similarity=0.087  Sum_probs=54.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc-cc-----ccccCHHHH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL-SE-----IMDKNYEMK  253 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~-~~-----~~~~~~~~~  253 (824)
                      .+|.|+|+.|+||||+|+.+ .  +..  |   .+++        ..++.++....-+..... ..     .........
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L-~--~~g--~---~~i~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   65 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL-K--ERG--A---KVIV--------MSDVVRKRYSIEAKPGERLMDFAKRLREIYGDGVV   65 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH-H--HTT--C---EEEE--------HHHHHHHHHHHHC---CCHHHHHHHHHHHHCTTHH
T ss_pred             cEEEEECCCCCCHHHHHHHH-H--HCC--C---cEEE--------HhHHHHHHHHhcCCChhHHHHHHHHHHhhCCHHHH
Confidence            47999999999999999999 4  322  1   1333        233444433332210000 00     000011223


Q ss_pred             HHHHHHhc-CCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          254 KIILHEYL-MTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       254 ~~~l~~~L-~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      ...+.+.+ ....-.+|+|++....+++.+...+.   ....+|.-..+.+++.
T Consensus        66 ~~~~~~~l~~~~~~~vi~dg~~~~~~~~~l~~~~~---~~~~~i~l~~~~~~~~  116 (179)
T 3lw7_A           66 ARLCVEELGTSNHDLVVFDGVRSLAEVEEFKRLLG---DSVYIVAVHSPPKIRY  116 (179)
T ss_dssp             HHHHHHHHCSCCCSCEEEECCCCHHHHHHHHHHHC---SCEEEEEEECCHHHHH
T ss_pred             HHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHhC---CCcEEEEEECCHHHHH
Confidence            34455555 23344578899966666666654433   2334554444444443

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=94.79  E-value=0.012  Score=61.42  Aligned_cols=46  Identities=15%  Similarity=0.177  Sum_probs=37.1

Q ss_pred             CCceechhhHHHHHHHHHcC------------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEG------------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.+..++.+...+...            .....-+-++|.+|+|||++|+.+.+
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   72 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   72 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHH
Confidence            46899999999998887641            11245677999999999999999988

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=94.79  E-value=0.028  Score=50.03  Aligned_cols=55  Identities=15%  Similarity=0.177  Sum_probs=46.8

Q ss_pred             eEEeecCCCCC--ccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCccCC
Q 003387          547 RYLKLNIPSLN--SLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       547 r~L~L~~~~i~--~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~  604 (824)
                      ..++.++.+++  .+|..+   -.+|++|+|++|.|+.+|.. |..+++|+.|+|++|.+.
T Consensus        11 ~~v~Cs~~~L~~~~vP~~l---p~~l~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~NP~~   68 (130)
T 3rfe_A           11 TLVDCGRRGLTWASLPTAF---PVDTTELVLTGNNLTALPPGLLDALPALRTAHLGANPWR   68 (130)
T ss_dssp             TEEECCSSCCCTTTSCSCC---CTTCSEEECTTSCCSSCCTTTGGGCTTCCEEECCSSCCB
T ss_pred             CEEEeCCCCCccccCCCCC---CcCCCEEECCCCcCCccChhhhhhccccCEEEecCCCee
Confidence            47888888988  999765   45799999999999999876 678999999999998764

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=94.58  E-value=0.017  Score=55.25  Aligned_cols=23  Identities=17%  Similarity=0.163  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|+.|+|||||++.+..
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~   31 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALAN   31 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999999988

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=94.55  E-value=0.2  Score=50.50  Aligned_cols=22  Identities=27%  Similarity=0.232  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|+|..|.|||||.+.+..
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~G   52 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISG   52 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhC
Confidence            4899999999999999999986

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=94.53  E-value=0.018  Score=59.95  Aligned_cols=37  Identities=14%  Similarity=0.003  Sum_probs=26.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      +.+||+|.|-|||||||.|..+.-  -....=..+.-|+
T Consensus        47 ~aKVIAIaGKGGVGKTTtavNLA~--aLA~~GkkVllID   83 (314)
T 3fwy_A           47 GAKVFAVYGKGGIGKSTTSSNLSA--AFSILGKRVLQIG   83 (314)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             CceEEEEECCCccCHHHHHHHHHH--HHHHCCCeEEEEe
Confidence            589999999999999999876654  2322222455555

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=94.43  E-value=0.015  Score=54.91  Aligned_cols=22  Identities=5%  Similarity=0.030  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|+|+.|+||||+|+.+.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~   25 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5789999999999999999987

>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics secsg; 1.80A {Caenorhabditis elegans} SCOP: c.10.1.1

Probab=94.34  E-value=0.018  Score=55.03  Aligned_cols=110  Identities=12%  Similarity=-0.001  Sum_probs=75.1

Q ss_pred             CCceeEeeccCC-CCCCCCcchhHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCC-----ccC
Q 003387          492 DSQLHSLLCCSP-ETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLN-----SLP  560 (824)
Q Consensus       492 ~~~Lr~L~l~~~-~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~-----~lp  560 (824)
                      .+.|+.|.+.++ .........+...+..-+.|+.|+|++|.+.     .+.+.+..-+.|++|+|++|.|.     .+-
T Consensus        40 n~~L~~L~L~~nn~igd~ga~~la~aL~~N~~L~~L~L~~n~igd~ga~alA~aL~~N~tL~~L~L~~N~Ig~~Ga~ala  119 (197)
T 1pgv_A           40 DTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLL  119 (197)
T ss_dssp             CSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHH
T ss_pred             CCCccEEECCCCCCCCHHHHHHHHHHHhhCCCcCEEEccCCCCChHHHHHHHHHHhcCCccCeEecCCCcCCHHHHHHHH
Confidence            567888888764 3321011245567777889999999999886     44455556678999999999987     333


Q ss_pred             hhhhhcCCCccEeecCCcc---cc-----ccchhhhccccCceecCCCcc
Q 003387          561 SSLLSNLLNLYTLDMPFSY---ID-----HTADEFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       561 ~~i~~~L~~L~~L~L~~~~---l~-----~lp~~i~~L~~L~~L~L~~~~  602 (824)
                      ..+ ..-+.|++|+|+++.   +.     .+...+..-+.|+.|+++.+.
T Consensus       120 ~aL-~~N~tL~~L~L~n~~~~~ig~~g~~~ia~aL~~N~tL~~L~l~~~~  168 (197)
T 1pgv_A          120 RST-LVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGISFAS  168 (197)
T ss_dssp             HHT-TTTCCCSEEECCCCSSCCCCHHHHHHHHHHHHHCSSCCEEECCCCC
T ss_pred             HHH-hhCCceeEEECCCCcCcCcCHHHHHHHHHHHHhCCCcCeEeccCCC
Confidence            444 555679999998653   23     234446667788999886554

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=94.29  E-value=0.065  Score=58.36  Aligned_cols=104  Identities=13%  Similarity=0.154  Sum_probs=62.4

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccc-cCCCceeEEEECCCCCCCC-HHHHHHHHHHHhCCC------
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYV-KHYFDCHAWITEPYSNEYD-ADQILDIVIKFLMPS------  239 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~-~~~F~~~~wv~~~vs~~~~-~~~~~~~i~~~l~~~------  239 (824)
                      +++.|..=. .-.-++|.|..|+|||+|++.+.+  .+ +.+-+.++++-  +.+..+ +.++..++...=...      
T Consensus       155 vID~l~pig-kGqr~gIfgg~GvGKT~L~~~l~~--~~a~~~~~v~V~~~--iGER~rEv~e~~~~~~~~~~l~~~~l~~  229 (498)
T 1fx0_B          155 VVNLLAPYR-RGGKIGLFGGAGVGKTVLIMELIN--NIAKAHGGVSVFGG--VGERTREGNDLYMEMKESGVINEQNIAE  229 (498)
T ss_dssp             THHHHSCCC-TTCCEEEEECSSSSHHHHHHHHHH--HTTTTCSSCEEEEE--ESCCSHHHHHHHHHHHHTTSSCSSTTCC
T ss_pred             Eeeeecccc-cCCeEEeecCCCCCchHHHHHHHH--HHHhhCCCEEEEEE--cccCcHHHHHHHHhhhcccccccccccc
Confidence            455554321 234689999999999999998877  33 23446778887  777654 446666766531111      


Q ss_pred             ---------CCcccccccCHHHHHHHHHHhcC---CCeEEEEEecCCCh
Q 003387          240 ---------SRLSEIMDKNYEMKKIILHEYLM---TKRYLIVIDDVWSI  276 (824)
Q Consensus       240 ---------~~~~~~~~~~~~~~~~~l~~~L~---~kr~LlVlDdv~~~  276 (824)
                               .+.|.....-.......+.++++   ++.+||++||+-.-
T Consensus       230 ~rtvvV~~t~d~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~DsitR~  278 (498)
T 1fx0_B          230 SKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIFRF  278 (498)
T ss_dssp             CCEEEEEECTTSCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSHHH
T ss_pred             cceEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHHH
Confidence                     01111111122333445556554   58999999999643

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=94.29  E-value=0.02  Score=53.72  Aligned_cols=22  Identities=9%  Similarity=0.025  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|.|+.|+||||+|+.+..
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~   23 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSK   23 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999987

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=94.22  E-value=0.024  Score=60.56  Aligned_cols=45  Identities=16%  Similarity=0.110  Sum_probs=35.7

Q ss_pred             CceechhhHHHHHHHHHc-------------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          157 DTVGLDDRMEELLDLLIE-------------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~-------------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.+..++.+...+..             .......|.++|++|+|||++|+.+.+
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~   73 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLAR   73 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            478999999988887731             111345788999999999999999998

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=94.21  E-value=0.027  Score=56.73  Aligned_cols=46  Identities=22%  Similarity=0.278  Sum_probs=33.4

Q ss_pred             CCCceechhhHHHHHHHHHc--C---------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIE--G---------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~--~---------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.+..+.++.+....  .         .-... +.|+|..|+||||||+.+.+
T Consensus        15 ~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g-~ll~G~~G~GKTtl~~~i~~   71 (254)
T 1ixz_A           15 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAG   71 (254)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSE-EEEECCTTSSHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCCCCHHHHHHHHHH
Confidence            45788988777766654431  1         00122 89999999999999999998

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=94.19  E-value=0.021  Score=54.15  Aligned_cols=23  Identities=9%  Similarity=0.224  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|+|+.|+|||||++.+..
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~   27 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLIT   27 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35899999999999999999987

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=94.17  E-value=0.11  Score=55.91  Aligned_cols=107  Identities=12%  Similarity=0.077  Sum_probs=58.0

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccc----cCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYV----KHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR  241 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~----~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~  241 (824)
                      ..+-++|..+=..-.++.|+|..|+|||||+..+.-....    ...-..++|++  ....++..++. .+++.++....
T Consensus       165 ~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid--~E~~~~~~rl~-~~a~~~gl~~~  241 (400)
T 3lda_A          165 KNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID--TEGTFRPVRLV-SIAQRFGLDPD  241 (400)
T ss_dssp             HHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEE--SSSCCCHHHHH-HHHHHTTCCHH
T ss_pred             hhHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEe--CCCccCHHHHH-HHHHHcCCChH
Confidence            3344444444233569999999999999999966421111    11234688998  66666665543 36666654210


Q ss_pred             -----cccccccCHH---HHHHHHHHhcC-CCeEEEEEecCCC
Q 003387          242 -----LSEIMDKNYE---MKKIILHEYLM-TKRYLIVIDDVWS  275 (824)
Q Consensus       242 -----~~~~~~~~~~---~~~~~l~~~L~-~kr~LlVlDdv~~  275 (824)
                           ..-....+..   +....+.+.+. .+.-+||+|.+-.
T Consensus       242 ~vleni~~~~~~~~~~~~~~l~~~~~~l~~~~~~llVIDs~t~  284 (400)
T 3lda_A          242 DALNNVAYARAYNADHQLRLLDAAAQMMSESRFSLIVVDSVMA  284 (400)
T ss_dssp             HHHHTEEEEECCSHHHHHHHHHHHHHHHHHSCEEEEEEETGGG
T ss_pred             hHhhcEEEeccCChHHHHHHHHHHHHHHHhcCCceEEecchhh
Confidence                 0001111222   22233333332 3567889998743

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=94.17  E-value=0.061  Score=56.93  Aligned_cols=104  Identities=13%  Similarity=0.139  Sum_probs=57.1

Q ss_pred             HHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC----ceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC----
Q 003387          170 DLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF----DCHAWITEPYSNEYDADQILDIVIKFLMPSSR----  241 (824)
Q Consensus       170 ~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F----~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~----  241 (824)
                      ++|..+=..-.++.|+|..|+|||||+..+..........    ..++|++  ....+...++ ..+++..+....    
T Consensus       122 ~lL~ggi~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~--~e~~~~~~~i-~~i~q~~~~~~~~v~~  198 (349)
T 1pzn_A          122 KLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID--TENTFRPERI-REIAQNRGLDPDEVLK  198 (349)
T ss_dssp             HHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE--SSSCCCHHHH-HHHHHTTTCCHHHHGG
T ss_pred             HHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEe--CCCCCCHHHH-HHHHHHcCCCHHHHhh
Confidence            3343332346899999999999999999987732111111    2458998  5554544443 334444432110    


Q ss_pred             ---ccc-ccccCHHHHHHHHHHhcC------CCeEEEEEecCCCh
Q 003387          242 ---LSE-IMDKNYEMKKIILHEYLM------TKRYLIVIDDVWSI  276 (824)
Q Consensus       242 ---~~~-~~~~~~~~~~~~l~~~L~------~kr~LlVlDdv~~~  276 (824)
                         ... .......++...+...++      .+.=+||+|.+-..
T Consensus       199 ni~~~~~~~~~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~  243 (349)
T 1pzn_A          199 HIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSH  243 (349)
T ss_dssp             GEEEEECCSHHHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTT
T ss_pred             CEEEEecCChHHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHh
Confidence               000 011112333444455553      46779999998654

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=94.09  E-value=0.049  Score=59.07  Aligned_cols=105  Identities=14%  Similarity=0.201  Sum_probs=59.4

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCC-HHHHHHHHHHHhCCC------
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD-ADQILDIVIKFLMPS------  239 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~-~~~~~~~i~~~l~~~------  239 (824)
                      ++++.|..=. .-.-++|+|..|+|||+|++.+.++. .+.+-+.++++-  +.+..+ +.++.+++.+.=...      
T Consensus       142 r~ID~l~pig-kGQr~~Ifgg~G~GKT~L~~~i~~~~-~~~~~~v~V~~~--iGER~rEv~e~~~~~~~~~~l~~~~~~~  217 (482)
T 2ck3_D          142 KVVDLLAPYA-KGGKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAG--VGERTREGNDLYHEMIESGVINLKDATS  217 (482)
T ss_dssp             HHHHHHSCEE-TTCEEEEEECTTSSHHHHHHHHHHHT-TTTCSSEEEEEE--ESCCHHHHHHHHHHHHHHTSSCSSSSCC
T ss_pred             EEEecccccc-cCCeeeeecCCCCChHHHHHHHHHhh-HhhCCCEEEEEE--CCCcchHHHHHHHHhhhccccccccCCc
Confidence            3555554311 13478999999999999999887731 123345667776  776653 346666766542111      


Q ss_pred             C--------CcccccccCHHHHHHHHHHhc---CCCeEEEEEecCCC
Q 003387          240 S--------RLSEIMDKNYEMKKIILHEYL---MTKRYLIVIDDVWS  275 (824)
Q Consensus       240 ~--------~~~~~~~~~~~~~~~~l~~~L---~~kr~LlVlDdv~~  275 (824)
                      .        +.|.....-.......+.+++   +++.+||++||+-.
T Consensus       218 rtvvV~~t~d~p~~~r~~~~~~a~tiAEyfrd~~G~dVLll~DsitR  264 (482)
T 2ck3_D          218 KVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFR  264 (482)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHH
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHHH
Confidence            0        000000001112223333443   47999999999954

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=94.04  E-value=0.027  Score=53.23  Aligned_cols=22  Identities=18%  Similarity=0.306  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|+|++|+||||+|+.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5799999999999999999986

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=94.03  E-value=0.023  Score=54.86  Aligned_cols=23  Identities=13%  Similarity=0.173  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.|+|+.|+||||+|+.+..
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=93.99  E-value=0.092  Score=54.08  Aligned_cols=36  Identities=19%  Similarity=0.107  Sum_probs=26.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ..+|+|+|.+|+||||++..+..  .....=..+.+++
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~--~~~~~g~~v~l~~  133 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAY--FYKKKGFKVGLVG  133 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH--HHHHCCCeEEEEe
Confidence            67999999999999999998876  3322223455665

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=93.96  E-value=0.073  Score=56.03  Aligned_cols=101  Identities=11%  Similarity=-0.014  Sum_probs=51.8

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcccc---CCCceeEEEECCCCCCCCHHHHHHHHHHHhCC-----
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVK---HYFDCHAWITEPYSNEYDADQILDIVIKFLMP-----  238 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~---~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~-----  238 (824)
                      ++++.+..-. .-..++|+|..|+|||||++.+.+  .+.   ..++++ ++-  +.+....-   .++.+.+..     
T Consensus       163 raID~~~pi~-rGQr~~IvG~sG~GKTtLl~~Iar--~i~~~~~~v~~I-~~l--IGER~~Ev---~~~~~~~~~~vV~a  233 (422)
T 3ice_A          163 RVLDLASPIG-RGQRGLIVAPPKAGKTMLLQNIAQ--SIAYNHPDCVLM-VLL--IDERPEEV---TEMQRLVKGEVVAS  233 (422)
T ss_dssp             HHHHHHSCCB-TTCEEEEECCSSSSHHHHHHHHHH--HHHHHCTTSEEE-EEE--ESSCHHHH---HHHHTTCSSEEEEE
T ss_pred             eeeeeeeeec-CCcEEEEecCCCCChhHHHHHHHH--HHhhcCCCeeEE-EEE--ecCChHHH---HHHHHHhCeEEEEe
Confidence            3445544322 235899999999999999998877  332   233333 455  55543222   223333311     


Q ss_pred             CCCcccccccCHHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          239 SSRLSEIMDKNYEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      ..+.|...........-.+.+++  +++.+||++||+-..
T Consensus       234 tadep~~~r~~~a~~alt~AEyfrd~G~dVLil~DslTR~  273 (422)
T 3ice_A          234 TFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRL  273 (422)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHHHHHHTSCEEEEEEECHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhcCCCEEEEEeCchHH
Confidence            11101000000111112223333  589999999999643

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=93.92  E-value=0.034  Score=58.56  Aligned_cols=42  Identities=21%  Similarity=0.166  Sum_probs=36.3

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|++..++.+...+..+.    -+-++|.+|+|||+||+.+.+
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~----~vll~G~pGtGKT~la~~la~   68 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG----HILLEGVPGLAKTLSVNTLAK   68 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC----CEEEESCCCHHHHHHHHHHHH
T ss_pred             cceeCcHHHHHHHHHHHHcCC----eEEEECCCCCcHHHHHHHHHH
Confidence            468899999999888887643    578899999999999999988

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=93.92  E-value=0.095  Score=53.96  Aligned_cols=86  Identities=14%  Similarity=0.047  Sum_probs=45.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccC-CCceeEEEECCCC-CCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFDCHAWITEPYS-NEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKI  255 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~~~vs-~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~  255 (824)
                      ..++|+|+|.+|+||||++..+..  .... .=..+..++  .. ......+.+....+..+...    ....+...+..
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~--~l~~~~G~~V~lv~--~D~~r~~a~eqL~~~~~~~gl~~----~~~~~~~~l~~  175 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAA--ISMLEKHKKIAFIT--TDTYRIAAVEQLKTYAELLQAPL----EVCYTKEEFQQ  175 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHH--HHHHTTCCCEEEEE--CCCSSTTHHHHHHHHHTTTTCCC----CBCSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH--HHHHhcCCEEEEEe--cCcccchHHHHHHHHHHhcCCCe----EecCCHHHHHH
Confidence            357999999999999999999876  3321 112455565  22 22233333333333332211    11123344444


Q ss_pred             HHHHhcCCCeEEEEEecC
Q 003387          256 ILHEYLMTKRYLIVIDDV  273 (824)
Q Consensus       256 ~l~~~L~~kr~LlVlDdv  273 (824)
                      .+.. + .+.=++++|-.
T Consensus       176 al~~-~-~~~dlvIiDT~  191 (296)
T 2px0_A          176 AKEL-F-SEYDHVFVDTA  191 (296)
T ss_dssp             HHHH-G-GGSSEEEEECC
T ss_pred             HHHH-h-cCCCEEEEeCC
Confidence            4443 3 33447788843

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=93.90  E-value=0.021  Score=53.55  Aligned_cols=22  Identities=9%  Similarity=0.249  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|+|+|+.|+||||+++.+..
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~   26 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQ   26 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999987

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=93.90  E-value=0.03  Score=52.55  Aligned_cols=23  Identities=35%  Similarity=0.611  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.++.
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~~   31 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHFK   31 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CEEEEEECCCCCCHHHHHHHHcc
Confidence            46899999999999999997664

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=93.84  E-value=0.052  Score=56.77  Aligned_cols=43  Identities=23%  Similarity=0.251  Sum_probs=32.6

Q ss_pred             eechhhHHHHHHHHHc--CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          159 VGLDDRMEELLDLLIE--GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       159 vGr~~~~~~l~~~L~~--~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      |+.+.-.+++++.+..  ..+....|.|+|+.|+||||+++.+..
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~   46 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQ   46 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHH
Confidence            4455666777777653  233467799999999999999998877

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=93.76  E-value=0.033  Score=52.40  Aligned_cols=23  Identities=22%  Similarity=0.294  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|+.|+||||+++.+..
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHH
Confidence            57899999999999999999876

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=93.74  E-value=0.033  Score=53.21  Aligned_cols=22  Identities=14%  Similarity=0.155  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|+|+.|.||||+++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            5789999999999999999975

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=93.72  E-value=0.02  Score=56.18  Aligned_cols=112  Identities=14%  Similarity=-0.041  Sum_probs=63.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILH  258 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~  258 (824)
                      -.++.|+|..|.||||++..+.+  +...+-..++.+.  ....  .+ -..++++.++....  ........+....+.
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~--r~~~~g~kVli~~--~~~d--~r-~~~~i~srlG~~~~--~~~~~~~~~i~~~i~   82 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLH--RLEYADVKYLVFK--PKID--TR-SIRNIQSRTGTSLP--SVEVESAPEILNYIM   82 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHH--HHHHTTCCEEEEE--ECCC--GG-GCSSCCCCCCCSSC--CEEESSTHHHHHHHH
T ss_pred             cEEEEEECCCCCcHHHHHHHHHH--HHHhcCCEEEEEE--eccC--ch-HHHHHHHhcCCCcc--ccccCCHHHHHHHHH
Confidence            46889999999999999987776  3333322344443  2221  11 11234444443221  122234456666666


Q ss_pred             HhcCCCeE-EEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          259 EYLMTKRY-LIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       259 ~~L~~kr~-LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      +.+.+.++ +||+|.+..-  +..+.+.. +.+  .|-.||+|-+..
T Consensus        83 ~~~~~~~~dvViIDEaQ~l~~~~ve~l~~-L~~--~gi~Vil~Gl~~  126 (223)
T 2b8t_A           83 SNSFNDETKVIGIDEVQFFDDRICEVANI-LAE--NGFVVIISGLDK  126 (223)
T ss_dssp             STTSCTTCCEEEECSGGGSCTHHHHHHHH-HHH--TTCEEEEECCSB
T ss_pred             HHhhCCCCCEEEEecCccCcHHHHHHHHH-HHh--CCCeEEEEeccc
Confidence            66655555 9999999642  34444432 222  267889888855

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=93.69  E-value=0.024  Score=53.89  Aligned_cols=23  Identities=17%  Similarity=0.330  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+.|.|+|+.|+||||+|+.+..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45788999999999999999987

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=93.64  E-value=0.04  Score=56.34  Aligned_cols=48  Identities=21%  Similarity=0.260  Sum_probs=34.9

Q ss_pred             CCCCCceechhhHHHHHHHHHc--C---------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLLIE--G---------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~--~---------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..-++++|.++.++++.+....  .         .-... +.|+|..|+||||||+.+.+
T Consensus        37 ~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~g-vll~Gp~GtGKTtl~~~i~~   95 (278)
T 1iy2_A           37 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAG   95 (278)
T ss_dssp             CCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCE-EEEECCTTSSHHHHHHHHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCcChHHHHHHHHHH
Confidence            3456789988877776655432  1         01122 89999999999999999998

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=93.62  E-value=0.051  Score=60.25  Aligned_cols=42  Identities=17%  Similarity=0.135  Sum_probs=36.2

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.+..++.+...+..+.    -|-++|.+|+|||+||+.+.+
T Consensus        22 ~~ivGq~~~i~~l~~al~~~~----~VLL~GpPGtGKT~LAraLa~   63 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKF   63 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTC----EEEEECCSSSSHHHHHHHGGG
T ss_pred             hhhHHHHHHHHHHHHHHhcCC----eeEeecCchHHHHHHHHHHHH
Confidence            467899999988888877653    678999999999999999998

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=93.62  E-value=0.036  Score=53.57  Aligned_cols=23  Identities=17%  Similarity=0.104  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|.|+|+.|.||||+|+.+..
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~   47 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQ   47 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999999988

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=93.60  E-value=0.032  Score=52.75  Aligned_cols=22  Identities=18%  Similarity=0.256  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .++|+|..|+|||||++.+...
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998763

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=93.59  E-value=0.09  Score=55.61  Aligned_cols=111  Identities=12%  Similarity=0.108  Sum_probs=64.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCce-eEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccc-cccCHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDC-HAWITEPYSNEYDADQILDIVIKFLMPSSRLSEI-MDKNYEMKKII  256 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~-~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~-~~~~~~~~~~~  256 (824)
                      -.+++|+|+.|.||||+.+.+.+  .+...... ++.+.+++.-....            ......+. ...+.......
T Consensus       123 ~g~i~I~GptGSGKTTlL~~l~g--~~~~~~~~~i~t~ed~~e~~~~~------------~~~~v~q~~~~~~~~~~~~~  188 (356)
T 3jvv_A          123 RGLVLVTGPTGSGKSTTLAAMLD--YLNNTKYHHILTIEDPIEFVHES------------KKCLVNQREVHRDTLGFSEA  188 (356)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHH--HHHHHCCCEEEEEESSCCSCCCC------------SSSEEEEEEBTTTBSCHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh--cccCCCCcEEEEccCcHHhhhhc------------cccceeeeeeccccCCHHHH
Confidence            34999999999999999999877  33322222 23333211110000            00000000 00111234457


Q ss_pred             HHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          257 LHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       257 l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      |...|....=+|++|.+-+.+.++.+....   ..|.-|++||-..+.+.
T Consensus       189 La~aL~~~PdvillDEp~d~e~~~~~~~~~---~~G~~vl~t~H~~~~~~  235 (356)
T 3jvv_A          189 LRSALREDPDIILVGEMRDLETIRLALTAA---ETGHLVFGTLHTTSAAK  235 (356)
T ss_dssp             HHHHTTSCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEESCSSHHH
T ss_pred             HHHHhhhCcCEEecCCCCCHHHHHHHHHHH---hcCCEEEEEEccChHHH
Confidence            888898888899999999877666655432   23666888887765544

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=93.59  E-value=0.033  Score=53.89  Aligned_cols=22  Identities=18%  Similarity=0.215  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|+|+.|+|||||++.+..
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~   29 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVK   29 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHHh
Confidence            5899999999999999999977

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=93.56  E-value=0.11  Score=56.32  Aligned_cols=24  Identities=21%  Similarity=0.206  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|.++|.+|+||||++..+..
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~  119 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAY  119 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999998876

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=93.56  E-value=0.04  Score=53.48  Aligned_cols=24  Identities=17%  Similarity=0.159  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|+|+.|.||||+|+.+..
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~   43 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQK   43 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999987

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=93.52  E-value=0.032  Score=53.86  Aligned_cols=23  Identities=22%  Similarity=0.225  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|+.|+||||+++.+..
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~   51 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVAD   51 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999987

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=93.49  E-value=0.031  Score=53.37  Aligned_cols=22  Identities=9%  Similarity=0.152  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|.|+.|+||||+|+.+.+
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~   23 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999987

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=93.43  E-value=0.077  Score=54.83  Aligned_cols=92  Identities=13%  Similarity=0.059  Sum_probs=48.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHH--HHHHHHHHHhCCCCCcccccccCHHHH-H
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDAD--QILDIVIKFLMPSSRLSEIMDKNYEMK-K  254 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~--~~~~~i~~~l~~~~~~~~~~~~~~~~~-~  254 (824)
                      ...+|.|+|.+|+||||++..+..  .....=..+.++.  . ..+...  +-+...++..+... .+.....+.... .
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~--~l~~~g~kV~lv~--~-D~~r~~a~eqL~~~~~~~gl~~-~~~~s~~~~~~v~~  176 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAK--MFVDEGKSVVLAA--A-DTFRAAAIEQLKIWGERVGATV-ISHSEGADPAAVAF  176 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHH--HHHHTTCCEEEEE--E-CTTCHHHHHHHHHHHHHHTCEE-ECCSTTCCHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHH--HHHhcCCEEEEEc--c-ccccHHHHHHHHHHHHHcCCcE-EecCCccCHHHHHH
Confidence            468999999999999999999887  3332222345554  2 222222  22334445444311 000111122222 2


Q ss_pred             HHHHHhcCCCeEEEEEecCCC
Q 003387          255 IILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       255 ~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      ..+...+..+.-++++|-.-.
T Consensus       177 ~al~~a~~~~~dvvIiDtpg~  197 (306)
T 1vma_A          177 DAVAHALARNKDVVIIDTAGR  197 (306)
T ss_dssp             HHHHHHHHTTCSEEEEEECCC
T ss_pred             HHHHHHHhcCCCEEEEECCCc
Confidence            344444444444788887643

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=93.39  E-value=0.041  Score=53.58  Aligned_cols=24  Identities=21%  Similarity=0.158  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|+|..|.|||||++.+..
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~   28 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALAR   28 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999887

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=93.36  E-value=0.029  Score=54.32  Aligned_cols=23  Identities=9%  Similarity=0.170  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|+.|+||||+|+.+..
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~   40 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAE   40 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999977

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=93.34  E-value=0.043  Score=53.18  Aligned_cols=22  Identities=27%  Similarity=0.320  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|+|+|+.|.||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=93.33  E-value=0.079  Score=51.40  Aligned_cols=23  Identities=17%  Similarity=-0.000  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|.|+.|+||||+|+.+.+
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~   26 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKD   26 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH
Confidence            36899999999999999999987

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=93.25  E-value=0.039  Score=51.51  Aligned_cols=24  Identities=17%  Similarity=0.261  Sum_probs=20.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~   29 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGL   29 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHH
T ss_pred             ccceEEEECCCCCCHHHHHHHHHH
Confidence            367999999999999999999977

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=93.23  E-value=0.046  Score=52.22  Aligned_cols=23  Identities=9%  Similarity=0.101  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|+.|+||||+|+.+..
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~   27 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALAT   27 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999976

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=93.23  E-value=0.083  Score=57.42  Aligned_cols=49  Identities=8%  Similarity=0.215  Sum_probs=32.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCC-ceeEEEECCCCCCC-CHHHHHHHHH
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYF-DCHAWITEPYSNEY-DADQILDIVI  233 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F-~~~~wv~~~vs~~~-~~~~~~~~i~  233 (824)
                      .++|+|..|+|||||++.+..+  ....+ +.++++-  +.+.. ...++..++.
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~--~~~~~~~i~V~~~--iGerttev~el~~~l~  203 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHN--IAQEHGGISVFAG--VGERTREGNDLYHEMK  203 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHH--HHHHTCCCEEEEE--ESSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhh--hhhccCcEEEEee--eccCchHHHHHHHHhh
Confidence            5899999999999999998873  32222 3455665  55553 3334555454

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=93.21  E-value=0.039  Score=53.44  Aligned_cols=23  Identities=9%  Similarity=0.192  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|+.|+||||+++.+..
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~   28 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFE   28 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999977

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=93.21  E-value=0.039  Score=53.36  Aligned_cols=22  Identities=18%  Similarity=0.229  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|+|+|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            4799999999999999999876

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=93.20  E-value=0.039  Score=53.69  Aligned_cols=23  Identities=9%  Similarity=0.202  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|+.|+|||||++.+..
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~   30 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFK   30 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECcCCCCHHHHHHHHHh
Confidence            46899999999999999999987

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=93.20  E-value=0.039  Score=52.65  Aligned_cols=22  Identities=23%  Similarity=0.243  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|.|+.|+||||+|+.+.+
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~   25 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMD   25 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999987

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=93.20  E-value=0.053  Score=58.19  Aligned_cols=46  Identities=13%  Similarity=0.097  Sum_probs=35.2

Q ss_pred             CCceechhhHHHHHHHHHc----------------------------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIE----------------------------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~----------------------------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.+..++.|...+..                            .......+.++|+.|+||||+|+.+.+
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~   94 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAK   94 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHH
Confidence            4578988888888777621                            111234688999999999999999998

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.15  E-value=0.076  Score=52.16  Aligned_cols=37  Identities=16%  Similarity=0.199  Sum_probs=27.4

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..+.+.+.+...  ...+|.|+|.+|+|||||+..+...
T Consensus        25 ~a~~~r~~~~~~--~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           25 LADKNRKLLNKH--GVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             HHHHHHHHHHHT--TCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC--CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            344444444333  4789999999999999999998873

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=93.14  E-value=0.048  Score=52.60  Aligned_cols=25  Identities=20%  Similarity=0.254  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +...+|+|+|+.|+||||+|+.+..
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHH
Confidence            3478999999999999999999987

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=93.11  E-value=0.047  Score=51.90  Aligned_cols=109  Identities=13%  Similarity=-0.027  Sum_probs=50.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHE  259 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  259 (824)
                      .++.|+|..|+||||++..+..... .... .++.+.  ...  |.+.-...+...++....  .....+.    ..+.+
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~-~~g~-~v~~~~--~~~--d~r~~~~~i~s~~g~~~~--~~~~~~~----~~~~~   71 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYK-LGKK-KVAVFK--PKI--DSRYHSTMIVSHSGNGVE--AHVIERP----EEMRK   71 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHH-HTTC-EEEEEE--EC-------CCCEECC----CEE--CEEESSG----GGGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH-HCCC-eEEEEe--ecc--ccccCcccEEecCCCcee--eEEECCH----HHHHH
Confidence            4788999999999999955554211 1122 233332  111  100000011111111100  0111111    22333


Q ss_pred             hcCCCeEEEEEecCCCh-hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          260 YLMTKRYLIVIDDVWSI-DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       260 ~L~~kr~LlVlDdv~~~-~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      .+.++.-+|++|.+... .+|......+.+.  |..|++|.++.
T Consensus        72 ~~~~~~dvviIDE~Q~~~~~~~~~l~~l~~~--~~~Vi~~Gl~~  113 (184)
T 2orw_A           72 YIEEDTRGVFIDEVQFFNPSLFEVVKDLLDR--GIDVFCAGLDL  113 (184)
T ss_dssp             GCCTTEEEEEECCGGGSCTTHHHHHHHHHHT--TCEEEEEEESB
T ss_pred             HhcCCCCEEEEECcccCCHHHHHHHHHHHHC--CCCEEEEeecc
Confidence            44455679999999754 3454444333222  67899988754

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=93.11  E-value=0.038  Score=53.39  Aligned_cols=21  Identities=24%  Similarity=0.471  Sum_probs=19.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +|+|.|+.|+||||+|+.+.+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISK   22 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHH
Confidence            689999999999999999987

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=93.08  E-value=0.12  Score=50.92  Aligned_cols=47  Identities=15%  Similarity=0.258  Sum_probs=31.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccc---cC-CCceeEEEECCCCCCCCHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYV---KH-YFDCHAWITEPYSNEYDAD  226 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~---~~-~F~~~~wv~~~vs~~~~~~  226 (824)
                      .-.+++|+|..|+|||||++.+......   .. .-..++|+.  -...+...
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~--~~~~~~~~   74 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID--TENTFRPE   74 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEE--SSSCCCHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEE--CCCCCCHH
Confidence            3579999999999999999999752111   11 234578887  44434433

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=93.06  E-value=0.036  Score=53.50  Aligned_cols=23  Identities=13%  Similarity=0.218  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|+|+.|+|||||++.+..
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35789999999999999999876

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=93.04  E-value=0.035  Score=53.83  Aligned_cols=23  Identities=9%  Similarity=0.250  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.|+|+.|+||||+++.+..
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~   34 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLS   34 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999977

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=93.03  E-value=0.074  Score=55.26  Aligned_cols=25  Identities=12%  Similarity=0.118  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ....+|||.|..|+||||+|+.+..
T Consensus        90 ~~p~iigI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           90 KVPYIIGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4577999999999999999999866

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=92.99  E-value=0.069  Score=53.37  Aligned_cols=38  Identities=13%  Similarity=-0.069  Sum_probs=27.5

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+.++............+|.|.|+.|+||||+|+.+.+
T Consensus        14 ~~~~~~~~~~~~~~~~~~I~l~G~~GsGKsT~a~~L~~   51 (243)
T 3tlx_A           14 LLNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKK   51 (243)
T ss_dssp             HHHHHHHHHHHHTSCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCcEEEEECCCCCCHHHHHHHHHH
Confidence            33444444433333567899999999999999999976

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=92.99  E-value=0.032  Score=53.04  Aligned_cols=30  Identities=13%  Similarity=0.195  Sum_probs=23.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCce
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDC  211 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~  211 (824)
                      +.|.|+|+.|+|||||++.+..  +....|..
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~--~~~~~~~~   31 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFA--EYPDSFGF   31 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH--HCTTTEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--hCCCCeEE
Confidence            4578999999999999999987  33444543

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=92.98  E-value=0.051  Score=54.63  Aligned_cols=24  Identities=4%  Similarity=0.117  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999876

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=92.97  E-value=0.038  Score=52.26  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|+.|+||||+|+.+..
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~   33 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELAS   33 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHH
Confidence            45788999999999999999986

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=92.96  E-value=0.05  Score=54.74  Aligned_cols=22  Identities=18%  Similarity=0.013  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.|+|+.|+||||||+.+..
T Consensus         2 ~li~I~G~~GSGKSTla~~La~   23 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQ   23 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            5789999999999999999976

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=92.96  E-value=0.055  Score=49.92  Aligned_cols=24  Identities=17%  Similarity=0.239  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+++|+|..|.|||||++.+..
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g   55 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQ   55 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            356999999999999999999987

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=92.95  E-value=0.052  Score=51.60  Aligned_cols=24  Identities=25%  Similarity=0.111  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+|.|+|+.|+||||+++.+..
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~   35 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLAD   35 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357899999999999999999987

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=92.95  E-value=0.057  Score=52.15  Aligned_cols=24  Identities=25%  Similarity=0.292  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|.|+.|+||||+|+.+.+
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~   37 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVK   37 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999986

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=92.93  E-value=0.078  Score=54.40  Aligned_cols=38  Identities=21%  Similarity=0.343  Sum_probs=27.8

Q ss_pred             hHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          164 RMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       164 ~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++++..+..+   .....+|.|+|++|+||||+|+.+..
T Consensus        15 ~~~~~~~~~l~~~~~~~~~~livl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           15 RLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             HHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            344444444433   23468999999999999999999976

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=92.91  E-value=0.051  Score=51.66  Aligned_cols=23  Identities=22%  Similarity=0.079  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|+|+.|+||||+|+.+.+
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=92.91  E-value=0.049  Score=50.69  Aligned_cols=24  Identities=13%  Similarity=0.068  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+++|+|..|+|||||+..+..
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~   26 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVA   26 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            367999999999999999999987

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=92.90  E-value=0.069  Score=52.26  Aligned_cols=40  Identities=23%  Similarity=0.192  Sum_probs=30.4

Q ss_pred             echhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          160 GLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.++..+.+.+.+...  ...+|.|+|.+|+|||||+..+..
T Consensus        13 ~~~~~~~~~~~~~~~~--~~~~i~i~G~~g~GKTTl~~~l~~   52 (221)
T 2wsm_A           13 ENKRLAEKNREALRES--GTVAVNIMGAIGSGKTLLIERTIE   52 (221)
T ss_dssp             HHHHHHHHHHHHHHHH--TCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hcHHHHHHHHHhhccc--CceEEEEEcCCCCCHHHHHHHHHH
Confidence            4445555565555433  378999999999999999999877

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=92.89  E-value=0.083  Score=56.12  Aligned_cols=37  Identities=19%  Similarity=0.116  Sum_probs=28.7

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++.+.+........+|+|+|.+|+|||||+..+..
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHH
Confidence            4455555554445688999999999999999998865

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=92.88  E-value=0.098  Score=54.49  Aligned_cols=37  Identities=16%  Similarity=0.099  Sum_probs=27.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ..++|+|+|.+|+||||++..+..  .....=..+.+++
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~--~l~~~g~kVllid  140 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMAN--YYAELGYKVLIAA  140 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHHHCCCeEEEEe
Confidence            468999999999999999999877  3333223455665

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=92.88  E-value=0.048  Score=53.70  Aligned_cols=22  Identities=18%  Similarity=0.211  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|+|+|+.|+||||+|+.+..
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999977

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=92.85  E-value=0.048  Score=52.98  Aligned_cols=23  Identities=13%  Similarity=0.053  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|+|||||++.+..
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~g   42 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRE   42 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            45899999999999999999876

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=92.84  E-value=0.056  Score=56.12  Aligned_cols=25  Identities=16%  Similarity=0.226  Sum_probs=22.5

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ....+|+|+|..|+|||||++.+..
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~g  112 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQA  112 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHh
Confidence            3468999999999999999999887

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=92.82  E-value=0.05  Score=54.48  Aligned_cols=23  Identities=22%  Similarity=0.161  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|+|+.|+|||||++.+.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999994

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=92.80  E-value=0.055  Score=51.35  Aligned_cols=23  Identities=22%  Similarity=0.111  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|.|.|+.|+||||+|+.+.+
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45799999999999999999976

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=92.79  E-value=0.056  Score=51.68  Aligned_cols=23  Identities=22%  Similarity=0.163  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|.|+.|+||||+|+.+.+
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~   25 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVE   25 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=92.77  E-value=0.041  Score=51.77  Aligned_cols=22  Identities=14%  Similarity=0.235  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.|+|+.|+||||+|+.+..
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~   26 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAK   26 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            3689999999999999999987

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=92.66  E-value=0.078  Score=53.30  Aligned_cols=40  Identities=18%  Similarity=0.142  Sum_probs=29.5

Q ss_pred             hhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          162 DDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       162 ~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +...+++++.+..+   .....+|.|+|++|+||||+|+.+..
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~i~l~G~~GsGKSTla~~L~~   54 (253)
T 2p5t_B           12 KHALARNLRSLTRGKKSSKQPIAILLGGQSGAGKTTIHRIKQK   54 (253)
T ss_dssp             HHHHHHHHHHHHTTCCCCSSCEEEEEESCGGGTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCCcccCCeEEEEECCCCCCHHHHHHHHHH
Confidence            34445555555543   23468999999999999999999977

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=92.65  E-value=0.13  Score=56.04  Aligned_cols=101  Identities=18%  Similarity=0.157  Sum_probs=54.2

Q ss_pred             HHHHHHc-CCCCeEEEEEEcCCCChHHHHH-HHHhCCccccCCCce-eEEEECCCCCCC-CHHHHHHHHHHHhCC-----
Q 003387          168 LLDLLIE-GPPQLSVVAILDSIGLDKTAFA-GEAYNSSYVKHYFDC-HAWITEPYSNEY-DADQILDIVIKFLMP-----  238 (824)
Q Consensus       168 l~~~L~~-~~~~~~vi~I~G~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~~~vs~~~-~~~~~~~~i~~~l~~-----  238 (824)
                      .++.|.. +.  -.-++|+|..|+|||+|| ..|.|.  .  .-+. ++++-  +.+.. .+.++.+++...=..     
T Consensus       165 aID~l~Pigr--GQR~~I~g~~g~GKT~Lal~~I~~~--~--~~dv~~V~~~--IGeR~~Ev~e~~~~~~~~g~m~rtvv  236 (515)
T 2r9v_A          165 AIDSMIPIGR--GQRELIIGDRQTGKTAIAIDTIINQ--K--GQGVYCIYVA--IGQKKSAIARIIDKLRQYGAMEYTTV  236 (515)
T ss_dssp             HHHHHSCEET--TCBEEEEEETTSSHHHHHHHHHHTT--T--TTTEEEEEEE--ESCCHHHHHHHHHHHHHTTGGGGEEE
T ss_pred             cccccccccc--CCEEEEEcCCCCCccHHHHHHHHHh--h--cCCcEEEEEE--cCCCcHHHHHHHHHHHhCCCcceeEE
Confidence            4555543 22  246899999999999995 588883  2  2443 35555  66654 334555555442110     


Q ss_pred             ---CCCcccccccCHHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          239 ---SSRLSEIMDKNYEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       239 ---~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                         ..+.|.....-.......+.+++  ++|.+||++||+..-
T Consensus       237 V~atad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~DslTr~  279 (515)
T 2r9v_A          237 VVASASDPASLQYIAPYAGCAMGEYFAYSGRDALVVYDDLSKH  279 (515)
T ss_dssp             EEECTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHHHH
T ss_pred             EEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEeccHHHH
Confidence               11111000000111122333333  579999999999643

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=92.61  E-value=0.063  Score=51.40  Aligned_cols=24  Identities=21%  Similarity=0.268  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+|+|+|+.|+||||+|+.+.+
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999999877

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=92.61  E-value=0.062  Score=54.31  Aligned_cols=23  Identities=13%  Similarity=0.313  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|++|+||||+|+.+..
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~   26 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAK   26 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=92.57  E-value=0.042  Score=52.13  Aligned_cols=22  Identities=9%  Similarity=0.110  Sum_probs=20.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|+|+.|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3589999999999999999977

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=92.55  E-value=0.056  Score=51.75  Aligned_cols=23  Identities=9%  Similarity=0.157  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|+.|+||||+|+.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~   31 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=92.52  E-value=0.058  Score=51.68  Aligned_cols=24  Identities=4%  Similarity=0.230  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-++|+|+|+.|+|||||++.+..
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~   41 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLS   41 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHh
Confidence            357899999999999999999986

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=92.51  E-value=0.1  Score=51.79  Aligned_cols=23  Identities=17%  Similarity=0.108  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||++.+..
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            45899999999999999999987

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=92.46  E-value=0.048  Score=53.49  Aligned_cols=23  Identities=17%  Similarity=0.252  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|+|||||++.+..
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g   45 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLN   45 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            45899999999999999999877

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=92.46  E-value=0.07  Score=53.36  Aligned_cols=23  Identities=4%  Similarity=0.088  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|..|.|||||++.+..
T Consensus        25 g~iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           25 PFLIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999999876

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=92.45  E-value=0.1  Score=51.92  Aligned_cols=22  Identities=18%  Similarity=0.246  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|+|..|.|||||.+.+..
T Consensus        25 e~~~liG~nGsGKSTLl~~l~G   46 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHhC
Confidence            7999999999999999999987

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=92.45  E-value=0.32  Score=51.18  Aligned_cols=35  Identities=23%  Similarity=0.118  Sum_probs=26.6

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++.+..=. .-.-++|+|..|+|||||++.+.+
T Consensus       163 iraID~l~Pig-rGQR~lIfg~~g~GKT~Ll~~Ia~  197 (427)
T 3l0o_A          163 TRLIDLFAPIG-KGQRGMIVAPPKAGKTTILKEIAN  197 (427)
T ss_dssp             HHHHHHHSCCB-TTCEEEEEECTTCCHHHHHHHHHH
T ss_pred             chhhhhccccc-CCceEEEecCCCCChhHHHHHHHH
Confidence            35666665422 234789999999999999999888

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=92.43  E-value=0.049  Score=51.01  Aligned_cols=22  Identities=14%  Similarity=0.143  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|.|+.|+||||+|+.+.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELAR   24 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999977

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=92.39  E-value=0.065  Score=51.08  Aligned_cols=23  Identities=22%  Similarity=0.192  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~   28 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999977

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=92.38  E-value=0.056  Score=51.89  Aligned_cols=23  Identities=13%  Similarity=0.167  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~   34 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVE   34 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=92.37  E-value=0.18  Score=54.41  Aligned_cols=36  Identities=17%  Similarity=0.022  Sum_probs=26.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ..+|.|+|.+|+||||++..+..  .....=..+..++
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~--~l~~~g~~Vllvd  133 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLAL--YYKGKGRRPLLVA  133 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHH--HHHTTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH--HHHHcCCeEEEee
Confidence            67999999999999999999887  3433323445555

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=92.34  E-value=0.1  Score=51.28  Aligned_cols=23  Identities=17%  Similarity=0.037  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||.+.+..
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~G   52 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGL   52 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999987

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=92.33  E-value=0.065  Score=49.84  Aligned_cols=21  Identities=5%  Similarity=0.018  Sum_probs=19.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.|.|+.|+||||+|+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSR   22 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=92.33  E-value=0.11  Score=52.90  Aligned_cols=23  Identities=26%  Similarity=0.254  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||++.+..
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHc
Confidence            35899999999999999999987

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=92.27  E-value=0.12  Score=55.15  Aligned_cols=110  Identities=14%  Similarity=0.201  Sum_probs=60.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeE-EEECCCCCCCCHHHHHHHHHHHhCCCCC-cccc-cccCHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHA-WITEPYSNEYDADQILDIVIKFLMPSSR-LSEI-MDKNYEMKKI  255 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~-wv~~~vs~~~~~~~~~~~i~~~l~~~~~-~~~~-~~~~~~~~~~  255 (824)
                      -.+++|+|..|.||||+++.+..  .+.......+ ++.+++.  +.           +..... .++. -..+......
T Consensus       136 g~~i~ivG~~GsGKTTll~~l~~--~~~~~~~g~I~~~e~~~e--~~-----------~~~~~~~v~Q~~~g~~~~~~~~  200 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIASMID--YINQTKSYHIITIEDPIE--YV-----------FKHKKSIVNQREVGEDTKSFAD  200 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHHHHH--HHHHHSCCEEEEEESSCC--SC-----------CCCSSSEEEEEEBTTTBSCSHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh--hcCcCCCcEEEEecccHh--hh-----------hccCceEEEeeecCCCHHHHHH
Confidence            56899999999999999999987  3332223333 4431111  10           000000 0000 0001122345


Q ss_pred             HHHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          256 ILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       256 ~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      .+...|....=+|++|.+.+.+.........   ..|.-|+.|+-..++..
T Consensus       201 ~l~~~L~~~pd~illdE~~d~e~~~~~l~~~---~~g~~vi~t~H~~~~~~  248 (372)
T 2ewv_A          201 ALRAALREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNTAID  248 (372)
T ss_dssp             HHHHHTTSCCSEEEESCCCSHHHHHHHHHHH---TTTCEEEECCCCCSHHH
T ss_pred             HHHHHhhhCcCEEEECCCCCHHHHHHHHHHH---hcCCEEEEEECcchHHH
Confidence            6777777677789999998765544433222   23666887776655433

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=92.27  E-value=0.35  Score=52.33  Aligned_cols=24  Identities=13%  Similarity=0.176  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...||.|+|.+|+||||++..+..
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLAR  122 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHH
Confidence            478999999999999999988876

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=92.25  E-value=0.063  Score=51.30  Aligned_cols=21  Identities=29%  Similarity=0.292  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +|+|.|+.|+||||+|+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=92.22  E-value=0.067  Score=53.78  Aligned_cols=23  Identities=13%  Similarity=0.164  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|+.|.||||+++.+..
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999985

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=92.20  E-value=0.064  Score=52.54  Aligned_cols=23  Identities=9%  Similarity=0.109  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        16 G~ii~l~GpsGsGKSTLlk~L~g   38 (219)
T 1s96_A           16 GTLYIVSAPSGAGKSSLIQALLK   38 (219)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            46999999999999999999987

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=92.18  E-value=0.072  Score=55.04  Aligned_cols=24  Identities=21%  Similarity=0.173  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|+|.+|+||||+++.+..
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            357999999999999999999876

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=92.16  E-value=0.069  Score=51.48  Aligned_cols=23  Identities=22%  Similarity=0.075  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|+.|+||||+|+.+..
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~   42 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAE   42 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999977

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=92.14  E-value=0.051  Score=51.42  Aligned_cols=23  Identities=22%  Similarity=0.190  Sum_probs=16.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~   27 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHE   27 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999976

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=92.12  E-value=0.12  Score=52.27  Aligned_cols=23  Identities=26%  Similarity=0.254  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||.+.+..
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999987

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=92.12  E-value=0.14  Score=55.82  Aligned_cols=95  Identities=12%  Similarity=0.069  Sum_probs=51.9

Q ss_pred             EEEEEEcCCCChHHHHH-HHHhCCccccCCCce-eEEEECCCCCCCC-HHHHHHHHHHHhCC--------CCCcccccc-
Q 003387          180 SVVAILDSIGLDKTAFA-GEAYNSSYVKHYFDC-HAWITEPYSNEYD-ADQILDIVIKFLMP--------SSRLSEIMD-  247 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~~~vs~~~~-~~~~~~~i~~~l~~--------~~~~~~~~~-  247 (824)
                      .-++|+|..|+|||+|| ..|.|.  ..  -+. ++++-  +.+..+ +.++.+++...=..        ..+.|.... 
T Consensus       164 QR~~Ifg~~g~GKT~Lal~~I~~~--~~--~dv~~V~~~--iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~  237 (507)
T 1fx0_A          164 QRELIIGDRQTGKTAVATDTILNQ--QG--QNVICVYVA--IGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQY  237 (507)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTC--CT--TTCEEEEEE--ESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTT
T ss_pred             CEEEEecCCCCCccHHHHHHHHHh--hc--CCcEEEEEE--cCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHH
Confidence            46799999999999995 688884  32  342 35555  665543 33444444331100        111111111 


Q ss_pred             ---cCHHHHHHHHHHhcCCCeEEEEEecCCCh-hhHHHH
Q 003387          248 ---KNYEMKKIILHEYLMTKRYLIVIDDVWSI-DMWDVI  282 (824)
Q Consensus       248 ---~~~~~~~~~l~~~L~~kr~LlVlDdv~~~-~~~~~l  282 (824)
                         ...-..++.+++  ++|.+||++||+... ..+.++
T Consensus       238 ~a~~~a~tiAEyfrd--~G~dVLli~Dsltr~A~A~REi  274 (507)
T 1fx0_A          238 LAPYTGAALAEYFMY--RERHTLIIYDDLSKQAQAYRQM  274 (507)
T ss_dssp             HHHHHHHHHHHHHHH--TTCEEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH--cCCcEEEEEecHHHHHHHHHHH
Confidence               112233444444  589999999998653 234444

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=92.11  E-value=0.075  Score=54.36  Aligned_cols=24  Identities=25%  Similarity=0.246  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999873

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=92.11  E-value=0.1  Score=56.27  Aligned_cols=91  Identities=12%  Similarity=0.131  Sum_probs=51.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCc----eeEEEECCCCCCC-CHHHHHHHHHHHh--CC------CCCcccccc
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFD----CHAWITEPYSNEY-DADQILDIVIKFL--MP------SSRLSEIMD  247 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~----~~~wv~~~vs~~~-~~~~~~~~i~~~l--~~------~~~~~~~~~  247 (824)
                      -++|.|..|+|||||+..+.+....  +-+    .++++-  +.+.. .+.++.+++.+.=  ..      ..+.|....
T Consensus       153 r~~Ifgg~G~GKt~L~~~Ia~~~~~--~~d~~~~~~V~~~--iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r  228 (465)
T 3vr4_D          153 KLPVFSGSGLPHKELAAQIARQATV--LDSSDDFAVVFAA--IGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIER  228 (465)
T ss_dssp             BCCEEECTTSCHHHHHHHHHHHCBC--SSCSSCEEEEEEE--EEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHH
T ss_pred             EEEEeCCCCcChHHHHHHHHHHHHh--ccCCCceEEEEEE--ecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHH
Confidence            4689999999999999999884332  223    455555  55543 3345556554421  00      011110011


Q ss_pred             cCHHHHHHHHHHhc---CCCeEEEEEecCCC
Q 003387          248 KNYEMKKIILHEYL---MTKRYLIVIDDVWS  275 (824)
Q Consensus       248 ~~~~~~~~~l~~~L---~~kr~LlVlDdv~~  275 (824)
                      .-.......+.+++   +++.+||++||+-.
T Consensus       229 ~~a~~~a~tiAEyfrd~~G~~VLl~~DslTr  259 (465)
T 3vr4_D          229 IATPRMALTAAEYLAYEKGMHVLVIMTDMTN  259 (465)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCEEEEEEECHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCeEEEEEcChHH
Confidence            11122233455555   37999999999964

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=92.10  E-value=0.062  Score=51.29  Aligned_cols=21  Identities=24%  Similarity=0.251  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +++|+|..|+|||||++.+..
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g   23 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASE   23 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHh
Confidence            689999999999999999876

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=92.03  E-value=0.053  Score=50.79  Aligned_cols=22  Identities=14%  Similarity=0.193  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|+|..|.|||||++.+..
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~   24 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMP   24 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999887

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=91.97  E-value=0.055  Score=57.33  Aligned_cols=45  Identities=18%  Similarity=0.145  Sum_probs=33.1

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+.++|.+..++.+...+....  ..-+-|+|..|+|||++|+.+.+
T Consensus        23 f~~i~G~~~~~~~l~~~~~~~~--~~~vLl~G~~GtGKT~la~~la~   67 (350)
T 1g8p_A           23 FSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALAA   67 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHHH
T ss_pred             chhccChHHHHHHHHHHhhCCC--CceEEEECCCCccHHHHHHHHHH
Confidence            4568999886665544444322  22388999999999999999987

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=91.96  E-value=0.32  Score=50.81  Aligned_cols=64  Identities=20%  Similarity=0.036  Sum_probs=41.6

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLM  237 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~  237 (824)
                      .|-+++ .+=..-.++.|.|.+|+||||+|..+..+...  .=..++|++    -+.+..++...++....
T Consensus        35 ~LD~~~-gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a~--~g~~Vl~fS----lEms~~ql~~Rlls~~~   98 (338)
T 4a1f_A           35 QLDNYT-SGFNKGSLVIIGARPSMGKTSLMMNMVLSALN--DDRGVAVFS----LEMSAEQLALRALSDLT   98 (338)
T ss_dssp             HHHHHH-CSBCTTCEEEEEECTTSCHHHHHHHHHHHHHH--TTCEEEEEE----SSSCHHHHHHHHHHHHH
T ss_pred             HHHHHh-cCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEe----CCCCHHHHHHHHHHHhh
Confidence            343444 34333568999999999999999988774222  113566665    34567777777766543

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=91.92  E-value=0.077  Score=51.64  Aligned_cols=23  Identities=4%  Similarity=-0.033  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|+.|+||||+|+.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~   31 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVE   31 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=91.91  E-value=0.24  Score=51.50  Aligned_cols=65  Identities=18%  Similarity=0.090  Sum_probs=43.2

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhC
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLM  237 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~  237 (824)
                      ..+-+++ .+=..-.++.|.|.+|+||||+|..+..+.-.+.  ..++|++  ..  .+..++...++....
T Consensus        56 ~~LD~~l-gGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~s--lE--~s~~~l~~R~~~~~~  120 (315)
T 3bh0_A           56 TELDRMT-YGYKRRNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHS--LE--MGKKENIKRLIVTAG  120 (315)
T ss_dssp             HHHHHHH-SSBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEE--SS--SCHHHHHHHHHHHHT
T ss_pred             HHHHhhc-CCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEE--CC--CCHHHHHHHHHHHHc
Confidence            3444444 4433456899999999999999988876322222  5677876  33  467777777776543

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=91.86  E-value=0.12  Score=54.48  Aligned_cols=24  Identities=25%  Similarity=0.257  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+++|+|..|+||||+++.+..
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag  179 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAH  179 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHh
Confidence            457999999999999999999876

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=91.84  E-value=0.25  Score=53.92  Aligned_cols=90  Identities=14%  Similarity=0.103  Sum_probs=49.5

Q ss_pred             EEEEEEcCCCChHHHHH-HHHhCCccccCCCce-eEEEECCCCCCC-CHHHHHHHHHHHhCCC--------CCccccccc
Q 003387          180 SVVAILDSIGLDKTAFA-GEAYNSSYVKHYFDC-HAWITEPYSNEY-DADQILDIVIKFLMPS--------SRLSEIMDK  248 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa-~~v~~~~~~~~~F~~-~~wv~~~vs~~~-~~~~~~~~i~~~l~~~--------~~~~~~~~~  248 (824)
                      .-++|+|..|+|||+|| ..|.|.  .  .-+. ++++-  +.+.. .+.++.+++...=...        .+.|.....
T Consensus       163 QR~~Ifg~~g~GKT~Lal~~I~~~--~--~~dv~~V~~~--iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~  236 (502)
T 2qe7_A          163 QRELIIGDRQTGKTTIAIDTIINQ--K--GQDVICIYVA--IGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLLY  236 (502)
T ss_dssp             CBCEEEECSSSCHHHHHHHHHHGG--G--SCSEEEEEEE--ESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHH
T ss_pred             CEEEEECCCCCCchHHHHHHHHHh--h--cCCcEEEEEE--CCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHH
Confidence            46799999999999995 578883  3  2343 35565  66654 3345555555421111        010000000


Q ss_pred             CHHHHHHHHHHhc--CCCeEEEEEecCCC
Q 003387          249 NYEMKKIILHEYL--MTKRYLIVIDDVWS  275 (824)
Q Consensus       249 ~~~~~~~~l~~~L--~~kr~LlVlDdv~~  275 (824)
                      -.......+.+++  ++|.+||++||+..
T Consensus       237 ~a~~~a~tiAEyfrd~G~dVLl~~Dsltr  265 (502)
T 2qe7_A          237 LAPYAGCAMGEYFMYKGKHALVVYDDLSK  265 (502)
T ss_dssp             HHHHHHHHHHHHHHTTTCEEEEEEECHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcEEEEEecHHH
Confidence            0011122333333  57999999999964

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=91.84  E-value=0.084  Score=57.25  Aligned_cols=52  Identities=15%  Similarity=0.182  Sum_probs=38.5

Q ss_pred             CCceechhhHHHHHHHHHcC------------CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          156 RDTVGLDDRMEELLDLLIEG------------PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      ..++|.+..++.+...+...            ....+-|.++|++|+||||+|+.+.+  .....|
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~--~l~~~~   78 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK--LANAPF   78 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHH--HTTCCE
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHH--HcCCCc
Confidence            46889999888887766321            11245688999999999999999988  444444

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=91.82  E-value=0.14  Score=51.03  Aligned_cols=23  Identities=17%  Similarity=0.192  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||.+.+..
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~G   54 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999987

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=91.81  E-value=0.12  Score=50.42  Aligned_cols=23  Identities=22%  Similarity=0.226  Sum_probs=21.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .+++|+|..|.|||||++.+..-
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            58999999999999999999873

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=91.79  E-value=0.12  Score=50.13  Aligned_cols=22  Identities=27%  Similarity=0.140  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|+|..|.|||||++.+..
T Consensus        23 e~~~liG~nGsGKSTLl~~l~G   44 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAV   44 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            3899999999999999999875

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=91.78  E-value=0.14  Score=51.75  Aligned_cols=23  Identities=22%  Similarity=0.196  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~G   72 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNL   72 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHc
Confidence            46899999999999999999987

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=91.78  E-value=0.089  Score=49.59  Aligned_cols=23  Identities=17%  Similarity=-0.002  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+|+|+|+.|+||||+++.+..
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999977

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=91.72  E-value=0.086  Score=51.40  Aligned_cols=25  Identities=16%  Similarity=0.187  Sum_probs=22.9

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+||.|.|++|+||||.|+.+.+
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~   51 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQ   51 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999999987

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=91.71  E-value=0.044  Score=53.37  Aligned_cols=22  Identities=18%  Similarity=0.173  Sum_probs=20.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|+|+|..|+||||+|+.+..
T Consensus         1 ~~I~i~G~~GsGKsTl~~~L~~   22 (214)
T 1gtv_A            1 MLIAIEGVDGAGKRTLVEKLSG   22 (214)
T ss_dssp             CEEEEEEEEEEEHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            3789999999999999999877

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=91.71  E-value=0.14  Score=51.14  Aligned_cols=23  Identities=17%  Similarity=0.192  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999987

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=91.69  E-value=0.14  Score=51.41  Aligned_cols=23  Identities=13%  Similarity=0.079  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||.+.+..
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~G   63 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIIST   63 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999987

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=91.68  E-value=0.095  Score=54.12  Aligned_cols=24  Identities=25%  Similarity=0.257  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+++|+|..|+||||+++.+..
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag  122 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAH  122 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357999999999999999999876

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=91.67  E-value=0.14  Score=51.50  Aligned_cols=23  Identities=17%  Similarity=0.148  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||.+.+..
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~G   55 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITG   55 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999987

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=91.67  E-value=0.098  Score=51.14  Aligned_cols=23  Identities=26%  Similarity=0.310  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999865

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=91.66  E-value=0.14  Score=51.11  Aligned_cols=23  Identities=17%  Similarity=0.098  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46999999999999999999976

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=91.62  E-value=0.14  Score=51.84  Aligned_cols=23  Identities=22%  Similarity=0.187  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            46899999999999999999987

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=91.62  E-value=0.15  Score=55.88  Aligned_cols=37  Identities=22%  Similarity=0.241  Sum_probs=28.0

Q ss_pred             HHHHHHHHHcCC-------CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          165 MEELLDLLIEGP-------PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       165 ~~~l~~~L~~~~-------~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+.|.+.|....       ..-.+++|+|..|+|||||++.+..
T Consensus       272 ~~~l~~~l~~~~~~Isl~i~~GeVI~LVGpNGSGKTTLl~~LAg  315 (503)
T 2yhs_A          272 KEEMGEILAKVDEPLNVEGKAPFVILMVGVNGVGKTTTIGKLAR  315 (503)
T ss_dssp             HHHHHHHHHTTBCCCCCCSCTTEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCceeeccCCeEEEEECCCcccHHHHHHHHHH
Confidence            445556664321       2457999999999999999999987

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=91.61  E-value=0.14  Score=50.48  Aligned_cols=24  Identities=21%  Similarity=0.177  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999883

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=91.60  E-value=0.14  Score=55.79  Aligned_cols=38  Identities=24%  Similarity=0.181  Sum_probs=28.7

Q ss_pred             hHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          164 RMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       164 ~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++.++|...       ....++|.|+|.+|+||||++..+..
T Consensus        78 ~~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~  122 (433)
T 2xxa_A           78 VRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGK  122 (433)
T ss_dssp             HHHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            345566666532       13478999999999999999988876

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=91.58  E-value=0.079  Score=51.44  Aligned_cols=23  Identities=4%  Similarity=-0.187  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|+.|+||||+|+.+.+
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~   32 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVE   32 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.56  E-value=0.15  Score=51.79  Aligned_cols=23  Identities=26%  Similarity=0.216  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~G   67 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQN   67 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999987

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=91.52  E-value=0.22  Score=63.59  Aligned_cols=99  Identities=18%  Similarity=0.007  Sum_probs=62.2

Q ss_pred             HHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCccc-
Q 003387          167 ELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSE-  244 (824)
Q Consensus       167 ~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~-  244 (824)
                      .+-.+|. .+=..-++|-|+|++|+||||||.++..  +....=..++|++  +...++...     ++.++..-+... 
T Consensus      1414 ~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~--ea~~~G~~v~Fi~--~e~~~~~l~-----a~~~G~dl~~l~v 1484 (2050)
T 3cmu_A         1414 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIA--AAQREGKTCAFID--AEHALDPIY-----ARKLGVDIDNLLC 1484 (2050)
T ss_dssp             HHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHH--HHHTTTCCEEEEC--TTSCCCHHH-----HHHTTCCTTTCEE
T ss_pred             HHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHH--HHHHcCCcEEEEE--cccccCHHH-----HHHcCCCchhcee
Confidence            3555554 3323467999999999999999999877  3333323677888  888777766     445543211000 


Q ss_pred             ccccCHHHHHHHHHHhcC-CCeEEEEEecCC
Q 003387          245 IMDKNYEMKKIILHEYLM-TKRYLIVIDDVW  274 (824)
Q Consensus       245 ~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~  274 (824)
                      ......++....+++..+ .+--+||+|.+.
T Consensus      1485 ~~~~~~E~~l~~~~~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1485 SQPDTGEQALEICDALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             ECCSSHHHHHHHHHHHHHHTCCSEEEESCGG
T ss_pred             ecCChHHHHHHHHHHHHhcCCCCEEEEcChh
Confidence            122234555555555543 466799999994

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=91.49  E-value=1.2  Score=43.74  Aligned_cols=105  Identities=16%  Similarity=0.101  Sum_probs=54.6

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC-ccccCCC-ceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS-SYVKHYF-DCHAWITEPYSNEYDADQILDIVIKFLMPSSR  241 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~-~~~~~~F-~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~  241 (824)
                      ..++++..+..+    +.+.|+|..|.||||+.....-+ ....... ...+.+.  +....-...+.+.+...++....
T Consensus        65 ~q~~~i~~i~~g----~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~--~p~~~la~q~~~~~~~~~~~~~~  138 (235)
T 3llm_A           65 FESEILEAISQN----SVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVT--QPRRISAVSVAERVAFERGEEPG  138 (235)
T ss_dssp             GHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEE--ESSHHHHHHHHHHHHHTTTCCTT
T ss_pred             HHHHHHHHHhcC----CEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEe--ccchHHHHHHHHHHHHHhccccC
Confidence            455566666554    47899999999999866544321 1111222 2233332  22222223444444444432210


Q ss_pred             ----------------cccccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          242 ----------------LSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       242 ----------------~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                                      ...+-..+.+.+...+...+++-+ +||+|.+..
T Consensus       139 ~~~g~~~~~~~~~~~~~~~Ivv~Tpg~l~~~l~~~l~~~~-~lVlDEah~  187 (235)
T 3llm_A          139 KSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAGIRGIS-HVIVDEIHE  187 (235)
T ss_dssp             SSEEEEETTEEECCCSSSEEEEEEHHHHHHHHHHCCTTCC-EEEECCTTS
T ss_pred             ceEEEeechhhccCCCCCeEEEECHHHHHHHHHhhhcCCc-EEEEECCcc
Confidence                            000112345666666766555444 789999986

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=91.45  E-value=0.062  Score=53.19  Aligned_cols=23  Identities=17%  Similarity=0.213  Sum_probs=16.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHh-C
Q 003387          179 LSVVAILDSIGLDKTAFAGEAY-N  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~-~  201 (824)
                      -.+++|+|+.|+|||||++.+. .
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~   50 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEK   50 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC-
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            3689999999999999999998 6

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=91.41  E-value=0.099  Score=51.93  Aligned_cols=24  Identities=17%  Similarity=0.328  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||++.+..-
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl   54 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLAE   54 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999999883

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=91.40  E-value=0.1  Score=50.73  Aligned_cols=23  Identities=13%  Similarity=-0.048  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|+.|+||||+|+.+..
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~   47 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEH   47 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999887

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=91.40  E-value=0.088  Score=50.74  Aligned_cols=23  Identities=9%  Similarity=-0.106  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|+.|+||||+++.+.+
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~   26 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIME   26 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHH
Confidence            35899999999999999999988

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.36  E-value=0.16  Score=51.42  Aligned_cols=23  Identities=9%  Similarity=0.060  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||.+.+..
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~G   55 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAG   55 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35899999999999999999987

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=91.34  E-value=0.48  Score=51.74  Aligned_cols=70  Identities=20%  Similarity=0.127  Sum_probs=42.7

Q ss_pred             eechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHH
Q 003387          159 VGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKF  235 (824)
Q Consensus       159 vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~  235 (824)
                      .|...-...+-+++ .+=..-.++.|.|.+|+||||+|..+..+.-.+  =..++|++    -+-+..++...++..
T Consensus       178 ~gi~TG~~~LD~~l-gGl~~G~liiIaG~pG~GKTtlal~ia~~~a~~--g~~vl~fS----lEms~~ql~~R~~~~  247 (444)
T 3bgw_A          178 TGVPSGFTELDRMT-YGYKRRNFVLIAARPSMGKTAFALKQAKNMSDN--DDVVNLHS----LEMGKKENIKRLIVT  247 (444)
T ss_dssp             CSBCCSCHHHHHHH-SSBCSSCEEEEEECSSSSHHHHHHHHHHHHHHT--TCEEEEEC----SSSCTTHHHHHHHHH
T ss_pred             CCcCCCcHHHHhhc-CCCCCCcEEEEEeCCCCChHHHHHHHHHHHHHc--CCEEEEEE----CCCCHHHHHHHHHHH
Confidence            34444445555555 343345789999999999999998887742222  12566665    233444555555544

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=91.29  E-value=0.11  Score=54.05  Aligned_cols=24  Identities=17%  Similarity=0.158  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|+|..|.|||||++.+..
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999887

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=91.27  E-value=0.22  Score=47.82  Aligned_cols=49  Identities=6%  Similarity=-0.014  Sum_probs=32.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHH
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      .|.|=|..|+||||.++.+.+  .....-..+++..  -.......+..++++
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~--~L~~~g~~v~~tr--eP~~t~~~~~ir~~l   50 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQ--YLEKRGKKVILKR--EPGGTETGEKIRKIL   50 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH--HHHHTTCCEEEEE--SSCSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH--HHHHCCCcEEEEE--CCCCCcHHHHHHHHh
Confidence            478889999999999999988  5555444556555  222323334444444

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=91.26  E-value=0.099  Score=50.99  Aligned_cols=21  Identities=14%  Similarity=0.166  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|+|.|+.|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999876

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=91.23  E-value=0.095  Score=51.66  Aligned_cols=23  Identities=17%  Similarity=0.185  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...|.|.|+.|+||||+|+.+..
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~   29 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITT   29 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=91.15  E-value=0.08  Score=52.98  Aligned_cols=22  Identities=14%  Similarity=0.140  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|+|+|+.|.||||+++.+..
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999987

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=91.14  E-value=0.11  Score=52.25  Aligned_cols=24  Identities=25%  Similarity=0.338  Sum_probs=21.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...++.+.|.||+||||++..+..
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~   36 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGR   36 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHH
Confidence            478899999999999999999875

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=91.09  E-value=0.11  Score=50.99  Aligned_cols=23  Identities=13%  Similarity=0.069  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...|.|.|+.|+||||+|+.+..
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~   26 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQE   26 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            45799999999999999999977

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=91.05  E-value=0.57  Score=55.90  Aligned_cols=21  Identities=10%  Similarity=-0.032  Sum_probs=19.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEA  199 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v  199 (824)
                      -.+++|+|+.|.||||+.+.+
T Consensus       662 g~i~~ItGpNGsGKSTlLr~i  682 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQT  682 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            579999999999999999998

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=91.05  E-value=0.11  Score=50.76  Aligned_cols=21  Identities=10%  Similarity=0.088  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|+|.|+.|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            488999999999999999876

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=91.03  E-value=0.11  Score=48.81  Aligned_cols=23  Identities=17%  Similarity=0.196  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+++|+|..|+|||||++.+..
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~   28 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIP   28 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHH
Confidence            57899999999999999999987

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=91.02  E-value=0.18  Score=51.39  Aligned_cols=23  Identities=13%  Similarity=-0.049  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~G   69 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNA   69 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35899999999999999999988

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=90.99  E-value=0.18  Score=49.71  Aligned_cols=24  Identities=21%  Similarity=0.295  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+|.|.|+.|+||||+++.+.+
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~   48 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYH   48 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHH
Confidence            357899999999999999999988

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=90.90  E-value=0.15  Score=50.88  Aligned_cols=22  Identities=9%  Similarity=0.253  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|+|..|.|||||.+.+..
T Consensus        27 e~~~liG~NGsGKSTLlk~l~G   48 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAG   48 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            5899999999999999999987

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=90.89  E-value=0.12  Score=51.85  Aligned_cols=23  Identities=17%  Similarity=0.138  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        29 Ge~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           29 GEVHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999988

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=90.85  E-value=0.12  Score=53.84  Aligned_cols=22  Identities=18%  Similarity=0.199  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|+|+|+.|+||||||+.+..
T Consensus         8 ~lI~I~GptgSGKTtla~~La~   29 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAK   29 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHH
Confidence            5899999999999999999887

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=90.79  E-value=0.14  Score=47.40  Aligned_cols=23  Identities=9%  Similarity=0.146  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..|+|+|.+|+|||||.+.+.+.
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            56899999999999999999874

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=90.78  E-value=0.12  Score=49.98  Aligned_cols=21  Identities=19%  Similarity=0.154  Sum_probs=20.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +|+|.|+.|+||||+|+.+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            899999999999999999977

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=90.77  E-value=0.18  Score=53.68  Aligned_cols=36  Identities=17%  Similarity=0.190  Sum_probs=27.3

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+++-+..+-..-++++|+|+.|.|||||++.+..
T Consensus       156 ~~~l~~~~~~i~~~~~i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          156 YDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             HHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHhcccccCCCCEEEEECCCCCCHHHHHHHHHh
Confidence            344444443434467999999999999999999987

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=90.77  E-value=0.12  Score=48.95  Aligned_cols=22  Identities=18%  Similarity=0.288  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|+|+|.+|+|||||++.+.+.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999999874

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=90.77  E-value=0.095  Score=56.85  Aligned_cols=93  Identities=13%  Similarity=0.054  Sum_probs=51.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCC--ceeEEEECCCCCCC-CHHHHHHHHHHHhCC--------CCCccccccc
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYF--DCHAWITEPYSNEY-DADQILDIVIKFLMP--------SSRLSEIMDK  248 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~--------~~~~~~~~~~  248 (824)
                      .-++|.|..|+|||+|+..|.++....+.=  +.++++-  +.+.. .+.++.+++...=..        ..+.|.....
T Consensus       153 Qr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~--iGER~~Ev~e~~~~~~~~g~m~rtvvV~~tsd~p~~~r~  230 (469)
T 2c61_A          153 QKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAA--MGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERI  230 (469)
T ss_dssp             CBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEE--EEECHHHHHHHHHHHHHHSGGGGEEEEEEETTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEE--ccCCcHHHHHHHHHHHhccCccceEEEEECCCCCHHHHH
Confidence            356889999999999999998854332211  3455655  55554 344566666543111        0111100111


Q ss_pred             CHHHHHHHHHHhcC---CCeEEEEEecCC
Q 003387          249 NYEMKKIILHEYLM---TKRYLIVIDDVW  274 (824)
Q Consensus       249 ~~~~~~~~l~~~L~---~kr~LlVlDdv~  274 (824)
                      -.......+.++++   ++.+||++||+-
T Consensus       231 ~~~~~a~tiAEyfrdd~G~dVLl~~Dslt  259 (469)
T 2c61_A          231 VTPRMALTAAEYLAYEHGMHVLVILTDIT  259 (469)
T ss_dssp             HHHHHHHHHHHHHHHHHCCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHhcCCeEEEEEeCHH
Confidence            11222334455554   699999999984

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=90.75  E-value=0.15  Score=48.69  Aligned_cols=36  Identities=14%  Similarity=0.193  Sum_probs=26.7

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+..++.. -+.-+.+.|+|++|.||||+|..+.+
T Consensus        45 ~~~l~~~~~~-iPkkn~ili~GPPGtGKTt~a~ala~   80 (212)
T 1tue_A           45 LGALKSFLKG-TPKKNCLVFCGPANTGKSYFGMSFIH   80 (212)
T ss_dssp             HHHHHHHHHT-CTTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHhc-CCcccEEEEECCCCCCHHHHHHHHHH
Confidence            4555555543 22345689999999999999988887

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=90.67  E-value=0.12  Score=52.21  Aligned_cols=24  Identities=21%  Similarity=0.201  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||++.+..-
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999999883

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=90.65  E-value=4.3  Score=42.73  Aligned_cols=25  Identities=12%  Similarity=0.193  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ....|+|+|.+|+|||||...+...
T Consensus       166 ~~~~v~lvG~~gvGKSTLin~L~~~  190 (357)
T 2e87_A          166 EIPTVVIAGHPNVGKSTLLKALTTA  190 (357)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHCSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999999875

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=90.64  E-value=0.1  Score=51.23  Aligned_cols=23  Identities=13%  Similarity=-0.139  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...|.|.|+.|+||||+|+.+.+
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~   27 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKT   27 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999999987

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=90.64  E-value=0.077  Score=57.18  Aligned_cols=93  Identities=12%  Similarity=0.114  Sum_probs=50.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCcccc--------CCCc-eeEEEECCCCCCC-CHHHHHHHHHHHhCC---------CC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVK--------HYFD-CHAWITEPYSNEY-DADQILDIVIKFLMP---------SS  240 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~--------~~F~-~~~wv~~~vs~~~-~~~~~~~~i~~~l~~---------~~  240 (824)
                      .-++|.|..|+|||||+..+.+.....        ++=+ .++++-  +.+.. .+.++.+++.+. +.         ..
T Consensus       148 Qr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~--iGeR~~Ev~e~~~~l~~~-g~~~rtvvv~~t~  224 (464)
T 3gqb_B          148 QKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAA--MGITQRELSYFIQEFERT-GALSRSVLFLNKA  224 (464)
T ss_dssp             CBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEE--EEECHHHHHHHHHHHHHT-SGGGGEEEEEEET
T ss_pred             CEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEE--ecCchHHHHHHHHHhhhc-ccccceEEEEECC
Confidence            356899999999999999998853331        1111 455555  55543 334455554432 10         00


Q ss_pred             CcccccccCHHHHHHHHHHhc---CCCeEEEEEecCCC
Q 003387          241 RLSEIMDKNYEMKKIILHEYL---MTKRYLIVIDDVWS  275 (824)
Q Consensus       241 ~~~~~~~~~~~~~~~~l~~~L---~~kr~LlVlDdv~~  275 (824)
                      +.|.....-.......+.+++   +++.+||++||+-.
T Consensus       225 d~p~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlTr  262 (464)
T 3gqb_B          225 DDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMTN  262 (464)
T ss_dssp             TSCTHHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChHH
Confidence            101001111122233445555   37999999999964

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=90.58  E-value=0.13  Score=51.85  Aligned_cols=23  Identities=22%  Similarity=0.287  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999987

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=90.56  E-value=0.27  Score=50.63  Aligned_cols=52  Identities=10%  Similarity=0.088  Sum_probs=34.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCc-eeEEEECCCCCCCCHHHHHHHHHHHh
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD-CHAWITEPYSNEYDADQILDIVIKFL  236 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~~~vs~~~~~~~~~~~i~~~l  236 (824)
                      -.+++|+|.+|+|||||++.+...  ....-. .++|+.  ..  ....++...+....
T Consensus        35 G~~~~i~G~~G~GKTTl~~~ia~~--~~~~~G~~v~~~~--~e--~~~~~~~~r~~~~~   87 (296)
T 1cr0_A           35 GEVIMVTSGSGMGKSTFVRQQALQ--WGTAMGKKVGLAM--LE--ESVEETAEDLIGLH   87 (296)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHHH--HHHTSCCCEEEEE--SS--SCHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH--HHHHcCCeEEEEe--Cc--CCHHHHHHHHHHHH
Confidence            468999999999999999998873  322222 456666  32  24455555555544

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=90.49  E-value=0.13  Score=55.49  Aligned_cols=35  Identities=23%  Similarity=0.232  Sum_probs=26.5

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++.+.|..-.....+++|+|..|+|||||.+.+..
T Consensus        57 ~i~~~L~~~~~~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           57 AISDALKEIDSSVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             HHHHHHHHHHHCCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             hhhhhhhhcccCCeEEEEECCCCCcHHHHHHHHhC
Confidence            34444433333467999999999999999999988

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=90.48  E-value=0.13  Score=49.09  Aligned_cols=24  Identities=17%  Similarity=0.264  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .-.|+|+|..|+|||||.+.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            568899999999999999998774

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=90.47  E-value=0.13  Score=51.50  Aligned_cols=24  Identities=17%  Similarity=0.196  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~Gl   54 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLGI   54 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            358999999999999999999873

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=90.47  E-value=0.36  Score=52.46  Aligned_cols=99  Identities=13%  Similarity=0.039  Sum_probs=54.3

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHH-HHHhCCccccCCCc-eeEEEECCCCCCCC-HHHHHHHHHHHhCCC-----
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFA-GEAYNSSYVKHYFD-CHAWITEPYSNEYD-ADQILDIVIKFLMPS-----  239 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa-~~v~~~~~~~~~F~-~~~wv~~~vs~~~~-~~~~~~~i~~~l~~~-----  239 (824)
                      .++.|..=. +-.-++|.|..|+|||+|| ..|.|.  .  .-+ .++++-  +.+..+ +.++.+++.+.=...     
T Consensus       152 aID~l~Pig-rGQR~~Ifg~~g~GKT~l~l~~I~n~--~--~~dv~~V~~~--IGeR~~ev~e~~~~l~~~g~m~~tvvV  224 (513)
T 3oaa_A          152 AVDSMIPIG-RGQRELIIGDRQTGKTALAIDAIINQ--R--DSGIKCIYVA--IGQKASTISNVVRKLEEHGALANTIVV  224 (513)
T ss_dssp             HHHHHSCCB-TTCBCEEEESSSSSHHHHHHHHHHTT--S--SSSCEEEEEE--ESCCHHHHHHHHHHHHHHSCSTTEEEE
T ss_pred             eeccccccc-cCCEEEeecCCCCCcchHHHHHHHhh--c--cCCceEEEEE--ecCChHHHHHHHHHHhhcCcccceEEE
Confidence            455554311 1236799999999999996 677773  2  233 345666  676543 345666654431111     


Q ss_pred             ---CCccc----ccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          240 ---SRLSE----IMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       240 ---~~~~~----~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                         .+.|.    ......-..++.+++  +++.+||++||+..
T Consensus       225 ~atad~p~~~r~~a~~~a~tiAEyfrd--~G~dVLli~Dsltr  265 (513)
T 3oaa_A          225 VATASESAALQYLAPYAGCAMGEYFRD--RGEDALIIYDDLSK  265 (513)
T ss_dssp             EECTTSCHHHHHHHHHHHHHHHHHHHH--TTCEEEEEEETHHH
T ss_pred             EECCCCChHHHHHHHHHHHHHHHHHHh--cCCCEEEEecChHH
Confidence               11110    000111222344443  68999999999964

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=90.45  E-value=0.26  Score=56.38  Aligned_cols=42  Identities=12%  Similarity=0.183  Sum_probs=36.4

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.++|.+..++.+...+..+    ..+.|+|..|+||||||+.+.+
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~   82 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAE   82 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhc
Confidence            56889988888887777765    3789999999999999999988

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=90.29  E-value=0.25  Score=53.91  Aligned_cols=106  Identities=14%  Similarity=0.087  Sum_probs=55.1

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHH-HHHhCCccc----cCCCc-eeEEEECCCCCCCC-HHHHHHHHHHHhCC--
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFA-GEAYNSSYV----KHYFD-CHAWITEPYSNEYD-ADQILDIVIKFLMP--  238 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa-~~v~~~~~~----~~~F~-~~~wv~~~vs~~~~-~~~~~~~i~~~l~~--  238 (824)
                      .++.|..=. .-.-++|+|..|+|||+|| ..|.|....    ..+-+ .++++-  +.+..+ +.++.+++...=..  
T Consensus       152 aID~l~Pig-rGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~--IGeR~~Ev~~~~~~~~~~g~m~~  228 (510)
T 2ck3_A          152 AVDSLVPIG-RGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVA--IGQKRSTVAQLVKRLTDADAMKY  228 (510)
T ss_dssp             HHHHHSCCB-TTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEE--ESCCHHHHHHHHHHHHHTTCGGG
T ss_pred             eeccccccc-cCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEE--CCCCcHHHHHHHHHHHhcCCccc
Confidence            455554311 1246799999999999994 577774321    02234 355666  666543 44555555542111  


Q ss_pred             ------CCCcccccccCHHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          239 ------SSRLSEIMDKNYEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       239 ------~~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                            ..+.|.....-.......+.+++  +++.+||++||+...
T Consensus       229 tvvV~atad~p~~~r~~a~~~a~tiAEyfrd~G~dVLli~Dsltr~  274 (510)
T 2ck3_A          229 TIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQ  274 (510)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHHHHHHTTTCEEEEEEETHHHH
T ss_pred             ceEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcCHHHH
Confidence                  11101000000111122333333  579999999999643

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=90.24  E-value=0.12  Score=51.15  Aligned_cols=24  Identities=29%  Similarity=0.243  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+|+|.|..|+||||+++.+..
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~   42 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEK   42 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHh
Confidence            457999999999999999999988

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=90.22  E-value=0.14  Score=50.42  Aligned_cols=23  Identities=22%  Similarity=0.166  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|.|+.|.||||+|+.+..
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999986

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=90.11  E-value=0.22  Score=51.40  Aligned_cols=23  Identities=13%  Similarity=0.209  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTT
T ss_pred             CCEEEEECCCCchHHHHHHHHHc
Confidence            46899999999999999999977

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=90.09  E-value=0.4  Score=52.72  Aligned_cols=59  Identities=14%  Similarity=0.106  Sum_probs=39.4

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHH-HHHHHH
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDAD-QILDIV  232 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~-~~~~~i  232 (824)
                      ++++.|..=. .-.-++|.|..|+|||+|++.+.+.    .+-+.++++-  +.+..+.- ++.+++
T Consensus       216 rvID~l~Pig-kGqr~~I~g~~g~GKT~L~~~ia~~----~~~~~~V~~~--iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          216 RVIDTFFPQA-KGGTAAIPGPAGSGKTVTQHQLAKW----SDAQVVIYIG--CGERGNEMTDVLEEF  275 (588)
T ss_dssp             HHHHHHSCEE-TTCEEEECSCCSHHHHHHHHHHHHH----SSCSEEEEEE--CCSSSSHHHHHHHHT
T ss_pred             chhhccCCcc-cCCeEEeecCCCCCHHHHHHHHHhc----cCCCEEEEEE--ecccHHHHHHHHHHH
Confidence            3555554311 1347899999999999999998772    2235677887  77766544 455554

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=90.07  E-value=0.16  Score=52.30  Aligned_cols=36  Identities=17%  Similarity=0.022  Sum_probs=26.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .++++|+|.+|+||||++..+..  .....=..+.+++
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~--~~~~~~~~v~l~~  133 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLAL--YYKGKGRRPLLVA  133 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH--HHHHcCCeEEEec
Confidence            57999999999999999999887  3332222455555

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=90.04  E-value=0.18  Score=47.43  Aligned_cols=26  Identities=15%  Similarity=0.051  Sum_probs=22.6

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .....|.|+|.+|+|||||...+.+.
T Consensus        14 ~~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           14 DQEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHhcC
Confidence            34567899999999999999999875

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=90.03  E-value=0.12  Score=50.44  Aligned_cols=23  Identities=9%  Similarity=-0.010  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...|.|.|+.|+||||+|+.+..
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~   27 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKK   27 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999999977

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=90.02  E-value=0.14  Score=55.70  Aligned_cols=37  Identities=30%  Similarity=0.316  Sum_probs=27.5

Q ss_pred             HHHHHHHHHcC------C-CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          165 MEELLDLLIEG------P-PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       165 ~~~l~~~L~~~------~-~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.+++...      . ....+|.|+|.+|+||||++..+..
T Consensus        78 ~~~l~~ll~~~~~~~~~~~~~~~vI~ivG~~GvGKTTla~~La~  121 (432)
T 2v3c_C           78 YEELVKLLGEEAKKLELNPKKQNVILLVGIQGSGKTTTAAKLAR  121 (432)
T ss_dssp             HHHHHHHHCCSCCCCCCCSSSCCCEEEECCSSSSTTHHHHHHHH
T ss_pred             HHHHHHHhCCCCcCccccCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            45566666432      1 2357999999999999999988877

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=90.02  E-value=0.15  Score=51.64  Aligned_cols=35  Identities=14%  Similarity=0.035  Sum_probs=25.1

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ++|+|.|-||+||||+|..+..  .....=..++-|+
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~--~la~~G~~VlliD   36 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTS--GLHAMGKTIMVVG   36 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH--HHHTTTCCEEEEE
T ss_pred             cEEEEecCCCCcHHHHHHHHHH--HHHHCCCcEEEEc
Confidence            6888899999999999988776  3333222455565

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=89.98  E-value=0.14  Score=49.03  Aligned_cols=24  Identities=17%  Similarity=0.264  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .-.|+|+|..|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            456899999999999999999874

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=89.91  E-value=0.44  Score=52.32  Aligned_cols=64  Identities=19%  Similarity=0.164  Sum_probs=39.5

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHH
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~  234 (824)
                      ...+-+++ .+=..-.++.|.|.+|+||||||..+..+.... .=..++|++  ..  .+..++...++.
T Consensus       190 ~~~LD~~~-gGl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~-~g~~Vl~~s--~E--~s~~~l~~r~~~  253 (454)
T 2r6a_A          190 FTELDRMT-SGFQRSDLIIVAARPSVGKTAFALNIAQNVATK-TNENVAIFS--LE--MSAQQLVMRMLC  253 (454)
T ss_dssp             CHHHHHHH-SSBCTTCEEEEECCTTSCHHHHHHHHHHHHHHH-SSCCEEEEE--SS--SCHHHHHHHHHH
T ss_pred             cHHHHhhc-CCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHh-CCCcEEEEE--CC--CCHHHHHHHHHH
Confidence            33444444 442335689999999999999999988742221 112577776  33  345666666543

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=89.90  E-value=0.16  Score=51.10  Aligned_cols=112  Identities=13%  Similarity=0.184  Sum_probs=59.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE-CCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHH
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT-EPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIIL  257 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l  257 (824)
                      -.+++|+|+.|.|||||++.+..  .....+...+++. .++...+... .  .++.+    .   .... +.......|
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g--~~~~~~~G~I~~~g~~i~~~~~~~-~--~~v~q----~---~~gl-~~~~l~~~l   91 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMID--YINQTKSYHIITIEDPIEYVFKHK-K--SIVNQ----R---EVGE-DTKSFADAL   91 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHH--HHHHHCCCEEEEEESSCCSCCCCS-S--SEEEE----E---EBTT-TBSCHHHHH
T ss_pred             CCEEEEECCCCccHHHHHHHHHH--hCCCCCCCEEEEcCCcceeecCCc-c--eeeeH----H---HhCC-CHHHHHHHH
Confidence            57999999999999999999887  3333223444443 1121111000 0  00000    0   0000 012234566


Q ss_pred             HHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          258 HEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       258 ~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      ...|..+.=+|++|..-+.+....+....   ..|.-|++||-+.++..
T Consensus        92 a~aL~~~p~illlDEp~D~~~~~~~l~~~---~~g~~vl~t~H~~~~~~  137 (261)
T 2eyu_A           92 RAALREDPDVIFVGEMRDLETVETALRAA---ETGHLVFGTLHTNTAID  137 (261)
T ss_dssp             HHHHHHCCSEEEESCCCSHHHHHHHHHHH---HTTCEEEEEECCSSHHH
T ss_pred             HHHHhhCCCEEEeCCCCCHHHHHHHHHHH---ccCCEEEEEeCcchHHH
Confidence            66665566688899997654433333221   23667888887765443

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=89.88  E-value=0.16  Score=46.34  Aligned_cols=23  Identities=13%  Similarity=0.190  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .-|.|+|.+|+|||||+..+.+.
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999998764

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=89.87  E-value=0.15  Score=50.00  Aligned_cols=21  Identities=14%  Similarity=0.104  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.|.|+.|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~   22 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKD   22 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999977

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=89.85  E-value=0.16  Score=52.05  Aligned_cols=23  Identities=17%  Similarity=0.200  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|+|.|.||+||||+|..+..
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA~   24 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLVA   24 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             ceEEEEeCCCcCcHHHHHHHHHH
Confidence            47899999999999999988776

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=89.82  E-value=0.15  Score=49.61  Aligned_cols=21  Identities=14%  Similarity=-0.016  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.|.|+.|+||||+|+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIME   22 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999977

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=89.76  E-value=0.2  Score=47.25  Aligned_cols=24  Identities=8%  Similarity=0.111  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ...|+|+|.+|+|||||.+.+.+.
T Consensus         7 ~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            7 SYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            467999999999999999999874

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=89.70  E-value=0.15  Score=52.87  Aligned_cols=23  Identities=9%  Similarity=0.209  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.|+|+.|+||||||..+..
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~   62 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAA   62 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999988

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=89.51  E-value=0.26  Score=54.51  Aligned_cols=24  Identities=17%  Similarity=0.162  Sum_probs=20.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.|+|.+|+||||++..+..
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~  123 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAY  123 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999998875

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=89.46  E-value=0.28  Score=51.50  Aligned_cols=35  Identities=17%  Similarity=0.200  Sum_probs=26.7

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++-+.-.-....+++|+|..|+|||||.+.+..
T Consensus        43 ~~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~g   77 (337)
T 2qm8_A           43 DLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGS   77 (337)
T ss_dssp             HHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHhCCcccCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            34444443334578999999999999999999874

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=89.44  E-value=0.18  Score=52.10  Aligned_cols=22  Identities=14%  Similarity=0.173  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.|+|+.|+||||||+.+..
T Consensus         6 ~~i~i~GptGsGKTtla~~La~   27 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALAD   27 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999987

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=89.37  E-value=0.18  Score=49.94  Aligned_cols=24  Identities=17%  Similarity=0.034  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|+|+.|.||||+++.+..
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999999999887

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=89.36  E-value=0.19  Score=46.69  Aligned_cols=24  Identities=29%  Similarity=0.303  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .--|.|+|.+|+|||||.+.+.+.
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            446899999999999999999875

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=89.30  E-value=0.18  Score=51.94  Aligned_cols=22  Identities=18%  Similarity=0.306  Sum_probs=20.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999986

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=89.25  E-value=0.28  Score=46.94  Aligned_cols=34  Identities=15%  Similarity=-0.021  Sum_probs=24.7

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +++.+.-..... .|+|+|.+|+|||||.+.+.++
T Consensus        15 ~l~~~~~~~~~~-ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           15 VLQFLGLYKKTG-KLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             HHHHHTCTTCCE-EEEEEEETTSSHHHHHHHHSCC
T ss_pred             HHHHhhccCCCc-EEEEECCCCCCHHHHHHHHhcC
Confidence            445443333234 5789999999999999999874

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=89.22  E-value=0.18  Score=51.13  Aligned_cols=21  Identities=14%  Similarity=0.425  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|+|..|+|||||.+.++.
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g   24 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFK   24 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999886

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=89.19  E-value=0.16  Score=50.18  Aligned_cols=23  Identities=17%  Similarity=0.039  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...|.|.|+.|+||||+|+.+.+
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~   38 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAK   38 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35799999999999999999987

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=89.18  E-value=0.28  Score=51.66  Aligned_cols=34  Identities=18%  Similarity=0.132  Sum_probs=25.6

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.+-+........+|+|+|.+|+||||++..+..
T Consensus        45 ~~~~l~~~~~~~~~i~i~G~~g~GKSTl~~~l~~   78 (341)
T 2p67_A           45 LLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGM   78 (341)
T ss_dssp             HHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHH
T ss_pred             HHHhCCcccCCCEEEEEEcCCCCCHHHHHHHHHH
Confidence            4433333334578999999999999999999864

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=89.17  E-value=0.44  Score=46.25  Aligned_cols=23  Identities=13%  Similarity=-0.035  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -..|.|.|+.|+||||+++.+.+
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~   28 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAE   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.15  E-value=0.57  Score=59.93  Aligned_cols=108  Identities=17%  Similarity=0.001  Sum_probs=67.8

Q ss_pred             ceechhhHHHHHHHHH-cCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHh
Q 003387          158 TVGLDDRMEELLDLLI-EGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFL  236 (824)
Q Consensus       158 ~vGr~~~~~~l~~~L~-~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l  236 (824)
                      +.+...-...|-.+|. .+=..-+++-|+|.+|+||||||.++...  ....=..++|++  ....++...     ++.+
T Consensus       361 ~~~I~TG~~~LD~lLG~GGl~~G~lilI~G~pGsGKTtLaLqia~~--~a~~G~~vlyis--~E~s~~~~~-----a~~l  431 (2050)
T 3cmu_A          361 VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFID--AEHALDPIY-----ARKL  431 (2050)
T ss_dssp             CCEECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHH--HHTTTCCEEEEC--TTSCCCHHH-----HHHT
T ss_pred             CceeeCCCHHHHHHhccCCccCCcEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEE--cCCCHHHHH-----HHHc
Confidence            4455555566666665 33234579999999999999999998873  333324688998  666666542     5556


Q ss_pred             CCCCCc-ccccccCHHHHHHHHHHhcC-CCeEEEEEecCC
Q 003387          237 MPSSRL-SEIMDKNYEMKKIILHEYLM-TKRYLIVIDDVW  274 (824)
Q Consensus       237 ~~~~~~-~~~~~~~~~~~~~~l~~~L~-~kr~LlVlDdv~  274 (824)
                      +...+. .-.+..+.++....+.+..+ .+--+||+|-+.
T Consensus       432 Gvd~~~L~I~~~~~~e~il~~~~~lv~~~~~~lIVIDSL~  471 (2050)
T 3cmu_A          432 GVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVA  471 (2050)
T ss_dssp             TCCTTTCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGG
T ss_pred             CCCHHHeEEeCCCCHHHHHHHHHHHHHhcCCcEEEECCHH
Confidence            543211 00233456666666665443 355699999985

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=89.09  E-value=0.29  Score=50.26  Aligned_cols=24  Identities=8%  Similarity=0.166  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-.+++|+|..|.|||||++.+..
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~g  148 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIH  148 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhh
Confidence            356899999999999999999987

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=88.96  E-value=0.67  Score=50.70  Aligned_cols=73  Identities=21%  Similarity=0.056  Sum_probs=45.7

Q ss_pred             echhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          160 GLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      |...-...+-+++ .+=..-.++.|.|.+|+||||+|..+..+.... .=..++|++  .  .-+..++...++.....
T Consensus       182 ~i~tG~~~LD~~l-gGl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~-~g~~vl~~s--l--E~~~~~l~~R~~~~~~~  254 (444)
T 2q6t_A          182 GVRTGFKELDQLI-GTLGPGSLNIIAARPAMGKTAFALTIAQNAALK-EGVGVGIYS--L--EMPAAQLTLRMMCSEAR  254 (444)
T ss_dssp             -CCCSCHHHHHHH-CCCCTTCEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEEE--S--SSCHHHHHHHHHHHHTT
T ss_pred             cccCCCHhhhhhc-CCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh-CCCeEEEEE--C--CCCHHHHHHHHHHHHcC
Confidence            4444445555555 553345689999999999999999887732211 113577776  3  34566777777655443

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=88.96  E-value=0.19  Score=46.83  Aligned_cols=23  Identities=13%  Similarity=0.055  Sum_probs=20.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..|+|+|.+|+|||||.+.+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999874

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=88.95  E-value=0.17  Score=51.62  Aligned_cols=23  Identities=22%  Similarity=0.120  Sum_probs=20.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.++.|+|.+|+|||||+..+..
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999998875

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=88.94  E-value=0.2  Score=46.11  Aligned_cols=22  Identities=27%  Similarity=0.234  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||.+.+.+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCc
Confidence            4789999999999999998764

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=88.92  E-value=0.32  Score=51.23  Aligned_cols=23  Identities=9%  Similarity=0.108  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~G   76 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNL   76 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHhc
Confidence            46899999999999999999987

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=88.92  E-value=0.22  Score=51.12  Aligned_cols=23  Identities=22%  Similarity=0.137  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.|+|+.|+||||||..+..
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~   25 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAK   25 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHHHHHH
Confidence            46899999999999999999987

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=88.92  E-value=0.19  Score=46.00  Aligned_cols=22  Identities=14%  Similarity=0.258  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||+..+.+.
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999998764

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=88.89  E-value=0.31  Score=51.25  Aligned_cols=23  Identities=17%  Similarity=0.146  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            35899999999999999999987

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=88.86  E-value=0.2  Score=46.09  Aligned_cols=24  Identities=4%  Similarity=0.076  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .--|.|+|.+|+|||||+..+.+.
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            446789999999999999998764

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=88.85  E-value=0.2  Score=51.24  Aligned_cols=24  Identities=21%  Similarity=0.177  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl   87 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGE   87 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcC
Confidence            468999999999999999999873

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=88.74  E-value=0.11  Score=53.24  Aligned_cols=23  Identities=9%  Similarity=0.141  Sum_probs=18.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|+|.|..|+||||+|+.+.+
T Consensus         5 ~~iIgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            5 HPIISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             SCEEEEESCC---CCTHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999876

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=88.73  E-value=0.22  Score=48.12  Aligned_cols=21  Identities=19%  Similarity=0.202  Sum_probs=19.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +|.|.|++|+||||.|+.+.+
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~   22 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAK   22 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            678999999999999999987

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=88.71  E-value=0.21  Score=46.06  Aligned_cols=23  Identities=17%  Similarity=0.203  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      --|.|+|.+|+|||||...+.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999999874

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=88.71  E-value=0.31  Score=45.35  Aligned_cols=25  Identities=24%  Similarity=0.309  Sum_probs=21.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ....|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999998774

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=88.71  E-value=0.2  Score=47.35  Aligned_cols=23  Identities=13%  Similarity=0.219  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      --|.|+|.+|+|||||+..+.+.
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46789999999999999999764

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=88.70  E-value=0.43  Score=48.04  Aligned_cols=38  Identities=16%  Similarity=0.167  Sum_probs=28.5

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +.++.+.+.......-.|+|+|..|+|||||...+...
T Consensus        22 l~~~~~~~~~~~~~~~~I~lvG~~g~GKSSLin~l~~~   59 (262)
T 3def_A           22 LIEFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGE   59 (262)
T ss_dssp             HHHHHHHHHHTTCCEEEEEEEECTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHhhccCCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            33444455554445678899999999999999999875

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=88.48  E-value=0.2  Score=49.77  Aligned_cols=36  Identities=17%  Similarity=0.113  Sum_probs=26.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      -.++.|+|.+|+||||||..+...  ....=..++|++
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~--~~~~~~~v~~~~   58 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWN--GLKMGEPGIYVA   58 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEE
Confidence            468999999999999998877652  222223577777

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=88.47  E-value=0.2  Score=46.01  Aligned_cols=24  Identities=25%  Similarity=0.264  Sum_probs=20.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         4 ~~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            346889999999999999998764

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=88.45  E-value=0.23  Score=46.32  Aligned_cols=25  Identities=16%  Similarity=0.223  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..--|.|+|..|+|||||...+.+.
T Consensus         8 ~~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            8 HLFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHhcC
Confidence            4567899999999999999999875

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=88.44  E-value=0.21  Score=54.18  Aligned_cols=24  Identities=25%  Similarity=0.249  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|.|+|+.|+||||+|+.+..
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~  280 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLV  280 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999999987

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=88.41  E-value=0.24  Score=45.51  Aligned_cols=23  Identities=22%  Similarity=0.255  Sum_probs=20.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      --|.|+|.+|+|||||.+.+.+.
T Consensus         4 ~ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            4 YKLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999998764

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=88.40  E-value=0.38  Score=56.83  Aligned_cols=46  Identities=15%  Similarity=0.164  Sum_probs=37.1

Q ss_pred             CCceechhhHHHHHHHHHcC-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEG-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|.+..++.+...+...       ......+-++|..|+|||++|+.+.+
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~  510 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSK  510 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHH
Confidence            45889999998888877532       12345789999999999999999988

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=88.37  E-value=0.34  Score=50.89  Aligned_cols=23  Identities=26%  Similarity=0.182  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        26 Ge~~~llGpnGsGKSTLLr~iaG   48 (348)
T 3d31_A           26 GEYFVILGPTGAGKTLFLELIAG   48 (348)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCccHHHHHHHHHc
Confidence            35899999999999999999987

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=88.32  E-value=0.47  Score=47.98  Aligned_cols=38  Identities=16%  Similarity=0.159  Sum_probs=27.9

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSS  203 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~  203 (824)
                      .++.+.+.......-.|.|+|.+|+|||||...+.+..
T Consensus        26 ~~~~~~~~~~~~~~~~I~vvG~~g~GKSSLin~l~~~~   63 (270)
T 1h65_A           26 LELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGER   63 (270)
T ss_dssp             HHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHHhhcCCCCeEEEEECCCCCCHHHHHHHHhCCC
Confidence            33444444444446788999999999999999998753

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=88.23  E-value=0.25  Score=45.55  Aligned_cols=24  Identities=17%  Similarity=0.050  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            456899999999999999998764

---

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	824
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	6e-12
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	4e-07
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	2e-06
d1xkua_	305	c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 99	3e-04
d2omza2	384	c.10.2.1 (A:33-416) Internalin A {Listeria monocyt	1e-04

>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 = 64.8 bits (157), Expect = 6e-12
 Identities = 28/160 (17%), Positives = 51/160 (31%), Gaps = 17/160 (10%)

Query: 154 KSRDTVGLDDRMEELLDLLIE-GPPQLSVVAILDSIGLDKTAFAGEAYNSS--YVKHYFD 210
           K       +  ++ ++  L E        + +    G  K+  A +A + S   +   +D
Sbjct: 18  KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYD 77

Query: 211 CHAWITEPYSNEYDADQILDIVIKFLMPSSRL------SEIMDKNYEMKKIILHEYLMTK 264
              W+ +                  LM  S        S     +  +K++I +  +   
Sbjct: 78  SIVWLKDS--GTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRP 135

Query: 265 RYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRI 304
             L V DDV   +     QE         R L+T  D+ I
Sbjct: 136 NTLFVFDDVVQEETIRWAQE------LRLRCLVTTRDVEI 169

>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 = 50.4 bits (119), Expect = 4e-07
 Identities = 42/251 (16%), Positives = 84/251 (33%), Gaps = 13/251 (5%)

Query: 523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH 582
           LRV+    L L + P  +        L L    +  +      NL NL+TL +  + I  
Sbjct: 12  LRVVQCSDLGLEKVPKDLPPD--TALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISK 69

Query: 583 T-ADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRN 641
                F  + KL  L      L   P K   +L+ L            + +   L  +  
Sbjct: 70  ISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRV-HENEITKVRKSVFNGLNQMIV 128

Query: 642 LRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNT 701
           + +  +   +  + + +   +  L  +++A+      ++ I       P SLT L     
Sbjct: 129 VELGTNPLKSSGIENGAFQGMKKLSYIRIAD----TNITTIPQG---LPPSLTELHLDGN 181

Query: 702 DLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNA 761
            +      +L+ L  L  L L  NS S       +      ++    + L      + + 
Sbjct: 182 KITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLAD- 240

Query: 762 AMPKLECLIIN 772
               ++ + ++
Sbjct: 241 -HKYIQVVYLH 250

>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 = 47.7 bits (112), Expect = 2e-06
 Identities = 40/208 (19%), Positives = 67/208 (32%), Gaps = 9/208 (4%)

Query: 523 LRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYID 581
           L  L L +  + +  P     L  L  L L+   L  LP  +   L  L   +   + + 
Sbjct: 57  LHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKVR 116

Query: 582 HTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRN 641
            +         +  L    +            ++ L++I  +     T    G  P+L  
Sbjct: 117 KSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIR-IADTNITTIPQGLPPSLTE 175

Query: 642 LRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNT 701
           L     L  N+ +       L  L +L     S     +    +    PH L  L  +N 
Sbjct: 176 L----HLDGNK-ITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPH-LRELHLNNN 229

Query: 702 DLMDDPMPTLEKLPLLQVLKLKQNSYSG 729
            L+  P   L     +QV+ L  N+ S 
Sbjct: 230 KLVKVPG-GLADHKYIQVVYLHNNNISA 256

>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 = 41.2 bits (95), Expect = 3e-04
 Identities = 18/190 (9%), Positives = 52/190 (27%), Gaps = 7/190 (3%)

Query: 488 LDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLR 547
           L +   +    L                      ++ +               + +  L 
Sbjct: 94  LPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLS 153

Query: 548 YLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHP 607
           Y+++   ++ ++P  L  +L  L+      + +D  A     +N L  L     ++ A  
Sbjct: 154 YIRIADTNITTIPQGLPPSLTELHLDGNKITKVD--AASLKGLNNLAKLGLSFNSISAVD 211

Query: 608 GKFCGSLENLNFISALH-PCCCTEDILGRLPNLRNLRIRG----DLSYNQSLLSKSLCRL 662
                +  +L  +   +         L     ++ + +       +  N         + 
Sbjct: 212 NGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKK 271

Query: 663 SCLESLKLAN 672
           +    + L +
Sbjct: 272 ASYSGVSLFS 281

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]} Length = 384

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]

 Score = 43.1 bits (100), Expect = 1e-04
 Identities = 34/188 (18%), Positives = 62/188 (32%), Gaps = 24/188 (12%)

Query: 517 CGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMP 576
            G+   L  L L     ++    + +L  L  L L    +++L    LS L  L  L + 
Sbjct: 215 LGILTNLDELSLNG-NQLKDIGTLASLTNLTDLDLANNQISNLAP--LSGLTKLTELKLG 271

Query: 577 FSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENL----NFISALHPCCCTEDI 632
            + I + +               +      P     +L  L    N IS + P       
Sbjct: 272 ANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISP------- 324

Query: 633 LGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHS 692
           +  L  L+ L      + N+     SL  L+ +  L   +     ++S +     L    
Sbjct: 325 VSSLTKLQRL----FFANNKVSDVSSLANLTNINWLSAGHN----QISDLTPLANL--TR 374

Query: 693 LTHLSFSN 700
           +T L  ++
Sbjct: 375 ITQLGLND 382

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	824
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.81
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.78
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.78
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	99.75
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.74
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.7
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.67
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.66
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.59
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.58
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.57
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	99.54
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.53
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.52
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	99.48
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.46
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.42
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	99.4
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.4
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.38
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.35
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.33
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.27
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	99.25
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	99.24
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.21
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.17
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	99.06
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.06
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	99.06
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	98.97
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.93
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.84
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	98.74
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.69
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.61
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.5
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.32
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.93
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.9
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.81
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.79
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.76
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.71
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.7
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.68
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.62
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.61
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.55
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.5
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.44
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.41
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.19
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.18
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.14
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	97.07
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.89
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.84
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.7
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	96.62
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.58
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.53
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.47
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.41
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	96.39
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.2
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	96.18
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.12
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.02
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.0
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.0
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	95.98
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.98
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	95.81
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	95.65
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	95.62
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.59
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	95.54
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.5
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	95.43
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	95.41
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.35
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.31
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.28
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.23
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.21
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	95.15
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.15
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.05
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	95.03
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	95.02
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	94.89
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	94.88
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	94.87
d2qy9a2	211	GTPase domain of the signal recognition particle r	94.84
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	94.81
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	94.81
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	94.79
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.62
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	94.6
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	94.32
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.3
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	94.26
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	94.15
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.03
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.01
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.0
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	93.85
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	93.8
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	93.61
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	93.52
d1okkd2	207	GTPase domain of the signal recognition particle r	93.49
d1j8yf2	211	GTPase domain of the signal sequence recognition p	93.44
d1vmaa2	213	GTPase domain of the signal recognition particle r	93.44
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	93.41
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	93.4
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	93.33
d1xpua3	289	Transcription termination factor Rho, ATPase domai	93.33
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	93.33
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	93.15
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	93.09
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	92.97
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	92.96
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	92.93
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	92.93
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	92.91
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	92.82
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	92.77
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	92.69
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	92.69
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	92.67
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	92.58
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	92.51
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	92.5
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	92.41
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	92.26
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	92.19
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	92.18
d1g2912	240	Maltose transport protein MalK, N-terminal domain	92.15
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	92.13
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	92.13
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	92.02
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	91.93
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.84
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	91.81
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	91.79
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	91.66
d2awna2	232	Maltose transport protein MalK, N-terminal domain	91.61
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	91.58
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	91.51
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.36
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	91.36
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	91.34
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	91.28
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	91.21
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	91.12
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	91.1
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	91.0
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	91.0
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	90.98
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	90.96
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.96
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	90.94
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	90.94
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	90.86
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	90.7
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	90.67
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	90.63
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	90.5
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	90.49
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	90.46
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	90.29
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	90.28
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	90.27
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	90.26
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	90.25
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.24
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	90.2
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	90.15
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	90.06
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	89.95
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	89.9
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	89.87
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	89.84
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	89.73
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	89.7
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	89.64
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	89.63
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	89.62
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	89.55
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	89.34
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	89.05
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	88.93
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	88.89
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	88.84
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	88.79
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	88.73
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	88.69
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	88.67
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	88.61
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	88.6
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	88.53
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	88.49
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	88.46
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	88.32
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	88.32
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	88.32
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	88.32
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	88.25
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	88.22
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	88.19
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	88.14
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	88.11
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	88.07
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	88.03
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	87.95
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	87.53
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	87.52
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	87.51
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	87.38
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	87.15
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	87.14
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	87.07
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	87.03
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	86.98
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	86.95
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	86.95
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	86.87
d2fh5b1	207	Signal recognition particle receptor beta-subunit	86.86
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	86.85
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	86.78
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	86.65
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	86.45
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	86.42
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	86.42
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	86.37
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	86.18
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	86.16
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	86.11
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	86.03
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	86.02
d1nrjb_	209	Signal recognition particle receptor beta-subunit	85.98
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	85.96
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	85.87
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	85.61
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	85.26
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	85.03
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	85.03
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	84.85
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	84.52
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	84.25
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	84.15
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	83.87
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	83.12
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	82.7
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	82.57
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	82.47
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	82.37
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	82.02
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	80.46

>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=1.9e-34  Score=298.15  Aligned_cols=218  Identities=16%  Similarity=0.129  Sum_probs=167.4

Q ss_pred             CCCCceechhhHHHHHHHHHc-CCCCeEEEEEEcCCCChHHHHHHHHhCCcc--ccCCCceeEEEECCCCCCCCHHHHHH
Q 003387          154 KSRDTVGLDDRMEELLDLLIE-GPPQLSVVAILDSIGLDKTAFAGEAYNSSY--VKHYFDCHAWITEPYSNEYDADQILD  230 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~-~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~--~~~~F~~~~wv~~~vs~~~~~~~~~~  230 (824)
                      .+..+|||+.++++|+++|.. .+.+.++|+|+||||+||||||+++|++.+  .+.+|++++||+  +++.++...+..
T Consensus        18 ~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~--vs~~~~~~~l~~   95 (277)
T d2a5yb3          18 KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLK--DSGTAPKSTFDL   95 (277)
T ss_dssp             CCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEE--CCCCSTTHHHHH
T ss_pred             CCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEE--ecCCCCHHHHHH
Confidence            356788999999999999975 455689999999999999999999998643  677899999999  999999887766


Q ss_pred             HHHHHh---CCCC--Cccc-ccccCHHHHHHHHHHhcCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHHH
Q 003387          231 IVIKFL---MPSS--RLSE-IMDKNYEMKKIILHEYLMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIRI  304 (824)
Q Consensus       231 ~i~~~l---~~~~--~~~~-~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~v  304 (824)
                      .+...+   +...  ..+. ....+.......+.+.|.+||+|+||||||+..+|+.+..      .|||||||||++.+
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~------~~srilvTTR~~~v  169 (277)
T d2a5yb3          96 FTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQE------LRLRCLVTTRDVEI  169 (277)
T ss_dssp             HHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHHHH------TTCEEEEEESBGGG
T ss_pred             HHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHhhhhhhcc------cCceEEEEeehHHH
Confidence            665444   3211  1111 2233345556678899999999999999999999987653      38999999999999


Q ss_pred             Hh---------------------hcccccC-CcCcCccccchhhHHHhcCCCchhHHHHHhHH------Hhhhhhhhc-c
Q 003387          305 II---------------------SFQFEDG-ENMRLDLVPTGGPLRATYKGRPFLILYHGSIS------LEENIREAV-E  355 (824)
Q Consensus       305 ~~---------------------~f~~~~~-~~~~~~~~~~~~~i~~~c~GlPlai~~~~~~l------~~~~~~~~~-~  355 (824)
                      +.                     +|..... ...++..++++++|+++|+|+|||++++|+.|      .|.+..+.+ +
T Consensus       170 ~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~~~~L~~  249 (277)
T d2a5yb3         170 SNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLES  249 (277)
T ss_dssp             GGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHHH
T ss_pred             HHhcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHHHHHHhc
Confidence            87                     4433221 12334567889999999999999999999999      333444444 2


Q ss_pred             CCC-cccccccc---cCCCCchHHHhHh
Q 003387          356 TPL-GLRYIKCL---MLPFCLKPCFIYL  379 (824)
Q Consensus       356 ~~~-~~~~~l~~---~L~~~lk~cfl~~  379 (824)
                      ... ++..++++   +||+++|.||-++
T Consensus       250 ~~~~~v~~il~~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         250 RGLVGVECITPYSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             HCSSTTCCCSSSSSSSHHHHHHHHHHTS
T ss_pred             CcHHHHHHHHHHHHhcccHHHHHHHHhC
Confidence            223 78888888   9999999999763

>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=99.81  E-value=2.7e-19  Score=194.05  Aligned_cols=283  Identities=19%  Similarity=0.219  Sum_probs=155.7

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      ..++++|.+.++....     + ..+..+++|++|+|++|.++.+|. ++++++|++|++++|.+..+++ + +++++|+
T Consensus        43 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~  113 (384)
T d2omza2          43 LDQVTTLQADRLGIKS-----I-DGVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQIADITP-L-ANLTNLT  113 (384)
T ss_dssp             HTTCCEEECCSSCCCC-----C-TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCCGG-G-TTCTTCC
T ss_pred             hCCCCEEECCCCCCCC-----c-cccccCCCCCEEeCcCCcCCCCcc-ccCCcccccccccccccccccc-c-ccccccc
Confidence            5567777777665542     1 235567777777777777777764 7777777777777777777664 4 7777777


Q ss_pred             EeecCCccccccchhhhccccCceecCCCccCCC----------------------------------------CCC-CC
Q 003387          572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPA----------------------------------------HPG-KF  610 (824)
Q Consensus       572 ~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~----------------------------------------~~~-p~  610 (824)
                      .|+++++.+..++.. .....+..+....+.+..                                        ... ..
T Consensus       114 ~L~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  192 (384)
T d2omza2         114 GLTLFNNQITDIDPL-KNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDISV  192 (384)
T ss_dssp             EEECCSSCCCCCGGG-TTCTTCSEEEEEEEEECCCGGGTTCTTCSEEEEEESCCCCGGGTTCTTCCEEECCSSCCCCCGG
T ss_pred             ccccccccccccccc-cccccccccccccccccccccccccccccccccccccchhhhhccccccccccccccccccccc
Confidence            777777665554432 122222222221111100                                        000 02


Q ss_pred             CCCCCCCCeeeccCC-CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccC--------CCCCccE
Q 003387          611 CGSLENLNFISALHP-CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANES--------KMPRLSK  681 (824)
Q Consensus       611 i~~L~~L~~l~~~~~-~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~--------~~~~L~~  681 (824)
                      ...++++..+.+..+ ...+.. ...+++|++|+++++.   ...+ ..+..+++|+.|++.++.        ..++|+.
T Consensus       193 ~~~l~~~~~l~l~~n~i~~~~~-~~~~~~L~~L~l~~n~---l~~~-~~l~~l~~L~~L~l~~n~l~~~~~~~~~~~L~~  267 (384)
T d2omza2         193 LAKLTNLESLIATNNQISDITP-LGILTNLDELSLNGNQ---LKDI-GTLASLTNLTDLDLANNQISNLAPLSGLTKLTE  267 (384)
T ss_dssp             GGGCTTCSEEECCSSCCCCCGG-GGGCTTCCEEECCSSC---CCCC-GGGGGCTTCSEEECCSSCCCCCGGGTTCTTCSE
T ss_pred             cccccccceeeccCCccCCCCc-ccccCCCCEEECCCCC---CCCc-chhhcccccchhccccCccCCCCcccccccCCE
Confidence            222333344433311 111112 3444555555555553   1111 134455566666655432        2233344


Q ss_pred             EEeCcc--------CcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCC
Q 003387          682 IVLAEY--------LFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWL  753 (824)
Q Consensus       682 l~l~~~--------~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l  753 (824)
                      +.+.+.        ..++.++.+.+..|.+.+  +..+..+++++.|++++|.+.+.   ..+..+|+|++|++++|. +
T Consensus       268 L~l~~~~l~~~~~~~~~~~l~~l~~~~n~l~~--~~~~~~~~~l~~L~ls~n~l~~l---~~l~~l~~L~~L~L~~n~-l  341 (384)
T d2omza2         268 LKLGANQISNISPLAGLTALTNLELNENQLED--ISPISNLKNLTYLTLYFNNISDI---SPVSSLTKLQRLFFANNK-V  341 (384)
T ss_dssp             EECCSSCCCCCGGGTTCTTCSEEECCSSCCSC--CGGGGGCTTCSEEECCSSCCSCC---GGGGGCTTCCEEECCSSC-C
T ss_pred             eeccCcccCCCCcccccccccccccccccccc--ccccchhcccCeEECCCCCCCCC---cccccCCCCCEEECCCCC-C
Confidence            443322        334555555555555432  33456677777777777766542   124567788888887774 5


Q ss_pred             ccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCC
Q 003387          754 EEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWP  798 (824)
Q Consensus       754 ~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c  798 (824)
                      +.++ .+..+|+|+.|++++|+ +..+++ +.++++|+.|+|+++
T Consensus       342 ~~l~-~l~~l~~L~~L~l~~N~-l~~l~~-l~~l~~L~~L~L~~N  383 (384)
T d2omza2         342 SDVS-SLANLTNINWLSAGHNQ-ISDLTP-LANLTRITQLGLNDQ  383 (384)
T ss_dssp             CCCG-GGGGCTTCCEEECCSSC-CCBCGG-GTTCTTCSEEECCCE
T ss_pred             CCCh-hHcCCCCCCEEECCCCc-CCCChh-hccCCCCCEeeCCCC
Confidence            5555 46677788888887775 445553 677778888877653

>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=99.78  E-value=9.2e-20  Score=192.05  Aligned_cols=244  Identities=20%  Similarity=0.195  Sum_probs=121.0

Q ss_pred             cccEEEeeCccCc---cCCccCCCCCcceEEeecC-CCCC-ccChhhhhcCCCccEeecCCccccccc-hhhhccccCce
Q 003387          522 LLRVLDLGSLVLI---QYPSGIENLFLLRYLKLNI-PSLN-SLPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRH  595 (824)
Q Consensus       522 ~Lr~L~L~~~~i~---~lp~~i~~l~~Lr~L~L~~-~~i~-~lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~  595 (824)
                      +++.|+|+++.+.   .+|..+++|++|++|+|++ |.+. .+|..+ ++|++|++|+|++|.+..++ ..+..+.+|++
T Consensus        51 ~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_          51 RVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAI-AKLTQLHYLYITHTNVSGAIPDFLSQIKTLVT  129 (313)
T ss_dssp             CEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGGG-GGCTTCSEEEEEEECCEEECCGGGGGCTTCCE
T ss_pred             EEEEEECCCCCCCCCCCCChHHhcCcccccccccccccccccccccc-ccccccchhhhccccccccccccccchhhhcc
Confidence            3555666665554   4566666666666666654 4444 566665 66666666666666555443 33555666666


Q ss_pred             ecCCCccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCC-CeEEEecc
Q 003387          596 LNFGSITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCL-ESLKLANE  673 (824)
Q Consensus       596 L~L~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L-~~L~l~~~  673 (824)
                      +++++|.+.. .+| .++                      .+++|+.++++++.  ....+|..+..+..+ +.+.++.|
T Consensus       130 l~l~~N~~~~-~~p~~l~----------------------~l~~L~~l~l~~n~--l~~~ip~~~~~l~~l~~~l~~~~n  184 (313)
T d1ogqa_         130 LDFSYNALSG-TLPPSIS----------------------SLPNLVGITFDGNR--ISGAIPDSYGSFSKLFTSMTISRN  184 (313)
T ss_dssp             EECCSSEEES-CCCGGGG----------------------GCTTCCEEECCSSC--CEEECCGGGGCCCTTCCEEECCSS
T ss_pred             cccccccccc-cCchhhc----------------------cCcccceeeccccc--cccccccccccccccccccccccc
Confidence            6666555432 222 222                      33333333333322  111222222233222 22332222


Q ss_pred             CCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCC
Q 003387          674 SKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWL  753 (824)
Q Consensus       674 ~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l  753 (824)
                          +++......+..+. +..++++.+...+..+..++.+++|+.+++.+|.+.+.  ....+.+++|+.|+|++|...
T Consensus       185 ----~l~~~~~~~~~~l~-~~~l~l~~~~~~~~~~~~~~~~~~l~~l~~~~~~l~~~--~~~~~~~~~L~~L~Ls~N~l~  257 (313)
T d1ogqa_         185 ----RLTGKIPPTFANLN-LAFVDLSRNMLEGDASVLFGSDKNTQKIHLAKNSLAFD--LGKVGLSKNLNGLDLRNNRIY  257 (313)
T ss_dssp             ----EEEEECCGGGGGCC-CSEEECCSSEEEECCGGGCCTTSCCSEEECCSSEECCB--GGGCCCCTTCCEEECCSSCCE
T ss_pred             ----cccccccccccccc-cccccccccccccccccccccccccccccccccccccc--ccccccccccccccCccCeec
Confidence                12222111112221 22344555544455555566666666666666555442  223455666666666666533


Q ss_pred             ccceeccCcccCccEEEEecCCCCCCCccccccCccCcEEEecCCc
Q 003387          754 EEWTMGNAAMPKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       754 ~~l~~~~~~lp~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~c~  799 (824)
                      ..+|..++.+++|+.|++++|.....+|. +.++++|+.+.+.+++
T Consensus       258 g~iP~~l~~L~~L~~L~Ls~N~l~g~iP~-~~~L~~L~~l~l~~N~  302 (313)
T d1ogqa_         258 GTLPQGLTQLKFLHSLNVSFNNLCGEIPQ-GGNLQRFDVSAYANNK  302 (313)
T ss_dssp             ECCCGGGGGCTTCCEEECCSSEEEEECCC-STTGGGSCGGGTCSSS
T ss_pred             ccCChHHhCCCCCCEEECcCCcccccCCC-cccCCCCCHHHhCCCc
Confidence            35666666666666666666654445553 3555666666655554

>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=99.78  E-value=1.1e-18  Score=182.92  Aligned_cols=263  Identities=18%  Similarity=0.153  Sum_probs=169.0

Q ss_pred             cccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCcccccc-chhhhccccCceecCCC
Q 003387          522 LLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHT-ADEFWKMNKLRHLNFGS  600 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~l-p~~i~~L~~L~~L~L~~  600 (824)
                      .+++++-++..++++|..+.  +++++|+|++|+++.+|+..|.++++|++|++++|.+..+ |..|.++++|++|++++
T Consensus        11 ~~~~~~C~~~~L~~lP~~l~--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~l~~n~~~~i~~~~f~~l~~L~~L~l~~   88 (305)
T d1xkua_          11 HLRVVQCSDLGLEKVPKDLP--PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSK   88 (305)
T ss_dssp             ETTEEECTTSCCCSCCCSCC--TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCS
T ss_pred             cCCEEEecCCCCCccCCCCC--CCCCEEECcCCcCCCcChhHhhccccccccccccccccccchhhhhCCCccCEecccC
Confidence            34566666666666666553  4666666666666666654336666666666666666665 34466666666666666


Q ss_pred             ccCCCCCCCCCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCC
Q 003387          601 ITLPAHPGKFCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPR  678 (824)
Q Consensus       601 ~~~~~~~~p~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~  678 (824)
                      |.+.  .+|. .....+..+....+  .......+.....+..+....+........+..+..+++|+.+.+..+    +
T Consensus        89 n~l~--~l~~-~~~~~l~~L~~~~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n----~  161 (305)
T d1xkua_          89 NQLK--ELPE-KMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADT----N  161 (305)
T ss_dssp             SCCS--BCCS-SCCTTCCEEECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSS----C
T ss_pred             CccC--cCcc-chhhhhhhhhccccchhhhhhhhhhccccccccccccccccccCCCccccccccccCccccccC----C
Confidence            6654  2331 01123334433311  111122244555666676665543333344455667788888888765    2


Q ss_pred             ccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCcccee
Q 003387          679 LSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTM  758 (824)
Q Consensus       679 L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~  758 (824)
                      +..+..   ..+++|++|++++|......+..+.+++.++.|++++|.+.. .....+.++++|++|+|++|. ++.+|.
T Consensus       162 l~~l~~---~~~~~L~~L~l~~n~~~~~~~~~~~~~~~l~~L~~s~n~l~~-~~~~~~~~l~~L~~L~L~~N~-L~~lp~  236 (305)
T d1xkua_         162 ITTIPQ---GLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISA-VDNGSLANTPHLRELHLNNNK-LVKVPG  236 (305)
T ss_dssp             CCSCCS---SCCTTCSEEECTTSCCCEECTGGGTTCTTCCEEECCSSCCCE-ECTTTGGGSTTCCEEECCSSC-CSSCCT
T ss_pred             ccccCc---ccCCccCEEECCCCcCCCCChhHhhccccccccccccccccc-cccccccccccceeeeccccc-cccccc
Confidence            332211   346788999999888777777888889999999999887754 223345678899999999985 778887


Q ss_pred             ccCcccCccEEEEecCCCCCCCcc-------ccccCccCcEEEecCCc
Q 003387          759 GNAAMPKLECLIINPCAYLKKMPE-------QLWYIKSLNKFDCWWPQ  799 (824)
Q Consensus       759 ~~~~lp~L~~L~l~~c~~l~~lp~-------~l~~l~~L~~L~l~~c~  799 (824)
                      .+..+++|+.|++++|. ++.++.       .....++|+.|+++++|
T Consensus       237 ~l~~l~~L~~L~Ls~N~-i~~i~~~~f~~~~~~~~~~~L~~L~L~~N~  283 (305)
T d1xkua_         237 GLADHKYIQVVYLHNNN-ISAIGSNDFCPPGYNTKKASYSGVSLFSNP  283 (305)
T ss_dssp             TTTTCSSCCEEECCSSC-CCCCCTTSSSCSSCCTTSCCCSEEECCSSS
T ss_pred             ccccccCCCEEECCCCc-cCccChhhccCcchhcccCCCCEEECCCCc
Confidence            78889999999999885 566543       23456789999999988

>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=99.75  E-value=9.4e-18  Score=181.73  Aligned_cols=274  Identities=19%  Similarity=0.158  Sum_probs=186.2

Q ss_pred             CCeeEEEEEecCCCccccccc--CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceE
Q 003387          471 KKAKRLNAVEREGDFACLDDY--DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRY  548 (824)
Q Consensus       471 ~~~r~lsl~~~~~~~~~~~~~--~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~  548 (824)
                      .+++.|.+. +.....+ +.+  +++|++|.+.++....    ..  .+..+++|++|++++|.+..++. ++.+++|++
T Consensus        44 ~~l~~L~l~-~~~I~~l-~gl~~L~nL~~L~Ls~N~l~~----l~--~l~~L~~L~~L~L~~n~i~~i~~-l~~l~~L~~  114 (384)
T d2omza2          44 DQVTTLQAD-RLGIKSI-DGVEYLNNLTQINFSNNQLTD----IT--PLKNLTKLVDILMNNNQIADITP-LANLTNLTG  114 (384)
T ss_dssp             TTCCEEECC-SSCCCCC-TTGGGCTTCCEEECCSSCCCC----CG--GGTTCTTCCEEECCSSCCCCCGG-GTTCTTCCE
T ss_pred             CCCCEEECC-CCCCCCc-cccccCCCCCEEeCcCCcCCC----Cc--cccCCcccccccccccccccccc-ccccccccc
Confidence            468899998 6555544 345  9999999999987653    22  38899999999999999988764 899999999


Q ss_pred             EeecCCCCCccChhh---------------------------------------------------------------hh
Q 003387          549 LKLNIPSLNSLPSSL---------------------------------------------------------------LS  565 (824)
Q Consensus       549 L~L~~~~i~~lp~~i---------------------------------------------------------------~~  565 (824)
                      |+++++.+..++...                                                               +.
T Consensus       115 L~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (384)
T d2omza2         115 LTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLSFGNQVTDLKPLANLTTLERLDISSNKVSDISVLA  194 (384)
T ss_dssp             EECCSSCCCCCGGGTTCTTCSEEEEEEEEECCCGGGTTCTTCSEEEEEESCCCCGGGTTCTTCCEEECCSSCCCCCGGGG
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccchhhhhccccccccccccccccccccccc
Confidence            999987765433211                                                               24


Q ss_pred             cCCCccEeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCC-cchhhhcCCCCccceEEE
Q 003387          566 NLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPC-CCTEDILGRLPNLRNLRI  644 (824)
Q Consensus       566 ~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~-~~~~~~l~~l~~L~~L~l  644 (824)
                      .+++++.|++++|.+..++. .+.+++|+.|++++|.+.  .++.+..+++|+.+++..+. ..+.. +..+++|+.|++
T Consensus       195 ~l~~~~~l~l~~n~i~~~~~-~~~~~~L~~L~l~~n~l~--~~~~l~~l~~L~~L~l~~n~l~~~~~-~~~~~~L~~L~l  270 (384)
T d2omza2         195 KLTNLESLIATNNQISDITP-LGILTNLDELSLNGNQLK--DIGTLASLTNLTDLDLANNQISNLAP-LSGLTKLTELKL  270 (384)
T ss_dssp             GCTTCSEEECCSSCCCCCGG-GGGCTTCCEEECCSSCCC--CCGGGGGCTTCSEEECCSSCCCCCGG-GTTCTTCSEEEC
T ss_pred             cccccceeeccCCccCCCCc-ccccCCCCEEECCCCCCC--CcchhhcccccchhccccCccCCCCc-ccccccCCEeec
Confidence            45556666666665555543 455566666666666554  34455555666666655221 22223 555666666666


Q ss_pred             ecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeec
Q 003387          645 RGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQ  724 (824)
Q Consensus       645 ~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~  724 (824)
                      +++.-   ..++ .+..++.++.+.+..+    .++.  +.....+++++.|++++|.+.+.  ..+..+|+|+.|++++
T Consensus       271 ~~~~l---~~~~-~~~~~~~l~~l~~~~n----~l~~--~~~~~~~~~l~~L~ls~n~l~~l--~~l~~l~~L~~L~L~~  338 (384)
T d2omza2         271 GANQI---SNIS-PLAGLTALTNLELNEN----QLED--ISPISNLKNLTYLTLYFNNISDI--SPVSSLTKLQRLFFAN  338 (384)
T ss_dssp             CSSCC---CCCG-GGTTCTTCSEEECCSS----CCSC--CGGGGGCTTCSEEECCSSCCSCC--GGGGGCTTCCEEECCS
T ss_pred             cCccc---CCCC-cccccccccccccccc----cccc--ccccchhcccCeEECCCCCCCCC--cccccCCCCCEEECCC
Confidence            55531   1111 2344555555555543    1222  12236678999999999988653  3488999999999999


Q ss_pred             cccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecC
Q 003387          725 NSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPC  774 (824)
Q Consensus       725 ~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c  774 (824)
                      |.++.  +. .+..+++|++|++++|. ++.++. +..+++|+.|+|++|
T Consensus       339 n~l~~--l~-~l~~l~~L~~L~l~~N~-l~~l~~-l~~l~~L~~L~L~~N  383 (384)
T d2omza2         339 NKVSD--VS-SLANLTNINWLSAGHNQ-ISDLTP-LANLTRITQLGLNDQ  383 (384)
T ss_dssp             SCCCC--CG-GGGGCTTCCEEECCSSC-CCBCGG-GTTCTTCSEEECCCE
T ss_pred             CCCCC--Ch-hHcCCCCCCEEECCCCc-CCCChh-hccCCCCCEeeCCCC
Confidence            98875  22 46789999999999886 666653 788999999999986

>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=99.74  E-value=6.1e-19  Score=185.64  Aligned_cols=225  Identities=17%  Similarity=0.193  Sum_probs=138.7

Q ss_pred             CceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeC-ccCc-cCCccCCCCCcceEEeecCCCCCccChhhhhcCCCc
Q 003387          493 SQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGS-LVLI-QYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNL  570 (824)
Q Consensus       493 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~-~~i~-~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L  570 (824)
                      .+++.|.+.++....  ...++..+.++++|++|+|++ |.+. .+|..|++|++|++|+|++|.+..++...+..+.+|
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  127 (313)
T d1ogqa_          50 YRVNNLDLSGLNLPK--PYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTL  127 (313)
T ss_dssp             CCEEEEEEECCCCSS--CEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTC
T ss_pred             EEEEEEECCCCCCCC--CCCCChHHhcCccccccccccccccccccccccccccccchhhhccccccccccccccchhhh
Confidence            357777777765531  113457889999999999997 5676 899999999999999999999998776655999999


Q ss_pred             cEeecCCc-cccccchhhhccccCceecCCCccCCCCCCC-CCCCCCCC-CeeeccCCCc--chhhhcCCCCccceEEEe
Q 003387          571 YTLDMPFS-YIDHTADEFWKMNKLRHLNFGSITLPAHPGK-FCGSLENL-NFISALHPCC--CTEDILGRLPNLRNLRIR  645 (824)
Q Consensus       571 ~~L~L~~~-~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L-~~l~~~~~~~--~~~~~l~~l~~L~~L~l~  645 (824)
                      +++++++| ....+|..++++++|+++++++|.+.+ .+| .++.+..+ ..+.+..+..  ..+..+..+.. ..+++.
T Consensus       128 ~~l~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~-~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~~~l~~-~~l~l~  205 (313)
T d1ogqa_         128 VTLDFSYNALSGTLPPSISSLPNLVGITFDGNRISG-AIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNL-AFVDLS  205 (313)
T ss_dssp             CEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCEE-ECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCCC-SEEECC
T ss_pred             cccccccccccccCchhhccCcccceeecccccccc-cccccccccccccccccccccccccccccccccccc-cccccc
Confidence            99999999 556778999999999999999998764 445 56566554 4444442110  11111333322 234443


Q ss_pred             cccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeecc
Q 003387          646 GDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQN  725 (824)
Q Consensus       646 ~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~  725 (824)
                      .+.  .....+..+..+++|+.+++..+.    +.. .+.....+++|+.|+|++|.+.+.+|..++++++|++|+|++|
T Consensus       206 ~~~--~~~~~~~~~~~~~~l~~l~~~~~~----l~~-~~~~~~~~~~L~~L~Ls~N~l~g~iP~~l~~L~~L~~L~Ls~N  278 (313)
T d1ogqa_         206 RNM--LEGDASVLFGSDKNTQKIHLAKNS----LAF-DLGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFN  278 (313)
T ss_dssp             SSE--EEECCGGGCCTTSCCSEEECCSSE----ECC-BGGGCCCCTTCCEEECCSSCCEECCCGGGGGCTTCCEEECCSS
T ss_pred             ccc--cccccccccccccccccccccccc----ccc-cccccccccccccccCccCeecccCChHHhCCCCCCEEECcCC
Confidence            332  233334444444555555544321    111 0111233344555555555444444444555555555555544


Q ss_pred             ccC
Q 003387          726 SYS  728 (824)
Q Consensus       726 ~~~  728 (824)
                      .+.
T Consensus       279 ~l~  281 (313)
T d1ogqa_         279 NLC  281 (313)
T ss_dssp             EEE
T ss_pred             ccc
Confidence            443

>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=99.70  E-value=2.2e-16  Score=165.10  Aligned_cols=240  Identities=15%  Similarity=0.149  Sum_probs=166.9

Q ss_pred             CcccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCC
Q 003387          521 KLLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFG  599 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~  599 (824)
                      +.+++|+|++|.++.+|+ .|.++++|++|++++|.+..+++..|.++++|++|++++|.++.+|..  ....|+.|++.
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 PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEK--MPKTLQELRVH  108 (305)
T ss_dssp             TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCSS--CCTTCCEEECC
T ss_pred             CCCCEEECcCCcCCCcChhHhhccccccccccccccccccchhhhhCCCccCEecccCCccCcCccc--hhhhhhhhhcc
Confidence            568888888888888875 577888888888888888877655448888888888888888888764  34567777777


Q ss_pred             CccCCCCCCC--CCCCCCCCCeeeccCC----CcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEecc
Q 003387          600 SITLPAHPGK--FCGSLENLNFISALHP----CCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANE  673 (824)
Q Consensus       600 ~~~~~~~~~p--~i~~L~~L~~l~~~~~----~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~  673 (824)
                      +|.+..  ++  .+.....+..+.....    .......+..+++|+.+.+.++.   ...++..  .+++|+.|++.++
T Consensus       109 ~n~l~~--l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~---l~~l~~~--~~~~L~~L~l~~n  181 (305)
T d1xkua_         109 ENEITK--VRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTN---ITTIPQG--LPPSLTELHLDGN  181 (305)
T ss_dssp             SSCCCB--BCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSC---CCSCCSS--CCTTCSEEECTTS
T ss_pred             ccchhh--hhhhhhhccccccccccccccccccCCCccccccccccCccccccCC---ccccCcc--cCCccCEEECCCC
Confidence            776652  22  3333444444444321    11112236777888888888774   2222222  3567888888765


Q ss_pred             CCCCCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCC
Q 003387          674 SKMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWL  753 (824)
Q Consensus       674 ~~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l  753 (824)
                      .    ........+..+++++.|++++|.+....+..+.++++|++|+|++|.+..  ++..+..+++|++|+|++|+ +
T Consensus       182 ~----~~~~~~~~~~~~~~l~~L~~s~n~l~~~~~~~~~~l~~L~~L~L~~N~L~~--lp~~l~~l~~L~~L~Ls~N~-i  254 (305)
T d1xkua_         182 K----ITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVK--VPGGLADHKYIQVVYLHNNN-I  254 (305)
T ss_dssp             C----CCEECTGGGTTCTTCCEEECCSSCCCEECTTTGGGSTTCCEEECCSSCCSS--CCTTTTTCSSCCEEECCSSC-C
T ss_pred             c----CCCCChhHhhccccccccccccccccccccccccccccceeeecccccccc--cccccccccCCCEEECCCCc-c
Confidence            2    333333444667888999999998877777788899999999999888764  45567788999999999875 6


Q ss_pred             ccceec-------cCcccCccEEEEecCCC
Q 003387          754 EEWTMG-------NAAMPKLECLIINPCAY  776 (824)
Q Consensus       754 ~~l~~~-------~~~lp~L~~L~l~~c~~  776 (824)
                      +.++..       ...+++|+.|.+++|+.
T Consensus       255 ~~i~~~~f~~~~~~~~~~~L~~L~L~~N~~  284 (305)
T d1xkua_         255 SAIGSNDFCPPGYNTKKASYSGVSLFSNPV  284 (305)
T ss_dssp             CCCCTTSSSCSSCCTTSCCCSEEECCSSSS
T ss_pred             CccChhhccCcchhcccCCCCEEECCCCcC
Confidence            666421       23468899999999984

>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=99.67  E-value=8.7e-17  Score=164.48  Aligned_cols=198  Identities=20%  Similarity=0.148  Sum_probs=117.5

Q ss_pred             ccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecC
Q 003387          519 MFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNF  598 (824)
Q Consensus       519 ~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L  598 (824)
                      ....+...+.+++.++.+|..+.  ++|++|+|++|.++.+|...|.++++|++|+|++|.++.+|. ++.+++|++|++
T Consensus         8 ~~~~~~~v~C~~~~L~~iP~~lp--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N~l~~l~~-~~~l~~L~~L~L   84 (266)
T d1p9ag_           8 KVASHLEVNCDKRNLTALPPDLP--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTKLQV-DGTLPVLGTLDL   84 (266)
T ss_dssp             CSTTCCEEECTTSCCSSCCSCCC--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCCEEEC-CSCCTTCCEEEC
T ss_pred             ccCCCeEEEccCCCCCeeCcCcC--cCCCEEECcCCcCCCcCHHHhhcccccccccccccccccccc-cccccccccccc
Confidence            44555666888888999998775  588999999999999987655899999999999999998875 678999999999


Q ss_pred             CCccCCCCCCC-CCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCC
Q 003387          599 GSITLPAHPGK-FCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMP  677 (824)
Q Consensus       599 ~~~~~~~~~~p-~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~  677 (824)
                      ++|.+..  .+ .+                      ..+++|+.|+++++.  .....+..+..+.+++.|.+..|    
T Consensus        85 s~N~l~~--~~~~~----------------------~~l~~L~~L~l~~~~--~~~~~~~~~~~l~~l~~L~l~~n----  134 (266)
T d1p9ag_          85 SHNQLQS--LPLLG----------------------QTLPALTVLDVSFNR--LTSLPLGALRGLGELQELYLKGN----  134 (266)
T ss_dssp             CSSCCSS--CCCCT----------------------TTCTTCCEEECCSSC--CCCCCSSTTTTCTTCCEEECTTS----
T ss_pred             ccccccc--ccccc----------------------ccccccccccccccc--cceeecccccccccccccccccc----
Confidence            9988752  22 33                      344445555444442  11111112223333444444332    


Q ss_pred             CccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCC
Q 003387          678 RLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSML  751 (824)
Q Consensus       678 ~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~  751 (824)
                      .++.+.......+++|+.|++++|.+....+..++.+++|++|+|++|.+..  ++.....+++|+.|.|++|+
T Consensus       135 ~l~~l~~~~~~~l~~l~~l~l~~N~l~~~~~~~~~~l~~L~~L~Ls~N~L~~--lp~~~~~~~~L~~L~L~~Np  206 (266)
T d1p9ag_         135 ELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLNGLENLDTLLLQENSLYT--IPKGFFGSHLLPFAFLHGNP  206 (266)
T ss_dssp             CCCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTTTCTTCCEEECCSSCCCC--CCTTTTTTCCCSEEECCSCC
T ss_pred             ccceeccccccccccchhcccccccccccCccccccccccceeecccCCCcc--cChhHCCCCCCCEEEecCCC
Confidence            1222222222334455555555555544444445555555555555555432  33333444555555555543

>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=99.66  E-value=8.7e-17  Score=166.31  Aligned_cols=201  Identities=19%  Similarity=0.180  Sum_probs=110.9

Q ss_pred             cccEEEeeCccCccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCc-cccccc-hhhhccccCceecC
Q 003387          522 LLRVLDLGSLVLIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFS-YIDHTA-DEFWKMNKLRHLNF  598 (824)
Q Consensus       522 ~Lr~L~L~~~~i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~-~l~~lp-~~i~~L~~L~~L~L  598 (824)
                      .+++|+|++|.|+.+|. .+..+++|++|+++++.+..++...+..+..++.++...+ .+..++ ..+.++++|++|++
T Consensus        33 ~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~l~~L~~L~l  112 (284)
T d1ozna_          33 ASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHL  112 (284)
T ss_dssp             TCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEEEC
T ss_pred             CCCEEECcCCcCCCCCHHHhhccccccccccccccccccccccccccccccccccccccccccccchhhcccccCCEEec
Confidence            34555555555554443 3455555555555555555544444444555555544433 444442 33455555555555


Q ss_pred             CCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCC
Q 003387          599 GSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPR  678 (824)
Q Consensus       599 ~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~  678 (824)
                      ++|.+..                      .....+..+++|+.++++++.  .....+..+..+++|++|++++|    +
T Consensus       113 ~~n~~~~----------------------~~~~~~~~~~~L~~l~l~~N~--l~~i~~~~f~~~~~L~~L~l~~N----~  164 (284)
T d1ozna_         113 DRCGLQE----------------------LGPGLFRGLAALQYLYLQDNA--LQALPDDTFRDLGNLTHLFLHGN----R  164 (284)
T ss_dssp             TTSCCCC----------------------CCTTTTTTCTTCCEEECCSSC--CCCCCTTTTTTCTTCCEEECCSS----C
T ss_pred             CCccccc----------------------ccccccchhcccchhhhcccc--ccccChhHhccccchhhcccccC----c
Confidence            5544431                      111124455566666666553  11111234555666777776655    3


Q ss_pred             ccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCC
Q 003387          679 LSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSML  751 (824)
Q Consensus       679 L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~  751 (824)
                      ++.+....+..+++|+.+.+++|.+.+..+..+..+++|++|++++|.+... ....++.+++|++|+|++++
T Consensus       165 l~~l~~~~f~~l~~L~~l~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~i~~~-~~~~~~~~~~L~~L~l~~N~  236 (284)
T d1ozna_         165 ISSVPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANNLSAL-PTEALAPLRALQYLRLNDNP  236 (284)
T ss_dssp             CCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSCC-CHHHHTTCTTCCEEECCSSC
T ss_pred             ccccchhhhccccccchhhhhhccccccChhHhhhhhhcccccccccccccc-cccccccccccCEEEecCCC
Confidence            5555544556667777777777776666666777777777777777766542 23345567777777777765

>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=99.59  E-value=1.9e-15  Score=154.36  Aligned_cols=198  Identities=20%  Similarity=0.165  Sum_probs=117.0

Q ss_pred             CCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccch-hhhccccCceecCCCccCCCCCCCCCCCCCCCCee
Q 003387          542 NLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFI  620 (824)
Q Consensus       542 ~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l  620 (824)
                      +...+...+.++++++.+|+.+ .  ++|++|+|++|.++.+|. .|.++++|++|+|++|.+.  .+|           
T Consensus         8 ~~~~~~~v~C~~~~L~~iP~~l-p--~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N~l~--~l~-----------   71 (266)
T d1p9ag_           8 KVASHLEVNCDKRNLTALPPDL-P--KDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELT--KLQ-----------   71 (266)
T ss_dssp             CSTTCCEEECTTSCCSSCCSCC-C--TTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCC--EEE-----------
T ss_pred             ccCCCeEEEccCCCCCeeCcCc-C--cCCCEEECcCCcCCCcCHHHhhcccccccccccccccc--ccc-----------
Confidence            4556666788999999999877 3  689999999999999985 5889999999999998775  111           


Q ss_pred             eccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeCccCcCCCceEEEEEc
Q 003387          621 SALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLAEYLFPHSLTHLSFSN  700 (824)
Q Consensus       621 ~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~  700 (824)
                                . ++.+++|+.|+++++.   ....+..+..+++|+.|+++.+    .+..+.......+.+++.|.+++
T Consensus        72 ----------~-~~~l~~L~~L~Ls~N~---l~~~~~~~~~l~~L~~L~l~~~----~~~~~~~~~~~~l~~l~~L~l~~  133 (266)
T d1p9ag_          72 ----------V-DGTLPVLGTLDLSHNQ---LQSLPLLGQTLPALTVLDVSFN----RLTSLPLGALRGLGELQELYLKG  133 (266)
T ss_dssp             ----------C-CSCCTTCCEEECCSSC---CSSCCCCTTTCTTCCEEECCSS----CCCCCCSSTTTTCTTCCEEECTT
T ss_pred             ----------c-cccccccccccccccc---cccccccccccccccccccccc----ccceeeccccccccccccccccc
Confidence                      1 4456777777777763   2222333445556666666543    12222222234445555555555


Q ss_pred             ccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccCccEEEEecCC
Q 003387          701 TDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPKLECLIINPCA  775 (824)
Q Consensus       701 ~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~L~~L~l~~c~  775 (824)
                      |.+....+..+..+++|+.|++++|.+... ....+..+++|++|+|++|. ++.+|.+...+++|+.|++++||
T Consensus       134 n~l~~l~~~~~~~l~~l~~l~l~~N~l~~~-~~~~~~~l~~L~~L~Ls~N~-L~~lp~~~~~~~~L~~L~L~~Np  206 (266)
T d1p9ag_         134 NELKTLPPGLLTPTPKLEKLSLANNNLTEL-PAGLLNGLENLDTLLLQENS-LYTIPKGFFGSHLLPFAFLHGNP  206 (266)
T ss_dssp             SCCCCCCTTTTTTCTTCCEEECTTSCCSCC-CTTTTTTCTTCCEEECCSSC-CCCCCTTTTTTCCCSEEECCSCC
T ss_pred             cccceeccccccccccchhccccccccccc-CccccccccccceeecccCC-CcccChhHCCCCCCCEEEecCCC
Confidence            555444444445555555555555544431 11223444555555555543 44444444445555555555544

>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=99.58  E-value=4.9e-15  Score=152.92  Aligned_cols=219  Identities=17%  Similarity=0.068  Sum_probs=132.6

Q ss_pred             EEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCccC
Q 003387          525 VLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITL  603 (824)
Q Consensus       525 ~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~  603 (824)
                      +++.+++.++.+|..+.  .++++|+|++|+|+.+|...|.++++|++|+++++.+..++.. +..+..+++++...+..
T Consensus        15 ~v~c~~~~L~~iP~~ip--~~~~~L~Ls~N~i~~i~~~~f~~l~~L~~L~ls~n~l~~i~~~~~~~~~~~~~l~~~~~~~   92 (284)
T d1ozna_          15 TTSCPQQGLQAVPVGIP--AASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQ   92 (284)
T ss_dssp             EEECCSSCCSSCCTTCC--TTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTT
T ss_pred             EEEcCCCCCCccCCCCC--CCCCEEECcCCcCCCCCHHHhhccccccccccccccccccccccccccccccccccccccc
Confidence            44667777888887765  4678888888888888876558888888888888888777644 45567777775433221


Q ss_pred             CCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEE
Q 003387          604 PAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIV  683 (824)
Q Consensus       604 ~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~  683 (824)
                      ..                     ......+..+++|+.|+++.+.  .....+..+                        
T Consensus        93 ~~---------------------~l~~~~~~~l~~L~~L~l~~n~--~~~~~~~~~------------------------  125 (284)
T d1ozna_          93 LR---------------------SVDPATFHGLGRLHTLHLDRCG--LQELGPGLF------------------------  125 (284)
T ss_dssp             CC---------------------CCCTTTTTTCTTCCEEECTTSC--CCCCCTTTT------------------------
T ss_pred             cc---------------------cccchhhcccccCCEEecCCcc--ccccccccc------------------------
Confidence            10                     0111126667777777777653  111111122                        


Q ss_pred             eCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcc
Q 003387          684 LAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAM  763 (824)
Q Consensus       684 l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~l  763 (824)
                          ..+++|+.+++++|.+....+..+..+++|+.|++++|.+.. .....+.++++|++|.+++|......+..+..+
T Consensus       126 ----~~~~~L~~l~l~~N~l~~i~~~~f~~~~~L~~L~l~~N~l~~-l~~~~f~~l~~L~~l~l~~N~l~~i~~~~f~~l  200 (284)
T d1ozna_         126 ----RGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRISS-VPERAFRGLHSLDRLLLHQNRVAHVHPHAFRDL  200 (284)
T ss_dssp             ----TTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCE-ECTTTTTTCTTCCEEECCSSCCCEECTTTTTTC
T ss_pred             ----chhcccchhhhccccccccChhHhccccchhhcccccCcccc-cchhhhccccccchhhhhhccccccChhHhhhh
Confidence                334555566666666554445556666666666666665542 112233456666666666665333334455666


Q ss_pred             cCccEEEEecCCCCCCCccccccCccCcEEEecC
Q 003387          764 PKLECLIINPCAYLKKMPEQLWYIKSLNKFDCWW  797 (824)
Q Consensus       764 p~L~~L~l~~c~~l~~lp~~l~~l~~L~~L~l~~  797 (824)
                      ++|+.|++++|......|..+..+++|+.|++++
T Consensus       201 ~~L~~L~l~~N~i~~~~~~~~~~~~~L~~L~l~~  234 (284)
T d1ozna_         201 GRLMTLYLFANNLSALPTEALAPLRALQYLRLND  234 (284)
T ss_dssp             TTCCEEECCSSCCSCCCHHHHTTCTTCCEEECCS
T ss_pred             hhcccccccccccccccccccccccccCEEEecC
Confidence            7777777776665444444566667777777765

>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=99.57  E-value=1.5e-14  Score=153.86  Aligned_cols=76  Identities=17%  Similarity=0.142  Sum_probs=41.9

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCC
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGS  600 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~  600 (824)
                      ++|++|+|++|.++.+|..+   .+|+.|++++|.++.++. +   .++|++|++++|.+..+|. ++.+++|++|++++
T Consensus        58 ~~L~~L~Ls~N~l~~lp~~~---~~L~~L~l~~n~l~~l~~-l---p~~L~~L~L~~n~l~~lp~-~~~l~~L~~L~l~~  129 (353)
T d1jl5a_          58 PHLESLVASCNSLTELPELP---QSLKSLLVDNNNLKALSD-L---PPLLEYLGVSNNQLEKLPE-LQNSSFLKIIDVDN  129 (353)
T ss_dssp             TTCSEEECCSSCCSSCCCCC---TTCCEEECCSSCCSCCCS-C---CTTCCEEECCSSCCSSCCC-CTTCTTCCEEECCS
T ss_pred             CCCCEEECCCCCCcccccch---hhhhhhhhhhcccchhhh-h---ccccccccccccccccccc-hhhhccceeecccc
Confidence            45666666666666665543   245555565555555442 1   1245666666666666654 45566666666655


Q ss_pred             ccCC
Q 003387          601 ITLP  604 (824)
Q Consensus       601 ~~~~  604 (824)
                      +.+.
T Consensus       130 ~~~~  133 (353)
T d1jl5a_         130 NSLK  133 (353)
T ss_dssp             SCCS
T ss_pred             cccc
Confidence            5443

>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=99.54  E-value=6.2e-14  Score=149.06  Aligned_cols=91  Identities=21%  Similarity=0.107  Sum_probs=76.8

Q ss_pred             CcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCC
Q 003387          521 KLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGS  600 (824)
Q Consensus       521 ~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~  600 (824)
                      .+|++|||+++.++.+|+.   +++|++|++++|+++++|..+    .+|+.|++++|.+..++. +  .++|++|++++
T Consensus        38 ~~l~~LdLs~~~L~~lp~~---~~~L~~L~Ls~N~l~~lp~~~----~~L~~L~l~~n~l~~l~~-l--p~~L~~L~L~~  107 (353)
T d1jl5a_          38 RQAHELELNNLGLSSLPEL---PPHLESLVASCNSLTELPELP----QSLKSLLVDNNNLKALSD-L--PPLLEYLGVSN  107 (353)
T ss_dssp             HTCSEEECTTSCCSCCCSC---CTTCSEEECCSSCCSSCCCCC----TTCCEEECCSSCCSCCCS-C--CTTCCEEECCS
T ss_pred             cCCCEEEeCCCCCCCCCCC---CCCCCEEECCCCCCcccccch----hhhhhhhhhhcccchhhh-h--ccccccccccc
Confidence            4689999999999999974   468999999999999999754    578899999998877764 1  24699999999


Q ss_pred             ccCCCCCCCCCCCCCCCCeeecc
Q 003387          601 ITLPAHPGKFCGSLENLNFISAL  623 (824)
Q Consensus       601 ~~~~~~~~p~i~~L~~L~~l~~~  623 (824)
                      |.+.  .+|.++.+++|+.+++.
T Consensus       108 n~l~--~lp~~~~l~~L~~L~l~  128 (353)
T d1jl5a_         108 NQLE--KLPELQNSSFLKIIDVD  128 (353)
T ss_dssp             SCCS--SCCCCTTCTTCCEEECC
T ss_pred             cccc--cccchhhhccceeeccc
Confidence            9987  67878889999999887

>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=99.53  E-value=3.7e-14  Score=140.90  Aligned_cols=190  Identities=22%  Similarity=0.242  Sum_probs=121.0

Q ss_pred             hcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCcee
Q 003387          517 CGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHL  596 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L  596 (824)
                      +..+.+|+.|++++|.++.++ .+.++++|++|++++|.+..+++ + .++++|+++++++|.++.++. +..+++|+.+
T Consensus        37 ~~~l~~L~~L~l~~~~i~~l~-~l~~l~~L~~L~ls~n~i~~~~~-l-~~l~~l~~l~~~~n~~~~i~~-l~~l~~L~~l  112 (227)
T d1h6ua2          37 QADLDGITTLSAFGTGVTTIE-GVQYLNNLIGLELKDNQITDLAP-L-KNLTKITELELSGNPLKNVSA-IAGLQSIKTL  112 (227)
T ss_dssp             HHHHHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-G-TTCCSCCEEECCSCCCSCCGG-GTTCTTCCEE
T ss_pred             HHHcCCcCEEECCCCCCCcch-hHhcCCCCcEeecCCceeecccc-c-ccccccccccccccccccccc-cccccccccc
Confidence            355677888888888887774 57778888888888888877664 4 788888888888887777664 7778888888


Q ss_pred             cCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCC
Q 003387          597 NFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKM  676 (824)
Q Consensus       597 ~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~  676 (824)
                      +++++...  .++.                      +...+.+..+.++++.....    ..+.++++|+.|.+.++.  
T Consensus       113 ~l~~~~~~--~~~~----------------------~~~~~~~~~l~~~~~~~~~~----~~~~~~~~L~~L~l~~n~--  162 (227)
T d1h6ua2         113 DLTSTQIT--DVTP----------------------LAGLSNLQVLYLDLNQITNI----SPLAGLTNLQYLSIGNAQ--  162 (227)
T ss_dssp             ECTTSCCC--CCGG----------------------GTTCTTCCEEECCSSCCCCC----GGGGGCTTCCEEECCSSC--
T ss_pred             cccccccc--ccch----------------------hccccchhhhhchhhhhchh----hhhccccccccccccccc--
Confidence            77766554  1222                      33344444554444321111    123445556666665431  


Q ss_pred             CCccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeecc
Q 003387          677 PRLSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKS  749 (824)
Q Consensus       677 ~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~  749 (824)
                        +..  ..++..+++|+.|++++|.+.+  ++.++++++|++|+|++|+++.  +. .+.++++|++|+|++
T Consensus       163 --~~~--~~~l~~l~~L~~L~Ls~n~l~~--l~~l~~l~~L~~L~Ls~N~lt~--i~-~l~~l~~L~~L~lsn  226 (227)
T d1h6ua2         163 --VSD--LTPLANLSKLTTLKADDNKISD--ISPLASLPNLIEVHLKNNQISD--VS-PLANTSNLFIVTLTN  226 (227)
T ss_dssp             --CCC--CGGGTTCTTCCEEECCSSCCCC--CGGGGGCTTCCEEECTTSCCCB--CG-GGTTCTTCCEEEEEE
T ss_pred             --ccc--chhhcccccceecccCCCccCC--ChhhcCCCCCCEEECcCCcCCC--Cc-ccccCCCCCEEEeeC
Confidence              111  1223456777788887777643  3447778888888888777654  22 356788888888764

>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=99.52  E-value=5.6e-15  Score=152.16  Aligned_cols=223  Identities=17%  Similarity=0.149  Sum_probs=138.1

Q ss_pred             ccEEEeeCccCccCCccCCCCCcceEEeecCCCCC-ccChhhhhcCCCccEeecCCcccc-ccchhhhccccCceecCCC
Q 003387          523 LRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLLNLYTLDMPFSYID-HTADEFWKMNKLRHLNFGS  600 (824)
Q Consensus       523 Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~-~lp~~i~~~L~~L~~L~L~~~~l~-~lp~~i~~L~~L~~L~L~~  600 (824)
                      +..+.++.+.+............|++|++++|.+. .....++.++++|++|++++|.+. ..+..+.++++|++|++++
T Consensus        25 ~~~lrl~~~~~~~~~~~~~~~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~Ls~  104 (284)
T d2astb2          25 VIAFRCPRSFMDQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSG  104 (284)
T ss_dssp             CSEEECTTCEECSCCCSCCCCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTT
T ss_pred             ceEeeccccccccchhhhccCCCCCEEECCCCccCHHHHHHHHHhCCCcccccccccCCCcHHHHHHhcCCCCcCccccc
Confidence            45666665554433333455678899999888765 222333488899999999888665 3456688888899998887


Q ss_pred             ccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccC-CCCCeEEEeccCCCCCc
Q 003387          601 ITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRL-SCLESLKLANESKMPRL  679 (824)
Q Consensus       601 ~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l-~~L~~L~l~~~~~~~~L  679 (824)
                      |....                    ...+......+++|++|++++|.......+...+... ++|+.|++++.  ..++
T Consensus       105 c~~it--------------------d~~l~~l~~~~~~L~~L~ls~c~~~~~~~~~~~~~~~~~~L~~L~l~~~--~~~i  162 (284)
T d2astb2         105 CSGFS--------------------EFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGY--RKNL  162 (284)
T ss_dssp             CBSCC--------------------HHHHHHHHHHCTTCCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSC--GGGS
T ss_pred             ccccc--------------------ccccchhhHHHHhccccccccccccccccchhhhcccccccchhhhccc--cccc
Confidence            64210                    2223333567899999999987644455555545443 67888887641  0112


Q ss_pred             cEEEeCcc-CcCCCceEEEEEccc-CCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccce
Q 003387          680 SKIVLAEY-LFPHSLTHLSFSNTD-LMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWT  757 (824)
Q Consensus       680 ~~l~l~~~-~~~~~L~~L~L~~~~-l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~  757 (824)
                      ..-.+... ..+++|++|++++|. +++..+..++++|+|++|++++|....+......+.+|+|+.|++.+|-.-..+.
T Consensus       163 ~~~~l~~l~~~~~~L~~L~L~~~~~itd~~~~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~L~l~~~~~d~~l~  242 (284)
T d2astb2         163 QKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGIVPDGTLQ  242 (284)
T ss_dssp             CHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTSSCTTCHH
T ss_pred             ccccccccccccccccccccccccCCCchhhhhhcccCcCCEEECCCCCCCChHHHHHHhcCCCCCEEeeeCCCCHHHHH
Confidence            21111111 356788888888774 5556667778888888888887643322223335667888888888773223333


Q ss_pred             eccCcccCcc
Q 003387          758 MGNAAMPKLE  767 (824)
Q Consensus       758 ~~~~~lp~L~  767 (824)
                      .-...+|+|+
T Consensus       243 ~l~~~lp~L~  252 (284)
T d2astb2         243 LLKEALPHLQ  252 (284)
T ss_dssp             HHHHHSTTSE
T ss_pred             HHHHhCcccc
Confidence            2233466655

>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=99.48  E-value=1.7e-13  Score=135.96  Aligned_cols=203  Identities=20%  Similarity=0.224  Sum_probs=148.6

Q ss_pred             EEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccCCC
Q 003387          526 LDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPA  605 (824)
Q Consensus       526 L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~  605 (824)
                      ++++.+.+..+. .+..+.+|++|++.+|+++.++ .+ .++++|++|++++|.+..++. +.++++|+++++++|.+. 
T Consensus        24 ~~l~~~~~~d~~-~~~~l~~L~~L~l~~~~i~~l~-~l-~~l~~L~~L~ls~n~i~~~~~-l~~l~~l~~l~~~~n~~~-   98 (227)
T d1h6ua2          24 IAAGKSNVTDTV-TQADLDGITTLSAFGTGVTTIE-GV-QYLNNLIGLELKDNQITDLAP-LKNLTKITELELSGNPLK-   98 (227)
T ss_dssp             HHTTCSSTTSEE-CHHHHHTCCEEECTTSCCCCCT-TG-GGCTTCCEEECCSSCCCCCGG-GTTCCSCCEEECCSCCCS-
T ss_pred             HHhCCCCcCCcC-CHHHcCCcCEEECCCCCCCcch-hH-hcCCCCcEeecCCceeecccc-cccccccccccccccccc-
Confidence            345555555332 3466788999999999999885 56 899999999999998888765 888999999988887654 


Q ss_pred             CCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCCccEEEeC
Q 003387          606 HPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPRLSKIVLA  685 (824)
Q Consensus       606 ~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~l~  685 (824)
                       .+                     .. +..+++|+.+.++.+.....    ..+...+.+..+.+..+.    +..  ..
T Consensus        99 -~i---------------------~~-l~~l~~L~~l~l~~~~~~~~----~~~~~~~~~~~l~~~~~~----~~~--~~  145 (227)
T d1h6ua2          99 -NV---------------------SA-IAGLQSIKTLDLTSTQITDV----TPLAGLSNLQVLYLDLNQ----ITN--IS  145 (227)
T ss_dssp             -CC---------------------GG-GTTCTTCCEEECTTSCCCCC----GGGTTCTTCCEEECCSSC----CCC--CG
T ss_pred             -cc---------------------cc-cccccccccccccccccccc----chhccccchhhhhchhhh----hch--hh
Confidence             12                     22 56677777777776642111    124456778888876531    211  12


Q ss_pred             ccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCccEEeeccCCCCccceeccCcccC
Q 003387          686 EYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLKVLHLKSMLWLEEWTMGNAAMPK  765 (824)
Q Consensus       686 ~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~~L~L~~~~~l~~l~~~~~~lp~  765 (824)
                      ....+++|+.|.+++|.+..  ...++++++|+.|++++|.+.+  + ..+.++++|++|+|++|+ ++.++ .+..+++
T Consensus       146 ~~~~~~~L~~L~l~~n~~~~--~~~l~~l~~L~~L~Ls~n~l~~--l-~~l~~l~~L~~L~Ls~N~-lt~i~-~l~~l~~  218 (227)
T d1h6ua2         146 PLAGLTNLQYLSIGNAQVSD--LTPLANLSKLTTLKADDNKISD--I-SPLASLPNLIEVHLKNNQ-ISDVS-PLANTSN  218 (227)
T ss_dssp             GGGGCTTCCEEECCSSCCCC--CGGGTTCTTCCEEECCSSCCCC--C-GGGGGCTTCCEEECTTSC-CCBCG-GGTTCTT
T ss_pred             hhcccccccccccccccccc--chhhcccccceecccCCCccCC--C-hhhcCCCCCCEEECcCCc-CCCCc-ccccCCC
Confidence            23567889999999998643  3458899999999999998765  2 236789999999999985 78776 4789999


Q ss_pred             ccEEEEec
Q 003387          766 LECLIINP  773 (824)
Q Consensus       766 L~~L~l~~  773 (824)
                      |+.|++++
T Consensus       219 L~~L~lsn  226 (227)
T d1h6ua2         219 LFIVTLTN  226 (227)
T ss_dssp             CCEEEEEE
T ss_pred             CCEEEeeC
Confidence            99999974

>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=1.2e-13  Score=135.21  Aligned_cols=165  Identities=23%  Similarity=0.224  Sum_probs=114.9

Q ss_pred             ccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecC
Q 003387          519 MFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNF  598 (824)
Q Consensus       519 ~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L  598 (824)
                      .+..|+.|++++|.++.++ .+..+++|++|++++|.++.+++ + +++++|++|++++|.++.+|. +..+++|+.|++
T Consensus        44 ~L~~L~~L~l~~~~i~~l~-~l~~l~~L~~L~L~~n~i~~l~~-~-~~l~~L~~L~l~~n~i~~l~~-l~~l~~L~~L~l  119 (210)
T d1h6ta2          44 ELNSIDQIIANNSDIKSVQ-GIQYLPNVTKLFLNGNKLTDIKP-L-ANLKNLGWLFLDENKVKDLSS-LKDLKKLKSLSL  119 (210)
T ss_dssp             HHHTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-G-TTCTTCCEEECCSSCCCCGGG-GTTCTTCCEEEC
T ss_pred             HhcCccEEECcCCCCCCch-hHhhCCCCCEEeCCCccccCccc-c-ccCcccccccccccccccccc-cccccccccccc
Confidence            4567888888888888765 37788888888888888888774 4 788888888888888888874 788888888888


Q ss_pred             CCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHHHHhccCCCCCeEEEeccCCCCC
Q 003387          599 GSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLSKSLCRLSCLESLKLANESKMPR  678 (824)
Q Consensus       599 ~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~~~l~~l~~L~~L~l~~~~~~~~  678 (824)
                      ++|.+.  .++.                      +..+++|+.+.++++.-.   . +..+..+++|+.+++++|    .
T Consensus       120 ~~~~~~--~~~~----------------------l~~l~~l~~l~~~~n~l~---~-~~~~~~l~~L~~l~l~~n----~  167 (210)
T d1h6ta2         120 EHNGIS--DING----------------------LVHLPQLESLYLGNNKIT---D-ITVLSRLTKLDTLSLEDN----Q  167 (210)
T ss_dssp             TTSCCC--CCGG----------------------GGGCTTCCEEECCSSCCC---C-CGGGGGCTTCSEEECCSS----C
T ss_pred             cccccc--cccc----------------------cccccccccccccccccc---c-cccccccccccccccccc----c
Confidence            877654  2222                      444555555555544211   1 112345566666666654    2


Q ss_pred             ccEEEeCccCcCCCceEEEEEcccCCCCCcccccCCCCCCeEEee
Q 003387          679 LSKIVLAEYLFPHSLTHLSFSNTDLMDDPMPTLEKLPLLQVLKLK  723 (824)
Q Consensus       679 L~~l~l~~~~~~~~L~~L~L~~~~l~~~~~~~l~~l~~L~~L~L~  723 (824)
                      +..  +..+..+++|+.|++++|.+.. + +.+.++++|++|+|+
T Consensus       168 l~~--i~~l~~l~~L~~L~Ls~N~i~~-l-~~l~~l~~L~~L~Ls  208 (210)
T d1h6ta2         168 ISD--IVPLAGLTKLQNLYLSKNHISD-L-RALAGLKNLDVLELF  208 (210)
T ss_dssp             CCC--CGGGTTCTTCCEEECCSSCCCB-C-GGGTTCTTCSEEEEE
T ss_pred             ccc--cccccCCCCCCEEECCCCCCCC-C-hhhcCCCCCCEEEcc
Confidence            332  2234567888888888888753 3 468889999999987

>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=99.42  E-value=4.1e-13  Score=130.16  Aligned_cols=81  Identities=19%  Similarity=0.209  Sum_probs=51.1

Q ss_pred             ccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecC
Q 003387          519 MFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNF  598 (824)
Q Consensus       519 ~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L  598 (824)
                      .++.|++|+++++.++.++ .+..+++|++|++++|.++.+++ + +++++|++|++++|.+..+|. +.++++|+.|++
T Consensus        38 ~l~~l~~L~l~~~~i~~l~-~l~~l~nL~~L~Ls~N~l~~~~~-l-~~l~~L~~L~l~~n~~~~~~~-l~~l~~L~~L~l  113 (199)
T d2omxa2          38 DLDQVTTLQADRLGIKSID-GVEYLNNLTQINFSNNQLTDITP-L-KNLTKLVDILMNNNQIADITP-LANLTNLTGLTL  113 (199)
T ss_dssp             HHTTCCEEECTTSCCCCCT-TGGGCTTCCEEECCSSCCCCCGG-G-TTCTTCCEEECCSSCCCCCGG-GTTCTTCSEEEC
T ss_pred             HhcCCCEEECCCCCCCCcc-ccccCCCcCcCccccccccCccc-c-cCCcccccccccccccccccc-cccccccccccc
Confidence            3556666777666666553 35666666666666666666654 4 666666666666666666653 566666666666


Q ss_pred             CCccC
Q 003387          599 GSITL  603 (824)
Q Consensus       599 ~~~~~  603 (824)
                      +++..
T Consensus       114 ~~~~~  118 (199)
T d2omxa2         114 FNNQI  118 (199)
T ss_dssp             CSSCC
T ss_pred             ccccc
Confidence            65544

>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=99.40  E-value=4.7e-14  Score=145.12  Aligned_cols=200  Identities=19%  Similarity=0.177  Sum_probs=133.1

Q ss_pred             ccCcccEEEeeCccCc--cCCccCCCCCcceEEeecCCCCC-ccChhhhhcCCCccEeecCCc-cccc--cchhhhcccc
Q 003387          519 MFKLLRVLDLGSLVLI--QYPSGIENLFLLRYLKLNIPSLN-SLPSSLLSNLLNLYTLDMPFS-YIDH--TADEFWKMNK  592 (824)
Q Consensus       519 ~~~~Lr~L~L~~~~i~--~lp~~i~~l~~Lr~L~L~~~~i~-~lp~~i~~~L~~L~~L~L~~~-~l~~--lp~~i~~L~~  592 (824)
                      ....|++||+++|.+.  .++..+.++++|++|+|++|.+. ..+..+ +++++|++|++++| .++.  +..-...+++
T Consensus        44 ~~~~L~~LdLs~~~i~~~~l~~l~~~c~~L~~L~L~~~~l~~~~~~~l-~~~~~L~~L~Ls~c~~itd~~l~~l~~~~~~  122 (284)
T d2astb2          44 SPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTL-AKNSNLVRLNLSGCSGFSEFALQTLLSSCSR  122 (284)
T ss_dssp             CCBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHH-TTCTTCSEEECTTCBSCCHHHHHHHHHHCTT
T ss_pred             cCCCCCEEECCCCccCHHHHHHHHHhCCCcccccccccCCCcHHHHHH-hcCCCCcCccccccccccccccchhhHHHHh
Confidence            3457888888888765  35555677888888888888776 444555 78888999998887 6653  3333567888


Q ss_pred             CceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhc-CCCCccceEEEecccc-cchhhHHHHhccCCCCCeEEE
Q 003387          593 LRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDIL-GRLPNLRNLRIRGDLS-YNQSLLSKSLCRLSCLESLKL  670 (824)
Q Consensus       593 L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l-~~l~~L~~L~l~~~~~-~~~~~l~~~l~~l~~L~~L~l  670 (824)
                      |++|++++|....                    ...+...+ ..+++|+.|+++++.. .....+.....++++|++|++
T Consensus       123 L~~L~ls~c~~~~--------------------~~~~~~~~~~~~~~L~~L~l~~~~~~i~~~~l~~l~~~~~~L~~L~L  182 (284)
T d2astb2         123 LDELNLSWCFDFT--------------------EKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDL  182 (284)
T ss_dssp             CCEEECCCCTTCC--------------------HHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEEC
T ss_pred             ccccccccccccc--------------------cccchhhhcccccccchhhhccccccccccccccccccccccccccc
Confidence            8999888764210                    11111112 2346788888887642 234455566677888999988


Q ss_pred             eccCCCCCccEEEeCccCcCCCceEEEEEcc-cCCCCCcccccCCCCCCeEEeeccccCCCeeeecCCCCCCcc
Q 003387          671 ANESKMPRLSKIVLAEYLFPHSLTHLSFSNT-DLMDDPMPTLEKLPLLQVLKLKQNSYSGRKLTCGSYGFPNLK  743 (824)
Q Consensus       671 ~~~~~~~~L~~l~l~~~~~~~~L~~L~L~~~-~l~~~~~~~l~~l~~L~~L~L~~~~~~~~~~~~~~~~~~~L~  743 (824)
                      +++   +.++.-.+.....+++|++|+|++| .++...+..++++|+|+.|++++| .....+......+|+|+
T Consensus       183 ~~~---~~itd~~~~~l~~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~L~l~~~-~~d~~l~~l~~~lp~L~  252 (284)
T d2astb2         183 SDS---VMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGI-VPDGTLQLLKEALPHLQ  252 (284)
T ss_dssp             TTC---TTCCGGGGGGGGGCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTS-SCTTCHHHHHHHSTTSE
T ss_pred             ccc---cCCCchhhhhhcccCcCCEEECCCCCCCChHHHHHHhcCCCCCEEeeeCC-CCHHHHHHHHHhCcccc
Confidence            753   2444444444567789999999997 455566677889999999999876 44433333334566665

>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=99.40  E-value=9.4e-13  Score=128.68  Aligned_cols=163  Identities=20%  Similarity=0.216  Sum_probs=112.2

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      ...++.|.+.++....     + ..+..+++|++|+|++|.++.++. ++.+++|++|++++|+++.+|. + +++++|+
T Consensus        45 L~~L~~L~l~~~~i~~-----l-~~l~~l~~L~~L~L~~n~i~~l~~-~~~l~~L~~L~l~~n~i~~l~~-l-~~l~~L~  115 (210)
T d1h6ta2          45 LNSIDQIIANNSDIKS-----V-QGIQYLPNVTKLFLNGNKLTDIKP-LANLKNLGWLFLDENKVKDLSS-L-KDLKKLK  115 (210)
T ss_dssp             HHTCCEEECTTSCCCC-----C-TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCGGG-G-TTCTTCC
T ss_pred             hcCccEEECcCCCCCC-----c-hhHhhCCCCCEEeCCCccccCccc-cccCcccccccccccccccccc-c-ccccccc
Confidence            4566777777665532     1 136778999999999999988774 7889999999999999998874 5 8899999


Q ss_pred             EeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCC-CcchhhhcCCCCccceEEEeccccc
Q 003387          572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHP-CCCTEDILGRLPNLRNLRIRGDLSY  650 (824)
Q Consensus       572 ~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~-~~~~~~~l~~l~~L~~L~l~~~~~~  650 (824)
                      .|++++|.+..++. +..+++|+.+++++|.+.  .++.++++++|+.++++.+ ...+.. +.++++|+.|+++++.  
T Consensus       116 ~L~l~~~~~~~~~~-l~~l~~l~~l~~~~n~l~--~~~~~~~l~~L~~l~l~~n~l~~i~~-l~~l~~L~~L~Ls~N~--  189 (210)
T d1h6ta2         116 SLSLEHNGISDING-LVHLPQLESLYLGNNKIT--DITVLSRLTKLDTLSLEDNQISDIVP-LAGLTKLQNLYLSKNH--  189 (210)
T ss_dssp             EEECTTSCCCCCGG-GGGCTTCCEEECCSSCCC--CCGGGGGCTTCSEEECCSSCCCCCGG-GTTCTTCCEEECCSSC--
T ss_pred             cccccccccccccc-cccccccccccccccccc--cccccccccccccccccccccccccc-ccCCCCCCEEECCCCC--
Confidence            99999998877764 888999999999888775  3334555566666665521 122233 5556666666666553  


Q ss_pred             chhhHHHHhccCCCCCeEEEe
Q 003387          651 NQSLLSKSLCRLSCLESLKLA  671 (824)
Q Consensus       651 ~~~~l~~~l~~l~~L~~L~l~  671 (824)
                       ...++ .+.++++|+.|+|+
T Consensus       190 -i~~l~-~l~~l~~L~~L~Ls  208 (210)
T d1h6ta2         190 -ISDLR-ALAGLKNLDVLELF  208 (210)
T ss_dssp             -CCBCG-GGTTCTTCSEEEEE
T ss_pred             -CCCCh-hhcCCCCCCEEEcc
Confidence             12222 34555555555554

>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=99.38  E-value=1.6e-12  Score=125.88  Aligned_cols=160  Identities=21%  Similarity=0.208  Sum_probs=119.3

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      .++++.|.+.++....     + ..+..+++|++|++++|.++.++. ++++++|++|++++|.+..++. + +++++|+
T Consensus        39 l~~l~~L~l~~~~i~~-----l-~~l~~l~nL~~L~Ls~N~l~~~~~-l~~l~~L~~L~l~~n~~~~~~~-l-~~l~~L~  109 (199)
T d2omxa2          39 LDQVTTLQADRLGIKS-----I-DGVEYLNNLTQINFSNNQLTDITP-LKNLTKLVDILMNNNQIADITP-L-ANLTNLT  109 (199)
T ss_dssp             HTTCCEEECTTSCCCC-----C-TTGGGCTTCCEEECCSSCCCCCGG-GTTCTTCCEEECCSSCCCCCGG-G-TTCTTCS
T ss_pred             hcCCCEEECCCCCCCC-----c-cccccCCCcCcCccccccccCccc-ccCCcccccccccccccccccc-c-ccccccc
Confidence            6678888888776642     1 236788999999999999988775 8899999999999999988875 5 8999999


Q ss_pred             EeecCCccccccchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCC-CcchhhhcCCCCccceEEEeccccc
Q 003387          572 TLDMPFSYIDHTADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHP-CCCTEDILGRLPNLRNLRIRGDLSY  650 (824)
Q Consensus       572 ~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~-~~~~~~~l~~l~~L~~L~l~~~~~~  650 (824)
                      .|++++|....++. +..+++|+.|++++|.+.  .++.+..+++|+.+++..+ -..+.. ++++++|+.|+++++.  
T Consensus       110 ~L~l~~~~~~~~~~-~~~l~~L~~L~l~~n~l~--~~~~l~~~~~L~~L~l~~n~l~~l~~-l~~l~~L~~L~ls~N~--  183 (199)
T d2omxa2         110 GLTLFNNQITDIDP-LKNLTNLNRLELSSNTIS--DISALSGLTSLQQLNFSSNQVTDLKP-LANLTTLERLDISSNK--  183 (199)
T ss_dssp             EEECCSSCCCCCGG-GTTCTTCSEEECCSSCCC--CCGGGTTCTTCSEEECCSSCCCCCGG-GTTCTTCCEEECCSSC--
T ss_pred             cccccccccccccc-cchhhhhHHhhhhhhhhc--ccccccccccccccccccccccCCcc-ccCCCCCCEEECCCCC--
Confidence            99999987777654 888999999999998875  4556777777777777632 223333 6777777777777763  


Q ss_pred             chhhHHHHhccCCCCCeE
Q 003387          651 NQSLLSKSLCRLSCLESL  668 (824)
Q Consensus       651 ~~~~l~~~l~~l~~L~~L  668 (824)
                       ...++ .+.++++|++|
T Consensus       184 -i~~i~-~l~~L~~L~~L  199 (199)
T d2omxa2         184 -VSDIS-VLAKLTNLESL  199 (199)
T ss_dssp             -CCCCG-GGGGCTTCSEE
T ss_pred             -CCCCc-cccCCCCCCcC
Confidence             12222 35566666654

>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=99.35  E-value=1.3e-12  Score=115.53  Aligned_cols=78  Identities=26%  Similarity=0.315  Sum_probs=68.4

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceecCCCccC
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLNFGSITL  603 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~L~~~~~  603 (824)
                      |+|+|++|.++.+|. ++++.+|++|++++|.+..+|+.+ +.+++|++|++++|.++.+|. +.++++|++|++++|.+
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~~N~i   77 (124)
T d1dcea3           1 RVLHLAHKDLTVLCH-LEQLLLVTHLDLSHNRLRALPPAL-AALRCLEVLQASDNALENVDG-VANLPRLQELLLCNNRL   77 (124)
T ss_dssp             SEEECTTSCCSSCCC-GGGGTTCCEEECCSSCCCCCCGGG-GGCTTCCEEECCSSCCCCCGG-GTTCSSCCEEECCSSCC
T ss_pred             CEEEcCCCCCCCCcc-cccCCCCCEEECCCCccCcchhhh-hhhhcccccccccccccccCc-cccccccCeEECCCCcc
Confidence            689999999988774 888999999999999999998887 889999999999998888875 88899999999998887


Q ss_pred             C
Q 003387          604 P  604 (824)
Q Consensus       604 ~  604 (824)
                      .
T Consensus        78 ~   78 (124)
T d1dcea3          78 Q   78 (124)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.33  E-value=1.1e-12  Score=131.40  Aligned_cols=74  Identities=15%  Similarity=0.186  Sum_probs=44.2

Q ss_pred             cEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccc-cch-hhhccccCceecCC
Q 003387          524 RVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDH-TAD-EFWKMNKLRHLNFG  599 (824)
Q Consensus       524 r~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~-lp~-~i~~L~~L~~L~L~  599 (824)
                      ++++.++..++.+|..+.  .++++|++++|.++.+|...|.++++|++|++++|.+.. +|. .+..++++++|.+.
T Consensus        11 ~~i~c~~~~l~~iP~~l~--~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~   86 (242)
T d1xwdc1          11 RVFLCQESKVTEIPSDLP--RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIE   86 (242)
T ss_dssp             SEEEEESCSCSSCCSCSC--SCCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEE
T ss_pred             CEEEEeCCCCCCcCCCCC--CCCCEEECcCCcCCccChhHhhccchhhhhhhccccccceeecccccccccccccccc
Confidence            566666666666665553  356666666666666666544666666666666664443 222 35556666666543

>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=99.27  E-value=3.2e-12  Score=118.83  Aligned_cols=86  Identities=16%  Similarity=0.018  Sum_probs=61.2

Q ss_pred             hcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCce
Q 003387          517 CGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRH  595 (824)
Q Consensus       517 ~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~  595 (824)
                      |.++..||.|+|++|.|+.+|..+..+.+|++|+|++|.+..++. + ..+++|++|++++|.+..+|.. +..+++|++
T Consensus        14 ~~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_          14 YTNAVRDRELDLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDG-F-PLLRRLKTLLVNNNRICRIGEGLDQALPDLTE   91 (162)
T ss_dssp             EECTTSCEEEECTTSCCCSCCCGGGGTTCCSEEECCSSCCCEECC-C-CCCSSCCEEECCSSCCCEECSCHHHHCTTCCE
T ss_pred             ccCcCcCcEEECCCCCCCccCccccccccCCEEECCCCCCCccCC-c-ccCcchhhhhcccccccCCCcccccccccccc
Confidence            345566777777777777776655667777777777777777743 4 7777777777777777777655 356777777


Q ss_pred             ecCCCccCC
Q 003387          596 LNFGSITLP  604 (824)
Q Consensus       596 L~L~~~~~~  604 (824)
                      |++++|.+.
T Consensus        92 L~L~~N~i~  100 (162)
T d1a9na_          92 LILTNNSLV  100 (162)
T ss_dssp             EECCSCCCC
T ss_pred             ceecccccc
Confidence            777777664

>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=99.25  E-value=2.5e-13  Score=149.74  Aligned_cols=109  Identities=15%  Similarity=0.029  Sum_probs=66.2

Q ss_pred             CCCceEEEEEcccCCCCCcccc----cCCCCCCeEEeeccccCCCe---eeecC-CCCCCccEEeeccCCCCcc-----c
Q 003387          690 PHSLTHLSFSNTDLMDDPMPTL----EKLPLLQVLKLKQNSYSGRK---LTCGS-YGFPNLKVLHLKSMLWLEE-----W  756 (824)
Q Consensus       690 ~~~L~~L~L~~~~l~~~~~~~l----~~l~~L~~L~L~~~~~~~~~---~~~~~-~~~~~L~~L~L~~~~~l~~-----l  756 (824)
                      ...|+.+.+++|.+.......+    ...++|++|+|++|.+.+..   +.... ...+.|++|+|++|. ++.     +
T Consensus       311 ~~~L~~l~l~~~~l~~~~~~~l~~~~~~~~~L~~L~Ls~N~i~~~g~~~l~~~l~~~~~~L~~L~Ls~n~-i~~~~~~~l  389 (460)
T d1z7xw1         311 GCQLESLWVKSCSFTAACCSHFSSVLAQNRFLLELQISNNRLEDAGVRELCQGLGQPGSVLRVLWLADCD-VSDSSCSSL  389 (460)
T ss_dssp             TCCCCEEECTTSCCBGGGHHHHHHHHHHCSSCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSC-CCHHHHHHH
T ss_pred             ccccccccccccchhhhhhhhcccccccccchhhhheeeecccCcccchhhhhhhcccCCCCEEECCCCC-CChHHHHHH
Confidence            3567888888877654433333    34568888888877765321   11112 245678888888885 442     2


Q ss_pred             eeccCcccCccEEEEecCCCCCC----Cccccc-cCccCcEEEecCCc
Q 003387          757 TMGNAAMPKLECLIINPCAYLKK----MPEQLW-YIKSLNKFDCWWPQ  799 (824)
Q Consensus       757 ~~~~~~lp~L~~L~l~~c~~l~~----lp~~l~-~l~~L~~L~l~~c~  799 (824)
                      ...+..+++|++|+|++|+.-..    +...+. +...|+.|.+.++.
T Consensus       390 ~~~l~~~~~L~~L~Ls~N~i~~~g~~~l~~~l~~~~~~L~~l~l~~~~  437 (460)
T d1z7xw1         390 AATLLANHSLRELDLSNNCLGDAGILQLVESVRQPGCLLEQLVLYDIY  437 (460)
T ss_dssp             HHHHHHCCCCCEEECCSSSCCHHHHHHHHHHHTSTTCCCCEEECTTCC
T ss_pred             HHHHhcCCCCCEEECCCCcCCHHHHHHHHHHHHhCCCccCEEECCCCC
Confidence            22344568888888888864221    222232 33468888888877

>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=99.24  E-value=8.6e-12  Score=124.76  Aligned_cols=99  Identities=17%  Similarity=0.188  Sum_probs=67.8

Q ss_pred             ceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchh-hhccccCceecCCCccCCCCCCC-CCCCCCCCCeeecc
Q 003387          546 LRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITLPAHPGK-FCGSLENLNFISAL  623 (824)
Q Consensus       546 Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~~~~~~p-~i~~L~~L~~l~~~  623 (824)
                      .+.++.++.+++.+|..+   ..++++|++++|.++.+|.. |.++++|++|++++|.+.....+ .+..++.+..+.+.
T Consensus        10 ~~~i~c~~~~l~~iP~~l---~~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~   86 (242)
T d1xwdc1          10 NRVFLCQESKVTEIPSDL---PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIE   86 (242)
T ss_dssp             SSEEEEESCSCSSCCSCS---CSCCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEE
T ss_pred             CCEEEEeCCCCCCcCCCC---CCCCCEEECcCCcCCccChhHhhccchhhhhhhccccccceeecccccccccccccccc
Confidence            468888998999999877   36899999999999999874 88999999999999987532112 44555555555443


Q ss_pred             C---CCcchhhhcCCCCccceEEEecc
Q 003387          624 H---PCCCTEDILGRLPNLRNLRIRGD  647 (824)
Q Consensus       624 ~---~~~~~~~~l~~l~~L~~L~l~~~  647 (824)
                      .   ........+..+++|+.|.+.++
T Consensus        87 ~~n~l~~~~~~~~~~l~~L~~l~l~~~  113 (242)
T d1xwdc1          87 KANNLLYINPEAFQNLPNLQYLLISNT  113 (242)
T ss_dssp             CCTTCCEECTTSEECCTTCCEEEEESC
T ss_pred             ccccccccccccccccccccccccchh
Confidence            1   11122222455555666655554

>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=99.21  E-value=8.6e-12  Score=115.83  Aligned_cols=107  Identities=14%  Similarity=0.077  Sum_probs=94.0

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCcc
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLY  571 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~  571 (824)
                      ..++|.|.+.++....     ++..+..+++|++|+|++|.++.++ .+..+++|++|++++|.+..+|+.++..+++|+
T Consensus        17 ~~~lr~L~L~~n~I~~-----i~~~~~~l~~L~~L~Ls~N~i~~l~-~~~~l~~L~~L~ls~N~i~~l~~~~~~~l~~L~   90 (162)
T d1a9na_          17 AVRDRELDLRGYKIPV-----IENLGATLDQFDAIDFSDNEIRKLD-GFPLLRRLKTLLVNNNRICRIGEGLDQALPDLT   90 (162)
T ss_dssp             TTSCEEEECTTSCCCS-----CCCGGGGTTCCSEEECCSSCCCEEC-CCCCCSSCCEEECCSSCCCEECSCHHHHCTTCC
T ss_pred             cCcCcEEECCCCCCCc-----cCccccccccCCEEECCCCCCCccC-CcccCcchhhhhcccccccCCCccccccccccc
Confidence            6689999999988753     2456678999999999999999885 588999999999999999999988768899999


Q ss_pred             EeecCCccccccch--hhhccccCceecCCCccCC
Q 003387          572 TLDMPFSYIDHTAD--EFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       572 ~L~L~~~~l~~lp~--~i~~L~~L~~L~L~~~~~~  604 (824)
                      +|++++|.+..+++  .+..+++|++|++++|.+.
T Consensus        91 ~L~L~~N~i~~~~~l~~l~~l~~L~~L~l~~N~i~  125 (162)
T d1a9na_          91 ELILTNNSLVELGDLDPLASLKSLTYLCILRNPVT  125 (162)
T ss_dssp             EEECCSCCCCCGGGGGGGGGCTTCCEEECCSSGGG
T ss_pred             cceeccccccccccccccccccccchhhcCCCccc
Confidence            99999999988874  5889999999999999875

>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=99.17  E-value=1.9e-11  Score=107.76  Aligned_cols=101  Identities=20%  Similarity=0.175  Sum_probs=88.0

Q ss_pred             eEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeec
Q 003387          496 HSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDM  575 (824)
Q Consensus       496 r~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L  575 (824)
                      |.|.+.++....     + ..+..++.|++|++++|.++.+|..++.+++|++|++++|.++.+|. + +++++|++|++
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   72 (124)
T d1dcea3           1 RVLHLAHKDLTV-----L-CHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDG-V-ANLPRLQELLL   72 (124)
T ss_dssp             SEEECTTSCCSS-----C-CCGGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCGG-G-TTCSSCCEEEC
T ss_pred             CEEEcCCCCCCC-----C-cccccCCCCCEEECCCCccCcchhhhhhhhcccccccccccccccCc-c-ccccccCeEEC
Confidence            566777776642     2 23788999999999999999999999999999999999999999975 6 99999999999


Q ss_pred             CCccccccc--hhhhccccCceecCCCccCC
Q 003387          576 PFSYIDHTA--DEFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       576 ~~~~l~~lp--~~i~~L~~L~~L~L~~~~~~  604 (824)
                      ++|.+..+|  ..++.+++|++|++++|.+.
T Consensus        73 ~~N~i~~~~~~~~l~~~~~L~~L~l~~N~i~  103 (124)
T d1dcea3          73 CNNRLQQSAAIQPLVSCPRLVLLNLQGNSLC  103 (124)
T ss_dssp             CSSCCCSSSTTGGGGGCTTCCEEECTTSGGG
T ss_pred             CCCccCCCCCchhhcCCCCCCEEECCCCcCC
Confidence            999999886  35889999999999999876

>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=99.06  E-value=8.2e-12  Score=137.27  Aligned_cols=303  Identities=17%  Similarity=0.112  Sum_probs=186.6

Q ss_pred             CceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCCcc-----Chh
Q 003387          493 SQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLNSL-----PSS  562 (824)
Q Consensus       493 ~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~~l-----p~~  562 (824)
                      .+|++|.+......   ...+...+..+++|++|+|++|.++     .++..+..+++|++|+|++|.++..     ...
T Consensus         2 ~~l~~ld~~~~~i~---~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~~~l~~~   78 (460)
T d1z7xw1           2 LDIQSLDIQCEELS---DARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQG   78 (460)
T ss_dssp             EEEEEEEEESCCCC---HHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHT
T ss_pred             CCCCEEEeeCCcCC---hHHHHHHHHhCCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcCCcCChHHHHHHHHH
Confidence            46889999887764   4455678889999999999999876     4556678899999999999998632     222


Q ss_pred             hhhcCCCccEeecCCccccc-----cchhhhccccCceecCCCccCCCCC---CC-CCCC--------------------
Q 003387          563 LLSNLLNLYTLDMPFSYIDH-----TADEFWKMNKLRHLNFGSITLPAHP---GK-FCGS--------------------  613 (824)
Q Consensus       563 i~~~L~~L~~L~L~~~~l~~-----lp~~i~~L~~L~~L~L~~~~~~~~~---~p-~i~~--------------------  613 (824)
                      +.....+|++|+|++|.++.     ++..+..+++|++|++++|.+....   ++ .+..                    
T Consensus        79 l~~~~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~~N~i~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~  158 (460)
T d1z7xw1          79 LQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQLEYCSLSAASC  158 (460)
T ss_dssp             TCSTTCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCBGGGH
T ss_pred             HhcCCCCCCEEECCCCCccccccccccchhhccccccccccccccchhhhhhhhhhcccccccccccccccccccchhhh
Confidence            21123579999999998764     4566788999999999998764210   00 0000                    


Q ss_pred             ---------CCCCCeeeccCCCcc------hhhhc-CCCCccceEEEeccccc--chhhHHHHhccCCCCCeEEEeccC-
Q 003387          614 ---------LENLNFISALHPCCC------TEDIL-GRLPNLRNLRIRGDLSY--NQSLLSKSLCRLSCLESLKLANES-  674 (824)
Q Consensus       614 ---------L~~L~~l~~~~~~~~------~~~~l-~~l~~L~~L~l~~~~~~--~~~~l~~~l~~l~~L~~L~l~~~~-  674 (824)
                               ...++.+.++.....      ....+ ..-.....+.+..+...  ........+...+.++.+.+..+. 
T Consensus       159 ~~~~~~l~~~~~~~~~~ls~~~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~~n~~  238 (460)
T d1z7xw1         159 EPLASVLRAKPDFKELTVSNNDINEAGVRVLCQGLKDSPCQLEALKLESCGVTSDNCRDLCGIVASKASLRELALGSNKL  238 (460)
T ss_dssp             HHHHHHHHHCTTCCEEECCSSBCHHHHHHHHHHHHHHSCCCCCEEECTTSCCBTTHHHHHHHHHHHCTTCCEEECCSSBC
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhcccccccccccccccchhhccc
Confidence                     111222222210000      00000 01112334444433211  112233445556677777776532 


Q ss_pred             --------------CCCCccEEEeCcc--------------CcCCCceEEEEEcccCCCCCcccc-----cCCCCCCeEE
Q 003387          675 --------------KMPRLSKIVLAEY--------------LFPHSLTHLSFSNTDLMDDPMPTL-----EKLPLLQVLK  721 (824)
Q Consensus       675 --------------~~~~L~~l~l~~~--------------~~~~~L~~L~L~~~~l~~~~~~~l-----~~l~~L~~L~  721 (824)
                                    ....++.+.+.++              ...+.++.+++++|.+.......+     ...+.|+.+.
T Consensus       239 ~~~~~~~~~~~~~~~~~~l~~l~l~~n~i~~~~~~~~~~~l~~~~~l~~l~l~~n~i~~~~~~~l~~~l~~~~~~L~~l~  318 (460)
T d1z7xw1         239 GDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGARLLCETLLEPGCQLESLW  318 (460)
T ss_dssp             HHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHHHHHHHHHHHTSTTCCCCEEE
T ss_pred             cccccchhhcccccccccccccccccccccccccccccccccccccccccccccccccccccchhhcccccccccccccc
Confidence                          3456777777664              345678888888776543222221     2346789999


Q ss_pred             eeccccCCCeee---ecCCCCCCccEEeeccCCCCcc-----ceecc-CcccCccEEEEecCCCCC----CCccccccCc
Q 003387          722 LKQNSYSGRKLT---CGSYGFPNLKVLHLKSMLWLEE-----WTMGN-AAMPKLECLIINPCAYLK----KMPEQLWYIK  788 (824)
Q Consensus       722 L~~~~~~~~~~~---~~~~~~~~L~~L~L~~~~~l~~-----l~~~~-~~lp~L~~L~l~~c~~l~----~lp~~l~~l~  788 (824)
                      +++|.+......   ......++|++|+|++|. +..     ++..+ ...+.|+.|++++|....    .++..+..++
T Consensus       319 l~~~~l~~~~~~~l~~~~~~~~~L~~L~Ls~N~-i~~~g~~~l~~~l~~~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~  397 (460)
T d1z7xw1         319 VKSCSFTAACCSHFSSVLAQNRFLLELQISNNR-LEDAGVRELCQGLGQPGSVLRVLWLADCDVSDSSCSSLAATLLANH  397 (460)
T ss_dssp             CTTSCCBGGGHHHHHHHHHHCSSCCEEECCSSB-CHHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCC
T ss_pred             ccccchhhhhhhhcccccccccchhhhheeeec-ccCcccchhhhhhhcccCCCCEEECCCCCCChHHHHHHHHHHhcCC
Confidence            988776543211   122346789999999886 432     22222 246789999999997432    2455677889


Q ss_pred             cCcEEEecCCc
Q 003387          789 SLNKFDCWWPQ  799 (824)
Q Consensus       789 ~L~~L~l~~c~  799 (824)
                      +|++|++++++
T Consensus       398 ~L~~L~Ls~N~  408 (460)
T d1z7xw1         398 SLRELDLSNNC  408 (460)
T ss_dssp             CCCEEECCSSS
T ss_pred             CCCEEECCCCc
Confidence            99999999997

>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=99.06  E-value=1.2e-10  Score=111.57  Aligned_cols=114  Identities=22%  Similarity=0.232  Sum_probs=56.9

Q ss_pred             cccccCCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCccC-CccCCCCCcceEEeecCCCCCccChhhhh
Q 003387          487 CLDDYDSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQY-PSGIENLFLLRYLKLNIPSLNSLPSSLLS  565 (824)
Q Consensus       487 ~~~~~~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~l-p~~i~~l~~Lr~L~L~~~~i~~lp~~i~~  565 (824)
                      +|..+.++++.|.+.++...   .......|..+++|+.|+|++|.+..+ +..+..+++|++|+|++|++..+|+..|.
T Consensus        23 iP~~lp~~l~~L~Ls~N~i~---~~~~~~~f~~l~~L~~L~L~~N~i~~~~~~~~~~~~~L~~L~Ls~N~l~~l~~~~F~   99 (192)
T d1w8aa_          23 IPRDIPLHTTELLLNDNELG---RISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNKMFL   99 (192)
T ss_dssp             CCSCCCTTCSEEECCSCCCC---SBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSCCCCEECSSSST
T ss_pred             cCCCCCCCCCEEEeCCCCCc---ccccccccCCCceEeeeeccccccccccccccccccccceeeeccccccccCHHHHh
Confidence            34333445555555555442   112234445555555555555555432 23344455555555555555555554445


Q ss_pred             cCCCccEeecCCccccccchh-hhccccCceecCCCccC
Q 003387          566 NLLNLYTLDMPFSYIDHTADE-FWKMNKLRHLNFGSITL  603 (824)
Q Consensus       566 ~L~~L~~L~L~~~~l~~lp~~-i~~L~~L~~L~L~~~~~  603 (824)
                      ++++|++|+|++|.++.+|.. |..+++|++|+|++|.+
T Consensus       100 ~l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~~N~~  138 (192)
T d1w8aa_         100 GLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPF  138 (192)
T ss_dssp             TCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCB
T ss_pred             CCCcccccccCCccccccCHHHhcCCccccccccccccc
Confidence            555555555555555555433 44555555555555543

>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=99.06  E-value=1.2e-11  Score=119.08  Aligned_cols=112  Identities=17%  Similarity=0.174  Sum_probs=86.8

Q ss_pred             hHhhhcccCcccEEEeeCccCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhcccc
Q 003387          513 WEKFCGMFKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNK  592 (824)
Q Consensus       513 ~~~~~~~~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~  592 (824)
                      ++..+..+++|++|+|++|.|+.++ .+..+++|++|+|++|.++.+|... ..+++|++|++++|.++.++. +..+++
T Consensus        40 l~~sl~~L~~L~~L~Ls~n~I~~i~-~l~~l~~L~~L~Ls~N~i~~i~~~~-~~~~~L~~L~l~~N~i~~l~~-~~~l~~  116 (198)
T d1m9la_          40 MDATLSTLKACKHLALSTNNIEKIS-SLSGMENLRILSLGRNLIKKIENLD-AVADTLEELWISYNQIASLSG-IEKLVN  116 (198)
T ss_dssp             CHHHHHHTTTCCEEECSEEEESCCC-CHHHHTTCCEEECCEEEECSCSSHH-HHHHHCCEEECSEEECCCHHH-HHHHHH
T ss_pred             hhhHHhcccccceeECcccCCCCcc-cccCCccccChhhcccccccccccc-ccccccccccccccccccccc-cccccc
Confidence            4467788889999999998888876 4788889999999998888888655 667789999998888888754 788889


Q ss_pred             CceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccc
Q 003387          593 LRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       593 L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      |++|++++|.+..                    ...+.. +..+++|+.|+++++.
T Consensus       117 L~~L~L~~N~i~~--------------------~~~~~~-l~~l~~L~~L~L~~N~  151 (198)
T d1m9la_         117 LRVLYMSNNKITN--------------------WGEIDK-LAALDKLEDLLLAGNP  151 (198)
T ss_dssp             SSEEEESEEECCC--------------------HHHHHH-HTTTTTCSEEEECSSH
T ss_pred             ccccccccchhcc--------------------cccccc-ccCCCccceeecCCCc
Confidence            9999888887752                    111223 6777788888887763

>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=98.97  E-value=6.9e-10  Score=106.18  Aligned_cols=121  Identities=17%  Similarity=0.247  Sum_probs=52.9

Q ss_pred             EEEeeCccCccCCccCCCCCcceEEeecCCCCCc-cChhhhhcCCCccEeecCCccccccc-hhhhccccCceecCCCcc
Q 003387          525 VLDLGSLVLIQYPSGIENLFLLRYLKLNIPSLNS-LPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       525 ~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~~i~~-lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~L~~~~  602 (824)
                      +++.+++.++.+|..+.  .++++|+|++|.|+. ++...|.++++|+.|+|++|.+..++ ..+..+++|++|++++|.
T Consensus        12 ~v~Cs~~~L~~iP~~lp--~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~~~~~~~~~~~L~~L~Ls~N~   89 (192)
T d1w8aa_          12 TVDCTGRGLKEIPRDIP--LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENK   89 (192)
T ss_dssp             EEECTTSCCSSCCSCCC--TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSCC
T ss_pred             EEEEeCCCcCccCCCCC--CCCCEEEeCCCCCcccccccccCCCceEeeeeccccccccccccccccccccceeeecccc
Confidence            44444444555554442  345555555555542 33333344555555555555444443 224445555555555554


Q ss_pred             CCCCCCC-CCCCCCCCCeeeccCC--CcchhhhcCCCCccceEEEeccc
Q 003387          603 LPAHPGK-FCGSLENLNFISALHP--CCCTEDILGRLPNLRNLRIRGDL  648 (824)
Q Consensus       603 ~~~~~~p-~i~~L~~L~~l~~~~~--~~~~~~~l~~l~~L~~L~l~~~~  648 (824)
                      +.. ..| .+.++++|+.|+++.+  ....+..+..+++|++|+++++.
T Consensus        90 l~~-l~~~~F~~l~~L~~L~L~~N~l~~i~~~~f~~l~~L~~l~L~~N~  137 (192)
T d1w8aa_          90 IKE-ISNKMFLGLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNP  137 (192)
T ss_dssp             CCE-ECSSSSTTCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCC
T ss_pred             ccc-cCHHHHhCCCcccccccCCccccccCHHHhcCCcccccccccccc
Confidence            431 111 2333333333333311  11112224556666666665553

>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=98.93  E-value=3.4e-10  Score=119.34  Aligned_cols=252  Identities=15%  Similarity=0.110  Sum_probs=157.3

Q ss_pred             hhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCCcc-----------ChhhhhcCCCccEeecCCc
Q 003387          515 KFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLNSL-----------PSSLLSNLLNLYTLDMPFS  578 (824)
Q Consensus       515 ~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~~l-----------p~~i~~~L~~L~~L~L~~~  578 (824)
                      ..+..+..|+.|+|++|.+.     .+...+...++|+.|+++++.....           ...+ ..+++|+.|+|++|
T Consensus        25 ~~L~~~~~l~~L~Ls~n~i~~~~~~~l~~~l~~~~~L~~l~l~~~~~~~~~~~~~~~~~~l~~~l-~~~~~L~~L~L~~n  103 (344)
T d2ca6a1          25 AVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQAL-LKCPKLHTVRLSDN  103 (344)
T ss_dssp             HHHHHCSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHH-TTCTTCCEEECCSC
T ss_pred             HHHhhCCCCCEEECcCCcCCHHHHHHHHHHHHhCCCCCEEECCCCcccccccccchHHHHHHHHH-hhCCCccccccccc
Confidence            45667888999999998764     4455677788999999987654422           2223 56788999999988


Q ss_pred             cccc-----cchhhhccccCceecCCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEeccc--ccc
Q 003387          579 YIDH-----TADEFWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDL--SYN  651 (824)
Q Consensus       579 ~l~~-----lp~~i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~--~~~  651 (824)
                      .+..     +...+..+++|++|++++|.+.......++.  .|..+       .........+.|+.|.++++.  ...
T Consensus       104 ~i~~~~~~~l~~~l~~~~~L~~L~l~~n~l~~~~~~~l~~--~l~~~-------~~~~~~~~~~~L~~l~l~~n~i~~~~  174 (344)
T d2ca6a1         104 AFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIAR--ALQEL-------AVNKKAKNAPPLRSIICGRNRLENGS  174 (344)
T ss_dssp             CCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHH--HHHHH-------HHHHHHHTCCCCCEEECCSSCCTGGG
T ss_pred             ccccccccchhhhhcccccchheecccccccccccccccc--ccccc-------ccccccccCcccceeecccccccccc
Confidence            6654     4455667889999988887653100000000  00000       000012345678888887764  122


Q ss_pred             hhhHHHHhccCCCCCeEEEeccC-CCCCccEEEeCccCcCCCceEEEEEcccCCCC----CcccccCCCCCCeEEeeccc
Q 003387          652 QSLLSKSLCRLSCLESLKLANES-KMPRLSKIVLAEYLFPHSLTHLSFSNTDLMDD----PMPTLEKLPLLQVLKLKQNS  726 (824)
Q Consensus       652 ~~~l~~~l~~l~~L~~L~l~~~~-~~~~L~~l~l~~~~~~~~L~~L~L~~~~l~~~----~~~~l~~l~~L~~L~L~~~~  726 (824)
                      ...+...+..+++|+.|+++.|. ...............+++|+.|+|++|.+...    ....+..+++|++|+|++|.
T Consensus       175 ~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~i~~~g~~~L~~~l~~~~~L~~L~Ls~n~  254 (344)
T d2ca6a1         175 MKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCL  254 (344)
T ss_dssp             HHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHHHGGGCTTCCEEECTTCC
T ss_pred             cccccchhhhhhhhcccccccccccccccccchhhhhcchhhhcccccccccccccccccccccccccccchhhhhhcCc
Confidence            34566677778889999887652 00001111112235678899999998876432    23456788999999999888


Q ss_pred             cCCCeeee---c--CCCCCCccEEeeccCCCCcc-----ceecc-CcccCccEEEEecCCCC
Q 003387          727 YSGRKLTC---G--SYGFPNLKVLHLKSMLWLEE-----WTMGN-AAMPKLECLIINPCAYL  777 (824)
Q Consensus       727 ~~~~~~~~---~--~~~~~~L~~L~L~~~~~l~~-----l~~~~-~~lp~L~~L~l~~c~~l  777 (824)
                      +.+.....   .  ...+++|++|+|++|. +..     +...+ ..+++|+.|++++|..-
T Consensus       255 i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~-i~~~~~~~l~~~l~~~~~~L~~L~l~~N~~~  315 (344)
T d2ca6a1         255 LSARGAAAVVDAFSKLENIGLQTLRLQYNE-IELDAVRTLKTVIDEKMPDLLFLELNGNRFS  315 (344)
T ss_dssp             CCHHHHHHHHHHHHTCSSCCCCEEECCSSC-CBHHHHHHHHHHHHHHCTTCCEEECTTSBSC
T ss_pred             cCchhhHHHHHHhhhccCCCCCEEECCCCc-CChHHHHHHHHHHHccCCCCCEEECCCCcCC
Confidence            75432111   1  1346789999999986 432     22222 25789999999998753

>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=98.84  E-value=2.2e-10  Score=110.02  Aligned_cols=125  Identities=20%  Similarity=0.214  Sum_probs=95.7

Q ss_pred             cCcccEEEeeCc--cCccCCccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccCceec
Q 003387          520 FKLLRVLDLGSL--VLIQYPSGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKLRHLN  597 (824)
Q Consensus       520 ~~~Lr~L~L~~~--~i~~lp~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L~~L~  597 (824)
                      ...++.+++++.  .++.+|.++..+++|++|+|++|.|+.++. + .+|++|++|+|++|.++.+|.....+++|++|+
T Consensus        22 ~~~~~~~~l~~~~~~i~~l~~sl~~L~~L~~L~Ls~n~I~~i~~-l-~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~   99 (198)
T d1m9la_          22 ATEAEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKISS-L-SGMENLRILSLGRNLIKKIENLDAVADTLEELW   99 (198)
T ss_dssp             CTTCSCEECCBCCTTCCCCHHHHHHTTTCCEEECSEEEESCCCC-H-HHHTTCCEEECCEEEECSCSSHHHHHHHCCEEE
T ss_pred             ccccceeeeecccCchhhhhhHHhcccccceeECcccCCCCccc-c-cCCccccChhhcccccccccccccccccccccc
Confidence            334566677665  366788889999999999999999998864 5 899999999999999998887666778899999


Q ss_pred             CCCccCCCCCCCCCCCCCCCCeeeccCCCcchhhhcCCCCccceEEEecccccchhhHH--HHhccCCCCCeEEEecc
Q 003387          598 FGSITLPAHPGKFCGSLENLNFISALHPCCCTEDILGRLPNLRNLRIRGDLSYNQSLLS--KSLCRLSCLESLKLANE  673 (824)
Q Consensus       598 L~~~~~~~~~~p~i~~L~~L~~l~~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~~~l~--~~l~~l~~L~~L~l~~~  673 (824)
                      +++|.+..                       +.. +..+++|+.|+++++.   ...++  ..+..+++|+.|++++|
T Consensus       100 l~~N~i~~-----------------------l~~-~~~l~~L~~L~L~~N~---i~~~~~~~~l~~l~~L~~L~L~~N  150 (198)
T d1m9la_         100 ISYNQIAS-----------------------LSG-IEKLVNLRVLYMSNNK---ITNWGEIDKLAALDKLEDLLLAGN  150 (198)
T ss_dssp             CSEEECCC-----------------------HHH-HHHHHHSSEEEESEEE---CCCHHHHHHHTTTTTCSEEEECSS
T ss_pred             cccccccc-----------------------ccc-ccccccccccccccch---hccccccccccCCCccceeecCCC
Confidence            99887641                       223 6678889999998874   22222  45677788888887765

>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=98.74  E-value=3.7e-09  Score=111.18  Aligned_cols=237  Identities=14%  Similarity=0.067  Sum_probs=134.5

Q ss_pred             CCceeEeeccCCCCCCCCcchhHhhhcccCcccEEEeeCccCcc-----------CCccCCCCCcceEEeecCCCCCc--
Q 003387          492 DSQLHSLLCCSPETRHLDPIDWEKFCGMFKLLRVLDLGSLVLIQ-----------YPSGIENLFLLRYLKLNIPSLNS--  558 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~~~~~~~~~~~~Lr~L~L~~~~i~~-----------lp~~i~~l~~Lr~L~L~~~~i~~--  558 (824)
                      ...++.|.+.++.........+...+...+.|+.|+++++....           +...+..+++|+.|+|++|.+..  
T Consensus        30 ~~~l~~L~Ls~n~i~~~~~~~l~~~l~~~~~L~~l~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~  109 (344)
T d2ca6a1          30 DDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTA  109 (344)
T ss_dssp             CSCCCEEECTTSEECHHHHHHHHHTTTTCTTCCEEECCSCCTTSCGGGSHHHHHHHHHHHTTCTTCCEEECCSCCCCTTT
T ss_pred             CCCCCEEECcCCcCCHHHHHHHHHHHHhCCCCCEEECCCCcccccccccchHHHHHHHHHhhCCCccccccccccccccc
Confidence            77888888887754311112345667788999999998875431           23445677899999999988764  


Q ss_pred             ---cChhhhhcCCCccEeecCCcccccc-----chh---------hhccccCceecCCCccCCCCCCCCCCCCCCCCeee
Q 003387          559 ---LPSSLLSNLLNLYTLDMPFSYIDHT-----ADE---------FWKMNKLRHLNFGSITLPAHPGKFCGSLENLNFIS  621 (824)
Q Consensus       559 ---lp~~i~~~L~~L~~L~L~~~~l~~l-----p~~---------i~~L~~L~~L~L~~~~~~~~~~p~i~~L~~L~~l~  621 (824)
                         +...+ ..+++|+.|++++|.+..-     ...         ....+.|+.|++++|.+....              
T Consensus       110 ~~~l~~~l-~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~~~~~~~~~~L~~l~l~~n~i~~~~--------------  174 (344)
T d2ca6a1         110 QEPLIDFL-SKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGS--------------  174 (344)
T ss_dssp             HHHHHHHH-HHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSSCCTGGG--------------
T ss_pred             ccchhhhh-cccccchheecccccccccccccccccccccccccccccCcccceeecccccccccc--------------
Confidence               44444 6789999999999865421     111         134567888888777654210              


Q ss_pred             ccCCCcchhhhcCCCCccceEEEecccccch---hhHHHHhccCCCCCeEEEeccCCCCCccEEE----eCccCcCCCce
Q 003387          622 ALHPCCCTEDILGRLPNLRNLRIRGDLSYNQ---SLLSKSLCRLSCLESLKLANESKMPRLSKIV----LAEYLFPHSLT  694 (824)
Q Consensus       622 ~~~~~~~~~~~l~~l~~L~~L~l~~~~~~~~---~~l~~~l~~l~~L~~L~l~~~~~~~~L~~l~----l~~~~~~~~L~  694 (824)
                          ...+...+..+++|+.|+++.+.-...   ..+...+..+++|+.|++++|.    +....    ...+..+++|+
T Consensus       175 ----~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~----i~~~g~~~L~~~l~~~~~L~  246 (344)
T d2ca6a1         175 ----MKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNT----FTHLGSSALAIALKSWPNLR  246 (344)
T ss_dssp             ----HHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSC----CHHHHHHHHHHHGGGCTTCC
T ss_pred             ----cccccchhhhhhhhcccccccccccccccccchhhhhcchhhhccccccccc----ccccccccccccccccccch
Confidence                011122244555666666666541111   1123334555666666666542    11000    01113456677


Q ss_pred             EEEEEcccCCCCCcccc----c--CCCCCCeEEeeccccCCCee---eecC-CCCCCccEEeeccCC
Q 003387          695 HLSFSNTDLMDDPMPTL----E--KLPLLQVLKLKQNSYSGRKL---TCGS-YGFPNLKVLHLKSML  751 (824)
Q Consensus       695 ~L~L~~~~l~~~~~~~l----~--~l~~L~~L~L~~~~~~~~~~---~~~~-~~~~~L~~L~L~~~~  751 (824)
                      +|+|++|.+.......+    .  ..+.|++|++++|.+....+   .... ..+++|++|+|++|.
T Consensus       247 ~L~Ls~n~i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~i~~~~~~~l~~~l~~~~~~L~~L~l~~N~  313 (344)
T d2ca6a1         247 ELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNR  313 (344)
T ss_dssp             EEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSCCBHHHHHHHHHHHHHHCTTCCEEECTTSB
T ss_pred             hhhhhcCccCchhhHHHHHHhhhccCCCCCEEECCCCcCChHHHHHHHHHHHccCCCCCEEECCCCc
Confidence            77777776544322222    2  23567777777776543211   1111 245677777777765

>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=98.69  E-value=1.7e-08  Score=92.29  Aligned_cols=88  Identities=16%  Similarity=0.086  Sum_probs=54.3

Q ss_pred             hhcccCcccEEEeeCcc-CccCCc-cCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccchhhhccccC
Q 003387          516 FCGMFKLLRVLDLGSLV-LIQYPS-GIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTADEFWKMNKL  593 (824)
Q Consensus       516 ~~~~~~~Lr~L~L~~~~-i~~lp~-~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp~~i~~L~~L  593 (824)
                      .+..+++|+.|+++++. ++.++. .|..+++|++|+|++|+++.+++..|..+++|++|+|++|.++.+|..+....+|
T Consensus        26 ~l~~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          26 HLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSL  105 (156)
T ss_dssp             TSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCCSTTTCSCCC
T ss_pred             cccCccccCeeecCCCccccccCchhhccccccCcceeeccccCCcccccccccccccceeccCCCCcccChhhhccccc
Confidence            34555666666665543 665543 3566666666666666666665554466666666666666666666655444566


Q ss_pred             ceecCCCccC
Q 003387          594 RHLNFGSITL  603 (824)
Q Consensus       594 ~~L~L~~~~~  603 (824)
                      ++|+|++|.+
T Consensus       106 ~~L~L~~Np~  115 (156)
T d2ifga3         106 QELVLSGNPL  115 (156)
T ss_dssp             CEEECCSSCC
T ss_pred             cccccCCCcc
Confidence            6666666654

>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=98.61  E-value=6.2e-08  Score=88.52  Aligned_cols=85  Identities=20%  Similarity=0.044  Sum_probs=74.7

Q ss_pred             cCcccEEEeeCccCccCCccCCCCCcceEEeecCC-CCCccChhhhhcCCCccEeecCCccccccc-hhhhccccCceec
Q 003387          520 FKLLRVLDLGSLVLIQYPSGIENLFLLRYLKLNIP-SLNSLPSSLLSNLLNLYTLDMPFSYIDHTA-DEFWKMNKLRHLN  597 (824)
Q Consensus       520 ~~~Lr~L~L~~~~i~~lp~~i~~l~~Lr~L~L~~~-~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp-~~i~~L~~L~~L~  597 (824)
                      +....+++.+++.+...|..+..+++|++|+++++ .++.++...|.++++|+.|++++|.++.++ ..|..+++|++|+
T Consensus         7 c~~~~~l~c~~~~~~~~p~~l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~   86 (156)
T d2ifga3           7 PHGSSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLN   86 (156)
T ss_dssp             CSSSSCEECCSSCCCTTTTTSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEE
T ss_pred             cCCCCeEEecCCCCccCcccccCccccCeeecCCCccccccCchhhccccccCcceeeccccCCccccccccccccccee
Confidence            33456788888888889999999999999999876 599998876699999999999999999995 4589999999999


Q ss_pred             CCCccCC
Q 003387          598 FGSITLP  604 (824)
Q Consensus       598 L~~~~~~  604 (824)
                      |++|.+.
T Consensus        87 Ls~N~l~   93 (156)
T d2ifga3          87 LSFNALE   93 (156)
T ss_dssp             CCSSCCS
T ss_pred             ccCCCCc
Confidence            9999986

>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=98.50  E-value=1.6e-07  Score=94.93  Aligned_cols=42  Identities=17%  Similarity=0.218  Sum_probs=36.1

Q ss_pred             CCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          154 KSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+.+|||++++++|.+.    .  .++|.|+|++|+|||||++++.+
T Consensus        10 ~~~~f~GR~~el~~l~~~----~--~~~i~i~G~~G~GKTsLl~~~~~   51 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKGL----R--APITLVLGLRRTGKSSIIKIGIN   51 (283)
T ss_dssp             SGGGSCCCHHHHHHHHHT----C--SSEEEEEESTTSSHHHHHHHHHH
T ss_pred             ChhhCCChHHHHHHHHhc----c--CCEEEEEcCCCCcHHHHHHHHHH
Confidence            457899999999998763    2  46889999999999999999987

>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=98.32  E-value=2e-06  Score=86.21  Aligned_cols=115  Identities=15%  Similarity=0.095  Sum_probs=83.7

Q ss_pred             CCCceechhhHHHHHHHHHc----CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCc-eeEEEECCCCCCCCHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIE----GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD-CHAWITEPYSNEYDADQIL  229 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~-~~~wv~~~vs~~~~~~~~~  229 (824)
                      +..++||+.++++|.++|..    .......+.|+|++|+||||+|+.+.+  .....+. ..+|+.  ...........
T Consensus        15 p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~--~l~~~~~~~~~~~~--~~~~~~~~~~~   90 (276)
T d1fnna2          15 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWE--LYKDKTTARFVYIN--GFIYRNFTAII   90 (276)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHH--HHTTSCCCEEEEEE--TTTCCSHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHH--HHhcccCCcEEEec--chhhhhhhhhh
Confidence            34689999999999999864    234567899999999999999999998  5544443 355776  77777888888


Q ss_pred             HHHHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCCh
Q 003387          230 DIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWSI  276 (824)
Q Consensus       230 ~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~~  276 (824)
                      ..+....+....   ............+.+.+.  .....+++|+++..
T Consensus        91 ~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~  136 (276)
T d1fnna2          91 GEIARSLNIPFP---RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL  136 (276)
T ss_dssp             HHHHHHTTCCCC---SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS
T ss_pred             hhhHHhhhhhhh---hhccchhHHHHHHHHHHhhcccccccchhHHHHh
Confidence            999888876543   233344555555555553  36777888888764

>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=97.93  E-value=2.5e-05  Score=76.57  Aligned_cols=129  Identities=17%  Similarity=0.189  Sum_probs=81.0

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC---ccccC-CCceeEEEECCCCCCCCHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS---SYVKH-YFDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~---~~~~~-~F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      +.++||++++++++..|....  -.-+.+||.+|||||+++..+...   .++.. .....+|.-+ .+.          
T Consensus        18 d~~igRd~Ei~~l~~iL~r~~--k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~-~~~----------   84 (268)
T d1r6bx2          18 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLD-IGS----------   84 (268)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECC-CC-----------
T ss_pred             CcccChHHHHHHHHHHHhcCc--cCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEee-ech----------
Confidence            468999999999999998665  234559999999999998777662   11222 2345666530 111          


Q ss_pred             HHHHhCCCCCcccccccCHHHHHHHHHHhc-CCCeEEEEEecCCCh----------hhHHHHHhhCCCCCCCcEEEEEec
Q 003387          232 VIKFLMPSSRLSEIMDKNYEMKKIILHEYL-MTKRYLIVIDDVWSI----------DMWDVIQEILPDNQNGSRVLITLT  300 (824)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L-~~kr~LlVlDdv~~~----------~~~~~l~~~~~~~~~gs~ilvTtR  300 (824)
                         -+.+..     ...+.++....+.+.+ +.+..++++||+...          .+...+..|.-..+ .=++|.||.
T Consensus        85 ---liag~~-----~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg-~i~vIgatT  155 (268)
T d1r6bx2          85 ---LLAGTK-----YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSG-KIRVIGSTT  155 (268)
T ss_dssp             -----CCCC-----CSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSC-CCEEEEEEC
T ss_pred             ---HhccCc-----cchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCC-CCeEEEeCC
Confidence               111111     1234566666566666 457799999998643          24455555444333 457888888


Q ss_pred             hHHHHh
Q 003387          301 DIRIII  306 (824)
Q Consensus       301 ~~~v~~  306 (824)
                      .++...
T Consensus       156 ~eey~~  161 (268)
T d1r6bx2         156 YQEFSN  161 (268)
T ss_dssp             HHHHHC
T ss_pred             HHHHHH
Confidence            887776

>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=97.90  E-value=1.2e-05  Score=80.89  Aligned_cols=115  Identities=15%  Similarity=0.141  Sum_probs=79.6

Q ss_pred             CCCCceechhhHHHHHHHHHc----CC---CCeEEEEEEcCCCChHHHHHHHHhCCccccC------CCceeEEEECCCC
Q 003387          154 KSRDTVGLDDRMEELLDLLIE----GP---PQLSVVAILDSIGLDKTAFAGEAYNSSYVKH------YFDCHAWITEPYS  220 (824)
Q Consensus       154 ~~~~~vGr~~~~~~l~~~L~~----~~---~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~------~F~~~~wv~~~vs  220 (824)
                      .++.++||+.++++|.+++..    +.   +...++.|+|++|+||||+|+.+.+.  +..      .....+++.  ..
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~--l~~~~~~~~~~~~~~~~~--~~   89 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKR--VSEAAAKEGLTVKQAYVN--AF   89 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHH--HHHHHHHTTCCEEEEEEE--GG
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHH--HHhhcccccCCceeeeec--cc
Confidence            356889999999999987742    22   22345677899999999999999983  321      123455666  77


Q ss_pred             CCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcC--CCeEEEEEecCCC
Q 003387          221 NEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLM--TKRYLIVIDDVWS  275 (824)
Q Consensus       221 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~--~kr~LlVlDdv~~  275 (824)
                      ...........+...+.....   ............+.+..+  +...++++|.+..
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~  143 (287)
T d1w5sa2          90 NAPNLYTILSLIVRQTGYPIQ---VRGAPALDILKALVDNLYVENHYLLVILDEFQS  143 (287)
T ss_dssp             GCCSHHHHHHHHHHHHTCCCC---CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHH
T ss_pred             cccchhhHHHHHhhhcccccc---cccchHHHHHHHHHHHHHhccCccccceeEEEE
Confidence            777888888888888876443   233445556666666553  4677888887753

>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=97.81  E-value=1.5e-05  Score=73.63  Aligned_cols=129  Identities=11%  Similarity=0.065  Sum_probs=75.9

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC---ccc-cCCCceeEEEECCCCCCCCHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS---SYV-KHYFDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~---~~~-~~~F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      +.++||+++++++++.|....  -.-+.+||.+|||||+++..+...   .++ ...-+.++|.-       |...++  
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~--k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~l-------d~~~Li--   90 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL-------DMGALV--   90 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEE-------CHHHHH--
T ss_pred             CCCcCcHHHHHHHHHHHhccC--CCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEe-------eHHHHh--
Confidence            468899999999999998755  234579999999999998777652   122 22335667665       332222  


Q ss_pred             HHHHhCCCCCcccccccCHHHHHHHHHHhc-C-CCeEEEEEecCCChh---------hHHHHHhhCCCCCCCcEEEEEec
Q 003387          232 VIKFLMPSSRLSEIMDKNYEMKKIILHEYL-M-TKRYLIVIDDVWSID---------MWDVIQEILPDNQNGSRVLITLT  300 (824)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L-~-~kr~LlVlDdv~~~~---------~~~~l~~~~~~~~~gs~ilvTtR  300 (824)
                           .+..     ...+.++....+.+.+ + ..+..|++||+...-         +...+..|.-..+ .=++|.||.
T Consensus        91 -----Ag~~-----~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~rg-~l~~IgatT  159 (195)
T d1jbka_          91 -----AGAK-----YRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARG-ELHCVGATT  159 (195)
T ss_dssp             -----TTTC-----SHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHHTT-SCCEEEEEC
T ss_pred             -----ccCC-----ccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHhCC-CceEEecCC
Confidence                 1111     1112344444444443 3 458999999996431         2223333322222 346777777


Q ss_pred             hHHHHh
Q 003387          301 DIRIII  306 (824)
Q Consensus       301 ~~~v~~  306 (824)
                      .++...
T Consensus       160 ~eey~~  165 (195)
T d1jbka_         160 LDEYRQ  165 (195)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766555

>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=97.79  E-value=1.2e-05  Score=77.93  Aligned_cols=122  Identities=11%  Similarity=0.164  Sum_probs=74.1

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC-CCce-eEEEECCCCCCCCHHHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFDC-HAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~~-~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      .++||.++.++.|.+++..+.  ...+-++|+.|+||||+|+.+.+  ++.. .+.. +.=+.  .+...+.........
T Consensus        14 ~divg~~~~~~~L~~~i~~~~--~~~lLl~Gp~G~GKttl~~~la~--~l~~~~~~~~~~e~~--~~~~~~~~~~~~~~~   87 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALAR--EIYGKNYSNMVLELN--ASDDRGIDVVRNQIK   87 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHH--HHHTTSHHHHEEEEC--TTSCCSHHHHHTHHH
T ss_pred             HHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChhHHHHHHHH--HhhcCCCcceeEEec--ccccCCeeeeecchh
Confidence            579999999999999998765  33466999999999999999988  4322 2222 22223  444444333222222


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      ......                   ....+++-.+|+|++...  ..-..+...+....+.++++++|...
T Consensus        88 ~~~~~~-------------------~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~  139 (227)
T d1sxjc2          88 DFASTR-------------------QIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYA  139 (227)
T ss_dssp             HHHHBC-------------------CSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             hccccc-------------------cccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcH
Confidence            111110                   111234558889999754  33344554444455678888887654

>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=97.76  E-value=1.7e-05  Score=76.62  Aligned_cols=124  Identities=14%  Similarity=0.142  Sum_probs=74.4

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC-ce-eEEEECCCCCCCCHHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF-DC-HAWITEPYSNEYDADQILDIV  232 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F-~~-~~wv~~~vs~~~~~~~~~~~i  232 (824)
                      -++++|-++.++++.+++..+.  ...+-++|+.|+||||+|+.+.+  ++...+ .. ++-+.  .+.......+...+
T Consensus        14 ~~d~ig~~~~~~~L~~~~~~~~--~~~~ll~Gp~G~GKTt~a~~la~--~l~~~~~~~~~~~~n--~~~~~~~~~i~~~~   87 (224)
T d1sxjb2          14 LSDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHCLAH--ELLGRSYADGVLELN--ASDDRGIDVVRNQI   87 (224)
T ss_dssp             GGGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHHHHH--HHHGGGHHHHEEEEC--TTSCCSHHHHHTHH
T ss_pred             HHHhcCCHHHHHHHHHHHHcCC--CCeEEEECCCCCCchhhHHHHHH--HHhcccccccccccc--ccccCCceehhhHH
Confidence            3678999999999999998765  44467899999999999999887  443322 22 33344  55554444443333


Q ss_pred             HHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          233 IKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       233 ~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                      .........                  .-.++.-++|+|++...  .....+...+......+++++||...
T Consensus        88 ~~~~~~~~~------------------~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2          88 KHFAQKKLH------------------LPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             HHHHHBCCC------------------CCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             HHHHHhhcc------------------CCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCch
Confidence            332221111                  01235568889999754  22333333333344456776666553

>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=97.71  E-value=3.6e-06  Score=76.93  Aligned_cols=85  Identities=20%  Similarity=0.028  Sum_probs=59.2

Q ss_pred             hHhhhcccCcccEEEeeCccCccCC---ccCCCCCcceEEeecCCCCCccChhhhhcCCCccEeecCCccccccc-----
Q 003387          513 WEKFCGMFKLLRVLDLGSLVLIQYP---SGIENLFLLRYLKLNIPSLNSLPSSLLSNLLNLYTLDMPFSYIDHTA-----  584 (824)
Q Consensus       513 ~~~~~~~~~~Lr~L~L~~~~i~~lp---~~i~~l~~Lr~L~L~~~~i~~lp~~i~~~L~~L~~L~L~~~~l~~lp-----  584 (824)
                      +...+..++.|++|+|++|.++.++   ..+..+++|++|+|++|.++.+++-.+.+..+|+.|++++|.+....     
T Consensus        57 l~~~~~~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~Npl~~~~~~~~~  136 (162)
T d1koha1          57 LRIIEENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLSDTFRDQST  136 (162)
T ss_dssp             HHHHHHHCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTSTTSSSSSSHHH
T ss_pred             hHHHHHhCCCCCEeeCCCccccCCchhHHHHhhCCcccccccccCccccchhhhhhhccccceeecCCCCcCcCcccchh
Confidence            3445567888888888888877553   44566888888888888888777632245557888888888665432     


Q ss_pred             ---hhhhccccCceec
Q 003387          585 ---DEFWKMNKLRHLN  597 (824)
Q Consensus       585 ---~~i~~L~~L~~L~  597 (824)
                         ..+..+|+|+.||
T Consensus       137 y~~~i~~~~P~L~~LD  152 (162)
T d1koha1         137 YISAIRERFPKLLRLD  152 (162)
T ss_dssp             HHHHHHTTSTTCCEET
T ss_pred             HHHHHHHHCCCCCEEC
Confidence               1245678888874

>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=97.70  E-value=1.3e-05  Score=78.99  Aligned_cols=46  Identities=11%  Similarity=-0.026  Sum_probs=36.3

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.++..+.|.+++..+.. ..-+-++|++|+||||+|+++.+
T Consensus        10 ~~diig~~~~~~~L~~~~~~~~~-~~~lll~Gp~G~GKTt~~~~la~   55 (252)
T d1sxje2          10 LNALSHNEELTNFLKSLSDQPRD-LPHLLLYGPNGTGKKTRCMALLE   55 (252)
T ss_dssp             GGGCCSCHHHHHHHHTTTTCTTC-CCCEEEECSTTSSHHHHHHTHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCCC-CCeEEEECCCCCCHHHHHHHHHH
Confidence            35799998888888877765432 33466999999999999999876

>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=97.68  E-value=1.1e-05  Score=78.71  Aligned_cols=132  Identities=14%  Similarity=0.080  Sum_probs=76.5

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCC---CceeEEEECCCCCCCCHHHHHHH
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHY---FDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~---F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      -++++|.++.++.+.+++..+.  ...+-++|+.|+||||+|+.+.+  ++...   ......+.  .+.......+...
T Consensus        11 ~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtl~~~i~~--~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~   84 (237)
T d1sxjd2          11 LDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILALTK--ELYGPDLMKSRILELN--ASDERGISIVREK   84 (237)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHHHH--HHHHHHHHTTSEEEEC--SSSCCCHHHHTTH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChHHHHHHHHH--HHcCCcccccchhhee--ccccccchHHHHH
Confidence            3568999999999999987664  44477999999999999999988  33211   12233344  5555555443333


Q ss_pred             HHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEech
Q 003387          232 VIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTD  301 (824)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~  301 (824)
                      +-........     ..    ....+......+.-.+|+|++...  ..+..+...+......+++++||..
T Consensus        85 ~~~~~~~~~~-----~~----~~~~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~  147 (237)
T d1sxjd2          85 VKNFARLTVS-----KP----SKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNY  147 (237)
T ss_dssp             HHHHHHSCCC-----CC----CTTHHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             HHHHhhhhhh-----hh----hHHHHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccc
Confidence            3222211111     00    011222333445557899998754  3444444444444456677777654

>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=97.62  E-value=1.5e-05  Score=77.47  Aligned_cols=45  Identities=20%  Similarity=0.223  Sum_probs=39.7

Q ss_pred             CCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|-+..++++.+++..+.  ...+-++|+.|+||||+|+.+.+
T Consensus        23 ~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtla~~iak   67 (231)
T d1iqpa2          23 LDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALAR   67 (231)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCcHHHHHHHHHH
Confidence            3679999999999999998775  45578999999999999999988

>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=97.61  E-value=0.00012  Score=71.25  Aligned_cols=45  Identities=22%  Similarity=0.196  Sum_probs=38.1

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+++|.++.++.+.+++..+. -...+-|+|..|+||||+|+.+.+
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~-~~~~~Ll~Gp~G~GKtt~a~~~~~   56 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAK   56 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTC-CCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHccChHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHH
Confidence            589999999999999998754 234577999999999999998766

>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=97.55  E-value=4.1e-06  Score=76.58  Aligned_cols=64  Identities=25%  Similarity=0.173  Sum_probs=48.1

Q ss_pred             CCCCCcceEEeecCCCCCccC---hhhhhcCCCccEeecCCccccccch-hhhccccCceecCCCccCC
Q 003387          540 IENLFLLRYLKLNIPSLNSLP---SSLLSNLLNLYTLDMPFSYIDHTAD-EFWKMNKLRHLNFGSITLP  604 (824)
Q Consensus       540 i~~l~~Lr~L~L~~~~i~~lp---~~i~~~L~~L~~L~L~~~~l~~lp~-~i~~L~~L~~L~L~~~~~~  604 (824)
                      ..++++|++|+|++|.++.++   ..+ .++++|+.|+|++|.++.+++ ...+..+|+.|++++|.+.
T Consensus        61 ~~~~~~L~~L~Ls~N~i~~l~~~~~~~-~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~Npl~  128 (162)
T d1koha1          61 EENIPELLSLNLSNNRLYRLDDMSSIV-QKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLS  128 (162)
T ss_dssp             HHHCTTCCCCCCCSSCCCCCSGGGTHH-HHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTSTTS
T ss_pred             HHhCCCCCEeeCCCccccCCchhHHHH-hhCCcccccccccCccccchhhhhhhccccceeecCCCCcC
Confidence            345788899999998888664   334 788889999999988888865 2334457888888888775

>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=97.50  E-value=0.00011  Score=69.81  Aligned_cols=123  Identities=16%  Similarity=0.094  Sum_probs=71.1

Q ss_pred             CCceechhh--HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHH
Q 003387          156 RDTVGLDDR--MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVI  233 (824)
Q Consensus       156 ~~~vGr~~~--~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~  233 (824)
                      .-++|-...  .+.+.++..........+.|+|..|+|||.|++++++  +.......+++++        ..++...+.
T Consensus        11 nF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~--~~~~~~~~~~~~~--------~~~~~~~~~   80 (213)
T d1l8qa2          11 NFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGN--EAKKRGYRVIYSS--------ADDFAQAMV   80 (213)
T ss_dssp             SCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHH--HHHHTTCCEEEEE--------HHHHHHHHH
T ss_pred             hccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHH--HhccCccceEEec--------hHHHHHHHH
Confidence            445675443  2334444444333344578999999999999999999  5555555666765        334444444


Q ss_pred             HHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh---hhHHHHHhh-CC-CCCCCcEEEEEechH
Q 003387          234 KFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI---DMWDVIQEI-LP-DNQNGSRVLITLTDI  302 (824)
Q Consensus       234 ~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~---~~~~~l~~~-~~-~~~~gs~ilvTtR~~  302 (824)
                      ..+...         ...+.    .+.++ .--+|++||+...   ..|+..... +. ....|.+||+||+..
T Consensus        81 ~~~~~~---------~~~~~----~~~~~-~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~  140 (213)
T d1l8qa2          81 EHLKKG---------TINEF----RNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRH  140 (213)
T ss_dssp             HHHHHT---------CHHHH----HHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSC
T ss_pred             HHHHcc---------chhhH----HHHHh-hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCc
Confidence            443221         11222    22222 3458999999754   355543322 22 124578899999764

>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=97.44  E-value=0.00011  Score=76.25  Aligned_cols=129  Identities=10%  Similarity=0.095  Sum_probs=68.3

Q ss_pred             CCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHH----HhCCccccCCCceeEEEECCCCCCCCHHHHHHH
Q 003387          156 RDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGE----AYNSSYVKHYFDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~----v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      ++++||+.+++++++.|.....  .-+.+||.+|||||+++..    +.+..--....+.++|.-       |...++..
T Consensus        22 d~~~gr~~ei~~~~~~L~r~~k--~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~l-------d~~~l~ag   92 (387)
T d1qvra2          22 DPVIGRDEEIRRVIQILLRRTK--NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSL-------QMGSLLAG   92 (387)
T ss_dssp             CCCCSCHHHHHHHHHHHHCSSC--CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEE-------CC------
T ss_pred             CCCcCcHHHHHHHHHHHhcCCC--CCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEe-------eHhhhhcc
Confidence            4688999999999999986542  2236789999999997744    444321233445677764       11111111


Q ss_pred             HHHHhCCCCCcccccccCHHHHHHHHHHhc-CC-CeEEEEEecCCChh---------hHHHHHhhCCCCCCCcEEEEEec
Q 003387          232 VIKFLMPSSRLSEIMDKNYEMKKIILHEYL-MT-KRYLIVIDDVWSID---------MWDVIQEILPDNQNGSRVLITLT  300 (824)
Q Consensus       232 i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L-~~-kr~LlVlDdv~~~~---------~~~~l~~~~~~~~~gs~ilvTtR  300 (824)
                             ..     .....++....+...+ +. ..+.|++|++...-         +...+..|.-..+ .=++|-||.
T Consensus        93 -------~~-----~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L~rg-~~~~I~~tT  159 (387)
T d1qvra2          93 -------AK-----YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALARG-ELRLIGATT  159 (387)
T ss_dssp             -----------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHTT-CCCEEEEEC
T ss_pred             -------cC-----cchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHHhCC-CcceeeecC
Confidence                   00     1123445555554444 33 47999999996531         2222222221122 246777777


Q ss_pred             hHHHHh
Q 003387          301 DIRIII  306 (824)
Q Consensus       301 ~~~v~~  306 (824)
                      .++...
T Consensus       160 ~~ey~~  165 (387)
T d1qvra2         160 LDEYRE  165 (387)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            766654

>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=97.41  E-value=0.00038  Score=67.63  Aligned_cols=53  Identities=19%  Similarity=0.109  Sum_probs=38.4

Q ss_pred             CCCceechhhHHHHHHHHH-------cC-CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          155 SRDTVGLDDRMEELLDLLI-------EG-PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~-------~~-~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      ..+++|..+.++.+++-..       .+ ....+-|-++|++|+|||++|+++.+  +....|
T Consensus         8 ~~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~--~~~~~~   68 (246)
T d1d2na_           8 MNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAE--ESNFPF   68 (246)
T ss_dssp             TTCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHH--HHTCSE
T ss_pred             ccCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhh--cccccc
Confidence            3568888887777666543       22 23467788999999999999999998  554443

>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=97.19  E-value=0.00024  Score=69.82  Aligned_cols=46  Identities=17%  Similarity=0.217  Sum_probs=36.9

Q ss_pred             CCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++|.++.+++|.+.+..           +-...+-|-++|++|.|||++|+++.+
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~   60 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN   60 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHH
Confidence            5689999999998887431           222356688999999999999999998

>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=97.18  E-value=0.001  Score=62.74  Aligned_cols=133  Identities=9%  Similarity=0.025  Sum_probs=67.6

Q ss_pred             echhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCC
Q 003387          160 GLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPS  239 (824)
Q Consensus       160 Gr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~  239 (824)
                      +.+...+++.+.+..+. -...+-++|+.|+||||+|+.+.+.  +-.. ...-+-.  .....+-    ..+.......
T Consensus         6 w~~~~~~~l~~~~~~~~-l~h~lLl~Gp~G~GKtt~a~~~a~~--l~~~-~~~~~~~--~~~~~~~----~~i~~~~~~~   75 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRY--LLCQ-QPQGHKS--CGHCRGC----QLMQAGTHPD   75 (207)
T ss_dssp             GGHHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHH--HTCS-SCBTTBC--CSCSHHH----HHHHHTCCTT
T ss_pred             ccHHHHHHHHHHHHcCC-cCeEEEEECCCCCcHHHHHHHHHHh--cccc-ccccccc--ccccchh----hhhhhccccc
Confidence            34556777888777654 2345888999999999999977651  1000 0000000  0000000    0111110000


Q ss_pred             C----CcccccccCHHHHHHHHHHhc-----CCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          240 S----RLSEIMDKNYEMKKIILHEYL-----MTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       240 ~----~~~~~~~~~~~~~~~~l~~~L-----~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                      .    ..........++. ..+.+.+     .+++-++|+||+...  +....+...+.....++++|.||++.+
T Consensus        76 ~~~~~~~~~~~~i~~~~i-r~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~  149 (207)
T d1a5ta2          76 YYTLAPEKGKNTLGVDAV-REVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPE  149 (207)
T ss_dssp             EEEECCCTTCSSBCHHHH-HHHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGG
T ss_pred             cchhhhhhcccccccchh-hHHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChh
Confidence            0    0000001112222 1222222     246679999999864  457777777776667888888887753

>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=97.14  E-value=0.00016  Score=70.96  Aligned_cols=107  Identities=14%  Similarity=0.073  Sum_probs=64.1

Q ss_pred             CCCceechhhHHHHHHHHHc---------------CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCC
Q 003387          155 SRDTVGLDDRMEELLDLLIE---------------GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPY  219 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~---------------~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~v  219 (824)
                      -.+++|.+..+++|.++|..               +....+.+-++|++|+||||+|+.+++  +..   -..+++.  .
T Consensus        13 ~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~--~~~---~~~~~~~--~   85 (253)
T d1sxja2          13 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQ--ELG---YDILEQN--A   85 (253)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHH--HTT---CEEEEEC--T
T ss_pred             HHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHH--HHH---hhhhccc--c
Confidence            46899999999999999864               122456889999999999999999998  332   2345665  5


Q ss_pred             CCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHhcCCCeEEEEEecCCC
Q 003387          220 SNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWS  275 (824)
Q Consensus       220 s~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~  275 (824)
                      +...+...+- ............  .....    .........++..++++|++..
T Consensus        86 ~~~~~~~~~~-~~~~~~~~~~~~--~~~~~----~~~~~~~~~~~~~vi~ide~~~  134 (253)
T d1sxja2          86 SDVRSKTLLN-AGVKNALDNMSV--VGYFK----HNEEAQNLNGKHFVIIMDEVDG  134 (253)
T ss_dssp             TSCCCHHHHH-HTGGGGTTBCCS--TTTTT----C----CCSSTTSEEEEECSGGG
T ss_pred             ccchhhHHHH-HHHHHHhhcchh--hhhhh----hhhhcccccccceEEEeeeccc
Confidence            5544444332 223322221110  00000    0111223346788999999864

>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=97.07  E-value=0.00034  Score=63.66  Aligned_cols=90  Identities=7%  Similarity=0.038  Sum_probs=58.6

Q ss_pred             hHhhhcccCcccEEEeeCcc-Cc-----cCCccCCCCCcceEEeecCCCCC-----ccChhhhhcCCCccEeecCCcccc
Q 003387          513 WEKFCGMFKLLRVLDLGSLV-LI-----QYPSGIENLFLLRYLKLNIPSLN-----SLPSSLLSNLLNLYTLDMPFSYID  581 (824)
Q Consensus       513 ~~~~~~~~~~Lr~L~L~~~~-i~-----~lp~~i~~l~~Lr~L~L~~~~i~-----~lp~~i~~~L~~L~~L~L~~~~l~  581 (824)
                      +.......+.|+.|+|+++. +.     .+-..+...++|++|+|++|.+.     .+...+ ...+.|++|+|++|.+.
T Consensus         7 l~~l~~n~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L-~~n~~L~~L~L~~n~i~   85 (167)
T d1pgva_           7 INRLREDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELI-ETSPSLRVLNVESNFLT   85 (167)
T ss_dssp             HHHHHTTCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHH-HHCSSCCEEECCSSBCC
T ss_pred             HHHHHhCCCCCcEEEeCCCCCCCHHHHHHHHHHHhhCCccceeeccccccchhHHHHHhhhh-hhcccccceeeehhhcc
Confidence            44555666888888888743 54     34445666777888888888775     233333 56677888888887665


Q ss_pred             c-----cchhhhccccCceecCCCccC
Q 003387          582 H-----TADEFWKMNKLRHLNFGSITL  603 (824)
Q Consensus       582 ~-----lp~~i~~L~~L~~L~L~~~~~  603 (824)
                      .     +-..+...+.|++|++++|..
T Consensus        86 ~~g~~~l~~aL~~n~sL~~L~l~~n~~  112 (167)
T d1pgva_          86 PELLARLLRSTLVTQSIVEFKADNQRQ  112 (167)
T ss_dssp             HHHHHHHHHHTTTTCCCSEEECCCCSS
T ss_pred             hHHHHHHHHHHHhCCcCCEEECCCCcC
Confidence            3     233455667778887776654

>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=96.89  E-value=0.00058  Score=66.16  Aligned_cols=46  Identities=20%  Similarity=0.230  Sum_probs=38.0

Q ss_pred             CCceechhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +++||-++.++++..++...   .....-+-++|++|+||||+|+.+.+
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~   57 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAH   57 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            57899999999988888642   22355677999999999999999998

>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=96.84  E-value=0.00024  Score=64.69  Aligned_cols=107  Identities=12%  Similarity=-0.016  Sum_probs=75.2

Q ss_pred             CCceeEeeccCCCCCCCCcc---hhHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCCc-----
Q 003387          492 DSQLHSLLCCSPETRHLDPI---DWEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLNS-----  558 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~~~~~---~~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~~-----  558 (824)
                      .+.|+.|.+.+.....  ..   .+...+...+.|+.|+|++|.+.     .+...+...+.|++|+|++|.+..     
T Consensus        14 ~~~L~~L~L~~~~~i~--~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~   91 (167)
T d1pgva_          14 DTDLKEVNINNMKRVS--KERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLAR   91 (167)
T ss_dssp             CSSCCEEECTTCCSSC--HHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHH
T ss_pred             CCCCcEEEeCCCCCCC--HHHHHHHHHHHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhhcchHHHHH
Confidence            5788999997643221  22   23456777888999999999876     333455667889999999998873     


Q ss_pred             cChhhhhcCCCccEeecCCccccc--------cchhhhccccCceecCCCc
Q 003387          559 LPSSLLSNLLNLYTLDMPFSYIDH--------TADEFWKMNKLRHLNFGSI  601 (824)
Q Consensus       559 lp~~i~~~L~~L~~L~L~~~~l~~--------lp~~i~~L~~L~~L~L~~~  601 (824)
                      +-..+ ...+.|++|+++++.+..        +...+...+.|+.|+++.+
T Consensus        92 l~~aL-~~n~sL~~L~l~~n~~~~~g~~~~~~l~~~L~~n~sL~~l~l~~~  141 (167)
T d1pgva_          92 LLRST-LVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGISFA  141 (167)
T ss_dssp             HHHHT-TTTCCCSEEECCCCSSCCCCHHHHHHHHHHHHHCSSCCEEECCCC
T ss_pred             HHHHH-HhCCcCCEEECCCCcCCCccHHHHHHHHHHHHhCCCccEeeCcCC
Confidence            33344 677889999998875443        3344566788888877554

>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=96.70  E-value=0.00068  Score=66.03  Aligned_cols=47  Identities=26%  Similarity=0.237  Sum_probs=36.1

Q ss_pred             CCCceechhhHHHHHHHH---HcC-------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLL---IEG-------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L---~~~-------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -++++|.++.+++|.+.+   ...       ....+-+-++|++|.|||++|+.+.+
T Consensus        11 ~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~   67 (256)
T d1lv7a_          11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG   67 (256)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHH
Confidence            468999999888876543   321       12356678999999999999999998

>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=96.62  E-value=0.00037  Score=67.56  Aligned_cols=47  Identities=21%  Similarity=0.175  Sum_probs=38.3

Q ss_pred             CCCceechhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+++||.+..+++|..++...   .....-+-++|++|+||||+|+.+.+
T Consensus         8 ~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~   57 (238)
T d1in4a2           8 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS   57 (238)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHh
Confidence            367999999999999988632   22344567999999999999999998

>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=96.58  E-value=0.00065  Score=65.87  Aligned_cols=49  Identities=22%  Similarity=0.316  Sum_probs=36.7

Q ss_pred             CCCCCceechhhHHHHHHHH---Hc-------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          153 SKSRDTVGLDDRMEELLDLL---IE-------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L---~~-------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.-++++|.++.+++|.+.+   ..       +....+-|-++|++|.|||++|+++.+
T Consensus         6 ~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~   64 (247)
T d1ixza_           6 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAG   64 (247)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHH
Confidence            44467999998887765543   22       122346688999999999999999998

>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=96.53  E-value=0.0023  Score=57.92  Aligned_cols=22  Identities=14%  Similarity=0.155  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.|.|++|+||||+|+.+..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999876

>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=96.47  E-value=0.007  Score=56.09  Aligned_cols=113  Identities=13%  Similarity=0.093  Sum_probs=68.1

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCc--cccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSS--YVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL  242 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~--~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~  242 (824)
                      ++.+.+++..+.  ...+-++|.+|.||||+|..+.+.-  ....|-| .+++. +-+....+.++- ++.+.+..... 
T Consensus         3 ~~~l~~~i~~~~--~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D-~~~i~-~~~~~I~Id~IR-~i~~~~~~~~~-   76 (198)
T d2gnoa2           3 LETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEID-PEGENIGIDDIR-TIKDFLNYSPE-   76 (198)
T ss_dssp             HHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEEC-CSSSCBCHHHHH-HHHHHHTSCCS-
T ss_pred             HHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHHhccccCCCC-EEEEe-CCcCCCCHHHHH-HHHHHHhhCcc-
Confidence            444555565554  7899999999999999999877621  1112223 44443 122233444443 34444443211 


Q ss_pred             ccccccCHHHHHHHHHHhcCCCeEEEEEecCCCh--hhHHHHHhhCCCCCCCcEEEEEechH
Q 003387          243 SEIMDKNYEMKKIILHEYLMTKRYLIVIDDVWSI--DMWDVIQEILPDNQNGSRVLITLTDI  302 (824)
Q Consensus       243 ~~~~~~~~~~~~~~l~~~L~~kr~LlVlDdv~~~--~~~~~l~~~~~~~~~gs~ilvTtR~~  302 (824)
                                         .+++=++|+|++...  ..++.+...+..-.+++.+|++|.+.
T Consensus        77 -------------------~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          77 -------------------LYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             -------------------SSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             -------------------cCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCCh
Confidence                               245558899999864  56777776665555677777777654

>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=96.41  E-value=0.0004  Score=68.37  Aligned_cols=47  Identities=30%  Similarity=0.261  Sum_probs=36.1

Q ss_pred             CCCceechhhHHHHHHHHHc-----------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          155 SRDTVGLDDRMEELLDLLIE-----------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       155 ~~~~vGr~~~~~~l~~~L~~-----------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|.++.+++|.+.+..           +-...+-|-++|+.|.|||+||+++.+
T Consensus         6 f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~   63 (265)
T d1r7ra3           6 WEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN   63 (265)
T ss_dssp             CSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHH
Confidence            45688988887777766531           222356688999999999999999998

>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=96.39  E-value=0.00089  Score=60.65  Aligned_cols=86  Identities=12%  Similarity=0.119  Sum_probs=51.8

Q ss_pred             hhHhhhcccCcccEEEeeCc-cCc-----cCCccCCCCCcceEEeecCCCCC-----ccChhhhhcCCCccEeecCCccc
Q 003387          512 DWEKFCGMFKLLRVLDLGSL-VLI-----QYPSGIENLFLLRYLKLNIPSLN-----SLPSSLLSNLLNLYTLDMPFSYI  580 (824)
Q Consensus       512 ~~~~~~~~~~~Lr~L~L~~~-~i~-----~lp~~i~~l~~Lr~L~L~~~~i~-----~lp~~i~~~L~~L~~L~L~~~~l  580 (824)
                      .+.......+.|+.|+|+++ .++     .+-..+...++|+.|+|++|.+.     .+-..+ ...++|+.|++++|.+
T Consensus         8 ~l~~~~~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l-~~~~~l~~l~l~~~~~   86 (166)
T d1io0a_           8 TLKRIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEML-KVNNTLKSLNVESNFI   86 (166)
T ss_dssp             HHHHHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHH-HHCSSCCEEECCSSCC
T ss_pred             HHHHHHhcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHH-hhcccchhhhhccccc
Confidence            34455566677888888764 354     34445556777777777777765     232333 5667777777777654


Q ss_pred             c-----ccchhhhccccCceecC
Q 003387          581 D-----HTADEFWKMNKLRHLNF  598 (824)
Q Consensus       581 ~-----~lp~~i~~L~~L~~L~L  598 (824)
                      .     .+...+...++|+.++|
T Consensus        87 ~~~g~~~l~~~l~~~~~L~~l~L  109 (166)
T d1io0a_          87 SGSGILALVEALQSNTSLIELRI  109 (166)
T ss_dssp             CHHHHHHHHHGGGGCSSCCEEEC
T ss_pred             cchhHHHHHHHHHhCccccEEee
Confidence            3     22344556666665544

>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=96.20  E-value=0.00085  Score=61.81  Aligned_cols=23  Identities=22%  Similarity=0.200  Sum_probs=21.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++.|.|.|+.|+||||||+++.+
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~   29 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAA   29 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            68899999999999999999988

>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=96.18  E-value=0.0011  Score=60.01  Aligned_cols=110  Identities=10%  Similarity=0.008  Sum_probs=76.5

Q ss_pred             CCceeEeeccCCCCCC-CCcchhHhhhcccCcccEEEeeCccCc-----cCCccCCCCCcceEEeecCCCCC-----ccC
Q 003387          492 DSQLHSLLCCSPETRH-LDPIDWEKFCGMFKLLRVLDLGSLVLI-----QYPSGIENLFLLRYLKLNIPSLN-----SLP  560 (824)
Q Consensus       492 ~~~Lr~L~l~~~~~~~-~~~~~~~~~~~~~~~Lr~L~L~~~~i~-----~lp~~i~~l~~Lr~L~L~~~~i~-----~lp  560 (824)
                      .+.|+.|.+.+..... .....+...+...++|+.|+|++|.+.     .+-..+....+|++|+++++.+.     .+.
T Consensus        16 ~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~~~~g~~~l~   95 (166)
T d1io0a_          16 DPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSGILALV   95 (166)
T ss_dssp             CTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHHHHHHH
T ss_pred             CCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhccccccchhHHHHH
Confidence            5788888887643221 001134456678899999999999876     34455667889999999998876     344


Q ss_pred             hhhhhcCCCccEeecC--Ccccc-----ccchhhhccccCceecCCCcc
Q 003387          561 SSLLSNLLNLYTLDMP--FSYID-----HTADEFWKMNKLRHLNFGSIT  602 (824)
Q Consensus       561 ~~i~~~L~~L~~L~L~--~~~l~-----~lp~~i~~L~~L~~L~L~~~~  602 (824)
                      ..+ ...++|+.++|+  ++.+.     .+...+...++|++|+++.+.
T Consensus        96 ~~l-~~~~~L~~l~L~l~~n~i~~~~~~~La~~L~~n~~L~~L~l~~~~  143 (166)
T d1io0a_          96 EAL-QSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHFTQ  143 (166)
T ss_dssp             HGG-GGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             HHH-HhCccccEEeeccCCCcCcHHHHHHHHHHHHhCCCcCEEeCcCCC
Confidence            555 788889886665  44553     355667788999999886553

>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=96.12  E-value=0.0024  Score=59.28  Aligned_cols=51  Identities=14%  Similarity=0.039  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHc-CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          164 RMEELLDLLIE-GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       164 ~~~~l~~~L~~-~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .++.|.+.... ...+.-+|||.|..|+||||||+.+..  .....+.....++
T Consensus         6 ~~~~~~~~~~~~~~~~~~iIgI~G~~GSGKSTla~~L~~--~l~~~~~~~~~~~   57 (198)
T d1rz3a_           6 RIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQ--TLREQGISVCVFH   57 (198)
T ss_dssp             HHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHhccCCCCEEEEEECCCCCCHHHHHHHHHH--Hhccccccceecc
Confidence            34455555443 244577999999999999999999987  4444443444443

>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=96.02  E-value=0.0008  Score=60.52  Aligned_cols=22  Identities=9%  Similarity=0.249  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.|.++|++|+||||+|+.+.+
T Consensus         3 k~I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4688899999999999999988

>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=96.00  E-value=0.0016  Score=57.77  Aligned_cols=22  Identities=18%  Similarity=0.306  Sum_probs=19.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.|+|++|+||||+|+.+..
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5788999999999999998865

>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=96.00  E-value=0.0025  Score=64.05  Aligned_cols=46  Identities=15%  Similarity=0.155  Sum_probs=37.0

Q ss_pred             CCceechhhHHHHHHHHHc-------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIE-------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~-------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|-++.++.+...+..       .+....++..+|+.|+|||.||+.+..
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~   74 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSK   74 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHh
Confidence            4678999999988776641       233466889999999999999999987

>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=95.98  E-value=0.0052  Score=61.60  Aligned_cols=45  Identities=20%  Similarity=0.289  Sum_probs=34.7

Q ss_pred             CceechhhHHHHHHHHHc-------CCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          157 DTVGLDDRMEELLDLLIE-------GPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~-------~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.++.++.|.+.+..       ......++..+|+.|+|||.+|+.+.+
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~   75 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA   75 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHH
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHH
Confidence            567888888888776642       122356888999999999999998877

>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=95.98  E-value=0.0093  Score=57.79  Aligned_cols=92  Identities=22%  Similarity=0.120  Sum_probs=63.3

Q ss_pred             CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCc-ccccccCHHHH
Q 003387          175 GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRL-SEIMDKNYEMK  253 (824)
Q Consensus       175 ~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~-~~~~~~~~~~~  253 (824)
                      +-..-+++-|+|..|+||||+|-.++...  +..=..++|++  .-..++.+.     +++++...+. --.+....++.
T Consensus        56 G~~~g~i~e~~G~~~~GKT~l~l~~~~~~--q~~g~~~vyID--tE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~  126 (269)
T d1mo6a1          56 GLPRGRVIEIYGPESSGKTTVALHAVANA--QAAGGVAAFID--AEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQA  126 (269)
T ss_dssp             SBCSSSEEEEECSSSSSHHHHHHHHHHHH--HHTTCEEEEEE--SSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHH
T ss_pred             CcccceeEEEecCCCcHHHHHHHHHHHHH--hcCCCEEEEEE--CCccCCHHH-----HHHhCCCHHHeEEecCCCHHHH
Confidence            43456899999999999999998877743  33334689999  888888765     5666653221 01344556777


Q ss_pred             HHHHHHhcC-CCeEEEEEecCCC
Q 003387          254 KIILHEYLM-TKRYLIVIDDVWS  275 (824)
Q Consensus       254 ~~~l~~~L~-~kr~LlVlDdv~~  275 (824)
                      .+.+...++ ++.-|||+|-+-.
T Consensus       127 ~~~~~~l~~~~~~~liIiDSi~a  149 (269)
T d1mo6a1         127 LEIADMLIRSGALDIVVIDSVAA  149 (269)
T ss_dssp             HHHHHHHHHTTCEEEEEEECSTT
T ss_pred             HHHHHHHHhcCCCCEEEEecccc
Confidence            666665554 4677999999954

>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=95.81  E-value=0.0018  Score=58.52  Aligned_cols=23  Identities=17%  Similarity=0.196  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.||+|+|..|+|||||++++.+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~   24 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIP   24 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            35899999999999999999987

>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=95.65  E-value=0.0018  Score=60.02  Aligned_cols=36  Identities=14%  Similarity=-0.110  Sum_probs=28.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      -.+|.++|++|+||||+|+.+..  +....+....++.
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~--~l~~~~~~~~~~~   54 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEE--YLVCHGIPCYTLD   54 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHH--HHHHTTCCEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH--HHHhcCCCccchh
Confidence            46888999999999999999988  5655555555554

>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=95.62  E-value=0.0027  Score=57.84  Aligned_cols=37  Identities=11%  Similarity=-0.068  Sum_probs=28.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccC-CCceeEEEE
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFDCHAWIT  216 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~  216 (824)
                      +-.+|.++|+.|+||||+|+.+..  ++.. .++...++.
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~--~L~~~~~~~~~~~~   42 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQV--TLNQQGGRSVSLLL   42 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH--HHHHHCSSCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHhhcCCCchhhhh
Confidence            357899999999999999999998  6543 345555555

>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=95.59  E-value=0.0021  Score=58.91  Aligned_cols=22  Identities=23%  Similarity=0.237  Sum_probs=20.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.|.|+|++|+|||||++++..
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~   23 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASE   23 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHH
Confidence            5689999999999999999987

>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=95.54  E-value=0.027  Score=52.95  Aligned_cols=51  Identities=14%  Similarity=0.331  Sum_probs=34.1

Q ss_pred             HHHHHHhcCCCeEEEEEecCCCh-------hhHHHHHhhCCCCCCCcEEEEEechHHHHh
Q 003387          254 KIILHEYLMTKRYLIVIDDVWSI-------DMWDVIQEILPDNQNGSRVLITLTDIRIII  306 (824)
Q Consensus       254 ~~~l~~~L~~kr~LlVlDdv~~~-------~~~~~l~~~~~~~~~gs~ilvTtR~~~v~~  306 (824)
                      .-.|.+.|..+.-+|++|..-..       +-|+.+....  ...|..||++|.+.+++.
T Consensus       153 RvaIAraL~~~P~lLllDEPTs~LD~~~~~~i~~~l~~l~--~~~g~tii~vTHd~~~a~  210 (230)
T d1l2ta_         153 RVAIARALANNPPIILADQPTGALDSKTGEKIMQLLKKLN--EEDGKTVVVVTHDINVAR  210 (230)
T ss_dssp             HHHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHH--HTTCCEEEEECSCHHHHT
T ss_pred             HHHHHhhhhcCCCEEEecCCccccCHHHHHHHHHHHHHHH--HhhCCEEEEECCCHHHHH
Confidence            45677777788889999998653       2244443321  234777888888888775

>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=95.50  E-value=0.0022  Score=57.78  Aligned_cols=25  Identities=8%  Similarity=0.015  Sum_probs=20.0

Q ss_pred             EEEEcCCCChHHHHHHHHhCCccccCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNSSYVKHY  208 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~~~~~~~  208 (824)
                      |.++||+|+||||+|+.+.+  +..-.
T Consensus         4 IvliG~~G~GKSTig~~La~--~l~~~   28 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAK--ALGVG   28 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHH--HHTCC
T ss_pred             EEEECCCCCCHHHHHHHHHH--HhCCC
Confidence            34569999999999999998  55433

>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=95.43  E-value=0.003  Score=57.05  Aligned_cols=22  Identities=18%  Similarity=0.273  Sum_probs=19.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..|.|+|++|+||||+|+.+.+
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~   26 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELAS   26 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            3477999999999999999987

>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=95.41  E-value=0.0043  Score=60.87  Aligned_cols=47  Identities=17%  Similarity=0.299  Sum_probs=33.2

Q ss_pred             chhhHHHHHHHHHcC---CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          161 LDDRMEELLDLLIEG---PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       161 r~~~~~~l~~~L~~~---~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      .++..++.++.+..+   ....+.|-++|++|+||||||+.+.+  .....|
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~--~~~~~~   60 (273)
T d1gvnb_          11 FENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFE--ETQGNV   60 (273)
T ss_dssp             HHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHH--HTTTCC
T ss_pred             HHHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHH--Hhhcce
Confidence            344455555556543   23567888999999999999999998  444443

>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=95.35  E-value=0.0031  Score=56.75  Aligned_cols=27  Identities=11%  Similarity=-0.044  Sum_probs=23.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHY  208 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~  208 (824)
                      +|++|+|..|+|||||+.++..  +.+..
T Consensus         2 kii~I~G~~gSGKTTli~~l~~--~L~~~   28 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVA--AAVRE   28 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH--HHHHT
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH--HHHhC
Confidence            6899999999999999999988  55444

>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=95.31  E-value=0.0025  Score=57.24  Aligned_cols=20  Identities=15%  Similarity=0.293  Sum_probs=18.7

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      |.|+||+|+||||+|+.+..
T Consensus         3 I~liG~~GsGKsTi~k~La~   22 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAK   22 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67889999999999999988

>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=95.28  E-value=0.016  Score=56.18  Aligned_cols=89  Identities=16%  Similarity=0.048  Sum_probs=61.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcc-cccccCHHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLS-EIMDKNYEMKKII  256 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~~~~~  256 (824)
                      .-+++-|+|.+|.||||+|-.+....+...  ..++|++  ....++..     ++++++...+.- -....+.++..+.
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiD--tE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~  126 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFID--AEHALDPV-----YARALGVNTDELLVSQPDNGEQALEI  126 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEE--SSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHH
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEE--CCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHH
Confidence            457999999999999999988877433222  4589999  77788874     677777643210 0344566776666


Q ss_pred             HHHhcCC-CeEEEEEecCCC
Q 003387          257 LHEYLMT-KRYLIVIDDVWS  275 (824)
Q Consensus       257 l~~~L~~-kr~LlVlDdv~~  275 (824)
                      +...++. +.-|||+|-+-.
T Consensus       127 ~~~l~~~~~~~liIiDSi~a  146 (268)
T d1xp8a1         127 MELLVRSGAIDVVVVDSVAA  146 (268)
T ss_dssp             HHHHHTTTCCSEEEEECTTT
T ss_pred             HHHHHhcCCCcEEEEecccc
Confidence            6666654 456899998843

>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=95.23  E-value=0.0047  Score=55.92  Aligned_cols=24  Identities=17%  Similarity=0.142  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +-++|.|.|+.|+||||+|+.+.+
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999987

>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=95.21  E-value=0.012  Score=57.08  Aligned_cols=88  Identities=17%  Similarity=0.016  Sum_probs=57.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCC-cccccccCHHHHHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSR-LSEIMDKNYEMKKII  256 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~-~~~~~~~~~~~~~~~  256 (824)
                      .-+++-|+|.+|+||||+|-.+.....  ..=..++|++  ....++...     ++.++...+ .--....+.++..+.
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q--~~g~~~vyid--tE~~~~~~~-----a~~~Gvd~d~v~~~~~~~~E~~~~~  123 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFID--AEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEI  123 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHH--HTTCCEEEEE--SSCCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHH--cCCCEEEEEc--cccccCHHH-----HHHhCCCHHHEEEecCCCHHHHHHH
Confidence            357999999999999999988887433  3334689999  777777643     566665321 101233455666666


Q ss_pred             HHHhcC-CCeEEEEEecCC
Q 003387          257 LHEYLM-TKRYLIVIDDVW  274 (824)
Q Consensus       257 l~~~L~-~kr~LlVlDdv~  274 (824)
                      +....+ ++.-|||+|-+-
T Consensus       124 i~~l~~~~~~~liViDSi~  142 (263)
T d1u94a1         124 CDALARSGAVDVIVVDSVA  142 (263)
T ss_dssp             HHHHHHHTCCSEEEEECGG
T ss_pred             HHHHHhcCCCCEEEEECcc
Confidence            655554 334488889884

>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=95.15  E-value=0.0036  Score=56.75  Aligned_cols=23  Identities=4%  Similarity=0.010  Sum_probs=21.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.|.|..|+||||+|+.+.+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~   25 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999999988

>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=95.15  E-value=0.0041  Score=56.95  Aligned_cols=22  Identities=23%  Similarity=0.243  Sum_probs=20.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.|.|+.|+||||+++.+..
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~   23 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMD   23 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999987

>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=95.05  E-value=0.0049  Score=55.72  Aligned_cols=24  Identities=21%  Similarity=0.097  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ....|.|.|++|+||||+|+.+.+
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~   27 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAA   27 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHH
Confidence            356789999999999999999987

>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=95.03  E-value=0.0056  Score=56.78  Aligned_cols=25  Identities=24%  Similarity=0.271  Sum_probs=23.1

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +...||.|.|++|+||||+|+.+.+
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~   30 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVK   30 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4588999999999999999999988

>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=95.02  E-value=0.005  Score=57.00  Aligned_cols=24  Identities=21%  Similarity=0.205  Sum_probs=22.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|.|+|++|+||||+|+.+.+
T Consensus         5 kp~iI~i~G~pGSGKsT~a~~La~   28 (194)
T d1qf9a_           5 KPNVVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999999987

>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=94.89  E-value=0.0067  Score=54.61  Aligned_cols=24  Identities=21%  Similarity=0.295  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+++.|+|+.|+||||+|+.+..
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~La~   28 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASEVAH   28 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999999987

>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=94.88  E-value=0.0071  Score=55.50  Aligned_cols=35  Identities=9%  Similarity=0.038  Sum_probs=25.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ++|.|.|+.|+||||+|+.+..  +.......+..+.
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
Confidence            6899999999999999999987  5544333333443

>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=94.87  E-value=0.0033  Score=56.89  Aligned_cols=22  Identities=14%  Similarity=0.143  Sum_probs=19.5

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +.|.++|++|+||||+|+.+.+
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~   24 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELAR   24 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHH
Confidence            3467889999999999999988

>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=94.84  E-value=0.03  Score=51.79  Aligned_cols=57  Identities=12%  Similarity=0.060  Sum_probs=38.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHH--HHHHHHHHHhCC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDAD--QILDIVIKFLMP  238 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~--~~~~~i~~~l~~  238 (824)
                      +...||.++|+.|+||||.+-++..  +.+ .....+.+-  ....|...  +-++..++.++.
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~--~~~-~~g~kV~li--t~Dt~R~gA~eQL~~~a~~l~v   65 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLAR--QFE-QQGKSVMLA--AGDTFRAAAVEQLQVWGQRNNI   65 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHH--HHH-TTTCCEEEE--CCCTTCHHHHHHHHHHHHHTTC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH--HHH-HCCCcEEEE--ecccccccchhhhhhhhhhcCC
Confidence            3578999999999999998877776  333 223445554  45666664  445566666655

>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=94.81  E-value=0.0066  Score=56.87  Aligned_cols=23  Identities=9%  Similarity=0.078  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+|.++|.+|+||||+|+++.+
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~   24 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTR   24 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>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=94.81  E-value=0.0064  Score=55.02  Aligned_cols=24  Identities=25%  Similarity=0.249  Sum_probs=21.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|.++|++|+||||+|+.+..
T Consensus        13 ~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          13 NPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999998876

>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=94.79  E-value=0.015  Score=56.13  Aligned_cols=113  Identities=15%  Similarity=0.241  Sum_probs=65.0

Q ss_pred             HHHHHHHc-CCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCC-CHHHHHHHHHHHhCC--CCCc
Q 003387          167 ELLDLLIE-GPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEY-DADQILDIVIKFLMP--SSRL  242 (824)
Q Consensus       167 ~l~~~L~~-~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~-~~~~~~~~i~~~l~~--~~~~  242 (824)
                      ++++.+.. +.  -.-++|.|..|+|||||+..+.++. .+.+=+.++++-  +.+.. .+.++.+++.+.--.  ....
T Consensus        57 raID~l~pigk--GQr~~If~~~g~GKt~l~~~i~~~~-~~~~~~v~V~~~--iGer~~ev~~~~~~~~~~~~~~~~~~~  131 (276)
T d2jdid3          57 KVVDLLAPYAK--GGKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAG--VGERTREGNDLYHEMIESGVINLKDAT  131 (276)
T ss_dssp             HHHHHHSCEET--TCEEEEEECTTSSHHHHHHHHHHHH-TTTCSSEEEEEE--ESCCHHHHHHHHHHHHHHTSSCSSSSC
T ss_pred             eeeeeeccccC--CCEEEeeCCCCCCHHHHHHHHHHHH-HhhCCCeEEEEE--eccChHHHHHHHHHHHhcCcccccccc
Confidence            46666654 22  2358999999999999999887731 222334567776  77654 445677777664211  1000


Q ss_pred             cc------ccccC------HHHHHHHHHHhc---CCCeEEEEEecCCCh-hhHHHHHh
Q 003387          243 SE------IMDKN------YEMKKIILHEYL---MTKRYLIVIDDVWSI-DMWDVIQE  284 (824)
Q Consensus       243 ~~------~~~~~------~~~~~~~l~~~L---~~kr~LlVlDdv~~~-~~~~~l~~  284 (824)
                      ..      ...++      ....+..+.+++   ++|.+|+++||+-.. +.+.++..
T Consensus       132 ~~tvvv~~~s~~~~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dsltr~A~A~reis~  189 (276)
T d2jdid3         132 SKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSA  189 (276)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTHHHHHHHHHHHG
T ss_pred             ceEEEEEECCCCCHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchhHHHHHHHHHHH
Confidence            00      00111      122233455665   379999999999654 34555443

>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=94.62  E-value=0.0086  Score=59.89  Aligned_cols=46  Identities=15%  Similarity=0.159  Sum_probs=35.0

Q ss_pred             CCceechhhHHHHHHHHHc----C--------CCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLIE----G--------PPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~~----~--------~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++|-++.++.+...+..    .        ....+-+..+|++|+|||.||+++.+
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~   71 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   71 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhh
Confidence            4678999888888765521    0        11346677899999999999999998

>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=94.60  E-value=0.007  Score=54.90  Aligned_cols=20  Identities=20%  Similarity=0.313  Sum_probs=19.1

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      |+|+|..|+|||||++.+..
T Consensus         3 i~I~G~~G~GKSTLl~~i~~   22 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVE   22 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHh
Confidence            89999999999999999987

>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=94.32  E-value=0.011  Score=57.78  Aligned_cols=35  Identities=14%  Similarity=0.035  Sum_probs=26.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      +.|+|+|-||+||||+|-.+..  .....=..++-|+
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~--~LA~~G~rVllID   36 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTS--GLHAMGKTIMVVG   36 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH--HHHTTTCCEEEEE
T ss_pred             CEEEEECCCcCCHHHHHHHHHH--HHHhCCCcEEEEe
Confidence            7899999999999999988766  4443333455555

>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=94.30  E-value=0.017  Score=57.89  Aligned_cols=65  Identities=14%  Similarity=0.014  Sum_probs=35.3

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCc--eeEEEECCCCCCCCHHHHHHHHHH
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD--CHAWITEPYSNEYDADQILDIVIK  234 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~~~vs~~~~~~~~~~~i~~  234 (824)
                      .++++.+....++..+|||.|.+|+|||||...+...  ....-.  .++-++  .+..++...++.+-.+
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~--~~~~g~~vavlavD--pss~~~ggailgdr~r  107 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGML--LIREGLKVAVIAVD--PSSPVTGGSILGDKTR  107 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHH--HHHTTCCEEEEEEC--CC--------------
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHH--HHhcCCceeeecCC--CceeeeccccccchhH
Confidence            4455555555567999999999999999999888762  222222  344555  6777776666665444

>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=94.26  E-value=0.02  Score=56.08  Aligned_cols=49  Identities=14%  Similarity=0.119  Sum_probs=32.8

Q ss_pred             hHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          164 RMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       164 ~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ++..+++.+...  +-+||.+.|-|||||||+|-.+..  .....=..+.-|+
T Consensus         7 ~~~~~~~~~~~~--~~~iii~sGKGGVGKTT~a~nLA~--~lA~~G~rVllvD   55 (279)
T d1ihua2           7 SLSALVDDIARN--EHGLIMLMGKGGVGKTTMAAAIAV--RLADMGFDVHLTT   55 (279)
T ss_dssp             CHHHHHHHHHTT--SCEEEEEECSTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             cHHHHHHHhhcC--CCEEEEEECCCCCCHHHHHHHHHH--HHHHCCCcEEEEe
Confidence            355566666644  489999999999999998766655  2222222455565

>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=94.15  E-value=0.011  Score=55.64  Aligned_cols=23  Identities=4%  Similarity=0.098  Sum_probs=20.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +-||||.|..|+||||+|+.+.+
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~   24 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQ   24 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999998876

>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=94.03  E-value=0.043  Score=54.03  Aligned_cols=81  Identities=12%  Similarity=0.081  Sum_probs=48.3

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCc--eeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHH
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFD--CHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKK  254 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~  254 (824)
                      ...-+|||.|..|+||||+|+.+..  .....+.  .+.-|+  ...-+-..+.+.+  +.+....+.|  +..|.+.+.
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~--lL~~~~~~~~v~~Is--~D~F~~~~~~l~~--~~~~~~~g~P--es~D~~~L~  149 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQA--LLSRWPEHRRVELIT--TDGFLHPNQVLKE--RGLMKKKGFP--ESYDMHRLV  149 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHH--HHTTSTTCCCEEEEE--GGGGBCCHHHHHH--HTCTTCTTSG--GGBCHHHHH
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHH--HHhhhcCCCceEEEe--eeeeECCchHHHH--hcCCccCCch--HhhhHHHHH
Confidence            4578999999999999999999877  5554442  233444  2322222222221  2222222222  456778888


Q ss_pred             HHHHHhcCCCe
Q 003387          255 IILHEYLMTKR  265 (824)
Q Consensus       255 ~~l~~~L~~kr  265 (824)
                      ..|.....++.
T Consensus       150 ~~L~~lk~g~~  160 (308)
T d1sq5a_         150 KFVSDLKSGVP  160 (308)
T ss_dssp             HHHHHHTTTCS
T ss_pred             HHHHHHHcCCC
Confidence            87777776643

>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=94.01  E-value=0.046  Score=50.52  Aligned_cols=56  Identities=13%  Similarity=-0.004  Sum_probs=35.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHH--HHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDAD--QILDIVIKFLMP  238 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~--~~~~~i~~~l~~  238 (824)
                      +.+||.++|+.|+||||.+.++..  +.+..-..+..++  . ..|...  +-++...+.++.
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~--~~~~~g~kV~lit--~-Dt~R~gA~eQL~~~a~~l~v   66 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLAL--YYKGKGRRPLLVA--A-DTQRPAAREQLRLLGEKVGV   66 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHH--HHHHTTCCEEEEE--C-CSSCHHHHHHHHHHHHHHTC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH--HHHHCCCcEEEEe--c-ccccchHHHHHHHHHHhcCC
Confidence            468999999999999988877765  3333333466665  3 344443  445556666554

>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=94.00  E-value=0.013  Score=53.79  Aligned_cols=23  Identities=22%  Similarity=0.271  Sum_probs=20.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHh
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAY  200 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~  200 (824)
                      ..-+|||+|+.|+||||+|+.+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            36799999999999999998774

>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=93.85  E-value=0.019  Score=57.39  Aligned_cols=37  Identities=16%  Similarity=0.207  Sum_probs=29.7

Q ss_pred             HHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          165 MEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       165 ~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..++++.+.....+..+|||.|.+|+|||||.-++..
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~   73 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGS   73 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHH
Confidence            4455555555556789999999999999999988876

>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=93.80  E-value=0.013  Score=54.02  Aligned_cols=22  Identities=23%  Similarity=0.205  Sum_probs=20.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+|.|.|++|+||||.|+.+++
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~   23 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVE   23 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999988

>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=93.61  E-value=0.017  Score=52.95  Aligned_cols=23  Identities=22%  Similarity=0.202  Sum_probs=20.3

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++++| |+|++|+||||+|+.+..
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
Confidence            46777 789999999999999987

>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=93.52  E-value=0.051  Score=52.44  Aligned_cols=102  Identities=13%  Similarity=0.095  Sum_probs=54.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCC-HHHHHHHHHHHhCC--------CCCcccccccCH
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYD-ADQILDIVIKFLMP--------SSRLSEIMDKNY  250 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~-~~~~~~~i~~~l~~--------~~~~~~~~~~~~  250 (824)
                      .-++|+|..|+|||+|+..+...  ...+-+.++++-  +.+... +.++..++.+.=..        ..+.+.....-.
T Consensus        68 Qr~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~--iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a  143 (276)
T d1fx0a3          68 QRELIIGDRQTGKTAVATDTILN--QQGQNVICVYVA--IGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLA  143 (276)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEE--ESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHH
T ss_pred             ceEeeccCCCCChHHHHHHHHhh--hcccCceeeeee--ecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHH
Confidence            34789999999999999865442  233345666665  555432 22333333221000        001110111112


Q ss_pred             HHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHHhh
Q 003387          251 EMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQEI  285 (824)
Q Consensus       251 ~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~~~  285 (824)
                      ...+..+.+++  ++|++|+++||+-.. ..+.++...
T Consensus       144 ~~~a~tiAEyfrd~G~~Vlll~Dsltr~A~A~rEis~~  181 (276)
T d1fx0a3         144 PYTGAALAEYFMYRERHTLIIYDDLSKQAQAYRQMSLL  181 (276)
T ss_dssp             HHHHHHHHHHHHHTTCEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCceeEEeeccHHHHHHHHHHHHH
Confidence            23344444544  479999999999654 455555543

>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=93.49  E-value=0.056  Score=49.81  Aligned_cols=57  Identities=16%  Similarity=0.019  Sum_probs=36.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCC-CCCHHHHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSN-EYDADQILDIVIKFLMP  238 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~-~~~~~~~~~~i~~~l~~  238 (824)
                      +.+||.++|+.|+||||.+-++..  +.+..=..+..|+  ... .....+-++..++.++.
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~--~~~~~g~kV~lit--~Dt~R~gA~eQL~~~a~~l~i   62 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGR--YYQNLGKKVMFCA--GDTFRAAGGTQLSEWGKRLSI   62 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH--HHHTTTCCEEEEC--CCCSSTTHHHHHHHHHHHHTC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--HHHHCCCcEEEEE--eccccccchhhHhhcccccCc
Confidence            468999999999999998877766  3332213566776  321 23334455555555554

>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=93.44  E-value=0.077  Score=48.99  Aligned_cols=38  Identities=16%  Similarity=-0.003  Sum_probs=22.7

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ....||.++|+.|+||||.+-++....+ ... ..+..|+
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~-~~g-~kV~lit   47 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYK-KKG-FKVGLVG   47 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHH-HTT-CCEEEEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH-HCC-CceEEEE
Confidence            4578999999999999998766665222 222 2466666

>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=93.44  E-value=0.058  Score=49.96  Aligned_cols=57  Identities=14%  Similarity=0.047  Sum_probs=37.2

Q ss_pred             CCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHH--HHHHHHHHHhCC
Q 003387          177 PQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDAD--QILDIVIKFLMP  238 (824)
Q Consensus       177 ~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~--~~~~~i~~~l~~  238 (824)
                      ....||.++|+.|+||||.+-++...  ....=..+..|+  . ..|...  +-++..++.++.
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~--~~~~~~kV~lit--~-Dt~R~gA~eQL~~~a~~l~i   67 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKM--FVDEGKSVVLAA--A-DTFRAAAIEQLKIWGERVGA   67 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHH--HHHTTCCEEEEE--E-CTTCHHHHHHHHHHHHHHTC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCceEEEe--e-cccccchhHHHHHHhhhcCc
Confidence            45789999999999999987777653  322224566665  2 334443  456666666654

>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=93.41  E-value=0.017  Score=57.10  Aligned_cols=36  Identities=11%  Similarity=0.031  Sum_probs=24.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .+.|+|.|-||+||||+|..+..  .....=..++-|+
T Consensus         2 Mr~IaisgKGGVGKTT~a~NLA~--~LA~~G~rVLlID   37 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNLVA--ALAEMGKKVMIVG   37 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             ccEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEe
Confidence            46788999999999998877655  3332222455565

>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=93.40  E-value=0.014  Score=53.38  Aligned_cols=32  Identities=13%  Similarity=0.182  Sum_probs=24.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHA  213 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~  213 (824)
                      +-|.|+|+.|+|||||++.+.+  +....|...+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~--~~~~~~~~~~   33 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFA--EYPDSFGFSV   33 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH--HCTTTEEECC
T ss_pred             CeEEEECCCCCCHHHHHHHHHH--hCCcceeEEE
Confidence            3478999999999999999988  4444565444

>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=93.33  E-value=0.016  Score=54.69  Aligned_cols=22  Identities=18%  Similarity=0.211  Sum_probs=20.9

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .||+|.|++|+||||+|+.+.+
T Consensus         4 piI~I~GppGSGKgT~ak~La~   25 (225)
T d1ckea_           4 PVITIDGPSGAGKGTLCKAMAE   25 (225)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4899999999999999999998

>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=93.33  E-value=0.012  Score=57.14  Aligned_cols=104  Identities=13%  Similarity=0.060  Sum_probs=54.3

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC-----CCC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP-----SSR  241 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~-----~~~  241 (824)
                      ++++.+..=. .-.-++|.|..|+|||||+..+.++.. ..+-++++.+.. +.+.  .++ ..++.+....     ..+
T Consensus        32 r~ID~l~Pig-rGQr~~I~g~~g~GKT~l~~~i~~~~~-~~~~~~v~~~~~-iger--~~e-v~~~~~~~~~~vv~~t~d  105 (289)
T d1xpua3          32 RVLDLASPIG-RGQRGLIVAPPKAGKTMLLQNIAQSIA-YNHPDCVLMVLL-IDER--PEE-VTEMQRLVKGEVVASTFD  105 (289)
T ss_dssp             HHHHHHSCCB-TTCEEEEEECSSSSHHHHHHHHHHHHH-HHCTTSEEEEEE-EEEC--HHH-HHHHHHHCSSEEEEEETT
T ss_pred             eeeeeccccc-CCCeeeEeCCCCCCHHHHHHHHHHHHh-hcCCCeEEEEEe-ecee--HHH-HHhHHhhcceEEEeccCC
Confidence            5777776522 134789999999999999999988422 223333333320 2222  122 2233333322     011


Q ss_pred             cccccccCHHHHHHHHHHhc--CCCeEEEEEecCCCh
Q 003387          242 LSEIMDKNYEMKKIILHEYL--MTKRYLIVIDDVWSI  276 (824)
Q Consensus       242 ~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~  276 (824)
                      .+.....-.......+.+++  +++.+|+++||+-..
T Consensus       106 ~~~~~r~~~~~~a~~iAEyfrd~G~dVLli~Dsltr~  142 (289)
T d1xpua3         106 EPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRL  142 (289)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTTCEEEEEESCHHHH
T ss_pred             CchhHHHHHHHHHHHHHHHHHHhccCceeecCcHHHH
Confidence            01000111122334444544  579999999999543

>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=93.33  E-value=0.025  Score=55.92  Aligned_cols=46  Identities=9%  Similarity=-0.041  Sum_probs=30.9

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHH
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQ  227 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~  227 (824)
                      ..++|.+.|-||+||||+|..+..  ...+.=..+.-|+  .....+...
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~--~lA~~G~rVLlvD--~Dp~~~l~~   52 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAI--RLAEQGKRVLLVS--TDPASNVGQ   52 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHH--HHHHTTCCEEEEE--CCTTCCHHH
T ss_pred             CCeEEEEECCCcChHHHHHHHHHH--HHHHCCCCEEEEe--CCCCCCHHH
Confidence            367889999999999998877766  3333323566777  544444443

>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=93.15  E-value=0.014  Score=53.61  Aligned_cols=23  Identities=13%  Similarity=-0.139  Sum_probs=20.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +..|.|.|++|+||||+|+.+.+
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~   25 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKT   25 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            34577999999999999999987

>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=93.09  E-value=0.02  Score=51.96  Aligned_cols=20  Identities=15%  Similarity=0.154  Sum_probs=18.7

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      |.|.|++|+||||+|+.+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~   22 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVA   22 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999977

>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=92.97  E-value=0.022  Score=53.69  Aligned_cols=22  Identities=18%  Similarity=0.034  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+|+|-|++|+||||+|+.+..
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~   25 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAK   25 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3688999999999999999988

>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=92.96  E-value=0.021  Score=52.31  Aligned_cols=23  Identities=22%  Similarity=0.222  Sum_probs=19.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...|.|.|++|+||||+|+.+..
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La~   28 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRITK   28 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceeEEEECCCCCCHHHHHHHHHH
Confidence            34566889999999999999988

>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=92.93  E-value=0.024  Score=53.72  Aligned_cols=36  Identities=8%  Similarity=0.026  Sum_probs=28.5

Q ss_pred             eEEEEEE-cCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAIL-DSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~-G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      .|||+|+ |-||+||||+|..+..  ...+.=..++.|+
T Consensus         1 ~kvIav~s~KGGvGKTtia~nlA~--~la~~g~~VlliD   37 (232)
T d1hyqa_           1 VRTITVASGKGGTGKTTITANLGV--ALAQLGHDVTIVD   37 (232)
T ss_dssp             CEEEEEEESSSCSCHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             CEEEEEECCCCCChHHHHHHHHHH--HHHhCCCCEEEEe
Confidence            3789998 9999999999998877  4444445678887

>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=92.93  E-value=0.017  Score=52.42  Aligned_cols=32  Identities=9%  Similarity=0.166  Sum_probs=25.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHA  213 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~  213 (824)
                      +.|.|+|+.|+|||||++.+..  +....|...+
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~--~~~~~~~~~v   35 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLIT--KHPDRFAYPI   35 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH--HCTTTEECCC
T ss_pred             CcEEEECCCCCCHHHHHHHHHH--hCCcCeeecc
Confidence            5789999999999999999987  4444564433

>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=92.91  E-value=0.034  Score=51.30  Aligned_cols=23  Identities=22%  Similarity=0.190  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~g   49 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTIST   49 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999987

>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=92.82  E-value=0.023  Score=51.68  Aligned_cols=22  Identities=14%  Similarity=0.122  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.|+|+.|+|||||++.+.+
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~   24 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRE   24 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            5788999999999999999977

>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=92.77  E-value=0.015  Score=53.47  Aligned_cols=28  Identities=14%  Similarity=0.228  Sum_probs=22.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCc
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFD  210 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~  210 (824)
                      -|.|+|+.|+|||||++.+..  +....|.
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~--~~~~~~~   29 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQ--EHSSIFG   29 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHH--HHTTTEE
T ss_pred             eEEEECCCCCCHHHHHHHHHH--hCCCcee
Confidence            367999999999999999987  4444443

>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=92.69  E-value=0.021  Score=51.86  Aligned_cols=21  Identities=24%  Similarity=0.134  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -|.|.|++|+||||+|+.+.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~   22 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAE   22 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            377889999999999999987

>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=92.69  E-value=0.026  Score=51.93  Aligned_cols=24  Identities=29%  Similarity=0.243  Sum_probs=21.7

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ...+|+|-|.-|+||||+|+.+.+
T Consensus         8 kp~~I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1           8 QPFTVLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999998876

>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=92.67  E-value=0.021  Score=51.88  Aligned_cols=21  Identities=14%  Similarity=0.153  Sum_probs=19.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.|.|++|+||||+|+.+.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~   22 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVE   22 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999988

>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=92.58  E-value=0.033  Score=51.83  Aligned_cols=37  Identities=8%  Similarity=-0.123  Sum_probs=27.8

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCCccccC-CCceeEEEE
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNSSYVKH-YFDCHAWIT  216 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~  216 (824)
                      .-.||-+.|++|+||||+|+.+..  +... .....++++
T Consensus        23 kg~vIwltGlsGsGKTTia~~L~~--~l~~~~~~~~~~ld   60 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKSTLAVELEH--QLVRDRRVHAYRLD   60 (208)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH--HHHHHHCCCEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHHHhcCceEEEEc
Confidence            467999999999999999999987  4432 223455665

>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=92.51  E-value=0.023  Score=52.30  Aligned_cols=23  Identities=9%  Similarity=0.134  Sum_probs=21.6

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .++|.|.|++|+||||+|+.+.+
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~   30 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQ   30 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999999987

>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=92.50  E-value=0.031  Score=56.75  Aligned_cols=48  Identities=15%  Similarity=0.149  Sum_probs=34.2

Q ss_pred             ceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccC
Q 003387          158 TVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKH  207 (824)
Q Consensus       158 ~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~  207 (824)
                      +.|.+...-...+.+..+.+.-+.+.++|++|+|||++|+.+.+  ....
T Consensus       133 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~--~~~~  180 (362)
T d1svma_         133 LPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLE--LCGG  180 (362)
T ss_dssp             STTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHH--HHCC
T ss_pred             ccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHH--HcCC
Confidence            33444444444455555655677999999999999999999999  4443

>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=92.41  E-value=0.049  Score=52.21  Aligned_cols=23  Identities=26%  Similarity=0.254  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            45999999999999999999987

>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=92.26  E-value=0.055  Score=50.93  Aligned_cols=122  Identities=13%  Similarity=0.113  Sum_probs=65.0

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEEC--------------CCCCCC------CH--------------
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITE--------------PYSNEY------DA--------------  225 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~--------------~vs~~~------~~--------------  225 (824)
                      .+++|+|+.|.|||||.+.+..-  . ..-...+|+..              -|.|.+      ++              
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl--~-~p~~G~I~~~G~~i~~~~~~~r~ig~v~Q~~~l~~~ltV~enl~~~l~~~~~~  101 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGI--V-KPDRGEVRLNGADITPLPPERRGIGFVPQDYALFPHLSVYRNIAYGLRNVERV  101 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS--S-CCSEEEEEETTEECTTSCTTTSCCBCCCSSCCCCTTSCHHHHHHTTCTTSCHH
T ss_pred             EEEEEECCCCChHHHHHHHHHcC--C-CCCceEEEECCEECCcCCHHHcCceeeccchhhcccchhhHhhhhhhcccCHH
Confidence            37889999999999999999882  1 12233444320              011111      11              


Q ss_pred             --HHHHHHHHHHhCCCCCccc-ccccCHHHH-HHHHHHhcCCCeEEEEEecCCCh-------hhHHHHHhhCCCCCCCcE
Q 003387          226 --DQILDIVIKFLMPSSRLSE-IMDKNYEMK-KIILHEYLMTKRYLIVIDDVWSI-------DMWDVIQEILPDNQNGSR  294 (824)
Q Consensus       226 --~~~~~~i~~~l~~~~~~~~-~~~~~~~~~-~~~l~~~L~~kr~LlVlDdv~~~-------~~~~~l~~~~~~~~~gs~  294 (824)
                        ++-..++++.++....... ....+..+. .-.|.+.|..+.-+|+||.--..       .-|+.+...-.  ..|..
T Consensus       102 ~~~~~v~~~l~~~gl~~~~~~~~~~LSGG~kQRvaiAral~~~P~illlDEPts~LD~~~~~~i~~~i~~l~~--~~g~t  179 (240)
T d2onka1         102 ERDRRVREMAEKLGIAHLLDRKPARLSGGERQRVALARALVIQPRLLLLDEPLSAVDLKTKGVLMEELRFVQR--EFDVP  179 (240)
T ss_dssp             HHHHHHHHHHHTTTCTTTTTCCGGGSCHHHHHHHHHHHHHTTCCSSBEEESTTSSCCHHHHHHHHHHHHHHHH--HHTCC
T ss_pred             HHHHHHHHHHHhcCcHhhhhCChhhCCHHHHHHHHHHHHHhccCCceEecCccccCCHHHHHHHHHHHHHHHH--hcCCe
Confidence              2334556666555321110 122233332 34667777788888899987643       22333332211  12455


Q ss_pred             EEEEechHHHHh
Q 003387          295 VLITLTDIRIII  306 (824)
Q Consensus       295 ilvTtR~~~v~~  306 (824)
                      ||++|.+.+.+.
T Consensus       180 vi~vtHd~~~~~  191 (240)
T d2onka1         180 ILHVTHDLIEAA  191 (240)
T ss_dssp             EEEEESCHHHHH
T ss_pred             EEEEeCCHHHHH
Confidence            777777755544

>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=92.19  E-value=0.047  Score=49.25  Aligned_cols=34  Identities=15%  Similarity=-0.003  Sum_probs=25.8

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +.+.+.-.....+ |.++|.+|+|||||...+...
T Consensus         3 ~~~~~~~~~k~~k-I~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_           3 VLQFLGLYKKTGK-LVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             HHHHHTCTTCCEE-EEEEEETTSSHHHHHHHHSCC
T ss_pred             hHHhccccCCCCE-EEEECCCCCCHHHHHHHHhCC
Confidence            4555555554455 669999999999999998775

>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=92.18  E-value=0.026  Score=56.99  Aligned_cols=46  Identities=17%  Similarity=0.120  Sum_probs=33.5

Q ss_pred             CCCCCceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHh
Q 003387          153 SKSRDTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAY  200 (824)
Q Consensus       153 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~  200 (824)
                      .+-.+++|.+..+..+.-......  ..-|-++|.+|+||||||+.+.
T Consensus         4 ~~f~~I~Gq~~~kral~laa~~~~--~h~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           4 FPFSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHH
T ss_pred             CChhhccCcHHHHHHHHHHHhccC--CCeEEEECCCCccHHHHHHHHH
Confidence            356789999987776554443211  2357899999999999999874

>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=92.15  E-value=0.058  Score=50.90  Aligned_cols=126  Identities=15%  Similarity=0.095  Sum_probs=67.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcc------------cc---C----CC--ceeEEEECCCC--CCCCHH---------
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSY------------VK---H----YF--DCHAWITEPYS--NEYDAD---------  226 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~------------~~---~----~F--~~~~wv~~~vs--~~~~~~---------  226 (824)
                      -.+++|+|..|.|||||++.++.-..            +.   .    .+  ..+.+|..+.+  ...++.         
T Consensus        29 Ge~~~liG~sGaGKSTll~~i~gl~~p~sG~I~~~g~~i~~~~~~~~~~~~~r~ig~v~Q~~~L~~~ltV~eni~~~~~~  108 (240)
T d1g2912          29 GEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKL  108 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTSSCCSEEEEEETTEEEEEGGGTEECCGGGSSEEEECSCCCCCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHHHhcCCCCCCCEEEECCEEecccchhhhcccccccceecccchhhcchhhhhHhhhhhHHH
Confidence            35899999999999999999977311            00   0    00  12334431111  111121         


Q ss_pred             ---------HHHHHHHHHhCCCCCccc-ccccCHHH-HHHHHHHhcCCCeEEEEEecCCCh-------hhHHHHHhhCCC
Q 003387          227 ---------QILDIVIKFLMPSSRLSE-IMDKNYEM-KKIILHEYLMTKRYLIVIDDVWSI-------DMWDVIQEILPD  288 (824)
Q Consensus       227 ---------~~~~~i~~~l~~~~~~~~-~~~~~~~~-~~~~l~~~L~~kr~LlVlDdv~~~-------~~~~~l~~~~~~  288 (824)
                               +...++++.++....... ....+..+ ..-.|.+.|..+.-+|++|.--..       .-|+.+..... 
T Consensus       109 ~~~~~~e~~~~v~~~l~~~~l~~~~~~~p~~LSGGqkQRv~IAraL~~~P~iLllDEPt~~LD~~~~~~i~~~l~~l~~-  187 (240)
T d1g2912         109 RKVPRQEIDQRVREVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQR-  187 (240)
T ss_dssp             TTCCHHHHHHHHHHHHHHHTCGGGTTCCGGGSCHHHHHHHHHHHHHHTCCSEEEEECTTTTSCHHHHHHHHHHHHHHHH-
T ss_pred             cCCCHHHHHHHHHHHHHHcCChhHhcCChhhCCHHHHHHHHHHHHHhcCCCEEEecCCCcccCHHHHHHHHHHHHHHHh-
Confidence                     223445555554211000 12223333 334677778788889999998653       12333332211 


Q ss_pred             CCCCcEEEEEechHHHHh
Q 003387          289 NQNGSRVLITLTDIRIII  306 (824)
Q Consensus       289 ~~~gs~ilvTtR~~~v~~  306 (824)
                       ..|..||++|.+.+.+.
T Consensus       188 -~~g~tvi~vTHd~~~~~  204 (240)
T d1g2912         188 -QLGVTTIYVTHDQVEAM  204 (240)
T ss_dssp             -HHTCEEEEEESCHHHHH
T ss_pred             -ccCCEEEEEcCCHHHHH
Confidence             12677888888877665

>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=92.13  E-value=0.074  Score=50.46  Aligned_cols=56  Identities=13%  Similarity=0.103  Sum_probs=37.0

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC----ceeEEEECCCCCCCCH
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF----DCHAWITEPYSNEYDA  225 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F----~~~~wv~~~vs~~~~~  225 (824)
                      |-++|..+=..-+++-|+|.+|+||||+|.++..+......+    ...+|++  ....++.
T Consensus        23 LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~--~~~~~~~   82 (251)
T d1szpa2          23 LDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID--TEGTFRP   82 (251)
T ss_dssp             HHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEE--SSSCCCG
T ss_pred             HHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEe--ecchHHH
Confidence            334444443346799999999999999998876643332222    4678888  5555543

>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=92.13  E-value=0.093  Score=51.74  Aligned_cols=26  Identities=12%  Similarity=0.003  Sum_probs=21.7

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKH  207 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~  207 (824)
                      .++-++|++|+|||.||+.+..  ++..
T Consensus       124 g~~l~~G~pG~GKT~la~ala~--~~~~  149 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGE--ALGG  149 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHH--HHHT
T ss_pred             ceEEEECCCCccHHHHHHHHHH--HhcC
Confidence            4566789999999999999998  6543

>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=92.02  E-value=0.034  Score=52.99  Aligned_cols=21  Identities=29%  Similarity=0.444  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ||+|+|+.|.|||||...+.+
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~   22 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGR   22 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHH
Confidence            899999999999999999865

>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=91.93  E-value=0.061  Score=51.33  Aligned_cols=23  Identities=26%  Similarity=0.218  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            46999999999999999999987

>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=91.84  E-value=0.047  Score=51.97  Aligned_cols=47  Identities=13%  Similarity=0.012  Sum_probs=36.1

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      |-+.|..+=..-.++-|+|.+|+|||++|.++..  ........++|++
T Consensus        15 LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~--~~~~~~~~~~~is   61 (242)
T d1tf7a2          15 LDEMCGGGFFKDSIILATGATGTGKTLLVSRFVE--NACANKERAILFA   61 (242)
T ss_dssp             HHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHH--HHHTTTCCEEEEE
T ss_pred             HHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHH--HHHHhccccceee
Confidence            3344444433467999999999999999999888  5666777888998

>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=91.81  E-value=0.037  Score=52.27  Aligned_cols=23  Identities=9%  Similarity=0.108  Sum_probs=21.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.++.
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHcC
Confidence            46999999999999999999988

>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=91.79  E-value=0.037  Score=50.14  Aligned_cols=20  Identities=15%  Similarity=0.177  Sum_probs=17.9

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      |.|.|++|+||||+|+.+.+
T Consensus         5 Ivl~G~pGSGKtT~a~~La~   24 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQE   24 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            44779999999999999987

>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=91.66  E-value=0.037  Score=49.99  Aligned_cols=21  Identities=14%  Similarity=-0.016  Sum_probs=18.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .|.|.|++|+||||+|+.+.+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~   22 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIME   22 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            366899999999999999987

>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=91.61  E-value=0.042  Score=51.60  Aligned_cols=23  Identities=13%  Similarity=0.098  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            35899999999999999999976

>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=91.58  E-value=0.044  Score=51.97  Aligned_cols=23  Identities=17%  Similarity=0.192  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -..++|+|..|.|||||++.+..
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35899999999999999999987

>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=91.51  E-value=0.048  Score=51.79  Aligned_cols=23  Identities=17%  Similarity=0.098  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999876

>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=91.36  E-value=0.058  Score=48.34  Aligned_cols=24  Identities=13%  Similarity=0.028  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ---|.|+|.+|+|||||...+.+.
T Consensus        16 ~~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          16 EVRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEEEECCCCCCHHHHHHHHhcC
Confidence            344779999999999999998774

>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=91.36  E-value=0.046  Score=51.52  Aligned_cols=23  Identities=17%  Similarity=0.086  Sum_probs=21.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHHc
Confidence            35899999999999999999877

>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=91.34  E-value=0.045  Score=52.36  Aligned_cols=23  Identities=22%  Similarity=0.186  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            45899999999999999999976

>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=91.28  E-value=0.084  Score=48.72  Aligned_cols=25  Identities=16%  Similarity=0.169  Sum_probs=21.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKH  207 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~  207 (824)
                      .|+|-|+.|+||||+++.+.+  +...
T Consensus         2 lI~ieG~dGsGKST~~~~L~~--~l~~   26 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSG--AFRA   26 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH--HHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH--HHHH
Confidence            589999999999999999887  5543

>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=91.21  E-value=0.044  Score=50.98  Aligned_cols=35  Identities=3%  Similarity=-0.094  Sum_probs=26.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      ..|+|-|+.|+||||+++.+.+  .....-..++++.
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
Confidence            5789999999999999999988  5544433445554

>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=91.12  E-value=0.049  Score=50.62  Aligned_cols=20  Identities=30%  Similarity=0.388  Sum_probs=18.1

Q ss_pred             EEEEEcCCCChHHHHHHHHh
Q 003387          181 VVAILDSIGLDKTAFAGEAY  200 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~  200 (824)
                      +|||+|+.|+||||+|+.+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998653

>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=91.10  E-value=0.046  Score=52.06  Aligned_cols=24  Identities=17%  Similarity=0.171  Sum_probs=22.0

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      +++.|+|-|+-|+||||+++.+.+
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~   24 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            368999999999999999999987

>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=91.00  E-value=0.057  Score=49.45  Aligned_cols=25  Identities=20%  Similarity=0.312  Sum_probs=22.1

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ++..|+|+|.+|+|||||...+.+.
T Consensus        22 ~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHhcCC
Confidence            4667999999999999999999863

>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=91.00  E-value=0.049  Score=51.00  Aligned_cols=23  Identities=26%  Similarity=0.182  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~G   48 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAG   48 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            35899999999999999999987

>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=90.98  E-value=0.038  Score=52.54  Aligned_cols=23  Identities=17%  Similarity=0.270  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .+.|+|-|+.|+||||+|+.+.+
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~   24 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQ   24 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999998877

>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=90.96  E-value=0.052  Score=52.86  Aligned_cols=24  Identities=25%  Similarity=0.165  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|+.|.|||||++.+..-
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCC
Confidence            468999999999999999999873

>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=90.96  E-value=0.045  Score=48.41  Aligned_cols=22  Identities=23%  Similarity=0.117  Sum_probs=19.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCCc
Q 003387          182 VAILDSIGLDKTAFAGEAYNSS  203 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~~  203 (824)
                      |.|+|.+|+|||||.+.+.++.
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            6799999999999999987753

>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=90.94  E-value=0.094  Score=50.81  Aligned_cols=82  Identities=9%  Similarity=0.056  Sum_probs=46.4

Q ss_pred             CCCeEEEEEEcCCCChHHHHHHHHhCCccccCCC--c-eeEEEECCCCCCCCHHHHHHHHHHHhCC-----CCCcccccc
Q 003387          176 PPQLSVVAILDSIGLDKTAFAGEAYNSSYVKHYF--D-CHAWITEPYSNEYDADQILDIVIKFLMP-----SSRLSEIMD  247 (824)
Q Consensus       176 ~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F--~-~~~wv~~~vs~~~~~~~~~~~i~~~l~~-----~~~~~~~~~  247 (824)
                      ....-+|||-|..|+||||||..+..  .+...+  . .++-++  ...-|-..+=...+.+....     ..+.|  ..
T Consensus        24 ~~~P~iIGi~G~qGSGKSTl~~~l~~--~L~~~~~~~~~v~~iS--~DdfY~t~~~r~~L~~~~~~~pl~~~RG~P--gT   97 (286)
T d1odfa_          24 NKCPLFIFFSGPQGSGKSFTSIQIYN--HLMEKYGGEKSIGYAS--IDDFYLTHEDQLKLNEQFKNNKLLQGRGLP--GT   97 (286)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHH--HHHHHHGGGSCEEEEE--GGGGBCCHHHHHHHHHHTTTCGGGSSSCST--TS
T ss_pred             CCCCEEEEeECCCCCCHHHHHHHHHH--HHHHHhCCCcceEeec--cCCCCCCHHHHHHHhhhccccccceecCCC--cc
Confidence            44577999999999999999998876  443332  2 344444  33333222323444444321     11222  34


Q ss_pred             cCHHHHHHHHHHhcCC
Q 003387          248 KNYEMKKIILHEYLMT  263 (824)
Q Consensus       248 ~~~~~~~~~l~~~L~~  263 (824)
                      -|...+.+.|....++
T Consensus        98 hD~~ll~~~l~~l~~~  113 (286)
T d1odfa_          98 HDMKLLQEVLNTIFNN  113 (286)
T ss_dssp             BCHHHHHHHHHHHTC-
T ss_pred             hhHHHHHHHHHHHHhh
Confidence            4666666776666654

>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=90.94  E-value=0.24  Score=46.91  Aligned_cols=56  Identities=14%  Similarity=0.110  Sum_probs=38.9

Q ss_pred             HHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCc----cccCCCceeEEEECCCCCCCCHHH
Q 003387          170 DLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSS----YVKHYFDCHAWITEPYSNEYDADQ  227 (824)
Q Consensus       170 ~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~----~~~~~F~~~~wv~~~vs~~~~~~~  227 (824)
                      ++|..+=..-+++-|+|.+|.|||++|.++..+.    .....+..+.|++  ....++...
T Consensus        28 ~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~   87 (258)
T d1v5wa_          28 KLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFID--TENTFRPDR   87 (258)
T ss_dssp             HHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEE--SSSCCCHHH
T ss_pred             HhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEec--hHHHHHHHH
Confidence            4444444456899999999999999998876421    2334566788998  666655443

>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=90.86  E-value=0.19  Score=47.70  Aligned_cols=57  Identities=19%  Similarity=0.250  Sum_probs=37.9

Q ss_pred             HHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcc----ccCCCceeEEEECCCCCCCCHHHH
Q 003387          170 DLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSY----VKHYFDCHAWITEPYSNEYDADQI  228 (824)
Q Consensus       170 ~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~----~~~~F~~~~wv~~~vs~~~~~~~~  228 (824)
                      ++|..+=..-+++-|+|.+|+||||+|.++..+..    ........+|+.  ....++...+
T Consensus        27 ~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~   87 (254)
T d1pzna2          27 KLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID--TENTFRPERI   87 (254)
T ss_dssp             HHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE--SSSCCCHHHH
T ss_pred             HhhcCCccCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEe--ccchhHHHHH
Confidence            44444434568999999999999999987765211    112345678888  6666665443

>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=90.70  E-value=0.054  Score=50.10  Aligned_cols=22  Identities=9%  Similarity=0.181  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|.|+|+.|+|||||.+.+..
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~   24 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLK   24 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            5788999999999999999987

>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=90.67  E-value=0.056  Score=47.33  Aligned_cols=21  Identities=10%  Similarity=-0.042  Sum_probs=18.7

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||.+.+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            569999999999999998764

>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=90.63  E-value=0.058  Score=48.77  Aligned_cols=34  Identities=24%  Similarity=0.198  Sum_probs=24.1

Q ss_pred             HHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          168 LLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       168 l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +.+.|.......+| .|+|.+|+|||||...+.+.
T Consensus         7 ~~~~l~~~~k~~KI-~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_           7 MFDKLWGSNKELRI-LILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             HHGGGTTCSSCEEE-EEEEETTSSHHHHHHHTCCS
T ss_pred             HHHHHhCCCceEEE-EEECCCCCCHHHHHHHHhcC
Confidence            33333344444554 59999999999999998664

>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=90.50  E-value=0.053  Score=48.07  Aligned_cols=21  Identities=10%  Similarity=0.189  Sum_probs=18.9

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.++|.+|+|||||+..+.++
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988764

>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=90.49  E-value=0.065  Score=50.64  Aligned_cols=35  Identities=11%  Similarity=0.023  Sum_probs=27.4

Q ss_pred             EEEEEE-cCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          180 SVVAIL-DSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~-G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      +||+|+ +-||+||||+|..+..  .....-..++-|+
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~--~la~~g~~VlliD   38 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSV--ALGDRGRKVLAVD   38 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCcHHHHHHHHHH--HHHhCCCCEEEEe
Confidence            689998 7899999999998876  4444444677777

>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=90.46  E-value=0.064  Score=47.52  Aligned_cols=21  Identities=5%  Similarity=0.161  Sum_probs=18.2

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.++|.+|+|||||+..+.++
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999877653

>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=90.29  E-value=0.066  Score=50.72  Aligned_cols=23  Identities=17%  Similarity=0.192  Sum_probs=21.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35999999999999999999988

>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=90.28  E-value=0.08  Score=47.15  Aligned_cols=21  Identities=19%  Similarity=0.284  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            569999999999999987765

>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=90.27  E-value=0.071  Score=47.18  Aligned_cols=21  Identities=14%  Similarity=0.061  Sum_probs=19.0

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||.+.+.++
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            669999999999999998774

>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=90.26  E-value=0.069  Score=50.49  Aligned_cols=125  Identities=12%  Similarity=0.158  Sum_probs=67.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCcc------------ccCCC----ceeEEEECC--CCCCCCHH--------------
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSY------------VKHYF----DCHAWITEP--YSNEYDAD--------------  226 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~------------~~~~F----~~~~wv~~~--vs~~~~~~--------------  226 (824)
                      -.++||+|+.|.|||||.+.+..-.+            +.+.-    ..+.++...  +-....+.              
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~~~p~~G~i~i~G~~i~~~~~~~~~~i~~vpq~~~~~~~ltv~e~l~~~~~~~~~~~  107 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTLIKPSSGIVTVFGKNVVEEPHEVRKLISYLPEEAGAYRNMQGIEYLRFVAGFYASSS  107 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEETTEETTTCHHHHHTTEEEECTTCCCCTTSBHHHHHHHHHHHHCCCH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCCCEEEECcEecccChHHHHhhEeEeeeccccCCCccHHHHHHHHHHhcCCCH
Confidence            46999999999999999999987311            00000    113344310  11122222              


Q ss_pred             ----HHHHHHHHHhCCCCCcc-cccccCHHHH-HHHHHHhcCCCeEEEEEecCCCh-------hhHHHHHhhCCCCCCCc
Q 003387          227 ----QILDIVIKFLMPSSRLS-EIMDKNYEMK-KIILHEYLMTKRYLIVIDDVWSI-------DMWDVIQEILPDNQNGS  293 (824)
Q Consensus       227 ----~~~~~i~~~l~~~~~~~-~~~~~~~~~~-~~~l~~~L~~kr~LlVlDdv~~~-------~~~~~l~~~~~~~~~gs  293 (824)
                          +..+.+++.++...... .....+..+. .-.|...|..+.=+|+||+.-..       .-|+-+.. +.  ..|-
T Consensus       108 ~~~~~~~~~~l~~~~l~~~~~~~~~~lSgG~~qrv~iA~al~~~p~illLDEPt~gLD~~~~~~i~~~i~~-~~--~~g~  184 (238)
T d1vpla_         108 SEIEEMVERATEIAGLGEKIKDRVSTYSKGMVRKLLIARALMVNPRLAILDEPTSGLDVLNAREVRKILKQ-AS--QEGL  184 (238)
T ss_dssp             HHHHHHHHHHHHHHCCGGGGGSBGGGCCHHHHHHHHHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHHH-HH--HTTC
T ss_pred             HHHHHHHHHHHHhCCCHHHHhhhhhhCCHHHHHHHHHHHHHhcCCCEEEecCCCCCCCHHHHHHHHHHHHH-HH--hcCC
Confidence                22333444444321100 0223333333 34667777788888899998643       12333332 22  2366


Q ss_pred             EEEEEechHHHHh
Q 003387          294 RVLITLTDIRIII  306 (824)
Q Consensus       294 ~ilvTtR~~~v~~  306 (824)
                      .||+||.+.+.+.
T Consensus       185 tii~~tH~l~~~~  197 (238)
T d1vpla_         185 TILVSSHNMLEVE  197 (238)
T ss_dssp             EEEEEECCHHHHT
T ss_pred             EEEEEeCCHHHHH
Confidence            7888888877766

>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=90.25  E-value=0.08  Score=50.51  Aligned_cols=45  Identities=20%  Similarity=0.127  Sum_probs=35.4

Q ss_pred             CceechhhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          157 DTVGLDDRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       157 ~~vGr~~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++||....++++.+.+..-...-.-|-|.|..|+|||++|+.+++
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~   45 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHK   45 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHH
Confidence            468888889999888876322222368899999999999999986

>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=90.24  E-value=0.12  Score=46.00  Aligned_cols=33  Identities=15%  Similarity=0.030  Sum_probs=23.9

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ++.+++...+  .+ |.|+|.+|+|||||...+.++
T Consensus         6 ~~~~~~~~k~--~k-I~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           6 RIWRLFNHQE--HK-VIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHTTSC--EE-EEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHhCCCe--EE-EEEECCCCCCHHHHHHHHhcC
Confidence            4454443332  44 669999999999999988775

>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=90.20  E-value=0.072  Score=47.49  Aligned_cols=22  Identities=14%  Similarity=0.196  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .|+|+|..|+|||||.+++.+.
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999763

>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=90.15  E-value=0.091  Score=49.48  Aligned_cols=23  Identities=26%  Similarity=0.189  Sum_probs=21.2

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||++.+..
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            36999999999999999999987

>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=90.06  E-value=0.07  Score=51.07  Aligned_cols=24  Identities=17%  Similarity=0.104  Sum_probs=21.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -.+++|+|+.|.|||||++.+..-
T Consensus        30 Gei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          30 GDVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHCC
Confidence            358999999999999999999883

>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=89.95  E-value=0.072  Score=49.26  Aligned_cols=22  Identities=27%  Similarity=0.320  Sum_probs=19.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+|||.|.-|+||||+|+.+-.
T Consensus         3 ~iIgITG~igSGKStv~~~l~~   24 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFTD   24 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999987643

>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=89.90  E-value=0.068  Score=47.85  Aligned_cols=21  Identities=14%  Similarity=0.237  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||+..+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            679999999999999987664

>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=89.87  E-value=0.096  Score=47.02  Aligned_cols=25  Identities=16%  Similarity=0.186  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ....|+|+|..|+|||||...+.+.
T Consensus         4 ~~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           4 YSGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3568999999999999999999874

>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=89.84  E-value=0.18  Score=48.74  Aligned_cols=115  Identities=12%  Similarity=0.057  Sum_probs=56.3

Q ss_pred             HHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcc-ccCCC----c-eeEEEECCCCCCCCH-HHHHHHHHHHhCCC
Q 003387          167 ELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSY-VKHYF----D-CHAWITEPYSNEYDA-DQILDIVIKFLMPS  239 (824)
Q Consensus       167 ~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~-~~~~F----~-~~~wv~~~vs~~~~~-~~~~~~i~~~l~~~  239 (824)
                      +.++.|..=. .-.-++|.|..|+|||+|+..+.+... ....-    . .++++-  +.+..+. .++.+.+...-...
T Consensus        57 raID~l~pig-~GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~--IGer~~E~~e~~~~~~~~~~~~  133 (285)
T d2jdia3          57 KAVDSLVPIG-RGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVA--IGQKRSTVAQLVKRLTDADAMK  133 (285)
T ss_dssp             HHHHHHSCCB-TTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEE--ESCCHHHHHHHHHHHHHTTCGG
T ss_pred             eEEecccCcc-CCCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEee--eCccHHHHHHHHHHhccccccc
Confidence            4555554311 124578999999999999876654211 11111    1 244555  5555433 34444443321110


Q ss_pred             --------CCcccccccCHHHHHHHHHHhc--CCCeEEEEEecCCCh-hhHHHHHh
Q 003387          240 --------SRLSEIMDKNYEMKKIILHEYL--MTKRYLIVIDDVWSI-DMWDVIQE  284 (824)
Q Consensus       240 --------~~~~~~~~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~-~~~~~l~~  284 (824)
                              .+.+.....-....+..+.+++  ++|.+|+++||+-.. +.+.++..
T Consensus       134 ~tvvv~~ts~~~~~~r~~~~~~a~tiAEyfrd~G~~VLll~Dsltr~A~A~rEis~  189 (285)
T d2jdia3         134 YTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSL  189 (285)
T ss_dssp             GEEEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCEEEEEEETHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCHHHHHHHHHHHHHHHHHHHHcCCcEEEEEcChHHHHHHHHHHHH
Confidence                    0100000000111122333333  689999999999654 34555544

>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=89.73  E-value=0.099  Score=46.82  Aligned_cols=25  Identities=12%  Similarity=0.206  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ....|+|+|..|+|||||..++.+.
T Consensus         4 ~~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           4 YCGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cccEEEEECCCCCCHHHHHHHHhCC
Confidence            3678999999999999999999864

>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=89.70  E-value=0.06  Score=48.54  Aligned_cols=21  Identities=10%  Similarity=0.150  Sum_probs=19.2

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |+|+|.+|+|||||...+.+.
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999763

>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=89.64  E-value=0.083  Score=46.97  Aligned_cols=21  Identities=29%  Similarity=0.271  Sum_probs=18.9

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|..|+|||||++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            678999999999999998774

>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=89.63  E-value=0.077  Score=46.91  Aligned_cols=21  Identities=14%  Similarity=0.184  Sum_probs=18.7

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||++.+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999988754

>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=89.62  E-value=0.08  Score=46.93  Aligned_cols=22  Identities=14%  Similarity=0.273  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||++.+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999887654

>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=89.55  E-value=0.08  Score=46.98  Aligned_cols=21  Identities=19%  Similarity=0.314  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|-+|+|||||.+.+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            668999999999999998764

>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=89.34  E-value=0.18  Score=46.84  Aligned_cols=28  Identities=14%  Similarity=0.010  Sum_probs=23.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHY  208 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~  208 (824)
                      -+.|+|-|+.|+||||+++.+.+  +.+.+
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~--~L~~~   30 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYK--KLQPN   30 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH--HTTTS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHH--HHHhC
Confidence            46799999999999999999987  55443

>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=89.05  E-value=0.088  Score=46.91  Aligned_cols=22  Identities=14%  Similarity=0.311  Sum_probs=19.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||.+.+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999988764

>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=88.93  E-value=0.082  Score=47.04  Aligned_cols=22  Identities=18%  Similarity=0.223  Sum_probs=18.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.++|.+|+|||||...+.++
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999987653

>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=88.89  E-value=0.095  Score=46.82  Aligned_cols=22  Identities=32%  Similarity=0.369  Sum_probs=19.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||...+.++
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999987653

>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=88.84  E-value=0.1  Score=47.23  Aligned_cols=22  Identities=23%  Similarity=0.258  Sum_probs=19.3

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|-+|+|||||+..+.++
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3679999999999999998874

>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=88.79  E-value=0.098  Score=46.46  Aligned_cols=21  Identities=24%  Similarity=0.357  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.++|.+|+|||+|.+...++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            568999999999999988765

>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=88.73  E-value=0.1  Score=46.46  Aligned_cols=21  Identities=10%  Similarity=0.181  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||++.+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            689999999999999887754

>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=88.69  E-value=0.054  Score=52.50  Aligned_cols=23  Identities=9%  Similarity=0.141  Sum_probs=17.5

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..||||.|..|.||||+|+.+.+
T Consensus         4 ~pIIgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           4 HPIISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             SCEEEEESCC---CCTHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHHHH
Confidence            45999999999999999998766

>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=88.67  E-value=0.1  Score=46.25  Aligned_cols=22  Identities=27%  Similarity=0.317  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|-+|+|||||+..+.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999888764

>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=88.61  E-value=0.1  Score=46.18  Aligned_cols=21  Identities=19%  Similarity=0.161  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|-+|+|||||+..+.++
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999987654

>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=88.60  E-value=0.071  Score=50.91  Aligned_cols=23  Identities=17%  Similarity=0.062  Sum_probs=20.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -..++|+|..|.|||||++.+..
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHh
Confidence            45899999999999999999875

>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=88.53  E-value=0.26  Score=48.69  Aligned_cols=104  Identities=15%  Similarity=0.170  Sum_probs=58.7

Q ss_pred             EEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCcccccccCHHHHHHHHHHh
Q 003387          181 VVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIMDKNYEMKKIILHEY  260 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~  260 (824)
                      -|.|+|..|.||||+.+++.+  .+... ..++-+.  -..+...           ..............-...+.++..
T Consensus       168 nili~G~tgSGKTT~l~al~~--~i~~~-~rivtiE--d~~El~l-----------~~~~~~~~~~~~~~~~~~~ll~~~  231 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIME--FIPKE-ERIISIE--DTEEIVF-----------KHHKNYTQLFFGGNITSADCLKSC  231 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGG--GSCTT-CCEEEEE--SSCCCCC-----------SSCSSEEEEECBTTBCHHHHHHHH
T ss_pred             CEEEEeeccccchHHHHHHhh--hcccc-cceeecc--chhhhhc-----------ccccccceeccccchhHHHHHHHH
Confidence            378899999999999999988  44332 2233332  1111110           000011111111112345667778


Q ss_pred             cCCCeEEEEEecCCChhhHHHHHhhCCCCCCCcEEEEEechHH
Q 003387          261 LMTKRYLIVIDDVWSIDMWDVIQEILPDNQNGSRVLITLTDIR  303 (824)
Q Consensus       261 L~~kr~LlVlDdv~~~~~~~~l~~~~~~~~~gs~ilvTtR~~~  303 (824)
                      |+...=-||+..+.+.+.|..+. ....++.|  ++.|....+
T Consensus       232 lR~~pd~iivgEiR~~ea~~~l~-a~~tGh~g--~~tT~Ha~s  271 (323)
T d1g6oa_         232 LRMRPDRIILGELRSSEAYDFYN-VLCSGHKG--TLTTLHAGS  271 (323)
T ss_dssp             TTSCCSEEEESCCCSTHHHHHHH-HHHTTCSC--EEEEECCSS
T ss_pred             hccCCCcccCCccCchhHHHHHH-HHHhcCCc--EEEEECCCC
Confidence            88777779999999988887654 44444445  355544333

>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=88.49  E-value=0.23  Score=47.49  Aligned_cols=40  Identities=15%  Similarity=0.199  Sum_probs=30.9

Q ss_pred             hhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          163 DRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       163 ~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..+.++...+.......--|.++|..|+|||||...+++.
T Consensus        16 ~~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          16 TKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            4555666666665545566789999999999999999875

>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=88.46  E-value=0.17  Score=46.78  Aligned_cols=35  Identities=11%  Similarity=0.073  Sum_probs=26.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCccccCC-CceeEEEE
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSSYVKHY-FDCHAWIT  216 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~~~~~~-F~~~~wv~  216 (824)
                      +.|+|-|+.|+||||+++.+.+  ..... +..+++..
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
Confidence            4688999999999999999987  44333 44555554

>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=88.32  E-value=0.087  Score=49.59  Aligned_cols=23  Identities=9%  Similarity=0.179  Sum_probs=21.0

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -.+++|+|..|.|||||.+.+..
T Consensus        25 Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          25 GEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35999999999999999999876

>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=88.32  E-value=0.11  Score=46.34  Aligned_cols=21  Identities=19%  Similarity=0.289  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||...+.++
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788999999999999887654

>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=88.32  E-value=0.1  Score=46.22  Aligned_cols=22  Identities=9%  Similarity=0.217  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||+..+.++
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3679999999999999988764

>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=88.32  E-value=0.11  Score=46.10  Aligned_cols=24  Identities=17%  Similarity=0.156  Sum_probs=19.8

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ..-|.|+|..|+|||||...+.++
T Consensus         4 ~~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           4 SRKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCcCHHHHHHHHHhC
Confidence            345788999999999999987653

>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=88.25  E-value=0.11  Score=45.93  Aligned_cols=21  Identities=14%  Similarity=0.297  Sum_probs=18.8

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||...+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788999999999999988764

>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=88.22  E-value=0.11  Score=47.45  Aligned_cols=22  Identities=9%  Similarity=0.194  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||+..+.++
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            3779999999999999987764

>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=88.19  E-value=0.12  Score=45.82  Aligned_cols=21  Identities=24%  Similarity=0.336  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|-.|+|||+|.+.+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            679999999999999987654

>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=88.14  E-value=3.1  Score=38.05  Aligned_cols=141  Identities=15%  Similarity=0.074  Sum_probs=73.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCCc-------------cccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCCCCCccccc
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNSS-------------YVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMPSSRLSEIM  246 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~~-------------~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~~~~~~~~~  246 (824)
                      +++.|.|+...||||+.+.|.-..             -.-..||. ++..  +...-++..                  .
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~-I~~~--~~~~d~~~~------------------~   94 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDG-IYTR--IGASDDLAG------------------G   94 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSE-EEEE--CCC------------------------C
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecce-EEEE--ECCCccccC------------------C
Confidence            378899999999999999875421             11123442 3443  222111100                  0


Q ss_pred             ccCHHHHHHHHHHhc--CCCeEEEEEecCCChh--------hHHHHHhhCCCCCCCcEEEEEechHHHHhh---------
Q 003387          247 DKNYEMKKIILHEYL--MTKRYLIVIDDVWSID--------MWDVIQEILPDNQNGSRVLITLTDIRIIIS---------  307 (824)
Q Consensus       247 ~~~~~~~~~~l~~~L--~~kr~LlVlDdv~~~~--------~~~~l~~~~~~~~~gs~ilvTtR~~~v~~~---------  307 (824)
                      ......-..++...+  .+++.|+++|.+....        .|. +...+.  ..++++++||...++...         
T Consensus        95 ~StF~~el~~~~~il~~~~~~sLvliDE~~~gT~~~eg~ala~a-ile~L~--~~~~~~i~tTH~~eL~~l~~~~~~~~~  171 (224)
T d1ewqa2          95 KSTFMVEMEEVALILKEATENSLVLLDEVGRGTSSLDGVAIATA-VAEALH--ERRAYTLFATHYFELTALGLPRLKNLH  171 (224)
T ss_dssp             CSHHHHHHHHHHHHHHHCCTTEEEEEESTTTTSCHHHHHHHHHH-HHHHHH--HHTCEEEEECCCHHHHTCCCTTEEEEE
T ss_pred             ccHHHHhHHHHHHHhccCCCCcEEeecccccCcchhhhcchHHH-HHHHHh--hcCcceEEeeechhhhhhhhcccceEE
Confidence            011111223333333  3688999999998652        122 122221  236889999999888761         


Q ss_pred             --cccccCCc-------CcCccccchhhHHHhcCCCchhHHHHHhHH
Q 003387          308 --FQFEDGEN-------MRLDLVPTGGPLRATYKGRPFLILYHGSIS  345 (824)
Q Consensus       308 --f~~~~~~~-------~~~~~~~~~~~i~~~c~GlPlai~~~~~~l  345 (824)
                        .....++.       ....-...|-++++++ |+|-.+.--|..+
T Consensus       172 ~~~~~~~~~~~f~Ykl~~G~~~~s~ai~iA~~~-Glp~~II~rA~~i  217 (224)
T d1ewqa2         172 VAAREEAGGLVFYHQVLPGPASKSYGVEVAAMA-GLPKEVVARARAL  217 (224)
T ss_dssp             EEEECCSSSCEEEEEEEESCCSSCCHHHHHHHT-TCCHHHHHHHHHH
T ss_pred             EEEEEeCCCeEEEEEEeeCCCCccHHHHHHHHh-CcCHHHHHHHHHH
Confidence              00011000       0011135677788776 6888777666543

>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=88.11  E-value=0.083  Score=47.76  Aligned_cols=21  Identities=10%  Similarity=0.102  Sum_probs=19.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -|+|+|.+|+|||||...+.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            389999999999999999865

>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=88.07  E-value=0.11  Score=46.32  Aligned_cols=22  Identities=9%  Similarity=0.199  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.++|.+|+|||||+..+.++
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999987643

>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=88.03  E-value=0.11  Score=46.74  Aligned_cols=22  Identities=5%  Similarity=0.045  Sum_probs=20.0

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|+|+|.+|+|||||..++.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999874

>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=87.95  E-value=0.12  Score=46.23  Aligned_cols=23  Identities=17%  Similarity=0.236  Sum_probs=19.4

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      --|.|+|.+|+|||||...+.++
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34679999999999999887664

>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=87.53  E-value=0.12  Score=46.13  Aligned_cols=22  Identities=14%  Similarity=0.270  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|..|+|||||+..+.++
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987664

>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=87.52  E-value=0.43  Score=43.74  Aligned_cols=56  Identities=13%  Similarity=0.102  Sum_probs=33.7

Q ss_pred             HHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCccc----cCCCceeEEEECCCCCCCCHHH
Q 003387          170 DLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYV----KHYFDCHAWITEPYSNEYDADQ  227 (824)
Q Consensus       170 ~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~----~~~F~~~~wv~~~vs~~~~~~~  227 (824)
                      ++|..+=..-+++-|.|.+|+||||+|..+..+...    ...+....++.  .........
T Consensus        14 ~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~   73 (242)
T d1n0wa_          14 KLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYID--TEGTFRPER   73 (242)
T ss_dssp             HHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEE--SSSCCCHHH
T ss_pred             HhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhh--hhhhhHHHH
Confidence            344333233579999999999999999877653211    12233455666  554544443

>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=87.51  E-value=0.13  Score=44.96  Aligned_cols=22  Identities=18%  Similarity=0.034  Sum_probs=19.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.++|.+|+|||||...+.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999988764

>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=87.38  E-value=0.18  Score=50.88  Aligned_cols=46  Identities=15%  Similarity=0.117  Sum_probs=33.3

Q ss_pred             CCceechhhHHHHHHHHH----------------------------cCCCCeEEEEEEcCCCChHHHHHHHHhC
Q 003387          156 RDTVGLDDRMEELLDLLI----------------------------EGPPQLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       156 ~~~vGr~~~~~~l~~~L~----------------------------~~~~~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ..+||-++.++.+-..+-                            +.+.....+-.+|+.|||||.||+.+..
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~   90 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAK   90 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHh
Confidence            467888888777654431                            1122356688899999999999999865

>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=87.15  E-value=0.14  Score=45.35  Aligned_cols=21  Identities=10%  Similarity=0.191  Sum_probs=18.1

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|..|+|||||...+.++
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999987654

>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=87.14  E-value=0.14  Score=45.30  Aligned_cols=24  Identities=25%  Similarity=0.264  Sum_probs=19.9

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +--|.|+|-+|+|||||++.+.++
T Consensus         4 ~~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCcCHHHHHHHHHhC
Confidence            345789999999999999987654

>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=87.07  E-value=0.23  Score=44.07  Aligned_cols=24  Identities=13%  Similarity=0.054  Sum_probs=20.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .++ |.|+|.+|+|||||.+.+.++
T Consensus        12 ~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          12 EMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhcC
Confidence            466 559999999999999999875

>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=87.03  E-value=0.14  Score=46.26  Aligned_cols=22  Identities=14%  Similarity=0.084  Sum_probs=19.2

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||.+.+.++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3789999999999999887664

>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=86.98  E-value=0.15  Score=45.41  Aligned_cols=21  Identities=19%  Similarity=0.276  Sum_probs=18.4

Q ss_pred             EEEEEcCCCChHHHHHHHHhC
Q 003387          181 VVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -|.++|.+|+|||||++.+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            367999999999999998765

>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=86.95  E-value=0.16  Score=48.12  Aligned_cols=22  Identities=9%  Similarity=-0.035  Sum_probs=20.3

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|||.|..|+||||+|+.+.+
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999998865

>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=86.95  E-value=0.15  Score=45.63  Aligned_cols=21  Identities=14%  Similarity=0.268  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||.+.+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999987654

>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=86.87  E-value=0.16  Score=45.02  Aligned_cols=22  Identities=18%  Similarity=0.232  Sum_probs=18.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|-+|+|||||+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999987553

>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=86.86  E-value=0.13  Score=47.35  Aligned_cols=23  Identities=13%  Similarity=0.016  Sum_probs=20.2

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +-|.|+|.+|+|||||..++.++
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999998764

>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=86.85  E-value=0.15  Score=45.89  Aligned_cols=22  Identities=23%  Similarity=0.274  Sum_probs=19.6

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|+|+|..|+|||||..++.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4799999999999999998864

>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=86.78  E-value=0.1  Score=46.40  Aligned_cols=21  Identities=19%  Similarity=0.332  Sum_probs=17.4

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||...+.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999987764

>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=86.65  E-value=0.15  Score=45.54  Aligned_cols=22  Identities=14%  Similarity=0.016  Sum_probs=18.8

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||+..+.++
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678999999999999887664

>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=86.45  E-value=0.16  Score=44.41  Aligned_cols=21  Identities=14%  Similarity=0.109  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |+|+|.+|+|||||..++.+.
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999998753

>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=86.42  E-value=0.15  Score=46.39  Aligned_cols=19  Identities=16%  Similarity=0.211  Sum_probs=17.1

Q ss_pred             EEEEEcCCCChHHHHHHHH
Q 003387          181 VVAILDSIGLDKTAFAGEA  199 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v  199 (824)
                      -|.|+|.+|+|||||+...
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3679999999999999887

>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=86.42  E-value=0.16  Score=44.73  Aligned_cols=21  Identities=14%  Similarity=0.118  Sum_probs=18.1

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|.+|+|||||...+.++
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            568999999999999987654

>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=86.37  E-value=0.17  Score=44.92  Aligned_cols=21  Identities=14%  Similarity=0.349  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.++|-.|+|||||++.+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999988764

>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=86.18  E-value=0.15  Score=47.64  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=22.6

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .+.|..|.|.-|.|||||.+.+.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            4789999999999999999999874

>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=86.16  E-value=0.17  Score=45.50  Aligned_cols=21  Identities=33%  Similarity=0.457  Sum_probs=18.6

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|..|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999987764

>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=86.11  E-value=0.17  Score=45.40  Aligned_cols=21  Identities=14%  Similarity=0.112  Sum_probs=18.4

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.++|..|+|||+|++.+.++
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999887664

>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=86.03  E-value=0.17  Score=45.82  Aligned_cols=21  Identities=10%  Similarity=0.017  Sum_probs=18.1

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.++|-+|+|||||.+....+
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            678999999999999887554

>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=86.02  E-value=0.23  Score=44.57  Aligned_cols=23  Identities=9%  Similarity=0.003  Sum_probs=19.6

Q ss_pred             EEEEEEcCCCChHHHHHHHHhCC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      --|.|+|.+|+|||||.+.+.++
T Consensus         6 iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35789999999999999887664

>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=85.98  E-value=0.18  Score=46.28  Aligned_cols=22  Identities=14%  Similarity=0.043  Sum_probs=19.9

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .|.|+|.+|+|||||...+.+.
T Consensus         5 ~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           5 SIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            6799999999999999999764

>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=85.96  E-value=0.28  Score=45.34  Aligned_cols=36  Identities=17%  Similarity=0.209  Sum_probs=27.7

Q ss_pred             hhHHHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCc
Q 003387          163 DRMEELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSS  203 (824)
Q Consensus       163 ~~~~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~  203 (824)
                      ..++.|.++|.+     +...++|..|||||||..++..+.
T Consensus        84 ~g~~~L~~~l~~-----kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          84 MGIEELKEYLKG-----KISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             TTHHHHHHHHSS-----SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             hhHhhHHHHhcC-----CeEEEECCCCCCHHHHHHhhcchh
Confidence            336677777732     366789999999999999998753

>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=85.87  E-value=0.17  Score=45.07  Aligned_cols=22  Identities=18%  Similarity=0.279  Sum_probs=18.5

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|-+|+|||||+..+.++
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999776553

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-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: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.61  E-value=1.3  Score=41.11  Aligned_cols=23  Identities=9%  Similarity=-0.018  Sum_probs=20.4

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      -+++.|.|+.+.||||+.|.|.-
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l   63 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTAL   63 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHH
Confidence            47899999999999999998755

>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=85.26  E-value=0.18  Score=44.99  Aligned_cols=22  Identities=9%  Similarity=0.135  Sum_probs=19.1

Q ss_pred             EEEEEcCCCChHHHHHHHHhCC
Q 003387          181 VVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       181 vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      -|.|+|.+|+|||||...+.++
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999987664

>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=85.03  E-value=0.19  Score=47.45  Aligned_cols=70  Identities=14%  Similarity=0.049  Sum_probs=41.1

Q ss_pred             HHHHHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCCcccc--------------CCCceeEEEECCCCCCCCHHHHHHH
Q 003387          166 EELLDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNSSYVK--------------HYFDCHAWITEPYSNEYDADQILDI  231 (824)
Q Consensus       166 ~~l~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~~~~~--------------~~F~~~~wv~~~vs~~~~~~~~~~~  231 (824)
                      ..|-++|..+=..-.++-|.|.+|+||||+|..+..+.-..              .....+.|++  ....++.. ....
T Consensus        21 ~~LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~--~e~~~~~~-~~~~   97 (258)
T d2i1qa2          21 SELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYID--TEGTFRPE-RIMQ   97 (258)
T ss_dssp             HHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEE--SSSCCCHH-HHHH
T ss_pred             HHHHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhcCceEEEEE--ecCCcCHH-HHHH
Confidence            33444444433345899999999999999998886532111              1123467887  55555533 3344


Q ss_pred             HHHHhCC
Q 003387          232 VIKFLMP  238 (824)
Q Consensus       232 i~~~l~~  238 (824)
                      +...+..
T Consensus        98 ~~~~~~~  104 (258)
T d2i1qa2          98 MAEHAGI  104 (258)
T ss_dssp             HHHHHTC
T ss_pred             HHhhcch
Confidence            4554443

>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=85.03  E-value=0.17  Score=45.40  Aligned_cols=25  Identities=16%  Similarity=-0.019  Sum_probs=21.5

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      +...|+|+|.+++|||||.+++.+.
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3567999999999999999988764

>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=84.85  E-value=0.21  Score=45.26  Aligned_cols=21  Identities=10%  Similarity=0.058  Sum_probs=18.0

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.++|-.|+|||+|+..+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999877654

>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=84.52  E-value=0.23  Score=45.85  Aligned_cols=22  Identities=9%  Similarity=-0.035  Sum_probs=19.3

Q ss_pred             EEEEEEcCC-CChHHHHHHHHhC
Q 003387          180 SVVAILDSI-GLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~g-GvGKTtLa~~v~~  201 (824)
                      +.+-|.|-| ||||||++-.+..
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~   24 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQ   24 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHH
Confidence            568899998 9999999987776

>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=84.25  E-value=0.44  Score=47.07  Aligned_cols=29  Identities=7%  Similarity=-0.044  Sum_probs=24.1

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYF  209 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F  209 (824)
                      +-.|.|=|.-|+||||+++.+.+  ......
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~--~l~~~~   34 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMAS--AASGGS   34 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHS--GGGCSS
T ss_pred             eEEEEEECCccCCHHHHHHHHHH--HhccCC
Confidence            56789999999999999999999  444443

>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=84.15  E-value=0.23  Score=43.08  Aligned_cols=25  Identities=16%  Similarity=0.235  Sum_probs=22.2

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      .-.+|.+.|-=|+||||++|.+.+.
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~   56 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhh
Confidence            4569999999999999999999873

>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=83.87  E-value=0.23  Score=45.04  Aligned_cols=21  Identities=14%  Similarity=0.109  Sum_probs=18.2

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.++|-+|+|||||.+.+.++
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            678999999999999987553

>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=83.12  E-value=0.55  Score=45.13  Aligned_cols=34  Identities=21%  Similarity=0.189  Sum_probs=28.2

Q ss_pred             HHHHHcCCCCeEEEEEEcCCCChHHHHHHHHhCC
Q 003387          169 LDLLIEGPPQLSVVAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       169 ~~~L~~~~~~~~vi~I~G~gGvGKTtLa~~v~~~  202 (824)
                      ++.|..-++.+.||+|+|.-+.||+||+..++..
T Consensus        22 l~~l~~~~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          22 LKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             HHHHHTCCSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             HHHHHcCCCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            3455555557999999999999999999999874

>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=82.70  E-value=0.19  Score=44.64  Aligned_cols=21  Identities=14%  Similarity=0.177  Sum_probs=8.3

Q ss_pred             EEEEcCCCChHHHHHHHHhCC
Q 003387          182 VAILDSIGLDKTAFAGEAYNS  202 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~~  202 (824)
                      |.|+|-+|+|||||...+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999877654

>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=82.57  E-value=0.29  Score=45.54  Aligned_cols=22  Identities=9%  Similarity=0.015  Sum_probs=18.8

Q ss_pred             EEEEEEcCCCChHHHHHHHHhC
Q 003387          180 SVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       180 ~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      .-|.++|.+|+|||||++.+..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999988754

>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=82.47  E-value=0.11  Score=45.50  Aligned_cols=20  Identities=15%  Similarity=0.283  Sum_probs=18.5

Q ss_pred             EEEEcCCCChHHHHHHHHhC
Q 003387          182 VAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       182 i~I~G~gGvGKTtLa~~v~~  201 (824)
                      |+++|.+|+|||||..++.+
T Consensus         3 I~liG~~n~GKSSLin~l~g   22 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLN   22 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999865

>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=82.37  E-value=0.23  Score=49.20  Aligned_cols=36  Identities=17%  Similarity=0.039  Sum_probs=26.7

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEE
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWIT  216 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~  216 (824)
                      +-.|+|=|.-|+||||+++.+.+  .....-..++++.
T Consensus         5 ~lrI~IEG~iGsGKSTl~~~L~~--~l~~~g~~v~~~~   40 (331)
T d1osna_           5 VLRIYLDGAYGIGKTTAAEEFLH--HFAITPNRILLIG   40 (331)
T ss_dssp             EEEEEEEESSSSCTTHHHHHHHH--TTTTSGGGEEEEC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH--HHhhcCCceEEEe
Confidence            44689999999999999999988  4433334455554

>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=82.02  E-value=0.33  Score=46.59  Aligned_cols=24  Identities=21%  Similarity=0.198  Sum_probs=21.4

Q ss_pred             CeEEEEEEcCCCChHHHHHHHHhC
Q 003387          178 QLSVVAILDSIGLDKTAFAGEAYN  201 (824)
Q Consensus       178 ~~~vi~I~G~gGvGKTtLa~~v~~  201 (824)
                      ++|-|+|+|-+|.|||||+-++..
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hceEEEEEeCCCCCHHHHHHHHHH
Confidence            578899999999999999988754

>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=80.46  E-value=0.84  Score=43.71  Aligned_cols=55  Identities=11%  Similarity=-0.004  Sum_probs=36.3

Q ss_pred             eEEEEEEcCCCChHHHHHHHHhCCccccCCCceeEEEECCCCCCCCHHHHHHHHHHHhCC
Q 003387          179 LSVVAILDSIGLDKTAFAGEAYNSSYVKHYFDCHAWITEPYSNEYDADQILDIVIKFLMP  238 (824)
Q Consensus       179 ~~vi~I~G~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~vs~~~~~~~~~~~i~~~l~~  238 (824)
                      -.++.|.|.+|+||||+|..+..+.-....+ .+++++    -+.+..++...++.....
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~-~v~~~s----~E~~~~~~~~r~~~~~~~   89 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAM----LEESVEETAEDLIGLHNR   89 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEE----SSSCHHHHHHHHHHHHTT
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhhhhccc-ceeEee----eccchhhHHhHHHHHhhc
Confidence            3578899999999999998876521122222 344544    345677777777776654