Citrus Sinensis ID: 003284

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830----
Protein Sequence
MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGGGFMS
Secondary Structure (PSIPRED)
cccccEEEEEEccccccccHHHHHHHHHHHHHHHHccccccccccccccEEEEEEEEEcccccccccEEEccccccHHHHHHHHccccccccccccHHHHHHHHHHHHHHcccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccccHHHHHHHHHHccEEEEEEcccccHHHHHHHHHHccccccccccccccccccEEEEEEcccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccHHHcccccccccEEHHHHHcccccccccccccEEEEEcccccHHHHHHHHHHHcccccccccccEEEccccccccccccccccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHcccHHHHHHHcccHHHHcccHHHHHHHHcHHHHHHcccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEEccHcccccHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEEccccccccEEEEccccccHHHHHHHHHccccccccHcHHHHHHHHHHHHHHcccccccccccccccccEEEEEEEcccccccccccccccccccccccccccccccccccHHHHHHHHHcccEEEEEEcccHHHHHHHHHHHcccccccccccccccccccEEEEEcccHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHcHHHHccHccccccccccccEEEEcccHcccccccccccccccEccccccccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccccEEEEEEEccccccccHHHHccccccHEEEEEEcHHHccccccccccEEEEEEccccccHHHHHHHcccEEEEEccccEEEEEcccccccEEEEEccccEEEEccccccHHHHHHcHHccccccHHHHHHHcccccHHHcccccccccHHccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccHHHHHHHcHcccccccccccccccc
Coil and Loop (DISEMBL)
MSEKQLIVAVEgtaamgpywQSIVSDYLEKIIRCFCVnelagqktsasNVELSLVTFNTHGsycaclvqrsgwtkDVDIFLHWLstipfagggfndAAIAEGLSEALMMFsvapngsqnqqnvdgqRHCILVaasnphplptpvyrpqmqnldqnenNEAQAESRLSDAETVAKSFVQCSVslsvicpkqlpkLTAIYNAakrnpraadppvdnsknphFLVLISENFMEARAAlsrpgvanlapnqnpvkmdiapvtsvtgpaptsipsvnginrppisvgnvptatvkvepstvtsmvngptfphipsvprpasqgvpslqtsspsstsqemitsgdsvpevkplvsgmsqplrpmapaaaNVNILNNLSQARQVMNNAaltggtsiglqsmgqtpmaMHMSNMIssgmassvptsqpvfssaqsgitsiggsgtltgtsqvpqnsglnsftsapsnlsgnsnpsisqpmgtlqggasmgqsvgmsqgnhsggqmvQNGISMNqnmmsglgpsgvssgtgtmiptpgmsqqaqsgmqplsvnnnTAVNMQLSQQTSSALHSSQSKYVKVWegslsgqrqgqpvFITKlegyrsasasetlaanwpptMQIVRLISQdhmnnkqyvgkaDFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIgmlfpgdmvvfkpqisSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLqqqqqipqlqqqsmpqlqqqqqlpqlqqqqqlpqmqqqqqlpqlqqqqqlsqpqqmvgsgmgqgyvqgpgrtqlvsqgqvssqgapnipgggfms
Flexible Loop (DISEMBL)
MSEKQLIVAvegtaamgpyWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVslsvicpkqlPKLTAIYNAAKRnpraadppvdnskNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTsipsvnginrppiSVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEgslsgqrqgqPVFITKLEGYRSASASetlaanwppTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSqgqvssqgapnipgggfms
Low Complexity Region (SEG)
MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVpslqtsspsstsqEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQsgitsiggsgtltgtsQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKpqissqqqqqlqqqqqqqqhqqmqsqlqhqqlsqlqqqqqqlpqlqqqipqlqqqqqipqlqqqsmpqlqqqqqlpqlqqqqqlpqmqqqqqlpqlqqqqqlsqpqqMVGSGMGQGYVQGPGRTQLvsqgqvssqgAPNIPGGGFMS
Disordered region (IsUnstruct)
*****LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSV**************RHCILVA**************************************VAKSFVQCSVSLSVICPKQLPKLTAIYNA******************HFLVLISENFMEAR**************************************************************************************************************************************IL********************************************************************************************************************************************************************************************************VKVWE**********PVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK***************************************************************************************************************************************************
Disordered Region (DISOPRED)
*SEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMF*****************HCILVAASNPHPLPTPVYRPQMQN*********QAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYN***************SKNPHFLVLIS*************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************QIVRLIS**********GKADFLVFRAM*********************************************************************************************************************************************************************************************P******
Disordered Region (DISEMBL)
MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQ****************TVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVP***************************SVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSG*****************GITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTP**********QPLSVNNNTAVNMQ****************VKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKP**************************************************************************************************************GMGQGYVQGPGRTQ**********GAPNIPGGGFMS
Disordered Region (DISPRO)
**EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELA***TSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQ*******AESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSR*******************************************VGNVPTATVKVEPSTVTSMVNGPTFPHI*S*********************************VKP*VSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMS*************SQ**************GSGTLTGTSQV********************NPSISQPMGT*****SM*****************************************TMIPTPGMSQ********************************QSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQ***************************************************************************************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNxxxxxxxxxxxxxxxxxxxxxAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLxxxxxxxxxxxxxxxxxxxxxxxxxxxxQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGGGFMS
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	834	2.2.26 [Sep-21-2011]
Q7XYY2	836	Mediator of RNA polymeras	yes	no	0.799	0.797	0.669	0.0
Q6GP15	801	Mediator of RNA polymeras	N/A	no	0.254	0.264	0.283	6e-18
A4IHD9	805	Mediator of RNA polymeras	yes	no	0.254	0.263	0.288	1e-17
A2VE44	746	Mediator of RNA polymeras	yes	no	0.233	0.261	0.284	2e-14
Q8VCB2	745	Mediator of RNA polymeras	yes	no	0.235	0.263	0.277	3e-14
Q71SY5	747	Mediator of RNA polymeras	yes	no	0.233	0.261	0.280	1e-13
Q9VDR1	863	Mediator of RNA polymeras	yes	no	0.249	0.241	0.224	5e-07

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

 Score =  875 bits (2261), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 464/693 (66%), Positives = 550/693 (79%), Gaps = 26/693 (3%)

Query: 4   KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY 63
           KQLIV  EGTAA+GPYWQ+IVSDYLEKIIR FC +EL G++   S VELSLV FN+HGSY
Sbjct: 6   KQLIVVAEGTAALGPYWQTIVSDYLEKIIRSFCGSELNGERNPVSTVELSLVIFNSHGSY 65

Query: 64  CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV 123
           CACLVQRSGWT+DVDIFLHWLS+I F GGGFN+ A AEGL+EALMMFS  P   Q Q + 
Sbjct: 66  CACLVQRSGWTRDVDIFLHWLSSIQFGGGGFNEVATAEGLAEALMMFS--PPSGQAQPSN 123

Query: 124 DGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSL 183
           D +RHCIL+ ASNPH LPTPVYRP++QN+++NEN +AQAESRLSDAETVA  F +CSVSL
Sbjct: 124 DLKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSL 183

Query: 184 SVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANL 243
           SV+CPKQLP + A+YNA K N ++AD  +D +KN  +LVLISENF+EA AALS     NL
Sbjct: 184 SVVCPKQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSH-SATNL 242

Query: 244 APNQNPVKMD---IAPVTSVTGPAPTSIPSVNGI--NRPPISVGNVPTATVKVEPSTVTS 298
              Q+PVK+D   +AP   VTG  P  + S NG   NR P+SVG VPTATVKVEPSTVTS
Sbjct: 243 PQTQSPVKVDRATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVEPSTVTS 302

Query: 299 MVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLV-SGMSQPLRP 357
           M   P+FPHIP+V RPA+Q +PS+QTSS S  SQ+M+++ ++ P++KP+V SGM+ PLR 
Sbjct: 303 MAPVPSFPHIPAVARPATQAIPSIQTSSASPVSQDMVSNAENAPDIKPVVVSGMTPPLRT 362

Query: 358 MAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPT 417
             P  ANVN+LNNLSQ RQVM++AA     +    S+GQ+ +AMHMSNMIS+GMA+S+P 
Sbjct: 363 GPPGGANVNLLNNLSQVRQVMSSAA----LAGAASSVGQSAVAMHMSNMISTGMATSLPP 418

Query: 418 SQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQG 477
           SQ VFS+ Q GITS+ GSG L G++Q  Q+ G N+  S  +  +  SN  +SQPM     
Sbjct: 419 SQTVFSTGQQGITSMAGSGALMGSAQTGQSPGPNNAFSPQTTSNVASNLGVSQPMQ---- 474

Query: 478 GASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSG 537
                   GM+QG+HSG  M+Q GISMNQNMMSGLG   VSSGTG M+PTPG+ QQAQSG
Sbjct: 475 --------GMNQGSHSGA-MMQGGISMNQNMMSGLGQGNVSSGTGGMMPTPGVGQQAQSG 525

Query: 538 MQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSAS 597
           +Q L  +N++A NMQLSQ +S A+ +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSAS
Sbjct: 526 IQQLGGSNSSAPNMQLSQPSSGAMQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSAS 585

Query: 598 ASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQ 657
           AS++LAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAM+QHGFLGQLQ+KKLCAVIQ
Sbjct: 586 ASDSLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMSQHGFLGQLQDKKLCAVIQ 645

Query: 658 LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 690
           LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI
Sbjct: 646 LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 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 = 93.6 bits (231), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 104/243 (42%), Gaps = 31/243 (12%)

Query: 6   LIVAVEGTAAMGPYWQSIVSDYLEKIIRCF-----CVNELAGQKTSASNVELSLVTFNTH 60
           ++  +EGTA +GPY++S+   YL   I  F        +  G        + SLV FNT 
Sbjct: 14  VVFVIEGTANLGPYFESLRKHYLLPAIEYFNGGPPAETDFGG---DYGGTQYSLVVFNTV 70

Query: 61  GSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQN 119
                  VQ    T     F+ WL +I F GGG    + IAEGLS AL +F    +  + 
Sbjct: 71  DCAPESYVQCHAPTSSAYEFVQWLDSIKFMGGGGESCSLIAEGLSTALQLF----DDFKK 126

Query: 120 QQNVDGQRH--CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFV 177
            +   GQ H  CIL+  S P+ LP                 E+   S  +  E + +   
Sbjct: 127 MREQIGQTHKVCILICNSPPYLLPA---------------VESTTYSGYT-TENLVQKIG 170

Query: 178 QCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSR 237
           +  +  S+I P++LP L  ++  A         P D S++P  ++L+    +    A S 
Sbjct: 171 ERGIHFSIISPRKLPALRTLFEKAMPVGLIEPQPKDYSQDPRHMILVRGMVLPVGGATSV 230

Query: 238 PGV 240
           PGV
Sbjct: 231 PGV 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 = 92.8 bits (229), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 104/243 (42%), Gaps = 31/243 (12%)

Query: 6   LIVAVEGTAAMGPYWQSIVSDYLEKIIRCF-----CVNELAGQKTSASNVELSLVTFNTH 60
           ++  +EGTA +GPY++S+   YL   I  F        +  G        + SLV FNT 
Sbjct: 15  VVFVIEGTANLGPYFESLRKHYLLPAIEYFNGGPPAETDFGG---DYGGTQYSLVVFNTV 71

Query: 61  GSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQN 119
                  VQ    T     F+ WL +I F GGG    + IAEGLS AL +F    +  + 
Sbjct: 72  DCAPESYVQCHAPTSSAYEFVQWLDSIRFMGGGGESCSLIAEGLSTALQLF----DDFKK 127

Query: 120 QQNVDGQRH--CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFV 177
            +   GQ H  CIL+  S P+ LP                 E+   S  +  E + +   
Sbjct: 128 MREQIGQTHKVCILICNSPPYLLPA---------------VESTTYSGYT-TENLVQKIG 171

Query: 178 QCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSR 237
           +  +  SVI P++LP L  ++  A         P D S++P  ++L+    +    A S 
Sbjct: 172 ERGIHFSVISPRKLPALRTLFEKAMPVGLIEPQPKDYSQDPRHMILVRGMVLPVGGATSV 231

Query: 238 PGV 240
           PGV
Sbjct: 232 PGV 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|A2VE44|MED25_BOVIN Mediator of RNA polymerase II transcription subunit 25 OS=Bos taurus GN=MED25 PE=2 SV=1

 Score = 81.6 bits (200), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 100/232 (43%), Gaps = 37/232 (15%)

Query: 5   QLIVAVEGTAAMGPYWQSIVSDYLEKIIRCF-----CVNELAGQKTSASNVELSLVTFNT 59
            ++  +EGTA +GPY++ +   YL   I  F        +  G        + SLV FNT
Sbjct: 17  DVVFVIEGTANLGPYFEGLRKHYLLPAIEYFNGGPPAETDFGGDY---GGTQYSLVVFNT 73

Query: 60  HGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQ 118
                   VQ    T     F+ WL  I F GGG    + IAEGLS AL +F    +  +
Sbjct: 74  VDCAPESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQLF----DDFK 129

Query: 119 NQQNVDGQRH--CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSF 176
             +   GQ H  C+L+  S P+ LP                 E+   S  +  ET+ +  
Sbjct: 130 KMREQIGQTHRVCLLICNSPPYLLPA---------------VESTTYSGCT-TETLVQKI 173

Query: 177 VQCSVSLSVICPKQLPKLTAIYNAAKRNPRA----ADPPVDNSKNPHFLVLI 224
            +  +  S++ P++LP L  ++  A   P A      PP D S++P  +VL+
Sbjct: 174 GERGIYFSIVSPRKLPALRLLFEKAA--PPAMLEPLQPPADVSQDPRHMVLV 223

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. Required for RARA/RXRA-mediated transcription.

Bos taurus (taxid: 9913)

>sp|Q8VCB2|MED25_MOUSE Mediator of RNA polymerase II transcription subunit 25 OS=Mus musculus GN=Med25 PE=1 SV=1

 Score = 81.3 bits (199), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 100/231 (43%), Gaps = 35/231 (15%)

Query: 5   QLIVAVEGTAAMGPYWQSIVSDYLEKIIRCF-----CVNELAGQKTSASNVELSLVTFNT 59
            ++  +EGTA +GPY++ +   YL   I  F        +  G        + SLV FNT
Sbjct: 17  DVVFVIEGTANLGPYFEELRKHYLLPAIEYFNGGPPAETDFGGDY---GGTQYSLVVFNT 73

Query: 60  HGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQ 118
                   VQ    T     F+ WL  I F GGG    + IAEGLS AL +F    +  +
Sbjct: 74  VDCAPESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQLF----DDFK 129

Query: 119 NQQNVDGQRH--CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSF 176
             +   GQ H  C+L+  S P+ LP                 E+   S  +  E++ +  
Sbjct: 130 KMREQIGQTHRVCLLICNSPPYLLPA---------------VESTTYSGCT-TESLVQKI 173

Query: 177 VQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADP---PVDNSKNPHFLVLI 224
            +  +  S++ P++LP L  ++  A   P   +P   P D S++P  +VL+
Sbjct: 174 GERGIHFSIVSPRKLPALRLLFEKAA-PPALLEPLQQPADVSQDPRHMVLV 223

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. Required for RARA/RXRA-mediated transcription.

Mus musculus (taxid: 10090)

>sp|Q71SY5|MED25_HUMAN Mediator of RNA polymerase II transcription subunit 25 OS=Homo sapiens GN=MED25 PE=1 SV=2

 Score = 79.3 bits (194), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 99/232 (42%), Gaps = 37/232 (15%)

Query: 5   QLIVAVEGTAAMGPYWQSIVSDYLEKIIRCF-----CVNELAGQKTSASNVELSLVTFNT 59
            ++  +EGTA +GPY++ +   YL   I  F        +  G        + SLV FNT
Sbjct: 17  DVVFVIEGTANLGPYFEGLRKHYLLPAIEYFNGGPPAETDFGGDY---GGTQYSLVVFNT 73

Query: 60  HGSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQ 118
                   VQ    T     F+ WL  I F GGG    + IAEGLS AL +F    +  +
Sbjct: 74  VDCAPESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQLF----DDFK 129

Query: 119 NQQNVDGQRH--CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSF 176
             +   GQ H  C+L+  S P+ LP                 E+   S  +  E + +  
Sbjct: 130 KMREQIGQTHRVCLLICNSPPYLLPA---------------VESTTYSGCT-TENLVQQI 173

Query: 177 VQCSVSLSVICPKQLPKLTAIYNAAKRNPRA----ADPPVDNSKNPHFLVLI 224
            +  +  S++ P++LP L  ++   K  P A      PP D S++P  +VL+
Sbjct: 174 GERGIHFSIVSPRKLPALRLLFE--KAAPPALLEPLQPPTDVSQDPRHMVLV 223

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. Required for RARA/RXRA-mediated transcription.

Homo sapiens (taxid: 9606)

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

 Score = 57.4 bits (137), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 53/236 (22%), Positives = 97/236 (41%), Gaps = 28/236 (11%)

Query: 5   QLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSL---VTFNTHG 61
            ++  +EG+A  G Y   + ++Y+   +  F    +  ++   +    +L   V + T  
Sbjct: 10  DVVFVIEGSAINGAYINELKTNYILPTLEHFTTGSIDEREYLIAERFATLYGIVVYRTAA 69

Query: 62  SYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQ 120
           +    +    G        +  +  +P  GGG    A +AEG + A   F       Q  
Sbjct: 70  NLLEPVCSTYGPFLQPQKVMETIERLPLVGGGMESCAHMAEGFAAAHGCFDDISERRQLL 129

Query: 121 QNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS 180
                QRHCIL+  S P+ +PT             E+ +   +S     E +A  F +  
Sbjct: 130 DQTSVQRHCILICNSPPYQMPT------------TESWKYPGKS----CEQLAALFNERK 173

Query: 181 VSLSVICPKQLPKLTAIYNAAKRNPRAADPPV---DNSKNPHFLVLISENFMEARA 233
           ++LS+I P+++P L  ++  A       D P+   + +KN   LVL+    ++ RA
Sbjct: 174 INLSIIAPRKMPVLFKLFMKAD-----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    0.353 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 298,473,552
Number of Sequences: 539616
Number of extensions: 12842162
Number of successful extensions: 261547
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: 67412
Number of HSP's gapped (non-prelim): 58345
length of query: 834
length of database: 191,569,459
effective HSP length: 126
effective length of query: 708
effective length of database: 123,577,843
effective search space: 87493112844
effective search space used: 87493112844
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	834
225423909	827	PREDICTED: uncharacterized protein LOC10	0.828	0.835	0.816	0.0
297737854	815	unnamed protein product [Vitis vinifera]	0.815	0.834	0.804	0.0
224111730	796	predicted protein [Populus trichocarpa]	0.817	0.856	0.798	0.0
449434652	858	PREDICTED: mediator of RNA polymerase II	0.811	0.789	0.726	0.0
356502460	879	PREDICTED: uncharacterized protein LOC10	0.814	0.772	0.728	0.0
312283021	852	unnamed protein product [Thellungiella h	0.796	0.779	0.677	0.0
30689268	836	phytochrome and flowering time regulator	0.799	0.797	0.669	0.0
297845606	832	hypothetical protein ARALYDRAFT_472815 [	0.799	0.801	0.673	0.0
255576521	561	conserved hypothetical protein [Ricinus	0.633	0.941	0.779	0.0
449519677	595	PREDICTED: mediator of RNA polymerase II	0.707	0.991	0.690	0.0

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

 Score = 1104 bits (2856), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 566/693 (81%), Positives = 623/693 (89%), Gaps = 2/693 (0%)

Query: 1   MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTH 60
           M+EKQL+VAVEGTAAMGPYWQ++VSDYL+KIIR FC NELAGQK S+SN ELSLV FN H
Sbjct: 1   MAEKQLVVAVEGTAAMGPYWQAVVSDYLDKIIRYFCGNELAGQKPSSSNFELSLVMFNAH 60

Query: 61  GSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQ 120
           GSYC+CLVQRSGWT+DVD+FL WLS +PFAGGGFNDAAIAEGL+EALMMFSVA NGSQ Q
Sbjct: 61  GSYCSCLVQRSGWTRDVDLFLQWLSALPFAGGGFNDAAIAEGLAEALMMFSVAANGSQTQ 120

Query: 121 QNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS 180
           QNVDGQRHCILVAA+NP+PLPTPVY+PQMQN++QNE+ E+Q ESRLSDAE VAKSF QCS
Sbjct: 121 QNVDGQRHCILVAANNPYPLPTPVYQPQMQNMEQNESIESQTESRLSDAEAVAKSFAQCS 180

Query: 181 VSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGV 240
           VSLSVICPKQLPKL +IYNA KRNPR ADPPVDN KNPHFLVLIS++FMEARAALSRPG+
Sbjct: 181 VSLSVICPKQLPKLKSIYNAGKRNPRVADPPVDNVKNPHFLVLISDSFMEARAALSRPGL 240

Query: 241 ANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGI-NRPPISVGNVPTATVKVEPSTVTSM 299
           +N+  NQ+PVKMDIA V  V+   P SIPSVNGI NRP I+VG VPTATVKVEPSTVTS+
Sbjct: 241 SNMTANQSPVKMDIASVPQVSAAPPASIPSVNGIMNRPTIAVGAVPTATVKVEPSTVTSI 300

Query: 300 VNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMA 359
            +GP FPHIPSVPR ASQGVPSLQTSSPSSTSQEMI++GD+V ++KP+VSG+SQ LRP+ 
Sbjct: 301 TSGPGFPHIPSVPRAASQGVPSLQTSSPSSTSQEMISNGDNVQDLKPIVSGISQTLRPVV 360

Query: 360 PAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQ 419
           PAAANV+ILNNLSQARQVM++AAL+GGTSIGLQSMG T MAMHMSNMISSGMASSVP +Q
Sbjct: 361 PAAANVSILNNLSQARQVMHSAALSGGTSIGLQSMGGTSMAMHMSNMISSGMASSVPATQ 420

Query: 420 PVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGA 479
            VFSS QS ++SI GSGTL GT+QV QNS L SFTSA SN+S NSN  ISQP+  LQGG 
Sbjct: 421 TVFSSGQSAVSSITGSGTLAGTAQVAQNSALGSFTSATSNMSVNSNLGISQPLSNLQGGV 480

Query: 480 SMGQSV-GMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGM 538
           SMGQ+V GMSQGN  GGQMVQ+GI MNQNMMSGLGPSG+SSGTGTMIPTPGMSQQ Q GM
Sbjct: 481 SMGQTVPGMSQGNLPGGQMVQSGIGMNQNMMSGLGPSGISSGTGTMIPTPGMSQQVQPGM 540

Query: 539 QPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASA 598
             L VNNN A NM L QQTS A+ ++QSKYVKVWEG+LSGQRQGQPVFIT+LEGYRSASA
Sbjct: 541 PSLGVNNNAAANMPLPQQTSGAMQTAQSKYVKVWEGNLSGQRQGQPVFITRLEGYRSASA 600

Query: 599 SETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQL 658
           SE+LAANWP TMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQL
Sbjct: 601 SESLAANWPATMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQL 660

Query: 659 PSQTLLLSVSDKACRLIGMLFPGDMVVFKPQIS 691
           PSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI+
Sbjct: 661 PSQTLLLSVSDKACRLIGMLFPGDMVVFKPQIT 693

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 1082 bits (2798), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 557/692 (80%), Positives = 613/692 (88%), Gaps = 12/692 (1%)

Query: 1   MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTH 60
           M+EKQL+VAVEGTAAMGPYWQ++VSDYL+KIIR FC NELAGQK S+SN ELSLV FN H
Sbjct: 1   MAEKQLVVAVEGTAAMGPYWQAVVSDYLDKIIRYFCGNELAGQKPSSSNFELSLVMFNAH 60

Query: 61  GSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQ 120
           GSYC+CLVQRSGWT+DVD+FL WLS +PFAGGGFNDAAIAEGL+EALMMFSVA NGSQ Q
Sbjct: 61  GSYCSCLVQRSGWTRDVDLFLQWLSALPFAGGGFNDAAIAEGLAEALMMFSVAANGSQTQ 120

Query: 121 QNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS 180
           QNVDGQRHCILVAA+NP+PLPTPVY+PQMQN++QNE+ E+Q ESRLSDAE VAKSF QCS
Sbjct: 121 QNVDGQRHCILVAANNPYPLPTPVYQPQMQNMEQNESIESQTESRLSDAEAVAKSFAQCS 180

Query: 181 VSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGV 240
           VSLSVICPKQLPKL +IYNA KRNPR ADPPVDN KNPHFLVLIS++FMEARAALSRPG+
Sbjct: 181 VSLSVICPKQLPKLKSIYNAGKRNPRVADPPVDNVKNPHFLVLISDSFMEARAALSRPGL 240

Query: 241 ANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNGI-NRPPISVGNVPTATVKVEPSTVTSM 299
           +N+  NQ+PVKMDIA V  V+   P SIPSVNGI NRP I+VG VPTATVKVEPSTVTS+
Sbjct: 241 SNMTANQSPVKMDIASVPQVSAAPPASIPSVNGIMNRPTIAVGAVPTATVKVEPSTVTSI 300

Query: 300 VNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMA 359
            +GP FPHIPSVPR ASQGVPSLQTSSPSSTSQEMI++GD+V ++KP+VSG+SQ LRP+ 
Sbjct: 301 TSGPGFPHIPSVPRAASQGVPSLQTSSPSSTSQEMISNGDNVQDLKPIVSGISQTLRPVV 360

Query: 360 PAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQ 419
           PAAANV+ILNNLSQARQVM++AAL+GGTSIGLQSMG T MAMHMSNMISSGMASSVP +Q
Sbjct: 361 PAAANVSILNNLSQARQVMHSAALSGGTSIGLQSMGGTSMAMHMSNMISSGMASSVPATQ 420

Query: 420 PVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGA 479
            VFSS QS ++SI GSGTL GT+QV QNS L SFTSA SN+S NSN  ISQP+       
Sbjct: 421 TVFSSGQSAVSSITGSGTLAGTAQVAQNSALGSFTSATSNMSVNSNLGISQPL------- 473

Query: 480 SMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQ 539
                 GMSQGN  GGQMVQ+GI MNQNMMSGLGPSG+SSGTGTMIPTPGMSQQ Q GM 
Sbjct: 474 ----IPGMSQGNLPGGQMVQSGIGMNQNMMSGLGPSGISSGTGTMIPTPGMSQQVQPGMP 529

Query: 540 PLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASAS 599
            L VNNN A NM L QQTS A+ ++QSKYVKVWEG+LSGQRQGQPVFIT+LEGYRSASAS
Sbjct: 530 SLGVNNNAAANMPLPQQTSGAMQTAQSKYVKVWEGNLSGQRQGQPVFITRLEGYRSASAS 589

Query: 600 ETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLP 659
           E+LAANWP TMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLP
Sbjct: 590 ESLAANWPATMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQLP 649

Query: 660 SQTLLLSVSDKACRLIGMLFPGDMVVFKPQIS 691
           SQTLLLSVSDKACRLIGMLFPGDMVVFKPQI+
Sbjct: 650 SQTLLLSVSDKACRLIGMLFPGDMVVFKPQIT 681

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 = 1076 bits (2783), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 555/695 (79%), Positives = 601/695 (86%), Gaps = 13/695 (1%)

Query: 1   MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTH 60
           M+EKQLIVAVEGTAAMGP+W  IVSDYLEKIIR          K   S VELS+VTFN+H
Sbjct: 1   MAEKQLIVAVEGTAAMGPFWSIIVSDYLEKIIR---------YKVPTSIVELSIVTFNSH 51

Query: 61  GSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQ 120
           GSY ACLVQRSGWT+DVDIFL WLS IPFAGGGFNDAAIAEGLSEALMMF + PNGSQ Q
Sbjct: 52  GSYSACLVQRSGWTRDVDIFLQWLSAIPFAGGGFNDAAIAEGLSEALMMFPIDPNGSQTQ 111

Query: 121 QNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS 180
            N+D QR+CIL+AASNPHPLPTPVYRPQ+QNL+Q EN +AQ ESRLSDAETVAKSF QCS
Sbjct: 112 SNIDEQRNCILIAASNPHPLPTPVYRPQIQNLEQIENIDAQNESRLSDAETVAKSFPQCS 171

Query: 181 VSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGV 240
           VSLS+ICPKQLPKL +IYNA KRN RAADPPVD+ KNPHFLVLISENFMEARAALS PGV
Sbjct: 172 VSLSIICPKQLPKLRSIYNAGKRNSRAADPPVDSVKNPHFLVLISENFMEARAALSLPGV 231

Query: 241 ANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNG--INRPPISVGNVPTATVKVEPSTVTS 298
            +L  NQ PVK+DIA VTSVTGPAPTSIPSVNG   NRP ISVGNVPTATVKVEPST+TS
Sbjct: 232 TSLTSNQTPVKVDIASVTSVTGPAPTSIPSVNGSITNRPTISVGNVPTATVKVEPSTITS 291

Query: 299 MVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPM 358
           M NGPTFPH PSVPRPASQGVP LQTSSPS+T+Q+M TSGD V ++KP VS M+Q  RP 
Sbjct: 292 MANGPTFPHNPSVPRPASQGVPILQTSSPSTTTQDMATSGDDVQDLKPNVSVMTQSARPG 351

Query: 359 APAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTS 418
            PAAANV+ILNN+SQARQVMN+A L+GGTS+GL S+ QT +AMHMSNMISSGMASSVP +
Sbjct: 352 PPAAANVSILNNISQARQVMNSAGLSGGTSLGLPSINQTSVAMHMSNMISSGMASSVPAA 411

Query: 419 QPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSN-PSISQPMGTLQG 477
             VFSS Q G++SI GSGTLTGT+Q+  NSGL SFTSA SN+SGNSN   ISQPMG LQ 
Sbjct: 412 PTVFSSGQPGVSSITGSGTLTGTTQIGPNSGLGSFTSATSNVSGNSNLGRISQPMGNLQA 471

Query: 478 GASMGQSV-GMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQS 536
           G S+GQS  GMSQGN SG QMVQ+G+  N N MSGLGPSGVSSG  TMIPTPGMSQQ QS
Sbjct: 472 GVSIGQSAPGMSQGNISGAQMVQSGMGANPNTMSGLGPSGVSSGLNTMIPTPGMSQQVQS 531

Query: 537 GMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSA 596
           GMQPL  NNN+A N+ +SQQT+  L   QSKYVKVWEG+LSGQRQGQPVFIT+LEGYRSA
Sbjct: 532 GMQPLGANNNSADNLSMSQQTAGGLQPPQSKYVKVWEGNLSGQRQGQPVFITRLEGYRSA 591

Query: 597 SASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVI 656
           SASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVI
Sbjct: 592 SASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVI 651

Query: 657 QLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQIS 691
           QLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQIS
Sbjct: 652 QLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQIS 686

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  951 bits (2459), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 503/692 (72%), Positives = 577/692 (83%), Gaps = 15/692 (2%)

Query: 1   MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTH 60
           M++KQLIV VEGTAAMGP+WQ++VSDY+EKI+R FC NEL GQK   SNVE SLVTF+TH
Sbjct: 1   MADKQLIVVVEGTAAMGPFWQTVVSDYIEKIVRSFCGNELTGQKPPTSNVEFSLVTFHTH 60

Query: 61  GSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQ 120
           GSYC CLVQR+GWT+DVDIF+ WLS IPF+GGGF+DAAIAEGL+EALMMF   PNG QNQ
Sbjct: 61  GSYCGCLVQRTGWTRDVDIFIQWLSAIPFSGGGFSDAAIAEGLAEALMMFPTQPNGGQNQ 120

Query: 121 QNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS 180
           Q +D Q+HCILVAASNP+PLPTPVYRP +QNL+Q++N E    S  S AETVAKSF QC 
Sbjct: 121 QTMDMQKHCILVAASNPYPLPTPVYRPAVQNLEQHDNVEP--GSSQSYAETVAKSFPQCF 178

Query: 181 VSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGV 240
           +SLSVICPKQLPKL AIY A KRNPRAADPP+DN K+P +LVLISENF+EARAALSRPG+
Sbjct: 179 ISLSVICPKQLPKLKAIYTAGKRNPRAADPPIDNVKSPSYLVLISENFVEARAALSRPGI 238

Query: 241 ANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNG--INRPPISVGNVPTATVKVEPSTVTS 298
            +L  NQ+PVKMDI+ V  VTGP PT+ PSVNG  INR P+SV N PTATVKVEP+TVTS
Sbjct: 239 TSLPANQSPVKMDISSVVPVTGPPPTTTPSVNGPIINRQPVSVPNGPTATVKVEPNTVTS 298

Query: 299 MVNGPTFP-HIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRP 357
           M NG  +P H+PSV R ASQGVPSLQTSSP S SQEMIT+ ++  ++KPLV+G+ QP+R 
Sbjct: 299 MTNGSGYPPHMPSVVRAASQGVPSLQTSSPLS-SQEMITNNENTQDLKPLVTGVPQPVRS 357

Query: 358 MAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPT 417
           + PA  NV+ILNN+SQAR VM+ AAL GGTSIGL SMGQTP+AMH+SNMISSGM SSVP 
Sbjct: 358 LGPA--NVSILNNISQAR-VMSTAALNGGTSIGLPSMGQTPIAMHVSNMISSGMGSSVPA 414

Query: 418 SQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQG 477
           +Q VFSS QSG+TSI GS TL   SQV  NSG++S TS  +N+SGN N + SQ +G LQG
Sbjct: 415 AQNVFSSGQSGMTSINGSSTL---SQVAPNSGISSLTSGNNNISGNPNIATSQAVGNLQG 471

Query: 478 GASMGQSV-GMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQS 536
             S+ QSV G+SQGN +G Q+VQ+GI ++QN+MS L   GVSSG GTMIPTPGM QQ Q+
Sbjct: 472 SVSVSQSVPGISQGNLAGTQVVQSGIGVSQNVMSNLTQPGVSSGNGTMIPTPGMPQQVQN 531

Query: 537 GMQPLSVNNNTAVNMQLSQQTSSALHS-SQSKYVKVWEGSLSGQRQGQPVFITKLEGYRS 595
           GM  L +NN  A NM L Q ++ AL   +QSKYVK WEG+LSGQRQGQPVFIT++EGYRS
Sbjct: 532 GMHSLGMNN-AAANMPLPQHSAGALQQQAQSKYVKFWEGNLSGQRQGQPVFITRMEGYRS 590

Query: 596 ASASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAV 655
           ASAS+ LAANWP TMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAV
Sbjct: 591 ASASDKLAANWPQTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAV 650

Query: 656 IQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK 687
           IQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK
Sbjct: 651 IQLPSQTLLLSVSDKACRLIGMLFPGDMVVFK 682

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  944 bits (2441), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 503/690 (72%), Positives = 565/690 (81%), Gaps = 11/690 (1%)

Query: 4   KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY 63
           KQLIVAVE TAAMGPYW +I+ DYL+K+IRCF  N+  GQK SASNVE +LVT+NTHG Y
Sbjct: 6   KQLIVAVESTAAMGPYWNTILMDYLDKMIRCFGGNDSTGQKFSASNVEFALVTYNTHGCY 65

Query: 64  CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV 123
            +CLVQRSGWT+D D+F  WLS+IPF GGGFNDAAIAEGLSEALMM   + +G+ NQQ+V
Sbjct: 66  SSCLVQRSGWTRDPDVFFSWLSSIPFNGGGFNDAAIAEGLSEALMMLWNSQSGAPNQQSV 125

Query: 124 DGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSL 183
           D  +HCILVAASNP+PL TPVY P+ QNL+Q+E  ++ + S L DAE VAK+F Q S+SL
Sbjct: 126 DMHKHCILVAASNPYPLQTPVYVPRPQNLEQSETIDSDSGSHLYDAEAVAKAFPQFSISL 185

Query: 184 SVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANL 243
           SVICPKQLPK+ +IYNA KRN RAADPP++ +K PHFL+LISE F EAR ALSR G+ +L
Sbjct: 186 SVICPKQLPKIKSIYNAGKRNNRAADPPLE-AKTPHFLILISEGFREARGALSRSGITSL 244

Query: 244 APNQNPVKMDIAPVTSVTGPAPTSIPSVNGI--NRPPISVGNVPTATVKVEPSTVTSMVN 301
             NQ+PVK+D   VT VTG  PTS+P VNG   NR P+  GNV  ATVKVEP  VTSMV+
Sbjct: 245 PSNQSPVKVDAVSVTPVTGAPPTSMP-VNGSIPNRQPVPAGNVAPATVKVEPVPVTSMVS 303

Query: 302 GPTFPHIPSVPRPAS--QGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMA 359
           GP FPH  SVPR  S  QGVPSLQTSSPSS SQ++IT+ ++  + KP VS +  PLRP+ 
Sbjct: 304 GPAFPHNSSVPRATSTSQGVPSLQTSSPSSVSQDIITNNETAQDTKPTVSML--PLRPVN 361

Query: 360 PAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQ 419
           P  ANVNILNNLSQARQVMN+AAL+GGTS+GL SMGQTP+AMHMSNMISSGM SSVP +Q
Sbjct: 362 PVQANVNILNNLSQARQVMNSAALSGGTSMGLPSMGQTPVAMHMSNMISSGMTSSVPAAQ 421

Query: 420 PVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGA 479
            VFSS QSGITS+  SG LT  +QV QNSGL S TS  SNLS +SN  ISQP+G LQG  
Sbjct: 422 NVFSSGQSGITSMTSSGPLTVPAQVGQNSGLGSLTSNTSNLSSSSNIGISQPLGNLQGVV 481

Query: 480 SMGQSV-GMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGM 538
           S+GQ V GMSQGN SG QMVQ G+SMNQN+MSGLG S VSSGTGTMIPTPGMSQ  QS M
Sbjct: 482 SIGQQVSGMSQGNLSGAQMVQGGVSMNQNVMSGLGQSVVSSGTGTMIPTPGMSQPVQSVM 541

Query: 539 QPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASA 598
           QPL   NN A NM LSQQTS  + S+QSKYVKVWEGSLSGQRQGQPVFITKLEGYR++SA
Sbjct: 542 QPLV--NNAAANMPLSQQTSGGMQSAQSKYVKVWEGSLSGQRQGQPVFITKLEGYRNSSA 599

Query: 599 SETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQL 658
           SETLAANWPP MQIVRLISQDHMNNKQYVGKADFLVFRAMN HGFLGQLQEKKLCAVIQL
Sbjct: 600 SETLAANWPPVMQIVRLISQDHMNNKQYVGKADFLVFRAMNPHGFLGQLQEKKLCAVIQL 659

Query: 659 PSQTLLLSVSDKACRLIGMLFPGDMVVFKP 688
           PSQTLLLSVSDKA RLIGMLFPGDMVVFKP
Sbjct: 660 PSQTLLLSVSDKAFRLIGMLFPGDMVVFKP 689

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  882 bits (2279), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 469/692 (67%), Positives = 547/692 (79%), Gaps = 28/692 (4%)

Query: 4   KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY 63
           KQLIV  EGTAA+GPYW +IVSDYLEKIIR FC +EL G++    NVELSLV FN+HGSY
Sbjct: 6   KQLIVVAEGTAALGPYWHTIVSDYLEKIIRSFCGSELNGER----NVELSLVIFNSHGSY 61

Query: 64  CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV 123
           CACLVQRSGWTKDVDIFLHWLS+I FAGGGF++AA AEGL+EALMMFS  P   Q Q + 
Sbjct: 62  CACLVQRSGWTKDVDIFLHWLSSIQFAGGGFSEAATAEGLAEALMMFS--PPSGQAQPSN 119

Query: 124 DGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSL 183
           D +RHCIL+ ASNPH LPTPVYRP++ N ++NEN +AQ+ESRLSDAETVA  F +CSVSL
Sbjct: 120 DLKRHCILITASNPHSLPTPVYRPKLPNAERNENGDAQSESRLSDAETVASYFSRCSVSL 179

Query: 184 SVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANL 243
           SVICPKQLPK+ A+YNA K NP++ D  +D  KN  +LVLI ENF+EARAALS     NL
Sbjct: 180 SVICPKQLPKIRALYNAGKLNPQSPDLSIDTVKNTFYLVLIPENFVEARAALSH-SATNL 238

Query: 244 APNQNPVKMD---IAPVTSVTGPAPTSIPSVNG--INRPPISVGNVPTATVKVEPSTVTS 298
              Q+PVK+D   +AP   VTG  P  +PS NG  +NR P+S+G VPTATVKVEPSTV S
Sbjct: 239 PQTQSPVKVDRSTVAPSLPVTGQPPAPVPSANGPILNRQPVSIGPVPTATVKVEPSTVPS 298

Query: 299 MVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPM 358
           M    TFPHI SV RPA+Q +PS+QTSSPS  SQEM+T+ ++ P+VKP+V+GM+ PLR  
Sbjct: 299 MAAVSTFPHIQSVARPATQAIPSIQTSSPSPVSQEMVTNAENAPDVKPVVTGMTPPLRTG 358

Query: 359 APAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTS 418
            P  ANVN+LNNLSQ RQVM++AA     +    S GQ+ +AMHMSNMIS+GMA+S+P S
Sbjct: 359 PPGGANVNLLNNLSQVRQVMSSAA----LAGAASSTGQSAVAMHMSNMISTGMATSLPPS 414

Query: 419 QPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGG 478
           Q VFSS Q GITS+ GSG L GT Q  Q+ G N+  S  +  +  SN  +SQPM      
Sbjct: 415 QTVFSSGQQGITSMAGSGALMGTVQAGQSPGPNNSFSPQTTSNVASNLGVSQPM------ 468

Query: 479 ASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGM 538
                  GM+QG+HSG QM+Q GI MNQNMMSGLG   VSSGTG M+PTPG+ QQAQSG+
Sbjct: 469 ------PGMNQGSHSGAQMMQGGIPMNQNMMSGLGQGNVSSGTGGMMPTPGVGQQAQSGI 522

Query: 539 QPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASA 598
           Q L  +N++A NMQLSQ +S+AL +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSASA
Sbjct: 523 QQLGGSNSSAPNMQLSQPSSAALQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSASA 582

Query: 599 SETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQL 658
           S++LAANWPPTMQIVRLISQDHMNNKQYVGKAD LVFRAM+QHGFLGQLQ+KKLCAVIQL
Sbjct: 583 SDSLAANWPPTMQIVRLISQDHMNNKQYVGKADSLVFRAMSQHGFLGQLQDKKLCAVIQL 642

Query: 659 PSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 690
           PSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI
Sbjct: 643 PSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 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 =  875 bits (2261), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 464/693 (66%), Positives = 550/693 (79%), Gaps = 26/693 (3%)

Query: 4   KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY 63
           KQLIV  EGTAA+GPYWQ+IVSDYLEKIIR FC +EL G++   S VELSLV FN+HGSY
Sbjct: 6   KQLIVVAEGTAALGPYWQTIVSDYLEKIIRSFCGSELNGERNPVSTVELSLVIFNSHGSY 65

Query: 64  CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV 123
           CACLVQRSGWT+DVDIFLHWLS+I F GGGFN+ A AEGL+EALMMFS  P   Q Q + 
Sbjct: 66  CACLVQRSGWTRDVDIFLHWLSSIQFGGGGFNEVATAEGLAEALMMFS--PPSGQAQPSN 123

Query: 124 DGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSL 183
           D +RHCIL+ ASNPH LPTPVYRP++QN+++NEN +AQAESRLSDAETVA  F +CSVSL
Sbjct: 124 DLKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSL 183

Query: 184 SVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANL 243
           SV+CPKQLP + A+YNA K N ++AD  +D +KN  +LVLISENF+EA AALS     NL
Sbjct: 184 SVVCPKQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSH-SATNL 242

Query: 244 APNQNPVKMD---IAPVTSVTGPAPTSIPSVNGI--NRPPISVGNVPTATVKVEPSTVTS 298
              Q+PVK+D   +AP   VTG  P  + S NG   NR P+SVG VPTATVKVEPSTVTS
Sbjct: 243 PQTQSPVKVDRATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVEPSTVTS 302

Query: 299 MVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLV-SGMSQPLRP 357
           M   P+FPHIP+V RPA+Q +PS+QTSS S  SQ+M+++ ++ P++KP+V SGM+ PLR 
Sbjct: 303 MAPVPSFPHIPAVARPATQAIPSIQTSSASPVSQDMVSNAENAPDIKPVVVSGMTPPLRT 362

Query: 358 MAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPT 417
             P  ANVN+LNNLSQ RQVM++AA     +    S+GQ+ +AMHMSNMIS+GMA+S+P 
Sbjct: 363 GPPGGANVNLLNNLSQVRQVMSSAA----LAGAASSVGQSAVAMHMSNMISTGMATSLPP 418

Query: 418 SQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQG 477
           SQ VFS+ Q GITS+ GSG L G++Q  Q+ G N+  S  +  +  SN  +SQPM     
Sbjct: 419 SQTVFSTGQQGITSMAGSGALMGSAQTGQSPGPNNAFSPQTTSNVASNLGVSQPMQ---- 474

Query: 478 GASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSG 537
                   GM+QG+HSG  M+Q GISMNQNMMSGLG   VSSGTG M+PTPG+ QQAQSG
Sbjct: 475 --------GMNQGSHSGA-MMQGGISMNQNMMSGLGQGNVSSGTGGMMPTPGVGQQAQSG 525

Query: 538 MQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSAS 597
           +Q L  +N++A NMQLSQ +S A+ +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSAS
Sbjct: 526 IQQLGGSNSSAPNMQLSQPSSGAMQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSAS 585

Query: 598 ASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQ 657
           AS++LAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAM+QHGFLGQLQ+KKLCAVIQ
Sbjct: 586 ASDSLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMSQHGFLGQLQDKKLCAVIQ 645

Query: 658 LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 690
           LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI
Sbjct: 646 LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 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 =  874 bits (2259), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 467/693 (67%), Positives = 550/693 (79%), Gaps = 26/693 (3%)

Query: 4   KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY 63
           KQLIV  EGTAA+GPYWQ+IVSDYLEKIIR FC +EL G++   S VELSLV FN+HGSY
Sbjct: 6   KQLIVVAEGTAALGPYWQTIVSDYLEKIIRSFCGSELNGERNPVSTVELSLVIFNSHGSY 65

Query: 64  CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV 123
           CACLVQRSGWT+DVDIFLHWLS+I F GGGFN+ A AEGL+EALMMFS  P   Q Q + 
Sbjct: 66  CACLVQRSGWTRDVDIFLHWLSSIQFGGGGFNEVATAEGLAEALMMFS--PPSGQAQPSN 123

Query: 124 DGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSL 183
           D +RHCIL+ ASNPH LPTPV+RP++Q++++NEN +AQAESRLSDAETVA  F +CSVSL
Sbjct: 124 DLKRHCILITASNPHTLPTPVFRPRLQSVERNENGDAQAESRLSDAETVASYFAKCSVSL 183

Query: 184 SVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANL 243
           SV+CPKQLPK+ A+YNA K NP++AD  +D +KN  +LVLISENF+EARAALS     NL
Sbjct: 184 SVVCPKQLPKIRALYNAGKLNPQSADLSIDTAKNTFYLVLISENFVEARAALSH-SATNL 242

Query: 244 APNQNPVKMD---IAPVTSVTGPAPTSIPSVNGI--NRPPISVGNVPTATVKVEPSTVTS 298
              Q+PVK+D   +AP   VTG  P  + S NG   NR P+SVG VPTATVKVEPSTVTS
Sbjct: 243 PQTQSPVKVDRATVAPSLPVTGQPPAPVTSANGPIQNRQPVSVGPVPTATVKVEPSTVTS 302

Query: 299 MVNGPTFPHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLV-SGMSQPLRP 357
           M   P FPHIPSV RPA+Q +PS+QTSS S  SQ+M+T+ ++ P++KP+V  GM+ PLR 
Sbjct: 303 MAPVPNFPHIPSVARPATQPIPSIQTSSASPVSQDMVTNAENAPDIKPVVVGGMTPPLRT 362

Query: 358 MAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPT 417
             P  ANVN+LNNLSQ RQVM++AAL G  S   QS     +AMHMSNMIS+GMA+S+P 
Sbjct: 363 GPPGGANVNLLNNLSQVRQVMSSAALAGAASSAGQSA----VAMHMSNMISTGMATSLPP 418

Query: 418 SQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQG 477
           SQ VFS+ Q GITS+ GSG L G++Q  Q+ G N+  S  +  +  SN  +SQPM     
Sbjct: 419 SQTVFSTGQQGITSMAGSGALMGSAQTGQSPGPNNAFSPQTTPNVASNLGVSQPMQ---- 474

Query: 478 GASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSG 537
                   GM+QG+HSG  M+Q GISMNQN++SGLG   VSSGTG M+PTPG+ QQAQSG
Sbjct: 475 --------GMNQGSHSGA-MMQGGISMNQNIVSGLGQGNVSSGTGGMMPTPGVGQQAQSG 525

Query: 538 MQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSAS 597
           +Q L  +N++A NMQLSQ +S AL +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSAS
Sbjct: 526 IQQLGGSNSSAPNMQLSQPSSGALQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSAS 585

Query: 598 ASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVIQ 657
           AS++LAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAM+QHGFLGQLQ+KKLCAVIQ
Sbjct: 586 ASDSLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMSQHGFLGQLQDKKLCAVIQ 645

Query: 658 LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 690
           LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI
Sbjct: 646 LPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQI 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 (2030), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/535 (77%), Positives = 461/535 (86%), Gaps = 7/535 (1%)

Query: 71  SGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMM-FSVAPNGSQNQQNVDGQRHC 129
           SGWT+DVDIFL WL+ IPFAGGGF+DAAIAEGLSEALMM F   PNGSQ QQN+DGQRHC
Sbjct: 30  SGWTRDVDIFLQWLAAIPFAGGGFSDAAIAEGLSEALMMMFPFVPNGSQAQQNIDGQRHC 89

Query: 130 ILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK 189
           IL+AASNPHPLPTPVYR Q+QNL+QNEN + Q ESRLSDAET+AKSF QCSVSLSVICPK
Sbjct: 90  ILIAASNPHPLPTPVYRQQIQNLEQNENIDPQTESRLSDAETIAKSFPQCSVSLSVICPK 149

Query: 190 QLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANLAPNQNP 249
           QLPKL AIYNA KRN RAADP VDN KNPHFLVLISENFMEARAALSRPGVANL  NQ+P
Sbjct: 150 QLPKLRAIYNAGKRNSRAADPTVDNVKNPHFLVLISENFMEARAALSRPGVANLPSNQSP 209

Query: 250 VKMDIAPVTSVTGPAPTSIPSVNG--INRPPISVGNVPTATVKVEPSTVTSMVNGPTFPH 307
           VKMD+A VTSV GP   SIPSVNG  ++RP  S+GNVPTATVKVEP+TVTSM  GP FPH
Sbjct: 210 VKMDVASVTSVAGPTSPSIPSVNGSIMSRP--SIGNVPTATVKVEPTTVTSMAPGPAFPH 267

Query: 308 IPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRPMAPAAANVNI 367
           IPS  RPASQ VPSLQTSSP +++QE+ITS ++V E+KP VSGM   +RP+ P AANV+I
Sbjct: 268 IPST-RPASQSVPSLQTSSPPTSTQEIITSSENVSEIKPTVSGMPHSVRPVPPGAANVSI 326

Query: 368 LNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPVFSSAQS 427
           LNNLSQARQVMN+AALTGGTSIGL S+ QTP+AMHMSNMISSGMASSVP +Q VFSS Q+
Sbjct: 327 LNNLSQARQVMNSAALTGGTSIGLPSINQTPVAMHMSNMISSGMASSVPAAQTVFSSGQT 386

Query: 428 GITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQGGASMGQSV-G 486
           GITSI GSGTLTGT+Q+  NSGL SFTS  +N+SGNSN  +SQPMG LQ G SMGQSV G
Sbjct: 387 GITSITGSGTLTGTTQIAPNSGLGSFTSTTTNVSGNSNLGMSQPMGNLQAGVSMGQSVPG 446

Query: 487 MSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSGMQPLSVNNN 546
           MSQGN SG QMVQ+GI M+QNMMSGLGPS VSSG  TMIPTPGM Q AQ+G+Q L VNNN
Sbjct: 447 MSQGNLSGAQMVQSGIGMSQNMMSGLGPSVVSSGASTMIPTPGMGQPAQTGIQSLGVNNN 506

Query: 547 TAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSASASET 601
           +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|449519677|ref|XP_004166861.1| PREDICTED: mediator of RNA polymerase II transcription subunit 25-like, partial [Cucumis sativus]

 Score =  768 bits (1984), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 418/605 (69%), Positives = 492/605 (81%), Gaps = 15/605 (2%)

Query: 1   MSEKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTH 60
           M++KQLIV VEGTAAMGP+WQ++VSDY+EKI+R FC NEL GQK   SNVE SLVTF+TH
Sbjct: 1   MADKQLIVVVEGTAAMGPFWQTVVSDYIEKIVRSFCGNELTGQKPPTSNVEFSLVTFHTH 60

Query: 61  GSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQ 120
           GSYC CLVQR+GWT+DVDIF+ WLS IPF+GGGF+DAAIAEGL+EALMMF   PNG QNQ
Sbjct: 61  GSYCGCLVQRTGWTRDVDIFIQWLSAIPFSGGGFSDAAIAEGLAEALMMFPTQPNGGQNQ 120

Query: 121 QNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS 180
           Q +D Q+HCILVAASNP+PLPTPVYRP +QNL+Q++N E    S  S AETVAKSF QC 
Sbjct: 121 QTMDMQKHCILVAASNPYPLPTPVYRPAVQNLEQHDNVE--PGSSQSYAETVAKSFPQCF 178

Query: 181 VSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGV 240
           +SLSVICPKQLPKL AIY A KRNPRAADPP+DN K+P +LVLISENF+EARAALSRPG+
Sbjct: 179 ISLSVICPKQLPKLKAIYTAGKRNPRAADPPIDNVKSPSYLVLISENFVEARAALSRPGI 238

Query: 241 ANLAPNQNPVKMDIAPVTSVTGPAPTSIPSVNG--INRPPISVGNVPTATVKVEPSTVTS 298
            +L  NQ+PVKMDI+ V  VTGP PT+ PSVNG  INR P+SV N PTATVKVEP+TVTS
Sbjct: 239 TSLPANQSPVKMDISSVVPVTGPPPTTTPSVNGPIINRQPVSVPNGPTATVKVEPNTVTS 298

Query: 299 MVNGPTF-PHIPSVPRPASQGVPSLQTSSPSSTSQEMITSGDSVPEVKPLVSGMSQPLRP 357
           M NG  + PH+PSV R ASQGVPSLQTSSP S SQEMIT+ ++  ++KPLV+G+ QP+R 
Sbjct: 299 MTNGSGYPPHMPSVVRAASQGVPSLQTSSPLS-SQEMITNNENTQDLKPLVTGVPQPVRS 357

Query: 358 MAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPT 417
           + P  ANV+ILNN+SQAR VM+ AAL GGTSIGL SMGQTP+AMH+SNMISSGM SSVP 
Sbjct: 358 LGP--ANVSILNNISQAR-VMSTAALNGGTSIGLPSMGQTPIAMHVSNMISSGMGSSVPA 414

Query: 418 SQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQG 477
           +Q VFSS QSG+TSI GS TL   SQV  NSG++S TS  +N+SGN N + SQ +G LQG
Sbjct: 415 AQNVFSSGQSGMTSINGSSTL---SQVAPNSGISSLTSGNNNISGNPNIATSQAVGNLQG 471

Query: 478 GASMGQSV-GMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQS 536
             S+ QSV G+SQGN +G Q+VQ+GI ++QN+MS L   GVSSG GTMIPTPGM QQ Q+
Sbjct: 472 SVSVSQSVPGISQGNLAGTQVVQSGIGVSQNVMSNLTQPGVSSGNGTMIPTPGMPQQVQN 531

Query: 537 GMQPLSVNNNTAVNMQLSQQTSSAL-HSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRS 595
           GM  L + NN A NM L Q ++ AL   +QSKYVK WEG+LSGQRQGQPVFIT++EGYRS
Sbjct: 532 GMHSLGM-NNAAANMPLPQHSAGALQQQAQSKYVKFWEGNLSGQRQGQPVFITRMEGYRS 590

Query: 596 ASASE 600
           ASAS+
Sbjct: 591 ASASD 595

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	834
TAIR|locus:2031200	836	PFT1 "PHYTOCHROME AND FLOWERIN	0.794	0.793	0.622	1.4e-220
UNIPROTKB|F1N3D4	743	MED25 "Mediator of RNA polymer	0.158	0.177	0.333	2.3e-12
UNIPROTKB|F1RHT9	746	MED25 "Uncharacterized protein	0.158	0.176	0.333	6.4e-12
MGI|MGI:1922863	745	Med25 "mediator of RNA polymer	0.158	0.177	0.333	7.4e-12
UNIPROTKB|A2VE44	746	MED25 "Mediator of RNA polymer	0.158	0.176	0.333	7.4e-12
UNIPROTKB|Q71SY5	747	MED25 "Mediator of RNA polymer	0.158	0.176	0.333	3.1e-10
ZFIN|ZDB-GENE-040426-2850	701	med25 "mediator of RNA polymer	0.292	0.348	0.268	6.4e-10
DICTYBASE|DDB_G0286967	1553	med25 "putative mediator compl	0.145	0.077	0.274	1.8e-07
WB|WBGene00019435	2232	K06A9.1 [Caenorhabditis elegan	0.384	0.143	0.219	1.2e-05
FB|FBgn0038760	863	MED25 "Mediator complex subuni	0.215	0.208	0.22	1.6e-05

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

 Score = 2090 (740.8 bits), Expect = 1.4e-220, Sum P(2) = 1.4e-220
 Identities = 430/691 (62%), Positives = 513/691 (74%)

Query:     4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY 63
             KQLIV  EGTAA+GPYWQ+IVSDYLEKIIR FC +EL G++   S VELSLV FN+HGSY
Sbjct:     6 KQLIVVAEGTAALGPYWQTIVSDYLEKIIRSFCGSELNGERNPVSTVELSLVIFNSHGSY 65

Query:    64 CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV 123
             CACLVQRSGWT+DVDIFLHWLS+I F GGGFN+ A AEGL+EALMMFS  P+G Q Q + 
Sbjct:    66 CACLVQRSGWTRDVDIFLHWLSSIQFGGGGFNEVATAEGLAEALMMFS-PPSG-QAQPSN 123

Query:   124 DGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSL 183
             D +RHCIL+ ASNPH LPTPVYRP++QN+++NEN +AQAESRLSDAETVA  F +CSVSL
Sbjct:   124 DLKRHCILITASNPHILPTPVYRPRLQNVERNENGDAQAESRLSDAETVASYFAKCSVSL 183

Query:   184 SVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPGVANL 243
             SV+CPKQLP + A+YNA K N ++AD  +D +KN  +LVLISENF+EA AALS     NL
Sbjct:   184 SVVCPKQLPTIRALYNAGKPNQQSADLSIDTAKNTFYLVLISENFVEACAALSH-SATNL 242

Query:   244 APNQNPVKMD---IAPVTSVTGPAPTSIPSVNGI--NRPPISVGNVPTATVKVEPSTVTS 298
                Q+PVK+D   +AP   VTG  P  + S NG   NR P+SVG VPTATVKVEPSTVTS
Sbjct:   243 PQTQSPVKVDRATVAPSIPVTGQPPAPVSSANGPIQNRQPVSVGPVPTATVKVEPSTVTS 302

Query:   299 MVNGPTFPHIPSVPRPASQGVXXXXXXXXXXXXXEMITSGDSVPEVKPLVSGMSQPLRPM 358
             M   P+FPHIP+V RPA+Q +             +M+++ ++ P++KP+V     P    
Sbjct:   303 MAPVPSFPHIPAVARPATQAIPSIQTSSASPVSQDMVSNAENAPDIKPVVVSGMTPPLRT 362

Query:   359 APAAANVNILNNLSQARQVMN--NAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVP 416
              P     N+ N L+   QV    ++A   G +    S+GQ+ +AMHMSNMIS+GMA+S+P
Sbjct:   363 GPPGG-ANV-NLLNNLSQVRQVMSSAALAGAA---SSVGQSAVAMHMSNMISTGMATSLP 417

Query:   417 TSQPVFSSAQXXXXXXXXXXXXXXXXQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQ 476
              SQ VFS+ Q                Q  Q+ G N+  S  +  +  SN  +SQPM    
Sbjct:   418 PSQTVFSTGQQGITSMAGSGALMGSAQTGQSPGPNNAFSPQTTSNVASNLGVSQPMQ--- 474

Query:   477 GGASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQS 536
                      GM+QG+HSG  M+Q GISMNQNMMSGLG   VSSGTG M+PTPG+ QQAQS
Sbjct:   475 ---------GMNQGSHSGA-MMQGGISMNQNMMSGLGQGNVSSGTGGMMPTPGVGQQAQS 524

Query:   537 GMQPLSVNNNTAVNMQLSQQTSSALHSSQSKYVKVWEGSLSGQRQGQPVFITKLEGYRSA 596
             G+Q L  +N++A NMQLSQ +S A+ +SQSKYVKVWEG+LSGQRQGQPV IT+LEGYRSA
Sbjct:   525 GIQQLGGSNSSAPNMQLSQPSSGAMQTSQSKYVKVWEGNLSGQRQGQPVLITRLEGYRSA 584

Query:   597 SASETLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMNQHGFLGQLQEKKLCAVI 656
             SAS++LAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAM+QHGFLGQLQ+KKLCAVI
Sbjct:   585 SASDSLAANWPPTMQIVRLISQDHMNNKQYVGKADFLVFRAMSQHGFLGQLQDKKLCAVI 644

Query:   657 QLPSQTLLLSVSDKACRLIGMLFPGDMVVFK 687
             QLPSQTLLLSVSDKACRLIGMLFPGDMVVFK
Sbjct:   645 QLPSQTLLLSVSDKACRLIGMLFPGDMVVFK 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 = 153 (58.9 bits), Expect = 2.3e-12, Sum P(3) = 2.3e-12
 Identities = 47/141 (33%), Positives = 66/141 (46%)

Query:     6 LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSAS--NVELSLVTFNTHGSY 63
             ++  +EGTA +GPY++ +   YL   I  F     A           + SLV FNT    
Sbjct:    18 VVFVIEGTANLGPYFEGLRKHYLLPAIEYFNGGPPAETDFGGDYGGTQYSLVVFNTVDCA 77

Query:    64 CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQN 122
                 VQ    T     F+ WL  I F GGG    + IAEGLS AL +F    +  + ++ 
Sbjct:    78 PESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQLFD---DFKKMREQ 134

Query:   123 VDGQRH--CILVAASNPHPLP 141
             + GQ H  C+L+  S P+ LP
Sbjct:   135 I-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 = 153 (58.9 bits), Expect = 6.4e-12, Sum P(2) = 6.4e-12
 Identities = 47/141 (33%), Positives = 66/141 (46%)

Query:     6 LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSAS--NVELSLVTFNTHGSY 63
             ++  +EGTA +GPY++ +   YL   I  F     A           + SLV FNT    
Sbjct:    18 VVFVIEGTANLGPYFEGLRKHYLLPAIEYFNGGPPAETDFGGDYGGTQYSLVVFNTVDCA 77

Query:    64 CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQN 122
                 VQ    T     F+ WL  I F GGG    + IAEGLS AL +F    +  + ++ 
Sbjct:    78 PESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQLFD---DFKKMREQ 134

Query:   123 VDGQRH--CILVAASNPHPLP 141
             + GQ H  C+L+  S P+ LP
Sbjct:   135 I-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 = 153 (58.9 bits), Expect = 7.4e-12, Sum P(3) = 7.4e-12
 Identities = 47/141 (33%), Positives = 66/141 (46%)

Query:     6 LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSAS--NVELSLVTFNTHGSY 63
             ++  +EGTA +GPY++ +   YL   I  F     A           + SLV FNT    
Sbjct:    18 VVFVIEGTANLGPYFEELRKHYLLPAIEYFNGGPPAETDFGGDYGGTQYSLVVFNTVDCA 77

Query:    64 CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQN 122
                 VQ    T     F+ WL  I F GGG    + IAEGLS AL +F    +  + ++ 
Sbjct:    78 PESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQLFD---DFKKMREQ 134

Query:   123 VDGQRH--CILVAASNPHPLP 141
             + GQ H  C+L+  S P+ LP
Sbjct:   135 I-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 = 153 (58.9 bits), Expect = 7.4e-12, Sum P(3) = 7.4e-12
 Identities = 47/141 (33%), Positives = 66/141 (46%)

Query:     6 LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSAS--NVELSLVTFNTHGSY 63
             ++  +EGTA +GPY++ +   YL   I  F     A           + SLV FNT    
Sbjct:    18 VVFVIEGTANLGPYFEGLRKHYLLPAIEYFNGGPPAETDFGGDYGGTQYSLVVFNTVDCA 77

Query:    64 CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQN 122
                 VQ    T     F+ WL  I F GGG    + IAEGLS AL +F    +  + ++ 
Sbjct:    78 PESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQLFD---DFKKMREQ 134

Query:   123 VDGQRH--CILVAASNPHPLP 141
             + GQ H  C+L+  S P+ LP
Sbjct:   135 I-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 = 153 (58.9 bits), Expect = 3.1e-10, Sum P(3) = 3.1e-10
 Identities = 47/141 (33%), Positives = 66/141 (46%)

Query:     6 LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSAS--NVELSLVTFNTHGSY 63
             ++  +EGTA +GPY++ +   YL   I  F     A           + SLV FNT    
Sbjct:    18 VVFVIEGTANLGPYFEGLRKHYLLPAIEYFNGGPPAETDFGGDYGGTQYSLVVFNTVDCA 77

Query:    64 CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQN 122
                 VQ    T     F+ WL  I F GGG    + IAEGLS AL +F    +  + ++ 
Sbjct:    78 PESYVQCHAPTSSAYEFVTWLDGIKFMGGGGESCSLIAEGLSTALQLFD---DFKKMREQ 134

Query:   123 VDGQRH--CILVAASNPHPLP 141
             + GQ H  C+L+  S P+ LP
Sbjct:   135 I-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 = 178 (67.7 bits), Expect = 6.4e-10, Sum P(3) = 6.4e-10
 Identities = 75/279 (26%), Positives = 128/279 (45%)

Query:     6 LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSAS--NVELSLVTFNTHGSY 63
             ++  +EGTA +GPY++S+ ++Y+   I  F     A           +  LV FNT    
Sbjct:    15 VVFVIEGTANLGPYFESLRNNYILPTIEYFNGGPPAETDFGGDYGGTQYGLVVFNTVDCA 74

Query:    64 CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQN 122
                 VQ    T     F+ W+ +I F GGG    + IAEGLS AL +F    +  + ++ 
Sbjct:    75 PESYVQCHAPTSSAFEFVSWIDSIQFMGGGAESCSLIAEGLSVALQLFD---DFKKMREQ 131

Query:   123 VDGQRH--CILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCS 180
             + GQ H  C+L+  S P+ LP                 E+ + +  + A+++ +      
Sbjct:   132 I-GQTHKVCVLLCNSPPYLLPAV---------------ESVSYTGCT-ADSLVQIIRDRG 174

Query:   181 VSLSVICPKQLPKLTAIYNAAKRN---PRAADPPVDNSKNPHFLVLISENFME-ARAALS 236
             +  SVI P++LP L +++  A      P ++ P  D S++P  +VL+    +  A    S
Sbjct:   175 IHFSVIAPRKLPALRSLFERASSVAGLPESSHP--DYSQDPFHMVLVRGIALPVAPGGGS 232

Query:   237 RP-GVANLAPNQN-PVKMD-IAPVTSVTGPAPTSIPSVN 272
              P  +  + P Q+ PV  + + PV S T P   +  +V+
Sbjct:   233 VPVSLKPVLPPQSLPVNQNPLVPVAS-TAPQMNTFQNVS 270

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

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

 Score = 110 (43.8 bits), Expect = 1.8e-07, Sum P(4) = 1.8e-07
 Identities = 37/135 (27%), Positives = 65/135 (48%)

Query:     4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY 63
             KQ+I  ++ +A M   + +I +DYL+ +   +  +E     +   N    LV F  +  Y
Sbjct:   146 KQIIFILDSSAMMAHSFPTIQNDYLDPLA-LYLKHE-----SKNFNFTYGLVLFRDYPPY 199

Query:    64 CACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDA-AIAEGLSEALMMFSVAPNGSQNQQN 122
                +   +  TKD+   L  ++T  F GGGF+   AI+EG+ +AL + S +       Q 
Sbjct:   200 SDFIASSTPLTKDLKTILTLMATTKFNGGGFSTGGAISEGICKALRLASCS-------QT 252

Query:   123 VDGQRHCILVAASNP 137
             +  +   IL+  +NP
Sbjct:   253 IIHEECFILITNNNP 267

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

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:   244 APNQNPVKMDIAPVTSVTGPAPTSIPSVNGINRPPISVGNVPTATVKVEPSTVTSMVNGP 303
             +PN +          +++G +   + +V+G     +S G+  T+   +  ST T   +  
Sbjct:   534 SPNPSSSPASTGSTITISGSSSIIVSTVSGST---VS-GSTGTSQSTLASSTATPG-SSS 588

Query:   304 TFPHIPSVPRPASQGVXXXXXXXXXXXXXEMITSGDSVPEVKPLVSGMSQPLRPMAPAAA 363
             T P   S P+P+SQ                   S    P            + P    A+
Sbjct:   589 TVPSSSS-PQPSSQSPAPNTGSTTPSQTSSQSPSPSMNPSSSTPTGSSQSTITPEGSTAS 647

Query:   364 NV--NILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPTSQPV 421
             +   +  +  S A +V + + +  G+S+G QS   +P    +S   +SGM  S  TS+P 
Sbjct:   648 SPTGSTGSTFSVATEVTSQSTVPSGSSLGTQSTNSSPSPSSLSPS-TSGM--STLTSEPS 704

Query:   422 FSSAQXXXXXXXXXXXXXXXXQVPQNSGLNSFTSAPSNLSGNS-----NPSISQPMGTLQ 476
              SS Q                Q    S L S TS  +  SG++     +PS S  +G+ Q
Sbjct:   705 PSSTQSSGAQSTLTTPSPNPSQ--STSSLESSTSGATTSSGSAGTTMTSPSQSSSVGSSQ 762

Query:   477 GGASMGQSVGMSQGNHSGG-QMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQ 535
             G  S   S    +    G  Q   + +S +  +++    S  ++  G+ +  P     + 
Sbjct:   763 GSTSPAASTTSGEMTSQGSTQTPGSSVSTSAAILTSTQQSVSTNSPGSTVTRPSTVSGST 822

Query:   536 SGMQPLSVNNNTAVNMQLSQQTSS-ALHSSQSKYVKVWEGS 575
             S    ++V +  A     S  +SS A  +SQ+       GS
Sbjct:   823 SSGSTVTVGSTEASTSGSSVASSSPAPSTSQNPNPSTSSGS 863

GO:0016021 "integral to membrane" evidence=IEA

FB|FBgn0038760 MED25 "Mediator complex subunit 25" [Drosophila melanogaster (taxid:7227)]

 Score = 114 (45.2 bits), Expect = 1.6e-05, Sum P(2) = 1.6e-05
 Identities = 44/200 (22%), Positives = 82/200 (41%)

Query:     6 LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSL---VTFNTHGS 62
             ++  +EG+A  G Y   + ++Y+   +  F    +  ++   +    +L   V + T  +
Sbjct:    11 VVFVIEGSAINGAYINELKTNYILPTLEHFTTGSIDEREYLIAERFATLYGIVVYRTAAN 70

Query:    63 YCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQNQQ 121
                 +    G        +  +  +P  GGG    A +AEG + A   F       Q   
Sbjct:    71 LLEPVCSTYGPFLQPQKVMETIERLPLVGGGMESCAHMAEGFAAAHGCFDDISERRQLLD 130

Query:   122 NVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSV 181
                 QRHCIL+  S P+ +PT             E+ +   +S     E +A  F +  +
Sbjct:   131 QTSVQRHCILICNSPPYQMPT------------TESWKYPGKS----CEQLAALFNERKI 174

Query:   182 SLSVICPKQLPKLTAIYNAA 201
             +LS+I P+++P L  ++  A
Sbjct:   175 NLSIIAPRKMPVLFKLFMKA 194

GO:0001104 "RNA polymerase II transcription cofactor activity" evidence=ISS

GO:0016592 "mediator complex" evidence=ISS

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

GO:0007399 "nervous system development" evidence=IMP

GO:0002805 "regulation of antimicrobial peptide biosynthetic process" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q7XYY2	MED25_ARATH	No assigned EC number	0.6695	0.7997	0.7978	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

Your Input: fgenesh4_pg.C_LG_X001175 hypothetical protein (796 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	834
pfam11265	226	pfam11265, Med25_VWA, Mediator complex subunit 25	6e-68
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	9e-16
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	8e-15
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	2e-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	3e-13
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	2e-12
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	6e-11
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	8e-11
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	9e-11
pfam13779	820	pfam13779, DUF4175, Domain of unknown function (DU	1e-10
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	5e-10
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	2e-09
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	2e-09
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	3e-09
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	4e-09
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	6e-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
COG3064	387	COG3064, TolA, Membrane protein involved in colici	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	3e-08
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	6e-08
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	8e-08
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	1e-07
PRK00286	438	PRK00286, xseA, exodeoxyribonuclease VII large sub	2e-07
PRK00286	438	PRK00286, xseA, exodeoxyribonuclease VII large sub	2e-07
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	2e-07
pfam09606	768	pfam09606, Med15, ARC105 or Med15 subunit of Media	3e-07
pfam09770	804	pfam09770, PAT1, Topoisomerase II-associated prote	6e-07
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	6e-07
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	8e-07
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	1e-06
COG1570	440	COG1570, XseA, Exonuclease VII, large subunit [DNA	2e-06
COG3264	835	COG3264, COG3264, Small-conductance mechanosensiti	2e-06
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	4e-06
pfam11498	476	pfam11498, Activator_LAG-3, Transcriptional activa	5e-06
COG3264	835	COG3264, COG3264, Small-conductance mechanosensiti	5e-06
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	5e-06
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	5e-06
pfam12128	1198	pfam12128, DUF3584, Protein of unknown function (D	5e-06
TIGR00237	432	TIGR00237, xseA, exodeoxyribonuclease VII, large s	5e-06
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	7e-06
PRK06800	228	PRK06800, fliH, flagellar assembly protein H; Vali	7e-06
COG3064	387	COG3064, TolA, Membrane protein involved in colici	8e-06
pfam11932	250	pfam11932, DUF3450, Protein of unknown function (D	8e-06
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	1e-05
PRK04863	1486	PRK04863, mukB, cell division protein MukB; Provis	1e-05
PRK10927	319	PRK10927, PRK10927, essential cell division protei	1e-05
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	1e-05
pfam02050	122	pfam02050, FliJ, Flagellar FliJ protein	1e-05
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	1e-05
pfam11498	476	pfam11498, Activator_LAG-3, Transcriptional activa	2e-05
COG1570	440	COG1570, XseA, Exonuclease VII, large subunit [DNA	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
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-05
pfam03280	189	pfam03280, Lipase_chap, Proteobacterial lipase cha	3e-05
PRK01294	336	PRK01294, PRK01294, lipase chaperone; Provisional	3e-05
PRK12757	256	PRK12757, PRK12757, cell division protein FtsN; Pr	4e-05
COG3264	835	COG3264, COG3264, Small-conductance mechanosensiti	4e-05
PRK10927	319	PRK10927, PRK10927, essential cell division protei	4e-05
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	5e-05
PRK10927	319	PRK10927, PRK10927, essential cell division protei	5e-05
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	5e-05
COG4372	499	COG4372, COG4372, Uncharacterized protein conserve	5e-05
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	6e-05
TIGR02473	141	TIGR02473, flagell_FliJ, flagellar export protein	6e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	7e-05
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	7e-05
pfam11068	131	pfam11068, DUF2869, Protein of unknown function (D	8e-05
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	9e-05
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	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
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	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
pfam03280	189	pfam03280, Lipase_chap, Proteobacterial lipase cha	1e-04
TIGR02473	141	TIGR02473, flagell_FliJ, flagellar export protein	1e-04
pfam11068	131	pfam11068, DUF2869, Protein of unknown function (D	1e-04
COG2959	391	COG2959, HemX, Uncharacterized enzyme of heme bios	1e-04
pfam12474	142	pfam12474, PKK, Polo kinase kinase	1e-04
COG1322	448	COG1322, COG1322, Predicted nuclease of restrictio	1e-04
PRK09510	387	PRK09510, tolA, cell envelope integrity inner memb	2e-04
PRK10263	1355	PRK10263, PRK10263, DNA translocase FtsK; Provisio	2e-04
TIGR00237	432	TIGR00237, xseA, exodeoxyribonuclease VII, large s	2e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	2e-04
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	2e-04
PRK11448	1123	PRK11448, hsdR, type I restriction enzyme EcoKI su	2e-04
pfam13904	261	pfam13904, DUF4207, Domain of unknown function (DU	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
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	2e-04
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	3e-04
pfam11932	250	pfam11932, DUF3450, Protein of unknown function (D	3e-04
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	3e-04
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	3e-04
pfam12795	239	pfam12795, MscS_porin, Mechanosensitive ion channe	3e-04
COG3115	324	COG3115, ZipA, Cell division protein [Cell divisio	3e-04
PRK11637	428	PRK11637, PRK11637, AmiB activator; Provisional	3e-04
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	4e-04
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	4e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
COG2959	391	COG2959, HemX, Uncharacterized enzyme of heme bios	4e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	4e-04
pfam12795	239	pfam12795, MscS_porin, Mechanosensitive ion channe	4e-04
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	4e-04
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	5e-04
pfam11068	131	pfam11068, DUF2869, Protein of unknown function (D	5e-04
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	5e-04
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	5e-04
TIGR02168	1179	TIGR02168, SMC_prok_B, chromosome segregation prot	5e-04
pfam11068	131	pfam11068, DUF2869, Protein of unknown function (D	6e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	6e-04
PRK03427	333	PRK03427, PRK03427, cell division protein ZipA; Pr	7e-04
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	7e-04
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	7e-04
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	7e-04
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	7e-04
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	7e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	7e-04
TIGR02302	851	TIGR02302, aProt_lowcomp, TIGR02302 family protein	7e-04
pfam04702	147	pfam04702, Vicilin_N, Vicilin N terminal region	8e-04
TIGR02794	346	TIGR02794, tolA_full, TolA protein	8e-04
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	8e-04
COG0419	908	COG0419, SbcC, ATPase involved in DNA repair [DNA	8e-04
pfam12128	1198	pfam12128, DUF3584, Protein of unknown function (D	9e-04
PRK11637	428	PRK11637, PRK11637, AmiB activator; Provisional	9e-04
smart00818	165	smart00818, Amelogenin, Amelogenins, cell adhesion	0.001
TIGR00237	432	TIGR00237, xseA, exodeoxyribonuclease VII, large s	0.001
pfam11932	250	pfam11932, DUF3450, Protein of unknown function (D	0.001
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	0.001
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	0.001
PRK10920	390	PRK10920, PRK10920, putative uroporphyrinogen III	0.001
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	0.001
pfam12037	276	pfam12037, DUF3523, Domain of unknown function (DU	0.001
pfam12037	276	pfam12037, DUF3523, Domain of unknown function (DU	0.001
pfam11180	192	pfam11180, DUF2968, Protein of unknown function (D	0.001
PRK01741	332	PRK01741, PRK01741, cell division protein ZipA; Pr	0.001
COG0845	372	COG0845, AcrA, Membrane-fusion protein [Cell envel	0.001
pfam03938	157	pfam03938, OmpH, Outer membrane protein (OmpH-like	0.001
pfam03938	157	pfam03938, OmpH, Outer membrane protein (OmpH-like	0.001
TIGR01843	423	TIGR01843, type_I_hlyD, type I secretion membrane	0.001
COG5380	283	COG5380, LimK, Lipase chaperone [Posttranslational	0.001
COG3064	387	COG3064, TolA, Membrane protein involved in colici	0.002
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	0.002
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	0.002
pfam02050	122	pfam02050, FliJ, Flagellar FliJ protein	0.002
TIGR04211	198	TIGR04211, SH3_and_anchor, SH3 domain protein	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
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	0.002
PRK11448	1123	PRK11448, hsdR, type I restriction enzyme EcoKI su	0.002
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.002
pfam07223	357	pfam07223, DUF1421, Protein of unknown function (D	0.002
TIGR02302	851	TIGR02302, aProt_lowcomp, TIGR02302 family protein	0.002
PRK12704	520	PRK12704, PRK12704, phosphodiesterase; Provisional	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
COG1570	440	COG1570, XseA, Exonuclease VII, large subunit [DNA	0.003
TIGR00618	1042	TIGR00618, sbcc, exonuclease SbcC	0.003
pfam12128	1198	pfam12128, DUF3584, Protein of unknown function (D	0.003
PRK10246	1047	PRK10246, PRK10246, exonuclease subunit SbcC; Prov	0.003
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.003
PRK11281	1113	PRK11281, PRK11281, hypothetical protein; Provisio	0.003
COG3166	206	COG3166, PilN, Tfp pilus assembly protein PilN [Ce	0.003
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.003
pfam13868	349	pfam13868, Trichoplein, Tumour suppressor, Mitosta	0.003
TIGR02302	851	TIGR02302, aProt_lowcomp, TIGR02302 family protein	0.003
pfam07321	152	pfam07321, YscO, Type III secretion protein YscO	0.003
pfam07321	152	pfam07321, YscO, Type III secretion protein YscO	0.003
COG4942	420	COG4942, COG4942, Membrane-bound metallopeptidase	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
pfam13388	422	pfam13388, DUF4106, Protein of unknown function (D	0.004
COG3115	324	COG3115, ZipA, Cell division protein [Cell divisio	0.004
PRK01741	332	PRK01741, PRK01741, cell division protein ZipA; Pr	0.004
COG5380	283	COG5380, LimK, Lipase chaperone [Posttranslational	0.004
COG4487	438	COG4487, COG4487, Uncharacterized protein conserve	0.004

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

 Score =  224 bits (572), Expect = 6e-68
 Identities = 77/230 (33%), Positives = 109/230 (47%), Gaps = 20/230 (8%)

Query: 3   EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASN--VELSLVTFNTH 60
              ++  +EGTA +GPY++++ ++Y+  II  F     A           + SLV FNT 
Sbjct: 13  VADVVFVIEGTANLGPYFETLKTNYILPIIEYFNGGPPAETDFGGEYGGTQYSLVVFNTV 72

Query: 61  GSYCACLVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAA-IAEGLSEALMMFSVAPNGSQN 119
            S     VQ  G T+DVD FLHWL +I F GGG    + IAEGL+EAL +F       Q 
Sbjct: 73  ASAPESYVQCHGPTRDVDEFLHWLDSIQFMGGGGESCSLIAEGLAEALQLFDDFSEMRQQ 132

Query: 120 QQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQC 179
               D  RHCIL+  S P+ LPT                 A  E + SD         + 
Sbjct: 133 IGQTDLHRHCILICNSPPYLLPT--------------VESASYEGKTSDQLAAI--IYER 176

Query: 180 SVSLSVICPKQLPKLTAIYNAAKRN-PRAADPPVDNSKNPHFLVLISENF 228
            + LS+I P++LP L  ++  AK +        +D +KNP  +VL+   F
Sbjct: 177 GIHLSIIAPRKLPALRLLFEKAKPDQQLPMKSSIDYAKNPFHMVLLRGIF 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 = 81.5 bits (202), Expect = 9e-16
 Identities = 37/130 (28%), Positives = 48/130 (36%), Gaps = 27/130 (20%)

Query: 696 QQLQQ--------QQQQQQHQQMQSQLQHQQLSQLQQQQQQL---------PQLQQQIPQ 738
           +QLQQ        Q  Q    +MQ  ++   L +  ++QQ L          Q   Q  +
Sbjct: 564 EQLQQMMENLQVTQGGQGGQSEMQQAME--GLGETLREQQGLSDETFRDLQEQFNAQRGE 621

Query: 739 LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLS-----QPQ 793
            Q QQ      Q    Q  QQ Q  Q QQQ Q  Q  Q  Q    ++QQ L      Q  
Sbjct: 622 QQGQQGQGGQGQG---QPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQQALRDELGRQRG 678

Query: 794 QMVGSGMGQG 803
            + G G   G
Sbjct: 679 GLPGMGGEAG 688

Length = 820

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

 Score = 78.4 bits (194), Expect = 8e-15
 Identities = 45/163 (27%), Positives = 59/163 (36%), Gaps = 32/163 (19%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQ-------------QQQLPQLQQ- 734
           Q++ Q Q+  QQ  Q         +L  Q L ++  +             QQ L QLQQ 
Sbjct: 511 QLAEQAQRNPQQGDQPPDQGNSM-ELTQQDLQRMMDRIEELMESGRRAEAQQLLEQLQQM 569

Query: 735 ----QIPQLQQQQQIPQLQQQSMPQL----QQQQQL-----PQLQQQQQLPQMQQQQQLP 781
               Q+ Q  Q  Q     QQ+M  L    ++QQ L       LQ+Q      + +QQ  
Sbjct: 570 MENLQVTQGGQGGQSEM--QQAMEGLGETLREQQGLSDETFRDLQEQFN--AQRGEQQGQ 625

Query: 782 QLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGA 824
           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 = 77.2 bits (191), Expect = 2e-14
 Identities = 47/159 (29%), Positives = 61/159 (38%), Gaps = 38/159 (23%)

Query: 696 QQLQQQQQQ--QQHQQMQSQLQHQQLSQ--LQQQ----------------QQQLPQLQQ- 734
           +QL +Q Q+  QQ  Q   Q    +L+Q  LQ+                 QQ L QLQQ 
Sbjct: 510 RQLAEQAQRNPQQGDQPPDQGNSMELTQQDLQRMMDRIEELMESGRRAEAQQLLEQLQQM 569

Query: 735 ----QIPQLQQQQQIPQLQQQSMPQL----QQQQQL-------PQLQQQQQLPQMQQQQQ 779
               Q+ Q  Q  Q     QQ+M  L    ++QQ L        Q Q   Q  + Q QQ 
Sbjct: 570 MENLQVTQGGQGGQSE--MQQAMEGLGETLREQQGLSDETFRDLQEQFNAQRGEQQGQQG 627

Query: 780 LPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQ 818
                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: 686 FKPQISSQQQQQLQQQQQQQQHQQM-----QSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 740
             P+      Q  Q   +Q Q QQ      Q+  Q     QL QQ   L Q Q      Q
Sbjct: 195 GPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQ 254

Query: 741 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ--LPQLQQQQQLSQPQQMVGS 798
                PQ  QQ     Q Q Q P   Q    P + Q Q   LP  QQ Q L   QQ  G 
Sbjct: 255 MPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQPQGQ 314

Query: 799 GMGQGYVQGP 808
             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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
               QQ  QL Q  QQ   Q M  +          +Q    PQ  Q  P+  Q QQ    
Sbjct: 163 LQQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPA 222

Query: 749 QQQSMPQLQQQQQLPQ----LQQQQQLPQMQQQQQLPQLQQQQQLSQPQ-------QMVG 797
             Q+  Q     QLPQ    LQQ Q     QQ    P    QQQ   PQ       Q   
Sbjct: 223 PSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQP 282

Query: 798 SGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPG 829
           +                 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 = 75.6 bits (186), Expect = 5e-14
 Identities = 45/139 (32%), Positives = 51/139 (36%), Gaps = 4/139 (2%)

Query: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           PQ    +Q     Q  Q   +Q+Q Q      SQ   Q    PQL QQ P LQQ Q    
Sbjct: 192 PQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGL 251

Query: 748 LQQQSMPQLQQQQQLPQ-LQQQQQLPQMQQQQQLPQLQQQQQLSQP---QQMVGSGMGQG 803
            QQ   P  Q  QQ  Q  Q Q Q P   Q    P L Q Q    P   Q  +   + Q 
Sbjct: 252 SQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPLVQQP 311

Query: 804 YVQGPGRTQLVSQGQVSSQ 822
             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: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           P    QQ   LQQ Q     QQM          Q  QQQQQ PQ Q Q P   Q    P 
Sbjct: 233 PPQLPQQPPPLQQPQFPGLSQQMP-----PPPPQPPQQQQQPPQPQAQPPPQNQPTPHPG 287

Query: 748 LQQQS--MPQLQQQQQLPQLQQQQQ--LPQMQQQQQLPQLQQQQQLSQPQQ 794
           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 = 3e-13
 Identities = 34/116 (29%), Positives = 36/116 (31%)

Query: 679 FPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQ 738
           +P        Q+  QQ      Q   Q     Q   Q   L Q Q               
Sbjct: 203 YPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQP 262

Query: 739 LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
            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 = 71.1 bits (175), Expect = 2e-12
 Identities = 28/100 (28%), Positives = 42/100 (42%), Gaps = 15/100 (15%)

Query: 693 QQQQQL-----QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           ++QQ L     +  Q+Q   Q+ + Q Q  Q      Q Q  P  Q Q  Q QQQ Q  Q
Sbjct: 598 REQQGLSDETFRDLQEQFNAQRGEQQGQQGQ----GGQGQGQPGQQGQQGQGQQQGQQGQ 653

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ 787
             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 = 66.1 bits (162), Expect = 6e-11
 Identities = 42/157 (26%), Positives = 57/157 (36%), Gaps = 34/157 (21%)

Query: 708 QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ--LQ---------------- 749
           Q+++  L    + QL +Q Q+ PQ   Q P      ++ Q  LQ                
Sbjct: 499 QELREALD-DYMRQLAEQAQRNPQQGDQPPDQGNSMELTQQDLQRMMDRIEELMESGRRA 557

Query: 750 --QQSMPQLQQ---QQQLPQLQQQQQLPQMQQQQQLPQ-LQQQQQLS---------QPQQ 794
             QQ + QLQQ     Q+ Q  Q  Q    Q  + L + L++QQ LS         Q   
Sbjct: 558 EAQQLLEQLQQMMENLQVTQGGQGGQSEMQQAMEGLGETLREQQGLSDETFRDLQEQFNA 617

Query: 795 MVGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGGG 831
             G   GQ    G G+ Q   QGQ          G G
Sbjct: 618 QRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQG 654

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: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 746
           KP+    Q  + Q Q Q    + +  +    QL Q QQ  Q     QQ +PQ    +Q  
Sbjct: 131 KPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAA 190

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQ 806
             QQ    Q     Q PQ   +Q  PQ           Q     Q  Q     + Q    
Sbjct: 191 FPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPP-LQQPQFP 249

Query: 807 GPGRTQLVSQGQVSSQGAP 825
           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 = 65.2 bits (159), Expect = 9e-11
 Identities = 31/95 (32%), Positives = 37/95 (38%), Gaps = 4/95 (4%)

Query: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQL-SQLQQQQQQLPQLQQQIPQLQQQQQIP 746
           PQ     QQ      Q  Q QQ   Q Q Q            LPQ Q       QQ Q+ 
Sbjct: 246 PQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLL 305

Query: 747 QLQQQSMPQL---QQQQQLPQLQQQQQLPQMQQQQ 778
            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|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175)

 Score = 64.9 bits (159), Expect = 1e-10
 Identities = 41/181 (22%), Positives = 58/181 (32%), Gaps = 48/181 (26%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           Q     Q+  QQ QQ Q  Q      Q  Q  Q QQQ QQ    Q     L ++QQ   L
Sbjct: 612 QEQFNAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGSLAERQQ--AL 669

Query: 749 QQQSMPQLQQQQQ-LPQL------------------------------------QQQQQL 771
           +     +L +Q+  LP +                                    +Q + L
Sbjct: 670 RD----ELGRQRGGLPGMGGEAGEAARDALGRAGRAMGGAEEALGQGDLAEAVDRQGRAL 725

Query: 772 PQMQQ--QQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGP-GRTQLVSQGQVSSQGAPNIP 828
             +++  +     + QQQ   Q  Q    G   G  + P GR     QG         +P
Sbjct: 726 EALREGARALGEAMAQQQGQQQGGQGQQQGRQGGNGRDPLGR-PRGGQGPDGGDRVK-VP 783

Query: 829 G 829
           G
Sbjct: 784 G 784

Length = 820

>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: 686 FKPQISSQQQQQLQQQQQQQ-----QHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 740
            +PQ     + Q Q Q   Q     +  + Q Q + Q     Q  QQ LPQ         
Sbjct: 132 PEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQAPQLPQPPQQVLPQGMPPRQAAF 191

Query: 741 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGM 800
            QQ  P+         Q   +  Q QQ    P     Q     Q  QQ    QQ    G+
Sbjct: 192 PQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGL 251

Query: 801 GQGYVQGPGRTQLVSQGQVSSQGAPN 826
            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 = 61.2 bits (148), Expect = 2e-09
 Identities = 53/145 (36%), Positives = 53/145 (36%), Gaps = 14/145 (9%)

Query: 693 QQQQQLQQQQQQ----------QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 742
            Q QQ    QQQ              Q Q Q Q Q   Q QQ  Q   QLQ Q  Q   Q
Sbjct: 181 NQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQ 240

Query: 743 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLP---QMQQQQQLPQLQQQQQLSQPQQMVG-S 798
           QQ P   Q  M Q QQ Q   Q QQ Q       MQQQ    Q QQ Q    P QM    
Sbjct: 241 QQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLGMLPNQMQQMP 300

Query: 799 GMGQGYVQGPGRTQLVSQGQVSSQG 823
           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 = 60.8 bits (147), Expect = 2e-09
 Identities = 50/152 (32%), Positives = 55/152 (36%), Gaps = 2/152 (1%)

Query: 673 RLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQL 732
           R+  M   G       Q S Q Q Q   Q   QQ Q         Q  Q    QQQ PQ+
Sbjct: 137 RVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQPPQM 196

Query: 733 QQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQ--QLPQLQQQQQLS 790
            Q        Q   Q Q Q   Q QQ  Q+ Q  Q QQ  QM QQQ     Q Q  QQ  
Sbjct: 197 GQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQGPADAQAQMGQQQQ 256

Query: 791 QPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQ 822
               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 = 60.4 bits (146), Expect = 3e-09
 Identities = 48/134 (35%), Positives = 56/134 (41%), Gaps = 2/134 (1%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           Q QQQ Q   QQQQ+ QMQ QLQ+QQ  Q+ QQQ      Q Q+ Q QQ Q   Q QQ  
Sbjct: 209 QMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQGPA-DAQAQMGQQQQGQGGMQPQQMQ 267

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQ 812
             Q+Q   Q    QQQ Q  Q+       Q         P Q       Q     P   Q
Sbjct: 268 GGQMQVPMQQQPPQQQPQQSQLGMLPNQMQQMPGGGQGGPGQP-MGPPPQRPGAVPQGGQ 326

Query: 813 LVSQGQVSSQGAPN 826
            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: 695 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMP 754
             + + Q  Q    Q Q Q   Q++  L++ + QL Q QQ       Q     L Q   P
Sbjct: 129 APKPEPQPPQAPESQPQPQTPAQKMLSLEEVEAQLQQRQQA--PQLPQPPQQVLPQGMPP 186

Query: 755 Q---LQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRT 811
           +     QQ    Q     Q PQ   +Q  PQ         P Q               + 
Sbjct: 187 RQAAFPQQGPPEQPPGYPQPPQGHPEQVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQP 246

Query: 812 QLVSQGQVSSQGAPNIPG 829
           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 = 58.7 bits (142), Expect = 6e-09
 Identities = 21/73 (28%), Positives = 44/73 (60%), Gaps = 3/73 (4%)

Query: 717 QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQ--LQQQQQLPQM 774
           +Q ++ QQQQ+   + ++Q  + ++QQQ  +LQQ+   + ++ +QL +  L  Q+Q  Q 
Sbjct: 62  EQYNRQQQQQKSAKRAEEQ-RKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQA 120

Query: 775 QQQQQLPQLQQQQ 787
           ++  +   L+Q+Q
Sbjct: 121 EEAAKQAALKQKQ 133

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: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
             ++  QQ  + QQQ  Q  Q        Q   Q Q Q     Q   Q+ Q  Q QQ  Q
Sbjct: 178 GGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQ 237

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ---QMVGSGMGQ-G 803
           + QQ  P   Q Q   Q Q Q  +   Q Q    Q+  QQQ  Q Q     +G    Q  
Sbjct: 238 MDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLGMLPNQMQ 297

Query: 804 YVQGPGRTQLVSQGQVSSQGAPNIPGGG 831
            + 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 = 58.1 bits (140), Expect = 1e-08
 Identities = 41/136 (30%), Positives = 45/136 (33%), Gaps = 2/136 (1%)

Query: 696 QQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQ 755
           QQ   Q Q QQ  QM  Q    Q       Q Q   + QQ P    Q  +P    Q   Q
Sbjct: 152 QQSSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQ 211

Query: 756 LQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVS 815
            Q Q    Q Q  Q   Q+Q QQQ  Q   QQQ     Q       QG      +     
Sbjct: 212 QQGQPGGQQQQNPQMQQQLQNQQQ--QQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGG 269

Query: 816 QGQVSSQGAPNIPGGG 831
           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: 693 QQQQQLQQ------QQQQQQHQQMQSQLQHQQ-LSQLQQQQQQLPQLQQQIPQLQQQQQI 745
           Q QQ+L +      +Q++Q+  Q+  +L+ Q     L QQQQ+L +LQQ++ +  +++  
Sbjct: 271 QLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRLQRALERRLR 330

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
              Q+      + QQQ PQ + ++   +++Q +Q  +   ++QL + +Q
Sbjct: 331 LAKQRLERLSQRLQQQNPQRRIERAQQRLEQLEQRLRRAMRRQLKRKRQ 379

Length = 438

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

 Score = 57.7 bits (139), Expect = 1e-08
 Identities = 26/107 (24%), Positives = 56/107 (52%), Gaps = 11/107 (10%)

Query: 682 DMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 741
           D V+  P    QQ  ++Q QQ   +  + Q +         ++++Q   +L+    Q  +
Sbjct: 51  DAVMVDPGAVVQQYGRIQSQQSSAKKGEQQRK---------KKEEQVAEELKP--KQAAE 99

Query: 742 QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           Q+++ QL+++ +   +QQ+Q  + ++Q QL Q QQ++Q  +   +Q+
Sbjct: 100 QERLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQK 146

Length = 387

>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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           Q++ QQ +    QQQ+ + Q+++ Q Q Q + Q QQQQQQ  Q QQ +  LQQQQQ+ QL
Sbjct: 324 QLAQQQNKMRLLQQQEMEMQRIEQQRQQQIMHQHQQQQQQEHQQQQML--LQQQQQMHQL 381

Query: 749 QQQSMPQ------LQQQQQLPQLQQ-------QQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           QQ            Q  Q    LQQ       +Q   Q QQ Q   Q QQQ Q       
Sbjct: 382 QQHHQMNGGGQFATQAHQHAAYLQQMQHMRLQEQIQHQQQQAQHHQQAQQQHQQPAQHGQ 441

Query: 796 VGSGMGQGYVQGP 808
           +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 = 57.3 bits (138), Expect = 2e-08
 Identities = 38/157 (24%), Positives = 45/157 (28%), Gaps = 2/157 (1%)

Query: 677 MLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQI 736
           +   G M +    +   Q  ++   Q   Q   M  Q   Q   Q QQ  Q  PQ  Q  
Sbjct: 117 LNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQP--QSQQPNQMGPQQGQAQ 174

Query: 737 PQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
            Q     Q  Q         Q  Q        Q   Q Q Q    Q Q  Q   Q Q   
Sbjct: 175 GQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQ 234

Query: 797 GSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGGGFM 833
              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 = 3e-08
 Identities = 25/102 (24%), Positives = 56/102 (54%), Gaps = 7/102 (6%)

Query: 700 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ- 758
           + +  Q+ QQ+Q +L      +L+Q++Q+L QL +++     ++ +   QQQ + +LQQ 
Sbjct: 262 RAELLQRLQQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLL-AQQQQRLDRLQQR 320

Query: 759 -----QQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
                +++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 = 55.6 bits (134), Expect = 6e-08
 Identities = 25/97 (25%), Positives = 52/97 (53%), Gaps = 14/97 (14%)

Query: 682 DMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 741
           D V+  P    +Q  + QQQQ+  +  + Q +         +++QQQ  +LQQ+  Q  +
Sbjct: 51  DAVMVDPGAVVEQYNRQQQQQKSAKRAEEQRK---------KKEQQQAEELQQK--QAAE 99

Query: 742 QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQ 778
           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 = 55.9 bits (134), Expect = 8e-08
 Identities = 44/116 (37%), Positives = 45/116 (38%), Gaps = 11/116 (9%)

Query: 680 PGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL 739
           P    V +PQ     QQQ QQ QQ    Q    Q Q     Q Q QQ Q P   Q   Q 
Sbjct: 747 PIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQ 806

Query: 740 QQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
            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: 458 SNLSGNSNPSISQPMGTLQGGASMGQSVG-MSQGNHSGGQMVQNGISMNQNMMSGLGPSG 516
           SNL  + N     PMG    G      VG M  G  +GG M Q+         + +GP  
Sbjct: 111 SNLLQSLNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQQSSGQPQSQQPNQMGPQQ 170

Query: 517 VSS--GTGTMIPTPGMSQQAQSGMQ-----PLSVNNNTAVNMQLSQQTSSALHSSQSKYV 569
             +    G M          Q   Q              +  Q         +    + +
Sbjct: 171 GQAQGQAGGMNQGQQGPVGQQQPPQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQL 230

Query: 570 KVWEGSLSGQRQGQPVFITKLEGYRSASASETLAANWPPTMQIVRLISQDHMNNKQYVGK 629
           +  +     Q+QG      ++   +               MQ+           +Q    
Sbjct: 231 QNQQQQQMDQQQGPADAQAQMGQQQQGQGGMQPQQMQGGQMQVPMQQQPPQQQPQQSQLG 290

Query: 630 ADFLVFRAMNQHGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQ 689
                    NQ   +    +      +  P Q              G++  G   + + +
Sbjct: 291 M------LPNQMQQMPGGGQGGPGQPMGPPPQRPGAVPQGGQAVQQGVMSAGQQQLKQMK 344

Query: 690 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 749
           + + + QQ  QQQQQQQ     +  Q Q   Q+ Q  Q +      I   Q       +Q
Sbjct: 345 LRNMRGQQQTQQQQQQQGGNHPAAHQQQMNQQVGQGGQMVALGYLNIQGNQGGLGANPMQ 404

Query: 750 QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGM 800
           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 = 54.0 bits (131), Expect = 2e-07
 Identities = 25/103 (24%), Positives = 55/103 (53%), Gaps = 8/103 (7%)

Query: 692 SQQQQQLQQQQQ--QQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 749
            Q++Q+L Q  +  + Q  +     Q Q+L +LQQ+ Q+  + + ++ + + ++   +LQ
Sbjct: 285 EQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRLQRALERRLRLAKQRLERLSQRLQ 344

Query: 750 QQSMPQLQQQQQLPQLQQQQQLPQM------QQQQQLPQLQQQ 786
           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 = 54.0 bits (131), Expect = 2e-07
 Identities = 26/106 (24%), Positives = 60/106 (56%), Gaps = 6/106 (5%)

Query: 691 SSQQQQQLQQQQQQ-QQHQQMQSQLQHQQLSQLQQQ-QQQLPQLQQQIPQLQQQQQIPQL 748
            ++  Q+LQQ QQ+  +  + + + + Q+L QL ++ + Q P+        QQQQ++ +L
Sbjct: 262 RAELLQRLQQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLA----QQQQRLDRL 317

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           QQ+    L+++ +L + + ++   ++QQQ    ++++ QQ  +  +
Sbjct: 318 QQRLQRALERRLRLAKQRLERLSQRLQQQNPQRRIERAQQRLEQLE 363

Length = 438

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

 Score = 52.7 bits (127), Expect = 2e-07
 Identities = 23/88 (26%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 702 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQL---QQQIPQLQQQQQIPQLQQQSMPQLQQ 758
               Q    Q QL  Q  + ++QQ  QL ++   +Q     +   QI Q  QQ  P    
Sbjct: 75  NSPTQLTDEQRQLLEQMQADMRQQPTQLSEVPYNEQTPQVPRSTVQIQQQAQQQQPPATT 134

Query: 759 QQQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
            Q  P    +Q    +Q Q   P   Q 
Sbjct: 135 AQPQPVTPPRQTTAPVQPQTPAPVRTQP 162

Length = 256

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

 Score = 53.9 bits (129), Expect = 3e-07
 Identities = 33/121 (27%), Positives = 44/121 (36%), Gaps = 1/121 (0%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           Q Q  +QQQ  QQQ QQ Q  +   Q+ Q+    Q  P      P  +        Q   
Sbjct: 270 QMQVPMQQQPPQQQPQQSQLGMLPNQMQQMPGGGQGGPGQPMGPPPQRPGAVPQGGQAVQ 329

Query: 753 MPQL-QQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRT 811
              +   QQQL Q++ +    Q Q QQQ  Q       +  QQM       G +   G  
Sbjct: 330 QGVMSAGQQQLKQMKLRNMRGQQQTQQQQQQQGGNHPAAHQQQMNQQVGQGGQMVALGYL 389

Query: 812 Q 812
            
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|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: 676 GMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQ 735
                   V     +S +       Q   +     +     Q    L     +      Q
Sbjct: 79  QNAPGAPSVGPDSDLSQKTSTFSPCQSGYEASTDPEYIPDLQPDPSLWGTAPKPEPQPPQ 138

Query: 736 IPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
            P+ Q Q Q P  +  S+ +++ Q    Q +QQ        QQ LPQ    +Q + PQQ 
Sbjct: 139 APESQPQPQTPAQKMLSLEEVEAQL---QQRQQAPQLPQPPQQVLPQGMPPRQAAFPQQG 195

Query: 796 VGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIP 828
                  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|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: 694 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ--QQLPQLQQQIPQLQQQQQIPQLQQQ 751
           +Q+   Q++QQQ  ++ + Q + +Q  Q Q+++  Q+  +  QQ  Q  + +  P  QQ+
Sbjct: 21  EQETRGQREQQQCERRCKEQYKEEQQQQRQREEDPQRRYEQCQQRCQQHEPRHRPTCQQR 80

Query: 752 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
              + +++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|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional

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

Query: 703 QQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQL 762
            QQ  Q +  Q Q+QQ  Q    Q Q  Q QQ +     Q Q  Q QQ   PQ Q QQ  
Sbjct: 752 VQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAP---QPQYQQPQQPVAPQPQYQQP- 807

Query: 763 PQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
               QQ   PQ Q QQ    +  Q Q  QPQQ V
Sbjct: 808 ----QQPVAPQPQYQQPQQPVAPQPQYQQPQQPV 837

Length = 1355

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

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

Query: 707 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSM-PQLQQQQQLPQL 765
           H Q+    Q    +   Q    +P L  Q P + QQ  +P   Q SM P    Q  LPQ 
Sbjct: 36  HHQIIPVSQQHPPTHTLQPHHHIPVLPAQQPVVPQQPLMPVPGQHSMTPTQHHQPNLPQP 95

Query: 766 QQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
            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|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication, recombination, and repair]

 Score = 51.1 bits (123), Expect = 2e-06
 Identities = 29/116 (25%), Positives = 61/116 (52%), Gaps = 22/116 (18%)

Query: 693 QQQQQLQQ----------QQQQQQHQQMQSQLQHQQLSQ-LQQQQQQLPQLQQQIPQL-- 739
           QQ  QLQ+           Q++Q+ + +  +LQ +   + L +QQQ+L +L  ++ +   
Sbjct: 268 QQLDQLQRRLHRALRRLLDQKKQRLEHLARRLQFRSPERLLSEQQQRLDELAIRLRRALE 327

Query: 740 ----QQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQ-----QQLPQLQQQ 786
                ++Q++ +L Q+  PQ+Q+QQQ  Q  +++    +++Q     ++L  L +Q
Sbjct: 328 NQLALKKQRLERLTQRLNPQIQRQQQRLQQLERRLDKALRRQLKRKRERLEALVEQ 383

Length = 440

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

 Score = 51.6 bits (124), Expect = 2e-06
 Identities = 31/160 (19%), Positives = 61/160 (38%), Gaps = 26/160 (16%)

Query: 661 QTLLLSVSDKACRLIGMLFPGDMVVFKPQISS----QQQQQLQQQQQQQQHQQMQSQLQH 716
           Q LL S  +        L   +    +  +         ++ ++ +   +  ++Q++L  
Sbjct: 10  QELLQSRRE--------LLTAESAQLEAALQLLQEAVNSKRQEEAEPAAEEAELQAELIQ 61

Query: 717 QQLSQLQQQQQQLPQLQQQIPQLQQQQ-----QIPQLQQQSMPQLQQQQQL--------P 763
           Q+L+   Q  Q L Q  +++  L          + QL Q S    +Q   L         
Sbjct: 62  QELAINDQLSQALNQQTERLNALASDDRQLANLLLQLLQSSRTIREQIAVLRGSLLLSRI 121

Query: 764 QLQQQQQLPQMQQQQQLPQL-QQQQQLSQPQQMVGSGMGQ 802
            LQQ   LP+  Q Q+  ++ Q++  L   +  + +  GQ
Sbjct: 122 LLQQLGPLPEAGQPQEQFEVTQERDALQAEKAYINALEGQ 161

Length = 835

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

 Score = 50.4 bits (120), Expect = 4e-06
 Identities = 22/117 (18%), Positives = 52/117 (44%), Gaps = 13/117 (11%)

Query: 690 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 749
             + QQ Q       Q+ +  + QL+ QQ   L+Q + ++ +L+ Q   L++ Q+     
Sbjct: 232 REALQQTQQSHAYLTQKREAQEEQLKKQQ--LLKQLRARIEELRAQEAVLEETQERINRA 289

Query: 750 QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQL-----------QQQQQLSQPQQM 795
           +++ 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|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: 686 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 745
                   ++  ++    +         +  Q ++QL QQQ ++  LQQQ     + Q+I
Sbjct: 289 AMEPEGETKKSPMEAGGDRMPQSAPPPAMNPQHIAQLAQQQNKMRLLQQQ---EMEMQRI 345

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQG-Y 804
            Q +QQ +    QQQQ  + QQQQ L  +QQQQQ+ QLQQ  Q++   Q          Y
Sbjct: 346 EQQRQQQIMHQHQQQQQQEHQQQQML--LQQQQQMHQLQQHHQMNGGGQFATQAHQHAAY 403

Query: 805 VQGPGRTQLVSQGQVSSQGA 824
           +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|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]

 Score = 50.1 bits (120), Expect = 5e-06
 Identities = 30/117 (25%), Positives = 48/117 (41%), Gaps = 10/117 (8%)

Query: 688 PQISSQQQQQLQQQQQQQQHQQMQSQL--QHQQLSQLQQQQQQLPQLQQQIPQLQQQ--Q 743
           P     + Q    QQ+   + Q+   L  Q ++L+ L    +QL  L  Q+ Q  +   +
Sbjct: 48  PAAEEAELQAELIQQELAINDQLSQALNQQTERLNALASDDRQLANLLLQLLQSSRTIRE 107

Query: 744 QIPQLQ---QQSMPQLQQQQQLP---QLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           QI  L+     S   LQQ   LP   Q Q+Q ++ Q +   Q  +        Q +Q
Sbjct: 108 QIAVLRGSLLLSRILLQQLGPLPEAGQPQEQFEVTQERDALQAEKAYINALEGQAEQ 164

Length = 835

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

 Score = 50.0 bits (120), Expect = 5e-06
 Identities = 32/126 (25%), Positives = 55/126 (43%), Gaps = 23/126 (18%)

Query: 689  QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
            +I  Q  +  + ++  QQH    +QL+   +S LQ   +Q  QL+Q   Q QQ Q+    
Sbjct: 898  EIREQLDEAEEAKRFVQQHGNALAQLE-PIVSVLQSDPEQFEQLKQDYQQAQQTQR--DA 954

Query: 749  QQQ------------------SMPQLQQQQQL-PQLQQQQQLPQMQQQQQLPQL-QQQQQ 788
            +QQ                  +   L +   L  +L+Q+ +  + ++ +   QL Q Q Q
Sbjct: 955  KQQAFALTEVVQRRAHFSYEDAAEMLAKNSDLNEKLRQRLEQAEQERTRAREQLRQAQAQ 1014

Query: 789  LSQPQQ 794
            L+Q  Q
Sbjct: 1015 LAQYNQ 1020

Length = 1486

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

 Score = 50.0 bits (120), Expect = 5e-06
 Identities = 24/126 (19%), Positives = 58/126 (46%), Gaps = 19/126 (15%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQ-----LSQLQQQQQQLPQLQQQIPQLQQQQ 743
           ++  Q+    Q QQ + +  +++ +L+ QQ     L++  ++  +    + ++ QLQ++ 
Sbjct: 504 RLREQRHLAEQLQQLRMRLSELEQRLRQQQRAERLLAEFCKRLGKNLDDEDELEQLQEEL 563

Query: 744 --QIPQLQQQSMPQLQQ----QQQLPQLQQQ-----QQLPQMQQ-QQQLPQLQQQ--QQL 789
             ++  L +      ++    +QQL QLQ +      + P     Q  L +L++Q  ++ 
Sbjct: 564 EARLESLSESVSEARERRMALRQQLEQLQARIQRLAARAPAWLAAQDALARLREQSGEEF 623

Query: 790 SQPQQM 795
              Q +
Sbjct: 624 EDSQDV 629

Length = 1486

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

 Score = 50.1 bits (120), Expect = 5e-06
 Identities = 28/112 (25%), Positives = 53/112 (47%), Gaps = 14/112 (12%)

Query: 690 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI---- 745
            ++ +Q +L  Q+ Q + Q ++ +L+     + QQ + QL QL  Q+ QL +QQQ     
Sbjct: 648 RTALKQARLDLQRLQNEQQSLKDKLELAIAERKQQAETQLRQLDAQLKQLLEQQQAFLEA 707

Query: 746 --PQLQQQSMPQLQQQQ--------QLPQLQQQQQLPQMQQQQQLPQLQQQQ 787
                ++    +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|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: 689 QISSQQQQQLQQQ---QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 745
           +I S  Q +L Q+      + H+     L HQ+ ++L+Q    L +   Q     QQ Q 
Sbjct: 251 EIVSPNQDELLQRLDGFNVRLHRAFD-TLLHQKKARLEQLVASLQRQHPQNKLALQQLQF 309

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
            +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|235316 PRK04863, mukB, cell division protein MukB; Provisional

 Score = 49.6 bits (119), Expect = 7e-06
 Identities = 24/115 (20%), Positives = 52/115 (45%), Gaps = 22/115 (19%)

Query: 696 QQLQQQQQQQQ--HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSM 753
           +QLQ++ + +     +  S+ + +++      +QQL QLQ +I +L  +       Q ++
Sbjct: 557 EQLQEELEARLESLSESVSEARERRM----ALRQQLEQLQARIQRLAARAPAWLAAQDAL 612

Query: 754 PQLQQQ--------QQLPQLQQQQQLPQMQQQQQLPQLQQQQQ--------LSQP 792
            +L++Q        Q + +  QQ    + +   +  +L  ++Q        LSQP
Sbjct: 613 ARLREQSGEEFEDSQDVTEYMQQLLERERELTVERDELAARKQALDEEIERLSQP 667

Length = 1486

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

 Score = 47.6 bits (113), Expect = 7e-06
 Identities = 30/105 (28%), Positives = 62/105 (59%), Gaps = 21/105 (20%)

Query: 683 MVVFKPQIS------SQQQQQLQ---------QQQQQQQHQQMQSQLQ--HQQLSQLQQQ 725
           M +FK +I       S++  +LQ         +++ Q+ H+++ +Q +  H++L+QL+Q+
Sbjct: 1   MSLFKNRIPKNSVSFSEETYELQFPKPIEVEVEEEIQKDHEELLAQQKSLHKELNQLRQE 60

Query: 726 QQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQ 770
           QQ+L + +QQ+  L  ++Q  +  QQ M +++  +Q  Q Q++QQ
Sbjct: 61  QQKLERERQQL--LADREQFQEHVQQQMKEIEAARQ--QFQKEQQ 101

Length = 228

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

 Score = 48.8 bits (116), Expect = 8e-06
 Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 712 SQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQL 771
                QQ  ++Q QQ    + +QQ  + +++Q   +L+     Q  +Q++L QL++++  
Sbjct: 57  PGAVVQQYGRIQSQQSSAKKGEQQ-RKKKEEQVAEELKP---KQAAEQERLKQLEKERLK 112

Query: 772 PQMQQQQQLPQLQQQQQLSQPQQ 794
            Q QQ+Q     +Q Q   + Q+
Sbjct: 113 AQEQQKQAEEAEKQAQLEQKQQE 135

Length = 387

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

 Score = 48.0 bits (115), Expect = 8e-06
 Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 6/83 (7%)

Query: 691 SSQQQQQLQQQ--QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ-QQQIPQ 747
            + Q Q+L  +  Q  ++ + ++      Q   +  QQQ++  LQQQI Q+++ +Q +  
Sbjct: 48  WADQTQELLAEIRQLLKEIENLRVYNDQLQ-RLVANQQQEIASLQQQIEQIEKTRQGLVP 106

Query: 748 LQQQSMPQLQQ--QQQLPQLQQQ 768
           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|197891 smart00818, Amelogenin, Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth

 Score = 45.9 bits (109), Expect = 1e-05
 Identities = 27/93 (29%), Positives = 34/93 (36%), Gaps = 2/93 (2%)

Query: 705 QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP-QLQQQSMPQLQQQQQLP 763
           QQH    +   H  +  L  QQ  +PQ Q  +P   Q    P Q  Q ++PQ  QQ   P
Sbjct: 44  QQHPPTHTLQPHHHIPVLPAQQPVVPQ-QPLMPVPGQHSMTPTQHHQPNLPQPAQQPFQP 102

Query: 764 QLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
           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 = 48.8 bits (117), Expect = 1e-05
 Identities = 24/105 (22%), Positives = 55/105 (52%), Gaps = 6/105 (5%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
              ++L ++ ++Q+H   Q Q    +LS+L+Q+ +Q  + ++ + +  ++       +  
Sbjct: 496 DVARELLRRLREQRHLAEQLQQLRMRLSELEQRLRQQQRAERLLAEFCKRLGKNLDDEDE 555

Query: 753 MPQLQQQQ--QLPQLQQQQ---QLPQMQQQQQLPQLQQQ-QQLSQ 791
           + QLQ++   +L  L +     +  +M  +QQL QLQ + Q+L+ 
Sbjct: 556 LEQLQEELEARLESLSESVSEARERRMALRQQLEQLQARIQRLAA 600

Length = 1486

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

 Score = 48.1 bits (114), Expect = 1e-05
 Identities = 32/108 (29%), Positives = 48/108 (44%), Gaps = 2/108 (1%)

Query: 685 VFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 744
           V  P+  + +Q+QL +Q Q    QQ    ++     Q  +Q+QQ  Q Q+Q  QL +QQ+
Sbjct: 108 VKTPEQLTPEQRQLLEQMQADMRQQPTQLVEVPWNEQTPEQRQQTLQRQRQAQQLAEQQR 167

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 792
           +   QQ    +   QQQ    Q      Q +Q +     Q  Q L Q 
Sbjct: 168 L-A-QQSRTTEQSWQQQTRTSQAAPVQAQPRQSKPASTQQPYQDLLQT 213

Length = 319

>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: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           P  +S Q +Q  QQ  + Q     +     + +Q   Q  Q P  Q Q  Q  QQ   PQ
Sbjct: 94  PPYASAQPRQPVQQPPEAQVPPQHA----PRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQ 149

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           +     P      Q  Q   Q   P    Q + P  +    + +P++
Sbjct: 150 VAPAPQPV-HSAPQPAQQAFQPAEPVAAPQPE-PVAEPAPVMDKPKR 194

Length = 333

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

 Score = 44.9 bits (107), Expect = 1e-05
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 10/80 (12%)

Query: 693 QQQQQLQQQQQQQQH--QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 750
           Q +++L++ QQ +    QQ+    Q    ++L+  Q  +  L + I   QQQQ++ Q ++
Sbjct: 16  QAEEKLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEAIA--QQQQELEQAEK 73

Query: 751 QSMPQLQQQQQLPQLQQQQQ 770
               Q++Q ++  Q Q+  Q
Sbjct: 74  ----QVEQARE--QWQEANQ 87

Length = 122

>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: 690 ISSQQQQQLQQQQQQQQHQQMQSQLQH-----------------------QQLSQLQQQQ 726
           +S   Q Q  QQQ   + Q++Q                            + L+QL+Q +
Sbjct: 727 LSLHSQLQTLQQQDVLEAQRLQKAQAQFDTALQASVFDDQQAFLAALLDEETLTQLEQLK 786

Query: 727 QQLP-QLQQQIPQLQQQQQIPQLQQQSMPQ-LQQQQQLPQLQQQ-QQLPQMQQQQQLPQL 783
           Q L  Q QQ    + Q  Q     QQ  P  L     + Q+QQ+  QL Q  ++    Q 
Sbjct: 787 QNLENQRQQAQTLVTQTAQALAQHQQHRPDGLDLTVTVEQIQQELAQLAQQLRENTTRQG 846

Query: 784 QQQQQLSQ 791
           + +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: 697 QLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQL 756
           +L   + + + ++   +    ++ Q        PQ   Q+ Q Q + ++ Q Q+  M ++
Sbjct: 286 ELDAMEPEGETKKSPMEAGGDRMPQSAPPPAMNPQHIAQLAQQQNKMRLLQQQEMEMQRI 345

Query: 757 QQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           +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|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication, recombination, and repair]

 Score = 48.0 bits (115), Expect = 2e-05
 Identities = 26/108 (24%), Positives = 54/108 (50%), Gaps = 12/108 (11%)

Query: 700 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL-------QQQQQIPQLQQQS 752
             +  QQ  Q+Q +L       L Q++Q+L  L +++          +QQQ++ +L  + 
Sbjct: 263 SAELLQQLDQLQRRLHRALRRLLDQKKQRLEHLARRLQFRSPERLLSEQQQRLDELAIRL 322

Query: 753 MPQLQ-----QQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
              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 = 48.0 bits (115), Expect = 2e-05
 Identities = 24/119 (20%), Positives = 54/119 (45%), Gaps = 24/119 (20%)

Query: 695 QQQLQQQ-----QQQQQHQQMQSQLQH--QQLSQLQQQ------------QQQLPQLQQQ 735
            ++  +        + Q QQ +SQL+   + LS L +               ++ ++++Q
Sbjct: 843 NRRRVELERALADHESQEQQQRSQLEQAKEGLSALNRLLPRLNLLADETLADRVEEIREQ 902

Query: 736 IPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQ-QQQLPQMQQQQQLPQLQQQQQLSQPQ 793
           + + ++ ++  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 = 33/95 (34%), Positives = 48/95 (50%), Gaps = 7/95 (7%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQIPQLQQ 750
           Q +Q L+ Q+QQ Q    Q+    Q L+Q QQ +     L   + Q+QQ+  Q   QL++
Sbjct: 784 QLKQNLENQRQQAQTLVTQTA---QALAQHQQHRPDGLDLTVTVEQIQQELAQLAQQLRE 840

Query: 751 QSMPQLQQQQQLPQ--LQQQQQLPQMQQQQQLPQL 783
            +  Q + +QQL Q    +QQQ   MQQ  Q  Q 
Sbjct: 841 NTTRQGEIRQQLKQDADNRQQQQALMQQIAQATQQ 875

Length = 1047

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

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 19/105 (18%), Positives = 50/105 (47%), Gaps = 10/105 (9%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
            +S     + +  + QQ+  ++Q +L   Q  QL + QQ+  +L+Q++  L+ + +  Q 
Sbjct: 57  YLSDTPSARERLPELQQELAELQEELAELQ-EQLAELQQENQELKQELSTLEAELERLQK 115

Query: 749 QQQSMPQLQQQ-----QQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           +   + 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 = 47.1 bits (112), Expect = 2e-05
 Identities = 15/92 (16%), Positives = 44/92 (47%)

Query: 703 QQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQL 762
                 Q  +++Q Q+    +++Q++  +L+QQ  + ++Q+   Q +Q+ + Q    ++ 
Sbjct: 44  DPGAVAQQANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQARQKELEQRAAAEKA 103

Query: 763 PQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
            +  +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|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: 675 IGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQ 734
           +G    G M   +P    Q  QQ Q   Q     +M             +     P    
Sbjct: 387 MGSPMGGAM--GQPPYYGQGPQQ-QFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAV 443

Query: 735 QIPQLQQQQQIPQLQQQSM---PQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
           + P    Q    +   Q +   P  Q       L Q Q      Q  Q  +L Q    + 
Sbjct: 444 RAPSRNAQNAAQKPPMQPVMYPPNYQSLPLSQDLPQPQSTA--SQGGQNKKLAQVLASAT 501

Query: 792 PQQ 794
           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|217472 pfam03280, Lipase_chap, Proteobacterial lipase chaperone protein

 Score = 45.3 bits (108), Expect = 3e-05
 Identities = 26/119 (21%), Positives = 45/119 (37%), Gaps = 21/119 (17%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
            Q   L  +Q+ ++   + +QL  + L + ++      +L Q   QLQ Q   PQ  +  
Sbjct: 71  AQDPSLSDEQKARRLAALIAQLP-EDLREARRNAALQQELAQATAQLQAQGASPQDLRA- 128

Query: 753 MPQLQQQ------QQLPQLQQ-----QQQLPQMQQQ------QQLPQLQQQQQLSQPQQ 794
                        Q+L QL Q     QQ+      +        L    +Q Q++Q +Q
Sbjct: 129 --ARAALVGPEAAQRLAQLDQERAAWQQRYDDYLAERDQILAAGLSDADKQAQIAQLRQ 185

Length = 189

>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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLS--QLQQQQQQL--PQLQQQIPQLQQQQQ 744
           Q+    +  LQ+ Q+QQ   Q  +QLQ    S  +L+  + QL  P+  Q++ QL QQ+ 
Sbjct: 218 QLPEDLRAALQESQRQQALLQQLAQLQASGASPQELRLMRAQLVGPEAAQRLEQLDQQRA 277

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ 787
                QQ       Q+   Q+     L    +Q Q+ QL+QQ+
Sbjct: 278 A---WQQRYDDYLAQRA--QILNAAGLSPQDRQAQIAQLRQQR 315

Length = 336

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

 Score = 45.8 bits (109), Expect = 4e-05
 Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 2/107 (1%)

Query: 687 KPQISSQQQQQLQQQQ--QQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 744
             Q++ +Q+Q L+Q Q   +QQ  Q+     ++Q  Q+ +   Q+ Q  QQ        Q
Sbjct: 77  PTQLTDEQRQLLEQMQADMRQQPTQLSEVPYNEQTPQVPRSTVQIQQQAQQQQPPATTAQ 136

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
              +          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 = 4e-05
 Identities = 19/101 (18%), Positives = 35/101 (34%), Gaps = 4/101 (3%)

Query: 698 LQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQ 757
           L      Q+  Q + +L   + +QL+   Q L +      Q + +    + + Q+    Q
Sbjct: 3   LAGNNVLQELLQSRRELLTAESAQLEAALQLLQEAVNSKRQEEAEPAAEEAELQAELIQQ 62

Query: 758 QQQQLPQLQQQ--QQLPQMQQ--QQQLPQLQQQQQLSQPQQ 794
           +     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 = 4e-05
 Identities = 29/95 (30%), Positives = 45/95 (47%), Gaps = 5/95 (5%)

Query: 702 QQQQQHQQMQSQLQHQ--QLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQ 759
           +Q+Q  +QMQ+ ++ Q  QL ++   +Q   Q QQ    LQ+Q+Q  QL +Q     Q +
Sbjct: 117 EQRQLLEQMQADMRQQPTQLVEVPWNEQTPEQRQQT---LQRQRQAQQLAEQQRLAQQSR 173

Query: 760 QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
                 QQQ +  Q    Q  P+  +     QP Q
Sbjct: 174 TTEQSWQQQTRTSQAAPVQAQPRQSKPASTQQPYQ 208

Length = 319

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

 Score = 46.5 bits (110), Expect = 5e-05
 Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 18/115 (15%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQH------QQLSQLQQQQQQLPQLQQQIPQLQQQ 742
           + ++  +QQ   ++Q++  Q + SQ  H         S  +   QQ   L Q I  LQQQ
Sbjct: 329 KRAAHVKQQSSIEEQRRLLQTLHSQEIHIRDAHEVATSIREISCQQH-TLTQHIHTLQQQ 387

Query: 743 QQIPQLQQQSMPQL------QQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
           +     + 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 = 45.8 bits (108), Expect = 5e-05
 Identities = 30/108 (27%), Positives = 45/108 (41%), Gaps = 6/108 (5%)

Query: 681 GDMVVFKPQISSQQQQQLQQQQQQQQHQQMQ------SQLQHQQLSQLQQQQQQLPQLQQ 734
           G  V    Q++ +Q+Q L+Q Q   + Q  Q      ++   +Q  Q  Q+Q+Q  QL +
Sbjct: 105 GGEVKTPEQLTPEQRQLLEQMQADMRQQPTQLVEVPWNEQTPEQRQQTLQRQRQAQQLAE 164

Query: 735 QIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQ 782
           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 = 45.9 bits (109), Expect = 5e-05
 Identities = 34/159 (21%), Positives = 46/159 (28%), Gaps = 18/159 (11%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ-QIPQLQQQ 751
            Q    Q  Q      Q Q        +        LP      P +Q +  Q+  +Q  
Sbjct: 67  PQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALP-AGPAGPTIQTEPGQLYPVQVP 125

Query: 752 SM----------PQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMG 801
            M           Q  QQ+ L QLQQ+   P   Q     Q  Q+   SQ QQ       
Sbjct: 126 VMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQSAQKNDESQLQQQPNGETP 185

Query: 802 QGYVQGPGRTQLVSQGQVSSQGAP------NIPGGGFMS 834
                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 = 5e-05
 Identities = 30/129 (23%), Positives = 56/129 (43%), Gaps = 4/129 (3%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQIPQLQ 749
             +  Q++Q+ Q    +   +Q + ++L++     QQ  Q  QQ      Q  QQI    
Sbjct: 192 KLRSAQIEQEAQNLATRANAAQARTEELARRAAAAQQTAQAIQQRDAQISQKAQQIAARA 251

Query: 750 QQSMPQLQQQQQLPQLQQ--QQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQG 807
           +Q   + +Q Q+L   Q   +Q++ Q++   Q     +QQ  +  +  V +G  Q   Q 
Sbjct: 252 EQIRERERQLQRLETAQARLEQEVAQLEAYYQAYVRLRQQAAATQRGQVLAGAAQRVAQA 311

Query: 808 PGRTQLVSQ 816
             + Q  +Q
Sbjct: 312 QAQAQAQAQ 320

Length = 499

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

 Score = 46.7 bits (111), Expect = 6e-05
 Identities = 30/106 (28%), Positives = 50/106 (47%), Gaps = 4/106 (3%)

Query: 689 QISSQQQQQLQQ-QQQQQQHQQMQSQLQHQQL--SQLQQQQQQLPQLQQQIPQLQQQQQI 745
            I+ Q Q  +Q     Q++H++    L  +     Q+    QQ+ Q QQQI Q +QQQ +
Sbjct: 589 NITLQPQDDIQPWLDAQEEHERQLRLLSQRHELQGQIAAHNQQIIQYQQQIEQ-RQQQLL 647

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
             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 = 43.5 bits (103), Expect = 6e-05
 Identities = 21/94 (22%), Positives = 46/94 (48%), Gaps = 6/94 (6%)

Query: 705 QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQ 764
           Q+   ++ + + Q   +L + Q +  +L+ Q+ QL + ++  + +QQ++ ++       +
Sbjct: 5   QKLLDLREKEEEQAKLELAKAQAEFERLETQLQQLIKYRE--EYEQQALEKVGAGTSALE 62

Query: 765 LQQQQ----QLPQMQQQQQLPQLQQQQQLSQPQQ 794
           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|236545 PRK09510, tolA, cell envelope integrity inner membrane protein TolA; Provisional

 Score = 45.6 bits (108), Expect = 7e-05
 Identities = 13/87 (14%), Positives = 44/87 (50%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           Q S+++ ++ +++++QQQ +++Q +   +Q    Q ++++L   +Q+    +  +Q    
Sbjct: 71  QKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAALK 130

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQ 775
           Q+Q+     +     + + + +  +  
Sbjct: 131 QKQAEEAAAKAAAAAKAKAEAEAKRAA 157

Length = 387

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

 Score = 45.8 bits (108), Expect = 7e-05
 Identities = 24/74 (32%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 716 HQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQ 775
           H+     +  QQ   Q   Q P +Q   Q PQ Q Q  P    QQ  PQ   QQ  PQ +
Sbjct: 195 HRHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQP-PQTE 253

Query: 776 QQQQLPQLQQQQQL 789
           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|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869)

 Score = 42.6 bits (101), Expect = 8e-05
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 7/83 (8%)

Query: 695 QQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           Q +LQ+Q  Q  Q+ QQ++ Q Q       +Q  QQ+ Q+QQQ+     +Q+  +  +Q 
Sbjct: 22  QAELQEQLTQLEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQQV-----EQERAKRLEQK 76

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQ 775
              L Q +Q+ +L    ++ Q Q
Sbjct: 77  NQLLFQIEQVQELPLGSEVKQGQ 99

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 = 9e-05
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 702 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 761
           +QQ Q+Q   +     QL+ LQ+ Q+     Q+Q  +   +QQ   L Q +  Q    +Q
Sbjct: 59  KQQAQNQTATNDALANQLTALQKAQES----QKQELEGILKQQAKALDQANRQQAALAKQ 114

Query: 762 LPQLQQQ 768
           L +LQQ+
Sbjct: 115 LDELQQK 121

Length = 390

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

 Score = 45.2 bits (107), Expect = 1e-04
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 740 QQQQQIPQLQQQSMPQLQQQQQLPQLQQ-----QQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           QQQQQ    + +   + ++QQQ  +LQQ     Q++L Q+++++   Q Q++Q     +Q
Sbjct: 67  QQQQQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQ 126

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: 687 KPQISSQQQQQLQQQ--QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 744
           +P     Q QQ QQ    Q Q  Q  Q      Q  Q QQ     PQ QQ    +  Q Q
Sbjct: 770 QPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQ 829

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQ 767
             Q QQ   PQ Q     P L +
Sbjct: 830 YQQPQQPVAPQPQDTLLHPLLMR 852

Length = 1355

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

 Score = 43.9 bits (104), Expect = 1e-04
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 717 QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQ 776
              +QL  +Q+QL + Q Q    QQ  Q+ ++          +  +   QQ QQ      
Sbjct: 75  NSPTQLTDEQRQLLE-QMQADMRQQPTQLSEVPYNEQTPQVPRSTVQIQQQAQQQQPPAT 133

Query: 777 QQQLPQLQQQQQLSQPQQ 794
             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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQ-IPQLQQQQQIPQ 747
           +   ++Q + +QQQQ+Q+ +  Q + +  Q    Q + +  P  QQ+   + +++QQ  Q
Sbjct: 34  ERRCKEQYKEEQQQQRQREEDPQRRYEQCQQRCQQHEPRHRPTCQQRCERRYEKEQQQQQ 93

Query: 748 LQ-QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQ 782
            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: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 746
           + Q   +++ + Q +++QQQ +Q +   Q ++  Q QQ+ QQ     +   Q + +++  
Sbjct: 28  REQQQCERRCKEQYKEEQQQQRQREEDPQ-RRYEQCQQRCQQHEPRHRPTCQQRCERRYE 86

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           + 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|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 45.7 bits (108), Expect = 1e-04
 Identities = 20/108 (18%), Positives = 46/108 (42%), Gaps = 7/108 (6%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQL------QQQIPQLQQQ 742
           + + ++Q + QQ  +Q + +  + + Q   L + Q++  +  +        + + Q++QQ
Sbjct: 249 REAQEEQLKKQQLLKQLRARIEELRAQEAVLEETQERINRARKAAPLAAHIKAVTQIEQQ 308

Query: 743 -QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQL 789
            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|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: 695 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQ-IPQLQQQQQIPQLQQQSM 753
              L Q++ + +      Q QH Q  +L  QQ Q  +L+++    L +Q +  + ++  +
Sbjct: 276 DTLLHQKKARLEQLVASLQRQHPQN-KLALQQLQFEKLEKRKQAALNKQLERTRQKKTRL 334

Query: 754 PQ-LQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
            + 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 = 41.9 bits (99), Expect = 1e-04
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 10/96 (10%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           +  + L + QQ+ +  + + +   Q   + +QQ     Q          Q  I  L +  
Sbjct: 2   KAARNLAEAQQELEQAEEKLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEAI 61

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
               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 = 20/110 (18%), Positives = 42/110 (38%), Gaps = 8/110 (7%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ-QQQQIPQLQQQ 751
            +  +L     +   +Q  + L+ Q  S    + Q     + +  Q   ++ +I   Q  
Sbjct: 20  AEDDKLDLAALRALLEQRAA-LRRQYFSA--DEAQAFFGDENRYDQYALERLRI--AQDP 74

Query: 752 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMG 801
           S+   Q+ ++L  L  Q  LP+  ++ +     QQ+      Q+   G  
Sbjct: 75  SLSDEQKARRLAALIAQ--LPEDLREARRNAALQQELAQATAQLQAQGAS 122

Length = 189

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

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 23/114 (20%), Positives = 37/114 (32%), Gaps = 14/114 (12%)

Query: 688 PQISSQQQQQLQQQQQQQQ--------HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL 739
           P +S +Q+ +       Q               Q   Q  +QLQ Q      L+     L
Sbjct: 74  PSLSDEQKARRLAALIAQLPEDLREARRNAALQQELAQATAQLQAQGASPQDLRAARAAL 133

Query: 740 QQQQQIPQLQQQSMPQLQQQQQLPQLQQQ------QQLPQMQQQQQLPQLQQQQ 787
              +   +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 = 42.3 bits (100), Expect = 1e-04
 Identities = 23/103 (22%), Positives = 54/103 (52%), Gaps = 10/103 (9%)

Query: 695 QQQLQQQQQQQQHQQMQSQLQH--QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           Q +L+  + Q + +++++QLQ   +   + +QQ  +         +L   Q+   ++Q  
Sbjct: 17  QAKLELAKAQAEFERLETQLQQLIKYREEYEQQALEKVGAGTSALELSNYQR--FIRQLD 74

Query: 753 MPQLQQQQQLPQLQQ-----QQQLPQMQQQ-QQLPQLQQQQQL 789
               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|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869)

 Score = 42.2 bits (100), Expect = 1e-04
 Identities = 31/77 (40%), Positives = 54/77 (70%), Gaps = 8/77 (10%)

Query: 708 QQMQSQLQHQQLSQLQQQQQQLP-QLQQQIPQLQQQ--QQIPQLQQQSMPQLQQQQQLPQ 764
           +++Q++LQ +QL+QL+Q+ QQL  Q Q+ I ++++Q  QQI Q+QQ    Q++Q++    
Sbjct: 19  EELQAELQ-EQLTQLEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQ----QVEQERAKRL 73

Query: 765 LQQQQQLPQMQQQQQLP 781
            Q+ Q L Q++Q Q+LP
Sbjct: 74  EQKNQLLFQIEQVQELP 90

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

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

 Score = 45.2 bits (107), Expect = 1e-04
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 5/82 (6%)

Query: 698 LQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQ 757
            QQQ   Q  +    Q Q + L   Q+ Q+ L QL+  I   QQQ ++ +L++Q      
Sbjct: 54  GQQQNVLQTQELQALQQQLKALQLAQENQKLLAQLESLIA--QQQAELDRLERQ---LET 108

Query: 758 QQQQLPQLQQQQQLPQMQQQQQ 779
            Q+QL +LQ++        ++ 
Sbjct: 109 LQKQLSELQKKVATISGSDRKD 130

Length = 391

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

 Score = 42.7 bits (101), Expect = 1e-04
 Identities = 21/118 (17%), Positives = 56/118 (47%), Gaps = 22/118 (18%)

Query: 693 QQQQQLQQQQQQQQHQ----------QMQSQLQHQQLSQLQQQQQQLPQLQQQI------ 736
            Q++QL+ +   ++ Q          Q++ Q +       Q+Q Q+L +L ++I      
Sbjct: 4   LQKEQLKDRFFLERTQLLKRHEKELEQLERQQKRTIEKLEQRQTQELRRLPKRIRAEQKT 63

Query: 737 ------PQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
                   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|224241 COG1322, COG1322, Predicted nuclease of restriction endonuclease-like fold, RmuC family [General function prediction only]

 Score = 44.7 bits (106), Expect = 1e-04
 Identities = 30/145 (20%), Positives = 58/145 (40%), Gaps = 18/145 (12%)

Query: 663 LLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQL 722
           + L+   +    +G L          Q+  +    L+Q       +    QL+      L
Sbjct: 15  VNLAFIRQLLLRLGRLE---------QMLGELAAVLEQLLLLLAFRAEAEQLR-TFARSL 64

Query: 723 QQQQQQLPQ-LQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQM--QQQQQ 779
           Q    +L Q L +   +LQQQ    + Q Q +  ++   QL   + Q+   ++  +  ++
Sbjct: 65  QALNLELIQELNELKARLQQQLLQSREQLQLL--IESLAQL-SSEFQELANEIFEELNRR 121

Query: 780 LPQLQQQ--QQLSQPQQMVGSGMGQ 802
           L +L QQ  +QL +P + V     +
Sbjct: 122 LAELNQQNLKQLLKPLREVLEKFRE 146

Length = 448

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

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 18/81 (22%), Positives = 44/81 (54%), Gaps = 9/81 (11%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           Q  S ++ + Q+++++QQ  +   +LQ +Q      +Q++L QL+++  +L  Q+Q  Q 
Sbjct: 70  QQKSAKRAEEQRKKKEQQQAE---ELQQKQ----AAEQERLKQLEKE--RLAAQEQKKQA 120

Query: 749 QQQSMPQLQQQQQLPQLQQQQ 769
           ++ +     +Q+Q  +   + 
Sbjct: 121 EEAAKQAALKQKQAEEAAAKA 141

Length = 387

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

 Score = 45.1 bits (106), Expect = 2e-04
 Identities = 50/197 (25%), Positives = 64/197 (32%), Gaps = 39/197 (19%)

Query: 656 IQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQ 715
           I+LPSQ       +KA       +         +I + QQ +L +Q  Q Q Q+   Q Q
Sbjct: 625 IKLPSQRA---AEEKAREAQRNQYDSGDQYNDDEIDAMQQDELARQFAQTQQQRYGEQYQ 681

Query: 716 HQQLSQLQQQQQQL-PQLQQQIPQLQQQQ------------------------------Q 744
           H      +        +L +Q  Q QQQ+                               
Sbjct: 682 HDVPVNAEDADAAAEAELARQFAQTQQQRYSGEQPAGANPFSLDDFEFSPMKALLDDGPH 741

Query: 745 IPQLQQQSMPQLQQQQQL---PQLQQQQQLPQMQQQQQLPQ--LQQQQQLSQPQQMVGSG 799
            P       P  Q QQ +    Q QQ QQ    Q Q Q PQ  +  Q Q  QPQQ V   
Sbjct: 742 EPLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQ 801

Query: 800 MGQGYVQGPGRTQLVSQ 816
                 Q P   Q   Q
Sbjct: 802 PQYQQPQQPVAPQPQYQ 818

Length = 1355

>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: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           +Q  Q +   QQ Q ++++ + Q     QL++ +Q+  +L +++ Q     QI + Q ++
Sbjct: 295 RQHPQNKLALQQLQFEKLEKRKQAALNKQLERTRQKKTRLTKRLTQTNPSPQILRAQTRT 354

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQ 775
               ++   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|234017 TIGR02794, tolA_full, TolA protein

 Score = 44.4 bits (105), Expect = 2e-04
 Identities = 17/92 (18%), Positives = 40/92 (43%), Gaps = 7/92 (7%)

Query: 695 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMP 754
                 QQ  +  QQ +   + +Q  Q + +QQ   + ++Q  +  +Q +  +L+Q    
Sbjct: 44  DPGAVAQQANRIQQQKKPAAKKEQERQKKLEQQA-EEAEKQ--RAAEQARQKELEQ---- 96

Query: 755 QLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
           +   ++   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|236892 PRK11281, PRK11281, hypothetical protein; Provisional

 Score = 45.3 bits (108), Expect = 2e-04
 Identities = 22/104 (21%), Positives = 42/104 (40%), Gaps = 11/104 (10%)

Query: 695 QQQLQQQQQQQQHQQMQSQLQH------QQLSQLQQQQQQLPQLQQQIPQLQQQ-QQIPQ 747
           Q QL    +Q+  +     +Q         L ++ +Q+++  QL+QQ+ Q   + +Q   
Sbjct: 42  QAQLDALNKQKLLEAEDKLVQQDLEQTLALLDKIDRQKEETEQLKQQLAQAPAKLRQA-- 99

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
             Q  +  L+        +    L   Q + +L Q   Q Q +Q
Sbjct: 100 --QAELEALKDDNDEETRETLSTLSLRQLESRLAQTLDQLQNAQ 141

Length = 1113

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

 Score = 44.9 bits (107), Expect = 2e-04
 Identities = 31/158 (19%), Positives = 61/158 (38%), Gaps = 41/158 (25%)

Query: 641 HGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLF-----------PGDMVVFKPQ 689
           H F G  +E  +                 K    + + F           PG  V   P+
Sbjct: 96  HEFHGDHREALMG---------------LKLAFRLAVWFHRTYGKDWDFKPGPFV--PPE 138

Query: 690 ISSQQQQQLQQQQQQQQHQ-QMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
                   LQQ+    + Q ++Q++ + Q  +  + QQQ+L  L+    +L+++QQ    
Sbjct: 139 DPENLLHALQQEVLTLKQQLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQ---- 194

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
                   + + QL QLQ++      +++Q+  ++  Q
Sbjct: 195 --------ELEAQLEQLQEKAAETSQERKQKRKEITDQ 224

Length = 1123

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

 Score = 43.9 bits (104), Expect = 2e-04
 Identities = 21/124 (16%), Positives = 57/124 (45%), Gaps = 18/124 (14%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQL-------QQQQQQLPQLQQQIPQLQQ 741
           Q   + Q+ L+++Q+Q++ ++ +     Q+L++        Q+ QQ   Q   +  +   
Sbjct: 99  QRQKKLQKLLEEKQKQEREKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHKKEAA 158

Query: 742 QQQIPQLQQQSMPQ-----------LQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLS 790
           +     L   + P+           LQ+ +     QQQQ+  + +++Q+  Q +++++  
Sbjct: 159 ESASSSLSGSAKPERNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEEERKQ 218

Query: 791 QPQQ 794
           + ++
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|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: 711 QSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQ 770
           Q   Q Q+ + L  +   L     +I QL++Q Q    + Q + QLQQ++    +  +Q 
Sbjct: 49  QIAEQQQRNALLTTEIALLDAEIAEIQQLKEQTQALLQRLQVIEQLQQKRAGWSVLLEQL 108

Query: 771 LPQMQQQQQLPQLQQQQQ 788
              + +   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 = 42.8 bits (101), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 701 QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ-IPQLQQQSMPQLQQQ 759
           Q +Q   QQ ++ L   +++ L  +  ++ QL++Q   L Q+ Q I QLQQ+        
Sbjct: 46  QDRQIAEQQQRNALLTTEIALLDAEIAEIQQLKEQTQALLQRLQVIEQLQQKRAGWSVLL 105

Query: 760 QQLP-QLQQQQQLPQMQQQQQ 779
           +QL   L +   L  ++QQ  
Sbjct: 106 EQLANLLPESVWLTSLKQQGD 126

Length = 206

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

 Score = 44.1 bits (105), Expect = 2e-04
 Identities = 6/96 (6%), Positives = 55/96 (57%), Gaps = 3/96 (3%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
            +    ++++++++ ++ + + +     Q+++++++  + ++   +LQ+++Q+ ++ ++ 
Sbjct: 52  LKALAEEEERERKRKEERR-EGRAVLQEQIEEREKR--RQEEYEERLQEREQMDEIIERI 108

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
             + + + 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|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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ-------QQLPQLQQQIPQLQQ 741
             SS     L  ++      Q   +L HQ  + L+ +        +++    Q   +L  
Sbjct: 725 NASSSLGSDLAAREDA--LNQSLKELMHQARTVLKARTEAHFNNNEEVTAALQTGAELSH 782

Query: 742 QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
                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|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450)

 Score = 43.4 bits (103), Expect = 3e-04
 Identities = 26/101 (25%), Positives = 46/101 (45%), Gaps = 6/101 (5%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQL-SQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 751
              QQ      Q Q +  +   Q Q+L ++++Q  +++  L+    QLQ+   +   QQQ
Sbjct: 29  AAAQQTVAAAAQSQKKIDKWADQTQELLAEIRQLLKEIENLRVYNDQLQRL--VAN-QQQ 85

Query: 752 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 792
            +  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|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: 700 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQ 759
                Q+H+  +   QHQ        Q + P  Q    Q+  Q      Q    P  Q  
Sbjct: 74  APANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPA 133

Query: 760 QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
            Q    Q  QQ    Q       +    Q +Q   
Sbjct: 134 YQPQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAF 168

Length = 333

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

 Score = 42.3 bits (100), Expect = 3e-04
 Identities = 17/87 (19%), Positives = 46/87 (52%), Gaps = 5/87 (5%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           + Q+QL + QQ+ Q  + +      +L +LQ++  ++ QL     +L ++ +  +L+++ 
Sbjct: 84  ELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLSANAIELDEENR--ELREEL 141

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQ 779
               + +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|221776 pfam12795, MscS_porin, Mechanosensitive ion channel porin domain

 Score = 43.0 bits (102), Expect = 3e-04
 Identities = 30/118 (25%), Positives = 55/118 (46%), Gaps = 19/118 (16%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQL-----QHQQLSQLQQQQQQLP----QLQQQIPQL 739
           Q++ ++    +Q+   Q  +Q  + L       Q+  Q Q+Q    P    +L+Q++  L
Sbjct: 5   QLNKRKLPTPEQKALIQDLEQALNFLDEIDKSKQKADQYQKQIDDAPKELRELRQELEAL 64

Query: 740 QQQQQ--IPQLQQQSMPQLQQQ--QQLPQLQQQQQLPQM------QQQQQLPQLQQQQ 787
           ++      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|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: 702 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 761
           Q  Q+H+  +   QHQ   +    Q ++P  Q            P        Q  ++ +
Sbjct: 74  QFTQEHEAARQSPQHQYQPEYASAQIKIPVPQPPQISDPPAHPQPTQPALDQEQPPEEAR 133

Query: 762 LPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
            P L Q+   PQ           Q  Q + P+Q V
Sbjct: 134 QPVLPQEAPAPQPVHSAAPQPAVQTVQPAVPEQQV 168

Length = 324

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

 Score = 43.9 bits (104), Expect = 3e-04
 Identities = 34/163 (20%), Positives = 62/163 (38%), Gaps = 65/163 (39%)

Query: 691 SSQQQQQLQQ---------QQQQQQHQQMQSQLQHQQLS------QLQQQQQQLPQLQQQ 735
           +  Q + +QQ         +QQQQQ   + +QL+ Q+ +      +L++ Q  L QL +Q
Sbjct: 45  NRDQLKSIQQDIAAKEKSVRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLNKQ 104

Query: 736 -------IPQLQQQQQ-------------------------------------------I 745
                  I +L+QQQ                                            +
Sbjct: 105 IDELNASIAKLEQQQAAQERLLAAQLDAAFRQGEHTGLQLILSGEESQRGERILAYFGYL 164

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
            Q +Q+++ +L+Q ++    Q+ +   +  QQ+ L   QQ QQ
Sbjct: 165 NQARQETIAELKQTREELAAQKAELEEKQSQQKTLLYEQQAQQ 207

Length = 428

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

 Score = 43.8 bits (103), Expect = 4e-04
 Identities = 19/127 (14%), Positives = 49/127 (38%), Gaps = 29/127 (22%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ-------- 744
           Q    L Q+++ Q+ Q  + QL  Q  +++++ + Q   L++   ++ + ++        
Sbjct: 240 QSHAYLTQKREAQEEQLKKQQLLKQLRARIEELRAQEAVLEETQERINRARKAAPLAAHI 299

Query: 745 --IPQLQQQSMPQLQ-------------------QQQQLPQLQQQQQLPQMQQQQQLPQL 783
             + Q++QQ+                         +QQ    +Q++ L  +  Q+   + 
Sbjct: 300 KAVTQIEQQAQRIHTELQSKMRSRAKLLMKRAAHVKQQSSIEEQRRLLQTLHSQEIHIRD 359

Query: 784 QQQQQLS 790
             +   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 = 43.1 bits (102), Expect = 4e-04
 Identities = 23/110 (20%), Positives = 35/110 (31%), Gaps = 1/110 (0%)

Query: 685 VFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 744
           V     ++Q+ +  +   Q Q      S    Q + Q  + Q       +      Q  Q
Sbjct: 71  VNHAPANAQEHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQ 130

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
            P  Q Q    LQQ    PQ+    Q      Q      Q  + ++ PQ 
Sbjct: 131 QPAYQPQPEQPLQQPVS-PQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQP 179

Length = 333

>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: 679 FPGDMVVFKP------QISSQQQQQLQQQQQQQQHQQMQSQL---------QHQ-----Q 718
             G M+  KP      Q   Q++  LQ Q  Q Q +  Q  +         Q        
Sbjct: 346 MHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGP 405

Query: 719 LSQLQQQQQQLPQLQQQIPQLQQQQQ-----IPQLQQQSMPQLQQQQQLPQLQQQ--QQL 771
             Q   Q    P++      +          +  +     P    Q    +   Q     
Sbjct: 406 QQQFNGQPLGWPRMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYP 465

Query: 772 PQMQQQQQLPQLQQQQ 787
           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|225507 COG2959, HemX, Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

 Score = 43.3 bits (102), Expect = 4e-04
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 707 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQ 766
             Q Q+ LQ Q+L  LQQQ + L   Q+    L Q + +   QQ  + +L++Q +     
Sbjct: 53  FGQQQNVLQTQELQALQQQLKALQLAQENQKLLAQLESLIAQQQAELDRLERQLE----T 108

Query: 767 QQQQLPQMQQQQQLPQLQQQQQ 788
            Q+QL ++Q++        ++ 
Sbjct: 109 LQKQLSELQKKVATISGSDRKD 130

Length = 391

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

 Score = 43.0 bits (102), Expect = 4e-04
 Identities = 13/93 (13%), Positives = 54/93 (58%), Gaps = 6/93 (6%)

Query: 694 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSM 753
           Q++  ++++Q+++ +  + + Q Q+L + +++Q +  + + Q    +++ +    +++ +
Sbjct: 210 QEEYERKERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQ----EERAEEEAERERML 265

Query: 754 PQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
            +  + ++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|221776 pfam12795, MscS_porin, Mechanosensitive ion channel porin domain

 Score = 42.6 bits (101), Expect = 4e-04
 Identities = 29/122 (23%), Positives = 57/122 (46%), Gaps = 11/122 (9%)

Query: 682 DMVVFKPQISSQQQQQLQQQ--QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL 739
                 P++++    QL+Q+  Q   Q Q++Q QLQ +  SQL + Q +  + QQQ+ + 
Sbjct: 67  TDAPVFPELANLSLSQLEQRLAQTLSQLQELQEQLQQEN-SQLIELQTRPERAQQQLSEA 125

Query: 740 QQQQQ-----IPQLQQQSMPQLQQQQQLPQLQQQ--QQLPQMQQQQQLPQLQQQQQLSQP 792
           +++ Q     +  L     P  Q Q+ L Q +    +   +  + + L     +Q+L + 
Sbjct: 126 RRRLQEIRNRLQALSPGGTPLAQAQRTLLQAELAALKAQIEELELELL-SNNNRQELLRL 184

Query: 793 QQ 794
           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|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: 699 QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL-----QQQQQIPQLQQQSM 753
            Q  Q  Q QQ Q+   HQ  SQL  QQ Q    Q    Q        Q Q P  QQ   
Sbjct: 79  PQSPQPDQQQQSQAPPSHQYPSQLPPQQVQSVPQQPTPQQEPYYPPPSQPQPPPAQQPQA 138

Query: 754 PQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
            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|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 43.6 bits (103), Expect = 5e-04
 Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 6/99 (6%)

Query: 699 QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ 758
           +Q Q      Q+ +  + Q L+  QQQQQ L  L +     Q+  +  Q  QQ++   ++
Sbjct: 216 EQVQSLTASLQVLTDEEKQLLTAQQQQQQSLNWLTRLDELQQEASRRQQALQQALAAEEK 275

Query: 759 QQ-QLPQLQQQQQLPQMQ-----QQQQLPQLQQQQQLSQ 791
            Q QL  L   Q   Q++      Q+Q   L   +Q  +
Sbjct: 276 AQPQLAALSLAQPARQLRPHWERIQEQSAALAHTRQQIE 314

Length = 1047

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

 Score = 40.3 bits (95), Expect = 5e-04
 Identities = 31/89 (34%), Positives = 54/89 (60%), Gaps = 9/89 (10%)

Query: 722 LQQQQQQLPQLQQQIPQLQQQQQ--IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ 779
             + Q+QL QL+Q++ QL+ Q Q  I ++++QS  Q++Q QQ  Q++Q++     Q+ Q 
Sbjct: 22  QAELQEQLTQLEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQ--QVEQERAKRLEQKNQL 79

Query: 780 LPQLQQQQQLSQPQQMVGSGMGQGYVQGP 808
           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|236795 PRK10920, PRK10920, putative uroporphyrinogen III C-methyltransferase; Provisional

 Score = 42.8 bits (101), Expect = 5e-04
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 751
            +QQ Q Q         Q+ + LQ  Q SQ Q+ +  L Q  + + Q  +QQ    L +Q
Sbjct: 58  GKQQAQNQTATNDALANQL-TALQKAQESQKQELEGILKQQAKALDQANRQQA--ALAKQ 114

Query: 752 SMPQLQQQ 759
            + +LQQ+
Sbjct: 115 -LDELQQK 121

Length = 390

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

 Score = 42.8 bits (101), Expect = 5e-04
 Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 8/68 (11%)

Query: 721 QLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 780
           Q Q Q      L  Q+  LQ+ Q+    +Q+    L+QQ +   L Q  +    QQ    
Sbjct: 61  QAQNQTATNDALANQLTALQKAQE--SQKQELEGILKQQAK--ALDQANR----QQAALA 112

Query: 781 PQLQQQQQ 788
            QL + QQ
Sbjct: 113 KQLDELQQ 120

Length = 390

>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common bacterial type

 Score = 43.5 bits (103), Expect = 5e-04
 Identities = 15/116 (12%), Positives = 58/116 (50%), Gaps = 11/116 (9%)

Query: 689 QISSQQQQQLQQQQQ-----QQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ 743
               + ++QL+  +      + Q   + ++++ +  ++L++ + +  +LQQ+I +L ++ 
Sbjct: 372 SRLEELEEQLETLRSKVAQLELQIASLNNEIE-RLEARLERLEDRRERLQQEIEELLKKL 430

Query: 744 QIPQLQQQSMPQLQQQQQLPQLQQ-----QQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           +  +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|220964 pfam11068, DUF2869, Protein of unknown function (DUF2869)

 Score = 40.3 bits (95), Expect = 6e-04
 Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 8/65 (12%)

Query: 692 SQQQQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQQQQLPQ----LQQQIPQLQQQQQI 745
            +Q  QL+Q+ QQ   Q Q+   +++ Q   Q++Q QQQ+ Q      +Q  QL  Q + 
Sbjct: 26  QEQLTQLEQELQQLEFQGQKAIKEIRKQSAQQIEQIQQQVEQERAKRLEQKNQLLFQIE- 84

Query: 746 PQLQQ 750
            Q+Q+
Sbjct: 85  -QVQE 88

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

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

 Score = 42.6 bits (101), Expect = 6e-04
 Identities = 7/100 (7%), Positives = 51/100 (51%), Gaps = 4/100 (4%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           QI  +++++ ++ +++ Q ++     +  +  Q + + +   + ++Q  +L+++      
Sbjct: 79  QIEEREKRRQEEYEERLQEREQ--MDEIIERIQEEDEAEAQEKREKQK-KLREEIDEFNE 135

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           ++    + +++++  +  +  +  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|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional

 Score = 42.3 bits (100), Expect = 7e-04
 Identities = 24/110 (21%), Positives = 38/110 (34%), Gaps = 4/110 (3%)

Query: 691 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ----QQQIP 746
             +  +   Q Q Q  +   Q +   QQ  + Q   Q  P+  Q  PQ  Q    Q Q  
Sbjct: 80  EHEAARPSPQHQYQPPYASAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPE 139

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
           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 = 7e-04
 Identities = 22/128 (17%), Positives = 29/128 (22%), Gaps = 3/128 (2%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
              Q      Q  Q        Q  Q       QQQ                        
Sbjct: 51  PSPQAPPPVAQLPQPLPQPPPTQALQALP-AGDQQQHNTPTGSPAANPPATFALPAGPAG 109

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ--QLSQPQQMVGSGMGQGYVQGPGR 810
                +  QL  +Q    + Q      L Q  QQ+  Q  Q +    +       Q   +
Sbjct: 110 PTIQTEPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQSAQ 169

Query: 811 TQLVSQGQ 818
               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 = 7e-04
 Identities = 23/112 (20%), Positives = 34/112 (30%), Gaps = 6/112 (5%)

Query: 685 VFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 744
           ++  Q+     Q        Q  QQ    LQ  Q         QLP  QQ      Q+  
Sbjct: 119 LYPVQVPVMVTQNPANSPLDQPAQQRA--LQQLQQRYGAPASGQLPSQQQ----SAQKND 172

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
             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 = 42.4 bits (100), Expect = 7e-04
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 15/80 (18%)

Query: 707 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQ 766
           H + Q+Q Q      L  Q   L + Q+      Q+Q++  + +      QQ + L Q  
Sbjct: 57  HGKQQAQNQTATNDALANQLTALQKAQE-----SQKQELEGILK------QQAKALDQAN 105

Query: 767 QQQQLPQMQQQQQLPQLQQQ 786
           +QQ        +QL +LQQ+
Sbjct: 106 RQQA----ALAKQLDELQQK 121

Length = 390

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

 Score = 43.0 bits (102), Expect = 7e-04
 Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 10/101 (9%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 751
             + + +QQ  +Q      +   Q ++  QL+QQ  Q P   +Q      Q ++  L+  
Sbjct: 55  EAEDKLVQQDLEQTLALLDKIDRQKEETEQLKQQLAQAPAKLRQA-----QAELEALKDD 109

Query: 752 SMPQLQQQ-QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
           +  + ++    L   Q + +L Q   Q Q      Q  L++
Sbjct: 110 NDEETRETLSTLSLRQLESRLAQTLDQLQ----NAQNDLAE 146

Length = 1113

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

 Score = 42.2 bits (100), Expect = 7e-04
 Identities = 9/101 (8%), Positives = 54/101 (53%), Gaps = 8/101 (7%)

Query: 693 QQQQQLQQQQQQQQHQQM----QSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           ++ +  +++++++  + M       L  ++  + ++++++         Q++++++  Q 
Sbjct: 30  KRIKAEEKEEERRIDEMMEEERLKALAEEEERERKRKEERREGRAVLQEQIEEREKRRQE 89

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQL 789
           + +   +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 = 42.8 bits (101), Expect = 7e-04
 Identities = 10/96 (10%), Positives = 56/96 (58%), Gaps = 14/96 (14%)

Query: 693 QQQQQLQQQQQQQQHQQMQS---------QLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ 743
           ++ ++L+ +  + +  ++++         +L+ + L +L+++ ++L +L+++I +L+++ 
Sbjct: 249 ERLEELKARLLEIESLELEALKIREEELRELE-RLLEELEEKIERLEELEREIEELEEEL 307

Query: 744 QIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ 779
           +  +   + + +L ++ +      +++L +++++ +
Sbjct: 308 EGLRALLEELEELLEKLK----SLEERLEKLEEKLE 339

Length = 908

>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein

 Score = 43.0 bits (101), Expect = 7e-04
 Identities = 34/141 (24%), Positives = 54/141 (38%), Gaps = 10/141 (7%)

Query: 696 QQLQQQQQQQQHQQMQSQLQHQQL---SQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           +QL QQ +    Q  +    + ++     LQ    Q+  L +   + Q +Q + QLQQ  
Sbjct: 541 RQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQLQQM- 599

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQL----QQQQQLSQPQQMVGSGMGQGYVQGP 808
           M  LQ  Q  P   QQ        +QQ+ +L    ++QQQL      +     +  ++G 
Sbjct: 600 MNNLQMGQ--PGQGQQMGDQSGDMEQQMNKLGELMRKQQQLRDETFKLDQDQRRDRMRGQ 657

Query: 809 GRTQLVSQGQVSSQGAPNIPG 829
              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|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: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           PQ   +Q QQ  QQ + +     Q + + +   + QQQQ+Q  + QQ+    QQQ+Q P+
Sbjct: 55  PQRRYEQCQQRCQQHEPRHRPTCQQRCERRYEKEQQQQQRQYQECQQRC---QQQEQRPR 111

Query: 748 LQQQSMPQLQQQQQLP 763
            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|234017 TIGR02794, tolA_full, TolA protein

 Score = 42.1 bits (99), Expect = 8e-04
 Identities = 16/97 (16%), Positives = 45/97 (46%), Gaps = 11/97 (11%)

Query: 687 KPQISSQQQQQL----QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 742
             Q +  QQQ+     ++Q++Q++ +Q   + + Q+      +Q +  +L+Q   +   +
Sbjct: 49  AQQANRIQQQKKPAAKKEQERQKKLEQQAEEAEKQR----AAEQARQKELEQ---RAAAE 101

Query: 743 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ 779
           +   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|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: 699 QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ 758
             QQ   Q+   Q  +Q+      QQ QQQ  Q  QQ       QQ PQ +Q      +Q
Sbjct: 203 PTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRSREQ 262

Query: 759 QQQ 761
             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|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication, recombination, and repair]

 Score = 42.8 bits (101), Expect = 8e-04
 Identities = 12/118 (10%), Positives = 71/118 (60%), Gaps = 11/118 (9%)

Query: 686 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQ---QQQQLPQLQQQIPQLQQQ 742
            + +I + +++  + ++++++ ++++++L   +  +L+    ++++L +L++ + +L+++
Sbjct: 230 LEQEIEALEERLAELEEEKERLEELKARLLEIESLELEALKIREEELRELERLLEELEEK 289

Query: 743 QQIPQLQQQ--SMPQLQQQQQL--PQLQQQQQLPQM--QQQQQLPQLQQQQQLSQPQQ 794
            +  +L++    + +L+++ +     L++ ++L +     +++L +L+++ +  + + 
Sbjct: 290 IE--RLEELEREIEELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESEL 345

Length = 908

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

 Score = 42.8 bits (101), Expect = 9e-04
 Identities = 28/108 (25%), Positives = 52/108 (48%), Gaps = 3/108 (2%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 751
            Q ++QL Q   + + Q+         L Q +   Q+L Q +QQ  + + +  I + +QQ
Sbjct: 624 KQAEEQLVQANAELEEQKRAEAEARTALKQARLDLQRL-QNEQQSLKDKLELAIAERKQQ 682

Query: 752 SMPQLQQ-QQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGS 798
           +  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|236942 PRK11637, PRK11637, AmiB activator; Provisional

 Score = 42.4 bits (100), Expect = 9e-04
 Identities = 27/101 (26%), Positives = 49/101 (48%), Gaps = 10/101 (9%)

Query: 697 QLQQQQQQQQH---QQMQS---QLQHQ--QLSQLQQQQQQLPQLQQQIPQLQQ--QQQIP 746
           +L+QQQ  Q+     Q+ +   Q +H   QL    ++ Q+  ++      L Q  Q+ I 
Sbjct: 114 KLEQQQAAQERLLAAQLDAAFRQGEHTGLQLILSGEESQRGERILAYFGYLNQARQETIA 173

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQ 787
           +L+Q       Q+ +L + Q QQ+    +QQ Q  +L+Q +
Sbjct: 174 ELKQTREELAAQKAELEEKQSQQKTLLYEQQAQQQKLEQAR 214

Length = 428

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

 Score = 40.2 bits (94), Expect = 0.001
 Identities = 33/102 (32%), Positives = 39/102 (38%), Gaps = 4/102 (3%)

Query: 695 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLP-QLQQQIPQLQQQQ-QIPQLQQQS 752
           Q  ++       ++ M   L HQ +   QQ       Q    IP L  QQ  +P  QQ  
Sbjct: 16  QSMIRHPYPSYGYEPMGGWLHHQIIPVSQQHPPTHTLQPHHHIPVLPAQQPVVP--QQPL 73

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           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|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: 654 AVIQLPSQTLLLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQ--QQQHQQMQ 711
           A I  P+Q  LL   D     +   F          +  Q++ +L+Q     Q+QH Q +
Sbjct: 250 AEIVSPNQDELLQRLDGFNVRLHRAFD--------TLLHQKKARLEQLVASLQRQHPQNK 301

Query: 712 SQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL---QQQSMPQLQQQQQLPQLQQQ 768
             LQ  Q  +L++++Q    L +Q+ + +Q++        Q    PQ+ + Q   + +Q 
Sbjct: 302 LALQQLQFEKLEKRKQA--ALNKQLERTRQKKTRLTKRLTQTNPSPQILRAQT--RTEQL 357

Query: 769 QQLPQMQQQQQLPQLQQQ 786
            +     +  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|204784 pfam11932, DUF3450, Protein of unknown function (DUF3450)

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 12/99 (12%)

Query: 691 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQL----PQLQQQIPQLQQQQQIP 746
           ++    Q     QQ      QSQ   +++ +   Q Q+L     QL ++I  L+      
Sbjct: 20  AAASLDQALAAAQQTVAAAAQSQ---KKIDKWADQTQELLAEIRQLLKEIENLRVYND-- 74

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQ 785
           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|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 42.1 bits (99), Expect = 0.001
 Identities = 31/118 (26%), Positives = 49/118 (41%), Gaps = 13/118 (11%)

Query: 687 KPQISSQQQQQ-----LQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 741
           K  +++QQQQQ     L +  + QQ    + Q   Q L+  ++ Q QL  L    P  Q 
Sbjct: 233 KQLLTAQQQQQQSLNWLTRLDELQQEASRRQQALQQALAAEEKAQPQLAALSLAQPARQL 292

Query: 742 QQQIPQLQQQSMPQLQQQQQLPQ----LQQQQQL----PQMQQQQQLPQLQQQQQLSQ 791
           +    ++Q+QS      +QQ+ +    LQ    L         +Q      QQQ L+ 
Sbjct: 293 RPHWERIQEQSAALAHTRQQIEEVNTRLQSTMALRARIRHHAAKQSAELQAQQQSLNT 350

Length = 1047

>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: 705 QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQ 764
           Q+ +Q ++ LQ  Q  QLQ + +QLP        + Q     Q  QQ   Q   Q     
Sbjct: 362 QRKEQRRAHLQ-DQFMQLQPRMRQLPMGSPMGGAMGQPPYYGQGPQQ---QFNGQPLGWP 417

Query: 765 LQQQQQLPQMQQQQQLPQL-----QQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQV 819
                  P        P         +      Q        Q  +  P       Q   
Sbjct: 418 RMSMMPTPMGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKPPMQPVMYPPN-----YQSLP 472

Query: 820 SSQGAPN 826
            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 = 42.3 bits (99), Expect = 0.001
 Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 699 QQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQ 758
           + +   +  QQ   Q   QQ +     QQ   Q QQQ  Q  QQ       QQ  PQ +Q
Sbjct: 196 RHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQP-PQTEQ 254

Query: 759 QQQLPQLQQQQQLPQMQQQQ 778
             +  + 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|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: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           P+ + Q   Q   QQ   Q+   Q Q Q QQ      QQ       QQ PQ +Q  +  +
Sbjct: 201 PKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRSR 260

Query: 748 LQ 749
            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|236795 PRK10920, PRK10920, putative uroporphyrinogen III C-methyltransferase; Provisional

 Score = 42.0 bits (99), Expect = 0.001
 Identities = 13/48 (27%), Positives = 27/48 (56%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQI 736
           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 = 0.001
 Identities = 27/126 (21%), Positives = 50/126 (39%), Gaps = 33/126 (26%)

Query: 698 LQQQQQQQQHQQMQSQLQHQQLSQLQQQ--QQQLPQLQQQI---PQLQQQQQI-PQLQQ- 750
            + Q+ + Q Q +Q  +  ++L+  ++   + Q      +I   P + Q+ +I  QL Q 
Sbjct: 234 ARIQRLEHQLQLLQEAINSKRLTLSEKTVQEAQSQDEAARIQANPLVAQELEINLQLSQR 293

Query: 751 -----QSMPQLQQQ-----QQLPQLQQQQQL--PQM--------------QQQQQLPQLQ 784
                + +  L QQ       L +L Q ++    Q+              QQQQ LP   
Sbjct: 294 LLKATEKLNTLTQQNLRVKNWLDRLTQSERNIKEQISVLKGSLLLSRILYQQQQALPSAD 353

Query: 785 QQQQLS 790
             + L+
Sbjct: 354 LIEGLA 359

Length = 1113

>gnl|CDD|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523)

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 21/91 (23%), Positives = 51/91 (56%), Gaps = 2/91 (2%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 751
           S+ Q++ +Q + + + ++ ++Q    +L + + + ++  +  Q+  Q QQ+QQ  Q Q +
Sbjct: 57  SKMQEKTRQAELEAKIKEYEAQQAQAKLERARVEAEERRKTLQE--QTQQEQQRAQYQDE 114

Query: 752 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQ 782
              +  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|221389 pfam12037, DUF3523, Domain of unknown function (DUF3523)

 Score = 41.3 bits (97), Expect = 0.001
 Identities = 18/109 (16%), Positives = 55/109 (50%), Gaps = 10/109 (9%)

Query: 694 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIP------QLQQQQQIPQ 747
           ++ + QQ Q + +  +++++ + + L +  QQ+QQ  Q Q ++       +L+QQ++   
Sbjct: 73  KEYEAQQAQAKLERARVEAEERRKTLQEQTQQEQQRAQYQDELARKRYQKELEQQRR--- 129

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
            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 = 40.5 bits (95), Expect = 0.001
 Identities = 29/96 (30%), Positives = 49/96 (51%), Gaps = 7/96 (7%)

Query: 703 QQQQHQQMQSQLQHQQL-SQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQ-- 759
            +Q  Q    +++  QL +Q  Q ++Q+   + +  +LQ   Q+ Q Q+Q +   QQQ  
Sbjct: 94  ARQTAQLADVEIRRAQLEAQKAQLERQIAASEARAERLQADLQLAQAQEQQVAARQQQAR 153

Query: 760 QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           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|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: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQIPQLQ 749
              + +  Q  Q Q     Q+ +    + + Q     +  +     QL+ +  +   ++ 
Sbjct: 115 QNHRSEPIQPTQPQYQSPTQTNVASMTIEETQSPNVPIEGINSSSEQLRVELAELAAEIY 174

Query: 750 QQSMPQLQQQQQLPQLQQQQQLPQ 773
             +  +++  +   + Q + +   
Sbjct: 175 SDASHRVELAKNFMEPQAETEAQP 198

Length = 332

>gnl|CDD|223914 COG0845, AcrA, Membrane-fusion protein [Cell envelope biogenesis, outer membrane]

 Score = 41.6 bits (97), Expect = 0.001
 Identities = 17/111 (15%), Positives = 37/111 (33%), Gaps = 4/111 (3%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           ++      Q    Q + Q  + Q+ L   +L  LQ++ + L   +  + Q +       L
Sbjct: 96  RLDPSAVLQAALDQAEAQLARAQALLAPAELGDLQREAK-LAAEKAAVSQAELDAAQALL 154

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQ---QQLPQLQQQQQLSQPQQMV 796
           +         Q  L   +   +  ++          +L +  QL    Q +
Sbjct: 155 RAAEALVEAAQAALASAKLNLEYTRITAPISGVIGARLVRVGQLVSAGQAL 205

Length = 372

>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like)

 Score = 39.9 bits (94), Expect = 0.001
 Identities = 23/84 (27%), Positives = 48/84 (57%), Gaps = 11/84 (13%)

Query: 708 QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQ 767
           +  Q QL+     + ++ Q +L + +++   LQ+++Q  Q Q  ++ +  ++ +  +LQQ
Sbjct: 34  KAAQKQLE----KEFKKLQAELQKKEKE---LQKEEQKLQKQAATLSEEARKAKQQELQQ 86

Query: 768 QQQLPQMQQQQQLPQLQQQQQLSQ 791
           +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|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like)

 Score = 39.9 bits (94), Expect = 0.001
 Identities = 31/93 (33%), Positives = 59/93 (63%), Gaps = 17/93 (18%)

Query: 700 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQ 759
           Q+Q +++ +++Q++LQ ++  +LQ+++Q+L   Q+Q   L ++ +     +    +LQQ+
Sbjct: 37  QKQLEKEFKKLQAELQKKE-KELQKEEQKL---QKQAATLSEEAR-----KAKQQELQQK 87

Query: 760 QQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 792
           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|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein, HlyD family

 Score = 41.5 bits (98), Expect = 0.001
 Identities = 20/102 (19%), Positives = 55/102 (53%), Gaps = 9/102 (8%)

Query: 694 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSM 753
           +  + QQ   + +   +++QL+   L+Q++Q + +L  LQ Q+  L+QQ ++   + ++ 
Sbjct: 126 ELIKGQQSLFESRKSTLRAQLE-LILAQIKQLEAELAGLQAQLQALRQQLEVISEELEAR 184

Query: 754 PQLQQQQQLPQLQ---QQQQLPQMQ-----QQQQLPQLQQQQ 787
            +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|227671 COG5380, LimK, Lipase chaperone [Posttranslational modification, protein turnover, chaperones]

 Score = 41.1 bits (96), Expect = 0.001
 Identities = 23/108 (21%), Positives = 52/108 (48%), Gaps = 5/108 (4%)

Query: 691 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 750
           S++QQ    ++ + ++    + ++        +++Q+    L   +P++Q+++   Q Q+
Sbjct: 129 SAEQQAFFAEENRLRELALERLRIYEDYGLSDEEKQRAWQALLLDLPKVQEERIFIQRQE 188

Query: 751 ---QSMPQLQQQQQLP--QLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
              Q +PQLQQ  Q P      +  L   +  Q+L +L +Q+   + Q
Sbjct: 189 ATAQLLPQLQQAGQGPTQIRLARVALVGEEGAQRLAELDRQRATWEQQ 236

Length = 283

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

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 17/69 (24%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           ++Q   + + +Q   Q+   QL+ ++L   +QQ+Q     +Q   QL+Q+QQ  Q ++ +
Sbjct: 85  EEQVAEELKPKQAAEQERLKQLEKERLKAQEQQKQAEEAEKQA--QLEQKQQEEQARKAA 142

Query: 753 MPQLQQQQQ 761
             Q ++ + 
Sbjct: 143 AEQKKKAEA 151

Length = 387

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

 Score = 41.9 bits (98), Expect = 0.002
 Identities = 25/121 (20%), Positives = 46/121 (38%), Gaps = 18/121 (14%)

Query: 689 QISSQQQ---QQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 745
           QI  Q Q    +LQ + + +    M+     +Q S +++Q++ L  L  Q   ++   ++
Sbjct: 304 QIEQQAQRIHTELQSKMRSRAKLLMKRAAHVKQQSSIEEQRRLLQTLHSQEIHIRDAHEV 363

Query: 746 PQL------QQQSMPQ--LQQQQQLPQLQQQQQLP-------QMQQQQQLPQLQQQQQLS 790
                    QQ ++ Q     QQQ   L Q+ Q         Q +Q     +    + L 
Sbjct: 364 ATSIREISCQQHTLTQHIHTLQQQKTTLTQKLQSLCKELDILQREQATIDTRTSAFRDLQ 423

Query: 791 Q 791
            
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|129705 TIGR00618, sbcc, exonuclease SbcC

 Score = 41.5 bits (97), Expect = 0.002
 Identities = 22/112 (19%), Positives = 39/112 (34%), Gaps = 15/112 (13%)

Query: 689 QISSQQ---QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ-QQLPQLQQQIP------- 737
           +IS QQ    Q +   QQQ+     + Q   ++L  LQ++Q     +             
Sbjct: 369 EISCQQHTLTQHIHTLQQQKTTLTQKLQSLCKELDILQREQATIDTRTSAFRDLQGQLAH 428

Query: 738 ----QLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQ 785
               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 = 38.4 bits (90), Expect = 0.002
 Identities = 20/100 (20%), Positives = 51/100 (51%), Gaps = 12/100 (12%)

Query: 689 QISSQQQQQLQ-QQQQQQQHQQMQSQLQHQQLSQLQ-------QQQQQLPQLQQQIPQLQ 740
           ++   QQ +L+ +QQ     Q + +       + +        QQQQ+L Q ++Q+ Q +
Sbjct: 20  KLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEAIAQQQQELEQAEKQVEQAR 79

Query: 741 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 780
           +Q Q    +++ + +L ++++    +++Q+    ++Q+ L
Sbjct: 80  EQWQEANQERKKLEKLLEREK----KKEQKEENRREQKLL 115

Length = 122

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

 Score = 40.4 bits (95), Expect = 0.002
 Identities = 22/75 (29%), Positives = 47/75 (62%), Gaps = 5/75 (6%)

Query: 717 QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQ 776
           + LS     +++LP+LQQ++ +L  Q+++ +LQ+Q   +LQQ+ Q  +L+Q+    + + 
Sbjct: 56  RYLSDTPSARERLPELQQELAEL--QEELAELQEQL-AELQQENQ--ELKQELSTLEAEL 110

Query: 777 QQQLPQLQQQQQLSQ 791
           ++   +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|234937 PRK01294, PRK01294, lipase chaperone; Provisional

 Score = 40.8 bits (96), Expect = 0.002
 Identities = 32/117 (27%), Positives = 49/117 (41%), Gaps = 16/117 (13%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
            Q   L   Q+  +   +++QL     + LQ+ Q+Q   L QQ+ QLQ     PQ  +  
Sbjct: 198 AQDPSLSDAQKAARLAALEAQLPEDLRAALQESQRQQ-ALLQQLAQLQASGASPQELRLM 256

Query: 753 MPQL---QQQQQLPQLQQQ------------QQLPQMQQQQQLPQLQQQQQLSQPQQ 794
             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 = 40.8 bits (96), Expect = 0.002
 Identities = 21/127 (16%), Positives = 45/127 (35%), Gaps = 16/127 (12%)

Query: 686 FKPQISSQQQQQLQQQQQQ--QQHQQMQSQLQ--------HQQLSQLQQQQQQLPQLQQQ 735
            + +I++Q  +    Q      +++   S L            L  LQQ       L+ +
Sbjct: 111 VEREIAAQLPEPADSQALDLWLRYKAYLSALAQLEDDGPGKLDLQALQQLLDARLALRAR 170

Query: 736 IPQLQQQQQI----PQLQQQSMPQLQ--QQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQL 789
                + Q       Q Q+ ++ +L+  Q   L   Q+  +L  ++ Q         Q+ 
Sbjct: 171 FFSDWEIQAFFGEENQYQRYALERLRIAQDPSLSDAQKAARLAALEAQLPEDLRAALQES 230

Query: 790 SQPQQMV 796
            + 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: 707 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQ 766
           H+   +    QQ +     QQ   Q   Q PQ Q QQQ  Q  QQ  PQ   QQ  PQ +
Sbjct: 195 HRHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQP-PQTE 253

Query: 767 QQQQLPQMQQQQQL 780
           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: 737 PQLQQQQQIPQLQ---QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
           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: 737 PQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           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|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: 689 QISSQQQQQLQQQQQ----QQQHQQMQSQLQHQQLSQ--LQQQQQQLPQLQQQIPQLQQQ 742
           Q+ S Q Q  + Q       Q+ QQ+++ L+  ++    L+  Q+ L Q +Q +   Q  
Sbjct: 150 QLVSLQTQPERAQAALYANSQRLQQIRNLLKGGKVGGKALRPSQRVLLQAEQALLNAQND 209

Query: 743 QQIPQLQQQSMPQ--LQQQQ-----QLPQLQQQQQLPQ--------MQQQQQLPQLQQQQ 787
            Q   L+  +  Q  LQ+Q+     ++ +L+ Q QL Q           ++ + + Q Q 
Sbjct: 210 LQRKSLEGNTQLQDLLQKQRDYLTARIQRLEHQLQLLQEAINSKRLTLSEKTVQEAQSQD 269

Query: 788 QLSQPQQ 794
           + ++ Q 
Sbjct: 270 EAARIQA 276

Length = 1113

>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: 725 QQQQLPQLQQQIPQLQQQ-QQIPQLQQQSMPQLQQQQQ----LPQLQQQQQLPQMQQQQQ 779
            +  L  LQQ++  L+QQ +   + + QS    + QQQ    L  L  + +  Q + + Q
Sbjct: 140 PENLLHALQQEVLTLKQQLELQAREKAQSQALAEAQQQELVALEGLAAELEEKQQELEAQ 199

Query: 780 LPQLQQQQQLSQPQQ 794
           L QLQ++   +  ++
Sbjct: 200 LEQLQEKAAETSQER 214

Length = 1123

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

 Score = 41.4 bits (98), Expect = 0.002
 Identities = 9/112 (8%), Positives = 56/112 (50%), Gaps = 16/112 (14%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQ----QQQLPQLQQQIPQ--------- 738
            ++ ++ ++++ +++ ++ + + +  +L   Q++    +++L +L+  + Q         
Sbjct: 160 REKAEREEEREAERRERKEEKEREVARLRAQQEEAEDEREELDELRADLYQEEYERKERQ 219

Query: 739 --LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQ-QQQLPQLQQQQ 787
              ++ ++  + +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|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: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQ---------QQIPQ 738
           P    Q  +        QQ           Q  Q  QQQQ               QQ+  
Sbjct: 50  PPAPEQVAKHELADAPLQQVNAALPPAPAPQSPQPDQQQQSQAPPSHQYPSQLPPQQVQS 109

Query: 739 LQQQQQIPQL-----QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
           + 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 = 41.1 bits (96), Expect = 0.002
 Identities = 36/138 (26%), Positives = 59/138 (42%), Gaps = 21/138 (15%)

Query: 689 QISSQQQQQLQQ----QQQQQQH---QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ 741
           Q+ SQ QQ +      Q  Q Q    Q    + Q  +L +L ++QQQL     ++ Q Q+
Sbjct: 591 QLLSQLQQMMNNLQMGQPGQGQQMGDQSGDMEQQMNKLGELMRKQQQLRDETFKLDQDQR 650

Query: 742 QQQ-------------IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           + +             +PQ   Q   Q     +L +LQQ++    + Q Q   +  +  Q
Sbjct: 651 RDRMRGQDGEQNFGDDMPQQDGQPNGQPNLHDRLRKLQQEEAKRGLGQSQGGLK-GELGQ 709

Query: 789 LSQPQQMVGSGMGQGYVQ 806
           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|237177 PRK12704, PRK12704, phosphodiesterase; Provisional

 Score = 41.3 bits (98), Expect = 0.002
 Identities = 14/96 (14%), Positives = 54/96 (56%), Gaps = 8/96 (8%)

Query: 687 KPQISSQQQQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ 744
           K +   + ++++ + + +  ++ ++ +++LQ  +  +L Q+++ L +  + + + +++  
Sbjct: 55  KKEALLEAKEEIHKLRNEFEKELRERRNELQKLE-KRLLQKEENLDRKLELLEKREEE-- 111

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 780
              L+++     Q+QQ+L + +++ +    +Q Q+L
Sbjct: 112 ---LEKKEKELEQKQQELEKKEEELEELIEEQLQEL 144

Length = 520

>gnl|CDD|148750 pfam07321, YscO, Type III secretion protein YscO

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 22/92 (23%), Positives = 49/92 (53%), Gaps = 5/92 (5%)

Query: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQ-LPQLQQQIPQLQQQQQI 745
           + Q ++   ++L++ QQQ    +       QQL++ +Q+ +    +L+Q   QLQ+ ++ 
Sbjct: 58  ELQGATVLLKELEKWQQQVGLLRENEASLEQQLAEAKQRLEAERQRLRQARQQLQEARK- 116

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQ 777
               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|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: 691 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 750
            + ++++     + +  ++   +L ++   +L+Q  Q L  L+ +I  LQ Q        
Sbjct: 539 PAVKKKEEAAAPKAETVKRSSKKLSYKLQRELEQLPQLLEDLEAEIEALQAQVADADFFS 598

Query: 751 QSMPQLQQQQQLPQLQQQQQ 770
           Q  P  Q Q+ L  L   +Q
Sbjct: 599 Q--PHEQTQKVLADLADAEQ 616

Length = 635

>gnl|CDD|113156 pfam04375, HemX, HemX

 Score = 40.7 bits (95), Expect = 0.002
 Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 718 QLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQ 777
            L Q+   Q +L  L Q++ QL Q  +    Q+  +     Q+ L QL++       Q  
Sbjct: 51  GLQQVAGLQIKLEALAQELTQLAQALEAQLAQEVRVLIRDNQEALAQLEKVLG----QLD 106

Query: 778 QQLPQLQQQQ 787
           + 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|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication, recombination, and repair]

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 21/82 (25%), Positives = 49/82 (59%), Gaps = 4/82 (4%)

Query: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
            ++ S+QQQ+L +   + + + +++QL  ++    +  Q+  PQ+Q+Q  +LQQ ++  +
Sbjct: 305 ERLLSEQQQRLDELAIRLR-RALENQLALKKQRLERLTQRLNPQIQRQQQRLQQLER--R 361

Query: 748 LQQQSMPQLQQ-QQQLPQLQQQ 768
           L +    QL++ +++L  L +Q
Sbjct: 362 LDKALRRQLKRKRERLEALVEQ 383

Length = 440

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

 Score = 40.7 bits (95), Expect = 0.003
 Identities = 21/139 (15%), Positives = 52/139 (37%), Gaps = 2/139 (1%)

Query: 681 GDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 740
           G   +   +                + +Q+  +        LQQ QQ    L Q+    +
Sbjct: 194 GKAELLTLRSQLLTLCTPCMPDTYHERKQVLEKELKHLREALQQTQQSHAYLTQKREAQE 253

Query: 741 QQQQIPQLQQQSMPQLQQ-QQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSG 799
           +Q +  QL +Q   ++++ + Q   L++ Q+    + ++  P     + ++Q +Q     
Sbjct: 254 EQLKKQQLLKQLRARIEELRAQEAVLEETQERIN-RARKAAPLAAHIKAVTQIEQQAQRI 312

Query: 800 MGQGYVQGPGRTQLVSQGQ 818
             +   +   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: 700 QQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ----QQIPQLQQQSMPQ 755
           + + +++ QQ +  LQ    ++ +Q ++QL Q   ++ + ++     +   +  +  + +
Sbjct: 602 ETELRERLQQAEEALQSAV-AKQKQAEEQLVQANAELEEQKRAEAEARTALKQARLDLQR 660

Query: 756 LQQQQQLPQLQQQQQLPQMQQQ--QQLPQL-QQQQQLSQPQQ 794
           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|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional

 Score = 40.9 bits (96), Expect = 0.003
 Identities = 33/129 (25%), Positives = 52/129 (40%), Gaps = 29/129 (22%)

Query: 689 QISSQQQQQLQQQQQ-QQQHQQMQSQLQHQQLS-------------------QLQQQQQQ 728
           QI++  QQ +Q QQQ +Q+ QQ+ + L    L+                     QQ+Q +
Sbjct: 624 QIAAHNQQIIQYQQQIEQRQQQLLTALAGYALTLPQEDEEASWLATRQQEAQSWQQRQNE 683

Query: 729 LPQLQQQIPQLQQ------QQQIPQLQQQSMPQLQQQQ---QLPQLQQQQQLPQMQQQQQ 779
           L  LQ +I QL        Q       ++++     +Q   Q   L  Q Q  Q Q   +
Sbjct: 684 LTALQNRIQQLTPLLETLPQSDDLPHSEETVALDNWRQVHEQCLSLHSQLQTLQQQDVLE 743

Query: 780 LPQLQQQQQ 788
             +LQ+ Q 
Sbjct: 744 AQRLQKAQA 752

Length = 1047

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

 Score = 40.1 bits (94), Expect = 0.003
 Identities = 17/114 (14%), Positives = 30/114 (26%), Gaps = 2/114 (1%)

Query: 683 MVVFKPQISSQQQQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 740
                P     QQ+ LQQ QQ+            Q       + Q QQ P  +    Q  
Sbjct: 131 NPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQQQSAQKNDESQLQQQPNGETPPQQTD 190

Query: 741 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
                       + +     +      +        +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|236892 PRK11281, PRK11281, hypothetical protein; Provisional

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 29/138 (21%), Positives = 58/138 (42%), Gaps = 36/138 (26%)

Query: 687 KPQISSQQQQQLQQQQQ--QQQHQQMQSQLQ-HQQLSQLQQQQQ-----QLPQLQQQIPQ 738
              +   Q+  LQ +Q     Q+   +  L+ + QL  L Q+Q+     ++ +L+ Q+  
Sbjct: 186 GKALRPSQRVLLQAEQALLNAQNDLQRKSLEGNTQLQDLLQKQRDYLTARIQRLEHQLQL 245

Query: 739 LQQ----------QQQIPQLQQ-------QSMPQLQQQ----QQLPQ--LQQQQQLPQMQ 775
           LQ+          ++ + + Q        Q+ P + Q+     QL Q  L+  ++L  + 
Sbjct: 246 LQEAINSKRLTLSEKTVQEAQSQDEAARIQANPLVAQELEINLQLSQRLLKATEKLNTLT 305

Query: 776 QQ-----QQLPQLQQQQQ 788
           QQ       L +L Q ++
Sbjct: 306 QQNLRVKNWLDRLTQSER 323

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 = 0.003
 Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 11/100 (11%)

Query: 674 LIGMLFPGDMVVFKPQISSQQQ--QQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQ 731
            I  L  G ++    QI+ QQQ    L  +      +         ++ QL++Q Q L Q
Sbjct: 35  GIAALALGGLLQD-RQIAEQQQRNALLTTEIALLDAEI-------AEIQQLKEQTQALLQ 86

Query: 732 LQQQIPQLQQQQQIPQLQQQSMP-QLQQQQQLPQLQQQQQ 770
             Q I QLQQ++    +  + +   L +   L  L+QQ  
Sbjct: 87  RLQVIEQLQQKRAGWSVLLEQLANLLPESVWLTSLKQQGD 126

Length = 206

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

 Score = 40.7 bits (96), Expect = 0.003
 Identities = 8/93 (8%), Positives = 55/93 (59%), Gaps = 6/93 (6%)

Query: 693 QQQQQLQQQQQQQQHQQM-QSQL-QHQQLSQLQQQQQQLPQLQ--QQIPQLQQQ-QQIPQ 747
           +++++ ++++++++ + + Q Q+ + ++  Q + +++   + Q  + I ++Q++ +   Q
Sbjct: 58  EEERERKRKEERREGRAVLQEQIEEREKRRQEEYEERLQEREQMDEIIERIQEEDEAEAQ 117

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 780
            +++   +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|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin

 Score = 40.3 bits (95), Expect = 0.003
 Identities = 11/87 (12%), Positives = 53/87 (60%), Gaps = 2/87 (2%)

Query: 695 QQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMP 754
           ++Q+++++++ Q ++ + + + +++ + Q + ++L Q   +  ++++ +   +L+QQ   
Sbjct: 240 EEQIEEKEERLQEERAEEEAERERMLEKQAEDEELEQENAEKRRMKRLEHRRELEQQIEE 299

Query: 755 QLQQQQQLPQ--LQQQQQLPQMQQQQQ 779
           + +++    +  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|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein

 Score = 40.7 bits (95), Expect = 0.003
 Identities = 42/154 (27%), Positives = 64/154 (41%), Gaps = 15/154 (9%)

Query: 683 MVVFKPQISSQQQQQLQQQQQ----------QQQHQQMQSQLQHQQLSQLQQQQQQ-LPQ 731
           M  +  Q++ Q +   QQ  +          QQ  Q M  Q+++   S  + Q +Q L Q
Sbjct: 536 MQTYMRQLAQQLRNNPQQLARPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQ 595

Query: 732 LQQQIPQLQ--QQQQIPQLQQQSMPQLQQQQQLPQL-QQQQQLPQMQQQQQLPQLQQQQQ 788
           LQQ +  LQ  Q  Q  Q+  QS    QQ  +L +L ++QQQL     +    Q + + +
Sbjct: 596 LQQMMNNLQMGQPGQGQQMGDQSGDMEQQMNKLGELMRKQQQLRDETFKLDQDQRRDRMR 655

Query: 789 LSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQ 822
               +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 = 38.9 bits (91), Expect = 0.003
 Identities = 15/60 (25%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 696 QQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQL--QQQIPQLQQQQQIPQLQQQSM 753
           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|148750 pfam07321, YscO, Type III secretion protein YscO

 Score = 38.9 bits (91), Expect = 0.003
 Identities = 31/124 (25%), Positives = 61/124 (49%), Gaps = 21/124 (16%)

Query: 692 SQQQQQLQQ--------QQQQQQHQQMQSQLQHQQLSQLQQQ---QQQLPQLQQQIPQL- 739
            +Q+Q L Q        QQ  Q ++Q + Q +++  ++LQ      ++L + QQQ+  L 
Sbjct: 21  KRQEQALVQARARHREAQQSLQDYRQWRQQEENRLFAELQGATVLLKELEKWQQQVGLLR 80

Query: 740 -------QQQQQIPQLQQQSMPQLQQ-QQQLPQLQQQQQ-LPQMQQQQQLPQLQQQQQLS 790
                  QQ  +  Q  +    +L+Q +QQL + ++ Q+   ++ +Q+Q     Q+Q L 
Sbjct: 81  ENEASLEQQLAEAKQRLEAERQRLRQARQQLQEARKAQEKFAELARQEQAEAQAQRQYLE 140

Query: 791 QPQQ 794
           + +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|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division and chromosome partitioning]

 Score = 40.5 bits (95), Expect = 0.003
 Identities = 14/107 (13%), Positives = 41/107 (38%), Gaps = 11/107 (10%)

Query: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ---- 743
           P +    +   +  +    +  +      +++  L+   +QL  ++ +I   Q +     
Sbjct: 133 PALLVSPEDAQRSVRLAIYYGALNPARA-ERIDALKATLKQLAAVRAEIAAEQAELTTLL 191

Query: 744 --QIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
             Q  Q  + +    ++++ L QL  +        Q++L +L+  + 
Sbjct: 192 SEQRAQQAKLAQLLEERKKTLAQLNSELS----ADQKKLEELRANES 234

Length = 420

>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: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           QQ+  L +QQQQ Q Q + ++ Q Q  +  +Q + QL +       L+QQQ++  +++Q 
Sbjct: 12  QQELLLLKQQQQIQKQLLIAEFQKQHENLTRQHEAQLQE------HLKQQQELLAMKRQQ 65

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQL 780
              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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLS-QLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           Q   Q+  + + +  +Q+ +++  +LQ Q    ++++ QQ+L QL+Q++ +  ++    Q
Sbjct: 318 QQRLQRALERRLRLAKQRLERLSQRLQQQNPQRRIERAQQRLEQLEQRLRRAMRR----Q 373

Query: 748 LQQQSMPQLQQQQQLPQLQQQ 768
           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: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           P + +QQ    QQ       Q   +  QH Q   L Q  QQ  Q Q   P   QQ   PQ
Sbjct: 59  PVLPAQQPVVPQQPLMPVPGQHSMTPTQHHQ-PNLPQPAQQPFQPQPLQPPQPQQPMQPQ 117

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQM 774
                +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|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106)

 Score = 40.4 bits (94), Expect = 0.004
 Identities = 18/73 (24%), Positives = 22/73 (30%)

Query: 707 HQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQ 766
           H                Q   Q P +Q    Q QQQ Q   +Q    P  Q   Q P   
Sbjct: 193 HGHRHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQT 252

Query: 767 QQQQLPQMQQQQQ 779
           +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|225657 COG3115, ZipA, Cell division protein [Cell division and chromosome partitioning]

 Score = 39.9 bits (93), Expect = 0.004
 Identities = 20/102 (19%), Positives = 31/102 (30%), Gaps = 1/102 (0%)

Query: 694 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ-S 752
           Q  Q  +  +Q    Q Q +    Q+     Q  Q+          Q      Q  ++  
Sbjct: 74  QFTQEHEAARQSPQHQYQPEYASAQIKIPVPQPPQISDPPAHPQPTQPALDQEQPPEEAR 133

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
            P L Q+   PQ           Q  Q    +QQ Q  +  +
Sbjct: 134 QPVLPQEAPAPQPVHSAAPQPAVQTVQPAVPEQQVQPEEVVE 175

Length = 324

>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: 701 QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQ 760
             Q+  +     + +  Q +Q Q Q      +     +  Q   +P     S  +  + +
Sbjct: 106 PNQEPAYYMQNHRSEPIQPTQPQYQSPTQTNVASMTIEETQSPNVPIEGINSSSEQLRVE 165

Query: 761 QLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGP 808
                 +       + +     ++ Q + ++ Q    +     YV  P
Sbjct: 166 LAELAAEIYSDASHRVELAKNFMEPQAE-TEAQPEATTNFIMLYVVAP 212

Length = 332

>gnl|CDD|227671 COG5380, LimK, Lipase chaperone [Posttranslational modification, protein turnover, chaperones]

 Score = 40.0 bits (93), Expect = 0.004
 Identities = 22/110 (20%), Positives = 46/110 (41%), Gaps = 9/110 (8%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           +      +++Q+     +    + Q+     Q+Q+      Q +PQLQQ  Q P   + +
Sbjct: 154 EDYGLSDEEKQRAWQALLLDLPKVQEERIFIQRQE---ATAQLLPQLQQAGQGPTQIRLA 210

Query: 753 MPQL---QQQQQLPQLQQQQQLPQMQQQ---QQLPQLQQQQQLSQPQQMV 796
              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 = 40.2 bits (94), Expect = 0.004
 Identities = 18/123 (14%), Positives = 53/123 (43%), Gaps = 13/123 (10%)

Query: 685 VFKPQISSQQQQQLQQQQQQQQHQQMQSQLQ-------HQQLSQLQQQQQQLPQLQQQIP 737
           + K + S + +Q   +Q +Q+   ++ + L+        ++      ++++L QL++Q+ 
Sbjct: 15  IPKCEDSIKGEQARYKQIEQEDQSRILNTLEEFEKEANEKRAQYRSAKKKELSQLEEQLI 74

Query: 738 QLQ------QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
             +        +QI Q +     ++ + + L  L  ++       +++L +L ++ Q   
Sbjct: 75  NQKKEQKNLFNEQIKQFELALQDEIAKLEALELLNLEKDKELELLEKELDELSKELQKQL 134

Query: 792 PQQ 794
              
Sbjct: 135 QNT 137

Length = 438

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	834
PF11265	226	Med25_VWA: Mediator complex subunit 25 von Willebr	100.0
cd01480	186	vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI	99.16
cd01482	164	vWA_collagen_alphaI-XII-like Collagen: The extrace	99.12
cd01469	177	vWA_integrins_alpha_subunit Integrins are a class	99.08
PF13519	172	VWA_2: von Willebrand factor type A domain; PDB: 3	99.03
cd01481	165	vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(V	99.03
cd01450	161	vWFA_subfamily_ECM Von Willebrand factor type A (v	99.03
cd01472	164	vWA_collagen von Willebrand factor (vWF) type A do	99.02
cd01473	192	vWA_CTRP CTRP for CS protein-TRAP-related protein:	98.9
cd01475	224	vWA_Matrilin VWA_Matrilin: In cartilaginous plate,	98.85
cd01474	185	vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxi	98.83
cd01453	183	vWA_transcription_factor_IIH_type Transcription fa	98.81
cd01476	163	VWA_integrin_invertebrates VWA_integrin (invertebr	98.79
cd01477	193	vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand	98.75
PF00092	178	VWA: von Willebrand factor type A domain; InterPro	98.68
cd01471	186	vWA_micronemal_protein Micronemal proteins: The To	98.62
cd00198	161	vWFA Von Willebrand factor type A (vWA) domain was	98.6
smart00187	423	INB Integrin beta subunits (N-terminal portion of	98.5
cd01456	206	vWA_ywmD_type VWA ywmD type:Von Willebrand factor	98.44
cd01467	180	vWA_BatA_type VWA BatA type: Von Willebrand factor	98.41
smart00327	177	VWA von Willebrand factor (vWF) type A domain. VWA	98.41
cd01470	198	vWA_complement_factors Complement factors B and C2	98.37
cd01452	187	VWA_26S_proteasome_subunit 26S proteasome plays a	98.35
PTZ00441	576	sporozoite surface protein 2 (SSP2); Provisional	98.31
PRK13685	326	hypothetical protein; Provisional	98.28
PF13768	155	VWA_3: von Willebrand factor type A domain	98.27
cd01451	178	vWA_Magnesium_chelatase Magnesium chelatase: Mg-ch	98.25
cd01463	190	vWA_VGCC_like VWA Voltage gated Calcium channel li	98.23
cd01465	170	vWA_subgroup VWA subgroup: Von Willebrand factor t	98.2
COG1240	261	ChlD Mg-chelatase subunit ChlD [Coenzyme metabolis	98.19
TIGR03436	296	acidobact_VWFA VWFA-related Acidobacterial domain.	98.17
cd01454	174	vWA_norD_type norD type: Denitrifying bacteria con	98.14
cd01461	171	vWA_interalpha_trypsin_inhibitor vWA_interalpha tr	98.09
cd01466	155	vWA_C3HC4_type VWA C3HC4-type: Von Willebrand fact	98.09
cd01464	176	vWA_subfamily VWA subfamily: Von Willebrand factor	98.05
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	97.99
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	97.98
cd01458	218	vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heter	97.91
cd01462	152	VWA_YIEM_type VWA YIEM type: Von Willebrand factor	97.82
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	97.74
PF00362	426	Integrin_beta: Integrin, beta chain; InterPro: IPR	97.74
cd01460	266	vWA_midasin VWA_Midasin: Midasin is a member of th	97.58
TIGR00868	863	hCaCC calcium-activated chloride channel protein 1	97.57
TIGR03788	596	marine_srt_targ marine proteobacterial sortase tar	97.46
cd01457	199	vWA_ORF176_type VWA ORF176 type: Von Willebrand fa	97.31
PF03731	224	Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; Inte	97.24
cd01455	191	vWA_F11C1-5a_type Von Willebrand factor type A (vW	97.07
PF04056	193	Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like pro	96.88
PF04811	243	Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: I	96.67
KOG3598	2220	consensus Thyroid hormone receptor-associated prot	96.66
KOG3598	2220	consensus Thyroid hormone receptor-associated prot	96.14
COG4245	207	TerY Uncharacterized protein encoded in toxicity p	96.04
TIGR00578	584	ku70 ATP-dependent DNA helicase ii, 70 kDa subunit	95.39
cd01468	239	trunk_domain trunk domain. COPII-coated vesicles c	94.82
cd01479	244	Sec24-like Sec24-like: Protein and membrane traffi	94.79
PF06707	205	DUF1194: Protein of unknown function (DUF1194); In	94.3
PF11498	468	Activator_LAG-3: Transcriptional activator LAG-3;	93.82
PF05762	222	VWA_CoxE: VWA domain containing CoxE-like protein;	93.54
PRK10997	487	yieM hypothetical protein; Provisional	92.89
KOG2807	378	consensus RNA polymerase II transcription initiati	91.89
COG5148	243	RPN10 26S proteasome regulatory complex, subunit R	91.49
PF11235	168	Med25_SD1: Mediator complex subunit 25 synapsin 1;	91.23
TIGR00627	279	tfb4 transcription factor tfb4. This family is bas	90.61
cd01478	267	Sec23-like Sec23-like: Protein and membrane traffi	88.8
KOG1226	783	consensus Integrin beta subunit (N-terminal portio	88.53
KOG1984	1007	consensus Vesicle coat complex COPII, subunit SFB3	88.08
KOG2884	259	consensus 26S proteasome regulatory complex, subun	87.88
PF03850	276	Tfb4: Transcription factor Tfb4; InterPro: IPR0046	86.8
PTZ00395	1560	Sec24-related protein; Provisional	86.0
PF10138	200	vWA-TerF-like: vWA found in TerF C terminus ; Inte	85.65
PF09967	126	DUF2201: VWA-like domain (DUF2201); InterPro: IPR0	83.9
PF11498	468	Activator_LAG-3: Transcriptional activator LAG-3;	82.8
PLN00162	761	transport protein sec23; Provisional	81.68

>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=2.3e-65  Score=526.10  Aligned_cols=210  Identities=43%  Similarity=0.699  Sum_probs=193.7

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCC--CCccEEEEEEeecCCCCcccceeeccCCCCHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTS--ASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIF   80 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~--~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~f   80 (834)
                      ++|||||||+||+||+||+.||+|||+|+||||++|+++|++++  ..+++||||+|++||||++++|++++||+|+++|
T Consensus        13 ~~~vVfvvEgTAalgpy~~~Lkt~Yl~P~le~f~~g~~~e~~~~~~~~~t~y~LVvf~t~d~~~~~~v~~~g~T~~~~~f   92 (226)
T PF11265_consen   13 QAQVVFVVEGTAALGPYWNTLKTNYLDPILEYFNGGPIAERDFGGDYSNTEYGLVVFNTADCYPEPIVQRSGPTSSPQKF   92 (226)
T ss_pred             cceEEEEEecchhhhhhHHHHHHHHHHHHHHHhcCCCcccccccccCCCceEEEEEEeccCCCcccceeccCCcCCHHHH
Confidence            58999999999999999999999999999999999999999974  3579999999999999999999999999999999


Q ss_pred             HHHhccCccCCCCCch-hhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           81 LHWLSTIPFAGGGFND-AAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~-~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      ++|||+|+|.|||+++ ++|+|||++||+|||+++..++.....+.+||||||||||||++|+..+            +.
T Consensus        93 l~~L~~I~f~GGG~e~~a~iaEGLa~AL~~fd~~~~~r~~~~~~~~~khcILI~nSpP~~~p~~~~------------~~  160 (226)
T PF11265_consen   93 LQWLDAIQFSGGGFESCAAIAEGLAEALQCFDDFKQMRQQQQQTDVQKHCILICNSPPYRLPVNEC------------PQ  160 (226)
T ss_pred             HHHHHccCcCCCCcccchhHHHHHHHHHHHhcchhhhccccCcccccceEEEEeCCCCccccccCC------------Cc
Confidence            9999999999999875 5599999999999999887777677788999999999999999997321            11


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccCCchhHHHHHHHhcCCCCC-CCCCCCCCCCCCeEEEeeccc
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRA-ADPPVDNSKNPHFLVLISENF  228 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrqlp~l~~Lfeka~~~~~~-~~~~~~~ak~p~hlVLLsg~~  228 (834)
                         + +..++|++|.++.||+|+||||||||+|+|++||||+++|.++ +++++||||||||||||||+|
T Consensus       161 ---~-~~~~~d~la~~~~~~~I~LSiisPrklP~l~~Lfeka~~~~~~~~~~~~~~ak~p~hlVLl~g~~  226 (226)
T PF11265_consen  161 ---Y-SGKTCDQLAVLISERNISLSIISPRKLPSLRSLFEKAKGNPRAAADPSKDYAKDPRHLVLLRGYF  226 (226)
T ss_pred             ---c-cCCCHHHHHHHHHhcCceEEEEcCccCHHHHHHHHhcCCCcccccccccccccCCCeEEEeecCC
Confidence               1 2258999999999999999999999999999999999999998 699999999999999999986

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 [].

>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=99.16  E-value=1.3e-09  Score=109.70  Aligned_cols=154  Identities=10%  Similarity=0.216  Sum_probs=111.5

Q ss_pred             CccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC---CCHH
Q 003284            3 EKQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT---KDVD   78 (834)
Q Consensus         3 ~~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT---sd~~   78 (834)
                      ..|||||||++++|+ ..|+.+| +++..+++.|...-  ..+......|+|||.|.+...      ..++|+   .|..
T Consensus         2 ~~dvv~vlD~S~Sm~~~~~~~~k-~~~~~~~~~l~~~~--~~~i~~~~~rvglv~fs~~~~------~~~~l~~~~~~~~   72 (186)
T cd01480           2 PVDITFVLDSSESVGLQNFDITK-NFVKRVAERFLKDY--YRKDPAGSWRVGVVQYSDQQE------VEAGFLRDIRNYT   72 (186)
T ss_pred             CeeEEEEEeCCCccchhhHHHHH-HHHHHHHHHHhhhh--ccCCCCCceEEEEEEecCCce------eeEecccccCCHH
Confidence            369999999999999 7888776 66778888885420  001112358999999997643      345565   7899


Q ss_pred             HHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           79 IFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        79 ~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      .+++.|++|.+.|||   -++.+||..|++.+.+.       ......|++||++|..+.....                
T Consensus        73 ~l~~~i~~l~~~gg~---T~~~~AL~~a~~~l~~~-------~~~~~~~~iillTDG~~~~~~~----------------  126 (186)
T cd01480          73 SLKEAVDNLEYIGGG---TFTDCALKYATEQLLEG-------SHQKENKFLLVITDGHSDGSPD----------------  126 (186)
T ss_pred             HHHHHHHhCccCCCC---ccHHHHHHHHHHHHhcc-------CCCCCceEEEEEeCCCcCCCcc----------------
Confidence            999999999988776   57889999999877531       2245689999999887642221                


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccCC--chhHHHHHH
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPKQ--LPKLTAIYN  199 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq--lp~l~~Lfe  199 (834)
                              .+.+..++.+.++||.+++|....  ...|++|-+
T Consensus       127 --------~~~~~~~~~~~~~gi~i~~vgig~~~~~~L~~IA~  161 (186)
T cd01480         127 --------GGIEKAVNEADHLGIKIFFVAVGSQNEEPLSRIAC  161 (186)
T ss_pred             --------hhHHHHHHHHHHCCCEEEEEecCccchHHHHHHHc
Confidence                    145678888999999999999875  233444443

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=99.12  E-value=4e-09  Score=103.72  Aligned_cols=162  Identities=14%  Similarity=0.263  Sum_probs=111.7

Q ss_pred             ccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            4 KQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         4 ~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      +|||||||++++|+ ..|+.+| +++.-+++.|.-        +....|+|||+|.+...   .. -.+.-+.+...++.
T Consensus         1 ~Dv~~vlD~S~Sm~~~~~~~~k-~~~~~l~~~~~~--------~~~~~rvgli~fs~~~~---~~-~~l~~~~~~~~l~~   67 (164)
T cd01482           1 ADIVFLVDGSWSIGRSNFNLVR-SFLSSVVEAFEI--------GPDGVQVGLVQYSDDPR---TE-FDLNAYTSKEDVLA   67 (164)
T ss_pred             CCEEEEEeCCCCcChhhHHHHH-HHHHHHHhheee--------CCCceEEEEEEECCCee---EE-EecCCCCCHHHHHH
Confidence            59999999999998 4787776 457777777732        12468999999999742   11 11223467889999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhh-cccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMM-FSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~-f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      .|+.|.+.||+   -.+.+||..|++. |...     .....+..|.+||++|..|.                       
T Consensus        68 ~l~~~~~~~g~---T~~~~aL~~a~~~~~~~~-----~~~r~~~~k~iillTDG~~~-----------------------  116 (164)
T cd01482          68 AIKNLPYKGGN---TRTGKALTHVREKNFTPD-----AGARPGVPKVVILITDGKSQ-----------------------  116 (164)
T ss_pred             HHHhCcCCCCC---ChHHHHHHHHHHHhcccc-----cCCCCCCCEEEEEEcCCCCC-----------------------
Confidence            99999998876   4688999888864 4321     11234567889999887653                       


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccCCchhHHHHHHHhcCCCCCCCCCCCCCCCCCeEEEeecc
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISEN  227 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPrqlp~l~~Lfeka~~~~~~~~~~~~~ak~p~hlVLLsg~  227 (834)
                           .|.+..|+.+.+.||.+++|.-.. ...+.|-+-|+..            +-.|+..+++|
T Consensus       117 -----~~~~~~a~~lk~~gi~i~~ig~g~-~~~~~L~~ia~~~------------~~~~~~~~~d~  164 (164)
T cd01482         117 -----DDVELPARVLRNLGVNVFAVGVKD-ADESELKMIASKP------------SETHVFNVADF  164 (164)
T ss_pred             -----chHHHHHHHHHHCCCEEEEEecCc-CCHHHHHHHhCCC------------chheEEEcCCC
Confidence                 145678899999999999998755 3344444433321            12488777664

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.

>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=99.08  E-value=6.7e-09  Score=103.91  Aligned_cols=164  Identities=11%  Similarity=0.164  Sum_probs=115.4

Q ss_pred             ccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccC--CCCHHHH
Q 003284            4 KQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGW--TKDVDIF   80 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gf--Tsd~~~f   80 (834)
                      .||+||||++++|++ .|+.+| .++.-+++.|.-+        ....|+|||.|.+...      ..+.|  ..+...+
T Consensus         1 ~Di~fvlD~S~S~~~~~f~~~k-~fi~~~i~~l~~~--------~~~~rvgvv~fs~~~~------~~~~l~~~~~~~~~   65 (177)
T cd01469           1 MDIVFVLDGSGSIYPDDFQKVK-NFLSTVMKKLDIG--------PTKTQFGLVQYSESFR------TEFTLNEYRTKEEP   65 (177)
T ss_pred             CcEEEEEeCCCCCCHHHHHHHH-HHHHHHHHHcCcC--------CCCcEEEEEEECCcee------EEEecCccCCHHHH
Confidence            499999999999997 888877 5688888888542        1358999999998732      22333  3466788


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      ++.++.+.+.||+   .++.+||..|+..+....    ...+....|.+|||+|...+.-.                   
T Consensus        66 ~~~i~~~~~~~g~---T~~~~AL~~a~~~l~~~~----~g~R~~~~kv~illTDG~~~~~~-------------------  119 (177)
T cd01469          66 LSLVKHISQLLGL---TNTATAIQYVVTELFSES----NGARKDATKVLVVITDGESHDDP-------------------  119 (177)
T ss_pred             HHHHHhCccCCCC---ccHHHHHHHHHHHhcCcc----cCCCCCCCeEEEEEeCCCCCCcc-------------------
Confidence            9999999988876   888999999997642111    11234578999999988876322                   


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEeccCCch----hHHHHHHHhcCCCCCCCCCCCCCCCCCeEEEeecc
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVICPKQLP----KLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISEN  227 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIsPrqlp----~l~~Lfeka~~~~~~~~~~~~~ak~p~hlVLLsg~  227 (834)
                             +.+.+++.+.+.||.+++|.--...    .+++|.+-|....            -.|+..++.|
T Consensus       120 -------~~~~~~~~~k~~gv~v~~Vgvg~~~~~~~~~~~L~~ias~p~------------~~h~f~~~~~  171 (177)
T cd01469         120 -------LLKDVIPQAEREGIIRYAIGVGGHFQRENSREELKTIASKPP------------EEHFFNVTDF  171 (177)
T ss_pred             -------ccHHHHHHHHHCCcEEEEEEecccccccccHHHHHHHhcCCc------------HHhEEEecCH
Confidence                   1266788889999999999876531    2344444332110            1488888776

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.

>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A

Probab=99.03  E-value=2e-09  Score=103.20  Aligned_cols=144  Identities=17%  Similarity=0.220  Sum_probs=105.2

Q ss_pred             cEEEEEeccccchHh------HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHH
Q 003284            5 QLIVAVEGTAAMGPY------WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVD   78 (834)
Q Consensus         5 dvVFVID~Tasmg~y------i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~   78 (834)
                      |||||||.|++|..+      |+.+|.- +.-+++.+.            ..+++||.|.+..      -..++||.|..
T Consensus         1 dvv~v~D~SgSM~~~~~~~~~~~~~~~~-~~~~~~~~~------------~~~v~l~~f~~~~------~~~~~~t~~~~   61 (172)
T PF13519_consen    1 DVVFVLDNSGSMNGYDGNRTRIDQAKDA-LNELLANLP------------GDRVGLVSFSDSS------RTLSPLTSDKD   61 (172)
T ss_dssp             EEEEEEE-SGGGGTTTSSS-HHHHHHHH-HHHHHHHHT------------TSEEEEEEESTSC------EEEEEEESSHH
T ss_pred             CEEEEEECCcccCCCCCCCcHHHHHHHH-HHHHHHHCC------------CCEEEEEEecccc------cccccccccHH
Confidence            899999999999999      7777644 666666652            2399999999853      23567899999


Q ss_pred             HHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           79 IFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        79 ~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      .|..+|+++...+.......+.+||.+|+++|++.+         ...|++|||+|..|.                    
T Consensus        62 ~~~~~l~~~~~~~~~~~~t~~~~al~~a~~~~~~~~---------~~~~~iv~iTDG~~~--------------------  112 (172)
T PF13519_consen   62 ELKNALNKLSPQGMPGGGTNLYDALQEAAKMLASSD---------NRRRAIVLITDGEDN--------------------  112 (172)
T ss_dssp             HHHHHHHTHHHHG--SSS--HHHHHHHHHHHHHC-S---------SEEEEEEEEES-TTH--------------------
T ss_pred             HHHHHhhcccccccCccCCcHHHHHHHHHHHHHhCC---------CCceEEEEecCCCCC--------------------
Confidence            999999999976555556889999999999997532         357899999987443                    


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccCCc----hhHHHHHHHhcCC
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPKQL----PKLTAIYNAAKRN  204 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrql----p~l~~Lfeka~~~  204 (834)
                              .+...+++.+.+++|++.+|.-..-    ..|+.|.+..++.
T Consensus       113 --------~~~~~~~~~~~~~~i~i~~v~~~~~~~~~~~l~~la~~tgG~  154 (172)
T PF13519_consen  113 --------SSDIEAAKALKQQGITIYTVGIGSDSDANEFLQRLAEATGGR  154 (172)
T ss_dssp             --------CHHHHHHHHHHCTTEEEEEEEES-TT-EHHHHHHHHHHTEEE
T ss_pred             --------cchhHHHHHHHHcCCeEEEEEECCCccHHHHHHHHHHhcCCE
Confidence                    1234488889999999999977654    3477777766543

>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=99.03  E-value=1.7e-08  Score=100.52  Aligned_cols=149  Identities=15%  Similarity=0.290  Sum_probs=108.0

Q ss_pred             ccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            4 KQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         4 ~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      +||||+||++++++ ..|+.+| ++|..+++.|.-+        ...+|+|||.|.+... .+   -.+.-..|...++.
T Consensus         1 ~DivfllD~S~Si~~~~f~~~k-~fi~~lv~~f~i~--------~~~~rVgvv~ys~~~~-~~---~~l~~~~~~~~l~~   67 (165)
T cd01481           1 KDIVFLIDGSDNVGSGNFPAIR-DFIERIVQSLDVG--------PDKIRVAVVQFSDTPR-PE---FYLNTHSTKADVLG   67 (165)
T ss_pred             CCEEEEEeCCCCcCHHHHHHHH-HHHHHHHhhccCC--------CCCcEEEEEEecCCee-EE---EeccccCCHHHHHH
Confidence            69999999999999 8888887 7799999999532        2358999999987642 11   12334557899999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      .++.|++.||+.  ..+.+||..+.+ +|... .+  ......+.|..|||+|-..+                       
T Consensus        68 ~i~~i~~~~g~~--t~t~~AL~~~~~~~f~~~-~g--~R~~~~~~kv~vviTdG~s~-----------------------  119 (165)
T cd01481          68 AVRRLRLRGGSQ--LNTGSALDYVVKNLFTKS-AG--SRIEEGVPQFLVLITGGKSQ-----------------------  119 (165)
T ss_pred             HHHhcccCCCCc--ccHHHHHHHHHHhhcCcc-cc--CCccCCCCeEEEEEeCCCCc-----------------------
Confidence            999999998753  356788888775 55421 11  11134577899999977543                       


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccCCchhHHHHHH
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYN  199 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPrqlp~l~~Lfe  199 (834)
                           .|.+..|+.+.+.||.+++|--.. ....+|-+
T Consensus       120 -----d~~~~~a~~lr~~gv~i~~vG~~~-~~~~eL~~  151 (165)
T cd01481         120 -----DDVERPAVALKRAGIVPFAIGARN-ADLAELQQ  151 (165)
T ss_pred             -----chHHHHHHHHHHCCcEEEEEeCCc-CCHHHHHH
Confidence                 145678999999999999998874 23444444

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=99.03  E-value=1e-08  Score=97.69  Aligned_cols=149  Identities=15%  Similarity=0.269  Sum_probs=109.1

Q ss_pred             ccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCC--HHHH
Q 003284            4 KQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKD--VDIF   80 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd--~~~f   80 (834)
                      .||+||||+|++|.. +|+.++ ..+..+++.|....        ...+++||.|.+...      ..+.|+++  ..++
T Consensus         1 ~di~~llD~S~Sm~~~~~~~~~-~~~~~~~~~~~~~~--------~~~~~~li~f~~~~~------~~~~~~~~~~~~~~   65 (161)
T cd01450           1 LDIVFLLDGSESVGPENFEKVK-DFIEKLVEKLDIGP--------DKTRVGLVQYSDDVR------VEFSLNDYKSKDDL   65 (161)
T ss_pred             CcEEEEEeCCCCcCHHHHHHHH-HHHHHHHHheeeCC--------CceEEEEEEEcCCce------EEEECCCCCCHHHH
Confidence            489999999999999 666665 44777777775421        367999999998522      23455544  8999


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      .++|+++.+.+|  +...+.|||..|++.+.....     .+....|++|||++..++.-.                   
T Consensus        66 ~~~i~~~~~~~~--~~t~~~~al~~a~~~~~~~~~-----~~~~~~~~iiliTDG~~~~~~-------------------  119 (161)
T cd01450          66 LKAVKNLKYLGG--GGTNTGKALQYALEQLFSESN-----ARENVPKVIIVLTDGRSDDGG-------------------  119 (161)
T ss_pred             HHHHHhcccCCC--CCccHHHHHHHHHHHhccccc-----ccCCCCeEEEEECCCCCCCCc-------------------
Confidence            999999988776  457889999999988764221     234567899999998775321                   


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEeccCC--chhHHHHHHH
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVICPKQ--LPKLTAIYNA  200 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq--lp~l~~Lfek  200 (834)
                             +.+.+++.+.+++|.+++|.-..  ...|++|-.+
T Consensus       120 -------~~~~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~~  154 (161)
T cd01450         120 -------DPKEAAAKLKDEGIKVFVVGVGPADEEELREIASC  154 (161)
T ss_pred             -------chHHHHHHHHHCCCEEEEEeccccCHHHHHHHhCC
Confidence                   35788999999999999998763  3444444443

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

>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins

Probab=99.02  E-value=1.3e-08  Score=99.66  Aligned_cols=151  Identities=13%  Similarity=0.248  Sum_probs=105.6

Q ss_pred             ccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            4 KQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      +|||||||.+++|.. .|+.+| +.+.-+++.|...        ....++|||+|.+...    .+..+....|...++.
T Consensus         1 ~Dvv~vlD~SgSm~~~~~~~~k-~~~~~~~~~l~~~--------~~~~~~giv~Fs~~~~----~~~~~~~~~~~~~~~~   67 (164)
T cd01472           1 ADIVFLVDGSESIGLSNFNLVK-DFVKRVVERLDIG--------PDGVRVGVVQYSDDPR----TEFYLNTYRSKDDVLE   67 (164)
T ss_pred             CCEEEEEeCCCCCCHHHHHHHH-HHHHHHHhhcccC--------CCCeEEEEEEEcCcee----EEEecCCCCCHHHHHH
Confidence            599999999999999 777776 4577777777421        1357999999997643    1122222488999999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQA  162 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~  162 (834)
                      .|+++.+.||+   -++.+||..|++.+.+..    ........|++|||+|.-+.    .                   
T Consensus        68 ~l~~l~~~~g~---T~~~~al~~a~~~l~~~~----~~~~~~~~~~iiliTDG~~~----~-------------------  117 (164)
T cd01472          68 AVKNLRYIGGG---TNTGKALKYVRENLFTEA----SGSREGVPKVLVVITDGKSQ----D-------------------  117 (164)
T ss_pred             HHHhCcCCCCC---chHHHHHHHHHHHhCCcc----cCCCCCCCEEEEEEcCCCCC----c-------------------
Confidence            99999987655   478899999998775321    11234467899999988431    0                   


Q ss_pred             hccCCCHHHHHHHHhhcCcEEEEeccCC--chhHHHHHHHhc
Q 003284          163 ESRLSDAETVAKSFVQCSVSLSVICPKQ--LPKLTAIYNAAK  202 (834)
Q Consensus       163 ~~~l~d~e~lA~~~~e~~I~LSvIsPrq--lp~l~~Lfeka~  202 (834)
                           +.+..+..+.+++|.++.|.-..  ...|+.|.+..+
T Consensus       118 -----~~~~~~~~l~~~gv~i~~ig~g~~~~~~L~~ia~~~~  154 (164)
T cd01472         118 -----DVEEPAVELKQAGIEVFAVGVKNADEEELKQIASDPK  154 (164)
T ss_pred             -----hHHHHHHHHHHCCCEEEEEECCcCCHHHHHHHHCCCc
Confidence                 12345566788999999997653  456666655444

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.

>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=98.90  E-value=8e-08  Score=98.06  Aligned_cols=154  Identities=17%  Similarity=0.285  Sum_probs=109.5

Q ss_pred             ccEEEEEeccccchHh-HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC----CHH
Q 003284            4 KQLIVAVEGTAAMGPY-WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----DVD   78 (834)
Q Consensus         4 ~dvVFVID~Tasmg~y-i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs----d~~   78 (834)
                      .||||+||++.+|+.. |+.-..+++.-+++.|.-+        ...+|+|||.|.+...      ..++|+.    |-.
T Consensus         1 ~Di~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~--------~~~~rvgvv~fs~~~~------~~~~~~~~~~~~~~   66 (192)
T cd01473           1 YDLTLILDESASIGYSNWRKDVIPFTEKIINNLNIS--------KDKVHVGILLFAEKNR------DVVPFSDEERYDKN   66 (192)
T ss_pred             CcEEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccC--------CCccEEEEEEecCCce------eEEecCcccccCHH
Confidence            3999999999999976 8864456788889988543        2368999999998753      3344543    456


Q ss_pred             HHHHHhccCc---cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccc
Q 003284           79 IFLHWLSTIP---FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQN  155 (834)
Q Consensus        79 ~fl~~Ld~I~---f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~  155 (834)
                      .++..++.|.   +.||   .-.+.+||..|++.|....     ....++.|..|||+|...+..-.             
T Consensus        67 ~l~~~i~~l~~~~~~~g---~T~~~~AL~~a~~~~~~~~-----~~r~~~~kv~IllTDG~s~~~~~-------------  125 (192)
T cd01473          67 ELLKKINDLKNSYRSGG---ETYIVEALKYGLKNYTKHG-----NRRKDAPKVTMLFTDGNDTSASK-------------  125 (192)
T ss_pred             HHHHHHHHHHhccCCCC---cCcHHHHHHHHHHHhccCC-----CCcccCCeEEEEEecCCCCCcch-------------
Confidence            7778777774   3344   3457888888888764311     12234689999999987763210             


Q ss_pred             cchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCCchhHHHHHHHhcCC
Q 003284          156 ENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRN  204 (834)
Q Consensus       156 e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrqlp~l~~Lfeka~~~  204 (834)
                                 .+....|+.+.++||.+++|---. ....+|..-|+-+
T Consensus       126 -----------~~~~~~a~~lk~~gV~i~~vGiG~-~~~~el~~ia~~~  162 (192)
T cd01473         126 -----------KELQDISLLYKEENVKLLVVGVGA-ASENKLKLLAGCD  162 (192)
T ss_pred             -----------hhHHHHHHHHHHCCCEEEEEEecc-ccHHHHHHhcCCC
Confidence                       135678999999999999999886 4566777766543

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.

>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity

Probab=98.85  E-value=7.2e-08  Score=99.96  Aligned_cols=150  Identities=15%  Similarity=0.213  Sum_probs=104.5

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccC--CCCHHH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGW--TKDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gf--Tsd~~~   79 (834)
                      ..|||||||++++|+. .|+.+| +++.-+++.|.-+        ....|+|||.|.+-.-      ..++|  ..|...
T Consensus         2 ~~DlvfllD~S~Sm~~~~~~~~k-~f~~~l~~~l~~~--------~~~~rvglv~fs~~~~------~~~~l~~~~~~~~   66 (224)
T cd01475           2 PTDLVFLIDSSRSVRPENFELVK-QFLNQIIDSLDVG--------PDATRVGLVQYSSTVK------QEFPLGRFKSKAD   66 (224)
T ss_pred             CccEEEEEeCCCCCCHHHHHHHH-HHHHHHHHhcccC--------CCccEEEEEEecCcee------EEecccccCCHHH
Confidence            3799999999999996 688777 6688888888432        1358999999998732      23444  467889


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      +...|+.|.+.|||-   .+.+||..|+. .|....  .-++......|.+|||+|..+.                    
T Consensus        67 l~~~i~~i~~~~~~t---~tg~AL~~a~~~~~~~~~--g~r~~~~~~~kvvillTDG~s~--------------------  121 (224)
T cd01475          67 LKRAVRRMEYLETGT---MTGLAIQYAMNNAFSEAE--GARPGSERVPRVGIVVTDGRPQ--------------------  121 (224)
T ss_pred             HHHHHHhCcCCCCCC---hHHHHHHHHHHHhCChhc--CCCCCCCCCCeEEEEEcCCCCc--------------------
Confidence            999999999988763   45567777775 343211  1122334457899999887542                    


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccCCchhHHHHHHHh
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAA  201 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrqlp~l~~Lfeka  201 (834)
                              .+.+.+++.+.+.||.+++|.--.. ....|.+-|
T Consensus       122 --------~~~~~~a~~lk~~gv~i~~VgvG~~-~~~~L~~ia  155 (224)
T cd01475         122 --------DDVSEVAAKARALGIEMFAVGVGRA-DEEELREIA  155 (224)
T ss_pred             --------ccHHHHHHHHHHCCcEEEEEeCCcC-CHHHHHHHh
Confidence                    1356788999999999999976653 234444433

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.

>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax

Probab=98.83  E-value=7.2e-08  Score=96.82  Aligned_cols=138  Identities=17%  Similarity=0.200  Sum_probs=95.5

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      ..|||||||++++|+..|..++ +++..+++.|..          ...|+|||.|.+...      ..++||++.+.+.+
T Consensus         4 ~~Dvv~llD~SgSm~~~~~~~~-~~~~~l~~~~~~----------~~~rvglv~Fs~~~~------~~~~l~~~~~~~~~   66 (185)
T cd01474           4 HFDLYFVLDKSGSVAANWIEIY-DFVEQLVDRFNS----------PGLRFSFITFSTRAT------KILPLTDDSSAIIK   66 (185)
T ss_pred             ceeEEEEEeCcCchhhhHHHHH-HHHHHHHHHcCC----------CCcEEEEEEecCCce------EEEeccccHHHHHH
Confidence            4799999999999999887765 667778888742          237999999997632      46788888776666


Q ss_pred             HhccCcc--CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           83 WLSTIPF--AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        83 ~Ld~I~f--~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      .|+.|..  .||   .-++.+||..|++.+.....     ......|++|||+|-.++.-..                  
T Consensus        67 ~l~~l~~~~~~g---~T~~~~aL~~a~~~l~~~~~-----~~r~~~~~villTDG~~~~~~~------------------  120 (185)
T cd01474          67 GLEVLKKVTPSG---QTYIHEGLENANEQIFNRNG-----GGRETVSVIIALTDGQLLLNGH------------------  120 (185)
T ss_pred             HHHHHhccCCCC---CCcHHHHHHHHHHHHHhhcc-----CCCCCCeEEEEEcCCCcCCCCC------------------
Confidence            6544432  233   36788999999865531111     1112238999999887742110                  


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                            .++...|+.+.+.||.++.|.-.
T Consensus       121 ------~~~~~~a~~l~~~gv~i~~vgv~  143 (185)
T cd01474         121 ------KYPEHEAKLSRKLGAIVYCVGVT  143 (185)
T ss_pred             ------cchHHHHHHHHHcCCEEEEEeec
Confidence                  13456678888999999999863

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.

>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=98.81  E-value=1.8e-07  Score=94.77  Aligned_cols=150  Identities=17%  Similarity=0.239  Sum_probs=102.6

Q ss_pred             ccEEEEEeccccch------HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCH
Q 003284            4 KQLIVAVEGTAAMG------PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDV   77 (834)
Q Consensus         4 ~dvVFVID~Tasmg------~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~   77 (834)
                      +|||||||.+.+|.      .-++.+|.. +..+++.+-..        ...-++|||+|++..+     ....++|.|.
T Consensus         4 r~ivi~lD~S~SM~a~D~~ptRl~~ak~~-~~~fi~~~~~~--------~~~~~vglv~f~~~~a-----~~~~PlT~D~   69 (183)
T cd01453           4 RHLIIVIDCSRSMEEQDLKPSRLAVVLKL-LELFIEEFFDQ--------NPISQLGIISIKNGRA-----EKLTDLTGNP   69 (183)
T ss_pred             eEEEEEEECcHHHhcCCCCchHHHHHHHH-HHHHHHHHhhc--------CccccEEEEEEcCCcc-----EEEECCCCCH
Confidence            69999999999998      466666644 45555444210        0235999999976644     2467889999


Q ss_pred             HHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCc-EEEEeecCCCCCCCCCcccCCcccccccc
Q 003284           78 DIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQR-HCILVAASNPHPLPTPVYRPQMQNLDQNE  156 (834)
Q Consensus        78 ~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qk-hCILIa~SpP~~lp~pv~~p~~~~~~~~e  156 (834)
                      ..|+..|+.+...+|   ..++.+||..|+.+|....        ....| ++||+++-.      .+            
T Consensus        70 ~~~~~~L~~~~~~~G---~t~l~~aL~~A~~~l~~~~--------~~~~~~iiil~sd~~------~~------------  120 (183)
T cd01453          70 RKHIQALKTARECSG---EPSLQNGLEMALESLKHMP--------SHGSREVLIIFSSLS------TC------------  120 (183)
T ss_pred             HHHHHHhhcccCCCC---chhHHHHHHHHHHHHhcCC--------ccCceEEEEEEcCCC------cC------------
Confidence            999999998722222   3689999999999985321        11234 445554310      00            


Q ss_pred             chhhhhhccCCCHHHHHHHHhhcCcEEEEeccC-CchhHHHHHHHhcCC
Q 003284          157 NNEAQAESRLSDAETVAKSFVQCSVSLSVICPK-QLPKLTAIYNAAKRN  204 (834)
Q Consensus       157 ~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr-qlp~l~~Lfeka~~~  204 (834)
                              ...+.+.+++.+++.+|.+++|.-- ..+.|++|-++.++.
T Consensus       121 --------~~~~~~~~~~~l~~~~I~v~~IgiG~~~~~L~~ia~~tgG~  161 (183)
T cd01453         121 --------DPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKATNGT  161 (183)
T ss_pred             --------ChhhHHHHHHHHHHcCcEEEEEEechHHHHHHHHHHHhCCe
Confidence                    0013467899999999999999876 356799999988765

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.

>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=98.79  E-value=3e-07  Score=89.55  Aligned_cols=152  Identities=13%  Similarity=0.231  Sum_probs=104.5

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHHH
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHW   83 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~~   83 (834)
                      .|||||||++++|...|+..| +++.-+++.|..+        ....|+|||.|.+...  ....-.+.++.+.+.++..
T Consensus         1 ldv~~llD~S~Sm~~~~~~~~-~~~~~~~~~l~~~--------~~~~~v~lv~f~~~~~--~~~~~~l~~~~~~~~l~~~   69 (163)
T cd01476           1 LDLLFVLDSSGSVRGKFEKYK-KYIERIVEGLEIG--------PTATRVALITYSGRGR--QRVRFNLPKHNDGEELLEK   69 (163)
T ss_pred             CCEEEEEeCCcchhhhHHHHH-HHHHHHHHhcCCC--------CCCcEEEEEEEcCCCc--eEEEecCCCCCCHHHHHHH
Confidence            489999999999999887665 6677888877432        1358999999987521  1222234556788999999


Q ss_pred             hccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhhh
Q 003284           84 LSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAE  163 (834)
Q Consensus        84 Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~~  163 (834)
                      ++.|...||+   .++.+||..|..++....  .   ......|.+||++|-.+..                        
T Consensus        70 i~~l~~~gg~---T~l~~aL~~a~~~l~~~~--~---~r~~~~~~villTDG~~~~------------------------  117 (163)
T cd01476          70 VDNLRFIGGT---TATGAAIEVALQQLDPSE--G---RREGIPKVVVVLTDGRSHD------------------------  117 (163)
T ss_pred             HHhCccCCCC---ccHHHHHHHHHHHhcccc--C---CCCCCCeEEEEECCCCCCC------------------------
Confidence            9999876654   578899999998774211  1   1123458889998754320                        


Q ss_pred             ccCCCHHHHHHHHhh-cCcEEEEeccCCc--hhHHHHHHHhc
Q 003284          164 SRLSDAETVAKSFVQ-CSVSLSVICPKQL--PKLTAIYNAAK  202 (834)
Q Consensus       164 ~~l~d~e~lA~~~~e-~~I~LSvIsPrql--p~l~~Lfeka~  202 (834)
                          ++...++.+.+ .+|+++.|.-..-  ..++.|-+-++
T Consensus       118 ----~~~~~~~~l~~~~~v~v~~vg~g~~~~~~~~~L~~ia~  155 (163)
T cd01476         118 ----DPEKQARILRAVPNIETFAVGTGDPGTVDTEELHSITG  155 (163)
T ss_pred             ----chHHHHHHHhhcCCCEEEEEECCCccccCHHHHHHHhC
Confidence                23456777777 9999999988664  44555554443

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.

>cd01477 vWA_F09G8-8_type VWA F09G8

Probab=98.75  E-value=1.8e-07  Score=95.82  Aligned_cols=159  Identities=11%  Similarity=0.163  Sum_probs=100.1

Q ss_pred             CccEEEEEeccccchHh-HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHH
Q 003284            3 EKQLIVAVEGTAAMGPY-WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y-i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~   79 (834)
                      ..|||||||++.+|++. |+.+|.. |..++..|..+..  .......+|+|||+|.+..-      ..|.++  .+...
T Consensus        19 ~~DivfvlD~S~Sm~~~~f~~~k~f-i~~~~~~~~~~~~--~~~~~~~~rVGlV~fs~~a~------~~~~L~d~~~~~~   89 (193)
T cd01477          19 WLDIVFVVDNSKGMTQGGLWQVRAT-ISSLFGSSSQIGT--DYDDPRSTRVGLVTYNSNAT------VVADLNDLQSFDD   89 (193)
T ss_pred             eeeEEEEEeCCCCcchhhHHHHHHH-HHHHHhhcccccc--ccCCCCCcEEEEEEccCceE------EEEecccccCHHH
Confidence            37999999999999854 6666643 5566666642100  00011358999999998743      223333  36678


Q ss_pred             HHHHhcc-C-ccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccc
Q 003284           80 FLHWLST-I-PFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNEN  157 (834)
Q Consensus        80 fl~~Ld~-I-~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~  157 (834)
                      +++.|+. + ....||  .-.+..||..|+++|....    +..+..+.|++|||++-.-..                  
T Consensus        90 ~~~ai~~~~~~~~~~g--gT~ig~aL~~A~~~l~~~~----~~~R~~v~kvvIllTDg~~~~------------------  145 (193)
T cd01477          90 LYSQIQGSLTDVSSTN--ASYLDTGLQAAEQMLAAGK----RTSRENYKKVVIVFASDYNDE------------------  145 (193)
T ss_pred             HHHHHHHHhhccccCC--cchHHHHHHHHHHHHHhhh----ccccCCCCeEEEEEecCccCC------------------
Confidence            8887774 2 222222  2467888999999886321    122345789999998641110                  


Q ss_pred             hhhhhhccCCCHHHHHHHHhhcCcEEEEeccCCc---hhHHHHHHHh
Q 003284          158 NEAQAESRLSDAETVAKSFVQCSVSLSVICPKQL---PKLTAIYNAA  201 (834)
Q Consensus       158 ~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrql---p~l~~Lfeka  201 (834)
                            .. .|++.+|+.+.+.||.++.|.--.-   ..+.+|-+-|
T Consensus       146 ------~~-~~~~~~a~~l~~~GI~i~tVGiG~~~d~~~~~~L~~ia  185 (193)
T cd01477         146 ------GS-NDPRPIAARLKSTGIAIITVAFTQDESSNLLDKLGKIA  185 (193)
T ss_pred             ------CC-CCHHHHHHHHHHCCCEEEEEEeCCCCCHHHHHHHHHhc
Confidence                  00 2567889999999999999976652   2355555433

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=98.68  E-value=4e-07  Score=88.47  Aligned_cols=148  Identities=18%  Similarity=0.265  Sum_probs=103.6

Q ss_pred             cEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHHHH
Q 003284            5 QLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIFL   81 (834)
Q Consensus         5 dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~fl   81 (834)
                      |||||||.+++|+. .|+.+| .+|..+++.|..        .....|++||.|.+..-      ..+.|+  .+..+++
T Consensus         1 DivflvD~S~sm~~~~~~~~~-~~v~~~i~~~~~--------~~~~~rv~iv~f~~~~~------~~~~~~~~~~~~~~~   65 (178)
T PF00092_consen    1 DIVFLVDTSGSMSGDNFEKAK-QFVKSIISRLSI--------SNNGTRVGIVTFSDSAR------VLFSLTDYQSKNDLL   65 (178)
T ss_dssp             EEEEEEE-STTSCHHHHHHHH-HHHHHHHHHSTB--------STTSEEEEEEEESSSEE------EEEETTSHSSHHHHH
T ss_pred             CEEEEEeCCCCCchHHHHHHH-HHHHHHHHhhhc--------cccccccceeeeecccc------ccccccccccccccc
Confidence            89999999999997 788866 668999998842        22468999999998844      334443  4688999


Q ss_pred             HHh-ccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           82 HWL-STIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        82 ~~L-d~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      ..+ +.+.+.||+-.   +++||..|++.|....    ...+....|.+|||++..++.-+.                  
T Consensus        66 ~~i~~~~~~~~g~t~---~~~aL~~a~~~l~~~~----~~~r~~~~~~iiliTDG~~~~~~~------------------  120 (178)
T PF00092_consen   66 NAINDSIPSSGGGTN---LGAALKFAREQLFSSN----NGGRPNSPKVIILITDGNSNDSDS------------------  120 (178)
T ss_dssp             HHHHTTGGCCBSSB----HHHHHHHHHHHTTSGG----GTTGTTSEEEEEEEESSSSSSHSG------------------
T ss_pred             ccccccccccchhhh---HHHHHhhhhhcccccc----cccccccccceEEEEeecccCCcc------------------
Confidence            988 88887776533   8889999998886421    112235678899999998864331                  


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEecc--CCchhHHHHHH
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVICP--KQLPKLTAIYN  199 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIsP--rqlp~l~~Lfe  199 (834)
                             ..+..++...+.+|.+..|..  .....|++|..
T Consensus       121 -------~~~~~~~~~~~~~i~~~~ig~~~~~~~~l~~la~  154 (178)
T PF00092_consen  121 -------PSEEAANLKKSNGIKVIAIGIDNADNEELRELAS  154 (178)
T ss_dssp             -------HHHHHHHHHHHCTEEEEEEEESCCHHHHHHHHSH
T ss_pred             -------hHHHHHHHHHhcCcEEEEEecCcCCHHHHHHHhC
Confidence                   123333333336999999998  23466666654

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 ....

>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell

Probab=98.62  E-value=9.3e-07  Score=88.37  Aligned_cols=141  Identities=17%  Similarity=0.267  Sum_probs=91.8

Q ss_pred             ccEEEEEeccccchHh--HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCccccee-eccCCCCHHHH
Q 003284            4 KQLIVAVEGTAAMGPY--WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQ-RSGWTKDVDIF   80 (834)
Q Consensus         4 ~dvVFVID~Tasmg~y--i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~-~~gfTsd~~~f   80 (834)
                      .|||||||++++|+..  |+.+| .++.-+++.|.-.        ....++|||+|.+..-   ..+. ...++.+...+
T Consensus         1 ~Dv~~vlD~SgSm~~~~~~~~~k-~~~~~~~~~~~~~--------~~~~~vglv~Fs~~~~---~~~~l~~~~~~~~~~~   68 (186)
T cd01471           1 LDLYLLVDGSGSIGYSNWVTHVV-PFLHTFVQNLNIS--------PDEINLYLVTFSTNAK---ELIRLSSPNSTNKDLA   68 (186)
T ss_pred             CcEEEEEeCCCCccchhhHHHHH-HHHHHHHHhcccC--------CCceEEEEEEecCCce---EEEECCCccccchHHH
Confidence            4999999999999955  55555 5577777777421        1357999999987632   1111 11234456664


Q ss_pred             HHHhcc---CccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccc
Q 003284           81 LHWLST---IPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNEN  157 (834)
Q Consensus        81 l~~Ld~---I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~  157 (834)
                      +.+++.   +.+.|||   -.+++||..|.+.+...     +....+..|++||++|..+..-.                
T Consensus        69 ~~~i~~l~~~~~~~G~---T~l~~aL~~a~~~l~~~-----~~~r~~~~~~villTDG~~~~~~----------------  124 (186)
T cd01471          69 LNAIRALLSLYYPNGS---TNTTSALLVVEKHLFDT-----RGNRENAPQLVIIMTDGIPDSKF----------------  124 (186)
T ss_pred             HHHHHHHHhCcCCCCC---ccHHHHHHHHHHHhhcc-----CCCcccCceEEEEEccCCCCCCc----------------
Confidence            445544   4444544   46889999998776431     11234567899999998764221                


Q ss_pred             hhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          158 NEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       158 ~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                                .+...++.+.+++|.+++|.--.
T Consensus       125 ----------~~~~~a~~l~~~gv~v~~igiG~  147 (186)
T cd01471         125 ----------RTLKEARKLRERGVIIAVLGVGQ  147 (186)
T ss_pred             ----------chhHHHHHHHHCCCEEEEEEeeh
Confidence                      22346788899999999998753

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.

>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=98.60  E-value=1.9e-06  Score=80.48  Aligned_cols=138  Identities=17%  Similarity=0.232  Sum_probs=96.8

Q ss_pred             ccEEEEEeccccc-hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC--CHHHH
Q 003284            4 KQLIVAVEGTAAM-GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDIF   80 (834)
Q Consensus         4 ~dvVFVID~Tasm-g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs--d~~~f   80 (834)
                      .||+||||.|++| ..+|+.++ .++.-+++.+...        ....+++||.|.+...      ....|+.  +...+
T Consensus         1 ~~v~~viD~S~Sm~~~~~~~~~-~~~~~~~~~~~~~--------~~~~~i~v~~f~~~~~------~~~~~~~~~~~~~~   65 (161)
T cd00198           1 ADIVFLLDVSGSMGGEKLDKAK-EALKALVSSLSAS--------PPGDRVGLVTFGSNAR------VVLPLTTDTDKADL   65 (161)
T ss_pred             CcEEEEEeCCCCcCcchHHHHH-HHHHHHHHhcccC--------CCCcEEEEEEecCccc------eeecccccCCHHHH
Confidence            4899999999999 67777777 5577777777542        2357999999998422      3344444  77888


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      ...++.+..  +......+.+||..++..+.+..       .....|.+|+|+|..++.-.                   
T Consensus        66 ~~~~~~~~~--~~~~~t~~~~al~~~~~~~~~~~-------~~~~~~~lvvitDg~~~~~~-------------------  117 (161)
T cd00198          66 LEAIDALKK--GLGGGTNIGAALRLALELLKSAK-------RPNARRVIILLTDGEPNDGP-------------------  117 (161)
T ss_pred             HHHHHhccc--CCCCCccHHHHHHHHHHHhcccC-------CCCCceEEEEEeCCCCCCCc-------------------
Confidence            888888876  12233556678888888776421       23356888999987664322                   


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                            .+.+.+.+.+.+++|.+.+|.-..
T Consensus       118 ------~~~~~~~~~~~~~~v~v~~v~~g~  141 (161)
T cd00198         118 ------ELLAEAARELRKLGITVYTIGIGD  141 (161)
T ss_pred             ------chhHHHHHHHHHcCCEEEEEEcCC
Confidence                  134667888889999999987763

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.

>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region)

Probab=98.50  E-value=3.1e-06  Score=95.70  Aligned_cols=174  Identities=11%  Similarity=0.061  Sum_probs=122.2

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC--Cc-----------------
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS--YC-----------------   64 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~--~~-----------------   64 (834)
                      .||.|++|-|.+|+++++.||+. ...+++.+..-        .+++|+|+=.|-|.+-  |-                 
T Consensus       100 vDLYyLMDlS~SM~ddl~~lk~l-g~~L~~~m~~i--------t~n~rlGfGsFVDK~v~P~~~t~p~~l~~PC~~~~~~  170 (423)
T smart00187      100 VDLYYLMDLSYSMKDDLDNLKSL-GDDLAREMKGL--------TSNFRLGFGSFVDKTVSPFVSTRPEKLENPCPNYNLT  170 (423)
T ss_pred             cceEEEEeCCccHHHHHHHHHHH-HHHHHHHHHhc--------ccCceeeEEEeecCccCCcccCCHHHhcCCCcCCCCC
Confidence            69999999999999999999977 67777777541        3468999998888631  11                 


Q ss_pred             ---cc-ceeeccCCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCc-cCCcEEEEeecCCCCC
Q 003284           65 ---AC-LVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV-DGQRHCILVAASNPHP  139 (834)
Q Consensus        65 ---~~-lv~~~gfTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~-~~qkhCILIa~SpP~~  139 (834)
                         .| +-....+|+|.+.|.+.+++...+|+.|.||.=.+||--|..|-+..       -|. ...|..|+++|+++|-
T Consensus       171 c~p~f~f~~~L~LT~~~~~F~~~V~~~~iSgN~D~PEgG~DAimQaaVC~~~I-------GWR~~a~rllv~~TDa~fH~  243 (423)
T smart00187      171 CEPPYGFKHVLSLTDDTDEFNEEVKKQRISGNLDAPEGGFDAIMQAAVCTEQI-------GWREDARRLLVFSTDAGFHF  243 (423)
T ss_pred             cCCCcceeeeccCCCCHHHHHHHHhhceeecCCcCCcccHHHHHHHHhhcccc-------ccCCCceEEEEEEcCCCccc
Confidence               11 11124459999999999999999999999999889988777554321       233 3567789999999996


Q ss_pred             CCC------------CcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEE-EeccCCchhHHHHHH
Q 003284          140 LPT------------PVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLS-VICPKQLPKLTAIYN  199 (834)
Q Consensus       140 lp~------------pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LS-vIsPrqlp~l~~Lfe  199 (834)
                      ...            .|++..  +.+|.++..+    ..-+..+|++.+.|++|.+= +|.-+..+.|++|-+
T Consensus       244 AGDGkLaGIv~PNDg~CHL~~--~g~Yt~s~~~----DYPSi~ql~~kL~e~nI~~IFAVT~~~~~~Y~~Ls~  310 (423)
T smart00187      244 AGDGKLAGIVQPNDGQCHLDN--NGEYTMSTTQ----DYPSIGQLNQKLAENNINPIFAVTKKQVSLYKELSA  310 (423)
T ss_pred             cCCcceeeEecCCCCcceeCC--CCCcCccCcC----CCCCHHHHHHHHHhcCceEEEEEcccchhHHHHHHH
Confidence            554            344321  1122222222    22356999999999999864 466666655544443

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).

>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=98.44  E-value=7.3e-06  Score=83.76  Aligned_cols=149  Identities=19%  Similarity=0.273  Sum_probs=97.6

Q ss_pred             ccEEEEEeccccch-------HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC----Ccc-----cc
Q 003284            4 KQLIVAVEGTAAMG-------PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS----YCA-----CL   67 (834)
Q Consensus         4 ~dvVFVID~Tasmg-------~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~----~~~-----~l   67 (834)
                      .+||||||+++||.       ..|+.+|.- +.-+++.+.           ...+++||+|.+...    +..     ++
T Consensus        21 ~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a-~~~~l~~l~-----------~~~~v~lv~F~~~~~~~~~~~~~~p~~~~   88 (206)
T cd01456          21 PNVAIVLDNSGSMREVDGGGETRLDNAKAA-LDETANALP-----------DGTRLGLWTFSGDGDNPLDVRVLVPKGCL   88 (206)
T ss_pred             CcEEEEEeCCCCCcCCCCCcchHHHHHHHH-HHHHHHhCC-----------CCceEEEEEecCCCCCCcccccccccccc
Confidence            78999999999997       466666644 444455442           246999999998421    111     11


Q ss_pred             e-eeccCC-CCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcc
Q 003284           68 V-QRSGWT-KDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVY  145 (834)
Q Consensus        68 v-~~~gfT-sd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~  145 (834)
                      . ...++. .+...+...|+.|...+||   -.+.+||..|+.+++  .         ...+++|||+|--+..-.    
T Consensus        89 ~~~~~~~~~~~~~~l~~~i~~i~~~~G~---T~l~~aL~~a~~~l~--~---------~~~~~iillTDG~~~~~~----  150 (206)
T cd01456          89 TAPVNGFPSAQRSALDAALNSLQTPTGW---TPLAAALAEAAAYVD--P---------GRVNVVVLITDGEDTCGP----  150 (206)
T ss_pred             ccccCCCCcccHHHHHHHHHhhcCCCCc---ChHHHHHHHHHHHhC--C---------CCcceEEEEcCCCccCCC----
Confidence            1 123443 5889999999999844443   578899999998884  1         113899999987553111    


Q ss_pred             cCCccccccccchhhhhhccCCCHHHHHHHHhh-----cCcEEEEeccCC---chhHHHHHHHhcCC
Q 003284          146 RPQMQNLDQNENNEAQAESRLSDAETVAKSFVQ-----CSVSLSVICPKQ---LPKLTAIYNAAKRN  204 (834)
Q Consensus       146 ~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e-----~~I~LSvIsPrq---lp~l~~Lfeka~~~  204 (834)
                                            +....++.+.+     ++|.|++|.--.   ...|+.|-+..++.
T Consensus       151 ----------------------~~~~~~~~~~~~~~~~~~i~i~~igiG~~~~~~~l~~iA~~tgG~  195 (206)
T cd01456         151 ----------------------DPCEVARELAKRRTPAPPIKVNVIDFGGDADRAELEAIAEATGGT  195 (206)
T ss_pred             ----------------------CHHHHHHHHHHhcCCCCCceEEEEEecCcccHHHHHHHHHhcCCe
Confidence                                  23344444444     499999998654   45677777766654

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

>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=98.41  E-value=5.2e-06  Score=82.04  Aligned_cols=137  Identities=18%  Similarity=0.223  Sum_probs=90.0

Q ss_pred             CccEEEEEeccccchHh-H-HHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHH
Q 003284            3 EKQLIVAVEGTAAMGPY-W-QSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIF   80 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y-i-~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~f   80 (834)
                      .+|||||||.+++|... | ..-|.++..-++..|... .       ...+++||+|.+...      ....|+.|...+
T Consensus         2 ~~~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~-~-------~~~~v~lv~f~~~~~------~~~~~~~~~~~~   67 (180)
T cd01467           2 GRDIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDR-R-------ENDRIGLVVFAGAAF------TQAPLTLDRESL   67 (180)
T ss_pred             CceEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHh-C-------CCCeEEEEEEcCCee------eccCCCccHHHH
Confidence            37999999999999753 2 011222333334334321 0       236999999976522      346788898888


Q ss_pred             HHHhccCcc--CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           81 LHWLSTIPF--AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        81 l~~Ld~I~f--~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      ...|+.|..  .||+   ..+.+||..|+.++....         ...+++|||+|-.+..-+                 
T Consensus        68 ~~~l~~l~~~~~~g~---T~l~~al~~a~~~l~~~~---------~~~~~iiliTDG~~~~g~-----------------  118 (180)
T cd01467          68 KELLEDIKIGLAGQG---TAIGDAIGLAIKRLKNSE---------AKERVIVLLTDGENNAGE-----------------  118 (180)
T ss_pred             HHHHHHhhhcccCCC---CcHHHHHHHHHHHHHhcC---------CCCCEEEEEeCCCCCCCC-----------------
Confidence            888888873  2332   467889999998885421         124889999988664211                 


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                              .+++.+++.+.+++|.|++|.-..
T Consensus       119 --------~~~~~~~~~~~~~gi~i~~i~ig~  142 (180)
T cd01467         119 --------IDPATAAELAKNKGVRIYTIGVGK  142 (180)
T ss_pred             --------CCHHHHHHHHHHCCCEEEEEEecC
Confidence                    134556777788999999987654

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

>smart00327 VWA von Willebrand factor (vWF) type A domain

Probab=98.41  E-value=2e-05  Score=75.93  Aligned_cols=140  Identities=16%  Similarity=0.274  Sum_probs=97.2

Q ss_pred             CccEEEEEeccccc-hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccC--CCCHHH
Q 003284            3 EKQLIVAVEGTAAM-GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGW--TKDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasm-g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gf--Tsd~~~   79 (834)
                      .+||+||||.|.+| +.+|+.++. ++.-+++.+...        ....++++|.|.+...      ..+.|  +++.+.
T Consensus         1 ~~~v~l~vD~S~SM~~~~~~~~~~-~~~~~~~~~~~~--------~~~~~i~ii~f~~~~~------~~~~~~~~~~~~~   65 (177)
T smart00327        1 PLDVVFLLDGSGSMGPNRFEKAKE-FVLKLVEQLDIG--------PDGDRVGLVTFSDDAT------VLFPLNDSRSKDA   65 (177)
T ss_pred             CccEEEEEeCCCccchHHHHHHHH-HHHHHHHhcCCC--------CCCcEEEEEEeCCCce------EEEcccccCCHHH
Confidence            37999999999999 888877774 466777766431        1257999999998532      23444  899999


Q ss_pred             HHHHhccCcc-CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           80 FLHWLSTIPF-AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        80 fl~~Ld~I~f-~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      +...++++.. .+|+   ..+.++|..|+..++....    .......+.+|+|+|..++.-                  
T Consensus        66 ~~~~i~~~~~~~~~~---~~~~~al~~~~~~~~~~~~----~~~~~~~~~iviitDg~~~~~------------------  120 (177)
T smart00327       66 LLEALASLSYKLGGG---TNLGAALQYALENLFSKSA----GSRRGAPKVLILITDGESNDG------------------  120 (177)
T ss_pred             HHHHHHhcCCCCCCC---chHHHHHHHHHHHhcCcCC----CCCCCCCeEEEEEcCCCCCCC------------------
Confidence            9999999997 3333   4455666666665531110    011123577888888777522                  


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                              .+.+.+++.+.+++|.+.+|..-.
T Consensus       121 --------~~~~~~~~~~~~~~i~i~~i~~~~  144 (177)
T smart00327      121 --------GDLLKAAKELKRSGVKVFVVGVGN  144 (177)
T ss_pred             --------ccHHHHHHHHHHCCCEEEEEEccC
Confidence                    245778888999999999998875

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.

>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation

Probab=98.37  E-value=6.1e-06  Score=83.67  Aligned_cols=122  Identities=11%  Similarity=0.221  Sum_probs=80.8

Q ss_pred             ccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCccccee-eccCCCCHHHHH
Q 003284            4 KQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQ-RSGWTKDVDIFL   81 (834)
Q Consensus         4 ~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~-~~gfTsd~~~fl   81 (834)
                      .|||||||++++|+ .-|+.+| .-|.-+++.+....        ...++|||+|.+...   ..+. +..++.|...++
T Consensus         1 ~di~~vlD~SgSM~~~~~~~~k-~~~~~l~~~l~~~~--------~~~~v~li~Fs~~~~---~~~~~~~~~~~~~~~~~   68 (198)
T cd01470           1 LNIYIALDASDSIGEEDFDEAK-NAIKTLIEKISSYE--------VSPRYEIISYASDPK---EIVSIRDFNSNDADDVI   68 (198)
T ss_pred             CcEEEEEECCCCccHHHHHHHH-HHHHHHHHHccccC--------CCceEEEEEecCCce---EEEecccCCCCCHHHHH
Confidence            48999999999997 5666666 34666666663211        246999999998733   1111 223566789999


Q ss_pred             HHhccCccCCCC-CchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           82 HWLSTIPFAGGG-FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        82 ~~Ld~I~f~GGG-~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      .+|+.+.+.+++ ...-.+++||..+++.++.... .....+....+.+|||+|--|.
T Consensus        69 ~~l~~~~~~~~~~~ggT~~~~Al~~~~~~l~~~~~-~~~~~~~~~~~~iillTDG~~~  125 (198)
T cd01470          69 KRLEDFNYDDHGDKTGTNTAAALKKVYERMALEKV-RNKEAFNETRHVIILFTDGKSN  125 (198)
T ss_pred             HHHHhCCcccccCccchhHHHHHHHHHHHHHHHHh-cCccchhhcceEEEEEcCCCcC
Confidence            999999876654 2346788999888876642111 0111223456778999988765

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.

>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins

Probab=98.35  E-value=2.1e-05  Score=80.71  Aligned_cols=148  Identities=20%  Similarity=0.184  Sum_probs=99.5

Q ss_pred             cEEEEEeccccchH------hHHHHHHHHHHHHH-HHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCH
Q 003284            5 QLIVAVEGTAAMGP------YWQSIVSDYLEKII-RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDV   77 (834)
Q Consensus         5 dvVFVID~Tasmg~------yi~~lkt~YI~p~l-e~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~   77 (834)
                      -+|||||.+.+|..      =|+..| +++.-++ +||...         ...++|||+|++...    . ...+.|.|.
T Consensus         5 a~vi~lD~S~sM~a~D~~PnRL~aak-~~i~~~~~~f~~~n---------p~~~vGlv~fag~~a----~-v~~plT~D~   69 (187)
T cd01452           5 ATMICIDNSEYMRNGDYPPTRFQAQA-DAVNLICQAKTRSN---------PENNVGLMTMAGNSP----E-VLVTLTNDQ   69 (187)
T ss_pred             EEEEEEECCHHHHcCCCCCCHHHHHH-HHHHHHHHHHHhcC---------CCccEEEEEecCCce----E-EEECCCCCH
Confidence            47999999999852      244444 3355555 444432         235999999998533    2 457889999


Q ss_pred             HHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccc
Q 003284           78 DIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNEN  157 (834)
Q Consensus        78 ~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~  157 (834)
                      ..++..|+.|...    ...++.+||..|+..|......      ...+|.+|+|+ |+=.     +             
T Consensus        70 ~~~~~~L~~i~~~----g~~~l~~AL~~A~~~L~~~~~~------~~~~rivi~v~-S~~~-----~-------------  120 (187)
T cd01452          70 GKILSKLHDVQPK----GKANFITGIQIAQLALKHRQNK------NQKQRIVAFVG-SPIE-----E-------------  120 (187)
T ss_pred             HHHHHHHHhCCCC----CcchHHHHHHHHHHHHhcCCCc------CCcceEEEEEe-cCCc-----C-------------
Confidence            9999999999853    2357889999999888543211      11124344443 3211     0             


Q ss_pred             hhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC----chhHHHHHHHhcC
Q 003284          158 NEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ----LPKLTAIYNAAKR  203 (834)
Q Consensus       158 ~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq----lp~l~~Lfeka~~  203 (834)
                             .-.+...+++.++++||.++||+--.    .++|++++++...
T Consensus       121 -------d~~~i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~~~~~~  163 (187)
T cd01452         121 -------DEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDAVNG  163 (187)
T ss_pred             -------CHHHHHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHHHHhcC
Confidence                   01246789999999999999998763    4888888887643

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.

>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional

Probab=98.31  E-value=1e-05  Score=94.43  Aligned_cols=138  Identities=18%  Similarity=0.257  Sum_probs=86.4

Q ss_pred             CccEEEEEeccccch-HhH-HHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC----C
Q 003284            3 EKQLIVAVEGTAAMG-PYW-QSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----D   76 (834)
Q Consensus         3 ~~dvVFVID~Tasmg-~yi-~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs----d   76 (834)
                      +.||+||||+++||+ +.| +.+| ..+..++..|..        ....++++||+|.+..-      ..+.+++    |
T Consensus        42 ~lDIvFLLD~SgSMg~~Nfle~AK-~Fa~~LV~~l~I--------s~D~V~VgiV~FSd~~r------~vfpL~s~~s~D  106 (576)
T PTZ00441         42 EVDLYLLVDGSGSIGYHNWITHVI-PMLMGLIQQLNL--------SDDAINLYMSLFSNNTT------ELIRLGSGASKD  106 (576)
T ss_pred             CceEEEEEeCCCccCCccHHHHHH-HHHHHHHHHhcc--------CCCceEEEEEEeCCCce------EEEecCCCcccc
Confidence            589999999999998 555 3333 445556666632        12468999999987732      2334433    3


Q ss_pred             HHHHHHHh---ccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccc
Q 003284           77 VDIFLHWL---STIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLD  153 (834)
Q Consensus        77 ~~~fl~~L---d~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~  153 (834)
                      ....+..|   ......|||   -.+.+||..|.+.+...      ....++.|++|||+|--+...             
T Consensus       107 k~~aL~~I~sL~~~~~pgGg---Tnig~AL~~Aae~L~sr------~~R~nvpKVVILLTDG~sns~-------------  164 (576)
T PTZ00441        107 KEQALIIVKSLRKTYLPYGK---TNMTDALLEVRKHLNDR------VNRENAIQLVILMTDGIPNSK-------------  164 (576)
T ss_pred             HHHHHHHHHHHHhhccCCCC---ccHHHHHHHHHHHHhhc------ccccCCceEEEEEecCCCCCc-------------
Confidence            23444433   333345554   44677777777666421      123456799999998776421             


Q ss_pred             cccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          154 QNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       154 ~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                                   .++...|+.+.++||.|++|---.
T Consensus       165 -------------~dvleaAq~LR~~GVeI~vIGVG~  188 (576)
T PTZ00441        165 -------------YRALEESRKLKDRNVKLAVIGIGQ  188 (576)
T ss_pred             -------------ccHHHHHHHHHHCCCEEEEEEeCC
Confidence                         134456778888888888887654

>PRK13685 hypothetical protein; Provisional

Probab=98.28  E-value=2.6e-05  Score=85.82  Aligned_cols=158  Identities=13%  Similarity=0.117  Sum_probs=101.2

Q ss_pred             ccEEEEEeccccchH------hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCH
Q 003284            4 KQLIVAVEGTAAMGP------YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDV   77 (834)
Q Consensus         4 ~dvVFVID~Tasmg~------yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~   77 (834)
                      .|||||||.++||..      -++.+|.. +..+++.+..           ..++|||+|.+...      ...++|.|.
T Consensus        89 ~~vvlvlD~S~SM~~~D~~p~RL~~ak~~-~~~~l~~l~~-----------~d~vglv~Fa~~a~------~~~p~t~d~  150 (326)
T PRK13685         89 AVVMLVIDVSQSMRATDVEPNRLAAAQEA-AKQFADELTP-----------GINLGLIAFAGTAT------VLVSPTTNR  150 (326)
T ss_pred             ceEEEEEECCccccCCCCCCCHHHHHHHH-HHHHHHhCCC-----------CCeEEEEEEcCcee------ecCCCCCCH
Confidence            589999999999984      46666644 4444554421           35899999998732      335789999


Q ss_pred             HHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccc
Q 003284           78 DIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNEN  157 (834)
Q Consensus        78 ~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~  157 (834)
                      +.+...|+++...||-    ++.+||..|++.++.... ..........+++||++|-....-..++             
T Consensus       151 ~~l~~~l~~l~~~~~T----~~g~al~~A~~~l~~~~~-~~~~~~~~~~~~IILlTDG~~~~~~~~~-------------  212 (326)
T PRK13685        151 EATKNAIDKLQLADRT----ATGEAIFTALQAIATVGA-VIGGGDTPPPARIVLMSDGKETVPTNPD-------------  212 (326)
T ss_pred             HHHHHHHHhCCCCCCc----chHHHHHHHHHHHHhhhc-ccccccCCCCCEEEEEcCCCCCCCCCCC-------------
Confidence            9999999999965432    345666666666542110 0000112235789999987543211110             


Q ss_pred             hhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC-----------------chhHHHHHHHhcCC
Q 003284          158 NEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ-----------------LPKLTAIYNAAKRN  204 (834)
Q Consensus       158 ~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq-----------------lp~l~~Lfeka~~~  204 (834)
                             ...+....++.+.+++|.+++|.--.                 -..|++|-+++++.
T Consensus       213 -------~~~~~~~aa~~a~~~gi~i~~Ig~G~~~g~~~~~g~~~~~~~d~~~L~~iA~~tgG~  269 (326)
T PRK13685        213 -------NPRGAYTAARTAKDQGVPISTISFGTPYGSVEINGQRQPVPVDDESLKKIAQLSGGE  269 (326)
T ss_pred             -------CcccHHHHHHHHHHcCCeEEEEEECCCCCCcCcCCceeeecCCHHHHHHHHHhcCCE
Confidence                   01134567888899999999997432                 24677777766654

>PF13768 VWA_3: von Willebrand factor type A domain

Probab=98.27  E-value=1.2e-05  Score=77.94  Aligned_cols=145  Identities=17%  Similarity=0.262  Sum_probs=93.8

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC-CcccceeeccCCCCHHHHHH
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS-YCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~-~~~~lv~~~gfTsd~~~fl~   82 (834)
                      +|||||||.+++|..++ .+.++-|.-+|+.+..           ..+|.||.|++... +...++...  ......+++
T Consensus         1 ~~vvilvD~S~Sm~g~~-~~~k~al~~~l~~L~~-----------~d~fnii~f~~~~~~~~~~~~~~~--~~~~~~a~~   66 (155)
T PF13768_consen    1 ADVVILVDTSGSMSGEK-ELVKDALRAILRSLPP-----------GDRFNIIAFGSSVRPLFPGLVPAT--EENRQEALQ   66 (155)
T ss_pred             CeEEEEEeCCCCCCCcH-HHHHHHHHHHHHhCCC-----------CCEEEEEEeCCEeeEcchhHHHHh--HHHHHHHHH
Confidence            58999999999999998 5555556666776643           45999999999743 111111111  245678899


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQA  162 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~  162 (834)
                      |++.++..+||   ..+.+||.+|+..+..          ....+++|||+|..|..-.                     
T Consensus        67 ~I~~~~~~~G~---t~l~~aL~~a~~~~~~----------~~~~~~IilltDG~~~~~~---------------------  112 (155)
T PF13768_consen   67 WIKSLEANSGG---TDLLAALRAALALLQR----------PGCVRAIILLTDGQPVSGE---------------------  112 (155)
T ss_pred             HHHHhcccCCC---ccHHHHHHHHHHhccc----------CCCccEEEEEEeccCCCCH---------------------
Confidence            99999984444   4566777777776521          3357999999988773211                     


Q ss_pred             hccCCCHHHHHHHH--hhcCcEEEEeccCC---chhHHHHHHHhcC
Q 003284          163 ESRLSDAETVAKSF--VQCSVSLSVICPKQ---LPKLTAIYNAAKR  203 (834)
Q Consensus       163 ~~~l~d~e~lA~~~--~e~~I~LSvIsPrq---lp~l~~Lfeka~~  203 (834)
                             +.+.+.+  ..+.|.++.+.--.   ...|++|-+..++
T Consensus       113 -------~~i~~~v~~~~~~~~i~~~~~g~~~~~~~L~~LA~~~~G  151 (155)
T PF13768_consen  113 -------EEILDLVRRARGHIRIFTFGIGSDADADFLRELARATGG  151 (155)
T ss_pred             -------HHHHHHHHhcCCCceEEEEEECChhHHHHHHHHHHcCCC
Confidence                   1222222  22568888776554   3667777665554

>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto)

Probab=98.25  E-value=2.9e-05  Score=77.72  Aligned_cols=152  Identities=15%  Similarity=0.197  Sum_probs=97.7

Q ss_pred             EEEEEeccccchHh--HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHHH
Q 003284            6 LIVAVEGTAAMGPY--WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHW   83 (834)
Q Consensus         6 vVFVID~Tasmg~y--i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~~   83 (834)
                      ||||||+++||+..  |+.+|     -+++.|....+      ....+++||+|.+...     ...+++|.+...+..+
T Consensus         3 v~lvlD~SgSM~~~~rl~~ak-----~a~~~~~~~~~------~~~d~v~lv~F~~~~~-----~~~~~~t~~~~~~~~~   66 (178)
T cd01451           3 VIFVVDASGSMAARHRMAAAK-----GAVLSLLRDAY------QRRDKVALIAFRGTEA-----EVLLPPTRSVELAKRR   66 (178)
T ss_pred             EEEEEECCccCCCccHHHHHH-----HHHHHHHHHhh------cCCCEEEEEEECCCCc-----eEEeCCCCCHHHHHHH
Confidence            79999999999852  33333     34444432111      1246999999986522     1245688899999999


Q ss_pred             hccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhhh
Q 003284           84 LSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAE  163 (834)
Q Consensus        84 Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~~  163 (834)
                      |+.+... |+   -.+.+||..|++.+....      ......+.+|||+|-.+..-..++                   
T Consensus        67 l~~l~~~-G~---T~l~~aL~~a~~~l~~~~------~~~~~~~~ivliTDG~~~~g~~~~-------------------  117 (178)
T cd01451          67 LARLPTG-GG---TPLAAGLLAAYELAAEQA------RDPGQRPLIVVITDGRANVGPDPT-------------------  117 (178)
T ss_pred             HHhCCCC-CC---CcHHHHHHHHHHHHHHHh------cCCCCceEEEEECCCCCCCCCCch-------------------
Confidence            9999753 33   466777777776651100      001124889999987654211110                   


Q ss_pred             ccCCCH-HHHHHHHhhcCcEEEEeccCC----chhHHHHHHHhcCCC
Q 003284          164 SRLSDA-ETVAKSFVQCSVSLSVICPKQ----LPKLTAIYNAAKRNP  205 (834)
Q Consensus       164 ~~l~d~-e~lA~~~~e~~I~LSvIsPrq----lp~l~~Lfeka~~~~  205 (834)
                         ... ..+++.+.+.+|.+.+|....    -..|++|-++.++.-
T Consensus       118 ---~~~~~~~~~~l~~~gi~v~~I~~~~~~~~~~~l~~iA~~tgG~~  161 (178)
T cd01451         118 ---ADRALAAARKLRARGISALVIDTEGRPVRRGLAKDLARALGGQY  161 (178)
T ss_pred             ---hHHHHHHHHHHHhcCCcEEEEeCCCCccCccHHHHHHHHcCCeE
Confidence               012 667888999999999998764    246888888877653

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=98.23  E-value=1.4e-05  Score=80.69  Aligned_cols=115  Identities=13%  Similarity=0.182  Sum_probs=71.6

Q ss_pred             ccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeec------cCCCC
Q 003284            4 KQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRS------GWTKD   76 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~------gfTsd   76 (834)
                      +|||||||+++||.. -|+.+| +-+.-+++.|.           ..-+++||.|.+...   .++.++      .++.+
T Consensus        14 ~~vv~llD~SgSM~~~~l~~ak-~~~~~ll~~l~-----------~~d~v~lv~F~~~~~---~~~~~~~~~~~~~~~~~   78 (190)
T cd01463          14 KDIVILLDVSGSMTGQRLHLAK-QTVSSILDTLS-----------DNDFFNIITFSNEVN---PVVPCFNDTLVQATTSN   78 (190)
T ss_pred             ceEEEEEECCCCCCcHHHHHHH-HHHHHHHHhCC-----------CCCEEEEEEeCCCee---EEeeecccceEecCHHH
Confidence            899999999999974 343333 22334444442           235899999999844   222111      13457


Q ss_pred             HHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCC
Q 003284           77 VDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNP  137 (834)
Q Consensus        77 ~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP  137 (834)
                      ...++.+|+.|...||    ..+.+||.+|+..+...........+....+++|||+|--+
T Consensus        79 ~~~~~~~l~~l~~~G~----T~~~~al~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~  135 (190)
T cd01463          79 KKVLKEALDMLEAKGI----ANYTKALEFAFSLLLKNLQSNHSGSRSQCNQAIMLITDGVP  135 (190)
T ss_pred             HHHHHHHHhhCCCCCc----chHHHHHHHHHHHHHHhhhcccccccCCceeEEEEEeCCCC
Confidence            8899999999997543    34667777777666431100111122345688999998765

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.

>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=98.20  E-value=4.7e-05  Score=74.17  Aligned_cols=149  Identities=15%  Similarity=0.149  Sum_probs=90.0

Q ss_pred             cEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHHHH
Q 003284            5 QLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIFL   81 (834)
Q Consensus         5 dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~fl   81 (834)
                      +||||||+|++|+. .|+.+|.- +.-+++.+..           ..+++||+|.+...      ..+.|+  .|...++
T Consensus         2 ~~~~vlD~S~SM~~~~~~~~k~a-~~~~~~~l~~-----------~~~v~li~f~~~~~------~~~~~~~~~~~~~l~   63 (170)
T cd01465           2 NLVFVIDRSGSMDGPKLPLVKSA-LKLLVDQLRP-----------DDRLAIVTYDGAAE------TVLPATPVRDKAAIL   63 (170)
T ss_pred             cEEEEEECCCCCCChhHHHHHHH-HHHHHHhCCC-----------CCEEEEEEecCCcc------EEecCcccchHHHHH
Confidence            79999999999964 36666643 4444444422           35899999998633      123343  4678888


Q ss_pred             HHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           82 HWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        82 ~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      ..|+++...| +   ..+.+||..|+..+.....       ....+++||++|..+..-+..                  
T Consensus        64 ~~l~~~~~~g-~---T~~~~al~~a~~~~~~~~~-------~~~~~~ivl~TDG~~~~~~~~------------------  114 (170)
T cd01465          64 AAIDRLTAGG-S---TAGGAGIQLGYQEAQKHFV-------PGGVNRILLATDGDFNVGETD------------------  114 (170)
T ss_pred             HHHHcCCCCC-C---CCHHHHHHHHHHHHHhhcC-------CCCeeEEEEEeCCCCCCCCCC------------------
Confidence            8898887533 3   2345555555554432110       112378999999877522110                  


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccCC---chhHHHHHHHhcCC
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPKQ---LPKLTAIYNAAKRN  204 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPrq---lp~l~~Lfeka~~~  204 (834)
                         + .++..+++.+.+++|.+++|.--.   ...|++|-...++.
T Consensus       115 ---~-~~~~~~~~~~~~~~v~i~~i~~g~~~~~~~l~~ia~~~~g~  156 (170)
T cd01465         115 ---P-DELARLVAQKRESGITLSTLGFGDNYNEDLMEAIADAGNGN  156 (170)
T ss_pred             ---H-HHHHHHHHHhhcCCeEEEEEEeCCCcCHHHHHHHHhcCCce
Confidence               0 123444555667899999987753   35566666544443

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

>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]

Probab=98.19  E-value=3.3e-05  Score=82.37  Aligned_cols=157  Identities=13%  Similarity=0.175  Sum_probs=109.7

Q ss_pred             ccEEEEEeccccchHh--HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHH
Q 003284            4 KQLIVAVEGTAAMGPY--WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFL   81 (834)
Q Consensus         4 ~dvVFVID~Tasmg~y--i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl   81 (834)
                      ..||||||+++||..+  +...|--. .-+|+.-+.          .+.++|||.|+.++.  +   -...+|+|++.+.
T Consensus        79 ~lvvfvVDASgSM~~~~Rm~aaKG~~-~~lL~dAYq----------~RdkvavI~F~G~~A--~---lll~pT~sv~~~~  142 (261)
T COG1240          79 NLIVFVVDASGSMAARRRMAAAKGAA-LSLLRDAYQ----------RRDKVAVIAFRGEKA--E---LLLPPTSSVELAE  142 (261)
T ss_pred             CcEEEEEeCcccchhHHHHHHHHHHH-HHHHHHHHH----------ccceEEEEEecCCcc--e---EEeCCcccHHHHH
Confidence            6899999999999999  99888663 444443333          478999999998865  2   2478999999999


Q ss_pred             HHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           82 HWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        82 ~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      +||..+..-|+  .  =+++||-.|.++|.+..-     ...+...+.|+|+|-=|-   .+.          +.     
T Consensus       143 ~~L~~l~~GG~--T--PL~~aL~~a~ev~~r~~r-----~~p~~~~~~vviTDGr~n---~~~----------~~-----  195 (261)
T COG1240         143 RALERLPTGGK--T--PLADALRQAYEVLAREKR-----RGPDRRPVMVVITDGRAN---VPI----------PL-----  195 (261)
T ss_pred             HHHHhCCCCCC--C--chHHHHHHHHHHHHHhhc-----cCCCcceEEEEEeCCccC---CCC----------CC-----
Confidence            99999984332  2  267888888888864221     112345677888876421   010          00     


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccCC----chhHHHHHHHhcCCC
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPKQ----LPKLTAIYNAAKRNP  205 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPrq----lp~l~~Lfeka~~~~  205 (834)
                        .-..+....|..+.+|++.+.||--..    +-..++|....+++-
T Consensus       196 --~~~~e~~~~a~~~~~~g~~~lvid~e~~~~~~g~~~~iA~~~Gg~~  241 (261)
T COG1240         196 --GPKAETLEAASKLRLRGIQLLVIDTEGSEVRLGLAEEIARASGGEY  241 (261)
T ss_pred             --chHHHHHHHHHHHhhcCCcEEEEecCCccccccHHHHHHHHhCCeE
Confidence              001356778888999999999997653    456677777777664

>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain

Probab=98.17  E-value=5e-05  Score=81.83  Aligned_cols=153  Identities=14%  Similarity=0.162  Sum_probs=102.3

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHHH
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHW   83 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~~   83 (834)
                      .+||||||++++|...|..+|.- +..+++.+..          ...+++||.|.+...      ..+.||.|...+...
T Consensus        54 ~~vvlvlD~SgSM~~~~~~a~~a-~~~~l~~~l~----------~~d~v~lv~f~~~~~------~~~~~t~~~~~l~~~  116 (296)
T TIGR03436        54 LTVGLVIDTSGSMRNDLDRARAA-AIRFLKTVLR----------PNDRVFVVTFNTRLR------LLQDFTSDPRLLEAA  116 (296)
T ss_pred             ceEEEEEECCCCchHHHHHHHHH-HHHHHHhhCC----------CCCEEEEEEeCCcee------EeecCCCCHHHHHHH
Confidence            68999999999999988777744 4455544211          346999999997521      236899999999999


Q ss_pred             hccCccCC-------CC----CchhhHHHHHHHH-HhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccc
Q 003284           84 LSTIPFAG-------GG----FNDAAIAEGLSEA-LMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQN  151 (834)
Q Consensus        84 Ld~I~f~G-------GG----~~~~AvaEGLa~A-L~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~  151 (834)
                      |+.+....       |.    .+..++.+||..| ++++.....      .....|.+|||++.....            
T Consensus       117 l~~l~~~~~~~~~~~~~~~~~~g~T~l~~al~~aa~~~~~~~~~------~~p~rk~iIllTDG~~~~------------  178 (296)
T TIGR03436       117 LNRLKPPLRTDYNSSGAFVRDGGGTALYDAITLAALEQLANALA------GIPGRKALIVISDGGDNR------------  178 (296)
T ss_pred             HHhccCCCccccccccccccCCCcchhHHHHHHHHHHHHHHhhc------CCCCCeEEEEEecCCCcc------------
Confidence            99998621       00    1234677776444 444432110      012357889998763210            


Q ss_pred             cccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCCc----------------hhHHHHHHHhcCC
Q 003284          152 LDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQL----------------PKLTAIYNAAKRN  204 (834)
Q Consensus       152 ~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrql----------------p~l~~Lfeka~~~  204 (834)
                                   ...+.+.+++.+.+.+|.+++|....+                ..|++|-+..++.
T Consensus       179 -------------~~~~~~~~~~~~~~~~v~vy~I~~~~~~~~~~~~~~~~~~~~~~~L~~iA~~TGG~  234 (296)
T TIGR03436       179 -------------SRDTLERAIDAAQRADVAIYSIDARGLRAPDLGAGAKAGLGGPEALERLAEETGGR  234 (296)
T ss_pred             -------------hHHHHHHHHHHHHHcCCEEEEeccCccccCCcccccccCCCcHHHHHHHHHHhCCe
Confidence                         012457788888999999999987632                4688888877765

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.

>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases

Probab=98.14  E-value=5.2e-05  Score=75.28  Aligned_cols=157  Identities=10%  Similarity=0.110  Sum_probs=98.3

Q ss_pred             cEEEEEeccccchH--hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCC--CCcccceeeccCCCCH-HH
Q 003284            5 QLIVAVEGTAAMGP--YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHG--SYCACLVQRSGWTKDV-DI   79 (834)
Q Consensus         5 dvVFVID~Tasmg~--yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~--~~~~~lv~~~gfTsd~-~~   79 (834)
                      -|+|+||+++||..  .|+.+|.- +.-+++.+..          ...+++||.|.+..  .....++....|+.+. ..
T Consensus         2 ~v~~llD~SgSM~~~~kl~~ak~a-~~~l~~~l~~----------~~d~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~   70 (174)
T cd01454           2 AVTLLLDLSGSMRSDRRIDVAKKA-AVLLAEALEA----------CGVPHAILGFTTDAGGRERVRWIKIKDFDESLHER   70 (174)
T ss_pred             EEEEEEECCCCCCCCcHHHHHHHH-HHHHHHHHHH----------cCCcEEEEEecCCCCCccceEEEEecCcccccchh
Confidence            48999999999988  67777754 3344444432          23689999999873  2111222333555543 35


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      ....|+.+..  ||  ...+.+||..|++.+...         ....|++|||+|--|..-...  .        ++   
T Consensus        71 ~~~~l~~~~~--~g--~T~~~~al~~a~~~l~~~---------~~~~~~iiliTDG~~~~~~~~--~--------~~---  124 (174)
T cd01454          71 ARKRLAALSP--GG--NTRDGAAIRHAAERLLAR---------PEKRKILLVISDGEPNDLDYY--E--------GN---  124 (174)
T ss_pred             HHHHHHccCC--CC--CCcHHHHHHHHHHHHhcC---------CCcCcEEEEEeCCCcCccccc--C--------cc---
Confidence            6677777764  22  356788899998887532         123689999999987643311  0        00   


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccCC------chhHHHHHHHh
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPKQ------LPKLTAIYNAA  201 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq------lp~l~~Lfeka  201 (834)
                         ...+.|+...++++.+.||.+++|---.      .+.++++|++-
T Consensus       125 ---~~~~~~~~~~~~~~~~~gi~v~~igig~~~~~~~~~~~~~~~~~~  169 (174)
T cd01454         125 ---VFATEDALRAVIEARKLGIEVFGITIDRDATTVDKEYLKNIFGEE  169 (174)
T ss_pred             ---hhHHHHHHHHHHHHHhCCcEEEEEEecCccccchHHHHHHhhCcc
Confidence               0011122223788889999999885442      56788888754

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.

>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=98.09  E-value=5.9e-05  Score=73.39  Aligned_cols=148  Identities=11%  Similarity=0.133  Sum_probs=94.9

Q ss_pred             CccEEEEEeccccchHh-HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeec-c-CCCCHHH
Q 003284            3 EKQLIVAVEGTAAMGPY-WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRS-G-WTKDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y-i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~-g-fTsd~~~   79 (834)
                      .+||+||||+++||..+ |+.++. .|..+++.+..           ..+++||+|.+..-   .+...+ . -..+...
T Consensus         2 ~~~v~~vlD~S~SM~~~~~~~~~~-al~~~l~~l~~-----------~~~~~l~~Fs~~~~---~~~~~~~~~~~~~~~~   66 (171)
T cd01461           2 PKEVVFVIDTSGSMSGTKIEQTKE-ALLTALKDLPP-----------GDYFNIIGFSDTVE---EFSPSSVSATAENVAA   66 (171)
T ss_pred             CceEEEEEECCCCCCChhHHHHHH-HHHHHHHhCCC-----------CCEEEEEEeCCCce---eecCcceeCCHHHHHH
Confidence            47999999999999755 666664 45666666532           24799999977522   111111 1 1234567


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      ++.+|+.+.. |||   ..+.+||..|+..+.+.         ....+.+|||+|-.+..-                   
T Consensus        67 ~~~~l~~~~~-~g~---T~l~~al~~a~~~l~~~---------~~~~~~iillTDG~~~~~-------------------  114 (171)
T cd01461          67 AIEYVNRLQA-LGG---TNMNDALEAALELLNSS---------PGSVPQIILLTDGEVTNE-------------------  114 (171)
T ss_pred             HHHHHHhcCC-CCC---cCHHHHHHHHHHhhccC---------CCCccEEEEEeCCCCCCH-------------------
Confidence            7888888877 443   45778888888777531         234689999998763210                   


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccC---CchhHHHHHHHhcCC
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPK---QLPKLTAIYNAAKRN  204 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr---qlp~l~~Lfeka~~~  204 (834)
                             .++...++...+.+|.++.|.-.   ..+.|+.|-++.++.
T Consensus       115 -------~~~~~~~~~~~~~~i~i~~i~~g~~~~~~~l~~ia~~~gG~  155 (171)
T cd01461         115 -------SQILKNVREALSGRIRLFTFGIGSDVNTYLLERLAREGRGI  155 (171)
T ss_pred             -------HHHHHHHHHhcCCCceEEEEEeCCccCHHHHHHHHHcCCCe
Confidence                   02233444444568999888764   357788888777654

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.

>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=98.09  E-value=5.1e-05  Score=74.42  Aligned_cols=145  Identities=17%  Similarity=0.161  Sum_probs=88.3

Q ss_pred             ccEEEEEeccccchHh-HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC-CCHHHHH
Q 003284            4 KQLIVAVEGTAAMGPY-WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT-KDVDIFL   81 (834)
Q Consensus         4 ~dvVFVID~Tasmg~y-i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT-sd~~~fl   81 (834)
                      .|||||||++++|... |+.+|. -|.-+++.+.           ...++|||+|.+..-.-.++   ..++ .+...+.
T Consensus         1 ~~v~~vlD~S~SM~~~rl~~ak~-a~~~l~~~l~-----------~~~~~~li~F~~~~~~~~~~---~~~~~~~~~~~~   65 (155)
T cd01466           1 VDLVAVLDVSGSMAGDKLQLVKH-ALRFVISSLG-----------DADRLSIVTFSTSAKRLSPL---RRMTAKGKRSAK   65 (155)
T ss_pred             CcEEEEEECCCCCCcHHHHHHHH-HHHHHHHhCC-----------CcceEEEEEecCCccccCCC---cccCHHHHHHHH
Confidence            4899999999999864 444432 2333344332           23589999999863311111   1122 2457888


Q ss_pred             HHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           82 HWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        82 ~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      .+|++|...||    -.+.+||..|++++....       .....+++|||+|-.+..-.                    
T Consensus        66 ~~i~~~~~~g~----T~~~~al~~a~~~~~~~~-------~~~~~~~iillTDG~~~~~~--------------------  114 (155)
T cd01466          66 RVVDGLQAGGG----TNVVGGLKKALKVLGDRR-------QKNPVASIMLLSDGQDNHGA--------------------  114 (155)
T ss_pred             HHHHhccCCCC----ccHHHHHHHHHHHHhhcc-------cCCCceEEEEEcCCCCCcch--------------------
Confidence            89999875332    467778888887775311       11235789999987652110                    


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccC---CchhHHHHHHHhcCC
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPK---QLPKLTAIYNAAKRN  204 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPr---qlp~l~~Lfeka~~~  204 (834)
                                ......+.+|.+++|.--   ....|++|-+..++.
T Consensus       115 ----------~~~~~~~~~v~v~~igig~~~~~~~l~~iA~~t~G~  150 (155)
T cd01466         115 ----------VVLRADNAPIPIHTFGLGASHDPALLAFIAEITGGT  150 (155)
T ss_pred             ----------hhhcccCCCceEEEEecCCCCCHHHHHHHHhccCce
Confidence                      011234578999988765   346677777766544

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,

>cd01464 vWA_subfamily VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=98.05  E-value=3.7e-05  Score=76.64  Aligned_cols=154  Identities=15%  Similarity=0.135  Sum_probs=87.9

Q ss_pred             CCCccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHH
Q 003284            1 MSEKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDI   79 (834)
Q Consensus         1 ~~~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~   79 (834)
                      |-..+||||||+++||+. .|+.++.- +.-+++.+...+     +...+.+++||.|.+..-      ..+++|...+.
T Consensus         1 ~~~~~v~~llD~SgSM~~~~~~~~k~a-~~~~~~~l~~~~-----~~~~~~~v~ii~F~~~a~------~~~~l~~~~~~   68 (176)
T cd01464           1 MRRLPIYLLLDTSGSMAGEPIEALNQG-LQMLQSELRQDP-----YALESVEISVITFDSAAR------VIVPLTPLESF   68 (176)
T ss_pred             CCCCCEEEEEECCCCCCChHHHHHHHH-HHHHHHHHhcCh-----hhccccEEEEEEecCCce------EecCCccHHhc
Confidence            667899999999999964 56666543 455555554321     112367999999998522      23445542211


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                         .++.+.. |||   -++.+||..|++++................+++|||+|--|..-.                  
T Consensus        69 ---~~~~l~~-~Gg---T~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~~------------------  123 (176)
T cd01464          69 ---QPPRLTA-SGG---TSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGEPTDDL------------------  123 (176)
T ss_pred             ---CCCcccC-CCC---CcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCCCCchH------------------
Confidence               2334443 333   577888888888774321100001112345789999987653111                  


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccCC---chhHHHHH
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPKQ---LPKLTAIY  198 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq---lp~l~~Lf  198 (834)
                             .++.+..+.+.++++.+++|.-=.   ...|++|-
T Consensus       124 -------~~~~~~~~~~~~~~~~i~~igiG~~~~~~~L~~ia  158 (176)
T cd01464         124 -------TAAIERIKEARDSKGRIVACAVGPKADLDTLKQIT  158 (176)
T ss_pred             -------HHHHHHHHhhcccCCcEEEEEeccccCHHHHHHHH
Confidence                   012345566666678888775443   34444443

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

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=97.99  E-value=0.00017  Score=85.64  Aligned_cols=160  Identities=15%  Similarity=0.143  Sum_probs=104.6

Q ss_pred             CccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHH
Q 003284            3 EKQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFL   81 (834)
Q Consensus         3 ~~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl   81 (834)
                      ...||||||+++||. .=|..+|.     +++.|-..      .+..+-+++||.|+...-  +   ...++|++.....
T Consensus       401 ~~~vvfvvD~SGSM~~~rl~~aK~-----a~~~ll~~------ay~~rD~v~lI~F~g~~a--~---~~lppT~~~~~~~  464 (584)
T PRK13406        401 ETTTIFVVDASGSAALHRLAEAKG-----AVELLLAE------AYVRRDQVALVAFRGRGA--E---LLLPPTRSLVRAK  464 (584)
T ss_pred             CccEEEEEECCCCCcHhHHHHHHH-----HHHHHHHh------hcCCCCEEEEEEECCCce--e---EEcCCCcCHHHHH
Confidence            478999999999994 34555553     33333211      112456999999976633  1   2467999999999


Q ss_pred             HHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           82 HWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        82 ~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      .+|++|...    +.-.+++||..|++++.....       ....+++|||+|--+.. +..            ..  ..
T Consensus       465 ~~L~~l~~g----GgTpL~~gL~~A~~~l~~~~~-------~~~~~~iVLlTDG~~n~-~~~------------~~--~~  518 (584)
T PRK13406        465 RSLAGLPGG----GGTPLAAGLDAAAALALQVRR-------KGMTPTVVLLTDGRANI-ARD------------GT--AG  518 (584)
T ss_pred             HHHhcCCCC----CCChHHHHHHHHHHHHHHhcc-------CCCceEEEEEeCCCCCC-Ccc------------cc--cc
Confidence            999988722    235788899888887754221       12358999999876531 100            00  00


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccCC--chhHHHHHHHhcCC
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPKQ--LPKLTAIYNAAKRN  204 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPrq--lp~l~~Lfeka~~~  204 (834)
                      ....+.|+..+|+.+.+.+|.+++|..-.  ...+++|-++.++.
T Consensus       519 ~~~~~~~~~~~a~~~~~~gi~~~vId~g~~~~~~~~~LA~~~gg~  563 (584)
T PRK13406        519 RAQAEEDALAAARALRAAGLPALVIDTSPRPQPQARALAEAMGAR  563 (584)
T ss_pred             ccchhhHHHHHHHHHHhcCCeEEEEecCCCCcHHHHHHHHhcCCe
Confidence            01123467888999999999999998753  34577777766554

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=97.98  E-value=0.00011  Score=87.26  Aligned_cols=165  Identities=15%  Similarity=0.182  Sum_probs=103.1

Q ss_pred             ccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            4 KQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      ..|+||||+++||.. -|+.+|     -+++.|...      .+..+-+++||+|++...  +   ..++||.+...+..
T Consensus       408 ~~v~fvvD~SGSM~~~rl~~aK-----~av~~Ll~~------~~~~~D~v~Li~F~~~~a--~---~~lp~t~~~~~~~~  471 (589)
T TIGR02031       408 RLLIFVVDASGSAAVARMSEAK-----GAVELLLGE------AYVHRDQVSLIAFRGTAA--E---VLLPPSRSVEQAKR  471 (589)
T ss_pred             ceEEEEEECCCCCChHHHHHHH-----HHHHHHHHh------hccCCCEEEEEEECCCCc--e---EECCCCCCHHHHHH
Confidence            568999999999964 344444     334444321      111345899999987642  1   23678999999999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQA  162 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~  162 (834)
                      +|+.|.. |||   -.+++||..|++.+.....       ....+++|||+|--+-- +  ...    ..+ ++..+.  
T Consensus       472 ~L~~l~~-gGg---TpL~~gL~~A~~~~~~~~~-------~~~~~~ivllTDG~~nv-~--~~~----~~~-~~~~~~--  530 (589)
T TIGR02031       472 RLDVLPG-GGG---TPLAAGLAAAFQTALQARS-------SGGTPTIVLITDGRGNI-P--LDG----DPE-SIKADR--  530 (589)
T ss_pred             HHhcCCC-CCC---CcHHHHHHHHHHHHHHhcc-------cCCceEEEEECCCCCCC-C--CCc----ccc-cccccc--
Confidence            9999975 333   4567778888777653110       13457999999875421 1  000    000 000000  


Q ss_pred             hccCCCHHHHHHHHhhcCcEEEEeccCC----chhHHHHHHHhcCCC
Q 003284          163 ESRLSDAETVAKSFVQCSVSLSVICPKQ----LPKLTAIYNAAKRNP  205 (834)
Q Consensus       163 ~~~l~d~e~lA~~~~e~~I~LSvIsPrq----lp~l~~Lfeka~~~~  205 (834)
                      +-...++..+|+.+.+.+|.++||-...    ...+++|-++.+++-
T Consensus       531 ~~~~~~~~~~a~~~~~~gi~~~vid~~~~~~~~~~~~~lA~~~~g~y  577 (589)
T TIGR02031       531 EQAAEEALALARKIREAGMPALVIDTAMRFVSTGFAQKLARKMGAHY  577 (589)
T ss_pred             hhHHHHHHHHHHHHHhcCCeEEEEeCCCCCccchHHHHHHHhcCCcE
Confidence            0011245788999999999999997753    345888888777653

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.

>cd01458 vWA_ku Ku70/Ku80 N-terminal domain

Probab=97.91  E-value=7e-05  Score=77.50  Aligned_cols=154  Identities=16%  Similarity=0.128  Sum_probs=92.9

Q ss_pred             cEEEEEeccccchHhHH---HHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC-----CcccceeeccCCCC
Q 003284            5 QLIVAVEGTAAMGPYWQ---SIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS-----YCACLVQRSGWTKD   76 (834)
Q Consensus         5 dvVFVID~Tasmg~yi~---~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~-----~~~~lv~~~gfTsd   76 (834)
                      -||||||.+.+|..--+   .-+=+....++..|-...+.    ....-++|||+|++...     |....+-+-.-+.|
T Consensus         3 ~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~----~~~~D~vGlilf~t~~~~~~~~~~~i~v~~~l~~~~   78 (218)
T cd01458           3 SVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKII----SSPKDLVGVVFYGTEESKNPVGYENIYVLLDLDTPG   78 (218)
T ss_pred             EEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhcee----CCCCCeEEEEEEcccCCCCcCCCCceEEeecCCCCC
Confidence            58999999999962110   01111122333333221111    11346999999999863     22222222223778


Q ss_pred             HHHHHHHhccCccC------CCC-CchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecC-CCCCCCCCcccCC
Q 003284           77 VDIFLHWLSTIPFA------GGG-FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAAS-NPHPLPTPVYRPQ  148 (834)
Q Consensus        77 ~~~fl~~Ld~I~f~------GGG-~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~S-pP~~lp~pv~~p~  148 (834)
                      ...+..+++-+.-.      +.| ....++.+||..|+.+|....       .....|++|||+|. .|+. ...     
T Consensus        79 ~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~aL~~a~~~~~~~~-------~~~~~k~IvL~TDg~~p~~-~~~-----  145 (218)
T cd01458          79 AERVEDLKELIEPGGLSFAGQVGDSGQVSLSDALWVCLDLFSKGK-------KKKSHKRIFLFTNNDDPHG-GDS-----  145 (218)
T ss_pred             HHHHHHHHHHhhcchhhhcccCCCCCCccHHHHHHHHHHHHHhcc-------ccccccEEEEECCCCCCCC-CCH-----
Confidence            88777777655321      112 236789999999999996411       13457999999986 4443 100     


Q ss_pred             ccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          149 MQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       149 ~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                               .+      ..+++.+|+.+.+++|.|.+|...-
T Consensus       146 ---------~~------~~~~~~~a~~l~~~gI~i~~i~i~~  172 (218)
T cd01458         146 ---------IK------DSQAAVKAEDLKDKGIELELFPLSS  172 (218)
T ss_pred             ---------HH------HHHHHHHHHHHHhCCcEEEEEecCC
Confidence                     00      1245789999999999999998754

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.

>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=97.82  E-value=0.00055  Score=66.23  Aligned_cols=132  Identities=14%  Similarity=0.180  Sum_probs=80.1

Q ss_pred             ccEEEEEeccccchHh-HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            4 KQLIVAVEGTAAMGPY-WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         4 ~dvVFVID~Tasmg~y-i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      +||+||||+++||... +... +.-+.-+++.+..          ...+++||.|.+.  +   .........+..+++.
T Consensus         1 ~~v~illD~SgSM~~~k~~~a-~~~~~~l~~~~~~----------~~~~v~li~F~~~--~---~~~~~~~~~~~~~~~~   64 (152)
T cd01462           1 GPVILLVDQSGSMYGAPEEVA-KAVALALLRIALA----------ENRDTYLILFDSE--F---QTKIVDKTDDLEEPVE   64 (152)
T ss_pred             CCEEEEEECCCCCCCCHHHHH-HHHHHHHHHHHHH----------cCCcEEEEEeCCC--c---eEEecCCcccHHHHHH
Confidence            6899999999999853 2222 2223333333321          1358999999877  1   1223446788899999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQA  162 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~  162 (834)
                      +|..+.. |||   -.+++||..++.++....         ...+.+|+|+|-..-..+                     
T Consensus        65 ~l~~~~~-~gg---T~l~~al~~a~~~l~~~~---------~~~~~ivliTDG~~~~~~---------------------  110 (152)
T cd01462          65 FLSGVQL-GGG---TDINKALRYALELIERRD---------PRKADIVLITDGYEGGVS---------------------  110 (152)
T ss_pred             HHhcCCC-CCC---cCHHHHHHHHHHHHHhcC---------CCCceEEEECCCCCCCCC---------------------
Confidence            9987754 344   356777778877764311         124678888875310000                     


Q ss_pred             hccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          163 ESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       163 ~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                          .++...+++..++++.+++|.--
T Consensus       111 ----~~~~~~~~~~~~~~~~v~~~~~g  133 (152)
T cd01462         111 ----DELLREVELKRSRVARFVALALG  133 (152)
T ss_pred             ----HHHHHHHHHHHhcCcEEEEEEec
Confidence                01112366666778999999654

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

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=97.74  E-value=0.00061  Score=81.69  Aligned_cols=158  Identities=18%  Similarity=0.223  Sum_probs=101.3

Q ss_pred             CccEEEEEeccccchH--hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHH
Q 003284            3 EKQLIVAVEGTAAMGP--YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIF   80 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~--yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~f   80 (834)
                      ...||||||+++||+.  -|..+|.- +.-++....          ..+.++|||.|++...  +   ..+++|++...+
T Consensus       465 ~~~vv~vvD~SgSM~~~~rl~~ak~a-~~~ll~~a~----------~~~D~v~lI~F~g~~a--~---~~~p~t~~~~~~  528 (633)
T TIGR02442       465 GNLVIFVVDASGSMAARGRMAAAKGA-VLSLLRDAY----------QKRDKVALITFRGEEA--E---VLLPPTSSVELA  528 (633)
T ss_pred             CceEEEEEECCccCCCccHHHHHHHH-HHHHHHHhh----------cCCCEEEEEEECCCCc--e---EEcCCCCCHHHH
Confidence            3689999999999974  35555533 223332211          1357999999986522  1   246889999999


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      ..+|+.+...||    -.+++||..|+.++.....     ......+.+|||+|--+---.            .+     
T Consensus       529 ~~~L~~l~~gG~----Tpl~~aL~~A~~~l~~~~~-----~~~~~~~~vvliTDG~~n~~~------------~~-----  582 (633)
T TIGR02442       529 ARRLEELPTGGR----TPLAAGLLKAAEVLSNELL-----RDDDGRPLLVVITDGRANVAD------------GG-----  582 (633)
T ss_pred             HHHHHhCCCCCC----CCHHHHHHHHHHHHHHhhc-----cCCCCceEEEEECCCCCCCCC------------CC-----
Confidence            999999985333    4566777777776652100     012345788999876442100            00     


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCC
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRN  204 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~  204 (834)
                        ...+.|+..+|+.+.+.+|.+.+|...    ....+++|-+..++.
T Consensus       583 --~~~~~~~~~~a~~l~~~~i~~~vIdt~~~~~~~~~~~~lA~~~gg~  628 (633)
T TIGR02442       583 --EPPTDDARTIAAKLAARGILFVVIDTESGFVRLGLAEDLARALGGE  628 (633)
T ss_pred             --CChHHHHHHHHHHHHhcCCeEEEEeCCCCCcchhHHHHHHHhhCCe
Confidence              001235677899999999999999763    346688888776654

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.

>PF00362 Integrin_beta: Integrin, beta chain; InterPro: IPR002369 Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [, ]

Probab=97.74  E-value=0.00031  Score=80.53  Aligned_cols=174  Identities=10%  Similarity=0.033  Sum_probs=104.6

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcc-----------------c
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCA-----------------C   66 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~-----------------~   66 (834)
                      .||.|++|-+.+|+++++.||+. =..+.+.+..  +      ..++|+|+=.|-|.+-+|-                 .
T Consensus       103 vDLYyLmDlS~Sm~ddl~~l~~l-g~~l~~~~~~--i------t~~~~~GfGsfvdK~~~P~~~~~p~~l~~pc~~~~~~  173 (426)
T PF00362_consen  103 VDLYYLMDLSYSMKDDLENLKSL-GQDLAEEMRN--I------TSNFRLGFGSFVDKPVMPFVSTTPEKLKNPCPSKNPN  173 (426)
T ss_dssp             EEEEEEEE-SGGGHHHHHHHCCC-CHHHHHHHHT--T-------SSEEEEEEEESSSSSTTTST-SSHCHHSTSCCTTS-
T ss_pred             eeEEEEeechhhhhhhHHHHHHH-HHHHHHHHHh--c------CccceEechhhcccccCCcccCChhhhcCcccccCCC
Confidence            59999999999999999999975 4456666643  1      2468999999988763211                 0


Q ss_pred             ceeecc------CCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCcc-CCcEEEEeecCCCCC
Q 003284           67 LVQRSG------WTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVD-GQRHCILVAASNPHP  139 (834)
Q Consensus        67 lv~~~g------fTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~-~qkhCILIa~SpP~~  139 (834)
                      +...|+      .|+|..+|...+.+..++|+-|.||+-.+||--|+.|-+..       -|.. ..|.+|+.+|+++|-
T Consensus       174 c~~~~~f~~~l~Lt~~~~~F~~~v~~~~is~n~D~PEgg~dal~Qa~vC~~~i-------gWr~~a~~llv~~TD~~fH~  246 (426)
T PF00362_consen  174 CQPPFSFRHVLSLTDDITEFNEEVNKQKISGNLDAPEGGLDALMQAAVCQEEI-------GWRNEARRLLVFSTDAGFHF  246 (426)
T ss_dssp             -B---SEEEEEEEES-HHHHHHHHHTS--B--SSSSBSHHHHHHHHHH-HHHH-------T--STSEEEEEEEESS-B--
T ss_pred             CCCCeeeEEeecccchHHHHHHhhhhccccCCCCCCccccchheeeeeccccc-------CcccCceEEEEEEcCCcccc
Confidence            112233      49999999999999999999999999999999887665311       1233 556778999999997


Q ss_pred             CCC------------CcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC-chhHHHHHH
Q 003284          140 LPT------------PVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ-LPKLTAIYN  199 (834)
Q Consensus       140 lp~------------pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq-lp~l~~Lfe  199 (834)
                      ...            .|++.. ++ .|.++    ..-..-...+|++.+.|++|..=+...+. ...|++|-+
T Consensus       247 agDg~l~gi~~pnd~~Chl~~-~~-~y~~~----~~~DYPSv~ql~~~l~e~~i~~IFAVt~~~~~~Y~~L~~  313 (426)
T PF00362_consen  247 AGDGKLAGIVKPNDGKCHLDD-NG-MYTAS----TEQDYPSVGQLVRKLSENNINPIFAVTKDVYSIYEELSN  313 (426)
T ss_dssp             TTGGGGGT--S---SS--BST-TS-BBGGG----GCS----HHHHHHHHHHTTEEEEEEEEGGGHHHHHHHHH
T ss_pred             ccccccceeeecCCCceEECC-CC-ccccc----ccccCCCHHHHHHHHHHcCCEEEEEEchhhhhHHHHHhh
Confidence            654            343321 00 11111    11122356899999999999865444444 444444433

The integrin receptors are composed of alpha and beta subunit heterodimers. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus. Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits []. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans []. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule []. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another. The structure of unliganded alphaV beta3 showed the molecule to be folded, with the head bent over towards the C termini of the legs which would normally be inserted into the membrane []. The head comprises a beta propeller domain at the end terminus of the alphaV subunit and an I/A domain inserted into a loop on the top of the hybrid domain in the beta subunit. The I/A domain consists of a Rossman fold with a core of beta parallel sheets surrounded by amphipathic alpha helices. Integrins are important therapeutic targets in conditions such as atherosclerosis, thrombosis, cancer and asthma []. At the N terminus of the beta subunit is a cysteine-containing domain reminiscent of that found in presenillins and semaphorins, which has hence been termed the PSI domain. C-terminal to the PSI domain is an A-domain, which has been predicted to adopt a Rossmann fold similar to that of the alpha subunit, but with additional loops between the second and third beta strands []. The murine gene Pactolus shares significant similarity with the beta subunit [], but lacks either one or both of the inserted loops. The C-terminal portion of the beta subunit extracellular domain contains an internally disulphide-bonded cysteine-rich region, while the intracellular tail contains putative sites of interaction with a variety of intracellular signalling and cytoskeletal proteins, such as focal adhesion kinase and alpha-actinin respectively []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first 20 amino acids of the beta-subunit cytoplasmic domain are also alpha helical, but the final 25 residues are disordered and, apart from a turn that follows a conserved NPxY motif, appear to lack defined structure, suggesting that this is adopted on effector binding. The two membrane-proximal helices mediate the link between the subunits via a series of hydrophobic and electrostatic contacts. This entry represents the N-terminal portion of the extracellular region of integrin beta subunits.; GO: 0005488 binding, 0007155 cell adhesion, 0007160 cell-matrix adhesion; PDB: 3VI4_B 3VI3_B 2VDQ_B 3IJE_B 1M1X_B 2VDR_B 3NIF_B 3NID_D 1TYE_F 2Q6W_F ....

>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family

Probab=97.58  E-value=0.00087  Score=72.50  Aligned_cols=136  Identities=13%  Similarity=0.108  Sum_probs=91.1

Q ss_pred             CccEEEEEeccccchHh------HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCC
Q 003284            3 EKQLIVAVEGTAAMGPY------WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKD   76 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y------i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd   76 (834)
                      +.+|||+||-+.||...      +++ + ..|..+++.+.            .-++|||.|....      ...++||.|
T Consensus        60 ~~qIvlaID~S~SM~~~~~~~~alea-k-~lIs~al~~Le------------~g~vgVv~Fg~~~------~~v~Plt~d  119 (266)
T cd01460          60 DYQILIAIDDSKSMSENNSKKLALES-L-CLVSKALTLLE------------VGQLGVCSFGEDV------QILHPFDEQ  119 (266)
T ss_pred             CceEEEEEecchhcccccccccHHHH-H-HHHHHHHHhCc------------CCcEEEEEeCCCc------eEeCCCCCC
Confidence            47999999999999774      221 1 12333444442            2599999999862      245788888


Q ss_pred             HHH--HHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCC--CCCCCCCcccCCcccc
Q 003284           77 VDI--FLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASN--PHPLPTPVYRPQMQNL  152 (834)
Q Consensus        77 ~~~--fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~Sp--P~~lp~pv~~p~~~~~  152 (834)
                      ...  ++..++...|..+|   -.|..+|.+|+.+|++...+.   ......+-+|||+|--  .|.             
T Consensus       120 ~~~~a~~~~l~~~~f~~~~---Tni~~aL~~a~~~f~~~~~~~---~s~~~~qlilLISDG~~~~~e-------------  180 (266)
T cd01460         120 FSSQSGPRILNQFTFQQDK---TDIANLLKFTAQIFEDARTQS---SSGSLWQLLLIISDGRGEFSE-------------  180 (266)
T ss_pred             chhhHHHHHhCcccCCCCC---CcHHHHHHHHHHHHHhhhccc---cccccccEEEEEECCCcccCc-------------
Confidence            875  55556555555444   569999999999997531100   1111358889998765  221             


Q ss_pred             ccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCCc
Q 003284          153 DQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQL  191 (834)
Q Consensus       153 ~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrql  191 (834)
                                    .....+++.+.+++|.+++|.-+..
T Consensus       181 --------------~~~~~~~r~a~e~~i~l~~I~ld~~  205 (266)
T cd01460         181 --------------GAQKVRLREAREQNVFVVFIIIDNP  205 (266)
T ss_pred             --------------cHHHHHHHHHHHcCCeEEEEEEcCC
Confidence                          1234568999999999999999874

The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.

>TIGR00868 hCaCC calcium-activated chloride channel protein 1

Probab=97.57  E-value=0.0014  Score=80.54  Aligned_cols=107  Identities=14%  Similarity=0.266  Sum_probs=64.2

Q ss_pred             CccEEEEEeccccchH--hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC-----C
Q 003284            3 EKQLIVAVEGTAAMGP--YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT-----K   75 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~--yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT-----s   75 (834)
                      .++||||||.+++|..  -|+.+|.     .++.|-...+      ....++|||.|.+...      ...+++     .
T Consensus       304 ~r~VVLVLDvSGSM~g~dRL~~lkq-----AA~~fL~~~l------~~~DrVGLVtFsssA~------vl~pLt~Its~~  366 (863)
T TIGR00868       304 QRIVCLVLDKSGSMTVEDRLKRMNQ-----AAKLFLLQTV------EKGSWVGMVTFDSAAY------IKNELIQITSSA  366 (863)
T ss_pred             CceEEEEEECCccccccCHHHHHHH-----HHHHHHHHhC------CCCCEEEEEEECCcee------EeeccccCCcHH
Confidence            4789999999999974  3544442     2332211111      1246999999999743      112332     2


Q ss_pred             CHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           76 DVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        76 d~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      |...+...|. +. .+||   -+|.+||.+|++++.....       ....+++||++|--+.
T Consensus       367 dr~aL~~~L~-~~-A~GG---T~I~~GL~~Alq~L~~~~~-------~~~~~~IILLTDGedn  417 (863)
T TIGR00868       367 ERDALTANLP-TA-ASGG---TSICSGLKAAFQVIKKSYQ-------STDGSEIVLLTDGEDN  417 (863)
T ss_pred             HHHHHHHhhc-cc-cCCC---CcHHHHHHHHHHHHHhccc-------ccCCCEEEEEeCCCCC
Confidence            3444444443 22 3333   6889999999998864221       1234799999986543

distributions. found a row in 1A13.INFO that was not parsed out

>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein

Probab=97.46  E-value=0.0012  Score=78.53  Aligned_cols=107  Identities=13%  Similarity=0.191  Sum_probs=69.6

Q ss_pred             ccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC-CCHHHHH
Q 003284            4 KQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT-KDVDIFL   81 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT-sd~~~fl   81 (834)
                      ++||||||+++||.. .|+.+|.- +.-+|+.+..           ..+|+||.|.+...  ...-.....+ .+.....
T Consensus       272 ~~vvfvlD~SgSM~g~~i~~ak~a-l~~~l~~L~~-----------~d~~~ii~F~~~~~--~~~~~~~~~~~~~~~~a~  337 (596)
T TIGR03788       272 RELVFVIDTSGSMAGESIEQAKSA-LLLALDQLRP-----------GDRFNIIQFDSDVT--LLFPVPVPATAHNLARAR  337 (596)
T ss_pred             ceEEEEEECCCCCCCccHHHHHHH-HHHHHHhCCC-----------CCEEEEEEECCcce--EeccccccCCHHHHHHHH
Confidence            789999999999964 46666643 4455555532           35999999987743  1111112222 3567788


Q ss_pred             HHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCC
Q 003284           82 HWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASN  136 (834)
Q Consensus        82 ~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~Sp  136 (834)
                      .||+.|...||    -.++.||..|+..+...        .....|++|||+|--
T Consensus       338 ~~i~~l~a~Gg----T~l~~aL~~a~~~~~~~--------~~~~~~~iillTDG~  380 (596)
T TIGR03788       338 QFVAGLQADGG----TEMAGALSAALRDDGPE--------SSGALRQVVFLTDGA  380 (596)
T ss_pred             HHHhhCCCCCC----ccHHHHHHHHHHhhccc--------CCCceeEEEEEeCCC
Confidence            89999986543    34777888888764211        123468999999874

Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).

>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=97.31  E-value=0.0029  Score=64.62  Aligned_cols=110  Identities=12%  Similarity=0.190  Sum_probs=65.3

Q ss_pred             CccEEEEEeccccchHh--------HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC
Q 003284            3 EKQLIVAVEGTAAMGPY--------WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT   74 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y--------i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT   74 (834)
                      .+|+|||||.|+||+..        |+.++.- +.-++..+..       +  ....++|++|.+...      ..++.+
T Consensus         2 ~~dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~-~~~l~~~~~~-------~--D~d~i~l~~f~~~~~------~~~~~~   65 (199)
T cd01457           2 NRDYTLLIDKSGSMAEADEAKERSRWEEAQES-TRALARKCEE-------Y--DSDGITVYLFSGDFR------RYDNVN   65 (199)
T ss_pred             CcCEEEEEECCCcCCCCCCCCCchHHHHHHHH-HHHHHHHHHh-------c--CCCCeEEEEecCCcc------ccCCcC
Confidence            48999999999999853        5666533 4444444321       1  224577888866532      112333


Q ss_pred             CCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhh-cccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           75 KDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMM-FSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        75 sd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~-f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                        ...+..++.++...||    -.+..+|..|+.. +..... .   ......+++|+|++--|+
T Consensus        66 --~~~v~~~~~~~~p~G~----T~l~~~l~~a~~~~~~~~~~-~---~~~p~~~~vIiiTDG~~~  120 (199)
T cd01457          66 --SSKVDQLFAENSPDGG----TNLAAVLQDALNNYFQRKEN-G---ATCPEGETFLVITDGAPD  120 (199)
T ss_pred             --HHHHHHHHhcCCCCCc----CcHHHHHHHHHHHHHHHHhh-c---cCCCCceEEEEEcCCCCC
Confidence              7888888988875544    3455566666533 221110 0   011125899999998876

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

>PF03731 Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; InterPro: IPR005161 The Ku heterodimer (composed of Ku70 P12956 from SWISSPROT and Ku80 P13010 from SWISSPROT) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway

Probab=97.24  E-value=0.0089  Score=61.90  Aligned_cols=144  Identities=12%  Similarity=0.137  Sum_probs=78.4

Q ss_pred             EEEEEeccccch-------HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCc--------ccceee
Q 003284            6 LIVAVEGTAAMG-------PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYC--------ACLVQR   70 (834)
Q Consensus         6 vVFVID~Tasmg-------~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~--------~~lv~~   70 (834)
                      +|||||++.+|.       .+|+.+++-.-.-+.+.+..         ++..++|||+|++...-.        ..++-.
T Consensus         2 ~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~---------~~kD~vgvvl~gt~~t~n~~~~~~~~~i~~l~   72 (224)
T PF03731_consen    2 TVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIIS---------SPKDEVGVVLFGTDETNNPDEDSGYENIFVLQ   72 (224)
T ss_dssp             EEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHT---------T---EEEEEEES-SS-BST-TTT-STTEEEEE
T ss_pred             EEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcC---------CCCCeEEEEEEcCCCCCCcccccCCCceEEee
Confidence            799999999999       34555553322222222222         233699999999887632        112222


Q ss_pred             ccCCCCHHHHHHHhccCcc------CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecC-CCCCCCCC
Q 003284           71 SGWTKDVDIFLHWLSTIPF------AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAAS-NPHPLPTP  143 (834)
Q Consensus        71 ~gfTsd~~~fl~~Ld~I~f------~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~S-pP~~lp~p  143 (834)
                      .-=..+++.+....+-+.-      ..++.....+.++|..|+.+|...-     .......|+++||+|. .||.-.  
T Consensus        73 ~l~~~~~~~l~~L~~~~~~~~~~~~~~~~~~~~~l~~al~v~~~~~~~~~-----~~~k~~~krI~l~Td~d~p~~~~--  145 (224)
T PF03731_consen   73 PLDPPSAERLKELEELLKPGDKFENFFSGSDEGDLSDALWVASDMFRERT-----CKKKKNKKRIFLFTDNDGPHEDD--  145 (224)
T ss_dssp             ECC--BHHHHHHHHTTSHHHHHHHHHC-SSS---HHHHHHHHHHHHHCHC-----TTS-ECEEEEEEEES-SSTTT-C--
T ss_pred             cCCccCHHHHHHHHHhhcccccccccCCCCCccCHHHHHHHHHHHHHHHh-----hcccCCCcEEEEEeCCCCCCCCH--
Confidence            1113355555554444432      2445567789999999999986310     1234567899999965 666411  


Q ss_pred             cccCCccccccccchhhhhhccCCCHHHH-----HHHHhhcCcEEEEecc
Q 003284          144 VYRPQMQNLDQNENNEAQAESRLSDAETV-----AKSFVQCSVSLSVICP  188 (834)
Q Consensus       144 v~~p~~~~~~~~e~~~~~~~~~l~d~e~l-----A~~~~e~~I~LSvIsP  188 (834)
                                             .+.+.+     ++.+.+.+|.|.++-.
T Consensus       146 -----------------------~~~~~~~~~l~~~Dl~~~~i~~~~~~l  172 (224)
T PF03731_consen  146 -----------------------DELERIIQKLKAKDLQDNGIEIELFFL  172 (224)
T ss_dssp             -----------------------CCHHHHHHHHHHHHHHHHTEEEEEEEC
T ss_pred             -----------------------HHHHHHHHhhccccchhcCcceeEeec
Confidence                                   122333     6669999999888865

This is the N-terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [].; PDB: 1JEQ_A 1JEY_A.

>cd01455 vWA_F11C1-5a_type Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)

Probab=97.07  E-value=0.013  Score=60.74  Aligned_cols=153  Identities=10%  Similarity=-0.009  Sum_probs=93.8

Q ss_pred             ccEEEEEeccccchHhHHH------HHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCccccee-eccCCCC
Q 003284            4 KQLIVAVEGTAAMGPYWQS------IVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQ-RSGWTKD   76 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~------lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~-~~gfTsd   76 (834)
                      |.|+||||-++||-. |+.      =|-+-+...++.|.+. .+  +.  ..-++|+  ++++.+  -+++. -+++|.|
T Consensus         1 ~~l~lavDlSgSM~~-~~~~dg~~~~RL~a~k~v~~~f~~f-~~--~r--~~DriG~--~g~~~~--~~~lt~d~p~t~d   70 (191)
T cd01455           1 KRLKLVVDVSGSMYR-FNGYDGRLDRSLEAVVMVMEAFDGF-ED--KI--QYDIIGH--SGDGPC--VPFVKTNHPPKNN   70 (191)
T ss_pred             CceEEEEECcHhHHH-HhccCCccccHHHHHHHHHHHHHHH-HH--hC--ccceeee--cCcccc--cCccccccCcccc
Confidence            579999999999986 341      1222333445556421 01  11  1246663  444432  33433 4777777


Q ss_pred             H---HHHHHHhccCccCCCCCchhhHHHHHHHHHhhcc-cCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccc
Q 003284           77 V---DIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFS-VAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNL  152 (834)
Q Consensus        77 ~---~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~-~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~  152 (834)
                      .   +.+...|+...+   |..+..-+|||..|+..|. ..         ....|.+||++|.+=..-            
T Consensus        71 ~~~~~~l~~~l~~~q~---g~ag~~TadAi~~av~rl~~~~---------~a~~kvvILLTDG~n~~~------------  126 (191)
T cd01455          71 KERLETLKMMHAHSQF---CWSGDHTVEATEFAIKELAAKE---------DFDEAIVIVLSDANLERY------------  126 (191)
T ss_pred             hhHHHHHHHHHHhccc---CccCccHHHHHHHHHHHHHhcC---------cCCCcEEEEEeCCCcCCC------------
Confidence            7   577778887765   2222222299999999985 42         223689999997653211            


Q ss_pred             ccccchhhhhhccCCCHHHH-HHHHhhcCcEEEEeccCC--chhHHHHHHHhcC
Q 003284          153 DQNENNEAQAESRLSDAETV-AKSFVQCSVSLSVICPKQ--LPKLTAIYNAAKR  203 (834)
Q Consensus       153 ~~~e~~~~~~~~~l~d~e~l-A~~~~e~~I~LSvIsPrq--lp~l~~Lfeka~~  203 (834)
                                  + -+++++ |++.++.||+++.|.-=.  -..|+.+-+..++
T Consensus       127 ------------~-i~P~~aAa~lA~~~gV~iytIgiG~~d~~~l~~iA~~tgG  167 (191)
T cd01455         127 ------------G-IQPKKLADALAREPNVNAFVIFIGSLSDEADQLQRELPAG  167 (191)
T ss_pred             ------------C-CChHHHHHHHHHhCCCEEEEEEecCCCHHHHHHHHhCCCC
Confidence                        1 266775 688889999999998654  4666666665443

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

>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex

Probab=96.88  E-value=0.022  Score=59.19  Aligned_cols=160  Identities=16%  Similarity=0.210  Sum_probs=107.3

Q ss_pred             EEeccccchH--hHHH---HHHHHHHHHH-HHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            9 AVEGTAAMGP--YWQS---IVSDYLEKII-RCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         9 VID~Tasmg~--yi~~---lkt~YI~p~l-e~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      |||.+.+|..  |-+.   +...|++..+ |||...++         ..+|+|+-|+.-     .-+...++.++.+..+
T Consensus         1 viD~S~~m~~~D~~PtRl~~~~~~l~~Fv~eff~qNPi---------Sqlgii~~~~~~-----a~~ls~lsgn~~~h~~   66 (193)
T PF04056_consen    1 VIDMSEAMREKDLKPTRLQCVLKALEEFVREFFDQNPI---------SQLGIIVMRDGR-----AERLSELSGNPQEHIE   66 (193)
T ss_pred             CeechHhHHhCcCCccHHHHHHHHHHHHHHHHHhcCCh---------hheeeeeeecce-----eEEeeecCCCHHHHHH
Confidence            6788887752  2221   1122233332 33444333         699999999873     2345678899999999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQA  162 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~  162 (834)
                      .|+++... +..++..+-.||..|...+...+        ....|-+++|..|-=                         
T Consensus        67 ~L~~~~~~-~~~G~~SLqN~Le~A~~~L~~~p--------~~~srEIlvi~gSl~-------------------------  112 (193)
T PF04056_consen   67 ALKKLRKL-EPSGEPSLQNGLEMARSSLKHMP--------SHGSREILVIFGSLT-------------------------  112 (193)
T ss_pred             HHHHhccC-CCCCChhHHHHHHHHHHHHhhCc--------cccceEEEEEEeecc-------------------------
Confidence            99888633 23345678899999998886433        234677777753321                         


Q ss_pred             hccCCCHHHHHHHHhhcCcEEEEeccC-CchhHHHHHHHhcCCCCCCCCCCCCCCCCCeEEEeeccchhh
Q 003284          163 ESRLSDAETVAKSFVQCSVSLSVICPK-QLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEA  231 (834)
Q Consensus       163 ~~~l~d~e~lA~~~~e~~I~LSvIsPr-qlp~l~~Lfeka~~~~~~~~~~~~~ak~p~hlVLLsg~~l~~  231 (834)
                      .+...|...+++.+.+.+|.+|||+.- .+-.+|+|.++.++.               |.|.|.+.-+++
T Consensus       113 t~Dp~di~~ti~~l~~~~IrvsvI~laaEv~I~k~i~~~T~G~---------------y~V~lde~H~~~  167 (193)
T PF04056_consen  113 TCDPGDIHETIESLKKENIRVSVISLAAEVYICKKICKETGGT---------------YGVILDEDHFKE  167 (193)
T ss_pred             cCCchhHHHHHHHHHHcCCEEEEEEEhHHHHHHHHHHHhhCCE---------------EEEecCHHHHHH
Confidence            112246788999999999999999876 478999999988863               667777655554

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

>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=96.67  E-value=0.017  Score=60.94  Aligned_cols=177  Identities=14%  Similarity=0.172  Sum_probs=85.9

Q ss_pred             EEEEEeccc--cchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCC----C-----------------
Q 003284            6 LIVAVEGTA--AMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHG----S-----------------   62 (834)
Q Consensus         6 vVFVID~Ta--smg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~----~-----------------   62 (834)
                      .|||||.|-  .-..+++.+++. |..+|+.+.         ...+.++|||+|.+.=    -                 
T Consensus         6 y~FvID~s~~av~~g~~~~~~~s-l~~~l~~l~---------~~~~~~vgiitfd~~V~~y~l~~~~~~~~~~v~~dl~~   75 (243)
T PF04811_consen    6 YVFVIDVSYEAVQSGLLQSLIES-LKSALDSLP---------GDERTRVGIITFDSSVHFYNLSSSLSQPQMIVVSDLDD   75 (243)
T ss_dssp             EEEEEE-SHHHHHHTHHHHHHHH-HHHHGCTSS---------TSTT-EEEEEEESSSEEEEETTTTSSSTEEEEEHHTTS
T ss_pred             EEEEEECchhhhhccHHHHHHHH-HHHHHHhcc---------CCCCcEEEEEEeCCEEEEEECCCCcCCCcccchHHHhh
Confidence            699999984  234455555533 333443332         1257999999997521    0                 


Q ss_pred             -----CcccceeeccCCCCHHHHHHHhccCccCCC-C-CchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecC
Q 003284           63 -----YCACLVQRSGWTKDVDIFLHWLSTIPFAGG-G-FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAAS  135 (834)
Q Consensus        63 -----~~~~lv~~~gfTsd~~~fl~~Ld~I~f~GG-G-~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~S  135 (834)
                           ..++++.....-..+..+++.|.. .|... + ..+.|...||.+|+.++....          .--++++.+.+
T Consensus        76 ~~~p~~~~llv~~~e~~~~i~~ll~~L~~-~~~~~~~~~~~~c~G~Al~~A~~ll~~~~----------~gGkI~~F~s~  144 (243)
T PF04811_consen   76 PFIPLPDGLLVPLSECRDAIEELLESLPS-IFPETAGKRPERCLGSALSAALSLLSSRN----------TGGKILVFTSG  144 (243)
T ss_dssp             HHSSTSSSSSEETTTCHHHHHHHHHHHHH-HSTT-TTB-----HHHHHHHHHHHHHHHT----------S-EEEEEEESS
T ss_pred             cccCCcccEEEEhHHhHHHHHHHHHHhhh-hcccccccCccccHHHHHHHHHHHHhccc----------cCCEEEEEecc
Confidence                 111122211111224444455554 22222 2 346889999999999986211          23466777777


Q ss_pred             CCCCCC-CCcccCCcc-ccccccc--hhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC----chhHHHHHHHhcCCC
Q 003284          136 NPHPLP-TPVYRPQMQ-NLDQNEN--NEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ----LPKLTAIYNAAKRNP  205 (834)
Q Consensus       136 pP~~lp-~pv~~p~~~-~~~~~e~--~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq----lp~l~~Lfeka~~~~  205 (834)
                      +|.-=| . +....-. +.+..+.  ..+.+... .-.+.||+.|.+.+|.+.+.+--.    +..|..|....+|+.
T Consensus       145 ~pt~G~Gg-~l~~~~~~~~~~~~~~~~~~~~~~~-~fY~~la~~~~~~~isvDlf~~~~~~~~l~tl~~l~~~TGG~l  220 (243)
T PF04811_consen  145 PPTYGPGG-SLKKREDSSHYDTEKEKALLLPPAN-EFYKKLAEECSKQGISVDLFVFSSDYVDLATLGPLARYTGGSL  220 (243)
T ss_dssp             ---SSSTT-SS-SBTTSCCCCHCTTHHCHSHSSS-HHHHHHHHHHHHCTEEEEEEEECSS--SHHHHTHHHHCTT-EE
T ss_pred             CCCCCCCc-eecccccccccccccchhhhccccc-hHHHHHHHHHHhcCCEEEEEeecCCCCCcHhHHHHHHhCceeE
Confidence            874333 1 1000000 1111011  11111111 125899999999999777654332    688888888777764

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 ....

>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]

Probab=96.66  E-value=0.00053  Score=85.19  Aligned_cols=23  Identities=9%  Similarity=0.166  Sum_probs=11.1

Q ss_pred             hhcCcEEEEeccCCchhHHHHHHHhc
Q 003284          177 VQCSVSLSVICPKQLPKLTAIYNAAK  202 (834)
Q Consensus       177 ~e~~I~LSvIsPrqlp~l~~Lfeka~  202 (834)
                      .+.|..+|  .+.|. +--+|||-.|
T Consensus      1709 kK~Glqvs--tkqk~-spwdlFEg~k 1731 (2220)
T KOG3598|consen 1709 KKNGLQVS--TKQKK-SPWDLFEGTK 1731 (2220)
T ss_pred             hhcCceec--ccccc-CcchhhccCC
Confidence            55555443  33332 2346777544

>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]

Probab=96.14  E-value=0.0013  Score=82.01  Aligned_cols=11  Identities=27%  Similarity=0.229  Sum_probs=5.5

Q ss_pred             CCCCCCCCccc
Q 003284          523 TMIPTPGMSQQ  533 (834)
Q Consensus       523 ~m~p~~gm~q~  533 (834)
                      +|+++.+|...
T Consensus      1995 a~g~~~~m~p~ 2005 (2220)
T KOG3598|consen 1995 AMGNTSSMPPS 2005 (2220)
T ss_pred             ccCCCCCcCCC
Confidence            45555555543

>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]

Probab=96.04  E-value=0.035  Score=57.38  Aligned_cols=160  Identities=21%  Similarity=0.188  Sum_probs=96.6

Q ss_pred             CCCccEEEEEeccccc-hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHH
Q 003284            1 MSEKQLIVAVEGTAAM-GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDI   79 (834)
Q Consensus         1 ~~~~dvVFVID~Tasm-g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~   79 (834)
                      |.+.-++|++|++++| |.-|+.|. +-|..+++.+...+.+.     .+.++++|+|..+--      ...+|| |+..
T Consensus         1 mrRlP~~lllDtSgSM~Ge~IealN-~Glq~m~~~Lkqdp~Al-----e~v~lsIVTF~~~a~------~~~pf~-~~~n   67 (207)
T COG4245           1 MRRLPCYLLLDTSGSMIGEPIEALN-AGLQMMIDTLKQDPYAL-----ERVELSIVTFGGPAR------VIQPFT-DAAN   67 (207)
T ss_pred             CCCCCEEEEEecCcccccccHHHHH-HHHHHHHHHHHhChhhh-----heeEEEEEEecCcce------EEechh-hHhh
Confidence            5667799999999999 55666665 66899999998866543     468999999986421      222333 3332


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      |.   =-+-+.+||-   .+..||..|+.|.++.....-.+.-.+..-.++||+|..|-    -.|.             
T Consensus        68 F~---~p~L~a~GgT---~lGaAl~~a~d~Ie~~~~~~~a~~kgdyrP~vfLiTDG~Pt----D~w~-------------  124 (207)
T COG4245          68 FN---PPILTAQGGT---PLGAALTLALDMIEERKRKYDANGKGDYRPWVFLITDGEPT----DDWQ-------------  124 (207)
T ss_pred             cC---CCceecCCCC---chHHHHHHHHHHHHHHHhhcccCCccccceEEEEecCCCcc----hHHH-------------
Confidence            21   1223344553   23445666777777643333333445566778999999882    2211             


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccC--CchhHHHHHHHhc
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPK--QLPKLTAIYNAAK  202 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr--qlp~l~~Lfeka~  202 (834)
                      +...-+    ++  +.-..++|..+.+-+.  +++.|+.|+|+-.
T Consensus       125 ~~~~~~----~~--~~~~~k~v~a~~~G~~~ad~~~L~qit~~V~  163 (207)
T COG4245         125 AGAALV----FQ--GERRAKSVAAFSVGVQGADNKTLNQITEKVR  163 (207)
T ss_pred             hHHHHh----hh--cccccceEEEEEecccccccHHHHHHHHhhc
Confidence            000000    11  1113355666666666  6899999998754

>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70)

Probab=95.39  E-value=0.13  Score=61.57  Aligned_cols=152  Identities=19%  Similarity=0.138  Sum_probs=86.7

Q ss_pred             cEEEEEeccccchHhHHH-----HHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC-----CcccceeeccCC
Q 003284            5 QLIVAVEGTAAMGPYWQS-----IVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS-----YCACLVQRSGWT   74 (834)
Q Consensus         5 dvVFVID~Tasmg~yi~~-----lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~-----~~~~lv~~~gfT   74 (834)
                      -|||+||++.+|..-...     =... +..|+..+....+-    ..+..++|||+|++-.+     |..++|-+.==.
T Consensus        12 ailflIDvs~sM~~~~~~~~~~s~~~~-al~~i~~l~q~kIi----s~~~D~vGivlfgT~~t~n~~~~~~i~v~~~L~~   86 (584)
T TIGR00578        12 SLIFLVDASKAMFEESQGEDELTPFDM-SIQCIQSVYTSKII----SSDKDLLAVVFYGTEKDKNSVNFKNIYVLQELDN   86 (584)
T ss_pred             EEEEEEECCHHHcCCCcCcCcCChHHH-HHHHHHHHHHhcCC----CCCCCeEEEEEEeccCCCCccCCCceEEEeeCCC
Confidence            389999999999841111     0111 22344444333221    22457999999999764     444444332223


Q ss_pred             CCHHHHHHHhccCccCCC---------CCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecC-CCCCCCCCc
Q 003284           75 KDVDIFLHWLSTIPFAGG---------GFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAAS-NPHPLPTPV  144 (834)
Q Consensus        75 sd~~~fl~~Ld~I~f~GG---------G~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~S-pP~~lp~pv  144 (834)
                      .|++.+ +.|+.|.-..|         ......++++|-.|+.+|....       .....|+++||+|. .||.-... 
T Consensus        87 p~a~~i-~~L~~l~~~~~~~~~~~~~~~~~~~~l~daL~~~~~~f~~~~-------~k~~~kRI~lfTd~D~P~~~~~~-  157 (584)
T TIGR00578        87 PGAKRI-LELDQFKGDQGPKKFRDTYGHGSDYSLSEVLWVCANLFSDVQ-------FRMSHKRIMLFTNEDNPHGNDSA-  157 (584)
T ss_pred             CCHHHH-HHHHHHhhccCccchhhccCCCCCCcHHHHHHHHHHHHHhcc-------hhhcCcEEEEECCCCCCCCCchh-
Confidence            344443 33333321101         1123478999999999996321       13357888888876 67642210 


Q ss_pred             ccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          145 YRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       145 ~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                                       ..   .-+.+.|+.|.+.||.|-++..+.
T Consensus       158 -----------------~~---~~a~~~a~dl~~~gi~ielf~l~~  183 (584)
T TIGR00578       158 -----------------KA---SRARTKAGDLRDTGIFLDLMHLKK  183 (584)
T ss_pred             -----------------HH---HHHHHHHHHHHhcCeEEEEEecCC
Confidence                             00   013568999999999999985543

Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.

>cd01468 trunk_domain trunk domain

Probab=94.82  E-value=0.66  Score=49.11  Aligned_cols=177  Identities=10%  Similarity=0.138  Sum_probs=94.8

Q ss_pred             cEEEEEecccc--chHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCC---c------cccee----
Q 003284            5 QLIVAVEGTAA--MGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY---C------ACLVQ----   69 (834)
Q Consensus         5 dvVFVID~Tas--mg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~---~------~~lv~----   69 (834)
                      -.|||||.+..  -..+++.+++- |.-+|+.+-.         ..+.++|||+|.++=.+   .      ..++-    
T Consensus         5 ~~vFvID~s~~ai~~~~l~~~~~s-l~~~l~~lp~---------~~~~~igiITf~~~V~~~~~~~~~~~~~~~v~~dl~   74 (239)
T cd01468           5 VFVFVIDVSYEAIKEGLLQALKES-LLASLDLLPG---------DPRARVGLITYDSTVHFYNLSSDLAQPKMYVVSDLK   74 (239)
T ss_pred             EEEEEEEcchHhccccHHHHHHHH-HHHHHHhCCC---------CCCcEEEEEEeCCeEEEEECCCCCCCCeEEEeCCCc
Confidence            36999999874  14456777754 5566665521         14689999999653111   1      01110    


Q ss_pred             ------eccCCCCH----HHHHHHhccCccCCC----CCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecC
Q 003284           70 ------RSGWTKDV----DIFLHWLSTIPFAGG----GFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAAS  135 (834)
Q Consensus        70 ------~~gfTsd~----~~fl~~Ld~I~f~GG----G~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~S  135 (834)
                            ..+|.-++    +.+...|+.|.-...    .-...|...||.+|+.++....          .--++++.+.+
T Consensus        75 d~f~p~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~----------~gGkI~~f~sg  144 (239)
T cd01468          75 DVFLPLPDRFLVPLSECKKVIHDLLEQLPPMFWPVPTHRPERCLGPALQAAFLLLKGTF----------AGGRIIVFQGG  144 (239)
T ss_pred             cCcCCCcCceeeeHHHHHHHHHHHHHhhhhhccccCCCCCcccHHHHHHHHHHHHhhcC----------CCceEEEEECC
Confidence                  01122222    344556666643332    2346888899999999886321          12345555556


Q ss_pred             CCC-CCCCCccc---CCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCCC
Q 003284          136 NPH-PLPTPVYR---PQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       136 pP~-~lp~pv~~---p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~~  205 (834)
                      +|- +...-..+   ..+.+  +.| .+..+... .-.+.||..|.+++|.+.+.+--    .+..+..|.+..++..
T Consensus       145 ~pt~GpG~l~~~~~~~~~~~--~~e-~~~~~~a~-~fY~~la~~~~~~~isvdlF~~~~~~~dl~~l~~l~~~TGG~v  218 (239)
T cd01468         145 LPTVGPGKLKSREDKEPIRS--HDE-AQLLKPAT-KFYKSLAKECVKSGICVDLFAFSLDYVDVATLKQLAKSTGGQV  218 (239)
T ss_pred             CCCCCCCccccCcccccCCC--ccc-hhcccccH-HHHHHHHHHHHHcCeEEEEEeccccccCHHHhhhhhhcCCceE
Confidence            663 22211000   00000  000 01111111 12378999999999999887532    3577888877777664

COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family possess a partial MIDAS motif that is a characteristic feature of most vWA domain proteins.

>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles

Probab=94.79  E-value=0.48  Score=50.59  Aligned_cols=176  Identities=13%  Similarity=0.182  Sum_probs=94.1

Q ss_pred             EEEEEeccccch--HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCC---cc-------cce----e
Q 003284            6 LIVAVEGTAAMG--PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY---CA-------CLV----Q   69 (834)
Q Consensus         6 vVFVID~Tasmg--~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~---~~-------~lv----~   69 (834)
                      .|||||.|..=-  .+++.+++- |.-+|+.+-.      +  -.+.++|||+|.+.=-+   ..       .++    .
T Consensus         6 ~~FvIDvs~~a~~~g~~~~~~~s-i~~~L~~lp~------~--~~~~~VgiITfd~~v~~y~l~~~~~~~q~~vv~dl~d   76 (244)
T cd01479           6 YVFLIDVSYNAIKSGLLATACEA-LLSNLDNLPG------D--DPRTRVGFITFDSTLHFFNLKSSLEQPQMMVVSDLDD   76 (244)
T ss_pred             EEEEEEccHHHHhhChHHHHHHH-HHHHHHhcCC------C--CCCeEEEEEEECCeEEEEECCCCCCCCeEEEeeCccc
Confidence            699999876221  145555544 4455555422      1  14689999999874211   00       011    0


Q ss_pred             e-----ccCCCCHH----HHHHHhccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           70 R-----SGWTKDVD----IFLHWLSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        70 ~-----~gfTsd~~----~fl~~Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      .     .+|.-++.    .+...|+.|.  |.-+.....|...||.+|+.++...            --++|+.+.++|-
T Consensus        77 ~f~P~~~~~lv~l~e~~~~i~~lL~~L~~~~~~~~~~~~c~G~Al~~A~~lL~~~------------GGkIi~f~s~~pt  144 (244)
T cd01479          77 PFLPLPDGLLVNLKESRQVIEDLLDQIPEMFQDTKETESALGPALQAAFLLLKET------------GGKIIVFQSSLPT  144 (244)
T ss_pred             ccCCCCcceeecHHHHHHHHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHhc------------CCEEEEEeCCCCC
Confidence            1     11222233    3334555553  2233345788999999999988621            1355666666654


Q ss_pred             CCC-CCcccC--CccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEec--cC--CchhHHHHHHHhcCCC
Q 003284          139 PLP-TPVYRP--QMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVIC--PK--QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       139 ~lp-~pv~~p--~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIs--Pr--qlp~l~~Lfeka~~~~  205 (834)
                      -=| .-+-+.  .+-+-+ .|. ...+... .-.+.+|..|.+++|.+.+.+  ..  .+..+..|-+..+|..
T Consensus       145 ~GpG~l~~~~~~~~~~~~-~e~-~~~~p~~-~fY~~la~~~~~~~isvDlF~~~~~~~dla~l~~l~~~TGG~v  215 (244)
T cd01479         145 LGAGKLKSREDPKLLSTD-KEK-QLLQPQT-DFYKKLALECVKSQISVDLFLFSNQYVDVATLGCLSRLTGGQV  215 (244)
T ss_pred             cCCcccccCccccccCch-hhh-hhcCcch-HHHHHHHHHHHHcCeEEEEEEccCcccChhhhhhhhhhcCceE
Confidence            222 111000  000000 111 1111111 124789999999999998875  22  3578888888888775

The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24

>PF06707 DUF1194: Protein of unknown function (DUF1194); InterPro: IPR010607 This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length

Probab=94.30  E-value=0.85  Score=48.06  Aligned_cols=161  Identities=18%  Similarity=0.221  Sum_probs=99.2

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC-----CCH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT-----KDV   77 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT-----sd~   77 (834)
                      +.+||+.||.++|+-..=-.|..   +=+..-|.+..+.+.=..+..-+++|-+|-=.++  ..-....+||     .|.
T Consensus         3 dlaLvLavDvS~SVD~~E~~lQ~---~G~A~Al~dp~V~~Ai~~g~~g~Iav~~~eWsg~--~~q~~~v~Wt~i~~~~da   77 (205)
T PF06707_consen    3 DLALVLAVDVSGSVDADEYRLQR---EGYAAALRDPEVIAAILSGPIGRIAVAVVEWSGP--GRQRVVVPWTRIDSPADA   77 (205)
T ss_pred             cceeeeeeeccCCCCHHHHHHHH---HHHHHHHCCHHHHHHHhcCCCCeEEEEEEEecCC--CCceEEeCCEEeCCHHHH
Confidence            35799999999999875333332   2344444443222111112223444444443332  2333457784     578


Q ss_pred             HHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccc
Q 003284           78 DIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNEN  157 (834)
Q Consensus        78 ~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~  157 (834)
                      ..|-..|...+...+++  -+|.+||..|+.+|+..+        ..+.|++|.|.--=|.                   
T Consensus        78 ~a~A~~l~~~~r~~~~~--Taig~Al~~a~~ll~~~~--------~~~~RrVIDvSGDG~~-------------------  128 (205)
T PF06707_consen   78 EAFAARLRAAPRRFGGR--TAIGSALDFAAALLAQNP--------FECWRRVIDVSGDGPN-------------------  128 (205)
T ss_pred             HHHHHHHHhCCCCCCCC--chHHHHHHHHHHHHHhCC--------CCCceEEEEECCCCCC-------------------
Confidence            88888999988777776  899999999999998533        3478899988622111                   


Q ss_pred             hhhhhhccCCCHHHHHHHHhhcCcEEEEeccCCc-h----hHHHHHHHhc
Q 003284          158 NEAQAESRLSDAETVAKSFVQCSVSLSVICPKQL-P----KLTAIYNAAK  202 (834)
Q Consensus       158 ~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrql-p----~l~~Lfeka~  202 (834)
                           .++....+.+-+.+..+||.+.-+.--.- +    .|.+-|+...
T Consensus       129 -----N~G~~p~~~ard~~~~~GitINgL~I~~~~~~~~~~L~~yy~~~V  173 (205)
T PF06707_consen  129 -----NQGPRPVTSARDAAVAAGITINGLAILDDDPFGGADLDAYYRRCV  173 (205)
T ss_pred             -----CCCCCccHHHHHHHHHCCeEEeeeEecCCCCCccccHHHHHhhhc
Confidence                 12222223556677888999987654432 3    5888888654

The function of this family is unknown.

>PF11498 Activator_LAG-3: Transcriptional activator LAG-3; InterPro: IPR021587 The C

Probab=93.82  E-value=0.017  Score=63.90  Aligned_cols=17  Identities=29%  Similarity=0.477  Sum_probs=0.0

Q ss_pred             CCCCcCccCCCCCCCCc
Q 003284          789 LSQPQQMVGSGMGQGYV  805 (834)
Q Consensus       789 qQqQqQ~~~~~~~q~~~  805 (834)
                      +..+...+|.|||-++-
T Consensus       427 q~hQn~~MGYgmPngyp  443 (468)
T PF11498_consen  427 QHHQNGGMGYGMPNGYP  443 (468)
T ss_dssp             -----------------
T ss_pred             chhhccCcccCCCCCCC
Confidence            33455667777765553

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 []. ; PDB: 2FO1_D.

>PF05762 VWA_CoxE: VWA domain containing CoxE-like protein; InterPro: IPR008912 This group of proteins contains a VWA type domain and the function of this family is unknown

Probab=93.54  E-value=0.48  Score=49.79  Aligned_cols=129  Identities=14%  Similarity=0.191  Sum_probs=70.1

Q ss_pred             cEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHHHh
Q 003284            5 QLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWL   84 (834)
Q Consensus         5 dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~~L   84 (834)
                      .||||+|.++||..|...+     ..++..+..      .+    -++-+++|.+.-.   .++..+ -..|+.+.+.-+
T Consensus        59 ~lvvl~DvSGSM~~~s~~~-----l~~~~~l~~------~~----~~~~~f~F~~~l~---~vT~~l-~~~~~~~~l~~~  119 (222)
T PF05762_consen   59 RLVVLCDVSGSMAGYSEFM-----LAFLYALQR------QF----RRVRVFVFSTRLT---EVTPLL-RRRDPEEALARL  119 (222)
T ss_pred             cEEEEEeCCCChHHHHHHH-----HHHHHHHHH------hC----CCEEEEEEeeehh---hhhhhh-ccCCHHHHHHHH
Confidence            7999999999999995433     334444432      11    2677788876521   111111 113555555544


Q ss_pred             c-cCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhhh
Q 003284           85 S-TIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAE  163 (834)
Q Consensus        85 d-~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~~  163 (834)
                      . .+...|||   -.|.++|.+++..+...        .. ....+|+|+|.  +...                      
T Consensus       120 ~~~~~~~~Gg---Tdi~~aL~~~~~~~~~~--------~~-~~t~vvIiSDg--~~~~----------------------  163 (222)
T PF05762_consen  120 SALVQSFGGG---TDIGQALREFLRQYARP--------DL-RRTTVVIISDG--WDTN----------------------  163 (222)
T ss_pred             HhhccCCCCc---cHHHHHHHHHHHHhhcc--------cc-cCcEEEEEecc--cccC----------------------
Confidence            3 22223333   33556666666655310        01 13455666663  1000                      


Q ss_pred             ccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          164 SRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       164 ~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                       ...+.+...+.+.+++-.|..+.|-
T Consensus       164 -~~~~~~~~l~~l~~r~~rviwLnP~  188 (222)
T PF05762_consen  164 -DPEPLAEELRRLRRRGRRVIWLNPL  188 (222)
T ss_pred             -ChHHHHHHHHHHHHhCCEEEEECCc
Confidence             0113456667788999999999996

It is found as part of a CO oxidising (Cox) system operon in several bacteria [].

>PRK10997 yieM hypothetical protein; Provisional

Probab=92.89  E-value=1.3  Score=52.09  Aligned_cols=141  Identities=15%  Similarity=0.243  Sum_probs=76.4

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHH---HHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHH
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEK---IIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIF   80 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p---~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~f   80 (834)
                      -.||+|||+++||..+    +.+|-.-   .+-+.--         ..+-+++|+.|.+.-.  .+   ...-......+
T Consensus       324 GpiII~VDtSGSM~G~----ke~~AkalAaAL~~iAl---------~q~dr~~li~Fs~~i~--~~---~l~~~~gl~~l  385 (487)
T PRK10997        324 GPFIVCVDTSGSMGGF----NEQCAKAFCLALMRIAL---------AENRRCYIMLFSTEVV--TY---ELTGPDGLEQA  385 (487)
T ss_pred             CcEEEEEECCCCCCCC----HHHHHHHHHHHHHHHHH---------hcCCCEEEEEecCCce--ee---ccCCccCHHHH
Confidence            5799999999999844    2222222   2222211         1234778999988532  11   12233457788


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      +..|+.. | |||   -.+..+|.+++.......       +.  .--+|+|+|=--...|                   
T Consensus       386 l~fL~~~-f-~GG---TDl~~aL~~al~~l~~~~-------~r--~adIVVISDF~~~~~~-------------------  432 (487)
T PRK10997        386 IRFLSQS-F-RGG---TDLAPCLRAIIEKMQGRE-------WF--DADAVVISDFIAQRLP-------------------  432 (487)
T ss_pred             HHHHHHh-c-CCC---CcHHHHHHHHHHHHcccc-------cC--CceEEEECCCCCCCCh-------------------
Confidence            8888754 4 444   224555566665553210       11  1124555532111111                   


Q ss_pred             hhhccCCCHHHHHHHHhh-cCcEEEEeccCC--chhHHHHHHHh
Q 003284          161 QAESRLSDAETVAKSFVQ-CSVSLSVICPKQ--LPKLTAIYNAA  201 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e-~~I~LSvIsPrq--lp~l~~Lfeka  201 (834)
                            .+.+.-.+.+.+ ++..|..|+--.  .|.|.++|++.
T Consensus       433 ------eel~~~L~~Lk~~~~~rf~~l~i~~~~~p~l~~ifD~~  470 (487)
T PRK10997        433 ------DELVAKVKELQRQHQHRFHAVAMSAHGKPGIMRIFDHI  470 (487)
T ss_pred             ------HHHHHHHHHHHHhcCcEEEEEEeCCCCCchHHHhcCee
Confidence                  012333345555 888888888764  69999999854

>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]

Probab=91.89  E-value=4  Score=45.63  Aligned_cols=150  Identities=17%  Similarity=0.232  Sum_probs=94.3

Q ss_pred             ccEEEEEeccccchH-----hHHHHHHHHHHHH-HHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCH
Q 003284            4 KQLIVAVEGTAAMGP-----YWQSIVSDYLEKI-IRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDV   77 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-----yi~~lkt~YI~p~-le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~   77 (834)
                      +-+++|||++-+|..     -.-.+...|++-. .|+|...++         ..+|||..+|---  +-+   ...|.++
T Consensus        61 Rhl~iviD~S~am~e~Df~P~r~a~~~K~le~Fv~eFFdQNPi---------SQigii~~k~g~A--~~l---t~ltgnp  126 (378)
T KOG2807|consen   61 RHLYIVIDCSRAMEEKDFRPSRFANVIKYLEGFVPEFFDQNPI---------SQIGIISIKDGKA--DRL---TDLTGNP  126 (378)
T ss_pred             eeEEEEEEhhhhhhhccCCchHHHHHHHHHHHHHHHHhccCch---------hheeEEEEecchh--hHH---HHhcCCH
Confidence            468999999988852     2223333344433 334444444         5899999998722  223   4568899


Q ss_pred             HHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccc
Q 003284           78 DIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNEN  157 (834)
Q Consensus        78 ~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~  157 (834)
                      .+-...|.++.+-+|-|+   +.-||.-|...+...+        ..+.|-+++|-.|=                     
T Consensus       127 ~~hI~aL~~~~~~~g~fS---LqNaLe~a~~~Lk~~p--------~H~sREVLii~ssl---------------------  174 (378)
T KOG2807|consen  127 RIHIHALKGLTECSGDFS---LQNALELAREVLKHMP--------GHVSREVLIIFSSL---------------------  174 (378)
T ss_pred             HHHHHHHhcccccCCChH---HHHHHHHHHHHhcCCC--------cccceEEEEEEeee---------------------
Confidence            999999999996666676   3344555555443222        22345554443221                     


Q ss_pred             hhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC-chhHHHHHHHhcC
Q 003284          158 NEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ-LPKLTAIYNAAKR  203 (834)
Q Consensus       158 ~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq-lp~l~~Lfeka~~  203 (834)
                          ..+..+|...+.+.+..-+|.+|||..-- .-..|+|..+.++
T Consensus       175 ----sT~DPgdi~~tI~~lk~~kIRvsvIgLsaEv~icK~l~kaT~G  217 (378)
T KOG2807|consen  175 ----STCDPGDIYETIDKLKAYKIRVSVIGLSAEVFICKELCKATGG  217 (378)
T ss_pred             ----cccCcccHHHHHHHHHhhCeEEEEEeechhHHHHHHHHHhhCC
Confidence                11223577788888999999999998874 5667777776653

>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]

Probab=91.49  E-value=3.5  Score=43.01  Aligned_cols=165  Identities=16%  Similarity=0.228  Sum_probs=102.1

Q ss_pred             cEEEEEecccc--chHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            5 QLIVAVEGTAA--MGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         5 dvVFVID~Tas--mg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      -+|++||-+-.  .|+|+++=..--+ ..+|.+....+++    ..-..+||+...++-+  ..   -+.||++..+|+.
T Consensus         5 atvvliDNse~s~NgDy~ptRFeAQk-d~ve~if~~K~nd----npEntiGli~~~~a~p--~v---lsT~T~~~gkilt   74 (243)
T COG5148           5 ATVVLIDNSEASQNGDYLPTRFEAQK-DAVESIFSKKFND----NPENTIGLIPLVQAQP--NV---LSTPTKQRGKILT   74 (243)
T ss_pred             eEEEEEeChhhhhcCCCCcHHHHHHH-HHHHHHHHHHhcC----CccceeeeeecccCCc--ch---hccchhhhhHHHH
Confidence            36788887755  4677665333222 2334333322221    1236899999988855  22   3779999999999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQA  162 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~  162 (834)
                      .|..|+..||-+    +..+|.-|+-.|....++      ...+|.+.+|| ||=.                 |+.|   
T Consensus        75 ~lhd~~~~g~a~----~~~~lqiaql~lkhR~nk------~q~qriVaFvg-Spi~-----------------esed---  123 (243)
T COG5148          75 FLHDIRLHGGAD----IMRCLQIAQLILKHRDNK------GQRQRIVAFVG-SPIQ-----------------ESED---  123 (243)
T ss_pred             HhccccccCcch----HHHHHHHHHHHHhcccCC------ccceEEEEEec-Cccc-----------------ccHH---
Confidence            999999998854    667778888777543322      11234444443 2211                 1111   


Q ss_pred             hccCCCHHHHHHHHhhcCcEEEEeccCCchhHHHHHHHhcCCCCCCCCCCCCCCCCCeEEEe
Q 003284          163 ESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLI  224 (834)
Q Consensus       163 ~~~l~d~e~lA~~~~e~~I~LSvIsPrqlp~l~~Lfeka~~~~~~~~~~~~~ak~p~hlVLL  224 (834)
                           ..-.+|+-+.++||-+.+|----+.-...|||+-+.        .|| .|..||+.+
T Consensus       124 -----eLirlak~lkknnVAidii~fGE~~n~~~l~efIda--------~N~-~dsshl~~~  171 (243)
T COG5148         124 -----ELIRLAKQLKKNNVAIDIIFFGEAANMAGLFEFIDA--------TNF-SDSSHLEVK  171 (243)
T ss_pred             -----HHHHHHHHHHhcCeeEEEEehhhhhhhhHHHHHHHh--------hcc-ccceeeEec
Confidence                 235789999999999999977766666666665431        222 456788766

>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=91.23  E-value=0.27  Score=49.07  Aligned_cols=77  Identities=18%  Similarity=0.210  Sum_probs=54.9

Q ss_pred             CCCCCCCCCCcccCCCCC-CCcCCCCCCCCCCCCCC-CC----------CccccCCccccceeecccccccCCCCCCCCC
Q 003284          240 VANLAPNQNPVKMDIAPV-TSVTGPAPTSIPSVNGI-NR----------PPISVGNVPTATVKVEPSTVTSMVNGPTFPH  307 (834)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~p~~~~~-~~----------~~~~~~~~~~~~~k~~~~~~~~m~~~p~f~~  307 (834)
                      .+.+.+++.+.....+.+ ++...++++.+|.|..+ +.          +.++..+||+|+..       +...|+||+.
T Consensus         9 pg~lq~KQ~Vp~pP~p~~~~~l~aaP~q~LPpVs~pq~qvp~n~tLsaAq~AAq~AVEAAknQ-------Kaglg~RF~p   81 (168)
T PF11235_consen    9 PGPLQPKQPVPLPPAPVSPAQLSAAPQQPLPPVSPPQYQVPGNSTLSAAQVAAQNAVEAAKNQ-------KAGLGPRFSP   81 (168)
T ss_pred             CCCCCCCCcccCCCCCCCccccccCCcCCCCCCCccccccCccccchHHHHHHHHHHHHHHhc-------cccCCCCCCC
Confidence            467888888777776655 77789999999999666 33          23567888866554       3457899999


Q ss_pred             CCCCCCCCCCCCCCcc
Q 003284          308 IPSVPRPASQGVPSLQ  323 (834)
Q Consensus       308 ~~p~~~~~~~~~~~~q  323 (834)
                      ++|+++..--|-|--|
T Consensus        82 i~p~~~a~~vgpPFsQ   97 (168)
T PF11235_consen   82 INPLQQAPGVGPPFSQ   97 (168)
T ss_pred             CCcccCCCCCCCCCcC
Confidence            9998886444444333

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 [].

>TIGR00627 tfb4 transcription factor tfb4

Probab=90.61  E-value=4.3  Score=44.71  Aligned_cols=168  Identities=15%  Similarity=0.146  Sum_probs=94.4

Q ss_pred             EEEEEeccccchHhHHH-----HHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC---Cccccee---ecc--
Q 003284            6 LIVAVEGTAAMGPYWQS-----IVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS---YCACLVQ---RSG--   72 (834)
Q Consensus         6 vVFVID~Tasmg~yi~~-----lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~---~~~~lv~---~~g--   72 (834)
                      ||+|||+..--|.-+..     -.++.|.-++-++|. .+.    .....++++|..+.+.+   |+.+...   ..+  
T Consensus         5 L~vvlD~np~~W~~~~~~~~~~~l~~~l~sllvF~Na-hL~----l~~~N~vaVIAs~~~~~~~LYps~~~~~~~~~~~~   79 (279)
T TIGR00627         5 LVVIIEANPCSWGMLALAHGKRTISKVLRAIVVFLNA-HLA----FNANNKLAVIASHSQDNKYLYPSTRCEDRNASELD   79 (279)
T ss_pred             EEEEEeCCHHHHHHHhhccCCCcHHHHHHHHHHHHHH-HHh----cCccCCEEEEEecCCcceEEecCCccccccccccc
Confidence            78999977644322211     234556666666654 221    12458999999988776   5544211   000  


Q ss_pred             ----------CCCCHH-HHH----HHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCC
Q 003284           73 ----------WTKDVD-IFL----HWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNP  137 (834)
Q Consensus        73 ----------fTsd~~-~fl----~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP  137 (834)
                                -++.++ .++    ..++...-..-......++.||.-||...-+..  ...+.....+.++++|..|+-
T Consensus        80 ~~~~~~~~y~~f~~v~~~v~~~l~~l~~~~~~~~~~~~~s~lagals~ALcyinr~~--~~~~~~~~~~~RIlii~~s~~  157 (279)
T TIGR00627        80 PKRLRELLYRDFRTVDETIVEEIKPLMAHADKHMKKDSRTVLAGALSDALGYINRSE--QSETASEKLKSRILVISITPD  157 (279)
T ss_pred             cccccchhccchhHHHHHHHHHHHHHHhhchhcccccccccchhHHHhhhhhhcccc--cccccCcCCcceEEEEECCCC
Confidence                      001111 112    222222211111245678899999997765421  011223456777777777754


Q ss_pred             CCCCCCcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccC---CchhHHHHHHHhcCC
Q 003284          138 HPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK---QLPKLTAIYNAAKRN  204 (834)
Q Consensus       138 ~~lp~pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr---qlp~l~~Lfeka~~~  204 (834)
                      +...   |.|.                     ...+.++.+.+|.++||...   ....|+.+-+..+|-
T Consensus       158 ~~~q---Yi~~---------------------mn~Ifaaqk~~I~Idv~~L~~e~~~~~lqQa~~~TgG~  203 (279)
T TIGR00627       158 MALQ---YIPL---------------------MNCIFSAQKQNIPIDVVSIGGDFTSGFLQQAADITGGS  203 (279)
T ss_pred             chHH---HHHH---------------------HHHHHHHHHcCceEEEEEeCCccccHHHHHHHHHhCCE
Confidence            4322   4433                     45677889999999999765   388999999988764

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd01478 Sec23-like Sec23-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles

Probab=88.80  E-value=6.9  Score=42.69  Aligned_cols=114  Identities=13%  Similarity=0.114  Sum_probs=60.5

Q ss_pred             HHhccCcc-----CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCC-CCcccCC---ccc-
Q 003284           82 HWLSTIPF-----AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLP-TPVYRPQ---MQN-  151 (834)
Q Consensus        82 ~~Ld~I~f-----~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp-~pv~~p~---~~~-  151 (834)
                      ..|+.|+-     .-+.....|...||..|+.+++...        ...--++++...++|--=| .-+.+..   +-. 
T Consensus       121 ~lLe~L~~~~~~~~~~~r~~r~~G~Al~~A~~ll~~~~--------~~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~  192 (267)
T cd01478         121 DLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEACF--------PNTGARIMLFAGGPCTVGPGAVVSTELKDPIRSH  192 (267)
T ss_pred             HHHHhCcccccccCCCCCCCCchHHHHHHHHHHHHhhc--------CCCCcEEEEEECCCCCCCCceeeccccccccccc
Confidence            46666643     2233346788889999988886210        1123456666666664322 1111100   000 


Q ss_pred             cc-cccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCC
Q 003284          152 LD-QNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRN  204 (834)
Q Consensus       152 ~~-~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~  204 (834)
                      .+ .+++.++.+... .-...+|..+.+++|.+.+.+--    .+..++.|.++.++.
T Consensus       193 ~d~~~~~~~~~~~a~-~fY~~la~~~~~~~vsvDlF~~s~d~vglaem~~l~~~TGG~  249 (267)
T cd01478         193 HDIDKDNAKYYKKAV-KFYDSLAKRLAANGHAVDIFAGCLDQVGLLEMKVLVNSTGGH  249 (267)
T ss_pred             cccccchhhhhhhHH-HHHHHHHHHHHhCCeEEEEEeccccccCHHHHHHHHHhcCcE
Confidence            00 011111111111 12367999999999998876633    357888888877765

The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 23 is very similar to Sec24. The Sec23 and Sec24

>KOG1226 consensus Integrin beta subunit (N-terminal portion of extracellular region) [Signal transduction mechanisms; Extracellular structures]

Probab=88.53  E-value=2.4  Score=51.89  Aligned_cols=177  Identities=12%  Similarity=0.065  Sum_probs=105.5

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC--------------Cccc--c
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS--------------YCAC--L   67 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~--------------~~~~--l   67 (834)
                      -||.+.+|=+.+|+++++.|++. =..+.+.++.=        .+++|+|.=.|-|.+-              .+++  +
T Consensus       133 VDLYyLMDlS~SM~DDl~~l~~L-G~~L~~~m~~l--------T~nfrlGFGSFVDK~v~P~i~~~pekl~npc~~~~~C  203 (783)
T KOG1226|consen  133 VDLYYLMDLSYSMKDDLENLKSL-GTDLAREMRKL--------TSNFRLGFGSFVDKTVSPYISTTPEKLRNPCPNYKNC  203 (783)
T ss_pred             eeEEEEeecchhhhhhHHHHHHH-HHHHHHHHHHH--------hccCCccccchhccccccccccCcHHhcCCCCCcccC
Confidence            59999999999999999999965 34444444321        1345666655555442              1221  1


Q ss_pred             eeeccC------CCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCC-ccCCcEEEEeecCCCCCC
Q 003284           68 VQRSGW------TKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQN-VDGQRHCILVAASNPHPL  140 (834)
Q Consensus        68 v~~~gf------Tsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~-~~~qkhCILIa~SpP~~l  140 (834)
                      .-.|+|      |.|++.|...+.+-..+|-=|.||-=.+|+--|..+=+..       -| +++.|..|+.+++-.|-.
T Consensus       204 ~ppfgfkhvLsLT~~~~~F~~~V~~q~ISgNlDaPEGGfDAimQaavC~~~I-------GWR~~a~~lLVF~td~~~H~a  276 (783)
T KOG1226|consen  204 APPFGFKHVLSLTNDAEEFNEEVGKQRISGNLDAPEGGFDAIMQAAVCTEKI-------GWRNDATRLLVFSTDAGFHFA  276 (783)
T ss_pred             CCCcccceeeecCCChHHHHHHHhhceeccCCCCCCchHHHHHhhhhccccc-------cccccceeEEEEEcCcceeee
Confidence            122444      9999999999999999998888776555554444333211       13 336778899999999976


Q ss_pred             CCCcccCCccc----cccccchhhh---hhccCCCHHHHHHHHhhcCcEEEE-eccCCchhHHHH
Q 003284          141 PTPVYRPQMQN----LDQNENNEAQ---AESRLSDAETVAKSFVQCSVSLSV-ICPKQLPKLTAI  197 (834)
Q Consensus       141 p~pv~~p~~~~----~~~~e~~~~~---~~~~l~d~e~lA~~~~e~~I~LSv-IsPrqlp~l~~L  197 (834)
                      ...-+..-+.-    =..+++..|+   ... .....+|++.+.+++|++.. |.-.+...+++|
T Consensus       277 ~DgkLaGiv~pnDG~CHL~~~g~Yt~S~~qd-yPSia~l~~kl~~~ni~~IFAVt~~~~~~Y~~l  340 (783)
T KOG1226|consen  277 GDGKLAGIVQPNDGQCHLDKNGEYTQSTTQD-YPSIAQLAQKLADNNINTIFAVTKNSQSLYEEL  340 (783)
T ss_pred             cccceeeEecCCCCccccCCCCccceecCCC-CCcHHHHHHHHhhhcchhHHHHhhhhhhHHHhh
Confidence            65211111100    0011221221   112 23558889999999987644 444444444443

>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.08  E-value=6  Score=49.19  Aligned_cols=160  Identities=16%  Similarity=0.251  Sum_probs=90.2

Q ss_pred             ccEEEEEecc--ccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCC------------------
Q 003284            4 KQLIVAVEGT--AAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY------------------   63 (834)
Q Consensus         4 ~dvVFVID~T--asmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~------------------   63 (834)
                      .-.||.||.|  |.+..-+..+.++ |..+|++|-.        .+++.|+|+|+|.+.=-|                  
T Consensus       418 pafvFmIDVSy~Ai~~G~~~a~ce~-ik~~l~~lp~--------~~p~~~Vgivtfd~tvhFfnl~s~L~qp~mliVsdv  488 (1007)
T KOG1984|consen  418 PAFVFMIDVSYNAISNGAVKAACEA-IKSVLEDLPR--------EEPNIRVGIVTFDKTVHFFNLSSNLAQPQMLIVSDV  488 (1007)
T ss_pred             ceEEEEEEeehhhhhcchHHHHHHH-HHHHHhhcCc--------cCCceEEEEEEecceeEeeccCccccCceEEEeecc
Confidence            4579999987  4455556666655 6777888843        136799999999764210                  


Q ss_pred             ccccee-eccC----CCCHHHHHHHhccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCC
Q 003284           64 CACLVQ-RSGW----TKDVDIFLHWLSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASN  136 (834)
Q Consensus        64 ~~~lv~-~~gf----Tsd~~~fl~~Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~Sp  136 (834)
                      .+++|= ..|+    -.+.......||.|.  |.+-+.-+.++..+|.+|+..+...          +.-|.+|....-|
T Consensus       489 ~dvfvPf~~g~~V~~~es~~~i~~lLd~Ip~mf~~sk~pes~~g~alqaa~lalk~~----------~gGKl~vF~s~Lp  558 (1007)
T KOG1984|consen  489 DDVFVPFLDGLFVNPNESRKVIELLLDSIPTMFQDSKIPESVFGSALQAAKLALKAA----------DGGKLFVFHSVLP  558 (1007)
T ss_pred             cccccccccCeeccchHHHHHHHHHHHHhhhhhccCCCCchhHHHHHHHHHHHHhcc----------CCceEEEEecccc
Confidence            111111 1222    233444555888884  5666666788888888888777531          1345555554444


Q ss_pred             CCCCCCCcccCCccccccccchhhhhhc--c---CCCHHHHHHHHhhcCcEEEEec
Q 003284          137 PHPLPTPVYRPQMQNLDQNENNEAQAES--R---LSDAETVAKSFVQCSVSLSVIC  187 (834)
Q Consensus       137 P~~lp~pv~~p~~~~~~~~e~~~~~~~~--~---l~d~e~lA~~~~e~~I~LSvIs  187 (834)
                      =+..+-     +|.+-++++-+.-.++-  |   -.+...||++|.|-+|+|.+-.
T Consensus       559 t~g~g~-----kl~~r~D~~l~~t~kek~l~~pq~~~y~~LA~e~v~~g~svDlF~  609 (1007)
T KOG1984|consen  559 TAGAGG-----KLSNRDDRRLIGTDKEKNLLQPQDKTYTTLAKEFVESGCSVDLFL  609 (1007)
T ss_pred             cccCcc-----cccccchhhhhcccchhhccCcchhHHHHHHHHHHHhCceEEEEE
Confidence            444441     11111111111000110  0   0124689999999999988764

>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]

Probab=87.88  E-value=13  Score=39.78  Aligned_cols=180  Identities=17%  Similarity=0.251  Sum_probs=108.5

Q ss_pred             EEEEEeccccc--hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHHH
Q 003284            6 LIVAVEGTAAM--GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHW   83 (834)
Q Consensus         6 vVFVID~Tasm--g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~~   83 (834)
                      .++|||-+-.|  |+|+++=..- =...++.+|...+...    .-.-+||+..-.+.+  ..   -..+|+|.-+++..
T Consensus         6 tmi~iDNse~mrNgDy~PtRf~a-Q~daVn~v~~~K~~sn----pEntvGiitla~a~~--~v---LsT~T~d~gkils~   75 (259)
T KOG2884|consen    6 TMICIDNSEYMRNGDYLPTRFQA-QKDAVNLVCQAKLRSN----PENTVGIITLANASV--QV---LSTLTSDRGKILSK   75 (259)
T ss_pred             EEEEEeChHHhhcCCCChHHHHH-HHHHHHHHHHhhhcCC----cccceeeEeccCCCc--ee---eeeccccchHHHHH
Confidence            57888887665  6777654322 1234555555433211    236899999888755  22   36799999999999


Q ss_pred             hccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhhh
Q 003284           84 LSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQAE  163 (834)
Q Consensus        84 Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~~  163 (834)
                      |.+|+..|+    +.+..||.-|.-.|....      .-+..+|.+++|+ ||=               ++.|       
T Consensus        76 lh~i~~~g~----~~~~~~i~iA~lalkhRq------nk~~~~riVvFvG-Spi---------------~e~e-------  122 (259)
T KOG2884|consen   76 LHGIQPHGK----ANFMTGIQIAQLALKHRQ------NKNQKQRIVVFVG-SPI---------------EESE-------  122 (259)
T ss_pred             hcCCCcCCc----ccHHHHHHHHHHHHHhhc------CCCcceEEEEEec-Ccc---------------hhhH-------
Confidence            999998775    456677777777775322      1122233334443 221               1111       


Q ss_pred             ccCCCHHHHHHHHhhcCcEEEEeccCCchhH-HHHHHHhcCCCCCCCCCCCCCCCCCeEEEeeccchhhhhhcCCCC
Q 003284          164 SRLSDAETVAKSFVQCSVSLSVICPKQLPKL-TAIYNAAKRNPRAADPPVDNSKNPHFLVLISENFMEARAALSRPG  239 (834)
Q Consensus       164 ~~l~d~e~lA~~~~e~~I~LSvIsPrqlp~l-~~Lfeka~~~~~~~~~~~~~ak~p~hlVLLsg~~l~~r~~~~r~~  239 (834)
                         .+...+|+-|.+.+|.+.||-=--...- .+||+.-.        ..|+.-+-.|||-+.-..+=.-..++-|-
T Consensus       123 ---keLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fid--------a~N~~~~gshlv~Vppg~~L~d~l~ssPi  188 (259)
T KOG2884|consen  123 ---KELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFID--------ALNGKGDGSHLVSVPPGPLLSDALLSSPI  188 (259)
T ss_pred             ---HHHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHH--------HhcCCCCCceEEEeCCCccHHHHhhcCce
Confidence               1457899999999999999976543222 23333211        12233566899988766654555554444

>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair

Probab=86.80  E-value=8.6  Score=42.30  Aligned_cols=169  Identities=15%  Similarity=0.145  Sum_probs=92.1

Q ss_pred             EEEEEeccccchHhHH--HHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC---Ccccce---eecc-----
Q 003284            6 LIVAVEGTAAMGPYWQ--SIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS---YCACLV---QRSG-----   72 (834)
Q Consensus         6 vVFVID~Tasmg~yi~--~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~---~~~~lv---~~~g-----   72 (834)
                      ||+|||+...-+.-..  .-.++.|+-++-++|. .+.    .....++++|.++.+.+   ||...-   ...+     
T Consensus         4 LvIILD~nP~~W~~~~~~~~l~~~l~~llvFlNa-hL~----l~~~N~vaVIAs~~~~s~~LYP~~~~~~~~~~~~~~~~   78 (276)
T PF03850_consen    4 LVIILDTNPLAWGQLSDQLSLSQFLDSLLVFLNA-HLA----LNHSNQVAVIASHSNSSKFLYPSPSSSESSNSGDVEMN   78 (276)
T ss_pred             EEEEEECCHHHHhhccccccHHHHHHHHHHHHHH-HHh----hCccCCEEEEEEcCCccEEEeCCCccccccCCCccccc
Confidence            7999998765443333  2234555555555554 221    12458999999988876   455441   0000     


Q ss_pred             --------CCCCHHHHH-HHhccC--ccCCCCCc--hhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEE-eecCCCC
Q 003284           73 --------WTKDVDIFL-HWLSTI--PFAGGGFN--DAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCIL-VAASNPH  138 (834)
Q Consensus        73 --------fTsd~~~fl-~~Ld~I--~f~GGG~~--~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCIL-Ia~SpP~  138 (834)
                              -++.+++++ +-|.++  +.......  ...++-||+.||+..-+...... ......+.++++ |..|+-+
T Consensus        79 ~~~~~~y~~f~~v~~~v~~~l~~l~~~~~~~~~~~~~s~LagALS~ALCyINR~~~~~~-~~~~~~~~RILv~~s~s~d~  157 (276)
T PF03850_consen   79 SSDSNKYRQFRNVDETVLEELKKLMSETSESSDSTTSSLLAGALSMALCYINRISRESP-SGGTSLKSRILVIVSGSPDS  157 (276)
T ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhhcccccccccchhhHHHHHHHHHHHhhhhhccc-CCCCCcCccEEEEEecCCCc
Confidence                    011111111 222211  12222222  37899999999988765421111 001233444444 7777776


Q ss_pred             CCCCCcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC--chhHHHHHHHhcCC
Q 003284          139 PLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ--LPKLTAIYNAAKRN  204 (834)
Q Consensus       139 ~lp~pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq--lp~l~~Lfeka~~~  204 (834)
                      ...   |.|.||                     .+=+..+.+|.+.++....  .+.|.-.-+..+|-
T Consensus       158 ~~Q---Yi~~MN---------------------~iFaAqk~~v~IDv~~L~~~~s~fLqQa~d~T~G~  201 (276)
T PF03850_consen  158 SSQ---YIPLMN---------------------CIFAAQKQKVPIDVCKLGGKDSTFLQQASDITGGI  201 (276)
T ss_pred             cHH---HHHHHH---------------------HHHHHhcCCceeEEEEecCCchHHHHHHHHHhCce
Confidence            555   555444                     3445678899999998886  67777766666554

The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex

>PTZ00395 Sec24-related protein; Provisional

Probab=86.00  E-value=4.1  Score=52.76  Aligned_cols=94  Identities=13%  Similarity=0.075  Sum_probs=50.7

Q ss_pred             HHHHHHHhccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccccc
Q 003284           77 VDIFLHWLSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQ  154 (834)
Q Consensus        77 ~~~fl~~Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~  154 (834)
                      -+.+...|+.|.  |.--...+.|+.-||.+|++++....         -.-|.|++.+.-|=+....-..+.  .+.  
T Consensus      1054 RevIe~LLDkLPemFt~t~~~esCLGSALqAA~~aLk~~G---------GGGKIiVF~SSLPniGpGaLK~Re--~~~-- 1120 (1560)
T PTZ00395       1054 IDKINTLIDTIKSVSTTMQSYGSCGNSALKIAMDMLKERN---------GLGSICMFYTTTPNCGIGAIKELK--KDL-- 1120 (1560)
T ss_pred             HHHHHHHHHHHHHHhhccCCCcccHHHHHHHHHHHHHhcC---------CCceEEEEEcCCCCCCCCcccccc--ccc--
Confidence            344555666664  22333457889999999999986311         123566666644522222210010  000  


Q ss_pred             ccchhh--hhhccCCCHHHHHHHHhhcCcEEEEec
Q 003284          155 NENNEA--QAESRLSDAETVAKSFVQCSVSLSVIC  187 (834)
Q Consensus       155 ~e~~~~--~~~~~l~d~e~lA~~~~e~~I~LSvIs  187 (834)
                      .|+...  .+.+    +..+|.+|.+.+|.|.+.+
T Consensus      1121 KEk~Ll~pqd~F----YK~LA~ECsk~qISVDLFL 1151 (1560)
T PTZ00395       1121 QENFLEVKQKIF----YDSLLLDLYAFNISVDIFI 1151 (1560)
T ss_pred             ccccccccchHH----HHHHHHHHHhcCCceEEEE
Confidence            111100  1122    3789999999999987654

>PF10138 vWA-TerF-like: vWA found in TerF C terminus ; InterPro: IPR019303 This entry represents the N-terminal domain of a family of proteins that confer resistance to the metalloid element tellurium and its salts

Probab=85.65  E-value=13  Score=39.20  Aligned_cols=145  Identities=12%  Similarity=0.214  Sum_probs=85.7

Q ss_pred             CccEEEEEeccccchHhHHH-HHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQS-IVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFL   81 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~-lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl   81 (834)
                      ++.|++|||.++||.++++. ...+.++.++-.-..  ++      ..-++=+++|.+..-.-.        .-..+.|.
T Consensus         1 rArV~LVLD~SGSM~~~yk~G~vQ~~~Er~lalA~~--~D------dDG~i~v~~Fs~~~~~~~--------~vt~~~~~   64 (200)
T PF10138_consen    1 RARVYLVLDISGSMRPLYKDGTVQRVVERILALAAQ--FD------DDGEIDVWFFSTEFDRLP--------DVTLDNYE   64 (200)
T ss_pred             CcEEEEEEeCCCCCchhhhCccHHHHHHHHHHHHhh--cC------CCCceEEEEeCCCCCcCC--------CcCHHHHH
Confidence            36799999999999998876 334444444433332  21      123677788877543111        22346777


Q ss_pred             HHhccCccC----C--CCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccc
Q 003284           82 HWLSTIPFA----G--GGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQN  155 (834)
Q Consensus        82 ~~Ld~I~f~----G--GG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~  155 (834)
                      .|++++...    +  ||   ..-+..|.+++..+-...       .....-.+|.|+|-.|+...              
T Consensus        65 ~~v~~~~~~~~~~~~~G~---t~y~~vm~~v~~~y~~~~-------~~~~P~~VlFiTDG~~~~~~--------------  120 (200)
T PF10138_consen   65 GYVDELHAGLPDWGRMGG---TNYAPVMEDVLDHYFKRE-------PSDAPALVLFITDGGPDDRR--------------  120 (200)
T ss_pred             HHHHHHhccccccCCCCC---cchHHHHHHHHHHHhhcC-------CCCCCeEEEEEecCCccchH--------------
Confidence            777776432    2  33   223334555565553211       11224689999998886322              


Q ss_pred             cchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC--chhHHHHHH
Q 003284          156 ENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ--LPKLTAIYN  199 (834)
Q Consensus       156 e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq--lp~l~~Lfe  199 (834)
                                  .++.+.++.+...|..+.|---.  .-.|++|=+
T Consensus       121 ------------~~~~~i~~as~~pifwqFVgiG~~~f~fL~kLD~  154 (200)
T PF10138_consen  121 ------------AIEKLIREASDEPIFWQFVGIGDSNFGFLEKLDD  154 (200)
T ss_pred             ------------HHHHHHHhccCCCeeEEEEEecCCcchHHHHhhc
Confidence                        24667777788889888886543  556666655

>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function

Probab=83.90  E-value=2.9  Score=40.43  Aligned_cols=76  Identities=20%  Similarity=0.266  Sum_probs=42.0

Q ss_pred             EEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHHHh
Q 003284            6 LIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHWL   84 (834)
Q Consensus         6 vVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~~L   84 (834)
                      |+++||+++||.+ .+.....+ |.-+++.+             ..++-| ++-|+.-+....+..         ....+
T Consensus         1 i~vaiDtSGSis~~~l~~fl~e-v~~i~~~~-------------~~~v~v-i~~D~~v~~~~~~~~---------~~~~~   56 (126)
T PF09967_consen    1 IVVAIDTSGSISDEELRRFLSE-VAGILRRF-------------PAEVHV-IQFDAEVQDVQVFRS---------LEDEL   56 (126)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH-HHHHHHhC-------------CCCEEE-EEECCEeeeeeEEec---------ccccc
Confidence            6899999999986 33333333 22233333             124434 444544433322222         33456


Q ss_pred             ccCccCCCCCc-hhhHHHHHHH
Q 003284           85 STIPFAGGGFN-DAAIAEGLSE  105 (834)
Q Consensus        85 d~I~f~GGG~~-~~AvaEGLa~  105 (834)
                      ..+++.|||.. ...+.|-+.+
T Consensus        57 ~~~~~~GgGGTdf~pvf~~~~~   78 (126)
T PF09967_consen   57 RDIKLKGGGGTDFRPVFEYLEE   78 (126)
T ss_pred             cccccCCCCCCcchHHHHHHHh
Confidence            67888888865 5667776654

>PF11498 Activator_LAG-3: Transcriptional activator LAG-3; InterPro: IPR021587 The C

Probab=82.80  E-value=0.39  Score=53.65  Aligned_cols=7  Identities=43%  Similarity=0.577  Sum_probs=0.0

Q ss_pred             CCCCCCC
Q 003284          135 SNPHPLP  141 (834)
Q Consensus       135 SpP~~lp  141 (834)
                      |||-.-|
T Consensus        11 sP~pEeP   17 (468)
T PF11498_consen   11 SPPPEEP   17 (468)
T ss_dssp             -------
T ss_pred             CCCCCCc
Confidence            3333333

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 []. ; PDB: 2FO1_D.

>PLN00162 transport protein sec23; Provisional

Probab=81.68  E-value=18  Score=45.11  Aligned_cols=37  Identities=16%  Similarity=0.109  Sum_probs=29.4

Q ss_pred             HHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCCC
Q 003284          169 AETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       169 ~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~~  205 (834)
                      .+.||+.+.+.+|.|.+.+--    .+..++.|.++.+|..
T Consensus       331 Y~~la~~~~~~gisvDlF~~s~dqvglaem~~l~~~TGG~v  371 (761)
T PLN00162        331 YEGLAKQLVAQGHVLDVFACSLDQVGVAEMKVAVERTGGLV  371 (761)
T ss_pred             HHHHHHHHHHcCceEEEEEccccccCHHHHhhhHhhcCcEE
Confidence            478999999999999887533    3688888888887764

---

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	834
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	4e-10
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	2e-09
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	4e-08
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-07
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	5e-07
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	1e-09
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	3e-09
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	4e-09
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	7e-09
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	1e-07
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	9e-06
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	1e-05
3lj5_A	725	Portal protein, protein GP1; DNA ejection, molecul	7e-04
1yvl_A	683	Signal transducer and activator of transcription 1	1e-07
1yvl_A	683	Signal transducer and activator of transcription 1	9e-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	3e-07
1f5n_A	592	Interferon-induced guanylate-binding protein 1; GB	3e-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	7e-05
3ghg_C	411	Fibrinogen gamma chain; triple-stranded coiled coi	2e-07
3ghg_C	411	Fibrinogen gamma chain; triple-stranded coiled coi	3e-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	5e-06
2es4_D	332	Lipase chaperone; protein-protein complex, steric	1e-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
3ibp_A	302	Chromosome partition protein MUKB; structural main	1e-05
3ibp_A	302	Chromosome partition protein MUKB; structural main	4e-05
3ibp_A	302	Chromosome partition protein MUKB; structural main	3e-04
2v71_A	189	Nuclear distribution protein NUDE-like 1; developm	1e-05
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	2e-05
1lwu_C	323	Fibrinogen gamma chain; heterotrimer, protein-pept	5e-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;	2e-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
3c8j_A	203	Natural killer cell receptor LY49C; MHC, virus, im	1e-04
1i84_S	1184	Smooth muscle myosin heavy chain; muscle protein,	2e-04
3ghg_A	562	Fibrinogen alpha chain; triple-stranded coiled coi	3e-04
3ajw_A	150	Flagellar FLIJ protein; flagellum, type III secret	3e-04
3o0z_A	168	RHO-associated protein kinase 1; coiled-coil, tran	3e-04
1vt0_M	602	Portal protein, protein GP1; portal protein, DNA e	5e-04
2h8n_A	112	HD4, histone deacetylase 4; alpha helix, polar zip	6e-04
1jad_A	251	PLC-beta, phospholipase C beta; alpha helical coil	8e-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 = 63.7 bits (154), Expect = 2e-10
 Identities = 20/133 (15%), Positives = 36/133 (27%)

Query: 690 ISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQ 749
           +S  +++   Q Q Q        Q   Q +         +   Q  +P       + Q Q
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 750 QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPG 809
             +  Q Q  QQ+ Q         +     +      Q     Q        Q  +  P 
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 810 RTQLVSQGQVSSQ 822
             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 = 62.5 bits (151), Expect = 4e-10
 Identities = 21/140 (15%), Positives = 31/140 (22%)

Query: 679 FPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQ 738
           +P   + +    +  QQ       Q      M                 Q   L     Q
Sbjct: 9   YPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQ 68

Query: 739 LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGS 798
           L QQ          M         P    Q Q+P         Q Q     +  Q     
Sbjct: 69  LHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAM 128

Query: 799 GMGQGYVQGPGRTQLVSQGQ 818
           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 = 61.0 bits (147), Expect = 1e-09
 Identities = 21/125 (16%), Positives = 31/125 (24%)

Query: 701 QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQ 760
             +++ + Q Q Q         Q  Q   PQ          Q  +P          QQ  
Sbjct: 3   HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62

Query: 761 QLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVS 820
              Q Q  QQ+ Q         L     +     M      Q       + Q ++     
Sbjct: 63  TPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYG 122

Query: 821 SQGAP 825
              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 = 60.6 bits (146), Expect = 2e-09
 Identities = 26/148 (17%), Positives = 39/148 (26%), Gaps = 2/148 (1%)

Query: 683 MVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 742
           M   K ++  Q Q Q  Q     Q        Q    + +   Q  +P         QQQ
Sbjct: 1   MSHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQ 60

Query: 743 QQIPQLQQ--QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGM 800
              P  +Q  Q + Q         L     +      Q    +Q    L Q QQ + +  
Sbjct: 61  FLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPA 120

Query: 801 GQGYVQGPGRTQLVSQGQVSSQGAPNIP 828
                   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 = 56.0 bits (134), Expect = 4e-08
 Identities = 23/120 (19%), Positives = 31/120 (25%)

Query: 676 GMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQ 735
           GM +    +  +  + S  QQQ     Q+Q HQQ+           L       P    Q
Sbjct: 39  GMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQ 98

Query: 736 IPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
                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 = 54.4 bits (130), Expect = 1e-07
 Identities = 23/124 (18%), Positives = 34/124 (27%), Gaps = 1/124 (0%)

Query: 712 SQLQHQQLSQLQQQQ-QQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQ 770
           S  + +   Q Q Q  Q    LQQ    +  Q             +  Q  +P + QQQ 
Sbjct: 2   SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61

Query: 771 LPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGAPNIPGG 830
           L   Q+Q      Q    ++         +       P     +       Q     P  
Sbjct: 62  LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121

Query: 831 GFMS 834
           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 = 52.9 bits (126), Expect = 3e-07
 Identities = 26/111 (23%), Positives = 38/111 (34%), Gaps = 2/111 (1%)

Query: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ--I 745
            Q  +  Q+QL QQ  Q         L +  L       Q    +Q   P  QQQQ    
Sbjct: 59  QQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAA 118

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
           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 = 52.5 bits (125), Expect = 5e-07
 Identities = 22/110 (20%), Positives = 35/110 (31%), Gaps = 3/110 (2%)

Query: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQ 747
           P +  QQ     Q+Q  QQ  Q  + +    L  +         +Q Q+P         Q
Sbjct: 54  PSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPN-AYMQPQVPVQMGTPLQQQ 112

Query: 748 LQQQSMPQLQQQQQLPQ--LQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
            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 = 60.5 bits (145), Expect = 1e-09
 Identities = 19/132 (14%), Positives = 44/132 (33%)

Query: 664 LLSVSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQ 723
           LL  + +      +L      +   +     +    +Q  Q   ++ ++  + Q L + Q
Sbjct: 538 LLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPETPEEQQWLVEAQ 597

Query: 724 QQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQL 783
           Q +Q          Q    Q   +L +     L  Q    +++ Q QL   +  +    +
Sbjct: 598 QAKQGQQDPAMVQAQGVLLQGQAELAKAQNQTLSLQIDAAKVEAQNQLNAARIAEIFNNM 657

Query: 784 QQQQQLSQPQQM 795
              +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 = 59.7 bits (143), Expect = 3e-09
 Identities = 20/126 (15%), Positives = 43/126 (34%), Gaps = 1/126 (0%)

Query: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 746
           K  I    ++    ++QQ   +  Q++   Q    + Q Q  L Q Q ++ + Q Q    
Sbjct: 574 KQLIQMGVKKPETPEEQQWLVEAQQAKQGQQDP-AMVQAQGVLLQGQAELAKAQNQTLSL 632

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQ 806
           Q+    +    Q       +    +   +Q +    L+      Q +        +  ++
Sbjct: 633 QIDAAKVEAQNQLNAARIAEIFNNMDLSKQSEFREFLKTVASFQQDRSEDARANAELLLK 692

Query: 807 GPGRTQ 812
           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 = 59.3 bits (142), Expect = 4e-09
 Identities = 22/118 (18%), Positives = 43/118 (36%), Gaps = 7/118 (5%)

Query: 686 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 745
               +     +QL Q   ++     + Q    +  Q +Q QQ    +Q Q   LQ Q ++
Sbjct: 564 GVEMMRDYANKQLIQMGVKKPETPEEQQWL-VEAQQAKQGQQDPAMVQAQGVLLQGQAEL 622

Query: 746 PQLQ------QQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVG 797
            + 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 = 58.5 bits (140), Expect = 7e-09
 Identities = 19/120 (15%), Positives = 42/120 (35%), Gaps = 2/120 (1%)

Query: 688 PQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQ-QLPQLQQQIPQLQQQQQIP 746
            +  + ++QQ   + QQ +  Q    +   Q   LQ Q +    Q Q    Q+   +   
Sbjct: 582 KKPETPEEQQWLVEAQQAKQGQQDPAMVQAQGVLLQGQAELAKAQNQTLSLQIDAAKVEA 641

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGYVQ 806
           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 = 54.7 bits (130), Expect = 1e-07
 Identities = 22/128 (17%), Positives = 46/128 (35%), Gaps = 1/128 (0%)

Query: 667 VSDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ 726
           + D A + +  +        + Q    + QQ +Q QQ     Q Q  L   Q ++L + Q
Sbjct: 568 MRDYANKQLIQMGVKKPETPEEQQWLVEAQQAKQGQQDPAMVQAQGVLLQGQ-AELAKAQ 626

Query: 727 QQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
            Q   LQ    +++ Q Q+   +   +       +  + ++  +     QQ +    +  
Sbjct: 627 NQTLSLQIDAAKVEAQNQLNAARIAEIFNNMDLSKQSEFREFLKTVASFQQDRSEDARAN 686

Query: 787 QQLSQPQQ 794
            +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 = 48.5 bits (114), Expect = 9e-06
 Identities = 18/112 (16%), Positives = 32/112 (28%)

Query: 684 VVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQ 743
                  S Q  +Q  + +  +   +        QL  LQ       +  + +     +Q
Sbjct: 516 CYTDVGPSFQSMKQQNRAEILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQ 575

Query: 744 QIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
            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 = 47.8 bits (112), Expect = 1e-05
 Identities = 22/107 (20%), Positives = 43/107 (40%), Gaps = 5/107 (4%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           Q +  +  +L  +  Q   +     LQ+  L   +  +       +Q+ Q+  ++     
Sbjct: 529 QQNRAEILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPETPE 588

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           +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 = 42.4 bits (98), Expect = 7e-04
 Identities = 25/168 (14%), Positives = 52/168 (30%), Gaps = 11/168 (6%)

Query: 668 SDKACRLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQ 727
             +   +         V    ++      + Q     +   +  + +     S  QQ + 
Sbjct: 474 VPRNVTITLEDGSEKDVQLMAEVVDLATGEKQVLNDIRGRYECYTDVGPSFQSMKQQNRA 533

Query: 728 QLPQLQQQIPQLQQQQQIPQLQ---------QQSMPQLQQQQQLPQLQQQQQLPQMQQ-- 776
           ++ +L  + PQ   + Q+  LQ          + M     +Q +    ++ + P+ QQ  
Sbjct: 534 EILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPETPEEQQWL 593

Query: 777 QQQLPQLQQQQQLSQPQQMVGSGMGQGYVQGPGRTQLVSQGQVSSQGA 824
            +     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: 641 HGFLGQLQEKKLCAVIQLPSQTLLLSVSDKACRLIGMLF---PGDMVVFKPQISSQQQQQ 697
           H  L QL ++   +   L +  LL     K+ R +   F   P  M +       ++++ 
Sbjct: 58  HDLLSQLDDQ--YSRFSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKI 115

Query: 698 LQQQQQQQQHQQMQSQL------QHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 751
           L+  Q+  Q Q    Q       Q +  S+++  + ++  ++ +I  L+  Q     + +
Sbjct: 116 LENAQRFNQAQSGNIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCK 175

Query: 752 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
           ++   + +        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 = 9e-06
 Identities = 11/104 (10%), Positives = 37/104 (35%), Gaps = 4/104 (3%)

Query: 689 QISSQQQQQLQQQQQ--QQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 746
                + + L+  Q     + + +Q++           Q+Q+   L++    L  +++  
Sbjct: 154 MCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRK-- 211

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLS 790
           ++  + +  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: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQ------QQQQQLPQLQQQIPQLQ 740
           +  +   +Q++L  + +  + + M  + + + L  LQ       +  Q  + +       
Sbjct: 131 QSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKS 190

Query: 741 QQQQIPQLQQQSMPQLQQQQQ--LPQLQQQQQLPQMQQQQ----QLPQLQQQQQLS 790
            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: 691 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQI-----PQLQQQQQI 745
              +  Q Q+Q   ++   M    + + + ++ +        Q  +      + +++QQ 
Sbjct: 186 GVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQS 245

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
             +       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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQ--LSQLQQQQQQLPQLQQQIPQLQQQQQIP 746
           + S +  Q   Q+   Q    + S L+ ++  L   Q+  Q      Q    L +Q+++ 
Sbjct: 84  RKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQRFNQAQSGNIQSTVMLDKQKELD 143

Query: 747 ----------QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
                        +  +  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: 691 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 750
            S +   L Q   ++  + +Q   Q   +         L + ++ +   Q+  Q      
Sbjct: 71  FSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQRFNQAQSGNI 130

Query: 751 QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           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: 693 QQQQQLQQQQQQQQH--QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 750
            +++++  +  +  +  +  Q+ L + +L + +++QQ           L Q Q    +  
Sbjct: 208 NKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVA 267

Query: 751 QSMPQLQQQ-QQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
           +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: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           Q ++       +   +Q Q  L+   L    ++++ + ++ + +   +  Q      +  
Sbjct: 178 QNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELV 237

Query: 753 MPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
             + +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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQ-LPQLQQQIPQLQQQQQIPQ 747
            +   Q +   + +  Q  +   + +      Q Q   ++    L  +  ++  +     
Sbjct: 162 SLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELL 221

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
              +         +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 = 53.4 bits (127), Expect = 2e-07
 Identities = 18/103 (17%), Positives = 50/103 (48%), Gaps = 6/103 (5%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           +        + Q  Q    ++ + +++  +    Q   + L ++Q++  Q+ +Q++  + 
Sbjct: 466 KSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKE--RS 523

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
            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 = 53.0 bits (126), Expect = 3e-07
 Identities = 16/98 (16%), Positives = 54/98 (55%), Gaps = 2/98 (2%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           Q   + +++ + ++ +   +Q   + L ++Q++ +Q+ + +++  Q   +Q   +++   
Sbjct: 480 QTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDR 539

Query: 753 MPQLQQQQQL--PQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           +  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 = 53.0 bits (126), Expect = 3e-07
 Identities = 19/104 (18%), Positives = 49/104 (47%), Gaps = 3/104 (2%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           +I  ++ +    Q   +   +MQ + +     + +  Q+ L QL +++    + Q + + 
Sbjct: 488 EIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMEN-DRVQLLKEQ 546

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 792
           ++    +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 = 49.2 bits (116), Expect = 4e-06
 Identities = 13/108 (12%), Positives = 48/108 (44%), Gaps = 1/108 (0%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ-IPQ 747
           +   +  Q  +  Q   + ++  +    Q    L ++++++   + +    Q   + + +
Sbjct: 449 EEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHE 508

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           +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 = 47.3 bits (111), Expect = 2e-05
 Identities = 12/109 (11%), Positives = 49/109 (44%), Gaps = 2/109 (1%)

Query: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 746
              +  +  ++ ++  Q ++  Q   + +      + Q  Q L + +++I   + + +  
Sbjct: 440 LQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESA 499

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           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 = 7e-05
 Identities = 16/129 (12%), Positives = 47/129 (36%), Gaps = 1/129 (0%)

Query: 668 SDKAC-RLIGMLFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQ 726
           S   C  L+ ++F       K  I S+        Q+ Q  ++   +   + +   +  Q
Sbjct: 403 SSDRCSGLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQ 462

Query: 727 QQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
             L   +     + Q  Q    +++ +   + + +  Q   +      ++ +Q+ + +++
Sbjct: 463 TYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKER 522

Query: 787 QQLSQPQQM 795
                 +Q+
Sbjct: 523 SYQEHLKQL 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 = 2e-07
 Identities = 19/137 (13%), Positives = 46/137 (33%), Gaps = 9/137 (6%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQ-QQQLPQLQQQIPQLQQQQQ------ 744
           S  Q ++ +  Q  +    Q + +  ++ QL +  Q      +   P +           
Sbjct: 30  STYQTKVDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKM 89

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQGY 804
           + ++ +     L     +  LQ+       Q+   L +   Q + +Q Q+     +    
Sbjct: 90  LEEIMKYEASILTHDSSIRYLQEIYNS-NNQKIVNLKEKVAQLE-AQCQEPCKDTVQIHD 147

Query: 805 VQGPGRTQLVSQGQVSS 821
           + 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 = 3e-05
 Identities = 12/111 (10%), Positives = 37/111 (33%), Gaps = 12/111 (10%)

Query: 686 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQ---QLSQLQQQQQQLPQLQQQI-PQLQQ 741
               + S +    Q + +  + +Q+   +Q       S             +++  ++ +
Sbjct: 36  VDKDLQSLEDILHQVENKTSEVKQLIKAIQLTYNPDESSKPNMIDAATLKSRKMLEEIMK 95

Query: 742 QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 792
            +        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: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQ 744
             + +      L+ ++  ++  + ++ +     S ++  Q+      Q+I  L+++  Q 
Sbjct: 73  SSKPNMIDAATLKSRKMLEEIMKYEASILTHD-SSIRYLQEIYNSNNQKIVNLKEKVAQL 131

Query: 745 IPQLQQQSMPQLQQQQQLPQ 764
             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: 686 FKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQI 745
            KP +   + +  +         Q  + + ++    L + Q+Q       + +   + ++
Sbjct: 98  VKPVLRDLKDRVAKFSDTSTTMYQYVNMIDNK----LVKTQKQRKDNDIILSEYNTEMEL 153

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGS 798
                +          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 = 49.6 bits (118), Expect = 3e-06
 Identities = 10/104 (9%), Positives = 27/104 (25%), Gaps = 5/104 (4%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
             S+   Q +     +    Q Q +     LS+   + +      +          +  L
Sbjct: 114 DTSTTMYQYVNMIDNKLVKTQKQRKDNDIILSEYNTEMELHYNYIKDNLDNNIPSSLRVL 173

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQP 792
           +       ++ 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 = 46.5 bits (110), Expect = 3e-05
 Identities = 7/84 (8%), Positives = 24/84 (28%), Gaps = 4/84 (4%)

Query: 694 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQ----LQQQIPQLQQQQQIPQLQ 749
            + Q Q++       +  ++++             +P     L+  I  L ++ Q  +  
Sbjct: 131 VKTQKQRKDNDIILSEYNTEMELHYNYIKDNLDNNIPSSLRVLRAVIDSLHKKIQKLENA 190

Query: 750 QQSMPQLQQQQQLPQLQQQQQLPQ 773
             +     +   +          +
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: 689 QISSQQQQQLQQQQQQ--QQHQQMQSQLQHQQLSQLQQQ--QQQLPQLQQQIPQLQQQQQ 744
           Q   Q+ + ++  Q      ++ ++SQ   Q L+   Q   +Q++ QL+Q +  L Q ++
Sbjct: 30  QDLEQKMKVVENLQDDFDFNYKTLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRR 89

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLS 790
              +  +    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: 694 QQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ--QQIPQLQQQ 751
             + L+ Q   Q        +  Q++ QL+Q    L Q+++ I          +  +Q+ 
Sbjct: 49  NYKTLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKT 108

Query: 752 SMPQLQQQQQLPQLQQQQQLP--QMQQQQQLPQLQQQ 786
                   ++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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           Q   ++ Q L+Q+ +  ++ Q      ++ L + Q   Q L    Q + + + QQ    L
Sbjct: 23  QDVRKRVQDLEQKMKVVENLQDDFDFNYKTL-KSQGDMQDLNGNNQSVTRQKMQQLEQML 81

Query: 749 QQQSMPQLQQQQQLPQ-LQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
                 +     +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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
            + SQ   Q      Q   +Q   QL+    +  Q ++  + +L   +  ++  Q+   L
Sbjct: 52  TLKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQK--TL 109

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
             + +   +++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: 702 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 761
           Q       + ++ Q      LQ  ++++  L+Q++  ++  Q       +++      Q 
Sbjct: 2   QANHPTAAVVTEKQQMLEQHLQDVRKRVQDLEQKMKVVENLQDDFDFNYKTLKSQGDMQD 61

Query: 762 LPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           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: 688 PQISSQQQQQLQQQQQQ-QQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQI-----PQLQQ 741
             ++   Q   +Q+ QQ +Q      Q++   +S+L      +  +Q+ +        ++
Sbjct: 60  QDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDEELADWKR 119

Query: 742 QQQIPQLQQQSMPQLQQQQQLPQL------QQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           +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: 686 FKPQISSQQQQQLQQQQQQQQHQQMQS------QLQHQQLSQLQQQQQQLPQLQQQI--- 736
            K Q   Q      Q   +Q+ QQ++       Q++   +S+L      +  +Q+ +   
Sbjct: 53  LKSQGDMQDLNGNNQSVTRQKMQQLEQMLTALDQMRRSIVSELAGLLSAMEYVQKTLTDE 112

Query: 737 --PQLQQQQQIPQLQQQSMPQLQQQQQ--------LPQLQQQ-QQLPQMQQQQQLPQLQQ 785
                +++QQI  +       L + +           Q +QQ ++L ++QQ+        
Sbjct: 113 ELADWKRRQQIACIGGPPNICLDRLENWITSLAESQLQTRQQIKKLEELQQKVSYKGDPI 172

Query: 786 QQQLSQPQQMVGS 798
            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: 689 QISSQQQQQLQQ--QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ-QQI 745
           ++ S+Q+Q L Q   +Q     ++   L    L+ L+   Q+   L  Q+          
Sbjct: 19  KLLSEQEQTLVQMIHEQSLLLNRLPPTLDENSLAPLKSLSQKQITLSGQMNTEMSALDAT 78

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
            +        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: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           Q    L   Q            Q Q L Q+  +Q  L               +  L Q+ 
Sbjct: 2   QGNPNLSSPQPILDTIYKLLSEQEQTLVQMIHEQSLLLNRLPPTLDENSLAPLKSLSQKQ 61

Query: 753 MPQLQQ-QQQLPQLQQ--QQQLPQMQQQQQLPQLQQQQQLSQPQ 793
           +    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: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQ-- 744
            P +SS Q       +   + +Q   Q+ H+Q   L +    L +      +   Q+Q  
Sbjct: 4   NPNLSSPQPILDTIYKLLSEQEQTLVQMIHEQSLLLNRLPPTLDENSLAPLKSLSQKQIT 63

Query: 745 IPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
           +       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: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ---- 742
            P +       L+   Q+Q     Q   +   L   ++     P    ++  L+Q     
Sbjct: 43  PPTLDENSLAPLKSLSQKQITLSGQMNTEMSALDATKKGMILEPTDLAKLFALKQDLQIQ 102

Query: 743 -QQIPQLQQQSMPQLQQQQQLPQLQQ----QQQLPQM 774
            +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 = 5e-06
 Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 6/115 (5%)

Query: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 746
           K    +    QL   ++ QQ      Q    +++ LQ+      Q++ QI Q    +   
Sbjct: 208 KAARLAALDAQLTPDERAQQAALHAQQDAVTKIADLQKAGATPDQMRAQIAQTLGPEAAA 267

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQ------LPQMQQQQQLPQLQQQQQLSQPQQM 795
           +  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 = 44.0 bits (103), Expect = 1e-04
 Identities = 15/103 (14%), Positives = 31/103 (30%), Gaps = 12/103 (11%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQ---------LQQQQQQLPQLQQQIPQLQQQ 742
              QQ    +    Q           Q++Q           Q QQ     Q +      +
Sbjct: 230 LHAQQDAVTKIADLQKAGATPDQMRAQIAQTLGPEAAARAAQMQQDDEAWQTRYQAYAAE 289

Query: 743 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQ 785
           +   ++  Q +    +  ++ QL+QQ       +  +   L +
Sbjct: 290 RD--RIAAQGLAPQDRDARIAQLRQQT-FTAPGEAIRAASLDR 329

>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: 699 QQQQQQQQHQQMQSQLQH--QQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQL 756
           +Q++   + + ++ ++     ++  L+  Q +     + +   + +        Q   QL
Sbjct: 3   KQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQL 62

Query: 757 QQQQQLPQLQQQ---------------QQLPQMQQQQQLPQLQQQQQLSQ 791
             ++    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: 687 KPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQ--------QQQQLPQLQQQIPQ 738
             +  +    +  Q+Q+Q   ++M   L +++   + +        +  Q   +  ++ +
Sbjct: 44  NREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVE 103

Query: 739 LQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
            +++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: 691 SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQ-----QQQQLPQLQQQIPQLQQQQQI 745
              +  Q Q+Q   ++   M    + + + ++ +     +  Q   +  ++ + +++QQ 
Sbjct: 51  GVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQS 110

Query: 746 PQLQQQSMPQLQQQQ--------QLPQLQQQ-QQLPQMQQQQQLPQLQQQQQLSQPQQMV 796
             +       L Q Q         L Q++QQ ++L +++Q+         +         
Sbjct: 111 ACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRT 170

Query: 797 GS 798
            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: 689 QISSQQQQQLQQQQQ--QQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIP 746
                + + L+  Q     + + +Q++           Q+Q+   L++    L  +++  
Sbjct: 19  MCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRK-- 76

Query: 747 QLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQL--QQQQQLSQPQQ 794
           ++  + +  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: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
           Q ++       +   +Q Q  L+   L    ++++ + ++ + +   +  Q    L    
Sbjct: 43  QNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQN--ALINDE 100

Query: 753 MPQLQQQQQLPQL--QQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
           + + +++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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           +I S +  Q +   + +  Q  + +      S  +Q+Q  L ++   +    +++++   
Sbjct: 24  EIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLML--DNKRKEVVHK 81

Query: 749 QQQSMPQLQQQQ------QLPQLQQQQQLPQ--MQQQQQLPQLQQQQQL 789
             + +   +  Q      +L + +++QQ           L QLQ    +
Sbjct: 82  IIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTI 130

>3ibp_A Chromosome partition protein MUKB; structural maintenance of chromosomes, SMC, condensin, chromosome segregation, hinge, dimerization domain; 3.10A {Escherichia coli} Length = 302

 Score = 47.0 bits (111), Expect = 1e-05
 Identities = 20/107 (18%), Positives = 45/107 (42%), Gaps = 4/107 (3%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
            I+S        ++++   +Q Q QLQ  ++  L Q+       Q  + QL +Q      
Sbjct: 4   MIASLSDSVSNAREERMALRQEQEQLQ-SRIQSLMQRAPVWLAAQNSLNQLSEQCGEEFT 62

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ-QQLSQPQQ 794
             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 = 45.5 bits (107), Expect = 4e-05
 Identities = 17/98 (17%), Positives = 38/98 (38%), Gaps = 7/98 (7%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQ-QQQIPQLQQ 750
           S     L       + ++M   L+ +Q    +Q Q ++  L Q+ P     Q  + QL +
Sbjct: 2   SHMIASLSDSVSNAREERMA--LRQEQ----EQLQSRIQSLMQRAPVWLAAQNSLNQLSE 55

Query: 751 QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           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 = 42.8 bits (100), Expect = 3e-04
 Identities = 15/102 (14%), Positives = 40/102 (39%), Gaps = 2/102 (1%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 751
           S  +++    +Q+Q+  Q + Q   Q+       Q  L QL +Q  +     Q   + + 
Sbjct: 13  SNAREERMALRQEQEQLQSRIQSLMQRAPVWLAAQNSLNQLSEQCGEEFTSSQ--DVTEY 70

Query: 752 SMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQ 793
               L+++++    + +    +    +++ +L Q       +
Sbjct: 71  LQQLLEREREAIVERDEVGARKNAVDEEIERLSQPGGSEDQR 112

>2v71_A Nuclear distribution protein NUDE-like 1; developmental protein, nuclear protein, neurogenesis, cytosk LIS1 binding, differentiation; 2.24A {Rattus norvegicus} Length = 189

 Score = 45.9 bits (108), Expect = 1e-05
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 691 SSQQQQQLQQQQQQQQHQQMQSQLQHQQL-SQLQQQQQQLPQLQQQIPQLQQQQQ--IPQ 747
           S + +Q  Q+ + +    Q  S+    +L +QL Q +Q+   LQ    +L+ + +    +
Sbjct: 19  SMKYKQSFQEARDELVEFQEGSRELEAELEAQLVQAEQRNRDLQADNQRLKYEVEALKEK 78

Query: 748 LQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           L+ Q     +Q   L     Q +  + Q  + + +L+Q   
Sbjct: 79  LEHQYAQSYKQVSVLEDDLSQTRAIKEQLHKYVRELEQAND 119

>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: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQS 752
             Q+ +Q+  ++ +  +        Q+ +L +  +     QQ + +LQQQ    +     
Sbjct: 2   SGQKTVQKILEEVRILEQIGVSHDAQIQELSEMWRVN---QQFVTRLQQQLVDIRQTCSR 58

Query: 753 MPQLQQQQQLPQLQ 766
             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 = 5e-05
 Identities = 12/74 (16%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 702 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 761
             Q+  Q++  +++  +         Q+ +L +       QQ + +LQQQ +   Q   +
Sbjct: 2   SGQKTVQKILEEVRILE-QIGVSHDAQIQELSEMW--RVNQQFVTRLQQQLVDIRQTCSR 58

Query: 762 LPQLQQQQQLPQMQ 775
             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 = 46.0 bits (108), Expect = 4e-05
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 1/101 (0%)

Query: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ-QQIPQLQQ 750
               Q+  Q  Q+ +  ++ +Q    +L +LQQ Q+      Q+  ++Q Q  Q+ QL  
Sbjct: 8   DAMSQKHLQINQRFEELRLITQDTENELKKLQQTQEYFIIQYQESLRIQAQFAQLGQLNP 67

Query: 751 QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
           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: 682 DMVVFKPQISSQQQQQLQQ--QQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQL 739
           +  + + Q S + Q Q  Q  Q   Q+    ++ LQ +Q+S     Q++   LQQ   +L
Sbjct: 43  EYFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLETWLQREAQTLQQYRVEL 102

Query: 740 QQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
            ++ 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 = 2e-04
 Identities = 21/105 (20%), Positives = 40/105 (38%), Gaps = 1/105 (0%)

Query: 698 LQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQ 757
           +      Q+H Q+  + +  +L   Q  + +L +LQQ       Q Q     Q    QL 
Sbjct: 5   VLVDAMSQKHLQINQRFEELRL-ITQDTENELKKLQQTQEYFIIQYQESLRIQAQFAQLG 63

Query: 758 QQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGSGMGQ 802
           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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
           Q +  + ++LQQ Q+    Q  +S     Q +QL Q   Q  +   +   LQQ+Q   + 
Sbjct: 29  QDTENELKKLQQTQEYFIIQYQESLRIQAQFAQLGQLNPQ--ERMSRETALQQKQVSLET 86

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
             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: 691 SSQQQQQLQQQQQQQQHQQMQSQLQH--QQLSQLQQ-------------QQQQLPQLQQQ 735
            + Q++  ++   QQ+   +++ LQ   Q L Q +              ++QQ   L  +
Sbjct: 65  LNPQERMSRETALQQKQVSLETWLQREAQTLQQYRVELAEKHQKTLQLLRKQQTIILDDE 124

Query: 736 IPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           + 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: 689 QISSQQQQQLQQQQQQQQH--------QQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 740
            I+   + +L++ QQ Q++         ++Q+Q         Q++  +   LQQ+   L+
Sbjct: 26  LITQDTENELKKLQQTQEYFIIQYQESLRIQAQFAQLGQLNPQERMSRETALQQKQVSLE 85

Query: 741 Q--QQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQMVGS 798
              Q++   LQQ  +   ++ Q+  QL ++QQ   +    +L Q +++QQL+        
Sbjct: 86  TWLQREAQTLQQYRVELAEKHQKTLQLLRKQQ--TIILDDELIQWKRRQQLAGNGGPPEG 143

Query: 799 GMGQ 802
            +  
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: 692 SQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQ 751
             ++Q L Q  +Q   +    ++  + +            +QQ               +Q
Sbjct: 69  PSEKQTLPQSIEQLTQK--SKKIIEEIIRYENTILAHENTIQQLTDMHIMNSNKITQLKQ 126

Query: 752 SMPQLQQQQQLPQLQQQQQLPQM 774
            + QL+   Q P     +     
Sbjct: 127 KIAQLESHCQEPCKDTAEIQETT 149

>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 = 43.0 bits (101), Expect = 1e-04
 Identities = 9/68 (13%), Positives = 19/68 (27%), Gaps = 1/68 (1%)

Query: 702 QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQ 761
           Q  Q  Q+    L H   S +Q+      ++      +  +     L+     Q  +   
Sbjct: 7   QYNQHKQETNETLNHHNCSNMQRAFNLKEEMLTNK-SIDCRPSNETLEYIKGEQHDRWDS 65

Query: 762 LPQLQQQQ 769
             +     
Sbjct: 66  KTKTVLDS 73

>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 = 2e-04
 Identities = 15/101 (14%), Positives = 49/101 (48%), Gaps = 6/101 (5%)

Query: 691  SSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQ 750
            +   + + Q  +++++ Q   ++L+ +  SQ     +++ +L+  I  LQ+  +    ++
Sbjct: 1081 AQIAELKAQLAKKEEELQAALARLEDET-SQKNNALKKIRELESHISDLQEDLES---EK 1136

Query: 751  QSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
             +  + ++Q++   L ++ +  + + +  L     QQ+L  
Sbjct: 1137 AARNKAEKQKR--DLSEELEALKTELEDTLDTTATQQELRG 1175

>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 = 43.3 bits (101), Expect = 3e-04
 Identities = 38/202 (18%), Positives = 67/202 (33%), Gaps = 4/202 (1%)

Query: 358 MAPAAANVNILNNLSQARQVMNNAALTGGTSIGLQSMGQTPMAMHMSNMISSGMASSVPT 417
           +         L ++ Q R  +        T  G  S G         N  S+G  +S  +
Sbjct: 222 LQKVPPEWKALTDMPQMRMELERPGGNEITRGGSTSYGTGSETESPRNPSSAGSWNSGSS 281

Query: 418 SQPVFSSAQSGITSIGGSGTLTGTSQVPQNSGLNSFTSAPSNLSGNSNPSISQPMGTLQG 477
                 +   G +  GG+ T    S  P ++G  +  S+ +  +GN NP   +P  T  G
Sbjct: 282 GPGSTGNRNPGSSGTGGTATWKPGSSGPGSTGSWNSGSSGTGSTGNQNPGSPRPGST--G 339

Query: 478 GASMGQSVGMSQGNHSGGQMVQNGISMNQNMMSGLGPSGVSSGTGTMIPTPGMSQQAQSG 537
             + G S   S G+ +      +G +   +  SG      S G+G   P        +  
Sbjct: 340 TWNPGSSERGSAGHWTSES-SVSGSTGQWHSESGSFRPD-SPGSGNARPNNPDWGTFEEV 397

Query: 538 MQPLSVNNNTAVNMQLSQQTSS 559
              +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: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
            ++     +  +   +++       L   +    QQ ++QL  L     + +        
Sbjct: 3   HMAQHGALETLKDLAEKEVDDAARLLGEMR-RGCQQAEEQLKMLIDYQNEYRSNLNTDMG 61

Query: 749 QQQSMPQLQQQQQ-LPQL-----QQQQQLPQMQQQ--QQLPQLQQQQQ 788
              +  +    QQ +  L     Q + QL Q  Q+    L   ++++Q
Sbjct: 62  NGIASNRWINYQQFIQTLEKAIEQHRLQLTQWTQKVDLALKSWREKKQ 109

>3o0z_A RHO-associated protein kinase 1; coiled-coil, transferase; HET: MSE; 2.33A {Homo sapiens} Length = 168

 Score = 41.3 bits (96), Expect = 3e-04
 Identities = 8/110 (7%), Positives = 38/110 (34%), Gaps = 3/110 (2%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQL---SQLQQQQQQLPQLQQQIPQLQQQQQI 745
           Q+         +     + ++  +++        S  ++ Q++   L+    Q  +    
Sbjct: 14  QLEEANDLLRTESDTAVRLRKSHTEMSKSISQLESLNRELQERNRILENSKSQTDKDYYQ 73

Query: 746 PQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQM 795
            Q   ++  + +          Q ++  +Q++ +  +   ++   + ++ 
Sbjct: 74  LQAILEAERRDRGHDSEMIGDLQARITSLQEEVKHLKHNLEKVEGERKEA 123

>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 = 42.7 bits (99), Expect = 5e-04
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 720 SQLQQQQQQLPQLQQQIPQLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQ 779
           S  QQ + ++ +L  + PQ   + Q+  LQ  ++   +  + +     +Q +    ++ +
Sbjct: 526 SMKQQNRAEILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPE 585

Query: 780 LPQLQQQQQLSQPQQMV 796
            P+  +QQ L + QQ  
Sbjct: 586 TPE--EQQWLVEAQQAK 600

>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: 678 LFPGDMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIP 737
           L P    + +P +  QQ QQ  +    +Q QQ+Q Q+   +    +Q +Q   Q + Q+ 
Sbjct: 13  LVPRGSHMAEPALREQQLQQ--ELLALKQKQQIQRQILIAEFQ--RQHEQLSRQHEAQLH 68

Query: 738 QLQQQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQL 780
           +  +QQQ     +     L+ Q++L + +Q+Q+L +  ++Q+L
Sbjct: 69  EHIKQQQEMLAMKHQQELLEHQRKLERHRQEQELEKQHREQKL 111

>1jad_A PLC-beta, phospholipase C beta; alpha helical coiled coil, hydrolase; 2.40A {Meleagris gallopavo} SCOP: h.4.10.1 Length = 251

 Score = 40.9 bits (95), Expect = 8e-04
 Identities = 8/100 (8%), Positives = 40/100 (40%), Gaps = 4/100 (4%)

Query: 693 QQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQ----LQQQIPQLQQQQQIPQL 748
            ++Q+ + ++ +++  + + +L  +      +           ++ +     +   + + 
Sbjct: 34  LKKQEKELKELERKGSKRREELLQKYSVLFLEPVYPRGLDSQVVELKERLEMELIHLGEE 93

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
               + + ++Q    Q  +  +L + +Q  +L  L++  +
Sbjct: 94  YHDGIRRRKEQHATEQTAKITELAREKQIAELKALKESSE 133

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	834
2iue_A	212	Pactolus I-domain; membrane protein, CD, ITC, limb	99.61
3vi3_B	454	Integrin beta-1; beta propeller fold, rossman fold	99.43
3v4v_B	503	Integrin beta-7; cell adhesion, madcam-1, membrane	99.4
3t3p_B	472	Integrin beta-3; integrin, cell adhesion, blood cl	99.39
3fcs_B	690	Integrin beta-3; beta propeller, rossmann fold, EG	99.38
3k6s_B	687	Integrin beta-2; cell receptor, adhesion molecule,	99.34
1ijb_A	202	VON willebrand factor; dinucleotide-binding fold,	99.05
2xgg_A	178	Microneme protein 2; A/I domain, cell adhesion, hy	99.0
1v7p_C	200	Integrin alpha-2; snake venom, C-type lectin, anta	98.99
1atz_A	189	VON willebrand factor; collagen-binding, hemostasi	98.98
3n2n_F	185	Anthrax toxin receptor 1; rossmann fold; 1.80A {Ho	98.94
1mf7_A	194	Integrin alpha M; cell adhesion; 1.25A {Homo sapie	98.89
3ibs_A	218	Conserved hypothetical protein BATB; structural ge	98.84
2b2x_A	223	Integrin alpha-1; computational design, antibody-a	98.83
1pt6_A	213	Integrin alpha-1; cell adhesion; 1.87A {Homo sapie	98.8
1shu_X	182	Anthrax toxin receptor 2; alpha/beta rossmann fold	98.79
1q0p_A	223	Complement factor B; VON willebrand factor, MAC-1,	98.78
1n3y_A	198	Integrin alpha-X; alpha/beta rossmann fold, cell a	98.73
4hqo_A	266	Sporozoite surface protein 2; malaria, gliding mot	98.72
4b4t_W	268	RPN10, 26S proteasome regulatory subunit RPN10; hy	98.71
4hqf_A	281	Thrombospondin-related anonymous protein, trap; ma	98.61
3zqk_A	199	VON willebrand factor; blood clotting, adamts-13,	98.6
3hrz_D	741	Complement factor B; serine protease, glycosilated	98.55
2x5n_A	192	SPRPN10, 26S proteasome regulatory subunit RPN10;	98.54
2odp_A	509	Complement C2; C3/C5 convertase, complement serin	98.54
1rrk_A	497	Complement factor B; BB, hydrolase; 2.00A {Homo sa	98.54
1mjn_A	179	Integrin alpha-L; rossmann fold, immune system; 1.	98.5
3k6s_A	1095	Integrin alpha-X; cell receptor, adhesion molecule	98.33
2x31_A	189	Magnesium-chelatase 60 kDa subunit; ligase, bacter	98.29
4fx5_A	464	VON willebrand factor type A; structural genomics,	98.13
1jey_B	565	KU80; double-strand DNA break repair, non-homologo	97.94
3rag_A	242	Uncharacterized protein; structural genomics, PSI-	97.91
1jey_A	609	KU70; double-strand DNA break repair, non-homologo	97.73
2ww8_A	893	RRGA, cell WALL surface anchor family protein; IGG	97.04
1yvr_A	538	RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein,	95.07
3iot_A	449	Maltose-binding protein, huntingtin fusion protei;	95.0
3iot_A	449	Maltose-binding protein, huntingtin fusion protei;	94.48
1pcx_A	810	Protein transport protein SEC24; 2.50A {Saccharomy	92.56
3eh1_A	751	Protein transport protein SEC24B; copii coat prote	92.55
2nut_A	769	Protein transport protein SEC23A; human copii SEC2	92.32
1m2v_B	926	SEC24, protein transport protein SEC24, SEC24P, SE	92.26
1m2o_A	768	SEC23, protein transport protein SEC23, SEC23P; zi	89.96
2nvo_A	535	RO sixty-related protein, RSR; alpha helical repea	88.0
3eh2_A	766	Protein transport protein SEC24C; copii-coat prote	85.91
3efo_B	770	SEC24 related gene family, member D; copii, coat p	83.96

>2iue_A Pactolus I-domain; membrane protein, CD, ITC, limbs, midas, admidas, membrane, integrin, titration, rossman fold, cell adhesion, transmembrane; NMR {Mus musculus}

Probab=99.61  E-value=7.8e-15  Score=150.48  Aligned_cols=166  Identities=8%  Similarity=0.098  Sum_probs=124.6

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHHH
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHW   83 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~~   83 (834)
                      .||+||||.|+||++|++.+|+. +..+++.+..  +      ..++|+|++.|+|+    . +...+.||+|.+.|.++
T Consensus         4 vDl~fl~D~S~SM~~di~~lk~~-~~~l~~~l~~--~------~~~~r~Gfg~f~Dk----~-~~~~l~lT~d~~~F~~~   69 (212)
T 2iue_A            4 VDLYFLMGLSGSAQGHLSNVQTL-GSDLLKALNE--I------SRSGRIGFGSIVNM----T-FQHILKLTADSSQFQRE   69 (212)
T ss_dssp             EEEEEEEECCGGGTTTHHHHHHH-HHHHHHHHHH--H------CSCEEEEEEEESSS----C-EEEEEEEESCHHHHHHH
T ss_pred             eEEEEEEeCCCcchhHHHHHHHH-HHHHHHHHHh--h------CcCceEEEEEEEcC----c-ceecCCcCCCHHHHHHH
Confidence            69999999999999999999977 7888777753  1      13689999999998    2 35678999999999999


Q ss_pred             hccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCC------------cccCCccc
Q 003284           84 LSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTP------------VYRPQMQN  151 (834)
Q Consensus        84 Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~p------------v~~p~~~~  151 (834)
                      ++++..+||++.||+..+||..|+.|.+..       .|....|.+||++|++||.....            |++-  .+
T Consensus        70 v~~~~vsg~~D~PE~g~dal~qa~~c~~~i-------~Wr~a~rllvl~TDa~~H~~gDg~l~gi~~pnd~~chl~--~g  140 (212)
T 2iue_A           70 LRKQLVSGKLATPKGQLDAVVQVAICLGEI-------GWRNGTRFLVLVTDNDFHLAKDKTLGTRQNTSDGRCHLD--DG  140 (212)
T ss_dssp             HHTCCCCCCSSSSBCHHHHHHHHHHCHHHH-------TCCSSEEEEEEECSSCBCCTTGGGGGTCCSCCCSSCCBS--SS
T ss_pred             HhhccccCCCCCCchHHHHHHHHHHhhhhc-------ccCCccEEEEEECcCCccccCCccccccccCCccccccC--CC
Confidence            999999999999999999999999875411       12335789999999999987542            2211  11


Q ss_pred             cccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC-chhHHHH
Q 003284          152 LDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ-LPKLTAI  197 (834)
Q Consensus       152 ~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq-lp~l~~L  197 (834)
                      +|. .    .......+++++.+.+.+++|.+....... ...+++|
T Consensus       141 ~y~-~----s~~~Dyps~~q~~~~l~~~~i~~ifavt~~~~~~Y~~l  182 (212)
T 2iue_A          141 MYR-S----RGEPDYQSVVQLASKLAENNIQPIFVVPSRMVKTYEKL  182 (212)
T ss_dssp             BBG-G----GGSSCCCCHHHHHHHHHHHTCEEEEEEEHHHHHHHHHH
T ss_pred             eec-c----CcccCCCCHHHHHHHHHhcCCcEEEEEccchhHHHHHH
Confidence            111 1    111123578999999999999975555543 3334444

>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=99.43  E-value=1.4e-12  Score=146.31  Aligned_cols=173  Identities=8%  Similarity=0.030  Sum_probs=128.5

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCC---------------------C
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHG---------------------S   62 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~---------------------~   62 (834)
                      .||+|++|.|++|+++++.||+. ...+++.+..-        ..++|+|++.|.|++                     |
T Consensus       123 VDLyyLmDlS~SM~ddl~~lk~l-g~~L~~~l~~~--------t~~~riGfGsFvDK~v~P~~~t~p~~~~nPC~~~~~c  193 (454)
T 3vi3_B          123 IDLYYLMDLSYSMKDDLENVKSL-GTDLMNEMRRI--------TSDFRIGFGSFVEKTVMPYISTTPAKLRNPCTSEQNC  193 (454)
T ss_dssp             EEEEEEEECSGGGHHHHHHHTTH-HHHHHHHHTTT--------CSSEEEEEEEECCCSSTTTSCCSTTTTTCCSCSSSCC
T ss_pred             eeEEEEecCCcchhhHHHHHHHH-HHHHHHHHHhc--------CCCeEEEEEEEeccccCCcccCChHHhcCCCcCccCC
Confidence            69999999999999999999987 68888888542        246899999999973                     2


Q ss_pred             Cccccee-eccCCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCC
Q 003284           63 YCACLVQ-RSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLP  141 (834)
Q Consensus        63 ~~~~lv~-~~gfTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp  141 (834)
                      .+.|..+ .+.+|+|..+|..+++++..+||+|.||+..|||..|+.|-+..       .|....|.+||++|+++|...
T Consensus       194 ~~~f~fr~~l~LT~d~~~F~~~V~~~~isGn~D~PEgg~DAl~Qaavc~~~i-------gWR~a~rllV~~TDa~fH~ag  266 (454)
T 3vi3_B          194 TTPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAVCGSLI-------GWRNVTRLLVFSTDAGFHFAG  266 (454)
T ss_dssp             CCCCSEEEEEEEESCHHHHHHHHTTCCCCCCSSSSBCHHHHHHHHHHCHHHH-------TCCSSEEEEEEEESSCBCCTT
T ss_pred             CCCcceeeeeecCCCHHHHHHHHhhccccCCCcCCchhHHHHHHHhcccccc-------CCccceEEEEEECCCCcCcCC
Confidence            2344444 57889999999999999999999999999999999988764311       133457888999999999766


Q ss_pred             C------------CcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcE-EEEeccCCchhHHHHHH
Q 003284          142 T------------PVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVS-LSVICPKQLPKLTAIYN  199 (834)
Q Consensus       142 ~------------pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~-LSvIsPrqlp~l~~Lfe  199 (834)
                      .            .|++-  +++| -.+..+    ..-...+|++.+.|++|. |++|.-+....|++|-+
T Consensus       267 DgkL~GIv~PNDg~CHL~--~~~Y-t~s~~~----DYPSv~ql~~~l~e~nI~~IFAVt~~~~~~Y~~L~~  330 (454)
T 3vi3_B          267 DGKLGGIVLPNDGQCHLE--NNMY-TMSHYY----DYPSIAHLVQKLSENNIQTIFAVTEEFQPVYKELKN  330 (454)
T ss_dssp             TTGGGTCCSCCCCCCCEE--TTEE-CCTTTS----CCCCHHHHHHHHHHTTEEEEEEEEGGGHHHHHHHHH
T ss_pred             CccccceecCCCCccEeC--CCcc-cccccC----CCCCHHHHHHHHHhcCCcEEEEEcCccchHHHHHHH
Confidence            5            23221  1222 111111    123579999999999999 66776666655555443

>3v4v_B Integrin beta-7; cell adhesion, madcam-1, membrane; HET: NAG BMA MAN 0DU; 3.10A {Homo sapiens} PDB: 3v4p_B*

Probab=99.40  E-value=2.7e-12  Score=145.25  Aligned_cols=173  Identities=10%  Similarity=0.054  Sum_probs=127.8

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCC----------------------
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHG----------------------   61 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~----------------------   61 (834)
                      .||+|+||.|.+|++|++.||+. ...+++.+..-        ..++|||++.|+|++                      
T Consensus       133 VDLyyLmDlS~SM~ddl~~lk~l-g~~L~~~l~~~--------t~~~RiGfGsFvDK~v~P~~~~~p~~l~~PC~~~~~~  203 (503)
T 3v4v_B          133 VDLYYLMDLSYSMKDDLERVRQL-GHALLVRLQEV--------THSVRIGFGSFVDKTVLPFVSTVPSKLRHPCPTRLER  203 (503)
T ss_dssp             EEEEEEEECSGGGHHHHHHHHHS-SHHHHHHHTTT--------CSCEEEEEEEECCCSSTTTSCCCHHHHHCCSSCSSSC
T ss_pred             eeEEEEEecCcchhhHHHHHHHH-HHHHHHHHHhh--------CcCcEEeeeeecccccCCcccCCHHHhcCCCcCCCCC
Confidence            69999999999999999999977 68888888541        246899999999963                      


Q ss_pred             CCccccee-eccCCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCC
Q 003284           62 SYCACLVQ-RSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPL  140 (834)
Q Consensus        62 ~~~~~lv~-~~gfTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~l  140 (834)
                      |.+.|..+ ...+|+|.++|..+++++..+||+|.||+..+||..|+.|-+..       .|....|.+||++|+++|..
T Consensus       204 c~p~f~fr~~l~LT~d~~~F~~~V~~~~iSGnlD~PEggfDAlmQaavC~~~I-------gWR~a~rllV~~TDA~fH~a  276 (503)
T 3v4v_B          204 CQSPFSFHHVLSLTGDAQAFEREVGRQSVSGNLDSPEGGFDAILQAALCQEQI-------GWRNVSRLLVFTSDDTFHTA  276 (503)
T ss_dssp             CCCCCSEEEEEEEESCSHHHHHHHTTCCCCCCSSSSBCHHHHHHHHHHCHHHH-------TCCSSEEEEEEEESSCBCCT
T ss_pred             CCCCcceEEEEEecCCHHHHHHHHhhcCccCCCCCCchHHHHHHHHhhccccc-------CCCcceEEEEEECCCCcCcC
Confidence            22344444 46789999999999999999999999999999999888654211       12335688999999999975


Q ss_pred             CC------------CcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcE-EEEeccCCchhHHHHH
Q 003284          141 PT------------PVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVS-LSVICPKQLPKLTAIY  198 (834)
Q Consensus       141 p~------------pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~-LSvIsPrqlp~l~~Lf  198 (834)
                      ..            .|++-. +++|. .    ......-...+|++.+.|++|. |+.|.-+....|++|-
T Consensus       277 gDgkLaGIv~pNDg~CHL~~-~~~Yt-~----s~~~DYPSv~ql~~kL~ennI~~IFAVt~~~~~~Y~~L~  341 (503)
T 3v4v_B          277 GDGKLGGIFMPSDGHCHLDS-NGLYS-R----STEFDYPSVGQVAQALSAANIQPIFAVTSAALPVYQELS  341 (503)
T ss_dssp             TGGGTTTCCSCCCSSCCBCT-TSBBG-G----GGGSCCCCHHHHHHHHHHHTEEEEEEECSSSHHHHHHHH
T ss_pred             CCccccceecCCCCCeEECC-CCccc-c----ccccCCCCHHHHHHHHHhcCCeEEEEEcccchhHHHHHH
Confidence            54            232210 12221 1    1122234679999999999998 6667666666555553

>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=99.39  E-value=4.6e-12  Score=142.84  Aligned_cols=174  Identities=9%  Similarity=-0.023  Sum_probs=127.0

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC---------------------
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS---------------------   62 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~---------------------   62 (834)
                      .||+|++|.|.+|++|++.||+. ...+++.+..-        ..++|||++.|+|++-                     
T Consensus       112 vDLy~LmDlS~SM~ddl~~lk~l-g~~L~~~l~~~--------t~~~riGfgsFvDk~v~P~~~~~p~~~l~nPc~~~~~  182 (472)
T 3t3p_B          112 VDIYYLMDLSYSMKDDLWSIQNL-GTKLATQMRKL--------TSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDMKT  182 (472)
T ss_dssp             EEEEEEEECSGGGHHHHHHTTTH-HHHHHHHHTTT--------CSCEEEEEEEECCCSSTTTSCCCSHHHHHCTTTTTTS
T ss_pred             ceEEEEEccCcchHHHHHHHHHH-HHHHHHHHHhc--------CcCcEEEEEEeeccccCccccCChhhhhcCCCccccc
Confidence            69999999999999999999987 78888888641        2468999999999632                     


Q ss_pred             --Cccccee-eccCCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCc-cCCcEEEEeecCCCC
Q 003284           63 --YCACLVQ-RSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV-DGQRHCILVAASNPH  138 (834)
Q Consensus        63 --~~~~lv~-~~gfTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~-~~qkhCILIa~SpP~  138 (834)
                        .+.|..+ .+.+|+|.++|..+++++..+||+|.||+..+||..|+.|-+..       .|. +..|.+||++|+++|
T Consensus       183 ~c~p~f~fr~~l~LT~d~~~F~~~V~~~~iSGn~D~PEgg~dAl~qaavC~~~i-------gWR~~a~rllV~~TDa~~H  255 (472)
T 3t3p_B          183 TCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKI-------GWRNDASHLLVFTTDAKTH  255 (472)
T ss_dssp             CCCCCCSEEEEEEEESCHHHHHHHHHHCCCCCCSSSSBCHHHHHHHHHHCHHHH-------TCCSSSEEEEEEEESSCBC
T ss_pred             CCCCCcceeEeeccCCCHHHHHHHHhhccccCCCCCCchHHHHHHHHhcchhhc-------CCCCCceEEEEEECCCCcC
Confidence              1233333 46789999999999999999999999999999999998654211       122 357888999999999


Q ss_pred             CCCC------------CcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcE-EEEeccCCchhHHHHHH
Q 003284          139 PLPT------------PVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVS-LSVICPKQLPKLTAIYN  199 (834)
Q Consensus       139 ~lp~------------pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~-LSvIsPrqlp~l~~Lfe  199 (834)
                      ....            .|++-. +++| ..    ......-...+|++.+.|++|. |+.|.-+....|++|-+
T Consensus       256 ~agDgkL~GIv~pnDg~CHL~~-~~~Y-~~----s~~~DYPSv~ql~~~l~e~nI~~IFAVt~~~~~~Y~~L~~  323 (472)
T 3t3p_B          256 IALDGRLAGIVQPNDGQCHVGS-DNHY-SA----STTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSE  323 (472)
T ss_dssp             CTTGGGGGTCCCCCCCCCCBCT-TCBB-TT----TTTSCCCCHHHHHHHHHHTTCEEEEEECGGGHHHHHHHHH
T ss_pred             cCCCccccceecCCCCceEECC-CCcc-cc----cccCCCCCHHHHHHHHHhcCccEEEEEeccchhHHHHHHH
Confidence            7554            232210 1111 11    1112224679999999999999 56666655565555543

>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=99.38  E-value=3.6e-12  Score=150.28  Aligned_cols=174  Identities=10%  Similarity=-0.010  Sum_probs=124.1

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCc-------------------
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYC-------------------   64 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~-------------------   64 (834)
                      .||+|+||.|++|++||+.||+. +..+++.+..  +      ..++|||++.|+|+...|                   
T Consensus       112 vDly~LmD~S~SM~ddi~~lk~l-~~~l~~~l~~--~------t~~~r~Gfgsf~Dk~~~P~~~~~p~~~~~~pc~~~~~  182 (690)
T 3fcs_B          112 VDIYYLMDLSYSMKDDLWSIQNL-GTKLATQMRK--L------TSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDMKT  182 (690)
T ss_dssp             EEEEEEEECSGGGHHHHHHTTTT-THHHHHHHHH--H------CSCEEEEEEEECCCSSTTTSCCCSTTTTTCTTSSSSS
T ss_pred             ccEEEEecCCcchHHHHHHHHHH-HHHHHHHHHh--h------CcCceEEeEEeeccccCCccccChhhhccCCCcCCCC
Confidence            69999999999999999999976 6778877754  1      246899999999966322                   


Q ss_pred             ----cccee-eccCCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCc-cCCcEEEEeecCCCC
Q 003284           65 ----ACLVQ-RSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNV-DGQRHCILVAASNPH  138 (834)
Q Consensus        65 ----~~lv~-~~gfTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~-~~qkhCILIa~SpP~  138 (834)
                          .|..+ .+.+|+|..+|..+|+++.++||+|.||+..+||..|+.+.+..       .|. ...|.+||++|+++|
T Consensus       183 ~c~~~f~f~~~l~lt~~~~~f~~~v~~~~isgn~D~PE~g~dAl~qa~~c~~~i-------gWr~~a~rllv~~TDa~~H  255 (690)
T 3fcs_B          183 TCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKI-------GWRNDASHLLVFTTDAKTH  255 (690)
T ss_dssp             CCCCCCSEEEEEEEESCHHHHHHHHTTCCCCCCSSSSBCHHHHHHHHHHCHHHH-------TCCSSSEEEEEEEESSCBC
T ss_pred             CCCCCccceeecccCCCHHHHHHHhhceeccCCCCCCchHHHHHHHHhhccccc-------CCCCCceEEEEEECCCccc
Confidence                12222 36779999999999999999999999999999999999665411       122 357888999999999


Q ss_pred             CCCC------------CcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC-chhHHHHHH
Q 003284          139 PLPT------------PVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ-LPKLTAIYN  199 (834)
Q Consensus       139 ~lp~------------pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq-lp~l~~Lfe  199 (834)
                      -...            .|++-. +++|. .    ......-+..+|++.|.|++|.+-++..+. +..|++|.+
T Consensus       256 ~agDg~l~gi~~pnd~~chl~~-~~~y~-~----s~~~DypSi~ql~~~l~~~~i~~ifavt~~~~~~y~~l~~  323 (690)
T 3fcs_B          256 IALDGRLAGIVQPNDGQCHVGS-DNHYS-A----STTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSE  323 (690)
T ss_dssp             CTTGGGGGTCCSCCCCCCCBCT-TCBBG-G----GGTSCCCCHHHHHHHHHHTTCEEEEEEEGGGHHHHHHHHH
T ss_pred             cCCCccccceecCCCcceeecC-CCccc-c----ccccCCCCHHHHHHHHHHcCCeEEEEEeCCchhhHHHHHh
Confidence            5433            222110 11111 1    111122358999999999999966555444 455555544

>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=99.34  E-value=1.9e-12  Score=152.43  Aligned_cols=174  Identities=7%  Similarity=-0.003  Sum_probs=124.6

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCC--------------------
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY--------------------   63 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~--------------------   63 (834)
                      .||+|+||.|.+|++||+.||+. +..+++.+..  +      ..++|||++.|+|+...                    
T Consensus       105 vDly~LmD~S~SM~ddi~~lk~l-~~~l~~~l~~--~------t~~~r~GfgsFvDk~~~P~~~~~p~~~~~Pc~~~~~~  175 (687)
T 3k6s_B          105 IDLYYLMDLSYSMLDDLRNVKKL-GGDLLRALNE--I------TESGRIGFGSFVDKTVLPFVNTHPDKLRNPCPNKEKE  175 (687)
T ss_dssp             CEEEEEEECSSTTHHHHHTTTTC-CTTHHHHHHS--S------CCSCEEEEEEECCCSSTTSSCCSSTTTTCCCCSCCCC
T ss_pred             eeEEEEEcCCcchHHHHHHHHHH-HHHHHHHHHh--h------CcCcEEeeEEeeccccCCccccCchhccCCCCCCCCC
Confidence            69999999999999999999976 7888888854  1      24689999999995431                    


Q ss_pred             --ccccee-eccCCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCC
Q 003284           64 --CACLVQ-RSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPL  140 (834)
Q Consensus        64 --~~~lv~-~~gfTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~l  140 (834)
                        +.|..+ ...+|+|+++|..+++++.++||+|.||+..+||..|+.+-+..       .|....|.+||++|+++|-.
T Consensus       176 c~~~f~f~~~l~lt~~~~~F~~~v~~~~isgn~D~PE~g~dAl~qa~vc~~~i-------gWr~a~rllV~~TDa~~H~a  248 (687)
T 3k6s_B          176 CQPPFAFRHVLKLTNNSNQFQTEVGKQLISGNLDAPEGGLDAMMQVAACPEEI-------GWRNVTRLLVFATDDGFHFA  248 (687)
T ss_dssp             CCCCCSCEEEEEEESCSHHHHHHHHTSCCCCCSSSSCCHHHHHHHHTTCHHHH-------CCCSSCCEEEEECSSCCCCT
T ss_pred             cCCcccceeecccCCCHHHHHHHHhhccccCCCCCCchHHHHHHHHhhccccc-------CCccceEEEEEECCCccccC
Confidence              222222 35679999999999999999999999999999999999443211       12336789999999999954


Q ss_pred             CC------------CcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEec-cCCchhHHHHHHH
Q 003284          141 PT------------PVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVIC-PKQLPKLTAIYNA  200 (834)
Q Consensus       141 p~------------pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIs-Prqlp~l~~Lfek  200 (834)
                      ..            .|++   .+-.+..+.+.    ..-+..+|++.|.|++|.+-++. -+.+..|++|.+.
T Consensus       249 gDg~l~gi~~pndg~Chl---~~~~y~~s~~~----DyPS~~ql~~~l~~~~I~~ifavt~~~~~~y~~l~~~  314 (687)
T 3k6s_B          249 GDGKLGAILTPNDGRCHL---EDNLYKRSNEF----DYPSVGQLAHKLAENNIQPIFAVTSRMVKTYEKLTEI  314 (687)
T ss_dssp             TGGGGGTCCCCCCSCCCC---SSSBCSSGGGS----CCCCGGGHHHHHHHTTCBCCEEECGGGHHHHHHHHHH
T ss_pred             CCccccceecCCCCcccc---CCCcccccccc----CCCCHHHHHHHHHHcCCeEEEEEeccchhhHHHHHhh
Confidence            43            2222   21111121111    12346899999999999865544 4445666666553

>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=99.05  E-value=2e-09  Score=107.22  Aligned_cols=149  Identities=15%  Similarity=0.201  Sum_probs=107.6

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~   79 (834)
                      ..|||||||++++|+. .|+.+| +++..+++.|.-+        ....|+|||.|.+..-      ..+.|+  .|...
T Consensus        13 ~~divfvlD~SgSm~~~~~~~~k-~~~~~~v~~l~~~--------~~~~rv~vv~fs~~~~------~~~~l~~~~~~~~   77 (202)
T 1ijb_A           13 LLDLVFLLDGSSRLSEAEFEVLK-AFVVDMMERLRVS--------QKWVRVAVVEYHDGSH------AYIGLKDRKRPSE   77 (202)
T ss_dssp             CEEEEEEEECBTTSCHHHHHHHH-HHHHHHHHTBCBS--------TTSEEEEEEEESSSEE------EEECTTCCCCHHH
T ss_pred             cccEEEEEECCCCCCHHHHHHHH-HHHHHHHHhcccC--------CCceEEEEEEECCCce------EEEecCCCCCHHH
Confidence            3799999999999985 788877 5678888887421        1357999999987622      234454  78899


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHH-hhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEAL-MMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL-~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      +...|+.|.+.|||  .-++.+||..|+ ++|..   .    .+....|.+|||+|..++.-                  
T Consensus        78 ~~~~i~~l~~~gg~--~T~~~~aL~~a~~~~~~~---~----~r~~~~~~iillTDG~~~~~------------------  130 (202)
T 1ijb_A           78 LRRIASQVKYAGSQ--VASTSEVLKYTLFQIFSK---I----DRPEASRIALLLMASQEPQR------------------  130 (202)
T ss_dssp             HHHHHHTCCCCCBS--CCCHHHHHHHHHHHTSSS---C----SCTTSEEEEEEEECCCCCGG------------------
T ss_pred             HHHHHHhCcCCCCC--cCcHHHHHHHHHHHHhcc---C----CCCCCCeEEEEEccCCCCcc------------------
Confidence            99999999998775  356778888887 45641   0    12346789999998876411                  


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccCC---chhHHHHHH
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPKQ---LPKLTAIYN  199 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq---lp~l~~Lfe  199 (834)
                            ...++...++.+.+++|.+++|.--.   ...|+.|-.
T Consensus       131 ------~~~~~~~~a~~l~~~gi~i~~igvG~~~~~~~L~~iA~  168 (202)
T 1ijb_A          131 ------MSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEK  168 (202)
T ss_dssp             ------GCTTHHHHHHHHHHTTEEEEEEEESTTSCHHHHHHHHH
T ss_pred             ------chHHHHHHHHHHHHCCCEEEEEecCCcCCHHHHHHHhC
Confidence                  01266788999999999999997653   244555544

>2xgg_A Microneme protein 2; A/I domain, cell adhesion, hydrolase; 2.05A {Toxoplasma gondii}

Probab=99.00  E-value=2.4e-09  Score=104.51  Aligned_cols=139  Identities=12%  Similarity=0.229  Sum_probs=101.0

Q ss_pred             CccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC----CH
Q 003284            3 EKQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----DV   77 (834)
Q Consensus         3 ~~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs----d~   77 (834)
                      ..|||||||++++|+ ..|+.+| +++..+++.|..+        ....++|||.|.+...      ..+.|+.    |.
T Consensus        17 ~~divfvlD~SgSm~~~~~~~~k-~~~~~~i~~l~~~--------~~~~rv~vv~F~~~~~------~~~~l~~~~~~~~   81 (178)
T 2xgg_A           17 QLDICFLIDSSGSIGIQNFRLVK-QFLHTFLMVLPIG--------PEEVNNAVVTYSTDVH------LQWDLQSPNAVDK   81 (178)
T ss_dssp             CEEEEEEEECCTTTCHHHHHHHH-HHHHHHHHHSCBS--------TTSEEEEEEEESSSEE------EEECTTSGGGSCH
T ss_pred             CeeEEEEEECCCCCCHHHHHHHH-HHHHHHHHhcCCC--------CCCeEEEEEEeCCceE------EEEeCCCCCccCH
Confidence            479999999999996 4788776 5578888887431        1358999999987632      2344544    88


Q ss_pred             HHHHHHhccCccCCCCCchhhHHHHHHHHHhh-cccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccccccc
Q 003284           78 DIFLHWLSTIPFAGGGFNDAAIAEGLSEALMM-FSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNE  156 (834)
Q Consensus        78 ~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~-f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e  156 (834)
                      ..|+.+|+.|.+.|||   ..+.+||..|++. |....     .......|.+|||+|..+..-                
T Consensus        82 ~~~~~~i~~l~~~~g~---T~~~~aL~~a~~~l~~~~~-----g~r~~~~~~iillTDG~~~~~----------------  137 (178)
T 2xgg_A           82 QLAAHAVLDMPYKKGS---TNTSDGLKACKQILFTGSR-----PGREHVPKLVIGMTDGESDSD----------------  137 (178)
T ss_dssp             HHHHHHHHHCCCCCCC---CCHHHHHHHHHHHHHHCCC-----TTCTTSCEEEEEEESSCCCHH----------------
T ss_pred             HHHHHHHHhCCCCCCC---ccHHHHHHHHHHHhcCccc-----CCCCCCCEEEEEEcCCCCCCC----------------
Confidence            9999999999987775   4677888888875 54211     112356799999998766410                


Q ss_pred             chhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          157 NNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       157 ~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                                .+++.+++.+.+++|.+++|.--.
T Consensus       138 ----------~~~~~~~~~l~~~gi~v~~igvG~  161 (178)
T 2xgg_A          138 ----------FRTVRAAKEIRELGGIVTVLAVGH  161 (178)
T ss_dssp             ----------HHHSHHHHHHHHTTCEEEEEECC-
T ss_pred             ----------ccHHHHHHHHHHCCCEEEEEEcCC
Confidence                      135678899999999999997654

>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=98.99  E-value=4e-09  Score=104.45  Aligned_cols=137  Identities=14%  Similarity=0.209  Sum_probs=100.6

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIF   80 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~f   80 (834)
                      ..|||||||++++|++ |+.+| +++..+++.|.-+        ....|+|||.|.+..-      ..++|+  .+...+
T Consensus         6 ~~div~vlD~SgSm~~-~~~~k-~~~~~~~~~l~~~--------~~~~rvglv~f~~~~~------~~~~l~~~~~~~~~   69 (200)
T 1v7p_C            6 LIDVVVVCDESNSIYP-WDAVK-NFLEKFVQGLDIG--------PTKTQVGLIQYANNPR------VVFNLNTYKTKEEM   69 (200)
T ss_dssp             CEEEEEEEECCTTCCC-HHHHH-HHHHHHHHTSCBS--------TTSEEEEEEEESSSEE------EEECTTTCSSHHHH
T ss_pred             cccEEEEEECCCCccc-HHHHH-HHHHHHHHhcCCC--------CCceEEEEEEECCCce------EEEeCCCcCCHHHH
Confidence            3799999999999995 77776 5577778777421        1358999999987621      234554  588999


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      +..|+.|...||+  ..++.+||..|++ +|....     .......|++|||+|-.++.   .                
T Consensus        70 ~~~i~~l~~~~G~--~T~~~~al~~a~~~~~~~~~-----g~r~~~~~~ivllTDG~~~~---~----------------  123 (200)
T 1v7p_C           70 IVATSQTSQYGGD--LTNTFGAIQYARKYAYSAAS-----GGRRSATKVMVVVTDGESHD---G----------------  123 (200)
T ss_dssp             HHHHHHCCCCCCS--CCCHHHHHHHHHHHTTSGGG-----TCCTTSEEEEEEEESSCCSC---G----------------
T ss_pred             HHHHHhhhccCCC--CCcHHHHHHHHHHhhccccc-----CCCCCCCeEEEEEccCCCCC---c----------------
Confidence            9999999987763  2468888899987 464211     11235678999999987751   0                


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEecc
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICP  188 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsP  188 (834)
                             .+++.+++.+.+++|.+++|.-
T Consensus       124 -------~~~~~~~~~~~~~gi~i~~igv  145 (200)
T 1v7p_C          124 -------SMLKAVIDQCNHDNILRFGIAV  145 (200)
T ss_dssp             -------GGHHHHHHHHHHTTEEEEEEEE
T ss_pred             -------ccHHHHHHHHHHCCCEEEEEEe
Confidence                   1356788999999999999976

>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=98.98  E-value=1.1e-08  Score=100.31  Aligned_cols=146  Identities=12%  Similarity=0.251  Sum_probs=103.8

Q ss_pred             CccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccC--CCCHHH
Q 003284            3 EKQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGW--TKDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gf--Tsd~~~   79 (834)
                      ..|||||||++++|+ ..|+.+| +++.-+++.|.-+        ....|+|||.|.+...      ..++|  +.|...
T Consensus         5 ~~div~vlD~SgSm~~~~~~~~k-~~~~~~~~~l~~~--------~~~~rv~lv~f~~~~~------~~~~l~~~~~~~~   69 (189)
T 1atz_A            5 PLDVILLLDGSSSFPASYFDEMK-SFAKAFISKANIG--------PRLTQVSVLQYGSITT------IDVPWNVVPEKAH   69 (189)
T ss_dssp             CEEEEEEEECSSSSCHHHHHHHH-HHHHHHHHHSCBS--------TTSEEEEEEEESSSEE------EEECTTCCCCHHH
T ss_pred             ceeEEEEEeCCCCCChhhHHHHH-HHHHHHHHhcCcC--------CCCeEEEEEEECCcce------EEEecCCCCCHHH
Confidence            479999999999998 6788877 4577788887421        1358999999976521      23455  899999


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      +...|+.|.+.|||   .++.+||..|++.+.....+    ......|++|+|++--+.                     
T Consensus        70 ~~~~i~~l~~~~g~---T~~~~aL~~a~~~l~~~~~g----~r~~~~~~vivltdg~~~---------------------  121 (189)
T 1atz_A           70 LLSLVDVMQREGGP---SQIGDALGFAVRYLTSEMHG----ARPGASKAVVILVTDVSV---------------------  121 (189)
T ss_dssp             HHHHHHTCCCCCCC---CCHHHHHHHHHHHHHSCCTT----CCTTSEEEEEEEECSCCS---------------------
T ss_pred             HHHHHHhCcCCCCc---chHHHHHHHHHHHHhccccC----CCCCCCcEEEEEeCCCCC---------------------
Confidence            99999999987765   57888888898766431111    112345778888766442                     


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccCCc---hhHHHHH
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPKQL---PKLTAIY  198 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrql---p~l~~Lf  198 (834)
                             .+++.+++.+.+++|.+++|.--.-   ..|+.|-
T Consensus       122 -------~~~~~~~~~~~~~gi~v~~igvG~~~~~~~L~~iA  156 (189)
T 1atz_A          122 -------DSVDAAADAARSNRVTVFPIGIGDRYDAAQLRILA  156 (189)
T ss_dssp             -------SCCHHHHHHHHHTTEEEEEEEESSSSCHHHHHHHT
T ss_pred             -------chHHHHHHHHHHCCCEEEEEEcCCcCCHHHHHHHH
Confidence                   1346788899999999999976542   3444443

>3n2n_F Anthrax toxin receptor 1; rossmann fold; 1.80A {Homo sapiens} SCOP: c.62.1.1

Probab=98.94  E-value=1.4e-09  Score=105.21  Aligned_cols=137  Identities=17%  Similarity=0.223  Sum_probs=99.8

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHHH
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLHW   83 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~~   83 (834)
                      .|||||||++++|+..|+.++ +++..+++.|..          ...++|||.|.+...      ..++||.|...+..+
T Consensus         8 ~div~vlD~SgSM~~~~~~~~-~~~~~~~~~~~~----------~~~~v~lv~f~~~~~------~~~~l~~~~~~~~~~   70 (185)
T 3n2n_F            8 FDLYFILDKSGSVLHHWNEIY-YFVEQLAHKFIS----------PQLRMSFIVFSTRGT------TLMKLTEDREQIRQG   70 (185)
T ss_dssp             EEEEEEEECSGGGGGGHHHHH-HHHHHHHHHCCC----------TTEEEEEEEESSSEE------EEEEEECCHHHHHHH
T ss_pred             eeEEEEEeCCCChhhhHHHHH-HHHHHHHHHhCC----------CCcEEEEEEEecCce------EEeccCCCHHHHHHH
Confidence            799999999999999888766 567788888732          257999999987632      356788899999999


Q ss_pred             hccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           84 LSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        84 Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      |++|.  +.|||   ..+.+||..|++.+.....     ......|++|||+|..+..-                     
T Consensus        71 i~~l~~~~~~g~---T~~~~al~~a~~~l~~~~~-----~~~~~~~~iillTDG~~~~~---------------------  121 (185)
T 3n2n_F           71 LEELQKVLPGGD---TYMHEGFERASEQIYYENR-----QGYRTASVIIALTDGELHED---------------------  121 (185)
T ss_dssp             HHHHHTCCCCSC---CCHHHHHHHHHHHHHHHHT-----TCBCEEEEEEEEECCCCCHH---------------------
T ss_pred             HHHHhhhcCCCC---ccHHHHHHHHHHHHhhccc-----cCCCCCcEEEEEcCCCCCCC---------------------
Confidence            99988  44665   4477777777764411000     11235789999998766310                     


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                         ...+++..++.+.+++|.+++|.-.
T Consensus       122 ---~~~~~~~~~~~~~~~gi~i~~igvg  146 (185)
T 3n2n_F          122 ---LFFYSEREANRSRDLGAIVYAVGVK  146 (185)
T ss_dssp             ---HHHHHHHHHHHHHHTTEEEEEEECS
T ss_pred             ---cccchHHHHHHHHHCCCEEEEEEec
Confidence               0013467899999999999999876

>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=98.89  E-value=5e-09  Score=102.88  Aligned_cols=138  Identities=12%  Similarity=0.186  Sum_probs=99.6

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC--CHHH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs--d~~~   79 (834)
                      ..|||||||++++|+. .|+.+| +++..+++.|..          ...|+|||.|.+...      ..++|+.  |...
T Consensus         5 ~~div~vlD~SgSm~~~~~~~~k-~~~~~~~~~l~~----------~~~~v~vv~f~~~~~------~~~~l~~~~~~~~   67 (194)
T 1mf7_A            5 DSDIAFLIDGSGSIIPHDFRRMK-EFVSTVMEQLKK----------SKTLFSLMQYSEEFR------IHFTFKEFQNNPN   67 (194)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHH-HHHHHHHHHHCC----------TTEEEEEEEESSSEE------EEECHHHHHHSCC
T ss_pred             CeeEEEEEeCCCCCCHHHHHHHH-HHHHHHHHhcCC----------CCeEEEEEEecCCce------EEEecCCcCCHHH
Confidence            3799999999999987 788777 567888888851          357999999987632      3455554  3457


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      +...|+.|.+.|||   ..+.+||..|++ +|....     ..+....|.+|||+|..+..-+  .              
T Consensus        68 ~~~~i~~l~~~~g~---T~~~~aL~~a~~~l~~~~~-----~~r~~~~~~iillTDG~~~~d~--~--------------  123 (194)
T 1mf7_A           68 PRSLVKPITQLLGR---THTATGIRKVVRELFNITN-----GARKNAFKILVVITDGEKFGDP--L--------------  123 (194)
T ss_dssp             HHHHHTTCCCCCSC---BCHHHHHHHHHHTTTSGGG-----TCCTTSEEEEEEEESSCCBSCS--S--------------
T ss_pred             HHHHHHhCcCCCCC---chHHHHHHHHHHHhcCccc-----CCCCCCCeEEEEEcCCCCCCCc--h--------------
Confidence            88899999987664   468889999995 664211     1123467899999998876211  1              


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                               +.+.+++.+.+++|.+++|.--.
T Consensus       124 ---------~~~~~~~~~~~~gi~v~~igvG~  146 (194)
T 1mf7_A          124 ---------GYEDVIPEADREGVIRYVIGVGD  146 (194)
T ss_dssp             ---------CGGGTHHHHHHTTEEEEEEEESG
T ss_pred             ---------hhHHHHHHHHHCCCEEEEEEecc
Confidence                     22445778899999999997654

>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=98.84  E-value=4.3e-08  Score=97.44  Aligned_cols=132  Identities=17%  Similarity=0.170  Sum_probs=99.2

Q ss_pred             CccEEEEEeccccchH------hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCC
Q 003284            3 EKQLIVAVEGTAAMGP------YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKD   76 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~------yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd   76 (834)
                      ..|||||||+++||..      -|+.+|. .+..+++.+.            ..++|||.|.+..      ...++||.|
T Consensus        11 ~~~iv~vlD~SgSM~~~d~~~~r~~~ak~-~~~~~~~~~~------------~~~v~lv~F~~~~------~~~~~~~~~   71 (218)
T 3ibs_A           11 GVEVIIALDISNSMLAQDVQPSRLEKAKR-LISRLVDELD------------NDKVGMIVFAGDA------FTQLPITSD   71 (218)
T ss_dssp             CCEEEEEEECSGGGGCCSSSSCHHHHHHH-HHHHHHHTCS------------SCEEEEEEESSSE------EEEEEEESC
T ss_pred             CCcEEEEEECCcCcccccCCcCHHHHHHH-HHHHHHHhCC------------CCeEEEEEECCCc------eEeCCCCCC
Confidence            4799999999999986      4777763 3555555441            3699999998762      245678999


Q ss_pred             HHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccccccc
Q 003284           77 VDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNE  156 (834)
Q Consensus        77 ~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e  156 (834)
                      ...+..+|+.|...........+.+||..|+.++...         ....|.+|||+|-.+..                 
T Consensus        72 ~~~~~~~l~~l~~~~~~~g~T~l~~al~~a~~~l~~~---------~~~~~~ivllTDG~~~~-----------------  125 (218)
T 3ibs_A           72 YISAKMFLESISPSLISKQGTAIGEAINLATRSFTPQ---------EGVGRAIIVITDGENHE-----------------  125 (218)
T ss_dssp             HHHHHHHHHTCCGGGCCSCSCCHHHHHHHHHTTSCSC---------SSCCEEEEEEECCTTCC-----------------
T ss_pred             HHHHHHHHHhcCcccCCCCCCcHHHHHHHHHHHHhhC---------CCCCcEEEEEcCCCCCC-----------------
Confidence            9999999999986422233467899999999988642         23568999999876531                 


Q ss_pred             chhhhhhccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          157 NNEAQAESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       157 ~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                                .+++.+++.+.+++|.+++|.--
T Consensus       126 ----------~~~~~~~~~~~~~~i~v~~igig  148 (218)
T 3ibs_A          126 ----------GGAVEAAKAAAEKGIQVSVLGVG  148 (218)
T ss_dssp             ----------SCHHHHHHHHHTTTEEEEEEEES
T ss_pred             ----------CcHHHHHHHHHhcCCEEEEEEec
Confidence                      14678899999999999999654

>2b2x_A Integrin alpha-1; computational design, antibody-antigen complex, immune syste; 2.20A {Rattus norvegicus} SCOP: c.62.1.1

Probab=98.83  E-value=2.8e-08  Score=100.15  Aligned_cols=140  Identities=14%  Similarity=0.248  Sum_probs=98.3

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      ..|||||||++++|+. |+.+| +++..+++.|.-        .....|+|||.|.+...    .+..+....+...++.
T Consensus        22 ~~div~vlD~SgSM~~-~~~~k-~~~~~~~~~l~~--------~~~~~rv~lv~F~~~~~----~~~~l~~~~~~~~~~~   87 (223)
T 2b2x_A           22 QLDIVIVLDGSNSIYP-WESVI-AFLNDLLKRMDI--------GPKQTQVGIVQYGENVT----HEFNLNKYSSTEEVLV   87 (223)
T ss_dssp             CEEEEEEEECSTTCCC-HHHHH-HHHHHHHTTSCC--------STTSCCEEEEEESSSEE----EEECTTTCCSHHHHHH
T ss_pred             cceEEEEEECCCChhh-HHHHH-HHHHHHHHhccc--------CCCCeEEEEEEeCCCcc----EEEecCCCCCHHHHHH
Confidence            3799999999999995 67666 446667766631        12358999999976522    1112233467889999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhh-cccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMM-FSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~-f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      .|+.|...||+  ...+.+||..|++. |+...     .......|++|||+|..+..-                     
T Consensus        88 ~i~~l~~~gG~--~T~~~~aL~~a~~~l~~~~~-----~~~~~~~~~iillTDG~~~~~---------------------  139 (223)
T 2b2x_A           88 AANKIVQRGGR--QTMTALGIDTARKEAFTEAR-----GARRGVKKVMVIVTDGESHDN---------------------  139 (223)
T ss_dssp             HHTTCCCCCCS--SCCHHHHHHHHHHTTSSGGG-----TCCTTSEEEEEEEESSCCTTG---------------------
T ss_pred             HHHhhhccCCC--CccHHHHHHHHHHHhcCccc-----CCCCCCCeEEEEEcCCCCCCC---------------------
Confidence            99999877663  24678889999875 64211     112346789999998766410                     


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                           .+++.+++.+.+++|.+++|.--
T Consensus       140 -----~~~~~~~~~~~~~gi~v~~igvG  162 (223)
T 2b2x_A          140 -----YRLKQVIQDCEDENIQRFSIAIL  162 (223)
T ss_dssp             -----GGHHHHHHHHHTTTEEEEEEEEC
T ss_pred             -----ccHHHHHHHHHHCCCEEEEEEec
Confidence                 14678899999999999999763

>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=98.80  E-value=4.6e-08  Score=97.69  Aligned_cols=140  Identities=14%  Similarity=0.223  Sum_probs=98.0

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      ..|||||||+++||+. |+.+| +++.-+++.|.-        .....++|||.|.+...    .+..+....+...++.
T Consensus         7 ~~div~vlD~SgSm~~-~~~~k-~~~~~~~~~l~~--------~~~~~~v~lv~F~~~~~----~~~~l~~~~~~~~~~~   72 (213)
T 1pt6_A            7 QLDIVIVLDGSNSIYP-WDSVT-AFLNDLLKRMDI--------GPKQTQVGIVQYGENVT----HEFNLNKYSSTEEVLV   72 (213)
T ss_dssp             CEEEEEEEECCTTCCC-HHHHH-HHHHHHHTTSCB--------STTSBEEEEEEESSSEE----EEECTTTCSSHHHHHH
T ss_pred             CccEEEEEECCCChhh-HHHHH-HHHHHHHHhcCC--------CCCCeEEEEEEeCCCcc----EEEeccccCCHHHHHH
Confidence            4799999999999995 67766 456666666631        12458999999987532    1112233467889999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhh-cccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMM-FSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~-f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      .|+.|...||..  ..+.+||..|++. |....     .......|.+|||+|-.+..-                     
T Consensus        73 ~i~~l~~~~G~~--T~~~~aL~~a~~~l~~~~~-----~~r~~~~~~iillTDG~~~~~---------------------  124 (213)
T 1pt6_A           73 AAKKIVQRGGRQ--TMTALGTDTARKEAFTEAR-----GARRGVKKVMVIVTDGESHDN---------------------  124 (213)
T ss_dssp             HHHTCCCCCCSS--CCHHHHHHHHHHTTTSGGG-----TCCTTCEEEEEEEESSCCSCS---------------------
T ss_pred             HHHhccCCCCCc--ccHHHHHHHHHHHhcCccc-----CCCCCCCeEEEEEcCCCCCCC---------------------
Confidence            999998876632  4577888888875 54211     112356789999998866410                     


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                           .+++.+++.+.+++|.+++|.--
T Consensus       125 -----~~~~~~~~~~~~~gi~i~~igig  147 (213)
T 1pt6_A          125 -----HRLKKVIQDCEDENIQRFSIAIL  147 (213)
T ss_dssp             -----HHHHHHHHHHHHTTEEEEEEEEC
T ss_pred             -----ccHHHHHHHHHHCCCEEEEEEec
Confidence                 13577889999999999999764

>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=98.79  E-value=2.1e-08  Score=96.73  Aligned_cols=137  Identities=18%  Similarity=0.191  Sum_probs=100.3

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      ..|||||||.+++|+..|.. +.+++..+++.|.+          ...++|||.|.+...      ..++||.|...+..
T Consensus         6 ~~dvv~vlD~SgSM~~~~~~-~~~~~~~~~~~~~~----------~~~~v~lv~f~~~~~------~~~~~~~~~~~~~~   68 (182)
T 1shu_X            6 AFDLYFVLDKSGSVANNWIE-IYNFVQQLAERFVS----------PEMRLSFIVFSSQAT------IILPLTGDRGKISK   68 (182)
T ss_dssp             CEEEEEEEECSGGGGGGHHH-HHHHHHHHHHHCCC----------TTEEEEEEEESSSEE------EEEEEECCHHHHHH
T ss_pred             ceeEEEEEECCCCcccCHHH-HHHHHHHHHHHhcC----------CCceEEEEEeCCCce------EEECCCCCHHHHHH
Confidence            37999999999999988776 44667777887732          357999999977522      35678889999988


Q ss_pred             HhccCcc--CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           83 WLSTIPF--AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        83 ~Ld~I~f--~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      +|+.|..  .+|   ...+.+||..|+.++.+..       .....|.+|||+|..+..-.                   
T Consensus        69 ~l~~l~~~~~~g---~T~~~~al~~a~~~l~~~~-------~~~~~~~iiliTDG~~~~~~-------------------  119 (182)
T 1shu_X           69 GLEDLKRVSPVG---ETYIHEGLKLANEQIQKAG-------GLKTSSIIIALTDGKLDGLV-------------------  119 (182)
T ss_dssp             HHHHHHTCCCCS---CCCHHHHHHHHHHHHHHHT-------GGGSCEEEEEEECCCCCTTH-------------------
T ss_pred             HHHhcccCCCCC---CchHHHHHHHHHHHHHhcc-------CCCCCeEEEEECCCCcCCCC-------------------
Confidence            8888763  233   3568888999998875421       13457899999998764110                   


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                           ..+.+.+++.+.+++|.+++|.--.
T Consensus       120 -----~~~~~~~~~~~~~~~i~i~~igvg~  144 (182)
T 1shu_X          120 -----PSYAEKEAKISRSLGASVYCVGVLD  144 (182)
T ss_dssp             -----HHHHHHHHHHHHHTTCEEEEEECSS
T ss_pred             -----chhHHHHHHHHHhCCCEEEEEeCCc
Confidence                 0124668889999999999998753

>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=98.78  E-value=8e-08  Score=95.40  Aligned_cols=123  Identities=14%  Similarity=0.168  Sum_probs=87.3

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCccccee-eccCCCCHHHH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQ-RSGWTKDVDIF   80 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~-~~gfTsd~~~f   80 (834)
                      ..|||||||++++|+. .|+.+| +++.-+++.|....        ...++|||.|.+...   ..+. ...++.|...+
T Consensus        15 ~~div~vlD~SgSM~~~~~~~~k-~~~~~~i~~l~~~~--------~~~~v~lv~f~~~~~---~~~~~~~~~~~~~~~~   82 (223)
T 1q0p_A           15 SMNIYLVLDGSDSIGASNFTGAK-KSLVNLIEKVASYG--------VKPRYGLVTYATYPK---IWVKVSEADSSNADWV   82 (223)
T ss_dssp             CEEEEEEEECSTTTCHHHHHHHH-HHHHHHHHHHHTTT--------CCCEEEEEEESSSEE---EEECTTSGGGGCHHHH
T ss_pred             ceeEEEEEeCCCCCchHHHHHHH-HHHHHHHHHHhcCC--------CCceEEEEEecCccc---eeeccccCCCCCHHHH
Confidence            3799999999999987 888887 55788888875421        246999999987632   1111 12567788999


Q ss_pred             HHHhccCccCCCC-CchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           81 LHWLSTIPFAGGG-FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        81 l~~Ld~I~f~GGG-~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      ...|++|.+.++. .+...+.+||..|+.++.+... ..+..+....|.+|||+|-.+.
T Consensus        83 ~~~i~~l~~~~~~~~g~T~~~~aL~~a~~~l~~~~~-~~~~~~~~~~~~iillTDG~~~  140 (223)
T 1q0p_A           83 TKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDD-VPPEGWNRTRHVIILMTDGLHN  140 (223)
T ss_dssp             HHHHHTCCTTSCSCTTCCCHHHHHHHHHHHHCCTTS-SCCTTGGGCEEEEEEEECSCCC
T ss_pred             HHHHHhcccccccCCCCccHHHHHHHHHHHhhcccc-ccccccccCCeEEEEECCCCCC
Confidence            9999999986432 1245788999999987764221 1122334567889999998775

>1n3y_A Integrin alpha-X; alpha/beta rossmann fold, cell adhesion; 1.65A {Homo sapiens} SCOP: c.62.1.1

Probab=98.73  E-value=2.7e-08  Score=97.48  Aligned_cols=138  Identities=12%  Similarity=0.209  Sum_probs=97.8

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC--CHHH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs--d~~~   79 (834)
                      ..|||||||++++|+. .|+.++ +++..+++.|.          ....+++||.|.+...      ..++|+.  +...
T Consensus         9 ~~div~vlD~SgSM~~~~~~~~~-~~~~~~~~~l~----------~~~~~v~lv~f~~~~~------~~~~~~~~~~~~~   71 (198)
T 1n3y_A            9 EQDIVFLIDGSGSISSRNFATMM-NFVRAVISQFQ----------RPSTQFSLMQFSNKFQ------THFTFEEFRRSSN   71 (198)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHH-HHHHHHHTTSC----------TTTEEEEEEEESSSEE------EEECHHHHHHCSS
T ss_pred             CeeEEEEEECCCCCCHHHHHHHH-HHHHHHHHhcC----------CCCcEEEEEEeCCCcc------EEEecCccCCHHH
Confidence            3799999999999988 677544 55677777664          1358999999998722      2344433  2245


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHH-hhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEAL-MMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL-~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      +..+|+.|.+.||   ...+.+||..|+ .+|....     ..+....|.+|||+|..+..-+                 
T Consensus        72 ~~~~i~~l~~~~g---~T~~~~al~~a~~~l~~~~~-----~~r~~~~~~iillTDG~~~~~~-----------------  126 (198)
T 1n3y_A           72 PLSLLASVHQLQG---FTYTATAIQNVVHRLFHASY-----GARRDAAKILIVITDGKKEGDS-----------------  126 (198)
T ss_dssp             GGGGGTTCCCCCS---CBCHHHHHHHHHTTTTSGGG-----TCCTTSEEEEEEEESSCCBSCS-----------------
T ss_pred             HHHHHhcCcCCCC---CchHHHHHHHHHHHHhCccc-----CCCCCCceEEEEECCCCCCCCc-----------------
Confidence            7788888887666   357888999999 5665311     1123457899999998775211                 


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                              .+++.+++.+.+++|.+++|.--.
T Consensus       127 --------~~~~~~~~~~~~~gi~i~~igvG~  150 (198)
T 1n3y_A          127 --------LDYKDVIPMADAAGIIRYAIGVGL  150 (198)
T ss_dssp             --------SCHHHHHHHHHHTTCEEEEEEESG
T ss_pred             --------ccHHHHHHHHHHCCCEEEEEEccc
Confidence                    256788899999999999987644

>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=98.72  E-value=4.9e-08  Score=101.77  Aligned_cols=139  Identities=19%  Similarity=0.267  Sum_probs=100.4

Q ss_pred             CccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCC----H
Q 003284            3 EKQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKD----V   77 (834)
Q Consensus         3 ~~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd----~   77 (834)
                      ..|||||||++++|+ ..|....++++.-+++.|.-+        ....++|||.|.+..-      ..+.++.+    .
T Consensus        18 ~~DivfvlD~SgSM~~~~~~~~~k~~~~~lv~~l~~~--------~~~~rvglv~Fs~~~~------~~~~l~~~~~~~~   83 (266)
T 4hqo_A           18 QVDLYLLVDGSGSIGYPNWITKVIPMLNGLINSLSLS--------RDTINLYMNLFGSYTT------ELIRLGSGQSIDK   83 (266)
T ss_dssp             CEEEEEEEECSTTTCHHHHHHTHHHHHHHHHHTCCBC--------TTSEEEEEEEESSSEE------EEECTTSHHHHCH
T ss_pred             ceeEEEEEECCCCcChhHHHHHHHHHHHHHHHHcccC--------CCCcEEEEEEecCCcc------eEEecCCCCccCH
Confidence            479999999999998 556434456678888888421        1358999999988622      34556554    6


Q ss_pred             HHHHHHhccCc---cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccccc
Q 003284           78 DIFLHWLSTIP---FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQ  154 (834)
Q Consensus        78 ~~fl~~Ld~I~---f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~  154 (834)
                      ..++..|+.|.   ..|||   -.+.+||..|..+|....      ......|.+|||+|-.|..   +           
T Consensus        84 ~~~~~~i~~l~~~~~~~G~---T~~~~AL~~a~~~l~~~~------~r~~~~~~iIllTDG~~~d---~-----------  140 (266)
T 4hqo_A           84 RQALSKVTELRKTYTPYGT---TSMTAALDEVQKHLNDRV------NREKAIQLVILMTDGVPNS---K-----------  140 (266)
T ss_dssp             HHHHHHHHHHHHHCCCCSC---CCHHHHHHHHHHHHHTTC------SCTTSEEEEEEEECSCCSC---H-----------
T ss_pred             HHHHHHHHHhhhccCCCCC---CCHHHHHHHHHHHHhhcc------ccCCCCeEEEEEccCCCCC---c-----------
Confidence            78888999986   55554   457788888888886421      2234579999999887641   0           


Q ss_pred             ccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          155 NENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       155 ~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                                  .+....++.+.+.||.+++|.--.
T Consensus       141 ------------~~~~~~a~~l~~~gi~i~~iGiG~  164 (266)
T 4hqo_A          141 ------------YRALEVANKLKQRNVRLAVIGIGQ  164 (266)
T ss_dssp             ------------HHHHHHHHHHHHTTCEEEEEECSS
T ss_pred             ------------hHHHHHHHHHHHCCCEEEEEecCc
Confidence                        145778999999999999998765

>4b4t_W RPN10, 26S proteasome regulatory subunit RPN10; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.71  E-value=2.1e-07  Score=98.57  Aligned_cols=160  Identities=13%  Similarity=0.140  Sum_probs=111.9

Q ss_pred             EEEEEeccccchH------hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHH
Q 003284            6 LIVAVEGTAAMGP------YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDI   79 (834)
Q Consensus         6 vVFVID~Tasmg~------yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~   79 (834)
                      +|||||.+.+|..      -|+..| +.+.-+++.+....        ...++|||+|.+..+    . ...++|.|..+
T Consensus         6 tViviD~S~SM~~~D~~PsRl~a~k-~Av~~li~~~~~~n--------Ped~VGLVtfag~~~----~-vl~plT~D~~~   71 (268)
T 4b4t_W            6 TVLVIDNSEYSRNGDFPRTRFEAQI-DSVEFIFQAKRNSN--------PENTVGLISGAGANP----R-VLSTFTAEFGK   71 (268)
T ss_dssp             EEEEECCSSTTSSTTSSSCHHHHHH-HHHHHHHHHHHHHC--------TTCEEEEEECCTTSC----E-EEEEEESCHHH
T ss_pred             EEEEEECCHHHhCCCCCCcHHHHHH-HHHHHHHHHHhhCC--------CcceEEEEEecCCcc----e-eccCCcchHHH
Confidence            8999999999952      255555 45666666553311        125999999986532    2 23578999999


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      ++..|++|+..|+    .++..||..|+..+....       .....+++||+.+++-.     +               
T Consensus        72 il~aL~~l~~~G~----T~l~~gL~~A~~aLk~~~-------~k~~~~rIIlf~ds~~~-----~---------------  120 (268)
T 4b4t_W           72 ILAGLHDTQIEGK----LHMATALQIAQLTLKHRQ-------NKVQHQRIVAFVCSPIS-----D---------------  120 (268)
T ss_dssp             HHHHHTTCCCCSC----CCHHHHHHHHHHHHHTCS-------CTTSEEEEEEEECSCCS-----S---------------
T ss_pred             HHHHhhhcCcCCC----CChHHHHHHHHHHHHhcc-------cCCCceEEEEEECCCCC-----C---------------
Confidence            9999999985433    567778888887775322       12345677888777532     1               


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCCCCCCCCCCCCCCCCCeEEEee
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLIS  225 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~~~~~~~~~~~ak~p~hlVLLs  225 (834)
                           .-.+++.+|+.+.++||.|+||.=-    .-.+|++|.++..++.          -+-.|||-|.
T Consensus       121 -----~~~~l~~lak~lkk~gI~v~vIgFG~~~~n~~kLe~l~~~~Ng~~----------~~~s~~v~v~  175 (268)
T 4b4t_W          121 -----SRDELIRLAKTLKKNNVAVDIINFGEIEQNTELLDEFIAAVNNPQ----------EETSHLLTVT  175 (268)
T ss_dssp             -----CHHHHHHHHHHHHHHTEEEEEEEESSCCSSCCHHHHHHHHHCSST----------TTSCEEEEEC
T ss_pred             -----CHHHHHHHHHHHHHcCCEEEEEEeCCCccchHHHHHHHHHhcCCC----------CCceeEEEeC
Confidence                 0025789999999999999999854    4588999999988752          1235888873

>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=98.61  E-value=1.3e-07  Score=98.80  Aligned_cols=138  Identities=13%  Similarity=0.235  Sum_probs=95.5

Q ss_pred             CccEEEEEeccccchH-hH-HHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC----C
Q 003284            3 EKQLIVAVEGTAAMGP-YW-QSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----D   76 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi-~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs----d   76 (834)
                      ..|||||||++++|+. .| +.+| +.+.-+++.|..+        ....++|||.|.+...      ..+.++.    |
T Consensus        21 ~~div~vlD~SgSM~~~~~~~~~k-~~~~~~v~~l~~~--------~~~~rvglv~Fs~~~~------~~~~l~~~~~~~   85 (281)
T 4hqf_A           21 EVDLYLLMDGSGSIRRHNWVNHAV-PLAMKLIQQLNLN--------DNAIHLYASVFSNNAR------EIIRLHSDASKN   85 (281)
T ss_dssp             CEEEEEEEECCCCSSTHHHHHHHH-HHHHHHHTTCCCC--------TTSEEEEEEEEETTEE------EEEEECSSCSSC
T ss_pred             ceeEEEEEeCCCCcCHHHHHHHHH-HHHHHHHHHhccC--------CCCcEEEEEEcCCCce------EEEEccccCccC
Confidence            4799999999999984 44 5454 5566666666421        2358999999987632      2233333    4


Q ss_pred             HHHHHHHhccCc---cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccc
Q 003284           77 VDIFLHWLSTIP---FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLD  153 (834)
Q Consensus        77 ~~~fl~~Ld~I~---f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~  153 (834)
                      ...++..|+.|.   +.|||   -.+.+||..|+..|....      ......|.+|||+|-.+..   +          
T Consensus        86 ~~~l~~~i~~l~~~~~~~G~---T~~~~aL~~a~~~l~~~~------~r~~~~~~iillTDG~~~d---~----------  143 (281)
T 4hqf_A           86 KEKALIIIKSLLSTNLPYGK---TSLTDALLQVRKHLNDRI------NRENANQLVVILTDGIPDS---I----------  143 (281)
T ss_dssp             HHHHHHHHHHHHHTTGGGCS---CCHHHHHHHHHHHHHTSC------CCTTCEEEEEEEESSCCSC---H----------
T ss_pred             HHHHHHHHHHHhhccCCCCC---ccHHHHHHHHHHHHHhcc------CCCCCCEEEEEEecCCCCC---c----------
Confidence            788888888886   45554   457788888887665321      1234578999999876641   0          


Q ss_pred             cccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          154 QNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       154 ~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                                   .+....++.+.++||.+++|.--.
T Consensus       144 -------------~~~~~~~~~l~~~gv~i~~igiG~  167 (281)
T 4hqf_A          144 -------------QDSLKESRKLSDRGVKIAVFGIGQ  167 (281)
T ss_dssp             -------------HHHHHHHHHHHHTTCEEEEEEESS
T ss_pred             -------------HHHHHHHHHHHHCCCEEEEEeCCC
Confidence                         145678889999999999997655

>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=98.60  E-value=2.4e-07  Score=92.04  Aligned_cols=114  Identities=13%  Similarity=0.244  Sum_probs=84.6

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~   79 (834)
                      ..|||||||++++|+. .|+.+| +++.-+++.|.-+        ....|+|||.|.+...      ..+.|+  .|...
T Consensus        21 ~~DivfvlD~S~Sm~~~~~~~~k-~~~~~~~~~l~~~--------~~~~rv~vv~fs~~~~------~~~~l~~~~~~~~   85 (199)
T 3zqk_A           21 VLDVAFVLEGSDKIGEADFNRSK-EFMEEVIQRMDVG--------QDSIHVTVLQYSYMVT------VEYPFSEAQSKGD   85 (199)
T ss_dssp             CCEEEEEEECCTTTCHHHHHHHH-HHHHHHHHHSCBS--------TTSBEEEEEEESSSEE------EEECTTSCCCHHH
T ss_pred             CcCEEEEEECCCCCCHHHHHHHH-HHHHHHHHhcCCC--------CCceEEEEEEECCccc------EEEecCCcCCHHH
Confidence            3799999999999995 588877 6688888888421        2358999999998632      234444  48899


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      ++..|++|.+.||+.  -++.+||..|++ +|....     ..+....|.+|||+|..+.
T Consensus        86 ~~~~i~~l~~~gg~~--T~~~~aL~~a~~~l~~~~~-----g~r~~~~~~iillTDG~~~  138 (199)
T 3zqk_A           86 ILQRLREIRYQGGNR--TNTGLALRYLSDHSFLVSQ-----GDREQAPNLVYMVTGNPAS  138 (199)
T ss_dssp             HHHHHHHCCCCCCSC--CCHHHHHHHCCCCCTCGGG-----TCCTTSCEEEEEEECSCCS
T ss_pred             HHHHHHhCcCCCCCc--ChHHHHHHHHHHHhhCccc-----CCCCCCCeEEEEEeCCCCc
Confidence            999999999988732  458888888886 453211     1234567999999998754

>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=98.55  E-value=3.8e-07  Score=106.87  Aligned_cols=119  Identities=13%  Similarity=0.160  Sum_probs=86.0

Q ss_pred             ccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC----CHH
Q 003284            4 KQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK----DVD   78 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs----d~~   78 (834)
                      .|||||||.+++|+. .|+.+| +.+..+++.|..++        ...|||||.|.+..-      ..+.++.    |.+
T Consensus       244 ~div~vlD~SgSM~~~~~~~~k-~~~~~~i~~l~~~~--------~~~rv~lv~f~~~~~------~~~~l~~~~~~~~~  308 (741)
T 3hrz_D          244 MNIYLVLDGSGSIGASDFTGAK-KCLVNLIEKVASYG--------VKPRYGLVTYATYPK------IWVKVSEADSSNAD  308 (741)
T ss_dssp             EEEEEEEECSTTTCHHHHHHHH-HHHHHHHHHHHHTT--------CCCEEEEEEESSSEE------EEECTTSGGGGCHH
T ss_pred             eeEEEEeccCCcccccchHHHH-HHHHHHHHhhhccC--------CCceEEEEEeccCCc------eeEeecccCCcCHH
Confidence            699999999999954 588877 55888888886421        257999999977522      3456655    899


Q ss_pred             HHHHHhccCccCCCC-CchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           79 IFLHWLSTIPFAGGG-FNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        79 ~fl~~Ld~I~f~GGG-~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      .++..|++|.+.++. ...-++.+||..|+++|.+... ..+..+....|.+|||+|--+.
T Consensus       309 ~~~~~i~~l~~~~~~~~ggT~~~~aL~~a~~~l~~~~~-~~~~~~~~~~~~iillTDG~~n  368 (741)
T 3hrz_D          309 WVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDD-VPPEGWNRTRHVIILMTDGLHN  368 (741)
T ss_dssp             HHHHHHTTCCGGGGSSSCCCCHHHHHHHHHHHHCCC---CCCTTGGGEEEEEEEEECSCCC
T ss_pred             HHHHHHHhcccccccCCCChHHHHHHHHHHHHHhhhhh-ccccchhccCeEEEEECCCccc
Confidence            999999999984332 1235688999999987743221 1233445678899999998665

>2x5n_A SPRPN10, 26S proteasome regulatory subunit RPN10; nuclear protein, nucleus, ubiquitin; 1.30A {Schizosaccharomyces pombe}

Probab=98.54  E-value=2e-06  Score=86.43  Aligned_cols=159  Identities=18%  Similarity=0.205  Sum_probs=105.3

Q ss_pred             ccEEEEEeccccchH------hHHHHHHHHHHHHHHHH-hccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCC
Q 003284            4 KQLIVAVEGTAAMGP------YWQSIVSDYLEKIIRCF-CVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKD   76 (834)
Q Consensus         4 ~dvVFVID~Tasmg~------yi~~lkt~YI~p~le~f-~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd   76 (834)
                      ..||||||.+.+|..      -|+..| ..+.-+++.| ...         ...++|||+|.+...   +  ...++|.|
T Consensus         3 e~lvlvlD~S~SM~~~D~~psRl~~ak-~~~~~~~~~~~~~~---------~~d~vGLV~fa~~~a---~--~~~plT~d   67 (192)
T 2x5n_A            3 EATMILIDNSEWMINGDYIPTRFEAQK-DTVHMIFNQKINDN---------PENMCGLMTIGDNSP---Q--VLSTLTRD   67 (192)
T ss_dssp             EEEEEEECCSGGGGCTTSSSCHHHHHH-HHHHHHHHHHHHHC---------TTCEEEEEECCTTSC---C--EEEEEESC
T ss_pred             eEEEEEEECCHhhccCCCCCCHHHHHH-HHHHHHHHHHHhcC---------CCCeEEEEEEcCCCc---E--EecCCCCC
Confidence            468999999999972      245554 3344444433 221         235999999998522   2  23578999


Q ss_pred             HHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcE-EEEeecCCCCCCCCCcccCCccccccc
Q 003284           77 VDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRH-CILVAASNPHPLPTPVYRPQMQNLDQN  155 (834)
Q Consensus        77 ~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkh-CILIa~SpP~~lp~pv~~p~~~~~~~~  155 (834)
                      ...++..|+.|...|    ..++.+||..|+.+|.....       ....++ +||+++ .=.  -.             
T Consensus        68 ~~~i~~~L~~l~~~g----~t~l~~aL~~A~~~l~~~~~-------~~~~~riiil~~~-~~~--~~-------------  120 (192)
T 2x5n_A           68 YGKFLSAMHDLPVRG----NAKFGDGIQIAQLALKHREN-------KIQRQRIVAFVGS-PIV--ED-------------  120 (192)
T ss_dssp             HHHHHHHHTTCCCCS----CCCHHHHHHHHHHHHHTCSC-------TTSEEEEEEEECS-CCS--SC-------------
T ss_pred             HHHHHHHHHcCCCCC----CchHHHHHHHHHHHHHhccc-------cCCCceEEEEEEC-CCC--CC-------------
Confidence            999999999988643    26899999999988864221       112233 455543 110  00             


Q ss_pred             cchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC----chhHHHHHHHhcCCCCCCCCCCCCCCCCCeEEEeecc
Q 003284          156 ENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ----LPKLTAIYNAAKRNPRAADPPVDNSKNPHFLVLISEN  227 (834)
Q Consensus       156 e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq----lp~l~~Lfeka~~~~~~~~~~~~~ak~p~hlVLLsg~  227 (834)
                                ..+.+.+++.++++||.+++|.--.    -. |++|.++.+.+.            -.|||-+..+
T Consensus       121 ----------~~~~~~~a~~lk~~gi~v~~Ig~G~~~~~~~-l~~la~~~n~~~------------~s~~~~~~~~  173 (192)
T 2x5n_A          121 ----------EKNLIRLAKRMKKNNVAIDIIHIGELQNESA-LQHFIDAANSSD------------SCHLVSIPPS  173 (192)
T ss_dssp             ----------HHHHHHHHHHHHHTTEEEEEEEESCC---CH-HHHHHHHHCSTT------------CCEEEEECCC
T ss_pred             ----------chhHHHHHHHHHHCCCEEEEEEeCCCCccHH-HHHHHHhccCCC------------ceEEEEecCc
Confidence                      0246789999999999999997642    24 899998876332            2588877665

>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=98.54  E-value=3.9e-07  Score=102.35  Aligned_cols=121  Identities=10%  Similarity=0.141  Sum_probs=84.2

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC----CCH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT----KDV   77 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT----sd~   77 (834)
                      ..|||||||.++||+. .|+.+| +.|..+++.|...        ....|+|||.|.+...      ..++++    .|.
T Consensus         9 ~~divfvlD~SgSM~~~~~~~~k-~~~~~l~~~l~~~--------~~~~rv~lv~f~~~~~------~~~~l~~~~~~~~   73 (509)
T 2odp_A            9 HLNLYLLLDASQSVSENDFLIFK-ESASLMVDRIFSF--------EINVSVAIITFASEPK------VLMSVLNDNSRDM   73 (509)
T ss_dssp             EEEEEEEEECSTTSCHHHHHHHH-HHHHHHHHHHHTT--------CCCEEEEEEEESSSEE------EEECTTSGGGGCH
T ss_pred             CeeEEEEEeCCCccchhhHHHHH-HHHHHHHHHhhcc--------CCCceEEEEEccCCCc------eeEeccCCCCCCH
Confidence            4899999999999987 677776 5588888888431        1347999999977532      234444    499


Q ss_pred             HHHHHHhccCccCCCCC-chhhHHHHHHHHHhhcccCCC--CCCCCCCccCCcEEEEeecCCCC
Q 003284           78 DIFLHWLSTIPFAGGGF-NDAAIAEGLSEALMMFSVAPN--GSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        78 ~~fl~~Ld~I~f~GGG~-~~~AvaEGLa~AL~~f~~~~~--~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      ..++..|++|.+.++.. ....+.+||..|+++|.....  ......+....|.+|||+|-.+.
T Consensus        74 ~~~~~~l~~l~~~~~~~~ggT~~~~aL~~a~~~l~~~~~~~~~~~~~~~~~~~~iillTDG~~~  137 (509)
T 2odp_A           74 TEVISSLENANYKDHENGTGTNTYAALNSVYLMMNNQMRLLGMETMAWQEIRHAIILLTDGKSN  137 (509)
T ss_dssp             HHHHHHHHTCCGGGGTTCCSCCHHHHHHHHHHHHHHHHHHHCTTSHHHHTEEEEEEEESCSCCC
T ss_pred             HHHHHHHHhcccccCCCCCCccHHHHHHHHHHHHhhcccccccccccccccceEEEEECCCCcc
Confidence            99999999999986432 346788888888887732110  00001122356889999998765

>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=98.54  E-value=4.8e-07  Score=101.07  Aligned_cols=122  Identities=14%  Similarity=0.189  Sum_probs=85.3

Q ss_pred             ccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCccccee-eccCCCCHHHHH
Q 003284            4 KQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQ-RSGWTKDVDIFL   81 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~-~~gfTsd~~~fl   81 (834)
                      .|||||||.++||+. .|+.+| +.+.-+++.|...        ....++|||.|.+...   ..+. ...+|.|.+.+.
T Consensus         2 ~div~vlD~SgSM~~~~~~~~k-~~~~~~~~~l~~~--------~~~~~v~lv~f~~~~~---~~~~~~~~~~~~~~~~~   69 (497)
T 1rrk_A            2 MNIYLVLDGSDSIGASNFTGAK-KVLVNLIEKVASY--------GVKPRYGLVTYATYPK---IWVKVSEADSSNADWVT   69 (497)
T ss_dssp             EEEEEEEECSTTTCHHHHHHHH-HHHHHHHHHHHHT--------TCCCEEEEEEESSSEE---EEECTTSGGGGCHHHHH
T ss_pred             eeEEEEEECCCCcchhhHHHHH-HHHHHHHHHhhcc--------CCCceEEEEEecCCce---EeeccccccccCHHHHH
Confidence            699999999999974 677777 4477888887432        1247999999986522   1111 125678999999


Q ss_pred             HHhccCccCCCCC-chhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           82 HWLSTIPFAGGGF-NDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        82 ~~Ld~I~f~GGG~-~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      ..|++|.+.|+.. ....+.+||..|+.++.+... ..+..+....|.+|||+|-.+.
T Consensus        70 ~~l~~l~~~~~~~~g~T~~~~al~~a~~~l~~~~~-~~~~~~~~~~~~iillTDG~~~  126 (497)
T 1rrk_A           70 KQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDD-VPPEGWNRTRHVIILMTDGLHN  126 (497)
T ss_dssp             HHHHHCCGGGSCCTTCCCHHHHHHHHHHHHCCC-------CGGGCEEEEEEEECSCCC
T ss_pred             HHHHhCcCccccccCccCHHHHHHHHHHHhhhhhc-cccccccccceEEEEEeCCCcc
Confidence            9999999866432 347788999999988743221 1122334567899999998765

>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=98.50  E-value=6.2e-07  Score=87.58  Aligned_cols=111  Identities=13%  Similarity=0.198  Sum_probs=78.3

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCH--HH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDV--DI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~--~~   79 (834)
                      ..|||||||++++|+. .|+.+| +++.-+++.|..          ...|+|||.|.+...      ..++|+...  ..
T Consensus         2 ~~divfvlD~S~Sm~~~~~~~~k-~~~~~~~~~l~~----------~~~rv~vv~fs~~~~------~~~~l~~~~~~~~   64 (179)
T 1mjn_A            2 NVDLVFLFDGSMSLQPDEFQKIL-DFMKDVMKKCSN----------TSYQFAAVQFSTSYK------TEFDFSDYVKRKD   64 (179)
T ss_dssp             CEEEEEEEECBTTCCHHHHHHHH-HHHHHHHHHTTT----------SSEEEEEEEESSSEE------EEECHHHHHHHCC
T ss_pred             CccEEEEEeCCCCCCHHHHHHHH-HHHHHHHHHhCC----------CCeEEEEEEECCcee------EEEcCcccCCHHH
Confidence            4799999999999987 587776 567788888721          357999999987632      235555422  24


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      +...++.|...+||   -++.+||..|++ +|....     .......|.+|||+|-.+.
T Consensus        65 ~~~~~~~i~~~~g~---T~~~~aL~~a~~~~~~~~~-----g~r~~~~~~iillTDG~~~  116 (179)
T 1mjn_A           65 PDALLKHVKHMLLL---TNTFGAINYVATEVFREEL-----GARPDATKVLIIITDGEAT  116 (179)
T ss_dssp             HHHHHTTCCCCCBC---CCHHHHHHHHHHHTSSGGG-----TCCTTSEEEEEEEESSCCS
T ss_pred             HHHHHHhcccCCCC---ChHHHHHHHHHHHhccccc-----CCCCCCCeEEEEEcCCCCC
Confidence            66777888877654   578899999984 674211     1123467899999998764

>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=98.33  E-value=7.5e-07  Score=110.28  Aligned_cols=138  Identities=12%  Similarity=0.192  Sum_probs=103.5

Q ss_pred             ccEEEEEeccccchHh-HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCC--CHHHH
Q 003284            4 KQLIVAVEGTAAMGPY-WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTK--DVDIF   80 (834)
Q Consensus         4 ~dvVFVID~Tasmg~y-i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTs--d~~~f   80 (834)
                      .|||||||++++|++. |+.+| +++..+++.|..          ...|+|||.|.+..      ...+.++.  |...+
T Consensus       131 ~DIvfvlD~SgSm~~~~f~~~k-~fv~~lv~~~~~----------~~~rVglV~Fs~~~------~~~~~lt~~~~~~~l  193 (1095)
T 3k6s_A          131 QDIVFLIDGSGSISSRNFATMM-NFVRAVISQFQR----------PSTQFSLMQFSNKF------QTHFTFEEFRRSSNP  193 (1095)
T ss_dssp             EEEEEEEECCTTSCSHHHHHHH-HHHHHHHHSSCS----------SSEEEEEEEESSSE------EEEECSHHHHSCSCG
T ss_pred             ccEEEEEcCCCCCChhHHHHHH-HHHHHHHHhccc----------cccEEEEEEECCeE------EEEecCcccCCHHHH
Confidence            7999999999999986 88776 667888888752          35899999998752      23456654  56677


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      ...++.|...|||   -++.+||..|++ +|...     +..+....|.+|||+|-.+..-+                  
T Consensus       194 ~~ai~~i~~~gG~---T~~g~AL~~a~~~lf~~~-----~g~R~~~~kviIllTDG~~~~d~------------------  247 (1095)
T 3k6s_A          194 LSLLASVHQLQGF---TYTATAIQNVVHRLFHAS-----YGARRDAAKILIVITDGKKEGDS------------------  247 (1095)
T ss_dssp             GGGTTTCCCCCSC---BCHHHHHHHHHTTTTSTT-----TTCCSSSEEEEEEEESSCCBSCS------------------
T ss_pred             HHHHhhhhcccCC---ChHHHHHHHHHHhhcccc-----ccCCCCCCeEEEEEeCCCcCCCc------------------
Confidence            8889999888774   678999999987 55421     11234567899999988774111                  


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccCCc
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPKQL  191 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrql  191 (834)
                             .+.+.+|+.+.+.||.+++|.--..
T Consensus       248 -------~~~~~~a~~~r~~GI~i~aIGVG~~  272 (1095)
T 3k6s_A          248 -------LDYKDVIPMADAAGIIRYAIGVGLA  272 (1095)
T ss_dssp             -------SCHHHHHHHHHHHCEEECCEEBSSG
T ss_pred             -------hhHHHHHHHHHHCCCEEEEEecccc
Confidence                   2567889999999999999987663

>2x31_A Magnesium-chelatase 60 kDa subunit; ligase, bacteriochlorophyll biosynthesis, photosynthesis; 7.50A {Rhodobacter capsulatus}

Probab=98.29  E-value=1.6e-06  Score=84.52  Aligned_cols=109  Identities=17%  Similarity=0.200  Sum_probs=76.3

Q ss_pred             CccEEEEEeccccc-hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHH
Q 003284            3 EKQLIVAVEGTAAM-GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFL   81 (834)
Q Consensus         3 ~~dvVFVID~Tasm-g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl   81 (834)
                      .+|||||||+++|| +..|+.+|.- +.-+++.+.          ....+++||.|.+...     ...+++|.|...+.
T Consensus         5 ~~~vv~vlD~SgSM~~~~~~~~k~~-~~~~~~~~~----------~~~~~v~lv~f~~~~~-----~~~~~~~~~~~~~~   68 (189)
T 2x31_A            5 DRVLIFAVDASGSAAVARLSEAKGA-VELLLGRAY----------AARDHVSLITFRGTAA-----QVLLQPSRSLTQTK   68 (189)
T ss_dssp             CCEEEEEEECCTTSCC--CHHHHHH-HHHHHHHSC----------TTTSCCCEEEESBSCC-----CBCTTTCSCHHHHH
T ss_pred             CeEEEEEEECCCCCCchHHHHHHHH-HHHHHHHhc----------CCCcEEEEEEECCCCc-----eEecCCCCCHHHHH
Confidence            48999999999999 5667766644 555555441          1346999999987422     13467889999999


Q ss_pred             HHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           82 HWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        82 ~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      .+|+.+...||    ..+.+||..|+.++....       .....+.+|||+|-.|.
T Consensus        69 ~~i~~l~~~g~----T~~~~al~~a~~~l~~~~-------~~~~~~~ivliTDG~~~  114 (189)
T 2x31_A           69 RQLQGLPGGGG----TPLASGMEMAMVTAKQAR-------SRGMTPTIALLTDGRGN  114 (189)
T ss_dssp             HHHHHCCCCBC----CCCHHHHHHHHHHHHTCT-------TTCSSEEEEECCBSCCS
T ss_pred             HHHhcCCCCCC----CCHHHHHHHHHHHHHhcc-------CCCCceEEEEECCCCCC
Confidence            99999986443    345677778887775321       12356899999998775

>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=98.13  E-value=2.4e-05  Score=88.56  Aligned_cols=105  Identities=13%  Similarity=0.128  Sum_probs=77.2

Q ss_pred             CccEEEEEeccccch---HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC-----
Q 003284            3 EKQLIVAVEGTAAMG---PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT-----   74 (834)
Q Consensus         3 ~~dvVFVID~Tasmg---~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT-----   74 (834)
                      ..|||||||+++||.   .-|+.+|.- +.-+++.|..           ..+++||.|.+...      ..+++|     
T Consensus        77 ~~dvv~VLD~SGSM~~~~~rl~~ak~a-~~~ll~~L~~-----------~drv~lV~Fs~~a~------~~~p~t~~l~~  138 (464)
T 4fx5_A           77 ENVEVIIIDCSGSMDYPRTKMMAAKEA-TKVAIDTLTD-----------GAFFAVVAGTEGAR------VVYPTGGQLLR  138 (464)
T ss_dssp             CEEEEEEEECCGGGGTTTHHHHHHHHH-HHHHHHHSCT-----------TCEEEEEEESSSEE------EEESSSSSCEE
T ss_pred             CceEEEEEEcCcccCCCCchHHHHHHH-HHHHHHhCCC-----------CCEEEEEEEcCceE------EEecCCccccc
Confidence            379999999999997   446666644 5666666642           35899999987632      233433     


Q ss_pred             ---CCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           75 ---KDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        75 ---sd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                         .|...+..+|++|...||    -.+.+||..|+.+|...         ....|++|||+|-.+.
T Consensus       139 ~~~~~~~~l~~~I~~L~~~Gg----T~l~~aL~~A~~~l~~~---------~~~~~~IILLTDG~~~  192 (464)
T 4fx5_A          139 ADYQSRAAAKEAVGRLHANGG----TAMGRWLAQAGRIFDTA---------PSAIKHAILLTDGKDE  192 (464)
T ss_dssp             CSHHHHHHHHHHHHTCCCCSC----CCHHHHHHHHHHHHTTC---------TTSEEEEEEEESSCCT
T ss_pred             CCHHHHHHHHHHHHcCCCCCC----CcHHHHHHHHHHHHhcC---------CCCCCEEEEEcCCCCC
Confidence               688899999999996443    56889999999988641         1345899999998664

>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=97.94  E-value=0.0001  Score=85.07  Aligned_cols=137  Identities=16%  Similarity=0.261  Sum_probs=87.7

Q ss_pred             ccEEEEEeccccchH-------hHHHHHHHHHHHHHHHH-hccccccccCCCCccEEEEEEeecCCC---------Cccc
Q 003284            4 KQLIVAVEGTAAMGP-------YWQSIVSDYLEKIIRCF-CVNELAGQKTSASNVELSLVTFNTHGS---------YCAC   66 (834)
Q Consensus         4 ~dvVFVID~Tasmg~-------yi~~lkt~YI~p~le~f-~~g~~~~~~~~~~~~~~gLVvY~d~~~---------~~~~   66 (834)
                      -+||||||.+.+|..       .|+.++. ++.-+++.. ..         ...-++|||+|++...         |...
T Consensus         8 e~iv~~iDvS~SM~~~d~~~~srl~~ak~-~i~~~i~~ki~~---------~~~D~vGlv~f~~~~~~~plt~d~~y~~i   77 (565)
T 1jey_B            8 AAVVLCMDVGFTMSNSIPGIESPFEQAKK-VITMFVQRQVFA---------ENKDEIALVLFGTDGTDNPLSGGDQYQNI   77 (565)
T ss_dssp             EEEEEEEECCGGGGCCBTTBCCHHHHHHH-HHHHHHHHHHHT---------TCCCEEEEEEESCSSCBSTTCTTTCSTTE
T ss_pred             eEEEEEEECChHhcccCCCCCCcHHHHHH-HHHHHHHHHhcC---------CCCCEEEEEEEccCCCCCccccccCCCce
Confidence            689999999999974       5666663 455555531 11         1246999999998753         1111


Q ss_pred             ceeeccCC-CCHHHHHHHhcc-CccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecC-CCCCCCCC
Q 003284           67 LVQRSGWT-KDVDIFLHWLST-IPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAAS-NPHPLPTP  143 (834)
Q Consensus        67 lv~~~gfT-sd~~~fl~~Ld~-I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~S-pP~~lp~p  143 (834)
                      .+. ...+ .+...+ ..|+. |.   +|....++.+||..|+.+|.....     ......|++||++|. .|+.   .
T Consensus        78 ~vl-~~l~~~~~~~l-~~l~~~l~---~~~~~t~i~~al~~A~~~l~~~~~-----~~k~~~krIiLlTDg~~~~~---~  144 (565)
T 1jey_B           78 TVH-RHLMLPDFDLL-EDIESKIQ---PGSQQADFLDALIVSMDVIQHETI-----GKKFEKRHIEIFTDLSSRFS---K  144 (565)
T ss_dssp             EEE-EEEECCCHHHH-HHHHTTCC---CCSSCCCHHHHHHHHHHHHHHHSS-----SSCCSEEEEEEECCCCSCCC---C
T ss_pred             EEe-ecCCCCCHHHH-HHHHhhcc---CCCccccHHHHHHHHHHHHHHHhh-----cccccccEEEEEeCCCCCCC---H
Confidence            111 2222 344444 44555 64   232456799999999999964210     011235899999975 3431   0


Q ss_pred             cccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEE-Ee
Q 003284          144 VYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLS-VI  186 (834)
Q Consensus       144 v~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LS-vI  186 (834)
                                             .+++.+|+.+.+.||.|+ +|
T Consensus       145 -----------------------~~~~~~a~~l~~~gI~i~~vi  165 (565)
T 1jey_B          145 -----------------------SQLDIIIHSLKKCDISLQFFL  165 (565)
T ss_dssp             -----------------------TTHHHHHHHHHHTTEEEEEEE
T ss_pred             -----------------------HHHHHHHHHHHhcCcEEEEEe
Confidence                                   267899999999999999 55

>3rag_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tructural genomics; 1.80A {Alicyclobacillus acidocaldarius subsp}

Probab=97.91  E-value=2.3e-05  Score=81.91  Aligned_cols=93  Identities=13%  Similarity=0.210  Sum_probs=70.6

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      ..||||+||+++||++-|+.+|.- |.-++..|..+        ..+.|+|||.|++...  +..+...+||++. .+..
T Consensus       134 ~~~vvfLVDtSgSM~~kl~~vk~a-l~~Ll~sl~~~--------~~~~~VavV~F~~~~~--~~~~ll~pfT~~~-~~~~  201 (242)
T 3rag_A          134 ALHLVVCLDTSASMRDKIPTVREA-VRDLALSLKVR--------SGPLAVSVIAFPGKGE--EATRLVQPFSSEV-NVAA  201 (242)
T ss_dssp             CEEEEEEEECSGGGTTTHHHHHHH-HHHHHHHHTTS--------SSCEEEEEEEESCSTT--CSCEEEEEEESSC-CHHH
T ss_pred             CCCEEEEEECcccHHHHHHHHHHH-HHHHHHHHhcc--------CCCcEEEEEEECCCCc--cceeecCCCCChH-HHHH
Confidence            479999999999999999999965 77777777532        1368999999998854  2222234899988 8888


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcc
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFS  111 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~  111 (834)
                      +|+.|.. ||+- +  +.+||..|+.+|+
T Consensus       202 ~l~~L~a-gG~T-p--lg~AL~~A~~~~~  226 (242)
T 3rag_A          202 LEAELVA-RGGT-P--TGPAIDHAADLLL  226 (242)
T ss_dssp             HHHHCCC-CSCC-C--HHHHHHHHHHHHH
T ss_pred             HHhhCCC-CCCC-c--HHHHHHHHHHHHH
Confidence            9999975 4542 2  7778888888885

>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=97.73  E-value=0.00024  Score=82.98  Aligned_cols=148  Identities=18%  Similarity=0.178  Sum_probs=88.9

Q ss_pred             CCcc-EEEEEeccccchH--------hHHHHHHHHHHHHHHH-HhccccccccCCCCccEEEEEEeecCCC-----Cccc
Q 003284            2 SEKQ-LIVAVEGTAAMGP--------YWQSIVSDYLEKIIRC-FCVNELAGQKTSASNVELSLVTFNTHGS-----YCAC   66 (834)
Q Consensus         2 ~~~d-vVFVID~Tasmg~--------yi~~lkt~YI~p~le~-f~~g~~~~~~~~~~~~~~gLVvY~d~~~-----~~~~   66 (834)
                      +.|| ||||||.+.+|..        .|+.++. +|.-+|.. +..         ...-++|||+|++...     ++..
T Consensus        33 ~~ke~ivf~IDvS~SM~~~d~~~~~srl~~a~~-~v~~~i~~kii~---------~~~D~vGlVlfgt~~t~n~l~~d~i  102 (609)
T 1jey_A           33 SGRDSLIFLVDASKAMFESQSEDELTPFDMSIQ-CIQSVYISKIIS---------SDRDLLAVVFYGTEKDKNSVNFKNI  102 (609)
T ss_dssp             -CEEEEEEEEECSGGGGCCCSSSSCCHHHHHHH-HHHHHHHHHHHT---------TCCCEEEEEEESCSSCBSTTCCTTE
T ss_pred             cCceEEEEEEECCHHHcCCCCCCCCChHHHHHH-HHHHHHHHhhCC---------CCCCeEEEEEEccCCCCCcCCCCCe
Confidence            3456 9999999999976        5666664 33333332 111         1236999999999873     3332


Q ss_pred             ceeeccC-CCCHHHHHHHhccCc---------cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecC-
Q 003284           67 LVQRSGW-TKDVDIFLHWLSTIP---------FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAAS-  135 (834)
Q Consensus        67 lv~~~gf-Tsd~~~fl~~Ld~I~---------f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~S-  135 (834)
                      ++.. .+ .-+.+.+..+.+-+.         ..|. ....++.+||..|+.+|....       .....|.+|||+|. 
T Consensus       103 ~v~~-~L~~~~~~~ik~l~~l~~~~~~~~~~~~~g~-~~~t~l~daL~~a~~~f~~~~-------~k~~~k~IiL~TDg~  173 (609)
T 1jey_A          103 YVLQ-ELDNPGAKRILELDQFKGQQGQKRFQDMMGH-GSDYSLSEVLWVCANLFSDVQ-------FKMSHKRIMLFTNED  173 (609)
T ss_dssp             EEEE-EEECCCHHHHHHHHTTSHHHHHHHHHHHHCC-SCCCCHHHHHHHHHHHHHTCS-------SCEEEEEEEEEESCS
T ss_pred             EEEe-cCCCCCHHHHHHHHHHhhcccchhhhhhcCC-CCCCCHHHHHHHHHHHHHhhc-------hhhcCCEEEEEcCCC
Confidence            3332 22 124443333332221         1232 235789999999999996421       12247899999985 


Q ss_pred             CCCCCCCCcccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          136 NPHPLPTPVYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       136 pP~~lp~pv~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                      +|+.-- .                 ..   ..+++.+|+.+.+.||.|.+|--.
T Consensus       174 ~p~~~~-~-----------------~~---~~~~~~~a~~l~~~gI~i~~igig  206 (609)
T 1jey_A          174 NPHGND-S-----------------AK---ASRARTKAGDLRDTGIFLDLMHLK  206 (609)
T ss_dssp             CTTTTC-H-----------------HH---HHHHHHHHHHHHHHTEEEEEEEBC
T ss_pred             CCCCCc-h-----------------HH---HHHHHHHHHHHHhcCcEEEEEecC
Confidence            444210 0                 00   014689999999999999999543

>2ww8_A RRGA, cell WALL surface anchor family protein; IGG, pilus, CNA_B, adhesin, integrin, cell adhesion; HET: EPE; 1.90A {Streptococcus pneumoniae}

Probab=97.04  E-value=0.0022  Score=78.06  Aligned_cols=118  Identities=13%  Similarity=0.152  Sum_probs=71.4

Q ss_pred             ccEEEEEeccccchHhH-------HHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCC----------cc-
Q 003284            4 KQLIVAVEGTAAMGPYW-------QSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY----------CA-   65 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi-------~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~----------~~-   65 (834)
                      +|||||||.++||...+       +.+| +-+..+|+.|...         ...|+|||.|.+..-.          .+ 
T Consensus       225 ~DIVfVLD~SGSM~~~~~~~~~Rl~~~K-~a~~~~ld~L~~~---------~~drVgLV~Fs~~a~~~~~~~v~~~~~~~  294 (893)
T 2ww8_A          225 LDVVILLDNSNSMSNIRNKNARRAERAG-EATRSLIDKITSD---------SENRVALVTYASTIFDGTEFTVEKGVADK  294 (893)
T ss_dssp             EEEEEEEECCGGGCTTHHHHCCHHHHHH-HHHHHHHHHHHTS---------TTCEEEEEEESSSBCBSCEEEEECCEECT
T ss_pred             ccEEEEEeCCCCCCCcCccchhHHHHHH-HHHHHHHHHhhcC---------CCcEEEEEEecCccccccccccccccccc
Confidence            79999999999998764       2233 3355556655321         2479999999974210          00 


Q ss_pred             ---------------c-ce---e---eccCCCCHHHHH---HHhccCcc--CCC-C---CchhhHHHHHHHHHhhcccCC
Q 003284           66 ---------------C-LV---Q---RSGWTKDVDIFL---HWLSTIPF--AGG-G---FNDAAIAEGLSEALMMFSVAP  114 (834)
Q Consensus        66 ---------------~-lv---~---~~gfTsd~~~fl---~~Ld~I~f--~GG-G---~~~~AvaEGLa~AL~~f~~~~  114 (834)
                                     . +.   .   ..+||.|...+.   ..|+.+.-  .|- +   ...-++.+||..|+++|+...
T Consensus       295 ~g~~~n~~~~w~~~~t~~t~~~~~~~~lpLT~d~~~i~~lk~~I~~~~~~~~G~~~l~~~GGT~i~~AL~~A~~lL~~~~  374 (893)
T 2ww8_A          295 NGKRLNDSLFWNYDQTSFTTNTKDYSYLKLTNDKNDIVELKNKVPTEAEDHDGNRLMYQFGATFTQKALMKADEILTQQA  374 (893)
T ss_dssp             TCCEECCCTTSCTTCCEEEEECCBCCEEEEECCHHHHHHHHHHSCSCCCCSCTTSGGGGGCSCCHHHHHHHHHHHHHHHS
T ss_pred             cccccccccccccccccccccccccccccccCCHHHHHHHHHHHhhhccccccccccccCCCChHHHHHHHHHHHHHhhc
Confidence                           0 00   0   125678886665   45544321  110 0   113568899999999986311


Q ss_pred             CCCCCCCCccCCcEEEEeecCCCC
Q 003284          115 NGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus       115 ~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                             .....|++|||+|--|.
T Consensus       375 -------~~~~~kvIILLTDG~pt  391 (893)
T 2ww8_A          375 -------RQNSQKVIFHITDGVPT  391 (893)
T ss_dssp             -------CSSSEEEEEEEESSCCS
T ss_pred             -------ccCCCeEEEEEcCCCCC
Confidence                   12356899999998775

>1yvr_A RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein, 60 kDa; heat repeat, VON willebrand factor A, rossmann fold, midas motif', RNA binding protein; 1.95A {Xenopus laevis} SCOP: a.118.25.1 c.62.1.5 PDB: 1yvp_A 2i91_A

Probab=95.07  E-value=0.088  Score=60.32  Aligned_cols=98  Identities=13%  Similarity=0.070  Sum_probs=55.3

Q ss_pred             CccEEEEEeccccchHh-----HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--C
Q 003284            3 EKQLIVAVEGTAAMGPY-----WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--K   75 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y-----i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--s   75 (834)
                      ..+|+||||.++||...     +.. +.--+.-.+..+..           +-+++||+|.+.  +     ...++|  .
T Consensus       368 ~~~v~lvvD~SgSM~~~~~~~~l~~-~~~Aa~l~~~~~~~-----------~d~vglv~Fs~~--~-----~~~~~t~~~  428 (538)
T 1yvr_A          368 GKRFLLAIDVSASMNQRVLGSILNA-SVVAAAMCMLVART-----------EKDSHMVAFSDE--M-----LPCPITVNM  428 (538)
T ss_dssp             CCCEEEEEECSGGGGSBSTTSSCBH-HHHHHHHHHHHHHH-----------CSSEEEEEESSS--E-----ECCSCCTTS
T ss_pred             CceEEEEEECccccCCCCCCCcHHH-HHHHHHHHHHHhcc-----------CCceEEEEECCC--c-----eEcCCCCcc
Confidence            37999999999999742     111 11100111111211           247999999863  1     122333  3


Q ss_pred             CHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCC
Q 003284           76 DVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNP  137 (834)
Q Consensus        76 d~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP  137 (834)
                      ++..++..|+.+  .|||   -++.+||..|+..-             ...+.+|||+|--.
T Consensus       429 ~l~~~l~~l~~~--~~Gg---T~i~~aL~~a~~~~-------------~~~~~iIliTDg~~  472 (538)
T 1yvr_A          429 LLHEVVEKMSDI--TMGS---TDCALPMLWAQKTN-------------TAADIFIVFTDCET  472 (538)
T ss_dssp             CHHHHHHHHTTC--CCSC---CCTTHHHHHHHHTT-------------CCCSEEEEEECCCC
T ss_pred             cHHHHHHHHhcC--CCCC---CcHHHHHHHHHhcc-------------CCCCEEEEEcCCCC
Confidence            466666677654  3444   33456777777641             12478999997644

>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=95.00  E-value=0.0047  Score=68.02  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=9.2

Q ss_pred             HHHHHHHhhc-CcEEEEec
Q 003284          170 ETVAKSFVQC-SVSLSVIC  187 (834)
Q Consensus       170 e~lA~~~~e~-~I~LSvIs  187 (834)
                      +.++++|.|+ ||+|.++.
T Consensus        21 ~~~~~~F~~~~gi~V~~~~   39 (449)
T 3iot_A           21 AEVGKKFEKDTGIKVTVEH   39 (449)
T ss_dssp             HHHHHHHHHHHSCCEEEEC
T ss_pred             HHHHHHHhhccCCEEEEEe
Confidence            4444444433 56666555

>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=94.48  E-value=0.0077  Score=66.30  Aligned_cols=11  Identities=18%  Similarity=0.063  Sum_probs=5.7

Q ss_pred             HHHHHHHHHhc
Q 003284           27 YLEKIIRCFCV   37 (834)
Q Consensus        27 YI~p~le~f~~   37 (834)
                      ++..+++.|+.
T Consensus        19 ~~~~~~~~F~~   29 (449)
T 3iot_A           19 GLAEVGKKFEK   29 (449)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhh
Confidence            34455555644

>1pcx_A Protein transport protein SEC24; 2.50A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 PDB: 1pd0_A 1pd1_A

Probab=92.56  E-value=1.3  Score=53.51  Aligned_cols=107  Identities=13%  Similarity=0.176  Sum_probs=61.9

Q ss_pred             HHHhccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccc---
Q 003284           81 LHWLSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQN---  155 (834)
Q Consensus        81 l~~Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~---  155 (834)
                      ...|+.|.  |..+.....|..-||.+|+.+++..            --++|+...++|--=|=.     |..-+..   
T Consensus       288 ~~lL~~L~~~~~~~~~~~~a~G~AL~~A~~lL~~~------------GGrI~~F~sg~pt~GpG~-----l~~r~~~~~~  350 (810)
T 1pcx_A          288 ETLLTKIPQIFQSNLITNFALGPALKSAYHLIGGV------------GGKIIVVSGTLPNLGIGK-----LQRRNESGVV  350 (810)
T ss_dssp             HHHHHHHHHHTTTCCCCCCCHHHHHHHHHHHHTTT------------CEEEEEEESSCCCSSTTC-----CCC-------
T ss_pred             HHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhc------------CCEEEEEecCCCCCCCCc-----cccccccccc
Confidence            34555553  5555566788999999999988621            136666677776432211     1111111   


Q ss_pred             ----cchhhhhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCCC
Q 003284          156 ----ENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       156 ----e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~~  205 (834)
                          |+....+... .-.+.||+.+.+.+|.+.+.+--    .+..|+.|-+..+|..
T Consensus       351 ~~~ke~~~l~~~a~-~fY~~la~~~~~~gi~VDlF~~s~~~~dla~l~~l~~~TGG~v  407 (810)
T 1pcx_A          351 NTSKETAQLLSCQD-SFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQT  407 (810)
T ss_dssp             -------------C-CHHHHHHHHHHHTTEEEEEEEEESSCCCHHHHHHHHHTTTCCE
T ss_pred             Ccccchhhhcccch-HHHHHHHHHHHHCCeEEEEEEccCCccChHHHHHHHhcCCcEE
Confidence                1000111111 12489999999999998877533    3578888988887764

>3eh1_A Protein transport protein SEC24B; copii coat protein, vesicle transport, transport signal sequence, cytoplasm, endoplasmic reticulum; 1.80A {Homo sapiens} PDB: 2nut_B 2nup_B 3egd_B 3egx_B

Probab=92.55  E-value=1.8  Score=51.89  Aligned_cols=175  Identities=10%  Similarity=0.126  Sum_probs=90.7

Q ss_pred             EEEEEecccc--chHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC-------C-----------cc
Q 003284            6 LIVAVEGTAA--MGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS-------Y-----------CA   65 (834)
Q Consensus         6 vVFVID~Tas--mg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~-------~-----------~~   65 (834)
                      .|||||.+..  -..+++.+++. |.-+|+.+-+         ..++++|||+|.+.=-       .           .+
T Consensus       163 yvFvIDvs~~a~~~g~l~~~~~s-l~~~L~~lp~---------~~~~~VG~ITfd~~vh~y~l~~~~~~~qmlvv~dl~d  232 (751)
T 3eh1_A          163 YLFVLDVSHNAVEAGYLTILCQS-LLENLDKLPG---------DSRTRIGFMTFDSTIHFYNLQEGLSQPQMLIVSDIDD  232 (751)
T ss_dssp             EEEEEECSHHHHHHTHHHHHHHH-HHHHTTTSSC---------CTTCEEEEEEESSSEEEEECCTTCSSCEEEEESCTTC
T ss_pred             EEEEEEccHhhhhhhHHHHHHHH-HHHHHHhcCC---------CcCcEEEEEEeCCEEEEEECCCCcccceeeccccccc
Confidence            5999998852  22345555533 2223332211         1468999999987311       0           00


Q ss_pred             ccee-eccC----CCCHHHHHHHhccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           66 CLVQ-RSGW----TKDVDIFLHWLSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        66 ~lv~-~~gf----Tsd~~~fl~~Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      ..+- ..+|    ...-+.+...|+.|.  |..+.....|..-||.+|+.++...            --++++...++|-
T Consensus       233 ~f~P~~~~~lv~l~e~~~~i~~lL~~Lp~~~~~~~~~~~~~G~AL~aA~~ll~~~------------GGrI~~F~sg~pt  300 (751)
T 3eh1_A          233 VFLPTPDSLLVNLYESKELIKDLLNALPNMFTNTRETHSALGPALQAAFKLMSPT------------GGRVSVFQTQLPS  300 (751)
T ss_dssp             TTSCCGGGTSEETTTTHHHHHHHHHHGGGTSTTCSCCCCCHHHHHHHHHHHHTTT------------CEEEEEEECSCCC
T ss_pred             cCCCChhhhcccHHHHHHHHHHHHHhhhHhhcCCCCCccchHHHHHHHHHHhhcC------------CCEEEEEecCCCC
Confidence            0000 0122    222333444566654  4444455688999999999988521            1355555566654


Q ss_pred             CCC-CCccc--CCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEec--cC--CchhHHHHHHHhcCCC
Q 003284          139 PLP-TPVYR--PQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVIC--PK--QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       139 ~lp-~pv~~--p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIs--Pr--qlp~l~~Lfeka~~~~  205 (834)
                      -=| .-+-+  +.+  ..+.|..+..+... .=.+.||+.+.+.+|.+.+.+  ..  .+..|+.|-+..+|..
T Consensus       301 ~GpG~l~~r~~~~~--~~~~ke~~~~~~a~-~fY~~la~~~~~~~i~VDlF~~s~~~~dlatl~~l~~~TGG~v  371 (751)
T 3eh1_A          301 LGAGLLQSREDPNQ--RSSTKVVQHLGPAT-DFYKKLALDCSGQQTAVDLFLLSSQYSDLASLACMSKYSAGCI  371 (751)
T ss_dssp             SSTTCCCCCCCSCG--GGGSSSCTTCSCSC-SHHHHHHHHHHHTTEEEEEEECCSSCCCHHHHTHHHHTTTCCE
T ss_pred             CCCCcccccccccc--CCCchhhhhhcchH-HHHHHHHHHHHhcCceEEEEEccCcccChHhHHHHHhhcCceE
Confidence            222 11100  000  00001001111111 125899999999998877654  33  3578888888887774

>2nut_A Protein transport protein SEC23A; human copii SEC23/24 complexed with SEC22, protein transport; 2.30A {Homo sapiens} PDB: 2nup_A 3egd_A 3eg9_A 3egx_A 3efo_A

Probab=92.32  E-value=0.66  Score=55.73  Aligned_cols=110  Identities=9%  Similarity=0.014  Sum_probs=63.0

Q ss_pred             HHhccCcc-----CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccccccc
Q 003284           82 HWLSTIPF-----AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNE  156 (834)
Q Consensus        82 ~~Ld~I~f-----~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e  156 (834)
                      ..|+.|+-     ..+.....|...||.+|+.+++...        ...--++++...++|-.=|-.     |...+.+|
T Consensus       246 ~lLe~L~~~~~~~~~~~~~~~a~G~Al~~A~~lL~~~~--------~~~GGrI~~F~sg~pt~GpG~-----l~~r~~~~  312 (769)
T 2nut_A          246 DLLGELQRDPWPVPQGKRPLRSSGVALSIAVGLLECTF--------PNTGARIMMFIGGPATQGPGM-----VVGDELKT  312 (769)
T ss_dssp             HHHHHCCCCSSCCCTTBCCCCCHHHHHHHHHHHHHHHS--------CSSCCEEEEEESSCCCSSSSC-----CSCSBTTS
T ss_pred             HHHHhcccccccccCCCCCccchHHHHHHHHHHHhhcc--------cCCCcEEEEEeCCCCCCCCCC-----CcCccccc
Confidence            45666643     3333445789999999999886311        112345666666776432211     11112211


Q ss_pred             c-----------hhhhhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCCC
Q 003284          157 N-----------NEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       157 ~-----------~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~~  205 (834)
                      .           .++.+... .-.+.+|+.+.+.+|.+.+.+--    .+..|+.|-+..+|.-
T Consensus       313 ~~rs~~d~~ke~~~~~~~a~-~fY~~la~~~~~~gi~VDlF~~~~~~vdla~l~~l~~~TGG~~  375 (769)
T 2nut_A          313 PIRSWHDIDKDNAKYVKKGT-KHFEALANRAATTGHVIDIYACALDQTGLLEMKCCPNLTGGYM  375 (769)
T ss_dssp             CCCCHHHHHTTCCTTHHHHH-HHHHHHHHHHHHHTCEEEEEEECSSCCCHHHHTHHHHHSSCCE
T ss_pred             ccccccccccchhhhccchH-HHHHHHHHHHHHCCeEEEEEeccCCccChHHHHHHhhcCCceE
Confidence            1           11111111 01478999999999999887543    2588899988888764

>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

Probab=92.26  E-value=1  Score=55.32  Aligned_cols=109  Identities=13%  Similarity=0.167  Sum_probs=64.3

Q ss_pred             HHHHHhccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccc-
Q 003284           79 IFLHWLSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQN-  155 (834)
Q Consensus        79 ~fl~~Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~-  155 (834)
                      .+...|+.|.  |..+.....|..-||.+|+.+++..            --++|+...++|--=|=.     |..-+.. 
T Consensus       402 ~I~~lLe~L~~~~~~~~~~~~~~G~AL~aA~~lL~~~------------GGrI~~F~sg~Pt~GpG~-----l~~re~~~  464 (926)
T 1m2v_B          402 NIETLLTKIPQIFQSNLITNFALGPALKSAYHLIGGV------------GGKIIVVSGTLPNLGIGK-----LQRRNESG  464 (926)
T ss_dssp             HHHHHHHHHHHHTSSCCCCCCCHHHHHHHHHHHHTTT------------CEEEEEEESSCCCSSTTC-----CCCCCC--
T ss_pred             HHHHHHHhhhhhhcCCCCCCccHHHHHHHHHHHHHhh------------CCEEEEEecCCCCCCCCc-----cccccccc
Confidence            3344555553  5555566788999999999988621            235666666666422211     1111111 


Q ss_pred             ------cchhhhhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCCC
Q 003284          156 ------ENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       156 ------e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~~  205 (834)
                            |+.+..+... .-.+.||+.|.+.+|.+.+.+-.    .+..|+.|.+..+|..
T Consensus       465 ~~~~~ke~~~ll~~a~-~FYk~LA~~~~~~gisVDlF~~s~~~vdla~l~~l~~~TGG~v  523 (926)
T 1m2v_B          465 VVNTSKETAQLLSCQD-SFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQT  523 (926)
T ss_dssp             --CCTTHHHHHTSCSS-THHHHHHHHHHHHTEEEEEEEEESSCCCHHHHHHHHHTTTCCE
T ss_pred             ccCcccchhhhccchH-HHHHHHHHHHHHcCeEEEEEEccCCCcChHHHHHHHhcCCceE
Confidence                  1100111111 12589999999999998877533    3688888988887764

>1m2o_A SEC23, protein transport protein SEC23, SEC23P; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 PDB: 1m2v_A 2qtv_A*

Probab=89.96  E-value=2  Score=51.60  Aligned_cols=110  Identities=10%  Similarity=0.086  Sum_probs=62.7

Q ss_pred             HHhccCcc-----CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccccccc
Q 003284           82 HWLSTIPF-----AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNE  156 (834)
Q Consensus        82 ~~Ld~I~f-----~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e  156 (834)
                      ..|+.|+-     ..+.....|..-||.+|+.+++...        ...--++++...++|--=|=.     |.+-+..|
T Consensus       240 ~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~--------~~~GGrI~~F~sg~pt~GpG~-----l~~r~~~~  306 (768)
T 1m2o_A          240 QLLENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCY--------KNIPARIILFASGPGTVAPGL-----IVNSELKD  306 (768)
T ss_dssp             HHHHTCCCSCSCCCTTBCCCCCHHHHHHHHHHHHHHHC--------TTSCCEEEEEESSCCCSSSSC-----CSCSBTTS
T ss_pred             HHHHhccccccccCCCCCCcccHHHHHHHHHHHHhhcc--------CCCCcEEEEEeCCCCCCCCcc-----cccccccc
Confidence            45666653     2333345688899999998886211        112245666666676432211     11111111


Q ss_pred             -----------chhhhhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCCC
Q 003284          157 -----------NNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       157 -----------~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~~  205 (834)
                                 +.++.+... .-.+.||+.+.+.+|.+.+.+--    .+..|+.|-+..+|..
T Consensus       307 ~~rs~~d~~k~~~~~~~~a~-~fY~~la~~~~~~gi~VDlF~~~~~~~dla~l~~l~~~TGG~v  369 (768)
T 1m2o_A          307 PLRSHHDIDSDHAQHYKKAC-KFYNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQLTDSTGGVL  369 (768)
T ss_dssp             CCCCHHHHHHTCCTTHHHHH-HHHHHHHHHHHHHTCEEEEEEECSSCCSHHHHHHHHHHHTCCE
T ss_pred             ccccccccccchhhhcCchH-HHHHHHHHHHHHCCeEEEEEEccCCccChHHHhhHhhcCCceE
Confidence                       111111111 12389999999999998877533    3588999999888764

>2nvo_A RO sixty-related protein, RSR; alpha helical repeats, VON willebrand factor A domain, beta- RNA binding protein; 1.89A {Deinococcus radiodurans}

Probab=88.00  E-value=2.1  Score=49.09  Aligned_cols=129  Identities=10%  Similarity=0.071  Sum_probs=65.9

Q ss_pred             CccEEEEEeccccchH-hHHH---H-HHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQS---I-VSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDV   77 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~---l-kt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~   77 (834)
                      +.+++++||.++||.. ....   + +.+ +--.+.+....         .+-+++||+|.+.  +     ....++.+ 
T Consensus       362 ~~~~lv~vDvSgSM~~~~~~~~~k~~~~e-~Aa~la~~~~r---------~~d~v~lv~Fs~~--~-----~~~~~~~~-  423 (535)
T 2nvo_A          362 NTRHLLALDVSGSMTCGDVAGVPGLTPNM-AAAAMSLIALR---------TEPDALTMGFAEQ--F-----RPLGITPR-  423 (535)
T ss_dssp             CSEEEEEECCSGGGGSCCGGGCTTCCHHH-HHHHHHHHHHH---------HSSEEEEEEEBSS--E-----EECCCCTT-
T ss_pred             CceEEEEEECCccccCCCCCCCCcccHHH-HHHHHHHHHcC---------cCCceEEEEECCc--c-----eEcCCCcc-
Confidence            3789999999999974 2110   0 111 11122222110         1248999999773  1     12234433 


Q ss_pred             HHHHHHhccCccC-CCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccccccc
Q 003284           78 DIFLHWLSTIPFA-GGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNE  156 (834)
Q Consensus        78 ~~fl~~Ld~I~f~-GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e  156 (834)
                      +.++..|+.|... |||-.   +..+|..|....             ...+.+|||+|-.-..-.               
T Consensus       424 ~~l~~~l~~l~~~~~ggTd---i~~~l~~a~~~~-------------~~~~~vIliTD~~~~~g~---------------  472 (535)
T 2nvo_A          424 DTLESAMQKAQSVSFGGTD---CAQPILWAAQER-------------LDVDTFVVYTDNETWAGQ---------------  472 (535)
T ss_dssp             CCHHHHHHHTCCSSBCCCC---TTHHHHHHHHTT-------------CCCSEEEEEESSCCCCCS---------------
T ss_pred             hhHHHHHHHHhhCCCCCcc---HHHHHHHHHHhc-------------CCCCEEEEEeCCCccCCC---------------
Confidence            3344444444332 44432   222344443321             123678999875332110               


Q ss_pred             chhhhhhccCCCHHHHHHHHhhc---CcEEEEeccCC
Q 003284          157 NNEAQAESRLSDAETVAKSFVQC---SVSLSVICPKQ  190 (834)
Q Consensus       157 ~~~~~~~~~l~d~e~lA~~~~e~---~I~LSvIsPrq  190 (834)
                                .++++.++.+.++   +++|.+|.-..
T Consensus       473 ----------~~~~~al~~~r~~~~~~~klv~i~l~~  499 (535)
T 2nvo_A          473 ----------VHPTVALDQYAQKMGRAPKLIVVGLTA  499 (535)
T ss_dssp             ----------SCHHHHHHHHHHHHSCCCEEEEEETTC
T ss_pred             ----------CCHHHHHHHHHHhhCCCCeEEEEeccC
Confidence                      1345566777766   78898886554

>3eh2_A Protein transport protein SEC24C; copii-coat protein, vesicle transport, cytoplasm, endoplasmic reticulum, ER-golgi transport, golgi apparatus; 2.35A {Homo sapiens}

Probab=85.91  E-value=9.4  Score=45.86  Aligned_cols=181  Identities=14%  Similarity=0.180  Sum_probs=89.2

Q ss_pred             EEEEEeccccc--hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC---------Cc---------c
Q 003284            6 LIVAVEGTAAM--GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS---------YC---------A   65 (834)
Q Consensus         6 vVFVID~Tasm--g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~---------~~---------~   65 (834)
                      .|||||.+..-  ..+++.+++. |.-+|+.+-.    +.....++.++|||+|...=-         .+         +
T Consensus       176 y~FvIDvs~~av~sg~l~~~~~s-i~~~L~~lp~----~~~~~~~~~~VG~ITfd~~vh~y~l~~~~~~~q~~vv~dl~d  250 (766)
T 3eh2_A          176 FIFMIDVSYNAIRTGLVRLLCEE-LKSLLDFLPR----EGGAEESAIRVGFVTYNKVLHFYNVKSSLAQPQMMVVSDVAD  250 (766)
T ss_dssp             EEEEEECSHHHHHTTHHHHHHHH-HHHHGGGCCC----CSSCSSCCCEEEEEEESSSEEEEECCTTCSSCEEEEECCTTT
T ss_pred             EEEEEECchhhccchHHHHHHHH-HHHHHHhCCc----ccccCCccceEEEEEeCCEEEEEECCCCCCCceEEEecChhh
Confidence            58999998421  1244444433 3333333311    101112468999999976411         01         1


Q ss_pred             ccee-eccCCCCH----HHHHHHhccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           66 CLVQ-RSGWTKDV----DIFLHWLSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        66 ~lv~-~~gfTsd~----~~fl~~Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      .++- ..+|.-++    +.+...|+.|+  |..-...+.+++-+|++|+.++...          ..--++++...+.|-
T Consensus       251 ~f~P~~~~~lv~l~e~~~~i~~lL~~L~~~~~~~~~~~t~~g~al~aa~~~l~~~----------~~GGkI~~F~s~lP~  320 (766)
T 3eh2_A          251 MFVPLLDGFLVNVNESRAVITSLLDQIPEMFADTRETETVFVPVIQAGMEALKAA----------ECAGKLFLFHTSLPI  320 (766)
T ss_dssp             CCCCCCTTSSBCTTTTHHHHHHHHHHHHHHHTTCCCCCCCSHHHHHHHHHHHHHT----------TCCEEEEEEECSCCC
T ss_pred             hccccccceeEeHHHHHHHHHHHHHhhhhhccCCCCCcchHHHHHHHHHHHhccC----------CCCcEEEEEecCCCC
Confidence            1110 11232222    23333455553  3222234567778888888776421          112455555566554


Q ss_pred             --CCCCCccc---CCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEec--cC--CchhHHHHHHHhcCCC
Q 003284          139 --PLPTPVYR---PQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVIC--PK--QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       139 --~lp~pv~~---p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIs--Pr--qlp~l~~Lfeka~~~~  205 (834)
                        +-..-+-+   ..+.+  .+|+ +..+... .=.+.||+.+.+.+|.+.+.+  ..  .+..|+.|.+..+|..
T Consensus       321 t~GpG~l~~r~~~~~~~s--dke~-~~~~~a~-~fY~~la~~~~~~~i~VDlF~~s~~~vdlatl~~l~~~TGG~v  392 (766)
T 3eh2_A          321 AEAPGKLKNRDDRKLINT--DKEK-TLFQPQT-GAYQTLAKECVAQGCCVDLFLFPNQYVDVATLSVVPQLTGGSV  392 (766)
T ss_dssp             SSSTTCCCCCCCGGGTTS--TTGG-GGTSCSS-THHHHHHHHHHHHTEEEEEEECCSSCCCHHHHTHHHHHTTCCE
T ss_pred             cCCCcccccccccccCCC--cchh-hhccchH-HHHHHHHHHHHhCCeEEEEEEecCCCcChHHHHHHHhhcCceE
Confidence              33321111   00000  1111 1222221 234899999999998777654  33  3588888888888764

>3efo_B SEC24 related gene family, member D; copii, coat protein, transport signal, disease mutation, endoplasmic reticulum, ER-golgi transport, golgi apparatus, membrane; 2.70A {Homo sapiens} PDB: 3eg9_B

Probab=83.96  E-value=11  Score=45.34  Aligned_cols=181  Identities=14%  Similarity=0.219  Sum_probs=89.6

Q ss_pred             EEEEEecccc-c-hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCC------------------cc
Q 003284            6 LIVAVEGTAA-M-GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY------------------CA   65 (834)
Q Consensus         6 vVFVID~Tas-m-g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~------------------~~   65 (834)
                      .|||||.+.. . ..+++.+++. |.-+|+.+-.   + .....++.++|||+|...=-+                  .+
T Consensus       180 y~FvIDvs~~av~sg~l~~~~~s-l~~~L~~lP~---~-~~~~~~~~~VG~ITfd~~vh~y~l~~~~~q~q~~vv~d~~d  254 (770)
T 3efo_B          180 FIFMIDVSYSNIKNGLVKLICEE-LKTMLEKIPK---E-EQEETSAIRVGFITYNKVLHFFNVKSNLAQPQMMVVTDVGE  254 (770)
T ss_dssp             EEEEEECSHHHHHTTHHHHHHHH-HHHHGGGCCC---C-TTSSSCSCEEEEEEESSSEEEEECCTTCSSCEEEEECCTTS
T ss_pred             EEEEEEcchhhccchHHHHHHHH-HHHHHHhCCc---c-ccccCccceEEEEEeCCEEEEEeCCCcccCceEEEeccccc
Confidence            6899998752 2 2355555544 3334443321   1 111124689999999764110                  01


Q ss_pred             ccee-eccCCCCH----HHHHHHhccCc--cCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           66 CLVQ-RSGWTKDV----DIFLHWLSTIP--FAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        66 ~lv~-~~gfTsd~----~~fl~~Ld~I~--f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      .++- ..+|.-++    +.+...|+.|+  |..-...+.+++-+|++|+.++...          ..--++++...+.|-
T Consensus       255 ~f~P~~~~~Lv~l~e~~~~i~~lL~~L~~~~~~~~~~~t~~g~al~aa~~~l~~~----------~~GGkI~~F~s~lP~  324 (770)
T 3efo_B          255 VFVPLLDGFLVNYQESQSVIHNLLDQIPDMFADSNENETVFAPVIQAGMEALKAA----------DCPGKLFIFHSSLPT  324 (770)
T ss_dssp             CCCCCSSSSSBCTTTTHHHHHHHHHHHHHHHHTCCCCCCCCHHHHHHHHHHHHHH----------TCCEEEEEEECSCCC
T ss_pred             ccCCCccceeeeHHHHHHHHHHHHHhhHhhccCCCCCcchHHHHHHHHHHHhccC----------CCCcEEEEEecCCCC
Confidence            1100 01222222    22333444442  3333344666777888888776420          012355555555454


Q ss_pred             --CCCCCccc---CCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEec--cCC--chhHHHHHHHhcCCC
Q 003284          139 --PLPTPVYR---PQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVIC--PKQ--LPKLTAIYNAAKRNP  205 (834)
Q Consensus       139 --~lp~pv~~---p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIs--Prq--lp~l~~Lfeka~~~~  205 (834)
                        .-..-+-+   ..+.+  .+|. +..+... .=.+.||+.|.+.+|.+.+.+  ...  +..|+.|.+..+|..
T Consensus       325 t~GpG~l~~r~~~~~~~t--~ke~-~~~~~a~-~fY~~lA~~~~~~~i~VDlF~~s~~~vdlatl~~l~~~TGG~v  396 (770)
T 3efo_B          325 AEAPGKLKNRDDKKLVNT--DKEK-ILFQPQT-NVYDSLAKDCVAHGCSVTLFLFPSQYVDVASLGLVPQLTGGTL  396 (770)
T ss_dssp             SSSTTCCCCCCCCCCSSC--SCGG-GGGSCSS-SHHHHHHHHHHHTTEEEEEEECCSSCCCHHHHTHHHHHTTCCE
T ss_pred             cCCCccccccccccccCC--cchh-hhhcchH-HHHHHHHHHHHHcCeEEEEEEecCCccChHHHHHHHhhcCceE
Confidence              22221100   00111  1111 1222211 235899999999998877654  332  578888888888764

---

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	834
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	7e-09
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	4e-07
d1f5na1	300	a.114.1.1 (A:284-583) Interferon-induced guanylate	2e-04
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	5e-08
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	6e-08
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	6e-08
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	2e-07
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	8e-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)	1e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	2e-06
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	1e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	3e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	4e-05
d2es4d1	280	a.137.15.1 (D:53-332) Lipase chaperone LifO (LipB)	4e-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	0.001
d1psya_	125	a.52.1.3 (A:) 2S albumin RicC3 {Castor bean (Ricin	0.003

>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 = 55.9 bits (134), Expect = 7e-09
 Identities = 17/104 (16%), Positives = 44/104 (42%), Gaps = 3/104 (2%)

Query: 683 MVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQ 742
           +   + +I  ++ +    Q   +   +MQ + +     + +  Q+ L QL +++   + Q
Sbjct: 199 LTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQ 258

Query: 743 QQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQ 786
                 +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 = 50.9 bits (121), Expect = 3e-07
 Identities = 15/106 (14%), Positives = 46/106 (43%), Gaps = 5/106 (4%)

Query: 689 QISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
            ++ ++++   ++ + +  Q     L   Q    Q  +Q+    Q+ + QL ++     +
Sbjct: 198 TLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQKERSYQEHLKQLTEK-----M 252

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQPQQ 794
           +   +  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 = 50.1 bits (119), Expect = 4e-07
 Identities = 14/108 (12%), Positives = 51/108 (47%), Gaps = 1/108 (0%)

Query: 682 DMVVFKPQISSQQQQQLQQQQQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQ-LQ 740
           +++    +        + Q  Q    ++ + +++  +    Q   + L ++Q++  Q ++
Sbjct: 176 EILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMME 235

Query: 741 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLPQLQQQQQ 788
           Q+++  Q   + + +  +  ++  L++Q++   ++ Q+Q   L++  Q
Sbjct: 236 QKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQ 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 = 42.0 bits (98), Expect = 2e-04
 Identities = 19/151 (12%), Positives = 59/151 (39%), Gaps = 5/151 (3%)

Query: 646 QLQEKKLCAVIQLPSQTLLLSVSDKACRLIG--MLFPGDMVVFKPQISSQQQQQLQQQQQ 703
           +    +   ++Q+    L   V        G   LF   +   K +   + ++ +Q ++ 
Sbjct: 118 EASSDRCSGLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEI 177

Query: 704 QQQHQQMQSQLQHQQLSQLQQQQQQLPQL---QQQIPQLQQQQQIPQLQQQSMPQLQQQQ 760
            Q + + +  +    L   Q   ++  ++   + +    Q   ++    Q+   Q+ +Q+
Sbjct: 178 LQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLHEMQRKNEQMMEQK 237

Query: 761 QLPQLQQQQQLPQMQQQQQLPQLQQQQQLSQ 791
           +    +  +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: 691 SSQQQQQLQQQQQQQQHQQ--MQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQQQQQIPQL 748
            S   QQ+++ +         M++  +  Q+S   +++        Q+  L ++   P +
Sbjct: 8   ESGCYQQMEEAEMLNHCGMYLMKNLGERSQVSPRMREEDHKQLCCMQLKNLDEKCMCPAI 67

Query: 749 QQQSMPQLQQQQQLPQLQQQQQLPQM 774
                  +  + +   +     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 = 0.003
 Identities = 20/101 (19%), Positives = 42/101 (41%), Gaps = 14/101 (13%)

Query: 691 SSQQQQQLQQQ----------QQQQQHQQMQSQLQHQQLSQLQQQQQQLPQLQQQIPQLQ 740
           S Q +Q++Q++          Q   +    +  L+       QQ+ QQL Q   Q+ Q++
Sbjct: 15  SQQCRQEVQRKDLSSCERYLRQSSSRRSTGEEVLRMPGDENQQQESQQLQQCCNQVKQVR 74

Query: 741 QQQQIPQLQQQSMPQLQQQQQLPQLQQQQQLPQMQQQQQLP 781
            + Q   ++  +  Q+QQ Q       ++     Q+  ++ 
Sbjct: 75  DECQCEAIKYIAEDQIQQGQL----HGEESERVAQRAGEIV 111

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	834
d1tyeb2	248	Integrin beta A domain {Human (Homo sapiens) [TaxI	99.72
d1pt6a_	192	Integrin alpha1-beta1 {Human (Homo sapiens) [TaxId	99.07
d1n3ya_	189	Integrin alpha-x beta2 {Human (Homo sapiens) [TaxI	99.05
d1atza_	184	von Willebrand factor A3 domain, vWA3 {Human (Homo	99.0
d1v7pc_	193	Integrin alpha2-beta1 {Human (Homo sapiens) [TaxId	98.99
d1shux_	181	Capillary morphogenesis protein 2 domain {Human (H	98.97
d1ijba_	202	von Willebrand factor A1 domain, vWA1 {Human (Homo	98.93
d1mf7a_	194	Integrin alpha M (CR3, CD11b/CD18, Mac-1 alpha sub	98.91
d1q0pa_	209	Complement factor B domain {Human (Homo sapiens) [	98.7
d1mjna_	179	Integrin CD11a/CD18 (Leukocyte function associated	98.64
d1jeyb2	236	Ku80 subunit N-terminal domain {Human (Homo sapien	98.45
d1jeya2	220	Ku70 subunit N-terminal domain {Human (Homo sapien	97.84
d1yvra2	174	60-kda SS-A/Ro ribonucleoprotein, RoRNP {African c	95.96
d2qtva3	271	Sec23 {Baker's yeast (Saccharomyces cerevisiae) [T	95.93
d1pd0a3	252	Sec24 {Baker's yeast (Saccharomyces cerevisiae) [T	95.74

>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=99.72  E-value=6.6e-17  Score=166.20  Aligned_cols=176  Identities=10%  Similarity=-0.027  Sum_probs=126.2

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcc------------------
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCA------------------   65 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~------------------   65 (834)
                      -|||||||+|+||++||+.+|+. +..+++.+..-        ...+|||+|.|+|+...+.                  
T Consensus         6 vDl~Fv~D~TgSM~~~i~~vk~~-i~~i~~~l~~~--------~~~~r~g~~~f~D~~~~p~~~~~~~~~~~~p~~~~~~   76 (248)
T d1tyeb2           6 VDIYYLMDLSYSMKDDLWSIQNL-GTKLATQMRKL--------TSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDMKT   76 (248)
T ss_dssp             EEEEEEEECSGGGGGGHHHHHHH-HHHHHHHHHHH--------CSCEEEEEEEECCCSSTTTSCCCSGGGGTCGGGGGTS
T ss_pred             eeEEEEEECCcCHHHHHHHHHHH-HHHHHHHHHhh--------CcCceEEEEEEEecccCccccccchhhccCccccccc
Confidence            59999999999999999999987 78888888642        1358999999999864221                  


Q ss_pred             -----cce-eeccCCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCC-ccCCcEEEEeecCCCC
Q 003284           66 -----CLV-QRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQN-VDGQRHCILVAASNPH  138 (834)
Q Consensus        66 -----~lv-~~~gfTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~-~~~qkhCILIa~SpP~  138 (834)
                           |.. ..++||+|+++|..+|+++...|||+.+|++.+||..|+.+.+..       .| .+..|.+|||+|+|||
T Consensus        77 ~~~~~f~~~~~~~~t~d~~~f~~~l~~~~~~GggD~pE~~~~Al~~a~~~~~~i-------~Wr~~a~r~viliTDA~~H  149 (248)
T d1tyeb2          77 TCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKI-------GWRNDASHLLVFTTDAKTH  149 (248)
T ss_dssp             CCCCCCSEEEEEEEESCHHHHHHHHTTCCCCCCSSSSBCHHHHHHHHHHCHHHH-------TCCTTSEEEEEEEESSCBC
T ss_pred             cccccccceecCCCCCCHHHHHHHHhheecccCCCCcchHHHHHHHHHHHhhhC-------CCCCCccEEEEEECCCCcc
Confidence                 111 235789999999999999999999999999999999998653211       11 2356888999999999


Q ss_pred             CCCCC------------cccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEecc-CCchhHHHHHHHh
Q 003284          139 PLPTP------------VYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICP-KQLPKLTAIYNAA  201 (834)
Q Consensus       139 ~lp~p------------v~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsP-rqlp~l~~Lfeka  201 (834)
                      ....-            |+.-     ..++- ..........+++|++.+.+++|.+.++.. +....+++|.+.-
T Consensus       150 ~~~d~~l~g~~~~~d~~~~~~-----~~~~~-~~~~~~dyps~~ql~~~l~~~~i~~ifavt~~~~~~Y~~l~~~~  219 (248)
T d1tyeb2         150 IALDGRLAGIVQPNDGQCHVG-----SDNHY-SASTTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSELI  219 (248)
T ss_dssp             CTTGGGGGTCCSCCCCCCCBC-----TTSBB-GGGGTSCCCCHHHHHHHHHHTTEEEEEEECGGGHHHHHHHHHTS
T ss_pred             cccccccccccccCCCccccC-----CCCcc-cccccccCCCHHHHHHHHHHhCcEEEEEECchhhHHHHHHHHhc
Confidence            65531            1100     00110 111222234679999999999999655444 4456677776644

>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=99.07  E-value=5e-10  Score=108.21  Aligned_cols=136  Identities=14%  Similarity=0.271  Sum_probs=98.8

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIF   80 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~f   80 (834)
                      +-|||||||++.+|+. |+.+| +++.-+++.|.-+        ...+|+|||.|.+..-      ..+.|+  .+...+
T Consensus         1 ~~DivfvlD~S~S~~~-~~~~k-~f~~~~i~~~~i~--------~~~~rv~vv~fs~~~~------~~~~l~~~~~~~~~   64 (192)
T d1pt6a_           1 QLDIVIVLDGSNSIYP-WDSVT-AFLNDLLKRMDIG--------PKQTQVGIVQYGENVT------HEFNLNKYSSTEEV   64 (192)
T ss_dssp             CEEEEEEEECCTTCCC-HHHHH-HHHHHHHTTSCBS--------TTSBEEEEEEESSSEE------EEECTTTCSSHHHH
T ss_pred             CeEEEEEEECCCCCCC-HHHHH-HHHHHHHHHhccC--------CCCcEEEEEEEeccEE------EEEeCCcchhhHHH
Confidence            4699999999999996 78776 6688888888421        2357999999986521      234443  478899


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      +..++++.+.||+...  ...||..|+. +|...     ...+..+.|.+|||++..++.-                   
T Consensus        65 ~~~i~~~~~~~g~~~~--~~~al~~~~~~~~~~~-----~g~R~~~~kviillTDG~~~d~-------------------  118 (192)
T d1pt6a_          65 LVAAKKIVQRGGRQTM--TALGTDTARKEAFTEA-----RGARRGVKKVMVIVTDGESHDN-------------------  118 (192)
T ss_dssp             HHHHHTCCCCCCSSCC--HHHHHHHHHHTTTSGG-----GTCCTTCEEEEEEEESSCCSCS-------------------
T ss_pred             HHHHhhhhhhhhhccc--hHHHHHHHHHhhhccc-----cCCCCCcceEEEEEecCCCCcc-------------------
Confidence            9999999988776543  3456777775 44321     1123467799999999876511                   


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEec
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVIC  187 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIs  187 (834)
                             .+.+.+|+.+.++||.+++|.
T Consensus       119 -------~~~~~~a~~lk~~gi~v~~ig  139 (192)
T d1pt6a_         119 -------HRLKKVIQDCEDENIQRFSIA  139 (192)
T ss_dssp             -------HHHHHHHHHHHHTTEEEEEEE
T ss_pred             -------hhhHHHHHHHHHCCCeEEEEE
Confidence                   135778999999999999996

>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=99.05  E-value=1.4e-10  Score=111.93  Aligned_cols=137  Identities=12%  Similarity=0.206  Sum_probs=100.1

Q ss_pred             CccEEEEEeccccchHh-HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHH
Q 003284            3 EKQLIVAVEGTAAMGPY-WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y-i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~   79 (834)
                      |+|||||||++++|+.+ |+.+| +++..+++.|..          ...|||||.|.+...      ..+.|+  .+...
T Consensus         2 e~DivfvlD~S~Sm~~~~~~~~k-~~~~~~i~~l~~----------~~~rv~vv~fs~~~~------~~~~l~~~~~~~~   64 (189)
T d1n3ya_           2 EQDIVFLIDGSGSISSRNFATMM-NFVRAVISQFQR----------PSTQFSLMQFSNKFQ------THFTFEEFRRSSN   64 (189)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHH-HHHHHHHTTSCT----------TTEEEEEEEESSSEE------EEECHHHHHHCSS
T ss_pred             CccEEEEEeCCCCCChHHHHHHH-HHHHHHHHHhCC----------CCCEEEEEEeeccce------eeccccccccHHH
Confidence            78999999999999865 87766 567777776632          357999999987732      223332  35567


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccch
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENN  158 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~  158 (834)
                      ++..|+++.+.||+-   .+.+||..|++ +|....     ..+..+.|.+||++|..++.-.                 
T Consensus        65 ~~~~i~~~~~~~g~t---~~~~al~~a~~~~f~~~~-----~~r~~~~kvivllTDG~~~~~~-----------------  119 (189)
T d1n3ya_          65 PLSLLASVHQLQGFT---YTATAIQNVVHRLFHASY-----GARRDAAKILIVITDGKKEGDS-----------------  119 (189)
T ss_dssp             GGGGGTTCCCCCSCB---CHHHHHHHHHTTTTSGGG-----TCCTTSEEEEEEEESSCCBSCS-----------------
T ss_pred             HHHHHHhhhhhhhhc---hHHHHHHHHHHHHhhhhc-----CCCCCCceEEEEEecCCCCCCc-----------------
Confidence            788899999988873   56788888886 443211     1234678999999998765322                 


Q ss_pred             hhhhhccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          159 EAQAESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       159 ~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                              .+.+.+++.+.++||.+++|.--
T Consensus       120 --------~~~~~~~~~~~~~gv~i~~Vgig  142 (189)
T d1n3ya_         120 --------LDYKDVIPMADAAGIIRYAIGVG  142 (189)
T ss_dssp             --------SCHHHHHHHHHHTTCEEEEEEES
T ss_pred             --------ccHHHHHHHHHHCCCceEEEecc
Confidence                    25688999999999999999643

>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=99.00  E-value=4e-09  Score=101.81  Aligned_cols=146  Identities=10%  Similarity=0.200  Sum_probs=103.6

Q ss_pred             ccEEEEEeccccc-hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            4 KQLIVAVEGTAAM-GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         4 ~dvVFVID~Tasm-g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      .|||||||++++| ...|+.+| +++..+++.|+-+        ...+|+|||.|.+..    ...-.+..+.|..+++.
T Consensus         3 lDivfliD~S~s~~~~~f~~~k-~~v~~~i~~~~i~--------~~~~rv~vv~f~~~~----~~~~~l~~~~~~~~l~~   69 (184)
T d1atza_           3 LDVILLLDGSSSFPASYFDEMK-SFAKAFISKANIG--------PRLTQVSVLQYGSIT----TIDVPWNVVPEKAHLLS   69 (184)
T ss_dssp             EEEEEEEECSSSSCHHHHHHHH-HHHHHHHHHSCBS--------TTSEEEEEEEESSSE----EEEECTTCCCCHHHHHH
T ss_pred             eEEEEEEeCCCCCCHHHHHHHH-HHHHHHHHhcCCC--------CCCcEEEEEEEeccc----eeeccccccccHHHHHH
Confidence            6999999999999 55677776 6688888888421        135799999997652    12223444679999999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQA  162 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~  162 (834)
                      .|++|.+.||+   ..+.+||..+++.+.....    ..+....|.+||+++..++.                       
T Consensus        70 ~i~~l~~~gg~---t~~~~al~~~~~~~~~~~~----g~R~~~~kvvvlltdg~~~d-----------------------  119 (184)
T d1atza_          70 LVDVMQREGGP---SQIGDALGFAVRYLTSEMH----GARPGASKAVVILVTDVSVD-----------------------  119 (184)
T ss_dssp             HHHTCCCCCCC---CCHHHHHHHHHHHHHSCCT----TCCTTSEEEEEEEECSCCSS-----------------------
T ss_pred             HHHhhhhcccc---cchhhhhhHHHHHhhhhhc----CCCCCCceEEEEEEecCccc-----------------------
Confidence            99999998776   3566777777765432111    12345688999999876541                       


Q ss_pred             hccCCCHHHHHHHHhhcCcEEEEeccCC---chhHHHH
Q 003284          163 ESRLSDAETVAKSFVQCSVSLSVICPKQ---LPKLTAI  197 (834)
Q Consensus       163 ~~~l~d~e~lA~~~~e~~I~LSvIsPrq---lp~l~~L  197 (834)
                           +.+..|+++.++||.+++|.--.   ...|+.|
T Consensus       120 -----~~~~~a~~lk~~gi~v~~igiG~~~~~~~L~~i  152 (184)
T d1atza_         120 -----SVDAAADAARSNRVTVFPIGIGDRYDAAQLRIL  152 (184)
T ss_dssp             -----CCHHHHHHHHHTTEEEEEEEESSSSCHHHHHHH
T ss_pred             -----hhhHHHHHHHHcCcEEEEEEeCCcCCHHHHHHH
Confidence                 34677899999999999998543   3445554

>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=98.99  E-value=1.8e-09  Score=104.46  Aligned_cols=135  Identities=14%  Similarity=0.216  Sum_probs=99.2

Q ss_pred             ccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHHHH
Q 003284            4 KQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIFL   81 (834)
Q Consensus         4 ~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~fl   81 (834)
                      -|||||||++.+|++ |+.+| +++..+++.|.-+        ....|+|||.|.+...      ..+.|+  .+..+++
T Consensus         2 ~DivfvlD~S~Sv~~-f~~~k-~f~~~ii~~~~i~--------~~~~rv~vv~fs~~~~------~~~~l~~~~~~~~~~   65 (193)
T d1v7pc_           2 IDVVVVCDESNSIYP-WDAVK-NFLEKFVQGLDIG--------PTKTQVGLIQYANNPR------VVFNLNTYKTKEEMI   65 (193)
T ss_dssp             EEEEEEEECCTTCCC-HHHHH-HHHHHHHHTSCBS--------TTSEEEEEEEESSSEE------EEECTTTCSSHHHHH
T ss_pred             EEEEEEEECCCCCcc-HHHHH-HHHHHHHHHcccC--------CCccEEEEEEeeccee------eeecccchhhHHHHH
Confidence            399999999999985 78776 6788888888432        2358999999987632      334554  5788999


Q ss_pred             HHhccCccCCCCCchhhHHHHHHHHHhhc-ccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           82 HWLSTIPFAGGGFNDAAIAEGLSEALMMF-SVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        82 ~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f-~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      ..++.+...+||.  ..+.+||..|++.+ ...     ...+..+.|.+||+++..|+.-                    
T Consensus        66 ~~i~~~~~~~g~~--t~~~~AL~~a~~~~f~~~-----~~~R~~~~kvvVllTDG~s~d~--------------------  118 (193)
T d1v7pc_          66 VATSQTSQYGGDL--TNTFGAIQYARKYAYSAA-----SGGRRSATKVMVVVTDGESHDG--------------------  118 (193)
T ss_dssp             HHHHHCCCCCCSC--CCHHHHHHHHHHHTTSGG-----GTCCTTSEEEEEEEESSCCSCG--------------------
T ss_pred             HHHHhhhhhccCc--cchHHHHHHHHHhccccc-----cCCCCCCceEEEEEecCCcCCC--------------------
Confidence            9999997776654  34678898888754 321     1233567899999999876511                    


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEec
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVIC  187 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIs  187 (834)
                            .+.+..++.+.+.||.++.|.
T Consensus       119 ------~~~~~~~~~~~~~gv~v~~Ig  139 (193)
T d1v7pc_         119 ------SMLKAVIDQCNHDNILRFGIA  139 (193)
T ss_dssp             ------GGHHHHHHHHHHTTEEEEEEE
T ss_pred             ------ccHHHHHHHHHhCCCEEEEEE
Confidence                  134567889999999999885

>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=98.97  E-value=1.1e-09  Score=104.73  Aligned_cols=139  Identities=17%  Similarity=0.168  Sum_probs=103.7

Q ss_pred             CccEEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            3 EKQLIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      ..|||||||++++|+..|..++ +++.-+++.|..          ...|+|||+|.+...      ..+.|+.|.+.+.+
T Consensus         5 ~~Div~llD~S~Sm~~~~~~~k-~~~~~~~~~~~~----------~~~rvglv~fs~~~~------~~~~l~~~~~~~~~   67 (181)
T d1shux_           5 AFDLYFVLDKSGSVANNWIEIY-NFVQQLAERFVS----------PEMRLSFIVFSSQAT------IILPLTGDRGKISK   67 (181)
T ss_dssp             CEEEEEEEECSGGGGGGHHHHH-HHHHHHHHHCCC----------TTEEEEEEEESSSEE------EEEEEECCHHHHHH
T ss_pred             ceEEEEEEeCCCCcccCHHHHH-HHHHHHHHHhcC----------CCCEEEEEEeecceE------EEEEecCCHHHHHH
Confidence            3799999999999999999876 668888888843          347999999988632      34677888888888


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQA  162 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~~  162 (834)
                      .|+.|...+++. ...+.+||..|++.|.+.       ......|.+|||+|..+.....                    
T Consensus        68 ~l~~l~~~~~~g-~t~~~~al~~~~~~~~~~-------~~~~~~~~ivliTDG~~~~~~~--------------------  119 (181)
T d1shux_          68 GLEDLKRVSPVG-ETYIHEGLKLANEQIQKA-------GGLKTSSIIIALTDGKLDGLVP--------------------  119 (181)
T ss_dssp             HHHHHHTCCCCS-CCCHHHHHHHHHHHHHHH-------TGGGSCEEEEEEECCCCCTTHH--------------------
T ss_pred             HhhhcccccCCC-cchHHHHHHHHHHHhhhc-------ccCCCceEEEEecCCCCCCCcc--------------------
Confidence            888887654332 246788888888776531       2345678999999987642110                    


Q ss_pred             hccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          163 ESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       163 ~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                          ......++.+.+.||.+..|.-..
T Consensus       120 ----~~~~~~~~~~k~~gv~v~~vgig~  143 (181)
T d1shux_         120 ----SYAEKEAKISRSLGASVYCVGVLD  143 (181)
T ss_dssp             ----HHHHHHHHHHHHTTCEEEEEECSS
T ss_pred             ----HHHHHHHHHHHHCCCEEEEEEeCc
Confidence                123578889999999999998764

>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=98.93  E-value=1.5e-08  Score=98.88  Aligned_cols=140  Identities=14%  Similarity=0.176  Sum_probs=102.7

Q ss_pred             ccEEEEEeccccch-HhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCCCCHHHHHH
Q 003284            4 KQLIVAVEGTAAMG-PYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWTKDVDIFLH   82 (834)
Q Consensus         4 ~dvVFVID~Tasmg-~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfTsd~~~fl~   82 (834)
                      .|||||||++++|+ ..|+.+| +++..+++.|.-+        ....|+|||.|.+...    ..-.+.++.+...+++
T Consensus        14 ~Dl~fvlD~S~S~~~~~f~~~k-~fv~~~i~~l~~~--------~~~~rvavv~y~~~~~----~~~~l~~~~~~~~l~~   80 (202)
T d1ijba_          14 LDLVFLLDGSSRLSEAEFEVLK-AFVVDMMERLRVS--------QKWVRVAVVEYHDGSH----AYIGLKDRKRPSELRR   80 (202)
T ss_dssp             EEEEEEEECBTTSCHHHHHHHH-HHHHHHHHTBCBS--------TTSEEEEEEEESSSEE----EEECTTCCCCHHHHHH
T ss_pred             eeEEEEEeCCCCCCHHHHHHHH-HHHHHHHHHhccC--------CCCcEEEEEEEeccee----eecCCcccchHHHHHH
Confidence            69999999999997 5688876 6789999998532        1358999999998632    1123455688899999


Q ss_pred             HhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhhh
Q 003284           83 WLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEAQ  161 (834)
Q Consensus        83 ~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~~  161 (834)
                      .++.|...||+..  .+.+||..++. +|..       ..+....|++|||++...+...                    
T Consensus        81 ~i~~l~~~~g~~~--~~~~al~~~~~~~~~~-------~~r~~~~k~vivitdg~~~~~~--------------------  131 (202)
T d1ijba_          81 IASQVKYAGSQVA--STSEVLKYTLFQIFSK-------IDRPEASRIALLLMASQEPQRM--------------------  131 (202)
T ss_dssp             HHHTCCCCCBSCC--CHHHHHHHHHHHTSSS-------CSCTTSEEEEEEEECCCCCGGG--------------------
T ss_pred             HHHhhhhhhhccc--cHHHHHHHHHHHhhhh-------ccCCCCcceEEEecccCCCccc--------------------
Confidence            9999998887653  45666777764 4431       1234568899999988653221                    


Q ss_pred             hhccCCCHHHHHHHHhhcCcEEEEeccC
Q 003284          162 AESRLSDAETVAKSFVQCSVSLSVICPK  189 (834)
Q Consensus       162 ~~~~l~d~e~lA~~~~e~~I~LSvIsPr  189 (834)
                          ..+.+..++.+.++||.+++|.--
T Consensus       132 ----~~~~~~~~~~l~~~gv~i~~Vgig  155 (202)
T d1ijba_         132 ----SRNFVRYVQGLKKKKVIVIPVGIG  155 (202)
T ss_dssp             ----CTTHHHHHHHHHHTTEEEEEEEES
T ss_pred             ----chHHHHHHHHHHHcCCeEEEEEeC
Confidence                125688899999999999999753

>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=98.91  E-value=1.8e-09  Score=104.53  Aligned_cols=139  Identities=12%  Similarity=0.129  Sum_probs=99.8

Q ss_pred             CccEEEEEeccccchH-hHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccC--CCCHHH
Q 003284            3 EKQLIVAVEGTAAMGP-YWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGW--TKDVDI   79 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~-yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gf--Tsd~~~   79 (834)
                      ..|||||||++++|+. .|+.+| .++..+++.|..          ..+|+|||.|.+...      ..+.|  ..|..+
T Consensus         5 ~~DivfvlD~S~s~~~~~~~~~k-~f~~~iv~~l~~----------~~~rv~vv~fs~~~~------~~~~l~~~~~~~~   67 (194)
T d1mf7a_           5 DSDIAFLIDGSGSIIPHDFRRMK-EFVSTVMEQLKK----------SKTLFSLMQYSEEFR------IHFTFKEFQNNPN   67 (194)
T ss_dssp             CEEEEEEEECCTTSCHHHHHHHH-HHHHHHHHHHCC----------TTEEEEEEEESSSEE------EEECHHHHHHSCC
T ss_pred             CeeEEEEEECCCCCCHHHHHHHH-HHHHHHHHHcCc----------CCceEEEEEEeccce------eEEeccccCCHHH
Confidence            4899999999999976 688766 568888888832          347999999987643      12233  335567


Q ss_pred             HHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchh
Q 003284           80 FLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNE  159 (834)
Q Consensus        80 fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~  159 (834)
                      +++.++.|.+.||+-   .+..||..|++.+-...    ......+.|.+|||++..++.-+.                 
T Consensus        68 ~~~~i~~i~~~~~~t---~~~~al~~~~~~~~~~~----~~~~~~~~kvvvliTDG~~~~~~~-----------------  123 (194)
T d1mf7a_          68 PRSLVKPITQLLGRT---HTATGIRKVVRELFNIT----NGARKNAFKILVVITDGEKFGDPL-----------------  123 (194)
T ss_dssp             HHHHHTTCCCCCSCB---CHHHHHHHHHHTTTSGG----GTCCTTSEEEEEEEESSCCBSCSS-----------------
T ss_pred             HHHHHhhhhhhhccc---hHHHHHHHHHHHHHhhh----ccCCCCCceEEEEEecCCCCCCch-----------------
Confidence            999999999988763   46677888887652111    112345678999999987764332                 


Q ss_pred             hhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          160 AQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       160 ~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                              +.+.+++.+.+.||.+++|..-.
T Consensus       124 --------~~~~~~~~~~~~gv~i~~VGi~~  146 (194)
T d1mf7a_         124 --------GYEDVIPEADREGVIRYVIGVGD  146 (194)
T ss_dssp             --------CGGGTHHHHHHTTEEEEEEEESG
T ss_pred             --------hHHHHHHHHHHcCCeeEEEecCC
Confidence                    23457888899999999997654

>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=98.70  E-value=2.6e-08  Score=96.16  Aligned_cols=168  Identities=13%  Similarity=0.104  Sum_probs=108.7

Q ss_pred             ccEEEEEeccccc-hHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCccccee-eccCCCCHHHHH
Q 003284            4 KQLIVAVEGTAAM-GPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQ-RSGWTKDVDIFL   81 (834)
Q Consensus         4 ~dvVFVID~Tasm-g~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~-~~gfTsd~~~fl   81 (834)
                      .|||||||.+++| +..|+.+| +.+.-+++.|..+        ....|+|||.|.+...   ..+. ...++.+...+.
T Consensus         2 lDivfvlD~SgSm~~~~~~~~k-~~~~~li~~l~~~--------~~~~rv~lv~f~~~~~---~~~~l~~~~~~~~~~l~   69 (209)
T d1q0pa_           2 MNIYLVLDGSDSIGASNFTGAK-KSLVNLIEKVASY--------GVKPRYGLVTYATYPK---IWVKVSEADSSNADWVT   69 (209)
T ss_dssp             EEEEEEEECSTTTCHHHHHHHH-HHHHHHHHHHHTT--------TCCCEEEEEEESSSEE---EEECTTSGGGGCHHHHH
T ss_pred             cCEEEEEeCCCCCChHHHHHHH-HHHHHHHHhcccC--------CCCcEEEEEEecCcee---EEecCccchhhHHHHHH
Confidence            4999999999999 57899988 6689999999542        2357999999987632   1111 123456688889


Q ss_pred             HHhccCccCCCCCc-hhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCccccccccchhh
Q 003284           82 HWLSTIPFAGGGFN-DAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQNENNEA  160 (834)
Q Consensus        82 ~~Ld~I~f~GGG~~-~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~~e~~~~  160 (834)
                      ..|++|.+.++... ...+.+||..|...+..... ..+..+..+.|.+||++|..|..-..+.           +..+.
T Consensus        70 ~~i~~i~~~~~~~~g~t~~~~al~~a~~~~~~~~~-~~~~~~~~~~kvvvl~TDG~~~~~~~~~-----------~~~~~  137 (209)
T d1q0pa_          70 KQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDD-VPPEGWNRTRHVIILMTDGLHNMGGDPI-----------TVIDE  137 (209)
T ss_dssp             HHHHTCCTTSCSCTTCCCHHHHHHHHHHHHCCTTS-SCCTTGGGCEEEEEEEECSCCCSSSCTH-----------HHHHH
T ss_pred             HHHHHhhhccccCCCCchHHHHHHHHHHHHHhhhc-cCccccCCCceEEEEEcCCCccCCCChH-----------HHHHH
Confidence            99999988776643 57899999999988854332 2234455677889999998775433221           00000


Q ss_pred             hhhccCCCHHHHHHHHhhcCcEEEEeccCCchhHHHH
Q 003284          161 QAESRLSDAETVAKSFVQCSVSLSVICPKQLPKLTAI  197 (834)
Q Consensus       161 ~~~~~l~d~e~lA~~~~e~~I~LSvIsPrqlp~l~~L  197 (834)
                      .+..  ......++.+.+.||.+++|.-..-.....|
T Consensus       138 ~~~~--~~~~~~~~~~~~~gi~i~~vgvg~~~~~~~L  172 (209)
T d1q0pa_         138 IRDL--LYIGKDRKNPREDYLDVYVFGVGPLVNQVNI  172 (209)
T ss_dssp             HHHH--TTCSCBTTBCCGGGEEEEEEECSSCCCHHHH
T ss_pred             HHHh--hhhHHHHHHHHhcCCceEEecCCccCCHHHH
Confidence            0000  0111124445677899998876544333333

>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=98.64  E-value=5.9e-08  Score=92.91  Aligned_cols=110  Identities=12%  Similarity=0.175  Sum_probs=79.5

Q ss_pred             ccEEEEEeccccchHh-HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--CCHHHH
Q 003284            4 KQLIVAVEGTAAMGPY-WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--KDVDIF   80 (834)
Q Consensus         4 ~dvVFVID~Tasmg~y-i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--sd~~~f   80 (834)
                      .|||||||++++|+.+ |+.+| +++..+++.|..          ..+|+|||.|.+..-      ..+.|+  .+...|
T Consensus         3 ~DivfllD~S~Si~~~~f~~~k-~f~~~~i~~i~~----------~~~rvgvv~fs~~~~------~~~~l~~~~~~~~~   65 (179)
T d1mjna_           3 VDLVFLFDGSMSLQPDEFQKIL-DFMKDVMKKCSN----------TSYQFAAVQFSTSYK------TEFDFSDYVKRKDP   65 (179)
T ss_dssp             EEEEEEEECBTTCCHHHHHHHH-HHHHHHHHHTTT----------SSEEEEEEEESSSEE------EEECHHHHHHHCCH
T ss_pred             eEEEEEEECCCCCCHHHHHHHH-HHHHHHHHHhCC----------CceEEEEEEEeeeee------EEechhhccchHHH
Confidence            6999999999999865 66665 678888887743          357999999987532      223443  466779


Q ss_pred             HHHhccCccCCCCCchhhHHHHHHHHHh-hcccCCCCCCCCCCccCCcEEEEeecCCCC
Q 003284           81 LHWLSTIPFAGGGFNDAAIAEGLSEALM-MFSVAPNGSQNQQNVDGQRHCILVAASNPH  138 (834)
Q Consensus        81 l~~Ld~I~f~GGG~~~~AvaEGLa~AL~-~f~~~~~~~~~~~~~~~qkhCILIa~SpP~  138 (834)
                      +..+++|.+.||+-   .+.+||..|++ +|....     ..+..+.|.+|||++..++
T Consensus        66 ~~~i~~i~~~~g~t---~~~~AL~~~~~~~f~~~~-----g~R~~~~kvvvllTDG~s~  116 (179)
T d1mjna_          66 DALLKHVKHMLLLT---NTFGAINYVATEVFREEL-----GARPDATKVLIIITDGEAT  116 (179)
T ss_dssp             HHHHTTCCCCCBCC---CHHHHHHHHHHHTSSGGG-----TCCTTSEEEEEEEESSCCS
T ss_pred             HHHHhhhhcccCcc---hHHHHHHHHHHHHhchhc-----CCCCCCCeEEEEEECCCCc
Confidence            99999999988763   55677777774 554211     1224567899999998664

>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=98.45  E-value=2.3e-06  Score=83.31  Aligned_cols=147  Identities=17%  Similarity=0.229  Sum_probs=90.5

Q ss_pred             CccEEEEEeccccchHh-------HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCC---------ccc
Q 003284            3 EKQLIVAVEGTAAMGPY-------WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY---------CAC   66 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y-------i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~---------~~~   66 (834)
                      +..||||||++++|..-       |+.+| +++..+++.+--   .     .+..++|||+|++....         ...
T Consensus         2 k~aiv~~lD~S~SM~~~~~~~~srl~~ak-~~~~~~v~~~~~---~-----~~~d~vglV~f~~~~t~~~~~~~~~~~~i   72 (236)
T d1jeyb2           2 KAAVVLCMDVGFTMSNSIPGIESPFEQAK-KVITMFVQRQVF---A-----ENKDEIALVLFGTDGTDNPLSGGDQYQNI   72 (236)
T ss_dssp             CEEEEEEEECCGGGGCCBTTBCCHHHHHH-HHHHHHHHHHHH---T-----TCCCEEEEEEESCSSCBSTTCTTTCSTTE
T ss_pred             CceEEEEEECChhhccCCCCCCCHHHHHH-HHHHHHHHHHhc---C-----CCCCeEEEEEEcCCCcccccccccccceE
Confidence            45699999999999754       77666 667777776521   1     12469999999876431         111


Q ss_pred             ceeeccCCCCHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCccc
Q 003284           67 LVQRSGWTKDVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYR  146 (834)
Q Consensus        67 lv~~~gfTsd~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~  146 (834)
                      .+....-+.+.. .+..+..+...+++  ...+.++|..|+.++.....     ......|++||++|...   +  +  
T Consensus        73 ~~~~~~~~~~~~-~~~~~~~~~~~~~~--~~~~~~al~~a~~~~~~~~~-----~~~~~~r~IiL~TDG~~---~--~--  137 (236)
T d1jeyb2          73 TVHRHLMLPDFD-LLEDIESKIQPGSQ--QADFLDALIVSMDVIQHETI-----GKKFEKRHIEIFTDLSS---R--F--  137 (236)
T ss_dssp             EEEEEEECCCHH-HHHHHHTTCCCCSS--CCCHHHHHHHHHHHHHHHSS-----SSCCSEEEEEEECCCCS---C--C--
T ss_pred             EEEeccccchhh-HHHHHhhhcccccc--ccchhHHHHHHHHHHHHhhh-----cccccccEEEEEecCCC---C--c--
Confidence            112222233333 44444444433333  23567777777766643211     12345789999998632   0  0  


Q ss_pred             CCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCCc
Q 003284          147 PQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQL  191 (834)
Q Consensus       147 p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrql  191 (834)
                                        .-.+++.+++.+.+.+|+|++|.....
T Consensus       138 ------------------~~~~~~~~a~~l~~~~I~i~~ig~g~~  164 (236)
T d1jeyb2         138 ------------------SKSQLDIIIHSLKKCDISLQFFLPFSL  164 (236)
T ss_dssp             ------------------CCTTHHHHHHHHHHTTEEEEEEESSCC
T ss_pred             ------------------ChHHHHHHHHHHHHcCCEEEEEecCCc
Confidence                              012678999999999999999998654

>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=97.84  E-value=3.9e-05  Score=73.89  Aligned_cols=148  Identities=16%  Similarity=0.132  Sum_probs=83.3

Q ss_pred             EEEEEeccccchHh--------HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCC----cccceeeccC
Q 003284            6 LIVAVEGTAAMGPY--------WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSY----CACLVQRSGW   73 (834)
Q Consensus         6 vVFVID~Tasmg~y--------i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~----~~~lv~~~gf   73 (834)
                      ||||||++++|...        |+.++ +++..+++.+...        ....++|||+|++....    .+.......+
T Consensus         5 ivf~ID~S~SM~~~d~~~~~s~~~~~~-~~~~~~~~~~i~~--------~~~d~vglv~f~t~~~~~~~~~~~~~~~~~l   75 (220)
T d1jeya2           5 LIFLVDASKAMFESQSEDELTPFDMSI-QCIQSVYISKIIS--------SDRDLLAVVFYGTEKDKNSVNFKNIYVLQEL   75 (220)
T ss_dssp             EEEEEECSGGGGCCCSSSSCCHHHHHH-HHHHHHHHHHHHT--------TCCCEEEEEEESCSSCBSTTCCTTEEEEEEE
T ss_pred             EEEEEECCcccCccccCCCCCHHHHHH-HHHHHHHHHHhhC--------CCCCEEEEEEeccccccCCCcccchhhhhcc
Confidence            99999999999543        44444 4566666666321        12469999999876431    1111111111


Q ss_pred             ----CCCHHHHHHHhcc-----CccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCC-CCCCCC
Q 003284           74 ----TKDVDIFLHWLST-----IPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNP-HPLPTP  143 (834)
Q Consensus        74 ----Tsd~~~fl~~Ld~-----I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP-~~lp~p  143 (834)
                          +.++..+..++..     +....+......+.+||..|+.+|....       .....|.+|||+|--+ +.-.. 
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~l~~al~~a~~~~~~~~-------~~~~~k~IiliTDg~~~~~~~~-  147 (220)
T d1jeya2          76 DNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQ-------FKMSHKRIMLFTNEDNPHGNDS-  147 (220)
T ss_dssp             ECCCHHHHHHHHTTSHHHHHHHHHHHHCCSCCCCHHHHHHHHHHHHHTCS-------SCEEEEEEEEEESCSCTTTTCH-
T ss_pred             cCchHHHHHhhhhhhhhhhhhhhhhcccCCCCccHHHHHHHHHHHHHhcc-------cccCCcEEEEEecCCCCCCCcc-
Confidence                2222222222211     0000011123458899999999996422       1234688999998743 21110 


Q ss_pred             cccCCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccCC
Q 003284          144 VYRPQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPKQ  190 (834)
Q Consensus       144 v~~p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPrq  190 (834)
                                    .+      ...+.+.|+.+.+++|.+++|.-..
T Consensus       148 --------------~~------~~~~~~~a~~~~~~gv~i~~i~ig~  174 (220)
T d1jeya2         148 --------------AK------ASRARTKAGDLRDTGIFLDLMHLKK  174 (220)
T ss_dssp             --------------HH------HHHHHHHHHHHHHHTEEEEEEEBCC
T ss_pred             --------------hh------hHHHHHHHHHHhhhcceEEEEEeCC
Confidence                          00      0134678888999999999996543

>d1yvra2 c.62.1.5 (A:364-537) 60-kda SS-A/Ro ribonucleoprotein, RoRNP {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: RoRNP C-terminal domain-like
domain: 60-kda SS-A/Ro ribonucleoprotein, RoRNP
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=95.96  E-value=0.017  Score=53.49  Aligned_cols=98  Identities=14%  Similarity=0.092  Sum_probs=53.4

Q ss_pred             CccEEEEEeccccchHh-----HHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCCCcccceeeccCC--C
Q 003284            3 EKQLIVAVEGTAAMGPY-----WQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGSYCACLVQRSGWT--K   75 (834)
Q Consensus         3 ~~dvVFVID~Tasmg~y-----i~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~~~~~lv~~~gfT--s   75 (834)
                      -+++|||||.++||+..     +..++.- +.-++..+.           .+-+++||+|.+..       ....++  .
T Consensus         5 g~~~vl~iD~SGSM~~~~~~~~~~~~~~a-~~~~~~~~~-----------~~~~~~vv~F~~~~-------~~~~~~~~~   65 (174)
T d1yvra2           5 GKRFLLAIDVSASMNQRVLGSILNASVVA-AAMCMLVAR-----------TEKDSHMVAFSDEM-------LPCPITVNM   65 (174)
T ss_dssp             CCCEEEEEECSGGGGSBSTTSSCBHHHHH-HHHHHHHHH-----------HCSSEEEEEESSSE-------ECCSCCTTS
T ss_pred             CCeEEEEEECccccCCcccCccHHHHHHH-HHHHHHhhc-----------cCCcEEEEEecCCc-------cccccCccc
Confidence            37899999999999642     2222221 111122221           12478999998751       223333  3


Q ss_pred             CHHHHHHHhccCccCCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCC
Q 003284           76 DVDIFLHWLSTIPFAGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNP  137 (834)
Q Consensus        76 d~~~fl~~Ld~I~f~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP  137 (834)
                      ++...+..++.+.  |||-.   +..+|..|+....             ..+.+|||+|.-.
T Consensus        66 ~~~~~~~~~~~~~--~ggT~---i~~al~~a~~~~~-------------~~~~ivllTDg~~  109 (174)
T d1yvra2          66 LLHEVVEKMSDIT--MGSTD---CALPMLWAQKTNT-------------AADIFIVFTDCET  109 (174)
T ss_dssp             CHHHHHHHHTTCC--CSCCC---TTHHHHHHHHTTC-------------CCSEEEEEECCCC
T ss_pred             hHHHHHHHhhccc--ccccc---HHHHHHHHHhhhc-------------cCCEEEEEeCCCc
Confidence            4555555555543  44432   3445666665322             1357999998743

>d2qtva3 c.62.1.2 (A:120-390) Sec23 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Trunk domain of Sec23/24
domain: Sec23
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.93  E-value=0.027  Score=56.58  Aligned_cols=108  Identities=10%  Similarity=0.100  Sum_probs=61.5

Q ss_pred             HHHHhccCccCC-----CCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEeecCCCCCCCCCcccCCcccccc
Q 003284           80 FLHWLSTIPFAG-----GGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVAASNPHPLPTPVYRPQMQNLDQ  154 (834)
Q Consensus        80 fl~~Ld~I~f~G-----GG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa~SpP~~lp~pv~~p~~~~~~~  154 (834)
                      +...|+.|.-..     +.....|...||.+|+.++....        .+.--++++..+++|--=|=.     |..-+.
T Consensus       119 i~~lL~~L~~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~--------~~~gGkI~~F~sg~pt~GpG~-----l~~r~~  185 (271)
T d2qtva3         119 LNQLLENLSPDQWSVPAGHRPLRATGSALNIASLLLQGCY--------KNIPARIILFASGPGTVAPGL-----IVNSEL  185 (271)
T ss_dssp             HHHHHHHCCCCCCCCCTTBCCCCCHHHHHHHHHHHHHHHC--------TTSCEEEEEEESSCCCSSSSC-----SSCSBT
T ss_pred             HHHHHHHhccCcccCCCCCCcccchHHHHHHHHHHHHhhc--------cCCCcEEEEEeCCCCCCCCcc-----cccccc
Confidence            344566664322     22234688999999998885211        122357777788888432211     111111


Q ss_pred             ccc--------------hhhhhhccCCCHHHHHHHHhhcCcEEEEecc--C--CchhHHHHHHHhcCC
Q 003284          155 NEN--------------NEAQAESRLSDAETVAKSFVQCSVSLSVICP--K--QLPKLTAIYNAAKRN  204 (834)
Q Consensus       155 ~e~--------------~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsP--r--qlp~l~~Lfeka~~~  204 (834)
                      +|.              +.....+    .+.||..+.+.+|.+.+.+-  .  .+..|..|.+..+|.
T Consensus       186 ~~~~rs~~d~~k~~~~~~~~a~~f----Y~~la~~~~~~~isvDlF~~s~~~~dl~~l~~l~~~TGG~  249 (271)
T d2qtva3         186 KDPLRSHHDIDSDHAQHYKKACKF----YNQIAQRVAANGHTVDIFAGCYDQIGMSEMKQLTDSTGGV  249 (271)
T ss_dssp             TSCCCCHHHHHTTCCTTHHHHHHH----HHHHHHHHHHHTEEEEEEEECSSCCSHHHHTHHHHTTTCC
T ss_pred             ccccCCccchhhhhhhhhhhHHHH----HHHHHHHHHHCCeEEEEEEecCccCChHHHHhHHhhCCce
Confidence            110              0011122    37899999999998776543  3  357788888877665

>d1pd0a3 c.62.1.2 (A:301-552) Sec24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: vWA-like
superfamily: vWA-like
family: Trunk domain of Sec23/24
domain: Sec24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.74  E-value=0.056  Score=53.56  Aligned_cols=178  Identities=11%  Similarity=0.119  Sum_probs=90.4

Q ss_pred             EEEEEeccccchHhHHHHHHHHHHHHHHHHhccccccccCCCCccEEEEEEeecCCC-C---------------------
Q 003284            6 LIVAVEGTAAMGPYWQSIVSDYLEKIIRCFCVNELAGQKTSASNVELSLVTFNTHGS-Y---------------------   63 (834)
Q Consensus         6 vVFVID~Tasmg~yi~~lkt~YI~p~le~f~~g~~~~~~~~~~~~~~gLVvY~d~~~-~---------------------   63 (834)
                      .|||||.|.      +.+.+.++.-+++.+.. .++.-.....+.++|||+|.+.=. |                     
T Consensus         6 ~vFvID~s~------~a~~~g~l~~~~~si~~-~l~~l~~~~~~~~VgiItf~~~V~~y~l~~~~~~~~~~~~~~~~~~~   78 (252)
T d1pd0a3           6 YCFLIDVSQ------SSIKSGLLATTINTLLQ-NLDSIPNHDERTRISILCVDNAIHYFKIPLDSENNEESADQINMMDI   78 (252)
T ss_dssp             EEEEEECSH------HHHHHTHHHHHHHHHHT-TTTTSCCTTSCCEECEEEESSSEEEEECCCGGGC-------CEEECC
T ss_pred             EEEEEECCH------HHhhhhHHHHHHHHHHH-HHHhCcCCCCCcEEEEEEECCEEEEEEccCCccccccccccccccch
Confidence            799999984      34444444444444332 222111112578999999976211 0                     


Q ss_pred             ---cccceee-c----cCCCCHHHHHHHhccCcc--CCCCCchhhHHHHHHHHHhhcccCCCCCCCCCCccCCcEEEEee
Q 003284           64 ---CACLVQR-S----GWTKDVDIFLHWLSTIPF--AGGGFNDAAIAEGLSEALMMFSVAPNGSQNQQNVDGQRHCILVA  133 (834)
Q Consensus        64 ---~~~lv~~-~----gfTsd~~~fl~~Ld~I~f--~GGG~~~~AvaEGLa~AL~~f~~~~~~~~~~~~~~~qkhCILIa  133 (834)
                         .+.++-+ .    .+-..-+.+...|+.|+-  ........|..-||..|+.++...            --++|+..
T Consensus        79 ~dl~~~~~p~~~~~lv~~~e~~~~i~~~L~~l~~~~~~~~~~~~~~G~Al~~a~~~l~~~------------gGkI~~f~  146 (252)
T d1pd0a3          79 ADLEEPFLPRPNSMVVSLKACRQNIETLLTKIPQIFQSNLITNFALGPALKSAYHLIGGV------------GGKIIVVS  146 (252)
T ss_dssp             CCTTCC-----TTTSEETTTTHHHHHHHHHHHHHHTTTCCCCCCCHHHHHHHHHHHHTTT------------CEEEEEEE
T ss_pred             hhhhhccCCCCccceeeHHHHHHHHHHHHHhChhhcccCCCCcccHHHHHHHHHHHHhcC------------CCEEEEEe
Confidence               0000000 0    123334455556676632  333344678889999999888521            13566666


Q ss_pred             cCCCCCCCCC-ccc---CCccccccccchhhhhhccCCCHHHHHHHHhhcCcEEEEeccC----CchhHHHHHHHhcCCC
Q 003284          134 ASNPHPLPTP-VYR---PQMQNLDQNENNEAQAESRLSDAETVAKSFVQCSVSLSVICPK----QLPKLTAIYNAAKRNP  205 (834)
Q Consensus       134 ~SpP~~lp~p-v~~---p~~~~~~~~e~~~~~~~~~l~d~e~lA~~~~e~~I~LSvIsPr----qlp~l~~Lfeka~~~~  205 (834)
                      +++|-.=|-. ..+   ..+++-+...  ...+ ....=.+.||..+.+++|++.+.+-.    .+..+..|-+..+|..
T Consensus       147 sg~pt~GpG~l~~r~~~~~~~~~~~~~--~~~~-~a~~fY~~la~~~~~~~isvdlF~~~~~~~dl~~l~~l~~~TGG~~  223 (252)
T d1pd0a3         147 GTLPNLGIGKLQRRNESGVVNTSKETA--QLLS-CQDSFYKNFTIDCSKVQITVDLFLASEDYMDVASLSNLSRFTAGQT  223 (252)
T ss_dssp             SSCCCSSTTCCCC-----------------------CCHHHHHHHHHTTTTEEEEEEEEESBCCCHHHHHHHHHTTTCCE
T ss_pred             cCCCCCCCcccccccccccccCcccch--hccc-chHHHHHHHHHHHHHCCEEEEEEeccccccCcHHHhhHhhcCCceE
Confidence            6666422211 100   0000000000  0000 00112479999999999988765443    4678899988887763