Citrus Sinensis ID: 003455

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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-------82
Protein Sequence
MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGGGFMS
Secondary Structure (PSIPRED)
cEEEEEHHHHHHHHHHHHHcccccccccccccccEEEEEEEEcccccccccEEEEcccccHHHHHHHHcccccccccccHHHHHHHHHHHHHHHcccccccccccccccccEEEEEEcccccccccccccccccccccccccccccccccccHHHHHHHHccccEEEEEEccccccHHHHHHHHcccccccccccccccccccEEEEEccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccEEEEEccccccccccHHHHccccccHHHHHHHHccccccccEEccccEEEEEcccccHHHHHHHHHHcccccccccccEEEEcccccHHHHccccccccEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHcHHHHHHHHcHHHHHHcccHHHHHHHcHHHHHHHccHHHHHHHHcHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEEEEHEEEEEEHHccccccccccccccccEEEEEEEcccccccHHHEEcccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccHHHHHHHHHHccccEEEEEEEcccHcHHHHHHHcccccccccccccHHHcccccEEEEEcccHHHHHHHHccccccccccccccEEEEEcccccccccccccccccccccccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccHHHEcccccHHcccccccccccccccccccHHHHHHHHHHHHHHHHHcHHHHccHccccccccccccEEEEcccHcccccccccccccccEccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccccEEEEEEEccccccccHHHHccccccHEEEEEEcHHHccccccccccEEEEEEccccccHHHHHHHcccEEEEEccccEEEEEcccccccEEEEEccccEEEEccccccHHHHHHcHHccccccHHHHHHHcccccHHHcccccccccHHccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccHHHHHHHcccccccccccccccccc
Coil and Loop (DISEMBL)
MCIYFYAYSKLSLYFHRCfcvnelagqktsasNVELSLVTFNTHGsycaclvqrsgwtkDVDIFLHWLstipfagggfndAAIAEGLSEALMMFsvapngsqnqqnvdgqRHCILVaasnphplptpvyrpqmqnldqnenNEAQAESRLSDAETVAKSFVQCSVslsvicpkqlpkLTAIYNAakrnpraadppvdnsknphFLVLISENFMEARAAlsrpgvanlapnqnpvkmdiapvtsvtgpaptsipsvnginrppisvgnvptatvkvepstvtsmvngptfphipsvprpasqgvpslqtsspsstsqemitsgdsvpevkplvsgmsqplrpmapaaaNVNILNNLSQARQVMNNAaltggtsiglqsmgqtpmaMHMSNMIssgmassvptsqpvfssaqsgitsiggsgtltgtsqvpqnsglnsftsapsnlsgnsnpsisqpmgtlqggasmgqsvgmsqgnhsggqmvQNGISMNqnmmsglgpsgvssgtgtmiptpgmsqqaqsgmqplsvnnnTAVNMQLSQQTSSALHSSQSKYVKVWegslsgqrqgqpvFITKlegyrsasasetlaanwpptMQIVRLISQdhmnnkqyvgkaDFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIgmlfpgdmvvfkpqisSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLqqqqqipqlqqqsmpqlqqqqqlpqlqqqqqlpqmqqqqqlpqlqqqqqlsqpqqmvgsgmgqgyvqgpgrtqlvsqgqvssqgapnipgggfms
Flexible Loop (DISEMBL)
MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVslsvicpkqlPKLTAIYNAAKRnpraadppvdnskNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTsipsvnginrppiSVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEgslsgqrqgqPVFITKLEGYRSASASetlaanwppTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSqgqvssqgapnipgggfms
Low Complexity Region (SEG)
MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVpslqtsspsstsqEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQsgitsiggsgtltgtsQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKpqissqqqqqlqqqqqqqqhqqmqsqlqhqqlsqlqqqqqqlpqlqqqipqlqqqqqipqlqqqsmpqlqqqqqlpqlqqqqqlpqmqqqqqlpqlqqqqqlsqpqqMVGSGMGQGYVQGPGRTQLvsqgqvssqgAPNIPGGGFMS
Disordered region (IsUnstruct)
*CIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSV**************RHCILVA**************************************VAKSFVQCSVSLSVICPKQLPKLTAIYNA******************HFLVLISENFMEAR**************************************************************************************************************************************IL********************************************************************************************************************************************************************************************************VKVWE**********PVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK***************************************************************************************************************************************************
Disordered Region (DISOPRED)
MCIYFYAYSKLSLYFHRCFCVNELAGQK**ASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMF*****************HCILVAASNPHPLPTPVYR****************ESRLSDAETVAKSFVQCSVSLSVICPKQLPKL*********************KNPHFLVLISEN************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************IVRL***************DFLVFR***********************************************************************************************************************************************************************************************P******
Disordered Region (DISEMBL)
MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQ****************TVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVP***************************SVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSG*****************GITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTP**********QPLSVNNNTAVNMQ****************VKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKP**************************************************************************************************************GMGQGYVQGPGRTQ**********GAPNIPGGGFMS
Disordered Region (DISPRO)
MCIYFYAYSKLSLYFHRCFCVNELA***TSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKR*PRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVT********************GNVPTATVKVEPSTVTSMVNGPTFPHIPS*****************************SVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMS************TSQPV************GSGTLTGTSQV*********************PSISQPMGT*****SM**S****************GI*MN*NMMSGL**********TMIPTPGMSQ********************************QSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQ***************************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNxxxxxxxxxxxxxxxxxxxxxAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLxxxxxxxxxxxxxxxxxxxxxxxxxxxxQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGGGFMS
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	818	2.2.26 [Sep-21-2011]
Q7XYY2	836	Mediator of RNA polymeras	yes	no	0.793	0.776	0.651	0.0
Q6GP15	801	Mediator of RNA polymeras	N/A	no	0.207	0.212	0.290	8e-12
A4IHD9	805	Mediator of RNA polymeras	yes	no	0.207	0.211	0.295	1e-11
Q9VDR1	863	Mediator of RNA polymeras	yes	no	0.157	0.149	0.272	4e-05

>sp|Q7XYY2|MED25_ARATH Mediator of RNA polymerase II transcription subunit 25 OS=Arabidopsis thaliana GN=MED25 PE=1 SV=1

 Score =  820 bits (2118), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 442/678 (65%), Positives = 528/678 (77%), Gaps = 29/678 (4%)

Query: 6   YAYSKLSLYFH---RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVD 62
           Y  + +S Y     R FC +EL G++   S VELSLV FN+HGSYCACLVQRSGWT+DVD
Sbjct: 21  YWQTIVSDYLEKIIRSFCGSELNGERNPVSTVELSLVIFNSHGSYCACLVQRSGWTRDVD 80

Query: 63  IFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH 122
           IFLHWLS+I F GGGFN+ A AEGL+EALMMFS  P   Q Q + D +RHCIL+ ASNPH
Sbjct: 81  IFLHWLSSIQFGGGGFNEVATAEGLAEALMMFS--PPSGQAQPSNDLKRHCILITASNPH 138

Query: 123 PLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIY 182
            LPTPVYRP++QN+++NEN +AQAESRLSDAETVA  F +CSVSLSV+CPKQLP + A+Y
Sbjct: 139 ILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSLSVVCPKQLPTIRALY 198

Query: 183 NAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMD---IA 239
           NA K N ++AD  +D +KN  +LVLISENF+EA AALS     NL   Q+PVK+D   +A
Sbjct: 199 NAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSH-SATNLPQTQSPVKVDRATVA 257

Query: 240 PVTSVTGPAPTSIPSVNGI--NRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPR 297
           P   VTG  P  + S NG   NR P+SVG VPTATVKVEPSTVTSM   P+FPHIP+V R
Sbjct: 258 PSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVEPSTVTSMAPVPSFPHIPAVAR 317

Query: 298 PASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLV-SGMSQPLRPMAPAAANVNILNNLS 356
           PA+Q +PS+QTSS S  SQ+M+++ ++ P++KP+V SGM+ PLR   P  ANVN+LNNLS
Sbjct: 318 PATQAIPSIQTSSASPVSQDMVSNAENAPDIKPVVVSGMTPPLRTGPPGGANVNLLNNLS 377

Query: 357 QARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSI 416
           Q RQVM++AA     +    S+GQ+ +AMHMSNMIS+GMA+S+P SQ VFS+ Q GITS+
Sbjct: 378 QVRQVMSSAA----LAGAASSVGQSAVAMHMSNMISTGMATSLPPSQTVFSTGQQGITSM 433

Query: 417 GGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNH 476
            GSG L G++Q  Q+ G N+  S  +  +  SN  +SQPM             GM+QG+H
Sbjct: 434 AGSGALMGSAQTGQSPGPNNAFSPQTTSNVASNLGVSQPMQ------------GMNQGSH 481

Query: 477 SGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQ 536
           SG  M+Q GISMNQNMMSGLG   VSSGTG M+PTPG+ QQAQSG+Q L  +N++A NMQ
Sbjct: 482 SGA-MMQGGISMNQNMMSGLGQGNVSSGTGGMMPTPGVGQQAQSGIQQLGGSNSSAPNMQ 540

Query: 537 LSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQI 596
           LSQ +S A+ +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSASAS++LAANWPPTMQI
Sbjct: 541 LSQPSSGAMQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSASASDSLAANWPPTMQI 600

Query: 597 VRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKAC 656
           VRLISQDHMNNKQYVGKADFLVFRAM+QHGFLGQLQ+KKLCAVIQLPSQTLLLSVSDKAC
Sbjct: 601 VRLISQDHMNNKQYVGKADFLVFRAMSQHGFLGQLQDKKLCAVIQLPSQTLLLSVSDKAC 660

Query: 657 RLIGMLFPGDMVVFKPQI 674
           RLIGMLFPGDMVVFKPQI
Sbjct: 661 RLIGMLFPGDMVVFKPQI 678

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. Positive regulator of shade avoidance and of jasmonate signaling. Acts in repression of PhyB-mediated light signaling and regulates the expression of FLOWERING LOCUS T (FT) and of CONSTANS (CO).
Arabidopsis thaliana (taxid: 3702)

>sp|Q6GP15|MED25_XENLA Mediator of RNA polymerase II transcription subunit 25 OS=Xenopus laevis GN=med25 PE=2 SV=1

 Score = 73.2 bits (178), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 56/193 (29%), Positives = 83/193 (43%), Gaps = 23/193 (11%)

Query: 35  ELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMM 93
           + SLV FNT        VQ    T     F+ WL +I F GGG    + IAEGLS AL +
Sbjct: 61  QYSLVVFNTVDCAPESYVQCHAPTSSAYEFVQWLDSIKFMGGGGESCSLIAEGLSTALQL 120

Query: 94  FSVAPNGSQNQQNVDGQRH--CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLS 151
           F    +  +  +   GQ H  CIL+  S P+ LP                 E+   S  +
Sbjct: 121 F----DDFKKMREQIGQTHKVCILICNSPPYLLPA---------------VESTTYSGYT 161

Query: 152 DAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISEN 211
             E + +   +  +  S+I P++LP L  ++  A         P D S++P  ++L+   
Sbjct: 162 -TENLVQKIGERGIHFSIISPRKLPALRTLFEKAMPVGLIEPQPKDYSQDPRHMILVRGM 220

Query: 212 FMEARAALSRPGV 224
            +    A S PGV
Sbjct: 221 VLPVGGATSVPGV 233

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Xenopus laevis (taxid: 8355)

>sp|A4IHD9|MED25_XENTR Mediator of RNA polymerase II transcription subunit 25 OS=Xenopus tropicalis GN=med25 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 83/193 (43%), Gaps = 23/193 (11%)

Query: 35  ELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMM 93
           + SLV FNT        VQ    T     F+ WL +I F GGG    + IAEGLS AL +
Sbjct: 62  QYSLVVFNTVDCAPESYVQCHAPTSSAYEFVQWLDSIRFMGGGGESCSLIAEGLSTALQL 121

Query: 94  FSVAPNGSQNQQNVDGQRH--CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLS 151
           F    +  +  +   GQ H  CIL+  S P+ LP                 E+   S  +
Sbjct: 122 F----DDFKKMREQIGQTHKVCILICNSPPYLLPA---------------VESTTYSGYT 162

Query: 152 DAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISEN 211
             E + +   +  +  SVI P++LP L  ++  A         P D S++P  ++L+   
Sbjct: 163 -TENLVQKIGERGIHFSVISPRKLPALRTLFEKAMPVGLIEPQPKDYSQDPRHMILVRGM 221

Query: 212 FMEARAALSRPGV 224
            +    A S PGV
Sbjct: 222 VLPVGGATSVPGV 234

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.

Xenopus tropicalis (taxid: 8364)

>sp|Q9VDR1|MED25_DROME Mediator of RNA polymerase II transcription subunit 25 OS=Drosophila melanogaster GN=MED25 PE=2 SV=1

 Score = 50.8 bits (120), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 68/154 (44%), Gaps = 25/154 (16%)

Query: 68  LSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPT 126
           +  +P  GGG    A +AEG + A   F       Q       QRHCIL+  S P+ +PT
Sbjct: 92  IERLPLVGGGMESCAHMAEGFAAAHGCFDDISERRQLLDQTSVQRHCILICNSPPYQMPT 151

Query: 127 PVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAK 186
                        E+ +   +S     E +A  F +  ++LS+I P+++P L  ++  A 
Sbjct: 152 ------------TESWKYPGKS----CEQLAALFNERKINLSIIAPRKMPVLFKLFMKAD 195

Query: 187 RNPRAADPPV---DNSKNPHFLVLISENFMEARA 217
                 D P+   + +KN   LVL+    ++ RA
Sbjct: 196 -----GDQPITSKNYAKNIRHLVLLKGYSLKERA 224


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.312    0.125    0.355 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 292,637,103
Number of Sequences: 539616
Number of extensions: 12623908
Number of successful extensions: 261095
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 1778
Number of HSP's successfully gapped in prelim test: 1782
Number of HSP's that attempted gapping in prelim test: 66969
Number of HSP's gapped (non-prelim): 58343
length of query: 818
length of database: 191,569,459
effective HSP length: 126
effective length of query: 692
effective length of database: 123,577,843
effective search space: 85515867356
effective search space used: 85515867356
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 66 (30.0 bits)

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (By similarity). Required for activated transcription of the MtnA, MtnB and MtnD genes.

Drosophila melanogaster (taxid: 7227)

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	818
225423909	827	PREDICTED: uncharacterized protein LOC10	0.819	0.810	0.802	0.0
224111730	796	predicted protein [Populus trichocarpa]	0.792	0.814	0.806	0.0
297737854	815	unnamed protein product [Vitis vinifera]	0.805	0.808	0.790	0.0
356502460	879	PREDICTED: uncharacterized protein LOC10	0.794	0.739	0.727	0.0
449434652	858	PREDICTED: mediator of RNA polymerase II	0.788	0.751	0.725	0.0
312283021	852	unnamed protein product [Thellungiella h	0.789	0.758	0.661	0.0
30689268	836	phytochrome and flowering time regulator	0.793	0.776	0.651	0.0
297845606	832	hypothetical protein ARALYDRAFT_472815 [	0.793	0.780	0.656	0.0
255576521	561	conserved hypothetical protein [Ricinus	0.645	0.941	0.779	0.0
123979422	759	phytochrome and flowering time protein 1	0.770	0.830	0.592	0.0

>gi|225423909|ref|XP_002278845.1| PREDICTED: uncharacterized protein LOC100259509 [Vitis vinifera]

 Score = 1042 bits (2695), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 542/675 (80%), Positives = 596/675 (88%), Gaps = 5/675 (0%)

Query: 6   YAYSKLSLYFH---RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVD 62
           Y  + +S Y     R FC NELAGQK S+SN ELSLV FN HGSYC+CLVQRSGWT+DVD
Sbjct: 19  YWQAVVSDYLDKIIRYFCGNELAGQKPSSSNFELSLVMFNAHGSYCSCLVQRSGWTRDVD 78

Query: 63  IFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH 122
           +FL WLS +PFAGGGFNDAAIAEGL+EALMMFSVA NGSQ QQNVDGQRHCILVAA+NP+
Sbjct: 79  LFLQWLSALPFAGGGFNDAAIAEGLAEALMMFSVAANGSQTQQNVDGQRHCILVAANNPY 138

Query: 123 PLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIY 182
           PLPTPVY+PQMQN++QNE+ E+Q ESRLSDAE VAKSF QCSVSLSVICPKQLPKL +IY
Sbjct: 139 PLPTPVYQPQMQNMEQNESIESQTESRLSDAEAVAKSFAQCSVSLSVICPKQLPKLKSIY 198

Query: 183 NAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVT 242
           NA KRNPR ADPPVDN KNPHFLVLIS++FMEARAALSRPG++N+  NQ+PVKMDIA V 
Sbjct: 199 NAGKRNPRVADPPVDNVKNPHFLVLISDSFMEARAALSRPGLSNMTANQSPVKMDIASVP 258

Query: 243 SVTGPAPTSIPSVNGI-NRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQ 301
            V+   P SIPSVNGI NRP I+VG VPTATVKVEPSTVTS+ +GP FPHIPSVPR ASQ
Sbjct: 259 QVSAAPPASIPSVNGIMNRPTIAVGAVPTATVKVEPSTVTSITSGPGFPHIPSVPRAASQ 318

Query: 302 GVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQV 361
           GVPSLQTSSPSSTSQEMI++GD+V ++KP+VSG+SQ LRP+ PAAANV+ILNNLSQARQV
Sbjct: 319 GVPSLQTSSPSSTSQEMISNGDNVQDLKPIVSGISQTLRPVVPAAANVSILNNLSQARQV 378

Query: 362 MNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGT 421
           M++AAL+GGTSIGLQSMG T MAMHMSNMISSGMASSVP +Q VFSS QS ++SI GSGT
Sbjct: 379 MHSAALSGGTSIGLQSMGGTSMAMHMSNMISSGMASSVPATQTVFSSGQSAVSSITGSGT 438

Query: 422 LTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSV-GMSQGNHSGGQ 480
           L GT+QV QNS L SFTSA SN+S NSN  ISQP+  LQGG SMGQ+V GMSQGN  GGQ
Sbjct: 439 LAGTAQVAQNSALGSFTSATSNMSVNSNLGISQPLSNLQGGVSMGQTVPGMSQGNLPGGQ 498

Query: 481 MVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQ 540
           MVQ+GI MNQNMMSGLGPSG+SSGTGTMIPTPGMSQQ Q GM  L VNNN A NM L QQ
Sbjct: 499 MVQSGIGMNQNMMSGLGPSGISSGTGTMIPTPGMSQQVQPGMPSLGVNNNAAANMPLPQQ 558

Query: 541 TSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLI 600
           TS A+ ++QSKYVKVWEG+LSGQRQGQPVFIT+LEGYRSASASE+LAANWP TMQIVRLI
Sbjct: 559 TSGAMQTAQSKYVKVWEGNLSGQRQGQPVFITRLEGYRSASASESLAANWPATMQIVRLI 618

Query: 601 SQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIG 660
           SQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIG
Sbjct: 619 SQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIG 678

Query: 661 MLFPGDMVVFKPQIS 675
           MLFPGDMVVFKPQI+
Sbjct: 679 MLFPGDMVVFKPQIT 693

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111730|ref|XP_002315956.1| predicted protein [Populus trichocarpa] gi|222864996|gb|EEF02127.1| predicted protein [Populus trichocarpa]

 Score = 1021 bits (2641), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 526/652 (80%), Positives = 570/652 (87%), Gaps = 4/652 (0%)

Query: 28  KTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGL 87
           K   S VELS+VTFN+HGSY ACLVQRSGWT+DVDIFL WLS IPFAGGGFNDAAIAEGL
Sbjct: 35  KVPTSIVELSIVTFNSHGSYSACLVQRSGWTRDVDIFLQWLSAIPFAGGGFNDAAIAEGL 94

Query: 88  SEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAE 147
           SEALMMF + PNGSQ Q N+D QR+CIL+AASNPHPLPTPVYRPQ+QNL+Q EN +AQ E
Sbjct: 95  SEALMMFPIDPNGSQTQSNIDEQRNCILIAASNPHPLPTPVYRPQIQNLEQIENIDAQNE 154

Query: 148 SRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVL 207
           SRLSDAETVAKSF QCSVSLS+ICPKQLPKL +IYNA KRN RAADPPVD+ KNPHFLVL
Sbjct: 155 SRLSDAETVAKSFPQCSVSLSIICPKQLPKLRSIYNAGKRNSRAADPPVDSVKNPHFLVL 214

Query: 208 ISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNG--INRPPISV 265
           ISENFMEARAALS PGV +L  NQ PVK+DIA VTSVTGPAPTSIPSVNG   NRP ISV
Sbjct: 215 ISENFMEARAALSLPGVTSLTSNQTPVKVDIASVTSVTGPAPTSIPSVNGSITNRPTISV 274

Query: 266 GNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSV 325
           GNVPTATVKVEPST+TSM NGPTFPH PSVPRPASQGVP LQTSSPS+T+Q+M TSGD V
Sbjct: 275 GNVPTATVKVEPSTITSMANGPTFPHNPSVPRPASQGVPILQTSSPSTTTQDMATSGDDV 334

Query: 326 PEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAM 385
            ++KP VS M+Q  RP  PAAANV+ILNN+SQARQVMN+A L+GGTS+GL S+ QT +AM
Sbjct: 335 QDLKPNVSVMTQSARPGPPAAANVSILNNISQARQVMNSAGLSGGTSLGLPSINQTSVAM 394

Query: 386 HMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLS 445
           HMSNMISSGMASSVP +  VFSS Q G++SI GSGTLTGT+Q+  NSGL SFTSA SN+S
Sbjct: 395 HMSNMISSGMASSVPAAPTVFSSGQPGVSSITGSGTLTGTTQIGPNSGLGSFTSATSNVS 454

Query: 446 GNSN-PSISQPMGTLQGGASMGQSV-GMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSS 503
           GNSN   ISQPMG LQ G S+GQS  GMSQGN SG QMVQ+G+  N N MSGLGPSGVSS
Sbjct: 455 GNSNLGRISQPMGNLQAGVSIGQSAPGMSQGNISGAQMVQSGMGANPNTMSGLGPSGVSS 514

Query: 504 GTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQ 563
           G  TMIPTPGMSQQ QSGMQPL  NNN+A N+ +SQQT+  L   QSKYVKVWEG+LSGQ
Sbjct: 515 GLNTMIPTPGMSQQVQSGMQPLGANNNSADNLSMSQQTAGGLQPPQSKYVKVWEGNLSGQ 574

Query: 564 RQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMN 623
           RQGQPVFIT+LEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMN
Sbjct: 575 RQGQPVFITRLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMN 634

Query: 624 QHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQIS 675
           QHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQIS
Sbjct: 635 QHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQIS 686

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737854|emb|CBI27055.3| unnamed protein product [Vitis vinifera]

 Score = 1019 bits (2635), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 533/674 (79%), Positives = 586/674 (86%), Gaps = 15/674 (2%)

Query: 6   YAYSKLSLYFH---RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVD 62
           Y  + +S Y     R FC NELAGQK S+SN ELSLV FN HGSYC+CLVQRSGWT+DVD
Sbjct: 19  YWQAVVSDYLDKIIRYFCGNELAGQKPSSSNFELSLVMFNAHGSYCSCLVQRSGWTRDVD 78

Query: 63  IFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH 122
           +FL WLS +PFAGGGFNDAAIAEGL+EALMMFSVA NGSQ QQNVDGQRHCILVAA+NP+
Sbjct: 79  LFLQWLSALPFAGGGFNDAAIAEGLAEALMMFSVAANGSQTQQNVDGQRHCILVAANNPY 138

Query: 123 PLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIY 182
           PLPTPVY+PQMQN++QNE+ E+Q ESRLSDAE VAKSF QCSVSLSVICPKQLPKL +IY
Sbjct: 139 PLPTPVYQPQMQNMEQNESIESQTESRLSDAEAVAKSFAQCSVSLSVICPKQLPKLKSIY 198

Query: 183 NAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVT 242
           NA KRNPR ADPPVDN KNPHFLVLIS++FMEARAALSRPG++N+  NQ+PVKMDIA V 
Sbjct: 199 NAGKRNPRVADPPVDNVKNPHFLVLISDSFMEARAALSRPGLSNMTANQSPVKMDIASVP 258

Query: 243 SVTGPAPTSIPSVNGI-NRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQ 301
            V+   P SIPSVNGI NRP I+VG VPTATVKVEPSTVTS+ +GP FPHIPSVPR ASQ
Sbjct: 259 QVSAAPPASIPSVNGIMNRPTIAVGAVPTATVKVEPSTVTSITSGPGFPHIPSVPRAASQ 318

Query: 302 GVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQV 361
           GVPSLQTSSPSSTSQEMI++GD+V ++KP+VSG+SQ LRP+ PAAANV+ILNNLSQARQV
Sbjct: 319 GVPSLQTSSPSSTSQEMISNGDNVQDLKPIVSGISQTLRPVVPAAANVSILNNLSQARQV 378

Query: 362 MNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGT 421
           M++AAL+GGTSIGLQSMG T MAMHMSNMISSGMASSVP +Q VFSS QS ++SI GSGT
Sbjct: 379 MHSAALSGGTSIGLQSMGGTSMAMHMSNMISSGMASSVPATQTVFSSGQSAVSSITGSGT 438

Query: 422 LTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQM 481
           L GT+QV QNS L SFTSA SN+S NSN  ISQP+             GMSQGN  GGQM
Sbjct: 439 LAGTAQVAQNSALGSFTSATSNMSVNSNLGISQPL-----------IPGMSQGNLPGGQM 487

Query: 482 VQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQT 541
           VQ+GI MNQNMMSGLGPSG+SSGTGTMIPTPGMSQQ Q GM  L VNNN A NM L QQT
Sbjct: 488 VQSGIGMNQNMMSGLGPSGISSGTGTMIPTPGMSQQVQPGMPSLGVNNNAAANMPLPQQT 547

Query: 542 SSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLIS 601
           S A+ ++QSKYVKVWEG+LSGQRQGQPVFIT+LEGYRSASASE+LAANWP TMQIVRLIS
Sbjct: 548 SGAMQTAQSKYVKVWEGNLSGQRQGQPVFITRLEGYRSASASESLAANWPATMQIVRLIS 607

Query: 602 QDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGM 661
           QDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGM
Sbjct: 608 QDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGM 667

Query: 662 LFPGDMVVFKPQIS 675
           LFPGDMVVFKPQI+
Sbjct: 668 LFPGDMVVFKPQIT 681

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356502460|ref|XP_003520037.1| PREDICTED: uncharacterized protein LOC100801664 [Glycine max]

 Score =  895 bits (2312), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 481/661 (72%), Positives = 539/661 (81%), Gaps = 11/661 (1%)

Query: 17  RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGG 76
           RCF  N+  GQK SASNVE +LVT+NTHG Y +CLVQRSGWT+D D+F  WLS+IPF GG
Sbjct: 35  RCFGGNDSTGQKFSASNVEFALVTYNTHGCYSSCLVQRSGWTRDPDVFFSWLSSIPFNGG 94

Query: 77  GFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNL 136
           GFNDAAIAEGLSEALMM   + +G+ NQQ+VD  +HCILVAASNP+PL TPVY P+ QNL
Sbjct: 95  GFNDAAIAEGLSEALMMLWNSQSGAPNQQSVDMHKHCILVAASNPYPLQTPVYVPRPQNL 154

Query: 137 DQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPV 196
           +Q+E  ++ + S L DAE VAK+F Q S+SLSVICPKQLPK+ +IYNA KRN RAADPP+
Sbjct: 155 EQSETIDSDSGSHLYDAEAVAKAFPQFSISLSVICPKQLPKIKSIYNAGKRNNRAADPPL 214

Query: 197 DNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVN 256
           + +K PHFL+LISE F EAR ALSR G+ +L  NQ+PVK+D   VT VTG  PTS+P VN
Sbjct: 215 E-AKTPHFLILISEGFREARGALSRSGITSLPSNQSPVKVDAVSVTPVTGAPPTSMP-VN 272

Query: 257 GI--NRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPAS--QGVPSLQTSSPS 312
           G   NR P+  GNV  ATVKVEP  VTSMV+GP FPH  SVPR  S  QGVPSLQTSSPS
Sbjct: 273 GSIPNRQPVPAGNVAPATVKVEPVPVTSMVSGPAFPHNSSVPRATSTSQGVPSLQTSSPS 332

Query: 313 STSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTS 372
           S SQ++IT+ ++  + KP VS +  PLRP+ P  ANVNILNNLSQARQVMN+AAL+GGTS
Sbjct: 333 SVSQDIITNNETAQDTKPTVSML--PLRPVNPVQANVNILNNLSQARQVMNSAALSGGTS 390

Query: 373 IGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNS 432
           +GL SMGQTP+AMHMSNMISSGM SSVP +Q VFSS QSGITS+  SG LT  +QV QNS
Sbjct: 391 MGLPSMGQTPVAMHMSNMISSGMTSSVPAAQNVFSSGQSGITSMTSSGPLTVPAQVGQNS 450

Query: 433 GLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSV-GMSQGNHSGGQMVQNGISMNQN 491
           GL S TS  SNLS +SN  ISQP+G LQG  S+GQ V GMSQGN SG QMVQ G+SMNQN
Sbjct: 451 GLGSLTSNTSNLSSSSNIGISQPLGNLQGVVSIGQQVSGMSQGNLSGAQMVQGGVSMNQN 510

Query: 492 MMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSK 551
           +MSGLG S VSSGTGTMIPTPGMSQ  QS MQPL   NN A NM LSQQTS  + S+QSK
Sbjct: 511 VMSGLGQSVVSSGTGTMIPTPGMSQPVQSVMQPLV--NNAAANMPLSQQTSGGMQSAQSK 568

Query: 552 YVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYV 611
           YVKVWEGSLSGQRQGQPVFITKLEGYR++SASETLAANWPP MQIVRLISQDHMNNKQYV
Sbjct: 569 YVKVWEGSLSGQRQGQPVFITKLEGYRNSSASETLAANWPPVMQIVRLISQDHMNNKQYV 628

Query: 612 GKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK 671
           GKADFLVFRAMN HGFLGQLQEKKLCAVIQLPSQTLLLSVSDKA RLIGMLFPGDMVVFK
Sbjct: 629 GKADFLVFRAMNPHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKAFRLIGMLFPGDMVVFK 688

Query: 672 P 672
           P
Sbjct: 689 P 689

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434652|ref|XP_004135110.1| PREDICTED: mediator of RNA polymerase II transcription subunit 25-like [Cucumis sativus]

 Score =  893 bits (2308), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 479/660 (72%), Positives = 546/660 (82%), Gaps = 15/660 (2%)

Query: 17  RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGG 76
           R FC NEL GQK   SNVE SLVTF+THGSYC CLVQR+GWT+DVDIF+ WLS IPF+GG
Sbjct: 33  RSFCGNELTGQKPPTSNVEFSLVTFHTHGSYCGCLVQRTGWTRDVDIFIQWLSAIPFSGG 92

Query: 77  GFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNL 136
           GF+DAAIAEGL+EALMMF   PNG QNQQ +D Q+HCILVAASNP+PLPTPVYRP +QNL
Sbjct: 93  GFSDAAIAEGLAEALMMFPTQPNGGQNQQTMDMQKHCILVAASNPYPLPTPVYRPAVQNL 152

Query: 137 DQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPV 196
           +Q++N E    S  S AETVAKSF QC +SLSVICPKQLPKL AIY A KRNPRAADPP+
Sbjct: 153 EQHDNVEP--GSSQSYAETVAKSFPQCFISLSVICPKQLPKLKAIYTAGKRNPRAADPPI 210

Query: 197 DNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVN 256
           DN K+P +LVLISENF+EARAALSRPG+ +L  NQ+PVKMDI+ V  VTGP PT+ PSVN
Sbjct: 211 DNVKSPSYLVLISENFVEARAALSRPGITSLPANQSPVKMDISSVVPVTGPPPTTTPSVN 270

Query: 257 G--INRPPISVGNVPTATVKVEPSTVTSMVNGPTFP-HIPSVPRPASQGVPSLQTSSPSS 313
           G  INR P+SV N PTATVKVEP+TVTSM NG  +P H+PSV R ASQGVPSLQTSSP S
Sbjct: 271 GPIINRQPVSVPNGPTATVKVEPNTVTSMTNGSGYPPHMPSVVRAASQGVPSLQTSSPLS 330

Query: 314 TSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSI 373
            SQEMIT+ ++  ++KPLV+G+ QP+R + PA  NV+ILNN+SQAR VM+ AAL GGTSI
Sbjct: 331 -SQEMITNNENTQDLKPLVTGVPQPVRSLGPA--NVSILNNISQAR-VMSTAALNGGTSI 386

Query: 374 GLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSG 433
           GL SMGQTP+AMH+SNMISSGM SSVP +Q VFSS QSG+TSI GS TL   SQV  NSG
Sbjct: 387 GLPSMGQTPIAMHVSNMISSGMGSSVPAAQNVFSSGQSGMTSINGSSTL---SQVAPNSG 443

Query: 434 LNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSV-GMSQGNHSGGQMVQNGISMNQNM 492
           ++S TS  +N+SGN N + SQ +G LQG  S+ QSV G+SQGN +G Q+VQ+GI ++QN+
Sbjct: 444 ISSLTSGNNNISGNPNIATSQAVGNLQGSVSVSQSVPGISQGNLAGTQVVQSGIGVSQNV 503

Query: 493 MSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHS-SQSK 551
           MS L   GVSSG GTMIPTPGM QQ Q+GM  L +NN  A NM L Q ++ AL   +QSK
Sbjct: 504 MSNLTQPGVSSGNGTMIPTPGMPQQVQNGMHSLGMNN-AAANMPLPQHSAGALQQQAQSK 562

Query: 552 YVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYV 611
           YVK WEG+LSGQRQGQPVFIT++EGYRSASAS+ LAANWP TMQIVRLISQDHMNNKQYV
Sbjct: 563 YVKFWEGNLSGQRQGQPVFITRMEGYRSASASDKLAANWPQTMQIVRLISQDHMNNKQYV 622

Query: 612 GKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK 671
           GKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK
Sbjct: 623 GKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK 682

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312283021|dbj|BAJ34376.1| unnamed protein product [Thellungiella halophila]

 Score =  830 bits (2143), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 448/677 (66%), Positives = 527/677 (77%), Gaps = 31/677 (4%)

Query: 6   YAYSKLSLYFH---RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVD 62
           Y ++ +S Y     R FC +EL G++    NVELSLV FN+HGSYCACLVQRSGWTKDVD
Sbjct: 21  YWHTIVSDYLEKIIRSFCGSELNGER----NVELSLVIFNSHGSYCACLVQRSGWTKDVD 76

Query: 63  IFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH 122
           IFLHWLS+I FAGGGF++AA AEGL+EALMMFS  P   Q Q + D +RHCIL+ ASNPH
Sbjct: 77  IFLHWLSSIQFAGGGFSEAATAEGLAEALMMFS--PPSGQAQPSNDLKRHCILITASNPH 134

Query: 123 PLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIY 182
            LPTPVYRP++ N ++NEN +AQ+ESRLSDAETVA  F +CSVSLSVICPKQLPK+ A+Y
Sbjct: 135 SLPTPVYRPKLPNAERNENGDAQSESRLSDAETVASYFSRCSVSLSVICPKQLPKIRALY 194

Query: 183 NAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMD---IA 239
           NA K NP++ D  +D  KN  +LVLI ENF+EARAALS     NL   Q+PVK+D   +A
Sbjct: 195 NAGKLNPQSPDLSIDTVKNTFYLVLIPENFVEARAALSH-SATNLPQTQSPVKVDRSTVA 253

Query: 240 PVTSVTGPAPTSIPSVNG--INRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPR 297
           P   VTG  P  +PS NG  +NR P+S+G VPTATVKVEPSTV SM    TFPHI SV R
Sbjct: 254 PSLPVTGQPPAPVPSANGPILNRQPVSIGPVPTATVKVEPSTVPSMAAVSTFPHIQSVAR 313

Query: 298 PASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQ 357
           PA+Q +PS+QTSSPS  SQEM+T+ ++ P+VKP+V+GM+ PLR   P  ANVN+LNNLSQ
Sbjct: 314 PATQAIPSIQTSSPSPVSQEMVTNAENAPDVKPVVTGMTPPLRTGPPGGANVNLLNNLSQ 373

Query: 358 ARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIG 417
            RQVM++AA     +    S GQ+ +AMHMSNMIS+GMA+S+P SQ VFSS Q GITS+ 
Sbjct: 374 VRQVMSSAA----LAGAASSTGQSAVAMHMSNMISTGMATSLPPSQTVFSSGQQGITSMA 429

Query: 418 GSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHS 477
           GSG L GT Q  Q+ G N+  S  +  +  SN  +SQPM             GM+QG+HS
Sbjct: 430 GSGALMGTVQAGQSPGPNNSFSPQTTSNVASNLGVSQPM------------PGMNQGSHS 477

Query: 478 GGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQL 537
           G QM+Q GI MNQNMMSGLG   VSSGTG M+PTPG+ QQAQSG+Q L  +N++A NMQL
Sbjct: 478 GAQMMQGGIPMNQNMMSGLGQGNVSSGTGGMMPTPGVGQQAQSGIQQLGGSNSSAPNMQL 537

Query: 538 SQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIV 597
           SQ +S+AL +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSASAS++LAANWPPTMQIV
Sbjct: 538 SQPSSAALQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSASASDSLAANWPPTMQIV 597

Query: 598 RLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACR 657
           RLISQDHMNNKQYVGKAD LVFRAM+QHGFLGQLQ+KKLCAVIQLPSQTLLLSVSDKACR
Sbjct: 598 RLISQDHMNNKQYVGKADSLVFRAMSQHGFLGQLQDKKLCAVIQLPSQTLLLSVSDKACR 657

Query: 658 LIGMLFPGDMVVFKPQI 674
           LIGMLFPGDMVVFKPQI
Sbjct: 658 LIGMLFPGDMVVFKPQI 674

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30689268|ref|NP_173925.3| phytochrome and flowering time regulatory protein 1 [Arabidopsis thaliana] gi|75145501|sp|Q7XYY2.1|MED25_ARATH RecName: Full=Mediator of RNA polymerase II transcription subunit 25; Short=AtMED25; AltName: Full=Phytochrome and flowering time 1 protein; AltName: Full=Phytochrome and flowering time regulatory protein 1 gi|32478899|gb|AAO39425.1| phytochrome and flowering time 1 protein [Arabidopsis thaliana] gi|332192518|gb|AEE30639.1| phytochrome and flowering time regulatory protein 1 [Arabidopsis thaliana]

 Score =  820 bits (2118), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 442/678 (65%), Positives = 528/678 (77%), Gaps = 29/678 (4%)

Query: 6   YAYSKLSLYFH---RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVD 62
           Y  + +S Y     R FC +EL G++   S VELSLV FN+HGSYCACLVQRSGWT+DVD
Sbjct: 21  YWQTIVSDYLEKIIRSFCGSELNGERNPVSTVELSLVIFNSHGSYCACLVQRSGWTRDVD 80

Query: 63  IFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH 122
           IFLHWLS+I F GGGFN+ A AEGL+EALMMFS  P   Q Q + D +RHCIL+ ASNPH
Sbjct: 81  IFLHWLSSIQFGGGGFNEVATAEGLAEALMMFS--PPSGQAQPSNDLKRHCILITASNPH 138

Query: 123 PLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIY 182
            LPTPVYRP++QN+++NEN +AQAESRLSDAETVA  F +CSVSLSV+CPKQLP + A+Y
Sbjct: 139 ILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSLSVVCPKQLPTIRALY 198

Query: 183 NAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMD---IA 239
           NA K N ++AD  +D +KN  +LVLISENF+EA AALS     NL   Q+PVK+D   +A
Sbjct: 199 NAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSH-SATNLPQTQSPVKVDRATVA 257

Query: 240 PVTSVTGPAPTSIPSVNGI--NRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPR 297
           P   VTG  P  + S NG   NR P+SVG VPTATVKVEPSTVTSM   P+FPHIP+V R
Sbjct: 258 PSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVEPSTVTSMAPVPSFPHIPAVAR 317

Query: 298 PASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLV-SGMSQPLRPMAPAAANVNILNNLS 356
           PA+Q +PS+QTSS S  SQ+M+++ ++ P++KP+V SGM+ PLR   P  ANVN+LNNLS
Sbjct: 318 PATQAIPSIQTSSASPVSQDMVSNAENAPDIKPVVVSGMTPPLRTGPPGGANVNLLNNLS 377

Query: 357 QARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSI 416
           Q RQVM++AA     +    S+GQ+ +AMHMSNMIS+GMA+S+P SQ VFS+ Q GITS+
Sbjct: 378 QVRQVMSSAA----LAGAASSVGQSAVAMHMSNMISTGMATSLPPSQTVFSTGQQGITSM 433

Query: 417 GGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNH 476
            GSG L G++Q  Q+ G N+  S  +  +  SN  +SQPM             GM+QG+H
Sbjct: 434 AGSGALMGSAQTGQSPGPNNAFSPQTTSNVASNLGVSQPMQ------------GMNQGSH 481

Query: 477 SGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQ 536
           SG  M+Q GISMNQNMMSGLG   VSSGTG M+PTPG+ QQAQSG+Q L  +N++A NMQ
Sbjct: 482 SGA-MMQGGISMNQNMMSGLGQGNVSSGTGGMMPTPGVGQQAQSGIQQLGGSNSSAPNMQ 540

Query: 537 LSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQI 596
           LSQ +S A+ +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSASAS++LAANWPPTMQI
Sbjct: 541 LSQPSSGAMQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSASASDSLAANWPPTMQI 600

Query: 597 VRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKAC 656
           VRLISQDHMNNKQYVGKADFLVFRAM+QHGFLGQLQ+KKLCAVIQLPSQTLLLSVSDKAC
Sbjct: 601 VRLISQDHMNNKQYVGKADFLVFRAMSQHGFLGQLQDKKLCAVIQLPSQTLLLSVSDKAC 660

Query: 657 RLIGMLFPGDMVVFKPQI 674
           RLIGMLFPGDMVVFKPQI
Sbjct: 661 RLIGMLFPGDMVVFKPQI 678

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297845606|ref|XP_002890684.1| hypothetical protein ARALYDRAFT_472815 [Arabidopsis lyrata subsp. lyrata] gi|297336526|gb|EFH66943.1| hypothetical protein ARALYDRAFT_472815 [Arabidopsis lyrata subsp. lyrata]

 Score =  819 bits (2116), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 445/678 (65%), Positives = 528/678 (77%), Gaps = 29/678 (4%)

Query: 6   YAYSKLSLYFH---RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVD 62
           Y  + +S Y     R FC +EL G++   S VELSLV FN+HGSYCACLVQRSGWT+DVD
Sbjct: 21  YWQTIVSDYLEKIIRSFCGSELNGERNPVSTVELSLVIFNSHGSYCACLVQRSGWTRDVD 80

Query: 63  IFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH 122
           IFLHWLS+I F GGGFN+ A AEGL+EALMMFS  P   Q Q + D +RHCIL+ ASNPH
Sbjct: 81  IFLHWLSSIQFGGGGFNEVATAEGLAEALMMFS--PPSGQAQPSNDLKRHCILITASNPH 138

Query: 123 PLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIY 182
            LPTPV+RP++Q++++NEN +AQAESRLSDAETVA  F +CSVSLSV+CPKQLPK+ A+Y
Sbjct: 139 TLPTPVFRPRLQSVERNENGDAQAESRLSDAETVASYFAKCSVSLSVVCPKQLPKIRALY 198

Query: 183 NAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMD---IA 239
           NA K NP++AD  +D +KN  +LVLISENF+EARAALS     NL   Q+PVK+D   +A
Sbjct: 199 NAGKLNPQSADLSIDTAKNTFYLVLISENFVEARAALSH-SATNLPQTQSPVKVDRATVA 257

Query: 240 PVTSVTGPAPTSIPSVNGI--NRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPR 297
           P   VTG  P  + S NG   NR P+SVG VPTATVKVEPSTVTSM   P FPHIPSV R
Sbjct: 258 PSLPVTGQPPAPVTSANGPIQNRQPVSVGPVPTATVKVEPSTVTSMAPVPNFPHIPSVAR 317

Query: 298 PASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLV-SGMSQPLRPMAPAAANVNILNNLS 356
           PA+Q +PS+QTSS S  SQ+M+T+ ++ P++KP+V  GM+ PLR   P  ANVN+LNNLS
Sbjct: 318 PATQPIPSIQTSSASPVSQDMVTNAENAPDIKPVVVGGMTPPLRTGPPGGANVNLLNNLS 377

Query: 357 QARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSI 416
           Q RQVM++AAL G  S   QS     +AMHMSNMIS+GMA+S+P SQ VFS+ Q GITS+
Sbjct: 378 QVRQVMSSAALAGAASSAGQSA----VAMHMSNMISTGMATSLPPSQTVFSTGQQGITSM 433

Query: 417 GGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNH 476
            GSG L G++Q  Q+ G N+  S  +  +  SN  +SQPM             GM+QG+H
Sbjct: 434 AGSGALMGSAQTGQSPGPNNAFSPQTTPNVASNLGVSQPMQ------------GMNQGSH 481

Query: 477 SGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQ 536
           SG  M+Q GISMNQN++SGLG   VSSGTG M+PTPG+ QQAQSG+Q L  +N++A NMQ
Sbjct: 482 SGA-MMQGGISMNQNIVSGLGQGNVSSGTGGMMPTPGVGQQAQSGIQQLGGSNSSAPNMQ 540

Query: 537 LSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQI 596
           LSQ +S AL +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSASAS++LAANWPPTMQI
Sbjct: 541 LSQPSSGALQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSASASDSLAANWPPTMQI 600

Query: 597 VRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKAC 656
           VRLISQDHMNNKQYVGKADFLVFRAM+QHGFLGQLQ+KKLCAVIQLPSQTLLLSVSDKAC
Sbjct: 601 VRLISQDHMNNKQYVGKADFLVFRAMSQHGFLGQLQDKKLCAVIQLPSQTLLLSVSDKAC 660

Query: 657 RLIGMLFPGDMVVFKPQI 674
           RLIGMLFPGDMVVFKPQI
Sbjct: 661 RLIGMLFPGDMVVFKPQI 678

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255576521|ref|XP_002529152.1| conserved hypothetical protein [Ricinus communis] gi|223531431|gb|EEF33265.1| conserved hypothetical protein [Ricinus communis]

 Score =  786 bits (2029), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/535 (77%), Positives = 461/535 (86%), Gaps = 7/535 (1%)

Query: 55  SGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMM-FSVAPNGSQNQQNVDGQRHC 113
           SGWT+DVDIFL WL+ IPFAGGGF+DAAIAEGLSEALMM F   PNGSQ QQN+DGQRHC
Sbjct: 30  SGWTRDVDIFLQWLAAIPFAGGGFSDAAIAEGLSEALMMMFPFVPNGSQAQQNIDGQRHC 89

Query: 114 ILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK 173
           IL+AASNPHPLPTPVYR Q+QNL+QNEN + Q ESRLSDAET+AKSF QCSVSLSVICPK
Sbjct: 90  ILIAASNPHPLPTPVYRQQIQNLEQNENIDPQTESRLSDAETIAKSFPQCSVSLSVICPK 149

Query: 174 QLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNP 233
           QLPKL AIYNA KRN RAADP VDN KNPHFLVLISENFMEARAALSRPGVANL  NQ+P
Sbjct: 150 QLPKLRAIYNAGKRNSRAADPTVDNVKNPHFLVLISENFMEARAALSRPGVANLPSNQSP 209

Query: 234 VKMDIAPVTSVTGPAPTSIPSVNG--INRPPISVGNVPTATVKVEPSTVTSMVNGPTFPH 291
           VKMD+A VTSV GP   SIPSVNG  ++RP  S+GNVPTATVKVEP+TVTSM  GP FPH
Sbjct: 210 VKMDVASVTSVAGPTSPSIPSVNGSIMSRP--SIGNVPTATVKVEPTTVTSMAPGPAFPH 267

Query: 292 IPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNI 351
           IPS  RPASQ VPSLQTSSP +++QE+ITS ++V E+KP VSGM   +RP+ P AANV+I
Sbjct: 268 IPST-RPASQSVPSLQTSSPPTSTQEIITSSENVSEIKPTVSGMPHSVRPVPPGAANVSI 326

Query: 352 LNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQS 411
           LNNLSQARQVMN+AALTGGTSIGL S+ QTP+AMHMSNMISSGMASSVP +Q VFSS Q+
Sbjct: 327 LNNLSQARQVMNSAALTGGTSIGLPSINQTPVAMHMSNMISSGMASSVPAAQTVFSSGQT 386

Query: 412 GITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSV-G 470
           GITSI GSGTLTGT+Q+  NSGL SFTS  +N+SGNSN  +SQPMG LQ G SMGQSV G
Sbjct: 387 GITSITGSGTLTGTTQIAPNSGLGSFTSTTTNVSGNSNLGMSQPMGNLQAGVSMGQSVPG 446

Query: 471 MSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNN 530
           MSQGN SG QMVQ+GI M+QNMMSGLGPS VSSG  TMIPTPGM Q AQ+G+Q L VNNN
Sbjct: 447 MSQGNLSGAQMVQSGIGMSQNMMSGLGPSVVSSGASTMIPTPGMGQPAQTGIQSLGVNNN 506

Query: 531 TAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASET 585
           +A NM LSQQT+SAL S+QSKYVKVWEG+LSGQRQGQPVFIT+LEGYRS SASET
Sbjct: 507 SAANMPLSQQTASALQSAQSKYVKVWEGNLSGQRQGQPVFITRLEGYRSGSASET 561

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|123979422|gb|ABM81545.1| phytochrome and flowering time protein 1 [Triticum aestivum]

 Score =  716 bits (1848), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/662 (59%), Positives = 478/662 (72%), Gaps = 32/662 (4%)

Query: 17  RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGG 76
           R FC  EL+GQK +    EL+LV F+THG Y A +VQRSGWTKD+D FL WLS I F+GG
Sbjct: 38  RSFCSTELSGQKLAGVPPELALVVFHTHGPYSAFIVQRSGWTKDMDAFLSWLSGISFSGG 97

Query: 77  GFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNL 136
           GF++AAI EGL+EALM+   + + SQN QN + Q+HC+LVAASNP+PLPTPVYRP +Q+ 
Sbjct: 98  GFSEAAICEGLAEALMILQGSSSSSQNHQNRELQKHCLLVAASNPYPLPTPVYRPSVQSS 157

Query: 137 DQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPV 196
           D  ++NEA  ES L+DAE VA SF QCSVSLSV+ PKQLP L AIYNA KRNP+A+DP V
Sbjct: 158 DHKKSNEATKESCLADAEAVAVSFAQCSVSLSVVSPKQLPTLKAIYNAGKRNPQASDPSV 217

Query: 197 DNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVN 256
           D++KNPHFLVL+SE+FMEAR ALS P   NL PN    KMD  P  +V GP   + PSVN
Sbjct: 218 DHAKNPHFLVLLSESFMEARTALSHPLPGNLVPNHTITKMDTTPAATVPGPPSNASPSVN 277

Query: 257 GINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQ 316
           G       +G  PTA VKVEP+T+  MV+ P F H+  +   ASQGV ++QTSSPS  SQ
Sbjct: 278 G-----TMMGRQPTANVKVEPTTIPPMVSAPAFSHMTPISNVASQGVSAMQTSSPSIISQ 332

Query: 317 EMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQ 376
           E   + + + E KPLV+ + Q +RP  P  ANV+ILNNLSQ R      +LT  TS+G  
Sbjct: 333 ETNVANEILQEHKPLVNPIQQQVRPGGP--ANVSILNNLSQHRH-----SLTAATSMG-P 384

Query: 377 SMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNS 436
           +MG TP+ +HMSNMISSGM     TS P        I+SI G+    G  Q+ QN+ L S
Sbjct: 385 NMGATPIQVHMSNMISSGM-----TSTPAV------ISSISGTVQPIGAQQLAQNTALGS 433

Query: 437 FTSAPSNLSGNSNPSISQPMGTLQGGASMGQSV-GMSQGN-HSGGQMVQNGISMNQNMMS 494
           F S  S +S NSN ++S  +  +Q   +MGQSV  M+QG   +G Q  Q GI  NQNM++
Sbjct: 434 FGSNTSTVSCNSNIAVSSSLANIQSNMAMGQSVPSMAQGGLMAGPQSGQGGIGTNQNMIN 493

Query: 495 GLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVK 554
            LG + ++S T TM+PTPGM Q  Q+G+  LS NN++A+NM L+Q  +       SKYVK
Sbjct: 494 NLGTTAINS-TPTMMPTPGMVQ--QTGVNALSANNSSAMNMPLAQHPNG---QQPSKYVK 547

Query: 555 VWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKA 614
           +WEG+LSGQRQGQPVFI KLEGYRS +AS TLA++WP TMQIVRLI+Q+HMNNKQYVGKA
Sbjct: 548 IWEGTLSGQRQGQPVFICKLEGYRSGTASGTLASDWPETMQIVRLIAQEHMNNKQYVGKA 607

Query: 615 DFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 674
           DFLVFR +NQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKA RLIGMLFPGDMVVFKPQ+
Sbjct: 608 DFLVFRTLNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKAGRLIGMLFPGDMVVFKPQV 667

Query: 675 SS 676
           S+
Sbjct: 668 ST 669

Source: Triticum aestivum

Species: Triticum aestivum

Genus: Triticum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	818
TAIR|locus:2031200	836	PFT1 "PHYTOCHROME AND FLOWERIN	0.775	0.758	0.611	1.3e-206
UNIPROTKB|F1N3D4	743	MED25 "Mediator of RNA polymer	0.106	0.117	0.372	2.5e-08
UNIPROTKB|F1RHT9	746	MED25 "Uncharacterized protein	0.106	0.116	0.372	7.3e-08
MGI|MGI:1922863	745	Med25 "mediator of RNA polymer	0.106	0.116	0.372	7.9e-08
UNIPROTKB|A2VE44	746	MED25 "Mediator of RNA polymer	0.106	0.116	0.372	8e-08
UNIPROTKB|Q71SY5	747	MED25 "Mediator of RNA polymer	0.106	0.116	0.372	3.2e-06
ZFIN|ZDB-GENE-040426-2850	701	med25 "mediator of RNA polymer	0.106	0.124	0.351	6.4e-06
WB|WBGene00019435	2232	K06A9.1 [Caenorhabditis elegan	0.392	0.143	0.219	1.2e-05
DICTYBASE|DDB_G0286967	1553	med25 "putative mediator compl	0.100	0.052	0.3	2.2e-05
POMBASE|SPAPB1E7.04c	1236	SPAPB1E7.04c "chitinase (predi	0.360	0.238	0.212	3.4e-05

TAIR|locus:2031200 PFT1 "PHYTOCHROME AND FLOWERING TIME 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1958 (694.3 bits), Expect = 1.3e-206, Sum P(2) = 1.3e-206
 Identities = 405/662 (61%), Positives = 486/662 (73%)

Query:    17 RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGG 76
             R FC +EL G++   S VELSLV FN+HGSYCACLVQRSGWT+DVDIFLHWLS+I F GG
Sbjct:    35 RSFCGSELNGERNPVSTVELSLVIFNSHGSYCACLVQRSGWTRDVDIFLHWLSSIQFGGG 94

Query:    77 GFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNL 136
             GFN+ A AEGL+EALMMFS  P+G Q Q + D +RHCIL+ ASNPH LPTPVYRP++QN+
Sbjct:    95 GFNEVATAEGLAEALMMFS-PPSG-QAQPSNDLKRHCILITASNPHILPTPVYRPRLQNV 152

Query:   137 DQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPV 196
             ++NEN +AQAESRLSDAETVA  F +CSVSLSV+CPKQLP + A+YNA K N ++AD  +
Sbjct:   153 ERNENGDAQAESRLSDAETVASYFAKCSVSLSVVCPKQLPTIRALYNAGKPNQQSADLSI 212

Query:   197 DNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMD---IAPVTSVTGPAPTSIP 253
             D +KN  +LVLISENF+EA AALS     NL   Q+PVK+D   +AP   VTG  P  + 
Sbjct:   213 DTAKNTFYLVLISENFVEACAALSH-SATNLPQTQSPVKVDRATVAPSIPVTGQPPAPVS 271

Query:   254 SVNGI--NRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVXXXXXXXX 311
             S NG   NR P+SVG VPTATVKVEPSTVTSM   P+FPHIP+V RPA+Q +        
Sbjct:   272 SANGPIQNRQPVSVGPVPTATVKVEPSTVTSMAPVPSFPHIPAVARPATQAIPSIQTSSA 331

Query:   312 XXXXXEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMN--NAALTG 369
                  +M+++ ++ P++KP+V     P     P     N+ N L+   QV    ++A   
Sbjct:   332 SPVSQDMVSNAENAPDIKPVVVSGMTPPLRTGPPGG-ANV-NLLNNLSQVRQVMSSAALA 389

Query:   370 GTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQXXXXXXXXXXXXXXXXQVP 429
             G +    S+GQ+ +AMHMSNMIS+GMA+S+P SQ VFS+ Q                Q  
Sbjct:   390 GAA---SSVGQSAVAMHMSNMISTGMATSLPPSQTVFSTGQQGITSMAGSGALMGSAQTG 446

Query:   430 QNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMN 489
             Q+ G N+  S  +  +  SN  +SQPM             GM+QG+HSG  M+Q GISMN
Sbjct:   447 QSPGPNNAFSPQTTSNVASNLGVSQPMQ------------GMNQGSHSGA-MMQGGISMN 493

Query:   490 QNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQ 549
             QNMMSGLG   VSSGTG M+PTPG+ QQAQSG+Q L  +N++A NMQLSQ +S A+ +SQ
Sbjct:   494 QNMMSGLGQGNVSSGTGGMMPTPGVGQQAQSGIQQLGGSNSSAPNMQLSQPSSGAMQTSQ 553

Query:   550 SKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQ 609
             SKYVKVWEG+LSGQRQGQPV IT+LEGYRSASAS++LAANWPPTMQIVRLISQDHMNNKQ
Sbjct:   554 SKYVKVWEGNLSGQRQGQPVLITRLEGYRSASASDSLAANWPPTMQIVRLISQDHMNNKQ 613

Query:   610 YVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVV 669
             YVGKADFLVFRAM+QHGFLGQLQ+KKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVV
Sbjct:   614 YVGKADFLVFRAMSQHGFLGQLQDKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVV 673

Query:   670 FK 671
             FK
Sbjct:   674 FK 675

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0003713 "transcription coactivator activity" evidence=NAS

GO:0010114 "response to red light" evidence=IMP

GO:0010218 "response to far red light" evidence=IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IMP

GO:0016592 "mediator complex" evidence=IDA

GO:0009909 "regulation of flower development" evidence=IMP

GO:0009585 "red, far-red light phototransduction" evidence=IMP

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=IMP

GO:0031349 "positive regulation of defense response" evidence=IMP

GO:0050832 "defense response to fungus" evidence=IMP

GO:0009911 "positive regulation of flower development" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F1N3D4 MED25 "Mediator of RNA polymerase II transcription subunit 25" [Bos taurus (taxid:9913)]

 Score = 115 (45.5 bits), Expect = 2.5e-08, Sum P(3) = 2.5e-08
 Identities = 35/94 (37%), Positives = 47/94 (50%)

Query:    35 ELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMM 93
             + SLV FNT        VQ    T     F+ WL  I F GGG    + IAEGLS AL +
Sbjct:    65 QYSLVVFNTVDCAPESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQL 124

Query:    94 FSVAPNGSQNQQNVDGQRH--CILVAASNPHPLP 125
             F    +  + ++ + GQ H  C+L+  S P+ LP
Sbjct:   125 FD---DFKKMREQI-GQTHRVCLLICNSPPYLLP 154

GO:2001178 "positive regulation of mediator complex assembly" evidence=IEA

GO:0071158 "positive regulation of cell cycle arrest" evidence=IEA

GO:0048147 "negative regulation of fibroblast proliferation" evidence=IEA

GO:0046965 "retinoid X receptor binding" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0035563 "positive regulation of chromatin binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|F1RHT9 MED25 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 115 (45.5 bits), Expect = 7.3e-08, Sum P(2) = 7.3e-08
 Identities = 35/94 (37%), Positives = 47/94 (50%)

Query:    35 ELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMM 93
             + SLV FNT        VQ    T     F+ WL  I F GGG    + IAEGLS AL +
Sbjct:    65 QYSLVVFNTVDCAPESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQL 124

Query:    94 FSVAPNGSQNQQNVDGQRH--CILVAASNPHPLP 125
             F    +  + ++ + GQ H  C+L+  S P+ LP
Sbjct:   125 FD---DFKKMREQI-GQTHRVCLLICNSPPYLLP 154

GO:2001178 "positive regulation of mediator complex assembly" evidence=IEA

GO:0071158 "positive regulation of cell cycle arrest" evidence=IEA

GO:0048147 "negative regulation of fibroblast proliferation" evidence=IEA

GO:0046965 "retinoid X receptor binding" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0035563 "positive regulation of chromatin binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

MGI|MGI:1922863 Med25 "mediator of RNA polymerase II transcription, subunit 25 homolog (yeast)" [Mus musculus (taxid:10090)]

 Score = 115 (45.5 bits), Expect = 7.9e-08, Sum P(3) = 7.9e-08
 Identities = 35/94 (37%), Positives = 47/94 (50%)

Query:    35 ELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMM 93
             + SLV FNT        VQ    T     F+ WL  I F GGG    + IAEGLS AL +
Sbjct:    65 QYSLVVFNTVDCAPESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQL 124

Query:    94 FSVAPNGSQNQQNVDGQRH--CILVAASNPHPLP 125
             F    +  + ++ + GQ H  C+L+  S P+ LP
Sbjct:   125 FD---DFKKMREQI-GQTHRVCLLICNSPPYLLP 154

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

GO:0035563 "positive regulation of chromatin binding" evidence=ISO

GO:0042974 "retinoic acid receptor binding" evidence=ISO;IPI

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0046965 "retinoid X receptor binding" evidence=ISO;IPI

GO:0048147 "negative regulation of fibroblast proliferation" evidence=ISO

GO:0071158 "positive regulation of cell cycle arrest" evidence=ISO

GO:2001178 "positive regulation of mediator complex assembly" evidence=ISO

UNIPROTKB|A2VE44 MED25 "Mediator of RNA polymerase II transcription subunit 25" [Bos taurus (taxid:9913)]

 Score = 115 (45.5 bits), Expect = 8.0e-08, Sum P(3) = 8.0e-08
 Identities = 35/94 (37%), Positives = 47/94 (50%)

Query:    35 ELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMM 93
             + SLV FNT        VQ    T     F+ WL  I F GGG    + IAEGLS AL +
Sbjct:    65 QYSLVVFNTVDCAPESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQL 124

Query:    94 FSVAPNGSQNQQNVDGQRH--CILVAASNPHPLP 125
             F    +  + ++ + GQ H  C+L+  S P+ LP
Sbjct:   125 FD---DFKKMREQI-GQTHRVCLLICNSPPYLLP 154

GO:0005634 "nucleus" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|Q71SY5 MED25 "Mediator of RNA polymerase II transcription subunit 25" [Homo sapiens (taxid:9606)]

 Score = 115 (45.5 bits), Expect = 3.2e-06, Sum P(3) = 3.2e-06
 Identities = 35/94 (37%), Positives = 47/94 (50%)

Query:    35 ELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMM 93
             + SLV FNT        VQ    T     F+ WL  I F GGG    + IAEGLS AL +
Sbjct:    65 QYSLVVFNTVDCAPESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQL 124

Query:    94 FSVAPNGSQNQQNVDGQRH--CILVAASNPHPLP 125
             F    +  + ++ + GQ H  C+L+  S P+ LP
Sbjct:   125 FD---DFKKMREQI-GQTHRVCLLICNSPPYLLP 154

GO:0042974 "retinoic acid receptor binding" evidence=IPI

GO:0046965 "retinoid X receptor binding" evidence=IPI

GO:0035563 "positive regulation of chromatin binding" evidence=IMP

GO:0008134 "transcription factor binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:2001178 "positive regulation of mediator complex assembly" evidence=IMP

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP

GO:0048147 "negative regulation of fibroblast proliferation" evidence=IMP

GO:0071158 "positive regulation of cell cycle arrest" evidence=IMP

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

ZFIN|ZDB-GENE-040426-2850 med25 "mediator of RNA polymerase II transcription, subunit 25 homolog (yeast)" [Danio rerio (taxid:7955)]

 Score = 112 (44.5 bits), Expect = 6.4e-06, Sum P(4) = 6.4e-06
 Identities = 33/94 (35%), Positives = 47/94 (50%)

Query:    35 ELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMM 93
             +  LV FNT        VQ    T     F+ W+ +I F GGG    + IAEGLS AL +
Sbjct:    62 QYGLVVFNTVDCAPESYVQCHAPTSSAFEFVSWIDSIQFMGGGAESCSLIAEGLSVALQL 121

Query:    94 FSVAPNGSQNQQNVDGQRH--CILVAASNPHPLP 125
             F    +  + ++ + GQ H  C+L+  S P+ LP
Sbjct:   122 FD---DFKKMREQI-GQTHKVCVLLCNSPPYLLP 151

GO:0003674 "molecular_function" evidence=ND

GO:0060021 "palate development" evidence=IMP

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

WB|WBGene00019435 K06A9.1 [Caenorhabditis elegans (taxid:6239)]

 Score = 144 (55.7 bits), Expect = 1.2e-05, P = 1.2e-05
 Identities = 75/341 (21%), Positives = 130/341 (38%)

Query:   228 APNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGP 287
             +PN +          +++G +   + +V+G     +S G+  T+   +  ST T   +  
Sbjct:   534 SPNPSSSPASTGSTITISGSSSIIVSTVSGST---VS-GSTGTSQSTLASSTATPG-SSS 588

Query:   288 TFPHIPSVPRPASQGVXXXXXXXXXXXXXEMITSGDSVPEVKPLVSGMSQPLRPMAPAAA 347
             T P   S P+P+SQ                   S    P            + P    A+
Sbjct:   589 TVPSSSS-PQPSSQSPAPNTGSTTPSQTSSQSPSPSMNPSSSTPTGSSQSTITPEGSTAS 647

Query:   348 NV--NILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPV 405
             +   +  +  S A +V + + +  G+S+G QS   +P    +S   +SGM  S  TS+P 
Sbjct:   648 SPTGSTGSTFSVATEVTSQSTVPSGSSLGTQSTNSSPSPSSLSPS-TSGM--STLTSEPS 704

Query:   406 FSSAQXXXXXXXXXXXXXXXXQVPQNSGLNSFTSAPSNLSGNS-----NPSISQPMGTLQ 460
              SS Q                Q    S L S TS  +  SG++     +PS S  +G+ Q
Sbjct:   705 PSSTQSSGAQSTLTTPSPNPSQ--STSSLESSTSGATTSSGSAGTTMTSPSQSSSVGSSQ 762

Query:   461 GGASMGQSVGMSQGNHSGG-QMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQ 519
             G  S   S    +    G  Q   + +S +  +++    S  ++  G+ +  P     + 
Sbjct:   763 GSTSPAASTTSGEMTSQGSTQTPGSSVSTSAAILTSTQQSVSTNSPGSTVTRPSTVSGST 822

Query:   520 SGMQPLSVNNNTAVNMQLSQQTSS-ALHSSQSKYVKVWEGS 559
             S    ++V +  A     S  +SS A  +SQ+       GS
Sbjct:   823 SSGSTVTVGSTEASTSGSSVASSSPAPSTSQNPNPSTSSGS 863

GO:0016021 "integral to membrane" evidence=IEA

DICTYBASE|DDB_G0286967 med25 "putative mediator complex subunit 25" [Dictyostelium discoideum (taxid:44689)]

 Score = 89 (36.4 bits), Expect = 2.2e-05, Sum P(4) = 2.2e-05
 Identities = 27/90 (30%), Positives = 43/90 (47%)

Query:    33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDA-AIAEGLSEAL 91
             N    LV F  +  Y   +   +  TKD+   L  ++T  F GGGF+   AI+EG+ +AL
Sbjct:   185 NFTYGLVLFRDYPPYSDFIASSTPLTKDLKTILTLMATTKFNGGGFSTGGAISEGICKAL 244

Query:    92 MMFSVAPNGSQNQQNVDGQRHCILVAASNP 121
              + S +       Q +  +   IL+  +NP
Sbjct:   245 RLASCS-------QTIIHEECFILITNNNP 267

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

POMBASE|SPAPB1E7.04c SPAPB1E7.04c "chitinase (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 137 (53.3 bits), Expect = 3.4e-05, P = 3.4e-05
 Identities = 67/316 (21%), Positives = 130/316 (41%)

Query:   242 TSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQ 301
             T++T    TS+ +    +   ++   V T+T+ +  S  TS++      ++ +V +PAS 
Sbjct:   387 TTITASGATSVTTTTKTDFDTVTTTIVSTSTL-ISASDSTSII---VSSYVSTVTQPAST 442

Query:   302 GVXXXXXXXXXXXXXE----MITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQ 357
              V             +    + +S  SVP    +    S P+   + A++  + L+  S+
Sbjct:   443 RVQTTTVSSISTSVKQPTASVASSSVSVPSSSSVQPQSSTPISSSSSASSPQSTLSTSSE 502

Query:   358 ARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQXXXXXXX 417
                 +++  L+G ++I   S   TP +  +S+ ++S ++SS  +S P  SS+        
Sbjct:   503 VVSEVSSTLLSGSSAIPSTS-SSTPSSSIISSPMTSVLSSS--SSIPT-SSSSDFSSSIT 558

Query:   418 XXXXXXXXXQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHS 477
                       +P     ++F+S  S LS     S S P  T    +S   S   S  + S
Sbjct:   559 TISSGISSSSIP-----STFSSVSSILSS----STSSPSSTSLSISSSSTSSTFSSASTS 609

Query:   478 GGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQL 537
                 + + IS +  ++S   PS  S    +     G S    S +  + ++++ +     
Sbjct:   610 SPSSISSSISSSSTILSSPTPSTSSLMISSSSIISGSSSILSSSISTIPISSSLSTYSSS 669

Query:   538 SQQTSSALHSSQSKYV 553
                +SS L SS S  +
Sbjct:   670 VIPSSSTLVSSSSSLI 685

GO:0000324 "fungal-type vacuole" evidence=IDA

GO:0000920 "cytokinetic cell separation" evidence=ISO

GO:0004568 "chitinase activity" evidence=ISO

GO:0005576 "extracellular region" evidence=IEA

GO:0009277 "fungal-type cell wall" evidence=ISO

GO:0009986 "cell surface" evidence=IC

GO:0034232 "ascospore wall chitin catabolic process" evidence=IC

GO:0046379 "extracellular polysaccharide metabolic process" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q7XYY2	MED25_ARATH	No assigned EC number	0.6519	0.7933	0.7763	yes	no

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	818
pfam11265	226	pfam11265, Med25_VWA, Mediator complex subunit 25	5e-52
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	6e-16
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	5e-15
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	1e-14
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-14
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	3e-14
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	5e-14
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-13
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-13
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	1e-12
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	4e-11
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	8e-11
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	8e-11
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	8e-11
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	5e-10
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	1e-09
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	2e-09
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	2e-09
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	4e-09
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	4e-09
COG3064	387	COG3064, TolA, Membrane protein involved in colici	7e-09
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	8e-09
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	1e-08
PRK00286	438	PRK00286, xseA, exodeoxyribonuclease VII large sub	1e-08
pfam11498	476	pfam11498, Activator_LAG-3, Transcriptional activa	1e-08
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	2e-08
PRK00286	438	PRK00286, xseA, exodeoxyribonuclease VII large sub	2e-08
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	3e-08
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	7e-08
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	1e-07
PRK00286	438	PRK00286, xseA, exodeoxyribonuclease VII large sub	1e-07
PRK00286	438	PRK00286, xseA, exodeoxyribonuclease VII large sub	1e-07
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	2e-07
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	2e-07
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	6e-07
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	6e-07
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	6e-07
COG3264	835	COG3264, COG3264, Small-conductance mechanosensiti	1e-06
COG1570	440	COG1570, XseA, Exonuclease VII, large subunit [DNA	1e-06
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	2e-06
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	3e-06
COG3264	835	COG3264, COG3264, Small-conductance mechanosensiti	4e-06
pfam12128	1198	pfam12128, DUF3584, Protein of unknown function (D	4e-06
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	4e-06
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	4e-06
COG3064	387	COG3064, TolA, Membrane protein involved in colici	5e-06
pfam11498	476	pfam11498, Activator_LAG-3, Transcriptional activa	5e-06
TIGR00237	432	TIGR00237, xseA, exodeoxyribonuclease VII, large s	5e-06
PRK06800	228	PRK06800, fliH, flagellar assembly protein H; Vali	5e-06
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	6e-06
pfam11932	250	pfam11932, DUF3450, Protein of unknown function (D	6e-06
PRK10927	319	PRK10927, PRK10927, essential cell division protei	8e-06
pfam02050	122	pfam02050, FliJ, Flagellar FliJ protein	9e-06
COG1570	440	COG1570, XseA, Exonuclease VII, large subunit [DNA	1e-05
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	1e-05
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	1e-05
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	1e-05
pfam11498	476	pfam11498, Activator_LAG-3, Transcriptional activa	2e-05
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	2e-05
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	2e-05
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	2e-05
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	2e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	2e-05
pfam03280	189	pfam03280, Lipase_chap, Proteobacterial lipase cha	2e-05
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	3e-05
COG3264	835	COG3264, COG3264, Small-conductance mechanosensiti	3e-05
PRK10927	319	PRK10927, PRK10927, essential cell division protei	3e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-05
PRK01294	336	PRK01294, PRK01294, lipase chaperone; Provisional	3e-05
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	4e-05
PRK10927	319	PRK10927, PRK10927, essential cell division protei	4e-05
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	4e-05
COG4372	499	COG4372, COG4372, Uncharacterized protein conserve	4e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	5e-05
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	5e-05
TIGR02473	141	TIGR02473, flagell_FliJ, flagellar export protein	5e-05
pfam11068	131	pfam11068, DUF2869, Protein of unknown function (D	5e-05
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	6e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	7e-05
pfam11068	131	pfam11068, DUF2869, Protein of unknown function (D	7e-05
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	8e-05
COG2959	391	COG2959, HemX, Uncharacterized enzyme of heme bios	8e-05
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	9e-05
TIGR02794	346	TIGR02794, tolA_full, TolA protein	9e-05
pfam03280	189	pfam03280, Lipase_chap, Proteobacterial lipase cha	9e-05
pfam12474	142	pfam12474, PKK, Polo kinase kinase	9e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	1e-04
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	1e-04
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	1e-04
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	1e-04
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	1e-04
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	1e-04
TIGR00237	432	TIGR00237, xseA, exodeoxyribonuclease VII, large s	1e-04
pfam02050	122	pfam02050, FliJ, Flagellar FliJ protein	1e-04
pfam03280	189	pfam03280, Lipase_chap, Proteobacterial lipase cha	1e-04
TIGR02473	141	TIGR02473, flagell_FliJ, flagellar export protein	1e-04
COG1322	448	COG1322, COG1322, Predicted nuclease of restrictio	1e-04
PRK11448	1123	PRK11448, hsdR, type I restriction enzyme EcoKI su	1e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	1e-04
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	1e-04
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	1e-04
TIGR00237	432	TIGR00237, xseA, exodeoxyribonuclease VII, large s	2e-04
pfam11932	250	pfam11932, DUF3450, Protein of unknown function (D	2e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	2e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-04
COG3166	206	COG3166, PilN, Tfp pilus assembly protein PilN [Ce	2e-04
COG3166	206	COG3166, PilN, Tfp pilus assembly protein PilN [Ce	2e-04
pfam12795	239	pfam12795, MscS_porin, Mechanosensitive ion channe	2e-04
PRK11637	428	PRK11637, PRK11637, AmiB activator; Provisional	2e-04
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	3e-04
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	3e-04
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	3e-04
pfam11068	131	pfam11068, DUF2869, Protein of unknown function (D	3e-04
COG2959	391	COG2959, HemX, Uncharacterized enzyme of heme bios	3e-04
pfam12795	239	pfam12795, MscS_porin, Mechanosensitive ion channe	3e-04
COG3115	324	COG3115, ZipA, Cell division protein [Cell divisio	3e-04
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	4e-04
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	4e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
pfam11068	131	pfam11068, DUF2869, Protein of unknown function (D	4e-04
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	4e-04
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	4e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	4e-04
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	4e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	4e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	5e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	5e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	5e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	5e-04
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	6e-04
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	6e-04
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	6e-04
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	6e-04
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	6e-04
TIGR02302	851	TIGR02302, aProt_lowcomp, TIGR02302 family protein	6e-04
COG0845	372	COG0845, AcrA, Membrane-fusion protein [Cell envel	6e-04
PRK11637	428	PRK11637, PRK11637, AmiB activator; Provisional	7e-04
pfam12037	276	pfam12037, DUF3523, Domain of unknown function (DU	7e-04
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	8e-04
pfam12128	1198	pfam12128, DUF3584, Protein of unknown function (D	8e-04
pfam11932	250	pfam11932, DUF3450, Protein of unknown function (D	8e-04
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	8e-04
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	8e-04
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	8e-04
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	8e-04
pfam03938	157	pfam03938, OmpH, Outer membrane protein (OmpH-like	8e-04
pfam03938	157	pfam03938, OmpH, Outer membrane protein (OmpH-like	8e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	9e-04
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	0.001
TIGR00237	432	TIGR00237, xseA, exodeoxyribonuclease VII, large s	0.001
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	0.001
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	0.001
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.001
pfam12037	276	pfam12037, DUF3523, Domain of unknown function (DU	0.001
pfam11180	192	pfam11180, DUF2968, Protein of unknown function (D	0.001
TIGR01843	423	TIGR01843, type_I_hlyD, type I secretion membrane	0.001
PRK01741	332	PRK01741, PRK01741, cell division protein ZipA; Pr	0.001
COG5380	283	COG5380, LimK, Lipase chaperone [Posttranslational	0.001
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	0.001
COG1570	440	COG1570, XseA, Exonuclease VII, large subunit [DNA	0.002
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	0.002
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	0.002
pfam02050	122	pfam02050, FliJ, Flagellar FliJ protein	0.002
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	0.002
PRK01294	336	PRK01294, PRK01294, lipase chaperone; Provisional	0.002
PRK01294	336	PRK01294, PRK01294, lipase chaperone; Provisional	0.002
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	0.002
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	0.002
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	0.002
PRK11448	1123	PRK11448, hsdR, type I restriction enzyme EcoKI su	0.002
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.002
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	0.002
COG3166	206	COG3166, PilN, Tfp pilus assembly protein PilN [Ce	0.002
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	0.002
TIGR02302	851	TIGR02302, aProt_lowcomp, TIGR02302 family protein	0.002
TIGR02302	851	TIGR02302, aProt_lowcomp, TIGR02302 family protein	0.002
pfam07321	152	pfam07321, YscO, Type III secretion protein YscO	0.002
pfam07321	152	pfam07321, YscO, Type III secretion protein YscO	0.002
pfam07321	152	pfam07321, YscO, Type III secretion protein YscO	0.002
PRK11147	635	PRK11147, PRK11147, ABC transporter ATPase compone	0.002
pfam04375	372	pfam04375, HemX, HemX	0.002
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	0.002
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	0.003
pfam12128	1198	pfam12128, DUF3584, Protein of unknown function (D	0.003
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.003
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	0.003
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.003
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.003
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	0.003
COG3115	324	COG3115, ZipA, Cell division protein [Cell divisio	0.003
COG5380	283	COG5380, LimK, Lipase chaperone [Posttranslational	0.003
COG4487	438	COG4487, COG4487, Uncharacterized protein conserve	0.003
pfam12203	92	pfam12203, HDAC4_Gln, Glutamine rich N terminal do	0.003
PRK00286	438	PRK00286, xseA, exodeoxyribonuclease VII large sub	0.004
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	0.004
PRK01294	336	PRK01294, PRK01294, lipase chaperone; Provisional	0.004
COG3115	324	COG3115, ZipA, Cell division protein [Cell divisio	0.004
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	0.004
PRK01741	332	PRK01741, PRK01741, cell division protein ZipA; Pr	0.004
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	0.004
TIGR03319	514	TIGR03319, RNase_Y, ribonuclease Y	0.004
COG0760	320	COG0760, SurA, Parvulin-like peptidyl-prolyl isome	0.004
pfam04156	186	pfam04156, IncA, IncA protein	0.004

>gnl|CDD|221051 pfam11265, Med25_VWA, Mediator complex subunit 25 von Willebrand factor type A

 Score =  180 bits (459), Expect = 5e-52
 Identities = 67/200 (33%), Positives = 88/200 (44%), Gaps = 20/200 (10%)

Query: 17  RCFCVNELAGQKTSASN--VELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFA 74
             F     A           + SLV FNT  S     VQ  G T+DVD FLHWL +I F 
Sbjct: 43  EYFNGGPPAETDFGGEYGGTQYSLVVFNTVASAPESYVQCHGPTRDVDEFLHWLDSIQFM 102

Query: 75  GGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQM 133
           GGG    + IAEGL+EAL +F       Q     D  RHCIL+  S P+ LPT       
Sbjct: 103 GGGGESCSLIAEGLAEALQLFDDFSEMRQQIGQTDLHRHCILICNSPPYLLPT------- 155

Query: 134 QNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRN-PRAA 192
                     A  E + SD         +  + LS+I P++LP L  ++  AK +     
Sbjct: 156 -------VESASYEGKTSDQLAAI--IYERGIHLSIIAPRKLPALRLLFEKAKPDQQLPM 206

Query: 193 DPPVDNSKNPHFLVLISENF 212
              +D +KNP  +VL+   F
Sbjct: 207 KSSIDYAKNPFHMVLLRGIF 226

The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex. Length = 226

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 81.9 bits (203), Expect = 6e-16
 Identities = 37/130 (28%), Positives = 48/130 (36%), Gaps = 27/130 (20%)

Query: 680 QQLQQ--------QQQQQQHQQMQSQLQHQQLSQLQQQQQQL---------PQLQQQIPQ 722
           +QLQQ        Q  Q    +MQ  ++   L +  ++QQ L          Q   Q  +
Sbjct: 564 EQLQQMMENLQVTQGGQGGQSEMQQAME--GLGETLREQQGLSDETFRDLQEQFNAQRGE 621

Query: 723 LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLS-----QPQ 777
            Q QQ      Q    Q  QQ Q  Q QQQ Q  Q  Q  Q    ++QQ L      Q  
Sbjct: 622 QQGQQGQGGQGQG---QPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQQALRDELGRQRG 678

Query: 778 QMVGSGMGQG 787
            + G G   G
Sbjct: 679 GLPGMGGEAG 688

Length = 820

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 79.2 bits (196), Expect = 5e-15
 Identities = 45/163 (27%), Positives = 59/163 (36%), Gaps = 32/163 (19%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQ-------------QQQLPQLQQ- 718
           Q++ Q Q+  QQ  Q         +L  Q L ++  +             QQ L QLQQ 
Sbjct: 511 QLAEQAQRNPQQGDQPPDQGNSM-ELTQQDLQRMMDRIEELMESGRRAEAQQLLEQLQQM 569

Query: 719 ----QIPQLQQQQQIPQLQQQSMPQL----QQQQQL-----PQLQQQQQLPQMQQQQQLP 765
               Q+ Q  Q  Q     QQ+M  L    ++QQ L       LQ+Q      + +QQ  
Sbjct: 570 MENLQVTQGGQGGQSEM--QQAMEGLGETLREQQGLSDETFRDLQEQFN--AQRGEQQGQ 625

Query: 766 QLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGA 808
           Q Q  Q   QP Q    G GQ   Q     Q         Q A
Sbjct: 626 QGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQQA 668

Length = 820

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 78.0 bits (193), Expect = 1e-14
 Identities = 47/159 (29%), Positives = 61/159 (38%), Gaps = 38/159 (23%)

Query: 680 QQLQQQQQQ--QQHQQMQSQLQHQQLSQ--LQQQ----------------QQQLPQLQQ- 718
           +QL +Q Q+  QQ  Q   Q    +L+Q  LQ+                 QQ L QLQQ 
Sbjct: 510 RQLAEQAQRNPQQGDQPPDQGNSMELTQQDLQRMMDRIEELMESGRRAEAQQLLEQLQQM 569

Query: 719 ----QIPQLQQQQQIPQLQQQSMPQL----QQQQQL-------PQLQQQQQLPQMQQQQQ 763
               Q+ Q  Q  Q     QQ+M  L    ++QQ L        Q Q   Q  + Q QQ 
Sbjct: 570 MENLQVTQGGQGGQSE--MQQAMEGLGETLREQQGLSDETFRDLQEQFNAQRGEQQGQQG 627

Query: 764 LPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQ 802
                Q Q   Q QQ  G   GQ    G G    +++ Q
Sbjct: 628 QGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQ 666

Length = 820

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 77.1 bits (190), Expect = 2e-14
 Identities = 39/130 (30%), Positives = 45/130 (34%), Gaps = 7/130 (5%)

Query: 670 FKPQISSQQQQQLQQQQQQQQHQQM-----QSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 724
             P+      Q  Q   +Q Q QQ      Q+  Q     QL QQ   L Q Q      Q
Sbjct: 195 GPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQ 254

Query: 725 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ--LPQLQQQQQLSQPQQMVGS 782
                PQ  QQ     Q Q Q P   Q    P + Q Q   LP  QQ Q L   QQ  G 
Sbjct: 255 MPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQ 314

Query: 783 GMGQGYVQGP 792
             G  + +  
Sbjct: 315 QRGPQFREQL 324

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 76.3 bits (188), Expect = 3e-14
 Identities = 38/152 (25%), Positives = 44/152 (28%), Gaps = 11/152 (7%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
               QQ  QL Q  QQ   Q M  +          +Q    PQ  Q  P+  Q QQ    
Sbjct: 163 LQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPA 222

Query: 733 QQQSMPQLQQQQQLPQ----LQQQQQLPQMQQQQQLPQLQQQQQLSQPQ-------QMVG 781
             Q+  Q     QLPQ    LQQ Q     QQ    P    QQQ   PQ       Q   
Sbjct: 223 PSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQP 282

Query: 782 SGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPG 813
           +                 Q Q+          
Sbjct: 283 TPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQ 314

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 76.0 bits (187), Expect = 5e-14
 Identities = 45/139 (32%), Positives = 51/139 (36%), Gaps = 4/139 (2%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           PQ    +Q     Q  Q   +Q+Q Q      SQ   Q    PQL QQ P LQQ Q    
Sbjct: 192 PQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGL 251

Query: 732 LQQQSMPQLQQQQQLPQ-LQQQQQLPQMQQQQQLPQLQQQQQLSQP---QQMVGSGMGQG 787
            QQ   P  Q  QQ  Q  Q Q Q P   Q    P L Q Q    P   Q  +   + Q 
Sbjct: 252 SQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQP 311

Query: 788 YVQGPGRTQLVSQGQVSSQ 806
             Q  G        Q+S Q
Sbjct: 312 QGQQRGPQFREQLVQLSQQ 330

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 74.0 bits (182), Expect = 2e-13
 Identities = 42/111 (37%), Positives = 47/111 (42%), Gaps = 9/111 (8%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           P    QQ   LQQ Q     QQM          Q  QQQQQ PQ Q Q P   Q    P 
Sbjct: 233 PPQLPQQPPPLQQPQFPGLSQQMP-----PPPPQPPQQQQQPPQPQAQPPPQNQPTPHPG 287

Query: 732 LQQQS--MPQLQQQQQLPQLQQQQQ--LPQMQQQQQLPQLQQQQQLSQPQQ 778
           L Q         QQ QL  L QQ Q      Q ++QL QL QQQ+ +  Q+
Sbjct: 288 LPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQLSQQQREALSQE 338

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 73.6 bits (181), Expect = 2e-13
 Identities = 34/116 (29%), Positives = 36/116 (31%)

Query: 663 FPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQ 722
           +P        Q+  QQ      Q   Q     Q   Q   L Q Q               
Sbjct: 203 YPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQP 262

Query: 723 LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
            QQQQQ PQ Q Q  PQ Q        Q Q       QQ QL  L QQ Q  Q   
Sbjct: 263 PQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQQRGP 318

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 71.5 bits (176), Expect = 1e-12
 Identities = 28/100 (28%), Positives = 42/100 (42%), Gaps = 15/100 (15%)

Query: 677 QQQQQL-----QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           ++QQ L     +  Q+Q   Q+ + Q Q  Q      Q Q  P  Q Q  Q QQQ Q  Q
Sbjct: 598 REQQGLSDETFRDLQEQFNAQRGEQQGQQGQ----GGQGQGQPGQQGQQGQGQQQGQQGQ 653

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ 771
             Q     L ++QQ   L+ +      +Q+  LP +  + 
Sbjct: 654 GGQGGQGSLAERQQ--ALRDELG----RQRGGLPGMGGEA 687

Length = 820

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 66.5 bits (163), Expect = 4e-11
 Identities = 42/157 (26%), Positives = 57/157 (36%), Gaps = 34/157 (21%)

Query: 692 QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ--LQ---------------- 733
           Q+++  L    + QL +Q Q+ PQ   Q P      ++ Q  LQ                
Sbjct: 499 QELREALD-DYMRQLAEQAQRNPQQGDQPPDQGNSMELTQQDLQRMMDRIEELMESGRRA 557

Query: 734 --QQSMPQLQQ---QQQLPQLQQQQQLPQMQQQQQLPQ-LQQQQQLS---------QPQQ 778
             QQ + QLQQ     Q+ Q  Q  Q    Q  + L + L++QQ LS         Q   
Sbjct: 558 EAQQLLEQLQQMMENLQVTQGGQGGQSEMQQAMEGLGETLREQQGLSDETFRDLQEQFNA 617

Query: 779 MVGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGGG 815
             G   GQ    G G+ Q   QGQ          G G
Sbjct: 618 QRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQG 654

Length = 820

>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 65.3 bits (160), Expect = 8e-11
 Identities = 41/181 (22%), Positives = 58/181 (32%), Gaps = 48/181 (26%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           Q     Q+  QQ QQ Q  Q      Q  Q  Q QQQ QQ    Q     L ++QQ   L
Sbjct: 612 QEQFNAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQQ--AL 669

Query: 733 QQQSMPQLQQQQQ-LPQL------------------------------------QQQQQL 755
           +     +L +Q+  LP +                                    +Q + L
Sbjct: 670 RD----ELGRQRGGLPGMGGEAGEAARDALGRAGRAMGGAEEALGQGDLAEAVDRQGRAL 725

Query: 756 PQMQQ--QQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGP-GRTQLVSQGQVSSQGAPNIP 812
             +++  +     + QQQ   Q  Q    G   G  + P GR     QG         +P
Sbjct: 726 EALREGARALGEAMAQQQGQQQGGQGQQQGRQGGNGRDPLGR-PRGGQGPDGGDRVK-VP 783

Query: 813 G 813
           G
Sbjct: 784 G 784

Length = 820

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 65.6 bits (160), Expect = 8e-11
 Identities = 33/139 (23%), Positives = 43/139 (30%), Gaps = 1/139 (0%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 730
           KP+    Q  + Q Q Q    + +  +    QL Q QQ  Q     QQ +PQ    +Q  
Sbjct: 131 KPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAA 190

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQ 790
             QQ    Q     Q PQ   +Q  PQ           Q     Q  Q     + Q    
Sbjct: 191 FPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPP-LQQPQFP 249

Query: 791 GPGRTQLVSQGQVSSQGAP 809
           G  +       Q   Q   
Sbjct: 250 GLSQQMPPPPPQPPQQQQQ 268

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 65.6 bits (160), Expect = 8e-11
 Identities = 31/95 (32%), Positives = 37/95 (38%), Gaps = 4/95 (4%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQL-SQLQQQQQQLPQLQQQIPQLQQQQQIP 730
           PQ     QQ      Q  Q QQ   Q Q Q            LPQ Q       QQ Q+ 
Sbjct: 246 PQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLL 305

Query: 731 QLQQQSMPQL---QQQQQLPQLQQQQQLPQMQQQQ 762
            L QQ   Q    Q ++QL QL QQQ+    Q++ 
Sbjct: 306 PLVQQPQGQQRGPQFREQLVQLSQQQREALSQEEA 340

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 62.9 bits (153), Expect = 5e-10
 Identities = 35/146 (23%), Positives = 44/146 (30%), Gaps = 5/146 (3%)

Query: 670 FKPQISSQQQQQLQQQQQQQ-----QHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 724
            +PQ     + Q Q Q   Q     +  + Q Q + Q     Q  QQ LPQ         
Sbjct: 132 PEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAF 191

Query: 725 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGM 784
            QQ  P+         Q   +  Q QQ    P     Q     Q  QQ    QQ    G+
Sbjct: 192 PQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGL 251

Query: 785 GQGYVQGPGRTQLVSQGQVSSQGAPN 810
            Q     P +     Q     Q  P 
Sbjct: 252 SQQMPPPPPQPPQQQQQPPQPQAQPP 277

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 61.6 bits (149), Expect = 1e-09
 Identities = 53/145 (36%), Positives = 53/145 (36%), Gaps = 14/145 (9%)

Query: 677 QQQQQLQQQQQQ----------QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 726
            Q QQ    QQQ              Q Q Q Q Q   Q QQ  Q   QLQ Q  Q   Q
Sbjct: 181 NQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQ 240

Query: 727 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLP---QMQQQQQLPQLQQQQQLSQPQQMVG-S 782
           QQ P   Q  M Q QQ Q   Q QQ Q       MQQQ    Q QQ Q    P QM    
Sbjct: 241 QQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLGMLPNQMQQMP 300

Query: 783 GMGQGYVQGPGRTQLVSQGQVSSQG 807
           G GQG    P        G V   G
Sbjct: 301 GGGQGGPGQPMGPPPQRPGAVPQGG 325

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 61.2 bits (148), Expect = 2e-09
 Identities = 50/152 (32%), Positives = 55/152 (36%), Gaps = 2/152 (1%)

Query: 657 RLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQL 716
           R+  M   G       Q S Q Q Q   Q   QQ Q         Q  Q    QQQ PQ+
Sbjct: 137 RVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQPPQM 196

Query: 717 QQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQ--QLPQLQQQQQLS 774
            Q        Q   Q Q Q   Q QQ  Q+ Q  Q QQ  QM QQQ     Q Q  QQ  
Sbjct: 197 GQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQGPADAQAQMGQQQQ 256

Query: 775 QPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQ 806
               M    M  G +Q P + Q   Q    SQ
Sbjct: 257 GQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQ 288

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 60.8 bits (147), Expect = 2e-09
 Identities = 48/134 (35%), Positives = 56/134 (41%), Gaps = 2/134 (1%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           Q QQQ Q   QQQQ+ QMQ QLQ+QQ  Q+ QQQ      Q Q+ Q QQ Q   Q QQ  
Sbjct: 209 QMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQGPA-DAQAQMGQQQQGQGGMQPQQMQ 267

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQ 796
             Q+Q   Q    QQQ Q  Q+       Q         P Q       Q     P   Q
Sbjct: 268 GGQMQVPMQQQPPQQQPQQSQLGMLPNQMQQMPGGGQGGPGQP-MGPPPQRPGAVPQGGQ 326

Query: 797 LVSQGQVSSQGAPN 810
            V QG +S+     
Sbjct: 327 AVQQGVMSAGQQQL 340

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 59.8 bits (145), Expect = 4e-09
 Identities = 31/138 (22%), Positives = 41/138 (29%), Gaps = 5/138 (3%)

Query: 679 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMP 738
             + + Q  Q    Q Q Q   Q++  L++ + QL Q QQ       Q     L Q   P
Sbjct: 129 APKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQA--PQLPQPPQQVLPQGMPP 186

Query: 739 Q---LQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRT 795
           +     QQ    Q     Q PQ   +Q  PQ         P Q               + 
Sbjct: 187 RQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQP 246

Query: 796 QLVSQGQVSSQGAPNIPG 813
           Q     Q      P  P 
Sbjct: 247 QFPGLSQQMPPPPPQPPQ 264

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 59.0 bits (143), Expect = 4e-09
 Identities = 21/73 (28%), Positives = 44/73 (60%), Gaps = 3/73 (4%)

Query: 701 QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQ--LQQQQQLPQM 758
           +Q ++ QQQQ+   + ++Q  + ++QQQ  +LQQ+   + ++ +QL +  L  Q+Q  Q 
Sbjct: 62  EQYNRQQQQQKSAKRAEEQ-RKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQA 120

Query: 759 QQQQQLPQLQQQQ 771
           ++  +   L+Q+Q
Sbjct: 121 EEAAKQAALKQKQ 133

Length = 387

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 58.4 bits (141), Expect = 7e-09
 Identities = 26/107 (24%), Positives = 56/107 (52%), Gaps = 11/107 (10%)

Query: 666 DMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 725
           D V+  P    QQ  ++Q QQ   +  + Q +         ++++Q   +L+    Q  +
Sbjct: 51  DAVMVDPGAVVQQYGRIQSQQSSAKKGEQQRK---------KKEEQVAEELKP--KQAAE 99

Query: 726 QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
           Q+++ QL+++ +   +QQ+Q  + ++Q QL Q QQ++Q  +   +Q+
Sbjct: 100 QERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQK 146

Length = 387

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 58.9 bits (142), Expect = 8e-09
 Identities = 42/148 (28%), Positives = 53/148 (35%), Gaps = 4/148 (2%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
             ++  QQ  + QQQ  Q  Q        Q   Q Q Q     Q   Q+ Q  Q QQ  Q
Sbjct: 178 GGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQ 237

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ---QMVGSGMGQ-G 787
           + QQ  P   Q Q   Q Q Q  +   Q Q    Q+  QQQ  Q Q     +G    Q  
Sbjct: 238 MDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLGMLPNQMQ 297

Query: 788 YVQGPGRTQLVSQGQVSSQGAPNIPGGG 815
            + G G+           Q    +P GG
Sbjct: 298 QMPGGGQGGPGQPMGPPPQRPGAVPQGG 325

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 58.5 bits (141), Expect = 1e-08
 Identities = 41/136 (30%), Positives = 45/136 (33%), Gaps = 2/136 (1%)

Query: 680 QQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQ 739
           QQ   Q Q QQ  QM  Q    Q       Q Q   + QQ P    Q  +P    Q   Q
Sbjct: 152 QQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQ 211

Query: 740 LQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVS 799
            Q Q    Q Q  Q   Q+Q QQQ  Q   QQQ     Q       QG      +     
Sbjct: 212 QQGQPGGQQQQNPQMQQQLQNQQQ--QQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGG 269

Query: 800 QGQVSSQGAPNIPGGG 815
           Q QV  Q  P      
Sbjct: 270 QMQVPMQQQPPQQQPQ 285

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed

 Score = 57.9 bits (141), Expect = 1e-08
 Identities = 29/109 (26%), Positives = 60/109 (55%), Gaps = 7/109 (6%)

Query: 677 QQQQQLQQ------QQQQQQHQQMQSQLQHQQ-LSQLQQQQQQLPQLQQQIPQLQQQQQI 729
           Q QQ+L +      +Q++Q+  Q+  +L+ Q     L QQQQ+L +LQQ++ +  +++  
Sbjct: 271 QLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRLQRALERRLR 330

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
              Q+      + QQQ PQ + ++   +++Q +Q  +   ++QL + +Q
Sbjct: 331 LAKQRLERLSQRLQQQNPQRRIERAQQRLEQLEQRLRRAMRRQLKRKRQ 379

Length = 438

>gnl|CDD|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3

 Score = 58.1 bits (139), Expect = 1e-08
 Identities = 49/133 (36%), Positives = 63/133 (47%), Gaps = 15/133 (11%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           Q++ QQ +    QQQ+ + Q+++ Q Q Q + Q QQQQQQ  Q QQ +  LQQQQQ+ QL
Sbjct: 324 QLAQQQNKMRLLQQQEMEMQRIEQQRQQQIMHQHQQQQQQEHQQQQML--LQQQQQMHQL 381

Query: 733 QQQSMPQ------LQQQQQLPQLQQ-------QQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           QQ            Q  Q    LQQ       +Q   Q QQ Q   Q QQQ Q       
Sbjct: 382 QQHHQMNGGGQFATQAHQHAAYLQQMQHMRLQEQIQHQQQQAQHHQQAQQQHQQPAQHGQ 441

Query: 780 VGSGMGQGYVQGP 792
           +G G+  GY    
Sbjct: 442 MGYGIPNGYPAHM 454

The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1. Length = 476

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 57.7 bits (139), Expect = 2e-08
 Identities = 38/157 (24%), Positives = 45/157 (28%), Gaps = 2/157 (1%)

Query: 661 MLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQI 720
           +   G M +    +   Q  ++   Q   Q   M  Q   Q   Q QQ  Q  PQ  Q  
Sbjct: 117 LNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQP--QSQQPNQMGPQQGQAQ 174

Query: 721 PQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
            Q     Q  Q         Q  Q        Q   Q Q Q    Q Q  Q   Q Q   
Sbjct: 175 GQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQ 234

Query: 781 GSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGGGFM 817
              M Q       + Q+  Q Q      P    GG M
Sbjct: 235 QQQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQM 271

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed

 Score = 56.7 bits (138), Expect = 2e-08
 Identities = 25/102 (24%), Positives = 56/102 (54%), Gaps = 7/102 (6%)

Query: 684 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ- 742
           + +  Q+ QQ+Q +L      +L+Q++Q+L QL +++     ++ +   QQQ + +LQQ 
Sbjct: 262 RAELLQRLQQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLL-AQQQQRLDRLQQR 320

Query: 743 -----QQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
                +++L   +Q+ +    + QQQ PQ + ++   + +Q+
Sbjct: 321 LQRALERRLRLAKQRLERLSQRLQQQNPQRRIERAQQRLEQL 362

Length = 438

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 56.4 bits (136), Expect = 3e-08
 Identities = 25/97 (25%), Positives = 52/97 (53%), Gaps = 14/97 (14%)

Query: 666 DMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 725
           D V+  P    +Q  + QQQQ+  +  + Q +         +++QQQ  +LQQ+  Q  +
Sbjct: 51  DAVMVDPGAVVEQYNRQQQQQKSAKRAEEQRK---------KKEQQQAEELQQK--QAAE 99

Query: 726 QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQ 762
           Q+++ QL+++   +L  Q+Q  Q ++  +   ++Q+Q
Sbjct: 100 QERLKQLEKE---RLAAQEQKKQAEEAAKQAALKQKQ 133

Length = 387

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 56.2 bits (135), Expect = 7e-08
 Identities = 44/116 (37%), Positives = 45/116 (38%), Gaps = 11/116 (9%)

Query: 664 PGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL 723
           P    V +PQ     QQQ QQ QQ    Q    Q Q     Q Q QQ Q P   Q   Q 
Sbjct: 747 PIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQ 806

Query: 724 QQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
            QQ   PQ      PQ QQ QQ    Q     PQ QQ QQ    Q Q  L  P  M
Sbjct: 807 PQQPVAPQ------PQYQQPQQPVAPQ-----PQYQQPQQPVAPQPQDTLLHPLLM 851

Length = 1355

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 55.0 bits (132), Expect = 1e-07
 Identities = 67/351 (19%), Positives = 104/351 (29%), Gaps = 17/351 (4%)

Query: 442 SNLSGNSNPSISQPMGTLQGGASMGQSVG-MSQGNHSGGQMVQNGISMNQNMMSGLGPSG 500
           SNL  + N     PMG    G      VG M  G  +GG M Q+         + +GP  
Sbjct: 111 SNLLQSLNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQ 170

Query: 501 VSS--GTGTMIPTPGMSQQAQSGMQ-----PLSVNNNTAVNMQLSQQTSSALHSSQSKYV 553
             +    G M          Q   Q              +  Q         +    + +
Sbjct: 171 GQAQGQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQL 230

Query: 554 KVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGK 613
           +  +     Q+QG      ++   +               MQ+           +Q    
Sbjct: 231 QNQQQQQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLG 290

Query: 614 ADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQ 673
                    NQ   +    +      +  P Q              G++  G   + + +
Sbjct: 291 M------LPNQMQQMPGGGQGGPGQPMGPPPQRPGAVPQGGQAVQQGVMSAGQQQLKQMK 344

Query: 674 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 733
           + + + QQ  QQQQQQQ     +  Q Q   Q+ Q  Q +      I   Q       +Q
Sbjct: 345 LRNMRGQQQTQQQQQQQGGNHPAAHQQQMNQQVGQGGQMVALGYLNIQGNQGGLGANPMQ 404

Query: 734 QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGM 784
           Q     +     +PQ+Q  Q +PQ  Q             SQP Q V  GM
Sbjct: 405 QGQPGMMSSPSPVPQVQTNQSMPQPPQPS---VPSPGGPGSQPPQSVSGGM 452

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed

 Score = 54.4 bits (132), Expect = 1e-07
 Identities = 25/103 (24%), Positives = 55/103 (53%), Gaps = 8/103 (7%)

Query: 676 SQQQQQLQQQQQ--QQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 733
            Q++Q+L Q  +  + Q  +     Q Q+L +LQQ+ Q+  + + ++ + + ++   +LQ
Sbjct: 285 EQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRLQRALERRLRLAKQRLERLSQRLQ 344

Query: 734 QQSMPQLQQQQQLPQLQQQQQLPQM------QQQQQLPQLQQQ 770
           QQ+  +  ++ Q    Q +Q+L +       +++Q+L  L QQ
Sbjct: 345 QQNPQRRIERAQQRLEQLEQRLRRAMRRQLKRKRQRLEALAQQ 387

Length = 438

>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed

 Score = 54.4 bits (132), Expect = 1e-07
 Identities = 26/106 (24%), Positives = 60/106 (56%), Gaps = 6/106 (5%)

Query: 675 SSQQQQQLQQQQQQ-QQHQQMQSQLQHQQLSQLQQQ-QQQLPQLQQQIPQLQQQQQIPQL 732
            ++  Q+LQQ QQ+  +  + + + + Q+L QL ++ + Q P+        QQQQ++ +L
Sbjct: 262 RAELLQRLQQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLA----QQQQRLDRL 317

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           QQ+    L+++ +L + + ++   ++QQQ    ++++ QQ  +  +
Sbjct: 318 QQRLQRALERRLRLAKQRLERLSQRLQQQNPQRRIERAQQRLEQLE 363

Length = 438

>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex non-fungal

 Score = 54.2 bits (130), Expect = 2e-07
 Identities = 33/121 (27%), Positives = 44/121 (36%), Gaps = 1/121 (0%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           Q Q  +QQQ  QQQ QQ Q  +   Q+ Q+    Q  P      P  +        Q   
Sbjct: 270 QMQVPMQQQPPQQQPQQSQLGMLPNQMQQMPGGGQGGPGQPMGPPPQRPGAVPQGGQAVQ 329

Query: 737 MPQL-QQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRT 795
              +   QQQL Q++ +    Q Q QQQ  Q       +  QQM       G +   G  
Sbjct: 330 QGVMSAGQQQLKQMKLRNMRGQQQTQQQQQQQGGNHPAAHQQQMNQQVGQGGQMVALGYL 389

Query: 796 Q 796
            
Sbjct: 390 N 390

The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. Length = 768

>gnl|CDD|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional

 Score = 53.1 bits (128), Expect = 2e-07
 Identities = 23/88 (26%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 686 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQL---QQQIPQLQQQQQIPQLQQQSMPQLQQ 742
               Q    Q QL  Q  + ++QQ  QL ++   +Q     +   QI Q  QQ  P    
Sbjct: 75  NSPTQLTDEQRQLLEQMQADMRQQPTQLSEVPYNEQTPQVPRSTVQIQQQAQQQQPPATT 134

Query: 743 QQQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
            Q  P    +Q    +Q Q   P   Q 
Sbjct: 135 AQPQPVTPPRQTTAPVQPQTPAPVRTQP 162

Length = 256

>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1

 Score = 52.8 bits (127), Expect = 6e-07
 Identities = 32/153 (20%), Positives = 46/153 (30%), Gaps = 4/153 (2%)

Query: 660 GMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQ 719
                   V     +S +       Q   +     +     Q    L     +      Q
Sbjct: 79  QNAPGAPSVGPDSDLSQKTSTFSPCQSGYEASTDPEYIPDLQPDPSLWGTAPKPEPQPPQ 138

Query: 720 IPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
            P+ Q Q Q P  +  S+ +++ Q    Q +QQ        QQ LPQ    +Q + PQQ 
Sbjct: 139 APESQPQPQTPAQKMLSLEEVEAQL---QQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQG 195

Query: 780 VGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIP 812
                  GY Q P       Q Q         P
Sbjct: 196 PP-EQPPGYPQPPQGHPEQVQPQQFLPAPSQAP 227

Members of this family are necessary for accurate chromosome transmission during cell division. Length = 804

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 52.8 bits (126), Expect = 6e-07
 Identities = 37/94 (39%), Positives = 41/94 (43%), Gaps = 8/94 (8%)

Query: 687 QQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQL 746
            QQ  Q +  Q Q+QQ  Q    Q Q  Q QQ +     Q Q  Q QQ   PQ Q QQ  
Sbjct: 752 VQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAP---QPQYQQPQQPVAPQPQYQQP- 807

Query: 747 PQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
               QQ   PQ Q QQ    +  Q Q  QPQQ V
Sbjct: 808 ----QQPVAPQPQYQQPQQPVAPQPQYQQPQQPV 837

Length = 1355

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 49.3 bits (117), Expect = 6e-07
 Identities = 30/97 (30%), Positives = 55/97 (56%), Gaps = 2/97 (2%)

Query: 678 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ--QQLPQLQQQIPQLQQQQQIPQLQQQ 735
           +Q+   Q++QQQ  ++ + Q + +Q  Q Q+++  Q+  +  QQ  Q  + +  P  QQ+
Sbjct: 21  EQETRGQREQQQCERRCKEQYKEEQQQQRQREEDPQRRYEQCQQRCQQHEPRHRPTCQQR 80

Query: 736 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
              + +++QQ  Q Q Q+   + QQQ+Q P+ QQQ Q
Sbjct: 81  CERRYEKEQQQQQRQYQECQQRCQQQEQRPRRQQQCQ 117

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]

 Score = 51.6 bits (124), Expect = 1e-06
 Identities = 31/160 (19%), Positives = 61/160 (38%), Gaps = 26/160 (16%)

Query: 645 QTLLLSVSDKACRLIGMLFPGDMVVFKPQISS----QQQQQLQQQQQQQQHQQMQSQLQH 700
           Q LL S  +        L   +    +  +         ++ ++ +   +  ++Q++L  
Sbjct: 10  QELLQSRRE--------LLTAESAQLEAALQLLQEAVNSKRQEEAEPAAEEAELQAELIQ 61

Query: 701 QQLSQLQQQQQQLPQLQQQIPQLQQQQ-----QIPQLQQQSMPQLQQQQQL--------P 747
           Q+L+   Q  Q L Q  +++  L          + QL Q S    +Q   L         
Sbjct: 62  QELAINDQLSQALNQQTERLNALASDDRQLANLLLQLLQSSRTIREQIAVLRGSLLLSRI 121

Query: 748 QLQQQQQLPQMQQQQQLPQL-QQQQQLSQPQQMVGSGMGQ 786
            LQQ   LP+  Q Q+  ++ Q++  L   +  + +  GQ
Sbjct: 122 LLQQLGPLPEAGQPQEQFEVTQERDALQAEKAYINALEGQ 161

Length = 835

>gnl|CDD|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication, recombination, and repair]

 Score = 51.1 bits (123), Expect = 1e-06
 Identities = 29/116 (25%), Positives = 61/116 (52%), Gaps = 22/116 (18%)

Query: 677 QQQQQLQQ----------QQQQQQHQQMQSQLQHQQLSQ-LQQQQQQLPQLQQQIPQL-- 723
           QQ  QLQ+           Q++Q+ + +  +LQ +   + L +QQQ+L +L  ++ +   
Sbjct: 268 QQLDQLQRRLHRALRRLLDQKKQRLEHLARRLQFRSPERLLSEQQQRLDELAIRLRRALE 327

Query: 724 ----QQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQ-----QQLPQLQQQ 770
                ++Q++ +L Q+  PQ+Q+QQQ  Q  +++    +++Q     ++L  L +Q
Sbjct: 328 NQLALKKQRLERLTQRLNPQIQRQQQRLQQLERRLDKALRRQLKRKRERLEALVEQ 383

Length = 440

>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth

 Score = 48.6 bits (116), Expect = 2e-06
 Identities = 29/89 (32%), Positives = 34/89 (38%), Gaps = 1/89 (1%)

Query: 691 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSM-PQLQQQQQLPQL 749
           H Q+    Q    +   Q    +P L  Q P + QQ  +P   Q SM P    Q  LPQ 
Sbjct: 36  HHQIIPVSQQHPPTHTLQPHHHIPVLPAQQPVVPQQPLMPVPGQHSMTPTQHHQPNLPQP 95

Query: 750 QQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
            QQ   PQ  Q  Q  Q  Q Q    P  
Sbjct: 96  AQQPFQPQPLQPPQPQQPMQPQPPVHPIP 124

They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide. Length = 165

>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 50.7 bits (121), Expect = 3e-06
 Identities = 22/117 (18%), Positives = 52/117 (44%), Gaps = 13/117 (11%)

Query: 674 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 733
             + QQ Q       Q+ +  + QL+ QQ   L+Q + ++ +L+ Q   L++ Q+     
Sbjct: 232 REALQQTQQSHAYLTQKREAQEEQLKKQQ--LLKQLRARIEELRAQEAVLEETQERINRA 289

Query: 734 QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQL-----------QQQQQLSQPQQM 779
           +++ P     + + Q++QQ Q    + Q ++              +QQ  + + +++
Sbjct: 290 RKAAPLAAHIKAVTQIEQQAQRIHTELQSKMRSRAKLLMKRAAHVKQQSSIEEQRRL 346

All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1042

>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]

 Score = 50.1 bits (120), Expect = 4e-06
 Identities = 30/117 (25%), Positives = 48/117 (41%), Gaps = 10/117 (8%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQL--QHQQLSQLQQQQQQLPQLQQQIPQLQQQ--Q 727
           P     + Q    QQ+   + Q+   L  Q ++L+ L    +QL  L  Q+ Q  +   +
Sbjct: 48  PAAEEAELQAELIQQELAINDQLSQALNQQTERLNALASDDRQLANLLLQLLQSSRTIRE 107

Query: 728 QIPQLQ---QQSMPQLQQQQQLP---QLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           QI  L+     S   LQQ   LP   Q Q+Q ++ Q +   Q  +        Q +Q
Sbjct: 108 QIAVLRGSLLLSRILLQQLGPLPEAGQPQEQFEVTQERDALQAEKAYINALEGQAEQ 164

Length = 835

>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584)

 Score = 50.5 bits (121), Expect = 4e-06
 Identities = 28/112 (25%), Positives = 53/112 (47%), Gaps = 14/112 (12%)

Query: 674 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI---- 729
            ++ +Q +L  Q+ Q + Q ++ +L+     + QQ + QL QL  Q+ QL +QQQ     
Sbjct: 648 RTALKQARLDLQRLQNEQQSLKDKLELAIAERKQQAETQLRQLDAQLKQLLEQQQAFLEA 707

Query: 730 --PQLQQQSMPQLQQQQ--------QLPQLQQQQQLPQMQQQQQLPQLQQQQ 771
                ++    +L + Q        QL QL    +  + Q + +L +L++Q 
Sbjct: 708 LKDDFRELRTERLAKWQVVEGELDNQLAQLSAAIEAARTQAKARLKELKKQY 759

This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. Length = 1198

>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional

 Score = 50.3 bits (121), Expect = 4e-06
 Identities = 24/126 (19%), Positives = 58/126 (46%), Gaps = 19/126 (15%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQ-----LSQLQQQQQQLPQLQQQIPQLQQQQ 727
           ++  Q+    Q QQ + +  +++ +L+ QQ     L++  ++  +    + ++ QLQ++ 
Sbjct: 504 RLREQRHLAEQLQQLRMRLSELEQRLRQQQRAERLLAEFCKRLGKNLDDEDELEQLQEEL 563

Query: 728 --QIPQLQQQSMPQLQQ----QQQLPQLQQQ-----QQLPQMQQ-QQQLPQLQQQ--QQL 773
             ++  L +      ++    +QQL QLQ +      + P     Q  L +L++Q  ++ 
Sbjct: 564 EARLESLSESVSEARERRMALRQQLEQLQARIQRLAARAPAWLAAQDALARLREQSGEEF 623

Query: 774 SQPQQM 779
              Q +
Sbjct: 624 EDSQDV 629

Length = 1486

>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional

 Score = 50.3 bits (121), Expect = 4e-06
 Identities = 32/126 (25%), Positives = 55/126 (43%), Gaps = 23/126 (18%)

Query: 673  QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
            +I  Q  +  + ++  QQH    +QL+   +S LQ   +Q  QL+Q   Q QQ Q+    
Sbjct: 898  EIREQLDEAEEAKRFVQQHGNALAQLE-PIVSVLQSDPEQFEQLKQDYQQAQQTQR--DA 954

Query: 733  QQQ------------------SMPQLQQQQQL-PQLQQQQQLPQMQQQQQLPQL-QQQQQ 772
            +QQ                  +   L +   L  +L+Q+ +  + ++ +   QL Q Q Q
Sbjct: 955  KQQAFALTEVVQRRAHFSYEDAAEMLAKNSDLNEKLRQRLEQAEQERTRAREQLRQAQAQ 1014

Query: 773  LSQPQQ 778
            L+Q  Q
Sbjct: 1015 LAQYNQ 1020

Length = 1486

>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell envelope biogenesis, outer membrane]

 Score = 49.6 bits (118), Expect = 5e-06
 Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 696 SQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQL 755
                QQ  ++Q QQ    + +QQ  + +++Q   +L+     Q  +Q++L QL++++  
Sbjct: 57  PGAVVQQYGRIQSQQSSAKKGEQQ-RKKKEEQVAEELKP---KQAAEQERLKQLEKERLK 112

Query: 756 PQMQQQQQLPQLQQQQQLSQPQQ 778
            Q QQ+Q     +Q Q   + Q+
Sbjct: 113 AQEQQKQAEEAEKQAQLEQKQQE 135

Length = 387

>gnl|CDD|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3

 Score = 49.6 bits (117), Expect = 5e-06
 Identities = 42/140 (30%), Positives = 63/140 (45%), Gaps = 6/140 (4%)

Query: 670 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 729
                   ++  ++    +         +  Q ++QL QQQ ++  LQQQ     + Q+I
Sbjct: 289 AMEPEGETKKSPMEAGGDRMPQSAPPPAMNPQHIAQLAQQQNKMRLLQQQ---EMEMQRI 345

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQG-Y 788
            Q +QQ +    QQQQ  + QQQQ L  +QQQQQ+ QLQQ  Q++   Q          Y
Sbjct: 346 EQQRQQQIMHQHQQQQQQEHQQQQML--LQQQQQMHQLQQHHQMNGGGQFATQAHQHAAY 403

Query: 789 VQGPGRTQLVSQGQVSSQGA 808
           +Q     +L  Q Q   Q A
Sbjct: 404 LQQMQHMRLQEQIQHQQQQA 423

The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1. Length = 476

>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit

 Score = 49.4 bits (118), Expect = 5e-06
 Identities = 25/110 (22%), Positives = 50/110 (45%), Gaps = 6/110 (5%)

Query: 673 QISSQQQQQLQQQ---QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 729
           +I S  Q +L Q+      + H+     L HQ+ ++L+Q    L +   Q     QQ Q 
Sbjct: 251 EIVSPNQDELLQRLDGFNVRLHRAFD-TLLHQKKARLEQLVASLQRQHPQNKLALQQLQF 309

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
            +L+++   Q    +QL + +Q++     +  Q  P  Q  +  ++ +Q+
Sbjct: 310 EKLEKRK--QAALNKQLERTRQKKTRLTKRLTQTNPSPQILRAQTRTEQL 357

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits [DNA metabolism, Degradation of DNA]. Length = 432

>gnl|CDD|180700 PRK06800, fliH, flagellar assembly protein H; Validated

 Score = 47.9 bits (114), Expect = 5e-06
 Identities = 30/105 (28%), Positives = 62/105 (59%), Gaps = 21/105 (20%)

Query: 667 MVVFKPQIS------SQQQQQLQ---------QQQQQQQHQQMQSQLQ--HQQLSQLQQQ 709
           M +FK +I       S++  +LQ         +++ Q+ H+++ +Q +  H++L+QL+Q+
Sbjct: 1   MSLFKNRIPKNSVSFSEETYELQFPKPIEVEVEEEIQKDHEELLAQQKSLHKELNQLRQE 60

Query: 710 QQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQ 754
           QQ+L + +QQ+  L  ++Q  +  QQ M +++  +Q  Q Q++QQ
Sbjct: 61  QQKLERERQQL--LADREQFQEHVQQQMKEIEAARQ--QFQKEQQ 101

Length = 228

>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional

 Score = 50.0 bits (120), Expect = 6e-06
 Identities = 24/115 (20%), Positives = 52/115 (45%), Gaps = 22/115 (19%)

Query: 680 QQLQQQQQQQQ--HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSM 737
           +QLQ++ + +     +  S+ + +++      +QQL QLQ +I +L  +       Q ++
Sbjct: 557 EQLQEELEARLESLSESVSEARERRM----ALRQQLEQLQARIQRLAARAPAWLAAQDAL 612

Query: 738 PQLQQQ--------QQLPQLQQQQQLPQMQQQQQLPQLQQQQQ--------LSQP 776
            +L++Q        Q + +  QQ    + +   +  +L  ++Q        LSQP
Sbjct: 613 ARLREQSGEEFEDSQDVTEYMQQLLERERELTVERDELAARKQALDEEIERLSQP 667

Length = 1486

>gnl|CDD|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450)

 Score = 48.4 bits (116), Expect = 6e-06
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 6/83 (7%)

Query: 675 SSQQQQQLQQQ--QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ-QQQIPQ 731
            + Q Q+L  +  Q  ++ + ++      Q   +  QQQ++  LQQQI Q+++ +Q +  
Sbjct: 48  WADQTQELLAEIRQLLKEIENLRVYNDQLQ-RLVANQQQEIASLQQQIEQIEKTRQGLVP 106

Query: 732 LQQQSMPQLQQ--QQQLPQLQQQ 752
           L  + +  L+Q     LP L+++
Sbjct: 107 LMYRMIDGLEQFVALDLPFLKEE 129

This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length. Length = 250

>gnl|CDD|236797 PRK10927, PRK10927, essential cell division protein FtsN; Provisional

 Score = 48.5 bits (115), Expect = 8e-06
 Identities = 32/108 (29%), Positives = 48/108 (44%), Gaps = 2/108 (1%)

Query: 669 VFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 728
           V  P+  + +Q+QL +Q Q    QQ    ++     Q  +Q+QQ  Q Q+Q  QL +QQ+
Sbjct: 108 VKTPEQLTPEQRQLLEQMQADMRQQPTQLVEVPWNEQTPEQRQQTLQRQRQAQQLAEQQR 167

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 776
           +   QQ    +   QQQ    Q      Q +Q +     Q  Q L Q 
Sbjct: 168 L-A-QQSRTTEQSWQQQTRTSQAAPVQAQPRQSKPASTQQPYQDLLQT 213

Length = 319

>gnl|CDD|202101 pfam02050, FliJ, Flagellar FliJ protein

 Score = 45.3 bits (108), Expect = 9e-06
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 10/80 (12%)

Query: 677 QQQQQLQQQQQQQQH--QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 734
           Q +++L++ QQ +    QQ+    Q    ++L+  Q  +  L + I   QQQQ++ Q ++
Sbjct: 16  QAEEKLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEAIA--QQQQELEQAEK 73

Query: 735 QSMPQLQQQQQLPQLQQQQQ 754
               Q++Q ++  Q Q+  Q
Sbjct: 74  ----QVEQARE--QWQEANQ 87

Length = 122

>gnl|CDD|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication, recombination, and repair]

 Score = 48.0 bits (115), Expect = 1e-05
 Identities = 26/108 (24%), Positives = 54/108 (50%), Gaps = 12/108 (11%)

Query: 684 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL-------QQQQQIPQLQQQS 736
             +  QQ  Q+Q +L       L Q++Q+L  L +++          +QQQ++ +L  + 
Sbjct: 263 SAELLQQLDQLQRRLHRALRRLLDQKKQRLEHLARRLQFRSPERLLSEQQQRLDELAIRL 322

Query: 737 MPQLQ-----QQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
              L+     ++Q+L +L Q+      +QQQ+L QL+++   +  +Q+
Sbjct: 323 RRALENQLALKKQRLERLTQRLNPQIQRQQQRLQQLERRLDKALRRQL 370

Length = 440

>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional

 Score = 49.2 bits (118), Expect = 1e-05
 Identities = 24/105 (22%), Positives = 55/105 (52%), Gaps = 6/105 (5%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
              ++L ++ ++Q+H   Q Q    +LS+L+Q+ +Q  + ++ + +  ++       +  
Sbjct: 496 DVARELLRRLREQRHLAEQLQQLRMRLSELEQRLRQQQRAERLLAEFCKRLGKNLDDEDE 555

Query: 737 MPQLQQQQ--QLPQLQQQQ---QLPQMQQQQQLPQLQQQ-QQLSQ 775
           + QLQ++   +L  L +     +  +M  +QQL QLQ + Q+L+ 
Sbjct: 556 LEQLQEELEARLESLSESVSEARERRMALRQQLEQLQARIQRLAA 600

Length = 1486

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 48.1 bits (115), Expect = 1e-05
 Identities = 26/107 (24%), Positives = 39/107 (36%), Gaps = 6/107 (5%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           P  +S Q +Q  QQ  + Q     +     + +Q   Q  Q P  Q Q  Q  QQ   PQ
Sbjct: 94  PPYASAQPRQPVQQPPEAQVPPQHA----PRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQ 149

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           +     P      Q  Q   Q   P    Q + P  +    + +P++
Sbjct: 150 VAPAPQPV-HSAPQPAQQAFQPAEPVAAPQPE-PVAEPAPVMDKPKR 194

Length = 333

>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 48.6 bits (116), Expect = 1e-05
 Identities = 34/128 (26%), Positives = 50/128 (39%), Gaps = 26/128 (20%)

Query: 674 ISSQQQQQLQQQQQQQQHQQMQSQLQH-----------------------QQLSQLQQQQ 710
           +S   Q Q  QQQ   + Q++Q                            + L+QL+Q +
Sbjct: 727 LSLHSQLQTLQQQDVLEAQRLQKAQAQFDTALQASVFDDQQAFLAALLDEETLTQLEQLK 786

Query: 711 QQLP-QLQQQIPQLQQQQQIPQLQQQSMPQ-LQQQQQLPQLQQQ-QQLPQMQQQQQLPQL 767
           Q L  Q QQ    + Q  Q     QQ  P  L     + Q+QQ+  QL Q  ++    Q 
Sbjct: 787 QNLENQRQQAQTLVTQTAQALAQHQQHRPDGLDLTVTVEQIQQELAQLAQQLRENTTRQG 846

Query: 768 QQQQQLSQ 775
           + +QQL Q
Sbjct: 847 EIRQQLKQ 854

Length = 1047

>gnl|CDD|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3

 Score = 47.7 bits (112), Expect = 2e-05
 Identities = 29/98 (29%), Positives = 50/98 (51%)

Query: 681 QLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQL 740
           +L   + + + ++   +    ++ Q        PQ   Q+ Q Q + ++ Q Q+  M ++
Sbjct: 286 ELDAMEPEGETKKSPMEAGGDRMPQSAPPPAMNPQHIAQLAQQQNKMRLLQQQEMEMQRI 345

Query: 741 QQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           +QQ+Q   + Q QQ  Q + QQQ   LQQQQQ+ Q QQ
Sbjct: 346 EQQRQQQIMHQHQQQQQQEHQQQQMLLQQQQQMHQLQQ 383

The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1. Length = 476

>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth

 Score = 45.6 bits (108), Expect = 2e-05
 Identities = 27/93 (29%), Positives = 34/93 (36%), Gaps = 2/93 (2%)

Query: 689 QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP-QLQQQSMPQLQQQQQLP 747
           QQH    +   H  +  L  QQ  +PQ Q  +P   Q    P Q  Q ++PQ  QQ   P
Sbjct: 44  QQHPPTHTLQPHHHIPVLPAQQPVVPQ-QPLMPVPGQHSMTPTQHHQPNLPQPAQQPFQP 102

Query: 748 QLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
           Q  Q  Q  Q  Q Q             P   +
Sbjct: 103 QPLQPPQPQQPMQPQPPVHPIPPLPPQPPLPPM 135

They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide. Length = 165

>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional

 Score = 48.4 bits (116), Expect = 2e-05
 Identities = 24/119 (20%), Positives = 54/119 (45%), Gaps = 24/119 (20%)

Query: 679 QQQLQQQ-----QQQQQHQQMQSQLQH--QQLSQLQQQ------------QQQLPQLQQQ 719
            ++  +        + Q QQ +SQL+   + LS L +               ++ ++++Q
Sbjct: 843 NRRRVELERALADHESQEQQQRSQLEQAKEGLSALNRLLPRLNLLADETLADRVEEIREQ 902

Query: 720 IPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQ-QQQLPQMQQQQQLPQLQQQQQLSQPQ 777
           + + ++ ++  Q    ++ QL  +  +  LQ   +Q  Q++Q  Q  Q QQ Q+ ++ Q
Sbjct: 903 LDEAEEAKRFVQQHGNALAQL--EPIVSVLQSDPEQFEQLKQDYQ--QAQQTQRDAKQQ 957

Length = 1486

>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 47.9 bits (114), Expect = 2e-05
 Identities = 35/97 (36%), Positives = 49/97 (50%), Gaps = 11/97 (11%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQIPQLQQ 734
           Q +Q L+ Q+QQ Q    Q+    Q L+Q QQ +     L   + Q+QQ+  Q   QL++
Sbjct: 784 QLKQNLENQRQQAQTLVTQTA---QALAQHQQHRPDGLDLTVTVEQIQQELAQLAQQLRE 840

Query: 735 QSMPQLQQQQQLPQ----LQQQQQLPQMQQQQQLPQL 767
            +  Q + +QQL Q     QQQQ L  MQQ  Q  Q 
Sbjct: 841 NTTRQGEIRQQLKQDADNRQQQQAL--MQQIAQATQQ 875

Length = 1047

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 46.2 bits (110), Expect = 2e-05
 Identities = 19/105 (18%), Positives = 50/105 (47%), Gaps = 10/105 (9%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
            +S     + +  + QQ+  ++Q +L   Q  QL + QQ+  +L+Q++  L+ + +  Q 
Sbjct: 57  YLSDTPSARERLPELQQELAELQEELAELQ-EQLAELQQENQELKQELSTLEAELERLQK 115

Query: 733 QQQSMPQLQQQ-----QQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
           +   + QL        ++  +L+++      + +Q+   L+ + +
Sbjct: 116 ELARIKQLSANAIELDEENRELREELA----ELKQENEALEAENE 156

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 47.5 bits (113), Expect = 2e-05
 Identities = 15/92 (16%), Positives = 44/92 (47%)

Query: 687 QQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQL 746
                 Q  +++Q Q+    +++Q++  +L+QQ  + ++Q+   Q +Q+ + Q    ++ 
Sbjct: 44  DPGAVAQQANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKA 103

Query: 747 PQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
            +  +Q      ++Q+Q  + + +Q      +
Sbjct: 104 AKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAK 135

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|217472 pfam03280, Lipase_chap, Proteobacterial lipase chaperone protein

 Score = 45.3 bits (108), Expect = 2e-05
 Identities = 26/119 (21%), Positives = 45/119 (37%), Gaps = 21/119 (17%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
            Q   L  +Q+ ++   + +QL  + L + ++      +L Q   QLQ Q   PQ  +  
Sbjct: 71  AQDPSLSDEQKARRLAALIAQLP-EDLREARRNAALQQELAQATAQLQAQGASPQDLRA- 128

Query: 737 MPQLQQQ------QQLPQLQQ-----QQQLPQMQQQ------QQLPQLQQQQQLSQPQQ 778
                        Q+L QL Q     QQ+      +        L    +Q Q++Q +Q
Sbjct: 129 --ARAALVGPEAAQRLAQLDQERAAWQQRYDDYLAERDQILAAGLSDADKQAQIAQLRQ 185

Length = 189

>gnl|CDD|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional

 Score = 46.2 bits (110), Expect = 3e-05
 Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 2/107 (1%)

Query: 671 KPQISSQQQQQLQQQQ--QQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 728
             Q++ +Q+Q L+Q Q   +QQ  Q+     ++Q  Q+ +   Q+ Q  QQ        Q
Sbjct: 77  PTQLTDEQRQLLEQMQADMRQQPTQLSEVPYNEQTPQVPRSTVQIQQQAQQQQPPATTAQ 136

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
              +          Q Q P   + Q    + Q  + P+++ +++  Q
Sbjct: 137 PQPVTPPRQTTAPVQPQTPAPVRTQPAAPVTQAVEAPKVEAEKEKEQ 183

Length = 256

>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]

 Score = 47.0 bits (112), Expect = 3e-05
 Identities = 19/101 (18%), Positives = 35/101 (34%), Gaps = 4/101 (3%)

Query: 682 LQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQ 741
           L      Q+  Q + +L   + +QL+   Q L +      Q + +    + + Q+    Q
Sbjct: 3   LAGNNVLQELLQSRRELLTAESAQLEAALQLLQEAVNSKRQEEAEPAAEEAELQAELIQQ 62

Query: 742 QQQQLPQLQQQ--QQLPQMQQ--QQQLPQLQQQQQLSQPQQ 778
           +     QL Q   QQ  ++               QL Q  +
Sbjct: 63  ELAINDQLSQALNQQTERLNALASDDRQLANLLLQLLQSSR 103

Length = 835

>gnl|CDD|236797 PRK10927, PRK10927, essential cell division protein FtsN; Provisional

 Score = 46.2 bits (109), Expect = 3e-05
 Identities = 29/95 (30%), Positives = 45/95 (47%), Gaps = 5/95 (5%)

Query: 686 QQQQQHQQMQSQLQHQ--QLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQ 743
           +Q+Q  +QMQ+ ++ Q  QL ++   +Q   Q QQ    LQ+Q+Q  QL +Q     Q +
Sbjct: 117 EQRQLLEQMQADMRQQPTQLVEVPWNEQTPEQRQQT---LQRQRQAQQLAEQQRLAQQSR 173

Query: 744 QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
                 QQQ +  Q    Q  P+  +     QP Q
Sbjct: 174 TTEQSWQQQTRTSQAAPVQAQPRQSKPASTQQPYQ 208

Length = 319

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 47.5 bits (113), Expect = 3e-05
 Identities = 25/123 (20%), Positives = 34/123 (27%), Gaps = 8/123 (6%)

Query: 659 IGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQ 718
           +G    G M   +P    Q  QQ Q   Q     +M             +     P    
Sbjct: 387 MGSPMGGAM--GQPPYYGQGPQQ-QFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAV 443

Query: 719 QIPQLQQQQQIPQLQQQSM---PQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
           + P    Q    +   Q +   P  Q       L Q Q      Q  Q  +L Q    + 
Sbjct: 444 RAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQSTA--SQGGQNKKLAQVLASAT 501

Query: 776 PQQ 778
           PQ 
Sbjct: 502 PQM 504

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|234937 PRK01294, PRK01294, lipase chaperone; Provisional

 Score = 46.6 bits (111), Expect = 3e-05
 Identities = 31/103 (30%), Positives = 49/103 (47%), Gaps = 9/103 (8%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLS--QLQQQQQQL--PQLQQQIPQLQQQQQ 728
           Q+    +  LQ+ Q+QQ   Q  +QLQ    S  +L+  + QL  P+  Q++ QL QQ+ 
Sbjct: 218 QLPEDLRAALQESQRQQALLQQLAQLQASGASPQELRLMRAQLVGPEAAQRLEQLDQQRA 277

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ 771
                QQ       Q+   Q+     L    +Q Q+ QL+QQ+
Sbjct: 278 A---WQQRYDDYLAQRA--QILNAAGLSPQDRQAQIAQLRQQR 315

Length = 336

>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 46.9 bits (111), Expect = 4e-05
 Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 18/115 (15%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQH------QQLSQLQQQQQQLPQLQQQIPQLQQQ 726
           + ++  +QQ   ++Q++  Q + SQ  H         S  +   QQ   L Q I  LQQQ
Sbjct: 329 KRAAHVKQQSSIEEQRRLLQTLHSQEIHIRDAHEVATSIREISCQQH-TLTQHIHTLQQQ 387

Query: 727 QQIPQLQQQSMPQL------QQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
           +     + QS+ +       +Q     +    + L     Q QL   ++QQ+L Q
Sbjct: 388 KTTLTQKLQSLCKELDILQREQATIDTRTSAFRDL-----QGQLAHAKKQQELQQ 437

All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1042

>gnl|CDD|236797 PRK10927, PRK10927, essential cell division protein FtsN; Provisional

 Score = 46.2 bits (109), Expect = 4e-05
 Identities = 30/108 (27%), Positives = 45/108 (41%), Gaps = 6/108 (5%)

Query: 665 GDMVVFKPQISSQQQQQLQQQQQQQQHQQMQ------SQLQHQQLSQLQQQQQQLPQLQQ 718
           G  V    Q++ +Q+Q L+Q Q   + Q  Q      ++   +Q  Q  Q+Q+Q  QL +
Sbjct: 105 GGEVKTPEQLTPEQRQLLEQMQADMRQQPTQLVEVPWNEQTPEQRQQTLQRQRQAQQLAE 164

Query: 719 QIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQ 766
           Q    QQ +   Q  QQ     Q      Q +Q +     Q  Q L Q
Sbjct: 165 QQRLAQQSRTTEQSWQQQTRTSQAAPVQAQPRQSKPASTQQPYQDLLQ 212

Length = 319

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 46.3 bits (110), Expect = 4e-05
 Identities = 34/159 (21%), Positives = 46/159 (28%), Gaps = 18/159 (11%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ-QIPQLQQQ 735
            Q    Q  Q      Q Q        +        LP      P +Q +  Q+  +Q  
Sbjct: 67  PQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALP-AGPAGPTIQTEPGQLYPVQVP 125

Query: 736 SM----------PQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMG 785
            M           Q  QQ+ L QLQQ+   P   Q     Q  Q+   SQ QQ       
Sbjct: 126 VMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQSAQKNDESQLQQQPNGETP 185

Query: 786 QGYVQGPGRTQLVSQGQVSSQGAP------NIPGGGFMS 818
                G G  +  +  ++               GGG M 
Sbjct: 186 PQQTDGAGDDESEALVRLREADGTLEQRIKGAEGGGAMK 224

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]

 Score = 46.6 bits (110), Expect = 4e-05
 Identities = 30/129 (23%), Positives = 56/129 (43%), Gaps = 4/129 (3%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQIPQLQ 733
             +  Q++Q+ Q    +   +Q + ++L++     QQ  Q  QQ      Q  QQI    
Sbjct: 192 KLRSAQIEQEAQNLATRANAAQARTEELARRAAAAQQTAQAIQQRDAQISQKAQQIAARA 251

Query: 734 QQSMPQLQQQQQLPQLQQ--QQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQG 791
           +Q   + +Q Q+L   Q   +Q++ Q++   Q     +QQ  +  +  V +G  Q   Q 
Sbjct: 252 EQIRERERQLQRLETAQARLEQEVAQLEAYYQAYVRLRQQAAATQRGQVLAGAAQRVAQA 311

Query: 792 PGRTQLVSQ 800
             + Q  +Q
Sbjct: 312 QAQAQAQAQ 320

Length = 499

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 46.0 bits (109), Expect = 5e-05
 Identities = 13/87 (14%), Positives = 44/87 (50%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           Q S+++ ++ +++++QQQ +++Q +   +Q    Q ++++L   +Q+    +  +Q    
Sbjct: 71  QKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALK 130

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQ 759
           Q+Q+     +     + + + +  +  
Sbjct: 131 QKQAEEAAAKAAAAAKAKAEAEAKRAA 157

Length = 387

>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 46.7 bits (111), Expect = 5e-05
 Identities = 30/106 (28%), Positives = 50/106 (47%), Gaps = 4/106 (3%)

Query: 673 QISSQQQQQLQQ-QQQQQQHQQMQSQLQHQQL--SQLQQQQQQLPQLQQQIPQLQQQQQI 729
            I+ Q Q  +Q     Q++H++    L  +     Q+    QQ+ Q QQQI Q +QQQ +
Sbjct: 589 NITLQPQDDIQPWLDAQEEHERQLRLLSQRHELQGQIAAHNQQIIQYQQQIEQ-RQQQLL 647

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
             L   ++   Q+ ++   L  +QQ  Q  QQ+Q      Q ++ Q
Sbjct: 648 TALAGYALTLPQEDEEASWLATRQQEAQSWQQRQNELTALQNRIQQ 693

Length = 1047

>gnl|CDD|131526 TIGR02473, flagell_FliJ, flagellar export protein FliJ

 Score = 43.8 bits (104), Expect = 5e-05
 Identities = 21/94 (22%), Positives = 46/94 (48%), Gaps = 6/94 (6%)

Query: 689 QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQ 748
           Q+   ++ + + Q   +L + Q +  +L+ Q+ QL + ++  + +QQ++ ++       +
Sbjct: 5   QKLLDLREKEEEQAKLELAKAQAEFERLETQLQQLIKYRE--EYEQQALEKVGAGTSALE 62

Query: 749 LQQQQ----QLPQMQQQQQLPQLQQQQQLSQPQQ 778
           L   Q    QL Q  QQQQ      QQ++   ++
Sbjct: 63  LSNYQRFIRQLDQRIQQQQQELALLQQEVEAKRE 96

Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems. Length = 141

>gnl|CDD|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869)

 Score = 43.4 bits (103), Expect = 5e-05
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 7/83 (8%)

Query: 679 QQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           Q +LQ+Q  Q  Q+ QQ++ Q Q       +Q  QQ+ Q+QQQ+     +Q+  +  +Q 
Sbjct: 22  QAELQEQLTQLEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQQV-----EQERAKRLEQK 76

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQ 759
              L Q +Q+ +L    ++ Q Q
Sbjct: 77  NQLLFQIEQVQELPLGSEVKQGQ 99

This bacterial family of proteins has no known function. Length = 131

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 45.8 bits (108), Expect = 6e-05
 Identities = 24/74 (32%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 700 HQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQ 759
           H+     +  QQ   Q   Q P +Q   Q PQ Q Q  P    QQ  PQ   QQ  PQ +
Sbjct: 195 HRHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQP-PQTE 253

Query: 760 QQQQLPQLQQQQQL 773
           Q  +  + Q  Q+ 
Sbjct: 254 QGHKRSREQGNQEF 267

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 45.6 bits (108), Expect = 7e-05
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 724 QQQQQIPQLQQQSMPQLQQQQQLPQLQQ-----QQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           QQQQQ    + +   + ++QQQ  +LQQ     Q++L Q+++++   Q Q++Q     +Q
Sbjct: 67  QQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQ 126

Length = 387

>gnl|CDD|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869)

 Score = 43.0 bits (102), Expect = 7e-05
 Identities = 31/77 (40%), Positives = 54/77 (70%), Gaps = 8/77 (10%)

Query: 692 QQMQSQLQHQQLSQLQQQQQQLP-QLQQQIPQLQQQ--QQIPQLQQQSMPQLQQQQQLPQ 748
           +++Q++LQ +QL+QL+Q+ QQL  Q Q+ I ++++Q  QQI Q+QQ    Q++Q++    
Sbjct: 19  EELQAELQ-EQLTQLEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQ----QVEQERAKRL 73

Query: 749 LQQQQQLPQMQQQQQLP 765
            Q+ Q L Q++Q Q+LP
Sbjct: 74  EQKNQLLFQIEQVQELP 90

This bacterial family of proteins has no known function. Length = 131

>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III C-methyltransferase; Provisional

 Score = 45.5 bits (108), Expect = 8e-05
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 686 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 745
           +QQ Q+Q   +     QL+ LQ+ Q+     Q+Q  +   +QQ   L Q +  Q    +Q
Sbjct: 59  KQQAQNQTATNDALANQLTALQKAQES----QKQELEGILKQQAKALDQANRQQAALAKQ 114

Query: 746 LPQLQQQ 752
           L +LQQ+
Sbjct: 115 LDELQQK 121

Length = 390

>gnl|CDD|225507 COG2959, HemX, Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

 Score = 45.6 bits (108), Expect = 8e-05
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 5/82 (6%)

Query: 682 LQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQ 741
            QQQ   Q  +    Q Q + L   Q+ Q+ L QL+  I   QQQ ++ +L++Q      
Sbjct: 54  GQQQNVLQTQELQALQQQLKALQLAQENQKLLAQLESLIA--QQQAELDRLERQ---LET 108

Query: 742 QQQQLPQLQQQQQLPQMQQQQQ 763
            Q+QL +LQ++        ++ 
Sbjct: 109 LQKQLSELQKKVATISGSDRKD 130

Length = 391

>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 45.7 bits (108), Expect = 9e-05
 Identities = 20/108 (18%), Positives = 46/108 (42%), Gaps = 7/108 (6%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQL------QQQIPQLQQQ 726
           + + ++Q + QQ  +Q + +  + + Q   L + Q++  +  +        + + Q++QQ
Sbjct: 249 REAQEEQLKKQQLLKQLRARIEELRAQEAVLEETQERINRARKAAPLAAHIKAVTQIEQQ 308

Query: 727 -QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQL 773
            Q+I    Q  M    +         +QQ    +Q++ L  L  Q+  
Sbjct: 309 AQRIHTELQSKMRSRAKLLMKRAAHVKQQSSIEEQRRLLQTLHSQEIH 356

All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1042

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 45.2 bits (107), Expect = 9e-05
 Identities = 17/92 (18%), Positives = 40/92 (43%), Gaps = 7/92 (7%)

Query: 679 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMP 738
                 QQ  +  QQ +   + +Q  Q + +QQ   + ++Q  +  +Q +  +L+Q    
Sbjct: 44  DPGAVAQQANRIQQQKKPAAKKEQERQKKLEQQA-EEAEKQ--RAAEQARQKELEQ---- 96

Query: 739 QLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
           +   ++   Q +Q  +  + +Q+Q      +Q
Sbjct: 97  RAAAEKAAKQAEQAAKQAEEKQKQAEEAKAKQ 128

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|217472 pfam03280, Lipase_chap, Proteobacterial lipase chaperone protein

 Score = 43.8 bits (104), Expect = 9e-05
 Identities = 20/110 (18%), Positives = 42/110 (38%), Gaps = 8/110 (7%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ-QQQQIPQLQQQ 735
            +  +L     +   +Q  + L+ Q  S    + Q     + +  Q   ++ +I   Q  
Sbjct: 20  AEDDKLDLAALRALLEQRAA-LRRQYFSA--DEAQAFFGDENRYDQYALERLRI--AQDP 74

Query: 736 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMG 785
           S+   Q+ ++L  L  Q  LP+  ++ +     QQ+      Q+   G  
Sbjct: 75  SLSDEQKARRLAALIAQ--LPEDLREARRNAALQQELAQATAQLQAQGAS 122

Length = 189

>gnl|CDD|204935 pfam12474, PKK, Polo kinase kinase

 Score = 43.1 bits (102), Expect = 9e-05
 Identities = 21/118 (17%), Positives = 56/118 (47%), Gaps = 22/118 (18%)

Query: 677 QQQQQLQQQQQQQQHQ----------QMQSQLQHQQLSQLQQQQQQLPQLQQQI------ 720
            Q++QL+ +   ++ Q          Q++ Q +       Q+Q Q+L +L ++I      
Sbjct: 4   LQKEQLKDRFFLERTQLLKRHEKELEQLERQQKRTIEKLEQRQTQELRRLPKRIRAEQKT 63

Query: 721 ------PQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
                   L+ +++  + + + +P+ Q+Q++     ++++  Q  Q+Q+   L +Q++
Sbjct: 64  RLKMFKESLKIEKKELKQEVEKLPRFQEQEKKRMKAEKEEQEQKHQKQEREFLAKQEE 121

This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam00069. Polo-like kinase 1 (Plx1) is essential during mitosis for the activation of Cdc25C, for spindle assembly, and for cyclin B degradation. This family is Polo kinase kinase (PKK) which phosphorylates Polo kinase and Polo-like kinase to activate them. PKK is a serine/threonine kinase. Length = 142

>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 44.8 bits (106), Expect = 1e-04
 Identities = 18/81 (22%), Positives = 44/81 (54%), Gaps = 9/81 (11%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           Q  S ++ + Q+++++QQ  +   +LQ +Q      +Q++L QL+++  +L  Q+Q  Q 
Sbjct: 70  QQKSAKRAEEQRKKKEQQQAE---ELQQKQ----AAEQERLKQLEKE--RLAAQEQKKQA 120

Query: 733 QQQSMPQLQQQQQLPQLQQQQ 753
           ++ +     +Q+Q  +   + 
Sbjct: 121 EEAAKQAALKQKQAEEAAAKA 141

Length = 387

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 45.5 bits (107), Expect = 1e-04
 Identities = 28/83 (33%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 671 KPQISSQQQQQLQQQ--QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 728
           +P     Q QQ QQ    Q Q  Q  Q      Q  Q QQ     PQ QQ    +  Q Q
Sbjct: 770 QPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQ 829

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQ 751
             Q QQ   PQ Q     P L +
Sbjct: 830 YQQPQQPVAPQPQDTLLHPLLMR 852

Length = 1355

>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

 Score = 45.5 bits (107), Expect = 1e-04
 Identities = 50/197 (25%), Positives = 64/197 (32%), Gaps = 39/197 (19%)

Query: 640 IQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQ 699
           I+LPSQ       +KA       +         +I + QQ +L +Q  Q Q Q+   Q Q
Sbjct: 625 IKLPSQRA---AEEKAREAQRNQYDSGDQYNDDEIDAMQQDELARQFAQTQQQRYGEQYQ 681

Query: 700 HQQLSQLQQQQQQL-PQLQQQIPQLQQQQ------------------------------Q 728
           H      +        +L +Q  Q QQQ+                               
Sbjct: 682 HDVPVNAEDADAAAEAELARQFAQTQQQRYSGEQPAGANPFSLDDFEFSPMKALLDDGPH 741

Query: 729 IPQLQQQSMPQLQQQQQL---PQLQQQQQLPQMQQQQQLPQ--LQQQQQLSQPQQMVGSG 783
            P       P  Q QQ +    Q QQ QQ    Q Q Q PQ  +  Q Q  QPQQ V   
Sbjct: 742 EPLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQ 801

Query: 784 MGQGYVQGPGRTQLVSQ 800
                 Q P   Q   Q
Sbjct: 802 PQYQQPQQPVAPQPQYQ 818

Length = 1355

>gnl|CDD|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 701 QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQ 760
              +QL  +Q+QL + Q Q    QQ  Q+ ++          +  +   QQ QQ      
Sbjct: 75  NSPTQLTDEQRQLLE-QMQADMRQQPTQLSEVPYNEQTPQVPRSTVQIQQQAQQQQPPAT 133

Query: 761 QQQLPQLQQQQQLSQPQQ 778
             Q   +   +Q + P Q
Sbjct: 134 TAQPQPVTPPRQTTAPVQ 151

Length = 256

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 42.8 bits (100), Expect = 1e-04
 Identities = 28/96 (29%), Positives = 52/96 (54%), Gaps = 2/96 (2%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQ-IPQLQQQQQIPQ 731
           +   ++Q + +QQQQ+Q+ +  Q + +  Q    Q + +  P  QQ+   + +++QQ  Q
Sbjct: 34  ERRCKEQYKEEQQQQRQREEDPQRRYEQCQQRCQQHEPRHRPTCQQRCERRYEKEQQQQQ 93

Query: 732 LQ-QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQ 766
            Q Q+   + QQQ+Q P+ QQQ Q    +Q Q+  +
Sbjct: 94  RQYQECQQRCQQQEQRPRRQQQCQRECREQYQEHGR 129

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 42.4 bits (99), Expect = 1e-04
 Identities = 31/102 (30%), Positives = 56/102 (54%), Gaps = 3/102 (2%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 730
           + Q   +++ + Q +++QQQ +Q +   Q ++  Q QQ+ QQ     +   Q + +++  
Sbjct: 28  REQQQCERRCKEQYKEEQQQQRQREEDPQ-RRYEQCQQRCQQHEPRHRPTCQQRCERRYE 86

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
           + QQQ   Q Q+ QQ  + QQQ+Q P+ QQQ Q    +Q Q+
Sbjct: 87  KEQQQQQRQYQECQQ--RCQQQEQRPRRQQQCQRECREQYQE 126

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit

 Score = 45.2 bits (107), Expect = 1e-04
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 3/101 (2%)

Query: 679 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQ-IPQLQQQQQIPQLQQQSM 737
              L Q++ + +      Q QH Q  +L  QQ Q  +L+++    L +Q +  + ++  +
Sbjct: 276 DTLLHQKKARLEQLVASLQRQHPQN-KLALQQLQFEKLEKRKQAALNKQLERTRQKKTRL 334

Query: 738 PQ-LQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
            + L Q    PQ+ + Q   +   ++       Q  L  PQ
Sbjct: 335 TKRLTQTNPSPQILRAQTRTEQLNRRLNALKNAQANLKLPQ 375

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits [DNA metabolism, Degradation of DNA]. Length = 432

>gnl|CDD|202101 pfam02050, FliJ, Flagellar FliJ protein

 Score = 42.2 bits (100), Expect = 1e-04
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 10/96 (10%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           +  + L + QQ+ +  + + +   Q   + +QQ     Q          Q  I  L +  
Sbjct: 2   KAARNLAEAQQELEQAEEKLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEAI 61

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
               QQQQ+L Q ++     Q++Q ++  Q Q+  Q
Sbjct: 62  A---QQQQELEQAEK-----QVEQARE--QWQEANQ 87

Length = 122

>gnl|CDD|217472 pfam03280, Lipase_chap, Proteobacterial lipase chaperone protein

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 23/114 (20%), Positives = 37/114 (32%), Gaps = 14/114 (12%)

Query: 672 PQISSQQQQQLQQQQQQQQ--------HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL 723
           P +S +Q+ +       Q               Q   Q  +QLQ Q      L+     L
Sbjct: 74  PSLSDEQKARRLAALIAQLPEDLREARRNAALQQELAQATAQLQAQGASPQDLRAARAAL 133

Query: 724 QQQQQIPQLQQQSMPQLQQQQQLPQLQQQ------QQLPQMQQQQQLPQLQQQQ 771
              +   +L Q    +   QQ+      +        L    +Q Q+ QL+QQ 
Sbjct: 134 VGPEAAQRLAQLDQERAAWQQRYDDYLAERDQILAAGLSDADKQAQIAQLRQQL 187

Length = 189

>gnl|CDD|131526 TIGR02473, flagell_FliJ, flagellar export protein FliJ

 Score = 42.7 bits (101), Expect = 1e-04
 Identities = 23/103 (22%), Positives = 54/103 (52%), Gaps = 10/103 (9%)

Query: 679 QQQLQQQQQQQQHQQMQSQLQH--QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           Q +L+  + Q + +++++QLQ   +   + +QQ  +         +L   Q+   ++Q  
Sbjct: 17  QAKLELAKAQAEFERLETQLQQLIKYREEYEQQALEKVGAGTSALELSNYQR--FIRQLD 74

Query: 737 MPQLQQQQQLPQLQQ-----QQQLPQMQQQ-QQLPQLQQQQQL 773
               QQQQ+L  LQQ     +++L + +++ + L +L++++Q 
Sbjct: 75  QRIQQQQQELALLQQEVEAKRERLLEARRELKALEKLKEKKQK 117

Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems. Length = 141

>gnl|CDD|224241 COG1322, COG1322, Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]

 Score = 45.1 bits (107), Expect = 1e-04
 Identities = 30/145 (20%), Positives = 58/145 (40%), Gaps = 18/145 (12%)

Query: 647 LLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQL 706
           + L+   +    +G L          Q+  +    L+Q       +    QL+      L
Sbjct: 15  VNLAFIRQLLLRLGRLE---------QMLGELAAVLEQLLLLLAFRAEAEQLR-TFARSL 64

Query: 707 QQQQQQLPQ-LQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQM--QQQQQ 763
           Q    +L Q L +   +LQQQ    + Q Q +  ++   QL   + Q+   ++  +  ++
Sbjct: 65  QALNLELIQELNELKARLQQQLLQSREQLQLL--IESLAQL-SSEFQELANEIFEELNRR 121

Query: 764 LPQLQQQ--QQLSQPQQMVGSGMGQ 786
           L +L QQ  +QL +P + V     +
Sbjct: 122 LAELNQQNLKQLLKPLREVLEKFRE 146

Length = 448

>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R; Provisional

 Score = 45.3 bits (108), Expect = 1e-04
 Identities = 31/158 (19%), Positives = 61/158 (38%), Gaps = 41/158 (25%)

Query: 625 HGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLF-----------PGDMVVFKPQ 673
           H F G  +E  +                 K    + + F           PG  V   P+
Sbjct: 96  HEFHGDHREALMG---------------LKLAFRLAVWFHRTYGKDWDFKPGPFV--PPE 138

Query: 674 ISSQQQQQLQQQQQQQQHQ-QMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
                   LQQ+    + Q ++Q++ + Q  +  + QQQ+L  L+    +L+++QQ    
Sbjct: 139 DPENLLHALQQEVLTLKQQLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQ---- 194

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
                   + + QL QLQ++      +++Q+  ++  Q
Sbjct: 195 --------ELEAQLEQLQEKAAETSQERKQKRKEITDQ 224

Length = 1123

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 44.5 bits (106), Expect = 1e-04
 Identities = 6/96 (6%), Positives = 55/96 (57%), Gaps = 3/96 (3%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
            +    ++++++++ ++ + + +     Q+++++++  + ++   +LQ+++Q+ ++ ++ 
Sbjct: 52  LKALAEEEERERKRKEERR-EGRAVLQEQIEEREKR--RQEEYEERLQEREQMDEIIERI 108

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
             + + + Q  + +Q++   ++ +  +    +++++
Sbjct: 109 QEEDEAEAQEKREKQKKLREEIDEFNEERIERKEEE 144

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional

 Score = 45.3 bits (108), Expect = 1e-04
 Identities = 22/104 (21%), Positives = 42/104 (40%), Gaps = 11/104 (10%)

Query: 679 QQQLQQQQQQQQHQQMQSQLQH------QQLSQLQQQQQQLPQLQQQIPQLQQQ-QQIPQ 731
           Q QL    +Q+  +     +Q         L ++ +Q+++  QL+QQ+ Q   + +Q   
Sbjct: 42  QAQLDALNKQKLLEAEDKLVQQDLEQTLALLDKIDRQKEETEQLKQQLAQAPAKLRQA-- 99

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
             Q  +  L+        +    L   Q + +L Q   Q Q +Q
Sbjct: 100 --QAELEALKDDNDEETRETLSTLSLRQLESRLAQTLDQLQNAQ 141

Length = 1113

>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207)

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 21/124 (16%), Positives = 57/124 (45%), Gaps = 18/124 (14%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQL-------QQQQQQLPQLQQQIPQLQQ 725
           Q   + Q+ L+++Q+Q++ ++ +     Q+L++        Q+ QQ   Q   +  +   
Sbjct: 99  QRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHKKEAA 158

Query: 726 QQQIPQLQQQSMPQ-----------LQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLS 774
           +     L   + P+           LQ+ +     QQQQ+  + +++Q+  Q +++++  
Sbjct: 159 ESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEEERKQ 218

Query: 775 QPQQ 778
           + ++
Sbjct: 219 KAEE 222

This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. Length = 261

>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 19/83 (22%), Positives = 40/83 (48%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           +Q  Q +   QQ Q ++++ + Q     QL++ +Q+  +L +++ Q     QI + Q ++
Sbjct: 295 RQHPQNKLALQQLQFEKLEKRKQAALNKQLERTRQKKTRLTKRLTQTNPSPQILRAQTRT 354

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQ 759
               ++   L   Q   +LPQ  
Sbjct: 355 EQLNRRLNALKNAQANLKLPQFG 377

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits [DNA metabolism, Degradation of DNA]. Length = 432

>gnl|CDD|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450)

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 6/101 (5%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQL-SQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 735
              QQ      Q Q +  +   Q Q+L ++++Q  +++  L+    QLQ+   +   QQQ
Sbjct: 29  AAAQQTVAAAAQSQKKIDKWADQTQELLAEIRQLLKEIENLRVYNDQLQRL--VAN-QQQ 85

Query: 736 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 776
            +  LQQQ +  +  +Q  +P M +      L+Q   L  P
Sbjct: 86  EIASLQQQIEQIEKTRQGLVPLMYRMID--GLEQFVALDLP 124

This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length. Length = 250

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 17/87 (19%), Positives = 46/87 (52%), Gaps = 5/87 (5%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           + Q+QL + QQ+ Q  + +      +L +LQ++  ++ QL     +L ++ +  +L+++ 
Sbjct: 84  ELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEENR--ELREEL 141

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQ 763
               + +Q+   L+ + +  Q  +Q++
Sbjct: 142 A---ELKQENEALEAENERLQENEQRR 165

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 43.7 bits (104), Expect = 2e-04
 Identities = 13/93 (13%), Positives = 54/93 (58%), Gaps = 6/93 (6%)

Query: 678 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSM 737
           Q++  ++++Q+++ +  + + Q Q+L + +++Q +  + + Q    +++ +    +++ +
Sbjct: 210 QEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQ----EERAEEEAERERML 265

Query: 738 PQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
            +  + ++L Q   +++  +M++ +   +L+QQ
Sbjct: 266 EKQAEDEELEQENAEKR--RMKRLEHRRELEQQ 296

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|225707 COG3166, PilN, Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 20/78 (25%), Positives = 35/78 (44%)

Query: 695 QSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQ 754
           Q   Q Q+ + L  +   L     +I QL++Q Q    + Q + QLQQ++    +  +Q 
Sbjct: 49  QIAEQQQRNALLTTEIALLDAEIAEIQQLKEQTQALLQRLQVIEQLQQKRAGWSVLLEQL 108

Query: 755 LPQMQQQQQLPQLQQQQQ 772
              + +   L  L+QQ  
Sbjct: 109 ANLLPESVWLTSLKQQGD 126

Length = 206

>gnl|CDD|225707 COG3166, PilN, Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 685 QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ-IPQLQQQSMPQLQQQ 743
           Q +Q   QQ ++ L   +++ L  +  ++ QL++Q   L Q+ Q I QLQQ+        
Sbjct: 46  QDRQIAEQQQRNALLTTEIALLDAEIAEIQQLKEQTQALLQRLQVIEQLQQKRAGWSVLL 105

Query: 744 QQLP-QLQQQQQLPQMQQQQQ 763
           +QL   L +   L  ++QQ  
Sbjct: 106 EQLANLLPESVWLTSLKQQGD 126

Length = 206

>gnl|CDD|221776 pfam12795, MscS_porin, Mechanosensitive ion channel porin domain

 Score = 43.4 bits (103), Expect = 2e-04
 Identities = 30/118 (25%), Positives = 55/118 (46%), Gaps = 19/118 (16%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQL-----QHQQLSQLQQQQQQLP----QLQQQIPQL 723
           Q++ ++    +Q+   Q  +Q  + L       Q+  Q Q+Q    P    +L+Q++  L
Sbjct: 5   QLNKRKLPTPEQKALIQDLEQALNFLDEIDKSKQKADQYQKQIDDAPKELRELRQELEAL 64

Query: 724 QQQQQ--IPQLQQQSMPQLQQQ--QQLPQLQQQQQLPQM------QQQQQLPQLQQQQ 771
           ++      P+L   S+ QL+Q+  Q L QLQ+ Q+  Q       + Q +  + QQQ 
Sbjct: 65  KKTDAPVFPELANLSLSQLEQRLAQTLSQLQELQEQLQQENSQLIELQTRPERAQQQL 122

The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux. Length = 239

>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 34/163 (20%), Positives = 62/163 (38%), Gaps = 65/163 (39%)

Query: 675 SSQQQQQLQQ---------QQQQQQHQQMQSQLQHQQLS------QLQQQQQQLPQLQQQ 719
           +  Q + +QQ         +QQQQQ   + +QL+ Q+ +      +L++ Q  L QL +Q
Sbjct: 45  NRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQ 104

Query: 720 -------IPQLQQQQQ-------------------------------------------I 729
                  I +L+QQQ                                            +
Sbjct: 105 IDELNASIAKLEQQQAAQERLLAAQLDAAFRQGEHTGLQLILSGEESQRGERILAYFGYL 164

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
            Q +Q+++ +L+Q ++    Q+ +   +  QQ+ L   QQ QQ
Sbjct: 165 NQARQETIAELKQTREELAAQKAELEEKQSQQKTLLYEQQAQQ 207

Length = 428

>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 44.2 bits (104), Expect = 3e-04
 Identities = 16/110 (14%), Positives = 35/110 (31%), Gaps = 9/110 (8%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ-------QQLPQLQQQIPQLQQ 725
             SS     L  ++      Q   +L HQ  + L+ +        +++    Q   +L  
Sbjct: 725 NASSSLGSDLAAREDA--LNQSLKELMHQARTVLKARTEAHFNNNEEVTAALQTGAELSH 782

Query: 726 QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
                Q   +   +     +  + +  Q++P  +    L      Q+  Q
Sbjct: 783 LAAEIQFFNRLREEDTHLLKTLEAEIGQEIPSDEDILNLQCETLVQEEEQ 832

All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1042

>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 44.2 bits (104), Expect = 3e-04
 Identities = 19/127 (14%), Positives = 49/127 (38%), Gaps = 29/127 (22%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ-------- 728
           Q    L Q+++ Q+ Q  + QL  Q  +++++ + Q   L++   ++ + ++        
Sbjct: 240 QSHAYLTQKREAQEEQLKKQQLLKQLRARIEELRAQEAVLEETQERINRARKAAPLAAHI 299

Query: 729 --IPQLQQQSMPQLQ-------------------QQQQLPQLQQQQQLPQMQQQQQLPQL 767
             + Q++QQ+                         +QQ    +Q++ L  +  Q+   + 
Sbjct: 300 KAVTQIEQQAQRIHTELQSKMRSRAKLLMKRAAHVKQQSSIEEQRRLLQTLHSQEIHIRD 359

Query: 768 QQQQQLS 774
             +   S
Sbjct: 360 AHEVATS 366

All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1042

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 43.5 bits (103), Expect = 3e-04
 Identities = 20/95 (21%), Positives = 27/95 (28%)

Query: 684 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQ 743
                Q+H+  +   QHQ        Q + P  Q    Q+  Q      Q    P  Q  
Sbjct: 74  APANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPA 133

Query: 744 QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
            Q    Q  QQ    Q       +    Q +Q   
Sbjct: 134 YQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAF 168

Length = 333

>gnl|CDD|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869)

 Score = 41.0 bits (97), Expect = 3e-04
 Identities = 31/89 (34%), Positives = 54/89 (60%), Gaps = 9/89 (10%)

Query: 706 LQQQQQQLPQLQQQIPQLQQQQQ--IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ 763
             + Q+QL QL+Q++ QL+ Q Q  I ++++QS  Q++Q QQ  Q++Q++     Q+ Q 
Sbjct: 22  QAELQEQLTQLEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQ--QVEQERAKRLEQKNQL 79

Query: 764 LPQLQQQQQLSQPQQMVGSGMGQGYVQGP 792
           L Q++Q Q+L      +GS + QG V+  
Sbjct: 80  LFQIEQVQELP-----LGSEVKQGQVESF 103

This bacterial family of proteins has no known function. Length = 131

>gnl|CDD|225507 COG2959, HemX, Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

 Score = 43.6 bits (103), Expect = 3e-04
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 691 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQ 750
             Q Q+ LQ Q+L  LQQQ + L   Q+    L Q + +   QQ  + +L++Q +     
Sbjct: 53  FGQQQNVLQTQELQALQQQLKALQLAQENQKLLAQLESLIAQQQAELDRLERQLE----T 108

Query: 751 QQQQLPQMQQQQQLPQLQQQQQ 772
            Q+QL ++Q++        ++ 
Sbjct: 109 LQKQLSELQKKVATISGSDRKD 130

Length = 391

>gnl|CDD|221776 pfam12795, MscS_porin, Mechanosensitive ion channel porin domain

 Score = 43.0 bits (102), Expect = 3e-04
 Identities = 29/122 (23%), Positives = 57/122 (46%), Gaps = 11/122 (9%)

Query: 666 DMVVFKPQISSQQQQQLQQQ--QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL 723
                 P++++    QL+Q+  Q   Q Q++Q QLQ +  SQL + Q +  + QQQ+ + 
Sbjct: 67  TDAPVFPELANLSLSQLEQRLAQTLSQLQELQEQLQQEN-SQLIELQTRPERAQQQLSEA 125

Query: 724 QQQQQ-----IPQLQQQSMPQLQQQQQLPQLQQQ--QQLPQMQQQQQLPQLQQQQQLSQP 776
           +++ Q     +  L     P  Q Q+ L Q +    +   +  + + L     +Q+L + 
Sbjct: 126 RRRLQEIRNRLQALSPGGTPLAQAQRTLLQAELAALKAQIEELELELL-SNNNRQELLRL 184

Query: 777 QQ 778
           Q+
Sbjct: 185 QR 186

The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux. Length = 239

>gnl|CDD|225657 COG3115, ZipA, Cell division protein [Cell division and chromosome partitioning]

 Score = 43.7 bits (103), Expect = 3e-04
 Identities = 21/95 (22%), Positives = 33/95 (34%)

Query: 686 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 745
           Q  Q+H+  +   QHQ   +    Q ++P  Q            P        Q  ++ +
Sbjct: 74  QFTQEHEAARQSPQHQYQPEYASAQIKIPVPQPPQISDPPAHPQPTQPALDQEQPPEEAR 133

Query: 746 LPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
            P L Q+   PQ           Q  Q + P+Q V
Sbjct: 134 QPVLPQEAPAPQPVHSAAPQPAVQTVQPAVPEQQV 168

Length = 324

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 43.1 bits (102), Expect = 4e-04
 Identities = 23/110 (20%), Positives = 35/110 (31%), Gaps = 1/110 (0%)

Query: 669 VFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 728
           V     ++Q+ +  +   Q Q      S    Q + Q  + Q       +      Q  Q
Sbjct: 71  VNHAPANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQ 130

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
            P  Q Q    LQQ    PQ+    Q      Q      Q  + ++ PQ 
Sbjct: 131 QPAYQPQPEQPLQQPVS-PQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQP 179

Length = 333

>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 43.6 bits (103), Expect = 4e-04
 Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 6/99 (6%)

Query: 683 QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ 742
           +Q Q      Q+ +  + Q L+  QQQQQ L  L +     Q+  +  Q  QQ++   ++
Sbjct: 216 EQVQSLTASLQVLTDEEKQLLTAQQQQQQSLNWLTRLDELQQEASRRQQALQQALAAEEK 275

Query: 743 QQ-QLPQLQQQQQLPQMQ-----QQQQLPQLQQQQQLSQ 775
            Q QL  L   Q   Q++      Q+Q   L   +Q  +
Sbjct: 276 AQPQLAALSLAQPARQLRPHWERIQEQSAALAHTRQQIE 314

Length = 1047

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 43.6 bits (103), Expect = 4e-04
 Identities = 24/136 (17%), Positives = 35/136 (25%), Gaps = 27/136 (19%)

Query: 663 FPGDMVVFKP------QISSQQQQQLQQQQQQQQHQQMQSQL---------QHQ-----Q 702
             G M+  KP      Q   Q++  LQ Q  Q Q +  Q  +         Q        
Sbjct: 346 MHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGP 405

Query: 703 LSQLQQQQQQLPQLQQQIPQLQQQQQ-----IPQLQQQSMPQLQQQQQLPQLQQQ--QQL 755
             Q   Q    P++      +          +  +     P    Q    +   Q     
Sbjct: 406 QQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYP 465

Query: 756 PQMQQQQQLPQLQQQQ 771
           P  Q       L Q Q
Sbjct: 466 PNYQSLPLSQDLPQPQ 481

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869)

 Score = 41.0 bits (97), Expect = 4e-04
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 8/65 (12%)

Query: 676 SQQQQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQQQQLPQ----LQQQIPQLQQQQQI 729
            +Q  QL+Q+ QQ   Q Q+   +++ Q   Q++Q QQQ+ Q      +Q  QL  Q + 
Sbjct: 26  QEQLTQLEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQQVEQERAKRLEQKNQLLFQIE- 84

Query: 730 PQLQQ 734
            Q+Q+
Sbjct: 85  -QVQE 88

This bacterial family of proteins has no known function. Length = 131

>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III C-methyltransferase; Provisional

 Score = 43.2 bits (102), Expect = 4e-04
 Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 8/68 (11%)

Query: 705 QLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 764
           Q Q Q      L  Q+  LQ+ Q+    +Q+    L+QQ +   L Q  +    QQ    
Sbjct: 61  QAQNQTATNDALANQLTALQKAQE--SQKQELEGILKQQAK--ALDQANR----QQAALA 112

Query: 765 PQLQQQQQ 772
            QL + QQ
Sbjct: 113 KQLDELQQ 120

Length = 390

>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III C-methyltransferase; Provisional

 Score = 43.2 bits (102), Expect = 4e-04
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 735
            +QQ Q Q         Q+ + LQ  Q SQ Q+ +  L Q  + + Q  +QQ    L +Q
Sbjct: 58  GKQQAQNQTATNDALANQL-TALQKAQESQKQELEGILKQQAKALDQANRQQA--ALAKQ 114

Query: 736 SMPQLQQQ 743
            + +LQQ+
Sbjct: 115 -LDELQQK 121

Length = 390

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 43.4 bits (103), Expect = 4e-04
 Identities = 7/100 (7%), Positives = 51/100 (51%), Gaps = 4/100 (4%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           QI  +++++ ++ +++ Q ++     +  +  Q + + +   + ++Q  +L+++      
Sbjct: 79  QIEEREKRRQEEYEERLQEREQ--MDEIIERIQEEDEAEAQEKREKQK-KLREEIDEFNE 135

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
           ++    + +++++  +  +  +  Q ++ ++  + + +++
Sbjct: 136 ERIERKEEEKEREREEELKILEY-QREKAEREEEREAERR 174

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 43.4 bits (102), Expect = 4e-04
 Identities = 37/93 (39%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 683 QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL-----QQQQQIPQLQQQSM 737
            Q  Q  Q QQ Q+   HQ  SQL  QQ Q    Q    Q        Q Q P  QQ   
Sbjct: 79  PQSPQPDQQQQSQAPPSHQYPSQLPPQQVQSVPQQPTPQQEPYYPPPSQPQPPPAQQPQA 138

Query: 738 PQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
            Q Q   Q+PQ QQ Q  PQ  Q QQ P  Q Q
Sbjct: 139 QQPQPPPQVPQQQQYQSPPQQPQYQQNPPPQAQ 171

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 43.9 bits (104), Expect = 4e-04
 Identities = 15/116 (12%), Positives = 58/116 (50%), Gaps = 11/116 (9%)

Query: 673 QISSQQQQQLQQQQQ-----QQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ 727
               + ++QL+  +      + Q   + ++++ +  ++L++ + +  +LQQ+I +L ++ 
Sbjct: 372 SRLEELEEQLETLRSKVAQLELQIASLNNEIE-RLEARLERLEDRRERLQQEIEELLKKL 430

Query: 728 QIPQLQQQSMPQLQQQQQLPQLQQ-----QQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           +  +L++      + +++L +LQ+     ++ L +++++ +  +        +  Q
Sbjct: 431 EEAELKELQAELEELEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQ 486

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein

 Score = 42.9 bits (101), Expect = 5e-04
 Identities = 16/97 (16%), Positives = 45/97 (46%), Gaps = 11/97 (11%)

Query: 671 KPQISSQQQQQL----QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 726
             Q +  QQQ+     ++Q++Q++ +Q   + + Q+      +Q +  +L+Q   +   +
Sbjct: 49  AQQANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQR----AAEQARQKELEQ---RAAAE 101

Query: 727 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ 763
           +   Q +Q +    ++Q+Q  + + +Q      + + 
Sbjct: 102 KAAKQAEQAAKQAEEKQKQAEEAKAKQAAEAKAKAEA 138

TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB [Transport and binding proteins, Other, Cellular processes, Pathogenesis]. Length = 346

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 43.0 bits (102), Expect = 5e-04
 Identities = 9/101 (8%), Positives = 54/101 (53%), Gaps = 8/101 (7%)

Query: 677 QQQQQLQQQQQQQQHQQM----QSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           ++ +  +++++++  + M       L  ++  + ++++++         Q++++++  Q 
Sbjct: 30  KRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQE 89

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQL 773
           + +   +LQ+++Q+   +  +++ +  + +   + ++Q++L
Sbjct: 90  EYEE--RLQEREQM--DEIIERIQEEDEAEAQEKREKQKKL 126

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 43.6 bits (103), Expect = 5e-04
 Identities = 10/96 (10%), Positives = 56/96 (58%), Gaps = 14/96 (14%)

Query: 677 QQQQQLQQQQQQQQHQQMQS---------QLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ 727
           ++ ++L+ +  + +  ++++         +L+ + L +L+++ ++L +L+++I +L+++ 
Sbjct: 249 ERLEELKARLLEIESLELEALKIREEELRELE-RLLEELEEKIERLEELEREIEELEEEL 307

Query: 728 QIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ 763
           +  +   + + +L ++ +      +++L +++++ +
Sbjct: 308 EGLRALLEELEELLEKLK----SLEERLEKLEEKLE 339

Length = 908

>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 43.6 bits (103), Expect = 5e-04
 Identities = 12/118 (10%), Positives = 71/118 (60%), Gaps = 11/118 (9%)

Query: 670 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQ---QQQQLPQLQQQIPQLQQQ 726
            + +I + +++  + ++++++ ++++++L   +  +L+    ++++L +L++ + +L+++
Sbjct: 230 LEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEK 289

Query: 727 QQIPQLQQQ--SMPQLQQQQQL--PQLQQQQQLPQM--QQQQQLPQLQQQQQLSQPQQ 778
            +  +L++    + +L+++ +     L++ ++L +     +++L +L+++ +  + + 
Sbjct: 290 IE--RLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESEL 345

Length = 908

>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 42.7 bits (101), Expect = 6e-04
 Identities = 24/110 (21%), Positives = 38/110 (34%), Gaps = 4/110 (3%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ----QQQIP 730
             +  +   Q Q Q  +   Q +   QQ  + Q   Q  P+  Q  PQ  Q    Q Q  
Sbjct: 80  EHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPE 139

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
           Q  QQ +         P     Q   Q  Q  +     Q + +++P  ++
Sbjct: 140 QPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPEPVAEPAPVM 189

Length = 333

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 42.4 bits (100), Expect = 6e-04
 Identities = 22/128 (17%), Positives = 29/128 (22%), Gaps = 3/128 (2%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
              Q      Q  Q        Q  Q       QQQ                        
Sbjct: 51  PSPQAPPPVAQLPQPLPQPPPTQALQALP-AGDQQQHNTPTGSPAANPPATFALPAGPAG 109

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ--QLSQPQQMVGSGMGQGYVQGPGR 794
                +  QL  +Q    + Q      L Q  QQ+  Q  Q +    +       Q   +
Sbjct: 110 PTIQTEPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQSAQ 169

Query: 795 TQLVSQGQ 802
               SQ Q
Sbjct: 170 KNDESQLQ 177

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 42.4 bits (100), Expect = 6e-04
 Identities = 23/112 (20%), Positives = 34/112 (30%), Gaps = 6/112 (5%)

Query: 669 VFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 728
           ++  Q+     Q        Q  QQ    LQ  Q         QLP  QQ      Q+  
Sbjct: 119 LYPVQVPVMVTQNPANSPLDQPAQQRA--LQQLQQRYGAPASGQLPSQQQ----SAQKND 172

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
             QLQQQ   +   QQ       + +     ++      Q+ +       M 
Sbjct: 173 ESQLQQQPNGETPPQQTDGAGDDESEALVRLREADGTLEQRIKGAEGGGAMK 224

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III C-methyltransferase; Provisional

 Score = 42.8 bits (101), Expect = 6e-04
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 15/80 (18%)

Query: 691 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQ 750
           H + Q+Q Q      L  Q   L + Q+      Q+Q++  + +      QQ + L Q  
Sbjct: 57  HGKQQAQNQTATNDALANQLTALQKAQE-----SQKQELEGILK------QQAKALDQAN 105

Query: 751 QQQQLPQMQQQQQLPQLQQQ 770
           +QQ        +QL +LQQ+
Sbjct: 106 RQQA----ALAKQLDELQQK 121

Length = 390

>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional

 Score = 43.4 bits (103), Expect = 6e-04
 Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 10/101 (9%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 735
             + + +QQ  +Q      +   Q ++  QL+QQ  Q P   +Q      Q ++  L+  
Sbjct: 55  EAEDKLVQQDLEQTLALLDKIDRQKEETEQLKQQLAQAPAKLRQA-----QAELEALKDD 109

Query: 736 SMPQLQQQ-QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
           +  + ++    L   Q + +L Q   Q Q      Q  L++
Sbjct: 110 NDEETRETLSTLSLRQLESRLAQTLDQLQ----NAQNDLAE 146

Length = 1113

>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein

 Score = 43.0 bits (101), Expect = 6e-04
 Identities = 34/141 (24%), Positives = 54/141 (38%), Gaps = 10/141 (7%)

Query: 680 QQLQQQQQQQQHQQMQSQLQHQQL---SQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           +QL QQ +    Q  +    + ++     LQ    Q+  L +   + Q +Q + QLQQ  
Sbjct: 541 RQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQLQQM- 599

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQL----QQQQQLSQPQQMVGSGMGQGYVQGP 792
           M  LQ  Q  P   QQ        +QQ+ +L    ++QQQL      +     +  ++G 
Sbjct: 600 MNNLQMGQ--PGQGQQMGDQSGDMEQQMNKLGELMRKQQQLRDETFKLDQDQRRDRMRGQ 657

Query: 793 GRTQLVSQGQVSSQGAPNIPG 813
              Q          G PN   
Sbjct: 658 DGEQNFGDDMPQQDGQPNGQP 678

Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model. Length = 851

>gnl|CDD|223914 COG0845, AcrA, Membrane-fusion protein [Cell envelope biogenesis, outer membrane]

 Score = 42.8 bits (100), Expect = 6e-04
 Identities = 17/111 (15%), Positives = 37/111 (33%), Gaps = 4/111 (3%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           ++      Q    Q + Q  + Q+ L   +L  LQ++ + L   +  + Q +       L
Sbjct: 96  RLDPSAVLQAALDQAEAQLARAQALLAPAELGDLQREAK-LAAEKAAVSQAELDAAQALL 154

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQ---QQLPQLQQQQQLSQPQQMV 780
           +         Q  L   +   +  ++          +L +  QL    Q +
Sbjct: 155 RAAEALVEAAQAALASAKLNLEYTRITAPISGVIGARLVRVGQLVSAGQAL 205

Length = 372

>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional

 Score = 42.4 bits (100), Expect = 7e-04
 Identities = 27/101 (26%), Positives = 49/101 (48%), Gaps = 10/101 (9%)

Query: 681 QLQQQQQQQQH---QQMQS---QLQHQ--QLSQLQQQQQQLPQLQQQIPQLQQ--QQQIP 730
           +L+QQQ  Q+     Q+ +   Q +H   QL    ++ Q+  ++      L Q  Q+ I 
Sbjct: 114 KLEQQQAAQERLLAAQLDAAFRQGEHTGLQLILSGEESQRGERILAYFGYLNQARQETIA 173

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ 771
           +L+Q       Q+ +L + Q QQ+    +QQ Q  +L+Q +
Sbjct: 174 ELKQTREELAAQKAELEEKQSQQKTLLYEQQAQQQKLEQAR 214

Length = 428

>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523)

 Score = 42.1 bits (99), Expect = 7e-04
 Identities = 21/91 (23%), Positives = 51/91 (56%), Gaps = 2/91 (2%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 735
           S+ Q++ +Q + + + ++ ++Q    +L + + + ++  +  Q+  Q QQ+QQ  Q Q +
Sbjct: 57  SKMQEKTRQAELEAKIKEYEAQQAQAKLERARVEAEERRKTLQE--QTQQEQQRAQYQDE 114

Query: 736 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQ 766
              +  Q++   Q +Q ++L +MQ++  L Q
Sbjct: 115 LARKRYQKELEQQRRQNEELLKMQEESVLRQ 145

This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with pfam00004. This domain has a conserved LER sequence motif. Length = 276

>gnl|CDD|218218 pfam04702, Vicilin_N, Vicilin N terminal region

 Score = 40.5 bits (94), Expect = 8e-04
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           PQ   +Q QQ  QQ + +     Q + + +   + QQQQ+Q  + QQ+    QQQ+Q P+
Sbjct: 55  PQRRYEQCQQRCQQHEPRHRPTCQQRCERRYEKEQQQQQRQYQECQQRC---QQQEQRPR 111

Query: 732 LQQQSMPQLQQQQQLP 747
            QQQ   + ++Q Q  
Sbjct: 112 RQQQCQRECREQYQEH 127

This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. Length = 147

>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584)

 Score = 42.8 bits (101), Expect = 8e-04
 Identities = 28/108 (25%), Positives = 52/108 (48%), Gaps = 3/108 (2%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 735
            Q ++QL Q   + + Q+         L Q +   Q+L Q +QQ  + + +  I + +QQ
Sbjct: 624 KQAEEQLVQANAELEEQKRAEAEARTALKQARLDLQRL-QNEQQSLKDKLELAIAERKQQ 682

Query: 736 SMPQLQQ-QQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGS 782
           +  QL+Q   QL QL +QQQ      +    +L+ ++  ++ Q + G 
Sbjct: 683 AETQLRQLDAQLKQLLEQQQAFLEALKDDFRELRTERL-AKWQVVEGE 729

This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. Length = 1198

>gnl|CDD|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450)

 Score = 41.4 bits (98), Expect = 8e-04
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 12/99 (12%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQL----PQLQQQIPQLQQQQQIP 730
           ++    Q     QQ      QSQ   +++ +   Q Q+L     QL ++I  L+      
Sbjct: 20  AAASLDQALAAAQQTVAAAAQSQ---KKIDKWADQTQELLAEIRQLLKEIENLRVYND-- 74

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQ 769
           QLQ+       QQQ++  LQQQ +  +  +Q  +P + +
Sbjct: 75  QLQRLV---ANQQQEIASLQQQIEQIEKTRQGLVPLMYR 110

This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length. Length = 250

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 42.3 bits (99), Expect = 8e-04
 Identities = 20/63 (31%), Positives = 25/63 (39%)

Query: 683 QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ 742
             QQ   Q+   Q  +Q+      QQ QQQ  Q  QQ       QQ PQ +Q      +Q
Sbjct: 203 PTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRSREQ 262

Query: 743 QQQ 745
             Q
Sbjct: 263 GNQ 265

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 42.3 bits (99), Expect = 8e-04
 Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 683 QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ 742
           + +   +  QQ   Q   QQ +     QQ   Q QQQ  Q  QQ       QQ  PQ +Q
Sbjct: 196 RHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQP-PQTEQ 254

Query: 743 QQQLPQLQQQQQLPQMQQQQ 762
             +  + Q  Q+  +M ++ 
Sbjct: 255 GHKRSREQGNQEFLKMLKED 274

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III C-methyltransferase; Provisional

 Score = 42.4 bits (100), Expect = 8e-04
 Identities = 13/48 (27%), Positives = 27/48 (56%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQI 720
           Q+++ Q+ Q  Q+Q+ +   + Q++   Q   Q     +QL +LQQ++
Sbjct: 75  QLTALQKAQESQKQELEGILKQQAKALDQANRQQAALAKQLDELQQKV 122

Length = 390

>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional

 Score = 42.6 bits (101), Expect = 8e-04
 Identities = 27/126 (21%), Positives = 50/126 (39%), Gaps = 33/126 (26%)

Query: 682 LQQQQQQQQHQQMQSQLQHQQLSQLQQQ--QQQLPQLQQQI---PQLQQQQQI-PQLQQ- 734
            + Q+ + Q Q +Q  +  ++L+  ++   + Q      +I   P + Q+ +I  QL Q 
Sbjct: 234 ARIQRLEHQLQLLQEAINSKRLTLSEKTVQEAQSQDEAARIQANPLVAQELEINLQLSQR 293

Query: 735 -----QSMPQLQQQ-----QQLPQLQQQQQL--PQM--------------QQQQQLPQLQ 768
                + +  L QQ       L +L Q ++    Q+              QQQQ LP   
Sbjct: 294 LLKATEKLNTLTQQNLRVKNWLDRLTQSERNIKEQISVLKGSLLLSRILYQQQQALPSAD 353

Query: 769 QQQQLS 774
             + L+
Sbjct: 354 LIEGLA 359

Length = 1113

>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like)

 Score = 40.3 bits (95), Expect = 8e-04
 Identities = 31/93 (33%), Positives = 59/93 (63%), Gaps = 17/93 (18%)

Query: 684 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQ 743
           Q+Q +++ +++Q++LQ ++  +LQ+++Q+L   Q+Q   L ++ +     +    +LQQ+
Sbjct: 37  QKQLEKEFKKLQAELQKKE-KELQKEEQKL---QKQAATLSEEAR-----KAKQQELQQK 87

Query: 744 QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 776
           QQ  +LQQ+QQ    QQ+ Q    Q+QQ+L QP
Sbjct: 88  QQ--ELQQKQQ--AAQQELQ----QKQQELLQP 112

This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery. Length = 157

>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like)

 Score = 40.3 bits (95), Expect = 8e-04
 Identities = 23/84 (27%), Positives = 48/84 (57%), Gaps = 11/84 (13%)

Query: 692 QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQ 751
           +  Q QL+     + ++ Q +L + +++   LQ+++Q  Q Q  ++ +  ++ +  +LQQ
Sbjct: 34  KAAQKQLE----KEFKKLQAELQKKEKE---LQKEEQKLQKQAATLSEEARKAKQQELQQ 86

Query: 752 QQQLPQMQQQQQLPQLQQQQQLSQ 775
           +QQ  ++QQ+QQ    QQ+ Q  Q
Sbjct: 87  KQQ--ELQQKQQ--AAQQELQQKQ 106

This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery. Length = 157

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 41.8 bits (99), Expect = 9e-04
 Identities = 9/112 (8%), Positives = 56/112 (50%), Gaps = 16/112 (14%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQ----QQQLPQLQQQIPQ--------- 722
            ++ ++ ++++ +++ ++ + + +  +L   Q++    +++L +L+  + Q         
Sbjct: 160 REKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQ 219

Query: 723 --LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQ-QQQLPQLQQQQ 771
              ++ ++  + +Q+     ++Q +  + + Q++  + +  ++++ + Q + 
Sbjct: 220 KEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAEEEAERERMLEKQAED 271

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 42.3 bits (99), Expect = 0.001
 Identities = 25/121 (20%), Positives = 46/121 (38%), Gaps = 18/121 (14%)

Query: 673 QISSQQQ---QQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 729
           QI  Q Q    +LQ + + +    M+     +Q S +++Q++ L  L  Q   ++   ++
Sbjct: 304 QIEQQAQRIHTELQSKMRSRAKLLMKRAAHVKQQSSIEEQRRLLQTLHSQEIHIRDAHEV 363

Query: 730 PQL------QQQSMPQ--LQQQQQLPQLQQQQQLP-------QMQQQQQLPQLQQQQQLS 774
                    QQ ++ Q     QQQ   L Q+ Q         Q +Q     +    + L 
Sbjct: 364 ATSIREISCQQHTLTQHIHTLQQQKTTLTQKLQSLCKELDILQREQATIDTRTSAFRDLQ 423

Query: 775 Q 775
            
Sbjct: 424 G 424

All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1042

>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 30/138 (21%), Positives = 56/138 (40%), Gaps = 17/138 (12%)

Query: 638 AVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQ--QQQHQQMQ 695
           A I  P+Q  LL   D     +   F          +  Q++ +L+Q     Q+QH Q +
Sbjct: 250 AEIVSPNQDELLQRLDGFNVRLHRAFD--------TLLHQKKARLEQLVASLQRQHPQNK 301

Query: 696 SQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL---QQQSMPQLQQQQQLPQLQQQ 752
             LQ  Q  +L++++Q    L +Q+ + +Q++        Q    PQ+ + Q   + +Q 
Sbjct: 302 LALQQLQFEKLEKRKQA--ALNKQLERTRQKKTRLTKRLTQTNPSPQILRAQT--RTEQL 357

Query: 753 QQLPQMQQQQQLPQLQQQ 770
            +     +  Q      Q
Sbjct: 358 NRRLNALKNAQANLKLPQ 375

This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits [DNA metabolism, Degradation of DNA]. Length = 432

>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 42.5 bits (100), Expect = 0.001
 Identities = 31/118 (26%), Positives = 49/118 (41%), Gaps = 13/118 (11%)

Query: 671 KPQISSQQQQQ-----LQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 725
           K  +++QQQQQ     L +  + QQ    + Q   Q L+  ++ Q QL  L    P  Q 
Sbjct: 233 KQLLTAQQQQQQSLNWLTRLDELQQEASRRQQALQQALAAEEKAQPQLAALSLAQPARQL 292

Query: 726 QQQIPQLQQQSMPQLQQQQQLPQ----LQQQQQL----PQMQQQQQLPQLQQQQQLSQ 775
           +    ++Q+QS      +QQ+ +    LQ    L         +Q      QQQ L+ 
Sbjct: 293 RPHWERIQEQSAALAHTRQQIEEVNTRLQSTMALRARIRHHAAKQSAELQAQQQSLNT 350

Length = 1047

>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 22/75 (29%), Positives = 47/75 (62%), Gaps = 5/75 (6%)

Query: 701 QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQ 760
           + LS     +++LP+LQQ++ +L  Q+++ +LQ+Q   +LQQ+ Q  +L+Q+    + + 
Sbjct: 56  RYLSDTPSARERLPELQQELAEL--QEELAELQEQL-AELQQENQ--ELKQELSTLEAEL 110

Query: 761 QQQLPQLQQQQQLSQ 775
           ++   +L + +QLS 
Sbjct: 111 ERLQKELARIKQLSA 125

Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Length = 198

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 26/127 (20%), Positives = 35/127 (27%), Gaps = 14/127 (11%)

Query: 689 QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQ 748
           Q+ +Q ++ LQ  Q  QLQ + +QLP        + Q     Q  QQ   Q   Q     
Sbjct: 362 QRKEQRRAHLQ-DQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQ---QFNGQPLGWP 417

Query: 749 LQQQQQLPQMQQQQQLPQL-----QQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQV 803
                  P        P         +      Q        Q  +  P       Q   
Sbjct: 418 RMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYPPN-----YQSLP 472

Query: 804 SSQGAPN 810
            SQ  P 
Sbjct: 473 LSQDLPQ 479

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 42.0 bits (98), Expect = 0.001
 Identities = 19/62 (30%), Positives = 25/62 (40%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           P+ + Q   Q   QQ   Q+   Q Q Q QQ      QQ       QQ PQ +Q  +  +
Sbjct: 201 PKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRSR 260

Query: 732 LQ 733
            Q
Sbjct: 261 EQ 262

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 41.4 bits (98), Expect = 0.001
 Identities = 8/93 (8%), Positives = 55/93 (59%), Gaps = 6/93 (6%)

Query: 677 QQQQQLQQQQQQQQHQQM-QSQL-QHQQLSQLQQQQQQLPQLQ--QQIPQLQQQ-QQIPQ 731
           +++++ ++++++++ + + Q Q+ + ++  Q + +++   + Q  + I ++Q++ +   Q
Sbjct: 58  EEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQ 117

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 764
            +++   +L+++      +++ +  + +++++ 
Sbjct: 118 EKREKQKKLREEIDE-FNEERIERKEEEKERER 149

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523)

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 18/109 (16%), Positives = 55/109 (50%), Gaps = 10/109 (9%)

Query: 678 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIP------QLQQQQQIPQ 731
           ++ + QQ Q + +  +++++ + + L +  QQ+QQ  Q Q ++       +L+QQ++   
Sbjct: 73  KEYEAQQAQAKLERARVEAEERRKTLQEQTQQEQQRAQYQDELARKRYQKELEQQRR--- 129

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
            Q + + ++Q++  L Q   ++   +   + +   ++++ +L +     
Sbjct: 130 -QNEELLKMQEESVLRQEAMRRATEEEILEMRRETIEEEAELERENIRA 177

This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with pfam00004. This domain has a conserved LER sequence motif. Length = 276

>gnl|CDD|221016 pfam11180, DUF2968, Protein of unknown function (DUF2968)

 Score = 40.9 bits (96), Expect = 0.001
 Identities = 29/96 (30%), Positives = 49/96 (51%), Gaps = 7/96 (7%)

Query: 687 QQQQHQQMQSQLQHQQL-SQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQ-- 743
            +Q  Q    +++  QL +Q  Q ++Q+   + +  +LQ   Q+ Q Q+Q +   QQQ  
Sbjct: 94  ARQTAQLADVEIRRAQLEAQKAQLERQIAASEARAERLQADLQLAQAQEQQVAARQQQAR 153

Query: 744 QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           Q+   L+ Q+Q      Q QL +LQ+Q +  Q QQ 
Sbjct: 154 QEAVALEAQRQ----AAQAQLRKLQRQIRQLQAQQN 185

This family of proteins has no known function. Length = 192

>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein, HlyD family

 Score = 41.9 bits (99), Expect = 0.001
 Identities = 20/102 (19%), Positives = 55/102 (53%), Gaps = 9/102 (8%)

Query: 678 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSM 737
           +  + QQ   + +   +++QL+   L+Q++Q + +L  LQ Q+  L+QQ ++   + ++ 
Sbjct: 126 ELIKGQQSLFESRKSTLRAQLE-LILAQIKQLEAELAGLQAQLQALRQQLEVISEELEAR 184

Query: 738 PQLQQQQQLPQLQ---QQQQLPQMQ-----QQQQLPQLQQQQ 771
            +L+++  + +L+    +++  + Q      + +L  L++Q 
Sbjct: 185 RKLKEKGLVSRLELLELERERAEAQGELGRLEAELEVLKRQI 226

Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins [Protein fate, Protein and peptide secretion and trafficking]. Length = 423

>gnl|CDD|234977 PRK01741, PRK01741, cell division protein ZipA; Provisional

 Score = 41.6 bits (98), Expect = 0.001
 Identities = 8/84 (9%), Positives = 29/84 (34%), Gaps = 2/84 (2%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQIPQLQ 733
              + +  Q  Q Q     Q+ +    + + Q     +  +     QL+ +  +   ++ 
Sbjct: 115 QNHRSEPIQPTQPQYQSPTQTNVASMTIEETQSPNVPIEGINSSSEQLRVELAELAAEIY 174

Query: 734 QQSMPQLQQQQQLPQLQQQQQLPQ 757
             +  +++  +   + Q + +   
Sbjct: 175 SDASHRVELAKNFMEPQAETEAQP 198

Length = 332

>gnl|CDD|227671 COG5380, LimK, Lipase chaperone [Posttranslational modification, protein turnover, chaperones]

 Score = 41.5 bits (97), Expect = 0.001
 Identities = 23/108 (21%), Positives = 52/108 (48%), Gaps = 5/108 (4%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 734
           S++QQ    ++ + ++    + ++        +++Q+    L   +P++Q+++   Q Q+
Sbjct: 129 SAEQQAFFAEENRLRELALERLRIYEDYGLSDEEKQRAWQALLLDLPKVQEERIFIQRQE 188

Query: 735 ---QSMPQLQQQQQLP--QLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
              Q +PQLQQ  Q P      +  L   +  Q+L +L +Q+   + Q
Sbjct: 189 ATAQLLPQLQQAGQGPTQIRLARVALVGEEGAQRLAELDRQRATWEQQ 236

Length = 283

>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 41.7 bits (99), Expect = 0.001
 Identities = 14/96 (14%), Positives = 54/96 (56%), Gaps = 8/96 (8%)

Query: 671 KPQISSQQQQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 728
           K +   + ++++ + + +  ++ ++ +++LQ  +  +L Q+++ L +  + + + +++  
Sbjct: 55  KKEALLEAKEEIHKLRNEFEKELRERRNELQKLE-KRLLQKEENLDRKLELLEKREEE-- 111

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 764
              L+++     Q+QQ+L + +++ +    +Q Q+L
Sbjct: 112 ---LEKKEKELEQKQQELEKKEEELEELIEEQLQEL 144

Length = 520

>gnl|CDD|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication, recombination, and repair]

 Score = 41.1 bits (97), Expect = 0.002
 Identities = 21/82 (25%), Positives = 49/82 (59%), Gaps = 4/82 (4%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
            ++ S+QQQ+L +   + + + +++QL  ++    +  Q+  PQ+Q+Q  +LQQ ++  +
Sbjct: 305 ERLLSEQQQRLDELAIRLR-RALENQLALKKQRLERLTQRLNPQIQRQQQRLQQLER--R 361

Query: 732 LQQQSMPQLQQ-QQQLPQLQQQ 752
           L +    QL++ +++L  L +Q
Sbjct: 362 LDKALRRQLKRKRERLEALVEQ 383

Length = 440

>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 33/102 (32%), Positives = 39/102 (38%), Gaps = 4/102 (3%)

Query: 679 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLP-QLQQQIPQLQQQQ-QIPQLQQQS 736
           Q  ++       ++ M   L HQ +   QQ       Q    IP L  QQ  +P  QQ  
Sbjct: 16  QSMIRHPYPSYGYEPMGGWLHHQIIPVSQQHPPTHTLQPHHHIPVLPAQQPVVP--QQPL 73

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           MP   Q    P    Q  LPQ  QQ   PQ  Q  Q  QP Q
Sbjct: 74  MPVPGQHSMTPTQHHQPNLPQPAQQPFQPQPLQPPQPQQPMQ 115

They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide. Length = 165

>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 41.9 bits (98), Expect = 0.002
 Identities = 22/112 (19%), Positives = 39/112 (34%), Gaps = 15/112 (13%)

Query: 673 QISSQQ---QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ-QQLPQLQQQIP------- 721
           +IS QQ    Q +   QQQ+     + Q   ++L  LQ++Q     +             
Sbjct: 369 EISCQQHTLTQHIHTLQQQKTTLTQKLQSLCKELDILQREQATIDTRTSAFRDLQGQLAH 428

Query: 722 ----QLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQ 769
               Q  QQ+             Q ++      Q+      +++QQL   +Q
Sbjct: 429 AKKQQELQQRYAELCAAAITCTAQCEKLEKIHLQESAQSLKEREQQLQTKEQ 480

All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1042

>gnl|CDD|202101 pfam02050, FliJ, Flagellar FliJ protein

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 20/100 (20%), Positives = 51/100 (51%), Gaps = 12/100 (12%)

Query: 673 QISSQQQQQLQ-QQQQQQQHQQMQSQLQHQQLSQLQ-------QQQQQLPQLQQQIPQLQ 724
           ++   QQ +L+ +QQ     Q + +       + +        QQQQ+L Q ++Q+ Q +
Sbjct: 20  KLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEAIAQQQQELEQAEKQVEQAR 79

Query: 725 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 764
           +Q Q    +++ + +L ++++    +++Q+    ++Q+ L
Sbjct: 80  EQWQEANQERKKLEKLLEREK----KKEQKEENRREQKLL 115

Length = 122

>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 41.3 bits (97), Expect = 0.002
 Identities = 33/129 (25%), Positives = 52/129 (40%), Gaps = 29/129 (22%)

Query: 673 QISSQQQQQLQQQQQ-QQQHQQMQSQLQHQQLS-------------------QLQQQQQQ 712
           QI++  QQ +Q QQQ +Q+ QQ+ + L    L+                     QQ+Q +
Sbjct: 624 QIAAHNQQIIQYQQQIEQRQQQLLTALAGYALTLPQEDEEASWLATRQQEAQSWQQRQNE 683

Query: 713 LPQLQQQIPQLQQ------QQQIPQLQQQSMPQLQQQQ---QLPQLQQQQQLPQMQQQQQ 763
           L  LQ +I QL        Q       ++++     +Q   Q   L  Q Q  Q Q   +
Sbjct: 684 LTALQNRIQQLTPLLETLPQSDDLPHSEETVALDNWRQVHEQCLSLHSQLQTLQQQDVLE 743

Query: 764 LPQLQQQQQ 772
             +LQ+ Q 
Sbjct: 744 AQRLQKAQA 752

Length = 1047

>gnl|CDD|234937 PRK01294, PRK01294, lipase chaperone; Provisional

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 32/117 (27%), Positives = 49/117 (41%), Gaps = 16/117 (13%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
            Q   L   Q+  +   +++QL     + LQ+ Q+Q   L QQ+ QLQ     PQ  +  
Sbjct: 198 AQDPSLSDAQKAARLAALEAQLPEDLRAALQESQRQQ-ALLQQLAQLQASGASPQELRLM 256

Query: 737 MPQL---QQQQQLPQLQQQ------------QQLPQMQQQQQLPQLQQQQQLSQPQQ 778
             QL   +  Q+L QL QQ             Q  Q+     L    +Q Q++Q +Q
Sbjct: 257 RAQLVGPEAAQRLEQLDQQRAAWQQRYDDYLAQRAQILNAAGLSPQDRQAQIAQLRQ 313

Length = 336

>gnl|CDD|234937 PRK01294, PRK01294, lipase chaperone; Provisional

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 21/127 (16%), Positives = 45/127 (35%), Gaps = 16/127 (12%)

Query: 670 FKPQISSQQQQQLQQQQQQ--QQHQQMQSQLQ--------HQQLSQLQQQQQQLPQLQQQ 719
            + +I++Q  +    Q      +++   S L            L  LQQ       L+ +
Sbjct: 111 VEREIAAQLPEPADSQALDLWLRYKAYLSALAQLEDDGPGKLDLQALQQLLDARLALRAR 170

Query: 720 IPQLQQQQQI----PQLQQQSMPQLQ--QQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQL 773
                + Q       Q Q+ ++ +L+  Q   L   Q+  +L  ++ Q         Q+ 
Sbjct: 171 FFSDWEIQAFFGEENQYQRYALERLRIAQDPSLSDAQKAARLAALEAQLPEDLRAALQES 230

Query: 774 SQPQQMV 780
            + Q ++
Sbjct: 231 QRQQALL 237

Length = 336

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 25/74 (33%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 691 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQ 750
           H+   +    QQ +     QQ   Q   Q PQ Q QQQ  Q  QQ  PQ   QQ  PQ +
Sbjct: 195 HRHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQP-PQTE 253

Query: 751 QQQQLPQMQQQQQL 764
           Q  +  + Q  Q+ 
Sbjct: 254 QGHKRSREQGNQEF 267

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 21/60 (35%), Positives = 25/60 (41%), Gaps = 3/60 (5%)

Query: 721 PQLQQQQQIPQLQ---QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
           P  Q   Q P  Q   Q    Q QQQ Q   +Q  QQ       QQ PQ +Q  + S+ Q
Sbjct: 203 PTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRSREQ 262

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 41.2 bits (96), Expect = 0.002
 Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 721 PQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           P+  QQ  +    QQ  P +Q   Q PQ Q QQQ  Q  QQ       QQ   ++   
Sbjct: 201 PKPTQQPTVQNPAQQ--PTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGH 256

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R; Provisional

 Score = 41.5 bits (98), Expect = 0.002
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 709 QQQQLPQLQQQIPQLQQQ-QQIPQLQQQSMPQLQQQQQ----LPQLQQQQQLPQMQQQQQ 763
            +  L  LQQ++  L+QQ +   + + QS    + QQQ    L  L  + +  Q + + Q
Sbjct: 140 PENLLHALQQEVLTLKQQLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQELEAQ 199

Query: 764 LPQLQQQQQLSQPQQ 778
           L QLQ++   +  ++
Sbjct: 200 LEQLQEKAAETSQER 214

Length = 1123

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 41.0 bits (97), Expect = 0.002
 Identities = 11/87 (12%), Positives = 53/87 (60%), Gaps = 2/87 (2%)

Query: 679 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMP 738
           ++Q+++++++ Q ++ + + + +++ + Q + ++L Q   +  ++++ +   +L+QQ   
Sbjct: 240 EEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQIEE 299

Query: 739 QLQQQQQLPQ--LQQQQQLPQMQQQQQ 763
           + +++    +  L++ ++L + + ++Q
Sbjct: 300 KEERRAAEREEELEEGERLREEEAERQ 326

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional

 Score = 41.4 bits (98), Expect = 0.002
 Identities = 29/127 (22%), Positives = 57/127 (44%), Gaps = 21/127 (16%)

Query: 673 QISSQQQQQLQQQQQ----QQQHQQMQSQLQHQQLSQ--LQQQQQQLPQLQQQIPQLQQQ 726
           Q+ S Q Q  + Q       Q+ QQ+++ L+  ++    L+  Q+ L Q +Q +   Q  
Sbjct: 150 QLVSLQTQPERAQAALYANSQRLQQIRNLLKGGKVGGKALRPSQRVLLQAEQALLNAQND 209

Query: 727 QQIPQLQQQSMPQ--LQQQQ-----QLPQLQQQQQLPQ--------MQQQQQLPQLQQQQ 771
            Q   L+  +  Q  LQ+Q+     ++ +L+ Q QL Q           ++ + + Q Q 
Sbjct: 210 LQRKSLEGNTQLQDLLQKQRDYLTARIQRLEHQLQLLQEAINSKRLTLSEKTVQEAQSQD 269

Query: 772 QLSQPQQ 778
           + ++ Q 
Sbjct: 270 EAARIQA 276

Length = 1113

>gnl|CDD|225707 COG3166, PilN, Tfp pilus assembly protein PilN [Cell motility and secretion / Intracellular trafficking and secretion]

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 11/100 (11%)

Query: 658 LIGMLFPGDMVVFKPQISSQQQ--QQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQ 715
            I  L  G ++    QI+ QQQ    L  +      +         ++ QL++Q Q L Q
Sbjct: 35  GIAALALGGLLQD-RQIAEQQQRNALLTTEIALLDAEI-------AEIQQLKEQTQALLQ 86

Query: 716 LQQQIPQLQQQQQIPQLQQQSMP-QLQQQQQLPQLQQQQQ 754
             Q I QLQQ++    +  + +   L +   L  L+QQ  
Sbjct: 87  RLQVIEQLQQKRAGWSVLLEQLANLLPESVWLTSLKQQGD 126

Length = 206

>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421)

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 35/120 (29%), Positives = 39/120 (32%), Gaps = 14/120 (11%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQ---------QQIPQ 722
           P    Q  +        QQ           Q  Q  QQQQ               QQ+  
Sbjct: 50  PPAPEQVAKHELADAPLQQVNAALPPAPAPQSPQPDQQQQSQAPPSHQYPSQLPPQQVQS 109

Query: 723 LQQQQQIPQL-----QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
           + QQ    Q        Q  P   QQ Q  Q Q   Q+PQ QQ Q  PQ  Q QQ   PQ
Sbjct: 110 VPQQPTPQQEPYYPPPSQPQPPPAQQPQAQQPQPPPQVPQQQQYQSPPQQPQYQQNPPPQ 169

This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function. Length = 357

>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 36/138 (26%), Positives = 59/138 (42%), Gaps = 21/138 (15%)

Query: 673 QISSQQQQQLQQ----QQQQQQH---QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 725
           Q+ SQ QQ +      Q  Q Q    Q    + Q  +L +L ++QQQL     ++ Q Q+
Sbjct: 591 QLLSQLQQMMNNLQMGQPGQGQQMGDQSGDMEQQMNKLGELMRKQQQLRDETFKLDQDQR 650

Query: 726 QQQ-------------IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
           + +             +PQ   Q   Q     +L +LQQ++    + Q Q   +  +  Q
Sbjct: 651 RDRMRGQDGEQNFGDDMPQQDGQPNGQPNLHDRLRKLQQEEAKRGLGQSQGGLK-GELGQ 709

Query: 773 LSQPQQMVGSGMGQGYVQ 790
           L Q  Q +G   G+G+ Q
Sbjct: 710 LGQGLQNLGIQPGKGFDQ 727

Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model. Length = 851

>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein

 Score = 41.1 bits (96), Expect = 0.002
 Identities = 42/154 (27%), Positives = 64/154 (41%), Gaps = 15/154 (9%)

Query: 667 MVVFKPQISSQQQQQLQQQQQ----------QQQHQQMQSQLQHQQLSQLQQQQQQ-LPQ 715
           M  +  Q++ Q +   QQ  +          QQ  Q M  Q+++   S  + Q +Q L Q
Sbjct: 536 MQTYMRQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQ 595

Query: 716 LQQQIPQLQ--QQQQIPQLQQQSMPQLQQQQQLPQL-QQQQQLPQMQQQQQLPQLQQQQQ 772
           LQQ +  LQ  Q  Q  Q+  QS    QQ  +L +L ++QQQL     +    Q + + +
Sbjct: 596 LQQMMNNLQMGQPGQGQQMGDQSGDMEQQMNKLGELMRKQQQLRDETFKLDQDQRRDRMR 655

Query: 773 LSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQ 806
               +Q  G  M Q   Q  G+  L        Q
Sbjct: 656 GQDGEQNFGDDMPQQDGQPNGQPNL-HDRLRKLQ 688

Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model. Length = 851

>gnl|CDD|148750 pfam07321, YscO, Type III secretion protein YscO

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 22/92 (23%), Positives = 49/92 (53%), Gaps = 5/92 (5%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQ-LPQLQQQIPQLQQQQQI 729
           + Q ++   ++L++ QQQ    +       QQL++ +Q+ +    +L+Q   QLQ+ ++ 
Sbjct: 58  ELQGATVLLKELEKWQQQVGLLRENEASLEQQLAEAKQRLEAERQRLRQARQQLQEARK- 116

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQ 761
               Q+   +L +Q+Q     Q+Q L +++Q+
Sbjct: 117 ---AQEKFAELARQEQAEAQAQRQYLEELEQE 145

This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis. Length = 152

>gnl|CDD|148750 pfam07321, YscO, Type III secretion protein YscO

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 31/124 (25%), Positives = 61/124 (49%), Gaps = 21/124 (16%)

Query: 676 SQQQQQLQQ--------QQQQQQHQQMQSQLQHQQLSQLQQQ---QQQLPQLQQQIPQL- 723
            +Q+Q L Q        QQ  Q ++Q + Q +++  ++LQ      ++L + QQQ+  L 
Sbjct: 21  KRQEQALVQARARHREAQQSLQDYRQWRQQEENRLFAELQGATVLLKELEKWQQQVGLLR 80

Query: 724 -------QQQQQIPQLQQQSMPQLQQ-QQQLPQLQQQQQ-LPQMQQQQQLPQLQQQQQLS 774
                  QQ  +  Q  +    +L+Q +QQL + ++ Q+   ++ +Q+Q     Q+Q L 
Sbjct: 81  ENEASLEQQLAEAKQRLEAERQRLRQARQQLQEARKAQEKFAELARQEQAEAQAQRQYLE 140

Query: 775 QPQQ 778
           + +Q
Sbjct: 141 ELEQ 144

This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis. Length = 152

>gnl|CDD|148750 pfam07321, YscO, Type III secretion protein YscO

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 15/60 (25%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 680 QQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQL--QQQIPQLQQQQQIPQLQQQSM 737
           QQL + +Q+ + ++ + +   QQL + ++ Q++  +L  Q+Q     Q+Q + +L+Q+  
Sbjct: 88  QQLAEAKQRLEAERQRLRQARQQLQEARKAQEKFAELARQEQAEAQAQRQYLEELEQEEF 147

This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis. Length = 152

>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed

 Score = 41.5 bits (98), Expect = 0.002
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 734
            + ++++     + +  ++   +L ++   +L+Q  Q L  L+ +I  LQ Q        
Sbjct: 539 PAVKKKEEAAAPKAETVKRSSKKLSYKLQRELEQLPQLLEDLEAEIEALQAQVADADFFS 598

Query: 735 QSMPQLQQQQQLPQLQQQQQ 754
           Q  P  Q Q+ L  L   +Q
Sbjct: 599 Q--PHEQTQKVLADLADAEQ 616

Length = 635

>gnl|CDD|113156 pfam04375, HemX, HemX

 Score = 41.0 bits (96), Expect = 0.002
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 702 QLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQ 761
            L Q+   Q +L  L Q++ QL Q  +    Q+  +     Q+ L QL++       Q  
Sbjct: 51  GLQQVAGLQIKLEALAQELTQLAQALEAQLAQEVRVLIRDNQEALAQLEKVLG----QLD 106

Query: 762 QQLPQLQQQQ 771
           + L +LQ + 
Sbjct: 107 KSLAELQDRV 116

This family consists of several bacterial HemX proteins. The hemX gene is not essential for haem synthesis in B. subtilis. HemX is a polytopic membrane protein which by an unknown mechanism down-regulates the level of HemA. Length = 372

>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 14/107 (13%), Positives = 41/107 (38%), Gaps = 11/107 (10%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ---- 727
           P +    +   +  +    +  +      +++  L+   +QL  ++ +I   Q +     
Sbjct: 133 PALLVSPEDAQRSVRLAIYYGALNPARA-ERIDALKATLKQLAAVRAEIAAEQAELTTLL 191

Query: 728 --QIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
             Q  Q  + +    ++++ L QL  +        Q++L +L+  + 
Sbjct: 192 SEQRAQQAKLAQLLEERKKTLAQLNSELS----ADQKKLEELRANES 234

Length = 420

>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 41.1 bits (96), Expect = 0.003
 Identities = 21/139 (15%), Positives = 52/139 (37%), Gaps = 2/139 (1%)

Query: 665 GDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 724
           G   +   +                + +Q+  +        LQQ QQ    L Q+    +
Sbjct: 194 GKAELLTLRSQLLTLCTPCMPDTYHERKQVLEKELKHLREALQQTQQSHAYLTQKREAQE 253

Query: 725 QQQQIPQLQQQSMPQLQQ-QQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSG 783
           +Q +  QL +Q   ++++ + Q   L++ Q+    + ++  P     + ++Q +Q     
Sbjct: 254 EQLKKQQLLKQLRARIEELRAQEAVLEETQERIN-RARKAAPLAAHIKAVTQIEQQAQRI 312

Query: 784 MGQGYVQGPGRTQLVSQGQ 802
             +   +   R +L+ +  
Sbjct: 313 HTELQSKMRSRAKLLMKRA 331

All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 1042

>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584)

 Score = 40.8 bits (96), Expect = 0.003
 Identities = 23/102 (22%), Positives = 53/102 (51%), Gaps = 8/102 (7%)

Query: 684 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ----QQIPQLQQQSMPQ 739
           + + +++ QQ +  LQ    ++ +Q ++QL Q   ++ + ++     +   +  +  + +
Sbjct: 602 ETELRERLQQAEEALQSAV-AKQKQAEEQLVQANAELEEQKRAEAEARTALKQARLDLQR 660

Query: 740 LQQQQQLPQLQQQQQLPQMQQQ--QQLPQL-QQQQQLSQPQQ 778
           LQ +QQ  + + +  + + +QQ   QL QL  Q +QL + QQ
Sbjct: 661 LQNEQQSLKDKLELAIAERKQQAETQLRQLDAQLKQLLEQQQ 702

This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. Length = 1198

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 17/114 (14%), Positives = 30/114 (26%), Gaps = 2/114 (1%)

Query: 667 MVVFKPQISSQQQQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 724
                P     QQ+ LQQ QQ+            Q       + Q QQ P  +    Q  
Sbjct: 131 NPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQSAQKNDESQLQQQPNGETPPQQTD 190

Query: 725 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
                       + +     +      +        +Q   Q +  ++ +  Q 
Sbjct: 191 GAGDDESEALVRLREADGTLEQRIKGAEGGGAMKVLKQPKKQAKSSKRRTIAQI 244

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 40.4 bits (94), Expect = 0.003
 Identities = 18/73 (24%), Positives = 22/73 (30%)

Query: 691 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQ 750
           H                Q   Q P +Q    Q QQQ Q   +Q    P  Q   Q P   
Sbjct: 193 HGHRHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQT 252

Query: 751 QQQQLPQMQQQQQ 763
           +Q      +Q  Q
Sbjct: 253 EQGHKRSREQGNQ 265

This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. Length = 422

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 10/116 (8%), Positives = 58/116 (50%), Gaps = 17/116 (14%)

Query: 677 QQQQQLQQQQQQQQ---HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ--------- 724
           Q++++  +++++Q+    +  + Q++ ++  +LQ+++ +    ++++ + Q         
Sbjct: 219 QKEKEEAEKRRRQKQELQRAREEQIEEKEE-RLQEERAEEEAERERMLEKQAEDEELEQE 277

Query: 725 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
             ++    + +   +L+QQ +  + ++  +  +  ++ +    + +++ ++ Q  +
Sbjct: 278 NAEKRRMKRLEHRRELEQQIEEKEERRAAEREEELEEGE----RLREEEAERQARI 329

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 40.3 bits (95), Expect = 0.003
 Identities = 13/112 (11%), Positives = 67/112 (59%), Gaps = 10/112 (8%)

Query: 674 ISSQQQQQLQQQQQQQ----QHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 729
              + +++ +++ +++    + ++  ++L+ QQ  + + ++++L +L+  + Q + +++ 
Sbjct: 159 QREKAEREEEREAERRERKEEKEREVARLRAQQE-EAEDEREELDELRADLYQEEYERKE 217

Query: 730 PQ-LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
            Q  ++++  + +Q+Q+L + +++Q   + ++ Q+    ++ ++ ++ ++M+
Sbjct: 218 RQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQE----ERAEEEAERERML 265

Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). Length = 349

>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional

 Score = 41.1 bits (97), Expect = 0.003
 Identities = 29/138 (21%), Positives = 58/138 (42%), Gaps = 36/138 (26%)

Query: 671 KPQISSQQQQQLQQQQQ--QQQHQQMQSQLQ-HQQLSQLQQQQQ-----QLPQLQQQIPQ 722
              +   Q+  LQ +Q     Q+   +  L+ + QL  L Q+Q+     ++ +L+ Q+  
Sbjct: 186 GKALRPSQRVLLQAEQALLNAQNDLQRKSLEGNTQLQDLLQKQRDYLTARIQRLEHQLQL 245

Query: 723 LQQ----------QQQIPQLQQ-------QSMPQLQQQ----QQLPQ--LQQQQQLPQMQ 759
           LQ+          ++ + + Q        Q+ P + Q+     QL Q  L+  ++L  + 
Sbjct: 246 LQEAINSKRLTLSEKTVQEAQSQDEAARIQANPLVAQELEINLQLSQRLLKATEKLNTLT 305

Query: 760 QQ-----QQLPQLQQQQQ 772
           QQ       L +L Q ++
Sbjct: 306 QQNLRVKNWLDRLTQSER 323

Length = 1113

>gnl|CDD|225657 COG3115, ZipA, Cell division protein [Cell division and chromosome partitioning]

 Score = 40.2 bits (94), Expect = 0.003
 Identities = 20/102 (19%), Positives = 31/102 (30%), Gaps = 1/102 (0%)

Query: 678 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ-S 736
           Q  Q  +  +Q    Q Q +    Q+     Q  Q+          Q      Q  ++  
Sbjct: 74  QFTQEHEAARQSPQHQYQPEYASAQIKIPVPQPPQISDPPAHPQPTQPALDQEQPPEEAR 133

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
            P L Q+   PQ           Q  Q    +QQ Q  +  +
Sbjct: 134 QPVLPQEAPAPQPVHSAAPQPAVQTVQPAVPEQQVQPEEVVE 175

Length = 324

>gnl|CDD|227671 COG5380, LimK, Lipase chaperone [Posttranslational modification, protein turnover, chaperones]

 Score = 40.0 bits (93), Expect = 0.003
 Identities = 22/110 (20%), Positives = 46/110 (41%), Gaps = 9/110 (8%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           +      +++Q+     +    + Q+     Q+Q+      Q +PQLQQ  Q P   + +
Sbjct: 154 EDYGLSDEEKQRAWQALLLDLPKVQEERIFIQRQE---ATAQLLPQLQQAGQGPTQIRLA 210

Query: 737 MPQL---QQQQQLPQLQQQQQLPQMQQQ---QQLPQLQQQQQLSQPQQMV 780
              L   +  Q+L +L +Q+   + Q Q        ++ + +LS  +Q  
Sbjct: 211 RVALVGEEGAQRLAELDRQRATWEQQFQDYYAARAAIEVRNELSASEQQT 260

Length = 283

>gnl|CDD|226889 COG4487, COG4487, Uncharacterized protein conserved in bacteria [Function unknown]

 Score = 40.6 bits (95), Expect = 0.003
 Identities = 18/123 (14%), Positives = 53/123 (43%), Gaps = 13/123 (10%)

Query: 669 VFKPQISSQQQQQLQQQQQQQQHQQMQSQLQ-------HQQLSQLQQQQQQLPQLQQQIP 721
           + K + S + +Q   +Q +Q+   ++ + L+        ++      ++++L QL++Q+ 
Sbjct: 15  IPKCEDSIKGEQARYKQIEQEDQSRILNTLEEFEKEANEKRAQYRSAKKKELSQLEEQLI 74

Query: 722 QLQ------QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
             +        +QI Q +     ++ + + L  L  ++       +++L +L ++ Q   
Sbjct: 75  NQKKEQKNLFNEQIKQFELALQDEIAKLEALELLNLEKDKELELLEKELDELSKELQKQL 134

Query: 776 PQQ 778
              
Sbjct: 135 QNT 137

Length = 438

>gnl|CDD|204848 pfam12203, HDAC4_Gln, Glutamine rich N terminal domain of histone deacetylase 4

 Score = 37.3 bits (86), Expect = 0.003
 Identities = 28/88 (31%), Positives = 55/88 (62%), Gaps = 7/88 (7%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           QQ+  L +QQQQ Q Q + ++ Q Q  +  +Q + QL +       L+QQQ++  +++Q 
Sbjct: 12  QQELLLLKQQQQIQKQLLIAEFQKQHENLTRQHEAQLQE------HLKQQQELLAMKRQQ 65

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQL 764
              L+++++L Q +Q+Q+L + +++QQL
Sbjct: 66  -ELLEKERKLEQQRQEQELEKHRREQQL 92

This domain is found in eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam00850. The domain forms an alpha helix which complexes to form a tetramer. The glutamine rich domains have many intra- and inter-helical interactions which are thought to be involved in reversible assembly and disassembly of proteins. The domain is part of histone deacetylase 4 (HDAC4) which removes acetyl groups from histones. This restores their positive charge to allow stronger DNA binding thus restricting transcriptional activity. Length = 92

>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed

 Score = 40.2 bits (95), Expect = 0.004
 Identities = 19/81 (23%), Positives = 45/81 (55%), Gaps = 12/81 (14%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLS-QLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           Q   Q+  + + +  +Q+ +++  +LQ Q    ++++ QQ+L QL+Q++ +  ++    Q
Sbjct: 318 QQRLQRALERRLRLAKQRLERLSQRLQQQNPQRRIERAQQRLEQLEQRLRRAMRR----Q 373

Query: 732 LQQQSMPQLQQQQQLPQLQQQ 752
           L+       +++Q+L  L QQ
Sbjct: 374 LK-------RKRQRLEALAQQ 387

Length = 438

>gnl|CDD|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 28/87 (32%), Positives = 34/87 (39%), Gaps = 1/87 (1%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           P + +QQ    QQ       Q   +  QH Q   L Q  QQ  Q Q   P   QQ   PQ
Sbjct: 59  PVLPAQQPVVPQQPLMPVPGQHSMTPTQHHQ-PNLPQPAQQPFQPQPLQPPQPQQPMQPQ 117

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQM 758
                +P L  Q  LP +   Q LP +
Sbjct: 118 PPVHPIPPLPPQPPLPPMFPMQPLPPL 144

They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide. Length = 165

>gnl|CDD|234937 PRK01294, PRK01294, lipase chaperone; Provisional

 Score = 39.7 bits (93), Expect = 0.004
 Identities = 33/133 (24%), Positives = 49/133 (36%), Gaps = 34/133 (25%)

Query: 672 PQISSQQQQQLQQQQQQ-----------QQHQQM---QSQLQHQQLSQLQ---------- 707
                   Q LQQ                + Q     ++Q Q   L +L+          
Sbjct: 147 DGPGKLDLQALQQLLDARLALRARFFSDWEIQAFFGEENQYQRYALERLRIAQDPSLSDA 206

Query: 708 QQQQQLPQLQQQIPQ-LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQ----- 761
           Q+  +L  L+ Q+P+ L+   Q  Q QQ  + QL Q Q        Q+L  M+ Q     
Sbjct: 207 QKAARLAALEAQLPEDLRAALQESQRQQALLQQLAQLQA--SGASPQELRLMRAQLVGPE 264

Query: 762 --QQLPQLQQQQQ 772
             Q+L QL QQ+ 
Sbjct: 265 AAQRLEQLDQQRA 277

Length = 336

>gnl|CDD|225657 COG3115, ZipA, Cell division protein [Cell division and chromosome partitioning]

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 7/105 (6%)

Query: 672 PQISSQQQQQLQQQQQQ-----QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 726
            + S Q Q Q +    Q      Q  Q+     H Q +Q    Q+Q P  + + P L Q+
Sbjct: 82  ARQSPQHQYQPEYASAQIKIPVPQPPQISDPPAHPQPTQPALDQEQ-PPEEARQPVLPQE 140

Query: 727 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ 771
              PQ    + PQ    Q +     +QQ+   +  +  P++++  
Sbjct: 141 APAPQPVHSAAPQ-PAVQTVQPAVPEQQVQPEEVVEPAPEVKRPP 184

Length = 324

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 40.4 bits (95), Expect = 0.004
 Identities = 14/109 (12%), Positives = 58/109 (53%), Gaps = 7/109 (6%)

Query: 678 QQQQLQQQQQQQQHQQMQSQL------QHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
            + + + ++ +++ + ++++L        +  S+L++ ++QL  L+ ++ QL+ Q     
Sbjct: 340 AELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLN 399

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQ-QQQQLSQPQQM 779
            + + +    ++ +  + + QQ++ ++ ++ +  +L+  Q +L + ++ 
Sbjct: 400 NEIERLEARLERLEDRRERLQQEIEELLKKLEEAELKELQAELEELEEE 448

SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]. Length = 1179

>gnl|CDD|234977 PRK01741, PRK01741, cell division protein ZipA; Provisional

 Score = 39.7 bits (93), Expect = 0.004
 Identities = 13/108 (12%), Positives = 33/108 (30%), Gaps = 1/108 (0%)

Query: 685 QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQ 744
             Q+  +     + +  Q +Q Q Q      +     +  Q   +P     S  +  + +
Sbjct: 106 PNQEPAYYMQNHRSEPIQPTQPQYQSPTQTNVASMTIEETQSPNVPIEGINSSSEQLRVE 165

Query: 745 QLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGP 792
                 +       + +     ++ Q + ++ Q    +     YV  P
Sbjct: 166 LAELAAEIYSDASHRVELAKNFMEPQAE-TEAQPEATTNFIMLYVVAP 212

Length = 332

>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 40.1 bits (94), Expect = 0.004
 Identities = 20/156 (12%), Positives = 57/156 (36%), Gaps = 8/156 (5%)

Query: 665 GDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 724
             +   + +I+++Q +      +Q+  Q   +QL  ++   L Q   +L   Q+++ +L+
Sbjct: 171 KQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELSADQKKLEELR 230

Query: 725 QQQQ-IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSG 783
             +  +      +     + ++       +      +  +  +  +  + + P++M    
Sbjct: 231 ANESRLKNEIASAEAAAAKARE--AAAAAEAAAARARAAEAKRTGETYKPTAPEKM---L 285

Query: 784 MGQGYVQGPGRTQLV--SQGQVSSQGAPNIPGGGFM 817
           +      G  R QL     G++  +      GG   
Sbjct: 286 ISSTGGFGALRGQLAWPVTGRILRRFGQADGGGLRW 321

Length = 420

>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y

 Score = 40.3 bits (95), Expect = 0.004
 Identities = 9/91 (9%), Positives = 53/91 (58%), Gaps = 6/91 (6%)

Query: 674 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 733
           + ++++    + + +++ ++ +++LQ  +  +L Q+++ L    +++  L ++++  + +
Sbjct: 54  LEAKEEVHKLRAELERELKERRNELQRLE-RRLLQREETL---DRKMESLDKKEENLEKK 109

Query: 734 QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 764
           ++ +    +++ L + +++ +    +Q+++L
Sbjct: 110 EKEL--SNKEKNLDEKEEELEELIAEQREEL 138

Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch [Transcription, Degradation of RNA]. Length = 514

>gnl|CDD|223831 COG0760, SurA, Parvulin-like peptidyl-prolyl isomerase [Posttranslational modification, protein turnover, chaperones]

 Score = 40.1 bits (93), Expect = 0.004
 Identities = 18/116 (15%), Positives = 41/116 (35%), Gaps = 5/116 (4%)

Query: 659 IGMLFPGDMVVFKPQISSQQQQ---QLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQ 715
           +       +V          Q+   + +   QQ++      QL  +QL  LQ   +   +
Sbjct: 23  VSASLVAGVVNAGAVAKVGAQEISAKEKLNAQQKERNIALEQL-GEQLLLLQAAAELGIK 81

Query: 716 L-QQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
           + QQ + QL  +  +     + +      +Q  QL  ++   Q  + +   +   +
Sbjct: 82  ISQQVVAQLIAEIAVLDKLAKELLLGLSDEQGKQLIAEKPAFQDVEGKFDARAYLK 137

Length = 320

>gnl|CDD|217933 pfam04156, IncA, IncA protein

 Score = 38.6 bits (90), Expect = 0.004
 Identities = 21/123 (17%), Positives = 53/123 (43%), Gaps = 15/123 (12%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQ----------QLSQLQQQQQQLPQLQQQI 720
            P  S + Q+  + Q +  + +Q  S+LQ +            S+L+  ++ L  L++ +
Sbjct: 64  APVQSVRPQKLEELQGELSELKQQLSELQEELEDLEERIAELESELEDLKEDLQLLRELL 123

Query: 721 PQLQQ-----QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
             L++     ++ I +L ++     Q  ++  +  +++     +  Q+L +  Q+ Q   
Sbjct: 124 KSLEERLESLEESIKELAKELRELRQDLREEVEELREELERLQENLQRLQEAIQELQSLL 183

Query: 776 PQQ 778
            Q 
Sbjct: 184 EQL 186

Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Length = 186

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	818
PF11265	226	Med25_VWA: Mediator complex subunit 25 von Willebr	100.0
cd01452	187	VWA_26S_proteasome_subunit 26S proteasome plays a	97.8
cd01480	186	vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI	97.79
cd01482	164	vWA_collagen_alphaI-XII-like Collagen: The extrace	97.66
cd01450	161	vWFA_subfamily_ECM Von Willebrand factor type A (v	97.58
cd01469	177	vWA_integrins_alpha_subunit Integrins are a class	97.43
cd01481	165	vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(V	97.28
cd01472	164	vWA_collagen von Willebrand factor (vWF) type A do	97.25
cd01453	183	vWA_transcription_factor_IIH_type Transcription fa	97.19
PF13519	172	VWA_2: von Willebrand factor type A domain; PDB: 3	97.1
cd01475	224	vWA_Matrilin VWA_Matrilin: In cartilaginous plate,	96.91
cd01476	163	VWA_integrin_invertebrates VWA_integrin (invertebr	96.5
cd01471	186	vWA_micronemal_protein Micronemal proteins: The To	96.46
cd01473	192	vWA_CTRP CTRP for CS protein-TRAP-related protein:	96.1
cd01474	185	vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxi	95.66
cd01458	218	vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heter	95.61
cd00198	161	vWFA Von Willebrand factor type A (vWA) domain was	95.58
cd01477	193	vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand	95.42
PF00092	178	VWA: von Willebrand factor type A domain; InterPro	95.34
KOG3598	2220	consensus Thyroid hormone receptor-associated prot	95.27
cd01456	206	vWA_ywmD_type VWA ywmD type:Von Willebrand factor	94.57
PF04056	193	Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like pro	94.57
smart00327	177	VWA von Willebrand factor (vWF) type A domain. VWA	94.35
cd01467	180	vWA_BatA_type VWA BatA type: Von Willebrand factor	94.0
PF11235	168	Med25_SD1: Mediator complex subunit 25 synapsin 1;	92.72
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	92.6
cd01451	178	vWA_Magnesium_chelatase Magnesium chelatase: Mg-ch	92.55
cd01463	190	vWA_VGCC_like VWA Voltage gated Calcium channel li	92.43
cd01470	198	vWA_complement_factors Complement factors B and C2	92.37
PRK13685	326	hypothetical protein; Provisional	92.31
PF04811	243	Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: I	92.31
cd01454	174	vWA_norD_type norD type: Denitrifying bacteria con	91.64
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	91.33
COG1240	261	ChlD Mg-chelatase subunit ChlD [Coenzyme metabolis	90.52
PTZ00441	576	sporozoite surface protein 2 (SSP2); Provisional	90.22
cd01461	171	vWA_interalpha_trypsin_inhibitor vWA_interalpha tr	89.85
TIGR03436	296	acidobact_VWFA VWFA-related Acidobacterial domain.	88.74
PF13768	155	VWA_3: von Willebrand factor type A domain	86.78
smart00187	423	INB Integrin beta subunits (N-terminal portion of	85.94
cd01466	155	vWA_C3HC4_type VWA C3HC4-type: Von Willebrand fact	85.02
cd01465	170	vWA_subgroup VWA subgroup: Von Willebrand factor t	81.56
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	81.2

>PF11265 Med25_VWA: Mediator complex subunit 25 von Willebrand factor type A; InterPro: IPR021419 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells

Probab=100.00  E-value=5.2e-65  Score=522.33  Aligned_cols=196  Identities=39%  Similarity=0.580  Sum_probs=179.1

Q ss_pred             CchhhHHHh-hhhHHHHHhhccccccccccCCC--cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCC
Q 003455            1 MCIYFYAYS-KLSLYFHRCFCVNELAGQKTSAS--NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGG   77 (818)
Q Consensus         1 m~~Y~~~l~-~YI~p~ie~f~~~~~~e~~~~~~--~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG   77 (818)
                      |++||+.|| +||+|+||||++|+++|++++++  +++|||||||+|||||+|+|+|+|||+|+++|++|||+|+|+|||
T Consensus        26 lgpy~~~Lkt~Yl~P~le~f~~g~~~e~~~~~~~~~t~y~LVvf~t~d~~~~~~v~~~g~T~~~~~fl~~L~~I~f~GGG  105 (226)
T PF11265_consen   26 LGPYWNTLKTNYLDPILEYFNGGPIAERDFGGDYSNTEYGLVVFNTADCYPEPIVQRSGPTSSPQKFLQWLDAIQFSGGG  105 (226)
T ss_pred             hhhhHHHHHHHHHHHHHHHhcCCCcccccccccCCCceEEEEEEeccCCCcccceeccCCcCCHHHHHHHHHccCcCCCC
Confidence            799999999 79999999999999999998555  899999999999999999999999999999999999999999999


Q ss_pred             -CChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHH
Q 003455           78 -FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETV  156 (818)
Q Consensus        78 -~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~l  156 (818)
                       +++++|||||++||+||+.....++...+.++|||||||||||||++|+.               |+..|++ +++|++
T Consensus       106 ~e~~a~iaEGLa~AL~~fd~~~~~r~~~~~~~~~khcILI~nSpP~~~p~~---------------~~~~~~~-~~~d~l  169 (226)
T PF11265_consen  106 FESCAAIAEGLAEALQCFDDFKQMRQQQQQTDVQKHCILICNSPPYRLPVN---------------ECPQYSG-KTCDQL  169 (226)
T ss_pred             cccchhHHHHHHHHHHHhcchhhhccccCcccccceEEEEeCCCCcccccc---------------CCCcccC-CCHHHH
Confidence             55577999999999999833333444456789999999999999999986               5566655 799999


Q ss_pred             HHHHhhcCceEEEeCCCcchHHHHHHHHhcCCCCC-CCCCCCCCCCCCeEEEeeccc
Q 003455          157 AKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRA-ADPPVDNSKNPHFLVLISENF  212 (818)
Q Consensus       157 a~~~~~~~I~lSiIsPrklp~L~~lf~~a~~~~~~-~~~~~d~ak~p~hlVLl~g~~  212 (818)
                      |.++.||+|+||||||||||+|++||||+++|++. +++++||||||||||||||+|
T Consensus       170 a~~~~~~~I~LSiisPrklP~l~~Lfeka~~~~~~~~~~~~~~ak~p~hlVLl~g~~  226 (226)
T PF11265_consen  170 AVLISERNISLSIISPRKLPSLRSLFEKAKGNPRAAADPSKDYAKDPRHLVLLRGYF  226 (226)
T ss_pred             HHHHHhcCceEEEEcCccCHHHHHHHHhcCCCcccccccccccccCCCeEEEeecCC
Confidence            99999999999999999999999999999999997 699999999999999999987

Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex [].

>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins

Probab=97.80  E-value=0.0005  Score=70.57  Aligned_cols=132  Identities=20%  Similarity=0.164  Sum_probs=91.4

Q ss_pred             hHHHhhhhHHHH-HhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            5 FYAYSKLSLYFH-RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         5 ~~~l~~YI~p~i-e~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      |+..|+++.-++ |||...+         ....|||+|.+..+|-     ...+|.|...++..|++|+..| |   +.|
T Consensus        26 L~aak~~i~~~~~~f~~~np---------~~~vGlv~fag~~a~v-----~~plT~D~~~~~~~L~~i~~~g-~---~~l   87 (187)
T cd01452          26 FQAQADAVNLICQAKTRSNP---------ENNVGLMTMAGNSPEV-----LVTLTNDQGKILSKLHDVQPKG-K---ANF   87 (187)
T ss_pred             HHHHHHHHHHHHHHHHhcCC---------CccEEEEEecCCceEE-----EECCCCCHHHHHHHHHhCCCCC-c---chH
Confidence            345556777776 5554433         3689999999855543     4678999999999999999642 2   578


Q ss_pred             HHHHHHHHhhhccCCCCCCCCCCCCCc-cEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhh
Q 003455           84 AEGLSEALMMFSVAPNGSQNQQNVDGQ-RHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQ  162 (818)
Q Consensus        84 aEGLa~AL~~~~~~~~~~~~~~~~~~q-khCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~  162 (818)
                      .+||..|+..|.-      +  ....+ +..|++..|+=-.                         .-.+.+.+|+.+.+
T Consensus        88 ~~AL~~A~~~L~~------~--~~~~~~~rivi~v~S~~~~-------------------------d~~~i~~~~~~lkk  134 (187)
T cd01452          88 ITGIQIAQLALKH------R--QNKNQKQRIVAFVGSPIEE-------------------------DEKDLVKLAKRLKK  134 (187)
T ss_pred             HHHHHHHHHHHhc------C--CCcCCcceEEEEEecCCcC-------------------------CHHHHHHHHHHHHH
Confidence            8999999988851      1  11222 2444444443111                         11357789999999


Q ss_pred             cCceEEEeCC----CcchHHHHHHHHhcC
Q 003455          163 CSVSLSVICP----KQLPKLTAIYNAAKR  187 (818)
Q Consensus       163 ~~I~lSiIsP----rklp~L~~lf~~a~~  187 (818)
                      +||.++||+=    ...++|+.+++....
T Consensus       135 ~~I~v~vI~~G~~~~~~~~l~~~~~~~~~  163 (187)
T cd01452         135 NNVSVDIINFGEIDDNTEKLTAFIDAVNG  163 (187)
T ss_pred             cCCeEEEEEeCCCCCCHHHHHHHHHHhcC
Confidence            9999999985    357889999988743

It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.

>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions

Probab=97.79  E-value=0.00066  Score=68.36  Aligned_cols=130  Identities=10%  Similarity=0.160  Sum_probs=94.4

Q ss_pred             hhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCC---CCHHHHHHHhccccCCCCCCC
Q 003455            3 IYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT---KDVDIFLHWLSTIPFAGGGFN   79 (818)
Q Consensus         3 ~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T---~~~~~fl~wL~~i~f~GGG~~   79 (818)
                      ..|+..|+++..+++.|...  ...+.....+.+|||+|.+...      ..+.|+   .|...++..|++|++.|||  
T Consensus        18 ~~~~~~k~~~~~~~~~l~~~--~~~~i~~~~~rvglv~fs~~~~------~~~~l~~~~~~~~~l~~~i~~l~~~gg~--   87 (186)
T cd01480          18 QNFDITKNFVKRVAERFLKD--YYRKDPAGSWRVGVVQYSDQQE------VEAGFLRDIRNYTSLKEAVDNLEYIGGG--   87 (186)
T ss_pred             hhHHHHHHHHHHHHHHHhhh--hccCCCCCceEEEEEEecCCce------eeEecccccCCHHHHHHHHHhCccCCCC--
Confidence            56788888888888888431  0001122358999999996532      234555   7899999999999998876  


Q ss_pred             hhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHH
Q 003455           80 DAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKS  159 (818)
Q Consensus        80 ~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~  159 (818)
                       ..+.+||..|+..+..       ..+....|+.||++.-.+.....                        .+.+..++.
T Consensus        88 -T~~~~AL~~a~~~l~~-------~~~~~~~~~iillTDG~~~~~~~------------------------~~~~~~~~~  135 (186)
T cd01480          88 -TFTDCALKYATEQLLE-------GSHQKENKFLLVITDGHSDGSPD------------------------GGIEKAVNE  135 (186)
T ss_pred             -ccHHHHHHHHHHHHhc-------cCCCCCceEEEEEeCCCcCCCcc------------------------hhHHHHHHH
Confidence             6889999999987741       12356789999998876633211                        256778888


Q ss_pred             HhhcCceEEEeCCCc
Q 003455          160 FVQCSVSLSVICPKQ  174 (818)
Q Consensus       160 ~~~~~I~lSiIsPrk  174 (818)
                      +.+.+|.+..|.-..
T Consensus       136 ~~~~gi~i~~vgig~  150 (186)
T cd01480         136 ADHLGIKIFFVAVGS  150 (186)
T ss_pred             HHHCCCEEEEEecCc
Confidence            999999999998865

The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.

>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions

Probab=97.66  E-value=0.0019  Score=63.56  Aligned_cols=121  Identities=14%  Similarity=0.200  Sum_probs=86.2

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      -|+..+++|..+++.|.-+        ...+++|||+|.+..   ...+ .+.-+.+..+++..|++|.+.||+   ..+
T Consensus        17 ~~~~~k~~~~~l~~~~~~~--------~~~~rvgli~fs~~~---~~~~-~l~~~~~~~~l~~~l~~~~~~~g~---T~~   81 (164)
T cd01482          17 NFNLVRSFLSSVVEAFEIG--------PDGVQVGLVQYSDDP---RTEF-DLNAYTSKEDVLAAIKNLPYKGGN---TRT   81 (164)
T ss_pred             hHHHHHHHHHHHHhheeeC--------CCceEEEEEEECCCe---eEEE-ecCCCCCHHHHHHHHHhCcCCCCC---ChH
Confidence            5677788888888888321        236899999999974   1111 122346789999999999999886   368


Q ss_pred             HHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhh
Q 003455           84 AEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQ  162 (818)
Q Consensus        84 aEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~  162 (818)
                      .+||-.|++ +|. ..    ...+....|.+||++.-.|..                            +++.+|+.+.+
T Consensus        82 ~~aL~~a~~~~~~-~~----~~~r~~~~k~iillTDG~~~~----------------------------~~~~~a~~lk~  128 (164)
T cd01482          82 GKALTHVREKNFT-PD----AGARPGVPKVVILITDGKSQD----------------------------DVELPARVLRN  128 (164)
T ss_pred             HHHHHHHHHHhcc-cc----cCCCCCCCEEEEEEcCCCCCc----------------------------hHHHHHHHHHH
Confidence            999998886 443 11    112355678888887765321                            55678899999


Q ss_pred             cCceEEEeCC
Q 003455          163 CSVSLSVICP  172 (818)
Q Consensus       163 ~~I~lSiIsP  172 (818)
                      .+|.+.+|.=
T Consensus       129 ~gi~i~~ig~  138 (164)
T cd01482         129 LGVNVFAVGV  138 (164)
T ss_pred             CCCEEEEEec
Confidence            9999999964

The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.

>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=97.58  E-value=0.0015  Score=62.05  Aligned_cols=126  Identities=12%  Similarity=0.126  Sum_probs=92.6

Q ss_pred             Cch-hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC--CHHHHHHHhccccCCCCC
Q 003455            1 MCI-YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDIFLHWLSTIPFAGGG   77 (818)
Q Consensus         1 m~~-Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~--~~~~fl~wL~~i~f~GGG   77 (818)
                      |.. +|+.+++.|..+++.|...+        ...+++||+|++..      ...+.|+.  +..+++.+|+++.+.+| 
T Consensus        13 m~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~li~f~~~~------~~~~~~~~~~~~~~~~~~i~~~~~~~~-   77 (161)
T cd01450          13 VGPENFEKVKDFIEKLVEKLDIGP--------DKTRVGLVQYSDDV------RVEFSLNDYKSKDDLLKAVKNLKYLGG-   77 (161)
T ss_pred             cCHHHHHHHHHHHHHHHHheeeCC--------CceEEEEEEEcCCc------eEEEECCCCCCHHHHHHHHHhcccCCC-
Confidence            444 67888888888888886422        35899999999842      12344444  48999999999998877 


Q ss_pred             CChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHH
Q 003455           78 FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVA  157 (818)
Q Consensus        78 ~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la  157 (818)
                       +...+.|||..|+..+.....     .+....|+.|||....+....                          +.++++
T Consensus        78 -~~t~~~~al~~a~~~~~~~~~-----~~~~~~~~iiliTDG~~~~~~--------------------------~~~~~~  125 (161)
T cd01450          78 -GGTNTGKALQYALEQLFSESN-----ARENVPKVIIVLTDGRSDDGG--------------------------DPKEAA  125 (161)
T ss_pred             -CCccHHHHHHHHHHHhccccc-----ccCCCCeEEEEECCCCCCCCc--------------------------chHHHH
Confidence             457889999999987751110     235677899999888664411                          467888


Q ss_pred             HHHhhcCceEEEeCCC
Q 003455          158 KSFVQCSVSLSVICPK  173 (818)
Q Consensus       158 ~~~~~~~I~lSiIsPr  173 (818)
                      +.+.+++|.+.+|+=.
T Consensus       126 ~~~~~~~v~v~~i~~g  141 (161)
T cd01450         126 AKLKDEGIKVFVVGVG  141 (161)
T ss_pred             HHHHHCCCEEEEEecc
Confidence            9999999999988654

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A

>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration

Probab=97.43  E-value=0.0029  Score=63.34  Aligned_cols=124  Identities=10%  Similarity=0.044  Sum_probs=88.6

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      .|+..++++..+++.|.-++        ..+.+|||+|.+.. .-.+.   +.-..+...++..++.|++.||+   ..+
T Consensus        17 ~f~~~k~fi~~~i~~l~~~~--------~~~rvgvv~fs~~~-~~~~~---l~~~~~~~~~~~~i~~~~~~~g~---T~~   81 (177)
T cd01469          17 DFQKVKNFLSTVMKKLDIGP--------TKTQFGLVQYSESF-RTEFT---LNEYRTKEEPLSLVKHISQLLGL---TNT   81 (177)
T ss_pred             HHHHHHHHHHHHHHHcCcCC--------CCcEEEEEEECCce-eEEEe---cCccCCHHHHHHHHHhCccCCCC---ccH
Confidence            68888999999999996432        35899999999873 11111   22234677899999999998887   788


Q ss_pred             HHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhc
Q 003455           84 AEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC  163 (818)
Q Consensus        84 aEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~  163 (818)
                      .+||..|+..+-. .   .+..+....|..||+++-.++.-+                          +.+.+++.+.+.
T Consensus        82 ~~AL~~a~~~l~~-~---~~g~R~~~~kv~illTDG~~~~~~--------------------------~~~~~~~~~k~~  131 (177)
T cd01469          82 ATAIQYVVTELFS-E---SNGARKDATKVLVVITDGESHDDP--------------------------LLKDVIPQAERE  131 (177)
T ss_pred             HHHHHHHHHHhcC-c---ccCCCCCCCeEEEEEeCCCCCCcc--------------------------ccHHHHHHHHHC
Confidence            9999999975420 1   112345688999999887766422                          225678888889


Q ss_pred             CceEEEeCC
Q 003455          164 SVSLSVICP  172 (818)
Q Consensus       164 ~I~lSiIsP  172 (818)
                      ||.+-.|.=
T Consensus       132 gv~v~~Vgv  140 (177)
T cd01469         132 GIIRYAIGV  140 (177)
T ss_pred             CcEEEEEEe
Confidence            998777653

Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.

>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions

Probab=97.28  E-value=0.0095  Score=59.45  Aligned_cols=126  Identities=12%  Similarity=0.151  Sum_probs=91.1

Q ss_pred             hhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhh
Q 003455            3 IYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA   82 (818)
Q Consensus         3 ~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~a   82 (818)
                      ..|+..|+||..+++.|.-++        ..+.+|||+|.+.. ..++.+   .-..+..+++..|++|+|.||+.  ..
T Consensus        16 ~~f~~~k~fi~~lv~~f~i~~--------~~~rVgvv~ys~~~-~~~~~l---~~~~~~~~l~~~i~~i~~~~g~~--t~   81 (165)
T cd01481          16 GNFPAIRDFIERIVQSLDVGP--------DKIRVAVVQFSDTP-RPEFYL---NTHSTKADVLGAVRRLRLRGGSQ--LN   81 (165)
T ss_pred             HHHHHHHHHHHHHHhhccCCC--------CCcEEEEEEecCCe-eEEEec---cccCCHHHHHHHHHhcccCCCCc--cc
Confidence            568999999999999996533        36999999998754 333333   23347899999999999998853  34


Q ss_pred             HHHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHh
Q 003455           83 IAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFV  161 (818)
Q Consensus        83 iaEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~  161 (818)
                      +++||..|.. +|.  .... ...+..+.|..|||++-...                            .+.+..|+.+.
T Consensus        82 t~~AL~~~~~~~f~--~~~g-~R~~~~~~kv~vviTdG~s~----------------------------d~~~~~a~~lr  130 (165)
T cd01481          82 TGSALDYVVKNLFT--KSAG-SRIEEGVPQFLVLITGGKSQ----------------------------DDVERPAVALK  130 (165)
T ss_pred             HHHHHHHHHHhhcC--cccc-CCccCCCCeEEEEEeCCCCc----------------------------chHHHHHHHHH
Confidence            6888988874 664  1111 11235678899999876432                            14677899999


Q ss_pred             hcCceEEEeCCC
Q 003455          162 QCSVSLSVICPK  173 (818)
Q Consensus       162 ~~~I~lSiIsPr  173 (818)
                      +.||.+=.|.-.
T Consensus       131 ~~gv~i~~vG~~  142 (165)
T cd01481         131 RAGIVPFAIGAR  142 (165)
T ss_pred             HCCcEEEEEeCC
Confidence            999998887665

The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.

>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins

Probab=97.25  E-value=0.012  Score=57.66  Aligned_cols=136  Identities=13%  Similarity=0.143  Sum_probs=90.9

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      .|+..++++..+++-|...        ....++|||+|.+....    +..+....|...++.-|+++++.||+   ..+
T Consensus        17 ~~~~~k~~~~~~~~~l~~~--------~~~~~~giv~Fs~~~~~----~~~~~~~~~~~~~~~~l~~l~~~~g~---T~~   81 (164)
T cd01472          17 NFNLVKDFVKRVVERLDIG--------PDGVRVGVVQYSDDPRT----EFYLNTYRSKDDVLEAVKNLRYIGGG---TNT   81 (164)
T ss_pred             HHHHHHHHHHHHHhhcccC--------CCCeEEEEEEEcCceeE----EEecCCCCCHHHHHHHHHhCcCCCCC---chH
Confidence            5677788888888888421        13579999999975322    22223348899999999999988665   468


Q ss_pred             HHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhc
Q 003455           84 AEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC  163 (818)
Q Consensus        84 aEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~  163 (818)
                      ++||..|++.+....    +..+....|+.|||+.--|..                            +.+..+..+.+.
T Consensus        82 ~~al~~a~~~l~~~~----~~~~~~~~~~iiliTDG~~~~----------------------------~~~~~~~~l~~~  129 (164)
T cd01472          82 GKALKYVRENLFTEA----SGSREGVPKVLVVITDGKSQD----------------------------DVEEPAVELKQA  129 (164)
T ss_pred             HHHHHHHHHHhCCcc----cCCCCCCCEEEEEEcCCCCCc----------------------------hHHHHHHHHHHC
Confidence            999999998774110    112345678889998773211                            223445667788


Q ss_pred             CceEEEeCCC--cchHHHHHHHHhc
Q 003455          164 SVSLSVICPK--QLPKLTAIYNAAK  186 (818)
Q Consensus       164 ~I~lSiIsPr--klp~L~~lf~~a~  186 (818)
                      +|.+-.|.-.  ....|+.|-+..+
T Consensus       130 gv~i~~ig~g~~~~~~L~~ia~~~~  154 (164)
T cd01472         130 GIEVFAVGVKNADEEELKQIASDPK  154 (164)
T ss_pred             CCEEEEEECCcCCHHHHHHHHCCCc
Confidence            9999988653  3455666655443

This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.

>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme

Probab=97.19  E-value=0.0076  Score=61.18  Aligned_cols=115  Identities=15%  Similarity=0.168  Sum_probs=79.4

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccE
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRH  112 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkh  112 (818)
                      ..++|||+|++..+|-     ...+|.|...|+..|+.+...+||   .++.+||..|+..|.  ..      .....|+
T Consensus        46 ~~~vglv~f~~~~a~~-----~~PlT~D~~~~~~~L~~~~~~~G~---t~l~~aL~~A~~~l~--~~------~~~~~~~  109 (183)
T cd01453          46 ISQLGIISIKNGRAEK-----LTDLTGNPRKHIQALKTARECSGE---PSLQNGLEMALESLK--HM------PSHGSRE  109 (183)
T ss_pred             cccEEEEEEcCCccEE-----EECCCCCHHHHHHHhhcccCCCCc---hhHHHHHHHHHHHHh--cC------CccCceE
Confidence            3689999997666643     566899999999999988222333   689999999999985  10      1122354


Q ss_pred             EEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCC-cchHHHHHHHHhcCC
Q 003455          113 CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK-QLPKLTAIYNAAKRN  188 (818)
Q Consensus       113 CILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPr-klp~L~~lf~~a~~~  188 (818)
                      .|||..+. ..                        +...+.+++++++.+.+|.+++|+=- ....|++|-++.++.
T Consensus       110 iiil~sd~-~~------------------------~~~~~~~~~~~~l~~~~I~v~~IgiG~~~~~L~~ia~~tgG~  161 (183)
T cd01453         110 VLIIFSSL-ST------------------------CDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKATNGT  161 (183)
T ss_pred             EEEEEcCC-Cc------------------------CChhhHHHHHHHHHHcCcEEEEEEechHHHHHHHHHHHhCCe
Confidence            55444321 00                        00014567899999999999999753 456799999998775

Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.

>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A

Probab=97.10  E-value=0.0033  Score=60.11  Aligned_cols=129  Identities=16%  Similarity=0.123  Sum_probs=88.3

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHH
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIA   84 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aia   84 (818)
                      ++..++.+.-+++.+.            ...++||.|.+..      -..+.||.|...|+.+|+++...+.......+.
T Consensus        22 ~~~~~~~~~~~~~~~~------------~~~v~l~~f~~~~------~~~~~~t~~~~~~~~~l~~~~~~~~~~~~t~~~   83 (172)
T PF13519_consen   22 IDQAKDALNELLANLP------------GDRVGLVSFSDSS------RTLSPLTSDKDELKNALNKLSPQGMPGGGTNLY   83 (172)
T ss_dssp             HHHHHHHHHHHHHHHT------------TSEEEEEEESTSC------EEEEEEESSHHHHHHHHHTHHHHG--SSS--HH
T ss_pred             HHHHHHHHHHHHHHCC------------CCEEEEEEecccc------cccccccccHHHHHHHhhcccccccCccCCcHH
Confidence            5666667766776651            2499999999843      235678999999999999999865445557889


Q ss_pred             HHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcC
Q 003455           85 EGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS  164 (818)
Q Consensus        85 EGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~  164 (818)
                      +||.+|+.+|+-.         ....|+.|||+.-.|.                            .+..++++.+.+++
T Consensus        84 ~al~~a~~~~~~~---------~~~~~~iv~iTDG~~~----------------------------~~~~~~~~~~~~~~  126 (172)
T PF13519_consen   84 DALQEAAKMLASS---------DNRRRAIVLITDGEDN----------------------------SSDIEAAKALKQQG  126 (172)
T ss_dssp             HHHHHHHHHHHC----------SSEEEEEEEEES-TTH----------------------------CHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHhC---------CCCceEEEEecCCCCC----------------------------cchhHHHHHHHHcC
Confidence            9999999999611         1466777888775222                            13334888889999


Q ss_pred             ceEEEeCCCc----chHHHHHHHHhcCC
Q 003455          165 VSLSVICPKQ----LPKLTAIYNAAKRN  188 (818)
Q Consensus       165 I~lSiIsPrk----lp~L~~lf~~a~~~  188 (818)
                      |.+-+|.=..    ...|+.|.+..++.
T Consensus       127 i~i~~v~~~~~~~~~~~l~~la~~tgG~  154 (172)
T PF13519_consen  127 ITIYTVGIGSDSDANEFLQRLAEATGGR  154 (172)
T ss_dssp             EEEEEEEES-TT-EHHHHHHHHHHTEEE
T ss_pred             CeEEEEEECCCccHHHHHHHHHHhcCCE
Confidence            9988775432    23588888776553

>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity

Probab=96.91  E-value=0.015  Score=60.38  Aligned_cols=124  Identities=14%  Similarity=0.122  Sum_probs=85.8

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      -|+..|++|..+++.|.-++        ..+.+|||+|.+-.- ..+   ...+..+..++...|++|++.|||   ..+
T Consensus        19 ~~~~~k~f~~~l~~~l~~~~--------~~~rvglv~fs~~~~-~~~---~l~~~~~~~~l~~~i~~i~~~~~~---t~t   83 (224)
T cd01475          19 NFELVKQFLNQIIDSLDVGP--------DATRVGLVQYSSTVK-QEF---PLGRFKSKADLKRAVRRMEYLETG---TMT   83 (224)
T ss_pred             HHHHHHHHHHHHHHhcccCC--------CccEEEEEEecCcee-EEe---cccccCCHHHHHHHHHhCcCCCCC---ChH
Confidence            58888899999999995422        258999999998631 111   233346788999999999999887   245


Q ss_pred             HHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhh
Q 003455           84 AEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQ  162 (818)
Q Consensus        84 aEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~  162 (818)
                      .+||..|+. +|.  .....|.......|..||+++-.+..                            +.+.+|+.+.+
T Consensus        84 g~AL~~a~~~~~~--~~~g~r~~~~~~~kvvillTDG~s~~----------------------------~~~~~a~~lk~  133 (224)
T cd01475          84 GLAIQYAMNNAFS--EAEGARPGSERVPRVGIVVTDGRPQD----------------------------DVSEVAAKARA  133 (224)
T ss_pred             HHHHHHHHHHhCC--hhcCCCCCCCCCCeEEEEEcCCCCcc----------------------------cHHHHHHHHHH
Confidence            678888885 453  11222323334578889987765321                            45677888888


Q ss_pred             cCceEEEeCC
Q 003455          163 CSVSLSVICP  172 (818)
Q Consensus       163 ~~I~lSiIsP  172 (818)
                      .+|.+-.|.=
T Consensus       134 ~gv~i~~Vgv  143 (224)
T cd01475         134 LGIEMFAVGV  143 (224)
T ss_pred             CCcEEEEEeC
Confidence            8998887754

Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.

>cd01476 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions

Probab=96.50  E-value=0.096  Score=50.90  Aligned_cols=126  Identities=15%  Similarity=0.201  Sum_probs=82.8

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCc-eeeccCCCCHHHHHHHhccccCCCCCCC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACL-VQRSGWTKDVDIFLHWLSTIPFAGGGFN   79 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~-v~~~g~T~~~~~fl~wL~~i~f~GGG~~   79 (818)
                      |...|+..++++.-+++.|..+        ....++|||+|.+..   ... .-...++.+...++.-|+.|++.||+  
T Consensus        13 m~~~~~~~~~~~~~~~~~l~~~--------~~~~~v~lv~f~~~~---~~~~~~~l~~~~~~~~l~~~i~~l~~~gg~--   79 (163)
T cd01476          13 VRGKFEKYKKYIERIVEGLEIG--------PTATRVALITYSGRG---RQRVRFNLPKHNDGEELLEKVDNLRFIGGT--   79 (163)
T ss_pred             hhhhHHHHHHHHHHHHHhcCCC--------CCCcEEEEEEEcCCC---ceEEEecCCCCCCHHHHHHHHHhCccCCCC--
Confidence            3446777888888888888532        235899999997741   111 11245567889999999999987764  


Q ss_pred             hhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHH
Q 003455           80 DAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKS  159 (818)
Q Consensus        80 ~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~  159 (818)
                       ..+++||..|+.++.  ....   .+....|..||++.=.+..                            +....++.
T Consensus        80 -T~l~~aL~~a~~~l~--~~~~---~r~~~~~~villTDG~~~~----------------------------~~~~~~~~  125 (163)
T cd01476          80 -TATGAAIEVALQQLD--PSEG---RREGIPKVVVVLTDGRSHD----------------------------DPEKQARI  125 (163)
T ss_pred             -ccHHHHHHHHHHHhc--cccC---CCCCCCeEEEEECCCCCCC----------------------------chHHHHHH
Confidence             478999999998774  1111   1223457788887632211                            23345666


Q ss_pred             Hhh-cCceEEEeCCC
Q 003455          160 FVQ-CSVSLSVICPK  173 (818)
Q Consensus       160 ~~~-~~I~lSiIsPr  173 (818)
                      +.+ .+|.+-.|.-.
T Consensus       126 l~~~~~v~v~~vg~g  140 (163)
T cd01476         126 LRAVPNIETFAVGTG  140 (163)
T ss_pred             HhhcCCCEEEEEECC
Confidence            777 77877777653

Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest any immunological functions for the invertebrate integrins. The members of this sub-group have the conserved MIDAS motif that is charateristic of this domain suggesting the involvement of the integrins in the recognition and binding of multi-ligands.

>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell

Probab=96.46  E-value=0.036  Score=55.32  Aligned_cols=124  Identities=15%  Similarity=0.174  Sum_probs=80.2

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceee-ccCCCCHHHHHHHhccc---cCCCCCCCh
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQR-SGWTKDVDIFLHWLSTI---PFAGGGFND   80 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~-~g~T~~~~~fl~wL~~i---~f~GGG~~~   80 (818)
                      |+..++++..+++.|.-.        .+.+.++||+|.+..-   ..+.. ..++.+...++.++++|   .+.|||   
T Consensus        19 ~~~~k~~~~~~~~~~~~~--------~~~~~vglv~Fs~~~~---~~~~l~~~~~~~~~~~~~~i~~l~~~~~~~G~---   84 (186)
T cd01471          19 VTHVVPFLHTFVQNLNIS--------PDEINLYLVTFSTNAK---ELIRLSSPNSTNKDLALNAIRALLSLYYPNGS---   84 (186)
T ss_pred             HHHHHHHHHHHHHhcccC--------CCceEEEEEEecCCce---EEEECCCccccchHHHHHHHHHHHhCcCCCCC---
Confidence            677788888888888532        1358999999986431   11111 12344666755555554   455554   


Q ss_pred             hhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHH
Q 003455           81 AAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSF  160 (818)
Q Consensus        81 ~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~  160 (818)
                      ..+++||..|...+...     +..+.+..|++||++.-.|-..+                          .+...|+.+
T Consensus        85 T~l~~aL~~a~~~l~~~-----~~~r~~~~~~villTDG~~~~~~--------------------------~~~~~a~~l  133 (186)
T cd01471          85 TNTTSALLVVEKHLFDT-----RGNRENAPQLVIIMTDGIPDSKF--------------------------RTLKEARKL  133 (186)
T ss_pred             ccHHHHHHHHHHHhhcc-----CCCcccCceEEEEEccCCCCCCc--------------------------chhHHHHHH
Confidence            45899999999777411     12345678999999987653211                          223567888


Q ss_pred             hhcCceEEEeCCC
Q 003455          161 VQCSVSLSVICPK  173 (818)
Q Consensus       161 ~~~~I~lSiIsPr  173 (818)
                      .+.+|.+.+|.=.
T Consensus       134 ~~~gv~v~~igiG  146 (186)
T cd01471         134 RERGVIIAVLGVG  146 (186)
T ss_pred             HHCCCEEEEEEee
Confidence            8999999998653

In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.

>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology

Probab=96.10  E-value=0.072  Score=54.53  Aligned_cols=141  Identities=13%  Similarity=0.154  Sum_probs=92.7

Q ss_pred             hH-HHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccC--CCCCCChh
Q 003455            5 FY-AYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPF--AGGGFNDA   81 (818)
Q Consensus         5 ~~-~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f--~GGG~~~~   81 (818)
                      |+ ..++++..+++.|.-++        ..+.+|||+|.+.. +-.+..... -..+-.+++..+++|..  ..||.  .
T Consensus        18 f~~~~~~f~~~lv~~l~i~~--------~~~rvgvv~fs~~~-~~~~~~~~~-~~~~~~~l~~~i~~l~~~~~~~g~--T   85 (192)
T cd01473          18 WRKDVIPFTEKIINNLNISK--------DKVHVGILLFAEKN-RDVVPFSDE-ERYDKNELLKKINDLKNSYRSGGE--T   85 (192)
T ss_pred             HHHHHHHHHHHHHHhCccCC--------CccEEEEEEecCCc-eeEEecCcc-cccCHHHHHHHHHHHHhccCCCCc--C
Confidence            66 46789999999996543        36899999999866 222222111 11345678888888852  32332  3


Q ss_pred             hHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHh
Q 003455           82 AIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFV  161 (818)
Q Consensus        82 aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~  161 (818)
                      .+++||..|++.|.  ...   ..+.+..|..||++....+.--                        ..++.+.|+.+.
T Consensus        86 ~~~~AL~~a~~~~~--~~~---~~r~~~~kv~IllTDG~s~~~~------------------------~~~~~~~a~~lk  136 (192)
T cd01473          86 YIVEALKYGLKNYT--KHG---NRRKDAPKVTMLFTDGNDTSAS------------------------KKELQDISLLYK  136 (192)
T ss_pred             cHHHHHHHHHHHhc--cCC---CCcccCCeEEEEEecCCCCCcc------------------------hhhHHHHHHHHH
Confidence            58899999998763  111   1234568999999987665410                        025678899999


Q ss_pred             hcCceEEEeCCCcchHHHHHHHHhcC
Q 003455          162 QCSVSLSVICPKQLPKLTAIYNAAKR  187 (818)
Q Consensus       162 ~~~I~lSiIsPrklp~L~~lf~~a~~  187 (818)
                      +.||.+-+|-=.. .....|..-|+.
T Consensus       137 ~~gV~i~~vGiG~-~~~~el~~ia~~  161 (192)
T cd01473         137 EENVKLLVVGVGA-ASENKLKLLAGC  161 (192)
T ss_pred             HCCCEEEEEEecc-ccHHHHHHhcCC
Confidence            9999999987654 345666666644

CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.

>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax

Probab=95.66  E-value=0.18  Score=50.64  Aligned_cols=123  Identities=16%  Similarity=0.110  Sum_probs=76.0

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCC--CCCC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFA--GGGF   78 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~--GGG~   78 (818)
                      |+..|....+++..+++.|..          ..+++|||+|.+..      -..+.||.+...+.+.|+.|...  ||| 
T Consensus        17 m~~~~~~~~~~~~~l~~~~~~----------~~~rvglv~Fs~~~------~~~~~l~~~~~~~~~~l~~l~~~~~~g~-   79 (185)
T cd01474          17 VAANWIEIYDFVEQLVDRFNS----------PGLRFSFITFSTRA------TKILPLTDDSSAIIKGLEVLKKVTPSGQ-   79 (185)
T ss_pred             hhhhHHHHHHHHHHHHHHcCC----------CCcEEEEEEecCCc------eEEEeccccHHHHHHHHHHHhccCCCCC-
Confidence            444555555788888888842          23899999998762      22466777776666665544432  333 


Q ss_pred             ChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHH
Q 003455           79 NDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAK  158 (818)
Q Consensus        79 ~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~  158 (818)
                        .++++||..|+..+.. ....   .+.. .|++|||+.-.+..-..                        .+....|+
T Consensus        80 --T~~~~aL~~a~~~l~~-~~~~---~r~~-~~~villTDG~~~~~~~------------------------~~~~~~a~  128 (185)
T cd01474          80 --TYIHEGLENANEQIFN-RNGG---GRET-VSVIIALTDGQLLLNGH------------------------KYPEHEAK  128 (185)
T ss_pred             --CcHHHHHHHHHHHHHh-hccC---CCCC-CeEEEEEcCCCcCCCCC------------------------cchHHHHH
Confidence              6789999999965421 1111   1112 28899998765532110                        13445677


Q ss_pred             HHhhcCceEEEeC
Q 003455          159 SFVQCSVSLSVIC  171 (818)
Q Consensus       159 ~~~~~~I~lSiIs  171 (818)
                      .+.+.+|.+-.|.
T Consensus       129 ~l~~~gv~i~~vg  141 (185)
T cd01474         129 LSRKLGAIVYCVG  141 (185)
T ss_pred             HHHHcCCEEEEEe
Confidence            7888889877765

ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.

>cd01458 vWA_ku Ku70/Ku80 N-terminal domain

Probab=95.61  E-value=0.13  Score=53.21  Aligned_cols=112  Identities=17%  Similarity=0.163  Sum_probs=76.2

Q ss_pred             cceEEEEEEccCC-----CCCcCceeeccCCCCHHHHHHHhccccCC------CCC-CChhhHHHHHHHHHhhhccCCCC
Q 003455           33 NVELSLVTFNTHG-----SYCACLVQRSGWTKDVDIFLHWLSTIPFA------GGG-FNDAAIAEGLSEALMMFSVAPNG  100 (818)
Q Consensus        33 ~~~yaLVvf~~~~-----~~~~~~v~~~g~T~~~~~fl~wL~~i~f~------GGG-~~~~aiaEGLa~AL~~~~~~~~~  100 (818)
                      .-+.|||+|++..     .|...+|-+---|.|...+..+++-++-.      +.| .....+.++|..|+.+|..   .
T Consensus        46 ~D~vGlilf~t~~~~~~~~~~~i~v~~~l~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~aL~~a~~~~~~---~  122 (218)
T cd01458          46 KDLVGVVFYGTEESKNPVGYENIYVLLDLDTPGAERVEDLKELIEPGGLSFAGQVGDSGQVSLSDALWVCLDLFSK---G  122 (218)
T ss_pred             CCeEEEEEEcccCCCCcCCCCceEEeecCCCCCHHHHHHHHHHhhcchhhhcccCCCCCCccHHHHHHHHHHHHHh---c
Confidence            4788999999975     35444444434477888887777765432      112 3458999999999999961   1


Q ss_pred             CCCCCCCCCccEEEEeecC-CCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCC
Q 003455          101 SQNQQNVDGQRHCILVAAS-NPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICP  172 (818)
Q Consensus       101 ~~~~~~~~~qkhCILi~nS-pP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsP  172 (818)
                          ......|+.||+++- .|+.--         .          ..  ..+++.+|+.+.+++|.|.+|.-
T Consensus       123 ----~~~~~~k~IvL~TDg~~p~~~~---------~----------~~--~~~~~~~a~~l~~~gI~i~~i~i  170 (218)
T cd01458         123 ----KKKKSHKRIFLFTNNDDPHGGD---------S----------IK--DSQAAVKAEDLKDKGIELELFPL  170 (218)
T ss_pred             ----cccccccEEEEECCCCCCCCCC---------H----------HH--HHHHHHHHHHHHhCCcEEEEEec
Confidence                123457888999885 455400         0          00  12567899999999999999975

The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.

>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=95.58  E-value=0.37  Score=44.65  Aligned_cols=123  Identities=18%  Similarity=0.188  Sum_probs=81.7

Q ss_pred             chhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC--CHHHHHHHhccccC-CCCCC
Q 003455            2 CIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDIFLHWLSTIPF-AGGGF   78 (818)
Q Consensus         2 ~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~--~~~~fl~wL~~i~f-~GGG~   78 (818)
                      ..||+..++++.-+++.+...        .....++||.|.+.      ......++.  +.+.+..-++.+.. .+|+ 
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~--------~~~~~i~v~~f~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   79 (161)
T cd00198          15 GEKLDKAKEALKALVSSLSAS--------PPGDRVGLVTFGSN------ARVVLPLTTDTDKADLLEAIDALKKGLGGG-   79 (161)
T ss_pred             cchHHHHHHHHHHHHHhcccC--------CCCcEEEEEEecCc------cceeecccccCCHHHHHHHHHhcccCCCCC-
Confidence            457788888888888888532        23579999999983      222344444  77888888888877 3333 


Q ss_pred             ChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHH
Q 003455           79 NDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAK  158 (818)
Q Consensus        79 ~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~  158 (818)
                        ..+.++|..|+..+....       .....|..|||.+-.+..-.                         .+.+.+.+
T Consensus        80 --t~~~~al~~~~~~~~~~~-------~~~~~~~lvvitDg~~~~~~-------------------------~~~~~~~~  125 (161)
T cd00198          80 --TNIGAALRLALELLKSAK-------RPNARRVIILLTDGEPNDGP-------------------------ELLAEAAR  125 (161)
T ss_pred             --ccHHHHHHHHHHHhcccC-------CCCCceEEEEEeCCCCCCCc-------------------------chhHHHHH
Confidence              445688888888774110       23456667777765443311                         25567788


Q ss_pred             HHhhcCceEEEeCCC
Q 003455          159 SFVQCSVSLSVICPK  173 (818)
Q Consensus       159 ~~~~~~I~lSiIsPr  173 (818)
                      .+.+.+|.+.+|.=.
T Consensus       126 ~~~~~~v~v~~v~~g  140 (161)
T cd00198         126 ELRKLGITVYTIGIG  140 (161)
T ss_pred             HHHHcCCEEEEEEcC
Confidence            888889999888554

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.

>cd01477 vWA_F09G8-8_type VWA F09G8

Probab=95.42  E-value=0.14  Score=52.73  Aligned_cols=131  Identities=11%  Similarity=0.153  Sum_probs=82.7

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhcc-c-cCCCCCCChhh
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLST-I-PFAGGGFNDAA   82 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~-i-~f~GGG~~~~a   82 (818)
                      |+..|+.|..++..|..+..  ....-..+..|||+|.+. .+.++.++   -..+..+|+..|+. + ....||  ...
T Consensus        37 f~~~k~fi~~~~~~~~~~~~--~~~~~~~~rVGlV~fs~~-a~~~~~L~---d~~~~~~~~~ai~~~~~~~~~~g--gT~  108 (193)
T cd01477          37 LWQVRATISSLFGSSSQIGT--DYDDPRSTRVGLVTYNSN-ATVVADLN---DLQSFDDLYSQIQGSLTDVSSTN--ASY  108 (193)
T ss_pred             HHHHHHHHHHHHhhcccccc--ccCCCCCcEEEEEEccCc-eEEEEecc---cccCHHHHHHHHHHHhhccccCC--cch
Confidence            56667778787887753110  000123589999999884 34444443   23477888888885 2 232223  246


Q ss_pred             HHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhh
Q 003455           83 IAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQ  162 (818)
Q Consensus        83 iaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~  162 (818)
                      +..||..|+++|...    .+..+....|+.|||+.-.-                        .... .+.+.+|+.+.+
T Consensus       109 ig~aL~~A~~~l~~~----~~~~R~~v~kvvIllTDg~~------------------------~~~~-~~~~~~a~~l~~  159 (193)
T cd01477         109 LDTGLQAAEQMLAAG----KRTSRENYKKVVIVFASDYN------------------------DEGS-NDPRPIAARLKS  159 (193)
T ss_pred             HHHHHHHHHHHHHhh----hccccCCCCeEEEEEecCcc------------------------CCCC-CCHHHHHHHHHH
Confidence            889999999988521    12234568999999985310                        0011 256788999999


Q ss_pred             cCceEEEeCC
Q 003455          163 CSVSLSVICP  172 (818)
Q Consensus       163 ~~I~lSiIsP  172 (818)
                      .||.+..|.=
T Consensus       160 ~GI~i~tVGi  169 (193)
T cd01477         160 TGIAIITVAF  169 (193)
T ss_pred             CCCEEEEEEe
Confidence            9999999854

8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo

>PF00092 VWA: von Willebrand factor type A domain; InterPro: IPR002035 The von Willebrand factor is a large multimeric glycoprotein found in blood plasma

Probab=95.34  E-value=0.25  Score=47.73  Aligned_cols=135  Identities=16%  Similarity=0.192  Sum_probs=90.3

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHh-ccccCCCCCCChhhH
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWL-STIPFAGGGFNDAAI   83 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL-~~i~f~GGG~~~~ai   83 (818)
                      |+..+++|..+++.|..        ....+.++||.|.+..-    .+-.+.-..+..+++..+ +.+.+.||+-.   +
T Consensus        17 ~~~~~~~v~~~i~~~~~--------~~~~~rv~iv~f~~~~~----~~~~~~~~~~~~~~~~~i~~~~~~~~g~t~---~   81 (178)
T PF00092_consen   17 FEKAKQFVKSIISRLSI--------SNNGTRVGIVTFSDSAR----VLFSLTDYQSKNDLLNAINDSIPSSGGGTN---L   81 (178)
T ss_dssp             HHHHHHHHHHHHHHSTB--------STTSEEEEEEEESSSEE----EEEETTSHSSHHHHHHHHHTTGGCCBSSB----H
T ss_pred             HHHHHHHHHHHHHhhhc--------cccccccceeeeecccc----cccccccccccccccccccccccccchhhh---H
Confidence            67788999999998842        23468999999998765    222333345688999998 89988887643   8


Q ss_pred             HHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhc
Q 003455           84 AEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC  163 (818)
Q Consensus        84 aEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~  163 (818)
                      ++||-+|+..|...    -...+....|..|||+...+..-+.                         ..+..+++..+.
T Consensus        82 ~~aL~~a~~~l~~~----~~~~r~~~~~~iiliTDG~~~~~~~-------------------------~~~~~~~~~~~~  132 (178)
T PF00092_consen   82 GAALKFAREQLFSS----NNGGRPNSPKVIILITDGNSNDSDS-------------------------PSEEAANLKKSN  132 (178)
T ss_dssp             HHHHHHHHHHTTSG----GGTTGTTSEEEEEEEESSSSSSHSG-------------------------HHHHHHHHHHHC
T ss_pred             HHHHhhhhhccccc----ccccccccccceEEEEeecccCCcc-------------------------hHHHHHHHHHhc
Confidence            99999999887511    1112347788889999988766331                         112223333335


Q ss_pred             CceEEEeCC--CcchHHHHHHH
Q 003455          164 SVSLSVICP--KQLPKLTAIYN  183 (818)
Q Consensus       164 ~I~lSiIsP--rklp~L~~lf~  183 (818)
                      +|.+=.|..  .....|++|..
T Consensus       133 ~i~~~~ig~~~~~~~~l~~la~  154 (178)
T PF00092_consen  133 GIKVIAIGIDNADNEELRELAS  154 (178)
T ss_dssp             TEEEEEEEESCCHHHHHHHHSH
T ss_pred             CcEEEEEecCcCCHHHHHHHhC
Confidence            788877777  23555776664

Mutant forms are involved in the aetiology of bleeding disorders []. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. Fold recognition algorithms were used to score sequence compatibility with a library of known structures: the vWF domain fold was predicted to be a doubly-wound, open, twisted beta-sheet flanked by alpha-helices []. 3D structures have been determined for the I-domains of integrins CD11b (with bound magnesium) [] and CD11a (with bound manganese) []. The domain adopts a classic alpha/beta Rossmann fold and contains an unusual metal ion coordination site at its surface. It has been suggested that this site represents a general metal ion-dependent adhesion site (MIDAS) for binding protein ligands []. The residues constituting the MIDAS motif in the CD11b and CD11a I-domains are completely conserved, but the manner in which the metal ion is coordinated differs slightly [].; GO: 0005515 protein binding; PDB: 2XGG_B 3ZQK_B 3GXB_A 3PPV_A 3PPX_A 3PPW_A 3PPY_A 1CQP_B 3TCX_B 2ICA_A ....

>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]

Probab=95.27  E-value=0.0099  Score=74.46  Aligned_cols=11  Identities=18%  Similarity=0.229  Sum_probs=4.8

Q ss_pred             CCeEEEeeccc
Q 003455          202 PHFLVLISENF  212 (818)
Q Consensus       202 p~hlVLl~g~~  212 (818)
                      ..|++-|+=.|
T Consensus      1730 ~k~~aplsW~w 1740 (2220)
T KOG3598|consen 1730 TKHLAPLSWKW 1740 (2220)
T ss_pred             CCCCCCcccee
Confidence            34444444333

>cd01456 vWA_ywmD_type VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=94.57  E-value=0.63  Score=47.54  Aligned_cols=92  Identities=16%  Similarity=0.179  Sum_probs=58.0

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCC----CCc-----Ccee-eccCC-CCHHHHHHHhcccc
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGS----YCA-----CLVQ-RSGWT-KDVDIFLHWLSTIP   72 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~----~~~-----~~v~-~~g~T-~~~~~fl~wL~~i~   72 (818)
                      .|+.+|+=+.-+++.+.           ....++||+|.+...    |-.     +... ..+++ .+...+..+|++|.
T Consensus        43 rl~~ak~a~~~~l~~l~-----------~~~~v~lv~F~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~~~i~~i~  111 (206)
T cd01456          43 RLDNAKAALDETANALP-----------DGTRLGLWTFSGDGDNPLDVRVLVPKGCLTAPVNGFPSAQRSALDAALNSLQ  111 (206)
T ss_pred             HHHHHHHHHHHHHHhCC-----------CCceEEEEEecCCCCCCccccccccccccccccCCCCcccHHHHHHHHHhhc
Confidence            44555554555555442           246899999998421    111     1111 23433 58899999999999


Q ss_pred             CCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCC
Q 003455           73 FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASN  120 (818)
Q Consensus        73 f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSp  120 (818)
                      +.+||   ..|.+||..|+.++.           ....+++|||+.--
T Consensus       112 ~~~G~---T~l~~aL~~a~~~l~-----------~~~~~~iillTDG~  145 (206)
T cd01456         112 TPTGW---TPLAAALAEAAAYVD-----------PGRVNVVVLITDGE  145 (206)
T ss_pred             CCCCc---ChHHHHHHHHHHHhC-----------CCCcceEEEEcCCC
Confidence            55554   578899999999883           11237888887653

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if

>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex

Probab=94.57  E-value=0.4  Score=49.85  Aligned_cols=130  Identities=15%  Similarity=0.135  Sum_probs=92.1

Q ss_pred             hhhHHHH-HhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHH
Q 003455           10 KLSLYFH-RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLS   88 (818)
Q Consensus        10 ~YI~p~i-e~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa   88 (818)
                      +|+.-.| |||..+|+         .+.|+|+.++.-+     -..+.++.++.+..+.|+++... ++.++..+-.||.
T Consensus        23 ~~l~~Fv~eff~qNPi---------Sqlgii~~~~~~a-----~~ls~lsgn~~~h~~~L~~~~~~-~~~G~~SLqN~Le   87 (193)
T PF04056_consen   23 KALEEFVREFFDQNPI---------SQLGIIVMRDGRA-----ERLSELSGNPQEHIEALKKLRKL-EPSGEPSLQNGLE   87 (193)
T ss_pred             HHHHHHHHHHHhcCCh---------hheeeeeeeccee-----EEeeecCCCHHHHHHHHHHhccC-CCCCChhHHHHHH
Confidence            4444433 56666666         8899999886432     23467888999999999888743 2345567888899


Q ss_pred             HHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEE
Q 003455           89 EALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLS  168 (818)
Q Consensus        89 ~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lS  168 (818)
                      .|...+.-.        ..-..|.+|+|..|-=.-                         ...|....++.|.+.+|.+|
T Consensus        88 ~A~~~L~~~--------p~~~srEIlvi~gSl~t~-------------------------Dp~di~~ti~~l~~~~Irvs  134 (193)
T PF04056_consen   88 MARSSLKHM--------PSHGSREILVIFGSLTTC-------------------------DPGDIHETIESLKKENIRVS  134 (193)
T ss_pred             HHHHHHhhC--------ccccceEEEEEEeecccC-------------------------CchhHHHHHHHHHHcCCEEE
Confidence            999877411        123567777776553211                         12478899999999999999


Q ss_pred             EeCC-CcchHHHHHHHHhcC
Q 003455          169 VICP-KQLPKLTAIYNAAKR  187 (818)
Q Consensus       169 iIsP-rklp~L~~lf~~a~~  187 (818)
                      ||+= -.+-.+|+|.++.+|
T Consensus       135 vI~laaEv~I~k~i~~~T~G  154 (193)
T PF04056_consen  135 VISLAAEVYICKKICKETGG  154 (193)
T ss_pred             EEEEhHHHHHHHHHHHhhCC
Confidence            9976 467789999998876

This domain is often found associated with the C2H2 type Zn-finger (IPR007087 from INTERPRO).; GO: 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent

>smart00327 VWA von Willebrand factor (vWF) type A domain

Probab=94.35  E-value=1.4  Score=42.21  Aligned_cols=137  Identities=18%  Similarity=0.211  Sum_probs=88.1

Q ss_pred             chhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeecc--CCCCHHHHHHHhccccC-CCCCC
Q 003455            2 CIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSG--WTKDVDIFLHWLSTIPF-AGGGF   78 (818)
Q Consensus         2 ~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g--~T~~~~~fl~wL~~i~f-~GGG~   78 (818)
                      ..+|+..++++.-+++.+...        ....+++||.|.+...      ....  .+++...+...++++.+ .+|+ 
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~--------~~~~~i~ii~f~~~~~------~~~~~~~~~~~~~~~~~i~~~~~~~~~~-   80 (177)
T smart00327       16 PNRFEKAKEFVLKLVEQLDIG--------PDGDRVGLVTFSDDAT------VLFPLNDSRSKDALLEALASLSYKLGGG-   80 (177)
T ss_pred             hHHHHHHHHHHHHHHHhcCCC--------CCCcEEEEEEeCCCce------EEEcccccCCHHHHHHHHHhcCCCCCCC-
Confidence            456777778888888877431        1358999999998321      1233  48999999999999998 3333 


Q ss_pred             ChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHH
Q 003455           79 NDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAK  158 (818)
Q Consensus        79 ~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~  158 (818)
                        ..+.++|..|+..+.  .. . ...+....+..|||..-.+...                          .+.+.+++
T Consensus        81 --~~~~~al~~~~~~~~--~~-~-~~~~~~~~~~iviitDg~~~~~--------------------------~~~~~~~~  128 (177)
T smart00327       81 --TNLGAALQYALENLF--SK-S-AGSRRGAPKVLILITDGESNDG--------------------------GDLLKAAK  128 (177)
T ss_pred             --chHHHHHHHHHHHhc--Cc-C-CCCCCCCCeEEEEEcCCCCCCC--------------------------ccHHHHHH
Confidence              456677777777663  01 0 0111222555666666555542                          36678888


Q ss_pred             HHhhcCceEEEeCCCc---chHHHHHHHHh
Q 003455          159 SFVQCSVSLSVICPKQ---LPKLTAIYNAA  185 (818)
Q Consensus       159 ~~~~~~I~lSiIsPrk---lp~L~~lf~~a  185 (818)
                      .+.+++|.+-+|.--.   ...|+.|....
T Consensus       129 ~~~~~~i~i~~i~~~~~~~~~~l~~~~~~~  158 (177)
T smart00327      129 ELKRSGVKVFVVGVGNDVDEEELKKLASAP  158 (177)
T ss_pred             HHHHCCCEEEEEEccCccCHHHHHHHhCCC
Confidence            8999999999887753   33355544433

VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.

>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=94.00  E-value=0.99  Score=44.48  Aligned_cols=96  Identities=22%  Similarity=0.253  Sum_probs=64.3

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccC--CCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCc
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPF--AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQ  110 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f--~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~q  110 (818)
                      ...++||+|.+..      .....||.+...+...|+.|..  .+|+   ..+.+||..|+.++...         ....
T Consensus        42 ~~~v~lv~f~~~~------~~~~~~~~~~~~~~~~l~~l~~~~~~g~---T~l~~al~~a~~~l~~~---------~~~~  103 (180)
T cd01467          42 NDRIGLVVFAGAA------FTQAPLTLDRESLKELLEDIKIGLAGQG---TAIGDAIGLAIKRLKNS---------EAKE  103 (180)
T ss_pred             CCeEEEEEEcCCe------eeccCCCccHHHHHHHHHHhhhcccCCC---CcHHHHHHHHHHHHHhc---------CCCC
Confidence            4689999997642      2245788888888889998873  2333   45788999999888511         1223


Q ss_pred             cEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeC
Q 003455          111 RHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVIC  171 (818)
Q Consensus       111 khCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIs  171 (818)
                      ++.|||+.-.+..-+                         .+.+++++.+.+.+|.+.+|.
T Consensus       104 ~~iiliTDG~~~~g~-------------------------~~~~~~~~~~~~~gi~i~~i~  139 (180)
T cd01467         104 RVIVLLTDGENNAGE-------------------------IDPATAAELAKNKGVRIYTIG  139 (180)
T ss_pred             CEEEEEeCCCCCCCC-------------------------CCHHHHHHHHHHCCCEEEEEE
Confidence            677777766543211                         234556777778899888775

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if

>PF11235 Med25_SD1: Mediator complex subunit 25 synapsin 1; InterPro: IPR021397 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells

Probab=92.72  E-value=0.15  Score=50.71  Aligned_cols=78  Identities=19%  Similarity=0.220  Sum_probs=56.8

Q ss_pred             CCCCCCCCCCCcccccCCC-CccCCCCCCCCCCCCCC-CCCC----------cccCCccccceeeccccccccCCCCCCC
Q 003455          223 GVANLAPNQNPVKMDIAPV-TSVTGPAPTSIPSVNGI-NRPP----------ISVGNVPTATVKVEPSTVTSMVNGPTFP  290 (818)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~----------~~~~~~~~~~~k~e~~~~~~m~~~p~f~  290 (818)
                      ..+.+++++.++....+.+ +.+++++++.+|.|..+ |..+          ++..+||+|+.       .+...|+||+
T Consensus         8 ~pg~lq~KQ~Vp~pP~p~~~~~l~aaP~q~LPpVs~pq~qvp~n~tLsaAq~AAq~AVEAAkn-------QKaglg~RF~   80 (168)
T PF11235_consen    8 VPGPLQPKQPVPLPPAPVSPAQLSAAPQQPLPPVSPPQYQVPGNSTLSAAQVAAQNAVEAAKN-------QKAGLGPRFS   80 (168)
T ss_pred             CCCCCCCCCcccCCCCCCCccccccCCcCCCCCCCccccccCccccchHHHHHHHHHHHHHHh-------ccccCCCCCC
Confidence            5688999999888887666 77788999999999666 4433          45677775554       4456789999


Q ss_pred             CCCCCCCCCCCCCCCcc
Q 003455          291 HIPSVPRPASQGVPSLQ  307 (818)
Q Consensus       291 ~~~p~~~~~~~~~~~~q  307 (818)
                      .|+|+++..--|-|--|
T Consensus        81 pi~p~~~a~~vgpPFsQ   97 (168)
T PF11235_consen   81 PINPLQQAPGVGPPFSQ   97 (168)
T ss_pred             CCCcccCCCCCCCCCcC
Confidence            99998886444444333

Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, this SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This The function of the SD domains is unclear [].

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=92.60  E-value=1.7  Score=52.28  Aligned_cols=130  Identities=17%  Similarity=0.212  Sum_probs=82.4

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccE
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRH  112 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkh  112 (818)
                      .-+++||+|++....     ....||++...+..+|+.|.. |||   ..+++||..|+.++..  .     ......++
T Consensus       443 ~D~v~Li~F~~~~a~-----~~lp~t~~~~~~~~~L~~l~~-gGg---TpL~~gL~~A~~~~~~--~-----~~~~~~~~  506 (589)
T TIGR02031       443 RDQVSLIAFRGTAAE-----VLLPPSRSVEQAKRRLDVLPG-GGG---TPLAAGLAAAFQTALQ--A-----RSSGGTPT  506 (589)
T ss_pred             CCEEEEEEECCCCce-----EECCCCCCHHHHHHHHhcCCC-CCC---CcHHHHHHHHHHHHHH--h-----cccCCceE
Confidence            357999999866521     235789999999999999975 444   5678888888887741  0     11244578


Q ss_pred             EEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCC----cchHHHHHHHHhcCC
Q 003455          113 CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRN  188 (818)
Q Consensus       113 CILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPr----klp~L~~lf~~a~~~  188 (818)
                      .|||+.=-+-- +.-      -+++ ++  ....+....++..+|+.+.+.+|.++||.-.    +.-.++.|-++.+++
T Consensus       507 ivllTDG~~nv-~~~------~~~~-~~--~~~~~~~~~~~~~~a~~~~~~gi~~~vid~~~~~~~~~~~~~lA~~~~g~  576 (589)
T TIGR02031       507 IVLITDGRGNI-PLD------GDPE-SI--KADREQAAEEALALARKIREAGMPALVIDTAMRFVSTGFAQKLARKMGAH  576 (589)
T ss_pred             EEEECCCCCCC-CCC------cccc-cc--cccchhHHHHHHHHHHHHHhcCCeEEEEeCCCCCccchHHHHHHHhcCCc
Confidence            88888653311 000      0000 00  0001111235678899999999999999773    344588888877665

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto)

Probab=92.55  E-value=1.8  Score=43.36  Aligned_cols=120  Identities=18%  Similarity=0.226  Sum_probs=78.3

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccE
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRH  112 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkh  112 (818)
                      ..+++||+|.+...+     ....+|.+...+..+|+.+.. ||+   ..+.+||..|+..+.  ...    ......+.
T Consensus        37 ~d~v~lv~F~~~~~~-----~~~~~t~~~~~~~~~l~~l~~-~G~---T~l~~aL~~a~~~l~--~~~----~~~~~~~~  101 (178)
T cd01451          37 RDKVALIAFRGTEAE-----VLLPPTRSVELAKRRLARLPT-GGG---TPLAAGLLAAYELAA--EQA----RDPGQRPL  101 (178)
T ss_pred             CCEEEEEEECCCCce-----EEeCCCCCHHHHHHHHHhCCC-CCC---CcHHHHHHHHHHHHH--HHh----cCCCCceE
Confidence            468999999865211     234678899999999999976 333   467788888887661  000    01123578


Q ss_pred             EEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCH-HHHHHHHhhcCceEEEeCCCc----chHHHHHHHHhcC
Q 003455          113 CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDA-ETVAKSFVQCSVSLSVICPKQ----LPKLTAIYNAAKR  187 (818)
Q Consensus       113 CILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~-e~la~~~~~~~I~lSiIsPrk----lp~L~~lf~~a~~  187 (818)
                      +|||+.-.+..-..+                     . ..+ .++++.+.+.+|.+.+|.-..    -..|+.|=++.++
T Consensus       102 ivliTDG~~~~g~~~---------------------~-~~~~~~~~~~l~~~gi~v~~I~~~~~~~~~~~l~~iA~~tgG  159 (178)
T cd01451         102 IVVITDGRANVGPDP---------------------T-ADRALAAARKLRARGISALVIDTEGRPVRRGLAKDLARALGG  159 (178)
T ss_pred             EEEECCCCCCCCCCc---------------------h-hHHHHHHHHHHHhcCCcEEEEeCCCCccCccHHHHHHHHcCC
Confidence            888886543321100                     0 112 677889999999999998653    3458888888776


Q ss_pred             CC
Q 003455          188 NP  189 (818)
Q Consensus       188 ~~  189 (818)
                      .-
T Consensus       160 ~~  161 (178)
T cd01451         160 QY  161 (178)
T ss_pred             eE
Confidence            53

In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding site. The BchD domain contains a AAA domain at its N-terminus and a VWA domain at its C-terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions.

>cd01463 vWA_VGCC_like VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta

Probab=92.43  E-value=0.59  Score=47.16  Aligned_cols=81  Identities=14%  Similarity=0.137  Sum_probs=50.2

Q ss_pred             cceEEEEEEccCCCCCcCceeec------cCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCC
Q 003455           33 NVELSLVTFNTHGSYCACLVQRS------GWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQN  106 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~------g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~  106 (818)
                      ..+++||.|.+..-   ..+.++      .++.+.+.++.||+.|+..||    ..+.+||.+|+..+............
T Consensus        48 ~d~v~lv~F~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~G~----T~~~~al~~a~~~l~~~~~~~~~~~~  120 (190)
T cd01463          48 NDFFNIITFSNEVN---PVVPCFNDTLVQATTSNKKVLKEALDMLEAKGI----ANYTKALEFAFSLLLKNLQSNHSGSR  120 (190)
T ss_pred             CCEEEEEEeCCCee---EEeeecccceEecCHHHHHHHHHHHhhCCCCCc----chHHHHHHHHHHHHHHhhhccccccc
Confidence            35899999998742   122111      234688999999999998543    45778888888766410001111122


Q ss_pred             CCCccEEEEeecCC
Q 003455          107 VDGQRHCILVAASN  120 (818)
Q Consensus       107 ~~~qkhCILi~nSp  120 (818)
                      ....+++|||+.=-
T Consensus       121 ~~~~~~iillTDG~  134 (190)
T cd01463         121 SQCNQAIMLITDGV  134 (190)
T ss_pred             CCceeEEEEEeCCC
Confidence            34567888888654

The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex.

>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation

Probab=92.37  E-value=1.4  Score=44.62  Aligned_cols=107  Identities=10%  Similarity=0.120  Sum_probs=65.7

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCC-CChhhH
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGG-FNDAAI   83 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG-~~~~ai   83 (818)
                      |+..|+-|.-+++.+...+        ...+++||+|.+..-. .+.. +..++.+...++.+|+++.+.+++ .....+
T Consensus        18 ~~~~k~~~~~l~~~l~~~~--------~~~~v~li~Fs~~~~~-~~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~ggT~~   87 (198)
T cd01470          18 FDEAKNAIKTLIEKISSYE--------VSPRYEIISYASDPKE-IVSI-RDFNSNDADDVIKRLEDFNYDDHGDKTGTNT   87 (198)
T ss_pred             HHHHHHHHHHHHHHccccC--------CCceEEEEEecCCceE-EEec-ccCCCCCHHHHHHHHHhCCcccccCccchhH
Confidence            5666667777777663211        1468999999887421 1111 134566889999999999886654 334678


Q ss_pred             HHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCC
Q 003455           84 AEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  122 (818)
Q Consensus        84 aEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~  122 (818)
                      .+||..|+..+..... ..........+..|||+.--|.
T Consensus        88 ~~Al~~~~~~l~~~~~-~~~~~~~~~~~~iillTDG~~~  125 (198)
T cd01470          88 AAALKKVYERMALEKV-RNKEAFNETRHVIILFTDGKSN  125 (198)
T ss_pred             HHHHHHHHHHHHHHHh-cCccchhhcceEEEEEcCCCcC
Confidence            9999998876631110 0011123456677888876544

They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation of an active protease that cleaves and activates complement C3. Complement C2 is in the classical pathway and complement B is in the alternative pathway. The interaction of C2 with C4 and of factor B with C3b are both dependent on Mg2+ binding sites within the VWA domains and the VWA domain of factor B has been shown to mediate the binding of C3. This is consistent with the common inferred function of VWA domains as magnesium-dependent protein interaction domains.

>PRK13685 hypothetical protein; Provisional

Probab=92.31  E-value=2.2  Score=47.20  Aligned_cols=108  Identities=16%  Similarity=0.187  Sum_probs=66.5

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccE
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRH  112 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkh  112 (818)
                      ..+.|||+|.+..-      ....+|.|-+.+...|++++..||    .++.+||..|++.+... .+..........|+
T Consensus       128 ~d~vglv~Fa~~a~------~~~p~t~d~~~l~~~l~~l~~~~~----T~~g~al~~A~~~l~~~-~~~~~~~~~~~~~~  196 (326)
T PRK13685        128 GINLGLIAFAGTAT------VLVSPTTNREATKNAIDKLQLADR----TATGEAIFTALQAIATV-GAVIGGGDTPPPAR  196 (326)
T ss_pred             CCeEEEEEEcCcee------ecCCCCCCHHHHHHHHHhCCCCCC----cchHHHHHHHHHHHHhh-hcccccccCCCCCE
Confidence            35789999997632      224689999999999999997543    34567888888776410 00000011223467


Q ss_pred             EEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeC
Q 003455          113 CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVIC  171 (818)
Q Consensus       113 CILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIs  171 (818)
                      .||++.-....-..+                    ....+..++++.+.+.+|.+++|.
T Consensus       197 IILlTDG~~~~~~~~--------------------~~~~~~~~aa~~a~~~gi~i~~Ig  235 (326)
T PRK13685        197 IVLMSDGKETVPTNP--------------------DNPRGAYTAARTAKDQGVPISTIS  235 (326)
T ss_pred             EEEEcCCCCCCCCCC--------------------CCcccHHHHHHHHHHcCCeEEEEE
Confidence            788776432210000                    011234567888889999999985

>PF04811 Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: IPR006896 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []

Probab=92.31  E-value=1.1  Score=47.33  Aligned_cols=166  Identities=13%  Similarity=0.121  Sum_probs=85.5

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCC--------------------------CCCcCceeeccC
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHG--------------------------SYCACLVQRSGW   57 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~--------------------------~~~~~~v~~~g~   57 (818)
                      +++.+++-|..+|+++..         ..++..|||+|.+.=                          +..+.+|.....
T Consensus        21 ~~~~~~~sl~~~l~~l~~---------~~~~~vgiitfd~~V~~y~l~~~~~~~~~~v~~dl~~~~~p~~~~llv~~~e~   91 (243)
T PF04811_consen   21 LLQSLIESLKSALDSLPG---------DERTRVGIITFDSSVHFYNLSSSLSQPQMIVVSDLDDPFIPLPDGLLVPLSEC   91 (243)
T ss_dssp             HHHHHHHHHHHHGCTSST---------STT-EEEEEEESSSEEEEETTTTSSSTEEEEEHHTTSHHSSTSSSSSEETTTC
T ss_pred             HHHHHHHHHHHHHHhccC---------CCCcEEEEEEeCCEEEEEECCCCcCCCcccchHHHhhcccCCcccEEEEhHHh
Confidence            445556666666666531         346899999997521                          112223333333


Q ss_pred             CCCHHHHHHHhccccCCCCC-CChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccc-c
Q 003455           58 TKDVDIFLHWLSTIPFAGGG-FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQ-N  135 (818)
Q Consensus        58 T~~~~~fl~wL~~i~f~GGG-~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~-~  135 (818)
                      -.....++++|.++--...+ ....+++.+|..|+.++...          ..--+.|+.+.++|-.=|=.++..... +
T Consensus        92 ~~~i~~ll~~L~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~----------~~gGkI~~F~s~~pt~G~Gg~l~~~~~~~  161 (243)
T PF04811_consen   92 RDAIEELLESLPSIFPETAGKRPERCLGSALSAALSLLSSR----------NTGGKILVFTSGPPTYGPGGSLKKREDSS  161 (243)
T ss_dssp             HHHHHHHHHHHHHHSTT-TTB-----HHHHHHHHHHHHHHH----------TS-EEEEEEESS---SSSTTSS-SBTTSC
T ss_pred             HHHHHHHHHHhhhhcccccccCccccHHHHHHHHHHHHhcc----------ccCCEEEEEeccCCCCCCCceeccccccc
Confidence            33455666666663222223 45589999999999998511          122345555666775555122222211 1


Q ss_pred             ccccchhhhhhhccCCC--HHHHHHHHhhcCceEEEeC-CC---cchHHHHHHHHhcCCC
Q 003455          136 LDQNENNEAQAESRLSD--AETVAKSFVQCSVSLSVIC-PK---QLPKLTAIYNAAKRNP  189 (818)
Q Consensus       136 l~~~~~~~~~~~~~l~~--~e~la~~~~~~~I~lSiIs-Pr---klp~L~~lf~~a~~~~  189 (818)
                      +...+ .|...+..-++  .+.||..|.+.+|.+.+.+ +.   -++.|..|....+|+.
T Consensus       162 ~~~~~-~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~tl~~l~~~TGG~l  220 (243)
T PF04811_consen  162 HYDTE-KEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSDYVDLATLGPLARYTGGSL  220 (243)
T ss_dssp             CCCHC-TTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS--SHHHHTHHHHCTT-EE
T ss_pred             ccccc-cchhhhccccchHHHHHHHHHHhcCCEEEEEeecCCCCCcHhHHHHHHhCceeE
Confidence            11111 11122222223  7899999999999887654 33   3788888888887764

COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain, an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the Sec23/24 alpha/beta trunk domain, which is formed from a single, approximately 250-residue segment plugged into the beta-barrel between strands beta-1 and beta-19. The trunk has an alpha/beta fold with a vWA topology, and it forms the dimer interface, primarily involving strand beta-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_A 2NUP_A 3EG9_A 3EFO_A 3EGX_A 2NUT_A 1PD0_A 1PD1_A 1M2V_B 1PCX_A ....

>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases

Probab=91.64  E-value=2.7  Score=41.66  Aligned_cols=121  Identities=12%  Similarity=0.163  Sum_probs=74.1

Q ss_pred             cceEEEEEEccCC--CCCcCceeeccCCCCH-HHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCC
Q 003455           33 NVELSLVTFNTHG--SYCACLVQRSGWTKDV-DIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDG  109 (818)
Q Consensus        33 ~~~yaLVvf~~~~--~~~~~~v~~~g~T~~~-~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~  109 (818)
                      ...++||+|.+..  .+...++....|+.+. ..+...|+.+..  ||  ...+++||..|+..+.         .....
T Consensus        37 ~d~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~g--~T~~~~al~~a~~~l~---------~~~~~  103 (174)
T cd01454          37 GVPHAILGFTTDAGGRERVRWIKIKDFDESLHERARKRLAALSP--GG--NTRDGAAIRHAAERLL---------ARPEK  103 (174)
T ss_pred             CCcEEEEEecCCCCCccceEEEEecCcccccchhHHHHHHccCC--CC--CCcHHHHHHHHHHHHh---------cCCCc
Confidence            4789999999874  1111222323444443 356777777764  33  3568899999998885         12345


Q ss_pred             ccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHH---HHHHhhcCceEEEeCC--Cc----chHHHH
Q 003455          110 QRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETV---AKSFVQCSVSLSVICP--KQ----LPKLTA  180 (818)
Q Consensus       110 qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~l---a~~~~~~~I~lSiIsP--rk----lp~L~~  180 (818)
                      .|+.|||+.--|......                   ...+..++++   ++.+.+.+|.+..|.=  ..    .+.|++
T Consensus       104 ~~~iiliTDG~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~gi~v~~igig~~~~~~~~~~~~~  164 (174)
T cd01454         104 RKILLVISDGEPNDLDYY-------------------EGNVFATEDALRAVIEARKLGIEVFGITIDRDATTVDKEYLKN  164 (174)
T ss_pred             CcEEEEEeCCCcCccccc-------------------CcchhHHHHHHHHHHHHHhCCcEEEEEEecCccccchHHHHHH
Confidence            788999998866543211                   0111123344   7777888999886632  22    677888


Q ss_pred             HHHHh
Q 003455          181 IYNAA  185 (818)
Q Consensus       181 lf~~a  185 (818)
                      +|++-
T Consensus       165 ~~~~~  169 (174)
T cd01454         165 IFGEE  169 (174)
T ss_pred             hhCcc
Confidence            88754

Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=91.33  E-value=3.1  Score=50.08  Aligned_cols=125  Identities=18%  Similarity=0.177  Sum_probs=82.0

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccE
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRH  112 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkh  112 (818)
                      .-+.+||+|++.+-.     -...+|++...+..||+.|... ||   ..|++||..|+.++...       ......++
T Consensus       437 rD~v~lI~F~g~~a~-----~~lppT~~~~~~~~~L~~l~~g-Gg---TpL~~gL~~A~~~l~~~-------~~~~~~~~  500 (584)
T PRK13406        437 RDQVALVAFRGRGAE-----LLLPPTRSLVRAKRSLAGLPGG-GG---TPLAAGLDAAAALALQV-------RRKGMTPT  500 (584)
T ss_pred             CCEEEEEEECCCcee-----EEcCCCcCHHHHHHHHhcCCCC-CC---ChHHHHHHHHHHHHHHh-------ccCCCceE
Confidence            468899999766432     1356899999999999988633 33   67889999999887511       01124578


Q ss_pred             EEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCC--cchHHHHHHHHhcCC
Q 003455          113 CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK--QLPKLTAIYNAAKRN  188 (818)
Q Consensus       113 CILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPr--klp~L~~lf~~a~~~  188 (818)
                      .|||+.=-+.. +..      ....        ....+.++..+|+.+.+.+|.+.+|.-.  ....+++|-+..++.
T Consensus       501 iVLlTDG~~n~-~~~------~~~~--------~~~~~~~~~~~a~~~~~~gi~~~vId~g~~~~~~~~~LA~~~gg~  563 (584)
T PRK13406        501 VVLLTDGRANI-ARD------GTAG--------RAQAEEDALAAARALRAAGLPALVIDTSPRPQPQARALAEAMGAR  563 (584)
T ss_pred             EEEEeCCCCCC-Ccc------cccc--------ccchhhHHHHHHHHHHhcCCeEEEEecCCCCcHHHHHHHHhcCCe
Confidence            89888654321 100      0000        0112346778899999999999999873  344577777766554

>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]

Probab=90.52  E-value=1  Score=48.87  Aligned_cols=123  Identities=16%  Similarity=0.185  Sum_probs=83.5

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccE
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRH  112 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkh  112 (818)
                      ..+.+||.|+.++.--     ...+|+|++++..||..+.. ||+   .=|++||-.|..+|.       ++....-.++
T Consensus       115 RdkvavI~F~G~~A~l-----ll~pT~sv~~~~~~L~~l~~-GG~---TPL~~aL~~a~ev~~-------r~~r~~p~~~  178 (261)
T COG1240         115 RDKVAVIAFRGEKAEL-----LLPPTSSVELAERALERLPT-GGK---TPLADALRQAYEVLA-------REKRRGPDRR  178 (261)
T ss_pred             cceEEEEEecCCcceE-----EeCCcccHHHHHHHHHhCCC-CCC---CchHHHHHHHHHHHH-------HhhccCCCcc
Confidence            5789999999876421     47899999999999999975 333   237899999999986       3333344456


Q ss_pred             EEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCC----cchHHHHHHHHhcCC
Q 003455          113 CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRN  188 (818)
Q Consensus       113 CILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPr----klp~L~~lf~~a~~~  188 (818)
                      |++|+=+.=.   +.|.               ....-..+....|..+..|++.|.||.=.    ++-..+.|....+++
T Consensus       179 ~~~vviTDGr---~n~~---------------~~~~~~~e~~~~a~~~~~~g~~~lvid~e~~~~~~g~~~~iA~~~Gg~  240 (261)
T COG1240         179 PVMVVITDGR---ANVP---------------IPLGPKAETLEAASKLRLRGIQLLVIDTEGSEVRLGLAEEIARASGGE  240 (261)
T ss_pred             eEEEEEeCCc---cCCC---------------CCCchHHHHHHHHHHHhhcCCcEEEEecCCccccccHHHHHHHHhCCe
Confidence            6555544322   1111               01111136667889999999999999653    355677888877765


Q ss_pred             C
Q 003455          189 P  189 (818)
Q Consensus       189 ~  189 (818)
                      -
T Consensus       241 ~  241 (261)
T COG1240         241 Y  241 (261)
T ss_pred             E
Confidence            4

>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional

Probab=90.22  E-value=2.6  Score=50.45  Aligned_cols=118  Identities=14%  Similarity=0.130  Sum_probs=68.5

Q ss_pred             HHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCC----CCHHHHHH---HhccccCCCCCC
Q 003455            6 YAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT----KDVDIFLH---WLSTIPFAGGGF   78 (818)
Q Consensus         6 ~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T----~~~~~fl~---wL~~i~f~GGG~   78 (818)
                      +..+..+..+|..|..+        .+.+.++||+|.+..      -..+.++    .|...++.   .|......||| 
T Consensus        62 e~AK~Fa~~LV~~l~Is--------~D~V~VgiV~FSd~~------r~vfpL~s~~s~Dk~~aL~~I~sL~~~~~pgGg-  126 (576)
T PTZ00441         62 THVIPMLMGLIQQLNLS--------DDAINLYMSLFSNNT------TELIRLGSGASKDKEQALIIVKSLRKTYLPYGK-  126 (576)
T ss_pred             HHHHHHHHHHHHHhccC--------CCceEEEEEEeCCCc------eEEEecCCCccccHHHHHHHHHHHHhhccCCCC-
Confidence            45556777777777432        236888899987652      1122332    23334444   44444446665 


Q ss_pred             ChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHH
Q 003455           79 NDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAK  158 (818)
Q Consensus        79 ~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~  158 (818)
                        ..+.+||..|...+.  .    +..+....|+.|||+.--+...                          .+....|+
T Consensus       127 --Tnig~AL~~Aae~L~--s----r~~R~nvpKVVILLTDG~sns~--------------------------~dvleaAq  172 (576)
T PTZ00441        127 --TNMTDALLEVRKHLN--D----RVNRENAIQLVILMTDGIPNSK--------------------------YRALEESR  172 (576)
T ss_pred             --ccHHHHHHHHHHHHh--h----cccccCCceEEEEEecCCCCCc--------------------------ccHHHHHH
Confidence              457778888877663  1    1134567899999987665321                          13334566


Q ss_pred             HHhhcCceEEEeCC
Q 003455          159 SFVQCSVSLSVICP  172 (818)
Q Consensus       159 ~~~~~~I~lSiIsP  172 (818)
                      .|.+.+|.+.+|.=
T Consensus       173 ~LR~~GVeI~vIGV  186 (576)
T PTZ00441        173 KLKDRNVKLAVIGI  186 (576)
T ss_pred             HHHHCCCEEEEEEe
Confidence            67777777666643

>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin)

Probab=89.85  E-value=5  Score=38.84  Aligned_cols=133  Identities=11%  Similarity=0.084  Sum_probs=79.6

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHH
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIA   84 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aia   84 (818)
                      ++..++.|..+++.+..           ...++||+|.+..-.- .......-+.+...++.+|+++.. |||   ..+.
T Consensus        20 ~~~~~~al~~~l~~l~~-----------~~~~~l~~Fs~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~-~g~---T~l~   83 (171)
T cd01461          20 IEQTKEALLTALKDLPP-----------GDYFNIIGFSDTVEEF-SPSSVSATAENVAAAIEYVNRLQA-LGG---TNMN   83 (171)
T ss_pred             HHHHHHHHHHHHHhCCC-----------CCEEEEEEeCCCceee-cCcceeCCHHHHHHHHHHHHhcCC-CCC---cCHH
Confidence            67777888887777632           2468999997652110 000001113456788889999887 444   4578


Q ss_pred             HHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcC
Q 003455           85 EGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS  164 (818)
Q Consensus        85 EGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~  164 (818)
                      +||..|+..+..         .....+.+|||+.-.+..                   +       .++...++...+.+
T Consensus        84 ~al~~a~~~l~~---------~~~~~~~iillTDG~~~~-------------------~-------~~~~~~~~~~~~~~  128 (171)
T cd01461          84 DALEAALELLNS---------SPGSVPQIILLTDGEVTN-------------------E-------SQILKNVREALSGR  128 (171)
T ss_pred             HHHHHHHHhhcc---------CCCCccEEEEEeCCCCCC-------------------H-------HHHHHHHHHhcCCC
Confidence            888888887741         234568888888765211                   0       12334444444457


Q ss_pred             ceEEEeCCC---cchHHHHHHHHhcCC
Q 003455          165 VSLSVICPK---QLPKLTAIYNAAKRN  188 (818)
Q Consensus       165 I~lSiIsPr---klp~L~~lf~~a~~~  188 (818)
                      |.+-.|.=.   ..+.|+.|=+..++.
T Consensus       129 i~i~~i~~g~~~~~~~l~~ia~~~gG~  155 (171)
T cd01461         129 IRLFTFGIGSDVNTYLLERLAREGRGI  155 (171)
T ss_pred             ceEEEEEeCCccCHHHHHHHHHcCCCe
Confidence            777666532   356688887777654

Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.

>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain

Probab=88.74  E-value=8.2  Score=41.70  Aligned_cols=116  Identities=20%  Similarity=0.263  Sum_probs=75.3

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCC--------------CCCCChhhHHHHHHHH-HhhhccC
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFA--------------GGGFNDAAIAEGLSEA-LMMFSVA   97 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~--------------GGG~~~~aiaEGLa~A-L~~~~~~   97 (818)
                      ..+++||.|.+..-      ....||.|...++..|+.+...              +||   .++.+||..| ++++...
T Consensus        88 ~d~v~lv~f~~~~~------~~~~~t~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~g~---T~l~~al~~aa~~~~~~~  158 (296)
T TIGR03436        88 NDRVFVVTFNTRLR------LLQDFTSDPRLLEAALNRLKPPLRTDYNSSGAFVRDGGG---TALYDAITLAALEQLANA  158 (296)
T ss_pred             CCEEEEEEeCCcee------EeecCCCCHHHHHHHHHhccCCCccccccccccccCCCc---chhHHHHHHHHHHHHHHh
Confidence            58999999996421      1358999999999999999873              233   4566776544 4555310


Q ss_pred             CCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCCcc--
Q 003455           98 PNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQL--  175 (818)
Q Consensus        98 ~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPrkl--  175 (818)
                       .     ......|..|||+.--..                         ....+.+++++.+.+.+|.+-.|.-..+  
T Consensus       159 -~-----~~~p~rk~iIllTDG~~~-------------------------~~~~~~~~~~~~~~~~~v~vy~I~~~~~~~  207 (296)
T TIGR03436       159 -L-----AGIPGRKALIVISDGGDN-------------------------RSRDTLERAIDAAQRADVAIYSIDARGLRA  207 (296)
T ss_pred             -h-----cCCCCCeEEEEEecCCCc-------------------------chHHHHHHHHHHHHHcCCEEEEeccCcccc
Confidence             0     011245666777653110                         1113667888889999999999887532  


Q ss_pred             --------------hHHHHHHHHhcCC
Q 003455          176 --------------PKLTAIYNAAKRN  188 (818)
Q Consensus       176 --------------p~L~~lf~~a~~~  188 (818)
                                    ..|+.|-+..++.
T Consensus       208 ~~~~~~~~~~~~~~~~L~~iA~~TGG~  234 (296)
T TIGR03436       208 PDLGAGAKAGLGGPEALERLAEETGGR  234 (296)
T ss_pred             CCcccccccCCCcHHHHHHHHHHhCCe
Confidence                          3477777777765

Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.

>PF13768 VWA_3: von Willebrand factor type A domain

Probab=86.78  E-value=2  Score=41.49  Aligned_cols=95  Identities=17%  Similarity=0.251  Sum_probs=61.1

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCC-CCcCceeeccCCCCHHHHHHHhccccCCCCCCC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGS-YCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFN   79 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~-~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~   79 (818)
                      |.-+++.+|+=|.-+|+.+.           ....|.||.|++... +...++...  ..+....+.||+.++..+||  
T Consensus        13 m~g~~~~~k~al~~~l~~L~-----------~~d~fnii~f~~~~~~~~~~~~~~~--~~~~~~a~~~I~~~~~~~G~--   77 (155)
T PF13768_consen   13 MSGEKELVKDALRAILRSLP-----------PGDRFNIIAFGSSVRPLFPGLVPAT--EENRQEALQWIKSLEANSGG--   77 (155)
T ss_pred             CCCcHHHHHHHHHHHHHhCC-----------CCCEEEEEEeCCEeeEcchhHHHHh--HHHHHHHHHHHHHhcccCCC--
Confidence            33344455555555555542           346899999999642 222222222  25668899999999996555  


Q ss_pred             hhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCC
Q 003455           80 DAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNP  121 (818)
Q Consensus        80 ~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP  121 (818)
                       ..+.++|.+|+..+.          .....++.||++.-.|
T Consensus        78 -t~l~~aL~~a~~~~~----------~~~~~~~IilltDG~~  108 (155)
T PF13768_consen   78 -TDLLAALRAALALLQ----------RPGCVRAIILLTDGQP  108 (155)
T ss_pred             -ccHHHHHHHHHHhcc----------cCCCccEEEEEEeccC
Confidence             456777778887652          3566789999997766

>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region)

Probab=85.94  E-value=16  Score=42.44  Aligned_cols=168  Identities=14%  Similarity=0.082  Sum_probs=98.0

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCC--CCCc--------------------C-ceeeccC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHG--SYCA--------------------C-LVQRSGW   57 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~--~~~~--------------------~-~v~~~g~   57 (818)
                      |+..++.||+-...+.+-...        ...+..+|+=.|-+.+  +|-+                    + +-..-..
T Consensus       112 M~ddl~~lk~lg~~L~~~m~~--------it~n~rlGfGsFVDK~v~P~~~t~p~~l~~PC~~~~~~c~p~f~f~~~L~L  183 (423)
T smart00187      112 MKDDLDNLKSLGDDLAREMKG--------LTSNFRLGFGSFVDKTVSPFVSTRPEKLENPCPNYNLTCEPPYGFKHVLSL  183 (423)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh--------cccCceeeEEEeecCccCCcccCCHHHhcCCCcCCCCCcCCCcceeeeccC
Confidence            666777788766666666643        2346777877777652  2211                    1 1233678


Q ss_pred             CCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCC------CCCcCc
Q 003455           58 TKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLP------TPVYRP  131 (818)
Q Consensus        58 T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp------~~~~~p  131 (818)
                      |+|..+|.+.+.+...+||......==+||--|..|-+  ..+-    +....|..|+++....|-.-      +..++-
T Consensus       184 T~~~~~F~~~V~~~~iSgN~D~PEgG~DAimQaaVC~~--~IGW----R~~a~rllv~~TDa~fH~AGDGkLaGIv~PND  257 (423)
T smart00187      184 TDDTDEFNEEVKKQRISGNLDAPEGGFDAIMQAAVCTE--QIGW----REDARRLLVFSTDAGFHFAGDGKLAGIVQPND  257 (423)
T ss_pred             CCCHHHHHHHHhhceeecCCcCCcccHHHHHHHHhhcc--cccc----CCCceEEEEEEcCCCccccCCcceeeEecCCC
Confidence            99999999999999999998554333333433333322  1111    34566777888888777321      000112


Q ss_pred             cccccccc-chhhhhhhccCCCHHHHHHHHhhcCceEEEeCC-CcchHHHHHHH
Q 003455          132 QMQNLDQN-ENNEAQAESRLSDAETVAKSFVQCSVSLSVICP-KQLPKLTAIYN  183 (818)
Q Consensus       132 ~~~~l~~~-~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsP-rklp~L~~lf~  183 (818)
                      .-|-|+.+ +-.++.+++- -++.+|++.+.|++|.+=|--- +..+.+++|-+
T Consensus       258 g~CHL~~~g~Yt~s~~~DY-PSi~ql~~kL~e~nI~~IFAVT~~~~~~Y~~Ls~  310 (423)
T smart00187      258 GQCHLDNNGEYTMSTTQDY-PSIGQLNQKLAENNINPIFAVTKKQVSLYKELSA  310 (423)
T ss_pred             CcceeCCCCCcCccCcCCC-CCHHHHHHHHHhcCceEEEEEcccchhHHHHHHH
Confidence            23344322 1111122222 3899999999999999988444 55555444443

Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).

>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=85.02  E-value=4.6  Score=39.49  Aligned_cols=74  Identities=20%  Similarity=0.266  Sum_probs=46.2

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCC-CCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCcc
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWT-KDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQR  111 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T-~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qk  111 (818)
                      ...++||+|.+..-. .....  .++ .+.+.+..||++|...||    ..+.+||..|+.++..  .     ......+
T Consensus        35 ~~~~~li~F~~~~~~-~~~~~--~~~~~~~~~~~~~i~~~~~~g~----T~~~~al~~a~~~~~~--~-----~~~~~~~  100 (155)
T cd01466          35 ADRLSIVTFSTSAKR-LSPLR--RMTAKGKRSAKRVVDGLQAGGG----TNVVGGLKKALKVLGD--R-----RQKNPVA  100 (155)
T ss_pred             cceEEEEEecCCccc-cCCCc--ccCHHHHHHHHHHHHhccCCCC----ccHHHHHHHHHHHHhh--c-----ccCCCce
Confidence            357999999985322 11111  122 256789999999876433    4677888888888741  0     1123457


Q ss_pred             EEEEeecCC
Q 003455          112 HCILVAASN  120 (818)
Q Consensus       112 hCILi~nSp  120 (818)
                      +.|||+.--
T Consensus       101 ~iillTDG~  109 (155)
T cd01466         101 SIMLLSDGQ  109 (155)
T ss_pred             EEEEEcCCC
Confidence            888888654

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,

>cd01465 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=81.56  E-value=40  Score=32.58  Aligned_cols=116  Identities=16%  Similarity=0.136  Sum_probs=66.5

Q ss_pred             ceEEEEEEccCCCCCcCceeeccCC--CCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCcc
Q 003455           34 VELSLVTFNTHGSYCACLVQRSGWT--KDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQR  111 (818)
Q Consensus        34 ~~yaLVvf~~~~~~~~~~v~~~g~T--~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qk  111 (818)
                      ..++||+|.+....      .+.|+  .+...++..|+++.. +||   ..+.+||..|+..+.  ...     .....+
T Consensus        36 ~~v~li~f~~~~~~------~~~~~~~~~~~~l~~~l~~~~~-~g~---T~~~~al~~a~~~~~--~~~-----~~~~~~   98 (170)
T cd01465          36 DRLAIVTYDGAAET------VLPATPVRDKAAILAAIDRLTA-GGS---TAGGAGIQLGYQEAQ--KHF-----VPGGVN   98 (170)
T ss_pred             CEEEEEEecCCccE------EecCcccchHHHHHHHHHcCCC-CCC---CCHHHHHHHHHHHHH--hhc-----CCCCee
Confidence            57999999986322      12333  467888888998875 333   345667777776663  110     112236


Q ss_pred             EEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCC---cchHHHHHHHHhcCC
Q 003455          112 HCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK---QLPKLTAIYNAAKRN  188 (818)
Q Consensus       112 hCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPr---klp~L~~lf~~a~~~  188 (818)
                      +.||++.-.+..-+..                      ..++.++++.+.+.+|.+.+|.=-   -...|++|-...++.
T Consensus        99 ~ivl~TDG~~~~~~~~----------------------~~~~~~~~~~~~~~~v~i~~i~~g~~~~~~~l~~ia~~~~g~  156 (170)
T cd01465          99 RILLATDGDFNVGETD----------------------PDELARLVAQKRESGITLSTLGFGDNYNEDLMEAIADAGNGN  156 (170)
T ss_pred             EEEEEeCCCCCCCCCC----------------------HHHHHHHHHHhhcCCeEEEEEEeCCCcCHHHHHHHHhcCCce
Confidence            7788877665431100                      013334455556678888877532   334466666555443

Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if n

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=81.20  E-value=10  Score=46.12  Aligned_cols=123  Identities=20%  Similarity=0.247  Sum_probs=79.0

Q ss_pred             cceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccE
Q 003455           33 NVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRH  112 (818)
Q Consensus        33 ~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkh  112 (818)
                      ...++||+|++....     -...||++...+..+|+.+.. |||   ..+++||..|+.++...     ........+.
T Consensus       502 ~D~v~lI~F~g~~a~-----~~~p~t~~~~~~~~~L~~l~~-gG~---Tpl~~aL~~A~~~l~~~-----~~~~~~~~~~  567 (633)
T TIGR02442       502 RDKVALITFRGEEAE-----VLLPPTSSVELAARRLEELPT-GGR---TPLAAGLLKAAEVLSNE-----LLRDDDGRPL  567 (633)
T ss_pred             CCEEEEEEECCCCce-----EEcCCCCCHHHHHHHHHhCCC-CCC---CCHHHHHHHHHHHHHHh-----hccCCCCceE
Confidence            478999999865311     146789999999999999976 333   45778888888877410     0011234566


Q ss_pred             EEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCC----cchHHHHHHHHhcCC
Q 003455          113 CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRN  188 (818)
Q Consensus       113 CILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPr----klp~L~~lf~~a~~~  188 (818)
                      .|||+.=-+-.-..                   ......++..+|+.+.+.+|.+.||...    +...+++|-+..++.
T Consensus       568 vvliTDG~~n~~~~-------------------~~~~~~~~~~~a~~l~~~~i~~~vIdt~~~~~~~~~~~~lA~~~gg~  628 (633)
T TIGR02442       568 LVVITDGRANVADG-------------------GEPPTDDARTIAAKLAARGILFVVIDTESGFVRLGLAEDLARALGGE  628 (633)
T ss_pred             EEEECCCCCCCCCC-------------------CCChHHHHHHHHHHHHhcCCeEEEEeCCCCCcchhHHHHHHHhhCCe
Confidence            67776432211000                   0011235678899999999999999762    356688887776553

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

---

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	818
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-08
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-07
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	1e-09
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	2e-09
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	2e-09
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	5e-09
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	7e-08
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	6e-06
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	8e-06
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	5e-04
1yvl_A	683	Signal transducer and activator of transcription 1	1e-07
1yvl_A	683	Signal transducer and activator of transcription 1	8e-06
1yvl_A	683	Signal transducer and activator of transcription 1	1e-05
1yvl_A	683	Signal transducer and activator of transcription 1	2e-05
1yvl_A	683	Signal transducer and activator of transcription 1	3e-05
1yvl_A	683	Signal transducer and activator of transcription 1	4e-05
1yvl_A	683	Signal transducer and activator of transcription 1	3e-04
1yvl_A	683	Signal transducer and activator of transcription 1	5e-04
1yvl_A	683	Signal transducer and activator of transcription 1	6e-04
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-07
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-07
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-07
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	4e-06
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	2e-05
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	6e-05
3ghg_C	411	Fibrinogen gamma chain; triple-stranded coiled coi	3e-07
3ghg_C	411	Fibrinogen gamma chain; triple-stranded coiled coi	4e-05
3ghg_C	411	Fibrinogen gamma chain; triple-stranded coiled coi	6e-05
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	5e-07
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	3e-06
1m1j_B	464	Fibrinogen beta chain; coiled coils, disulfide rin	3e-05
1bg1_A	596	Protein (transcription factor STAT3B); protein-DNA	2e-06
1bg1_A	596	Protein (transcription factor STAT3B); protein-DNA	4e-06
1bg1_A	596	Protein (transcription factor STAT3B); protein-DNA	8e-06
1bg1_A	596	Protein (transcription factor STAT3B); protein-DNA	2e-05
1bg1_A	596	Protein (transcription factor STAT3B); protein-DNA	2e-05
1bg1_A	596	Protein (transcription factor STAT3B); protein-DNA	3e-05
1bg1_A	596	Protein (transcription factor STAT3B); protein-DNA	3e-05
1uur_A	473	Stata protein, STAT protein; transcription activat	4e-06
1uur_A	473	Stata protein, STAT protein; transcription activat	5e-06
1uur_A	473	Stata protein, STAT protein; transcription activat	2e-05
1uur_A	473	Stata protein, STAT protein; transcription activat	7e-04
2es4_D	332	Lipase chaperone; protein-protein complex, steric	4e-06
2es4_D	332	Lipase chaperone; protein-protein complex, steric	1e-04
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	8e-06
3ibp_A	302	Chromosome partition protein MUKB; structural main	8e-06
3ibp_A	302	Chromosome partition protein MUKB; structural main	3e-05
3ibp_A	302	Chromosome partition protein MUKB; structural main	2e-04
1bf5_A	575	Signal transducer and activator of transcription 1	1e-05
1bf5_A	575	Signal transducer and activator of transcription 1	1e-05
1bf5_A	575	Signal transducer and activator of transcription 1	1e-05
1bf5_A	575	Signal transducer and activator of transcription 1	4e-05
1bf5_A	575	Signal transducer and activator of transcription 1	5e-05
1bf5_A	575	Signal transducer and activator of transcription 1	7e-05
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	2e-05
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	6e-05
1y1u_A	585	Signal transducer and activator of transcription;	4e-05
1y1u_A	585	Signal transducer and activator of transcription;	8e-05
1y1u_A	585	Signal transducer and activator of transcription;	1e-04
1y1u_A	585	Signal transducer and activator of transcription;	2e-04
1y1u_A	585	Signal transducer and activator of transcription;	2e-04
1y1u_A	585	Signal transducer and activator of transcription;	5e-04
1m1j_C	409	Fibrinogen gamma chain; coiled coils, disulfide ri	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	1e-04
3c8j_A	203	Natural killer cell receptor LY49C; MHC, virus, im	2e-04
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	2e-04
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	2e-04
3ajw_A	150	Flagellar FLIJ protein; flagellum, type III secret	3e-04
1vt0_M	602	Portal protein, protein GP1; portal protein, DNA e	4e-04
1jad_A	251	PLC-beta, phospholipase C beta; alpha helical coil	5e-04
2h8n_A	112	HD4, histone deacetylase 4; alpha helix, polar zip	6e-04
4dci_A	150	Uncharacterized protein; PSI-biology, midwest cent	6e-04

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 63.3 bits (153), Expect = 2e-10
 Identities = 20/133 (15%), Positives = 36/133 (27%)

Query: 674 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 733
           +S  +++   Q Q Q        Q   Q +         +   Q  +P       + Q Q
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 734 QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPG 793
             +  Q Q  QQ+ Q         +     +      Q     Q        Q  +  P 
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 794 RTQLVSQGQVSSQ 806
             Q  +    + +
Sbjct: 121 YGQPSAAMGQNMR 133

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 62.2 bits (150), Expect = 6e-10
 Identities = 21/140 (15%), Positives = 31/140 (22%)

Query: 663 FPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQ 722
           +P   + +    +  QQ       Q      M                 Q   L     Q
Sbjct: 9   YPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQ 68

Query: 723 LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGS 782
           L QQ          M         P    Q Q+P         Q Q     +  Q     
Sbjct: 69  LHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAM 128

Query: 783 GMGQGYVQGPGRTQLVSQGQ 802
           G     +       L+++  
Sbjct: 129 GQNMRPMNQLYPIDLLTELP 148

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 60.2 bits (145), Expect = 2e-09
 Identities = 21/125 (16%), Positives = 31/125 (24%)

Query: 685 QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQ 744
             +++ + Q Q Q         Q  Q   PQ          Q  +P          QQ  
Sbjct: 3   HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62

Query: 745 QLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVS 804
              Q Q  QQ+ Q         L     +     M      Q       + Q ++     
Sbjct: 63  TPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYG 122

Query: 805 SQGAP 809
              A 
Sbjct: 123 QPSAA 127

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 59.8 bits (144), Expect = 2e-09
 Identities = 26/148 (17%), Positives = 39/148 (26%), Gaps = 2/148 (1%)

Query: 667 MVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 726
           M   K ++  Q Q Q  Q     Q        Q    + +   Q  +P         QQQ
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 727 QQIPQLQQ--QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGM 784
              P  +Q  Q + Q         L     +      Q    +Q    L Q QQ + +  
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 785 GQGYVQGPGRTQLVSQGQVSSQGAPNIP 812
                   G+                +P
Sbjct: 121 YGQPSAAMGQNMRPMNQLYPIDLLTELP 148

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 55.6 bits (133), Expect = 5e-08
 Identities = 23/120 (19%), Positives = 31/120 (25%)

Query: 660 GMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQ 719
           GM +    +  +  + S  QQQ     Q+Q HQQ+           L       P    Q
Sbjct: 39  GMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQ 98

Query: 720 IPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
                Q     Q QQQ M      Q    + Q  +         L               
Sbjct: 99  PQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPP 158

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 54.1 bits (129), Expect = 2e-07
 Identities = 23/124 (18%), Positives = 34/124 (27%), Gaps = 1/124 (0%)

Query: 696 SQLQHQQLSQLQQQQ-QQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQ 754
           S  + +   Q Q Q  Q    LQQ    +  Q             +  Q  +P + QQQ 
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 755 LPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGG 814
           L   Q+Q      Q    ++         +       P     +       Q     P  
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121

Query: 815 GFMS 818
           G  S
Sbjct: 122 GQPS 125

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 52.5 bits (125), Expect = 5e-07
 Identities = 26/111 (23%), Positives = 38/111 (34%), Gaps = 2/111 (1%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ--I 729
            Q  +  Q+QL QQ  Q         L +  L       Q    +Q   P  QQQQ    
Sbjct: 59  QQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAA 118

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
           P   Q S    Q  + + QL     L ++        L     +  P++M+
Sbjct: 119 PAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERML 169

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926

 Score = 52.1 bits (124), Expect = 6e-07
 Identities = 22/110 (20%), Positives = 35/110 (31%), Gaps = 3/110 (2%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 731
           P +  QQ     Q+Q  QQ  Q  + +    L  +         +Q Q+P         Q
Sbjct: 54  PSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPN-AYMQPQVPVQMGTPLQQQ 112

Query: 732 LQQQSMPQLQQQQQLPQ--LQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
            Q  + P   Q        ++   QL  +    +LP       L  P  +
Sbjct: 113 QQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLV 162

>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA packaging podoviridae, virus assembly, tail tube, trunk domain; 7.50A {Enterobacteria phage P22} Length = 725

 Score = 61.2 bits (147), Expect = 1e-09
 Identities = 19/132 (14%), Positives = 44/132 (33%)

Query: 648 LLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQ 707
           LL  + +      +L      +   +     +    +Q  Q   ++ ++  + Q L + Q
Sbjct: 538 LLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPETPEEQQWLVEAQ 597

Query: 708 QQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQL 767
           Q +Q          Q    Q   +L +     L  Q    +++ Q QL   +  +    +
Sbjct: 598 QAKQGQQDPAMVQAQGVLLQGQAELAKAQNQTLSLQIDAAKVEAQNQLNAARIAEIFNNM 657

Query: 768 QQQQQLSQPQQM 779
              +Q    + +
Sbjct: 658 DLSKQSEFREFL 669

>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA packaging podoviridae, virus assembly, tail tube, trunk domain; 7.50A {Enterobacteria phage P22} Length = 725

 Score = 60.5 bits (145), Expect = 2e-09
 Identities = 20/126 (15%), Positives = 43/126 (34%), Gaps = 1/126 (0%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 730
           K  I    ++    ++QQ   +  Q++   Q    + Q Q  L Q Q ++ + Q Q    
Sbjct: 574 KQLIQMGVKKPETPEEQQWLVEAQQAKQGQQDP-AMVQAQGVLLQGQAELAKAQNQTLSL 632

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQ 790
           Q+    +    Q       +    +   +Q +    L+      Q +        +  ++
Sbjct: 633 QIDAAKVEAQNQLNAARIAEIFNNMDLSKQSEFREFLKTVASFQQDRSEDARANAELLLK 692

Query: 791 GPGRTQ 796
           G  +T 
Sbjct: 693 GDEQTH 698

>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA packaging podoviridae, virus assembly, tail tube, trunk domain; 7.50A {Enterobacteria phage P22} Length = 725

 Score = 60.1 bits (144), Expect = 2e-09
 Identities = 22/118 (18%), Positives = 43/118 (36%), Gaps = 7/118 (5%)

Query: 670 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 729
               +     +QL Q   ++     + Q    +  Q +Q QQ    +Q Q   LQ Q ++
Sbjct: 564 GVEMMRDYANKQLIQMGVKKPETPEEQQWL-VEAQQAKQGQQDPAMVQAQGVLLQGQAEL 622

Query: 730 PQLQ------QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVG 781
            + Q      Q    +++ Q QL   +  +    M   +Q    +  + ++  QQ   
Sbjct: 623 AKAQNQTLSLQIDAAKVEAQNQLNAARIAEIFNNMDLSKQSEFREFLKTVASFQQDRS 680

>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA packaging podoviridae, virus assembly, tail tube, trunk domain; 7.50A {Enterobacteria phage P22} Length = 725

 Score = 58.9 bits (141), Expect = 5e-09
 Identities = 19/120 (15%), Positives = 42/120 (35%), Gaps = 2/120 (1%)

Query: 672 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQ-QLPQLQQQIPQLQQQQQIP 730
            +  + ++QQ   + QQ +  Q    +   Q   LQ Q +    Q Q    Q+   +   
Sbjct: 582 KKPETPEEQQWLVEAQQAKQGQQDPAMVQAQGVLLQGQAELAKAQNQTLSLQIDAAKVEA 641

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQ 790
           Q Q  +    +    +   +Q +    ++      Q  + +      +++  G  Q + Q
Sbjct: 642 QNQLNAARIAEIFNNMDLSKQSEFREFLKTVASFQQ-DRSEDARANAELLLKGDEQTHKQ 700

>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA packaging podoviridae, virus assembly, tail tube, trunk domain; 7.50A {Enterobacteria phage P22} Length = 725

 Score = 55.1 bits (131), Expect = 7e-08
 Identities = 22/128 (17%), Positives = 46/128 (35%), Gaps = 1/128 (0%)

Query: 651 VSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ 710
           + D A + +  +        + Q    + QQ +Q QQ     Q Q  L   Q ++L + Q
Sbjct: 568 MRDYANKQLIQMGVKKPETPEEQQWLVEAQQAKQGQQDPAMVQAQGVLLQGQ-AELAKAQ 626

Query: 711 QQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
            Q   LQ    +++ Q Q+   +   +       +  + ++  +     QQ +    +  
Sbjct: 627 NQTLSLQIDAAKVEAQNQLNAARIAEIFNNMDLSKQSEFREFLKTVASFQQDRSEDARAN 686

Query: 771 QQLSQPQQ 778
            +L     
Sbjct: 687 AELLLKGD 694

>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA packaging podoviridae, virus assembly, tail tube, trunk domain; 7.50A {Enterobacteria phage P22} Length = 725

 Score = 48.9 bits (115), Expect = 6e-06
 Identities = 18/112 (16%), Positives = 32/112 (28%)

Query: 668 VVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ 727
                  S Q  +Q  + +  +   +        QL  LQ       +  + +     +Q
Sbjct: 516 CYTDVGPSFQSMKQQNRAEILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQ 575

Query: 728 QIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
            I    ++     +QQ  +   Q +Q        Q    L Q Q      Q 
Sbjct: 576 LIQMGVKKPETPEEQQWLVEAQQAKQGQQDPAMVQAQGVLLQGQAELAKAQN 627

>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA packaging podoviridae, virus assembly, tail tube, trunk domain; 7.50A {Enterobacteria phage P22} Length = 725

 Score = 48.5 bits (114), Expect = 8e-06
 Identities = 22/107 (20%), Positives = 43/107 (40%), Gaps = 5/107 (4%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           Q +  +  +L  +  Q   +     LQ+  L   +  +       +Q+ Q+  ++     
Sbjct: 529 QQNRAEILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPETPE 588

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           +QQ + + QQ +     Q QQ    +Q Q  L Q Q +   +Q Q +
Sbjct: 589 EQQWLVEAQQAK-----QGQQDPAMVQAQGVLLQGQAELAKAQNQTL 630

>3lj5_A Portal protein, protein GP1; DNA ejection, molecular motor, DNA packaging podoviridae, virus assembly, tail tube, trunk domain; 7.50A {Enterobacteria phage P22} Length = 725

 Score = 42.8 bits (99), Expect = 5e-04
 Identities = 25/168 (14%), Positives = 52/168 (30%), Gaps = 11/168 (6%)

Query: 652 SDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQ 711
             +   +         V    ++      + Q     +   +  + +     S  QQ + 
Sbjct: 474 VPRNVTITLEDGSEKDVQLMAEVVDLATGEKQVLNDIRGRYECYTDVGPSFQSMKQQNRA 533

Query: 712 QLPQLQQQIPQLQQQQQIPQLQ---------QQSMPQLQQQQQLPQLQQQQQLPQMQQ-- 760
           ++ +L  + PQ   + Q+  LQ          + M     +Q +    ++ + P+ QQ  
Sbjct: 534 EILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPETPEEQQWL 593

Query: 761 QQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGA 808
            +     Q QQ  +  Q       GQ  +       L  Q   +   A
Sbjct: 594 VEAQQAKQGQQDPAMVQAQGVLLQGQAELAKAQNQTLSLQIDAAKVEA 641

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 54.1 bits (129), Expect = 1e-07
 Identities = 25/160 (15%), Positives = 64/160 (40%), Gaps = 11/160 (6%)

Query: 625 HGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLF---PGDMVVFKPQISSQQQQQ 681
           H  L QL ++   +   L +  LL     K+ R +   F   P  M +       ++++ 
Sbjct: 58  HDLLSQLDDQ--YSRFSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKI 115

Query: 682 LQQQQQQQQHQQMQSQL------QHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 735
           L+  Q+  Q Q    Q       Q +  S+++  + ++  ++ +I  L+  Q     + +
Sbjct: 116 LENAQRFNQAQSGNIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCK 175

Query: 736 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
           ++   + +        Q+Q   + ++  L    +++++  
Sbjct: 176 TLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVH 215

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 48.3 bits (114), Expect = 8e-06
 Identities = 11/104 (10%), Positives = 37/104 (35%), Gaps = 4/104 (3%)

Query: 673 QISSQQQQQLQQQQQ--QQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 730
                + + L+  Q     + + +Q++           Q+Q+   L++    L  +++  
Sbjct: 154 MCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRK-- 211

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLS 774
           ++  + +  L   +         +L + +++QQ   +       
Sbjct: 212 EVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNAC 255

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 48.0 bits (113), Expect = 1e-05
 Identities = 15/116 (12%), Positives = 49/116 (42%), Gaps = 12/116 (10%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQ------QQQQQLPQLQQQIPQLQ 724
           +  +   +Q++L  + +  + + M  + + + L  LQ       +  Q  + +       
Sbjct: 131 QSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKS 190

Query: 725 QQQQIPQLQQQSMPQLQQQQQ--LPQLQQQQQLPQMQQQQ----QLPQLQQQQQLS 774
            Q+Q   L ++    L  +++  + ++ +   + ++ Q      +L + +++QQ +
Sbjct: 191 DQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSA 246

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 47.2 bits (111), Expect = 2e-05
 Identities = 15/108 (13%), Positives = 38/108 (35%), Gaps = 5/108 (4%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQI-----PQLQQQQQI 729
              +  Q Q+Q   ++   M    + + + ++ +        Q  +      + +++QQ 
Sbjct: 186 GVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQS 245

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
             +       L Q Q    +  +      QQ ++L +L+Q+       
Sbjct: 246 ACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDP 293

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 46.8 bits (110), Expect = 3e-05
 Identities = 17/120 (14%), Positives = 42/120 (35%), Gaps = 12/120 (10%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQ--LSQLQQQQQQLPQLQQQIPQLQQQQQIP 730
           + S +  Q   Q+   Q    + S L+ ++  L   Q+  Q      Q    L +Q+++ 
Sbjct: 84  RKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQRFNQAQSGNIQSTVMLDKQKELD 143

Query: 731 ----------QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
                        +  +  L+  Q     + +    +  +   + +  Q+Q+    ++M 
Sbjct: 144 SKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMY 203

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 46.0 bits (108), Expect = 4e-05
 Identities = 16/105 (15%), Positives = 37/105 (35%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 734
            S +   L Q   ++  + +Q   Q   +         L + ++ +   Q+  Q      
Sbjct: 71  FSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQRFNQAQSGNI 130

Query: 735 QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           QS   L +Q++L    +  +   M  + ++  L+  Q     +  
Sbjct: 131 QSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCK 175

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 43.3 bits (101), Expect = 3e-04
 Identities = 16/97 (16%), Positives = 44/97 (45%), Gaps = 3/97 (3%)

Query: 677 QQQQQLQQQQQQQQH--QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 734
            +++++  +  +  +  +  Q+ L + +L + +++QQ           L Q Q    +  
Sbjct: 208 NKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVA 267

Query: 735 QSMPQLQQQ-QQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
           +S+ Q++QQ ++L +L+Q+         +    L  +
Sbjct: 268 ESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDR 304

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 42.6 bits (99), Expect = 5e-04
 Identities = 14/103 (13%), Positives = 37/103 (35%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           Q ++       +   +Q Q  L+   L    ++++ + ++ + +   +  Q      +  
Sbjct: 178 QNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELV 237

Query: 737 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
             + +QQ           L Q+Q    +     QQ   Q +++
Sbjct: 238 EWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKL 280

>1yvl_A Signal transducer and activator of transcription 1-alpha/beta; signaling protein; HET: PTR; 3.00A {Homo sapiens} Length = 683

 Score = 42.6 bits (99), Expect = 6e-04
 Identities = 10/104 (9%), Positives = 31/104 (29%), Gaps = 1/104 (0%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQ-LPQLQQQIPQLQQQQQIPQ 731
            +   Q +   + +  Q  +   + +      Q Q   ++    L  +  ++  +     
Sbjct: 162 SLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELL 221

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
              +         +L + +++QQ   +         Q Q   + 
Sbjct: 222 NVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTI 265

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 53.8 bits (128), Expect = 2e-07
 Identities = 18/103 (17%), Positives = 50/103 (48%), Gaps = 6/103 (5%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           +        + Q  Q    ++ + +++  +    Q   + L ++Q++  Q+ +Q++  + 
Sbjct: 466 KSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKE--RS 523

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
            Q+ + QL ++ +      + QL + Q++    +LQ+Q+QL +
Sbjct: 524 YQEHLKQLTEKME----NDRVQLLKEQERTLALKLQEQEQLLK 562

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 53.4 bits (127), Expect = 2e-07
 Identities = 16/98 (16%), Positives = 54/98 (55%), Gaps = 2/98 (2%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           Q   + +++ + ++ +   +Q   + L ++Q++ +Q+ + +++  Q   +Q   +++   
Sbjct: 480 QTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDR 539

Query: 737 MPQLQQQQQL--PQLQQQQQLPQMQQQQQLPQLQQQQQ 772
           +  L++Q++    +LQ+Q+QL +   Q++   ++ + Q
Sbjct: 540 VQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQ 577

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 53.4 bits (127), Expect = 2e-07
 Identities = 19/104 (18%), Positives = 49/104 (47%), Gaps = 3/104 (2%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           +I  ++ +    Q   +   +MQ + +     + +  Q+ L QL +++    + Q + + 
Sbjct: 488 EIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMEN-DRVQLLKEQ 546

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 776
           ++    +LQ+Q+QL +   Q++   M+ + Q   LQ + +  + 
Sbjct: 547 ERTLALKLQEQEQLLKEGFQKESRIMKNEIQ--DLQTKMRRRKA 588

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 49.6 bits (117), Expect = 4e-06
 Identities = 13/108 (12%), Positives = 48/108 (44%), Gaps = 1/108 (0%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ-IPQ 731
           +   +  Q  +  Q   + ++  +    Q    L ++++++   + +    Q   + + +
Sbjct: 449 EEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHE 508

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           +Q+++   ++Q+++  Q   +Q   +M+  +     +Q++ L+   Q 
Sbjct: 509 MQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQE 556

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 47.6 bits (112), Expect = 2e-05
 Identities = 12/109 (11%), Positives = 49/109 (44%), Gaps = 2/109 (1%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 730
              +  +  ++ ++  Q ++  Q   + +      + Q  Q L + +++I   + + +  
Sbjct: 440 LQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESA 499

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           Q   + + ++Q++ +  Q+ +Q++    +  +QL +  +  ++   ++ 
Sbjct: 500 QASAKMLHEMQRKNE--QMMEQKERSYQEHLKQLTEKMENDRVQLLKEQ 546

>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP hydrolysis, GDP, GMP, dynamin related, large GTPase family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens} SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A* 2bc9_A* 2d4h_A* Length = 592

 Score = 45.3 bits (106), Expect = 6e-05
 Identities = 22/166 (13%), Positives = 57/166 (34%), Gaps = 5/166 (3%)

Query: 618 VFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLL---SVSDKAC-RLIGMLFPGDMVVFKPQ 673
           VF   +        Q K+L A ++             S   C  L+ ++F       K  
Sbjct: 367 VFIRSSFKDVDHLFQ-KELAAQLEKKRDDFCKQNQEASSDRCSGLLQVIFSPLEEEVKAG 425

Query: 674 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 733
           I S+        Q+ Q  ++   +   + +   +  Q  L   +     + Q  Q    +
Sbjct: 426 IYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEK 485

Query: 734 QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           ++ +   + + +  Q   +      ++ +Q+ + +++      +Q+
Sbjct: 486 EKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQL 531

>3ghg_C Fibrinogen gamma chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 1deq_C Length = 411

 Score = 53.0 bits (127), Expect = 3e-07
 Identities = 19/137 (13%), Positives = 46/137 (33%), Gaps = 9/137 (6%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQ-QQQLPQLQQQIPQLQQQQQ------ 728
           S  Q ++ +  Q  +    Q + +  ++ QL +  Q      +   P +           
Sbjct: 30  STYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKM 89

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGY 788
           + ++ +     L     +  LQ+       Q+   L +   Q + +Q Q+     +    
Sbjct: 90  LEEIMKYEASILTHDSSIRYLQEIYNS-NNQKIVNLKEKVAQLE-AQCQEPCKDTVQIHD 147

Query: 789 VQGPGRTQLVSQGQVSS 805
           + G     + ++G   S
Sbjct: 148 ITGKDCQDIANKGAKQS 164

>3ghg_C Fibrinogen gamma chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 1deq_C Length = 411

 Score = 46.0 bits (109), Expect = 4e-05
 Identities = 12/111 (10%), Positives = 37/111 (33%), Gaps = 12/111 (10%)

Query: 670 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQ---QLSQLQQQQQQLPQLQQQI-PQLQQ 725
               + S +    Q + +  + +Q+   +Q       S             +++  ++ +
Sbjct: 36  VDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKMLEEIMK 95

Query: 726 QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 776
            +        S+  LQ+          Q++  ++++      Q + Q  +P
Sbjct: 96  YEASILTHDSSIRYLQEIYN----SNNQKIVNLKEKVA----QLEAQCQEP 138

>3ghg_C Fibrinogen gamma chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 1deq_C Length = 411

 Score = 45.3 bits (107), Expect = 6e-05
 Identities = 10/80 (12%), Positives = 31/80 (38%), Gaps = 3/80 (3%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQ 728
             + +      L+ ++  ++  + ++ +     S ++  Q+      Q+I  L+++  Q 
Sbjct: 73  SSKPNMIDAATLKSRKMLEEIMKYEASILTHD-SSIRYLQEIYNSNNQKIVNLKEKVAQL 131

Query: 729 IPQLQQQSMPQLQQQQQLPQ 748
             Q Q+     +Q      +
Sbjct: 132 EAQCQEPCKDTVQIHDITGK 151

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B* Length = 464

 Score = 51.9 bits (124), Expect = 5e-07
 Identities = 13/113 (11%), Positives = 33/113 (29%), Gaps = 5/113 (4%)

Query: 670 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 729
            KP +   + +  +         Q  + + ++    L + Q+Q       + +   + ++
Sbjct: 98  VKPVLRDLKDRVAKFSDTSTTMYQYVNMIDNK----LVKTQKQRKDNDIILSEYNTEMEL 153

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGS 782
                +          L  L+        ++ Q+L      Q        V S
Sbjct: 154 HYNYIKDNLDNNIPSSLRVLRAVIDS-LHKKIQKLENAIATQTDYCRSPCVAS 205

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B* Length = 464

 Score = 49.2 bits (117), Expect = 3e-06
 Identities = 10/104 (9%), Positives = 27/104 (25%), Gaps = 5/104 (4%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
             S+   Q +     +    Q Q +     LS+   + +      +          +  L
Sbjct: 114 DTSTTMYQYVNMIDNKLVKTQKQRKDNDIILSEYNTEMELHYNYIKDNLDNNIPSSLRVL 173

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 776
           +       ++ Q+L     +  +       + P +         
Sbjct: 174 RAVIDSLHKKIQKL-----ENAIATQTDYCRSPCVASCNIPVVS 212

>1m1j_B Fibrinogen beta chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_B* Length = 464

 Score = 46.2 bits (109), Expect = 3e-05
 Identities = 7/84 (8%), Positives = 24/84 (28%), Gaps = 4/84 (4%)

Query: 678 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQ----LQQQIPQLQQQQQIPQLQ 733
            + Q Q++       +  ++++             +P     L+  I  L ++ Q  +  
Sbjct: 131 VKTQKQRKDNDIILSEYNTEMELHYNYIKDNLDNNIPSSLRVLRAVIDSLHKKIQKLENA 190

Query: 734 QQSMPQLQQQQQLPQLQQQQQLPQ 757
             +     +   +          +
Sbjct: 191 IATQTDYCRSPCVASCNIPVVSGR 214

>1bg1_A Protein (transcription factor STAT3B); protein-DNA complex, cytokine activation, complex (transcription factor/DNA), transcription/DNA complex; HET: DNA PTR; 2.25A {Mus musculus} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 3cwg_A Length = 596

 Score = 50.6 bits (120), Expect = 2e-06
 Identities = 18/106 (16%), Positives = 47/106 (44%), Gaps = 6/106 (5%)

Query: 673 QISSQQQQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQ--QQQLPQLQQQIPQLQQQQQ 728
           Q   Q+ + ++  Q      ++ ++SQ   Q L+   Q   +Q++ QL+Q +  L Q ++
Sbjct: 30  QDLEQKMKVVENLQDDFDFNYKTLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRR 89

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLS 774
              +  +    L   + + +    ++L   +++QQ+  +     + 
Sbjct: 90  --SIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIACIGGPPNIC 133

>1bg1_A Protein (transcription factor STAT3B); protein-DNA complex, cytokine activation, complex (transcription factor/DNA), transcription/DNA complex; HET: DNA PTR; 2.25A {Mus musculus} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 3cwg_A Length = 596

 Score = 49.5 bits (117), Expect = 4e-06
 Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 9/97 (9%)

Query: 678 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQIPQLQQQ 735
             + L+ Q   Q        +  Q++ QL+Q    L Q+++ I          +  +Q+ 
Sbjct: 49  NYKTLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKT 108

Query: 736 SMPQLQQQQQLPQLQQQQQLP--QMQQQQQLPQLQQQ 770
                   ++L   +++QQ+          L +L+  
Sbjct: 109 -----LTDEELADWKRRQQIACIGGPPNICLDRLENW 140

>1bg1_A Protein (transcription factor STAT3B); protein-DNA complex, cytokine activation, complex (transcription factor/DNA), transcription/DNA complex; HET: DNA PTR; 2.25A {Mus musculus} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 3cwg_A Length = 596

 Score = 48.3 bits (114), Expect = 8e-06
 Identities = 18/104 (17%), Positives = 43/104 (41%), Gaps = 2/104 (1%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           Q   ++ Q L+Q+ +  ++ Q      ++ L + Q   Q L    Q + + + QQ    L
Sbjct: 23  QDVRKRVQDLEQKMKVVENLQDDFDFNYKTL-KSQGDMQDLNGNNQSVTRQKMQQLEQML 81

Query: 733 QQQSMPQLQQQQQLPQ-LQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
                 +     +L   L   + + +    ++L   +++QQ++ 
Sbjct: 82  TALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKRRQQIAC 125

>1bg1_A Protein (transcription factor STAT3B); protein-DNA complex, cytokine activation, complex (transcription factor/DNA), transcription/DNA complex; HET: DNA PTR; 2.25A {Mus musculus} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 3cwg_A Length = 596

 Score = 47.2 bits (111), Expect = 2e-05
 Identities = 16/105 (15%), Positives = 42/105 (40%), Gaps = 2/105 (1%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
            + SQ   Q      Q   +Q   QL+    +  Q ++  + +L   +  ++  Q+   L
Sbjct: 52  TLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQK--TL 109

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
             + +   +++QQ+  +     +   + +  +  L + Q  ++ Q
Sbjct: 110 TDEELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQ 154

>1bg1_A Protein (transcription factor STAT3B); protein-DNA complex, cytokine activation, complex (transcription factor/DNA), transcription/DNA complex; HET: DNA PTR; 2.25A {Mus musculus} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 3cwg_A Length = 596

 Score = 47.2 bits (111), Expect = 2e-05
 Identities = 16/94 (17%), Positives = 37/94 (39%)

Query: 686 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 745
           Q       + ++ Q      LQ  ++++  L+Q++  ++  Q       +++      Q 
Sbjct: 2   QANHPTAAVVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGDMQD 61

Query: 746 LPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           L    Q     +MQQ +Q+     Q + S   ++
Sbjct: 62  LNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSEL 95

>1bg1_A Protein (transcription factor STAT3B); protein-DNA complex, cytokine activation, complex (transcription factor/DNA), transcription/DNA complex; HET: DNA PTR; 2.25A {Mus musculus} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 3cwg_A Length = 596

 Score = 46.8 bits (110), Expect = 3e-05
 Identities = 18/120 (15%), Positives = 46/120 (38%), Gaps = 12/120 (10%)

Query: 672 PQISSQQQQQLQQQQQQ-QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQI-----PQLQQ 725
             ++   Q   +Q+ QQ +Q      Q++   +S+L      +  +Q+ +        ++
Sbjct: 60  QDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKR 119

Query: 726 QQQIPQLQQQSMPQLQQQQQLPQL------QQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           +QQI  +       L + +           Q +QQ+ ++++ QQ    +    +     +
Sbjct: 120 RQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPIVQHRPML 179

>1bg1_A Protein (transcription factor STAT3B); protein-DNA complex, cytokine activation, complex (transcription factor/DNA), transcription/DNA complex; HET: DNA PTR; 2.25A {Mus musculus} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 3cwg_A Length = 596

 Score = 46.8 bits (110), Expect = 3e-05
 Identities = 22/133 (16%), Positives = 49/133 (36%), Gaps = 20/133 (15%)

Query: 670 FKPQISSQQQQQLQQQQQQQQHQQMQS------QLQHQQLSQLQQQQQQLPQLQQQI--- 720
            K Q   Q      Q   +Q+ QQ++       Q++   +S+L      +  +Q+ +   
Sbjct: 53  LKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDE 112

Query: 721 --PQLQQQQQIPQLQQQSMPQLQQQQQ--------LPQLQQQ-QQLPQMQQQQQLPQLQQ 769
                +++QQI  +       L + +           Q +QQ ++L ++QQ+        
Sbjct: 113 ELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPI 172

Query: 770 QQQLSQPQQMVGS 782
            Q     ++ +  
Sbjct: 173 VQHRPMLEERIVE 185

>1uur_A Stata protein, STAT protein; transcription activator, SH2, signal transduction, transducer, transcription factor; HET: PTR; 2.7A {Dictyostelium discoideum} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 1uus_A* Length = 473

 Score = 49.2 bits (116), Expect = 4e-06
 Identities = 22/109 (20%), Positives = 37/109 (33%), Gaps = 4/109 (3%)

Query: 673 QISSQQQQQLQQ--QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ-QQI 729
           ++ S+Q+Q L Q   +Q     ++   L    L+ L+   Q+   L  Q+          
Sbjct: 19  KLLSEQEQTLVQMIHEQSLLLNRLPPTLDENSLAPLKSLSQKQITLSGQMNTEMSALDAT 78

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
            +        L +   L Q   Q Q  Q+       Q     Q S P+ 
Sbjct: 79  KKGMILEPTDLAKLFALKQ-DLQIQFKQLSLLHNEIQSILNPQHSAPKP 126

>1uur_A Stata protein, STAT protein; transcription activator, SH2, signal transduction, transducer, transcription factor; HET: PTR; 2.7A {Dictyostelium discoideum} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 1uus_A* Length = 473

 Score = 48.8 bits (115), Expect = 5e-06
 Identities = 18/104 (17%), Positives = 31/104 (29%), Gaps = 3/104 (2%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           Q    L   Q            Q Q L Q+  +Q  L               +  L Q+ 
Sbjct: 2   QGNPNLSSPQPILDTIYKLLSEQEQTLVQMIHEQSLLLNRLPPTLDENSLAPLKSLSQKQ 61

Query: 737 MPQLQQ-QQQLPQLQQ--QQQLPQMQQQQQLPQLQQQQQLSQPQ 777
           +    Q   ++  L    +  + +     +L  L+Q  Q+   Q
Sbjct: 62  ITLSGQMNTEMSALDATKKGMILEPTDLAKLFALKQDLQIQFKQ 105

>1uur_A Stata protein, STAT protein; transcription activator, SH2, signal transduction, transducer, transcription factor; HET: PTR; 2.7A {Dictyostelium discoideum} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 1uus_A* Length = 473

 Score = 47.3 bits (111), Expect = 2e-05
 Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 2/109 (1%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ-- 728
            P +SS Q       +   + +Q   Q+ H+Q   L +    L +      +   Q+Q  
Sbjct: 4   NPNLSSPQPILDTIYKLLSEQEQTLVQMIHEQSLLLNRLPPTLDENSLAPLKSLSQKQIT 63

Query: 729 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
           +       M  L   ++   L+          +Q L    +Q  L   +
Sbjct: 64  LSGQMNTEMSALDATKKGMILEPTDLAKLFALKQDLQIQFKQLSLLHNE 112

>1uur_A Stata protein, STAT protein; transcription activator, SH2, signal transduction, transducer, transcription factor; HET: PTR; 2.7A {Dictyostelium discoideum} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 PDB: 1uus_A* Length = 473

 Score = 41.9 bits (97), Expect = 7e-04
 Identities = 15/97 (15%), Positives = 30/97 (30%), Gaps = 9/97 (9%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ---- 726
            P +       L+   Q+Q     Q   +   L   ++     P    ++  L+Q     
Sbjct: 43  PPTLDENSLAPLKSLSQKQITLSGQMNTEMSALDATKKGMILEPTDLAKLFALKQDLQIQ 102

Query: 727 -QQIPQLQQQSMPQLQQQQQLPQLQQ----QQQLPQM 758
            +Q+  L  +    L  Q   P+       + Q   +
Sbjct: 103 FKQLSLLHNEIQSILNPQHSAPKPNVALVLKSQPFPV 139

>2es4_D Lipase chaperone; protein-protein complex, steric chaperone, triacylglycerol hydrolase, all alpha helix protein, A/B hydrolase fold; 1.85A {Burkholderia glumae} SCOP: a.137.15.1 Length = 332

 Score = 48.6 bits (115), Expect = 4e-06
 Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 6/115 (5%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 730
           K    +    QL   ++ QQ      Q    +++ LQ+      Q++ QI Q    +   
Sbjct: 208 KAARLAALDAQLTPDERAQQAALHAQQDAVTKIADLQKAGATPDQMRAQIAQTLGPEAAA 267

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQ------LPQMQQQQQLPQLQQQQQLSQPQQM 779
           +  Q        Q +      ++       L    +  ++ QL+QQ   +  + +
Sbjct: 268 RAAQMQQDDEAWQTRYQAYAAERDRIAAQGLAPQDRDARIAQLRQQTFTAPGEAI 322

>2es4_D Lipase chaperone; protein-protein complex, steric chaperone, triacylglycerol hydrolase, all alpha helix protein, A/B hydrolase fold; 1.85A {Burkholderia glumae} SCOP: a.137.15.1 Length = 332

 Score = 44.4 bits (104), Expect = 1e-04
 Identities = 15/103 (14%), Positives = 31/103 (30%), Gaps = 12/103 (11%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQ---------LQQQQQQLPQLQQQIPQLQQQ 726
              QQ    +    Q           Q++Q           Q QQ     Q +      +
Sbjct: 230 LHAQQDAVTKIADLQKAGATPDQMRAQIAQTLGPEAAARAAQMQQDDEAWQTRYQAYAAE 289

Query: 727 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQ 769
           +   ++  Q +    +  ++ QL+QQ       +  +   L +
Sbjct: 290 RD--RIAAQGLAPQDRDARIAQLRQQT-FTAPGEAIRAASLDR 329

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus} Length = 189

 Score = 46.3 bits (109), Expect = 8e-06
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQHQQL-SQLQQQQQQLPQLQQQIPQLQQQQQ--IPQ 731
           S + +Q  Q+ + +    Q  S+    +L +QL Q +Q+   LQ    +L+ + +    +
Sbjct: 19  SMKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKEK 78

Query: 732 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
           L+ Q     +Q   L     Q +  + Q  + + +L+Q   
Sbjct: 79  LEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQAND 119

>3ibp_A Chromosome partition protein MUKB; structural maintenance of chromosomes, SMC, condensin, chromosome segregation, hinge, dimerization domain; 3.10A {Escherichia coli} Length = 302

 Score = 47.4 bits (112), Expect = 8e-06
 Identities = 20/107 (18%), Positives = 45/107 (42%), Gaps = 4/107 (3%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
            I+S        ++++   +Q Q QLQ  ++  L Q+       Q  + QL +Q      
Sbjct: 4   MIASLSDSVSNAREERMALRQEQEQLQ-SRIQSLMQRAPVWLAAQNSLNQLSEQCGEEFT 62

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ-QQLSQPQQ 778
             Q + +  QQ    + +   +  ++  ++    + ++ ++LSQP  
Sbjct: 63  SSQDVTEYLQQLLEREREAIVERDEVGARKN--AVDEEIERLSQPGG 107

>3ibp_A Chromosome partition protein MUKB; structural maintenance of chromosomes, SMC, condensin, chromosome segregation, hinge, dimerization domain; 3.10A {Escherichia coli} Length = 302

 Score = 45.9 bits (108), Expect = 3e-05
 Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 7/98 (7%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ-QQQIPQLQQ 734
           S     L       + ++M   L+ +Q    +Q Q ++  L Q+ P     Q  + QL +
Sbjct: 2   SHMIASLSDSVSNAREERMA--LRQEQ----EQLQSRIQSLMQRAPVWLAAQNSLNQLSE 55

Query: 735 QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
           Q   +    Q + +  QQ    + +   +  ++  ++ 
Sbjct: 56  QCGEEFTSSQDVTEYLQQLLEREREAIVERDEVGARKN 93

>3ibp_A Chromosome partition protein MUKB; structural maintenance of chromosomes, SMC, condensin, chromosome segregation, hinge, dimerization domain; 3.10A {Escherichia coli} Length = 302

 Score = 43.2 bits (101), Expect = 2e-04
 Identities = 17/103 (16%), Positives = 42/103 (40%), Gaps = 4/103 (3%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQ-LQQQQQIPQLQQ 734
           S  +++    +Q+Q+  Q + Q   Q+       Q  L QL +Q  +     Q + +  Q
Sbjct: 13  SNAREERMALRQEQEQLQSRIQSLMQRAPVWLAAQNSLNQLSEQCGEEFTSSQDVTEYLQ 72

Query: 735 QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
           Q    L+++++    + +    +    +++ +L Q       +
Sbjct: 73  Q---LLEREREAIVERDEVGARKNAVDEEIERLSQPGGSEDQR 112

>1bf5_A Signal transducer and activator of transcription 1-alpha/beta; complex (SH2 domain/DNA), SH2 domain, transcription factor; HET: DNA PTR; 2.90A {Homo sapiens} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 Length = 575

 Score = 47.9 bits (113), Expect = 1e-05
 Identities = 10/110 (9%), Positives = 37/110 (33%), Gaps = 17/110 (15%)

Query: 683 QQQQQQQQHQQMQSQLQH--QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQL 740
           +Q++   + + ++ ++     ++  L+  Q +     + +   + +        Q   QL
Sbjct: 3   KQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQL 62

Query: 741 QQQQQLPQLQQQ---------------QQLPQMQQQQQLPQLQQQQQLSQ 775
             ++    L  +               +         +L + +++QQ + 
Sbjct: 63  LLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSAC 112

>1bf5_A Signal transducer and activator of transcription 1-alpha/beta; complex (SH2 domain/DNA), SH2 domain, transcription factor; HET: DNA PTR; 2.90A {Homo sapiens} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 Length = 575

 Score = 47.6 bits (112), Expect = 1e-05
 Identities = 16/115 (13%), Positives = 44/115 (38%), Gaps = 8/115 (6%)

Query: 671 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQ--------QQQQLPQLQQQIPQ 722
             +  +    +  Q+Q+Q   ++M   L +++   + +        +  Q   +  ++ +
Sbjct: 44  NREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVE 103

Query: 723 LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 777
            +++QQ   +       L Q Q    +  +      QQ ++L +L+Q+       
Sbjct: 104 WKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDP 158

>1bf5_A Signal transducer and activator of transcription 1-alpha/beta; complex (SH2 domain/DNA), SH2 domain, transcription factor; HET: DNA PTR; 2.90A {Homo sapiens} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 Length = 575

 Score = 47.6 bits (112), Expect = 1e-05
 Identities = 17/122 (13%), Positives = 45/122 (36%), Gaps = 14/122 (11%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQ-----QQQQLPQLQQQIPQLQQQQQI 729
              +  Q Q+Q   ++   M    + + + ++ +     +  Q   +  ++ + +++QQ 
Sbjct: 51  GVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQS 110

Query: 730 PQLQQQSMPQLQQQQ--------QLPQLQQQ-QQLPQMQQQQQLPQLQQQQQLSQPQQMV 780
             +       L Q Q         L Q++QQ ++L +++Q+         +         
Sbjct: 111 ACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRT 170

Query: 781 GS 782
            S
Sbjct: 171 FS 172

>1bf5_A Signal transducer and activator of transcription 1-alpha/beta; complex (SH2 domain/DNA), SH2 domain, transcription factor; HET: DNA PTR; 2.90A {Homo sapiens} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 Length = 575

 Score = 46.0 bits (108), Expect = 4e-05
 Identities = 14/110 (12%), Positives = 40/110 (36%), Gaps = 6/110 (5%)

Query: 673 QISSQQQQQLQQQQQ--QQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 730
                + + L+  Q     + + +Q++           Q+Q+   L++    L  +++  
Sbjct: 19  MCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRK-- 76

Query: 731 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQL--QQQQQLSQPQQ 778
           ++  + +  L   +         +L + +++QQ   +       L Q Q 
Sbjct: 77  EVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQN 126

>1bf5_A Signal transducer and activator of transcription 1-alpha/beta; complex (SH2 domain/DNA), SH2 domain, transcription factor; HET: DNA PTR; 2.90A {Homo sapiens} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 Length = 575

 Score = 45.6 bits (107), Expect = 5e-05
 Identities = 15/105 (14%), Positives = 41/105 (39%), Gaps = 4/105 (3%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
           Q ++       +   +Q Q  L+   L    ++++ + ++ + +   +  Q    L    
Sbjct: 43  QNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQN--ALINDE 100

Query: 737 MPQLQQQQQLPQL--QQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
           + + +++QQ   +       L Q+Q    +     QQ   Q +++
Sbjct: 101 LVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKL 145

>1bf5_A Signal transducer and activator of transcription 1-alpha/beta; complex (SH2 domain/DNA), SH2 domain, transcription factor; HET: DNA PTR; 2.90A {Homo sapiens} SCOP: a.47.1.1 b.2.5.5 d.93.1.1 Length = 575

 Score = 45.2 bits (106), Expect = 7e-05
 Identities = 16/109 (14%), Positives = 42/109 (38%), Gaps = 10/109 (9%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           +I S +  Q +   + +  Q  + +      S  +Q+Q  L ++   +    +++++   
Sbjct: 24  EIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLML--DNKRKEVVHK 81

Query: 733 QQQSMPQLQQQQ------QLPQLQQQQQLPQ--MQQQQQLPQLQQQQQL 773
             + +   +  Q      +L + +++QQ           L QLQ    +
Sbjct: 82  IIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTI 130

>1lwu_C Fibrinogen gamma chain; heterotrimer, protein-peptide complex, blood clotting; HET: NDG MAN NAG BMA GAL; 2.80A {Petromyzon marinus} SCOP: d.171.1.1 h.1.8.1 PDB: 1n73_C* Length = 323

 Score = 46.3 bits (110), Expect = 2e-05
 Identities = 11/74 (14%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 736
             Q+ +Q+  ++ +  +        Q+ +L +  +     QQ + +LQQQ    +     
Sbjct: 2   SGQKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVN---QQFVTRLQQQLVDIRQTCSR 58

Query: 737 MPQLQQQQQLPQLQ 750
             Q     ++  + 
Sbjct: 59  PCQDTTANKISPIT 72

>1lwu_C Fibrinogen gamma chain; heterotrimer, protein-peptide complex, blood clotting; HET: NDG MAN NAG BMA GAL; 2.80A {Petromyzon marinus} SCOP: d.171.1.1 h.1.8.1 PDB: 1n73_C* Length = 323

 Score = 45.2 bits (107), Expect = 6e-05
 Identities = 12/74 (16%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 686 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 745
             Q+  Q++  +++  +         Q+ +L +       QQ + +LQQQ +   Q   +
Sbjct: 2   SGQKTVQKILEEVRILE-QIGVSHDAQIQELSEMW--RVNQQFVTRLQQQLVDIRQTCSR 58

Query: 746 LPQLQQQQQLPQMQ 759
             Q     ++  + 
Sbjct: 59  PCQDTTANKISPIT 72

>1y1u_A Signal transducer and activator of transcription; STAT, DNA-binding, SH2 domain, transcription REGU signaling protein; 3.21A {Mus musculus} Length = 585

 Score = 46.3 bits (109), Expect = 4e-05
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 1/101 (0%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ-QQIPQLQQ 734
               Q+  Q  Q+ +  ++ +Q    +L +LQQ Q+      Q+  ++Q Q  Q+ QL  
Sbjct: 8   DAMSQKHLQINQRFEELRLITQDTENELKKLQQTQEYFIIQYQESLRIQAQFAQLGQLNP 67

Query: 735 QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
           Q     +   Q  Q+  +  L +  Q  Q  +++  ++  +
Sbjct: 68  QERMSRETALQQKQVSLETWLQREAQTLQQYRVELAEKHQK 108

>1y1u_A Signal transducer and activator of transcription; STAT, DNA-binding, SH2 domain, transcription REGU signaling protein; 3.21A {Mus musculus} Length = 585

 Score = 45.2 bits (106), Expect = 8e-05
 Identities = 23/112 (20%), Positives = 45/112 (40%), Gaps = 2/112 (1%)

Query: 666 DMVVFKPQISSQQQQQLQQ--QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL 723
           +  + + Q S + Q Q  Q  Q   Q+    ++ LQ +Q+S     Q++   LQQ   +L
Sbjct: 43  EYFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLETWLQREAQTLQQYRVEL 102

Query: 724 QQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
            ++ Q      +    +    +L Q +++QQL       +      Q    +
Sbjct: 103 AEKHQKTLQLLRKQQTIILDDELIQWKRRQQLAGNGGPPEGSLDVLQSWCEK 154

>1y1u_A Signal transducer and activator of transcription; STAT, DNA-binding, SH2 domain, transcription REGU signaling protein; 3.21A {Mus musculus} Length = 585

 Score = 44.4 bits (104), Expect = 1e-04
 Identities = 21/105 (20%), Positives = 40/105 (38%), Gaps = 1/105 (0%)

Query: 682 LQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQ 741
           +      Q+H Q+  + +  +L   Q  + +L +LQQ       Q Q     Q    QL 
Sbjct: 5   VLVDAMSQKHLQINQRFEELRL-ITQDTENELKKLQQTQEYFIIQYQESLRIQAQFAQLG 63

Query: 742 QQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQ 786
           Q     ++ ++  L Q Q   +    ++ Q L Q +  +     +
Sbjct: 64  QLNPQERMSRETALQQKQVSLETWLQREAQTLQQYRVELAEKHQK 108

>1y1u_A Signal transducer and activator of transcription; STAT, DNA-binding, SH2 domain, transcription REGU signaling protein; 3.21A {Mus musculus} Length = 585

 Score = 43.7 bits (102), Expect = 2e-04
 Identities = 26/107 (24%), Positives = 48/107 (44%), Gaps = 2/107 (1%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
           Q +  + ++LQQ Q+    Q  +S     Q +QL Q   Q  +   +   LQQ+Q   + 
Sbjct: 29  QDTENELKKLQQTQEYFIIQYQESLRIQAQFAQLGQLNPQ--ERMSRETALQQKQVSLET 86

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
             Q   Q  QQ ++   ++ Q+  Q+ ++QQ   L  +    + +Q 
Sbjct: 87  WLQREAQTLQQYRVELAEKHQKTLQLLRKQQTIILDDELIQWKRRQQ 133

>1y1u_A Signal transducer and activator of transcription; STAT, DNA-binding, SH2 domain, transcription REGU signaling protein; 3.21A {Mus musculus} Length = 585

 Score = 43.7 bits (102), Expect = 2e-04
 Identities = 22/119 (18%), Positives = 46/119 (38%), Gaps = 15/119 (12%)

Query: 675 SSQQQQQLQQQQQQQQHQQMQSQLQH--QQLSQLQQ-------------QQQQLPQLQQQ 719
            + Q++  ++   QQ+   +++ LQ   Q L Q +              ++QQ   L  +
Sbjct: 65  LNPQERMSRETALQQKQVSLETWLQREAQTLQQYRVELAEKHQKTLQLLRKQQTIILDDE 124

Query: 720 IPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           + Q +++QQ+          L   Q   +   +      QQ ++   L QQ  +  P +
Sbjct: 125 LIQWKRRQQLAGNGGPPEGSLDVLQSWCEKLAEIIWQNRQQIRRAEHLCQQLPIPGPVE 183

>1y1u_A Signal transducer and activator of transcription; STAT, DNA-binding, SH2 domain, transcription REGU signaling protein; 3.21A {Mus musculus} Length = 585

 Score = 42.5 bits (99), Expect = 5e-04
 Identities = 26/124 (20%), Positives = 56/124 (45%), Gaps = 12/124 (9%)

Query: 673 QISSQQQQQLQQQQQQQQH--------QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 724
            I+   + +L++ QQ Q++         ++Q+Q         Q++  +   LQQ+   L+
Sbjct: 26  LITQDTENELKKLQQTQEYFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLE 85

Query: 725 Q--QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGS 782
              Q++   LQQ  +   ++ Q+  QL ++QQ   +    +L Q +++QQL+        
Sbjct: 86  TWLQREAQTLQQYRVELAEKHQKTLQLLRKQQ--TIILDDELIQWKRRQQLAGNGGPPEG 143

Query: 783 GMGQ 786
            +  
Sbjct: 144 SLDV 147

>1m1j_C Fibrinogen gamma chain; coiled coils, disulfide rings, fibrinogen, blood clotting; HET: NDG NAG; 2.70A {Gallus gallus} SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_C Length = 409

 Score = 44.1 bits (104), Expect = 1e-04
 Identities = 11/83 (13%), Positives = 24/83 (28%), Gaps = 2/83 (2%)

Query: 676 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 735
             ++Q L Q  +Q   +    ++  + +            +QQ               +Q
Sbjct: 69  PSEKQTLPQSIEQLTQK--SKKIIEEIIRYENTILAHENTIQQLTDMHIMNSNKITQLKQ 126

Query: 736 SMPQLQQQQQLPQLQQQQQLPQM 758
            + QL+   Q P     +     
Sbjct: 127 KIAQLESHCQEPCKDTAEIQETT 149

>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184

 Score = 44.4 bits (105), Expect = 1e-04
 Identities = 15/101 (14%), Positives = 49/101 (48%), Gaps = 6/101 (5%)

Query: 675  SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 734
            +   + + Q  +++++ Q   ++L+ +  SQ     +++ +L+  I  LQ+  +    ++
Sbjct: 1081 AQIAELKAQLAKKEEELQAALARLEDET-SQKNNALKKIRELESHISDLQEDLES---EK 1136

Query: 735  QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
             +  + ++Q++   L ++ +  + + +  L     QQ+L  
Sbjct: 1137 AARNKAEKQKR--DLSEELEALKTELEDTLDTTATQQELRG 1175

>3c8j_A Natural killer cell receptor LY49C; MHC, virus, immune system; 2.60A {Mus musculus} SCOP: d.169.1.1 PDB: 3c8k_D 1p4l_D 1ja3_A 1p1z_D Length = 203

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 9/68 (13%), Positives = 19/68 (27%), Gaps = 1/68 (1%)

Query: 686 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 745
           Q  Q  Q+    L H   S +Q+      ++      +  +     L+     Q  +   
Sbjct: 7   QYNQHKQETNETLNHHNCSNMQRAFNLKEEMLTNK-SIDCRPSNETLEYIKGEQHDRWDS 65

Query: 746 LPQLQQQQ 753
             +     
Sbjct: 66  KTKTVLDS 73

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens} Length = 168

 Score = 42.0 bits (98), Expect = 2e-04
 Identities = 8/110 (7%), Positives = 38/110 (34%), Gaps = 3/110 (2%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQL---SQLQQQQQQLPQLQQQIPQLQQQQQI 729
           Q+         +     + ++  +++        S  ++ Q++   L+    Q  +    
Sbjct: 14  QLEEANDLLRTESDTAVRLRKSHTEMSKSISQLESLNRELQERNRILENSKSQTDKDYYQ 73

Query: 730 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
            Q   ++  + +          Q ++  +Q++ +  +   ++   + ++ 
Sbjct: 74  LQAILEAERRDRGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEA 123

>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets, alpha helices, AMY amyloidosis, blood coagulation, disease mutation, glycoprot phosphoprotein; HET: NAG NDG BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A* 2a45_G* Length = 562

 Score = 43.7 bits (102), Expect = 2e-04
 Identities = 38/202 (18%), Positives = 67/202 (33%), Gaps = 4/202 (1%)

Query: 342 MAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPT 401
           +         L ++ Q R  +        T  G  S G         N  S+G  +S  +
Sbjct: 222 LQKVPPEWKALTDMPQMRMELERPGGNEITRGGSTSYGTGSETESPRNPSSAGSWNSGSS 281

Query: 402 SQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQG 461
                 +   G +  GG+ T    S  P ++G  +  S+ +  +GN NP   +P  T  G
Sbjct: 282 GPGSTGNRNPGSSGTGGTATWKPGSSGPGSTGSWNSGSSGTGSTGNQNPGSPRPGST--G 339

Query: 462 GASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSG 521
             + G S   S G+ +      +G +   +  SG      S G+G   P        +  
Sbjct: 340 TWNPGSSERGSAGHWTSES-SVSGSTGQWHSESGSFRPD-SPGSGNARPNNPDWGTFEEV 397

Query: 522 MQPLSVNNNTAVNMQLSQQTSS 543
              +S       + +    +  
Sbjct: 398 SGNVSPGTRREYHTEKLVTSKG 419

>3ajw_A Flagellar FLIJ protein; flagellum, type III secretion, coiled-coil, protein transpor; 2.10A {Salmonella typhimurium} Length = 150

 Score = 41.0 bits (96), Expect = 3e-04
 Identities = 16/108 (14%), Positives = 37/108 (34%), Gaps = 9/108 (8%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
            ++     +  +   +++       L   +    QQ ++QL  L     + +        
Sbjct: 3   HMAQHGALETLKDLAEKEVDDAARLLGEMR-RGCQQAEEQLKMLIDYQNEYRSNLNTDMG 61

Query: 733 QQQSMPQLQQQQQ-LPQL-----QQQQQLPQMQQQ--QQLPQLQQQQQ 772
              +  +    QQ +  L     Q + QL Q  Q+    L   ++++Q
Sbjct: 62  NGIASNRWINYQQFIQTLEKAIEQHRLQLTQWTQKVDLALKSWREKKQ 109

>1vt0_M Portal protein, protein GP1; portal protein, DNA ejection, molecular motor, DNA packaging podoviridae; 3.25A {Enterobacteria phage P22} PDB: 3lj4_A Length = 602

 Score = 43.1 bits (100), Expect = 4e-04
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 704 SQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ 763
           S  QQ + ++ +L  + PQ   + Q+  LQ  ++   +  + +     +Q +    ++ +
Sbjct: 526 SMKQQNRAEILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPE 585

Query: 764 LPQLQQQQQLSQPQQMV 780
            P+  +QQ L + QQ  
Sbjct: 586 TPE--EQQWLVEAQQAK 600

>1jad_A PLC-beta, phospholipase C beta; alpha helical coiled coil, hydrolase; 2.40A {Meleagris gallopavo} SCOP: h.4.10.1 Length = 251

 Score = 41.7 bits (97), Expect = 5e-04
 Identities = 8/100 (8%), Positives = 40/100 (40%), Gaps = 4/100 (4%)

Query: 677 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQ----LQQQIPQLQQQQQIPQL 732
            ++Q+ + ++ +++  + + +L  +      +           ++ +     +   + + 
Sbjct: 34  LKKQEKELKELERKGSKRREELLQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEE 93

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
               + + ++Q    Q  +  +L + +Q  +L  L++  +
Sbjct: 94  YHDGIRRRKEQHATEQTAKITELAREKQIAELKALKESSE 133

>2h8n_A HD4, histone deacetylase 4; alpha helix, polar zipper, transcription; 2.60A {Homo sapiens} PDB: 2o94_A Length = 112

 Score = 39.4 bits (91), Expect = 6e-04
 Identities = 27/103 (26%), Positives = 53/103 (51%), Gaps = 4/103 (3%)

Query: 662 LFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIP 721
           L P    + +P +  QQ QQ  +    +Q QQ+Q Q+   +    +Q +Q   Q + Q+ 
Sbjct: 13  LVPRGSHMAEPALREQQLQQ--ELLALKQKQQIQRQILIAEFQ--RQHEQLSRQHEAQLH 68

Query: 722 QLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 764
           +  +QQQ     +     L+ Q++L + +Q+Q+L +  ++Q+L
Sbjct: 69  EHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 111

>4dci_A Uncharacterized protein; PSI-biology, midwest center for structural genomics, MCSG, S genomics, unknown function; 2.82A {Synechococcus SP} Length = 150

 Score = 40.0 bits (93), Expect = 6e-04
 Identities = 21/101 (20%), Positives = 43/101 (42%), Gaps = 4/101 (3%)

Query: 668 VVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ 727
            V  P    + ++++         Q  Q + + Q +    ++Q   P   +   Q+   Q
Sbjct: 20  AVVTPTWKEEAEREISNGIANADQQLAQLEQEGQTVVDQVRRQSANPLDPRVQEQVANIQ 79

Query: 728 QIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQ 768
           Q  Q+  +     +Q++ L  LQQQ Q+ +++  Q + Q Q
Sbjct: 80  Q--QVAGKRSELEEQKRNL--LQQQAQVRELEMDQIVEQGQ 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	818
2iue_A	212	Pactolus I-domain; membrane protein, CD, ITC, limb	98.17
4b4t_W	268	RPN10, 26S proteasome regulatory subunit RPN10; hy	97.66
1ijb_A	202	VON willebrand factor; dinucleotide-binding fold,	97.63
3fcs_B	690	Integrin beta-3; beta propeller, rossmann fold, EG	97.6
3k6s_B	687	Integrin beta-2; cell receptor, adhesion molecule,	97.45
1atz_A	189	VON willebrand factor; collagen-binding, hemostasi	97.44
1v7p_C	200	Integrin alpha-2; snake venom, C-type lectin, anta	97.28
2xgg_A	178	Microneme protein 2; A/I domain, cell adhesion, hy	97.27
3t3p_B	472	Integrin beta-3; integrin, cell adhesion, blood cl	97.26
3vi3_B	454	Integrin beta-1; beta propeller fold, rossman fold	97.25
2x5n_A	192	SPRPN10, 26S proteasome regulatory subunit RPN10;	97.24
3ibs_A	218	Conserved hypothetical protein BATB; structural ge	97.02
3v4v_B	503	Integrin beta-7; cell adhesion, madcam-1, membrane	96.98
2b2x_A	223	Integrin alpha-1; computational design, antibody-a	96.94
3n2n_F	185	Anthrax toxin receptor 1; rossmann fold; 1.80A {Ho	96.81
1pt6_A	213	Integrin alpha-1; cell adhesion; 1.87A {Homo sapie	96.74
1mf7_A	194	Integrin alpha M; cell adhesion; 1.25A {Homo sapie	96.64
1n3y_A	198	Integrin alpha-X; alpha/beta rossmann fold, cell a	96.55
1q0p_A	223	Complement factor B; VON willebrand factor, MAC-1,	96.23
1shu_X	182	Anthrax toxin receptor 2; alpha/beta rossmann fold	95.9
3zqk_A	199	VON willebrand factor; blood clotting, adamts-13,	95.86
4hqo_A	266	Sporozoite surface protein 2; malaria, gliding mot	95.68
2x31_A	189	Magnesium-chelatase 60 kDa subunit; ligase, bacter	95.32
1rrk_A	497	Complement factor B; BB, hydrolase; 2.00A {Homo sa	95.31
3hrz_D	741	Complement factor B; serine protease, glycosilated	95.1
4hqf_A	281	Thrombospondin-related anonymous protein, trap; ma	94.91
3k6s_A	1095	Integrin alpha-X; cell receptor, adhesion molecule	93.89
2odp_A	509	Complement C2; C3/C5 convertase, complement serin	93.35
3iot_A	449	Maltose-binding protein, huntingtin fusion protei;	93.07
1jey_B	565	KU80; double-strand DNA break repair, non-homologo	92.46
1mjn_A	179	Integrin alpha-L; rossmann fold, immune system; 1.	91.87
4fx5_A	464	VON willebrand factor type A; structural genomics,	90.31
3rag_A	242	Uncharacterized protein; structural genomics, PSI-	88.55
1jey_A	609	KU70; double-strand DNA break repair, non-homologo	87.2

>2iue_A Pactolus I-domain; membrane protein, CD, ITC, limbs, midas, admidas, membrane, integrin, titration, rossman fold, cell adhesion, transmembrane; NMR {Mus musculus}

Probab=98.17  E-value=1.9e-05  Score=80.97  Aligned_cols=155  Identities=10%  Similarity=0.072  Sum_probs=111.6

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCCh
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFND   80 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~   80 (818)
                      |+.|++.+|+-+..+++-+..        ...++.+|++.|+++     .+.....+|+|..+|..+|+++..+||+...
T Consensus        16 M~~di~~lk~~~~~l~~~l~~--------~~~~~r~Gfg~f~Dk-----~~~~~l~lT~d~~~F~~~v~~~~vsg~~D~P   82 (212)
T 2iue_A           16 AQGHLSNVQTLGSDLLKALNE--------ISRSGRIGFGSIVNM-----TFQHILKLTADSSQFQRELRKQLVSGKLATP   82 (212)
T ss_dssp             GTTTHHHHHHHHHHHHHHHHH--------HCSCEEEEEEEESSS-----CEEEEEEEESCHHHHHHHHHTCCCCCCSSSS
T ss_pred             chhHHHHHHHHHHHHHHHHHh--------hCcCceEEEEEEEcC-----cceecCCcCCCHHHHHHHHhhccccCCCCCC
Confidence            889999999888888877742        123699999999998     2456788999999999999999999999777


Q ss_pred             hhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCC----CCcCcc--cccccccchhhhhhhccCCCHH
Q 003455           81 AAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPT----PVYRPQ--MQNLDQNENNEAQAESRLSDAE  154 (818)
Q Consensus        81 ~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~----~~~~p~--~~~l~~~~~~~~~~~~~l~~~e  154 (818)
                      .+.-|||-.|+.|.+  ..+-    +. ..|.+||++..+||...=    ..+.|.  -|.|.++.-..+..+ ...+++
T Consensus        83 E~g~dal~qa~~c~~--~i~W----r~-a~rllvl~TDa~~H~~gDg~l~gi~~pnd~~chl~~g~y~~s~~~-Dyps~~  154 (212)
T 2iue_A           83 KGQLDAVVQVAICLG--EIGW----RN-GTRFLVLVTDNDFHLAKDKTLGTRQNTSDGRCHLDDGMYRSRGEP-DYQSVV  154 (212)
T ss_dssp             BCHHHHHHHHHHCHH--HHTC----CS-SEEEEEEECSSCBCCTTGGGGGTCCSCCCSSCCBSSSBBGGGGSS-CCCCHH
T ss_pred             chHHHHHHHHHHhhh--hccc----CC-ccEEEEEECcCCccccCCccccccccCCccccccCCCeeccCccc-CCCCHH
Confidence            788889999987732  0000    23 779999999999998531    122233  233332211111122 235999


Q ss_pred             HHHHHHhhcCceEEEeCCCcch
Q 003455          155 TVAKSFVQCSVSLSVICPKQLP  176 (818)
Q Consensus       155 ~la~~~~~~~I~lSiIsPrklp  176 (818)
                      ++.+.+.+++|.+-+...+...
T Consensus       155 q~~~~l~~~~i~~ifavt~~~~  176 (212)
T 2iue_A          155 QLASKLAENNIQPIFVVPSRMV  176 (212)
T ss_dssp             HHHHHHHHHTCEEEEEEEHHHH
T ss_pred             HHHHHHHhcCCcEEEEEccchh
Confidence            9999999999998888776543

>4b4t_W RPN10, 26S proteasome regulatory subunit RPN10; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.66  E-value=0.00046  Score=72.99  Aligned_cols=135  Identities=16%  Similarity=0.139  Sum_probs=95.4

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHH
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIA   84 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aia   84 (818)
                      |+..++.+.-+++.+....        .....|||+|....+    .| ...+|+|..+++..|++|+..|+    ..++
T Consensus        26 l~a~k~Av~~li~~~~~~n--------Ped~VGLVtfag~~~----~v-l~plT~D~~~il~aL~~l~~~G~----T~l~   88 (268)
T 4b4t_W           26 FEAQIDSVEFIFQAKRNSN--------PENTVGLISGAGANP----RV-LSTFTAEFGKILAGLHDTQIEGK----LHMA   88 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHC--------TTCEEEEEECCTTSC----EE-EEEEESCHHHHHHHHTTCCCCSC----CCHH
T ss_pred             HHHHHHHHHHHHHHHhhCC--------CcceEEEEEecCCcc----ee-ccCCcchHHHHHHHhhhcCcCCC----CChH
Confidence            4556667777777653211        136899999976432    22 25789999999999999986433    5788


Q ss_pred             HHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcC
Q 003455           85 EGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS  164 (818)
Q Consensus        85 EGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~  164 (818)
                      .||..|+..+.       ........++.||+..++=..                         .-.+++.+|+.+.++|
T Consensus        89 ~gL~~A~~aLk-------~~~~k~~~~rIIlf~ds~~~~-------------------------~~~~l~~lak~lkk~g  136 (268)
T 4b4t_W           89 TALQIAQLTLK-------HRQNKVQHQRIVAFVCSPISD-------------------------SRDELIRLAKTLKKNN  136 (268)
T ss_dssp             HHHHHHHHHHH-------TCSCTTSEEEEEEEECSCCSS-------------------------CHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHH-------hcccCCCceEEEEEECCCCCC-------------------------CHHHHHHHHHHHHHcC
Confidence            89999998884       112344556677777774110                         0137889999999999


Q ss_pred             ceEEEeCC----CcchHHHHHHHHhcCC
Q 003455          165 VSLSVICP----KQLPKLTAIYNAAKRN  188 (818)
Q Consensus       165 I~lSiIsP----rklp~L~~lf~~a~~~  188 (818)
                      |.|+||.=    .+-..|++|.++..++
T Consensus       137 I~v~vIgFG~~~~n~~kLe~l~~~~Ng~  164 (268)
T 4b4t_W          137 VAVDIINFGEIEQNTELLDEFIAAVNNP  164 (268)
T ss_dssp             EEEEEEEESSCCSSCCHHHHHHHHHCSS
T ss_pred             CEEEEEEeCCCccchHHHHHHHHHhcCC
Confidence            99999984    3577799999999765

>1ijb_A VON willebrand factor; dinucleotide-binding fold, blood clotting; 1.80A {Homo sapiens} SCOP: c.62.1.1 PDB: 1ijk_A 1auq_A 1u0n_A 3hxo_A 1uex_C 3hxq_A 1sq0_A 1m10_A 1fns_A 1oak_A 1u0o_C

Probab=97.63  E-value=0.00068  Score=66.98  Aligned_cols=133  Identities=17%  Similarity=0.182  Sum_probs=93.8

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCC--CCHHHHHHHhccccCCCCCCChh
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIFLHWLSTIPFAGGGFNDA   81 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T--~~~~~fl~wL~~i~f~GGG~~~~   81 (818)
                      -|+.+|+++..+++.|.-++        ..+.+|||.|.+..-      ..+.++  .|...|...|++|++.|||.  .
T Consensus        30 ~~~~~k~~~~~~v~~l~~~~--------~~~rv~vv~fs~~~~------~~~~l~~~~~~~~~~~~i~~l~~~gg~~--T   93 (202)
T 1ijb_A           30 EFEVLKAFVVDMMERLRVSQ--------KWVRVAVVEYHDGSH------AYIGLKDRKRPSELRRIASQVKYAGSQV--A   93 (202)
T ss_dssp             HHHHHHHHHHHHHHTBCBST--------TSEEEEEEEESSSEE------EEECTTCCCCHHHHHHHHHTCCCCCBSC--C
T ss_pred             HHHHHHHHHHHHHHhcccCC--------CceEEEEEEECCCce------EEEecCCCCCHHHHHHHHHhCcCCCCCc--C
Confidence            57888999999999995321        358999999987631      123333  78999999999999988753  5


Q ss_pred             hHHHHHHHHH-hhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHH
Q 003455           82 AIAEGLSEAL-MMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSF  160 (818)
Q Consensus        82 aiaEGLa~AL-~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~  160 (818)
                      .+++||..|+ ++|.   .    ..+....|..|||+.-.+..                        ....++...|+.+
T Consensus        94 ~~~~aL~~a~~~~~~---~----~~r~~~~~~iillTDG~~~~------------------------~~~~~~~~~a~~l  142 (202)
T 1ijb_A           94 STSEVLKYTLFQIFS---K----IDRPEASRIALLLMASQEPQ------------------------RMSRNFVRYVQGL  142 (202)
T ss_dssp             CHHHHHHHHHHHTSS---S----CSCTTSEEEEEEEECCCCCG------------------------GGCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhc---c----CCCCCCCeEEEEEccCCCCc------------------------cchHHHHHHHHHH
Confidence            6788899998 5664   1    12346778899999876532                        0123677889999


Q ss_pred             hhcCceEEEeCCCc---chHHHHHHH
Q 003455          161 VQCSVSLSVICPKQ---LPKLTAIYN  183 (818)
Q Consensus       161 ~~~~I~lSiIsPrk---lp~L~~lf~  183 (818)
                      .+.+|.+-.|.=-.   ...|+.|=.
T Consensus       143 ~~~gi~i~~igvG~~~~~~~L~~iA~  168 (202)
T 1ijb_A          143 KKKKVIVIPVGIGPHANLKQIRLIEK  168 (202)
T ss_dssp             HHTTEEEEEEEESTTSCHHHHHHHHH
T ss_pred             HHCCCEEEEEecCCcCCHHHHHHHhC
Confidence            99999988875321   234555544

>3fcs_B Integrin beta-3; beta propeller, rossmann fold, EGF domain, cell adhesion, DI mutation, glycoprotein, HOST-virus interaction, M phosphoprotein; HET: NAG MAN; 2.55A {Homo sapiens} PDB: 4g1e_B* 3ije_B* 4g1m_B* 1jv2_B* 1l5g_B* 1m1x_B* 1u8c_B*

Probab=97.60  E-value=0.00068  Score=80.16  Aligned_cols=170  Identities=9%  Similarity=0.029  Sum_probs=112.6

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCc-----------------------Cc-eeecc
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCA-----------------------CL-VQRSG   56 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~-----------------------~~-v~~~g   56 (818)
                      |+.|++.||+.+..+++-+..        ...++.+|++.|+++.-.|.                       +. -....
T Consensus       124 M~ddi~~lk~l~~~l~~~l~~--------~t~~~r~Gfgsf~Dk~~~P~~~~~p~~~~~~pc~~~~~~c~~~f~f~~~l~  195 (690)
T 3fcs_B          124 MKDDLWSIQNLGTKLATQMRK--------LTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLT  195 (690)
T ss_dssp             GHHHHHHTTTTTHHHHHHHHH--------HCSCEEEEEEEECCCSSTTTSCCCSTTTTTCTTSSSSSCCCCCCSEEEEEE
T ss_pred             hHHHHHHHHHHHHHHHHHHHh--------hCcCceEEeEEeeccccCCccccChhhhccCCCcCCCCCCCCCccceeecc
Confidence            788999999988888888753        23469999999999663221                       11 12257


Q ss_pred             CCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCC----CCcCc-
Q 003455           57 WTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPT----PVYRP-  131 (818)
Q Consensus        57 ~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~----~~~~p-  131 (818)
                      +|+|..+|..+|+++..+||+....+.-|||..|+.+.+  ..+    =+....|..||++..++|..--    ..++| 
T Consensus       196 lt~~~~~f~~~v~~~~isgn~D~PE~g~dAl~qa~~c~~--~ig----Wr~~a~rllv~~TDa~~H~agDg~l~gi~~pn  269 (690)
T 3fcs_B          196 LTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDE--KIG----WRNDASHLLVFTTDAKTHIALDGRLAGIVQPN  269 (690)
T ss_dssp             EESCHHHHHHHHTTCCCCCCSSSSBCHHHHHHHHHHCHH--HHT----CCSSSEEEEEEEESSCBCCTTGGGGGTCCSCC
T ss_pred             cCCCHHHHHHHhhceeccCCCCCCchHHHHHHHHhhccc--ccC----CCCCceEEEEEECCCccccCCCccccceecCC
Confidence            899999999999999999999777777799999985542  000    0346788899999999983110    01112 


Q ss_pred             -cccccccc-chhhhhhhccCCCHHHHHHHHhhcCceEEEeCCCcc-hHHHHHHHHh
Q 003455          132 -QMQNLDQN-ENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQL-PKLTAIYNAA  185 (818)
Q Consensus       132 -~~~~l~~~-~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPrkl-p~L~~lf~~a  185 (818)
                       ..+-|+.. .-..+..+ -.-++.+|++.|.+++|.+-|...+.. ...++|.+..
T Consensus       270 d~~chl~~~~~y~~s~~~-DypSi~ql~~~l~~~~i~~ifavt~~~~~~y~~l~~~i  325 (690)
T 3fcs_B          270 DGQCHVGSDNHYSASTTM-DYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSELI  325 (690)
T ss_dssp             CCCCCBCTTCBBGGGGTS-CCCCHHHHHHHHHHTTCEEEEEEEGGGHHHHHHHHHHS
T ss_pred             CcceeecCCCcccccccc-CCCCHHHHHHHHHHcCCeEEEEEeCCchhhHHHHHhhc
Confidence             22223211 00011111 123699999999999999888777654 4445554443

>3k6s_B Integrin beta-2; cell receptor, adhesion molecule, cell adhesion, pyrrolidone carboxylic acid; HET: NAG MAN; 3.50A {Homo sapiens} PDB: 3k71_B* 3k72_B*

Probab=97.45  E-value=0.00051  Score=81.13  Aligned_cols=169  Identities=8%  Similarity=0.008  Sum_probs=111.3

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCc----------------------C-ceeeccC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCA----------------------C-LVQRSGW   57 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~----------------------~-~v~~~g~   57 (818)
                      |+.|++.+|+.+..+++-+..        ...++.+|++.|+++.-.|-                      + +-....+
T Consensus       117 M~ddi~~lk~l~~~l~~~l~~--------~t~~~r~GfgsFvDk~~~P~~~~~p~~~~~Pc~~~~~~c~~~f~f~~~l~l  188 (687)
T 3k6s_B          117 MLDDLRNVKKLGGDLLRALNE--------ITESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKECQPPFAFRHVLKL  188 (687)
T ss_dssp             THHHHHTTTTCCTTHHHHHHS--------SCCSCEEEEEEECCCSSTTSSCCSSTTTTCCCCSCCCCCCCCCSCEEEEEE
T ss_pred             hHHHHHHHHHHHHHHHHHHHh--------hCcCcEEeeEEeeccccCCccccCchhccCCCCCCCCCcCCcccceeeccc
Confidence            888999999888888887753        23479999999999542221                      1 1123568


Q ss_pred             CCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCC----CCc--Cc
Q 003455           58 TKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPT----PVY--RP  131 (818)
Q Consensus        58 T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~----~~~--~p  131 (818)
                      |+|..+|..+|+++..+||+....+.-|||..|+.+-+  ..+-    +. ..|..||++..++|..--    ..+  +-
T Consensus       189 t~~~~~F~~~v~~~~isgn~D~PE~g~dAl~qa~vc~~--~igW----r~-a~rllV~~TDa~~H~agDg~l~gi~~pnd  261 (687)
T 3k6s_B          189 TNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPE--EIGW----RN-VTRLLVFATDDGFHFAGDGKLGAILTPND  261 (687)
T ss_dssp             ESCSHHHHHHHHTSCCCCCSSSSCCHHHHHHHHTTCHH--HHCC----CS-SCCEEEEECSSCCCCTTGGGGGTCCCCCC
T ss_pred             CCCHHHHHHHHhhccccCCCCCCchHHHHHHHHhhccc--ccCC----cc-ceEEEEEECCCccccCCCccccceecCCC
Confidence            99999999999999999999777677789988884431  0000    23 778889999999883110    011  22


Q ss_pred             ccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCCc-chHHHHHHHHh
Q 003455          132 QMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ-LPKLTAIYNAA  185 (818)
Q Consensus       132 ~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPrk-lp~L~~lf~~a  185 (818)
                      ..+-|..+.-..+..++ .-++.+|++.|.+++|.+-|...+. +..+++|.+..
T Consensus       262 g~Chl~~~~y~~s~~~D-yPS~~ql~~~l~~~~I~~ifavt~~~~~~y~~l~~~i  315 (687)
T 3k6s_B          262 GRCHLEDNLYKRSNEFD-YPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEII  315 (687)
T ss_dssp             SCCCCSSSBCSSGGGSC-CCCGGGHHHHHHHTTCBCCEEECGGGHHHHHHHHHHS
T ss_pred             CccccCCCccccccccC-CCCHHHHHHHHHHcCCeEEEEEeccchhhHHHHHhhc
Confidence            22334311101111121 2368999999999999988777654 45556665544

>1atz_A VON willebrand factor; collagen-binding, hemostasis, dinucleotide binding fold; 1.80A {Homo sapiens} SCOP: c.62.1.1 PDB: 4dmu_B 2adf_A 1fe8_A 1ao3_A

Probab=97.44  E-value=0.0014  Score=63.54  Aligned_cols=123  Identities=11%  Similarity=0.157  Sum_probs=85.9

Q ss_pred             hhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhh
Q 003455            3 IYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA   82 (818)
Q Consensus         3 ~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~a   82 (818)
                      .-|+.+|++|..+++.|.-++        ..++++||.|.+..-    .+-.+..+.|...+...|++|.+.|||   ..
T Consensus        21 ~~~~~~k~~~~~~~~~l~~~~--------~~~rv~lv~f~~~~~----~~~~l~~~~~~~~~~~~i~~l~~~~g~---T~   85 (189)
T 1atz_A           21 SYFDEMKSFAKAFISKANIGP--------RLTQVSVLQYGSITT----IDVPWNVVPEKAHLLSLVDVMQREGGP---SQ   85 (189)
T ss_dssp             HHHHHHHHHHHHHHHHSCBST--------TSEEEEEEEESSSEE----EEECTTCCCCHHHHHHHHHTCCCCCCC---CC
T ss_pred             hhHHHHHHHHHHHHHhcCcCC--------CCeEEEEEEECCcce----EEEecCCCCCHHHHHHHHHhCcCCCCc---ch
Confidence            457888899999999985321        358999999976421    111223389999999999999998776   57


Q ss_pred             HHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhh
Q 003455           83 IAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQ  162 (818)
Q Consensus        83 iaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~  162 (818)
                      +++||..|+..+.....+    .+....|++||+..--+..                            +.+.+++.+.+
T Consensus        86 ~~~aL~~a~~~l~~~~~g----~r~~~~~~vivltdg~~~~----------------------------~~~~~~~~~~~  133 (189)
T 1atz_A           86 IGDALGFAVRYLTSEMHG----ARPGASKAVVILVTDVSVD----------------------------SVDAAADAARS  133 (189)
T ss_dssp             HHHHHHHHHHHHHSCCTT----CCTTSEEEEEEEECSCCSS----------------------------CCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccC----CCCCCCcEEEEEeCCCCCc----------------------------hHHHHHHHHHH
Confidence            889999999766411111    1234567788887654321                            34678888999


Q ss_pred             cCceEEEeCC
Q 003455          163 CSVSLSVICP  172 (818)
Q Consensus       163 ~~I~lSiIsP  172 (818)
                      .+|.+.+|.=
T Consensus       134 ~gi~v~~igv  143 (189)
T 1atz_A          134 NRVTVFPIGI  143 (189)
T ss_dssp             TTEEEEEEEE
T ss_pred             CCCEEEEEEc
Confidence            9999988854

>1v7p_C Integrin alpha-2; snake venom, C-type lectin, antagonist, cell adhes glycoprotein, toxin-cell adhesion complex; HET: NAG; 1.90A {Homo sapiens} SCOP: c.62.1.1 PDB: 1aox_A 1dzi_A

Probab=97.28  E-value=0.0024  Score=62.60  Aligned_cols=124  Identities=11%  Similarity=0.099  Sum_probs=88.8

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCC--CCHHHHHHHhccccCCCCCC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIFLHWLSTIPFAGGGF   78 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T--~~~~~fl~wL~~i~f~GGG~   78 (818)
                      |+. |+.+|+++..+++.|.-+        .....++||+|.+.. +     ..+.+|  .+...++..|++|.+.||+.
T Consensus        19 m~~-~~~~k~~~~~~~~~l~~~--------~~~~rvglv~f~~~~-~-----~~~~l~~~~~~~~~~~~i~~l~~~~G~~   83 (200)
T 1v7p_C           19 IYP-WDAVKNFLEKFVQGLDIG--------PTKTQVGLIQYANNP-R-----VVFNLNTYKTKEEMIVATSQTSQYGGDL   83 (200)
T ss_dssp             CCC-HHHHHHHHHHHHHTSCBS--------TTSEEEEEEEESSSE-E-----EEECTTTCSSHHHHHHHHHHCCCCCCSC
T ss_pred             ccc-HHHHHHHHHHHHHhcCCC--------CCceEEEEEEECCCc-e-----EEEeCCCcCCHHHHHHHHHhhhccCCCC
Confidence            443 788889999999998532        135899999998753 1     123343  68899999999999887742


Q ss_pred             ChhhHHHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHH
Q 003455           79 NDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVA  157 (818)
Q Consensus        79 ~~~aiaEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la  157 (818)
                        ..+++||..|+. +|..  .   ...+....|..|||+.-.+..                         . .+.+.+|
T Consensus        84 --T~~~~al~~a~~~~~~~--~---~g~r~~~~~~ivllTDG~~~~-------------------------~-~~~~~~~  130 (200)
T 1v7p_C           84 --TNTFGAIQYARKYAYSA--A---SGGRRSATKVMVVVTDGESHD-------------------------G-SMLKAVI  130 (200)
T ss_dssp             --CCHHHHHHHHHHHTTSG--G---GTCCTTSEEEEEEEESSCCSC-------------------------G-GGHHHHH
T ss_pred             --CcHHHHHHHHHHhhccc--c---cCCCCCCCeEEEEEccCCCCC-------------------------c-ccHHHHH
Confidence              458899999997 4641  1   112346788999999876542                         0 1456788


Q ss_pred             HHHhhcCceEEEeCC
Q 003455          158 KSFVQCSVSLSVICP  172 (818)
Q Consensus       158 ~~~~~~~I~lSiIsP  172 (818)
                      +.+.+.+|.+.+|.=
T Consensus       131 ~~~~~~gi~i~~igv  145 (200)
T 1v7p_C          131 DQCNHDNILRFGIAV  145 (200)
T ss_dssp             HHHHHTTEEEEEEEE
T ss_pred             HHHHHCCCEEEEEEe
Confidence            899999999998865

>2xgg_A Microneme protein 2; A/I domain, cell adhesion, hydrolase; 2.05A {Toxoplasma gondii}

Probab=97.27  E-value=0.001  Score=64.33  Aligned_cols=120  Identities=14%  Similarity=0.203  Sum_probs=86.7

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC----CHHHHHHHhccccCCCCCCC
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----DVDIFLHWLSTIPFAGGGFN   79 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~----~~~~fl~wL~~i~f~GGG~~   79 (818)
                      .|+.+|++|..+++.|..+        ...+.++||.|.+..-      ..+.++.    +...|+.+|++|.+.|||  
T Consensus        34 ~~~~~k~~~~~~i~~l~~~--------~~~~rv~vv~F~~~~~------~~~~l~~~~~~~~~~~~~~i~~l~~~~g~--   97 (178)
T 2xgg_A           34 NFRLVKQFLHTFLMVLPIG--------PEEVNNAVVTYSTDVH------LQWDLQSPNAVDKQLAAHAVLDMPYKKGS--   97 (178)
T ss_dssp             HHHHHHHHHHHHHHHSCBS--------TTSEEEEEEEESSSEE------EEECTTSGGGSCHHHHHHHHHHCCCCCCC--
T ss_pred             HHHHHHHHHHHHHHhcCCC--------CCCeEEEEEEeCCceE------EEEeCCCCCccCHHHHHHHHHhCCCCCCC--
Confidence            5788889999999998532        2358999999987531      1233333    889999999999998875  


Q ss_pred             hhhHHHHHHHHHhh-hccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHH
Q 003455           80 DAAIAEGLSEALMM-FSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAK  158 (818)
Q Consensus        80 ~~aiaEGLa~AL~~-~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~  158 (818)
                       ..+++||..|+.. |.  ...   ..+....|..|||+.-.+..                   +       .+++.+++
T Consensus        98 -T~~~~aL~~a~~~l~~--~~~---g~r~~~~~~iillTDG~~~~-------------------~-------~~~~~~~~  145 (178)
T 2xgg_A           98 -TNTSDGLKACKQILFT--GSR---PGREHVPKLVIGMTDGESDS-------------------D-------FRTVRAAK  145 (178)
T ss_dssp             -CCHHHHHHHHHHHHHH--CCC---TTCTTSCEEEEEEESSCCCH-------------------H-------HHHSHHHH
T ss_pred             -ccHHHHHHHHHHHhcC--ccc---CCCCCCCEEEEEEcCCCCCC-------------------C-------ccHHHHHH
Confidence             4688899999975 54  111   11346788999998865432                   0       14567889


Q ss_pred             HHhhcCceEEEeC
Q 003455          159 SFVQCSVSLSVIC  171 (818)
Q Consensus       159 ~~~~~~I~lSiIs  171 (818)
                      .+.+.+|.+.+|.
T Consensus       146 ~l~~~gi~v~~ig  158 (178)
T 2xgg_A          146 EIRELGGIVTVLA  158 (178)
T ss_dssp             HHHHTTCEEEEEE
T ss_pred             HHHHCCCEEEEEE
Confidence            9999999999884

>3t3p_B Integrin beta-3; integrin, cell adhesion, blood clotting, fibrinogen, platele; HET: NAG BMA MAN; 2.20A {Homo sapiens} PDB: 3t3m_B* 3nig_B* 3nif_B* 3nid_B* 2vdr_B* 2vc2_B* 2vdk_B* 2vdm_B* 2vdn_B* 2vdl_B* 2vdp_B* 2vdq_B* 2vdo_B* 3fcu_B* 1txv_B* 1ty3_B* 1ty5_B* 1ty6_B* 1ty7_B* 1tye_B*

Probab=97.26  E-value=0.0047  Score=69.95  Aligned_cols=166  Identities=9%  Similarity=0.029  Sum_probs=111.4

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCC--C---------------------CcCcee-ecc
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGS--Y---------------------CACLVQ-RSG   56 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~--~---------------------~~~~v~-~~g   56 (818)
                      |+.|++.+|+-...+++-+..        ...+..+|++.|++++-  |                     +.+... ...
T Consensus       124 M~ddl~~lk~lg~~L~~~l~~--------~t~~~riGfgsFvDk~v~P~~~~~p~~~l~nPc~~~~~~c~p~f~fr~~l~  195 (472)
T 3t3p_B          124 MKDDLWSIQNLGTKLATQMRK--------LTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLT  195 (472)
T ss_dssp             GHHHHHHTTTHHHHHHHHHTT--------TCSCEEEEEEEECCCSSTTTSCCCSHHHHHCTTTTTTSCCCCCCSEEEEEE
T ss_pred             hHHHHHHHHHHHHHHHHHHHh--------cCcCcEEEEEEeeccccCccccCChhhhhcCCCcccccCCCCCcceeEeec
Confidence            788899999888888888853        24579999999999642  2                     122111 357


Q ss_pred             CCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCC------CcC
Q 003455           57 WTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTP------VYR  130 (818)
Q Consensus        57 ~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~------~~~  130 (818)
                      +|+|..+|..++.++..+||+....+.-|||-.|+.|-+  ..+    =+....|..||++..++|..--.      .++
T Consensus       196 LT~d~~~F~~~V~~~~iSGn~D~PEgg~dAl~qaavC~~--~ig----WR~~a~rllV~~TDa~~H~agDgkL~GIv~pn  269 (472)
T 3t3p_B          196 LTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDE--KIG----WRNDASHLLVFTTDAKTHIALDGRLAGIVQPN  269 (472)
T ss_dssp             EESCHHHHHHHHHHCCCCCCSSSSBCHHHHHHHHHHCHH--HHT----CCSSSEEEEEEEESSCBCCTTGGGGGTCCCCC
T ss_pred             cCCCHHHHHHHHhhccccCCCCCCchHHHHHHHHhcchh--hcC----CCCCceEEEEEECCCCcCcCCCccccceecCC
Confidence            899999999999999999999777777899998886542  000    03467888999999999853211      112


Q ss_pred             ccccccccc-chhhhhhhccCCCHHHHHHHHhhcCceEEEeCCCc-chHHHHH
Q 003455          131 PQMQNLDQN-ENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ-LPKLTAI  181 (818)
Q Consensus       131 p~~~~l~~~-~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPrk-lp~L~~l  181 (818)
                      -.-|-|+.+ .-..+..++ .-++.+|++.+.|++|.+=+...+. ...+++|
T Consensus       270 Dg~CHL~~~~~Y~~s~~~D-YPSv~ql~~~l~e~nI~~IFAVt~~~~~~Y~~L  321 (472)
T 3t3p_B          270 DGQCHVGSDNHYSASTTMD-YPSLGLMTEKLSQKNINLIFAVTENVVNLYQNY  321 (472)
T ss_dssp             CCCCCBCTTCBBTTTTTSC-CCCHHHHHHHHHHTTCEEEEEECGGGHHHHHHH
T ss_pred             CCceEECCCCcccccccCC-CCCHHHHHHHHHhcCccEEEEEeccchhHHHHH
Confidence            233334321 111111222 2389999999999999987766654 3333444

>3vi3_B Integrin beta-1; beta propeller fold, rossman fold, beta sandwich, fibronecti receptor, cell adhesion-immune system complex; HET: NAG BMA MAN; 2.90A {Homo sapiens} PDB: 3vi4_B*

Probab=97.25  E-value=0.0048  Score=69.52  Aligned_cols=158  Identities=8%  Similarity=-0.004  Sum_probs=109.3

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCC---------------C------CCcCcee-eccCC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHG---------------S------YCACLVQ-RSGWT   58 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~---------------~------~~~~~v~-~~g~T   58 (818)
                      |+.+++.+|+-...+++-...        ...+..+|++.|.+++               |      -+.+... ...+|
T Consensus       135 M~ddl~~lk~lg~~L~~~l~~--------~t~~~riGfGsFvDK~v~P~~~t~p~~~~nPC~~~~~c~~~f~fr~~l~LT  206 (454)
T 3vi3_B          135 MKDDLENVKSLGTDLMNEMRR--------ITSDFRIGFGSFVEKTVMPYISTTPAKLRNPCTSEQNCTTPFSYKNVLSLT  206 (454)
T ss_dssp             GHHHHHHHTTHHHHHHHHHTT--------TCSSEEEEEEEECCCSSTTTSCCSTTTTTCCSCSSSCCCCCCSEEEEEEEE
T ss_pred             hhhHHHHHHHHHHHHHHHHHh--------cCCCeEEEEEEEeccccCCcccCChHHhcCCCcCccCCCCCcceeeeeecC
Confidence            777888888888888887753        2347999999999963               1      1222222 47889


Q ss_pred             CCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCC------CCcCcc
Q 003455           59 KDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPT------PVYRPQ  132 (818)
Q Consensus        59 ~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~------~~~~p~  132 (818)
                      +|..+|..++.++..+||+....+.-|||-.|+.|-+  ..+-    +. ..|..||++..++|..--      ..++-.
T Consensus       207 ~d~~~F~~~V~~~~isGn~D~PEgg~DAl~Qaavc~~--~igW----R~-a~rllV~~TDa~fH~agDgkL~GIv~PNDg  279 (454)
T 3vi3_B          207 NKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAVCGS--LIGW----RN-VTRLLVFSTDAGFHFAGDGKLGGIVLPNDG  279 (454)
T ss_dssp             SCHHHHHHHHTTCCCCCCSSSSBCHHHHHHHHHHCHH--HHTC----CS-SEEEEEEEESSCBCCTTTTGGGTCCSCCCC
T ss_pred             CCHHHHHHHHhhccccCCCcCCchhHHHHHHHhcccc--ccCC----cc-ceEEEEEECCCCcCcCCCccccceecCCCC
Confidence            9999999999999999999888788899998887632  0000    23 778889999999985321      112334


Q ss_pred             cccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCCc
Q 003455          133 MQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  174 (818)
Q Consensus       133 ~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPrk  174 (818)
                      -|-|+.+.-..+..++- -++.+|++.+.|++|.+=|...++
T Consensus       280 ~CHL~~~~Yt~s~~~DY-PSv~ql~~~l~e~nI~~IFAVt~~  320 (454)
T 3vi3_B          280 QCHLENNMYTMSHYYDY-PSIAHLVQKLSENNIQTIFAVTEE  320 (454)
T ss_dssp             CCCEETTEECCTTTSCC-CCHHHHHHHHHHTTEEEEEEEEGG
T ss_pred             ccEeCCCcccccccCCC-CCHHHHHHHHHhcCCcEEEEEcCc
Confidence            45555222111122222 389999999999999987776654

>2x5n_A SPRPN10, 26S proteasome regulatory subunit RPN10; nuclear protein, nucleus, ubiquitin; 1.30A {Schizosaccharomyces pombe}

Probab=97.24  E-value=0.0032  Score=62.89  Aligned_cols=111  Identities=19%  Similarity=0.234  Sum_probs=76.7

Q ss_pred             ceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEE
Q 003455           34 VELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHC  113 (818)
Q Consensus        34 ~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhC  113 (818)
                      .+.|||+|.+...+-     ...+|.|..+++..|++|...| |   .++++||..|+.+|.-  .     ......++.
T Consensus        46 d~vGLV~fa~~~a~~-----~~plT~d~~~i~~~L~~l~~~g-~---t~l~~aL~~A~~~l~~--~-----~~~~~~~ri  109 (192)
T 2x5n_A           46 NMCGLMTIGDNSPQV-----LSTLTRDYGKFLSAMHDLPVRG-N---AKFGDGIQIAQLALKH--R-----ENKIQRQRI  109 (192)
T ss_dssp             CEEEEEECCTTSCCE-----EEEEESCHHHHHHHHTTCCCCS-C---CCHHHHHHHHHHHHHT--C-----SCTTSEEEE
T ss_pred             CeEEEEEEcCCCcEE-----ecCCCCCHHHHHHHHHcCCCCC-C---chHHHHHHHHHHHHHh--c-----cccCCCceE
Confidence            789999999753332     2578899999999999988754 2   6899999999998851  1     111223334


Q ss_pred             EEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCC----cchHHHHHHHHhc
Q 003455          114 ILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAK  186 (818)
Q Consensus       114 ILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPr----klp~L~~lf~~a~  186 (818)
                      ||+..+. +.   .                     ...+.+.+|+.+.+.+|.+++|.=-    .-. |+.|.++..
T Consensus       110 iil~~~~-~~---~---------------------~~~~~~~~a~~lk~~gi~v~~Ig~G~~~~~~~-l~~la~~~n  160 (192)
T 2x5n_A          110 VAFVGSP-IV---E---------------------DEKNLIRLAKRMKKNNVAIDIIHIGELQNESA-LQHFIDAAN  160 (192)
T ss_dssp             EEEECSC-CS---S---------------------CHHHHHHHHHHHHHTTEEEEEEEESCC---CH-HHHHHHHHC
T ss_pred             EEEEECC-CC---C---------------------CchhHHHHHHHHHHCCCEEEEEEeCCCCccHH-HHHHHHhcc
Confidence            4444331 10   0                     0125788999999999999998741    225 999998875

>3ibs_A Conserved hypothetical protein BATB; structural genomics, protein structure, midwest center for S genomics, MCSG, PSI-2; HET: MSE; 2.10A {Bacteroides thetaiotaomicron}

Probab=97.02  E-value=0.0053  Score=60.37  Aligned_cols=114  Identities=18%  Similarity=0.134  Sum_probs=83.4

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      .|+..|+.+..+++.+.            ...++||+|.+.      ....+.+|.|...+..+|++|...........+
T Consensus        33 r~~~ak~~~~~~~~~~~------------~~~v~lv~F~~~------~~~~~~~~~~~~~~~~~l~~l~~~~~~~g~T~l   94 (218)
T 3ibs_A           33 RLEKAKRLISRLVDELD------------NDKVGMIVFAGD------AFTQLPITSDYISAKMFLESISPSLISKQGTAI   94 (218)
T ss_dssp             HHHHHHHHHHHHHHTCS------------SCEEEEEEESSS------EEEEEEEESCHHHHHHHHHTCCGGGCCSCSCCH
T ss_pred             HHHHHHHHHHHHHHhCC------------CCeEEEEEECCC------ceEeCCCCCCHHHHHHHHHhcCcccCCCCCCcH
Confidence            46677777777777662            368999999865      223467888999999999999874222223668


Q ss_pred             HHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhc
Q 003455           84 AEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC  163 (818)
Q Consensus        84 aEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~  163 (818)
                      .+||..|+.+|.         ......|.+|||+.-.+..                           .+++.+++.+.++
T Consensus        95 ~~al~~a~~~l~---------~~~~~~~~ivllTDG~~~~---------------------------~~~~~~~~~~~~~  138 (218)
T 3ibs_A           95 GEAINLATRSFT---------PQEGVGRAIIVITDGENHE---------------------------GGAVEAAKAAAEK  138 (218)
T ss_dssp             HHHHHHHHTTSC---------SCSSCCEEEEEEECCTTCC---------------------------SCHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHh---------hCCCCCcEEEEEcCCCCCC---------------------------CcHHHHHHHHHhc
Confidence            999999998885         1135677888887654322                           1577889999999


Q ss_pred             CceEEEeC
Q 003455          164 SVSLSVIC  171 (818)
Q Consensus       164 ~I~lSiIs  171 (818)
                      +|.+.+|.
T Consensus       139 ~i~v~~ig  146 (218)
T 3ibs_A          139 GIQVSVLG  146 (218)
T ss_dssp             TEEEEEEE
T ss_pred             CCEEEEEE
Confidence            99999885

>3v4v_B Integrin beta-7; cell adhesion, madcam-1, membrane; HET: NAG BMA MAN 0DU; 3.10A {Homo sapiens} PDB: 3v4p_B*

Probab=96.98  E-value=0.013  Score=66.64  Aligned_cols=165  Identities=12%  Similarity=0.068  Sum_probs=109.1

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCC--CC--------------------CcCcee-eccC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHG--SY--------------------CACLVQ-RSGW   57 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~--~~--------------------~~~~v~-~~g~   57 (818)
                      |+.|++.+|+-...+++-+..        ...+..+|++.|++++  +|                    +.+... ...+
T Consensus       145 M~ddl~~lk~lg~~L~~~l~~--------~t~~~RiGfGsFvDK~v~P~~~~~p~~l~~PC~~~~~~c~p~f~fr~~l~L  216 (503)
T 3v4v_B          145 MKDDLERVRQLGHALLVRLQE--------VTHSVRIGFGSFVDKTVLPFVSTVPSKLRHPCPTRLERCQSPFSFHHVLSL  216 (503)
T ss_dssp             GHHHHHHHHHSSHHHHHHHTT--------TCSCEEEEEEEECCCSSTTTSCCCHHHHHCCSSCSSSCCCCCCSEEEEEEE
T ss_pred             hhhHHHHHHHHHHHHHHHHHh--------hCcCcEEeeeeecccccCCcccCCHHHhcCCCcCCCCCCCCCcceEEEEEe
Confidence            778889999888888888753        3457999999999963  11                    122222 3578


Q ss_pred             CCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCC----CC--cCc
Q 003455           58 TKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPT----PV--YRP  131 (818)
Q Consensus        58 T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~----~~--~~p  131 (818)
                      |+|..+|..++.++..+||+....+.-|||-.|+.|-+  ..+=    +. ..|..||++..++|..--    ..  ++-
T Consensus       217 T~d~~~F~~~V~~~~iSGnlD~PEggfDAlmQaavC~~--~IgW----R~-a~rllV~~TDA~fH~agDgkLaGIv~pND  289 (503)
T 3v4v_B          217 TGDAQAFEREVGRQSVSGNLDSPEGGFDAILQAALCQE--QIGW----RN-VSRLLVFTSDDTFHTAGDGKLGGIFMPSD  289 (503)
T ss_dssp             ESCSHHHHHHHTTCCCCCCSSSSBCHHHHHHHHHHCHH--HHTC----CS-SEEEEEEEESSCBCCTTGGGTTTCCSCCC
T ss_pred             cCCHHHHHHHHhhcCccCCCCCCchHHHHHHHHhhccc--ccCC----Cc-ceEEEEEECCCCcCcCCCccccceecCCC
Confidence            99999999999999999999777777899988886542  0110    12 558889999999985211    11  122


Q ss_pred             cccccccc-chhhhhhhccCCCHHHHHHHHhhcCceEEEeCCC-cchHHHHH
Q 003455          132 QMQNLDQN-ENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK-QLPKLTAI  181 (818)
Q Consensus       132 ~~~~l~~~-~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPr-klp~L~~l  181 (818)
                      .-|-|+.+ .-..+..++ .-++.+|++.+.+++|.+=|...+ .....++|
T Consensus       290 g~CHL~~~~~Yt~s~~~D-YPSv~ql~~kL~ennI~~IFAVt~~~~~~Y~~L  340 (503)
T 3v4v_B          290 GHCHLDSNGLYSRSTEFD-YPSVGQVAQALSAANIQPIFAVTSAALPVYQEL  340 (503)
T ss_dssp             SSCCBCTTSBBGGGGGSC-CCCHHHHHHHHHHHTEEEEEEECSSSHHHHHHH
T ss_pred             CCeEECCCCccccccccC-CCCHHHHHHHHHhcCCeEEEEEcccchhHHHHH
Confidence            33444321 111122222 248999999999999987665554 34444443

>2b2x_A Integrin alpha-1; computational design, antibody-antigen complex, immune syste; 2.20A {Rattus norvegicus} SCOP: c.62.1.1

Probab=96.94  E-value=0.0077  Score=60.10  Aligned_cols=123  Identities=11%  Similarity=0.076  Sum_probs=86.1

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHH
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIA   84 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aia   84 (818)
                      |+.+|+++..+++.|.-+        .....++||.|.+.. +..   -......+...++..|++|.+.||+.  ..++
T Consensus        38 ~~~~k~~~~~~~~~l~~~--------~~~~rv~lv~F~~~~-~~~---~~l~~~~~~~~~~~~i~~l~~~gG~~--T~~~  103 (223)
T 2b2x_A           38 WESVIAFLNDLLKRMDIG--------PKQTQVGIVQYGENV-THE---FNLNKYSSTEEVLVAANKIVQRGGRQ--TMTA  103 (223)
T ss_dssp             HHHHHHHHHHHHTTSCCS--------TTSCCEEEEEESSSE-EEE---ECTTTCCSHHHHHHHHTTCCCCCCSS--CCHH
T ss_pred             HHHHHHHHHHHHHhcccC--------CCCeEEEEEEeCCCc-cEE---EecCCCCCHHHHHHHHHhhhccCCCC--ccHH
Confidence            678888999999888421        236899999997642 111   11234467899999999999887632  4588


Q ss_pred             HHHHHHHhh-hccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhc
Q 003455           85 EGLSEALMM-FSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC  163 (818)
Q Consensus        85 EGLa~AL~~-~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~  163 (818)
                      +||..|+.. |..  .   +..+....|+.|||+.-.+..                        .  .+.+.+++.+.+.
T Consensus       104 ~aL~~a~~~l~~~--~---~~~~~~~~~~iillTDG~~~~------------------------~--~~~~~~~~~~~~~  152 (223)
T 2b2x_A          104 LGIDTARKEAFTE--A---RGARRGVKKVMVIVTDGESHD------------------------N--YRLKQVIQDCEDE  152 (223)
T ss_dssp             HHHHHHHHTTSSG--G---GTCCTTSEEEEEEEESSCCTT------------------------G--GGHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcCc--c---cCCCCCCCeEEEEEcCCCCCC------------------------C--ccHHHHHHHHHHC
Confidence            899999975 531  0   112346778899998765432                        0  1567888999999


Q ss_pred             CceEEEeCC
Q 003455          164 SVSLSVICP  172 (818)
Q Consensus       164 ~I~lSiIsP  172 (818)
                      +|.+.+|.=
T Consensus       153 gi~v~~igv  161 (223)
T 2b2x_A          153 NIQRFSIAI  161 (223)
T ss_dssp             TEEEEEEEE
T ss_pred             CCEEEEEEe
Confidence            999998853

>3n2n_F Anthrax toxin receptor 1; rossmann fold; 1.80A {Homo sapiens} SCOP: c.62.1.1

Probab=96.81  E-value=0.0034  Score=60.06  Aligned_cols=124  Identities=15%  Similarity=0.141  Sum_probs=87.2

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhcccc--CCCCCC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIP--FAGGGF   78 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~--f~GGG~   78 (818)
                      |+..|+.+++++..+++.|..          ....++||.|.+..      -..+.+|.|...+..+|++|.  +.||| 
T Consensus        20 M~~~~~~~~~~~~~~~~~~~~----------~~~~v~lv~f~~~~------~~~~~l~~~~~~~~~~i~~l~~~~~~g~-   82 (185)
T 3n2n_F           20 VLHHWNEIYYFVEQLAHKFIS----------PQLRMSFIVFSTRG------TTLMKLTEDREQIRQGLEELQKVLPGGD-   82 (185)
T ss_dssp             GGGGHHHHHHHHHHHHHHCCC----------TTEEEEEEEESSSE------EEEEEEECCHHHHHHHHHHHHTCCCCSC-
T ss_pred             hhhhHHHHHHHHHHHHHHhCC----------CCcEEEEEEEecCc------eEEeccCCCHHHHHHHHHHHhhhcCCCC-
Confidence            556788888999999998832          25899999997642      224577889999999999998  45776 


Q ss_pred             ChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHH
Q 003455           79 NDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAK  158 (818)
Q Consensus        79 ~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~  158 (818)
                        ..+.+||..|+..+.....     ......|+.|||+.-.+..                        ....+.+..++
T Consensus        83 --T~~~~al~~a~~~l~~~~~-----~~~~~~~~iillTDG~~~~------------------------~~~~~~~~~~~  131 (185)
T 3n2n_F           83 --TYMHEGFERASEQIYYENR-----QGYRTASVIIALTDGELHE------------------------DLFFYSEREAN  131 (185)
T ss_dssp             --CCHHHHHHHHHHHHHHHHT-----TCBCEEEEEEEEECCCCCH------------------------HHHHHHHHHHH
T ss_pred             --ccHHHHHHHHHHHHhhccc-----cCCCCCcEEEEEcCCCCCC------------------------CcccchHHHHH
Confidence              4478888888874410000     1123678889998765422                        01114567899


Q ss_pred             HHhhcCceEEEeCC
Q 003455          159 SFVQCSVSLSVICP  172 (818)
Q Consensus       159 ~~~~~~I~lSiIsP  172 (818)
                      .+.+.+|.+-.|.=
T Consensus       132 ~~~~~gi~i~~igv  145 (185)
T 3n2n_F          132 RSRDLGAIVYAVGV  145 (185)
T ss_dssp             HHHHTTEEEEEEEC
T ss_pred             HHHHCCCEEEEEEe
Confidence            99999999998854

>1pt6_A Integrin alpha-1; cell adhesion; 1.87A {Homo sapiens} SCOP: c.62.1.1 PDB: 4a0q_A 1qcy_A 1qc5_A 1qc5_B 1ck4_A 1mhp_A

Probab=96.74  E-value=0.014  Score=57.70  Aligned_cols=123  Identities=11%  Similarity=0.070  Sum_probs=85.8

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHH
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIA   84 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aia   84 (818)
                      |+.+|+++..+++.|.-+        .....++||+|.+..- .   +-......+...++..|++|.+.||..  ..++
T Consensus        23 ~~~~k~~~~~~~~~l~~~--------~~~~~v~lv~F~~~~~-~---~~~l~~~~~~~~~~~~i~~l~~~~G~~--T~~~   88 (213)
T 1pt6_A           23 WDSVTAFLNDLLKRMDIG--------PKQTQVGIVQYGENVT-H---EFNLNKYSSTEEVLVAAKKIVQRGGRQ--TMTA   88 (213)
T ss_dssp             HHHHHHHHHHHHTTSCBS--------TTSBEEEEEEESSSEE-E---EECTTTCSSHHHHHHHHHTCCCCCCSS--CCHH
T ss_pred             HHHHHHHHHHHHHhcCCC--------CCCeEEEEEEeCCCcc-E---EEeccccCCHHHHHHHHHhccCCCCCc--ccHH
Confidence            678888999999888421        2368999999986431 1   111234467899999999999887732  3488


Q ss_pred             HHHHHHHhh-hccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhc
Q 003455           85 EGLSEALMM-FSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC  163 (818)
Q Consensus        85 EGLa~AL~~-~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~  163 (818)
                      +||..|+.. |..  .   +..+....|..|||+.-.+..-                          .+.+.+++.+.+.
T Consensus        89 ~aL~~a~~~l~~~--~---~~~r~~~~~~iillTDG~~~~~--------------------------~~~~~~~~~~~~~  137 (213)
T 1pt6_A           89 LGTDTARKEAFTE--A---RGARRGVKKVMVIVTDGESHDN--------------------------HRLKKVIQDCEDE  137 (213)
T ss_dssp             HHHHHHHHTTTSG--G---GTCCTTCEEEEEEEESSCCSCS--------------------------HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcCc--c---cCCCCCCCeEEEEEcCCCCCCC--------------------------ccHHHHHHHHHHC
Confidence            899999975 531  0   1123467888999998755320                          1456788889999


Q ss_pred             CceEEEeCC
Q 003455          164 SVSLSVICP  172 (818)
Q Consensus       164 ~I~lSiIsP  172 (818)
                      +|.+.+|.=
T Consensus       138 gi~i~~igi  146 (213)
T 1pt6_A          138 NIQRFSIAI  146 (213)
T ss_dssp             TEEEEEEEE
T ss_pred             CCEEEEEEe
Confidence            999988864

>1mf7_A Integrin alpha M; cell adhesion; 1.25A {Homo sapiens} SCOP: c.62.1.1 PDB: 1na5_A 1jlm_A 1ido_A 1m1u_A 3q3g_G 1n9z_A 1bhq_1 1bho_1 1idn_1 3qa3_G

Probab=96.64  E-value=0.0051  Score=59.71  Aligned_cols=120  Identities=13%  Similarity=0.097  Sum_probs=83.8

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC--CHHHHHHHhccccCCCCCCChh
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDIFLHWLSTIPFAGGGFNDA   81 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~--~~~~fl~wL~~i~f~GGG~~~~   81 (818)
                      .|+.+|+++..+++.|.          ...++++||.|.+..-      ..+.|+.  +...+...|++|.+.|||   .
T Consensus        22 ~~~~~k~~~~~~~~~l~----------~~~~~v~vv~f~~~~~------~~~~l~~~~~~~~~~~~i~~l~~~~g~---T   82 (194)
T 1mf7_A           22 DFRRMKEFVSTVMEQLK----------KSKTLFSLMQYSEEFR------IHFTFKEFQNNPNPRSLVKPITQLLGR---T   82 (194)
T ss_dssp             HHHHHHHHHHHHHHHHC----------CTTEEEEEEEESSSEE------EEECHHHHHHSCCHHHHHTTCCCCCSC---B
T ss_pred             HHHHHHHHHHHHHHhcC----------CCCeEEEEEEecCCce------EEEecCCcCCHHHHHHHHHhCcCCCCC---c
Confidence            57888899999999985          1258999999977531      2244444  456789999999987775   4


Q ss_pred             hHHHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHH
Q 003455           82 AIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSF  160 (818)
Q Consensus        82 aiaEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~  160 (818)
                      .+.+||..|+. +|..  .   ...+....|..|||+.-.+..-+.                         +.+++++.+
T Consensus        83 ~~~~aL~~a~~~l~~~--~---~~~r~~~~~~iillTDG~~~~d~~-------------------------~~~~~~~~~  132 (194)
T 1mf7_A           83 HTATGIRKVVRELFNI--T---NGARKNAFKILVVITDGEKFGDPL-------------------------GYEDVIPEA  132 (194)
T ss_dssp             CHHHHHHHHHHTTTSG--G---GTCCTTSEEEEEEEESSCCBSCSS-------------------------CGGGTHHHH
T ss_pred             hHHHHHHHHHHHhcCc--c---cCCCCCCCeEEEEEcCCCCCCCch-------------------------hhHHHHHHH
Confidence            68899999995 6641  0   112345778899999877652111                         223456778


Q ss_pred             hhcCceEEEeCC
Q 003455          161 VQCSVSLSVICP  172 (818)
Q Consensus       161 ~~~~I~lSiIsP  172 (818)
                      .+.+|.+..|.=
T Consensus       133 ~~~gi~v~~igv  144 (194)
T 1mf7_A          133 DREGVIRYVIGV  144 (194)
T ss_dssp             HHTTEEEEEEEE
T ss_pred             HHCCCEEEEEEe
Confidence            889999888854

>1n3y_A Integrin alpha-X; alpha/beta rossmann fold, cell adhesion; 1.65A {Homo sapiens} SCOP: c.62.1.1

Probab=96.55  E-value=0.0061  Score=59.02  Aligned_cols=120  Identities=13%  Similarity=0.090  Sum_probs=83.9

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC--CHHHHHHHhccccCCCCCCChh
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDIFLHWLSTIPFAGGGFNDA   81 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~--~~~~fl~wL~~i~f~GGG~~~~   81 (818)
                      .|+.+++++..+++.|.          .....++||+|.+..      ...+.++.  +...++.+|+.|.+.|||   .
T Consensus        26 ~~~~~~~~~~~~~~~l~----------~~~~~v~lv~f~~~~------~~~~~~~~~~~~~~~~~~i~~l~~~~g~---T   86 (198)
T 1n3y_A           26 NFATMMNFVRAVISQFQ----------RPSTQFSLMQFSNKF------QTHFTFEEFRRSSNPLSLLASVHQLQGF---T   86 (198)
T ss_dssp             HHHHHHHHHHHHHTTSC----------TTTEEEEEEEESSSE------EEEECHHHHHHCSSGGGGGTTCCCCCSC---B
T ss_pred             HHHHHHHHHHHHHHhcC----------CCCcEEEEEEeCCCc------cEEEecCccCCHHHHHHHHhcCcCCCCC---c
Confidence            57777889988888885          235899999998862      12233332  335688899999887764   5


Q ss_pred             hHHHHHHHHH-hhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHH
Q 003455           82 AIAEGLSEAL-MMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSF  160 (818)
Q Consensus        82 aiaEGLa~AL-~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~  160 (818)
                      .+.+||..|+ .+|..  .   +..+....|..|||+.-.+..-+                         .+.+.+++.+
T Consensus        87 ~~~~al~~a~~~l~~~--~---~~~r~~~~~~iillTDG~~~~~~-------------------------~~~~~~~~~~  136 (198)
T 1n3y_A           87 YTATAIQNVVHRLFHA--S---YGARRDAAKILIVITDGKKEGDS-------------------------LDYKDVIPMA  136 (198)
T ss_dssp             CHHHHHHHHHTTTTSG--G---GTCCTTSEEEEEEEESSCCBSCS-------------------------SCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhCc--c---cCCCCCCceEEEEECCCCCCCCc-------------------------ccHHHHHHHH
Confidence            6889999999 66641  1   11134567888999887654211                         2567788899


Q ss_pred             hhcCceEEEeCC
Q 003455          161 VQCSVSLSVICP  172 (818)
Q Consensus       161 ~~~~I~lSiIsP  172 (818)
                      .+.+|.+.+|.=
T Consensus       137 ~~~gi~i~~igv  148 (198)
T 1n3y_A          137 DAAGIIRYAIGV  148 (198)
T ss_dssp             HHTTCEEEEEEE
T ss_pred             HHCCCEEEEEEc
Confidence            999999988753

>1q0p_A Complement factor B; VON willebrand factor, MAC-1, I domain, A domain, hydrolase; 1.80A {Homo sapiens} SCOP: c.62.1.1

Probab=96.23  E-value=0.034  Score=54.55  Aligned_cols=107  Identities=14%  Similarity=0.093  Sum_probs=71.3

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCcee-eccCCCCHHHHHHHhccccCCCCC-CChh
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQ-RSGWTKDVDIFLHWLSTIPFAGGG-FNDA   81 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~-~~g~T~~~~~fl~wL~~i~f~GGG-~~~~   81 (818)
                      .|+.+|+++.-+++.|...+        ....++||.|.+..-.   .+. ....|.|...+...|++|.+.++. -...
T Consensus        32 ~~~~~k~~~~~~i~~l~~~~--------~~~~v~lv~f~~~~~~---~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~g~T  100 (223)
T 1q0p_A           32 NFTGAKKSLVNLIEKVASYG--------VKPRYGLVTYATYPKI---WVKVSEADSSNADWVTKQLNEINYEDHKLKSGT  100 (223)
T ss_dssp             HHHHHHHHHHHHHHHHHTTT--------CCCEEEEEEESSSEEE---EECTTSGGGGCHHHHHHHHHTCCTTSCSCTTCC
T ss_pred             HHHHHHHHHHHHHHHHhcCC--------CCceEEEEEecCccce---eeccccCCCCCHHHHHHHHHhcccccccCCCCc
Confidence            78889999999998885422        2478999999875421   111 125567889999999999986431 1235


Q ss_pred             hHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCC
Q 003455           82 AIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  122 (818)
Q Consensus        82 aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~  122 (818)
                      .+.+||..|+.+|... ....+.......|..|||+.-.+.
T Consensus       101 ~~~~aL~~a~~~l~~~-~~~~~~~~~~~~~~iillTDG~~~  140 (223)
T 1q0p_A          101 NTKKALQAVYSMMSWP-DDVPPEGWNRTRHVIILMTDGLHN  140 (223)
T ss_dssp             CHHHHHHHHHHHHCCT-TSSCCTTGGGCEEEEEEEECSCCC
T ss_pred             cHHHHHHHHHHHhhcc-ccccccccccCCeEEEEECCCCCC
Confidence            6899999999877411 111111123567778888887654

>1shu_X Anthrax toxin receptor 2; alpha/beta rossmann fold, membrane protein; 1.50A {Homo sapiens} SCOP: c.62.1.1 PDB: 1tzn_a 1sht_X 1t6b_Y*

Probab=95.90  E-value=0.027  Score=53.55  Aligned_cols=122  Identities=18%  Similarity=0.103  Sum_probs=83.6

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccC--CCCCC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPF--AGGGF   78 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f--~GGG~   78 (818)
                      |...+..+++++..+++.|..          ....++||.|.+..      ...+.||.+...+..+|++|..  .+|| 
T Consensus        19 M~~~~~~~~~~~~~~~~~~~~----------~~~~v~lv~f~~~~------~~~~~~~~~~~~~~~~l~~l~~~~~~g~-   81 (182)
T 1shu_X           19 VANNWIEIYNFVQQLAERFVS----------PEMRLSFIVFSSQA------TIILPLTGDRGKISKGLEDLKRVSPVGE-   81 (182)
T ss_dssp             GGGGHHHHHHHHHHHHHHCCC----------TTEEEEEEEESSSE------EEEEEEECCHHHHHHHHHHHHTCCCCSC-
T ss_pred             cccCHHHHHHHHHHHHHHhcC----------CCceEEEEEeCCCc------eEEECCCCCHHHHHHHHHhcccCCCCCC-
Confidence            444444455788888888732          35899999997642      2346678899999999988874  3443 


Q ss_pred             ChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHH
Q 003455           79 NDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAK  158 (818)
Q Consensus        79 ~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~  158 (818)
                        ..+.+||..|+.++...       ......|..|||+.-.+..-                        .....+.+++
T Consensus        82 --T~~~~al~~a~~~l~~~-------~~~~~~~~iiliTDG~~~~~------------------------~~~~~~~~~~  128 (182)
T 1shu_X           82 --TYIHEGLKLANEQIQKA-------GGLKTSSIIIALTDGKLDGL------------------------VPSYAEKEAK  128 (182)
T ss_dssp             --CCHHHHHHHHHHHHHHH-------TGGGSCEEEEEEECCCCCTT------------------------HHHHHHHHHH
T ss_pred             --chHHHHHHHHHHHHHhc-------cCCCCCeEEEEECCCCcCCC------------------------CchhHHHHHH
Confidence              56889999999877411       12356788899988765320                        0013456788


Q ss_pred             HHhhcCceEEEeCC
Q 003455          159 SFVQCSVSLSVICP  172 (818)
Q Consensus       159 ~~~~~~I~lSiIsP  172 (818)
                      .+.+.+|.+.+|.=
T Consensus       129 ~~~~~~i~i~~igv  142 (182)
T 1shu_X          129 ISRSLGASVYCVGV  142 (182)
T ss_dssp             HHHHTTCEEEEEEC
T ss_pred             HHHhCCCEEEEEeC
Confidence            88999999988864

>3zqk_A VON willebrand factor; blood clotting, adamts-13, force sensor, VON willebrand DISE domain, haemostasis; HET: NAG; 1.70A {Homo sapiens} PDB: 3ppv_A 3ppx_A 3ppw_A 3ppy_A 3gxb_A*

Probab=95.86  E-value=0.04  Score=54.09  Aligned_cols=101  Identities=10%  Similarity=0.069  Sum_probs=71.0

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      -|+.+|+++..+++.|.-+        ...+.++||.|.+..-.    +-.+..+.+...++..|++|++.||+.  ..+
T Consensus        38 ~~~~~k~~~~~~~~~l~~~--------~~~~rv~vv~fs~~~~~----~~~l~~~~~~~~~~~~i~~l~~~gg~~--T~~  103 (199)
T 3zqk_A           38 DFNRSKEFMEEVIQRMDVG--------QDSIHVTVLQYSYMVTV----EYPFSEAQSKGDILQRLREIRYQGGNR--TNT  103 (199)
T ss_dssp             HHHHHHHHHHHHHHHSCBS--------TTSBEEEEEEESSSEEE----EECTTSCCCHHHHHHHHHHCCCCCCSC--CCH
T ss_pred             HHHHHHHHHHHHHHhcCCC--------CCceEEEEEEECCcccE----EEecCCcCCHHHHHHHHHhCcCCCCCc--ChH
Confidence            4788889999999999532        23689999999875321    111223458999999999999998743  347


Q ss_pred             HHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCC
Q 003455           84 AEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHP  123 (818)
Q Consensus        84 aEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~  123 (818)
                      ++||..|+. +|.  ..   ...+....|..|||+.-.+..
T Consensus       104 ~~aL~~a~~~l~~--~~---~g~r~~~~~~iillTDG~~~d  139 (199)
T 3zqk_A          104 GLALRYLSDHSFL--VS---QGDREQAPNLVYMVTGNPASD  139 (199)
T ss_dssp             HHHHHHCCCCCTC--GG---GTCCTTSCEEEEEEECSCCSS
T ss_pred             HHHHHHHHHHhhC--cc---cCCCCCCCeEEEEEeCCCCch
Confidence            888888886 453  11   112346788999999886543

>4hqo_A Sporozoite surface protein 2; malaria, gliding motility, VWA domain, TSR domain, extensibl ribbon, receptor on sporozoite, vaccine target; HET: FUC BGC; 2.19A {Plasmodium vivax} PDB: 4hql_A* 4hqn_A*

Probab=95.68  E-value=0.044  Score=56.59  Aligned_cols=121  Identities=15%  Similarity=0.125  Sum_probs=85.5

Q ss_pred             hh-HHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC----CHHHHHHHhcccc---CCC
Q 003455            4 YF-YAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----DVDIFLHWLSTIP---FAG   75 (818)
Q Consensus         4 Y~-~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~----~~~~fl~wL~~i~---f~G   75 (818)
                      -| +.+++++.-+++.|.-++        ..+.++||+|.+..      -..+.++.    +...++..|++|.   ..|
T Consensus        35 ~~~~~~k~~~~~lv~~l~~~~--------~~~rvglv~Fs~~~------~~~~~l~~~~~~~~~~~~~~i~~l~~~~~~~  100 (266)
T 4hqo_A           35 NWITKVIPMLNGLINSLSLSR--------DTINLYMNLFGSYT------TELIRLGSGQSIDKRQALSKVTELRKTYTPY  100 (266)
T ss_dssp             HHHHTHHHHHHHHHHTCCBCT--------TSEEEEEEEESSSE------EEEECTTSHHHHCHHHHHHHHHHHHHHCCCC
T ss_pred             HHHHHHHHHHHHHHHHcccCC--------CCcEEEEEEecCCc------ceEEecCCCCccCHHHHHHHHHHhhhccCCC
Confidence            35 467789999999985322        35899999998752      12234443    4788999999997   666


Q ss_pred             CCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHH
Q 003455           76 GGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAET  155 (818)
Q Consensus        76 GG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~  155 (818)
                      ||   ..+++||..|..+|.  ..+    .+....|..|||+.-.|..   +                       .++..
T Consensus       101 G~---T~~~~AL~~a~~~l~--~~~----~r~~~~~~iIllTDG~~~d---~-----------------------~~~~~  145 (266)
T 4hqo_A          101 GT---TSMTAALDEVQKHLN--DRV----NREKAIQLVILMTDGVPNS---K-----------------------YRALE  145 (266)
T ss_dssp             SC---CCHHHHHHHHHHHHH--TTC----SCTTSEEEEEEEECSCCSC---H-----------------------HHHHH
T ss_pred             CC---CCHHHHHHHHHHHHh--hcc----ccCCCCeEEEEEccCCCCC---c-----------------------hHHHH
Confidence            65   457889999988886  111    2345678999998765541   0                       25678


Q ss_pred             HHHHHhhcCceEEEeCCC
Q 003455          156 VAKSFVQCSVSLSVICPK  173 (818)
Q Consensus       156 la~~~~~~~I~lSiIsPr  173 (818)
                      .|+.+.+.+|.+.+|.=-
T Consensus       146 ~a~~l~~~gi~i~~iGiG  163 (266)
T 4hqo_A          146 VANKLKQRNVRLAVIGIG  163 (266)
T ss_dssp             HHHHHHHTTCEEEEEECS
T ss_pred             HHHHHHHCCCEEEEEecC
Confidence            889999999999988643

>2x31_A Magnesium-chelatase 60 kDa subunit; ligase, bacteriochlorophyll biosynthesis, photosynthesis; 7.50A {Rhodobacter capsulatus}

Probab=95.32  E-value=0.0071  Score=58.35  Aligned_cols=94  Identities=14%  Similarity=0.105  Sum_probs=63.5

Q ss_pred             hhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhh
Q 003455            3 IYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA   82 (818)
Q Consensus         3 ~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~a   82 (818)
                      ..|+..|+.+.-+++.+.          .....++||.|.+...     -....+|.+...+..+|+.+...||    ..
T Consensus        21 ~~~~~~k~~~~~~~~~~~----------~~~~~v~lv~f~~~~~-----~~~~~~~~~~~~~~~~i~~l~~~g~----T~   81 (189)
T 2x31_A           21 ARLSEAKGAVELLLGRAY----------AARDHVSLITFRGTAA-----QVLLQPSRSLTQTKRQLQGLPGGGG----TP   81 (189)
T ss_dssp             --CHHHHHHHHHHHHHSC----------TTTSCCCEEEESBSCC-----CBCTTTCSCHHHHHHHHHHCCCCBC----CC
T ss_pred             hHHHHHHHHHHHHHHHhc----------CCCcEEEEEEECCCCc-----eEecCCCCCHHHHHHHHhcCCCCCC----CC
Confidence            456777777777776551          1246889999986332     1245688899999999999986443    35


Q ss_pred             HHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCC
Q 003455           83 IAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  122 (818)
Q Consensus        83 iaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~  122 (818)
                      +.+||..|+.++..  .     ......|..|||+.-.|.
T Consensus        82 ~~~al~~a~~~l~~--~-----~~~~~~~~ivliTDG~~~  114 (189)
T 2x31_A           82 LASGMEMAMVTAKQ--A-----RSRGMTPTIALLTDGRGN  114 (189)
T ss_dssp             CHHHHHHHHHHHHT--C-----TTTCSSEEEEECCBSCCS
T ss_pred             HHHHHHHHHHHHHh--c-----cCCCCceEEEEECCCCCC
Confidence            67889999988851  1     112456788888876554

>1rrk_A Complement factor B; BB, hydrolase; 2.00A {Homo sapiens} SCOP: b.47.1.2 c.62.1.1 PDB: 1rs0_A* 1rtk_A* 2win_I* 1dle_A

Probab=95.31  E-value=0.078  Score=58.80  Aligned_cols=108  Identities=14%  Similarity=0.095  Sum_probs=71.7

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCcee-eccCCCCHHHHHHHhccccCCCCC-CChh
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQ-RSGWTKDVDIFLHWLSTIPFAGGG-FNDA   81 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~-~~g~T~~~~~fl~wL~~i~f~GGG-~~~~   81 (818)
                      .|+.+|+.|.-+++.|...+        ...+++||+|.+..-   ..+. ....|.|...++..|++|.+.++. ....
T Consensus        18 ~~~~~k~~~~~~~~~l~~~~--------~~~~v~lv~f~~~~~---~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~g~T   86 (497)
T 1rrk_A           18 NFTGAKKVLVNLIEKVASYG--------VKPRYGLVTYATYPK---IWVKVSEADSSNADWVTKQLNEINYEDHKLKSGT   86 (497)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT--------CCCEEEEEEESSSEE---EEECTTSGGGGCHHHHHHHHHHCCGGGSCCTTCC
T ss_pred             hHHHHHHHHHHHHHHhhccC--------CCceEEEEEecCCce---EeeccccccccCHHHHHHHHHhCcCccccccCcc
Confidence            57888889999999884322        247899999985321   1111 125678999999999999986542 2237


Q ss_pred             hHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCC
Q 003455           82 AIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHP  123 (818)
Q Consensus        82 aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~  123 (818)
                      .+++||..|+.+|... ....+.......|..|||+.-.+..
T Consensus        87 ~~~~al~~a~~~l~~~-~~~~~~~~~~~~~~iillTDG~~~~  127 (497)
T 1rrk_A           87 NTKKALQAVYSMMSWP-DDVPPEGWNRTRHVIILMTDGLHNM  127 (497)
T ss_dssp             CHHHHHHHHHHHHCCC-------CGGGCEEEEEEEECSCCCS
T ss_pred             CHHHHHHHHHHHhhhh-hccccccccccceEEEEEeCCCccc
Confidence            7899999999877411 1111222245778899999876543

>3hrz_D Complement factor B; serine protease, glycosilated, multi-domain, complement SYST convertase, complement alternate pathway; HET: NAG P6G; 2.20A {Homo sapiens} PDB: 2xwj_I* 3hs0_D* 2ok5_A* 2xwb_F*

Probab=95.10  E-value=0.041  Score=64.22  Aligned_cols=101  Identities=15%  Similarity=0.101  Sum_probs=71.5

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC----CHHHHHHHhccccC----CC
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----DVDIFLHWLSTIPF----AG   75 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~----~~~~fl~wL~~i~f----~G   75 (818)
                      -|+.+|+.+..+|+.|..++        ..+.+|||+|.+..      ...+.+|.    |.+.++..|++|++    .|
T Consensus       260 ~~~~~k~~~~~~i~~l~~~~--------~~~rv~lv~f~~~~------~~~~~l~~~~~~~~~~~~~~i~~l~~~~~~~~  325 (741)
T 3hrz_D          260 DFTGAKKCLVNLIEKVASYG--------VKPRYGLVTYATYP------KIWVKVSEADSSNADWVTKQLNEINYEDHKLK  325 (741)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT--------CCCEEEEEEESSSE------EEEECTTSGGGGCHHHHHHHHTTCCGGGGSSS
T ss_pred             chHHHHHHHHHHHHhhhccC--------CCceEEEEEeccCC------ceeEeecccCCcCHHHHHHHHHhcccccccCC
Confidence            47888899999999986422        25799999997642      22344554    89999999999998    55


Q ss_pred             CCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCC
Q 003455           76 GGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  122 (818)
Q Consensus        76 GG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~  122 (818)
                      ||   .++++||..|+.+|... ....+..+....|..|||+.--+.
T Consensus       326 gg---T~~~~aL~~a~~~l~~~-~~~~~~~~~~~~~~iillTDG~~n  368 (741)
T 3hrz_D          326 SG---TNTKKALQAVYSMMSWP-DDVPPEGWNRTRHVIILMTDGLHN  368 (741)
T ss_dssp             CC---CCHHHHHHHHHHHHCCC---CCCTTGGGEEEEEEEEECSCCC
T ss_pred             CC---hHHHHHHHHHHHHHhhh-hhccccchhccCeEEEEECCCccc
Confidence            54   56899999999877311 112223345678888999987554

>4hqf_A Thrombospondin-related anonymous protein, trap; malaria, parasite motility, I domain, TSR domain, receptor O sporozoite, vaccine target; 2.20A {Plasmodium falciparum} PDB: 4hqk_A 2bbx_A

Probab=94.91  E-value=0.085  Score=54.63  Aligned_cols=119  Identities=9%  Similarity=0.145  Sum_probs=80.9

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC----CHHHHHHHhcccc---CCCCC
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----DVDIFLHWLSTIP---FAGGG   77 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~----~~~~fl~wL~~i~---f~GGG   77 (818)
                      ++.+++++.-+++.|..+        ...+.++||+|.+..      -..+.++.    +...++..|++|.   +.|||
T Consensus        40 ~~~~k~~~~~~v~~l~~~--------~~~~rvglv~Fs~~~------~~~~~l~~~~~~~~~~l~~~i~~l~~~~~~~G~  105 (281)
T 4hqf_A           40 VNHAVPLAMKLIQQLNLN--------DNAIHLYASVFSNNA------REIIRLHSDASKNKEKALIIIKSLLSTNLPYGK  105 (281)
T ss_dssp             HHHHHHHHHHHHTTCCCC--------TTSEEEEEEEEETTE------EEEEEECSSCSSCHHHHHHHHHHHHHTTGGGCS
T ss_pred             HHHHHHHHHHHHHHhccC--------CCCcEEEEEEcCCCc------eEEEEccccCccCHHHHHHHHHHHhhccCCCCC
Confidence            377778888888888532        236899999998642      11223333    4788888888887   56665


Q ss_pred             CChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHH
Q 003455           78 FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVA  157 (818)
Q Consensus        78 ~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la  157 (818)
                         ..+++||..|+..|.  ...    .+....|..|||+.-.+..                         . .+....|
T Consensus       106 ---T~~~~aL~~a~~~l~--~~~----~r~~~~~~iillTDG~~~d-------------------------~-~~~~~~~  150 (281)
T 4hqf_A          106 ---TSLTDALLQVRKHLN--DRI----NRENANQLVVILTDGIPDS-------------------------I-QDSLKES  150 (281)
T ss_dssp             ---CCHHHHHHHHHHHHH--TSC----CCTTCEEEEEEEESSCCSC-------------------------H-HHHHHHH
T ss_pred             ---ccHHHHHHHHHHHHH--hcc----CCCCCCEEEEEEecCCCCC-------------------------c-HHHHHHH
Confidence               458889999987764  111    2235688889988765431                         0 2566788


Q ss_pred             HHHhhcCceEEEeCC
Q 003455          158 KSFVQCSVSLSVICP  172 (818)
Q Consensus       158 ~~~~~~~I~lSiIsP  172 (818)
                      +.+.+.+|.+-+|.=
T Consensus       151 ~~l~~~gv~i~~igi  165 (281)
T 4hqf_A          151 RKLSDRGVKIAVFGI  165 (281)
T ss_dssp             HHHHHTTCEEEEEEE
T ss_pred             HHHHHCCCEEEEEeC
Confidence            888899999888753

>3k6s_A Integrin alpha-X; cell receptor, adhesion molecule, cell adhesion, pyrrolidone carboxylic acid; HET: NAG MAN; 3.50A {Homo sapiens} PDB: 3k71_A* 3k72_A*

Probab=93.89  E-value=0.12  Score=64.20  Aligned_cols=120  Identities=13%  Similarity=0.089  Sum_probs=87.0

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC--CHHHHHHHhccccCCCCCCChhh
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDIFLHWLSTIPFAGGGFNDAA   82 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~--~~~~fl~wL~~i~f~GGG~~~~a   82 (818)
                      |+.+|+++..+++.|..          ..+.+|||+|.+..      -..+.++.  |...++..+++|+..|||   .+
T Consensus       148 f~~~k~fv~~lv~~~~~----------~~~rVglV~Fs~~~------~~~~~lt~~~~~~~l~~ai~~i~~~gG~---T~  208 (1095)
T 3k6s_A          148 FATMMNFVRAVISQFQR----------PSTQFSLMQFSNKF------QTHFTFEEFRRSSNPLSLLASVHQLQGF---TY  208 (1095)
T ss_dssp             HHHHHHHHHHHHHSSCS----------SSEEEEEEEESSSE------EEEECSHHHHSCSCGGGGTTTCCCCCSC---BC
T ss_pred             HHHHHHHHHHHHHhccc----------cccEEEEEEECCeE------EEEecCcccCCHHHHHHHHhhhhcccCC---Ch
Confidence            78888999999999951          25899999997642      22345553  666788889999998875   67


Q ss_pred             HHHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHh
Q 003455           83 IAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFV  161 (818)
Q Consensus        83 iaEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~  161 (818)
                      +++||..|+. +|.  ..   +..+....|..|||+.-.+..-+                         .+.+.+|+.+.
T Consensus       209 ~g~AL~~a~~~lf~--~~---~g~R~~~~kviIllTDG~~~~d~-------------------------~~~~~~a~~~r  258 (1095)
T 3k6s_A          209 TATAIQNVVHRLFH--AS---YGARRDAAKILIVITDGKKEGDS-------------------------LDYKDVIPMAD  258 (1095)
T ss_dssp             HHHHHHHHHTTTTS--TT---TTCCSSSEEEEEEEESSCCBSCS-------------------------SCHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcc--cc---ccCCCCCCeEEEEEeCCCcCCCc-------------------------hhHHHHHHHHH
Confidence            8999999996 553  11   11235678899999876553211                         26778889999


Q ss_pred             hcCceEEEeCCC
Q 003455          162 QCSVSLSVICPK  173 (818)
Q Consensus       162 ~~~I~lSiIsPr  173 (818)
                      +.+|.+-.|.=.
T Consensus       259 ~~GI~i~aIGVG  270 (1095)
T 3k6s_A          259 AAGIIRYAIGVG  270 (1095)
T ss_dssp             HHCEEECCEEBS
T ss_pred             HCCCEEEEEecc
Confidence            999998887654

>2odp_A Complement C2; C3/C5 convertase, complement serin protease, human complement system, glycoprotein, SP, VWFA,; HET: NAG; 1.90A {Homo sapiens} PDB: 2odq_A* 2i6q_A* 2i6s_A*

Probab=93.35  E-value=0.3  Score=54.41  Aligned_cols=110  Identities=13%  Similarity=0.145  Sum_probs=69.0

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCC-CChhh
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGG-FNDAA   82 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG-~~~~a   82 (818)
                      -|+..|+.|..+++.|....        ...+++||+|.+..-. .+.+ ....+.|..+++..|++|.+.++. .....
T Consensus        26 ~~~~~k~~~~~l~~~l~~~~--------~~~rv~lv~f~~~~~~-~~~l-~~~~~~~~~~~~~~l~~l~~~~~~~~ggT~   95 (509)
T 2odp_A           26 DFLIFKESASLMVDRIFSFE--------INVSVAIITFASEPKV-LMSV-LNDNSRDMTEVISSLENANYKDHENGTGTN   95 (509)
T ss_dssp             HHHHHHHHHHHHHHHHHTTC--------CCEEEEEEEESSSEEE-EECT-TSGGGGCHHHHHHHHHTCCGGGGTTCCSCC
T ss_pred             hHHHHHHHHHHHHHHhhccC--------CCceEEEEEccCCCce-eEec-cCCCCCCHHHHHHHHHhcccccCCCCCCcc
Confidence            46788889999999884311        2489999999763311 1111 112344999999999999998633 13367


Q ss_pred             HHHHHHHHHhhhccCCC--CCCCCCCCCCccEEEEeecCCCCC
Q 003455           83 IAEGLSEALMMFSVAPN--GSQNQQNVDGQRHCILVAASNPHP  123 (818)
Q Consensus        83 iaEGLa~AL~~~~~~~~--~~~~~~~~~~qkhCILi~nSpP~~  123 (818)
                      +++||..|+.+|.....  +..........|..|||+.-.+..
T Consensus        96 ~~~aL~~a~~~l~~~~~~~~~~~~~~~~~~~~iillTDG~~~~  138 (509)
T 2odp_A           96 TYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSNM  138 (509)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTSHHHHTEEEEEEEESCSCCCS
T ss_pred             HHHHHHHHHHHHhhcccccccccccccccceEEEEECCCCccC
Confidence            88889999987741000  000000113567889998876543

>3iot_A Maltose-binding protein, huntingtin fusion protei; HTT-EX1, HD, sugar transport, transport, apoptos disease mutation, nucleus; 3.50A {Escherichia coli k-12} PDB: 3io6_A 3io4_A 3ior_A 3iou_A 3iov_A 3iow_A

Probab=93.07  E-value=0.018  Score=63.14  Aligned_cols=20  Identities=25%  Similarity=0.388  Sum_probs=15.0

Q ss_pred             HHHHHHHHhhc-CceEEEeCC
Q 003455          153 AETVAKSFVQC-SVSLSVICP  172 (818)
Q Consensus       153 ~e~la~~~~~~-~I~lSiIsP  172 (818)
                      .+.+++.|.+. +|++.++..
T Consensus        20 ~~~~~~~F~~~~gi~V~~~~~   40 (449)
T 3iot_A           20 LAEVGKKFEKDTGIKVTVEHP   40 (449)
T ss_dssp             HHHHHHHHHHHHSCCEEEECC
T ss_pred             HHHHHHHHhhccCCEEEEEec
Confidence            56777888665 888888874

>1jey_B KU80; double-strand DNA break repair, non-homologous END-joining, protein/nucleic acid complex, alpha/beta domain, beta barrel; HET: DNA; 2.50A {Homo sapiens} SCOP: b.131.1.2 c.62.1.4 PDB: 1jeq_B*

Probab=92.46  E-value=0.89  Score=52.28  Aligned_cols=123  Identities=20%  Similarity=0.284  Sum_probs=74.0

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCC---------CCcCceeeccCC-CCHHHHHHHhcc-cc
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGS---------YCACLVQRSGWT-KDVDIFLHWLST-IP   72 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~---------~~~~~v~~~g~T-~~~~~fl~wL~~-i~   72 (818)
                      .|+..+++|.-+++-..        .....-+.|||+|++...         |..++|-. ..+ .+.+.+ .-|+. |.
T Consensus        30 rl~~ak~~i~~~i~~ki--------~~~~~D~vGlv~f~~~~~~~plt~d~~y~~i~vl~-~l~~~~~~~l-~~l~~~l~   99 (565)
T 1jey_B           30 PFEQAKKVITMFVQRQV--------FAENKDEIALVLFGTDGTDNPLSGGDQYQNITVHR-HLMLPDFDLL-EDIESKIQ   99 (565)
T ss_dssp             HHHHHHHHHHHHHHHHH--------HTTCCCEEEEEEESCSSCBSTTCTTTCSTTEEEEE-EEECCCHHHH-HHHHTTCC
T ss_pred             cHHHHHHHHHHHHHHHh--------cCCCCCEEEEEEEccCCCCCccccccCCCceEEee-cCCCCCHHHH-HHHHhhcc
Confidence            34555666665555310        011347899999998762         22222221 222 344444 45665 53


Q ss_pred             CCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecC-CCCCCCCCCcCcccccccccchhhhhhhccCC
Q 003455           73 FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAAS-NPHPLPTPVYRPQMQNLDQNENNEAQAESRLS  151 (818)
Q Consensus        73 f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nS-pP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~  151 (818)
                         +|....+|.+||..|+.+|.  ....   ......|+.||+++- +|+.                          -.
T Consensus       100 ---~~~~~t~i~~al~~A~~~l~--~~~~---~~k~~~krIiLlTDg~~~~~--------------------------~~  145 (565)
T 1jey_B          100 ---PGSQQADFLDALIVSMDVIQ--HETI---GKKFEKRHIEIFTDLSSRFS--------------------------KS  145 (565)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHH--HHSS---SSCCSEEEEEEECCCCSCCC--------------------------CT
T ss_pred             ---CCCccccHHHHHHHHHHHHH--HHhh---cccccccEEEEEeCCCCCCC--------------------------HH
Confidence               23345779999999999995  1100   112246888888854 3432                          02


Q ss_pred             CHHHHHHHHhhcCceEE-Ee
Q 003455          152 DAETVAKSFVQCSVSLS-VI  170 (818)
Q Consensus       152 ~~e~la~~~~~~~I~lS-iI  170 (818)
                      +++++|+.+.+.||.|. ||
T Consensus       146 ~~~~~a~~l~~~gI~i~~vi  165 (565)
T 1jey_B          146 QLDIIIHSLKKCDISLQFFL  165 (565)
T ss_dssp             THHHHHHHHHHTTEEEEEEE
T ss_pred             HHHHHHHHHHhcCcEEEEEe
Confidence            78899999999999999 66

>1mjn_A Integrin alpha-L; rossmann fold, immune system; 1.30A {Homo sapiens} SCOP: c.62.1.1 PDB: 3hi6_A 1mq8_B* 3eoa_I 3eob_I 1rd4_A* 1lfa_A 1zon_A 1zoo_A 1zop_A 1dgq_A 1xdd_A* 1xdg_A* 1xuo_A* 3e2m_A* 3bqn_B* 1cqp_A* 3bqm_B* 2ica_A* 2o7n_A* 3m6f_A* ...

Probab=91.87  E-value=0.26  Score=47.46  Aligned_cols=96  Identities=8%  Similarity=0.016  Sum_probs=65.3

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCC--CHHHHHHHhccccCCCCCCChh
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDIFLHWLSTIPFAGGGFNDA   81 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~--~~~~fl~wL~~i~f~GGG~~~~   81 (818)
                      -|+..++++..+++.|.  +        ..+.++||.|.+..-      ..+.|+.  +...+...+++|++.+||   .
T Consensus        19 ~~~~~k~~~~~~~~~l~--~--------~~~rv~vv~fs~~~~------~~~~l~~~~~~~~~~~~~~~i~~~~g~---T   79 (179)
T 1mjn_A           19 EFQKILDFMKDVMKKCS--N--------TSYQFAAVQFSTSYK------TEFDFSDYVKRKDPDALLKHVKHMLLL---T   79 (179)
T ss_dssp             HHHHHHHHHHHHHHHTT--T--------SSEEEEEEEESSSEE------EEECHHHHHHHCCHHHHHTTCCCCCBC---C
T ss_pred             HHHHHHHHHHHHHHHhC--C--------CCeEEEEEEECCcee------EEEcCcccCCHHHHHHHHHhcccCCCC---C
Confidence            47888889999999882  1        347999999986431      1244443  223466778888887764   5


Q ss_pred             hHHHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCC
Q 003455           82 AIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHP  123 (818)
Q Consensus        82 aiaEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~  123 (818)
                      ++++||..|+. +|..  .   +..+....|.+||++.-.+..
T Consensus        80 ~~~~aL~~a~~~~~~~--~---~g~r~~~~~~iillTDG~~~~  117 (179)
T 1mjn_A           80 NTFGAINYVATEVFRE--E---LGARPDATKVLIIITDGEATD  117 (179)
T ss_dssp             CHHHHHHHHHHHTSSG--G---GTCCTTSEEEEEEEESSCCSS
T ss_pred             hHHHHHHHHHHHhccc--c---cCCCCCCCeEEEEEcCCCCCC
Confidence            78999999994 7741  1   112345788999999876653

>4fx5_A VON willebrand factor type A; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, blood clotting; HET: MSE; 1.73A {Catenulispora acidiphila}

Probab=90.31  E-value=1.4  Score=49.49  Aligned_cols=89  Identities=12%  Similarity=0.067  Sum_probs=63.3

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccC--------CCCHHHHHHHhccccCCC
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGW--------TKDVDIFLHWLSTIPFAG   75 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~--------T~~~~~fl~wL~~i~f~G   75 (818)
                      -|+..|+-+.-+|+.+..           ...++||.|.+..-.      .+.+        ..+...+..+|++|...|
T Consensus        96 rl~~ak~a~~~ll~~L~~-----------~drv~lV~Fs~~a~~------~~p~t~~l~~~~~~~~~~l~~~I~~L~~~G  158 (464)
T 4fx5_A           96 KMMAAKEATKVAIDTLTD-----------GAFFAVVAGTEGARV------VYPTGGQLLRADYQSRAAAKEAVGRLHANG  158 (464)
T ss_dssp             HHHHHHHHHHHHHHHSCT-----------TCEEEEEEESSSEEE------EESSSSSCEECSHHHHHHHHHHHHTCCCCS
T ss_pred             hHHHHHHHHHHHHHhCCC-----------CCEEEEEEEcCceEE------EecCCcccccCCHHHHHHHHHHHHcCCCCC
Confidence            366777777777777742           357999999765321      2232        368899999999999644


Q ss_pred             CCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCC
Q 003455           76 GGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  122 (818)
Q Consensus        76 GG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~  122 (818)
                       |   ..+.+||..|+.+|.  .       .....|+.|||+.--+.
T Consensus       159 -g---T~l~~aL~~A~~~l~--~-------~~~~~~~IILLTDG~~~  192 (464)
T 4fx5_A          159 -G---TAMGRWLAQAGRIFD--T-------APSAIKHAILLTDGKDE  192 (464)
T ss_dssp             -C---CCHHHHHHHHHHHHT--T-------CTTSEEEEEEEESSCCT
T ss_pred             -C---CcHHHHHHHHHHHHh--c-------CCCCCCEEEEEcCCCCC
Confidence             3   558999999999985  1       22456888999887654

>3rag_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tructural genomics; 1.80A {Alicyclobacillus acidocaldarius subsp}

Probab=88.55  E-value=0.77  Score=47.91  Aligned_cols=80  Identities=11%  Similarity=0.080  Sum_probs=58.0

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCCh
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFND   80 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~   80 (818)
                      |+.=|+..|+.|.-++..|....        ..++++||.|+.....-  .+-.-.||++. .+..+|+.|.. ||+-. 
T Consensus       147 M~~kl~~vk~al~~Ll~sl~~~~--------~~~~VavV~F~~~~~~~--~~ll~pfT~~~-~~~~~l~~L~a-gG~Tp-  213 (242)
T 3rag_A          147 MRDKIPTVREAVRDLALSLKVRS--------GPLAVSVIAFPGKGEEA--TRLVQPFSSEV-NVAALEAELVA-RGGTP-  213 (242)
T ss_dssp             GTTTHHHHHHHHHHHHHHHTTSS--------SCEEEEEEEESCSTTCS--CEEEEEEESSC-CHHHHHHHCCC-CSCCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHhccC--------CCcEEEEEEECCCCccc--eeecCCCCChH-HHHHHHhhCCC-CCCCc-
Confidence            33346777888888888885321        25899999999876522  22224889998 88899999974 66533 


Q ss_pred             hhHHHHHHHHHhhhc
Q 003455           81 AAIAEGLSEALMMFS   95 (818)
Q Consensus        81 ~aiaEGLa~AL~~~~   95 (818)
                        +++||..|+.+|+
T Consensus       214 --lg~AL~~A~~~~~  226 (242)
T 3rag_A          214 --TGPAIDHAADLLL  226 (242)
T ss_dssp             --HHHHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHH
Confidence              8899999998885

>1jey_A KU70; double-strand DNA break repair, non-homologous END-joining, protein/nucleic acid complex, alpha/beta domain, beta barrel; HET: DNA; 2.50A {Homo sapiens} SCOP: b.131.1.1 c.62.1.3 PDB: 1jeq_A* 3rzx_B

Probab=87.20  E-value=2.4  Score=49.31  Aligned_cols=110  Identities=20%  Similarity=0.152  Sum_probs=65.7

Q ss_pred             cceEEEEEEccCCC-----CCcCceeeccCCCCHHHHHHHhcccc---------CCCCCCChhhHHHHHHHHHhhhccCC
Q 003455           33 NVELSLVTFNTHGS-----YCACLVQRSGWTKDVDIFLHWLSTIP---------FAGGGFNDAAIAEGLSEALMMFSVAP   98 (818)
Q Consensus        33 ~~~yaLVvf~~~~~-----~~~~~v~~~g~T~~~~~fl~wL~~i~---------f~GGG~~~~aiaEGLa~AL~~~~~~~   98 (818)
                      .-+.|||+|++...     |..++|.+.==..+...+..+.+-+.         ..|. ....+|++||..|+.+|.  .
T Consensus        80 ~D~vGlVlfgt~~t~n~l~~d~i~v~~~L~~~~~~~ik~l~~l~~~~~~~~~~~~~g~-~~~t~l~daL~~a~~~f~--~  156 (609)
T 1jey_A           80 RDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGH-GSDYSLSEVLWVCANLFS--D  156 (609)
T ss_dssp             CCEEEEEEESCSSCBSTTCCTTEEEEEEEECCCHHHHHHHHTTSHHHHHHHHHHHHCC-SCCCCHHHHHHHHHHHHH--T
T ss_pred             CCeEEEEEEccCCCCCcCCCCCeEEEecCCCCCHHHHHHHHHHhhcccchhhhhhcCC-CCCCCHHHHHHHHHHHHH--h
Confidence            47899999999882     33334433111123333332222221         1121 234789999999999996  1


Q ss_pred             CCCCCCCCCCCccEEEEeecC-CCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeC
Q 003455           99 NGSQNQQNVDGQRHCILVAAS-NPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVIC  171 (818)
Q Consensus        99 ~~~~~~~~~~~qkhCILi~nS-pP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIs  171 (818)
                      .     ......|+.||+++- +|+.--                   ...  ..+++.+|+.+.+.||.|-+|-
T Consensus       157 ~-----~~k~~~k~IiL~TDg~~p~~~~-------------------~~~--~~~~~~~a~~l~~~gI~i~~ig  204 (609)
T 1jey_A          157 V-----QFKMSHKRIMLFTNEDNPHGND-------------------SAK--ASRARTKAGDLRDTGIFLDLMH  204 (609)
T ss_dssp             C-----SSCEEEEEEEEEESCSCTTTTC-------------------HHH--HHHHHHHHHHHHHHTEEEEEEE
T ss_pred             h-----chhhcCCEEEEEcCCCCCCCCc-------------------hHH--HHHHHHHHHHHHhcCcEEEEEe
Confidence            1     112247888888874 455310                   000  1257899999999999999983

---

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	818
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	4e-09
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	3e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	1e-04
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	3e-08
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	4e-08
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	4e-08
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	1e-07
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	5e-07
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	6e-07
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	7e-07
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	1e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	8e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	2e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	2e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	2e-04
d1s6da_	103	a.52.1.3 (A:) Methionine-rich 2S protein (albumin	0.001
g1pnb.1	106	a.52.1.3 (A:,B:) Napin BNIb {Rape (Brassica napus)	0.001
d2oeza1	245	e.68.1.1 (A:1-245) Uncharacterized protein VP2528	0.002
d1psya_	125	a.52.1.3 (A:) 2S albumin RicC3 {Castor bean (Ricin	0.002
d1fxka_	107	a.2.5.1 (A:) Prefoldin beta subunit {Archaeon Meth	0.004

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.3 bits (135), Expect = 4e-09
 Identities = 17/104 (16%), Positives = 44/104 (42%), Gaps = 3/104 (2%)

Query: 667 MVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 726
           +   + +I  ++ +    Q   +   +MQ + +     + +  Q+ L QL +++   + Q
Sbjct: 199 LTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQ 258

Query: 727 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 770
                 +Q+    L+ Q+Q   L++  Q      + ++  LQ +
Sbjct: 259 LLK---EQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTK 299

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 2e-07
 Identities = 15/106 (14%), Positives = 46/106 (43%), Gaps = 5/106 (4%)

Query: 673 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
            ++ ++++   ++ + +  Q     L   Q    Q  +Q+    Q+ + QL ++     +
Sbjct: 198 TLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEK-----M 252

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 778
           +   +  L++Q++   L+ Q+Q   +++  Q      + ++   Q 
Sbjct: 253 ENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQT 298

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 3e-07
 Identities = 16/110 (14%), Positives = 50/110 (45%), Gaps = 5/110 (4%)

Query: 666 DMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 725
           +++    +        + Q  Q    ++ + +++  +    Q   + L ++Q++    Q 
Sbjct: 176 EILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRK--NEQM 233

Query: 726 QQQIPQLQQQSMPQLQQQQQ---LPQLQQQQQLPQMQQQQQLPQLQQQQQ 772
            +Q  +  Q+ + QL ++ +   +  L++Q++   ++ Q+Q   L++  Q
Sbjct: 234 MEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQ 283

>d1f5na1 a.114.1.1 (A:284-583) Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 300

class: All alpha proteins
fold: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
superfamily: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
family: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
domain: Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 1e-04
 Identities = 19/151 (12%), Positives = 59/151 (39%), Gaps = 5/151 (3%)

Query: 630 QLQEKKLCAVIQLPSQTLLLSVSDKACRLIG--MLFPGDMVVFKPQISSQQQQQLQQQQQ 687
           +    +   ++Q+    L   V        G   LF   +   K +   + ++ +Q ++ 
Sbjct: 118 EASSDRCSGLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEI 177

Query: 688 QQQHQQMQSQLQHQQLSQLQQQQQQLPQL---QQQIPQLQQQQQIPQLQQQSMPQLQQQQ 744
            Q + + +  +    L   Q   ++  ++   + +    Q   ++    Q+   Q+ +Q+
Sbjct: 178 LQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQK 237

Query: 745 QLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 775
           +    +  +QL +  +  ++  L++Q++   
Sbjct: 238 ERSYQEHLKQLTEKMENDRVQLLKEQERTLA 268

>d1s6da_ a.52.1.3 (A:) Methionine-rich 2S protein (albumin 8) {Common sunflower (Helianthus annuus) [TaxId: 4232]} Length = 103

class: All alpha proteins
fold: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
superfamily: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
family: Seed storage protein, 2S albumin
domain: Methionine-rich 2S protein (albumin 8)
species: Common sunflower (Helianthus annuus) [TaxId: 4232]

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 11/86 (12%), Positives = 30/86 (34%), Gaps = 2/86 (2%)

Query: 675 SSQQQQQLQQQQQQQQHQQ--MQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 732
            S   QQ+++ +         M++  +  Q+S   +++        Q+  L ++   P +
Sbjct: 8   ESGCYQQMEEAEMLNHCGMYLMKNLGERSQVSPRMREEDHKQLCCMQLKNLDEKCMCPAI 67

Query: 733 QQQSMPQLQQQQQLPQLQQQQQLPQM 758
                  +  + +   +     LP  
Sbjct: 68  MMMLNEPMWIRMRDQVMSMAHNLPIE 93

>d1psya_ a.52.1.3 (A:) 2S albumin RicC3 {Castor bean (Ricinus communis) [TaxId: 3988]} Length = 125

class: All alpha proteins
fold: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
superfamily: Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
family: Seed storage protein, 2S albumin
domain: 2S albumin RicC3
species: Castor bean (Ricinus communis) [TaxId: 3988]

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 20/101 (19%), Positives = 42/101 (41%), Gaps = 14/101 (13%)

Query: 675 SSQQQQQLQQQ----------QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 724
           S Q +Q++Q++          Q   +    +  L+       QQ+ QQL Q   Q+ Q++
Sbjct: 15  SQQCRQEVQRKDLSSCERYLRQSSSRRSTGEEVLRMPGDENQQQESQQLQQCCNQVKQVR 74

Query: 725 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLP 765
            + Q   ++  +  Q+QQ Q       ++     Q+  ++ 
Sbjct: 75  DECQCEAIKYIAEDQIQQGQL----HGEESERVAQRAGEIV 111

>d1fxka_ a.2.5.1 (A:) Prefoldin beta subunit {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} Length = 107

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Prefoldin
family: Prefoldin
domain: Prefoldin beta subunit
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 16/102 (15%), Positives = 44/102 (43%), Gaps = 7/102 (6%)

Query: 685 QQQQQQHQQMQSQLQ--HQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ 742
           Q Q  Q QQ+Q Q Q    Q   ++ Q  +  +  +++ +     ++ +     + ++ +
Sbjct: 4   QHQLAQFQQLQQQAQAISVQKQTVEMQINETQKALEELSRAADDAEVYKSSGNILIRVAK 63

Query: 743 QQQLPQLQQ-----QQQLPQMQQQQQLPQLQQQQQLSQPQQM 779
            +   +LQ+     Q +   +++Q++    + Q+     Q+ 
Sbjct: 64  DELTEELQEKLETLQLREKTIERQEERVMKKLQEMQVNIQEA 105

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	818
d1tyeb2	248	Integrin beta A domain {Human (Homo sapiens) [TaxI	98.75
d1ijba_	202	von Willebrand factor A1 domain, vWA1 {Human (Homo	97.43
d1pt6a_	192	Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId	97.42
d1atza_	184	von Willebrand factor A3 domain, vWA3 {Human (Homo	97.38
d1v7pc_	193	Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId	97.38
d1n3ya_	189	Integrin alpha-x beta2 {Human (Homo sapiens) [TaxI	97.3
d1mf7a_	194	Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha sub	96.61
d1shux_	181	Capillary morphogenesis protein 2 domain {Human (H	96.6
d1q0pa_	209	Complement factor B domain {Human (Homo sapiens) [	96.38
d1mjna_	179	Integrin CD11a/CD18 (Leukocyte function associated	95.8
d1jeyb2	236	Ku80 subunit N-terminal domain {Human (Homo sapien	95.42
d1jeya2	220	Ku70 subunit N-terminal domain {Human (Homo sapien	86.13

>d1tyeb2 c.62.1.1 (B:107-354) Integrin beta A domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin beta A domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.75  E-value=8.1e-08  Score=97.37  Aligned_cols=172  Identities=9%  Similarity=0.011  Sum_probs=119.2

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCc------------------------eeecc
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACL------------------------VQRSG   56 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~------------------------v~~~g   56 (818)
                      |+.|++.+|+-|..+++.+..        ......+|||.|+++...+...                        .....
T Consensus        18 M~~~i~~vk~~i~~i~~~l~~--------~~~~~r~g~~~f~D~~~~p~~~~~~~~~~~~p~~~~~~~~~~~f~~~~~~~   89 (248)
T d1tyeb2          18 MKDDLWSIQNLGTKLATQMRK--------LTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLT   89 (248)
T ss_dssp             GGGGHHHHHHHHHHHHHHHHH--------HCSCEEEEEEEECCCSSTTTSCCCSGGGGTCGGGGGTSCCCCCCSEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHh--------hCcCceEEEEEEEecccCccccccchhhccCccccccccccccccceecCC
Confidence            899999999999999998853        1236899999999986433111                        12358


Q ss_pred             CCCCHHHHHHHhccccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCC------CcC
Q 003455           57 WTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTP------VYR  130 (818)
Q Consensus        57 ~T~~~~~fl~wL~~i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~------~~~  130 (818)
                      ||+|..+|..+|+++...|||....+.-+||..|+.|.+  ..+    =+....|..|||+..|||...--      -++
T Consensus        90 ~t~d~~~f~~~l~~~~~~GggD~pE~~~~Al~~a~~~~~--~i~----Wr~~a~r~viliTDA~~H~~~d~~l~g~~~~~  163 (248)
T d1tyeb2          90 LTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDE--KIG----WRNDASHLLVFTTDAKTHIALDGRLAGIVQPN  163 (248)
T ss_dssp             EESCHHHHHHHHTTCCCCCCSSSSBCHHHHHHHHHHCHH--HHT----CCTTSEEEEEEEESSCBCCTTGGGGGTCCSCC
T ss_pred             CCCCHHHHHHHHhheecccCCCCcchHHHHHHHHHHHhh--hCC----CCCCccEEEEEECCCCcccccccccccccccC
Confidence            999999999999999999999888899999999886642  011    13567789999999999953210      011


Q ss_pred             cccccccccchhhhhhhccCCCHHHHHHHHhhcCceEEEeCCCc-chHHHHHHHHhc
Q 003455          131 PQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ-LPKLTAIYNAAK  186 (818)
Q Consensus       131 p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~~I~lSiIsPrk-lp~L~~lf~~a~  186 (818)
                      ...|.+...............+++++++.+.+++|.+-++..++ +..+++|-+...
T Consensus       164 d~~~~~~~~~~~~~~~~~dyps~~ql~~~l~~~~i~~ifavt~~~~~~Y~~l~~~~~  220 (248)
T d1tyeb2         164 DGQCHVGSDNHYSASTTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSELIP  220 (248)
T ss_dssp             CCCCCBCTTSBBGGGGTSCCCCHHHHHHHHHHTTEEEEEEECGGGHHHHHHHHHTST
T ss_pred             CCccccCCCCcccccccccCCCHHHHHHHHHHhCcEEEEEECchhhHHHHHHHHhcC
Confidence            22222221111111222233479999999999999987777654 566666666553

>d1ijba_ c.62.1.1 (A:) von Willebrand factor A1 domain, vWA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: von Willebrand factor A1 domain, vWA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.43  E-value=0.00059  Score=65.38  Aligned_cols=134  Identities=15%  Similarity=0.145  Sum_probs=96.1

Q ss_pred             hhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhh
Q 003455            3 IYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA   82 (818)
Q Consensus         3 ~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~a   82 (818)
                      ..|+.+|+++..+++.|.-++        ..+++|||+|.+..-    .+-.+.++.+..+++.-++.|.+.||+..  .
T Consensus        29 ~~f~~~k~fv~~~i~~l~~~~--------~~~rvavv~y~~~~~----~~~~l~~~~~~~~l~~~i~~l~~~~g~~~--~   94 (202)
T d1ijba_          29 AEFEVLKAFVVDMMERLRVSQ--------KWVRVAVVEYHDGSH----AYIGLKDRKRPSELRRIASQVKYAGSQVA--S   94 (202)
T ss_dssp             HHHHHHHHHHHHHHHTBCBST--------TSEEEEEEEESSSEE----EEECTTCCCCHHHHHHHHHTCCCCCBSCC--C
T ss_pred             HHHHHHHHHHHHHHHHhccCC--------CCcEEEEEEEeccee----eecCCcccchHHHHHHHHHhhhhhhhccc--c
Confidence            458899999999999996433        258999999988541    11235566899999999999999988764  4


Q ss_pred             HHHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHh
Q 003455           83 IAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFV  161 (818)
Q Consensus        83 iaEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~  161 (818)
                      +.++|..|+. +|.       +..+....|+.|||.......-                        ...+++..|+.+.
T Consensus        95 ~~~al~~~~~~~~~-------~~~r~~~~k~vivitdg~~~~~------------------------~~~~~~~~~~~l~  143 (202)
T d1ijba_          95 TSEVLKYTLFQIFS-------KIDRPEASRIALLLMASQEPQR------------------------MSRNFVRYVQGLK  143 (202)
T ss_dssp             HHHHHHHHHHHTSS-------SCSCTTSEEEEEEEECCCCCGG------------------------GCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhh-------hccCCCCcceEEEecccCCCcc------------------------cchHHHHHHHHHH
Confidence            6777888875 443       1234568899999998754321                        1136789999999


Q ss_pred             hcCceEEEeCC--C-cchHHHHH
Q 003455          162 QCSVSLSVICP--K-QLPKLTAI  181 (818)
Q Consensus       162 ~~~I~lSiIsP--r-klp~L~~l  181 (818)
                      +.||.+-+|.=  . ....|+.|
T Consensus       144 ~~gv~i~~Vgig~~~~~~~L~~i  166 (202)
T d1ijba_         144 KKKVIVIPVGIGPHANLKQIRLI  166 (202)
T ss_dssp             HTTEEEEEEEESTTSCHHHHHHH
T ss_pred             HcCCeEEEEEeCCcCCHHHHHHH
Confidence            99999888853  2 23335554

>d1pt6a_ c.62.1.1 (A:) Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin alpha1-beta1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.42  E-value=0.0008  Score=63.48  Aligned_cols=123  Identities=11%  Similarity=0.095  Sum_probs=87.2

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccC--CCCHHHHHHHhccccCCCCCC
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGW--TKDVDIFLHWLSTIPFAGGGF   78 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~--T~~~~~fl~wL~~i~f~GGG~   78 (818)
                      |+. |+..|+++..+++.|+-++        ..+.+|||.|.+..      ...+.+  +.+...++..++++.+.||+.
T Consensus        14 ~~~-~~~~k~f~~~~i~~~~i~~--------~~~rv~vv~fs~~~------~~~~~l~~~~~~~~~~~~i~~~~~~~g~~   78 (192)
T d1pt6a_          14 IYP-WDSVTAFLNDLLKRMDIGP--------KQTQVGIVQYGENV------THEFNLNKYSSTEEVLVAAKKIVQRGGRQ   78 (192)
T ss_dssp             CCC-HHHHHHHHHHHHTTSCBST--------TSBEEEEEEESSSE------EEEECTTTCSSHHHHHHHHHTCCCCCCSS
T ss_pred             CCC-HHHHHHHHHHHHHHhccCC--------CCcEEEEEEEeccE------EEEEeCCcchhhHHHHHHHhhhhhhhhhc
Confidence            444 7888999999999995433        35799999997542      112333  347889999999999988875


Q ss_pred             ChhhHHHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHH
Q 003455           79 NDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVA  157 (818)
Q Consensus        79 ~~~aiaEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la  157 (818)
                      ..  .+.||..|+. +|.  .   .+..+....|.+||++...++.-                          .+.++.|
T Consensus        79 ~~--~~~al~~~~~~~~~--~---~~g~R~~~~kviillTDG~~~d~--------------------------~~~~~~a  125 (192)
T d1pt6a_          79 TM--TALGTDTARKEAFT--E---ARGARRGVKKVMVIVTDGESHDN--------------------------HRLKKVI  125 (192)
T ss_dssp             CC--HHHHHHHHHHTTTS--G---GGTCCTTCEEEEEEEESSCCSCS--------------------------HHHHHHH
T ss_pred             cc--hHHHHHHHHHhhhc--c---ccCCCCCcceEEEEEecCCCCcc--------------------------hhhHHHH
Confidence            44  4567877775 443  1   11124578899999998765420                          1466889


Q ss_pred             HHHhhcCceEEEeC
Q 003455          158 KSFVQCSVSLSVIC  171 (818)
Q Consensus       158 ~~~~~~~I~lSiIs  171 (818)
                      +.+.+.||.+-+|.
T Consensus       126 ~~lk~~gi~v~~ig  139 (192)
T d1pt6a_         126 QDCEDENIQRFSIA  139 (192)
T ss_dssp             HHHHHTTEEEEEEE
T ss_pred             HHHHHCCCeEEEEE
Confidence            99999999988874

>d1atza_ c.62.1.1 (A:) von Willebrand factor A3 domain, vWA3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: von Willebrand factor A3 domain, vWA3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.38  E-value=0.00072  Score=63.92  Aligned_cols=132  Identities=11%  Similarity=0.145  Sum_probs=92.4

Q ss_pred             hhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhh
Q 003455            3 IYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA   82 (818)
Q Consensus         3 ~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~a   82 (818)
                      ..|+.+|+++..+++.|+-++        ..+.+|||.|++.. +   .+-....+++..+++..|++|.+.||+   ..
T Consensus        18 ~~f~~~k~~v~~~i~~~~i~~--------~~~rv~vv~f~~~~-~---~~~~l~~~~~~~~l~~~i~~l~~~gg~---t~   82 (184)
T d1atza_          18 SYFDEMKSFAKAFISKANIGP--------RLTQVSVLQYGSIT-T---IDVPWNVVPEKAHLLSLVDVMQREGGP---SQ   82 (184)
T ss_dssp             HHHHHHHHHHHHHHHHSCBST--------TSEEEEEEEESSSE-E---EEECTTCCCCHHHHHHHHHTCCCCCCC---CC
T ss_pred             HHHHHHHHHHHHHHHhcCCCC--------CCcEEEEEEEeccc-e---eeccccccccHHHHHHHHHhhhhcccc---cc
Confidence            468888999999999995332        25789999996432 1   112345567999999999999998876   35


Q ss_pred             HHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhh
Q 003455           83 IAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQ  162 (818)
Q Consensus        83 iaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~  162 (818)
                      +++||..|+..+.. ....   .+....|..||++...|+.                            +.+..|+++.+
T Consensus        83 ~~~al~~~~~~~~~-~~~g---~R~~~~kvvvlltdg~~~d----------------------------~~~~~a~~lk~  130 (184)
T d1atza_          83 IGDALGFAVRYLTS-EMHG---ARPGASKAVVILVTDVSVD----------------------------SVDAAADAARS  130 (184)
T ss_dssp             HHHHHHHHHHHHHS-CCTT---CCTTSEEEEEEEECSCCSS----------------------------CCHHHHHHHHH
T ss_pred             hhhhhhHHHHHhhh-hhcC---CCCCCceEEEEEEecCccc----------------------------hhhHHHHHHHH
Confidence            68888888865431 1111   2456788999998875432                            34577889999


Q ss_pred             cCceEEEeC--CC-cchHHHHH
Q 003455          163 CSVSLSVIC--PK-QLPKLTAI  181 (818)
Q Consensus       163 ~~I~lSiIs--Pr-klp~L~~l  181 (818)
                      .||.+-+|.  .. ....|+.|
T Consensus       131 ~gi~v~~igiG~~~~~~~L~~i  152 (184)
T d1atza_         131 NRVTVFPIGIGDRYDAAQLRIL  152 (184)
T ss_dssp             TTEEEEEEEESSSSCHHHHHHH
T ss_pred             cCcEEEEEEeCCcCCHHHHHHH
Confidence            999998887  22 23335555

>d1v7pc_ c.62.1.1 (C:) Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin alpha2-beta1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.38  E-value=0.00078  Score=63.73  Aligned_cols=120  Identities=11%  Similarity=0.073  Sum_probs=86.6

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCC--CCHHHHHHHhccccCCCCCCChhh
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIFLHWLSTIPFAGGGFNDAA   82 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T--~~~~~fl~wL~~i~f~GGG~~~~a   82 (818)
                      |+..|+++..+++.|.-++        ..+.+|||.|.+..-      ..+.++  .+..+++..++++.+.+||..  .
T Consensus        17 f~~~k~f~~~ii~~~~i~~--------~~~rv~vv~fs~~~~------~~~~l~~~~~~~~~~~~i~~~~~~~g~~t--~   80 (193)
T d1v7pc_          17 WDAVKNFLEKFVQGLDIGP--------TKTQVGLIQYANNPR------VVFNLNTYKTKEEMIVATSQTSQYGGDLT--N   80 (193)
T ss_dssp             HHHHHHHHHHHHHTSCBST--------TSEEEEEEEESSSEE------EEECTTTCSSHHHHHHHHHHCCCCCCSCC--C
T ss_pred             HHHHHHHHHHHHHHcccCC--------CccEEEEEEeeccee------eeecccchhhHHHHHHHHHhhhhhccCcc--c
Confidence            7889999999999995432        358999999976531      113333  588899999999988777653  4


Q ss_pred             HHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhh
Q 003455           83 IAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQ  162 (818)
Q Consensus        83 iaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~  162 (818)
                      +++||..|+..+-    ...+..+....|.+||++...|+.-                          .+.+..++.+.+
T Consensus        81 ~~~AL~~a~~~~f----~~~~~~R~~~~kvvVllTDG~s~d~--------------------------~~~~~~~~~~~~  130 (193)
T d1v7pc_          81 TFGAIQYARKYAY----SAASGGRRSATKVMVVVTDGESHDG--------------------------SMLKAVIDQCNH  130 (193)
T ss_dssp             HHHHHHHHHHHTT----SGGGTCCTTSEEEEEEEESSCCSCG--------------------------GGHHHHHHHHHH
T ss_pred             hHHHHHHHHHhcc----ccccCCCCCCceEEEEEecCCcCCC--------------------------ccHHHHHHHHHh
Confidence            7888999997541    1122235678899999999876531                          134467888889


Q ss_pred             cCceEEEe
Q 003455          163 CSVSLSVI  170 (818)
Q Consensus       163 ~~I~lSiI  170 (818)
                      .+|.+-.|
T Consensus       131 ~gv~v~~I  138 (193)
T d1v7pc_         131 DNILRFGI  138 (193)
T ss_dssp             TTEEEEEE
T ss_pred             CCCEEEEE
Confidence            89987666

>d1n3ya_ c.62.1.1 (A:) Integrin alpha-x beta2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin alpha-x beta2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=0.0002  Score=67.65  Aligned_cols=120  Identities=13%  Similarity=0.068  Sum_probs=85.8

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhHH
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIA   84 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~aia   84 (818)
                      |+.+|+++..+++.|..          ..+.+|||.|.+..-   ..+ .+..+.+..+++..|+++.+.|||   ..++
T Consensus        20 ~~~~k~~~~~~i~~l~~----------~~~rv~vv~fs~~~~---~~~-~l~~~~~~~~~~~~i~~~~~~~g~---t~~~   82 (189)
T d1n3ya_          20 FATMMNFVRAVISQFQR----------PSTQFSLMQFSNKFQ---THF-TFEEFRRSSNPLSLLASVHQLQGF---TYTA   82 (189)
T ss_dssp             HHHHHHHHHHHHTTSCT----------TTEEEEEEEESSSEE---EEE-CHHHHHHCSSGGGGGTTCCCCCSC---BCHH
T ss_pred             HHHHHHHHHHHHHHhCC----------CCCEEEEEEeeccce---eec-cccccccHHHHHHHHHhhhhhhhh---chHH
Confidence            77788899999988842          247899999987531   111 122334667888999999999987   3577


Q ss_pred             HHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhc
Q 003455           85 EGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC  163 (818)
Q Consensus        85 EGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~  163 (818)
                      .||..|+. +|..     ....+....|.+||++.-.+..-+                         .+.+.+++.+.+.
T Consensus        83 ~al~~a~~~~f~~-----~~~~r~~~~kvivllTDG~~~~~~-------------------------~~~~~~~~~~~~~  132 (189)
T d1n3ya_          83 TAIQNVVHRLFHA-----SYGARRDAAKILIVITDGKKEGDS-------------------------LDYKDVIPMADAA  132 (189)
T ss_dssp             HHHHHHHTTTTSG-----GGTCCTTSEEEEEEEESSCCBSCS-------------------------SCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhh-----hcCCCCCCceEEEEEecCCCCCCc-------------------------ccHHHHHHHHHHC
Confidence            89999985 4531     111245778999999987654311                         3678899999999


Q ss_pred             CceEEEeC
Q 003455          164 SVSLSVIC  171 (818)
Q Consensus       164 ~I~lSiIs  171 (818)
                      +|.+-.|.
T Consensus       133 gv~i~~Vg  140 (189)
T d1n3ya_         133 GIIRYAIG  140 (189)
T ss_dssp             TCEEEEEE
T ss_pred             CCceEEEe
Confidence            99998885

>d1mf7a_ c.62.1.1 (A:) Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.61  E-value=0.0018  Score=61.21  Aligned_cols=124  Identities=12%  Similarity=-0.004  Sum_probs=86.4

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      .|+.+|+++..+++.|..          ..+.+|||.|.+..- .+..   +..+.+..+++..|++|.+.||+-   .+
T Consensus        22 ~~~~~k~f~~~iv~~l~~----------~~~rv~vv~fs~~~~-~~~~---l~~~~~~~~~~~~i~~i~~~~~~t---~~   84 (194)
T d1mf7a_          22 DFRRMKEFVSTVMEQLKK----------SKTLFSLMQYSEEFR-IHFT---FKEFQNNPNPRSLVKPITQLLGRT---HT   84 (194)
T ss_dssp             HHHHHHHHHHHHHHHHCC----------TTEEEEEEEESSSEE-EEEC---HHHHHHSCCHHHHHTTCCCCCSCB---CH
T ss_pred             HHHHHHHHHHHHHHHcCc----------CCceEEEEEEeccce-eEEe---ccccCCHHHHHHHHhhhhhhhccc---hH
Confidence            578888999999998832          247999999976542 1111   223346678999999999998762   46


Q ss_pred             HHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHHhhc
Q 003455           84 AEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC  163 (818)
Q Consensus        84 aEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~~~~  163 (818)
                      +.||..|+..+-    ..-+..+....|..|||+...++.-+.                         +.+.+++.+.+.
T Consensus        85 ~~al~~~~~~~~----~~~~~~~~~~~kvvvliTDG~~~~~~~-------------------------~~~~~~~~~~~~  135 (194)
T d1mf7a_          85 ATGIRKVVRELF----NITNGARKNAFKILVVITDGEKFGDPL-------------------------GYEDVIPEADRE  135 (194)
T ss_dssp             HHHHHHHHHTTT----SGGGTCCTTSEEEEEEEESSCCBSCSS-------------------------CGGGTHHHHHHT
T ss_pred             HHHHHHHHHHHH----hhhccCCCCCceEEEEEecCCCCCCch-------------------------hHHHHHHHHHHc
Confidence            788988887652    111112356789999999877654331                         334568888899


Q ss_pred             CceEEEeCCC
Q 003455          164 SVSLSVICPK  173 (818)
Q Consensus       164 ~I~lSiIsPr  173 (818)
                      +|.+=+|..-
T Consensus       136 gv~i~~VGi~  145 (194)
T d1mf7a_         136 GVIRYVIGVG  145 (194)
T ss_dssp             TEEEEEEEES
T ss_pred             CCeeEEEecC
Confidence            9999888654

>d1shux_ c.62.1.1 (X:) Capillary morphogenesis protein 2 domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Capillary morphogenesis protein 2 domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.60  E-value=0.0029  Score=58.84  Aligned_cols=125  Identities=16%  Similarity=0.069  Sum_probs=87.5

Q ss_pred             CchhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCCh
Q 003455            1 MCIYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFND   80 (818)
Q Consensus         1 m~~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~   80 (818)
                      |+.=|+.+++++.-+++.|..          ..+.+|||+|.+..      -..+.++.+.+.+...|+.|...+++- .
T Consensus        18 m~~~~~~~k~~~~~~~~~~~~----------~~~rvglv~fs~~~------~~~~~l~~~~~~~~~~l~~l~~~~~~g-~   80 (181)
T d1shux_          18 VANNWIEIYNFVQQLAERFVS----------PEMRLSFIVFSSQA------TIILPLTGDRGKISKGLEDLKRVSPVG-E   80 (181)
T ss_dssp             GGGGHHHHHHHHHHHHHHCCC----------TTEEEEEEEESSSE------EEEEEEECCHHHHHHHHHHHHTCCCCS-C
T ss_pred             cccCHHHHHHHHHHHHHHhcC----------CCCEEEEEEeecce------EEEEEecCCHHHHHHHhhhcccccCCC-c
Confidence            444466678899999999943          24799999998743      223667788888888888888765431 2


Q ss_pred             hhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCCCCCCCcCcccccccccchhhhhhhccCCCHHHHHHHH
Q 003455           81 AAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSF  160 (818)
Q Consensus        81 ~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e~la~~~  160 (818)
                      ..+++||-.|+..|.       +..+....|..|||+...+-.-.                        .......++.+
T Consensus        81 t~~~~al~~~~~~~~-------~~~~~~~~~~ivliTDG~~~~~~------------------------~~~~~~~~~~~  129 (181)
T d1shux_          81 TYIHEGLKLANEQIQ-------KAGGLKTSSIIIALTDGKLDGLV------------------------PSYAEKEAKIS  129 (181)
T ss_dssp             CCHHHHHHHHHHHHH-------HHTGGGSCEEEEEEECCCCCTTH------------------------HHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHhh-------hcccCCCceEEEEecCCCCCCCc------------------------cHHHHHHHHHH
Confidence            468899999998774       11235667889999988654311                        01345778889


Q ss_pred             hhcCceEEEeCCC
Q 003455          161 VQCSVSLSVICPK  173 (818)
Q Consensus       161 ~~~~I~lSiIsPr  173 (818)
                      .+.+|.+=.|.-.
T Consensus       130 k~~gv~v~~vgig  142 (181)
T d1shux_         130 RSLGASVYCVGVL  142 (181)
T ss_dssp             HHTTCEEEEEECS
T ss_pred             HHCCCEEEEEEeC
Confidence            9999987777543

>d1q0pa_ c.62.1.1 (A:) Complement factor B domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Complement factor B domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.38  E-value=0.0055  Score=57.61  Aligned_cols=110  Identities=14%  Similarity=0.070  Sum_probs=77.0

Q ss_pred             hhhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCC-CChh
Q 003455            3 IYFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGG-FNDA   81 (818)
Q Consensus         3 ~Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG-~~~~   81 (818)
                      ..|+.+|+.+..+|+.|..+        ...+.++||.|.+..-.- +.+ ...++.+...+...|++|.+.++. -...
T Consensus        17 ~~~~~~k~~~~~li~~l~~~--------~~~~rv~lv~f~~~~~~~-~~l-~~~~~~~~~~l~~~i~~i~~~~~~~~g~t   86 (209)
T d1q0pa_          17 SNFTGAKKSLVNLIEKVASY--------GVKPRYGLVTYATYPKIW-VKV-SEADSSNADWVTKQLNEINYEDHKLKSGT   86 (209)
T ss_dssp             HHHHHHHHHHHHHHHHHHTT--------TCCCEEEEEEESSSEEEE-ECT-TSGGGGCHHHHHHHHHTCCTTSCSCTTCC
T ss_pred             HHHHHHHHHHHHHHHhcccC--------CCCcEEEEEEecCceeEE-ecC-ccchhhHHHHHHHHHHHhhhccccCCCCc
Confidence            57899999999999999542        236899999998642110 000 234556788889999999988776 3347


Q ss_pred             hHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCCCCC
Q 003455           82 AIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHP  123 (818)
Q Consensus        82 aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~  123 (818)
                      .+++||-.|+..+... ....+..+....|.+||++...|-.
T Consensus        87 ~~~~al~~a~~~~~~~-~~~~~~~~~~~~kvvvl~TDG~~~~  127 (209)
T d1q0pa_          87 NTKKALQAVYSMMSWP-DDVPPEGWNRTRHVIILMTDGLHNM  127 (209)
T ss_dssp             CHHHHHHHHHHHHCCT-TSSCCTTGGGCEEEEEEEECSCCCS
T ss_pred             hHHHHHHHHHHHHHhh-hccCccccCCCceEEEEEcCCCccC
Confidence            8899999999877522 2222344566788899999876543

>d1mjna_ c.62.1.1 (A:) Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Integrin A (or I) domain
domain: Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.80  E-value=0.0071  Score=56.46  Aligned_cols=98  Identities=8%  Similarity=-0.045  Sum_probs=68.2

Q ss_pred             hhHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCCCcCceeeccCCCCHHHHHHHhccccCCCCCCChhhH
Q 003455            4 YFYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAI   83 (818)
Q Consensus         4 Y~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~~~~~v~~~g~T~~~~~fl~wL~~i~f~GGG~~~~ai   83 (818)
                      -|+.+|++|..+++.|..          ..+.+|||.|.+..- -++   .+..+.+..+|+..|++|.+.||+   ..+
T Consensus        19 ~f~~~k~f~~~~i~~i~~----------~~~rvgvv~fs~~~~-~~~---~l~~~~~~~~~~~~i~~i~~~~g~---t~~   81 (179)
T d1mjna_          19 EFQKILDFMKDVMKKCSN----------TSYQFAAVQFSTSYK-TEF---DFSDYVKRKDPDALLKHVKHMLLL---TNT   81 (179)
T ss_dssp             HHHHHHHHHHHHHHHTTT----------SSEEEEEEEESSSEE-EEE---CHHHHHHHCCHHHHHTTCCCCCBC---CCH
T ss_pred             HHHHHHHHHHHHHHHhCC----------CceEEEEEEEeeeee-EEe---chhhccchHHHHHHHhhhhcccCc---chH
Confidence            378899999999997732          358999999976331 111   122235777899999999999887   356


Q ss_pred             HHHHHHHHh-hhccCCCCCCCCCCCCCccEEEEeecCCCCC
Q 003455           84 AEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHP  123 (818)
Q Consensus        84 aEGLa~AL~-~~~~~~~~~~~~~~~~~qkhCILi~nSpP~~  123 (818)
                      ++||..|+. +|.  ..   ...+....|.+|||+...+..
T Consensus        82 ~~AL~~~~~~~f~--~~---~g~R~~~~kvvvllTDG~s~d  117 (179)
T d1mjna_          82 FGAINYVATEVFR--EE---LGARPDATKVLIIITDGEATD  117 (179)
T ss_dssp             HHHHHHHHHHTSS--GG---GTCCTTSEEEEEEEESSCCSS
T ss_pred             HHHHHHHHHHHhc--hh---cCCCCCCCeEEEEEECCCCcc
Confidence            788888874 664  11   112356789999999886553

>d1jeyb2 c.62.1.4 (B:6-241) Ku80 subunit N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Ku80 subunit N-terminal domain
domain: Ku80 subunit N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.42  E-value=0.19  Score=47.26  Aligned_cols=127  Identities=20%  Similarity=0.219  Sum_probs=77.9

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCC---------CCcCceeeccCCCCHHHHHHHhccccCCC
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGS---------YCACLVQRSGWTKDVDIFLHWLSTIPFAG   75 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~---------~~~~~v~~~g~T~~~~~fl~wL~~i~f~G   75 (818)
                      |+..|+++.-+|+-+.-        .....+.|||+|++...         +..+.+-+.--+.+ ...+.-+..+...+
T Consensus        26 l~~ak~~~~~~v~~~~~--------~~~~d~vglV~f~~~~t~~~~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~~   96 (236)
T d1jeyb2          26 FEQAKKVITMFVQRQVF--------AENKDEIALVLFGTDGTDNPLSGGDQYQNITVHRHLMLPD-FDLLEDIESKIQPG   96 (236)
T ss_dssp             HHHHHHHHHHHHHHHHH--------TTCCCEEEEEEESCSSCBSTTCTTTCSTTEEEEEEEECCC-HHHHHHHHTTCCCC
T ss_pred             HHHHHHHHHHHHHHHhc--------CCCCCeEEEEEEcCCCcccccccccccceEEEEeccccch-hhHHHHHhhhcccc
Confidence            67777888888876532        11347899999988642         11122222222333 34444444444444


Q ss_pred             CCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCC-CCCCCCCCcCcccccccccchhhhhhhccCCCHH
Q 003455           76 GGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASN-PHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAE  154 (818)
Q Consensus        76 GG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSp-P~~lp~~~~~p~~~~l~~~~~~~~~~~~~l~~~e  154 (818)
                      ++.  ..+.++|..|+.++...     ........|+.||+++-. |+.                          -.+.+
T Consensus        97 ~~~--~~~~~al~~a~~~~~~~-----~~~~~~~~r~IiL~TDG~~~~~--------------------------~~~~~  143 (236)
T d1jeyb2          97 SQQ--ADFLDALIVSMDVIQHE-----TIGKKFEKRHIEIFTDLSSRFS--------------------------KSQLD  143 (236)
T ss_dssp             SSC--CCHHHHHHHHHHHHHHH-----SSSSCCSEEEEEEECCCCSCCC--------------------------CTTHH
T ss_pred             ccc--cchhHHHHHHHHHHHHh-----hhcccccccEEEEEecCCCCcC--------------------------hHHHH
Confidence            443  35777888888766411     112345678889998853 221                          12678


Q ss_pred             HHHHHHhhcCceEEEeCCC
Q 003455          155 TVAKSFVQCSVSLSVICPK  173 (818)
Q Consensus       155 ~la~~~~~~~I~lSiIsPr  173 (818)
                      .+|+.+.+.+|+|.+|..-
T Consensus       144 ~~a~~l~~~~I~i~~ig~g  162 (236)
T d1jeyb2         144 IIIHSLKKCDISLQFFLPF  162 (236)
T ss_dssp             HHHHHHHHTTEEEEEEESS
T ss_pred             HHHHHHHHcCCEEEEEecC
Confidence            9999999999999999874

>d1jeya2 c.62.1.3 (A:34-253) Ku70 subunit N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Ku70 subunit N-terminal domain
domain: Ku70 subunit N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.13  E-value=2.3  Score=39.14  Aligned_cols=127  Identities=16%  Similarity=0.102  Sum_probs=68.7

Q ss_pred             hHHHhhhhHHHHHhhccccccccccCCCcceEEEEEEccCCCC-----CcCceeeccCC----CCHHHHHHHhcc-----
Q 003455            5 FYAYSKLSLYFHRCFCVNELAGQKTSASNVELSLVTFNTHGSY-----CACLVQRSGWT----KDVDIFLHWLST-----   70 (818)
Q Consensus         5 ~~~l~~YI~p~ie~f~~~~~~e~~~~~~~~~yaLVvf~~~~~~-----~~~~v~~~g~T----~~~~~fl~wL~~-----   70 (818)
                      |+..++++..+++-|...        .....+|||+|++....     ....+- ...+    .++..+..+++.     
T Consensus        27 ~~~~~~~~~~~~~~~i~~--------~~~d~vglv~f~t~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~   97 (220)
T d1jeya2          27 FDMSIQCIQSVYISKIIS--------SDRDLLAVVFYGTEKDKNSVNFKNIYVL-QELDNPGAKRILELDQFKGQQGQKR   97 (220)
T ss_dssp             HHHHHHHHHHHHHHHHHT--------TCCCEEEEEEESCSSCBSTTCCTTEEEE-EEEECCCHHHHHHHHTTSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhC--------CCCCEEEEEEeccccccCCCcccchhhh-hcccCchHHHHHhhhhhhhhhhhhh
Confidence            445556777776666321        12468999999876531     111111 1111    122222222211     


Q ss_pred             ---ccCCCCCCChhhHHHHHHHHHhhhccCCCCCCCCCCCCCccEEEEeecCC-CCCCCCCCcCcccccccccchhhhhh
Q 003455           71 ---IPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASN-PHPLPTPVYRPQMQNLDQNENNEAQA  146 (818)
Q Consensus        71 ---i~f~GGG~~~~aiaEGLa~AL~~~~~~~~~~~~~~~~~~qkhCILi~nSp-P~~lp~~~~~p~~~~l~~~~~~~~~~  146 (818)
                         +.-.+|+   ..+.+||..|+.+|.  ..     ......|..|||++-- |+.-...                  .
T Consensus        98 ~~~~~~~~~~---t~l~~al~~a~~~~~--~~-----~~~~~~k~IiliTDg~~~~~~~~~------------------~  149 (220)
T d1jeya2          98 FQDMMGHGSD---YSLSEVLWVCANLFS--DV-----QFKMSHKRIMLFTNEDNPHGNDSA------------------K  149 (220)
T ss_dssp             HHHHHCCSCC---CCHHHHHHHHHHHHH--TC-----SSCEEEEEEEEEESCSCTTTTCHH------------------H
T ss_pred             hhhcccCCCC---ccHHHHHHHHHHHHH--hc-----ccccCCcEEEEEecCCCCCCCcch------------------h
Confidence               1112222   358899999999996  11     1223457788888764 4431100                  0


Q ss_pred             hccCCCHHHHHHHHhhcCceEEEeC
Q 003455          147 ESRLSDAETVAKSFVQCSVSLSVIC  171 (818)
Q Consensus       147 ~~~l~~~e~la~~~~~~~I~lSiIs  171 (818)
                         ...+.+.|+.+.+.+|.+.+|.
T Consensus       150 ---~~~~~~~a~~~~~~gv~i~~i~  171 (220)
T d1jeya2         150 ---ASRARTKAGDLRDTGIFLDLMH  171 (220)
T ss_dssp             ---HHHHHHHHHHHHHHTEEEEEEE
T ss_pred             ---hHHHHHHHHHHhhhcceEEEEE
Confidence               0235577888899999999984